Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr7
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: 47983841
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869652 characters in sequence are not A, C, G, or T
File 100 of 153
Found at i:31526402 original size:3 final size:3
Alignment explanation
Indices: 31526394--31526427 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
31526384 ACCCCTTTTT
31526394 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
31526428 TAAAGAGTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:31526859 original size:18 final size:18
Alignment explanation
Indices: 31526815--31526860 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
31526805 TAAATAGATA
* *
31526815 TTAAACTTATTCATAAAT
1 TTAAATTTAATCATAAAT
*
31526833 TTAAAATTTAATCATGAAT
1 TT-AAATTTAATCATAAAT
31526852 TTAAATTTA
1 TTAAATTTA
31526861 TATATATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.46
Consensus pattern (18 bp):
TTAAATTTAATCATAAAT
Found at i:31527959 original size:26 final size:28
Alignment explanation
Indices: 31527902--31527953 Score: 81
Period size: 26 Copynumber: 1.9 Consensus size: 28
31527892 TTGAATCTAA
*
31527902 AAAAATTGTTTGAAAATTAAAAAAATAT
1 AAAAATTGTTAGAAAATTAAAAAAATAT
31527930 AAAAATT-TTAGAAAA-TAAAAAAAT
1 AAAAATTGTTAGAAAATTAAAAAAAT
31527954 TCAAAAGGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 9 0.39
27 7 0.30
28 7 0.30
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (28 bp):
AAAAATTGTTAGAAAATTAAAAAAATAT
Found at i:31529816 original size:23 final size:24
Alignment explanation
Indices: 31529790--31529846 Score: 82
Period size: 23 Copynumber: 2.5 Consensus size: 24
31529780 TTTTAAAACT
31529790 TTATATATTTTTTGAAT-TTTAAA
1 TTATATATTTTTTGAATGTTTAAA
* *
31529813 TTATATA-TATTTGAATGTTTAAG
1 TTATATATTTTTTGAATGTTTAAA
31529836 TTATATATTTT
1 TTATATATTTT
31529847 CGAATAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
22 8 0.28
23 19 0.66
24 2 0.07
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (24 bp):
TTATATATTTTTTGAATGTTTAAA
Found at i:31533474 original size:40 final size:39
Alignment explanation
Indices: 31533388--31533536 Score: 156
Period size: 40 Copynumber: 3.7 Consensus size: 39
31533378 CACACCAGTT
* * * *
31533388 TGTGGACAAGCCACCA-ATATTACATATAAACTGTCAGTAA
1 TGTGGACAAGCCACCAGA-ATTGCAAACAAA-TTTCAGTAA
* *
31533428 TATGGACAAGCCACCAGAATTGCAAACAAATTTCTAGTAT
1 TGTGGACAAGCCACCAGAATTGCAAACAAATTTC-AGTAA
* * * *
31533468 TGTGGACAAGCCACTAAAATTGCAAACAAGTTGCCAGTAA
1 TGTGGACAAGCCACCAGAATTGCAAACAAATT-TCAGTAA
*
31533508 TGTGGACAAGCCACCAGAATTGCAGACAA
1 TGTGGACAAGCCACCAGAATTGCAAACAA
31533537 CCTACTAGTA
Statistics
Matches: 91, Mismatches: 15, Indels: 6
0.81 0.13 0.05
Matches are distributed among these distances:
39 3 0.03
40 86 0.95
41 2 0.02
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.21
Consensus pattern (39 bp):
TGTGGACAAGCCACCAGAATTGCAAACAAATTTCAGTAA
Found at i:31535591 original size:25 final size:26
Alignment explanation
Indices: 31535536--31535591 Score: 89
Period size: 25 Copynumber: 2.2 Consensus size: 26
31535526 AAATGTTAAG
31535536 TAAATATATTATATTATTATATATAA
1 TAAATATATTATATTATTATATATAA
*
31535562 T-AATATATTATGTTATTATA-ATAA
1 TAAATATATTATATTATTATATATAA
31535586 TAAATA
1 TAAATA
31535592 AATAAAAAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 5 0.18
25 22 0.79
26 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (26 bp):
TAAATATATTATATTATTATATATAA
Found at i:31536553 original size:41 final size:38
Alignment explanation
Indices: 31536506--31536618 Score: 102
Period size: 41 Copynumber: 2.9 Consensus size: 38
31536496 TTCGACTTCT
*
31536506 AGTCGATGAGACACTGGGTGTCAATTTAGTACTTTGGATTA
1 AGTCGATGAGACACTGGGTGTCAA-TTA-TACTTCGG-TTA
* ** * * *
31536547 ATTCGATGAGACGTTGGATGTGAATT-TACTTCGGTTT
1 AGTCGATGAGACACTGGGTGTCAATTATACTTCGGTTA
*
31536584 AGCCGATGAGACACTGGGTGTCAAATTATTACTTC
1 AGTCGATGAGACACTGGGTGTC-AATTA-TACTTC
31536619 AAATTATCTG
Statistics
Matches: 56, Mismatches: 13, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
37 18 0.32
38 11 0.20
40 8 0.14
41 19 0.34
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.35
Consensus pattern (38 bp):
AGTCGATGAGACACTGGGTGTCAATTATACTTCGGTTA
Found at i:31541912 original size:15 final size:15
Alignment explanation
Indices: 31541892--31541934 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
31541882 TGTTAAGTAA
31541892 ATATATTATATTATT
1 ATATATTATATTATT
31541907 ATATA-TA-A-TA--
1 ATATATTATATTATT
31541917 ATATATTATATTATT
1 ATATATTATATTATT
31541932 ATA
1 ATA
31541935 ATAAAACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 10
0.70 0.00 0.30
Matches are distributed among these distances:
10 5 0.22
11 2 0.09
12 3 0.13
13 3 0.13
14 2 0.09
15 8 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATATTATATTATT
Found at i:31541919 original size:25 final size:24
Alignment explanation
Indices: 31541891--31541938 Score: 87
Period size: 25 Copynumber: 2.0 Consensus size: 24
31541881 ATGTTAAGTA
31541891 AATATATTATATTATTATATATAAT
1 AATATATTATATTATTATA-ATAAT
31541916 AATATATTATATTATTATAATAA
1 AATATATTATATTATTATAATAA
31541939 AACAAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 4 0.17
25 19 0.83
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
AATATATTATATTATTATAATAAT
Found at i:31542040 original size:27 final size:27
Alignment explanation
Indices: 31541952--31542043 Score: 73
Period size: 27 Copynumber: 3.3 Consensus size: 27
31541942 AAATAAATAA
* *
31541952 AAAGAAAAAGGAAATAGAA-AAAGAAGG
1 AAAGAAAAA-GAAAGAAAAGAAAGAAGG
* * *
31541979 AAAGAAACAGAGAAAGCCAAACGAAACATGG
1 AAAGAAA-A-AGAAAG--AAAAGAAAGAAGG
31542010 --AGAAAAAGAAAGAAAAGAAAGAAGG
1 AAAGAAAAAGAAAGAAAAGAAAGAAGG
31542035 AAAGAAAAA
1 AAAGAAAAA
31542044 TTAGGGTTTC
Statistics
Matches: 50, Mismatches: 8, Indels: 14
0.69 0.11 0.19
Matches are distributed among these distances:
25 10 0.20
27 20 0.40
28 6 0.12
29 6 0.12
30 2 0.04
31 6 0.12
ACGTcount: A:0.68, C:0.05, G:0.24, T:0.02
Consensus pattern (27 bp):
AAAGAAAAAGAAAGAAAAGAAAGAAGG
Found at i:31546454 original size:24 final size:24
Alignment explanation
Indices: 31546425--31546481 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
31546415 GTTATTACTG
31546425 TTTTGATGAGAACTTTGTAGGTGT
1 TTTTGATGAGAACTTTGTAGGTGT
*
31546449 TTTTGATGAGACCTTTGTAGGTGT
1 TTTTGATGAGAACTTTGTAGGTGT
31546473 TTTTGATGA
1 TTTTGATGA
31546482 AAGTTCAACC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.19, C:0.05, G:0.28, T:0.47
Consensus pattern (24 bp):
TTTTGATGAGAACTTTGTAGGTGT
Found at i:31561278 original size:17 final size:18
Alignment explanation
Indices: 31561247--31561282 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
31561237 CATGTTGTTG
31561247 GCTCGTGTAGGCCCACAC
1 GCTCGTGTAGGCCCACAC
31561265 GCTCGTGT-GGCCCACAC
1 GCTCGTGTAGGCCCACAC
31561282 G
1 G
31561283 GCCCAAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.14, C:0.39, G:0.31, T:0.17
Consensus pattern (18 bp):
GCTCGTGTAGGCCCACAC
Found at i:31574021 original size:16 final size:17
Alignment explanation
Indices: 31574000--31574033 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
31573990 ATTATTTTGG
*
31574000 ATTTTTGG-GTATTTCC
1 ATTTTTGGTATATTTCC
31574016 ATTTTTGGTATATTTCC
1 ATTTTTGGTATATTTCC
31574033 A
1 A
31574034 GTCAAATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.18, C:0.12, G:0.15, T:0.56
Consensus pattern (17 bp):
ATTTTTGGTATATTTCC
Found at i:31578178 original size:29 final size:29
Alignment explanation
Indices: 31578145--31578211 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
31578135 GGTTTAATGG
***
31578145 TTTAGGGTTTAGGGTTTAAGATTTATGAT
1 TTTAGGGTTTACAATTTAAGATTTATGAT
* *
31578174 TTTAGGGTTTACAATTTATGATTTATGGT
1 TTTAGGGTTTACAATTTAAGATTTATGAT
31578203 TTTAGGGTT
1 TTTAGGGTT
31578212 AATTTATGGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.22, C:0.01, G:0.25, T:0.51
Consensus pattern (29 bp):
TTTAGGGTTTACAATTTAAGATTTATGAT
Found at i:31578206 original size:22 final size:22
Alignment explanation
Indices: 31578152--31578197 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
31578142 TGGTTTAGGG
31578152 TTTAGGGTTTA-AGATTTATGAT
1 TTTAGGGTTTACA-ATTTATGAT
31578174 TTTAGGGTTTACAATTTATGAT
1 TTTAGGGTTTACAATTTATGAT
31578196 TT
1 TT
31578198 ATGGTTTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.26, C:0.02, G:0.20, T:0.52
Consensus pattern (22 bp):
TTTAGGGTTTACAATTTATGAT
Found at i:31578364 original size:22 final size:22
Alignment explanation
Indices: 31578339--31578385 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
31578329 TGTTTAGGGT
*
31578339 TTAAGAGG-TTAAAGTTTAAAGG
1 TTAAG-GGTTTAAAGTCTAAAGG
*
31578361 TTAAGGGTTTAAAGTCTAAGGG
1 TTAAGGGTTTAAAGTCTAAAGG
31578383 TTA
1 TTA
31578386 GGGGCTTATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.36, C:0.02, G:0.28, T:0.34
Consensus pattern (22 bp):
TTAAGGGTTTAAAGTCTAAAGG
Found at i:31578370 original size:15 final size:15
Alignment explanation
Indices: 31578334--31578384 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
31578324 TTTATTGTTT
31578334 AGGGTTTAAGAGGTTA
1 AGGGTTTAA-AGGTTA
*
31578350 A-AGTTTAAAGGTTA
1 AGGGTTTAAAGGTTA
31578364 AGGGTTTAAA-GTCTA
1 AGGGTTTAAAGGT-TA
31578379 AGGGTT
1 AGGGTT
31578385 AGGGGCTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 9 0.29
15 21 0.68
16 1 0.03
ACGTcount: A:0.33, C:0.02, G:0.31, T:0.33
Consensus pattern (15 bp):
AGGGTTTAAAGGTTA
Found at i:31578465 original size:23 final size:23
Alignment explanation
Indices: 31578434--31578479 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
31578424 ATTTAAGGGT
*
31578434 TATGCTAAAAATATAAAAAAATA
1 TATGCTAAAAATAGAAAAAAATA
*
31578457 TATGTTAAAAATAGAAAAAAATA
1 TATGCTAAAAATAGAAAAAAATA
31578480 AAATAGTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.65, C:0.02, G:0.07, T:0.26
Consensus pattern (23 bp):
TATGCTAAAAATAGAAAAAAATA
Found at i:31578943 original size:115 final size:115
Alignment explanation
Indices: 31578600--31579058 Score: 473
Period size: 115 Copynumber: 4.0 Consensus size: 115
31578590 TTGTCTGATT
* * * * * * *
31578600 TTTTGGTGGCGTTTTTTCTAAAATGCCGCAAAAGGAGT-TATATTAGTGGCGTTTCTACGAAAAA
1 TTTTAGTGGCGTTTTTACTAAAACGCCGCAAAAGGA-TATGTGTTAGTGGCGTTTTTACTAAAAA
* ** * *
31578664 CGCCGCAATTATGTTTTTTTGTCTTTGTTAAACGTTGTCGTTTTTATCTACG
65 CGCCGCAATTATG-TTATAAGTGTTTGCTAAACGTTGTCGTTTTTATCTACG
* * * **
31578716 TTTTCAGTGGCGTTTTTTCCAAAACGCCGCAAAATGATATGTGTTAGTGGCG-TTTT-C-AGGTA
1 TTTT-AGTGGCGTTTTTACTAAAACGCCGCAAAAGGATATGTGTTAGTGGCGTTTTTACTA-AAA
* * * *
31578778 ACGCCGCAATTATGTTATTAGTCTTTTG-TAAACGTTGTTGTTTTTATCTACA
64 ACGCCGCAATTATGTTATAAGT-GTTTGCTAAACGTTGTCGTTTTTATCTACG
* * * * *
31578830 TTATTAGTGGCATTTTTACAAAAATGCCGCAAAAGGTTATGTGGTAGTGGCGTTTTTA-TAAAAA
1 TT-TTAGTGGCGTTTTTACTAAAACGCCGCAAAAGGATATGTGTTAGTGGCGTTTTTACTAAAAA
*
31578894 TGCCGCAATTATGTTATAAGTGTTTGCTAAACGTTGTCGTTTTTATCTACG
65 CGCCGCAATTATGTTATAAGTGTTTGCTAAACGTTGTCGTTTTTATCTACG
* * * * * * *
31578945 TTTTTAGTGGCGTTTGTACTAAAACGCCAG-TAAAGGATATGTTTTCGTGGCATTTTTATTATAA
1 -TTTTAGTGGCGTTTTTACTAAAACGCC-GCAAAAGGATATGTGTTAGTGGCGTTTTTACTAAAA
*
31579009 ACGCCGCAATTATGTTTTAAGTGTTTGCTAAACGTTGTCGTTTTCTATCT
64 ACGCCGCAATTATGTTATAAGTGTTTGCTAAACGTTGTCGTTTT-TATCT
31579059 GGGATTTTTT
Statistics
Matches: 289, Mismatches: 41, Indels: 25
0.81 0.12 0.07
Matches are distributed among these distances:
114 75 0.26
115 112 0.39
116 58 0.20
117 44 0.15
ACGTcount: A:0.24, C:0.14, G:0.20, T:0.41
Consensus pattern (115 bp):
TTTTAGTGGCGTTTTTACTAAAACGCCGCAAAAGGATATGTGTTAGTGGCGTTTTTACTAAAAAC
GCCGCAATTATGTTATAAGTGTTTGCTAAACGTTGTCGTTTTTATCTACG
Found at i:31578947 original size:229 final size:234
Alignment explanation
Indices: 31578605--31579058 Score: 559
Period size: 229 Copynumber: 2.0 Consensus size: 234
31578595 TGATTTTTTG
* * *
