Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 78 of 345
Found at i:21527091 original size:21 final size:21
Alignment explanation
Indices: 21527043--21527109 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
21527033 TATAAATAGA
21527043 ATAAATAACATATAATAAAA---
1 ATAAA-AA-ATATAATAAAATTT
*
21527063 ATATAAAATATAATAAAATTT
1 ATAAAAAATATAATAAAATTT
* *
21527084 ATAAAAAATGT-ATATAATATT
1 ATAAAAAATATAATAAAAT-TT
21527105 ATAAA
1 ATAAA
21527110 TAATGAAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
18 11 0.28
19 2 0.05
20 10 0.26
21 16 0.41
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (21 bp):
ATAAAAAATATAATAAAATTT
Found at i:21527112 original size:25 final size:25
Alignment explanation
Indices: 21527084--21527132 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
21527074 AATAAAATTT
21527084 ATAA-AAAATGTATATAATATTATAA
1 ATAATAAAAT-TATATAATATTATAA
* *
21527109 ATAATGAAATTATATATTATTATA
1 ATAATAAAATTATATAATATTATA
21527133 TACAACTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (25 bp):
ATAATAAAATTATATAATATTATAA
Found at i:21527158 original size:2 final size:2
Alignment explanation
Indices: 21527146--21527177 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
21527136 AACTAATGTT
*
21527146 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21527178 GTATTTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:21527221 original size:28 final size:28
Alignment explanation
Indices: 21527180--21527233 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
21527170 TATATATAGT
21527180 ATTTAAAATAAATTGAATTTCAAAAAAA
1 ATTTAAAATAAATTGAATTTCAAAAAAA
* * * *
21527208 ATTTAAATTTAATTTAATTTTAAAAA
1 ATTTAAAATAAATTGAATTTCAAAAA
21527234 TTTAGGGTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (28 bp):
ATTTAAAATAAATTGAATTTCAAAAAAA
Found at i:21528697 original size:44 final size:44
Alignment explanation
Indices: 21528642--21529107 Score: 604
Period size: 44 Copynumber: 10.8 Consensus size: 44
21528632 GATGTCCTTG
* *
21528642 AGAGACGCCAAATCTGCTATCTTCAATCTGCTCTCTGACAATAT
1 AGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATAC
* *
21528686 AGAGACACCAAATCTGCTATCTTCGATTTGCTCTCTGACAATAC
1 AGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATAC
* * * * *
21528730 AGAGATGCCAAATCTACTATCTTCAATCTGCTCTCTGACAACAT
1 AGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATAC
* *
21528774 AGAGACACCAAATCTGCTATCTTCGATATGCTCTCTGACAATAC
1 AGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATAC
* *
21528818 AGAGATGCCAAATCTGCTATCTTCGATCTACTCTCTGACAATAC
1 AGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATAC
* *
21528862 AGAGACACCAAATCTGCTATCTTCGATCTGCTCTCTAACAATAC
1 AGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATAC
* * * * *
21528906 AAAGACGCCAAATCTACAATCTTTGATCTACTCTCTGACAATAC
1 AGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATAC
* *
21528950 AGAGACGCTAAATCTGCTATCTTCGATCTGCTCTCTGACAATAT
1 AGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATAC
* *
21528994 AAAGACGCCAAATCTGCTA------A-CTGCTCTTTGACAATAC
1 AGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATAC
* * *
21529031 AGAGACGCCAAATCTACTATCTTCGATCTACTTTCTGACAATAC
1 AGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATAC
* * * *
21529075 AGAGATGCCAAATTTGTTATCTTCGATATGCTC
1 AGAGACGCCAAATCTGCTATCTTCGATCTGCTC
21529108 CTTGTAAACA
Statistics
Matches: 359, Mismatches: 56, Indels: 14
0.84 0.13 0.03
Matches are distributed among these distances:
37 32 0.09
38 1 0.00
43 1 0.00
44 325 0.91
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.29
Consensus pattern (44 bp):
AGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATAC
Found at i:21529058 original size:81 final size:81
Alignment explanation
Indices: 21528936--21529087 Score: 232
Period size: 81 Copynumber: 1.9 Consensus size: 81
21528926 CTTTGATCTA
* * * *
21528936 CTCTCTGACAATACAGAGACGCTAAATCTGCTATCTTCGATCTGCTCTCTGACAATATAAAGACG
1 CTCTCTGACAATACAGAGACGCCAAATCTACTATCTTCGATCTACTCTCTGACAATACAAAGACG
21529001 CCAAATCTGCTAACTG
66 CCAAATCTGCTAACTG
* * * *
21529017 CTCTTTGACAATACAGAGACGCCAAATCTACTATCTTCGATCTACTTTCTGACAATACAGAGATG
1 CTCTCTGACAATACAGAGACGCCAAATCTACTATCTTCGATCTACTCTCTGACAATACAAAGACG
21529082 CCAAAT
66 CCAAAT
21529088 TTGTTATCTT
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
81 63 1.00
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.28
Consensus pattern (81 bp):
CTCTCTGACAATACAGAGACGCCAAATCTACTATCTTCGATCTACTCTCTGACAATACAAAGACG
CCAAATCTGCTAACTG
Found at i:21543213 original size:27 final size:30
Alignment explanation
Indices: 21543176--21543240 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
21543166 TAGAATAATC
* *
21543176 AATATATATAG-T-AACAATATATAAT-AA
1 AATATAAATAGATAAACAACATATAATAAA
*
21543203 AATATAAATAGAATAAATAACATATAATAAA
1 AATATAAATAG-ATAAACAACATATAATAAA
21543234 AATATAA
1 AATATAA
21543241 CATATAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 10 0.32
29 1 0.03
30 11 0.35
31 9 0.29
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (30 bp):
AATATAAATAGATAAACAACATATAATAAA
Found at i:21543227 original size:20 final size:18
Alignment explanation
Indices: 21543198--21543252 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 18
21543188 AACAATATAT
*
21543198 AATAAAATATAAATAGAATA
1 AATAACATATAAATA-AA-A
21543218 AATAACATAT-AATAAAA
1 AATAACATATAAATAAAA
21543235 ATATAACATAT-AATAAAA
1 A-ATAACATATAAATAAAA
21543253 TTTAAAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
17 2 0.06
18 18 0.55
19 4 0.12
20 9 0.27
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.25
Consensus pattern (18 bp):
AATAACATATAAATAAAA
Found at i:21543815 original size:26 final size:26
Alignment explanation
Indices: 21543779--21543914 Score: 236
Period size: 26 Copynumber: 5.2 Consensus size: 26
21543769 TGATACAAAT
21543779 TGATAATAGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
21543805 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
21543831 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
21543857 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
21543883 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
21543909 TGATAA
1 TGATAA
21543915 GAATTTCATG
Statistics
Matches: 107, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 107 1.00
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:21549253 original size:18 final size:18
Alignment explanation
Indices: 21549222--21549278 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
21549212 AGATTTTTTC
21549222 TTTTTTAAGTTTTATATTAT
1 TTTTTTAA--TTTATATTAT
* **
21549242 TTTTTTAATTTATTTTGC
1 TTTTTTAATTTATATTAT
*
21549260 TTATTTAATTTATATTAT
1 TTTTTTAATTTATATTAT
21549278 T
1 T
21549279 AATTTTAAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
18 22 0.73
20 8 0.27
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTTTTAATTTATATTAT
Found at i:21549337 original size:21 final size:23
Alignment explanation
Indices: 21549281--21549353 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 23
21549271 ATATTATTAA
*
21549281 TTTTAAAACA-TTTGTAATATAT
1 TTTTAAAACATTTTATAATATAT
* **
21549303 ATTTAAAATGTTTTATAATAT-T
1 TTTTAAAACATTTTATAATATAT
*
21549325 TTTTAAAA-ATTTTA-ATTATTAT
1 TTTTAAAACATTTTATAATA-TAT
21549347 TTTTAAA
1 TTTTAAA
21549354 TATATTTTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
20 3 0.07
21 6 0.15
22 23 0.56
23 9 0.22
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (23 bp):
TTTTAAAACATTTTATAATATAT
Found at i:21549572 original size:2 final size:2
Alignment explanation
Indices: 21549565--21549592 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
21549555 GTTTAAATAA
21549565 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21549593 TTATTATAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21549670 original size:26 final size:27
Alignment explanation
Indices: 21549634--21549694 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 27
21549624 GTGACTATTA
*
21549634 ATAAATTTATATA-TAAATATAAATTTT
1 ATAAATATATATATTAAATAT-AATTTT
*
21549661 A-AAATATATATATTAAATATTATTTT
1 ATAAATATATATATTAAATATAATTTT
21549687 ATAAATAT
1 ATAAATAT
21549695 TAAATATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 16 0.53
27 14 0.47
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
ATAAATATATATATTAAATATAATTTT
Found at i:21549709 original size:23 final size:21
Alignment explanation
Indices: 21549665--21549706 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
21549655 AATTTTAAAA
*
21549665 TATATATATTAAATATTATTT
1 TATAAATATTAAATATTATTT
21549686 TATAAATATTAAATA-TATTT
1 TATAAATATTAAATATTATTT
21549706 T
1 T
21549707 TTTTCTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TATAAATATTAAATATTATTT
Found at i:21549907 original size:26 final size:27
Alignment explanation
Indices: 21549858--21549920 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 27
21549848 TTTTAAATAC
* *
21549858 AATTTTTAAATACATTTAAAAAATTAT
1 AATTTTTAAATACATATAAAAAATCAT
* *
21549885 AATTTTTTAATA-ATATAAGAAATCAT
1 AATTTTTAAATACATATAAAAAATCAT
*
21549911 AATATTTAAA
1 AATTTTTAAA
21549921 ATATTTTTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 19 0.63
27 11 0.37
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (27 bp):
AATTTTTAAATACATATAAAAAATCAT
Found at i:21549997 original size:17 final size:17
Alignment explanation
Indices: 21549969--21550011 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
21549959 CTTTTTTGAA
21549969 ATTTTATGTTTTTT-TCTT
1 ATTTTAT-TTTTTTAT-TT
21549987 ATTTTATTTTTTTATTT
1 ATTTTATTTTTTTATTT
21550004 ATTTTATT
1 ATTTTATT
21550012 ATTAATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.79
Consensus pattern (17 bp):
ATTTTATTTTTTTATTT
Found at i:21550006 original size:12 final size:12
Alignment explanation
Indices: 21549970--21550021 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
21549960 TTTTTTGAAA
21549970 TTTTATGTT-TTT
1 TTTTAT-TTATTT
21549982 TTCTTATTTTATTT
1 TT-TTA-TTTATTT
21549996 TTTTATTTATTT
1 TTTTATTTATTT
* *
21550008 TATTATTAATTT
1 TTTTATTTATTT
21550020 TT
1 TT
21550022 AAAATTTTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
12 20 0.59
13 8 0.24
14 6 0.18
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.79
Consensus pattern (12 bp):
TTTTATTTATTT
Found at i:21550028 original size:21 final size:21
Alignment explanation
Indices: 21550016--21550090 Score: 71
Period size: 21 Copynumber: 3.4 Consensus size: 21
21550006 TTTATTATTA
* *
21550016 ATTTTTAAAATTTTGTAATGT
1 ATTTTTAAAATTTTATAATAT
*
21550037 ATATTTAAAATGTTTTATAATAT
1 ATTTTTAAAA--TTTTATAATAT
*
21550060 ATTTTTTACAATTTTA-AATATT
1 A-TTTTTAAAATTTTATAATA-T
21550082 ATTTTTAAA
1 ATTTTTAAA
21550091 TTCTTTTTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
