Fragment Cluster 1: 5016c,3003b,3003a,5016a,5015a Fragment Coverage tRNA-Cys-GCA-8:TLE_Z tRNA-Cys-GCA-4:A_DSLE_CSL_TLE_Z tRNA-Cys-GCA-5:TLE_Z tRNA-Cys-GCA-2:A_DSLE_CSL_TLE_Z tRNA-Cys-GCA-7:TLE_Z tRNA-Cys-GCA-11:TLE_Z tRNA-Cys-GCA-14:TLE_Z Fragment Aminos Cys Fragment Alignment # STOCKHOLM 1.0 tRNA-Cys-GCA-2 -GGGGGUAUAGCUCAGU--GGU--AGAGCAUUUGACUGCAGAUCAAGAGGUCCCCGGUUCAAAUCCGGGUGCCCCCUCCA [1] tRNA-Cys-GCA-4 -GGGGGUAUAGCUCAGU--GGU--AGAGCAUUUGACUGCAGAUCAAGAGGUCCCUGGUUCAAAUCCGGGUGCCCCCUCCA [2] tRNA-Cys-GCA-5 -GGGGGUAUAGCUCAGU--GGGU-AGAGCAUUUGACUGCAGAUCAAGAGGUCCCCGGUUCAAAUCCGGGUGCCCCCUCCA [3] tRNA-Cys-GCA-7 -GGGGGUAUAGCUCAGGU-GGU--AGAGCAUUUGACUGCAGAUCAAGAGGUCCCCGGUUCAAAUCCGGGUGCCCCCUCCA [4] tRNA-Cys-GCA-8 -GGGGGUAUAGCUCAGG--GGU--AGAGCAUUUGACUGCAGAUCAAGAGGUCCCCGGUUCAAAUCCGGGUGCCCCCUCCA [5] tRNA-Cys-GCA-11 -GGGGGUAUAGCUUAGC--GGU--AGAGCAUUUGACUGCAGAUCAAGAGGUCCCCGGUUCAAAUCCGGGUGCCCCCUCCA [6] tRNA-Cys-GCA-14 -GGGGGUAUAGCUCAGG--GGU--AGAGCAUUUGACUGCAGAUCAAGAAGUCCCCGGUUCAAAUCCGGGUGCCCCCUCCA [7] 5015a .GGGGGUAUAGCUC.................................................................. [1,2,3,4,5,7] 5016a .GGGGGUAUAGCUCAG................................................................ [1,2,3,4,5,7] 5016c .GGGGGUAUAGCUCAGU--GGU--AGAGCAUUUGACU........................................... [1,2] 3003b ..........................................................UCAAAUCCGGGUGCCCCCUCCA [1,2,3,4,5,6,7] 3003a ...............................................................UCCGGGUGCCCCCUCCA [1,2,3,4,5,6,7] #=GC SS_cons :(((((((,,<<<<___________>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))):::: #=GC RF +=======++====+++++++++++====+=====++***++=====+++++=====+++++++============++++ // Fragment Cluster 2: 3021b,3021a Fragment Coverage tRNA-Ala-TGC-2:TLE_Z tRNA-Ala-CGC-1:TLE_Z tRNA-Ala-CGC-3:TLE_Z tRNA-Ala-CGC-2:TLE_Z tRNA-Ala-TGC-4:TLE_Z tRNA-Ala-TGC-3:TLE_Z Fragment Aminos Ala Fragment Alignment # STOCKHOLM 1.0 tRNA-Ala-CGC-1 -GGGGAUGUAGCUCAGU--GGU--AGAGCGCAUGCUUCGCAUGUAUGAGGUCCCGGGUUCGAUCCCCGGCAUCUCCACCA [1] tRNA-Ala-CGC-2 -GGGGAUGUAGCUCAGU--GGU--AGAGCGCAUGCUUCGCAUGUAUGAGGCCCCGGGUUCGAUCCCCGGCAUCUCCACCA [2] tRNA-Ala-CGC-3 -GGGGAUGUAGCUCAGU--GGU--AGAGCGCGCGCUUCGCAUGUGUGAGGUCCCGGGUUCAAUCCCCGGCAUCUCCACCA [3] tRNA-Ala-TGC-2 -GGGGAUGUAGCUCAGU--GGU--AGAGCGCAUGCUUUGCAUGUAUGAGGUCCCGGGUUCGAUCCCCGGCAUCUCCACCA [4] tRNA-Ala-TGC-3 -GGGGAUGUAGCUCAGU--GGU--AGAGCGCAUGCUUUGCAUGUAUGAGGCCCCGGGUUCGAUCCCCGGCAUCUCCACCA [5] tRNA-Ala-TGC-4 -GGGGAUGUAGCUCAGU--GGU--AGAGCGCAUGCUUUGCACGUAUGAGGCCCCGGGUUCAAUCCCCGGCAUCUCCACCA [6] 3021b ..........................................................UCGAUCCCCGGCAUCUCCACCA [1,2,4,5] 3021a ..............................................................UCCCCGGCAUCUCCACCA [1,2,3,4,5,6] #=GC SS_cons :(((((((,,<<<<___________>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))):::: #=GC RF +=======++====+++++++++++====+=====++***++=====+++++=====+++++++============++++ // Fragment Cluster 3: 5013b,5013c,5012b,5012a,5011a,3002a,3002b Fragment Coverage tRNA-Pro-CGG-1:A_DSLE_CS_TLE_Z tRNA-Pro-CGG-2:A_DSLE_CS_TLE_Z tRNA-Pro-AGG-2:A_DSLE_CS_TLE_Z tRNA-Pro-AGG-1:A_DSLE_CS_TLE_Z tRNA-Pro-TGG-3:A_DSLE_CS_TLE_Z tRNA-Pro-TGG-2:A_DSLE_TLE_Z tRNA-Pro-TGG-1:A_DSL_TLE_Z tRNA-Pro-AGG-3:A_DSL_TLE_Z Fragment Aminos Pro Fragment Alignment # STOCKHOLM 1.0 tRNA-Pro-AGG-1 -GGCUCGUUGGUCUAGG--GGU--AUGAUUCUCGCUUAGGAUGCGAGAGGUCCCGGGUUCAAAUCCCGGACGAGCCCCCA [1] tRNA-Pro-AGG-2 -GGCUCGUUGGUCUAGG--GGU--AUGAUUCUCGCUUAGGGUGCGAGAGGUCCCGGGUUCAAAUCCCGGACGAGCCCCCA [2] tRNA-Pro-AGG-3 -GGCUCGUUGGUCUAGG--GGUG--UGGUUCUCGCUUAGGGCGGGAGA-GUCCCGGGUUCAAAUCCCGGACGAGCCCCCA [3] tRNA-Pro-CGG-1 -GGCUCGUUGGUCUAGG--GGU--AUGAUUCUCGCUUCGGGUGCGAGAGGUCCCGGGUUCAAAUCCCGGACGAGCCCCCA [4] tRNA-Pro-CGG-2 -GGCUCGUUGGUCUAGG--GGU--AUGAUUCUCGCUUCGGGUGUGAGAGGUCCCGGGUUCAAAUCCCGGACGAGCCCCCA [5] tRNA-Pro-TGG-1 -GGCUCGUUGGUCUAGU--GGU--AUGAUUCUCGCUUUGGGUGCGAGAGGUCCCGGGUUCAAAUCCCGGACGAGCCCCCA [6] tRNA-Pro-TGG-2 -GGCUCGUUGGUCUAGG--GGU--AUGAUUCUCGGUUUGGGUCCGAGAGGUCCCGGGUUCAAAUCCCGGACGAGCCCCCA [7] tRNA-Pro-TGG-3 -GGCUCGUUGGUCUAGG--GGU--AUGAUUCUCGCUUUGGGUGCGAGAGGUCCCGGGUUCAAAUCCCGGACGAGCCCCCA [8] 5011a .GGCUCGUUGGUCUAG................................................................ [1,2,3,4,5,6,7,8] 5012a .GGCUCGUUGGUCUAGG--G............................................................ [1,2,3,4,5,7,8] 5013b .GGCUCGUUGGUCUAGG--GGU--AU...................................................... [1,2,4,5,7,8] 5012b .GGCUCGUUGGUCUAGG--GGU--AUGA.................................................... [1,2,4,5,7,8] 5013c .GGCUCGUUGGUCUAGG--GGU--AUGAUUCUCGC............................................. [1,2,4,5,8] 3002b ..........................................................UCAAAUCCCGGACGAGCCCCCA [1,2,3,4,5,6,7,8] 3002a ..............................................................AUCCCGGACGAGCCCCCA [1,2,3,4,5,6,7,8] #=GC SS_cons :(((((((,,<<<<___________>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))):::: #=GC RF +=======++====+++++++++++====+=====++***++=====+++++=====+++++++============++++ // Fragment Cluster 4: 5032c,3024a,3024b,5032a,3025b,3025a,5032b Fragment Coverage tRNA-Asp-GTC-10:TLE_Z tRNA-Asp-GTC-1:A_DSL_TLE_Z tRNA-Asp-GTC-2:A_DSLE_CSL_TLE_Z