Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 115 of 125
Found at i:35561885 original size:25 final size:24
Alignment explanation
Indices: 35561815--35561886 Score: 58
Period size: 25 Copynumber: 2.9 Consensus size: 24
35561805 TTAATTTAAT
* *
35561815 TATATAAATAAAAGAATTTTAAAAA
1 TATATAAA-ATAAGAATTTAAAAAA
* *
35561840 T-TATTAAATTCAA-AATATAAACAAA
1 TATA-TAAAAT-AAGAATTTAAA-AAA
35561865 TATATAAAATAAGAATTTAAAA
1 TATATAAAATAAGAATTTAAAA
35561887 CACATTTTAG
Statistics
Matches: 36, Mismatches: 6, Indels: 11
0.68 0.11 0.21
Matches are distributed among these distances:
24 11 0.31
25 23 0.64
26 2 0.06
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (24 bp):
TATATAAAATAAGAATTTAAAAAA
Found at i:35562943 original size:22 final size:22
Alignment explanation
Indices: 35562918--35562959 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
35562908 TCGTGAACAC
35562918 TTTTATGTGTTT-AATGTTTAGA
1 TTTTATGT-TTTAAATGTTTAGA
*
35562940 TTTTTTGTTTTAAATGTTTA
1 TTTTATGTTTTAAATGTTTA
35562960 ACAAAAATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.21, C:0.00, G:0.14, T:0.64
Consensus pattern (22 bp):
TTTTATGTTTTAAATGTTTAGA
Found at i:35569261 original size:13 final size:13
Alignment explanation
Indices: 35569243--35569267 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35569233 TACAATCCCC
35569243 AAAAGATATATAA
1 AAAAGATATATAA
35569256 AAAAGATATATA
1 AAAAGATATATA
35569268 TAATCCATTT
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:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (13 bp):
AAAAGATATATAA
Found at i:35574625 original size:3 final size:3
Alignment explanation
Indices: 35574617--35574664 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
35574607 GCCTTCAATT
35574617 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
35574665 AAGTACTAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:35579808 original size:33 final size:33
Alignment explanation
Indices: 35579771--35579847 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 33
35579761 CTAGTCAAAG
* ** * *
35579771 TTGTTTATTTTATTAATTTTGTTTTGATTAAAT
1 TTGTTTATTTTACTAATTTCATTTTGACTAAAA
*
35579804 TTG-TTATTTTCCTAATTTCATTTTGACTAAAA
1 TTGTTTATTTTACTAATTTCATTTTGACTAAAA
*
35579836 TTATTTATTTTA
1 TTGTTTATTTTA
35579848 AATAAATAGG
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
32 25 0.71
33 10 0.29
ACGTcount: A:0.26, C:0.05, G:0.06, T:0.62
Consensus pattern (33 bp):
TTGTTTATTTTACTAATTTCATTTTGACTAAAA
Found at i:35590910 original size:16 final size:17
Alignment explanation
Indices: 35590873--35590910 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
35590863 CTTTTAAAAT
*
35590873 ATTATTTTATTCTTTCA
1 ATTATTTTATTCTTTAA
35590890 ATTATTTTATT-TTTAA
1 ATTATTTTATTCTTTAA
35590906 ATTAT
1 ATTAT
35590911 AAAAATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (17 bp):
ATTATTTTATTCTTTAA
Found at i:35590924 original size:24 final size:25
Alignment explanation
Indices: 35590896--35590942 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
35590886 TTCAATTATT
*
35590896 TTATTT-TTAAATTATAAAAATATA
1 TTATTTATTAAATTAGAAAAATATA
35590920 TTATTTATTAAATTAGAAAAATA
1 TTATTTATTAAATTAGAAAAATA
35590943 ATCGCTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (25 bp):
TTATTTATTAAATTAGAAAAATATA
Found at i:35591348 original size:1 final size:1
Alignment explanation
Indices: 35591342--35591371 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
35591332 TAGACTTAAG
35591342 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
35591372 ATAGTAGTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:35592913 original size:20 final size:21
Alignment explanation
Indices: 35592888--35592933 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
35592878 AGTGTCTTAT
35592888 AAAAAT-ATAATAAAATATTA
1 AAAAATAATAATAAAATATTA
* *
35592908 AAAAATACATAATAATATTTTA
1 AAAAATA-ATAATAAAATATTA
35592930 AAAA
1 AAAA
35592934 TACTTAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 6 0.27
22 16 0.73
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (21 bp):
AAAAATAATAATAAAATATTA
Found at i:35592932 original size:21 final size:22
Alignment explanation
Indices: 35592887--35592941 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
35592877 AAGTGTCTTA
35592887 TAAAAAT--ATAATAAAATATT
1 TAAAAATACATAATAAAATATT
* *
35592907 AAAAAATACATAATAATAT-TT
1 TAAAAATACATAATAAAATATT
*
35592928 TAAAAATACTTAAT
1 TAAAAATACATAAT
35592942 TATGAAATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 6 0.21
21 14 0.48
22 9 0.31
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (22 bp):
TAAAAATACATAATAAAATATT
Found at i:35594122 original size:58 final size:59
Alignment explanation
Indices: 35594051--35594164 Score: 140
Period size: 58 Copynumber: 1.9 Consensus size: 59
35594041 CCAATGTGGA
* * * * *
35594051 AACAATTATCAAGTTCATAGTCTAACTTGAAC-AAAAGAAATTCAAACCCCAATATAAG
1 AACAATTACCAAGTTCAGAGCCTAACTTAAACAAAAAGAAATTCAAACCACAATATAAG
* * * *
35594109 AACAATTGCCAAGTTTAGAGCCTAACTTAAACAAAAATAAATTCAAATCACAATAT
1 AACAATTACCAAGTTCAGAGCCTAACTTAAACAAAAAGAAATTCAAACCACAATAT
35594165 GAAAAAAATT
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
58 26 0.57
59 20 0.43
ACGTcount: A:0.49, C:0.18, G:0.08, T:0.25
Consensus pattern (59 bp):
AACAATTACCAAGTTCAGAGCCTAACTTAAACAAAAAGAAATTCAAACCACAATATAAG
Found at i:35597608 original size:23 final size:23
Alignment explanation
Indices: 35597582--35597761 Score: 236
Period size: 23 Copynumber: 7.8 Consensus size: 23
35597572 TTAATGTTCA
**
35597582 CGAACATGTTCATTTAAC-TTAAT
1 CGAACATGTTCA-CGAACATTAAT
*
35597605 CGAACATGTTTACGAACATTAAT
1 CGAACATGTTCACGAACATTAAT
* *
35597628 CTAACATATTCACGAACATTAAT
1 CGAACATGTTCACGAACATTAAT
*
35597651 CGAATATGTTCACGAACATTAAT
1 CGAACATGTTCACGAACATTAAT
*
35597674 CGAACATATTCACGAACATTAAT
1 CGAACATGTTCACGAACATTAAT
* *
35597697 CGAATATGTTCACGAACATTAAA
1 CGAACATGTTCACGAACATTAAT
*
35597720 CGAACATGTTCATGAACATATAAT
1 CGAACATGTTCACGAACAT-TAAT
*
35597744 TGAACATGTTCACGAACA
1 CGAACATGTTCACGAACA
35597762 ATGATAATGA
Statistics
Matches: 136, Mismatches: 19, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
22 3 0.02
23 114 0.84
24 19 0.14
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.29
Consensus pattern (23 bp):
CGAACATGTTCACGAACATTAAT
Found at i:35597884 original size:12 final size:12
Alignment explanation
Indices: 35597856--35597914 Score: 77
Period size: 12 Copynumber: 5.0 Consensus size: 12
35597846 TCATTAATAA
*
35597856 ATAAACGAGC-C
1 ATAAACGAGCTT
35597867 ATAAACGAG-TT
1 ATAAACGAGCTT
35597878 AATAAACGAGCTT
1 -ATAAACGAGCTT
35597891 ATAAACGAGCTT
1 ATAAACGAGCTT
*
35597903 TTAAACGAGCTT
1 ATAAACGAGCTT
35597915 GTTCGTGAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
11 9 0.21
12 32 0.74
13 2 0.05
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.24
Consensus pattern (12 bp):
ATAAACGAGCTT
Found at i:35601103 original size:18 final size:18
Alignment explanation
Indices: 35601080--35601117 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
35601070 ACAAAGAAAT
35601080 TTAAATTATAGGTTTTTG
1 TTAAATTATAGGTTTTTG
35601098 TTAAATTATAGGTTTTTG
1 TTAAATTATAGGTTTTTG
35601116 TT
1 TT
35601118 CTTAGTGTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.16, T:0.58
Consensus pattern (18 bp):
TTAAATTATAGGTTTTTG
Found at i:35607687 original size:2 final size:2
Alignment explanation
Indices: 35607680--35607705 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
35607670 CTCACATGGC
35607680 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
35607706 GGCCAACATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35608124 original size:4 final size:4
Alignment explanation
Indices: 35608115--35608143 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
35608105 GAGAAGCTTT
35608115 AGCC AGCC AGCC AGCC AGCC A-CC AGCC AG
1 AGCC AGCC AGCC AGCC AGCC AGCC AGCC AG
35608144 GGTCAACTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.28, C:0.48, G:0.24, T:0.00
Consensus pattern (4 bp):
AGCC
Found at i:35609760 original size:20 final size:20
Alignment explanation
Indices: 35609735--35609774 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
35609725 AAGACATGAA
35609735 ACAAGAGCCCTTTACTTGTT
1 ACAAGAGCCCTTTACTTGTT
35609755 ACAAGAGCCCTTTACTTGTT
1 ACAAGAGCCCTTTACTTGTT
35609775 GAAAGTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (20 bp):
ACAAGAGCCCTTTACTTGTT
Found at i:35610365 original size:13 final size:13
