Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 102 of 204
Found at i:31208987 original size:88 final size:89
Alignment explanation
Indices: 31208811--31208980 Score: 245
Period size: 88 Copynumber: 1.9 Consensus size: 89
31208801 TAGTGTCGTA
31208811 GTAGTAGAGTCGAACTAATCCGAAGCTTTAACTTTTCCTTGAATTAAGTCTGATTGTGGTTTATC
1 GTAGTAGAGTCGAACTAATCCGAAGCTTTAACTTTTCCTTGAATTAAGTCTGATTGTGGTTTATC
** * *
31208876 TTGATCTCGATAACTAGGATCATT
66 TTGATCTAAATAAATAAGATCATT
* * * *
31208900 GTAGTAGAGTCGAAC-AATCCTAAGCTTTAGCTTTTCCTTTATTTAAGT-TCGATTGTGGTTTAT
1 GTAGTAGAGTCGAACTAATCCGAAGCTTTAACTTTTCCTTGAATTAAGTCT-GATTGTGGTTTAT
31208963 CTTGATCTAAATAAATAA
65 CTTGATCTAAATAAATAA
31208981 TTTCATTTAA
Statistics
Matches: 72, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
87 1 0.01
88 56 0.78
89 15 0.21
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (89 bp):
GTAGTAGAGTCGAACTAATCCGAAGCTTTAACTTTTCCTTGAATTAAGTCTGATTGTGGTTTATC
TTGATCTAAATAAATAAGATCATT
Found at i:31209699 original size:27 final size:27
Alignment explanation
Indices: 31209652--31209879 Score: 216
Period size: 27 Copynumber: 8.4 Consensus size: 27
31209642 TTGGTCTAGT
* *
31209652 GGTAGAATGA-CTAAAACACCCTCATAG
1 GGTAAAATGACCT-AAATACCCTCATAG
31209679 GGTAAAATGACCTAAATACCCTCATAG
1 GGTAAAATGACCTAAATACCCTCATAG
* *
31209706 GGTAAAATGACCAAAATACCCCCATAG
1 GGTAAAATGACCTAAATACCCTCATAG
*
31209733 GGTAAAATGA-CTGAAATACCCCCATAG
1 GGTAAAATGACCT-AAATACCCTCATAG
* * *
31209760 GATAAAATGAACGAAATACCC-CAATAG
1 GGTAAAATGACCTAAATACCCTC-ATAG
* *
31209787 GGTAAAAATGA-TTGAAGTAACCCT-ATAG
1 GGT-AAAATGACCT-AAAT-ACCCTCATAG
* *
31209815 GGTAAAATTACCAAAATACCCTCATAG
1 GGTAAAATGACCTAAATACCCTCATAG
* *
31209842 GGTAAAATGATCGAAATACCC-CTATAG
1 GGTAAAATGACCTAAATACCCTC-ATAG
*
31209869 AGTAAAATGAC
1 GGTAAAATGAC
31209880 TGTTATACCC
Statistics
Matches: 170, Mismatches: 20, Indels: 22
0.80 0.09 0.10
Matches are distributed among these distances:
26 8 0.05
27 138 0.81
28 20 0.12
29 4 0.02
ACGTcount: A:0.44, C:0.20, G:0.17, T:0.20
Consensus pattern (27 bp):
GGTAAAATGACCTAAATACCCTCATAG
Found at i:31209841 original size:82 final size:81
Alignment explanation
Indices: 31209652--31209879 Score: 253
Period size: 82 Copynumber: 2.8 Consensus size: 81
31209642 TTGGTCTAGT
* * * * *
31209652 GGTAGAATGACTAAAACACCCTCATAGGGTAAAATGACCTAAATACCCTCATAGGGT-AAAATGA
1 GGTAAAATGACCAAAATACCCTCATAGGGTAAAATGAACGAAATACCC-CATAGGGTAAAAATGA
*
31209716 CCAAAATACCCCCATAG
65 CCAAAATAACCCCATAG
** * *
31209733 GGTAAAATGACTGAAATACCCCCATAGGATAAAATGAACGAAATACCCCAATAGGGTAAAAATGA
1 GGTAAAATGACCAAAATACCCTCATAGGGTAAAATGAACGAAATACCCC-ATAGGGTAAAAATGA
*** * *
31209798 TTGAAGTAACCCTATAG
65 CCAAAATAACCCCATAG
* * *
31209815 GGTAAAATTACCAAAATACCCTCATAGGGTAAAATGATCGAAATACCCCTATAGAGT-AAAATGA
1 GGTAAAATGACCAAAATACCCTCATAGGGTAAAATGAACGAAATACCCC-ATAGGGTAAAAATGA
31209879 C
65 C
31209880 TGTTATACCC
Statistics
Matches: 123, Mismatches: 22, Indels: 4
0.83 0.15 0.03
Matches are distributed among these distances:
80 1 0.01
81 55 0.45
82 67 0.54
ACGTcount: A:0.44, C:0.20, G:0.17, T:0.20
Consensus pattern (81 bp):
GGTAAAATGACCAAAATACCCTCATAGGGTAAAATGAACGAAATACCCCATAGGGTAAAAATGAC
CAAAATAACCCCATAG
Found at i:31209887 original size:27 final size:27
Alignment explanation
Indices: 31209857--31209912 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
31209847 AATGATCGAA
31209857 ATACCCCTATAGAG-TAAAATGACTGTT
1 ATACCCCTA-AGAGATAAAATGACTGTT
* *
31209884 ATACCCCTAGGAGATGAAATGACTGTT
1 ATACCCCTAAGAGATAAAATGACTGTT
31209911 AT
1 AT
31209913 GGCTTTATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 3 0.12
27 23 0.88
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (27 bp):
ATACCCCTAAGAGATAAAATGACTGTT
Found at i:31209889 original size:54 final size:54
Alignment explanation
Indices: 31209652--31209879 Score: 264
Period size: 54 Copynumber: 4.2 Consensus size: 54
31209642 TTGGTCTAGT
* * * * *
31209652 GGTAGAATGACTAAAACACCCTCATAGGGTAAAATGACCTAAATA-CCCTCATAG
1 GGTAAAATGACCAAAATACCCTCATAGGGTAAAATGATCGAAATACCCCT-ATAG
* *
31209706 GGTAAAATGACCAAAATACCCCCATAGGGTAAAATGA-CTGAAATACCCCCATAG
1 GGTAAAATGACCAAAATACCCTCATAGGGTAAAATGATC-GAAATACCCCTATAG
* * * * * *
31209760 GATAAAATGAACGAAATACCC-CAATAGGGTAAAAATGATTGAAGTAACCCTATAG
1 GGTAAAATGACCAAAATACCCTC-ATAGGGT-AAAATGATCGAAATACCCCTATAG
*
31209815 GGTAAAATTACCAAAATACCCTCATAGGGTAAAATGATCGAAATACCCCTATAG
1 GGTAAAATGACCAAAATACCCTCATAGGGTAAAATGATCGAAATACCCCTATAG
*
31209869 AGTAAAATGAC
1 GGTAAAATGAC
31209880 TGTTATACCC
Statistics
Matches: 146, Mismatches: 22, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
53 2 0.01
54 97 0.66
55 46 0.32
56 1 0.01
ACGTcount: A:0.44, C:0.20, G:0.17, T:0.20
Consensus pattern (54 bp):
GGTAAAATGACCAAAATACCCTCATAGGGTAAAATGATCGAAATACCCCTATAG
Found at i:31214339 original size:13 final size:12
Alignment explanation
Indices: 31214294--31214341 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
31214284 ATTTCATGTT
31214294 ATTTAAAAAAAA
1 ATTTAAAAAAAA
* *
31214306 ATTGAAAAAAAC
1 ATTTAAAAAAAA
* *
31214318 TTTTGAAAAGAAA
1 ATTT-AAAAAAAA
31214331 ATTTAAAAAAA
1 ATTTAAAAAAA
31214342 TAAAAAAATT
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
12 18 0.67
13 9 0.33
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.25
Consensus pattern (12 bp):
ATTTAAAAAAAA
Found at i:31215812 original size:19 final size:19
Alignment explanation
Indices: 31215770--31215812 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
31215760 ACTTTGTTCT
*
31215770 CTAAAAAAAAGAAAAAAAA
1 CTAATAAAAAGAAAAAAAA
* *
31215789 C-AATAAAAAGGAGAAAAA
1 CTAATAAAAAGAAAAAAAA
31215807 CTAATA
1 CTAATA
31215813 TTTTTTTTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.74, C:0.07, G:0.09, T:0.09
Consensus pattern (19 bp):
CTAATAAAAAGAAAAAAAA
Found at i:31218171 original size:21 final size:20
Alignment explanation
Indices: 31218126--31218171 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
31218116 TTGTTGGAAT
31218126 GGTT-AATTTAATCAATTTA
1 GGTTGAATTTAATCAATTTA
*
31218145 GATTGAATTTAATTC-ATGTTA
1 GGTTGAATTTAA-TCAAT-TTA
31218166 GGTTGA
1 GGTTGA
31218172 TTGCATTTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.14
20 9 0.41
21 10 0.45
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (20 bp):
GGTTGAATTTAATCAATTTA
Found at i:31228601 original size:22 final size:22
Alignment explanation
Indices: 31228575--31228619 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
31228565 ATTATATGTA
31228575 TTAATTCATAATATAA-TTAATT
1 TTAATTCAT-ATATAATTTAATT
* *
31228597 TTAATTTATATCTAATTTAATT
1 TTAATTCATATATAATTTAATT
31228619 T
1 T
31228620 GAGTTAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (22 bp):
TTAATTCATATATAATTTAATT
Found at i:31229030 original size:18 final size:19
Alignment explanation
Indices: 31229002--31229038 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
31228992 GCATTCACAT
31229002 CTTTCCTCTCTTCTCTCCA
1 CTTTCCTCTCTTCTCTCCA
*
31229021 CTTT-CTCTCTTCTTTCCA
1 CTTTCCTCTCTTCTCTCCA
31229039 TTCCAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.05, C:0.43, G:0.00, T:0.51
Consensus pattern (19 bp):
CTTTCCTCTCTTCTCTCCA
Found at i:31229323 original size:21 final size:20
Alignment explanation
Indices: 31229278--31229323 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
31229268 TTGTTGGAAT
31229278 GGTT-AATTTAATCAATTTA
1 GGTTGAATTTAATCAATTTA
*
31229297 GCTTGAATTTAATTC-ATGTTA
1 GGTTGAATTTAA-TCAAT-TTA
31229318 GGTTGA
1 GGTTGA
31229324 TTGCATTTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.14
20 9 0.41
21 10 0.45
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.46
Consensus pattern (20 bp):
GGTTGAATTTAATCAATTTA
Found at i:31241521 original size:44 final size:45
Alignment explanation
Indices: 31241457--31241549 Score: 161
Period size: 44 Copynumber: 2.1 Consensus size: 45
31241447 GGTAACCCAC
* *
31241457 TAACAAAATCCATCGTTACACACTTTCCCTTCCACTGGGGAATCT
1 TAACAAAATCCATCGTTACACACTTTCACTTCCACTAGGGAATCT
31241502 TAAC-AAATCCATCGTTACACACTTTCACTTCCACTAGGGAATCT
1 TAACAAAATCCATCGTTACACACTTTCACTTCCACTAGGGAATCT
31241546 TAAC
1 TAAC
31241550 TGGTTGAAGC
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
44 42 0.91
45 4 0.09
ACGTcount: A:0.31, C:0.30, G:0.10, T:0.29
Consensus pattern (45 bp):
TAACAAAATCCATCGTTACACACTTTCACTTCCACTAGGGAATCT
Found at i:31247389 original size:50 final size:49
Alignment explanation
Indices: 31247328--31247575 Score: 289
Period size: 50 Copynumber: 4.9 Consensus size: 49
31247318 ACATGAGAGT
* * * *
31247328 TCTCATATCGGTGCCCATGCCATGTCCTAGACATGGTCTTACGAGGGACC
1 TCTCATCTCGGTACCAATGCCATGTCCCAGACATGGTCTTACG-GGGACC
* ***
31247378 TCTCATCTCGGTAACAATGCCATGTCATGGACATGGTCTTACGGGGGACC
1 TCTCATCTCGGTACCAATGCCATGTCCCAGACATGGTCTTAC-GGGGACC
31247428 TCTCATCTCGGTACCAATGCCATGTCCCAGACATGGTCTTACGGGGAACC
1 TCTCATCTCGGTACCAATGCCATGTCCCAGACATGGTCTTACGGGG-ACC
* *
31247478 TCTCATCTCGGTACCAACGCCATGTCCCAGACATGGTCTTACTTGGGACC
1 TCTCATCTCGGTACCAATGCCATGTCCCAGACATGGTCTTAC-GGGGACC
** *
31247528 TCTCATAACCTCAATAATGCCAATGCCATGTCCCAGATATGGTCTTAC
1 TCTCAT---CTCGGT-A--CCAATGCCATGTCCCAGACATGGTCTTAC
31247576 ATAGGGTCTC
Statistics
Matches: 173, Mismatches: 16, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
49 4 0.02
50 133 0.77
51 4 0.02
53 4 0.02
54 1 0.01
56 27 0.16
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.26
Consensus pattern (49 bp):
TCTCATCTCGGTACCAATGCCATGTCCCAGACATGGTCTTACGGGGACC
Found at i:31250159 original size:22 final size:22
Alignment explanation
Indices: 31250091--31250159 Score: 61
Period size: 22 Copynumber: 3.1 Consensus size: 22
31250081 AAATTCCAAC
*
31250091 AAAGTAAAAAG-AAGGAAAAAGGA
1 AAAG-AAAAAGAAAGG-AAAGGGA
**
31250114 AAAGAAAAAGAAA-GAAAGAAA
1 AAAGAAAAAGAAAGGAAAGGGA
* *
31250135 AAATAAAAATAAAGGAAAGGGA
1 AAAGAAAAAGAAAGGAAAGGGA
31250157 AAA
1 AAA
31250160 AAAGAATTAA
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
21 15 0.41
22 16 0.43
23 6 0.16
ACGTcount: A:0.74, C:0.00, G:0.22, T:0.04
Consensus pattern (22 bp):
AAAGAAAAAGAAAGGAAAGGGA
Found at i:31250930 original size:19 final size:20
Alignment explanation
Indices: 31250894--31250931 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
31250884 CTACGGTGAT
*
31250894 ACCTTTAGAAACACTCGATC
1 ACCTATAGAAACACTCGATC
31250914 ACCTATAGAAA-ACTCGAT
1 ACCTATAGAAACACTCGAT
31250932 ATCTTTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.39, C:0.26, G:0.11, T:0.24
Consensus pattern (20 bp):
ACCTATAGAAACACTCGATC
Found at i:31258127 original size:24 final size:24
Alignment explanation
Indices: 31258099--31258150 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
31258089 TTCCAAGAAG
*
31258099 ATTTAGTATTTATTA-CTATAATAT
1 ATTTAGCATTTATTAGC-ATAATAT
*
31258123 ATTTAGCATTTATTAGCATAATCT
1 ATTTAGCATTTATTAGCATAATAT
