Tandem Repeats Finder Program written by: Gary Benson Program in Bioinformatics Boston University Version 4.09 Sequence: A05 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: 100714657 ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32 Warning! 3970000 characters in sequence are not A, C, G, or T File 73 of 318 Found at i:25254894 original size:3 final size:3 Alignment explanation
Indices: 25254857--25254881 Score: 50 Period size: 3 Copynumber: 8.3 Consensus size: 3 25254847 ATTGTAGATC 25254857 TTA TTA TTA TTA TTA TTA TTA TTA T 1 TTA TTA TTA TTA TTA TTA TTA TTA T 25254882 ATACTCTTAT Statistics Matches: 22, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 22 1.00 ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68 Consensus pattern (3 bp): TTA Found at i:25265538 original size:37 final size:37 Alignment explanation
Indices: 25265477--25265622 Score: 233 Period size: 37 Copynumber: 4.0 Consensus size: 37 25265467 TACGTATGAT * * 25265477 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC 1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC * 25265512 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC 1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC * 25265549 CACTTATCACTTTGTTTCTTGATCAGATAAGTGCAGC 1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC * 25265586 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC 1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC 25265623 TAAAACTATC Statistics Matches: 102, Mismatches: 7, Indels: 2 0.92 0.06 0.02 Matches are distributed among these distances: 35 9 0.09 36 3 0.03 37 90 0.88 ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36 Consensus pattern (37 bp): CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC Found at i:25265639 original size:46 final size:46 Alignment explanation
Indices: 25265586--25265802 Score: 272 Period size: 46 Copynumber: 4.6 Consensus size: 46 25265576 TAAGTGCAGC * * * * 25265586 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAACTAT 1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTAT * * 25265632 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT 1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTAT * 25265678 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT 1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTAT * * * * 25265724 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC 1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTATAGCCAAAGCTAT * 25265776 CACTTATCACTTTATCACTTGATCAGA 1 CACTTATCACTTTGTCACTTGATCAGA 25265803 AGTACTCAAA Statistics Matches: 153, Mismatches: 12, Indels: 12 0.86 0.07 0.07 Matches are distributed among these distances: 46 111 0.73 48 1 0.01 50 1 0.01 52 40 0.26 ACGTcount: A:0.29, C:0.22, G:0.13, T:0.35 Consensus pattern (46 bp): CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTAT Found at i:25265754 original size:52 final size:52 Alignment explanation
Indices: 25265675--25265788 Score: 158 Period size: 52 Copynumber: 2.2 Consensus size: 52 25265665 TAGCCGAAGC * ** 25265675 TATCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT 1 TATCACTT-TCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTACCACT * * 25265728 TATCACTTTCCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT 1 TATCACTTT-CACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTACCACT 25265780 TATCACTTT 1 TATCACTTT 25265789 ATCACTTGAT Statistics Matches: 55, Mismatches: 5, Indels: 3 0.87 0.08 0.05 Matches are distributed among these distances: 52 44 0.80 53 11 0.20 ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36 Consensus pattern (52 bp): TATCACTTTCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTACCACT Found at i:25277363 original size:44 final size:44 Alignment explanation
Indices: 25277312--25277403 Score: 132 Period size: 44 Copynumber: 2.1 Consensus size: 44 25277302 CTGAAGTATC * 25277312 AGTAACAGTACGAGACACA-AAGTGCCTCATCGACACAAAGTCGA 1 AGTAACAGTACGACAC-CATAAGTGCCTCATCGACACAAAGTCGA * * * 25277356 AGTAACAGTACGACACCATTAGTGCCTCATCGACTCAAGGTCGA 1 AGTAACAGTACGACACCATAAGTGCCTCATCGACACAAAGTCGA 25277400 AGTA 1 AGTA 25277404 TCCTGAACAT Statistics Matches: 43, Mismatches: 4, Indels: 2 0.88 0.08 0.04 Matches are distributed among these distances: 43 2 0.05 44 41 0.95 ACGTcount: A:0.37, C:0.25, G:0.21, T:0.17 Consensus pattern (44 bp): AGTAACAGTACGACACCATAAGTGCCTCATCGACACAAAGTCGA Found at i:25287832 original size:8 final size:8 Alignment explanation
Indices: 25287821--25287864 Score: 63 Period size: 8 Copynumber: 5.5 Consensus size: 8 25287811 CTTTTATGTT 25287821 TTATTATA 1 TTATTATA 25287829 TTATT-TAA 1 TTATTAT-A 25287837 TTATTATA 1 TTATTATA * 25287845 TTAATATA 1 TTATTATA 25287853 TTATTATA 1 TTATTATA 25287861 TTAT 1 TTAT 25287865 ATAGTTAAGT Statistics Matches: 32, Mismatches: 2, Indels: 4 0.84 0.05 0.11 Matches are distributed among these distances: 7 1 0.03 8 30 0.94 9 1 0.03 ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61 Consensus pattern (8 bp): TTATTATA Found at i:25287840 original size:16 final size:17 Alignment explanation
Indices: 25287821--25287867 Score: 71 Period size: 16 Copynumber: 2.9 Consensus size: 17 25287811 CTTTTATGTT * 25287821 TTATTATATTATTTA-A 1 TTATTATATTATATATA 25287837 TTATTATATTA-ATATA 1 TTATTATATTATATATA 25287853 TTATTATATTATATA 1 TTATTATATTATATA 25287868 GTTAAGTCTT Statistics Matches: 28, Mismatches: 1, Indels: 3 0.88 0.03 0.09 Matches are distributed among these distances: 15 2 0.07 16 23 0.82 17 3 0.11 ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60 Consensus pattern (17 bp): TTATTATATTATATATA Found at i:25287863 original size:24 final size:24 Alignment explanation
Indices: 25287825--25287872 Score: 64 Period size: 24 Copynumber: 2.0 Consensus size: 24 25287815 TATGTTTTAT 25287825 TATATTATTTAATTATTATA-TTAA 1 TATATTATTTAATTA-TATAGTTAA 25287849 TATATTA-TTATATTATATAGTTAA 1 TATATTATTTA-ATTATATAGTTAA 25287873 GTCTTAAGTA Statistics Matches: 22, Mismatches: 0, Indels: 4 0.85 0.00 0.15 Matches are distributed among these distances: 23 7 0.32 24 15 0.68 ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56 Consensus pattern (24 bp): TATATTATTTAATTATATAGTTAA Found at i:25303125 original size:21 final size:21 Alignment explanation
Indices: 25303091--25303130 Score: 55 Period size: 21 Copynumber: 1.9 Consensus size: 21 25303081 AGATGAAAAT * 25303091 AAAAACTAAACCTCGAAACAC 1 AAAAACTAAACCTCAAAACAC 25303112 AAAAAC-AAACCCTCAAAAC 1 AAAAACTAAA-CCTCAAAAC 25303131 GTAAACACAA Statistics Matches: 17, Mismatches: 1, Indels: 2 0.85 0.05 0.10 Matches are distributed among these distances: 20 3 0.18 21 14 0.82 ACGTcount: A:0.60, C:0.30, G:0.03, T:0.07 Consensus pattern (21 bp): AAAAACTAAACCTCAAAACAC Found at i:25304649 original size:45 final size:45 Alignment explanation
Indices: 25304583--25304672 Score: 135 Period size: 45 Copynumber: 2.0 Consensus size: 45 25304573 GAAAAATTTA * * 25304583 GTAAAAATATCCATCATCTGATCTCTGATTTGCAATAAATCAGTT 1 GTAAAAATATCCATCACCTGATCTCTGATTTGCAATAAACCAGTT ** * 25304628 GTAAAAATATCTGTCACCTGATCTTTGATTTGCAATAAACCAGTT 1 GTAAAAATATCCATCACCTGATCTCTGATTTGCAATAAACCAGTT 25304673 TCTTCAATAT Statistics Matches: 40, Mismatches: 5, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 45 40 1.00 ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36 Consensus pattern (45 bp): GTAAAAATATCCATCACCTGATCTCTGATTTGCAATAAACCAGTT Found at i:25309109 original size:19 final size:18 Alignment explanation
Indices: 25309046--25309109 Score: 56 Period size: 19 Copynumber: 3.4 Consensus size: 18 25309036 GTTCGGAAAA * 25309046 TTTTATAAATTTTTAATT 1 TTTTATAATTTTTTAATT * * * 25309064 AGTCTATAATTTTTTTATT 1 -TTTTATAATTTTTTAATT * 25309083 TTAATATAATTTTTATAATT 1 TT-TTATAATTTTT-TAATT 25309103 TTTTATA 1 TTTTATA 25309110 GAGAAAAAAG Statistics Matches: 35, Mismatches: 8, Indels: 4 0.74 0.17 0.09 Matches are distributed among these distances: 18 1 0.03 19 28 0.80 20 6 0.17 ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64 Consensus pattern (18 bp): TTTTATAATTTTTTAATT Found at i:25320682 original size:75 final size:75 Alignment explanation
Indices: 25320559--25320709 Score: 257 Period size: 75 Copynumber: 2.0 Consensus size: 75 25320549 GCGAGAATGA * ** * 25320559 ACTCACCTCCAAGAGGGGACCACCAAGGAGTCACTAGGGTGTAACATTGTACTACCTCAGCCAAT 1 ACTCACCTCCAAAAGGGGACCACCAAGGAACCACTAGGGTGTAACATTGTACTACCTCAGCCAAG 25320624 GGAATGTTAG 66 GGAATGTTAG * 25320634 ACTCACCTCCAAAAGGGGACCACCAAGGAACCACTAGGGTGTAACATTGTACTACCTCAGCTAAG 1 ACTCACCTCCAAAAGGGGACCACCAAGGAACCACTAGGGTGTAACATTGTACTACCTCAGCCAAG 25320699 GGAATGTTAG 66 GGAATGTTAG 25320709 A 1 A 25320710 ACAATACCAT Statistics Matches: 71, Mismatches: 5, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 75 71 1.00 ACGTcount: A:0.32, C:0.25, G:0.23, T:0.19 Consensus pattern (75 bp): ACTCACCTCCAAAAGGGGACCACCAAGGAACCACTAGGGTGTAACATTGTACTACCTCAGCCAAG GGAATGTTAG Found at i:25330270 original size:16 final size:15 Alignment explanation
Indices: 25330239--25330278 Score: 57 Period size: 14 Copynumber: 2.8 Consensus size: 15 25330229 TTTCTTACAT 25330239 TCTTTTTCTTTTTCA 1 TCTTTTTCTTTTTCA 25330254 TCTTTTTC-TTTTC- 1 TCTTTTTCTTTTTCA * 25330267 TCATTTTCTTTT 1 TCTTTTTCTTTT 25330279 CACTTTCTTT Statistics Matches: 23, Mismatches: 1, Indels: 3 0.85 0.04 0.11 Matches are distributed among these distances: 13 7 0.30 14 8 0.35 15 8 0.35 ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75 Consensus pattern (15 bp): TCTTTTTCTTTTTCA Found at i:25330275 original size:13 final size:14 Alignment explanation
Indices: 25330242--25330280 Score: 53 Period size: 13 Copynumber: 2.8 Consensus size: 14 25330232 CTTACATTCT * 25330242 TTTTCTTTTTCATCT 1 TTTTC-TTTTCATCA 25330257 TTTTCTTTTC-TCA 1 TTTTCTTTTCATCA 25330270 TTTTCTTTTCA 1 TTTTCTTTTCA 25330281 CTTTCTTTTG Statistics Matches: 22, Mismatches: 1, Indels: 3 0.85 0.04 0.12 Matches are distributed among these distances: 13 12 0.55 14 5 0.23 15 5 0.23 ACGTcount: A:0.08, C:0.21, G:0.00, T:0.72 Consensus pattern (14 bp): TTTTCTTTTCATCA Found at i:25330346 original size:18 final size:17 Alignment explanation
