Tandem Repeats Finder Program written by: Gary Benson Program in Bioinformatics Boston University Version 4.09 Sequence: VEPZ01008100.1 Hibiscus syriacus cultivar Beakdansim tig00110630_pilon, whole genome shotgun sequence Parameters: 2 7 7 80 10 50 1000 Pmatch=0.80,Pindel=0.10 tuple sizes 0,4,5,7 tuple distances 0, 29, 159, 1000 Length: 1372717 ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33 File 6 of 7 Found at i:1073451 original size:22 final size:22 Alignment explanation
Indices: 1073413--1073492 Score: 85 Period size: 22 Copynumber: 3.7 Consensus size: 22 1073403 AATTTAAAAA * 1073413 AATATTATTT-AAATAATAATT 1 AATATTATTTAAAATAATAAAT * 1073434 AATATTATTTAAAATAATAACT 1 AATATTATTTAAAATAATAAAT * * * 1073456 AATATGATTTTAAATATTAAAT 1 AATATTATTTAAAATAATAAAT 1073478 -A-ATTACTTTAAAATA 1 AATATTA-TTTAAAATA 1073493 TTTTTATAAT Statistics Matches: 50, Mismatches: 7, Indels: 4 0.82 0.11 0.07 Matches are distributed among these distances: 20 3 0.06 21 19 0.38 22 28 0.56 ACGTcount: A:0.53, C:0.03, G:0.01, T:0.44 Consensus pattern (22 bp): AATATTATTTAAAATAATAAAT Found at i:1074136 original size:36 final size:37 Alignment explanation
Indices: 1074073--1074143 Score: 101 Period size: 36 Copynumber: 1.9 Consensus size: 37 1074063 CTTATACTAC * 1074073 ATTTTTAAAAAAACACATAAATGTTAATACTATTAATA 1 ATTTTTAAAAAAACACATAAATATTAATA-TATTAATA * 1074111 ATTTTTTAAAAAA-A-ATAAATATTAATATATTAA 1 ATTTTTAAAAAAACACATAAATATTAATATATTAA 1074144 ATTTTTGAAC Statistics Matches: 31, Mismatches: 2, Indels: 3 0.86 0.06 0.08 Matches are distributed among these distances: 35 6 0.19 36 12 0.39 37 1 0.03 38 12 0.39 ACGTcount: A:0.55, C:0.04, G:0.01, T:0.39 Consensus pattern (37 bp): ATTTTTAAAAAAACACATAAATATTAATATATTAATA Found at i:1075144 original size:6 final size:6 Alignment explanation
Indices: 1075135--1075204 Score: 106 Period size: 6 Copynumber: 11.5 Consensus size: 6 1075125 TATTACTATT * 1075135 ACCACG ACCACG GCCACG ACCACG ACCACG ACCACG ACCACG ACC-CGAG 1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCAC--G 1075184 ACCACG ACCACG ACCACG ACC 1 ACCACG ACCACG ACCACG ACC 1075205 CGAGACGAGA Statistics Matches: 59, Mismatches: 2, Indels: 6 0.88 0.03 0.09 Matches are distributed among these distances: 5 1 0.02 6 53 0.90 7 4 0.07 8 1 0.02 ACGTcount: A:0.31, C:0.50, G:0.19, T:0.00 Consensus pattern (6 bp): ACCACG Found at i:1075192 original size:25 final size:25 Alignment explanation
Indices: 1075135--1075210 Score: 120 Period size: 25 Copynumber: 3.1 Consensus size: 25 1075125 TATTACTATT * 1075135 ACCACGACCACGGCCACGA-CC-ACG 1 ACCACGACCACGACCACGACCCGA-G 1075159 ACCACGACCACGACCACGACCCGAG 1 ACCACGACCACGACCACGACCCGAG 1075184 ACCACGACCACGACCACGACCCGAG 1 ACCACGACCACGACCACGACCCGAG 1075209 AC 1 AC 1075211 GAGACGGCGG Statistics Matches: 49, Mismatches: 1, Indels: 3 0.92 0.02 0.06 Matches are distributed among these distances: 24 18 0.37 25 30 0.61 26 1 0.02 ACGTcount: A:0.32, C:0.49, G:0.20, T:0.00 Consensus pattern (25 bp): ACCACGACCACGACCACGACCCGAG Found at i:1086378 original size:114 final size:113 Alignment explanation
Indices: 1086250--1086503 Score: 252 Period size: 114 Copynumber: 2.2 Consensus size: 113 1086240 AAAACAGTTA ** ** * * 1086250 TTGAAAACGTATAATATATATTTTTTTGAAAA-AAATGGTTTTTGA-AAATATATATAATATGGT 1 TTGAAAATATATAATATATATTTTTTTGAAAACAAATGGAATAT-ATAAATATATATAATATAGT * 1086313 TTTGAAAATACGATTTAAAAACATATAT-TATATA-ATTTTGAAAATATTT 65 TTTGAAAAT--GATTTAAAAACATATATATATATAGATTTTAAAAATATTT * * ** * * 1086362 TTGAAAACATATATAATATATA-GTTTTCGAAAACATTTTGAATATATATATATATATAATATAG 1 TTG-AAA-ATATATAATATATATTTTTTTGAAAACAAATGGAATATATAAATATATATAATATAG * * * 1086426 TTTTTAAAATGTTTTAAAAACATATATAATATATAGTTTTTAAAAATATTT 64 TTTTGAAAATGATTTAAAAACATATAT-ATATATAGATTTTAAAAATATTT 1086477 TTGAAAATATAT--TATATAGTTTTTTTG 1 TTGAAAATATATAATATATA-TTTTTTTG 1086504 TTAATATATT Statistics Matches: 115, Mismatches: 18, Indels: 17 0.77 0.12 0.11 Matches are distributed among these distances: 111 6 0.05 112 19 0.17 113 24 0.21 114 50 0.43 115 16 0.14 ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45 Consensus pattern (113 bp): TTGAAAATATATAATATATATTTTTTTGAAAACAAATGGAATATATAAATATATATAATATAGTT TTGAAAATGATTTAAAAACATATATATATATAGATTTTAAAAATATTT Found at i:1086405 original size:26 final size:25 Alignment explanation
Indices: 1086347--1086410 Score: 71 Period size: 26 Copynumber: 2.6 Consensus size: 25 1086337 ATATTATATA * 1086347 ATTTTGAA-A-ATATTTTTGAAAAC 1 ATTTTGAATATATATTTTCGAAAAC * 1086370 ATATAT-AATATATAGTTTTCGAAAAC 1 AT-TTTGAATATATA-TTTTCGAAAAC 1086396 ATTTTGAATATATAT 1 ATTTTGAATATATAT 1086411 ATATATATAA Statistics Matches: 33, Mismatches: 3, Indels: 8 0.75 0.07 0.18 Matches are distributed among these distances: 23 4 0.12 24 3 0.09 25 6 0.18 26 20 0.61 ACGTcount: A:0.44, C:0.05, G:0.08, T:0.44 Consensus pattern (25 bp): ATTTTGAATATATATTTTCGAAAAC Found at i:1086451 original size:34 final size:34 Alignment explanation
Indices: 1086413--1086500 Score: 106 Period size: 34 Copynumber: 2.5 Consensus size: 34 1086403 ATATATATAT * 1086413 ATATATAATATAGTTTTT-AAAATGTTTTAAAAA 1 ATATATAATATAGTTTTTAAAAATATTTTAAAAA ** 1086446 CATATATAATATATAGTTTTTAAAAATATTTTTGAAA 1 -ATATAT-A-ATATAGTTTTTAAAAATATTTTAAAAA * 1086483 ATATATTATATAGTTTTT 1 ATATATAATATAGTTTTT 1086501 TTGTTAATAT Statistics Matches: 47, Mismatches: 4, Indels: 6 0.82 0.07 0.11 Matches are distributed among these distances: 34 17 0.36 35 1 0.02 36 17 0.36 37 12 0.26 ACGTcount: A:0.44, C:0.01, G:0.06, T:0.49 Consensus pattern (34 bp): ATATATAATATAGTTTTTAAAAATATTTTAAAAA Found at i:1086461 original size:77 final size:78 Alignment explanation
Indices: 1086335--1086494 Score: 216 Period size: 77 Copynumber: 2.1 Consensus size: 78 1086325 ATTTAAAAAC * * * * 1086335 ATATATTATATAATTTTGAAAATATTTTTGAAAACATATATAATATATAGTTTTCGAAAACA-TT 1 ATATATAATATAATTTTGAAAATAGTTTTAAAAACATATATAATATATAGTTTTCAAAAACATTT * 1086399 TTGAATATATATAT 66 TTGAAAATATAT-T * * * * 1086413 ATATATAATATAGTTTTTAAAAT-GTTTTAAAAACATATATAATATATAGTTTTTAAAAATATTT 1 ATATATAATATAATTTTGAAAATAGTTTTAAAAACATATATAATATATAGTTTTCAAAAACATTT 1086477 TTGAAAATATATT 66 TTGAAAATATATT 1086490 ATATA 1 ATATA 1086495 GTTTTTTTGT Statistics Matches: 72, Mismatches: 9, Indels: 3 0.86 0.11 0.04 Matches are distributed among these distances: 77 39 0.54 78 33 0.46 ACGTcount: A:0.46, C:0.03, G:0.06, T:0.46 Consensus pattern (78 bp): ATATATAATATAATTTTGAAAATAGTTTTAAAAACATATATAATATATAGTTTTCAAAAACATTT TTGAAAATATATT Found at i:1086494 original size:36 final size:38 Alignment explanation
Indices: 1086188--1086494 Score: 196 Period size: 36 Copynumber: 8.2 Consensus size: 38 1086178 TTTATAACAA * 1086188 TATAGTATAGTTTTTGAAAATATTTTCT-AAAAGCGTATA- 1 TATA-TATAGTTTTTGAAAATATTTT-TGAAAA-CATATAT * * * * * 1086227 -ACATATAGTTTTT-AAAACAGTTATTGAAAACGTATAA 1 TATATATAGTTTTTGAAAATA-TTTTTGAAAACATATAT * * * 1086264 TATATAT-TTTTTTGAAAAAAATGGTTTTTGAAAATATATA- 1 TATATATAGTTTTTG---AAAAT-ATTTTTGAAAACATATAT * ** * 1086304 TA-ATAT-GGTTTTGAAAATACGATTTAAAAACATATAT 1 TATATATAGTTTTTGAAAATA-TTTTTGAAAACATATAT 1086341 TATATA-A--TTTTGAAAATATTTTTGAAAACATATAT 1 TATATATAGTTTTTGAAAATATTTTTGAAAACATATAT * * * * 1086376 AATATATAGTTTTCGAAAACA-TTTTGAATATATATATAT 1 TATATATAGTTTTTGAAAATATTTTTGAA-A-ACATATAT * * 1086415 ATATAATATAGTTTTT-AAAAT-GTTTTAAAAACATATAT 1 -TAT-ATATAGTTTTTGAAAATATTTTTGAAAACATATAT * * 1086453 AATATATAGTTTTTAAAAATATTTTTG-AAA-ATATAT 1 TATATATAGTTTTTGAAAATATTTTTGAAAACATATAT 1086489 TATATA 1 TATATA 1086495 GTTTTTTTGT Statistics Matches: 212, Mismatches: 33, Indels: 49 0.72 0.11 0.17 Matches are distributed among these distances: 35 19 0.09 36 63 0.30 37 41 0.19 38 31 0.15 39 17 0.08 40 14 0.07 41 27 0.13 ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43 Consensus pattern (38 bp): TATATATAGTTTTTGAAAATATTTTTGAAAACATATAT Found at i:1086519 original size:3 final size:3 Alignment explanation
Indices: 1086513--1086598 Score: 77 Period size: 3 Copynumber: 26.7 Consensus size: 3 1086503 GTTAATATAT 1086513 TTA TTA TTA TTA TTA TTCA TTA -TA TTTA TTTA TTA TATA TTA TATA 1 TTA TTA TTA TTA TTA TT-A TTA TTA -TTA -TTA TTA T-TA TTA T-TA * 1086559 TTA TTA TTA TTCA TTA -TA TTTA TTT TTA GTTA TTA TTA TT 1 TTA TTA TTA TT-A TTA TTA -TTA TTA TTA -TTA TTA TTA TT 1086599 TCTTTTAGGG Statistics Matches: 72, Mismatches: 2, Indels: 18 0.78 0.02 0.20 Matches are distributed among these distances: 2 4 0.06 3 45 0.62 4 23 0.32 ACGTcount: A:0.31, C:0.02, G:0.01, T:0.65 Consensus pattern (3 bp): TTA Found at i:1086547 original size:20 final size:20 Alignment explanation
Indices: 1086522--1086583 Score: 92 Period size: 20 Copynumber: 3.1 Consensus size: 20 1086512 TTTATTATTA 1086522 TTATTATTCATTATATTTAT 1 TTATTATTCATTATATTTAT 1086542 TTATTATAT-ATTATATATTA- 1 TTATTAT-TCATTATAT-TTAT 1086562 TTATTATTCATTATATTTAT 1 TTATTATTCATTATATTTAT 1086582 TT 1 TT 1086584 TTAGTTATTA Statistics Matches: 38, Mismatches: 0, Indels: 8 0.83 0.00 0.17 Matches are distributed among these distances: 19 4 0.11 20 30 0.79 21 4 0.11 ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65 Consensus pattern (20 bp): TTATTATTCATTATATTTAT Found at i:1086553 original size:40 final size:38 Alignment explanation
Indices: 1086507--1086598 Score: 141 Period size: 40 Copynumber: 2.3 Consensus size: 38 1086497 TTTTTTGTTA 1086507 ATATATTTATTATTATTATTATTCATTATATTTATTTATT 1 ATATA-TTATTATTATTATTATTCATTATATTTATTT-TT 1086547 ATATATTATATATTATTATTATTCATTATATTTATTTTT 1 ATATATTAT-TATTATTATTATTCATTATATTTATTTTT 1086586 AGT-TATTATTATT 1 A-TATATTATTATT 1086599 TCTTTTAGGG Statistics Matches: 50, Mismatches: 0, Indels: 6 0.89 0.00 0.11 Matches are distributed among these distances: 38 4 0.08 39 13 0.26 40 33 0.66 ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64 Consensus pattern (38 bp): ATATATTATTATTATTATTATTCATTATATTTATTTTT Found at i:1086581 original size:13 final size:13 Alignment explanation
Indices: 1086507--1086598 Score: 86 Period size: 13 Copynumber: 7.0 Consensus size: 13 1086497 TTTTTTGTTA 1086507 ATATATTTATTATT 1 ATATA-TTATTATT 1086521 AT-TATTATTCATT 1 ATATATTATT-ATT 1086534 ATAT-TTATTTATT 1 ATATATTA-TTATT 1086547 ATATATTATATATT 1 ATATATTAT-TATT 1086561 AT-TATTATTCATT 1 ATATATTATT-ATT * 1086574 ATAT-TTATTTTT 1 ATATATTATTATT 1086586 AGT-TATTATTATT 1 A-TATATTATTATT 1086599 TCTTTTAGGG Statistics Matches: 67, Mismatches: 2, Indels: 19 0.76 0.02 0.22 Matches are distributed among these distances: 12 10 0.15 13 42 0.63 14 15 0.22 ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64 Consensus pattern (13 bp): ATATATTATTATT Found at i:1087481 original size:17 final size:18 Alignment explanation
Indices: 1087450--1087484 Score: 54 Period size: 18 Copynumber: 2.0 Consensus size: 18 1087440 AGAGTTGAGA 1087450 GGTTTTTTAGAGGTTTGG 1 GGTTTTTTAGAGGTTTGG * 1087468 GGTTTTTTTG-GGTTTGG 1 GGTTTTTTAGAGGTTTGG 1087485 TTAAAAATGA Statistics Matches: 16, Mismatches: 1, Indels: 1 0.89 0.06 0.06 Matches are distributed among these distances: 17 7 0.44 18 9 0.56 ACGTcount: A:0.06, C:0.00, G:0.40, T:0.54 Consensus pattern (18 bp): GGTTTTTTAGAGGTTTGG Found at i:1087869 original size:29 final size:28 Alignment explanation