31578605 GTGGCGTTTTTTCTAAAATGCCGCAAAAGGAGTTATATTAGTGGCGTTTCTACGAAAAACGCCGC
1 GTGGCATTTTTACAAAAATGCCGCAAAAGGAGTTATATTAGTGGCGTTTCTACGAAAAACGCCGC
* ** * * *
31578670 AATTATGTTTTTTTGTCTTTGTTAAACGTTGTCGTTTTTATCTACGTTTTCAGTGGCGTTTTTTC
66 AATTATGTTTATAAGTCTTTGCTAAACGTTGTCGTTTTTATCTACGTTTTCAGTGGCGTTTGTAC
* * *
31578735 CAAAACGCC-GCAAAATGATATGTGTTAGTGGCGTTTTCA-GGT-AACGCCGCAATTATGTTATT
131 CAAAACGCCAG-AAAAGGATATGTGTTAGTGGCATTTTCATGATAAACGCCGCAATTATGTT-TT
* *
31578797 -AGTCTTTTG-TAAACGTTGTTGTTTT-TATCTACATTATTA
194 AAGT-GTTTGCTAAACGTTGTCGTTTTCTATCTACATTATTA
* * * *
31578836 GTGGCATTTTTACAAAAATGCCGCAAAA-G-GTTATGTGGTAGTGGCGTTTTTA-TAAAAATGCC
1 GTGGCATTTTTACAAAAATGCCGCAAAAGGAGTTATAT--TAGTGGCGTTTCTACGAAAAACGCC
* *
31578898 GCAATTATG-TTATAAGTGTTTGCTAAACGTTGTCGTTTTTATCTACGTTTTTAGTGGCGTTTGT
64 GCAATTATGTTTATAAGTCTTTGCTAAACGTTGTCGTTTTTATCTACGTTTTCAGTGGCGTTTGT
* * * * * *
31578962 ACTAAAACGCCAGTAAAGGATATGTTTTCGTGGCATTTTTATTATAAACGCCGCAATTATGTTTT
129 ACCAAAACGCCAGAAAAGGATATGTGTTAGTGGCATTTTCATGATAAACGCCGCAATTATGTTTT
31579027 AAGTGTTTGCTAAACGTTGTCGTTTTCTATCT
194 AAGTGTTTGCTAAACGTTGTCGTTTTCTATCT
31579059 GGGATTTTTT
Statistics
Matches: 189, Mismatches: 26, Indels: 15
0.82 0.11 0.07
Matches are distributed among these distances:
229 85 0.45
230 26 0.14
231 73 0.39
232 5 0.03
ACGTcount: A:0.24, C:0.14, G:0.20, T:0.41
Consensus pattern (234 bp):
GTGGCATTTTTACAAAAATGCCGCAAAAGGAGTTATATTAGTGGCGTTTCTACGAAAAACGCCGC
AATTATGTTTATAAGTCTTTGCTAAACGTTGTCGTTTTTATCTACGTTTTCAGTGGCGTTTGTAC
CAAAACGCCAGAAAAGGATATGTGTTAGTGGCATTTTCATGATAAACGCCGCAATTATGTTTTAA
GTGTTTGCTAAACGTTGTCGTTTTCTATCTACATTATTA
Found at i:31579192 original size:14 final size:14
Alignment explanation
Indices: 31579173--31579200 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
31579163 CCCCACTCTG
31579173 ATTTCCCTAATTTC
1 ATTTCCCTAATTTC
31579187 ATTTCCCTAATTTC
1 ATTTCCCTAATTTC
31579201 CCATTTCCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.29, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTTCCCTAATTTC
Found at i:31580752 original size:13 final size:13
Alignment explanation
Indices: 31580728--31580761 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
31580718 ATTTCAAACT
31580728 TTAAATATAAAAAA
1 TTAAA-ATAAAAAA
*
31580742 TTAAAATAAAAAG
1 TTAAAATAAAAAA
31580755 TTAAAAT
1 TTAAAAT
31580762 CTCTATTAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (13 bp):
TTAAAATAAAAAA
Found at i:31580975 original size:12 final size:12
Alignment explanation
Indices: 31580958--31580983 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
31580948 TTCTTAATAA
31580958 TTATATATAAGC
1 TTATATATAAGC
31580970 TTATATATAAGC
1 TTATATATAAGC
31580982 TT
1 TT
31580984 GCATAACTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (12 bp):
TTATATATAAGC
Found at i:31581001 original size:12 final size:12
Alignment explanation
Indices: 31580986--31581043 Score: 54
Period size: 12 Copynumber: 5.2 Consensus size: 12
31580976 ATAAGCTTGC
31580986 ATAACTTACATA
1 ATAACTTACATA
31580998 ATAACTTAC---
1 ATAACTTACATA
*
31581007 ATAACTTATAT-
1 ATAACTTACATA
*
31581018 ATAA-TAACATA
1 ATAACTTACATA
*
31581029 ATAAATTACATA
1 ATAACTTACATA
31581041 ATA
1 ATA
31581044 CATAACTTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
9 8 0.21
10 4 0.11
11 8 0.21
12 18 0.47
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.34
Consensus pattern (12 bp):
ATAACTTACATA
Found at i:31581010 original size:9 final size:9
Alignment explanation
Indices: 31580998--31582138 Score: 797
Period size: 9 Copynumber: 130.4 Consensus size: 9
31580988 AACTTACATA
31580998 ATAACTTAC
1 ATAACTTAC
*
31581007 ATAACTTAT
1 ATAACTTAC
31581016 AT-A--TA-
1 ATAACTTAC
*
31581021 ATAACATA-
1 ATAACTTAC
*
31581029 ATAAATTAC
1 ATAACTTAC
31581038 ATAA--TAC
1 ATAACTTAC
*
31581045 ATAACTTATAT
1 ATAAC-T-TAC
*
31581056 ATAAGCTTGC
1 ATAA-CTTAC
31581066 ATAACTTAC
1 ATAACTTAC
31581075 ATAA--TAC
1 ATAACTTAC
**
31581082 ACCACTTAC
1 ATAACTTAC
31581091 ATAACTTAC
1 ATAACTTAC
*
31581100 ATAGCTTAC
1 ATAACTTAC
*
31581109 AT-TC-TAC
1 ATAACTTAC
*
31581116 ACAACTTAC
1 ATAACTTAC
*
31581125 ATAACATAC
1 ATAACTTAC
31581134 ATAA--TAC
1 ATAACTTAC
*
31581141 AGAACTTAC
1 ATAACTTAC
*
31581150 ATAA--AAC
1 ATAACTTAC
*
31581157 ACAACTTAC
1 ATAACTTAC
*
31581166 ATATCTTAC
1 ATAACTTAC
31581175 ATAA--TAC
1 ATAACTTAC
31581182 ATAACTTAC
1 ATAACTTAC
31581191 ATAA--TAC
1 ATAACTTAC
*
31581198 A-ACATTTAC
1 ATA-ACTTAC
* *
31581207 ACAACTTAA
1 ATAACTTAC
*
31581216 ATAACTTAT
1 ATAACTTAC
*
31581225 ATAACTTGC
1 ATAACTTAC
*
31581234 ATAACTTAT
1 ATAACTTAC
*
31581243 ATAA-TAAC
1 ATAACTTAC
*
31581251 ATAACAACTAAC
1 AT---AACTTAC
** *
31581263 ATAAAATAT
1 ATAACTTAC
*
31581272 ATAAACATATAT
1 AT-AAC-T-TAC
* *
31581284 AGAAACTTGC
1 A-TAACTTAC
*
31581294 ATAACTTAT
1 ATAACTTAC
*
31581303 ATAA-TAAC
1 ATAACTTAC
*
31581311 ATAA-TAAC
1 ATAACTTAC
31581319 -TAACATAATAC
1 ATAAC-T--TAC
31581330 ATAACTTAC
1 ATAACTTAC
31581339 ATAACTTAC
1 ATAACTTAC
31581348 ATAACTTAC
1 ATAACTTAC
*
31581357 ATAAATTA-
1 ATAACTTAC
31581365 AGTAACTTAC
1 A-TAACTTAC
31581375 ATAACTTAC
1 ATAACTTAC
31581384 ATAACTTAC
1 ATAACTTAC
31581393 ATAACTTAC
1 ATAACTTAC
* *
31581402 ATAAATTAA
1 ATAACTTAC
31581411 ATAACTTAC
1 ATAACTTAC
31581420 ATAACTTAC
1 ATAACTTAC
*
31581429 ATAACTTAA
1 ATAACTTAC
31581438 ATAACTTAC
1 ATAACTTAC
31581447 ATAA--TAC
1 ATAACTTAC
31581454 ATAACCTT-C
1 ATAA-CTTAC
*
31581463 CTAACTTAC
1 ATAACTTAC
* *
31581472 ATTATTTAC
1 ATAACTTAC
31581481 ATAA--TAC
1 ATAACTTAC
* *
31581488 A-ATGCCTAC
1 ATA-ACTTAC
31581497 ATAACTTAC
1 ATAACTTAC
31581506 ATAACTTAC
1 ATAACTTAC
* *
31581515 ATAAATTAA
1 ATAACTTAC
31581524 ATAACTTAC
1 ATAACTTAC
31581533 ATAACTTAC
1 ATAACTTAC
*
31581542 ATAACTTAA
1 ATAACTTAC
31581551 ATAACTTAC
1 ATAACTTAC
31581560 ATAA--TAC
1 ATAACTTAC
31581567 ATAACCTT-C
1 ATAA-CTTAC
*
31581576 CTAACTTAC
1 ATAACTTAC
* *
31581585 ATTATTTAC
1 ATAACTTAC
31581594 ATAA--TAC
1 ATAACTTAC
* *
31581601 A-ATGCCTAC
1 ATA-ACTTAC
31581610 ATAACTTAC
1 ATAACTTAC
31581619 ATAACTTAC
1 ATAACTTAC
* *
31581628 ATAAATTAA
1 ATAACTTAC
31581637 ATAACTTAC
1 ATAACTTAC
31581646 ATAACTTAC
1 ATAACTTAC
*
31581655 ATAACTTAA
1 ATAACTTAC
31581664 ATAACTTAC
1 ATAACTTAC
31581673 ATAA--TAC
1 ATAACTTAC
31581680 ATAACCTT-C
1 ATAA-CTTAC
*
31581689 CTAACTTAC
1 ATAACTTAC
* *
31581698 ATTATTTAC
1 ATAACTTAC
31581707 ATAA--TAC
1 ATAACTTAC
* *
31581714 A-ATGCCTAC
1 ATA-ACTTAC
31581723 ATAACTTAC
1 ATAACTTAC
31581732 ATAACTTAC
1 ATAACTTAC
* *
31581741 ATAAATTAA
1 ATAACTTAC
31581750 ATAACTTAC
1 ATAACTTAC
31581759 ATAACTTAC
1 ATAACTTAC
*
31581768 ATAACTTAA
1 ATAACTTAC
31581777 ATAACTTAC
1 ATAACTTAC
31581786 ATAA--TAC
1 ATAACTTAC
31581793 ATAACCTT-C
1 ATAA-CTTAC
*
31581802 CTAACTTAC
1 ATAACTTAC
* *
31581811 ATTATTTAC
1 ATAACTTAC
31581820 ATAA--TAC
1 ATAACTTAC
* *
31581827 A-ATGCCTAC
1 ATA-ACTTAC
31581836 ATAACTTAC
1 ATAACTTAC
31581845 ATAACTTAC
1 ATAACTTAC
* *
31581854 ATAAATTAA
1 ATAACTTAC
31581863 ATAACTTAC
1 ATAACTTAC
31581872 ATAACTTAC
1 ATAACTTAC
*
31581881 ATAACTTAA
1 ATAACTTAC
*
31581890 ATAACTTAA
1 ATAACTTAC
31581899 ATAACTTAC
1 ATAACTTAC
31581908 ATAA--TAC
1 ATAACTTAC
*
31581915 ATAACTTTC
1 ATAACTTAC
*
31581924 CTAACTTAC
1 ATAACTTAC
* *
31581933 ATTATTTAC
1 ATAACTTAC
31581942 ATAA--TAC
1 ATAACTTAC
** **
31581949 ATTGCCCAC
1 ATAACTTAC
31581958 ATAACTTAC
1 ATAACTTAC
31581967 ATAACTTAC
1 ATAACTTAC
* *
31581976 ATAAATTAA
1 ATAACTTAC
31581985 ATAACTTAC
1 ATAACTTAC
31581994 ATAACTTAC
1 ATAACTTAC
*
31582003 ATAACTTAA
1 ATAACTTAC
31582012 ATAACTTAC
1 ATAACTTAC
31582021 ATAA-TTA-
1 ATAACTTAC
*
31582028 AT-ATTATAC
1 ATAACT-TAC
* *
31582037 ACAATTTAC
1 ATAACTTAC
31582046 ATAA--TAC
1 ATAACTTAC
*
31582053 ATTACTTAC
1 ATAACTTAC
31582062 ATAACTTAC
1 ATAACTTAC
*
31582071 ATTACTTAC
1 ATAACTTAC
31582080 AGT-ACTTTAC
1 A-TAAC-TTAC
31582090 TTATAGTACTTAC
1 --ATA--ACTTAC
*
31582103 GTAA--TAC
1 ATAACTTAC
31582110 ATAA--TAC
1 ATAACTTAC
31582117 ATAACTTAC
1 ATAACTTAC
31582126 ATAACTTAC
1 ATAACTTAC
31582135 ATAA
1 ATAA
31582139 TACATAAAAA
Statistics
Matches: 902, Mismatches: 141, Indels: 178
0.74 0.12 0.15
Matches are distributed among these distances:
5 2 0.00
6 9 0.01
7 120 0.13
8 43 0.05
9 660 0.73
10 27 0.03
11 16 0.02
12 19 0.02
13 4 0.00
14 2 0.00
ACGTcount: A:0.46, C:0.19, G:0.01, T:0.33
Consensus pattern (9 bp):
ATAACTTAC
Found at i:31581151 original size:41 final size:41
Alignment explanation
Indices: 31581114--31581194 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 41
31581104 CTTACATTCT
31581114 ACACAACTTACATAACATACATAATACAGAACTTACATAAA
1 ACACAACTTACATAACATACATAATACAGAACTTACATAAA
* * *
31581155 ACACAACTTACATATCTTACATAATACATAACTTACATAA
1 ACACAACTTACATAACATACATAATACAGAACTTACATAA
31581195 TACAACATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.51, C:0.22, G:0.01, T:0.26
Consensus pattern (41 bp):
ACACAACTTACATAACATACATAATACAGAACTTACATAAA
Found at i:31581207 original size:41 final size:41
Alignment explanation
Indices: 31581085--31582072 Score: 324
Period size: 43 Copynumber: 23.2 Consensus size: 41
31581075 ATAATACACC
* **
31581085 ACTTACATAACTTACATAGCTTACATTCTACACAACTTACATA
1 ACTTACATAA--TACATAACTTACATAATACACAACTTACATA
* * *
31581128 ACATACATAATACAGAACTTACATAAAACACAACTTACATA
1 ACTTACATAATACATAACTTACATAATACACAACTTACATA
* * *
31581169 TCTTACATAATACATAACTTACATAATACA-ACATTTACACA
1 ACTTACATAATACATAACTTACATAATACACA-ACTTACATA
* * * * * *
31581210 ACTTAAATAACTTATATAACTTGCATAACTTATATAA-TAACATAACA
1 ACTTACATAA--TACATAACTTACATAA--TACACAACTTACAT---A
* * * *
31581257 ACTAACATAA-A-ATATA-TAAACATATATAGA-AACTTGCATA
1 ACTTACATAATACATA-ACT-TACATA-ATACACAACTTACATA
* * *
31581297 ACTTATATAATAACATAA-TAAC-T-A-ACATAA--TACATA
1 ACTTACATAAT-ACATAACTTACATAATACACAACTTACATA
*
31581333 ACTTACATAACTTACATAACTTACATAAATTA-AGTAACTTACATA
1 ACTTACATAA--TACATAACTTACAT-AA-TACA-CAACTTACATA
* *
31581378 ACTTACATAACTTACATAACTTACATAAATTAAATAACTTACATA
1 ACTTACATAA--TACATAACTTACAT-AA-TACACAACTTACATA
* * *
31581423 ACTTACATAACTTAAATAACTTACATAATACATAACCTT-CCTA
1 ACTTACATAA--TACATAACTTACATAATACACAA-CTTACATA
* ** *
31581466 ACTTACATTATTTACATAA--TACAATGCCTACATAACTTACATA
1 ACTTACA-TA-ATACATAACTTAC-AT-AATACACAACTTACATA
* * *
31581509 ACTTACATAAATTAAATAACTTACATAACTTACATAACTTAAATA
1 ACTTACAT-AA-TACATAACTTACATAA--TACACAACTTACATA
*
31581554 ACTTACATAATACATAAC---C-T--T-C-CTAACTTACATT
1 ACTTACATAATACATAACTTACATAATACAC-AACTTACATA
* * * *
31581588 ATTTACATAATACA-ATGCCTACATAACTTACATAACTTACATA
1 ACTTACATAATACATA-ACTTACATAA--TACACAACTTACATA
* * * *
31581631 AATTAAATAACTTACATAACTTACATAACTTAAATAACTTACATA
1 ACTTACATAA--TACATAACTTACATAA--TACACAACTTACATA
* * * *
31581676 A--TACATAACCTTCCTAACTTACATTATTTACATAA--TACA-A
1 ACTTACATAA--TACATAACTTACA-TA-ATACACAACTTACATA
* * * *
31581716 TGCCTACATAACTTACATAACTTACATAAATTAAATAACTTACATA
1 -ACTTACATAA--TACATAACTTACAT-AA-TACACAACTTACATA
* * *
31581762 ACTTACATAACTTAAATAACTTACATAATACATAACCTT-CCTA
1 ACTTACATAA--TACATAACTTACATAATACACAA-CTTACATA
* ** *
31581805 ACTTACATTATTTACATAA--TACAATGCCTACATAACTTACATA
1 ACTTACA-TA-ATACATAACTTAC-AT-AATACACAACTTACATA
* * *
31581848 ACTTACATAAATTAAATAACTTACATAACTTACATAACTTAAATA
1 ACTTACAT-AA-TACATAACTTACATAA--TACACAACTTACATA
* * *
31581893 ACTTAAATAACTTACATAA--TACATAACTTTC-CTAACTTACATT
1 ACTTACATAA--TACATAACTTACATAA--TACAC-AACTTACATA
* ** ** *
31581936 ATTTACATAATACATTGCCCACATAACTTACATAACTTACATA
1 ACTTACATAATACATAACTTACATAA--TACACAACTTACATA
* * * *
31581979 AATTAAATAACTTACATAACTTACATAACTTAAATAACTTACATA
1 ACTTACATAA--TACATAACTTACATAA--TACACAACTTACATA
* * **
31582024 A-TTA-ATATTATACACAATTTACATAATACATTACTTACATA
1 ACTTACATA--ATACATAACTTACATAATACACAACTTACATA
31582065 ACTTACAT
1 ACTTACAT
31582073 TACTTACAGT
Statistics
Matches: 746, Mismatches: 110, Indels: 178
0.72 0.11 0.17
Matches are distributed among these distances:
33 1 0.00
34 23 0.03
35 1 0.00
36 14 0.02
37 9 0.01
38 8 0.01