21 20 0.45
22 7 0.16
23 10 0.23
24 7 0.16
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (21 bp):
ATTTTTAAAATTTTATAATAT
Found at i:21550223 original size:18 final size:18
Alignment explanation
Indices: 21550200--21550238 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
21550190 GTAACGATTA
*
21550200 ATAAATTTAAATATAAAT
1 ATAAATTTAAAAATAAAT
*
21550218 ATAAATTTAAAAATATAT
1 ATAAATTTAAAAATAAAT
21550236 ATA
1 ATA
21550239 TTAAATATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAAATTTAAAAATAAAT
Found at i:21555543 original size:30 final size:30
Alignment explanation
Indices: 21555507--21555628 Score: 140
Period size: 30 Copynumber: 4.1 Consensus size: 30
21555497 GTCCCAGAGC
* *
21555507 AGTTCATATAACTCGGACATAGGTGGTTCG
1 AGTTCATATCACCCGGACATAGGTGGTTCG
* * *
21555537 AGTTCATATCA-CCGGACAT-GTATGTTTCA
1 AGTTCATATCACCCGGACATAG-GTGGTTCG
* *
21555566 AGTTCATATCACCCAGACATGGGTGGTTCG
1 AGTTCATATCACCCGGACATAGGTGGTTCG
* *
21555596 AGTTCATATCACCCGGATATAGGCGGTTCG
1 AGTTCATATCACCCGGACATAGGTGGTTCG
21555626 AGT
1 AGT
21555629 CCATTTGACC
Statistics
Matches: 76, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
28 1 0.01
29 23 0.30
30 51 0.67
31 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (30 bp):
AGTTCATATCACCCGGACATAGGTGGTTCG
Found at i:21559131 original size:20 final size:18
Alignment explanation
Indices: 21559083--21559224 Score: 59
Period size: 18 Copynumber: 7.9 Consensus size: 18
21559073 AATGTATTTT
*
21559083 TTAAAAATATTTTATAATA
1 TTAAATATATTTTA-AATA
*
21559102 -T--ATATTTTTTAAATA
1 TTAAATATATTTTAAATA
*
21559117 TTAAAAATATATTTTCAA-A
1 TT--AAATATATTTTAAATA
21559136 TT--AT-T-TTTTAAATA
1 TTAAATATATTTTAAATA
*
21559150 TTAAATATATTTTTAATA
1 TTAAATATATTTTAAATA
* * *
21559168 TTATAAAACATTTAAAATGA
1 TTA-AATATATTTTAAAT-A
* *
21559188 TTTAAAATATTTTTTAATATT
1 -TT-AAATATATTTTAA-ATA
*
21559209 TTAAAT-GATTTTAAAT
1 TTAAATATATTTTAAAT
21559225 TTTTTTAAAT
Statistics
Matches: 91, Mismatches: 17, Indels: 32
0.65 0.12 0.23
Matches are distributed among these distances:
13 6 0.07
14 4 0.04
15 6 0.07
16 11 0.12
17 3 0.03
18 18 0.20
19 17 0.19
20 13 0.14
21 10 0.11
22 3 0.03
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (18 bp):
TTAAATATATTTTAAATA
Found at i:21559146 original size:33 final size:33
Alignment explanation
Indices: 21559083--21559171 Score: 121
Period size: 33 Copynumber: 2.7 Consensus size: 33
21559073 AATGTATTTT
21559083 TTAAAAATAT-TTTATAATATATATTTTTTAAATA
1 TTAAAAATATATTT-TAATAT-TATTTTTTAAATA
21559117 TTAAAAATATATTTTCAA-ATTATTTTTTAAATA
1 TTAAAAATATATTTT-AATATTATTTTTTAAATA
*
21559150 TTAAATATAT-TTTTAATATTAT
1 TTAAAAATATATTTTAATATTAT
21559172 AAAACATTTA
Statistics
Matches: 51, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
31 2 0.04
32 9 0.18
33 22 0.43
34 13 0.25
35 5 0.10
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (33 bp):
TTAAAAATATATTTTAATATTATTTTTTAAATA
Found at i:21559180 original size:19 final size:19
Alignment explanation
Indices: 21559140--21559213 Score: 62
Period size: 19 Copynumber: 3.8 Consensus size: 19
21559130 TTCAAATTAT
*
21559140 TTTTTAAATATTA-AATATA
1 TTTTT-AATATTATAAAATA
*
21559159 TTTTTAATATTATAAAACA
1 TTTTTAATATTATAAAATA
**
21559178 TTTAAAATGATT-TAAAATA
1 TTTTTAAT-ATTATAAAATA
*
21559197 TTTTTTAATATTTTAAA
1 -TTTTTAATATTATAAA
21559214 TGATTTTAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
18 7 0.16
19 24 0.55
20 13 0.30
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (19 bp):
TTTTTAATATTATAAAATA
Found at i:21559214 original size:19 final size:19
Alignment explanation
Indices: 21559125--21559220 Score: 70
Period size: 20 Copynumber: 4.8 Consensus size: 19
21559115 TATTAAAAAT
21559125 ATATTTTCAAATTATTTTTTA
1 ATATTTT-AAA-TATTTTTTA
*
21559146 A-ATATTAAATATATTTTTA
1 ATATTTTAAATAT-TTTTTA
* * **
21559165 ATATTATAAA-ACATTTAAA
1 ATATTTTAAATA-TTTTTTA
*
21559184 ATGATTTAAAATATTTTTTA
1 AT-ATTTTAAATATTTTTTA
21559204 ATATTTTAAATGATTTT
1 ATATTTTAAAT-ATTTT
21559221 AAATTTTTTT
Statistics
Matches: 57, Mismatches: 12, Indels: 13
0.70 0.15 0.16
Matches are distributed among these distances:
18 3 0.05
19 25 0.44
20 27 0.47
21 2 0.04
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (19 bp):
ATATTTTAAATATTTTTTA
Found at i:21559219 original size:10 final size:9
Alignment explanation
Indices: 21559141--21559238 Score: 56
Period size: 10 Copynumber: 10.6 Consensus size: 9
21559131 TCAAATTATT
21559141 TTTTAAATA
1 TTTTAAATA
*
21559150 -TTAAATATA
1 TTTTAA-ATA
*
21559159 TTTTTAATA
1 TTTTAAATA
* *
21559168 TTATAAAACA
1 TT-TTAAATA
*
21559178 TTTAAAATGA
1 TTTTAAAT-A
*
21559188 TTTAAAATA
1 TTTTAAATA
*
21559197 TTTTTTAATA
1 -TTTTAAATA
21559207 TTTTAAATGA
1 TTTTAAAT-A
*
21559217 TTTTAAATT
1 TTTTAAATA
*
21559226 TTTTTAA-A
1 TTTTAAATA
21559234 TTTTA
1 TTTTA
21559239 CATAGAATTT
Statistics
Matches: 69, Mismatches: 14, Indels: 13
0.72 0.15 0.14
Matches are distributed among these distances:
8 8 0.12
9 27 0.39
10 34 0.49
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (9 bp):
TTTTAAATA
Found at i:21559248 original size:29 final size:28
Alignment explanation
Indices: 21559177--21559256 Score: 90
Period size: 29 Copynumber: 2.8 Consensus size: 28
21559167 ATTATAAAAC
* *
21559177 ATTTAAAATGATTTAAAATATTTTTTAAT
1 ATTTTAAATGATTTTAAAT-TTTTTTAAT
21559206 ATTTTAAATGATTTTAAATTTTTTTAA-
1 ATTTTAAATGATTTTAAATTTTTTTAAT
*
21559233 ATTTTACATAGAATTTTGAAATTT
1 ATTTTAAAT-G-ATTTT-AAATTT
21559257 ATAATTTTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
27 8 0.18
28 9 0.20
29 22 0.49
30 6 0.13
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.54
Consensus pattern (28 bp):
ATTTTAAATGATTTTAAATTTTTTTAAT
Found at i:21559976 original size:37 final size:36
Alignment explanation
Indices: 21559906--21559976 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 36
21559896 ATTAATTATT
*
21559906 TTTTTAAAATTCTAAAAAATTAATTTGAAAAATACA
1 TTTTTAAAATTCTAAAAAATTAATTTCAAAAATACA
*
21559942 TTTTTAAAATT-TATAAATAATTAATTTCACAAATA
1 TTTTTAAAATTCTA-AAA-AATTAATTTCAAAAATA
21559977 TATATATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
35 2 0.06
36 14 0.45
37 15 0.48
ACGTcount: A:0.51, C:0.06, G:0.01, T:0.42
Consensus pattern (36 bp):
TTTTTAAAATTCTAAAAAATTAATTTCAAAAATACA
Found at i:21560045 original size:22 final size:21
Alignment explanation
Indices: 21560000--21560040 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
21559990 AAAAAATATT
21560000 TTTAAAAATAATAATTAAAAA
1 TTTAAAAATAATAATTAAAAA
21560021 TTTAAAAA-AAT-ATTATAAAA
1 TTTAAAAATAATAATTA-AAAA
21560041 CATTTTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 7 0.37
21 8 0.42
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
TTTAAAAATAATAATTAAAAA
Found at i:21560047 original size:23 final size:22
Alignment explanation
Indices: 21559999--21560072 Score: 62
Period size: 23 Copynumber: 3.4 Consensus size: 22
21559989 AAAAAAATAT
*
21559999 TTTTAAAAATAATAAT-TAAAAA
1 TTTTAAAAA-AATATTATAAAAA
21560021 -TTTAAAAAAATATTATAAAACA
1 TTTTAAAAAAATATTATAAAA-A
* * * **
21560043 TTTTAAATATATATTACAAATT
1 TTTTAAAAAAATATTATAAAAA
21560065 TTTTAAAA
1 TTTTAAAA
21560073 TTAATAATAT
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
20 5 0.12
21 13 0.31
22 8 0.19
23 16 0.38
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (22 bp):
TTTTAAAAAAATATTATAAAAA
Found at i:21560120 original size:36 final size:36
Alignment explanation
Indices: 21560075--21560148 Score: 89
Period size: 36 Copynumber: 2.0 Consensus size: 36
21560065 TTTTAAAATT
*
21560075 AATAATATAAA-TTAAATAAGTAAAATAAAT-TAAGAA
1 AATAATATAAACTTAAAAAAG-AAAA-AAATCTAAGAA
*
21560111 AATATTATAAAGCTTAAAAAAGAAAAAAATCTAAGAA
1 AATAATATAAA-CTTAAAAAAGAAAAAAATCTAAGAA
21560148 A
1 A
21560149 GAGACAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
36 14 0.42
37 11 0.33
38 8 0.24
ACGTcount: A:0.66, C:0.03, G:0.07, T:0.24
Consensus pattern (36 bp):
AATAATATAAACTTAAAAAAGAAAAAAATCTAAGAA
Found at i:21560184 original size:7 final size:8
Alignment explanation
Indices: 21560165--21560194 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
21560155 AAATATAAGA
21560165 AAAAAAGT
1 AAAAAAGT
21560173 AAAAAAGT
1 AAAAAAGT
*
21560181 AAAAAAAT
1 AAAAAAGT
21560189 AAAAAA
1 AAAAAA
21560195 ATTTAAGAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.83, C:0.00, G:0.07, T:0.10
Consensus pattern (8 bp):
AAAAAAGT
Found at i:21565045 original size:2 final size:2
Alignment explanation
Indices: 21565040--21565080 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
21565030 AACATGAAAG
21565040 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
21565081 TAGTAAGCTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:21569563 original size:2 final size:2
Alignment explanation
Indices: 21569556--21569580 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
21569546 CGTAACATTG
21569556 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
21569581 ATGTTTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21572681 original size:46 final size:46
Alignment explanation
Indices: 21572631--21572806 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
21572621 TGGTTGAGCA
21572631 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
21572677 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
21572722 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
21572770 CCCGATCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
21572807 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 64 0.58
47 28 0.25
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:21572787 original size:93 final size:93
Alignment explanation
Indices: 21572628--21572798 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
21572618 GGATGGTTGA
* *
21572628 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
21572693 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
21572721 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGATCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
21572786 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
21572799 ACTTATGGGC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:21585143 original size:5 final size:6
Alignment explanation
Indices: 21585126--21585153 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
21585116 AAACAGAACT
21585126 AGAAAA AGAAAA AGAAAA AGAAAA AGAA
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAA
21585154 TCAAACTCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:21585969 original size:2 final size:2
Alignment explanation
Indices: 21585964--21585992 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
21585954 CTCTTTTTTG
21585964 AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21585993 TCTTGTTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21590545 original size:41 final size:41