Indices: 1087817--1087874 Score: 80 Period size: 28 Copynumber: 2.0 Consensus size: 28 1087807 TTACTCTAAA * * * 1087817 AAATTAACATTTTTCTTTGTTTTTCTTT 1 AAATTAACATTTTTCTATCTTTTTATTT 1087845 AAATTAACATTTTTCTCATCTTTTTATTT 1 AAATTAACATTTTTCT-ATCTTTTTATTT 1087874 A 1 A 1087875 TTTATTTCCT Statistics Matches: 26, Mismatches: 3, Indels: 1 0.87 0.10 0.03 Matches are distributed among these distances: 28 16 0.62 29 10 0.38 ACGTcount: A:0.26, C:0.12, G:0.02, T:0.60 Consensus pattern (28 bp): AAATTAACATTTTTCTATCTTTTTATTT Found at i:1087962 original size:11 final size:11 Alignment explanation
Indices: 1087948--1087994 Score: 53 Period size: 11 Copynumber: 4.4 Consensus size: 11 1087938 TTTCTTAACC 1087948 TTTTTATTTAT 1 TTTTTATTTAT 1087959 TTTTTATTTCA- 1 TTTTTATTT-AT * 1087970 TATTTATTTAT 1 TTTTTATTTAT * 1087981 TTATT-TTTAT 1 TTTTTATTTAT 1087991 TTTT 1 TTTT 1087995 ACGATCTAAC Statistics Matches: 30, Mismatches: 4, Indels: 5 0.77 0.10 0.13 Matches are distributed among these distances: 10 9 0.30 11 20 0.67 12 1 0.03 ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79 Consensus pattern (11 bp): TTTTTATTTAT Found at i:1087991 original size:18 final size:17 Alignment explanation
Indices: 1087948--1087992 Score: 63 Period size: 18 Copynumber: 2.5 Consensus size: 17 1087938 TTTCTTAACC 1087948 TTTTTATTTATTTTTTA 1 TTTTTATTTATTTTTTA * 1087965 TTTCATATTTATTTATTTA 1 TTT-TTATTTATTT-TTTA 1087984 TTTTTATTT 1 TTTTTATTT 1087993 TTACGATCTA Statistics Matches: 24, Mismatches: 2, Indels: 3 0.83 0.07 0.10 Matches are distributed among these distances: 17 3 0.12 18 14 0.58 19 7 0.29 ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78 Consensus pattern (17 bp): TTTTTATTTATTTTTTA Found at i:1092249 original size:46 final size:46 Alignment explanation
Indices: 1092191--1092286 Score: 113 Period size: 46 Copynumber: 2.1 Consensus size: 46 1092181 ATTATTCTTT * * * 1092191 ATTTTCATTTATAACATTCATCCATGTTTATAATGCA-CCATTATGC 1 ATTTTCAGTTATAACATACATCCATGTTGATAATGCACCCA-TATGC * * ** 1092237 ATTTTCAGTTATAGCATACTTTTATGTTGATAATGCACCCATATGC 1 ATTTTCAGTTATAACATACATCCATGTTGATAATGCACCCATATGC 1092283 ATTT 1 ATTT 1092287 CAACTATGAC Statistics Matches: 42, Mismatches: 7, Indels: 2 0.82 0.14 0.04 Matches are distributed among these distances: 46 39 0.93 47 3 0.07 ACGTcount: A:0.29, C:0.18, G:0.09, T:0.44 Consensus pattern (46 bp): ATTTTCAGTTATAACATACATCCATGTTGATAATGCACCCATATGC Found at i:1092349 original size:45 final size:45 Alignment explanation
Indices: 1092266--1092384 Score: 143 Period size: 45 Copynumber: 2.6 Consensus size: 45 1092256 TTTTATGTTG * * * * 1092266 ATAATGCACCCATATGCATT-TCAACTATGACACACTTTCATTCCA 1 ATAATGCACCCATATGCATTAT-TATTTTGACACACTTTCATTACA * * 1092311 ATAATGCACCCATATGCATTATTATTTTGGCATC-CTTTCATTACG 1 ATAATGCACCCATATGCATTATTATTTTGACA-CACTTTCATTACA * 1092356 GTAATGCACCCATATGCATTATTATTTTG 1 ATAATGCACCCATATGCATTATTATTTTG 1092385 TTCATTCGTT Statistics Matches: 65, Mismatches: 7, Indels: 4 0.86 0.09 0.05 Matches are distributed among these distances: 45 63 0.97 46 2 0.03 ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37 Consensus pattern (45 bp): ATAATGCACCCATATGCATTATTATTTTGACACACTTTCATTACA Found at i:1095673 original size:45 final size:45 Alignment explanation
Indices: 1095622--1095919 Score: 384 Period size: 45 Copynumber: 6.6 Consensus size: 45 1095612 ATTTATGTTG * * * ** 1095622 ATAATGCACCCATATGCATT-TCAACTATGAAATCCTTTCATGCCA 1 ATAATGCACCCATATGCATTAT-TATTTTGGCATCCTTTCATGCCA * 1095667 ATAATGCACCCATATGCATTATTATTTTGGCATCATTTCATGCCA 1 ATAATGCACCCATATGCATTATTATTTTGGCATCCTTTCATGCCA * * * * * 1095712 ATAATGCACCCATATTCTTTATTATTTTGGGATACTTTCATGCTA 1 ATAATGCACCCATATGCATTATTATTTTGGCATCCTTTCATGCCA * * * * 1095757 ATAATGCACCTATATTCATTATTATTTTGGCATCCTTTCATGTCG 1 ATAATGCACCCATATGCATTATTATTTTGGCATCCTTTCATGCCA * 1095802 ATAATGCACCTATATG-ATTATTATTTTGGCATCCTTTCATGCCA 1 ATAATGCACCCATATGCATTATTATTTTGGCATCCTTTCATGCCA * * * * 1095846 ATAATGCACCTATCTGCATTATTATTTTGGTATCCTTTCATGCCG 1 ATAATGCACCCATATGCATTATTATTTTGGCATCCTTTCATGCCA * 1095891 ATAATGCACCCATATTCATTATTATTTTG 1 ATAATGCACCCATATGCATTATTATTTTG 1095920 TTCATTCGTT Statistics Matches: 223, Mismatches: 28, Indels: 4 0.87 0.11 0.02 Matches are distributed among these distances: 44 41 0.18 45 181 0.81 46 1 0.00 ACGTcount: A:0.28, C:0.21, G:0.11, T:0.41 Consensus pattern (45 bp): ATAATGCACCCATATGCATTATTATTTTGGCATCCTTTCATGCCA Found at i:1095868 original size:134 final size:135 Alignment explanation
Indices: 1095653--1095919 Score: 410 Period size: 134 Copynumber: 2.0 Consensus size: 135 1095643 CAACTATGAA 1095653 ATCCTTTCATGCCAATAATGCACCCATATGCATTATTATTTTGGCATCATTTCATGCCAATAATG 1 ATCCTTTCATGCCAATAATGCACCCATATGCATTATTATTTTGGCATCATTTCATGCCAATAATG * * * * 1095718 CACCCATATTCTTTATTATTTTGGGATACTTTCATGCTAATAATGCACCTATATTCATTATTATT 66 CACCCATATGCATTATTATTTTGGGATACTTTCATGCCAATAATGCACCCATATTCATTATTATT 1095783 TTGGC 131 TTGGC * * * * 1095788 ATCCTTTCATGTCGATAATGCACCTATATG-ATTATTATTTTGGCATCCTTTCATGCCAATAATG 1 ATCCTTTCATGCCAATAATGCACCCATATGCATTATTATTTTGGCATCATTTCATGCCAATAATG * * * * * 1095852 CACCTATCTGCATTATTATTTTGGTATCCTTTCATGCCGATAATGCACCCATATTCATTATTATT 66 CACCCATATGCATTATTATTTTGGGATACTTTCATGCCAATAATGCACCCATATTCATTATTATT 1095917 TTG 131 TTG 1095920 TTCATTCGTT Statistics Matches: 119, Mismatches: 13, Indels: 1 0.89 0.10 0.01 Matches are distributed among these distances: 134 92 0.77 135 27 0.23 ACGTcount: A:0.26, C:0.21, G:0.11, T:0.42 Consensus pattern (135 bp): ATCCTTTCATGCCAATAATGCACCCATATGCATTATTATTTTGGCATCATTTCATGCCAATAATG CACCCATATGCATTATTATTTTGGGATACTTTCATGCCAATAATGCACCCATATTCATTATTATT TTGGC Found at i:1096348 original size:22 final size:21 Alignment explanation
Indices: 1096306--1096376 Score: 85 Period size: 22 Copynumber: 3.5 Consensus size: 21 1096296 TGGCTCTTCA * 1096306 GTATCGATAC-CCATACCATG 1 GTATCGATACTCCATACTATG 1096326 GTATCGATACTACCATACTATG 1 GTATCGATACT-CCATACTATG * * 1096348 GTACCGATACT--ATGCTATG 1 GTATCGATACTCCATACTATG 1096367 GTATCGATAC 1 GTATCGATAC 1096377 CATTTTTACA Statistics Matches: 45, Mismatches: 4, Indels: 5 0.83 0.07 0.09 Matches are distributed among these distances: 19 16 0.36 20 10 0.22 22 19 0.42 ACGTcount: A:0.30, C:0.24, G:0.17, T:0.30 Consensus pattern (21 bp): GTATCGATACTCCATACTATG Found at i:1099358 original size:35 final size:35 Alignment explanation
Indices: 1099265--1099497 Score: 161 Period size: 36 Copynumber: 6.4 Consensus size: 35 1099255 AAAAAACCAG * ** 1099265 TTTTTGAAAATATATATAATATGGTTTTGAAAATA 1 TTTTTGAAAACATATATAATATAATTTTGAAAATA ** * * 1099300 CGATTTAAAAACATATATTATATAATTTTGAAAATA 1 -TTTTTGAAAACATATATAATATAATTTTGAAAATA * 1099336 TTTTTGAAAACATATATAATATATAGTTTTTGAAAACA 1 TTTTTGAAAACATATATAATATA-A--TTTTGAAAATA * * 1099374 -TTTTGAATATATATATATAATATATATAGTTTTTAAAAT- 1 TTTTTGAA-A-ACATATAT-A-ATATA-A-TTTTGAAAATA * * * 1099413 GTTTTAAAAACATATATTATATATAGTTTTGAAAATA 1 TTTTTGAAAACATATA-TA-ATATAATTTTGAAAATA * * 1099450 TTTTTG-AAA-ATATATTATATAGTTTTGAAAA-A 1 TTTTTGAAAACATATATAATATAATTTTGAAAATA 1099482 TGGGTTTTGAAAACAT 1 T---TTTTGAAAACAT 1099498 TTTGGAAATT Statistics Matches: 159, Mismatches: 23, Indels: 29 0.75 0.11 0.14 Matches are distributed among these distances: 32 2 0.01 33 15 0.09 34 1 0.01 35 29 0.18 36 44 0.28 37 13 0.08 38 24 0.15 39 9 0.06 40 15 0.09 41 7 0.04 ACGTcount: A:0.44, C:0.03, G:0.09, T:0.44 Consensus pattern (35 bp): TTTTTGAAAACATATATAATATAATTTTGAAAATA Found at i:1099382 original size:26 final size:25 Alignment explanation
Indices: 1099324--1099387 Score: 80 Period size: 26 Copynumber: 2.6 Consensus size: 25 1099314 ATATTATATA 1099324 ATTTTGAA-A-ATATTTTTGAAAAC 1 ATTTTGAATATATATTTTTGAAAAC * 1099347 ATATAT-AATATATAGTTTTTGAAAAC 1 AT-TTTGAATATATA-TTTTTGAAAAC 1099373 ATTTTGAATATATAT 1 ATTTTGAATATATAT 1099388 ATATAATATA Statistics Matches: 34, Mismatches: 2, Indels: 8 0.77 0.05 0.18 Matches are distributed among these distances: 23 4 0.12 24 3 0.09 25 6 0.18 26 21 0.62 ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45 Consensus pattern (25 bp): ATTTTGAATATATATTTTTGAAAAC Found at i:1099439 original size:77 final size:79 Alignment explanation
Indices: 1099318--1099470 Score: 213 Period size: 77 Copynumber: 2.0 Consensus size: 79 1099308 AAACATATAT * * * 1099318 TATATAATTTTGAAAATATTTTTGAAAACATATATAATATATAGTTTTTGAAAACA-TTTTGAAT 1 TATATAATTTTGAAAATAGTTTTAAAAACATATATAATATATAG-TTTTGAAAACATTTTTGAAA 1099382 ATATA-TATATAATA 65 ATATATTATATAATA * * * * 1099396 TATATAGTTTTTAAAAT-GTTTTAAAAACATATATTATATATAGTTTTGAAAATATTTTTGAAAA 1 TATATAATTTTGAAAATAGTTTTAAAAACATATATAATATATAGTTTTGAAAACATTTTTGAAAA 1099460 TATATTATATA 66 TATATTATATA 1099471 GTTTTGAAAA Statistics Matches: 66, Mismatches: 7, Indels: 4 0.86 0.09 0.05 Matches are distributed among these distances: 76 10 0.15 77 35 0.53 78 21 0.32 ACGTcount: A:0.45, C:0.02, G:0.07, T:0.46 Consensus pattern (79 bp): TATATAATTTTGAAAATAGTTTTAAAAACATATATAATATATAGTTTTGAAAACATTTTTGAAAA TATATTATATAATA Found at i:1099522 original size:3 final size:3 Alignment explanation
Indices: 1099516--1099587 Score: 71 Period size: 3 Copynumber: 23.7 Consensus size: 3 1099506 TTTTTTTTTG 1099516 TTA TTA TATA TTA TTCA TTA -TA TTTA TTA -TA TATA TTA TTA TTA -TA 1 TTA TTA T-TA TTA TT-A TTA TTA -TTA TTA TTA T-TA TTA TTA TTA TTA 1099562 TTA TTA -TA TTA TTA TTTA TTA TTA TT 1 TTA TTA TTA TTA TTA -TTA TTA TTA TT 1099588 TCTTTTAGGG Statistics Matches: 60, Mismatches: 0, Indels: 18 0.77 0.00 0.23 Matches are distributed among these distances: 2 8 0.13 3 38 0.63 4 14 0.23 ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64 Consensus pattern (3 bp): TTA Found at i:1099546 original size:23 final size:23 Alignment explanation
Indices: 1099516--1099588 Score: 96 Period size: 23 Copynumber: 3.1 Consensus size: 23 1099506 TTTTTTTTTG 1099516 TTATTATATATTATTCATTA-TAT 1 TTATTATATATTATT-ATTATTAT 1099539 TTATTATATA-TATTATTATTAT 1 TTATTATATATTATTATTATTAT 1099561 ATTATTATATTATTATTTATTATTAT 1 -TTATTATA-TATTA-TTATTATTAT 1099587 TT 1 TT 1099589 CTTTTAGGGT Statistics Matches: 45, Mismatches: 0, Indels: 8 0.85 0.00 0.15 Matches are distributed among these distances: 21 4 0.09 22 7 0.16 23 18 0.40 24 2 0.04 25 4 0.09 26 10 0.22 ACGTcount: A:0.34, C:0.01, G:0.00, T:0.64 Consensus pattern (23 bp): TTATTATATATTATTATTATTAT Found at i:1099587 original size:13 final size:13 Alignment explanation
Indices: 1099516--1099586 Score: 87 Period size: 13 Copynumber: 5.5 Consensus size: 13 1099506 TTTTTTTTTG 1099516 TTATTATATATTA 1 TTATTATATATTA 1099529 TTCATTATAT-TTA 1 TT-ATTATATATTA 1099542 TTA-TATATATTA 1 TTATTATATATTA 1099554 TTATTATATTATTA 1 TTATTATA-TATTA 1099568 -TATTAT-TATTTA 1 TTATTATATA-TTA 1099580 TTATTAT 1 TTATTAT 1099587 TTCTTTTAGG Statistics Matches: 52, Mismatches: 0, Indels: 12 0.81 0.00 0.19 Matches are distributed among these distances: 11 7 0.13 12 10 0.19 13 23 0.44 14 12 0.23 ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63 Consensus pattern (13 bp): TTATTATATATTA Found at i:1104670 original size:93 final size:92 Alignment explanation
Indices: 1104535--1104719 Score: 361 Period size: 93 Copynumber: 2.0 Consensus size: 92 1104525 TTCCATATTA 1104535 GCACCCCAAATATGTTTTAGGCCTTCAATAGTCAAGACCCATTAGTACCACTCCAAAGTGAAGGG 1 GCACCCCAAATATGTTTTAGGCCTTCAATAGTCAAGACCCATTAGTACCACTCCAAAGTGAAGGG 1104600 GATCGGGTCCTCCCATTTATACTTTTC 66 GATCGGGTCCTCCCATTTATACTTTTC 1104627 GCACCCCAAATATGTTTTAGGCCTTTCAATAGTCAAGACCCATTAGTACCACTCCAAAGTGAAGG 1 GCACCCCAAATATGTTTTAGGCC-TTCAATAGTCAAGACCCATTAGTACCACTCCAAAGTGAAGG 1104692 GGATCGGGTCCTCCCATTTATACTTTTC 65 GGATCGGGTCCTCCCATTTATACTTTTC 1104720 TCGAAGAATC Statistics Matches: 92, Mismatches: 0, Indels: 1 0.99 0.00 0.01 Matches are distributed among these distances: 92 23 0.25 93 69 0.75 ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29 Consensus pattern (92 bp): GCACCCCAAATATGTTTTAGGCCTTCAATAGTCAAGACCCATTAGTACCACTCCAAAGTGAAGGG GATCGGGTCCTCCCATTTATACTTTTC Found at i:1107477 original size:25 final size:25 Alignment explanation
