Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168470.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_7, whole genome shotgun sequence
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: 26282861
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 74000 characters in sequence are not A, C, G, or T
File 63 of 133
Found at i:12802728 original size:32 final size:31
Alignment explanation
Indices: 12802693--12802995 Score: 154
Period size: 32 Copynumber: 9.6 Consensus size: 31
12802683 GCAGGCACTC
* *
12802693 AAATTTAAGCCAGTTTAGTTGGCACCTAATGC
1 AAATTTAAGCCAGTTTAGCTGGCACC-AATGA
* * *
12802725 AAATTTAACCCTAGATTAACTGGCACCCAA-G-
1 AAATTTAAGCC-AGTTTAGCTGGCA-CCAATGA
* * * * *
12802756 --TTTTAAACCTAGTTTAGCTAGCACCCATAA
1 AAATTTAAGCC-AGTTTAGCTGGCACCAATGA
** * *
12802786 AAATTTAAGCCTAGTTTAATTGGTACCTATGA
1 AAATTTAAGCC-AGTTTAGCTGGCACCAATGA
* **
12802818 AAATTTAAGCTCAATTTAGCCAGCACCAAT-A
1 AAATTTAAGC-CAGTTTAGCTGGCACCAATGA
* * * *
12802849 CAAAGTTAAGCCTAGGTTAGCTAGCACAAAT-A
1 -AAATTTAAGCC-AGTTTAGCTGGCACCAATGA
* *
12802881 AAATTTAAGCTCAGTTTAGCTGACA-CTATGA
1 AAATTTAAGC-CAGTTTAGCTGGCACCAATGA
* *
12802912 AAATTTAAGCTTAGTTTAGTTGGCACCAATGA
1 AAATTTAAGC-CAGTTTAGCTGGCACCAATGA
** **
12802944 AAATTTAAAATCAGTTTAATTGGCACCCAAT-A
1 AAATTT-AAGCCAGTTTAGCTGGCA-CCAATGA
*
12802976 AAATTTTAAGTCTAGTTTAG
1 AAA-TTTAAG-CCAGTTTAG
12802996 TTAGCATACA
Statistics
Matches: 206, Mismatches: 49, Indels: 31
0.72 0.17 0.11
Matches are distributed among these distances:
28 3 0.01
29 18 0.09
30 2 0.01
31 44 0.21
32 108 0.52
33 29 0.14
34 2 0.01
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (31 bp):
AAATTTAAGCCAGTTTAGCTGGCACCAATGA
Found at i:12805359 original size:3 final size:3
Alignment explanation
Indices: 12805345--12805400 Score: 69
Period size: 3 Copynumber: 18.7 Consensus size: 3
12805335 TAAAAATGAA
* * *
12805345 AAT AAT AA- AAT AAT AAAT AAT AAT AAT AGT AAT AGT AAT AGT AAT
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
12805390 AAT AAT AAT AA
1 AAT AAT AAT AA
12805401 ATAAATAAAC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
2 2 0.04
3 40 0.89
4 3 0.07
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:12805418 original size:13 final size:13
Alignment explanation
Indices: 12805398--12805422 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12805388 ATAATAATAA
12805398 TAAATAAATAAAC
1 TAAATAAATAAAC
12805411 TAAATAAATAAA
1 TAAATAAATAAA
12805423 AGATTTTTTA
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:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAATAAATAAAC
Found at i:12805755 original size:13 final size:13
Alignment explanation
Indices: 12805739--12805778 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
12805729 TAAAACTTCG
12805739 AAATGAAACCTTA
1 AAATGAAACCTTA
*
12805752 AAATGAAACC-GA
1 AAATGAAACCTTA
*
12805764 AAATAAAACCTTA
1 AAATGAAACCTTA
12805777 AA
1 AA
12805779 CTAGAATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.60, C:0.15, G:0.07, T:0.17
Consensus pattern (13 bp):
AAATGAAACCTTA
Found at i:12807613 original size:20 final size:19
Alignment explanation
Indices: 12807588--12807631 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
12807578 TAGGGTAAGT
*
12807588 AAACCCAAAAACCTTAGGTG
1 AAACCCAAAAACC-TAGGAG
* *
12807608 AAACCCTAAATCCTAGGAG
1 AAACCCAAAAACCTAGGAG
12807627 AAACC
1 AAACC
12807632 TTAAACCCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.45, C:0.27, G:0.14, T:0.14
Consensus pattern (19 bp):
AAACCCAAAAACCTAGGAG
Found at i:12807629 original size:19 final size:19
Alignment explanation
Indices: 12807588--12807655 Score: 57
Period size: 19 Copynumber: 3.6 Consensus size: 19
12807578 TAGGGTAAGT
* *
12807588 AAACCCAAAAACCTTAGGTG
1 AAACCCTAAAACC-TAGGAG
*
12807608 AAACCCTAAATCCTAGGAG
1 AAACCCTAAAACCTAGGAG
* * *
12807627 AAACCTTAAACCCTA-GAT
1 AAACCCTAAAACCTAGGAG
*
12807645 AAAACCTAAAA
1 AAACCCTAAAA
12807656 GCTCTAAGTG
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
18 10 0.26
19 18 0.46
20 11 0.28
ACGTcount: A:0.49, C:0.25, G:0.10, T:0.16
Consensus pattern (19 bp):
AAACCCTAAAACCTAGGAG
Found at i:12807684 original size:19 final size:19
Alignment explanation
Indices: 12807659--12807724 Score: 73
Period size: 19 Copynumber: 3.5 Consensus size: 19
12807649 CCTAAAAGCT
12807659 CTAAGTGAAATCCTAAACC
1 CTAAGTGAAATCCTAAACC
*
12807678 TTAAGTG-AA-CCTGAAACC
1 CTAAGTGAAATCCT-AAACC
* *
12807696 CTAGGTGAAATCCTAAACT
1 CTAAGTGAAATCCTAAACC
*
12807715 CTAAGCGAAA
1 CTAAGTGAAA
12807725 CCCCAAAGCT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
17 3 0.08
18 12 0.32
19 20 0.53
20 3 0.08
ACGTcount: A:0.41, C:0.23, G:0.15, T:0.21
Consensus pattern (19 bp):
CTAAGTGAAATCCTAAACC
Found at i:12807762 original size:20 final size:21
Alignment explanation
Indices: 12807739--12807792 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
12807729 AAAGCTTTAG
12807739 TTGAAACCCTAAATTAAA-CC
1 TTGAAACCCTAAATTAAAGCC
*
12807759 TTGAAACCCCAAA-TAAAGCC
1 TTGAAACCCTAAATTAAAGCC
* *
12807779 TTAAAACCTTAAAT
1 TTGAAACCCTAAAT
12807793 CCACTTAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 4 0.14
20 24 0.86
ACGTcount: A:0.46, C:0.24, G:0.06, T:0.24
Consensus pattern (21 bp):
TTGAAACCCTAAATTAAAGCC
Found at i:12815794 original size:22 final size:21
Alignment explanation
Indices: 12815743--12815804 Score: 58
Period size: 22 Copynumber: 3.0 Consensus size: 21
12815733 ATTTTTAATG
12815743 TTAAATATTAATTTT---ATA
1 TTAAATATTAATTTTAAAATA
* *
12815761 TTTAATTTTAATTTTAAAATA
1 TTAAATATTAATTTTAAAATA
* *
12815782 TTGAAATATTAATATAAAAATA
1 TT-AAATATTAATTTTAAAATA
12815804 T
1 T
12815805 ATTTTTAACA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
18 13 0.38
21 5 0.15
22 16 0.47
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
TTAAATATTAATTTTAAAATA
Found at i:12824809 original size:42 final size:42
Alignment explanation
Indices: 12824762--12824845 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
12824752 AGCAGGCACA
*
12824762 GTTATAGAGTAGAAACAAGTATGCGAGTAATCATTTAGGAAT
1 GTTATAGAGTAGAAACAAGTATGCAAGTAATCATTTAGGAAT
12824804 GTTATAGAGTAGAAACAAGTATGCAAGTAATCATTTAGGAAT
1 GTTATAGAGTAGAAACAAGTATGCAAGTAATCATTTAGGAAT
12824846 CATTATTACA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.42, C:0.07, G:0.23, T:0.29
Consensus pattern (42 bp):
GTTATAGAGTAGAAACAAGTATGCAAGTAATCATTTAGGAAT
Found at i:12827698 original size:16 final size:17
Alignment explanation
Indices: 12827677--12827713 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
12827667 CCAATACCTT
12827677 AACTAAAGAAA-TAAAG
1 AACTAAAGAAACTAAAG
*
12827693 AACTAAAGAAACTAGAG
1 AACTAAAGAAACTAAAG
12827710 AACT
1 AACT
12827714 TAAAAAAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.62, C:0.11, G:0.14, T:0.14
Consensus pattern (17 bp):
AACTAAAGAAACTAAAG
Found at i:12841121 original size:33 final size:33
Alignment explanation
Indices: 12841075--12841151 Score: 93
Period size: 33 Copynumber: 2.4 Consensus size: 33
12841065 AAAGTACTAT
* **
12841075 TGCAT-AAAGAAATCATGGCGATGCAAAAAGCA
1 TGCATGAAACAAATCATGAAGATGCAAAAAGCA
*
12841107 TGCATGAAACAAATCATGAAGATGCATAAAGCA
1 TGCATGAAACAAATCATGAAGATGCAAAAAGCA
**
12841140 TAAATGAAACAA
1 TGCATGAAACAA
12841152 TAGAGAAGGT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
32 5 0.13
33 33 0.87
ACGTcount: A:0.51, C:0.14, G:0.18, T:0.17
Consensus pattern (33 bp):
TGCATGAAACAAATCATGAAGATGCAAAAAGCA
Found at i:12860164 original size:18 final size:18
Alignment explanation
Indices: 12860137--12860183 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
12860127 GGGTTTGCAT
* *
12860137 GATTTGGGGTTGTGG-TTG
1 GATTTAGGGTT-TGGATTA
12860155 GATTTAGGGTTTGGATTA
1 GATTTAGGGTTTGGATTA
12860173 GATTTAGGGTT
1 GATTTAGGGTT
12860184 ATAAGCTAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 3 0.12
18 23 0.88
ACGTcount: A:0.15, C:0.00, G:0.40, T:0.45
Consensus pattern (18 bp):
GATTTAGGGTTTGGATTA
Found at i:12860203 original size:37 final size:33
Alignment explanation
Indices: 12860157--12860241 Score: 95
Period size: 30 Copynumber: 2.5 Consensus size: 33
12860147 TGTGGTTGGA
12860157 TTTAGGGTTTGGATTAGATTTAGGGTTATAAGCTAGG
1 TTTAGGGTTTGGATT---TTTAGGGTT-TAAGCTAGG
*
12860194 TTTAGGGTTT-G--TTTTAGGGTTTAAGCTTGG
1 TTTAGGGTTTGGATTTTTAGGGTTTAAGCTAGG
12860224 TTTAGGGTTTAGGATTTT
1 TTTAGGGTTT-GGATTTT
12860242 GGTTTTAGGG
Statistics
Matches: 43, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
30 18 0.42
31 9 0.21
32 1 0.02
34 4 0.09
36 1 0.02
37 10 0.23
ACGTcount: A:0.19, C:0.02, G:0.32, T:0.47
Consensus pattern (33 bp):
TTTAGGGTTTGGATTTTTAGGGTTTAAGCTAGG
Found at i:12860219 original size:30 final size:31
Alignment explanation
Indices: 12860175--12860233 Score: 102
Period size: 30 Copynumber: 1.9 Consensus size: 31
12860165 TTGGATTAGA
12860175 TTTAGGGTTATAAGCTAGGTTTAGGGTTTGT
1 TTTAGGGTTATAAGCTAGGTTTAGGGTTTGT
*
12860206 TTTAGGGTT-TAAGCTTGGTTTAGGGTTT
1 TTTAGGGTTATAAGCTAGGTTTAGGGTTT
12860234 AGGATTTTGG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 18 0.67
31 9 0.33
ACGTcount: A:0.17, C:0.03, G:0.32, T:0.47
Consensus pattern (31 bp):
TTTAGGGTTATAAGCTAGGTTTAGGGTTTGT
Found at i:12860250 original size:39 final size:37
Alignment explanation
Indices: 12860191--12860273 Score: 112
Period size: 39 Copynumber: 2.2 Consensus size: 37
12860181 GTTATAAGCT
12860191 AGGTTTAGGGTTTGTTTTAGGGTTTAAGCTTGGTTTA
1 AGGTTTAGGGTTTGTTTTAGGGTTTAAGCTTGGTTTA
* * * *
12860228 GGGTTTAGGATTTTGGTTTTAGGGTTTGAGGTTGGTTTA
1 AGGTTTAGG-GTTT-GTTTTAGGGTTTAAGCTTGGTTTA
12860267 AGGTTTA
1 AGGTTTA
12860274 TGTTTGAGGT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
37 8 0.21
38 3 0.08
39 28 0.72
ACGTcount: A:0.16, C:0.01, G:0.35, T:0.48
Consensus pattern (37 bp):
AGGTTTAGGGTTTGTTTTAGGGTTTAAGCTTGGTTTA
Found at i:12860279 original size:24 final size:24
Alignment explanation
Indices: 12860251--12860297 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
12860241 TGGTTTTAGG
12860251 GTTTGAGGTTGGTTTAAGGTTTAT
1 GTTTGAGGTTGGTTTAAGGTTTAT
*
12860275 GTTTGAGGTTGGTTTAGGGTTTA
1 GTTTGAGGTTGGTTTAAGGTTTA
12860298 GGTAAGAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.15, C:0.00, G:0.36, T:0.49
Consensus pattern (24 bp):
GTTTGAGGTTGGTTTAAGGTTTAT
Found at i:12860310 original size:19 final size:18
Alignment explanation
Indices: 12860286--12860348 Score: 62
Period size: 19 Copynumber: 3.6 Consensus size: 18
12860276 TTTGAGGTTG
12860286 GTTTAGGGTTTAGGTAAGA
