Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 188 of 193
Found at i:58640468 original size:14 final size:15
Alignment explanation
Indices: 58640435--58640469 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
58640425 CTATTTTTTA
58640435 TTTTTTTTAATTCTG
1 TTTTTTTTAATTCTG
* *
58640450 TTTTTTTTATTTTTG
1 TTTTTTTTAATTCTG
58640465 TTTTT
1 TTTTT
58640470 CTCCAGATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.09, C:0.03, G:0.06, T:0.83
Consensus pattern (15 bp):
TTTTTTTTAATTCTG
Found at i:58644756 original size:7 final size:7
Alignment explanation
Indices: 58644744--58644773 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
58644734 ATGCTTTGAA
58644744 TTTTCTT
1 TTTTCTT
58644751 TTTTCTT
1 TTTTCTT
58644758 TTTTCTT
1 TTTTCTT
58644765 TTTT-TT
1 TTTTCTT
58644771 TTT
1 TTT
58644774 CCTTAAACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (7 bp):
TTTTCTT
Found at i:58645109 original size:14 final size:15
Alignment explanation
Indices: 58645085--58645113 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
58645075 TTTAATTCAA
58645085 CTTTTTCCTTTCTTT
1 CTTTTTCCTTTCTTT
58645100 CTTTTT-CTTTCTTT
1 CTTTTTCCTTTCTTT
58645114 TATAAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (15 bp):
CTTTTTCCTTTCTTT
Found at i:58647598 original size:33 final size:33
Alignment explanation
Indices: 58647534--58647598 Score: 76
Period size: 33 Copynumber: 2.0 Consensus size: 33
58647524 CTTAGATCGC
* ** **
58647534 ACACCTGCAAGCTCATCCAAATCTGTGAGCTCT
1 ACACCAGCAAGCTCATCCAAAGATGCAAGCTCT
*
58647567 ACACCAGCAAGCTCATCCACAGATGCAAGCTC
1 ACACCAGCAAGCTCATCCAAAGATGCAAGCTC
58647599 ATTCAAAGCT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.31, C:0.35, G:0.15, T:0.18
Consensus pattern (33 bp):
ACACCAGCAAGCTCATCCAAAGATGCAAGCTCT
Found at i:58647630 original size:18 final size:18
Alignment explanation
Indices: 58647607--58647667 Score: 86
Period size: 18 Copynumber: 3.4 Consensus size: 18
58647597 TCATTCAAAG
58647607 CTGCGAGATCAAACACAA
1 CTGCGAGATCAAACACAA
* ** *
58647625 CTGCGAGCTCATTCAAAA
1 CTGCGAGATCAAACACAA
58647643 CTGCGAGATCAAACACAA
1 CTGCGAGATCAAACACAA
58647661 CTGCGAG
1 CTGCGAG
58647668 CTCATCAAAG
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.38, C:0.28, G:0.20, T:0.15
Consensus pattern (18 bp):
CTGCGAGATCAAACACAA
Found at i:58647641 original size:36 final size:36
Alignment explanation
Indices: 58647594--58647677 Score: 152
Period size: 36 Copynumber: 2.4 Consensus size: 36
58647584 CACAGATGCA
58647594 AGCTCATTCAAAGCTGCGAGATCAAACACAACTGCG
1 AGCTCATTCAAAGCTGCGAGATCAAACACAACTGCG
*
58647630 AGCTCATTCAAAACTGCGAGATCAAACACAACTGCG
1 AGCTCATTCAAAGCTGCGAGATCAAACACAACTGCG
58647666 AGCTCA-TCAAAG
1 AGCTCATTCAAAG
58647678 ATGTAAGCTC
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
35 5 0.11
36 41 0.89
ACGTcount: A:0.38, C:0.27, G:0.18, T:0.17
Consensus pattern (36 bp):
AGCTCATTCAAAGCTGCGAGATCAAACACAACTGCG
Found at i:58647676 original size:21 final size:21
Alignment explanation
Indices: 58647614--58647676 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 21
58647604 AAGCTGCGAG
58647614 ATCAAACACAACTGCGAGCTC
1 ATCAAACACAACTGCGAGCTC
58647635 ATTC--A-A-AACTGCGAG---
1 A-TCAAACACAACTGCGAGCTC
58647650 ATCAAACACAACTGCGAGCTC
1 ATCAAACACAACTGCGAGCTC
58647671 ATCAAA
1 ATCAAA
58647677 GATGTAAGCT
Statistics
Matches: 34, Mismatches: 0, Indels: 16
0.68 0.00 0.32
Matches are distributed among these distances:
14 2 0.06
15 1 0.03
16 1 0.03
17 1 0.03
18 18 0.53
19 1 0.03
20 1 0.03
21 7 0.21
22 2 0.06
ACGTcount: A:0.41, C:0.29, G:0.14, T:0.16
Consensus pattern (21 bp):
ATCAAACACAACTGCGAGCTC
Found at i:58654290 original size:120 final size:119
Alignment explanation
Indices: 58654078--58654320 Score: 371
Period size: 120 Copynumber: 2.0 Consensus size: 119
58654068 GTTGTCAACA
*
58654078 ATGGCCTTTACAAAACTAAATACACTTCGTTTAACCTAGCATGAGGGTTCCTACGTTTCTATATT
1 ATGGCCTTTACAAAACTAAATACACTTCGTTTAACCTAGCATGAGGGTTCCTACGTTTCTACATT
* * *
58654143 TCAGCAGCTAACTCTCCCACCCCCTCTC-GAAAATTTATCTACATGGTATCTTTG
66 TCAGCAGCTAACTCTACCACCCCCTCTCTG-AAATTTAGCAACATGGTATCTTTG
* * *
58654197 ATGGCCTTTTCAAAACTAAATACACTTTCGTTTAACCTAGTATGAGGGTTCCTACGTTTCTGCAT
1 ATGGCCTTTACAAAACTAAATACAC-TTCGTTTAACCTAGCATGAGGGTTCCTACGTTTCTACAT
* * *
58654262 TTTAGCAGCTTACTCTACCACCCTCTCTCTGAAATTTAGCAACATGGTATCTTTG
65 TTCAGCAGCTAACTCTACCACCCCCTCTCTGAAATTTAGCAACATGGTATCTTTG
58654317 ATGG
1 ATGG
58654321 AAGGGTAAAT
Statistics
Matches: 112, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
119 24 0.21
120 87 0.78
121 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.35
Consensus pattern (119 bp):
ATGGCCTTTACAAAACTAAATACACTTCGTTTAACCTAGCATGAGGGTTCCTACGTTTCTACATT
TCAGCAGCTAACTCTACCACCCCCTCTCTGAAATTTAGCAACATGGTATCTTTG
Found at i:58654968 original size:18 final size:20
Alignment explanation
Indices: 58654941--58654978 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
58654931 AAAGTGTTGA
*
58654941 AACAACCTA-GAG-GAAAAG
1 AACAAACTAGGAGAGAAAAG
58654959 AACAAACTAGGAGAGAAAAG
1 AACAAACTAGGAGAGAAAAG
58654979 TCAAAGACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 3 0.18
20 6 0.35
ACGTcount: A:0.58, C:0.13, G:0.24, T:0.05
Consensus pattern (20 bp):
AACAAACTAGGAGAGAAAAG
Found at i:58659326 original size:19 final size:20
Alignment explanation
Indices: 58659302--58659339 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
58659292 TTACAAAAAG
58659302 AAAAA-TCAAAATAATTTTC
1 AAAAATTCAAAATAATTTTC
58659321 AAAAATTCAAAATAATTTT
1 AAAAATTCAAAATAATTTT
58659340 TTATATTCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (20 bp):
AAAAATTCAAAATAATTTTC
Found at i:58669640 original size:17 final size:18
Alignment explanation
Indices: 58669615--58669650 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
58669605 ATTTCATGTT
58669615 TAAAATTTTATAA-ATAA
1 TAAAATTTTATAATATAA
*
58669632 TAAACTTTTATAATATAA
1 TAAAATTTTATAATATAA
58669650 T
1 T
58669651 CTAATATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAAATTTTATAATATAA
Found at i:58670848 original size:3 final size:3
Alignment explanation
Indices: 58670842--58670893 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
58670832 TAATAATATA
58670842 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
58670890 TCT T
1 TCT T
58670894 TATTATATAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:58671996 original size:8 final size:8
Alignment explanation
Indices: 58671985--58672025 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
58671975 TAATTTTTTA
58671985 AAAATTAT
1 AAAATTAT
58671993 AAAA-TAT
1 AAAATTAT
58672000 -AAATTATT
1 AAAATTA-T
*
58672008 AAAATGAT
1 AAAATTAT
58672016 AAAATTAT
1 AAAATTAT
58672024 AA
1 AA
58672026 TTTTATTATC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
6 3 0.11
7 5 0.18
8 15 0.54
9 5 0.18
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (8 bp):
AAAATTAT
Found at i:58672005 original size:14 final size:16
Alignment explanation
Indices: 58671985--58672025 Score: 59
Period size: 14 Copynumber: 2.6 Consensus size: 16
58671975 TAATTTTTTA
58671985 AAAATTATAAAAT-AT
1 AAAATTATAAAATGAT
58672000 -AAATTATTAAAATGAT
1 AAAATTA-TAAAATGAT
58672016 AAAATTATAA
1 AAAATTATAA
58672026 TTTTATTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 6 0.26
15 6 0.26
16 5 0.22
17 6 0.26
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (16 bp):
AAAATTATAAAATGAT
Found at i:58675725 original size:22 final size:24
Alignment explanation
Indices: 58675699--58675742 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
58675689 TTTAAAAAAT
58675699 TATTTAT-ATTATAT-TATTTTAA
1 TATTTATAATTATATATATTTTAA
*
58675721 TATTTATAATTTTATATATTTT
1 TATTTATAATTATATATATTTT
58675743 TATGTATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 6 0.32
24 6 0.32
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (24 bp):
TATTTATAATTATATATATTTTAA
Found at i:58675739 original size:16 final size:16
Alignment explanation
Indices: 58675703--58675741 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
58675693 AAAAATTATT
*
58675703 TATATTATATTATTTTA
1 TATATT-TATAATTTTA
58675720 -ATATTTATAATTTTA
1 TATATTTATAATTTTA
58675735 TATATTT
1 TATATTT
58675742 TTATGTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TATATTTATAATTTTA
Found at i:58676237 original size:19 final size:19
Alignment explanation
Indices: 58676213--58676310 Score: 54
Period size: 19 Copynumber: 5.0 Consensus size: 19
58676203 TTTAAATCCT
58676213 TTTTTTACAATTTTTAATA
1 TTTTTTACAATTTTTAATA
** * *
58676232 TTTTTTCACAA-ACTTACTT
