Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
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: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 100 of 216
Found at i:31242018 original size:24 final size:24
Alignment explanation
Indices: 31241991--31242036 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
31241981 TTAAAACTAC
31241991 TTCTAAATAAAACTC-AAGAGAAAA
1 TTCTAAA-AAAACTCAAAGAGAAAA
* *
31242015 TTCTTAAAGAACTCAAAGAGAA
1 TTCTAAAAAAACTCAAAGAGAA
31242037 TTTTCACTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.54, C:0.13, G:0.11, T:0.22
Consensus pattern (24 bp):
TTCTAAAAAAACTCAAAGAGAAAA
Found at i:31243250 original size:50 final size:51
Alignment explanation
Indices: 31243182--31243313 Score: 151
Period size: 50 Copynumber: 2.6 Consensus size: 51
31243172 GTGTGTTCTG
* * *
31243182 CATTTAATAAAGTTATGCATTATGTAACTTCCATGCTAG-TTAAGTATGCAT
1 CATTAAAT-AAGTCATGCATTATGTAACTCCCATGCTAGTTTAAGTATGCAT
* * *
31243233 CA-TAAATAATGTCATGCATTATGTAACTCCCATGTTAGTTTAAGTCTGTAT
1 CATTAAATAA-GTCATGCATTATGTAACTCCCATGCTAGTTTAAGTATGCAT
* *
31243284 CATTAAATTAAGTCTTGCATTAAGTAACTC
1 CATTAAA-TAAGTCATGCATTATGTAACTC
31243314 ATTTGTCATT
Statistics
Matches: 69, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
49 2 0.03
50 29 0.42
51 14 0.20
52 21 0.30
53 3 0.04
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (51 bp):
CATTAAATAAGTCATGCATTATGTAACTCCCATGCTAGTTTAAGTATGCAT
Found at i:31245086 original size:36 final size:36
Alignment explanation
Indices: 31245003--31245074 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
31244993 GAAATGAAAG
31245003 TGATAGTTGAATGTGCATATTATAAATGTCTTATAA
1 TGATAGTTGAATGTGCATATTATAAATGTCTTATAA
*
31245039 TGATAGTTGAATGTGCATATTATATATGTCTTATAA
1 TGATAGTTGAATGTGCATATTATAAATGTCTTATAA
31245075 CTTGTTGTGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.43
Consensus pattern (36 bp):
TGATAGTTGAATGTGCATATTATAAATGTCTTATAA
Found at i:31245808 original size:27 final size:27
Alignment explanation
Indices: 31245770--31245822 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
31245760 TGTTTGTAGG
*
31245770 TACATGCATGGACAGCATTGAAGATAA
1 TACATGCATGGACAGCAATGAAGATAA
31245797 TACATGCATGGACAGCAATGAAGATA
1 TACATGCATGGACAGCAATGAAGATA
31245823 CTTCAATGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.21
Consensus pattern (27 bp):
TACATGCATGGACAGCAATGAAGATAA
Found at i:31252153 original size:13 final size:13
Alignment explanation
Indices: 31252137--31252181 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
31252127 TCTCTTTGAG
31252137 TTTTCTCCAAGAA
1 TTTTCTCCAAGAA
* * *
31252150 TTTTGT-CTAGAG
1 TTTTCTCCAAGAA
31252162 TTTTCTCCAAGAA
1 TTTTCTCCAAGAA
31252175 TTTTCTC
1 TTTTCTC
31252182 TTGAGTTTTC
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
12 9 0.36
13 16 0.64
ACGTcount: A:0.22, C:0.20, G:0.11, T:0.47
Consensus pattern (13 bp):
TTTTCTCCAAGAA
Found at i:31252162 original size:25 final size:25
Alignment explanation
Indices: 31252134--31252192 Score: 100
Period size: 25 Copynumber: 2.4 Consensus size: 25
31252124 AATTCTCTTT
*
31252134 GAGTTTTCTCCAAGAATTTTGTCTA
1 GAGTTTTCTCCAAGAATTTTCTCTA
*
31252159 GAGTTTTCTCCAAGAATTTTCTCTT
1 GAGTTTTCTCCAAGAATTTTCTCTA
31252184 GAGTTTTCT
1 GAGTTTTCT
31252193 TTGGAAGTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (25 bp):
GAGTTTTCTCCAAGAATTTTCTCTA
Found at i:31255758 original size:15 final size:16
Alignment explanation
Indices: 31255736--31255774 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
31255726 CATAACCTGG
31255736 ACAATTAAAA-TACAC
1 ACAATTAAAACTACAC
* *
31255751 ATAATTAAAACTAGAC
1 ACAATTAAAACTACAC
31255767 ACAATTAA
1 ACAATTAA
31255775 TTAAGTTAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.59, C:0.15, G:0.03, T:0.23
Consensus pattern (16 bp):
ACAATTAAAACTACAC
Found at i:31255777 original size:20 final size:20
Alignment explanation
Indices: 31255752--31255796 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
31255742 AAAATACACA
31255752 TAATTAAAACT-AGACACAAT
1 TAATT-AAACTAAGACACAAT
**
31255772 TAATTAAGTTAAGACACAAT
1 TAATTAAACTAAGACACAAT
31255792 TAATT
1 TAATT
31255797 TGGTTGGACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.51, C:0.11, G:0.07, T:0.31
Consensus pattern (20 bp):
TAATTAAACTAAGACACAAT
Found at i:31257592 original size:26 final size:26
Alignment explanation
Indices: 31257562--31257612 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
31257552 ACCAATGAAC
*
31257562 CGGGGAATCAGCACTTAGCAACCCCT
1 CGGGGAATCAGCACATAGCAACCCCT
31257588 CGGGGAATCAGCACATAGCAACCCC
1 CGGGGAATCAGCACATAGCAACCCC
31257613 CTTTCACATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.35, G:0.24, T:0.12
Consensus pattern (26 bp):
CGGGGAATCAGCACATAGCAACCCCT
Found at i:31257652 original size:103 final size:104
Alignment explanation
Indices: 31257468--31257690 Score: 369
Period size: 103 Copynumber: 2.2 Consensus size: 104
31257458 AATGGATATC
31257468 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
31257533 GGATATCGCACTTAGCACCACCAATGAACCGGGGAATCA
66 GGATATCGCACATAGCACCACCAATAAACCGGGGAATCA
31257572 GCACTTAGCAACCCCTC-GGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
31257636 GGATCA-CGCACATAGCACCACCCATAAATCGGGGAATCA
66 GGAT-ATCGCACATAGCACCACCAATAAACCGGGGAATCA
**
31257675 GCACACAGCAACCCCT
1 GCACTTAGCAACCCCT
31257691 TTTATTACAA
Statistics
Matches: 112, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
103 94 0.84
104 18 0.16
ACGTcount: A:0.31, C:0.32, G:0.19, T:0.18
Consensus pattern (104 bp):
GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
GGATATCGCACATAGCACCACCAATAAACCGGGGAATCA
Found at i:31258050 original size:29 final size:29
Alignment explanation
Indices: 31258017--31258080 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
31258007 TAATCCACCA
31258017 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
31258046 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
31258076 CCCAA
1 CCCAA
31258081 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:31258054 original size:30 final size:30
Alignment explanation
Indices: 31258024--31258080 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
31258014 CCACCCAACT
31258024 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
31258053 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
31258081 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:31260330 original size:18 final size:18
Alignment explanation
Indices: 31260307--31260341 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
31260297 TTTTTCTTTT
31260307 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
31260325 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
31260342 TTTCTTTTCT
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:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:31260350 original size:18 final size:18
Alignment explanation
Indices: 31260329--31260449 Score: 118
Period size: 18 Copynumber: 6.6 Consensus size: 18
31260319 TCAATCTCAA
31260329 TTTCTTTTTCAATTTTCTTT
1 TTTCTTTTTC-ATTTTC-TT
* * *
31260349 TCTTCGTTTTCTTTTTCTC
1 T-TTCTTTTTCATTTTCTT
**
31260368 TCACTTTTTCGA-TTTCTT
1 TTTCTTTTTC-ATTTTCTT
* *
31260386 TTTCTTTTGCAATTTCTT
1 TTTCTTTTTCATTTTCTT
31260404 TTTCTTTTTCATTTTCTT
1 TTTCTTTTTCATTTTCTT
* *
31260422 TTTCTTCTTCACTTTCTT
1 TTTCTTTTTCATTTTCTT
31260440 TTTCTTTTTC
1 TTTCTTTTTC
31260450 TTCTTTTTCA
Statistics
Matches: 82, Mismatches: 16, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
17 1 0.01
18 65 0.79
19 2 0.02
20 6 0.07
21 8 0.10
ACGTcount: A:0.07, C:0.21, G:0.02, T:0.70
Consensus pattern (18 bp):
TTTCTTTTTCATTTTCTT
Found at i:31260463 original size:6 final size:6
Alignment explanation
Indices: 31260329--31260451 Score: 93
Period size: 6 Copynumber: 20.0 Consensus size: 6
31260319 TCAATCTCAA
* * * ** **
31260329 TTTCTT TTTCAAT TTTCTTT TCTTCGT TTTCTT TTTCTC TCACTT TTTCGA
1 TTTCTT TTTC-TT TTTC-TT T-TTCTT TTTCTT TTTCTT TTTCTT TTTCTT
* ** *