31258147 ATTT
1 ATTT
31258151 GACCTACAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 24 0.96
25 1 0.04
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.52
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:31258999 original size:13 final size:13
Alignment explanation
Indices: 31258981--31259005 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31258971 TAAAGACCGA
31258981 GCATTAGCGGCGG
1 GCATTAGCGGCGG
31258994 GCATTAGCGGCG
1 GCATTAGCGGCG
31259006 TTTTTCGAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.24, G:0.44, T:0.16
Consensus pattern (13 bp):
GCATTAGCGGCGG
Found at i:31259660 original size:105 final size:105
Alignment explanation
Indices: 31259572--31259761 Score: 260
Period size: 105 Copynumber: 1.8 Consensus size: 105
31259562 TGTGATTTAG
* * *
31259572 GGGTTAAGGG-TTAGGGGTTAGGGATT-TGGGTTAGAG-TTTAGGGTTTAGATTAATTAGTATTT
1 GGGTTAAGGGTTTA-GGGTTAGGGATTAAGAGTTAGAGATTTAAGGTTTAGATTAATTAGTA-TT
31259634 TTTTAATTTACATATTAAATAAGGTTTAGGGTTAGTAGTTAA
64 TTTTAATTTACATATTAAATAAGGTTTAGGGTTAGTAGTTAA
** * *
31259676 GGGTTTGGGGTTTAGGGTTAGGGGTTAAGAGTTAGTGATTTAAGGTTTAGATTAATTAGTATTTT
1 GGGTTAAGGGTTTAGGGTTAGGGATTAAGAGTTAGAGATTTAAGGTTTAGATTAATTAGTATTTT
* *
31259741 TTAATTTATATATTAATTAAG
66 TTAATTTACATATTAAATAAG
31259762 TTCTTATATA
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
104 19 0.26
105 33 0.45
106 22 0.30
ACGTcount: A:0.28, C:0.01, G:0.28, T:0.44
Consensus pattern (105 bp):
GGGTTAAGGGTTTAGGGTTAGGGATTAAGAGTTAGAGATTTAAGGTTTAGATTAATTAGTATTTT
TTAATTTACATATTAAATAAGGTTTAGGGTTAGTAGTTAA
Found at i:31259709 original size:14 final size:14
Alignment explanation
Indices: 31259656--31259710 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
31259646 TATTAAATAA
* *
31259656 GGTTTAGGGTTAGT
1 GGTTAAGGGTTAGG
* *
31259670 AGTTAAGGGTTTGG
1 GGTTAAGGGTTAGG
*
31259684 GGTTTAGGGTTAGG
1 GGTTAAGGGTTAGG
*
31259698 GGTTAAGAGTTAG
1 GGTTAAGGGTTAG
31259711 TGATTTAAGG
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.20, C:0.00, G:0.44, T:0.36
Consensus pattern (14 bp):
GGTTAAGGGTTAGG
Found at i:31259717 original size:28 final size:28
Alignment explanation
Indices: 31259658--31259722 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 28
31259648 TTAAATAAGG
* * * *
31259658 TTTAGGGTTAGTAGTTAAGGGTTTGGGG
1 TTTAGGGTTAGGAGTTAAGAGTTAGGGA
* *
31259686 TTTAGGGTTAGGGGTTAAGAGTTAGTGA
1 TTTAGGGTTAGGAGTTAAGAGTTAGGGA
*
31259714 TTTAAGGTT
1 TTTAGGGTT
31259723 TAGATTAATT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.22, C:0.00, G:0.38, T:0.40
Consensus pattern (28 bp):
TTTAGGGTTAGGAGTTAAGAGTTAGGGA
Found at i:31259845 original size:15 final size:15
Alignment explanation
Indices: 31259827--31259855 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
31259817 TATGATTTAG
31259827 GGTTTAGGAGATAGA
1 GGTTTAGGAGATAGA
31259842 GGTTTAGGAGATAG
1 GGTTTAGGAGATAG
31259856 TTTAAATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.41, T:0.28
Consensus pattern (15 bp):
GGTTTAGGAGATAGA
Found at i:31262075 original size:31 final size:31
Alignment explanation
Indices: 31262037--31262098 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
31262027 TATGTGATAG
* *
31262037 AGTCTCGTTTGTGTTTGTTTTTAGCCCAGGT
1 AGTCTCGTCTGTGTTTGTTTTTAACCCAGGT
31262068 AGTCTCGTCTGTGTTTGTTTTTAACCCAGGT
1 AGTCTCGTCTGTGTTTGTTTTTAACCCAGGT
31262099 GCTTTTATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.11, C:0.18, G:0.24, T:0.47
Consensus pattern (31 bp):
AGTCTCGTCTGTGTTTGTTTTTAACCCAGGT
Found at i:31265105 original size:43 final size:43
Alignment explanation
Indices: 31265009--31265272 Score: 282
Period size: 43 Copynumber: 6.2 Consensus size: 43
31264999 AGATTATGTT
* ** * * *
31265009 TTTAGCGGCGTTTTTGCTAGAAGCGCCACTAAAGGT-TTGTTC
1 TTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGGTCGTGGTC
* ** * *
31265051 TTTAGTGGCGTTTGTGATAAAAGCGCTGCTAAAGGTCGTGGTC
1 TTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGGTCGTGGTC
* *
31265094 TTTAGTGGCGTTTGTGGGAGAAGTGCCGCTAAAGGTCGTGGTC
1 TTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGGTCGTGGTC
* *
31265137 TTTAGCGGCCTTTGTGGGAAAAGCGCCGCTAAAGGTCAG-GGTC
1 TTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGGTC-GTGGTC
* * * * *
31265180 TATCGCGACGTTTGTGGGAGAAGCGTCGCTAAAGGTCAG-CGTC
1 TTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGGTC-GTGGTC
* * *
31265223 TTTAGCAGCGTTTGTAGGAGAAGCGCCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGGTCGTGGTC
31265266 TTTAGCG
1 TTTAGCG
31265273 CCGCTAAAGA
Statistics
Matches: 186, Mismatches: 33, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
42 30 0.16
43 155 0.83
44 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.29
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGGTCGTGGTC
Found at i:31266618 original size:24 final size:24
Alignment explanation
Indices: 31266591--31266642 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
31266581 TTTCTAAAAG
*
31266591 ATTTAGTATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
*
31266615 ATTTAGCATTTATTAGCATAATTT
1 ATTTAGCATTTATTAGCATAATAT
31266639 ATTT
1 ATTT
31266643 GACCTAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.35, C:0.06, G:0.08, T:0.52
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:31269705 original size:18 final size:16
Alignment explanation
Indices: 31269682--31269726 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 16
31269672 TCATTTCATA
31269682 TTCCATTTCACATCTCCT
1 TTCCATTTCACA--TCCT
*
31269700 TTCCATTTCTCATCCT
1 TTCCATTTCACATCCT
31269716 TTACCATTTCA
1 TT-CCATTTCA
31269727 ATATCAAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 6 0.25
17 7 0.29
18 11 0.46
ACGTcount: A:0.18, C:0.36, G:0.00, T:0.47
Consensus pattern (16 bp):
TTCCATTTCACATCCT
Found at i:31271468 original size:23 final size:23
Alignment explanation
Indices: 31271437--31271481 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
31271427 TGAGATGAAG
31271437 AACAATAAGCTC-TATCGAGCTGA
1 AACAATAAGCTCATA-CGAGCTGA
*
31271460 AACAGTAAGCTCATACGAGCTG
1 AACAATAAGCTCATACGAGCTG
31271482 TGGTGAGTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (23 bp):
AACAATAAGCTCATACGAGCTGA
Found at i:31275361 original size:25 final size:26
Alignment explanation
Indices: 31275332--31275400 Score: 86
Period size: 26 Copynumber: 2.7 Consensus size: 26
31275322 TCACATCCCA
*
31275332 ATTTTACTCC-AATAAAACTTTGACG
1 ATTTTACCCCTAATAAAACTTTGACG
* * *
31275357 ATTTTACCCCTATTAAAATTTTGATG
1 ATTTTACCCCTAATAAAACTTTGACG
*
31275383 ATTTTACCCCTAGTAAAA
1 ATTTTACCCCTAATAAAA
31275401 TTTCAAGAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
25 9 0.24
26 29 0.76
ACGTcount: A:0.35, C:0.19, G:0.07, T:0.39
Consensus pattern (26 bp):
ATTTTACCCCTAATAAAACTTTGACG
Found at i:31275379 original size:26 final size:26
Alignment explanation
Indices: 31275344--31275403 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
31275334 TTTACTCCAA
* *
31275344 TAAAACTTTGACGATTTTACCCCTAT
1 TAAAATTTTGACGATTTTACCCCTAG
*
31275370 TAAAATTTTGATGATTTTACCCCTAG
1 TAAAATTTTGACGATTTTACCCCTAG
31275396 TAAAATTT
1 TAAAATTT
31275404 CAAGAAAATC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.33, C:0.17, G:0.08, T:0.42
Consensus pattern (26 bp):
TAAAATTTTGACGATTTTACCCCTAG
Found at i:31279906 original size:22 final size:22
Alignment explanation
Indices: 31279872--31279949 Score: 120
Period size: 22 Copynumber: 3.5 Consensus size: 22
31279862 TATCAATGGC
* * *
31279872 CATGAGGGTTTAGTTCGTTAAA
1 CATGAGAGCTTAGTACGTTAAA
31279894 CATGAGAGCTTAGTACGTTAAA
1 CATGAGAGCTTAGTACGTTAAA
*
31279916 CATGAGAGCTTAGTACGTGAAA
1 CATGAGAGCTTAGTACGTTAAA
31279938 CATGAGAGCTTA
1 CATGAGAGCTTA
31279950 ATATCCTCAA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAAA
Found at i:31283766 original size:30 final size:31
Alignment explanation
Indices: 31283727--31283786 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
31283717 TGAGGTGGGA
*
31283727 TGGGAAGAGAATAAAAGTTTTAGAGGAAAAG
1 TGGGAAGAGAATAAAAATTTTAGAGGAAAAG
* * *
31283758 TGGG-AGAGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGAGAATAAAAATTTTAGAGGAAAA
31283787 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.45, C:0.00, G:0.35, T:0.20
Consensus pattern (31 bp):
TGGGAAGAGAATAAAAATTTTAGAGGAAAAG
Found at i:31286609 original size:25 final size:25
Alignment explanation
Indices: 31286549--31286609 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 25
31286539 CTCCTAAATT
*
31286549 TTAATTTAATTATCTAATTTTTCAA
1 TTAATTAAATTATCTAATTTTTCAA
* *
31286574 TTTATTGAATTAT-TAATATTTT-ATA
1 TTAATTAAATTATCTAAT-TTTTCA-A
31286599 TTAATTAAATT
1 TTAATTAAATT
31286610 TTTGAGAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
24 5 0.17
25 25 0.83
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (25 bp):
TTAATTAAATTATCTAATTTTTCAA
Found at i:31289639 original size:14 final size:14
Alignment explanation
Indices: 31289620--31289646 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
31289610 GTGGTCCAGT
31289620 TGAACTGAACCGAG
1 TGAACTGAACCGAG
31289634 TGAACTGAACCGA
1 TGAACTGAACCGA
31289647 CCAAGAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.22, G:0.26, T:0.15
Consensus pattern (14 bp):
TGAACTGAACCGAG
Found at i:31293078 original size:16 final size:18
Alignment explanation
Indices: 31293052--31293085 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
31293042 ATATACATCA
31293052 TAAATTAA-TTTCTCAAT
1 TAAATTAATTTTCTCAAT
31293069 TAAA-TAATTTTCTCAAT
1 TAAATTAATTTTCTCAAT
31293086 CTGGTTCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.19
17 13 0.81
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (18 bp):
TAAATTAATTTTCTCAAT
Found at i:31293207 original size:37 final size:37
Alignment explanation
Indices: 31293162--31293235 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
31293152 ATTTTCTACG
31293162 TTCAACAAATTCACCATGACCAATTAATTTAATTTCA
1 TTCAACAAATTCACCATGACCAATTAATTTAATTTCA
31293199 TTCAACAAATTCACCATGACCAATTAATTTAATTTCA
1 TTCAACAAATTCACCATGACCAATTAATTTAATTTCA
31293236 GTTTTTGAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.41, C:0.22, G:0.03, T:0.35
Consensus pattern (37 bp):
TTCAACAAATTCACCATGACCAATTAATTTAATTTCA
Found at i:31300727 original size:27 final size:27
Alignment explanation
Indices: 31300685--31301288 Score: 610
Period size: 27 Copynumber: 22.3 Consensus size: 27
31300675 AGAGGTCAAT
31300685 AAATGACCGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * **
31300712 AAAT-AACAAAACTACCTTCATAGGGTA
1 AAATGACCGAAA-TACCCCCATAGGGTA
* **
31300739 GAATGACCGAAATACCTTCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
31300766 GAATGACCGAAATAGCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
31300793 AATTGACCGAAATA-CCCCATTGGATA
1 AAATGACCGAAATACCCCCATAGGGTA
* * * *
31300819 AAATAACTGAAATGCCCTCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * * *
31300846 GAATGACTGAAACAGCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
31300873 AAATGATCGAAATACCTCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
31300900 AAATGACCAAAATACCCTCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
31300927 AAATGATCGAAATACCCCCATTGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
31300954 AAATGATCGAAATACCCCCATTGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * * *
31300981 AAATGATCGAAATA-CACTATAGGTTA
1 AAATGACCGAAATACCCCCATAGGGTA
*
31301007 AATTGACCGAAATA-CCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
31301033 AAATGACCGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
31301060 GAATGACCGAAATACCTCCATAAGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
31301087 GAATGATCGAAATACCTCTATACCCTTACAGGGTA
1 AAATGACCGAAATA-C-C----CCC--ATAGGGTA
* * *
31301122 AAATG-GCTAAAGTACCCCTATAGGGTA
1 AAATGACCGAAA-TACCCCCATAGGGTA
*
31301149 AAATGACCGAAATACCCCTATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
**
31301176 AAATGAATGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * * * *
31301203 GAATGATCGAAATA-CACTATAGGTTA
1 AAATGACCGAAATACCCCCATAGGGTA
*
31301229 AATTGACCGAAATA-CCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
31301255 AAATGACCGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
31301282 AAATGAC
1 AAATGAC
31301289 TGTTATACCC
Statistics
Matches: 481, Mismatches: 81, Indels: 30
0.81 0.14 0.05
Matches are distributed among these distances:
26 109 0.23
27 339 0.70
28 10 0.02
29 3 0.01
33 3 0.01
34 5 0.01
35 12 0.02
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.20
Consensus pattern (27 bp):
AAATGACCGAAATACCCCCATAGGGTA
Found at i:31301181 original size:89 final size:81
Alignment explanation
Indices: 31301114--31301288 Score: 198
Period size: 79 Copynumber: 2.2 Consensus size: 81
31301104 CTATACCCTT
* *
31301114 ACAGGGTAAAATG-GCTAAAGTACCCCTATAGGGTAAAATGACCGAAATACCCCTATAGGGTAAA
1 ACAGGGTAAAATGACCGAAA-TACCCCTATAGGGTAAAATGACCGAAATACCCC-ATAGGGTAAA
31301178 ATGAAT-GAAATA-CCCCC
64 ATG-ATCGAAATACCCCCC
* * * * * *
31301195 ATAGGGTAGAATGATCGAAATA-CACTATAGGTTAAATTGACCGAAATACCCCATAGGGTAAAAT
1 ACAGGGTAAAATGACCGAAATACCCCTATAGGGTAAAATGACCGAAATACCCCATAGGGTAAAAT
*
31301259 GACCGAAATA-CCCCC
66 GATCGAAATACCCCCC
*
31301274 ATAGGGTAAAATGAC
1 ACAGGGTAAAATGAC
31301289 TGTTATACCC
Statistics
Matches: 82, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
78 1 0.01
79 37 0.45
80 27 0.33
81 13 0.16
82 4 0.05
ACGTcount: A:0.41, C:0.19, G:0.20, T:0.19
Consensus pattern (81 bp):
ACAGGGTAAAATGACCGAAATACCCCTATAGGGTAAAATGACCGAAATACCCCATAGGGTAAAAT
GATCGAAATACCCCCC
Found at i:31301191 original size:222 final size:214
Alignment explanation
Indices: 31300685--31301288 Score: 741
Period size: 222 Copynumber: 2.8 Consensus size: 214
31300675 AGAGGTCAAT
* * * * * **
31300685 AAATGACCGAAATACCCCCATAGGGTAAAAT-AACAAAACTA-CCTTCATAGGGTAGAATGACCG
1 AAATGACCAAAATACCCCTATAGGGTAAAATGAACGAAA-TACCCCT-ATAGGGTAAAATGAATG
** * * * *
31300748 AAATACCTTCATAGGGTAGAATGACCGAAATAGCCCCATAGGGTAAATTGACCGAAATACCCCAT
64 AAATACCCCCATAGGGTAGAATGATCGAAATA-CACTATAGGTTAAATTGACCGAAATACCCCAT
* * * * * * * *
31300813 TGGATAAAATAACTGAAATGCCCTCATAGGGTAGAATGACTGAAACAGCCCCATAGGGTAAAATG
128 AGGGTAAAATGACCGAAATACCCCCATAGGGTAGAATGACCGAAACAGCCCCATAAGGTAAAATG
*
31300878 ATCGAAATACCTCCATAGGGTA
193 ATCGAAATACCTCCACAGGGTA
* * *
31300900 AAATGACCAAAATA-CCCTCATAGGGTAAAATGATCGAAATACCCCCATTGGGTAAAATG-ATCG
1 AAATGACCAAAATACCCCT-ATAGGGTAAAATGAACGAAATACCCCTATAGGGTAAAATGAAT-G
* *
31300963 AAATACCCCCATTGGGTAAAATGATCGAAATACACTATAGGTTAAATTGACCGAAATACCCCATA
64 AAATACCCCCATAGGGTAGAATGATCGAAATACACTATAGGTTAAATTGACCGAAATACCCCATA
* *
31301028 GGGTAAAATGACCGAAATACCCCCATAGGGTAGAATGACCGAAATA-CCTCCATAAGGTAGAATG
129 GGGTAAAATGACCGAAATACCCCCATAGGGTAGAATGACCGAAACAGCC-CCATAAGGTAAAATG
31301092 ATCGAAATACCTCTATACCCTTACAGGGTA
193 ATCGAAATA-C-C--T--CC--ACAGGGTA
* * * *
31301122 AAATGGCTAAAGTACCCCTATAGGGTAAAATGACCGAAATACCCCTATAGGGTAAAATGAATGAA
1 AAATGACCAAAATACCCCTATAGGGTAAAATGAACGAAATACCCCTATAGGGTAAAATGAATGAA
31301187 ATACCCCCATAGGGTAGAATGATCGAAATACACTATAGGTTAAATTGACCGAAATACCCCATAGG
66 ATACCCCCATAGGGTAGAATGATCGAAATACACTATAGGTTAAATTGACCGAAATACCCCATAGG
*
31301252 GTAAAATGACCGAAATACCCCCATAGGGTAAAATGAC
131 GTAAAATGACCGAAATACCCCCATAGGGTAGAATGAC
31301289 TGTTATACCC
Statistics
Matches: 336, Mismatches: 38, Indels: 23
0.85 0.10 0.06
Matches are distributed among these distances:
213 2 0.01
214 93 0.28
215 67 0.20
216 8 0.02
218 1 0.00
220 2 0.01
222 157 0.47
223 6 0.02
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.20
Consensus pattern (214 bp):
AAATGACCAAAATACCCCTATAGGGTAAAATGAACGAAATACCCCTATAGGGTAAAATGAATGAA
ATACCCCCATAGGGTAGAATGATCGAAATACACTATAGGTTAAATTGACCGAAATACCCCATAGG
GTAAAATGACCGAAATACCCCCATAGGGTAGAATGACCGAAACAGCCCCATAAGGTAAAATGATC
GAAATACCTCCACAGGGTA
Found at i:31304498 original size:27 final size:27
Alignment explanation
Indices: 31304437--31304498 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
31304427 TTGAGATCTT
* *
31304437 CATGTTTAGTGTCCCGACGAACTATTC
1 CATGTTTAGTGTCCCAACGAACTATCC
*
31304464 CATATTTAGTGTCCCAAC-AGACTATCC
1 CATGTTTAGTGTCCCAACGA-ACTATCC
*
31304491 CGTGTTTA
1 CATGTTTA
31304499 ATATTTTATT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
26 1 0.03
27 28 0.97
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (27 bp):
CATGTTTAGTGTCCCAACGAACTATCC
Found at i:31304814 original size:45 final size:45
Alignment explanation
Indices: 31304710--31304814 Score: 147
Period size: 45 Copynumber: 2.3 Consensus size: 45
31304700 TTCAACCAGG
* * *
31304710 GTCTTACTTATTTCCAAAATGATGTCATAGCATCTTTCAGTTATT
1 GTCTTACTCATTTCTAAAATGATGTCATAGAATCTTTCAGTTATT
* ** *
31304755 ATCTTACTCATTTCTATCATGATGTCATAGAATCTTTTAGTTATT
1 GTCTTACTCATTTCTAAAATGATGTCATAGAATCTTTCAGTTATT
31304800 GTCTTACTCATTTCT
1 GTCTTACTCATTTCT
31304815 GGCATATAGC
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.25, C:0.18, G:0.10, T:0.48
Consensus pattern (45 bp):
GTCTTACTCATTTCTAAAATGATGTCATAGAATCTTTCAGTTATT
Found at i:31307781 original size:20 final size:20
Alignment explanation
Indices: 31307756--31307806 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
31307746 ATCGTAAAAC
*
31307756 GGTATCGATACCAGGATAAA
1 GGTATCGATACCAGAATAAA
* *
31307776 GGTATCGATACTATAATAAA
1 GGTATCGATACCAGAATAAA
*
31307796 GGTATCAATAC
1 GGTATCGATAC
31307807 TTTAATAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (20 bp):
GGTATCGATACCAGAATAAA
Found at i:31307807 original size:20 final size:20
Alignment explanation
Indices: 31307771--31307820 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
31307761 CGATACCAGG
*
31307771 ATAAAGGTATCGATACTATA
1 ATAAAGGTATCAATACTATA
*
31307791 ATAAAGGTATCAATACTTTA
1 ATAAAGGTATCAATACTATA
*
31307811 ATAAAAGTAT
1 ATAAAGGTAT
31307821 TAAAACTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.32
Consensus pattern (20 bp):
ATAAAGGTATCAATACTATA
Found at i:31307828 original size:20 final size:20
Alignment explanation
Indices: 31307789--31307829 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
31307779 ATCGATACTA
* *
31307789 TAATAAAGGTATCAATACTT
1 TAATAAAAGTATCAAAACTT
*
31307809 TAATAAAAGTATTAAAACTT
1 TAATAAAAGTATCAAAACTT
31307829 T
1 T
31307830 GAGAAAAGCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.37
Consensus pattern (20 bp):
TAATAAAAGTATCAAAACTT
Found at i:31307865 original size:20 final size:20
Alignment explanation
Indices: 31307803--31307869 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 20
31307793 AAAGGTATCA
* * *
31307803 ATACTTTAATAAAAGTATTA
1 ATACTTTGAGAAAAGTATTG
* * *
31307823 AAACTTTGAGAAAAGCATCG
1 ATACTTTGAGAAAAGTATTG
31307843 ATACTTTGAGAAAAGTATTG
1 ATACTTTGAGAAAAGTATTG
31307863 ATACTTT
1 ATACTTT
31307870 AAGGAATGTA
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.34
Consensus pattern (20 bp):
ATACTTTGAGAAAAGTATTG
Found at i:31311497 original size:11 final size:10
Alignment explanation
Indices: 31311466--31311534 Score: 52
Period size: 10 Copynumber: 6.8 Consensus size: 10
31311456 TATTTATGAG
*
31311466 TTTTATGAAT
1 TTTTATAAAT
*
31311476 TTTTATGAAT
1 TTTTATAAAT
*
31311486 TTTTATAAAA
1 TTTTATAAAT
31311496 TTTTA-AATAT
1 TTTTATAA-AT
*
31311506 GTTTTATTAA-
1 -TTTTATAAAT
*
31311516 TTTTATAATTT
1 TTTTATAA-AT
31311527 TTTTATAA
1 TTTTATAA
31311535 TTTATTAGAC
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
9 9 0.19
10 24 0.50
11 14 0.29
12 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (10 bp):
TTTTATAAAT
Found at i:31311500 original size:10 final size:10
Alignment explanation
Indices: 31311435--31311491 Score: 59
Period size: 10 Copynumber: 5.9 Consensus size: 10
31311425 TTATATATAT
31311435 AATTTATTA-G
1 AATTT-TTATG
31311445 AATTTTTAT-
1 AATTTTTATG
31311454 -ATTATTTATG
1 AATT-TTTATG
*
31311464 -AGTTTTATG
1 AATTTTTATG
31311473 AATTTTTATG
1 AATTTTTATG
31311483 AATTTTTAT
1 AATTTTTAT
31311492 AAAATTTTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
8 3 0.07
9 14 0.34
10 24 0.59
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.60
Consensus pattern (10 bp):
AATTTTTATG
Found at i:31311517 original size:20 final size:19
Alignment explanation
Indices: 31311465--31311537 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 19
31311455 TTATTTATGA
31311465 GTTTTATGAATTTTTATGAATT
1 GTTTTAT-AA-TTTTAT-AATT
*
31311487 -TTTATAAAATTTTA-AATAT
1 GTTT-TATAATTTTATAAT-T
31311506 GTTTTATTAATTTTATAATT
1 GTTTTA-TAATTTTATAATT
*
31311526 TTTTTATAATTT
1 GTTTTATAATTT
31311538 ATTAGACTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
18 3 0.07
19 9 0.21
20 21 0.49
21 8 0.19
22 2 0.05
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (19 bp):
GTTTTATAATTTTATAATT
Found at i:31312982 original size:17 final size:14
Alignment explanation
Indices: 31312948--31312978 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
31312938 TAGCTATTAC
31312948 TATAACTATTAATA
1 TATAACTATTAATA
*
31312962 TATAACTATTATTA
1 TATAACTATTAATA
31312976 TAT
1 TAT
31312979 TATAGATTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (14 bp):
TATAACTATTAATA
Found at i:31313281 original size:16 final size:17
Alignment explanation
Indices: 31313260--31313292 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
31313250 ATGACTAAAT
31313260 CTATTAATATA-TATAA
1 CTATTAATATATTATAA
*
31313276 CTATTACTATATTATAA
1 CTATTAATATATTATAA
31313293 ATTATAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (17 bp):
CTATTAATATATTATAA
Found at i:31313298 original size:28 final size:28
Alignment explanation
Indices: 31313245--31313298 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
31313235 ATATAGTATT
*
31313245 TAACTATGACTAAATCTATTAATATATA