1 TTTTTT-ACAATTTTTAATA
** *
58676251 TTTTTTTTAATTTCTAATA
1 TTTTTTACAATTTTTAATA
* * *
58676270 TTTCTCACAACTTTTAATAA
1 TTTTTTACAATTTTTAAT-A
*
58676290 TTTTTTTACATTTTTTTAATA
1 -TTTTTTACA-ATTTTTAATA
58676311 AGTATTTGTA
Statistics
Matches: 53, Mismatches: 21, Indels: 8
0.65 0.26 0.10
Matches are distributed among these distances:
18 2 0.04
19 31 0.58
20 5 0.09
21 8 0.15
22 7 0.13
ACGTcount: A:0.29, C:0.11, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTTTTACAATTTTTAATA
Found at i:58676324 original size:22 final size:22
Alignment explanation
Indices: 58676281--58676326 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
58676271 TTCTCACAAC
* *
58676281 TTTTAATAATTTTTTTACATTT
1 TTTTAATAATATTTGTACATTT
58676303 TTTTAATAAGTATTTGTA-ATTT
1 TTTTAATAA-TATTTGTACATTT
58676325 TT
1 TT
58676327 AATCTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.65
Consensus pattern (22 bp):
TTTTAATAATATTTGTACATTT
Found at i:58677319 original size:22 final size:24
Alignment explanation
Indices: 58677280--58677339 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 24
58677270 AAACGGAACA
* *
58677280 AACAGAGAGTACCGAAGTACT-G-
1 AACAGAGAGCACAGAAGTACTAGC
* *
58677302 AACAGAGAGCACATAAGTGCTAGGC
1 AACAGAGAGCACAGAAGTACTA-GC
58677327 AACAGAGAGCACA
1 AACAGAGAGCACA
58677340 CAAAGTGCTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
22 17 0.55
24 1 0.03
25 13 0.42
ACGTcount: A:0.43, C:0.20, G:0.27, T:0.10
Consensus pattern (24 bp):
AACAGAGAGCACAGAAGTACTAGC
Found at i:58677353 original size:23 final size:23
Alignment explanation
Indices: 58677279--58677492 Score: 151
Period size: 23 Copynumber: 9.5 Consensus size: 23
58677269 TAAACGGAAC
* * *
58677279 AAACAGAGAGTAC-CGAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
* *
58677301 GAACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
58677323 AGGCAACAGAGAGCACACAAAGTGCT
1 A---AACAGAGAGCACACAAAGTGCT
* *
58677349 AAACAAAGAGTACACAAA--G-T
1 AAACAGAGAGCACACAAAGTGCT
*
58677369 --AC--TGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
58677388 AATCAGAGAGCACACGAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* * *
58677411 AATCGGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
58677434 AATAACAGAGAGCACGA-GACGTGCT
1 -A-AACAGAGAGCAC-ACAAAGTGCT
*
58677459 AAACAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
58677482 AATCAGAGAGC
1 AAACAGAGAGC
58677493 GCGCTAGTGT
Statistics
Matches: 151, Mismatches: 25, Indels: 31
0.73 0.12 0.15
Matches are distributed among these distances:
16 10 0.07
18 3 0.02
19 1 0.01
20 1 0.01
21 2 0.01
22 18 0.12
23 77 0.51
24 2 0.01
25 28 0.19
26 9 0.06
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:58677358 original size:25 final size:25
Alignment explanation
Indices: 58677302--58677366 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
58677292 CGAAGTACTG
* **
58677302 AACAGAGAGCACATAAGTGCTAGGC
1 AACAGAGAGCACAAAAGTGCTAAAC
58677327 AACAGAGAGCACACAAAGTGCTAAAC
1 AACAGAGAGCACA-AAAGTGCTAAAC
58677353 AA-AGAGTA-CACAAA
1 AACAGAG-AGCACAAA
58677367 GTACTGAGCA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
24 2 0.06
25 21 0.60
26 12 0.34
ACGTcount: A:0.49, C:0.20, G:0.22, T:0.09
Consensus pattern (25 bp):
AACAGAGAGCACAAAAGTGCTAAAC
Found at i:58677387 original size:39 final size:39
Alignment explanation
Indices: 58677333--58677407 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
58677323 AGGCAACAGA
*
58677333 GAGCACACAAAGTGCTAAACAAAGAGTACACAAAGTACT
1 GAGCACACAAAGTGCTAAACAAAGAGCACACAAAGTACT
* * *
58677372 GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGT
1 GAGCACACAAAGTGCTAAACAAAGAGCACACAAAGT
58677408 GCTAATCGGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.12
Consensus pattern (39 bp):
GAGCACACAAAGTGCTAAACAAAGAGCACACAAAGTACT
Found at i:58677446 original size:48 final size:46
Alignment explanation
Indices: 58677372--58677492 Score: 172
Period size: 48 Copynumber: 2.6 Consensus size: 46
58677362 ACAAAGTACT
* * *
58677372 GAGCACACAAAGTGCTAATCAGAGAGCAC-ACGAAGTGCTAATCGGA
1 GAGCACACACAGTGCTAATCAGAGAGCACGA-GAAGTGCTAAACAGA
*
58677418 GAGCACACACAGTGCTAATAACAGAGAGCACGAGACGTGCTAAACAGA
1 GAGCACACACAGTGCTAAT--CAGAGAGCACGAGAAGTGCTAAACAGA
58677466 GAGCACACACAGTGCTAATCAGAGAGC
1 GAGCACACACAGTGCTAATCAGAGAGC
58677493 GCGCTAGTGT
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
46 26 0.38
48 41 0.60
49 1 0.01
ACGTcount: A:0.40, C:0.23, G:0.26, T:0.12
Consensus pattern (46 bp):
GAGCACACACAGTGCTAATCAGAGAGCACGAGAAGTGCTAAACAGA
Found at i:58678580 original size:33 final size:36
Alignment explanation
Indices: 58678519--58678584 Score: 93
Period size: 33 Copynumber: 1.9 Consensus size: 36
58678509 CTCTTTTACC
* *
58678519 CCTTGCTCTACTCTTTTCCTTTGTCTTCAATTTGAT
1 CCTTGCTCTACTCTTCTCCTTTCTCTTCAATTTGAT
58678555 CCTTGC-CT-CTCTTCT-CTTTCTCTTCAATTT
1 CCTTGCTCTACTCTTCTCCTTTCTCTTCAATTT
58678585 CACATAAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 14 0.50
34 6 0.21
35 2 0.07
36 6 0.21
ACGTcount: A:0.09, C:0.32, G:0.06, T:0.53
Consensus pattern (36 bp):
CCTTGCTCTACTCTTCTCCTTTCTCTTCAATTTGAT
Found at i:58678609 original size:7 final size:7
Alignment explanation
Indices: 58678597--58678622 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
58678587 CATAAACACA
58678597 TATAAGC
1 TATAAGC
58678604 TATAAGC
1 TATAAGC
58678611 TATAAGC
1 TATAAGC
58678618 TATAA
1 TATAA
58678623 TTCAATAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.31
Consensus pattern (7 bp):
TATAAGC
Found at i:58680116 original size:15 final size:15
Alignment explanation
Indices: 58680072--58680124 Score: 63
Period size: 15 Copynumber: 3.4 Consensus size: 15
58680062 AGTTCTGAAA
*
58680072 TTTAATTTTTAT-AT
1 TTTATTTTTTATAAT
58680086 TTTAATTTTTAATATAAT
1 TTT-ATTTTT--TATAAT
58680104 TTTATTTTTTATAAT
1 TTTATTTTTTATAAT
58680119 TTTATT
1 TTTATT
58680125 AATTAATTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 3 0.09
15 17 0.50
17 9 0.26
18 5 0.15
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTATTTTTTATAAT
Found at i:58683543 original size:21 final size:21
Alignment explanation
Indices: 58683517--58683556 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
58683507 TACCCTGCAC
*
58683517 TTCTACCGAAACATACATGGG
1 TTCTACCGAAACAAACATGGG
58683538 TTCTACCGAAACAAACATG
1 TTCTACCGAAACAAACATG
58683557 CCAAATCTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.25, G:0.15, T:0.23
Consensus pattern (21 bp):
TTCTACCGAAACAAACATGGG
Found at i:58684249 original size:52 final size:51
Alignment explanation
Indices: 58684062--58684249 Score: 200
Period size: 52 Copynumber: 3.6 Consensus size: 51
58684052 TTTCATTTAA
* ** * *
58684062 TACTTACGATGACA-TATAGTCATCGGACCTCTTGTTCCATATAGGAATTCATA
1 TACTCACGATGACACT-TAGTCATCGGACCT-TTAATCCATAAAGG-ATTCATT
* * *
58684115 TACTCACGATGACACTAAGTCATCGGACCTTTAATCCATCATGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
* * **
58684166 TACTCACGATGACACTTAATCATCGAACCTTTCATAT-TGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTT-A-ATCCATAAAGGATTCATT
*
58684218 TACTCACGATGACACTTAGTCATCGGGCCTTT
1 TACTCACGATGACACTTAGTCATCGGACCTTT
58684250 TTGTTTATAG
Statistics
Matches: 114, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
51 35 0.31
52 50 0.44
53 28 0.25
54 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.33
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
Found at i:58687369 original size:24 final size:25
Alignment explanation
Indices: 58687338--58687391 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
58687328 TCGAAAAAAT
58687338 TAATAAGA-TTTTTTTGTGGAGGTA
1 TAATAAGATTTTTTTTGTGGAGGTA
*
58687362 TAATAAGATTTTTTTTTTGGAGGTA
1 TAATAAGATTTTTTTTGTGGAGGTA
58687387 TAATA
1 TAATA
58687392 CTATGACAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
24 8 0.29
25 20 0.71
ACGTcount: A:0.31, C:0.00, G:0.20, T:0.48
Consensus pattern (25 bp):
TAATAAGATTTTTTTTGTGGAGGTA
Found at i:58689466 original size:3 final size:3
Alignment explanation
Indices: 58689458--58689495 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
58689448 TTTATTTTGT
58689458 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
58689496 GTATAAAAGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:58689636 original size:18 final size:17
Alignment explanation
Indices: 58689609--58689642 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
58689599 TAAAAATTGT
*
58689609 GATAATTATATATTTAAA
1 GATAAGTATA-ATTTAAA
58689627 GATAAGTATAATTTAA
1 GATAAGTATAATTTAA
