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 171 of 193
Found at i:53328766 original size:107 final size:105
Alignment explanation
Indices: 53328530--53328943 Score: 416
Period size: 107 Copynumber: 3.9 Consensus size: 105
53328520 CTTACTCTTG
* * **
53328530 AGCAATAACATGAAGAAATATAATGCCTTGGTCATGTTGTC-AGCATCGAGTAAGCAGCAATGAG
1 AGCAATAACATGAAGAAATATAATGCATTGGTCATGTTGTCTA-CATCAAGTAAGCAATAATGAG
* *
53328594 TATGCAAA-TGTAATGTAACCCTTCCTAGGCGATCCAAGAGTA
65 TATGCAAACTG--ATGTACCCCTTCCTAGGCGATGCAAGAGTA
** * * **
53328636 AGCGGTAACATGAAGAAATATAATGTC-TCGGTCATGCTGTCTACATTGAGTAAGCAATAATGAG
1 AGCAATAACATGAAGAAATATAATG-CATTGGTCATGTTGTCTACATCAAGTAAGCAATAATGAG
* * * *
53328700 CATGCAAACCTTGATGTACCCCTTGCTAGGTGATGCATGAGTA
65 TATGCAAA-C-TGATGTACCCCTTCCTAGGCGATGCAAGAGTA
*
53328743 AGCAATAACATGAAGAAATATAATGCATTTGTC--G-TGT-TACGA-CAAGTAAG-AAGTAATGA
1 AGCAATAACATGAAGAAATATAATGCATTGGTCATGTTGTCTAC-ATCAAGTAAGCAA-TAATGA
* *
53328802 GTATACGAAACTGATGAACCCCTTCCTAGGCGATGCACA-AGTA
64 GTATGC-AAACTGATGTACCCCTTCCTAGGCGATGCA-AGAGTA
* * * * * *
53328845 AGCAAATGACATAAAGAAATATAATGCTTTGGTCATGTTGTCCACATCAAGTAGGCAATAATGGG
1 AGC-AATAACATGAAGAAATATAATGCATTGGTCATGTTGTCTACATCAAGTAAGCAATAATGAG
*
53328910 TATGCATACCTGATGTACCCCTTCCTAGGCGATG
65 TATGCA-AACTGATGTACCCCTTCCTAGGCGATG
53328944 AACAGGAACA
Statistics
Matches: 255, Mismatches: 35, Indels: 35
0.78 0.11 0.11
Matches are distributed among these distances:
102 32 0.13
103 46 0.18
104 7 0.03
105 2 0.01
106 66 0.26
107 98 0.38
108 2 0.01
109 2 0.01
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.26
Consensus pattern (105 bp):
AGCAATAACATGAAGAAATATAATGCATTGGTCATGTTGTCTACATCAAGTAAGCAATAATGAGT
ATGCAAACTGATGTACCCCTTCCTAGGCGATGCAAGAGTA
Found at i:53330335 original size:2 final size:2
Alignment explanation
Indices: 53330328--53330356 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
53330318 ATAAATCAAA
53330328 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
53330357 TGAAAAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:53338059 original size:2 final size:2
Alignment explanation
Indices: 53338052--53338097 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
53338042 CTTTGAGGAA
53338052 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
53338094 AG AG
1 AG AG
53338098 TTGAAGCTAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:53338661 original size:21 final size:21
Alignment explanation
Indices: 53338615--53338667 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
53338605 AGTTTTATGC
53338615 TAATTGAAAT-TTTATTTAATA
1 TAATT-AAATATTTATTTAATA
* *
53338636 T-ATTAAATATTTATTTCATT
1 TAATTAAATATTTATTTAATA
*
53338656 TAATTAGATATT
1 TAATTAAATATT
53338668 CAATTACATA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 4 0.15
20 13 0.48
21 10 0.37
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.55
Consensus pattern (21 bp):
TAATTAAATATTTATTTAATA
Found at i:53338824 original size:19 final size:20
Alignment explanation
Indices: 53338781--53338826 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
53338771 CAAAATTTTA
53338781 TATTATTT-TCTTAAGATTT
1 TATTATTTATCTTAAGATTT
*
53338800 TA-TATTTATTTTAA-ATTT
1 TATTATTTATCTTAAGATTT
53338818 TATTATTTA
1 TATTATTTA
53338827 AATGCATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (20 bp):
TATTATTTATCTTAAGATTT
Found at i:53342312 original size:28 final size:28
Alignment explanation
Indices: 53342275--53342331 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
53342265 GGTCCCATGT
* *
53342275 TTTTATAATATTATTAATTATTTTAATA
1 TTTTATAATATTATTAATTAGTTAAATA
53342303 TTTTATAATATTATTAATTAGTTAAATA
1 TTTTATAATATTATTAATTAGTTAAATA
53342331 T
1 T
53342332 AGTTATTATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (28 bp):
TTTTATAATATTATTAATTAGTTAAATA
Found at i:53342591 original size:26 final size:26
Alignment explanation
Indices: 53342543--53342593 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
53342533 ATCTTTTTAA
* * *
53342543 TATATTTAAATTTGAGATTTAATTTT
1 TATATTTAAATTTCAAATATAATTTT
*
53342569 TATATTTTAATTTCAAATATAATTT
1 TATATTTAAATTTCAAATATAATTT
53342594 GAACTCTATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (26 bp):
TATATTTAAATTTCAAATATAATTTT
Found at i:53347644 original size:19 final size:19
Alignment explanation
Indices: 53347622--53347679 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
53347612 TTAATGTTAA
*
53347622 ATTTTTATTTTAATAATAT
1 ATTTTAATTTTAATAATAT
**
53347641 ATTTTAACATTAATAATA-
1 ATTTTAATTTTAATAATAT
53347659 ATTTTAAATTTTAAATAATAT
1 ATTTT-AATTTT-AATAATAT
53347680 TCTTATATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
18 5 0.16
19 19 0.61
20 7 0.23
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTTTAATTTTAATAATAT
Found at i:53347677 original size:20 final size:19
Alignment explanation
Indices: 53347628--53347691 Score: 62
Period size: 19 Copynumber: 3.3 Consensus size: 19
53347618 TTAAATTTTT
53347628 ATTTTAATAATATATTTTAA
1 ATTTTAATAATA-ATTTTAA
53347648 CA--TTAATAATAATTTTAA
1 -ATTTTAATAATAATTTTAA
*
53347666 ATTTTAAATAAT-ATTCTTAT
1 ATTTT-AATAATAATT-TTAA
53347686 ATTTTA
1 ATTTTA
53347692 TTAAAACTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
17 1 0.03
18 7 0.18
19 15 0.39
20 14 0.37
21 1 0.03
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTTTAATAATAATTTTAA
Found at i:53347786 original size:24 final size:23
Alignment explanation
Indices: 53347744--53347789 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
53347734 TATTATAATT
*
53347744 TATAAATATTTAATAATATAAAA
1 TATAAACATTTAATAATATAAAA
53347767 TATAAACATTATAATAATATAAA
1 TATAAACATT-TAATAATATAAA
53347790 TATGAATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (23 bp):
TATAAACATTTAATAATATAAAA
Found at i:53348541 original size:16 final size:17
Alignment explanation
Indices: 53348511--53348551 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
53348501 TGAAAATTTA
* *
53348511 AAAAGAAATGTAAAATG
1 AAAAGAAATGGAAAAAG
53348528 AAAA-AAATGGAAAAAG
1 AAAAGAAATGGAAAAAG
53348544 AAAAGAAA
1 AAAAGAAA
53348552 AGTTAATATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.73, C:0.00, G:0.17, T:0.10
Consensus pattern (17 bp):
AAAAGAAATGGAAAAAG
Found at i:53348582 original size:12 final size:12
Alignment explanation
Indices: 53348544--53348583 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
53348534 ATGGAAAAAG
53348544 AAAAGAAAAGTT
1 AAAAGAAAAGTT
* *
53348556 AATATGAAAATTT
1 AA-AAGAAAAGTT
53348569 AAAAGAAAAGTT
1 AAAAGAAAAGTT
53348581 AAA
1 AAA
53348584 CATTGCCTCG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.23
Consensus pattern (12 bp):
AAAAGAAAAGTT
Found at i:53356132 original size:71 final size:69
Alignment explanation
Indices: 53356016--53356211 Score: 259
Period size: 71 Copynumber: 2.8 Consensus size: 69
53356006 ACACTAGCGC
*
53356016 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACTGTGTGTGCTCTCTGTTTAGCACGTC
1 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACTTTGTGTGCTCTCTGTTTAGCAC-TC
53356081 T-CGT
65 TGCGT
* * * *
53356085 GCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATCAGTACTTTGTGTACTCTCTGTTTAGCACT
1 GCTCTCTG--ATTAGCACTGTGTGTGCTCTCTGTTTAGCACTTTGTGTGCTCTCTGTTTAGCACT
* *
53356150 TTGTGT
64 CTGCGT
* * * *
53356156 GCTCTCTGATCAGTACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTCTCTGTT
1 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACTTTGTGTGCTCTCTGTT
53356212 GCCCTGCACT
Statistics
Matches: 109, Mismatches: 15, Indels: 6
0.84 0.12 0.05
Matches are distributed among these distances:
69 48 0.44
70 2 0.02
71 59 0.54
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.44
Consensus pattern (69 bp):
GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACTTTGTGTGCTCTCTGTTTAGCACTCT
GCGT
Found at i:53356210 original size:23 final size:23
Alignment explanation
Indices: 53356016--53356211 Score: 232
Period size: 23 Copynumber: 8.4 Consensus size: 23
53356006 ACACTAGCGC
* *
53356016 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTTTGTGT
*
53356039 GCTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTTTGTGT
* *
53356062 GCTCTCTGTTTAGCACGTCT-CGT
1 GCTCTCTGTTTAGCAC-TTTGTGT
*
53356085 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG-T-TTAGCACTTTGTGT
* * *
53356110 GCTCTCTGATCAGTACTTTGTGT
1 GCTCTCTGTTTAGCACTTTGTGT
*
53356133 ACTCTCTGTTTAGCACTTTGTGT
1 GCTCTCTGTTTAGCACTTTGTGT
* * *
53356156 GCTCTCTGATCAGTACTTTGTGT
1 GCTCTCTGTTTAGCACTTTGTGT
*
53356179 ACTCTCTGTTTAGCACTTTGTGT
1 GCTCTCTGTTTAGCACTTTGTGT
53356202 GCTCTCTGTT
1 GCTCTCTGTT
53356212 GCCCTGCACT
Statistics
Matches: 147, Mismatches: 22, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
23 125 0.85
24 5 0.03
25 17 0.12
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.44
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTTTGTGT
Found at i:53356232 original size:71 final size:68
Alignment explanation
Indices: 53356016--53356259 Score: 242
Period size: 71 Copynumber: 3.5 Consensus size: 68
53356006 ACACTAGCGC
* * * * *
53356016 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACTGTGTGTGCTCTCTGTTTAGCACGTC
1 GCTCTCTGATCAGCACTGTGTGTACTCTCTGTTTAGCACTTTGTGTGCTCTCTGTTTAGCACTTA
53356081 TCGT
66 T-GT
* * * * * *
53356085 GCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATCAGTACTTTGTGTACTCTCTGTTTAGCACT
1 GCTCTCTG--ATCAGCACTGTGTGTACTCTCTGTTTAGCACTTTGTGTGCTCTCTGTTTAGCAC-
*
53356150 TTGTGT
63 TTATGT
* *
53356156 GCTCTCTGATCAGTACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTCTCTGTTGCCCT-GCA
1 GCTCTCTGATCAGCACTGTGTGTACTCTCTGTTTAGCACTTTGTGTGCTCTCTGTT----TAGCA
53356220 CTTATGT
62 CTTATGT
* *
53356227 GCTCTCTGTTCAGTACT-TCG-GTACTCTCTGTTT
1 GCTCTCTGATCAGCACTGT-GTGTACTCTCTGTTT
53356260 GTTCCGTTTA
Statistics
Matches: 150, Mismatches: 17, Indels: 15
0.82 0.09 0.08
Matches are distributed among these distances:
69 48 0.32
70 14 0.09
71 81 0.54
72 6 0.04
73 1 0.01
ACGTcount: A:0.11, C:0.24, G:0.21, T:0.43
Consensus pattern (68 bp):
GCTCTCTGATCAGCACTGTGTGTACTCTCTGTTTAGCACTTTGTGTGCTCTCTGTTTAGCACTTA
TGT
Found at i:53357565 original size:15 final size:17
Alignment explanation
Indices: 53357539--53357570 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
53357529 TTAGCAATAG
53357539 AAAAGTAGATAT-TCAT
1 AAAAGTAGATATGTCAT
53357555 AAAAG-AGATATGTCAT
1 AAAAGTAGATATGTCAT
53357571 CAATGAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.50, C:0.06, G:0.16, T:0.28
Consensus pattern (17 bp):
AAAAGTAGATATGTCAT
Found at i:53357714 original size:8 final size:8
Alignment explanation
Indices: 53357696--53357729 Score: 59