Indices: 25330303--25330346 Score: 54 Period size: 18 Copynumber: 2.5 Consensus size: 17 25330293 GTTTTTCCTC 25330303 TCTTTTTCTCATTTTTAT 1 TCTTTTT-TCATTTTTAT 25330321 T-TTCTTTTACATTTTTAT 1 TCTT-TTTT-CATTTTTAT 25330339 TCTTTTTT 1 TCTTTTTT 25330347 TTTCTCTCAT Statistics Matches: 23, Mismatches: 0, Indels: 6 0.79 0.00 0.21 Matches are distributed among these distances: 17 3 0.13 18 18 0.78 19 2 0.09 ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75 Consensus pattern (17 bp): TCTTTTTTCATTTTTAT Found at i:25332826 original size:74 final size:74 Alignment explanation
Indices: 25332714--25332863 Score: 264 Period size: 74 Copynumber: 2.0 Consensus size: 74 25332704 TAAGTATAAA * * * 25332714 GATAGGTAATGGAAATAGGTTCAAAATTGGCTAAGTATAAGTTGATTAGGTTCGGCTAACAAAGA 1 GATAGGTAATAGAAATAGGTTCAAAATTGGATAAGTATAAGTTGATTAGGTTCGACTAACAAAGA 25332779 AAGTAAATT 66 AAGTAAATT * 25332788 GATAGGTAATAGAAATAGGTTTAAAATTGGATAAGTATAAGTTGATTAGGTTCGACTAACAAAGA 1 GATAGGTAATAGAAATAGGTTCAAAATTGGATAAGTATAAGTTGATTAGGTTCGACTAACAAAGA 25332853 AAGTAAATT 66 AAGTAAATT 25332862 GA 1 GA 25332864 ATAGTTTAGA Statistics Matches: 72, Mismatches: 4, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 74 72 1.00 ACGTcount: A:0.43, C:0.05, G:0.23, T:0.29 Consensus pattern (74 bp): GATAGGTAATAGAAATAGGTTCAAAATTGGATAAGTATAAGTTGATTAGGTTCGACTAACAAAGA AAGTAAATT Found at i:25334130 original size:10 final size:10 Alignment explanation
Indices: 25334103--25334132 Score: 51 Period size: 10 Copynumber: 3.0 Consensus size: 10 25334093 AGAAATAAAG * 25334103 ATGAGCTCAA 1 ATGAGCTGAA 25334113 ATGAGCTGAA 1 ATGAGCTGAA 25334123 ATGAGCTGAA 1 ATGAGCTGAA 25334133 CTAAGCTCAT Statistics Matches: 19, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 10 19 1.00 ACGTcount: A:0.40, C:0.13, G:0.27, T:0.20 Consensus pattern (10 bp): ATGAGCTGAA Found at i:25342261 original size:29 final size:29 Alignment explanation
Indices: 25342219--25342277 Score: 109 Period size: 29 Copynumber: 2.0 Consensus size: 29 25342209 TCAAGATGAG 25342219 GAATTTAATGAAATGATTACATTATCTAT 1 GAATTTAATGAAATGATTACATTATCTAT * 25342248 GAATTTAATGAAATGATTACATTCTCTAT 1 GAATTTAATGAAATGATTACATTATCTAT 25342277 G 1 G 25342278 TATTAAATAA Statistics Matches: 29, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 29 29 1.00 ACGTcount: A:0.39, C:0.08, G:0.12, T:0.41 Consensus pattern (29 bp): GAATTTAATGAAATGATTACATTATCTAT Found at i:25342290 original size:29 final size:29 Alignment explanation
Indices: 25342219--25342290 Score: 90 Period size: 29 Copynumber: 2.5 Consensus size: 29 25342209 TCAAGATGAG * * 25342219 GAATTTAATGAAATGATTACATTATCTAT 1 GAATTAAATAAAATGATTACATTATCTAT * * * 25342248 GAATTTAATGAAATGATTACATTCTCTAT 1 GAATTAAATAAAATGATTACATTATCTAT * 25342277 GTATTAAATAAAAT 1 GAATTAAATAAAAT 25342291 ACTATTAAGT Statistics Matches: 39, Mismatches: 4, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 29 39 1.00 ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40 Consensus pattern (29 bp): GAATTAAATAAAATGATTACATTATCTAT Found at i:25342703 original size:12 final size:14 Alignment explanation
Indices: 25342666--25342732 Score: 63 Period size: 11 Copynumber: 5.0 Consensus size: 14 25342656 TTTTAATTTG * 25342666 TTAAATTGATTATGAT 1 TTAAATTAATTAT--T 25342682 TTAAATTAATT-TT 1 TTAAATTAATTATT 25342695 TTAAA-TAATTATT 1 TTAAATTAATTATT 25342708 TT---TTAATTATT 1 TTAAATTAATTATT * 25342719 TTGAATTAATTATT 1 TTAAATTAATTATT 25342733 ATACAAATTA Statistics Matches: 45, Mismatches: 1, Indels: 12 0.78 0.02 0.21 Matches are distributed among these distances: 11 10 0.22 12 5 0.11 13 10 0.22 14 9 0.20 15 1 0.02 16 10 0.22 ACGTcount: A:0.37, C:0.00, G:0.04, T:0.58 Consensus pattern (14 bp): TTAAATTAATTATT Found at i:25343685 original size:18 final size:17 Alignment explanation
Indices: 25343635--25343689 Score: 60 Period size: 17 Copynumber: 3.2 Consensus size: 17 25343625 TTTCTTAGAA * 25343635 TTTTGT-ATCTCGTAACT 1 TTTTGTAATCTCATAA-T * 25343652 TTTTGTATTC-CATAAT 1 TTTTGTAATCTCATAAT 25343668 TATTTGTAATCTCATAAT 1 T-TTTGTAATCTCATAAT 25343686 TTTT 1 TTTT 25343690 AGTATGATAT Statistics Matches: 32, Mismatches: 3, Indels: 6 0.78 0.07 0.15 Matches are distributed among these distances: 16 2 0.06 17 21 0.66 18 9 0.28 ACGTcount: A:0.24, C:0.13, G:0.07, T:0.56 Consensus pattern (17 bp): TTTTGTAATCTCATAAT Found at i:25344872 original size:49 final size:48 Alignment explanation
Indices: 25344806--25344900 Score: 120 Period size: 48 Copynumber: 2.0 Consensus size: 48 25344796 TGTGACACAC * * * 25344806 CCGTGTGAGGTGGCTTAGGACGTGTTTAGAGTCTGCTAAATAGACACGG 1 CCGTGTGAGGTGACTTAGGACGTG-TTACAATCTGCTAAATAGACACGG * * 25344855 CCGTGTG-GTGTGACTTAGGCCGTGTTACAATCTGTTAAATAGACAC 1 CCGTGTGAG-GTGACTTAGGACGTGTTACAATCTGCTAAATAGACAC 25344901 AGGTGTGTGA Statistics Matches: 40, Mismatches: 5, Indels: 3 0.83 0.10 0.06 Matches are distributed among these distances: 48 20 0.50 49 20 0.50 ACGTcount: A:0.23, C:0.18, G:0.31, T:0.28 Consensus pattern (48 bp): CCGTGTGAGGTGACTTAGGACGTGTTACAATCTGCTAAATAGACACGG Found at i:25350165 original size:20 final size:20 Alignment explanation
Indices: 25350075--25350181 Score: 64 Period size: 20 Copynumber: 5.3 Consensus size: 20 25350065 TACTTCACAA * 25350075 ATATATACATATACT-AAAAT 1 ATATATA-ATATAATAAAAAT * 25350095 ATACATAATA-ATATATAAAAT 1 ATATATAATATA-ATA-AAAAT * 25350116 ATA-AT-AT-TAAAAAACACAT 1 ATATATAATATAATAAA-A-AT * * 25350135 GTATATGATAT-ATGAAAAAT 1 ATATATAATATAAT-AAAAAT 25350155 ATATATAATATAATAAAAAT 1 ATATATAATATAATAAAAAT * 25350175 ACATATA 1 ATATATA 25350182 TATGTAATAC Statistics Matches: 68, Mismatches: 8, Indels: 22 0.69 0.08 0.22 Matches are distributed among these distances: 17 2 0.03 18 4 0.06 19 11 0.16 20 33 0.49 21 14 0.21 22 4 0.06 ACGTcount: A:0.59, C:0.06, G:0.03, T:0.33 Consensus pattern (20 bp): ATATATAATATAATAAAAAT Found at i:25350180 original size:22 final size:22 Alignment explanation
Indices: 25350114--25350183 Score: 58 Period size: 22 Copynumber: 3.2 Consensus size: 22 25350104 AATATATAAA * * 25350114 ATATAATATTA-AAAAACACAT 1 ATATAATATAATAAAAATACAT * 25350135 GTAT-ATGATATATGAAAAAT--AT 1 ATATAAT-ATA-AT-AAAAATACAT 25350157 ATATAATATAATAAAAATACAT 1 ATATAATATAATAAAAATACAT 25350179 ATATA 1 ATATA 25350184 TGTAATACAT Statistics Matches: 38, Mismatches: 4, Indels: 13 0.69 0.07 0.24 Matches are distributed among these distances: 20 8 0.21 21 7 0.18 22 16 0.42 23 2 0.05 24 5 0.13 ACGTcount: A:0.59, C:0.04, G:0.04, T:0.33 Consensus pattern (22 bp): ATATAATATAATAAAAATACAT Found at i:25350623 original size:3 final size:3 Alignment explanation
Indices: 25350615--25350655 Score: 57 Period size: 3 Copynumber: 14.0 Consensus size: 3 25350605 GAAATATACT * * 25350615 TAA TAA TAA TAA GAA TAA TAG TAA TAA T-A TAA TAA TAA TAA 1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA 25350656 ACATATAAAA Statistics Matches: 33, Mismatches: 4, Indels: 2 0.85 0.10 0.05 Matches are distributed among these distances: 2 2 0.06 3 31 0.94 ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32 Consensus pattern (3 bp): TAA Found at i:25350663 original size:17 final size:17 Alignment explanation
Indices: 25350615--25350655 Score: 55 Period size: 17 Copynumber: 2.4 Consensus size: 17 25350605 GAAATATACT * 25350615 TAATAATAATAAGAATAA 1 TAATAATAAT-ATAATAA * 25350633 TAGTAATAATATAATAA 1 TAATAATAATATAATAA 25350650 TAATAA 1 TAATAA 25350656 ACATATAAAA Statistics Matches: 20, Mismatches: 3, Indels: 1 0.83 0.12 0.04 Matches are distributed among these distances: 17 11 0.55 18 9 0.45 ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32 Consensus pattern (17 bp): TAATAATAATATAATAA Found at i:25351156 original size:18 final size:19 Alignment explanation
Indices: 25351133--25351186 Score: 58 Period size: 21 Copynumber: 2.8 Consensus size: 19 25351123 AAAGAAAAAA 25351133 AAAGAGA-AGAAGGGAGAG 1 AAAGAGAGAGAAGGGAGAG * 25351151 AAAGAGAGAGGAGGGAGAAGGG 1 AAAGAGAGAGAAGGGAG-A--G 25351173 AAAG-GAGAGAAGGG 1 AAAGAGAGAGAAGGG 25351187 GGGCTACCGG Statistics Matches: 30, Mismatches: 2, Indels: 5 0.81 0.05 0.14 Matches are distributed among these distances: 18 7 0.23 19 8 0.27 20 1 0.03 21 9 0.30 22 5 0.17 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (19 bp): AAAGAGAGAGAAGGGAGAG Found at i:25351167 original size:19 final size:18 Alignment explanation
Indices: 25351133--25351168 Score: 54 Period size: 19 Copynumber: 1.9 Consensus size: 18 25351123 AAAGAAAAAA 25351133 AAAGAGAAGAAGGGAGAG 1 AAAGAGAAGAAGGGAGAG * 25351151 AAAGAGAGAGGAGGGAGA 1 AAAGAGA-AGAAGGGAGA 25351169 AGGGAAAGGA Statistics Matches: 16, Mismatches: 1, Indels: 1 0.89 0.06 0.06 Matches are distributed among these distances: 18 7 0.44 19 9 0.56 ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00 Consensus pattern (18 bp): AAAGAGAAGAAGGGAGAG Found at i:25359118 original size:19 final size:21 Alignment explanation
Indices: 25359076--25359118 Score: 56 Period size: 21 Copynumber: 2.1 Consensus size: 21 25359066 TTACTCAAAG 25359076 AAAGCCGATTGATCCATCTCA 1 AAAGCCGATTGATCCATCTCA 25359097 AAAGCCGGATT-ATCC-T-TCA 1 AAAGCC-GATTGATCCATCTCA 25359116 AAA 1 AAA 25359119 CTGAAGATCT Statistics Matches: 21, Mismatches: 0, Indels: 4 0.84 0.00 0.16 Matches are distributed among these distances: 19 6 0.29 20 1 0.05 21 10 0.48 22 4 0.19 ACGTcount: A:0.37, C:0.26, G:0.14, T:0.23 Consensus pattern (21 bp): AAAGCCGATTGATCCATCTCA Found at i:25362690 original size:22 final size:21 Alignment explanation
Indices: 25362652--25362695 Score: 54 Period size: 22 Copynumber: 2.0 Consensus size: 21 25362642 CTTTTCTCTC * 25362652 TATTCTCTTGTTATTTACTGT 1 TATTCTCTTGTTATTTAATGT 25362673 TATT-TCTTGTTTATTTTAATGT 1 TATTCTCTTG-TTA-TTTAATGT 25362695 T 1 T 25362696 TTTTATGATA Statistics Matches: 20, Mismatches: 1, Indels: 3 0.83 0.04 0.12 Matches are distributed among these distances: 20 5 0.25 21 7 0.35 22 8 0.40 ACGTcount: A:0.16, C:0.09, G:0.09, T:0.66 Consensus pattern (21 bp): TATTCTCTTGTTATTTAATGT Found at i:25364266 original size:14 final size:15 Alignment explanation