1 GTTTAGGGTTTAGGT-AGA
12860305 GTTTAGGGTTT---TA-A
1 GTTTAGGGTTTAGGTAGA
*
12860319 TTTTAGGGTTTAGGTTAGA
1 GTTTAGGGTTTAGG-TAGA
*
12860338 GTTTAAGGTTT
1 GTTTAGGGTTT
12860349 TGATTTTAGG
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
14 11 0.31
15 1 0.03
16 1 0.03
18 2 0.06
19 21 0.58
ACGTcount: A:0.22, C:0.00, G:0.32, T:0.46
Consensus pattern (18 bp):
GTTTAGGGTTTAGGTAGA
Found at i:12860325 original size:33 final size:33
Alignment explanation
Indices: 12860287--12860363 Score: 127
Period size: 33 Copynumber: 2.3 Consensus size: 33
12860277 TTGAGGTTGG
*
12860287 TTTAGGGTTTAGGTAAGAGTTTAGGGTTTTAAT
1 TTTAGGGTTTAGGTAAGAGTTTAAGGTTTTAAT
* *
12860320 TTTAGGGTTTAGGTTAGAGTTTAAGGTTTTGAT
1 TTTAGGGTTTAGGTAAGAGTTTAAGGTTTTAAT
12860353 TTTAGGGTTTA
1 TTTAGGGTTTA
12860364 AGATAAGGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.22, C:0.00, G:0.30, T:0.48
Consensus pattern (33 bp):
TTTAGGGTTTAGGTAAGAGTTTAAGGTTTTAAT
Found at i:12860417 original size:19 final size:19
Alignment explanation
Indices: 12860395--12860440 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
12860385 GTTTGAGGTT
12860395 GGTTTAGGGTGTAAGTTAG
1 GGTTTAGGGTGTAAGTTAG
* *
12860414 GGTTTTGGGTTTAAGTTAG
1 GGTTTAGGGTGTAAGTTAG
12860433 GGTTTAGG
1 GGTTTAGG
12860441 TTTTGATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.41, T:0.41
Consensus pattern (19 bp):
GGTTTAGGGTGTAAGTTAG
Found at i:12860443 original size:44 final size:44
Alignment explanation
Indices: 12860353--12860436 Score: 109
Period size: 44 Copynumber: 2.0 Consensus size: 44
12860343 AGGTTTTGAT
* * *
12860353 TTTAGGGTTTAAGATAAGGTTTTGGTTTTATAGTTTGAGGTTGG
1 TTTAGGGTGTAAGATAAGGTTTTGGGTTTATAGTTAGAGGTTGG
* *
12860397 TTTAGGGTGTAAGTTAGGGTTTTGGGTTTA-AGTTAG-GGTT
1 TTTAGGGTGTAAGATAAGGTTTTGGGTTTATAGTTAGAGGTT
12860437 TAGGTTTTGA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 4 0.11
43 5 0.14
44 26 0.74
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.46
Consensus pattern (44 bp):
TTTAGGGTGTAAGATAAGGTTTTGGGTTTATAGTTAGAGGTTGG
Found at i:12862327 original size:144 final size:143
Alignment explanation
Indices: 12862021--12862327 Score: 420
Period size: 144 Copynumber: 2.1 Consensus size: 143
12862011 AATACCTTCG
* * *
12862021 AAGAGCATTTTGGTAATTTCACCTTTTTGAGGTGCAATCAAGGTTTTTAATGCATCAAAATTCAT
1 AAGAGCATTTTGGTAATTTAACCTTTTTGAGGTACAATCAAAGTTTTTAATGCATCAAAATTCAT
* * ** * *
12862086 GGAATAATATTAAAACATGATCTAGAGTTTTTCACGAAAAGTTGACCTCAAAAAGGTTAAATTAT
66 GGAATAATATTAAAACATGATCTAGAGTTTTTCAAGAAAAATAAACCTCAAAAAGGTAAAATTAC
* ** *
12862151 AAGAATATGCGTA
131 AAAAATACCCCTA
* *
12862164 AAGGGCATTTTGGTAAATTTAACCTTTTTGAGGTACAATCAAAGTTTTTAATGTATCAAAATTCA
1 AAGAGCATTTTGGT-AATTTAACCTTTTTGAGGTACAATCAAAGTTTTTAATGCATCAAAATTCA
*
12862229 TGGAATAATATTAAAAGCATGATCTAGAGTTTTTCAATAAAAATAAACCTCAAAAAGGTAAAATT
65 TGGAATAATATTAAAA-CATGATCTAGAGTTTTTCAAGAAAAATAAACCTCAAAAAGGTAAAATT
12862294 ACAAAAATACCCCTA
129 ACAAAAATACCCCTA
12862309 GAA-AGCATTCTT-GTAATTT
1 -AAGAGCATT-TTGGTAATTT
12862328 CTCTCATACA
Statistics
Matches: 143, Mismatches: 17, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
143 13 0.09
144 67 0.47
145 59 0.41
146 4 0.03
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (143 bp):
AAGAGCATTTTGGTAATTTAACCTTTTTGAGGTACAATCAAAGTTTTTAATGCATCAAAATTCAT
GGAATAATATTAAAACATGATCTAGAGTTTTTCAAGAAAAATAAACCTCAAAAAGGTAAAATTAC
AAAAATACCCCTA
Found at i:12867848 original size:15 final size:12
Alignment explanation
Indices: 12867816--12867841 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12867806 CTTCTCTTTT
12867816 TTCTTTTCTTAG
1 TTCTTTTCTTAG
12867828 TTCTTTTCTTAG
1 TTCTTTTCTTAG
12867840 TT
1 TT
12867842 ATTCTTTAGT
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:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (12 bp):
TTCTTTTCTTAG
Found at i:12869510 original size:31 final size:31
Alignment explanation
Indices: 12869468--12869561 Score: 89
Period size: 36 Copynumber: 2.9 Consensus size: 31
12869458 TAAGATGTGT
* *
12869468 ATGACATGGAATGCATGTACTACCTATATGC
1 ATGAAATGGAATGCATGTACTACCTATATGA
* *
12869499 ATGAAATGGAATACATGTACTATCCTTAAGACATGA
1 ATGAAATGGAATGCATGTACTA-CC-T---ATATGA
* *
12869535 ATGAAATGAAATGCATGTACTATCTAT
1 ATGAAATGGAATGCATGTACTACCTAT
12869562 TGATGTCTGT
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
31 21 0.42
32 2 0.04
33 1 0.02
34 1 0.02
35 1 0.02
36 24 0.48
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (31 bp):
ATGAAATGGAATGCATGTACTACCTATATGA
Found at i:12871703 original size:18 final size:18
Alignment explanation
Indices: 12871680--12871714 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12871670 CATGATATGA
12871680 ATGACAAGGTATGAATGC
1 ATGACAAGGTATGAATGC
**
12871698 ATGACAATTTATGAATG
1 ATGACAAGGTATGAATG
12871715 TATATAATAA
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:0.40, C:0.09, G:0.23, T:0.29
Consensus pattern (18 bp):
ATGACAAGGTATGAATGC
Found at i:12871801 original size:19 final size:19
Alignment explanation
Indices: 12871766--12871828 Score: 83
Period size: 18 Copynumber: 3.3 Consensus size: 19
12871756 TGTTTGGTTT
*
12871766 GGTTTTGGAAGGTGGTTTAG
1 GGTTTCGGAA-GTGGTTTAG
12871786 GGTTTCGGAAGTGG-TTAG
1 GGTTTCGGAAGTGGTTTAG
* *
12871804 GGTTTGGGATGTGGTTTAG
1 GGTTTCGGAAGTGGTTTAG
12871823 GGTTTC
1 GGTTTC
12871829 AAATTTTGGT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
18 16 0.42
19 13 0.34
20 9 0.24
ACGTcount: A:0.13, C:0.03, G:0.44, T:0.40
Consensus pattern (19 bp):
GGTTTCGGAAGTGGTTTAG
Found at i:12874381 original size:9 final size:9
Alignment explanation
Indices: 12874367--12874395 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
12874357 TAGAAGTTGC
12874367 AAGGTAGTT
1 AAGGTAGTT
12874376 AAGGTAGTT
1 AAGGTAGTT
12874385 AAGGTAGTT
1 AAGGTAGTT
12874394 AA
1 AA
12874396 ATTCAATTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (9 bp):
AAGGTAGTT
Found at i:12877941 original size:145 final size:143
Alignment explanation
Indices: 12877609--12877944 Score: 363
Period size: 145 Copynumber: 2.3 Consensus size: 143
12877599 TAAAATTGTG
* * * * * *
12877609 ATTTTAATGCACTGAAAATCATGATTGTACCTCAAAAAGTTTAAATTACCAAAATATCCTTTAAA
1 ATTTTAATGCATTAAAAACCTTGATTGTACCTCAAAAGGTTGAAATTACCAAAATATCCTTTAAA
12877674 GGTATTTTCATAATTTTATCATTCTAAGGTTGATTTTTCACAAAAAGCTCCAAATCATGTTTTGA
66 GGTATTTTCATAATTTTATCATTCTAAGGTTGATTTTTCACAAAAAGCTCCAAATCATGTTTTGA
**
12877739 TATTATTTCATGA
131 TATTATTTCAAAA
* * ** *
12877752 ATTTTCATGCATTAAAAACCTTGATTGCACCCTGGAATGGTTGAAATTACCAAAA-ATGCCCTTT
1 ATTTTAATGCATTAAAAACCTTGATTGTA-CCTCAAAAGGTTGAAATTACCAAAATAT--CCTTT
* ** * **** * * *
12877816 AGAGGTATTTTTGTAATTTTA-CCTTCCCT-AGGTTGATTTTTTGTGAAAAGCTCTAGATCGTGT
63 AAAGGTATTTTCATAATTTTATCATT--CTAAGGTTGATTTTTCACAAAAAGCTCCAAATCATGT
*
12877879 TTTGATATTATTTTAAAA
126 TTTGATATTATTTCAAAA
*
12877897 ATTTTAATGCATTAAAAACCTTGATCGTACCTCAAAAGGATTGAAATT
1 ATTTTAATGCATTAAAAACCTTGATTGTACCTCAAAAGG-TTGAAATT
12877945 GAATTACTAA
Statistics
Matches: 156, Mismatches: 31, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
143 25 0.16
144 30 0.19
145 99 0.63
146 2 0.01
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (143 bp):
ATTTTAATGCATTAAAAACCTTGATTGTACCTCAAAAGGTTGAAATTACCAAAATATCCTTTAAA
GGTATTTTCATAATTTTATCATTCTAAGGTTGATTTTTCACAAAAAGCTCCAAATCATGTTTTGA
TATTATTTCAAAA
Found at i:12879798 original size:31 final size:29
Alignment explanation
Indices: 12879770--12879941 Score: 99
Period size: 31 Copynumber: 5.8 Consensus size: 29
12879760 AGCAAACCTT
12879770 AAACTCTAAACCAAATCCTAAACCAAACCC
1 AAACTCTAAACCAAA-CCTAAACCAAACCC
*
12879800 AAA-TGCTAAACC---CC-AAATCAAACCC
1 AAACT-CTAAACCAAACCTAAACCAAACCC
* * * *
12879825 AAACCCCAAACTAAACCATAAACCAAACCTG
1 AAACTCTAAACCAAACC-TAAACCAAACC-C
*
12879856 AAACCCTAAACCAAACACTAAACCCTAAA-CC
1 AAACTCTAAACCAAAC-CTAAA-CC-AAACCC
* *
12879887 AAACTCTAAA-TAGAACCCTAAACCAAACCTT
1 AAACTCTAAACCA-AA-CCTAAACCAAACC-C
*
12879918 AAA-TCCTAAATCAAACCCTAAACC
1 AAACT-CTAAACCAAA-CCTAAACC
12879942 CTAAATTGAA
Statistics
Matches: 112, Mismatches: 13, Indels: 33
0.71 0.08 0.21
Matches are distributed among these distances:
25 18 0.16
26 2 0.02
28 2 0.02
29 4 0.04
30 24 0.21
31 53 0.47
32 6 0.05
33 3 0.03
ACGTcount: A:0.50, C:0.35, G:0.02, T:0.13
Consensus pattern (29 bp):
AAACTCTAAACCAAACCTAAACCAAACCC
Found at i:12879904 original size:43 final size:43
Alignment explanation
Indices: 12879857--12879939 Score: 123
Period size: 43 Copynumber: 1.9 Consensus size: 43
12879847 CCAAACCTGA
*
12879857 AACCCTAAACCAAACAC-TAAACCCTAAACCAAACTCTAAATAG
1 AACCCTAAACCAAAC-CTTAAACCCTAAACCAAACCCTAAATAG
* *
12879900 AACCCTAAACCAAACCTTAAATCCTAAATCAAACCCTAAA
1 AACCCTAAACCAAACCTTAAACCCTAAACCAAACCCTAAA
12879940 CCCTAAATTG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 1 0.03
43 35 0.97
ACGTcount: A:0.51, C:0.33, G:0.01, T:0.16
Consensus pattern (43 bp):
AACCCTAAACCAAACCTTAAACCCTAAACCAAACCCTAAATAG
Found at i:12879939 original size:12 final size:12
Alignment explanation
Indices: 12879770--12879920 Score: 63
Period size: 12 Copynumber: 12.8 Consensus size: 12
12879760 AGCAAACCTT
*
12879770 AAACTCTAAACC
1 AAACCCTAAACC
*
12879782 AAATCCTAAACC
1 AAACCCTAAACC
*
12879794 AAACCC-AAATGCT
1 AAACCCTAAA--CC
* *
12879807 AAACCCCAAATC
1 AAACCCTAAACC
12879819 AAACCC-AAACCCC
1 AAACCCTAAA--CC
12879832 AAA--CTAAACC
1 AAACCCTAAACC
*
12879842 ATAAACC-AAACC
1 A-AACCCTAAACC
12879854 TGAAACCCTAAACC
1 --AAACCCTAAACC
*
12879868 AAA--C---ACT
1 AAACCCTAAACC
12879875 AAACCCTAAACC
1 AAACCCTAAACC
* *
12879887 AAACTCTAAA-T
1 AAACCCTAAACC
12879898 AGAACCCTAAACC
1 A-AACCCTAAACC
*
12879911 AAACCTTAAA
1 AAACCCTAAA
12879921 TCCTAAATCA
Statistics
Matches: 105, Mismatches: 15, Indels: 38
0.66 0.09 0.24
Matches are distributed among these distances:
7 5 0.05
9 1 0.01
10 4 0.04
11 10 0.10
12 59 0.56
13 17 0.16
14 9 0.09
ACGTcount: A:0.51, C:0.34, G:0.02, T:0.13
Consensus pattern (12 bp):
AAACCCTAAACC
Found at i:12879947 original size:19 final size:19
Alignment explanation
Indices: 12879757--12879995 Score: 135
Period size: 19 Copynumber: 12.8 Consensus size: 19
12879747 CCCTTAAGCT
* * *
12879757 TAAAGCAAACCTTAAACTC
1 TAAACCAAACCCTAAACCC
*
12879776 TAAACCAAATCCTAAA-CC
1 TAAACCAAACCCTAAACCC
**
12879794 -AAACCCAAATGCTAAACCC
1 TAAA-CCAAACCCTAAACCC
* *
12879813 CAAATCAAACCC-AAA-CC
1 TAAACCAAACCCTAAACCC
*
12879830 ----CCAAA--CTAAACCA
1 TAAACCAAACCCTAAACCC
12879843 TAAACCAAA-CCTGAAACCC
1 TAAACCAAACCCT-AAACCC
*
12879862 TAAACCAAACACTAAACCC
