Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A07
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: 92880876
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2857347 characters in sequence are not A, C, G, or T
File 178 of 290
Found at i:57603703 original size:34 final size:33
Alignment explanation
Indices: 57603631--57603703 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
57603621 CTCTCCCTCA
* * *
57603631 TTTAAATGCCGTCCATTGCATGTGGAACATCTC
1 TTTAATTGCCGTCCATTGCATGTAGAACAACTC
*
57603664 ATTAATTGCCGTTCCA-TGCATGTAGAACAACATC
1 TTTAATTGCCG-TCCATTGCATGTAGAACAAC-TC
57603698 TTTAAT
1 TTTAAT
57603704 CCATGTCTTG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
33 22 0.67
34 11 0.33
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (33 bp):
TTTAATTGCCGTCCATTGCATGTAGAACAACTC
Found at i:57606013 original size:18 final size:18
Alignment explanation
Indices: 57605992--57606051 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
57605982 GACCTCACTC
57605992 TCTTTTTTGATTTCTTTT
1 TCTTTTTTGATTTCTTTT
** *
57606010 TCTTTTTCAATCTCTTTT
1 TCTTTTTTGATTTCTTTT
57606028 TCTTTTCTTTTGATTTCTTTT
1 TC--TT-TTTTGATTTCTTTT
57606049 TCT
1 TCT
57606052 CGCTTGCACT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
18 17 0.52
19 1 0.03
20 2 0.06
21 13 0.39
ACGTcount: A:0.07, C:0.17, G:0.03, T:0.73
Consensus pattern (18 bp):
TCTTTTTTGATTTCTTTT
Found at i:57607030 original size:13 final size:12
Alignment explanation
Indices: 57606985--57607023 Score: 78
Period size: 12 Copynumber: 3.2 Consensus size: 12
57606975 AAAAAAAAAA
57606985 TTTGAATTTTTT
1 TTTGAATTTTTT
57606997 TTTGAATTTTTT
1 TTTGAATTTTTT
57607009 TTTGAATTTTTT
1 TTTGAATTTTTT
57607021 TTT
1 TTT
57607024 CAAATTTCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (12 bp):
TTTGAATTTTTT
Found at i:57608682 original size:40 final size:40
Alignment explanation
Indices: 57608628--57608819 Score: 213
Period size: 40 Copynumber: 4.8 Consensus size: 40
57608618 TATAACCACA
* ** *
57608628 AGCACAAATTCCTTCGGGTCTTAGCCCGGATTTAGTAACT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATAACT
* * * *
57608668 CGCACAAATGCCTTCGGATCTTAGTCCGGATAAAATCACT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATAACT
* * * * **
57608708 AGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATAACT
* *
57608748 CGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATCACT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATAACT
* * *
57608788 AGCACAATTGCCTACGGGACTTAGCCCGGATA
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATA
57608820 TCATTCAAAT
Statistics
Matches: 122, Mismatches: 30, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
40 122 1.00
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
AGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATAACT
Found at i:57608748 original size:80 final size:80
Alignment explanation
Indices: 57608628--57608820 Score: 298
Period size: 80 Copynumber: 2.4 Consensus size: 80
57608618 TATAACCACA
* *
57608628 AGCACAAATT-CCTTCGGGTCTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGATCTTAG
1 AGCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGATCTTAG
*
57608692 TCCGGATAAAATCACT
65 CCCGGATAAAATCACT
* * *
57608708 AGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCACAAATGCCTTCGGGTCTTAGC
1 AGCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGATCTTAGC
57608773 CCGGATAAAATCACT
66 CCGGATAAAATCACT
* *
57608788 AGCACAATTGCCTACGGGACTTAGCCCGGATAT
1 AGCACAATTGCCTTCGGGTCTTAGCCCGGATAT
57608821 CATTCAAATG
Statistics
Matches: 102, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
79 4 0.04
80 98 0.96
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (80 bp):
AGCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGATCTTAGC
CCGGATAAAATCACT
Found at i:57613028 original size:21 final size:21
Alignment explanation
Indices: 57613004--57613045 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
57612994 TCATCAAATC
*
57613004 TACACCTTGAGGCATCGGGGG
1 TACACCTTGAGGAATCGGGGG
**
57613025 TACAGGTTGAGGAATCGGGGG
1 TACACCTTGAGGAATCGGGGG
57613046 AGGTAGGGGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.21, C:0.17, G:0.43, T:0.19
Consensus pattern (21 bp):
TACACCTTGAGGAATCGGGGG
Found at i:57615308 original size:30 final size:30
Alignment explanation
Indices: 57615274--57615334 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
57615264 CATTTAATAC
*
57615274 AAACTTTGGCACAATTACATTTTTGCCCCT
1 AAACTTTGGCACAATTACACTTTTGCCCCT
* *
57615304 AAACTTTTGCATAATTACACTTTTGCCCCT
1 AAACTTTGGCACAATTACACTTTTGCCCCT
57615334 A
1 A
57615335 GGTTCGAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.28, C:0.26, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGCACAATTACACTTTTGCCCCT
Found at i:57616753 original size:30 final size:30
Alignment explanation
Indices: 57616667--57616754 Score: 88
Period size: 30 Copynumber: 2.9 Consensus size: 30
57616657 CTAACTCACT
* *
57616667 TTCAACTCACGAGCTAAACCTTAGCTCAAC
1 TTCAGCTCACGAGCTAAAGCTTAGCTCAAC
* * ** *
57616697 TTCAGCTTAGGAG-TTTAGCCTCAGCTCAAC
1 TTCAGCTCACGAGCTAAAG-CTTAGCTCAAC
*
57616727 TTTAGCTCACGAGCTAAAGCTTAGCTCA
1 TTCAGCTCACGAGCTAAAGCTTAGCTCA
57616755 TTTTAGTTTA
Statistics
Matches: 43, Mismatches: 13, Indels: 4
0.72 0.22 0.07
Matches are distributed among these distances:
29 2 0.05
30 38 0.88
31 3 0.07
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.27
Consensus pattern (30 bp):
TTCAGCTCACGAGCTAAAGCTTAGCTCAAC
Found at i:57618865 original size:15 final size:15
Alignment explanation
Indices: 57618817--57618885 Score: 61
Period size: 15 Copynumber: 4.7 Consensus size: 15
57618807 TAAAGAGAAC
*
57618817 AAGAAAACC-GAATA
1 AAGAAACCCAGAATA
* *
57618831 AAGAAATCCA-AGATT
1 AAGAAACCCAGA-ATA
*
57618846 GAGAAACCCAGAATA
1 AAGAAACCCAGAATA
* *
57618861 AAGAAATCCATAATA
1 AAGAAACCCAGAATA
57618876 AAGAAACCCA
1 AAGAAACCCA
57618886 AGATACGATA
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
14 9 0.21
15 33 0.77
16 1 0.02
ACGTcount: A:0.58, C:0.17, G:0.13, T:0.12
Consensus pattern (15 bp):
AAGAAACCCAGAATA
Found at i:57618881 original size:30 final size:30
Alignment explanation
Indices: 57618817--57618885 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
57618807 TAAAGAGAAC
* *
57618817 AAGAAAACC-GAATAAAGAAATCCAAGATT
1 AAGAAACCCAGAATAAAGAAATCCAAGATA
*
57618846 GAGAAACCCAGAATAAAGAAATCCATA-ATA
1 AAGAAACCCAGAATAAAGAAATCCA-AGATA
57618876 AAGAAACCCA
1 AAGAAACCCA
57618886 AGATACGATA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 7 0.21
30 26 0.76
31 1 0.03
ACGTcount: A:0.58, C:0.17, G:0.13, T:0.12
Consensus pattern (30 bp):
AAGAAACCCAGAATAAAGAAATCCAAGATA
Found at i:57622661 original size:30 final size:30
Alignment explanation
Indices: 57622627--57622723 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
57622617 TAAACTAAAA
*
57622627 TGAGCTAAGCTTTAGCTTGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
57622657 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
57622687 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
57622717 TGAGCTA
1 TGAGCTA
57622724 GGAGTGAGCT
Statistics
Matches: 49, Mismatches: 15, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
29 2 0.04
30 41 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:57623320 original size:46 final size:46
Alignment explanation
Indices: 57623253--57623468 Score: 206
Period size: 46 Copynumber: 4.7 Consensus size: 46
57623243 TGTAACCCGC
* * * * *
57623253 CCATAAGCGAACTTGGACTCAACTCAATGAGCTCGGCCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCAGACGTTCGCAT
* *
57623299 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATACCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTC--AGA-C--GTTCGCAT
* * * *
57623349 -C-TCA-CGAACTTGGACTCAACTCAACGAGTTCAGACGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCAGACGTTCGCAT
* * * * *
57623392 CCATAATTGAACTCGGACTCAACTCAATGAGTTTAGATGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCAGACGTTCGCAT
*
57623438 CCATAAGTGAACTCGGACTCAATTCAACGAG
1 CCATAAGTGAACTCGGACTCAACTCAACGAG
