Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397257.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_95.0, 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: 12062019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 103452 characters in sequence are not A, C, G, or T
File 15 of 26
Found at i:5632386 original size:24 final size:24
Alignment explanation
Indices: 5632353--5632410 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
5632343 ATAGATGTGG
* * *
5632353 CAAAATATGTAATAAAATACGTGA
1 CAAAACATGTAATAAAACACATGA
5632377 CAAAACATGTAATAAAACACATGA
1 CAAAACATGTAATAAAACACATGA
5632401 CAAATACATG
1 CAAA-ACATG
5632411 ACAAAACATA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 25 0.83
25 5 0.17
ACGTcount: A:0.55, C:0.14, G:0.10, T:0.21
Consensus pattern (24 bp):
CAAAACATGTAATAAAACACATGA
Found at i:5635389 original size:29 final size:31
Alignment explanation
Indices: 5635318--5635393 Score: 86
Period size: 29 Copynumber: 2.5 Consensus size: 31
5635308 TTAAAAAAAC
5635318 TTAAATAAATTTTT-TATTCTTTTATTACAT
1 TTAAATAAATTTTTATATTCTTTTATTACAT
* * * **
5635348 TCAATTAACTTTTTATA-T-TTTTATTTTAT
1 TTAAATAAATTTTTATATTCTTTTATTACAT
5635377 TTAAATAAATTTTTATA
1 TTAAATAAATTTTTATA
5635394 ATTAATAATT
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
29 23 0.62
30 12 0.32
31 2 0.05
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (31 bp):
TTAAATAAATTTTTATATTCTTTTATTACAT
Found at i:5635643 original size:31 final size:29
Alignment explanation
Indices: 5635591--5635660 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 29
5635581 GGTATAAGAG
5635591 TTTG-TTTAAATGAAATTAAAAATATAAAAA
1 TTTGATTTAAATGAAA-TAAAAA-ATAAAAA
5635621 TTTGATTTAATAT-AAATAAAAAATAAAAA
1 TTTGATTTAA-ATGAAATAAAAAATAAAAA
5635650 TTT-ATTTAAAT
1 TTTGATTTAAAT
5635661 TCTCTTGAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
27 2 0.05
28 6 0.16
29 10 0.26
30 10 0.26
31 8 0.21
32 2 0.05
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (29 bp):
TTTGATTTAAATGAAATAAAAAATAAAAA
Found at i:5648972 original size:28 final size:28
Alignment explanation
Indices: 5648932--5648985 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
5648922 AAGTAAACCT
*
5648932 ACTGATTAAAGTTCATTTATATGGACCC
1 ACTGATTAAAGTTCATTTACATGGACCC
5648960 ACTGATTAAAGTTCATTTACATGGAC
1 ACTGATTAAAGTTCATTTACATGGAC
5648986 TGAAGTTCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (28 bp):
ACTGATTAAAGTTCATTTACATGGACCC
Found at i:5659902 original size:20 final size:20
Alignment explanation
Indices: 5659860--5659903 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
5659850 CAATCAACGG
*
5659860 AAAAGAAAAAAAATTTAAAA
1 AAAAGAAAAAAAATTAAAAA
5659880 AAAAG-AAAAAAATTAAAATA
1 AAAAGAAAAAAAATTAAAA-A
5659900 AAAA
1 AAAA
5659904 AGTTTAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.14
Consensus pattern (20 bp):
AAAAGAAAAAAAATTAAAAA
Found at i:5665017 original size:17 final size:16
Alignment explanation
Indices: 5664977--5665019 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
5664967 ATATTAGTAA
*
5664977 TTAAATTAT-ATATGT
1 TTAAATTATAATATAT
*
5664992 TTTAATTATAATAATAT
1 TTAAATTATAAT-ATAT
5665009 TTAAATTATAA
1 TTAAATTATAA
5665020 ATAAAATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 8 0.35
16 2 0.09
17 13 0.57
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
TTAAATTATAATATAT
Found at i:5665023 original size:21 final size:20
Alignment explanation
Indices: 5664999--5665044 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
5664989 TGTTTTAATT
5664999 ATAATAATATTTAA-ATTATAA
1 ATAATAATA-TTAATATT-TAA
5665020 ATAA-AATATTAATATTTAA
1 ATAATAATATTAATATTTAA
5665039 A-AATAA
1 ATAATAA
5665045 AATAAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
18 2 0.09
19 10 0.43
20 7 0.30
21 4 0.17
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
ATAATAATATTAATATTTAA
Found at i:5665032 original size:26 final size:26
Alignment explanation
Indices: 5665003--5665053 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
5664993 TTAATTATAA
*
5665003 TAATATTT-AAATTATAAATAAAATAT
1 TAATATTTAAAAATA-AAATAAAATAT
5665029 TAATATTTAAAAATAAAATAAAATA
1 TAATATTTAAAAATAAAATAAAATA
5665054 ATCCTATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (26 bp):
TAATATTTAAAAATAAAATAAAATAT
Found at i:5666120 original size:16 final size:15
Alignment explanation
Indices: 5666093--5666122 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
5666083 CATAGTTATC
5666093 ATTTTATTTATTCTT
1 ATTTTATTTATTCTT
5666108 ATTTTATTTTATTCT
1 ATTTTA-TTTATTCT
5666123 CATAAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (15 bp):
ATTTTATTTATTCTT
Found at i:5669511 original size:17 final size:18
Alignment explanation
Indices: 5669478--5669513 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
5669468 TTTAGACATT
*
5669478 AGCCCAATCAAATCAAAC
1 AGCCCAATCAAACCAAAC
5669496 AGCCCAA-CAAACCAAAC
1 AGCCCAATCAAACCAAAC
5669513 A
1 A
5669514 AAAAAGTGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.53, C:0.36, G:0.06, T:0.06
Consensus pattern (18 bp):
AGCCCAATCAAACCAAAC
Found at i:5670017 original size:45 final size:46
Alignment explanation
Indices: 5669929--5670027 Score: 112
Period size: 45 Copynumber: 2.2 Consensus size: 46
5669919 GATGTTTAAT
* * * *
5669929 TTTTTATTTTAGAGAATTAAGTATGTGATTTAATATTTCTTTGGAG
1 TTTTCATTTTAGAGAATTAAGTAAGTAACTTAATATTTCTTTGGAG
* *
5669975 TTTTCATTTTAGAGAA-TCAGTAAGTAACTTAATATCTT-TTTGGTG
1 TTTTCATTTTAGAGAATTAAGTAAGTAACTTAATAT-TTCTTTGGAG
*
5670020 CTTTCATT
1 TTTTCATT
5670028 CATAAAAATC
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
45 28 0.62
46 17 0.38
ACGTcount: A:0.27, C:0.07, G:0.15, T:0.51
Consensus pattern (46 bp):
TTTTCATTTTAGAGAATTAAGTAAGTAACTTAATATTTCTTTGGAG
Found at i:5684085 original size:12 final size:12
Alignment explanation
Indices: 5684068--5684092 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5684058 TTCAAGGGTG
5684068 GGTTGAAATTTT
1 GGTTGAAATTTT
5684080 GGTTGAAATTTT
1 GGTTGAAATTTT
5684092 G
1 G
5684093 AACATGAGTA
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:0.24, C:0.00, G:0.28, T:0.48
Consensus pattern (12 bp):
GGTTGAAATTTT
Found at i:5686427 original size:26 final size:26
Alignment explanation
Indices: 5686398--5686452 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
5686388 TTTTAATACT
5686398 TAGTAAAATTTTAAATTAATTCTTTA
1 TAGTAAAATTTTAAATTAATTCTTTA
5686424 TAGTAAAATTTTAAATTAATTCTTTA
1 TAGTAAAATTTTAAATTAATTCTTTA
5686450 TAG
1 TAG
5686453 GATAGATACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.49
Consensus pattern (26 bp):
TAGTAAAATTTTAAATTAATTCTTTA
Found at i:5690714 original size:20 final size:22
Alignment explanation
Indices: 5690689--5690730 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
5690679 AAATTACTAT
5690689 TATATAA-TTTTTA-AAAAAAA
1 TATATAATTTTTTACAAAAAAA
5690709 TATATAATTTTTTACAAAAAAA
1 TATATAATTTTTTACAAAAAAA
5690731 ATTAGAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 7 0.35
21 6 0.30
22 7 0.35
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
TATATAATTTTTTACAAAAAAA
Found at i:5691605 original size:14 final size:15
Alignment explanation
Indices: 5691571--5691608 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
5691561 TAGACAATTA
5691571 TATTTTAT-TTTAGT
1 TATTTTATATTTAGT
*
5691585 TAATTTATATTTA-T
1 TATTTTATATTTAGT
5691599 TATTTTATAT
1 TATTTTATAT
5691609 ATTTGTCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 17 0.81
15 4 0.19
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (15 bp):
TATTTTATATTTAGT
Found at i:5702179 original size:20 final size:20
Alignment explanation
Indices: 5702154--5702193 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
5702144 GTATGCCATA
5702154 TTTTCCAATCAACTTACTTT
1 TTTTCCAATCAACTTACTTT
5702174 TTTTCCAATCAACTTACTTT
1 TTTTCCAATCAACTTACTTT
5702194 CTGTGTTGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTTCCAATCAACTTACTTT
Found at i:5709401 original size:25 final size:24
Alignment explanation
Indices: 5709357--5709403 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
5709347 AAATGATTGG
*
5709357 AAAGTTCTGAATCTATTTGTTGTT
1 AAAGTTCTGAATCTACTTGTTGTT
5709381 AAAGTATCTGAAGTCT-CTTGTTG
1 AAAGT-TCTGAA-TCTACTTGTTG
5709404 ATGTTTCTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 5 0.25
25 12 0.60
26 3 0.15
ACGTcount: A:0.26, C:0.11, G:0.19, T:0.45
Consensus pattern (24 bp):
AAAGTTCTGAATCTACTTGTTGTT