Alignment explanation
Indices: 35610347--35610409 Score: 78
Period size: 13 Copynumber: 5.0 Consensus size: 13
35610337 TAAATCAAAC
35610347 TTTTTTAAAAATA
1 TTTTTTAAAAATA
35610360 TTTTTTAAAAATA
1 TTTTTTAAAAATA
*
35610373 TTTTTTTAAAACT-
1 -TTTTTTAAAAATA
*
35610386 CTTTTT--AAATA
1 TTTTTTAAAAATA
35610397 TTTTTTAAAAATA
1 TTTTTTAAAAATA
35610410 ATGCTAAACT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
10 3 0.07
11 5 0.12
12 5 0.12
13 18 0.43
14 11 0.26
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTTTTAAAAATA
Found at i:35620761 original size:14 final size:14
Alignment explanation
Indices: 35620742--35620777 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
35620732 TTTGGTGTCT
*
35620742 AAAATTTTAAAAAG
1 AAAATTTTAAAAAC
*
35620756 AAAATTTTAAAACC
1 AAAATTTTAAAAAC
35620770 AAAATTTT
1 AAAATTTT
35620778 GGGAAATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.33
Consensus pattern (14 bp):
AAAATTTTAAAAAC
Found at i:35627321 original size:17 final size:16
Alignment explanation
Indices: 35627286--35627317 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
35627276 TAGCGGCGCT
35627286 TATAAGCACCGCTAAA
1 TATAAGCACCGCTAAA
*
35627302 TATAAGCGCCGCTAAA
1 TATAAGCACCGCTAAA
35627318 ATATTTAGCG
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:0.41, C:0.25, G:0.16, T:0.19
Consensus pattern (16 bp):
TATAAGCACCGCTAAA
Found at i:35627460 original size:43 final size:43
Alignment explanation
Indices: 35627366--35627485 Score: 150
Period size: 43 Copynumber: 2.8 Consensus size: 43
35627356 CGCTAATGAT
* * * * *
35627366 AACGCCGTTATAGAACATGTTCTTTAGCAGTGCTTCTCCCCCA
1 AACGCCGCTAAAGAACGTGTTCTTTAGCGGCGCTTCTCCCCCA
* * * *
35627409 AGCACCGCTAAAGAACGTGTTCTTTAGCGGCGCTTTTCCCTCA
1 AACGCCGCTAAAGAACGTGTTCTTTAGCGGCGCTTCTCCCCCA
*
35627452 AACGCCGCTAAAGATCGTGTTCTTTAGCGGCGCT
1 AACGCCGCTAAAGAACGTGTTCTTTAGCGGCGCT
35627486 CAGATTTTTA
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 65 1.00
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (43 bp):
AACGCCGCTAAAGAACGTGTTCTTTAGCGGCGCTTCTCCCCCA
Found at i:35627565 original size:15 final size:15
Alignment explanation
Indices: 35627545--35627577 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
35627535 TTTTCCTGTA
*
35627545 AATTCAAATCCAACC
1 AATTCAAACCCAACC
35627560 AATTCAAACCCAACC
1 AATTCAAACCCAACC
35627575 AAT
1 AAT
35627578 AACTTCAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.48, C:0.33, G:0.00, T:0.18
Consensus pattern (15 bp):
AATTCAAACCCAACC
Found at i:35639333 original size:28 final size:29
Alignment explanation
Indices: 35639288--35639342 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
35639278 ATTTCCTTTT
35639288 TATTCTTTTTTCCTTCCTTT-CTTTTTCA
1 TATTCTTTTTTCCTTCCTTTCCTTTTTCA
*
35639316 TATT-TTTTATTCTTTCCTTTCCTTTTT
1 TATTCTTTT-TTCCTTCCTTTCCTTTTT
35639343 TTTTTCCGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 4 0.17
28 14 0.58
29 6 0.25
ACGTcount: A:0.07, C:0.22, G:0.00, T:0.71
Consensus pattern (29 bp):
TATTCTTTTTTCCTTCCTTTCCTTTTTCA
Found at i:35641039 original size:5 final size:5
Alignment explanation
Indices: 35641029--35641054 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
35641019 ATAATTAAAA
35641029 ATTCT ATTCT ATTCT ATTCT ATTCT A
1 ATTCT ATTCT ATTCT ATTCT ATTCT A
35641055 CTCGAAGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.00, T:0.58
Consensus pattern (5 bp):
ATTCT
Found at i:35644200 original size:20 final size:18
Alignment explanation
Indices: 35644177--35644226 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 18
35644167 AAACTTATTG
35644177 AAAATTAGAAACAAAATATA
1 AAAATT-GAAA-AAAATATA
*
35644197 AAAATTGTAAAAAATATA
1 AAAATTGAAAAAAATATA
35644215 AAAATTGTAAAA
1 AAAATTG-AAAA
35644227 TTTTATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 15 0.56
19 6 0.22
20 6 0.22
ACGTcount: A:0.68, C:0.02, G:0.06, T:0.24
Consensus pattern (18 bp):
AAAATTGAAAAAAATATA
Found at i:35644209 original size:9 final size:9
Alignment explanation
Indices: 35644189--35644254 Score: 71
Period size: 9 Copynumber: 7.3 Consensus size: 9
35644179 AATTAGAAAC
35644189 AAAA-TATA
1 AAAATTATA
*
35644197 AAAATTGTA
1 AAAATTATA
*
35644206 AAAAATATA
1 AAAATTATA
*
35644215 AAAATTGTA
1 AAAATTATA
*
35644224 AAATTTTATA
1 AAA-ATTATA
*
35644234 AAAATCATA
1 AAAATTATA
35644243 AAAATTATA
1 AAAATTATA
35644252 AAA
1 AAA
35644255 TGTATCAAAA
Statistics
Matches: 46, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
8 4 0.09
9 35 0.76
10 7 0.15
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.30
Consensus pattern (9 bp):
AAAATTATA
Found at i:35644264 original size:28 final size:27
Alignment explanation
Indices: 35644189--35644265 Score: 88
Period size: 28 Copynumber: 2.9 Consensus size: 27
35644179 AATTAGAAAC
35644189 AAAA-TATAAAAATTGTA-AAAAATATA
1 AAAATTAT-AAAATTGTATAAAAATATA
* *
35644215 AAAATTGTAAAATTTTATAAAAATCATA
1 AAAATTATAAAATTGTATAAAAAT-ATA
35644243 AAAATTATAAAA-TGTATCAAAAA
1 AAAATTATAAAATTGTAT-AAAAA
35644266 GGTCCTTTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
26 12 0.28
27 12 0.28
28 19 0.44
ACGTcount: A:0.64, C:0.03, G:0.04, T:0.30
Consensus pattern (27 bp):
AAAATTATAAAATTGTATAAAAATATA
Found at i:35646134 original size:40 final size:41
Alignment explanation
Indices: 35646090--35646170 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 41
35646080 CATCCTTACT
*
35646090 TTTTAAAATTTAATTCTT-ATACTTTAAATAAAAA-TAAAAA
1 TTTTAAAAATT-ATTCTTCATACTTTAAATAAAAATTAAAAA
* *
35646130 TTTTAAAAATTATTTTTCATATTTTAAATAAAAATTAAAAA
1 TTTTAAAAATTATTCTTCATACTTTAAATAAAAATTAAAAA
35646171 CTTATGAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
39 5 0.14
40 25 0.69
41 6 0.17
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (41 bp):
TTTTAAAAATTATTCTTCATACTTTAAATAAAAATTAAAAA
Found at i:35647178 original size:214 final size:214
Alignment explanation
Indices: 35646809--35647239 Score: 844
Period size: 214 Copynumber: 2.0 Consensus size: 214
35646799 GCTTTTATAC
35646809 ATAACTTAAACAAGCCTTTCAACATATATCGTTTTGGCTTACTAACATAGTATTTAAGTGAATAC
1 ATAACTTAAACAAGCCTTTCAACATATATCGTTTTGGCTTACTAACATAGTATTTAAGTGAATAC
35646874 AAAATAACTCCTTGAAAATAACTATTATTTTATTAACAATCAAAGCACAATTAAACGAAGATATG
66 AAAATAACTCCTTGAAAATAACTATTATTTTATTAACAATCAAAGCACAATTAAACGAAGATATG
35646939 CTCTCCAAAACAACAATAAAATCTTGATTAATCATCCACGTTCCAAGGCTTGAATTGATTCACTT
131 CTCTCCAAAACAACAATAAAATCTTGATTAATCATCCACGTTCCAAGGCTTGAATTGATTCACTT
35647004 GTGTCCAATCCAATCTTCA
196 GTGTCCAATCCAATCTTCA
*
35647023 ATAACTTAGACAAGCCTTTCAACATATATCGTTTTGGCTTACTAACATAGTATTTAAGTGAATAC
1 ATAACTTAAACAAGCCTTTCAACATATATCGTTTTGGCTTACTAACATAGTATTTAAGTGAATAC
*
35647088 AAAATAACTCCTTGAAAATAGCTATTATTTTATTAACAATCAAAGCACAATTAAACGAAGATATG
66 AAAATAACTCCTTGAAAATAACTATTATTTTATTAACAATCAAAGCACAATTAAACGAAGATATG
35647153 CTCTCCAAAACAACAATAAAATCTTGATTAATCATCCACGTTCCAAGGCTTGAATTGATTCACTT
131 CTCTCCAAAACAACAATAAAATCTTGATTAATCATCCACGTTCCAAGGCTTGAATTGATTCACTT
35647218 GTGTCCAATCCAATCTTCA
196 GTGTCCAATCCAATCTTCA
35647237 ATA
1 ATA
35647240 GCCAAGCATT
Statistics
Matches: 215, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
214 215 1.00
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (214 bp):
ATAACTTAAACAAGCCTTTCAACATATATCGTTTTGGCTTACTAACATAGTATTTAAGTGAATAC
AAAATAACTCCTTGAAAATAACTATTATTTTATTAACAATCAAAGCACAATTAAACGAAGATATG
CTCTCCAAAACAACAATAAAATCTTGATTAATCATCCACGTTCCAAGGCTTGAATTGATTCACTT
GTGTCCAATCCAATCTTCA
Found at i:35649692 original size:14 final size:15
Alignment explanation
Indices: 35649663--35649692 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
35649653 TTTCATTAAG
35649663 AATAATTTTAAAAAA
1 AATAATTTTAAAAAA
*
35649678 AATAATTTCAAAAAA
1 AATAATTTTAAAAAA
35649693 TCTTATTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (15 bp):
AATAATTTTAAAAAA
Found at i:35650414 original size:18 final size:18
Alignment explanation
Indices: 35650370--35650417 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
35650360 TCTATGAACA
35650370 AAAAATTT-TAAAAAATTC
1 AAAAATTTAT-AAAAATTC
*
35650388 AAAATATTTATAAAAATTT
1 AAAA-ATTTATAAAAATTC
*
35650407 TAAAATTTATA
1 AAAAATTTATA
35650418 TTTTTAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 11 0.42
19 14 0.54
20 1 0.04
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (18 bp):
AAAAATTTATAAAAATTC
Found at i:35657273 original size:17 final size:18
Alignment explanation
Indices: 35657253--35657286 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