57623469 TTTGGATGCC
Statistics
Matches: 139, Mismatches: 22, Indels: 18
0.78 0.12 0.10
Matches are distributed among these distances:
42 3 0.02
43 3 0.02
44 2 0.01
45 4 0.03
46 93 0.67
47 24 0.17
48 2 0.01
49 2 0.01
50 3 0.02
51 3 0.02
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCAGACGTTCGCAT
Found at i:57625373 original size:42 final size:41
Alignment explanation
Indices: 57625303--57625383 Score: 99
Period size: 42 Copynumber: 2.0 Consensus size: 41
57625293 TTCTCTTTAA
* ** * *
57625303 TCTCTTTTTCAATTTCTTTTTCACTCTCAAATTTCTTTTCGT
1 TCTCTTTTTCAATCTCAATCTCAATCTC-AATTTCTTTTCGT
*
57625345 TCTCTTTTTCAATCTCAATCTCAATCTCATTTTCTTTTC
1 TCTCTTTTTCAATCTCAATCTCAATCTCAATTTCTTTTC
57625384 TTTGTTTTTC
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
41 10 0.30
42 23 0.70
ACGTcount: A:0.16, C:0.26, G:0.01, T:0.57
Consensus pattern (41 bp):
TCTCTTTTTCAATCTCAATCTCAATCTCAATTTCTTTTCGT
Found at i:57625401 original size:19 final size:20
Alignment explanation
Indices: 57625377--57625417 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
57625367 AATCTCATTT
57625377 TCTTTTCTTTGTTT-TTCTC
1 TCTTTTCTTTGTTTCTTCTC
57625396 TCTTTTCTTTGTTTCTTCTC
1 TCTTTTCTTTGTTTCTTCTC
57625416 TC
1 TC
57625418 GATTTCATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.00, C:0.24, G:0.05, T:0.71
Consensus pattern (20 bp):
TCTTTTCTTTGTTTCTTCTC
Found at i:57627590 original size:13 final size:13
Alignment explanation
Indices: 57627572--57627596 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
57627562 TAACCTACAA
57627572 AATTAAATAACAT
1 AATTAAATAACAT
57627585 AATTAAATAACA
1 AATTAAATAACA
57627597 CACAACTATT
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:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (13 bp):
AATTAAATAACAT
Found at i:57627876 original size:20 final size:21
Alignment explanation
Indices: 57627821--57627869 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
57627811 AAAAAGGAAT
* *
57627821 GAGCTGAAACGAGCTAAATTC
1 GAGCTCAAACGAGCTAAAATC
57627842 GAGCTCAAACGAGCTAAAAT-
1 GAGCTCAAACGAGCTAAAATC
57627862 GAGCTCAA
1 GAGCTCAA
57627870 GTGAGCTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 8 0.31
21 18 0.69
ACGTcount: A:0.41, C:0.20, G:0.22, T:0.16
Consensus pattern (21 bp):
GAGCTCAAACGAGCTAAAATC
Found at i:57629862 original size:29 final size:29
Alignment explanation
Indices: 57629829--57629887 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
57629819 TAGACAACTC
*
57629829 CTTTAATGCCGTTCTATGCA-TCAGCAGCT
1 CTTTAATGCCGTTCCATGCACT-AGCAGCT
*
57629858 CTTTAATGCTGTTCCATGCACTAGCAGCT
1 CTTTAATGCCGTTCCATGCACTAGCAGCT
57629887 C
1 C
57629888 AATTAATGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 26 0.96
30 1 0.04
ACGTcount: A:0.20, C:0.29, G:0.17, T:0.34
Consensus pattern (29 bp):
CTTTAATGCCGTTCCATGCACTAGCAGCT
Found at i:57632640 original size:19 final size:19
Alignment explanation
Indices: 57632616--57632655 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
57632606 AGCTCCCATG
57632616 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
57632635 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
57632654 TA
1 TA
57632656 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:57633920 original size:14 final size:14
Alignment explanation
Indices: 57633903--57633944 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
57633893 ACCGACCAAA
*
57633903 TTGTTCATACCATT
1 TTGTTCCTACCATT
*
57633917 TTGTTCCTACCCTT
1 TTGTTCCTACCATT
*
57633931 TCGTTCCTACCATT
1 TTGTTCCTACCATT
57633945 CCATTCGTAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.14, C:0.31, G:0.07, T:0.48
Consensus pattern (14 bp):
TTGTTCCTACCATT
Found at i:57634091 original size:18 final size:17
Alignment explanation
Indices: 57634068--57634153 Score: 63
Period size: 18 Copynumber: 5.1 Consensus size: 17
57634058 TCGTATCACA
57634068 TTTTCTTTTTCATTCTCT
1 TTTTCTTTTTCATT-TCT
*
57634086 TTTTCTTTCTCTATTTCT
1 TTTTCTTTTTC-ATTTCT
** *
57634104 TTTTCACTTTCGTTTTCT
1 TTTTCTTTTTC-ATTTCT
*
57634122 TTTTC--TTTCTTTTC-
1 TTTTCTTTTTCATTTCT
*
57634136 TCTTCTTTTT-ATTTCT
1 TTTTCTTTTTCATTTCT
57634152 TT
1 TT
57634154 ACAACTTGAA
Statistics
Matches: 55, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
14 4 0.07
15 9 0.16
16 8 0.15
18 31 0.56
19 3 0.05
ACGTcount: A:0.05, C:0.21, G:0.01, T:0.73
Consensus pattern (17 bp):
TTTTCTTTTTCATTTCT
Found at i:57634092 original size:6 final size:6
Alignment explanation
Indices: 57634068--57634129 Score: 61
Period size: 6 Copynumber: 10.3 Consensus size: 6
57634058 TCGTATCACA
* * * * * * *
57634068 TTTTCT TTTTCA TTCTCT TTTTCT TTCTCT ATTTCT TTTTCA CTTTCG
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
57634116 TTTTCT TTTTCT TT
1 TTTTCT TTTTCT TT
57634130 CTTTTCTCTT
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.05, C:0.21, G:0.02, T:0.73
Consensus pattern (6 bp):
TTTTCT
Found at i:57635091 original size:34 final size:33
Alignment explanation
Indices: 57635052--57635118 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
57635042 TACAACAAAA
*
57635052 AATCTCAACACATGAATTTTTTTTGAATTTTTTT
1 AATCTCAACACATGAA-TTTTTTTAAATTTTTTT
*
57635086 AATCTCAATACATGAATTTTTTTAAATTTTTTT
1 AATCTCAACACATGAATTTTTTTAAATTTTTTT
57635119 CACTACATGA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 16 0.52
34 15 0.48
ACGTcount: A:0.31, C:0.10, G:0.04, T:0.54
Consensus pattern (33 bp):
AATCTCAACACATGAATTTTTTTAAATTTTTTT
Found at i:57635350 original size:14 final size:14
Alignment explanation
Indices: 57635333--57635372 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
57635323 CGAATGGAAT
*
57635333 GGTAGGAACGAAAG
1 GGTAGGAACAAAAG
57635347 GGTAGGAACAAAAG
1 GGTAGGAACAAAAG
* *
57635361 GATATGAACAAA
1 GGTAGGAACAAA
57635373 TTGGTCGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.50, C:0.07, G:0.33, T:0.10
Consensus pattern (14 bp):
GGTAGGAACAAAAG
Found at i:57641623 original size:72 final size:73
Alignment explanation
Indices: 57641510--57641657 Score: 183
Period size: 72 Copynumber: 2.0 Consensus size: 73
57641500 TTTAATGCTA
* * * *
57641510 TCCCAAGTCCCATGCACACACTAAATTCGGCTGGTTGGG-AAAATACAACAG-CAACTTTCGCTT
1 TCCCAAGTCCCATGCACACAATAAATTCGACAGCTTGGGAAAAATACAACAGCCAACTTT-GCTT
57641573 TAAATGCCG
65 TAAATGCCG
* * * * * *
57641582 TCCCAAGTCCCATGCACTCAATAAATTCGACAGCTTTGGAAAAATGCAGCAGCCACCTTTTCTTT
1 TCCCAAGTCCCATGCACACAATAAATTCGACAGCTTGGGAAAAATACAACAGCCAACTTTGCTTT
57641647 AAATGCCG
66 AAATGCCG
57641655 TCC
1 TCC
57641658 ATGTACCTGC
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
72 33 0.52
73 25 0.39
74 6 0.09
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.25
Consensus pattern (73 bp):
TCCCAAGTCCCATGCACACAATAAATTCGACAGCTTGGGAAAAATACAACAGCCAACTTTGCTTT
AAATGCCG
Found at i:57642858 original size:14 final size:14
Alignment explanation
Indices: 57642839--57642868 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
57642829 CCAATTACGA
57642839 ACAAGATTGTTATT
1 ACAAGATTGTTATT
57642853 ACAAGATTGTTATT
1 ACAAGATTGTTATT
57642867 AC
1 AC
57642869 CATCCAAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.40
Consensus pattern (14 bp):
ACAAGATTGTTATT
Found at i:57644898 original size:11 final size:12
Alignment explanation
Indices: 57644876--57644902 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
57644866 TCAAAAAAAA
57644876 TTTTGAATTTTT
1 TTTTGAATTTTT
57644888 TTTTGAATTTTT
1 TTTTGAATTTTT
57644900 TTT
1 TTT
57644903 CAAATTTCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (12 bp):
TTTTGAATTTTT
Found at i:57654819 original size:27 final size:27
Alignment explanation
Indices: 57654788--57654965 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
57654778 TAAATTGTAC
57654788 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
57654815 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
57654841 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
57654869 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
57654897 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
