Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 10 of 322
Found at i:2517320 original size:16 final size:16
Alignment explanation
Indices: 2517299--2517332 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2517289 TCACTAACAG
* *
2517299 TCTTCAAGTCCCTAAA
1 TCTTCAAATACCTAAA
2517315 TCTTCAAATACCTAAA
1 TCTTCAAATACCTAAA
2517331 TC
1 TC
2517333 GATAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.32
Consensus pattern (16 bp):
TCTTCAAATACCTAAA
Found at i:2517709 original size:117 final size:117
Alignment explanation
Indices: 2517501--2517711 Score: 287
Period size: 117 Copynumber: 1.8 Consensus size: 117
2517491 TTTGATTAGT
* * *
2517501 TGGTTATTTGTGATTTACTATTGCAATTTGAGTACAAAAATGTAGGGTTTGTTTTGTCGATTTTT
1 TGGTTAATTGTGATTTACTATTGCAATTTCAGTACAAAAATGTAGGGTTTGTTTTGTCGATTTGT
* *** * *
2517566 GATGCGATGGTGGTCCTAATGTTGTTGATAAAATTGTTGTAAAAATTGTAGA
66 GATGAGACAATGGTCCCAATGATGTTGATAAAATTGTTGTAAAAATTGTAGA
* * * * *
2517618 TGGTTAATTGTGATTTATTATTGCAATTTCAGTGCTAGAATGTGGGGTTTGTTTTGTCGATTTGT
1 TGGTTAATTGTGATTTACTATTGCAATTTCAGTACAAAAATGTAGGGTTTGTTTTGTCGATTTGT
*
2517683 GATGAGACAATGGTCCCGATGATGTTGAT
66 GATGAGACAATGGTCCCAATGATGTTGAT
2517712 TTCTGTTACC
Statistics
Matches: 79, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
117 79 1.00
ACGTcount: A:0.24, C:0.07, G:0.26, T:0.43
Consensus pattern (117 bp):
TGGTTAATTGTGATTTACTATTGCAATTTCAGTACAAAAATGTAGGGTTTGTTTTGTCGATTTGT
GATGAGACAATGGTCCCAATGATGTTGATAAAATTGTTGTAAAAATTGTAGA
Found at i:2518642 original size:51 final size:51
Alignment explanation
Indices: 2518573--2518725 Score: 225
Period size: 51 Copynumber: 3.0 Consensus size: 51
2518563 GTTGCTGGTA
* *
2518573 ATAAATATGCTAGTGATTTTACAACATCAGATGGAGTGGATAATGTTGCTG
1 ATAAATATGCTGGTGATTTTGCAACATCAGATGGAGTGGATAATGTTGCTG
* * * *
2518624 ATAAATATGTTGGTGATTTTGCAACATCAGATAGAGTGGATAATATTGCTA
1 ATAAATATGCTGGTGATTTTGCAACATCAGATGGAGTGGATAATGTTGCTG
* * *
2518675 ATAAATATGCTGGTGACTTTGCAACATCAGATGGACTAGATAATGTTGCTG
1 ATAAATATGCTGGTGATTTTGCAACATCAGATGGAGTGGATAATGTTGCTG
2518726 CTACACATAG
Statistics
Matches: 89, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 89 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (51 bp):
ATAAATATGCTGGTGATTTTGCAACATCAGATGGAGTGGATAATGTTGCTG
Found at i:2521526 original size:22 final size:22
Alignment explanation
Indices: 2521500--2521544 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
2521490 TCATATGCTT
*
2521500 TTGTAAAGAACATTTATCGAAA
1 TTGTAAAGAACATTTATCCAAA
*
2521522 TTGTAAAGTACATTTATCCAAA
1 TTGTAAAGAACATTTATCCAAA
2521544 T
1 T
2521545 GATCAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (22 bp):
TTGTAAAGAACATTTATCCAAA
Found at i:2522541 original size:32 final size:32
Alignment explanation
Indices: 2522505--2522578 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 32
2522495 TTTGGTTCTA
* *
2522505 AGGGATTTCACGATTTCG-TTCCTAATAGTTTT
1 AGGGATTTCACGATTT-GATTCCTAAAAATTTT
*
2522537 AGGGA-TTCAACGATTTGATTCGTAAAAATTTT
1 AGGGATTTC-ACGATTTGATTCCTAAAAATTTT
2522569 AGGGATTTCA
1 AGGGATTTCA
2522579 AGAAGATTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
31 4 0.11
32 29 0.81
33 3 0.08
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.39
Consensus pattern (32 bp):
AGGGATTTCACGATTTGATTCCTAAAAATTTT
Found at i:2522643 original size:18 final size:16
Alignment explanation
Indices: 2522600--2522635 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2522590 GAATGCTATC
* *
2522600 GATTTAGGTATTTGAA
1 GATTTAGGGACTTGAA
2522616 GATTTAGGGACTTGAA
1 GATTTAGGGACTTGAA
2522632 GATT
1 GATT
2522636 GTTAGGGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.03, G:0.28, T:0.39
Consensus pattern (16 bp):
GATTTAGGGACTTGAA
Found at i:2536669 original size:21 final size:20
Alignment explanation
Indices: 2536639--2536686 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
2536629 TTAAGAATTA
* *
2536639 TTTTAGTATTATTTTTATTT
1 TTTTAATATTATTTTTATGT
*
2536659 GTTTTAATATTTGTTTTTATGT
1 -TTTTAATA-TTATTTTTATGT
2536681 TTTTAA
1 TTTTAA
2536687 ATATATTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.71
Consensus pattern (20 bp):
TTTTAATATTATTTTTATGT
Found at i:2543925 original size:16 final size:16
Alignment explanation
Indices: 2543888--2543931 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
2543878 TTCATTTTTC
* *
2543888 TTAATTTTTTTA-TCT
1 TTAACTTTTTTATTAT
*
2543903 TTCACTTTTTTATTAT
1 TTAACTTTTTTATTAT
2543919 TTAACTTTTTTAT
1 TTAACTTTTTTAT
2543932 AAAAGTTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.70
Consensus pattern (16 bp):
TTAACTTTTTTATTAT
Found at i:2546475 original size:7 final size:7
Alignment explanation
Indices: 2546463--2546487 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2546453 AAAATACAAT
2546463 TTTATTA
1 TTTATTA
2546470 TTTATTA
1 TTTATTA
2546477 TTTATTA
1 TTTATTA
2546484 TTTA
1 TTTA
2546488 CGAATGGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTATTA
Found at i:2547211 original size:28 final size:28
Alignment explanation
Indices: 2547171--2547233 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
2547161 GTCATTATCA
2547171 ACCCCATAAGTTATAAAACTTTTCCTAT
1 ACCCCATAAGTTATAAAACTTTTCCTAT
* * *
2547199 ACCCCATAAGTTATGAGACTTTTCCTGT
1 ACCCCATAAGTTATAAAACTTTTCCTAT
2547227 ACCCCAT
1 ACCCCAT
2547234 TAATATGGGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (28 bp):
ACCCCATAAGTTATAAAACTTTTCCTAT
Found at i:2551634 original size:27 final size:27
Alignment explanation
Indices: 2551603--2551655 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
2551593 AATAAGAAAC
*
2551603 GTAAATAACTAAGTAATGAGGAAATAA
1 GTAAATAACTAAGTAATGAGAAAATAA
2551630 GTAAATAACTAAGTAATGAGAAAATA
1 GTAAATAACTAAGTAATGAGAAAATA
2551656 TGTACAGTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.57, C:0.04, G:0.17, T:0.23
Consensus pattern (27 bp):
GTAAATAACTAAGTAATGAGAAAATAA
Found at i:2551972 original size:45 final size:45
Alignment explanation
Indices: 2551908--2552079 Score: 263
Period size: 45 Copynumber: 3.8 Consensus size: 45
2551898 TTATTTATAG
* * *
2551908 CTTCAATCTGTTCTACTGCAACTTCAGGGGAATAAGATTTGCTAT
1 CTTCAGTCTGCTCTACTGCAACTTCAGGGAAATAAGATTTGCTAT
2551953 CTTCAGTCTGCTCTACTGCAACTTCAGGGAAATAAGATTTGCTAT
1 CTTCAGTCTGCTCTACTGCAACTTCAGGGAAATAAGATTTGCTAT
* * *
2551998 CTTCAGTCTGCTCGACTGTAACTTTAGGGAAATAAGATTTGCTAT
1 CTTCAGTCTGCTCTACTGCAACTTCAGGGAAATAAGATTTGCTAT
* * *
2552043 CTTCAGTCTGCTCCACTACAACTTCAGGGAGATAAGA
1 CTTCAGTCTGCTCTACTGCAACTTCAGGGAAATAAGA
2552080 CATGTGACTT
Statistics
Matches: 116, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 116 1.00
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.33
Consensus pattern (45 bp):
CTTCAGTCTGCTCTACTGCAACTTCAGGGAAATAAGATTTGCTAT
Found at i:2552330 original size:43 final size:43
Alignment explanation
Indices: 2552180--2552381 Score: 163
Period size: 43 Copynumber: 4.6 Consensus size: 43
2552170 TAGCTTCGAT
* * * * *
2552180 CTGTTTCCCTACTGCTTAGGGTGATGAGATCTGCAAATCTTCAAC
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAA--TTCAAC
* * * ** ** *
2552225 CTATTACCTTACTGCTTAGGGGGTTAAG-GCTTGTCACCTTTGAT
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATC-TGT-AAATTCAAC
* *
2552269 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAGATTCAAC
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAAC
* * *
2552312 CTGTTACCCTACTGCTTAGGGGTTTAAGGTCTGTAAATTCAGC
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAAC
* ** *
2552355 TTACTACCCTACTACTTAGGGGGTTAA
1 CTGTTACCCTACTGCTTAGGGGGTTAA
2552382 AGCCCATCAC
Statistics
Matches: 122, Mismatches: 32, Indels: 8
0.75 0.20 0.05
Matches are distributed among these distances:
43 64 0.52
44 32 0.26
45 25 0.20
46 1 0.01
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.35
Consensus pattern (43 bp):
CTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAAC
Found at i:2552339 original size:87 final size:88
Alignment explanation
Indices: 2552177--2552340 Score: 240
Period size: 89 Copynumber: 1.9 Consensus size: 88
2552167 TCATAGCTTC
* * *
2552177 GATCTGTTTCCCTACTGCTTAGGGTGATGAGATCTGCAAATCTTCAACCTATTACCTTACTGCTT
1 GATCTGTTTCCCTACTGCTTAGGGGGATAAGATCTGCAAA-CTTCAACCTATTACCCTACTGCTT
2552242 AGGGGGTTAAGGCTTGTCACCTTT
65 AGGGGGTTAAGGCTTGTCACCTTT
* * * *
2552266 GATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAGA-TTCAACCTGTTACCCTACTGCTTA
1 GATCTGTTTCCCTACTGCTTAGGGGGATAAGATCTGCAAACTTCAACCTATTACCCTACTGCTTA
*
2552330 GGGGTTTAAGG
66 GGGGGTTAAGG
2552341 TCTGTAAATT
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
87 32 0.48
89 35 0.52
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.35
Consensus pattern (88 bp):
GATCTGTTTCCCTACTGCTTAGGGGGATAAGATCTGCAAACTTCAACCTATTACCCTACTGCTTA
GGGGGTTAAGGCTTGTCACCTTT
Found at i:2565113 original size:26 final size:27
Alignment explanation
Indices: 2565077--2565141 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
2565067 TATGTACACA
2565077 ATATATATAATATAT-TAAAAATATAC
1 ATATATATAATATATATAAAAATATAC
* *
2565103 ATATATATAATATTTATAAAAATATAT
1 ATATATATAATATATATAAAAATATAC
2565130 ATATAGTATAAT
1 ATATA-TATAAT
2565142 GTTAATATGT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
26 14 0.40
27 15 0.43
28 6 0.17
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (27 bp):
ATATATATAATATATATAAAAATATAC
Found at i:2566512 original size:28 final size:28
Alignment explanation
Indices: 2566473--2566544 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 28
2566463 AAAATTTTTT
* * *
2566473 TAGG-TTTGGGCTTTGTGGGTTAGAAGA
1 TAGGTTTTGGGCTTAGGGGGTTAGAAAA
2566500 TAGGTTTTGGGC-TAGGGGGTTAGAAAA
1 TAGGTTTTGGGCTTAGGGGGTTAGAAAA
*
2566527 TGGGTTTTGGGC-TAGGGG
1 TAGGTTTTGGGCTTAGGGG
2566545 CCAAATGGGC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
27 33 0.82
28 7 0.17
ACGTcount: A:0.18, C:0.04, G:0.44, T:0.33
Consensus pattern (28 bp):
TAGGTTTTGGGCTTAGGGGGTTAGAAAA
Found at i:2566519 original size:27 final size:27