Found at i:5723082 original size:221 final size:213
Alignment explanation
Indices: 5722574--5723084 Score: 544
Period size: 215 Copynumber: 2.3 Consensus size: 213
5722564 TAAATATTAT
* ** * ** * * * *
5722574 ATATATTTAATTTATATATAAGTATTCCTATACTTATAATAAACTTTATTAATATGATTATACTT
1 ATATATTTAATTTATACATAAGTATTAGTA-ACTTATAATAAAATGAATTTATAAGATTACATTT
** ** ** * * *
5722639 AATAACCTTATTAACTATCATCTTAGTTTTTATAACATATTGTTTATAATTACTTATTATTTATA
65 AATAATTTTATTAGTTATTGTCTTAATTTTTATAACATAATGTTTATAATTAATTATTATTTATA
* *
5722704 CAAATTTTGATATGAAATACTATAACATATAAGTTGTGTCATTAATTTCATACATAATAATAAAG
130 CAAACTTTGATATAAAATACTATAACATATAAGTTGTGTCATTAATTTCATACATAATAATAAAG
5722769 TAATATATTATACATACAC
195 TAATATATTATACATACAC
* * ** *
5722788 ATATATTTAATTTATACATAAGTATTACGGTAACTTATAATAGACTTTATTTATATGATTACATT
1 ATATATTTAATTTATACATAAGTATTA--GTAACTTATAATAAAATGAATTTATAAGATTACATT
5722853 TAATAATTTTATTAGTTATTGTCTTAATTTTTATAACATAATGTTTATAATTAATTATTATTTAT
64 TAATAATTTTATTAGTTATTGTCTTAATTTTTATAACATAATGTTTATAATTAATTATTATTTAT
* *
5722918 GCAAACTTTGATATAAAAATTAAAACATTATAACATATAAGTTGTGTCATTAATTTCATATAT-A
129 ACAAACTTTGATAT-AAAA-T---AC--TATAACATATAAGTTGTGTCATTAATTTCATACATAA
* *
5722982 TAATAAAGTAATATATTATATATATAC
187 TAATAAAGTAATATATTATACATACAC
* * * **
5723009 ATATATTTAATTTATATATAATTCTTA-TATTTTATAATTATAAATGAAGTTTATAAGTATTA-A
1 ATATATTTAATTTATACATAAGTATTAGTAACTTATAA-TA-AAATGAA-TTTATAAG-ATTACA
5723072 TCTT-ATAATTTTA
62 T-TTAATAATTTTA
5723085 AAAAAATGAT
Statistics
Matches: 251, Mismatches: 32, Indels: 21
0.83 0.11 0.07
Matches are distributed among these distances:
214 25 0.10
215 97 0.39
216 5 0.02
217 1 0.00
218 8 0.03
219 2 0.01
220 5 0.02
221 68 0.27
222 40 0.16
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.47
Consensus pattern (213 bp):
ATATATTTAATTTATACATAAGTATTAGTAACTTATAATAAAATGAATTTATAAGATTACATTTA
ATAATTTTATTAGTTATTGTCTTAATTTTTATAACATAATGTTTATAATTAATTATTATTTATAC
AAACTTTGATATAAAATACTATAACATATAAGTTGTGTCATTAATTTCATACATAATAATAAAGT
AATATATTATACATACAC
Found at i:5723174 original size:26 final size:26
Alignment explanation
Indices: 5723145--5723204 Score: 120
Period size: 26 Copynumber: 2.3 Consensus size: 26
5723135 TAATTCTATA
5723145 TTTGGTCGGTTAGGTCTTTCTTTATG
1 TTTGGTCGGTTAGGTCTTTCTTTATG
5723171 TTTGGTCGGTTAGGTCTTTCTTTATG
1 TTTGGTCGGTTAGGTCTTTCTTTATG
5723197 TTTGGTCG
1 TTTGGTCG
5723205 ATTTTGATCG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.07, C:0.12, G:0.28, T:0.53
Consensus pattern (26 bp):
TTTGGTCGGTTAGGTCTTTCTTTATG
Found at i:5725731 original size:16 final size:17
Alignment explanation
Indices: 5725710--5725742 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5725700 TATCTTTTTT
5725710 TTATTA-ATTTAAAAAA
1 TTATTATATTTAAAAAA
5725726 TTATTATATTTAAAAAA
1 TTATTATATTTAAAAAA
5725743 AATTTAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TTATTATATTTAAAAAA
Found at i:5725855 original size:21 final size:21
Alignment explanation
Indices: 5725805--5725855 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
5725795 CGATTGAGGG
5725805 AAGGGAGCATCGGTTCTCCTT
1 AAGGGAGCATCGGTTCTCCTT
*
5725826 AAGGAAGCATCGAG-T-TCCTT
1 AAGGGAGCATCG-GTTCTCCTT
5725846 AAGAGGAGCA
1 AAG-GGAGCA
5725856 CCAGGTGCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 8 0.31
21 17 0.65
22 1 0.04
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.22
Consensus pattern (21 bp):
AAGGGAGCATCGGTTCTCCTT
Found at i:5726668 original size:119 final size:119
Alignment explanation
Indices: 5726512--5726754 Score: 409
Period size: 119 Copynumber: 2.0 Consensus size: 119
5726502 GTTAAGTTCA
*
5726512 GTTTTAATTTTTCTCTTCTTCATAGATTAATGCTGTGTTGAAATTATGAATGAAAGTGTGTGTTA
1 GTTTTAATTTTTCTCTTCTTCATAGATTAATGCTGTGTTGAAATTATGAATGAAACTGTGTGTTA
*
5726577 ATCTTCTTTCTTCTGTAGACAACTATTATTTTTTTTTGT-TTGCTCTTGCTTTTT
66 ATCTTCTTTCTTCTGCAGACAACTATTATTTTTTTTT-TCTTGCTCTTGCTTTTT
* * *
5726631 GTTTTAATTTTTCTCTTCTTTAT-GTATTAATGTTGTGTTGAAGTTATGAATGAAACTGTGTGTT
1 GTTTTAATTTTTCTCTTCTTCATAG-ATTAATGCTGTGTTGAAATTATGAATGAAACTGTGTGTT
5726695 AATCTTCTTTCTTCTGCAGACAACTATTATTTTTTTTTTCTTGCTCTTGCTTTTT
65 AATCTTCTTTCTTCTGCAGACAACTATTATTTTTTTTTTCTTGCTCTTGCTTTTT
5726750 GTTTT
1 GTTTT
5726755 TTTGTCAAGT
Statistics
Matches: 117, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
118 2 0.02
119 115 0.98
ACGTcount: A:0.19, C:0.12, G:0.14, T:0.55
Consensus pattern (119 bp):
GTTTTAATTTTTCTCTTCTTCATAGATTAATGCTGTGTTGAAATTATGAATGAAACTGTGTGTTA
ATCTTCTTTCTTCTGCAGACAACTATTATTTTTTTTTTCTTGCTCTTGCTTTTT
Found at i:5733400 original size:16 final size:17
Alignment explanation
Indices: 5733362--5733404 Score: 70
Period size: 16 Copynumber: 2.6 Consensus size: 17
5733352 AAACTTGTAT
5733362 GCTACTATAATCCAAAA
1 GCTACTATAATCCAAAA
*
5733379 GTTACTATAATCC-AAA
1 GCTACTATAATCCAAAA
5733395 GCTACTATAA
1 GCTACTATAA
5733405 ACTTGTATGC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 12 0.50
17 12 0.50
ACGTcount: A:0.44, C:0.21, G:0.07, T:0.28
Consensus pattern (17 bp):
GCTACTATAATCCAAAA
Found at i:5741696 original size:38 final size:38
Alignment explanation
Indices: 5741641--5741713 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
5741631 AATGAAGAGA
5741641 AAGAGTGAAAAACAGGTTTGAATATGTAAGGTTTTGGG
1 AAGAGTGAAAAACAGGTTTGAATATGTAAGGTTTTGGG
*
5741679 AAGAGTGAAAAAGAGGTTTGAATATGTAAGGTTTT
1 AAGAGTGAAAAACAGGTTTGAATATGTAAGGTTTT
5741714 AGAAGGCTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.38, C:0.01, G:0.30, T:0.30
Consensus pattern (38 bp):
AAGAGTGAAAAACAGGTTTGAATATGTAAGGTTTTGGG
Found at i:5751674 original size:2 final size:2
Alignment explanation
Indices: 5751669--5751715 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
5751659 ACACATGCTT
* * * *
5751669 AC AC AC AC GC GC AC AC GC AC AC AC AC CC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
5751711 AC AC A
1 AC AC A
5751716 TATAGGAGAT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.43, C:0.51, G:0.06, T:0.00
Consensus pattern (2 bp):
AC
Found at i:5759885 original size:22 final size:24
Alignment explanation
Indices: 5759842--5759891 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
5759832 TTCAAAATTA
5759842 AAAATCTTAAAAAATAAATA-TTT
1 AAAATCTTAAAAAATAAATATTTT
* **
5759865 AAAAT-TTTAAAAATATTTATTTT
1 AAAATCTTAAAAAATAAATATTTT
5759888 AAAA
1 AAAA
5759892 GACTTTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (24 bp):
AAAATCTTAAAAAATAAATATTTT
Found at i:5788225 original size:2 final size:2
Alignment explanation
Indices: 5788218--5788253 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
5788208 ATTCATAGTA
*
5788218 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5788254 CCACAAAAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5791945 original size:2 final size:2
Alignment explanation
Indices: 5791899--5791930 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5791889 GAATGCGTGC
5791899 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
5791931 GAGTGATGGA
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:5802033 original size:15 final size:15
Alignment explanation
Indices: 5802013--5802047 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
5802003 TGCCTACTTT
5802013 ATTATTATTGTTATA
1 ATTATTATTGTTATA
*
5802028 ATTATTATTGTTATT
1 ATTATTATTGTTATA
5802043 ATTAT
1 ATTAT
5802048 GGTACATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (15 bp):
ATTATTATTGTTATA
Found at i:5808331 original size:71 final size:71
Alignment explanation
Indices: 5808215--5808363 Score: 208
Period size: 71 Copynumber: 2.1 Consensus size: 71
5808205 CCGGGGCATT
* * * * *
5808215 CCATTACTATCTTCCTTATCATTGATATTCACTTTATTCCTAATGTTGTCAACAAAGGTAGATCT
1 CCATTATTATCTTCCTTATCACTGATATTCACTTTATCCCTAATGTTATCAACAAAGGTAGACCT
5808280 AACAAA
66 AACAAA
* * ** *
5808286 CCATTATTATCTTCCTTATCACTGTTATTCGCTTTATCCCTAATGTTATCAATGATGGTAGACCT
1 CCATTATTATCTTCCTTATCACTGATATTCACTTTATCCCTAATGTTATCAACAAAGGTAGACCT
5808351 AACAAA
66 AACAAA
5808357 CCATTAT
1 CCATTAT
5808364 CAACATTTTT
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
71 68 1.00
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.39
Consensus pattern (71 bp):
CCATTATTATCTTCCTTATCACTGATATTCACTTTATCCCTAATGTTATCAACAAAGGTAGACCT
AACAAA
Found at i:5815251 original size:20 final size:21
Alignment explanation
Indices: 5815226--5815265 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
5815216 TAGAGCCCTC
*
5815226 CTATTTTCTTT-TATTTTTTG
1 CTATTTACTTTATATTTTTTG
*
