Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 129432109
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: 129432109
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 135 of 425
Found at i:40713710 original size:80 final size:81
Alignment explanation
Indices: 40713573--40713791 Score: 247
Period size: 80 Copynumber: 2.8 Consensus size: 81
40713563 GAATCACGTA
**
40713573 CCTTCGGAAT-TTAA-CCGGATATAG-CTACTC-GTTCAAATGCCTTCGGGACTTAGCCCGG-TT
1 CCTTCGG-ATCTTAACCCGGATATAGTC-ACTCAGCACAAATGCCTTCGGGACTTAGCCCGGATT
40713633 ATAGTAACTCGCACAAATG
64 -TAGTAACTCGCACAAATG
* * * *
40713652 CCTTCAGGA-CTTAACCCGGATTTAGTGAC-CCGCACAAATGCCTTCGGGACTTAACCCGGATTT
1 CCTTC-GGATCTTAACCCGGATATAGTCACTCAGCACAAATGCCTTCGGGACTTAGCCCGGATTT
* *
40713715 AGTAACTCGCCCCAATG
65 AGTAACTCGCACAAATG
** *
40713732 CCTTCGGATCTTAGTCCGGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 CCTTCGGATCTTAACCCGGATATAGTCACTCAGCACAAATGCCTTCGGGACTTAGCCCGGA
40713792 CATCATTCGA
Statistics
Matches: 118, Mismatches: 14, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
79 14 0.12
80 95 0.81
81 9 0.08
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (81 bp):
CCTTCGGATCTTAACCCGGATATAGTCACTCAGCACAAATGCCTTCGGGACTTAGCCCGGATTTA
GTAACTCGCACAAATG
Found at i:40717175 original size:16 final size:16
Alignment explanation
Indices: 40717151--40717187 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
40717141 TTTTGAAAGG
*
40717151 AAAACAAATGAATCTT
1 AAAAAAAATGAATCTT
*
40717167 AAAAAAAATGAGTCTT
1 AAAAAAAATGAATCTT
40717183 AAAAA
1 AAAAA
40717188 CTTAATGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.62, C:0.08, G:0.08, T:0.22
Consensus pattern (16 bp):
AAAAAAAATGAATCTT
Found at i:40723868 original size:49 final size:50
Alignment explanation
Indices: 40723815--40723915 Score: 159
Period size: 50 Copynumber: 2.0 Consensus size: 50
40723805 TTTAGTTATT
*
40723815 TTAGTTTAATTAATTAAGTT-TTTTTAATTGTCTTTAGTTGAATAAATAA
1 TTAGTTTAATTAATTAAATTGTTTTTAATTGTCTTTAGTTGAATAAATAA
* **
40723864 TTAGTTTAATTAATTAAATTGTTTTTAATTTTCTTTAGTTGCTTAAATAA
1 TTAGTTTAATTAATTAAATTGTTTTTAATTGTCTTTAGTTGAATAAATAA
40723914 TT
1 TT
40723916 TCTGCAATTA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
49 19 0.40
50 28 0.60
ACGTcount: A:0.33, C:0.03, G:0.09, T:0.55
Consensus pattern (50 bp):
TTAGTTTAATTAATTAAATTGTTTTTAATTGTCTTTAGTTGAATAAATAA
Found at i:40723925 original size:50 final size:49
Alignment explanation
Indices: 40723822--40723927 Score: 131
Period size: 50 Copynumber: 2.1 Consensus size: 49
40723812 ATTTTAGTTT
* * **
40723822 AATTAATTAAGTTTTTTTAATTGTCTTTAGTTGAATAAATAATTAGTTT
1 AATTAATTAAATTTTTTTAATTGTCTTTAGTTGAATAAATAATTACTGC
* ** *
40723871 AATTAATTAAATTGTTTTTAATTTTCTTTAGTTGCTTAAATAATTTCTGC
1 AATTAATTAAATT-TTTTTAATTGTCTTTAGTTGAATAAATAATTACTGC
40723921 AATTAAT
1 AATTAAT
40723928 ATGTTCCAGC
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
49 12 0.25
50 36 0.75
ACGTcount: A:0.34, C:0.05, G:0.08, T:0.53
Consensus pattern (49 bp):
AATTAATTAAATTTTTTTAATTGTCTTTAGTTGAATAAATAATTACTGC
Found at i:40723980 original size:17 final size:17
Alignment explanation
Indices: 40723958--40723990 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
40723948 TTGCTATAGC
40723958 CATTTAACTTGTTTAAA
1 CATTTAACTTGTTTAAA
40723975 CATTTAACTTGTTTAA
1 CATTTAACTTGTTTAA
40723991 TTGTGCTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.33, C:0.12, G:0.06, T:0.48
Consensus pattern (17 bp):
CATTTAACTTGTTTAAA
Found at i:40725771 original size:40 final size:40
Alignment explanation
Indices: 40725726--40725910 Score: 204
Period size: 40 Copynumber: 4.7 Consensus size: 40
40725716 GCTACTCGTT
*
40725726 CAAATGCCTTCGGGACATAGCCCGG-TTATCGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTAT-GTAACTCGCA
* *
40725766 TAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTAT-GTAACTCGCA
40725806 CAAATGCCTTCGGG-CTTAGCCCGGGATTA-GTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCC-GGATTATGTAACTCGCA
* * * *
40725845 CAAATGCCTTC-GGATCTTAGTCCGTA-TATAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTAT-GTAAC-TCGCA
40725886 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
40725911 CATCATTCGA
Statistics
Matches: 124, Mismatches: 12, Indels: 18
0.81 0.08 0.12
Matches are distributed among these distances:
38 4 0.03
39 30 0.24
40 77 0.62
41 13 0.10
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTATGTAACTCGCA
Found at i:40725839 original size:79 final size:81
Alignment explanation
Indices: 40725726--40725909 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
40725716 GCTACTCGTT
* *
40725726 CAAATGCCTTCGGGACATAGCCC-GGTTATCGTAACTCGCATAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGGTTA-CGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
40725789 GGATTTAGTAAC-TCGCA
64 GGATATAGTAACTTAGCA
**
40725806 CAAATGCCTTCGGG-CTTAGCCCGGGATTA-GTAACTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGG-TTACGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
40725869 TATATAGTCACTTAGCA
65 GATATAGTAACTTAGCA
40725886 CAAA-GCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
40725910 ACATCATTCG
Statistics
Matches: 91, Mismatches: 8, Indels: 10
0.83 0.07 0.09
Matches are distributed among these distances:
78 3 0.03
79 51 0.56
80 34 0.37
81 3 0.03
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGGTTACGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:40729252 original size:16 final size:17
Alignment explanation
Indices: 40729197--40729252 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 17
40729187 AAAAGAAGCG
40729197 AGAAAAAGAAATTGAGAGA
1 AGAAAAAGAAATT--GAGA
* *
40729216 AGAAAAA-AAAATGATA
1 AGAAAAAGAAATTGAGA
40729232 A-AAAAAGAAATTGA-A
1 AGAAAAAGAAATTGAGA
40729247 AGAAAA
1 AGAAAA
40729253 GAGAGCTTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
15 7 0.22
16 14 0.44
18 4 0.12
19 7 0.22
ACGTcount: A:0.71, C:0.00, G:0.18, T:0.11
Consensus pattern (17 bp):
AGAAAAAGAAATTGAGA
Found at i:40729299 original size:18 final size:16
Alignment explanation
Indices: 40729276--40729341 Score: 60
Period size: 18 Copynumber: 3.7 Consensus size: 16
40729266 AAAGGAGAAA
40729276 GAAAAAGAAAAAGAATGT
1 GAAAAAGAAAAA-AAT-T
*
40729294 GAAAAATCAAAGAAAATT
1 GAAAAA-GAAA-AAAATT
40729312 GAAAAAGAGAAAAAGATT
1 GAAAAAGA-AAAAA-ATT
40729330 GAAGAAAGAAAA
1 GAA-AAAGAAAA
40729342 GAAAGAATGC
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
17 4 0.10
18 24 0.59
19 11 0.27
20 2 0.05
ACGTcount: A:0.68, C:0.02, G:0.20, T:0.11
Consensus pattern (16 bp):
GAAAAAGAAAAAAATT
Found at i:40731106 original size:50 final size:49
Alignment explanation
Indices: 40731021--40731121 Score: 175
Period size: 50 Copynumber: 2.0 Consensus size: 49
40731011 TTTAGTTATT
*
40731021 TTAGTTTAATTAATTAAGTTTTTTTAATTGTCTTTAGTTGCTTAAATAA
1 TTAGCTTAATTAATTAAGTTTTTTTAATTGTCTTTAGTTGCTTAAATAA
*
40731070 TTAGCTTAATTAATTAAGTTGTTTTTAATTTTCTTTAGTTGCTTAAATAA
1 TTAGCTTAATTAATTAAGTT-TTTTTAATTGTCTTTAGTTGCTTAAATAA
40731120 TT
1 TT
40731122 TCGGCAATTA
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
49 19 0.39
50 30 0.61
ACGTcount: A:0.30, C:0.05, G:0.10, T:0.55
Consensus pattern (49 bp):
TTAGCTTAATTAATTAAGTTTTTTTAATTGTCTTTAGTTGCTTAAATAA
Found at i:40731186 original size:17 final size:17
Alignment explanation
Indices: 40731164--40731196 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
40731154 TTGCTATAGC
40731164 CATTTAACTTGTTTAAA
1 CATTTAACTTGTTTAAA
40731181 CATTTAACTTGTTTAA
1 CATTTAACTTGTTTAA
40731197 TTGTGCTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.33, C:0.12, G:0.06, T:0.48
Consensus pattern (17 bp):
CATTTAACTTGTTTAAA
Found at i:40732651 original size:2 final size:2
Alignment explanation
Indices: 40732644--40732671 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
40732634 ACTTATTATA
40732644 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
40732672 AATTTATATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:40733122 original size:23 final size:21
Alignment explanation
Indices: 40733078--40733124 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
40733068 GTAGTGTAAT
**
40733078 ATATATTAAAAATTGTTCTAA
1 ATATATTAAAAATTGTGATAA
40733099 ATATATTATAAAATATGTGATAA
1 ATATATTA-AAAAT-TGTGATAA
40733122 ATA
1 ATA
40733125 CTGTAATAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 8 0.36
22 5 0.23
23 9 0.41
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.40
Consensus pattern (21 bp):
ATATATTAAAAATTGTGATAA
Found at i:40742547 original size:34 final size:33
Alignment explanation
Indices: 40742495--40742560 Score: 87
Period size: 34 Copynumber: 2.0 Consensus size: 33
40742485 CTCAGTTAGA
*
40742495 GCCTTAGCCCATACAGTAACAATATCAATATAG
1 GCCTTAACCCATACAGTAACAATATCAATATAG
* * *
40742528 GCCTTAACCCAATTCAGTAATAGTATCAATATA
1 GCCTTAACCC-ATACAGTAACAATATCAATATA
40742561 AAATGCAAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 9 0.32
34 19 0.68
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (33 bp):
GCCTTAACCCATACAGTAACAATATCAATATAG
Found at i:40751506 original size:47 final size:47
Alignment explanation
Indices: 40751386--40751527 Score: 257
Period size: 49 Copynumber: 3.0 Consensus size: 47
40751376 ATGTATGAGA
40751386 TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
1 TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
*
40751433 TGTATATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAG
1 TG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
40751482 TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
40751528 TATATGTGTG
Statistics
Matches: 91, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
47 45 0.49
49 46 0.51
ACGTcount: A:0.33, C:0.08, G:0.28, T:0.30
Consensus pattern (47 bp):
TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
Found at i:40751593 original size:48 final size:47
Alignment explanation
Indices: 40751519--40751718 Score: 276
Period size: 48 Copynumber: 4.2 Consensus size: 47
40751509 CGATGTGATG
* * * *
40751519 AATGTGAAATATATGTGTGATGTGTATATGTGGTAAAGCCGAAGGGCT
1 AATGTGAAA-ATATATATGATATGTATATGTGGTAAAGCCGAATGGCT
*
40751567 AATGTGAAACATATATAAGATATGTATATGTGGTAAAGCCGAATGGCT
1 AATGTGAAA-ATATATATGATATGTATATGTGGTAAAGCCGAATGGCT
*
40751615 AATGTG-AAATATATGAGTGATATGTATATGTGGTAAAGCCGAATGACT
1 AATGTGAAAATATAT-A-TGATATGTATATGTGGTAAAGCCGAATGGCT
* *
40751663 AATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCT
1 AATGTGAAA-ATATATATGATATGTATATGTGGTAAAGCCGAATGGCT
40751711 AATGTGAA
1 AATGTGAA
40751719 TGTTGTAACA
Statistics
Matches: 137, Mismatches: 11, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
46 6 0.04
47 3 0.02
48 121 0.88
49 2 0.01
50 5 0.04
ACGTcount: A:0.36, C:0.07, G:0.27, T:0.31
Consensus pattern (47 bp):
AATGTGAAAATATATATGATATGTATATGTGGTAAAGCCGAATGGCT
Found at i:40751619 original size:96 final size:96
Alignment explanation
Indices: 40751519--40751718 Score: 328
Period size: 96 Copynumber: 2.1 Consensus size: 96
40751509 CGATGTGATG
* * *
40751519 AATGTGAAATATATGTGTGATGTGTATATGTGGTAAAGCCGAAGGGCTAATGTGAAACATATATA
1 AATGTGAAATATATGAGTGATATGTATATGTGGTAAAGCCGAAGGACTAATGTGAAACATATATA
40751584 AGATATGTATATGTGGTAAAGCCGAATGGCT
66 AGATATGTATATGTGGTAAAGCCGAATGGCT
* * * *
40751615 AATGTGAAATATATGAGTGATATGTATATGTGGTAAAGCCGAATGACTAATGTGAAATATATGTG
1 AATGTGAAATATATGAGTGATATGTATATGTGGTAAAGCCGAAGGACTAATGTGAAACATATATA
*
40751680 TGATATGTATATGTGGTAAAGCCGAATGGCT
66 AGATATGTATATGTGGTAAAGCCGAATGGCT
40751711 AATGTGAA
1 AATGTGAA
40751719 TGTTGTAACA
Statistics
Matches: 96, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
96 96 1.00
ACGTcount: A:0.36, C:0.07, G:0.27, T:0.31
Consensus pattern (96 bp):
AATGTGAAATATATGAGTGATATGTATATGTGGTAAAGCCGAAGGACTAATGTGAAACATATATA
AGATATGTATATGTGGTAAAGCCGAATGGCT
Found at i:40751809 original size:37 final size:37
Alignment explanation
Indices: 40751758--40751885 Score: 229
Period size: 37 Copynumber: 3.4 Consensus size: 37
40751748 AACTTGGAAA
*
40751758 TATGTTCCGGGTGAGACCCGATGACTACGTGTGGAGAT
1 TATG-TCCGGGTAAGACCCGATGACTACGTGTGGAGAT
*
40751796 TATGTCCGGGTGAGACCCGATGACTACGTGTGGAGAT