Alignment explanation
Indices: 2566489--2566544 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
2566479 TGGGCTTTGT
*
2566489 GGGTTAGAAGATAGGTTTTGGGCTAGG
1 GGGTTAGAAAATAGGTTTTGGGCTAGG
*
2566516 GGGTTAGAAAATGGGTTTTGGGCTAGG
1 GGGTTAGAAAATAGGTTTTGGGCTAGG
2566543 GG
1 GG
2566545 CCAAATGGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.21, C:0.04, G:0.46, T:0.29
Consensus pattern (27 bp):
GGGTTAGAAAATAGGTTTTGGGCTAGG
Found at i:2568086 original size:28 final size:28
Alignment explanation
Indices: 2568046--2568108 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
2568036 GTCATTATCG
2568046 ACCCCATAAGTTATAAAACTCTTCCTAT
1 ACCCCATAAGTTATAAAACTCTTCCTAT
* * *
2568074 ACCCCATAAGTTATGAGACTTTTCCTAT
1 ACCCCATAAGTTATAAAACTCTTCCTAT
2568102 ACCCCAT
1 ACCCCAT
2568109 TAATATGGGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.32, C:0.30, G:0.06, T:0.32
Consensus pattern (28 bp):
ACCCCATAAGTTATAAAACTCTTCCTAT
Found at i:2568525 original size:20 final size:20
Alignment explanation
Indices: 2568502--2568570 Score: 61
Period size: 20 Copynumber: 3.3 Consensus size: 20
2568492 CAAAAATTAC
2568502 AAAAAAATCAAAATAATTTT
1 AAAAAAATCAAAATAATTTT
* *
2568522 AAAAAATTAAAAAT-A-TTT
1 AAAAAAATCAAAATAATTTT
2568540 ATAAAAAATCCAAAATTTATATTTT
1 A-AAAAAAT-CAAAA--TA-ATTTT
2568565 AAAAAA
1 AAAAAA
2568571 GTTAAAAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
18 4 0.11
19 7 0.18
20 16 0.42
22 1 0.03
24 6 0.16
25 4 0.11
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (20 bp):
AAAAAAATCAAAATAATTTT
Found at i:2568527 original size:19 final size:20
Alignment explanation
Indices: 2568503--2568584 Score: 80
Period size: 19 Copynumber: 4.0 Consensus size: 20
2568493 AAAAATTACA
2568503 AAAAAATCAAAATA-ATTTT
1 AAAAAATCAAAATATATTTT
*
2568522 AAAAAATTAAAA-ATATTTAT
1 AAAAAATCAAAATATATTT-T
2568542 AAAAAATCCAAAATTTATATTTT
1 AAAAAAT-CAAAA--TATATTTT
*
2568565 AAAAAAGTTAAAA-ATATTTT
1 AAAAAA-TCAAAATATATTTT
2568585 TAAGGAATAT
Statistics
Matches: 53, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
18 1 0.02
19 15 0.28
20 15 0.28
21 4 0.08
23 11 0.21
24 7 0.13
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.35
Consensus pattern (20 bp):
AAAAAATCAAAATATATTTT
Found at i:2568578 original size:44 final size:39
Alignment explanation
Indices: 2568503--2568583 Score: 117
Period size: 44 Copynumber: 1.9 Consensus size: 39
2568493 AAAAATTACA
2568503 AAAAAATCAAAATAATTTTAAAAAATTAAAAATATTTAT
1 AAAAAATCAAAATAATTTTAAAAAATTAAAAATATTTAT
2568542 AAAAAATCCAAAATTTATATTTTAAAAAAGTTAAAAATATTT
1 AAAAAAT-CAAAA--TA-ATTTTAAAAAA-TTAAAAATATTT
2568584 TTAAGGAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
39 7 0.19
40 5 0.14
42 2 0.05
43 11 0.30
44 12 0.32
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.35
Consensus pattern (39 bp):
AAAAAATCAAAATAATTTTAAAAAATTAAAAATATTTAT
Found at i:2568583 original size:20 final size:19
Alignment explanation
Indices: 2568511--2568584 Score: 76
Period size: 20 Copynumber: 3.5 Consensus size: 19
2568501 CAAAAAAATC
2568511 AAAATAATTTTAAAAAATTA
1 AAAAT-ATTTTAAAAAATTA
*
2568531 AAAATATTTATAAAAAATCCA
1 AAAATATTT-TAAAAAAT-TA
2568552 AAATTTATATTTTAAAAAAGTTA
1 AAA---ATATTTTAAAAAA-TTA
2568575 AAAATATTTT
1 AAAATATTTT
2568585 TAAGGAATAT
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
19 4 0.09
20 20 0.43
21 4 0.09
23 11 0.24
24 7 0.15
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (19 bp):
AAAATATTTTAAAAAATTA
Found at i:2569027 original size:15 final size:16
Alignment explanation
Indices: 2569007--2569046 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
2568997 TTTCTTTATT
*
2569007 TTTTTTATT-TTTCAC
1 TTTTTTATTATTTAAC
2569022 TTTTTTATTATTTAAC
1 TTTTTTATTATTTAAC
2569038 TTTATTTAT
1 TTT-TTTAT
2569047 AAAAATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.41
16 8 0.36
17 5 0.23
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTTTATTATTTAAC
Found at i:2572418 original size:21 final size:21
Alignment explanation
Indices: 2572392--2572454 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
2572382 TATTTAATAT
2572392 TATTATATTTACCATTATTCA
1 TATTATATTTACCATTATTCA
2572413 TA-T-TA--T--CATTATT-A
1 TATTATATTTACCATTATTCA
*
2572427 TTATTATATTGACCATTATTCA
1 -TATTATATTTACCATTATTCA
2572449 TATTAT
1 TATTAT
2572455 CATTATTATT
Statistics
Matches: 33, Mismatches: 1, Indels: 16
0.66 0.02 0.32
Matches are distributed among these distances:
14 1 0.03
15 9 0.27
16 1 0.03
17 3 0.09
19 2 0.06
20 1 0.03
21 15 0.45
22 1 0.03
ACGTcount: A:0.33, C:0.11, G:0.02, T:0.54
Consensus pattern (21 bp):
TATTATATTTACCATTATTCA
Found at i:2572428 original size:3 final size:3
Alignment explanation
Indices: 2572413--2572525 Score: 63
Period size: 3 Copynumber: 37.0 Consensus size: 3
2572403 CCATTATTCA
* * * *
2572413 TAT TAT CAT TAT TAT TAT TA- TAT TGAC CAT TAT TCA- TAT TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT T-AT TAT TAT TAT
* * * *
2572458 TAT TAT TAA CA- TAT TAT TAT TTT TAAT GTAT TAT TAT TAC TAGT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT T-AT -TAT TAT TAT TAT TA-T TAT
*
2572505 TAT TAT T-T CTAG TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT
2572526 ATATAATATT
Statistics
Matches: 83, Mismatches: 17, Indels: 20
0.69 0.14 0.17
Matches are distributed among these distances:
2 5 0.06
3 70 0.84
4 7 0.08
5 1 0.01
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:2572433 original size:36 final size:36
Alignment explanation
Indices: 2572389--2572465 Score: 145
Period size: 36 Copynumber: 2.1 Consensus size: 36
2572379 TATTATTTAA
*
2572389 TATTATTATATTTACCATTATTCATATTATCATTAT
1 TATTATTATATTGACCATTATTCATATTATCATTAT
2572425 TATTATTATATTGACCATTATTCATATTATCATTAT
1 TATTATTATATTGACCATTATTCATATTATCATTAT
2572461 TATTA
1 TATTA
2572466 ACATATTATT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.34, C:0.10, G:0.01, T:0.55
Consensus pattern (36 bp):
TATTATTATATTGACCATTATTCATATTATCATTAT
Found at i:2572478 original size:17 final size:17
Alignment explanation
Indices: 2572456--2572496 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
2572446 TCATATTATC
2572456 ATTATTATTAACATATT
1 ATTATTATTAACATATT
* **
2572473 ATTATTTTTAATGTATT
1 ATTATTATTAACATATT
2572490 ATTATTA
1 ATTATTA
2572497 CTAGTTATTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (17 bp):
ATTATTATTAACATATT
Found at i:2572494 original size:31 final size:31
Alignment explanation
Indices: 2572456--2572525 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
2572446 TCATATTATC
2572456 ATTATTATTAACATA-TTATTATT-TTTA-ATGT
1 ATTATTATT-AC-TAGTTATTATTATTTATA-GT
*
2572487 ATTATTATTACTAGTTATTATTATTTCTAGT
1 ATTATTATTACTAGTTATTATTATTTATAGT
2572518 ATTATTAT
1 ATTATTAT
2572526 ATATAATATT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
29 2 0.06
30 10 0.29
31 22 0.63
32 1 0.03
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (31 bp):
ATTATTATTACTAGTTATTATTATTTATAGT
Found at i:2572941 original size:17 final size:17
Alignment explanation
Indices: 2572919--2572976 Score: 73
Period size: 17 Copynumber: 3.4 Consensus size: 17
2572909 GAAAAATGAG
2572919 AATTTTTAAAACACGAA
1 AATTTTTAAAACACGAA
* *
2572936 AATTTTGAAAGCACGAA
1 AATTTTTAAAACACGAA
*
2572953 AATTTTTGAAAC-CTGAA
1 AATTTTTAAAACAC-GAA
2572970 AATTTTT
1 AATTTTT
2572977 TTTTAGAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
16 1 0.03
17 34 0.97
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.34
Consensus pattern (17 bp):
AATTTTTAAAACACGAA
Found at i:2584827 original size:12 final size:11
Alignment explanation
Indices: 2584810--2584863 Score: 54
Period size: 12 Copynumber: 4.6 Consensus size: 11
2584800 TTCTGTTTTT
2584810 TTATATTTATTA
1 TTATA-TTATTA
2584822 TTATATTATTA
1 TTATATTATTA
* *
2584833 TTACAATTATTC
1 TTA-TATTATTA
2584845 TTATCATTATTA
1 TTAT-ATTATTA
*
2584857 GTATATT
1 TTATATT
2584864 CCTACGATAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
11 12 0.34
12 23 0.66
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.59
Consensus pattern (11 bp):
TTATATTATTA
Found at i:2586666 original size:21 final size:21
Alignment explanation
Indices: 2586641--2586681 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2586631 GTCGCTATAA
* *
2586641 TATTAATATTATTACTATATT
1 TATTAATATTAATAATATATT
*
2586662 TATTATTATTAATAATATAT
1 TATTAATATTAATAATATAT
2586682 ATTTTTTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
TATTAATATTAATAATATATT
Found at i:2586973 original size:27 final size:26
Alignment explanation
Indices: 2586942--2587015 Score: 78
Period size: 27 Copynumber: 2.7 Consensus size: 26
2586932 TTTTTAATAC
2586942 TATATTTTTAATACCATATATATTG-TG
1 TATATTTTTAATA--ATATATATTGATG
* *
2586969 TATATTCTTAATATTATATATTGTATG
1 TATATTTTTAATAATATATATTG-ATG
*
2586996 TATTTTTTTAATAACTATAT
1 TATATTTTTAATAA-TATAT
2587016 TATATGTATA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
25 9 0.23
27 25 0.64
28 5 0.13
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.55
Consensus pattern (26 bp):
TATATTTTTAATAATATATATTGATG
Found at i:2587057 original size:23 final size:21
Alignment explanation
Indices: 2587023--2587217 Score: 78
Period size: 23 Copynumber: 8.7 Consensus size: 21
2587013 TATTATATGT
2587023 ATATATATTATGTACATATTTTTA
1 ATAT-TATTATGT--ATATTTTTA
*
2587047 ATATTATTATGTATTTTTTTA
1 ATATTATTATGTATATTTTTA
*
2587068 ATATATATATGTGTATATTTATGTA
1 ATAT-TAT-TATGTATATTT-T-TA
*
2587093 ATATTATTAATAGT-TGTTTTTTA
1 ATATTATT-AT-GTAT-ATTTTTA
* *
2587116 ACATTATTA--T-TATTTCTA
1 ATATTATTATGTATATTTTTA
* *
2587134 ATATGTA-TATATATA-TTTCA
1 ATAT-TATTATGTATATTTTTA
*
2587154 ATAACTAAATTATGTATGTATTTTTA
1 AT-A-T-TATTATGTA--TATTTTTA
* * *
2587180 ATACTATTTTATGTACATACTTTA
1 ATA-T-TATTATGTATAT-TTTTA
2587204 ATATTATTATGTAT
1 ATATTATTATGTAT
2587218 TTTATTATAA
Statistics
Matches: 132, Mismatches: 21, Indels: 38
0.69 0.11 0.20