Alignment explanation
Indices: 21590487--21590647 Score: 146
Period size: 41 Copynumber: 3.9 Consensus size: 41
21590477 AAAGGCAGCA
* *
21590487 AAAAACT-AAGCAGTAGCGGCGTTTTTGGTCCAAGCGCCACT
1 AAAAACTGAA-CAATAGCGGCGTTTTTGGTCCAAACGCCACT
* * *
21590528 AAAAACTGAACAATAGCGGCATTTTTTGGTCAAAAAGCCACT
1 AAAAACTGAACAATAGCGGC-GTTTTTGGTCCAAACGCCACT
* * * ** *
21590570 AAAAACCGAGCAATAGAGGCGTTTTTAATCCAAACGCCGC-
1 AAAAACTGAACAATAGCGGCGTTTTTGGTCCAAACGCCACT
* * * *
21590610 AAAAAGTTGAGCTATAGCAGCGTTTTTGGTCCAAACGC
1 AAAAA-CTGAACAATAGCGGCGTTTTTGGTCCAAACGC
21590648 TGCAAAAAGT
Statistics
Matches: 96, Mismatches: 21, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
40 5 0.05
41 55 0.57
42 36 0.38
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (41 bp):
AAAAACTGAACAATAGCGGCGTTTTTGGTCCAAACGCCACT
Found at i:21590555 original size:42 final size:41
Alignment explanation
Indices: 21590487--21590595 Score: 112
Period size: 42 Copynumber: 2.6 Consensus size: 41
21590477 AAAGGCAGCA
* * * **
21590487 AAAAACT-AAGCAGTAGCGGCGTTTTTGGTCCAAGCGCCACT
1 AAAAACTGAA-CAATAGCGGCTTTTTTGGTCAAAAAGCCACT
21590528 AAAAACTGAACAATAGCGGCATTTTTTGGTCAAAAAGCCACT
1 AAAAACTGAACAATAGCGGC-TTTTTTGGTCAAAAAGCCACT
* * * *
21590570 AAAAACCGAGCAATAGAGGCGTTTTT
1 AAAAACTGAACAATAGCGGCTTTTTT
21590596 AATCCAAACG
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
41 21 0.37
42 36 0.63
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (41 bp):
AAAAACTGAACAATAGCGGCTTTTTTGGTCAAAAAGCCACT
Found at i:21590954 original size:22 final size:21
Alignment explanation
Indices: 21590926--21590998 Score: 83
Period size: 22 Copynumber: 3.3 Consensus size: 21
21590916 TGGCTTTCTC
*
21590926 TAAACCCCTAATCCTTAAACCT
1 TAAA-CCCTAATCCTAAAACCT
* * *
21590948 TAAACCCTAATTTCTAAAAACA
1 TAAACCCTAA-TCCTAAAACCT
21590970 TAAACCCTAAATCCTAAAACCT
1 TAAACCCT-AATCCTAAAACCT
21590992 TAAACCC
1 TAAACCC
21590999 CAAAAAAATC
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
21 6 0.14
22 34 0.81
23 2 0.05
ACGTcount: A:0.44, C:0.32, G:0.00, T:0.25
Consensus pattern (21 bp):
TAAACCCTAATCCTAAAACCT
Found at i:21591710 original size:40 final size:39
Alignment explanation
Indices: 21591655--21591757 Score: 136
Period size: 40 Copynumber: 2.6 Consensus size: 39
21591645 GGCATTAACG
*
21591655 GCGCTTTTTGAAAAACGCCGCTAAAGATCAAGTATTAGC
1 GCGCTTTTTGAAAAACGCCGCTAAAGATCAAGAATTAGC
* *
21591694 AGCGCTTTTTGAAAAACGACGCTAAAGATCGAGAATTAGC
1 -GCGCTTTTTGAAAAACGCCGCTAAAGATCAAGAATTAGC
* * *
21591734 GGGCTTTTTCAAAAATGCCG-TAAA
1 GCGCTTTTTGAAAAACGCCGCTAAA
21591758 AAGTTTAATT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
38 4 0.07
39 16 0.29
40 36 0.64
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.25
Consensus pattern (39 bp):
GCGCTTTTTGAAAAACGCCGCTAAAGATCAAGAATTAGC
Found at i:21595350 original size:24 final size:24
Alignment explanation
Indices: 21595269--21595398 Score: 199
Period size: 24 Copynumber: 5.2 Consensus size: 24
21595259 CATGAAATTC
21595269 TTATCATGAAACATTTACCTAACCCA
1 TTATCATG-AACATTTACCTAA-CCA
21595295 TTATCATGAAACATTTACCTAACCCA
1 TTATCATG-AACATTTACCTAA-CCA
21595321 TTATCATGAACATTTACCTAACCA
1 TTATCATGAACATTTACCTAACCA
21595345 TTATCATGGAA-ATTTACCTAACCA
1 TTATCAT-GAACATTTACCTAACCA
*
21595369 TTATCATGAACATTTACCTAACTA
1 TTATCATGAACATTTACCTAACCA
21595393 TTATCA
1 TTATCA
21595399 ATTTGTATCA
Statistics
Matches: 101, Mismatches: 1, Indels: 6
0.94 0.01 0.06
Matches are distributed among these distances:
23 3 0.03
24 48 0.48
25 16 0.16
26 34 0.34
ACGTcount: A:0.38, C:0.24, G:0.05, T:0.34
Consensus pattern (24 bp):
TTATCATGAACATTTACCTAACCA
Found at i:21601047 original size:26 final size:26
Alignment explanation
Indices: 21601011--21601146 Score: 218
Period size: 26 Copynumber: 5.2 Consensus size: 26
21601001 CATGAAATTC
21601011 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
*
21601037 TTATCATGAAACATTTACCTAACTCA
1 TTATCATGAAACATTTACCTAACCCA
21601063 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* * *
21601089 TTATCATGGAATATTTACCTAATCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
21601115 TTGTCATGAAACATTTACCTAACTCA
1 TTATCATGAAACATTTACCTAACCCA
21601141 TTATCA
1 TTATCA
21601147 ATTTGTATCA
Statistics
Matches: 99, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 99 1.00
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:21604125 original size:9 final size:9
Alignment explanation
Indices: 21604102--21604139 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
21604092 TTAAAGTTTA
21604102 AATTT-CAT
1 AATTTACAT
*
21604110 AACTTACAT
1 AATTTACAT
21604119 AATTTACAT
1 AATTTACAT
*
21604128 AACTTACAT
1 AATTTACAT
21604137 AAT
1 AAT
21604140 ACATAAATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
8 4 0.16
9 21 0.84
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (9 bp):
AATTTACAT
Found at i:21604130 original size:18 final size:18
Alignment explanation
Indices: 21604102--21604274 Score: 84
Period size: 18 Copynumber: 9.2 Consensus size: 18
21604092 TTAAAGTTTA
21604102 AATTT-CATAACTTACAT
1 AATTTACATAACTTACAT
21604119 AATTTACATAACTTACAT
1 AATTTACATAACTTACAT
* *
21604137 AA--TACATAAATATATAT
1 AATTTACATAACT-TACAT
* *
21604154 CATAT-CATAACTTACAT
1 AATTTACATAACTTACAT
* * *
21604171 AACTCACACAACTTACAT
1 AATTTACATAACTTACAT
* *
21604189 AATAACTTATATATATCATATCAT
1 AAT---TTACATA-A-CTTA-CAT
* *
21604213 AACTTACATAACTCACAT
1 AATTTACATAACTTACAT
* *
21604231 AACTTACATACCTCACCTCACAT
1 AATTTACATA----A-CTTACAT
*
21604254 AACTTACATAACTTACAT
1 AATTTACATAACTTACAT
21604272 AAT
1 AAT
21604275 ACATAAATAG
Statistics
Matches: 119, Mismatches: 21, Indels: 31
0.70 0.12 0.18
Matches are distributed among these distances:
16 8 0.07
17 15 0.13
18 54 0.45
19 4 0.03
20 1 0.01
21 10 0.08
22 2 0.02
23 20 0.17
24 5 0.04
ACGTcount: A:0.45, C:0.22, G:0.00, T:0.34
Consensus pattern (18 bp):
AATTTACATAACTTACAT
Found at i:21604171 original size:9 final size:9
Alignment explanation
Indices: 21604159--21604311 Score: 87
Period size: 9 Copynumber: 16.0 Consensus size: 9
21604149 TATATCATAT
21604159 CATAACTTA
1 CATAACTTA
*
21604168 CATAACTCA
1 CATAACTTA
*
21604177 CACAACTTA
1 CATAACTTA
21604186 CATAATAACTTA
1 C---ATAACTTA
* *
21604198 TATATATCATA
1 CATA-A-CTTA
21604209 TCATAACTTA
1 -CATAACTTA
*
21604219 CATAACTCA
1 CATAACTTA
21604228 CATAACTTA
1 CATAACTTA
*
21604237 CATACCTCACCTCA
1 CATA----A-CTTA
21604251 CATAACTTA
1 CATAACTTA
21604260 CATAACTTA
1 CATAACTTA
21604269 CATAA--TA
1 CATAACTTA
*
21604276 CATAA-ATA
1 CATAACTTA
* * *
21604284 GATATCATA
1 CATAACTTA
21604293 TCATAACTTA
1 -CATAACTTA
21604303 CATAACTTA
1 CATAACTTA
21604312 ATTATACTTA
Statistics
Matches: 113, Mismatches: 17, Indels: 28
0.72 0.11 0.18
Matches are distributed among these distances:
7 7 0.06
8 5 0.04
9 68 0.60
10 11 0.10
11 4 0.04
12 10 0.09
13 1 0.01
14 7 0.06
ACGTcount: A:0.44, C:0.24, G:0.01, T:0.31
Consensus pattern (9 bp):
CATAACTTA
Found at i:21604222 original size:51 final size:52
Alignment explanation
Indices: 21604106--21604240 Score: 211
Period size: 51 Copynumber: 2.6 Consensus size: 52
21604096 AGTTTAAATT
* *
21604106 TCATAACTTACATAATTTACATAACTTACATAATACATAAATATATATCATA
1 TCATAACTTACATAACTCACATAACTTACATAATACATAAATATATATCATA
* *
21604158 TCATAACTTACATAACTCACACAACTTACATAATA-ACT-TATATATATCATA
1 TCATAACTTACATAACTCACATAACTTACATAATACA-TAAATATATATCATA
21604209 TCATAACTTACATAACTCACATAACTTACATA
1 TCATAACTTACATAACTCACATAACTTACATA
21604241 CCTCACCTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
51 44 0.57
52 33 0.43
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (52 bp):
TCATAACTTACATAACTCACATAACTTACATAATACATAAATATATATCATA
Found at i:21604463 original size:15 final size:15
Alignment explanation
Indices: 21604443--21604481 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
21604433 AGTAAAAACT
21604443 TTTCTAAATTTTGTA
1 TTTCTAAATTTTGTA
21604458 TTTCTAAATTTTGTA
1 TTTCTAAATTTTGTA
*
21604473 TTTCAAAAT
1 TTTCTAAAT
21604482 GCAAGCCAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.31, C:0.08, G:0.05, T:0.56
Consensus pattern (15 bp):
TTTCTAAATTTTGTA
Found at i:21608804 original size:13 final size:14
Alignment explanation
Indices: 21608788--21608816 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
21608778 TTTTAAATAT
21608788 TTATAAT-GTTTAA
1 TTATAATGGTTTAA
21608801 TTATAATGGTTTAA
1 TTATAATGGTTTAA
21608815 TT
1 TT
21608817 CGTCATTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (14 bp):
TTATAATGGTTTAA
Found at i:21613165 original size:21 final size:21
Alignment explanation
Indices: 21613103--21613165 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
21613093 ATTTGTTTGC
*
21613103 TTATTGTAAGAATATTTTTAA
1 TTATTGTAAGAATATTTTAAA
* *
21613124 -CATTGT-A-AAT-TTTAAAA
1 TTATTGTAAGAATATTTTAAA
*
21613141 TTATTGTAAGAATATTTTGAA
1 TTATTGTAAGAATATTTTAAA
21613162 TTAT
1 TTAT
21613166 ACTTCATTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
17 5 0.16
18 8 0.25
19 2 0.06
20 8 0.25
21 9 0.28
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.49
Consensus pattern (21 bp):
TTATTGTAAGAATATTTTAAA
Found at i:21613486 original size:14 final size:14
Alignment explanation
Indices: 21613465--21613497 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
21613455 ACTTATAGAC
21613465 CTAAAAAAATGCC-
1 CTAAAAAAATGCCA
21613478 CTAAAAAAATGCCA
1 CTAAAAAAATGCCA
21613492 CTAAAA
1 CTAAAA
21613498 GTCTGTTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.58, C:0.21, G:0.06, T:0.15
Consensus pattern (14 bp):
CTAAAAAAATGCCA
Found at i:21618178 original size:24 final size:24
Alignment explanation
Indices: 21618151--21618198 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
21618141 ACAATATGAT
21618151 AACACCAGCAATTCATAGAGCATC
1 AACACCAGCAATTCATAGAGCATC
21618175 AACACCAGCAATTCATAGAGCATC
1 AACACCAGCAATTCATAGAGCATC
21618199 TTACTTGTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.29, G:0.12, T:0.17
Consensus pattern (24 bp):
AACACCAGCAATTCATAGAGCATC
Found at i:21624006 original size:6 final size:6
Alignment explanation
Indices: 21623995--21624043 Score: 62
Period size: 6 Copynumber: 7.5 Consensus size: 6
21623985 GGCAACCCAA
21623995 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT ATATATATAT TTTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT -T-T-T-TAT TTTTAT TTT
21624044 CTTGAGTGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
6 30 0.77
7 2 0.05
8 2 0.05
9 2 0.05
10 3 0.08
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTTAT
Found at i:21624230 original size:20 final size:19
Alignment explanation
Indices: 21624205--21624248 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
