Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr1
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 35726063
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1821929 characters in sequence are not A, C, G, or T
File 64 of 109
Found at i:20702894 original size:59 final size:58
Alignment explanation
Indices: 20702713--20702895 Score: 141
Period size: 56 Copynumber: 3.1 Consensus size: 58
20702703 ATATAATTTA
*
20702713 ATAAAATTGTTAATA-AA-TATTCTTATATGAATTTACTAATAAAATCATAATATATAATACT
1 ATAAAATT-TTAATATAATTATTCTTATATGAATTTAC---T-AAATCATAATATATAATAAT
* * * * *
20702774 A-AAATATAATTTAAAATAATTATTATTAAACAT-AATTTAAT-AA--A-AATATATAAT-TT
1 ATAAA-AT--TTTAATATAATTATTCTT--ATATGAATTTACTAAATCATAATATATAATAAT
20702830 AATAAAATTCTTAATATAATTATTCTTATATGAATTTACTAAATCATAATATATAATAAT
1 -ATAAAATT-TTAATATAATTATTCTTATATGAATTTACTAAATCATAATATATAATAAT
20702890 ATAAAA
1 ATAAAA
20702896 ATAATATATA
Statistics
Matches: 96, Mismatches: 10, Indels: 34
0.69 0.07 0.24
Matches are distributed among these distances:
54 3 0.03
55 8 0.08
56 18 0.19
57 13 0.14
58 5 0.05
59 16 0.17
60 6 0.06
61 3 0.03
62 6 0.06
63 3 0.03
64 6 0.06
65 6 0.06
66 3 0.03
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (58 bp):
ATAAAATTTTAATATAATTATTCTTATATGAATTTACTAAATCATAATATATAATAAT
Found at i:20704243 original size:38 final size:38
Alignment explanation
Indices: 20704189--20704264 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
20704179 CGGTTGAGGA
*
20704189 AAGGGAAAAAAAAGCAATTACTTTACCAAAATGGATCC
1 AAGGGAAAAAAAAGCAACTACTTTACCAAAATGGATCC
*
20704227 AAGGGAAAAAAGAGCAACTACTTTACCAAAATGGATCC
1 AAGGGAAAAAAAAGCAACTACTTTACCAAAATGGATCC
20704265 TAATACAAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.49, C:0.17, G:0.17, T:0.17
Consensus pattern (38 bp):
AAGGGAAAAAAAAGCAACTACTTTACCAAAATGGATCC
Found at i:20709540 original size:4 final size:4
Alignment explanation
Indices: 20709531--20709555 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
20709521 TAATGAAAGC
20709531 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
20709556 ATTATAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:20709930 original size:3 final size:3
Alignment explanation
Indices: 20709924--20710176 Score: 497
Period size: 3 Copynumber: 84.0 Consensus size: 3
20709914 CTACTACTAC
20709924 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
20709972 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
20710020 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
20710068 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
20710116 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
20710164 TAA TAA TTAA TAA
1 TAA TAA -TAA TAA
20710177 AAAATAGCAA
Statistics
Matches: 249, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
3 246 0.99
4 3 0.01
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:20711538 original size:18 final size:17
Alignment explanation
Indices: 20711521--20711554 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
20711511 CATTTATTTA
*
20711521 ATTCGACTTAATTTTTT
1 ATTCGAATTAATTTTTT
*
20711538 ATTTGAATTAATTTTTT
1 ATTCGAATTAATTTTTT
20711555 TAATATTTCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.62
Consensus pattern (17 bp):
ATTCGAATTAATTTTTT
Found at i:20714849 original size:20 final size:21
Alignment explanation
Indices: 20714811--20714849 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
20714801 GATGTCATAC
20714811 AAATTAAAAAATATCATTTAA
1 AAATTAAAAAATATCATTTAA
*
20714832 AAATTAAAATATAT-ATTT
1 AAATTAAAAAATATCATTT
20714850 TTTGTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (21 bp):
AAATTAAAAAATATCATTTAA
Found at i:20715540 original size:30 final size:31
Alignment explanation
Indices: 20715501--20715560 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
20715491 GGAGGTGAGA
*
20715501 TGGGAAGGGAATAAAAGTTTTAGGG-GAAAAG
1 TGGGAAGGGAATAAAAATTTT-GGGAGAAAAG
*
20715532 TGGG-AGGGAGTAAAAATTTTGGGAGAAAA
1 TGGGAAGGGAATAAAAATTTTGGGAGAAAA
20715561 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 3 0.12
30 19 0.73
31 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTGGGAGAAAAG
Found at i:20723792 original size:27 final size:27
Alignment explanation
Indices: 20723754--20723805 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
20723744 TCTTATGTTA
20723754 GCTTCTAATTCTAGTTCCAAAGAACAG
1 GCTTCTAATTCTAGTTCCAAAGAACAG
20723781 GCTTCTAATTCTAGTTCCAAAGAAC
1 GCTTCTAATTCTAGTTCCAAAGAAC
20723806 CATTTTTCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31
Consensus pattern (27 bp):
GCTTCTAATTCTAGTTCCAAAGAACAG
Found at i:20727443 original size:41 final size:40
Alignment explanation
Indices: 20727398--20727482 Score: 91
Period size: 40 Copynumber: 2.1 Consensus size: 40
20727388 GGCCGACCCG
20727398 AATATATAATAAATATA-TATTTTTAATTTTTTAATTTTCAA
1 AATAT-TAATAAA-ATACTATTTTTAATTTTTTAATTTTCAA
** * * * *
20727439 AATATTTTTAAAATACTTTTTTTTATTTTTTTATTTTTAA
1 AATATTAATAAAATACTATTTTTAATTTTTTAATTTTCAA
20727479 AATA
1 AATA
20727483 ATTTTTTGGT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
39 3 0.08
40 29 0.78
41 5 0.14
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (40 bp):
AATATTAATAAAATACTATTTTTAATTTTTTAATTTTCAA
Found at i:20729776 original size:47 final size:47
Alignment explanation
Indices: 20729707--20729846 Score: 217
Period size: 47 Copynumber: 2.9 Consensus size: 47
20729697 TGCTTACTCC
20729707 TACTTGACGTGGTGATAAGTTTTTGTTGTAAAATGTCAAGGGGAGAT
1 TACTTGACGTGGTGATAAGTTTTTGTTGTAAAATGTCAAGGGGAGAT
* * *
20729754 TACTTGAAGTGGTGATGAGTTTTTGTTGTAAAATGTCAAAGGGAGAT
1 TACTTGACGTGGTGATAAGTTTTTGTTGTAAAATGTCAAGGGGAGAT
* *
20729801 TACTTGACGTGGTGATAAGTTTTTGTTCTATAAAATGTGAAGGGGA
1 TACTTGACGTGGTGATAAGTTTTTG-T-TGTAAAATGTCAAGGGGA
20729847 TCAGAAAGTT
Statistics
Matches: 83, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
47 67 0.81
48 1 0.01
49 15 0.18
ACGTcount: A:0.29, C:0.06, G:0.29, T:0.36
Consensus pattern (47 bp):
TACTTGACGTGGTGATAAGTTTTTGTTGTAAAATGTCAAGGGGAGAT
Found at i:20751658 original size:18 final size:18
Alignment explanation
Indices: 20751624--20751659 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
20751614 AATTTTTAAA
*
20751624 TTTGAATAACTCAAATAT
1 TTTGAATAAATCAAATAT
*
20751642 TTTGAATAAATCGAATAT
1 TTTGAATAAATCAAATAT
20751660 AAACCATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.39
Consensus pattern (18 bp):
TTTGAATAAATCAAATAT
Found at i:20752191 original size:2 final size:2
Alignment explanation
Indices: 20752184--20752218 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
20752174 ACATGGAGCA
20752184 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20752219 AGATAATTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20756775 original size:16 final size:16
Alignment explanation
Indices: 20756751--20756781 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20756741 AATTATTCGA
*
20756751 ATTTTTTTATTAAATC
1 ATTTGTTTATTAAATC
20756767 ATTTGTTTATTAAAT
1 ATTTGTTTATTAAAT
20756782 TTTTCTTAAA
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:0.32, C:0.03, G:0.03, T:0.61
Consensus pattern (16 bp):
ATTTGTTTATTAAATC
Found at i:20757657 original size:21 final size:21
Alignment explanation
Indices: 20757631--20757681 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
20757621 AATAAAATAC
* * *
20757631 TTTAAAATTTTTTTTATTTTT
1 TTTAAAAATTTTTTAATGTTT
20757652 TTTAAATAATTTTTTAATGTTT
1 TTTAAA-AATTTTTTAATGTTT
*
20757674 ATTAAAAA
1 TTTAAAAA
20757682 ATGGGTCGGG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 8 0.32
22 17 0.68
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
TTTAAAAATTTTTTAATGTTT
Found at i:20758026 original size:24 final size:23
Alignment explanation
Indices: 20757999--20758046 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
20757989 TCAATCAGGG
*
20757999 TTTTA-AATATTAATGGGTATTAAA
1 TTTTATAAT-TTAATGGAT-TTAAA
20758023 TTTTATAATTTAATGGATTTAAA
1 TTTTATAATTTAATGGATTTAAA
20758046 T
1 T
20758047 AGGGCGAGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 6 0.27
24 13 0.59
25 3 0.14
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (23 bp):
TTTTATAATTTAATGGATTTAAA
Found at i:20767282 original size:15 final size:15
Alignment explanation
Indices: 20767262--20767292 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
20767252 CCAACCTTCA
20767262 AATTTTACCTCAATT
1 AATTTTACCTCAATT
20767277 AATTTTACCTCAATT
1 AATTTTACCTCAATT
20767292 A
1 A
20767293 TACATAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.19, G:0.00, T:0.45
Consensus pattern (15 bp):
AATTTTACCTCAATT
Found at i:20770688 original size:18 final size:17
Alignment explanation
Indices: 20770660--20770694 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
20770650 ATTTTTAAGA
*
20770660 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
20770677 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
20770695 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:20770948 original size:16 final size:16
Alignment explanation
Indices: 20770927--20770965 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
20770917 TTGATTTGCT
*
20770927 ATTACACAGCTTTTCC
1 ATTACACAGCTATTCC
**
20770943 ATTACACCTCTATTCC
1 ATTACACAGCTATTCC
20770959 ATTACAC
1 ATTACAC
20770966 CTCTAATCCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.33, G:0.03, T:0.36
Consensus pattern (16 bp):
ATTACACAGCTATTCC
Found at i:20770966 original size:16 final size:16
Alignment explanation
Indices: 20770940--20770996 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
20770930 ACACAGCTTT
* *
20770940 TCCATTACACCTCTAT
1 TCCAATACACCTCTAA
*
20770956 TCCATTACACCTCTAA
1 TCCAATACACCTCTAA
20770972 TCCAATACACCTCTAA
1 TCCAATACACCTCTAA
20770988 TCCAATACA
1 TCCAATACA
20770997 GCGAACCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (16 bp):
TCCAATACACCTCTAA