tRNA-Asp-GTC-3:A_DSLE_TLE_Z Fragment Aminos Asp Fragment Alignment # STOCKHOLM 1.0 tRNA-Asp-GTC-1 -UCCUCGUUAGUAUAGU--GGUU-AGUAUCCCCGCCUGUCACGCGGGAGA-CCGGGGUUCAAUUCCCCGACGGGGAGCCA [1] tRNA-Asp-GTC-2 -UCCUCGUUAGUAUAGU--GGUG-AGUAUCCCCGCCUGUCACGCGGGAGA-CCGGGGUUCGAUUCCCCGACGGGGAGCCA [2] tRNA-Asp-GTC-3 -UCCUCGUUAGUAUAGU--GGUG-AGUGUCCCCGUCUGUCACGCGGGAGA-CCGGGGUUCGAUUCCCCGACGGGGAGCCA [3] tRNA-Asp-GTC-10 -UCCUUGUUACUAUAGU--GGUG-AGUAUCUCUGCCUGUCAUGCGUGAGA-GAGGGGGUCGAUUCCCCGACGGGGAGCCA [4] 5032a .UCCUCGUUAGUAUAGU--GG........................................................... [1,2,3] 5032b .UCCUCGUUAGUAUAGU--GGUG-AGU..................................................... [2,3] 5032c .UCCUCGUUAGUAUAGU--GGUG-AGUAUCCCCGCC............................................ [2] 3024b ..........................................................UCGAUUCCCCGACGGGGAGCCA [2,3,4] 3025b ..........................................................UCGAUUCCCCGACGGGGAGCCA [2,3,4] 3024a ..............................................................UUCCCCGACGGGGAGCCA [1,2,3,4] 3025a ..............................................................UUCCCCGACGGGGAGCCA [1,2,3,4] #=GC SS_cons :(((((((,,<<<<___________>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))):::: #=GC RF +=======++====+++++++++++====+=====++***++=====+++++=====+++++++============++++ // Fragment Cluster 5: 3012a,3012b,3011a,3011b,5023b,5023a Fragment Coverage tRNA-Leu-CAG-1:A_DSLE_TLE_Z tRNA-Leu-CAG-2:A_DSLE_TLE_Z tRNA-Leu-CAA-6:A_DSL tRNA-Leu-CAA-2:TLE_Z tRNA-Leu-CAA-4:TLE_Z tRNA-Leu-CAA-3:TLE_Z tRNA-Leu-CAA-1:TLE_Z Fragment Aminos Leu Fragment Alignment # STOCKHOLM 1.0 tRNA-Leu-CAA-1 -GUCAGGAUGGCCGAGU--GGUCUAAGGCGCCAGACUCAAGUUCUGGU-G-CGUGGGUUCGAAUCCCACUUCUGACACCA [1] tRNA-Leu-CAA-2 -GUCAGGAUGGCCGAGU--GGUCUAAGGCGCCAGACUCAAGUUCUGGU-G-CGUGGGUUCGAAUCCCACUUCUGACACCA [2] tRNA-Leu-CAA-3 -GUCAGGAUGGCCGAGU--GGUCUAAGGCGCCAGACUCAAGUUCUGGU-G-CGUGGGUUCGAAUCCCACUUCUGACACCA [3] tRNA-Leu-CAA-4 -GUCAGGAUGGCCGAGU--GGUCUAAGGCGCCAGACUCAAGUUCUGGU-G-CGUGGGUUCGAAUCCCACUUCUGACACCA [4] tRNA-Leu-CAA-6 -GUCAGGAUGGCCGAGCA-GUCUUAAGGCGCUGCGUUCAAAUCGCA-CCG-CGUGGGUUCGAAUCCCACUUUUGACACCA [5] tRNA-Leu-CAG-1 -GUCAGGAUGGCCGAGC--GGUCUAAGGCGCUGCGUUCAGGUCGCAGU-G-CGUGGGUUCGAAUCCCACUCCUGACACCA [6] tRNA-Leu-CAG-2 -GUCAGGAUGGCCGAGC--GGUCUAAGGCGCUGCGUUCAGGUCGCAGU-G-CGUGGGUUCGAAUCCCACUUCUGACACCA [7] 5023a .GUCAGGAUGGCCGAGC............................................................... [5,6,7] 5023b .GUCAGGAUGGCCGAGC--GGUCUAA...................................................... [6,7] 3012b ..........................................................UCGAAUCCCACUUCUGACACCA [1,2,3,4,7] 3011b ..........................................................UCGAAUCCCACUCCUGACACCA [6] 3012a ..............................................................AUCCCACUUCUGACACCA [1,2,3,4,7] 3011a ..............................................................AUCCCACUCCUGACACCA [6] #=GC SS_cons :(((((((,,<<<<___________>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))):::: #=GC RF +=======++====+++++++++++====+=====++***++=====+++++=====+++++++============++++ // Fragment Cluster 6: 5022a,5022b,3014a,3014b Fragment Coverage tRNA-Ser-TGA-4:A_DSLE tRNA-Ser-TGA-2:A_DSLE_TLE_Z tRNA-Ser-TGA-3:A_DSLE_TLE_Z tRNA-Ser-AGA-4:A_DSL_TLE_Z tRNA-Ser-AGA-3:A_DSLE_TLE_Z tRNA-Ser-AGA-2:A_DSLE_TLE_Z tRNA-Ser-AGA-1:A_DSLE_TLE_Z Fragment Aminos Ser Fragment Alignment # STOCKHOLM 1.0 tRNA-Ser-AGA-1 -GUAGUCGUGGCCGAGU--GGUU-AAGGCGAUGGACUAGAAAUCCAUU-G-CGCAGGUUCGAAUCCUGCCGACUACGCCA [1] tRNA-Ser-AGA-2 -GUAGUCGUGGCCGAGU--GGUU-AAGGCGAUGGACUAGAAAUCCAUU-G-CGCAGGUUCGAAUCCUGCCGACUACGCCA [2] tRNA-Ser-AGA-3 -GUAGUCGUGGCCGAGU--GGUU-AAGGCGAUGGACUAGAAAUCCAUU-A-CGCAGGUUCGAAUCCUGCCGACUACGCCA [3] tRNA-Ser-AGA-4 -GUAGUCGUGGCCGAGU--GGUU-AAGGUGAUGGACUAGAAACCCAUU-G-CGCAGGUUCGAAUCCUGCCGACUACGCCA [4] tRNA-Ser-TGA-2 -GUAGUCGUGGCCGAGU--GGUU-AAGGCGAUGGACUUGAAAUCCAUU-G-CGCAGGUUCGAAUCCUGCCGACUACGCCA [5] tRNA-Ser-TGA-3 -GUAGUCGUGGCCGAGU--GGUU-AAGGCGAUGGACUUGAAAUCCAUU-G-CGCAGGUUCGAAUCCUGCCGACUACGCCA [6] tRNA-Ser-TGA-4 -GUAGUCGUGGCCGAGU--GGUU-AAGGCGAUGGACUUGAAAUCCAUU-G-CGCAGGUUCGAAUCCUGUCGGCUACGCCA [7] 5022a .GUAGUCGUGGCCGA................................................................. [1,2,3,4,5,6,7] 5022b .GUAGUCGUGGCCGAGU--GGUU-AAGGC................................................... [1,2,3,5,6,7] 3014b ..........................................................UCGAAUCCUGCCGACUACGCCA [1,2,3,4,5,6] 3014a ..............................................................AUCCUGCCGACUACGCCA [1,2,3,4,5,6] #=GC SS_cons :(((((((,,<<<<___________>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))):::: #=GC RF +=======++====+++++++++++====+=====++***++=====+++++=====+++++++============++++ // Fragment Cluster 7: 5017a,5017b,3020a,3020b,5017c Fragment Coverage tRNA-Ala-CGC-4:A_DSLE_CS tRNA-Ala-TGC-1:TLE_Z tRNA-Ala-TGC-6:TLE_Z tRNA-Ala-AGC-2:A_DSLE_CS_TLE_Z tRNA-Ala-AGC-5:A_DSLE_CS tRNA-Ala-AGC-3:A_DSLE_CS_TLE_Z tRNA-Ala-AGC-7:A_DSLE_CS_TLE_Z Fragment Aminos Ala Fragment Alignment # STOCKHOLM 1.0 tRNA-Ala-AGC-2 -GGGGGUGUAGCUCAGU--GGU--AGAGCGCGUGCUUAGCAUGCACGAGGCCCCGGGUUCAAUCCCCGGCACCUCCACCA [1] tRNA-Ala-AGC-3 -GGGGGUGUAGCUCAGU--GGU--AGAGCGCGUGCUUAGCAUGUACGAGGUCCCGGGUUCAAUCCCCGGCACCUCCACCA [2] tRNA-Ala-AGC-5 -GGGGGUGUAGCUCAGU--GGU--AGAGCGCGUGCUUAGCAUGCACGAGGCCCUGGGUUCAAUCCCCAGCACCUCCACCA [3] tRNA-Ala-AGC-7 -GGGGGUGUAGCUCAGU--GGU--AGAGCGCGUGCUUAGCAUGCACGAGGCCCCGGGUUCAAUCCCCGGCACCUCCACCA [4] tRNA-Ala-CGC-4 -GGGGGUGUAGCUCAGU--GGU--AGAGCGCGUGCUUCGCAUGUACGAGGCCCCGGGUUCGACCCCCGGCUCCUCCACCA [5] tRNA-Ala-TGC-1 -GGGGGUGUAGCUCAGU--GGU--AGAGCGCAUGCUUUGCAUGUAUGAGGUCCCGGGUUCGAUCCCCGGCACCUCCACCA [6] tRNA-Ala-TGC-6 -GGGGGUGUAGCUCAGU--GGU--AGAGCACAUGCUUUGCAUGUGUGAGGCCCCGGGUUCGAUCCCCGGCACCUCCACCA [7] 5017a .GGGGGUGUAGCUC.................................................................. [1,2,3,4,5,6,7] 5017b .GGGGGUGUAGCUCAGU--GGU--AGAGC................................................... [1,2,3,4,5,6,7] 5017c .GGGGGUGUAGCUCAGU--GGU--AGAGCGCGUGC............................................. [1,2,3,4,5] 3020b ..........................................................UCGAUCCCCGGCACCUCCACCA [6,7] 3020a ..............................................................UCCCCGGCACCUCCACCA [1,2,4,6,7] #=GC SS_cons :(((((((,,<<<<___________>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))):::: #=GC RF +=======++====+++++++++++====+=====++***++=====+++++=====+++++++============++++ // Fragment Cluster 8: 5021a,3004b,5021b,3004a Fragment Coverage tRNA-Gln-CTG-8:A_DSL tRNA-Gln-CTG-10:A_DSL tRNA-Gln-CTG-12:A_DSL tRX-Gln-NNN-3:A_DSL tRNA-Gln-CTG-5:A_DSL_TLE_Z tRNA-Gln-CTG-4:A_DSL_TE_Z tRNA-Gln-CTG-7:A_DSL tRNA-Gln-CTG-1:A_DSL_TLE_Z tRNA-Gln-CTG-3:A_DSL_TE_Z tRNA-Gln-CTG-2:A_DSL_TE_Z Fragment Aminos Gln Fragment Alignment # STOCKHOLM 1.0 tRNA-Gln-CTG-1 -GGUUCCAUGGUGUAAU--GGUU-AGCACUCUGGACUCUGAAUCCAGCGA-UCCGAGUUCAAAUCUCGGUG.GAACCUCCA [1] tRNA-Gln-CTG-2 -GGUUCCAUGGUGUAAU--GGUU-AGCACUCUGGACUCUGAAUCCAGCGA-UCCGAGUUCAAGUCUCGGUG.GAACCUCCA [2] tRNA-Gln-CTG-3 -GGUUCCAUGGUGUAAU--GGUG-AGCACUCUGGACUCUGAAUCCAGCGA-UCCGAGUUCGAGUCUCGGUG.GAACCUCCA [3] tRNA-Gln-CTG-4 -GGUUCCAUGGUGUAAU--GGUA-AGCACUCUGGACUCUGAAUCCAGCGA-UCCGAGUUCGAGUCUCGGUG.GAACCUCCA [4] tRNA-Gln-CTG-5 -GGUUCCAUGGUGUAAU--GGUU-AGCACUCUGGACUCUGAAUCCGGUAA-UCCGAGUUCAAAUCUCGGUG.GAACCUCCA [5] tRNA-Gln-CTG-7 -GGUUCCAUGGUGUAAU--GGUA-AGCACUCUGGACUCUGAAUCCAGCCA-UCUGAGUUCGAGUCUCUGUG.GAACCUCCA [6] tRNA-Gln-CTG-8 -GGUUCCAUGGUGUAAU--GGUG-AGCACUUUGGACUCUGAAUACAGUGAUCA-GAGUUCAAGUCUCACUG.GGACCUCCA [7] tRNA-Gln-CTG-10 -GGUUCCAUGGUGUAAU--GGUG-ACCACUUUGGACUCUGAAUACAGUGAUCA-GAGUUCAAGUCUCACUG.GAACCUCCA [8] tRNA-Gln-CTG-12 -GGUUCCAUGGUGUAAU--GGUA-AGCACCCUGGACUCUGAAUCCAGCAA-CCAGAGUUCCAGUCUCAGCGuGGACCUCCA [9] tRX-Gln-NNN-3 -GGUUCCAUGGUGUAAU--GGUG-AGCACUUUGGACUCUGAAUACAGUGAUCA-GAGUUCAAGUCUCACUG.GAACCUCCA [10] 5021a .GGUUCCAUGGUGUA.................................................................. [1,2,3,4,5,6,7,8,9,10] 5021b .GGUUCCAUGGUGUAAU--GG............................................................ [1,2,3,4,5,6,7,8,9,10] 3004b ..........................................................UCAAAUCUCGGUG.GAACCUCCA [1,5] 3004a ...............................................................UCUCGGUG.GAACCUCCA [1,2,3,4,5] #=GC SS_cons :(((((((,,<<<<___________>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>)).))))):::: #=GC RF +=======++====+++++++++++====+=====++***++=====+++++=====+++++++=======.=====++++ // Fragment Cluster 9: 3005a,3005b Fragment Coverage tRNA-Gln-TTG-2:TE_Z tRNA-Gln-TTG-3:TLE_Z tRNA-Gln-TTG-1:TLE_Z Fragment Aminos Gln Fragment Alignment # STOCKHOLM 1.0 tRNA-Gln-TTG-1 -GGUCCCAUGGUGUAAU--GGUU-AGCACUCUGGACUUUGAAUCCAGCGA-UCCGAGUUCAAAUCUCGGUGGGACCUCCA [1] tRNA-Gln-TTG-2 -GGUCCCAUGGUGUAAU--GGUU-AGCACUCUGGACUUUGAAUCCAGCAA-UCCGAGUUCGAAUCUCGGUGGGACCUCCA [2] tRNA-Gln-TTG-3 -GGCCCCAUGGUGUAAU--GGUU-AGCACUCUGGACUUUGAAUCCAGCGA-UCCGAGUUCAAAUCUCGGUGGGACCUCCA [3] 3005b ..........................................................UCAAAUCUCGGUGGGACCUCCA [1,3] 3005a ...............................................................UCUCGGUGGGACCUCCA [1,2,3] #=GC SS_cons :(((((((,,<<<<___________>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))):::: #=GC RF +=======++====+++++++++++====+=====++***++=====+++++=====+++++++============++++ // Fragment Cluster 10: 3018b,3018a Fragment Coverage tRNA-Met-CAT-4:TLE_Z tRNA-Met-CAT-2:TLE_Z tRNA-Met-CAT-7:TLE_Z tRNA-Met-CAT-5:TLE_Z Fragment Aminos Met Fragment Alignment # STOCKHOLM 1.0 tRNA-Met-CAT-2 -GCCCUCUUAGCGCAGU--GGGC-AGCGCGUCAGUCUCAUAAUCUGAAGGUCCUGAGUUCGAGCCUCAGAGAGGGCACCA [1] tRNA-Met-CAT-4 -GCCCUCUUAGCGCAGC--GGGC-AGCGCGUCAGUCUCAUAAUCUGAAGGUCCUGAGUUCGAGCCUCAGAGAGGGCACCA [2] tRNA-Met-CAT-5 -GCCCUCUUAGCGCAGCU-GGC--AGCGCGUCAGUCUCAUAAUCUGAAGGUCCUGAGUUCAAGCCUCAGAGAGGGCACCA [3] tRNA-Met-CAT-7 -GCCCUCUUAGUGCAGCU-GGC--AGCGCGUCAGUUUCAUAAUCUGAAAGUCCUGAGUUCAAGCCUCAGAGAGGGCACCA [4] 3018b ..........................................................UCGAGCCUCAGAGAGGGCACCA [1,2] 3018a .............................................................AGCCUCAGAGAGGGCACCA [1,2,3,4] #=GC SS_cons :(((((((,,<<<<___________>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))):::: #=GC RF +=======++====+++++++++++====+=====++***++=====+++++=====+++++++============++++ // Fragment Cluster 11: 5010a,3022b,3022a Fragment Coverage tRNA-Ile-AAT-8:A_DSL_TLE_Z