5815246 CTATTTAGTTTATATTTTTT
1 CTATTTACTTTATATTTTTT
5815266 AGGCAACTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.15, C:0.07, G:0.05, T:0.72
Consensus pattern (21 bp):
CTATTTACTTTATATTTTTTG
Found at i:5827170 original size:18 final size:19
Alignment explanation
Indices: 5827139--5827178 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
5827129 CGTAATTAAA
*
5827139 AAATTATTTAAAATTTTTT
1 AAATAATTTAAAATTTTTT
5827158 AAATAATTT-AAATTTTTT
1 AAATAATTTAAAATTTTTT
5827176 AAA
1 AAA
5827179 AATATTATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
AAATAATTTAAAATTTTTT
Found at i:5831735 original size:2 final size:2
Alignment explanation
Indices: 5831728--5831764 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5831718 CCTTGGTCCT
5831728 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
5831765 TCAAAACCGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:5844646 original size:2 final size:2
Alignment explanation
Indices: 5844596--5844627 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5844586 ATAAACTTTA
5844596 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
5844628 CCATCTCCAT
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:5846281 original size:23 final size:22
Alignment explanation
Indices: 5846250--5846326 Score: 57
Period size: 23 Copynumber: 3.4 Consensus size: 22
5846240 TTCTTGCTAC
5846250 TGATCTGCTACCATGTTTGTTGT
1 TGATCTGCT-CCATGTTTGTTGT
* * * *
5846273 TGATTTGCTGC-TGGTTTGGTGC
1 TGATCTGCTCCAT-GTTTGTTGT
* *
5846295 TGATCTGCTGCCATGTCTGTTTT
1 TGATCTGCT-CCATGTTTGTTGT
*
5846318 TGATTTGCT
1 TGATCTGCT
5846327 GCTGGTTTGG
Statistics
Matches: 40, Mismatches: 11, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
21 1 0.03
22 16 0.40
23 22 0.55
24 1 0.03
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (22 bp):
TGATCTGCTCCATGTTTGTTGT
Found at i:5846321 original size:45 final size:45
Alignment explanation
Indices: 5846249--5846338 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 45
5846239 ATTCTTGCTA
*
5846249 CTGATCTGCTACCATGTTTGTTGTTGATTTGCTGCTGGTTTGGTG
1 CTGATCTGCTACCATGTCTGTTGTTGATTTGCTGCTGGTTTGGTG
* *
5846294 CTGATCTGCTGCCATGTCTGTTTTTGATTTGCTGCTGGTTTGGTG
1 CTGATCTGCTACCATGTCTGTTGTTGATTTGCTGCTGGTTTGGTG
5846339 AATAATTTGT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.08, C:0.17, G:0.29, T:0.47
Consensus pattern (45 bp):
CTGATCTGCTACCATGTCTGTTGTTGATTTGCTGCTGGTTTGGTG
Found at i:5853027 original size:16 final size:17
Alignment explanation
Indices: 5853006--5853038 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
5852996 AAATGTTATT
5853006 AATATTTATAAT-AAAA
1 AATATTTATAATGAAAA
*
5853022 AATATTTTTAATGAAAA
1 AATATTTATAATGAAAA
5853039 TAATTTGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
AATATTTATAATGAAAA
Found at i:5857946 original size:15 final size:15
Alignment explanation
Indices: 5857926--5857955 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5857916 AATCATTGAT
*
5857926 CAAACTGCGAGAAAA
1 CAAACTGCAAGAAAA
5857941 CAAACTGCAAGAAAA
1 CAAACTGCAAGAAAA
5857956 ATGAAATAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.20, G:0.17, T:0.07
Consensus pattern (15 bp):
CAAACTGCAAGAAAA
Found at i:5858832 original size:13 final size:13
Alignment explanation
Indices: 5858816--5858842 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5858806 GTAATGGATT
5858816 TCATCAATGCAGA
1 TCATCAATGCAGA
5858829 TCATCAATGCAGA
1 TCATCAATGCAGA
5858842 T
1 T
5858843 TGATAATTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (13 bp):
TCATCAATGCAGA
Found at i:5877297 original size:2 final size:2
Alignment explanation
Indices: 5877290--5877324 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5877280 TCACATGGTT
5877290 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5877325 TCAATAGGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5887028 original size:31 final size:33
Alignment explanation
Indices: 5886966--5887031 Score: 100
Period size: 31 Copynumber: 2.1 Consensus size: 33
5886956 CAAGATATTA
*
5886966 TGTTGAGATTTTCTTTTGTTTTTTTTTTTAAAT
1 TGTTGAGATTTTCTTTTGTTTTTGTTTTTAAAT
*
5886999 TGTTGATATTTT-TTTTG-TTTTGTTTTTAAAT
1 TGTTGAGATTTTCTTTTGTTTTTGTTTTTAAAT
5887030 TG
1 TG
5887032 AATAATAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 15 0.48
32 5 0.16
33 11 0.35
ACGTcount: A:0.15, C:0.02, G:0.14, T:0.70
Consensus pattern (33 bp):
TGTTGAGATTTTCTTTTGTTTTTGTTTTTAAAT
Found at i:5890251 original size:40 final size:40
Alignment explanation
Indices: 5890196--5890272 Score: 154
Period size: 40 Copynumber: 1.9 Consensus size: 40
5890186 GATTTGATCG
5890196 TGAAATGTTAGATTTGATTGGATCTATGGAAGGAAGCATC
1 TGAAATGTTAGATTTGATTGGATCTATGGAAGGAAGCATC
5890236 TGAAATGTTAGATTTGATTGGATCTATGGAAGGAAGC
1 TGAAATGTTAGATTTGATTGGATCTATGGAAGGAAGC
5890273 GCGAGATCTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.32, C:0.06, G:0.29, T:0.32
Consensus pattern (40 bp):
TGAAATGTTAGATTTGATTGGATCTATGGAAGGAAGCATC
Found at i:5914783 original size:127 final size:128
Alignment explanation
Indices: 5914596--5914830 Score: 346
Period size: 127 Copynumber: 1.8 Consensus size: 128
5914586 AAATTATACT
* *
5914596 GTGTATGCATGTGTGTGTAAAATAAATAAATAAATGATCAACATATAACATTTAAAATATATAAA
1 GTGTATGCATGTGTGTGTAAAACAAATAAATAAATGATAAACATATAACATTTAAAATATATAAA
*
5914661 ATATTCAAACAATATAAATTCAAATTTGAGTACTAAATATATAGAAATTGATAATATAACAAC
66 ATAGTCAAACAATATAAATTCAAATTTGAGTACTAAATATATAGAAATTGATAATATAACAAC
*** * * * *
5914724 GTGTATGCATGTGTGTG-AAAACGTGTATATAAATGATAAATATGTATCATTTAAAATATATAAA
1 GTGTATGCATGTGTGTGTAAAACAAATAAATAAATGATAAACATATAACATTTAAAATATATAAA
* * *
5914788 ATAGTCTAACAATATAAATTCAAATTTGGGTACTACATATATA
66 ATAGTCAAACAATATAAATTCAAATTTGAGTACTAAATATATA
5914831 TGTTTGTGTA
Statistics
Matches: 94, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
127 77 0.82
128 17 0.18
ACGTcount: A:0.47, C:0.08, G:0.11, T:0.34
Consensus pattern (128 bp):
GTGTATGCATGTGTGTGTAAAACAAATAAATAAATGATAAACATATAACATTTAAAATATATAAA
ATAGTCAAACAATATAAATTCAAATTTGAGTACTAAATATATAGAAATTGATAATATAACAAC
Found at i:5920841 original size:4 final size:4
Alignment explanation
Indices: 5920832--5920856 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
5920822 GTTTTAACCA
5920832 TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
5920857 AAGTTCAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:5940526 original size:19 final size:20
Alignment explanation
Indices: 5940487--5940526 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
5940477 TTACAAAATG
* *
5940487 AGTGAAGAAGAGGAAGTTGC
1 AGTGAAGAAGAAGAAGCTGC
5940507 AGTGAAG-AGAAGAAGCTGC
1 AGTGAAGAAGAAGAAGCTGC
5940526 A
1 A
5940527 ACCAGTTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.42, C:0.07, G:0.38, T:0.12
Consensus pattern (20 bp):
AGTGAAGAAGAAGAAGCTGC
Found at i:5945220 original size:17 final size:17
Alignment explanation
Indices: 5945198--5945232 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
5945188 AGGTGACCTT
*
5945198 GACTAATATCTTTTGAA
1 GACTAAGATCTTTTGAA
*
5945215 GACTAAGGTCTTTTGAA
1 GACTAAGATCTTTTGAA
5945232 G
1 G
5945233 TTTTTTGGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.37
Consensus pattern (17 bp):
GACTAAGATCTTTTGAA
Found at i:5960501 original size:18 final size:18
Alignment explanation
Indices: 5960478--5960515 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
5960468 TTGCAAATAA
5960478 AGAATTT-AAAATAGTAAT
1 AGAATTTGAAAAT-GTAAT
*
5960496 AGAATTTGATAATGTAAT
1 AGAATTTGAAAATGTAAT
5960514 AG
1 AG
5960516 TATTCAAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.50, C:0.00, G:0.16, T:0.34
Consensus pattern (18 bp):
AGAATTTGAAAATGTAAT
Found at i:5965391 original size:5 final size:5
Alignment explanation
Indices: 5965383--5965407 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
5965373 AAAAATGAAG
5965383 GAAAA GAAAA GAAAA GAAAA GAAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA
5965408 CACATTGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:5967732 original size:24 final size:24
Alignment explanation
Indices: 5967679--5967726 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
5967669 TATTGAACAT
5967679 ATTCTGATTTTTTACTTGGGCAAA
1 ATTCTGATTTTTTACTTGGGCAAA
5967703 ATTCTGATTTTTTA-TTCGGGCAAA
1 ATTCTGATTTTTTACTT-GGGCAAA
5967727 TATCTGCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 2 0.09
24 21 0.91
ACGTcount: A:0.25, C:0.12, G:0.17, T:0.46
Consensus pattern (24 bp):
ATTCTGATTTTTTACTTGGGCAAA