Period size: 8 Copynumber: 4.1 Consensus size: 8
53357686 AAAATTTTCA
53357696 TTTAAATAT
1 TTTAAA-AT
53357705 TTTAAAAT
1 TTTAAAAT
53357713 TTTAAAAT
1 TTTAAAAT
53357721 TTTAAAAT
1 TTTAAAAT
53357729 T
1 T
53357730 AATAAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 19 0.76
9 6 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (8 bp):
TTTAAAAT
Found at i:53366699 original size:38 final size:40
Alignment explanation
Indices: 53366625--53366712 Score: 135
Period size: 38 Copynumber: 2.2 Consensus size: 40
53366615 TAAAAAGTAT
*
53366625 TTATATTAAAAACATTAATATAAATATAATAAATATTTTA
1 TTATATTAAAAACATCAATATAAATATAATAAATATTTTA
*
53366665 TTATATTAAAAAC-TCAA-ATAAATATAATATATATTTTA
1 TTATATTAAAAACATCAATATAAATATAATAAATATTTTA
*
53366703 TTGTATTAAA
1 TTATATTAAA
53366713 TATAAATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
38 29 0.64
39 3 0.07
40 13 0.29
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.43
Consensus pattern (40 bp):
TTATATTAAAAACATCAATATAAATATAATAAATATTTTA
Found at i:53367621 original size:27 final size:27
Alignment explanation
Indices: 53367591--53367678 Score: 65
Period size: 26 Copynumber: 3.3 Consensus size: 27
53367581 AAGTGCGGTA
*
53367591 AAAAAATATTTTTAAAAAGTAATTTTT
1 AAAAAATATTATTAAAAAGTAATTTTT
* ** *
53367618 -AAAAAT-TTGGTTAAAGATTTAATTGTT
1 AAAAAATATT-ATTAAA-AAGTAATTTTT
* * *
53367645 AAAAATTACTATCAAAAAGT-ATTTTT
1 AAAAAATATTATTAAAAAGTAATTTTT
53367671 AAAAAATA
1 AAAAAATA
53367679 AAATATTTAT
Statistics
Matches: 45, Mismatches: 12, Indels: 9
0.68 0.18 0.14
Matches are distributed among these distances:
25 2 0.04
26 23 0.51
27 10 0.22
28 9 0.20
29 1 0.02
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.40
Consensus pattern (27 bp):
AAAAAATATTATTAAAAAGTAATTTTT
Found at i:53367931 original size:14 final size:14
Alignment explanation
Indices: 53367894--53367935 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
53367884 TTATATTTTA
53367894 AATATTTAAATA-T
1 AATATTTAAATATT
53367907 AATCA-TTAAATATT
1 AAT-ATTTAAATATT
*
53367921 TATATTTAAATATT
1 AATATTTAAATATT
53367935 A
1 A
53367936 GTACAGTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (14 bp):
AATATTTAAATATT
Found at i:53370461 original size:83 final size:83
Alignment explanation
Indices: 53370313--53370480 Score: 309
Period size: 83 Copynumber: 2.0 Consensus size: 83
53370303 TTATATTGTC
*
53370313 TAATTTGATTAGCTGTACTACAGTATACTACTCACTTACATCCAAGTCCGAGTTACATAGCTATG
1 TAATGTGATTAGCTGTACTACAGTATACTACTCACTTACATCCAAGTCCGAGTTACATAGCTATG
53370378 CTTCGACTTTAACTCAGT
66 CTTCGACTTTAACTCAGT
* *
53370396 TAATGTGATTATCTGTACTACAGTATACTACTCACTTACATCCAAGTCCGAGTTACATAGTTATG
1 TAATGTGATTAGCTGTACTACAGTATACTACTCACTTACATCCAAGTCCGAGTTACATAGCTATG
53370461 CTTCGACTTTAACTCAGT
66 CTTCGACTTTAACTCAGT
53370479 TA
1 TA
53370481 TTACTCTTTC
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 82 1.00
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (83 bp):
TAATGTGATTAGCTGTACTACAGTATACTACTCACTTACATCCAAGTCCGAGTTACATAGCTATG
CTTCGACTTTAACTCAGT
Found at i:53375352 original size:22 final size:23
Alignment explanation
Indices: 53375322--53375377 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
53375312 AACAATCTAT
53375322 ATATATATATATAATTCAGAGAAA
1 ATATATATA-ATAATTCAGAGAAA
**
53375346 ATATATATAATTTTTCAGAGAAA
1 ATATATATAATAATTCAGAGAAA
*
53375369 A-AAATATAA
1 ATATATATAA
53375378 AGAAGTATCC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 7 0.24
23 13 0.45
24 9 0.31
ACGTcount: A:0.55, C:0.04, G:0.07, T:0.34
Consensus pattern (23 bp):
ATATATATAATAATTCAGAGAAA
Found at i:53375370 original size:24 final size:24
Alignment explanation
Indices: 53375322--53375369 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
53375312 AACAATCTAT
53375322 ATATATATATATAATTCAGAGAAA
1 ATATATATATATAATTCAGAGAAA
**
53375346 ATATATATA-ATTTTTCAGAGAAA
1 ATATATATATATAATTCAGAGAAA
53375369 A
1 A
53375370 AAATATAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.52, C:0.04, G:0.08, T:0.35
Consensus pattern (24 bp):
ATATATATATATAATTCAGAGAAA
Found at i:53380007 original size:60 final size:59
Alignment explanation
Indices: 53379895--53380271 Score: 460
Period size: 61 Copynumber: 6.3 Consensus size: 59
53379885 AATTAGTACA
* * *
53379895 TTTTTGGATGTAGGCTATCAAATGGCCGACACCTCCTATTCTCGAGAAAAAAATTTCAATT
1 TTTTTGG-TGTTGGCCATCAAATGGCCGACACC-CCTTTTCTCGAGAAAAAAATTTCAATT
** * *
53379956 TTTTTGGTGTTGGCCATCAAATGATCGGCACTCCTCTTTTCTCGAGAAAAAAAATTGC-A--
1 TTTTTGGTGTTGGCCATCAAATGGCCGACAC-CC-CTTTTCTCGAG-AAAAAAATTTCAATT
* *
53380015 TTTTTGGATATTGGCCATCAAATGGCCGACACCCCTTATTCTCGAGAAAAAAATTTCAAAT
1 TTTTTGG-TGTTGGCCATCAAATGGCCGACACCCCTT-TTCTCGAGAAAAAAATTTCAATT
* * *
53380076 TTTTTGATGTTGACCATCAAATGGCCGACACCCCTTTTTCTC--GAAAAAAATTT-AAAT
1 TTTTTGGTGTTGGCCATCAAATGGCCGACACCCC-TTTTCTCGAGAAAAAAATTTCAATT
* * *
53380133 TTTTGGGTGTTGGTCATCAAATGGCAGACACCCCTTATTCTCGAGAAAAAAATTTCAAATT
1 TTTTTGGTGTTGGCCATCAAATGGCCGACACCCCTT-TTCTCGAGAAAAAAATTTC-AATT
*
53380194 TTTTTTGTGTTGGCCATCAAATGGCCGACACCCCCTTTTCTCGAGAAAAAAATTTCAAATT
1 TTTTTGGTGTTGGCCATCAAATGGCCGACA-CCCCTTTTCTCGAGAAAAAAATTTC-AATT
53380255 TTTTTGGTGTTGGCCAT
1 TTTTTGGTGTTGGCCAT
53380272 TAACTTCTCC
Statistics
Matches: 275, Mismatches: 26, Indels: 30
0.83 0.08 0.09
Matches are distributed among these distances:
56 2 0.01
57 38 0.14
58 24 0.09
59 29 0.11
60 70 0.25
61 96 0.35
62 16 0.06
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.34
Consensus pattern (59 bp):
TTTTTGGTGTTGGCCATCAAATGGCCGACACCCCTTTTCTCGAGAAAAAAATTTCAATT
Found at i:53381158 original size:26 final size:26
Alignment explanation
Indices: 53381129--53381178 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
53381119 AAATACACAA
53381129 GAAATT-CGAAATTAAATTAAAAAAAC
1 GAAATTAC-AAATTAAATTAAAAAAAC
*
53381155 GAAATTACAAATTAAATTTAAAAA
1 GAAATTACAAATTAAATTAAAAAA
53381179 GTAAAGGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 21 0.95
27 1 0.05
ACGTcount: A:0.62, C:0.06, G:0.06, T:0.26
Consensus pattern (26 bp):
GAAATTACAAATTAAATTAAAAAAAC
Found at i:53382296 original size:13 final size:13
Alignment explanation
Indices: 53382278--53382302 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53382268 ATTTCGAAAA
53382278 TGTAAAAAATATT
1 TGTAAAAAATATT
53382291 TGTAAAAAATAT
1 TGTAAAAAATAT
53382303 CAAATATTTA
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:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (13 bp):
TGTAAAAAATATT
Found at i:53383744 original size:45 final size:46
Alignment explanation
Indices: 53383689--53383843 Score: 128
Period size: 44 Copynumber: 3.5 Consensus size: 46
53383679 TTTATTTAAA
*
53383689 GATATAAAATTAATAAATAATGTATTGTCAAATCAACACATTATAT
1 GATATAAAATTAATAAATAATGTATTATCAAATCAACACATTATAT
* * **** * *
53383735 GATA-AAAATTGTAATATAATAAT-AATAAT--AATTTTTA-TTTA-AA
1 GATATAAAA-T-TAATA-AATAATGTATTATCAAATCAACACATTATAT
53383778 GATATAAAATTAATAAATAATGTATTATCAAATCAACACATTATAT
1 GATATAAAATTAATAAATAATGTATTATCAAATCAACACATTATAT
*
53383824 G--ATAAAATTTATAATATAAT
1 GATATAAAATTAATAA-ATAAT
53383844 AATAATTTGT
Statistics
Matches: 81, Mismatches: 18, Indels: 21
0.68 0.15 0.17
Matches are distributed among these distances:
41 6 0.07
42 9 0.11
43 6 0.07
44 23 0.28
45 16 0.20
46 7 0.09
47 8 0.10
48 6 0.07
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.37
Consensus pattern (46 bp):
GATATAAAATTAATAAATAATGTATTATCAAATCAACACATTATAT
Found at i:53383783 original size:89 final size:88
Alignment explanation
Indices: 53383560--53383929 Score: 482
Period size: 89 Copynumber: 4.3 Consensus size: 88
53383550 TAAATTTAAA
*
53383560 ATATGATAAAAATTGTA-AT-ATAATAATAATAATTTTTATTTAAAGACATAAAATTAATAAATA
1 ATATGATAAAAATTGTATATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATA
*
53383623 ATGTATTGTCAAATCAACA-TTT
66 ATGTATTGTCAAATCAACACATT
53383645 AAAATATGATAAAAATTG----TAAT-ATAATAATAATTTTTATTTAAAGATATAAAATTAATAA
1 ---ATATGATAAAAATTGTATATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAA
53383705 ATAATGTATTGTCAAATCAACACATT
63 ATAATGTATTGTCAAATCAACACATT
53383731 ATATGATAAAAATTGTAATATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAAT
1 ATATGATAAAAATTGT-ATATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAAT
*
53383796 AATGTATTATCAAATCAACACATT
65 AATGTATTGTCAAATCAACACATT
* *
53383820 ATATGAT-AAAA-T-T-TATAAT-ATAATAATAATTTGTACTTT-AA-ATATGAAAATTTGATAA
1 ATATGATAAAAATTGTATATAATAATAATAATAATTTTTA-TTTAAAGATAT-AAAA-TTAATAA
* *
53383878 ATAATGTATTGTCAAATTAACACAAT
63 ATAATGTATTGTCAAATCAACACATT
* *
53383904 ATTTGATATAAATTGTAATATAATAA
1 ATATGATAAAAATTGT-ATATAATAA
53383930 CTATCTTTTT
Statistics
Matches: 255, Mismatches: 10, Indels: 32
0.86 0.03 0.11
Matches are distributed among these distances:
82 4 0.02
83 36 0.14
84 44 0.17
85 63 0.25
86 6 0.02
87 2 0.01
88 23 0.09
89 76 0.30
90 1 0.00
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.39
Consensus pattern (88 bp):
ATATGATAAAAATTGTATATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATA
ATGTATTGTCAAATCAACACATT
Found at i:53384082 original size:11 final size:12
Alignment explanation
Indices: 53384060--53384108 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
53384050 AAACATGTTC
53384060 ATTAATTTTCAA
1 ATTAATTTTCAA
*
53384072 ATTAATTTCAACTTAA
1 ATTAATTT----TCAA
53384088 ATTAATTTTCAA
1 ATTAATTTTCAA
53384100 ATTAATTTT
1 ATTAATTTT
53384109 TATACAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
12 20 0.65
16 11 0.35
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (12 bp):
ATTAATTTTCAA
Found at i:53384106 original size:16 final size:16
Alignment explanation
Indices: 53384070--53384104 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
53384060 ATTAATTTTC
*
53384070 AAATTAATTTCAACTT
1 AAATTAATTTCAAATT
53384086 AAATTAATTTTCAAATT
1 AAATTAA-TTTCAAATT
53384103 AA
1 AA
53384105 TTTTTATACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.43
Consensus pattern (16 bp):
AAATTAATTTCAAATT
Found at i:53385853 original size:6 final size:6
Alignment explanation
Indices: 53385844--53385919 Score: 70
Period size: 6 Copynumber: 13.0 Consensus size: 6
53385834 ATTTTGATTT
* * * *
53385844 TTTAAG TTTAAA -TTAAT TTTAAA TTTAAA TTTATTTA TTTAAA TTT-AT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA--AA TTTAAA TTTAAA
53385892 TTTAAA TTTAAA TTT-AA -TTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
53385920 ATGATATTAA
Statistics
Matches: 57, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
4 2 0.04
5 12 0.21
6 38 0.67
8 5 0.09
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:53385885 original size:14 final size:16