tRNA-Ile-AAT-2:A_DSL tRNA-Ile-AAT-1:A_DSL_TLE_Z tRNA-Ile-AAT-6:A_DSL tRNA-Ile-AAT-7:A_DSL_TLE_Z tRNA-Ile-AAT-4:A_DSL tRNA-Ile-AAT-5:A_DSL_TLE_Z tRNA-Ile-AAT-12:A_DSL tRNA-Ile-GAT-1:A_DSL Fragment Aminos Ile Fragment Alignment # STOCKHOLM 1.0 tRNA-Ile-AAT-1 -GGCCGGUUAGCUCAGUU-GGUU-AGAGCGUGGCGCUAAUAACGCCAAGGUCGCGGGUUCGAUCCCCGUACGGGCCACCA [1] tRNA-Ile-AAT-2 -GGCCGGUUAGCUCAGUU-GGUU-AGAGCGUGGUGCUAAUAACGCCAAGGUCGCGGGUUCGAUCCCCGUACUGGCCACCA [2] tRNA-Ile-AAT-4 -GGCCGGUUAGCUCAGUU-GGUU-AGAGCGUGGUGCUAAUAACGCCAAGGUCGCGGGUUCGAACCCCGUACGGGCCACCA [3] tRNA-Ile-AAT-5 -GGCCGGUUAGCUCAGUU-GGUU-AGAGCGUGGUGCUAAUAACGCCAAGGUCGCGGGUUCGAUCCCCGUACGGGCCACCA [4] tRNA-Ile-AAT-6 -GGCCGGUUAGCUCAGUU-GGUU-AGAGCGUGGUGCUAAUAACGCUAAGGUCGCGGGUUCGAUCCCCGUACUGGCCACCA [5] tRNA-Ile-AAT-7 -GGCCGGUUAGCUCAGUU-GGUC-AGAGCGUGGUGCUAAUAACGCCAAGGUCGCGGGUUCGAUCCCCGUACGGGCCACCA [6] tRNA-Ile-AAT-8 -GGCCGGUUAGCUCAGUC-GGCU-AGAGCGUGGUGCUAAUAACGCCAAGGUCGCGGGUUCGAUCCCCGUACGGGCCACCA [7] tRNA-Ile-AAT-12 -GGCCGGUUAGCUCAGUC-GGUU-AGAGCGUGGUGCUAAUAACGCCAAGGUCGCGGGUUCGAUCCCCGUGCCGGUCACCA [8] tRNA-Ile-GAT-1 -GGCCGGUUAGCUCAGUU-GGUA-AGAGCGUGGUGCUGAUAACACCAAGGUCGCGGGCUCGACUCCCGCACCGGCCACCA [9] 5010a .GGCCGGUUAGCUCAG................................................................ [1,2,3,4,5,6,7,8,9] 3022b ..........................................................UCGAUCCCCGUACGGGCCACCA [1,4,6,7] 3022a ..............................................................UCCCCGUACGGGCCACCA [1,4,6,7] #=GC SS_cons :(((((((,,<<<<___________>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))):::: #=GC RF +=======++====+++++++++++====+=====++***++=====+++++=====+++++++============++++ // Fragment Cluster 12: 5026a,5026b,5026c,5027c,5027b,3008b,3008a Fragment Coverage tRNA-Val-AAC-1:A_DSLE_CS_TLE_Z tRNA-Val-AAC-2:A_DSLE_CS_TLE_Z tRNA-Val-AAC-3:A_DSLE_CS tRNA-Val-AAC-4:A_DSLE_CS_TLE_Z tRNA-Val-AAC-5:A_DSLE tRX-Val-NNN-1:TE_Z tRNA-Val-CAC-1:A_DSLE_CS_TLE_Z tRNA-Val-CAC-7:A_DSL tRNA-Val-CAC-4:A_DSLE_CS tRNA-Val-CAC-5:A_DSLE_CS_TLE_Z tRNA-Val-CAC-14:A_DSLE Fragment Aminos Val Fragment Alignment # STOCKHOLM 1.0 tRNA-Val-AAC-1 -GUUUCCGUAGUGUAGU--GGUU-AUCACGUUCGCCUAACACGCGAAAGGUCCCCGGUUCGAAACCGGGCGGAAACACCA [1] tRNA-Val-AAC-2 -GUUUCCGUAGUGUAGU--GGUC-AUCACGUUCGCCUAACACGCGAAAGGUCCCCGGUUCGAAACCGGGCGGAAACACCA [2] tRNA-Val-AAC-3 -GUUUCCGUAGUGUAGU--GGUU-AUCACGUUCGCCUAACACGCGAAAGGUCCCUGGAUCAAAACCAGGCGGAAACACCA [3] tRNA-Val-AAC-4 -GUUUCCGUAGUGUAGU--GGUU-AUCACGUUCGCCUAACACGCGAAAGGUCCGCGGUUCGAAACCGGGCGGAAACACCA [4] tRNA-Val-AAC-5 -GUUUCCGUAGUGUAGU--GGUU-AUCACGUUUGCCUAACACGCGAAAGGUCCCCGGUUCGAAACCGGGCAGAAACACCA [5] tRNA-Val-CAC-1 -GUUUCCGUAGUGUAGU--GGUU-AUCACGUUCGCCUCACACGCGAAAGGUCCCCGGUUCGAAACCGGGCGGAAACACCA [6] tRNA-Val-CAC-4 -GUUUCCGUAGUGUAGU--GGUU-AUCACGUUCGCCUCACACGCGAAAGGUCCCCGGUUCGAAACUGGGCGGAAACACCA [7] tRNA-Val-CAC-5 -GUUUCCGUAGUGUAGU--GGUU-AUCACGUUCGCCUCACACGCGAAAGGUCCCCGGUUCGAAACCGGGCGGAAACACCA [8] tRNA-Val-CAC-7 -GUUUCCGUAGUGUAGU--GGUU-AUUAUGUUCGCCUCACACGCGAAAAGUCCCCGGUUCGAAAUCAGGCGGGAACACCA [9] tRNA-Val-CAC-14 -GUUUCCGUAGUGUAGU--GGUU-AUCAUGUUCGCCUCACACGCGAAAGGUCCCCGGUUCGAAACUGGAUGGAAACACCA [10] tRX-Val-NNN-1 -GUUUCCAUAGCGUAGU--AAUU-AUCAAGUUUGCCUAACACGCGAAAUGUCCCCGGUUCAAAACCGGGCGGAAACACCA [11] 5026a .GUUUCCGUAGUGUAGU--GG........................................................... [1,2,3,4,5,6,7,8,9,10] 5026b .GUUUCCGUAGUGUAGU--GGUC-AUC..................................................... [2] 5027b .GUUUCCGUAGUGUAGU--GGUU-AUC..................................................... [1,3,4,5,6,7,8,10] 5026c .GUUUCCGUAGUGUAGU--GGUC-AUCACGUUCGC............................................. [2] 5027c .GUUUCCGUAGUGUAGU--GGUU-AUCACGUUCGC............................................. [1,3,4,6,7,8] 3008b ..........................................................UCGAAACCGGGCGGAAACACCA [1,2,4,6,8] 3008a ...............................................................ACCGGGCGGAAACACCA [1,2,4,6,8,11] #=GC SS_cons :(((((((,,<<<<___________>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))):::: #=GC RF +=======++====+++++++++++====+=====++***++=====+++++=====+++++++============++++ // Fragment Cluster 13: 5020b,5020c,5020a,3017b,3017a Fragment Coverage tRX-Val-NNN-2:A_DSL tRNA-Val-TAC-1:A_DSLE_CS_TLE_Z tRNA-Val-TAC-3:A_DSLE_TLE_Z tRNA-Val-TAC-2:A_DSL_TLE_Z Fragment Aminos Val Fragment Alignment # STOCKHOLM 1.0 tRX-Val-NNN-2 -GGUUCCAUAGUGUAAC--AGUU-AUCAUGUCUGCUUUACACACUGAAGGUCCUGGGUUCAAACUCCAGUGGAACCACCA [1] tRNA-Val-TAC-1 -GGUUCCAUAGUGUAGU--GGUU-AUCACGUCUGCUUUACACGCAGAAGGUCCUGGGUUCGAGCCCCAGUGGAACCACCA [2] tRNA-Val-TAC-2 -GGUUCCAUAGUGUAGC--GGUU-AUCACGUCUGCUUUACACGCAGAAGGUCCUGGGUUCGAGCCCCAGUGGAACCACCA [3] tRNA-Val-TAC-3 -GGUUCCAUAGUGUAGU--GGUU-AUCACAUCUGCUUUACACGCAGAAGGUCCUGGGUUCAAGCCCCAGUGGAACCACCA [4] 5020a .GGUUCCAUAGUGUA................................................................. [1,2,3,4] 5020b .GGUUCCAUAGUGUAGU--GGUU-AUC..................................................... [2,4] 5020c .GGUUCCAUAGUGUAGU--GGUU-AUCACGUCUGC............................................. [2] 3017b ..........................................................UCGAGCCCCAGUGGAACCACCA [2,3] 3017a .............................................................AGCCCCAGUGGAACCACCA [2,3,4] #=GC SS_cons :(((((((,,<<<<___________>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))):::: #=GC RF +=======++====+++++++++++====+=====++***++=====+++++=====+++++++============++++ // Fragment Cluster 14: 3009a,3009b Fragment Coverage tRNA-Leu-TAA-1:TLE_Z Fragment Aminos Leu Fragment Alignment # STOCKHOLM 1.0 tRNA-Leu-TAA-1 -ACCAGGAUGGCCGAGU--GGUU-AAGGCGUUGGACUUAAGAUCCAAU-G-CGUGGGUUCGAACCCCACUCCUGGUACCA [1] 3009b ..........................................................UCGAACCCCACUCCUGGUACCA [1] 3009a ..............................................................ACCCCACUCCUGGUACCA [1] #=GC SS_cons :(((((((,,<<<<___________>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))):::: #=GC RF +=======++====+++++++++++====+=====++***++=====+++++=====+++++++============++++ // Fragment Cluster 15: 3026b,5008b,3026a,5008c Fragment Coverage tRNA-Gly-TCC-4:A_DSLE tRNA-Gly-TCC-1:TLE_Z tRNA-Gly-TCC-2:A_DSLE_CS_TLE_Z tRNA-Gly-TCC-3:TLE_Z Fragment Aminos Gly Fragment Alignment # STOCKHOLM 1.0 tRNA-Gly-TCC-1 -GCGUUGGUGGUAUAGU--GGUU-AGCAUAGCUGCCUUCCAAGCAGUUGA-CCCGGGUUCGAUUCCCGGCCAACGCACCA [1] tRNA-Gly-TCC-2 -GCGUUGGUGGUAUAGU--GGUG-AGCAUAGCUGCCUUCCAAGCAGUUGA-CCCGGGUUCGAUUCCCGGCCAACGCACCA [2] tRNA-Gly-TCC-3 -GCGUUGGUGGUAUAGU--GGUA-AGCAUAGCUGCCUUCCAAGCAGUUGA-CCCGGGUUCGAUUCCCGGCCAACGCACCA [3] tRNA-Gly-TCC-4 -GCGUUGGUGGUAUAGU--GGUG-AGCAUAGUUGCCUUCCAAGCAGUUGA-CCCGGGCUCGAUUCCCGCCCAACGCACCA [4] 5008b .GCGUUGGUGGUAUAGU--GGUG-AGC..................................................... [2,4] 5008c .GCGUUGGUGGUAUAGU--GGUG-AGCAUAGCUG.............................................. [2] 3026b ..........................................................UCGAUUCCCGGCCAACGCACCA [1,2,3] 3026a ..............................................................UUCCCGGCCAACGCACCA [1,2,3] #=GC SS_cons :(((((((,,<<<<___________>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))):::: #=GC RF +=======++====+++++++++++====+=====++***++=====+++++=====+++++++============++++ // Fragment Cluster 16: 3013b,3013a Fragment Coverage tRNA-His-GTG-1:TLE_Z tRNA-His-GTG-2:TLE_Z Fragment Aminos His Fragment Alignment # STOCKHOLM 1.0 tRNA-His-GTG-1 GGCCGUGAUCGUAUAGU--GGUU-AGUACUCUGCGUUGUGGCCGCAGCAA-CCUCGGUUCGAAUCCGAGUCACGGCACCA [1] tRNA-His-GTG-2 GGCCAUGAUCGUAUAGU--GGUU-AGUACUCUGCGCUGUGGCCGCAGCAA-CCUCGAUUCGAAUCCGAGUCACGGCACCA [2] 3013b ..........................................................UCGAAUCCGAGUCACGGCACCA [1,2] 3013a ...............................................................UCCGAGUCACGGCACCA [1,2] #=GC SS_cons :(((((((,,<<<<___________>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))):::: #=GC RF +=======++====+++++++++++====+=====++***++=====+++++=====+++++++============++++ // Fragment Cluster 17: 5002b,5002c,5002a Fragment Coverage tRNA-Arg-CCG-2:A_DSLE_CS Fragment Aminos Arg Fragment Alignment # STOCKHOLM 1.0 tRNA-Arg-CCG-2 -GACCCAGUGGCCUAAU--GGAU-AAGGCAUCAGCCUCCGGAGCUGGGGAUUGUGGGUUCGAGUCCCAUCUGGGUCGCCA [1] 5002a .GACCCAGUGGCCUA................................................................. [1] 5002b .GACCCAGUGGCCUAAU--GGA.......................................................... [1] 5002c .GACCCAGUGGCCUAAU--GGAU-AAGGCAUCAGC............................................. [1] #=GC SS_cons :(((((((,,<<<<___________>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))):::: #=GC RF +=======++====+++++++++++====+=====++***++=====+++++=====+++++++============++++ // Fragment Cluster 18: 3027a,3027b,5004b,5004c Fragment Coverage tRNA-Gly-GCC-2:A_DSLE_CSL_TLE_Z tRNA-Gly-GCC-3:A_DSLE_CSL tRNA-Gly-CCC-5:TE_Z tRNA-Gly-CCC-1:A_DSLE_CSL_TE_Z tRNA-Gly-GCC-5:A_DSLE_CSL Fragment Aminos Gly Fragment Alignment # STOCKHOLM 1.0 tRNA-Gly-CCC-1 -GCAUUGGUGGUUCAGU--GGU--AGAAUUCUCGCCUCCCACGCGGGAGA-CCCGGGUUCAAUUCCCG.GCCAAUGCACCA [1] tRNA-Gly-CCC-5 -GCCUUGGUGGUGCAGU--GGU--AGAAUUCUCGCCUCCCACGUGGGAGA-CCCGGGUUCAAUUCCCG.GCCAAUGCACCA [2] tRNA-Gly-GCC-2 -GCAUUGGUGGUUCAGU--GGU--AGAAUUCUCGCCUGCCACGCGGGAGG-CCCGGGUUCGAUUCCCG.GCCAAUGCACCA [3] tRNA-Gly-GCC-3 -GCAUUGGUGGUUCAGU--GGU--AGAAUUCUCGCCUGCCACGCGGGAGG-CCCGGGUUUGAUUCCCG.GCCAGUGCACCA [4] tRNA-Gly-GCC-5 -GCAUUGGUGGUUCAGU--GGU--AGAAUUCUCGCCUGCCAUGCGGGCGG-CCGGGCUUCGAUU-CCUgGCCAAUGCACCA [5] 5004b .GCAUUGGUGGUUCAGU--GGU--AGA...................................................... [1,3,4,5] 5004c .GCAUUGGUGGUUCAGU--GGU--AGAAUUCUCGCC............................................. [1,3,4,5] 3027b ..........................................................UCGAUUCCCG.GCCAAUGCACCA [3] 3027a ...............................................................UCCCG.GCCAAUGCACCA [1,2,3] #=GC SS_cons :(((((((,,<<<<___________>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>.>))))))):::: #=GC RF +=======++====+++++++++++====+=====++***++=====+++++=====+++++++====.========++++ // Fragment Cluster 19: 5003c,5003b,3028a,3028b Fragment Coverage tRNA-Gly-GCC-1:A_DSLE_CSL_TLE_Z Fragment Aminos Gly Fragment Alignment # STOCKHOLM 1.0 tRNA-Gly-GCC-1 -GCAUGGGUGGUUCAGU--GGU--AGAAUUCUCGCCUGCCACGCGGGAGG-CCCGGGUUCGAUUCCCGGCCCAUGCACCA [1] 5003b .GCAUGGGUGGUUCAGU--GGU--AGA..................................................... [1] 5003c .GCAUGGGUGGUUCAGU--GGU--AGAAUUCUCGCC............................................ [1] 3028b ..........................................................UCGAUUCCCGGCCCAUGCACCA [1] 3028a ...............................................................UCCCGGCCCAUGCACCA [1] #=GC SS_cons :(((((((,,<<<<___________>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))):::: #=GC RF +=======++====+++++++++++====+=====++***++=====+++++=====+++++++============++++ // Fragment Cluster 20: 5009c,5009b,5009a Fragment Coverage tRNA-Val-CAC-2:A_DSLE_CS Fragment Aminos Val Fragment Alignment # STOCKHOLM 1.0 tRNA-Val-CAC-2 -GCUUCUGUAGUGUAGU--GGUU-AUCACGUUCGCCUCACACGCGAAAGGUCCCCGGUUCGAAACCGGGCAGAAGCACCA [1] 5009a .GCUUCUGUAGUGUAG................................................................ [1] 5009b .GCUUCUGUAGUGUAGU--GGUU-AUC..................................................... [1] 5009c .GCUUCUGUAGUGUAGU--GGUU-AUCACGUUCGC............................................. [1] #=GC SS_cons :(((((((,,<<<<___________>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))):::: #=GC RF +=======++====+++++++++++====+=====++***++=====+++++=====+++++++============++++ // Fragment Cluster 21: 5007a,5007c Fragment Coverage tRNA-Gly-CCC-2:A_DSLE_CS Fragment Aminos Gly Fragment Alignment # STOCKHOLM 1.0 tRNA-Gly-CCC-2 -GCGCCGCUGGUGUAGU--GGU--AUCAUGCAAGAUUCCCAUUCUUGCGA-CCCGGGUUCGAUUCCCGGGCGGCGCACCA [1] 5007a .GCGCCGCUGGUGUAG................................................................ [1] 5007c .GCGCCGCUGGUGUAGU--GGU--AUCAUGCAAGA............................................. [1] #=GC SS_cons :(((((((,,<<<<___________>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))):::: #=GC RF +=======++====+++++++++++====+=====++***++=====+++++=====+++++++============++++ // Fragment Cluster 22: 5001b,5001a,3031b,3030b,3030a,3031a Fragment Coverage tRNA-Tyr-GTA-7:A_DSLE_TLE_Z tRNA-Tyr-GTA-6:A_DSLE_V_TSLE_Z tRNA-Tyr-GTA-5:A_DSLE_TLE_Z tRNA-Tyr-GTA-4:A_DSLE tRNA-Tyr-GTA-3:A_DSL_V_TSLE_Z tRNA-Tyr-GTA-2:A_DSL_TLE_Z tRNA-Tyr-GTA-1:A_DSL Fragment Aminos Tyr Fragment Alignment # STOCKHOLM 1.0 tRNA-Tyr-GTA-1 -CCUUCGAUAGCUCAGUU-GGU--AGAGCGGAGGACUGUAGAUCCUUAG-------------------GUCGCUGGUUCGAAUCCGGCUCGAAGGACCA [1] tRNA-Tyr-GTA-2 -CCUUCGAUAGCUCAGUU-GGU--AGAGCGGAGGACUGUAGAUCCUUAG-------------------GUCGCUGGUUCGAUUCCGGCUCGAAGGACCA [2] tRNA-Tyr-GTA-3 -CCUUCGAUAGCUCAGUU-GGU--AGAGCGGAGGACUGUAGAUCCUUAG-------------------GUCGCUGGUUCGAAUCCGGCUCGGAGGACCA [3] tRNA-Tyr-GTA-4 -CCUUCGAUAGCUCAGCU-GGU--AGAGCGGAGGACUGUAGAUCCUUAG-------------------GUCGCUGGUUCGAUUCCAGCUCGAAGGACCA [4] tRNA-Tyr-GTA-5 -CCUUCGAUAGCUCAGCU-GGU--AGAGCGGAGGACUGUAGAUCCUUAG-------------------GUCGCUGGUUCGAUUCCGGCUCGAAGGACCA [5] tRNA-Tyr-GTA-6 -CCUUCGAUAGCUCAGCU-GGU--AGAGCGGAGGACUGUAGAUCCUUAG-------------------GUCGCUGGUUCGAAUCCGGCUCGGAGGACCA [6] tRNA-Tyr-GTA-7 -CCUUCGAUAGCUCAGCU-GGU--AGAGCGGAGGACUGUAGAUCCUUAG-------------------GUCGCUGGUUCAAUUCCGGCUCGAAGGACCA [7] 5001a .CCUUCGAUAGCUCAG................................................................................... [1,2,3,4,5,6,7] 5001b .CCUUCGAUAGCUCAGCU-GGU--AGAGC...................................................................... [4,5,6,7] 3031b .....................................................................UCGCUGGUUCGAAUCCGGCUCGGAGGACCA [3,6] 3030b .............................................................................UCGAUUCCGGCUCGAAGGACCA [2,5] 3030a .................................................................................UUCCGGCUCGAAGGACCA [2,5,7] 3031a ..................................................................................UCCGGCUCGGAGGACCA [3,6] #=GC SS_cons :(((((((,,<<<<___________>>>>,<<<<<_______>>>>>,,<<<<<<<_____>>>>>>>,,,<<<<<_______>>>>>))))))):::: #=GC RF +=======++====+++++++++++====+=====++***++=====++=======+++++=======+++=====+++++++============++++ // Fragment Cluster 23: 3007b,3007a Fragment Coverage tRNA-Thr-TGT-3:TLE_Z tRNA-Thr-TGT-6:TE_Z tRNA-Thr-TGT-5:TE_Z tRNA-Thr-TGT-4:TE_Z Fragment Aminos Thr Fragment Alignment # STOCKHOLM 1.0 tRNA-Thr-TGT-3 -GGCUCCAUAGCUCAGG--GGUU-AGAGCGCUGGUCUUGUAAACCAGGGGUCGCGAGUUCAAUUCUCGCUGGGGCCUCCA [1] tRNA-Thr-TGT-4 -GGCUCCAUAGCUCAGG--GGUU-AGAGCACUGGUCUUGUAAACCAGGGGUCGCGAGUUCAAAUCUCGCUGGGGCCUCCA [2] tRNA-Thr-TGT-5 -GGCCCUAUAGCUCAGG--GGUU-AGAGCACUGGUCUUGUAAACCAGGGGUCGCGAGUUCAAAUCUCGCUGGGGCCUCCA [3] tRNA-Thr-TGT-6 -GGCUCCAUAGCUCAGG--GGUU-AGAGCACUGGUCUUGUAAACCAGG-GUCGCGAGUUCAAAUCUCGCUGGGGCCUCCA [4] 3007b ..........................................................UCAAUUCUCGCUGGGGCCUCCA [1] 3007a ...............................................................UCUCGCUGGGGCCUCCA [1,2,3,4] #=GC SS_cons :(((((((,,<<<<___________>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))):::: #=GC RF +=======++====+++++++++++====+=====++***++=====+++++=====+++++++============++++ // Fragment Cluster 24: 5019b,5019a,3001a Fragment Coverage tRNA-Leu-AAG-4:TLE_Z tRNA-Leu-AAG-3:A_DSLE_TLE_Z tRNA-Leu-AAG-2:A_DSLE_TLE_Z tRNA-Leu-AAG-1:A_DSLE_TLE_Z tRNA-Leu-TAG-3:TLE_Z tRNA-Leu-TAG-1:A_DSLE_TLE_Z Fragment Aminos Leu Fragment Alignment # STOCKHOLM 1.0 tRNA-Leu-AAG-1 -GGUAGCGUGGCCGAGC--GGUCUAAGGCGCUGGAUUAAGGCUCCAGU-G-CGUGGGUUCGAAUCCCACCGCUGCCACCA [1] tRNA-Leu-AAG-2 -GGUAGCGUGGCCGAGC--GGUCUAAGGCGCUGGAUUAAGGCUCCAGU-G-CGUGGGUUCGAAUCCCACCGCUGCCACCA [2] tRNA-Leu-AAG-3 -GGUAGCGUGGCCGAGC--GGUCUAAGGCGCUGGAUUAAGGCUCCAGU-G-CGUGGGUUCAAAUCCCACCGCUGCCACCA [3] tRNA-Leu-AAG-4 -GGUAGCGUGGCCGAGU--GGUCUAAGACGCUGGAUUAAGGCUCCAGU-G-CGUGGGUUUGAAUCCCACCGCUGCCACCA [4] tRNA-Leu-TAG-1 -GGUAGCGUGGCCGAGC--GGUCUAAGGCGCUGGAUUUAGGCUCCAGU-G-CGUGGGUUCGAAUCCCACCGCUGCCACCA [5] tRNA-Leu-TAG-3 -GGUAGCGUGGCCGAGU--GGUCUAAGGCGCUGGAUUUAGGCUCCAGU-G-CGUGGGUUCGAAUCCCACCGCUGCCACCA [6] 5019a .GGUAGCGUGGCCGAGC............................................................... [1,2,3,5] 5019b .GGUAGCGUGGCCGAGC--GGUCUAAG..................................................... [1,2,3,5] 3001a ..............................................................AUCCCACCGCUGCCACCA [1,2,3,4,5,6] #=GC SS_cons :(((((((,,<<<<___________>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))):::: #=GC RF +=======++====+++++++++++====+=====++***++=====+++++=====+++++++============++++ // Fragment Cluster 25: 3023a,3023b Fragment Coverage tRNA-Phe-GAA-4:TE_Z tRNA-Phe-GAA-1:TLE_Z tRNA-Phe-GAA-2:TE_Z tRNA-Phe-GAA-3:TE_Z Fragment Aminos Phe Fragment Alignment # STOCKHOLM 1.0 tRNA-Phe-GAA-1 -GCCGAAAUAGCUCAGUU-GGG--AGAGCGUUAGACUGAAGAUCU.AAAGGUCCCUGGUUCGAUCCCGGGUUUCGGCACCA [1] tRNA-Phe-GAA-2 -GCCGAAAUAGCUCAGUU-GGG--AGAGCGUUAGACUGAAGAUCU.AAAGGUCCCUGGUUCAAUCCCGGGUUUCGGCACCA [2] tRNA-Phe-GAA-3 -GCCGAGAUAGCUCAGUU-GGG--AGAGCGUUAGACUGAAGAUCU.AAAGGUCCCUGGUUCAAUCCCGGGUUUCGGCACCA [3] tRNA-Phe-GAA-4 -GCCGAAAUAGCUCAGUU-GGG--AGAGCGUUAGACCGAAGAUCUuAAAGGUCCCUGGUUCAAUCCCGGGUUUCGGCACCA [4] 3023b ...........................................................UCGAUCCCGGGUUUCGGCACCA [1] 3023a ................................................................CCCGGGUUUCGGCACCA [1,2,3,4] #=GC SS_cons :(((((((,,<<<<___________>>>>,<<<<<_______>>>.>>,,,,,<<<<<_______>>>>>))))))):::: #=GC RF +=======++====+++++++++++====+=====++***++===.==+++++=====+++++++============++++ // Fragment Cluster 26: 5005a,5006c,5005c_2,3016a,5005b_2,3016b Fragment Coverage tRNA-Lys-CTT-3:A_DSLE_CS_TLE_Z tRNA-Lys-CTT-2:A_DSLE_CS_TLE_Z tRNA-Lys-CTT-1:A_DSLE_CSL_TLE_Z tRNA-Lys-CTT-5:A_DSL tRNA-Lys-CTT-4:A_DSLE_CSL_TLE_Z Fragment Aminos Lys Fragment Alignment # STOCKHOLM 1.0 tRNA-Lys-CTT-1 -GCCCGGCUAGCUCAGUC-GGU--AGAGCAUGGGACUCUUAAUCCCAGGGUCGUGGGUUCGAGCCCCACGUUGGGCGCCA [1] tRNA-Lys-CTT-2 -GCCCGGCUAGCUCAGUC-GGU--AGAGCAUGAGACUCUUAAUCUCAGGGUCGUGGGUUCGAGCCCCACGUUGGGCGCCA [2] tRNA-Lys-CTT-3 -GCCCGGCUAGCUCAGUC-GGU--AGAGCAUGAGACCCUUAAUCUCAGGGUCGUGGGUUCGAGCCCCACGUUGGGCGCCA [3] tRNA-Lys-CTT-4 -GCCCGGCUAGCUCAGUC-GGU--AGAGCAUGGGACUCUUAAUCUCAGGGUCGUGGGUUCGAGCCCCACGUUGGGCGCCA [4] tRNA-Lys-CTT-5 -GCCCGGCUAGCUCAGUC-GAU--AGAGCAUGAGACUCUUAAUCUCAGGGUCGUGGGUUCGAGCCGCACGUUGGGCGCCA [5] 5005a .GCCCGGCUAGCUCAG................................................................ [1,2,3,4,5] 5005b_2 .GCCCGGCUAGCUCAGUC-GGU--AGAGC................................................... [1,2,3,4] 5005c_2 .GCCCGGCUAGCUCAGUC-GGU--AGAGCAUGAGA............................................. [2,3] 5006c .GCCCGGCUAGCUCAGUC-GGU--AGAGCAUGGGAC............................................ [1,4] 3016b ..........................................................UCGAGCCCCACGUUGGGCGCCA [1,2,3,4] 3016a .............................................................AGCCCCACGUUGGGCGCCA [1,2,3,4] #=GC SS_cons :(((((((,,<<<<___________>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))):::: #=GC RF +=======++====+++++++++++====+=====++***++=====+++++=====+++++++============++++ // Fragment Cluster 27: 3006a,3006b,5005c_1,5005b_1 Fragment Coverage tRNA-Lys-TTT-5:A_DSLE_CS_TLE_Z tRNA-Lys-TTT-3:A_DSLE_CS_TLE_Z Fragment Aminos Lys Fragment Alignment # STOCKHOLM 1.0 tRNA-Lys-TTT-3 -GCCCGGAUAGCUCAGUC-GGU--AGAGCAUCAGACUUUUAAUCUGAGGGUCCAGGGUUCAAGUCCCUGUUCGGGCGCCA [1] tRNA-Lys-TTT-5 -GCCCGGAUAGCUCAGUC-GGU--AGAGCAUCAGACUUUUAAUCUGAGGGUCCGGGGUUCAAGUCCCUGUUCGGGCGCCA [2] 5005b_1 .GCCCGGAUAGCUCAGUC-GG........................................................... [1,2] 5005c_1 .GCCCGGAUAGCUCAGUC-GGU--AGAGCAUCAGA............................................. [1,2] 3006b ..........................................................UCAAGUCCCUGUUCGGGCGCCA [1,2] 3006a ...............................................................UCCCUGUUCGGGCGCCA [1,2] #=GC SS_cons :(((((((,,<<<<___________>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))):::: #=GC RF +=======++====+++++++++++====+=====++***++=====+++++=====+++++++============++++ // Fragment Cluster 28: 3019a,3019b Fragment Coverage tRNA-Ala-AGC-1:TLE_Z Fragment Aminos Ala Fragment Alignment # STOCKHOLM 1.0 tRNA-Ala-AGC-1 -GGGGGUAUAGCUCAGU--GGU--AGAGCGCGUGCUUAGCAUGCACGAGGUCCUGGGUUCGAUCCCCAGUACCUCCACCA [1] 3019b ..........................................................UCGAUCCCCAGUACCUCCACCA [1] 3019a ..............................................................UCCCCAGUACCUCCACCA [1] #=GC SS_cons :(((((((,,<<<<___________>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))):::: #=GC RF +=======++====+++++++++++====+=====++***++=====+++++=====+++++++============++++ // Fragment Cluster 29: 3010b,3010a Fragment Coverage tRNA-Leu-TAG-2:TLE_Z Fragment Aminos