1 TATGTCCGGGTAAGACCCGATGACTACGTGTGGAGAT
40751833 TATGTCCGGGTAAGACCCGATGACTACGTGTGGAGAT
1 TATGTCCGGGTAAGACCCGATGACTACGTGTGGAGAT
40751870 TATGTCCGGGTAAGAC
1 TATGTCCGGGTAAGAC
40751886 TTCGTAATAA
Statistics
Matches: 89, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
37 85 0.96
38 4 0.04
ACGTcount: A:0.23, C:0.19, G:0.34, T:0.25
Consensus pattern (37 bp):
TATGTCCGGGTAAGACCCGATGACTACGTGTGGAGAT
Found at i:40753769 original size:40 final size:40
Alignment explanation
Indices: 40753721--40754001 Score: 445
Period size: 40 Copynumber: 7.0 Consensus size: 40
40753711 GAGAGTGATA
40753721 TATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGACG
1 TATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGACG
*
40753761 TATCCGGACTAAGTTCCGAGGAGCATTCGTGCTAGTGACG
1 TATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGACG
*
40753801 TATCCGGACTAAGCTCCGAAGAGCATTCGTGCTAGTGACG
1 TATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGACG
* *
40753841 TATCCGGACTAAGTTCCGAGGAGCATTCGTGCTAGTGATG
1 TATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGACG
* *
40753881 TATCCGGACTAAGTTCCGAGGAGCATTCGTGCTAGTGATG
1 TATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGACG
*
40753921 TATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
1 TATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGACG
* * * * * *
40753961 TATCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGTGACG
1 TATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGACG
40754001 T
1 T
40754002 GTATTCGGGC
Statistics
Matches: 227, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 227 1.00
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.25
Consensus pattern (40 bp):
TATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGACG
Found at i:40761595 original size:20 final size:20
Alignment explanation
Indices: 40761572--40761623 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
40761562 TGAAAATAAA
*
40761572 CTACCAATAATGCAGACAAG
1 CTACCAATAATGCAAACAAG
*
40761592 CTACCAGTAATGCAAACAAG
1 CTACCAATAATGCAAACAAG
*
40761612 CCACCAATAATG
1 CTACCAATAATG
40761624 TAGATAAACT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.44, C:0.27, G:0.13, T:0.15
Consensus pattern (20 bp):
CTACCAATAATGCAAACAAG
Found at i:40761601 original size:40 final size:40
Alignment explanation
Indices: 40761545--40761623 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 40
40761535 CCAGTAATAT
* * *
40761545 AGACAAGCCACTAGTAATGAAAATAAACTACCAATAATGC
1 AGACAAGCCACCAGTAATGAAAACAAACCACCAATAATGC
* * *
40761585 AGACAAGCTACCAGTAATGCAAACAAGCCACCAATAATG
1 AGACAAGCCACCAGTAATGAAAACAAACCACCAATAATG
40761624 TAGATAAACT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.48, C:0.23, G:0.14, T:0.15
Consensus pattern (40 bp):
AGACAAGCCACCAGTAATGAAAACAAACCACCAATAATGC
Found at i:40765800 original size:79 final size:81
Alignment explanation
Indices: 40765691--40765873 Score: 241
Period size: 79 Copynumber: 2.3 Consensus size: 81
40765681 TACTCGTTCA
* *
40765691 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
40765754 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
**
40765771 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
*
40765834 TATAGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
40765850 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
40765874 CATCATTCGA
Statistics
Matches: 91, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
78 3 0.03
79 60 0.66
80 28 0.31
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:40765873 original size:40 final size:40
Alignment explanation
Indices: 40765670--40765873 Score: 247
Period size: 40 Copynumber: 5.1 Consensus size: 40
40765660 CGGAATTTAA
** *
40765670 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
40765710 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
40765750 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
40765789 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* *
40765829 CCGGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
40765869 CCGGA
1 CCGGA
40765874 CATCATTCGA
Statistics
Matches: 142, Mismatches: 15, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 95 0.67
41 12 0.08
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:40773773 original size:79 final size:81
Alignment explanation
Indices: 40773664--40773846 Score: 241
Period size: 79 Copynumber: 2.3 Consensus size: 81
40773654 TACTCGTTCA
* *
40773664 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
40773727 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
**
40773744 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
*
40773807 TATAGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
40773823 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
40773847 CATCATTCGA
Statistics
Matches: 91, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
78 3 0.03
79 60 0.66
80 28 0.31
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:40773846 original size:40 final size:40
Alignment explanation
Indices: 40773643--40773846 Score: 247
Period size: 40 Copynumber: 5.1 Consensus size: 40
40773633 CGGAATTTAA
** *
40773643 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
40773683 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
40773723 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
40773762 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* *
40773802 CCGGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
40773842 CCGGA
1 CCGGA
40773847 CATCATTCGA
Statistics
Matches: 142, Mismatches: 15, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 95 0.67
41 12 0.08
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:40777431 original size:14 final size:14
Alignment explanation
Indices: 40777412--40777440 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
40777402 GATGAGTAAG
40777412 TTTAAATAATTTGA
1 TTTAAATAATTTGA
40777426 TTTAAATAATTTGA
1 TTTAAATAATTTGA
40777440 T
1 T
40777441 GTAATGATGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (14 bp):
TTTAAATAATTTGA
Found at i:40788776 original size:29 final size:30
Alignment explanation
Indices: 40788719--40788837 Score: 106
Period size: 29 Copynumber: 4.2 Consensus size: 30
40788709 TACATACATG
* **
40788719 CATATGGCCC-GCTAGGCCC-AATTTTATT
1 CATATGGCCCATCTAGGCCCAAATCATATT
* *
40788747 CAAATGGCCCATCTA-GCCCAGATCATATT
1 CATATGGCCCATCTAGGCCCAAATCATATT
* * ** *
40788776 CTTAGGGCCCA-CTAGGCCCACTTCACATT
1 CATATGGCCCATCTAGGCCCAAATCATATT
40788805 CATATGGCCCAT-TAGGCCCAAATCATATT
1 CATATGGCCCATCTAGGCCCAAATCATATT
40788834 -ATAT
1 CATAT
40788838 TCATGTTCAT
Statistics
Matches: 71, Mismatches: 16, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
28 20 0.28
29 51 0.72
ACGTcount: A:0.27, C:0.30, G:0.15, T:0.28
Consensus pattern (30 bp):
CATATGGCCCATCTAGGCCCAAATCATATT
Found at i:40788939 original size:19 final size:18
Alignment explanation
Indices: 40788906--40788942 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
40788896 TGGGCCCAAC
40788906 AGCCCATCAGGCCCATTT
1 AGCCCATCAGGCCCATTT
*
40788924 AGCCCATTCTGGCCCATTT
1 AGCCCA-TCAGGCCCATTT
40788943 GGCCAATCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.19, C:0.38, G:0.16, T:0.27
Consensus pattern (18 bp):
AGCCCATCAGGCCCATTT
Found at i:40789075 original size:8 final size:8
Alignment explanation
Indices: 40789047--40789098 Score: 52
Period size: 8 Copynumber: 6.6 Consensus size: 8
40789037 CGTAGCCCAA
40789047 CTTTT-GG
1 CTTTTCGG
40789054 CTTTTCGG
1 CTTTTCGG
* *
40789062 CATTTCAG
1 CTTTTCGG
*
40789070 CTTTTCAG
1 CTTTTCGG
*
40789078 CTATTCGG
1 CTTTTCGG
*
40789086 CATTTCGG
1 CTTTTCGG
40789094 CTTTT
1 CTTTT
40789099 GTCGATTCAT
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
7 5 0.14
8 31 0.86
ACGTcount: A:0.10, C:0.23, G:0.19, T:0.48
Consensus pattern (8 bp):
CTTTTCGG
Found at i:40790421 original size:42 final size:41
Alignment explanation
Indices: 40790374--40790528 Score: 168
Period size: 42 Copynumber: 3.7 Consensus size: 41
40790364 TAGCATACCA
*
40790374 ATGCCATATCCCAGATATGGTCTTACATGTAATCTCTTATTG
1 ATGCCATATCCCAGATATGGTCTTACACG-AATCTCTTATTG
* * **
40790416 ATGCCAATAGCCCAGCTATGGTCTTACACGAAATCT-TATATCA
1 ATGCC-ATATCCCAGATATGGTCTTACACG-AATCTCT-TATTG
* ** *
40790459 ATGCCATATCCCAAATATTATCTTACACGAAGTCTCATATTG
1 ATGCCATATCCCAGATATGGTCTTACACGAA-TCTCTTATTG
*
40790501 ATGCCATATCCCAGATATAGTCTTACAC
1 ATGCCATATCCCAGATATGGTCTTACAC
40790529 ATAGACTTAG
Statistics
Matches: 92, Mismatches: 17, Indels: 8
0.79 0.15 0.07
Matches are distributed among these distances:
41 2 0.02
42 56 0.61
43 34 0.37
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.32
Consensus pattern (41 bp):
ATGCCATATCCCAGATATGGTCTTACACGAATCTCTTATTG
Found at i:40793729 original size:42 final size:42
Alignment explanation
Indices: 40793611--40793731 Score: 116
Period size: 43 Copynumber: 2.9 Consensus size: 42
40793601 CACACGGTAC
* * * ***
40793611 CATACCAATGCCATATCCCAGATATAGTCTTATATGTAATCT
1 CATATCAATGCCATATCCCAGATATGGTCTTACACAAAATCT
** * * * * *
40793653 CATATTGATGACAATAGCCCGGCTATGGTATTACACAAAATCT
1 CATATCAATG-CCATATCCCAGATATGGTCTTACACAAAATCT
40793696 CATATCAATGCCATATCCCAGATATGGTCTTACACA
1 CATATCAATGCCATATCCCAGATATGGTCTTACACA
40793732 TAGACTTGGT
Statistics
Matches: 58, Mismatches: 20, Indels: 2
0.73 0.25 0.03
Matches are distributed among these distances:
42 28 0.48
43 30 0.52
ACGTcount: A:0.34, C:0.24, G:0.12, T:0.30
Consensus pattern (42 bp):
CATATCAATGCCATATCCCAGATATGGTCTTACACAAAATCT
Found at i:40801865 original size:94 final size:94
Alignment explanation
Indices: 40801756--40801948 Score: 377
Period size: 94 Copynumber: 2.1 Consensus size: 94
40801746 AATAATTTAT
40801756 TTTATTGATTCAATTAAACAAAAAAATATTTGTTTATGATGTGTTTTATTCCTAATGTATGTAAA
1 TTTATTGATTCAATTAAACAAAAAAATATTTGTTTATGATGTGTTTTATTCCTAATGTATGTAAA
40801821 TATTTTTATTTATTTAAAATTATTATAAA
66 TATTTTTATTTATTTAAAATTATTATAAA
*
40801850 TTTATTGATTCAATTAAACAAAAAAATATTTGTTTATGATGTGTTTTATTCCTTATGTATGTAAA
1 TTTATTGATTCAATTAAACAAAAAAATATTTGTTTATGATGTGTTTTATTCCTAATGTATGTAAA
40801915 TATTTTTATTTATTTAAAATTATTATAAA
66 TATTTTTATTTATTTAAAATTATTATAAA
40801944 TTTAT
1 TTTAT
40801949 ACAACTTTTA
Statistics
Matches: 98, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
94 98 1.00
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.51
Consensus pattern (94 bp):
TTTATTGATTCAATTAAACAAAAAAATATTTGTTTATGATGTGTTTTATTCCTAATGTATGTAAA
TATTTTTATTTATTTAAAATTATTATAAA
Found at i:40802003 original size:2 final size:2
Alignment explanation
Indices: 40801996--40802035 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
40801986 TAACTCTTTC
40801996 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40802036 TTGTGTTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40809303 original size:39 final size:40
Alignment explanation
Indices: 40809198--40809404 Score: 242
Period size: 40 Copynumber: 5.2 Consensus size: 40
40809188 TATTCAAATG
* * *
40809198 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACT
*
40809239 ATATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACT
* *
40809279 A-ATTCCGGGCTAAG-CCCGAAGGCATTGGTGTGAGTTACT
1 ATA-TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
40809318 AAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* * **
40809358 ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CT
40809398 ATATCCG
1 ATATCCG
40809405 ATTAAATCCC
Statistics
Matches: 143, Mismatches: 17, Indels: 13
0.83 0.10 0.08
Matches are distributed among these distances:
39 36 0.25
40 78 0.55
41 28 0.20
42 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:40809338 original size:79 final size:81
Alignment explanation
Indices: 40809198--40809384 Score: 247
Period size: 79 Copynumber: 2.3 Consensus size: 81
40809188 TATTCAAATG
* * *
40809198 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGC
40809263 ATTTGTGCGAGTTACT
66 ATTTGTGCGAGTTACT
* * **
40809279 A-ATTCCGGGCTAAG-CCCGAAGGCATTGGTG-TGAGTTACTAAATCCGGGTTAAG-TCCCGAAG
1 ATA-TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACTAAATCCGGACTAAGAT-CCGAAG