Matches are distributed among these distances:
18 10 0.08
19 4 0.03
20 6 0.05
21 15 0.11
22 14 0.11
23 35 0.27
24 18 0.14
25 24 0.18
26 6 0.05
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.55
Consensus pattern (21 bp):
ATATTATTATGTATATTTTTA
Found at i:2587097 original size:55 final size:56
Alignment explanation
Indices: 2586957--2587109 Score: 149
Period size: 55 Copynumber: 2.7 Consensus size: 56
2586947 TTTTAATACC
* *
2586957 ATATATAT-TGTGTATA-TTCT-TAATA-TTAT-ATATTGTATGTATTTTTTTAATA
1 ATATATATATGTGTATATTTATGTAATATTTTTAATATTGTATGTATTTTTTT-ATA
* *
2587009 ACTATATTATATGTATATATATTATGTACATATTTTTAATATTATTATGTA-TTTTTT-TA
1 A-TATA-TATATGTGTATAT-TTATGTA-ATATTTTTAATATT-GTATGTATTTTTTTATA
*
2587068 ATATATATATGTGTATATTTATGTAATATTATTAATAGTTGT
1 ATATATATATGTGTATATTTATGTAATATTTTTAATA-TTGT
2587110 TTTTTAACAT
Statistics
Matches: 83, Mismatches: 7, Indels: 19
0.76 0.06 0.17
Matches are distributed among these distances:
52 1 0.01
53 4 0.05
54 3 0.04
55 19 0.23
56 9 0.11
57 15 0.18
58 6 0.07
59 6 0.07
60 3 0.04
61 11 0.13
62 6 0.07
ACGTcount: A:0.34, C:0.02, G:0.08, T:0.56
Consensus pattern (56 bp):
ATATATATATGTGTATATTTATGTAATATTTTTAATATTGTATGTATTTTTTTATA
Found at i:2587302 original size:69 final size:69
Alignment explanation
Indices: 2587207--2587337 Score: 169
Period size: 69 Copynumber: 1.9 Consensus size: 69
2587197 TACTTTAATA
* *
2587207 TTATTATGTATTTTATTATAATGTATATGTACATATCTATGTAGTATTAT-TA-ATATATATTTT
1 TTATTATGTATTTTAATATAATGTATATGTACAT-TCTATATA-TATTATGTATATATATATTTT
2587270 TTTATG
64 TTTATG
* * *
2587276 TTATTA-GTATTTCTAATATATTGTATATGTTCATTTTATATATATTATGTATATATATATTT
1 TTATTATGTATTT-TAATATAATGTATATGTACATTCTATATATATTATGTATATATATATTT
2587338 AGTATTATTA
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
67 6 0.11
68 14 0.26
69 34 0.63
ACGTcount: A:0.32, C:0.03, G:0.08, T:0.57
Consensus pattern (69 bp):
TTATTATGTATTTTAATATAATGTATATGTACATTCTATATATATTATGTATATATATATTTTTT
TATG
Found at i:2587349 original size:157 final size:158
Alignment explanation
Indices: 2587011--2587351 Score: 362
Period size: 157 Copynumber: 2.2 Consensus size: 158
2587001 TTTTAATAAC
* * *
2587011 TATAT-TATATGTATATATATTATGTACATATTTTTAATATTATTATGTATTTTTTTAATATATA
1 TATATATATATTTATATATATTATGTACATATCTTTAATATTATTATGTATTTTATTAATATATA
** * * *
2587075 TATGTGTATATTTATGTAATATTATTAATAGTTGTTTTTTAACATTATTATTATTTCTAATATGT
66 TATGTACATATCTATGTAATATTATTAATAGTTATTTTTTAACATTATTAGTATTTCTAATATGT
2587140 ATATATATATTTCAATAACTAAATTATG
131 ATATATATATTTCAATAACTAAATTATG
* *
2587168 TATGTAT-T-TTTAATACTATTTTATGTACATA-CTTTAATATTATTATGTATTTTATT-ATAAT
1 TATATATATATTT-ATA-TATATTATGTACATATCTTTAATATTATTATGTATTTTATTAAT-AT
* * * **
2587229 GTATATGTACATATCTATGTAGTATTATTAATA-TATATTTTTTTATGTTATTAGTATTTCTAAT
63 ATATATGTACATATCTATGTAATATTATTAATAGT-TATTTTTTAACATTATTAGTATTTCTAAT
* * *
2587293 A--TAT-TGTATATGTTCATTTTATA-TATATTATG
127 ATGTATATATATAT-TTCA--ATA-ACTAAATTATG
2587325 TATATATATATTTAGTAT-TATTATGTA
1 TATATATATATTTA-TATATATTATGTA
2587352 TACACTTTTC
Statistics
Matches: 152, Mismatches: 20, Indels: 24
0.78 0.10 0.12
Matches are distributed among these distances:
154 6 0.04
155 7 0.05
156 5 0.03
157 110 0.72
158 19 0.12
159 5 0.03
ACGTcount: A:0.34, C:0.04, G:0.07, T:0.55
Consensus pattern (158 bp):
TATATATATATTTATATATATTATGTACATATCTTTAATATTATTATGTATTTTATTAATATATA
TATGTACATATCTATGTAATATTATTAATAGTTATTTTTTAACATTATTAGTATTTCTAATATGT
ATATATATATTTCAATAACTAAATTATG
Found at i:2588548 original size:17 final size:17
Alignment explanation
Indices: 2588526--2588558 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2588516 AAAATCTTTT
2588526 TTAAAAAATTAAAAAAA
1 TTAAAAAATTAAAAAAA
*
2588543 TTAAAAATTTAAAAAA
1 TTAAAAAATTAAAAAA
2588559 GTTATAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
TTAAAAAATTAAAAAAA
Found at i:2590075 original size:18 final size:18
Alignment explanation
Indices: 2590052--2590106 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
2590042 AAATTACCAA
* *
2590052 AAAATTCAAAGTATTTTT
1 AAAATTCAAAATATTTAT
*
2590070 AAAATTTAAAATATTTAT
1 AAAATTCAAAATATTTAT
*
2590088 AAAATTTCCAAA-ATTTAT
1 AAAA-TTCAAAATATTTAT
2590106 A
1 A
2590107 TTTTTAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
18 26 0.84
19 5 0.16
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (18 bp):
AAAATTCAAAATATTTAT
Found at i:2599259 original size:29 final size:30
Alignment explanation
Indices: 2599205--2599282 Score: 88
Period size: 29 Copynumber: 2.6 Consensus size: 30
2599195 TTTAATTCTT
* *
2599205 TTTAATAGTATAGGGATTAAATTGATACA-
1 TTTAATAGTAGAGGGACTAAATTGATACAG
*
2599234 TTTAATAGTAGAGGGACT-AATGTGATCCAG
1 TTTAATAGTAGAGGGACTAAAT-TGATACAG
*
2599264 TTTATATAATAGAGGGACT
1 TTTA-ATAGTAGAGGGACT
2599283 TGGCAGGTAC
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
28 3 0.07
29 22 0.52
30 4 0.10
31 13 0.31
ACGTcount: A:0.37, C:0.06, G:0.22, T:0.35
Consensus pattern (30 bp):
TTTAATAGTAGAGGGACTAAATTGATACAG
Found at i:2604504 original size:56 final size:58
Alignment explanation
Indices: 2604438--2604555 Score: 213
Period size: 58 Copynumber: 2.1 Consensus size: 58
2604428 CTACACAATA
2604438 TTAACTTGAAAATTAATAATAACA-GG-GTTTTGCAAGAGTACATTTAGAATACTCTT
1 TTAACTTGAAAATTAATAATAACAGGGTGTTTTGCAAGAGTACATTTAGAATACTCTT
*
2604494 TTAACTTGAAAATTAATAATAACAGGGTGTTTTGCAAGAGTACTTTTAGAATACTCTT
1 TTAACTTGAAAATTAATAATAACAGGGTGTTTTGCAAGAGTACATTTAGAATACTCTT
2604552 TTAA
1 TTAA
2604556 GGGTGGTTCA
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
56 24 0.41
57 2 0.03
58 33 0.56
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.37
Consensus pattern (58 bp):
TTAACTTGAAAATTAATAATAACAGGGTGTTTTGCAAGAGTACATTTAGAATACTCTT
Found at i:2606096 original size:30 final size:30
Alignment explanation
Indices: 2606062--2606130 Score: 122
Period size: 30 Copynumber: 2.3 Consensus size: 30
2606052 AAATAATCAC
2606062 TCAATATTTATTAATTATATTAATTCACTT
1 TCAATATTTATTAATTATATTAATTCACTT
2606092 TCAATATTTATTAATTATATTAATTCACTT
1 TCAATATTTATTAATTATATTAATTCACTT
*
2606122 TTAAT-TTTA
1 TCAATATTTA
2606131 AATATATTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
29 4 0.11
30 34 0.89
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (30 bp):
TCAATATTTATTAATTATATTAATTCACTT
Found at i:2606131 original size:26 final size:28
Alignment explanation
Indices: 2606069--2606138 Score: 90
Period size: 30 Copynumber: 2.5 Consensus size: 28
2606059 CACTCAATAT
*
2606069 TTATTAATTATATTAATTCACTTTCAATAT
1 TTATTAATTATATTAATTCACTTT--ATAA
2606099 TTATTAATTATATTAATTCACTTT-TAA
1 TTATTAATTATATTAATTCACTTTATAA
*
2606126 TT-TTAAATATATT
1 TTATTAATTATATT
2606139 TAACCCTCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
26 10 0.26
27 4 0.11
30 24 0.63
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (28 bp):
TTATTAATTATATTAATTCACTTTATAA
Found at i:2606258 original size:30 final size:30
Alignment explanation
Indices: 2606223--2606299 Score: 100
Period size: 30 Copynumber: 2.6 Consensus size: 30
2606213 GTCCAAAACA
* *
2606223 TATTTTAATATCGAGCCAAAAAAAATTATT
1 TATTTTAAAATCGAACCAAAAAAAATTATT
* * *
2606253 TATTTTAAAATTGAACCACAATAAATTATT
1 TATTTTAAAATCGAACCAAAAAAAATTATT
*
2606283 TATTTTAAAATCAAACC
1 TATTTTAAAATCGAACC
2606300 CACCAACACA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.47, C:0.12, G:0.04, T:0.38
Consensus pattern (30 bp):
TATTTTAAAATCGAACCAAAAAAAATTATT
Found at i:2610102 original size:27 final size:28
Alignment explanation
Indices: 2610079--2610131 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
2610069 GAGTAAATAT
2610079 ATCAAATATCAAATTAAA-ATTAAAAAA
1 ATCAAATATCAAATTAAATATTAAAAAA
* * *
2610106 ATTATATATTAAATTAAATATTAAAA
1 ATCAAATATCAAATTAAATATTAAAA
2610132 TTAAACTCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 15 0.68
28 7 0.32
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (28 bp):
ATCAAATATCAAATTAAATATTAAAAAA
Found at i:2610134 original size:13 final size:13
Alignment explanation
Indices: 2610103--2610136 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
2610093 TAAAATTAAA
*
2610103 AAAATTATATATT
1 AAAATTAAATATT
2610116 -AAATTAAATATT
1 AAAATTAAATATT
2610128 AAAATTAAA
1 AAAATTAAA
2610137 CTCATTTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AAAATTAAATATT
Found at i:2618079 original size:13 final size:13
Alignment explanation
Indices: 2618061--2618087 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2618051 ATATATATAT
2618061 AAGAAACAAAAGA
1 AAGAAACAAAAGA
2618074 AAGAAACAAAAGA
1 AAGAAACAAAAGA
2618087 A
1 A
2618088 TAAAAAGAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.78, C:0.07, G:0.15, T:0.00
Consensus pattern (13 bp):
AAGAAACAAAAGA
Found at i:2619198 original size:23 final size:23
Alignment explanation
Indices: 2619168--2619254 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 23
2619158 GCTTTATCGA
* *
2619168 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTCATGTGTCGTATT
*
2619191 TCAGGCACCTCGTGTGTCGTA--
1 TCAGGCACCTCATGTGTCGTATT
*
2619212 TCAGGCACCTCGTGTGTCGT-TT
1 TCAGGCACCTCATGTGTCGTATT
* *
2619234 T-AGGCACTTTATGTGTCGTAT
1 TCAGGCACCTCATGTGTCGTAT
2619255 ACTGATCAGG
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
21 35 0.64
22 2 0.04
23 18 0.33
ACGTcount: A:0.15, C:0.22, G:0.25, T:0.38
Consensus pattern (23 bp):
TCAGGCACCTCATGTGTCGTATT
Found at i:2623000 original size:76 final size:74
Alignment explanation
Indices: 2622858--2623000 Score: 232
Period size: 74 Copynumber: 1.9 Consensus size: 74
2622848 NNNNNNNNNN
* * *
2622858 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAATT
1 AAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGACACGCCGAGGTATTTTCAATT
2622923 TCTGTTGTC
66 TCTGTTGTC
*
2622932 AAAAAAATCAACTCGTATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTTCAA
1 AAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGG--ACACGCCGAGGTATTTTCAA
2622997 TTTC
64 TTTC
2623001 CGTTTTTCAA