Indices: 1107442--1107501 Score: 102 Period size: 25 Copynumber: 2.4 Consensus size: 25 1107432 AGGTTTTGCT * 1107442 CCTTAAACCCGCTAGGAGCTCCGCC 1 CCTTAACCCCGCTAGGAGCTCCGCC 1107467 CCTTAACCCCGCTAGGAGCTCCGCC 1 CCTTAACCCCGCTAGGAGCTCCGCC 1107492 CCTTGAACCC 1 CCTT-AACCC 1107502 TTAGTAGGAA Statistics Matches: 33, Mismatches: 1, Indels: 1 0.94 0.03 0.03 Matches are distributed among these distances: 25 28 0.85 26 5 0.15 ACGTcount: A:0.18, C:0.47, G:0.18, T:0.17 Consensus pattern (25 bp): CCTTAACCCCGCTAGGAGCTCCGCC Found at i:1107631 original size:35 final size:36 Alignment explanation
Indices: 1107585--1107653 Score: 131 Period size: 35 Copynumber: 1.9 Consensus size: 36 1107575 TTGATATGAA 1107585 CATTATTTGACATGCATGGTT-TAGCCCCATATTTG 1 CATTATTTGACATGCATGGTTATAGCCCCATATTTG 1107620 CATTATTTGACATGCATGGTTATAGCCCCATATT 1 CATTATTTGACATGCATGGTTATAGCCCCATATT 1107654 GCAATGGTTT Statistics Matches: 33, Mismatches: 0, Indels: 1 0.97 0.00 0.03 Matches are distributed among these distances: 35 21 0.64 36 12 0.36 ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39 Consensus pattern (36 bp): CATTATTTGACATGCATGGTTATAGCCCCATATTTG Found at i:1108109 original size:182 final size:184 Alignment explanation
Indices: 1107801--1108166 Score: 709 Period size: 182 Copynumber: 2.0 Consensus size: 184 1107791 GATTAACAAA 1107801 AAATGTGAAGATGCTTGAGAAGCAATCTTTGTAATTAAGATTCGAGATTCTCCAATTGGCTTGGG 1 AAATGTGAAGATGCTTGAGAAGCAATCTTTGTAATTAAGATTCGAGATTCTCCAATTGGCTTGGG * 1107866 ATGGGCCACCTTAGTTTGGTTTTGGGCTATAATCATTGCATTTCCTTACTGTTTTATATCTATAT 66 ATGGGCCACCTTAGTTTGGTTTTGGGCTATAATCATTGAATTTCCTTACTGTTTTATATCTATAT 1107931 TGTATGTGATGC-ATGAATGGTATATTAGCATGCTAATAGATTGATGAGATCAT 131 TGTATGTGATGCAATGAATGGTATATTAGCATGCTAATAGATTGATGAGATCAT 1107984 AAATGTGAAGATGCTTGAGAAGCAATCTTTGT-ATTAAGATTCGAGATTCTCCAATTGGCTTGGG 1 AAATGTGAAGATGCTTGAGAAGCAATCTTTGTAATTAAGATTCGAGATTCTCCAATTGGCTTGGG 1108048 ATGGGCCACCTTAGTTTGGTTTTGGGCTATAATCATTGAATTTCCTTACTGTTTTATATCTATAT 66 ATGGGCCACCTTAGTTTGGTTTTGGGCTATAATCATTGAATTTCCTTACTGTTTTATATCTATAT 1108113 TGTATGTGATGCAATGAATGGTATATTAGCATGCTAATAGATTGATGAGATCAT 131 TGTATGTGATGCAATGAATGGTATATTAGCATGCTAATAGATTGATGAGATCAT 1108167 TAAGGGCCTA Statistics Matches: 181, Mismatches: 1, Indels: 2 0.98 0.01 0.01 Matches are distributed among these distances: 182 108 0.60 183 73 0.40 ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38 Consensus pattern (184 bp): AAATGTGAAGATGCTTGAGAAGCAATCTTTGTAATTAAGATTCGAGATTCTCCAATTGGCTTGGG ATGGGCCACCTTAGTTTGGTTTTGGGCTATAATCATTGAATTTCCTTACTGTTTTATATCTATAT TGTATGTGATGCAATGAATGGTATATTAGCATGCTAATAGATTGATGAGATCAT Found at i:1111944 original size:34 final size:34 Alignment explanation
Indices: 1111901--1112001 Score: 175 Period size: 34 Copynumber: 3.0 Consensus size: 34 1111891 GGTTTCTGTC * 1111901 TATGAGACATTGTATTTCTCTTTCGAAGGAAATG 1 TATGAGACATAGTATTTCTCTTTCGAAGGAAATG * 1111935 TATGAGACATGGTATTTCTCTTTCGAAGGAAATG 1 TATGAGACATAGTATTTCTCTTTCGAAGGAAATG * 1111969 TATGAGACATAGTATTTCTCTTTAGAAGGAAAT 1 TATGAGACATAGTATTTCTCTTTCGAAGGAAAT 1112002 TTATCCTTCA Statistics Matches: 64, Mismatches: 3, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 34 64 1.00 ACGTcount: A:0.32, C:0.11, G:0.21, T:0.37 Consensus pattern (34 bp): TATGAGACATAGTATTTCTCTTTCGAAGGAAATG Found at i:1113712 original size:2 final size:2 Alignment explanation
Indices: 1113705--1113744 Score: 80 Period size: 2 Copynumber: 20.0 Consensus size: 2 1113695 TGTATCGTTA 1113705 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 1113745 GCACGTGTAA Statistics Matches: 38, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 38 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:1115302 original size:87 final size:89 Alignment explanation
Indices: 1115131--1115302 Score: 296 Period size: 89 Copynumber: 2.0 Consensus size: 89 1115121 TCCCGAATAT * 1115131 TTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCTCTAATATGATTAG 1 TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCTCTAATATGATTAG 1115196 GGTAACTTGGATATAAAAGGATTA 66 GGTAACTTGGATATAAAAGGATTA 1115220 TTAAATTCTAATTAATT-AATATAGATTTAATTAATTTGAAATAATAAAA-C-CTAATATGATTA 1 TTAAATTC-AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCTCTAATATGATTA * 1115282 GGGTAACTTGGCTATAAAAGG 65 GGGTAACTTGGATATAAAAGG 1115303 GTGCGTTGGG Statistics Matches: 80, Mismatches: 2, Indels: 4 0.93 0.02 0.05 Matches are distributed among these distances: 87 32 0.40 88 1 0.01 89 39 0.49 90 8 0.10 ACGTcount: A:0.45, C:0.05, G:0.12, T:0.38 Consensus pattern (89 bp): TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCTCTAATATGATTAG GGTAACTTGGATATAAAAGGATTA Found at i:1126294 original size:35 final size:36 Alignment explanation
Indices: 1126226--1126296 Score: 108 Period size: 35 Copynumber: 2.0 Consensus size: 36 1126216 AATTTAAAAT * 1126226 GGGTATTTTTCAAATACAACTGTCCCACAAAACATC 1 GGGTATTTTTCAAATACAACTGCCCCACAAAACATC * * 1126262 GGGTGTTTTTCAAATA-AATTGCCCCACAAAACATC 1 GGGTATTTTTCAAATACAACTGCCCCACAAAACATC 1126297 AAGTGCAGTT Statistics Matches: 32, Mismatches: 3, Indels: 1 0.89 0.08 0.03 Matches are distributed among these distances: 35 17 0.53 36 15 0.47 ACGTcount: A:0.35, C:0.24, G:0.13, T:0.28 Consensus pattern (36 bp): GGGTATTTTTCAAATACAACTGCCCCACAAAACATC Found at i:1126855 original size:63 final size:63 Alignment explanation
Indices: 1126756--1126901 Score: 240 Period size: 63 Copynumber: 2.3 Consensus size: 63 1126746 TTGACGAGGA * * * 1126756 AGATCATTCAACAAATCT-ATTCCAATACAGTTTGATGGGGAAGATCATTCAAAAAGTATTTGT 1 AGATCACTCAACAAAT-TGATTCCAATACAGTTTGATGAGGAAGATAATTCAAAAAGTATTTGT 1126819 AGATCACTCAACAAATTGATTCCAATACAGTTTGATGAGGAAGATAATTCAAAAAGTATTTGT 1 AGATCACTCAACAAATTGATTCCAATACAGTTTGATGAGGAAGATAATTCAAAAAGTATTTGT * 1126882 AAATCACTCAACAAATTGAT 1 AGATCACTCAACAAATTGAT 1126902 GAGGAAGATC Statistics Matches: 78, Mismatches: 4, Indels: 2 0.93 0.05 0.02 Matches are distributed among these distances: 62 1 0.01 63 77 0.99 ACGTcount: A:0.41, C:0.14, G:0.14, T:0.30 Consensus pattern (63 bp): AGATCACTCAACAAATTGATTCCAATACAGTTTGATGAGGAAGATAATTCAAAAAGTATTTGT Found at i:1128737 original size:18 final size:18 Alignment explanation
Indices: 1128714--1128771 Score: 100 Period size: 18 Copynumber: 3.3 Consensus size: 18 1128704 ACCGGTCACA 1128714 ACCCGACCCGACCCGTTG 1 ACCCGACCCGACCCGTTG * 1128732 ACCCGA-CCGACCCGTTT 1 ACCCGACCCGACCCGTTG 1128749 ACCCGACCCGACCCGTTG 1 ACCCGACCCGACCCGTTG 1128767 ACCCG 1 ACCCG 1128772 TTGACCGTTG Statistics Matches: 37, Mismatches: 2, Indels: 2 0.90 0.05 0.05 Matches are distributed among these distances: 17 16 0.43 18 21 0.57 ACGTcount: A:0.17, C:0.50, G:0.21, T:0.12 Consensus pattern (18 bp): ACCCGACCCGACCCGTTG Found at i:1128781 original size:7 final size:8 Alignment explanation
Indices: 1128758--1128792 Score: 63 Period size: 8 Copynumber: 4.5 Consensus size: 8 1128748 TACCCGACCC 1128758 GACCCGTT 1 GACCCGTT 1128766 GACCCGTT 1 GACCCGTT 1128774 GA-CCGTT 1 GACCCGTT 1128781 GACCCGTT 1 GACCCGTT 1128789 GACC 1 GACC 1128793 GGAGTTGATA Statistics Matches: 26, Mismatches: 0, Indels: 2 0.93 0.00 0.07 Matches are distributed among these distances: 7 7 0.27 8 19 0.73 ACGTcount: A:0.14, C:0.37, G:0.26, T:0.23 Consensus pattern (8 bp): GACCCGTT Found at i:1128781 original size:15 final size:15 Alignment explanation
Indices: 1128761--1128793 Score: 66 Period size: 15 Copynumber: 2.2 Consensus size: 15 1128751 CCGACCCGAC 1128761 CCGTTGACCCGTTGA 1 CCGTTGACCCGTTGA 1128776 CCGTTGACCCGTTGA 1 CCGTTGACCCGTTGA 1128791 CCG 1 CCG 1128794 GAGTTGATAA Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 18 1.00 ACGTcount: A:0.12, C:0.36, G:0.27, T:0.24 Consensus pattern (15 bp): CCGTTGACCCGTTGA Found at i:1131751 original size:18 final size:18 Alignment explanation
Indices: 1131728--1131798 Score: 82 Period size: 18 Copynumber: 4.3 Consensus size: 18 1131718 ACCGGTCACA 1131728 ACCCGACCCGACCCGTTG 1 ACCCGACCCGACCCGTTG 1131746 ACCCGA-CCGACCCGTT- 1 ACCCGACCCGACCCGTTG * * 1131762 ----TACCCGACCCGTTT 1 ACCCGACCCGACCCGTTG 1131776 ACCCGACCCGACCCGTTG 1 ACCCGACCCGACCCGTTG 1131794 ACCCG 1 ACCCG 1131799 TTGACCGTTG Statistics Matches: 44, Mismatches: 3, Indels: 12 0.75 0.05 0.20 Matches are distributed among these distances: 12 1 0.02 13 10 0.23 17 10 0.23 18 23 0.52 ACGTcount: A:0.17, C:0.49, G:0.20, T:0.14 Consensus pattern (18 bp): ACCCGACCCGACCCGTTG Found at i:1131768 original size:30 final size:31 Alignment explanation
Indices: 1131732--1131798 Score: 109 Period size: 30 Copynumber: 2.2 Consensus size: 31 1131722 GTCACAACCC 1131732 GACCCGACCCGTTGACCCGA-CCGACCCGTT 1 GACCCGACCCGTTGACCCGACCCGACCCGTT * * 1131762 TACCCGACCCGTTTACCCGACCCGACCCGTT 1 GACCCGACCCGTTGACCCGACCCGACCCGTT 1131793 GACCCG 1 GACCCG 1131799 TTGACCGTTG Statistics Matches: 33, Mismatches: 3, Indels: 1 0.89 0.08 0.03 Matches are distributed among these distances: 30 18 0.55 31 15 0.45 ACGTcount: A:0.16, C:0.48, G:0.21, T:0.15 Consensus pattern (31 bp): GACCCGACCCGTTGACCCGACCCGACCCGTT Found at i:1131798 original size:13 final size:13 Alignment explanation
Indices: 1131732--1131785 Score: 54 Period size: 13 Copynumber: 3.8 Consensus size: 13 1131722 GTCACAACCC 1131732 GACCCGACCCGTT 1 GACCCGACCCGTT 1131745 GACCCGACCGACCCGTT 1 GA--C--CCGACCCGTT * 1131762 TACCCGACCCGTT 1 GACCCGACCCGTT * 1131775 TACCCGACCCG 1 GACCCGACCCG 1131786 ACCCGTTGAC Statistics Matches: 36, Mismatches: 1, Indels: 8 0.80 0.02 0.18 Matches are distributed among these distances: 13 23 0.64 15 2 0.06 17 11 0.31 ACGTcount: A:0.17, C:0.48, G:0.20, T:0.15 Consensus pattern (13 bp): GACCCGACCCGTT Found at i:1131808 original size:7 final size:7 Alignment explanation
Indices: 1131788--1131819 Score: 55 Period size: 7 Copynumber: 4.4 Consensus size: 7 1131778 CCGACCCGAC 1131788 CCGTTGA 1 CCGTTGA 1131795 CCCGTTGA 1 -CCGTTGA 1131803 CCGTTGA 1 CCGTTGA 1131810 CCGTTGA 1 CCGTTGA 1131817 CCG 1 CCG 1131820 GAGTTGATAA Statistics Matches: 24, Mismatches: 0, Indels: 1 0.96 0.00 0.04 Matches are distributed among these distances: 7 17 0.71 8 7 0.29 ACGTcount: A:0.12, C:0.34, G:0.28, T:0.25 Consensus pattern (7 bp): CCGTTGA Found at i:1133577 original size:30 final size:30 Alignment explanation
Indices: 1133533--1133607 Score: 100 Period size: 30 Copynumber: 2.5 Consensus size: 30 1133523 GCACAAACTT 1133533 AAACATAAAGGACTAAAATA-ATAAAAATAG 1 AAACATAAAGGACTAAAATAGA-AAAAATAG * 1133563 AAAC-TAAAGGGACTAAAATAGAAAAATTAG 1 AAACATAAA-GGACTAAAATAGAAAAAATAG * 1133593 AAACTTAAAGGACTA 1 AAACATAAAGGACTA 1133608 TACATTAATT Statistics Matches: 41, Mismatches: 1, Indels: 6 0.85 0.02 0.12 Matches are distributed among these distances: 29 4 0.10 30 32 0.78 31 5 0.12 ACGTcount: A:0.61, C:0.08, G:0.13, T:0.17 Consensus pattern (30 bp): AAACATAAAGGACTAAAATAGAAAAAATAG Found at i:1134870 original size:9 final size:8 Alignment explanation