58689643 TTTATTACTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (17 bp):
GATAAGTATAATTTAAA
Found at i:58691045 original size:12 final size:12
Alignment explanation
Indices: 58691028--58691057 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
58691018 AGAATAAGAG
58691028 AAATCCGAACCT
1 AAATCCGAACCT
58691040 AAATCCGAACCT
1 AAATCCGAACCT
58691052 AAATCC
1 AAATCC
58691058 TTTTGGGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.43, C:0.33, G:0.07, T:0.17
Consensus pattern (12 bp):
AAATCCGAACCT
Found at i:58705268 original size:124 final size:123
Alignment explanation
Indices: 58705043--58705291 Score: 322
Period size: 124 Copynumber: 2.0 Consensus size: 123
58705033 CGCATAAATC
* * * * *
58705043 ATTAAGGCAATAACATATTATGAATCTGTTATAATTTGTAATATCTATTTGAGATCTAATATTAT
1 ATTAAGGCAATAACATACTATGAATATGTTATAATTGGTAATATCTATCTGAGAGCTAATATTAT
* * * * * *
58705108 GATTTTAGGTTCTTGAGCATACATGAATGGCTCATTTATGAACTTTATCCCCTAGAAT
66 GATGTTAGATTCTTGAGAATACATGAATGGCTCATTTATGAACTTAAACCCCAAGAAT
* * *
58705166 ATTAAGGCAATCATATACTATGAATATGTTATATATTGGTAATGTCTATCTGAGAGCTAATATTA
1 ATTAAGGCAATAACATACTATGAATATGTTATA-ATTGGTAATATCTATCTGAGAGCTAATATTA
*
58705231 TGATGTTAGATTCTTGAGAATGCAT-ACATGG-TACATTTATGAACTTAAACCCCAAGAAT
65 TGATGTTAGATTCTTGAGAATACATGA-ATGGCT-CATTTATGAACTTAAACCCCAAGAAT
58705290 AT
1 AT
58705292 CTATCTAGCT
Statistics
Matches: 108, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
123 31 0.29
124 77 0.71
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (123 bp):
ATTAAGGCAATAACATACTATGAATATGTTATAATTGGTAATATCTATCTGAGAGCTAATATTAT
GATGTTAGATTCTTGAGAATACATGAATGGCTCATTTATGAACTTAAACCCCAAGAAT
Found at i:58706614 original size:27 final size:26
Alignment explanation
Indices: 58706524--58706617 Score: 68
Period size: 27 Copynumber: 3.5 Consensus size: 26
58706514 GTGGTTTCAG
*
58706524 TTTGCACAAATAAAAATGTGGATTTC
1 TTTGCACAAATAAAAATGTAGATTTC
** * * *
58706550 TTTAAAATAAATTAAAAAT-TAAATATC
1 TTT-GCACAAA-TAAAAATGTAGATTTC
58706577 TTTG-ACGAAATAAAAATGT-GATTTC
1 TTTGCAC-AAATAAAAATGTAGATTTC
58706602 AGTTTGCACAAATAAA
1 --TTTGCACAAATAAA
58706618 TTAAAATACA
Statistics
Matches: 51, Mismatches: 10, Indels: 13
0.69 0.14 0.18
Matches are distributed among these distances:
25 12 0.24
26 7 0.14
27 23 0.45
28 9 0.18
ACGTcount: A:0.47, C:0.09, G:0.11, T:0.34
Consensus pattern (26 bp):
TTTGCACAAATAAAAATGTAGATTTC
Found at i:58717546 original size:9 final size:9
Alignment explanation
Indices: 58717532--58717569 Score: 67
Period size: 9 Copynumber: 4.1 Consensus size: 9
58717522 ATGATAATAG
58717532 AAAATTTTT
1 AAAATTTTT
58717541 AAAATTTTT
1 AAAATTTTT
58717550 AAAATTTTT
1 AAAATTTTT
58717559 AAAATTATTT
1 AAAATT-TTT
58717569 A
1 A
58717570 TATATTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
9 24 0.86
10 4 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
AAAATTTTT
Found at i:58717596 original size:14 final size:14
Alignment explanation
Indices: 58717577--58717608 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
58717567 TTATATATTT
*
58717577 TTTTAAATTATAAA
1 TTTTAAAATATAAA
58717591 TTTTAAAATATAAA
1 TTTTAAAATATAAA
58717605 TTTT
1 TTTT
58717609 GGAATTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TTTTAAAATATAAA
Found at i:58717621 original size:18 final size:19
Alignment explanation
Indices: 58717598--58717634 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
58717588 AAATTTTAAA
58717598 ATATAAAT-TTTGGAATTT
1 ATATAAATATTTGGAATTT
*
58717616 ATATAAATATTTTGAATTT
1 ATATAAATATTTGGAATTT
58717635 TAATTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (19 bp):
ATATAAATATTTGGAATTT
Found at i:58721596 original size:16 final size:17
Alignment explanation
Indices: 58721575--58721611 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
58721565 TTAAAATTTC
58721575 AATAAAAAATAAAA-AA
1 AATAAAAAATAAAAGAA
*
58721591 AAT-AAAGATAAAAGAA
1 AATAAAAAATAAAAGAA
58721607 AATAA
1 AATAA
58721612 CATGTATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 9 0.50
16 8 0.44
17 1 0.06
ACGTcount: A:0.81, C:0.00, G:0.05, T:0.14
Consensus pattern (17 bp):
AATAAAAAATAAAAGAA
Found at i:58724421 original size:20 final size:19
Alignment explanation
Indices: 58724382--58724432 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
58724372 ATTAATTATT
58724382 TATAAATTTAATTAAAATA
1 TATAAATTTAATTAAAATA
* *
58724401 TATAAATTATATTTTAAATA
1 TATAAATT-TAATTAAAATA
* *
58724421 TTTAAATATAAT
1 TATAAATTTAAT
58724433 CATTAAATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 11 0.42
20 15 0.58
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TATAAATTTAATTAAAATA
Found at i:58728750 original size:23 final size:23
Alignment explanation
Indices: 58728720--58728770 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
58728710 CAGCCGATAT
58728720 CATGCTCATAATTGCAATAGGAG
1 CATGCTCATAATTGCAATAGGAG
58728743 CATGCTCATAATTGCAATAGGAG
1 CATGCTCATAATTGCAATAGGAG
58728766 CATGC
1 CATGC
58728771 AACCACCGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (23 bp):
CATGCTCATAATTGCAATAGGAG
Found at i:58740128 original size:3 final size:3
Alignment explanation
Indices: 58740120--58740147 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
58740110 AACGTAAGTC
58740120 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
58740148 GCTGAATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:58742853 original size:33 final size:33
Alignment explanation
Indices: 58742794--58742880 Score: 95
Period size: 33 Copynumber: 2.6 Consensus size: 33
58742784 GGATCAGTAG
* * *
58742794 GAGTTTCTTCA-TCCAGGTTAGTGGGAATGCTAT
1 GAGTTTCTTCACTCAAGGTT-GAGGGAATACTAT
* *
58742827 GATTTTCTTCACTCGAGGTTGAGGGAATACTAT
1 GAGTTTCTTCACTCAAGGTTGAGGGAATACTAT
* *
58742860 GAGTTCCTTCACCCAAGGTTG
1 GAGTTTCTTCACTCAAGGTTG
58742881 CAGGAAGGGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
33 38 0.84
34 7 0.16
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.34
Consensus pattern (33 bp):
GAGTTTCTTCACTCAAGGTTGAGGGAATACTAT
Found at i:58743813 original size:33 final size:33
Alignment explanation
Indices: 58743776--58743860 Score: 98
Period size: 33 Copynumber: 2.5 Consensus size: 33
58743766 GATGGATGGG
* * *
58743776 AGTTTCTTCATCCAAGTTTGGAGGAATGCTACA
1 AGTTTCTTCACCCAAGTTTGAAGGAATGCAACA
* ** *
58743809 AGTTTCTTCACCCGAGGGTGAAGGAATGGAACA
1 AGTTTCTTCACCCAAGTTTGAAGGAATGCAACA
58743842 AGTTTCTTCACCCACAGTT
1 AGTTTCTTCACCCA-AGTT
58743861 GCAGGAACAC
Statistics
Matches: 41, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
33 39 0.95
34 2 0.05
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.29
Consensus pattern (33 bp):
AGTTTCTTCACCCAAGTTTGAAGGAATGCAACA
Found at i:58747874 original size:174 final size:174
Alignment explanation
Indices: 58747558--58747877 Score: 414
Period size: 174 Copynumber: 1.8 Consensus size: 174
58747548 AAAACCCTGG
* ** *
58747558 CTCCATTTACCTCATTCTGAGCCTTGGCTTCACCACCTGAAACATCATACCTTGAACCCAAATCA
1 CTCCATTTACCTCATTCTGAGCCCTACCTTCACCACCTGAAACATCATACCTTGAACCCAAACCA
** **
58747623 CTGGCTGCACCACCTTCACTATCTAAGGTACTCAGATTACCCTCCAAACCAACTTCATCAGGCTC
66 CTCACTGCACCACAGTCACTATCTAAGGTACTCAGATTACCCTCCAAACCAACTTCATCAGGCTC
*
58747688 ATTATGACCACAAACTACATCATTAGAACAAGACCGAACCACAC
131 ATTATAACCACAAACTACATCATTAGAACAAGACCGAACCACAC
* * *
58747732 CTCCATTTACCTCATTCTGAGCCCTACCTTCCCCACCTGAAACCTCATTCCTTGAACCCAAACCA
1 CTCCATTTACCTCATTCTGAGCCCTACCTTCACCACCTGAAACATCATACCTTGAACCCAAACCA
*** * * *
58747797 -TCCACTGCATGGCAGTCACTATCTAAGGTTCTCA-AGTTACCCTCCAAACCAACTTTA-CTGGA
66 CT-CACTGCACCACAGTCACTATCTAAGGTACTCAGA-TTACCCTCCAAACCAACTTCATCAGG-
58747859 CTC-TTCATAACCACAAACT
128 CTCATT-ATAACCACAAACT
58747878 GCTTCACCAA
Statistics
Matches: 124, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
173 7 0.06
174 117 0.94
ACGTcount: A:0.30, C:0.36, G:0.10, T:0.25
Consensus pattern (174 bp):
CTCCATTTACCTCATTCTGAGCCCTACCTTCACCACCTGAAACATCATACCTTGAACCCAAACCA
CTCACTGCACCACAGTCACTATCTAAGGTACTCAGATTACCCTCCAAACCAACTTCATCAGGCTC
ATTATAACCACAAACTACATCATTAGAACAAGACCGAACCACAC
Found at i:58750753 original size:59 final size:59
Alignment explanation
Indices: 58750687--58750806 Score: 240
Period size: 59 Copynumber: 2.0 Consensus size: 59
58750677 CAAAAAGAAT
58750687 TTTAAATGCTTTAATTTAATTAAATCCGAGAATCTCCTCCAAATAATACTCCATCCAAG
1 TTTAAATGCTTTAATTTAATTAAATCCGAGAATCTCCTCCAAATAATACTCCATCCAAG
58750746 TTTAAATGCTTTAATTTAATTAAATCCGAGAATCTCCTCCAAATAATACTCCATCCAAG
1 TTTAAATGCTTTAATTTAATTAAATCCGAGAATCTCCTCCAAATAATACTCCATCCAAG
58750805 TT
1 TT
58750807 CTGTCCACGA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.37, C:0.22, G:0.07, T:0.35
