Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 45 of 171
Found at i:19183866 original size:17 final size:18
Alignment explanation
Indices: 19183844--19183883 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
19183834 TAAAAATTAC
19183844 AAAATTTAT-ATTTTTAA
1 AAAATTTATAATTTTTAA
*
19183861 AAAA-TTATAATTTTTTA
1 AAAATTTATAATTTTTAA
19183878 AAAATT
1 AAAATT
19183884 CTAAAGAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 4 0.20
17 15 0.75
18 1 0.05
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AAAATTTATAATTTTTAA
Found at i:19183918 original size:17 final size:17
Alignment explanation
Indices: 19183817--19183918 Score: 53
Period size: 17 Copynumber: 5.6 Consensus size: 17
19183807 AATAATTTTT
*
19183817 AAATTTCAAAATATTTATA
1 AAATTT-AAAAAATTTA-A
* * *
19183836 AAAATTACAAAATTTAT
1 AAATTTAAAAAATTTAA
**
19183853 ATTTTTAAAAAA-TTATA
1 AAATTTAAAAAATTTA-A
** *
19183870 ATTTTTTAAAAATTCTAA
1 AAATTTAAAAAATT-TAA
19183888 AGAATATATAAAAAATTTAA
1 A-AAT-T-TAAAAAATTTAA
19183908 AAATTTAAAAA
1 AAATTTAAAAA
19183919 TAAGTTAATT
Statistics
Matches: 64, Mismatches: 13, Indels: 14
0.70 0.14 0.15
Matches are distributed among these distances:
16 3 0.05
17 25 0.39
18 12 0.19
19 11 0.17
20 5 0.08
21 8 0.12
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (17 bp):
AAATTTAAAAAATTTAA
Found at i:19184235 original size:10 final size:10
Alignment explanation
Indices: 19184220--19184244 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
19184210 TTATTTGGGT
19184220 TTTTTTTTTC
1 TTTTTTTTTC
19184230 TTTTTTTTTC
1 TTTTTTTTTC
19184240 TTTTT
1 TTTTT
19184245 GCGAATGTAG
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:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:19184465 original size:29 final size:30
Alignment explanation
Indices: 19184404--19184481 Score: 104
Period size: 29 Copynumber: 2.6 Consensus size: 30
19184394 TTAACCATTT
* *
19184404 TACATGAACTATGATTTAATGTGTAATTGTA
1 TACATGAAATTTGATTT-ATGTGTAATTGTA
*
19184435 TACATGAAATTTGATTT-TGTGTAATTTTA
1 TACATGAAATTTGATTTATGTGTAATTGTA
19184464 TACATGAAATTTTGATTT
1 TACATGAAA-TTTGATTT
19184482 GATCCAATTC
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
29 20 0.47
30 8 0.19
31 15 0.35
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.47
Consensus pattern (30 bp):
TACATGAAATTTGATTTATGTGTAATTGTA
Found at i:19196086 original size:30 final size:32
Alignment explanation
Indices: 19196007--19196088 Score: 82
Period size: 30 Copynumber: 2.6 Consensus size: 32
19195997 TTTTTTATTT
* *
19196007 AATATTAATATAATTTATTGTTATATATTTTTGGA
1 AATATT-ATATAA--TATTTTTATATATTTTTGAA
*
19196042 AATATT-TAT-TTATTTTTATATA-TTTT-AA
1 AATATTATATAATATTTTTATATATTTTTGAA
19196070 AATATTATATAATATTTTT
1 AATATTATATAATATTTTT
19196089 TGTCAACAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
28 7 0.17
29 7 0.17
30 18 0.44
33 3 0.07
35 6 0.15
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.59
Consensus pattern (32 bp):
AATATTATATAATATTTTTATATATTTTTGAA
Found at i:19199544 original size:27 final size:27
Alignment explanation
Indices: 19199506--19199559 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
19199496 GAGAGAATAT
19199506 TTATCTTAGATATTTAATATCTATCTC
1 TTATCTTAGATATTTAATATCTATCTC
19199533 TTATCTTAGATATTTAATATCTATCTC
1 TTATCTTAGATATTTAATATCTATCTC
19199560 ATATATTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.15, G:0.04, T:0.52
Consensus pattern (27 bp):
TTATCTTAGATATTTAATATCTATCTC
Found at i:19206499 original size:24 final size:25
Alignment explanation
Indices: 19206456--19206505 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
19206446 TAGAAATTTT
**
19206456 TAAAATTTTTATAATGTTTTAAAAA
1 TAAAATTTTTATAAAATTTTAAAAA
*
19206481 TAAAA-TTTTATAAAATTTTAGAAA
1 TAAAATTTTTATAAAATTTTAAAAA
19206505 T
1 T
19206506 TTAAAGTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (25 bp):
TAAAATTTTTATAAAATTTTAAAAA
Found at i:19210977 original size:26 final size:26
Alignment explanation
Indices: 19210941--19210993 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
19210931 CACATTTTTT
19210941 CACTTTTCACAATCTAGCCATCATAG
1 CACTTTTCACAATCTAGCCATCATAG
19210967 CACTTTTCACAATCTAGCCATCATAG
1 CACTTTTCACAATCTAGCCATCATAG
19210993 C
1 C
19210994 TTTCTTAACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.32, G:0.08, T:0.30
Consensus pattern (26 bp):
CACTTTTCACAATCTAGCCATCATAG
Found at i:19211149 original size:23 final size:23
Alignment explanation
Indices: 19211125--19211224 Score: 155
Period size: 23 Copynumber: 4.3 Consensus size: 23
19211115 TGCTGGGTAA
* *
19211125 CAGAGGGCACACAAAGTGCTAAA
1 CAGAGAGCACACAAAGTGCTAAT
*
19211148 CAGAGAGTACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
*
19211171 CAGAGAGCACACACAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
*
19211194 CAGAGAGTACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
19211217 CAGAGAGC
1 CAGAGAGC
19211225 GCGCTAGTGT
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 69 1.00
ACGTcount: A:0.42, C:0.21, G:0.24, T:0.13
Consensus pattern (23 bp):
CAGAGAGCACACAAAGTGCTAAT
Found at i:19211189 original size:46 final size:46
Alignment explanation
Indices: 19211125--19211224 Score: 173
Period size: 46 Copynumber: 2.2 Consensus size: 46
19211115 TGCTGGGTAA
*
19211125 CAGAGGGCACACAAAGTGCTAAACAGAGAGTACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAACAGAGAGTACACAAAGTGCTAAT
* *
19211171 CAGAGAGCACACACAGTGCTAATCAGAGAGTACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAACAGAGAGTACACAAAGTGCTAAT
19211217 CAGAGAGC
1 CAGAGAGC
19211225 GCGCTAGTGT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 51 1.00
ACGTcount: A:0.42, C:0.21, G:0.24, T:0.13
Consensus pattern (46 bp):
CAGAGAGCACACAAAGTGCTAAACAGAGAGTACACAAAGTGCTAAT
Found at i:19221675 original size:28 final size:27
Alignment explanation
Indices: 19221610--19221663 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
19221600 ATAAATTTTG
*
19221610 AAATTTTTATAAATGTTTTGAATTTTAA
1 AAATTTTT-TAAATGTTTTGAAATTTAA
19221638 AAATTATTTTAAAT-TTTTGAAATTTA
1 AAATT-TTTTAAATGTTTTGAAATTTA
19221664 CTTAAATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 11 0.46
28 10 0.42
29 3 0.12
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.54
Consensus pattern (27 bp):
AAATTTTTTAAATGTTTTGAAATTTAA
Found at i:19230763 original size:138 final size:138
Alignment explanation
Indices: 19230515--19230794 Score: 533
Period size: 138 Copynumber: 2.0 Consensus size: 138
19230505 CCGACCAATT
* *
19230515 TTTATCTAACCAGCCAATTTGCTTCATGATTATGTTATTATATTAATAGCAGTCACAACAATAAA
1 TTTATCTAACCAGCCAATTCGCTTCATGATTATGTTATCATATTAATAGCAGTCACAACAATAAA
19230580 ATAAACTACTAACAATCTAAAATGATTAATCTATAAGATCATTAAATTATTAGTAAATTTACGTG
66 ATAAACTACTAACAATCTAAAATGATTAATCTATAAGATCATTAAATTATTAGTAAATTTACGTG
19230645 TTGGTCAC
131 TTGGTCAC
*
19230653 TTTATCTAACCAGCCAATTCGCTTCATGATTATGTTATCATATTAGTAGCAGTCACAACAATAAA
1 TTTATCTAACCAGCCAATTCGCTTCATGATTATGTTATCATATTAATAGCAGTCACAACAATAAA
19230718 ATAAACTACTAACAATCTAAAATGATTAATCTATAAGATCATTAAATTATTAGTAAATTTACGTG
66 ATAAACTACTAACAATCTAAAATGATTAATCTATAAGATCATTAAATTATTAGTAAATTTACGTG
19230783 TTGGTCAC
131 TTGGTCAC
19230791 TTTA
1 TTTA
19230795 AAAAGTTATG
Statistics
Matches: 139, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
138 139 1.00
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.36
Consensus pattern (138 bp):
TTTATCTAACCAGCCAATTCGCTTCATGATTATGTTATCATATTAATAGCAGTCACAACAATAAA
ATAAACTACTAACAATCTAAAATGATTAATCTATAAGATCATTAAATTATTAGTAAATTTACGTG
TTGGTCAC
Found at i:19230853 original size:31 final size:31
Alignment explanation
Indices: 19230817--19230878 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
19230807 ATAATCATTG
*
19230817 AATTATTCGAAAGTTTTCATTTAAT-TCACTA
1 AATTATTCGAAAATTTTCATTT-ATGTCACTA
* *
19230848 AATTATTTGAAAATTTTTATTTATGTCACTA
1 AATTATTCGAAAATTTTCATTTATGTCACTA
19230879 GTCTGTCAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 2 0.07
31 25 0.93
ACGTcount: A:0.35, C:0.10, G:0.06, T:0.48
Consensus pattern (31 bp):
AATTATTCGAAAATTTTCATTTATGTCACTA
Found at i:19231716 original size:24 final size:25
Alignment explanation
Indices: 19231683--19231739 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
19231673 AACTTCTTTT
**
19231683 AAAATGATAAAATT-TTAATTTAATA
1 AAAAT-ATAAAATTATTAAAATAATA
19231708 AAAATAT-AAATTATTAAAATAATA
1 AAAATATAAAATTATTAAAATAATA
*
19231732 AAATTATA
1 AAAATATA
19231740 TTTTTACCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 5 0.19
24 17 0.63
25 5 0.19
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (25 bp):
AAAATATAAAATTATTAAAATAATA
Found at i:19235789 original size:12 final size:12
Alignment explanation
Indices: 19235772--19235797 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
19235762 TTGCTATTAT
19235772 ACACGCACACAC
1 ACACGCACACAC
19235784 ACACGCACACAC
1 ACACGCACACAC
19235796 AC
1 AC
19235798 CTATAGTATG
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:0.42, C:0.50, G:0.08, T:0.00