Found at i:5984120 original size:29 final size:29
Alignment explanation
Indices: 5984085--5984150 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
5984075 TGTTCTCGTG
* *
5984085 TACTTATTCACGTATACATTCGTCTCTTA
1 TACTTATTCACGTACACATTCGTCTATTA
* **
5984114 TACTTATTCATGTACACATTTTTCTATTA
1 TACTTATTCACGTACACATTCGTCTATTA
5984143 -ACTTATTC
1 TACTTATTC
5984151 TTGTATAGCT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 8 0.25
29 24 0.75
ACGTcount: A:0.26, C:0.21, G:0.05, T:0.48
Consensus pattern (29 bp):
TACTTATTCACGTACACATTCGTCTATTA
Found at i:5989463 original size:22 final size:22
Alignment explanation
Indices: 5989421--5989463 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
5989411 ACATTTATAA
*
5989421 AAACCTAATAAACAAATTAAAC
1 AAACCTAACAAACAAATTAAAC
*
5989443 AAACC-AACAAACCAATATAAA
1 AAACCTAACAAACAAAT-TAAA
5989464 ATAGATAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.65, C:0.21, G:0.00, T:0.14
Consensus pattern (22 bp):
AAACCTAACAAACAAATTAAAC
Found at i:5992029 original size:23 final size:23
Alignment explanation
Indices: 5991998--5992041 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
5991988 ATGAAATATG
*
5991998 ACTTCAAAGAATAAATAAAGATA
1 ACTTCAAAGAACAAATAAAGATA
* *
5992021 ACTTGAAAGAACAAGTAAAGA
1 ACTTCAAAGAACAAATAAAGA
5992042 AAGAAAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.59, C:0.09, G:0.14, T:0.18
Consensus pattern (23 bp):
ACTTCAAAGAACAAATAAAGATA
Found at i:5992096 original size:23 final size:23
Alignment explanation
Indices: 5992070--5992145 Score: 75
Period size: 23 Copynumber: 3.2 Consensus size: 23
5992060 GAAAGTATTT
*
5992070 GAAAACTAAAGAAAGAGAAGCAA
1 GAAAACTAAAGAAAGAGAAGTAA
* *
5992093 GAAATAACTATA-AAAGA-AAGTATTT
1 G-AA-AACTAAAGAAAGAGAAGTA--A
5992118 GAAAACTAAAGAAAGAGAAGTAA
1 GAAAACTAAAGAAAGAGAAGTAA
5992141 GAAAA
1 GAAAA
5992146 TAACTATAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
23 16 0.38
24 14 0.33
25 12 0.29
ACGTcount: A:0.63, C:0.05, G:0.18, T:0.13
Consensus pattern (23 bp):
GAAAACTAAAGAAAGAGAAGTAA
Found at i:5992102 original size:25 final size:25
Alignment explanation
Indices: 5992073--5992163 Score: 77
Period size: 25 Copynumber: 3.8 Consensus size: 25
5992063 AGTATTTGAA
*
5992073 AACTAAAGAAAGAGAAGCAAGAAAT
1 AACTAAAGAAAGAGAAGTAAGAAAT
* *
5992098 AACTATA-AAAGA-AAGTATTTG-AA-
1 AACTAAAGAAAGAGAAGTA--AGAAAT
5992121 AACTAAAGAAAGAGAAGTAAGAAAAT
1 AACTAAAGAAAGAGAAGTAAG-AAAT
*
5992147 AACTATA-AAAGA-AAGTA
1 AACTAAAGAAAGAGAAGTA
5992164 TATGAAGAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
23 11 0.21
24 17 0.32
25 19 0.36
26 6 0.11
ACGTcount: A:0.63, C:0.05, G:0.16, T:0.15
Consensus pattern (25 bp):
AACTAAAGAAAGAGAAGTAAGAAAT
Found at i:5992103 original size:48 final size:49
Alignment explanation
Indices: 5992042--5992169 Score: 222
Period size: 48 Copynumber: 2.6 Consensus size: 49
5992032 CAAGTAAAGA
*
5992042 AAGAAAAAAACTATAAAAGAAAGTATTTGAAAACTAAAGAAAGAGAAGC
1 AAGAAAATAACTATAAAAGAAAGTATTTGAAAACTAAAGAAAGAGAAGC
*
5992091 AAG-AAATAACTATAAAAGAAAGTATTTGAAAACTAAAGAAAGAGAAGT
1 AAGAAAATAACTATAAAAGAAAGTATTTGAAAACTAAAGAAAGAGAAGC
*
5992139 AAGAAAATAACTATAAAAGAAAGTATATGAA
1 AAGAAAATAACTATAAAAGAAAGTATTTGAA
5992170 GAGAGAAAGA
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
48 46 0.61
49 29 0.39
ACGTcount: A:0.62, C:0.05, G:0.16, T:0.17
Consensus pattern (49 bp):
AAGAAAATAACTATAAAAGAAAGTATTTGAAAACTAAAGAAAGAGAAGC
Found at i:5994529 original size:27 final size:27
Alignment explanation
Indices: 5994494--5994553 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
5994484 ACATTAAAAT
*
5994494 AATATATACGATGTATTATTTTGATAAA
1 AATA-ATACAATGTATTATTTTGATAAA
* *
5994522 GATAATACAATTTATTATTTTGATAAA
1 AATAATACAATGTATTATTTTGATAAA
5994549 AATAA
1 AATAA
5994554 ATAATAAAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 25 0.89
28 3 0.11
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (27 bp):
AATAATACAATGTATTATTTTGATAAA
Found at i:5994589 original size:14 final size:13
Alignment explanation
Indices: 5994572--5994605 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
5994562 ACATAGAAAA
5994572 TATTTTTATCTTTT
1 TATTTTTAT-TTTT
5994586 TATTATTTATTTTT
1 TATT-TTTATTTTT
5994600 TATTTT
1 TATTTT
5994606 AAAATTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 2 0.11
14 12 0.63
15 5 0.26
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (13 bp):
TATTTTTATTTTT
Found at i:6008970 original size:3 final size:3
Alignment explanation
Indices: 6008962--6008987 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
6008952 TTAATTTGTT
6008962 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
6008988 TAAATTTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:6018536 original size:15 final size:18
Alignment explanation
Indices: 6018516--6018553 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
6018506 TATATATATA
6018516 AAAGAAA-A-AGAA-AAG
1 AAAGAAAGATAGAAGAAG
6018531 AAAGAAAGATAGAAGAAG
1 AAAGAAAGATAGAAGAAG
6018549 AAAGA
1 AAAGA
6018554 GTACCTGATC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 7 0.35
16 1 0.05
17 4 0.20
18 8 0.40
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.03
Consensus pattern (18 bp):
AAAGAAAGATAGAAGAAG
Found at i:6018719 original size:5 final size:5
Alignment explanation
Indices: 6018711--6018746 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
6018701 AATTTACAGC
* *
6018711 CCTAA CCTAA CCTAA CCTAA GCTAG CCTAA CCTAA C
1 CCTAA CCTAA CCTAA CCTAA CCTAA CCTAA CCTAA C
6018747 AAAGAAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.36, C:0.39, G:0.06, T:0.19
Consensus pattern (5 bp):
CCTAA
Found at i:6030924 original size:27 final size:23
Alignment explanation
Indices: 6030871--6030921 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
6030861 ATTATGCTAG
6030871 CTTTCCACAAACAAAACAACTAT
1 CTTTCCACAAACAAAACAACTAT
*
6030894 CTTTCCACAAACAAAACAACTAC
1 CTTTCCACAAACAAAACAACTAT
6030917 CTTTC
1 CTTTC
6030922 TTTTTGAAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.43, C:0.33, G:0.00, T:0.24
Consensus pattern (23 bp):
CTTTCCACAAACAAAACAACTAT
Found at i:6048888 original size:12 final size:12
Alignment explanation
Indices: 6048871--6048896 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
6048861 GAAGAGGGAT
6048871 AACACCGACGCC
1 AACACCGACGCC
6048883 AACACCGACGCC
1 AACACCGACGCC
6048895 AA
1 AA
6048897 GTGCCGTAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.46, G:0.15, T:0.00
Consensus pattern (12 bp):
AACACCGACGCC
Found at i:6051285 original size:2 final size:2
Alignment explanation
Indices: 6051278--6051312 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
6051268 TTTCTATTTC
* *
6051278 AT AT AT AT AA AT AA AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6051313 ATTTCTTCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:6051532 original size:2 final size:2
Alignment explanation
Indices: 6051525--6051575 Score: 75
Period size: 2 Copynumber: 25.5 Consensus size: 2
6051515 TTTATTATGT
* * *
6051525 TC TC TC TC TG TC TC TC TG TC TC TG TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
6051567 TC TC TC TC T
1 TC TC TC TC T
6051576 ATATATATAT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.43, G:0.06, T:0.51
Consensus pattern (2 bp):
TC
Found at i:6051548 original size:14 final size:14
Alignment explanation
Indices: 6051525--6051575 Score: 84
Period size: 14 Copynumber: 3.6 Consensus size: 14
6051515 TTTATTATGT
6051525 TCTCTCTCTGTCTC
1 TCTCTCTCTGTCTC
*
6051539 TCTGTCTCTGTCTC
1 TCTCTCTCTGTCTC
*
6051553 TCTCTCTCTCTCTC
1 TCTCTCTCTGTCTC
6051567 TCTCTCTCT
1 TCTCTCTCT
6051576 ATATATATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 34 1.00
ACGTcount: A:0.00, C:0.43, G:0.06, T:0.51
Consensus pattern (14 bp):
TCTCTCTCTGTCTC
Found at i:6052108 original size:2 final size:2
Alignment explanation
Indices: 6052103--6052127 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6052093 TCTCTCTCTC
6052103 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
6052128 CAAAATTTTG
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:6055289 original size:22 final size:22
Alignment explanation
Indices: 6055261--6055303 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
6055251 AATTATGCTC
6055261 CTAAGAAAGTCTAGTCCAGCTA
1 CTAAGAAAGTCTAGTCCAGCTA
6055283 CTAAGAAAGTCTAGTCCAGCT
1 CTAAGAAAGTCTAGTCCAGCT
6055304 TTCAAGGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (22 bp):