Found at i:20772436 original size:32 final size:30
Alignment explanation
Indices: 20772378--20772437 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
20772368 AACATATTAT
* * *
20772378 TATATATATACATACATATACTAAAAATGC
1 TATATATATACATAAAAATACCAAAAATGC
20772408 TATATATATACATATAAAAATACCAAAAAT
1 TATATATATAC--ATAAAAATACCAAAAAT
20772438 ATTTTCATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 11 0.44
32 14 0.56
ACGTcount: A:0.55, C:0.12, G:0.02, T:0.32
Consensus pattern (30 bp):
TATATATATACATAAAAATACCAAAAATGC
Found at i:20772634 original size:27 final size:28
Alignment explanation
Indices: 20772576--20772634 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 28
20772566 ATGAACCAAT
**
20772576 AATAATATCAATTTTGAAAATAAAATAC
1 AATAATAGAAATTTTGAAAATAAAATAC
* *
20772604 -ATAATAGAAATTTTG-AAATAATATTC
1 AATAATAGAAATTTTGAAAATAAAATAC
20772630 AATAA
1 AATAA
20772635 ATTTAAAGCA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
26 9 0.35
27 17 0.65
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.34
Consensus pattern (28 bp):
AATAATAGAAATTTTGAAAATAAAATAC
Found at i:20773738 original size:131 final size:131
Alignment explanation
Indices: 20773504--20773765 Score: 506
Period size: 131 Copynumber: 2.0 Consensus size: 131
20773494 CTACTCATTT
20773504 GTTCGTCTCTTACAGGTACGGTGTGCAGAGGTACGGACGTGGCACGTACGGAGGTGAAGGCGCAC
1 GTTCGTCTCTTACAGGTACGGTGTGCAGAGGTACGGACGTGGCACGTACGGAGGTGAAGGCGCAC
20773569 GCGTACGAGGGCTCGTCACGCGCAGAGGGAGAGCGAGGGGACATCACTACTGCGGTGCTGGGAAC
66 GCGTACGAGGGCTCGTCACGCGCAGAGGGAGAGCGAGGGGACATCACTACTGCGGTGCTGGGAAC
20773634 C
131 C
*
20773635 GTTCGTCTCTTACAGGTACGGTGTGCAGAGGTGCGGACGTGGCACGTACGGAGGTGAAGGCGCAC
1 GTTCGTCTCTTACAGGTACGGTGTGCAGAGGTACGGACGTGGCACGTACGGAGGTGAAGGCGCAC
*
20773700 GCGTACGAGGGCTCGTCACGCGCAGAGGGAGAGCGAGGGGACGTCACTACTGCGGTGCTGGGAAC
66 GCGTACGAGGGCTCGTCACGCGCAGAGGGAGAGCGAGGGGACATCACTACTGCGGTGCTGGGAAC
20773765 C
131 C
20773766 CTTGCTGCTA
Statistics
Matches: 129, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
131 129 1.00
ACGTcount: A:0.20, C:0.24, G:0.40, T:0.16
Consensus pattern (131 bp):
GTTCGTCTCTTACAGGTACGGTGTGCAGAGGTACGGACGTGGCACGTACGGAGGTGAAGGCGCAC
GCGTACGAGGGCTCGTCACGCGCAGAGGGAGAGCGAGGGGACATCACTACTGCGGTGCTGGGAAC
C
Found at i:20774126 original size:3 final size:3
Alignment explanation
Indices: 20774118--20774152 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
20774108 TATGAAAATA
20774118 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
20774153 AAGGTTGAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:20781487 original size:72 final size:72
Alignment explanation
Indices: 20781401--20781599 Score: 398
Period size: 72 Copynumber: 2.8 Consensus size: 72
20781391 TAAGTAATTA
20781401 ATATAAATATTTATATAACTAATGGTGCATGAAATATTTTAAAATTTTAAAATATTTCATGCACC
1 ATATAAATATTTATATAACTAATGGTGCATGAAATATTTTAAAATTTTAAAATATTTCATGCACC
20781466 ATTAGTT
66 ATTAGTT
20781473 ATATAAATATTTATATAACTAATGGTGCATGAAATATTTTAAAATTTTAAAATATTTCATGCACC
1 ATATAAATATTTATATAACTAATGGTGCATGAAATATTTTAAAATTTTAAAATATTTCATGCACC
20781538 ATTAGTT
66 ATTAGTT
20781545 ATATAAATATTTATATAACTAATGGTGCATGAAATATTTTAAAATTTTAAAATAT
1 ATATAAATATTTATATAACTAATGGTGCATGAAATATTTTAAAATTTTAAAATAT
20781600 AATGATAAAT
Statistics
Matches: 127, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 127 1.00
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.42
Consensus pattern (72 bp):
ATATAAATATTTATATAACTAATGGTGCATGAAATATTTTAAAATTTTAAAATATTTCATGCACC
ATTAGTT
Found at i:20781628 original size:21 final size:22
Alignment explanation
Indices: 20781604--20781649 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
20781594 AAATATAATG
*
20781604 ATAAATT-ATTAT-TTTAATATA
1 ATAAATTAATAATATTTAA-ATA
20781625 AT-AATTAATAATATTTAAATA
1 ATAAATTAATAATATTTAAATA
20781646 ATAA
1 ATAA
20781650 TAAATGTTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
20 4 0.19
21 11 0.52
22 6 0.29
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
ATAAATTAATAATATTTAAATA
Found at i:20785134 original size:18 final size:19
Alignment explanation
Indices: 20785096--20785135 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
20785086 TACAAAAATG
*
20785096 AAATTTAAAATAATTTTTA
1 AAATTTAAAATAATTTATA
20785115 AAATTTAAAAT-ATTTATA
1 AAATTTAAAATAATTTATA
20785133 AAA
1 AAA
20785136 ACTCCAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATTTAAAATAATTTATA
Found at i:20785550 original size:20 final size:21
Alignment explanation
Indices: 20785510--20785550 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
20785500 AAAAAGAAAT
* *
20785510 ACACCAAAAAATGGCTGAAAG
1 ACACCAAAAAATGACTAAAAG
20785531 ACACCAAAAAAT-ACTAAAAG
1 ACACCAAAAAATGACTAAAAG
20785551 TACAAAGTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.59, C:0.20, G:0.12, T:0.10
Consensus pattern (21 bp):
ACACCAAAAAATGACTAAAAG
Found at i:20786245 original size:8 final size:8
Alignment explanation
Indices: 20786232--20786256 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
20786222 AGAAGCATAG
20786232 TATGGGTT
1 TATGGGTT
20786240 TATGGGTT
1 TATGGGTT
20786248 TATGGGTT
1 TATGGGTT
20786256 T
1 T
20786257 TGGTTATAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.36, T:0.52
Consensus pattern (8 bp):
TATGGGTT
Found at i:20792038 original size:18 final size:18
Alignment explanation
Indices: 20792005--20792048 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
20791995 TTTTTATGTG
* * *
20792005 TGTTTATTTTTGTTTTTA
1 TGTTTATGTTTATTTTAA
20792023 TGTTTATGTTTATTTTAA
1 TGTTTATGTTTATTTTAA
*
20792041 TTTTTATG
1 TGTTTATG
20792049 CATTTTTCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.16, C:0.00, G:0.11, T:0.73
Consensus pattern (18 bp):
TGTTTATGTTTATTTTAA
Found at i:20799117 original size:58 final size:58
Alignment explanation
Indices: 20798974--20799120 Score: 179
Period size: 58 Copynumber: 2.6 Consensus size: 58
20798964 GAAACAAATT
* * * *
20798974 ACATCCCTCC-AAACACACCAGAGAGCACTGAAGTGCTAAAATTGAAAACAATAGATC
1 ACATCCCTCCAAAACACACCAAAAAGCACTAAAGTGATAAAATTGAAAACAATAGATC
* * *** * * *
20799031 AAATCCCTCCAAAAAACATTGAATAGCACTAAAGTGATAAACTTGAAGACAATAGATC
1 ACATCCCTCCAAAACACACCAAAAAGCACTAAAGTGATAAAATTGAAAACAATAGATC
20799089 ACATCCCTCCAAAACACACCAAAAAGCACTAA
1 ACATCCCTCCAAAACACACCAAAAAGCACTAA
20799121 GGTGCTAAGC
Statistics
Matches: 72, Mismatches: 17, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
57 9 0.12
58 63 0.88
ACGTcount: A:0.47, C:0.26, G:0.11, T:0.16
Consensus pattern (58 bp):
ACATCCCTCCAAAACACACCAAAAAGCACTAAAGTGATAAAATTGAAAACAATAGATC
Found at i:20802324 original size:21 final size:20
Alignment explanation
Indices: 20802289--20802328 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
20802279 ACCAGTTATA
20802289 AAAGTCCTTAAACAATCCATT
1 AAAGTCCTTAAACAA-CCATT
**
20802310 AAAGTCCTTTTACAACCAT
1 AAAGTCCTTAAACAACCAT
20802329 CAACAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.40, C:0.25, G:0.05, T:0.30
Consensus pattern (20 bp):
AAAGTCCTTAAACAACCATT
Found at i:20815492 original size:3 final size:3
Alignment explanation
Indices: 20815484--20815523 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
20815474 ATATGTAAGG
* *
20815484 ATA ATA ATA ACA ATA ATA ATA ATA ATA ATA ATA GTA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
20815524 AGTCATAGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:20818507 original size:48 final size:48
Alignment explanation
Indices: 20818449--20818544 Score: 165
Period size: 48 Copynumber: 2.0 Consensus size: 48
20818439 GCGCTTCCAT
* *
20818449 AAGCGCCGCAAAAAATGCCACTAACGAAAACGTCGCAAACTTTTGCAG
1 AAGCGCCGCAAAAAATACCACTAACAAAAACGTCGCAAACTTTTGCAG
*
20818497 AAGCGCCGCAAAAAATACCGCTAACAAAAACGTCGCAAACTTTTGCAG
1 AAGCGCCGCAAAAAATACCACTAACAAAAACGTCGCAAACTTTTGCAG
20818545 CGTTTACAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.41, C:0.27, G:0.18, T:0.15
Consensus pattern (48 bp):
AAGCGCCGCAAAAAATACCACTAACAAAAACGTCGCAAACTTTTGCAG
Found at i:20818613 original size:42 final size:42
Alignment explanation
Indices: 20818556--20818846 Score: 501
Period size: 42 Copynumber: 6.9 Consensus size: 42
20818546 GTTTACAAAC
*
20818556 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
*
20818598 AAAAACGCCGCTAAAGATCATGTTCTTTCGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
*
20818640 AAAAACGCCGCTAAAGATCATGTTCTTTCGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
*
20818682 AAAAACGCCGCTAAAGATCATGTTCTTTCGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
*
20818724 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
* *
20818766 GAAAAACGCCACTAAAGATCATGTTCTTTAGCGGTGCTTAGAA
1 -AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
*
20818809 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTT
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT
20818847 TTATACAAAA
Statistics
Matches: 238, Mismatches: 10, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
42 199 0.84
43 39 0.16
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.23
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
Found at i:20819214 original size:21 final size:21
Alignment explanation
Indices: 20819190--20819236 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
20819180 TTGCAGCTTT
20819190 TGCTTCCCTCGCTGCAGCCGC
1 TGCTTCCCTCGCTGCAGCCGC
* *
20819211 TGCTTCCCTCGCTGCCGCCTC
1 TGCTTCCCTCGCTGCAGCCGC
20819232 TGCTT
1 TGCTT
20819237 TAAGTTGTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.02, C:0.47, G:0.21, T:0.30
Consensus pattern (21 bp):
TGCTTCCCTCGCTGCAGCCGC
Found at i:20826283 original size:24 final size:24
Alignment explanation
Indices: 20826256--20826336 Score: 92
Period size: 24 Copynumber: 3.2 Consensus size: 24
20826246 TGTATCATTC
20826256 ATTTAAATAATTAATTACCTATCT
1 ATTTAAATAATTAATTACCTATCT
*
20826280 ATTTAAACAATTAATTACCTA-CAAATT
1 ATTTAAATAATTAATTACCTATC----T