40809340 GCATTTGTGCGAGTTACT
64 GCATTTGTGCGAGTTACT
* *
40809358 ATAACCGGGCTATGTCCCGAAGGCATT
1 ATATCCGGGCTAAGTCCCGAAGGCATT
40809385 TGAACGAGTA
Statistics
Matches: 93, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
78 1 0.01
79 52 0.56
80 28 0.30
81 12 0.13
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (81 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGC
ATTTGTGCGAGTTACT
Found at i:40809415 original size:79 final size:80
Alignment explanation
Indices: 40809202--40809419 Score: 241
Period size: 79 Copynumber: 2.7 Consensus size: 80
40809192 CAAATGATAT
* * *
40809202 CCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGT-GACTATATCCGGACTAAGAT-CCGAAGGCAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTAG-CTATATCCGGATTAA-ATCCCGAAGGCAT
*
40809265 TTGTGCGAGTTACTAATT
63 TTGTGCGAGTTACTAATA
* * * * *
40809283 CCGGGCTAAG-CCCGAAGGCATTGGTGTGAGTTA-CTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TAGCTATATCCGGATTAAATCCCGAAGGCATTT
40809346 GTGCGAGTTACT-ATAA
65 GTGCGAGTTACTAAT-A
* **
40809362 CCGGGCTATGTCCCGAAGGCATTTGAACGAGTAGCTATATCC-GATTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGCTATATCCGGATTAAATCCCGAAGG
40809420 TATGTGATTC
Statistics
Matches: 114, Mismatches: 17, Indels: 14
0.79 0.12 0.10
Matches are distributed among these distances:
78 3 0.03
79 63 0.55
80 38 0.33
81 10 0.09
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGCTATATCCGGATTAAATCCCGAAGGCATTTG
TGCGAGTTACTAATA
Found at i:40813581 original size:25 final size:25
Alignment explanation
Indices: 40813547--40813597 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
40813537 CTCAAATGGG
40813547 ATGCAGGTAGGCTTTAAGGATTTTA
1 ATGCAGGTAGGCTTTAAGGATTTTA
40813572 ATGCAGGTAGGCTTTAAGGATTTTA
1 ATGCAGGTAGGCTTTAAGGATTTTA
40813597 A
1 A
40813598 ACGATCTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.29, C:0.08, G:0.27, T:0.35
Consensus pattern (25 bp):
ATGCAGGTAGGCTTTAAGGATTTTA
Found at i:40814590 original size:33 final size:34
Alignment explanation
Indices: 40814519--40814583 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
40814509 TGCATTTTAT
*
40814519 ACTGATACTGTTACTATATTGGGCTAAGGCCCAC
1 ACTGATACTGTTACTATATTGGGCTAAAGCCCAC
40814553 ACTGATACTGTTACTATA-TGGGCTAAAGCCC
1 ACTGATACTGTTACTATATTGGGCTAAAGCCC
40814584 TAACTGAGAC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 12 0.40
34 18 0.60
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (34 bp):
ACTGATACTGTTACTATATTGGGCTAAAGCCCAC
Found at i:40817234 original size:37 final size:37
Alignment explanation
Indices: 40817184--40817311 Score: 229
Period size: 37 Copynumber: 3.4 Consensus size: 37
40817174 TTATTACGAA
*
40817184 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
1 GTCTCACCCGGACATAATCTCCACACGTAGTCATCGG
*
40817221 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
1 GTCTCACCCGGACATAATCTCCACACGTAGTCATCGG
40817258 GTCTCACCCGGACATAATCTCCACACGTAGTCATCGG
1 GTCTCACCCGGACATAATCTCCACACGTAGTCATCGG
40817295 GTCTCACCCGGAACATA
1 GTCTCACCCGG-ACATA
40817312 TTTCCAAGTT
Statistics
Matches: 89, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
37 84 0.94
38 5 0.06
ACGTcount: A:0.25, C:0.34, G:0.19, T:0.23
Consensus pattern (37 bp):
GTCTCACCCGGACATAATCTCCACACGTAGTCATCGG
Found at i:40817414 original size:48 final size:48
Alignment explanation
Indices: 40817351--40817598 Score: 397
Period size: 48 Copynumber: 5.2 Consensus size: 48
40817341 TGTTACAACA
40817351 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
* *
40817399 TTCACATTAGTCATTCGGCTTTACCACATATACATATCACTCATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
* *
40817447 TTCACATTAGCCATTCGGCTTTACCATATATACATATCACTCATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
* ** * *
40817495 TTCACATTAGTCATTCGGCTTTACCACATATACATATCTTATATATGT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
* *
40817543 TTCACATTAGCCCTTCGGCTTTACCACATATACACATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
40817591 TTCACATT
1 TTCACATT
40817599 CATCACATCG
Statistics
Matches: 182, Mismatches: 18, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 182 1.00
ACGTcount: A:0.31, C:0.26, G:0.06, T:0.37
Consensus pattern (48 bp):
TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
Found at i:40817647 original size:47 final size:47
Alignment explanation
Indices: 40817590--40817731 Score: 257
Period size: 49 Copynumber: 3.0 Consensus size: 47
40817580 CACACATATA
40817590 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
40817637 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACAC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACAC
40817686 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
40817732 TCTCATACAT
Statistics
Matches: 91, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
47 45 0.49
49 46 0.51
ACGTcount: A:0.30, C:0.28, G:0.08, T:0.33
Consensus pattern (47 bp):
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
Found at i:40821550 original size:40 final size:40
Alignment explanation
Indices: 40821501--40821772 Score: 445
Period size: 40 Copynumber: 6.8 Consensus size: 40
40821491 CCAGCATGAT
* * *
40821501 TGCTCTTCGGGACCTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
40821541 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
*
40821581 TGCTCCTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
* *
40821621 TGCTCCTCGGAACTTAGTCCGGATACGTCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
* *
40821661 TGCTCTTCGGAGCTTAGTCCGGATACGTCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
* *
40821701 TGCTCCTCGGAACTTAGTCCGGATACGTCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
*
40821741 TGCTCTTCGGAACTTAGTCCGGATATATCACT
1 TGCTCTTCGGAACTTAGTCCGGATACATCACT
40821773 CTCAATTCTC
Statistics
Matches: 220, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 220 1.00
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (40 bp):
TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
Found at i:40823697 original size:38 final size:37
Alignment explanation
Indices: 40823600--40823727 Score: 204
Period size: 37 Copynumber: 3.4 Consensus size: 37
40823590 TTATTACGAA
*
40823600 GTCTTACCCGGACA-AATTCTCCACACGTAGTCATCGG
1 GTCTCACCCGGACATAA-TCTCCACACGTAGTCATCGG
*
40823637 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
1 GTCTCACCCGGACATAATCTCCACACGTAGTCATCGG
40823674 GTCTCACCCGGGACATAATCTCCACACGTAGTCATCGG
1 GTCTCACCC-GGACATAATCTCCACACGTAGTCATCGG
*
40823712 GTCTCACCCGAACATA
1 GTCTCACCCGGACATA
40823728 TTTCCAAGTT
Statistics
Matches: 87, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
37 48 0.55
38 39 0.45
ACGTcount: A:0.25, C:0.34, G:0.19, T:0.23
Consensus pattern (37 bp):
GTCTCACCCGGACATAATCTCCACACGTAGTCATCGG
Found at i:40831363 original size:29 final size:29
Alignment explanation
Indices: 40831273--40831432 Score: 180
Period size: 29 Copynumber: 5.5 Consensus size: 29
40831263 ACTCGATTTC
* * **
40831273 GCACACTTAGTGCCATGTGATTT-AAGCCC
1 GCACACTTAGTGCCATAT-ATTTCCAGCAT
* *** *
40831302 GCACACATAGTGCCATACCCTTCGAGC-T
1 GCACACTTAGTGCCATATATTTCCAGCAT
** *
40831330 CGCACACCCAGTGCCGTATATTTCCAGCAT
1 -GCACACTTAGTGCCATATATTTCCAGCAT
40831360 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
40831389 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
40831418 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
40831433 ATCTCGTCAC
Statistics
Matches: 111, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
28 2 0.02
29 108 0.97
30 1 0.01
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (29 bp):
GCACACTTAGTGCCATATATTTCCAGCAT
Found at i:40834023 original size:43 final size:43
Alignment explanation
Indices: 40833975--40834144 Score: 132
Period size: 43 Copynumber: 4.0 Consensus size: 43
40833965 ATTACCGAGA
40833975 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
** * *
40834018 TGTGATTATGTGTAAGACCATGTTTGGAACATTGGCATCAT-TA-
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCAT--TGTAT
* * * * * * *
40834061 TATGATTTCGTGTAAGACCATGTCTAGGATAGTGGCATCG-AT
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
* * * * * *
40834103 ACGTTATAACATGTAAGACCATATCCGGGATA-TGGCATTGTA
1 -TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTA
40834145 CGAGCTATAT
Statistics
Matches: 98, Mismatches: 23, Indels: 12
0.74 0.17 0.09
Matches are distributed among these distances:
41 1 0.01
42 7 0.07
43 87 0.89
44 2 0.02
45 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (43 bp):
TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
Found at i:40836623 original size:40 final size:39
Alignment explanation
Indices: 40836568--40836769 Score: 260
Period size: 40 Copynumber: 5.1 Consensus size: 39
40836558 TGAATAATAC
* * *
40836568 CCGGGCTAAGTCCCGAAGACATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTG-TTATAT
* * *
40836608 CCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTG-TTATAT
*
40836648 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGTTATAT
* *
40836688 CTGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGTTATAT
* *
40836728 CCGGGCTAAGACCCGAAGGCATTCGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGT-GTTATAT
40836768 CC
1 CC
40836770 AGAGATATTC
Statistics
Matches: 145, Mismatches: 15, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
39 1 0.01
40 142 0.98
41 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (39 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGTTATAT
Found at i:40844733 original size:40 final size:40
Alignment explanation
Indices: 40844678--40844841 Score: 179
Period size: 40 Copynumber: 4.1 Consensus size: 40
40844668 TGAATGATAC
* *
40844678 CCGGGCTAAGTCCCGAAGACATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGACATTTGTGCTAGTGATTATAT
* * * *
40844718 CCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACTATAT
1 CCGGGCTAAGACCCGAAGACATTTGTGCTAGTGATTATAT
* *
40844758 CCGGGCTAAGACCCGAAGGA-TTTTGTGCGAGTTG-TTATAT
1 CCGGGCTAAGACCCGAA-GACATTTGTGCTAG-TGATTATAT
* * * * *
40844798 CCGGGCTAAGAACCGAAGGCATTCGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGACATTTGTGCTAGTGATTATAT
40844838 CCGG
1 CCGG
40844842 TTATATTCCG
Statistics
Matches: 102, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
39 3 0.03
40 96 0.94
41 3 0.03
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGACATTTGTGCTAGTGATTATAT
Found at i:40844814 original size:80 final size:80
Alignment explanation
Indices: 40844678--40844841 Score: 199
Period size: 80 Copynumber: 2.0 Consensus size: 80
40844668 TGAATGATAC
* * * *
40844678 CCGGGCTAAGTCCCGAAGACATTTATGCTAGTGATTATATCCGGGTTAAGACCCGAAGGCAATT-
1 CCGGGCTAAGACCCGAAGACATTTATGCGAGTGATTATATCCGGGCTAAGAACCGAAGGC-ATTC
40844742 GTGCTAGTGACTATAT
65 GTGCTAGTGACTATAT
* *
40844758 CCGGGCTAAGACCCGAAGGA-TTTTGTGCGAGTTG-TTATATCCGGGCTAAGAACCGAAGGCATT
1 CCGGGCTAAGACCCGAA-GACATTTATGCGAG-TGATTATATCCGGGCTAAGAACCGAAGGCATT
* **
40844821 CGTGCTTGTGGTTATAT
64 CGTGCTAGTGACTATAT
40844838 CCGG
1 CCGG
40844842 TTATATTCCG
Statistics
Matches: 72, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
79 3 0.04
80 65 0.90
81 4 0.06
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.27
Consensus pattern (80 bp):
CCGGGCTAAGACCCGAAGACATTTATGCGAGTGATTATATCCGGGCTAAGAACCGAAGGCATTCG
TGCTAGTGACTATAT
Found at i:40869221 original size:40 final size:39
Alignment explanation
Indices: 40869177--40869369 Score: 251
Period size: 39 Copynumber: 4.9 Consensus size: 39
40869167 GTTCAAAACA
* * ** * *
40869177 CCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAATG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
* *
40869217 CCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
*
40869257 CCTTCGGGCTTAGCCCGGATATCATAGCTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
* *
40869296 CCTTCGGGCTTAGCCCGGATATCACAATTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
* *
40869335 CCTTCGGGCTTAGCCCGGATATCACAATTCGCACA
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACA
40869370 TTCATTCACA
Statistics
Matches: 139, Mismatches: 14, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 99 0.71