21624195 GCTTTAAACT
21624205 CACCCAAACCTACGCCCAAA
1 CACCC-AACCTACGCCCAAA
*
21624225 CACCCACCCTACGCCCAAA
1 CACCCAACCTACGCCCAAA
21624244 CACCC
1 CACCC
21624249 TTCTTATTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.34, C:0.57, G:0.05, T:0.05
Consensus pattern (19 bp):
CACCCAACCTACGCCCAAA
Found at i:21625337 original size:8 final size:7
Alignment explanation
Indices: 21625319--21625356 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
21625309 TATATTCTTA
21625319 AAAAAAG
1 AAAAAAG
*
21625326 AAAAATG
1 AAAAAAG
21625333 AAAAAAG
1 AAAAAAG
21625340 AAAAAAG
1 AAAAAAG
21625347 AAAAAA-
1 AAAAAAG
21625353 AAAA
1 AAAA
21625357 GAGGGAGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
6 4 0.14
7 25 0.86
ACGTcount: A:0.87, C:0.00, G:0.11, T:0.03
Consensus pattern (7 bp):
AAAAAAG
Found at i:21633429 original size:36 final size:37
Alignment explanation
Indices: 21633382--21633456 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 37
21633372 ACACATTATA
21633382 CTTCATTTAATTGTATTTACTCC-TTTTGTCCTATTT
1 CTTCATTTAATTGTATTTACTCCTTTTTGTCCTATTT
21633418 CTTCATTTAATTGTATTTACTCCTTTTTGTCCTATTT
1 CTTCATTTAATTGTATTTACTCCTTTTTGTCCTATTT
21633455 CT
1 CT
21633457 ACTACCATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 23 0.61
37 15 0.39
ACGTcount: A:0.16, C:0.20, G:0.05, T:0.59
Consensus pattern (37 bp):
CTTCATTTAATTGTATTTACTCCTTTTTGTCCTATTT
Found at i:21633434 original size:18 final size:19
Alignment explanation
Indices: 21633380--21633438 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 19
21633370 ATACACATTA
21633380 TACTTCATTTAATTGTATT
1 TACTTCATTTAATTGTATT
* ** **
21633399 TAC-TCCTTTTGTCCTATT
1 TACTTCATTTAATTGTATT
21633417 T-CTTCATTTAATTGTATT
1 TACTTCATTTAATTGTATT
21633435 TACT
1 TACT
21633439 CCTTTTTGTC
Statistics
Matches: 28, Mismatches: 10, Indels: 4
0.67 0.24 0.10
Matches are distributed among these distances:
17 1 0.04
18 22 0.79
19 5 0.18
ACGTcount: A:0.20, C:0.17, G:0.05, T:0.58
Consensus pattern (19 bp):
TACTTCATTTAATTGTATT
Found at i:21633799 original size:29 final size:30
Alignment explanation
Indices: 21633767--21633829 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 30
21633757 AAGTTTTATG
*
21633767 TATAAAATTATACA-AAATCAAAATTCATA
1 TATAAAATTACACATAAATCAAAATTCATA
*
21633796 TATAACATTACACATTAAATCAAAATTCATA
1 TATAAAATTACACA-TAAATCAAAATTCATA
21633827 TAT
1 TAT
21633830 GATTTTAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 12 0.40
31 18 0.60
ACGTcount: A:0.54, C:0.13, G:0.00, T:0.33
Consensus pattern (30 bp):
TATAAAATTACACATAAATCAAAATTCATA
Found at i:21637333 original size:75 final size:75
Alignment explanation
Indices: 21637210--21637359 Score: 300
Period size: 75 Copynumber: 2.0 Consensus size: 75
21637200 AGTTCTAACA
21637210 TGGTTAAAATGAACTTAAGATGATTTGTTATATGAAATGCACATGTTATATGGAAATATGATATG
1 TGGTTAAAATGAACTTAAGATGATTTGTTATATGAAATGCACATGTTATATGGAAATATGATATG
21637275 AAAAGCACAT
66 AAAAGCACAT
21637285 TGGTTAAAATGAACTTAAGATGATTTGTTATATGAAATGCACATGTTATATGGAAATATGATATG
1 TGGTTAAAATGAACTTAAGATGATTTGTTATATGAAATGCACATGTTATATGGAAATATGATATG
21637350 AAAAGCACAT
66 AAAAGCACAT
21637360 GTTTATGAAA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 75 1.00
ACGTcount: A:0.41, C:0.07, G:0.19, T:0.33
Consensus pattern (75 bp):
TGGTTAAAATGAACTTAAGATGATTTGTTATATGAAATGCACATGTTATATGGAAATATGATATG
AAAAGCACAT
Found at i:21637429 original size:43 final size:43
Alignment explanation
Indices: 21637381--21637463 Score: 166
Period size: 43 Copynumber: 1.9 Consensus size: 43
21637371 TTACTACATG
21637381 ATGAGTTCATCTTTGATTCTTGAAATTTATGTGAAGTAATGAT
1 ATGAGTTCATCTTTGATTCTTGAAATTTATGTGAAGTAATGAT
21637424 ATGAGTTCATCTTTGATTCTTGAAATTTATGTGAAGTAAT
1 ATGAGTTCATCTTTGATTCTTGAAATTTATGTGAAGTAAT
21637464 AACTAACATG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.30, C:0.07, G:0.18, T:0.45
Consensus pattern (43 bp):
ATGAGTTCATCTTTGATTCTTGAAATTTATGTGAAGTAATGAT
Found at i:21654340 original size:47 final size:47
Alignment explanation
Indices: 21654271--21654366 Score: 183
Period size: 47 Copynumber: 2.0 Consensus size: 47
21654261 ACATGCATGT
21654271 TATCCCATGTTTTTATTTTTCCTTTTTGGTTTACAAATATCACTGTA
1 TATCCCATGTTTTTATTTTTCCTTTTTGGTTTACAAATATCACTGTA
*
21654318 TATCCCATGTTTTTATTTTTCCTTTTTGGTTTACAAATATCACTTTA
1 TATCCCATGTTTTTATTTTTCCTTTTTGGTTTACAAATATCACTGTA
21654365 TA
1 TA
21654367 CTTTCCAACG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.22, C:0.17, G:0.07, T:0.54
Consensus pattern (47 bp):
TATCCCATGTTTTTATTTTTCCTTTTTGGTTTACAAATATCACTGTA
Found at i:21654639 original size:129 final size:126
Alignment explanation
Indices: 21654460--21654784 Score: 425
Period size: 129 Copynumber: 2.5 Consensus size: 126
21654450 TAAAAATTCC
*
21654460 TTAAAACGAAGGCAATGTTTGATGTTTGGAAATTCGGGAAATCGTGCCCTACCGTGCTGGGTTTC
1 TTAAAAC-AAGGCAATGTTTGATG-TTGGAAATTCGGGGAATCGTGCCCTACCGTGCTGGGTTTC
* * *
21654525 GATTTCCCGTTTGTTCAAAATAATCGAACCTTCCTTTAGAATTTCATTCGTTTTTCTTCTAAATT
64 GATTTCCCGTTTGTTCAAAATAATCAAACATTCCTTTAGAATTTCATTCG-TATTCTT-TAAATT
* * * * *
21654590 TTAAAACAATGCAATGTTTGATGCTTGGAAATTTGGGGAACCGTGCCCTATCGTGTTGGGTTTCG
1 TTAAAACAAGGCAATGTTTGATG-TTGGAAATTCGGGGAATCGTGCCCTACCGTGCTGGGTTTCG
* * * * *
21654655 ATTTCTCTTTTGTTCAAAATAATCAAATATTCCTTTAGAATTTCGTTTGTATTCTTTAAATT
65 ATTTCCCGTTTGTTCAAAATAATCAAACATTCCTTTAGAATTTCATTCGTATTCTTTAAATT
* ** * * *
21654717 CTAAAACAAGGCAATGTTCAATGTTTGAAGTTCGAGGAATCGTGCCCTACCGTGCTGGGTTTCGA
1 TTAAAACAAGGCAATGTTTGATGTTGGAAATTCGGGGAATCGTGCCCTACCGTGCTGGGTTTCGA
21654782 TTT
66 TTT
21654785 TTTGTTGGAC
Statistics
Matches: 169, Mismatches: 26, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
126 38 0.22
127 25 0.15
128 6 0.04
129 93 0.55
130 7 0.04
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.38
Consensus pattern (126 bp):
TTAAAACAAGGCAATGTTTGATGTTGGAAATTCGGGGAATCGTGCCCTACCGTGCTGGGTTTCGA
TTTCCCGTTTGTTCAAAATAATCAAACATTCCTTTAGAATTTCATTCGTATTCTTTAAATT
Found at i:21666233 original size:44 final size:43
Alignment explanation
Indices: 21666170--21666600 Score: 293
Period size: 44 Copynumber: 9.7 Consensus size: 43
21666160 AATTATGGCA
* * * *
21666170 AATCTTATCTTCTTGAAGTTGCAGTGAAGCAGATTAAAGCCATT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-CATT
* * * *
21666214 AATCTTATCTCCTTGAAGTTGCAGTGGAGCAAAATGAAG-ATGGCG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCAT---T
* *
21666259 AATCTTATCTCCCTGAAGTTGTAGTGGTGCAGATTGAAGACATT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-CATT
* * * * * ** *
21666303 AACCCTATCTCTCTAAAGATGCAGTGGATTAGGTTGAAG--TT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCATT
* * * * *
21666344 ACAAGTTTTATCTCCCTGAAGTTGCAATGGGGCAGACTGAAG-ATGGCG
1 --AA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCAT---T
*
21666392 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGCCATT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-CATT
* * * ** *
21666436 AACCTTATCTCCCTGAAGATGCAGTGAATTAGGTTGAAG--TT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCATT
* *
21666477 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGGGCAGACTGAAG-ATGGT
1 --AA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCAT--T
* * *
21666524 GAA-CTTTATCTCCTTGAAGTTACAGTGGAGCAGATCGAAGCCATT
1 -AATC-TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-CATT
* *
21666569 AACCTTATCTCCCTGAAGTTGCAGTCGAGCAG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAG
21666601 TTACAGTAGA
Statistics
Matches: 298, Mismatches: 65, Indels: 48
0.73 0.16 0.12
Matches are distributed among these distances:
41 4 0.01
42 2 0.01
43 4 0.01
44 177 0.59
45 100 0.34
46 4 0.01
47 7 0.02
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (43 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCATT
Found at i:21666418 original size:133 final size:133
Alignment explanation
Indices: 21666216--21666593 Score: 578
Period size: 133 Copynumber: 2.8 Consensus size: 133
21666206 AAGCCATTAA
* * * * *
21666216 TCTTATCTCCTTGAAGTTGCAGTGGAGCAAAATGAAGATGGCGAATCTTATCTCCCTGAAGTTGT
1 TCTTATCTCCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCGAATCTTATCTCCCTGAAGTTGC
* * * * * * *
21666281 AGTGGTGCAGATTGAAGACATTAACCCTATCTCTCTAAAGATGCAGTGGATTAGGTTGAAGTTAC
66 AGTGGAGCAGATCGAAGCCATTAACCTTATCTCCCTGAAGATGCAGTGAATTAGGTTGAAGTTAC
21666346 AAG
131 AAG
* *
21666349 TTTTATCTCCCTGAAGTTGCAATGGGGCAGACTGAAGATGGCGAATCTTATCTCCCTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCGAATCTTATCTCCCTGAAGTTGC
21666414 AGTGGAGCAGATCGAAGCCATTAACCTTATCTCCCTGAAGATGCAGTGAATTAGGTTGAAGTTAC
66 AGTGGAGCAGATCGAAGCCATTAACCTTATCTCCCTGAAGATGCAGTGAATTAGGTTGAAGTTAC
21666479 AAG
131 AAG
* * *
21666482 TCTTATCTCCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGTGAA-CTTTATCTCCTTGAAGTTA
1 TCTTATCTCCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCGAATC-TTATCTCCCTGAAGTTG
*
21666546 CAGTGGAGCAGATCGAAGCCATTAACCTTATCTCCCTGAAGTTGCAGT
65 CAGTGGAGCAGATCGAAGCCATTAACCTTATCTCCCTGAAGATGCAGT
21666594 CGAGCAGTTA
Statistics
Matches: 224, Mismatches: 20, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
132 1 0.00
133 223 1.00
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (133 bp):
TCTTATCTCCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCGAATCTTATCTCCCTGAAGTTGC
AGTGGAGCAGATCGAAGCCATTAACCTTATCTCCCTGAAGATGCAGTGAATTAGGTTGAAGTTAC
AAG
Found at i:21666583 original size:89 final size:86
Alignment explanation
Indices: 21666174--21666600 Score: 308
Period size: 89 Copynumber: 4.8 Consensus size: 86
21666164 ATGGCAAATC
* * * * *
21666174 TTATCTTCTTGAAGTTGCAGTGAAGCAGATTAAAGCCATTAATCTTATCTCCTTGAAGTTGCAGT
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCATTAATCTTATCTCCCTGAAGTTGCAGT
* *
21666239 GGAGCAAAATGAAGATGGCGAA-T
66 GGAGC-AGATGAAGAT--TGAACT
* * * * * * * *
21666262 CTTATCTCCCTGAAGTTGTAGTGGTGCAGATTGAAGACATTAACCCTATCTCTCTAAAGATGCAG
1 -TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCATTAATCTTATCTCCCTGAAGTTGCAG
** * * *
21666327 TGGATTAGGTTGAAG-TTACAAGTT
65 TGGAGCA-GATGAAGATT-GAA-CT
* * * *
21666351 TTATCTCCCTGAAGTTGCAATGGGGCAGACTGAAG--ATGGCGAATCTTATCTCCCTGAAGTTGC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCAT---TAATCTTATCTCCCTGAAGTTGC
*
21666414 AGTGGAGCAGATCGAAGCCATT-AACC
63 AGTGGAGCAGAT-GAAG--ATTGAACT
* * ** * ** *
21666440 TTATCTCCCTGAAGATGCAGTGAATTAGGTTGAAGTTA-CAAGTCTTATCTCCCTGAAGTTGCAG
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCATTAA-TCTTATCTCCCTGAAGTTGCAG
*
21666504 TGGGGCAGACTGAAGATGGTGAACT
65 TGGAGCAGA-TGAAGAT--TGAACT
* * * *
21666529 TTATCTCCTTGAAGTTACAGTGGAGCAGATCGAAGCCATTAACCTTATCTCCCTGAAGTTGCAGT
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCATTAATCTTATCTCCCTGAAGTTGCAGT
*
21666594 CGAGCAG
66 GGAGCAG
21666601 TTACAGTAGA
Statistics
Matches: 260, Mismatches: 59, Indels: 38