*
20826307 AATTTAAATAATTAATTACCTATTT
1 -ATTTAAATAATTAATTACCTATCT
20826332 ATTTA
1 ATTTA
20826337 TTTGTTTATT
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
23 1 0.02
24 25 0.52
25 1 0.02
27 1 0.02
28 20 0.42
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (24 bp):
ATTTAAATAATTAATTACCTATCT
Found at i:20826339 original size:28 final size:26
Alignment explanation
Indices: 20826256--20826339 Score: 82
Period size: 28 Copynumber: 3.2 Consensus size: 26
20826246 TGTATCATTC
*
20826256 ATTTAAATAATTAATTACC--TATCT
1 ATTTAAATAATTAATTACCTATATTT
* * *
20826280 ATTTAAACAATTAATTACCTACAAATTA
1 ATTTAAATAATTAATTACCT--ATATTT
20826308 ATTTAAATAATTAATTACCTATTTATTT
1 ATTTAAATAATTAATTACCTA--TATTT
20826336 ATTT
1 ATTT
20826340 GTTTATTTAT
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
24 18 0.38
26 1 0.02
28 28 0.60
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (26 bp):
ATTTAAATAATTAATTACCTATATTT
Found at i:20826744 original size:29 final size:29
Alignment explanation
Indices: 20826706--20826769 Score: 119
Period size: 29 Copynumber: 2.2 Consensus size: 29
20826696 ATGACCGTTG
20826706 AAACCCTAAACCCCAAATCCATTACCCCT
1 AAACCCTAAACCCCAAATCCATTACCCCT
*
20826735 AAACCTTAAACCCCAAATCCATTACCCCT
1 AAACCCTAAACCCCAAATCCATTACCCCT
20826764 AAACCC
1 AAACCC
20826770 GATCTTGAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.39, C:0.44, G:0.00, T:0.17
Consensus pattern (29 bp):
AAACCCTAAACCCCAAATCCATTACCCCT
Found at i:20826909 original size:7 final size:7
Alignment explanation
Indices: 20826899--20826936 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
20826889 CTCTTAACAT
20826899 CTAACCC
1 CTAACCC
20826906 CTAA--C
1 CTAACCC
20826911 CTAACCC
1 CTAACCC
20826918 CTAACCC
1 CTAACCC
20826925 CTAACCC
1 CTAACCC
*
20826932 TTAAC
1 CTAAC
20826937 ATAAACCTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
5 5 0.18
7 23 0.82
ACGTcount: A:0.32, C:0.50, G:0.00, T:0.18
Consensus pattern (7 bp):
CTAACCC
Found at i:20826910 original size:14 final size:14
Alignment explanation
Indices: 20826893--20826938 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
20826883 CCCTAACTCT
20826893 TAACATCTAACCCC
1 TAACATCTAACCCC
20826907 TAAC--CTAACCCC
1 TAACATCTAACCCC
** *
20826919 TAACCCCTAACCCT
1 TAACATCTAACCCC
20826933 TAACAT
1 TAACAT
20826939 AAACCTTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 12 0.44
14 15 0.56
ACGTcount: A:0.35, C:0.43, G:0.00, T:0.22
Consensus pattern (14 bp):
TAACATCTAACCCC
Found at i:20826916 original size:12 final size:12
Alignment explanation
Indices: 20826899--20826923 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20826889 CTCTTAACAT
20826899 CTAACCCCTAAC
1 CTAACCCCTAAC
20826911 CTAACCCCTAAC
1 CTAACCCCTAAC
20826923 C
1 C
20826924 CCTAACCCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.52, G:0.00, T:0.16
Consensus pattern (12 bp):
CTAACCCCTAAC
Found at i:20826922 original size:26 final size:26
Alignment explanation
Indices: 20826884--20826936 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
20826874 ACCCTAAATC
* * *
20826884 CCTAACTCTTAACATCTAACCCCTAA
1 CCTAACCCCTAACACCTAACCCCTAA
* *
20826910 CCTAACCCCTAACCCCTAACCCTTAA
1 CCTAACCCCTAACACCTAACCCCTAA
20826936 C
1 C
20826937 ATAAACCTTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.32, C:0.45, G:0.00, T:0.23
Consensus pattern (26 bp):
CCTAACCCCTAACACCTAACCCCTAA
Found at i:20826995 original size:14 final size:14
Alignment explanation
Indices: 20826961--20827004 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
20826951 TCACATTAAC
* *
20826961 CCTTAAACCAGAAT
1 CCTTAATCCATAAT
*
20826975 CCCTAATCCATAAT
1 CCTTAATCCATAAT
20826989 CCTTAATTCCATAAT
1 CCTTAA-TCCATAAT
20827004 C
1 C
20827005 TATAAAACTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
14 16 0.64
15 9 0.36
ACGTcount: A:0.36, C:0.32, G:0.02, T:0.30
Consensus pattern (14 bp):
CCTTAATCCATAAT
Found at i:20827085 original size:22 final size:21
Alignment explanation
Indices: 20827038--20827143 Score: 54
Period size: 21 Copynumber: 5.0 Consensus size: 21
20827028 CCCCCAGCCT
* *
20827038 TTAAACCATAAACTATAACCC
1 TTAAACCATAAACCATAAACC
* *
20827059 CTAAACCCATAATCCATAAACC
1 TTAAA-CCATAAACCATAAACC
*** *
20827081 TTAAAATGGTAACACC-TAAACT
1 TT-AAACCATAA-ACCATAAACC
*
20827103 TTAAACTC-TAAACCATATACC
1 TTAAAC-CATAAACCATAAACC
* * *
20827124 CTAAACCAAAAACCCTAAAC
1 TTAAACCATAAACCATAAAC
20827144 TATAGTGATA
Statistics
Matches: 61, Mismatches: 18, Indels: 12
0.67 0.20 0.13
Matches are distributed among these distances:
20 4 0.07
21 28 0.46
22 24 0.39
23 5 0.08
ACGTcount: A:0.47, C:0.29, G:0.02, T:0.22
Consensus pattern (21 bp):
TTAAACCATAAACCATAAACC
Found at i:20827127 original size:14 final size:14
Alignment explanation
Indices: 20827105--20827143 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
20827095 CCTAAACTTT
* *
20827105 AAACTCTAAACCAT
1 AAACCCTAAACCAA
*
20827119 ATACCCTAAACCAA
1 AAACCCTAAACCAA
20827133 AAACCCTAAAC
1 AAACCCTAAAC
20827144 TATAGTGATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.51, C:0.33, G:0.00, T:0.15
Consensus pattern (14 bp):
AAACCCTAAACCAA
Found at i:20827883 original size:114 final size:113
Alignment explanation
Indices: 20827597--20827922 Score: 342
Period size: 113 Copynumber: 2.9 Consensus size: 113
20827587 ATTACTGAGC
* *
20827597 ATTAGCGGCGCTT-TACAAAAAACGCCACTAAAT-CCCGAAAGCTCAGAAAACGGCGTCGTTGTG
1 ATTAGCGGCGCTTCTA-AAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGG
* * * *
20827660 CTTAGGTTATTTGTGGCGCTTTATCTAAAACGCCGCTAAATCTCTGGAT
65 CTCAGGTTATTTGTGGCACTTTATCTAAAACGCCGCGAAAGCTCTGGAT
** * *
20827709 ATTAGCGGCGCTTACTTGAAAAACGCCGCTAAATCCACGAAAGCTC-GAAAACGGCATCGTTGGG
1 ATTAGCGGCGCTT-CTAAAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGG
* * *
20827773 CTCAGTTTTTTTTTGTGGCAC-TTAGT-TGAAAACGCCGCGAAAGC-CTGGGT
65 CTCAG--GTTATTTGTGGCACTTTA-TCT-AAAACGCCGCGAAAGCTCTGGAT
* * * *
20827823 ATTAGCGTCGCTTCTAAAAAAACGCCGCTAATTCCCCGAAAGCTCAGAAAATGGCGTCGTTGGGA
1 ATTAGCGGCGCTTCTAAAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGC
* * * * *
20827888 TTAGGTGT-TTTGCGGCGCTTTCTCGAAAACGCCGC
66 TCAGGT-TATTTGTGGCACTTTATCTAAAACGCCGC
20827923 TAATGCTTAT
Statistics
Matches: 176, Mismatches: 27, Indels: 22
0.78 0.12 0.10
Matches are distributed among these distances:
112 33 0.19
113 66 0.38
114 51 0.29
115 26 0.15
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.26
Consensus pattern (113 bp):
ATTAGCGGCGCTTCTAAAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGC
TCAGGTTATTTGTGGCACTTTATCTAAAACGCCGCGAAAGCTCTGGAT
Found at i:20829701 original size:45 final size:44
Alignment explanation
Indices: 20829615--20829702 Score: 115
Period size: 45 Copynumber: 2.0 Consensus size: 44
20829605 AAATCTGTTC
* * *
20829615 CATTCAACCAAACACAATAATATTATTACAGTTCTATTCCATTG
1 CATTCAACCAAACACAATAATATGATTACAATTCTAGTCCATTG
*
20829659 CATTCAACCAAACA-ATTAATCACTGATTACAATTCTAGTCCATT
1 CATTCAACCAAACACAATAAT-A-TGATTACAATTCTAGTCCATT
20829703 ACAGTTTTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
43 5 0.13
44 15 0.39
45 18 0.47
ACGTcount: A:0.39, C:0.24, G:0.05, T:0.33
Consensus pattern (44 bp):
CATTCAACCAAACACAATAATATGATTACAATTCTAGTCCATTG
Found at i:20832208 original size:79 final size:81
Alignment explanation
Indices: 20832086--20832249 Score: 199
Period size: 82 Copynumber: 2.0 Consensus size: 81
20832076 AAAAATTCTG
** * *
20832086 ACACACACCCAAAGTTTCAAACCAACATAACAAAGCCAGAACTTC-TTTTCATCTCCCTTAACCA
1 ACACACACCCAAAGTTTCAAACCAACATAACAAAAACAAAACTTCTTTTTCATCTCCCTCAACCA
20832150 TTCTG-TCACTTTTATC
66 TTC-GATCACTTTTATC
* ** * *
20832166 ACACACACCCAAAG-TTCAAACCCATGTCACAAAAACAAAACTTCTTTTTTTCATCTCTCTCAAC
1 ACACACACCCAAAGTTTCAAACCAACATAACAAAAACAAAACTTC--TTTTTCATCTCCCTCAAC
20832230 CATTCGATCACTTTTATC
64 CATTCGATCACTTTTATC
20832248 AC
1 AC
20832250 TTGAAAATTT
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
79 23 0.32
80 14 0.20
81 1 0.01
82 33 0.46
ACGTcount: A:0.34, C:0.32, G:0.04, T:0.29
Consensus pattern (81 bp):
ACACACACCCAAAGTTTCAAACCAACATAACAAAAACAAAACTTCTTTTTCATCTCCCTCAACCA
TTCGATCACTTTTATC
Found at i:20832600 original size:9 final size:9
Alignment explanation
Indices: 20832586--20832617 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
20832576 AAATTTAAAT
20832586 TTCGAGTTA
1 TTCGAGTTA
20832595 TTCGAGTTA
1 TTCGAGTTA
*
20832604 ATCGAGTTA
1 TTCGAGTTA
20832613 TTCGA
1 TTCGA
20832618 ATCAACTCGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.25, C:0.12, G:0.22, T:0.41
Consensus pattern (9 bp):
TTCGAGTTA
Found at i:20832935 original size:30 final size:31
Alignment explanation
Indices: 20832901--20832960 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
20832891 AAACCTTTTA
*
20832901 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAAATTTTACTCCCTTCCCAC
* *
20832931 TTTTCCCCTAAAAATTTTATTCCCTTCCCA
1 TTTTCCCCCAAAAATTTTACTCCCTTCCCA
20832961 TCCCACCTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.22, C:0.38, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAAATTTTACTCCCTTCCCAC
Found at i:20833096 original size:19 final size:19
Alignment explanation
Indices: 20833052--20833107 Score: 55
Period size: 20 Copynumber: 3.0 Consensus size: 19
20833042 ACTTTTCCTC
*
20833052 AAACTTTTA--TT-CCCCA
1 AAACTTTTATTTTCCCCCT
20833068 AAACTTTTTATTTTCCCCCT
1 AAAC-TTTTATTTTCCCCCT
*
20833088 AAACTTTTACTTTTCACCCT
1 AAACTTTTA-TTTTCCCCCT
20833108 TTACTCTCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
16 4 0.12
17 5 0.15
19 7 0.21
20 17 0.52
ACGTcount: A:0.25, C:0.30, G:0.00, T:0.45
Consensus pattern (19 bp):
AAACTTTTATTTTCCCCCT
Found at i:20838102 original size:8 final size:8
Alignment explanation
Indices: 20838089--20838119 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
20838079 CCCAAATTAT
20838089 TTTTTTTC
1 TTTTTTTC
*
20838097 TTTTTTTG