40 40 0.29
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.23
Consensus pattern (39 bp):
CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
Found at i:40869288 original size:39 final size:39
Alignment explanation
Indices: 40869207--40869369 Score: 263
Period size: 39 Copynumber: 4.2 Consensus size: 39
40869197 TATGGTAACC
* *
40869207 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
* *
40869247 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
40869286 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
40869325 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
40869364 CGCACA
1 CGCACA
40869370 TTCATTCACA
Statistics
Matches: 116, Mismatches: 7, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
39 99 0.85
40 17 0.15
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.23
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:40876972 original size:40 final size:39
Alignment explanation
Indices: 40876928--40877081 Score: 191
Period size: 39 Copynumber: 3.9 Consensus size: 39
40876918 GTTCAAAACA
* * ** * *
40876928 CCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAATG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
* *
40876968 CCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
*
40877008 CCTTCGGGCTTAGCCCGGATATCATAGCTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
* *
40877047 CCTTCGGGCTTAGCCCGGATATCACAATTCGCACA
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACA
40877082 TTCATTCACA
Statistics
Matches: 100, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
39 60 0.60
40 40 0.40
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.23
Consensus pattern (39 bp):
CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
Found at i:40877039 original size:39 final size:39
Alignment explanation
Indices: 40876958--40877081 Score: 194
Period size: 39 Copynumber: 3.2 Consensus size: 39
40876948 TATGGTAACC
* *
40876958 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
* *
40876998 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
40877037 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
40877076 CGCACA
1 CGCACA
40877082 TTCATTCACA
Statistics
Matches: 77, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
39 60 0.78
40 17 0.22
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.23
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:40880847 original size:32 final size:32
Alignment explanation
Indices: 40880807--40880876 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
40880797 ATATAAGGCT
*
40880807 ATCT-ACCAAGCCTTTTCCACCTTGAAACAAA
1 ATCTAACCAAGCCTTTGCCACCTTGAAACAAA
40880838 ATCTAACCAAGCCTTTGCCACCTTGAAACAAA
1 ATCTAACCAAGCCTTTGCCACCTTGAAACAAA
40880870 ATCTAAC
1 ATCTAAC
40880877 ATTAACCAAC
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
31 4 0.11
32 33 0.89
ACGTcount: A:0.37, C:0.31, G:0.07, T:0.24
Consensus pattern (32 bp):
ATCTAACCAAGCCTTTGCCACCTTGAAACAAA
Found at i:40885251 original size:46 final size:48
Alignment explanation
Indices: 40885143--40885260 Score: 161
Period size: 48 Copynumber: 2.5 Consensus size: 48
40885133 GGCTATTACA
40885143 CATGTCCCAAACATGTCTTACACTGGCTTAAATATCTCAAGGCTGATG
1 CATGTCCCAAACATGTCTTACACTGGCTTAAATATCTCAAGGCTGATG
* * **
40885191 CGTGTCCCAAACATGTCTTACACTGGCTCT-TATA-CTGTA-GCTGATG
1 CATGTCCCAAACATGTCTTACACTGGCT-TAAATATCTCAAGGCTGATG
*
40885237 CATGTCCCAGACATGTCTTACACT
1 CATGTCCCAAACATGTCTTACACT
40885261 AGCACACATA
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
46 29 0.46
47 3 0.05
48 30 0.48
49 1 0.02
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (48 bp):
CATGTCCCAAACATGTCTTACACTGGCTTAAATATCTCAAGGCTGATG
Found at i:40894957 original size:46 final size:47
Alignment explanation
Indices: 40894839--40895065 Score: 198
Period size: 46 Copynumber: 4.8 Consensus size: 47
40894829 GGGGTAAGGT
* * * * *
40894839 GCCGATGCCATGTCCCAAACATGGTCTTACACAAGCTCTAGCATATC-TG
1 GCCGATGCCATGTCCCAGACAT-GTCTTACACTAGCTCT--CGTCTCAAG
* * * *
40894888 TGCCGATACCATGTCCCAGACATGTCTTACCCT-GACT-TATGTCTCGAG
1 -GCCGATGCCATGTCCCAGACATGTCTTACACTAG-CTCT-CGTCTCAAG
* *
40894936 GCCGATG-CATGTCCCAAACATGTCTTACACTAGCTCTCGTCTCAAT
1 GCCGATGCCATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCAAG
* * *
40894982 GCCGATGCCATGTCCCAGACATGTTCTTACACTGGCTCT--TATAATATG
1 GCCGATGCCATGTCCCAGACATG-TCTTACACTAGCTCTCGTCTCA-A-G
40895030 GCCGATG-CATGTCCCAGACATGTCTTACACTAGCTC
1 GCCGATGCCATGTCCCAGACATGTCTTACACTAGCTC
40895066 ACAATAACCC
Statistics
Matches: 148, Mismatches: 21, Indels: 20
0.78 0.11 0.11
Matches are distributed among these distances:
46 53 0.36
47 41 0.28
48 24 0.16
49 10 0.07
50 20 0.14
ACGTcount: A:0.23, C:0.31, G:0.18, T:0.28
Consensus pattern (47 bp):
GCCGATGCCATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCAAG
Found at i:40895051 original size:94 final size:92
Alignment explanation
Indices: 40894839--40895065 Score: 260
Period size: 94 Copynumber: 2.4 Consensus size: 92
40894829 GGGGTAAGGT
* **
40894839 GCCGATGCCATGTCCCAAACATGGTCTTACACAAGCTCTAGCATATCTGTGCCGATACCATGTCC
1 GCCGATG-CATGTCCCAAACAT-GTCTTACACTAGCTCTA-CATATCAATGCCGATACCATGTCC
* * *
40894904 CAGACATGTCTTACCCTGACTTATGTCTCGAG
63 CAGACATGTCTTACACTGACTTATATAT--AG
* * *
40894936 GCCGATGCATGTCCCAAACATGTCTTACACTAGCTCT-CGTCTCAATGCCGATGCCATGTCCCAG
1 GCCGATGCATGTCCCAAACATGTCTTACACTAGCTCTACATATCAATGCCGATACCATGTCCCAG
*
40895000 ACATGTTCTTACACTGGCTCT-TATAATATG
66 ACATG-TCTTACACTGACT-TATAT-ATA-G
*
40895030 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTC
1 GCCGATGCATGTCCCAAACATGTCTTACACTAGCTC
40895066 ACAATAACCC
Statistics
Matches: 115, Mismatches: 11, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
93 28 0.24
94 49 0.43
95 17 0.15
96 14 0.12
97 7 0.06
ACGTcount: A:0.23, C:0.31, G:0.18, T:0.28
Consensus pattern (92 bp):
GCCGATGCATGTCCCAAACATGTCTTACACTAGCTCTACATATCAATGCCGATACCATGTCCCAG
ACATGTCTTACACTGACTTATATATAG
Found at i:40900233 original size:27 final size:27
Alignment explanation
Indices: 40900097--40900254 Score: 192
Period size: 27 Copynumber: 5.9 Consensus size: 27
40900087 ATATATACAT
* *
40900097 CACAT-AGGGCAAAACAGTCATATTAC
1 CACATAAGGGCAAAATAGTCATTTTAC
* *
40900123 CATACAAGGGCAAAATAGTCATTTTAC
1 CACATAAGGGCAAAATAGTCATTTTAC
* * *
40900150 CATATAAGGGCACAACAGTCATTTTAC
1 CACATAAGGGCAAAATAGTCATTTTAC
*
40900177 CACATAAGGGAAAAATAGTCATTTTAC
1 CACATAAGGGCAAAATAGTCATTTTAC
* * *
40900204 CACATAAGGGAAAAATAATCATCTTAC
1 CACATAAGGGCAAAATAGTCATTTTAC
* *
40900231 CACCTAAGGGGAAAATAGTCATTT
1 CACATAAGGGCAAAATAGTCATTT
40900255 AATTAATTTT
Statistics
Matches: 114, Mismatches: 17, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
26 3 0.03
27 111 0.97
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.24
Consensus pattern (27 bp):
CACATAAGGGCAAAATAGTCATTTTAC
Found at i:40902716 original size:80 final size:80
Alignment explanation
Indices: 40902632--40902780 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
40902622 TATGGTAACC
* * * *
40902632 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
40902696 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
40902712 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
40902777 CCGG
66 CCGG
40902781 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:40902722 original size:40 final size:38
Alignment explanation
Indices: 40902673--40902780 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
40902663 ATCACGATTT
*
40902673 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
40902713 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
40902753 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
40902781 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:40910075 original size:47 final size:47
Alignment explanation
Indices: 40910021--40910629 Score: 894
Period size: 47 Copynumber: 13.0 Consensus size: 47
40910011 TTAGGATTTT
** *
40910021 ATGTGATGAATGTGAATGTGTATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
40910068 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
40910115 ATGTGGTGAATATGAACATGTATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
40910162 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * *
40910209 ATGTGGTGAATATGAACATGTATAAATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
40910256 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGTCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
40910303 ATGTGGTGAATATGAACATGTATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
40910350 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * * *
40910397 ATGTGGTGAATATGAACATGCATATATGTGATTAGGCCGAACGGCCT
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
40910444 ATGTGATGAATGTGAACATGCATCTATGTGATGAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
40910491 ATGTGATGAATGTGAGCATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
40910538 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * *
40910585 ATGTGGTGAATATGAACATGCATATATGTGGTAAAGCCGAATGGC
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGC
40910630 TAGTGTGAAA
Statistics
Matches: 500, Mismatches: 62, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 500 1.00
ACGTcount: A:0.32, C:0.12, G:0.30, T:0.27
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:40910137 original size:94 final size:94
Alignment explanation
Indices: 40910021--40910629 Score: 1029
Period size: 94 Copynumber: 6.5 Consensus size: 94
40910011 TTAGGATTTT
* * **
40910021 ATGTGATGAATGTGAATGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAGCA
1 ATGTGGTGAATATGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAGCA
40910086 TGCATATGTGTGATAAGGCCGAATGGCCA
66 TGCATATGTGTGATAAGGCCGAATGGCCA
40910115 ATGTGGTGAATATGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAGCA
1 ATGTGGTGAATATGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAGCA
40910180 TGCATATGTGTGATAAGGCCGAATGGCCA
66 TGCATATGTGTGATAAGGCCGAATGGCCA
*
40910209 ATGTGGTGAATATGAACATGTATAAATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAGCA
1 ATGTGGTGAATATGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAGCA
*
40910274 TGCATATGTGTGATAAGGCCGAATGGTCA
66 TGCATATGTGTGATAAGGCCGAATGGCCA
40910303 ATGTGGTGAATATGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAGCA
1 ATGTGGTGAATATGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAGCA
40910368 TGCATATGTGTGATAAGGCCGAATGGCCA
66 TGCATATGTGTGATAAGGCCGAATGGCCA
* * * * *
40910397 ATGTGGTGAATATGAACATGCATATATGTGATTAGGCCGAACGGCCTATGTGATGAATGTGAACA
1 ATGTGGTGAATATGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAGCA
* * *
40910462 TGCATCTATGTGATGAGGCCGAATGGCCA
66 TGCATATGTGTGATAAGGCCGAATGGCCA
* * * *
40910491 ATGTGATGAATGTGAGCATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAGCA
1 ATGTGGTGAATATGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAGCA
40910556 TGCATATGTGTGATAAGGCCGAATGGCCA
66 TGCATATGTGTGATAAGGCCGAATGGCCA
* * *
40910585 ATGTGGTGAATATGAACATGCATATATGTGGTAAAGCCGAATGGC
1 ATGTGGTGAATATGAACATGTATATATGTGATAAGGCCGAATGGC
40910630 TAGTGTGAAA
Statistics
Matches: 484, Mismatches: 31, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
94 484 1.00
ACGTcount: A:0.32, C:0.12, G:0.30, T:0.27
Consensus pattern (94 bp):
ATGTGGTGAATATGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAGCA
TGCATATGTGTGATAAGGCCGAATGGCCA
Found at i:40910405 original size:25 final size:25
Alignment explanation
Indices: 40910330--40910405 Score: 63
Period size: 23 Copynumber: 3.2 Consensus size: 25
40910320 ATGTATATAT
40910330 GTGATAAGGCCGAATGGCCAATGTG
1 GTGATAAGGCCGAATGGCCAATGTG
* * * *
40910355 ATGA-ATGTG-AGCAT-G-CATATGT-
1 GTGATAAG-GCCGAATGGCCA-ATGTG
40910377 GTGATAAGGCCGAATGGCCAATGTG
1 GTGATAAGGCCGAATGGCCAATGTG
40910402 GTGA
1 GTGA
40910406 ATATGAACAT
Statistics
Matches: 36, Mismatches: 8, Indels: 14
0.62 0.14 0.24
Matches are distributed among these distances:
22 6 0.17
23 10 0.28
24 10 0.28
25 10 0.28
ACGTcount: A:0.29, C:0.13, G:0.34, T:0.24
Consensus pattern (25 bp):
GTGATAAGGCCGAATGGCCAATGTG