Consensus pattern (12 bp):
ACACGCACACAC
Found at i:19246602 original size:29 final size:28
Alignment explanation
Indices: 19246570--19246647 Score: 75
Period size: 29 Copynumber: 2.7 Consensus size: 28
19246560 ATTTATTTAG
*
19246570 AATTATAAAATATAAAAGAATTGACTAAA
1 AATTATAAAATATAAAA-AATTAACTAAA
* * *
19246599 AATTATAATAATATTAGAAATTAATTAAA
1 AATTATAA-AATATAAAAAATTAACTAAA
* *
19246628 AACTATAAAATTTATAAAAA
1 AATTATAAAATATA-AAAAA
19246648 CAATTTACTG
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
28 4 0.10
29 28 0.72
30 7 0.18
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.32
Consensus pattern (28 bp):
AATTATAAAATATAAAAAATTAACTAAA
Found at i:19246734 original size:15 final size:16
Alignment explanation
Indices: 19246716--19246749 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
19246706 ATTAAATATG
*
19246716 AATGTTTTA-ATAATA
1 AATGTTTTATAAAATA
19246731 AATGTTTTATAAAATA
1 AATGTTTTATAAAATA
19246747 AAT
1 AAT
19246750 ATAAATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (16 bp):
AATGTTTTATAAAATA
Found at i:19248144 original size:23 final size:23
Alignment explanation
Indices: 19248114--19248173 Score: 113
Period size: 23 Copynumber: 2.7 Consensus size: 23
19248104 CATAAAACCA
19248114 ATATATATATTATATATATATAT
1 ATATATATATTATATATATATAT
19248137 ATATATATATTATATATATATAT
1 ATATATATATTATATATATATAT
19248160 ATATATATA-TATAT
1 ATATATATATTATAT
19248174 TAAATCAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 5 0.14
23 32 0.86
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
ATATATATATTATATATATATAT
Found at i:19248192 original size:2 final size:2
Alignment explanation
Indices: 19248114--19248173 Score: 106
Period size: 2 Copynumber: 31.0 Consensus size: 2
19248104 CATAAAACCA
19248114 AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19248154 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
19248174 TAAATCAAAT
Statistics
Matches: 56, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 54 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:19248793 original size:30 final size:29
Alignment explanation
Indices: 19248712--19248793 Score: 76
Period size: 28 Copynumber: 2.8 Consensus size: 29
19248702 ATATTATATT
* * * *
19248712 AATTATGATTTAATGTGCAATTGTATATATA
1 AATTTTGATTTGATGT--AATTTTATACATA
* *
19248743 AATTTTGATCTG-TATAATTTTATACATA
1 AATTTTGATTTGATGTAATTTTATACATA
19248771 CAATTTTGATTTGATGTAATTTT
1 -AATTTTGATTTGATGTAATTTT
19248794 TATAAAATAT
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
28 11 0.27
29 11 0.27
30 10 0.24
31 9 0.22
ACGTcount: A:0.34, C:0.05, G:0.11, T:0.50
Consensus pattern (29 bp):
AATTTTGATTTGATGTAATTTTATACATA
Found at i:19254691 original size:2 final size:2
Alignment explanation
Indices: 19254684--19254731 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
19254674 CAAACAAATA
19254684 AT AT AT AT AT AT AT 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 AT AT AT AT
19254726 AT AT AT
1 AT AT AT
19254732 TATTTAGATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19255798 original size:21 final size:22
Alignment explanation
Indices: 19255772--19255812 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
19255762 AGATAACGTA
*
19255772 GTTTTGTCTTTTAA-TTTAATT
1 GTTTTGACTTTTAACTTTAATT
19255793 GTTTTGACTTTTAACTTTAA
1 GTTTTGACTTTTAACTTTAA
19255813 AAAAAGTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.22, C:0.07, G:0.10, T:0.61
Consensus pattern (22 bp):
GTTTTGACTTTTAACTTTAATT
Found at i:19259393 original size:19 final size:19
Alignment explanation
Indices: 19259369--19259407 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
19259359 TTTATTATTA
*
19259369 ATATATTTATAATTATAAT
1 ATATATTTATAATTAAAAT
*
19259388 ATATATTTATTATTAAAAT
1 ATATATTTATAATTAAAAT
19259407 A
1 A
19259408 AAATTGTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATATATTTATAATTAAAAT
Found at i:19290548 original size:24 final size:24
Alignment explanation
Indices: 19290519--19290565 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
19290509 TATAAATAAT
*
19290519 AAAATTAT-AAATTAAAAAATAAAC
1 AAAATTATGAAAAT-AAAAATAAAC
*
19290543 AAAATTTTGAAAATAAAAATAAA
1 AAAATTATGAAAATAAAAATAAA
19290566 TAAATGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATTATGAAAATAAAAATAAAC
Found at i:19296697 original size:10 final size:10
Alignment explanation
Indices: 19296684--19296732 Score: 64
Period size: 10 Copynumber: 5.0 Consensus size: 10
19296674 ATTTTTGAGA
19296684 TTTTTTTATT
1 TTTTTTTATT
19296694 TTTTTTTATT
1 TTTTTTTATT
*
19296704 TTTTTTTATA
1 TTTTTTTATT
*
19296714 ATTTTTT-TT
1 TTTTTTTATT
*
19296723 TTTATTTATT
1 TTTTTTTATT
19296733 ATGTAGTACG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
9 6 0.18
10 27 0.82
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (10 bp):
TTTTTTTATT
Found at i:19302237 original size:21 final size:21
Alignment explanation
Indices: 19302172--19302240 Score: 59
Period size: 21 Copynumber: 3.1 Consensus size: 21
19302162 TGATTAATTT
* *
19302172 TGATGAGATTAAAAATAATAA
1 TGATAAGATTAAAATTAATAA
* *
19302193 TGGTGATAAAATTAATTATT-ATAA
1 ---TGATAAGATTAA-AATTAATAA
19302217 TGATAAGATTAAAATTAATAA
1 TGATAAGATTAAAATTAATAA
19302238 TGA
1 TGA
19302241 AATACTTGTT
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
20 3 0.08
21 18 0.49
24 14 0.38
25 2 0.05
ACGTcount: A:0.52, C:0.00, G:0.13, T:0.35
Consensus pattern (21 bp):
TGATAAGATTAAAATTAATAA
Found at i:19314749 original size:12 final size:12
Alignment explanation
Indices: 19314729--19314769 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
19314719 CCTTTGTTTA
*
19314729 AAAACTTAATTC
1 AAAATTTAATTC
*
19314741 AAAATTTAATTT
1 AAAATTTAATTC
19314753 AAAATTTAA-TC
1 AAAATTTAATTC
19314764 AAAATT
1 AAAATT
19314770 AAATATAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
11 7 0.27
12 19 0.73
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (12 bp):
AAAATTTAATTC
Found at i:19315475 original size:16 final size:16
Alignment explanation
Indices: 19315454--19315488 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
19315444 AATTAAATTA
19315454 ATTTATTTTAAAAAAT
1 ATTTATTTTAAAAAAT
* *
19315470 ATTTATTTTTAAAATT
1 ATTTATTTTAAAAAAT
19315486 ATT
1 ATT
19315489 CAATAATGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTTATTTTAAAAAAT
Found at i:19315502 original size:31 final size:32
Alignment explanation
Indices: 19315466--19315526 Score: 99
Period size: 31 Copynumber: 1.9 Consensus size: 32
19315456 TTATTTTAAA
19315466 AAATATTTAT-TTTTAAAATT-ATTCAATAATG
1 AAATATTT-TCTTTTAAAATTGATTCAATAATG
19315497 AAATATTTTCTTTTAAAATTGATTCAATAA
1 AAATATTTTCTTTTAAAATTGATTCAATAA
19315527 GTGGAGTGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
30 1 0.04
31 18 0.64
32 9 0.32
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (32 bp):
AAATATTTTCTTTTAAAATTGATTCAATAATG
Found at i:19334283 original size:31 final size:31
Alignment explanation
Indices: 19334242--19334343 Score: 79
Period size: 31 Copynumber: 3.3 Consensus size: 31
19334232 ATTATATTAA
*
19334242 TAATTTATAAGAATTTGATCAAATTAAAATT
1 TAATATATAAGAATTTGATCAAATTAAAATT
*
19334273 TAATATATAAG-A-TTG-TACAAAATCAAAATT
1 TAATATATAAGAATTTGAT-C-AAATTAAAATT
* * *
19334303 T-ATATAT-AGAATTATAGATTAAACTAAAAAT
1 TAATATATAAGAATT-T-GATCAAATTAAAATT
*
19334334 TAATGTATAA
1 TAATATATAA
19334344 TTTTAAGATT
Statistics
Matches: 55, Mismatches: 7, Indels: 16
0.71 0.09 0.21
Matches are distributed among these distances:
28 3 0.05
29 11 0.20
30 13 0.24
31 20 0.36
32 6 0.11
33 2 0.04
ACGTcount: A:0.52, C:0.04, G:0.07, T:0.37
Consensus pattern (31 bp):
TAATATATAAGAATTTGATCAAATTAAAATT
Found at i:19334756 original size:22 final size:22
Alignment explanation
Indices: 19334723--19334774 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
19334713 TAAAAATTAA
* *
19334723 AATTTCTT-AATTTGGTATTGG
1 AATTTTTTCAATTTGATATTGG
*
19334744 AATTTTTTCAATTTGATATTTG
1 AATTTTTTCAATTTGATATTGG
*
19334766 AGTTTTTTC
1 AATTTTTTC
19334775 CTCAATTAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 7 0.27
22 19 0.73
ACGTcount: A:0.23, C:0.06, G:0.13, T:0.58
Consensus pattern (22 bp):
AATTTTTTCAATTTGATATTGG
Found at i:19341352 original size:2 final size:2
Alignment explanation
Indices: 19341345--19341369 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19341335 TCTCCAAATC
19341345 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 T
19341370 TAAATGTTCA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19349110 original size:1 final size:1
Alignment explanation
Indices: 19349104--19349140 Score: 56
Period size: 1 Copynumber: 37.0 Consensus size: 1
19349094 CAGCCATCTC
* *
19349104 TTTTTTTTTCTTTTTTTCTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
19349141 GGCCTTAACC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.05, G:0.00, T:0.95
Consensus pattern (1 bp):
T
Found at i:19349138 original size:18 final size:18
Alignment explanation