1 TTTTTTTC
20838105 TTTTTTTC
1 TTTTTTTC
20838113 TTTTTTT
1 TTTTTTT
20838120 TTTATGCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.00, C:0.06, G:0.03, T:0.90
Consensus pattern (8 bp):
TTTTTTTC
Found at i:20838110 original size:16 final size:16
Alignment explanation
Indices: 20838089--20838119 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
20838079 CCCAAATTAT
20838089 TTTTTTTCTTTTTTTG
1 TTTTTTTCTTTTTTTG
20838105 TTTTTTTCTTTTTTT
1 TTTTTTTCTTTTTTT
20838120 TTTATGCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.06, G:0.03, T:0.90
Consensus pattern (16 bp):
TTTTTTTCTTTTTTTG
Found at i:20843592 original size:20 final size:20
Alignment explanation
Indices: 20843567--20843609 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
20843557 AGGGGTAAAT
20843567 AATTGAAATGAGAAAATTTG
1 AATTGAAATGAGAAAATTTG
20843587 AATTGAAATGAGAAAATTTG
1 AATTGAAATGAGAAAATTTG
20843607 AAT
1 AAT
20843610 AAGTGTGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.51, C:0.00, G:0.19, T:0.30
Consensus pattern (20 bp):
AATTGAAATGAGAAAATTTG
Found at i:20849199 original size:31 final size:30
Alignment explanation
Indices: 20849164--20849224 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
20849154 AAAACAGAAA
*
20849164 ATTTTA-ATGAAAGTGACTAATTTAAATAATT
1 ATTTTATATG-AAGTGACTAAATT-AATAATT
*
20849195 ATTTTATTTGAAGTGACTAAATTAATAATT
1 ATTTTATATGAAGTGACTAAATTAATAATT
20849225 TCTTTTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 7 0.26
31 18 0.67
32 2 0.07
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (30 bp):
ATTTTATATGAAGTGACTAAATTAATAATT
Found at i:20851536 original size:110 final size:110
Alignment explanation
Indices: 20851339--20851540 Score: 325
Period size: 110 Copynumber: 1.8 Consensus size: 110
20851329 AATTAAGTTA
** *
20851339 TTACAGGAAGATAGGTAAATTTACCTTTTGGTGTCATGGCAGTTTGTTTTGTGAATGCCAACTGG
1 TTACAGGAAGATAGGTAAATTTACCTTTTGGTGTCATACCAGTTTGTGTTGTGAATGCCAACTGG
*
20851404 GCTGGCTTGAGGGTTTTGAGAGGCTTATTTTAGCTGCGACTTGAG
66 GCTGGCTTGAGGGATTTGAGAGGCTTATTTTAGCTGCGACTTGAG
* *
20851449 TTACAGGAAGATAGGTAAATTTACCTTTTTGTGTCATACCAGTTTGTGTTGTGAATGCCGACTGG
1 TTACAGGAAGATAGGTAAATTTACCTTTTGGTGTCATACCAGTTTGTGTTGTGAATGCCAACTGG
*
20851514 GTTGGCTTGA-GGATTTGAAGAGGCTTA
66 GCTGGCTTGAGGGATTTG-AGAGGCTTA
20851541 CTTAAGAAAA
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
109 6 0.07
110 78 0.93
ACGTcount: A:0.22, C:0.12, G:0.29, T:0.36
Consensus pattern (110 bp):
TTACAGGAAGATAGGTAAATTTACCTTTTGGTGTCATACCAGTTTGTGTTGTGAATGCCAACTGG
GCTGGCTTGAGGGATTTGAGAGGCTTATTTTAGCTGCGACTTGAG
Found at i:20857669 original size:25 final size:24
Alignment explanation
Indices: 20857641--20857700 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 24
20857631 CTGTAAGGTT
*
20857641 AAAAATAGTGTTAAGACATTCATACA
1 AAAAATA-T-TTAAGACATTCAGACA
20857667 AAATAATATTTAAGACATTCAGACA
1 AAA-AATATTTAAGACATTCAGACA
20857692 AAAATATAT
1 AAAA-ATAT
20857701 CAATAATTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
24 1 0.03
25 22 0.71
26 4 0.13
27 4 0.13
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (24 bp):
AAAAATATTTAAGACATTCAGACA
Found at i:20858978 original size:21 final size:21
Alignment explanation
Indices: 20858954--20859015 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
20858944 TTGTCCAGCT
* *
20858954 TCCGGCGGGGCTTGTGGTTGC
1 TCCGGCGGGGATTCTGGTTGC
20858975 TCCGGCGGGGATTCTGGTT-C
1 TCCGGCGGGGATTCTGGTTGC
*
20858995 ATCCGGTAGGGGA-TCTGGTTG
1 -TCCGG-CGGGGATTCTGGTTG
20859016 TCAGTGTTGG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 1 0.03
21 29 0.83
22 5 0.14
ACGTcount: A:0.06, C:0.21, G:0.44, T:0.29
Consensus pattern (21 bp):
TCCGGCGGGGATTCTGGTTGC
Found at i:20859282 original size:18 final size:18
Alignment explanation
Indices: 20859256--20859298 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
20859246 GACTAGAAAA
* * *
20859256 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGCT
20859274 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
20859292 AGGATAC
1 AGGATAC
20859299 GCACCTGGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.28, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:20862918 original size:11 final size:11
Alignment explanation
Indices: 20862904--20863001 Score: 62
Period size: 11 Copynumber: 9.3 Consensus size: 11
20862894 GAGAAATTTA
20862904 AGAGGAAATTG
1 AGAGGAAATTG
*
20862915 AGAGCAAATTG
1 AGAGGAAATTG
**
20862926 AGATTAAA-T-
1 AGAGGAAATTG
* *
20862935 A-TGG-ATTTG
1 AGAGGAAATTG
*
20862944 AGA-GAAATTT
1 AGAGGAAATTG
20862954 AGAAGGAAATTG
1 AG-AGGAAATTG
* *
20862966 AGAGCAATTTG
1 AGAGGAAATTG
*
20862977 AGAAGAAATTG
1 AGAGGAAATTG
*
20862988 AGAGAAAATTG
1 AGAGGAAATTG
20862999 AGA
1 AGA
20863002 AAATAATTGA
Statistics
Matches: 63, Mismatches: 18, Indels: 12
0.68 0.19 0.13
Matches are distributed among these distances:
7 1 0.02
8 1 0.02
9 3 0.05
10 6 0.10
11 44 0.70
12 8 0.13
ACGTcount: A:0.47, C:0.02, G:0.28, T:0.23
Consensus pattern (11 bp):
AGAGGAAATTG
Found at i:20862935 original size:51 final size:51
Alignment explanation
Indices: 20862880--20862979 Score: 157
Period size: 51 Copynumber: 2.0 Consensus size: 51
20862870 AATTAACTAA
20862880 AAATAAGGATTTAAGAGAAATTTA-AGAGGAAATTGAGAGCAAATTGAGATT
1 AAATAAGGATTTAAGAGAAATTTAGA-AGGAAATTGAGAGCAAATTGAGATT
* * *
20862931 AAATATGGATTTGAGAGAAATTTAGAAGGAAATTGAGAGCAATTTGAGA
1 AAATAAGGATTTAAGAGAAATTTAGAAGGAAATTGAGAGCAAATTGAGA
20862980 AGAAATTGAG
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 44 0.98
52 1 0.02
ACGTcount: A:0.47, C:0.02, G:0.25, T:0.26
Consensus pattern (51 bp):
AAATAAGGATTTAAGAGAAATTTAGAAGGAAATTGAGAGCAAATTGAGATT
Found at i:20862976 original size:33 final size:33
Alignment explanation
Indices: 20862939--20863001 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
20862929 TTAAATATGG
* *
20862939 ATTTGAG-AGAAATTTAGAAGGAAATTGAGAGCA
1 ATTTGAGAAGAAATTGAG-AGAAAATTGAGAGCA
20862972 ATTTGAGAAGAAATTGAGAGAAAATTGAGA
1 ATTTGAGAAGAAATTGAGAGAAAATTGAGA
20863002 AAATAATTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 18 0.67
34 9 0.33
ACGTcount: A:0.48, C:0.02, G:0.27, T:0.24
Consensus pattern (33 bp):
ATTTGAGAAGAAATTGAGAGAAAATTGAGAGCA
Found at i:20863011 original size:12 final size:11
Alignment explanation
Indices: 20862960--20863015 Score: 58
Period size: 11 Copynumber: 5.0 Consensus size: 11
20862950 ATTTAGAAGG
**
20862960 AAATTGAGAGC
1 AAATTGAGAAA
* *
20862971 AATTTGAGAAG
1 AAATTGAGAAA
*
20862982 AAATTGAGAGA
1 AAATTGAGAAA
20862993 AAATTGAGAAA
1 AAATTGAGAAA
20863004 ATAATTGAGAAA
1 A-AATTGAGAAA
20863016 GGATTAATTT
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
11 27 0.73
12 10 0.27
ACGTcount: A:0.54, C:0.02, G:0.23, T:0.21
Consensus pattern (11 bp):
AAATTGAGAAA
Found at i:20868782 original size:33 final size:34
Alignment explanation
Indices: 20868745--20868815 Score: 110
Period size: 33 Copynumber: 2.1 Consensus size: 34
20868735 ATATGCTTGG
20868745 GCCTCGGTTTACTCGGGCT-AGCAC-TTTTTTTGC
1 GCCTCGGTTTACTCGGG-TGAGCACTTTTTTTTGC
*
20868778 GCCTCGGTTTACTCGGGTGAGCGCTTTTTTTTGC
1 GCCTCGGTTTACTCGGGTGAGCACTTTTTTTTGC
20868812 GCCT
1 GCCT
20868816 TGCACCTCAG
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
32 1 0.03
33 21 0.60
34 13 0.37
ACGTcount: A:0.07, C:0.27, G:0.27, T:0.39
Consensus pattern (34 bp):
GCCTCGGTTTACTCGGGTGAGCACTTTTTTTTGC
Found at i:20869920 original size:1 final size:1
Alignment explanation
Indices: 20869914--20869992 Score: 131
Period size: 1 Copynumber: 79.0 Consensus size: 1
20869904 AATCCTATGC
* *
20869914 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
20869979 AAAAGAAAAAAAAA
1 AAAAAAAAAAAAAA
20869993 GAAGAGAAAA
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
1 72 1.00
ACGTcount: A:0.96, C:0.00, G:0.04, T:0.00
Consensus pattern (1 bp):
A
Found at i:20870000 original size:15 final size:14
Alignment explanation
Indices: 20869914--20870002 Score: 110
Period size: 13 Copynumber: 6.3 Consensus size: 14
20869904 AATCCTATGC
20869914 AAAAAAAAAAAAA-
1 AAAAAAAAAAAAAG
20869927 AAAAAAAAAAAAA-
1 AAAAAAAAAAAAAG
*
20869940 AAAAAAAAAAAAAA
1 AAAAAAAAAAAAAG
*
20869954 AAAAAAAAGAAAAAA
1 AAAAAAAA-AAAAAG
20869969 AAAGAAAAAAAAAAG
1 AAA-AAAAAAAAAAG
*
20869984 AAAAAAAAAGAAGAG
1 AAAAAAAAA-AAAAG
20869999 AAAA
1 AAAA
20870003 TGAAAGAAGA
Statistics
Matches: 70, Mismatches: 2, Indels: 6
0.90 0.03 0.08
Matches are distributed among these distances:
13 26 0.37
14 14 0.20
15 25 0.36
16 5 0.07
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAAAG
Found at i:20872454 original size:348 final size:346
Alignment explanation
Indices: 20871797--20872498 Score: 1197
Period size: 348 Copynumber: 2.0 Consensus size: 346
20871787 TCTCCAATCC
* * * *
20871797 AAAATTAGAATTAGGAGTGATCCTGAAGGATAGGCCTCAGTTGGGATTCTAAAAGCTTCCAAGTG
1 AAAATGAGAACTAGGAGAGATACTGAAGGATAGGCCTCAGTTGGGATTCTAAAAGCTTCCAAGTG
20871862 CAAAAGGCTGTCTATTGTCACCATAGAAGTTAGGCATTTGCCAATAGCCTTATTGTTTTTTGGGA
66 CAAAAGGCTGTCTATTGTCACCATAGAAGTTAGGCATTTGCCAATAGCCTTATTGTTTTTTGGGA
20871927 GTGCTGAACTCTTAGTTCTAGAGAGTAGTGACCAAGGGTCAAAGCTTCAGAAACCTCCAATATAA
131 GTGCTGAACTCTTAGTTCTAGAGAGTAGTGACCAAGGGTCAAAGCTTCAGAAACCTCCAATATAA
* *
20871992 AAGGAATAAGTAGGAATCAGACCATGAGGTTTTAAGTTTCACTCATGTCCACCGCAGAATAACTT
196 AAGGAATAAGTAGGAATCAGACCATGAGGTTTTAAGCTTCACTCATGTCCACCACAGAATAACTT
*
20872057 ATCTGCCCTTCAATTAAAAGTTGGATTTGTAACTGTCTCCTTTTTGCTAAATTCTTTAGGCAAAT
261 ATCTGCCCTTCAAATAAAAGTTGGATTTGTAACTGTCTCCTTTTTGCTAAATTCTTTAGGCAAAT
* *
20872122 CCTATGTCTGTGAATCATTTA
326 CCTATGTATATGAATCATTTA
* *
20872143 AAAATGAGAACTAGGAGAGATACTGAAGGATAGGCCTTAGTTGGGATTCTAAAAGCTTCCCAGTG
1 AAAATGAGAACTAGGAGAGATACTGAAGGATAGGCCTCAGTTGGGATTCTAAAAGCTTCCAAGTG
* * * *
20872208 CAAAAGGCTGTCTGTTGTCACCATAGAAGTTAGGCATTTTCCAATGGCCTTGTTGTTTTTTGGTA
66 CAAAAGGCTGTCTATTGTCACCATAGAAGTTAGGCATTTGCCAATAGCCTTATTGTTTTTTGG--
* *