39 2 0.00
40 13 0.02
41 100 0.13
42 23 0.03
43 281 0.38
44 37 0.05
45 221 0.30
46 4 0.01
47 9 0.01
ACGTcount: A:0.47, C:0.19, G:0.01, T:0.33
Consensus pattern (41 bp):
ACTTACATAATACATAACTTACATAATACACAACTTACATA
Found at i:31581304 original size:31 final size:29
Alignment explanation
Indices: 31581227--31581319 Score: 89
Period size: 29 Copynumber: 3.1 Consensus size: 29
31581217 TAACTTATAT
*
31581227 AACTTGCATAACTTATATAATAACATAAC
1 AACTTGCATAACTTATATAATAACATAAA
** ** *
31581256 AACTAACATAAAATATATAA-ACATATATAGA
1 AACTTGCATAACTTATATAATA-ACATA-A-A
*
31581287 AACTTGCATAACTTATATAATAACATAAT
1 AACTTGCATAACTTATATAATAACATAAA
31581316 AACT
1 AACT
31581320 AACATAATAC
Statistics
Matches: 48, Mismatches: 12, Indels: 8
0.71 0.18 0.12
Matches are distributed among these distances:
28 1 0.02
29 24 0.50
30 2 0.04
31 20 0.42
32 1 0.02
ACGTcount: A:0.53, C:0.14, G:0.03, T:0.30
Consensus pattern (29 bp):
AACTTGCATAACTTATATAATAACATAAA
Found at i:31581521 original size:113 final size:113
Alignment explanation
Indices: 31581381--31582025 Score: 1182
Period size: 113 Copynumber: 5.6 Consensus size: 113
31581371 TTACATAACT
31581381 TACATAACTTACATAACTTACATAAATTAAATAACTTACATAACTTACATAACTTAAATAACTTA
1 TACATAACTTACATAACTTACATAAATTAAATAACTTACATAACTTACATAACTTAAATAACTTA
31581446 CATAATACATAACCTTCCTAACTTACATTATTTACATAATACAATGCC
66 CATAATACATAACCTTCCTAACTTACATTATTTACATAATACAATGCC
31581494 TACATAACTTACATAACTTACATAAATTAAATAACTTACATAACTTACATAACTTAAATAACTTA
1 TACATAACTTACATAACTTACATAAATTAAATAACTTACATAACTTACATAACTTAAATAACTTA
31581559 CATAATACATAACCTTCCTAACTTACATTATTTACATAATACAATGCC
66 CATAATACATAACCTTCCTAACTTACATTATTTACATAATACAATGCC
31581607 TACATAACTTACATAACTTACATAAATTAAATAACTTACATAACTTACATAACTTAAATAACTTA
1 TACATAACTTACATAACTTACATAAATTAAATAACTTACATAACTTACATAACTTAAATAACTTA
31581672 CATAATACATAACCTTCCTAACTTACATTATTTACATAATACAATGCC
66 CATAATACATAACCTTCCTAACTTACATTATTTACATAATACAATGCC
31581720 TACATAACTTACATAACTTACATAAATTAAATAACTTACATAACTTACATAACTTAAATAACTTA
1 TACATAACTTACATAACTTACATAAATTAAATAACTTACATAACTTACATAACTTAAATAACTTA
31581785 CATAATACATAACCTTCCTAACTTACATTATTTACATAATACAATGCC
66 CATAATACATAACCTTCCTAACTTACATTATTTACATAATACAATGCC
31581833 TACATAACTTACATAACTTACATAAATTAAATAACTTACATAACTTACATAACTTAAATAACTTA
1 TACATAACTTACATAACTTACATAAATTAAATAACTTACATAAC-T---T-AC----ATAACTTA
* *
31581898 AATAACTTACATAATACATAACTTTCCTAACTTACATTATTTACATAATACATTGCC
57 AATAACTTACATAATACATAACCTTCCTAACTTACATTATTTACATAATACAATGCC
*
31581955 CACATAACTTACATAACTTACATAAATTAAATAACTTACATAACTTACATAACTTAAATAACTTA
1 TACATAACTTACATAACTTACATAAATTAAATAACTTACATAACTTACATAACTTAAATAACTTA
31582020 CATAAT
66 CATAAT
31582026 TAATATTATA
Statistics
Matches: 520, Mismatches: 3, Indels: 18
0.96 0.01 0.03
Matches are distributed among these distances:
113 406 0.78
114 1 0.00
117 3 0.01
118 3 0.01
121 1 0.00
122 106 0.20
ACGTcount: A:0.46, C:0.20, G:0.01, T:0.34
Consensus pattern (113 bp):
TACATAACTTACATAACTTACATAAATTAAATAACTTACATAACTTACATAACTTAAATAACTTA
CATAATACATAACCTTCCTAACTTACATTATTTACATAATACAATGCC
Found at i:31582037 original size:122 final size:120
Alignment explanation
Indices: 31581721--31582030 Score: 517
Period size: 122 Copynumber: 2.6 Consensus size: 120
31581711 TACAATGCCT
31581721 ACATAACTTACATAACTTACATAAATTAAATAACTTACATAACTTACATAACTTAAATAACTTAC
1 ACATAACTTACATAACTTACATAAATTAAATAACTTACATAACTTACATAACTTAAATAACTTAC
*
31581786 -------ATAATACATAACCTTCCTAACTTACATTATTTACATAATACAATGCCT
66 ATAATTAATAATACATAACCTTCCTAACTTACATTATTTACATAATACAATGCCC
*
31581834 ACATAACTTACATAACTTACATAAATTAAATAACTTACATAACTTACATAACTTAAATAACTTAA
1 ACATAACTTACATAACTTACATAAATTAAATAACTTACATAACTTACATAACTTAAATAACTTAC
* *
31581899 ATAACTTACATAATACATAACTTTCCTAACTTACATTATTTACATAATACATTGCCC
66 ATAA-TTA-ATAATACATAACCTTCCTAACTTACATTATTTACATAATACAATGCCC
31581956 ACATAACTTACATAACTTACATAAATTAAATAACTTACATAACTTACATAACTTAAATAACTTAC
1 ACATAACTTACATAACTTACATAAATTAAATAACTTACATAACTTACATAACTTAAATAACTTAC
31582021 ATAATTAATA
66 ATAATTAATA
31582031 TTATACACAA
Statistics
Matches: 183, Mismatches: 5, Indels: 11
0.92 0.03 0.06
Matches are distributed among these distances:
113 64 0.35
120 3 0.02
121 3 0.02
122 113 0.62
ACGTcount: A:0.46, C:0.19, G:0.01, T:0.34
Consensus pattern (120 bp):
ACATAACTTACATAACTTACATAAATTAAATAACTTACATAACTTACATAACTTAAATAACTTAC
ATAATTAATAATACATAACCTTCCTAACTTACATTATTTACATAATACAATGCCC
Found at i:31582046 original size:226 final size:230
Alignment explanation
Indices: 31581313--31582145 Score: 1133
Period size: 226 Copynumber: 3.6 Consensus size: 230
31581303 ATAATAACAT
* * * * * *
31581313 AATAACTAACATAATACATAACTTACATAACTTACATAACTTACATAAATTA-AGTAACTTACAT
1 AATAACTTACATAATACATAACTT-CCTAAC-TACAT-ATTTACAT-AA-TACAAT-GCCTACAT
* * * *
31581377 AACTTACATAACTTACATAACTTACATAAATTAAATAACTTACATAACTTACATAACTTAAATAA
60 AACTTACATAACTTACATAAATTAAATAACTTACATAAC-TACATAAC-TACATAACTTAAATAA
31581442 CTTACATAATACATAACCTTCCTAACTTACATTATTTACATAATACAATGCCTACATAACTTACA
123 CTTACATAATACATAACCTTCCTAACTTACATTATTTACATAATACAATGCCTACATAACTTACA
31581507 TAACTTACATAAATTAAATAACTTACATAACTTACATAACTTA
188 TAACTTACATAAATTAAATAACTTACATAACTTACATAACTTA
31581550 AATAACTTACATAATACATAACCTTCCTAACTTACATTATTTACATAATACAATGCCTACATAAC
1 AATAACTTACATAATACATAA-CTTCCTAAC-TACA-TATTTACATAATACAATGCCTACATAAC
31581615 TTACATAACTTACATAAATTAAATAACTTACAT-A--AC-T---TACATAACTTAAATAACTTAC
63 TTACATAACTTACATAAATTAAATAACTTACATAACTACATAACTACATAACTTAAATAACTTAC
31581673 ATAATACATAACCTTCCTAACTTACATTATTTACATAATACAATGCCTACATAACTTACATAACT
128 ATAATACATAACCTTCCTAACTTACATTATTTACATAATACAATGCCTACATAACTTACATAACT
31581738 TACATAAATTAAATAACTTACATAACTTACATAACTTA
193 TACATAAATTAAATAACTTACATAACTTACATAACTTA
31581776 AATAACTTACATAATACATAACCTTCCTAACTTACATTATTTACATAATACAATGCCTACATAAC
1 AATAACTTACATAATACATAA-CTTCCTAAC-TACA-TATTTACATAATACAATGCCTACATAAC
*
31581841 TTACATAACTTACATAAATTAAATAACTTACATAACTTACATAACTTAAATAACTTAAATAACTT
63 TTACATAACTTACATAAATTAAATAACTTACATAAC-TACATAAC-TACATAACTTAAATAACTT
* * *
31581906 ACATAATACATAACTTTCCTAACTTACATTATTTACATAATACATTGCCCACATAACTTACATAA
126 ACATAATACATAACCTTCCTAACTTACATTATTTACATAATACAATGCCTACATAACTTACATAA
31581971 CTTACATAAATTAAATAACTTACATAACTTACATAACTTA
191 CTTACATAAATTAAATAACTTACATAACTTACATAACTTA
* * * *
31582011 AATAACTTACATAATTA-AT-A-TT-AT-AC-ACA-ATTTACATAATACATTACTTACATAACTT
1 AATAACTTACATAA-TACATAACTTCCTAACTACATATTTACATAATACAATGCCTACATAACTT
* ** * * *
31582069 ACATTACTTACAGTACTTTACTTATAGTACTTACGTAA-TACATAA-TACATAACTTACATAACT
65 ACATAACTTACA-TAAATTA--AATA--ACTTACATAACTACATAACTACATAACTTAAATAACT
31582132 TACATAATACATAA
125 TACATAATACATAA
31582146 AAATATACCA
Statistics
Matches: 553, Mismatches: 25, Indels: 46
0.89 0.04 0.07
Matches are distributed among these distances:
226 259 0.47
227 36 0.07
228 3 0.01
229 10 0.02
230 5 0.01
231 13 0.02
232 2 0.00
234 2 0.00
235 176 0.32
236 6 0.01
237 37 0.07
238 4 0.01
ACGTcount: A:0.46, C:0.19, G:0.01, T:0.34
Consensus pattern (230 bp):
AATAACTTACATAATACATAACTTCCTAACTACATATTTACATAATACAATGCCTACATAACTTA
CATAACTTACATAAATTAAATAACTTACATAACTACATAACTACATAACTTAAATAACTTACATA
ATACATAACCTTCCTAACTTACATTATTTACATAATACAATGCCTACATAACTTACATAACTTAC
ATAAATTAAATAACTTACATAACTTACATAACTTA
Found at i:31585066 original size:21 final size:20
Alignment explanation
Indices: 31585040--31585090 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
31585030 TACAACTTAT
* *
31585040 AGCAGAGGTGGCAGCGAGGGA
1 AGCAGAGGT-ACAGCGAGAGA
31585061 AGCAGAGGCTACAGCGAGAGA
1 AGCAGAGG-TACAGCGAGAGA
*
31585082 AGTAGAGGT
1 AGCAGAGGT
31585091 TCAAAAGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 1 0.04
21 24 0.92
22 1 0.04
ACGTcount: A:0.33, C:0.14, G:0.45, T:0.08
Consensus pattern (20 bp):
AGCAGAGGTACAGCGAGAGA
Found at i:31585702 original size:85 final size:85
Alignment explanation
Indices: 31585521--31585732 Score: 259
Period size: 85 Copynumber: 2.5 Consensus size: 85
31585511 TTTGTGAAGA
* * * * *
31585521 AAGCGCCGCTAAAGAACATGATCTTTAGCGACATC-TTTCTCTAAGCGCCACTAAAGAACATGAT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTCTTTTTTCTAAACGCCACTAAAGAACATGAC
*
31585585 CTTTAGTGGCGTTTTTCTCC
66 CTTTAGCGGCGTTTTTCTCC
* * * *
31585605 ATGCGCCACTAAAGAACATGATCTTTAGCGGCGTCTTTTTTTTAAACGCCGCTAAAGAACATGAC
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTCTTTTTTCTAAACGCCACTAAAGAACATGAC
* *
31585670 CTTTAGCGGC-TTTTGTTTCT
66 CTTTAGCGGCGTTTT-TCTCC
* * *
31585690 AAGCGCCGCTAAAGAACATGACCTTAAGCGGTGT-TTTTTTCTA
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTCTTTTTTCTA
31585733 TAAATACTGC
Statistics
Matches: 108, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
84 43 0.40
85 65 0.60
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (85 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTCTTTTTTCTAAACGCCACTAAAGAACATGAC
CTTTAGCGGCGTTTTTCTCC
Found at i:31585731 original size:42 final size:42
Alignment explanation
Indices: 31585521--31585732 Score: 255
Period size: 42 Copynumber: 5.0 Consensus size: 42
31585511 TTTGTGAAGA
* * * *
31585521 AAGCGCCGCTAAAGAACATGATCTTTAGCGACATCTTTCTCT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCT
* * * *
31585563 AAGCGCCACTAAAGAACATGATCTTTAGTGGCGTTTTTCTCC
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCT
* * *
31585605 ATGCGCCACTAAAGAACATGATCTTTAGCGGCGTCTTTTTTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGT-TTTTTTCT
* *
31585648 AAACGCCGCTAAAGAACATGACCTTTAGCGGC-TTTTGTTTCT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTT-TTTCT
* * *
31585690 AAGCGCCGCTAAAGAACATGACCTTAAGCGGTGTTTTTTTCT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCT
31585732 A
1 A
31585733 TAAATACTGC
Statistics
Matches: 148, Mismatches: 19, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
41 3 0.02
42 108 0.73
43 37 0.25
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (42 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCT
Found at i:31595052 original size:12 final size:12
Alignment explanation
Indices: 31595037--31595063 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
31595027 TAAGGAGGGG
31595037 ATCGTGGAGAAA
1 ATCGTGGAGAAA
31595049 ATCGTGGAGAAA
1 ATCGTGGAGAAA
31595061 ATC
1 ATC
31595064 AATGGGATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.11, G:0.30, T:0.19
Consensus pattern (12 bp):
ATCGTGGAGAAA
Found at i:31596354 original size:18 final size:17
Alignment explanation
Indices: 31596331--31596364 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
31596321 GTGGGCCGAA
31596331 ATGGGCCATATGGGCCCG
1 ATGGGCCA-ATGGGCCCG
*
31596349 ATGGGCTAATGGGCCC
1 ATGGGCCAATGGGCCC
31596365 AACACGGGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.18, C:0.26, G:0.38, T:0.18
Consensus pattern (17 bp):
ATGGGCCAATGGGCCCG
Found at i:31602237 original size:346 final size:353
Alignment explanation
Indices: 31601554--31602246 Score: 933
Period size: 346 Copynumber: 2.0 Consensus size: 353
31601544 GGGGTAGTTG
31601554 TTTACTCCATCCATCTTTTTAGTCAAAAGCCTTAGCTTAATGAGTGAGTCCCATTCAAATTGTGA
1 TTTACTCCATCCATCTTTTTAGTCAAAAGCCTTAGCTTAATGAG-GAGTCCCATTCAAATTGTGA
* * * * * *
31601619 CATGATTGAGTTTCTAGCAATTCGGTTTATACTCCACTGTGATTGTTGAGTAAAAAATTCTTATG
65 AATAATTGAGTATCTAGCAATTCAGTTTATACTCCACTGTGATTGTCGAGTAAAAAATTCATATG
31601684 AAAAGTTGAATCCCCTAATAAAAAATATAAAAAATAAATGTGCATGTATTTGAGTATGTATAAGG
130 AAAAGTTGAATCCCCTAATAAAAAATATAAAAAATAAA---G-A-GTA-TT-AGTATGTATAAGG
* * * *
31601749 CCAATAAAAAAGAGAGGAAAAAATGAAACTGGGTTTTGTTAAAAGATGAAATGGGTAAATTAGGA
188 CCAATAAAAAAGAGAGAAAAAAATGAAACTAGGTTTAGTTAAAAGATGAAATAGGTAAATTAGGA
* *
31601814 GATACTTGCTATAGTGGAAGTTTATGGATACTTACGATTTCTTGTTTTTAGGGCAATACTTTCTA
253 GATACTTGCTATAGTGGAAGTGTATGGATACTTACGAGTTCTTGTTTTTAGGGCAATACTTTCTA
** *
31601879 AATTGTCTTTCCTGAAT-AGCTAAAAGGTTAATTGT
318 AACGGCCTTTCCTGAATGAGCTAAAAGGTTAATTGT
*
31601914 TTTA-TCCATCCATCTTTTTAGTCAAAAGCCTTAGCTTCATGA-GAGTCCCATTCAAATTGTGAA