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
74 41 0.65
76 22 0.35
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (74 bp):
AAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGACACGCCGAGGTATTTTCAATT
TCTGTTGTC
Found at i:2623080 original size:167 final size:161
Alignment explanation
Indices: 2622858--2623297 Score: 602
Period size: 167 Copynumber: 2.7 Consensus size: 161
2622848 NNNNNNNNNN
*
2622858 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAATT
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATT
* * * *
2622923 TCTG-TTGTCAAAAAAATCAACTCGTATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACGCCGAG
66 TCTGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG--ACACACCGAG
* *
2622987 GTATTTTCAATTTCCGTTTTTCAATTTCTGCCTTTC
129 GTATTTTCAATTT-C--TGTTCAATTTATGCCTTTC
* * *
2623023 AAAAAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGTTGAGGTAATTTCAA
1 --AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAA
**
2623088 TTTCTGTTTGTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACATTGA
64 TTTCTGTTTGTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACACCGA
**
2623153 GGTATTTTCAATTTCTGTTCAATTTATGTTTTTC
128 GGTATTTTCAATTTCTGTTCAATTTATGCCTTTC
* ** *
2623187 --AAAAATCAGCTCATATTGCGAGAAATGAGTTGAGCCACAGGACACGCTGAGGTATTTTCAATT
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATT
*
2623250 TCTGTTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
66 TCTGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
2623298 GGGGCACGCT
Statistics
Matches: 249, Mismatches: 22, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
157 38 0.15
160 65 0.26
164 15 0.06
166 1 0.00
167 85 0.34
168 5 0.02
169 40 0.16
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (161 bp):
AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATT
TCTGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACACCGAGGT
ATTTTCAATTTCTGTTCAATTTATGCCTTTC
Found at i:2623449 original size:74 final size:74
Alignment explanation
Indices: 2623351--2623614 Score: 309
Period size: 74 Copynumber: 3.5 Consensus size: 74
2623341 TTTCAAAAAN
*
2623351 TGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTGTCAAAAAAATCAACTCATAT
1 TGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCTGTTGTCAAAAAAATCAACTCATAT
2623416 TGCGAGAAA
66 TGCGAGAAA
* * * *
2623425 TGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTTTTGTCTTTC-AAAAAATCAACTCATA
1 TGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCTGT-TGTCAAAAAAATCAACTCATA
**
2623489 TTGCGAGAGG
65 TTGCGAGAAA
* *
2623499 TGAGTCGAGCCTC-AGAACACGTTGAGGTAATTTCAATTTCTGTTGTCAAAAAAATCAACT-AGT
1 TGAGTTGAGCCTCAAG-ACACGCTGAGGTAATTTCAATTTCTGTTGTCAAAAAAATCAACTCA-T
* ***
2623562 ATTGTGAGCGG
64 ATTGCGAGAAA
* * * *
2623573 CGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTTCAATTTC
1 TGAGTTGAGCCTCAAG--ACACGCTGAGGTAATTTCAATTTC
2623615 CGTTTTTCAC
Statistics
Matches: 162, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
73 6 0.04
74 131 0.81
75 4 0.02
76 21 0.13
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (74 bp):
TGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCTGTTGTCAAAAAAATCAACTCATAT
TGCGAGAAA
Found at i:2623455 original size:140 final size:142
Alignment explanation
Indices: 2623191--2623558 Score: 404
Period size: 148 Copynumber: 2.6 Consensus size: 142
2623181 TTTTTCAAAA
* * * *
2623191 ATCAGCTCATATTGCGAGAAA-TGAGTTGAGCCACAGGACACGCTGAGGTATTTTCAATTTCTGT
1 ATCAACTCATATTGC-AAAAAGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTG-
* ** ** *
2623255 TTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAAGTATTGT
64 TTGTCAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAAGTATTGT
*
2623318 CAATTTTTGTGTTT
129 CAATTTTTGTCTTT
* * * * *
2623332 -T-AATTTATGTTTCAAAAANTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTT
1 ATCAACTCATATTGCAAAAAGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTT
* * *
2623395 GTCAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCA
66 GTCAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAAGTATTGTCA
2623460 ATTTTTGTCTTT
131 ATTTTTGTCTTT
* * * * * *
2623472 CAAAAAATCAACTCATATTGCGAGAGGTGAGTCGAGCCTCAGAACACGTTGAGGTAATTTCAATT
1 ------ATCAACTCATATTGCAAAAAGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
2623537 TCTGTTGTCAAAAAAATCAACT
60 TCTGTTGTCAAAAAAATCAACT
2623559 AGTATTGTGA
Statistics
Matches: 187, Mismatches: 29, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
138 8 0.04
139 47 0.25
140 64 0.34
147 1 0.01
148 67 0.36
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (142 bp):
ATCAACTCATATTGCAAAAAGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTT
GTCAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAAGTATTGTCA
ATTTTTGTCTTT
Found at i:2623763 original size:168 final size:168
Alignment explanation
Indices: 2623482--2624284 Score: 1332
Period size: 168 Copynumber: 4.8 Consensus size: 168
2623472 CAAAAAATCA
* ** * * * * *
2623482 ACTCATATTGCGAGAGGTGAGTCGAGCCTCAG--AACACGTTGAGGTAATTTCAATTTCTGT-TG
1 ACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACACGCTGAGCTATTTTCAATTTCTGTCTT
* ** * * *
2623544 TCAAAAAAATCAACT-AGTATTGTGAGCGGCGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTT
66 TAAAAAAAATCAACTCA-TATTACGAGAGGTGAGTTGAGCCTCAGATCACACGCCGAGGTATTTT
2623608 CAATTTCCGTTTTTCACTTTCTGCCGTTCAAATAAATTG
130 CAATTTCCGTTTTTCACTTTCTGCCGTTCAAATAAATTG
2623647 ACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACACGCTGAGCTATTTTCAATTTCTGTCTT
1 ACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACACGCTGAGCTATTTTCAATTTCTGTCTT
2623712 TAAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGATCACACGCCGAGGTATTTTC
66 TAAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGATCACACGCCGAGGTATTTTC
2623777 AATTTCCGTTTTTCACTTTCTGCCGTTCAAATAAATTG
131 AATTTCCGTTTTTCACTTTCTGCCGTTCAAATAAATTG
2623815 ACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACACGCTGAGCTATTTTCAATTTCTGTCTT
1 ACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACACGCTGAGCTATTTTCAATTTCTGTCTT
2623880 TAAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGATCACACGCCGAGGTATTTTC
66 TAAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGATCACACGCCGAGGTATTTTC
2623945 AATTTCCGTTTTTCACTTTCTGCCGTTCAAATAAATTG
131 AATTTCCGTTTTTCACTTTCTGCCGTTCAAATAAATTG
2623983 ACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACACGCTGAGCTATTTTCAATTTCTGTCTT
1 ACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACACGCTGAGCTATTTTCAATTTCTGTCTT
2624048 TAAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGATCACACGCCGAGGTATTTTC
66 TAAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGATCACACGCCGAGGTATTTTC
2624113 AATTTCCGTTTTTCACTTTCTGCCGTTCAAATAAATTG
131 AATTTCCGTTTTTCACTTTCTGCCGTTCAAATAAATTG
*
2624151 ACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATTTTCAATTTCTGT-TT
1 ACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACACGCTGAGCTATTTTCAATTTCTGTCTT
* * * ** * **
2624215 TCTAAAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCA-A-GACACGTTGAGGTATTTT
66 T-AAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGATCACACGCCGAGGTATTTT
2624278 CAATTTC
130 CAATTTC
2624285 TATTTTCAAA
Statistics
Matches: 610, Mismatches: 23, Indels: 9
0.95 0.04 0.01
Matches are distributed among these distances:
165 29 0.05
166 22 0.04
167 28 0.05
168 530 0.87
169 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (168 bp):
ACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACACGCTGAGCTATTTTCAATTTCTGTCTT
TAAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGATCACACGCCGAGGTATTTTC
AATTTCCGTTTTTCACTTTCTGCCGTTCAAATAAATTG
Found at i:2624249 original size:77 final size:74
Alignment explanation
Indices: 2624151--2624381 Score: 261
Period size: 75 Copynumber: 3.1 Consensus size: 74
2624141 AAATAAATTG
* *
2624151 ACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATTTTCAATTTCTGTTTT
1 ACTCATATTGCGAGAGGTGAGTTGAGCCTTGG--CACACGCTGAGGTATTTTCAATTTCTGTTTT
2624216 CTAAAAAATTCA
64 CTAAAAAA-TCA
** ** * *
2624228 ACTCATATTGCGAGAAATGAGTTGAGCCTCAAG-ACACGTTGAGGTATTTTCAATTTCTATTTTC
1 ACTCATATTGCGAGAGGTGAGTTGAGCCT-TGGCACACGCTGAGGTATTTTCAATTTCTGTTTTC
*
2624292 AAAAAAAATCA
65 -TAAAAAATCA
* * * *
2624303 ACTTATATTGCGAGAGGTGAGTTGAGCCTCAGG-ACATGCTGAGGTATTTTCAATTTTTGTTTT-
1 ACTCATATTGCGAGAGGTGAGTTGAGCCT-TGGCACACGCTGAGGTATTTTCAATTTCTGTTTTC
*
2624366 TCAAAAATCA
65 TAAAAAATCA
2624376 ACTCAT
1 ACTCAT
2624382 NNNNNNNNNN
Statistics
Matches: 132, Mismatches: 20, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
73 13 0.10
75 85 0.64
76 6 0.05
77 27 0.20
78 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (74 bp):
ACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCACACGCTGAGGTATTTTCAATTTCTGTTTTCT
AAAAAATCA
Found at i:2633363 original size:46 final size:46
Alignment explanation
Indices: 2633299--2633516 Score: 366
Period size: 46 Copynumber: 4.7 Consensus size: 46
2633289 AACCCGCCCC
* * *
2633299 TAAGTGAACTCGGACTCAACTCAACGAGCTTAGG-CGTTCGCATCCC
1 TAAGTGAACTCGGACTCAACTCAACGAG-TTCGGACATTCGCATCCA
* * *
2633345 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
2633391 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
2633437 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
2633483 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
2633517 TGCTCAACCA
Statistics
Matches: 165, Mismatches: 6, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
45 3 0.02
46 162 0.98
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.21
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:2636169 original size:46 final size:46
Alignment explanation
Indices: 2636097--2636266 Score: 168
Period size: 46 Copynumber: 3.7 Consensus size: 46
2636087 TGTAACCCAC
* * *
2636097 CCATAAATGAACTCGAACTCAACTCAACGAGCTCGGGCGTTTGCAT
1 CCATCAATGAACTCGGACTCAACTCAACGAGCTCGGGCATTTGCAT
* *