20872273 GAGTGCTGAACTCTTAGTTCTAGCGAGTAGTGACCATGGGTCAAAGCTTCAGAAACCTCCAATAT
129 GAGTGCTGAACTCTTAGTTCTAGAGAGTAGTGACCAAGGGTCAAAGCTTCAGAAACCTCCAATAT
* *
20872338 AAAAGGAATAAGTAGGAATCAGACCATGAGGTTTTAAGCTTCACTCATGTCCAGCACAGAATTAC
194 AAAAGGAATAAGTAGGAATCAGACCATGAGGTTTTAAGCTTCACTCATGTCCACCACAGAATAAC
* *
20872403 TTATCTGCCCTTTAAATAGAAGTTGGATTTGTAACTGTCTCCTTTTTGCTAAATTCTTTAGGCAA
259 TTATCTGCCCTTCAAATAAAAGTTGGATTTGTAACTGTCTCCTTTTTGCTAAATTCTTTAGGCAA
20872468 ATCCTATGTATATGAATCATTTA
324 ATCCTATGTATATGAATCATTTA
20872491 AAAATGAG
1 AAAATGAG
20872499 TGTTTCATCC
Statistics
Matches: 333, Mismatches: 21, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
346 118 0.35
348 215 0.65
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (346 bp):
AAAATGAGAACTAGGAGAGATACTGAAGGATAGGCCTCAGTTGGGATTCTAAAAGCTTCCAAGTG
CAAAAGGCTGTCTATTGTCACCATAGAAGTTAGGCATTTGCCAATAGCCTTATTGTTTTTTGGGA
GTGCTGAACTCTTAGTTCTAGAGAGTAGTGACCAAGGGTCAAAGCTTCAGAAACCTCCAATATAA
AAGGAATAAGTAGGAATCAGACCATGAGGTTTTAAGCTTCACTCATGTCCACCACAGAATAACTT
ATCTGCCCTTCAAATAAAAGTTGGATTTGTAACTGTCTCCTTTTTGCTAAATTCTTTAGGCAAAT
CCTATGTATATGAATCATTTA
Found at i:20892939 original size:17 final size:18
Alignment explanation
Indices: 20892906--20892939 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20892896 TGTTAACGCT
*
20892906 TAAAATAATATTATATAG
1 TAAAATAATAGTATATAG
20892924 TAAAATAAT-GTATATA
1 TAAAATAATAGTATATA
20892940 CAAAAAATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (18 bp):
TAAAATAATAGTATATAG
Found at i:20894205 original size:23 final size:23
Alignment explanation
Indices: 20894177--20894224 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
20894167 ATTGGGCTAG
*
20894177 GGTTTAATGGGTAATTCGGGTTA
1 GGTTTAATGAGTAATTCGGGTTA
* * *
20894200 GGTTTAGTTAGTATTTCGGGTTA
1 GGTTTAATGAGTAATTCGGGTTA
20894223 GG
1 GG
20894225 GTATTTTACT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.19, C:0.04, G:0.35, T:0.42
Consensus pattern (23 bp):
GGTTTAATGAGTAATTCGGGTTA
Found at i:20894736 original size:48 final size:48
Alignment explanation
Indices: 20894680--20894835 Score: 142
Period size: 48 Copynumber: 3.2 Consensus size: 48
20894670 CGTTGTTGTA
20894680 GCTTTAATCTTTTTAACTGCAATGTCGGAGAAACGATTTACCGATGTG
1 GCTTTAATCTTTTTAACTGCAATGTCGGAGAAACGATTTACCGATGTG
* * * * *
20894728 GCTTTAATCTGTTCT-ACTGC-ATCGCCTGGGGAGTAA-GA-TT-CGCTATTGTA
1 GCTTTAATCT-TTTTAACTGCAAT-G--T-CGGAGAAACGATTTAC-CGA-TGTG
* * *
20894778 GCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCGATTCACCGATGTG
1 GCTTTAATCTTTTTAACTGCAATGTCGGAGAAACGATTTACCGATGTG
20894826 GCTTTAATCT
1 GCTTTAATCT
20894836 GTTCCACGAT
Statistics
Matches: 83, Mismatches: 13, Indels: 24
0.69 0.11 0.20
Matches are distributed among these distances:
47 6 0.07
48 33 0.40
49 13 0.16
50 23 0.28
51 8 0.10
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (48 bp):
GCTTTAATCTTTTTAACTGCAATGTCGGAGAAACGATTTACCGATGTG
Found at i:20894764 original size:98 final size:98
Alignment explanation
Indices: 20894630--20894842 Score: 336
Period size: 98 Copynumber: 2.2 Consensus size: 98
20894620 CGCTGTTGTA
* * *
20894630 GCTTCAATCTGTTCCACTACACCGCCTGGGAAGTAAGATTCGTTGTTGTAGCTTTAATCTTTTTA
1 GCTTTAATCTGTTCCACTACACCGCCTGGGAAGTAAGATTCGCTATTGTAGCTTTAATCTTTTTA
*
20894695 ACTGCAATGTCGGAGAAACGATTTACCGATGTG
66 ACTGCAATGTCGGAGAAACGATTCACCGATGTG
* * * *
20894728 GCTTTAATCTGTTCTACTGCATCGCCTGGGGAGTAAGATTCGCTATTGTAGCTTTAATCTTTTTA
1 GCTTTAATCTGTTCCACTACACCGCCTGGGAAGTAAGATTCGCTATTGTAGCTTTAATCTTTTTA
* *
20894793 ACTGCAATGTCGGGGAAGCGATTCACCGATGTG
66 ACTGCAATGTCGGAGAAACGATTCACCGATGTG
20894826 GCTTTAATCTGTTCCAC
1 GCTTTAATCTGTTCCAC
20894843 GATGTGGCTT
Statistics
Matches: 104, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
98 104 1.00
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.35
Consensus pattern (98 bp):
GCTTTAATCTGTTCCACTACACCGCCTGGGAAGTAAGATTCGCTATTGTAGCTTTAATCTTTTTA
ACTGCAATGTCGGAGAAACGATTCACCGATGTG
Found at i:20894786 original size:50 final size:50
Alignment explanation
Indices: 20894614--20894787 Score: 137
Period size: 50 Copynumber: 3.5 Consensus size: 50
20894604 TCGACGAAGC
* * * * * *
20894614 AAGATTCGCTGTTGTAGCTTCAATCTGTTCCACTACACCGCCTGGGAAGT
1 AAGATTCGCTATTGTAGCTTTAATCTGTTCTACTGCATCGCCTGGGGAGT
* * * * *
20894664 AAGATTCGTTGTTGTAGCTTTAATCT-TTTTAACTGCAAT-G--T-CGGAGA
1 AAGATTCGCTATTGTAGCTTTAATCTGTTCT-ACTGC-ATCGCCTGGGGAGT
* *
20894711 AACGATTTAC-CGA-TGTGGCTTTAATCTGTTCTACTGCATCGCCTGGGGAGT
1 AA-GA-TT-CGCTATTGTAGCTTTAATCTGTTCTACTGCATCGCCTGGGGAGT
20894762 AAGATTCGCTATTGTAGCTTTAATCT
1 AAGATTCGCTATTGTAGCTTTAATCT
20894788 TTTTAACTGC
Statistics
Matches: 94, Mismatches: 18, Indels: 24
0.69 0.13 0.18
Matches are distributed among these distances:
47 7 0.07
48 23 0.24
49 11 0.12
50 46 0.49
51 7 0.07
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.36
Consensus pattern (50 bp):
AAGATTCGCTATTGTAGCTTTAATCTGTTCTACTGCATCGCCTGGGGAGT
Found at i:20894845 original size:23 final size:23
Alignment explanation
Indices: 20894819--20894864 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
20894809 AGCGATTCAC
20894819 CGATGTGGCTTTAATCTGTTCCA
1 CGATGTGGCTTTAATCTGTTCCA
20894842 CGATGTGGCTTTAATCTGTTCCA
1 CGATGTGGCTTTAATCTGTTCCA
20894865 TTGCACCGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.39
Consensus pattern (23 bp):
CGATGTGGCTTTAATCTGTTCCA
Found at i:20894937 original size:50 final size:50
Alignment explanation
Indices: 20894874--20895151 Score: 196
Period size: 50 Copynumber: 5.6 Consensus size: 50
20894864 ATTGCACCGC
* **
20894874 CAGGGAAGTAAGATTTGCTGTTGTAGCTTTAACCTTTTTAACTGCAATGT
1 CAGGGAAGCAAGATTCACTGTTGTAGCTTTAACCTTTTTAACTGCAATGT
* * * * ** **
20894924 CGGGGAAGCAAGATTCACCTATATG--GCTTTAATCTGTTCCACTGCACCG-
1 CAGGGAAGCAAGATTCA-CTGT-TGTAGCTTTAACCTTTTTAACTGCAATGT
* ** *
20894973 CTAGGGAAGTAAGATTTGCTGTTGTAGCTTTAACCTTTTTAACTACAATGT
1 C-AGGGAAGCAAGATTCACTGTTGTAGCTTTAACCTTTTTAACTGCAATGT
* * * * * * ** *
20895024 AAGGGAAGC--GATTCACCGATGTGGCTTTAATCTGTTCCACTGC-ATCGC
1 CAGGGAAGCAAGATTCACTGTTGTAGCTTTAACCTTTTTAACTGCAAT-GT
20895072 CTA-GGAAGCAAGATTCACTGTTGTAGCTTTAACCTTTTTAACTGCAATGT
1 C-AGGGAAGCAAGATTCACTGTTGTAGCTTTAACCTTTTTAACTGCAATGT
* * * *
20895122 CGGGGAAGC--GATTCACCGATGTGGCTTTAA
1 CAGGGAAGCAAGATTCACTGTTGTAGCTTTAA
20895152 TCTGTTCCAC
Statistics
Matches: 167, Mismatches: 49, Indels: 26
0.69 0.20 0.11
Matches are distributed among these distances:
47 2 0.01
48 51 0.31
49 5 0.03
50 102 0.61
51 5 0.03
52 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (50 bp):
CAGGGAAGCAAGATTCACTGTTGTAGCTTTAACCTTTTTAACTGCAATGT
Found at i:20895043 original size:221 final size:219
Alignment explanation
Indices: 20894630--20895063 Score: 645
Period size: 221 Copynumber: 2.0 Consensus size: 219
20894620 CGCTGTTGTA
* * *
20894630 GCTTCAATCTGTTCCACTACACCGCCTGGGAAGTAAGATTCGTTGTTGTAGCTTTAATCTTTTTA
1 GCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAGATTCGCTGTTGTAGCTTTAACCTTTTTA
* * * * * *
20894695 ACTGCAATGTCGGAGAAACGATTTACCGATGTGGCTTTAATCTGTTCTACTGCATCGCCTGGGGA
66 ACTGCAATGTCGGAGAAAAGATTCACCGATATGGCTTTAATCTGTTCCACTGCACCGCCTGGGAA
* * **
20894760 GTAAGATTCGCTATTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCGATTCACCGATGT
131 GTAAGATTCGCTATTGTAGCTTTAACCTTTTTAACTACAATGTAAGGGAAGCGATTCACCGATGT
20894825 GGCTTTAATCTGTTCCACGATGTG
196 GGCTTTAATCTGTTCCACGATGTG
* * * *
20894849 GCTTTAATCTGTTCCATTGCACCGCCAGGGAAGTAAGATTTGCTGTTGTAGCTTTAACCTTTTTA
1 GCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAGATTCGCTGTTGTAGCTTTAACCTTTTTA
* *
20894914 ACTGCAATGTCGGGGAAGCAAGATTCACCTATATGGCTTTAATCTGTTCCACTGCACCG-CTAGG
66 ACTGCAATGTCGGAGAA--AAGATTCACCGATATGGCTTTAATCTGTTCCACTGCACCGCCT-GG
* *
20894978 GAAGTAAGATTTGCTGTTGTAGCTTTAACCTTTTTAACTACAATGTAAGGGAAGCGATTCACCGA
128 GAAGTAAGATTCGCTATTGTAGCTTTAACCTTTTTAACTACAATGTAAGGGAAGCGATTCACCGA
20895043 TGTGGCTTTAATCTGTTCCAC
193 TGTGGCTTTAATCTGTTCCAC
20895064 TGCATCGCCT
Statistics
Matches: 191, Mismatches: 21, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
219 74 0.39
220 2 0.01
221 115 0.60
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (219 bp):
GCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAGATTCGCTGTTGTAGCTTTAACCTTTTTA
ACTGCAATGTCGGAGAAAAGATTCACCGATATGGCTTTAATCTGTTCCACTGCACCGCCTGGGAA
GTAAGATTCGCTATTGTAGCTTTAACCTTTTTAACTACAATGTAAGGGAAGCGATTCACCGATGT
GGCTTTAATCTGTTCCACGATGTG
Found at i:20895079 original size:48 final size:48
Alignment explanation
Indices: 20895026--20895177 Score: 180
Period size: 48 Copynumber: 3.1 Consensus size: 48
20895016 TACAATGTAA
20895026 GGGAAGCGATTCACCGATGTGGCTTTAATCTGTTCCACTGCATCGCCT
1 GGGAAGCGATTCACCGATGTGGCTTTAATCTGTTCCACTGCATCGCCT
* * * * * * ** * *
20895074 AGGAAGCAAGATTCACTGTTGTAGCTTTAACCTTTTTAACTGCAAT-GTCG
1 GGGAAGC--GATTCACCGATGTGGCTTTAATCTGTTCCACTGC-ATCGCCT
20895124 GGGAAGCGATTCACCGATGTGGCTTTAATCTGTTCCACTGCATCGCCT
1 GGGAAGCGATTCACCGATGTGGCTTTAATCTGTTCCACTGCATCGCCT
20895172 GGGAAG
1 GGGAAG
20895178 TAAGATTCTT
Statistics
Matches: 80, Mismatches: 20, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
47 2 0.03
48 41 0.51
50 35 0.44
51 2 0.03
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.30
Consensus pattern (48 bp):
GGGAAGCGATTCACCGATGTGGCTTTAATCTGTTCCACTGCATCGCCT
Found at i:20895101 original size:98 final size:99
Alignment explanation
Indices: 20894842--20895185 Score: 534
Period size: 98 Copynumber: 3.5 Consensus size: 99
20894832 ATCTGTTCCA
* *
20894842 CGATGTGGCTTTAATCTGTTCCATTGCACCGCC-AGGGAAGTAAGATTTGCTGTTGTAGCTTTAA
1 CGATGTGGCTTTAATCTGTTCCACTGCACCGCCTAGGGAAGTAAGATTCGCTGTTGTAGCTTTAA
20894906 CCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCAC
66 CCTTTTTAACTGCAATGTCGGGGAAGC--GATTCAC
* * *
20894942 CTATATGGCTTTAATCTGTTCCACTGCACCG-CTAGGGAAGTAAGATTTGCTGTTGTAGCTTTAA
1 CGATGTGGCTTTAATCTGTTCCACTGCACCGCCTAGGGAAGTAAGATTCGCTGTTGTAGCTTTAA
* **
20895006 CCTTTTTAACTACAATGTAAGGGAAGCGATTCAC