1 TAAACCAAACCCTAAACCC
*
12879881 TAAACCAAACTCTAAATAGAACCC
1 TAAACCAAAC-C---CTA-AACCC
* *
12879905 TAAACCAAACCTTAAATCC
1 TAAACCAAACCCTAAACCC
*
12879924 TAAATCAAACCCTAAACCC
1 TAAACCAAACCCTAAACCC
***
12879943 TAAATTGAACCC-AAAGCCC
1 TAAACCAAACCCTAAA-CCC
*
12879962 -AAACCAAACCTTAAACCC
1 TAAACCAAACCCTAAACCC
* *
12879980 CAAACCAAGCCCTAAA
1 TAAACCAAACCCTAAA
12879996 TAGAATTGAA
Statistics
Matches: 173, Mismatches: 27, Indels: 40
0.72 0.11 0.17
Matches are distributed among these distances:
11 1 0.01
12 3 0.02
13 5 0.03
17 10 0.06
18 30 0.17
19 99 0.57
20 7 0.04
23 3 0.02
24 15 0.09
ACGTcount: A:0.49, C:0.35, G:0.03, T:0.13
Consensus pattern (19 bp):
TAAACCAAACCCTAAACCC
Found at i:12882610 original size:20 final size:20
Alignment explanation
Indices: 12882582--12882620 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12882572 GACTTTATGA
*
12882582 TTTAAGGTTTTATTTAGGGC
1 TTTAAGGTTTTATCTAGGGC
*
12882602 TTTAGGGTTTTATCTAGGG
1 TTTAAGGTTTTATCTAGGG
12882621 TTTCAGATGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.05, G:0.28, T:0.49
Consensus pattern (20 bp):
TTTAAGGTTTTATCTAGGGC
Found at i:12882666 original size:25 final size:26
Alignment explanation
Indices: 12882638--12882694 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 26
12882628 TGTCACTTAA
* *
12882638 GGTTTCAG-TTTTTACATAGGGTTTT
1 GGTTTCAGACTTTTACATAGGGTTTC
*
12882663 GGTTT-TGACTTTTACATAGGGTTTC
1 GGTTTCAGACTTTTACATAGGGTTTC
12882688 GGTTTCA
1 GGTTTCA
12882695 CCTAAGGTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 1 0.04
25 25 0.96
ACGTcount: A:0.16, C:0.11, G:0.25, T:0.49
Consensus pattern (26 bp):
GGTTTCAGACTTTTACATAGGGTTTC
Found at i:12882747 original size:27 final size:27
Alignment explanation
Indices: 12882699--12882766 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
12882689 GTTTCACCTA
*
12882699 AGGTTTCATTTTAAGATTTTAATTTTG
1 AGGTTTCATTTTAAGATCTTAATTTTG
*
12882726 AGGTTTCGTTTTAATG-TCTTAATTTTAG
1 AGGTTTCATTTTAA-GATCTTAATTTT-G
* *
12882754 AGTTTTAATTTTA
1 AGGTTTCATTTTA
12882767 GAAATTTATG
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
27 22 0.65
28 12 0.35
ACGTcount: A:0.25, C:0.04, G:0.15, T:0.56
Consensus pattern (27 bp):
AGGTTTCATTTTAAGATCTTAATTTTG
Found at i:12882761 original size:14 final size:14
Alignment explanation
Indices: 12882706--12882768 Score: 51
Period size: 14 Copynumber: 4.6 Consensus size: 14
12882696 CTAAGGTTTC
12882706 ATTTTA-AGATTTTA
1 ATTTTAGAG-TTTTA
* *
12882720 ATTTT-GAGGTTTC
1 ATTTTAGAGTTTTA
* *
12882733 GTTTTA-ATGTCTTA
1 ATTTTAGA-GTTTTA
12882747 ATTTTAGAGTTTTA
1 ATTTTAGAGTTTTA
12882761 ATTTTAGA
1 ATTTTAGA
12882769 AATTTATGAA
Statistics
Matches: 37, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
13 8 0.22
14 28 0.76
15 1 0.03
ACGTcount: A:0.27, C:0.03, G:0.14, T:0.56
Consensus pattern (14 bp):
ATTTTAGAGTTTTA
Found at i:12883010 original size:22 final size:21
Alignment explanation
Indices: 12882985--12883025 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
12882975 TTTCCATTAA
12882985 ATTTTATTATTATTTATTTATC
1 ATTTTATTATTA-TTATTTATC
*
12883007 ATTTTATTTTTATTATTTA
1 ATTTTATTATTATTATTTA
12883026 ATAATTCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (21 bp):
ATTTTATTATTATTATTTATC
Found at i:12884873 original size:20 final size:19
Alignment explanation
Indices: 12884844--12884884 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
12884834 TATTTAATTA
12884844 TTTAATTTTTATTAC-TATT
1 TTTAATTTTTA-TACATATT
12884863 TTTATATTTTTATACATATT
1 TTTA-ATTTTTATACATATT
12884883 TT
1 TT
12884885 GTTTGGCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTAATTTTTATACATATT
Found at i:12885457 original size:160 final size:159
Alignment explanation
Indices: 12885191--12885488 Score: 429
Period size: 160 Copynumber: 1.9 Consensus size: 159
12885181 CTCGAATACT
***
12885191 ACCTTTTAAAACCCTTTTTTCTTTACTTTTTTGGTTTTTTGTTTTTTTCCTTTGTATTTTTTTTA
1 ACCTTTTAAAACCCTTTTTTCTTTACTTTTTCACTTTTTTGTTTTTTTCCTTTGTATTTTTTTTA
* * *
12885256 TAGATCAAGACAACATCACAAATCAAAATAAATGACAACCAAGATAACACT-GTAAGTCGGAGAA
66 TAGATCAAGACAACATCACAAATCAAAATAAAGGACAACCAAGATAACACTACT-AGTCAGAGAA
*
12885320 TAAAGAATGATCGGGACAACATCATAAGTC
130 CAAAGAATGATCGGGACAACATCATAAGTC
*
12885350 ACCTTTTAAAACCC-TTTTTCTTTACTTTTTCACTTTTTTGGTTTTTTTTTCTTTGTATTTTTTT
1 ACCTTTTAAAACCCTTTTTTCTTTACTTTTTCACTTTTTT-G-TTTTTTTCCTTTGTATTTTTTT
** * * * *
12885414 TATAGATCGGGACAACATCATAAATCGAAATAAAGGCCAACCAAGGTAACACTACTAGTCAGAGA
64 TATAGATCAAGACAACATCACAAATCAAAATAAAGGACAACCAAGATAACACTACTAGTCAGAGA
12885479 ACAAAGAATG
129 ACAAAGAATG
12885489 TTTAGGATAA
Statistics
Matches: 122, Mismatches: 14, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
158 22 0.18
159 15 0.12
160 84 0.69
161 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.39
Consensus pattern (159 bp):
ACCTTTTAAAACCCTTTTTTCTTTACTTTTTCACTTTTTTGTTTTTTTCCTTTGTATTTTTTTTA
TAGATCAAGACAACATCACAAATCAAAATAAAGGACAACCAAGATAACACTACTAGTCAGAGAAC
AAAGAATGATCGGGACAACATCATAAGTC
Found at i:12885680 original size:36 final size:36
Alignment explanation
Indices: 12885517--12885681 Score: 109
Period size: 36 Copynumber: 4.6 Consensus size: 36
12885507 GTTAAAATAA
* * * * *
12885517 AAAGAACGACCTGAACAACA-TCGCAAGTCAAAAAAT
1 AAAGAATGACCAGGACAACACT-GCAAGTCGAGAAAT
* * * * *
12885553 AAAGGATGATCGGGACAACACTGCAAGTCAAAAAAT
1 AAAGAATGACCAGGACAACACTGCAAGTCGAGAAAT
* * *
12885589 AAAAAATGACCAAGACAACATTGCAAGTCGAGAAA-
1 AAAGAATGACCAGGACAACACTGCAAGTCGAGAAAT
* ** * * * *
12885624 CAAGAACAACTAGAATAACACTGTAAGTCGAGAAAT
1 AAAGAATGACCAGGACAACACTGCAAGTCGAGAAAT
**
12885660 AAAGAATGATTAGGACAACACT
1 AAAGAATGACCAGGACAACACT
12885682 AAAGTCATAA
Statistics
Matches: 98, Mismatches: 29, Indels: 4
0.75 0.22 0.03
Matches are distributed among these distances:
35 25 0.26
36 72 0.73
37 1 0.01
ACGTcount: A:0.51, C:0.18, G:0.18, T:0.14
Consensus pattern (36 bp):
AAAGAATGACCAGGACAACACTGCAAGTCGAGAAAT
Found at i:12886037 original size:16 final size:16
Alignment explanation
Indices: 12886016--12886080 Score: 76
Period size: 17 Copynumber: 3.9 Consensus size: 16
12886006 TTATTTAAAG
12886016 TTGTTTTTGTTTTTTT
1 TTGTTTTTGTTTTTTT
*
12886032 TTGTTTTTCTTCTTTTT
1 TTGTTTTTGTT-TTTTT
12886049 TTGTTTTATGTTTTTTT
1 TTGTTTT-TGTTTTTTT
***
12886066 CCCTTTTTGTTTTTT
1 TTGTTTTTGTTTTTT
12886081 ACATTTACTT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
16 18 0.43
17 21 0.50
18 3 0.07
ACGTcount: A:0.02, C:0.08, G:0.09, T:0.82
Consensus pattern (16 bp):
TTGTTTTTGTTTTTTT
Found at i:12894301 original size:3 final size:3
Alignment explanation
Indices: 12894293--12894342 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
12894283 AACACATGGT
12894293 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
12894341 AT
1 AT
12894343 TATCATTATT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:12898167 original size:9 final size:8
Alignment explanation
Indices: 12898155--12898197 Score: 54
Period size: 8 Copynumber: 5.4 Consensus size: 8
12898145 TAAAATTTCA
12898155 TTTTATTAT
1 TTTTA-TAT
12898164 TTTTAT-T
1 TTTTATAT
12898171 ATTTTATAT
1 -TTTTATAT
12898180 TTTTATAT
1 TTTTATAT
12898188 TTTT-TAT
1 TTTTATAT
12898195 TTT
1 TTT
12898198 AATAAACTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
7 7 0.22
8 19 0.59
9 6 0.19
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTATAT
Found at i:12898174 original size:22 final size:22
Alignment explanation
Indices: 12898139--12898196 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 22
12898129 TGGGTGCAAC
**
12898139 TATTTTTAAAATTTCAT-TTTAT
1 TATTTTTATTATTTCATATTT-T
*
12898161 TATTTTTATTATTTTATATTTT
1 TATTTTTATTATTTCATATTTT
12898183 TATATTTT-TTATTT
1 TAT-TTTTATTATTT
12898197 TAATAAACTG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
22 24 0.77
23 7 0.23
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (22 bp):
TATTTTTATTATTTCATATTTT
Found at i:12898176 original size:17 final size:16
Alignment explanation
Indices: 12898154--12898197 Score: 65
Period size: 15 Copynumber: 2.8 Consensus size: 16
12898144 TTAAAATTTC
12898154 ATTTTATTATTTTTATT
1 ATTTTATTATTTTTA-T
12898171 ATTTTA-TATTTTTAT
1 ATTTTATTATTTTTAT
12898186 ATTTT-TTATTTT
1 ATTTTATTATTTT
12898198 AATAAACTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 12 0.46
16 8 0.31
17 6 0.23
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
ATTTTATTATTTTTAT
Found at i:12898453 original size:12 final size:12
Alignment explanation
Indices: 12898417--12898458 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
12898407 TTTACAGTTC
12898417 AGGGTTTTACCT
1 AGGGTTTTACCT
* *
12898429 AAGGCTTTA--T
1 AGGGTTTTACCT
12898439 AGGGTTTTACCT
1 AGGGTTTTACCT
12898451 AGGGTTTT
1 AGGGTTTT
12898459 GATTTTCACT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
10 8 0.33
12 16 0.67
ACGTcount: A:0.19, C:0.12, G:0.26, T:0.43
Consensus pattern (12 bp):
AGGGTTTTACCT
Found at i:12898515 original size:38 final size:38
Alignment explanation
Indices: 12898443--12898516 Score: 114
Period size: 38 Copynumber: 1.9 Consensus size: 38
12898433 CTTTATAGGG
*
12898443 TTTTACCTAGGGTTTTGATTTTCACTTAATGTTTCAGC
1 TTTTACCTAGGGTTTTGATTTTCACTTAAGGTTTCAGC
*
12898481 TTTTACCTAGGGTTTTGGTTTTCA-TCTAAGGTTTCA
1 TTTTACCTAGGGTTTTGATTTTCACT-TAAGGTTTCA
12898517 TTTTAAGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
37 1 0.03
38 32 0.97
ACGTcount: A:0.18, C:0.15, G:0.18, T:0.50
Consensus pattern (38 bp):
TTTTACCTAGGGTTTTGATTTTCACTTAAGGTTTCAGC
Found at i:12898550 original size:14 final size:15
Alignment explanation
Indices: 12898516--12898556 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
12898506 CTAAGGTTTC
12898516 ATTTTA-AGATTTTA
1 ATTTTAGAGATTTTA
12898530 ATTTTAGAG-TTTTA
1 ATTTTAGAGATTTTA
*
12898544 ATTTTAGAAATTT
1 ATTTTAGAGATTT
12898557 ACGAGCCTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 19 0.79
15 5 0.21
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.56
Consensus pattern (15 bp):
ATTTTAGAGATTTTA
Found at i:12898786 original size:14 final size:14
Alignment explanation
Indices: 12898767--12898806 Score: 50
Period size: 12 Copynumber: 3.1 Consensus size: 14
12898757 TTCCATTAAA
12898767 ATTTATTATTATTT
1 ATTTATTATTATTT
*
12898781 ATTTATCA-T-TTT
1 ATTTATTATTATTT
12898793 ATTT-TTATTATTT
1 ATTTATTATTATTT
12898806 A
1 A
12898807 ATAATTTCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
11 2 0.09
12 8 0.36
13 5 0.23
14 7 0.32
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (14 bp):