Indices: 25364247--25364276 Score: 53 Period size: 14 Copynumber: 2.1 Consensus size: 15 25364237 TTTATTTATT 25364247 ATTTTTAT-GTTTTA 1 ATTTTTATCGTTTTA 25364261 ATTTTTATCGTTTTA 1 ATTTTTATCGTTTTA 25364276 A 1 A 25364277 AACTATTTTT Statistics Matches: 15, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 14 8 0.53 15 7 0.47 ACGTcount: A:0.23, C:0.03, G:0.07, T:0.67 Consensus pattern (15 bp): ATTTTTATCGTTTTA Found at i:25373927 original size:40 final size:41 Alignment explanation
Indices: 25373875--25373966 Score: 114 Period size: 40 Copynumber: 2.2 Consensus size: 41 25373865 TAATATTCTG * * 25373875 ATCTGCATTCTATATTTGATAGGACTGAGGCCCTA-ATATAT 1 ATCTG-ATTCTATATCTGATAGGACTAAGGCCCTATATATAT * * * 25373916 TTCTGATTCTATATCTGATTGGGCTAAGGCCCTATTATATAT 1 ATCTGATTCTATATCTGATAGGACTAAGGCCCTA-TATATAT 25373958 ATCTGATTC 1 ATCTGATTC 25373967 GGCATCCGAG Statistics Matches: 43, Mismatches: 6, Indels: 3 0.83 0.12 0.06 Matches are distributed among these distances: 40 25 0.58 41 4 0.09 42 14 0.33 ACGTcount: A:0.26, C:0.17, G:0.16, T:0.40 Consensus pattern (41 bp): ATCTGATTCTATATCTGATAGGACTAAGGCCCTATATATAT Found at i:25378406 original size:20 final size:20 Alignment explanation
Indices: 25378381--25378419 Score: 78 Period size: 20 Copynumber: 1.9 Consensus size: 20 25378371 TAATTTTTAA 25378381 ATATAAAATTTTCATCAATT 1 ATATAAAATTTTCATCAATT 25378401 ATATAAAATTTTCATCAAT 1 ATATAAAATTTTCATCAAT 25378420 AAACTCCACA Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 20 19 1.00 ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44 Consensus pattern (20 bp): ATATAAAATTTTCATCAATT Found at i:25384817 original size:18 final size:18 Alignment explanation
Indices: 25384794--25384831 Score: 67 Period size: 18 Copynumber: 2.1 Consensus size: 18 25384784 AATATATATT 25384794 AACCCAAGTACCCAACCC 1 AACCCAAGTACCCAACCC * 25384812 AACCCAATTACCCAACCC 1 AACCCAAGTACCCAACCC 25384830 AA 1 AA 25384832 TCATAAAAAT Statistics Matches: 19, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 18 19 1.00 ACGTcount: A:0.42, C:0.47, G:0.03, T:0.08 Consensus pattern (18 bp): AACCCAAGTACCCAACCC Found at i:25384824 original size:13 final size:13 Alignment explanation
Indices: 25384808--25384832 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 25384798 CAAGTACCCA 25384808 ACCCAACCCAATT 1 ACCCAACCCAATT 25384821 ACCCAACCCAAT 1 ACCCAACCCAAT 25384833 CATAAAAATT Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.40, C:0.48, G:0.00, T:0.12 Consensus pattern (13 bp): ACCCAACCCAATT Found at i:25384912 original size:18 final size:18 Alignment explanation
Indices: 25384889--25384957 Score: 70 Period size: 18 Copynumber: 3.8 Consensus size: 18 25384879 TTTATACAAA 25384889 TAATTCGGTTAATTTAGT 1 TAATTCGGTTAATTTAGT ** * 25384907 TAATTCAGG-TAATTCGGG 1 TAATTC-GGTTAATTTAGT * 25384925 TAATTCGGTTAA-TTCGAT 1 TAATTCGGTTAATTTAG-T 25384943 TAATTCGGTTAATTT 1 TAATTCGGTTAATTT 25384958 TATACTTATT Statistics Matches: 41, Mismatches: 6, Indels: 7 0.76 0.11 0.13 Matches are distributed among these distances: 17 4 0.10 18 33 0.80 19 4 0.10 ACGTcount: A:0.28, C:0.09, G:0.19, T:0.45 Consensus pattern (18 bp): TAATTCGGTTAATTTAGT Found at i:25384928 original size:27 final size:27 Alignment explanation
Indices: 25384889--25384957 Score: 86 Period size: 27 Copynumber: 2.6 Consensus size: 27 25384879 TTTATACAAA 25384889 TAATTCGGTTAATTTAGTTAATTC-AGG 1 TAATTCGGTTAATTTAGTTAATTCGA-G * ** * 25384916 TAATTCGGGTAATTCGGTTAATTCGAT 1 TAATTCGGTTAATTTAGTTAATTCGAG 25384943 TAATTCGGTTAATTT 1 TAATTCGGTTAATTT 25384958 TATACTTATT Statistics Matches: 35, Mismatches: 6, Indels: 2 0.81 0.14 0.05 Matches are distributed among these distances: 27 34 0.97 28 1 0.03 ACGTcount: A:0.28, C:0.09, G:0.19, T:0.45 Consensus pattern (27 bp): TAATTCGGTTAATTTAGTTAATTCGAG Found at i:25388000 original size:20 final size:20 Alignment explanation
Indices: 25387975--25388012 Score: 76 Period size: 20 Copynumber: 1.9 Consensus size: 20 25387965 ATGAGGTTTA 25387975 AAAAATGGGTTAAAAACCAC 1 AAAAATGGGTTAAAAACCAC 25387995 AAAAATGGGTTAAAAACC 1 AAAAATGGGTTAAAAACC 25388013 CCATTTTTGT Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 20 18 1.00 ACGTcount: A:0.55, C:0.13, G:0.16, T:0.16 Consensus pattern (20 bp): AAAAATGGGTTAAAAACCAC Found at i:25400567 original size:18 final size:18 Alignment explanation
Indices: 25400536--25400593 Score: 80 Period size: 18 Copynumber: 3.2 Consensus size: 18 25400526 TCTATTATAA 25400536 TATTAATTAATAAAATAT 1 TATTAATTAATAAAATAT * * 25400554 TATTACTTATTAAAATAT 1 TATTAATTAATAAAATAT * * 25400572 TATTATTTAATAAAAAAT 1 TATTAATTAATAAAATAT 25400590 TATT 1 TATT 25400594 TGAAAGTCAT Statistics Matches: 35, Mismatches: 5, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 18 35 1.00 ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48 Consensus pattern (18 bp): TATTAATTAATAAAATAT Found at i:25401707 original size:39 final size:40 Alignment explanation
Indices: 25401612--25401708 Score: 119 Period size: 39 Copynumber: 2.5 Consensus size: 40 25401602 CTTTGATTAG * * 25401612 CCGATGATGCACTATGTGCTAGTATATTTACTTCGTTTAT 1 CCGATGATGCACTATATGCTAGTATATTTACTTCGTATAT * * 25401652 -CTATGATGCACTTATATGCTAGTATA-TTGCTTCGATATAT 1 CCGATGATGCAC-TATATGCTAGTATATTTACTTCG-TATAT 25401692 CCGATGATGCA-TATATG 1 CCGATGATGCACTATATG 25401709 TTCCAATATA Statistics Matches: 49, Mismatches: 5, Indels: 7 0.80 0.08 0.11 Matches are distributed among these distances: 39 23 0.47 40 17 0.35 41 9 0.18 ACGTcount: A:0.26, C:0.16, G:0.18, T:0.40 Consensus pattern (40 bp): CCGATGATGCACTATATGCTAGTATATTTACTTCGTATAT Found at i:25412944 original size:15 final size:15 Alignment explanation
Indices: 25412926--25412991 Score: 55 Period size: 14 Copynumber: 4.3 Consensus size: 15 25412916 TATTACAAAA 25412926 ATTTATTATTAATAT 1 ATTTATTATTAATAT * 25412941 ATTTATAATTGTAATAAAT 1 ATTTATTA-T-TAAT--AT * 25412960 ATTTATTATTAAAAT 1 ATTTATTATTAATAT * 25412975 A-TTAATATTAA-AT 1 ATTTATTATTAATAT 25412988 ATTT 1 ATTT 25412992 TCAATAATAT Statistics Matches: 42, Mismatches: 4, Indels: 11 0.74 0.07 0.19 Matches are distributed among these distances: 13 3 0.07 14 11 0.26 15 10 0.24 16 1 0.02 17 7 0.17 18 1 0.02 19 9 0.21 ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53 Consensus pattern (15 bp): ATTTATTATTAATAT Found at i:25413041 original size:16 final size:16 Alignment explanation
Indices: 25413010--25413046 Score: 58 Period size: 16 Copynumber: 2.3 Consensus size: 16 25413000 ATGTGAATAA 25413010 TATTATTTAAAATTAT 1 TATTATTTAAAATTAT 25413026 TATT-TTTAAAATTTAT 1 TATTATTTAAAA-TTAT 25413042 TATTA 1 TATTA 25413047 AAATAAAATT Statistics Matches: 19, Mismatches: 0, Indels: 3 0.86 0.00 0.14 Matches are distributed among these distances: 15 7 0.37 16 12 0.63 ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59 Consensus pattern (16 bp): TATTATTTAAAATTAT Found at i:25413098 original size:22 final size:22 Alignment explanation
Indices: 25413058--25413113 Score: 62 Period size: 22 Copynumber: 2.6 Consensus size: 22 25413048 AATAAAATTG * 25413058 AAATATTAAA-TA-ATTTATTA 1 AAATAATAAATTATATTTATTA 25413078 AAATAATAAATTATATTTATTA 1 AAATAATAAATTATATTTATTA * * * 25413100 TATTAATAATTTAT 1 AAATAATAAATTAT 25413114 TATATGACTA Statistics Matches: 30, Mismatches: 4, Indels: 2 0.83 0.11 0.06 Matches are distributed among these distances: 20 9 0.30 21 2 0.07 22 19 0.63 ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48 Consensus pattern (22 bp): AAATAATAAATTATATTTATTA Found at i:25417825 original size:20 final size:21 Alignment explanation
Indices: 25417802--25417851 Score: 77 Period size: 20 Copynumber: 2.5 Consensus size: 21 25417792 ATTTTAATAT 25417802 TATATTATATATAT-TTTTCA 1 TATATTATATATATGTTTTCA * 25417822 TATATTATATATATGTTTTTA 1 TATATTATATATATGTTTTCA 25417843 -ATATTATAT 1 TATATTATAT 25417852 TTTATATATT Statistics Matches: 28, Mismatches: 1, Indels: 2 0.90 0.03 0.06 Matches are distributed among these distances: 20 23 0.82 21 5 0.18 ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60 Consensus pattern (21 bp): TATATTATATATATGTTTTCA Found at i:25417862 original size:34 final size:37 Alignment explanation
Indices: 25417807--25417887 Score: 105 Period size: 35 Copynumber: 2.2 Consensus size: 37 25417797 AATATTATAT * 25417807 TATATATATTTTTCATATATTA-TATATATGTTTTTAA 1 TATATATA-TTTTCATATATTATTATATATATTTTTAA * * 25417844 TAT-TATATTTT-ATATATTATTATGTATATTTTTAG 1 TATATATATTTTCATATATTATTATATATATTTTTAA 25417879 TATATATAT 1 TATATATAT 25417888 ATTTGTGAAG Statistics Matches: 39, Mismatches: 3, Indels: 5 0.83 0.06 0.11 Matches are distributed among these distances: 34 8 0.21 35 19 0.49 36 9 0.23 37 3 0.08 ACGTcount: A:0.35, C:0.01, G:0.04, T:0.60 Consensus pattern (37 bp): TATATATATTTTCATATATTATTATATATATTTTTAA Found at i:25418815 original size:15 final size:15 Alignment explanation
Indices: 25418797--25418830 Score: 50 Period size: 15 Copynumber: 2.3 Consensus size: 15 25418787 TTTATACTAT * 25418797 GTATATATATATTTA 1 GTATATATATATTCA * 25418812 GTATGTATATATTCA 1 GTATATATATATTCA 25418827 GTAT 1 GTAT 25418831 TATTATGCGT Statistics Matches: 17, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 15 17 1.00 ACGTcount: A:0.35, C:0.03, G:0.12, T:0.50 Consensus pattern (15 bp): GTATATATATATTCA Found at i:25418837 original size:21 final size:20 Alignment explanation
Indices: 25418777--25418837 Score: 56 Period size: 21 Copynumber: 3.0 Consensus size: 20 25418767 ATTCCTAATA 25418777 TATATATTCAT-TTATACTATG 1 TATATATTCATATTAT--TATG * 25418798 TATATA-T-ATATTTAGTATG 1 TATATATTCATA-TTATTATG 25418817 TATATATTCAGTATTATTATG 1 TATATATTCA-TATTATTATG 25418838 CGTGTATTTT Statistics Matches: 33, Mismatches: 2, Indels: 10 0.73 0.04 0.22 Matches are distributed among these distances: 19 12 0.36 20 2 0.06 21 17 0.52 22 2 0.06 ACGTcount: A:0.34, C:0.05, G:0.08, T:0.52 Consensus pattern (20 bp): TATATATTCATATTATTATG Found at i:25422708 original size:16 final size:16 Alignment explanation