57654924 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
57654951 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
57654966 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:57654902 original size:82 final size:81
Alignment explanation
Indices: 57654789--57654944 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
57654779 AAATTGTACA
* *
57654789 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
57654853 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
57654870 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
57654935 TGCGAGTTGA
65 TGCGAATTGA
57654945 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:57654956 original size:82 final size:81
Alignment explanation
Indices: 57654785--57654965 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
57654775 GATTAAATTG
* *
57654785 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
57654850 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
57654866 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
57654930 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
57654948 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
57654966 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:57663004 original size:27 final size:27
Alignment explanation
Indices: 57662973--57663150 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
57662963 TAAATTGTAC
57662973 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
57663000 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
57663026 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
57663054 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
57663082 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
57663109 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
57663136 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
57663151 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:57663087 original size:82 final size:81
Alignment explanation
Indices: 57662974--57663129 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
57662964 AAATTGTACA
* *
57662974 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
57663038 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
57663055 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
57663120 TGCGAGTTGA
65 TGCGAATTGA
57663130 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:57663141 original size:82 final size:81
Alignment explanation
Indices: 57662970--57663150 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
57662960 GATTAAATTG
* *
57662970 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
57663035 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
57663051 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
57663115 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
57663133 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
57663151 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:57666450 original size:49 final size:49
Alignment explanation
Indices: 57666386--57666551 Score: 179
Period size: 50 Copynumber: 3.3 Consensus size: 49
57666376 CTGGTACGCA
* * *
57666386 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCAGGTACACG
*** * * *
57666435 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCGTCTGATACATG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC-AATTATCAGGTACACG
* * * *
57666485 TAGTAGCCTGCACTTTGTACTACACACGTGATCGAAGTTATCAGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-CCAA-TTATCAGGTACACG
*
57666536 TAGTAGCCTACACTTA
1 TAGTAGCCTGCACTTA
57666552 TGACTATTAG
Statistics
Matches: 94, Mismatches: 20, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
49 31 0.33
50 42 0.45
51 21 0.22
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.27
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCAGGTACACG
Found at i:57668575 original size:49 final size:50
Alignment explanation
Indices: 57668465--57668593 Score: 179
Period size: 49 Copynumber: 2.6 Consensus size: 50
57668455 GATCGTATCA
* * *
57668465 AGCCTGCACTTAGTACTACACACGTGATCGAATTTATCAAGTACGCATAGT
1 AGCCTGCACTTAGTACTACACATGTGA-CCAATTTATCAAGTACACATAGT
* * *
57668516 AGCCTGCACTTAGTACTACACATGCGACCAA-TTATCTAGTACACGTAGT
1 AGCCTGCACTTAGTACTACACATGTGACCAATTTATCAAGTACACATAGT
*
57668565 AGCCTACACTTAGTACTACACATGTGACC
1 AGCCTGCACTTAGTACTACACATGTGACC
57668594 TCACAATAGC
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
49 42 0.60
50 3 0.04
51 25 0.36
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.26
Consensus pattern (50 bp):
AGCCTGCACTTAGTACTACACATGTGACCAATTTATCAAGTACACATAGT
Found at i:57669275 original size:30 final size:30
Alignment explanation
Indices: 57669241--57669300 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
57669231 CTTTAATACG
57669241 AACTTTGGCAAAATTAC-CATTTTGCCCCTA
1 AACTTTGGCAAAATTACAC-TTTTGCCCCTA
* *
57669271 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTGCCCCTA
57669301 GGCTCGAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.28, C:0.27, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGCAAAATTACACTTTTGCCCCTA
Found at i:57671141 original size:14 final size:14
Alignment explanation
Indices: 57671122--57671166 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
57671112 AACTCATCTT
*
57671122 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
57671136 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
57671149 AATTTAATTTAATG
1 AGTTTAATTTAATG
57671163 AGTT
1 AGTT
57671167 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:57672178 original size:29 final size:29
Alignment explanation
Indices: 57672145--57672204 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
57672135 ATAACCAAAC
*
57672145 CTACAAAAACTTTATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
57672174 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
57672203 CT
1 CT
57672205 TTGAATCCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.30, G:0.00, T:0.28
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:57672197 original size:15 final size:15
Alignment explanation
Indices: 57672151--57672198 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
57672141 AAACCTACAA
*
57672151 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
57672166 AAAC-CCATCTACAT
1 AAACTTCATATCCAT
57672180 AAACTTCATATCCAT
1 AAACTTCATATCCAT
57672195 AAAC
1 AAAC
57672199 CCATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:57675018 original size:12 final size:13
Alignment explanation
Indices: 57675001--57675030 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
57674991 TGCAAAGCTG
57675001 AAAAAT-AAAATA
1 AAAAATAAAAATA
57675013 AAAAATAAAAATA
1 AAAAATAAAAATA
57675026 AAAAA
1 AAAAA
57675031 AAGTTCAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (13 bp):
AAAAATAAAAATA
Found at i:57681499 original size:30 final size:30
Alignment explanation
Indices: 57681465--57681561 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
57681455 TAAACTAAAA
* *
57681465 TGAGCTAAGCTTTAGCTTGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
* * * * *
57681495 TGAGCTAAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
* *
57681525 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGATTTAGCTCGTGAGCT-AAAGT
57681555 TGAGCTA
1 TGAGCTA
57681562 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
30 49 0.94
31 3 0.06
ACGTcount: A:0.30, C:0.13, G:0.27, T:0.30
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
Found at i:57683745 original size:30 final size:30
Alignment explanation
Indices: 57683674--57683756 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
57683664 CTTTTGTTTC
* *
57683674 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
57683705 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
57683734 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
57683757 GCTTTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.11
30 32 0.71
31 8 0.18
ACGTcount: A:0.13, C:0.22, G:0.01, T:0.64
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:57683756 original size:18 final size:18