Indices: 19349102--19349137 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
19349092 CACAGCCATC
19349102 TCTTTTTTTTTCTTTTTT
1 TCTTTTTTTTTCTTTTTT
19349120 TCTTTTTTTTT-TTTTTT
1 TCTTTTTTTTTCTTTTTT
19349137 T
1 T
19349138 TTTGGCCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (18 bp):
TCTTTTTTTTTCTTTTTT
Found at i:19356414 original size:3 final size:3
Alignment explanation
Indices: 19356406--19356430 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
19356396 AATACAATCC
19356406 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
19356431 AAGAGGTAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:19361059 original size:14 final size:15
Alignment explanation
Indices: 19361040--19361068 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
19361030 AAATCGTCTA
19361040 TATTTTT-ATAATTT
1 TATTTTTAATAATTT
19361054 TATTTTTAATAATTT
1 TATTTTTAATAATTT
19361069 AAAATTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TATTTTTAATAATTT
Found at i:19363873 original size:28 final size:29
Alignment explanation
Indices: 19363841--19363896 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
19363831 TTTGCATACA
19363841 TAATAAAAAAATAGA-TTATTTTTATAAT
1 TAATAAAAAAATAGAGTTATTTTTATAAT
* *
19363869 TAATAAAAAATTCGAGTTATTTTTATAA
1 TAATAAAAAAATAGAGTTATTTTTATAA
19363897 AAAAAGTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 13 0.52
29 12 0.48
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (29 bp):
TAATAAAAAAATAGAGTTATTTTTATAAT
Found at i:19365652 original size:15 final size:16
Alignment explanation
Indices: 19365616--19365655 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
19365606 ATAGTAAAAA
19365616 TATAATTTTATCATTTT
1 TATAA-TTTATCATTTT
*
19365633 AATAATTTAT-ATTTT
1 TATAATTTATCATTTT
19365648 TATAATTT
1 TATAATTT
19365656 TAAAAAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 12 0.57
16 5 0.24
17 4 0.19
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
TATAATTTATCATTTT
Found at i:19365656 original size:8 final size:8
Alignment explanation
Indices: 19365616--19365657 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
19365606 ATAGTAAAAA
19365616 TATAATTT
1 TATAATTT
*
19365624 TATCATTT
1 TATAATTT
19365632 TAATAA-TT
1 T-ATAATTT
*
19365640 TATATTTT
1 TATAATTT
19365648 TATAATTT
1 TATAATTT
19365656 TA
1 TA
19365658 AAAAATTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 3 0.11
8 22 0.79
9 3 0.11
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (8 bp):
TATAATTT
Found at i:19369382 original size:18 final size:18
Alignment explanation
Indices: 19369356--19369393 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
19369346 TTGAATTTCG
*
19369356 AATTTGAAT-AACTCGAAT
1 AATTCGAATAAAC-CGAAT
19369374 AATTCGAATAAACCGAAT
1 AATTCGAATAAACCGAAT
19369392 AA
1 AA
19369394 AACTATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.50, C:0.13, G:0.11, T:0.26
Consensus pattern (18 bp):
AATTCGAATAAACCGAAT
Found at i:19377144 original size:2 final size:2
Alignment explanation
Indices: 19377137--19377168 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
19377127 GTGTTTATGC
19377137 AT AT 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
19377169 TGCATATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19377302 original size:90 final size:90
Alignment explanation
Indices: 19377149--19377331 Score: 366
Period size: 90 Copynumber: 2.0 Consensus size: 90
19377139 ATATATATAT
19377149 ATATATATATATATATATATTGCATATTATTACATCTAAAAAATATGAAAAAATAATATAATTAA
1 ATATATATATATATATATATTGCATATTATTACATCTAAAAAATATGAAAAAATAATATAATTAA
19377214 AGTTAATTAGCAAAAATATGCATAC
66 AGTTAATTAGCAAAAATATGCATAC
19377239 ATATATATATATATATATATTGCATATTATTACATCTAAAAAATATGAAAAAATAATATAATTAA
1 ATATATATATATATATATATTGCATATTATTACATCTAAAAAATATGAAAAAATAATATAATTAA
19377304 AGTTAATTAGCAAAAATATGCATAC
66 AGTTAATTAGCAAAAATATGCATAC
19377329 ATA
1 ATA
19377332 CCGCAGCAAC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
90 93 1.00
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.36
Consensus pattern (90 bp):
ATATATATATATATATATATTGCATATTATTACATCTAAAAAATATGAAAAAATAATATAATTAA
AGTTAATTAGCAAAAATATGCATAC
Found at i:19390076 original size:40 final size:41
Alignment explanation
Indices: 19389999--19390114 Score: 144
Period size: 40 Copynumber: 2.9 Consensus size: 41
19389989 AATATTTAAT
* * * *
19389999 TAGTTGGAAAGTAATTCTAACGTTTCATATATCAAGTTATA
1 TAGTTGGAAAGTATTTCTAATGTTTGATATGTCAAGTTATA
* * * *
19390040 TATTTTGAAAGTATTT-TAATGTTTGATTTGTCAAGTTTTA
1 TAGTTGGAAAGTATTTCTAATGTTTGATATGTCAAGTTATA
*
19390080 TAGTTGGAAAGTATTTCTAATGTTTGGTATGTCAA
1 TAGTTGGAAAGTATTTCTAATGTTTGATATGTCAA
19390115 ATTTTATTTA
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
40 33 0.53
41 29 0.47
ACGTcount: A:0.31, C:0.06, G:0.17, T:0.46
Consensus pattern (41 bp):
TAGTTGGAAAGTATTTCTAATGTTTGATATGTCAAGTTATA
Found at i:19390113 original size:41 final size:41
Alignment explanation
Indices: 19389999--19390121 Score: 149
Period size: 41 Copynumber: 3.0 Consensus size: 41
19389989 AATATTTAAT
* * * * *
19389999 TAGTTGGAAAGTAATTCTAACGTTTCATATATCAAGTTATA
1 TAGTTGGAAAGTATTTCTAATGTTTGATATGTCAAGTTTTA
* * *
19390040 TATTTTGAAAGTATTT-TAATGTTTGATTTGTCAAGTTTTA
1 TAGTTGGAAAGTATTTCTAATGTTTGATATGTCAAGTTTTA
* *
19390080 TAGTTGGAAAGTATTTCTAATGTTTGGTATGTCAAATTTTA
1 TAGTTGGAAAGTATTTCTAATGTTTGATATGTCAAGTTTTA
19390121 T
1 T
19390122 TTAATTTTAT
Statistics
Matches: 68, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
40 33 0.49
41 35 0.51
ACGTcount: A:0.31, C:0.06, G:0.16, T:0.47
Consensus pattern (41 bp):
TAGTTGGAAAGTATTTCTAATGTTTGATATGTCAAGTTTTA
Found at i:19390738 original size:21 final size:21
Alignment explanation
Indices: 19390714--19390765 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 21
19390704 ATCTACCACA
19390714 AAGGTAGAGAAAACGTACCGC
1 AAGGTAGAGAAAACGTACCGC
*
19390735 AAGGT--AG-AAACGTGCCGC
1 AAGGTAGAGAAAACGTACCGC
*
19390753 AAGGCAGAGAAAA
1 AAGGTAGAGAAAA
19390766 AACGTACCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 14 0.54
19 2 0.08
20 2 0.08
21 8 0.31
ACGTcount: A:0.44, C:0.17, G:0.31, T:0.08
Consensus pattern (21 bp):
AAGGTAGAGAAAACGTACCGC
Found at i:19390804 original size:13 final size:13
Alignment explanation
Indices: 19390786--19390819 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
19390776 AAAAGCAAAT
19390786 AAAAACTAGAAAA
1 AAAAACTAGAAAA
*
19390799 AAAAACTATAAAA
1 AAAAACTAGAAAA
*
19390812 AATAACTA
1 AAAAACTA
19390820 AATATAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.74, C:0.09, G:0.03, T:0.15
Consensus pattern (13 bp):
AAAAACTAGAAAA
Found at i:19392150 original size:19 final size:19
Alignment explanation
Indices: 19392077--19392142 Score: 53
Period size: 19 Copynumber: 3.4 Consensus size: 19
19392067 TAATATTTTC
*
19392077 ATATTTTCACAACATATTATTA
1 ATATTTTCA-AA-ATTTTA-TA
* * *
19392099 ATATCTT-ATAATTTTCTA
1 ATATTTTCAAAATTTTATA
*
19392117 TTATTTTCAAAATTTTATA
1 ATATTTTCAAAATTTTATA
19392136 ATATTTT
1 ATATTTT
19392143 AACAATTTAT
Statistics
Matches: 34, Mismatches: 9, Indels: 5
0.71 0.19 0.10
Matches are distributed among these distances:
18 7 0.21
19 19 0.56
20 1 0.03
21 1 0.03
22 6 0.18
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (19 bp):
ATATTTTCAAAATTTTATA
Found at i:19392324 original size:16 final size:16
Alignment explanation
Indices: 19392299--19392338 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
19392289 TGTTTGGTTC
19392299 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
* *
19392315 GCTGTTATGGAATAGG
1 GCTGTAATGGAATAGA
19392331 GCTGTAAT
1 GCTGTAAT
19392339 CAGTAATTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.30, C:0.07, G:0.33, T:0.30
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:19392523 original size:48 final size:49
Alignment explanation
Indices: 19392427--19392520 Score: 188
Period size: 49 Copynumber: 1.9 Consensus size: 49
19392417 TAATAGCATA
19392427 AGAAAAAATGCTTAAATGACTAAAGTACCCTTAACAAATTTTTTTTAGT
1 AGAAAAAATGCTTAAATGACTAAAGTACCCTTAACAAATTTTTTTTAGT
19392476 AGAAAAAATGCTTAAATGACTAAAGTACCCTTAACAAATTTTTTT
1 AGAAAAAATGCTTAAATGACTAAAGTACCCTTAACAAATTTTTTT
19392521 AGTTAGATGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.34
Consensus pattern (49 bp):
AGAAAAAATGCTTAAATGACTAAAGTACCCTTAACAAATTTTTTTTAGT
Found at i:19392617 original size:54 final size:52
Alignment explanation
Indices: 19392553--19392655 Score: 145
Period size: 54 Copynumber: 1.9 Consensus size: 52
19392543 AATTTTAATG
*
19392553 ATTATTATTAAATATAATTTAAAAAATTAATTAATTTAAT-TATATTTTAACATA
1 ATTATCATTAAATATAATTTAAAAAA-T-A-TAATTTAATATATATTTTAACATA
*
19392607 ATTATCATTAAATATAATTTAATAAATATAATTTAATAATATATTTTAA
1 ATTATCATTAAATATAATTTAAAAAATATAATTTAAT-ATATATTTTAA
19392656 TATATATTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
51 9 0.20
52 1 0.02
53 11 0.24
54 24 0.53
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (52 bp):
ATTATCATTAAATATAATTTAAAAAATATAATTTAATATATATTTTAACATA