CTAAGAAAGTCTAGTCCAGCTA
Found at i:6059395 original size:22 final size:21
Alignment explanation
Indices: 6059355--6059395 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
6059345 CAAATCAATT
**
6059355 AATATTAATTTATTTTTTATC
1 AATATTAATTTATCATTTATC
6059376 AATATTAAATTTATCATTTA
1 AATATT-AATTTATCATTTA
6059396 CTTTTTAACG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (21 bp):
AATATTAATTTATCATTTATC
Found at i:6060115 original size:17 final size:17
Alignment explanation
Indices: 6060093--6060126 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
6060083 AATTTGACAA
6060093 TTATTATATG-TTTATTT
1 TTATTAT-TGTTTTATTT
6060110 TTATTATTGTTTTATTT
1 TTATTATTGTTTTATTT
6060127 AATATCATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 14 0.88
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.74
Consensus pattern (17 bp):
TTATTATTGTTTTATTT
Found at i:6067543 original size:2 final size:2
Alignment explanation
Indices: 6067536--6067560 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6067526 TCTAAACAAT
6067536 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
6067561 TACTTAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:6074560 original size:23 final size:23
Alignment explanation
Indices: 6074481--6074560 Score: 54
Period size: 23 Copynumber: 3.3 Consensus size: 23
6074471 AGTACAAATA
* *
6074481 TTTAAATAAATTATACATTATTC
1 TTTAATTAAATTATACAATATTC
* * * * *
6074504 CTTAATTATACTAT-CAATTTAATG
1 TTTAATTAAATTATACAA--TATTC
6074528 TTTGACATTAAATTATACAATATTC
1 TTT-A-ATTAAATTATACAATATTC
6074553 TTTAATTA
1 TTTAATTA
6074561 TACTATCAAT
Statistics
Matches: 40, Mismatches: 12, Indels: 10
0.65 0.19 0.16
Matches are distributed among these distances:
22 2 0.05
23 14 0.35
24 6 0.15
25 7 0.17
26 8 0.20
27 3 0.08
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.47
Consensus pattern (23 bp):
TTTAATTAAATTATACAATATTC
Found at i:6075136 original size:15 final size:16
Alignment explanation
Indices: 6075102--6075151 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 16
6075092 AATTATCAAG
*
6075102 TAAAAATTATT-AAAT
1 TAAAAAATATTAAAAT
* *
6075117 AAAAAAAT-TTAAAGT
1 TAAAAAATATTAAAAT
6075132 T-AAAAATATTAAAAT
1 TAAAAAATATTAAAAT
6075147 TAAAA
1 TAAAA
6075152 TATGTAACTA
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
14 8 0.30
15 16 0.59
16 3 0.11
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (16 bp):
TAAAAAATATTAAAAT
Found at i:6083520 original size:2 final size:2
Alignment explanation
Indices: 6083513--6083581 Score: 50
Period size: 2 Copynumber: 34.5 Consensus size: 2
6083503 TTCTCCCTCG
* * * * * *
6083513 CT CT CT CT C- CT CT GT CT CT GT CT CT GT CT CT GT CT CT TT AAT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT -CT
* *
6083555 CT TT AT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
6083582 AATTTAATTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
1 1 0.02
2 49 0.96
3 1 0.02
ACGTcount: A:0.04, C:0.39, G:0.06, T:0.51
Consensus pattern (2 bp):
CT
Found at i:6083533 original size:6 final size:6
Alignment explanation
Indices: 6083522--6083549 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
6083512 GCTCTCTCTC
6083522 CTCTGT CTCTGT CTCTGT CTCTGT CTCT
1 CTCTGT CTCTGT CTCTGT CTCTGT CTCT
6083550 TTAATCTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.14, T:0.50
Consensus pattern (6 bp):
CTCTGT
Found at i:6084242 original size:1 final size:1
Alignment explanation
Indices: 6084236--6084263 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
6084226 CAAACTGGGA
6084236 GGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGG
6084264 TAGATAGGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:6092525 original size:4 final size:4
Alignment explanation
Indices: 6092518--6092576 Score: 50
Period size: 4 Copynumber: 15.2 Consensus size: 4
6092508 TATTTAATTA
* * * *
6092518 TAAT TAAT TAAT TAAA AAAT TATT TAAT T-A- TAAT TAAT TAAT TAAA
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT
* *
6092564 AAAT TATT TAAT T
1 TAAT TAAT TAAT T
6092577 TTAAATAAAA
Statistics
Matches: 41, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
2 1 0.02
3 2 0.05
4 38 0.93
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (4 bp):
TAAT
Found at i:6092543 original size:30 final size:30
Alignment explanation
Indices: 6092507--6092576 Score: 140
Period size: 30 Copynumber: 2.3 Consensus size: 30
6092497 AAATGATATT
6092507 TTATTTAATTATAATTAATTAATTAAAAAA
1 TTATTTAATTATAATTAATTAATTAAAAAA
6092537 TTATTTAATTATAATTAATTAATTAAAAAA
1 TTATTTAATTATAATTAATTAATTAAAAAA
6092567 TTATTTAATT
1 TTATTTAATT
6092577 TTAAATAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (30 bp):
TTATTTAATTATAATTAATTAATTAAAAAA
Found at i:6096139 original size:23 final size:24
Alignment explanation
Indices: 6096096--6096141 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
6096086 GGAGAATAAT
*
6096096 AATAAAATATTAATGTATTTTTAA
1 AATAAAAAATTAATGTATTTTTAA
*
6096120 AATAAAAAATT-ATGTTTTTTTA
1 AATAAAAAATTAATGTATTTTTA
6096142 TATGAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
AATAAAAAATTAATGTATTTTTAA
Found at i:6100003 original size:17 final size:19
Alignment explanation
Indices: 6099972--6100007 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
6099962 ATGTATATTT
6099972 TTAATAAAAATTAAATTAA
1 TTAATAAAAATTAAATTAA
6099991 TTAA-AAAAA-TAAATTAA
1 TTAATAAAAATTAAATTAA
6100008 AGTTTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
18 5 0.29
19 4 0.24
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
TTAATAAAAATTAAATTAA
Found at i:6101003 original size:3 final size:3
Alignment explanation
Indices: 6100995--6101028 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
6100985 TTATACCATA
*
6100995 TCT TCT TCT GCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
6101029 ATTCCTTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.32, G:0.03, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:6103995 original size:2 final size:2
Alignment explanation
Indices: 6103971--6104014 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
6103961 TTCCCTCCCT
* *
6103971 TC TC TG TC TC TG TC TC T- TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
6104012 TC T
1 TC T
6104015 GCTGTAACTC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.00, C:0.43, G:0.05, T:0.52
Consensus pattern (2 bp):
TC
Found at i:6104603 original size:13 final size:13
Alignment explanation
Indices: 6104585--6104609 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6104575 ACATCGAGCA
6104585 GGTGATTTTGTTG
1 GGTGATTTTGTTG
6104598 GGTGATTTTGTT
1 GGTGATTTTGTT
6104610 TGTATTTTAA
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:0.00, G:0.36, T:0.56
Consensus pattern (13 bp):
GGTGATTTTGTTG
Found at i:6112951 original size:19 final size:19
Alignment explanation
Indices: 6112924--6112968 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
6112914 AAGTAAAATA
*
6112924 CTAATTAATATAAAATAAG-
1 CTAAATAATATAAAAT-AGC
*
6112943 CTAAATAATCTAAAATAGC
1 CTAAATAATATAAAATAGC
6112962 CTAAATA
1 CTAAATA
6112969 TATGTAAAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 2 0.09
19 21 0.91
ACGTcount: A:0.56, C:0.11, G:0.04, T:0.29
Consensus pattern (19 bp):
CTAAATAATATAAAATAGC
Found at i:6130396 original size:13 final size:14
Alignment explanation
Indices: 6130378--6130409 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
6130368 TAAACAGCTT
6130378 ATTTATAAAA-CAA
1 ATTTATAAAAGCAA
6130391 ATTTATAAAAGCAA
1 ATTTATAAAAGCAA
6130405 ATTTA
1 ATTTA
6130410 CCAAATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.34
Consensus pattern (14 bp):
ATTTATAAAAGCAA
Found at i:6151813 original size:18 final size:19
Alignment explanation
Indices: 6151782--6151822 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
6151772 TTCCTACTTT
* *
6151782 TTTTTTATTATTTTTTTTA
1 TTTTTTACTATTTTTTCTA
6151801 TTTTTTACT-TTTTTTCTA
1 TTTTTTACTATTTTTTCTA
6151819 TTTT
1 TTTT
6151823 AACTTAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.12, C:0.05, G:0.00, T:0.83
Consensus pattern (19 bp):
TTTTTTACTATTTTTTCTA
Found at i:6152083 original size:15 final size:15
Alignment explanation
Indices: 6152033--6152084 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
6152023 TTGACATGAC
*
6152033 ATAATTAATTATAAT
1 ATAATTAATAATAAT
**
6152048 ATAATATGTTAATATATT
1 ATAAT-TAATAATA-A-T
6152066 ATAATTAATAATAAT