Alignment explanation
Indices: 57683707--57683762 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
57683697 CACTCTCAAA
* *
57683707 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
57683724 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
57683742 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
57683761 TT
1 TT
57683763 CAAAGGCTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:57683763 original size:12 final size:12
Alignment explanation
Indices: 57683732--57683756 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
57683722 TTTTTCAATC
57683732 TCATTTTCTTTT
1 TCATTTTCTTTT
57683744 TCATTTTCTTTT
1 TCATTTTCTTTT
57683756 T
1 T
57683757 GCTTTTCAAA
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:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:57683774 original size:12 final size:12
Alignment explanation
Indices: 57683759--57683789 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
57683749 TTCTTTTTGC
57683759 TTTTCAAAGGCT
1 TTTTCAAAGGCT
57683771 TTTTCAAAGGCT
1 TTTTCAAAGGCT
57683783 TTTTCAA
1 TTTTCAA
57683790 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:57683859 original size:108 final size:108
Alignment explanation
Indices: 57683742--57684080 Score: 651
Period size: 108 Copynumber: 3.1 Consensus size: 108
57683732 TCATTTTCTT
*
57683742 TTTCATTTTCTTTTTGCTTTTCAAAGGCTTTTTCAAAGGCTTTTTCAAGTTCTCTCAAGATTCGC
1 TTTCATTTTCTTTTTGCTTTTTAAAGGCTTTTTCAAAGGCTTTTTCAAGTTCTCTCAAGATTCGC
57683807 TCATTTTCTCTCTTACTTGCCTCTTGCCTCTCTTTTCTTTTTA
66 TCATTTTCTCTCTTACTTGCCTCTTGCCTCTCTTTTCTTTTTA
57683850 TTTCATTTTCTTTTTGCTTTTTAAAGGCTTTTTCAAAGGCTTTTTCAAGTTCTCTCAAGATTCGC
1 TTTCATTTTCTTTTTGCTTTTTAAAGGCTTTTTCAAAGGCTTTTTCAAGTTCTCTCAAGATTCGC
* *
57683915 TCATTTTCTCTTTTACTTGCCTCTTGCCTCTCTTTTCTTTCTA
66 TCATTTTCTCTCTTACTTGCCTCTTGCCTCTCTTTTCTTTTTA
57683958 TTTCATTTTCTTTTTGCTTTTTAAAGGCTTTTTCAAAGGCTTTTTCAAGTTCTCTCAAGATTCGC
1 TTTCATTTTCTTTTTGCTTTTTAAAGGCTTTTTCAAAGGCTTTTTCAAGTTCTCTCAAGATTCGC
57684023 TCATTTTCTCTCTTACTTGCCTCTTGCCTCTCTTTTCTTTTTA
66 TCATTTTCTCTCTTACTTGCCTCTTGCCTCTCTTTTCTTTTTA
57684066 TTTCATTTTCTTTTT
1 TTTCATTTTCTTTTT
57684081 CTTCTTTTGC
Statistics
Matches: 226, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
108 226 1.00
ACGTcount: A:0.14, C:0.23, G:0.09, T:0.55
Consensus pattern (108 bp):
TTTCATTTTCTTTTTGCTTTTTAAAGGCTTTTTCAAAGGCTTTTTCAAGTTCTCTCAAGATTCGC
TCATTTTCTCTCTTACTTGCCTCTTGCCTCTCTTTTCTTTTTA
Found at i:57683882 original size:12 final size:12
Alignment explanation
Indices: 57683865--57683897 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
57683855 TTTTCTTTTT
57683865 GCTTTTT-AAAG
1 GCTTTTTCAAAG
57683876 GCTTTTTCAAAG
1 GCTTTTTCAAAG
57683888 GCTTTTTCAA
1 GCTTTTTCAA
57683898 GTTCTCTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.33
12 14 0.67
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.45
Consensus pattern (12 bp):
GCTTTTTCAAAG
Found at i:57683990 original size:12 final size:12
Alignment explanation
Indices: 57683973--57684005 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
57683963 TTTTCTTTTT
57683973 GCTTTTT-AAAG
1 GCTTTTTCAAAG
57683984 GCTTTTTCAAAG
1 GCTTTTTCAAAG
57683996 GCTTTTTCAA
1 GCTTTTTCAA
57684006 GTTCTCTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.33
12 14 0.67
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.45
Consensus pattern (12 bp):
GCTTTTTCAAAG
Found at i:57684063 original size:5 final size:5
Alignment explanation
Indices: 57684053--57684109 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
57684043 CTCTTGCCTC
*
57684053 TCTTT TCTTT T-TATT TCATTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
57684100 TCTTT TCTTT
1 TCTTT TCTTT
57684110 GTTTCCTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:57684093 original size:15 final size:14
Alignment explanation
Indices: 57684053--57684109 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
57684043 CTCTTGCCTC
*
57684053 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
57684068 TCATTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
57684083 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
57684100 TCTTTTCTTT
1 TCTTTTCTTT
57684110 GTTTCCTCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 12 0.32
16 14 0.38
17 7 0.19
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:57685046 original size:11 final size:11
Alignment explanation
Indices: 57685032--57685072 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
57685022 ATTTTTTTTC
57685032 TTTTTGAATTT
1 TTTTTGAATTT
57685043 TTTTTGAATTT
1 TTTTTGAATTT
* *
57685054 TGTTTTCAAATT
1 T-TTTTGAATTT
57685066 TTTTTGA
1 TTTTTGA
57685073 CTTGTATAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 17 0.65
12 9 0.35
ACGTcount: A:0.20, C:0.02, G:0.10, T:0.68
Consensus pattern (11 bp):
TTTTTGAATTT
Found at i:57686827 original size:30 final size:30
Alignment explanation
Indices: 57686742--57686838 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
57686732 TAAACTAAAA
* * * *
57686742 TGAGCTAAGCTTTAGCTTGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGTTGAAGT
* * * * *
57686772 TGAGCTGAGATTAAACTCCTAAGTTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGTTGAAGT
*
57686802 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGATTTAGCTCGTGAGTTG-AAGT
57686832 TGAGCTA
1 TGAGCTA
57686839 GGAATGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
30 48 0.94
31 3 0.06
ACGTcount: A:0.29, C:0.12, G:0.28, T:0.31
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGTTGAAGT
Found at i:57693697 original size:13 final size:13
Alignment explanation
Indices: 57693679--57693709 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
57693669 TTGTAGATTC
57693679 AAAAAAATCG-GA
1 AAAAAAATCGAGA
57693691 AAAAAAATCGAGA
1 AAAAAAATCGAGA
57693704 AAAAAA
1 AAAAAA
57693710 TTTTTTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.56
13 8 0.44
ACGTcount: A:0.74, C:0.06, G:0.13, T:0.06
Consensus pattern (13 bp):
AAAAAAATCGAGA
Found at i:57693722 original size:12 final size:12
Alignment explanation
Indices: 57693707--57693733 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
57693697 ATCGAGAAAA
57693707 AAATTTTTTTTT
1 AAATTTTTTTTT
57693719 AAATTTTTTTTT
1 AAATTTTTTTTT
57693731 AAA
1 AAA
57693734 AAAAATTGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
AAATTTTTTTTT
Found at i:57695959 original size:31 final size:33
Alignment explanation
Indices: 57695898--57695959 Score: 76
Period size: 32 Copynumber: 1.9 Consensus size: 33
57695888 AAAGAAATCG
* *
57695898 AGAGAGAGAAAAAAAATGAAAAGAATAAAGAAA
1 AGAGAGAGAAAAAAAATAAAAACAATAAAGAAA
57695931 AGAGA-AGAAAAGAAAA-AAAAACAA-AAAGA
1 AGAGAGAGAAAA-AAAATAAAAACAATAAAGA
57695960 CGAGTGATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
31 5 0.19
32 12 0.46
33 9 0.35
ACGTcount: A:0.76, C:0.02, G:0.19, T:0.03
Consensus pattern (33 bp):
AGAGAGAGAAAAAAAATAAAAACAATAAAGAAA
Found at i:57699070 original size:21 final size:21
Alignment explanation
Indices: 57699025--57699087 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
57699015 TTTGAACCAT
* *
57699025 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
57699047 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
*
57699068 TACCATTTCGTAACAATTCC
1 TACCATTTCGTACCAATTCC
57699088 CAAATACCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
21 24 0.67
22 12 0.33
ACGTcount: A:0.35, C:0.32, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:57708472 original size:19 final size:19
Alignment explanation
Indices: 57708427--57708472 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
57708417 ATTAACACAC
*
57708427 AATTAATTAAAATATAACT
1 AATTAATAAAAATATAACT
*
57708446 -ATTCATAAAAATCATAA-T
1 AATTAATAAAAAT-ATAACT
57708464 AATTAATAA
1 AATTAATAA
57708473 TTAAACAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.35
Consensus pattern (19 bp):
AATTAATAAAAATATAACT
Found at i:57708699 original size:10 final size:10
Alignment explanation
Indices: 57708686--57708720 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