2636143 CCATCAATGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACAT
1 CCATCAATGAACTCGGACTCAACTCAACGAGCTCGG--G-C-ATTTGCAT
* * * * * *
2636193 -C-TC-ACGAACTTGGACTCAACTCAACGAGTTCAGACATTCGCAT
1 CCATCAATGAACTCGGACTCAACTCAACGAGCTCGGGCATTTGCAT
2636236 CCAT-AAGTGAACTCGGACTCAACTCAACGAG
1 CCATCAA-TGAACTCGGACTCAACTCAACGAG
2636267 TTCAGATGCC
Statistics
Matches: 101, Mismatches: 15, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
43 5 0.05
44 2 0.02
45 2 0.02
46 56 0.55
47 26 0.26
48 3 0.03
49 2 0.02
50 5 0.05
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.21
Consensus pattern (46 bp):
CCATCAATGAACTCGGACTCAACTCAACGAGCTCGGGCATTTGCAT
Found at i:2636743 original size:30 final size:30
Alignment explanation
Indices: 2636696--2636755 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
2636686 ATTTAATAAG
*
2636696 AACTTTGGCAAAGTTACATTTTTGCCCCTA
1 AACTTTGGCAAAGTTACACTTTTGCCCCTA
*
2636726 AACTTTTGCATAA-TTACACTTTTGCCCCTA
1 AACTTTGGCA-AAGTTACACTTTTGCCCCTA
2636756 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 25 0.93
31 2 0.07
ACGTcount: A:0.27, C:0.25, G:0.10, T:0.38
Consensus pattern (30 bp):
AACTTTGGCAAAGTTACACTTTTGCCCCTA
Found at i:2643847 original size:41 final size:41
Alignment explanation
Indices: 2643802--2643883 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
2643792 ACTTTAGTCC
*
2643802 TAATTTTAAGTAAATCAATAAATATATAAAATTGTTCAATT
1 TAATTTTAAGTAAATCAATAAACATATAAAATTGTTCAATT
2643843 TAATTTTAAGTAAATCAATAAACATATAAAATTGTTCAATT
1 TAATTTTAAGTAAATCAATAAACATATAAAATTGTTCAATT
2643884 GGATAAAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.49, C:0.06, G:0.05, T:0.40
Consensus pattern (41 bp):
TAATTTTAAGTAAATCAATAAACATATAAAATTGTTCAATT
Found at i:2644077 original size:31 final size:32
Alignment explanation
Indices: 2644032--2644094 Score: 119
Period size: 31 Copynumber: 2.0 Consensus size: 32
2644022 TTGTTAATTT
2644032 GAGATTAAAAAGTTAATAATTAAGCCATTTTC
1 GAGATTAAAAAGTTAATAATTAAGCCATTTTC
2644064 GAGATT-AAAAGTTAATAATTAAGCCATTTTC
1 GAGATTAAAAAGTTAATAATTAAGCCATTTTC
2644095 TTCTATACTT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 25 0.81
32 6 0.19
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.35
Consensus pattern (32 bp):
GAGATTAAAAAGTTAATAATTAAGCCATTTTC
Found at i:2650448 original size:17 final size:17
Alignment explanation
Indices: 2650426--2650459 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2650416 CTTTTAAGTG
2650426 TTTATAACTGTTATTGA
1 TTTATAACTGTTATTGA
2650443 TTTATAACTGTTATTGA
1 TTTATAACTGTTATTGA
2650460 AGTGCATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.06, G:0.12, T:0.53
Consensus pattern (17 bp):
TTTATAACTGTTATTGA
Found at i:2654897 original size:14 final size:14
Alignment explanation
Indices: 2654860--2654916 Score: 69
Period size: 15 Copynumber: 3.9 Consensus size: 14
2654850 GAATTTTTTG
* *
2654860 TTAAATTTATTTCA
1 TTAAATTTTTTTAA
2654874 TTACAATTTTTTTAA
1 TTA-AATTTTTTTAA
2654889 TTAAATTTTTTATAA
1 TTAAATTTTTT-TAA
*
2654904 GTAAATTTTTTTA
1 TTAAATTTTTTTA
2654917 TTTCAAAATG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
14 13 0.34
15 25 0.66
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60
Consensus pattern (14 bp):
TTAAATTTTTTTAA
Found at i:2660940 original size:15 final size:16
Alignment explanation
Indices: 2660920--2660956 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
2660910 CCGTGTAAAC
*
2660920 ACAAAACAAACAAAA-
1 ACAAAACAAAAAAAAT
2660935 ACAAAACAAAAAAAAT
1 ACAAAACAAAAAAAAT
2660951 ACAAAA
1 ACAAAA
2660957 AATATATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.81, C:0.16, G:0.00, T:0.03
Consensus pattern (16 bp):
ACAAAACAAAAAAAAT
Found at i:2660941 original size:11 final size:11
Alignment explanation
Indices: 2660916--2660957 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
2660906 GGGCCCGTGT
2660916 AAACACAAAAC-
1 AAACA-AAAACA
2660927 AAACAAAAACA
1 AAACAAAAACA
2660938 AAACAAAAA-A
1 AAACAAAAACA
2660948 AATACAAAAA
1 AA-ACAAAAA
2660958 ATATATAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 8 0.28
11 21 0.72
ACGTcount: A:0.81, C:0.17, G:0.00, T:0.02
Consensus pattern (11 bp):
AAACAAAAACA
Found at i:2663749 original size:130 final size:130
Alignment explanation
Indices: 2663569--2663941 Score: 406
Period size: 130 Copynumber: 2.9 Consensus size: 130
2663559 AAAATTATTC
* * ** *
2663569 AAAACAAAGACGAAATTTGATGTTCAGCGATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAA
1 AAAACGAAGACGAGATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAA
* * * * *
2663634 TTTCGCGTTCGCTCAAAATAATCGAATTTCCCTTTGAAATTTCATTCATATCTTTTAAAATCCCT
66 TTTCGCATTCGCTCAAAATAATCGAATATCACTTTAAAATTTCACTCATATCTTTTAAAATCCCT
* * * *
2663699 TAAATGAAGATGAGATTTGATGTTTGGCAATTCGCGGAATTGTGCCCTAACGTGTTGGGTTGCAA
1 AAAACGAAGACGAGATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAA
* * * ** * * *
2663764 TTTCGCATTTGTTCAAAATAATCGAATATCATTTTAAAATTTTGCTCGTGTCTTTTAAAATCTCT
66 TTTCGCATTCGCTCAAAATAATCGAATATCACTTTAAAATTTCACTCATATCTTTTAAAATCCCT
* * * * * * *
2663829 AAAACGAAGGCGATATGTGATATTTGGCAATTCACGGGATCGTGCCCTAACGTGTTGGGTAGCAA
1 AAAACGAAGACGAGATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAA
* * * * * * *
2663894 TTCCCCGATT-GTTTAAAATAATCAAATATCCCTTCAAAATTTCACTCA
66 TTTCGC-ATTCGCTCAAAATAATCGAATATCACTTTAAAATTTCACTCA
2663942 GCCCCTCTAA
Statistics
Matches: 199, Mismatches: 43, Indels: 2
0.82 0.18 0.01
Matches are distributed among these distances:
130 196 0.98
131 3 0.02
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34
Consensus pattern (130 bp):
AAAACGAAGACGAGATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAA
TTTCGCATTCGCTCAAAATAATCGAATATCACTTTAAAATTTCACTCATATCTTTTAAAATCCCT
Found at i:2666521 original size:162 final size:161
Alignment explanation
Indices: 2666037--2666522 Score: 618
Period size: 163 Copynumber: 3.0 Consensus size: 161
2666027 ATTGAGTCGA
* * *
2666037 GGCAAGGTGGATTTTATCTAAAACCG-CCCCAA-TATGCCCTGAAAATTTCAGCCAAGCAACTAA
1 GGCAAGGTGGATTTTATCTAAAACCGCCCCCAACT-TGCCCTGAAAATTTCAGCTAAGAAACCAA
* * * **
2666100 CATGCCTAGCCTCTGAACTTGATTGTCAGATAAAAGAAAGACCCATAAGGTGAGGTTGAAACCTG
65 CATGCCTAGCCTCCGAACTTGATTGTCAGATAAAAGAAAGACCTATAGGGTGAGGTTGAAACCCA
* * *
2666165 AAAAGTTGGGTTATTTTTCCTCATATATGTTCGG
130 AAAAGTT-CGTT-TTTTTCCCCATATAAGTTCGG
* * * * *
2666199 GGCAATGTGGATTTTATCTACAACCACTCCCAACCTGCCCTGAAAATTTCAGCTAAGAAACCAAC
1 GGCAAGGTGGATTTTATCTAAAACCGCCCCCAACTTGCCCTGAAAATTTCAGCTAAGAAACCAAC
* *
2666264 ATGCCTAGCCTCCGAACTCGATTGTCAGATAAAAGAAAGCCCTATAGGGTGAGGTTGAAACCCAA
66 ATGCCTAGCCTCCGAACTTGATTGTCAGATAAAAGAAAGACCTATAGGGTGAGGTTGAAACCCAA
* * *
2666329 AAAGTTCGCTTGTTTCTCCCATATAAGTTCGT
131 AAAGTTCGTTTTTTTC-CCCATATAAGTTCGG
* * * *
2666361 GGCAAGGTGGATTTTATCTAGAACTGCCCCACAACTTGCCCCGAAAATTTCAGATAAGAAACCAA
1 GGCAAGGTGGATTTTATCTAAAACCGCCCC-CAACTTGCCCTGAAAATTTCAGCTAAGAAACCAA
* * *
2666426 CATGCCTAGCCTCCGAACTTGATTGTGAGATAAAA-AAAGACATATAGGGGGAGGTTGAAACCCA
65 CATGCCTAGCCTCCGAACTTGATTGTCAGATAAAAGAAAGACCTATAGGGTGAGGTTGAAACCCA
* **
2666490 AAAATTTCAGTTTTTTTCCCCATGCAAGTTCGG
130 AAAAGTTC-GTTTTTTTCCCCATATAAGTTCGG
2666523 TTGAAACTCG
Statistics
Matches: 279, Mismatches: 40, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
161 5 0.02
162 107 0.38
163 167 0.60
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (161 bp):
GGCAAGGTGGATTTTATCTAAAACCGCCCCCAACTTGCCCTGAAAATTTCAGCTAAGAAACCAAC
ATGCCTAGCCTCCGAACTTGATTGTCAGATAAAAGAAAGACCTATAGGGTGAGGTTGAAACCCAA
AAAGTTCGTTTTTTTCCCCATATAAGTTCGG
Found at i:2667071 original size:29 final size:29
Alignment explanation
Indices: 2667029--2667086 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
2667019 AAACAAAAGA
2667029 AAGTCAAATTATTGCCCAGATTGTTCGTT
1 AAGTCAAATTATTGCCCAGATTGTTCGTT
2667058 AAGTCAAATTATTGCCCAGATTGTTCGTT
1 AAGTCAAATTATTGCCCAGATTGTTCGTT
2667087 GTTGTTTAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (29 bp):
AAGTCAAATTATTGCCCAGATTGTTCGTT
Found at i:2668110 original size:14 final size:15
Alignment explanation
Indices: 2668058--2668108 Score: 77
Period size: 15 Copynumber: 3.5 Consensus size: 15
2668048 ATAAAACGTT
2668058 AATATAAATAATTAA
1 AATATAAATAATTAA
* *
2668073 AATAT-AATACTTTA
1 AATATAAATAATTAA
2668087 AATATAAATAATTAA
1 AATATAAATAATTAA
2668102 AATATAA
1 AATATAA
2668109 TATGAGATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
14 12 0.39
15 19 0.61
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (15 bp):
AATATAAATAATTAA
Found at i:2669474 original size:17 final size:17
Alignment explanation
Indices: 2669446--2669479 Score: 52
Period size: 16 Copynumber: 2.0 Consensus size: 17
2669436 TTCATTTTTC
2669446 TTAAAAAAAA-TTAGTA
1 TTAAAAAAAATTTAGTA
2669462 TTAAAACAAAATTTAGTA
1 TTAAAA-AAAATTTAGTA
2669480 CAAATGATGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 4 0.25
18 6 0.38
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.32
Consensus pattern (17 bp):
TTAAAAAAAATTTAGTA
Found at i:2670244 original size:21 final size:21
Alignment explanation
Indices: 2670220--2670259 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2670210 TGAATTAACT
2670220 CAACTTTATCCAAAATTTATA
1 CAACTTTATCCAAAATTTATA
* *
2670241 CAACTTTTTCCGAAATTTA
1 CAACTTTATCCAAAATTTA
2670260 CACACCCCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.20, G:0.03, T:0.40
Consensus pattern (21 bp):
CAACTTTATCCAAAATTTATA
Found at i:2687026 original size:17 final size:18
Alignment explanation
Indices: 2686999--2687034 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
2686989 CTCCCTAAAA
*
2686999 TTTACATTTTTAAACTTT
1 TTTACATTTTTAAAATTT
2687017 TTTA-ATTTTTAAAATTT
1 TTTACATTTTTAAAATTT
2687034 T
1 T
2687035 AAATTTGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTACATTTTTAAAATTT
Found at i:2687034 original size:16 final size:17
Alignment explanation
Indices: 2686999--2687045 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
2686989 CTCCCTAAAA
*
2686999 TTTACATTTTTAAACTTT