1 TAACTATGACTAAATCTATAAATATATA
* *
31313273 TAACTATTACTATAT-TATAAAT-TATA
1 TAACTATGACTAAATCTATAAATATATA
31313299 ACAAAAGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 4 0.17
27 6 0.26
28 13 0.57
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (28 bp):
TAACTATGACTAAATCTATAAATATATA
Found at i:31314201 original size:15 final size:15
Alignment explanation
Indices: 31314181--31314224 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
31314171 ATGAATTACT
31314181 AAATTTAAAATTAAA
1 AAATTTAAAATTAAA
* *
31314196 ATATTTATAATCTAAA
1 AAATTTAAAAT-TAAA
*
31314212 AAATTCAAAATTA
1 AAATTTAAAATTA
31314225 TTTGAATGTA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (15 bp):
AAATTTAAAATTAAA
Found at i:31315742 original size:26 final size:26
Alignment explanation
Indices: 31315713--31315764 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
31315703 AATATTGACA
*
31315713 TAAACAATATTTATCTTAATGATAAT
1 TAAACAATATTTATATTAATGATAAT
* *
31315739 TAAATAATATTTATATTTATGATAAT
1 TAAACAATATTTATATTAATGATAAT
31315765 ATTATTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (26 bp):
TAAACAATATTTATATTAATGATAAT
Found at i:31315784 original size:21 final size:21
Alignment explanation
Indices: 31315741--31315797 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
31315731 ATGATAATTA
* * **
31315741 AATAATATTTATATTTATGAT
1 AATATTATTTATTTTTACAAT
31315762 AATATTATTTATTTTTACAAT
1 AATATTATTTATTTTTACAAT
* *
31315783 AATTTTATATATTTT
1 AATATTATTTATTTT
31315798 CATATTCTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (21 bp):
AATATTATTTATTTTTACAAT
Found at i:31316492 original size:23 final size:23
Alignment explanation
Indices: 31316466--31316545 Score: 78
Period size: 23 Copynumber: 3.4 Consensus size: 23
31316456 AGTTAAAAAA
31316466 AATTTTATTATCTGAAAAAACAT
1 AATTTTATTATCTGAAAAAACAT
31316489 AATTTTATTTTTATCT-ATTTAAAAA-A-
1 AATTTTA---TTATCTGA---AAAAACAT
31316515 AA-TTTATTATCTGAAAAAACAT
1 AATTTTATTATCTGAAAAAACAT
31316537 AATTTTATT
1 AATTTTATT
31316546 TTTATCTATT
Statistics
Matches: 47, Mismatches: 0, Indels: 20
0.70 0.00 0.30
Matches are distributed among these distances:
20 5 0.11
21 1 0.02
22 8 0.17
23 14 0.30
25 5 0.11
26 8 0.17
27 1 0.02
28 5 0.11
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (23 bp):
AATTTTATTATCTGAAAAAACAT
Found at i:31316518 original size:26 final size:26
Alignment explanation
Indices: 31316489--31316576 Score: 64
Period size: 26 Copynumber: 3.5 Consensus size: 26
31316479 GAAAAAACAT
31316489 AATTTTATTTTTATCTATTTAAAAAA
1 AATTTTATTTTTATCTATTTAAAAAA
31316515 AA-TTTA---TTATCTGA---AAAAACA
1 AATTTTATTTTTATCT-ATTTAAAAA-A
* **
31316536 TAATTTTATTTTTATCTATTTATAATT
1 -AATTTTATTTTTATCTATTTAAAAAA
31316563 AATTTTAATTTTTA
1 AATTTT-ATTTTTA
31316577 AGGTGTAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 21
0.67 0.04 0.29
Matches are distributed among these distances:
20 5 0.10
21 1 0.02
22 8 0.17
23 5 0.10
25 5 0.10
26 14 0.29
27 7 0.15
28 3 0.06
ACGTcount: A:0.40, C:0.05, G:0.01, T:0.55
Consensus pattern (26 bp):
AATTTTATTTTTATCTATTTAAAAAA
Found at i:31316522 original size:48 final size:49
Alignment explanation
Indices: 31316458--31316557 Score: 193
Period size: 48 Copynumber: 2.1 Consensus size: 49
31316448 AGAATATAAG
31316458 TTAAAAAAAATTTTATTATCTGAAAAAACATAATTTTATTTTTATCTAT
1 TTAAAAAAAATTTTATTATCTGAAAAAACATAATTTTATTTTTATCTAT
31316507 TTAAAAAAAA-TTTATTATCTGAAAAAACATAATTTTATTTTTATCTAT
1 TTAAAAAAAATTTTATTATCTGAAAAAACATAATTTTATTTTTATCTAT
31316555 TTA
1 TTA
31316558 TAATTAATTT
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
48 41 0.80
49 10 0.20
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (49 bp):
TTAAAAAAAATTTTATTATCTGAAAAAACATAATTTTATTTTTATCTAT
Found at i:31321216 original size:28 final size:28
Alignment explanation
Indices: 31321179--31321233 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
31321169 TAATAGTGTG
* * *
31321179 TGGGCTTTAGCCTAATGTAGTAACAGTC
1 TGGGCCTTAGCCCAATATAGTAACAGTC
31321207 TGGGCCTTAGCCCAATATAGTAACAGT
1 TGGGCCTTAGCCCAATATAGTAACAGT
31321234 ACAATGCAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (28 bp):
TGGGCCTTAGCCCAATATAGTAACAGTC
Found at i:31321369 original size:26 final size:26
Alignment explanation
Indices: 31321340--31321436 Score: 97
Period size: 26 Copynumber: 3.7 Consensus size: 26
31321330 CACCAATATC
*
31321340 GCAGCAAAGTTGTCAGTAATAGTGAT
1 GCAGCAAAGTTGCCAGTAATAGTGAT
*
31321366 GCAGCAATGTTGCCAGTAATAGTGAT
1 GCAGCAAAGTTGCCAGTAATAGTGAT
* * * * *
31321392 GCAGTAATA-CTGCCAGTAACAGTAAC
1 GCAGCAA-AGTTGCCAGTAATAGTGAT
* *
31321418 ACAGCAAAGCTGCCAGTAA
1 GCAGCAAAGTTGCCAGTAA
31321437 CAGTATATGT
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
25 1 0.02
26 58 0.98
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.22
Consensus pattern (26 bp):
GCAGCAAAGTTGCCAGTAATAGTGAT
Found at i:31321398 original size:14 final size:14
Alignment explanation
Indices: 31321353--31321400 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
31321343 GCAAAGTTGT
31321353 CAGTAATAGTGATG
1 CAGTAATAGTGATG
*
31321367 CAGCAAT-GT--TG
1 CAGTAATAGTGATG
31321378 CCAGTAATAGTGATG
1 -CAGTAATAGTGATG
31321393 CAGTAATA
1 CAGTAATA
31321401 CTGCCAGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
11 2 0.07
12 6 0.21
13 4 0.14
14 14 0.50
15 2 0.07
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.27
Consensus pattern (14 bp):
CAGTAATAGTGATG
Found at i:31321684 original size:27 final size:27
Alignment explanation
Indices: 31321624--31321793 Score: 161
Period size: 27 Copynumber: 6.3 Consensus size: 27
31321614 GGGTATAACA
* *
31321624 ATCATTTTACCCTTCG-GGAGT-TTTCG
1 ATCATTTTACCTTTCGAGG-GTATTTTG
*
31321650 ATCATTTTATCTTTCGAGGGTATTTTG
1 ATCATTTTACCTTTCGAGGGTATTTTG
31321677 ATCATTTTA-CTCTTCGAGGGTATTTT-
1 ATCATTTTACCT-TTCGAGGGTATTTTG
**
31321703 AGTCATTTTACCCTTT-GAGGGTATTTCC
1 A-TCATTTTA-CCTTTCGAGGGTATTTTG
* * *
31321731 ATCATTTTACCCTTCGGGGGTATTTCG
1 ATCATTTTACCTTTCGAGGGTATTTTG
* *
31321758 ATCATTCTACCCTTCGAGGGTATTTTG
1 ATCATTTTACCTTTCGAGGGTATTTTG
* *
31321785 GTTATTTTA
1 ATCATTTTA
31321794 GGCCCATTAC
Statistics
Matches: 123, Mismatches: 13, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
26 23 0.19
27 95 0.77
28 3 0.02
29 2 0.02
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.46
Consensus pattern (27 bp):
ATCATTTTACCTTTCGAGGGTATTTTG
Found at i:31321725 original size:54 final size:54
Alignment explanation
Indices: 31321624--31321793 Score: 186
Period size: 54 Copynumber: 3.2 Consensus size: 54
31321614 GGGTATAACA
* *
31321624 ATCATTTTACCCTTCG-GGAGT-TTTCGATCATTTTA-TCTTTCGAGGGTATTTTG
1 ATCATTTTACCCTTCGAGG-GTATTTAGATCATTTTACCCTTT-GAGGGTATTTTG
* **
31321677 ATCATTTTACTCTTCGAGGGTATTTTAG-TCATTTTACCCTTTGAGGGTATTTCC
1 ATCATTTTACCCTTCGAGGGTA-TTTAGATCATTTTACCCTTTGAGGGTATTTTG
* * * *
31321731 ATCATTTTACCCTTCGGGGGTATTTCGATCATTCTACCCTTCGAGGGTATTTTG
1 ATCATTTTACCCTTCGAGGGTATTTAGATCATTTTACCCTTTGAGGGTATTTTG
* *
31321785 GTTATTTTA
1 ATCATTTTA
31321794 GGCCCATTAC
Statistics
Matches: 98, Mismatches: 14, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
53 21 0.21
54 69 0.70
55 8 0.08
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.46
Consensus pattern (54 bp):
ATCATTTTACCCTTCGAGGGTATTTAGATCATTTTACCCTTTGAGGGTATTTTG
Found at i:31321773 original size:81 final size:80
Alignment explanation
Indices: 31321625--31321793 Score: 223
Period size: 81 Copynumber: 2.1 Consensus size: 80
31321615 GGTATAACAA
* * * * * *
31321625 TCATTTTACCCTTCGGGAGTTTTCGATCATTTTATCTTTCGAGGGTATTTTGATCATTTTACTCT
1 TCATTTTACCCTTCGGGAGTTTTCCATCATTTTACCCTTCGAGGGTATTTCGATCATTCTACCCT
31321690 TCGAGGGTATTTTAG
66 TCGAGGGTATTTTAG
* *
31321705 TCATTTTACCCTTTGAGG-GTATTTCCATCATTTTACCCTTCGGGGGTATTTCGATCATTCTACC
1 TCATTTTACCCTTCG-GGAGT-TTTCCATCATTTTACCCTTCGAGGGTATTTCGATCATTCTACC
*
31321769 CTTCGAGGGTATTTTGG
64 CTTCGAGGGTATTTTAG
*
31321786 TTATTTTA
1 TCATTTTA
31321794 GGCCCATTAC
Statistics
Matches: 77, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
80 16 0.21
81 61 0.79
ACGTcount: A:0.17, C:0.18, G:0.18, T:0.46
Consensus pattern (80 bp):
TCATTTTACCCTTCGGGAGTTTTCCATCATTTTACCCTTCGAGGGTATTTCGATCATTCTACCCT
TCGAGGGTATTTTAG
Found at i:31330602 original size:43 final size:42
Alignment explanation
Indices: 31330544--31330740 Score: 279
Period size: 43 Copynumber: 4.6 Consensus size: 42
31330534 CAATGCCTAC
* * *
31330544 GTCCCAGACGA-GGTCTTACATGTAATCAAATATCGATGCCACT
1 GTCCCAGAC-ATGGTCTTACACGTAATCATATA-CGATGCCAAT
* *
31330587 GTCCCAGACAGGGTCTTATACGTAAATCATATACGATGCCAAT
1 GTCCCAGACATGGTCTTACACGT-AATCATATACGATGCCAAT
*
31330630 GTCCCAGACATGGTCTTACACGTAAATCTTATACGATGCCAAT
1 GTCCCAGACATGGTCTTACACGT-AATCATATACGATGCCAAT
31330673 GTCCCAGACATGGTCTTACACGTAACTCATATACGATGCCAAT
1 GTCCCAGACATGGTCTTACACGTAA-TCATATACGATGCCAAT
*
31330716 GTCCTAGACATGGTCTTACACGTAA
1 GTCCCAGACATGGTCTTACACGTAA
31330741 ATCTCAAATC
Statistics
Matches: 142, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
42 3 0.02
43 131 0.92
44 8 0.06
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.26
Consensus pattern (42 bp):
GTCCCAGACATGGTCTTACACGTAATCATATACGATGCCAAT
Found at i:31330667 original size:86 final size:87
Alignment explanation
Indices: 31330544--31330776 Score: 307
Period size: 86 Copynumber: 2.7 Consensus size: 87
31330534 CAATGCCTAC
* * * *
31330544 GTCCCAGACGA-GGTCTTACATGT-AATCAAATATCGATGCCACTGTCCCAGACAGGGTCTTATA
1 GTCCCAGAC-ATGGTCTTACACGTAAATCTAATATCGATGCCAATGTCCCAGACAGGGTCTTACA
31330607 CGTAAATCATATACGATGCCAAT
65 CGTAAATCATATACGATGCCAAT
* *
31330630 GTCCCAGACATGGTCTTACACGTAAATCTTATA-CGATGCCAATGTCCCAGACATGGTCTTACAC
1 GTCCCAGACATGGTCTTACACGTAAATCTAATATCGATGCCAATGTCCCAGACAGGGTCTTACAC
*
31330694 GTAACTCATATACGATGCCAAT
66 GTAAATCATATACGATGCCAAT
* *
31330716 GTCCTAGACATGGTCTTACACGTAAATCTCAA-ATCAATGCC-ATCGTCCCAGAC-GTGGTCTT
1 GTCCCAGACATGGTCTTACACGTAAATCT-AATATCGATGCCAAT-GTCCCAGACAG-GGTCTT
31330777 TCTCAATATT
Statistics
Matches: 130, Mismatches: 11, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
85 1 0.01
86 100 0.77
87 29 0.22
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.27
Consensus pattern (87 bp):
GTCCCAGACATGGTCTTACACGTAAATCTAATATCGATGCCAATGTCCCAGACAGGGTCTTACAC
GTAAATCATATACGATGCCAAT
Found at i:31338642 original size:24 final size:21
Alignment explanation
Indices: 31338559--31338656 Score: 121
Period size: 21 Copynumber: 4.7 Consensus size: 21
31338549 TCTTCAAGGA
*
31338559 TATGTAATCTTAGATATGA--
1 TATGCAATCTTAGATATGATT
*
31338578 TATGCAATCTTAGATATGATA
1 TATGCAATCTTAGATATGATT
31338599 TATGCAATCTTAGATATGATT
1 TATGCAATCTTAGATATGATT
31338620 TATGCAATCTTAGAAGATATGATT
1 TATGCAATCTT---AGATATGATT
*
31338644 T-TGTAATCTTAGA
1 TATGCAATCTTAGA
31338657 GATTTAATTT
Statistics
Matches: 71, Mismatches: 3, Indels: 9