Leu Fragment Alignment # STOCKHOLM 1.0 tRNA-Leu-TAG-2 -GGUAGUGUGGCCGAGC--GGUCUAAGGCGCUGGAUUUAGGCUCCAGU-G-CGUGGGUUCGAAUCCCACCACUGCCACCA [1] 3010b ..........................................................UCGAAUCCCACCACUGCCACCA [1] 3010a ..............................................................AUCCCACCACUGCCACCA [1] #=GC SS_cons :(((((((,,<<<<___________>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))):::: #=GC RF +=======++====+++++++++++====+=====++***++=====+++++=====+++++++============++++ // Fragment Cluster 30: 5030c,5030b,3029a,3029b Fragment Coverage tRNA-Glu-TTC-4:TLE_Z tRNA-Glu-TTC-14:TLE_Z tRNA-Glu-CTC-2:A_DSLE_CS tRNA-Glu-CTC-3:TLE_Z tRNA-Glu-CTC-1:A_DSLE_CS_TLE_Z Fragment Aminos Glu Fragment Alignment # STOCKHOLM 1.0 tRNA-Glu-CTC-1 -UC.CCUGGUGGUCUAGU--GGUU-AGGAUUCGGCGCUCUCACCGCCGCGG-CCCGGGUUCGAUUCCCGGUCAGGGAACCA [1] tRNA-Glu-CTC-2 -UC.CCUGGUGGUCUAGU--GGUU-AGGAUUCGGCGCUCUCACCGCCGCGG-CCCGGGUUCGAUUCCCGGUCAGGAAACCA [2] tRNA-Glu-CTC-3 -UCcCCUGGUGGUCUAGU--GCUU-AGGAUUCGGUGCUCUCACCGCUGCUG-CCUGCGUUCGAUUCCCGGUCAGGGAACCA [3] tRNA-Glu-TTC-4 -UC.CCUGGUGGUCUAGU--GGCU-AGGAUUCGGCGCUUUCACCGCCGCGG-CCCGGGUUCGAUUCCCGGUCAGGGAACCA [4] tRNA-Glu-TTC-14 -UC.CCUGGUGGUCUAGU--GGCU-AGGAUUCGGCGCUUUCACCGCUGCGG-CCCGGGUUCGAUUCCCGGUCAGGGAACCA [5] 5030b .UC.CCUGGUGGUCUAGU--GGUU-AGG..................................................... [1,2] 5030c .UC.CCUGGUGGUCUAGU--GGUU-AGGAUUCGGCG............................................. [1,2] 3029b ...........................................................UCGAUUCCCGGUCAGGGAACCA [1,3,4,5] 3029a ...............................................................UUCCCGGUCAGGGAACCA [1,3,4,5] #=GC SS_cons :((.(((((,,<<<<___________>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))):::: #=GC RF +==.=====++====+++++++++++====+=====++***++=====+++++=====+++++++============++++ // Fragment Cluster 31: 5029a,5029b Fragment Coverage tRNA-Glu-TTC-1:A_DSLE Fragment Aminos Glu Fragment Alignment # STOCKHOLM 1.0 tRNA-Glu-TTC-1 -UCCCAUAUGGUCUAGC--GGUU-AGGAUUCCUGGUUUUCACCCAGGUGG-CCCGGGUUCGACUCCCGGUAUGGGAACCA [1] 5029a .UCCCAUAUGGUCUAGC--GG........................................................... [1] 5029b .UCCCAUAUGGUCUAGC--GGUU-AGG..................................................... [1] #=GC SS_cons :(((((((,,<<<<___________>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))):::: #=GC RF +=======++====+++++++++++====+=====++***++=====+++++=====+++++++============++++ // Fragment Cluster 32: 5028b,5028c,5028a,3015a,3015b Fragment Coverage tRNA-Glu-TTC-2:A_DSLE_CS_TLE_Z Fragment Aminos Glu Fragment Alignment # STOCKHOLM 1.0 tRNA-Glu-TTC-2 -UCCCACAUGGUCUAGC--GGUU-AGGAUUCCUGGUUUUCACCCAGGCGG-CCCGGGUUCGACUCCCGGUGUGGGAACCA [1] 5028a .UCCCACAUGGUCUAGC--GG........................................................... [1] 5028b .UCCCACAUGGUCUAGC--GGUU-AGG..................................................... [1] 5028c .UCCCACAUGGUCUAGC--GGUU-AGGAUUCCUGG............................................. [1] 3015b ..........................................................UCGACUCCCGGUGUGGGAACCA [1] 3015a .............................................................ACUCCCGGUGUGGGAACCA [1] #=GC SS_cons :(((((((,,<<<<___________>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))):::: #=GC RF +=======++====+++++++++++====+=====++***++=====+++++=====+++++++============++++ // Fragment Cluster 33: 5014a Fragment Coverage tRNA-Arg-ACG-2:A_DSL tRNA-Arg-ACG-1:A_DSL Fragment Aminos Arg Fragment Alignment # STOCKHOLM 1.0 tRNA-Arg-ACG-1 -GGGCCAGUGGCGCAAU--GGAU-AACGCGUCUGACUACGGAUCAGAAGAUUCCAGGUUCGACUCCUGGCUGGCUCGCCA [1] tRNA-Arg-ACG-2 -GGGCCAGUGGCGCAAU--GGAU-AACGCGUCUGACUACGGAUCAGAAGAUUCUAGGUUCGACUCCUGGCUGGCUCGCCA [2] 5014a .GGGCCAGUGGCGCAAU--GG........................................................... [1,2] #=GC SS_cons :(((((((,,<<<<___________>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))):::: #=GC RF +=======++====+++++++++++====+=====++***++=====+++++=====+++++++============++++ // Fragment Cluster 34: 3033a Fragment Coverage tRNA-Asn-GTT-5:TE_Z tRNA-Asn-GTT-4:TE_Z tRNA-Asn-GTT-1:TE_Z tRNA-Asn-GTT-3:TE_Z tRNA-Asn-GTT-2:TE_Z tRNA-Asn-GTT-24:TE_Z Fragment Aminos Asn Fragment Alignment # STOCKHOLM 1.0 tRNA-Asn-GTT-1 -GUCUCUGUGGCGCAAUC-GGUU-AGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAUCCCACCCAGGGACGCCA [1] tRNA-Asn-GTT-2 -GUCUCUGUGGCGCAAUC-GGUU-AGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGCCCACCCAGGGACGCCA [2] tRNA-Asn-GTT-3 -GUCUCUGUGGCGCAAUC-GGUU-AGCGCAUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGCCCACCCAGGGACGCCA [3] tRNA-Asn-GTT-4 -GUCUCUGUGGCGCAAUC-GGUU-AGCGCGUUCGGCUGUUAACCGAAAGAUUGGUGGUUCGAGCCCACCCAGGGACGCCA [4] tRNA-Asn-GTT-5 -GUCUCUGUGGCGCAAUC-GGUU-AGCGCGUUCGGCUGUUAACUGAAAGGUUGGUGGUUCGAGCCCACCCAGGGACGCCA [5] tRNA-Asn-GTT-24 -GUCUCUGUGGCGCAAUC-GGUU-AGCGCGUUCGGCUGUUAACCGCAAGGUUGGUGGUUCCAGCCCACCCAGGGACGCCA [6] 3033a ...............................................................CCCACCCAGGGACGCCA [1,2,3,4,5,6] #=GC SS_cons :(((((((,,<<<<___________>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))):::: #=GC RF +=======++====+++++++++++====+=====++***++=====+++++=====+++++++============++++ //