Indices: 1134848--1134895 Score: 55 Period size: 9 Copynumber: 5.9 Consensus size: 8 1134838 GTAAATTGTA 1134848 AATAAAAT 1 AATAAAAT 1134856 ATATAATAAT 1 A-ATAA-AAT 1134866 AATAATAAT 1 AATAA-AAT 1134875 AATAAAAT 1 AATAAAAT 1134883 -ATAAAA- 1 AATAAAAT 1134889 AATAAAA 1 AATAAAA 1134896 AAAAGACTCG Statistics Matches: 37, Mismatches: 0, Indels: 7 0.84 0.00 0.16 Matches are distributed among these distances: 7 12 0.32 8 4 0.11 9 17 0.46 10 4 0.11 ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27 Consensus pattern (8 bp): AATAAAAT Found at i:1135301 original size:134 final size:134 Alignment explanation
Indices: 1135128--1135377 Score: 349 Period size: 134 Copynumber: 1.9 Consensus size: 134 1135118 GAGTTCTTTT * * 1135128 CATCTTTAGGAAGGGTGATAACTCGATTCTTACGCGATGAAGACAGCTGGTTATCTAGGGGTGAC 1 CATCTTTAGGAAGGGTGATAACTCGATTCCTACGCGATGAAGACAGCAGGTTATCTAGGGGTGAC * * * * 1135193 ACGGCTCCTACGTGATGAGGAGGTCTGGTCAAGGGATGACACGGTTCCTACGTGATGAGGATGGT 66 ACAGCTCCTACGTGATAAGGAGGTATAGTCAAGGGATGACACGGTTCCTACGTGATGAGGATGGT 1135258 TGGC 131 TGGC * * * * * * 1135262 CATCTTTAGG-AGTGGTGATAACTCGGTTCCTACGTGATGACGACGGCAGGTTATCTATGGTTGA 1 CATCTTTAGGAAG-GGTGATAACTCGATTCCTACGCGATGAAGACAGCAGGTTATCTAGGGGTGA * * * 1135326 CACAGCTCCTACGTTATAAGGAGGTATAGTCAGGGGATGACATGGTTCCTAC 65 CACAGCTCCTACGTGATAAGGAGGTATAGTCAAGGGATGACACGGTTCCTAC 1135378 AGAATGAGGA Statistics Matches: 100, Mismatches: 15, Indels: 2 0.85 0.13 0.02 Matches are distributed among these distances: 133 2 0.02 134 98 0.98 ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27 Consensus pattern (134 bp): CATCTTTAGGAAGGGTGATAACTCGATTCCTACGCGATGAAGACAGCAGGTTATCTAGGGGTGAC ACAGCTCCTACGTGATAAGGAGGTATAGTCAAGGGATGACACGGTTCCTACGTGATGAGGATGGT TGGC Found at i:1135385 original size:134 final size:134 Alignment explanation
Indices: 1135128--1135405 Score: 344 Period size: 134 Copynumber: 2.1 Consensus size: 134 1135118 GAGTTCTTTT * * 1135128 CATCTTTAGGAAGGGTGATAACTCGATTCTTACGCGATGAAGACAGCTGGTTATCTAGGGGTGAC 1 CATCTTTAGGAAGGGTGATAACTCGATTCCTACGCGATGAAGACAGCAGGTTATCTAGGGGTGAC * * * * * * * 1135193 ACGGCTCCTACGTGATGAGGAGGTCTGGTCAAGGGATGACACGGTTCCTACGTGATGAGGATGGT 66 ACAGCTCCTACGTGATAAGGAGGTATAGTCAAGGGATGACACGGTTCCTACGTAATGAGGACGAT * 1135258 TGGC 131 TGAC * * * * * * 1135262 CATCTTTAGG-AGTGGTGATAACTCGGTTCCTACGTGATGACGACGGCAGGTTATCTATGGTTGA 1 CATCTTTAGGAAG-GGTGATAACTCGATTCCTACGCGATGAAGACAGCAGGTTATCTAGGGGTGA * * * 1135326 CACAGCTCCTACGTTATAAGGAGGTATAGTCAGGGGATGACATGGTTCCTACAG-AATGAGGACG 65 CACAGCTCCTACGTGATAAGGAGGTATAGTCAAGGGATGACACGGTTCCTAC-GTAATGAGGACG 1135390 ATTGAC 129 ATTGAC * 1135396 CATCCTTAGG 1 CATCTTTAGG 1135406 GATTATGGTT Statistics Matches: 122, Mismatches: 20, Indels: 4 0.84 0.14 0.03 Matches are distributed among these distances: 133 2 0.02 134 119 0.98 135 1 0.01 ACGTcount: A:0.24, C:0.18, G:0.31, T:0.26 Consensus pattern (134 bp): CATCTTTAGGAAGGGTGATAACTCGATTCCTACGCGATGAAGACAGCAGGTTATCTAGGGGTGAC ACAGCTCCTACGTGATAAGGAGGTATAGTCAAGGGATGACACGGTTCCTACGTAATGAGGACGAT TGAC Found at i:1135453 original size:28 final size:28 Alignment explanation
Indices: 1135421--1135509 Score: 92 Period size: 28 Copynumber: 3.1 Consensus size: 28 1135411 TGGTTTCAGG 1135421 AGAAACCAACTCAAAGATTTGTTTCAAA 1 AGAAACCAACTCAAAGATTTGTTTCAAA * * 1135449 AGAAA-CATACTTAAAGATTTATTTCAAGA 1 AGAAACCA-ACTCAAAGATTTGTTTCAA-A * 1135478 A-AAACAAACTCAAAGATGATGTGTTTCAAA 1 AGAAACCAACTCAAAGAT--T-TGTTTCAAA 1135508 AG 1 AG 1135510 CAACTGTCTC Statistics Matches: 49, Mismatches: 5, Indels: 11 0.75 0.08 0.17 Matches are distributed among these distances: 27 2 0.04 28 34 0.69 29 3 0.06 30 3 0.06 31 7 0.14 ACGTcount: A:0.48, C:0.13, G:0.12, T:0.26 Consensus pattern (28 bp): AGAAACCAACTCAAAGATTTGTTTCAAA Found at i:1135591 original size:63 final size:67 Alignment explanation
Indices: 1135469--1135597 Score: 167 Period size: 63 Copynumber: 2.0 Consensus size: 67 1135459 TTAAAGATTT * * 1135469 ATTTCAAGAAAAACAAACTCAAAGATGATGTGTTTCAAAAGCAACTGTCTCAAAAGAGACAAAAT 1 ATTTCAAGAAAAACAAACTCAAAGATGATCTGTTTCAAAAGAAACTGTCTCAAAAGAGACAAAAT 1135534 TC 66 TC * * * ** 1135536 ATTTCAAGAGAAAC-GACTCAAAGATGA-CT-TTT-AAAGGAAACTGTCTCAAGCGAGACAAAAT 1 ATTTCAAGAAAAACAAACTCAAAGATGATCTGTTTCAAAAGAAACTGTCTCAAAAGAGACAAAAT 1135597 T 66 T 1135598 TTTTTTAAGG Statistics Matches: 55, Mismatches: 7, Indels: 4 0.83 0.11 0.06 Matches are distributed among these distances: 63 26 0.47 64 3 0.05 65 1 0.02 66 12 0.22 67 13 0.24 ACGTcount: A:0.46, C:0.16, G:0.16, T:0.22 Consensus pattern (67 bp): ATTTCAAGAAAAACAAACTCAAAGATGATCTGTTTCAAAAGAAACTGTCTCAAAAGAGACAAAAT TC Found at i:1135674 original size:66 final size:63 Alignment explanation
Indices: 1135511--1135675 Score: 159 Period size: 66 Copynumber: 2.6 Consensus size: 63 1135501 TTTCAAAAGC * 1135511 AACTGTCTCAAAAGAGACAAAATTCATTTCAAGAGAAACGACTCAAAGATGACTTTTAAAGGA 1 AACTGTCTCAAAAGAGACAAAATTCATTTCAAGGGAAACGACTCAAAGATGACTTTTAAAGGA ** ** * * ** * ** ** 1135574 AACTGTCTCAAGCGAGACAAAATTTTTTTTAAGGGAAGCGTTTTTAAAGATCGGTGTTTTATGGG 1 AACTGTCTCAAAAGAGACAAAATTCATTTCAAGGGAAACG-ACTCAAAGAT--GACTTTTAAAGG 1135639 A 63 A * * 1135640 AACTGTCTCAAATGAGACAAAATTCGTTTCAAGGGA 1 AACTGTCTCAAAAGAGACAAAATTCATTTCAAGGGA 1135676 CATGATCTCA Statistics Matches: 80, Mismatches: 19, Indels: 3 0.78 0.19 0.03 Matches are distributed among these distances: 63 33 0.41 64 7 0.09 66 40 0.50 ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28 Consensus pattern (63 bp): AACTGTCTCAAAAGAGACAAAATTCATTTCAAGGGAAACGACTCAAAGATGACTTTTAAAGGA Found at i:1136028 original size:28 final size:28 Alignment explanation
Indices: 1135967--1136020 Score: 81 Period size: 28 Copynumber: 1.9 Consensus size: 28 1135957 AGAGAAATAA * * 1135967 ACTCAAAGATTTTTTTCAAAAGGAACAG 1 ACTCAAAGATTTGTTTCAAAAGAAACAG * 1135995 ACTCAAAGATTTGTTTCAAGAGAAAC 1 ACTCAAAGATTTGTTTCAAAAGAAAC 1136021 TGTCTCAAGA Statistics Matches: 23, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 28 23 1.00 ACGTcount: A:0.43, C:0.15, G:0.15, T:0.28 Consensus pattern (28 bp): ACTCAAAGATTTGTTTCAAAAGAAACAG Found at i:1136284 original size:36 final size:37 Alignment explanation
Indices: 1136241--1136313 Score: 103 Period size: 36 Copynumber: 2.0 Consensus size: 37 1136231 TTGTATCTCA * 1136241 GAGAAAAAATGTCTCAAGCGAAAC-GAAATTTGTTTT 1 GAGAAAAAATGTCTCAAGCGAAACAAAAATTTGTTTT * * * 1136277 GAGAAAAATTTTCTCAAGCGAGACAAAAATTTGTTTT 1 GAGAAAAAATGTCTCAAGCGAAACAAAAATTTGTTTT 1136314 AAAATTCTCA Statistics Matches: 32, Mismatches: 4, Indels: 1 0.86 0.11 0.03 Matches are distributed among these distances: 36 21 0.66 37 11 0.34 ACGTcount: A:0.41, C:0.11, G:0.18, T:0.30 Consensus pattern (37 bp): GAGAAAAAATGTCTCAAGCGAAACAAAAATTTGTTTT Found at i:1143639 original size:3 final size:3 Alignment explanation
Indices: 1143631--1143661 Score: 53 Period size: 3 Copynumber: 10.3 Consensus size: 3 1143621 AATTGTAAAT * 1143631 ATA ATA ATA ATA ATA ATA ATA ACA ATA ATA A 1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A 1143662 ATATAAAATA Statistics Matches: 26, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 3 26 1.00 ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29 Consensus pattern (3 bp): ATA Found at i:1143667 original size:15 final size:15 Alignment explanation
Indices: 1143626--1143685 Score: 59 Period size: 15 Copynumber: 3.8 Consensus size: 15 1143616 GTGTAAATTG * 1143626 TAAATATAATAATAA 1 TAAATATAACAATAA 1143641 TAATAATAATAACAATAA 1 T-A-AAT-ATAACAATAA 1143659 TAAATATAA-AATAAA 1 TAAATATAACAAT-AA * 1143674 TAAATAAAACAA 1 TAAATATAACAA 1143686 AAAAAAAAGA Statistics Matches: 38, Mismatches: 2, Indels: 9 0.78 0.04 0.18 Matches are distributed among these distances: 14 3 0.08 15 15 0.39 16 6 0.16 17 4 0.11 18 10 0.26 ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27 Consensus pattern (15 bp): TAAATATAACAATAA Found at i:1147770 original size:28 final size:28 Alignment explanation
Indices: 1147712--1147802 Score: 110 Period size: 28 Copynumber: 3.2 Consensus size: 28 1147702 TGAATAAAAT * * * 1147712 TTTATAGGGTTTTTGAGATTATGATATAA 1 TTTATAGGG-TTTAGAGTTTATGATGTAA 1147741 TTTATAGGGTTTAGAGTTTATGATGTAA 1 TTTATAGGGTTTAGAGTTTATGATGTAA * * * * 1147769 TTTATAGGATTTGGAATTTATGACGTAA 1 TTTATAGGGTTTAGAGTTTATGATGTAA 1147797 TTTATA 1 TTTATA 1147803 TGATTTGGAC Statistics Matches: 55, Mismatches: 7, Indels: 1 0.87 0.11 0.02 Matches are distributed among these distances: 28 46 0.84 29 9 0.16 ACGTcount: A:0.31, C:0.01, G:0.21, T:0.47 Consensus pattern (28 bp): TTTATAGGGTTTAGAGTTTATGATGTAA Found at i:1147807 original size:28 final size:28 Alignment explanation
Indices: 1147738--1147811 Score: 103 Period size: 28 Copynumber: 2.6 Consensus size: 28 1147728 GATTATGATA * * * * 1147738 TAATTTATAGGGTTTAGAGTTTATGATG 1 TAATTTATAGGATTTGGAATTTATGACG 1147766 TAATTTATAGGATTTGGAATTTATGACG 1 TAATTTATAGGATTTGGAATTTATGACG * 1147794 TAATTTATATGATTTGGA 1 TAATTTATAGGATTTGGA 1147812 CTAATTTACA Statistics Matches: 41, Mismatches: 5, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 28 41 1.00 ACGTcount: A:0.31, C:0.01, G:0.22, T:0.46 Consensus pattern (28 bp): TAATTTATAGGATTTGGAATTTATGACG Found at i:1148044 original size:3 final size:3 Alignment explanation
Indices: 1148036--1148099 Score: 92 Period size: 3 Copynumber: 21.0 Consensus size: 3 1148026 ACCATTATAT ** * 1148036 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA AAA ATA TTA 1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA 1148084 TTA TTA TTA TTTA TTA 1 TTA TTA TTA -TTA TTA 1148100 CAAACCCAAT Statistics Matches: 56, Mismatches: 4, Indels: 2 0.90 0.06 0.03 Matches are distributed among these distances: 3 53 0.95 4 3 0.05 ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62 Consensus pattern (3 bp): TTA Found at i:1148156 original size:18 final size:18 Alignment explanation
Indices: 1148119--1148158 Score: 53 Period size: 18 Copynumber: 2.2 Consensus size: 18 1148109 TACCTAACAT * * 1148119 CCAAACCCAAACCCTGGC 1 CCAAACCAAAACCCTAGC * 1148137 CCAAACCAAAACCTTAGC 1 CCAAACCAAAACCCTAGC 1148155 CCAA 1 CCAA 1148159 CACCTAAACT Statistics Matches: 19, Mismatches: 3, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 18 19 1.00 ACGTcount: A:0.40, C:0.45, G:0.07, T:0.07 Consensus pattern (18 bp): CCAAACCAAAACCCTAGC Found at i:1148883 original size:19 final size:19 Alignment explanation
Indices: 1148856--1148892 Score: 56 Period size: 19 Copynumber: 1.9 Consensus size: 19 1148846 TCAGCCGAGC * 1148856 AGAGGAAAAGAGAGAGTTG 1 AGAGAAAAAGAGAGAGTTG * 1148875 AGAGAAAAAGGGAGAGTT 1 AGAGAAAAAGAGAGAGTT 1148893 TTTTTGGGTT Statistics Matches: 16, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 19 16 1.00 ACGTcount: A:0.49, C:0.00, G:0.41, T:0.11 Consensus pattern (19 bp): AGAGAAAAAGAGAGAGTTG Found at i:1162296 original size:79 final size:79 Alignment explanation
Indices: 1162201--1162371 Score: 256 Period size: 79 Copynumber: 2.2 Consensus size: 79 1162191 AGAAGTTCAA * * 1162201 AATGAGAAGAACTTATTTAACCTTAGCTAGATTCCATCATAG-AATGAGGTTG-ATCAACATTTC 1 AATGAGAAGAACTTATTCAACCTTAGCTAGATTCCATCACAGAAAT-AGG-TGAATCAACATTTC 1162264 CAATGGAAGGGTTCGT 64 CAATGGAAGGGTTCGT * * * 1162280 AATGAGAAGAACTTATTCAACCTTAGCTCGATTCCATCACAGAAATATGTGAATCAATATTTCCA 1 AATGAGAAGAACTTATTCAACCTTAGCTAGATTCCATCACAGAAATAGGTGAATCAACATTTCCA 1162345 ATGGAAGGGTTCGT 66 ATGGAAGGGTTCGT * 1162359 AATAAGAAGAACT 1 AATGAGAAGAACT 1162372 CGTCCTATGA Statistics Matches: 84, Mismatches: 6, Indels: 4 0.89 0.06 0.04 Matches are distributed among these distances: 78 2 0.02 79 79 0.94 80 3 0.04 ACGTcount: A:0.37, C:0.16, G:0.19, T:0.29 Consensus pattern (79 bp): AATGAGAAGAACTTATTCAACCTTAGCTAGATTCCATCACAGAAATAGGTGAATCAACATTTCCA ATGGAAGGGTTCGT Found at i:1162678 original size:115 final size:118 Alignment explanation