Alignment explanation
Indices: 53385843--53385919 Score: 86
Period size: 17 Copynumber: 4.8 Consensus size: 16
53385833 GATTTTGATT
*
53385843 TTTTAAGTTTAAATTAA
1 TTTTAA-TTTAAATTTA
53385860 TTTTAAATTTAAATTTA
1 TTTT-AATTTAAATTTA
53385877 -TTT-ATTTAAATTTA
1 TTTTAATTTAAATTTA
53385891 TTTTAAATTTAAATTTA
1 TTTT-AATTTAAATTTA
* *
53385908 ATTAAATTTAAA
1 TTTTAATTTAAA
53385920 ATGATATTAA
Statistics
Matches: 53, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
14 11 0.21
15 3 0.06
16 11 0.21
17 26 0.49
18 2 0.04
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (16 bp):
TTTTAATTTAAATTTA
Found at i:53385928 original size:17 final size:16
Alignment explanation
Indices: 53385893--53385935 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
53385883 TAAATTTATT
* *
53385893 TTAAATTTAAATTTAA
1 TTAAATTTAAAATGAA
53385909 TTAAATTTAAAATGATA
1 TTAAATTTAAAATGA-A
*
53385926 TTAAAATTAA
1 TTAAATTTAA
53385936 TAAATTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (16 bp):
TTAAATTTAAAATGAA
Found at i:53386657 original size:27 final size:27
Alignment explanation
Indices: 53386619--53386671 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
53386609 ATAACAATTA
*
53386619 TAATAAATATTAAT-ATTAAATAATAT
1 TAATAAATATTAATAATAAAATAATAT
*
53386645 TAATAAAATATTAGTAATAAAATAATA
1 TAAT-AAATATTAATAATAAAATAATA
53386672 AACAAAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 4 0.17
27 9 0.39
28 10 0.43
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (27 bp):
TAATAAATATTAATAATAAAATAATAT
Found at i:53387807 original size:30 final size:30
Alignment explanation
Indices: 53387771--53388082 Score: 176
Period size: 29 Copynumber: 10.5 Consensus size: 30
53387761 CCCGAACTTT
53387771 CTAAAATTCCATTTTTAACCCCGATTTCAC
1 CTAAAATTCCATTTTTAACCCCGATTTCAC
*
53387801 CAAAAATTACCA-TTTT-ACCCTCGAACTTT---
1 CTAAAATT-CCATTTTTAACCC-CG-A-TTTCAC
*
53387830 CTAAAATTCCATTTTTAACCCC-AGTTTTAC
1 CTAAAATTCCATTTTTAACCCCGA-TTTCAC
* * * * *** **
53387860 CAAAAATT--ACTATTATACCCCCAAACCTT
1 CTAAAATTCCATTTTTA-ACCCCGATTTCAC
*
53387889 CTAAAATTCCATTTTTAACCCTGATTTCAC
1 CTAAAATTCCATTTTTAACCCCGATTTCAC
* * **
53387919 CAAAAATTATCA-TTTT-ACCCTCGAACTC-C
1 CTAAAATT-CCATTTTTAACCC-CGATTTCAC
*
53387948 CTAAAATTCCATTTTT-ACCCCGGTTTCACC
1 CTAAAATTCCATTTTTAACCCCGATTTCA-C
*
53387978 TCTAAAATTCCATTTTTAACCTCGATTTCA-
1 -CTAAAATTCCATTTTTAACCCCGATTTCAC
*
53388008 CTAAAATTACCA-TTTT-ACCCCTAAACTTT--C
1 CTAAAATT-CCATTTTTAACCCC--GA-TTTCAC
53388038 C-AAAATTCCATTTTTAAACCCCGATTTCAC
1 CTAAAATTCCATTTTT-AACCCCGATTTCAC
53388068 C-AAAATTACCATTTT
1 CTAAAATT-CCATTTT
53388083 CCCCCCGGGT
Statistics
Matches: 214, Mismatches: 37, Indels: 61
0.69 0.12 0.20
Matches are distributed among these distances:
27 4 0.02
28 24 0.11
29 71 0.33
30 60 0.28
31 42 0.20
32 13 0.06
ACGTcount: A:0.32, C:0.29, G:0.03, T:0.36
Consensus pattern (30 bp):
CTAAAATTCCATTTTTAACCCCGATTTCAC
Found at i:53387833 original size:59 final size:59
Alignment explanation
Indices: 53387741--53387977 Score: 343
Period size: 59 Copynumber: 4.0 Consensus size: 59
53387731 CCCAAACAGT
53387741 CCAAAAATTACCATTTTACCCCCGAACTTTCTAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCGAACTTTCTAAAATTCCATTTTTAACCCCGATTTCA
* *
53387800 CCAAAAATTACCATTTTACCCTCGAACTTTCTAAAATTCCATTTTTAACCCC-AGTTTTA
1 CCAAAAATTACCATTTTACCCCCGAACTTTCTAAAATTCCATTTTTAACCCCGA-TTTCA
* * * * *
53387859 CCAAAAATTACTATTATACCCCCAAACCTTCTAAAATTCCATTTTTAACCCTGATTTCA
1 CCAAAAATTACCATTTTACCCCCGAACTTTCTAAAATTCCATTTTTAACCCCGATTTCA
* * ** *
53387918 CCAAAAATTATCATTTTACCCTCGAACTCCCTAAAATTCCATTTTT-ACCCCGGTTTCA
1 CCAAAAATTACCATTTTACCCCCGAACTTTCTAAAATTCCATTTTTAACCCCGATTTCA
53387976 CC
1 CC
53387978 TCTAAAATTC
Statistics
Matches: 157, Mismatches: 19, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
58 13 0.08
59 143 0.91
60 1 0.01
ACGTcount: A:0.32, C:0.30, G:0.03, T:0.35
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCCCGAACTTTCTAAAATTCCATTTTTAACCCCGATTTCA
Found at i:53387988 original size:90 final size:90
Alignment explanation
Indices: 53387742--53388068 Score: 245
Period size: 89 Copynumber: 3.7 Consensus size: 90
53387732 CCAAACAGTC
** * * *
53387742 CAAAAATTACCATTTTACCCCCGAACTTTCTAAAATTCCATTTTTAACCCCGATTTCA-C-CAAA
1 CAAAAATTACCATTTTACCCCTAAACTTCCCAAAATTCCATTTTTAACCCCGATTTCACCTCTAA
*
53387805 AATTACCA-TTTTACCCTCGAACTTT--
66 AATT-CCATTTTTAACCTCG-A-TTTCA
* *** * * * * *
53387830 CTAAAATT-CCATTTTTAACCCC-AGTTTTACCAAAAATT--ACTATTATACCCCCA---AACCT
1 CAAAAATTACCA-TTTT-ACCCCTAAACTT-CCCAAAATTCCATTTTTA-ACCCCGATTTCACC-
53387888 TCTAAAATTCCATTTTTAACC-CTGATTTCA
61 TCTAAAATTCCATTTTTAACCTC-GATTTCA
* * *
53387918 CCAAAAATTATCATTTTA-CCCTCGAAC-TCCCTAAAATTCCATTTTT-ACCCCGGTTTCACCTC
1 -CAAAAATTACCATTTTACCCCT-AAACTTCCC-AAAATTCCATTTTTAACCCCGATTTCACCTC
53387980 TAAAATTCCATTTTTAACCTCGATTTCA
63 TAAAATTCCATTTTTAACCTCGATTTCA
* *
53388008 CTAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAAACCCCGATTTCACC
1 CAAAAATTACCATTTTACCCCTAAACTTCCCAAAATTCCATTTTT-AACCCCGATTTCACC
53388069 AAAATTACCA
Statistics
Matches: 183, Mismatches: 30, Indels: 49
0.70 0.11 0.19
Matches are distributed among these distances:
85 1 0.01
86 4 0.02
87 18 0.10
88 47 0.26
89 55 0.30
90 41 0.22
91 17 0.09
ACGTcount: A:0.32, C:0.29, G:0.03, T:0.35
Consensus pattern (90 bp):
CAAAAATTACCATTTTACCCCTAAACTTCCCAAAATTCCATTTTTAACCCCGATTTCACCTCTAA
AATTCCATTTTTAACCTCGATTTCA
Found at i:53387992 original size:59 final size:59
Alignment explanation
Indices: 53387741--53388023 Score: 331
Period size: 59 Copynumber: 4.8 Consensus size: 59
53387731 CCCAAACAGT
* *
53387741 CCAAAAATTACCATTTTACCCCCGAACTTTCTAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCTCGAACTCTCTAAAATTCCATTTTTAACCCCGATTTCA
* *
53387800 CCAAAAATTACCATTTTACCCTCGAACTTTCTAAAATTCCATTTTTAACCCC-AGTTTTA
1 CCAAAAATTACCATTTTACCCTCGAACTCTCTAAAATTCCATTTTTAACCCCGA-TTTCA
* * * * *
53387859 CCAAAAATTACTATTATACCCCCAAAC-CTTCTAAAATTCCATTTTTAACCCTGATTTCA
1 CCAAAAATTACCATTTTACCCTCGAACTC-TCTAAAATTCCATTTTTAACCCCGATTTCA
* * *
53387918 CCAAAAATTATCATTTTACCCTCGAACTCCCTAAAATTCCATTTTT-ACCCCGGTTTCA
1 CCAAAAATTACCATTTTACCCTCGAACTCTCTAAAATTCCATTTTTAACCCCGATTTCA
* * ** *
53387976 CCTCTAAAATT-CCATTTTTAACCTCGATTTCACTAAAATTACCATTTT
1 -C-CAAAAATTACCA-TTTTACCCTCGAACTCTCTAAAATT-CCATTTT
53388024 ACCCCTAAAC
Statistics
Matches: 193, Mismatches: 23, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
58 11 0.06
59 145 0.75
60 30 0.16
61 7 0.04
ACGTcount: A:0.32, C:0.29, G:0.03, T:0.36
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCTCGAACTCTCTAAAATTCCATTTTTAACCCCGATTTCA
Found at i:53388098 original size:58 final size:58
Alignment explanation
Indices: 53387981--53388124 Score: 173
Period size: 58 Copynumber: 2.5 Consensus size: 58
53387971 TTTCACCTCT
* * * *
53387981 AAAATTCCATTTTTAACCTCGATTTCACTAAAATTACCATTTTACCCCTAAACTTTCC
1 AAAATTCCATTTTTAACCCCGATTTCACCAAAATTACCATTTTACCCCCAAACTATCC
****
53388039 AAAATTCCATTTTTAAACCCCGATTTCACCAAAATTACCATTTT-CCCCCCGGGTATCC
1 AAAATTCCATTTTT-AACCCCGATTTCACCAAAATTACCATTTTACCCCCAAACTATCC
* *
53388097 AAAAGTCCCATTTTTAATCCCGATTTCA
1 AAAA-TTCCATTTTTAACCCCGATTTCA
53388125 TCGTTTCTTC
Statistics
Matches: 74, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
58 38 0.51
59 36 0.49
ACGTcount: A:0.31, C:0.29, G:0.05, T:0.35
Consensus pattern (58 bp):
AAAATTCCATTTTTAACCCCGATTTCACCAAAATTACCATTTTACCCCCAAACTATCC
Found at i:53390648 original size:19 final size:19
Alignment explanation
Indices: 53390616--53390657 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
53390606 ATTTTCAAAA
53390616 CAAAA-TATTTAATA-AAT
1 CAAAATTATTTAATACAAT
53390633 CAAAATTATATTAATACAAT
1 CAAAATTAT-TTAATACAAT
53390653 -AAAAT
1 CAAAAT
53390658 ATAAATCTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.23
18 3 0.14
19 11 0.50
20 3 0.14
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (19 bp):
CAAAATTATTTAATACAAT
Found at i:53391492 original size:60 final size:60
Alignment explanation
Indices: 53391298--53391922 Score: 612
Period size: 60 Copynumber: 10.5 Consensus size: 60
53391288 GGAGAAGTTG
*
53391298 GTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTGAAATTTTTTTATTCGAGAAAAAGGG-
1 GTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTG-AATTTTTTT-CTCGA-AAAAAGGGA
*
53391360 GTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTAAAATTTTTTTCTC-AAGAAAAGGGA
1 GTGTCGGCCATTTGATGGCCAACACCAAAAAAATTT-GAATTTTTTTCTCGAA-AAAAGGGA
* *
53391421 GGTGTCTGCCATTTGATGG-CAAGCACCAAAAAAATTTGAATTTTTTTCTCGAAAATAGGGA
1 -GTGTCGGCCATTTGATGGCCAA-CACCAAAAAAATTTGAATTTTTTTCTCGAAAAAAGGGA
* *
53391482 GTGTCGGCCATTTGATGGCCAACACC-CAAAAA--TGCAA-TTTTTT-TCGAGAAAAGGGA
1 GTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTG-AATTTTTTTCTCGAAAAAAGGGA
* * *
53391538 GTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTGAAATTTTTTTCTCGAGAATAGGGG
1 GTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTG-AATTTTTTTCTCGAAAAAAGGGA
* * *
53391599 GTGTTGGCCATTTGATGGCCAACATC-TAAAAA--TGCAATTTTTTTTCTCGAGAAAAAGAGG-
1 GTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTG-AA-TTTTTTTCTCGA-AAAAAG-GGA
* * * * *
53391659 GTGTCGACCATTTGATGGCCAATACAAAAAAAATTTGAATTTTTTTCTCGAGAATAGAGG-
1 GTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTGAATTTTTTTCTCGAAAAAAG-GGA
* * * *
53391719 GTGTCGGCCATTTGATGGCCAACACC-CAAAAATAT-AATTTTTTT-TCGAGAAAAGAGA
1 GTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTGAATTTTTTTCTCGAAAAAAGGGA
* * * * *
53391776 GTGTCGGCCATTTGATGGCCTACACTAAAAAATTTTGAATTTTTTTTTCTG-AAACA-GGA
1 GTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTGAATTTTTTTCTC-GAAAAAAGGGA
*** * * * * * *
53391835 GATGTCGGCCATGCAATGACCAACACC-CAAAAATGT-AA-TTTTTTATAGAAAATA-GG-
1 G-TGTCGGCCATTTGATGGCCAACACCAAAAAAATTTGAATTTTTTTCTCGAAAAAAGGGA
* *
53391891 GTGTCGACCATTTGATGCCCAACACCAAAAAA
1 GTGTCGGCCATTTGATGGCCAACACCAAAAAA
53391923 CACAAATTTT
Statistics
Matches: 476, Mismatches: 60, Indels: 60
0.80 0.10 0.10
Matches are distributed among these distances:
55 20 0.04
56 44 0.09
57 59 0.12
58 23 0.05
59 47 0.10
60 119 0.25
61 82 0.17
62 80 0.17
63 2 0.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (60 bp):
GTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTGAATTTTTTTCTCGAAAAAAGGGA
Found at i:53391595 original size:117 final size:117
Alignment explanation
Indices: 53391298--53391922 Score: 730
Period size: 117 Copynumber: 5.3 Consensus size: 117
53391288 GGAGAAGTTG
* *
53391298 GTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTGAAATTTTTTTATTCGAGAAAAAGGGGTG
1 GTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTG-AATTTTTTT-CTCGAG-AATAGGGGTG