35657243 TGAACTCATT
35657253 CATGAAATG-AATTAAAA
1 CATGAAATGAAATTAAAA
*
35657270 CATGAATTGAAATTAAA
1 CATGAAATGAAATTAAA
35657287 TAGTGCACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.26
Consensus pattern (18 bp):
CATGAAATGAAATTAAAA
Found at i:35657362 original size:20 final size:20
Alignment explanation
Indices: 35657315--35657371 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 20
35657305 ATCATTTCAT
35657315 ATTTATATATTTCTAATTTAAA
1 ATTTAT-TATTT-TAATTTAAA
*
35657337 ATTTATTATTTTAATTGTAAT
1 ATTTATTATTTTAATT-TAAA
*
35657358 ATTATATTTTTTTA
1 ATT-TATTATTTTA
35657372 CAATTATTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 5 0.16
21 11 0.35
22 15 0.48
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (20 bp):
ATTTATTATTTTAATTTAAA
Found at i:35663971 original size:18 final size:18
Alignment explanation
Indices: 35663938--35663972 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
35663928 CACGCTTTTT
* *
35663938 TTCTGCCTTGTGGCACGC
1 TTCTGCCTTATAGCACGC
35663956 TTCTGCCTTATAGCACG
1 TTCTGCCTTATAGCACG
35663973 TTTTCGTCTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.11, C:0.31, G:0.23, T:0.34
Consensus pattern (18 bp):
TTCTGCCTTATAGCACGC
Found at i:35669008 original size:21 final size:24
Alignment explanation
Indices: 35668967--35669009 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
35668957 GAGAGAGAAA
35668967 ACTAATTATAAGATGAAAATAATG
1 ACTAATTATAAGATGAAAATAATG
35668991 ACTAATTA-AA-AT-AAAATAA
1 ACTAATTATAAGATGAAAATAA
35669010 GAGAGAAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
22 2 0.11
23 2 0.11
24 8 0.42
ACGTcount: A:0.60, C:0.05, G:0.07, T:0.28
Consensus pattern (24 bp):
ACTAATTATAAGATGAAAATAATG
Found at i:35670758 original size:17 final size:17
Alignment explanation
Indices: 35670736--35670806 Score: 106
Period size: 17 Copynumber: 4.2 Consensus size: 17
35670726 ATCAAACCAT
**
35670736 TTTGAATTTGTTTTAAA
1 TTTGAATTTAATTTAAA
35670753 TTTGAATTTAATTTAAA
1 TTTGAATTTAATTTAAA
35670770 TTTGAATTTAATTTAAA
1 TTTGAATTTAATTTAAA
* *
35670787 TTTGGATTAAATTTAAA
1 TTTGAATTTAATTTAAA
35670804 TTT
1 TTT
35670807 ATTATAAATT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 50 1.00
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (17 bp):
TTTGAATTTAATTTAAA
Found at i:35670765 original size:11 final size:11
Alignment explanation
Indices: 35670751--35670816 Score: 55
Period size: 11 Copynumber: 5.9 Consensus size: 11
35670741 ATTTGTTTTA
*
35670751 AATTTGAATTT
1 AATTTAAATTT
35670762 AATTTAAATTT
1 AATTTAAATTT
35670773 GAATTT-AATTT
1 -AATTTAAATTT
** *
35670784 AAATTTGGATTA
1 -AATTTAAATTT
35670796 AATTTAAATTT
1 AATTTAAATTT
35670807 -ATTATAAATT
1 AATT-TAAATT
35670817 CAATGTCCAA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
10 3 0.07
11 34 0.76
12 8 0.18
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:35670767 original size:5 final size:6
Alignment explanation
Indices: 35670736--35670790 Score: 53
Period size: 6 Copynumber: 9.7 Consensus size: 6
35670726 ATCAAACCAT
* * *
35670736 TTTGAA TTTG-T TTTAAA TTTGAA TTT-AA TTTAAA TTTGAA TTT-AA
1 TTTGAA TTTGAA TTTGAA TTTGAA TTTGAA TTTGAA TTTGAA TTTGAA
*
35670781 TTTAAA TTTG
1 TTTGAA TTTG
35670791 GATTAAATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
5 13 0.32
6 27 0.68
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (6 bp):
TTTGAA
Found at i:35670802 original size:6 final size:6
Alignment explanation
Indices: 35670747--35670807 Score: 65
Period size: 6 Copynumber: 10.7 Consensus size: 6
35670737 TTGAATTTGT
* * **
35670747 TTTAAA TTTGAA TTT-AA TTTAAA TTTGAA TTT-AA TTTAAA TTTGGA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
35670793 -TTAAA TTTAAA TTTA
1 TTTAAA TTTAAA TTTA
35670808 TTATAAATTC
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
5 13 0.28
6 33 0.72
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:35672404 original size:29 final size:26
Alignment explanation
Indices: 35672372--35672487 Score: 65
Period size: 29 Copynumber: 4.0 Consensus size: 26
35672362 TTATATCTTG
35672372 ACCCCAAACTTTCTAAAAATTACCATTTT
1 ACCCCAAA-TTTC-AAAAATT-CCATTTT
*
35672401 ACCCCTAAATTTACCAAAATTCCACTTTT
1 ACCCC-AAATTT-CAAAAATTCCA-TTTT
*
35672430 GA-CCCTAATTTCACCAAAATTTACCATTTT
1 -ACCCCAAATTTCA--AAAA-TT-CCATTTT
*
35672460 ACCCCCGAACTTTTC-AAAATTCCATTTT
1 A-CCCC-AA-ATTTCAAAAATTCCATTTT
35672488 TGACCTCGGT
Statistics
Matches: 70, Mismatches: 5, Indels: 25
0.70 0.05 0.25
Matches are distributed among these distances:
27 1 0.01
28 15 0.21
29 28 0.40
30 15 0.21
31 6 0.09
32 1 0.01
33 4 0.06
ACGTcount: A:0.34, C:0.29, G:0.02, T:0.35
Consensus pattern (26 bp):
ACCCCAAATTTCAAAAATTCCATTTT
Found at i:35672602 original size:58 final size:57
Alignment explanation
Indices: 35672386--35672604 Score: 228
Period size: 59 Copynumber: 3.7 Consensus size: 57
35672376 CAAACTTTCT
* * *
35672386 AAAAATTACCATTTTACCCCTAAATTTACCAAAATTCCACTTTTGACCCTAATTTCACC
1 AAAAATTACCATTTTACCCCGAAATTT-CCAAAATTCCATTTTTGACCCTGATTTCA-C
* * * * *
35672445 AAAATTTACCATTTTACCCCCGAACTTTTCAAAATTCCATTTTTGACCTCGGTTTTGC-C
1 AAAAATTACCATTTTA-CCCCGAAATTTCCAAAATTCCATTTTTGACC-CTGATTT-CAC
* *
35672504 AAAATTTACCATTTTACCCTCCAAACTTTCC-AAATTCCATTTTT-AGCCCTGATTTCAC
1 AAAAATTACCATTTTACCC-CGAAA-TTTCCAAAATTCCATTTTTGA-CCCTGATTTCAC
**
35672562 AAAAATTACCATTTTACCCCGAAAAGTCCAAAATTACCATTTT
1 AAAAATTACCATTTTACCCCGAAATTTCCAAAATT-CCATTTT
35672605 GCCCTCGGGT
Statistics
Matches: 134, Mismatches: 17, Indels: 19
0.79 0.10 0.11
Matches are distributed among these distances:
56 3 0.02
57 10 0.07
58 35 0.26
59 68 0.51
60 17 0.13
61 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.36
Consensus pattern (57 bp):
AAAAATTACCATTTTACCCCGAAATTTCCAAAATTCCATTTTTGACCCTGATTTCAC
Found at i:35676830 original size:16 final size:15
Alignment explanation
Indices: 35676809--35676857 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
35676799 TGATGGAGAT
35676809 ATTATTTTGATAATTA
1 ATTATTTT-ATAATTA
35676825 ATTATTTT-TATATT-
1 ATTATTTTATA-ATTA
35676839 A-TATTTTAGTAATTA
1 ATTATTTTA-TAATTA
35676854 ATTA
1 ATTA
35676858 GTTAAGTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
13 6 0.21
14 6 0.21
15 6 0.21
16 10 0.36
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (15 bp):
ATTATTTTATAATTA
Found at i:35677106 original size:30 final size:25
Alignment explanation
Indices: 35677029--35677097 Score: 102
Period size: 25 Copynumber: 2.7 Consensus size: 25
35677019 AAAAATATTT
35677029 AAAATTTTATATTAATTTTTTATAACA
1 AAAATTTTAT-TTAA-TTTTTATAACA
35677056 AAAATTTTATTTAATTTTTATAACA
1 AAAATTTTATTTAATTTTTATAACA
* *
35677081 AAAAATTTATTTTATTT
1 AAAATTTTATTTAATTT
35677098 AATTTTTATC
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
25 26 0.65
26 4 0.10
27 10 0.25
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (25 bp):
AAAATTTTATTTAATTTTTATAACA
Found at i:35678785 original size:10 final size:10
Alignment explanation
Indices: 35678772--35678796 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
35678762 ACTCCATTTA
35678772 AAATAATTCT
1 AAATAATTCT
35678782 AAATAATTCT
1 AAATAATTCT
35678792 AAATA
1 AAATA
35678797 TTATATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (10 bp):
AAATAATTCT
Found at i:35688244 original size:1 final size:1
Alignment explanation
Indices: 35688238--35688275 Score: 76
Period size: 1 Copynumber: 38.0 Consensus size: 1
35688228 CAGGAAAGGT
35688238 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
35688276 ATGACAAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:35696237 original size:59 final size:57
Alignment explanation
Indices: 35696174--35696285 Score: 145
Period size: 59 Copynumber: 1.9 Consensus size: 57
35696164 TTTTGTGAGA
* * *
35696174 TTTAAAAATATCACGAAAATATGTGAAAAAAAAATCATAAAAAAT-CCAATTTGGTAAGG
1 TTTAAAAATATCACGAAAAGA-AT--AAAAAAAATCACAAAAAATCCCAATTTGGTAAGG
* *
35696233 TTTAAAAATGTCACGAAAAGAATAAAAAACATCACAAAAAATCCCAATTTGGT
1 TTTAAAAATATCACGAAAAGAATAAAAAAAATCACAAAAAATCCCAATTTGGT
35696286 GAGCTCTCAC
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
56 17 0.36
57 10 0.21
58 1 0.02
59 19 0.40
ACGTcount: A:0.54, C:0.12, G:0.11, T:0.24
Consensus pattern (57 bp):
TTTAAAAATATCACGAAAAGAATAAAAAAAATCACAAAAAATCCCAATTTGGTAAGG
Found at i:35699128 original size:2 final size:2
Alignment explanation
Indices: 35699116--35699148 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
35699106 AAACGAGTTG