1 TTTACTCCATCCATCTTTTTAGTCAAAAGCCTTAGCTTAATGAGGAGTCCCATTCAAATTGTGAA
* * *
31601977 ATAATTGAGTATCTGGCAATTCAGTTTATGCTCCATTGTGATTGTCGAGTCAAAAAA-TCATATG
66 ATAATTGAGTATCTAGCAATTCAGTTTATACTCCACTGTGATTGTCGAGT-AAAAAATTCATATG
* *
31602041 AAAAGTTGAATGCCCTAATAAAAAATATAATAAAT-AA-A-TA-T-GTATGTATAAGGCCAGCA-
130 AAAAGTTGAATCCCCTAATAAAAAATATAAAAAATAAAGAGTATTAGTATGTATAAGGCCA--AT
*
31602100 AAAAAATG-GAGAAAAAAATGAAA-TCAGGTTTAGTTAAAAGATGAACTAGGTAAATTAGGAGAT
193 AAAAAA-GAGAGAAAAAAATGAAACT-AGGTTTAGTTAAAAGATGAAATAGGTAAATTAGGAGAT
* * * * **
31602163 ACTTGCTATAGTGGAAGTGTATGGGTACTTAGGAGTTCTTGTTTTTAGGGCAATATTTTTTGCAC
256 ACTTGCTATAGTGGAAGTGTATGGATACTTACGAGTTCTTGTTTTTAGGGCAATACTTTCTAAAC
31602228 GGCCTTTCCTGAATGAGCT
321 GGCCTTTCCTGAATGAGCT
31602247 TATGAAACAT
Statistics
Matches: 299, Mismatches: 28, Indels: 25
0.85 0.08 0.07
Matches are distributed among these distances:
345 16 0.05
346 122 0.41
347 7 0.02
349 2 0.01
351 1 0.00
356 2 0.01
357 102 0.34
358 6 0.02
359 37 0.12
360 4 0.01
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (353 bp):
TTTACTCCATCCATCTTTTTAGTCAAAAGCCTTAGCTTAATGAGGAGTCCCATTCAAATTGTGAA
ATAATTGAGTATCTAGCAATTCAGTTTATACTCCACTGTGATTGTCGAGTAAAAAATTCATATGA
AAAGTTGAATCCCCTAATAAAAAATATAAAAAATAAAGAGTATTAGTATGTATAAGGCCAATAAA
AAAGAGAGAAAAAAATGAAACTAGGTTTAGTTAAAAGATGAAATAGGTAAATTAGGAGATACTTG
CTATAGTGGAAGTGTATGGATACTTACGAGTTCTTGTTTTTAGGGCAATACTTTCTAAACGGCCT
TTCCTGAATGAGCTAAAAGGTTAATTGT
Found at i:31633368 original size:6 final size:6
Alignment explanation
Indices: 31633351--31633380 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
31633341 TCAGATCTTG
31633351 TATTTAA TATTTA TATTTA TATTTA TATTT
1 TATTT-A TATTTA TATTTA TATTTA TATTT
31633381 GTTCGCTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 18 0.78
7 5 0.22
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TATTTA
Found at i:31641271 original size:43 final size:43
Alignment explanation
Indices: 31641237--31641320 Score: 141
Period size: 43 Copynumber: 2.0 Consensus size: 43
31641227 ATATACATGG
*
31641237 TTTGGCACACGACCGTGTGGCCCTATTTCTAATATACACACGA
1 TTTGGCACACGACCGTGTGGCCCTATTTCAAATATACACACGA
* *
31641280 TTTGGCACACGACCATGTGGCCCTATTTCAAATATTCACAC
1 TTTGGCACACGACCGTGTGGCCCTATTTCAAATATACACAC
31641321 AGGTGGACAC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.29
Consensus pattern (43 bp):
TTTGGCACACGACCGTGTGGCCCTATTTCAAATATACACACGA
Found at i:31641332 original size:43 final size:43
Alignment explanation
Indices: 31641239--31641333 Score: 129
Period size: 43 Copynumber: 2.2 Consensus size: 43
31641229 ATACATGGTT
* * **
31641239 TGGCACACGACCGTGTGGCCCTATTTCTAATATACACACGATT
1 TGGCACACGACCATGTGGCCCTATTTCAAATATACACACGAGG
*
31641282 TGGCACACGACCATGTGGCCCTATTTCAAATATTCACAC-AGG
1 TGGCACACGACCATGTGGCCCTATTTCAAATATACACACGAGG
31641324 TGGACACACG
1 TGG-CACACG
31641334 GGCTGAGACA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 4 0.09
43 42 0.91
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (43 bp):
TGGCACACGACCATGTGGCCCTATTTCAAATATACACACGAGG
Found at i:31643376 original size:44 final size:44
Alignment explanation
Indices: 31643302--31643508 Score: 158
Period size: 44 Copynumber: 4.8 Consensus size: 44
31643292 GGCATTACAT
* * ** *
31643302 GATTTCATATAAGACCATAGATGGGCTATGGCATCGATATATGA
1 GATTTCGTGTAAGACCATATCTGGGATATGGCATCGATATATGA
* * *
31643346 GACTTTC-TATAAGACCATATCTGGGATATGGCATTGATATATGT
1 GA-TTTCGTGTAAGACCATATCTGGGATATGGCATCGATATATGA
* * * * **
31643390 GATTACGTGTAAGACCATGTTTGGGACATTGGCATTAATATAT--
1 GATTTCGTGTAAGACCATATCTGGGATA-TGGCATCGATATATGA
* *
31643433 GA-TTCGTGTAAGACCAT-TGCTGGGCTATTGGCATCGATATGTGA
1 GATTTCGTGTAAGACCATAT-CTGGGATA-TGGCATCGATATATGA
* * *
31643477 TA-AT-ATGTAAGACCATATCTGGGATATGGCAT
1 GATTTCGTGTAAGACCATATCTGGGATATGGCAT
31643509 TGTATGTGAT
Statistics
Matches: 134, Mismatches: 22, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
41 1 0.01
42 37 0.28
43 23 0.17
44 56 0.42
45 17 0.13
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.33
Consensus pattern (44 bp):
GATTTCGTGTAAGACCATATCTGGGATATGGCATCGATATATGA
Found at i:31643507 original size:42 final size:43
Alignment explanation
Indices: 31643355--31643519 Score: 162
Period size: 42 Copynumber: 3.9 Consensus size: 43
31643345 AGACTTTCTA
* *
31643355 TAAGACCATATCTGGGATA-TGGCATTGATATATGTGATTACGTG
1 TAAGACCATATCTGGGATATTGGCATTG--ATATGTGATAATGTG
* * * * *
31643399 TAAGACCATGTTTGGGACATTGGCATTAATATATGAT--TCGTG
1 TAAGACCATATCTGGGATATTGGCATTGATATGTGATAAT-GTG
* * *
31643441 TAAGACCAT-TGCTGGGCTATTGGCATCGATATGTGATAATATG
1 TAAGACCATAT-CTGGGATATTGGCATTGATATGTGATAATGTG
31643484 TAAGACCATATCTGGGATA-TGGCATTG-TATGTGATA
1 TAAGACCATATCTGGGATATTGGCATTGATATGTGATA
31643520 CACGAGACTT
Statistics
Matches: 100, Mismatches: 15, Indels: 15
0.77 0.12 0.12
Matches are distributed among these distances:
41 10 0.10
42 39 0.39
43 26 0.26
44 18 0.18
45 7 0.07
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.34
Consensus pattern (43 bp):
TAAGACCATATCTGGGATATTGGCATTGATATGTGATAATGTG
Found at i:31644047 original size:15 final size:16
Alignment explanation
Indices: 31644027--31644064 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
31644017 ACTTGATGCA
*
31644027 ATTATTT-GTAATGTG
1 ATTATTTAGTAATATG
31644042 ATTATTTAGTAATATG
1 ATTATTTAGTAATATG
31644058 AGTTATT
1 A-TTATT
31644065 ATATTACAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 7 0.35
16 8 0.40
17 5 0.25
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.53
Consensus pattern (16 bp):
ATTATTTAGTAATATG
Found at i:31647901 original size:27 final size:26
Alignment explanation
Indices: 31647848--31647904 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
31647838 CAATATCTGC
*
31647848 ACCGAAATACCCCACAAGATAACATG
1 ACCGAAATACCCCACAAGATAAAATG
*
31647874 ACCGAAATACCCC-CATAGGGTAAAATG
1 ACCGAAATACCCCACA-A-GATAAAATG
31647901 ACCG
1 ACCG
31647905 TGTAATAGCC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 2 0.07
26 14 0.52
27 11 0.41
ACGTcount: A:0.42, C:0.30, G:0.16, T:0.12
Consensus pattern (26 bp):
ACCGAAATACCCCACAAGATAAAATG
Found at i:31650696 original size:27 final size:26
Alignment explanation
Indices: 31650653--31650761 Score: 137
Period size: 27 Copynumber: 4.1 Consensus size: 26
31650643 GGATGTTACA
** *
31650653 GACCGAAATACTTCATAGGATAAAAT
1 GACCGAAATACCCCATAGGGTAAAAT
*
31650679 GACCAAAATACCCCCATAGGGTAAAAT
1 GACCGAAATA-CCCCATAGGGTAAAAT
* *
31650706 AATCGAAATACCCCATAGGGTAAAAT
1 GACCGAAATACCCCATAGGGTAAAAT
*
31650732 GACTGAAATATCCCCATAGGGTAAAAT
1 GACCGAAATA-CCCCATAGGGTAAAAT
31650759 GAC
1 GAC
31650762 TGTTATACCC
Statistics
Matches: 71, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
26 32 0.45
27 39 0.55
ACGTcount: A:0.44, C:0.20, G:0.17, T:0.19
Consensus pattern (26 bp):
GACCGAAATACCCCATAGGGTAAAAT
Found at i:31650762 original size:27 final size:26
Alignment explanation
Indices: 31650657--31650776 Score: 127
Period size: 27 Copynumber: 4.6 Consensus size: 26
31650647 GTTACAGACC
** * *
31650657 GAAATACTTCATAGGATAAAATGACC
1 GAAATACCCCATAGGGTAAAATGACT
* *
31650683 AAAATACCCCCATAGGGTAAAAT-AAT
1 GAAATA-CCCCATAGGGTAAAATGACT
31650709 CGAAATACCCCATAGGGTAAAATGACT
1 -GAAATACCCCATAGGGTAAAATGACT
31650736 GAAATATCCCCATAGGGTAAAATGACT
1 GAAATA-CCCCATAGGGTAAAATGACT
**
31650763 GTTATACCCC-TAGG
1 GAAATACCCCATAGG
31650777 AGATGAAATG
Statistics
Matches: 80, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
25 4 0.05
26 32 0.40
27 44 0.55
ACGTcount: A:0.42, C:0.20, G:0.17, T:0.22
Consensus pattern (26 bp):
GAAATACCCCATAGGGTAAAATGACT
Found at i:31650772 original size:53 final size:53
Alignment explanation
Indices: 31650656--31650758 Score: 152
Period size: 53 Copynumber: 1.9 Consensus size: 53
31650646 TGTTACAGAC
**
31650656 CGAAATACTTCATAGGATAAAATGACCAAAATACCCCCATAGGGTAAAATAAT
1 CGAAATACCCCATAGGATAAAATGACCAAAATACCCCCATAGGGTAAAATAAT
* ** *
31650709 CGAAATACCCCATAGGGTAAAATGACTGAAATATCCCCATAGGGTAAAAT
1 CGAAATACCCCATAGGATAAAATGACCAAAATACCCCCATAGGGTAAAAT
31650759 GACTGTTATA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 44 1.00
ACGTcount: A:0.45, C:0.19, G:0.16, T:0.20
Consensus pattern (53 bp):
CGAAATACCCCATAGGATAAAATGACCAAAATACCCCCATAGGGTAAAATAAT
Found at i:31654074 original size:4 final size:4
Alignment explanation
Indices: 31654065--31654113 Score: 98
Period size: 4 Copynumber: 12.2 Consensus size: 4
31654055 TCAATTATTC
31654065 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
31654113 T
1 T
31654114 ACAAGAGCCT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 45 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:31654629 original size:21 final size:21
Alignment explanation
Indices: 31654604--31654643 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
31654594 CCATCACTCA
31654604 TTTTAACCAT-TTATTAATATT
1 TTTTAACCATATT-TTAATATT
*
31654625 TTTTAATCATATTTTAATA
1 TTTTAACCATATTTTAATA
31654644 CCGTGTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTAACCATATTTTAATATT
Found at i:31654974 original size:44 final size:43
Alignment explanation
Indices: 31654926--31655018 Score: 105
Period size: 44 Copynumber: 2.1 Consensus size: 43
31654916 TAGTTAAAAA
* *
31654926 TAAAATATAATAAAAGTTGTCATAATTATACATTTAAAAATGAT
1 TAAAATATAATAAAAGTTGTCATAATTATACAATT-AAAATAAT
* * ** * *
31654970 TAAAATTTAATAGATTTTGTGATAATTATATAATTAAAATAAT
1 TAAAATATAATAAAAGTTGTCATAATTATACAATTAAAATAAT
31655013 TAAAAT
1 TAAAAT
31655019 TAAAATTAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
43 13 0.32
44 28 0.68
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (43 bp):
TAAAATATAATAAAAGTTGTCATAATTATACAATTAAAATAAT
Found at i:31655021 original size:15 final size:17
Alignment explanation
Indices: 31654991--31655042 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 17
31654981 AGATTTTGTG
31654991 ATAATTATATAATTAAA
1 ATAATTATATAATTAAA
31655008 ATAATTA-A-AATTAAA
1 ATAATTATATAATTAAA
31655023 ATTAAAATTAT-TAATTAAA
1 A-T--AATTATATAATTAAA
31655042 A
1 A
31655043 AAAGTTGTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
15 8 0.27
16 2 0.07
17 7 0.23
18 5 0.17
19 8 0.27
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATAATTATATAATTAAA
Found at i:31655027 original size:12 final size:13
Alignment explanation
Indices: 31655010--31655042 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
31655000 TAATTAAAAT
31655010 AATTAAAATTA-A
1 AATTAAAATTATA
*
31655022 AATTAAAATTATT
1 AATTAAAATTATA
31655035 AATTAAAA
1 AATTAAAA
31655043 AAAGTTGTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AATTAAAATTATA
Found at i:31663554 original size:20 final size:21
Alignment explanation
Indices: 31663525--31663576 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
31663515 TTAGGAAGAA
*
31663525 TTAAATTTTTTTA-TATGTTCT
1 TTAAA-TTTTTTAGAATGTTCT
*
31663546 TTAAATTTTTTAGAATTTTCT
1 TTAAATTTTTTAGAATGTTCT
*
31663567 TTTAATTTTT
1 TTAAATTTTT
31663577 ATAATTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 7 0.26
21 20 0.74
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.67
Consensus pattern (21 bp):
TTAAATTTTTTAGAATGTTCT
Found at i:31663577 original size:20 final size:21
Alignment explanation
Indices: 31663525--31663590 Score: 66
Period size: 20 Copynumber: 3.2 Consensus size: 21
31663515 TTAGGAAGAA
* *
31663525 TTAAATTTTTTTA-TATGTTCT
1 TTAAA-TTTTTTAGAATTTTCT
31663546 TTAAATTTTTTAGAATTTTCT
1 TTAAATTTTTTAGAATTTTCT
* *
31663567 TTTAA-TTTTTATAATTTT-T
1 TTAAATTTTTTAGAATTTTCT
31663586 TTAAA
1 TTAAA
31663591 ATATAAATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
19 5 0.13
20 19 0.49
21 15 0.38
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (21 bp):
TTAAATTTTTTAGAATTTTCT
Found at i:31669385 original size:42 final size:42
Alignment explanation
Indices: 31669317--31669440 Score: 153
Period size: 42 Copynumber: 3.0 Consensus size: 42
31669307 ACTGAGATGT
* * * *
31669317 GATTTGTGTAAGACCATGTCTAGGACATTGGCATCGGTATGA