* ** *
53391363 TCGGCCATTTGATGGCCAACACCAAAAAAATTTAAAATTTTTTTCTCAAGAAAAGGGA
63 TCGGCCATTTGATGGCCAACACC-CAAAAA--TGCAATTTTTTTCTCGAGAAAAGGGA
* *
53391421 GGTGTCTGCCATTTGATGG-CAAGCACCAAAAAAATTTGAATTTTTTTCTCGAAAATAGGGAGTG
1 -GTGTCGGCCATTTGATGGCCAA-CACCAAAAAAATTTGAATTTTTTTCTCGAGAATAGGG-GTG
53391485 TCGGCCATTTGATGGCCAACACCCAAAAATGCAA-TTTTTT-TCGAGAAAAGGGA
63 TCGGCCATTTGATGGCCAACACCCAAAAATGCAATTTTTTTCTCGAGAAAAGGGA
53391538 GTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTGAAATTTTTTTCTCGAGAATAGGGGGTGT
1 GTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTG-AATTTTTTTCTCGAGAATA-GGGGTGT
* * *
53391603 TGGCCATTTGATGGCCAACATCTAAAAATGCAATTTTTTTTCTCGAGAAAAAGAGG-
64 CGGCCATTTGATGGCCAACACCCAAAAATGCAA-TTTTTTTCTCGAG-AAAAG-GGA
* * *
53391659 GTGTCGACCATTTGATGGCCAATACAAAAAAAATTTGAATTTTTTTCTCGAGAATAGAGGGTGTC
1 GTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTGAATTTTTTTCTCGAGAATAG-GGGTGTC
** *
53391724 GGCCATTTGATGGCCAACACCCAAAAATATAATTTTTTT-TCGAGAAAAGAGA
65 GGCCATTTGATGGCCAACACCCAAAAATGCAATTTTTTTCTCGAGAAAAGGGA
* * * * * *
53391776 GTGTCGGCCATTTGATGGCCTACACTAAAAAATTTTGAATTTTTTTTTCTGA-AACAGGAGATGT
1 GTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTGAATTTTTTTCTC-GAGAATAGG-GGTGT
*** * * * *
53391840 CGGCCATGCAATGACCAACACCCAAAAATGTAA-TTTTTTAT--AGAAAATAGG-
64 CGGCCATTTGATGGCCAACACCCAAAAATGCAATTTTTTTCTCGAGAAAA-GGGA
* *
53391891 GTGTCGACCATTTGATGCCCAACACCAAAAAA
1 GTGTCGGCCATTTGATGGCCAACACCAAAAAA
53391923 CACAAATTTT
Statistics
Matches: 444, Mismatches: 41, Indels: 41
0.84 0.08 0.08
Matches are distributed among these distances:
115 34 0.08
116 41 0.09
117 152 0.34
118 16 0.04
119 17 0.04
120 58 0.13
121 50 0.11
122 32 0.07
123 12 0.03
124 32 0.07
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (117 bp):
GTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTGAATTTTTTTCTCGAGAATAGGGGTGTCG
GCCATTTGATGGCCAACACCCAAAAATGCAATTTTTTTCTCGAGAAAAGGGA
Found at i:53391869 original size:237 final size:232
Alignment explanation
Indices: 53391298--53391922 Score: 776
Period size: 237 Copynumber: 2.6 Consensus size: 232
53391288 GGAGAAGTTG
*
53391298 GTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTGAAATTTTTTTATTCGAGAAAAAGGGGTG
1 GTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTG-AATTTTTTT-TTC-TGAAAAAGGGGTG
* *
53391363 TCGGCCATTTGATGGCCAACACCAAAAAAATTTAAAATTTTTTTCTCAAGAAAAGGGAGGTGTCT
63 TCGGCCATTTGATGGCCAACACC-AAAAAA--TGAAATTTTTTTCTC-AGAAAAGAG-GGTGTC-
53391428 G-CCATTTGATGG-CAAGCACCAAAAAAATTTGAATTTTTTTCTCGAAAATAGGGAGTGTCGGCC
122 GACCATTTGATGGCCAA-CACCAAAAAAATTTGAATTTTTTTCTCGAAAATAGGGAGTGTCGGCC
* *
53391491 ATTTGATGGCCAACACCCAAAAATGCAATTTTTTTCGAGAAAAGGGA
186 ATTTGATGGCCAACACCCAAAAATACAATTTTTTTCGAGAAAAGAGA
* *
53391538 GTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTGAA-ATTTTTTTCTCGAGAATAGGGGGTG
1 GTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTGAATTTTTTTTTCT-GA-AA-AAGGGGTG
* * * *
53391602 TTGGCCATTTGATGGCCAACATCTAAAAATGCAATTTTTTTTCTCGAGAAAAAGAGGGTGTCGAC
63 TCGGCCATTTGATGGCCAACACCAAAAAATG-AAATTTTTTTCTC-AG-AAAAGAGGGTGTCGAC
* * *
53391667 CATTTGATGGCCAATACAAAAAAAATTTGAATTTTTTTCTCGAGAATAGAGG-GTGTCGGCCATT
125 CATTTGATGGCCAACACCAAAAAAATTTGAATTTTTTTCTCGAAAATAG-GGAGTGTCGGCCATT
*
53391731 TGATGGCCAACACCCAAAAATATAATTTTTTTTCGAGAAAAGAGA
189 TGATGGCCAACACCCAAAAATACAA-TTTTTTTCGAGAAAAGAGA
* * * * *
53391776 GTGTCGGCCATTTGATGGCCTACACTAAAAAATTTTGAATTTTTTTTTCTGAAACAGGAGATGTC
1 GTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTGAATTTTTTTTTCTGAAAAAGG-GGTGTC
*** * * * * *
53391841 GGCCATGCAATGACCAACACCCAAAAATGTAA-TTTTTTAT-AGAAAATAGGGTGTCGACCATTT
65 GGCCATTTGATGGCCAACACCAAAAAATGAAATTTTTTTCTCAGAAAAGAGGGTGTCGACCATTT
*
53391904 GATGCCCAACACCAAAAAA
130 GATGGCCAACACCAAAAAA
53391923 CACAAATTTT
Statistics
Matches: 337, Mismatches: 37, Indels: 30
0.83 0.09 0.07
Matches are distributed among these distances:
232 36 0.11
233 2 0.01
235 7 0.02
236 5 0.01
237 132 0.39
238 79 0.23
239 39 0.12
240 37 0.11
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (232 bp):
GTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTGAATTTTTTTTTCTGAAAAAGGGGTGTCG
GCCATTTGATGGCCAACACCAAAAAATGAAATTTTTTTCTCAGAAAAGAGGGTGTCGACCATTTG
ATGGCCAACACCAAAAAAATTTGAATTTTTTTCTCGAAAATAGGGAGTGTCGGCCATTTGATGGC
CAACACCCAAAAATACAATTTTTTTCGAGAAAAGAGA
Found at i:53392584 original size:20 final size:20
Alignment explanation
Indices: 53392541--53392585 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
53392531 GAAGTATAAA
*
53392541 AAAAATCATGAGAGAGTACG
1 AAAAATCATGAGAGAGTACC
* * *
53392561 AAAAATTATGAGGGATTACC
1 AAAAATCATGAGAGAGTACC
53392581 AAAAA
1 AAAAA
53392586 AGATACGAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.53, C:0.09, G:0.20, T:0.18
Consensus pattern (20 bp):
AAAAATCATGAGAGAGTACC
Found at i:53392615 original size:20 final size:20
Alignment explanation
Indices: 53392592--53392692 Score: 66
Period size: 20 Copynumber: 5.2 Consensus size: 20
53392582 AAAAAGATAC
53392592 GAGAATATAAAAAATTATGA
1 GAGAATATAAAAAATTATGA
* *
53392612 GAGATTATAAAAAATTTTGA
1 GAGAATATAAAAAATTATGA
* * * *
53392632 AAAAATATAACAGA-TATGA
1 GAGAATATAAAAAATTATGA
* * **
53392651 G-TATTATAAAAAA-TGCGA
1 GAGAATATAAAAAATTATGA
*
53392669 -AAAAGTATAAAAAATTATGA
1 GAGAA-TATAAAAAATTATGA
53392689 GAGA
1 GAGA
53392693 CTACCGCAAA
Statistics
Matches: 57, Mismatches: 20, Indels: 7
0.68 0.24 0.08
Matches are distributed among these distances:
18 12 0.21
19 13 0.23
20 30 0.53
21 2 0.04
ACGTcount: A:0.57, C:0.02, G:0.15, T:0.26
Consensus pattern (20 bp):
GAGAATATAAAAAATTATGA
Found at i:53392688 original size:38 final size:40
Alignment explanation
Indices: 53392595--53392692 Score: 121
Period size: 38 Copynumber: 2.5 Consensus size: 40
53392585 AAGATACGAG
**
53392595 AATATAAAAAATTATGAGAGATTATAAAAAATTTTGAAAA
1 AATATAAAAAATTATGAGAGATTATAAAAAATTGCGAAAA
* * *
53392635 AATATAACAGA-TATGAG-TATTATAAAAAA-TGCGAAAA
1 AATATAAAAAATTATGAGAGATTATAAAAAATTGCGAAAA
*
53392672 AGTATAAAAAATTATGAGAGA
1 AATATAAAAAATTATGAGAGA
53392693 CTACCGCAAA
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
37 14 0.30
38 17 0.36
39 7 0.15
40 9 0.19
ACGTcount: A:0.58, C:0.02, G:0.13, T:0.27
Consensus pattern (40 bp):
AATATAAAAAATTATGAGAGATTATAAAAAATTGCGAAAA
Found at i:53393802 original size:16 final size:16
Alignment explanation
Indices: 53393776--53393813 Score: 67
Period size: 16 Copynumber: 2.3 Consensus size: 16
53393766 TTTTGTTCGT
53393776 TGTCTTGTTCAAACTTA
1 TGTC-TGTTCAAACTTA
53393793 TGTCTGTTCAAACTTA
1 TGTCTGTTCAAACTTA
53393809 TGTCT
1 TGTCT
53393814 AGACATAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.21, C:0.18, G:0.13, T:0.47
Consensus pattern (16 bp):
TGTCTGTTCAAACTTA
Found at i:53394473 original size:21 final size:19
Alignment explanation
Indices: 53394452--53394513 Score: 70
Period size: 20 Copynumber: 3.1 Consensus size: 19
53394442 TTGATCTTTA
53394452 AAAATCATTTAATTTCATTT
1 AAAATCATTTAATTT-ATTT
* *
53394472 AAAATAATTTATTATTTAATT
1 AAAATCATTTA--ATTTATTT
53394493 AAAATCATTTAATTTTATTT
1 AAAATCATTTAA-TTTATTT
53394513 A
1 A
53394514 TCACTTCCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
19 1 0.03
20 17 0.49
21 13 0.37
22 4 0.11
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.52
Consensus pattern (19 bp):
AAAATCATTTAATTTATTT
Found at i:53394557 original size:18 final size:18
Alignment explanation
Indices: 53394523--53394573 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
53394513 ATCACTTCCA
* *
53394523 AATTTATTACTTAAATTT
1 AATTTATTCCTTTAATTT
*
53394541 CATTTATTCCTTTAA-TT
1 AATTTATTCCTTTAATTT
53394558 AATTT-TTCCTTTAATT
1 AATTTATTCCTTTAATT
53394574 ATTTAATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
16 9 0.32
17 7 0.25
18 12 0.43
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.59
Consensus pattern (18 bp):
AATTTATTCCTTTAATTT
Found at i:53394568 original size:16 final size:17
Alignment explanation
Indices: 53394523--53394590 Score: 63
Period size: 16 Copynumber: 4.1 Consensus size: 17
53394513 ATCACTTCCA
* *
53394523 AATTTATTACTTAAATTT
1 AATTTATTCCTTTAA-TT
*
53394541 CATTTATTCCTTTAATT
1 AATTTATTCCTTTAATT
53394558 AATTT-TTCCTTTAATT
1 AATTTATTCCTTTAATT
53394574 -ATTTAATT--TTTAATT
1 AATTT-ATTCCTTTAATT
53394589 AA
1 AA
53394591 AATCATTTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
15 11 0.26
16 12 0.28
17 8 0.19
18 12 0.28
ACGTcount: A:0.32, C:0.09, G:0.00, T:0.59
Consensus pattern (17 bp):
AATTTATTCCTTTAATT
Found at i:53396388 original size:30 final size:30
Alignment explanation
Indices: 53396331--53396388 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
53396321 ACGTAAAATC
* **
53396331 AAAATCCCTTAAAACTGAATTCACAAAAAA
1 AAAATCCCCTAAAACTGAAAACACAAAAAA
*
53396361 AAAATCCCCTAAAACTGAAAACTCAAAA
1 AAAATCCCCTAAAACTGAAAACACAAAA
53396389 TTGAAGTGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.57, C:0.22, G:0.03, T:0.17
Consensus pattern (30 bp):
AAAATCCCCTAAAACTGAAAACACAAAAAA
Found at i:53398408 original size:24 final size:24
Alignment explanation
Indices: 53398339--53398411 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 24
53398329 ATAGCATTCA
* *
53398339 AACAACCAAAATAACAATCAAAAC
1 AACAACAAAAATAACAATAAAAAC
** * *
53398363 AACAGTAAAAATAATAGA-AAAAAT
1 AACAACAAAAATAACA-ATAAAAAC
*
53398387 AGCAACAAAAATAACAATAAAAAC
1 AACAACAAAAATAACAATAAAAAC
53398411 A
1 A
53398412 GTACCAAAAT
Statistics
Matches: 36, Mismatches: 11, Indels: 4
0.71 0.22 0.08
Matches are distributed among these distances:
23 1 0.03
24 34 0.94
25 1 0.03
ACGTcount: A:0.70, C:0.15, G:0.04, T:0.11
Consensus pattern (24 bp):
AACAACAAAAATAACAATAAAAAC
Found at i:53398432 original size:48 final size:47
Alignment explanation
Indices: 53398341--53398443 Score: 120
Period size: 47 Copynumber: 2.2 Consensus size: 47
53398331 AGCATTCAAA
* *
53398341 CAACCAAAATAACAATCAAAACAACAGTAAAAATAATAGAAAAAATAG
1 CAACAAAAATAACAAT-AAAACAACAGTAAAAATAATAAAAAAAATAG
* *
53398389 CAACAAAAATAACAAT-AAA-AACAGTACCAAAATAGTAAAAAAAATTG
1 CAACAAAAATAACAATAAAACAACAGTA--AAAATAATAAAAAAAATAG
*
53398436 CATCAAAA
1 CAACAAAA
53398444 CAGCAACTAA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
45 7 0.15
46 3 0.06
47 23 0.48
48 15 0.31
ACGTcount: A:0.66, C:0.15, G:0.06, T:0.14
Consensus pattern (47 bp):
CAACAAAAATAACAATAAAACAACAGTAAAAATAATAAAAAAAATAG
Found at i:53398477 original size:22 final size:21
Alignment explanation
Indices: 53398452--53398520 Score: 79
Period size: 22 Copynumber: 3.3 Consensus size: 21
53398442 AACAGCAACT
53398452 AAAACAGTAAAAATATAACACC
1 AAAACAGTAAAAA-ATAACACC