1 TTTA-ATTTTTAAACATT
2687017 TTTAATTTTTAAA-ATT
1 TTTAATTTTTAAACATT
* *
2687033 TTAAATTTGTAAA
1 TTTAATTTTTAAA
2687046 TGTAAAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 13 0.50
17 9 0.35
18 4 0.15
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.57
Consensus pattern (17 bp):
TTTAATTTTTAAACATT
Found at i:2691135 original size:32 final size:32
Alignment explanation
Indices: 2691099--2691164 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
2691089 TTACGACAGT
*
2691099 GAACATTTCATAATTTCATTCTAATCAAGTCA
1 GAACATTTCATAATATCATTCTAATCAAGTCA
*
2691131 GAACATTTGATAATATCATTCTAATCAAGTCA
1 GAACATTTCATAATATCATTCTAATCAAGTCA
2691163 GA
1 GA
2691165 GGAAAATTGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (32 bp):
GAACATTTCATAATATCATTCTAATCAAGTCA
Found at i:2696318 original size:14 final size:15
Alignment explanation
Indices: 2696292--2696322 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
2696282 TCCTGGCTCA
2696292 TCAACACATTTTTCT
1 TCAACACATTTTTCT
2696307 TCAACA-ATTTTTCT
1 TCAACACATTTTTCT
2696321 TC
1 TC
2696323 CCATTTCTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (15 bp):
TCAACACATTTTTCT
Found at i:2699028 original size:17 final size:18
Alignment explanation
Indices: 2699006--2699039 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2698996 ATGACTTCTA
2699006 TTAAAT-TATAATTATTT
1 TTAAATGTATAATTATTT
*
2699023 TTAAATGTATATTTATT
1 TTAAATGTATAATTATT
2699040 ACGACTTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (18 bp):
TTAAATGTATAATTATTT
Found at i:2700405 original size:26 final size:25
Alignment explanation
Indices: 2700347--2700412 Score: 69
Period size: 26 Copynumber: 2.6 Consensus size: 25
2700337 AACATACTTC
*
2700347 TAATTATTTTTATTTCATTAATTATA
1 TAATTATTTTTA-TTAATTAATTATA
* * *
2700373 TATTTATTTTTATTAATTAGTGTATT
1 TAATTATTTTTATTAATTAAT-TATA
*
2700399 TAATTATTATTATT
1 TAATTATTTTTATT
2700413 TAAAGATATT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
25 7 0.21
26 26 0.79
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.64
Consensus pattern (25 bp):
TAATTATTTTTATTAATTAATTATA
Found at i:2700428 original size:24 final size:22
Alignment explanation
Indices: 2700395--2700438 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
2700385 TTAATTAGTG
2700395 TATTTAATTATTATTATTTAAAGA
1 TATTTAATTA-T-TTATTTAAAGA
*
2700419 TATTTGATTATTTATTTAAA
1 TATTTAATTATTTATTTAAA
2700439 AATGTATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 1 0.05
24 9 0.47
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (22 bp):
TATTTAATTATTTATTTAAAGA
Found at i:2700454 original size:22 final size:23
Alignment explanation
Indices: 2700401--2700455 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
2700391 AGTGTATTTA
* *
2700401 ATTATTATTATTTAAAGATATTTG
1 ATTATT-TTATTTAAAAATATATG
*
2700425 ATTA-TTTATTTAAAAATGTAT-
1 ATTATTTTATTTAAAAATATATG
2700446 ATTATTTTAT
1 ATTATTTTAT
2700456 GTAATGTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 4 0.15
22 18 0.67
23 1 0.04
24 4 0.15
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (23 bp):
ATTATTTTATTTAAAAATATATG
Found at i:2703261 original size:12 final size:11
Alignment explanation
Indices: 2703231--2703298 Score: 52
Period size: 12 Copynumber: 6.0 Consensus size: 11
2703221 CCGTATTTAC
*
2703231 TTATATTTTTA
1 TTATATTATTA
2703242 CTTATATTATTA
1 -TTATATTATTA
*
2703254 TTACTATTATCA
1 TTA-TATTATTA
2703266 TTATGA-T-TTA
1 TTAT-ATTATTA
2703276 TTACT-TTATTA
1 TTA-TATTATTA
2703287 TTATCATTATTA
1 TTAT-ATTATTA
2703299 CTGCCATTGT
Statistics
Matches: 46, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
10 7 0.15
11 12 0.26
12 27 0.59
ACGTcount: A:0.31, C:0.07, G:0.01, T:0.60
Consensus pattern (11 bp):
TTATATTATTA
Found at i:2716088 original size:87 final size:85
Alignment explanation
Indices: 2715989--2716189 Score: 212
Period size: 87 Copynumber: 2.3 Consensus size: 85
2715979 TTCATAAGAT
* **
2715989 CTTAAACCCCTAAGCAGTAGGGTAACAGACCAAATTGT-AGATCTTATTTCCCTAAGCC-G-TAG
1 CTTAACCCCCTAAGCAGTAGGGTAACAGACCAAATT-TAAGATC-TAAATCCCTAA-CCGGTTAG
* *
2716051 TGGAGCAGATCGAA-GATTGACAAGC
63 -GAAACAGATC-AATGA-TGACAAGC
* * ****
2716076 CTTAACCCCCTAAACAGTAGGGTAACTGGTTGAATTTACAGATCTAAATCCCTAACCGGTTAGGA
1 CTTAACCCCCTAAGCAGTAGGGTAACAGACCAAATTTA-AGATCTAAATCCCTAACCGGTTAGGA
2716141 AACAGATCAATGATGACAAGC
65 AACAGATCAATGATGACAAGC
2716162 CTTAACCCCCTAAGCAGTAGGGTAACAG
1 CTTAACCCCCTAAGCAGTAGGGTAACAG
2716190 GCTGAAAATC
Statistics
Matches: 96, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
86 39 0.41
87 49 0.51
88 8 0.08
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.22
Consensus pattern (85 bp):
CTTAACCCCCTAAGCAGTAGGGTAACAGACCAAATTTAAGATCTAAATCCCTAACCGGTTAGGAA
ACAGATCAATGATGACAAGC
Found at i:2717790 original size:3 final size:3
Alignment explanation
Indices: 2717784--2717852 Score: 58
Period size: 3 Copynumber: 23.7 Consensus size: 3
2717774 TTATTAATCG
* *
2717784 TAT TAT TAC TAT TAT T-T CT-T TAT TTT TAT T-T TA- TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT
2717825 TCAT TAT TAGT TAT TAT TAT TAT TAT TA
1 T-AT TAT TA-T TAT TAT TAT TAT TAT TA
2717853 GTTTTAGCTT
Statistics
Matches: 55, Mismatches: 4, Indels: 14
0.75 0.05 0.19
Matches are distributed among these distances:
2 8 0.15
3 41 0.75
4 6 0.11
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:2717839 original size:19 final size:19
Alignment explanation
Indices: 2717817--2717855 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
2717807 TTTTATTTTA
2717817 TATTA-TATTCATTATTAGT
1 TATTATTATT-ATTATTAGT
2717836 TATTATTATTATTATTAGT
1 TATTATTATTATTATTAGT
2717855 T
1 T
2717856 TTAGCTTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.62
Consensus pattern (19 bp):
TATTATTATTATTATTAGT
Found at i:2717931 original size:18 final size:20
Alignment explanation
Indices: 2717908--2717944 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
2717898 ATTATTAATA
2717908 ATTATT-TTTTTAA-ACATT
1 ATTATTATTTTTAATACATT
2717926 ATTATTATTTTTAATACAT
1 ATTATTATTTTTAATACAT
2717945 GCATATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 7 0.41
20 4 0.24
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTATTATTTTTAATACATT
Found at i:2718158 original size:29 final size:29
Alignment explanation
Indices: 2718122--2718182 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
2718112 TTATTTATCG
2718122 TTATT-ATA-AATA-TATTGTTTT-CATTC
1 TTATTAATATAATATTATTGTTTTCCA-TC
*
2718148 TTATTAATATATTATTATTGTTTTCCATC
1 TTATTAATATAATATTATTGTTTTCCATC
2718177 TTATTA
1 TTATTA
2718183 TTATTACTAG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 5 0.17
27 3 0.10
28 3 0.10
29 17 0.57
30 2 0.07
ACGTcount: A:0.30, C:0.08, G:0.03, T:0.59
Consensus pattern (29 bp):
TTATTAATATAATATTATTGTTTTCCATC
Found at i:2718186 original size:3 final size:3
Alignment explanation
Indices: 2718073--2718116 Score: 61
Period size: 3 Copynumber: 14.3 Consensus size: 3
2718063 ACTATTATGC
* *
2718073 TAT TAT TAT TAT TAT TAT TAT TAT TAT AAT CAT TCAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT T
2718117 TATCGTTATT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:2718284 original size:12 final size:12
Alignment explanation
Indices: 2718267--2718341 Score: 93
Period size: 12 Copynumber: 6.2 Consensus size: 12
2718257 CTCTCTGTAT
2718267 TTACTTATATTA
1 TTACTTATATTA
2718279 TTACTTATATTA
1 TTACTTATATTA
2718291 TTACTTATATTA
1 TTACTTATATTA
2718303 TTA-TTACTATTA
1 TTACTTA-TATTA
*
2718315 TCA-TTATGATTTA
1 TTACTTAT-A-TTA
2718328 TTACTT-TATTA
1 TTACTTATATTA
2718339 TTA
1 TTA
2718342 TCATTATTAC
Statistics
Matches: 57, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
11 10 0.18
12 39 0.68
13 6 0.11
14 2 0.04
ACGTcount: A:0.32, C:0.08, G:0.01, T:0.59
Consensus pattern (12 bp):
TTACTTATATTA
Found at i:2718304 original size:15 final size:13
Alignment explanation
Indices: 2718267--2718321 Score: 60
Period size: 15 Copynumber: 4.1 Consensus size: 13
2718257 CTCTCTGTAT
2718267 TTAC-TTATATTA
1 TTACTTTATATTA
2718279 TTAC-TTATATTA
1 TTACTTTATATTA
2718291 TTACTTATATTATTA
1 TTACTT-TA-TATTA
2718306 TTACTATTATCATTA
1 TTACT-TTAT-ATTA
2718321 T
1 T
2718322 GATTTATTAC
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
12 16 0.42
13 1 0.03
14 3 0.08
15 17 0.45
16 1 0.03
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.58
Consensus pattern (13 bp):
TTACTTTATATTA
Found at i:2718348 original size:27 final size:25
Alignment explanation
Indices: 2718271--2718348 Score: 92
Period size: 27 Copynumber: 3.2 Consensus size: 25
2718261 CTGTATTTAC
2718271 TTATATTATTACTTATATTATTA-C-
1 TTATATTATTACTT-TATTATTATCA
*
2718295 TTATATTATTA--TTACTATTATCA
1 TTATATTATTACTTTATTATTATCA
2718318 TTATGATTTATTACTTTATTATTATCA
1 TTAT-A-TTATTACTTTATTATTATCA
2718345 TTAT
1 TTAT
2718349 TACTGCCATT
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
21 7 0.15
22 2 0.04
23 4 0.09
24 12 0.26
25 6 0.13
27 15 0.33
ACGTcount: A:0.32, C:0.08, G:0.01, T:0.59
Consensus pattern (25 bp):
TTATATTATTACTTTATTATTATCA
Found at i:2718350 original size:12 final size:11
Alignment explanation
Indices: 2718271--2718350 Score: 76
Period size: 12 Copynumber: 7.0 Consensus size: 11
2718261 CTGTATTTAC
2718271 TTATATTATTA
1 TTATATTATTA
2718282 CTTATATTATTA
1 -TTATATTATTA
2718294 CTTATATTATTA
1 -TTATATTATTA
*
2718306 TTACTATTATCA
1 TTA-TATTATTA
2718318 TTATGA-T-TTA
1 TTAT-ATTATTA
2718328 TTACT-TTATTA
1 TTA-TATTATTA
2718339 TTATCATTATTA
1 TTAT-ATTATTA
2718351 CTGCCATTGT
Statistics
Matches: 59, Mismatches: 2, Indels: 14
0.79 0.03 0.19
Matches are distributed among these distances:
10 7 0.12
11 12 0.20
12 40 0.68
ACGTcount: A:0.33, C:0.07, G:0.01, T:0.59
Consensus pattern (11 bp):
TTATATTATTA
Found at i:2718370 original size:3 final size:3
Alignment explanation
Indices: 2718274--2718350 Score: 61
Period size: 3 Copynumber: 25.7 Consensus size: 3