ATTTATTATTATTT
Found at i:12898813 original size:22 final size:22
Alignment explanation
Indices: 12898768--12898813 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
12898758 TCCATTAAAA
*
12898768 TTTATTATTATTTATTTATCAT
1 TTTATTATTATTTATTTATAAT
*
12898790 TTTATTTTTA-TTATTTAATAAT
1 TTTATTATTATTTATTT-ATAAT
12898812 TT
1 TT
12898814 CCAACAACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTATTATTATTTATTTATAAT
Found at i:12900592 original size:13 final size:13
Alignment explanation
Indices: 12900568--12900602 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
12900558 CTTCGATTTT
12900568 TTATTT-TTTTAA
1 TTATTTATTTTAA
12900580 TTATTTATTTTAA
1 TTATTTATTTTAA
12900593 TTA-TTATTTT
1 TTATTTATTTT
12900603 TATATTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 13 0.59
13 9 0.41
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
TTATTTATTTTAA
Found at i:12900603 original size:13 final size:12
Alignment explanation
Indices: 12900568--12900604 Score: 56
Period size: 13 Copynumber: 2.9 Consensus size: 12
12900558 CTTCGATTTT
12900568 TTATTTTTTTAA
1 TTATTTTTTTAA
12900580 TTATTTATTTTAA
1 TTATTT-TTTTAA
12900593 TTATTATTTTTA
1 TTATT-TTTTTA
12900605 TATTTTATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 6 0.26
13 16 0.70
14 1 0.04
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
TTATTTTTTTAA
Found at i:12903458 original size:6 final size:6
Alignment explanation
Indices: 12903447--12903493 Score: 53
Period size: 6 Copynumber: 7.8 Consensus size: 6
12903437 AGACTTCAAG
*
12903447 TATTTT TATTTT TATTTT TATTCTT GTTTTTT TA-TTT TA-TTT TATTT
1 TATTTT TATTTT TATTTT TATT-TT -TATTTT TATTTT TATTTT TATTT
12903494 ATTTAATTGC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
5 10 0.28
6 19 0.53
7 4 0.11
8 3 0.08
ACGTcount: A:0.15, C:0.02, G:0.02, T:0.81
Consensus pattern (6 bp):
TATTTT
Found at i:12906152 original size:10 final size:10
Alignment explanation
Indices: 12906137--12906165 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
12906127 CAGAATAGAA
12906137 GTACATCGAT
1 GTACATCGAT
12906147 GTACATCGAT
1 GTACATCGAT
12906157 GTACATCGA
1 GTACATCGA
12906166 CCATTTGAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28
Consensus pattern (10 bp):
GTACATCGAT
Found at i:12915366 original size:50 final size:50
Alignment explanation
Indices: 12915280--12915395 Score: 162
Period size: 50 Copynumber: 2.3 Consensus size: 50
12915270 AACCAACAAA
* * *
12915280 CTTTTCAAAGATAAG-ATTTCAAAGTTTCAAAGCCTCTGTTTAAGATGAG
1 CTTTTCAAAGATAAGAATTTCAAAGTTTCAAACCCTCTATTTAAGAGGAG
* * * *
12915329 CTTTTCAAAGGTAAGAATTTTAAAGTTTCAATCCCTCTATTTATGAGGAG
1 CTTTTCAAAGATAAGAATTTCAAAGTTTCAAACCCTCTATTTAAGAGGAG
12915379 CTTTTCAAAGATAAGAA
1 CTTTTCAAAGATAAGAA
12915396 GCCTCTGTTT
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
49 14 0.24
50 44 0.76
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (50 bp):
CTTTTCAAAGATAAGAATTTCAAAGTTTCAAACCCTCTATTTAAGAGGAG
Found at i:12915491 original size:26 final size:26
Alignment explanation
Indices: 12915458--12915509 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
12915448 CTTTTCAAAG
12915458 ATAAGATTTTTTAAGTTTCAAAGCAT
1 ATAAGATTTTTTAAGTTTCAAAGCAT
12915484 ATAAGATTTTTTAAGTTTCAAAGCAT
1 ATAAGATTTTTTAAGTTTCAAAGCAT
12915510 CTATTTAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (26 bp):
ATAAGATTTTTTAAGTTTCAAAGCAT
Found at i:12915552 original size:59 final size:60
Alignment explanation
Indices: 12915489--12915611 Score: 158
Period size: 60 Copynumber: 2.1 Consensus size: 60
12915479 AGCATATAAG
* *
12915489 ATTTTTT-AAGTTTCAAAGCATCTATTTAGAAAGAACTTTTCAAAGTTAAGATTTTAAAA
1 ATTTTTTAAAATTTCAAAGCATCTATTTAGAAAGAACTTTTCAAAGATAAGATTTTAAAA
* * * * * * *
12915548 ATTTTTTAAAATTTCAAAGCCTTTGTTTAGAAGGAGCTTTTGAAAGATAAGATTTTTAAA
1 ATTTTTTAAAATTTCAAAGCATCTATTTAGAAAGAACTTTTCAAAGATAAGATTTTAAAA
12915608 ATTT
1 ATTT
12915612 CAAAACCTCT
Statistics
Matches: 54, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
59 7 0.13
60 47 0.87
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.42
Consensus pattern (60 bp):
ATTTTTTAAAATTTCAAAGCATCTATTTAGAAAGAACTTTTCAAAGATAAGATTTTAAAA
Found at i:12915625 original size:50 final size:50
Alignment explanation
Indices: 12915550--12915658 Score: 139
Period size: 50 Copynumber: 2.2 Consensus size: 50
12915540 TTTTAAAAAT
* * *
12915550 TTTTTAAAATTTCAAAGCCTTTGTTTAGAAGGAGCT-TTTGAAAGATAAGA
1 TTTTTAAAATTTCAAAACCTCTGTTTAGAAGGAG-TGTTTCAAAGATAAGA
* * * *
12915600 TTTTTAAAATTTCAAAACCTCTGTTTAGGAGTAGTGTTTCAAAGTTAAGT
1 TTTTTAAAATTTCAAAACCTCTGTTTAGAAGGAGTGTTTCAAAGATAAGA
12915650 TTTTTAAAA
1 TTTTTAAAA
12915659 ACTTTAAAGC
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
49 1 0.02
50 50 0.98
ACGTcount: A:0.35, C:0.08, G:0.16, T:0.41
Consensus pattern (50 bp):
TTTTTAAAATTTCAAAACCTCTGTTTAGAAGGAGTGTTTCAAAGATAAGA
Found at i:12918082 original size:19 final size:18
Alignment explanation
Indices: 12918060--12918186 Score: 130
Period size: 18 Copynumber: 6.8 Consensus size: 18
12918050 CATCAAGCTA
* *
12918060 AAACCAAACGTTAAATCCT
1 AAACCAAAC-CTAAACCCT
*
12918079 AAACCAAACCTTCAACCCT
1 AAACCAAACC-TAAACCCT
*
12918098 AAACCAAACCCAAACCCT
1 AAACCAAACCTAAACCCT
* *
12918116 AGACCAAACCTAAACACT
1 AAACCAAACCTAAACCCT
*
12918134 AAACCAAACCCAAACTCC-
1 AAACCAAACCTAAAC-CCT
*
12918152 AAACTAAACCTTAAACCCT
1 AAACCAAACC-TAAACCCT
12918171 AAACCAAACCCTAAAC
1 AAACCAAA-CCTAAAC
12918187 TCAATTCCAA
Statistics
Matches: 89, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
18 45 0.51
19 42 0.47
20 2 0.02
ACGTcount: A:0.49, C:0.37, G:0.02, T:0.13
Consensus pattern (18 bp):
AAACCAAACCTAAACCCT
Found at i:12918107 original size:12 final size:12
Alignment explanation
Indices: 12918092--12918250 Score: 73
Period size: 12 Copynumber: 12.9 Consensus size: 12
12918082 CCAAACCTTC
12918092 AACCCTAAACCA
1 AACCCTAAACCA
12918104 AACCC-AAACCCTA
1 AACCCTAAA-CC-A
*
12918117 GA-CC-AAACCTA
1 AACCCTAAACC-A
*
12918128 AACACTAAACCA
1 AACCCTAAACCA
12918140 AACCC-AAACTCCA
1 AACCCTAAA--CCA
12918153 AA--CTAAACCTTA
1 AACCCTAAACC--A
12918165 AACCCTAAACCA
1 AACCCTAAACCA
12918177 AACCCTAAACTCA
1 AACCCTAAAC-CA
** *
12918190 ATTCCAAACACCA
1 AACCCTAA-ACCA
** *
12918203 AACGTTAAATCA
1 AACCCTAAACCA
12918215 AA--CTGAAATCCTA
1 AACCCT-AAA-CC-A
*
12918228 AATCCTAAACCA
1 AACCCTAAACCA
12918240 AACCCTAAACC
1 AACCCTAAACC
12918251 CCAAACTAAA
Statistics
Matches: 113, Mismatches: 16, Indels: 36
0.68 0.10 0.22
Matches are distributed among these distances:
10 3 0.03
11 15 0.13
12 52 0.46
13 29 0.26
14 12 0.11
15 2 0.02
ACGTcount: A:0.48, C:0.36, G:0.02, T:0.14
Consensus pattern (12 bp):
AACCCTAAACCA
Found at i:12918115 original size:18 final size:18
Alignment explanation
Indices: 12918076--12918250 Score: 124
Period size: 19 Copynumber: 9.4 Consensus size: 18
12918066 AACGTTAAAT
12918076 CCTAAACCAAACCTTC-AAC
1 CCTAAACCAAACC--CAAAC
12918095 CCTAAACCAAACCCAAAC
1 CCTAAACCAAACCCAAAC
* *
12918113 CCTAGACCAAACCTAAAC
1 CCTAAACCAAACCCAAAC
*
12918131 ACTAAACCAAACCCAAAC
1 CCTAAACCAAACCCAAAC
* *
12918149 TCC-AAACTAAACCTTAAAC
1 -CCTAAACCAAACC-CAAAC
12918168 CCTAAACCAAACCCTAAAC
1 CCTAAACCAAACCC-AAAC
* *
12918187 TC-AATTCCAAACACCAAAC
1 CCTAA-ACCAAAC-CCAAAC
** * ** *
12918206 GTTAAATCAAACTGAAAT
1 CCTAAACCAAACCCAAAC
12918224 CCTAAATCCTAAA-CCAAAC
1 CCTAAA-CC-AAACCCAAAC
12918243 CCTAAACC
1 CCTAAACC
12918251 CCAAACTAAA
Statistics
Matches: 121, Mismatches: 25, Indels: 21
0.72 0.15 0.13
Matches are distributed among these distances:
17 1 0.01
18 56 0.46
19 57 0.47
20 7 0.06
ACGTcount: A:0.47, C:0.37, G:0.02, T:0.14
Consensus pattern (18 bp):
CCTAAACCAAACCCAAAC
Found at i:12918126 original size:37 final size:38
Alignment explanation
Indices: 12918075--12918188 Score: 162
Period size: 37 Copynumber: 3.1 Consensus size: 38
12918065 AAACGTTAAA
*
12918075 TCCTAAACCAAACCTTCAACCCTAAACCAAACCCAAAC
1 TCCTAAACCAAACCTTAAACCCTAAACCAAACCCAAAC
* *
12918113 -CCTAGACCAAACC-TAAACACTAAACCAAACCCAAAC
1 TCCTAAACCAAACCTTAAACCCTAAACCAAACCCAAAC
*
12918149 TCC-AAACTAAACCTTAAACCCTAAACCAAACCCTAAAC
1 TCCTAAACCAAACCTTAAACCCTAAACCAAACCC-AAAC
12918187 TC
1 TC
12918189 AATTCCAAAC
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
36 29 0.43
37 32 0.48
38 6 0.09
ACGTcount: A:0.46, C:0.39, G:0.01, T:0.13
Consensus pattern (38 bp):
TCCTAAACCAAACCTTAAACCCTAAACCAAACCCAAAC
Found at i:12918404 original size:19 final size:19
Alignment explanation
Indices: 12918315--12918405 Score: 87
Period size: 19 Copynumber: 4.8 Consensus size: 19
12918305 ATTAACCCAG
*
12918315 ACCCCAAACCAAATCC-TAA
1 ACCCTAAACCAAA-CCTTAA
* *
12918334 ACCTTAAACCAAGCCTTAA
1 ACCCTAAACCAAACCTTAA
* *
12918353 A-CCTTAATCAAAGCCTTAA
1 ACCCTAAACCAAA-CCTTAA
*
12918372 ACCCTAAACTAAACCTTAA
1 ACCCTAAACCAAACCTTAA
*
12918391 GCCCTAAACCAAACC
1 ACCCTAAACCAAACC
12918406 CAAAACTGAC
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
18 9 0.16
19 40 0.70
20 8 0.14
ACGTcount: A:0.44, C:0.35, G:0.03, T:0.18
Consensus pattern (19 bp):
ACCCTAAACCAAACCTTAA
Found at i:12918478 original size:31 final size:30
Alignment explanation
Indices: 12918370--12918503 Score: 84
Period size: 31 Copynumber: 4.4 Consensus size: 30
12918360 TCAAAGCCTT
*
12918370 AAACCCTAAACTAAACCTTAAGCCCTAAA-CC-
1 AAACCCTAAACTAAACC--AA-ACCTAAACCCA
* * *
12918401 AAACCCAAAACT-GACTCAAACACCAAACCTCA
1 AAACCCTAAACTAAAC-CAAAC-CTAAACC-CA
*
12918433 AAA--CTAAACTTAAACACTAACCTAAACCCA
1 AAACCCTAAAC-TAAAC-CAAACCTAAACCCA
12918463 AAACCCTAAACTAAACCCCAAACC-AAACCCA
1 AAACCCTAAACTAAA--CCAAACCTAAACCCA
12918494 AAACCC-AAAC
1 AAACCCTAAAC
12918504 CGAACCCTAA
Statistics
Matches: 82, Mismatches: 10, Indels: 23
0.71 0.09 0.20
Matches are distributed among these distances:
28 1 0.01
29 6 0.07
30 17 0.21
31 37 0.45
32 20 0.24
33 1 0.01
ACGTcount: A:0.51, C:0.37, G:0.01, T:0.11
Consensus pattern (30 bp):
AAACCCTAAACTAAACCAAACCTAAACCCA
Found at i:12918486 original size:19 final size:19
Alignment explanation
Indices: 12918370--12918486 Score: 71
Period size: 19 Copynumber: 6.3 Consensus size: 19
12918360 TCAAAGCCTT
**
12918370 AAACCCTAAACTAAACCTT
1 AAACCCTAAACTAAACCCC
* *
12918389 AAGCCCTAAACCAAA-CCC
1 AAACCCTAAACTAAACCCC
* * *
12918407 AAA-ACT-GACTCAAACACC
1 AAACCCTAAACT-AAACCCC
* **
12918425 AAACCTCAAAACTAAA-CTT
1 AAACC-CTAAACTAAACCCC
* * *
12918444 AAACACTAACCTAAACCCA
1 AAACCCTAAACTAAACCCC
12918463 AAACCCTAAACTAAACCCC
1 AAACCCTAAACTAAACCCC
12918482 AAACC
1 AAACC
12918487 AAACCCAAAA