35699116 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35699149 TAGAGGAGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35703471 original size:3 final size:3
Alignment explanation
Indices: 35703463--35703514 Score: 68
Period size: 3 Copynumber: 17.3 Consensus size: 3
35703453 CTTTTATACT
* * * *
35703463 TTC TTC TTC TTC TTC TTC TTC TTC TTC ATC TTC ATC TTC ATC TTC TGC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
35703511 TTC T
1 TTC T
35703515 CTTTATTCAT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.06, C:0.33, G:0.02, T:0.60
Consensus pattern (3 bp):
TTC
Found at i:35707376 original size:22 final size:22
Alignment explanation
Indices: 35707334--35707376 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
35707324 TTTAGCCCAA
* *
35707334 ATAAAAAGTTGGGCTCTTGTAG
1 ATAAAAAATTGGGCTCATGTAG
*
35707356 ATAAAAAATTGGGTTCATGTA
1 ATAAAAAATTGGGCTCATGTA
35707377 ATTAAGCTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (22 bp):
ATAAAAAATTGGGCTCATGTAG
Found at i:35707654 original size:12 final size:12
Alignment explanation
Indices: 35707637--35707662 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
35707627 AAAGGCGATC
35707637 CCAAGTCCAAGA
1 CCAAGTCCAAGA
35707649 CCAAGTCCAAGA
1 CCAAGTCCAAGA
35707661 CC
1 CC
35707663 GGCGGTTCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.38, G:0.15, T:0.08
Consensus pattern (12 bp):
CCAAGTCCAAGA
Found at i:35715002 original size:5 final size:5
Alignment explanation
Indices: 35714992--35715017 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
35714982 ACTTTATGTC
35714992 AAATT AAATT AAATT AAATT AAATT A
1 AAATT AAATT AAATT AAATT AAATT A
35715018 GAGGCTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AAATT
Found at i:35715045 original size:6 final size:6
Alignment explanation
Indices: 35715034--35715058 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
35715024 AAAATTGCGT
35715034 GTTAGG GTTAGG GTTAGG GTTAGG G
1 GTTAGG GTTAGG GTTAGG GTTAGG G
35715059 GCATGGATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.52, T:0.32
Consensus pattern (6 bp):
GTTAGG
Found at i:35719537 original size:41 final size:42
Alignment explanation
Indices: 35719486--35719573 Score: 169
Period size: 41 Copynumber: 2.1 Consensus size: 42
35719476 ATGTCCCAAA
35719486 AAATTGCATATCAAGCATAATTCAAAACAATTAACGCGACTC
1 AAATTGCATATCAAGCATAATTCAAAACAATTAACGCGACTC
35719528 AAATT-CATATCAAGCATAATTCAAAACAATTAACGCGACTC
1 AAATTGCATATCAAGCATAATTCAAAACAATTAACGCGACTC
35719569 AAATT
1 AAATT
35719574 TAAGCTACAT
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 41 0.89
42 5 0.11
ACGTcount: A:0.47, C:0.20, G:0.08, T:0.25
Consensus pattern (42 bp):
AAATTGCATATCAAGCATAATTCAAAACAATTAACGCGACTC
Found at i:35727356 original size:8 final size:8
Alignment explanation
Indices: 35727343--35727367 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
35727333 TAGTATAGTG
35727343 GGGTATTT
1 GGGTATTT
35727351 GGGTATTT
1 GGGTATTT
35727359 GGGTATTT
1 GGGTATTT
35727367 G
1 G
35727368 AAAGGTGGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.40, T:0.48
Consensus pattern (8 bp):
GGGTATTT
Found at i:35728095 original size:12 final size:12
Alignment explanation
Indices: 35728055--35728096 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 12
35728045 GTGACTGGGA
35728055 AAAAAATTATAT
1 AAAAAATTATAT
35728067 AACAATATATT-TAT
1 AA-AA-A-ATTATAT
35728081 AAAAAATTATAT
1 AAAAAATTATAT
35728093 AAAA
1 AAAA
35728097 TTTAAATCAG
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
11 3 0.12
12 10 0.38
13 4 0.15
14 6 0.23
15 3 0.12
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAAAATTATAT
Found at i:35764575 original size:5 final size:5
Alignment explanation
Indices: 35764565--35764590 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
35764555 GAACAAATAT
35764565 ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG A
35764591 ATTCTATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (5 bp):
ATTCG
Found at i:35770325 original size:20 final size:19
Alignment explanation
Indices: 35770302--35770360 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 19
35770292 CAAATGCTCT
35770302 TTTGAACCGATTCATTTTTG
1 TTTGAACCGATTC-TTTTTG
** *
35770322 TTTGAATTGATTGTTTATTG
1 TTTGAACCGATTCTTT-TTG
35770342 TTTGAAGCCGATTCTTTTT
1 TTTGAA-CCGATTCTTTTT
35770361 TTATTAACTT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
19 3 0.10
20 21 0.68
21 7 0.23
ACGTcount: A:0.19, C:0.10, G:0.17, T:0.54
Consensus pattern (19 bp):
TTTGAACCGATTCTTTTTG
Found at i:35775522 original size:13 final size:13
Alignment explanation
Indices: 35775504--35775535 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
35775494 GGAGAATGAC
35775504 TTGACAAATCTTA
1 TTGACAAATCTTA
*
35775517 TTGACAGATCTTA
1 TTGACAAATCTTA
35775530 TTGACA
1 TTGACA
35775536 CAAAAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (13 bp):
TTGACAAATCTTA
Found at i:35782992 original size:20 final size:21
Alignment explanation
Indices: 35782956--35783000 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
35782946 TATAAAAATC
35782956 TAATTAGTACAAATTATAAAA
1 TAATTAGTACAAATTATAAAA
* *
35782977 TAATTAGTA-TAATTATAACA
1 TAATTAGTACAAATTATAAAA
35782997 TAAT
1 TAAT
35783001 AAAGTTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.38
Consensus pattern (21 bp):
TAATTAGTACAAATTATAAAA
Found at i:35784096 original size:26 final size:29
Alignment explanation
Indices: 35784061--35784114 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
35784051 ATCAAAATAA
35784061 ATTTAAA-TTT-CA-AATAATTAGAAAAT
1 ATTTAAATTTTACATAATAATTAGAAAAT
*
35784087 ATTTAAATTTTAGATAATAATTAGAAAA
1 ATTTAAATTTTACATAATAATTAGAAAA
35784115 CCCGCAAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 7 0.29
27 3 0.12
28 1 0.04
29 13 0.54
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.39
Consensus pattern (29 bp):
ATTTAAATTTTACATAATAATTAGAAAAT
Found at i:35785649 original size:21 final size:20
Alignment explanation
Indices: 35785611--35785651 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
35785601 TAATATTTCG
**
35785611 TTATTTTTCTCTTTATTTTA
1 TTATTTTTCTCTACATTTTA
35785631 TTATTTTTCTGCTACATTTTA
1 TTATTTTTCT-CTACATTTTA
35785652 ATTTCGTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.17, C:0.12, G:0.02, T:0.68
Consensus pattern (20 bp):
TTATTTTTCTCTACATTTTA
Found at i:35786400 original size:39 final size:38
Alignment explanation
Indices: 35786327--35786404 Score: 97
Period size: 39 Copynumber: 2.0 Consensus size: 38
35786317 ACCTTGTGGA
* *
35786327 TTAATTTAAAATTTGTTAATAATAAATATTATTAAATAT
1 TTAATTCAAAATTTGTTAATAATAAATATCATT-AATAT
35786366 TTAATTCAAATATTT-TTAATAATAAA-ATACATTAATAT
1 TTAATTCAAA-ATTTGTTAATAATAAATAT-CATTAATAT
35786404 T
1 T
35786405 ATTTTTATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
38 8 0.23
39 23 0.66
40 4 0.11
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (38 bp):
TTAATTCAAAATTTGTTAATAATAAATATCATTAATAT
Found at i:35792810 original size:2 final size:2
Alignment explanation
Indices: 35792803--35792839 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
35792793 ACTATTTTAT
35792803 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35792840 TTAAAAAGCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:35793801 original size:30 final size:28
Alignment explanation
Indices: 35793767--35793823 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
35793757 CAATTGATTT
35793767 TTAAAATAAAAAATAAAAAGATTAAATTCA
1 TTAAAAT-AAAAATAAAAA-ATTAAATTCA
* *
35793797 TTAAAATAAAAGTAGAAAATTAAATTC
1 TTAAAATAAAAATAAAAAATTAAATTC
35793824 TAAATGTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 9 0.36
29 9 0.36
30 7 0.28
ACGTcount: A:0.63, C:0.04, G:0.05, T:0.28
Consensus pattern (28 bp):
TTAAAATAAAAATAAAAAATTAAATTCA
Found at i:35798567 original size:21 final size:21
Alignment explanation
Indices: 35798543--35798591 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
35798533 AAAATCTTAA
35798543 ATTTTATTAAAAAAAATGAAT
1 ATTTTATTAAAAAAAATGAAT
* * * *
35798564 ATTTGATTTAAATATATGAAT
1 ATTTTATTAAAAAAAATGAAT
35798585 -TTTTATT
1 ATTTTATT
35798592 GCTATAAGTA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (21 bp):
ATTTTATTAAAAAAAATGAAT
Found at i:35801004 original size:17 final size:17
Alignment explanation
Indices: 35800984--35801016 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
35800974 AAAATTAAAA
35800984 TTAAAAATAAATATTTT
1 TTAAAAATAAATATTTT