2718264 TATTTACTTA
* *
2718274 TAT TAT TACT TA- TAT TAT TACT TA- TAT TAT TAT TAC TAT TAT CAT
1 TAT TAT TA-T TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT
* * *
2718319 TAT GATT TAT TAC T-T TAT TAT TAT CAT TAT TA
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TA
2718351 CTGCCATTGT
Statistics
Matches: 58, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
2 5 0.09
3 45 0.78
4 8 0.14
ACGTcount: A:0.32, C:0.08, G:0.01, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:2719619 original size:32 final size:32
Alignment explanation
Indices: 2719583--2719648 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
2719573 TTACGACAGT
*
2719583 GAACATTTCATAATTTCATTCTAATCAAGTCA
1 GAACATTTCATAATATCATTCTAATCAAGTCA
*
2719615 GAACATTTGATAATATCATTCTAATCAAGTCA
1 GAACATTTCATAATATCATTCTAATCAAGTCA
2719647 GA
1 GA
2719649 GGAAAATTGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (32 bp):
GAACATTTCATAATATCATTCTAATCAAGTCA
Found at i:2724802 original size:14 final size:15
Alignment explanation
Indices: 2724776--2724806 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
2724766 TCCTGGCTCA
2724776 TCAACACATTTTTCT
1 TCAACACATTTTTCT
2724791 TCAACA-ATTTTTCT
1 TCAACACATTTTTCT
2724805 TC
1 TC
2724807 CCATTTCTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (15 bp):
TCAACACATTTTTCT
Found at i:2728193 original size:26 final size:25
Alignment explanation
Indices: 2728135--2728200 Score: 69
Period size: 26 Copynumber: 2.6 Consensus size: 25
2728125 AACATACTTC
*
2728135 TAATTATTTTTATTTCATTAATTAAT
1 TAATTATTTTTA-TTAATTAATTAAT
* * *
2728161 TATTTATTTTTATTAATTAGTTTATT
1 TAATTATTTTTATTAATTA-ATTAAT
*
2728187 TAATTATTATTATT
1 TAATTATTTTTATT
2728201 TAAAGATATA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
25 6 0.18
26 27 0.82
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (25 bp):
TAATTATTTTTATTAATTAATTAAT
Found at i:2728237 original size:21 final size:22
Alignment explanation
Indices: 2728191--2728240 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
2728181 TTTATTTAAT
*
2728191 TATTA-TTATTTAAAGATATAA
1 TATTATTTATTTAAAAATATAA
* *
2728212 GATTATTTATTTAAAAATGT-A
1 TATTATTTATTTAAAAATATAA
2728233 TATTATTT
1 TATTATTT
2728241 TATGTAATGT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (22 bp):
TATTATTTATTTAAAAATATAA
Found at i:2728242 original size:22 final size:23
Alignment explanation
Indices: 2728189--2728243 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
2728179 AGTTTATTTA
*
2728189 ATTATTATTATTTAAAGATATAAG
1 ATTATT-TTATTTAAAAATATAAG
* *
2728213 ATTA-TTTATTTAAAAATGT-AT
1 ATTATTTTATTTAAAAATATAAG
2728234 ATTATTTTAT
1 ATTATTTTAT
2728244 GTAATGTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 5 0.19
22 17 0.63
23 1 0.04
24 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (23 bp):
ATTATTTTATTTAAAAATATAAG
Found at i:2729266 original size:18 final size:17
Alignment explanation
Indices: 2729233--2729266 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2729223 AAAAGAAAGT
*
2729233 AAAAGAAAGAAGAACAG
1 AAAAGAAACAAGAACAG
2729250 AAAAGAAACAGAGAACA
1 AAAAGAAACA-AGAACA
2729267 AAACGAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.71, C:0.09, G:0.21, T:0.00
Consensus pattern (17 bp):
AAAAGAAACAAGAACAG
Found at i:2729717 original size:17 final size:17
Alignment explanation
Indices: 2729681--2729714 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2729671 TAAAAGAGTT
*
2729681 AATTAGGATTAAATTGG
1 AATTAGGAATAAATTGG
2729698 AATTAAGGAATAAATTG
1 AATT-AGGAATAAATTG
2729715 AATAAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.47, C:0.00, G:0.21, T:0.32
Consensus pattern (17 bp):
AATTAGGAATAAATTGG
Found at i:2730253 original size:27 final size:27
Alignment explanation
Indices: 2730213--2730292 Score: 74
Period size: 27 Copynumber: 2.9 Consensus size: 27
2730203 ATGCCTTATT
* *
2730213 GGTGTATTTGGGAGGATATGA-TATACC
1 GGTGTGTTTAGGAGGATAT-ATTATACC
* *
2730240 GGTGTGTTTAGGAGGCTATATTATACT
1 GGTGTGTTTAGGAGGATATATTATACC
2730267 GGTGTG-TTATGGAGGATTTATATTAT
1 GGTGTGTTTA-GGAGGA--TATATTAT
2730293 TCTGGGTGTG
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
26 4 0.09
27 32 0.73
29 8 0.18
ACGTcount: A:0.24, C:0.05, G:0.31, T:0.40
Consensus pattern (27 bp):
GGTGTGTTTAGGAGGATATATTATACC
Found at i:2731253 original size:20 final size:19
Alignment explanation
Indices: 2731216--2731254 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
2731206 TATATAGCTG
*
2731216 ATTAACTACTTTAACAACT
1 ATTAACTACTTGAACAACT
*
2731235 ATTAACTGACTTGACCAACT
1 ATTAACT-ACTTGAACAACT
2731255 TACTAACCAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.38, C:0.23, G:0.05, T:0.33
Consensus pattern (19 bp):
ATTAACTACTTGAACAACT
Found at i:2735806 original size:20 final size:19
Alignment explanation
Indices: 2735769--2735807 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
2735759 TATATAGCTA
* *
2735769 ATTAACTACTTTAGCAACT
1 ATTAACTACTTGACCAACT
2735788 ATTAACTGACTTGACCAACT
1 ATTAACT-ACTTGACCAACT
2735808 TACTAACCAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.33
Consensus pattern (19 bp):
ATTAACTACTTGACCAACT
Found at i:2737722 original size:25 final size:26
Alignment explanation
Indices: 2737664--2737737 Score: 116
Period size: 25 Copynumber: 2.9 Consensus size: 26
2737654 TGAGCTTTCC
*
2737664 AATGTGCAAGCTGCAAG-TTCAGCAAA
1 AATGTGTAAGCTGCAAGCTT-AGCAAA
2737690 AATGTGTAAGCTGCAAGCTTAGC-AA
1 AATGTGTAAGCTGCAAGCTTAGCAAA
2737715 AATGTGTAAGCTGCAAGCTTAGC
1 AATGTGTAAGCTGCAAGCTTAGC
2737738 GAGAAGTGAG
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
25 25 0.54
26 19 0.41
27 2 0.04
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.23
Consensus pattern (26 bp):
AATGTGTAAGCTGCAAGCTTAGCAAA
Found at i:2740074 original size:51 final size:51
Alignment explanation
Indices: 2739975--2740075 Score: 121
Period size: 51 Copynumber: 2.0 Consensus size: 51
2739965 GGTATGTATA
* * * *
2739975 TAAAGGGATTACATCATTTTCGGTCAAATAAGGTGGTTTGAACCGACTTTG
1 TAAAGGGATTACACCAGTTTCGGTCAAATAAGGTGATTTGAACAGACTTTG
* * * * *
2740026 TAAAGGGATTACACCAGTTTCGGTGAGATAAGTTGATTTTAATAGACTTT
1 TAAAGGGATTACACCAGTTTCGGTCAAATAAGGTGATTTGAACAGACTTT
2740076 TATGCATTCC
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
51 41 1.00
ACGTcount: A:0.31, C:0.12, G:0.23, T:0.35
Consensus pattern (51 bp):
TAAAGGGATTACACCAGTTTCGGTCAAATAAGGTGATTTGAACAGACTTTG
Found at i:2741020 original size:21 final size:21
Alignment explanation
Indices: 2740991--2741030 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2740981 TTTGATTTTT
2740991 TTCAAGATGAAAATACTGAAA
1 TTCAAGATGAAAATACTGAAA
* * *
2741012 TTCAGGATGAGAATGCTGA
1 TTCAAGATGAAAATACTGA
2741031 TATGGCATAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.10, G:0.23, T:0.25
Consensus pattern (21 bp):
TTCAAGATGAAAATACTGAAA
Found at i:2747617 original size:15 final size:16
Alignment explanation
Indices: 2747597--2747626 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2747587 TAACTAATGT
2747597 AAAATAAT-GTTATTC
1 AAAATAATAGTTATTC
2747612 AAAATAATAGTTATT
1 AAAATAATAGTTATT
2747627 TAACATAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (16 bp):
AAAATAATAGTTATTC
Found at i:2748652 original size:31 final size:31
Alignment explanation
Indices: 2748617--2748683 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
2748607 CTTCCTGCAT
* *
2748617 TAAAATCCAACCAAATACAACAAATATAATA
1 TAAAATCCAACCAAAAACAACAAATATAACA
* * * *
2748648 TAAAATGCAGCCAAAAACAGCAAATTTAACA
1 TAAAATCCAACCAAAAACAACAAATATAACA
2748679 TAAAA
1 TAAAA
2748684 AATACAAACA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.60, C:0.18, G:0.04, T:0.18
Consensus pattern (31 bp):
TAAAATCCAACCAAAAACAACAAATATAACA
Found at i:2748955 original size:21 final size:20
Alignment explanation
Indices: 2748931--2748988 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
2748921 TCTGCTACCA
*
2748931 TCGCTCGTGCCTCTGCCTCTC
1 TCGCT-GTGCCTCTGCCTCCC
*
2748952 TCGCTGTAGCCGCTGCCTCCC
1 TCGCTGT-GCCTCTGCCTCCC
*
2748973 TCTCTGCTGCCTCTGC
1 TCGCTG-TGCCTCTGC
2748989 TCTAAGTTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 2 0.06
21 28 0.90
22 1 0.03
ACGTcount: A:0.02, C:0.47, G:0.21, T:0.31
Consensus pattern (20 bp):
TCGCTGTGCCTCTGCCTCCC
Found at i:2754550 original size:9 final size:9
Alignment explanation
Indices: 2754536--2754755 Score: 131
Period size: 9 Copynumber: 23.9 Consensus size: 9
2754526 TATTTAAGTA
2754536 TTATGTAAG
1 TTATGTAAG
*
2754545 TTATGTAAT
1 TTATGTAAG
*
2754554 TTATGATATG
1 TTATG-TAAG
* * *
2754564 ATATAT-AT
1 TTATGTAAG
*
2754572 TTATGTAAA
1 TTATGTAAG
* *
2754581 TTATAT-AT
1 TTATGTAAG
*
2754589 TTATCTAAG
1 TTATGTAAG
*
2754598 TTATATAAG
1 TTATGTAAG
2754607 TTATGTAAG
1 TTATGTAAG
*
2754616 TTATGTAAA
1 TTATGTAAG
*
2754625 TTATGATATAAAA
1 TTATG---T-AAG
*
2754638 TATATTTAAG
1 T-TATGTAAG
*
2754648 TATTTTGTAAG
1 --TTATGTAAG
2754659 TTATGTAAG
1 TTATGTAAG
* *
2754668 TTATAT-AT
1 TTATGTAAG
*
2754676 TTATCTAAG
1 TTATGTAAG
*
2754685 TTATATAAG
1 TTATGTAAG
*
2754694 TTATATAAG
1 TTATGTAAG
*
2754703 TTATGTATG
1 TTATGTAAG
*
2754712 TTATATAAG
1 TTATGTAAG
2754721 TTATGTAAG
1 TTATGTAAG
* *
2754730 TTATATATG
1 TTATGTAAG
*
2754739 TTATATAAG
1 TTATGTAAG
2754748 TTATGTAA
1 TTATGTAA
2754756 ATTAAGATAT
Statistics
Matches: 164, Mismatches: 36, Indels: 22
0.74 0.16 0.10
Matches are distributed among these distances:
8 16 0.10
9 125 0.76
10 7 0.04
11 7 0.04
12 2 0.01
13 4 0.02
14 3 0.02
ACGTcount: A:0.38, C:0.01, G:0.13, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:2754615 original size:18 final size:18
Alignment explanation
Indices: 2754536--2754751 Score: 150
Period size: 18 Copynumber: 11.7 Consensus size: 18
2754526 TATTTAAGTA
* *
2754536 TTATGTAAGTTATGTAAT
1 TTATGTAAGTTATATAAG
* * *
2754554 TTATGATATGATATAT-AT
1 TTATG-TAAGTTATATAAG
* *
2754572 TTATGTAAATTATAT-AT
1 TTATGTAAGTTATATAAG
*
2754589 TTATCTAAGTTATATAAG