Statistics
Matches: 69, Mismatches: 23, Indels: 12
0.66 0.22 0.12
Matches are distributed among these distances:
16 2 0.03
17 5 0.07
18 16 0.23
19 39 0.57
20 4 0.06
21 3 0.04
ACGTcount: A:0.50, C:0.36, G:0.02, T:0.13
Consensus pattern (19 bp):
AAACCCTAAACTAAACCCC
Found at i:12918525 original size:30 final size:31
Alignment explanation
Indices: 12918454--12918532 Score: 90
Period size: 30 Copynumber: 2.6 Consensus size: 31
12918444 AAACACTAAC
*
12918454 CTAAACCCAAAACCCTAAACTAAACCCCAAA
1 CTAAACCCAAAACCCTAAACCAAACCCCAAA
* * *
12918485 CCAAACCCAAAACCC-AAACCGAACCCTAAA
1 CTAAACCCAAAACCCTAAACCAAACCCCAAA
* *
12918515 TTAAATCC-AAACCCTAAA
1 CTAAACCCAAAACCCTAAA
12918533 TTTAGACCCC
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
29 6 0.15
30 20 0.50
31 14 0.35
ACGTcount: A:0.51, C:0.38, G:0.01, T:0.10
Consensus pattern (31 bp):
CTAAACCCAAAACCCTAAACCAAACCCCAAA
Found at i:12922178 original size:7 final size:7
Alignment explanation
Indices: 12922162--12922278 Score: 99
Period size: 7 Copynumber: 16.4 Consensus size: 7
12922152 TTAGGTATGC
12922162 TTTAGGG
1 TTTAGGG
*
12922169 TTTAGAG
1 TTTAGGG
12922176 TTTAGGG
1 TTTAGGG
*
12922183 TTTTAGGT
1 -TTTAGGG
*
12922191 TTTAAGG
1 TTTAGGG
12922198 TTTAGGG
1 TTTAGGG
*
12922205 TTTACGG
1 TTTAGGG
*
12922212 TTTAAGG
1 TTTAGGG
*
12922219 TTTAAGG
1 TTTAGGG
*
12922226 TTTAAGG
1 TTTAGGG
*
12922233 TTTAAGG
1 TTTAGGG
*
12922240 TTTAAGG
1 TTTAGGG
*
12922247 TTTAGGT
1 TTTAGGG
**
12922254 TTTATAG
1 TTTAGGG
12922261 TCTTAGGG
1 T-TTAGGG
*
12922269 TTTAAGG
1 TTTAGGG
12922276 TTT
1 TTT
12922279 TAAATTTGGG
Statistics
Matches: 92, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
7 81 0.88
8 11 0.12
ACGTcount: A:0.21, C:0.02, G:0.30, T:0.47
Consensus pattern (7 bp):
TTTAGGG
Found at i:12922208 original size:21 final size:21
Alignment explanation
Indices: 12922162--12922281 Score: 113
Period size: 21 Copynumber: 5.6 Consensus size: 21
12922152 TTAGGTATGC
* *
12922162 TTTAGGGTTT-AGAGTTTAGGG
1 TTTAGGTTTTAAG-GTTTAAGG
*
12922183 TTTTAGGTTTTAAGGTTTAGGG
1 -TTTAGGTTTTAAGGTTTAAGG
12922205 TTTACGG-TTTAAGGTTTAAGG
1 TTTA-GGTTTTAAGGTTTAAGG
12922226 TTTAAGG-TTTAAGGTTTAAGG
1 TTT-AGGTTTTAAGGTTTAAGG
*
12922247 TTTAGGTTTTATA-GTCTTAGGG
1 TTTAGGTTTTA-AGGT-TTAAGG
12922269 TTTAAGGTTTTAA
1 TTT-AGGTTTTAA
12922282 ATTTGGGATT
Statistics
Matches: 88, Mismatches: 3, Indels: 14
0.84 0.03 0.13
Matches are distributed among these distances:
20 3 0.03
21 45 0.51
22 30 0.34
23 10 0.11
ACGTcount: A:0.23, C:0.02, G:0.29, T:0.47
Consensus pattern (21 bp):
TTTAGGTTTTAAGGTTTAAGG
Found at i:12922303 original size:17 final size:16
Alignment explanation
Indices: 12922281--12922335 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 16
12922271 TAAGGTTTTA
12922281 AATTTGGGATTTCATGG
1 AATTTGGG-TTTCATGG
*
12922298 AATTTGGCGTTTTATGG
1 AATTTGG-GTTTCATGG
*
12922315 GATTTGAGGTTTCATGG
1 AATTTG-GGTTTCATGG
12922332 AATT
1 AATT
12922336 AAGCATGCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
17 30 0.94
18 2 0.06
ACGTcount: A:0.22, C:0.05, G:0.29, T:0.44
Consensus pattern (16 bp):
AATTTGGGTTTCATGG
Found at i:12924307 original size:20 final size:20
Alignment explanation
Indices: 12924284--12924350 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
12924274 TTTGGACATT
12924284 TTTGACTAATTTTGATCAAA
1 TTTGACTAATTTTGATCAAA
* * *
12924304 TTTGACT-TTATTTGACCAAG
1 TTTGACTAAT-TTTGATCAAA
12924324 TTTGACTAATTTTGATCAAA
1 TTTGACTAATTTTGATCAAA
12924344 TTTGACT
1 TTTGACT
12924351 TTAAGGTATT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
19 1 0.03
20 37 0.95
21 1 0.03
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.46
Consensus pattern (20 bp):
TTTGACTAATTTTGATCAAA
Found at i:12924604 original size:15 final size:16
Alignment explanation
Indices: 12924584--12924616 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
12924574 CTGAAAGGGT
12924584 TTTGTTTG-TTTCATG
1 TTTGTTTGTTTTCATG
12924599 TTTGTTTGTTTTCATG
1 TTTGTTTGTTTTCATG
12924615 TT
1 TT
12924617 AAAGCAAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.06, C:0.06, G:0.18, T:0.70
Consensus pattern (16 bp):
TTTGTTTGTTTTCATG
Found at i:12924712 original size:51 final size:49
Alignment explanation
Indices: 12924643--12924801 Score: 138
Period size: 53 Copynumber: 3.1 Consensus size: 49
12924633 TTGACATGAC
*
12924643 TTTAAAAATCATAGGCAAGTGACTTTAAAAATCTTTTTTTTTGAAAAATGCT
1 TTTATAAA-CATAGGCAAGTGACTTTAAAAA-C-TTTTTTTTGAAAAATGCT
* * * *
12924695 TTTATAAACATAAGCAAGTGATTTTTAAAAAAACTTTTTTTTGCAAAAGTACT
1 TTTATAAACATAGGCAAGTGA-CTTT--AAAAACTTTTTTTTG-AAAAATGCT
** * * * * *
12924748 CCTATAAATATAGGCAAGTCACTTAAAAAAATTTTTTTTGAAAATTGCT
1 TTTATAAACATAGGCAAGTGACTTTAAAAACTTTTTTTTGAAAAATGCT
*
12924797 ATTAT
1 TTTAT
12924802 GAAGGTAGGC
Statistics
Matches: 86, Mismatches: 17, Indels: 11
0.75 0.15 0.10
Matches are distributed among these distances:
49 10 0.12
50 14 0.16
51 12 0.14
52 21 0.24
53 24 0.28
54 5 0.06
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (49 bp):
TTTATAAACATAGGCAAGTGACTTTAAAAACTTTTTTTTGAAAAATGCT
Found at i:12924889 original size:51 final size:49
Alignment explanation
Indices: 12924807--12924941 Score: 200
Period size: 51 Copynumber: 2.7 Consensus size: 49
12924797 ATTATGAAGG
*
12924807 TAGGCAACAAACTCTAAAAATCTCATTTTGAAAAGAGCTTCTATCAAA-A
1 TAGGCAACAAACTTTAAAAATCTCATTTTGAAAAGAGCTTCTAT-AAAGA
* *
12924856 TATGCAACAAACTTTTAAAAAATCTCATTTTGAAAAGGGCTTCTATAAAGA
1 TAGGCAACAAAC-TTT-AAAAATCTCATTTTGAAAAGAGCTTCTATAAAGA
*
12924907 TAGGCAATAAACTTTAAAAATCTCATTTTGAAAAG
1 TAGGCAACAAACTTTAAAAATCTCATTTTGAAAAG
12924942 GTTTTAATGT
Statistics
Matches: 78, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
49 31 0.40
50 8 0.10
51 39 0.50
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.30
Consensus pattern (49 bp):
TAGGCAACAAACTTTAAAAATCTCATTTTGAAAAGAGCTTCTATAAAGA
Found at i:12927543 original size:46 final size:46
Alignment explanation
Indices: 12927484--12927579 Score: 129
Period size: 46 Copynumber: 2.1 Consensus size: 46
12927474 GATTTTGGCA
* * * *
12927484 ATTTTGGTGTGGGCTATGACCCACTTATTGTTGTATTTTTACTTTT
1 ATTTTGGTATGGGCTATGACCCACTAATTATTGTATTTTAACTTTT
* * *
12927530 ATTTTGGTATGGGCTATGGCCCACTAATTATTTTATTTTAATTTTT
1 ATTTTGGTATGGGCTATGACCCACTAATTATTGTATTTTAACTTTT
12927576 ATTT
1 ATTT
12927580 CTATTTTATT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.19, C:0.11, G:0.17, T:0.53
Consensus pattern (46 bp):
ATTTTGGTATGGGCTATGACCCACTAATTATTGTATTTTAACTTTT
Found at i:12928485 original size:30 final size:29
Alignment explanation
Indices: 12928421--12928487 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 29
12928411 GCTTCTTTTT
**
12928421 TTTTCATTTTATTTTCTATTTTGAATTTCT
1 TTTT-ATTTTATTTTCTATTTTGAATTTAA
*
12928451 TTTTATTTTATTTTTCCTATTTT-ATTTTAA
1 TTTTATTTTA-TTTT-CTATTTTGAATTTAA
12928481 TTTTATT
1 TTTTATT
12928488 ATATATATCT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 6 0.19
30 19 0.59
31 7 0.22
ACGTcount: A:0.18, C:0.07, G:0.01, T:0.73
Consensus pattern (29 bp):
TTTTATTTTATTTTCTATTTTGAATTTAA
Found at i:12928895 original size:38 final size:38
Alignment explanation
Indices: 12928844--12928941 Score: 121
Period size: 38 Copynumber: 2.6 Consensus size: 38
12928834 ATAATTTTAC
12928844 AATAAAATCTCACCAAACTATTGAGAGAGT-TGCATCAA
1 AATAAAATCTCACCAAACTATTGAGAGA-TCTGCATCAA
* * *
12928882 AATAAAATCTCACCAAACGATGGGGAGATCTGCATCAA
1 AATAAAATCTCACCAAACTATTGAGAGATCTGCATCAA
*
12928920 AGT-AAATCAT-ACCAAACTATTG
1 AATAAAATC-TCACCAAACTATTG
12928942 GAGGATTTTA
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
37 16 0.31
38 36 0.69
ACGTcount: A:0.44, C:0.19, G:0.14, T:0.22
Consensus pattern (38 bp):
AATAAAATCTCACCAAACTATTGAGAGATCTGCATCAA
Found at i:12936692 original size:21 final size:21
Alignment explanation
Indices: 12936653--12936692 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
12936643 CTTTGGATTG
*
12936653 CAAAATGCTAGGGTAACATAT
1 CAAAATGCTAGAGTAACATAT
* *
12936674 CAAAATGCTATAGTGACAT
1 CAAAATGCTAGAGTAACAT
12936693 TCTTTCATGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.25
Consensus pattern (21 bp):
CAAAATGCTAGAGTAACATAT
Found at i:12940364 original size:43 final size:44
Alignment explanation
Indices: 12940203--12940353 Score: 193
Period size: 43 Copynumber: 3.5 Consensus size: 44
12940193 GTTAGAGGAT
* * * * * *
12940203 TATTTTAAATTTATTTAGCCTCTAAATAGAGAAACTCATTT-TC
1 TATTTTAAAGTTGTTTAGCCTCTGAATAGAGGAGCCCATTTCTC
*
12940246 TATTTTAAAGTTG-TTAGCCTCTGAATAGAGGAGCCCA-TTCCC
1 TATTTTAAAGTTGTTTAGCCTCTGAATAGAGGAGCCCATTTCTC
* *
12940288 TATTTTAAAGTTCTTTAGCCTATGAATAGAGGAGCCCATTTCTC
1 TATTTTAAAGTTGTTTAGCCTCTGAATAGAGGAGCCCATTTCTC
12940332 -ATTTTAAAGTTGTTTAGCCTCT
1 TATTTTAAAGTTGTTTAGCCTCT
12940354 ATTTAGAGGA
Statistics
Matches: 93, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
41 2 0.02
42 33 0.35
43 54 0.58
44 4 0.04
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.40
Consensus pattern (44 bp):
TATTTTAAAGTTGTTTAGCCTCTGAATAGAGGAGCCCATTTCTC
Found at i:12941598 original size:19 final size:18
Alignment explanation
Indices: 12941563--12941610 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
12941553 TCCTTTTTTC
12941563 ATTTTATTTTCTAATTTG
1 ATTTTATTTTCTAATTTG
*
12941581 ATTTTACTTTTCCT-ATTTT
1 ATTTTA-TTTT-CTAATTTG
12941600 ATTTTCATTTT
1 ATTTT-ATTTT
12941611 ATTATATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 6 0.23
19 17 0.65
20 3 0.12
ACGTcount: A:0.19, C:0.10, G:0.02, T:0.69
Consensus pattern (18 bp):
ATTTTATTTTCTAATTTG
Found at i:12942459 original size:79 final size:79
Alignment explanation
Indices: 12942325--12942477 Score: 209
Period size: 79 Copynumber: 1.9 Consensus size: 79
12942315 TCTAGTTTCA
* * * * * * *
12942325 TAAACTCGAATCTACTATTTAAAGATACATAAGTCAATCTTGGGGCTTCTTTTTAAATA-AGACA
1 TAAACTAGAATCTAATATTTAAAGATACATAAATCAATCTTAGGACTCCTCTTTAAATAGA-ACA
12942389 GATTCAGTCTGGTTG
65 GATTCAGTCTGGTTG
* *
12942404 TAAACTAGAATCTAATATTTAAAGATACCTAAATCAATCTTAGGACTCCTCTTTAAATAGAATAG
1 TAAACTAGAATCTAATATTTAAAGATACATAAATCAATCTTAGGACTCCTCTTTAAATAGAACAG
12942469 ATTCAGTCT
66 ATTCAGTCT
12942478 ATTGGTCATT
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
79 63 0.98
80 1 0.02
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (79 bp):
TAAACTAGAATCTAATATTTAAAGATACATAAATCAATCTTAGGACTCCTCTTTAAATAGAACAG
ATTCAGTCTGGTTG
Found at i:12946489 original size:13 final size:13
Alignment explanation
Indices: 12946471--12946495 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12946461 AGTTACTCAC