31260380 TTTCTT TTTCTT TTGCAA TTTCTT TTTCTT TTTCAT TTTCTT TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
* **
31260428 CTTCAC TTTCTT TTTCTT TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT
31260452 CTTTTTCATT
Statistics
Matches: 86, Mismatches: 29, Indels: 4
0.72 0.24 0.03
Matches are distributed among these distances:
6 74 0.86
7 9 0.10
8 3 0.03
ACGTcount: A:0.07, C:0.20, G:0.02, T:0.71
Consensus pattern (6 bp):
TTTCTT
Found at i:31262178 original size:78 final size:78
Alignment explanation
Indices: 31262049--31262205 Score: 314
Period size: 78 Copynumber: 2.0 Consensus size: 78
31262039 GGCAATGTGA
31262049 TTGCTTTTCGTTCGAGCTCTTTGTTGTTCATAGGCAAGCTCACATCATTCCCCTCGAAAGGTTGC
1 TTGCTTTTCGTTCGAGCTCTTTGTTGTTCATAGGCAAGCTCACATCATTCCCCTCGAAAGGTTGC
31262114 GAGCTCAAAGCTG
66 GAGCTCAAAGCTG
31262127 TTGCTTTTCGTTCGAGCTCTTTGTTGTTCATAGGCAAGCTCACATCATTCCCCTCGAAAGGTTGC
1 TTGCTTTTCGTTCGAGCTCTTTGTTGTTCATAGGCAAGCTCACATCATTCCCCTCGAAAGGTTGC
31262192 GAGCTCAAAGCTG
66 GAGCTCAAAGCTG
31262205 T
1 T
31262206 CACATCTTGA
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 79 1.00
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (78 bp):
TTGCTTTTCGTTCGAGCTCTTTGTTGTTCATAGGCAAGCTCACATCATTCCCCTCGAAAGGTTGC
GAGCTCAAAGCTG
Found at i:31262853 original size:10 final size:11
Alignment explanation
Indices: 31262837--31262872 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
31262827 TTCACACTCT
*
31262837 TTTTTTTTGAA
1 TTTTTTTCGAA
*
31262848 TTTTTTTCGAT
1 TTTTTTTCGAA
31262859 TTTTTTTCGAA
1 TTTTTTTCGAA
31262870 TTT
1 TTT
31262873 CCTCTTCTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.14, C:0.06, G:0.08, T:0.72
Consensus pattern (11 bp):
TTTTTTTCGAA
Found at i:31262961 original size:12 final size:12
Alignment explanation
Indices: 31262944--31262974 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
31262934 AATAAAACCT
31262944 TTTTTTTTGAAC
1 TTTTTTTTGAAC
31262956 TTTTTTTTGAAC
1 TTTTTTTTGAAC
*
31262968 TTCTTTT
1 TTTTTTT
31262975 ATATATCACA
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:0.13, C:0.10, G:0.06, T:0.71
Consensus pattern (12 bp):
TTTTTTTTGAAC
Found at i:31264060 original size:21 final size:21
Alignment explanation
Indices: 31264034--31264096 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
31264024 TTGGTATTTG
31264034 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
31264055 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
31264076 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
31264097 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:31265191 original size:10 final size:10
Alignment explanation
Indices: 31265176--31265217 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
31265166 TTTGCAAGTT
31265176 TTGAGCTAAA
1 TTGAGCTAAA
* *
31265186 TTGAGCTGAT
1 TTGAGCTAAA
*
31265196 TTGAGCT-CA
1 TTGAGCTAAA
31265205 TTGAGCTAAA
1 TTGAGCTAAA
31265215 TTG
1 TTG
31265218 GAAGTTAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
9 7 0.27
10 19 0.73
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.36
Consensus pattern (10 bp):
TTGAGCTAAA
Found at i:31267975 original size:18 final size:18
Alignment explanation
Indices: 31267954--31267988 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
31267944 TTTTTCTTTT
31267954 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
31267972 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
31267989 TTCCTTTTCT
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:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:31267985 original size:6 final size:6
Alignment explanation
Indices: 31267976--31268106 Score: 66
Period size: 6 Copynumber: 21.0 Consensus size: 6
31267966 TCAATCTCAA
** * * ** **
31267976 TTTCTT TTTCAA TTTCCT TTTCTT CGTTTTCTT TTTCTC TCACTT TTTCGA
1 TTTCTT TTTCTT TTTCTT TTTCTT --T-TTCTT TTTCTT TTTCTT TTTCTT
* ** *
31268027 TTTCTT TTTCTTTT TTTCTT TTACAA TTTCTT TTTCTT TTTCATT TTT-AT
1 TTTCTT TTTC--TT TTTCTT TTTCTT TTTCTT TTTCTT TTTC-TT TTTCTT
* **
31268077 TTTCTT CTTCAC TTTCTT TTTCTT TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
31268107 CTTTTTCATT
Statistics
Matches: 89, Mismatches: 29, Indels: 14
0.67 0.22 0.11
Matches are distributed among these distances:
5 4 0.04
6 67 0.75
7 6 0.07
8 7 0.08
9 5 0.06
ACGTcount: A:0.08, C:0.20, G:0.02, T:0.71
Consensus pattern (6 bp):
TTTCTT
Found at i:31268039 original size:18 final size:17
Alignment explanation
Indices: 31268027--31268119 Score: 88
Period size: 18 Copynumber: 5.5 Consensus size: 17
31268017 ACTTTTTCGA
31268027 TTTCTTTTTC--TT-TT
1 TTTCTTTTTCATTTCTT
*
31268041 TTTCTTTTACAATTTCTT
1 TTTCTTTTTC-ATTTCTT
*
31268059 TTTCTTTTTCATTTTTAT
1 TTTCTTTTTCATTTCT-T
*
31268077 TTTCTTCTTCACTTTCTT
1 TTTCTTTTTCA-TTTCTT
31268095 TTTCTTTTTC--TTCTT
1 TTTCTTTTTCATTTCTT
31268110 TTTCATTTTT
1 TTTC-TTTTT
31268120 ATTACAATGT
Statistics
Matches: 66, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
14 9 0.14
15 9 0.14
16 5 0.08
17 7 0.11
18 32 0.48
19 4 0.06
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTCTTTTTCATTTCTT
Found at i:31268074 original size:26 final size:26
Alignment explanation
Indices: 31268026--31268075 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
31268016 CACTTTTTCG
*
31268026 ATTTCTTTTTCTTTTTTTCTTTTACA
1 ATTTCTTTTTCTTTTTATCTTTTACA
31268052 ATTTCTTTTTCTTTTTCAT-TTTTA
1 ATTTCTTTTTCTTTTT-ATCTTTTA
31268076 TTTTCTTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 21 0.95
27 1 0.05
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.74
Consensus pattern (26 bp):
ATTTCTTTTTCTTTTTATCTTTTACA
Found at i:31272759 original size:12 final size:12
Alignment explanation
Indices: 31272730--31272804 Score: 64
Period size: 12 Copynumber: 6.2 Consensus size: 12
31272720 AAACAACATG
31272730 TGAAAAAGAAAA
1 TGAAAAAGAAAA
** *
31272742 ACAAAAAGAAAT
1 TGAAAAAGAAAA
31272754 TGAAAAAGAAAA
1 TGAAAAAGAAAA
* *
31272766 TGAACATG-AAA
1 TGAAAAAGAAAA
*
31272777 -GAAAATAAGAAAT
1 TG-AAA-AAGAAAA
31272790 TGAAAAAGAAAA
1 TGAAAAAGAAAA
31272802 TGA
1 TGA
31272805 GAGTGAGAGT
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
10 1 0.02
11 5 0.11
12 35 0.74
13 5 0.11
14 1 0.02
ACGTcount: A:0.69, C:0.03, G:0.16, T:0.12
Consensus pattern (12 bp):
TGAAAAAGAAAA
Found at i:31272836 original size:45 final size:45
Alignment explanation
Indices: 31272774--31272890 Score: 119
Period size: 45 Copynumber: 2.6 Consensus size: 45
31272764 AATGAACATG
* * **
31272774 AAAGAAAATAAGAAATTGAAAAAGAAAATGAGA-GTGAGAGTGAGAA
1 AAAGAAAA-AAGAAATTGAAAAAGAAAAAG-GATGTGAAAAAGAGAA
* **
31272820 AAAGAAAAAAGAAATTGAGATTGAAAAAGGATGTGAAAAAGAGAA
1 AAAGAAAAAAGAAATTGAAAAAGAAAAAGGATGTGAAAAAGAGAA
**
31272865 AATCAAAAAAGAAATTGAAGAAAGAA
1 AAAGAAAAAAGAAATTGAA-AAAGAA
31272891 GAGAAAATGA
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
44 2 0.04
45 43 0.75
46 12 0.21
ACGTcount: A:0.63, C:0.01, G:0.23, T:0.13
Consensus pattern (45 bp):
AAAGAAAAAAGAAATTGAAAAAGAAAAAGGATGTGAAAAAGAGAA
Found at i:31272838 original size:27 final size:26
Alignment explanation
Indices: 31272791--31272847 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
31272781 ATAAGAAATT
* *
31272791 GAAAAAGAAAATGAGAGTGAGAGTGA
1 GAAAAAGAAAAAGAAAGTGAGAGTGA
* *
31272817 GAAAAAGAAAAAAGAAATTGAGATTGA
1 GAAAAAG-AAAAAGAAAGTGAGAGTGA
31272844 -AAAA
1 GAAAA
31272848 GGATGTGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 11 0.42
27 15 0.58
ACGTcount: A:0.61, C:0.00, G:0.26, T:0.12
Consensus pattern (26 bp):
GAAAAAGAAAAAGAAAGTGAGAGTGA
Found at i:31276506 original size:20 final size:20
Alignment explanation
Indices: 31276481--31276525 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
31276471 TAAATACACA
31276481 TAATTAAAACT-AGACACAAT
1 TAATT-AAACTAAGACACAAT
**
31276501 TAATTAAGTTAAGACACAAT
1 TAATTAAACTAAGACACAAT
31276521 TAATT
1 TAATT
31276526 CGGTTGTACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.51, C:0.11, G:0.07, T:0.31
Consensus pattern (20 bp):
TAATTAAACTAAGACACAAT