Indices: 1162274--1162689 Score: 577 Period size: 118 Copynumber: 3.6 Consensus size: 118 1162264 CAATGGAAGG * * ** * * * 1162274 GTTCGTAATGAGAAGAACTTATTCAACCTTAGCTCGATTCCATCACAGAAATATGTGAATCAATA 1 GTTCATAATGAGAAGAACTTATTCAACCTTAGCTCAATTCCATCACAGAAGGAGGTGGATCAACA * * * 1162339 TTTCCAATGGAAGGGTTCGTAATAAGAAGAACTCGTCCTATGAGGGAGAAGAA 66 TTTCCAATGGAAGGGTTCGTAATGAGAAGAACTCATCCGATGAGGGAGAAGAA * * * * * 1162392 GTTCATAATGAGAAGAACTTATTCAACCTTAGCTCAATTCCATCATAGAATGAGGAGGGTTAACA 1 GTTCATAATGAGAAGAACTTATTCAACCTTAGCTCAATTCCATCACAGAAGGAGGTGGATCAACA * 1162457 TTTCCAATGGAAGGGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAA 66 TTTCCAATGGAAGGGTTCGTAATGAGAAGAACTCATCCGATGAGGGAGAAGAA * * 1162510 GTTCACAATGAGAAGAACTTATTCAACCTTATCTCAATTCCATCACAGAAGGAGGTGGATCAACA 1 GTTCATAATGAGAAGAACTTATTCAACCTTAGCTCAATTCCATCACAGAAGGAGGTGGATCAACA * * 1162575 TTTCTAATAGAAGGGTTCGTAATGAGAAGAACTCATCCGATGAGGGAG-A-AA 66 TTTCCAATGGAAGGGTTCGTAATGAGAAGAACTCATCCGATGAGGGAGAAGAA * * * * * * 1162626 -TTCGTAATGAGAAGAACTTATTCAACCTTAGCTCGATTCCATCATATAAGGAGTTGGAACAACA 1 GTTCATAATGAGAAGAACTTATTCAACCTTAGCTCAATTCCATCACAGAAGGAGGTGGATCAACA 1162690 CAATCTTGGC Statistics Matches: 265, Mismatches: 33, Indels: 3 0.88 0.11 0.01 Matches are distributed among these distances: 115 56 0.21 116 2 0.01 117 1 0.00 118 206 0.78 ACGTcount: A:0.37, C:0.17, G:0.21, T:0.25 Consensus pattern (118 bp): GTTCATAATGAGAAGAACTTATTCAACCTTAGCTCAATTCCATCACAGAAGGAGGTGGATCAACA TTTCCAATGGAAGGGTTCGTAATGAGAAGAACTCATCCGATGAGGGAGAAGAA Found at i:1163061 original size:23 final size:23 Alignment explanation
Indices: 1163035--1163079 Score: 81 Period size: 23 Copynumber: 2.0 Consensus size: 23 1163025 TATTTTATTT * 1163035 TATTATTATTATTTATTACAAAA 1 TATTATTATTATTTATGACAAAA 1163058 TATTATTATTATTTATGACAAA 1 TATTATTATTATTTATGACAAA 1163080 CCCAATACCC Statistics Matches: 21, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 23 21 1.00 ACGTcount: A:0.42, C:0.04, G:0.02, T:0.51 Consensus pattern (23 bp): TATTATTATTATTTATGACAAAA Found at i:1163070 original size:3 final size:3 Alignment explanation
Indices: 1162974--1163052 Score: 83 Period size: 3 Copynumber: 26.3 Consensus size: 3 1162964 TTTTTCAACC * * 1162974 ATT A-T ATT ATT ATT ATT ATAA AAT ATT ATT ATT ATT ATT ATT ATT 1 ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT * 1163019 ATAA ATT ATT -TT ATT -TT ATT ATT ATT ATTT ATT A 1 AT-T ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT A 1163053 CAAAATATTA Statistics Matches: 64, Mismatches: 6, Indels: 12 0.78 0.07 0.15 Matches are distributed among these distances: 2 6 0.09 3 52 0.81 4 6 0.09 ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62 Consensus pattern (3 bp): ATT Found at i:1163846 original size:19 final size:19 Alignment explanation
Indices: 1163819--1163855 Score: 56 Period size: 19 Copynumber: 1.9 Consensus size: 19 1163809 TCGATTGAGC * 1163819 AGAGGAAAAGAGAGAGTTG 1 AGAGAAAAAGAGAGAGTTG * 1163838 AGAGAAAAAGGGAGAGTT 1 AGAGAAAAAGAGAGAGTT 1163856 TTTTTAGGTT Statistics Matches: 16, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 19 16 1.00 ACGTcount: A:0.49, C:0.00, G:0.41, T:0.11 Consensus pattern (19 bp): AGAGAAAAAGAGAGAGTTG Found at i:1169181 original size:51 final size:51 Alignment explanation
Indices: 1169126--1169252 Score: 139 Period size: 51 Copynumber: 2.5 Consensus size: 51 1169116 ACGCATGGTA * * * * * 1169126 AGGCGCGATGCATGGG-CTGCTCCTTACTGTCGTGTGACACACGCACCAAAT 1 AGGCGCGGTGCATGGGCCT-CGCCTTACTGTCATCTGACACAAGCACCAAAT * * * 1169177 AGGCGCGGTGCATGGGCCTCGCCTTGCTGTCATCTGACACAAGCGCCAGAT 1 AGGCGCGGTGCATGGGCCTCGCCTTACTGTCATCTGACACAAGCACCAAAT * * * 1169228 AGGCACGGTGCATGGGTCACGCCTT 1 AGGCGCGGTGCATGGGCCTCGCCTT 1169253 GTATAATTAT Statistics Matches: 64, Mismatches: 11, Indels: 2 0.83 0.14 0.03 Matches are distributed among these distances: 51 62 0.97 52 2 0.03 ACGTcount: A:0.19, C:0.30, G:0.31, T:0.20 Consensus pattern (51 bp): AGGCGCGGTGCATGGGCCTCGCCTTACTGTCATCTGACACAAGCACCAAAT Found at i:1169360 original size:29 final size:29 Alignment explanation
Indices: 1169309--1169375 Score: 82 Period size: 29 Copynumber: 2.3 Consensus size: 29 1169299 TATAAATATG * * * 1169309 CTCTCAACCCGTAAACATTCACAACAATC 1 CTCTCAACCCGTAAAAATACACAACAAAC 1169338 CTCTCAACCCG-AAAAATCACACAACAAAC 1 CTCTCAACCCGTAAAAAT-ACACAACAAAC * 1169367 CTTTCAACC 1 CTCTCAACC 1169376 GCTAAATATC Statistics Matches: 33, Mismatches: 4, Indels: 2 0.85 0.10 0.05 Matches are distributed among these distances: 28 5 0.15 29 28 0.85 ACGTcount: A:0.40, C:0.39, G:0.03, T:0.18 Consensus pattern (29 bp): CTCTCAACCCGTAAAAATACACAACAAAC Found at i:1169465 original size:18 final size:21 Alignment explanation
Indices: 1169444--1169484 Score: 61 Period size: 21 Copynumber: 2.1 Consensus size: 21 1169434 TGTAAGGTAA 1169444 TTTTT-TAA-TATAT-AATAT 1 TTTTTATAATTATATGAATAT 1169462 TTTTTATAATTATATGAATAT 1 TTTTTATAATTATATGAATAT 1169483 TT 1 TT 1169485 GAAAAAAAAT Statistics Matches: 20, Mismatches: 0, Indels: 3 0.87 0.00 0.13 Matches are distributed among these distances: 18 5 0.25 19 3 0.15 20 5 0.25 21 7 0.35 ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61 Consensus pattern (21 bp): TTTTTATAATTATATGAATAT Found at i:1174207 original size:23 final size:23 Alignment explanation
Indices: 1174181--1174231 Score: 93 Period size: 23 Copynumber: 2.2 Consensus size: 23 1174171 TAATTTTTAT * 1174181 TATACACTAGATAAAATGATTAG 1 TATACACTAGATAAAATGATTAA 1174204 TATACACTAGATAAAATGATTAA 1 TATACACTAGATAAAATGATTAA 1174227 TATAC 1 TATAC 1174232 CAAATCACTT Statistics Matches: 27, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 23 27 1.00 ACGTcount: A:0.49, C:0.10, G:0.10, T:0.31 Consensus pattern (23 bp): TATACACTAGATAAAATGATTAA Found at i:1175158 original size:13 final size:13 Alignment explanation
Indices: 1175142--1175193 Score: 50 Period size: 13 Copynumber: 3.8 Consensus size: 13 1175132 TAACTGCAAA 1175142 AAATAAAATAATT 1 AAATAAAATAATT ** 1175155 AAATAAAATACTAAA 1 AAATAAAATA--ATT * 1175170 AAATTTAAATAATT 1 AAA-TAAAATAATT 1175184 AAATAAAATA 1 AAATAAAATA 1175194 CTAACAAAAT Statistics Matches: 30, Mismatches: 6, Indels: 6 0.71 0.14 0.14 Matches are distributed among these distances: 13 16 0.53 14 4 0.13 15 4 0.13 16 6 0.20 ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29 Consensus pattern (13 bp): AAATAAAATAATT Found at i:1175179 original size:29 final size:29 Alignment explanation
Indices: 1175139--1175211 Score: 112 Period size: 29 Copynumber: 2.5 Consensus size: 29 1175129 TTATAACTGC * 1175139 AAAAAA-TAAAATAATTAAATAAAATACT 1 AAAAAATTTAAATAATTAAATAAAATACT 1175167 AAAAAATTTAAATAATTAAATAAAATACT 1 AAAAAATTTAAATAATTAAATAAAATACT 1175196 AACAAAATATTAAATA 1 AA-AAAAT-TTAAATA 1175212 GAATAAAATA Statistics Matches: 41, Mismatches: 1, Indels: 3 0.91 0.02 0.07 Matches are distributed among these distances: 28 6 0.15 29 23 0.56 30 5 0.12 31 7 0.17 ACGTcount: A:0.68, C:0.04, G:0.00, T:0.27 Consensus pattern (29 bp): AAAAAATTTAAATAATTAAATAAAATACT Found at i:1175190 original size:21 final size:19 Alignment explanation
Indices: 1175140--1175193 Score: 56 Period size: 21 Copynumber: 2.6 Consensus size: 19 1175130 TATAACTGCA 1175140 AAAAATAAAATAATTAAAT 1 AAAAATAAAATAATTAAAT 1175159 AAAATACTAAAA-AATTTAAAT 1 AAAA-A-TAAAATAA-TTAAAT 1175180 AATTAAATAAAATA 1 AA--AAATAAAATA 1175194 CTAACAAAAT Statistics Matches: 29, Mismatches: 0, Indels: 9 0.76 0.00 0.24 Matches are distributed among these distances: 19 4 0.14 20 3 0.10 21 18 0.62 22 2 0.07 23 2 0.07 ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28 Consensus pattern (19 bp): AAAAATAAAATAATTAAAT Found at i:1175491 original size:40 final size:41 Alignment explanation
Indices: 1175407--1175484 Score: 113 Period size: 40 Copynumber: 1.9 Consensus size: 41 1175397 GTGTGTCAGT * * 1175407 TGGCAGAAAGGCGTGGCCCATGCACCGTGCCTTACCCTACG 1 TGGCAGAAAGGCATGGCCCATGCACCGCGCCTTACCCTACG * * 1175448 TGGCA-AAAGGCATGTCCCATGCATCGCGCCTTACCCT 1 TGGCAGAAAGGCATGGCCCATGCACCGCGCCTTACCCT 1175485 GTGTGGCGCC Statistics Matches: 33, Mismatches: 4, Indels: 1 0.87 0.11 0.03 Matches are distributed among these distances: 40 28 0.85 41 5 0.15 ACGTcount: A:0.21, C:0.35, G:0.26, T:0.19 Consensus pattern (41 bp): TGGCAGAAAGGCATGGCCCATGCACCGCGCCTTACCCTACG Found at i:1182879 original size:78 final size:79 Alignment explanation
Indices: 1182685--1182873 Score: 326 Period size: 78 Copynumber: 2.4 Consensus size: 79 1182675 GCGAAACATT * * * 1182685 CTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGTTGACAATGTACCCATATACATT 1 CTTTCATGCCAATAATGCAACCATATGCATTATTCCTTTATGCTGACAATGTACCCATATACATT 1182750 TCAGCTATGGCATC 66 TCAGCTATGGCATC * * 1182764 ATTTCATGCCAATAATGC-ACCATATGAATTATTCCTTTATGCTGACAATGTACCCATATACATT 1 CTTTCATGCCAATAATGCAACCATATGCATTATTCCTTTATGCTGACAATGTACCCATATACATT 1182828 TCAGCTATGGCATC 66 TCAGCTATGGCATC 1182842 CTTTCATGCCAATAATGCAACCATATGCATTA 1 CTTTCATGCCAATAATGCAACCATATGCATTA 1182874 CCCTTTTTCA Statistics Matches: 102, Mismatches: 7, Indels: 2 0.92 0.06 0.02 Matches are distributed among these distances: 78 73 0.72 79 29 0.28 ACGTcount: A:0.30, C:0.24, G:0.11, T:0.35 Consensus pattern (79 bp): CTTTCATGCCAATAATGCAACCATATGCATTATTCCTTTATGCTGACAATGTACCCATATACATT TCAGCTATGGCATC Found at i:1183313 original size:20 final size:22 Alignment explanation
Indices: 1183290--1183336 Score: 62 Period size: 20 Copynumber: 2.2 Consensus size: 22 1183280 TCAAAGTATC * 1183290 GATACTACTACCCT-A-GTACT 1 GATACTACTACACTAAGGTACT * 1183310 GATACTTCTACACTAAGGTACT 1 GATACTACTACACTAAGGTACT 1183332 GATAC 1 GATAC 1183337 CCCTTCCTAG Statistics Matches: 23, Mismatches: 2, Indels: 2 0.85 0.07 0.07 Matches are distributed among these distances: 20 12 0.52 21 1 0.04 22 10 0.43 ACGTcount: A:0.32, C:0.26, G:0.13, T:0.30 Consensus pattern (22 bp): GATACTACTACACTAAGGTACT Found at i:1183448 original size:19 final size:22 Alignment explanation
Indices: 1183399--1183450 Score: 65 Period size: 19 Copynumber: 2.5 Consensus size: 22 1183389 CCCTCTATGT * 1183399 GGTATCGATACTACCCTTCTAT 1 GGTATCGATACTACCCTTCTAC * 1183421 GGTACCGATACT-CCC-T-TAC 1 GGTATCGATACTACCCTTCTAC 1183440 GGTATCGATAC 1 GGTATCGATAC 1183451 CGAAATTAGA Statistics Matches: 27, Mismatches: 3, Indels: 3 0.82 0.09 0.09 Matches are distributed among these distances: 19 12 0.44 20 1 0.04 21 3 0.11 22 11 0.41 ACGTcount: A:0.23, C:0.29, G:0.17, T:0.31 Consensus pattern (22 bp): GGTATCGATACTACCCTTCTAC Found at i:1189671 original size:34 final size:34 Alignment explanation
Indices: 1189633--1189831 Score: 101 Period size: 34 Copynumber: 5.2 Consensus size: 34 1189623 TCAGCGAGGC 1189633 ATTCTTTCATGCCAATAATGCACCCATATGCATT 1 ATTCTTTCATGCCAATAATGCACCCATATGCATT * ** * * * 1189667 ATTCTTTTATGCTGACAATGTACCCATATACATTTCAGCT 1 ATTCTTTCATGCCAATAATGCACCCATATGCA--T----T 1189707 ATGTCATCATTTCATGCCAATAATGCACCCATATGCATT 1 A--T--TC-TTTCATGCCAATAATGCACCCATATGCATT * ** * * 1189746 ATTCTTTTATGCTGACAATGCACCCATATACATTTCAACT 1 ATTCTTTCATGCCAATAATGCACCCATATGCA--T----T 1189786 ATGGCATCCTTTCATGCCAATAATGCACCCATATGCATT 1 AT----T-CTTTCATGCCAATAATGCACCCATATGCATT 1189825 ATTCTTT 1 ATTCTTT 1189832 TATGTTGAAA Statistics Matches: 121, Mismatches: 22, Indels: 44 0.65 0.12 0.24 Matches are distributed among these distances: 34 53 0.44 35 3 0.02 36 2 0.02 37 1 0.01 39 5 0.04 40 5 0.04 42 1 0.01 43 2 0.02 44 3 0.02 45 46 0.38 ACGTcount: A:0.29, C:0.25, G:0.10, T:0.37 Consensus pattern (34 bp): ATTCTTTCATGCCAATAATGCACCCATATGCATT Found at i:1189889 original size:157 final size:158 Alignment explanation