Found at i:40910460 original size:22 final size:22
Alignment explanation
Indices: 40910435--40910505 Score: 54
Period size: 22 Copynumber: 3.1 Consensus size: 22
40910425 TGATTAGGCC
40910435 GAACGGCCTATGTGATGAATGT
1 GAACGGCCTATGTGATGAATGT
* * *
40910457 GAACATGCATCTATGTGATG-AGGCC
1 GAAC-GGC--CTATGTGATGAATG-T
* *
40910482 GAATGGCCAATGTGATGAATGT
1 GAACGGCCTATGTGATGAATGT
40910504 GA
1 GA
40910506 GCATGCATAT
Statistics
Matches: 36, Mismatches: 8, Indels: 10
0.67 0.15 0.19
Matches are distributed among these distances:
22 15 0.42
23 4 0.11
24 4 0.11
25 13 0.36
ACGTcount: A:0.30, C:0.14, G:0.31, T:0.25
Consensus pattern (22 bp):
GAACGGCCTATGTGATGAATGT
Found at i:40910521 original size:25 final size:25
Alignment explanation
Indices: 40910491--40910569 Score: 69
Period size: 25 Copynumber: 3.3 Consensus size: 25
40910481 CGAATGGCCA
40910491 ATGTGATGAATGTGAGCATGCATAT
1 ATGTGATGAATGTGAGCATGCATAT
* * *
40910516 ATGTGAT-AA-G-GCCGAATGGC-CA-
1 ATGTGATGAATGTG-AGCAT-GCATAT
40910538 ATGTGATGAATGTGAGCATGCATAT
1 ATGTGATGAATGTGAGCATGCATAT
*
40910563 GTGTGAT
1 ATGTGAT
40910570 AAGGCCGAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 14
0.66 0.11 0.23
Matches are distributed among these distances:
22 8 0.20
23 9 0.22
24 9 0.22
25 14 0.35
ACGTcount: A:0.30, C:0.10, G:0.30, T:0.29
Consensus pattern (25 bp):
ATGTGATGAATGTGAGCATGCATAT
Found at i:40910593 original size:25 final size:25
Alignment explanation
Indices: 40910518--40910593 Score: 63
Period size: 23 Copynumber: 3.2 Consensus size: 25
40910508 ATGCATATAT
40910518 GTGATAAGGCCGAATGGCCAATGTG
1 GTGATAAGGCCGAATGGCCAATGTG
* * * *
40910543 ATGA-ATGTG-AGCAT-G-CATATGT-
1 GTGATAAG-GCCGAATGGCCA-ATGTG
40910565 GTGATAAGGCCGAATGGCCAATGTG
1 GTGATAAGGCCGAATGGCCAATGTG
40910590 GTGA
1 GTGA
40910594 ATATGAACAT
Statistics
Matches: 36, Mismatches: 8, Indels: 14
0.62 0.14 0.24
Matches are distributed among these distances:
22 6 0.17
23 10 0.28
24 10 0.28
25 10 0.28
ACGTcount: A:0.29, C:0.13, G:0.34, T:0.24
Consensus pattern (25 bp):
GTGATAAGGCCGAATGGCCAATGTG
Found at i:40910842 original size:37 final size:37
Alignment explanation
Indices: 40910792--40910974 Score: 303
Period size: 37 Copynumber: 4.9 Consensus size: 37
40910782 GGAAATATAT
* * *
40910792 TCCGGGTGAGACCCGATGACTACGTGTGGAGAGTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
40910829 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* *
40910866 TCCGAGTAAGACCCGATGACTACATGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
40910903 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* *
40910940 TCCGGGTAAGACCCGATAACTTCGTGTGGAGATTT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTT
40910975 CGTCGAGCTA
Statistics
Matches: 137, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 137 1.00
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.26
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:40913438 original size:54 final size:54
Alignment explanation
Indices: 40913296--40913439 Score: 245
Period size: 54 Copynumber: 2.7 Consensus size: 54
40913286 TGGAGGAAGC
*
40913296 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGCGGCTCTGCCACATATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
40913350 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
* *
40913404 GTTCTGGTGGCTCTGCCACAA-TATCTGTATCTGGTG
1 GTCCTGGTGGCTATGCCACAATTATCTG-ATCTGGTG
40913440 ACTTCGTCAC
Statistics
Matches: 86, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
53 6 0.07
54 80 0.93
ACGTcount: A:0.17, C:0.26, G:0.24, T:0.33
Consensus pattern (54 bp):
GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
Found at i:40913450 original size:27 final size:27
Alignment explanation
Indices: 40913299--40913457 Score: 184
Period size: 27 Copynumber: 5.9 Consensus size: 27
40913289 AGGAAGCGTC
*
40913299 CTGGTGGCTATGCCACAATTATCTG-AT
1 CTGGTGGCTCTGCCACAA-TATCTGTAT
* *
40913326 CTGGCGGCTCTGCCACATATATCTGT-C
1 CTGGTGGCTCTGCCACA-ATATCTGTAT
*
40913353 CTGGTGGCTATGCCACAATTATCTG-AT
1 CTGGTGGCTCTGCCACAA-TATCTGTAT
40913380 CTGGTGGCTCTGCCACATATATCTGT-T
1 CTGGTGGCTCTGCCACA-ATATCTGTAT
40913407 CTGGTGGCTCTGCCACAATATCTGTAT
1 CTGGTGGCTCTGCCACAATATCTGTAT
* *
40913434 CTGGTGACT-TCGTCACAATATCTG
1 CTGGTGGCTCT-GCCACAATATCTG
40913458 GCAGCCTCGC
Statistics
Matches: 115, Mismatches: 9, Indels: 16
0.82 0.06 0.11
Matches are distributed among these distances:
26 10 0.09
27 103 0.90
28 2 0.02
ACGTcount: A:0.19, C:0.26, G:0.22, T:0.33
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATATCTGTAT
Found at i:40913451 original size:81 final size:80
Alignment explanation
Indices: 40913299--40913457 Score: 207
Period size: 81 Copynumber: 2.0 Consensus size: 80
40913289 AGGAAGCGTC
*
40913299 CTGGTGGCTATGCCACAATTATCTGATCTGGCGGCTCTGCCACATATATCTGTCCTGGTGGCTAT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGCGGCTCTGCCACATATATCTGTCCTGGTGACTAT
40913364 GCCACAATTATCTGAT
66 GCCACAA-TATCTGAT
* * * *
40913380 CTGGTGGCTCTGCCAC-ATATATCTGTTCTGGTGGCTCTGCCACA-ATATCTGTATCTGGTGACT
1 CTGGTGGCTATGCCACAAT-TATCTGATCTGGCGGCTCTGCCACATATATCTGT-CCTGGTGACT
*
40913443 -TCGTCACAATATCTG
64 AT-GCCACAATATCTG
40913458 GCAGCCTCGC
Statistics
Matches: 69, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
80 17 0.25
81 52 0.75
ACGTcount: A:0.19, C:0.26, G:0.22, T:0.33
Consensus pattern (80 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGCGGCTCTGCCACATATATCTGTCCTGGTGACTAT
GCCACAATATCTGAT
Found at i:40920531 original size:54 final size:54
Alignment explanation
Indices: 40920390--40920532 Score: 234
Period size: 54 Copynumber: 2.6 Consensus size: 54
40920380 GGAGGAAGCA
**
40920390 TCCTGGTGGCTCTGCCACAATTATCTGATCTGGCAGCTCTGCCACATATATCTG
1 TCCTGGTGGCTCTGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTG
*
40920444 TCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTG
1 TCCTGGTGGCTCTGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTG
*
40920498 TTCTGGTGGCTCTGCCACAA-TATCTGTATCTGGTG
1 TCCTGGTGGCTCTGCCACAATTATCTG-ATCTGGTG
40920533 ACTTCGTCAC
Statistics
Matches: 83, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
53 6 0.07
54 77 0.93
ACGTcount: A:0.17, C:0.27, G:0.22, T:0.34
Consensus pattern (54 bp):
TCCTGGTGGCTCTGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTG
Found at i:40920543 original size:27 final size:27
Alignment explanation
Indices: 40920392--40920550 Score: 184
Period size: 27 Copynumber: 5.9 Consensus size: 27
40920382 AGGAAGCATC
40920392 CTGGTGGCTCTGCCACAATTATCTG-AT
1 CTGGTGGCTCTGCCACAA-TATCTGTAT
** *
40920419 CTGGCAGCTCTGCCACATATATCTGT-C
1 CTGGTGGCTCTGCCACA-ATATCTGTAT
*
40920446 CTGGTGGCTATGCCACAATTATCTG-AT
1 CTGGTGGCTCTGCCACAA-TATCTGTAT
40920473 CTGGTGGCTCTGCCACATATATCTGT-T
1 CTGGTGGCTCTGCCACA-ATATCTGTAT
40920500 CTGGTGGCTCTGCCACAATATCTGTAT
1 CTGGTGGCTCTGCCACAATATCTGTAT
* *
40920527 CTGGTGACT-TCGTCACAATATCTG
1 CTGGTGGCTCT-GCCACAATATCTG
40920551 GCAGCCTCGC
Statistics
Matches: 114, Mismatches: 10, Indels: 16
0.81 0.07 0.11
Matches are distributed among these distances:
26 10 0.09
27 102 0.89
28 2 0.02
ACGTcount: A:0.19, C:0.26, G:0.21, T:0.33
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATATCTGTAT
Found at i:40920544 original size:81 final size:80
Alignment explanation
Indices: 40920392--40920550 Score: 207
Period size: 81 Copynumber: 2.0 Consensus size: 80
40920382 AGGAAGCATC
*
40920392 CTGGTGGCTCTGCCACAATTATCTGATCTGGCAGCTCTGCCACATATATCTGTCCTGGTGGCTAT
1 CTGGTGGCTCTGCCACAATTATCTGATCTGGCAGCTCTGCCACATATATCTGTCCTGGTGACTAT
40920457 GCCACAATTATCTGAT
66 GCCACAA-TATCTGAT
* ** *
40920473 CTGGTGGCTCTGCCAC-ATATATCTGTTCTGGTGGCTCTGCCACA-ATATCTGTATCTGGTGACT
1 CTGGTGGCTCTGCCACAAT-TATCTGATCTGGCAGCTCTGCCACATATATCTGT-CCTGGTGACT
*
40920536 -TCGTCACAATATCTG
64 AT-GCCACAATATCTG
40920551 GCAGCCTCGC
Statistics
Matches: 69, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
80 17 0.25
81 52 0.75
ACGTcount: A:0.19, C:0.26, G:0.21, T:0.33
Consensus pattern (80 bp):
CTGGTGGCTCTGCCACAATTATCTGATCTGGCAGCTCTGCCACATATATCTGTCCTGGTGACTAT
GCCACAATATCTGAT
Found at i:40923843 original size:21 final size:21
Alignment explanation
Indices: 40923818--40923887 Score: 122
Period size: 21 Copynumber: 3.3 Consensus size: 21
40923808 AATTGCACAT
* *
40923818 GGCCGTGTGGGTTAATGGTCA
1 GGCCGTGTGGGTCAATGGCCA
40923839 GGCCGTGTGGGTCAATGGCCA
1 GGCCGTGTGGGTCAATGGCCA
40923860 GGCCGTGTGGGTCAATGGCCA
1 GGCCGTGTGGGTCAATGGCCA
40923881 GGCCGTG
1 GGCCGTG
40923888 GTCGACACCC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.13, C:0.21, G:0.44, T:0.21
Consensus pattern (21 bp):
GGCCGTGTGGGTCAATGGCCA
Found at i:40926686 original size:40 final size:40
Alignment explanation
Indices: 40926631--40926852 Score: 331
Period size: 40 Copynumber: 5.6 Consensus size: 40
40926621 TATTCAGATG
* * *
40926631 ATATCTGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
*
40926671 ATATCCGGGCTAAGTCCCGAAGGCCTTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
*
40926711 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
40926751 ATATCCGGGCTAAATCCTGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
40926791 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
*
40926831 ATATCC-GGCTAATTCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
40926853 TACTTGGGTT
Statistics
Matches: 166, Mismatches: 15, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
39 14 0.08
40 150 0.90
41 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.28
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:40931763 original size:39 final size:39
Alignment explanation
Indices: 40931662--40931892 Score: 394
Period size: 39 Copynumber: 6.0 Consensus size: 39
40931652 AAGACACTAA
40931662 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
*
40931701 AAATATAT-CGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
* *
40931739 AAATATATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
40931778 AAATGTATCC-GGCTAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
*
40931816 AAATGTATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
* *
40931855 AAATGTATCCGGGTTAAAGTCCCGCAGGCTTTGTGCTG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTG
40931893 ATAATATAAT
Statistics
Matches: 182, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
38 75 0.41
39 107 0.59
ACGTcount: A:0.22, C:0.26, G:0.29, T:0.23
Consensus pattern (39 bp):
AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
Found at i:40931766 original size:77 final size:77
Alignment explanation
Indices: 40931662--40931900 Score: 390
Period size: 77 Copynumber: 3.1 Consensus size: 77
40931652 AAGACACTAA
* * *
40931662 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGGAAATATATCGGGCTAAAGTCCCGCAG
1 AAATATATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGGAAATGTATCGGGCTAAAGTCCCGCAG
40931727 GCTTCGTGCTGG
66 GCTTCGTGCTGG
*
40931739 AAATATATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGGAAATGTATCCGGCTAAAGTCCCGCAG
1 AAATATATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGGAAATGTATCGGGCTAAAGTCCCGCAG
40931804 GCTTCGTGCTGG
66 GCTTCGTGCTGG
* *
40931816 AAATGTATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGGAAATGTATCCGGGTTAAAGTCCCGCA
1 AAATATATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGGAAATGTAT-CGGGCTAAAGTCCCGCA
*
40931881 GGCTTTGTGCT-G
65 GGCTTCGTGCTGG
40931893 ATAATATA
1 A-AATATA
40931901 ATTTCGGGTT
Statistics
Matches: 151, Mismatches: 9, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
77 121 0.80
78 30 0.20
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.24
Consensus pattern (77 bp):
AAATATATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGGAAATGTATCGGGCTAAAGTCCCGCAG
GCTTCGTGCTGG
Found at i:40938478 original size:11 final size:11
Alignment explanation
Indices: 40938461--40938509 Score: 53
Period size: 11 Copynumber: 4.3 Consensus size: 11
40938451 AGATAAATAT
40938461 TATTTTATTAA
1 TATTTTATTAA
* *
40938472 TACTTTAATAAGA
1 TA-TTTTATTA-A
*
40938485 TATTTTATTAT
1 TATTTTATTAA
40938496 TATTTTATTAA
1 TATTTTATTAA
40938507 TAT
1 TAT
40938510 ATAAAGAAAG