12946471 CTCTCAGAGAACT
1 CTCTCAGAGAACT
12946484 CTCTCAGAGAAC
1 CTCTCAGAGAAC
12946496 CACCGATTTC
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:0.32, C:0.32, G:0.16, T:0.20
Consensus pattern (13 bp):
CTCTCAGAGAACT
Found at i:12948500 original size:13 final size:13
Alignment explanation
Indices: 12948482--12948506 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12948472 TTTATAGTTT
12948482 TTTGTTTATTTTC
1 TTTGTTTATTTTC
12948495 TTTGTTTATTTT
1 TTTGTTTATTTT
12948507 GTAGTTTTTT
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:0.08, C:0.04, G:0.08, T:0.80
Consensus pattern (13 bp):
TTTGTTTATTTTC
Found at i:12948506 original size:24 final size:24
Alignment explanation
Indices: 12948485--12948545 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
12948475 ATAGTTTTTT
*
12948485 GTTTATTTTCTTTGTTTATTTTGTA
1 GTTT-TTTTATTTGTTTATTTTGTA
*
12948510 GTTTTTTTATTTTTTTATTTATGT-
1 GTTTTTTTATTTGTTTATTT-TGTA
*
12948534 GTTTGTTTATTT
1 GTTTTTTTATTT
12948546 TTTTGGAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 25 0.78
25 7 0.22
ACGTcount: A:0.11, C:0.02, G:0.11, T:0.75
Consensus pattern (24 bp):
GTTTTTTTATTTGTTTATTTTGTA
Found at i:12948522 original size:8 final size:8
Alignment explanation
Indices: 12948454--12948549 Score: 50
Period size: 8 Copynumber: 11.6 Consensus size: 8
12948444 AGTCAAACTG
*
12948454 TTTTGATT
1 TTTTTATT
12948462 TTTTTATACT
1 TTTTTAT--T
* *
12948472 TTTATAGT
1 TTTTTATT
*
12948480 TTTTTGTT
1 TTTTTATT
*
12948488 TATTTTCTT
1 T-TTTTATT
*
12948497 TGTTTA-T
1 TTTTTATT
*
12948504 TTTGTAGTT
1 TTTTTA-TT
12948513 TTTTTATT
1 TTTTTATT
12948521 TTTTTATT
1 TTTTTATT
* * *
12948529 TATGTGTT
1 TTTTTATT
*
12948537 TGTTTATT
1 TTTTTATT
12948545 TTTTT
1 TTTTT
12948550 GGAATATTTT
Statistics
Matches: 64, Mismatches: 19, Indels: 10
0.69 0.20 0.11
Matches are distributed among these distances:
7 5 0.08
8 40 0.62
9 13 0.20
10 6 0.09
ACGTcount: A:0.12, C:0.02, G:0.09, T:0.76
Consensus pattern (8 bp):
TTTTTATT
Found at i:12948546 original size:24 final size:24
Alignment explanation
Indices: 12948499--12948549 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
12948489 ATTTTCTTTG
*
12948499 TTTATTTTGTAGTTTTTTTATTTT
1 TTTATTTTGTAGTTTGTTTATTTT
12948523 TTTATTTATGT-GTTTGTTTATTTT
1 TTTATTT-TGTAGTTTGTTTATTTT
12948547 TTT
1 TTT
12948550 GGAATATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.12, C:0.00, G:0.10, T:0.78
Consensus pattern (24 bp):
TTTATTTTGTAGTTTGTTTATTTT
Found at i:12948550 original size:12 final size:12
Alignment explanation
Indices: 12948479--12948550 Score: 63
Period size: 12 Copynumber: 5.6 Consensus size: 12
12948469 ACTTTTATAG
12948479 TTTTTTGTTTAT
1 TTTTTTGTTTAT
12948491 TTTCTTTGTTTATT
1 TTT-TTTGTTTA-T
*
12948505 TTGTAGTTTTTTTAT
1 TT-T--TTTGTTTAT
*
12948520 TTTTTTATTTAT
1 TTTTTTGTTTAT
* *
12948532 GTGTTTGTTTAT
1 TTTTTTGTTTAT
12948544 TTTTTTG
1 TTTTTTG
12948551 GAATATTTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
12 25 0.52
13 8 0.17
14 4 0.08
15 4 0.08
16 7 0.15
ACGTcount: A:0.10, C:0.01, G:0.11, T:0.78
Consensus pattern (12 bp):
TTTTTTGTTTAT
Found at i:12948758 original size:79 final size:79
Alignment explanation
Indices: 12948627--12948785 Score: 282
Period size: 79 Copynumber: 2.0 Consensus size: 79
12948617 AAGTTGAAAG
* * *
12948627 TATCAATTTTTCTTGTACAAAAGCATTGAGTTTTTGAAGAGAAAAGGATTTATATCAAAGATTGA
1 TATCAATTTTCCCTGTACAAAAGCATTGAGTTTTTGAAGAGAAAAGGATTTATATCAAAGATTAA
12948692 ATCATTATTCTTTT
66 ATCATTATTCTTTT
12948706 TATCAATTTTCCCTGTACAAAAGCATTGAGTTTTTGAAGAGAAAAGGATTTATATCAAAGATTAA
1 TATCAATTTTCCCTGTACAAAAGCATTGAGTTTTTGAAGAGAAAAGGATTTATATCAAAGATTAA
*
12948771 ATCATTATTTTTTT
66 ATCATTATTCTTTT
12948785 T
1 T
12948786 TTATTTATTT
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
79 76 1.00
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.42
Consensus pattern (79 bp):
TATCAATTTTCCCTGTACAAAAGCATTGAGTTTTTGAAGAGAAAAGGATTTATATCAAAGATTAA
ATCATTATTCTTTT
Found at i:12953269 original size:63 final size:63
Alignment explanation
Indices: 12953196--12953378 Score: 294
Period size: 63 Copynumber: 2.9 Consensus size: 63
12953186 TGGTACTGAG
*
12953196 AAGCTTATGAATGATGACCAAGTGATAGATGATGAAATTTATTTTGAAATGGCTAGTATTAAA
1 AAGCTTATGAATGATGACCAAGTGACAGATGATGAAATTTATTTTGAAATGGCTAGTATTAAA
* *
12953259 AAGCTTATGAATGATGACCAAGTGACAGATGATGAAATTTGTTTTGAAATGGCTAGTATTGAA
1 AAGCTTATGAATGATGACCAAGTGACAGATGATGAAATTTATTTTGAAATGGCTAGTATTAAA
* ** * *
12953322 AAGCTTATGAAAGATGACCAAGTGACAGAAAATAAAATTTATTTTGAAATGGTTAGT
1 AAGCTTATGAATGATGACCAAGTGACAGATGATGAAATTTATTTTGAAATGGCTAGT
12953379 GTTGATAAGC
Statistics
Matches: 111, Mismatches: 9, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
63 111 1.00
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.32
Consensus pattern (63 bp):
AAGCTTATGAATGATGACCAAGTGACAGATGATGAAATTTATTTTGAAATGGCTAGTATTAAA
Found at i:12954044 original size:21 final size:21
Alignment explanation
Indices: 12953997--12954046 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
12953987 CCTTTTGAAT
12953997 AAAATCTTTGAATTTCAAAAG
1 AAAATCTTTGAATTTCAAAAG
*
12954018 AGAATCTTTGAATTTC-AAAG
1 AAAATCTTTGAATTTCAAAAG
12954038 AAAAATCTT
1 -AAAATCTT
12954047 GGAGCTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 4 0.15
21 22 0.85
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.34
Consensus pattern (21 bp):
AAAATCTTTGAATTTCAAAAG
Found at i:12954517 original size:41 final size:41
Alignment explanation
Indices: 12954395--12954656 Score: 190
Period size: 41 Copynumber: 6.4 Consensus size: 41
12954385 ATGATTGTCA
* * * * * *
12954395 AGGAGCCATTTATTTTTCAAAAGTTTTGATGCCTCTATTGAG
1 AGGAGCAATTTA-TTTTCTAAAGTTGTGGTGCCTCTGTTTAG
* * * * * *
12954437 AGGAGCCATTTATTTTTTAAAAGTTCTGTTGTCTTTGTTTAG
1 AGGAGCAATTTATTTTCT-AAAGTTGTGGTGCCTCTGTTTAG
* *
12954479 AAGAGCAATTTATTTTCTAAAGTTATGGTGCCTCTGTTTAG
1 AGGAGCAATTTATTTTCTAAAGTTGTGGTGCCTCTGTTTAG
* * * *
12954520 AGGAGCAATTTAATTTCCAAAGTTGTGGTGTCTCTATTTAG
1 AGGAGCAATTTATTTTCTAAAGTTGTGGTGCCTCTGTTTAG
* * * *
12954561 AGGAAC-ATTTACTTTTC-AAAGTCGTTGAGCCTCTGTTTAG
1 AGGAGCAATTTA-TTTTCTAAAGTTGTGGTGCCTCTGTTTAG
** * * ***
12954601 AGGAGCTTTGTTTATTATCCAAAGTTGTTAAGCCTCTGTTTAG
1 AGGAGC--AATTTATTTTCTAAAGTTGTGGTGCCTCTGTTTAG
12954644 AGGAGC--TTTATTT
1 AGGAGCAATTTATTT
12954657 ATTTTTCCAA
Statistics
Matches: 180, Mismatches: 34, Indels: 15
0.79 0.15 0.07
Matches are distributed among these distances:
39 6 0.03
40 28 0.16
41 67 0.37
42 48 0.27
43 31 0.17
ACGTcount: A:0.25, C:0.13, G:0.20, T:0.42
Consensus pattern (41 bp):
AGGAGCAATTTATTTTCTAAAGTTGTGGTGCCTCTGTTTAG
Found at i:12954600 original size:40 final size:40
Alignment explanation
Indices: 12954472--12954827 Score: 164
Period size: 43 Copynumber: 8.6 Consensus size: 40
12954462 CTGTTGTCTT
* * * ** * *
12954472 TGTTTAGAAGAGCAATTTATTTTCTAAAGTTATGGTGCCTC
1 TGTTTAGAGGAACTATTTATTTTC-AAAGTCGTTGAGCCTC
* * * * * * *
12954513 TGTTTAGAGGAGCAATTTAATTTCCAAAGTTGTGGTGTCTC
1 TGTTTAGAGGAACTATTT-ATTTTCAAAGTCGTTGAGCCTC
*
12954554 TATTTAGAGGAAC-ATTTACTTTTCAAAGTCGTTGAGCCTC
1 TGTTTAGAGGAACTATTTA-TTTTCAAAGTCGTTGAGCCTC
* * * * *
12954594 TGTTTAGAGGAGCTTTGTTTATTATCCAAAGTTGTTAAGCCTC
1 TGTTTAGAGGAAC--TATTTATT-TTCAAAGTCGTTGAGCCTC
* **
12954637 TGTTTAGAGGAGCTTTATTTATTTTTCCAAAAGTCGTTGAGTTTC
1 TGTTTAGAGGAAC--TATTTA-TTTT-C-AAAGTCGTTGAGCCTC
* *
12954682 TGATTAGAGG-A--GTTTATTTTCCAAAGTCGTTGAGCCTC
1 TGTTTAGAGGAACTATTTATTTT-CAAAGTCGTTGAGCCTC
** * * * * * *
12954720 TAATTAGAAGAGCCATTTAGTTTCAAGGTCGTGGAGCCTC
1 TGTTTAGAGGAACTATTTATTTTCAAAGTCGTTGAGCCTC
* * * * *
12954760 TATTTAGAGGAACTTTGTTTATTTTTTAAA-CCTGTTGAGCTTC
1 TGTTTAGAGGAAC--TATTTA-TTTTCAAAGTC-GTTGAGCCTC
*
12954803 TGTTTAGAGGAGCTTTATTTATTTT
1 TGTTTAGAGGAAC--TATTTATTTT
12954828 TTTTATTTTT
Statistics
Matches: 250, Mismatches: 49, Indels: 31
0.76 0.15 0.09
Matches are distributed among these distances:
38 22 0.09
39 7 0.03
40 60 0.24
41 49 0.20
42 16 0.06
43 72 0.29
44 3 0.01
45 21 0.08
ACGTcount: A:0.24, C:0.13, G:0.21, T:0.42
Consensus pattern (40 bp):
TGTTTAGAGGAACTATTTATTTTCAAAGTCGTTGAGCCTC
Found at i:12954691 original size:45 final size:43
Alignment explanation
Indices: 12954577--12954956 Score: 203
Period size: 43 Copynumber: 8.8 Consensus size: 43
12954567 ATTTACTTTT
*
12954577 CAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTGTTTATTATC
1 CAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTATTTATTATC
* * *
12954620 CAAAGTTGTTAAGCCTCTGTTTAGAGGAGCTTTATTTATTTTTC
1 CAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTATTTA-TTATC
** *
12954664 CAAAAGTCGTTGAGTTTCTGATTAGAGGAG-TTTA--T-TT-TC
1 C-AAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTATTTATTATC
** * *
12954703 CAAAGTCGTTGAGCCTCTAATTAGAAGAGC--CATTTAGTT-T-
1 CAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTATTTA-TTATC
* * * * * * *
12954743 CAAGGTCGTGGAGCCTCTATTTAGAGGAACTTTGTTTATTTTT
1 CAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTATTTATTATC
* * *
12954786 TAAA-CCTGTTGAGCTTCTGTTTAGAGGAGCTTTATTTATTTTTTTTATTTTTC
1 CAAAGTC-GTTGAGCCTCTGTTTAGAGGAGCTTTATTTA------TTA----TC
* * * * * *
12954839 CAAATTCATTGAGTCTTTGTTTA-AGGAGCTTTGTTTATTTTTC
1 CAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTATTTA-TTATC
** *
12954882 TGAAGTTGTTGAGCCTCTGTTTAGAGGAGCAATTTA-TT-TT-TC
1 CAAAGTCGTTGAGCCTCTGTTTAGAGGAGC--TTTATTTATTATC
* * * *
12954924 CAAAGTCATTTAGCCTCTGCTTAAAGGAGCTTT
1 CAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTT
12954957 TGTTTATTTT
Statistics
Matches: 257, Mismatches: 54, Indels: 55
0.70 0.15 0.15
Matches are distributed among these distances:
37 1 0.00
38 24 0.09
39 4 0.02
40 30 0.12
41 5 0.02
42 32 0.12
43 83 0.32
44 15 0.06
45 25 0.10
46 3 0.01
47 3 0.01
49 2 0.01
52 13 0.05
53 16 0.06
54 1 0.00
ACGTcount: A:0.23, C:0.14, G:0.20, T:0.43
Consensus pattern (43 bp):
CAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTATTTATTATC
Found at i:12954933 original size:85 final size:87
Alignment explanation
Indices: 12954829--12954988 Score: 234
Period size: 87 Copynumber: 1.9 Consensus size: 87
12954819 ATTTATTTTT
* * * * *
12954829 TTTATTTTTCCAAATTCATTGAGTCTTTG-TTTAAGGAGC-TTTGTTTATTTTTCTGAAGTTGTT
1 TTTATTTTTCCAAAGTCATTGAGCCTCTGCTTAAAGGAGCTTTTGTTTATTTTTCTAAAGTTGTT
*
12954892 GAGCCTCTGTTTAGAGGAGCAA
66 AAGCCTCTGTTTAGAGGAGCAA
*
12954914 TTTATTTTTCCAAAGTCATTTAGCCTCTGCTTAAAGGAGCTTTTGTTTATTTTTCTAAAGTTGTT