*
35801001 TTAAAAATTAATATTT
1 TTAAAAATAAATATTT
35801017 ACTTTTATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTAAAAATAAATATTTT
Found at i:35824793 original size:20 final size:20
Alignment explanation
Indices: 35824768--35824820 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 20
35824758 ATTATAAATT
*
35824768 TAAAAATTAGAAATAATA-TA
1 TAAAAATTAGAAA-AAAACTA
35824788 TAAAAATT-GAAAAAAACTA
1 TAAAAATTAGAAAAAAACTA
*
35824807 GAAAAATTAGAAAA
1 TAAAAATTAGAAAA
35824821 GGTATTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 3 0.10
19 13 0.45
20 13 0.45
ACGTcount: A:0.68, C:0.02, G:0.08, T:0.23
Consensus pattern (20 bp):
TAAAAATTAGAAAAAAACTA
Found at i:35824922 original size:23 final size:23
Alignment explanation
Indices: 35824872--35824934 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
35824862 TTTAAATTCC
**
35824872 ATTTTAGAATTTTATAATTATAT
1 ATTTTAGAATTTTATAAAAATAT
35824895 ATTTTAGAATTTTATGAAAAATAT
1 ATTTTAGAATTTTAT-AAAAATAT
*
35824919 -TTTTAAACATTTTATA
1 ATTTTAGA-ATTTTATA
35824935 GTTTTTTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 22 0.63
24 13 0.37
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (23 bp):
ATTTTAGAATTTTATAAAAATAT
Found at i:35827790 original size:186 final size:185
Alignment explanation
Indices: 35827433--35827799 Score: 447
Period size: 186 Copynumber: 2.0 Consensus size: 185
35827423 TGGATTTAAA
* ** * * * *
35827433 GTATGTTTTTCTACTTGTCAATAGGTATTGATCTATCGTACCGACCATCGGATTGTCATTAGGAG
1 GTATGTTCTTCTACTCATCAATAGGTACTGATCTACCATACCAACCATCGGATTGTCATTAGGAG
* *
35827498 CTCGCTGACGAAATTTGAAAAAAAAACATAACACCCGAATGATTCCGTGATCAAATTGTAACGTT
66 CTCGCTGACGAAATTT-AAAAAAAAACATAACACCCGAATAATTCAGTGATCAAATTGTAACGTT
* * *
35827563 TTTTCATTAAATGATCAAAACGAAAATACTCATAGTTTAATGCCTAATGATCTAAG
130 TTTTCATTAAATGATCAAAACAAAAATACTCATAATTTAATGACTAATGATCTAAG
* * * *
35827619 GTATGTTCTTCTACTCATCAATATGTACTGATCTACCATATCAACCATCGGATTGTCCTTTGGAG
1 GTATGTTCTTCTACTCATCAATAGGTACTGATCTACCATACCAACCATCGGATTGTCATTAGGAG
* * * *
35827684 CTCGTTGGA-GAAATTT-TAAAAAAACGTAACATCCGAATAATTCAGTGATCAAATTGTAAC-TT
66 CTCGCT-GACGAAATTTAAAAAAAAACATAACACCCGAATAATTCAGTGATCAAATTGTAACGTT
*
35827746 TTTTTAGTTAAATGA-CTAAAACAAAAATTTAC-CTATAATTTAATGACTAATGAT
130 TTTTCA-TTAAATGATC-AAAACAAAAA--TACTC-ATAATTTAATGACTAATGAT
35827800 GTAATTTCTT
Statistics
Matches: 154, Mismatches: 21, Indels: 12
0.82 0.11 0.06
Matches are distributed among these distances:
183 8 0.05
184 56 0.36
185 1 0.01
186 87 0.56
187 2 0.01
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (185 bp):
GTATGTTCTTCTACTCATCAATAGGTACTGATCTACCATACCAACCATCGGATTGTCATTAGGAG
CTCGCTGACGAAATTTAAAAAAAAACATAACACCCGAATAATTCAGTGATCAAATTGTAACGTTT
TTTCATTAAATGATCAAAACAAAAATACTCATAATTTAATGACTAATGATCTAAG
Found at i:35829214 original size:2 final size:2
Alignment explanation
Indices: 35829207--35829231 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
35829197 AATGTGGAGA
35829207 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
35829232 AGTCATTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:35829762 original size:19 final size:19
Alignment explanation
Indices: 35829719--35829756 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
35829709 GAGAAAATTA
*
35829719 ACATTTTATCTATTATATT
1 ACATTTTATCTATTACATT
*
35829738 ACATTTTGTCTATTACATT
1 ACATTTTATCTATTACATT
35829757 TAATTTGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.29, C:0.13, G:0.03, T:0.55
Consensus pattern (19 bp):
ACATTTTATCTATTACATT
Found at i:35832089 original size:60 final size:59
Alignment explanation
Indices: 35832019--35832130 Score: 143
Period size: 60 Copynumber: 1.9 Consensus size: 59
35832009 TCAAATCGAA
* * *
35832019 CAAAAAAATTAACTATCAAATTAAAAAAAAAAGTCAAATTCAAGTACCAAATTGAATACT
1 CAAAAAAATTAAATACCAAATTAAAAAAAAAA-TAAAATTCAAGTACCAAATTGAATACT
* * * * *
35832079 CAAAAAAATTAAATACCAATTTAAGAAAAATATAAAATTTAAGTATCAAATT
1 CAAAAAAATTAAATACCAAATTAAAAAAAAAATAAAATTCAAGTACCAAATT
35832131 AAGAAAAAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
59 17 0.39
60 27 0.61
ACGTcount: A:0.59, C:0.11, G:0.04, T:0.26
Consensus pattern (59 bp):
CAAAAAAATTAAATACCAAATTAAAAAAAAAATAAAATTCAAGTACCAAATTGAATACT
Found at i:35832149 original size:32 final size:33
Alignment explanation
Indices: 35832104--35832179 Score: 95
Period size: 32 Copynumber: 2.4 Consensus size: 33
35832094 CCAATTTAAG
* *
35832104 AAAAATATAAAATTTA-AGTATCAAATT-AAGAA
1 AAAAATATTAAATTTAGA-TACCAAATTGAAGAA
*
35832136 AAAAATATTAAATTTAGATACCAAATTGAATAA
1 AAAAATATTAAATTTAGATACCAAATTGAAGAA
35832169 AAAAA-ATTAAA
1 AAAAATATTAAA
35832180 CATAAAATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
32 29 0.74
33 10 0.26
ACGTcount: A:0.63, C:0.04, G:0.05, T:0.28
Consensus pattern (33 bp):
AAAAATATTAAATTTAGATACCAAATTGAAGAA
Found at i:35832208 original size:90 final size:88
Alignment explanation
Indices: 35832022--35832200 Score: 204
Period size: 91 Copynumber: 2.0 Consensus size: 88
35832012 AATCGAACAA
* *
35832022 AAAAATTAACTATCAAATTAAAAAAAAAAGTCAAATTCAAGTACCAAATTGAATACTCAAAAAAA
1 AAAATTTAAGTATCAAATTAAAAAAAAAAGTCAAATTCAAGTACCAAATTGAATA--CAAAAAAA
* * *
35832087 TTAAATACCAATTTAAGAAAAATAT
64 TTAAACACAAAATTAAGAAAAATAT
* *
35832112 AAAATTTAAGTATCAAATTAAGAAAAAAATA-TTAAATT-TAGATACCAAATTGAATA-AAAAAA
1 AAAATTTAAGTATCAAATTAA-AAAAAAA-AGTCAAATTCAAG-TACCAAATTGAATACAAAAAA
*
35832174 ATTAAACATAAAATTAA-AAAATATAT
63 ATTAAACACAAAATTAAGAAAA-ATAT
35832200 A
1 A
35832201 TCAAATTTTA
Statistics
Matches: 77, Mismatches: 8, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
87 4 0.05
88 24 0.31
90 21 0.27
91 27 0.35
92 1 0.01
ACGTcount: A:0.61, C:0.08, G:0.04, T:0.26
Consensus pattern (88 bp):
AAAATTTAAGTATCAAATTAAAAAAAAAAGTCAAATTCAAGTACCAAATTGAATACAAAAAAATT
AAACACAAAATTAAGAAAAATAT
Found at i:35833088 original size:16 final size:16
Alignment explanation
Indices: 35833046--35833112 Score: 54
Period size: 16 Copynumber: 4.4 Consensus size: 16
35833036 ATATCATAAC
*
35833046 TTATAAATTCAAATTA
1 TTATATATTCAAATTA
* *
35833062 -AATATCTTTCAAATTA
1 TTATAT-ATTCAAATTA
*
35833078 TTATATATTCAAATGA
1 TTATATATTCAAATTA
35833094 TTA-ATA-T-AAATTA
1 TTATATATTCAAATTA
35833107 TT-TATA
1 TTATATA
35833113 AAATTTAATT
Statistics
Matches: 41, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
13 10 0.24
14 1 0.02
15 6 0.15
16 20 0.49
17 4 0.10
ACGTcount: A:0.46, C:0.06, G:0.01, T:0.46
Consensus pattern (16 bp):
TTATATATTCAAATTA
Found at i:35833137 original size:22 final size:23
Alignment explanation
Indices: 35833094--35833139 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
35833084 ATTCAAATGA
*
35833094 TTAATATAAATTATTTATAAAAT
1 TTAATATAAATTATATATAAAAT
*
35833117 TTAATTTAAA-TATATATAAAAT
1 TTAATATAAATTATATATAAAAT
35833139 T
1 T
35833140 ATTTAATCTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TTAATATAAATTATATATAAAAT
Found at i:35853672 original size:13 final size:13
Alignment explanation
Indices: 35853654--35853683 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
35853644 ATTCATTTAT
35853654 TAAAAAAATAAAA
1 TAAAAAAATAAAA
35853667 TAAAAAAATAAAA
1 TAAAAAAATAAAA
35853680 -AAAA
1 TAAAA
35853684 GTTTGAACGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (13 bp):
TAAAAAAATAAAA
Found at i:35855467 original size:31 final size:31
Alignment explanation
Indices: 35855429--35855495 Score: 134
Period size: 31 Copynumber: 2.2 Consensus size: 31
35855419 TTCCTACCCC
35855429 TAAATTTTATATATTAAAAAATAATTAAGAA
1 TAAATTTTATATATTAAAAAATAATTAAGAA
35855460 TAAATTTTATATATTAAAAAATAATTAAGAA
1 TAAATTTTATATATTAAAAAATAATTAAGAA
35855491 TAAAT
1 TAAAT
35855496 AAATGAATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (31 bp):
TAAATTTTATATATTAAAAAATAATTAAGAA
Found at i:35858561 original size:20 final size:20
Alignment explanation
Indices: 35858528--35858566 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
35858518 GAGGTTAATA
*
35858528 TTCCATATGATCATATATTC
1 TTCCATACGATCATATATTC
* *
35858548 TTCCATACGTTCATGTATT
1 TTCCATACGATCATATATT
35858567 TTGGAGGCAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.21, G:0.08, T:0.46
Consensus pattern (20 bp):
TTCCATACGATCATATATTC
Found at i:35863954 original size:223 final size:224
Alignment explanation
Indices: 35863560--35864017 Score: 787
Period size: 223 Copynumber: 2.0 Consensus size: 224
35863550 ATCCACCACA
* *
35863560 TCAGTTTCATTTCATCAAATCTTGCTAAATCACCTTTTGATCACGAAAGTAAATAACATCTTCCG