Consensus pattern (59 bp):
TTTAAATGCTTTAATTTAATTAAATCCGAGAATCTCCTCCAAATAATACTCCATCCAAG
Found at i:58750998 original size:23 final size:24
Alignment explanation
Indices: 58750966--58751010 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
58750956 GATTATGACA
58750966 ATGCAATATTTTATAAAAATTTAT
1 ATGCAATATTTTATAAAAATTTAT
* *
58750990 ATGC-ATATTTTTTCAAAATTT
1 ATGCAATATTTTATAAAAATTT
58751011 CCTTCTCATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49
Consensus pattern (24 bp):
ATGCAATATTTTATAAAAATTTAT
Found at i:58753595 original size:54 final size:53
Alignment explanation
Indices: 58753501--58753606 Score: 149
Period size: 54 Copynumber: 2.0 Consensus size: 53
58753491 AAACCCAGTG
* * *
58753501 TTCCATTTCTTCGGCTTAAATATCAGGGTTGAAGGCCAGGTGCCAAATTTATT
1 TTCCATTTCTTCGGCTTAAATAGCAGGGTTGAAGGACAGGTGCCAAAATTATT
* * *
58753554 TTCCATTTGTTCGGCTTAAAATAGCAGGGTTGAATGACAGGTGGCAAAATTAT
1 TTCCATTTCTTCGGCTT-AAATAGCAGGGTTGAAGGACAGGTGCCAAAATTAT
58753607 GGAGCATAGA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
53 16 0.35
54 30 0.65
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (53 bp):
TTCCATTTCTTCGGCTTAAATAGCAGGGTTGAAGGACAGGTGCCAAAATTATT
Found at i:58754493 original size:63 final size:63
Alignment explanation
Indices: 58754387--58754592 Score: 385
Period size: 63 Copynumber: 3.3 Consensus size: 63
58754377 AGGGAACACC
*
58754387 GATATATTGAAGATGAATATATCAACTCCAACCTCATGTAGGTTTCTCTACTTTGAACCAAGA
1 GATACATTGAAGATGAATATATCAACTCCAACCTCATGTAGGTTTCTCTACTTTGAACCAAGA
*
58754450 GATACACTGAAGATGAATATATCAACTCCAACCTCATGTAGGTTTCTCTACTTTGAACCAAGA
1 GATACATTGAAGATGAATATATCAACTCCAACCTCATGTAGGTTTCTCTACTTTGAACCAAGA
*
58754513 GATACATTGAGGATGAATATATCAACTCCAACCTCATGTAGGTTTCTCTACTTTGAACCAAGA
1 GATACATTGAAGATGAATATATCAACTCCAACCTCATGTAGGTTTCTCTACTTTGAACCAAGA
58754576 GATACATTGAAGATGAA
1 GATACATTGAAGATGAA
58754593 CATCTAATTT
Statistics
Matches: 138, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 138 1.00
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (63 bp):
GATACATTGAAGATGAATATATCAACTCCAACCTCATGTAGGTTTCTCTACTTTGAACCAAGA
Found at i:58755402 original size:33 final size:33
Alignment explanation
Indices: 58755355--58755431 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 33
58755345 GAGGAATAGT
* * *
58755355 AGTTCCTTCGCTGAATGACGGAGGAACAGCTGG
1 AGTTTCTTCACTGAATGACGGAGGAACAGATGG
** *
58755388 AGTTTCTTCACTGAATGTTGGAGGAAGAGATGG
1 AGTTTCTTCACTGAATGACGGAGGAACAGATGG
58755421 AGTTTCTTCAC
1 AGTTTCTTCAC
58755432 CCAAGGTTTC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.29
Consensus pattern (33 bp):
AGTTTCTTCACTGAATGACGGAGGAACAGATGG
Found at i:58755446 original size:33 final size:33
Alignment explanation
Indices: 58755376--58755446 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 33
58755366 TGAATGACGG
* ** * *
58755376 AGGAACAGCTGGAGTTTCTTCACTGAATGTTGG
1 AGGAACAGATGGAGTTTCTTCACCCAAGGTTGC
* *
58755409 AGGAAGAGATGGAGTTTCTTCACCCAAGGTTTC
1 AGGAACAGATGGAGTTTCTTCACCCAAGGTTGC
58755442 AGGAA
1 AGGAA
58755447 TACTGGAGCT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.27
Consensus pattern (33 bp):
AGGAACAGATGGAGTTTCTTCACCCAAGGTTGC
Found at i:58762616 original size:15 final size:16
Alignment explanation
Indices: 58762585--58762626 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
58762575 AAACTTTCAT
*
58762585 ATTGT-AATTTTCAAA
1 ATTGTAAATTCTCAAA
58762600 ATTGTAAATTCTCAAA
1 ATTGTAAATTCTCAAA
*
58762616 TAATGTAAATT
1 -ATTGTAAATT
58762627 AGTCTTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 5 0.22
16 9 0.39
17 9 0.39
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (16 bp):
ATTGTAAATTCTCAAA
Found at i:58765490 original size:82 final size:82
Alignment explanation
Indices: 58765322--58765495 Score: 210
Period size: 82 Copynumber: 2.1 Consensus size: 82
58765312 ATTTATCTCT
* * * *
58765322 TTTAAAATTTTTAAAATTTTAAAATAATAAAAATAAAATTATACTTTGAACCCTTAAAATGAAAA
1 TTTAAAATTTTTAAAATTTTAAAATAATAAAAATAAAATTACAATTTGAACCCTAAAAATAAAAA
* *
58765387 ATTTTCTATTTAGACAT
66 ATTTTCAATTTAGACAC
* * *
58765404 TTTAAAATTTTTATAATTTTAAATTAATAAAAATAAAATTACAATTT-AGCTCTCTAAAAATAAT
1 TTTAAAATTTTTAAAATTTTAAAATAATAAAAATAAAATTACAATTTGAAC-C-CTAAAAATAA-
*
58765468 AAAATTTT-AATTTA-ACCC
63 AAAATTTTCAATTTAGACAC
58765486 TTTAAAATTT
1 TTTAAAATTT
58765496 ACATTTTTAC
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
81 2 0.03
82 56 0.71
83 13 0.16
84 8 0.10
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.42
Consensus pattern (82 bp):
TTTAAAATTTTTAAAATTTTAAAATAATAAAAATAAAATTACAATTTGAACCCTAAAAATAAAAA
ATTTTCAATTTAGACAC
Found at i:58765492 original size:30 final size:29
Alignment explanation
Indices: 58765427--58765492 Score: 69
Period size: 30 Copynumber: 2.2 Consensus size: 29
58765417 TAATTTTAAA
* *
58765427 TTAATAAAAATAAAATTACAATTTAGCTCT
1 TTAA-AAAAATAAAATTACAATTTAACCCT
* **
58765457 CTAAAAATAATAAAATTTTAATTTAACCCT
1 TTAAAAA-AATAAAATTACAATTTAACCCT
58765487 TTAAAA
1 TTAAAA
58765493 TTTACATTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
29 3 0.10
30 26 0.90
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.36
Consensus pattern (29 bp):
TTAAAAAAATAAAATTACAATTTAACCCT
Found at i:58769741 original size:23 final size:23
Alignment explanation
Indices: 58769715--58769784 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
58769705 TTCATTTAAT
*
58769715 TTAATCAAACATGTTCACGAACA
1 TTAATCGAACATGTTCACGAACA
* **
58769738 TTAAACGAACATGTTCATAAACA
1 TTAATCGAACATGTTCACGAACA
*
58769761 TATAATTGAACATGTTCACGAACA
1 T-TAATCGAACATGTTCACGAACA
58769785 ATGTTAATGA
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
23 20 0.53
24 18 0.47
ACGTcount: A:0.44, C:0.19, G:0.10, T:0.27
Consensus pattern (23 bp):
TTAATCGAACATGTTCACGAACA
Found at i:58769776 original size:24 final size:23
Alignment explanation
Indices: 58769722--58769784 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 23
58769712 AATTTAATCA
*
58769722 AACATGTTCACGAACATTAAACG
1 AACATGTTCACAAACATTAAACG
* **
58769745 AACATGTTCATAAACATATAATTG
1 AACATGTTCACAAACAT-TAAACG
*
58769769 AACATGTTCACGAACA
1 AACATGTTCACAAACA
58769785 ATGTTAATGA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 15 0.45
24 18 0.55
ACGTcount: A:0.44, C:0.19, G:0.11, T:0.25
Consensus pattern (23 bp):
AACATGTTCACAAACATTAAACG
Found at i:58769891 original size:12 final size:12
Alignment explanation
Indices: 58769874--58769921 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
58769864 ATCATTAATA
58769874 AATAAACGAG-T
1 AATAAACGAGCT
*
58769885 CAATAAATGAGCT
1 -AATAAACGAGCT
58769898 AATAAACGAGCT
1 AATAAACGAGCT
**
58769910 TTTAAACGAGCT
1 AATAAACGAGCT
58769922 TGTTCGTGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
12 30 0.97
13 1 0.03
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.23
Consensus pattern (12 bp):
AATAAACGAGCT
Found at i:58770925 original size:6 final size:6
Alignment explanation
Indices: 58770916--58770940 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
58770906 GAAATGGAAA
58770916 TGGGTT TGGGTT TGGGTT TGGGTT T
1 TGGGTT TGGGTT TGGGTT TGGGTT T
58770941 TAGTACCTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (6 bp):
TGGGTT
Found at i:58771506 original size:26 final size:25
Alignment explanation
Indices: 58771477--58771557 Score: 74
Period size: 26 Copynumber: 3.1 Consensus size: 25
58771467 ATTCAAAATA
*
58771477 TTTATAAAAATTTCAAAATATATATT
1 TTTA-AAAAATTTCAAAATATATAAT
* * *
58771503 TTTAAAAAAATTATAAAAAAATAAAAT
1 TTT-AAAAAATT-TCAAAATATATAAT
*
58771530 TTGAAAAAATTTCTAAAATA-ATAAT
1 TTTAAAAAATTTC-AAAATATATAAT
58771555 TTT
1 TTT
58771558 GGACATGATT
Statistics
Matches: 43, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
25 7 0.16
26 23 0.53
27 13 0.30
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (25 bp):
TTTAAAAAATTTCAAAATATATAAT
Found at i:58771558 original size:26 final size:26
Alignment explanation
Indices: 58771482--58771558 Score: 77
Period size: 27 Copynumber: 3.0 Consensus size: 26
58771472 AAATATTTAT
*
58771482 AAAAATTTC-AAAAT-ATATATTTTTA
1 AAAAATTTCTAAAATAATA-ATTTTGA
* * * *
58771507 AAAAAATTATAAAAAAATAAAATTTGA
1 AAAAATTTCTAAAATAAT-AATTTTGA
58771534 AAAAATTTCTAAAATAATAATTTTG
1 AAAAATTTCTAAAATAATAATTTTG
58771559 GACATGATTC
Statistics
Matches: 40, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
25 7 0.17
26 10 0.25
27 22 0.55
28 1 0.03
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (26 bp):
AAAAATTTCTAAAATAATAATTTTGA
Found at i:58775337 original size:102 final size:102