* * *
53398474 AAAACAATAAAAAATAGCAATC
1 AAAACAGTAAAAAATAAC-ACC
53398496 AAAACAGTAAAAAA-AA-ACC
1 AAAACAGTAAAAAATAACACC
53398515 AAAACA
1 AAAACA
53398521 ACAATATAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
19 8 0.20
21 5 0.12
22 27 0.68
ACGTcount: A:0.70, C:0.16, G:0.04, T:0.10
Consensus pattern (21 bp):
AAAACAGTAAAAAATAACACC
Found at i:53398493 original size:44 final size:41
Alignment explanation
Indices: 53398440--53398521 Score: 112
Period size: 44 Copynumber: 1.9 Consensus size: 41
53398430 AAATTGCATC
53398440 AAAACAGCAA-CTAAAACAGTAAAAATATAACACCAAAACAATAA
1 AAAACAGCAATC-AAAACAGTAAAAA-A-AA-ACCAAAACAATAA
*
53398484 AAAATAGCAATCAAAACAGTAAAAAAAAACCAAAACAA
1 AAAACAGCAATCAAAACAGTAAAAAAAAACCAAAACAA
53398522 CAATATAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
41 10 0.28
42 2 0.06
43 1 0.03
44 22 0.61
45 1 0.03
ACGTcount: A:0.68, C:0.17, G:0.05, T:0.10
Consensus pattern (41 bp):
AAAACAGCAATCAAAACAGTAAAAAAAAACCAAAACAATAA
Found at i:53398907 original size:33 final size:33
Alignment explanation
Indices: 53398836--53398909 Score: 89
Period size: 33 Copynumber: 2.2 Consensus size: 33
53398826 TCCACACCGT
*
53398836 ATTTAAATCTCATATTCTTTTCCTTCTTTTTAA
1 ATTTAAATCTCATATTCTTTTCATTCTTTTTAA
*
53398869 ATTTAAATC-C-TATTCATTTTCATTGTTTATTAA
1 ATTTAAATCTCATATTC-TTTTCATTCTTT-TTAA
*
53398902 CTTTAAAT
1 ATTTAAAT
53398910 TCTTTTTACT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 5 0.14
32 11 0.31
33 20 0.56
ACGTcount: A:0.28, C:0.15, G:0.01, T:0.55
Consensus pattern (33 bp):
ATTTAAATCTCATATTCTTTTCATTCTTTTTAA
Found at i:53398970 original size:14 final size:14
Alignment explanation
Indices: 53398951--53399002 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 14
53398941 TCATTTATCC
53398951 TTTAATTAAAATCA
1 TTTAATTAAAATCA
* *
53398965 TTTAATTTAATTTATCC
1 TTTAA-TTAA--AATCA
*
53398982 TTTGATTAAAATCA
1 TTTAATTAAAATCA
53398996 TTTAATT
1 TTTAATT
53399003 TCATTTATTA
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
14 14 0.48
15 4 0.14
16 4 0.14
17 7 0.24
ACGTcount: A:0.38, C:0.08, G:0.02, T:0.52
Consensus pattern (14 bp):
TTTAATTAAAATCA
Found at i:53398972 original size:31 final size:31
Alignment explanation
Indices: 53398934--53399010 Score: 136
Period size: 31 Copynumber: 2.5 Consensus size: 31
53398924 AATTTATTAT
53398934 TTTAATTTCATTTATCCTTTAATTAAAATCA
1 TTTAATTTCATTTATCCTTTAATTAAAATCA
* *
53398965 TTTAATTTAATTTATCCTTTGATTAAAATCA
1 TTTAATTTCATTTATCCTTTAATTAAAATCA
53398996 TTTAATTTCATTTAT
1 TTTAATTTCATTTAT
53399011 TACTTTTAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.34, C:0.10, G:0.01, T:0.55
Consensus pattern (31 bp):
TTTAATTTCATTTATCCTTTAATTAAAATCA
Found at i:53409464 original size:13 final size:13
Alignment explanation
Indices: 53409446--53409494 Score: 98
Period size: 13 Copynumber: 3.8 Consensus size: 13
53409436 TTCGAGTACC
53409446 TGTGTGTGCAAGG
1 TGTGTGTGCAAGG
53409459 TGTGTGTGCAAGG
1 TGTGTGTGCAAGG
53409472 TGTGTGTGCAAGG
1 TGTGTGTGCAAGG
53409485 TGTGTGTGCA
1 TGTGTGTGCA
53409495 TTATCAACGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 36 1.00
ACGTcount: A:0.14, C:0.08, G:0.45, T:0.33
Consensus pattern (13 bp):
TGTGTGTGCAAGG
Found at i:53411069 original size:29 final size:30
Alignment explanation
Indices: 53411010--53411078 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
53411000 AACTTATATC
*
53411010 TTTATAATTTTTAAAAGATTAAATTCAAAT
1 TTTATAATTTTTAAAAGATTAAAATCAAAT
* * **
53411040 TTTATCATTTTTTAAA-ATTAAAATGTAAT
1 TTTATAATTTTTAAAAGATTAAAATCAAAT
*
53411069 TTTATTATTT
1 TTTATAATTT
53411079 ATTATCATAT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 19 0.58
30 14 0.42
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (30 bp):
TTTATAATTTTTAAAAGATTAAAATCAAAT
Found at i:53413044 original size:17 final size:15
Alignment explanation
Indices: 53413003--53413044 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 15
53412993 GGTAAATAGT
53413003 AAAATTAGA-AAAAA
1 AAAATTAGAGAAAAA
53413017 AAAATTAAGAGAACATAA
1 AAAATT-AGAGAA-A-AA
53413035 AAAATTAGAG
1 AAAATTAGAG
53413045 TATTCTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 6 0.25
15 3 0.12
16 2 0.08
17 5 0.21
18 8 0.33
ACGTcount: A:0.69, C:0.02, G:0.12, T:0.17
Consensus pattern (15 bp):
AAAATTAGAGAAAAA
Found at i:53413737 original size:31 final size:29
Alignment explanation
Indices: 53413670--53413745 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 29
53413660 TTATCAACTT
*
53413670 AAAATTTCATGTATAAAATTACACAAAATC
1 AAAA-TTCATGTATAAAATTACACAAAACC
*
53413700 AAAATTCATGTATATAATTACACATTAAACC
1 AAAATTCATGTATAAAATTACACA--AAACC
* *
53413731 ATAATTCATATATAA
1 AAAATTCATGTATAA
53413746 TCTTGATATT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
29 19 0.49
30 4 0.10
31 16 0.41
ACGTcount: A:0.51, C:0.13, G:0.03, T:0.33
Consensus pattern (29 bp):
AAAATTCATGTATAAAATTACACAAAACC
Found at i:53415710 original size:17 final size:15
Alignment explanation
Indices: 53415669--53415710 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 15
53415659 GGTAAATAGT
53415669 AAAATTAGA-AAAAA
1 AAAATTAGAGAAAAA
53415683 AAAATTAAGAGAACATAA
1 AAAATT-AGAGAA-A-AA
53415701 AAAATTAGAG
1 AAAATTAGAG
53415711 TATTCTATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 6 0.25
15 3 0.12
16 2 0.08
17 5 0.21
18 8 0.33
ACGTcount: A:0.69, C:0.02, G:0.12, T:0.17
Consensus pattern (15 bp):
AAAATTAGAGAAAAA
Found at i:53416369 original size:29 final size:30
Alignment explanation
Indices: 53416327--53416385 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
53416317 GAATTTTATC
*
53416327 AAATTAAAATTTCATGTATAAAATTACACA
1 AAATCAAAATTTCATGTATAAAATTACACA
*
53416357 AAATCAAAA-TTCATGTATATAATTACACA
1 AAATCAAAATTTCATGTATAAAATTACACA
53416386 TTAAACCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 19 0.70
30 8 0.30
ACGTcount: A:0.53, C:0.12, G:0.03, T:0.32
Consensus pattern (30 bp):
AAATCAAAATTTCATGTATAAAATTACACA
Found at i:53416399 original size:31 final size:29
Alignment explanation
Indices: 53416332--53416407 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 29
53416322 TTATCAAATT
*
53416332 AAAATTTCATGTATAAAATTACACAAAATC
1 AAAA-TTCATGTATAAAATTACACAAAACC
*
53416362 AAAATTCATGTATATAATTACACATTAAACC
1 AAAATTCATGTATAAAATTACACA--AAACC
* *
53416393 ATAATTCATATATAA
1 AAAATTCATGTATAA
53416408 TCTTGATATT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
29 19 0.49
30 4 0.10
31 16 0.41
ACGTcount: A:0.51, C:0.13, G:0.03, T:0.33
Consensus pattern (29 bp):
AAAATTCATGTATAAAATTACACAAAACC
Found at i:53416768 original size:2 final size:2
Alignment explanation
Indices: 53416761--53416786 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
53416751 TAATTCACCA
53416761 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
53416787 GATTATGACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53417161 original size:18 final size:17
Alignment explanation
Indices: 53417116--53417172 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 17
53417106 GAATTTAAAC
53417116 ATAATATAAATAATTAAAGT
1 ATAATATAAA-AATT-AA-T
53417136 ATAATATAAAAATTAAT
1 ATAATATAAAAATTAAT
*
53417153 ATGAATATAAGAATTTAAT
1 AT-AATATAA-AAATTAAT
53417172 A
1 A
53417173 CAGTAAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
17 3 0.09
18 9 0.26
19 12 0.35
20 10 0.29
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (17 bp):
ATAATATAAAAATTAAT
Found at i:53418381 original size:18 final size:18
Alignment explanation
Indices: 53418346--53418383 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
53418336 AAATTGAAGT
*
53418346 ATCAAATTAAATGTTTAA
1 ATCAAATTAAATGATTAA
53418364 ATCAAATTTAAAT-ATTAA
1 ATCAAA-TTAAATGATTAA
53418382 AT
1 AT
53418384 TAAAAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (18 bp):
ATCAAATTAAATGATTAA
Found at i:53419675 original size:106 final size:105
Alignment explanation
Indices: 53419492--53419702 Score: 345
Period size: 106 Copynumber: 2.0 Consensus size: 105
53419482 ATAGAATTTT
53419492 ATTTAATTAGTTGTTTTAAATTTTAACTTATTTTTTGGTCAACATTTGCTTCTTCTTTTTTATTG
1 ATTTAATTAGTTGTTTTAAATTTTAACTTATTTTTTGGTCAACATTTGCTTCTTCTTTTTTATTG
*
53419557 TGTATTTAGTTCATTCCTCATTTCTTCTTTTAATGGTGAA
66 TGTATTTAGTTCATTCCTCATTTCTTATTTTAATGGTGAA
* * *
53419597 ATTTAATTAGTTGTTTT-AATTTTAATTTA-TTTTTGGTCAGCATTTGCTCTCTTTTTTGGTTTA
1 ATTTAATTAGTTGTTTTAAATTTTAACTTATTTTTTGGTCAACATTTGCT-TCTTCTTT--TTTA
53419660 TTGTGTATTTAGTTCATTCCTCATTTCTTATTTTAATGGTGAA
63 TTGTGTATTTAGTTCATTCCTCATTTCTTATTTTAATGGTGAA
53419703 TTTGGTTCAT
Statistics
Matches: 99, Mismatches: 4, Indels: 5
0.92 0.04 0.05
Matches are distributed among these distances:
103 18 0.18
104 18 0.18
105 17 0.17
106 46 0.46
ACGTcount: A:0.20, C:0.10, G:0.12, T:0.57
Consensus pattern (105 bp):
ATTTAATTAGTTGTTTTAAATTTTAACTTATTTTTTGGTCAACATTTGCTTCTTCTTTTTTATTG
TGTATTTAGTTCATTCCTCATTTCTTATTTTAATGGTGAA
Found at i:53426555 original size:52 final size:51
Alignment explanation
Indices: 53426497--53426685 Score: 225
Period size: 52 Copynumber: 3.6 Consensus size: 51
53426487 ATTTCACTTC
* * ** *
53426497 ATTCATATACTCACGATGACACATAGCCACCGAACCTTATAATCCACGAGGG
1 ATTCATATACTCACGATGACACATAGTCATCGAACCTT-TAATCCATAAAGG
* * * *
53426549 ATTCATATACTCACGATGACACAGAATCATCGGACCTCTTAATCCGTAAAGG
1 ATTCATATACTCACGATGACACATAGTCATCGAACCT-TTAATCCATAAAGG
* * *
53426601 ATCCATATACTCATGATGACACTTAGTCATCGAACCTTTAAATCCATAAAGG
1 ATTCATATACTCACGATGACACATAGTCATCGAACCTTT-AATCCATAAAGG
*
53426653 ATTTCATATACTCACGATGACACTTAGTCATCG
1 A-TTCATATACTCACGATGACACATAGTCATCG
53426686 GACCCTTTTT
Statistics
Matches: 116, Mismatches: 18, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
51 2 0.02
52 84 0.72
53 30 0.26
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.26
Consensus pattern (51 bp):
ATTCATATACTCACGATGACACATAGTCATCGAACCTTTAATCCATAAAGG
Found at i:53433787 original size:53 final size:52
Alignment explanation
Indices: 53433602--53433846 Score: 217
Period size: 52 Copynumber: 4.7 Consensus size: 52
53433592 ATTTCACTTC
* * * * * * *
53433602 ATTCATATACTCACGATGTCATTTAGCCACCAGACCTTATAATCCACAAGGG
1 ATTCATATACTCACGATGACACTTAGTCATCAGACCTCATAATCCATAAAGG
** * * * ** *
53433654 ATTTGTATATTCACGATGATA-TAGAGTCATTGGACCTCTTAATCCGA-AAAGG
1 ATTCATATACTCACGATGACACT-TAGTCATCAGACCTCATAATCC-ATAAAGG
* * *
53433706 ATACATATACTTACGATGACACTTAGTCATCAGACCT-TTAAATCCATAAAGG
1 ATTCATATACTCACGATGACACTTAGTCATCAGACCTCAT-AATCCATAAAGG
* * * *
53433758 ATTTCATATACTCACGGTAACACTTAGTCATCGGACCTCATAATCCATAAAAG
1 A-TTCATATACTCACGATGACACTTAGTCATCAGACCTCATAATCCATAAAGG
* *
53433811 ATTCATTTACTCACAATGACACTTAGTCATCAGACC