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
11 15 0.50
12 12 0.40
13 3 0.10
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:40938506 original size:27 final size:27
Alignment explanation
Indices: 40938429--40938508 Score: 76
Period size: 27 Copynumber: 3.0 Consensus size: 27
40938419 GAGATATTTT
* *
40938429 GATATTTTATAATTATTTAATTAGATAA
1 GATATTTTATTATTATTTTATTA-ATAA
**
40938457 -ATATTATT-TTATTAATACT-TTAATAA
1 GATATT-TTATTATT-ATTTTATTAATAA
40938483 GATATTTTATTATTATTTTATTAATA
1 GATATTTTATTATTATTTTATTAATA
40938509 TATAAAGAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
26 9 0.22
27 28 0.68
28 4 0.10
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (27 bp):
GATATTTTATTATTATTTTATTAATAA
Found at i:40938511 original size:24 final size:24
Alignment explanation
Indices: 40938456--40938511 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
40938446 TAATTAGATA
40938456 AATATTATTTTATTAATACTTTAAT
1 AATA-TATTTTATTAATACTTTAAT
* * * *
40938481 AAGATATTTTATTATTATTTTATT
1 AATATATTTTATTAATACTTTAAT
40938505 AATATAT
1 AATATAT
40938512 AAAGAAAGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (24 bp):
AATATATTTTATTAATACTTTAAT
Found at i:40940683 original size:38 final size:40
Alignment explanation
Indices: 40940633--40940977 Score: 324
Period size: 46 Copynumber: 8.0 Consensus size: 40
40940623 CTGATATGAA
40940633 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC-TG
1 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCATG
40940672 -TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATGTG
1 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC--A--TG
40940715 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC-TG
1 --ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCATG
40940756 -TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG
1 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC----ATG
*
40940799 AAATGTGTAAGACCATGGTTGGAAGATACCATGGCAACCTGATATGAG
1 --ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC----AT--G
40940847 ATGTGTAAGACCATGGTTG-AAGATACCATGGCAACGTGACATG
1 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC----CATG
* **
40940890 AAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGACATG
1 --ATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC----CATG
* *
40940936 AAAAGAGTAAGACCATGGTTGAAAGATACCATGGCAA-CATG
1 --ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCATG
40940977 A
1 A
40940978 CAGAAAATGA
Statistics
Matches: 276, Mismatches: 5, Indels: 50
0.83 0.02 0.15
Matches are distributed among these distances:
38 72 0.26
39 1 0.00
41 6 0.02
43 5 0.02
45 34 0.12
46 156 0.57
48 1 0.00
49 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.26, T:0.22
Consensus pattern (40 bp):
ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCATG
Found at i:40940739 original size:46 final size:46
Alignment explanation
Indices: 40940672--40941017 Score: 451
Period size: 46 Copynumber: 7.7 Consensus size: 46
40940662 TGGCAACCTG
*
40940672 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATGTGAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
40940718 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACC-----TG---
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
40940756 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
* *
40940802 TGTGTAAGACCATGGTTGGAAGATACCATGGCAACCTGATATGAGA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
* *
40940848 TGTGTAAGACCATGGTTG-AAGATACCATGGCAACGTGACATGAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
* ** * *
40940893 AGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
* * * *
40940939 AGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG-AAA
* * * *
40940985 TGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCA
40941018 TCACGTCAAA
Statistics
Matches: 276, Mismatches: 14, Indels: 20
0.89 0.05 0.06
Matches are distributed among these distances:
38 36 0.13
41 2 0.01
43 2 0.01
45 40 0.14
46 196 0.71
ACGTcount: A:0.38, C:0.16, G:0.25, T:0.21
Consensus pattern (46 bp):
TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
Found at i:40940758 original size:84 final size:86
Alignment explanation
Indices: 40940623--40941017 Score: 496
Period size: 84 Copynumber: 4.5 Consensus size: 86
40940613 AGTGTGCTCT
40940623 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC-TG-TGTGTAAGACCATG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCATGATGTGTAAGACCATG
40940686 GTTGAAAGATACCATGGCAAC
66 GTTGAAAGATACCATGGCAAC
*
40940707 CTGATGTGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC-TG-TGTGTAAGACCATG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCATGATGTGTAAGACCATG
40940770 GTTGAAAGATACCATGGCAAC
66 GTTGAAAGATACCATGGCAAC
*
40940791 CTGATATGAAATGTGTAAGACCATGGTTGGAAGATACCATGGCAACCTGATATGAGATGTGTAAG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC----AT--GATGTGTAAG
40940856 ACCATGGTTG-AAGATACCATGGCAAC
60 ACCATGGTTGAAAGATACCATGGCAAC
* * * ** * *
40940882 GTGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAGTAAG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC----CATG--ATGTGTAAG
40940947 ACCATGGTTGAAAGATACCATGGCAAC
60 ACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
40940974 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
40941018 TCACGTCAAA
Statistics
Matches: 278, Mismatches: 17, Indels: 24
0.87 0.05 0.08
Matches are distributed among these distances:
84 128 0.46
89 2 0.01
91 77 0.28
92 70 0.25
95 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.25, T:0.22
Consensus pattern (86 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCATGATGTGTAAGACCATG
GTTGAAAGATACCATGGCAAC
Found at i:40940880 original size:91 final size:92
Alignment explanation
Indices: 40940756--40941017 Score: 366
Period size: 91 Copynumber: 2.9 Consensus size: 92
40940746 TGGCAACCTG
* * * *
40940756 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGG
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGAGTAAGACCATGGTTGA
* *
40940821 AAGATACCATGGCAACCTGATATGAGA
66 AAGATACCATGGCAACCTGACATGAAA
* * *
40940848 TGTGTAAGACCATGGTTG-AAGATACCATGGCAACGTGACATGAAAAGAATAAGACCATGGTTGA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGAGTAAGACCATGGTTGA
*
40940912 AAGATACCATGGCAACGTGACATGAAA
66 AAGATACCATGGCAACCTGACATGAAA
* * *
40940939 AGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAATGAGTAAGACCATAGTTG
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGACATG-AAATGAGTAAGACCATGGTTG
* *
40941003 AAAGACACTATGGCA
65 AAAGATACCATGGCA
40941018 TCACGTCAAA
Statistics
Matches: 151, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
91 81 0.54
92 70 0.46
ACGTcount: A:0.39, C:0.15, G:0.25, T:0.21
Consensus pattern (92 bp):
TGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGAGTAAGACCATGGTTGA
AAGATACCATGGCAACCTGACATGAAA
Found at i:40940949 original size:137 final size:129
Alignment explanation
Indices: 40940637--40941004 Score: 457
Period size: 137 Copynumber: 2.8 Consensus size: 129
40940627 TATGAAATGT
*
40940637 GTAAGACCATGGTTGAAAGATACCATGGCAACCTG---T-----GTGTAAGACCATGGTTGAAAG
1 GTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAAAGAGTAAGACCATGGTTGAAAG
* *
40940694 ATACCATGGCAACCTGATGTGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGTGT
66 ATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTG-AAGATACCATGGCAACCTGTGA
* * * *
40940759 GTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGGAAG
1 GTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAAAGAGTAAGACCATGGTTGAAAG
* *
40940824 ATACCATGGCAACCTGATATGAGATGTGTAAGACCATGGTTGAAGATACCATGGCAACGTGACAT
66 ATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAGATACCATGGCAACCTG---T
40940889 GAAAA
128 G---A
*
40940894 GAATAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAGTAAGACCATGGTTGAA
1 G--TAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAAAGAGTAAGACCATGGTTGAA
* * * *
40940959 AGATACCATGGCAACATGACA-GAAAATGAGTAAGACCATAGTTGAA
64 AGATACCATGGCAACCTGATATG-AAATGTGTAAGACCATGGTTGAA
40941005 AGACACTATG
Statistics
Matches: 214, Mismatches: 15, Indels: 19
0.86 0.06 0.08
Matches are distributed among these distances:
122 35 0.16
125 1 0.00
129 18 0.08
130 60 0.28
132 2 0.01
135 1 0.00
136 1 0.00
137 96 0.45
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.21
Consensus pattern (129 bp):
GTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAAAGAGTAAGACCATGGTTGAAAG
ATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAGATACCATGGCAACCTGTGA
Found at i:40941958 original size:71 final size:71
Alignment explanation
Indices: 40941842--40941983 Score: 284
Period size: 71 Copynumber: 2.0 Consensus size: 71
40941832 TAGAATCAGT
40941842 TTATAAGTATACGAACAGTCTTCTATGTCTAGAAATCGTTTGCATTTTAATTAAGAAATATGAAC
1 TTATAAGTATACGAACAGTCTTCTATGTCTAGAAATCGTTTGCATTTTAATTAAGAAATATGAAC
40941907 AATCAA
66 AATCAA
40941913 TTATAAGTATACGAACAGTCTTCTATGTCTAGAAATCGTTTGCATTTTAATTAAGAAATATGAAC
1 TTATAAGTATACGAACAGTCTTCTATGTCTAGAAATCGTTTGCATTTTAATTAAGAAATATGAAC
40941978 AATCAA
66 AATCAA
40941984 ATGAAATAGT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (71 bp):
TTATAAGTATACGAACAGTCTTCTATGTCTAGAAATCGTTTGCATTTTAATTAAGAAATATGAAC
AATCAA
Found at i:40944013 original size:22 final size:21
Alignment explanation
Indices: 40943971--40944019 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
40943961 AAAATGATTG
* *
40943971 TAACAAATATAAGTTTCATAA
1 TAACAAATATAAATATCATAA
40943992 TTAACAAATATATAATAT-ATAA
1 -TAACAAATATA-AATATCATAA
40944014 TAACAA
1 TAACAA
40944020 TTTTTAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 6 0.25
22 15 0.62
23 3 0.12
ACGTcount: A:0.57, C:0.08, G:0.02, T:0.33
Consensus pattern (21 bp):
TAACAAATATAAATATCATAA
Found at i:40946578 original size:5 final size:5
Alignment explanation
Indices: 40946568--40946595 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
40946558 TTTTTAATCC
40946568 TTTTA TTTTA TTTTA TTTTA TTTTA TTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTT
40946596 ATTATTTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:40947153 original size:23 final size:23
Alignment explanation
Indices: 40947127--40947171 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
40947117 TATACTAAAT
**
40947127 ATATATATTTTTTATTTTTAATC
1 ATATATACATTTTATTTTTAATC
*
40947150 ATATTTACATTTTATTTTTAAT
1 ATATATACATTTTATTTTTAAT
40947172 TTTAATATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.64
Consensus pattern (23 bp):
ATATATACATTTTATTTTTAATC
Found at i:40948890 original size:18 final size:17
Alignment explanation
Indices: 40948869--40948911 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
40948859 TTCAAAAAAA
* *
40948869 TTTAATTTTTGATACTTT
1 TTTAATATTT-ATAATTT
*
40948887 TTTAAGATTTATAATTT
1 TTTAATATTTATAATTT
40948904 TTTAATAT
1 TTTAATAT
40948912 AAATTTAGTA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (17 bp):
TTTAATATTTATAATTT
Found at i:40949101 original size:23 final size:23
Alignment explanation
Indices: 40949075--40949120 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
40949065 TACTAGTTTG
40949075 GGGTGGTGAGGGATGGCCAAAGA
1 GGGTGGTGAGGGATGGCCAAAGA
*
40949098 GGGTGGTGAGGGATGGCTAAAGA
1 GGGTGGTGAGGGATGGCCAAAGA
40949121 TCAATGATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.26, C:0.07, G:0.52, T:0.15
Consensus pattern (23 bp):
GGGTGGTGAGGGATGGCCAAAGA
Found at i:40956184 original size:11 final size:11
Alignment explanation
Indices: 40956167--40956215 Score: 53
Period size: 11 Copynumber: 4.3 Consensus size: 11
40956157 AGATAAATAT
40956167 TATTTTATTAA
1 TATTTTATTAA
* *
40956178 TACTTTAATAAGA
1 TA-TTTTATTA-A
*
40956191 TATTTTATTAT
1 TATTTTATTAA
40956202 TATTTTATTAA
1 TATTTTATTAA
40956213 TAT
1 TAT
40956216 ATAAAGAAAG
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
11 15 0.50
12 12 0.40
13 3 0.10
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:40956212 original size:27 final size:27
Alignment explanation
Indices: 40956135--40956214 Score: 76
Period size: 27 Copynumber: 3.0 Consensus size: 27
40956125 GAGATATTTT
* *