Found at i:31276797 original size:30 final size:30
Alignment explanation
Indices: 31276749--31276809 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
31276739 TCTAATTGGA
* *
31276749 ATTGAGCTGAATTTGAGCTTA-TTCGAGCTC
1 ATTGAGCTGAAATGGAGCTTAGTTC-AGCTC
*
31276779 ATTGAGTTGAAATGGAGCTTAGTTCAGCTC
1 ATTGAGCTGAAATGGAGCTTAGTTCAGCTC
31276809 A
1 A
31276810 CAACAAATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 24 0.89
31 3 0.11
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (30 bp):
ATTGAGCTGAAATGGAGCTTAGTTCAGCTC
Found at i:31286578 original size:19 final size:21
Alignment explanation
Indices: 31286555--31286600 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
31286545 AAAAAAATTC
31286555 AAAAAA-TTGAAAAA-ATCAA
1 AAAAAATTTGAAAAATATCAA
*
31286574 AAAAAATTTGAAAAATATTAA
1 AAAAAATTTGAAAAATATCAA
31286595 AAAAAA
1 AAAAAA
31286601 AGAGTTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 6 0.25
20 8 0.33
21 10 0.42
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.20
Consensus pattern (21 bp):
AAAAAATTTGAAAAATATCAA
Found at i:31286578 original size:20 final size:21
Alignment explanation
Indices: 31286555--31286601 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
31286545 AAAAAAATTC
31286555 AAAAAATTGAAAAA-ATCAAA
1 AAAAAATTGAAAAATATCAAA
* *
31286575 AAAAATTTGAAAAATATTAAA
1 AAAAAATTGAAAAATATCAAA
31286596 AAAAAA
1 AAAAAA
31286602 GAGTTTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.19
Consensus pattern (21 bp):
AAAAAATTGAAAAATATCAAA
Found at i:31287823 original size:33 final size:33
Alignment explanation
Indices: 31287755--31287826 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 33
31287745 AGAAAACGAA
*
31287755 AGTGGAAAAGAAAAAGAGCCTGAAAAGAAATCG
1 AGTGAAAAAGAAAAAGAGCCTGAAAAGAAATCG
* *
31287788 AGTGAAAAAGAAAGAGAGTCTGTAAAAGAAA-CG
1 AGTGAAAAAGAAAAAGAGCCTG-AAAAGAAATCG
31287821 AGTGAA
1 AGTGAA
31287827 GACAGTAATC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
33 27 0.77
34 8 0.23
ACGTcount: A:0.54, C:0.07, G:0.28, T:0.11
Consensus pattern (33 bp):
AGTGAAAAAGAAAAAGAGCCTGAAAAGAAATCG
Found at i:31296869 original size:20 final size:21
Alignment explanation
Indices: 31296844--31296893 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
31296834 AAAAGAAAAG
31296844 AAAGAAGAGAGATTGAGAG-A
1 AAAGAAGAGAGATTGAGAGAA
** *
31296864 AAAGAATCGAGATTGTGAGAA
1 AAAGAAGAGAGATTGAGAGAA
31296885 AAAGAAGAG
1 AAAGAAGAG
31296894 CAATGAAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.54, C:0.02, G:0.32, T:0.12
Consensus pattern (21 bp):
AAAGAAGAGAGATTGAGAGAA
Found at i:31305737 original size:26 final size:26
Alignment explanation
Indices: 31305701--31305750 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
31305691 GTGTTGTGTT
*
31305701 CATTAATGTGCACGATGAGCCTTGCC
1 CATTAATGTGCACGAAGAGCCTTGCC
*
31305727 CATTAGTGTGCACGAAGAGCCTTG
1 CATTAATGTGCACGAAGAGCCTTG
31305751 AGCTGAATAA
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:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (26 bp):
CATTAATGTGCACGAAGAGCCTTGCC
Found at i:31306377 original size:14 final size:14
Alignment explanation
Indices: 31306320--31306379 Score: 52
Period size: 14 Copynumber: 4.2 Consensus size: 14
31306310 TAAAACATTC
31306320 AAAC-AAGTAATT-
1 AAACTAAGTAATTA
* *
31306332 AAGCTATAGGAATTA
1 AAACTA-AGTAATTA
*
31306347 AAACATAATTAAATTA
1 AAAC-TAAGT-AATTA
31306363 AAACTAAGTAATTA
1 AAACTAAGTAATTA
31306377 AAA
1 AAA
31306380 TATCTAAGAA
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
12 3 0.08
13 1 0.03
14 14 0.38
15 8 0.22
16 11 0.30
ACGTcount: A:0.58, C:0.07, G:0.08, T:0.27
Consensus pattern (14 bp):
AAACTAAGTAATTA
Found at i:31309353 original size:20 final size:20
Alignment explanation
Indices: 31309328--31309366 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
31309318 CGTCCTTGGT
31309328 TCAGCTCACTT-GAGCTCAAG
1 TCAGCTCA-TTCGAGCTCAAG
*
31309348 TCAGCTTATTCGAGCTCAA
1 TCAGCTCATTCGAGCTCAA
31309367 ATTATCTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (20 bp):
TCAGCTCATTCGAGCTCAAG
Found at i:31309774 original size:16 final size:16
Alignment explanation
Indices: 31309736--31309777 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
31309726 GTATGGGAGT
*
31309736 ATACATGAATGGCTGA
1 ATACATGGATGGCTGA
*
31309752 ATACATGGATGGCTGG
1 ATACATGGATGGCTGA
*
31309768 ATTCATGGAT
1 ATACATGGAT
31309778 ATGGCTCATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.31, C:0.12, G:0.29, T:0.29
Consensus pattern (16 bp):
ATACATGGATGGCTGA
Found at i:31311880 original size:12 final size:13
Alignment explanation
Indices: 31311863--31311910 Score: 61
Period size: 12 Copynumber: 4.1 Consensus size: 13
31311853 ATTTATTCCA
31311863 GCAAAA-TAAAAT
1 GCAAAACTAAAAT
31311875 GCAAAACT-AAAT
1 GCAAAACTAAAAT
31311887 GCAAAACT-AAA-
1 GCAAAACTAAAAT
31311898 G-AAAACTAAAAT
1 GCAAAACTAAAAT
31311910 G
1 G
31311911 AGTTTATTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
10 6 0.18
11 4 0.12
12 22 0.67
13 1 0.03
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (13 bp):
GCAAAACTAAAAT
Found at i:31313070 original size:21 final size:21
Alignment explanation
Indices: 31313019--31313075 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
31313009 CTCAATCTCT
*
31313019 CTTCTTTC-TTTTCTTTTTCA
1 CTTCTTTCAATTTCTTTTTCA
* *
31313039 CTCTCTCTCAATTTCTTTTTCT
1 CT-TCTTTCAATTTCTTTTTCA
* *
31313061 GTTCTTTCAAATTCT
1 CTTCTTTCAATTTCT
31313076 CCAAAGATTG
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
20 2 0.07
21 16 0.55
22 11 0.38
ACGTcount: A:0.11, C:0.26, G:0.02, T:0.61
Consensus pattern (21 bp):
CTTCTTTCAATTTCTTTTTCA
Found at i:31315285 original size:14 final size:13
Alignment explanation
Indices: 31315266--31315291 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31315256 AATAATACTC
31315266 TTTTTTTTTACAA
1 TTTTTTTTTACAA
31315279 TTTTTTTTTACAA
1 TTTTTTTTTACAA
31315292 ACTCACTCCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTTTTTTACAA
Found at i:31316744 original size:12 final size:13
Alignment explanation
Indices: 31316727--31316774 Score: 61
Period size: 12 Copynumber: 4.1 Consensus size: 13
31316717 ATTTATTCCA
31316727 GCAAAA-TAAAAT
1 GCAAAACTAAAAT
31316739 GCAAAACT-AAAT
1 GCAAAACTAAAAT
31316751 GCAAAACT-AAA-
1 GCAAAACTAAAAT
31316762 G-AAAACTAAAAT
1 GCAAAACTAAAAT
31316774 G
1 G
31316775 AGTTTATTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
10 6 0.18
11 4 0.12
12 22 0.67
13 1 0.03
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (13 bp):
GCAAAACTAAAAT
Found at i:31318211 original size:6 final size:6
Alignment explanation
Indices: 31318200--31318257 Score: 64
Period size: 6 Copynumber: 9.7 Consensus size: 6
31318190 ACATTGTAGT
* ** *
31318200 GAAAAA GAAAAA GAAAACA -AAAAT GAAAAA GAAAAA GAAATT GCAAAA
1 GAAAAA GAAAAA GAAAA-A GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA
31318248 GAAAAA GAAA
1 GAAAAA GAAA
31318258 TCAAAAAAGT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
6 41 0.98
7 1 0.02
ACGTcount: A:0.76, C:0.03, G:0.16, T:0.05
Consensus pattern (6 bp):
GAAAAA
Found at i:31318266 original size:18 final size:17
Alignment explanation
Indices: 31318206--31318264 Score: 73
Period size: 18 Copynumber: 3.4 Consensus size: 17
31318196 TAGTGAAAAA
*
31318206 GAAAAAGAAAACAAAAAT
1 GAAAAAGAAAA-AGAAAT
31318224 GAAAAAGAAAAAGAAATT
1 GAAAAAGAAAAAGAAA-T
*
31318242 GCAAAAGAAAAAGAAAT
1 GAAAAAGAAAAAGAAAT
*
31318259 CAAAAA
1 GAAAAA
31318265 AGTGAGAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
17 9 0.25
18 27 0.75
ACGTcount: A:0.75, C:0.05, G:0.14, T:0.07
Consensus pattern (17 bp):
GAAAAAGAAAAAGAAAT
Found at i:31320099 original size:20 final size:19
Alignment explanation
Indices: 31320044--31320100 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 19
31320034 ATATATACGA
** *
31320044 AATT-AAAAAAAGGAAGTA
1 AATTAAAAAAAAGGTTGTG
**
31320062 AATTAAAAAAAATTTTGTG
1 AATTAAAAAAAAGGTTGTG
31320081 AATTAAAAAAAAGGGTTGTG
1 AATTAAAAAAAA-GGTTGTG