Alignment explanation
Indices: 58775148--58775337 Score: 317
Period size: 102 Copynumber: 1.9 Consensus size: 102
58775138 TTACCGCATT
* * *
58775148 GAGGGCCCCTTCGAGCTCTCCCCATAAGCTCTTCCTCAAGCATTACACGGGACACTATTACACTC
1 GAGGGCCCCTTCGAGCACTCCCCATAAGCTCTTCCTCAAGCATTACACAGGACACTACTACACTC
* *
58775213 GCCTTTAGCGCGTCTAAACGACCTCAAGGGCCTCGTG
66 GCCTTTAGCACGTCCAAACGACCTCAAGGGCCTCGTG
*
58775250 GAGGGCCCCTTCGAGCACTCCCCATAAGCTCTTCCTCAAGCATTACACAGGACACTACTCCACTC
1 GAGGGCCCCTTCGAGCACTCCCCATAAGCTCTTCCTCAAGCATTACACAGGACACTACTACACTC
*
58775315 GCCTTTAGCACGTCCAAGCGACC
66 GCCTTTAGCACGTCCAAACGACC
58775338 CTTGATGTCC
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
102 81 1.00
ACGTcount: A:0.23, C:0.37, G:0.19, T:0.21
Consensus pattern (102 bp):
GAGGGCCCCTTCGAGCACTCCCCATAAGCTCTTCCTCAAGCATTACACAGGACACTACTACACTC
GCCTTTAGCACGTCCAAACGACCTCAAGGGCCTCGTG
Found at i:58778675 original size:5 final size:5
Alignment explanation
Indices: 58778665--58778706 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
58778655 AAAAGAATGA
* *
58778665 AAAAT AAAAT AAAAG AAAAGT TAAA- AAAAT AAAAT AAAAT AA
1 AAAAT AAAAT AAAAT AAAA-T AAAAT AAAAT AAAAT AAAAT AA
58778707 CAAAATTGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
4 3 0.10
5 25 0.81
6 3 0.10
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:58779576 original size:3 final size:3
Alignment explanation
Indices: 58779568--58779597 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
58779558 CATGTCAAGC
58779568 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
58779598 AGAAGGATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:58785155 original size:19 final size:18
Alignment explanation
Indices: 58785133--58785194 Score: 70
Period size: 19 Copynumber: 3.3 Consensus size: 18
58785123 CTTTTGGAAT
58785133 TTTTTATAAATATTTTGAA
1 TTTTTA-AAATATTTTGAA
*
58785152 TTTTAAAAATTATTTTGAA
1 TTTTTAAAA-TATTTTGAA
* *
58785171 TTTCTAAAATGTATTTGAA
1 TTTTTAAAATAT-TTTGAA
58785190 TTTTT
1 TTTTT
58785195 TTATAATTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
18 5 0.14
19 31 0.86
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.56
Consensus pattern (18 bp):
TTTTTAAAATATTTTGAA
Found at i:58785977 original size:22 final size:21
Alignment explanation
Indices: 58785952--58785999 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
58785942 CAAATATTGA
*
58785952 TTAATAATAGGATAAATTAAGG
1 TTAATAAGAGGATAAATTAA-G
* * *
58785974 TTAAAAAGATGATTAATTAAG
1 TTAATAAGAGGATAAATTAAG
58785995 TTAAT
1 TTAAT
58786000 TATGAAAGTC
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (21 bp):
TTAATAAGAGGATAAATTAAG
Found at i:58786903 original size:41 final size:41
Alignment explanation
Indices: 58786794--58787021 Score: 276
Period size: 41 Copynumber: 5.5 Consensus size: 41
58786784 GGTGCATAAA
* * * ** *
58786794 AAGGAAGACTCATGTCTCGGGTTGAGCATGAGAAATTGTATA
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTTTG-ATT
*
58786836 AATGGAAGACTCATGTCTCGAAATGAGAATGAGATTTTGATT
1 AA-GGAAGACTCATGTCTCGAGATGAGAATGAGATTTTGATT
* * *
58786878 AAGGAATACTCATGTCTCGAGATGAGAATGAGATTATGAAT
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTTTGATT
*
58786919 AAGGAAGACTCATGTCTCGAAATGAGAATGAGATTTTGATT
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTTTGATT
* * * *
58786960 AAGAAAGACTCATGTCTCGAGATGAGAATGAGAATATGGTT
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTTTGATT
* *
58787001 AAAGGAAGACTTATGACTCGA
1 -AAGGAAGACTCATGTCTCGA
58787022 AAGAGCATAC
Statistics
Matches: 161, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
41 108 0.67
42 23 0.14
43 30 0.19
ACGTcount: A:0.37, C:0.11, G:0.25, T:0.27
Consensus pattern (41 bp):
AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTTTGATT
Found at i:58786944 original size:82 final size:82
Alignment explanation
Indices: 58786794--58787023 Score: 318
Period size: 82 Copynumber: 2.8 Consensus size: 82
58786784 GGTGCATAAA
* * * * *
58786794 AAGGAAGACTCATGTCTCGGGTTGAGCATGAGAAATTGTATAAATGGAAGACTCATGTCTCGAAA
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATA-TGAATAAA-GGAAGACTCATGTCTCGAAA
58786859 TGAGAATGAGATTTTGATT
64 TGAGAATGAGATTTTGATT
*
58786878 AAGGAATACTCATGTCTCGAGATGAGAATGAGATTATGAAT-AAGGAAGACTCATGTCTCGAAAT
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGA-TATGAATAAAGGAAGACTCATGTCTCGAAAT
58786942 GAGAATGAGATTTTGATT
65 GAGAATGAGATTTTGATT
* ** * *
58786960 AAGAAAGACTCATGTCTCGAGATGAGAATGAGAATATGGTTAAAGGAAGACTTATGACTCGAAA
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAG-ATATGAATAAAGGAAGACTCATGTCTCGAAA
58787024 GAGCATACGG
Statistics
Matches: 131, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
82 74 0.56
83 23 0.18
84 33 0.25
85 1 0.01
ACGTcount: A:0.38, C:0.10, G:0.25, T:0.27
Consensus pattern (82 bp):
AAGGAAGACTCATGTCTCGAGATGAGAATGAGATATGAATAAAGGAAGACTCATGTCTCGAAATG
AGAATGAGATTTTGATT
Found at i:58788065 original size:19 final size:19
Alignment explanation
Indices: 58788008--58788065 Score: 57
Period size: 19 Copynumber: 3.0 Consensus size: 19
58787998 GAGCACATAT
58788008 GGTTACATGATACAATTACA
1 GGTT-CATGATACAATTACA
*
58788028 GGTT-ATGAAAGC-ATATACA
1 GGTTCATGATA-CAAT-TACA
*
58788047 GTTTCATGATACAATTACA
1 GGTTCATGATACAATTACA
58788066 CCTAGTGTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 9
0.72 0.07 0.21
Matches are distributed among these distances:
18 7 0.23
19 13 0.42
20 11 0.35
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.31
Consensus pattern (19 bp):
GGTTCATGATACAATTACA
Found at i:58797015 original size:28 final size:28
Alignment explanation
Indices: 58796955--58797015 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
58796945 TTACATGGAC
*
58796955 TGATTATTTAACTAGTAAACGAAATACA
1 TGATTATTTAACTAATAAACGAAATACA
*
58796983 AGATTATTTAACTACATAAAC-AATATA-A
1 TGATTATTTAACTA-ATAAACGAA-ATACA
58797011 TGATT
1 TGATT
58797016 TTGCCTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
28 20 0.71
29 8 0.29
ACGTcount: A:0.48, C:0.10, G:0.08, T:0.34
Consensus pattern (28 bp):
TGATTATTTAACTAATAAACGAAATACA
Found at i:58798540 original size:27 final size:27
Alignment explanation
Indices: 58798466--58798561 Score: 129
Period size: 27 Copynumber: 3.5 Consensus size: 27
58798456 CCATACGAGC
**
58798466 CCAAAATCAGAATAACGCTCTTACGAG
1 CCAAAATCAGAATAACGCTCTTTTGAG
* *
58798493 CCCAGAATCAGAATAACGCTCTTTTAAG
1 -CCAAAATCAGAATAACGCTCTTTTGAG
*
58798521 CCAAAATCAGAATAATGCTCTTTTGAG
1 CCAAAATCAGAATAACGCTCTTTTGAG
*
58798548 CCAGAATCAGAATA
1 CCAAAATCAGAATA
58798562 CTCCTCAAGC
Statistics
Matches: 60, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
27 37 0.62
28 23 0.38
ACGTcount: A:0.40, C:0.23, G:0.15, T:0.23
Consensus pattern (27 bp):
CCAAAATCAGAATAACGCTCTTTTGAG
Found at i:58807490 original size:20 final size:20
Alignment explanation
Indices: 58807444--58807532 Score: 85
Period size: 20 Copynumber: 4.4 Consensus size: 20
58807434 ATATTTTTAT
*
58807444 AATTTTTTAAAATATAAAATTTG
1 AATTTTTTAAAAT-T--ATTTTG
58807467 -ATTTTTTATAAA-TATTTTG
1 AATTTTTTA-AAATTATTTTG
* *
58807486 AA-TTTTAAAAATTATTTTA
1 AATTTTTTAAAATTATTTTG
*
58807505 AATTTTTGAAAATTATTTTG
1 AATTTTTTAAAATTATTTTG
58807525 AATTTTTT
1 AATTTTTT
58807533 TTGTAATTTT
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
18 3 0.05
19 18 0.32
20 23 0.41
21 1 0.02
22 8 0.14
23 3 0.05
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.56
Consensus pattern (20 bp):
AATTTTTTAAAATTATTTTG
Found at i:58807491 original size:19 final size:19
Alignment explanation
Indices: 58807463--58807531 Score: 86
Period size: 19 Copynumber: 3.6 Consensus size: 19
58807453 AAATATAAAA
*
58807463 TTTGATTTTTTATAAA-TAT
1 TTTGAATTTTTA-AAATTAT
*
58807482 TTTGAATTTTAAAAATTAT
1 TTTGAATTTTTAAAATTAT
*
58807501 TTTAAATTTTTGAAAATTAT
1 TTTGAATTTTT-AAAATTAT
58807521 TTTGAATTTTT
1 TTTGAATTTTT
58807532 TTTGTAATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
18 3 0.07
19 22 0.51
20 18 0.42
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (19 bp):
TTTGAATTTTTAAAATTAT
Found at i:58812770 original size:28 final size:28
Alignment explanation
Indices: 58812739--58812793 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 28
58812729 AGAAATTATT
* * *
58812739 AATAATATTATTTAAATTATAATATATG
1 AATAATAATATTCAAATCATAATATATG
* *
58812767 AATATTAATATTCAAATCATGATATAT
1 AATAATAATATTCAAATCATAATATAT
58812794 TTTATATTAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.44
Consensus pattern (28 bp):
AATAATAATATTCAAATCATAATATATG
Found at i:58815339 original size:9 final size:8