Found at i:19392634 original size:14 final size:14
Alignment explanation
Indices: 19392615--19392662 Score: 71
Period size: 14 Copynumber: 3.5 Consensus size: 14
19392605 TAATTATCAT
19392615 TAAATATAATTTAA
1 TAAATATAATTTAA
19392629 TAAATATAATTTAA
1 TAAATATAATTTAA
*
19392643 T-AATATATTTTAA
1 TAAATATAATTTAA
*
19392656 TATATAT
1 TAAATAT
19392663 TTTTATTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
13 12 0.39
14 19 0.61
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TAAATATAATTTAA
Found at i:19396538 original size:23 final size:23
Alignment explanation
Indices: 19396464--19396792 Score: 286
Period size: 23 Copynumber: 14.5 Consensus size: 23
19396454 TAAACGGAAC
* *
19396464 AAACAGAGAGTAC-CAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
* *
19396486 GAACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
19396508 GGGCAACAGAGAGCACACAAAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
*
19396534 AAACAGAGAGTACACAAA--G-T
1 AAACAGAGAGCACACAAAGTGCT
*
19396554 --AC--TGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
19396573 AATCAGAGAGCACACGAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
19396596 AATCAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
19396619 AATAACAGAGAGCACGA-GACGTGCT
1 -A-AACAGAGAGCAC-ACAAAGTGCT
*
19396644 AAACAGAGAGCACACATAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* * *
19396667 AATCAGAGAGCACGA-GACGTGCT
1 AAACAGAGAGCAC-ACAAAGTGCT
*
19396690 AAACAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* * *
19396713 AATCAGAGAGCACGA-GACGTGCT
1 AAACAGAGAGCAC-ACAAAGTGCT
*
19396736 AAACAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
19396759 AATCAGAGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
19396782 AATCAGAGAGC
1 AAACAGAGAGC
19396793 GCGCTAGTGT
Statistics
Matches: 247, Mismatches: 40, Indels: 39
0.76 0.12 0.12
Matches are distributed among these distances:
16 10 0.04
18 3 0.01
19 1 0.00
20 1 0.00
21 2 0.01
22 20 0.08
23 169 0.68
24 4 0.02
25 29 0.12
26 8 0.03
ACGTcount: A:0.42, C:0.22, G:0.25, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:19396539 original size:48 final size:45
Alignment explanation
Indices: 19396464--19396792 Score: 332
Period size: 46 Copynumber: 7.2 Consensus size: 45
19396454 TAAACGGAAC
* * *
19396464 AAACAGAGAGTAC-CAAAGTACTGAA-CAGAGAGCACATAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT-AATCAGAGAGCACAGAAGTGCT
* * * * *
19396508 GGGCAACAGAGAGCACACAAAGTGCTAAACAGAGAGTACACAA-AG-T
1 ---AAACAGAGAGCACACAAAGTGCTAATCAGAGAGCACAGAAGTGCT
*
19396554 --AC--TGAGCACACAAAGTGCTAATCAGAGAGCACACGAAGTGCT
1 AAACAGAGAGCACACAAAGTGCTAATCAGAGAGCACA-GAAGTGCT
* * *
19396596 AATCAGAGAGCACACACAGTGCTAATAACAGAGAGCACGAGACGTGCT
1 AAACAGAGAGCACACAAAGTGCTAAT--CAGAGAGCAC-AGAAGTGCT
* *
19396644 AAACAGAGAGCACACATAGTGCTAATCAGAGAGCACGAGACGTGCT
1 AAACAGAGAGCACACAAAGTGCTAATCAGAGAGCAC-AGAAGTGCT
* *
19396690 AAACAGAGAGCACACACAGTGCTAATCAGAGAGCACGAGACGTGCT
1 AAACAGAGAGCACACAAAGTGCTAATCAGAGAGCAC-AGAAGTGCT
* *
19396736 AAACAGAGAGCACACACAGTGCTAATCAGAGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCTAATCAGAGAGCACA-GAAGTGCT
*
19396782 AATCAGAGAGC
1 AAACAGAGAGC
19396793 GCGCTAGTGT
Statistics
Matches: 248, Mismatches: 21, Indels: 27
0.84 0.07 0.09
Matches are distributed among these distances:
39 28 0.11
40 2 0.01
41 3 0.01
42 1 0.00
44 1 0.00
45 1 0.00
46 136 0.55
47 14 0.06
48 61 0.25
49 1 0.00
ACGTcount: A:0.42, C:0.22, G:0.25, T:0.12
Consensus pattern (45 bp):
AAACAGAGAGCACACAAAGTGCTAATCAGAGAGCACAGAAGTGCT
Found at i:19396572 original size:39 final size:39
Alignment explanation
Indices: 19396518--19396592 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
19396508 GGGCAACAGA
*
19396518 GAGCACACAAAGTGCTAAACAGAGAGTACACAAAGTACT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
* *
19396557 GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGT
19396593 GCTAATCAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (39 bp):
GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
Found at i:19396792 original size:46 final size:46
Alignment explanation
Indices: 19396557--19396771 Score: 360
Period size: 46 Copynumber: 4.6 Consensus size: 46
19396547 ACAAAGTACT
* * *
19396557 GAGCACACAAAGTGCTAATCAGAGAGCAC-ACGAAGTGCTAATCAGA
1 GAGCACACACAGTGCTAATCAGAGAGCACGA-GACGTGCTAAACAGA
19396603 GAGCACACACAGTGCTAATAACAGAGAGCACGAGACGTGCTAAACAGA
1 GAGCACACACAGTGCTAAT--CAGAGAGCACGAGACGTGCTAAACAGA
*
19396651 GAGCACACATAGTGCTAATCAGAGAGCACGAGACGTGCTAAACAGA
1 GAGCACACACAGTGCTAATCAGAGAGCACGAGACGTGCTAAACAGA
19396697 GAGCACACACAGTGCTAATCAGAGAGCACGAGACGTGCTAAACAGA
1 GAGCACACACAGTGCTAATCAGAGAGCACGAGACGTGCTAAACAGA
19396743 GAGCACACACAGTGCTAATCAGAGAGCAC
1 GAGCACACACAGTGCTAATCAGAGAGCAC
19396772 ACAAAGTGCT
Statistics
Matches: 161, Mismatches: 5, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
46 119 0.74
48 41 0.25
49 1 0.01
ACGTcount: A:0.40, C:0.23, G:0.25, T:0.12
Consensus pattern (46 bp):
GAGCACACACAGTGCTAATCAGAGAGCACGAGACGTGCTAAACAGA
Found at i:19402592 original size:16 final size:16
Alignment explanation
Indices: 19402569--19402640 Score: 126
Period size: 16 Copynumber: 4.5 Consensus size: 16
19402559 CGTTTGGTTC
19402569 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
* *
19402585 GGTGTAATGAAATAGA
1 GCTGTAATGGAATAGA
19402601 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
19402617 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
19402633 GCTGTAAT
1 GCTGTAAT
19402641 CAGTAATTCA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 52 1.00
ACGTcount: A:0.38, C:0.06, G:0.31, T:0.26
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:19402681 original size:46 final size:44
Alignment explanation
Indices: 19402622--19402715 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 44
19402612 ATAGAGCTGT
* *
19402622 AATGGAATAGAGCTGTAATCAGTAATTCAAT-TGTTTGGTTGATTGG
1 AATGGAATAGAGCTGTAAT-AAT-ATTC-ATGTGTTTGGTTGAATGG
*
19402668 AATGGAATAGAGCTGTAATAATATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAGCTGTAATAATATTCATGTGTTTGGTTGAATGG
19402712 AATG
1 AATG
19402716 ATGCTGTAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
43 1 0.02
44 22 0.50
45 2 0.05
46 19 0.43
ACGTcount: A:0.31, C:0.05, G:0.27, T:0.37
Consensus pattern (44 bp):
AATGGAATAGAGCTGTAATAATATTCATGTGTTTGGTTGAATGG
Found at i:19402840 original size:16 final size:16
Alignment explanation
Indices: 19402821--19402914 Score: 50
Period size: 16 Copynumber: 6.0 Consensus size: 16
19402811 GATTATTATT
19402821 AAATATAATTTAATAA
1 AAATATAATTTAATAA
**
19402837 AAATATTAA-TTAATTT
1 AAATA-TAATTTAATAA
* * *
19402853 AATTATATTTTAATAT
1 AAATATAATTTAATAA
* * *
19402869 AATTATTATTAAAT-A
1 AAATATAATTTAATAA
* **
19402884 AAATTTAATAAAAT-A
1 AAATATAATTTAATAA
*
19402899 ATATATAATTTAATAA
1 AAATATAATTTAATAA
19402915 TATTTTTAAT
Statistics
Matches: 58, Mismatches: 17, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
15 23 0.40
16 32 0.55
17 3 0.05
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AAATATAATTTAATAA
Found at i:19402843 original size:26 final size:26
Alignment explanation
Indices: 19402803--19402948 Score: 94
Period size: 32 Copynumber: 5.1 Consensus size: 26
19402793 CTTATTAAAT
*
19402803 TTTAATAAGATTATTATTAAATATAA
1 TTTAATAAAATTATTATTAAATATAA
* *
19402829 TTTAATAAAAATATTAATTAATTTAATTATAT
1 TTTAAT--AAA-ATT-ATT-A-TTAAATATAA
* *
19402861 TTTAATATAATTATTATTAAATAAAA
1 TTTAATAAAATTATTATTAAATATAA
* *
19402887 TTTAATAAAATAATATATAATTTAATAATATT
1 TTTAATAAAAT--TAT-T-ATTAAAT-ATA-A
*
19402919 TTTAATATAATTATTATTAAAATATGAA
1 TTTAATAAAATTATTATT-AAATAT-AA
19402947 TT
1 TT
19402949 AGTAAAAATT
Statistics
Matches: 92, Mismatches: 14, Indels: 26
0.70 0.11 0.20
Matches are distributed among these distances:
26 23 0.25
27 1 0.01
28 15 0.16
29 12 0.13
30 14 0.15
31 3 0.03
32 24 0.26
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (26 bp):
TTTAATAAAATTATTATTAAATATAA
Found at i:19402874 original size:58 final size:58
Alignment explanation
Indices: 19402796--19402966 Score: 206
Period size: 58 Copynumber: 2.9 Consensus size: 58
19402786 GATTATTCTT
* *
19402796 ATTAAATTTTAATA-AGATTATTATTAAATATAATTTAATAAAAATATTA-ATTAATTTA
1 ATTATATTTTAATATA-ATTATTATTAAATATAATTTAATAAAAATAATATA-TAATTTA
*
19402854 ATTATATTTTAATATAATTATTATTAAATAAAATTTAAT-AAAATAATATATAATTTA
1 ATTATATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAATATATAATTTA
* * *
19402911 ATAATATTTTTAATATAATTATTATTAAAATATGAA-TTAGTAAAAATTATAATATA
1 ATTATA-TTTTAATATAATTATTATT-AAATAT-AATTTAATAAAAATAAT-ATATA
19402967 TAATATTAGA
Statistics
Matches: 99, Mismatches: 7, Indels: 11
0.85 0.06 0.09
Matches are distributed among these distances:
57 20 0.20
58 55 0.56
59 10 0.10
60 9 0.09
61 5 0.05
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (58 bp):
ATTATATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAATATATAATTTA
Found at i:19402933 original size:15 final size:15
Alignment explanation
Indices: 19402846--19402938 Score: 52