0.86 0.04 0.11
Matches are distributed among these distances:
19 18 0.25
20 3 0.04
21 31 0.44
23 8 0.11
24 11 0.15
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.41
Consensus pattern (21 bp):
TATGCAATCTTAGATATGATT
Found at i:31352006 original size:6 final size:6
Alignment explanation
Indices: 31351995--31352031 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
31351985 AGTATACTTT
*
31351995 TATACA TATACA TATACA TATTCA TATACA TATACA T
1 TATACA TATACA TATACA TATACA TATACA TATACA T
31352032 CTGCATGTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.46, C:0.16, G:0.00, T:0.38
Consensus pattern (6 bp):
TATACA
Found at i:31353929 original size:12 final size:12
Alignment explanation
Indices: 31353912--31353940 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
31353902 TTCTTTTCGG
31353912 TTTTAGTTTTTA
1 TTTTAGTTTTTA
31353924 TTTTAGTTTTTA
1 TTTTAGTTTTTA
31353936 TTTTA
1 TTTTA
31353941 CCAGGATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (12 bp):
TTTTAGTTTTTA
Found at i:31355266 original size:8 final size:8
Alignment explanation
Indices: 31355227--31355267 Score: 82
Period size: 8 Copynumber: 5.1 Consensus size: 8
31355217 TTTTAAATAA
31355227 TATTTTAT
1 TATTTTAT
31355235 TATTTTAT
1 TATTTTAT
31355243 TATTTTAT
1 TATTTTAT
31355251 TATTTTAT
1 TATTTTAT
31355259 TATTTTAT
1 TATTTTAT
31355267 T
1 T
31355268 GTTTAGTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 33 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:31356764 original size:2 final size:2
Alignment explanation
Indices: 31356759--31356787 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
31356749 TATATATATA
31356759 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
31356788 TTTATTATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:31358809 original size:26 final size:26
Alignment explanation
Indices: 31358780--31358830 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
31358770 GATGTCCCAT
* *
31358780 AAGATAGTCCTTGGCGAACTTTCCAA
1 AAGATAGTCCATGACGAACTTTCCAA
*
31358806 AAGATAGTCCATGACGGACTTTCCA
1 AAGATAGTCCATGACGAACTTTCCA
31358831 GATATGATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (26 bp):
AAGATAGTCCATGACGAACTTTCCAA
Found at i:31360176 original size:22 final size:23
Alignment explanation
Indices: 31360141--31360184 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
31360131 TTATTATATA
*
31360141 AAATAAAATTAATTATTATGTAGG
1 AAATAAAA-TAATTATAATGTAGG
31360165 AAATAAAA-AATTATAATGTA
1 AAATAAAATAATTATAATGTA
31360185 TAAATTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 11 0.58
24 8 0.42
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34
Consensus pattern (23 bp):
AAATAAAATAATTATAATGTAGG
Found at i:31366001 original size:3 final size:3
Alignment explanation
Indices: 31365993--31366058 Score: 105
Period size: 3 Copynumber: 22.0 Consensus size: 3
31365983 CATGTTATAC
*
31365993 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
31366041 TAT CAT TAT CAT TAT TAT
1 TAT TAT TAT TAT TAT TAT
31366059 AGTTATTGCT
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:31366361 original size:23 final size:21
Alignment explanation
Indices: 31366335--31366377 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
31366325 TTAAACACAT
31366335 ATTTTTATATATAATATATACAC
1 ATTTTTATA-AT-ATATATACAC
*
31366358 ATTTTTTTAATATATATACA
1 ATTTTTATAATATATATACA
31366378 TTTTTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 9 0.47
22 2 0.11
23 8 0.42
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (21 bp):
ATTTTTATAATATATATACAC
Found at i:31366370 original size:19 final size:19
Alignment explanation
Indices: 31366346--31366386 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
31366336 TTTTTATATA
31366346 TAATATATACACATTTTTT
1 TAATATATACACATTTTTT
*
31366365 TAATATATATACATTTTTT
1 TAATATATACACATTTTTT
31366384 TAA
1 TAA
31366387 AGCTTTTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (19 bp):
TAATATATACACATTTTTT
Found at i:31366374 original size:21 final size:22
Alignment explanation
Indices: 31366329--31366386 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 22
31366319 TATGTATTAA
31366329 ACACATATTTTTATATATAATATAT
1 ACACAT-TTTTT-TA-ATAATATAT
31366354 ACACATTTTTTTAAT-ATATAT
1 ACACATTTTTTTAATAATATAT
31366375 --ACATTTTTTTAA
1 ACACATTTTTTTAA
31366387 AGCTTTTATG
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
19 12 0.36
21 6 0.18
22 2 0.06
23 2 0.06
24 5 0.15
25 6 0.18
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.52
Consensus pattern (22 bp):
ACACATTTTTTTAATAATATAT
Found at i:31368466 original size:19 final size:20
Alignment explanation
Indices: 31368422--31368466 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
31368412 AACGTCTCTT
*
31368422 TATGCA-TTCATTTCATGCA
1 TATGCATTTCATTACATGCA
31368441 T-TCGCATTTCATTACAT-CA
1 TAT-GCATTTCATTACATGCA
31368460 TATGCAT
1 TATGCAT
31368467 CAAAGATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
18 1 0.05
19 11 0.50
20 10 0.45
ACGTcount: A:0.27, C:0.22, G:0.09, T:0.42
Consensus pattern (20 bp):
TATGCATTTCATTACATGCA
Found at i:31371112 original size:47 final size:46
Alignment explanation
Indices: 31371048--31371181 Score: 191
Period size: 45 Copynumber: 2.9 Consensus size: 46
31371038 TAAAAGGTGG
31371048 GACCAAGGTGAAAGCCTACAAAGGGCGCTTTGAGTCAAAAAAAAAA
1 GACCAAGGTGAAAGCCTACAAAGGGCGCTTTGAGTCAAAAAAAAAA
* *
31371094 GGGCCAAGGTGAAAGCCTACAAAGGGCTCTTTGAGTC-AAAAAAAAA
1 -GACCAAGGTGAAAGCCTACAAAGGGCGCTTTGAGTCAAAAAAAAAA
* * * *
31371140 GACCAGGGTGAAACCCTACAAAGGGAGCCTTGAGT-AAAAAAA
1 GACCAAGGTGAAAGCCTACAAAGGGCGCTTTGAGTCAAAAAAA
31371182 GGAAAAAAAA
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
45 35 0.45
46 9 0.12
47 34 0.44
ACGTcount: A:0.43, C:0.18, G:0.25, T:0.13
Consensus pattern (46 bp):
GACCAAGGTGAAAGCCTACAAAGGGCGCTTTGAGTCAAAAAAAAAA
Found at i:31371150 original size:45 final size:46
Alignment explanation
Indices: 31371047--31371181 Score: 193
Period size: 47 Copynumber: 3.0 Consensus size: 46
31371037 CTAAAAGGTG
31371047 GGACCAAGGTGAAAGCCTACAAAGGGCGCTTTGAGTCAAAAAAAAAA
1 GGACCAAGGTGAAAGCCTACAAAGGGCGCTTTGAGTC-AAAAAAAAA
* *
31371094 GGGCCAAGGTGAAAGCCTACAAAGGGCTCTTTGAGTCAAAAAAAAA
1 GGACCAAGGTGAAAGCCTACAAAGGGCGCTTTGAGTCAAAAAAAAA
* * * *
31371140 -GACCAGGGTGAAACCCTACAAAGGGAGCCTTGAGT-AAAAAAA
1 GGACCAAGGTGAAAGCCTACAAAGGGCGCTTTGAGTCAAAAAAA
31371182 GGAAAAAAAA
Statistics
Matches: 80, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
44 7 0.09
45 29 0.36
46 9 0.11
47 35 0.44
ACGTcount: A:0.43, C:0.18, G:0.26, T:0.13
Consensus pattern (46 bp):
GGACCAAGGTGAAAGCCTACAAAGGGCGCTTTGAGTCAAAAAAAAA
Found at i:31372820 original size:177 final size:177
Alignment explanation
Indices: 31372454--31372909 Score: 538
Period size: 177 Copynumber: 2.6 Consensus size: 177
31372444 TGAATACAAA
* * * * * *
31372454 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCCAAGAAAGCAGATCTTATCTTCATGTACT
1 AGATCTTGTCTTCCTATACTGGTAGTGAAGTAGATCAAAG-ATGCAGATCTTGTCTTCATGTACT
* * *
31372519 AGCGTG-AGCAGATCAAAGATAGCAGATCTTGTCTTCCCATACTGGTGGCGGAGTAGATCGAAGA
65 AGCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGA
* * * *
31372583 AAGTAAATCTTGTCTTCATGTACTGACGTGAAGTAGATCAAAGATAGC
130 AAGCAAATCTTATCTTCATGTACTGACGTGAAGTAGATCAAAGAAAAC
* * * * * *
31372631 AAATCCTGTCTTCCTATATTGGTAGTGAAGTGGATCGAAGATGCAGATCTTGTCTTCATGTATTA
1 AGATCTTGTCTTCCTATACTGGTAGTGAAGTAGATCAAAGATGCAGATCTTGTCTTCATGTACTA
* *
31372696 GCGTGAAGTAGATCGAAGATAGTAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAG
66 GCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAA
* * **
31372761 AGCAAATCTTATCTTCATGTATTGGCGTGAAGTAGATTGAAGAAAAC
131 AGCAAATCTTATCTTCATGTACTGACGTGAAGTAGATCAAAGAAAAC
* * * ** ***
31372808 AGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAAAGATAATAGATCTTGTCTTCCCATACT
1 AGATCTTGTCTTCCTATACTGGTAGTGAAGTAGATCAAAGAT-GCAGATCTTGTCTTCATGTACT
* * * *
31372872 GGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTC
65 AG-CGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTC
31372910 ATGTACTGGC
Statistics
Matches: 233, Mismatches: 43, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
176 43 0.18
177 159 0.68
178 31 0.13
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (177 bp):
AGATCTTGTCTTCCTATACTGGTAGTGAAGTAGATCAAAGATGCAGATCTTGTCTTCATGTACTA
GCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAA
AGCAAATCTTATCTTCATGTACTGACGTGAAGTAGATCAAAGAAAAC
Found at i:31372828 original size:89 final size:89
Alignment explanation
Indices: 31372454--31372909 Score: 497
Period size: 88 Copynumber: 5.1 Consensus size: 89
31372444 TGAATACAAA
* *
31372454 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCCAAGAAAGCAGATCTTATCTTCATGTACT
1 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTACT
* * *
31372519 AGCGTG-AGCAGATCAAAGATAGC
66 GGCGTGAAGTAGATCGAAGATAGC
* * *
31372542 AGATCTTGTCTTCCCATACTGGTGGCGGAGTAGATCGAAGAAAGTAAATCTTGTCTTCATGTACT
1 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTACT
* *
31372607 GACGTGAAGTAGATCAAAGATAGC
66 GGCGTGAAGTAGATCGAAGATAGC
* * * * * * * * *
31372631 AAATCCTGTCTTCCTATATTGGTAGTGAAGTGGATCGAAG-ATGCAGATCTTGTCTTCATGTATT
1 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTACT
* *
31372695 AGCGTGAAGTAGATCGAAGATAGT
66 GGCGTGAAGTAGATCGAAGATAGC
* * * *
31372719 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAGAGCAAATCTTATCTTCATGTATT
1 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTACT
* * *
31372784 GGCGTGAAGTAGATTGAAGAAAAC
66 GGCGTGAAGTAGATCGAAGATAGC
*** * * * * ***
31372808 AGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAAAGATAA-TAGATCTTGTCTTCCCATAC
1 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGA-AAGCAGATCTTGTCTTCATGTAC
* * *
31372871 TGGTGGCGAAGTAGATCGAAGAAAGC
65 TGG-CGTGAAGTAGATCGAAGATAGC
31372897 AGATCTTGTCTTC
1 AGATCTTGTCTTC
31372910 ATGTACTGGC
Statistics
Matches: 306, Mismatches: 58, Indels: 7
0.82 0.16 0.02
Matches are distributed among these distances:
88 168 0.55
89 138 0.45
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (89 bp):
AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTACT
GGCGTGAAGTAGATCGAAGATAGC
Found at i:31372910 original size:89 final size:89
Alignment explanation
Indices: 31372789--31372979 Score: 301
Period size: 89 Copynumber: 2.1 Consensus size: 89
31372779 GTATTGGCGT
*
31372789 GAAGTAGATTGAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAATAG
1 GAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAATAG
* *
31372854 ATCTTGTCTTCCCATACTGGTGGC
66 ATCCTGTCTTCCCATACTGGTAGC
* *
31372878 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAGTAG
1 GAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAATAG
* * *
31372943 GTCCTGTCTTCCTATATTGGTAGC