57708676 AAGCTCGGTT
57708686 GAGCTCAAAC
1 GAGCTCAAAC
*
57708696 GAGCTGAAAC
1 GAGCTCAAAC
*
57708706 GAGCTCAAAT
1 GAGCTCAAAC
57708716 GAGCT
1 GAGCT
57708721 GAGTTGAGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.37, C:0.23, G:0.26, T:0.14
Consensus pattern (10 bp):
GAGCTCAAAC
Found at i:57708729 original size:20 final size:20
Alignment explanation
Indices: 57708683--57708730 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
57708673 AGTAAGCTCG
57708683 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
*** *
57708703 AACGAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
57708723 GTTGAGCT
1 GTTGAGCT
57708731 GGACGGAGCT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.31, C:0.19, G:0.29, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:57712482 original size:49 final size:49
Alignment explanation
Indices: 57712422--57712641 Score: 278
Period size: 49 Copynumber: 4.4 Consensus size: 49
57712412 CCAAAGCTAT
* *
57712422 CTGCACATAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGC
1 CTGCACTTAGTACTACACATGTGACCAATTATCCGGTACACGTAGTAGC
*
57712471 CTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACGTAGTAGC
1 CTGCACTTAGTACTACACATGTGACCAATTATCCGGTACACGTAGTAGC
* ** * * *
57712520 CTGCACTTAGTACTACACACGTGACCTAACCATCTGATAGACGTAGTAGC
1 CTGCACTTAGTACTACACATGTGACC-AATTATCCGGTACACGTAGTAGC
* * * * * *
57712570 CTACACTTAGTACTACACATGTGATCACAGTTTTCGGGTACGCATAGTAGC
1 CTGCACTTAGTACTACACATGTGA-C-CAATTATCCGGTACACGTAGTAGC
57712621 CTGCACTTAGTACTACACATG
1 CTGCACTTAGTACTACACATG
57712642 CAACCTCACA
Statistics
Matches: 148, Mismatches: 20, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
49 72 0.49
50 40 0.27
51 35 0.24
52 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.25
Consensus pattern (49 bp):
CTGCACTTAGTACTACACATGTGACCAATTATCCGGTACACGTAGTAGC
Found at i:57715188 original size:12 final size:13
Alignment explanation
Indices: 57715173--57715201 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
57715163 TATTTTTATT
57715173 TTTATTTATTTA-
1 TTTATTTATTTAG
57715185 TTTATTTATTTAG
1 TTTATTTATTTAG
57715198 TTTA
1 TTTA
57715202 AATTTTTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.72
Consensus pattern (13 bp):
TTTATTTATTTAG
Found at i:57720688 original size:17 final size:18
Alignment explanation
Indices: 57720666--57720702 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
57720656 CTCTCTTTTG
57720666 TTTTCTT-TTTCT-TATTT
1 TTTTCTTCTTT-TATATTT
57720683 TTTTCTTCTTTTATATTT
1 TTTTCTTCTTTTATATTT
57720701 TT
1 TT
57720703 ACAATCTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.08, C:0.11, G:0.00, T:0.81
Consensus pattern (18 bp):
TTTTCTTCTTTTATATTT
Found at i:57720696 original size:16 final size:18
Alignment explanation
Indices: 57720666--57720702 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
57720656 CTCTCTTTTG
*
57720666 TTTTCTTTTTCTTAT-TT
1 TTTTCTTCTTCTTATATT
57720683 TTTTCTTCTT-TTATATT
1 TTTTCTTCTTCTTATATT
57720700 TTT
1 TTT
57720703 ACAATCTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.08, C:0.11, G:0.00, T:0.81
Consensus pattern (18 bp):
TTTTCTTCTTCTTATATT
Found at i:57722814 original size:10 final size:10
Alignment explanation
Indices: 57722792--57722874 Score: 80
Period size: 10 Copynumber: 8.3 Consensus size: 10
57722782 AATGTTCTAG
57722792 TTTCAATTTTT
1 TTTCAA-TTTT
57722803 TTTCAATTTT
1 TTTCAATTTT
*
57722813 TTTTAA-TTT
1 TTTCAATTTT
*
57722822 TTTAAATTTT
1 TTTCAATTTT
*
57722832 TTTCGAAATTT
1 TTTC-AATTTT
*
57722843 TTT-GATTTT
1 TTTCAATTTT
*
57722852 TTTTAATTTT
1 TTTCAATTTT
*
57722862 TTTCGATTTT
1 TTTCAATTTT
57722872 TTT
1 TTT
57722875 TTGAAACTTT
Statistics
Matches: 60, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
9 15 0.25
10 31 0.52
11 14 0.23
ACGTcount: A:0.19, C:0.05, G:0.04, T:0.72
Consensus pattern (10 bp):
TTTCAATTTT
Found at i:57722832 original size:30 final size:29
Alignment explanation
Indices: 57722799--57722875 Score: 100
Period size: 30 Copynumber: 2.6 Consensus size: 29
57722789 TAGTTTCAAT
57722799 TTTTTTTCAATTTTTTTTAATTTTTTAAA
1 TTTTTTTCAATTTTTTTTAATTTTTTAAA
* * * *
57722828 TTTTTTTCGAAATTTTTTGATTTTTTTTAA
1 TTTTTTTC-AATTTTTTTTAATTTTTTAAA
*
57722858 TTTTTTTCGATTTTTTTT
1 TTTTTTTCAATTTTTTTT
57722876 TGAAACTTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
29 15 0.38
30 25 0.62
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.74
Consensus pattern (29 bp):
TTTTTTTCAATTTTTTTTAATTTTTTAAA
Found at i:57724337 original size:12 final size:13
Alignment explanation
Indices: 57724320--57724349 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
57724310 TGCAAAGCTG
57724320 AAAAAT-AAAATA
1 AAAAATAAAAATA
57724332 AAAAATAAAAATA
1 AAAAATAAAAATA
57724345 AAAAA
1 AAAAA
57724350 AGTTCAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (13 bp):
AAAAATAAAAATA
Found at i:57734830 original size:18 final size:19
Alignment explanation
Indices: 57734807--57734845 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
57734797 TTTATCTCAA
*
57734807 TTTCTTTTTC-CACTCTTT
1 TTTCTTGTTCACACTCTTT
*
57734825 TTTCTTGTTCACATTCTTT
1 TTTCTTGTTCACACTCTTT
57734844 TT
1 TT
57734846 CTCTCTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.08, C:0.23, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTCTTGTTCACACTCTTT
Found at i:57734884 original size:18 final size:18
Alignment explanation
Indices: 57734863--57734906 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
57734853 AAACTCTTTT
57734863 TCATTCTCTTTTTCAATC
1 TCATTCTCTTTTTCAATC
* *
57734881 TCATTTTCTTTTTCACTC
1 TCATTCTCTTTTTCAATC
*
57734899 TCAATCTC
1 TCATTCTC
57734907 AATCTCTTTT
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:0.30, G:0.00, T:0.55
Consensus pattern (18 bp):
TCATTCTCTTTTTCAATC
Found at i:57734891 original size:30 final size:30
Alignment explanation
Indices: 57734857--57734924 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 30
57734847 TCTCTCAAAC
* ** *
57734857 TCTTTTTCATTCTCTTTTTCAATCTCATTT
1 TCTTTTTCACTCTCAATCTCAATCTCATTT
*
57734887 TCTTTTTCACTCTCAATCTCAATCTCTTTT
1 TCTTTTTCACTCTCAATCTCAATCTCATTT
57734917 TCTTTTTC
1 TCTTTTTC
57734925 TTTCATTTCT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.13, C:0.26, G:0.00, T:0.60
Consensus pattern (30 bp):
TCTTTTTCACTCTCAATCTCAATCTCATTT
Found at i:57734902 original size:24 final size:24
Alignment explanation
Indices: 57734838--57734919 Score: 83
Period size: 24 Copynumber: 3.4 Consensus size: 24
57734828 CTTGTTCACA
* *
57734838 TTCTTTTTCTCTCTCAAACTCTTT
1 TTCTTTTTCTCTCTCAATCTCATT
* * * *
57734862 TTCATTCTCTTTTTCAATCTCATT
1 TTCTTTTTCTCTCTCAATCTCATT
* *
57734886 TTCTTTTTCACTCTCAATCTCAAT
1 TTCTTTTTCTCTCTCAATCTCATT
*
57734910 CTCTTTTTCT
1 TTCTTTTTCT
57734920 TTTTCTTTCA
Statistics
Matches: 44, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.15, C:0.28, G:0.00, T:0.57
Consensus pattern (24 bp):
TTCTTTTTCTCTCTCAATCTCATT
Found at i:57737402 original size:10 final size:10
Alignment explanation
Indices: 57737389--57737423 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
57737379 AAGCTCGGTT
57737389 GAGCTCAAAC
1 GAGCTCAAAC
*
57737399 GAGCTGAAAC
1 GAGCTCAAAC
*
57737409 GAGCTCAAAT
1 GAGCTCAAAC
57737419 GAGCT
1 GAGCT
57737424 AAGTTGAGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.37, C:0.23, G:0.26, T:0.14
Consensus pattern (10 bp):
GAGCTCAAAC
Found at i:57737432 original size:20 final size:21
Alignment explanation
Indices: 57737386--57737433 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
57737376 AGTAAGCTCG
57737386 GTTGAGCTCAAACGAGCTGAA
1 GTTGAGCTCAAACGAGCTGAA
** *
57737407 -ACGAGCTCAAATGAGCT-AA
1 GTTGAGCTCAAACGAGCTGAA
57737426 GTTGAGCT
1 GTTGAGCT
57737434 GGACGGAGCT
Statistics
Matches: 21, Mismatches: 5, Indels: 3
0.72 0.17 0.10
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (21 bp):
GTTGAGCTCAAACGAGCTGAA
Found at i:57742784 original size:20 final size:20
Alignment explanation
Indices: 57742761--57742807 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
57742751 GGGTTAAGAT