66 CCTTTTTAACTGCAATGTCGGGGAAGCGATTCAC
* * *
20895040 CGATGTGGCTTTAATCTGTTCCACTGCATCGCCTA-GGAAGCAAGATTCACTGTTGTAGCTTTAA
1 CGATGTGGCTTTAATCTGTTCCACTGCACCGCCTAGGGAAGTAAGATTCGCTGTTGTAGCTTTAA
20895104 CCTTTTTAACTGCAATGTCGGGGAAGCGATTCAC
66 CCTTTTTAACTGCAATGTCGGGGAAGCGATTCAC
*
20895138 CGATGTGGCTTTAATCTGTTCCACTGCATCGCCT-GGGAAGTAAGATTC
1 CGATGTGGCTTTAATCTGTTCCACTGCACCGCCTAGGGAAGTAAGATTC
20895186 TTGATTTCAC
Statistics
Matches: 225, Mismatches: 16, Indels: 8
0.90 0.06 0.03
Matches are distributed among these distances:
98 138 0.61
99 4 0.02
100 83 0.37
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (99 bp):
CGATGTGGCTTTAATCTGTTCCACTGCACCGCCTAGGGAAGTAAGATTCGCTGTTGTAGCTTTAA
CCTTTTTAACTGCAATGTCGGGGAAGCGATTCAC
Found at i:20896430 original size:15 final size:15
Alignment explanation
Indices: 20896405--20896439 Score: 54
Period size: 14 Copynumber: 2.3 Consensus size: 15
20896395 AGCCTCTCTA
20896405 TTTTTACTTTTTCATT
1 TTTTTAC-TTTTCATT
20896421 TTTTTA-TTTTCATT
1 TTTTTACTTTTCATT
20896435 TTTTT
1 TTTTT
20896440 GACTCAAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 13 0.68
16 6 0.32
ACGTcount: A:0.11, C:0.09, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTTACTTTTCATT
Found at i:20897268 original size:13 final size:14
Alignment explanation
Indices: 20897252--20897281 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
20897242 TCTATTTTTA
20897252 TTTTCTT-TTTCTT
1 TTTTCTTCTTTCTT
20897265 TTTTCTTCTTTCTT
1 TTTTCTTCTTTCTT
20897279 TTT
1 TTT
20897282 CTCCTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTCTTCTTTCTT
Found at i:20904410 original size:129 final size:130
Alignment explanation
Indices: 20904256--20904514 Score: 511
Period size: 129 Copynumber: 2.0 Consensus size: 130
20904246 TTTAAAAAAG
20904256 GGTCAGGCCTCTGGTAAGGCATTTTTTGCCCCGACCCGACCCGGCCCGAATTCACTAAAGGACAA
1 GGTCAGGCCTCTGGTAAGGCATTTTTTGCCCCGACCCGACCCGGCCCGAATTCACTAAAGGACAA
20904321 AAAAATCTATTTTTTTAATGTTATTTTCTTGTTATTTTCTCCCTATTTTGCTAT-ATTTTACTAT
66 AAAAATCTATTTTTTTAATGTTATTTTCTTGTTATTTTCTCCCTATTTTGCTATCATTTTACTAT
20904385 GGTCAGGCCTCTGGTAAGGCATTTTTTGCCCCGACCCGACCCGGCCCGAATTCACTAAAGGACAA
1 GGTCAGGCCTCTGGTAAGGCATTTTTTGCCCCGACCCGACCCGGCCCGAATTCACTAAAGGACAA
20904450 AAAAATCTATTTTTTTAATGTTATTTTCTTGTTATTTTCTCCCTATTTTGCTATCATTTTACTAT
66 AAAAATCTATTTTTTTAATGTTATTTTCTTGTTATTTTCTCCCTATTTTGCTATCATTTTACTAT
20904515 TATGTTGCTA
Statistics
Matches: 129, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
129 119 0.92
130 10 0.08
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.39
Consensus pattern (130 bp):
GGTCAGGCCTCTGGTAAGGCATTTTTTGCCCCGACCCGACCCGGCCCGAATTCACTAAAGGACAA
AAAAATCTATTTTTTTAATGTTATTTTCTTGTTATTTTCTCCCTATTTTGCTATCATTTTACTAT
Found at i:20909800 original size:27 final size:27
Alignment explanation
Indices: 20909761--20909858 Score: 126
Period size: 27 Copynumber: 3.6 Consensus size: 27
20909751 GCATCCTGTC
*
20909761 AGCCTTTGTGGCGTACTCTGAATGAAT
1 AGCCTTTGTGGCGTACTCTGTATGAAT
* * *
20909788 CGCCTTTGTGGCGTACCCTCTAT-AGAT
1 AGCCTTTGTGGCGTACTCTGTATGA-AT
*
20909815 AGCCTTTGTGGCGTACTCTGTATGGAT
1 AGCCTTTGTGGCGTACTCTGTATGAAT
*
20909842 TGCCTTTGTGGCGTACT
1 AGCCTTTGTGGCGTACT
20909859 TTGATTATAT
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
26 1 0.02
27 59 0.98
ACGTcount: A:0.15, C:0.22, G:0.27, T:0.36
Consensus pattern (27 bp):
AGCCTTTGTGGCGTACTCTGTATGAAT
Found at i:20909870 original size:27 final size:26
Alignment explanation
Indices: 20909762--20909870 Score: 98
Period size: 27 Copynumber: 4.0 Consensus size: 26
20909752 CATCCTGTCA
*
20909762 GCCTTTGTGGCGTACTCTGA-ATGAATC
1 GCCTTTGTGGCGTACTCTGATAT--ATT
* *
20909789 GCCTTTGTGGCGTACCCTCT-ATAGATA
1 GCCTTTGTGGCGTA--CTCTGATATATT
20909816 GCCTTTGTGGCGTACTCTG-TATGGATT
1 GCCTTTGTGGCGTACTCTGATAT--ATT
*
20909843 GCCTTTGTGGCGTACTTTGATTATATT
1 GCCTTTGTGGCGTACTCTGA-TATATT
20909870 G
1 G
20909871 TTTTAGAGCA
Statistics
Matches: 69, Mismatches: 5, Indels: 16
0.77 0.06 0.18
Matches are distributed among these distances:
25 6 0.09
27 54 0.78
28 1 0.01
29 8 0.12
ACGTcount: A:0.16, C:0.20, G:0.26, T:0.39
Consensus pattern (26 bp):
GCCTTTGTGGCGTACTCTGATATATT
Found at i:20914929 original size:6 final size:6
Alignment explanation
Indices: 20914911--20914951 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
20914901 ACACCCCCAT
*
20914911 TTACCA TTTACCA TTACCA TTACCA TTAACCA ATACCA TTA
1 TTACCA -TTACCA TTACCA TTACCA TT-ACCA TTACCA TTA
20914952 ACTTCCTTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
6 20 0.65
7 11 0.35
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (6 bp):
TTACCA
Found at i:20914929 original size:13 final size:13
Alignment explanation
Indices: 20914907--20914950 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
20914897 ATCTACACCC
20914907 CCATTTACCATTTA
1 CCATTTACCA-TTA
20914921 CCA-TTACCATTA
1 CCATTTACCATTA
* *
20914933 CCATTAACCAATA
1 CCATTTACCATTA
20914946 CCATT
1 CCATT
20914951 AACTTCCTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
12 6 0.22
13 18 0.67
14 3 0.11
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (13 bp):
CCATTTACCATTA
Found at i:20914935 original size:19 final size:19
Alignment explanation
Indices: 20914911--20914951 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
20914901 ACACCCCCAT
* *
20914911 TTACCATTTACCATTACCA
1 TTACCATTAACCAATACCA
20914930 TTACCATTAACCAATACCA
1 TTACCATTAACCAATACCA
20914949 TTA
1 TTA
20914952 ACTTCCTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (19 bp):
TTACCATTAACCAATACCA
Found at i:20920584 original size:16 final size:16
Alignment explanation
Indices: 20920563--20920596 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
20920553 GCTAACATTC
*
20920563 TTTATTAAATTATTAT
1 TTTATTAAATTAATAT
*
20920579 TTTATTTAATTAATAT
1 TTTATTAAATTAATAT
20920595 TT
1 TT
20920597 GAGAAAGTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTATTAAATTAATAT
Found at i:20924090 original size:21 final size:21
Alignment explanation
Indices: 20924066--20924105 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
20924056 GAGATTTGAG
*
20924066 ATTCAGGGTTCAGGATTTAAT
1 ATTCAAGGTTCAGGATTTAAT
* *
20924087 ATTCAAGGTTTATGATTTA
1 ATTCAAGGTTCAGGATTTA
20924106 GGGTTATTGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.07, G:0.20, T:0.42
Consensus pattern (21 bp):
ATTCAAGGTTCAGGATTTAAT
Found at i:20924936 original size:17 final size:19
Alignment explanation
Indices: 20924904--20924938 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
20924894 ATAAAAAAAA
20924904 AAAAAACGTTGTAAAGAAC
1 AAAAAACGTTGTAAAGAAC
20924923 AAAAAA-GTTG-AAAGAA
1 AAAAAACGTTGTAAAGAA
20924939 AGTGTTATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 4 0.25
19 6 0.38
ACGTcount: A:0.63, C:0.06, G:0.17, T:0.14
Consensus pattern (19 bp):
AAAAAACGTTGTAAAGAAC
Found at i:20926155 original size:25 final size:24
Alignment explanation
Indices: 20926126--20926173 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
20926116 TATATTGTAA
*
20926126 TATATATTTTCCACTAAAATATTAG
1 TATAT-TTTTCCAATAAAATATTAG
**
20926151 TATATTTTTTTAATAAAATATTA
1 TATATTTTTCCAATAAAATATTA
20926174 AGATTATTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.50
Consensus pattern (24 bp):
TATATTTTTCCAATAAAATATTAG
Found at i:20937059 original size:3 final size:3
Alignment explanation
Indices: 20937051--20937105 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
20937041 AGGAAAACGA
20937051 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
20937099 ATT ATT A
1 ATT ATT A
20937106 AGAGAATAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:20937844 original size:22 final size:22
Alignment explanation
Indices: 20937819--20937861 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
20937809 TAAGTCTCTA
20937819 TTTT-TATTTTTGAGAATTTAAC
1 TTTTGTATTTTTGA-AATTTAAC
*
20937841 TTTTGTATTTTTTAAATTTAA
1 TTTTGTATTTTTGAAATTTAA
20937862 AAATTCACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.28, C:0.02, G:0.07, T:0.63
Consensus pattern (22 bp):
TTTTGTATTTTTGAAATTTAAC
Found at i:20937982 original size:7 final size:7
Alignment explanation
Indices: 20937970--20938010 Score: 66
Period size: 7 Copynumber: 5.9 Consensus size: 7
20937960 ATCAGATCAT
20937970 ATTAAAA
1 ATTAAAA
20937977 ATT-AAA
1 ATTAAAA
20937983 ATATAAAA
1 AT-TAAAA
20937991 ATTAAAA
1 ATTAAAA
20937998 ATTAAAA
1 ATTAAAA
20938005 ATTAAA
1 ATTAAA
20938011 TTTAAATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 5 0.16
7 22 0.69
8 5 0.16
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
ATTAAAA
Found at i:20943181 original size:25 final size:25
Alignment explanation
Indices: 20943151--20943217 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 25
20943141 TTGCTCGTAT
20943151 GAGCTTCTCGATAATTGGATCTCCG
1 GAGCTTCTCGATAATTGGATCTCCG
** * *
20943176 GAGCTTC-CTGATAAAAGGCTCTCTG
1 GAGCTTCTC-GATAATTGGATCTCCG
20943201 GAGCTTCTCGAT-ATTGG
1 GAGCTTCTCGATAATTGG
20943218 CTCACATGAG
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
24 4 0.12
25 29 0.85
26 1 0.03
ACGTcount: A:0.21, C:0.22, G:0.25, T:0.31
Consensus pattern (25 bp):
GAGCTTCTCGATAATTGGATCTCCG
Found at i:20943242 original size:24 final size:24
Alignment explanation
Indices: 20943215--20943281 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 24
20943205 TTCTCGATAT
*
20943215 TGGCTCACATGAGCTTCCCAATTA
1 TGGCTCACACGAGCTTCCCAATTA
** *
20943239 TGGCTCTTACGAGCTTCCCGATTA
1 TGGCTCACACGAGCTTCCCAATTA
**
20943263 TGGCTCTTACGAGCTTCCC
1 TGGCTCACACGAGCTTCCC
20943282 GTTACATGGC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.18, C:0.31, G:0.19, T:0.31
Consensus pattern (24 bp):
TGGCTCACACGAGCTTCCCAATTA
Found at i:20943282 original size:24 final size:24
Alignment explanation
Indices: 20943225--20943282 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
20943215 TGGCTCACAT