Alignment explanation
Indices: 58815318--58815356 Score: 53
Period size: 8 Copynumber: 4.8 Consensus size: 8
58815308 TCTGTTTATC
58815318 AAAAAAGA
1 AAAAAAGA
58815326 AAAAAAGA
1 AAAAAAGA
58815334 AGAAAAAGA
1 A-AAAAAGA
58815343 AAAAGAA-A
1 AAAA-AAGA
58815351 AAAAAA
1 AAAAAA
58815357 TAGCAATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
7 2 0.07
8 17 0.59
9 10 0.34
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:58815342 original size:6 final size:6
Alignment explanation
Indices: 58815319--58815356 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
58815309 CTGTTTATCA
*
58815319 AAAAAG AAAAA- AAGAAG AAAAAG AAAAAG AAAAA- AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
58815357 TAGCAATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
5 8 0.28
6 21 0.72
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:58823989 original size:23 final size:23
Alignment explanation
Indices: 58823915--58824105 Score: 123
Period size: 23 Copynumber: 8.5 Consensus size: 23
58823905 TAAACGGAAC
* * *
58823915 AAACAGAGAGTAC-CGAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
* *
58823937 GAACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
58823959 GGGCAACAGAGAGCACACAAAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
*
58823985 AAACAGAGAGTACACAAA--G-T
1 AAACAGAGAGCACACAAAGTGCT
*
58824005 --AC--TGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* * *
58824024 AATCGGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
58824047 AATAACAGAGAGCACGA-GACGTGCT
1 -A-AACAGAGAGCAC-ACAAAGTGCT
*
58824072 AAACAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
58824095 AATCAGAGAGC
1 AAACAGAGAGC
58824106 GCGCTAGTGT
Statistics
Matches: 131, Mismatches: 22, Indels: 31
0.71 0.12 0.17
Matches are distributed among these distances:
16 10 0.08
18 3 0.02
19 1 0.01
20 1 0.01
21 2 0.02
22 18 0.14
23 58 0.44
24 2 0.02
25 28 0.21
26 8 0.06
ACGTcount: A:0.42, C:0.21, G:0.25, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:58824057 original size:25 final size:23
Alignment explanation
Indices: 58824008--58824105 Score: 126
Period size: 23 Copynumber: 4.2 Consensus size: 23
58823998 ACAAAGTACT
* *
58824008 GAGCACACAAAGTGCTAATCGGA
1 GAGCACACACAGTGCTAATCAGA
58824031 GAGCACACACAGTGCTAATAACAGA
1 GAGCACACACAGTGCTAAT--CAGA
* *
58824056 GAGCACGAGAC-GTGCTAAACAGA
1 GAGCAC-ACACAGTGCTAATCAGA
58824079 GAGCACACACAGTGCTAATCAGA
1 GAGCACACACAGTGCTAATCAGA
58824102 GAGC
1 GAGC
58824106 GCGCTAGTGT
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
22 3 0.05
23 43 0.66
25 16 0.25
26 3 0.05
ACGTcount: A:0.40, C:0.23, G:0.26, T:0.11
Consensus pattern (23 bp):
GAGCACACACAGTGCTAATCAGA
Found at i:58826027 original size:14 final size:13
Alignment explanation
Indices: 58826010--58826058 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 13
58826000 ATTCCAATAG
58826010 GTTAATTTAAGTTA
1 GTTAATTTAA-TTA
58826024 GTTAATTTAATTA
1 GTTAATTTAATTA
*
58826037 GTTCAAATTAATATA
1 GTT-AATTTAAT-TA
58826052 -TTAATTT
1 GTTAATTT
58826059 GGATCAACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 10 0.32
14 19 0.61
15 2 0.06
ACGTcount: A:0.39, C:0.02, G:0.08, T:0.51
Consensus pattern (13 bp):
GTTAATTTAATTA
Found at i:58831940 original size:22 final size:22
Alignment explanation
Indices: 58831912--58831954 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
58831902 ACGAATGTAT
58831912 TAATTAAAATCTTTG-TTTTGGA
1 TAATTAAAATC-TTGATTTTGGA
58831934 TAATTAAAATCTTGATTTTGG
1 TAATTAAAATCTTGATTTTGG
58831955 TTACTGTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.49
Consensus pattern (22 bp):
TAATTAAAATCTTGATTTTGGA
Found at i:58837751 original size:35 final size:34
Alignment explanation
Indices: 58837682--58837751 Score: 90
Period size: 35 Copynumber: 2.0 Consensus size: 34
58837672 CAAACCAACA
58837682 TTTTAGCAACTTTTACTCTTTATCTTTCTCCTTT
1 TTTTAGCAACTTTTACTCTTTATCTTTCTCCTTT
*
58837716 TTTTAGCAAACTATTTAC-CTTT-TTTTCTCTCCTTT
1 TTTTAGC-AACT-TTTACTCTTTATCTT-TCTCCTTT
58837751 T
1 T
58837752 AGAGAATTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
34 10 0.31
35 17 0.53
36 5 0.16
ACGTcount: A:0.16, C:0.23, G:0.03, T:0.59
Consensus pattern (34 bp):
TTTTAGCAACTTTTACTCTTTATCTTTCTCCTTT
Found at i:58844341 original size:16 final size:16
Alignment explanation
Indices: 58844286--58844334 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
58844276 TGTATAACAT
*
58844286 AAATAAAATAATAATAA
1 AAATATAATAA-AATAA
* *
58844303 TAATTATAATACAATAA
1 -AAATATAATAAAATAA
58844320 AAATATAATAAAATA
1 AAATATAATAAAATA
58844335 CGAATATTGA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
16 13 0.50
17 5 0.19
18 8 0.31
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (16 bp):
AAATATAATAAAATAA
Found at i:58847795 original size:20 final size:20
Alignment explanation
Indices: 58847770--58847808 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
58847760 TTGAATTTAA
* *
58847770 TTATCAATTTTTTTGAAAGG
1 TTATCAATCTTTTAGAAAGG
58847790 TTATCAATCTTTTAGAAAG
1 TTATCAATCTTTTAGAAAG
58847809 AGCTGAATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (20 bp):
TTATCAATCTTTTAGAAAGG
Found at i:58847933 original size:18 final size:18
Alignment explanation
Indices: 58847912--58847946 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
58847902 CGATTTTTTT
* *
58847912 TATTTTTTACATTTTAAG
1 TATTTTTAAAATTTTAAG
58847930 TATTTTTAAAATTTTAA
1 TATTTTTAAAATTTTAA
58847947 ATTATTTGTT
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:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (18 bp):
TATTTTTAAAATTTTAAG
Found at i:58850462 original size:23 final size:23
Alignment explanation
Indices: 58850418--58850463 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
58850408 ACATTGTTCG
* *
58850418 TGAACATGTTCGATTAAGTTAAA
1 TGAACATGTTCGATGAAATTAAA
58850441 TGAACATGTTCG-TGAACATTAAA
1 TGAACATGTTCGATGAA-ATTAAA
58850464 CAAACGAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (23 bp):
TGAACATGTTCGATGAAATTAAA
Found at i:58854986 original size:43 final size:43
Alignment explanation
Indices: 58854910--58854993 Score: 123
Period size: 43 Copynumber: 2.0 Consensus size: 43
58854900 TGCATAACAA
* * *
58854910 GGCTTATTGTTTACATCTTATAAAGATAATGCCTAAAATATGT
1 GGCTTATTCTTAACATCTCATAAAGATAATGCCTAAAATATGT
* *
58854953 GGCTTATTCTTAACATCTCATAATGATAGTGCCTAAAATAT
1 GGCTTATTCTTAACATCTCATAAAGATAATGCCTAAAATAT
58854994 TTACCAAGTG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (43 bp):
GGCTTATTCTTAACATCTCATAAAGATAATGCCTAAAATATGT
Found at i:58865572 original size:22 final size:22
Alignment explanation
Indices: 58865544--58865711 Score: 228
Period size: 22 Copynumber: 7.4 Consensus size: 22
58865534 TGCTGGGGGA
58865544 AACAGAAGCACACACAGTGCTG
1 AACAGAAGCACACACAGTGCTG
*
58865566 AACAGAAGCACAGACAGTGCTG
1 AACAGAAGCACACACAGTGCTG
*
58865588 AACAGAAGCACAGACAGTGCTG
1 AACAGAAGCACACACAGTGCTG
*
58865610 ATCAGAAGCACACACAGTGCTG
1 AACAGAAGCACACACAGTGCTG
*
58865632 AACAGAAGCACACATAGTGCTG
1 AACAGAAGCACACACAGTGCTG
* * *
58865654 ATCAGAAGTACACACAATGCTGGGG
1 AACAGAAGCACACACAGTGCT---G
58865679 AAACAGAAGCACACACAGTGCTG
1 -AACAGAAGCACACACAGTGCTG
58865702 AACAGTAAGC
1 AACAG-AAGC
58865712 GCGCTAACAT
Statistics
Matches: 129, Mismatches: 12, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
22 105 0.81
23 5 0.04
25 1 0.01
26 18 0.14
ACGTcount: A:0.40, C:0.24, G:0.24, T:0.11
Consensus pattern (22 bp):
AACAGAAGCACACACAGTGCTG
Found at i:58868059 original size:30 final size:32
Alignment explanation
Indices: 58868014--58868092 Score: 83
Period size: 30 Copynumber: 2.5 Consensus size: 32
58868004 ATCTAAATTT
*
58868014 TTTTGCTTCAATTTGGTAATC-AAACTTGACACC
1 TTTT-CTT-AATTTGGTAACCTAAACTTGACACC
* *
58868047 TTTTC-TAATTTGGT-ACCTAAATTTGACACT
1 TTTTCTTAATTTGGTAACCTAAACTTGACACC
*
58868077 TTTTCTTAAGTTGGTA
1 TTTTCTTAATTTGGTA
58868093 CTTGATCTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
29 2 0.05
30 23 0.59
31 9 0.23
32 1 0.03
33 4 0.10
ACGTcount: A:0.25, C:0.16, G:0.13, T:0.46
Consensus pattern (32 bp):
TTTTCTTAATTTGGTAACCTAAACTTGACACC
Found at i:58868120 original size:60 final size:58
Alignment explanation
Indices: 58868053--58868180 Score: 148
Period size: 60 Copynumber: 2.2 Consensus size: 58
58868043 CACCTTTTCT
* * * *
58868053 AATTTGGTACCTAAATTTGACACTTTTTCTTAAGTTGGTACTTGATCTTTTTTTAGGTCC
1 AATTTGGTACCTAAACTTGACACTTTTTCCTAAGTTGGTACCTGATATTTTTTT--GTCC
* * * * * *
58868113 AATTTGGTACTTGAACTTGACTCTTTTTCCTAATTTGGTGCCTGATATTTTTTTGTTC