1 TTATGTAAGTTATATAAG
* *
2754607 TTATGTAAGTTATGTAAA
1 TTATGTAAGTTATATAAG
* *
2754625 TTATGATATAAAATATATTTAAG
1 TTATG---T-AAGT-TATATAAG
* *
2754648 TATTTTGTAAGTTATGTAAG
1 --TTATGTAAGTTATATAAG
* * *
2754668 TTATAT-ATTTATCTAAG
1 TTATGTAAGTTATATAAG
*
2754685 TTATATAAGTTATATAAG
1 TTATGTAAGTTATATAAG
*
2754703 TTATGTATGTTATATAAG
1 TTATGTAAGTTATATAAG
*
2754721 TTATGTAAGTTATATATG
1 TTATGTAAGTTATATAAG
*
2754739 TTATATAAGTTAT
1 TTATGTAAGTTAT
2754752 GTAAATTAAG
Statistics
Matches: 159, Mismatches: 29, Indels: 20
0.76 0.14 0.10
Matches are distributed among these distances:
17 37 0.23
18 90 0.57
19 7 0.04
20 7 0.04
21 4 0.03
22 4 0.03
23 6 0.04
25 4 0.03
ACGTcount: A:0.38, C:0.01, G:0.12, T:0.49
Consensus pattern (18 bp):
TTATGTAAGTTATATAAG
Found at i:2754628 original size:27 final size:27
Alignment explanation
Indices: 2754589--2754755 Score: 147
Period size: 27 Copynumber: 6.0 Consensus size: 27
2754579 AATTATATAT
*
2754589 TTATCTAAGTTATATAAGTTATGTAAG
1 TTATGTAAGTTATATAAGTTATGTAAG
* * *
2754616 TTATGTAAATTATGATATAAAATATATTTAAG
1 TTATGT-AAGT-T-ATAT-AAGT-TATGTAAG
* * * *
2754648 TATTTTGTAAGTTATGTAAGTTATAT-AT
1 --TTATGTAAGTTATATAAGTTATGTAAG
* *
2754676 TTATCTAAGTTATATAAGTTATATAAG
1 TTATGTAAGTTATATAAGTTATGTAAG
*
2754703 TTATGTATGTTATATAAGTTATGTAAG
1 TTATGTAAGTTATATAAGTTATGTAAG
* *
2754730 TTATATATGTTATATAAGTTATGTAA
1 TTATGTAAGTTATATAAGTTATGTAA
2754756 ATTAAGATAT
Statistics
Matches: 114, Mismatches: 18, Indels: 16
0.77 0.12 0.11
Matches are distributed among these distances:
26 21 0.18
27 55 0.48
28 4 0.04
29 5 0.04
30 7 0.06
31 6 0.05
32 8 0.07
33 3 0.03
34 5 0.04
ACGTcount: A:0.38, C:0.01, G:0.13, T:0.47
Consensus pattern (27 bp):
TTATGTAAGTTATATAAGTTATGTAAG
Found at i:2754646 original size:114 final size:114
Alignment explanation
Indices: 2754512--2754733 Score: 304
Period size: 114 Copynumber: 1.9 Consensus size: 114
2754502 ACTAGTTATG
* * * *
2754512 TATGATATGATATATATTTAAGTATTATGTAAGTTATGTAATTTATGATATGATATAT-ATTTAT
1 TATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTAT-ATAT-ATATATAAGTTAT
* *
2754576 GTAAATTATAT-ATTTATCTAAGTTATATAAGTTATGTAAGTTATGTAAAT
64 ATAAATTATATAAGTTATCTAAGTTATATAAGTTATGTAAGTTATGTAAAT
* * *
2754626 TATGATATAAAATATATTTAAGTATTTTGTAAGTTATGTAAGTTATATATTTATCTAAGTTATAT
1 TATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTATATATATATATAAGTTATAT
* * *
2754691 AAGTTATATAAGTTATGTATGTTATATAAGTTATGTAAGTTAT
66 AAATTATATAAGTTATCTAAGTTATATAAGTTATGTAAGTTAT
2754734 ATATGTTATA
Statistics
Matches: 94, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
112 4 0.04
113 18 0.19
114 72 0.77
ACGTcount: A:0.38, C:0.01, G:0.13, T:0.48
Consensus pattern (114 bp):
TATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTATATATATATATAAGTTATAT
AAATTATATAAGTTATCTAAGTTATATAAGTTATGTAAGTTATGTAAAT
Found at i:2754886 original size:15 final size:15
Alignment explanation
Indices: 2754866--2754921 Score: 73
Period size: 15 Copynumber: 3.8 Consensus size: 15
2754856 AAGTAGCGGG
2754866 ATTAAATAATATTTA
1 ATTAAATAATATTTA
2754881 ATTAAATAATATTT-
1 ATTAAATAATATTTA
2754895 A-TAAA-AATTATTTTA
1 ATTAAATAA-TA-TTTA
2754910 ATTAAATAATAT
1 ATTAAATAATAT
2754922 ACATGTCATT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
12 2 0.06
13 6 0.17
14 4 0.11
15 16 0.44
16 6 0.17
17 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
ATTAAATAATATTTA
Found at i:2755126 original size:24 final size:24
Alignment explanation
Indices: 2755098--2755165 Score: 93
Period size: 24 Copynumber: 2.8 Consensus size: 24
2755088 ACTTAAATGG
2755098 TAAAACGGACGATAATATTTGTAA
1 TAAAACGGACGATAATATTTGTAA
* *
2755122 TAAAACGGA-GAATAGTATTTGTGA
1 TAAAACGGACG-ATAATATTTGTAA
*
2755146 TAAAACGGACGAGAATATTT
1 TAAAACGGACGATAATATTT
2755166 CAATAATAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
23 1 0.03
24 36 0.95
25 1 0.03
ACGTcount: A:0.44, C:0.07, G:0.21, T:0.28
Consensus pattern (24 bp):
TAAAACGGACGATAATATTTGTAA
Found at i:2759230 original size:14 final size:15
Alignment explanation
Indices: 2759206--2759235 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
2759196 CACAAACTTC
2759206 AGAATTTATGTATTT
1 AGAATTTATGTATTT
2759221 AGAA-TTATGTATTT
1 AGAATTTATGTATTT
2759235 A
1 A
2759236 TATAAACACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (15 bp):
AGAATTTATGTATTT
Found at i:2761216 original size:28 final size:28
Alignment explanation
Indices: 2761146--2761238 Score: 84
Period size: 28 Copynumber: 3.2 Consensus size: 28
2761136 TTTTTGTGGG
2761146 GGGTTTAGGGTTT-TGGAGTTTATAGA-TTA
1 GGGTTTAGGGTTTAT-GA-TTTA-AGATTTA
* * * *
2761175 GTGTTTATGTTTTATGATTTAAAATTTA
1 GGGTTTAGGGTTTATGATTTAAGATTTA
2761203 GGGTTTAGGGTTTAATG-TTTAAGATTTAA
1 GGGTTTAGGGTTT-ATGATTTAAGATTT-A
2761232 GGGTTTA
1 GGGTTTA
2761239 CAGAAAGCCA
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
27 2 0.04
28 26 0.50
29 23 0.44
30 1 0.02
ACGTcount: A:0.25, C:0.00, G:0.27, T:0.48
Consensus pattern (28 bp):
GGGTTTAGGGTTTATGATTTAAGATTTA
Found at i:2761573 original size:41 final size:40
Alignment explanation
Indices: 2761528--2761785 Score: 193
Period size: 41 Copynumber: 6.6 Consensus size: 40
2761518 AACTTTTTGC
*
2761528 GGCGTTTGGACCAAAAACGCCGCTATTAATCAGTTTTTAGT
1 GGCGTTTGGA-CAAAAACGCCGCTATTGATCAGTTTTTAGT
* * *
2761569 GGCGTTTTGGATAAAAACGCCACAATTGATCAGCTTTTT-GT
1 GGCG-TTTGGACAAAAACGCCGCTATTGATCAG-TTTTTAGT
2761610 GGCGTTTGGGACAAAAACGCCGC-----A--A---TTTAGT
1 GGCGTTT-GGACAAAAACGCCGCTATTGATCAGTTTTTAGT
** * *
2761641 GGCGTTTGAGATTAAAACGCCACTATTGATCAGCTTTTAGT
1 GGCGTTTG-GACAAAAACGCCGCTATTGATCAGTTTTTAGT
* * * *
2761682 GGCGTTTTGATAAAAACGCCGCTATTGACCAATTTTTAGT
1 GGCGTTTGGACAAAAACGCCGCTATTGATCAGTTTTTAGT
* * * * *
2761722 GGCGTTTTTGG-CAAAAATGCCGCTATAGTTTAGCTTTTAGT
1 GGCG--TTTGGACAAAAACGCCGCTATTGATCAGTTTTTAGT
2761763 GGCGTTTCGGAC--AAACGCCGCTA
1 GGCGTTT-GGACAAAAACGCCGCTA
2761786 ATGTATATTA
Statistics
Matches: 173, Mismatches: 25, Indels: 40
0.73 0.11 0.17
Matches are distributed among these distances:
30 4 0.02
31 20 0.12
34 1 0.01
36 2 0.01
38 1 0.01
39 13 0.08
40 36 0.21
41 81 0.47
42 15 0.09
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.32
Consensus pattern (40 bp):
GGCGTTTGGACAAAAACGCCGCTATTGATCAGTTTTTAGT
Found at i:2761658 original size:72 final size:71
Alignment explanation
Indices: 2761563--2761703 Score: 212
Period size: 72 Copynumber: 2.0 Consensus size: 71
2761553 TTAATCAGTT
*
2761563 TTTAGTGGCGTTTTGGATAAAAACGCCACAATTGATCAGCTTTTTGTGGCGTTTGGGACAAAAAC
1 TTTAGTGGCGTTTTGGATAAAAACGCCACAATTGATCAGCTTTTAGTGGCGTTT-GGACAAAAAC
2761628 GCCGCAA
65 GCCGCAA
* * * *
2761635 TTTAGTGGCG-TTTGAGATTAAAACGCCACTATTGATCAGCTTTTAGTGGCGTTTTGATAAAAAC
1 TTTAGTGGCGTTTTG-GATAAAAACGCCACAATTGATCAGCTTTTAGTGGCGTTTGGACAAAAAC
2761699 GCCGC
65 GCCGC
2761704 TATTGACCAA
Statistics
Matches: 63, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
71 17 0.27
72 46 0.73
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (71 bp):
TTTAGTGGCGTTTTGGATAAAAACGCCACAATTGATCAGCTTTTAGTGGCGTTTGGACAAAAACG
CCGCAA
Found at i:2767112 original size:21 final size:22
Alignment explanation
Indices: 2767083--2767129 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
2767073 CAGAAGGAGT
*
2767083 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
2767105 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
2767126 GAGT
1 GAGT
2767130 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:2775275 original size:13 final size:13
Alignment explanation
Indices: 2775255--2775288 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
2775245 GGTAGTGGGT
2775255 TTAA-TGGGTAGG
1 TTAATTGGGTAGG
2775267 TTAATTGGGTAGG
1 TTAATTGGGTAGG
2775280 TTAATTGGG
1 TTAATTGGG
2775289 CTGAAGGTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.19
13 17 0.81
ACGTcount: A:0.24, C:0.00, G:0.38, T:0.38
Consensus pattern (13 bp):
TTAATTGGGTAGG
Found at i:2779263 original size:25 final size:23
Alignment explanation
Indices: 2779234--2779298 Score: 66
Period size: 25 Copynumber: 2.9 Consensus size: 23
2779224 AATAAAAAAC
*
2779234 TTTAAAATATAATAAATCAAATACA
1 TTTAAAACATAA-AAAT-AAATACA
2779259 TTTAAAACATAAAAATAAAT--A
1 TTTAAAACATAAAAATAAATACA
*
2779280 -TTAAAACA-AAAAACAAATA
1 TTTAAAACATAAAAATAAATA
2779299 AAAAATGAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
19 9 0.24
20 8 0.22
21 1 0.03
23 4 0.11
24 4 0.11
25 11 0.30
ACGTcount: A:0.66, C:0.08, G:0.00, T:0.26
Consensus pattern (23 bp):
TTTAAAACATAAAAATAAATACA
Found at i:2779291 original size:19 final size:20
Alignment explanation
Indices: 2779260--2779298 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
2779250 TCAAATACAT
*
2779260 TTAAAACATAAAAATAAATA
1 TTAAAACATAAAAACAAATA
2779280 TTAAAACA-AAAAACAAATA
1 TTAAAACATAAAAACAAATA
2779299 AAAAATGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.21
Consensus pattern (20 bp):
TTAAAACATAAAAACAAATA
Found at i:2780179 original size:17 final size:17
Alignment explanation
Indices: 2780146--2780179 Score: 52
Period size: 16 Copynumber: 2.0 Consensus size: 17
2780136 TTTAATTAAG
2780146 TAAATTATTAAAAATTA
1 TAAATTATTAAAAATTA
2780163 TAAA-TATTAAAATATTA
1 TAAATTATTAAAA-ATTA
2780180 GATAATAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAATTATTAAAAATTA
Found at i:2782490 original size:22 final size:19
Alignment explanation
Indices: 2782465--2782535 Score: 67
Period size: 16 Copynumber: 3.6 Consensus size: 19
2782455 TTAATTTTAA
2782465 TATTATTTATACTATTATATTT
1 TATTATTTAT--TATTATA-TT
2782487 TATTACTATTATTATTATATT
1 TATTA-T-TTATTATTATATT
*
2782508 TATTA--T-TTATTGTATT
1 TATTATTTATTATTATATT
2782524 TATTATTTATTA
1 TATTATTTATTA
2782536 GCATTAGTAT
Statistics
Matches: 43, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
16 14 0.33
17 1 0.02
18 1 0.02
19 3 0.07
21 7 0.16
22 12 0.28
23 1 0.02
24 4 0.09
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (19 bp):
TATTATTTATTATTATATT
Done.