1 GATTCGTGTAAGACCATGTCTAGGACATTAGCACCGATATGA
* *
31669359 GATTCGTGTAAGACCATGTTTGGGACATTAGCACCGATATGA
1 GATTCGTGTAAGACCATGTCTAGGACATTAGCACCGATATGA
*
31669401 GATTCGTGTAAGACCATAG-CTAGG-CTATTAGCATCGATAT
1 GATTCGTGTAAGACCAT-GTCTAGGAC-ATTAGCACCGATAT
31669441 ATGATAGTAT
Statistics
Matches: 71, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
41 1 0.01
42 69 0.97
43 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (42 bp):
GATTCGTGTAAGACCATGTCTAGGACATTAGCACCGATATGA
Found at i:31672373 original size:2 final size:2
Alignment explanation
Indices: 31672366--31672399 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
31672356 ATATAGGCAT
*
31672366 CA CA CA CA CA TA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
31672400 TATATATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.47, G:0.00, T:0.03
Consensus pattern (2 bp):
CA
Found at i:31674917 original size:11 final size:11
Alignment explanation
Indices: 31674895--31674952 Score: 80
Period size: 11 Copynumber: 5.2 Consensus size: 11
31674885 AACTAATCCT
31674895 CTCTCAAATTTC
1 CTCTC-AATTTC
31674907 CTCTCAATTTC
1 CTCTCAATTTC
*
31674918 CTCTAAATTTC
1 CTCTCAATTTC
*
31674929 CTCTCAATTTG
1 CTCTCAATTTC
*
31674940 CTCTCAAATTC
1 CTCTCAATTTC
31674951 CT
1 CT
31674953 TCCAAATTTC
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
11 36 0.88
12 5 0.12
ACGTcount: A:0.22, C:0.33, G:0.02, T:0.43
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:31674928 original size:22 final size:23
Alignment explanation
Indices: 31674895--31674970 Score: 97
Period size: 22 Copynumber: 3.4 Consensus size: 23
31674885 AACTAATCCT
31674895 CTCTCAAATTTCCTCTCAATTTC
1 CTCTCAAATTTCCTCTCAATTTC
*
31674918 CTCT-AAATTTCCTCTCAATTTG
1 CTCTCAAATTTCCTCTCAATTTC
31674940 CTCTCAAA-TTCCT-TCCAAATTT-
1 CTCTCAAATTTCCTCT-C-AATTTC
31674962 CTCTCAAAT
1 CTCTCAAAT
31674971 CCATATTTAA
Statistics
Matches: 48, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
21 1 0.02
22 35 0.73
23 12 0.25
ACGTcount: A:0.25, C:0.32, G:0.01, T:0.42
Consensus pattern (23 bp):
CTCTCAAATTTCCTCTCAATTTC
Found at i:31674944 original size:33 final size:33
Alignment explanation
Indices: 31674894--31674968 Score: 98
Period size: 33 Copynumber: 2.2 Consensus size: 33
31674884 AAACTAATCC
* *
31674894 TCTCTCAAATTTCCTCTCAATTTCC-TCTAAATT
1 TCTCTC-AATTTCCTCTCAAATTCCTTCCAAATT
*
31674927 TCCTCTCAATTTGCTCTCAAATTCCTTCCAAATT
1 T-CTCTCAATTTCCTCTCAAATTCCTTCCAAATT
31674961 TCTCTCAA
1 TCTCTCAA
31674969 ATCCATATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 24 0.65
34 13 0.35
ACGTcount: A:0.24, C:0.32, G:0.01, T:0.43
Consensus pattern (33 bp):
TCTCTCAATTTCCTCTCAAATTCCTTCCAAATT
Found at i:31674969 original size:11 final size:11
Alignment explanation
Indices: 31674894--31674970 Score: 72
Period size: 11 Copynumber: 6.9 Consensus size: 11
31674884 AAACTAATCC
31674894 TCTCTCAAATT
1 TCTCTCAAATT
31674905 TCCTCTC-AATT
1 T-CTCTCAAATT
31674916 TC-CTCTAAATT
1 TCTCTC-AAATT
31674927 TCCTCTC-AATT
1 T-CTCTCAAATT
31674938 TGCTCTCAAATT
1 T-CTCTCAAATT
*
31674950 CCT-TCCAAATT
1 TCTCT-CAAATT
31674961 TCTCTCAAAT
1 TCTCTCAAAT
31674971 CCATATTTAA
Statistics
Matches: 55, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
9 3 0.05
10 2 0.04
11 36 0.65
12 11 0.20
13 3 0.05
ACGTcount: A:0.25, C:0.31, G:0.01, T:0.43
Consensus pattern (11 bp):
TCTCTCAAATT
Found at i:31676091 original size:7 final size:7
Alignment explanation
Indices: 31676079--31676104 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
31676069 TAGTCGATTG
31676079 GTATTTA
1 GTATTTA
31676086 GTATTTA
1 GTATTTA
31676093 GTATTTA
1 GTATTTA
31676100 GTATT
1 GTATT
31676105 ATGTATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:31677286 original size:25 final size:25
Alignment explanation
Indices: 31677250--31677332 Score: 121
Period size: 25 Copynumber: 3.3 Consensus size: 25
31677240 TATTTTGATA
* * *
31677250 TTATTTGTTGTAATAAAATGGACGT
1 TTATTTGATGTAATAAAATAGAAGT
31677275 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
*
31677300 TTATTTGATGTAATAAAATAGAAAT
1 TTATTTGATGTAATAAAATAGAAGT
*
31677325 TTTTTTGA
1 TTATTTGA
31677333 GTTATTTTGA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 53 1.00
ACGTcount: A:0.39, C:0.01, G:0.16, T:0.45
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:31677403 original size:95 final size:94
Alignment explanation
Indices: 31677206--31677376 Score: 231
Period size: 95 Copynumber: 1.8 Consensus size: 94
31677196 ATTTTGATTT
*
31677206 TATTTT-ATGTAATAAAATAAAAAAATTTTTGAGTTATTTTGATATTATTTGTTGTAATAAAATG
1 TATTTTGATGTAATAAAATAAAAAAATTTTTGAGTTATTTTGATATTATTTGATGTAATAAAATG
* * *
31677270 GACGTTTATTTGATGTAATAAAATAGAAG
66 GACGATTAATTAATGTAATAAAATAGAAG
* * ** *
31677299 TTTATTTGATGTAATAAAATAGAAATTTTTTTGAGTTATTTTGATATTATTTGATGTAATAACAT
1 TAT-TTTGATGTAATAAAATAAAAAAATTTTTGAGTTATTTTGATATTATTTGATGTAATAAAAT
31677364 -GA-GATTAATTAAT
65 GGACGATTAATTAAT
31677377 TTGTACAAAT
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
93 10 0.15
94 5 0.07
95 52 0.78
ACGTcount: A:0.39, C:0.01, G:0.13, T:0.46
Consensus pattern (94 bp):
TATTTTGATGTAATAAAATAAAAAAATTTTTGAGTTATTTTGATATTATTTGATGTAATAAAATG
GACGATTAATTAATGTAATAAAATAGAAG
Found at i:31680799 original size:124 final size:124
Alignment explanation
Indices: 31680554--31680925 Score: 586
Period size: 124 Copynumber: 3.0 Consensus size: 124
31680544 CAAACATGCT
31680554 ACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGGTA
1 ACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGGTA
*
31680619 GAAGGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCTAGGACCA
66 GAAGCATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCTAGGACCA
* * * *
31680678 ACTGTAGCAAAAGTGCGTCCACGAGGGCGCGATTTCAGAAATTCTTCTCA-AATAGCATCCTGCT
1 ACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAA-AGCATCCTGGT
* * * *
31680742 TGAAGCATTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATAATTTTTTC-AGGACCT
65 AGAAGCA-TTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCTAGGACCA
*
31680802 ACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTAACAAATTCTTCTCATAAAGCATCCTGGTA
1 ACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGGTA
* * *
31680867 AAAGCGATTTTATACTATTTGCTCAGAAACGTCAAATCGAAATTATTTCTTATAGGACC
66 GAAGC-ATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCTAGGACC
31680926 TAAAAACCCT
Statistics
Matches: 223, Mismatches: 20, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
123 2 0.01
124 169 0.76
125 52 0.23
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.30
Consensus pattern (124 bp):
ACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGGTA
GAAGCATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCTAGGACCA
Found at i:31685096 original size:7 final size:7
Alignment explanation
Indices: 31685084--31685136 Score: 88
Period size: 7 Copynumber: 7.6 Consensus size: 7
31685074 AAATATATAT
*
31685084 TTTTTTA
1 TTTTTAA
*
31685091 TTTTTTA
1 TTTTTAA
31685098 TTTTTAA
1 TTTTTAA
31685105 TTTTTAA
1 TTTTTAA
31685112 TTTTTAA
1 TTTTTAA
31685119 TTTTTAA
1 TTTTTAA
31685126 TTTTTAA
1 TTTTTAA
31685133 TTTT
1 TTTT
31685137 AAAACACTTT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
7 45 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTAA
Found at i:31685174 original size:23 final size:26
Alignment explanation
Indices: 31685144--31685201 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 26
31685134 TTTAAAACAC
*
31685144 TTTT-AAAAT-ATTTTTT-AT-TTTT
1 TTTTAAAAATAATTTTTTAATGTTTA
31685166 TTTTAAAAATAATTTTTTAATGTTTA
1 TTTTAAAAATAATTTTTTAATGTTTA
31685192 TTTTAAAAAT
1 TTTTAAAAAT
31685202 GGGCCAGGCC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 4 0.13
23 5 0.16
24 7 0.23
25 2 0.06
26 13 0.42
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (26 bp):
TTTTAAAAATAATTTTTTAATGTTTA
Found at i:31685564 original size:31 final size:31
Alignment explanation
Indices: 31685520--31685608 Score: 101
Period size: 31 Copynumber: 2.8 Consensus size: 31
31685510 CCGAATATAA
31685520 TAAATATATTTTTTATTTTTATTTTTTAATTT
1 TAAA-ATATTTTTTATTTTTATTTTTTAATTT
*
31685552 TAAAATACTTTTTT-TTTATT-TTTTTTATTTT
1 TAAAATA-TTTTTTATTT-TTATTTTTTAATTT
*
31685583 TAAAATGATTTTTTAATGTTTATTTT
1 TAAAAT-ATTTTTT-ATTTTTATTTT
31685609 AAAAATGGGC
Statistics
Matches: 49, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
31 28 0.57
32 15 0.31
33 6 0.12
ACGTcount: A:0.27, C:0.01, G:0.02, T:0.70
Consensus pattern (31 bp):
TAAAATATTTTTTATTTTTATTTTTTAATTT
Found at i:31686457 original size:19 final size:21
Alignment explanation
Indices: 31686433--31686477 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
31686423 ACATCATTTC
*
31686433 CAGAAGC-CCGAAG-GCTAAA
1 CAGAAGCACAGAAGTGCTAAA
*
31686452 CAGAAGCACATAAGTGCTAAA
1 CAGAAGCACAGAAGTGCTAAA
31686473 CAGAA
1 CAGAA
31686478 ACCCATAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 7 0.32
20 4 0.18
21 11 0.50
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (21 bp):
CAGAAGCACAGAAGTGCTAAA
Found at i:31686497 original size:42 final size:42
Alignment explanation
Indices: 31686448--31686600 Score: 180
Period size: 42 Copynumber: 3.6 Consensus size: 42
31686438 GCCCGAAGGC
* *
31686448 TAAACAGAAGCACATAAGTGCTAAACAGAAACCCATAAGGGT
1 TAAACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGT
* ** * *
31686490 TGAACAGAAGCTTGTAAGAGCTGAACAAAAACCCATAAGGGT
1 TAAACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGT
* * *
31686532 TAAACAGAAACTCAAAAGAGCTAAACGGAAACCCATAAGGGT
1 TAAACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGT
* * * *
31686574 TAAACATAAACTCATATGAGTTAAACA
1 TAAACAGAAGCTCATAAGAGCTAAACA
31686601 AAAGCTCGTG
Statistics
Matches: 91, Mismatches: 20, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 91 1.00
ACGTcount: A:0.48, C:0.18, G:0.18, T:0.16
Consensus pattern (42 bp):
TAAACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGT
Found at i:31686584 original size:21 final size:21
Alignment explanation
Indices: 31686448--31686600 Score: 108
Period size: 21 Copynumber: 7.3 Consensus size: 21
31686438 GCCCGAAGGC
* * * *
31686448 TAAACAGAAGCACATAAGTGC
1 TAAACAGAAACCCATAAGAGT
*
31686469 TAAACAGAAACCCATAAGGGT
1 TAAACAGAAACCCATAAGAGT
* * *** *
31686490 TGAACAGAAGCTTGTAAGAGC
1 TAAACAGAAACCCATAAGAGT
* * *
31686511 TGAACAAAAACCCATAAGGGT
1 TAAACAGAAACCCATAAGAGT
* * *
31686532 TAAACAGAAACTCAAAAGAGC
1 TAAACAGAAACCCATAAGAGT
* *
31686553 TAAACGGAAACCCATAAGGGT
1 TAAACAGAAACCCATAAGAGT
* * *
31686574 TAAACATAAACTCATATGAGT
1 TAAACAGAAACCCATAAGAGT
31686595 TAAACA
1 TAAACA
31686601 AAAGCTCGTG
Statistics
Matches: 98, Mismatches: 34, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 98 1.00
ACGTcount: A:0.48, C:0.18, G:0.18, T:0.16
Consensus pattern (21 bp):
TAAACAGAAACCCATAAGAGT
Found at i:31688231 original size:19 final size:19
Alignment explanation
Indices: 31688203--31688249 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
31688193 GGCATAGTTA
31688203 TAAAAA-ATATGTATATAT
1 TAAAAATATATGTATATAT
31688221 TAAAAATATATGTATATAT
1 TAAAAATATATGTATATAT
31688240 TAAAAATATA
1 TAAAAATATA
31688250 CGTAAGAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 6 0.21
19 22 0.79
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.38
Consensus pattern (19 bp):
TAAAAATATATGTATATAT
Found at i:31697908 original size:21 final size:21
Alignment explanation
Indices: 31697867--31697908 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
31697857 AAAATTTTAG
* *
31697867 AAATTTCTAAAATATATAAAT
1 AAATTTCAAAAATATAAAAAT
31697888 AAATATTCAAAAATA-AAAAAT
1 AAAT-TTCAAAAATATAAAAAT
31697909 TAGTTAAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (21 bp):
AAATTTCAAAAATATAAAAAT
Found at i:31699496 original size:11 final size:11
Alignment explanation
Indices: 31699462--31699505 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 11