31320101 TTTCAAGTTC
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
18 4 0.13
19 21 0.70
20 5 0.17
ACGTcount: A:0.56, C:0.00, G:0.18, T:0.26
Consensus pattern (19 bp):
AATTAAAAAAAAGGTTGTG
Found at i:31325921 original size:27 final size:27
Alignment explanation
Indices: 31325891--31326095 Score: 205
Period size: 27 Copynumber: 7.6 Consensus size: 27
31325881 ATATTAAGTC
* *
31325891 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
31325918 CGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
*
31325946 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAATCAACT
** ** *
31325973 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
** **
31326000 CGCACACTTAGTGC-ATCATTTTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* ** *
31326027 CGCACACTTAGTGCAACATGGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
** *
31326054 CGCACACTTAGTGCTACATAGCCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
31326081 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
31326096 GTACAATTTA
Statistics
Matches: 155, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
27 129 0.83
28 26 0.17
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:31326030 original size:54 final size:54
Alignment explanation
Indices: 31325891--31326094 Score: 257
Period size: 54 Copynumber: 3.8 Consensus size: 54
31325881 ATATTAAGTC
* * * **
31325891 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCACATGGTCAAA-T
* *
31325946 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCACATGGTCAAAT
** ** *
31326000 CGCACACTTAGTGC-ATCATTTTCATTTCGCACACTTAGTGCAACATGGTCAAAT
1 CGCACACTTAGTGCTA-CATAGTCAACTCGCACACTTAGTGCCACATGGTCAAAT
* *
31326054 CGCACACTTAGTGCTACATAGCCAAATCGCACACTTAGTGC
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGC
31326095 TGTACAATTT
Statistics
Matches: 128, Mismatches: 19, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
53 1 0.01
54 80 0.62
55 47 0.37
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCACATGGTCAAAT
Found at i:31326060 original size:81 final size:81
Alignment explanation
Indices: 31325945--31326094 Score: 228
Period size: 81 Copynumber: 1.9 Consensus size: 81
31325935 ATAATCAAAC
* * * * * *
31325945 TCGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCGCATGGTCAATTCGCACACTTA
1 TCGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGCCACATAGCCAAATCGCACACTTA
31326010 GTGCATCATTTTCATT
66 GTGCATCATTTTCATT
* *
31326026 TCGCACACTTAGTGCAACATGGTCAAATCGCACACTTAGTGCTACATAGCCAAATCGCACACTTA
1 TCGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGCCACATAGCCAAATCGCACACTTA
31326091 GTGC
66 GTGC
31326095 TGTACAATTT
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 61 1.00
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (81 bp):
TCGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGCCACATAGCCAAATCGCACACTTA
GTGCATCATTTTCATT
Found at i:31334747 original size:10 final size:10
Alignment explanation
Indices: 31334734--31334789 Score: 62
Period size: 10 Copynumber: 5.6 Consensus size: 10
31334724 CACTCACTTG
*
31334734 AGCTCAAGTC
1 AGCTCAATTC
31334744 AGCTC-ATTC
1 AGCTCAATTC
*
31334753 GAGCTCAAGTC
1 -AGCTCAATTC
31334764 AGCTC-ATTC
1 AGCTCAATTC
31334773 GAGCTCAATTC
1 -AGCTCAATTC
31334784 AGCTCA
1 AGCTCA
31334790 TTGAGCTCGT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
9 6 0.15
10 26 0.67
11 7 0.18
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:31334756 original size:20 final size:20
Alignment explanation
Indices: 31334733--31334797 Score: 114
Period size: 20 Copynumber: 3.3 Consensus size: 20
31334723 TCACTCACTT
31334733 GAGCTCAAGTCAGCTCATTC
1 GAGCTCAAGTCAGCTCATTC
31334753 GAGCTCAAGTCAGCTCATTC
1 GAGCTCAAGTCAGCTCATTC
*
31334773 GAGCTCAATTCAGCTCATT-
1 GAGCTCAAGTCAGCTCATTC
31334792 GAGCTC
1 GAGCTC
31334798 GTTATTAGCT
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
19 6 0.14
20 38 0.86
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.26
Consensus pattern (20 bp):
GAGCTCAAGTCAGCTCATTC
Found at i:31339315 original size:19 final size:21
Alignment explanation
Indices: 31339281--31339327 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
31339271 TTAGCTCAAG
*
31339281 TGAGCTAATTGGAGCTGAAA-
1 TGAGCTAATGGGAGCTGAAAT
31339301 TGAGCTAA-GGGAGCTGAAAT
1 TGAGCTAATGGGAGCTGAAAT
31339321 TGAGCTA
1 TGAGCTA
31339328 CAGTCAGGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.34, C:0.11, G:0.32, T:0.23
Consensus pattern (21 bp):
TGAGCTAATGGGAGCTGAAAT
Found at i:31341455 original size:18 final size:18
Alignment explanation
Indices: 31341422--31341468 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
31341412 TTTTTCATCA
* *
31341422 TCTTTTTCATTTTCAATT
1 TCTTTTTCAATCTCAATT
31341440 T-TTTTCTCAATCTCAATT
1 TCTTTT-TCAATCTCAATT
31341458 TCTTTTTCAAT
1 TCTTTTTCAAT
31341469 TTTCTTTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 4 0.16
18 17 0.68
19 4 0.16
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.62
Consensus pattern (18 bp):
TCTTTTTCAATCTCAATT
Found at i:31342433 original size:14 final size:14
Alignment explanation
Indices: 31342427--31342459 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
31342417 TTTTTTTGAC
31342427 TTTTTTTTTGAATT
1 TTTTTTTTTGAATT
*
31342441 TCTTTTTTTGAATT
1 TTTTTTTTTGAATT
31342455 TTTTT
1 TTTTT
31342460 AAACTTCGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.12, C:0.03, G:0.06, T:0.79
Consensus pattern (14 bp):
TTTTTTTTTGAATT
Found at i:31343954 original size:19 final size:20
Alignment explanation
Indices: 31343930--31343967 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
31343920 TGAGCTGATT
31343930 GGAGCTGAAA-TGAGCTAAG
1 GGAGCTGAAATTGAGCTAAG
31343949 GGAGCTGAAATTGAGCTAA
1 GGAGCTGAAATTGAGCTAA
31343968 AGTCAGGTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.37, C:0.11, G:0.34, T:0.18
Consensus pattern (20 bp):
GGAGCTGAAATTGAGCTAAG
Found at i:31352489 original size:14 final size:14
Alignment explanation
Indices: 31352470--31352496 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
31352460 TGCATCTCCC
31352470 CATGCATGAATCTA
1 CATGCATGAATCTA
31352484 CATGCATGAATCT
1 CATGCATGAATCT
31352497 GCCCAATGTA
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:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (14 bp):
CATGCATGAATCTA
Found at i:31356140 original size:33 final size:34
Alignment explanation
Indices: 31356092--31356166 Score: 107
Period size: 33 Copynumber: 2.2 Consensus size: 34
31356082 AGATTTAAAC
*
31356092 AAATTAATTACTAACACTTATTTAAGCTGAACTA
1 AAATTAATTACTAACACTTATTTAAGATGAACTA
* *
31356126 AAATT-ATTTCTAACACTTATTTGAGATGAACTA
1 AAATTAATTACTAACACTTATTTAAGATGAACTA
*
31356159 AATTTAAT
1 AAATTAAT
31356167 AAACTAACTC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
33 29 0.81
34 7 0.19
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.39
Consensus pattern (34 bp):
AAATTAATTACTAACACTTATTTAAGATGAACTA
Found at i:31366386 original size:27 final size:28
Alignment explanation
Indices: 31366355--31366466 Score: 111
Period size: 27 Copynumber: 4.0 Consensus size: 28
31366345 TGATTCAAAA
* *
31366355 ATATATATTAAGTCCGCACACTCAGTGCT
1 ATATA-ATCAAGTCCGCACACTTAGTGCT
*
31366384 ATATAATCAACT-CGCACACTTAGTGCT
1 ATATAATCAAGTCCGCACACTTAGTGCT
31366411 ATATAATCAAG-CTCGCACACTTAGTGCT
1 ATATAATCAAGTC-CGCACACTTAGTGCT
* * * **
31366439 GTACAATTTAAACCCGCACACTTAGTGC
1 ATATAA-TCAAGTCCGCACACTTAGTGC
31366467 CAATCTCATG
Statistics
Matches: 71, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
27 24 0.34
28 24 0.34
29 22 0.31
30 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.29
Consensus pattern (28 bp):
ATATAATCAAGTCCGCACACTTAGTGCT
Found at i:31374111 original size:29 final size:27
Alignment explanation
Indices: 31374093--31374162 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
31374083 ATATTAAGTC
31374093 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
*
31374120 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