1 ATAATTAATAATAAT
6152081 ATAA
1 ATAA
6152085 CATATTAATG
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
15 10 0.34
16 6 0.21
17 7 0.24
18 6 0.21
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (15 bp):
ATAATTAATAATAAT
Found at i:6152098 original size:13 final size:13
Alignment explanation
Indices: 6152073--6152109 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
6152063 ATTATAATTA
6152073 ATAATAATATAAC
1 ATAATAATATAAC
* *
6152086 ATATTAATGTAAC
1 ATAATAATATAAC
6152099 ATAATAATATA
1 ATAATAATATA
6152110 TTCATAGGAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (13 bp):
ATAATAATATAAC
Found at i:6152103 original size:33 final size:33
Alignment explanation
Indices: 6152031--6152107 Score: 93
Period size: 33 Copynumber: 2.4 Consensus size: 33
6152021 TATTGACATG
* * *
6152031 ACATAATTAATTATAATATAATATGTTAATATA
1 ACATAATTAATAATAATATAACATATTAATATA
** *
6152064 TTATAATTAATAATAATATAACATATTAATGTA
1 ACATAATTAATAATAATATAACATATTAATATA
6152097 ACATAA-TAATA
1 ACATAATTAATA
6152108 TATTCATAGG
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
32 5 0.14
33 31 0.86
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.40
Consensus pattern (33 bp):
ACATAATTAATAATAATATAACATATTAATATA
Found at i:6155218 original size:105 final size:105
Alignment explanation
Indices: 6155036--6155227 Score: 312
Period size: 105 Copynumber: 1.8 Consensus size: 105
6155026 TGAGTTGTGC
6155036 AGCACATTAGAGGGTCATTTCTGACTTTTTGTAGTTCCCATTTCAAATTGTGAATTCAACAAACT
1 AGCACATTAGAGGGTCATTTCTGACTTTTTGTAGTTCCCATTTCAAATTGTGAATTCAACAAACT
6155101 CTAACACATATTCAAGTCATGCGTTTTTTCGGGGTTCTTT
66 CTAACACATATTCAAGTCATGCGTTTTTTCGGGGTTCTTT
* * * **
6155141 AGCACATTAGAGTGTCATTTCTGACTTTTTGTAGTTCTCATTTCAAATTTTGAATTGGACAAACT
1 AGCACATTAGAGGGTCATTTCTGACTTTTTGTAGTTCCCATTTCAAATTGTGAATTCAACAAACT
** *
6155206 CTAATGCATATTCAATTCATGC
66 CTAACACATATTCAAGTCATGC
6155228 CCTTTTTTTC
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
105 79 1.00
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (105 bp):
AGCACATTAGAGGGTCATTTCTGACTTTTTGTAGTTCCCATTTCAAATTGTGAATTCAACAAACT
CTAACACATATTCAAGTCATGCGTTTTTTCGGGGTTCTTT
Found at i:6169294 original size:22 final size:22
Alignment explanation
Indices: 6169269--6169313 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
6169259 TACATAAAGT
6169269 TGAGACAATTACAATACAAGAA
1 TGAGACAATTACAATACAAGAA
6169291 TGAGACAATTACAATACAAGAA
1 TGAGACAATTACAATACAAGAA
6169313 T
1 T
6169314 AAGTAAGAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.53, C:0.13, G:0.13, T:0.20
Consensus pattern (22 bp):
TGAGACAATTACAATACAAGAA
Found at i:6171883 original size:14 final size:14
Alignment explanation
Indices: 6171864--6171890 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6171854 TCAAAATTAT
6171864 AACTTATAAAAAAG
1 AACTTATAAAAAAG
6171878 AACTTATAAAAAA
1 AACTTATAAAAAA
6171891 AATTACCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.07, G:0.04, T:0.22
Consensus pattern (14 bp):
AACTTATAAAAAAG
Found at i:6187906 original size:18 final size:17
Alignment explanation
Indices: 6187880--6187914 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
6187870 ACCTGCAATT
6187880 GGGGAAGCAATTGGATTA
1 GGGGAAGCAATT-GATTA
*
6187898 GGGGCAGCAATTGATTA
1 GGGGAAGCAATTGATTA
6187915 CTTGTCTGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.31, C:0.09, G:0.37, T:0.23
Consensus pattern (17 bp):
GGGGAAGCAATTGATTA
Found at i:6190279 original size:7 final size:7
Alignment explanation
Indices: 6190264--6190293 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
6190254 GCTGCATAGT
*
6190264 CATCGTG
1 CATCATG
6190271 CATCATG
1 CATCATG
6190278 CATCATG
1 CATCATG
6190285 CATCATG
1 CATCATG
6190292 CA
1 CA
6190294 CAACAAACAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.27
Consensus pattern (7 bp):
CATCATG
Found at i:6193137 original size:15 final size:16
Alignment explanation
Indices: 6193110--6193139 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6193100 AGATTCAAAG
6193110 AAAAAATAGATTTATC
1 AAAAAATAGATTTATC
6193126 AAAAAATA-ATTTAT
1 AAAAAATAGATTTAT
6193140 ATATTAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.33
Consensus pattern (16 bp):
AAAAAATAGATTTATC
Found at i:6195286 original size:27 final size:27
Alignment explanation
Indices: 6195256--6195416 Score: 133
Period size: 27 Copynumber: 5.9 Consensus size: 27
6195246 TGGTATACGA
* ** *
6195256 ATGTTGAAAATATCCTTATTACATATT
1 ATGTTGAAAATTTAATTATTACATGTT
* * * *
6195283 ATGTTGAAGATTTAGTTGTTACACGTT
1 ATGTTGAAAATTTAATTATTACATGTT
6195310 ATGTTGAAAATTTAATTATTACATGTT
1 ATGTTGAAAATTTAATTATTACATGTT
* * *
6195337 ATGTTGAAAAATGTAATTGTTACACGTT
1 ATGTTG-AAAATTTAATTATTACATGTT
* * * * **
6195365 ATATTGAAAATTCAATTGTTTCCCGTT
1 ATGTTGAAAATTTAATTATTACATGTT
* *
6195392 ATATTGAAAAAATTAATTATTACAT
1 ATGTTG-AAAATTTAATTATTACAT
6195417 ACTATGATGA
Statistics
Matches: 107, Mismatches: 25, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
27 72 0.67
28 35 0.33
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.43
Consensus pattern (27 bp):
ATGTTGAAAATTTAATTATTACATGTT
Found at i:6195374 original size:55 final size:55
Alignment explanation
Indices: 6195229--6195381 Score: 175
Period size: 54 Copynumber: 2.8 Consensus size: 55
6195219 TTTAAACGTC
* * * * * **
6195229 ATGTTAAAAAATGTAATTGGTATACG-AATGTTGAAAATATCCTTATTACATATT
1 ATGTTGAAAAATGTAATTGTTACACGTTATGTTGAAAATTTAATTATTACATATT
* * * *
6195283 ATGTTG-AAGATTTAGTTGTTACACGTTATGTTGAAAATTTAATTATTACATGTT
1 ATGTTGAAAAATGTAATTGTTACACGTTATGTTGAAAATTTAATTATTACATATT
* *
6195337 ATGTTGAAAAATGTAATTGTTACACGTTATATTGAAAATTCAATT
1 ATGTTGAAAAATGTAATTGTTACACGTTATGTTGAAAATTTAATT
6195382 GTTTCCCGTT
Statistics
Matches: 81, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
53 14 0.17
54 34 0.42
55 33 0.41
ACGTcount: A:0.37, C:0.07, G:0.14, T:0.42
Consensus pattern (55 bp):
ATGTTGAAAAATGTAATTGTTACACGTTATGTTGAAAATTTAATTATTACATATT
Found at i:6195399 original size:55 final size:55
Alignment explanation
Indices: 6195298--6195415 Score: 148
Period size: 55 Copynumber: 2.1 Consensus size: 55
6195288 GAAGATTTAG
* * * *
6195298 TTGTTACACGTTATGTTGAAAATTTAATTATTACATGTTATGTTG-AAAAATGTAA
1 TTGTTACACGTTATATTGAAAATTCAATTATTACACGTTATATTGAAAAAAT-TAA
* * *
6195353 TTGTTACACGTTATATTGAAAATTCAATTGTTTCCCGTTATATTGAAAAAATTAA
1 TTGTTACACGTTATATTGAAAATTCAATTATTACACGTTATATTGAAAAAATTAA
*
6195408 TTATTACA
1 TTGTTACA
6195416 TACTATGATG
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
55 48 0.89
56 6 0.11
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.43
Consensus pattern (55 bp):
TTGTTACACGTTATATTGAAAATTCAATTATTACACGTTATATTGAAAAAATTAA
Found at i:6195674 original size:4 final size:4
Alignment explanation
Indices: 6195665--6195689 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
6195655 CCAAATTAAA
6195665 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
6195690 TTGTGTTGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:6196216 original size:21 final size:22
Alignment explanation
Indices: 6196190--6196230 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
6196180 TATTTGAATG
*
6196190 GATAAAA-TTATAAAATTTTAA
1 GATAAAACATATAAAATTTTAA
6196211 GATAAAACATATAAAATTTT
1 GATAAAACATATAAAATTTT
6196231 TAAATTTTAT
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:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (22 bp):
GATAAAACATATAAAATTTTAA
Found at i:6196262 original size:17 final size:19
Alignment explanation
Indices: 6196228--6196270 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
6196218 CATATAAAAT
*
6196228 TTTTAAATTTTATAAAGA-
1 TTTTAAATTTAATAAAGAG
*
6196246 TTTTATATTTAAT-AAGAG
1 TTTTAAATTTAATAAAGAG
6196264 TTTTAAA
1 TTTTAAA
6196271 AAAGAATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (19 bp):
TTTTAAATTTAATAAAGAG
Found at i:6200969 original size:15 final size:15
Alignment explanation
Indices: 6200949--6200978 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6200939 AACAATCAAG
*
6200949 TAATATGATTATAAA
1 TAATATAATTATAAA
6200964 TAATATAATTATAAA
1 TAATATAATTATAAA
6200979 AAAAATAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (15 bp):
TAATATAATTATAAA
Found at i:6208051 original size:49 final size:49
Alignment explanation
Indices: 6207979--6208075 Score: 158
Period size: 49 Copynumber: 2.0 Consensus size: 49
6207969 CGGCTCCTAT
*
6207979 AAAGCATTAAATGATTCAATGTAAGGATCCAGTCCAAGTACCACACTAC