1 AATTTGGTACCTAAACTTGACACTTTTTCCTAAGTTGGTACCTGATATTTTTTTGTCC
58868171 AATTTGGTAC
1 AATTTGGTAC
58868181 TTGAACGTTT
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
58 13 0.22
60 45 0.78
ACGTcount: A:0.20, C:0.15, G:0.16, T:0.49
Consensus pattern (58 bp):
AATTTGGTACCTAAACTTGACACTTTTTCCTAAGTTGGTACCTGATATTTTTTTGTCC
Found at i:58868151 original size:31 final size:31
Alignment explanation
Indices: 58868036--58868151 Score: 82
Period size: 31 Copynumber: 3.8 Consensus size: 31
58868026 TTGGTAATCA
* * *
58868036 AACTTGACACCTTTT-CTAATTTGGTACCTA
1 AACTTGACACTTTTTCCTAATTTGGTACTTG
* * *
58868066 AATTTGACACTTTTTCTTAAGTTGGTACTTG
1 AACTTGACACTTTTTCCTAATTTGGTACTTG
* *
58868097 ATCTT----TTTTTAGGTCC-AATTTGGTACTTG
1 AACTTGACACTTTT---TCCTAATTTGGTACTTG
*
58868126 AACTTGACTCTTTTTCCTAATTTGGT
1 AACTTGACACTTTTTCCTAATTTGGT
58868152 GCCTGATATT
Statistics
Matches: 64, Mismatches: 13, Indels: 17
0.68 0.14 0.18
Matches are distributed among these distances:
27 4 0.06
29 16 0.25
30 18 0.28
31 22 0.34
33 4 0.06
ACGTcount: A:0.22, C:0.17, G:0.14, T:0.47
Consensus pattern (31 bp):
AACTTGACACTTTTTCCTAATTTGGTACTTG
Found at i:58869306 original size:16 final size:16
Alignment explanation
Indices: 58869275--58869309 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
58869265 AATATTTAGT
58869275 TTTATTGAATATAAAA
1 TTTATTGAATATAAAA
*
58869291 TTTATATGAATAAAAAA
1 TTTAT-TGAATATAAAA
58869308 TT
1 TT
58869310 GAATTGAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (16 bp):
TTTATTGAATATAAAA
Found at i:58869643 original size:9 final size:9
Alignment explanation
Indices: 58869621--58869687 Score: 50
Period size: 9 Copynumber: 7.6 Consensus size: 9
58869611 CATAAAAAAA
*
58869621 TATAAAATA
1 TATAAAATT
58869630 T-TAAAATT
1 TATAAAATT
58869638 TATAAAA--
1 TATAAAATT
*
58869645 AATAAAATT
1 TATAAAATT
*
58869654 TAAAAAAATT
1 T-ATAAAATT
* *
58869664 CATAAAAACT
1 TAT-AAAATT
58869674 TATAAAATT
1 TATAAAATT
58869683 TATAA
1 TATAA
58869688 TAAATGATAA
Statistics
Matches: 44, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
7 6 0.14
8 7 0.16
9 17 0.39
10 14 0.32
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (9 bp):
TATAAAATT
Found at i:58869650 original size:16 final size:16
Alignment explanation
Indices: 58869621--58869662 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
58869611 CATAAAAAAA
*
58869621 TATAAAATATTAAAATT
1 TATAAAA-AATAAAATT
58869638 TATAAAAAATAAAATT
1 TATAAAAAATAAAATT
58869654 TA-AAAAAAT
1 TATAAAAAAT
58869663 TCATAAAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 7 0.29
16 10 0.42
17 7 0.29
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
TATAAAAAATAAAATT
Found at i:58869661 original size:15 final size:15
Alignment explanation
Indices: 58869617--58869662 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
58869607 ATCTCATAAA
* * *
58869617 AAAATATAAAATATT
1 AAAATTTAAAAAAAT
58869632 AAAATTTATAAAAAAT
1 AAAATTTA-AAAAAAT
58869648 AAAATTTAAAAAAAT
1 AAAATTTAAAAAAAT
58869663 TCATAAAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
15 14 0.52
16 13 0.48
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAATTTAAAAAAAT
Found at i:58869838 original size:21 final size:21
Alignment explanation
Indices: 58869812--58869851 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
58869802 CAGTAATTAT
58869812 AAAACTTATACAAA-ATTCATA
1 AAAACTTATA-AAAGATTCATA
58869833 AAAACTTATAAAAGATTCA
1 AAAACTTATAAAAGATTCA
58869852 AAACAAGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.57, C:0.12, G:0.03, T:0.28
Consensus pattern (21 bp):
AAAACTTATAAAAGATTCATA
Found at i:58869906 original size:10 final size:10
Alignment explanation
Indices: 58869888--58869934 Score: 55
Period size: 9 Copynumber: 5.0 Consensus size: 10
58869878 TAATATTTTA
*
58869888 AAAAAATTAT
1 AAAATATTAT
58869898 AAAATATTA-
1 AAAATATTAT
58869907 AAAATA-TAT
1 AAAATATTAT
58869916 AAAAT-TTAT
1 AAAATATTAT
*
58869925 AAAAAATTAT
1 AAAATATTAT
58869935 TGGTTCCTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
8 2 0.06
9 18 0.56
10 12 0.38
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (10 bp):
AAAATATTAT
Found at i:58869907 original size:19 final size:18
Alignment explanation
Indices: 58869884--58869934 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
58869874 AAAATAATAT
58869884 TTTAAAAAAATTATAAAA
1 TTTAAAAAAATTATAAAA
*
58869902 TATTAAAAATA-TATAAAA
1 T-TTAAAAAAATTATAAAA
58869920 TTTATAAAAAATTAT
1 TTTA-AAAAAATTAT
58869935 TGGTTCCTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 3 0.11
18 14 0.50
19 11 0.39
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TTTAAAAAAATTATAAAA
Found at i:58869928 original size:18 final size:17
Alignment explanation
Indices: 58869889--58869934 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 17
58869879 AATATTTTAA
58869889 AAAAATTATAAAATATT
1 AAAAATTATAAAATATT
*
58869906 AAAAATATATAAAATTTATA
1 AAAAAT-TATAAAA--TATT
58869926 AAAAATTAT
1 AAAAATTAT
58869935 TGGTTCCTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 6 0.24
18 7 0.28
19 3 0.12
20 9 0.36
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AAAAATTATAAAATATT
Found at i:58870618 original size:15 final size:15
Alignment explanation
Indices: 58870598--58870636 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
58870588 GCACATCAAA
*
58870598 CAAGAATTAATATAT
1 CAAGAATTAATAAAT
*
58870613 CAAGAA-TACTAAAT
1 CAAGAATTAATAAAT
58870627 CAAGAATTAA
1 CAAGAATTAA
58870637 GCACACATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.56, C:0.10, G:0.08, T:0.26
Consensus pattern (15 bp):
CAAGAATTAATAAAT
Found at i:58871150 original size:13 final size:13
Alignment explanation
Indices: 58871129--58871162 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
58871119 ACAATATAAC
58871129 AATAATAATCCTA
1 AATAATAATCCTA
*
58871142 AATATTAATCCTA
1 AATAATAATCCTA
*
58871155 AAAAATAA
1 AATAATAA
58871163 AATTTAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATAATCCTA
Found at i:58875330 original size:17 final size:19
Alignment explanation
Indices: 58875282--58875330 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
58875272 TTTTTATAAA
*
58875282 TTTTATAACTTTAATAAGT
1 TTTTATAATTTTAATAAGT
*
58875301 TTATATCAATTTTAAT-A-T
1 TTTTAT-AATTTTAATAAGT
58875319 TTTTATAATTTT
1 TTTTATAATTTT
58875331 TAATGAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 6 0.23
18 6 0.23
19 6 0.23
20 8 0.31
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (19 bp):
TTTTATAATTTTAATAAGT
Found at i:58875813 original size:22 final size:23
Alignment explanation
Indices: 58875788--58875847 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 23
58875778 CAATTAAATT
*
58875788 ATATATTTTTATGATAATAA-AA
1 ATATATTTTTATAATAATAATAA
* **
58875810 ATATAATTTTATAATTTTAATAA
1 ATATATTTTTATAATAATAATAA
*
58875833 TTATATTTTTATAAT
1 ATATATTTTTATAAT
58875848 TTTTTTAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
22 16 0.52
23 15 0.48
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
ATATATTTTTATAATAATAATAA
Found at i:58875890 original size:27 final size:28
Alignment explanation
Indices: 58875860--58875922 Score: 78
Period size: 27 Copynumber: 2.3 Consensus size: 28
58875850 TTTTAAAATT
*
58875860 AAATTA-AATTTTAATATTTTTAGA-TTA
1 AAATTATAATTTTAATATTATTA-ATTTA
*
58875887 AAA-TATAATTTTATTATTATTAATTTA
1 AAATTATAATTTTAATATTATTAATTTA
58875914 AAATTATAA
1 AAATTATAA
58875923 AAAATTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 3 0.10
27 23 0.74
28 5 0.16
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (28 bp):
AAATTATAATTTTAATATTATTAATTTA
Found at i:58880711 original size:13 final size:13
Alignment explanation
Indices: 58880693--58880735 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
58880683 AACGTAAATT
*
58880693 TAAAAAATAAAAAA
1 TAAAAAAT-TAAAA
*
58880707 TAAAAAATTTAAA
1 TAAAAAATTAAAA
*
58880720 TAGAAAATTAAAA
1 TAAAAAATTAAAA
58880733 TAA
1 TAA
58880736 TTTTTTTTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
13 16 0.67
14 8 0.33
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (13 bp):
TAAAAAATTAAAA
Found at i:58880720 original size:20 final size:22
Alignment explanation
Indices: 58880697--58880738 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
58880687 TAAATTTAAA
58880697 AAATA-AAAAATAAAA-AATTT
1 AAATAGAAAAATAAAATAATTT
*
58880717 AAATAGAAAATTAAAATAATTT
1 AAATAGAAAAATAAAATAATTT
58880739 TTTTTTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 9 0.47
22 5 0.26
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (22 bp):