*
20943225 GAGCTTCCCAATTATGGCTCTTAC
1 GAGCTTCCCGATTATGGCTCTTAC
20943249 GAGCTTCCCGATTATGGCTCTTAC
1 GAGCTTCCCGATTATGGCTCTTAC
20943273 GAGCTTCCCG
1 GAGCTTCCCG
20943283 TTACATGGCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.17, C:0.31, G:0.21, T:0.31
Consensus pattern (24 bp):
GAGCTTCCCGATTATGGCTCTTAC
Found at i:20948584 original size:15 final size:15
Alignment explanation
Indices: 20948566--20948770 Score: 137
Period size: 15 Copynumber: 13.9 Consensus size: 15
20948556 TCACATGTAA
20948566 GGTTCACACATATAG
1 GGTTCACACATATAG
* * * *
20948581 GGTTCGCGCATACAT
1 GGTTCACACATATAG
*
20948596 GGTTCACACATACA-
1 GGTTCACACATATAG
*
20948610 GGTTCGCACATATAG
1 GGTTCACACATATAG
*
20948625 GGTTCACACATATTG
1 GGTTCACACATATAG
* * * *
20948640 GTTTCGCACATACAA
1 GGTTCACACATATAG
** *
20948655 GAAT-AGACATATAG
1 GGTTCACACATATAG
* * *
20948669 TGTTCAAACGTATA-
1 GGTTCACACATATAG
* *
20948683 GGTTCTCACATTTAG
1 GGTTCACACATATAG
*
20948698 GGTTTACACATATAG
1 GGTTCACACATATAG
* *** *
20948713 GATTTTTACATGTAG
1 GGTTCACACATATAG
* *
20948728 GGTTCACACATACAA
1 GGTTCACACATATAG
*
20948743 GGTTCGCACATATAG
1 GGTTCACACATATAG
20948758 GGTTCACACATAT
1 GGTTCACACATAT
20948771 TAATTCACAA
Statistics
Matches: 138, Mismatches: 49, Indels: 6
0.72 0.25 0.03
Matches are distributed among these distances:
14 28 0.20
15 110 0.80
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.30
Consensus pattern (15 bp):
GGTTCACACATATAG
Found at i:20948650 original size:44 final size:44
Alignment explanation
Indices: 20948564--20948771 Score: 159
Period size: 44 Copynumber: 4.7 Consensus size: 44
20948554 GTTCACATGT
* * * *
20948564 AAGGTTCACACATATAGGGTTCGCGCATACATGGTTCACACATAC
1 AAGGTTCGCACATATAGGGTTCACACATA-TTGGTTCACACATAC
*
20948609 -AGGTTCGCACATATAGGGTTCACACATATTGGTTTCGCACATAC
1 AAGGTTCGCACATATAGGGTTCACACATATTGG-TTCACACATAC
** * * * * * * **
20948653 AAGAATAG-ACATATAGTGTTCAAACGTATAGGTTCTCACATTT
1 AAGGTTCGCACATATAGGGTTCACACATATTGGTTCACACATAC
* ** * *** * *
20948696 AGGGTTTACACATATAGGATTTTTACATGTAGGGTTCACACATAC
1 AAGGTTCGCACATATAGGGTTCACACATAT-TGGTTCACACATAC
20948741 AAGGTTCGCACATATAGGGTTCACACATATT
1 AAGGTTCGCACATATAGGGTTCACACATATT
20948772 AATTCACAAA
Statistics
Matches: 119, Mismatches: 40, Indels: 9
0.71 0.24 0.05
Matches are distributed among these distances:
43 14 0.12
44 69 0.58
45 36 0.30
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (44 bp):
AAGGTTCGCACATATAGGGTTCACACATATTGGTTCACACATAC
Found at i:20948833 original size:34 final size:34
Alignment explanation
Indices: 20948783--20948899 Score: 130
Period size: 34 Copynumber: 3.4 Consensus size: 34
20948773 ATTCACAAAG
* * *
20948783 TACATAACAT-GTGGGTTCATATACTATGA-CGTAC
1 TACATAACATAG-GGGTTCACATACTA-CATCATAC
*
20948817 TACATAACATAGGGGTTTACATACTACATCATAC
1 TACATAACATAGGGGTTCACATACTACATCATAC
* *
20948851 TATATAACATAGGGGTTCACATACTACTTCATAC
1 TACATAACATAGGGGTTCACATACTACATCATAC
*
20948885 TATATAACATTAGGG
1 TACATAACA-TAGGG
20948900 TTCGCTTACT
Statistics
Matches: 73, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
33 1 0.01
34 66 0.90
35 6 0.08
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.32
Consensus pattern (34 bp):
TACATAACATAGGGGTTCACATACTACATCATAC
Found at i:20948910 original size:34 final size:34
Alignment explanation
Indices: 20948814--20948899 Score: 136
Period size: 34 Copynumber: 2.5 Consensus size: 34
20948804 TACTATGACG
* *
20948814 TACTACATAACATAGGGGTTTACATACTACATCA
1 TACTATATAACATAGGGGTTCACATACTACATCA
*
20948848 TACTATATAACATAGGGGTTCACATACTACTTCA
1 TACTATATAACATAGGGGTTCACATACTACATCA
20948882 TACTATATAACATTAGGG
1 TACTATATAACA-TAGGG
20948900 TTCGCTTACT
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
34 43 0.90
35 5 0.10
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (34 bp):
TACTATATAACATAGGGGTTCACATACTACATCA
Found at i:20953641 original size:16 final size:16
Alignment explanation
Indices: 20953605--20953643 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
20953595 AGTTTTTTGA
* *
20953605 ATTTCAAAAAATTTCT
1 ATTTAAAAAAATTTAT
*
20953621 TTTTAAAAAAATTTAT
1 ATTTAAAAAAATTTAT
20953637 ATTTAAA
1 ATTTAAA
20953644 GTGGGTCATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (16 bp):
ATTTAAAAAAATTTAT
Found at i:20955972 original size:2 final size:2
Alignment explanation
Indices: 20955965--20955997 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
20955955 TCAACATTCA
*
20955965 AT AT AT AT AT AT AT AT AT AT AT AT TT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20955998 TTCTAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:20962366 original size:23 final size:23
Alignment explanation
Indices: 20962339--20962384 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 23
20962329 TAATTTGTTA
20962339 TATTAA-ACATATATTAACCTTAT
1 TATTAATAC-TATATTAACCTTAT
20962362 TATTAATTTACTATATTAACCTT
1 TATTAA--TACTATATTAACCTT
20962385 TACTAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 6 0.30
25 12 0.60
26 2 0.10
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.48
Consensus pattern (23 bp):
TATTAATACTATATTAACCTTAT
Found at i:20966810 original size:19 final size:21
Alignment explanation
Indices: 20966772--20966810 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
20966762 AATAATTGAT
*
20966772 TATATTGTTGTTATTATTTTG
1 TATATTGTTGTTAATATTTTG
20966793 TATATT-TTG-TAATATTTT
1 TATATTGTTGTTAATATTTT
20966811 TTGTTTTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (21 bp):
TATATTGTTGTTAATATTTTG
Found at i:20968733 original size:24 final size:24
Alignment explanation
Indices: 20968706--20968751 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
20968696 CATTTTTTTT
20968706 TATATATTTTGGTAAATAAAAATA
1 TATATATTTTGGTAAATAAAAATA
*
20968730 TATATTTTTTGGTAAATAAAAA
1 TATATATTTTGGTAAATAAAAA
20968752 AAACTTATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (24 bp):
TATATATTTTGGTAAATAAAAATA
Found at i:20968824 original size:74 final size:77
Alignment explanation
Indices: 20968739--20968883 Score: 192
Period size: 75 Copynumber: 1.9 Consensus size: 77
20968729 ATATATTTTT
*
20968739 TGGTAAATAAAAAAA-ACTTATAACATTTTGGT-TATTTTTAATTTTTT-TAATATATTT-GT-A
1 TGGTAAATAAAAAAATACTTATAACATTTTCGTAT-TTTTTAATTTTTTGTAATAT-TTTGGTAA
20968799 AAAACCCATTATTC
64 AAAACCCATTATTC
** * *
20968813 TGGTAAATAAAAAAATTTTTATAATATTTTCGTATTTTTTTATTTTTTGTAATATTTTGGTAAAA
1 TGGTAAATAAAAAAATACTTATAACATTTTCGTATTTTTTAATTTTTTGTAATATTTTGGTAAAA
20968878 AACCCA
66 AACCCA
20968884 AAATAAACCA
Statistics
Matches: 61, Mismatches: 5, Indels: 7
0.84 0.07 0.10
Matches are distributed among these distances:
74 15 0.25
75 28 0.46
76 9 0.15
77 9 0.15
ACGTcount: A:0.38, C:0.07, G:0.08, T:0.48
Consensus pattern (77 bp):
TGGTAAATAAAAAAATACTTATAACATTTTCGTATTTTTTAATTTTTTGTAATATTTTGGTAAAA
AACCCATTATTC
Found at i:20969362 original size:4 final size:4
Alignment explanation
Indices: 20969334--20969508 Score: 118
Period size: 4 Copynumber: 43.8 Consensus size: 4
20969324 CTTCCTCTTC
* * *
20969334 TTCT TT-T TTTT TTCT CTTC- TCCT TTC- TT-T TTCT TTCC TTCT TTCT
1 TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT
20969379 TTCT TT-T TTCT TCTCCT TTCCT TT-T CTTC- TTCT TTCT TTCT TTCT
1 TTCT TTCT TTCT T-T-CT TT-CT TTCT -TTCT TTCT TTCT TTCT TTCT
* * *
20969424 TTTT TTCT CTTC- TCCT TTCCTT TTCT TTCC TTC- TT-T TTCT TTCT TTCAT
1 TTCT TTCT -TTCT TTCT TT-C-T TTCT TTCT TTCT TTCT TTCT TTCT TTC-T
* *
20969473 CTCCT TTCT TTCT TTTT TTCT TTCT TTCT TTCT TTC
1 -TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTC
20969509 CCTCTCCTTC
Statistics
Matches: 138, Mismatches: 14, Indels: 38
0.73 0.07 0.20
Matches are distributed among these distances:
3 22 0.16
4 91 0.66
5 17 0.12
6 8 0.06
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.71
Consensus pattern (4 bp):
TTCT
Found at i:20969386 original size:44 final size:44
Alignment explanation
Indices: 20969310--20969507 Score: 181
Period size: 44 Copynumber: 4.7 Consensus size: 44
20969300 TTTCTTTTCT
* *
20969310 TTTCTTTTTCCTTCCTTCCTCTTC-TTCTTTTTTTTTTCTCTTCTCC
1 TTTCCTTTTCTTTCCTT-CT-TTCTTTC-TTTTTTTTTCTCTTCTCC
*
20969356 TTTCTTTTTCTTTCCTTCTTTCTTTC----TTTTT-TCTTCTCC
1 TTTCCTTTTCTTTCCTTCTTTCTTTCTTTTTTTTTCTCTTCTCC
20969395 TTTCCTTTTC-TT-CTTCTTTCTTTCTTTCTTTTTTTCTCTTCTCC
1 TTTCCTTTTCTTTCCTTCTTTCTTTC-TT-TTTTTTTCTCTTCTCC
**
20969439 TTTCCTTTTCTTTCCTTC-TT-TTTCTTTCTTTCATCTCCTT-T-C
1 TTTCCTTTTCTTTCCTTCTTTCTTTCTTT-TTTTTTCT-CTTCTCC
*
20969481 TTT-CTTTT-TTTCTTTCTTTCTTTCTTT
1 TTTCCTTTTCTTTCCTTCTTTCTTTCTTT
20969508 CCCTCTCCTT
Statistics
Matches: 133, Mismatches: 5, Indels: 32
0.78 0.03 0.19
Matches are distributed among these distances:
37 12 0.09
38 2 0.02
39 17 0.13
40 12 0.09
41 7 0.05
42 12 0.09
43 14 0.11
44 28 0.21
45 9 0.07
46 20 0.15
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.71
Consensus pattern (44 bp):
TTTCCTTTTCTTTCCTTCTTTCTTTCTTTTTTTTTCTCTTCTCC
Found at i:20969445 original size:49 final size:48
Alignment explanation
Indices: 20969357--20969485 Score: 152
Period size: 49 Copynumber: 2.6 Consensus size: 48
20969347 CTCTTCTCCT
* * * *
20969357 TTCTTTTTCTTTCCTTCTTTCTTTCTTTTTTCTTCTCCTTTCCTTTTC
1 TTCTTTTTCTTTCTTTCTTTCTTTCTTTCTCCTTCTCCTTTCCTTTCC
* *
20969405 TTCTTCTTTCTTTCTTTCTTTTTTTCTCTTCTCCTT-TCCTTTTCTTTCC
1 TTCTT-TTTCTTTCTTTCTTTCTTTCT-TTCTCCTTCTCCTTTCCTTTCC
*
20969454 TTCTTTTTCTTTCTTTCATCTCCTTTCTTTCT
1 TTCTTTTTCTTTCTTTC-T-TTCTTTCTTTCT
20969486 TTTTTTCTTT
Statistics
Matches: 69, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
48 17 0.25
49 40 0.58
50 12 0.17
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.70
Consensus pattern (48 bp):
TTCTTTTTCTTTCTTTCTTTCTTTCTTTCTCCTTCTCCTTTCCTTTCC
Found at i:20969504 original size:62 final size:61
Alignment explanation
Indices: 20969300--20969505 Score: 166
Period size: 60 Copynumber: 3.4 Consensus size: 61
20969290 AAAAAAACAT