1 ATTCATATACTCACGATGACACTTAGTCATCAGACC
53433847 CTTTTTCATT
Statistics
Matches: 152, Mismatches: 34, Indels: 14
0.76 0.17 0.07
Matches are distributed among these distances:
51 4 0.03
52 102 0.67
53 45 0.30
54 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.29
Consensus pattern (52 bp):
ATTCATATACTCACGATGACACTTAGTCATCAGACCTCATAATCCATAAAGG
Found at i:53434723 original size:22 final size:21
Alignment explanation
Indices: 53434679--53434728 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
53434669 TTAGACTTTT
53434679 TTATTAACTTAATTAATCACA
1 TTATTAACTTAATTAATCACA
* *
53434700 TTTTTAACCTTAA-TAATTCCCA
1 TTATTAA-CTTAATTAA-TCACA
53434722 TTATTAA
1 TTATTAA
53434729 TCAATATTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.38, C:0.16, G:0.00, T:0.46
Consensus pattern (21 bp):
TTATTAACTTAATTAATCACA
Found at i:53437740 original size:3 final size:3
Alignment explanation
Indices: 53437732--53437771 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
53437722 ATACAACGAG
53437732 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
53437772 ATAAAGTTGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:53440427 original size:20 final size:21
Alignment explanation
Indices: 53440389--53440428 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
53440379 CTGTAACTGT
53440389 CACCAATTTCCTCGTGAACCC
1 CACCAATTTCCTCGTGAACCC
*
53440410 CACCATTTTCCTCG-GAACC
1 CACCAATTTCCTCGTGAACC
53440429 ATTCAAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.23, C:0.42, G:0.10, T:0.25
Consensus pattern (21 bp):
CACCAATTTCCTCGTGAACCC
Found at i:53445049 original size:2 final size:2
Alignment explanation
Indices: 53445042--53445071 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
53445032 CAATCAATAT
53445042 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
53445072 AGCAAAATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:53456532 original size:9 final size:9
Alignment explanation
Indices: 53456515--53456572 Score: 53
Period size: 9 Copynumber: 6.2 Consensus size: 9
53456505 TTTAATTAAT
*
53456515 TTTTTAAAA
1 TTTTAAAAA
*
53456524 TTTGAAAAA
1 TTTTAAAAA
*
53456533 TTTGAAAATTA
1 TTTTAAAA--A
*
53456544 TTTTTAAAA
1 TTTTAAAAA
*
53456553 TTTTTAAAA
1 TTTTAAAAA
53456562 TTTTAAAAA
1 TTTTAAAAA
53456571 TT
1 TT
53456573 AATTAAATGA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
9 35 0.83
11 7 0.17
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (9 bp):
TTTTAAAAA
Found at i:53465869 original size:13 final size:13
Alignment explanation
Indices: 53465851--53465878 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
53465841 AATATAGGGG
53465851 AAAATGTACCATT
1 AAAATGTACCATT
53465864 AAAATGTACCATT
1 AAAATGTACCATT
53465877 AA
1 AA
53465879 CGAATTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.14, G:0.07, T:0.29
Consensus pattern (13 bp):
AAAATGTACCATT
Found at i:53469161 original size:2 final size:2
Alignment explanation
Indices: 53469154--53469207 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
53469144 TCTTATCACA
53469154 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
53469196 AT AT AT AT AT AT
1 AT AT AT AT AT AT
53469208 TAATTAATCA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53469820 original size:20 final size:20
Alignment explanation
Indices: 53469795--53469832 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
53469785 GGATTTCTCG
*
53469795 AAAAAAGTCAACGGTCAACC
1 AAAAAAGTCAACGATCAACC
53469815 AAAAAAGTCAACGATCAA
1 AAAAAAGTCAACGATCAA
53469833 TAACAGTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.21, G:0.13, T:0.11
Consensus pattern (20 bp):
AAAAAAGTCAACGATCAACC
Found at i:53469919 original size:27 final size:27
Alignment explanation
Indices: 53469864--53469926 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
53469854 AAGTCAACGG
* *
53469864 TTCGATTCAATCAACGGTTCAGTTTGA
1 TTCGATTCGATCAACGGTTCAGTTCGA
*
53469891 TTCGGTTCGATCAACGGTTC-GATTCGA
1 TTCGATTCGATCAACGGTTCAG-TTCGA
53469918 TTCGATTCG
1 TTCGATTCG
53469927 GGTTGTTGGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 1 0.03
27 30 0.97
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.37
Consensus pattern (27 bp):
TTCGATTCGATCAACGGTTCAGTTCGA
Found at i:53478576 original size:21 final size:21
Alignment explanation
Indices: 53478550--53478594 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
53478540 GAATTTTTCA
* *
53478550 TTTCTTTAC-ATTTTTTATAAT
1 TTTC-TTACGATTTTATAAAAT
53478571 TTTCTTACGATTTTATAAAAT
1 TTTCTTACGATTTTATAAAAT
53478592 TTT
1 TTT
53478595 ATAATTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.27, C:0.09, G:0.02, T:0.62
Consensus pattern (21 bp):
TTTCTTACGATTTTATAAAAT
Found at i:53484116 original size:29 final size:31
Alignment explanation
Indices: 53484064--53484133 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 31
53484054 AAAAACTAAT
* *
53484064 AATTTGATTCTTTTTGAAATATTAACGGTTA
1 AATTTGATTCTTTTTGAAATATTAAAGGATA
**
53484095 AATTTGATT-TTTTTTTAA-ATTAAAGGATA
1 AATTTGATTCTTTTTGAAATATTAAAGGATA
*
53484124 AATTTAATTC
1 AATTTGATTC
53484134 AAAAAATAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
29 17 0.52
30 7 0.21
31 9 0.27
ACGTcount: A:0.36, C:0.04, G:0.10, T:0.50
Consensus pattern (31 bp):
AATTTGATTCTTTTTGAAATATTAAAGGATA
Found at i:53484649 original size:10 final size:9
Alignment explanation
Indices: 53484600--53484736 Score: 57
Period size: 9 Copynumber: 14.8 Consensus size: 9
53484590 TAAAATACTA
53484600 AAAAATTAT
1 AAAAATTAT
*
53484609 ATAAACTTAT
1 A-AAAATTAT
*
53484619 AAAATTTTAT
1 AAAA-ATTAT
* *
53484629 AAAAGTCAT
1 AAAAATTAT
53484638 AATAAATTAT
1 AA-AAATTAT
*
53484648 AAAAAATA-
1 AAAAATTAT
* *
53484656 AAAAAATAA
1 AAAAATTAT
*
53484665 AAAAATTAG
1 AAAAATTAT
**
53484674 AACTATTCAT
1 AAAAATT-AT
* *
53484684 -AAACTTAC
1 AAAAATTAT
53484692 AAATAATTAT
1 AAA-AATTAT
53484702 AAATAAATTAT
1 -AA-AAATTAT
53484713 -AAAA-TAT
1 AAAAATTAT
*
53484720 TAAAATTAT
1 AAAAATTAT
53484729 ATAAAATT
1 A-AAAATT
53484737 TTATTTATTA
Statistics
Matches: 97, Mismatches: 19, Indels: 23
0.70 0.14 0.17
Matches are distributed among these distances:
7 3 0.03
8 16 0.16
9 35 0.36
10 34 0.35
11 8 0.08
12 1 0.01
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.33
Consensus pattern (9 bp):
AAAAATTAT
Found at i:53496812 original size:43 final size:44
Alignment explanation
Indices: 53496723--53496818 Score: 117
Period size: 44 Copynumber: 2.2 Consensus size: 44
53496713 TGGAACATGC
* *
53496723 TTTTTTTACTATGTTTGGCTAATGAATTTTAGTGTTCACAAGTT
1 TTTTTTTACTAAGTTTGGCTAATGAATTTTAGTGTTCAAAAGTT
* *
53496767 TTTTTTTACTAAGTTTGG-TCAATGAATTTTATTG-T-AAATATTT
1 TTTTTTTACTAAGTTTGGCT-AATGAATTTTAGTGTTCAAA-AGTT
53496810 TTTTTTTAC
1 TTTTTTTAC
53496819 CTTTTTACAG
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
42 2 0.04
43 14 0.30
44 30 0.65
ACGTcount: A:0.24, C:0.07, G:0.12, T:0.56
Consensus pattern (44 bp):
TTTTTTTACTAAGTTTGGCTAATGAATTTTAGTGTTCAAAAGTT
Found at i:53505518 original size:24 final size:25
Alignment explanation
Indices: 53505491--53505567 Score: 90
Period size: 24 Copynumber: 3.2 Consensus size: 25
53505481 TAATCATTTC
53505491 AAAATTTAATA-AATAATTAAAATT
1 AAAATTTAATACAATAATTAAAATT
53505515 AAAATTTCAA-ACAA-AATTAAAATT
1 AAAATTT-AATACAATAATTAAAATT
* *
53505539 AAAATTAAATTACAATAA-TAAATTT
1 AAAATTTAA-TACAATAATTAAAATT
53505564 AAAA
1 AAAA
53505568 AATAATGATA
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
23 2 0.04
24 24 0.52
25 18 0.39
26 2 0.04
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (25 bp):
AAAATTTAATACAATAATTAAAATT
Found at i:53505566 original size:6 final size:6
Alignment explanation
Indices: 53505505--53505547 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
53505495 TTTAATAAAT
* *
53505505 AATTAA AATTAA AATTTCA AA-CAA AATTAA AATTAA AATTAA A
1 AATTAA AATTAA AA-TTAA AATTAA AATTAA AATTAA AATTAA A
53505548 TTACAATAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
5 3 0.10
6 23 0.74
7 5 0.16
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (6 bp):
AATTAA
Found at i:53506105 original size:9 final size:9
Alignment explanation
Indices: 53506086--53506119 Score: 59
Period size: 9 Copynumber: 3.7 Consensus size: 9
53506076 AGTTATATTA
53506086 TTTTAAGTTT
1 TTTTAA-TTT
53506096 TTTTAATTT
1 TTTTAATTT
53506105 TTTTAATTT
1 TTTTAATTT
53506114 TTTTAA
1 TTTTAA
53506120 AAAAACTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 18 0.75
10 6 0.25
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (9 bp):
TTTTAATTT
Found at i:53506374 original size:5 final size:5
Alignment explanation
Indices: 53506366--53506391 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
53506356 TATAAAAATA
53506366 ATATT ATATT ATATT ATATT ATATT A
1 ATATT ATATT ATATT ATATT ATATT A
53506392 AGAATACTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
ATATT
Found at i:53509807 original size:23 final size:21
Alignment explanation
Indices: 53509781--53509833 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
53509771 AAATATATTC
53509781 ATATTAAAAAAACATTATTATGA
1 ATATTAAAAAAACATT-TTAT-A
* *
53509804 ATA-T-AATAAACATTTTATT
1 ATATTAAAAAAACATTTTATA
53509823 ATATTAAAAAA
1 ATATTAAAAAA
53509834 CATAAGTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
19 3 0.12
20 5 0.20
21 13 0.52
22 1 0.04
23 3 0.12
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.38
Consensus pattern (21 bp):
ATATTAAAAAAACATTTTATA
Found at i:53509834 original size:20 final size:21
Alignment explanation
Indices: 53509776--53509836 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 21
53509766 CATTAAAATA
53509776 TATTCATATTAAAAAAACATTAT
1 TATT-ATATT-AAAAAACATTAT
* *
53509799 TATGA-ATATAATAAACATT-T
1 TATTATAT-TAAAAAACATTAT
53509819 TATTATATTAAAAAACAT
1 TATTATATTAAAAAACAT
53509837 AAGTTATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
20 14 0.44
21 13 0.41
22 2 0.06
23 3 0.09
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (21 bp):
TATTATATTAAAAAACATTAT
Found at i:53516294 original size:13 final size:13
Alignment explanation
Indices: 53516276--53516300 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53516266 GTACATTGTT
53516276 TTATATTTAATTA
1 TTATATTTAATTA
53516289 TTATATTTAATT
1 TTATATTTAATT
53516301 TTTTATATGA
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTATATTTAATTA
Found at i:53519634 original size:14 final size:15
Alignment explanation
Indices: 53519615--53519647 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
53519605 GCAACATCAC
53519615 AATTAAAT-TAAATA
1 AATTAAATCTAAATA
*
53519629 AATTAAATCTAAGTA