Indices: 1189585--1189910 Score: 503 Period size: 157 Copynumber: 2.1 Consensus size: 158 1189575 TTCCATTTAA * * * * * * * 1189585 ATTATACTTTTATTTCTGATAATGCACCCCTACGCATTTCAGCGAGGCATTCTTTCATGCCAATA 1 ATTATTCTTTTATTGCTGACAATGCACCCATACACATTTCAACGAGGCATCCTTTCATGCCAATA * 1189650 ATGCACCCATATGCATTATTCTTTTATGCTGACAATGTACCCATATACATTTCAGCTATGTCATC 66 ATGCACCCATATGCATTATTCTTTTATGCTGACAATGTACCCATATACATTTCAGCTATGGCATC 1189715 ATTTCATGCCAATAATGCACCCATATGC 131 ATTTCATGCCAATAATGCACCCATATGC * * 1189743 ATTATTCTTTTA-TGCTGACAATGCACCCATATACATTTCAACTATGGCATCCTTTCATGCCAAT 1 ATTATTCTTTTATTGCTGACAATGCACCCATACACATTTCAACGA-GGCATCCTTTCATGCCAAT * 1189807 AATGCACCCATATGCATTATTCTTTTATGTTGA-AATGTACCCATATACATTTCAGCTATGGCAT 65 AATGCACCCATATGCATTATTCTTTTATGCTGACAATGTACCCATATACATTTCAGCTATGGCAT * * 1189871 CCTTTCATTCCAATAATGCACCCATATGC 130 CATTTCATGCCAATAATGCACCCATATGC * 1189900 ATTACTCTTTT 1 ATTATTCTTTT 1189911 TCATTCATTT Statistics Matches: 153, Mismatches: 14, Indels: 3 0.90 0.08 0.02 Matches are distributed among these distances: 157 92 0.60 158 61 0.40 ACGTcount: A:0.28, C:0.25, G:0.10, T:0.37 Consensus pattern (158 bp): ATTATTCTTTTATTGCTGACAATGCACCCATACACATTTCAACGAGGCATCCTTTCATGCCAATA ATGCACCCATATGCATTATTCTTTTATGCTGACAATGTACCCATATACATTTCAGCTATGGCATC ATTTCATGCCAATAATGCACCCATATGC Found at i:1189930 original size:78 final size:79 Alignment explanation
Indices: 1189619--1189910 Score: 489 Period size: 79 Copynumber: 3.7 Consensus size: 79 1189609 CACCCCTACG * * 1189619 CATTTCAGCGA-GGCATTCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCTGAC 1 CATTTCAGCTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCTGAC 1189683 AATGTACCCATATA 66 AATGTACCCATATA * * 1189697 CATTTCAGCTATGTCATCATTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCTGAC 1 CATTTCAGCTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCTGAC * 1189762 AATGCACCCATATA 66 AATGTACCCATATA * * 1189776 CATTTCAACTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGTTGA- 1 CATTTCAGCTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCTGAC 1189840 AATGTACCCATATA 66 AATGTACCCATATA * * 1189854 CATTTCAGCTATGGCATCCTTTCATTCCAATAATGCACCCATATGCATTACTCTTTT 1 CATTTCAGCTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTT 1189911 TCATTCATTT Statistics Matches: 200, Mismatches: 13, Indels: 2 0.93 0.06 0.01 Matches are distributed among these distances: 78 77 0.38 79 123 0.62 ACGTcount: A:0.28, C:0.25, G:0.11, T:0.36 Consensus pattern (79 bp): CATTTCAGCTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCTGAC AATGTACCCATATA Found at i:1190551 original size:94 final size:94 Alignment explanation
Indices: 1190379--1190556 Score: 209 Period size: 94 Copynumber: 1.9 Consensus size: 94 1190369 CCTTCCTGGC * * * * 1190379 ATCGATACCAAAATTAGGTTGATGTTTCATGGTATCGATACCCTCTACGTGGTATTGATACTACC 1 ATCGATACCAAAATTAGATTGATGTTTCATGGTATCGATACCCTCTACATAGTATCGATACTACC * *** 1190444 CTTCTATGGTATCGATACTCCCTTAAGGT 66 CTTCAACAATATCGATACTCCCTTAAGGT * * * 1190473 ATCGATACCGAAATTAGATTCGATGTTTGCTTGGTATCGATACCCTTTTA-ATAGTATCGATACT 1 ATCGATACCAAAATTAGATT-GATGTTT-CATGGTATCGATACCC-TCTACATAGTATCGATACT 1190537 A-CC-TCAACAATATCGATACT 63 ACCCTTCAACAATATCGATACT 1190557 GATTGAAACA Statistics Matches: 70, Mismatches: 11, Indels: 6 0.80 0.13 0.07 Matches are distributed among these distances: 94 31 0.44 95 9 0.13 96 27 0.39 97 3 0.04 ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35 Consensus pattern (94 bp): ATCGATACCAAAATTAGATTGATGTTTCATGGTATCGATACCCTCTACATAGTATCGATACTACC CTTCAACAATATCGATACTCCCTTAAGGT Found at i:1193813 original size:2 final size:2 Alignment explanation
Indices: 1193806--1193841 Score: 72 Period size: 2 Copynumber: 18.0 Consensus size: 2 1193796 TGTGTAATTA 1193806 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 1193842 TTACACATTA Statistics Matches: 34, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 34 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:1194727 original size:21 final size:21 Alignment explanation
Indices: 1194701--1194800 Score: 83 Period size: 21 Copynumber: 4.8 Consensus size: 21 1194691 GTATCGAATA ** 1194701 AGTTGGTATTGATACCAGATG 1 AGTTGGTATCAATACCAGATG * 1194722 AGTTGGTATCAATACCAGATA 1 AGTTGGTATCAATACCAGATG * * * * * 1194743 AATTGATGTCCATACCATATG 1 AGTTGGTATCAATACCAGATG * * * * 1194764 AATTAGTATCCATAACAGATG 1 AGTTGGTATCAATACCAGATG * 1194785 AGTTGGTATCCATACC 1 AGTTGGTATCAATACC 1194801 GTGTCGAAAT Statistics Matches: 62, Mismatches: 17, Indels: 0 0.78 0.22 0.00 Matches are distributed among these distances: 21 62 1.00 ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31 Consensus pattern (21 bp): AGTTGGTATCAATACCAGATG Found at i:1194797 original size:42 final size:42 Alignment explanation
Indices: 1194698--1194800 Score: 107 Period size: 42 Copynumber: 2.5 Consensus size: 42 1194688 GATGTATCGA ** * * * 1194698 ATAAGTTGGTATTGATACCAGATGAGTTGGTATCAATACCAG 1 ATAAGTTGGTATCCATACCAGATGAATTAGTATCAATAACAG * * * * * 1194740 ATAAATTGATGTCCATACCATATGAATTAGTATCCATAACAG 1 ATAAGTTGGTATCCATACCAGATGAATTAGTATCAATAACAG * 1194782 ATGAGTTGGTATCCATACC 1 ATAAGTTGGTATCCATACC 1194801 GTGTCGAAAT Statistics Matches: 47, Mismatches: 14, Indels: 0 0.77 0.23 0.00 Matches are distributed among these distances: 42 47 1.00 ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31 Consensus pattern (42 bp): ATAAGTTGGTATCCATACCAGATGAATTAGTATCAATAACAG Found at i:1202795 original size:74 final size:74 Alignment explanation
Indices: 1202595--1203170 Score: 487 Period size: 74 Copynumber: 8.0 Consensus size: 74 1202585 GGTAGTAAAA * ** * * * 1202595 TGTCTCGACTGAGATGAAAGTTGTTTTAAGGCAAACTATCTCAAGTGACATAAAATTTTTGTTTC 1 TGTCTCGAGTGAGACAAAACTTGTTTTAAGGAAAACTATCTCAAGTGAGATAAAATTTTTGTTTC * 1202660 AGGAGAAAC 66 AAGAGAAAC ** * * * * * * * 1202669 AATCTTGATTGAGACAAAATTTGTTTTAAAGG-AAATTTTCTTAAGAGAGATAAAATTTTTGTTT 1 TGTCTCGAGTGAGACAAAACTTGTTTT-AAGGAAAACTATCTCAAGTGAGATAAAATTTTTGTTT * 1202733 CGAGAGAAAC 65 CAAGAGAAAC * ** 1202743 TGTCTCGAGTGAGACAAAACTTGTTTTAAGGAAAAATATCTCAAGTTTGATAAAATTTTTGTTTC 1 TGTCTCGAGTGAGACAAAACTTGTTTTAAGGAAAACTATCTCAAGTGAGATAAAATTTTTGTTTC * * ** 1202808 GAG-GTGAGT 66 AAGAG-AAAC * 1202817 TGTCTCGAGTGAGA-AGAAACTTGTTTTAAGGAAAACTATCTCAAGTGAGATAGAATTTTTGTTT 1 TGTCTCGAGTGAGACA-AAACTTGTTTTAAGGAAAACTATCTCAAGTGAGATAAAATTTTTGTTT 1202881 CAA-ATGAAAC 65 CAAGA-GAAAC * * * 1202891 TGTCTC----GAGACACAACTTGTTTTAAGG-----GA----AAGTGAGACAAAATTTTTGTTTC 1 TGTCTCGAGTGAGACAAAACTTGTTTTAAGGAAAACTATCTCAAGTGAGATAAAATTTTTGTTTC * ** * 1202943 TATTGAAAA 66 AAGAGAAAC * * 1202952 TGTCTCGAGTGAGACGAAA-TTGATTTTAAGGAAAATTATCTCAAGTGAGATAAAATTTTTGTTT 1 TGTCTCGAGTGAGACAAAACTTG-TTTTAAGGAAAACTATCTCAAGTGAGATAAAATTTTTGTTT * 1203016 CAAAAGAAAC 65 CAAGAGAAAC * * * * * * 1203026 TGTCTTGAGTTAGA-AGAAATTTGTTTTAAAGAAAACTATGTGAAGTGAGATAAAATTTTTGTTT 1 TGTCTCGAGTGAGACA-AAACTTGTTTTAAGGAAAACTATCTCAAGTGAGATAAAATTTTTGTTT * 1203090 TAAGA-AAAC 65 CAAGAGAAAC * * * * * 1203099 TATCTCGAG-GAGACGAAATTTG-TTTAATGAAAA-TCATCTTAAGTGAGATAAAAATATTTTGT 1 TGTCTCGAGTGAGACAAAACTTGTTTTAAGGAAAACT-ATCTCAAGTGAGAT-AAAAT-TTTTGT 1203161 TTCAAGAGAA 63 TTCAAGAGAA 1203171 TCTATCTCAA Statistics Matches: 405, Mismatches: 68, Indels: 58 0.76 0.13 0.11 Matches are distributed among these distances: 61 32 0.08 64 3 0.01 65 16 0.04 70 20 0.05 71 23 0.06 72 15 0.04 73 29 0.07 74 259 0.64 75 8 0.02 ACGTcount: A:0.37, C:0.09, G:0.19, T:0.34 Consensus pattern (74 bp): TGTCTCGAGTGAGACAAAACTTGTTTTAAGGAAAACTATCTCAAGTGAGATAAAATTTTTGTTTC AAGAGAAAC Found at i:1203188 original size:40 final size:37 Alignment explanation
Indices: 1203071--1203210 Score: 101 Period size: 40 Copynumber: 3.7 Consensus size: 37 1203061 CTATGTGAAG * * * 1203071 TGAGATAAAATTTTTGTTTTAAGA-AAACTATCTC-GA 1 TGAGATAAAATTTTTGTTTCAAGAGAATC-ATCTCAAA * ** * * * 1203107 GGAGACGAAA--TTTGTTT-AATGAAAATCATCTTAAG 1 TGAGATAAAATTTTTGTTTCAA-GAGAATCATCTCAAA 1203142 TGAGATAAAAATATTTTGTTTCAAGAGAATCTATCTCAAA 1 TGAGAT-AAAAT-TTTTGTTTCAAGAGAATC-ATCTCAAA 1203182 TGAGATAAAATTTTTGTTTCTGAAGAGAA 1 TGAGATAAAATTTTTGTTTC--AAGAGAA 1203211 CCTCTTAAAA Statistics Matches: 80, Mismatches: 13, Indels: 18 0.72 0.12 0.16 Matches are distributed among these distances: 33 2 0.03 34 13 0.16 35 7 0.09 36 10 0.12 38 9 0.11 39 18 0.22 40 21 0.26 ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36 Consensus pattern (37 bp): TGAGATAAAATTTTTGTTTCAAGAGAATCATCTCAAA Found at i:1203192 original size:39 final size:38 Alignment explanation
Indices: 1203117--1203210 Score: 102 Period size: 40 Copynumber: 2.4 Consensus size: 38 1203107 GGAGACGAAA * * * 1203117 TTTGTTT-AATGAAAATCATCTTAAGTGAGATAAAAATAT 1 TTTGTTTCAA-GAGAATCATCTCAAATGAGATAAAAAT-T 1203156 TTTGTTTCAAGAGAATCTATCTCAAATGAGAT-AAAATT 1 TTTGTTTCAAGAGAATC-ATCTCAAATGAGATAAAAATT 1203194 TTTGTTTCTGAAGAGAA 1 TTTGTTTC--AAGAGAA 1203211 CCTCTTAAAA Statistics Matches: 48, Mismatches: 3, Indels: 7 0.83 0.05 0.12 Matches are distributed among these distances: 38 9 0.19 39 18 0.38 40 21 0.44 ACGTcount: A:0.39, C:0.07, G:0.15, T:0.38 Consensus pattern (38 bp): TTTGTTTCAAGAGAATCATCTCAAATGAGATAAAAATT Found at i:1204185 original size:15 final size:16 Alignment explanation
Indices: 1204150--1204185 Score: 65 Period size: 16 Copynumber: 2.3 Consensus size: 16 1204140 AAAAAGTAGT 1204150 GCAAAAAGTGTTTCCC 1 GCAAAAAGTGTTTCCC 1204166 GCAAAAAGTGTTTCCC 1 GCAAAAAGTGTTTCCC 1204182 -CAAA 1 GCAAA 1204186 GATGAAATTC Statistics Matches: 20, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 15 4 0.20 16 16 0.80 ACGTcount: A:0.36, C:0.25, G:0.17, T:0.22 Consensus pattern (16 bp): GCAAAAAGTGTTTCCC Found at i:1205580 original size:21 final size:21 Alignment explanation
Indices: 1205556--1205603 Score: 69 Period size: 21 Copynumber: 2.3 Consensus size: 21 1205546 TTAAATGTCC * 1205556 TGCAAAATACAAAGATGTAAA 1 TGCAAAATACAAAGATGCAAA * * 1205577 TGCAGAATACAAAGATGCAAG 1 TGCAAAATACAAAGATGCAAA 1205598 TGCAAA 1 TGCAAA 1205604 TGTAAATGTA Statistics Matches: 23, Mismatches: 4, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 21 23 1.00 ACGTcount: A:0.52, C:0.12, G:0.19, T:0.17 Consensus pattern (21 bp): TGCAAAATACAAAGATGCAAA Found at i:1208028 original size:16 final size:14 Alignment explanation
Indices: 1208007--1208048 Score: 50 Period size: 14 Copynumber: 2.9 Consensus size: 14 1207997 TAAAAACGAA 1208007 GAAAATAATAAATAG 1 GAAAAT-ATAAATAG 1208022 TGAAAATATAAA-AG 1 -GAAAATATAAATAG 1208036 GAAAATGATAAAT 1 GAAAAT-ATAAAT 1208049 GAAAAGTAAA Statistics Matches: 24, Mismatches: 0, Indels: 5 0.83 0.00 0.17 Matches are distributed among these distances: 13 6 0.25 14 7 0.29 15 5 0.21 16 6 0.25 ACGTcount: A:0.64, C:0.00, G:0.14, T:0.21 Consensus pattern (14 bp): GAAAATATAAATAG Found at i:1208116 original size:26 final size:24 Alignment explanation
Indices: 1208087--1208148 Score: 67 Period size: 24 Copynumber: 2.6 Consensus size: 24 1208077 AAAATATGTA * 1208087 AATATATATAATATAATATGATACAT 1 AATATATATAATATAATAT-A-AAAT * 1208113 AATA-A-ATATTATAATATAAAAT 1 AATATATATAATATAATATAAAAT 1208135 -ATATATATAATATA 1 AATATATATAATATA 1208149 GAAAAATTAA Statistics Matches: 31, Mismatches: 3, Indels: 7 0.76 0.07 0.17 Matches are distributed among these distances: 21 3 0.10 22 4 0.13 23 8 0.26 24 11 0.35 25 1 0.03 26 4 0.13 ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39 Consensus pattern (24 bp): AATATATATAATATAATATAAAAT Found at i:1212670 original size:31 final size:31 Alignment explanation