1 TCAGTGTCATTTCATCAAATATTGCTAAATCACCTTTTGATCACGAAAGTAAATAACATCTTCCG
* * *
35863625 ATCACCAATATATGCAATAATGATATGTATAATTAATCTAAAGAAACTAAAAGAAGTAATTGCAT
66 ATCACCAAAATATGCAATAATGATACGAATAATTAATCTAAAGAAACTAAAAGAAGTAATTGCAT
*
35863690 TATCATCTAAAAACCTATGAGAAACAAGCCCTTAATCATAAAACA-AGAATGAAGACATGCCTAG
131 TATCATCTAAAAACCAATGAGAAACAAGCCCTTAATCATAAAACAGAGAATGAAGACATGCCTAG
35863754 ATAAGAAGTAAGAGCCCACCGATTCCAAC
196 ATAAGAAGTAAGAGCCCACCGATTCCAAC
*
35863783 TCAGTGTCATTTCATCTAATATTGCTAAATCACCTTTTGATCACGAAAGTAAATAACATCGTT-C
1 TCAGTGTCATTTCATCAAATATTGCTAAATCACCTTTTGATCACGAAAGTAAATAACATC-TTCC
35863847 GATCACCAAAATATGCAATAATGATACGAATAATTAATCTAAAGAAA-TGAAAAGAAGTAATTGC
65 GATCACCAAAATATGCAATAATGATACGAATAATTAATCTAAAGAAACT-AAAAGAAGTAATTGC
* *
35863911 ATTATCGTCTACAAACCAATGAGAAACAAGCCCTTAATCATAAAACATGAGAATGAAGACATGCC
129 ATTATCATCTAAAAACCAATGAGAAACAAGCCCTTAATCATAAAACA-GAGAATGAAGACATGCC
35863976 TAGATAAGAAGTAAGAGCCCACCGATTCCAAC
193 TAGATAAGAAGTAAGAGCCCACCGATTCCAAC
35864008 TCAGTGTCAT
1 TCAGTGTCAT
35864018 CCTCTTCCCT
Statistics
Matches: 222, Mismatches: 9, Indels: 6
0.94 0.04 0.03
Matches are distributed among these distances:
222 1 0.00
223 161 0.73
224 2 0.01
225 58 0.26
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.26
Consensus pattern (224 bp):
TCAGTGTCATTTCATCAAATATTGCTAAATCACCTTTTGATCACGAAAGTAAATAACATCTTCCG
ATCACCAAAATATGCAATAATGATACGAATAATTAATCTAAAGAAACTAAAAGAAGTAATTGCAT
TATCATCTAAAAACCAATGAGAAACAAGCCCTTAATCATAAAACAGAGAATGAAGACATGCCTAG
ATAAGAAGTAAGAGCCCACCGATTCCAAC
Found at i:35870465 original size:18 final size:18
Alignment explanation
Indices: 35870425--35870467 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
35870415 GTTCAAGGTG
35870425 TAATTAATTTAAAATATT
1 TAATTAATTTAAAATATT
* *
35870443 CAATTAA-TTAAATTTATT
1 TAATTAATTTAAA-ATATT
35870461 TAATTAA
1 TAATTAA
35870468 AAAATATTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (18 bp):
TAATTAATTTAAAATATT
Found at i:35871075 original size:28 final size:29
Alignment explanation
Indices: 35871028--35871086 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 29
35871018 TTGAAGGGTT
* * * *
35871028 TTTTTTTGTTTTTAATTTTGCAAATGAAA
1 TTTTTTTGTTTTAAAGTTTGAAAAAGAAA
35871057 TTTTTTTG-TTTAAAGTTTGAAAAAGAAA
1 TTTTTTTGTTTTAAAGTTTGAAAAAGAAA
35871085 TT
1 TT
35871087 CATGTCATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 18 0.69
29 8 0.31
ACGTcount: A:0.32, C:0.02, G:0.12, T:0.54
Consensus pattern (29 bp):
TTTTTTTGTTTTAAAGTTTGAAAAAGAAA
Found at i:35879173 original size:29 final size:30
Alignment explanation
Indices: 35879123--35879179 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
35879113 AAAATTTATC
*
35879123 TGAAAAAATTTATAAAATTAAA-AAAAACT
1 TGAAAAAATTTATAAAAATAAATAAAAACT
35879152 TGAAAAAATTTA-AATAAATAAATAAAAA
1 TGAAAAAATTTATAA-AAATAAATAAAAA
35879180 TTGTAGCTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 2 0.08
29 18 0.72
30 5 0.20
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (30 bp):
TGAAAAAATTTATAAAAATAAATAAAAACT
Found at i:35894776 original size:3 final size:3
Alignment explanation
Indices: 35894768--35894797 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
35894758 GAAAAGATAA
35894768 AAG AAG AAG AAG AAG AAG AAG AAG AA- AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
35894798 GAGGAGGTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:35898160 original size:30 final size:30
Alignment explanation
Indices: 35898086--35898162 Score: 77
Period size: 29 Copynumber: 2.6 Consensus size: 30
35898076 AAAATTTTAA
* * * *
35898086 TTTAATAATTATAGAATTTTATTTTGATTC
1 TTTAATAATTATAAAAATTTAATTTAATTC
* *
35898116 ATTAA-AA-TATTAAAAATTTAATTTAATTT
1 TTTAATAATTA-TAAAAATTTAATTTAATTC
35898145 TTTAATAATTATAAAAAT
1 TTTAATAATTATAAAAAT
35898163 ATAAATTATT
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
28 2 0.05
29 20 0.54
30 13 0.35
31 2 0.05
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (30 bp):
TTTAATAATTATAAAAATTTAATTTAATTC
Found at i:35898171 original size:15 final size:17
Alignment explanation
Indices: 35898151--35898189 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
35898141 ATTTTTTAAT
35898151 AATTATAAAAAT-AT-A
1 AATTATAAAAATAATAA
*
35898166 AATTATTAAAATAATAA
1 AATTATAAAAATAATAA
35898183 AATTATA
1 AATTATA
35898190 TTTATTATCG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 11 0.55
16 2 0.10
17 7 0.35
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AATTATAAAAATAATAA
Found at i:35900332 original size:23 final size:23
Alignment explanation
Indices: 35900280--35900332 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
35900270 AAGGGGGCTG
* *
35900280 AAATT-AAATTATAATTTTTACA
1 AAATTAAAAATATAATTTTTAAA
***
35900302 ATCGTAAAAATATAATTTTTAAA
1 AAATTAAAAATATAATTTTTAAA
35900325 AAATTAAA
1 AAATTAAA
35900333 TTAAAATTTT
Statistics
Matches: 22, Mismatches: 8, Indels: 1
0.71 0.26 0.03
Matches are distributed among these distances:
22 2 0.09
23 20 0.91
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40
Consensus pattern (23 bp):
AAATTAAAAATATAATTTTTAAA
Found at i:35908098 original size:17 final size:18
Alignment explanation
Indices: 35908063--35908097 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
35908053 AGTTAAATTT
35908063 ATTATTATACCAATAAAA
1 ATTATTATACCAATAAAA
35908081 ATTA-TATA-CAATAAAA
1 ATTATTATACCAATAAAA
35908097 A
1 A
35908098 AATGAACTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 4 0.24
18 4 0.24
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.31
Consensus pattern (18 bp):
ATTATTATACCAATAAAA
Found at i:35908852 original size:31 final size:31
Alignment explanation
Indices: 35908817--35908885 Score: 120
Period size: 31 Copynumber: 2.2 Consensus size: 31
35908807 TTTTTAGGTG
*
35908817 TATTTTTATGCTATCATGTTTTAATTATTTT
1 TATTTTTATGCTATCACGTTTTAATTATTTT
*
35908848 TATTTTTATGTTATCACGTTTTAATTATTTT
1 TATTTTTATGCTATCACGTTTTAATTATTTT
35908879 TATTTTT
1 TATTTTT
35908886 CTATCTTGAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.22, C:0.06, G:0.06, T:0.67
Consensus pattern (31 bp):
TATTTTTATGCTATCACGTTTTAATTATTTT
Found at i:35917883 original size:2 final size:2
Alignment explanation
Indices: 35917876--35917900 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
35917866 TATTATAACA
35917876 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
35917901 ATTGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35918750 original size:245 final size:245
Alignment explanation
Indices: 35918320--35919207 Score: 1697
Period size: 245 Copynumber: 3.6 Consensus size: 245
35918310 AATATAGACT
* *
35918320 TAAAAATCAAAAGTCAAAATCACTTTCACTTTTTTTCATCACATCCCTATATTTTAACCTTTTTA
1 TAAAAATCAAAAGTCAAAACCACTTTCACTTTTTTTCATCACATCCCTATATCTTAACCTTTTTA
*
35918385 ATAATATTTTTACATTATGGTTAAAGATGAATTGATTGTTACATAACATATAATCACATCTTATC
66 ATAATATTTTTACATTATGGTTAAGGATGAATTGATTGTTACATAACATATAATCACATCTTATC
35918450 TTCTTAATAATATTTTTACATC-GGAAGTTAAACCCAATTTTCATTAAGAATAGGAAATTTGATA
131 TTCTTAATAATATTTTTACATCGGGAA-TTAAACCCAATTTTCATTAAGAATAGGAAATTTGATA
35918514 GAGATTTTCTTTCATAATATAGACTTATAGGAGATGAAAAATAAGAGAAAA
195 GAGATTTTCTTTCATAATATAGACTTATAGGAGATGAAAAATAAGAGAAAA
35918565 TAAAAATCAAAAGTCAAAACCACTTTCACTTTTTTTCATCACATCCCTATATCTTAACCTTTTTA
1 TAAAAATCAAAAGTCAAAACCACTTTCACTTTTTTTCATCACATCCCTATATCTTAACCTTTTTA
35918630 ATAATATTTTTACATTATGGTTAAGGATGAATTGATTGTTACATAACATATAATCACATCTTATC
66 ATAATATTTTTACATTATGGTTAAGGATGAATTGATTGTTACATAACATATAATCACATCTTATC
35918695 TTCTTAATAATATTTTTACATCGGGAATTAAACCCAATTTTCATTAAGAATAGGAAATTTGATAG
131 TTCTTAATAATATTTTTACATCGGGAATTAAACCCAATTTTCATTAAGAATAGGAAATTTGATAG
35918760 AGATTTTCTTTCATAATATAGACTTATAGGAGATGAAAAATAAGAGAAAA
196 AGATTTTCTTTCATAATATAGACTTATAGGAGATGAAAAATAAGAGAAAA
35918810 TAAAAATCAAAAGTCAAAACCACTTTCACTTTTTTTCATCACATCCCTATATCTTAACCTTTTTA
1 TAAAAATCAAAAGTCAAAACCACTTTCACTTTTTTTCATCACATCCCTATATCTTAACCTTTTTA
*
35918875 ATAATATTTTTACATTATGGTTAAGGATGAATTGATTGTTACATAATATATAATCACATCTTATC
66 ATAATATTTTTACATTATGGTTAAGGATGAATTGATTGTTACATAACATATAATCACATCTTATC
* *
35918940 TTCTTAATAATATTTTTACATCGGGAGTTAAACTCAATTTTCATTAAGAATAGGAAATTTGATAG
131 TTCTTAATAATATTTTTACATCGGGAATTAAACCCAATTTTCATTAAGAATAGGAAATTTGATAG
35919005 AGATTTTCTTTCATAATATAGACTTATAGGAGATGAAAAATAAGAGAAAA
196 AGATTTTCTTTCATAATATAGACTTATAGGAGATGAAAAATAAGAGAAAA
35919055 TAAAAATCAAAAGTCAAAACCACTTTCACTTTTTTTCATCACATCCCTATATCTTAACCTTTTTA
1 TAAAAATCAAAAGTCAAAACCACTTTCACTTTTTTTCATCACATCCCTATATCTTAACCTTTTTA