Indices: 25422687--25422722 Score: 63 Period size: 16 Copynumber: 2.2 Consensus size: 16 25422677 GTATAACTAA 25422687 CATTCATTTATGCATT 1 CATTCATTTATGCATT * 25422703 CATTCATTTATTCATT 1 CATTCATTTATGCATT 25422719 CATT 1 CATT 25422723 GCATATCCCA Statistics Matches: 19, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 16 19 1.00 ACGTcount: A:0.25, C:0.19, G:0.03, T:0.53 Consensus pattern (16 bp): CATTCATTTATGCATT Found at i:25431147 original size:68 final size:74 Alignment explanation
Indices: 25431025--25431207 Score: 234 Period size: 68 Copynumber: 2.6 Consensus size: 74 25431015 TATTTCTGTT * * ** * * 25431025 TTCAAAATTCGACTCATATTGCGAGAAATGAGTTGAGCCTCAAGAAAAGTTGAGGTATTTTC-A- 1 TTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGAAAAGCTGAGGTAATTTCAAT 25431088 A-T-T-TTG 66 ATTCTATTG * * * 25431094 TT-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAAT 1 TTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGAAAAGCTGAGGTAATTTCAAT * 25431158 ATTCTATTT 66 ATTCTATTG 25431167 TTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC 1 TTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC 25431208 GGCTCACATG Statistics Matches: 98, Mismatches: 10, Indels: 7 0.85 0.09 0.06 Matches are distributed among these distances: 68 50 0.51 69 3 0.03 70 1 0.01 71 1 0.01 72 1 0.01 73 4 0.04 74 38 0.39 ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31 Consensus pattern (74 bp): TTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGAAAAGCTGAGGTAATTTCAAT ATTCTATTG Found at i:25431401 original size:171 final size:164 Alignment explanation
Indices: 25431096--25431408 Score: 412 Period size: 171 Copynumber: 1.9 Consensus size: 164 25431086 CAATTTTGTT * * 25431096 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATATT 1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAGGACACGCTGAGGTAATTTCAAAATT * * * 25431161 CTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGTTGAGGTA 66 CTATTTTTCAAAAACCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGCTGAGCTA * 25431226 TTTTCAGTTTCTGTTTTTTTAATTTATATTTTTC 131 TTTTCAATTTCTGTTTTTTTAATTTATATTTTTC * * * * * * 25431260 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAATCTCGGGTCATATGTTGAGGTATTTTCAAAA 1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAGG--ACACGCTGAGGTAATTTCAAAA * * * 25431325 TCTGCTTTTAAGTTTCAAAAAACCAACTCATATTGCG-GAGGTGAGTTGAGCCTTGGCTCACGTG 64 T-T-CTATT---TTTC-AAAAACCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATG 25431389 CTGAGCTATTTTCAATTTCT 123 CTGAGCTATTTTCAATTTCT 25431409 ACTTTAATGT Statistics Matches: 126, Mismatches: 15, Indels: 9 0.84 0.10 0.06 Matches are distributed among these distances: 164 38 0.30 166 18 0.14 167 1 0.01 168 4 0.03 171 46 0.37 172 19 0.15 ACGTcount: A:0.28, C:0.16, G:0.20, T:0.35 Consensus pattern (164 bp): AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAGGACACGCTGAGGTAATTTCAAAATT CTATTTTTCAAAAACCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGCTGAGCTA TTTTCAATTTCTGTTTTTTTAATTTATATTTTTC Found at i:25432536 original size:21 final size:21 Alignment explanation
Indices: 25432506--25432556 Score: 59 Period size: 21 Copynumber: 2.4 Consensus size: 21 25432496 CCACCGGAAA 25432506 TCCCCTTCTCCCCACTCTCC-TT 1 TCCCC-TCTCCCCACTC-CCATT * 25432528 TCCCCTCTCCCCTCTCCCATT 1 TCCCCTCTCCCCACTCCCATT * 25432549 TCCTCTCT 1 TCCCCTCT 25432557 TCTTTTTTTC Statistics Matches: 26, Mismatches: 2, Indels: 3 0.84 0.06 0.10 Matches are distributed among these distances: 20 2 0.08 21 19 0.73 22 5 0.19 ACGTcount: A:0.04, C:0.59, G:0.00, T:0.37 Consensus pattern (21 bp): TCCCCTCTCCCCACTCCCATT Found at i:25433369 original size:20 final size:19 Alignment explanation
Indices: 25433346--25433542 Score: 86 Period size: 20 Copynumber: 10.6 Consensus size: 19 25433336 ATTTTAATAT 25433346 TATATTATATATATTTTTCA 1 TATATTATATATATTTTT-A 25433366 TATATTATATATATGTTTT- 1 TATATTATATATAT-TTTTA 25433385 TA-A-TAT-TATATTTTATA 1 TATATTATATATATTTT-TA * 25433402 TATCATTATGTATATTTTTA 1 TAT-ATTATATATATTTTTA * * 25433422 -ATA-TATATAT-TTGTGA 1 TATATTATATATATTTTTA * 25433438 -AGTATTATCA-ATAGTTTT- 1 TA-TATTAT-ATATATTTTTA 25433456 T-TATTAT-TATTATTTTTA 1 TATATTATATA-TATTTTTA * * 25433474 -ATATGTATATAT-TGTGTA 1 TATAT-TATATATATTTTTA * ** 25433492 TATATTTTA-ATACTACATTA 1 TATATTATATATA-T-TTTTA 25433512 TATA-TATATAT-TTTTTA 1 TATATTATATATATTTTTA 25433529 TATTATGTATATAT 1 TA-TAT-TATATAT 25433543 TTCAAGTATT Statistics Matches: 135, Mismatches: 16, Indels: 52 0.67 0.08 0.26 Matches are distributed among these distances: 15 3 0.02 16 12 0.09 17 32 0.24 18 20 0.15 19 20 0.15 20 36 0.27 21 12 0.09 ACGTcount: A:0.35, C:0.03, G:0.05, T:0.58 Consensus pattern (19 bp): TATATTATATATATTTTTA Found at i:25433374 original size:25 final size:23 Alignment explanation
Indices: 25433322--25433404 Score: 89 Period size: 22 Copynumber: 3.6 Consensus size: 23 25433312 CTAATATGTA * * 25433322 TATATTATGTAAATATTTTAATAT 1 TATATTATATATAT-TTTTAATAT * 25433346 TATATTATATATATTTTTCATA- 1 TATATTATATATATTTTTAATAT * 25433368 TAT-TATATATATGTTTTTAATAT 1 TATAT-TATATATATTTTTAATAT * 25433391 TATATTTTATATAT 1 TATATTATATATAT 25433405 CATTATGTAT Statistics Matches: 49, Mismatches: 7, Indels: 7 0.78 0.11 0.11 Matches are distributed among these distances: 21 1 0.02 22 18 0.37 23 17 0.35 24 13 0.27 ACGTcount: A:0.37, C:0.01, G:0.02, T:0.59 Consensus pattern (23 bp): TATATTATATATATTTTTAATAT Found at i:25433425 original size:35 final size:36 Alignment explanation
Indices: 25433351--25433433 Score: 109 Period size: 36 Copynumber: 2.3 Consensus size: 36 25433341 AATATTATAT 25433351 TATATATATTTTTCATATATTATATATATGTTTTTAA 1 TATATATATTTTTCATATATTATATATA-GTTTTTAA * 25433388 TAT-TATATTTTAT-ATATCATTATGTATA-TTTTTAA 1 TATATATATTTT-TCATAT-ATTATATATAGTTTTTAA 25433423 TATATATATTT 1 TATATATATTT 25433434 GTGAAGTATT Statistics Matches: 42, Mismatches: 1, Indels: 7 0.84 0.02 0.14 Matches are distributed among these distances: 35 10 0.24 36 19 0.45 37 13 0.31 ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60 Consensus pattern (36 bp): TATATATATTTTTCATATATTATATATAGTTTTTAA Found at i:25433486 original size:26 final size:27 Alignment explanation
Indices: 25433457--25433543 Score: 63 Period size: 27 Copynumber: 3.1 Consensus size: 27 25433447 AATAGTTTTT 25433457 TATTAT-TATTATTTTTAATATGTATA 1 TATTATATATTATTTTTAATATGTATA * * ** 25433483 TATTGTGTA-TATATTTTAATACTACATTA 1 TATTATATATTAT-TTTTAATA-TGTA-TA * 25433512 TATATATATATT-TTTTATATTATGTATA 1 TAT-TATATATTATTTT-TAATATGTATA 25433540 TATT 1 TATT 25433544 TCAAGTATTA Statistics Matches: 46, Mismatches: 8, Indels: 13 0.69 0.12 0.19 Matches are distributed among these distances: 26 8 0.17 27 11 0.24 28 7 0.15 29 10 0.22 30 9 0.20 31 1 0.02 ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59 Consensus pattern (27 bp): TATTATATATTATTTTTAATATGTATA Found at i:25434347 original size:21 final size:19 Alignment explanation
Indices: 25434323--25434374 Score: 68 Period size: 19 Copynumber: 2.6 Consensus size: 19 25434313 TAATATGTAT 25434323 TGTATATATTTATTTATACTA 1 TGTATATATTTA-TT-TACTA * * 25434344 TGTATATATATATTTAGTA 1 TGTATATATTTATTTACTA 25434363 TGTATATATTTA 1 TGTATATATTTA 25434375 GTATTATTAT Statistics Matches: 28, Mismatches: 3, Indels: 2 0.85 0.09 0.06 Matches are distributed among these distances: 19 15 0.54 20 2 0.07 21 11 0.39 ACGTcount: A:0.35, C:0.02, G:0.08, T:0.56 Consensus pattern (19 bp): TGTATATATTTATTTACTA Found at i:25434363 original size:15 final size:15 Alignment explanation
Indices: 25434345--25434378 Score: 59 Period size: 15 Copynumber: 2.3 Consensus size: 15 25434335 TTTATACTAT 25434345 GTATATATATATTTA 1 GTATATATATATTTA * 25434360 GTATGTATATATTTA 1 GTATATATATATTTA 25434375 GTAT 1 GTAT 25434379 TATTATGCGT Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 15 18 1.00 ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53 Consensus pattern (15 bp): GTATATATATATTTA Found at i:25434385 original size:21 final size:19 Alignment explanation
Indices: 25434323--25434385 Score: 72 Period size: 21 Copynumber: 3.1 Consensus size: 19 25434313 TAATATGTAT 25434323 TGTATATATTTATTTATACTA 1 TGTATATATTTATTTAT--TA * * 25434344 TGTATATATATATTTAGTA 1 TGTATATATTTATTTATTA 25434363 TGTATATATTTAGTATTATTA 1 TGTATATATTTA-T-TTATTA 25434384 TG 1 TG 25434386 CGTGTATTTT Statistics Matches: 36, Mismatches: 4, Indels: 4 0.82 0.09 0.09 Matches are distributed among these distances: 19 13 0.36 20 1 0.03 21 22 0.61 ACGTcount: A:0.33, C:0.02, G:0.10, T:0.56 Consensus pattern (19 bp): TGTATATATTTATTTATTA Found at i:25434632 original size:34 final size:34 Alignment explanation
Indices: 25434579--25434644 Score: 89 Period size: 34 Copynumber: 1.9 Consensus size: 34 25434569 TACTATCGCA ** 25434579 CGTATATTGTTAATGTTTTA-TATATTGTCTATTT 1 CGTATATTGTTAACCTTTTATTAT-TTGTCTATTT * 25434613 CGTATATTTTTAACCTTTTATTATTTGTCTAT 1 CGTATATTGTTAACCTTTTATTATTTGTCTAT 25434645 CCCGAATTTA Statistics Matches: 28, Mismatches: 3, Indels: 2 0.85 0.09 0.06 Matches are distributed among these distances: 34 25 0.89 35 3 0.11 ACGTcount: A:0.23, C:0.09, G:0.09, T:0.59 Consensus pattern (34 bp): CGTATATTGTTAACCTTTTATTATTTGTCTATTT Found at i:25438931 original size:3 final size:3 Alignment explanation
Indices: 25438923--25439291 Score: 134 Period size: 3 Copynumber: 121.7 Consensus size: 3 25438913 TAATTTAATA * * * 25438923 TAT TAT TAT TACT TAT TAT T-T TAC TAT TAT TGT CTAA TA- TAT TAT 1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT * * * * * * 25438968 TAT CAC TAT TAT TAT TAC T-T TAC TAT TGT AATT TAT GGTAT TAT TAT 1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT --TAT TAT TAT * * 25439015 TAC TCT TAT T-T TCAT TAT TAT TAT TAT TAT TAT TAT TATT TAT T-T 1 TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT * * * * * * * * 25439060 TCT T-T T-T TAC TAT TGT TAT TAGT GACC TAT TAC TAT TCT TAT TAG 1 TAT TAT TAT TAT TAT TAT TAT TA-T TA-T TAT TAT TAT TAT TAT TAT * * * * * * 25439105 CA- TAC TAT TAT T-T CCTAT T-T TA- TAT TAT TAT TGT TAT CAA CAT 1 TAT TAT TAT TAT TAT --TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT * * ** 25439148 ATAT TAT TAT CAT TAAT GTAT TGT TAT TCCC TAT TAT TAT TAT TAT TAT 1 -TAT TAT TAT TAT T-AT -TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT * * * 25439197 TAT TAT TAT TCCT T-T TAT TATT TAT TAT CAA TA- TAT TAT TAT TAT 1 TAT TAT TAT T-AT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT * * * * * ** * 25439242 TAT TGT TAT TAT TGT TAT TGT TGT TAT TGT TAT TGC TAT TGT TAT TAT 1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT 25439290 TA 1 TA 25439292 CCACCTTATT Statistics Matches: 268, Mismatches: 70, Indels: 56 0.68 0.18 0.14 Matches are distributed among these distances: 2 23 0.09 3 213 0.79 4 27 0.10 5 5 0.02 ACGTcount: A:0.28, C:0.08, G:0.05, T:0.59 Consensus pattern (3 bp): TAT Found at i:25439404 original size:17 final size:17 Alignment explanation