57742761 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTTGAA
* * *
57742781 TGAGTTGACTTGAGCTTGAG
1 TGAGCTGAATTGAGCTTGAA
57742801 TGAGCTG
1 TGAGCTG
57742808 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.11, G:0.34, T:0.32
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTTGAA
Found at i:57746135 original size:20 final size:20
Alignment explanation
Indices: 57746112--57746158 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
57746102 GGGTTAAGAT
*
57746112 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
57746132 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
57746152 TGAGCTG
1 TGAGCTG
57746159 GAAACGAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:57750502 original size:11 final size:11
Alignment explanation
Indices: 57750486--57750528 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
57750476 ATATACTTCG
57750486 ATTTTTTTTTA
1 ATTTTTTTTTA
57750497 ATTTTTTTTTCA
1 ATTTTTTTTT-A
*
57750509 A-TTTTTTTAA
1 ATTTTTTTTTA
57750519 ATTTTTTTTT
1 ATTTTTTTTT
57750529 CGAATTTCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 2 0.07
11 24 0.86
12 2 0.07
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (11 bp):
ATTTTTTTTTA
Found at i:57750513 original size:22 final size:23
Alignment explanation
Indices: 57750482--57750535 Score: 83
Period size: 22 Copynumber: 2.4 Consensus size: 23
57750472 TTTTATATAC
* *
57750482 TTCGATTTTTTTTTAATTTTTTT
1 TTCGAATTTTTTTAAATTTTTTT
57750505 TTC-AATTTTTTTAAATTTTTTT
1 TTCGAATTTTTTTAAATTTTTTT
57750527 TTCGAATTT
1 TTCGAATTT
57750536 CCTCTTCTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 20 0.71
23 8 0.29
ACGTcount: A:0.19, C:0.06, G:0.04, T:0.72
Consensus pattern (23 bp):
TTCGAATTTTTTTAAATTTTTTT
Found at i:57766875 original size:10 final size:10
Alignment explanation
Indices: 57766860--57766914 Score: 56
Period size: 10 Copynumber: 5.4 Consensus size: 10
57766850 AACTCCGACC
57766860 AGCTCAATTG
1 AGCTCAATTG
* *
57766870 AGCTCATTTT
1 AGCTCAATTG
*
57766880 AGCTCAATCG
1 AGCTCAATTG
*
57766890 AGCTCAATTT
1 AGCTCAATTG
*
57766900 AGCTACAATTC
1 AGCT-CAATTG
57766911 AGCT
1 AGCT
57766915 TATTTATTTT
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
10 27 0.75
11 9 0.25
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.33
Consensus pattern (10 bp):
AGCTCAATTG
Found at i:57766883 original size:20 final size:20
Alignment explanation
Indices: 57766860--57766919 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
57766850 AACTCCGACC
57766860 AGCTCAATTGAGCTCATTTT
1 AGCTCAATTGAGCTCATTTT
* *
57766880 AGCTCAATCGAGCTCAATTT
1 AGCTCAATTGAGCTCATTTT
* *
57766900 AGCTACAATTCAGCTTATTT
1 AGCT-CAATTGAGCTCATTT
57766920 ATTTTATTGG
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 22 0.67
21 11 0.33
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (20 bp):
AGCTCAATTGAGCTCATTTT
Found at i:57768624 original size:18 final size:18
Alignment explanation
Indices: 57768598--57768647 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
57768588 AAATTGAAAG
*
57768598 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAAACGA
** *
57768616 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAAACGA
57768634 AAAAGAAAAAGAAA
1 AAAAGAAAAAGAAA
57768648 TCAAAATAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.76, C:0.06, G:0.14, T:0.04
Consensus pattern (18 bp):
AAAAGAAAAAGAAAACGA
Found at i:57768626 original size:6 final size:6
Alignment explanation
Indices: 57768594--57768647 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
57768584 AAAGAAATTG
* * ** *
57768594 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
57768641 AAAGAA A
1 AAAGAA A
57768648 TCAAAATAGT
Statistics
Matches: 38, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
5 3 0.08
6 35 0.92
ACGTcount: A:0.76, C:0.06, G:0.15, T:0.04
Consensus pattern (6 bp):
AAAGAA
Found at i:57768707 original size:18 final size:18
Alignment explanation
Indices: 57768686--57768720 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
57768676 AGAAAAGAAA
57768686 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
57768704 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
57768721 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:57770804 original size:10 final size:10
Alignment explanation
Indices: 57770788--57770845 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
57770778 CAACTCCGAC
57770788 CAGCTCAATT
1 CAGCTCAATT
* *
57770798 GAGCTCATTT
1 CAGCTCAATT
57770808 CAGCTCAA-T
1 CAGCTCAATT
57770817 CGAGCTCAATT
1 C-AGCTCAATT
*
57770828 TAGCTACAATT
1 CAGCT-CAATT
57770839 CAGCTCA
1 CAGCTCA
57770846 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:57770811 original size:20 final size:20
Alignment explanation
Indices: 57770788--57770848 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
57770778 CAACTCCGAC
57770788 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
57770808 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
57770829 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
57770849 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:57783928 original size:15 final size:15
Alignment explanation
Indices: 57783908--57783936 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
57783898 TTGTAATGAA
57783908 AAATGAAAGAAAAAT
1 AAATGAAAGAAAAAT
57783923 AAATGAAAGAAAAA
1 AAATGAAAGAAAAA
57783937 GAGTGTGAAA
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:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (15 bp):
AAATGAAAGAAAAAT
Found at i:57784026 original size:18 final size:19
Alignment explanation
Indices: 57783985--57784030 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
57783975 AAATGAAATT
57783985 GAAAAAGA-AAGTGAAAAA
1 GAAAAAGAGAAGTGAAAAA
57784003 -ACAAAAGAGAAG-GAAAAA
1 GA-AAAAGAGAAGTGAAAAA
57784021 GAAAAAGAGA
1 GAAAAAGAGA
57784031 TCGAGAGTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 1 0.04
18 20 0.80
19 4 0.16
ACGTcount: A:0.72, C:0.02, G:0.24, T:0.02
Consensus pattern (19 bp):
GAAAAAGAGAAGTGAAAAA
Found at i:57785432 original size:13 final size:13
Alignment explanation
Indices: 57785414--57785442 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
57785404 CGGCTAACCT
57785414 ACATAATTAAATA
1 ACATAATTAAATA
57785427 ACATAATTAAATA
1 ACATAATTAAATA
57785440 ACA
1 ACA
57785443 CACAACTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (13 bp):
ACATAATTAAATA
Found at i:57785700 original size:10 final size:10
Alignment explanation
Indices: 57785667--57785715 Score: 55
Period size: 10 Copynumber: 4.8 Consensus size: 10
57785657 AAAAAGGAAT
*
57785667 GAGCTGAAAC
1 GAGCTCAAAC
57785677 GAGCT-AAATTC
1 GAGCTCAAA--C
57785688 GAGCTCAAAC
1 GAGCTCAAAC
*
57785698 GAGCTAAAAC
1 GAGCTCAAAC
57785708 GAGCTCAA
1 GAGCTCAA
57785716 GTGAGCTGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 3 0.09
10 22 0.65
11 6 0.18
12 3 0.09
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.14
Consensus pattern (10 bp):
GAGCTCAAAC
Found at i:57785722 original size:20 final size:21
Alignment explanation
Indices: 57785667--57785715 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
57785657 AAAAAGGAAT
* *
57785667 GAGCTGAAACGAGCTAAATTC
1 GAGCTCAAACGAGCTAAATAC
57785688 GAGCTCAAACGAGCTAAA-AC
1 GAGCTCAAACGAGCTAAATAC
57785708 GAGCTCAA
1 GAGCTCAA
57785716 GTGAGCTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.14
Consensus pattern (21 bp):
GAGCTCAAACGAGCTAAATAC
Found at i:57786065 original size:30 final size:29
Alignment explanation
Indices: 57786031--57786102 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 29
57786021 AGCTCACTCC
57786031 TAGCTCACTTTCAACTCACGAGCTAAACCT
1 TAGCTCACTTT-AACTCACGAGCTAAACCT
* * *
57786061 TAGCTCAACTTTAGCTCATGAGCTAAAGCT
1 TAGCTC-ACTTTAACTCACGAGCTAAACCT
*
57786091 TAGCTCATTTTA
1 TAGCTCACTTTA
57786103 GTTTAAACTC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 5 0.14
30 27 0.73
31 5 0.14
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.32
Consensus pattern (29 bp):
TAGCTCACTTTAACTCACGAGCTAAACCT