Indices: 1212571--1212674 Score: 86 Period size: 31 Copynumber: 3.2 Consensus size: 31 1212561 GTCGGTGCTA * ** 1212571 AACCTATACAAGGAATTACCAACAACGACTG 1 AACCTATACAATGAATTACCAACAGGGACTG * * 1212602 AACCTGCTAGAGATAAGGAATTACCAATC-GGTG-CTG 1 AACCT-ATACA-AT---GAATTACCAA-CAGG-GACTG 1212638 AACCTATACAATGAATTACCAACAGGGACTG 1 AACCTATACAATGAATTACCAACAGGGACTG 1212669 AACCTA 1 AACCTA 1212675 CAAAGTCTTC Statistics Matches: 57, Mismatches: 7, Indels: 18 0.70 0.09 0.22 Matches are distributed among these distances: 30 2 0.04 31 26 0.46 32 3 0.05 33 1 0.02 34 2 0.04 35 3 0.05 36 18 0.32 37 2 0.04 ACGTcount: A:0.40, C:0.23, G:0.17, T:0.19 Consensus pattern (31 bp): AACCTATACAATGAATTACCAACAGGGACTG Found at i:1219666 original size:27 final size:27 Alignment explanation
Indices: 1219621--1219672 Score: 79 Period size: 27 Copynumber: 1.9 Consensus size: 27 1219611 TCCTAACAAG * 1219621 TTTGACCAATTGAATAAGTTTGATAAA 1 TTTGACCAATTGAACAAGTTTGATAAA 1219648 TTTGACCAATTTG-ACAAGTTTGATA 1 TTTGACCAA-TTGAACAAGTTTGATA 1219673 TGCAAATGAT Statistics Matches: 23, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 27 20 0.87 28 3 0.13 ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38 Consensus pattern (27 bp): TTTGACCAATTGAACAAGTTTGATAAA Found at i:1221965 original size:23 final size:23 Alignment explanation
Indices: 1221939--1222002 Score: 119 Period size: 23 Copynumber: 2.8 Consensus size: 23 1221929 ATGTTGTGAG * 1221939 TTCTAGAATAGTTTGTTAGTTAA 1 TTCTAGAATAGTTTGTTAGCTAA 1221962 TTCTAGAATAGTTTGTTAGCTAA 1 TTCTAGAATAGTTTGTTAGCTAA 1221985 TTCTAGAATAGTTTGTTA 1 TTCTAGAATAGTTTGTTA 1222003 TCTTGTAGCA Statistics Matches: 40, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 23 40 1.00 ACGTcount: A:0.30, C:0.06, G:0.17, T:0.47 Consensus pattern (23 bp): TTCTAGAATAGTTTGTTAGCTAA Found at i:1226396 original size:23 final size:23 Alignment explanation
Indices: 1226368--1226422 Score: 110 Period size: 23 Copynumber: 2.4 Consensus size: 23 1226358 CCTGGTTTTG 1226368 TGCAAGCTGGTGATGGTTTAGTT 1 TGCAAGCTGGTGATGGTTTAGTT 1226391 TGCAAGCTGGTGATGGTTTAGTT 1 TGCAAGCTGGTGATGGTTTAGTT 1226414 TGCAAGCTG 1 TGCAAGCTG 1226423 CATAAAGCAA Statistics Matches: 32, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 23 32 1.00 ACGTcount: A:0.18, C:0.11, G:0.35, T:0.36 Consensus pattern (23 bp): TGCAAGCTGGTGATGGTTTAGTT Found at i:1233936 original size:22 final size:22 Alignment explanation
Indices: 1233901--1233954 Score: 90 Period size: 22 Copynumber: 2.5 Consensus size: 22 1233891 ACTTATGATG * 1233901 GTATCGATACCGTAGTTCAGAA 1 GTATCGGTACCGTAGTTCAGAA * 1233923 GTATCGGTATCGTAGTTCAGAA 1 GTATCGGTACCGTAGTTCAGAA 1233945 GTATCGGTAC 1 GTATCGGTAC 1233955 TTTAGTTAAG Statistics Matches: 29, Mismatches: 3, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 22 29 1.00 ACGTcount: A:0.28, C:0.17, G:0.26, T:0.30 Consensus pattern (22 bp): GTATCGGTACCGTAGTTCAGAA Found at i:1235751 original size:14 final size:14 Alignment explanation
Indices: 1235732--1235763 Score: 55 Period size: 14 Copynumber: 2.3 Consensus size: 14 1235722 GTATGAGCAG * 1235732 GAGTTCATTTGAAT 1 GAGTTCATTCGAAT 1235746 GAGTTCATTCGAAT 1 GAGTTCATTCGAAT 1235760 GAGT 1 GAGT 1235764 AGATACACCC Statistics Matches: 17, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 14 17 1.00 ACGTcount: A:0.28, C:0.09, G:0.25, T:0.38 Consensus pattern (14 bp): GAGTTCATTCGAAT Found at i:1237742 original size:17 final size:17 Alignment explanation
Indices: 1237717--1237758 Score: 75 Period size: 17 Copynumber: 2.5 Consensus size: 17 1237707 TCCATGATAG * 1237717 CTACCTCAATGACTAAA 1 CTACTTCAATGACTAAA 1237734 CTACTTCAATGACTAAA 1 CTACTTCAATGACTAAA 1237751 CTACTTCA 1 CTACTTCA 1237759 GAAGGGAGTT Statistics Matches: 24, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 17 24 1.00 ACGTcount: A:0.38, C:0.29, G:0.05, T:0.29 Consensus pattern (17 bp): CTACTTCAATGACTAAA Found at i:1249560 original size:22 final size:22 Alignment explanation
Indices: 1249532--1249583 Score: 86 Period size: 22 Copynumber: 2.4 Consensus size: 22 1249522 ACTCTCTTTC 1249532 TATATATACATACATACATACA 1 TATATATACATACATACATACA * * 1249554 TATATATACATATATATATACA 1 TATATATACATACATACATACA 1249576 TATATATA 1 TATATATA 1249584 TATATAGATA Statistics Matches: 28, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 22 28 1.00 ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38 Consensus pattern (22 bp): TATATATACATACATACATACA Found at i:1249582 original size:4 final size:4 Alignment explanation
Indices: 1249532--1249616 Score: 107 Period size: 4 Copynumber: 21.2 Consensus size: 4 1249522 ACTCTCTTTC * * * * * * 1249532 TATA TATA CATA CATA CATA CATA TATA TACA TATA TATA TACA TATA 1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA * 1249580 TATA TATA TAGA TATA TATA TATA TATA TATA TATA T 1 TATA TATA TATA TATA TATA TATA TATA TATA TATA T 1249617 CACTGTTTCT Statistics Matches: 73, Mismatches: 8, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 4 73 1.00 ACGTcount: A:0.49, C:0.07, G:0.01, T:0.42 Consensus pattern (4 bp): TATA Found at i:1254380 original size:2 final size:2 Alignment explanation
Indices: 1254373--1254399 Score: 54 Period size: 2 Copynumber: 13.5 Consensus size: 2 1254363 AGGGATTCAC 1254373 TA TA TA TA TA TA TA TA TA TA TA TA TA T 1 TA TA TA TA TA TA TA TA TA TA TA TA TA T 1254400 TAATCACACT Statistics Matches: 25, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 25 1.00 ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52 Consensus pattern (2 bp): TA Found at i:1266248 original size:20 final size:20 Alignment explanation
Indices: 1266220--1266261 Score: 59 Period size: 20 Copynumber: 2.1 Consensus size: 20 1266210 AGGTGTTATG 1266220 ATGAATTTTTA-AAGTTTTTA 1 ATGAATTTTTATAA-TTTTTA * 1266240 ATGATTTTTTATAATTTTTA 1 ATGAATTTTTATAATTTTTA 1266260 AT 1 AT 1266262 TCATCATAAT Statistics Matches: 20, Mismatches: 1, Indels: 2 0.87 0.04 0.09 Matches are distributed among these distances: 20 18 0.90 21 2 0.10 ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60 Consensus pattern (20 bp): ATGAATTTTTATAATTTTTA Found at i:1266865 original size:87 final size:87 Alignment explanation
Indices: 1266768--1266941 Score: 287 Period size: 87 Copynumber: 2.0 Consensus size: 87 1266758 AAGAGGGAGT * * * 1266768 TGAACATTTTCATACTTTTTTCGACAATTGGTATCTTTTTCATTAAATATTTTAATAAGGG-GAG 1 TGAACATTTTCATACTTTTTCCGACAATTGATATCTTTTT-ATTAAATAATTTAATAAGGGAGAG 1266832 TTTTGCCAAAAACAATTTTTCAA 65 TTTTGCCAAAAACAATTTTTCAA * 1266855 TGAACATTTTCATACTTTTTCCGACAATTGATATCTTTTTATTAAATAATTTATTAAGGGAGAGT 1 TGAACATTTTCATACTTTTTCCGACAATTGATATCTTTTTATTAAATAATTTAATAAGGGAGAGT * 1266920 TTTGCCAAAAATAATTTTTCAA 66 TTTGCCAAAAACAATTTTTCAA 1266942 ATGTTTTGTT Statistics Matches: 81, Mismatches: 5, Indels: 2 0.92 0.06 0.02 Matches are distributed among these distances: 86 18 0.22 87 63 0.78 ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44 Consensus pattern (87 bp): TGAACATTTTCATACTTTTTCCGACAATTGATATCTTTTTATTAAATAATTTAATAAGGGAGAGT TTTGCCAAAAACAATTTTTCAA Found at i:1271146 original size:32 final size:31 Alignment explanation
Indices: 1271071--1271219 Score: 131 Period size: 31 Copynumber: 4.7 Consensus size: 31 1271061 TCAACCTAAG * * * * 1271071 GGAATGCCTTGGGGTCTTAGAGCATACCC-AA 1 GGAATACCTTGGGGCCTGAGAGC-GACCCAAA * * * * 1271102 GAAATATCTTGGGGCCTCAGAGTCGACCCAAT 1 GGAATACCTTGGGGCCTGAGAG-CGACCCAAA * * 1271134 GGAGTACCTTGGGGCCTGAGAGCCTA-CCAAA 1 GGAATACCTTGGGGCCTGAGAG-CGACCCAAA 1271165 GGAATACCTTGGGGCCTGAGAGCTGACCCAAA 1 GGAATACCTTGGGGCCTGAGAGC-GACCCAAA * * * 1271197 GGAATATCTCGGGGCCTAAGAGC 1 GGAATACCTTGGGGCCTGAGAGC 1271220 CTACCTAAGA Statistics Matches: 95, Mismatches: 19, Indels: 7 0.79 0.16 0.06 Matches are distributed among these distances: 30 1 0.01 31 47 0.49 32 47 0.49 ACGTcount: A:0.27, C:0.24, G:0.30, T:0.19 Consensus pattern (31 bp): GGAATACCTTGGGGCCTGAGAGCGACCCAAA Found at i:1271176 original size:63 final size:63 Alignment explanation
Indices: 1271071--1271229 Score: 176 Period size: 63 Copynumber: 2.5 Consensus size: 63 1271061 TCAACCTAAG * * * * * * * 1271071 GGAATGCCTTGGGGTCTTAGAGCATACCCAAGAAATATCTTGGGGCCTCAGAG-TCGACCCAAT 1 GGAATACCTTGGGGCCTAAGAGCCTACCAAAGAAATACCTTGGGGCCTCAGAGCT-GACCCAAA * * * * 1271134 GGAGTACCTTGGGGCCTGAGAGCCTACCAAAGGAATACCTTGGGGCCTGAGAGCTGACCCAAA 1 GGAATACCTTGGGGCCTAAGAGCCTACCAAAGAAATACCTTGGGGCCTCAGAGCTGACCCAAA * * * 1271197 GGAATATCTCGGGGCCTAAGAGCCTACCTAAGA 1 GGAATACCTTGGGGCCTAAGAGCCTACCAAAGA 1271230 GTCACCTTAG Statistics Matches: 79, Mismatches: 16, Indels: 2 0.81 0.16 0.02 Matches are distributed among these distances: 63 78 0.99 64 1 0.01 ACGTcount: A:0.28, C:0.25, G:0.29, T:0.19 Consensus pattern (63 bp): GGAATACCTTGGGGCCTAAGAGCCTACCAAAGAAATACCTTGGGGCCTCAGAGCTGACCCAAA Found at i:1277079 original size:20 final size:20 Alignment explanation
Indices: 1277032--1277403 Score: 304 Period size: 20 Copynumber: 18.2 Consensus size: 20 1277022 AATGACCAAC * * 1277032 AAAATCGCAACGCGATAT-C 1 AAAATCGCAACGCGATTTAG * 1277051 AAAACCGCAACGCGATTTAG 1 AAAATCGCAACGCGATTTAG * * ** 1277071 AAAAGCGCAACGTTGA-AAAG 1 AAAATCGCAACG-CGATTTAG * * ** 1277091 AAGATCGCAACACGATCTTCC 1 AAAATCGCAACGCGAT-TTAG * * * 1277112 AAGAATCGCAATGCGATTCAT 1 AA-AATCGCAACGCGATTTAG ** 1277133 AAAATCGCAACGCGATCTTCC 1 AAAATCGCAACGCGAT-TTAG * 1277154 AAGAATCGCAACGCGATTCAG 1 AA-AATCGCAACGCGATTTAG * 1277175 AAAATCGCAACGCGATTCAG 1 AAAATCGCAACGCGATTTAG * 1277195 AAAATCGCAACGCGATTCAG 1 AAAATCGCAACGCGATTTAG ** 1277215 AAAATCGCAACGCGATCTTCC 1 AAAATCGCAACGCGAT-TTAG * 1277236 AAGAATCGCAACGCGATTAAG 1 AA-AATCGCAACGCGATTTAG * 1277257 AAAATCGCAACGCGATTCCA- 1 AAAATCGCAACGCGATT-TAG * ** 1277277 AGAATCGCAACGCGATCTTCC 1 AAAATCGCAACGCGAT-TTAG * 1277298 AAGAATCGCAACGCGATTAAG 1 AA-AATCGCAACGCGATTTAG * 1277319 AAAATCGCAACGCGATTCCA- 1 AAAATCGCAACGCGATT-TAG * * 1277339 AGAATCGCAACGCGATCTT-C 1 AAAATCGCAACGCGAT-TTAG * * 1277359 CAAATCGCAACGCGATTAAG 1 AAAATCGCAACGCGATTTAG * 1277379 AAAATCGCAACGCGATTAAG 1 AAAATCGCAACGCGATTTAG 1277399 AAAAT 1 AAAAT 1277404 GAGTAAATTC Statistics Matches: 286, Mismatches: 50, Indels: 33 0.78 0.14 0.09 Matches are distributed among these distances: 19 19 0.07 20 187 0.65 21 27 0.09 22 53 0.19 ACGTcount: A:0.39, C:0.26, G:0.19, T:0.16 Consensus pattern (20 bp): AAAATCGCAACGCGATTTAG Found at i:1277142 original size:62 final size:61 Alignment explanation
Indices: 1277035--1277400 Score: 388 Period size: 62 Copynumber: 6.0 Consensus size: 61 1277025 GACCAACAAA * * * * * * 1277035 ATCGCAACGCGAT-AT-CAA-AACCGCAACGCGATTTAGAAAAGCGCAACGTTGAAAAGAAG 1 ATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACG-CGATAAGAAG * * * * *** 1277094 ATCGCAACACGATCTTCCAAGAATCGCAATGCGATTCATAAAATCGCAACGCGATCTTCCAAG 1 ATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGA--TAAGAAG * * * * 1277157 AATCGCAACGCGA--TT-CAGAAAATCGCAACGCGATTCAGAAAATCGCAACGCGATTCAGAAA 1 -ATCGCAACGCGATCTTCCA-AGAATCGCAACGCGATTAAGAAAATCGCAACGCGA-TAAGAAG *** 1277218 ATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATTCCAAG 1 ATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATAAGAAG *** 1277279 AATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATTCCAAG 1 -ATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATAAGAAG 1277341 AATCGCAACGCGATCTTCC-A-AATCGCAACGCGATTAAGAAAATCGCAACGCGATTAAGAA 1 -ATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGA-TAAGAA 1277401 AATGAGTAAA Statistics Matches: 265, Mismatches: 30, Indels: 22 0.84 0.09 0.07 Matches are distributed among these distances: 59 12 0.05 60 46 0.17 61 17 0.06 62 174 0.66 63 5 0.02 64 11 0.04 ACGTcount: A:0.39, C:0.26, G:0.19, T:0.16 Consensus pattern (61 bp): ATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATAAGAAG Found at i:1277201 original size:82 final size:81 Alignment explanation