Indices: 25439382--25439415 Score: 59 Period size: 17 Copynumber: 2.0 Consensus size: 17 25439372 TTTTATTATC 25439382 ATTATTACTATCATATT 1 ATTATTACTATCATATT * 25439399 ATTATTACTATTATATT 1 ATTATTACTATCATATT 25439416 TTCATCTATA Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 17 16 1.00 ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56 Consensus pattern (17 bp): ATTATTACTATCATATT Found at i:25439643 original size:13 final size:14 Alignment explanation
Indices: 25439627--25439691 Score: 55 Period size: 13 Copynumber: 4.7 Consensus size: 14 25439617 TTTAATTTCA 25439627 ATTT-TTTTAGCTT 1 ATTTATTTTAGCTT * 25439640 ATTTATTATT-TCTTT 1 ATTTATT-TTAGC-TT * 25439655 TTTTATTTTAGCTT 1 ATTTATTTTAGCTT * 25439669 ATTCATTTTA-CTT 1 ATTTATTTTAGCTT * 25439682 ATTTGTTTTA 1 ATTTATTTTA 25439692 TCTTTTCTCT Statistics Matches: 41, Mismatches: 7, Indels: 8 0.73 0.12 0.14 Matches are distributed among these distances: 13 15 0.37 14 15 0.37 15 11 0.27 ACGTcount: A:0.18, C:0.08, G:0.05, T:0.69 Consensus pattern (14 bp): ATTTATTTTAGCTT Found at i:25442431 original size:15 final size:15 Alignment explanation
Indices: 25442413--25442443 Score: 53 Period size: 15 Copynumber: 2.1 Consensus size: 15 25442403 TTTTAATAAA 25442413 TTTTTTAAAAAAAAT 1 TTTTTTAAAAAAAAT * 25442428 TTTTTTAAAAATAAT 1 TTTTTTAAAAAAAAT 25442443 T 1 T 25442444 AATAGAAATT Statistics Matches: 15, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 15 15 1.00 ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52 Consensus pattern (15 bp): TTTTTTAAAAAAAAT Found at i:25442562 original size:16 final size:16 Alignment explanation
Indices: 25442541--25442571 Score: 53 Period size: 16 Copynumber: 1.9 Consensus size: 16 25442531 GATGAGTTCA 25442541 AAATTAAAAAAAATAG 1 AAATTAAAAAAAATAG * 25442557 AAATTATAAAAAATA 1 AAATTAAAAAAAATA 25442572 TTAATAATGA Statistics Matches: 14, Mismatches: 1, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 16 14 1.00 ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23 Consensus pattern (16 bp): AAATTAAAAAAAATAG Found at i:25446411 original size:28 final size:29 Alignment explanation
Indices: 25446379--25446458 Score: 99 Period size: 29 Copynumber: 2.8 Consensus size: 29 25446369 GTTGAGAGAT 25446379 GAAGAGCCTTGATGAAAGA-ATGAAAGAC 1 GAAGAGCCTTGATGAAAGAGATGAAAGAC * * * 25446407 GAAGAGCTTTGATAAAAGAGATGAGAGAC 1 GAAGAGCCTTGATGAAAGAGATGAAAGAC * * * 25446436 GAAGAGTCTAGATGAAAGGGATG 1 GAAGAGCCTTGATGAAAGAGATG 25446459 TGAGAGGGAT Statistics Matches: 43, Mismatches: 8, Indels: 1 0.83 0.15 0.02 Matches are distributed among these distances: 28 17 0.40 29 26 0.60 ACGTcount: A:0.44, C:0.07, G:0.33, T:0.16 Consensus pattern (29 bp): GAAGAGCCTTGATGAAAGAGATGAAAGAC Found at i:25446440 original size:29 final size:28 Alignment explanation
Indices: 25446371--25446441 Score: 97 Period size: 28 Copynumber: 2.5 Consensus size: 28 25446361 GCAGCCAAGT * * 25446371 TGAGAGATGAAGAGCCTTGATGAAAGAA 1 TGAGAGACGAAGAGCCTTGATAAAAGAA * * 25446399 TGAAAGACGAAGAGCTTTGATAAAAGAGA 1 TGAGAGACGAAGAGCCTTGATAAAAGA-A 25446428 TGAGAGACGAAGAG 1 TGAGAGACGAAGAG 25446442 TCTAGATGAA Statistics Matches: 37, Mismatches: 5, Indels: 1 0.86 0.12 0.02 Matches are distributed among these distances: 28 23 0.62 29 14 0.38 ACGTcount: A:0.45, C:0.07, G:0.32, T:0.15 Consensus pattern (28 bp): TGAGAGACGAAGAGCCTTGATAAAAGAA Found at i:25446453 original size:29 final size:28 Alignment explanation
Indices: 25446371--25446463 Score: 98 Period size: 29 Copynumber: 3.2 Consensus size: 28 25446361 GCAGCCAAGT * 25446371 TGAGAGATGAAGAGCCTTGATGAAAGA-A 1 TGAGAGACGAAGAG-CTTGATGAAAGAGA * * 25446399 TGAAAGACGAAGAGCTTTGATAAAAGAGA 1 TGAGAGACGAAGAGC-TTGATGAAAGAGA * * 25446428 TGAGAGACGAAGAGTCTAGATGAAAGGGA 1 TGAGAGACGAAGAG-CTTGATGAAAGAGA * 25446457 TGTGAGA 1 TGAGAGA 25446464 GGGATTTTCA Statistics Matches: 54, Mismatches: 8, Indels: 5 0.81 0.12 0.07 Matches are distributed among these distances: 27 1 0.02 28 22 0.41 29 30 0.56 30 1 0.02 ACGTcount: A:0.43, C:0.06, G:0.33, T:0.17 Consensus pattern (28 bp): TGAGAGACGAAGAGCTTGATGAAAGAGA Found at i:25448067 original size:25 final size:26 Alignment explanation
Indices: 25448039--25448094 Score: 69 Period size: 26 Copynumber: 2.2 Consensus size: 26 25448029 TTGAAACTTG * * 25448039 ATTTTTTT-TAGTTTTTAAATTTTTA 1 ATTTTTTTATAATTTCTAAATTTTTA * 25448064 ATTTTTTTATAATTTCTAATTTTTTA 1 ATTTTTTTATAATTTCTAAATTTTTA * 25448090 GTTTT 1 ATTTT 25448095 GAACTCATCT Statistics Matches: 26, Mismatches: 4, Indels: 1 0.84 0.13 0.03 Matches are distributed among these distances: 25 8 0.31 26 18 0.69 ACGTcount: A:0.23, C:0.02, G:0.04, T:0.71 Consensus pattern (26 bp): ATTTTTTTATAATTTCTAAATTTTTA Found at i:25448071 original size:18 final size:18 Alignment explanation
Indices: 25448050--25448088 Score: 62 Period size: 18 Copynumber: 2.2 Consensus size: 18 25448040 TTTTTTTTAG * 25448050 TTTTTA-AATTTTTAATT 1 TTTTTATAATTTCTAATT 25448067 TTTTTATAATTTCTAATT 1 TTTTTATAATTTCTAATT 25448085 TTTT 1 TTTT 25448089 AGTTTTGAAC Statistics Matches: 20, Mismatches: 1, Indels: 1 0.91 0.05 0.05 Matches are distributed among these distances: 17 6 0.30 18 14 0.70 ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72 Consensus pattern (18 bp): TTTTTATAATTTCTAATT Found at i:25450934 original size:19 final size:19 Alignment explanation
Indices: 25450899--25450940 Score: 50 Period size: 19 Copynumber: 2.2 Consensus size: 19 25450889 AATTAAACTT * * 25450899 GAAAATTAGACCTAAGATG 1 GAAAATTAGACCCAAGATC 25450918 GAAAATT-GAACCCAAGATC 1 GAAAATTAG-ACCCAAGATC 25450937 GAAA 1 GAAA 25450941 CCCAAAAATT Statistics Matches: 20, Mismatches: 2, Indels: 2 0.83 0.08 0.08 Matches are distributed among these distances: 18 1 0.05 19 19 0.95 ACGTcount: A:0.50, C:0.14, G:0.19, T:0.17 Consensus pattern (19 bp): GAAAATTAGACCCAAGATC Found at i:25451463 original size:32 final size:32 Alignment explanation
Indices: 25451426--25451497 Score: 81 Period size: 32 Copynumber: 2.2 Consensus size: 32 25451416 CGATGGTTGT 25451426 GACGACAACGATCCGGCGACCGACAGATGGTC 1 GACGACAACGATCCGGCGACCGACAGATGGTC * * **** 25451458 GACGACAATGGTTTTTCGACCGACAGATGGTC 1 GACGACAACGATCCGGCGACCGACAGATGGTC * 25451490 GGCGACAA 1 GACGACAA 25451498 TAATTCTTTG Statistics Matches: 33, Mismatches: 7, Indels: 0 0.82 0.17 0.00 Matches are distributed among these distances: 32 33 1.00 ACGTcount: A:0.28, C:0.26, G:0.31, T:0.15 Consensus pattern (32 bp): GACGACAACGATCCGGCGACCGACAGATGGTC Found at i:25452098 original size:12 final size:12 Alignment explanation
Indices: 25452077--25452127 Score: 57 Period size: 12 Copynumber: 4.2 Consensus size: 12 25452067 TGACGTGGCA * 25452077 GAGGAGGACGAT 1 GAGGATGACGAT * * 25452089 GAGGAAGACGAA 1 GAGGATGACGAT * 25452101 GATGATGACGAT 1 GAGGATGACGAT * 25452113 GACGATGACGAT 1 GAGGATGACGAT 25452125 GAG 1 GAG 25452128 CTATATGGCG Statistics Matches: 32, Mismatches: 7, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 12 32 1.00 ACGTcount: A:0.37, C:0.10, G:0.41, T:0.12 Consensus pattern (12 bp): GAGGATGACGAT Found at i:25452113 original size:6 final size:6 Alignment explanation
Indices: 25452083--25452126 Score: 52 Period size: 6 Copynumber: 7.3 Consensus size: 6 25452073 GGCAGAGGAG * * * * 25452083 GACGAT GAGGAA GACGAA GATGAT GACGAT GACGAT GACGAT GA 1 GACGAT GACGAT GACGAT GACGAT GACGAT GACGAT GACGAT GA 25452127 GCTATATGGC Statistics Matches: 32, Mismatches: 6, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 6 32 1.00 ACGTcount: A:0.39, C:0.11, G:0.36, T:0.14 Consensus pattern (6 bp): GACGAT Found at i:25461335 original size:2 final size:2 Alignment explanation
Indices: 25461328--25461364 Score: 74 Period size: 2 Copynumber: 18.5 Consensus size: 2 25461318 GACCAATTAT 25461328 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A 1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A 25461365 TATAATTATA Statistics Matches: 35, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 35 1.00 ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00 Consensus pattern (2 bp): AC Found at i:25468385 original size:15 final size:15 Alignment explanation
Indices: 25468363--25468410 Score: 55 Period size: 15 Copynumber: 3.3 Consensus size: 15 25468353 TTTTTTAAGA 25468363 TTACATTTTAATCAC 1 TTACATTTTAATCAC * * 25468378 TTATATTTGAAAT-A- 1 TTACATTT-TAATCAC 25468392 TTACATTTTAATCAC 1 TTACATTTTAATCAC 25468407 TTAC 1 TTAC 25468411 GTTATCATTT Statistics Matches: 26, Mismatches: 4, Indels: 6 0.72 0.11 0.17 Matches are distributed among these distances: 13 3 0.12 14 8 0.31 15 12 0.46 16 3 0.12 ACGTcount: A:0.35, C:0.15, G:0.02, T:0.48 Consensus pattern (15 bp): TTACATTTTAATCAC Found at i:25472633 original size:35 final size:37 Alignment explanation
Indices: 25472588--25472658 Score: 110 Period size: 37 Copynumber: 1.9 Consensus size: 37 25472578 AGAACAACTA * 25472588 AATTATACAAAAC-ATAAAGAAATCATGACACTGGTT 1 AATTATACAAAACTAAAAAGAAATCATGACACTGGTT 25472624 AATT-TACAAAACTTAAAAAGAAATCATGACACTGG 1 AATTATACAAAAC-TAAAAAGAAATCATGACACTGG 25472659 AAGCTATATT Statistics Matches: 32, Mismatches: 1, Indels: 3 0.89 0.03 0.08 Matches are distributed among these distances: 35 8 0.25 36 4 0.12 37 20 0.62 ACGTcount: A:0.51, C:0.14, G:0.11, T:0.24 Consensus pattern (37 bp): AATTATACAAAACTAAAAAGAAATCATGACACTGGTT Found at i:25480472 original size:39 final size:39 Alignment explanation