Period size: 15 Copynumber: 6.3 Consensus size: 15
19402836 AAAATATTAA
*
19402846 TTAATTTAATTATATT
1 TTAATATAATTAT-TT
*
19402862 TTAATATAATTATTA
1 TTAATATAATTATTT
*
19402877 TTAA-ATAA-AATTT
1 TTAATATAATTATTT
* * *
19402890 AATAAAATAATATATAAT
1 -TTAATATAAT-TAT-TT
19402908 TT-A-ATAA-TATTT
1 TTAATATAATTATTT
*
19402920 TTAATATAATTATTA
1 TTAATATAATTATTT
19402935 TTAA
1 TTAA
19402939 AATATGAATT
Statistics
Matches: 59, Mismatches: 10, Indels: 17
0.69 0.12 0.20
Matches are distributed among these distances:
12 3 0.05
13 7 0.12
14 11 0.19
15 21 0.36
16 13 0.22
17 3 0.05
18 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TTAATATAATTATTT
Found at i:19406647 original size:25 final size:25
Alignment explanation
Indices: 19406618--19406666 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
19406608 CAAAACTTGT
19406618 AGTCTTATTTCTTAATCCTAAACTG
1 AGTCTTATTTCTTAATCCTAAACTG
19406643 AGTCTTATTTCTTAATCCTAAACT
1 AGTCTTATTTCTTAATCCTAAACT
19406667 AATATACTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.29, C:0.20, G:0.06, T:0.45
Consensus pattern (25 bp):
AGTCTTATTTCTTAATCCTAAACTG
Found at i:19407821 original size:137 final size:139
Alignment explanation
Indices: 19407484--19407900 Score: 704
Period size: 139 Copynumber: 3.0 Consensus size: 139
19407474 TAAGCGACAC
* * *
19407484 TCAATATTTGGGTCTGAAAACATAGTTTCTGCAAACATGGTTGTGCAGAATCAGAAGCAATATAA
1 TCAATATTTGGGTCTCAAAACACAGTTTCTGCAAACATGGTTGTGCAGAATCAGAAGCAACATAA
*
19407549 TATTTGTACAACCAACAACACATTGAACCTCCTAGAACAAAATAACAGAATCAACAAAGTATCCT
66 TATTTGTACAACCAGCAACACATTGAACCTCCTAGAACAAAATAACAGAATCAACAAAGTATCCT
19407614 AACAGAATG
131 AACAGAATG
*
19407623 TCAATATTTAGGTCTCAAAACACAGTTTCTGCAAACATGGTTGTGCAGAATCAGAAGCAACATAA
1 TCAATATTTGGGTCTCAAAACACAGTTTCTGCAAACATGGTTGTGCAGAATCAGAAGCAACATAA
19407688 TATTTGTACAACCAGCAACACATTGAACC-CCTTAGAAC-AAATAACAGAATCAACAAAGTATCC
66 TATTTGTACAACCAGCAACACATTGAACCTCC-TAGAACAAAATAACAGAATCAACAAAGTATCC
19407751 TAACAGAATG
130 TAACAGAATG
*
19407761 TCAATA-TTGGGTCTCAAAACACAGTTTCTGCAAACATGGTTGTGCAAAATC-GAAAGCAACATA
1 TCAATATTTGGGTCTCAAAACACAGTTTCTGCAAACATGGTTGTGCAGAATCAG-AAGCAACATA
19407824 AT-TTTGTACAA-CAGCAACACATTGAACCTCCTAGAACAAAATAACAGAATCAAC-AAGTATCC
65 ATATTTGTACAACCAGCAACACATTGAACCTCCTAGAACAAAATAACAGAATCAACAAAGTATCC
19407886 TAACAGAATG
130 TAACAGAATG
*
19407896 GCAAT
1 TCAAT
19407901 GGATGATGAC
Statistics
Matches: 266, Mismatches: 8, Indels: 12
0.93 0.03 0.04
Matches are distributed among these distances:
135 45 0.17
136 28 0.11
137 55 0.21
138 43 0.16
139 95 0.36
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.24
Consensus pattern (139 bp):
TCAATATTTGGGTCTCAAAACACAGTTTCTGCAAACATGGTTGTGCAGAATCAGAAGCAACATAA
TATTTGTACAACCAGCAACACATTGAACCTCCTAGAACAAAATAACAGAATCAACAAAGTATCCT
AACAGAATG
Found at i:19408750 original size:39 final size:35
Alignment explanation
Indices: 19408707--19408797 Score: 92
Period size: 39 Copynumber: 2.4 Consensus size: 35
19408697 TACGGCCGAG
19408707 TCGAAGGAAGAAAGGCTGGAATCGGTGCTATGACAGTAA
1 TCGAAGGAAGAAA-G-TGGAA--GGTGCTATGACAGTAA
* *
19408746 TCGAAAGAGAGGGTAAAGTGGGAGGTGCTATGACAGTAA
1 TCG-AAG-GA-AG-AAAGTGGAAGGTGCTATGACAGTAA
19408785 TCGAAGGAAGAAA
1 TCGAAGGAAGAAA
19408798 AAGGGCAGGG
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
35 3 0.07
36 1 0.02
37 2 0.04
38 3 0.07
39 22 0.49
40 3 0.07
41 6 0.13
42 2 0.04
43 3 0.07
ACGTcount: A:0.38, C:0.10, G:0.35, T:0.16
Consensus pattern (35 bp):
TCGAAGGAAGAAAGTGGAAGGTGCTATGACAGTAA
Found at i:19413157 original size:18 final size:19
Alignment explanation
Indices: 19413134--19413178 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
19413124 CCAAAAAGTT
19413134 CATTTTTTCCCATTTC-TC
1 CATTTTTTCCCATTTCATC
*
19413152 CATTTTTTTCCATTTCTATC
1 CATTTTTTCCCATTTC-ATC
19413172 CATTTTT
1 CATTTTT
19413179 GTTCATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 15 0.62
20 9 0.38
ACGTcount: A:0.13, C:0.27, G:0.00, T:0.60
Consensus pattern (19 bp):
CATTTTTTCCCATTTCATC
Found at i:19414941 original size:15 final size:15
Alignment explanation
Indices: 19414906--19414948 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
19414896 AAAAGTAACG
19414906 AAGAAA-TAAAAAGA
1 AAGAAATTAAAAAGA
*
19414920 AAAAAATTAAAGAA-A
1 AAGAAATTAAA-AAGA
19414935 AAGAAATTAAAAAG
1 AAGAAATTAAAAAG
19414949 GAAATGAGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
14 7 0.29
15 15 0.62
16 2 0.08
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.12
Consensus pattern (15 bp):
AAGAAATTAAAAAGA
Found at i:19427379 original size:29 final size:31
Alignment explanation
Indices: 19427328--19427387 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 31
19427318 GTCAACTATT
*
19427328 TGTCTATCACTATCAACTAGAAGAGAAATAA
1 TGTCTATCACTATAAACTAGAAGAGAAATAA
*
19427359 TGTCTAT-A-TATAAACTGGAAGAGAAATAA
1 TGTCTATCACTATAAACTAGAAGAGAAATAA
19427388 GGGAAATTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 19 0.70
30 1 0.04
31 7 0.26
ACGTcount: A:0.47, C:0.12, G:0.15, T:0.27
Consensus pattern (31 bp):
TGTCTATCACTATAAACTAGAAGAGAAATAA
Found at i:19430695 original size:21 final size:21
Alignment explanation
Indices: 19430656--19430695 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
19430646 CCATAGGGTC
* *
19430656 AATTTTTTCTTTTTCTTTTTT
1 AATTTTTTCTCTTACTTTTTT
*
19430677 AATTTTTTCTCTTAGTTTT
1 AATTTTTTCTCTTACTTTT
19430696 CATTTCTATG
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:0.12, C:0.10, G:0.03, T:0.75
Consensus pattern (21 bp):
AATTTTTTCTCTTACTTTTTT
Found at i:19433638 original size:28 final size:30
Alignment explanation
Indices: 19433595--19433650 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
19433585 TAGTTTAATA
19433595 TGTAGTTTTATATATG-AATTTTAATTTTG
1 TGTAGTTTTATATATGAAATTTTAATTTTG
*
19433624 TGTA-TTTTATATATGAAATTTTGATTT
1 TGTAGTTTTATATATGAAATTTTAATTT
19433651 GATTTAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 11 0.44
29 14 0.56
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.59
Consensus pattern (30 bp):
TGTAGTTTTATATATGAAATTTTAATTTTG
Found at i:19435080 original size:27 final size:28
Alignment explanation
Indices: 19435050--19435109 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 28
19435040 TTTATATAAA
19435050 ATATTATTTAAAGAATAATTATTTTATAT
1 ATATTATTTAAA-AATAATTATTTTATAT
* *
19435079 ATCATTTTTTAAATATAATTATTTTATAT
1 AT-ATTATTTAAAAATAATTATTTTATAT
19435108 AT
1 AT
19435110 CGATAATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 19 0.68
30 9 0.32
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (28 bp):
ATATTATTTAAAAATAATTATTTTATAT
Found at i:19435094 original size:14 final size:15
Alignment explanation
Indices: 19435067--19435110 Score: 63
Period size: 14 Copynumber: 3.0 Consensus size: 15
19435057 TTAAAGAATA
19435067 ATTATTTTATATATC
1 ATTATTTTATATATC
* *
19435082 ATT-TTTTAAATATA
1 ATTATTTTATATATC
19435096 ATTATTTTATATATC
1 ATTATTTTATATATC
19435111 GATAATTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTATTTTATATATC
Found at i:19435109 original size:15 final size:15
Alignment explanation
Indices: 19435064--19435109 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
19435054 TATTTAAAGA
19435064 ATAATTATTTTATAT
1 ATAATTATTTTATAT
* *
19435079 ATCATT-TTTTAAAT
1 ATAATTATTTTATAT
19435093 ATAATTATTTTATAT
1 ATAATTATTTTATAT
19435108 AT
1 AT
19435110 CGATAATTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
14 12 0.46
15 14 0.54
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (15 bp):
ATAATTATTTTATAT
Found at i:19437637 original size:17 final size:17
Alignment explanation
Indices: 19437602--19437635 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
19437592 GTTATATCAA
*
19437602 TAATTATATTAATAATT
1 TAATTAAATTAATAATT
19437619 TAATTAAATTAA-AATT
1 TAATTAAATTAATAATT
19437635 T
1 T
19437636 TATGTATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TAATTAAATTAATAATT
Found at i:19437685 original size:33 final size:32
Alignment explanation
Indices: 19437624--19437684 Score: 97
Period size: 31 Copynumber: 1.9 Consensus size: 32
19437614 TAATTTAATT
*
19437624 AAATTAAAATTTTATGTATAAAATTATATACA
1 AAATTAAAAGTTTATGTATAAAATTATATACA
*
19437656 AAATT-AAAGTTTATGTATATAATTATATA
1 AAATTAAAAGTTTATGTATAAAATTATATA
19437685 TTAAAACATG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 22 0.81
32 5 0.19
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.43
Consensus pattern (32 bp):
AAATTAAAAGTTTATGTATAAAATTATATACA
Found at i:19439476 original size:3 final size:3
Alignment explanation
Indices: 19439468--19439498 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
19439458 CGTCCTTTTT
*
19439468 ACA ACA ACA ACA ACA ATA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
19439499 TAATAATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.68, C:0.29, G:0.00, T:0.03
Consensus pattern (3 bp):
ACA
Found at i:19439490 original size:15 final size:15
Alignment explanation
Indices: 19439470--19439501 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