35919120 ATAATATTTTTACATTATGGTTAAGGATGAATTGATTGTTACATAACATATAATCACATCTTATC
66 ATAATATTTTTACATTATGGTTAAGGATGAATTGATTGTTACATAACATATAATCACATCTTATC
*
35919185 TTCTTAATAATATTTTTATATCG
131 TTCTTAATAATATTTTTACATCG
35919208 TAATTATTAC
Statistics
Matches: 634, Mismatches: 8, Indels: 2
0.98 0.01 0.00
Matches are distributed among these distances:
245 630 0.99
246 4 0.01
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.39
Consensus pattern (245 bp):
TAAAAATCAAAAGTCAAAACCACTTTCACTTTTTTTCATCACATCCCTATATCTTAACCTTTTTA
ATAATATTTTTACATTATGGTTAAGGATGAATTGATTGTTACATAACATATAATCACATCTTATC
TTCTTAATAATATTTTTACATCGGGAATTAAACCCAATTTTCATTAAGAATAGGAAATTTGATAG
AGATTTTCTTTCATAATATAGACTTATAGGAGATGAAAAATAAGAGAAAA
Found at i:35920063 original size:19 final size:20
Alignment explanation
Indices: 35920027--35920065 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
35920017 AAAATTATAT
* *
35920027 TAATTTAATAATATTATTAA
1 TAATTTAATAAAAATATTAA
35920047 TAATTT-ATAAAAATATTAA
1 TAATTTAATAAAAATATTAA
35920066 ATTAAAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TAATTTAATAAAAATATTAA
Found at i:35950171 original size:6 final size:6
Alignment explanation
Indices: 35950160--35950204 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
35950150 TTTGTGATCA
* * * *
35950160 AAATTG AAATTG AAAGTG AAAGTG AAAGTG AAATTG GAATTG AAA
1 AAATTG AAATTG AAATTG AAATTG AAATTG AAATTG AAATTG AAA
35950205 GTGATAAGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.24, T:0.24
Consensus pattern (6 bp):
AAATTG
Found at i:35966438 original size:24 final size:22
Alignment explanation
Indices: 35966411--35966465 Score: 56
Period size: 24 Copynumber: 2.4 Consensus size: 22
35966401 TTTGGATTTT
35966411 TTTTAAAAATAATTTTATTATAAA
1 TTTTAAAAATAATTTTA-TAT-AA
* * *
35966435 TTTTGATAATTATTTTATATAA
1 TTTTAAAAATAATTTTATATAA
35966457 TATTTAAAA
1 T-TTTAAAA
35966466 TTATTTATAG
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
22 3 0.12
23 8 0.32
24 14 0.56
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
TTTTAAAAATAATTTTATATAA
Found at i:35969825 original size:29 final size:28
Alignment explanation
Indices: 35969793--35969852 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 28
35969783 AAATAGATAT
35969793 ACTAAATTTTTAAA-AATAAAAATATAAAA
1 ACTAAA-TTTTAAATAA-AAAAATATAAAA
35969822 ACTAAATTTTAAATTCAAAAAAATATAAAA
1 ACTAAATTTTAAA-T-AAAAAAATATAAAA
35969852 A
1 A
35969853 ATATGACATA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
28 7 0.25
29 6 0.21
30 13 0.46
31 2 0.07
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (28 bp):
ACTAAATTTTAAATAAAAAAATATAAAA
Found at i:35974441 original size:30 final size:30
Alignment explanation
Indices: 35974397--35974455 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
35974387 TCGAGCTTCT
*
35974397 TCCAACCGCCCTGCTTTTCTCGGTAAGTTC
1 TCCAACAGCCCTGCTTTTCTCGGTAAGTTC
* *
35974427 TCCAACAGCTCTGCTTTTCTCGTTAAGTT
1 TCCAACAGCCCTGCTTTTCTCGGTAAGTT
35974456 TTTCCCTTCG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.15, C:0.32, G:0.15, T:0.37
Consensus pattern (30 bp):
TCCAACAGCCCTGCTTTTCTCGGTAAGTTC
Found at i:35979621 original size:30 final size:31
Alignment explanation
Indices: 35979561--35979629 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
35979551 TATTATATTT
* * * *
35979561 AATAAATTTAAAAATATATATAATATATT-A
1 AATATATTTAAAAATATATAAAAAAAATTAA
35979591 AATATATTTAAAAATAT-TAAAAAAAAATTAA
1 AATATATTTAAAAATATAT-AAAAAAAATTAA
35979622 AATATATT
1 AATATATT
35979630 AAATTTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 1 0.03
30 23 0.70
31 9 0.27
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (31 bp):
AATATATTTAAAAATATATAAAAAAAATTAA
Found at i:35979738 original size:11 final size:11
Alignment explanation
Indices: 35979657--35979738 Score: 62
Period size: 11 Copynumber: 7.6 Consensus size: 11
35979647 AACAGCTGTA
35979657 AATAAAATAAT
1 AATAAAATAAT
*
35979668 AA-AAAATAAC
1 AATAAAATAAT
*
35979678 AATAAAA-CAT
1 AATAAAATAAT
***
35979688 AAATTCTATAAT
1 -AATAAAATAAT
* *
35979700 ATTTAAATAAT
1 AATAAAATAAT
*
35979711 ATTAAAA-AAT
1 AATAAAATAAT
35979721 AATAAAATAAT
1 AATAAAATAAT
35979732 AATAAAA
1 AATAAAA
35979739 AGACAAAAAA
Statistics
Matches: 55, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
10 19 0.35
11 34 0.62
12 2 0.04
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:35979748 original size:21 final size:21
Alignment explanation
Indices: 35979704--35979753 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
35979694 TATAATATTT
* *
35979704 AAATAATATTAAAAAATAATA
1 AAATAATAATAAAAAACAATA
35979725 AAATAATAATAAAAAGACAA-A
1 AAATAATAATAAAAA-ACAATA
35979746 AAA-AATAA
1 AAATAATAA
35979754 CACTTAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 5 0.19
21 18 0.69
22 3 0.12
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (21 bp):
AAATAATAATAAAAAACAATA
Found at i:35979805 original size:12 final size:12
Alignment explanation
Indices: 35979760--35979844 Score: 57
Period size: 12 Copynumber: 7.2 Consensus size: 12
35979750 ATAACACTTA
*
35979760 AATAACAAAAAC
1 AATAACAAAAAT
*
35979772 AACAATC-AAAAT
1 AATAA-CAAAAAT
* *
35979784 AAAAATAAAAAT
1 AATAACAAAAAT
* *
35979796 AATAGC-AAAAC
1 AATAACAAAAAT
*
35979807 AACAACAAAAAT
1 AATAACAAAAAT
* **
35979819 AGTAGTAAAAAT
1 AATAACAAAAAT
35979831 AATAACAAAAAT
1 AATAACAAAAAT
35979843 AA
1 AA
35979845 CAATATCAAA
Statistics
Matches: 52, Mismatches: 18, Indels: 6
0.68 0.24 0.08
Matches are distributed among these distances:
11 8 0.15
12 43 0.83
13 1 0.02
ACGTcount: A:0.72, C:0.11, G:0.04, T:0.14
Consensus pattern (12 bp):
AATAACAAAAAT
Found at i:35979818 original size:35 final size:35
Alignment explanation
Indices: 35979760--35979840 Score: 101
Period size: 35 Copynumber: 2.3 Consensus size: 35
35979750 ATAACACTTA
35979760 AATAACAAAAACAACAATCAAAATAAAAATAAAAAT
1 AATAAC-AAAACAACAATCAAAATAAAAATAAAAAT
* ** *
35979796 AATAGCAAAACAACAA-CAAAAATAGTAGTAAAAAT
1 AATAACAAAACAACAATC-AAAATAAAAATAAAAAT
35979831 AATAACAAAA
1 AATAACAAAA
35979841 ATAACAATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
34 1 0.03
35 33 0.85
36 5 0.13
ACGTcount: A:0.72, C:0.11, G:0.04, T:0.14
Consensus pattern (35 bp):
AATAACAAAACAACAATCAAAATAAAAATAAAAAT
Found at i:35979875 original size:21 final size:20
Alignment explanation
Indices: 35979849--35979905 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
35979839 AAATAACAAT
*
35979849 ATCAAAATAGTAAAAAATAAC
1 ATCAAAATAGCAAAAAA-AAC
*
35979870 ATCAAAATAGCAAACAAAAC
1 ATCAAAATAGCAAAAAAAAC
* *
35979890 AGCAAAAAAGCAAAAA
1 ATCAAAATAGCAAAAA
35979906 CAGTAAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
20 16 0.52
21 15 0.48
ACGTcount: A:0.68, C:0.14, G:0.07, T:0.11
Consensus pattern (20 bp):
ATCAAAATAGCAAAAAAAAC
Found at i:35981288 original size:17 final size:18
Alignment explanation
Indices: 35981253--35981290 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
35981243 AAACATAAAA
35981253 TTAAAATTTTATAAATAT
1 TTAAAATTTTATAAATAT
*
35981271 TTAAAATTTTA-CAATAT
1 TTAAAATTTTATAAATAT
35981288 TTA
1 TTA
35981291 TCATCAAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
TTAAAATTTTATAAATAT
Found at i:35982814 original size:3 final size:3
Alignment explanation
Indices: 35982808--35982840 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
35982798 ATGATGGGAG
35982808 TTA TTA TTA TTA TTA TTA TTA TT- TT- TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
35982841 TGGTTATAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 4 0.14
3 25 0.86
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (3 bp):
TTA
Found at i:35990864 original size:90 final size:89
Alignment explanation
Indices: 35990575--35990852 Score: 412
Period size: 90 Copynumber: 3.1 Consensus size: 89
35990565 ACTATTTGAA
**
35990575 CGTCGCCGTCTTCTCCAAGACGAAGATAAACTTCCGGTTGTCGGCCATTCCGATTGGACTTCCTT
1 CGTCGCCGTCTTCTCCAAGACGAAGATGGACTTCCGGTTGTCGGCCATTCCGATTGGAC-TCCTT
* *
35990640 TTTAGAAAGAACCAAGGAATGGAAT
65 TTTAGAACGAAACAAGGAATGGAAT
* *
35990665 CGTCGTCGTCTTCTCCAAGACGAAGATGGACTTCCAGTTGTCGGCCATTCCGATTGGACTGCCTT
1 CGTCGCCGTCTTCTCCAAGACGAAGATGGACTTCCGGTTGTCGGCCATTCCGATTGGACT-CCTT
*
35990730 TTTAGAACGAAACACGGAATGGAAT
65 TTTAGAACGAAACAAGGAATGGAAT
* ** *
35990755 CGTCGCCGTCTTCTCCAAGATGAAGATGGACTTCCGGTTGTCGGCCACGCTGATTGGACATCCTT
1 CGTCGCCGTCTTCTCCAAGACGAAGATGGACTTCCGGTTGTCGGCCATTCCGATTGGAC-TCCTT
*
35990820 TTTAGAACGAAACAAGGAATGGAAC
65 TTTAGAACGAAACAAGGAATGGAAT
*
35990845 CGCCGCCG
1 CGTCGCCG