66 ATCCTGTCTTCCCATACTGGTAGC
*
31372967 GAAGTGGATCGAA
1 GAAGTAGATCGAA
31372980 TACACATCTT
Statistics
Matches: 93, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
89 93 1.00
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (89 bp):
GAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAATAG
ATCCTGTCTTCCCATACTGGTAGC
Found at i:31372951 original size:133 final size:133
Alignment explanation
Indices: 31372454--31372953 Score: 567
Period size: 133 Copynumber: 3.8 Consensus size: 133
31372444 TGAATACAAA
* *
31372454 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCCAAGAAAGCAGATCTTATCTTCATGTACT
1 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAAATCTTATCTTCATGTACT
* * *** * * *
31372519 AGCGTG-AGCAGATCAAAGATAGCAGATCTTGTCTTCCCATACTGGTGGCGGAGTAGATCGAAGA
66 GGCGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCGAAGA
31372583 -AAGT
130 TAA-T
* *** ** * * * * * * * *
31372587 AAATCTTGTCTTCATGTACT-GACGTGAAGTAGATCAAAGATAGCAAATCCTGTCTTCCTATATT
1 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAAATCTTATCTTCATGTACT
* * * * *
31372651 GGTAGTGAAGTGGATCGAAGAT-GCAGATCTTGTCTTCATGTATTAGCGTGAAGTAGATCGAAGA
66 GG-CGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCGAAGA
*
31372715 TAGT
130 TAAT
* *
31372719 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAGAGCAAATCTTATCTTCATGTATT
1 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAAATCTTATCTTCATGTACT
** * * *
31372784 GGCGTGAAGTAGATTGAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAT
66 GGCGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCGAAGAT
31372849 AAT
131 AAT
* *
31372852 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTACT
1 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAAATCTTATCTTCATGTACT
* * *
31372917 GGCGTGAAGTAGATCAAAGATAGTAGGTCCTGTCTTC
66 GGCGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTC
31372954 CTATATTGGT
Statistics
Matches: 300, Mismatches: 62, Indels: 10
0.81 0.17 0.03
Matches are distributed among these distances:
132 81 0.27
133 208 0.69
134 11 0.04
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (133 bp):
AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAAATCTTATCTTCATGTACT
GGCGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCGAAGAT
AAT
Found at i:31375145 original size:21 final size:20
Alignment explanation
Indices: 31375059--31375144 Score: 86
Period size: 19 Copynumber: 4.3 Consensus size: 20
31375049 AATACGCATG
* **
31375059 TTTTTTACAATATATATGCA
1 TTTTTTATAATATATACACA
* *
31375079 TTTTTTAT-GTATTAAACACA
1 TTTTTTATAATA-TATACACA
31375099 TATTTTTATAATATATACACA
1 T-TTTTTATAATATATACACA
*
31375120 TTTTTT-TAATATATATACA
1 TTTTTTATAATATATACACA
31375139 TTTTTT
1 TTTTTT
31375145 TAAAGCTTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
19 20 0.36
20 18 0.33
21 15 0.27
22 2 0.04
ACGTcount: A:0.35, C:0.08, G:0.02, T:0.55
Consensus pattern (20 bp):
TTTTTTATAATATATACACA
Found at i:31380500 original size:40 final size:41
Alignment explanation
Indices: 31380456--31380565 Score: 120
Period size: 39 Copynumber: 2.8 Consensus size: 41
31380446 CAAAAAACGT
*
31380456 CGCTAAAAATCGAGTATTAGCGGCGCTTTTAC-G-AAAACAC
1 CGCTAAAAATAGAGTATTAGCGGCGCTTTT-CTGAAAAACAC
* * * *
31380496 CGCT-AAAATAGAGCATTATCGGTGC-TTTCTGAAAAACGC
1 CGCTAAAAATAGAGTATTAGCGGCGCTTTTCTGAAAAACAC
* *
31380535 CGCTAAAAATAAAGTATTAGCGGCGTTTTTC
1 CGCTAAAAATAGAGTATTAGCGGCGCTTTTC
31380566 AGGAAGCGCC
Statistics
Matches: 56, Mismatches: 10, Indels: 7
0.77 0.14 0.10
Matches are distributed among these distances:
37 1 0.02
38 4 0.07
39 27 0.48
40 20 0.36
41 4 0.07
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (41 bp):
CGCTAAAAATAGAGTATTAGCGGCGCTTTTCTGAAAAACAC
Found at i:31380677 original size:41 final size:41
Alignment explanation
Indices: 31380620--31380906 Score: 412
Period size: 41 Copynumber: 7.0 Consensus size: 41
31380610 AGCTTTTCGA
* *
31380620 GGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAAAGCTCTG
1 GGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCTG
* * *
31380661 GGCTTTAGTGGCGTTTTTGGAGAAGTGCCGCTAATGCTCTA
1 GGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCTG
*
31380702 GGCTTTAGCGGCGTTTTTGGAGAAGCGCCGTTAATGCTCTG
1 GGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCTG
* * *
31380743 GGCTTTAGCGGCGCTTTTAGAGAAGCGCCGCTAATGTTCTG
1 GGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCTG
* * *
31380784 GGCTTTAGCGGTGTTTTTGGAAAATCGCCGCTAATGCTCTG
1 GGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCTG
* * *
31380825 GGCTTTAGCGGCGTTTTTGGGGAAGTGCCACTAATGCTCTG
1 GGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCTG
*
31380866 GACTTTAGCGGCGTTTTTGGGAGAAGCGCCGCTTAATGCTC
1 GGCTTTAGCGGCGTTTTT-GGAGAAGCGCCGC-TAATGCTC
31380907 CCGGGATTTT
Statistics
Matches: 215, Mismatches: 29, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
41 197 0.92
42 10 0.05
43 8 0.04
ACGTcount: A:0.17, C:0.20, G:0.32, T:0.31
Consensus pattern (41 bp):
GGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCTG
Found at i:31381288 original size:21 final size:23
Alignment explanation
Indices: 31381262--31381304 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
31381252 TTAATTGGTT
31381262 AATTTA-TATTAATT-AATATTC
1 AATTTATTATTAATTGAATATTC
*
31381283 AATTTATTTTTAATTGAATATT
1 AATTTATTATTAATTGAATATT
31381305 TAAAATCTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 7 0.37
23 6 0.32
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (23 bp):
AATTTATTATTAATTGAATATTC
Found at i:31381549 original size:14 final size:14
Alignment explanation
Indices: 31381530--31381619 Score: 67
Period size: 14 Copynumber: 6.4 Consensus size: 14
31381520 TATCACTATA
*
31381530 GTTTAGGGTTTTTG
1 GTTTAGGGTTTATG
*
31381544 GTTTAGGGTATATG
1 GTTTAGGGTTTATG
* *
31381558 GTTTAGAGTTTAAG
1 GTTTAGGGTTTATG
*
31381572 GTTTAGGTGTTACCAT-
1 GTTTAGG-GTT--TATG
*
31381588 -TTTAAGGTTTATG
1 GTTTAGGGTTTATG
* *
31381601 ATTTATGGTTTATG
1 GTTTAGGGTTTATG
31381615 GTTTA
1 GTTTA
31381620 AAGGCTGGGG
Statistics
Matches: 59, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
12 2 0.03
14 48 0.81
15 8 0.14
17 1 0.02
ACGTcount: A:0.20, C:0.02, G:0.28, T:0.50
Consensus pattern (14 bp):
GTTTAGGGTTTATG
Found at i:31381700 original size:20 final size:21
Alignment explanation
Indices: 31381655--31381706 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 21
31381645 TTATGTGTTA
31381655 AGGGTTTATGGGTTTATAATTTT
1 AGGGTTTA--GGTTTATAATTTT
*
31381678 AGGGTTTAGGTTTATGA-TTT
1 AGGGTTTAGGTTTATAATTTT
31381698 AGGGTTTAG
1 AGGGTTTAG
31381707 ATTAACTAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 12 0.43
21 8 0.29
23 8 0.29
ACGTcount: A:0.21, C:0.00, G:0.31, T:0.48
Consensus pattern (21 bp):
AGGGTTTAGGTTTATAATTTT
Found at i:31381771 original size:14 final size:14
Alignment explanation
Indices: 31381752--31381796 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
31381742 TTAATTATCA
31381752 TTATAGTTTAAGGT
1 TTATAGTTTAAGGT
31381766 TTATAGTTT-AGTGT
1 TTATAGTTTAAG-GT
* *
31381780 ATATGGTTTAAGGT
1 TTATAGTTTAAGGT
31381794 TTA
1 TTA
31381797 AGATTTAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 2 0.08
14 22 0.85
15 2 0.08
ACGTcount: A:0.27, C:0.00, G:0.22, T:0.51
Consensus pattern (14 bp):
TTATAGTTTAAGGT
Found at i:31382790 original size:21 final size:21
Alignment explanation
Indices: 31382748--31382790 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
31382738 GCCATTTTAT
* * *
31382748 CCCCAAATTTCCCTCGTGAAA
1 CCCCAAATTTCCCCCCTAAAA
*
31382769 CCCCTAATTTCCCCCCTAAAA
1 CCCCAAATTTCCCCCCTAAAA
31382790 C
1 C
31382791 TCTTAACTTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.44, G:0.05, T:0.23
Consensus pattern (21 bp):
CCCCAAATTTCCCCCCTAAAA
Found at i:31382837 original size:4 final size:4
Alignment explanation
Indices: 31382828--31382853 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
31382818 CTTGCTTTCT
31382828 CTCC CTCC CTCC CTCC CTCC CTCC CT
1 CTCC CTCC CTCC CTCC CTCC CTCC CT
31382854 GCGACATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.73, G:0.00, T:0.27
Consensus pattern (4 bp):
CTCC
Found at i:31382987 original size:9 final size:9
Alignment explanation
Indices: 31382973--31383005 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
31382963 AGTAAAACAT
31382973 GTTACAGAG
1 GTTACAGAG
*
31382982 GTTACATAG
1 GTTACAGAG
31382991 GTTACAGAG
1 GTTACAGAG
31383000 GTTACA
1 GTTACA
31383006 ACCATTGCTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.27
Consensus pattern (9 bp):
GTTACAGAG
Found at i:31385512 original size:22 final size:22
Alignment explanation
Indices: 31385486--31385527 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
31385476 CGTTTGTGTG
*
31385486 AAAAGCGCCGCTAAAGGCCTAA
1 AAAAGCGCCGCTAAAAGCCTAA
31385508 AAAAGCGCCGCTAAAAGCCT
1 AAAAGCGCCGCTAAAAGCCT
31385528 GTTTTGGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.29, G:0.21, T:0.10
Consensus pattern (22 bp):
AAAAGCGCCGCTAAAAGCCTAA
Found at i:31388418 original size:5 final size:5
Alignment explanation
Indices: 31388408--31388450 Score: 50
Period size: 5 Copynumber: 8.0 Consensus size: 5
31388398 TCCAAATAAG
*
31388408 TAAAA TAAAA TAAAA TAAAG TAAAAA TAATAA TAAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA T-AAAA TAA-AA T-AAAA TAAAA
31388451 ATTGGGTTGC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
5 21 0.64
6 10 0.30
7 2 0.06
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (5 bp):
TAAAA
Found at i:31388423 original size:10 final size:11
Alignment explanation
Indices: 31388409--31388450 Score: 59
Period size: 12 Copynumber: 3.8 Consensus size: 11
31388399 CCAAATAAGT
31388409 AAAATAAAAT-
1 AAAATAAAATA
*
31388419 AAAATAAAGTA
1 AAAATAAAATA
31388430 AAAATAATAATA
1 AAAATAA-AATA
31388442 AAAATAAAA
1 AAAATAAAA
31388451 ATTGGGTTGC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 9 0.32
11 9 0.32
12 10 0.36
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:31395593 original size:24 final size:24
Alignment explanation
Indices: 31395548--31395594 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
31395538 GGAATTGGGG
**
31395548 AGAGAGAAAACAAATTTTCTAAAA
1 AGAGAGAAAACAAATTAACTAAAA
31395572 AGAGAGAAAA-AAATTGAACTAAA
1 AGAGAGAAAACAAATT-AACTAAA
31395595 TCAGATAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.62, C:0.06, G:0.15, T:0.17
Consensus pattern (24 bp):
AGAGAGAAAACAAATTAACTAAAA
Found at i:31397063 original size:21 final size:21
Alignment explanation
Indices: 31397025--31397078 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
31397015 TGCTAGTTAC
*
31397025 TAATATCATGATTTAAA-TAAA
1 TAATATCAT-ATTCAAATTAAA
31397046 TAATATCATATCTCAAATTAAA
1 TAATATCATAT-TCAAATTAAA
*
31397068 TATACATCATA
1 TA-ATATCATA