*
31374148 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
31374163 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:31374156 original size:28 final size:28
Alignment explanation
Indices: 31374093--31374190 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
31374083 ATATTAAGTC
*
31374093 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
31374120 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
31374148 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
31374177 CGCACACTTAGTGC
1 CGCACACTTAGTGC
31374191 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:31375656 original size:21 final size:21
Alignment explanation
Indices: 31375613--31375658 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
31375603 TTTACATAGG
**
31375613 AATTAAATCATAAAGTCTAAA
1 AATTAAATCATAAAGAATAAA
*
31375634 AATTAAATCATAAAGAATTAA
1 AATTAAATCATAAAGAATAAA
31375655 AATT
1 AATT
31375659 TTACAAATTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.59, C:0.07, G:0.04, T:0.30
Consensus pattern (21 bp):
AATTAAATCATAAAGAATAAA
Found at i:31387650 original size:21 final size:21
Alignment explanation
Indices: 31387621--31387660 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
31387611 TTAATGAGCT
*
31387621 GAAATTTCCAGAAAAATTCAA
1 GAAAATTCCAGAAAAATTCAA
*
31387642 GAAAATTCCAGGAAAATTC
1 GAAAATTCCAGAAAAATTC
31387661 TCCAGCAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.15, G:0.12, T:0.23
Consensus pattern (21 bp):
GAAAATTCCAGAAAAATTCAA
Found at i:31390328 original size:12 final size:12
Alignment explanation
Indices: 31390295--31390375 Score: 53
Period size: 12 Copynumber: 6.8 Consensus size: 12
31390285 TTTTCACTCG
31390295 ATTTC-TTTTCA
1 ATTTCTTTTTCA
** *
31390306 AGCTCTCTTTCA
1 ATTTCTTTTTCA
31390318 ATTTCTTTTTCCA
1 ATTTCTTTTT-CA
*
31390331 CTCTTTCTTTTTC-
1 --ATTTCTTTTTCA
*
31390344 --TTCTCTTTCA
1 ATTTCTTTTTCA
31390354 ATTTCTTTTTCA
1 ATTTCTTTTTCA
*
31390366 ATCTCTTTTT
1 ATTTCTTTTT
31390376 GGTTTTCACT
Statistics
Matches: 53, Mismatches: 10, Indels: 13
0.70 0.13 0.17
Matches are distributed among these distances:
9 8 0.15
11 3 0.06
12 30 0.57
13 2 0.04
14 1 0.02
15 9 0.17
ACGTcount: A:0.12, C:0.25, G:0.01, T:0.62
Consensus pattern (12 bp):
ATTTCTTTTTCA
Found at i:31390336 original size:21 final size:20
Alignment explanation
Indices: 31390310--31390365 Score: 59
Period size: 18 Copynumber: 3.0 Consensus size: 20
31390300 TTTTCAAGCT
31390310 CTCTTTCAATTTCTTTTTCCA
1 CTCTTTCAATTTCTTTTT-CA
*
31390331 CTCTTTC--TTT-TTCTT--
1 CTCTTTCAATTTCTTTTTCA
31390346 CTCTTTCAATTTCTTTTTCA
1 CTCTTTCAATTTCTTTTTCA
31390366 ATCTCTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 11
0.68 0.05 0.27
Matches are distributed among these distances:
15 7 0.25
17 3 0.11
18 8 0.29
19 3 0.11
21 7 0.25
ACGTcount: A:0.11, C:0.27, G:0.00, T:0.62
Consensus pattern (20 bp):
CTCTTTCAATTTCTTTTTCA
Found at i:31395520 original size:21 final size:21
Alignment explanation
Indices: 31395475--31395537 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
31395465 TTTGAACCAT
* *
31395475 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
31395497 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
31395518 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
31395538 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 24 0.65
22 13 0.35
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:31398106 original size:40 final size:40
Alignment explanation
Indices: 31398047--31398294 Score: 320
Period size: 40 Copynumber: 6.2 Consensus size: 40
31398037 CATTTGAATG
*
31398047 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * *
31398087 TTATCCGGGTTAAGACCCGAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* *
31398127 TTATCCGGGTTAAGACCCGAAGGCATTTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * *
31398167 TTATCTGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-T
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* *
31398207 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* * * * *
31398247 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
31398287 ATATCCGG
1 ATATCCGG
31398295 CCAAATTCCG
Statistics
Matches: 188, Mismatches: 17, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
39 2 0.01
40 183 0.97
41 3 0.02
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.29
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
Found at i:31403459 original size:10 final size:10
Alignment explanation
Indices: 31403444--31403485 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
31403434 TTTGCAAGTT
31403444 TTGAGCTAAA
1 TTGAGCTAAA
* *
31403454 TTGAGCTGAT
1 TTGAGCTAAA
*
31403464 TTGAGCT-CA
1 TTGAGCTAAA
31403473 TTGAGCTAAA
1 TTGAGCTAAA
31403483 TTG
1 TTG
31403486 GAAGTTAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
9 7 0.27
10 19 0.73
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.36
Consensus pattern (10 bp):
TTGAGCTAAA
Found at i:31409502 original size:18 final size:18
Alignment explanation
Indices: 31409475--31409516 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
31409465 TGCTGGAATA
*
31409475 AATTAATTAAGTT-AGTTT
1 AATTAATTAA-TTCAGCTT
*
31409493 AATTAGTTAATTCAGCTT
1 AATTAATTAATTCAGCTT
31409511 AATTAA
1 AATTAA
31409517 ATGTTGAGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (18 bp):
AATTAATTAATTCAGCTT
Found at i:31412769 original size:6 final size:6
Alignment explanation
Indices: 31412760--31412788 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
31412750 TTTTTCTTTT
31412760 TCTCAC TCTCAC TCTCAC TCTCAC TCTCA
1 TCTCAC TCTCAC TCTCAC TCTCAC TCTCA
31412789 TTTTCTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.48, G:0.00, T:0.34
Consensus pattern (6 bp):
TCTCAC
Found at i:31415711 original size:19 final size:20
Alignment explanation
Indices: 31415676--31415713 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
31415666 CAAGCTGACT
*
31415676 TTAGCTCAATTTGAGCTCCC
1 TTAGCTCAATTTCAGCTCCC
31415696 TTAGCTC-ATTTCAGCTCC
1 TTAGCTCAATTTCAGCTCC
31415714 AATCAGCTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.18, C:0.32, G:0.13, T:0.37
Consensus pattern (20 bp):
TTAGCTCAATTTCAGCTCCC
Found at i:31419696 original size:25 final size:24
Alignment explanation
Indices: 31419668--31419714 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
31419658 ATGAAAAAAA
31419668 GAAAACAAAA-GTAGGAAAAGAAAGT
1 GAAAACAAAATG-A-GAAAAGAAAGT
*
31419693 GAAAAGAAAATGAGAAAAGAAA
1 GAAAACAAAATGAGAAAAGAAA
31419715 AACAAGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 9 0.45
25 10 0.50
26 1 0.05
ACGTcount: A:0.68, C:0.02, G:0.23, T:0.06
Consensus pattern (24 bp):
GAAAACAAAATGAGAAAAGAAAGT
Found at i:31419715 original size:13 final size:12
Alignment explanation
Indices: 31419644--31419715 Score: 58
Period size: 13 Copynumber: 5.8 Consensus size: 12
31419634 AAGAAAGTGA
31419644 AAAAGAAAAGA-
1 AAAAGAAAAGAG
*
31419655 AAAATGAAAAAAAG
1 AAAA-G-AAAAGAG
*
31419669 AAAACAAAAGTAGG
1 AAAAGAAAAG-A-G
*
31419683 AAAAG-AAAGTG
1 AAAAGAAAAGAG
31419694 AAAAGAAAATGAG
1 AAAAGAAAA-GAG
31419707 AAAAGAAAA
1 AAAAGAAAA
31419716 ACAAGAAAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
11 10 0.21
12 8 0.17
13 21 0.44
14 9 0.19
ACGTcount: A:0.74, C:0.01, G:0.19, T:0.06
Consensus pattern (12 bp):
AAAAGAAAAGAG
Found at i:31427194 original size:19 final size:18
Alignment explanation
Indices: 31427158--31427197 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
31427148 TTTTCACTCG
*
31427158 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
31427176 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
31427195 TTT
1 TTT
31427198 GTTTGTTGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:31428271 original size:17 final size:17
Alignment explanation
Indices: 31428249--31428283 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
31428239 AAACTAGCTC
31428249 TTTTTTTTCACAATTTTT
1 TTTTTTTTCA-AATTTTT
31428267 TTTTTTTTCAAATTTTT
1 TTTTTTTTCAAATTTTT