19439460 TCCTTTTTAC
19439470 AACAACAACAACAAT
1 AACAACAACAACAAT
19439485 AACAACAACAACAAT
1 AACAACAACAACAAT
19439500 AA
1 AA
19439502 TAATAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.69, C:0.25, G:0.00, T:0.06
Consensus pattern (15 bp):
AACAACAACAACAAT
Found at i:19440745 original size:50 final size:50
Alignment explanation
Indices: 19440605--19440737 Score: 203
Period size: 50 Copynumber: 2.7 Consensus size: 50
19440595 GAACAGTGTC
* *
19440605 GAGATACGTATGAAGTCTTTTCATCTTTTTGAAGCTGACACGTTTATGTA
1 GAGATAAGTATGAAGTCTTTTCATCTTTTTGAAGCTGACACGTTCATGTA
* * *
19440655 GAGATAAGTATGAAATCTCTTCATCTTTTTTAAGCTGACACGTTCATGTA
1 GAGATAAGTATGAAGTCTTTTCATCTTTTTGAAGCTGACACGTTCATGTA
* *
19440705 GAGATAAGTATCATGTCTTTTCATCTTTTTGAA
1 GAGATAAGTATGAAGTCTTTTCATCTTTTTGAA
19440738 ATTGACACCT
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 73 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (50 bp):
GAGATAAGTATGAAGTCTTTTCATCTTTTTGAAGCTGACACGTTCATGTA
Found at i:19446354 original size:25 final size:26
Alignment explanation
Indices: 19446307--19446359 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
19446297 AAGTGCTGGG
*
19446307 TAACAGAGGGCACACGAAGTGCT-AA
1 TAACAGAGGGCACACGAAATGCTGAA
19446332 TAACAGAGGGCACAC-ACAATGCTGAA
1 TAACAGAGGGCACACGA-AATGCTGAA
19446358 TA
1 TA
19446360 GAGGGCATGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 1 0.04
25 20 0.80
26 4 0.16
ACGTcount: A:0.42, C:0.21, G:0.25, T:0.13
Consensus pattern (26 bp):
TAACAGAGGGCACACGAAATGCTGAA
Found at i:19454318 original size:2 final size:2
Alignment explanation
Indices: 19454302--19454343 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
19454292 AAACACTAGT
*
19454302 TA TA -A TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19454343 T
1 T
19454344 TAAAATTGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19454584 original size:18 final size:19
Alignment explanation
Indices: 19454552--19454587 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
19454542 CTCGATAATT
*
19454552 TATATTTTTTATTTTGACC
1 TATAATTTTTATTTTGACC
19454571 TATAATTTTT-TTTTGAC
1 TATAATTTTTATTTTGAC
19454588 TTCACCATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.22, C:0.08, G:0.06, T:0.64
Consensus pattern (19 bp):
TATAATTTTTATTTTGACC
Found at i:19457384 original size:7 final size:7
Alignment explanation
Indices: 19457372--19457406 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
19457362 TAATGTAAGA
19457372 TTTTAAT
1 TTTTAAT
19457379 TTTTAAT
1 TTTTAAT
19457386 TTTTAAT
1 TTTTAAT
*
19457393 ATTTAAT
1 TTTTAAT
19457400 ATTTTAA
1 -TTTTAA
19457407 AAATTTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 20 0.80
8 5 0.20
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (7 bp):
TTTTAAT
Found at i:19461400 original size:29 final size:29
Alignment explanation
Indices: 19461345--19461400 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
19461335 TTAGAGCTAT
* *
19461345 TTTTTTTATTTGAAAATTGATTTTTTTCA
1 TTTTTTTATTTCAAAATTGATTATTTTCA
*
19461374 TTTTTTTATTTTCAAAATTTA-TATTTT
1 TTTTTTTA-TTTCAAAATTGATTATTTT
19461401 AATCAAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 13 0.57
30 10 0.43
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.68
Consensus pattern (29 bp):
TTTTTTTATTTCAAAATTGATTATTTTCA
Found at i:19472752 original size:85 final size:86
Alignment explanation
Indices: 19472649--19472810 Score: 299
Period size: 85 Copynumber: 1.9 Consensus size: 86
19472639 ATTTACAACA
*
19472649 CTTCTCCCTTTGCTTCTCCTCATGTAGTTCTTACTTCCCTGATTTTGTTTTGACTTAGAAATTAT
1 CTTCTCCCTTTGCTTCTCCTCATGTAGTTCTTACTTCCCTGATTTTGTTTTGACTTAGAAATGAT
19472714 TACAAGACCTAACTTACAGCG
66 TACAAGACCTAACTTACAGCG
*
19472735 CTTCTCCC-TTGCTTCTCCTCATGTAGTTCTTACTTCCCTGATTTTGTTTTGACTTAGAAATGGT
1 CTTCTCCCTTTGCTTCTCCTCATGTAGTTCTTACTTCCCTGATTTTGTTTTGACTTAGAAATGAT
19472799 TACAAGACCTAA
66 TACAAGACCTAA
19472811 TGTCTGGTTG
Statistics
Matches: 74, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
85 66 0.89
86 8 0.11
ACGTcount: A:0.20, C:0.25, G:0.12, T:0.42
Consensus pattern (86 bp):
CTTCTCCCTTTGCTTCTCCTCATGTAGTTCTTACTTCCCTGATTTTGTTTTGACTTAGAAATGAT
TACAAGACCTAACTTACAGCG
Found at i:19474315 original size:20 final size:20
Alignment explanation
Indices: 19474279--19474316 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
19474269 GTAATTTTTT
*
19474279 TAAAAATTTGAAGAGTTTAG
1 TAAAAATTTGAAAAGTTTAG
19474299 TAAAAATATT-AAAAGTTT
1 TAAAAAT-TTGAAAAGTTT
19474317 TGTGAGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.88
21 2 0.12
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (20 bp):
TAAAAATTTGAAAAGTTTAG
Found at i:19474808 original size:20 final size:20
Alignment explanation
Indices: 19474749--19474808 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
19474739 ATAGACAAAT
*
19474749 TATTAATTAAAATTAT-TTAA
1 TATTAATTAAAATGATATT-A
**
19474769 TATTAA-TATATTTG-TATTA
1 TATTAATTA-AAATGATATTA
19474788 TATTAATTAAAATGATATTA
1 TATTAATTAAAATGATATTA
19474808 T
1 T
19474809 GAATTACTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
19 13 0.42
20 18 0.58
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (20 bp):
TATTAATTAAAATGATATTA
Found at i:19474979 original size:7 final size:7
Alignment explanation
Indices: 19474967--19475000 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
19474957 CCATTGCCAG
19474967 GGTGATC
1 GGTGATC
*
19474974 GGTGATT
1 GGTGATC
19474981 GGTGATC
1 GGTGATC
*
19474988 GCTGATC
1 GGTGATC
19474995 GGTGAT
1 GGTGAT
19475001 GCTTCGCAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.15, C:0.12, G:0.41, T:0.32
Consensus pattern (7 bp):
GGTGATC
Found at i:19478577 original size:20 final size:20
Alignment explanation
Indices: 19478541--19478578 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
19478531 ATGTAATTTT
*
19478541 TAAAAATTTGAAGAGTTTAG
1 TAAAAATTTGAAAAGTTTAG
19478561 TAAAAATATT-AAAAGTTT
1 TAAAAAT-TTGAAAAGTTT
19478579 TGTGAGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.88
21 2 0.12
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (20 bp):
TAAAAATTTGAAAAGTTTAG
Found at i:19479071 original size:20 final size:20
Alignment explanation
Indices: 19479012--19479071 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
19479002 ATAGACAAAT
*
19479012 TATTAATTAAAATTAT-TTAA
1 TATTAATTAAAATGATATT-A
**
19479032 TATTAA-TATATTTG-TATTA
1 TATTAATTA-AAATGATATTA
19479051 TATTAATTAAAATGATATTA
1 TATTAATTAAAATGATATTA
19479071 T
1 T
19479072 GAATTACTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
19 13 0.42
20 18 0.58
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (20 bp):
TATTAATTAAAATGATATTA
Found at i:19479241 original size:7 final size:7
Alignment explanation
Indices: 19479229--19479262 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
19479219 CCATTGCCAG
19479229 GGTGATC
1 GGTGATC
*
19479236 GGTGATT
1 GGTGATC
19479243 GGTGATC
1 GGTGATC
*
19479250 GCTGATC
1 GGTGATC
19479257 GGTGAT
1 GGTGAT
19479263 GCTTCGCAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.15, C:0.12, G:0.41, T:0.32
Consensus pattern (7 bp):
GGTGATC
Found at i:19481099 original size:131 final size:131
Alignment explanation
Indices: 19480865--19481107 Score: 459
Period size: 131 Copynumber: 1.9 Consensus size: 131
19480855 GTGAAGGGTC
*
19480865 CTTGAATCTCATATCCCCATAATCATGTGTCGGATACTAGTGTTAGATATAGGTACTTTTAAGAA
1 CTTGAAGCTCATATCCCCATAATCATGTGTCGGATACTAGTGTTAGATATAGGTACTTTTAAGAA
*
19480930 AAATGAAGAGTTGGAGCAACATAGATTCAATATGTTATATCAGAAAAATAATGTTAGATATAGGT
66 AAATGAAGAGTTGGAGCAACACAGATTCAATATGTTATATCAGAAAAATAATGTTAGATATAGGT
19480995 A
131 A
*
19480996 CTTGAAGCTCATGTCCCCATAATCATGTGTCGGATACTAGTGTTAGATATAGGTACTTTTAAGAA
1 CTTGAAGCTCATATCCCCATAATCATGTGTCGGATACTAGTGTTAGATATAGGTACTTTTAAGAA
19481061 AAATGAAGAGTTGGAGCAACACAGATTCAATATGTTATATCAGAAAA
66 AAATGAAGAGTTGGAGCAACACAGATTCAATATGTTATATCAGAAAA
19481108 TAAATCACAT
Statistics
Matches: 109, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
131 109 1.00
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (131 bp):
CTTGAAGCTCATATCCCCATAATCATGTGTCGGATACTAGTGTTAGATATAGGTACTTTTAAGAA
AAATGAAGAGTTGGAGCAACACAGATTCAATATGTTATATCAGAAAAATAATGTTAGATATAGGT
A
Found at i:19484096 original size:27 final size:27
Alignment explanation
Indices: 19484038--19484096 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
19484028 CAAATACGTT
* *
19484038 TTTGAACTAACCTAGTATATACAATGA
1 TTTGGACTAACCTAGTATATACAAAGA
* *
19484065 TTTGGACTAACCTATTATATATAAAGA
1 TTTGGACTAACCTAGTATATACAAAGA
19484092 TTTGG
1 TTTGG
19484097 TTTTAGGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (27 bp):
TTTGGACTAACCTAGTATATACAAAGA
Found at i:19485566 original size:21 final size:21
Alignment explanation
Indices: 19485533--19485574 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
19485523 TAACGTGGCA
*
19485533 AATTAACTGGTCACATCAACT
1 AATTAACTAGTCACATCAACT
* *
19485554 AATTTACTAGTCACGTCAACT