0.73 0.17 0.11
Matches are distributed among these distances:
86 4 0.02
87 4 0.02
88 70 0.27
89 175 0.67
90 4 0.02
91 1 0.00
92 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (86 bp):
TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCATTAATCTTATCTCCCTGAAGTTGCAGT
GGAGCAGATGAAGATTGAACT
Found at i:21668542 original size:19 final size:17
Alignment explanation
Indices: 21668505--21668540 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
21668495 TAAAATCACC
21668505 ATTTTGAAGTTTTTTAT
1 ATTTTGAAGTTTTTTAT
21668522 ATTTTGAAGTTTTTTAT
1 ATTTTGAAGTTTTTTAT
21668539 AT
1 AT
21668541 ATCATATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.25, C:0.00, G:0.11, T:0.64
Consensus pattern (17 bp):
ATTTTGAAGTTTTTTAT
Found at i:21670432 original size:24 final size:22
Alignment explanation
Indices: 21670384--21670437 Score: 67
Period size: 21 Copynumber: 2.4 Consensus size: 22
21670374 ACATATATGT
21670384 ATAATAAT-GATGAAAATAATA
1 ATAATAATAGATGAAAATAATA
21670405 ATAATAATAG-TGAAAATAAATAA
1 ATAATAATAGATGAAAAT-AAT-A
21670428 GATAATAATA
1 -ATAATAATA
21670438 AATATAATAG
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
21 15 0.52
22 4 0.14
23 1 0.03
24 9 0.31
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.28
Consensus pattern (22 bp):
ATAATAATAGATGAAAATAATA
Found at i:21670524 original size:3 final size:3
Alignment explanation
Indices: 21670509--21670600 Score: 50
Period size: 3 Copynumber: 31.3 Consensus size: 3
21670499 TGCTAACATG
* * ** *
21670509 AAT AAT GAT AAT AAT ACT AAT AAT AAT AAT AA- AAT ACG AAG AAGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T
* * *
21670554 -AT ATAT AAT -AT AAT AAT AAT ATT AA- AAT -AC AAT AATT AAA AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT
21670597 AAT A
1 AAT A
21670601 TTATATATAA
Statistics
Matches: 67, Mismatches: 14, Indels: 16
0.69 0.14 0.16
Matches are distributed among these distances:
2 8 0.12
3 53 0.79
4 6 0.09
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:21670613 original size:26 final size:26
Alignment explanation
Indices: 21670553--21670617 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
21670543 TACGAAGAAG
* *
21670553 TATATATAATATAATAATAATATTAA
1 TATAAATAATATAAAAATAATATTAA
*
21670579 AATACAATAAT-TAAAAATAATATTATA
1 TATA-AATAATATAAAAATAATATTA-A
21670606 TATAAAT-ATATA
1 TATAAATAATATA
21670618 CAATATTCAC
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
25 2 0.06
26 21 0.66
27 9 0.28
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (26 bp):
TATAAATAATATAAAAATAATATTAA
Found at i:21670667 original size:3 final size:3
Alignment explanation
Indices: 21670649--21670689 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
21670639 AAACGTATAC
*
21670649 TAA TATA TAG TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
21670690 TTGGAAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:21671945 original size:17 final size:16
Alignment explanation
Indices: 21671908--21671950 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
21671898 TTTTAATTAC
*
21671908 TGGGTT-TTGGGCTGT
1 TGGGTTATTGGGCTGA
21671923 TGGGGTTATTGGGCTGAA
1 T-GGGTTATTGGGCTG-A
21671941 TGGGTTATTG
1 TGGGTTATTG
21671951 TTGTTTGGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 1 0.04
16 5 0.21
17 17 0.71
18 1 0.04
ACGTcount: A:0.09, C:0.05, G:0.44, T:0.42
Consensus pattern (16 bp):
TGGGTTATTGGGCTGA
Found at i:21672479 original size:128 final size:127
Alignment explanation
Indices: 21672240--21672558 Score: 440
Period size: 128 Copynumber: 2.5 Consensus size: 127
21672230 TAAAAATTCC
* *
21672240 TTAAAACGAAGGCAATGTTTGATGTTTGGAAATTCAGGAAATCGTGCCCTACCGTGCTAGGTTTC
1 TTAAAAC-AAGGCAATGTTTGATGTTTGGAAATTCGGGGAATCGTGCCCTACCGTGCTAGGTTTC
* * * * *
21672305 GATTTCCCGTTTGTTCAAAATAATCGAACCTTCTTTTAGAATTTCATTCGTGTTTTTCTAAATT
65 GATTTCCCGTTTGTTCAAAATAATCAAACATTCCTTTAGAATTTCATTCGTATTCTT-TAAATT
* * * *
21672369 TTAAAACAACGCAATGTTTGATGCTTGGAAATTCGGGGAACCGTGCCCTATCGTGCTAGGTTTCG
1 TTAAAACAAGGCAATGTTTGATGTTTGGAAATTCGGGGAATCGTGCCCTACCGTGCTAGGTTTCG
* *
21672434 ATTTCTCGTTTGTTCAAAATAATCAAATATTCCTTTAGAATTTCATTCGTATTCTTTAAATT
66 ATTTCCCGTTTGTTCAAAATAATCAAACATTCCTTTAGAATTTCATTCGTATTCTTTAAATT
* ** * * * *
21672496 CTAAAACAAGGCAATGTTCAATGTTTGGAAGTTCGAGGAATCGTGCCCTACCATGCTGGGTTT
1 TTAAAACAAGGCAATGTTTGATGTTTGGAAATTCGGGGAATCGTGCCCTACCGTGCTAGGTTT
21672559 TGGTTTTTTG
Statistics
Matches: 166, Mismatches: 24, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
127 58 0.35
128 101 0.61
129 7 0.04
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.37
Consensus pattern (127 bp):
TTAAAACAAGGCAATGTTTGATGTTTGGAAATTCGGGGAATCGTGCCCTACCGTGCTAGGTTTCG
ATTTCCCGTTTGTTCAAAATAATCAAACATTCCTTTAGAATTTCATTCGTATTCTTTAAATT
Found at i:21677386 original size:11 final size:11
Alignment explanation
Indices: 21677372--21677439 Score: 54
Period size: 11 Copynumber: 6.5 Consensus size: 11
21677362 TTAAATTTTA
21677372 ATAAAAAATAT
1 ATAAAAAATAT
*
21677383 ATAAAAATTAT
1 ATAAAAAATAT
* *
21677394 -TAAAAATTAC
1 ATAAAAAATAT
*
21677404 AAAAAAAAT-T
1 ATAAAAAATAT
* *
21677414 AT-GAAAATCT
1 ATAAAAAATAT
21677424 -TAAAAAATAT
1 ATAAAAAATAT
21677434 ATAAAA
1 ATAAAA
21677440 TTTGTAAAAT
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
9 6 0.14
10 17 0.39
11 21 0.48
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.28
Consensus pattern (11 bp):
ATAAAAAATAT
Found at i:21677447 original size:20 final size:19
Alignment explanation
Indices: 21677406--21677478 Score: 60
Period size: 19 Copynumber: 3.8 Consensus size: 19
21677396 AAAATTACAA
21677406 AAAAAATTATGAAAATCTT
1 AAAAAATTATGAAAATCTT
*
21677425 AAAAAATATAT-AAAATTTGT
1 AAAAAAT-TATGAAAATCT-T
** * *
21677445 AAAATTTTATAAAAATCAT
1 AAAAAATTATGAAAATCTT
*
21677464 AAAAATTTA-GAAAAT
1 AAAAAATTATGAAAAT
21677479 ATATAGAAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
18 5 0.11
19 25 0.57
20 14 0.32
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.33
Consensus pattern (19 bp):
AAAAAATTATGAAAATCTT
Found at i:21677448 original size:28 final size:28
Alignment explanation
Indices: 21677407--21677478 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 28
21677397 AAATTACAAA
21677407 AAAAATTATGAAAATCTTA-AAAAAT-AT
1 AAAAATT-TGAAAATCTTATAAAAATCAT
*
21677434 ATAAAATTTGTAAAATTTTATAAAAATCAT
1 A-AAAATTTG-AAAATCTTATAAAAATCAT
21677464 AAAAATTTAGAAAAT
1 AAAAATTT-GAAAAT
21677479 ATATAGAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
27 3 0.08
28 14 0.36
29 18 0.46
30 4 0.10
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.33
Consensus pattern (28 bp):
AAAAATTTGAAAATCTTATAAAAATCAT
Found at i:21677577 original size:9 final size:9
Alignment explanation
Indices: 21677318--21677579 Score: 86
Period size: 10 Copynumber: 27.0 Consensus size: 9
21677308 ACATGTGGCA
*
21677318 AAAAATGAT
1 AAAAATTAT
*
21677327 AAAAA-AAT
1 AAAAATTAT
*
21677335 AAAAATCAAT
1 AAAAAT-TAT
*
21677345 AAAAGTTAT
1 AAAAATTAT
*
21677354 AAAAATAATT
1 AAAAATTA-T
**
21677364 AAATTTTAAT
1 AAAAATT-AT
21677374 AAAAAATATAT
1 -AAAAAT-TAT
21677385 AAAAATTATT
1 AAAAATTA-T
*
21677395 AAAAATTACAAA
1 AAAAATT---AT
21677407 AAAAATTAT
1 AAAAATTAT
*
21677416 GAAAATCT-T
1 AAAAAT-TAT
21677425 AAAAAATATAT
1 -AAAAAT-TAT
* *
21677436 AAAATTTGT
1 AAAAATTAT
*
21677445 AAAATTTTAT
1 AAAA-ATTAT
*
21677455 AAAAATCAT
1 AAAAATTAT
21677464 AAAAATT-T
1 AAAAATTAT
21677472 AGAAAATATAT
1 A-AAAAT-TAT
* * *
21677483 AGAAATACAA
1 AAAAAT-TAT
21677493 AAACAATTAT
1 AAA-AATTAT
*
21677503 -AAAATTTT
1 AAAAATTAT
* *
21677511 ATAAAGTCAT
1 A-AAAATTAT
21677521 AAGAAAATTAT
1 -A-AAAATTAT
21677532 AAAAAATGTA-
1 -AAAAAT-TAT
21677542 AAAAATTAT
1 AAAAATTAT
21677551 -AAAATTCAT
1 AAAAATT-AT
21677560 AAAAAAATTAT
1 --AAAAATTAT
21677571 AAAAATTAT
1 AAAAATTAT
21677580 CATACTAAAA
Statistics
Matches: 192, Mismatches: 34, Indels: 54
0.69 0.12 0.19
Matches are distributed among these distances:
8 22 0.11
9 61 0.32
10 68 0.35
11 26 0.14
12 14 0.07
13 1 0.01
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.30
Consensus pattern (9 bp):
AAAAATTAT
Found at i:21677796 original size:30 final size:29
Alignment explanation
Indices: 21677701--21677804 Score: 93
Period size: 29 Copynumber: 3.5 Consensus size: 29
21677691 TTTTTGATGC
* *
21677701 ATTTTATAATTTTTTATGACTTTTA-TAAA
1 ATTTAATAATTTTTTAT-ATTTTTATTAAA
* * * * *
21677730 ATTTTACAATATTTTATATTTTTTTTCCTAA
1 ATTTAATAATTTTTTATATTTTTATT--AAA
*
21677761 TTTTAATAATATTTTTATATTTTTATTAAA
1 ATTTAATAAT-TTTTTATATTTTTATTAAA
21677791 ATTTAATAATTTTT
1 ATTTAATAATTTTT
21677805 ATAACTTTTA
Statistics
Matches: 59, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
28 5 0.08
29 20 0.34
30 11 0.19
31 9 0.15
32 14 0.24
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.62
Consensus pattern (29 bp):
ATTTAATAATTTTTTATATTTTTATTAAA
Found at i:21677838 original size:9 final size:9
Alignment explanation
Indices: 21677702--21677839 Score: 57
Period size: 9 Copynumber: 14.4 Consensus size: 9
21677692 TTTTGATGCA
21677702 TTTTATAATT
1 TTTTATAA-T
* *
21677712 TTTTATGAC
1 TTTTATAAT
*
21677721 TTTTATAAAA
1 TTTTAT-AAT
*
21677731 TTTTACAAT
1 TTTTATAAT
*
21677740 ATTTTATATTTT
1 -TTTTATA--AT
*
21677752 TTTTCCTAAT
1 TTTT-ATAAT
*
21677762 TTTAATAAT
1 TTTTATAAT
21677771 ATTTT-TATAT
1 -TTTTATA-AT
*
21677781 TTTTATTAAAA
1 TTTTA-T-AAT
*
21677792 TTTAATAAT
1 TTTTATAAT
*
21677801 TTTTATAAC
1 TTTTATAAT
*
21677810 TTTTATTTAT
1 TTTTA-TAAT
21677820 TTTTAT--T
1 TTTTATAAT
21677827 TTTTATAAT
1 TTTTATAAT
21677836 TTTT
1 TTTT
21677840 TTGCCACATG
Statistics
Matches: 95, Mismatches: 20, Indels: 27
0.67 0.14 0.19
Matches are distributed among these distances:
7 7 0.07
9 38 0.40
10 36 0.38
11 10 0.11
12 4 0.04
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (9 bp):
TTTTATAAT
Found at i:21678046 original size:84 final size:86
Alignment explanation
Indices: 21677926--21678118 Score: 254
Period size: 84 Copynumber: 2.3 Consensus size: 86
21677916 TCAAAAAGTA
* **
21677926 TTTTTGATGCATTTT-AAAGTTTAAGTACTTAATTGAGTGCCAAAAAAA-TCAGGGGCTTAATT-
1 TTTTTAATGCATTTTGAAAGTTTAAGTACCCAATTGAGTG--AAAAAAAGT-AGGGGCTTAATTA
* *
21677988 TTTTTT-AAAAA-GTTTG-TGGGC
63 TTTTTTAAAAAAGGTTTGAAGGCC
21678009 TTTTTAATGCATTTTGAAAGTTTAAGTACCCAATTGAGTGAAAAAAAGTAGGGGCTTAATTACTT
1 TTTTTAATGCATTTTGAAAGTTTAAGTACCCAATTGAGTGAAAAAAAGTAGGGGCTTAATTA-TT
21678074 TTTTAAAAAATGGTTTGAAGGCC
65 TTTTAAAAAA-GGTTTGAAGGCC
21678097 TTTTTAATGCATTTTGAAAGTT
1 TTTTTAATGCATTTTGAAAGTT
21678119 AAAACACCCA
Statistics
Matches: 97, Mismatches: 5, Indels: 11
0.86 0.04 0.10
Matches are distributed among these distances:
82 19 0.20
83 15 0.15
84 28 0.29
85 5 0.05
87 5 0.05
88 25 0.26
ACGTcount: A:0.33, C:0.08, G:0.19, T:0.40
Consensus pattern (86 bp):