Found at i:57787784 original size:11 final size:11
Alignment explanation
Indices: 57787765--57787799 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
57787755 GTTATACAAG
57787765 TCAAAAAAAAA
1 TCAAAAAAAAA
*
57787776 TCGAAAAAAAAT
1 TC-AAAAAAAAA
57787788 TCAAAAAAAAA
1 TCAAAAAAAAA
57787799 T
1 T
57787800 TTCGAAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.74, C:0.09, G:0.03, T:0.14
Consensus pattern (11 bp):
TCAAAAAAAAA
Found at i:57787784 original size:12 final size:12
Alignment explanation
Indices: 57787767--57787813 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
57787757 TATACAAGTC
57787767 AAAAAAAAATCG
1 AAAAAAAAATCG
*
57787779 AAAAAAAATTC-
1 AAAAAAAAATCG
57787790 AAAAAAAAATTTCG
1 AAAAAAAAA--TCG
57787804 AAAAGAAAAA
1 AAAA-AAAAA
57787814 AAAATCTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
11 8 0.28
12 10 0.34
13 2 0.07
14 4 0.14
15 5 0.17
ACGTcount: A:0.74, C:0.06, G:0.06, T:0.13
Consensus pattern (12 bp):
AAAAAAAAATCG
Found at i:57787826 original size:19 final size:19
Alignment explanation
Indices: 57787790--57787829 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
57787780 AAAAAAATTC
*
57787790 AAAAAAAAATTTCGAAAAG
1 AAAAAAAAATCTCGAAAAG
57787809 AAAAAAAAATCT-GAAAA-
1 AAAAAAAAATCTCGAAAAG
57787826 AAAA
1 AAAA
57787830 GTGTTTAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 4 0.20
18 5 0.25
19 11 0.55
ACGTcount: A:0.75, C:0.05, G:0.07, T:0.12
Consensus pattern (19 bp):
AAAAAAAAATCTCGAAAAG
Found at i:57788771 original size:21 final size:20
Alignment explanation
Indices: 57788737--57788780 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
57788727 ACATTCTTGT
57788737 AAAGAGAAAACAAAGAAAAGA
1 AAAGAGAAAACAAA-AAAAGA
*
57788758 AAAGA-AAAAGCAAAAGAAGA
1 AAAGAGAAAA-CAAAAAAAGA
57788778 AAA
1 AAA
57788781 ATAAAATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.77, C:0.05, G:0.18, T:0.00
Consensus pattern (20 bp):
AAAGAGAAAACAAAAAAAGA
Found at i:57788882 original size:11 final size:12
Alignment explanation
Indices: 57788852--57788882 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
57788842 TTGAGAGAAC
*
57788852 TTGAAAAAGCCT
1 TTGAAAAACCCT
57788864 TTGAAAAACCCT
1 TTGAAAAACCCT
57788876 TTGAAAA
1 TTGAAAA
57788883 GCAAAAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.26
Consensus pattern (12 bp):
TTGAAAAACCCT
Found at i:57788919 original size:30 final size:31
Alignment explanation
Indices: 57788885--57788966 Score: 87
Period size: 30 Copynumber: 2.7 Consensus size: 31
57788875 TTTGAAAAGC
* *
57788885 AAAAAGAAAATTAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATCAAAAAGAAATATGAGAGTG
* * *
57788915 AAAAAGAGAA-CGAAAAGAAATTTGAGAGTG
1 AAAAAGAAAATCAAAAAGAAATATGAGAGTG
* *
57788945 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATCAAAAAGAAAT
57788967 TGAAACAAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
29 8 0.20
30 24 0.59
31 9 0.22
ACGTcount: A:0.65, C:0.01, G:0.21, T:0.13
Consensus pattern (31 bp):
AAAAAGAAAATCAAAAAGAAATATGAGAGTG
Found at i:57793347 original size:29 final size:29
Alignment explanation
Indices: 57793314--57793373 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
57793304 ATAACCAAAC
* *
57793314 CTACAAAAACTTTATATCCATAAATCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
* *
57793343 CTACATAAACTTCATATCTATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
57793372 CT
1 CT
57793374 TTGAATCCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.42, C:0.27, G:0.00, T:0.32
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:57793603 original size:9 final size:9
Alignment explanation
Indices: 57793589--57793624 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
57793579 AGTAAGTTTC
57793589 AAAAAAATG
1 AAAAAAATG
*
57793598 AAAAAAACG
1 AAAAAAATG
57793607 AAAAAAAATG
1 -AAAAAAATG
57793617 AAAAAAAT
1 AAAAAAAT
57793625 TTCAAACAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.81, C:0.03, G:0.08, T:0.08
Consensus pattern (9 bp):
AAAAAAATG
Found at i:57793604 original size:10 final size:10
Alignment explanation
Indices: 57793589--57793623 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
57793579 AGTAAGTTTC
57793589 AAAAAAATG-
1 AAAAAAATGA
*
57793598 AAAAAAACGA
1 AAAAAAATGA
57793608 AAAAAAATGA
1 AAAAAAATGA
57793618 AAAAAA
1 AAAAAA
57793624 TTTCAAACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.83, C:0.03, G:0.09, T:0.06
Consensus pattern (10 bp):
AAAAAAATGA
Found at i:57794730 original size:30 final size:28
Alignment explanation
Indices: 57794694--57794749 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
57794684 AAGCAAAAAA
* *
57794694 GAAAAAGAGTGTGTGCAAGAAAGTAAAGTT
1 GAAAAAGAGAGTGAGCAA-AAAG-AAAGTT
57794724 GAAAAAGAGAGTGAGCAAAAAGAAAG
1 GAAAAAGAGAGTGAGCAAAAAGAAAG
57794750 CGTGGAAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
29 4 0.17
30 16 0.67
ACGTcount: A:0.54, C:0.04, G:0.30, T:0.12
Consensus pattern (28 bp):
GAAAAAGAGAGTGAGCAAAAAGAAAGTT
Found at i:57798421 original size:12 final size:12
Alignment explanation
Indices: 57798406--57798436 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
57798396 TTCTTTTTGC
57798406 TTTTCAAAGGCT
1 TTTTCAAAGGCT
57798418 TTTTCAAAGGCT
1 TTTTCAAAGGCT
57798430 TTTTCAA
1 TTTTCAA
57798437 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:57798494 original size:5 final size:5
Alignment explanation
Indices: 57798484--57798551 Score: 50
Period size: 5 Copynumber: 13.0 Consensus size: 5
57798474 CTCTTGCCTC
* *
57798484 TCTTT TCTTT T-TAAT TCATTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
*
57798531 TCTTT TCTTT GCTTT CTCTTT
1 TCTTT TCTTT TCTTT -TCTTT
57798552 ACAAGAATGT
Statistics
Matches: 50, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
4 4 0.08
5 32 0.64
6 9 0.18
7 5 0.10
ACGTcount: A:0.04, C:0.19, G:0.03, T:0.74
Consensus pattern (5 bp):
TCTTT
Found at i:57798524 original size:15 final size:14
Alignment explanation
Indices: 57798484--57798540 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
57798474 CTCTTGCCTC
*
57798484 TCTTTTCTTTTTAAT
1 TCTTTTCTTTTT-CT
57798499 TCATTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
57798514 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
57798531 TCTTTTCTTT
1 TCTTTTCTTT
57798541 GCTTTCTCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 12 0.32
16 14 0.38
17 7 0.19
ACGTcount: A:0.05, C:0.18, G:0.02, T:0.75
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:57798541 original size:21 final size:21
Alignment explanation
Indices: 57798502--57798551 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
57798492 TTTTAATTCA
57798502 TTTTCTTTTTCTTCTTTTGCT
1 TTTTCTTTTTCTTCTTTTGCT
*
57798523 TTTTC-TTTTCTTTTCTTTGCT
1 TTTTCTTTTTCTTCT-TTTGCT
*
57798544 TTCTCTTT
1 TTTTCTTT
57798552 ACAAGAATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 8 0.32
21 15 0.60
22 2 0.08
ACGTcount: A:0.00, C:0.20, G:0.04, T:0.76
Consensus pattern (21 bp):
TTTTCTTTTTCTTCTTTTGCT
Found at i:57806085 original size:30 final size:30
Alignment explanation
Indices: 57805999--57806098 Score: 103
Period size: 30 Copynumber: 3.3 Consensus size: 30
57805989 TAAACTAAAA
* *
57805999 TGAGCTAAGCTTTAGCTCGTGAGCTAAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCT-GAAGT
* * * * * *
57806030 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
57806060 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
57806089 ATGAGCTAAG
1 -TGAGCTAAG
57806099 AGTGAGCTCG
Statistics
Matches: 54, Mismatches: 14, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
29 1 0.02
30 35 0.65
31 18 0.33
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.27
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
Found at i:57817512 original size:12 final size:12
Alignment explanation
Indices: 57817497--57817527 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
57817487 TCTTTTTTTC
57817497 TTTTCAAAGGCT
1 TTTTCAAAGGCT
57817509 TTTTCAAAGGCT
1 TTTTCAAAGGCT
57817521 TTTTCAA
1 TTTTCAA
57817528 GTGCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:57817615 original size:21 final size:22