31397079 AAAAAGAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 2 0.07
21 13 0.46
22 6 0.21
23 7 0.25
ACGTcount: A:0.50, C:0.11, G:0.02, T:0.37
Consensus pattern (21 bp):
TAATATCATATTCAAATTAAA
Found at i:31406386 original size:222 final size:219
Alignment explanation
Indices: 31406036--31406454 Score: 578
Period size: 222 Copynumber: 1.9 Consensus size: 219
31406026 CTTTGACGAC
* *
31406036 TAGTCAATTTGGGGAAAAAAATACAATGACTGATTTATTGGGGTCAATTTTGAGAAAAATGATTT
1 TAGTCAATTTGGGGAAAAAAATACAATGACTGATTTATGGGGGTCAATTTTGAGAAAAAGGATTT
* * * *
31406101 TATTAAGTTTATTAAACATGATGAAAATGGGAAAGGGGTTAAAGTTATTTGGTCGGAATTGAAGA
66 TAATAAGTTAATTAAACATGATGAAAATGGGAAAGGGGTCAAAGTTATTGGGTCGGAATTGAAGA
*
31406166 AGAGGGTTTGGATAAGAAGGGCCATAGATGCGATTCTAGGCTT-GAGGCAGTCTGAAAATTTGGA
131 AGAGGGTTTGGATAAGAAGGGCCATAGATGCGATTCTAGGCTTAGAGGCAGTCTGAAAATGTGGA
31406230 TTTTGGGCTTGGGGGTAGTCTGAA
196 TTTTGGGCTTGGGGGTAGTCTGAA
* * *
31406254 TAGTCAATTTGGGGAAAAAAAAGATACGATGGCTGATTTATCGGGGGTCAATTTT-AGAAAAGGG
1 TAGTCAATTTGGGG--AAAAAA-ATACAATGACTGATTTAT-GGGGGTCAATTTTGAGAAAAAGG
* *
31406318 AATTTTAATAAGTTAATTAAACATGATGAAAATGGGAAA-GGG-CAAAGGTTGTTGGG-CTGGTC
62 -ATTTTAATAAGTTAATTAAACATGATGAAAATGGGAAAGGGGTCAAA-GTTATTGGGTC-GG-A
* * * * *
31406380 ATTGAAGAAGGGGGTTTGGATAAGATGGGCCATAGGTGCGATTCTAGGCTTAGGGGCAGTCTGAT
123 ATTGAAGAAGAGGGTTTGGATAAGAAGGGCCATAGATGCGATTCTAGGCTTAGAGGCAGTCTGAA
31406445 AATGTGGATT
188 AATGTGGATT
31406455 CTGATTATTT
Statistics
Matches: 175, Mismatches: 17, Indels: 13
0.85 0.08 0.06
Matches are distributed among these distances:
218 14 0.08
220 10 0.06
221 35 0.20
222 96 0.55
223 20 0.11
ACGTcount: A:0.33, C:0.07, G:0.30, T:0.30
Consensus pattern (219 bp):
TAGTCAATTTGGGGAAAAAAATACAATGACTGATTTATGGGGGTCAATTTTGAGAAAAAGGATTT
TAATAAGTTAATTAAACATGATGAAAATGGGAAAGGGGTCAAAGTTATTGGGTCGGAATTGAAGA
AGAGGGTTTGGATAAGAAGGGCCATAGATGCGATTCTAGGCTTAGAGGCAGTCTGAAAATGTGGA
TTTTGGGCTTGGGGGTAGTCTGAA
Found at i:31412895 original size:13 final size:14
Alignment explanation
Indices: 31412879--31412910 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
31412869 TGTTTATACC
31412879 TTTTATTTATT-TA
1 TTTTATTTATTATA
31412892 TTTTA-TTATTATA
1 TTTTATTTATTATA
31412905 TTTTAT
1 TTTTAT
31412911 GATTTTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTTATTTATTATA
Found at i:31413049 original size:23 final size:25
Alignment explanation
Indices: 31413002--31413048 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
31412992 TTTAGATTTA
*
31413002 TTATCATATATTTGTTTTTAAAAAT
1 TTATCATATATTTATTTTTAAAAAT
31413027 TTATCATATA-TTATTTTTAAAA
1 TTATCATATATTTATTTTTAAAA
31413049 TGTTGTCTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.55
Consensus pattern (25 bp):
TTATCATATATTTATTTTTAAAAAT
Found at i:31418460 original size:23 final size:22
Alignment explanation
Indices: 31418428--31418470 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
31418418 TTTGAGTCAT
31418428 AAAAATAAAAA-TGAAAAATGAA
1 AAAAATAAAAAGT-AAAAATGAA
31418450 AAAAATGAAAAAGTAAAAATG
1 AAAAAT-AAAAAGTAAAAATG
31418471 GAGAGGCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.32
23 12 0.63
24 1 0.05
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.14
Consensus pattern (22 bp):
AAAAATAAAAAGTAAAAATGAA
Found at i:31419674 original size:50 final size:50
Alignment explanation
Indices: 31419611--31420250 Score: 446
Period size: 50 Copynumber: 12.8 Consensus size: 50
31419601 GGTGAAGACA
* * * *
31419611 GAATCTTATTTCCCGGGCAGTGCAGTGGAACAGATTAAAGCCACATCGGT
1 GAATCTTACTTCCCTGGCAGTGCAGTGGAAAAGATTAAAGCCACAACGGT
* *** * * * **
31419661 GAATCTTGCTTCCCCAACATTGCAGTTGAAAAGATTAAAGCTACAACAAT
1 GAATCTTACTTCCCTGGCAGTGCAGTGGAAAAGATTAAAGCCACAACGGT
* * * * * *
31419711 TAATCTTATTTCCCTGGCGGTGCAGTGGAACAGATTAACGCCACAACGGC
1 GAATCTTACTTCCCTGGCAGTGCAGTGGAAAAGATTAAAGCCACAACGGT
* * * * ** * * *
31419761 GAACCTTGCTTCCCCT-ACATTGCAGTTAAAAAGATTAAAGCTACAACAGC
1 GAATCTTACTT-CCCTGGCAGTGCAGTGGAAAAGATTAAAGCCACAACGGT
* * * *
31419811 GAATCTTAC-TCCCAGGC-GATGCAGTGGAACAGATTAAAGCCACATCGAT
1 GAATCTTACTTCCCTGGCAG-TGCAGTGGAAAAGATTAAAGCCACAACGGT
* * * ** * * *
31419860 GAATCTTGCTTCCCTGACATTGCAGTTAAAAATATTAAAGCTACAACAGT
1 GAATCTTACTTCCCTGGCAGTGCAGTGGAAAAGATTAAAGCCACAACGGT
* * * * *
31419910 GAATCTTATTTCCCTGGCGGTGCAGTGGAACAGATTAAGGCCACAACGGC
1 GAATCTTACTTCCCTGGCAGTGCAGTGGAAAAGATTAAAGCCACAACGGT
* * * * * ** * *
31419960 GAACCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACAACAGT
1 GAATCTTACTTCCCTGGCAGTGCAGTGGAAAAGATTAAAGCCACAACGGT
* * *
31420010 GAATCTTACTCCCCAGGC-GATGCAGTGGAACAGATTAAAGCCACATA-GGT
1 GAATCTTACTTCCCTGGCAG-TGCAGTGGAAAAGATTAAAGCCACA-ACGGT
* * * * ** * * *
31420060 GAATCTTGCTTCCCTGACATTGCAATTAAAAAGATTAAAGCTACAACTGC
1 GAATCTTACTTCCCTGGCAGTGCAGTGGAAAAGATTAAAGCCACAACGGT
* * *
31420110 GAATCTTACTTCCCTAGCGGTGCAGTGGAATAGATTAAAGCCACAACGGT
1 GAATCTTACTTCCCTGGCAGTGCAGTGGAAAAGATTAAAGCCACAACGGT
* * ** * ** * * * *
31420160 GAATCTTGCTTCCCCGAAATTGCAGTTAAAAATATTAAAGCTACAACAGC
1 GAATCTTACTTCCCTGGCAGTGCAGTGGAAAAGATTAAAGCCACAACGGT
* * *
31420210 AAATCTTACTTCCCTGGCCGTGCAAT-GAAACAGATTAAAGC
1 GAATCTTACTTCCCTGGCAGTGCAGTGGAAA-AGATTAAAGC
31420251 TACGACGGCA
Statistics
Matches: 429, Mismatches: 151, Indels: 20
0.71 0.25 0.03
Matches are distributed among these distances:
48 3 0.01
49 36 0.08
50 385 0.90
51 5 0.01
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.24
Consensus pattern (50 bp):
GAATCTTACTTCCCTGGCAGTGCAGTGGAAAAGATTAAAGCCACAACGGT
Found at i:31419785 original size:100 final size:100
Alignment explanation
Indices: 31419611--31420274 Score: 877
Period size: 100 Copynumber: 6.7 Consensus size: 100
31419601 GGTGAAGACA
* * * *
31419611 GAATCTTATTTCCCGGGCAGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCC
1 GAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCTTCCCC
* * **
31419676 AACATTGCAGTTGAAAAGATTAAAGCTACAACAAT
66 TACATTGCAGTTAAAAAGATTAAAGCTACAACAGC
* * * * *
31419711 TAATCTTATTTCCCTGGCGGTGCAGTGGAACAGATTAACGCCACAACGGCGAACCTTGCTTCCCC
1 GAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCTTCCCC
31419776 TACATTGCAGTTAAAAAGATTAAAGCTACAACAGC
66 TACATTGCAGTTAAAAAGATTAAAGCTACAACAGC
* * * *
31419811 GAATCTTAC-TCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGATGAATCTTGCTT-CCC
1 GAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCTTCCCC
* *
31419874 TGACATTGCAGTTAAAAATATTAAAGCTACAACAGT
66 T-ACATTGCAGTTAAAAAGATTAAAGCTACAACAGC
* * * *
31419910 GAATCTTATTTCCCTGGCGGTGCAGTGGAACAGATTAAGGCCACAACGGCGAACCTTGCTTCCCC
1 GAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCTTCCCC
* *
31419975 GACATTGCAGTTAAAAAGATTAAAGCTACAACAGT
66 TACATTGCAGTTAAAAAGATTAAAGCTACAACAGC
* * *
31420010 GAATCTTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATA-GGTGAATCTTGCTT-CC
1 GAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTAAAGCCACA-ACGGTGAATCTTGCTTCCC
* *
31420073 CTGACATTGCAATTAAAAAGATTAAAGCTACAACTGC
65 CT-ACATTGCAGTTAAAAAGATTAAAGCTACAACAGC
* *
31420110 GAATCTTACTTCCCTAGCGGTGCAGTGGAATAGATTAAAGCCACAACGGTGAATCTTGCTTCCCC
1 GAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCTTCCCC
* * *
31420175 GAAATTGCAGTTAAAAATATTAAAGCTACAACAGC
66 TACATTGCAGTTAAAAAGATTAAAGCTACAACAGC
* * * * * * ** *
31420210 AAATCTTACTTCCCTGGCCGTGCAATGAAACAGATTAAAGCTACGACGGCAAATCTTGTTTCCCC
1 GAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCTTCCCC
31420275 GACGCTGCAG
Statistics
Matches: 493, Mismatches: 64, Indels: 14
0.86 0.11 0.02
Matches are distributed among these distances:
98 4 0.01
99 88 0.18
100 394 0.80
101 7 0.01
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.25
Consensus pattern (100 bp):
GAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCTTCCCC
TACATTGCAGTTAAAAAGATTAAAGCTACAACAGC
Found at i:31420267 original size:200 final size:200
Alignment explanation
Indices: 31419611--31420250 Score: 980
Period size: 200 Copynumber: 3.2 Consensus size: 200
31419601 GGTGAAGACA
* *
31419611 GAATCTTATTTCCCGGGC-AGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCC
1 GAATCTTACTTCCCAGGCGA-TGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCC
** * * *
31419675 CAACATTGCAGTTGAAAAGATTAAAGCTACAACAATTAATCTTATTTCCCTGGCGGTGCAGTGGA
65 TGACATTGCAGTTAAAAAGATTAAAGCTACAACAGTGAATCTTATTTCCCTGGCGGTGCAGTGGA
* *
31419740 ACAGATTAACGCCACAACGGCGAACCTTGCTTCCCCTACATTGCAGTTAAAAAGATTAAAGCTAC
130 ACAGATTAAAGCCACAACGGCGAACCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTAC
31419805 AACAGC
195 AACAGC
*
31419811 GAATCTTAC-TCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGATGAATCTTGCTTCCCT
1 GAATCTTACTTCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCT
*
31419875 GACATTGCAGTTAAAAATATTAAAGCTACAACAGTGAATCTTATTTCCCTGGCGGTGCAGTGGAA
66 GACATTGCAGTTAAAAAGATTAAAGCTACAACAGTGAATCTTATTTCCCTGGCGGTGCAGTGGAA
*
31419940 CAGATTAAGGCCACAACGGCGAACCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACA
131 CAGATTAAAGCCACAACGGCGAACCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACA
*
31420005 ACAGT
196 ACAGC
* *
31420010 GAATCTTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATAGGTGAATCTTGCTTCCCT
1 GAATCTTACTTCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCT
* * * * *
31420075 GACATTGCAATTAAAAAGATTAAAGCTACAACTGCGAATCTTACTTCCCTAGCGGTGCAGTGGAA
66 GACATTGCAGTTAAAAAGATTAAAGCTACAACAGTGAATCTTATTTCCCTGGCGGTGCAGTGGAA
* * * * *
31420140 TAGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGAAATTGCAGTTAAAAATATTAAAGCTACA
131 CAGATTAAAGCCACAACGGCGAACCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACA
31420205 ACAGC
196 ACAGC
* * * *
31420210 AAATCTTACTTCCCTGGCCG-TGCAATGAAACAGATTAAAGC
1 GAATCTTACTTCCCAGG-CGATGCAGTGGAACAGATTAAAGC
31420251 TACGACGGCA
Statistics
Matches: 404, Mismatches: 33, Indels: 6
0.91 0.07 0.01
Matches are distributed among these distances:
199 186 0.46
200 216 0.53
201 2 0.00
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.24
Consensus pattern (200 bp):
GAATCTTACTTCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCT
GACATTGCAGTTAAAAAGATTAAAGCTACAACAGTGAATCTTATTTCCCTGGCGGTGCAGTGGAA
CAGATTAAAGCCACAACGGCGAACCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACA
ACAGC
Found at i:31430710 original size:27 final size:27
Alignment explanation
Indices: 31430649--31430914 Score: 155
Period size: 27 Copynumber: 10.2 Consensus size: 27
31430639 TCATCTCCTA
**
31430649 GGGGTATAACAGTCATTTTAACCTATG
1 GGGGTATTTCAGTCATTTTAACCTATG
*
31430676 AGGGTATTTCAGTCATTTTAACCTATG
1 GGGGTATTTCAGTCATTTTAACCTATG
*
31430703 AGGGTATTTCA-TC----T--CCTA-G
1 GGGGTATTTCAGTCATTTTAACCTATG
* * *
31430722 GGGTGT-TTT-GGTCATTTTACCCTGTG
1 GGG-GTATTTCAGTCATTTTAACCTATG
** ***
31430748 GGGGTATTTC-GATCATTCCATTTTAT-
1 GGGGTATTTCAG-TCATTTTAACCTATG
* * *
31430774 GGGGTATTTCGGTAATTCT-ACCTTATG
1 GGGGTATTTCAGTCATTTTAACC-TATG
* *
31430801 GGGGTATTTCAGACATTTTATCCTATG