Indices: 1277115--1277394 Score: 354 Period size: 82 Copynumber: 3.4 Consensus size: 81 1277105 ATCTTCCAAG * * 1277115 AATCGCAATGCGATTCATAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAAAAT 1 AATCGCAACGCGATTCAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAAAAT 1277180 CGCAACGCGATTCAGAA 66 CGCAACGCGATTCA-AA * 1277197 AATCGCAACGCGATTCAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAAT 1 AATCGCAACGCGATTCAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAAAAT * 1277262 CGCAACGCGATTCCAAG 66 CGCAACGCGATT-CAAA * *** 1277279 AATCGCAACGCGATCTTCCA-AGAATCGCAACGCGAT-TAAGAA-AATCGCAACGCGATTCCA-A 1 AATCGCAACGCGA--TT-CAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATT-CAGA * * 1277340 GAATCGCAACGCGATCTTC-CA 62 AAATCGCAACGCGA--TTCAAA * 1277361 AATCGCAACGCGATTAAGAAAATCGCAACGCGAT 1 AATCGCAACGCGATTCAGAAAATCGCAACGCGAT 1277395 TAAGAAAATG Statistics Matches: 176, Mismatches: 14, Indels: 18 0.85 0.07 0.09 Matches are distributed among these distances: 79 1 0.01 80 17 0.10 82 130 0.74 83 7 0.04 84 19 0.11 85 2 0.01 ACGTcount: A:0.38, C:0.27, G:0.19, T:0.17 Consensus pattern (81 bp): AATCGCAACGCGATTCAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAAAAT CGCAACGCGATTCAAA Found at i:1277491 original size:20 final size:19 Alignment explanation
Indices: 1277468--1277519 Score: 59 Period size: 19 Copynumber: 2.7 Consensus size: 19 1277458 TTCTTTTCAA * * 1277468 CGTTGCGCTTTTCTAAATCG 1 CGTTGCGATTTT-GAAATCG * * 1277488 CGTTGCGGTTTTGATATCG 1 CGTTGCGATTTTGAAATCG 1277507 CGTTGCGATTTTG 1 CGTTGCGATTTTG 1277520 TTGGTCATTT Statistics Matches: 28, Mismatches: 4, Indels: 1 0.85 0.12 0.03 Matches are distributed among these distances: 19 17 0.61 20 11 0.39 ACGTcount: A:0.12, C:0.19, G:0.27, T:0.42 Consensus pattern (19 bp): CGTTGCGATTTTGAAATCG Found at i:1283947 original size:55 final size:54 Alignment explanation
Indices: 1283888--1284191 Score: 279 Period size: 54 Copynumber: 5.5 Consensus size: 54 1283878 TAGAATTAAC 1283888 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCAAAAGT 1 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCAAAA-T * *** 1283943 GATTGAGCACCTCTGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAAAAAAT 1 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGT---G-T---AGCCAAAAT * ** * * * * 1284004 GACTGAGCACCTCTGTGCTTCAGCCGGGAGCTAACACCTCTGTGTAGCTAAGAT 1 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCAAAAT * * * 1284058 GATTGAGCACCTCTGTGCTTCAATCGAG-GACTGACACCTTTGTGCAGCCAACTAT 1 GATTGAGCACCTCTGTGCTTCAATCGAGAG-CTGACACCTCTGTGTAGCCAA-AAT * * * * * **** 1284113 GATTGAGCACCTCTGTGCTTCAATCTAAATTCTGGCACCTCTGTGCA-TTGGAAT 1 GATTGAGCACCTCTGTGCTTCAATCGAGA-GCTGACACCTCTGTGTAGCCAAAAT * 1284167 GATTGAGCACCTCTGTGCTACAATC 1 GATTGAGCACCTCTGTGCTTCAATC 1284192 TAAAATCAAG Statistics Matches: 204, Mismatches: 34, Indels: 23 0.78 0.13 0.09 Matches are distributed among these distances: 53 1 0.00 54 72 0.35 55 70 0.34 56 14 0.07 57 1 0.00 58 2 0.01 59 1 0.00 61 38 0.19 62 5 0.02 ACGTcount: A:0.26, C:0.25, G:0.22, T:0.27 Consensus pattern (54 bp): GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCAAAAT Found at i:1283986 original size:27 final size:27 Alignment explanation
Indices: 1283895--1283987 Score: 91 Period size: 27 Copynumber: 3.4 Consensus size: 27 1283885 AACGATTGAG * 1283895 CACCTCTGTGCTTCAATCGAGAGCTGA 1 CACCTCTGTGCTTCAATCGAGAACTGA * ** * * 1283922 CACCTCTGTG-TAGCCAAAAGTG-ATTGA 1 CACCTCTGTGCT--TCAATCGAGAACTGA 1283949 GCACCTCTGTGCTTCAATCGAGAACTGA 1 -CACCTCTGTGCTTCAATCGAGAACTGA 1283977 CACCTCTGTGC 1 CACCTCTGTGC 1283988 AGTTAAAAAA Statistics Matches: 50, Mismatches: 11, Indels: 10 0.70 0.15 0.14 Matches are distributed among these distances: 26 1 0.02 27 29 0.58 28 19 0.38 29 1 0.02 ACGTcount: A:0.24, C:0.29, G:0.22, T:0.26 Consensus pattern (27 bp): CACCTCTGTGCTTCAATCGAGAACTGA Found at i:1284095 original size:27 final size:28 Alignment explanation
Indices: 1284061--1284137 Score: 77 Period size: 27 Copynumber: 2.8 Consensus size: 28 1284051 CTAAGATGAT 1284061 TGAGCACCTCTGTGCTTCAATCGAGGAC 1 TGAGCACCTCTGTGCTTCAATCGAGGAC * ** * * * 1284089 TGA-CACCTTTGTGCAGCCAA-CTATGAT 1 TGAGCACCTCTGTGC-TTCAATCGAGGAC 1284116 TGAGCACCTCTGTGCTTCAATC 1 TGAGCACCTCTGTGCTTCAATC 1284138 TAAATTCTGG Statistics Matches: 37, Mismatches: 9, Indels: 6 0.71 0.17 0.12 Matches are distributed among these distances: 27 20 0.54 28 17 0.46 ACGTcount: A:0.22, C:0.29, G:0.21, T:0.29 Consensus pattern (28 bp): TGAGCACCTCTGTGCTTCAATCGAGGAC Found at i:1284095 original size:54 final size:55 Alignment explanation
Indices: 1283888--1284137 Score: 236 Period size: 55 Copynumber: 4.5 Consensus size: 55 1283878 TAGAATTAAC * * * * 1283888 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCAA-AAGT 1 GATTGAGCACCTCTGTGCTTCAATCGGGAGCTAACACCTCTGTGCAGCCAACGA-T * * * ** ** 1283943 GATTGAGCACCTCTGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAAAAAAT 1 GATTGAGCACCTCTGTGCTTCAATCGGGAGCTAACACCTCTGTGCAG------CCAACGAT * ** * * 1284004 GACTGAGCACCTCTGTGCTTCAGCCGGGAGCTAACACCTCTGTGTAGCTAA-GAT 1 GATTGAGCACCTCTGTGCTTCAATCGGGAGCTAACACCTCTGTGCAGCCAACGAT * * * 1284058 GATTGAGCACCTCTGTGCTTCAATCGAGGA-CTGACACCTTTGTGCAGCCAACTAT 1 GATTGAGCACCTCTGTGCTTCAATCG-GGAGCTAACACCTCTGTGCAGCCAACGAT 1284113 GATTGAGCACCTCTGTGCTTCAATC 1 GATTGAGCACCTCTGTGCTTCAATC 1284138 TAAATTCTGG Statistics Matches: 164, Mismatches: 22, Indels: 18 0.80 0.11 0.09 Matches are distributed among these distances: 54 42 0.26 55 77 0.47 61 43 0.26 62 2 0.01 ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26 Consensus pattern (55 bp): GATTGAGCACCTCTGTGCTTCAATCGGGAGCTAACACCTCTGTGCAGCCAACGAT Found at i:1284096 original size:115 final size:116 Alignment explanation
Indices: 1283891--1284104 Score: 349 Period size: 115 Copynumber: 1.9 Consensus size: 116 1283881 AATTAACGAT * * 1283891 TGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCAAAAGTGATTGAGCACCTC 1 TGAGCACCTCTGTGCTTCAACCGAGAGCTAACACCTCTGTGTAGCCAAAAGTGATTGAGCACCTC 1283956 TGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAAAAAATGAC 66 TGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAAAAAATGAC * * * * 1284007 TGAGCACCTCTGTGCTTCAGCCGGGAGCTAACACCTCTGTGTAGCTAAGA-TGATTGAGCACCTC 1 TGAGCACCTCTGTGCTTCAACCGAGAGCTAACACCTCTGTGTAGCCAAAAGTGATTGAGCACCTC * * 1284071 TGTGCTTCAATCGAGGACTGACACCTTTGTGCAG 66 TGTGCTTCAATCGAGAACTGACACCTCTGTGCAG 1284105 CCAACTATGA Statistics Matches: 90, Mismatches: 8, Indels: 1 0.91 0.08 0.01 Matches are distributed among these distances: 115 46 0.51 116 44 0.49 ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25 Consensus pattern (116 bp): TGAGCACCTCTGTGCTTCAACCGAGAGCTAACACCTCTGTGTAGCCAAAAGTGATTGAGCACCTC TGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAAAAAATGAC Found at i:1285046 original size:37 final size:36 Alignment explanation
Indices: 1285000--1285078 Score: 106 Period size: 37 Copynumber: 2.2 Consensus size: 36 1284990 ATATATATAT * * * 1285000 ATATATATAATAATTATTAAATTTACTCTCTCAAAAA 1 ATATATATAAAAACTATTAAATTTAAT-TCTCAAAAA * 1285037 ATATGTATAAAAACTATTAAATTTAATTCTCAAAAA 1 ATATATATAAAAACTATTAAATTTAATTCTCAAAAA 1285073 AT-TATA 1 ATATATA 1285079 CTATTTTAGA Statistics Matches: 37, Mismatches: 5, Indels: 2 0.84 0.11 0.05 Matches are distributed among these distances: 35 3 0.08 36 11 0.30 37 23 0.62 ACGTcount: A:0.51, C:0.09, G:0.01, T:0.39 Consensus pattern (36 bp): ATATATATAAAAACTATTAAATTTAATTCTCAAAAA Found at i:1285227 original size:17 final size:18 Alignment explanation
Indices: 1285205--1285253 Score: 57 Period size: 17 Copynumber: 2.8 Consensus size: 18 1285195 TTCTTTGTTT * 1285205 AGTTGTTCATCTT-TTTG 1 AGTTGTTCATCTTCATTG * 1285222 AGTTGTTTATCTTCATTG 1 AGTTGTTCATCTTCATTG * 1285240 AGTTGATCAT-TTCA 1 AGTTGTTCATCTTCA 1285254 ATCAAGTTAT Statistics Matches: 27, Mismatches: 4, Indels: 2 0.82 0.12 0.06 Matches are distributed among these distances: 17 16 0.59 18 11 0.41 ACGTcount: A:0.18, C:0.12, G:0.16, T:0.53 Consensus pattern (18 bp): AGTTGTTCATCTTCATTG Found at i:1286230 original size:24 final size:24 Alignment explanation
Indices: 1286201--1286248 Score: 69 Period size: 24 Copynumber: 2.0 Consensus size: 24 1286191 TCGATAATCC * 1286201 GTTTGTTTATATTCATTCGTTTAT 1 GTTTGTTTATATTCATTCATTTAT * * 1286225 GTTTGTTTATGTTCGTTCATTTAT 1 GTTTGTTTATATTCATTCATTTAT 1286249 ATTTAGCCTA Statistics Matches: 21, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 24 21 1.00 ACGTcount: A:0.15, C:0.08, G:0.15, T:0.62 Consensus pattern (24 bp): GTTTGTTTATATTCATTCATTTAT Found at i:1287650 original size:22 final size:23 Alignment explanation
Indices: 1287625--1287671 Score: 60 Period size: 23 Copynumber: 2.1 Consensus size: 23 1287615 AAGATAAATG * 1287625 AACATGCCA-AAAAGCAGAAGAA 1 AACATGCCATAAAAACAGAAGAA * * 1287647 AACATGTCATAAAAACAGATGAA 1 AACATGCCATAAAAACAGAAGAA 1287670 AA 1 AA 1287672 TGTGCAACAC Statistics Matches: 21, Mismatches: 3, Indels: 1 0.84 0.12 0.04 Matches are distributed among these distances: 22 8 0.38 23 13 0.62 ACGTcount: A:0.60, C:0.15, G:0.15, T:0.11 Consensus pattern (23 bp): AACATGCCATAAAAACAGAAGAA Found at i:1291840 original size:21 final size:20 Alignment explanation
Indices: 1291802--1291840 Score: 51 Period size: 21 Copynumber: 1.9 Consensus size: 20 1291792 TAATGGATGG * 1291802 TTGTTTTTATATGTTGTTAT 1 TTGTTTTTATATGATGTTAT * 1291822 TTGTTTTGTTTATGATGTT 1 TTGTTTT-TATATGATGTT 1291841 TAATGCCTTA Statistics Matches: 16, Mismatches: 2, Indels: 1 0.84 0.11 0.05 Matches are distributed among these distances: 20 7 0.44 21 9 0.56 ACGTcount: A:0.13, C:0.00, G:0.18, T:0.69 Consensus pattern (20 bp): TTGTTTTTATATGATGTTAT Found at i:1292442 original size:19 final size:21 Alignment explanation
Indices: 1292399--1292443 Score: 58 Period size: 23 Copynumber: 2.1 Consensus size: 21 1292389 CTAAATTTAC 1292399 TTTTGCCAAGACATTTCTATCCA 1 TTTTGCCAAGACA-TTC-ATCCA 1292422 TTTTGCCAAGACA-TC-TCCA 1 TTTTGCCAAGACATTCATCCA 1292441 TTT 1 TTT 1292444 GCTGCCGCAT Statistics Matches: 22, Mismatches: 0, Indels: 4 0.85 0.00 0.15 Matches are distributed among these distances: 19 7 0.32 21 2 0.09 23 13 0.59 ACGTcount: A:0.24, C:0.27, G:0.09, T:0.40 Consensus pattern (21 bp): TTTTGCCAAGACATTCATCCA Found at i:1294020 original size:20 final size:20 Alignment explanation
Indices: 1293995--1294033 Score: 53 Period size: 20 Copynumber: 1.9 Consensus size: 20 1293985 TAGGATTCTT * 1293995 GATTTT-AATATATAGGATGG 1 GATTTTGAAGATA-AGGATGG 1294015 GATTTTGAAGATAAGGATG 1 GATTTTGAAGATAAGGATG 1294034 TGTTAGATGA Statistics Matches: 17, Mismatches: 1, Indels: 2 0.85 0.05 0.10 Matches are distributed among these distances: 20 12 0.71 21 5 0.29 ACGTcount: A:0.36, C:0.00, G:0.28, T:0.36 Consensus pattern (20 bp): GATTTTGAAGATAAGGATGG Done.