31699452 ATTTTAAAAA
*
31699462 TAAAAATTTTT
1 TAAAAATATTT
31699473 TACAAAAAGTATTT
1 T--AAAAA-TATTT
31699487 TAAAAATATTT
1 TAAAAATATTT
31699498 TAAAAATA
1 TAAAAATA
31699506 AAAAAATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
11 14 0.48
12 5 0.17
13 5 0.17
14 5 0.17
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (11 bp):
TAAAAATATTT
Found at i:31703012 original size:81 final size:79
Alignment explanation
Indices: 31702861--31703016 Score: 242
Period size: 81 Copynumber: 1.9 Consensus size: 79
31702851 TAAGAATGTT
* * *
31702861 TAGAAGTTCCATTTTTAAGTTGTGAGTTACTAAAGAAAATAAAAGTTGACAGACACAAAAAAACT
1 TAGAAGTGCCATTTTTAAGTTGTGAGTTACTAAAAAAAATAAAAGTTGAAAGACACAAAAAAACT
31702926 CCTTGATTGAAGAC
66 CCTTGATTGAAGAC
31702940 TAGAAGTGCCATTTTTAAGTTGTGTGAGTTACTAAAAAAAAATAAAAGTTGAAAGACAC-AAAAA
1 TAGAAGTGCCATTTTTAAG-T-TGTGAGTTACT-AAAAAAAATAAAAGTTGAAAGACACAAAAAA
*
31703004 ACTTCTTGATTGA
63 ACTCCTTGATTGA
31703017 TGAGCAAGTA
Statistics
Matches: 70, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
79 18 0.26
80 1 0.01
81 28 0.40
82 23 0.33
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.29
Consensus pattern (79 bp):
TAGAAGTGCCATTTTTAAGTTGTGAGTTACTAAAAAAAATAAAAGTTGAAAGACACAAAAAAACT
CCTTGATTGAAGAC
Found at i:31712937 original size:45 final size:45
Alignment explanation
Indices: 31712884--31712974 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
31712874 AAATAAATGA
31712884 ATTTCAAGTTGCTATAACATATGGATTATGACATATAAACTAAAG
1 ATTTCAAGTTGCTATAACATATGGATTATGACATATAAACTAAAG
*
31712929 ATTTCAAGTTGCTATAACATATGGATTTTGACATATAAACTAAAG
1 ATTTCAAGTTGCTATAACATATGGATTATGACATATAAACTAAAG
31712974 A
1 A
31712975 AATTATATAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (45 bp):
ATTTCAAGTTGCTATAACATATGGATTATGACATATAAACTAAAG
Found at i:31712955 original size:24 final size:24
Alignment explanation
Indices: 31712884--31712956 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 24
31712874 AAATAAATGA
31712884 ATTTCAAGTTGCTATAACATATGG
1 ATTTCAAGTTGCTATAACATATGG
**
31712908 A-TT--A--TGACATATAA-ACTAAAG
1 ATTTCAAGTTG-C-TATAACA-TATGG
31712929 ATTTCAAGTTGCTATAACATATGG
1 ATTTCAAGTTGCTATAACATATGG
31712953 ATTT
1 ATTT
31712957 TGACATATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 18
0.62 0.07 0.31
Matches are distributed among these distances:
19 2 0.06
20 2 0.06
21 10 0.28
22 2 0.06
23 2 0.06
24 14 0.39
25 2 0.06
26 2 0.06
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (24 bp):
ATTTCAAGTTGCTATAACATATGG
Found at i:31713498 original size:16 final size:16
Alignment explanation
Indices: 31713477--31713512 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
31713467 CTGAATTACT
* *
31713477 ATTACAGCTCTATTTC
1 ATTACACCTCTATTCC
31713493 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
31713509 ATTA
1 ATTA
31713513 TAGTGAACCA
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:0.28, C:0.28, G:0.03, T:0.42
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:31713903 original size:9 final size:9
Alignment explanation
Indices: 31713889--31713919 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
31713879 GTTAAACGAA
31713889 TCGAGTTAT
1 TCGAGTTAT
*
31713898 TCGAGTTAA
1 TCGAGTTAT
31713907 TCGAGTTAT
1 TCGAGTTAT
31713916 TCGA
1 TCGA
31713920 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:31713989 original size:9 final size:9
Alignment explanation
Indices: 31713975--31714008 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
31713965 GTTTTCGAAT
31713975 TCGAATAAC
1 TCGAATAAC
*
31713984 TCGAATAAT
1 TCGAATAAC
*
31713993 TCGAATAAG
1 TCGAATAAC
31714002 TCGAATA
1 TCGAATA
31714009 TCAAACTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:31713993 original size:18 final size:18
Alignment explanation
Indices: 31713972--31714008 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
31713962 TGAGTTTTCG
31713972 AATTCGAATAACTCGAAT
1 AATTCGAATAACTCGAAT
*
31713990 AATTCGAATAAGTCGAAT
1 AATTCGAATAACTCGAAT
31714008 A
1 A
31714009 TCAAACTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.27
Consensus pattern (18 bp):
AATTCGAATAACTCGAAT
Found at i:31714270 original size:30 final size:31
Alignment explanation
Indices: 31714222--31714281 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
31714212 AAACCTTTTA
* *
31714222 TTTTCCCCCCAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
31714252 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
31714282 TCTCAGCTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.18, C:0.42, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:31716065 original size:21 final size:21
Alignment explanation
Indices: 31716041--31716080 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
31716031 TTTAAAATTA
31716041 GATTGTTTTCTA-AATTTTAAG
1 GATT-TTTTCTAGAATTTTAAG
*
31716062 GATTTTTTTTAGAATTTTA
1 GATTTTTTCTAGAATTTTA
31716081 GATATTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.28, C:0.03, G:0.12, T:0.57
Consensus pattern (21 bp):
GATTTTTTCTAGAATTTTAAG
Found at i:31717586 original size:12 final size:12
Alignment explanation
Indices: 31717569--31717601 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
31717559 ATTTTAACAC
31717569 TATTATTATCAT
1 TATTATTATCAT
31717581 TATTATTATCAT
1 TATTATTATCAT
31717593 TATTATTAT
1 TATTATTAT
31717602 ACTTACGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (12 bp):
TATTATTATCAT
Found at i:31717784 original size:27 final size:24
Alignment explanation
Indices: 31717717--31717784 Score: 64
Period size: 27 Copynumber: 2.7 Consensus size: 24
31717707 TTCGTAGTTT
*
31717717 TTATATATATGTATATACATTTATA
1 TTATATA-ATATATATACATTTATA
* *
31717742 TTTTATAATATTTATACATTTTCCATA
1 TTATATAATATATATACA-TTT--ATA
*
31717769 TTATATAATCTATATA
1 TTATATAATATATATA
31717785 TATGTTTATA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
24 9 0.26
25 9 0.26
27 16 0.47
ACGTcount: A:0.38, C:0.07, G:0.01, T:0.53
Consensus pattern (24 bp):
TTATATAATATATATACATTTATA
Found at i:31717871 original size:8 final size:8
Alignment explanation
Indices: 31717858--31717910 Score: 54
Period size: 8 Copynumber: 6.4 Consensus size: 8
31717848 TTTCTTAGTT
31717858 TTTATATA
1 TTTATATA
31717866 TTTATATA
1 TTTATATA
*
31717874 TGTATATACA
1 T-T-TATATA
31717884 TTTATAT-
1 TTTATATA
31717891 TTTATAATA
1 TTTAT-ATA
*
31717900 TCTATATA
1 TTTATATA
31717908 TTT
1 TTT
31717911 TCCATATTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
7 5 0.14
8 20 0.54
9 6 0.16
10 6 0.16
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (8 bp):
TTTATATA
Found at i:31717887 original size:26 final size:26
Alignment explanation
Indices: 31717858--31717934 Score: 77
Period size: 27 Copynumber: 2.9 Consensus size: 26
31717848 TTTCTTAGTT
*
31717858 TTTATATATTTAT-ATATGTATATACA
1 TTTATAT-TTTATAATATCTATATACA
*
31717884 TTTATATTTTATAATATCTATATA-T
1 TTTATATTTTATAATATCTATATACA
* *
31717909 TTTCCATATTTTATAATCTATATATA
1 TTT--ATATTTTATAATATCTATATA
31717935 TATGTTTATA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
25 8 0.18
26 17 0.39
27 19 0.43
ACGTcount: A:0.36, C:0.06, G:0.01, T:0.56
Consensus pattern (26 bp):
TTTATATTTTATAATATCTATATACA
Found at i:31717911 original size:148 final size:143
Alignment explanation
Indices: 31717692--31717966 Score: 426
Period size: 148 Copynumber: 1.9 Consensus size: 143
31717682 ATTATTATCA
*
31717692 TATTATTATTTTATTTTCGTAGTTTTTATATATATGTATATACATTTATATTTTATAATATTTAT
1 TATTATTATTTTATTTTCGTAGTTTTTATATATATGTATATACATTTATATTTTATAATATCTAT
*
31717757 ACATTTTCCATATTATATAATC-TATATATATGTTTATACATTTTTTATAATATGAATATATATA
66 ACATTTTCCATATTATATAATCATATATATATGTTTATACATTCTTTATAATATGAATATATATA
31717821 CATATACATCTTT
131 CATATACATCTTT
*
31717834 TATTATTATTTTATTTTCTTAGTTTTTATATATTTATATATGTATATACATTTATATTTTATAAT
1 TATTATTATTTTATTTTCGTAG--TTT-T-TA--TATATATGTATATACATTTATATTTTATAAT
* * *
31717899 ATCTATATATTTTCCATATTTTATAATCTATATATATATGTTTATACATTCTTTATAATATGTAT
60 ATCTATACATTTTCCATATTATATAATC-ATATATATATGTTTATACATTCTTTATAATATGAAT
31717964 ATA
124 ATA
31717967 CATATTTTCT
Statistics
Matches: 119, Mismatches: 6, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
142 21 0.18
144 3 0.03
145 1 0.01
146 2 0.02
148 56 0.47
150 36 0.30
ACGTcount: A:0.34, C:0.07, G:0.03, T:0.56
Consensus pattern (143 bp):
TATTATTATTTTATTTTCGTAGTTTTTATATATATGTATATACATTTATATTTTATAATATCTAT
ACATTTTCCATATTATATAATCATATATATATGTTTATACATTCTTTATAATATGAATATATATA
CATATACATCTTT
Found at i:31719790 original size:16 final size:16
Alignment explanation
Indices: 31719765--31719795 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31719755 TGTGTTTTGT
*
31719765 TTTGATTGCATGACAC
1 TTTGACTGCATGACAC
31719781 TTTGACTGCATGACA
1 TTTGACTGCATGACA
31719796 TTTCATTATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (16 bp):
TTTGACTGCATGACAC
Found at i:31724589 original size:41 final size:40
Alignment explanation
Indices: 31724489--31725023 Score: 354
Period size: 41 Copynumber: 12.7 Consensus size: 40
31724479 AAACCGGTGA
* * * * *
31724489 AATCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAA
1 AATCAGTCTTATCTCCCTGAAGTTGCAGTAGAGCAGA-TAG
* * *
31724530 AATCAGATCTTATCTCTCTGAAGTTGCAGAAGAGCAGATCG
1 AATCAG-TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATAG
* * * * *
31724571 CATCCAGTCTTATCTCTCTGAAGTTGCAGTGGAGCGGATTAA
1 AAT-CAGTCTTATCTCCCTGAAGTTGCAGTAGAGCAGA-TAG
* * *
31724613 AATCAGATCTTATCTCTCTGAAGTTGCAATAGAGCAGATCG
1 AATCAG-TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATAG
* *
31724654 CATCCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGA-AG
1 AAT-CAGTCTTATCTCCCTGAAGTTGCAGT--AG-AG-CAGATAG
* * * * * *
31724698 AAATCAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAA
1 -AATCAGTCTTATCTCCCTGAAGTTGCAGTAGAGCAGA-TAG
** * *
31724740 AATCAGATCTTATCTCTTTGAAGTTGCAGAAGAGCAGATCG
1 AATCAG-TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATAG
* *
31724781 CATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATAGAAG
1 AAT-CAGTCTTATCTCCCTGAAGTTGCAGTAGAGCAGAT---AG
* * * *
31724825 AAATCAATCCTATCTCCCTGAAGTTGCAGT-GAAGCGGATTAA
1 -AATCAGTCTTATCTCCCTGAAGTTGCAGTAG-AGCAGA-TAG
* * * *
31724867 AATCAGATCTTATCTCTCTGAAGTTGCAGAAGAGTAGATCG
1 AATCAG-TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATAG
* * * * ** *
31724908 CATCCAGTCCTATCTCCCTGAGGTTGCAGTGGAGTGGATTAAA
1 AAT-CAGTCTTATCTCCCTGAAGTTGCAGTAGAGCAGA-T-AG
** * *
31724951 AATTACAGATCTTATCTCTTTGAAGTTGCATTAGAGCAGATCG
1 AA-T-CAG-TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATAG
*
31724994 CATCCAGTCTTATCTCCCTGAAGTTGCAGT
1 AAT-CAGTCTTATCTCCCTGAAGTTGCAGT
31725024 GGAGTAGACT
Statistics
Matches: 381, Mismatches: 86, Indels: 54
0.73 0.17 0.10
Matches are distributed among these distances:
40 3 0.01
41 154 0.40
42 124 0.33
43 6 0.02
44 62 0.16
45 32 0.08
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.28
Consensus pattern (40 bp):
AATCAGTCTTATCTCCCTGAAGTTGCAGTAGAGCAGATAG
Found at i:31724637 original size:83 final size:83
Alignment explanation
Indices: 31724498--31725027 Score: 559
Period size: 83 Copynumber: 6.3 Consensus size: 83
31724488 AAATCAATCC
31724498 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCTGAAGTTGCAGAAGA
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCTGAAGTTGCAGAAGA
31724563 GCAGATCGCATCCAGTCT
66 GCAGATCGCATCCAGTCT
*
31724581 TATCTCTCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCTGAAGTTGCA-ATAG
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCTGAAGTTGCAGA-AG
*
31724645 AGCAGATCGCATCCAATCT
65 AGCAGATCGCATCCAGTCT
* ** * * * *
31724664 TATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCA-ATCCTATCTCCCTAAAGTTGCAGT
1 TATCTCCCTGAAGTTGCAGTGGAGC-G-GATTA-AAATCAGATCTTATCTCTCTGAAGTTGCAGA
* * ***
31724728 GGAGCGGATTAAAAT-CAGATCT
63 AGAGCAGA-TCGCATCCAG-TCT
** ** * *** * **
31724750 TATCTCTTTGAAGTTGCAGAAGAGCAGA-TCGCATCCAG-TCTTATCTCCCTGAAGTTGCAGTGG