TTTTTAATGCATTTTGAAAGTTTAAGTACCCAATTGAGTGAAAAAAAGTAGGGGCTTAATTATTT
TTTAAAAAAGGTTTGAAGGCC
Found at i:21678128 original size:88 final size:83
Alignment explanation
Indices: 21677956--21678131 Score: 221
Period size: 88 Copynumber: 2.0 Consensus size: 83
21677946 TTAAGTACTT
* *
21677956 AATTGAGTGCCAAAAAAATCAGGGGCTTAATTTTTTTTAAAAAGTTTGTGGGCTTTTTAATGCAT
1 AATTGAGTG-CAAAAAAATCAGGGGCTTAATTTTTTTTAAAAAGTTTGAGGCCTTTTTAATGCAT
* **
21678021 TTTGAAAGTTTAAGTACCC
65 TTTGAAAGTTAAAACACCC
21678040 AATTGAGTG-AAAAAAAGT-AGGGGCTTAATTACTTTTTTAAAAAATGGTTTGAAGGCCTTTTTA
1 AATTGAGTGCAAAAAAA-TCAGGGGCTTAATT--TTTTTT-AAAAA--GTTTG-AGGCCTTTTTA
21678103 ATGCATTTTGAAAGTTAAAACACCC
59 ATGCATTTTGAAAGTTAAAACACCC
21678128 AATT
1 AATT
21678132 TAAAAAACTT
Statistics
Matches: 80, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
82 19 0.24
83 1 0.01
84 15 0.19
85 5 0.06
87 5 0.06
88 35 0.44
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.36
Consensus pattern (83 bp):
AATTGAGTGCAAAAAAATCAGGGGCTTAATTTTTTTTAAAAAGTTTGAGGCCTTTTTAATGCATT
TTGAAAGTTAAAACACCC
Found at i:21686221 original size:6 final size:6
Alignment explanation
Indices: 21686202--21686231 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
21686192 CATGGAGCCT
*
21686202 AAGGGC AAGAGC AAGGGC AAGGGC AAGGGC
1 AAGGGC AAGGGC AAGGGC AAGGGC AAGGGC
21686232 TCAAATCATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.47, T:0.00
Consensus pattern (6 bp):
AAGGGC
Found at i:21691634 original size:52 final size:51
Alignment explanation
Indices: 21691433--21691638 Score: 205
Period size: 53 Copynumber: 3.9 Consensus size: 51
21691423 CCATGGCAAC
* * * * ** *
21691433 AAGTGATAAGCGATATCCTTATAAGACTATAGCTGGGCTATGACATCTAAAAA
1 AAGTGATAAGTG-T-TCCGTATAAGACCATAGCTGGGCTATGGCATCGGAGAA
* * **
21691486 CAAGTGATAAGTGATTTTCGTATAAGACCATAGCTGGGCTATGGCTTCGGATTA
1 -AAGTGATAAGTG--TTCCGTATAAGACCATAGCTGGGCTATGGCATCGGAGAA
*
21691540 AAGTGATACAAGTGATCCGTATAAGACCATAGCTGGGCTATGGCATCGGAGAA
1 AAGTGAT--AAGTGTTCCGTATAAGACCATAGCTGGGCTATGGCATCGGAGAA
* * *
21691593 AAGTGATAAGTGCTTCCGTGTAAGACCATATCTGGGATATGGCATC
1 AAGTGATAAGTG-TTCCGTATAAGACCATAGCTGGGCTATGGCATC
21691639 AGTATGATAT
Statistics
Matches: 128, Mismatches: 20, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
51 5 0.04
52 29 0.23
53 48 0.38
54 40 0.31
55 6 0.05
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.27
Consensus pattern (51 bp):
AAGTGATAAGTGTTCCGTATAAGACCATAGCTGGGCTATGGCATCGGAGAA
Found at i:21694164 original size:2 final size:2
Alignment explanation
Indices: 21694157--21694183 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
21694147 AAACAAAATC
21694157 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
21694184 CAACAGCGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21695945 original size:17 final size:16
Alignment explanation
Indices: 21695913--21695943 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
21695903 ATAATATCTC
21695913 TTTTTTTAAATATTTA
1 TTTTTTTAAATATTTA
21695929 TTTTTTTAAATATTT
1 TTTTTTTAAATATTT
21695944 TACTATACTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTTTTAAATATTTA
Found at i:21706171 original size:18 final size:18
Alignment explanation
Indices: 21706148--21706183 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
21706138 TGGGTTTTTG
21706148 ATAAATCGTATGTTCTTC
1 ATAAATCGTATGTTCTTC
21706166 ATAAATCGTATGTTCTTC
1 ATAAATCGTATGTTCTTC
21706184 TTATTTATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.44
Consensus pattern (18 bp):
ATAAATCGTATGTTCTTC
Found at i:21712604 original size:55 final size:55
Alignment explanation
Indices: 21712471--21712614 Score: 175
Period size: 55 Copynumber: 2.6 Consensus size: 55
21712461 TGTGAAGGTC
**
21712471 CACACCCGTGTTGTTTTGACAGGTTTGCCCACGGTTACTTGGCACGGGCGTGTCG
1 CACACCCGTGTTGTTTTGACAGGTTTGCCCACGGTTACAAGGCACGGGCGTGTCG
** **
21712526 CACACCTTTGTTAATTTGACAGGTTTAG-CCACAGGTT-CAAGGCACGGGCGTGTCG
1 CACACCCGTGTTGTTTTGACAGGTTT-GCCCAC-GGTTACAAGGCACGGGCGTGTCG
* * *
21712581 CACACCCGTGTTGTTTTGGCAGGTTCGCCTACGG
1 CACACCCGTGTTGTTTTGACAGGTTTGCCCACGG
21712615 CCATGTTGCA
Statistics
Matches: 73, Mismatches: 13, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
54 3 0.04
55 65 0.89
56 5 0.07
ACGTcount: A:0.16, C:0.26, G:0.29, T:0.28
Consensus pattern (55 bp):
CACACCCGTGTTGTTTTGACAGGTTTGCCCACGGTTACAAGGCACGGGCGTGTCG
Found at i:21712626 original size:55 final size:53
Alignment explanation
Indices: 21712471--21712632 Score: 139
Period size: 55 Copynumber: 2.9 Consensus size: 53
21712461 TGTGAAGGTC
* *
21712471 CACACCCGTGTTGTTTTGACAGGTTTGCCCACGGTTACT-TGGCACGGGCGTGTCG
1 CACACCCGTGTTGTTTTGACAGGTTAG-CCACGGTCA-TGT-GCACGGGCGTGTCG
** ** *
21712526 CACACCTTTGTTAATTTGACAGGTTTAGCCACAGGTTCAAG-GCACGGGCGTGTCG
1 CACACCCGTGTTGTTTTGACAGG-TTAGCCAC-GG-TCATGTGCACGGGCGTGTCG
* * * *
21712581 CACACCCGTGTTGTTTTGGCAGGTTCGCCTACGGCCATGTTGCACGGTCGTG
1 CACACCCGTGTTGTTTTGACAGGTTAGCC-ACGGTCATG-TGCACGGGCGTG
21712633 GTGATTTATC
Statistics
Matches: 84, Mismatches: 16, Indels: 14
0.74 0.14 0.12
Matches are distributed among these distances:
53 3 0.04
54 7 0.08
55 67 0.80
56 5 0.06
57 2 0.02
ACGTcount: A:0.15, C:0.27, G:0.30, T:0.28
Consensus pattern (53 bp):
CACACCCGTGTTGTTTTGACAGGTTAGCCACGGTCATGTGCACGGGCGTGTCG
Found at i:21713931 original size:27 final size:27
Alignment explanation
Indices: 21713892--21714047 Score: 194
Period size: 27 Copynumber: 5.8 Consensus size: 27
21713882 AGGCTGCCAA
* *
21713892 ATATTGTGACAGAGTCACCAGATACAG
1 ATATTGTGGCAGAGCCACCAGATACAG
21713919 ATATTGTGGCAGAGCCACCAGA-ACAG
1 ATATTGTGGCAGAGCCACCAGATACAG
21713945 ATATATGTGGCAGAGCCACCAGAT-CAG
1 ATAT-TGTGGCAGAGCCACCAGATACAG
* * *
21713972 ATAATTGTGGTATAGCCACCAG-GACAG
1 AT-ATTGTGGCAGAGCCACCAGATACAG
21713999 ATATATGTGGCAGAGCCACCAGAT-CAG
1 ATAT-TGTGGCAGAGCCACCAGATACAG
*
21714026 ATAATTGTGGCATAGCCACCAG
1 AT-ATTGTGGCAGAGCCACCAG
21714048 GACGCTTCCT
Statistics
Matches: 113, Mismatches: 9, Indels: 14
0.83 0.07 0.10
Matches are distributed among these distances:
26 10 0.09
27 99 0.88
28 4 0.04
ACGTcount: A:0.34, C:0.21, G:0.25, T:0.20
Consensus pattern (27 bp):
ATATTGTGGCAGAGCCACCAGATACAG
Found at i:21714048 original size:54 final size:54
Alignment explanation
Indices: 21713892--21714050 Score: 250
Period size: 54 Copynumber: 3.0 Consensus size: 54
21713882 AGGCTGCCAA
* * * *
21713892 ATAT-TGTGACAGAGTCACCAGATACAGAT-ATTGTGGCAGAGCCACCAGAACAG
1 ATATATGTGGCAGAGCCACCAGAT-CAGATAATTGTGGCATAGCCACCAGGACAG
*
21713945 ATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGTATAGCCACCAGGACAG
1 ATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCACCAGGACAG
21713999 ATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCACCAGGAC
1 ATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCACCAGGAC
21714051 GCTTCCTCCA
Statistics
Matches: 98, Mismatches: 6, Indels: 3
0.92 0.06 0.03
Matches are distributed among these distances:
53 9 0.09
54 89 0.91
ACGTcount: A:0.34, C:0.21, G:0.25, T:0.19
Consensus pattern (54 bp):
ATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCACCAGGACAG
Found at i:21715675 original size:26 final size:26
Alignment explanation
Indices: 21715644--21715751 Score: 173
Period size: 26 Copynumber: 4.2 Consensus size: 26
21715634 TGAAATGCCC
21715644 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAAACCATT
*
21715670 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATT
* *
21715696 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAAACCATT
21715722 ATCATGGAACATTTACCT-AACCTATT
1 ATCATGGAACATTTACCTAAACC-ATT
21715748 ATCA
1 ATCA
21715752 ATTTGTACCA
Statistics
Matches: 76, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
25 3 0.04
26 73 0.96
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAAACCATT
Found at i:21717981 original size:49 final size:48
Alignment explanation
Indices: 21717909--21718102 Score: 201
Period size: 50 Copynumber: 3.9 Consensus size: 48
21717899 GCCAAAGCTA
* *
21717909 TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACAG
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACC-ACAG
* *
21717958 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTCACTA-
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGA-C-CAC-AG
** * * * *
21718008 TCTAATACACATATTAGCCTGCACTTAGTACTACACACGTGATCATAG
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCACAG
* * *
21718056 TTTTCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC
1 ---TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACC
21718103 TCACAATAGA
Statistics
Matches: 120, Mismatches: 18, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
47 1 0.01
48 2 0.02
49 38 0.32
50 41 0.34
51 38 0.32
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (48 bp):
TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCACAG
Found at i:21718042 original size:26 final size:26
Alignment explanation
Indices: 21717963--21718044 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
21717953 AACAGTCTGG
* *
21717963 TACACGTAGTAGCCTGCACTTAGTAC
1 TACACATATTAGCCTGCACTTAGTAC
** * * *
21717989 TACACACGTGA-CCT-CAC-TATCTAA
1 TACACATATTAGCCTGCACTTA-GTAC
21718013 TACACATATTAGCCTGCACTTAGTAC
1 TACACATATTAGCCTGCACTTAGTAC
21718039 TACACA
1 TACACA
21718045 CGTGATCATA
Statistics
Matches: 40, Mismatches: 12, Indels: 8
0.67 0.20 0.13
Matches are distributed among these distances:
23 2 0.05
24 13 0.32
25 6 0.15
26 17 0.43
27 2 0.05
ACGTcount: A:0.32, C:0.29, G:0.12, T:0.27
Consensus pattern (26 bp):
TACACATATTAGCCTGCACTTAGTAC
Found at i:21718093 original size:101 final size:99
Alignment explanation
Indices: 21717918--21718106 Score: 254
Period size: 101 Copynumber: 1.9 Consensus size: 99
21717908 ATCTGGTACG
* * *
21717918 CATAGTAGCCTGCACTTAGTACTACACATGCGACCAACAGTCTGGTACACGTAGTAGCCTGCACT
1 CATAGTAGCCTGCACTTAGTACTACACACGCGACCAACAGTCGGGTACACATAGTAGCCTGCACT
*
21717983 TAGTACTACACACGTGACCTCACTATCTAATACA
66 TAGTACTACACACGCGACCTCACTATCTAATACA
* * * * *
21718017 CATATTAGCCTGCACTTAGTACTACACACGTGATC-ATAGTTTTCGGGTACGCATAGTAGCCTGC
1 CATAGTAGCCTGCACTTAGTACTACACACGCGACCAACAG---TCGGGTACACATAGTAGCCTGC
*
21718081 ACTTAGTACTACACATGCGACCTCAC
63 ACTTAGTACTACACACGCGACCTCAC
21718107 AATAGATCAT
Statistics
Matches: 77, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
98 3 0.04
99 31 0.40
101 43 0.56
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.26
Consensus pattern (99 bp):
CATAGTAGCCTGCACTTAGTACTACACACGCGACCAACAGTCGGGTACACATAGTAGCCTGCACT
TAGTACTACACACGCGACCTCACTATCTAATACA
Found at i:21719565 original size:25 final size:24
Alignment explanation
Indices: 21719527--21719573 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
21719517 AAATATAACA
* *
21719527 TAAAAGAAATAAAACAAATGAAACG
1 TAAAAGAAACAAAA-AAAGGAAACG
*
21719552 TAAAAGAAGCAAAAAAAGGAAA