Alignment explanation
Indices: 57817591--57817631 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
57817581 ATTTTTATTT
*
57817591 CTTTTTCTTTT-TCTTCTTTTG
1 CTTTTTATTTTCTCTTCTTTTG
*
57817612 CTTTTTATTTTCTTTTCTTT
1 CTTTTTATTTTCTCTTCTTT
57817632 ATTTTCTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.78
Consensus pattern (22 bp):
CTTTTTATTTTCTCTTCTTTTG
Found at i:57817643 original size:25 final size:26
Alignment explanation
Indices: 57817593--57817643 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 26
57817583 TTTTATTTCT
*
57817593 TTTTCTTTTTCTTCTTTTGCTTTTTA
1 TTTTCTTTTTCTTCTTTTGCTCTTTA
*
57817619 TTTTC-TTTTCTT-TATTTTCTCTTTA
1 TTTTCTTTTTCTTCT-TTTGCTCTTTA
57817644 CAAGAATGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 1 0.05
25 16 0.73
26 5 0.23
ACGTcount: A:0.06, C:0.16, G:0.02, T:0.76
Consensus pattern (26 bp):
TTTTCTTTTTCTTCTTTTGCTCTTTA
Found at i:57818609 original size:14 final size:14
Alignment explanation
Indices: 57818573--57818612 Score: 59
Period size: 13 Copynumber: 3.1 Consensus size: 14
57818563 TTTTTTTTCC
57818573 TTTTTTTC-G-ATT
1 TTTTTTTCTGAATT
57818585 TTTTTTT-TGAATT
1 TTTTTTTCTGAATT
57818598 TTTTTTTCTGAATT
1 TTTTTTTCTGAATT
57818612 T
1 T
57818613 CTTATCTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 8 0.32
13 10 0.40
14 7 0.28
ACGTcount: A:0.12, C:0.05, G:0.07, T:0.75
Consensus pattern (14 bp):
TTTTTTTCTGAATT
Found at i:57818708 original size:13 final size:14
Alignment explanation
Indices: 57818692--57818730 Score: 53
Period size: 13 Copynumber: 2.7 Consensus size: 14
57818682 CAACTCAAAA
57818692 TTTTTTTTTTGA-T
1 TTTTTTTTTTGACT
57818705 TTTTTTTTTTGACT
1 TTTTTTTTTTGACT
57818719 TCCTTTTTTTTT
1 T--TTTTTTTTT
57818731 CGTTACAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 12 0.52
14 2 0.09
16 9 0.39
ACGTcount: A:0.05, C:0.08, G:0.05, T:0.82
Consensus pattern (14 bp):
TTTTTTTTTTGACT
Found at i:57820368 original size:30 final size:30
Alignment explanation
Indices: 57820334--57820430 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
57820324 TAAACTAAAA
57820334 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
57820364 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
57820394 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
57820423 ATGAGCTA
1 -TGAGCTA
57820431 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:57822700 original size:6 final size:6
Alignment explanation
Indices: 57822684--57822733 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
57822674 TTTCTTTTTA
*
57822684 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
57822733 T
1 T
57822734 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:57822716 original size:37 final size:37
Alignment explanation
Indices: 57822673--57822743 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
57822663 CTTGCCTCTC
57822673 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
57822710 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
57822744 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:57822744 original size:16 final size:16
Alignment explanation
Indices: 57822669--57822729 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
57822659 GCCTCTTGCC
*
57822669 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
57822685 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
57822701 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
57822717 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
57822730 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:57823695 original size:13 final size:13
Alignment explanation
Indices: 57823669--57823706 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 13
57823659 TTTTTTTTCC
57823669 TTTTTTTC-G-AT
1 TTTTTTTCTGAAT
57823680 TTTTTTT-TGAAT
1 TTTTTTTCTGAAT
57823692 TTTTTTTCTGAAT
1 TTTTTTTCTGAAT
57823705 TT
1 TT
57823707 CTTCTCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 8 0.33
12 9 0.38
13 7 0.29
ACGTcount: A:0.13, C:0.05, G:0.08, T:0.74
Consensus pattern (13 bp):
TTTTTTTCTGAAT
Found at i:57825504 original size:30 final size:29
Alignment explanation
Indices: 57825403--57825505 Score: 89
Period size: 30 Copynumber: 3.4 Consensus size: 29
57825393 CTGAGTTAAA
* * *
57825403 CTAAAATGAGCTAAGCTTTAAGCTCGTGAG
1 CTAAATTGAGCTGAGGTTT-AGCTCGTGAG
* * * * *
57825433 CTAAAGTTGAGCTGAGGCTAAACTCCTAAG
1 CTAAA-TTGAGCTGAGGTTTAGCTCGTGAG
*
57825463 CTGAAGTTGAGCTGAGGTTTAGCTCGTGAG
1 CT-AAATTGAGCTGAGGTTTAGCTCGTGAG
57825493 CTAAATATGAGCT
1 CTAAAT-TGAGCT
57825506 AGGAGTGAGC
Statistics
Matches: 55, Mismatches: 15, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
29 3 0.05
30 41 0.75
31 11 0.20
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.27
Consensus pattern (29 bp):
CTAAATTGAGCTGAGGTTTAGCTCGTGAG
Found at i:57827786 original size:5 final size:5
Alignment explanation
Indices: 57827763--57827822 Score: 52
Period size: 5 Copynumber: 11.4 Consensus size: 5
57827753 CTTGCCTCTC
*
57827763 TTTCT TTT-T ATTTCAT TTTCTT TTTCT TCTCT TGCTT-T TTTCT TTTCT
1 TTTCT TTTCT -TTTC-T TTTC-T TTTCT TTTCT T--TTCT TTTCT TTTCT
57827811 TTTCT TTTCT TT
1 TTTCT TTTCT TT
57827823 GTTTCTCTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
4 3 0.07
5 30 0.65
6 11 0.24
7 2 0.04
ACGTcount: A:0.03, C:0.18, G:0.02, T:0.77
Consensus pattern (5 bp):
TTTCT
Found at i:57827818 original size:16 final size:16
Alignment explanation
Indices: 57827763--57827822 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
57827753 CTTGCCTCTC
*
57827763 TTTCTTTTT-ATTTCAT
1 TTTCTTTTTCTTTTC-T
*
57827779 TTTCTTTTTCTTCTC-
1 TTTCTTTTTCTTTTCT
*
57827794 TTGCTTTTTTCTTTTCT
1 TTTC-TTTTTCTTTTCT
57827811 TTTC-TTTTCTTT
1 TTTCTTTTTCTTT
57827823 GTTTCTCTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
15 11 0.31
16 19 0.53
17 6 0.17
ACGTcount: A:0.03, C:0.18, G:0.02, T:0.77
Consensus pattern (16 bp):
TTTCTTTTTCTTTTCT
Found at i:57835917 original size:21 final size:22
Alignment explanation
Indices: 57835873--57835922 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
57835863 GAGGCCCGTC
*
57835873 AGCTCAATTCAGCTTGCATTTG
1 AGCTCAATTCAGCTCGCATTTG
* *
57835895 AGCTCATTTCAGCTCG-TTTTG
1 AGCTCAATTCAGCTCGCATTTG
57835916 AGCTCAA
1 AGCTCAA
57835923 CCAAGCTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (22 bp):
AGCTCAATTCAGCTCGCATTTG
Found at i:57842100 original size:12 final size:12
Alignment explanation
Indices: 57842083--57842149 Score: 53
Period size: 12 Copynumber: 5.2 Consensus size: 12
57842073 TATACAAGTT
57842083 AAAAAAATAAAA
1 AAAAAAATAAAA
*
57842095 AAAAAATTCGAAAA
1 AAAAAAAT--AAAA
* **
57842109 AACAAAATTCGAA
1 AA-AAAAATAAAA
*
57842122 AAAAAAATCAAA
1 AAAAAAATAAAA
57842134 AAAAAAATCAAAA
1 AAAAAAAT-AAAA
57842147 AAA
1 AAA
57842150 GTGTTATTTG
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
12 23 0.51
13 10 0.22
14 6 0.13
15 6 0.13
ACGTcount: A:0.79, C:0.07, G:0.03, T:0.10
Consensus pattern (12 bp):
AAAAAAATAAAA
Found at i:57842126 original size:16 final size:14
Alignment explanation
Indices: 57842091--57842149 Score: 74
Period size: 12 Copynumber: 4.5 Consensus size: 14
57842081 TTAAAAAAAT
57842091 AAAAAAAAAATTCG
1 AAAAAAAAAATTCG
57842105 AAAAAACAAAATTCG
1 AAAAAA-AAAATTCG
57842120 -AAAAAAAAA-TC-
1 AAAAAAAAAATTCG
57842131 AAAAAAAAAA-TC-
1 AAAAAAAAAATTCG
57842143 AAAAAAA
1 AAAAAAA
57842150 GTGTTATTTG
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
12 20 0.47
13 4 0.09
14 11 0.26
15 8 0.19
ACGTcount: A:0.78, C:0.08, G:0.03, T:0.10
Consensus pattern (14 bp):
AAAAAAAAAATTCG
Found at i:57843146 original size:10 final size:10
Alignment explanation
Indices: 57843130--57843187 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
57843120 CAACTCCGAC
57843130 CAGCTCAATT
1 CAGCTCAATT
* *
57843140 GAGCTCATTT
1 CAGCTCAATT
57843150 CAGCTCAA-T
1 CAGCTCAATT
57843159 CGAGCTCAATT
1 C-AGCTCAATT
*
57843170 TAGCTACAATT
1 CAGCT-CAATT
57843181 CAGCTCA
1 CAGCTCA
57843188 TTTATTTATT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Done.