1 AATTAACTAGTCACATCAACT
19485575 CTCTCATTAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.36, C:0.24, G:0.10, T:0.31
Consensus pattern (21 bp):
AATTAACTAGTCACATCAACT
Found at i:19493138 original size:31 final size:31
Alignment explanation
Indices: 19493100--19493158 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
19493090 TCAAAGCTGT
*
19493100 GGTAAACTTGAACTAAATTATAAAGGACGTA
1 GGTAAACTTGAACCAAATTATAAAGGACGTA
* *
19493131 GGTAAACTTTAACCAAATTATCAAGGAC
1 GGTAAACTTGAACCAAATTATAAAGGAC
19493159 ATTTTAGTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.44, C:0.14, G:0.17, T:0.25
Consensus pattern (31 bp):
GGTAAACTTGAACCAAATTATAAAGGACGTA
Found at i:19499175 original size:21 final size:21
Alignment explanation
Indices: 19499146--19499185 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
19499136 ATTTCATTAA
* *
19499146 ATTATATTTAATAATAATATT
1 ATTAAATTTAATAACAATATT
19499167 ATTAAATTTAATAACAATA
1 ATTAAATTTAATAACAATA
19499186 ATCATCTACT
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:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (21 bp):
ATTAAATTTAATAACAATATT
Found at i:19499355 original size:16 final size:16
Alignment explanation
Indices: 19499334--19499388 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
19499324 TGAATTACTG
*
19499334 ATTACAGTCCTATTCC
1 ATTACAGACCTATTCC
*
19499350 ATTACA-ACCCTATTTC
1 ATTACAGA-CCTATTCC
19499366 ATTACA-ACTCTATTCC
1 ATTACAGAC-CTATTCC
19499382 ATTACAG
1 ATTACAG
19499389 CGAACTAAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
15 1 0.03
16 32 0.97
ACGTcount: A:0.31, C:0.29, G:0.04, T:0.36
Consensus pattern (16 bp):
ATTACAGACCTATTCC
Found at i:19500223 original size:14 final size:14
Alignment explanation
Indices: 19500191--19500224 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
19500181 ACCATTTCAT
* *
19500191 TATTATGTTGTTAT
1 TATTTTGTTGTTAA
19500205 TATTTTGTTGTTAA
1 TATTTTGTTGTTAA
19500219 TATTTT
1 TATTTT
19500225 AATTTGTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.21, C:0.00, G:0.12, T:0.68
Consensus pattern (14 bp):
TATTTTGTTGTTAA
Found at i:19502627 original size:3 final size:3
Alignment explanation
Indices: 19502619--19502654 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
19502609 TACATATTTA
19502619 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
19502655 TTCTCTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:19504311 original size:22 final size:22
Alignment explanation
Indices: 19504276--19504318 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
19504266 AATTGTAATT
*
19504276 AAAATTATAGTATTAAAAATAC
1 AAAATTATAATATTAAAAATAC
*
19504298 AAAATTGTAATATTAAAAATA
1 AAAATTATAATATTAAAAATA
19504319 TTTCTAAGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (22 bp):
AAAATTATAATATTAAAAATAC
Found at i:19507349 original size:16 final size:16
Alignment explanation
Indices: 19507328--19507359 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
19507318 ACTGTCTAAT
19507328 GTAAGGCATATTTGTC
1 GTAAGGCATATTTGTC
19507344 GTAAGGCATATTTGTC
1 GTAAGGCATATTTGTC
19507360 ATACCCAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (16 bp):
GTAAGGCATATTTGTC
Found at i:19507458 original size:52 final size:52
Alignment explanation
Indices: 19507382--19507486 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
19507372 ACGTTTTGAC
19507382 TTGAGCAGTGAATGAGTAGAAATTTCTCATGCAATTTCATGCAGACAAATTT
1 TTGAGCAGTGAATGAGTAGAAATTTCTCATGCAATTTCATGCAGACAAATTT
19507434 TTGAGCAGTGAATGAGTAGAAATTTCTCATGCAATTTCATGCAGACAAATTT
1 TTGAGCAGTGAATGAGTAGAAATTTCTCATGCAATTTCATGCAGACAAATTT
19507486 T
1 T
19507487 CATGAAAAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.33
Consensus pattern (52 bp):
TTGAGCAGTGAATGAGTAGAAATTTCTCATGCAATTTCATGCAGACAAATTT
Found at i:19511608 original size:20 final size:20
Alignment explanation
Indices: 19511583--19511627 Score: 58
Period size: 18 Copynumber: 2.3 Consensus size: 20
19511573 ATCTGCTAAA
*
19511583 TATTTAATTTTTTTATA-TAG
1 TATTTAA-TTTTTTATACAAG
19511603 TATTT-ATTTTTTATACAAG
1 TATTTAATTTTTTATACAAG
19511622 TATTTA
1 TATTTA
19511628 CTATATAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 9 0.41
19 8 0.36
20 5 0.23
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.62
Consensus pattern (20 bp):
TATTTAATTTTTTATACAAG
Found at i:19512360 original size:17 final size:17
Alignment explanation
Indices: 19512335--19512376 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
19512325 GAAAAAAACA
*
19512335 GTTACAAGAATATGAAAG
1 GTTA-AAGAAGATGAAAG
*
19512353 GTTAAAGAAGATGGAAG
1 GTTAAAGAAGATGAAAG
19512370 GTTAAAG
1 GTTAAAG
19512377 GTTAAGGGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.48, C:0.02, G:0.29, T:0.21
Consensus pattern (17 bp):
GTTAAAGAAGATGAAAG
Found at i:19517738 original size:17 final size:17
Alignment explanation
Indices: 19517712--19517748 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
19517702 AAGTAGATAC
*
19517712 AAGAATATGAAAAGTTA
1 AAGAAGATGAAAAGTTA
*
19517729 AAGAAGATGAAAGGTTA
1 AAGAAGATGAAAAGTTA
19517746 AAG
1 AAG
19517749 GTTAAGAGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.24, T:0.19
Consensus pattern (17 bp):
AAGAAGATGAAAAGTTA
Found at i:19522566 original size:2 final size:2
Alignment explanation
Indices: 19522561--19522590 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
19522551 CCCCCCCCCC
19522561 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
19522591 AGATTTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:19526297 original size:17 final size:18
Alignment explanation
Indices: 19526275--19526308 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
19526265 ATTCAATTTT
*
19526275 AAAAACTCAAAA-TATTC
1 AAAAACTAAAAAGTATTC
19526292 AAAAACTAAAAAGTATT
1 AAAAACTAAAAAGTATT
19526309 GCTTTTCTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.62, C:0.12, G:0.03, T:0.24
Consensus pattern (18 bp):
AAAAACTAAAAAGTATTC
Found at i:19527592 original size:12 final size:12
Alignment explanation
Indices: 19527577--19527601 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19527567 CACACTTACA
19527577 TTCTTTTTTTTT
1 TTCTTTTTTTTT
19527589 TTCTTTTTTTTT
1 TTCTTTTTTTTT
19527601 T
1 T
19527602 GAGTTTAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TTCTTTTTTTTT
Found at i:19533252 original size:11 final size:12
Alignment explanation
Indices: 19533236--19533265 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
19533226 AAATGATGAA
19533236 ATTATATA-TTT
1 ATTATATATTTT
19533247 ATTATATATTTT
1 ATTATATATTTT
19533259 ATTATAT
1 ATTATAT
19533266 TTATATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.44
12 10 0.56
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
ATTATATATTTT
Found at i:19537091 original size:62 final size:59
Alignment explanation
Indices: 19536964--19537094 Score: 183
Period size: 59 Copynumber: 2.2 Consensus size: 59
19536954 AAAATTGGGA
* * * *
19536964 TGTTGGCCATGCAATGGCTGACACCTCCTTTTTGTCAAAAAAAATTCAAATTTTTTTGG
1 TGTTGGCCATGCAATGGCCGACACCCCCCTTTTCTCAAAAAAAATTCAAATTTTTTTGG
19537023 TGTTGGCCAT-CAAATGGCCGACACCCCCCTTTTCTCGAGAAAAAAATTCAAATTTTTTTTGG
1 TGTTGGCCATGC-AATGGCCGACACCCCCCTTTTCTC-A-AAAAAAATTCAAA-TTTTTTTGG
19537085 TGTTGGCCAT
1 TGTTGGCCAT
19537095 TTTTCTCGAT
Statistics
Matches: 64, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
58 1 0.02
59 30 0.47
60 1 0.02
61 13 0.20
62 19 0.30
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (59 bp):
TGTTGGCCATGCAATGGCCGACACCCCCCTTTTCTCAAAAAAAATTCAAATTTTTTTGG
Found at i:19538512 original size:12 final size:12
Alignment explanation
Indices: 19538492--19538525 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
19538482 ATACTGGGGA
*
19538492 TCAGGTTGGTGC
1 TCAGGTTGGTAC
*
19538504 TCCGGTTGGTAC
1 TCAGGTTGGTAC
19538516 TCAGGTTGGT
1 TCAGGTTGGT
19538526 CCTGAGGCTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.09, C:0.18, G:0.38, T:0.35
Consensus pattern (12 bp):
TCAGGTTGGTAC
Found at i:19540536 original size:80 final size:80
Alignment explanation
Indices: 19540438--19540944 Score: 729
Period size: 80 Copynumber: 6.3 Consensus size: 80
19540428 TAAATATAAA
* **
19540438 ATATGCTAAAAATTGTAATATAAAAATTTTTATTTAAAGATATAAAATTAATAAATAATGTATTG
1 ATATGATAAAAATTGTAATATAAAAAAATTTATTTAAAGATATAAAATTAATAAATAATGTATTG
19540503 TCAAATCAACACATT
66 TCAAATCAACACATT
*
19540518 ATATGATAAAAATTGTAATATAAAAAAAATTATTTAAAGATATAAAATTAATAAATAATGTATTG
1 ATATGATAAAAATTGTAATATAAAAAAATTTATTTAAAGATATAAAATTAATAAATAATGTATTG
*
19540583 TCAAATCAAGACATT
66 TCAAATCAACACATT
*
19540598 ATAT-ATGATAAATTGTAATATAAAAAAATTTATTTAAAGATATAAAATTAATAAATAATGTATT
1 ATATGAT-AAAAATTGTAATATAAAAAAATTTATTTAAAGATATAAAATTAATAAATAATGTATT
19540662 GTCAAATCAACACATT
65 GTCAAATCAACACATT
*
19540678 ATATGAT--AAATTGTAATATAAAAAAA-TTATTTGAAGATATAAAATTAATAAATAATGTATTG
1 ATATGATAAAAATTGTAATATAAAAAAATTTATTTAAAGATATAAAATTAATAAATAATGTATTG
* *
19540740 TCAAATCAAGAAATT
66 TCAAATCAACACATT
* *