40956135 GATATTTTATAATTATTTAATTAGATAA
1 GATATTTTATTATTATTTTATTA-ATAA
**
40956163 -ATATTATT-TTATTAATACT-TTAATAA
1 GATATT-TTATTATT-ATTTTATTAATAA
40956189 GATATTTTATTATTATTTTATTAATA
1 GATATTTTATTATTATTTTATTAATA
40956215 TATAAAGAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
26 9 0.22
27 28 0.68
28 4 0.10
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (27 bp):
GATATTTTATTATTATTTTATTAATAA
Found at i:40956217 original size:24 final size:24
Alignment explanation
Indices: 40956162--40956217 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
40956152 TAATTAGATA
40956162 AATATTATTTTATTAATACTTTAAT
1 AATA-TATTTTATTAATACTTTAAT
* * * *
40956187 AAGATATTTTATTATTATTTTATT
1 AATATATTTTATTAATACTTTAAT
40956211 AATATAT
1 AATATAT
40956218 AAAGAAAGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (24 bp):
AATATATTTTATTAATACTTTAAT
Found at i:40958445 original size:46 final size:46
Alignment explanation
Indices: 40958378--40958722 Score: 451
Period size: 46 Copynumber: 7.7 Consensus size: 46
40958368 TGGCAACCTG
*
40958378 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATGTGAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
40958424 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACC-----T---A
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
40958462 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
*
40958508 TGTGTAAGACCATGGTTG-AAGATACCATGGCAACCTGATATGAGA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
* *
40958553 TGTGTAAGACCATGGTTG-AAGATACCATGGCAACGTGACATGAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
* ** * *
40958598 AGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
* * * *
40958644 AGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG-AAA
* * * *
40958690 TGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCA
40958723 TCACGTCAAA
Statistics
Matches: 276, Mismatches: 13, Indels: 20
0.89 0.04 0.06
Matches are distributed among these distances:
38 37 0.13
41 1 0.00
43 1 0.00
45 84 0.30
46 153 0.55
ACGTcount: A:0.38, C:0.16, G:0.25, T:0.21
Consensus pattern (46 bp):
TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
Found at i:40958470 original size:84 final size:86
Alignment explanation
Indices: 40958329--40958722 Score: 487
Period size: 84 Copynumber: 4.5 Consensus size: 86
40958319 AGTGTGCTCT
*
40958329 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC-T-GTGTGTAAGACCATG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCATAATGTGTAAGACCATG
40958392 GTTGAAAGATACCATGGCAAC
66 GTTGAAAGATACCATGGCAAC
*
40958413 CTGATGTGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC-T-ATGTGTAAGACCATG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCATAATGTGTAAGACCATG
40958476 GTTGAAAGATACCATGGCAAC
66 GTTGAAAGATACCATGGCAAC
40958497 CTGATATGAAATGTGTAAGACCATGGTTG-AAGATACCATGGCAACCTGATATGAGATGTGTAAG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC----AT-A-ATGTGTAAG
40958561 ACCATGGTTG-AAGATACCATGGCAAC
60 ACCATGGTTGAAAGATACCATGGCAAC
* * * ** * *
40958587 GTGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAGTAAG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC----CAT--AATGTGTAAG
40958652 ACCATGGTTGAAAGATACCATGGCAAC
60 ACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
40958679 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
40958723 TCACGTCAAA
Statistics
Matches: 277, Mismatches: 17, Indels: 24
0.87 0.05 0.08
Matches are distributed among these distances:
83 17 0.06
84 110 0.40
88 1 0.00
90 40 0.14
91 55 0.20
92 53 0.19
95 1 0.00
ACGTcount: A:0.38, C:0.16, G:0.25, T:0.22
Consensus pattern (86 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCATAATGTGTAAGACCATG
GTTGAAAGATACCATGGCAAC
Found at i:40958629 original size:91 final size:92
Alignment explanation
Indices: 40958461--40958722 Score: 368
Period size: 91 Copynumber: 2.9 Consensus size: 92
40958451 ATGGCAACCT
* * * *
40958461 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTG
1 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAAAGAGTAAGACCATGGTTG
* *
40958526 -AAGATACCATGGCAACCTGATATGAG
66 AAAGATACCATGGCAACCTGACATGAA
* *
40958552 ATGTGTAAGACCATGGTTG-AAGATACCATGGCAACGTGACATGAAAAGAATAAGACCATGGTTG
1 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAAAGAGTAAGACCATGGTTG
*
40958616 AAAGATACCATGGCAACGTGACATGAA
66 AAAGATACCATGGCAACCTGACATGAA
* * *
40958643 AAGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAATGAGTAAGACCATAGTT
1 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAAA-GAGTAAGACCATGGTT
* *
40958707 GAAAGACACTATGGCA
65 GAAAGATACCATGGCA
40958723 TCACGTCAAA
Statistics
Matches: 153, Mismatches: 15, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
90 40 0.26
91 64 0.42
92 49 0.32
ACGTcount: A:0.39, C:0.15, G:0.25, T:0.21
Consensus pattern (92 bp):
ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAAAGAGTAAGACCATGGTTG
AAAGATACCATGGCAACCTGACATGAA
Found at i:40959663 original size:71 final size:71
Alignment explanation
Indices: 40959547--40959688 Score: 284
Period size: 71 Copynumber: 2.0 Consensus size: 71
40959537 TAGAATCAGT
40959547 TTATAAGTATACGAACAGTCTTCTATGTCTAGAAATCGTTTGCATTTTAATTAAGAAATATGAAC
1 TTATAAGTATACGAACAGTCTTCTATGTCTAGAAATCGTTTGCATTTTAATTAAGAAATATGAAC
40959612 AATCAA
66 AATCAA
40959618 TTATAAGTATACGAACAGTCTTCTATGTCTAGAAATCGTTTGCATTTTAATTAAGAAATATGAAC
1 TTATAAGTATACGAACAGTCTTCTATGTCTAGAAATCGTTTGCATTTTAATTAAGAAATATGAAC
40959683 AATCAA
66 AATCAA
40959689 ATGAAATAGT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (71 bp):
TTATAAGTATACGAACAGTCTTCTATGTCTAGAAATCGTTTGCATTTTAATTAAGAAATATGAAC
AATCAA
Found at i:40961707 original size:22 final size:21
Alignment explanation
Indices: 40961665--40961713 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
40961655 AAAATGATTG
* *
40961665 TAACAAATATAAGTTTCATAA
1 TAACAAATATAAATATCATAA
40961686 TTAACAAATATATAATAT-ATAA
1 -TAACAAATATA-AATATCATAA
40961708 TAACAA
1 TAACAA
40961714 TTTTTAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 6 0.25
22 15 0.62
23 3 0.12
ACGTcount: A:0.57, C:0.08, G:0.02, T:0.33
Consensus pattern (21 bp):
TAACAAATATAAATATCATAA
Found at i:40964271 original size:5 final size:5
Alignment explanation
Indices: 40964261--40964288 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
40964251 TTTTTAATCC
40964261 TTTTA TTTTA TTTTA TTTTA TTTTA TTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTT
40964289 ATTATTTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:40964845 original size:24 final size:23
Alignment explanation
Indices: 40964818--40964863 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
40964808 TATATACTAA
*
40964818 ATATATATATTTTTATTTTTAATC
1 ATATATACA-TTTTATTTTTAATC
*
40964842 ATATTTACATTTTATTTTTAAT
1 ATATATACATTTTATTTTTAAT
40964864 TTTAATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (23 bp):
ATATATACATTTTATTTTTAATC
Found at i:40971408 original size:40 final size:40
Alignment explanation
Indices: 40971353--40971556 Score: 214
Period size: 40 Copynumber: 5.1 Consensus size: 40
40971343 TGAATGATAC
* * * *
40971353 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCAAGTGATTATAT
*
40971393 CCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTG-TTATAT
1 CCGGGCTAAGACCCGAAGGCAATT-GTGCAAG-TGATTATAT
* ** *
40971433 CCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTACCAAAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCAAGTGATTATAT
* * ** *
40971473 CCGGGTTAAGACCCGAAGGCAATTGTGCAAGTTACCAAAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCAAGTGATTATAT
* ** *
40971513 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCAAGTGATTATAT
40971553 CCGG
1 CCGG
40971557 TTAAATCCCG
Statistics
Matches: 143, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
39 3 0.02
40 135 0.94
41 5 0.03
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCAATTGTGCAAGTGATTATAT
Found at i:40971555 original size:80 final size:80
Alignment explanation
Indices: 40971353--40971570 Score: 244
Period size: 80 Copynumber: 2.7 Consensus size: 80
40971343 TGAATGATAC
* * * *
40971353 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATATCCGGGCTAAGACCCGAAGGCATTCG
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATATCCGGGTTAAGACCCGAAGGCATTCG
* *** *
40971418 TGCGAGTTGTTATAT
66 TGCAAGTTACCAAAT
* * ** *
40971433 CCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTACCAAATCCGGGTTAAGACCCGAAGGCAATT-
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATATCCGGGTTAAGACCCGAAGGC-ATTC
40971497 GTGCAAGTTACCAAAT
65 GTGCAAGTTACCAAAT
* * *
40971513 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATATCC-GGTTAA-ATCCCGAAGG
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATATCCGGGTTAAGA-CCCGAAGG
40971571 TACGTGACTC
Statistics
Matches: 114, Mismatches: 22, Indels: 5
0.81 0.16 0.04
Matches are distributed among these distances:
78 1 0.01
79 14 0.12
80 96 0.84
81 3 0.03
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (80 bp):
CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATATCCGGGTTAAGACCCGAAGGCATTCG
TGCAAGTTACCAAAT
Found at i:40979544 original size:40 final size:40
Alignment explanation
Indices: 40979489--40979692 Score: 214
Period size: 40 Copynumber: 5.1 Consensus size: 40
40979479 TGAATGATAC
* * * *
40979489 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCAAGTGATTATAT
*
40979529 CCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTG-TTATAT
1 CCGGGCTAAGACCCGAAGGCAATT-GTGCAAG-TGATTATAT
* ** *
40979569 CCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTACCAAAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCAAGTGATTATAT
* * ** *
40979609 CCGGGTTAAGACCCGAAGGCAATTGTGCAAGTTACCAAAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCAAGTGATTATAT
* ** *
40979649 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCAAGTGATTATAT
40979689 CCGG
1 CCGG
40979693 TTGAATCCCG
Statistics
Matches: 143, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
39 3 0.02
40 135 0.94
41 5 0.03
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCAATTGTGCAAGTGATTATAT
Found at i:40979691 original size:80 final size:80
Alignment explanation
Indices: 40979489--40979692 Score: 239
Period size: 80 Copynumber: 2.5 Consensus size: 80
40979479 TGAATGATAC
* * *
40979489 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATATCCGGGCTAAGACCCGAAGGCATTCG
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATATCCGGGCTAAGACCCGAAGGCATTCG
* *** *
40979554 TGCGAGTTGTTATAT
66 TGCAAGTTACCAAAT
* * ** * *
40979569 CCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTACCAAATCCGGGTTAAGACCCGAAGGCAATT-
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATATCCGGGCTAAGACCCGAAGGC-ATTC
40979633 GTGCAAGTTACCAAAT
65 GTGCAAGTTACCAAAT
* * *
40979649 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATATCCGG
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATATCCGG
40979693 TTGAATCCCG
Statistics
Matches: 101, Mismatches: 22, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
80 98 0.97
81 3 0.03
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.24
Consensus pattern (80 bp):
CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATATCCGGGCTAAGACCCGAAGGCATTCG
TGCAAGTTACCAAAT
Found at i:40987381 original size:40 final size:40
Alignment explanation
Indices: 40987268--40987404 Score: 175
Period size: 40 Copynumber: 3.4 Consensus size: 40
40987258 CTCGAGAATA
* ** *
40987268 TAAAGTGGATAGGATTCATTCCTGATTCACTATAATACCT
1 TAAAGTGGATAGGATTTATTCCTGATTCACTATGGTAACT
* * *
40987308 CAAAGTGGATAGGATTTGTTCCTGATTCACTATGGTAATT
1 TAAAGTGGATAGGATTTATTCCTGATTCACTATGGTAACT
*
40987348 TAAAGTGAATAGGATTTATTCCTGATTCACTATGGTAACT
1 TAAAGTGGATAGGATTTATTCCTGATTCACTATGGTAACT
* **
40987388 TAAGGCAGATAGGATTT
1 TAAAGTGGATAGGATTT
40987405 GACCTGAAAA
Statistics
Matches: 82, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 82 1.00
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (40 bp):
TAAAGTGGATAGGATTTATTCCTGATTCACTATGGTAACT
Found at i:40987460 original size:78 final size:78
Alignment explanation
Indices: 40987370--40987521 Score: 261