Indices: 25480429--25480529 Score: 139 Period size: 39 Copynumber: 2.6 Consensus size: 39 25480419 ATCGTGATCT * * 25480429 GAAGCCCGAAATCTAGCTAAAGCACATAAGTGCTAAACG 1 GAAGCCCGAAAGCTAACTAAAGCACATAAGTGCTAAACG * * 25480468 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG 1 GAAGCCCGAAAGCTAACTAAAGCACATAAGTGCTAAACG * * * 25480507 GAAGCCCGGAGGCTAACTGAAGC 1 GAAGCCCGAAAGCTAACTAAAGC 25480530 TCATCAGAGC Statistics Matches: 57, Mismatches: 5, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 39 57 1.00 ACGTcount: A:0.38, C:0.24, G:0.26, T:0.13 Consensus pattern (39 bp): GAAGCCCGAAAGCTAACTAAAGCACATAAGTGCTAAACG Found at i:25480511 original size:21 final size:21 Alignment explanation
Indices: 25480448--25480511 Score: 80 Period size: 21 Copynumber: 3.2 Consensus size: 21 25480438 AATCTAGCTA 25480448 AAGCACATAAGTGCTAAACGG 1 AAGCACATAAGTGCTAAACGG ** * 25480469 AAGC-CCGAAG-GCT-AACTG 1 AAGCACATAAGTGCTAAACGG 25480487 AAGCACATAAGTGCTAAACGG 1 AAGCACATAAGTGCTAAACGG 25480508 AAGC 1 AAGC 25480512 CCGGAGGCTA Statistics Matches: 34, Mismatches: 6, Indels: 6 0.74 0.13 0.13 Matches are distributed among these distances: 18 8 0.24 19 7 0.21 20 7 0.21 21 12 0.35 ACGTcount: A:0.41, C:0.22, G:0.25, T:0.12 Consensus pattern (21 bp): AAGCACATAAGTGCTAAACGG Found at i:25484334 original size:25 final size:25 Alignment explanation
Indices: 25484300--25484389 Score: 92 Period size: 25 Copynumber: 3.6 Consensus size: 25 25484290 ATATTATTAT * 25484300 TATTTTTTATTTTAAGTTTTTCTTA 1 TATTATTTATTTTAAGTTTTTCTTA * * 25484325 TATTATTTATTTTAAATTGTT-TTA 1 TATTATTTATTTTAAGTTTTTCTTA * *** 25484349 TTATTTTTTATTTTAAGTTTTTCACG 1 -TATTATTTATTTTAAGTTTTTCTTA * 25484375 TATTATGTATTTTAA 1 TATTATTTATTTTAA 25484390 ACTATTATCC Statistics Matches: 52, Mismatches: 11, Indels: 4 0.78 0.16 0.06 Matches are distributed among these distances: 24 3 0.06 25 49 0.94 ACGTcount: A:0.24, C:0.03, G:0.06, T:0.67 Consensus pattern (25 bp): TATTATTTATTTTAAGTTTTTCTTA Found at i:25484350 original size:50 final size:50 Alignment explanation
Indices: 25484296--25484390 Score: 154 Period size: 50 Copynumber: 1.9 Consensus size: 50 25484286 AACTATATTA ** * 25484296 TTATTATTTTTTATTTTAAGTTTTTCTTATATTATTTATTTTAAATTGTT 1 TTATTATTTTTTATTTTAAGTTTTTCACATATTATGTATTTTAAATTGTT * 25484346 TTATTATTTTTTATTTTAAGTTTTTCACGTATTATGTATTTTAAA 1 TTATTATTTTTTATTTTAAGTTTTTCACATATTATGTATTTTAAA 25484391 CTATTATCCA Statistics Matches: 41, Mismatches: 4, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 50 41 1.00 ACGTcount: A:0.25, C:0.03, G:0.05, T:0.66 Consensus pattern (50 bp): TTATTATTTTTTATTTTAAGTTTTTCACATATTATGTATTTTAAATTGTT Found at i:25484472 original size:27 final size:28 Alignment explanation
Indices: 25484419--25484545 Score: 102 Period size: 28 Copynumber: 4.5 Consensus size: 28 25484409 ATTTTAAAGG 25484419 TTATTTATTTTAAA--ATTTTTATATATA 1 TTATTTATTTTAAATTATTTTT-TATATA * 25484446 TTATTTATTTTGAATTATTTTTTTATATA 1 TTATTTATTTTAAATTA-TTTTTTATATA * * * * 25484475 TATCTTTTATTTTTAAACTA--TTTTGTACA 1 T-T-ATTTA-TTTTAAATTATTTTTTATATA * 25484504 TTATTTATTTTAAATT-TCTTTTTACATA 1 TTATTTATTTTAAATTAT-TTTTTATATA * 25484532 TTATTTATCTTAAA 1 TTATTTATTTTAAA 25484546 CTCTTTTATA Statistics Matches: 79, Mismatches: 12, Indels: 17 0.73 0.11 0.16 Matches are distributed among these distances: 26 8 0.10 27 17 0.22 28 20 0.25 29 16 0.20 30 6 0.08 31 4 0.05 32 8 0.10 ACGTcount: A:0.31, C:0.05, G:0.02, T:0.63 Consensus pattern (28 bp): TTATTTATTTTAAATTATTTTTTATATA Found at i:25484529 original size:26 final size:26 Alignment explanation
Indices: 25484419--25484686 Score: 162 Period size: 26 Copynumber: 10.2 Consensus size: 26 25484409 ATTTTAAAGG 25484419 TTATTTATTTTAAAATTT-TTATATATA 1 TTATTTATTTT-AAATTTCTT-TATATA * 25484446 TTATTTATTTTGAATTATTTTTTTATATA 1 TTATTTATTTT-AA--ATTTCTTTATATA * * * * 25484475 TATCTTTTATTTTTAAACTAT-TTTGTACA 1 T-T-ATTTA-TTTTAAA-TTTCTTTATATA * 25484504 TTATTTATTTTAAATTTCTTTTTACATA 1 TTATTTATTTTAAATTTC--TTTATATA * * 25484532 TTATTTATCTTAAA-CTCTTT-TATA 1 TTATTTATTTTAAATTTCTTTATATA * * 25484556 -T-GTTATTTTAAAGTGTC-TTATATA 1 TTATTTATTTTAAA-TTTCTTTATATA * * * 25484580 TTATCTATTTTAAATTGCTTTGTATA 1 TTATTTATTTTAAATTTCTTTATATA * * 25484606 TTATCTATTTT-AATTTGTTTATATA 1 TTATTTATTTTAAATTTCTTTATATA * * * 25484631 TTATTTATTTTAAA-ATGTTT-TATG 1 TTATTTATTTTAAATTTCTTTATATA * * 25484655 GTATTTACTTTAAATTGT-TTTATATA 1 TTATTTATTTTAAATT-TCTTTATATA 25484681 TTATTT 1 TTATTT 25484687 TGTTTTGTTT Statistics Matches: 189, Mismatches: 32, Indels: 41 0.72 0.12 0.16 Matches are distributed among these distances: 22 9 0.05 23 3 0.02 24 24 0.13 25 37 0.20 26 44 0.23 27 19 0.10 28 19 0.10 29 19 0.10 30 5 0.03 31 6 0.03 32 4 0.02 ACGTcount: A:0.29, C:0.05, G:0.04, T:0.62 Consensus pattern (26 bp): TTATTTATTTTAAATTTCTTTATATA Found at i:25484685 original size:50 final size:48 Alignment explanation
Indices: 25484503--25484686 Score: 165 Period size: 50 Copynumber: 3.7 Consensus size: 48 25484493 TATTTTGTAC * * * * * 25484503 ATTATTTATTTTAAATTTCTTTTTACATATTATTTATCTTAAACTCTTTT 1 ATTATTTATTTTAAA-TT-GTTTTATATATTATTTATTTTAAAATGTTTT * * * * 25484553 A-TATGTTATTTTAAAGTGTCTTATATATTATCTATTTTAAATTGCTTTGTAT 1 ATTAT-TTATTTTAAATTGTTTTATATATTATTTATTTTAAAATG--TT-T-T * * 25484605 ATTATCTATTTTAATTTG-TTTATATATTATTTATTTTAAAATGTTTT 1 ATTATTTATTTTAAATTGTTTTATATATTATTTATTTTAAAATGTTTT * 25484652 ATGGTATTTACTTTAAATTGTTTTATATATTATTT 1 AT--TATTTATTTTAAATTGTTTTATATATTATTT 25484687 TGTTTTGTTT Statistics Matches: 108, Mismatches: 17, Indels: 18 0.76 0.12 0.13 Matches are distributed among these distances: 47 3 0.03 48 21 0.19 49 19 0.18 50 27 0.25 51 23 0.21 52 12 0.11 53 3 0.03 ACGTcount: A:0.29, C:0.05, G:0.05, T:0.60 Consensus pattern (48 bp): ATTATTTATTTTAAATTGTTTTATATATTATTTATTTTAAAATGTTTT Found at i:25488476 original size:15 final size:17 Alignment explanation
Indices: 25488445--25488479 Score: 56 Period size: 15 Copynumber: 2.2 Consensus size: 17 25488435 CTACACGTGG 25488445 TAATTTTATTTTAGTTT 1 TAATTTTATTTTAGTTT 25488462 TAATTTT-TTTT-GTTT 1 TAATTTTATTTTAGTTT 25488477 TAA 1 TAA 25488480 AATATTATAT Statistics Matches: 18, Mismatches: 0, Indels: 2 0.90 0.00 0.10 Matches are distributed among these distances: 15 7 0.39 16 4 0.22 17 7 0.39 ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71 Consensus pattern (17 bp): TAATTTTATTTTAGTTT Found at i:25511564 original size:18 final size:18 Alignment explanation
Indices: 25511541--25511609 Score: 66 Period size: 18 Copynumber: 3.7 Consensus size: 18 25511531 GCACATAAGT 25511541 GCTAACGGAAGCCCGAAG 1 GCTAACGGAAGCCCGAAG * ** 25511559 GCTAACTGAAGCACATAAG 1 GCTAACGGAAGC-CCGAAG * 25511578 TGCTAAACGGAAGCCCGGAG 1 -GCT-AACGGAAGCCCGAAG * 25511598 GCTAACTGAAGC 1 GCTAACGGAAGC 25511610 TCATCAGAGC Statistics Matches: 40, Mismatches: 8, Indels: 6 0.74 0.15 0.11 Matches are distributed among these distances: 18 19 0.47 19 7 0.17 20 6 0.15 21 8 0.20 ACGTcount: A:0.35, C:0.25, G:0.29, T:0.12 Consensus pattern (18 bp): GCTAACGGAAGCCCGAAG Found at i:25511600 original size:39 final size:38 Alignment explanation
Indices: 25511510--25511609 Score: 146 Period size: 38 Copynumber: 2.6 Consensus size: 38 25511500 ATCGTGATCT ** * * 25511510 GAAGCCCGAAATCTAGCTAAAGCACATAAGTGCTAACG 1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAACG 25511548 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG 1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCT-AACG * 25511587 GAAGCCCGGAGGCTAACTGAAGC 1 GAAGCCCGAAGGCTAACTGAAGC 25511610 TCATCAGAGC Statistics Matches: 56, Mismatches: 5, Indels: 1 0.90 0.08 0.02 Matches are distributed among these distances: 38 30 0.54 39 26 0.46 ACGTcount: A:0.37, C:0.24, G:0.26, T:0.13 Consensus pattern (38 bp): GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAACG Found at i:25515145 original size:24 final size:24 Alignment explanation
Indices: 25515117--25515198 Score: 85 Period size: 24 Copynumber: 3.4 Consensus size: 24 25515107 TTATTATTTT 25515117 TTATTTTAAGTTTTTCTTATATTA 1 TTATTTTAAGTTTTTCTTATATTA * * * 25515141 TTATTTTAAATTGTT-TTATTATTT 1 TTATTTTAAGTTTTTCTTA-TATTA *** 25515165 TTATTTTAAGTTTTTCACGTATTA 1 TTATTTTAAGTTTTTCTTATATTA 25515189 TGTATTTTAA 1 T-TATTTTAA 25515199 ACTATTATCC Statistics Matches: 46, Mismatches: 9, Indels: 5 0.77 0.15 0.08 Matches are distributed among these distances: 23 3 0.07 24 35 0.76 25 8 0.17 ACGTcount: A:0.26, C:0.04, G:0.06, T:0.65 Consensus pattern (24 bp): TTATTTTAAGTTTTTCTTATATTA Found at i:25515213 original size:48 final size:47 Alignment explanation
Indices: 25515105--25515213 Score: 112 Period size: 48 Copynumber: 2.3 Consensus size: 47 25515095 AAAACTATAT * ** * 25515105 TATTATTATTTTTTATTTTAAGTTTTTCTTATATTATTATTTTAAATTG 1 TATTATCA-TTTTTATTTTAAGTTTTTCACATATTATTATTTTAAA-TC * * * 25515154 TTTTATTATTTTTATTTTAAGTTTTTCACGTATTATGTATTTTAAA-C 1 TATTATCATTTTTATTTTAAGTTTTTCACATATTAT-TATTTTAAATC 25515201 TATTATCCATTTT 1 TATTAT-CATTTT 25515214 AAATATTTTA Statistics Matches: 51, Mismatches: 7, Indels: 5 0.81 0.11 0.08 Matches are distributed among these distances: 47 5 0.10 48 30 0.59 49 16 0.31 ACGTcount: A:0.26, C:0.06, G:0.05, T:0.64 Consensus pattern (47 bp): TATTATCATTTTTATTTTAAGTTTTTCACATATTATTATTTTAAATC Found at i:25515279 original size:26 final size:26 Alignment explanation
Indices: 25515191--25515493 Score: 162 Period size: 26 Copynumber: 11.7 Consensus size: 26 25515181 ACGTATTATG * ** 25515191 TATTTTAAACTATTATCCATTTTAAA- 1 TATTTTATA-TATTATTTATTTTAAAT ** 25515217 TATTTTA-AGGTTATTTATTTTAAAAT 1 TATTTTATATATTATTTATTTT-AAAT * 25515243 T-TTTATATATATTATTTATTTTGAAT 1 TATTT-TATATATTATTTATTTTAAAT * * 25515269 TATTTTTTATATATATCTTTTATTTTTAAAC 1 TA--TTTTATATAT-T-ATTTA-TTTTAAAT * * 25515300 TATTTTGTACATTATTTATTTTAAATT 1 TATTTTATATATTATTTATTTTAAA-T * * * * 25515327 TCTTTTTACATATTATTTATCTTAAAC 1 T-ATTTTATATATTATTTATTTTAAAT * * * 25515354 T-CTTT-TATA-T-GTTATTTTAAAG 1 TATTTTATATATTATTTATTTTAAAT * * * 25515376 TGTCTTATATATTATCTATTTTAAAT 1 TATTTTATATATTATTTATTTTAAAT ** * * 25515402 TGCTTTGTATATTATCTATTTT-AAT 1 TATTTTATATATTATTTATTTTAAAT 25515427 T-TGTTTATATATTATTTATTTTAAA- 1 TAT-TTTATATATTATTTATTTTAAAT ** * 25515452 -ATGTTT-TATGGTATTTACTTTAAAT 1 TAT-TTTATATATTATTTATTTTAAAT * 25515477 TGTTTTATATATTATTT 1 TATTTTATATATTATTT 25515494 TGTTTTGTTT Statistics Matches: 213, Mismatches: 42, Indels: 44 0.71 0.14 0.15 Matches are distributed among these distances: 22 10 0.05 23 3 0.01 24 31 0.15 25 40 0.19 26 60 0.28 27 18 0.08 28 27 0.13 29 12 0.06 30 4 0.02 31 8 0.04 ACGTcount: A:0.30, C:0.05, G:0.05, T:0.60 Consensus pattern (26 bp): TATTTTATATATTATTTATTTTAAAT Found at i:25515492 original size:50 final size:48 Alignment explanation