19540755 ATATGATAAAAATTGTAATATAAAAAAATTTATTTAAAGATATAAAATTAATAAATATTGTATTA
1 ATATGATAAAAATTGTAATATAAAAAAATTTATTTAAAGATATAAAATTAATAAATAATGTATTG
19540820 TCAAATCAACACATT
66 TCAAATCAACACATT
*
19540835 ATATGATAAAAATTGTAATATAATACTAATAATTTGTACTTT-AAG-TATGAAAATTTGATAAAT
1 ATATGATAAAAATTGTAATATAA-A--AA-AA-TT-TA-TTTAAAGATAT-AAAA-TTAATAAAT
* * *
19540898 AATGTATTGTCAAATTAATACAAT
57 AATGTATTGTCAAATCAACACATT
* *
19540922 ATTTGATATAAATTGTAATATAA
1 ATATGATAAAAATTGTAATATAA
19540945 TAACTATTTT
Statistics
Matches: 389, Mismatches: 24, Indels: 21
0.90 0.06 0.05
Matches are distributed among these distances:
77 55 0.14
78 19 0.05
79 21 0.05
80 222 0.57
81 3 0.01
83 2 0.01
84 2 0.01
85 5 0.01
86 9 0.02
87 51 0.13
ACGTcount: A:0.52, C:0.04, G:0.07, T:0.37
Consensus pattern (80 bp):
ATATGATAAAAATTGTAATATAAAAAAATTTATTTAAAGATATAAAATTAATAAATAATGTATTG
TCAAATCAACACATT
Found at i:19540782 original size:157 final size:157
Alignment explanation
Indices: 19540438--19540944 Score: 725
Period size: 157 Copynumber: 3.1 Consensus size: 157
19540428 TAAATATAAA
* **
19540438 ATATGCTAAAAATTGTAATATAAAAATTTTTATTTAAAGATATAAAATTAATAAATAATGTATTG
1 ATATGATAAAAATTGTAATATAAAAAAATTTATTTAAAGATATAAAATTAATAAATAATGTATTG
19540503 TCAAATCAACACATTATATGATAAAAATTGTAATATAAAAAAAATTATTTAAAGATATAAAATTA
66 TCAAATCAACACATTATATGAT-AAAATTGTAATAT-AAAAAAATTATTT-AAGATATAAAATTA
*
19540568 ATAAATAATGTATTGTCAAATCAAGACATT
128 ATAAATAATGTATTGTCAAATCAAGAAATT
*
19540598 ATAT-ATGATAAATTGTAATATAAAAAAATTTATTTAAAGATATAAAATTAATAAATAATGTATT
1 ATATGAT-AAAAATTGTAATATAAAAAAATTTATTTAAAGATATAAAATTAATAAATAATGTATT
19540662 GTCAAATCAACACATTATATGAT-AAATTGTAATATAAAAAAATTATTTGAAGATATAAAATTAA
65 GTCAAATCAACACATTATATGATAAAATTGTAATATAAAAAAATTATTT-AAGATATAAAATTAA
19540726 TAAATAATGTATTGTCAAATCAAGAAATT
129 TAAATAATGTATTGTCAAATCAAGAAATT
* *
19540755 ATATGATAAAAATTGTAATATAAAAAAATTTATTTAAAGATATAAAATTAATAAATATTGTATTA
1 ATATGATAAAAATTGTAATATAAAAAAATTTATTTAAAGATATAAAATTAATAAATAATGTATTG
19540820 TCAAATCAACACATTATATGATAAAAATTGTAATATAATACTAATAATTTGTACTTTAAG-TATG
66 TCAAATCAACACATTATATGAT-AAAATTGTAATATAA-A--AA-AA--T-TA-TTTAAGATAT-
* * *
19540884 AAAATTTGATAAATAATGTATTGTCAAATTAATACAA-T
121 AAAA-TTAATAAATAATGTATTGTCAAATCAAGA-AATT
* *
19540922 ATTTGATATAAATTGTAATATAA
1 ATATGATAAAAATTGTAATATAA
19540945 TAACTATTTT
Statistics
Matches: 318, Mismatches: 14, Indels: 23
0.90 0.04 0.06
Matches are distributed among these distances:
157 137 0.43
158 14 0.04
159 15 0.05
160 82 0.26
162 2 0.01
163 2 0.01
165 4 0.01
166 9 0.03
167 51 0.16
168 2 0.01
ACGTcount: A:0.52, C:0.04, G:0.07, T:0.37
Consensus pattern (157 bp):
ATATGATAAAAATTGTAATATAAAAAAATTTATTTAAAGATATAAAATTAATAAATAATGTATTG
TCAAATCAACACATTATATGATAAAATTGTAATATAAAAAAATTATTTAAGATATAAAATTAATA
AATAATGTATTGTCAAATCAAGAAATT
Found at i:19541140 original size:16 final size:16
Alignment explanation
Indices: 19541087--19541129 Score: 86
Period size: 16 Copynumber: 2.7 Consensus size: 16
19541077 CATTAATTTC
19541087 TAAATTAATTTCAACT
1 TAAATTAATTTCAACT
19541103 TAAATTAATTTCAACT
1 TAAATTAATTTCAACT
19541119 TAAATTAATTT
1 TAAATTAATTT
19541130 TCAAATTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (16 bp):
TAAATTAATTTCAACT
Found at i:19544756 original size:59 final size:60
Alignment explanation
Indices: 19544551--19544812 Score: 286
Period size: 59 Copynumber: 4.4 Consensus size: 60
19544541 AGGAGAAGTT
*
19544551 GGTGTCGGCCATTTGATGGCCAACACTAAAAAAAATTTGAAATTTTTTTCTCGAGAATAAAG
1 GGTGTCGGCCATTTGATGGCCAACAC--AAAAAAATTTGAAATTTTTTTCTCGAGAATAAGG
* * **
19544613 AGTGTCGGCCATTTGATGGCCAACATCAAAAAAATTTG-AA-TTTTTTCTCGAGAAAAATT
1 GGTGTCGGCCATTTGATGGCCAACA-CAAAAAAATTTGAAATTTTTTTCTCGAGAATAAGG
* * * * * *
19544672 GGTGTCGACCAGTTGATGGTCAACACAAAAAAATTTG-AATTTTTTTCTCAAGAACAGGG
1 GGTGTCGGCCATTTGATGGCCAACACAAAAAAATTTGAAATTTTTTTCTCGAGAATAAGG
** * * *
19544731 GGTGTCGGCCATTTGATGGCCAACACCCAAAAA--TGCAATTTTTTT-TTGA-AATAGGG
1 GGTGTCGGCCATTTGATGGCCAACACAAAAAAATTTGAAATTTTTTTCTCGAGAATAAGG
* *
19544787 GGTGTCAGCCATTTGATGACCAACAC
1 GGTGTCGGCCATTTGATGGCCAACAC
19544813 CCAAAATGTA
Statistics
Matches: 174, Mismatches: 23, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
56 30 0.17
57 4 0.02
58 23 0.13
59 79 0.45
60 2 0.01
61 11 0.06
62 24 0.14
63 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.30
Consensus pattern (60 bp):
GGTGTCGGCCATTTGATGGCCAACACAAAAAAATTTGAAATTTTTTTCTCGAGAATAAGG
Found at i:19544799 original size:56 final size:54
Alignment explanation
Indices: 19544727--19544853 Score: 191
Period size: 56 Copynumber: 2.3 Consensus size: 54
19544717 TCTCAAGAAC
* *
19544727 AGGGGGTGTCGGCCATTTGATGGCCAACACCCAAAAATGCAATTTTTTTTTGAAAT
1 AGGGGGTGTCAGCCATTTGATGACCAACACCC-AAAATGCAA-TTTTTTTTGAAAT
*
19544783 AGGGGGTGTCAGCCATTTGATGACCAACACCCAAAATGTAATTTTTTTTGAAAT
1 AGGGGGTGTCAGCCATTTGATGACCAACACCCAAAATGCAATTTTTTTTGAAAT
* *
19544837 AGGGAGTGTCAGTCATT
1 AGGGGGTGTCAGCCATT
19544854 GCATAGCTAA
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
54 28 0.42
55 8 0.12
56 30 0.45
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.31
Consensus pattern (54 bp):
AGGGGGTGTCAGCCATTTGATGACCAACACCCAAAATGCAATTTTTTTTGAAAT
Found at i:19544874 original size:55 final size:55
Alignment explanation
Indices: 19544727--19544853 Score: 175
Period size: 54 Copynumber: 2.3 Consensus size: 55
19544717 TCTCAAGAAC
* * *
19544727 AGGGGGTGTCGGCCATTTGATGGCCAACACCCAAAAATGCAATTTTTTTTTGAAAT
1 AGGGAGTGTCAGCCATTTGATGACCAACA-CCAAAAATGCAATTTTTTTTTGAAAT
* * *
19544783 AGGGGGTGTCAGCCATTTGATGACCAACACCCAAAATGTAA-TTTTTTTTGAAAT
1 AGGGAGTGTCAGCCATTTGATGACCAACACCAAAAATGCAATTTTTTTTTGAAAT
*
19544837 AGGGAGTGTCAGTCATT
1 AGGGAGTGTCAGCCATT
19544854 GCATAGCTAA
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 28 0.43
55 10 0.15
56 27 0.42
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.31
Consensus pattern (55 bp):
AGGGAGTGTCAGCCATTTGATGACCAACACCAAAAATGCAATTTTTTTTTGAAAT
Found at i:19545617 original size:26 final size:26
Alignment explanation
Indices: 19545581--19545650 Score: 131
Period size: 26 Copynumber: 2.7 Consensus size: 26
19545571 CACGTTAGGC
19545581 TCTAATTATTTTAATATTTAAATTAA
1 TCTAATTATTTTAATATTTAAATTAA
19545607 TCTAATTATTTTAATATTTAAATTAA
1 TCTAATTATTTTAATATTTAAATTAA
*
19545633 TCTAATTATTTTTATATT
1 TCTAATTATTTTAATATT
19545651 AATATATGAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (26 bp):
TCTAATTATTTTAATATTTAAATTAA
Found at i:19548738 original size:24 final size:23
Alignment explanation
Indices: 19548687--19548751 Score: 78
Period size: 24 Copynumber: 2.8 Consensus size: 23
19548677 TTAATGTTCA
*
19548687 CGAACATGTTCATTTAAC-TTAAT
1 CGAACATGTTCA-TGAACATTAAT
19548710 CGAACATGTTCATGAACATATAAT
1 CGAACATGTTCATGAACAT-TAAT
* *
19548734 TGAACATGTTCACGAACA
1 CGAACATGTTCATGAACA
19548752 ATGTTAATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
22 4 0.11
23 13 0.35
24 20 0.54
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.31
Consensus pattern (23 bp):
CGAACATGTTCATGAACATTAAT
Found at i:19554726 original size:2 final size:2
Alignment explanation
Indices: 19554715--19554755 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
19554705 CTTTAGAAAA
19554715 AT AT -T AT AT AT AT 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 AT AT AT AT
19554756 TTTTTTTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:19568978 original size:150 final size:150
Alignment explanation
Indices: 19568707--19569009 Score: 606
Period size: 150 Copynumber: 2.0 Consensus size: 150
19568697 AATGATGTTT
19568707 TCCCTTAATGGTTAACAATGTCAGGTGCAAAATTTGATTAGCTCCTTCAGGACCATGCATGATGC
1 TCCCTTAATGGTTAACAATGTCAGGTGCAAAATTTGATTAGCTCCTTCAGGACCATGCATGATGC
19568772 CATTTAAATTGGCACTTACCTTTTCTTGGTGGGGCTCTCTCTCACATAAAACTTGAAGGTTAACT
66 CATTTAAATTGGCACTTACCTTTTCTTGGTGGGGCTCTCTCTCACATAAAACTTGAAGGTTAACT
19568837 GATTATTGAAACATACCAAC
131 GATTATTGAAACATACCAAC
19568857 TCCCTTAATGGTTAACAATGTCAGGTGCAAAATTTGATTAGCTCCTTCAGGACCATGCATGATGC
1 TCCCTTAATGGTTAACAATGTCAGGTGCAAAATTTGATTAGCTCCTTCAGGACCATGCATGATGC
19568922 CATTTAAATTGGCACTTACCTTTTCTTGGTGGGGCTCTCTCTCACATAAAACTTGAAGGTTAACT
66 CATTTAAATTGGCACTTACCTTTTCTTGGTGGGGCTCTCTCTCACATAAAACTTGAAGGTTAACT
19568987 GATTATTGAAACATACCAAC
131 GATTATTGAAACATACCAAC
19569007 TCC
1 TCC
19569010 TACATGTTAT
Statistics
Matches: 153, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
150 153 1.00
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (150 bp):
TCCCTTAATGGTTAACAATGTCAGGTGCAAAATTTGATTAGCTCCTTCAGGACCATGCATGATGC
CATTTAAATTGGCACTTACCTTTTCTTGGTGGGGCTCTCTCTCACATAAAACTTGAAGGTTAACT
GATTATTGAAACATACCAAC
Found at i:19578894 original size:18 final size:18
Alignment explanation
Indices: 19578868--19578902 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
19578858 AGTGTTTGGA
*
19578868 TGAATAATTTTGAAATTT
1 TGAAGAATTTTGAAATTT
*
19578886 TGAAGAATTTTTAAATT
1 TGAAGAATTTTGAAATT
19578903 GTTCCATTCA
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:0.00, G:0.11, T:0.49
Consensus pattern (18 bp):
TGAAGAATTTTGAAATTT
Done.