1 TTTATTTTTCCAAAGTCATTGAGCCTCTGCTTAAAGGAGCTTTTGTTTATTTTTCTAAAGTTGTT
*
12954979 AAGTCTCTGT
66 AAGCCTCTGT
12954989 CATTGAGCTT
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
85 25 0.38
86 9 0.14
87 31 0.48
ACGTcount: A:0.21, C:0.13, G:0.17, T:0.48
Consensus pattern (87 bp):
TTTATTTTTCCAAAGTCATTGAGCCTCTGCTTAAAGGAGCTTTTGTTTATTTTTCTAAAGTTGTT
AAGCCTCTGTTTAGAGGAGCAA
Found at i:12954939 original size:42 final size:42
Alignment explanation
Indices: 12954829--12954954 Score: 119
Period size: 42 Copynumber: 3.0 Consensus size: 42
12954819 ATTTATTTTT
* * * **
12954829 TTTATTTTTCCAAATTCATTGAGTCTTTGTTTAAGGAGCTTTG
1 TTTATTTTTCCAAAGTCATTGAGCCTCTGTTTAAGGAGC-TAA
** **
12954872 TTTATTTTTCTGAAGTTGTTGAGCCTCTGTTTAGAGGAGC-AA
1 TTTATTTTTCCAAAGTCATTGAGCCTCTGTTTA-AGGAGCTAA
* *
12954914 TTTATTTTTCCAAAGTCATTTAGCCTCTGCTTAAAGGAGCT
1 TTTATTTTTCCAAAGTCATTGAGCCTCTG-TTTAAGGAGCT
12954955 TTTGTTTATT
Statistics
Matches: 65, Mismatches: 15, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
42 30 0.46
43 29 0.45
44 6 0.09
ACGTcount: A:0.22, C:0.14, G:0.18, T:0.45
Consensus pattern (42 bp):
TTTATTTTTCCAAAGTCATTGAGCCTCTGTTTAAGGAGCTAA
Found at i:12954987 original size:45 final size:44
Alignment explanation
Indices: 12954861--12954987 Score: 132
Period size: 42 Copynumber: 2.9 Consensus size: 44
12954851 GTCTTTGTTT
* * *
12954861 AAGGAGCTTTGTTTATTTTTCTGAAGTTGTTGAGCCTCTGTTTA
1 AAGGAGCTTTGTTTATTTTTCTAAAGTTGTTAAGCCTCTGCTTA
* ** * ** *
12954905 GAGGAGC--AATTTATTTTTCCAAAGTCATTTAGCCTCTGCTTA
1 AAGGAGCTTTGTTTATTTTTCTAAAGTTGTTAAGCCTCTGCTTA
*
12954947 AAGGAGCTTTTGTTTATTTTTCTAAAGTTGTTAAGTCTCTG
1 AAGGAGC-TTTGTTTATTTTTCTAAAGTTGTTAAGCCTCTG
12954988 TCATTGAGCT
Statistics
Matches: 63, Mismatches: 17, Indels: 5
0.74 0.20 0.06
Matches are distributed among these distances:
42 33 0.52
44 6 0.10
45 24 0.38
ACGTcount: A:0.22, C:0.13, G:0.20, T:0.45
Consensus pattern (44 bp):
AAGGAGCTTTGTTTATTTTTCTAAAGTTGTTAAGCCTCTGCTTA
Found at i:12956765 original size:14 final size:14
Alignment explanation
Indices: 12956746--12956774 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
12956736 TCCATCATTG
12956746 ACAATTCACCCCGA
1 ACAATTCACCCCGA
12956760 ACAATTCACCCCGA
1 ACAATTCACCCCGA
12956774 A
1 A
12956775 GCGGTTCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.41, G:0.07, T:0.14
Consensus pattern (14 bp):
ACAATTCACCCCGA
Found at i:12957830 original size:13 final size:12
Alignment explanation
Indices: 12957802--12957887 Score: 57
Period size: 12 Copynumber: 6.7 Consensus size: 12
12957792 CCGTTTTGAT
12957802 TTTTTTTGGTTT-
1 TTTTTTT-GTTTA
12957814 TTTTTATTGTTTA
1 TTTTT-TTGTTTA
12957827 TTTTCTTTGTTTA
1 TTTT-TTTGTTTA
*
12957840 TTTTGTAGTTTTTTTA
1 -TTT-T--TTTGTTTA
**
12957856 TTTTTTAATTTA
1 TTTTTTTGTTTA
* *
12957868 TGTGTTTGTTTA
1 TTTTTTTGTTTA
12957880 TTTTTTTG
1 TTTTTTTG
12957888 GGAATATTTT
Statistics
Matches: 58, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
12 29 0.50
13 13 0.22
14 5 0.09
15 4 0.07
16 7 0.12
ACGTcount: A:0.10, C:0.01, G:0.12, T:0.77
Consensus pattern (12 bp):
TTTTTTTGTTTA
Found at i:12965827 original size:11 final size:11
Alignment explanation
Indices: 12965771--12965839 Score: 54
Period size: 11 Copynumber: 6.4 Consensus size: 11
12965761 AACAAAGTAA
12965771 AATGTGATGTA-
1 AATGTGATG-AG
*
12965782 AATGCG-TGAG
1 AATGTGATGAG
* *
12965792 AATGTCATGGAA
1 AATGTGAT-GAG
* *
12965804 AATGGGATAAG
1 AATGTGATGAG
12965815 AATGTGATGAG
1 AATGTGATGAG
12965826 AATGTGATGA-
1 AATGTGATGAG
12965836 AATG
1 AATG
12965840 CAAGAAAAAG
Statistics
Matches: 45, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
9 1 0.02
10 10 0.22
11 26 0.58
12 8 0.18
ACGTcount: A:0.39, C:0.03, G:0.32, T:0.26
Consensus pattern (11 bp):
AATGTGATGAG
Found at i:12974814 original size:20 final size:20
Alignment explanation
Indices: 12974789--12974828 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
12974779 CAAGATTTCC
12974789 AAAAAATTATGTTTGATTTT
1 AAAAAATTATGTTTGATTTT
12974809 AAAAAATTATGTTTGATTTT
1 AAAAAATTATGTTTGATTTT
12974829 CTTTTCTTTC
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:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (20 bp):
AAAAAATTATGTTTGATTTT
Found at i:12975182 original size:43 final size:43
Alignment explanation
Indices: 12975127--12975582 Score: 427
Period size: 43 Copynumber: 10.3 Consensus size: 43
12975117 CCATCGAGGA
* * *
12975127 AAACAAATTTAAATTAAGAAATGGGCTCATCTATACAGAGGCT
1 AAACAACTTTAAAATAAGAAATGGGCTCCTCTATACAGAGGCT
* * ** * *
12975170 AAATAATTTTAAAATAAGAAATGAACTCTTCTATGCAGAGGCT
1 AAACAACTTTAAAATAAGAAATGGGCTCCTCTATACAGAGGCT
* *
12975213 AAACAACTTTAAAATAAGAAATGGTCTCCAT-TATACATAGGCT
1 AAACAACTTTAAAATAAGAAATGGGCTCC-TCTATACAGAGGCT
* *
12975256 AAACAACTTTAAAATAGTTAAAATAGGAAATGGGCTCCAT-TATAAATAGGCT
1 AAACAACTTT-AAA-A--T---A-A-GAAATGGGCTCC-TCTATACAGAGGCT
* * **
12975308 AAACAACTTTAAAATATGAAATGGACTCCTCTATGTAGAGGCT
1 AAACAACTTTAAAATAAGAAATGGGCTCCTCTATACAGAGGCT
* *
12975351 AAACAACTTTAAAATTAAAAAATGGGCTCCTCTACACAGAGGCT
1 AAACAACTTTAAAA-TAAGAAATGGGCTCCTCTATACAGAGGCT
* * *
12975395 AAAACAACTTTAAAATAGGAAATGGG-TCCTTTATACATAGGCT
1 -AAACAACTTTAAAATAAGAAATGGGCTCCTCTATACAGAGGCT
* * * * *
12975438 AAAATAACTTTAAAATAGGAAATGGGCTCTTTTATACAGA-TCTT
1 -AAACAACTTTAAAATAAGAAATGGGCTCCTCTATACAGAGGC-T
* *
12975482 AAACAACTTTAAAAT-AGAAAATGGACTCCTCTATATAGAGGCT
1 AAACAACTTTAAAATAAG-AAATGGGCTCCTCTATACAGAGGCT
* * *
12975525 AAAACAACTTTAAATTAAGAAATAGGCTCCTCTATACAAAGGCT
1 -AAACAACTTTAAAATAAGAAATGGGCTCCTCTATACAGAGGCT
*
12975569 AAATAACTTTAAAA
1 AAACAACTTTAAAA
12975583 ACTTTAAATA
Statistics
Matches: 344, Mismatches: 50, Indels: 38
0.80 0.12 0.09
Matches are distributed among these distances:
42 2 0.01
43 198 0.58
44 84 0.24
45 18 0.05
47 1 0.00
48 1 0.00
50 2 0.01
51 4 0.01
52 34 0.10
ACGTcount: A:0.44, C:0.15, G:0.14, T:0.27
Consensus pattern (43 bp):
AAACAACTTTAAAATAAGAAATGGGCTCCTCTATACAGAGGCT
Found at i:12975299 original size:52 final size:52
Alignment explanation
Indices: 12975221--12975323 Score: 179
Period size: 52 Copynumber: 2.0 Consensus size: 52
12975211 CTAAACAACT
* *
12975221 TTAAAATAAGAAATGGTCTCCATTATACATAGGCTAAACAACTTTAAAATAG
1 TTAAAATAAGAAATGGGCTCCATTATAAATAGGCTAAACAACTTTAAAATAG
*
12975273 TTAAAATAGGAAATGGGCTCCATTATAAATAGGCTAAACAACTTTAAAATA
1 TTAAAATAAGAAATGGGCTCCATTATAAATAGGCTAAACAACTTTAAAATA
12975324 TGAAATGGAC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.28
Consensus pattern (52 bp):
TTAAAATAAGAAATGGGCTCCATTATAAATAGGCTAAACAACTTTAAAATAG
Found at i:12975437 original size:87 final size:88
Alignment explanation
Indices: 12975273--12975582 Score: 364
Period size: 87 Copynumber: 3.6 Consensus size: 88
12975263 TTTAAAATAG
* * * *
12975273 TTAAAA-TAGGAAATGGGCTCCAT-TATAAATAGGCTAAACAACTTTAAAATATGAAATGGACTC
1 TTAAAATTAAGAAATGGGCTCC-TCTATACAGAGGCTAAACAACTTTAAAATAGGAAATGGACTC
*
12975336 CTCTATGTAGAGGCT-AAACAACT
65 CTCTATATAGAGGCTAAAACAACT
* * *
12975359 TTAAAATTAAAAAATGGGCTCCTCTACACAGAGGCTAAAACAACTTTAAAATAGGAAATGG-GTC
1 TTAAAATTAAGAAATGGGCTCCTCTATACAGAGGCT-AAACAACTTTAAAATAGGAAATGGACTC
* * * *
12975423 CTTTATACATAGGCTAAAATAACT
65 CTCTATATAGAGGCTAAAACAACT
* * * * *
12975447 TTAAAA-TAGGAAATGGGCTCTTTTATACAGA-TCTTAAACAACTTTAAAATAGAAAATGGACTC
1 TTAAAATTAAGAAATGGGCTCCTCTATACAGAGGC-TAAACAACTTTAAAATAGGAAATGGACTC
12975510 CTCTATATAGAGGCTAAAACAACT
65 CTCTATATAGAGGCTAAAACAACT
* * *
12975534 TT-AAATTAAGAAATAGGCTCCTCTATACAAAGGCTAAATAACTTTAAAA
1 TTAAAATTAAGAAATGGGCTCCTCTATACAGAGGCTAAACAACTTTAAAA
12975583 ACTTTAAATA
Statistics
Matches: 185, Mismatches: 31, Indels: 15
0.80 0.13 0.06
Matches are distributed among these distances:
86 34 0.18
87 114 0.62
88 37 0.20
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.27
Consensus pattern (88 bp):
TTAAAATTAAGAAATGGGCTCCTCTATACAGAGGCTAAACAACTTTAAAATAGGAAATGGACTCC
TCTATATAGAGGCTAAAACAACT
Found at i:12975954 original size:17 final size:17
Alignment explanation
Indices: 12975932--12976195 Score: 95
Period size: 17 Copynumber: 15.5 Consensus size: 17
12975922 TTTACAGAGG
12975932 TTTTAGATTCACAAGAA
1 TTTTAGATTCACAAGAA
*
12975949 TTTTAGTTTCACAAGAA
1 TTTTAGATTCACAAGAA
* * * *
12975966 -TCTAAAGTTCATAAGGA
1 TTTTAGA-TTCACAAGAA
* * **
12975983 -TTCATATTTGCAAGAA
1 TTTTAGATTCACAAGAA
*
12975999 TTTTTAGATTCATAAGAA
1 -TTTTAGATTCACAAGAA
*
12976017 -TTTAGATTCACAAGAC
1 TTTTAGATTCACAAGAA
* *
12976033 TTTAAAGATTCACAAGAC
1 TTT-TAGATTCACAAGAA
* * *
12976051 TTTCAGATTCGCAAGGA
1 TTTTAGATTCACAAGAA
* * * * *
12976068 TCTAAGTTTCATAAAAA
1 TTTTAGATTCACAAGAA
*
12976085 TTTCAGATTCACAAGAA
1 TTTTAGATTCACAAGAA
* * * ** *
12976102 CTTCAGGTTTGCAAGAG
1 TTTTAGATTCACAAGAA
* * * *
12976119 CTTTAGGTTCTCAAGAG
1 TTTTAGATTCACAAGAA
* * * *
12976136 CTTCA-AGTTTATAAGAA
1 TTTTAGA-TTCACAAGAA
*
12976153 TTTTAGGTTCACAAGAA
1 TTTTAGATTCACAAGAA
* * *
12976170 TTTAAGGTTCGCAAGAA
1 TTTTAGATTCACAAGAA
*
12976187 TTTAAGATT
1 TTTTAGATT
12976196 TGTAAGAATT
Statistics
Matches: 181, Mismatches: 59, Indels: 14
0.71 0.23 0.06
Matches are distributed among these distances:
16 23 0.13
17 131 0.72
18 27 0.15
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (17 bp):
TTTTAGATTCACAAGAA
Found at i:12976031 original size:34 final size:34
Alignment explanation
Indices: 12975932--12976101 Score: 121
Period size: 34 Copynumber: 5.0 Consensus size: 34
12975922 TTTACAGAGG
* *
12975932 TTTT-AGATTCACAAGAATTTTAGTTTCACAAGAA
1 TTTTAAGATTCATAAGAA-TTTAGATTCACAAGAA
* * * * * **
12975966 TCTAAAG-TTCATAAGGATTCATATTTGCAAGAA
1 TTTTAAGATTCATAAGAATTTAGATTCACAAGAA
* *
12975999 TTTTTAGATTCATAAGAATTTAGATTCACAAGAC
1 TTTTAAGATTCATAAGAATTTAGATTCACAAGAA
* * * * *
12976033 TTTAAAGATTCACAAGACTTTCAGATTCGCAAGGA
1 TTTTAAGATTCATAAGAATTT-AGATTCACAAGAA
* * *
12976068 -TCTAAGTTTCATAAAAATTTCAGATTCACAAGAA
1 TTTTAAGATTCATAAGAATTT-AGATTCACAAGAA
12976102 CTTCAGGTTT
Statistics
Matches: 100, Mismatches: 33, Indels: 6
0.72 0.24 0.04
Matches are distributed among these distances:
33 15 0.15
34 73 0.73
35 12 0.12
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (34 bp):
TTTTAAGATTCATAAGAATTTAGATTCACAAGAA
Found at i:12976214 original size:18 final size:17
Alignment explanation
Indices: 12976164--12976221 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 17
12976154 TTTAGGTTCA
* *
12976164 CAAGAATTTAAGGTTCG
1 CAAGAATTTAAGATTTG
12976181 CAAGAATTTAAGATTTG
1 CAAGAATTTAAGATTTG
* *
12976198 TAAGAATTTTTAGATTTG
1 CAAGAA-TTTAAGATTTG
12976216 CAAGAA
1 CAAGAA
12976222 ATTCAACTTC
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