31428284 AATTTTAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTTTTTCAAATTTTT
Found at i:31428282 original size:13 final size:13
Alignment explanation
Indices: 31428266--31428330 Score: 76
Period size: 13 Copynumber: 4.8 Consensus size: 13
31428256 TCACAATTTT
31428266 TTTTTTTTTCAAA
1 TTTTTTTTTCAAA
*
31428279 TTTTTAATTTTAAAGA
1 TTTTT--TTTTCAA-A
**
31428295 TTTTTTTTTTGAA
1 TTTTTTTTTCAAA
31428308 TTTTTTTTTCAAA
1 TTTTTTTTTCAAA
31428321 TTTTTTTTTC
1 TTTTTTTTTC
31428331 GAGAAACTAC
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
13 27 0.61
14 5 0.11
15 6 0.14
16 6 0.14
ACGTcount: A:0.22, C:0.05, G:0.03, T:0.71
Consensus pattern (13 bp):
TTTTTTTTTCAAA
Found at i:31428282 original size:16 final size:15
Alignment explanation
Indices: 31428249--31428329 Score: 62
Period size: 15 Copynumber: 5.4 Consensus size: 15
31428239 AAACTAGCTC
31428249 TTTTTTTTCACAATTTTT
1 TTTTTTTTCA-AA--TTT
31428267 TTTTTTTTCAAATTT
1 TTTTTTTTCAAATTT
** *
31428282 TTAATTTT-AAAGATT
1 TTTTTTTTCAAA-TTT
*
31428297 TTTTTTTT-GAA--T
1 TTTTTTTTCAAATTT
31428309 TTTTTTTTCAAATTT
1 TTTTTTTTCAAATTT
31428324 TTTTTT
1 TTTTTT
31428330 CGAGAAACTA
Statistics
Matches: 52, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
12 9 0.17
13 2 0.04
14 3 0.06
15 26 0.50
17 2 0.04
18 10 0.19
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.72
Consensus pattern (15 bp):
TTTTTTTTCAAATTT
Found at i:31428289 original size:17 final size:18
Alignment explanation
Indices: 31428251--31428289 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
31428241 ACTAGCTCTT
**
31428251 TTTTTTCACAATTTTTTT
1 TTTTTTCACAATTTTTAA
31428269 TTTTTTCA-AATTTTTAA
1 TTTTTTCACAATTTTTAA
31428286 TTTT
1 TTTT
31428290 AAAGATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTTTCACAATTTTTAA
Found at i:31440640 original size:20 final size:20
Alignment explanation
Indices: 31440617--31440681 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
31440607 AAGCTCAAAC
31440617 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGTAAGCTAAATT
31440637 GAGCTCAAACG--AGCTAAATT
1 GAGCT-AAA-GTAAGCTAAATT
* * * *
31440657 AAGCTTATGTAAGCTAAATC
1 GAGCTAAAGTAAGCTAAATT
31440677 GAGCT
1 GAGCT
31440682 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (20 bp):
GAGCTAAAGTAAGCTAAATT
Found at i:31440680 original size:30 final size:29
Alignment explanation
Indices: 31440607--31440681 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 29
31440597 AACTTAAGCC
31440607 AAGCTCAAACGAGCTAAAGTAAGCTAAATT
1 AAGCT-AAACGAGCTAAAGTAAGCTAAATT
* * *
31440637 GAGCTCAAACGAGCTAAATTAAGCT-TATGT
1 AAGCT-AAACGAGCTAAAGTAAGCTAAAT-T
31440667 AAGCTAAATCGAGCT
1 AAGCTAAA-CGAGCT
31440682 GGGAAAAACT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
29 5 0.13
30 34 0.87
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.23
Consensus pattern (29 bp):
AAGCTAAACGAGCTAAAGTAAGCTAAATT
Found at i:31442492 original size:33 final size:33
Alignment explanation
Indices: 31442454--31442516 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
31442444 GATTACTCAG
31442454 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
31442487 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
31442517 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.25, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:31442543 original size:21 final size:21
Alignment explanation
Indices: 31442514--31442569 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
31442504 CAAGCTCTCT
*
31442514 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
31442535 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
31442556 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
31442570 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:31442562 original size:14 final size:14
Alignment explanation
Indices: 31442513--31442569 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
31442503 TCAAGCTCTC
31442513 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
31442526 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
31442540 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
31442554 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
31442568 TT
1 TT
31442570 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:31442597 original size:18 final size:18
Alignment explanation
Indices: 31442531--31442649 Score: 87
Period size: 18 Copynumber: 6.4 Consensus size: 18
31442521 TCTTTTTTCG
31442531 CTTTTTCTTTTTCAATTTT
1 CTTTTTCTTTTTCAA-TTT
* **
31442550 CTTTTCTTCATTTTCTTTTT
1 C-TTT-TTCTTTTTCAATTT
* ** *
31442570 CTCTCACTTTTTCGATTT
1 CTTTTTCTTTTTCAATTT
*
31442588 CTTTTTCTTTTGCAATTT
1 CTTTTTCTTTTTCAATTT
**
31442606 CTTTTTC-TTTTCGTTTT
1 CTTTTTCTTTTTCAATTT
*
31442623 CTTTTGTTTTCTTTCAATTT
1 CTTTT-TCTT-TTTCAATTT
31442643 CTTTTTC
1 CTTTTTC
31442650 AATCTCTTTC
Statistics
Matches: 74, Mismatches: 21, Indels: 10
0.70 0.20 0.10
Matches are distributed among these distances:
17 12 0.16
18 30 0.41
19 5 0.07
20 19 0.26
21 8 0.11
ACGTcount: A:0.08, C:0.19, G:0.03, T:0.70
Consensus pattern (18 bp):
CTTTTTCTTTTTCAATTT
Found at i:31442633 original size:10 final size:11
Alignment explanation
Indices: 31442603--31442636 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
31442593 TCTTTTGCAA
*
31442603 TTTCTTTTTCT
1 TTTCGTTTTCT
31442614 TTTCGTTTTCT
1 TTTCGTTTTCT
31442625 TTT-GTTTTCT
1 TTTCGTTTTCT
31442635 TT
1 TT
31442637 CAATTTCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 9 0.41
11 13 0.59
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (11 bp):
TTTCGTTTTCT
Found at i:31442649 original size:6 final size:6
Alignment explanation
Indices: 31442531--31442627 Score: 61
Period size: 6 Copynumber: 15.8 Consensus size: 6
31442521 TCTTTTTTCG
* * * **
31442531 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** *
31442582 CGATTT CTTTTT CTTTTG CAATTT CTTTTT C-TTTT CGTTTT CTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTT
31442628 GTTTTCTTTC
Statistics
Matches: 66, Mismatches: 22, Indels: 6
0.70 0.23 0.06
Matches are distributed among these distances:
5 5 0.08
6 49 0.74
7 9 0.14
8 3 0.05
ACGTcount: A:0.07, C:0.20, G:0.03, T:0.70
Consensus pattern (6 bp):
CTTTTT
Found at i:31443691 original size:14 final size:14
Alignment explanation
Indices: 31443649--31443694 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
31443639 CTCGCAAGAC
31443649 TTTTCACTTTTTTT
1 TTTTCACTTTTTTT
** *
31443663 TTTAAACTTGATTTT
1 TTTTCACTT-TTTTT
31443678 TTTTCACTTTTTTT
1 TTTTCACTTTTTTT
31443692 TTT
1 TTT
31443695 GAATTTTTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
14 14 0.56
15 11 0.44
ACGTcount: A:0.13, C:0.11, G:0.02, T:0.74
Consensus pattern (14 bp):
TTTTCACTTTTTTT
Found at i:31446629 original size:22 final size:22
Alignment explanation
Indices: 31446599--31446645 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
31446589 TTTGGTATTT
31446599 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
31446621 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
31446643 GGG
1 GGG
31446646 TTCAAAAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.32, C:0.04, G:0.40, T:0.23
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:31448345 original size:15 final size:15
Alignment explanation
Indices: 31448325--31448377 Score: 72
Period size: 17 Copynumber: 3.5 Consensus size: 15
31448315 TAGATTCTTC
31448325 TTTTTTTCACGAAATTT
1 TTTTTTTCACGAAA--T
*
31448342 TTTTTTTCACGAATT
1 TTTTTTTCACGAAAT
31448357 TTTTTTTCAC-AAAT
1 TTTTTTTCACGAAAT
31448371 TTTTTTT
1 TTTTTTT
31448378 TTGAATTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
14 10 0.29
15 11 0.32
17 13 0.38
ACGTcount: A:0.21, C:0.11, G:0.04, T:0.64
Consensus pattern (15 bp):
TTTTTTTCACGAAAT
Found at i:31448347 original size:17 final size:17
Alignment explanation
Indices: 31448325--31448379 Score: 89
Period size: 15 Copynumber: 3.4 Consensus size: 17
31448315 TAGATTCTTC
31448325 TTTTTTTCACGAAATTT
1 TTTTTTTCACGAAATTT