1 GGGGTATTTCAGTCATTTTAACCTATG
* * *
31430828 GGGGTATTTCGGTCATTCTATCCTATG
1 GGGGTATTTCAGTCATTTTAACCTATG
* * *
31430855 GGGGTATTTTAGTCATTCTACCCTATG
1 GGGGTATTTCAGTCATTTTAACCTATG
* * * *
31430882 AGGGTAATTC-GATCATTTTACCCTGTG
1 GGGGTATTTCAG-TCATTTTAACCTATG
31430909 GGGGTA
1 GGGGTA
31430915 ATTCGATCAT
Statistics
Matches: 188, Mismatches: 34, Indels: 34
0.73 0.13 0.13
Matches are distributed among these distances:
19 8 0.04
20 6 0.03
22 1 0.01
23 1 0.01
25 5 0.03
26 29 0.15
27 136 0.72
28 2 0.01
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (27 bp):
GGGGTATTTCAGTCATTTTAACCTATG
Found at i:31430847 original size:54 final size:54
Alignment explanation
Indices: 31430721--31430914 Score: 194
Period size: 54 Copynumber: 3.6 Consensus size: 54
31430711 TCATCTCCTA
* * * * * **
31430721 GGGGTGTTTTGGTCATTTTACCCTGTGGGGGTATTTC-GATCATTCCATTTTAT-
1 GGGGTATTTCGGTCATTCTACCCTATGGGGGTATTTCAGA-CATTCTATCCTATG
* * *
31430774 GGGGTATTTCGGTAATTCTACCTTATGGGGGTATTTCAGACATTTTATCCTATG
1 GGGGTATTTCGGTCATTCTACCCTATGGGGGTATTTCAGACATTCTATCCTATG
* * * *
31430828 GGGGTATTTCGGTCATTCTATCCTATGGGGGTATTTTAGTCATTCTACCCTATG
1 GGGGTATTTCGGTCATTCTACCCTATGGGGGTATTTCAGACATTCTATCCTATG
* * * * *
31430882 AGGGTAATTCGATCATTTTACCCTGTGGGGGTA
1 GGGGTATTTCGGTCATTCTACCCTATGGGGGTA
31430915 ATTCGATCAT
Statistics
Matches: 116, Mismatches: 23, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
53 40 0.34
54 76 0.66
ACGTcount: A:0.18, C:0.16, G:0.26, T:0.41
Consensus pattern (54 bp):
GGGGTATTTCGGTCATTCTACCCTATGGGGGTATTTCAGACATTCTATCCTATG
Found at i:31430900 original size:81 final size:81
Alignment explanation
Indices: 31430733--31430925 Score: 246
Period size: 81 Copynumber: 2.4 Consensus size: 81
31430723 GGTGTTTTGG
** * *
31430733 TCATTTTACCCTGTGGGGGTATTTCGATCATTCCATTTTATGGGGTATTTCGGTAATTCTACCTT
1 TCATTTTACCCTGTGGGGGTATTTCGATCATTCCATCCTATGGGGTATTTCAGTAATTCTACCCT
* *
31430798 ATGGGGGTATTTCAGA
66 ATGAGGGTAATTCAGA
* * * * * *
31430814 -CATTTTATCCTATGGGGGTATTTCGGTCATTCTATCCTATGGGGGTATTTTAGTCATTCTACCC
1 TCATTTTACCCTGTGGGGGTATTTCGATCATTCCATCCTAT-GGGGTATTTCAGTAATTCTACCC
31430878 TATGAGGGTAATTC-GA
65 TATGAGGGTAATTCAGA
*
31430894 TCATTTTACCCTGTGGGGGTAATTCGATCATT
1 TCATTTTACCCTGTGGGGGTATTTCGATCATT
31430926 TATTGACCTT
Statistics
Matches: 94, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
80 36 0.38
81 58 0.62
ACGTcount: A:0.19, C:0.17, G:0.23, T:0.41
Consensus pattern (81 bp):
TCATTTTACCCTGTGGGGGTATTTCGATCATTCCATCCTATGGGGTATTTCAGTAATTCTACCCT
ATGAGGGTAATTCAGA
Found at i:31430926 original size:27 final size:27
Alignment explanation
Indices: 31430733--31430925 Score: 176
Period size: 27 Copynumber: 7.2 Consensus size: 27
31430723 GGTGTTTTGG
* *
31430733 TCATTTTACCCTGTGGGGGTATTTCGA
1 TCATTCTACCCTATGGGGGTATTTCGA
* *** *
31430760 TCATTCCATTTTAT-GGGGTATTTCGG
1 TCATTCTACCCTATGGGGGTATTTCGA
* *
31430786 TAATTCTACCTTATGGGGGTATTTCAGA
1 TCATTCTACCCTATGGGGGTATTTC-GA
* * *
31430814 -CATTTTATCCTATGGGGGTATTTCGG
1 TCATTCTACCCTATGGGGGTATTTCGA
* *
31430840 TCATTCTATCCTATGGGGGTATTT-TA
1 TCATTCTACCCTATGGGGGTATTTCGA
* *
31430866 GTCATTCTACCCTATGAGGGTAATTCGA
1 -TCATTCTACCCTATGGGGGTATTTCGA
* * *
31430894 TCATTTTACCCTGTGGGGGTAATTCGA
1 TCATTCTACCCTATGGGGGTATTTCGA
31430921 TCATT
1 TCATT
31430926 TATTGACCTT
Statistics
Matches: 134, Mismatches: 27, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 22 0.16
27 110 0.82
28 2 0.01
ACGTcount: A:0.19, C:0.17, G:0.23, T:0.41
Consensus pattern (27 bp):
TCATTCTACCCTATGGGGGTATTTCGA
Found at i:31436429 original size:30 final size:30
Alignment explanation
Indices: 31436380--31436468 Score: 124
Period size: 30 Copynumber: 3.0 Consensus size: 30
31436370 TCGCATGGCT
* * *
31436380 GTGTGTCACTCATGACTGAGGCACACGCCC
1 GTGTTTCACACATGACTGAGACACACGCCC
*
31436410 GTGTTTCACACATGGCTGAGACACACGCCC
1 GTGTTTCACACATGACTGAGACACACGCCC
* *
31436440 ATGTTTCACACATGACTAAGACACACGCC
1 GTGTTTCACACATGACTGAGACACACGCC
31436469 TGTGGCAACA
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 52 1.00
ACGTcount: A:0.26, C:0.33, G:0.21, T:0.20
Consensus pattern (30 bp):
GTGTTTCACACATGACTGAGACACACGCCC
Found at i:31448198 original size:26 final size:26
Alignment explanation
Indices: 31448167--31448216 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
31448157 TGTGAGGAGC
* *
31448167 CCATTTCGTAGCTCGTGTGAGCAAAT
1 CCATTTCATAGCTCATGTGAGCAAAT
31448193 CCATTTCATAGCTCATGTGAGCAA
1 CCATTTCATAGCTCATGTGAGCAA
31448217 CGATGTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (26 bp):
CCATTTCATAGCTCATGTGAGCAAAT
Found at i:31453496 original size:5 final size:5
Alignment explanation
Indices: 31453486--31453512 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
31453476 CAAAAGATGG
31453486 AGAAA AGAAA AGAAA AGAAA AGAAA AG
1 AGAAA AGAAA AGAAA AGAAA AGAAA AG
31453513 CTGGCAGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:31462598 original size:16 final size:16
Alignment explanation
Indices: 31462579--31462621 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
31462569 CGAAGTGACA
*
31462579 AGCTGGCGAAGGGGCG
1 AGCTAGCGAAGGGGCG
* *
31462595 AGCTAGTGAAGTGGCG
1 AGCTAGCGAAGGGGCG
*
31462611 AGCTAGTGAAG
1 AGCTAGCGAAG
31462622 TGGAACGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.26, C:0.14, G:0.47, T:0.14
Consensus pattern (16 bp):
AGCTAGCGAAGGGGCG
Found at i:31462622 original size:16 final size:16
Alignment explanation
Indices: 31462586--31462624 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
31462576 ACAAGCTGGC
*
31462586 GAAGGGGCGAGCTAGT
1 GAAGTGGCGAGCTAGT
31462602 GAAGTGGCGAGCTAGT
1 GAAGTGGCGAGCTAGT
31462618 GAAGTGG
1 GAAGTGG
31462625 AACGAATAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.26, C:0.10, G:0.49, T:0.15
Consensus pattern (16 bp):
GAAGTGGCGAGCTAGT
Found at i:31462995 original size:6 final size:6
Alignment explanation
Indices: 31462986--31463011 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
31462976 TAATAAATTC
31462986 AAATAT AAATAT AAATAT AAATAT AA
1 AAATAT AAATAT AAATAT AAATAT AA
31463012 TGTCTATACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AAATAT
Found at i:31465304 original size:23 final size:23
Alignment explanation
Indices: 31465278--31465445 Score: 183
Period size: 23 Copynumber: 7.3 Consensus size: 23
31465268 ATAAGTGCCA
*
31465278 CACTGATATGTAGCCGAAGTTAC
1 CACTGATATGTAGCCGAAGCTAC
* * * *
31465301 CACTAATACGTAGCTGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
31465324 CACTGAAATGTAGCTGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
31465347 CACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* * *
31465370 CACTAAAATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
31465393 CACTGATATGTAGCTGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* * *
31465416 CATTGAAATTTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
31465439 CATTGAT
1 CACTGAT
31465446 CAATAACACT
Statistics
Matches: 118, Mismatches: 27, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 118 1.00
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:31465348 original size:46 final size:46
Alignment explanation
Indices: 31465278--31465445 Score: 237
Period size: 46 Copynumber: 3.7 Consensus size: 46
31465268 ATAAGTGCCA
* * * *
31465278 CACTGATATGTAGCCGAAGTTACCACTAATACGTAGCTGTAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGATATGTAGCTGTAGCTAC
* *
31465324 CACTGAAATGTAGCTGAAGCTACCACTGATATGTAGCCGTAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGATATGTAGCTGTAGCTAC
* *
31465370 CACTAAAATGTAGCCAAAGCTACCACTGATATGTAGCTGTAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGATATGTAGCTGTAGCTAC
* * *
31465416 CATTGAAATTTAGCCGAAGCTACCATTGAT
1 CACTGAAATGTAGCCGAAGCTACCACTGAT
31465446 CAATAACACT
Statistics
Matches: 107, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 107 1.00
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (46 bp):
CACTGAAATGTAGCCGAAGCTACCACTGATATGTAGCTGTAGCTAC
Found at i:31465391 original size:69 final size:69
Alignment explanation
Indices: 31465278--31465440 Score: 218
Period size: 69 Copynumber: 2.4 Consensus size: 69
31465268 ATAAGTGCCA
* * ***
31465278 CACTGATATGTAGCCGAAGTTACCACTAATACGTAGCTGTAGCTACCACTGAAATGTAGCTGAAG
1 CACTGATATGTAGCCGAAGCTACCACTAAAACGTAGCCAAAGCTACCACTGAAATGTAGCTGAAG
31465343 CTAC
66 CTAC
* * * *
31465347 CACTGATATGTAGCCGTAGCTACCACTAAAATGTAGCCAAAGCTACCACTGATATGTAGCTGTAG
1 CACTGATATGTAGCCGAAGCTACCACTAAAACGTAGCCAAAGCTACCACTGAAATGTAGCTGAAG
31465412 CTAC
66 CTAC
* * *
31465416 CATTGAAATTTAGCCGAAGCTACCA
1 CACTGATATGTAGCCGAAGCTACCA
31465441 TTGATCAATA
Statistics
Matches: 81, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
69 81 1.00
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.25
Consensus pattern (69 bp):
CACTGATATGTAGCCGAAGCTACCACTAAAACGTAGCCAAAGCTACCACTGAAATGTAGCTGAAG
CTAC
Found at i:31467408 original size:22 final size:23
Alignment explanation
Indices: 31467366--31467410 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
31467356 TTCAATTTAG
* *
31467366 TATTTATATAATTTAATAAAAAC
1 TATTAATATAATTTAAGAAAAAC
31467389 TATTAATATAA-TTAAGAAAAAC
1 TATTAATATAATTTAAGAAAAAC
31467411 ATTTGGCATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (23 bp):
TATTAATATAATTTAAGAAAAAC
Found at i:31469819 original size:23 final size:22
Alignment explanation
Indices: 31469764--31469806 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
31469754 ACAGAGTTGA
*
31469764 CGTCCCGACGAGGAAGAGGCGT
1 CGTCCCGACGAGGAAGAGACGT
31469786 CGTCCCGACGA-GAAGAGACGT
1 CGTCCCGACGAGGAAGAGACGT
31469807 ATTGTCCCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.26, C:0.28, G:0.37, T:0.09
Consensus pattern (22 bp):
CGTCCCGACGAGGAAGAGACGT
Found at i:31471325 original size:6 final size:6
Alignment explanation
Indices: 31471316--31471402 Score: 138
Period size: 6 Copynumber: 14.5 Consensus size: 6
31471306 GAGATGCAGA
* *
31471316 TGGGGT TGGGGT TGGGGT TGGGGA TGGGGT CGGGGT TGGGGT TGGGGT
1 TGGGGT TGGGGT TGGGGT TGGGGT TGGGGT TGGGGT TGGGGT TGGGGT
* *
31471364 TGGGGT TGGGGT TGGGGT TGGGGA TGGGGT GGGGGT TGG
1 TGGGGT TGGGGT TGGGGT TGGGGT TGGGGT TGGGGT TGG
31471403 AGTAGCAGCT
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 73 1.00
ACGTcount: A:0.02, C:0.01, G:0.68, T:0.29
Consensus pattern (6 bp):
TGGGGT
Found at i:31475101 original size:17 final size:18
Alignment explanation
Indices: 31475079--31475121 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
31475069 GTTTAGAAAT
*
31475079 TATTTTTATCAT-ACTAA
1 TATTTTTATAATAACTAA
*
31475096 TATTTTTTATAATAATTAA
1 TA-TTTTTATAATAACTAA
31475115 TATTTTT
1 TATTTTT
31475122 TTTAAATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 2 0.09
18 14 0.64
19 6 0.27
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (18 bp):
TATTTTTATAATAACTAA
Done.