1 AAAGCATTAAATGATTCAATGTAAGGATCCAGTCCAAGCACCACACTAC
* * *
6208028 AAAGCTTTAAATGATTCTATGTAAGGATTCAGTCCAAGCACCACACTA
1 AAAGCATTAAATGATTCAATGTAAGGATCCAGTCCAAGCACCACACTA
6208076 AATAGAAGAG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.25
Consensus pattern (49 bp):
AAAGCATTAAATGATTCAATGTAAGGATCCAGTCCAAGCACCACACTAC
Found at i:6212167 original size:23 final size:23
Alignment explanation
Indices: 6212137--6212185 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
6212127 ATGACGGTAC
*
6212137 CTTTGATTTAAATCTACTTCAAT
1 CTTTGATTTAAATATACTTCAAT
6212160 CTTTGATTTAAATATACTTCAAT
1 CTTTGATTTAAATATACTTCAAT
6212183 CTT
1 CTT
6212186 AATATCTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.31, C:0.16, G:0.04, T:0.49
Consensus pattern (23 bp):
CTTTGATTTAAATATACTTCAAT
Found at i:6227001 original size:20 final size:20
Alignment explanation
Indices: 6226972--6227010 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
6226962 TAAAAACAAA
6226972 TCTATAAATAAATAAATAAT
1 TCTATAAATAAATAAATAAT
*
6226992 TCTATCAATAAATAAATAA
1 TCTATAAATAAATAAATAA
6227011 CAATTGTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (20 bp):
TCTATAAATAAATAAATAAT
Found at i:6227349 original size:16 final size:16
Alignment explanation
Indices: 6227328--6227371 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
6227318 TATGCAAATA
6227328 AAAAAAAAAAGAGAAG
1 AAAAAAAAAAGAGAAG
* *
6227344 AAAAAAAGATGAGAAG
1 AAAAAAAAAAGAGAAG
*
6227360 AAGAAGAAAAAG
1 AA-AAAAAAAAG
6227372 GCAAGAAGGT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
16 16 0.73
17 6 0.27
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (16 bp):
AAAAAAAAAAGAGAAG
Found at i:6228515 original size:22 final size:23
Alignment explanation
Indices: 6228489--6228534 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
6228479 ATTATTGAAT
6228489 AATTT-ATGAT-TAGTATTAAAAA
1 AATTTAATGATATAGT-TTAAAAA
6228511 AATTTAAATGATATAGTTTAAAAA
1 AATTT-AATGATATAGTTTAAAAA
6228535 TATTATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 5 0.24
24 12 0.57
25 4 0.19
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (23 bp):
AATTTAATGATATAGTTTAAAAA
Found at i:6230236 original size:15 final size:15
Alignment explanation
Indices: 6230222--6230299 Score: 68
Period size: 15 Copynumber: 5.3 Consensus size: 15
6230212 CTGTAAAATT
*
6230222 ATATTTTTAATAATT
1 ATATTTTTAATAATC
* * *
6230237 ACATTTTCAACAATC
1 ATATTTTTAATAATC
* **
6230252 ATATATCCAATAATC
1 ATATTTTTAATAATC
*
6230267 ACATTTTTAATAATC
1 ATATTTTTAATAATC
*
6230282 ATATTTTTTATAAT-
1 ATATTTTTAATAATC
6230296 ATAT
1 ATAT
6230300 CAAATACAAT
Statistics
Matches: 49, Mismatches: 14, Indels: 1
0.77 0.22 0.02
Matches are distributed among these distances:
14 4 0.08
15 45 0.92
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATTTTTAATAATC
Found at i:6230295 original size:30 final size:30
Alignment explanation
Indices: 6230222--6230295 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 30
6230212 CTGTAAAATT
*
6230222 ATATTTTTAATAATTACATTTTCAACAATC
1 ATATTTTTAATAATCACATTTTCAACAATC
* ** * *
6230252 ATATATCCAATAATCACATTTTTAATAATC
1 ATATTTTTAATAATCACATTTTCAACAATC
*
6230282 ATATTTTTTATAAT
1 ATATTTTTAATAAT
6230296 ATATCAAATA
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (30 bp):
ATATTTTTAATAATCACATTTTCAACAATC
Found at i:6237056 original size:29 final size:30
Alignment explanation
Indices: 6237006--6237067 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
6236996 AGTCAAAGAT
6237006 TTTAAATTTGAAAAAGTGAAAA-TGAAAAA
1 TTTAAATTTGAAAAAGTGAAAATTGAAAAA
*
6237035 TTTAATATTTGAAAGAA-T-AAAATTGTAAAA
1 TTTAA-ATTTGAAA-AAGTGAAAATTGAAAAA
6237065 TTT
1 TTT
6237068 TTAAAAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 9 0.31
30 18 0.62
31 2 0.07
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.35
Consensus pattern (30 bp):
TTTAAATTTGAAAAAGTGAAAATTGAAAAA
Found at i:6239753 original size:19 final size:20
Alignment explanation
Indices: 6239716--6239764 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
6239706 GGTAATCCAT
* *
6239716 ATTTTTTAAAATATGATAATA
1 ATTTTTT-AAATATAATAAAA
6239737 ATTTTTTAAAT-TAATAAAA
1 ATTTTTTAAATATAATAAAA
*
6239756 ATATTTTAA
1 ATTTTTTAA
6239765 TTTTTTATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 14 0.56
20 4 0.16
21 7 0.28
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
ATTTTTTAAATATAATAAAA
Found at i:6239761 original size:21 final size:20
Alignment explanation
Indices: 6239714--6239762 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
6239704 TTGGTAATCC
* *
6239714 ATATTTTTTAAAATATGATA
1 ATATTTTTTAAAATATAAAA
*
6239734 ATAATTTTTTAAATTAATAAAA
1 AT-ATTTTTTAAAAT-ATAAAA
6239756 ATATTTT
1 ATATTTT
6239763 AATTTTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 2 0.08
21 16 0.67
22 6 0.25
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
ATATTTTTTAAAATATAAAA
Found at i:6240032 original size:12 final size:12
Alignment explanation
Indices: 6240008--6240040 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
6239998 TTAATTTAAA
6240008 TTTAAAA-ATAT
1 TTTAAAATATAT
6240019 TTTAAAATATAT
1 TTTAAAATATAT
6240031 TTTAATAATA
1 TTTAA-AATA
6240041 AATAGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 7 0.35
12 9 0.45
13 4 0.20
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
TTTAAAATATAT
Found at i:6240690 original size:19 final size:20
Alignment explanation
Indices: 6240653--6240700 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
6240643 GGTACTCCAT
* *
6240653 ATTTTTTAAAATATGATAATA
1 ATTTTTT-AAATATAATAAAA
6240674 ATTTTTTAAAT-TAATAAAA
1 ATTTTTTAAATATAATAAAA
*
6240693 ATATTTTA
1 ATTTTTTA
6240701 TTTTTTTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 13 0.54
20 4 0.17
21 7 0.29
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
ATTTTTTAAATATAATAAAA
Found at i:6240698 original size:21 final size:20
Alignment explanation
Indices: 6240651--6240699 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
6240641 TTGGTACTCC
* *
6240651 ATATTTTTTAAAATATGATA
1 ATATTTTTTAAAATATAAAA
*
6240671 ATAATTTTTTAAATTAATAAAA
1 AT-ATTTTTTAAAAT-ATAAAA
6240693 ATATTTT
1 ATATTTT
6240700 ATTTTTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 2 0.08
21 16 0.67
22 6 0.25
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
ATATTTTTTAAAATATAAAA
Found at i:6240732 original size:937 final size:954
Alignment explanation
Indices: 6239332--6241266 Score: 2955
Period size: 937 Copynumber: 2.0 Consensus size: 954
6239322 ACAAAAGTGA
*
6239332 ATCTTAAAATTAAGAGTAAAATACTTTAATCTCTTTAAGTTTTAATCCAAATTACATAAAAATTT
1 ATCTTAAAATTAAAAGTAAAATACTTTAATCTCTTTAAGTTTTAATCCAAATTACATAAAAATTT
*
6239397 ATTAATTTTTAAAATAAACATTTTATTTCAAAAAATTATTTGTCATTGGATACGTGGATTCAGCT
66 ATTAATTTTTAAAATAAACATTTCATTTCAAAAAATTATTTGTCATTGGATACGTGGATTCAGCT
* * *
6239462 ATTTAGTTAATCATTAATATTTTCATCAACTTGCTAAAGTGACAAAGATAAAAAAAAAATTTATT
131 ATTTAGTTAATCATTAATATTTTCATCAACTTGCTAAAATGACAAAAATAAAAAAAAAATTTATC
*
6239527 TTTATTAATTTTTATAATTATAATTATATAATTATTTTTTTTTCATTAATTTTTTTTTAAAAAAG
196 TTTATTAATTTTTATAATTATAATTATATAATTATTTTTTTTTCATTAATTTTTTTTAAAAAAAG
6239592 CTCCCCATTGGCGAGCACCGATGCTCCCTTTGGGAGCCCGATTTGGGAGCCTGGGCTTCCCAAGG
261 CTCCCCATT----------G-TG----C---GGGAGCCCGATTTGGGAGCCTGGGCTTCCCAAGG
* *
6239657 AGCGAGGGAGCACCGGTGCCCCCCCTTCAAGGGGAGCTGGGGAGAGATTGGTAATCCATATTTTT
308 AGCGAGGCAGCACCGGCGCCCCCCCTTCAAGGGGAGCTGGGGAGAGATTGGTAATCCATATTTTT
6239722 TAAAATATGATAATAATTTTTTAAATTAATAAAAATATTTTAATTTTTTATTATTTTTATTAATA
373 TAAAATATGATAATAATTTTTTAAATTAATAAAAATATTTTAATTTTTTATTATTTTTATTAATA
* *
6239787 ATATTTGTAGTTTTAAAATGAAGTATTTATTTTAAAAATTAATAAATTTTTATATCTTTTTAATT
438 ATATTTGTAGTTTTAAAATGAAGTACTTATTTTAAAAATTAATAAATTTTTATATCATTTTAATT
6239852 AAAATTTAAGAAATCAGTATATTTTACCTTAAAATTAAAGGTACCCAAAGG-TCAAGTTGCTTGT
503 AAAATTTAAGAAATCAGTATATTTTACCTTAAAATTAAAGGTACCC-AAGGATCAAGTTGCTTGT
6239916 CTAGGTCCTG-A-AG-T-GTC-GA-G-CTTGGGCATCAATTTTTAGGCTTAAAAAGAACAATTAT
567 CTAGGTCCTGAAGAGCTAGTCTGACGACTTGGGCATCAATTTTTAGGCTTAAAAAGAACAATTAT
6239974 ATTAACAAAAAATATTA-TT-TTT-ATTT-AA-TT-TA-A-ATTTAAAAATAT-TTTAAAATATA
632 ATTAACAAAAAATATTATTTATTTAATTTAAATTTATATATATTTAAAAATATATTTAAAATATA
*
6240030 TTTTAATAATAAATAGAAAATTAAATTTCAATAATATATCAAAATAATTTCTTAACATTAAGTCT
697 TTTTAATAATAAATAGAAAATTAAATTTCAATAATATATCAAAATAATTTCTTAACATTAAATCT
*
6240095 TCAACCCTTGTATCCCGCAGCAAAATTGCAAAGTCGACGGCTTGGAACAGATTTGGCCAAAAGCA
762 TCAACCCTTGTATCCAGCAGCAAAATTGCAAAGTCGACGGCTTGGAACAGATTTGGCCAAAAGCA