* * * * *
20969300 TTTC-TTTTCTTTTCTT-TTTCCTTC-CTTCCTCTTCTTCTT-TTTTT-TTTCTCT-TCTCC
1 TTTCTTTTTTTTTTCTTCTTTCTTTCTCTT-TTCTTCTCCTTCTTTTTCTTTCTTTCTCTCC
* * * * *
20969356 TTTCTTTTTCTTTCCTTCTTTCTTTCTTTTTTCTTCTCCTTTCCTTTTC-TTC-TTCT-TTC
1 TTTCTTTTTTTTTTCTTCTTTCTTTCTCTTTTCTTCTCC-TTCTTTTTCTTTCTTTCTCTCC
20969415 TTTCTTTCTTTTTTTC-TCTTCTCCTTTC-CTTTTCTT-TCCTTCTTTTTCTTTCTTTCATCTCC
1 TTTCTTT-TTTTTTTCTTCTT-T-CTTTCTCTTTTCTTCTCCTTCTTTTTCTTTCTTTC-TCTCC
20969477 TTTCTTTCTTTTTTTCTTTCTTTCTTTCT
1 TTTCTTT-TTTTTTTC-TTCTTTCTTTCT
20969506 TTCCCTCTCC
Statistics
Matches: 120, Mismatches: 13, Indels: 27
0.75 0.08 0.17
Matches are distributed among these distances:
56 4 0.03
57 11 0.09
58 22 0.18
59 24 0.20
60 25 0.21
61 6 0.05
62 23 0.19
63 1 0.01
64 4 0.03
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (61 bp):
TTTCTTTTTTTTTTCTTCTTTCTTTCTCTTTTCTTCTCCTTCTTTTTCTTTCTTTCTCTCC
Found at i:20969517 original size:62 final size:60
Alignment explanation
Indices: 20969300--20969519 Score: 181
Period size: 62 Copynumber: 3.6 Consensus size: 60
20969290 AAAAAAACAT
* * *
20969300 TTTCTTTTCTTT-TCTT-TTTCCTTCCTTCCTCTTCTTCTTTTT-TTT-TTCTCTTCTCCTTTC
1 TTTCTTTT-TTTCT-TTCTTTCTTTCTTTCCTCTCCTTCTTTTTCTTTCTT-TC-TCTCCTTTC
* * *
20969360 TTT-TTCTTTCCTTCTTTCTTTCTTT-TTTCTTCTCCTTTCCTTTTC-TTC-TTCT-TTCTTTC
1 TTTCTT-TTT--TTCTTTCTTTCTTTCTTTCCTCTCC-TTCTTTTTCTTTCTTTCTCTCCTTTC
* * *
20969419 TTTCTTTTTTTCTCTTC-TCCTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCATCTCCTTTC
1 TTTCTTTTTTTCT-TTCTTTCTTT-CTTTCCTCTCCTTCTTTTTCTTTCTTTC-TCTCCTTTC
20969481 TTTCTTTTTTTCTTTCTTTCTTTCTTTCCCTCTCCTTCT
1 TTTCTTTTTTTCTTTCTTTCTTTCTTT-CCTCTCCTTCT
20969520 GGTCCCCCCA
Statistics
Matches: 127, Mismatches: 15, Indels: 34
0.72 0.09 0.19
Matches are distributed among these distances:
57 9 0.07
58 11 0.09
59 25 0.20
60 11 0.09
61 21 0.17
62 50 0.39
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (60 bp):
TTTCTTTTTTTCTTTCTTTCTTTCTTTCCTCTCCTTCTTTTTCTTTCTTTCTCTCCTTTC
Found at i:20969573 original size:27 final size:27
Alignment explanation
Indices: 20969535--20969604 Score: 106
Period size: 27 Copynumber: 2.6 Consensus size: 27
20969525 CCCCAATAAA
20969535 CATTGGTGCCGCCAATGG-TATTGGCAC
1 CATTGGTGCCGCCAATGGCT-TTGGCAC
20969562 CATTGGTGCCGCCAATGGCTTTGGCAC
1 CATTGGTGCCGCCAATGGCTTTGGCAC
* *
20969589 CTTTCGTGCCGCCAAT
1 CATTGGTGCCGCCAAT
20969605 CCCATTGGCG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
27 39 0.98
28 1 0.03
ACGTcount: A:0.16, C:0.30, G:0.27, T:0.27
Consensus pattern (27 bp):
CATTGGTGCCGCCAATGGCTTTGGCAC
Found at i:20969612 original size:27 final size:27
Alignment explanation
Indices: 20969535--20969613 Score: 95
Period size: 27 Copynumber: 2.9 Consensus size: 27
20969525 CCCCAATAAA
* *
20969535 CATTGGTGCCGCCAATGGTATTGGCAC
1 CATTCGTGCCGCCAATGGCATTGGCAC
* *
20969562 CATTGGTGCCGCCAATGGCTTTGGCAC
1 CATTCGTGCCGCCAATGGCATTGGCAC
* **
20969589 CTTTCGTGCCGCCAATCCCATTGGC
1 CATTCGTGCCGCCAATGGCATTGGC
20969614 GTGACCAAGG
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.15, C:0.32, G:0.27, T:0.27
Consensus pattern (27 bp):
CATTCGTGCCGCCAATGGCATTGGCAC
Found at i:20969706 original size:23 final size:23
Alignment explanation
Indices: 20969674--20969719 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
20969664 TTTGTTTTTT
20969674 TATATATTTTGGTAAATAAAAAA
1 TATATATTTTGGTAAATAAAAAA
*
20969697 TATATTTTTTGGTAAATAAAAAA
1 TATATATTTTGGTAAATAAAAAA
20969720 AAGTTATAAC
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:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (23 bp):
TATATATTTTGGTAAATAAAAAA
Found at i:20970545 original size:43 final size:43
Alignment explanation
Indices: 20970480--20970618 Score: 235
Period size: 43 Copynumber: 3.2 Consensus size: 43
20970470 CGGCATTTAT
20970480 GCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACCCACAAAC
1 GCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACCCACAAAC
* *
20970523 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTA-CCAGAAAC
1 GCCGCTAAAGAACATGATCTTTAGCGGCGC-TTTACCCACAAAC
20970566 GCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACCCACAAAC
1 GCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACCCACAAAC
*
20970609 GCCACTAAAG
1 GCCGCTAAAG
20970619 GTCATAAAAA
Statistics
Matches: 89, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
42 4 0.04
43 81 0.91
44 4 0.04
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.20
Consensus pattern (43 bp):
GCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACCCACAAAC
Found at i:20974189 original size:13 final size:13
Alignment explanation
Indices: 20974166--20974200 Score: 61
Period size: 13 Copynumber: 2.6 Consensus size: 13
20974156 TTTTTATTTC
20974166 ATTTTTATTTTTGT
1 ATTTTT-TTTTTGT
20974180 ATTTTTTTTTTGT
1 ATTTTTTTTTTGT
20974193 ATTTTTTT
1 ATTTTTTT
20974201 CTTATAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 15 0.71
14 6 0.29
ACGTcount: A:0.11, C:0.00, G:0.06, T:0.83
Consensus pattern (13 bp):
ATTTTTTTTTTGT
Found at i:20974552 original size:14 final size:15
Alignment explanation
Indices: 20974533--20974561 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
20974523 ACCCTTGAAT
20974533 CCCTAAAT-CCTAAC
1 CCCTAAATCCCTAAC
20974547 CCCTAAATCCCTAAC
1 CCCTAAATCCCTAAC
20974562 TCTTAACCCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.34, C:0.45, G:0.00, T:0.21
Consensus pattern (15 bp):
CCCTAAATCCCTAAC
Found at i:20974555 original size:22 final size:22
Alignment explanation
Indices: 20974530--20974574 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
20974520 CCGACCCTTG
20974530 AATCCCTAAATCCTAACCCCTA
1 AATCCCTAAATCCTAACCCCTA
* *
20974552 AATCCCTAACTCTTAACCCCTA
1 AATCCCTAAATCCTAACCCCTA
20974574 A
1 A
20974575 CTACTAACCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.40, G:0.00, T:0.24
Consensus pattern (22 bp):
AATCCCTAAATCCTAACCCCTA
Found at i:20974713 original size:21 final size:18
Alignment explanation
Indices: 20974671--20974724 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 18
20974661 CAAAACACGT
*
20974671 AAAAAACTGAACTGGATA
1 AAAAAACTGAACCGGATA
20974689 AAAAAACTGAACCGAGCACTA
1 AAAAAACTGAACCG-G-A-TA
*
20974710 AAAATACTGAACCGG
1 AAAAAACTGAACCGG
20974725 GATGGATAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 13 0.42
19 1 0.03
20 2 0.06
21 15 0.48
ACGTcount: A:0.52, C:0.19, G:0.17, T:0.13
Consensus pattern (18 bp):
AAAAAACTGAACCGGATA
Found at i:20975029 original size:114 final size:114
Alignment explanation
Indices: 20974766--20975475 Score: 1077
Period size: 114 Copynumber: 6.2 Consensus size: 114
20974756 GCTTATATCG
* *
20974766 GGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTATTAAAAACA-CTGCT
1 GGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAA-AGCCGCT
* * * *
20974830 AAATCCCCAAAAGCTCAGAAAACAGCGTCGTTGGGCTTAGG-TTTTTTGT
65 AAATCCCCGAAAGCTCAAAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGC
* *
20974879 GGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCATTCTTAAAAAAGCAGCTA
1 GGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAAAGCCGCTA
20974944 AATCCCCGAAAGCTCAAAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGC
66 AATCCCCGAAAGCTCAAAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGC
* * *
20974993 GGCGCTTTCTCAAAAATGCCGCTAAAGCCCTAAGCATTAGCGGCGCATTCTTAAAAAAGCCGCTA
1 GGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAAAGCCGCTA
*
20975058 AATCCCCGAAAGCTCAAAAAACGGCGTTGTTGGGCTTAGGTTTTTTTGC
66 AATCCCCGAAAGCTCAAAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGC
* *
20975107 GGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGTGCTTTATTAAAAAA-CATCGC
1 GGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAAAGC--CGC
* *
20975171 TAAATCCCCGAAAGCTCAGAAAACGGTGTCGTTGGGCTTAGG-TTTTTTGC
64 TAAATCCCCGAAAGCTCAAAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGC
* *
20975221 GGCGCTTTCTCAAAAACGCCGCTAAAGCCATGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTA
1 GGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAAAGCCGCTA
* * * * * *
20975286 AATCTCTGAAAGCTCAGAAAATGGTGTCGTTGGGCGTAGGTTTTTTTGC
66 AATCCCCGAAAGCTCAAAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGC
* * *
20975335 GGCGCTTTCTCAAAAACACCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCAA
1 GGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAAAGCCGCTA
*
20975400 AATCCCCGAAAGCTCAAAAAACGGCGTCATTGGGCTTAGGTTTTTTTTGC
66 AATCCCCGAAAGCTCAAAAAACGGCGTCGTTGGGCTTAGG-TTTTTTTGC
* * *
20975450 GGCGCTTTCTTAAAAATGCCACTAAA
1 GGCGCTTTCTCAAAAACGCCGCTAAA
20975476 TCCCCGACAG
Statistics
Matches: 549, Mismatches: 41, Indels: 12
0.91 0.07 0.02
Matches are distributed among these distances:
112 1 0.00
113 139 0.25
114 335 0.61
115 74 0.13
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (114 bp):
GGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAAAGCCGCTA
AATCCCCGAAAGCTCAAAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGC
Found at i:20975459 original size:74 final size:73
Alignment explanation
Indices: 20975374--20975544 Score: 234
Period size: 74 Copynumber: 2.3 Consensus size: 73
20975364 CTGAGCATTA
*
20975374 GCGGCGCTTTCTTAAAAACGCCGCAAAATCCCCGAAAGCTCAAAAAACGGCGTCATTGGGCTTAG
1 GCGGCGCTTTCTTAAAAACGCCACAAAATCCCCGAAAGCTCAAAAAACGGCGTCATTGGGCTTAG
20975439 GTTTTTTTT
66 G-TTTTTTT
* * * ** * *
20975448 GCGGCGCTTTCTTAAAAATGCCACTAAATCCCCGACAGCTCGGAAAACGGTGTCGTTGGGCTTAG
1 GCGGCGCTTTCTTAAAAACGCCACAAAATCCCCGAAAGCTCAAAAAACGGCGTCATTGGGCTTAG
20975513 GTTTTTTT
66 GTTTTTTT
* * *
20975521 GCGGCGGTTTCTCAAAAATGCCAC
1 GCGGCGCTTTCTTAAAAACGCCAC
20975545 TAAAGCCCTG
Statistics
Matches: 87, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
73 29 0.33
74 58 0.67
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (73 bp):
GCGGCGCTTTCTTAAAAACGCCACAAAATCCCCGAAAGCTCAAAAAACGGCGTCATTGGGCTTAG
GTTTTTTT
Done.