31448342 TTTTTTTCACG-AA-TT
1 TTTTTTTCACGAAATTT
31448357 TTTTTTTCAC-AAATTT
1 TTTTTTTCACGAAATTT
31448373 TTTTTTT
1 TTTTTTT
31448380 GAATTTTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
15 14 0.39
16 11 0.31
17 11 0.31
ACGTcount: A:0.20, C:0.11, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTTTTTCACGAAATTT
Found at i:31448386 original size:11 final size:11
Alignment explanation
Indices: 31448372--31448414 Score: 63
Period size: 11 Copynumber: 4.0 Consensus size: 11
31448362 TTCACAAATT
31448372 TTTTTTTTGAA
1 TTTTTTTTGAA
31448383 TTTTTTTTG-A
1 TTTTTTTTGAA
31448393 -TTTTTTTGAAA
1 TTTTTTTTG-AA
31448404 TTTTTTTTGAA
1 TTTTTTTTGAA
31448415 GAAACTACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
9 8 0.28
10 1 0.03
11 12 0.41
12 8 0.28
ACGTcount: A:0.19, C:0.00, G:0.09, T:0.72
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:31448396 original size:21 final size:21
Alignment explanation
Indices: 31448373--31448413 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
31448363 TCACAAATTT
31448373 TTTTTTTG-AATTTTTTTTGA
1 TTTTTTTGAAATTTTTTTTGA
31448393 TTTTTTTGAAATTTTTTTTGA
1 TTTTTTTGAAATTTTTTTTGA
31448414 AGAAACTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.17, C:0.00, G:0.10, T:0.73
Consensus pattern (21 bp):
TTTTTTTGAAATTTTTTTTGA
Found at i:31449448 original size:21 final size:23
Alignment explanation
Indices: 31449403--31449449 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
31449393 TCACCTGCAA
* *
31449403 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
31449426 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
31449447 TAA
1 TAA
31449450 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:31455490 original size:30 final size:30
Alignment explanation
Indices: 31455456--31455552 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
31455446 AGCTCACTCC
31455456 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
31455486 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
31455516 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
31455546 TAGCTCA
1 TAGCTCA
31455553 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:31476849 original size:20 final size:20
Alignment explanation
Indices: 31476826--31476872 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
31476816 GGGTTAAGAT
31476826 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTTGAG
* *
31476846 TGAGTTGACTTGAGCTTGAG
1 TGAGCTGAATTGAGCTTGAG
31476866 TGAGCTG
1 TGAGCTG
31476873 GAAACGAGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.11, G:0.36, T:0.32
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTTGAG
Found at i:31480168 original size:20 final size:20
Alignment explanation
Indices: 31480145--31480191 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
31480135 GGGTTAAGAT
*
31480145 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
31480165 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
31480185 TGAGCTG
1 TGAGCTG
31480192 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:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:31484205 original size:10 final size:10
Alignment explanation
Indices: 31484190--31484251 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
31484180 TTTGAACCAT
*
31484190 TACCAATTCG
1 TACCAATTCA
*
31484200 TACCAAATACCA
1 TACC-AAT-TCA
*
31484212 TACCATTTCA
1 TACCAATTCA
31484222 TACCAATTCCA
1 TACCAATT-CA
* *
31484233 TACCATTTCG
1 TACCAATTCA
31484243 TACCAATTC
1 TACCAATTC
31484252 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:31484235 original size:21 final size:21
Alignment explanation
Indices: 31484190--31484252 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
31484180 TTTGAACCAT
* *
31484190 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
31484212 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
31484233 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
31484253 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:31491349 original size:24 final size:23
Alignment explanation
Indices: 31491295--31491393 Score: 80
Period size: 21 Copynumber: 4.4 Consensus size: 23
31491285 GGATAATTAA
**
31491295 GAAATGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGAATTGGTAC
***
31491318 GTTTTGGTATTTTGGAATTGGTAC
1 GAAATGGTA-TTTGGAATTGGTAC
*
31491342 GAAATGGTA--TGGAATTGGTAT
1 GAAATGGTATTTGGAATTGGTAC
*
31491363 GAAATGGTA--TGGTATTTGGTAC
1 GAAATGGTATTTGG-AATTGGTAC
*
31491385 GAATTGGTA
1 GAAATGGTA
31491394 ATGGTTCAAA
Statistics
Matches: 62, Mismatches: 12, Indels: 5
0.78 0.15 0.06
Matches are distributed among these distances:
21 23 0.37
22 15 0.24
23 6 0.10
24 18 0.29
ACGTcount: A:0.25, C:0.03, G:0.31, T:0.40
Consensus pattern (23 bp):
GAAATGGTATTTGGAATTGGTAC
Found at i:31491356 original size:21 final size:21
Alignment explanation
Indices: 31491330--31491393 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
31491320 TTTGGTATTT
31491330 TGGAATTGGTACGAAATGGTA
1 TGGAATTGGTACGAAATGGTA
*
31491351 TGGAATTGGTATGAAATGGTA
1 TGGAATTGGTACGAAATGGTA
* *
31491372 TGGTATTTGGTACGAATTGGTA
1 TGG-AATTGGTACGAAATGGTA
31491394 ATGGTTCAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
21 23 0.61
22 15 0.39
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.34
Consensus pattern (21 bp):
TGGAATTGGTACGAAATGGTA
Found at i:31495341 original size:10 final size:10
Alignment explanation
Indices: 31495317--31495365 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
31495307 AGCTCGTTTC
*
31495317 CAGCTCACTT
1 CAGCTCAATT
* *
31495327 GAGCTCAAGT
1 CAGCTCAATT
31495337 CAGCTC-ATT
1 CAGCTCAATT
31495346 CGAGCTCAATT
1 C-AGCTCAATT
31495357 CAGCTCAAT
1 CAGCTCAAT
31495366 CTTAACCCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
9 3 0.09
10 25 0.78
11 4 0.12
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.27
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:31495342 original size:20 final size:20
Alignment explanation
Indices: 31495317--31495363 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
31495307 AGCTCGTTTC
31495317 CAGCTCACTT-GAGCTCAAGT
1 CAGCTCA-TTCGAGCTCAAGT
*
31495337 CAGCTCATTCGAGCTCAATT
1 CAGCTCATTCGAGCTCAAGT
31495357 CAGCTCA
1 CAGCTCA
31495364 ATCTTAACCC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.26
Consensus pattern (20 bp):
CAGCTCATTCGAGCTCAAGT
Found at i:31496728 original size:13 final size:13
Alignment explanation
Indices: 31496710--31496735 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31496700 ACCTGAAAGC
31496710 AATTTAATTCATA
1 AATTTAATTCATA
31496723 AATTTAATTCATA
1 AATTTAATTCATA
31496736 TTAGGACACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
AATTTAATTCATA
Found at i:31497150 original size:20 final size:21
Alignment explanation
Indices: 31497125--31497163 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
31497115 TCAAACAAGC
31497125 AAATGAGCTCAA-TGAGCTGG
1 AAATGAGCTCAATTGAGCTGG
*
31497145 AAATGAGCTGAATTGAGCT
1 AAATGAGCTCAATTGAGCT
31497164 CAACGAGCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.36, C:0.13, G:0.28, T:0.23
Consensus pattern (21 bp):
AAATGAGCTCAATTGAGCTGG
Found at i:31497680 original size:20 final size:20
Alignment explanation
Indices: 31497655--31497701 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
31497645 AGCTCGTTTC
*
31497655 CAGCTCACTT-GAGCTCAAGT
1 CAGCTCA-TTCGAGCCCAAGT
*
31497675 CAGCTCATTCGAGCCCAATT
1 CAGCTCATTCGAGCCCAAGT
31497695 CAGCTCA
1 CAGCTCA
31497702 ATCTTAACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.26, C:0.34, G:0.17, T:0.23
Consensus pattern (20 bp):
CAGCTCATTCGAGCCCAAGT
Found at i:31512987 original size:20 final size:20
Alignment explanation
Indices: 31512941--31512987 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
31512931 AGCTCGTTTC
*
31512941 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
31512961 CAACTCACTCAAGCTTAATT
1 CAGCTCACTCAAGCTCAAGT
31512981 CAGCTCA
1 CAGCTCA
31512988 ATCTTAACCC