6240160 AAAAAGAATTAAA-AGGGGCTTTAATTTGAAAGCCTTTTCTTTTGTTTTGTGAGATGGTGGGAAA
827 AAAAAGAATTAAAGA-GGGCTTTAATTTGAAAGCCTTTTCTTTTGTTTTGTGAGATGGTGGGAAA
6240224 GACAATAAAACAGAAATCAGAGGGAAACAGAGAAAGAGAGAGA-CC-GGCCAAAATACCTTTGG
891 GACAATAAAACAGAAATCAGAGGGAAACAGAGAAAGAGAGAGATCCAGGCCAAAATACCTTTGG
* * * *
6240286 ATCTTAAAATTAAAAGTAAAATATTTTAATCTTTTTAAGTTTTAATCGAAATTATATAAAAATTT
1 ATCTTAAAATTAAAAGTAAAATACTTTAATCTCTTTAAGTTTTAATCCAAATTACATAAAAATTT
* *
6240351 ATTAATTTTTAAAATAAATATTTCATTTCAAAAAATTATTTGTCATT-GATTACGTGGATTCCGC
66 ATTAATTTTTAAAATAAACATTTCATTTCAAAAAATTATTTGTCATTGGA-TACGTGGATTCAGC
* * * *
6240415 TATTTAGTTAATTATTAATATTTTCATCAACTTGTTAAAATGATAAAAATAAAAAAATAATTTTA
130 TATTTAGTTAATCATTAATATTTTCATCAACTTGCTAAAATGACAAAAATAAAAAAA-AAATTTA
6240480 TCTTTATTAATTTTTATAATTATAATTATATAATTATATTATTTTTTCATTAATTTTTTTTAAAA
194 TCTTTATTAATTTTTATAATTATAATTATATAATTAT-TT-TTTTTTCATTAATTTTTTTTAAAA
6240545 AAAGCTCCCCA-T-TG-GGGAGCCCGATTTGGGAGCCTGGGCTTCCCAAGGGAGCGAGGCAGCAC
257 AAAGCTCCCCATTGTGCGGGAGCCCGATTTGGGAGCCTGGGCTTCCCAA-GGAGCGAGGCAGCAC
*
6240607 CGGCGCCCCCCCTTCAAGGGGAGCTGGGGAGAGATTGGTACTCCATATTTTTTAAAATATGATAA
321 CGGCGCCCCCCCTTCAAGGGGAGCTGGGGAGAGATTGGTAATCCATATTTTTTAAAATATGATAA
*
6240672 TAATTTTTTAAATTAATAAAAATATTTTATTTTTTTATTATTTTTATTAATAATATTTGTAGTTT
386 TAATTTTTTAAATTAATAAAAATATTTTAATTTTTTATTATTTTTATTAATAATATTTGTAGTTT
*
6240737 TAAAATGGAGTACTTATTTTAAAAATTAATAAATTTTTATATCATTTTAATTAAAATTTAAGAAA
451 TAAAATGAAGTACTTATTTTAAAAATTAATAAATTTTTATATCATTTTAATTAAAATTTAAGAAA
* *
6240802 TCAGTATATTTTACCTTAAAATTAAAGGTGCGCAAGGATCAAGTTGCTTGTCTAGGTCCTGAAGT
516 TCAGTATATTTTACCTTAAAATTAAAGGTACCCAAGGATCAAGTTGCTTGTCTAGGTCCTGAA--
6240867 GTCGAGCTTGAGTCTTGACTCGCGGCGAACTTGGGCATCAATTTTTAGGCTTAAAAAGAACAATT
579 ---GAGC-T-AGTC-TGA-------CG-ACTTGGGCATCAATTTTTAGGCTTAAAAAGAACAATT
*
6240932 ATATTAACAAATAATATTATTTTATTTAATTTAAATTTAAAAATATATATTTAAAAATATATTTA
630 ATATTAACAAAAAATATTA-TTTATTTAATTTAAATTT----ATATATATTTAAAAATATATTTA
*
6240997 AAATATATTTTGATAATAAATAGAAAATTAAATTTCAATAATATATCAAAATAATTTCTTAACAT
690 AAATATATTTTAATAATAAATAGAAAATTAAATTTCAATAATATATCAAAATAATTTCTTAACAT
* *
6241062 TAAATCTTCAACCCTTGTATCCAGCAGGAAAATTGCAAAGTCGACGGTTTGGAACAGATTTGGCC
755 TAAATCTTCAACCCTTGTATCCAGCAGCAAAATTGCAAAGTCGACGGCTTGGAACAGATTTGGCC
**
6241127 AAAAGCCGAAAAGAATTAAAGAGGGCTTTAATTTGAAAGCCTTTTCTTTTGTTTTGTGAGATGGT
820 AAAAGCAAAAAAGAATTAAAGAGGGCTTTAATTTGAAAGCCTTTTCTTTTGTTTTGTGAGATGGT
* *
6241192 GGGAAAGACAATAAAACAGAAATCAGAGGGAAAGAGAGAAAGAGAGAGATCCAAGGGCCAAAATC
885 GGGAAAGACAATAAAACAGAAATCAGAGGGAAACAGAGAAAGAGAGAGATCC-A-GGCCAAAATA
6241257 CCTTTGG
948 CCTTTGG
6241264 ATC
1 ATC
6241267 CGAGACACGG
Statistics
Matches: 898, Mismatches: 35, Indels: 72
0.89 0.03 0.07
Matches are distributed among these distances:
936 36 0.04
937 257 0.29
938 1 0.00
944 4 0.00
946 1 0.00
948 3 0.00
950 2 0.00
953 2 0.00
954 170 0.19
955 42 0.05
956 3 0.00
957 34 0.04
958 1 0.00
960 54 0.06
962 2 0.00
963 3 0.00
964 4 0.00
965 2 0.00
966 2 0.00
971 2 0.00
972 1 0.00
973 12 0.01
974 238 0.27
975 3 0.00
978 19 0.02
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (954 bp):
ATCTTAAAATTAAAAGTAAAATACTTTAATCTCTTTAAGTTTTAATCCAAATTACATAAAAATTT
ATTAATTTTTAAAATAAACATTTCATTTCAAAAAATTATTTGTCATTGGATACGTGGATTCAGCT
ATTTAGTTAATCATTAATATTTTCATCAACTTGCTAAAATGACAAAAATAAAAAAAAAATTTATC
TTTATTAATTTTTATAATTATAATTATATAATTATTTTTTTTTCATTAATTTTTTTTAAAAAAAG
CTCCCCATTGTGCGGGAGCCCGATTTGGGAGCCTGGGCTTCCCAAGGAGCGAGGCAGCACCGGCG
CCCCCCCTTCAAGGGGAGCTGGGGAGAGATTGGTAATCCATATTTTTTAAAATATGATAATAATT
TTTTAAATTAATAAAAATATTTTAATTTTTTATTATTTTTATTAATAATATTTGTAGTTTTAAAA
TGAAGTACTTATTTTAAAAATTAATAAATTTTTATATCATTTTAATTAAAATTTAAGAAATCAGT
ATATTTTACCTTAAAATTAAAGGTACCCAAGGATCAAGTTGCTTGTCTAGGTCCTGAAGAGCTAG
TCTGACGACTTGGGCATCAATTTTTAGGCTTAAAAAGAACAATTATATTAACAAAAAATATTATT
TATTTAATTTAAATTTATATATATTTAAAAATATATTTAAAATATATTTTAATAATAAATAGAAA
ATTAAATTTCAATAATATATCAAAATAATTTCTTAACATTAAATCTTCAACCCTTGTATCCAGCA
GCAAAATTGCAAAGTCGACGGCTTGGAACAGATTTGGCCAAAAGCAAAAAAGAATTAAAGAGGGC
TTTAATTTGAAAGCCTTTTCTTTTGTTTTGTGAGATGGTGGGAAAGACAATAAAACAGAAATCAG
AGGGAAACAGAGAAAGAGAGAGATCCAGGCCAAAATACCTTTGG
Found at i:6240985 original size:14 final size:13
Alignment explanation
Indices: 6240966--6241004 Score: 62
Period size: 12 Copynumber: 3.0 Consensus size: 13
6240956 TTTAATTTAA
6240966 ATTTAAAAATATAT
1 ATTT-AAAATATAT
6240980 ATTTAAAA-ATAT
1 ATTTAAAATATAT
6240992 ATTTAAAATATAT
1 ATTTAAAATATAT
6241005 TTTGATAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.50
13 8 0.33
14 4 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATTTAAAATATAT
Found at i:6241001 original size:11 final size:12
Alignment explanation
Indices: 6240966--6241006 Score: 57
Period size: 11 Copynumber: 3.3 Consensus size: 12
6240956 TTTAATTTAA
6240966 ATTTAAAAATATAT
1 ATTT-AAAA-ATAT
6240980 ATTTAAAAATAT
1 ATTTAAAAATAT
6240992 ATTT-AAAATAT
1 ATTTAAAAATAT
6241003 ATTT
1 ATTT
6241007 TGATAATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.41
12 8 0.30
13 4 0.15
14 4 0.15
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
ATTTAAAAATAT
Found at i:6252250 original size:48 final size:49
Alignment explanation
Indices: 6252135--6252281 Score: 262
Period size: 49 Copynumber: 3.0 Consensus size: 49
6252125 GCCCGGTGGA
6252135 CCGCAGGGGGGAATCGGGACTCGTGGGAGCCGGAGGGGGGCGGGCAGGG
1 CCGCAGGGGGGAATCGGGACTCGTGGGAGCCGGAGGGGGGCGGGCAGGG
*
6252184 CCGCAGGGGGGAACCGGGACTCGTGGGAGCCGGAGGGGGGCGGGCAGGG
1 CCGCAGGGGGGAATCGGGACTCGTGGGAGCCGGAGGGGGGCGGGCAGGG
6252233 CCGCA-GGGGGAATCGGGACTCGTGGGAGCCGGAGGAGGGG-GGGCAGGG
1 CCGCAGGGGGGAATCGGGACTCGTGGGAGCCGGAGG-GGGGCGGGCAGGG
6252281 C
1 C
6252282 TAGCCCGGCC
Statistics
Matches: 95, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
48 38 0.40
49 57 0.60
ACGTcount: A:0.15, C:0.21, G:0.59, T:0.05
Consensus pattern (49 bp):
CCGCAGGGGGGAATCGGGACTCGTGGGAGCCGGAGGGGGGCGGGCAGGG
Found at i:6252777 original size:112 final size:113
Alignment explanation
Indices: 6252544--6252786 Score: 343
Period size: 112 Copynumber: 2.2 Consensus size: 113
6252534 AAATACAAGT
*
6252544 TTAATACATTTATATTTTTTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTTTAAT
1 TTAATATATTT-TATTTTTTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTTTAAT
* * *
6252609 GTCATATATTTTATTTTTATTTATTATTATAATCTTATATATTTTATTT
65 GTCATATATTTTATTTTTATATATTATTATAATATTATATATTTTATTA
*
6252658 TTAATATA-TTTATTTTTTATTATTAATTTTTATATTATATCATCTCTTAAATATATTTTTAATG
1 TTAATATATTTTATTTTTTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTTTAATG
**
6252722 TCATATATTTTATTTTTAATATATTTATT-TTTTATTAT-TAATTTGTA-TA
66 TCATATATTTTATTTTT-ATATA-TTATTATAATATTATAT-ATTT-TATTA
6252771 TT-ATATATTTTATTTT
1 TTAATATATTTTATTTT
6252787 AGTTTATTTT
Statistics
Matches: 117, Mismatches: 7, Indels: 11
0.87 0.05 0.08
Matches are distributed among these distances:
112 76 0.65
113 27 0.23
114 14 0.12
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.63
Consensus pattern (113 bp):
TTAATATATTTTATTTTTTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTTTAATG
TCATATATTTTATTTTTATATATTATTATAATATTATATATTTTATTA
Found at i:6252797 original size:79 final size:78
Alignment explanation
Indices: 6252612--6252907 Score: 267
Period size: 79 Copynumber: 3.6 Consensus size: 78
6252602 TTTTAATGTC
*
6252612 ATATATTTTATTTTTATTTATTATTATAATCTTATATATTTTATTTTTAATATATTTATTTTTTA
1 ATATATTTTA-TTTTATTTA-T-TT-TAATATTATATATTTTATTTTTAATATATTTATTTTTTA
6252677 TTATTAATTTTTATATT
62 TTATTAATTTTTATATT
** * * *
6252694 ATATCATCTCTTA-AATATAT-TTTTAATGTCATATATTTTATTTTTAATATATTTATTTTTTAT
1 ATAT-AT-T-TTATTTTATTTATTTTAATATTATATATTTTATTTTTAATATATTTATTTTTTAT
*
6252757 TATTAATTTGTATATT
63 TATTAATTTTTATATT
*
6252773 ATATATTTTATTTTAGTTTATTTTACTTATATTATATAAATTTTAATTTTTTATAT-TTTATTTA
1 ATATATTTTATTTTA-TTTATTTTA---ATATTATAT--ATTTT-ATTTTTAATATATTTA-TT-
* *
6252837 TTTTAATTTTTTATTTTTATATT
57 TTTT-ATTATTAATTTTTATATT
* * * * *
6252860 ATATATTTTATTTTA-ATATTTTTATAATAATATAATATATTTTTAATA
1 ATATATTTTATTTTATTTATTTTAAT-ATTATATATTTTATTTTTAATA
6252908 AAATAATAAA
Statistics
Matches: 177, Mismatches: 21, Indels: 34
0.76 0.09 0.15
Matches are distributed among these distances:
76 3 0.02
77 3 0.02
78 4 0.02
79 62 0.35
80 11 0.06
81 4 0.02
82 13 0.07
83 12 0.07
84 10 0.06
85 21 0.12
86 4 0.02
87 30 0.17
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.65
Consensus pattern (78 bp):
ATATATTTTATTTTATTTATTTTAATATTATATATTTTATTTTTAATATATTTATTTTTTATTAT
TAATTTTTATATT
Done.