1 TAAAAGAAACAAAAAAAGGAAA
21719574 GAAAGTTACA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 7 0.37
25 12 0.63
ACGTcount: A:0.70, C:0.06, G:0.15, T:0.09
Consensus pattern (24 bp):
TAAAAGAAACAAAAAAAGGAAACG
Found at i:21720571 original size:41 final size:41
Alignment explanation
Indices: 21720525--21720625 Score: 102
Period size: 38 Copynumber: 2.5 Consensus size: 41
21720515 TCGACCTCGA
*
21720525 GTCGATGAGACACTGGGTGTCACTAAATTT-CTTCGGATAG
1 GTCGATGAGACACTGGGTGTCACCAAATTTACTTCGGATAG
* ** * *
21720565 ATTCGATGAGGTACT-GG-GT-ACCAACTTTACTTCGGCTAG
1 -GTCGATGAGACACTGGGTGTCACCAAATTTACTTCGGATAG
*
21720604 GCCGATGAGACACTGGGTGTCA
1 GTCGATGAGACACTGGGTGTCA
21720626 ACTATTACTT
Statistics
Matches: 46, Mismatches: 10, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
38 17 0.37
39 13 0.28
40 4 0.09
41 12 0.26
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.28
Consensus pattern (41 bp):
GTCGATGAGACACTGGGTGTCACCAAATTTACTTCGGATAG
Found at i:21720634 original size:39 final size:39
Alignment explanation
Indices: 21720527--21720661 Score: 123
Period size: 39 Copynumber: 3.4 Consensus size: 39
21720517 GACCTCGAGT
* * *
21720527 CGATGAGACACTGGGTGTC-ACTAAATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCAACT--ATTACTTCGGCTAG-TC
** ** *
21720568 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
*
21720606 CGATGAGACACTGGGTGTCAACTATTACTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAACTATTACTTCG-GCTAGTC
*
21720645 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
21720662 CCATATTGGT
Statistics
Matches: 76, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
38 19 0.25
39 36 0.47
40 3 0.04
41 15 0.20
42 3 0.04
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.27
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
Found at i:21727218 original size:46 final size:46
Alignment explanation
Indices: 21727168--21727296 Score: 231
Period size: 46 Copynumber: 2.8 Consensus size: 46
21727158 TGGTTGAGCA
*
21727168 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
21727214 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* *
21727260 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
21727297 GCGGGTTACA
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 80 1.00
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:21734079 original size:46 final size:46
Alignment explanation
Indices: 21734015--21734338 Score: 393
Period size: 46 Copynumber: 7.0 Consensus size: 46
21734005 TTATCTTTGA
* * * * *
21734015 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATAT
* **
21734061 CATGTTGCCAT-GTCGTCTTTCAACCATGGTCTTGTTCATTTCATAT
1 CATGTTGCCATGGT-ATCTTTCAACCATGGTCTTACTCATTTCATAT
* * *
21734107 CACGTTGCCATGGTATCTTTCAACTATGGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATAT
** **
21734153 CATGTTGCCATGGCGTCTTTCAACCATGGTCTTGTTCATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
* * *
21734199 CACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAA
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
* *
21734245 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
* * *
21734291 CAGGTTGCCATTGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
21734337 CA
1 CA
21734339 AAGAGCACAC
Statistics
Matches: 245, Mismatches: 28, Indels: 10
0.87 0.10 0.04
Matches are distributed among these distances:
45 10 0.04
46 229 0.93
47 6 0.02
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.40
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
Found at i:21734139 original size:92 final size:92
Alignment explanation
Indices: 21734020--21734331 Score: 448
Period size: 92 Copynumber: 3.4 Consensus size: 92
21734010 TTTGACATGA
* * * *
21734020 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTCATGTTGCCATGTCGTCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCTGTCATGTTGCCATGTCGTCTTTCAAC
21734085 CATGGTCTTGTTCATTTCATATCACGT
66 CATGGTCTTGTTCATTTCATATCACGT
* * *
21734112 TGCCATGGTATCTTTCAACTATGGTCTTACTCATTTTCTGTCATGTTGCCATGGCGTCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCTGTCATGTTGCCATGTCGTCTTTCAAC
21734177 CATGGTCTTGTTCATTTCATATCACGT
66 CATGGTCTTGTTCATTTCATATCACGT
** * *
21734204 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATAACAGGTTGCCATGGT-ATCTTTCA
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTC-TGTCATGTTGCCAT-GTCGTCTTTCA
*** *
21734267 ACCATGGTCTTACACATTTCATATCAGGT
64 ACCATGGTCTTGTTCATTTCATATCACGT
*
21734296 TGCCATTGTATCTTTCAACCATGGTCTTACACATTT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTT
21734332 CATATCAAAG
Statistics
Matches: 202, Mismatches: 15, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
91 4 0.02
92 195 0.97
93 3 0.01
ACGTcount: A:0.20, C:0.24, G:0.15, T:0.41
Consensus pattern (92 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCTGTCATGTTGCCATGTCGTCTTTCAAC
CATGGTCTTGTTCATTTCATATCACGT
Found at i:21738084 original size:49 final size:50
Alignment explanation
Indices: 21737844--21738089 Score: 280
Period size: 49 Copynumber: 4.9 Consensus size: 50
21737834 ATCTATTGTG
* * *
21737844 AGGTCACGTGTGTAGTACTAAGTGCAGGATACTACGTGTACCGGATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * * * *
21737894 A-GTCGCATGTGTAGTACTAAATGCAGGCTACTATGCGTACCTGATAACTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-TT
* * * * * * **
21737944 CGATCACGTGTGTAGTACTAAGTGTAGGTTACTACGTGTATCAGATGGTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* *
21737994 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * *
21738044 -GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
21738090 GCCTTGTCTA
Statistics
Matches: 161, Mismatches: 33, Indels: 5
0.81 0.17 0.03
Matches are distributed among these distances:
49 80 0.50
50 47 0.29
51 34 0.21
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.29
Consensus pattern (50 bp):
AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
Found at i:21746170 original size:53 final size:55
Alignment explanation
Indices: 21746103--21746226 Score: 155
Period size: 53 Copynumber: 2.3 Consensus size: 55
21746093 TTACCATTTT
* * *
21746103 CATGTCTTGACATGGTCTTACGTGGTATCC-TTGCCTTAT-G-AACTCACCAATGC
1 CATGTCTTGACATGGTCTTACATGGGA-CCTTTACCTTATAGTAACTCACCAATGC
* * *
21746156 CATGCCTTGGCATGGTCTTACATGGGACCTTTACCTTATAGTAACTCATCAATGC
1 CATGTCTTGACATGGTCTTACATGGGACCTTTACCTTATAGTAACTCACCAATGC
*
21746211 GATGTCTTGACATGGT
1 CATGTCTTGACATGGT
21746227 ATCCTTAACC
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
52 2 0.03
53 31 0.53
54 1 0.02
55 25 0.42
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (55 bp):
CATGTCTTGACATGGTCTTACATGGGACCTTTACCTTATAGTAACTCACCAATGC
Found at i:21753008 original size:2 final size:2
Alignment explanation
Indices: 21753001--21753042 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
21752991 CTACAGCTCC
21753001 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21753043 ATTATAAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21753048 original size:10 final size:11
Alignment explanation
Indices: 21753001--21753053 Score: 67
Period size: 10 Copynumber: 5.0 Consensus size: 11
21752991 CTACAGCTCC
21753001 TATATATAT-A
1 TATATATATAA
21753011 TATATATAT-A
1 TATATATATAA
21753021 TATATATATATA
1 TATATATATA-A
21753033 TATATATATAA
1 TATATATATAA
*
21753044 T-TATAAATAA
1 TATATATATAA
21753054 GTGACACTCC
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
10 27 0.68
11 2 0.05
12 11 0.28
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TATATATATAA
Found at i:21756548 original size:26 final size:26
Alignment explanation
Indices: 21756512--21756621 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
21756502 TGATACAAAT
*
21756512 TGATAATAGGTTAGGTAAATGTTTAA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
21756538 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
21756564 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
21756590 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
21756616 TGATAA
1 TGATAA
21756622 GAATTTCATG
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 80 1.00
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:21758273 original size:27 final size:27
Alignment explanation
Indices: 21758230--21758329 Score: 119
Period size: 27 Copynumber: 3.7 Consensus size: 27
21758220 GAGGAAGCGT
*
21758230 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* * *
21758257 TCTGGTGGCTCTTCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
21758284 TCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* *
21758312 TCTGGTGACTCTGTCACA
1 TCTGGTGGCTCTGCCACA
21758330 TTATCTTTTG
Statistics
Matches: 60, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
27 45 0.75
28 15 0.25
ACGTcount: A:0.18, C:0.25, G:0.22, T:0.35
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:21758335 original size:54 final size:54
Alignment explanation
Indices: 21758228--21758335 Score: 148
Period size: 54 Copynumber: 2.0 Consensus size: 54
21758218 TGGAGGAAGC
*
21758228 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTTCCACATATATCT
1 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTTCCACATATATCT
* * *
21758282 GTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGT-CACAT-TATCT
1 GTTCTGGTGGCTATGCCACAAATATCTG-ATCTGGTGACTCT-TCCACATATATCT
21758336 TTTGGCAGCC
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
54 30 0.62
55 17 0.35
56 1 0.02
ACGTcount: A:0.18, C:0.24, G:0.21, T:0.37
Consensus pattern (54 bp):
GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTTCCACATATATCT
Found at i:21761266 original size:25 final size:26
Alignment explanation
Indices: 21761177--21761285 Score: 168
Period size: 26 Copynumber: 4.2 Consensus size: 26
21761167 TGATACAAAT
21761177 TGATAATAGGTTAGGTAAATG-TTCAA
1 TGATAATAGGTTAGGTAAATGTTTC-A
*
21761203 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
21761229 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
21761255 TG-TAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
21761280 TGATAA
1 TGATAA
21761286 GAATTTCATG
Statistics
Matches: 78, Mismatches: 3, Indels: 4
0.92 0.04 0.05
Matches are distributed among these distances:
25 25 0.32
26 51 0.65
27 2 0.03
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:21761284 original size:51 final size:52
Alignment explanation
Indices: 21761177--21761285 Score: 168
Period size: 51 Copynumber: 2.1 Consensus size: 52
21761167 TGATACAAAT
21761177 TGATAATAGGTTAGGTAAATGTTCAATGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCAATGATAATAGGTTAGGTAAATGTTCCA
* * *
21761229 TGATAATGGGTTAGGTAAATGTTTC-ATG-TAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATG-TTCAATGATAATAGGTTAGGTAAATGTTCCA
21761280 TGATAA
1 TGATAA
21761286 GAATTTCATG