Indices: 25515310--25515493 Score: 165 Period size: 50 Copynumber: 3.7 Consensus size: 48 25515300 TATTTTGTAC * * * * * 25515310 ATTATTTATTTTAAATTTCTTTTTACATATTATTTATCTTAAACTCTTTT 1 ATTATTTATTTTAAA-TT-GTTTTATATATTATTTATTTTAAAATGTTTT * * * * 25515360 A-TATGTTATTTTAAAGTGTCTTATATATTATCTATTTTAAATTGCTTTGTAT 1 ATTAT-TTATTTTAAATTGTTTTATATATTATTTATTTTAAAATG--TT-T-T * * 25515412 ATTATCTATTTTAATTTG-TTTATATATTATTTATTTTAAAATGTTTT 1 ATTATTTATTTTAAATTGTTTTATATATTATTTATTTTAAAATGTTTT * 25515459 ATGGTATTTACTTTAAATTGTTTTATATATTATTT 1 AT--TATTTATTTTAAATTGTTTTATATATTATTT 25515494 TGTTTTGTTT Statistics Matches: 108, Mismatches: 17, Indels: 18 0.76 0.12 0.13 Matches are distributed among these distances: 47 3 0.03 48 21 0.19 49 19 0.18 50 27 0.25 51 23 0.21 52 12 0.11 53 3 0.03 ACGTcount: A:0.29, C:0.05, G:0.05, T:0.60 Consensus pattern (48 bp): ATTATTTATTTTAAATTGTTTTATATATTATTTATTTTAAAATGTTTT Found at i:25519253 original size:15 final size:17 Alignment explanation
Indices: 25519222--25519256 Score: 56 Period size: 15 Copynumber: 2.2 Consensus size: 17 25519212 CTACACGTGG 25519222 TAATTTTATTTTAGTTT 1 TAATTTTATTTTAGTTT 25519239 TAATTTT-TTTT-GTTT 1 TAATTTTATTTTAGTTT 25519254 TAA 1 TAA 25519257 AATATTATAT Statistics Matches: 18, Mismatches: 0, Indels: 2 0.90 0.00 0.10 Matches are distributed among these distances: 15 7 0.39 16 4 0.22 17 7 0.39 ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71 Consensus pattern (17 bp): TAATTTTATTTTAGTTT Found at i:25532502 original size:22 final size:21 Alignment explanation
Indices: 25532462--25532515 Score: 63 Period size: 22 Copynumber: 2.5 Consensus size: 21 25532452 GTGTTTGAGG * * * 25532462 TCTCGAAACAATTGTTCTTAGA 1 TCTCGAGACAAGTGGTCTT-GA * 25532484 TCTCGAGACAAGTGGTCTTTA 1 TCTCGAGACAAGTGGTCTTGA 25532505 TCTCGAGACAA 1 TCTCGAGACAA 25532516 AAGAACATCA Statistics Matches: 28, Mismatches: 4, Indels: 1 0.85 0.12 0.03 Matches are distributed among these distances: 21 12 0.43 22 16 0.57 ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31 Consensus pattern (21 bp): TCTCGAGACAAGTGGTCTTGA Found at i:25537948 original size:13 final size:13 Alignment explanation
Indices: 25537930--25537977 Score: 51 Period size: 13 Copynumber: 3.6 Consensus size: 13 25537920 TTCTTCCTTC 25537930 TCTTCTCTTCTCT 1 TCTTCTCTTCTCT * * 25537943 TCTTCTATTTTCT 1 TCTTCTCTTCTCT * * 25537956 TTTTCTCATTCTTT 1 TCTTCTC-TTCTCT 25537970 TCTTCTCT 1 TCTTCTCT 25537978 AGCCGAAACA Statistics Matches: 27, Mismatches: 7, Indels: 2 0.75 0.19 0.06 Matches are distributed among these distances: 13 17 0.63 14 10 0.37 ACGTcount: A:0.04, C:0.29, G:0.00, T:0.67 Consensus pattern (13 bp): TCTTCTCTTCTCT Found at i:25539441 original size:46 final size:45 Alignment explanation
Indices: 25539388--25539563 Score: 205 Period size: 46 Copynumber: 3.8 Consensus size: 45 25539378 TATTTGGGCA 25539388 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G ** * * 25539434 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATAT-AACTAG-GCA- 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC---ACTTATGGA-T-GCGAAG * 25539481 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G * * 25539527 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG 25539564 GCGGGTTACA Statistics Matches: 111, Mismatches: 10, Indels: 18 0.80 0.07 0.13 Matches are distributed among these distances: 43 1 0.01 44 7 0.06 45 1 0.01 46 65 0.59 47 28 0.25 48 1 0.01 49 7 0.06 50 1 0.01 ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28 Consensus pattern (45 bp): TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG Found at i:25539543 original size:93 final size:93 Alignment explanation
Indices: 25539384--25539555 Score: 308 Period size: 93 Copynumber: 1.8 Consensus size: 93 25539374 AGGATATTTG * * 25539384 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG 1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG 25539449 TTGAGTCCGAGTTCGAGAGATATAACTA 66 TTGAGTCCGAGTTCGAGAGATATAACTA * * 25539477 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG 1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG 25539542 TTGAGTCCGAGTTC 66 TTGAGTCCGAGTTC 25539556 ACTTATGGGC Statistics Matches: 75, Mismatches: 4, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 93 75 1.00 ACGTcount: A:0.22, C:0.22, G:0.30, T:0.27 Consensus pattern (93 bp): GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG TTGAGTCCGAGTTCGAGAGATATAACTA Found at i:25550502 original size:19 final size:20 Alignment explanation
Indices: 25550475--25550521 Score: 69 Period size: 21 Copynumber: 2.4 Consensus size: 20 25550465 CGAATACGCC * 25550475 AACAAAAGCTCG-AAAGCTG 1 AACAGAAGCTCGAAAAGCTG 25550494 AACAGAAGCTCGTAAAAGCTG 1 AACAGAAGCTCG-AAAAGCTG 25550515 AACAGAA 1 AACAGAA 25550522 AGTAAAACAC Statistics Matches: 25, Mismatches: 1, Indels: 2 0.89 0.04 0.07 Matches are distributed among these distances: 19 11 0.44 21 14 0.56 ACGTcount: A:0.49, C:0.19, G:0.21, T:0.11 Consensus pattern (20 bp): AACAGAAGCTCGAAAAGCTG Found at i:25554655 original size:22 final size:21 Alignment explanation
Indices: 25554616--25554660 Score: 56 Period size: 22 Copynumber: 2.1 Consensus size: 21 25554606 ATTTAAAAAT 25554616 TATTTTATACTAACATTTTATA 1 TATTTTATACTAACA-TTTATA * 25554638 TATTTTATAATTAA-ATTTATA 1 TATTTTAT-ACTAACATTTATA 25554659 TA 1 TA 25554661 AAAATTTTAA Statistics Matches: 21, Mismatches: 1, Indels: 3 0.84 0.04 0.12 Matches are distributed among these distances: 21 8 0.38 22 9 0.43 23 4 0.19 ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56 Consensus pattern (21 bp): TATTTTATACTAACATTTATA Found at i:25554808 original size:20 final size:21 Alignment explanation
Indices: 25554783--25554833 Score: 79 Period size: 20 Copynumber: 2.5 Consensus size: 21 25554773 GCAAATTAAT * 25554783 AGACCTATCCATGGGTTGGG- 1 AGACCTATCCATGGGTCGGGC 25554803 AGACCTATCCATGGGTCGGGC 1 AGACCTATCCATGGGTCGGGC 25554824 AG-CCTATCCA 1 AGACCTATCCA 25554834 GCTAGACTAA Statistics Matches: 29, Mismatches: 1, Indels: 2 0.91 0.03 0.06 Matches are distributed among these distances: 20 27 0.93 21 2 0.07 ACGTcount: A:0.22, C:0.27, G:0.29, T:0.22 Consensus pattern (21 bp): AGACCTATCCATGGGTCGGGC Found at i:25555597 original size:25 final size:25 Alignment explanation
Indices: 25555569--25555620 Score: 86 Period size: 25 Copynumber: 2.1 Consensus size: 25 25555559 ATCAAGTGAG * 25555569 TATTTTTTATTTTAAAATATTACAT 1 TATTTTTTATTTCAAAATATTACAT * 25555594 TATTTTTTATTTCAAAATGTTACAT 1 TATTTTTTATTTCAAAATATTACAT 25555619 TA 1 TA 25555621 ATAAATTTAA Statistics Matches: 25, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 25 25 1.00 ACGTcount: A:0.35, C:0.06, G:0.02, T:0.58 Consensus pattern (25 bp): TATTTTTTATTTCAAAATATTACAT Found at i:25558374 original size:22 final size:22 Alignment explanation
Indices: 25558316--25558374 Score: 59 Period size: 22 Copynumber: 2.6 Consensus size: 22 25558306 TAAGTATAAA 25558316 AAAATAAATAAAA-AACATTTGT 1 AAAA-AAATAAAATAACATTTGT * * 25558338 ATAAAAATATTAATAAC-TTTGT 1 AAAAAAATA-AAATAACATTTGT 25558360 AAAAAGAATAAAATA 1 AAAAA-AATAAAATA 25558375 TAGTTTTAGT Statistics Matches: 30, Mismatches: 4, Indels: 6 0.75 0.10 0.15 Matches are distributed among these distances: 21 5 0.17 22 18 0.60 23 7 0.23 ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29 Consensus pattern (22 bp): AAAAAAATAAAATAACATTTGT Found at i:25564241 original size:23 final size:23 Alignment explanation
Indices: 25564179--25564242 Score: 76 Period size: 23 Copynumber: 2.8 Consensus size: 23 25564169 TCGGAATTTT * 25564179 TCATAACATATAACATATCGAAA 1 TCATATCATATAACATATCGAAA * * 25564202 TCATATTATTTAACATATC-AAA 1 TCATATCATATAACATATCGAAA * 25564224 GTCATATCATATATCATAT 1 -TCATATCATATAACATAT 25564243 AATATATCAA Statistics Matches: 34, Mismatches: 6, Indels: 2 0.81 0.14 0.05 Matches are distributed among these distances: 22 3 0.09 23 31 0.91 ACGTcount: A:0.45, C:0.16, G:0.03, T:0.36 Consensus pattern (23 bp): TCATATCATATAACATATCGAAA Found at i:25566182 original size:18 final size:18 Alignment explanation
Indices: 25566136--25566184 Score: 57 Period size: 17 Copynumber: 2.8 Consensus size: 18 25566126 GAGAGGAAAG 25566136 AAAGAATAAAAAA-TAAA 1 AAAGAATAAAAAATTAAA * * * 25566153 AGAGGA-ACAAAATTAAA 1 AAAGAATAAAAAATTAAA 25566170 AAAGAATAAAAAATT 1 AAAGAATAAAAAATT 25566185 GCGAGTGATT Statistics Matches: 24, Mismatches: 6, Indels: 3 0.73 0.18 0.09 Matches are distributed among these distances: 16 5 0.21 17 12 0.50 18 7 0.29 ACGTcount: A:0.73, C:0.02, G:0.10, T:0.14 Consensus pattern (18 bp): AAAGAATAAAAAATTAAA Found at i:25571250 original size:14 final size:16 Alignment explanation
Indices: 25571221--25571250 Score: 53 Period size: 15 Copynumber: 1.9 Consensus size: 16 25571211 AAATCACTAA 25571221 TAATATTAATTTTTTT 1 TAATATTAATTTTTTT 25571237 TAAT-TTAATTTTTT 1 TAATATTAATTTTTT 25571251 CAATGAATTA Statistics Matches: 14, Mismatches: 0, Indels: 1 0.93 0.00 0.07 Matches are distributed among these distances: 15 10 0.71 16 4 0.29 ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70 Consensus pattern (16 bp): TAATATTAATTTTTTT Found at i:25573764 original size:40 final size:40 Alignment explanation
Indices: 25573709--25573829 Score: 181 Period size: 40 Copynumber: 3.0 Consensus size: 40 25573699 ATTTGATGTG 25573709 TATCCGGGCTTAAAGACCCGCAGGCTATATGCTGGAATTA 1 TATCCGGGCTTAAAGACCCGCAGGCTATATGCTGGAATTA * 25573749 TATCCGGGCTTAAAGACCCGTAGGCTATATGCTGGAATTA 1 TATCCGGGCTTAAAGACCCGCAGGCTATATGCTGGAATTA * * ** * 25573789 TACCCGGACTT-AAGGTCCGCAGGCTATGTGCTGGAATTA 1 TATCCGGGCTTAAAGACCCGCAGGCTATATGCTGGAATTA 25573828 TA 1 TA 25573830 ACCAGACTTA Statistics Matches: 74, Mismatches: 7, Indels: 1 0.90 0.09 0.01 Matches are distributed among these distances: 39 26 0.35 40 48 0.65 ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26 Consensus pattern (40 bp): TATCCGGGCTTAAAGACCCGCAGGCTATATGCTGGAATTA Found at i:25573824 original size:39 final size:39 Alignment explanation