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAAT-CAGATCTTATCTCTCTGAAGTTGCAGAAG
* * * *
31724813 AGCAGATAGAAGAAAT-CAATCC
65 AGCAGAT---CG-CATCCAGTCT
*
31724835 TATCTCCCTGAAGTTGCAGTGAAGCGGATTAAAATCAGATCTTATCTCTCTGAAGTTGCAGAAGA
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCTGAAGTTGCAGAAGA
* *
31724900 GTAGATCGCATCCAGTCC
66 GCAGATCGCATCCAGTCT
* * * **
31724918 TATCTCCCTGAGGTTGCAGTGGAGTGGATTAAAAATTACAGATCTTATCTCTTTGAAGTTGCATT
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATT-AAAA-T-CAGATCTTATCTCTCTGAAGTTGCAGA
31724983 AGAGCAGATCGCATCCAGTCT
63 AGAGCAGATCGCATCCAGTCT
31725004 TATCTCCCTGAAGTTGCAGTGGAG
1 TATCTCCCTGAAGTTGCAGTGGAG
31725028 TAGACTAGAG
Statistics
Matches: 371, Mismatches: 57, Indels: 35
0.80 0.12 0.08
Matches are distributed among these distances:
82 6 0.02
83 166 0.45
84 6 0.02
85 58 0.16
86 135 0.36
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (83 bp):
TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCTGAAGTTGCAGAAGA
GCAGATCGCATCCAGTCT
Found at i:31724722 original size:44 final size:43
Alignment explanation
Indices: 31724487--31724895 Score: 255
Period size: 42 Copynumber: 9.7 Consensus size: 43
31724477 ACAAACCGGT
* * **
31724487 GAAATCAATCCTATCTCCCTGAAGTTGCAGTGGAGC-GGATTA
1 GAAATCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGCAGAA
* * *
31724529 -AAATCAGATCTTATCTCTCTGAAGTTGCA--GAAG-AGCAGATC
1 GAAATCA-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGCAGA-A
* * * * **
31724570 G-CATCCAGTCTTATCTCTCTGAAGTTGCAGTGGAGC-GGATTA
1 GAAAT-CAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGCAGAA
* * *
31724612 -AAATCAGATCTTATCTCTCTGAAGTTGCAAT--AG-AGCAGATC
1 GAAATCA-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGCAGA-A
*
31724653 G-CATCCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAA
1 GAAAT-CAATCTTATCTCCCTGAAGTTGCAGTGGAGCAG-CAGAA
* * * **
31724697 GAAATCAATCCTATCTCCCTAAAGTTGCAGTGGAGC-GGATTA
1 GAAATCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGCAGAA
** * *
31724739 -AAATCAGATCTTATCTCTTTGAAGTTGCA--GAAG-AGCAGATC
1 GAAATCA-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGCAGA-A
* * *
31724780 G-CATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATAGAA
1 GAAAT-CAATCTTATCTCCCTGAAGTTGCAGTGGAGCAG-CAGAA
* * * **
31724824 GAAATCAATCCTATCTCCCTGAAGTTGCAGTGAAGC-GGATTA
1 GAAATCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGCAGAA
*
31724866 -AAATCAGATCTTATCTCTCTGAAGTTGCAG
1 GAAATCA-ATCTTATCTCCCTGAAGTTGCAG
31724896 AAGAGTAGAT
Statistics
Matches: 281, Mismatches: 56, Indels: 60
0.71 0.14 0.15
Matches are distributed among these distances:
40 14 0.05
41 88 0.31
42 93 0.33
43 12 0.04
44 63 0.22
45 11 0.04
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (43 bp):
GAAATCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGCAGAA
Found at i:31724741 original size:127 final size:127
Alignment explanation
Indices: 31724581--31724941 Score: 625
Period size: 127 Copynumber: 2.8 Consensus size: 127
31724571 CATCCAGTCT
*
31724581 TATCTCTCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCTGAAGTTGCA-ATAG
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCTGAAGTTGCAGA-AG
*
31724645 AGCAGATCGCATCCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCC
65 AGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCC
* *
31724708 TATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTTTGAAGTTGCAGAAGA
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCTGAAGTTGCAGAAGA
*
31724773 GCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATAGAAGAAATCAATCC
66 GCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCC
*
31724835 TATCTCCCTGAAGTTGCAGTGAAGCGGATTAAAATCAGATCTTATCTCTCTGAAGTTGCAGAAGA
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCTGAAGTTGCAGAAGA
* * *
31724900 GTAGATCGCATCCAGTCCTATCTCCCTGAGGTTGCAGTGGAG
66 GCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAG
31724942 TGGATTAAAA
Statistics
Matches: 222, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
127 221 1.00
128 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.27
Consensus pattern (127 bp):
TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCTGAAGTTGCAGAAGA
GCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCC
Found at i:31726306 original size:3 final size:3
Alignment explanation
Indices: 31726298--31726346 Score: 80
Period size: 3 Copynumber: 16.0 Consensus size: 3
31726288 ATTTTTACAC
*
31726298 TAT TAT TAT CAT TAT TAT TAT TAT TATT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT
31726344 TAT
1 TAT
31726347 ACTTACGTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
3 40 0.93
4 3 0.07
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:31726514 original size:27 final size:26
Alignment explanation
Indices: 31726460--31726561 Score: 73
Period size: 27 Copynumber: 3.7 Consensus size: 26
31726450 TTTTCATAGT
31726460 TTTTATATATATGTATATACATTTATA
1 TTTTATA-ATATGTATATACATTTATA
31726487 TTTTATAATAT-T-TATACATTTTCCATA
1 TTTTATAATATGTATATACA-TTT--ATA
* * * **
31726514 TTATATAATCTATATATATGTTTATACA
1 TTTTATAATATGTATATACATTTAT--A
31726542 TTTTTTATAATATGTATATA
1 --TTTTATAATATGTATATA
31726562 TATATACATA
Statistics
Matches: 59, Mismatches: 7, Indels: 15
0.73 0.09 0.19
Matches are distributed among these distances:
24 6 0.10
25 4 0.07
26 6 0.10
27 19 0.32
28 5 0.08
29 4 0.07
30 15 0.25
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.55
Consensus pattern (26 bp):
TTTTATAATATGTATATACATTTATA
Found at i:31726644 original size:24 final size:24
Alignment explanation
Indices: 31726613--31726680 Score: 75
Period size: 27 Copynumber: 2.6 Consensus size: 24
31726603 TTTCATAGTT
31726613 TTTATATATTTAT-ATATGCATATACA
1 TTTATAT-TTTATAATAT-C-TATACA
31726639 TTTATATTTTATAATATCTATACA
1 TTTATATTTTATAATATCTATACA
31726663 TTTTCCATATTTTATAAT
1 -TTT--ATATTTTATAAT
31726681 CTATATATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
24 6 0.16
25 9 0.24
26 11 0.29
27 12 0.32
ACGTcount: A:0.35, C:0.09, G:0.01, T:0.54
Consensus pattern (24 bp):
TTTATATTTTATAATATCTATACA
Found at i:31726696 original size:158 final size:154
Alignment explanation
Indices: 31726410--31726724 Score: 490
Period size: 158 Copynumber: 2.0 Consensus size: 154
31726400 ATGTTTTTAA
*
31726410 ATACATATACATATTTTATTATTATCATATTATTATTTTATTTTCATAGTTTTTATATATATGTA
1 ATACATATACATATTTTATTATTAT-ATATTATTATTTTATTTTCATAGTTTTTATATATATGCA
* **
31726475 TATACATTTATATTTTATAATATTTATACATTTTCCATATTATATAATCTATATATATGTTTATA
65 TATACATTTATATTTTATAATATCTATACATTTTCCATATTATATAATCTATATATAAATTTATA
* *
31726540 CATTTTTTATAATATGTATATATAT
130 CATTCTTTATAATATGCATATATAT
31726565 ATACATATACATATTTTATTATTAT-T-TTATTATTTTATTTTCATAGTTTTTATATATTTATAT
1 ATACATATACATATTTTATTATTATATATTATTATTTTATTTTCATAG--TTT-T-TA--TATAT
*
31726628 ATGCATATACATTTATATTTTATAATATCTATACATTTTCCATATTTTATAATCTATATATAAAT
60 ATGCATATACATTTATATTTTATAATATCTATACATTTTCCATATTATATAATCTATATATAAAT
31726693 TTATACATTCTTTATAATATGCATATATAT
125 TTATACATTCTTTATAATATGCATATATAT
31726723 AT
1 AT
31726725 TCTTACACTA
Statistics
Matches: 147, Mismatches: 7, Indels: 9
0.90 0.04 0.06
Matches are distributed among these distances:
152 20 0.14
153 1 0.01
154 3 0.02
155 26 0.18
156 2 0.01
158 95 0.65
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (154 bp):
ATACATATACATATTTTATTATTATATATTATTATTTTATTTTCATAGTTTTTATATATATGCAT
ATACATTTATATTTTATAATATCTATACATTTTCCATATTATATAATCTATATATAAATTTATAC
ATTCTTTATAATATGCATATATAT
Found at i:31726719 original size:30 final size:28
Alignment explanation
Indices: 31726645--31726719 Score: 57
Period size: 30 Copynumber: 2.6 Consensus size: 28
31726635 TACATTTATA
31726645 TTTTATAATAT-C-TATACATTT-TCCAT
1 TTTTATAATATGCATATACATTTAT-CAT
* ** *
31726671 ATTTTATAATCTATATATAAATTTATACAT
1 -TTTTATAATATGCATATACATTTAT-CAT
31726701 TCTTTATAATATGCATATA
1 T-TTTATAATATGCATATA
31726720 TATATTCTTA
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
27 10 0.27
29 9 0.24
30 18 0.49
ACGTcount: A:0.37, C:0.11, G:0.01, T:0.51
Consensus pattern (28 bp):
TTTTATAATATGCATATACATTTATCAT
Found at i:31726777 original size:158 final size:157
Alignment explanation
Indices: 31726465--31726793 Score: 396
Period size: 158 Copynumber: 2.1 Consensus size: 157
31726455 ATAGTTTTTA
* *
31726465 TATATATGTATATACATTTATATTTTATAATATTTATACATTTTCCATATTATATAATCTATATA
1 TATATATGCATATACATTTATATTTTATAATATCTATACATTTTCCATATTATATAATCTATATA
** * * * ** *
31726530 TATGTTTATACATTTTTTATAATATGTATATATATATACATATACATATTTTATTATTATTTTAT
66 TAAATTTATACATTCTTTATAATATGCATATATATATACATATACATATTTCAAAACTA-TTTAT
* * * **
31726595 TATTTTATTTTCATAGTTTTTATATATT
130 AAATATATTTTCATAGTTTTTATATACG
*
31726623 TATATATGCATATACATTTATATTTTATAATATCTATACATTTTCCATATTTTATAATCTATATA
1 TATATATGCATATACATTTATATTTTATAATATCTATACATTTTCCATATTATATAATCTATATA
*
31726688 TAAATTTATACATTCTTTATAATATGCATATATATATTC-T-TACACTA-TTCAAAACTA-TTAT
66 TAAATTTATACATTCTTTATAATATGCATATATATATACATATACA-TATTTCAAAACTATTTAT
**
31726749 AAATATATTTTCCACATTTTTTTATATATACG
130 AAATATATTTT---CATAGTTTT-TATATACG
*
31726781 TATATATCCATAT
1 TATATATGCATAT
31726794 TTTCATAATT
Statistics
Matches: 146, Mismatches: 20, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
154 12 0.08
156 10 0.07
157 10 0.07
158 114 0.78
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.53
Consensus pattern (157 bp):
TATATATGCATATACATTTATATTTTATAATATCTATACATTTTCCATATTATATAATCTATATA
TAAATTTATACATTCTTTATAATATGCATATATATATACATATACATATTTCAAAACTATTTATA
AATATATTTTCATAGTTTTTATATACG
Found at i:31726819 original size:158 final size:155
Alignment explanation
Indices: 31726448--31726819 Score: 375
Period size: 158 Copynumber: 2.4 Consensus size: 155
31726438 ATTATTATTT
* * * *
31726448 TATTTTCATAGTTTTTATATA--TATGTAT--ATACATTTATATTTTATAATATTTATACATTTT
1 TATTTTCACAGTTTTTATATATGTATATATCCATATATTTATAATTTATAATATTTATACATTTT
** * *
31726509 CCATATTATATAATCTATATATATGTTTATACATTTTTTATAATATGTATATATATATACATATA
66 CCATATTATATAATCTATATATAAATTTATACATTCTTTATAATATGCATATATATATACATATA
* ** * * * *
31726574 CATATTTTATTATTATTTTATTATTT
131 CATATTTCAAAACTA-TTTATAAATA
* * * * *
31726600 TATTTTCATAGTTTTTATATATTTATATATGCATATACATTTATATTTTATAATATCTATACATT
1 TATTTTCACAGTTTTTATATATGTATATATCCATAT--ATTTATAATTTATAATATTTATACATT
* *
31726665 TTCCATATTTTATAATCTATATATAAATTTATACATTCTTTATAATATGCATATATATATTC-T-
64 TTCCATATTATATAATCTATATATAAATTTATACATTCTTTATAATATGCATATATATATACATA
31726728 TACACTA-TTCAAAACTA-TTATAAATA
129 TACA-TATTTCAAAACTATTTATAAATA
*
31726754 TATTTTCCACATTTTTTTATATATACGTATATATCCATAT-TTTCATAATTTACTAATATATTAT
1 TATTTT-CACA-GTTTTTATATAT--GTATATATCCATATATTT-ATAATTTA-TAATAT-TTAT
31726818 AC
59 AC
31726820 TTATATATAT
Statistics
Matches: 184, Mismatches: 22, Indels: 22
0.81 0.10 0.10
Matches are distributed among these distances:
152 21 0.11
154 18 0.10
155 6 0.03
156 31 0.17
157 9 0.05
158 99 0.54
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.53
Consensus pattern (155 bp):
TATTTTCACAGTTTTTATATATGTATATATCCATATATTTATAATTTATAATATTTATACATTTT
CCATATTATATAATCTATATATAAATTTATACATTCTTTATAATATGCATATATATATACATATA
CATATTTCAAAACTATTTATAAATA
Found at i:31726858 original size:2 final size:2
Alignment explanation
Indices: 31726851--31726875 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31726841 ATGCATCTAT
31726851 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 T
31726876 TATTGTTTTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31730922 original size:17 final size:17
Alignment explanation
Indices: 31730897--31730935 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
31730887 CAGAATTAAA
*
31730897 ATTTGATTGAGAAATTT
1 ATTTAATTGAGAAATTT
31730914 ATTTAATTGAGAAATTT
1 ATTTAATTGAGAAATTT
31730931 ATTTA
1 ATTTA
31730936 GTTAATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (17 bp):
ATTTAATTGAGAAATTT