1 AATTAAATCTAAATA
53519644 AATT
1 AATT
53519648 TGATATATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (15 bp):
AATTAAATCTAAATA
Found at i:53530782 original size:24 final size:23
Alignment explanation
Indices: 53530720--53530783 Score: 56
Period size: 24 Copynumber: 2.7 Consensus size: 23
53530710 AATTTAATTC
* *
53530720 TTAATAATTATATTTTTTATTAAT
1 TTAATTATTA-ATTTTTAATTAAT
** * *
53530744 TTGTTTTTTATTTTTTAATTAAAT
1 TTAATTATTAATTTTTAATT-AAT
53530768 TTAATTATTAATTTTT
1 TTAATTATTAATTTTT
53530784 TAAAAAGAAT
Statistics
Matches: 29, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
23 8 0.28
24 21 0.72
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (23 bp):
TTAATTATTAATTTTTAATTAAT
Found at i:53533421 original size:22 final size:22
Alignment explanation
Indices: 53533395--53533444 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
53533385 AATCAATTAT
53533395 GTTGAATAGCAATGACAAAGGA
1 GTTGAATAGCAATGACAAAGGA
53533417 GTTGAATAGCAATGACAAAGGA
1 GTTGAATAGCAATGACAAAGGA
53533439 GTTGAA
1 GTTGAA
53533445 ATCGAGAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.44, C:0.08, G:0.28, T:0.20
Consensus pattern (22 bp):
GTTGAATAGCAATGACAAAGGA
Found at i:53541819 original size:31 final size:31
Alignment explanation
Indices: 53541753--53541819 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
53541743 TTTTGTTATT
* ** * *
53541753 TTTTTTATAACGTCAGTGACTGTTTTGTTAT
1 TTTTTGATAACGTCAGTGACTGACTTGTCAC
*
53541784 TTTTTGATAACGTCAGTGATTGACTTGTCAC
1 TTTTTGATAACGTCAGTGACTGACTTGTCAC
53541815 TTTTT
1 TTTTT
53541820 CAAAATTGAG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.19, C:0.12, G:0.16, T:0.52
Consensus pattern (31 bp):
TTTTTGATAACGTCAGTGACTGACTTGTCAC
Found at i:53541819 original size:32 final size:31
Alignment explanation
Indices: 53541733--53541805 Score: 119
Period size: 31 Copynumber: 2.3 Consensus size: 31
53541723 AAAATATTAA
*
53541733 TCAGTGATTGTTTTGTTATTTTTTTTATAACG
1 TCAGTGATTGTTTTGTTA-TTTTTTGATAACG
*
53541765 TCAGTGACTGTTTTGTTATTTTTTGATAACG
1 TCAGTGATTGTTTTGTTATTTTTTGATAACG
53541796 TCAGTGATTG
1 TCAGTGATTG
53541806 ACTTGTCACT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
31 21 0.55
32 17 0.45
ACGTcount: A:0.19, C:0.08, G:0.19, T:0.53
Consensus pattern (31 bp):
TCAGTGATTGTTTTGTTATTTTTTGATAACG
Found at i:53543137 original size:23 final size:23
Alignment explanation
Indices: 53543096--53543146 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
53543086 TTTTACATGT
53543096 TTAT-TTTTAAATTTATTAAATAA
1 TTATATTTTAAATTTATTAAA-AA
53543119 -TATATTTTAGAATTT-TTAAAAA
1 TTATATTTTA-AATTTATTAAAAA
53543141 TTATAT
1 TTATAT
53543147 ATAAGATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
22 5 0.20
23 15 0.60
24 5 0.20
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (23 bp):
TTATATTTTAAATTTATTAAAAA
Found at i:53543424 original size:28 final size:27
Alignment explanation
Indices: 53543377--53543430 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
53543367 ATAAATTAGT
53543377 AATGATAAAATTACACTTTAACCTTTCA
1 AATGATAAAATTACACTTTAA-CTTTCA
53543405 AATGATAAAAATTTA-A-TTTAACTTTC
1 AATGAT-AAAA-TTACACTTTAACTTTC
53543431 TAAAAATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
27 5 0.21
28 11 0.46
29 5 0.21
30 3 0.12
ACGTcount: A:0.44, C:0.13, G:0.04, T:0.39
Consensus pattern (27 bp):
AATGATAAAATTACACTTTAACTTTCA
Found at i:53547731 original size:10 final size:10
Alignment explanation
Indices: 53547716--53547762 Score: 60
Period size: 10 Copynumber: 4.6 Consensus size: 10
53547706 TAATTATAAA
53547716 TATTAATTAT
1 TATTAATTAT
53547726 TATTAATTAT
1 TATTAATTAT
*
53547736 TATTATAATTGT
1 TA-T-TAATTAT
53547748 TATTAA-TAT
1 TATTAATTAT
53547757 TATTAA
1 TATTAA
53547763 CAATCAAAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
9 8 0.24
10 15 0.45
11 2 0.06
12 8 0.24
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (10 bp):
TATTAATTAT
Found at i:53547750 original size:12 final size:13
Alignment explanation
Indices: 53547721--53547761 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 13
53547711 ATAAATATTA
53547721 ATTATTATTAATT
1 ATTATTATTAATT
53547734 ATTATTA-TAATT
1 ATTATTATTAATT
* *
53547746 GTTATTAAT-ATT
1 ATTATTATTAATT
53547758 ATTA
1 ATTA
53547762 ACAATCAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 17 0.68
13 8 0.32
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (13 bp):
ATTATTATTAATT
Found at i:53551940 original size:20 final size:20
Alignment explanation
Indices: 53551855--53551940 Score: 75
Period size: 20 Copynumber: 4.1 Consensus size: 20
53551845 ATTTTATAAT
53551855 TTTTTAAAAATATAGATTTTGAAA
1 TTTTTAAAAAT-T--ATTTTG-AA
* *
53551879 TTTTTTATAAA-TATTTTAAA
1 -TTTTTAAAAATTATTTTGAA
* *
53551899 ATTTTAAAAATTATTTTCAA
1 TTTTTAAAAATTATTTTGAA
*
53551919 TTTTTGAAAATTATTTTGAA
1 TTTTTAAAAATTATTTTGAA
53551939 TT
1 TT
53551941 ATTTTATAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
19 8 0.15
20 29 0.56
21 5 0.10
23 1 0.02
25 9 0.17
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.53
Consensus pattern (20 bp):
TTTTTAAAAATTATTTTGAA
Found at i:53558289 original size:58 final size:56
Alignment explanation
Indices: 53558188--53558347 Score: 164
Period size: 58 Copynumber: 2.8 Consensus size: 56
53558178 ATTTTTCTAA
* *
53558188 AATTATATATT-ATAATTTTTACT-AATTCATATTTTAATAATAATTATATTAAAAATAT
1 AATTAAATATTAAT-ATTTTTATTAAATT-ATA-TTTAATAATAATTATATT-AAAATAT
* * * *
53558246 TATTAAAT-TTCATATTATTTTATTAAATTGTATTTAATAATAATTATGTTAAAATAT
1 AATTAAATATTAATA-T-TTTTATTAAATTATATTTAATAATAATTATATTAAAATAT
*
53558303 AATTAAATAAATTAATATTTTTATTCAATTATATTTAATAATAAT
1 AATTAAAT--ATTAATATTTTTATTAAATTATATTTAATAATAAT
53558348 CATTAAAATT
Statistics
Matches: 86, Mismatches: 9, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
57 17 0.20
58 51 0.59
59 9 0.10
60 9 0.10
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.51
Consensus pattern (56 bp):
AATTAAATATTAATATTTTTATTAAATTATATTTAATAATAATTATATTAAAATAT
Found at i:53558485 original size:39 final size:44
Alignment explanation
Indices: 53558430--53558534 Score: 114
Period size: 46 Copynumber: 2.5 Consensus size: 44
53558420 TTTCTTATGC
*
53558430 TATTACAGCATC-ATTCCATT-CAACCAA-ACACAA-GAA-TA-T
1 TATTACAGC-TCTATTCCATTCCAACCAACAAACAATGAATTACT
*
53558469 TATTACAGCTCTATTCCATTCCAATCAACTAAACAATTGAATTACT
1 TATTACAGCTCTATTCCATTCCAACCAAC-AAACAA-TGAATTACT
*
53558515 GATTACAGCTCTATTCCATT
1 TATTACAGCTCTATTCCATT
53558535 ACAGCTATAT
Statistics
Matches: 55, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
38 2 0.04
39 17 0.31
40 6 0.11
42 5 0.09
44 3 0.05
45 2 0.04
46 20 0.36
ACGTcount: A:0.37, C:0.25, G:0.06, T:0.32
Consensus pattern (44 bp):
TATTACAGCTCTATTCCATTCCAACCAACAAACAATGAATTACT
Found at i:53558537 original size:16 final size:16
Alignment explanation
Indices: 53558516--53558587 Score: 108
Period size: 16 Copynumber: 4.5 Consensus size: 16
53558506 TGAATTACTG
53558516 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
53558532 ATTACAGCTATATTCC
1 ATTACAGCTCTATTCC
*
53558548 ATTACAGTTCTATTCC
1 ATTACAGCTCTATTCC
* *
53558564 ATTACACCTCTATTCT
1 ATTACAGCTCTATTCC
53558580 ATTACAGC
1 ATTACAGC
53558588 GAACCAAACG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.28, C:0.28, G:0.06, T:0.39
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:53560290 original size:59 final size:59
Alignment explanation
Indices: 53560214--53560438 Score: 285
Period size: 59 Copynumber: 3.8 Consensus size: 59
53560204 TGGATACCCG
* ** *
53560214 GGGGCAAAATGGTAATTTTGGTGTCATCGAGGTTAAAAATAGAATTTTAAAAGAGTCAA
1 GGGGTAAAATGGTAATTTTGGTGAAATCGAGGTTAAAAATAGAATTTTAAAAGATTCAA
* * *
53560273 GGGGTAAAATGGTAATTTTTGGTGAAACCGAGGTTAAAAATGGAATTTTAAAAGATTC-G
1 GGGGTAAAATGGTAA-TTTTGGTGAAATCGAGGTTAAAAATAGAATTTTAAAAGATTCAA
* * *
53560332 GGGGTAAAATGGTAATTTTCGGTGAAGTCGGGGTTAAAAAT-GAAATTTTAGAAGATTCAA
1 GGGGTAAAATGGTAATTTT-GGTGAAATCGAGGTTAAAAATAG-AATTTTAAAAGATTCAA
* *
53560392 -GGGTAAAATGGTAAATTTTGGTGAAATCGGGGTTAAAAATAGGATTT
1 GGGGTAAAATGGT-AATTTTGGTGAAATCGAGGTTAAAAATAGAATTT
53560439 AGGAAAGTTT
Statistics
Matches: 146, Mismatches: 14, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
58 5 0.03
59 97 0.66
60 44 0.30
ACGTcount: A:0.37, C:0.05, G:0.28, T:0.30
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTGGTGAAATCGAGGTTAAAAATAGAATTTTAAAAGATTCAA
Found at i:53560344 original size:118 final size:117
Alignment explanation
Indices: 53560212--53560466 Score: 322
Period size: 118 Copynumber: 2.2 Consensus size: 117
53560202 TATGGATACC
* *
53560212 CGGGGGCAAAATGGTAATTTT-GGTGTCA-TCGAGGTTAAAAAT-AGAATTTTAAAAGAGTCAAG
1 CGGGGGTAAAATGGTAATTTTCGGTG-AAGTCGAGGTTAAAAATGA-AATTTTAAAAGAGTCAA-
*
53560274 GGGTAAAATGGTAATTTTTGGTGAAACCGAGGTTAAAAAT-GGAATTTTA-AAAGATT
63 GGGTAAAATGGTAAATTTTGGTGAAACCGAGGTTAAAAATAGG-A-TTTAGAAAG-TT
* * *
53560330 CGGGGGTAAAATGGTAATTTTCGGTGAAGTCGGGGTTAAAAATGAAATTTTAGAAGATTCAAGGG
1 CGGGGGTAAAATGGTAATTTTCGGTGAAGTCGAGGTTAAAAATGAAATTTTAAAAGAGTCAAGGG
* *
53560395 TAAAATGGTAAATTTTGGTGAAATCGGGGTTAAAAATAGGATTTAGGAAAGTT
66 TAAAATGGTAAATTTTGGTGAAACCGAGGTTAAAAATAGGATTTA-GAAAGTT
* *
53560448 TGGGGGTAAAATGATAATT
1 CGGGGGTAAAATGGTAATT
53560467 GTTGAAAGTT
Statistics
Matches: 121, Mismatches: 10, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
117 4 0.03
118 78 0.64
119 38 0.31
120 1 0.01
ACGTcount: A:0.37, C:0.05, G:0.28, T:0.30
Consensus pattern (117 bp):
CGGGGGTAAAATGGTAATTTTCGGTGAAGTCGAGGTTAAAAATGAAATTTTAAAAGAGTCAAGGG
TAAAATGGTAAATTTTGGTGAAACCGAGGTTAAAAATAGGATTTAGAAAGTT
Found at i:53560370 original size:30 final size:30
Alignment explanation
Indices: 53560273--53560429 Score: 94
Period size: 30 Copynumber: 5.3 Consensus size: 30
53560263 AAAGAGTCAA
* *
53560273 GGGG-TAAAATGGTAATTTTTGGTGAAACC
1 GGGGTTAAAATGGTAATTTTAGGTGAAATC
* *** *
53560302 GAGGTTAAAAATGG-AATTTTAAAAG-ATTC
1 GGGGTT-AAAATGGTAATTTTAGGTGAAATC
* * *
53560331 GGGGGTAAAATGGTAATTTTCGGTGAAGTC
1 GGGGTTAAAATGGTAATTTTAGGTGAAATC
* ** *
53560361 GGGGTTAAAAAT-GAAATTTTAGAAG-ATTC
1 GGGGTT-AAAATGGTAATTTTAGGTGAAATC
*
53560390 AAGGG-TAAAATGGTAAATTTT-GGTGAAATC
1 -GGGGTTAAAATGGT-AATTTTAGGTGAAATC
53560420 GGGGTTAAAA
1 GGGGTTAAAA
53560430 ATAGGATTTA
Statistics
Matches: 92, Mismatches: 26, Indels: 19
0.67 0.19 0.14
Matches are distributed among these distances:
28 12 0.13
29 26 0.28
30 42 0.46
31 12 0.13
ACGTcount: A:0.37, C:0.04, G:0.29, T:0.30
Consensus pattern (30 bp):
GGGGTTAAAATGGTAATTTTAGGTGAAATC
Found at i:53560455 original size:59 final size:58
Alignment explanation
Indices: 53560212--53560466 Score: 268
Period size: 59 Copynumber: 4.3 Consensus size: 58