Indices: 25573726--25573853 Score: 175 Period size: 39 Copynumber: 3.3 Consensus size: 39 25573716 GCTTAAAGAC * * ** 25573726 CCGCAGGCTATATGCTGGAATTATATCCGGGCTTAAAGAC 1 CCGCAGGCTATATGCTGGAATTATAACCGGACTT-AAGGT * * 25573766 CCGTAGGCTATATGCTGGAATTATACCCGGACTTAAGGT 1 CCGCAGGCTATATGCTGGAATTATAACCGGACTTAAGGT * * 25573805 CCGCAGGCTATGTGCTGGAATTATAACCAGACTTAAGGT 1 CCGCAGGCTATATGCTGGAATTATAACCGGACTTAAGGT 25573844 CCGCAGGCTA 1 CCGCAGGCTA 25573854 CGCGCTGGAA Statistics Matches: 79, Mismatches: 9, Indels: 1 0.89 0.10 0.01 Matches are distributed among these distances: 39 48 0.61 40 31 0.39 ACGTcount: A:0.27, C:0.23, G:0.26, T:0.25 Consensus pattern (39 bp): CCGCAGGCTATATGCTGGAATTATAACCGGACTTAAGGT Found at i:25573861 original size:39 final size:39 Alignment explanation
Indices: 25573779--25573863 Score: 134 Period size: 39 Copynumber: 2.2 Consensus size: 39 25573769 TAGGCTATAT * * * * 25573779 GCTGGAATTATACCCGGACTTAAGGTCCGCAGGCTATGT 1 GCTGGAATTATAACCAGACTTAAGGTCCGCAGGCTACGC 25573818 GCTGGAATTATAACCAGACTTAAGGTCCGCAGGCTACGC 1 GCTGGAATTATAACCAGACTTAAGGTCCGCAGGCTACGC 25573857 GCTGGAA 1 GCTGGAA 25573864 ATATGTCCGG Statistics Matches: 42, Mismatches: 4, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 39 42 1.00 ACGTcount: A:0.26, C:0.24, G:0.28, T:0.22 Consensus pattern (39 bp): GCTGGAATTATAACCAGACTTAAGGTCCGCAGGCTACGC Found at i:25576323 original size:23 final size:21 Alignment explanation
Indices: 25576251--25576325 Score: 69 Period size: 21 Copynumber: 3.5 Consensus size: 21 25576241 CCTGATCAGT ** * 25576251 ATACGACACATAAAGTGCCTA 1 ATACGACACACGAGGTGCCTA * ** * 25576272 AAACGGTACACGAGGTGCCTG 1 ATACGACACACGAGGTGCCTA 25576293 ATACGACACACGAGGTGCCTAAA 1 ATACGACACACGAGGTGCCT--A 25576316 ATACGACACA 1 ATACGACACA 25576326 TAAAGTGCCT Statistics Matches: 41, Mismatches: 11, Indels: 2 0.76 0.20 0.04 Matches are distributed among these distances: 21 31 0.76 23 10 0.24 ACGTcount: A:0.39, C:0.25, G:0.21, T:0.15 Consensus pattern (21 bp): ATACGACACACGAGGTGCCTA Found at i:25576650 original size:15 final size:15 Alignment explanation
Indices: 25576625--25576682 Score: 89 Period size: 15 Copynumber: 3.8 Consensus size: 15 25576615 TCATATATAT 25576625 TATATAATTCAATCAA 1 TATA-AATTCAATCAA 25576641 TATAAATTCAATCAA 1 TATAAATTCAATCAA * * 25576656 AATAATTTCAATCAA 1 TATAAATTCAATCAA 25576671 TATAAATTCAAT 1 TATAAATTCAAT 25576683 AAATTCATCG Statistics Matches: 38, Mismatches: 4, Indels: 1 0.88 0.09 0.02 Matches are distributed among these distances: 15 34 0.89 16 4 0.11 ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36 Consensus pattern (15 bp): TATAAATTCAATCAA Found at i:25577042 original size:8 final size:8 Alignment explanation
Indices: 25577029--25577067 Score: 51 Period size: 8 Copynumber: 4.8 Consensus size: 8 25577019 TATCTTTATT 25577029 ATATAATA 1 ATATAATA 25577037 ATATAATA 1 ATATAATA 25577045 ATATAATA 1 ATATAATA * * 25577053 ACATACTAA 1 ATATAAT-A 25577062 ATATAA 1 ATATAA 25577068 AAAAAAATCT Statistics Matches: 26, Mismatches: 4, Indels: 1 0.84 0.13 0.03 Matches are distributed among these distances: 8 21 0.81 9 5 0.19 ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33 Consensus pattern (8 bp): ATATAATA Found at i:25582459 original size:24 final size:25 Alignment explanation
Indices: 25582430--25582479 Score: 93 Period size: 24 Copynumber: 2.0 Consensus size: 25 25582420 TAAATTGTGT 25582430 TAGGTTTTTTTTTT-AAATTCTAGC 1 TAGGTTTTTTTTTTAAAATTCTAGC 25582454 TAGGTTTTTTTTTTAAAATTCTAGC 1 TAGGTTTTTTTTTTAAAATTCTAGC 25582479 T 1 T 25582480 TGTTTTAGGT Statistics Matches: 25, Mismatches: 0, Indels: 1 0.96 0.00 0.04 Matches are distributed among these distances: 24 14 0.56 25 11 0.44 ACGTcount: A:0.22, C:0.08, G:0.12, T:0.58 Consensus pattern (25 bp): TAGGTTTTTTTTTTAAAATTCTAGC Found at i:25583903 original size:40 final size:39 Alignment explanation
Indices: 25583848--25583980 Score: 176 Period size: 40 Copynumber: 3.4 Consensus size: 39 25583838 ATTTGATGTG * * 25583848 TATCCGGGCTTAAAGACCCGCAGGCTATATGCTGGAATTA 1 TATCCGGACTT-AAGACCCACAGGCTATATGCTGGAATTA * 25583888 TATCCGGGCTTAAAGACCCACAGGCTATATGCTGGAATTA 1 TATCCGGACTT-AAGACCCACAGGCTATATGCTGGAATTA * ** * 25583928 TACCCGGACTTAAGGTCCACAGGCTATGTGCTGGAATTA 1 TATCCGGACTTAAGACCCACAGGCTATATGCTGGAATTA * 25583967 TAACCGGACTTAAG 1 TATCCGGACTTAAG 25583981 GTCCGCAGGC Statistics Matches: 86, Mismatches: 7, Indels: 1 0.91 0.07 0.01 Matches are distributed among these distances: 39 38 0.44 40 48 0.56 ACGTcount: A:0.29, C:0.23, G:0.24, T:0.25 Consensus pattern (39 bp): TATCCGGACTTAAGACCCACAGGCTATATGCTGGAATTA Found at i:25583960 original size:39 final size:39 Alignment explanation
Indices: 25583868--25583992 Score: 178 Period size: 39 Copynumber: 3.2 Consensus size: 39 25583858 TAAAGACCCG * * ** 25583868 CAGGCTATATGCTGGAATTATATCCGGGCTTAAAGACCCA 1 CAGGCTATATGCTGGAATTATAACCGGACTT-AAGGTCCA * 25583908 CAGGCTATATGCTGGAATTATACCCGGACTTAAGGTCCA 1 CAGGCTATATGCTGGAATTATAACCGGACTTAAGGTCCA * * 25583947 CAGGCTATGTGCTGGAATTATAACCGGACTTAAGGTCCG 1 CAGGCTATATGCTGGAATTATAACCGGACTTAAGGTCCA 25583986 CAGGCTA 1 CAGGCTA 25583993 CGCGCTGGAA Statistics Matches: 78, Mismatches: 7, Indels: 1 0.91 0.08 0.01 Matches are distributed among these distances: 39 49 0.63 40 29 0.37 ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25 Consensus pattern (39 bp): CAGGCTATATGCTGGAATTATAACCGGACTTAAGGTCCA Found at i:25585553 original size:18 final size:18 Alignment explanation
Indices: 25585516--25585553 Score: 51 Period size: 18 Copynumber: 2.1 Consensus size: 18 25585506 GTTCACCTCT * 25585516 TTTCTTAGTATTTATTAG 1 TTTCTTAGTATTTATGAG 25585534 TTTC-TAGTATTATATGAG 1 TTTCTTAGTATT-TATGAG 25585552 TT 1 TT 25585554 GTGGGTGATT Statistics Matches: 18, Mismatches: 1, Indels: 2 0.86 0.05 0.10 Matches are distributed among these distances: 17 7 0.39 18 11 0.61 ACGTcount: A:0.24, C:0.05, G:0.13, T:0.58 Consensus pattern (18 bp): TTTCTTAGTATTTATGAG Found at i:25586226 original size:6 final size:6 Alignment explanation
Indices: 25586203--25586240 Score: 60 Period size: 6 Copynumber: 6.3 Consensus size: 6 25586193 TTTTTAACTA 25586203 ATAATT ATAAATT A-AATT ATAATT ATAATT ATAATT AT 1 ATAATT AT-AATT ATAATT ATAATT ATAATT ATAATT AT 25586241 CACAATTTTT Statistics Matches: 30, Mismatches: 0, Indels: 4 0.88 0.00 0.12 Matches are distributed among these distances: 5 5 0.17 6 20 0.67 7 5 0.17 ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47 Consensus pattern (6 bp): ATAATT Found at i:25590190 original size:18 final size:19 Alignment explanation
Indices: 25590154--25590192 Score: 55 Period size: 18 Copynumber: 2.1 Consensus size: 19 25590144 ACTAAATAAT 25590154 AAAATATAATAATTATTTA 1 AAAATATAATAATTATTTA 25590173 AAAATAT-AT-ATTACTTTA 1 AAAATATAATAATTA-TTTA 25590191 AA 1 AA 25590193 TTTTAAAATA Statistics Matches: 19, Mismatches: 0, Indels: 3 0.86 0.00 0.14 Matches are distributed among these distances: 17 4 0.21 18 8 0.42 19 7 0.37 ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41 Consensus pattern (19 bp): AAAATATAATAATTATTTA Found at i:25591301 original size:28 final size:28 Alignment explanation
Indices: 25591261--25591318 Score: 98 Period size: 28 Copynumber: 2.1 Consensus size: 28 25591251 GTTTTGAGTA * 25591261 TAAGTTTCCCTATTCATTCTATTATTAT 1 TAAGTTTCCCTATTCATTCTATTATCAT * 25591289 TAAGTTTCCCTATTCGTTCTATTATCAT 1 TAAGTTTCCCTATTCATTCTATTATCAT 25591317 TA 1 TA 25591319 TGAAATTTAT Statistics Matches: 28, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 28 28 1.00 ACGTcount: A:0.24, C:0.19, G:0.05, T:0.52 Consensus pattern (28 bp): TAAGTTTCCCTATTCATTCTATTATCAT Found at i:25597003 original size:25 final size:24 Alignment explanation
Indices: 25596981--25597027 Score: 67 Period size: 24 Copynumber: 1.9 Consensus size: 24 25596971 TCGAAAAATG 25596981 AAAAAAAAATACATGCTACAAAAGC 1 AAAAAAAAAT-CATGCTACAAAAGC * * 25597006 AAACAAAAATCGTGCTACAAAA 1 AAAAAAAAATCATGCTACAAAA 25597028 ATAGACCAAA Statistics Matches: 20, Mismatches: 2, Indels: 1 0.87 0.09 0.04 Matches are distributed among these distances: 24 11 0.55 25 9 0.45 ACGTcount: A:0.62, C:0.17, G:0.09, T:0.13 Consensus pattern (24 bp): AAAAAAAAATCATGCTACAAAAGC Found at i:25598377 original size:24 final size:28 Alignment explanation
Indices: 25598317--25598375 Score: 84 Period size: 28 Copynumber: 2.1 Consensus size: 28 25598307 TGTCATAATG * 25598317 ATATATACACATATGGTATTAAGAATAT 1 ATATATACACATATAGTATTAAGAATAT * 25598345 ATATATACA-ATATAGTATTTAAAAATAT 1 ATATATACACATATAGTA-TTAAGAATAT 25598373 ATA 1 ATA 25598376 CATAAGATGG Statistics Matches: 28, Mismatches: 2, Indels: 2 0.88 0.06 0.06 Matches are distributed among these distances: 27 7 0.25 28 21 0.75 ACGTcount: A:0.51, C:0.05, G:0.07, T:0.37 Consensus pattern (28 bp): ATATATACACATATAGTATTAAGAATAT Found at i:25599172 original size:3 final size:3 Alignment explanation
Indices: 25599166--25599209 Score: 61 Period size: 3 Copynumber: 14.7 Consensus size: 3 25599156 AAACATAAGC * * * 25599166 TAA TAA TGA TAA TAA TAA TAA TAA TAA TAG TAA TAA TAC TAA TA 1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA 25599210 TTATAAAAAT Statistics Matches: 35, Mismatches: 6, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 3 35 1.00 ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34 Consensus pattern (3 bp): TAA Found at i:25599859 original size:13 final size:13 Alignment explanation
Indices: 25599812--25599863 Score: 52 Period size: 13 Copynumber: 3.8 Consensus size: 13 25599802 AAAAAGGTAA 25599812 ATTTTTTT-TTAAT 1 ATTTTTTTATT-AT * 25599825 ATTTGTTTTGTATAT 1 ATTT-TTTTAT-TAT * 25599840 ATATTTTTATTAT 1 ATTTTTTTATTAT 25599853 ATTTTTTTATT 1 ATTTTTTTATT 25599864 TATGATGTAT Statistics Matches: 33, Mismatches: 3, Indels: 6 0.79 0.07 0.14 Matches are distributed among these distances: 13 17 0.52 14 9 0.27 15 6 0.18 16 1 0.03 ACGTcount: A:0.23, C:0.00, G:0.04, T:0.73 Consensus pattern (13 bp): ATTTTTTTATTAT Done.