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:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:31514494 original size:12 final size:12
Alignment explanation
Indices: 31514477--31514512 Score: 51
Period size: 10 Copynumber: 3.2 Consensus size: 12
31514467 AAAAGAGAAG
31514477 AAATTCAGAAAA
1 AAATTCAGAAAA
31514489 AAATTCA-AAAA
1 AAATTCAGAAAA
31514500 AAA-TC-GAAAA
1 AAATTCAGAAAA
31514510 AAA
1 AAA
31514513 AGGAAGTGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 9 0.39
11 7 0.30
12 7 0.30
ACGTcount: A:0.72, C:0.08, G:0.06, T:0.14
Consensus pattern (12 bp):
AAATTCAGAAAA
Found at i:31518406 original size:18 final size:18
Alignment explanation
Indices: 31518385--31518419 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
31518375 TTTTTCTTTT
31518385 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
31518403 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
31518420 TTTCTTTTCT
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:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:31519335 original size:13 final size:13
Alignment explanation
Indices: 31519317--31519350 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
31519307 TATACTTCGA
31519317 TTTTTTTTTGAAT
1 TTTTTTTTTGAAT
*
31519330 TTTTTTTTTGGAT
1 TTTTTTTTTGAAT
31519343 TTTTTTTT
1 TTTTTTTT
31519351 CAAATTTCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.09, C:0.00, G:0.09, T:0.82
Consensus pattern (13 bp):
TTTTTTTTTGAAT
Found at i:31523489 original size:20 final size:20
Alignment explanation
Indices: 31523443--31523489 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
31523433 AGCTCGTTTC
*
31523443 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
31523463 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
31523483 CAGCTCA
1 CAGCTCA
31523490 ATCTTAACCC
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:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:31527596 original size:11 final size:11
Alignment explanation
Indices: 31527566--31527599 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
31527556 TAAAAAAAAG
*
31527566 GAAAAAAAATT
1 GAAAAAAATTT
*
31527577 AAAAAAAATTT
1 GAAAAAAATTT
31527588 GAAAAAAATTT
1 GAAAAAAATTT
31527599 G
1 G
31527600 TATTCAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.09, T:0.24
Consensus pattern (11 bp):
GAAAAAAATTT
Found at i:31527709 original size:17 final size:16
Alignment explanation
Indices: 31527677--31527708 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
31527667 AAAAAGAAGT
31527677 TTCAGAAGTAAAAAAA
1 TTCAGAAGTAAAAAAA
*
31527693 TTCAGAATTAAAAAAA
1 TTCAGAAGTAAAAAAA
31527709 AAGAAGAGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.62, C:0.06, G:0.09, T:0.22
Consensus pattern (16 bp):
TTCAGAAGTAAAAAAA
Found at i:31528623 original size:18 final size:17
Alignment explanation
Indices: 31528611--31528649 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
31528601 GAGAAAATGA
31528611 AAATGAAAAAGAAAAAG
1 AAATGAAAAAGAAAAAG
31528628 AAATG--AAAGAAAAAG
1 AAATGAAAAAGAAAAAG
31528643 AAGATGA
1 AA-ATGA
31528650 GTGTGAGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 12 0.60
16 3 0.15
17 5 0.25
ACGTcount: A:0.72, C:0.00, G:0.21, T:0.08
Consensus pattern (17 bp):
AAATGAAAAAGAAAAAG
Found at i:31528638 original size:15 final size:16
Alignment explanation
Indices: 31528618--31528649 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
31528608 TGAAAATGAA
31528618 AAAGAAAAAGAA-ATG
1 AAAGAAAAAGAAGATG
31528633 AAAGAAAAAGAAGATG
1 AAAGAAAAAGAAGATG
31528649 A
1 A
31528650 GTGTGAGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (16 bp):
AAAGAAAAAGAAGATG
Found at i:31531752 original size:10 final size:10
Alignment explanation
Indices: 31531723--31531765 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
31531713 TTCAGTATTG
*
31531723 TAAAAAAAAG
1 TAAAAAAAAT
*
31531733 GAAAAAAAAT
1 TAAAAAAAAT
31531743 TAAAAAAAATT
1 TAAAAAAAA-T
31531754 TGAAAAAAAAT
1 T-AAAAAAAAT
31531765 T
1 T
31531766 GTATTCAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 16 0.57
11 4 0.14
12 8 0.29
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (10 bp):
TAAAAAAAAT
Found at i:31531759 original size:12 final size:12
Alignment explanation
Indices: 31531733--31531765 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
31531723 TAAAAAAAAG
31531733 GAAAAAAAA-TT
1 GAAAAAAAATTT
31531744 -AAAAAAAATTT
1 GAAAAAAAATTT
31531755 GAAAAAAAATT
1 GAAAAAAAATT
31531766 GTATTCAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 8 0.40
11 2 0.10
12 10 0.50
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (12 bp):
GAAAAAAAATTT
Found at i:31531832 original size:21 final size:22
Alignment explanation
Indices: 31531807--31531859 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
31531797 ATTCAGTACT
31531807 GAAAAAAAAGAGAA-ATTCA-AA
1 GAAAAAAAA-AGAAGATTCAGAA
*
31531828 GAAAAAAAAAGAAGTTTCAGAA
1 GAAAAAAAAAGAAGATTCAGAA
*
31531850 GTAAAAAAAA
1 GAAAAAAAAA
31531860 TTCAGAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 4 0.14
21 13 0.46
22 11 0.39
ACGTcount: A:0.70, C:0.04, G:0.15, T:0.11
Consensus pattern (22 bp):
GAAAAAAAAAGAAGATTCAGAA
Found at i:31531877 original size:18 final size:17
Alignment explanation
Indices: 31531843--31531876 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
31531833 AAAAAGAAGT
31531843 TTCAGAAGTAAAAAAAA
1 TTCAGAAGTAAAAAAAA
*
31531860 TTCAGAATTAAAAAAAA
1 TTCAGAAGTAAAAAAAA
31531877 AAGAAGAGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.65, C:0.06, G:0.09, T:0.21
Consensus pattern (17 bp):
TTCAGAAGTAAAAAAAA
Found at i:31532792 original size:18 final size:17
Alignment explanation
Indices: 31532780--31532818 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
31532770 GAGAAAATGA
31532780 AAATGAAAAAGAAAAAG
1 AAATGAAAAAGAAAAAG
31532797 AAATG--AAAGAAAAAG
1 AAATGAAAAAGAAAAAG
31532812 AAGATGA
1 AA-ATGA
31532819 GTGTGAGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 12 0.60
16 3 0.15
17 5 0.25
ACGTcount: A:0.72, C:0.00, G:0.21, T:0.08
Consensus pattern (17 bp):
AAATGAAAAAGAAAAAG
Found at i:31532807 original size:15 final size:16
Alignment explanation
Indices: 31532787--31532818 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
31532777 TGAAAATGAA
31532787 AAAGAAAAAGAA-ATG
1 AAAGAAAAAGAAGATG
31532802 AAAGAAAAAGAAGATG
1 AAAGAAAAAGAAGATG
31532818 A
1 A
31532819 GTGTGAGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (16 bp):
AAAGAAAAAGAAGATG
Found at i:31535921 original size:10 final size:10
Alignment explanation
Indices: 31535892--31535934 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
31535882 TTCAGTATTG
*
31535892 TAAAAAAAAG
1 TAAAAAAAAT
*
31535902 GAAAAAAAAT
1 TAAAAAAAAT
31535912 TAAAAAAAATT
1 TAAAAAAAA-T
31535923 TGAAAAAAAAT
1 T-AAAAAAAAT
31535934 T
1 T
31535935 GTATTCAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 16 0.57
11 4 0.14
12 8 0.29
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (10 bp):
TAAAAAAAAT
Found at i:31535928 original size:12 final size:12
Alignment explanation
Indices: 31535902--31535934 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
31535892 TAAAAAAAAG
31535902 GAAAAAAAA-TT
1 GAAAAAAAATTT
31535913 -AAAAAAAATTT
1 GAAAAAAAATTT
31535924 GAAAAAAAATT
1 GAAAAAAAATT
31535935 GTATTCAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 8 0.40
11 2 0.10
12 10 0.50
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (12 bp):
GAAAAAAAATTT
Found at i:31536003 original size:21 final size:23
Alignment explanation
Indices: 31535977--31536029 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
31535967 TTCAGTACTG
*
31535977 AAAAAAAAAGAGAAATTCA-AAG-
1 AAAAAAAAAGA-AGATTCAGAAGT
*
31535999 AAAAAAAAAGAAGTTTCAGAAGT
1 AAAAAAAAAGAAGATTCAGAAGT
31536022 AAAAAAAA
1 AAAAAAAA
31536030 TTCAGAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 5 0.19
22 14 0.52
23 8 0.30
ACGTcount: A:0.72, C:0.04, G:0.13, T:0.11
Consensus pattern (23 bp):
AAAAAAAAAGAAGATTCAGAAGT
Done.