53560202 TATGGATACC
* ** *
53560212 CGGGGGCAAAATGGTAATTTTGGTGTCATCGAGGTTAAAAATAGAATTTTA-AAAGAGT
1 CGGGGGTAAAATGGTAATTTTGGTGAAATCGAGGTTAAAAAT-GAATTTTAGAAAGATT
* *
53560270 CAAGGGGTAAAATGGTAATTTTTGGTGAAACCGAGGTTAAAAATGGAATTTTA-AAAGATT
1 C-GGGGGTAAAATGGTAA-TTTTGGTGAAATCGAGGTTAAAAAT-GAATTTTAGAAAGATT
* *
53560330 CGGGGGTAAAATGGTAATTTTCGGTGAAGTCGGGGTTAAAAATGAAATTTTAG-AAGATT
1 CGGGGGTAAAATGGTAATTTT-GGTGAAATCGAGGTTAAAAATG-AATTTTAGAAAGATT
** * *
53560389 CAAGGGTAAAATGGTAAATTTTGGTGAAATCGGGGTTAAAAATAGGA-TTTAGGAAAG-TT
1 CGGGGGTAAAATGGT-AATTTTGGTGAAATCGAGGTTAAAAAT-GAATTTTA-GAAAGATT
* *
53560448 TGGGGGTAAAATGATAATT
1 CGGGGGTAAAATGGTAATT
53560467 GTTGAAAGTT
Statistics
Matches: 169, Mismatches: 19, Indels: 18
0.82 0.09 0.09
Matches are distributed among these distances:
58 14 0.08
59 108 0.64
60 47 0.28
ACGTcount: A:0.37, C:0.05, G:0.28, T:0.30
Consensus pattern (58 bp):
CGGGGGTAAAATGGTAATTTTGGTGAAATCGAGGTTAAAAATGAATTTTAGAAAGATT
Found at i:53560499 original size:19 final size:19
Alignment explanation
Indices: 53560475--53560529 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
53560465 TTGTTGAAAG
53560475 TTTTGGGGTCAAAATGTAA
1 TTTTGGGGTCAAAATGTAA
53560494 TTTT--GG--AAAA-G---
1 TTTTGGGGTCAAAATGTAA
53560505 TTTTGGGGTCAAAATGTAA
1 TTTTGGGGTCAAAATGTAA
53560524 TTTTGG
1 TTTTGG
53560530 AAAAGTTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 16
0.64 0.00 0.36
Matches are distributed among these distances:
11 4 0.14
13 2 0.07
14 1 0.04
15 8 0.29
16 1 0.04
17 2 0.07
19 10 0.36
ACGTcount: A:0.29, C:0.04, G:0.27, T:0.40
Consensus pattern (19 bp):
TTTTGGGGTCAAAATGTAA
Found at i:53560565 original size:119 final size:120
Alignment explanation
Indices: 53560436--53560787 Score: 498
Period size: 119 Copynumber: 3.0 Consensus size: 120
53560426 AAAAATAGGA
* *
53560436 TTTAGGAAAGTTTGGGGGTAAAATGATAATTGTT-G-AAAGTTTTGGGGTCAAAATGTAATTTTG
1 TTTAGAAAAGTTTAGGGGTAAAATGATAATT-TTAGAAAAGTTTTGGGGTCAAAATGTAATTTTG
*
53560499 GAAAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTTAAAAGGTAAT
65 GAAAAGTTTTAGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTTAAAAGGTAAT
* * *
53560555 TTTAGAAAAGTTTTAGGGTTAAAAT-ATAATTTTAGAAAAG-TTTAGGGTCAAAATGTAATTTTA
1 TTTAGAAAAG-TTTAGGGGTAAAATGATAATTTTAGAAAAGTTTTGGGGTCAAAATGTAATTTTG
* * *
53560618 GAAAAGTTTTAGGGTTAAAATGTAATTTTAGAAAAGTTTTGGGGTTAAAATGTAAT
65 GAAAAGTTTTAGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTTAAAAGGTAAT
* *
53560674 TTTAGAAAAATTTTGGGGTCAAAATG-TAATTTTAGAAAAGTTTTGGGGTCAAAATGTAATTTTG
1 TTTAGAAAAGTTTAGGGGT-AAAATGATAATTTTAGAAAAGTTTTGGGGTCAAAATGTAATTTTG
* * * * *
53560738 GAAATGTTTTAGGGTCGAAATATAATTTTGGAAAAGTTCTGGGGTCAAAA
65 GAAAAGTTTTAGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTTAAAA
53560788 CATGATTTTT
Statistics
Matches: 206, Mismatches: 21, Indels: 11
0.87 0.09 0.05
Matches are distributed among these distances:
118 9 0.04
119 117 0.57
120 80 0.39
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.37
Consensus pattern (120 bp):
TTTAGAAAAGTTTAGGGGTAAAATGATAATTTTAGAAAAGTTTTGGGGTCAAAATGTAATTTTGG
AAAAGTTTTAGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTTAAAAGGTAAT
Found at i:53560796 original size:30 final size:30
Alignment explanation
Indices: 53560436--53560787 Score: 469
Period size: 30 Copynumber: 11.8 Consensus size: 30
53560426 AAAAATAGGA
* *
53560436 TTTAGGAAAGTTTGGGGGT-AAAATGATAAT
1 TTTAGAAAAGTTTTGGGGTCAAAATG-TAAT
53560466 TGTT-G-AAAGTTTTGGGGTCAAAATGTAAT
1 T-TTAGAAAAGTTTTGGGGTCAAAATGTAAT
*
53560495 TTTGGAAAAGTTTTGGGGTCAAAATGTAAT
1 TTTAGAAAAGTTTTGGGGTCAAAATGTAAT
* * *
53560525 TTTGGAAAAGTTTTGGGGTTAAAAGGTAAT
1 TTTAGAAAAGTTTTGGGGTCAAAATGTAAT
* * *
53560555 TTTAGAAAAGTTTTAGGGTTAAAATATAAT
1 TTTAGAAAAGTTTTGGGGTCAAAATGTAAT
*
53560585 TTTAGAAAAG-TTTAGGGTCAAAATGTAAT
1 TTTAGAAAAGTTTTGGGGTCAAAATGTAAT
* *
53560614 TTTAGAAAAGTTTTAGGGTTAAAATGTAAT
1 TTTAGAAAAGTTTTGGGGTCAAAATGTAAT
*
53560644 TTTAGAAAAGTTTTGGGGTTAAAATGTAAT
1 TTTAGAAAAGTTTTGGGGTCAAAATGTAAT
*
53560674 TTTAGAAAAATTTTGGGGTCAAAATGTAAT
1 TTTAGAAAAGTTTTGGGGTCAAAATGTAAT
53560704 TTTAGAAAAGTTTTGGGGTCAAAATGTAAT
1 TTTAGAAAAGTTTTGGGGTCAAAATGTAAT
* * * * *
53560734 TTTGGAAATGTTTTAGGGTCGAAATATAAT
1 TTTAGAAAAGTTTTGGGGTCAAAATGTAAT
* *
53560764 TTTGGAAAAGTTCTGGGGTCAAAA
1 TTTAGAAAAGTTTTGGGGTCAAAA
53560788 CATGATTTTT
Statistics
Matches: 294, Mismatches: 23, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
28 2 0.01
29 45 0.15
30 245 0.83
31 2 0.01
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.37
Consensus pattern (30 bp):
TTTAGAAAAGTTTTGGGGTCAAAATGTAAT
Found at i:53561802 original size:7 final size:7
Alignment explanation
Indices: 53561792--53561852 Score: 67
Period size: 7 Copynumber: 9.3 Consensus size: 7
53561782 TTATTTCGAT
53561792 ATTATTA
1 ATTATTA
53561799 ATTATTA
1 ATTATTA
53561806 A-TATTA
1 ATTATTA
*
53561812 ACTA-TA
1 ATTATTA
*
53561818 ATCA-TA
1 ATTATTA
*
53561824 AATATTA
1 ATTATTA
53561831 ATTA-TA
1 ATTATTA
53561837 ATTATTA
1 ATTATTA
53561844 ATTATTA
1 ATTATTA
53561851 AT
1 AT
53561853 AATATTTTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
6 20 0.43
7 26 0.57
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (7 bp):
ATTATTA
Found at i:53561812 original size:13 final size:14
Alignment explanation
Indices: 53561792--53561852 Score: 67
Period size: 13 Copynumber: 4.6 Consensus size: 14
53561782 TTATTTCGAT
53561792 ATTATTAATTATTA
1 ATTATTAATTATTA
*
53561806 A-TATTAACTA-TA
1 ATTATTAATTATTA
* *
53561818 ATCA-TAAATATTA
1 ATTATTAATTATTA
53561831 ATTA-TAATTATTA
1 ATTATTAATTATTA
53561844 ATTATTAAT
1 ATTATTAAT
53561853 AATATTTTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
12 8 0.21
13 26 0.67
14 5 0.13
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (14 bp):
ATTATTAATTATTA
Found at i:53562539 original size:6 final size:6
Alignment explanation
Indices: 53562528--53562594 Score: 86
Period size: 6 Copynumber: 11.7 Consensus size: 6
53562518 GAATTTATAA
*
53562528 TAAATT TAAATT TAAA-T TAAATC TAAATT TAAA-T TAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
* *
53562574 TAAA-A TAAATT TAATTT TAAA
1 TAAATT TAAATT TAAATT TAAA
53562595 ACAAATTCAA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
5 14 0.27
6 38 0.73
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (6 bp):
TAAATT
Found at i:53562547 original size:11 final size:11
Alignment explanation
Indices: 53562519--53562573 Score: 69
Period size: 11 Copynumber: 4.9 Consensus size: 11
53562509 TTGGACTTTG
53562519 AATTTATAA-TA
1 AATTTA-AATTA
53562530 AATTTAAATTTA
1 AATTTAAA-TTA
53562542 AA-TTAAATCTA
1 AATTTAAAT-TA
53562553 AATTTAAATTA
1 AATTTAAATTA
53562564 AATTTAAATT
1 AATTTAAATT
53562574 TAAAATAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 3 0.08
11 27 0.68
12 10 0.25
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (11 bp):
AATTTAAATTA
Found at i:53562582 original size:11 final size:12
Alignment explanation
Indices: 53562528--53562594 Score: 86
Period size: 11 Copynumber: 5.8 Consensus size: 12
53562518 GAATTTATAA
53562528 TAAATTTAAATT
1 TAAATTTAAATT
*
53562540 TAAA-TTAAATC
1 TAAATTTAAATT
53562551 TAAATTTAAA-T
1 TAAATTTAAATT
53562562 TAAATTTAAATT
1 TAAATTTAAATT
*
53562574 TAAA-ATAAATT
1 TAAATTTAAATT
*
53562585 TAATTTTAAA
1 TAAATTTAAA
53562595 ACAAATTCAA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
11 29 0.62
12 18 0.38
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (12 bp):
TAAATTTAAATT
Found at i:53562595 original size:17 final size:17
Alignment explanation
Indices: 53562519--53562601 Score: 112
Period size: 17 Copynumber: 4.9 Consensus size: 17
53562509 TTGGACTTTG
*
53562519 AATTTATAATAAATTTA
1 AATTTAAAATAAATTTA
* *
53562536 AATTTAAATTAAATCTA
1 AATTTAAAATAAATTTA
*
53562553 AATTTAAATTAAATTTA
1 AATTTAAAATAAATTTA
53562570 AATTTAAAATAAATTTA
1 AATTTAAAATAAATTTA
* *
53562587 ATTTTAAAACAAATT
1 AATTTAAAATAAATT
53562602 CAAAATGGTT
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 59 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
AATTTAAAATAAATTTA
Found at i:53563012 original size:68 final size:69
Alignment explanation
Indices: 53562915--53563056 Score: 232
Period size: 68 Copynumber: 2.0 Consensus size: 69
53562905 GAAAATGATC
*
53562915 TTGCTCTTACTTCAACAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTCCGAGGGG
1 TTGCTCTTACTT--ACAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTCCAAGGGG
53562980 ATGACG
64 ATGACG
* *
53562986 TTGCTCTTACTT-CAATTTCAGAGATAAAGATGTGTTATCCACTCTACTTCAATTTCAAGGGGAT
1 TTGCTCTTACTTACAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTCCAAGGGGAT
53563050 GACG
66 GACG
53563054 TTG
1 TTG
53563057 AGACCTGCAG
Statistics
Matches: 68, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
68 56 0.82
71 12 0.18
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.34
Consensus pattern (69 bp):
TTGCTCTTACTTACAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTCCAAGGGGAT
GACG
Found at i:53574987 original size:58 final size:57
Alignment explanation
Indices: 53574925--53575088 Score: 188
Period size: 58 Copynumber: 2.8 Consensus size: 57
53574915 ATGGATACCC
* **
53574925 GGGGGCAAATGGTAATTTTGGTGTCATCGAGGTTAAAAATGGAATTTTAAAAGATTCG
1 GGGGGAAAATGGTAATTTTGGTGAAATCGAGGTTAAAAATGGAATTTT-AAAGATTCG
* * *
53574983 GGGGGTAAAATGGTAATTTTCGATGAAACCGGGGTT-AAAATGGAATTTTAAAGATTCG
1 GGGGG-AAAATGGTAATTTT-GGTGAAATCGAGGTTAAAAATGGAATTTTAAAGATTCG
* * *
53575041 AGGGTAAAATGGTAAATTTTGGTGAAATC-AGGGTTAAAAATGGGATTT
1 GGGGGAAAATGGT-AATTTTGGTGAAATCGA-GGTTAAAAATGGAATTT
53575089 AGGGAAGTTT
Statistics
Matches: 89, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
57 19 0.21
58 34 0.38
59 26 0.29
60 10 0.11
ACGTcount: A:0.35, C:0.05, G:0.29, T:0.30
Consensus pattern (57 bp):
GGGGGAAAATGGTAATTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAAAGATTCG
Found at i:53574992 original size:29 final size:27
Alignment explanation
Indices: 53574960--53575052 Score: 87
Period size: 30 Copynumber: 3.3 Consensus size: 27
53574950 ATCGAGGTTA
53574960 AAAATGGAATTTTAAAAGATTCGGGGGGT
1 AAAATGGAATTTT-AAAGATTC-GGGGGT
* * ** *
53574989 AAAATGGTAATTTTCGATGAAACCGGGGTT
1 AAAATGG-AATTTT-AAAG-ATTCGGGGGT
*
53575019 AAAATGGAATTTTAAAGATTCGAGGGT
1 AAAATGGAATTTTAAAGATTCGGGGGT
53575046 AAAATGG
1 AAAATGG
53575053 TAAATTTTGG
Statistics
Matches: 50, Mismatches: 12, Indels: 6
0.74 0.18 0.09
Matches are distributed among these distances:
27 13 0.26
28 2 0.04
29 13 0.26
30 20 0.40
31 2 0.04
ACGTcount: A:0.39, C:0.05, G:0.28, T:0.28
Consensus pattern (27 bp):
AAAATGGAATTTTAAAGATTCGGGGGT
Done.