AAATAGAAAAATAAAATAATTT
Found at i:58882151 original size:2 final size:2
Alignment explanation
Indices: 58882146--58882184 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
58882136 ACTTACCCAC
58882146 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
58882185 CTTAGATTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:58885352 original size:19 final size:19
Alignment explanation
Indices: 58885328--58885369 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
58885318 AATTAAAATT
*
58885328 TTTTCTTAGGTTTTATAGG
1 TTTTCTTAGGTTTTATAAG
*
58885347 TTTTCTTATGTTTTATAAG
1 TTTTCTTAGGTTTTATAAG
58885366 TTTT
1 TTTT
58885370 TTAATTCATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.17, C:0.05, G:0.14, T:0.64
Consensus pattern (19 bp):
TTTTCTTAGGTTTTATAAG
Found at i:58889521 original size:17 final size:17
Alignment explanation
Indices: 58889476--58889523 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 17
58889466 AAGTTCGTAG
* *
58889476 TACAACACAGGTTTGCA
1 TACAACATAGGTTCGCA
*
58889493 TAACATCATAGGTTCGCA
1 T-ACAACATAGGTTCGCA
58889511 TACAACATAGGTT
1 TACAACATAGGTT
58889524 TGTAATATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (17 bp):
TACAACATAGGTTCGCA
Found at i:58892632 original size:17 final size:18
Alignment explanation
Indices: 58892600--58892633 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
58892590 AAACATAACA
*
58892600 TTTTAAAAGATTATAATT
1 TTTTAAAAGATAATAATT
58892618 TTTTAAAA-ATAATAAT
1 TTTTAAAAGATAATAAT
58892634 ATATATAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
TTTTAAAAGATAATAATT
Found at i:58892750 original size:20 final size:20
Alignment explanation
Indices: 58892725--58892779 Score: 110
Period size: 20 Copynumber: 2.8 Consensus size: 20
58892715 GGATCGAATT
58892725 GATTGGATCAAGAACCAACC
1 GATTGGATCAAGAACCAACC
58892745 GATTGGATCAAGAACCAACC
1 GATTGGATCAAGAACCAACC
58892765 GATTGGATCAAGAAC
1 GATTGGATCAAGAAC
58892780 TAATTGGGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.40, C:0.22, G:0.22, T:0.16
Consensus pattern (20 bp):
GATTGGATCAAGAACCAACC
Found at i:58892899 original size:18 final size:19
Alignment explanation
Indices: 58892876--58892913 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
58892866 AGTTGAATCA
58892876 ATTTTTATAA-TTTTTAAT
1 ATTTTTATAATTTTTTAAT
*
58892894 ATTTTTTTAATTTTTTAAT
1 ATTTTTATAATTTTTTAAT
58892913 A
1 A
58892914 ATTTATTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
ATTTTTATAATTTTTTAAT
Found at i:58892915 original size:11 final size:10
Alignment explanation
Indices: 58892877--58892917 Score: 50
Period size: 9 Copynumber: 4.2 Consensus size: 10
58892867 GTTGAATCAA
58892877 TTTTTATAAT
1 TTTTTATAAT
*
58892887 TTTTAAT-AT
1 TTTTTATAAT
58892896 TTTTT-TAAT
1 TTTTTATAAT
58892905 TTTTTAATAAT
1 TTTTT-ATAAT
58892916 TT
1 TT
58892918 ATTTGGTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
8 1 0.04
9 13 0.50
10 6 0.23
11 6 0.23
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:58898007 original size:41 final size:38
Alignment explanation
Indices: 58897914--58898010 Score: 97
Period size: 41 Copynumber: 2.5 Consensus size: 38
58897904 CAATAAAGTA
*
58897914 ACACCCAGTGTCTCATCG-ACCTAACCGAAGTAAAGTG
1 ACACCCAGTGTCTCATCGAACCTAACCGAAGTAAAATG
** ** * *
58897951 GTACCCAGTACCTCATCGAATCTATCCGAAGTAAAATAATG
1 ACACCCAGTGTCTCATCGAACCTAACCGAAGT--AA-AATG
58897992 ACACCCAGTGTCTCATCGA
1 ACACCCAGTGTCTCATCGA
58898011 CTCAAGGTCG
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
37 14 0.31
38 11 0.24
40 2 0.04
41 18 0.40
ACGTcount: A:0.33, C:0.29, G:0.16, T:0.22
Consensus pattern (38 bp):
ACACCCAGTGTCTCATCGAACCTAACCGAAGTAAAATG
Found at i:58901331 original size:35 final size:33
Alignment explanation
Indices: 58901291--58901355 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 33
58901281 ATATTGCATG
58901291 TGTTATTCTATTA-ATTAATTTCAAATTACATATTT
1 TGTTATT-TATTATATT-ATTTCAAA-TACATATTT
*
58901326 TGTTATTTATTATATTATTTTAAATACATA
1 TGTTATTTATTATATTATTTCAAATACATA
58901356 ATTTATACAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 6 0.21
34 12 0.43
35 10 0.36
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.55
Consensus pattern (33 bp):
TGTTATTTATTATATTATTTCAAATACATATTT
Found at i:58901778 original size:30 final size:30
Alignment explanation
Indices: 58901738--58901804 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
58901728 ATCATTAATA
* * * *
58901738 ATTTTTCGTTATAGACGTAATGAAACTGTC
1 ATTTTCCGTTACAGACATAATAAAACTGTC
*
58901768 ATTTTCCGTTACAGATATAATAAAACTGTC
1 ATTTTCCGTTACAGACATAATAAAACTGTC
*
58901798 ACTTTCC
1 ATTTTCC
58901805 ATCCTTCTCT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (30 bp):
ATTTTCCGTTACAGACATAATAAAACTGTC
Found at i:58921392 original size:2 final size:2
Alignment explanation
Indices: 58921385--58921424 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
58921375 ATTTGTTTTA
58921385 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
58921425 ATGGATGTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:58921538 original size:2 final size:2
Alignment explanation
Indices: 58921531--58921569 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
58921521 ACCTAAATTC
58921531 CT CT CT CT CT CT CT CT CT 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 CT CT CT CT CT CT C
58921570 ACAATGAGTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:58921706 original size:2 final size:2
Alignment explanation
Indices: 58921699--58921740 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
58921689 TTGATTATTG
58921699 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
58921741 TCAAGTCATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58922280 original size:23 final size:23
Alignment explanation
Indices: 58922253--58922306 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
58922243 TAATTTATAT
*
58922253 ATTAAAATTAAATT-TTACAAATA
1 ATTAAAATT-AATTGTTAAAAATA
*
58922276 ATTAATATTAATTGTTAAAAATA
1 ATTAAAATTAATTGTTAAAAATA
*
58922299 TTTAAAAT
1 ATTAAAAT
58922307 ATTCCTTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
22 4 0.15
23 22 0.85
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
ATTAAAATTAATTGTTAAAAATA
Found at i:58927642 original size:28 final size:29
Alignment explanation
Indices: 58927587--58927643 Score: 89
Period size: 31 Copynumber: 1.9 Consensus size: 29
58927577 TTCTATTTTA
58927587 AAATAATGATATTTATTATTCACAAAAAAAT
1 AAATAATGATATTTATTATT--CAAAAAAAT
58927618 AAATAATGATATTTATTATT-AAAAAA
1 AAATAATGATATTTATTATTCAAAAAA
58927644 GGAATAGCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 6 0.23
31 20 0.77
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.37
Consensus pattern (29 bp):
AAATAATGATATTTATTATTCAAAAAAAT
Found at i:58934826 original size:176 final size:176
Alignment explanation
Indices: 58934532--58934884 Score: 688
Period size: 176 Copynumber: 2.0 Consensus size: 176
58934522 TTAAAAAATA
58934532 AGCTAACACGACACATTCTCAATAAGTTAAGTCGGATTTTATTTTATTTTGTATATATTAAGTGA
1 AGCTAACACGACACATTCTCAATAAGTTAAGTCGGATTTTATTTTATTTTGTATATATTAAGTGA
58934597 AAGTTTAGATGGGTGATGTGGCATATTTAATCTACTTTTGGTCTCACGTTATAGTATCTTATTTC
66 AAGTTTAGATGGGTGATGTGGCATATTTAATCTACTTTTGGTCTCACGTTATAGTATCTTATTTC
*
58934662 ACCATCACTGTTGTTTTTACACTAATCACAGGTAAACATACTGTTC
131 ACCATCACTGCTGTTTTTACACTAATCACAGGTAAACATACTGTTC
*
58934708 AGCTAACACGACACATTCTCAATATGTTAAGTCGGATTTTATTTTATTTTGTATATATTAAGTGA
1 AGCTAACACGACACATTCTCAATAAGTTAAGTCGGATTTTATTTTATTTTGTATATATTAAGTGA
58934773 AAGTTTAGATGGGTGATGTGGCATATTTAATCTACTTTTGGTCTCACGTTATAGTATCTTATTTC
66 AAGTTTAGATGGGTGATGTGGCATATTTAATCTACTTTTGGTCTCACGTTATAGTATCTTATTTC
58934838 ACCATCACTGCTGTTTTTACACTAATCACAGGTAAACATACTGTTC
131 ACCATCACTGCTGTTTTTACACTAATCACAGGTAAACATACTGTTC
58934884 A
1 A
58934885 TCCAAATCCA
Statistics
Matches: 175, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
176 175 1.00
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (176 bp):
AGCTAACACGACACATTCTCAATAAGTTAAGTCGGATTTTATTTTATTTTGTATATATTAAGTGA
AAGTTTAGATGGGTGATGTGGCATATTTAATCTACTTTTGGTCTCACGTTATAGTATCTTATTTC
ACCATCACTGCTGTTTTTACACTAATCACAGGTAAACATACTGTTC
Found at i:58935084 original size:18 final size:18
Alignment explanation
Indices: 58935059--58935102 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
58935049 ATATAAAATA
*
58935059 ATTA-TAATTATAATTATT
1 ATTATTAATAATAATT-TT
58935077 -TTATTAATAATAATTTT
1 ATTATTAATAATAATTTT
58935094 ATTATTAAT
1 ATTATTAAT
58935103 GTTATCGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTATTAATAATAATTTT
Done.