Period size: 78 Copynumber: 1.9 Consensus size: 78
40987360 GATTTATTCC
40987370 TGATTCACTATGGTAA-CTTAAGGCAGATAGGATTTGACCTGAAAAGGTAATCCTGATTCACTAC
1 TGATTCACTATGGTAATC-TAAGGCAGATAGGATTTGACCTGAAAAGGTAATCCTGATTCACTAC
40987434 AGTTACATGATATA
65 AGTTACATGATATA
* **
40987448 TGATTCATTATGGTAATCTAAGGTGGATAGGATTTGACCTGAAAAGGTAATCCTGATTCACTACA
1 TGATTCACTATGGTAATCTAAGGCAGATAGGATTTGACCTGAAAAGGTAATCCTGATTCACTACA
40987513 GTTACATGA
66 GTTACATGA
40987522 GATGTGACTC
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
78 69 0.99
79 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (78 bp):
TGATTCACTATGGTAATCTAAGGCAGATAGGATTTGACCTGAAAAGGTAATCCTGATTCACTACA
GTTACATGATATA
Found at i:40990151 original size:6 final size:6
Alignment explanation
Indices: 40990133--40990245 Score: 56
Period size: 6 Copynumber: 18.3 Consensus size: 6
40990123 AAGAAACATT
* * *
40990133 ATCAGA A-CTAGA ATCAGA ATCAGA ATTAGGTA A-CA-A ATTAAA ATCAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA
* * *
40990181 ATCAGT ATCAGGTA A-CAGA ATCAAA ATCAGA ATCAGT ATCAGGTA A-CAGA
1 ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA
*
40990231 ATCAAAA ATCAGA AT
1 ATC-AGA ATCAGA AT
40990246 GTGAATGCAA
Statistics
Matches: 81, Mismatches: 13, Indels: 26
0.68 0.11 0.22
Matches are distributed among these distances:
4 2 0.02
5 6 0.07
6 55 0.68
7 14 0.17
8 4 0.05
ACGTcount: A:0.50, C:0.14, G:0.15, T:0.20
Consensus pattern (6 bp):
ATCAGA
Found at i:40990201 original size:19 final size:19
Alignment explanation
Indices: 40990177--40990234 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
40990167 AAATTAAAAT
40990177 CAGAATCAGTATCAGGTAA
1 CAGAATCAGTATCAGGTAA
*
40990196 CAGAATCA--A--A---AT
1 CAGAATCAGTATCAGGTAA
40990208 CAGAATCAGTATCAGGTAA
1 CAGAATCAGTATCAGGTAA
40990227 CAGAATCA
1 CAGAATCA
40990235 AAAATCAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 14
0.65 0.04 0.30
Matches are distributed among these distances:
12 9 0.30
14 1 0.03
15 1 0.03
16 1 0.03
17 1 0.03
19 17 0.57
ACGTcount: A:0.47, C:0.17, G:0.17, T:0.19
Consensus pattern (19 bp):
CAGAATCAGTATCAGGTAA
Found at i:40990210 original size:31 final size:31
Alignment explanation
Indices: 40990144--40990245 Score: 161
Period size: 31 Copynumber: 3.3 Consensus size: 31
40990134 TCAGAACTAG
* * *
40990144 AATCAGAATCAGAATTAGGTAACA-AATTAA
1 AATCAGAATCAGTATCAGGTAACAGAATCAA
40990174 AATCAGAATCAGTATCAGGTAACAGAATCAA
1 AATCAGAATCAGTATCAGGTAACAGAATCAA
40990205 AATCAGAATCAGTATCAGGTAACAGAATCAAA
1 AATCAGAATCAGTATCAGGTAACAGAATC-AA
40990237 AATCAGAAT
1 AATCAGAAT
40990246 GTGAATGCAA
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
30 22 0.33
31 34 0.51
32 11 0.16
ACGTcount: A:0.51, C:0.14, G:0.15, T:0.21
Consensus pattern (31 bp):
AATCAGAATCAGTATCAGGTAACAGAATCAA
Found at i:40990431 original size:28 final size:27
Alignment explanation
Indices: 40990382--40990457 Score: 80
Period size: 28 Copynumber: 2.8 Consensus size: 27
40990372 GCTCAATTAT
* * * *
40990382 CAGATATTGTGACAGAGTCACCAGATA
1 CAGATATTGTGGCAAAGCCACCAGAAA
* *
40990409 TAGATATTTGTGGCATAGCCACCAGAAA
1 CAGATA-TTGTGGCAAAGCCACCAGAAA
*
40990437 CAGATAATGTGGCAAAGCCAC
1 CAGATATTGTGGCAAAGCCAC
40990458 TTAACAGAAT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
27 18 0.45
28 22 0.55
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.21
Consensus pattern (27 bp):
CAGATATTGTGGCAAAGCCACCAGAAA
Found at i:40990644 original size:22 final size:22
Alignment explanation
Indices: 40990616--40990680 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
40990606 GCAAATACGT
*
40990616 TTGGCACACAGCCATAATCAGG
1 TTGGCACAAAGCCATAATCAGG
* *
40990638 TTGGCACAGAGCCAT-ATGTAGG
1 TTGGCACAAAGCCATAAT-CAGG
*
40990660 TTGACACAAAGCCATAATCAG
1 TTGGCACAAAGCCATAATCAG
40990681 AAGGCTTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 2 0.06
22 32 0.89
23 2 0.06
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAGCCATAATCAGG
Found at i:40990957 original size:16 final size:16
Alignment explanation
Indices: 40990936--40990966 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40990926 ATCCCAACCC
*
40990936 ATGCAACATGTCATGT
1 ATGCAAAATGTCATGT
40990952 ATGCAAAATGTCATG
1 ATGCAAAATGTCATG
40990967 CCCATATTTG
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:0.35, C:0.16, G:0.19, T:0.29
Consensus pattern (16 bp):
ATGCAAAATGTCATGT
Found at i:40991569 original size:27 final size:27
Alignment explanation
Indices: 40991107--40991561 Score: 583
Period size: 27 Copynumber: 17.0 Consensus size: 27
40991097 GGGGCAAAAT
* * * *
40991107 GGTAATTTTACCCCACA-AGGTATCTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
40991133 GGTAATTCCACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
40991160 AGTAATTCTACCCTACATGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
40991187 AGTAATTCTACCCTACAGGGGTATTGC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
40991214 GATAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
40991241 GGTAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
*
40991268 GGTAATTCTACCCTACAGGGCTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
40991295 GGTAATTCTACCCTACA--GGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
40991320 GGTATTTCTACCCTACAAGGGTAGTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * * *
40991347 GGTATTTCTACCTTACAAGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
40991374 AGTAATTCTACCCTACAGGGGAATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
40991401 GGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
40991428 GGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
40991455 GGTAATTCTATCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
40991482 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* ** *
40991509 GGTATTTCTACCCTACAAAGGTATTTA
1 GGTAATTCTACCCTACAGGGGTATTTC
*
40991536 GGTAATTCTACACTACAGGGGTATTT
1 GGTAATTCTACCCTACAGGGGTATTT
40991562 TAATAATTTT
Statistics
Matches: 375, Mismatches: 51, Indels: 5
0.87 0.12 0.01
Matches are distributed among these distances:
25 23 0.06
26 14 0.04
27 338 0.90
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:40991639 original size:81 final size:81
Alignment explanation
Indices: 40991554--40991738 Score: 201
Period size: 81 Copynumber: 2.3 Consensus size: 81
40991544 TACACTACAG
* * ** *
40991554 GGGTATTTTAATAATTTTGTAAATCAAAGGTAGAAC-GATAATTTTGTAAATCGGGGGTACTTTG
1 GGGTATTTTAGTAATTTTATAAATCAAAGGTAGAACAG-TAATTTTACAAATCAGGGGTACTTTG
* *
40991618 GTAATTTTACAAATCGA
65 GTAATTTTACAAACCAA
* * * * * *** *
40991635 GGGTATTTCAGTAATTTCACAAATCGAGGGTATTTCAGTAATTTTACAAATCAGGGGTATTTTGG
1 GGGTATTTTAGTAATTTTATAAATCAAAGGTAGAACAGTAATTTTACAAATCAGGGGTACTTTGG
40991700 TAATTTTACAAACCAA
66 TAATTTTACAAACCAA
*
40991716 GGGTATTTTGGTAATTTTATAAA
1 GGGTATTTTAGTAATTTTATAAA
40991739 CCAGGGGTAT
Statistics
Matches: 83, Mismatches: 20, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
81 82 0.99
82 1 0.01
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.38
Consensus pattern (81 bp):
GGGTATTTTAGTAATTTTATAAATCAAAGGTAGAACAGTAATTTTACAAATCAGGGGTACTTTGG
TAATTTTACAAACCAA
Found at i:40991650 original size:54 final size:54
Alignment explanation
Indices: 40991608--40991807 Score: 251
Period size: 54 Copynumber: 3.7 Consensus size: 54
40991598 TGTAAATCGG
* ** * * *
40991608 GGGTACTTTGGTAATTTTACAAATC-GAGGGTATTTCAGTAATTTCACAAATCGA
1 GGGTATTTTGGTAATTTTACAAATCAG-GGGTATTTTGGTAATTTTACAAACCAA
**
40991662 GGGTATTTCAGTAATTTTACAAATCAGGGGTATTTTGGTAATTTTACAAACCAA
1 GGGTATTTTGGTAATTTTACAAATCAGGGGTATTTTGGTAATTTTACAAACCAA
* * **
40991716 GGGTATTTTGGTAATTTTATAAACCAGGGGTATTTTGGTAATTTTGTAAACCAA
1 GGGTATTTTGGTAATTTTACAAATCAGGGGTATTTTGGTAATTTTACAAACCAA
*
40991770 TGGTATTTTGGTAATTTTACAAA-CTAGGGGTATTTTGG
1 GGGTATTTTGGTAATTTTACAAATC-AGGGGTATTTTGG
40991808 CGATTTGGTA
Statistics
Matches: 128, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
53 1 0.01
54 126 0.98
55 1 0.01
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.39
Consensus pattern (54 bp):
GGGTATTTTGGTAATTTTACAAATCAGGGGTATTTTGGTAATTTTACAAACCAA
Found at i:40991747 original size:81 final size:81
Alignment explanation
Indices: 40991592--40991807 Score: 254
Period size: 81 Copynumber: 2.7 Consensus size: 81
40991582 GGTAGAACGA
* * * * **
40991592 TAATTTTGTAAATCGGGGGTACTTTGGTAATTTTACAAATCGAGGGTATTTCAGTAATTTCACAA
1 TAATTTTGTAAATCAGGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTGGTAATTTCACAA
*
40991657 ATCGAGGGTATTTCAG
66 ACCGAGGGTATTTCAG
** * *
40991673 TAATTTTACAAATCAGGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTGGTAATTTTATAA
1 TAATTTTGTAAATCAGGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTGGTAATTTCACAA
**
40991738 ACC-AGGGGTATTTTGG
66 ACCGA-GGGTATTTCAG
* ** * *
40991754 TAATTTTGTAAACCAATGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGG
1 TAATTTTGTAAATCAGGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTGG
40991808 CGATTTGGTA
Statistics
Matches: 114, Mismatches: 20, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
80 1 0.01
81 113 0.99
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.39
Consensus pattern (81 bp):
TAATTTTGTAAATCAGGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTGGTAATTTCACAA
ACCGAGGGTATTTCAG
Found at i:40991813 original size:27 final size:27
Alignment explanation
Indices: 40991607--40991807 Score: 226
Period size: 27 Copynumber: 7.4 Consensus size: 27
40991597 TTGTAAATCG
* *
40991607 GGGGTACTTTGGTAATTTTACAAATC-
1 GGGGTATTTTGGTAATTTTACAAACCA
** * *
40991633 GAGGGTATTTCAGTAATTTCACAAATC-
1 G-GGGTATTTTGGTAATTTTACAAACCA
** *
40991660 GAGGGTATTTCAGTAATTTTACAAATCA
1 G-GGGTATTTTGGTAATTTTACAAACCA
40991688 GGGGTATTTTGGTAATTTTACAAACCA
1 GGGGTATTTTGGTAATTTTACAAACCA
* *
40991715 AGGGTATTTTGGTAATTTTATAAACCA
1 GGGGTATTTTGGTAATTTTACAAACCA
**
40991742 GGGGTATTTTGGTAATTTTGTAAACCA
1 GGGGTATTTTGGTAATTTTACAAACCA
** *
40991769 ATGGTATTTTGGTAATTTTACAAACTA
1 GGGGTATTTTGGTAATTTTACAAACCA
40991796 GGGGTATTTTGG
1 GGGGTATTTTGG
40991808 CGATTTGGTA
Statistics
Matches: 154, Mismatches: 19, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
26 1 0.01
27 152 0.99
28 1 0.01
ACGTcount: A:0.30, C:0.09, G:0.22, T:0.39
Consensus pattern (27 bp):
GGGGTATTTTGGTAATTTTACAAACCA
Found at i:40993232 original size:46 final size:47
Alignment explanation
Indices: 40993087--40993259 Score: 187
Period size: 46 Copynumber: 3.7 Consensus size: 47
40993077 GTTATCGTGG
* * *
40993087 GCTAGTGTAAAACATGTCTGGGACAT-GCATCAGCCACATT---ATGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGGCATC-G--GCATTGAGACGAGA
* *
40993133 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACGAGT
1 GCTAGTGTAAGA-CATGTCTGGGACATGGCATCGGCATTGAGACGAGA
* * *
40993181 GCTAGTGTAAGACATGTCTGGGACAT-TCATCGGCCTTGGGACGTA-A
1 GCTAGTGTAAGACATGTCTGGGACATGGCATCGGCATTGAGACG-AGA
40993227 GCTAGTGTAAGACATGTCTGGGACATGGCATCG
1 GCTAGTGTAAGACATGTCTGGGACATGGCATCG
40993260 ACAACTTGCC
Statistics
Matches: 109, Mismatches: 11, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
45 4 0.04
46 50 0.46
47 35 0.32
48 20 0.18
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.24
Consensus pattern (47 bp):
GCTAGTGTAAGACATGTCTGGGACATGGCATCGGCATTGAGACGAGA
Found at i:40996752 original size:22 final size:22
Alignment explanation
Indices: 40996709--40996753 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
40996699 CCACACTGGT
*
40996709 ATGTGCCCCTTTTCACATGGGC
1 ATGTGCCCCTTTTCACAAGGGC
*
40996731 ATGTG-CCCTTTCTCATAAGGGC
1 ATGTGCCCCTTT-TCACAAGGGC
40996753 A
1 A
40996754 CTTGACCTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.18, C:0.29, G:0.22, T:0.31
Consensus pattern (22 bp):
ATGTGCCCCTTTTCACAAGGGC
Found at i:41000094 original size:17 final size:17
Alignment explanation
Indices: 41000055--41000094 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
41000045 TTCAAAGCAA
41000055 ATAAATTATAAAAAAAT
1 ATAAATTATAAAAAAAT
* **
41000072 AAAAATTATAAAATTAT
1 ATAAATTATAAAAAAAT
41000089 ATAAAT
1 ATAAAT
41000095 CAATTCAACT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATAAATTATAAAAAAAT
Done.