17 20 0.57
18 15 0.43
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.34
Consensus pattern (17 bp):
CAAGAATTTAAGATTTG
Found at i:12976437 original size:22 final size:22
Alignment explanation
Indices: 12976412--12976482 Score: 72
Period size: 22 Copynumber: 3.1 Consensus size: 22
12976402 ATTTTAGGGT
*
12976412 TTCATATCCAAAATTTCAAAGA
1 TTCACATCCAAAATTTCAAAGA
* *
12976434 TTCACATTCAAACAATTT-TAAGAA
1 TTCACA-TCCAA-AATTTCAAAG-A
*
12976458 TTCCCATCCAAAATTTCAAAGA
1 TTCACATCCAAAATTTCAAAGA
12976480 TTC
1 TTC
12976483 TCATTTGAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
22 14 0.36
23 14 0.36
24 11 0.28
ACGTcount: A:0.42, C:0.21, G:0.04, T:0.32
Consensus pattern (22 bp):
TTCACATCCAAAATTTCAAAGA
Found at i:12976451 original size:46 final size:46
Alignment explanation
Indices: 12976380--12976560 Score: 143
Period size: 46 Copynumber: 4.0 Consensus size: 46
12976370 ACCTCTAGAA
** * ** *
12976380 TTCAAAGATTCTTATTTGAAAAATTTTAGGGTTTCATATCCAAAAT
1 TTCAAAGATTCACATTTCAAAAATTTTAGGAATTCACATCCAAAAT
* *
12976426 TTCAAAGATTCACA-TTCAAACAATTTTAAGAATTCCCATCCAAAAT
1 TTCAAAGATTCACATTTCAAA-AATTTTAGGAATTCACATCCAAAAT
* * * **
12976472 TTCAAAGATTCTCATTTGAAAAATTTTA-GAGATTCACATCTAAGGT
1 TTCAAAGATTCACATTTCAAAAATTTTAGGA-ATTCACATCCAAAAT
* *** * * *
12976518 TTCAAAG-GTCTTTTTTCAAAAACTTTATGAATTCACATTCAAA
1 TTCAAAGATTCACATTTCAAAAATTTTAGGAATTCACATCCAAA
12976561 GATTCTTATT
Statistics
Matches: 109, Mismatches: 22, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
45 32 0.29
46 72 0.66
47 5 0.05
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (46 bp):
TTCAAAGATTCACATTTCAAAAATTTTAGGAATTCACATCCAAAAT
Found at i:12976537 original size:92 final size:91
Alignment explanation
Indices: 12976380--12976624 Score: 204
Period size: 92 Copynumber: 2.7 Consensus size: 91
12976370 ACCTCTAGAA
* * * *
12976380 TTCAAAGATTCTTATTTGAAAAATTTTAGGGTTTCATATCCAAAATTTCAAAGATTCACATTCAA
1 TTCAAAGATTCTCATTTGAAAAATTTTAGAGATTCACATCCAAAATTTCAAAGATTCACATTCAA
* *
12976445 ACAATTTTAAGAATTCCCATCCAAAAT
66 A-AACTTTAAGAATTCACATCCAAAAT
* ** * ***
12976472 TTCAAAGATTCTCATTTGAAAAATTTTAGAGATTCACATCTAAGGTTTCAAAG-GTCTTTTTTCA
1 TTCAAAGATTCTCATTTGAAAAATTTTAGAGATTCACATCCAAAATTTCAAAGATTC-ACATTCA
*
12976536 AAAACTTTATGAATT--CA--C---A-
65 AAAACTTTAAGAATTCACATCCAAAAT
* * * *
12976555 TTCAAAGATTCTTATTTGAAAAAAATTTTA-AGGTTTCGCATCCAAAATTTCAAAGATTCTCATT
1 TTCAAAGATTCTCATTTG--AAAAATTTTAGA-GATTCACATCCAAAATTTCAAAGATTCACATT
*
12976619 CGAAAA
63 CAAAAA
12976625 GCTCTTTTAA
Statistics
Matches: 125, Mismatches: 23, Indels: 17
0.76 0.14 0.10
Matches are distributed among these distances:
83 17 0.14
84 2 0.02
85 36 0.29
86 2 0.02
87 1 0.01
89 2 0.02
91 13 0.10
92 52 0.42
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (91 bp):
TTCAAAGATTCTCATTTGAAAAATTTTAGAGATTCACATCCAAAATTTCAAAGATTCACATTCAA
AAACTTTAAGAATTCACATCCAAAAT
Found at i:12977131 original size:139 final size:138
Alignment explanation
Indices: 12976853--12977249 Score: 325
Period size: 139 Copynumber: 2.8 Consensus size: 138
12976843 GATTCACATG
* * * *
12976853 TTCCCTACAAGATGCAAATGCATGCCTCAACCATGATGCAAATACAATTATCAAGGATTTAAATA
1 TTCCCTACAAGATGAAAATGCATGCCCCAACCATGATGCAAACACAATTATCAAGGATGTAAATA
* * * * * * *
12976918 CAATGTAAACATAATATATGTAATGTAGATGTCACTACATATTCTTAAGGATTTAAATACAATGC
66 CAATGTAAACATAATATATG-AATGCAAATGTCACAACATATTCTCAAGGAATGAAAGACAATGC
12976983 AAATGCATA
130 AAATGCATA
* *
12976992 TTCCCTACATGATGAAAATGCATGCCCCAACCATGATGTAAACACAATTATCAAGGATGTAAATA
1 TTCCCTACAAGATGAAAATGCATGCCCCAACCATGATGCAAACACAATTATCAAGGATGTAAATA
* * * **
12977057 TAATGTATACATAATGTATG-ATGCAAATG-CAACAACCCATATTCTCATTGAATGATGGAA-AT
66 CAATGTAAACATAATATATGAATGCAAATGTC-ACAA--CATATTCTCAAGGAATGA---AAGA-
*
12977119 GCAAATGTCATATAATGATTCAAA
124 -C-AATG-C--A-AATG---CATA
* * * * *
12977143 GGTTCCCTA-AATGATGCAAATGCATACCTCAACCATGATGCAAATACAATTATCAAGGATTTAA
1 --TTCCCTACAA-GATGAAAATGCATGCCCCAACCATGATGCAAACACAATTATCAAGGATGTAA
* * * *
12977207 ATACAATGTAAACACAATGTATGTAATGCAGATGTCACTACAT
63 ATACAATGTAAACATAATATATG-AATGCAAATGTCACAACAT
12977250 CAATATCGTG
Statistics
Matches: 206, Mismatches: 30, Indels: 30
0.77 0.11 0.11
Matches are distributed among these distances:
136 1 0.00
137 10 0.05
139 89 0.43
141 1 0.00
142 2 0.01
143 1 0.00
144 4 0.02
145 1 0.00
147 1 0.00
148 4 0.02
151 3 0.01
152 1 0.00
153 76 0.37
155 11 0.05
156 1 0.00
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.28
Consensus pattern (138 bp):
TTCCCTACAAGATGAAAATGCATGCCCCAACCATGATGCAAACACAATTATCAAGGATGTAAATA
CAATGTAAACATAATATATGAATGCAAATGTCACAACATATTCTCAAGGAATGAAAGACAATGCA
AATGCATA
Found at i:12978718 original size:32 final size:32
Alignment explanation
Indices: 12978677--12978744 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 32
12978667 GGAATTTGGG
*
12978677 AATAGATATAGGAAAAGATGTTAAAAGGTAAA
1 AATAGATATAGAAAAAGATGTTAAAAGGTAAA
12978709 AATAGATATAGAAAAAGATGTTAAAAGGTAAA
1 AATAGATATAGAAAAAGATGTTAAAAGGTAAA
12978741 AATA
1 AATA
12978745 TATGATGATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.59, C:0.00, G:0.19, T:0.22
Consensus pattern (32 bp):
AATAGATATAGAAAAAGATGTTAAAAGGTAAA
Found at i:12990357 original size:16 final size:16
Alignment explanation
Indices: 12990338--12990368 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
12990328 GTTTATTGAG
12990338 TCCACCCATTATATAC
1 TCCACCCATTATATAC
12990354 TCCACCCATTATATA
1 TCCACCCATTATATA
12990369 AGCCTTACTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.35, G:0.00, T:0.32
Consensus pattern (16 bp):
TCCACCCATTATATAC
Found at i:12997565 original size:21 final size:21
Alignment explanation
Indices: 12997540--12997579 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
12997530 TAGGCATTAG
*
12997540 GGGATTAATCCCCTCATGTAA
1 GGGATCAATCCCCTCATGTAA
*
12997561 GGGATCGATCCCCTCATGT
1 GGGATCAATCCCCTCATGT
12997580 TATGAGATAG
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:0.23, C:0.28, G:0.23, T:0.28
Consensus pattern (21 bp):
GGGATCAATCCCCTCATGTAA
Found at i:13007307 original size:141 final size:142
Alignment explanation
Indices: 13007113--13007375 Score: 376
Period size: 141 Copynumber: 1.9 Consensus size: 142
13007103 TTTTTTTTAT
*
13007113 TAATTTTACATATAAATATTCCATTTTCACTAATTATTTGTTATCCTATTATCAAATAATTAATC
1 TAATTTTACATATAAATATTCCATTTTCACAAATTATTTGTTATCCTATTATCAAATAATTAATC
* *
13007178 ATTTTTATTAA-TTTC-TATAAAAATATACATTTCCTTATTTATTTATTTTATATATAGATTTTT
66 ATTTTTATTAATTTTCATATAAAAATAGACATTTCCTT-TTTA-TTAATTTATATATAGATTTTT
13007241 TTATTAATAAATAA
129 TTATTAATAAATAA
*
13007255 TAATTTTACATTTAAATATTCC-TTTTCACAAATTATTT-TTGA-CC-ATGGTATCAAATAATTA
1 TAATTTTACATATAAATATTCCATTTTCACAAATTATTTGTT-ATCCTAT--TATCAAATAATTA
** *
13007316 ATTGTTTTTATTAATTTTCATATAAATATAGACATTTCCTTTTTATTAATTTATATATAG
63 ATCATTTTTATTAATTTTCATATAAAAATAGACATTTCCTTTTTATTAATTTATATATAG
13007376 TGTTTTCTTG
Statistics
Matches: 109, Mismatches: 7, Indels: 11
0.86 0.06 0.09
Matches are distributed among these distances:
139 2 0.02
140 4 0.04
141 55 0.50
142 29 0.27
143 19 0.17
ACGTcount: A:0.36, C:0.10, G:0.03, T:0.51
Consensus pattern (142 bp):
TAATTTTACATATAAATATTCCATTTTCACAAATTATTTGTTATCCTATTATCAAATAATTAATC
ATTTTTATTAATTTTCATATAAAAATAGACATTTCCTTTTTATTAATTTATATATAGATTTTTTT
ATTAATAAATAA
Found at i:13008014 original size:2 final size:2
Alignment explanation
Indices: 13008007--13008042 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
13007997 AAAACCCCTC
*
13008007 AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13008043 AAGTAAGAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:13013374 original size:16 final size:18
Alignment explanation
Indices: 13013347--13013381 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
13013337 AAGGGACTTC
13013347 ATATGACATTATC-TTTT
1 ATATGACATTATCATTTT
13013364 ATATG-CATTATCATTTT
1 ATATGACATTATCATTTT
13013381 A
1 A
13013382 GAAAGATGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.31, C:0.11, G:0.06, T:0.51
Consensus pattern (18 bp):
ATATGACATTATCATTTT
Found at i:13021982 original size:21 final size:22
Alignment explanation
Indices: 13021939--13021982 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
13021929 AAGCCTAAAC
*
13021939 TTAAAAGATTGCAAATTAAGAA
1 TTAAAAGATTGCAAATCAAGAA
*
13021961 TTAAAAGATTGTAAA-CAAGAA
1 TTAAAAGATTGCAAATCAAGAA
13021982 T
1 T
13021983 GTTAAATTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.55, C:0.05, G:0.14, T:0.27
Consensus pattern (22 bp):
TTAAAAGATTGCAAATCAAGAA
Found at i:13022274 original size:17 final size:17
Alignment explanation
Indices: 13022254--13022298 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
13022244 CCAATACCTT
13022254 AACTAAAAGAACTAA-A
1 AACTAAAAGAACTAAGA
* *
13022270 GAACTAAAAAAACTTAGA
1 -AACTAAAAGAACTAAGA
13022288 AACTAAAAGAA
1 AACTAAAAGAA
13022299 AGAAAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 23 0.96
18 1 0.04
ACGTcount: A:0.67, C:0.11, G:0.09, T:0.13
Consensus pattern (17 bp):
AACTAAAAGAACTAAGA
Found at i:13026445 original size:14 final size:14
Alignment explanation
Indices: 13026426--13026471 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
13026416 AAATTTTAAG
13026426 TGAATTTAGCAATT
1 TGAATTTAGCAATT
13026440 TGAATTTTA--AA--
1 TGAA-TTTAGCAATT
13026451 TGAATTTAGCAATT
1 TGAATTTAGCAATT
13026465 TGAATTT
1 TGAATTT
13026472 TAAATGAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
10 4 0.15
11 4 0.15
12 2 0.07
13 2 0.07
14 11 0.41
15 4 0.15
ACGTcount: A:0.37, C:0.04, G:0.13, T:0.46
Consensus pattern (14 bp):
TGAATTTAGCAATT
Found at i:13026445 original size:25 final size:25
Alignment explanation
Indices: 13026411--13026483 Score: 128
Period size: 25 Copynumber: 2.9 Consensus size: 25
13026401 TTGTAATTTA
* *
13026411 AATTTAAATTTTAAGTGAATTTAGC
1 AATTTGAATTTTAAATGAATTTAGC
13026436 AATTTGAATTTTAAATGAATTTAGC
1 AATTTGAATTTTAAATGAATTTAGC
13026461 AATTTGAATTTTAAATGAATTTA
1 AATTTGAATTTTAAATGAATTTA
13026484 TTAACTAAGT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 46 1.00
ACGTcount: A:0.41, C:0.03, G:0.11, T:0.45
Consensus pattern (25 bp):
AATTTGAATTTTAAATGAATTTAGC
Found at i:13029180 original size:18 final size:17
Alignment explanation
Indices: 13029147--13029180 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
13029137 TTTAGATATT
13029147 ATTTTAAATTCAAATTA
1 ATTTTAAATTCAAATTA
*
13029164 ATTTTATAATTCCAATT
1 ATTTTA-AATTCAAATT
13029181 TAAAAGATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTTAAATTCAAATTA
Done.