35990853 AATGCTCCAA
Statistics
Matches: 170, Mismatches: 16, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
89 1 0.01
90 168 0.99
91 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (89 bp):
CGTCGCCGTCTTCTCCAAGACGAAGATGGACTTCCGGTTGTCGGCCATTCCGATTGGACTCCTTT
TTAGAACGAAACAAGGAATGGAAT
Found at i:35992061 original size:51 final size:51
Alignment explanation
Indices: 35991979--35992456 Score: 627
Period size: 51 Copynumber: 9.4 Consensus size: 51
35991969 GAGTCCCTTA
* * * ** * *
35991979 CTCCCCAGATCTTTCCGTTGGTAAAGTTGAAAATAATGGATTGACCCCTAC
1 CTCCCCAGATCTTTCCGCTAGCAAACCTGAAAACAATGGGTTGACCCCTAC
* **
35992030 CTCCCCAGATCTTTTCC-CTAGCAAACCTGAAAATAATGGGTTGACCCCTTT
1 CTCCCCAGATC-TTTCCGCTAGCAAACCTGAAAACAATGGGTTGACCCCTAC
*
35992081 CTCCCCAGATCTTTCCGCTAGCAAACCTGAAAACAATGGGTTGACCCCTGC
1 CTCCCCAGATCTTTCCGCTAGCAAACCTGAAAACAATGGGTTGACCCCTAC
* *
35992132 CTCCCCAGATCTTTCCGCTAGCAAACATGAAAACAATGGGTTAACCCCTGA-
1 CTCCCCAGATCTTTCCGCTAGCAAACCTGAAAACAATGGGTTGACCCCT-AC
*
35992183 CTCCCCAGATCTTTCCGCTAGCAAACCTGAAAACAATGGATTGACCCCTAC
1 CTCCCCAGATCTTTCCGCTAGCAAACCTGAAAACAATGGGTTGACCCCTAC
* * *
35992234 CTCCTCAGATCTTTCCGCTGGCAAACCTGAAAACAATGGGTTGATCCCTAC
1 CTCCCCAGATCTTTCCGCTAGCAAACCTGAAAACAATGGGTTGACCCCTAC
* * * *
35992285 TTCCCCAGATCTTTACTCTAGCAAACCTGAAAACAATGGGTTGATCCCTAC
1 CTCCCCAGATCTTTCCGCTAGCAAACCTGAAAACAATGGGTTGACCCCTAC
* * * * * * *
35992336 TTCTCCAGATCTTTCCGCTAGTAAACCTGAAAATAATGGTTTGACTCCTAT
1 CTCCCCAGATCTTTCCGCTAGCAAACCTGAAAACAATGGGTTGACCCCTAC
* * * *
35992387 CTCCCCAGATCTTTCCACTAGCAAACCTGAAAACAATGGATTAACCCCTAT
1 CTCCCCAGATCTTTCCGCTAGCAAACCTGAAAACAATGGGTTGACCCCTAC
*
35992438 CTCTCCAGATCTTTCCGCT
1 CTCCCCAGATCTTTCCGCT
35992457 GGTAACACTG
Statistics
Matches: 378, Mismatches: 45, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
50 6 0.02
51 367 0.97
52 5 0.01
ACGTcount: A:0.28, C:0.31, G:0.15, T:0.27
Consensus pattern (51 bp):
CTCCCCAGATCTTTCCGCTAGCAAACCTGAAAACAATGGGTTGACCCCTAC
Found at i:35993348 original size:14 final size:15
Alignment explanation
Indices: 35993319--35993352 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
35993309 GTAATTTATT
35993319 TTTTAATTTGTTTTA
1 TTTTAATTTGTTTTA
*
35993334 TTTTGATTT-TTTTA
1 TTTTAATTTGTTTTA
35993348 TTTTA
1 TTTTA
35993353 GTGGAAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (15 bp):
TTTTAATTTGTTTTA
Found at i:35993614 original size:48 final size:49
Alignment explanation
Indices: 35993510--35993621 Score: 138
Period size: 47 Copynumber: 2.3 Consensus size: 49
35993500 CATAAGAAAA
*
35993510 TATTATCATATATTTTTGTTTCAGTTAATATCATTATTAAGTTATTAATAT
1 TATTAT-ATATATTGTTGTTT-AGTTAATATCATTATTAAGTTATTAATAT
* * *
35993561 TATTATATATATTGTT-TTT-GTTAATATTATTATTAAGTTGTTAGTAAT
1 TATTATATATATTGTTGTTTAGTTAATATCATTATTAAGTTATTAAT-AT
*
35993609 TATTATACATATT
1 TATTATATATATT
35993622 TTATAAATTT
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
47 23 0.42
48 14 0.25
49 3 0.05
50 9 0.16
51 6 0.11
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.56
Consensus pattern (49 bp):
TATTATATATATTGTTGTTTAGTTAATATCATTATTAAGTTATTAATAT
Found at i:35997185 original size:16 final size:17
Alignment explanation
Indices: 35997166--35997207 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
35997156 TTTTTTTCTA
**
35997166 GTTTTTATTTGTTG-AT
1 GTTTTTATTTGCGGTAT
35997182 GTTTTT-TTTGCGGTAT
1 GTTTTTATTTGCGGTAT
35997198 GTTTTTATTT
1 GTTTTTATTT
35997208 TGCCTTATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 5 0.23
16 14 0.64
17 3 0.14
ACGTcount: A:0.10, C:0.02, G:0.19, T:0.69
Consensus pattern (17 bp):
GTTTTTATTTGCGGTAT
Found at i:35997243 original size:17 final size:18
Alignment explanation
Indices: 35997205--35997244 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
35997195 TATGTTTTTA
*
35997205 TTTTGCCTTATGACACGT
1 TTTTGCCTTATAACACGT
35997223 TTTTGCCTTATAACACGT
1 TTTTGCCTTATAACACGT
35997241 TTTT
1 TTTT
35997245 ATCTATCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.17, C:0.20, G:0.12, T:0.50
Consensus pattern (18 bp):
TTTTGCCTTATAACACGT
Found at i:35998110 original size:20 final size:21
Alignment explanation
Indices: 35998072--35998111 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
35998062 AAAAATATAT
*
35998072 AAAATTGATTGATGAATTAAA
1 AAAATTGATTAATGAATTAAA
*
35998093 AAAATTG-TTAATGGATTAA
1 AAAATTGATTAATGAATTAA
35998112 TTTTCCATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (21 bp):
AAAATTGATTAATGAATTAAA
Found at i:36004334 original size:31 final size:30
Alignment explanation
Indices: 36004282--36004341 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
36004272 ATAAATGTGA
36004282 AATTTATATATAAATTATGATTTAATGTAC
1 AATTTATATATAAATTATGATTTAATGTAC
* * *
36004312 AATTTGATATATGAATTTTGATTTAGTGTA
1 AATTT-ATATATAAATTATGATTTAATGTA
36004342 ATTGTAAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 5 0.19
31 21 0.81
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (30 bp):
AATTTATATATAAATTATGATTTAATGTAC
Found at i:36013671 original size:26 final size:25
Alignment explanation
Indices: 36013642--36013717 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 25
36013632 TAATATGATT
36013642 ATATAAAAAATTTTAATAAATAAAAA
1 ATATAAAAAATTTTAA-AAATAAAAA
* *
36013668 ATATATAAAATTATTAAATATTAAAATA
1 ATATAAAAAATT-TTAAA-AATAAAA-A
36013696 ATATAATATAAATATTTAAAAA
1 ATATAA-A-AAAT-TTTAAAAA
36013718 AAATAAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
26 12 0.30
27 10 0.25
28 6 0.15
29 2 0.05
30 9 0.22
31 1 0.03
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (25 bp):
ATATAAAAAATTTTAAAAATAAAAA
Found at i:36013723 original size:22 final size:21
Alignment explanation
Indices: 36013672--36013723 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
36013662 TAAAAAATAT
*
36013672 ATAAAATTATTAAATATTAAA
1 ATAAAATAATTAAATATTAAA
*
36013693 ATAATATAATATAAATATTTAAA
1 ATAAAATAAT-TAAATA-TTAAA
36013716 A-AAAATAA
1 ATAAAATAA
36013724 AAAATAACAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 8 0.31
22 12 0.46
23 6 0.23
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
ATAAAATAATTAAATATTAAA
Found at i:36013837 original size:16 final size:16
Alignment explanation
Indices: 36013816--36013856 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
36013806 ATGCTTAAAT
36013816 CTGACCCAAATCAAGC
1 CTGACCCAAATCAAGC
*
36013832 CTGACCCAAATCTAGC
1 CTGACCCAAATCAAGC
*
36013848 CTAACCCAA
1 CTGACCCAA
36013857 CCCATGATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.37, C:0.39, G:0.10, T:0.15
Consensus pattern (16 bp):
CTGACCCAAATCAAGC
Found at i:36018533 original size:2 final size:2
Alignment explanation
Indices: 36018526--36018564 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
36018516 GATTTATTCC
36018526 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
36018565 GCATTAACTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:36023066 original size:4 final size:4
Alignment explanation
Indices: 36023055--36023083 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
36023045 AAAAACAAAC
36023055 AAAT -AAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
36023084 GAACAAAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:36025903 original size:20 final size:20
Alignment explanation
Indices: 36025880--36025922 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
36025870 ATTTTTGTTT
36025880 TTAAGAAT-TTAAAATATATG
1 TTAAGAATGTTAAAATAT-TG
* *
36025900 TTAATATTGTTAAAATATTG
1 TTAAGAATGTTAAAATATTG
36025920 TTA
1 TTA
36025923 TTAAATAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (20 bp):
TTAAGAATGTTAAAATATTG
Found at i:36029557 original size:17 final size:17
Alignment explanation
Indices: 36029535--36029569 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
36029525 TTTTGTCTCT
36029535 TTTTTTTATTAAATTAA
1 TTTTTTTATTAAATTAA
36029552 TTTTTTTATTAAATTAA
1 TTTTTTTATTAAATTAA
36029569 T
1 T
36029570 AGTTAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTTTTATTAAATTAA
Found at i:36037312 original size:15 final size:15
Alignment explanation
Indices: 36037294--36037332 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
36037284 ATTCAATAAA
36037294 AAATATAAAATTATT
1 AAATATAAAATTATT
*
36037309 AAATATTAAA-TATT
1 AAATATAAAATTATT
36037323 AAA-ATAAAAT
1 AAATATAAAAT
36037333 AAAATAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
13 5 0.24
14 7 0.33
15 9 0.43
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
AAATATAAAATTATT
Done.