Found at i:31738253 original size:7 final size:7
Alignment explanation
Indices: 31738241--31738268 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
31738231 AAGTCCATAT
31738241 ATATTTA
1 ATATTTA
31738248 ATATTTA
1 ATATTTA
31738255 ATATTTA
1 ATATTTA
31738262 ATATTTA
1 ATATTTA
31738269 CGAGTTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
ATATTTA
Found at i:31739771 original size:76 final size:76
Alignment explanation
Indices: 31739627--31739773 Score: 174
Period size: 76 Copynumber: 1.9 Consensus size: 76
31739617 GCGCTGGGCA
* * * *
31739627 CAACTCATTATTGGTACATCCAACTAGTGCTGAGCACACATTTGATATTGTCAATTTACTCGATT
1 CAACTCATTATTGGTACATCCAACTAGTGCTGAGCACACATATGATATCGTCAATTTACTCAACT
31739692 AGCACTAGGCG
66 AGCACTAGGCG
* ** *
31739703 CAACTCATTGTTGGTACATTTAACTAAG-GCTCGA-CACACATATGATATCGTCGATTTA-TCTA
1 CAACTCATTATTGGTACATCCAACT-AGTGCT-GAGCACACATATGATATCGTCAATTTACTC-A
31739765 ACTAGCACT
63 ACTAGCACT
31739774 GGGGGCAAGC
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
75 2 0.03
76 54 0.90
77 4 0.07
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (76 bp):
CAACTCATTATTGGTACATCCAACTAGTGCTGAGCACACATATGATATCGTCAATTTACTCAACT
AGCACTAGGCG
Found at i:31750738 original size:76 final size:75
Alignment explanation
Indices: 31750522--31750755 Score: 216
Period size: 76 Copynumber: 3.1 Consensus size: 75
31750512 GGTACATCAA
* * * ** *
31750522 ACTAGTGTTGGGCACACATTTGGTATCATCAGTTTACCCGACTAGCGTTGGGCACAACTCATTAT
1 ACTAGTGCTGGGCACACATTTGATATCATCAGTTTA-CTGACTAGCACTGGGCACAACTCATTGT
** *
31750587 TGGTACATCCA
65 TGGTTTATCCG
* * * * * ** ** *
31750598 ACTAGTGCAGTGCATATATTTGATATCGTTGGTTTACTCGACTAGCACTGGGTGCAACTTATTGT
1 ACTAGTGCTGGGCACACATTTGATATCATCAGTTTACT-GACTAGCACTGGGCACAACTCATTGT
* *
31750663 TTGTTTATCTG
65 TGGTTTATCCG
* **
31750674 ACTAGTGCTGGGCACACATTTGATATCATCAGTTTATCTGACTAGCCCTGGGCACAAAACATTGT
1 ACTAGTGCTGGGCACACATTTGATATCATCAGTTTA-CTGACTAGCACTGGGCACAACTCATTGT
*
31750739 TGGTTTCTCCG
65 TGGTTTATCCG
31750750 ACTAGT
1 ACTAGT
31750756 ACAAGGCAAA
Statistics
Matches: 119, Mismatches: 37, Indels: 4
0.74 0.23 0.03
Matches are distributed among these distances:
75 1 0.01
76 116 0.97
77 2 0.02
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (75 bp):
ACTAGTGCTGGGCACACATTTGATATCATCAGTTTACTGACTAGCACTGGGCACAACTCATTGTT
GGTTTATCCG
Found at i:31762308 original size:17 final size:17
Alignment explanation
Indices: 31762286--31762320 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
31762276 TAAGACAATT
31762286 CGGGCATATGGGCCACA
1 CGGGCATATGGGCCACA
* *
31762303 CGGGCATGTGGGCTACA
1 CGGGCATATGGGCCACA
31762320 C
1 C
31762321 AGGTAAGGCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.20, C:0.29, G:0.37, T:0.14
Consensus pattern (17 bp):
CGGGCATATGGGCCACA
Found at i:31765836 original size:46 final size:46
Alignment explanation
Indices: 31765783--31765875 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
31765773 TTACCGAATT
31765783 TCATCTTTGACCACGTTGATCATTAAAATCAACTAATGGACTAATC
1 TCATCTTTGACCACGTTGATCATTAAAATCAACTAATGGACTAATC
31765829 TCATCTTTGACCACGTTGATCATTAAAATCAACTAATGGACTAATC
1 TCATCTTTGACCACGTTGATCATTAAAATCAACTAATGGACTAATC
31765875 T
1 T
31765876 GATAGCAACA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.34, C:0.22, G:0.11, T:0.33
Consensus pattern (46 bp):
TCATCTTTGACCACGTTGATCATTAAAATCAACTAATGGACTAATC
Found at i:31765934 original size:10 final size:9
Alignment explanation
Indices: 31765921--31766038 Score: 107
Period size: 10 Copynumber: 12.7 Consensus size: 9
31765911 CATTTTCATC
31765921 ATAAAAATT
1 ATAAAAATT
*
31765930 CAT-AAAACT
1 -ATAAAAATT
*
31765939 ATAAAAATC
1 ATAAAAATT
31765948 ATAAAAA-T
1 ATAAAAATT
* *
31765956 AAAAAAATC
1 ATAAAAATT
31765965 ATTAAAAACTT
1 A-TAAAAA-TT
*
31765976 ATAAAACTT
1 ATAAAAATT
31765985 ATAAAAATAT
1 ATAAAAAT-T
31765995 ATAAAAACTT
1 ATAAAAA-TT
31766005 AT-AAAATT
1 ATAAAAATT
31766013 ATAAAAAATT
1 AT-AAAAATT
31766023 ATAAAAAATT
1 AT-AAAAATT
31766033 ATAAAA
1 ATAAAA
31766039 TTGTAATATA
Statistics
Matches: 90, Mismatches: 10, Indels: 17
0.77 0.09 0.15
Matches are distributed among these distances:
8 12 0.13
9 34 0.38
10 41 0.46
11 3 0.03
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (9 bp):
ATAAAAATT
Found at i:31765944 original size:18 final size:17
Alignment explanation
Indices: 31765921--31766029 Score: 92
Period size: 18 Copynumber: 5.9 Consensus size: 17
31765911 CATTTTCATC
*
31765921 ATAAAAATTCATAAAACT
1 ATAAAAATT-ATAAAAAT
*
31765939 ATAAAAATCATAAAAAT
1 ATAAAAATTATAAAAAT
* *
31765956 AAAAAAATCATTAAAAACTT
1 ATAAAAATTA-TAAAAA--T
*
31765976 ATAAAACTTATAAAAATAT
1 ATAAAAATTAT-AAAA-AT
*
31765995 ATAAAAACTTATAAAATT
1 ATAAAAA-TTATAAAAAT
31766013 ATAAAAAATTATAAAAA
1 AT-AAAAATTATAAAAA
31766030 ATTATAAAAT
Statistics
Matches: 75, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
17 16 0.21
18 25 0.33
19 17 0.23
20 16 0.21
21 1 0.01
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (17 bp):
ATAAAAATTATAAAAAT
Found at i:31765979 original size:28 final size:27
Alignment explanation
Indices: 31765940--31766040 Score: 107
Period size: 28 Copynumber: 3.6 Consensus size: 27
31765930 CATAAAACTA
* *
31765940 TAAAAA-TCATAAAAATAAAAAAATCAT
1 TAAAAACTTATAAAATTAAAAAAAT-AT
*
31765967 TAAAAACTTATAAAACTTATAAAAATAT
1 TAAAAACTTATAAAA-TTAAAAAAATAT
31765995 ATAAAAACTTATAAAATTATAAAAAAT-T
1 -TAAAAACTTATAAAATTA-AAAAAATAT
*
31766023 ATAAAAAATTATAAAATT
1 -TAAAAACTTATAAAATT
31766041 GTAATATATT
Statistics
Matches: 65, Mismatches: 5, Indels: 7
0.84 0.06 0.09
Matches are distributed among these distances:
27 6 0.09
28 30 0.46
29 29 0.45
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (27 bp):
TAAAAACTTATAAAATTAAAAAAATAT
Found at i:31765989 original size:37 final size:38
Alignment explanation
Indices: 31765921--31766038 Score: 124
Period size: 38 Copynumber: 3.2 Consensus size: 38
31765911 CATTTTCATC
*
31765921 ATAAAAA-TTCATAAAAC-TATAAAAATCATAAAAATA-
1 ATAAAAACTT-ATAAAACTTATAAAAATTATAAAAATAT
*
31765957 A-AAAAATCATTA-AAAACTTATAAAACTTATAAAAATAT
1 ATAAAAA-C-TTATAAAACTTATAAAAATTATAAAAATAT
31765995 ATAAAAACTTATAAAA-TTATAAAAAATTATAAAAA-ATT
1 ATAAAAACTTATAAAACTTAT-AAAAATTATAAAAATA-T
31766033 ATAAAA
1 ATAAAA
31766039 TTGTAATATA
Statistics
Matches: 70, Mismatches: 3, Indels: 16
0.79 0.03 0.18
Matches are distributed among these distances:
35 5 0.07
36 6 0.09
37 26 0.37
38 28 0.40
39 5 0.07
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (38 bp):
ATAAAAACTTATAAAACTTATAAAAATTATAAAAATAT
Found at i:31766774 original size:20 final size:19
Alignment explanation
Indices: 31766751--31766802 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
31766741 TTTTTTTTAC
*
31766751 ATTTTTATAGGTTTTTGTGA
1 ATTTTTATAGGTTTTTAT-A
*
31766771 ATTTTTATAAGTTTTTATA
1 ATTTTTATAGGTTTTTATA
*
31766790 AGTTTTATAGGTT
1 ATTTTTATAGGTT
31766803 CATATATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.25, C:0.00, G:0.15, T:0.60
Consensus pattern (19 bp):
ATTTTTATAGGTTTTTATA
Found at i:31766798 original size:9 final size:10
Alignment explanation
Indices: 31766752--31766795 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
31766742 TTTTTTTACA
*
31766752 TTTTTATAGG
1 TTTTTATAAG
*
31766762 TTTTTGTGAA-
1 TTTTTAT-AAG
31766772 TTTTTATAAG
1 TTTTTATAAG
31766782 TTTTTATAAG
1 TTTTTATAAG
31766792 TTTT
1 TTTT
31766796 ATAGGTTCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
9 2 0.07
10 26 0.90
11 1 0.03
ACGTcount: A:0.23, C:0.00, G:0.14, T:0.64
Consensus pattern (10 bp):
TTTTTATAAG
Found at i:31766846 original size:21 final size:20
Alignment explanation
Indices: 31766833--31766877 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 20
31766823 TTATGGTTTA
31766833 TTTATAAGCTTTTATGAATTT
1 TTTATAAG-TTTTATGAATTT
*
31766854 TTTATAAGTTTTAT-AATTA
1 TTTATAAGTTTTATGAATTT
31766873 TTTAT
1 TTTAT
31766878 TTATGATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.39
20 6 0.26
21 8 0.35
ACGTcount: A:0.31, C:0.02, G:0.07, T:0.60
Consensus pattern (20 bp):
TTTATAAGTTTTATGAATTT
Found at i:31766876 original size:19 final size:21
Alignment explanation
Indices: 31766830--31766877 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
31766820 TATTTATGGT
31766830 TTATTTATAAGCTTTTATGAA
1 TTATTTATAAGCTTTTATGAA
*
31766851 TTTTTTATAAG-TTTTAT-AA
1 TTATTTATAAGCTTTTATGAA
31766870 TTATTTAT
1 TTATTTAT
31766878 TTATGATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 9 0.36
20 6 0.24
21 10 0.40
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.60
Consensus pattern (21 bp):
TTATTTATAAGCTTTTATGAA
Found at i:31767072 original size:57 final size:57
Alignment explanation
Indices: 31767002--31767142 Score: 160
Period size: 60 Copynumber: 2.4 Consensus size: 57
31766992 TAATGGATAA
*
31767002 GCTTAATTAATTTTTTTTATTAACAAC-AACTCAATT-GAGTGCGAACTAAGTTGAGGG
1 GCTTAATTGATTTTTTTTATTAACAACAAACTCAATTAGAGT--GAACTAAGTTGAGGG
* * * *
31767059 GTTTAATTGATTTTTTTAATTAACAACAAAAATTCAATTAGGAGTGAAGTAAGTTGAGGG
1 GCTTAATTGATTTTTTTTATTAACAAC--AAACTCAATTA-GAGTGAACTAAGTTGAGGG
*
31767119 GCTTAATTGATTTATTTTTCTTAA
1 GCTTAATTGATTT-TTTTTATTAA
31767143 GAATCTCATA
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
57 24 0.34
60 34 0.49
61 8 0.11
62 4 0.06
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.40
Consensus pattern (57 bp):
GCTTAATTGATTTTTTTTATTAACAACAAACTCAATTAGAGTGAACTAAGTTGAGGG
Found at i:31767593 original size:8 final size:8
Alignment explanation
Indices: 31767580--31767615 Score: 65
Period size: 8 Copynumber: 4.6 Consensus size: 8
31767570 AAGTCATTAC
31767580 TTTTTTTG
1 TTTTTTTG
31767588 TTTTTTTG
1 TTTTTTTG
31767596 TTTTTTTG
1 TTTTTTTG
31767604 TTTTTTT-
1 TTTTTTTG
31767611 TTTTT
1 TTTTT
31767616 GCCCTTTAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 5 0.18
8 23 0.82
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (8 bp):
TTTTTTTG
Found at i:31769237 original size:26 final size:26
Alignment explanation
Indices: 31769189--31769243 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
31769179 TTTGAAATTT
* * *
31769189 ATTCGAATCGAATCAAGTGGAATGAA
1 ATTCGAATCGAATCAAATCGAATAAA
* *
31769215 ATTCGAGTCGAGTCAAATCGAATAAA
1 ATTCGAATCGAATCAAATCGAATAAA
31769241 ATT
1 ATT
31769244 GTTTAAGTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.42, C:0.13, G:0.20, T:0.25
Consensus pattern (26 bp):
ATTCGAATCGAATCAAATCGAATAAA
Found at i:31769494 original size:17 final size:18
Alignment explanation
Indices: 31769472--31769511 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
31769462 TTTTTTAGAT
*
31769472 TTTTTTAAAAATTAT-AA
1 TTTTTTAAAAAATATAAA
31769489 TTTTTTAAAAAATATAAA
1 TTTTTTAAAAAATATAAA
31769507 TTTTT
1 TTTTT
31769512 GAATTTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTTTTTAAAAAATATAAA
Found at i:31769538 original size:20 final size:19
Alignment explanation
Indices: 31769501--31769555 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
31769491 TTTTAAAAAA
31769501 TATAAAT-TTTTGAATTTT
1 TATAAATATTTTGAATTTT
*
31769519 TATAAATATTTTGATTTTT
1 TATAAATATTTTGAATTTT
*
31769538 TAAAAATTATTTTGAATT
1 TATAAA-TATTTTGAATT
31769556 ATTTTTTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
18 7 0.22
19 15 0.47
20 10 0.31
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.58
Consensus pattern (19 bp):
TATAAATATTTTGAATTTT
Found at i:31770965 original size:19 final size:19
Alignment explanation
Indices: 31770943--31770993 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
31770933 ATGTTGTTTA
*
31770943 TATTTATATTTTTTATTTG
1 TATTTATATTTTTTATTTC
*
31770962 TATTTAT-TGTATTTATTTC
1 TATTTATAT-TTTTTATTTC
31770981 TA--TATATTTTTTA
1 TATTTATATTTTTTA
31770994 GATACCCATA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
17 8 0.30
18 2 0.07
19 17 0.63
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.71
Consensus pattern (19 bp):
TATTTATATTTTTTATTTC
Done.