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
51 27 0.51
52 23 0.43
53 3 0.06
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.37
Consensus pattern (52 bp):
TGATAATAGGTTAGGTAAATGTTCAATGATAATAGGTTAGGTAAATGTTCCA
Found at i:21762942 original size:27 final size:27
Alignment explanation
Indices: 21762899--21763011 Score: 120
Period size: 27 Copynumber: 4.2 Consensus size: 27
21762889 GAGGAAGCGT
*
21762899 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* * *
21762926 TCTGGTGGCTCTTCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
21762953 TCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* * * *
21762981 TCTGGTGACTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
21763007 TCTGG
1 TCTGG
21763012 CAGCCATGCT
Statistics
Matches: 73, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
26 5 0.07
27 53 0.73
28 15 0.21
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.37
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:21763004 original size:54 final size:54
Alignment explanation
Indices: 21762897--21763011 Score: 162
Period size: 54 Copynumber: 2.1 Consensus size: 54
21762887 TGGAGGAAGC
*
21762897 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTTCCACATATATCT
1 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTTCCACATATATCT
* * *
21762951 GTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGT-CACAT-TATCT
1 GTTCTGGTGGCTATGCCACAAATATCTG-ATCTGGTGACTCT-TCCACATATATCT
21763005 GTTCTGG
1 GTTCTGG
21763012 CAGCCATGCT
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
54 37 0.67
55 17 0.31
56 1 0.02
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37
Consensus pattern (54 bp):
GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTTCCACATATATCT
Found at i:21765361 original size:43 final size:43
Alignment explanation
Indices: 21765214--21765364 Score: 214
Period size: 43 Copynumber: 3.5 Consensus size: 43
21765204 TGTCCTGGAT
* * *
21765214 ATGGTATTACATGTAATCTCATATCGATGCCAATGTCCCAGAC
1 ATGGTCTTACATGTAATCACATAACGATGCCAATGTCCCAGAC
*** * *
21765257 ATGGTCTTACACAAAATCATATAACGATGCCAATGTCTCAGAC
1 ATGGTCTTACATGTAATCACATAACGATGCCAATGTCCCAGAC
21765300 ATGGTCTTACATGTAATCACA-ACACGATGCCAATGTCCCAGAC
1 ATGGTCTTACATGTAATCACATA-ACGATGCCAATGTCCCAGAC
21765343 ATGGTCTTACATGTAATCACAT
1 ATGGTCTTACATGTAATCACAT
21765365 CTCGGTAGTC
Statistics
Matches: 93, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
42 1 0.01
43 92 0.99
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (43 bp):
ATGGTCTTACATGTAATCACATAACGATGCCAATGTCCCAGAC
Found at i:21768333 original size:4 final size:4
Alignment explanation
Indices: 21768324--21768370 Score: 51
Period size: 4 Copynumber: 11.8 Consensus size: 4
21768314 GAAACAATAA
* * *
21768324 AAAT AAAT AAA- ATAG AAAT AAAG AAAT AAAT AATAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA-AT AAAT AAAT AAA
21768371 ACAAAATGAG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
3 2 0.06
4 30 0.83
5 4 0.11
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:21772067 original size:361 final size:362
Alignment explanation
Indices: 21771394--21772120 Score: 1224
Period size: 361 Copynumber: 2.0 Consensus size: 362
21771384 CTAAATCAAT
* * * *
21771394 GAAGTAAGAGCACTCACAGATGATGGTGCCTAAGAATGAGTGTTGGCACTAAATCGATTGGGTCA
1 GAAGTAAGAGCACTCACAGATGATGGTGCCCAAAAATAAGTGTTGGCACTAAATCGATTGGATCA
*
21771459 AGATGGAGATGGACCAGGTGAAAACATTCAACTACCTTGTGAACTTGCAATAGGTAAGGAATTAA
66 AGATGGAGATGGACCAGGTGAAAACATACAACTACCTTGTGAACTTGCAATAGGTAAGGAATTAA
21771524 AAATAGGCACAGATGGGTTGAATAAAGGCATCCAAGATTGCATTTGAGGCCCAACACCAAAATTA
131 AAATAGGCACAGATGGGTTGAATAAAGGCATCCAAGATTGCATTTGAGGCCCAACACCAAAATTA
* * *
21771589 CACATGTTTGTTTGAGATGGAAGCATGTATGAAACACTTTTATAAGAAGCATGAAAATGATAATA
196 CACATGTTTGTTTGAGATGGAAGCATGCATGAAACACTTTTATAAAAAGCATGAAAACGATAATA
* * *
21771654 AAAATGGTCAACAAGATAACCTGTCTTACCACACAAATGATATTAGATTTCAGAATCAGAAGAAC
261 AAAATGGTCAACAAGATAACCCGTCTTACCACACAAATGACACTAGATTTCAGAATCAGAAGAAC
* * * **
21771719 GACTACGCCCATATCTTCAAAATGAACCAGGACCAAA
326 GACCACGCCCACATCCTCAAAATGAACCAAAACCAAA
* *
21771756 GAAGT-AGTAGCACTCACAGGTGATGGTGCCCAAAAATAAGTGTTGGCACTAAATTGATTGGATC
1 GAAGTAAG-AGCACTCACAGATGATGGTGCCCAAAAATAAGTGTTGGCACTAAATCGATTGGATC
*
21771820 AAGATGGAGGTGGA-CAGGTGAAAACATACAACTACCTTGTGAACTTGCAATAGGTAAGGAATTA
65 AAGATGGAGATGGACCAGGTGAAAACATACAACTACCTTGTGAACTTGCAATAGGTAAGGAATTA
*
21771884 AAAATAGGTACAGATGGGTTGAATAAAGGCATCCAAGATTGCATTTGAGGCCCAACACCAAAATT
130 AAAATAGGCACAGATGGGTTGAATAAAGGCATCCAAGATTGCATTTGAGGCCCAACACCAAAATT
*
21771949 ACACATGTTTGTTTGAGATGGAAGCCTGCATGAAACACTTTTATAAAAAGCATGAAAACGATAAT
195 ACACATGTTTGTTTGAGATGGAAGCATGCATGAAACACTTTTATAAAAAGCATGAAAACGATAAT
* *
21772014 AACAATGGTCAACAAGATGACCCGTCTTACCACACAAATGACACTAGATTTCAGAATCAGAAGAA
260 AAAAATGGTCAACAAGATAACCCGTCTTACCACACAAATGACACTAGATTTCAGAATCAGAAGAA
21772079 CGACCACGCCCACATCCTCAAAATGAACCAAAACCAAA
325 CGACCACGCCCACATCCTCAAAATGAACCAAAACCAAA
21772117 GAAG
1 GAAG
21772121 GGCTTATAAG
Statistics
Matches: 341, Mismatches: 23, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
361 273 0.80
362 68 0.20
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.22
Consensus pattern (362 bp):
GAAGTAAGAGCACTCACAGATGATGGTGCCCAAAAATAAGTGTTGGCACTAAATCGATTGGATCA
AGATGGAGATGGACCAGGTGAAAACATACAACTACCTTGTGAACTTGCAATAGGTAAGGAATTAA
AAATAGGCACAGATGGGTTGAATAAAGGCATCCAAGATTGCATTTGAGGCCCAACACCAAAATTA
CACATGTTTGTTTGAGATGGAAGCATGCATGAAACACTTTTATAAAAAGCATGAAAACGATAATA
AAAATGGTCAACAAGATAACCCGTCTTACCACACAAATGACACTAGATTTCAGAATCAGAAGAAC
GACCACGCCCACATCCTCAAAATGAACCAAAACCAAA
Found at i:21773453 original size:19 final size:19
Alignment explanation
Indices: 21773404--21773455 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 19
21773394 TTGAGAGATA
*
21773404 ATTT-TTTTAGTTTTTTAC
1 ATTTATTTTATTTTTTTAC
* * * *
21773422 ATATAATTAATTTTTTTAT
1 ATTTATTTTATTTTTTTAC
21773441 ATTTATTTTATTTTT
1 ATTTATTTTATTTTT
21773456 ATATTTTTTT
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
18 3 0.12
19 22 0.88
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (19 bp):
ATTTATTTTATTTTTTTAC
Found at i:21773466 original size:17 final size:17
Alignment explanation
Indices: 21773434--21773465 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
21773424 ATAATTAATT
21773434 TTTTTATATTTATTTTA
1 TTTTTATATTTATTTTA
21773451 TTTTTATATTT-TTTT
1 TTTTTATATTTATTTT
21773466 TTGAGATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTTATATTTATTTTA
Found at i:21776845 original size:18 final size:19
Alignment explanation
Indices: 21776822--21776870 Score: 75
Period size: 18 Copynumber: 2.7 Consensus size: 19
21776812 CTTGGCCCAT
21776822 TGCAGTAACAGTAAAT-AG
1 TGCAGTAACAGTAAATCAG
*
21776840 TGCAGTAACAGT-TATCAG
1 TGCAGTAACAGTAAATCAG
21776858 TGCAGTAACAGTA
1 TGCAGTAACAGTA
21776871 TACAAGTCCT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 2 0.07
18 26 0.93
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.24
Consensus pattern (19 bp):
TGCAGTAACAGTAAATCAG
Found at i:21777237 original size:27 final size:27
Alignment explanation
Indices: 21777190--21777549 Score: 425
Period size: 27 Copynumber: 13.3 Consensus size: 27
21777180 TACATCAAAT
* * * *
21777190 AGGGCAAAACAATCATCTTACCATATA
1 AGGGCAAAATAGTCATTTTACCACATA
*
21777217 AGGGCAAAATAGTTATTTTACCACATA
1 AGGGCAAAATAGTCATTTTACCACATA
* * *
21777244 AAGGCAGAATAGTCATTTTACCATATA
1 AGGGCAAAATAGTCATTTTACCACATA
* * *
21777271 AGGGCAAAACAATCATTTTACCACTTA
1 AGGGCAAAATAGTCATTTTACCACATA
*
21777298 AGGGCAAAATAGTTATTTTACCACATA
1 AGGGCAAAATAGTCATTTTACCACATA
* * *
21777325 AGGGC-AGATCAATCATTTTATCACATA
1 AGGGCAAAAT-AGTCATTTTACCACATA
* *
21777352 AGGGCAAAACAGTCATTTTACCACTTA
1 AGGGCAAAATAGTCATTTTACCACATA
*
21777379 AAGGCAAAATAGTCATTTTACCACATA
1 AGGGCAAAATAGTCATTTTACCACATA
* * ** *
21777406 AGGGTAGAATAGAAATTTTATCACATA
1 AGGGCAAAATAGTCATTTTACCACATA
* * *
21777433 AGGGCAAAACAATCATTTTACCACTTA
1 AGGGCAAAATAGTCATTTTACCACATA
*
21777460 AGGACAAAATAGTCATTTTACCACATA
1 AGGGCAAAATAGTCATTTTACCACATA
* *
21777487 AGGGAAAAATAGTCATTTTATCACATA
1 AGGGCAAAATAGTCATTTTACCACATA
* *
21777514 AGGGCAAAACAGTCATTTTACCACTTA
1 AGGGCAAAATAGTCATTTTACCACATA
21777541 AGGGCAAAA
1 AGGGCAAAA
21777550 CAACCATTTT
Statistics
Matches: 275, Mismatches: 56, Indels: 4
0.82 0.17 0.01
Matches are distributed among these distances:
26 3 0.01
27 270 0.98
28 2 0.01
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (27 bp):
AGGGCAAAATAGTCATTTTACCACATA
Found at i:21777325 original size:81 final size:81
Alignment explanation
Indices: 21777190--21777549 Score: 544
Period size: 81 Copynumber: 4.4 Consensus size: 81
21777180 TACATCAAAT
* * *
21777190 AGGGCAAAACAATCATCTTACCA-TATAAGGGCAAAATAGTTATTTTACCACATAAAGGCAGAAT
1 AGGGCAAAACAATCATTTTACCACT-TAAGGGCAAAATAGTCATTTTACCACATAAGGGCAGAAT
* *
21777254 AGTCATTTTACCATATA
65 AGTCATTTTATCACATA
*
21777271 AGGGCAAAACAATCATTTTACCACTTAAGGGCAAAATAGTTATTTTACCACATAAGGGCAG-ATC
1 AGGGCAAAACAATCATTTTACCACTTAAGGGCAAAATAGTCATTTTACCACATAAGGGCAGAAT-
*
21777335 AATCATTTTATCACATA
65 AGTCATTTTATCACATA
* * *
21777352 AGGGCAAAACAGTCATTTTACCACTTAAAGGCAAAATAGTCATTTTACCACATAAGGGTAGAATA
1 AGGGCAAAACAATCATTTTACCACTTAAGGGCAAAATAGTCATTTTACCACATAAGGGCAGAATA
**
21777417 GAAATTTTATCACATA
66 GTCATTTTATCACATA
* * *
21777433 AGGGCAAAACAATCATTTTACCACTTAAGGACAAAATAGTCATTTTACCACATAAGGGAAAAATA
1 AGGGCAAAACAATCATTTTACCACTTAAGGGCAAAATAGTCATTTTACCACATAAGGGCAGAATA
21777498 GTCATTTTATCACATA
66 GTCATTTTATCACATA
*
21777514 AGGGCAAAACAGTCATTTTACCACTTAAGGGCAAAA
1 AGGGCAAAACAATCATTTTACCACTTAAGGGCAAAA
21777550 CAACCATTTT
Statistics
Matches: 255, Mismatches: 21, Indels: 6
0.90 0.07 0.02
Matches are distributed among these distances:
80 2 0.01
81 250 0.98
82 3 0.01
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (81 bp):
AGGGCAAAACAATCATTTTACCACTTAAGGGCAAAATAGTCATTTTACCACATAAGGGCAGAATA
GTCATTTTATCACATA
Found at i:21781047 original size:18 final size:17
Alignment explanation
Indices: 21781024--21781059 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
21781014 CTTGGCCCAT
21781024 TGCAGTAACAGTAAACAG
1 TGCAGTAACAGT-AACAG
21781042 TGCAGTAACAGTAACAG
1 TGCAGTAACAGTAACAG
21781059 T
1 T
21781060 AATCAGCACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.42, C:0.17, G:0.22, T:0.19
Consensus pattern (17 bp):
TGCAGTAACAGTAACAG
Found at i:21781078 original size:24 final size:24
Alignment explanation
Indices: 21781026--21781071 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
21781016 TGGCCCATTG
**
21781026 CAGTAACAGTAAACAGTGCAGTAA
1 CAGTAACAGTAAACAGCACAGTAA
*
21781050 CAGTAACAGTAATCAGCACAGT
1 CAGTAACAGTAAACAGCACAGT
21781072 GATAGTATAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.43, C:0.20, G:0.20, T:0.17
Consensus pattern (24 bp):
CAGTAACAGTAAACAGCACAGTAA
Done.