Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 69 of 132
Found at i:19703465 original size:29 final size:30
Alignment explanation
Indices: 19703402--19703476 Score: 75
Period size: 30 Copynumber: 2.5 Consensus size: 30
19703392 CTCTCAAATT
*
19703402 TTTTTAATATTTTTTCTTCAAAATTTTATTC
1 TTTTTAATATTTTTTCCTCAAAATTTTA-TC
19703433 TTTTT-AT-TTTTTTCCCTCAAAATTTTA-C
1 TTTTTAATATTTTTT-CCTCAAAATTTTATC
* *
19703461 ATTTTCAAAATTTTTT
1 -TTTTTAATATTTTTT
19703477 GTTTTTTCCC
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
28 1 0.03
29 10 0.27
30 15 0.41
31 11 0.30
ACGTcount: A:0.25, C:0.12, G:0.00, T:0.63
Consensus pattern (30 bp):
TTTTTAATATTTTTTCCTCAAAATTTTATC
Found at i:19703912 original size:18 final size:17
Alignment explanation
Indices: 19703889--19703959 Score: 52
Period size: 18 Copynumber: 3.9 Consensus size: 17
19703879 CAATTTCACA
19703889 TTTTATTTTTAAAATAAT
1 TTTTA-TTTTAAAATAAT
**
19703907 TTTTATTAAAAAATAATAT
1 TTTTATTTTAAAAT-A-AT
* * *
19703926 TTTTACATTTAATATATT
1 TTTTA-TTTTAAAATAAT
19703944 TTTTAATTTTAAAATA
1 TTTT-ATTTTAAAATA
19703960 CATAGTTACA
Statistics
Matches: 40, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
17 7 0.17
18 19 0.47
19 9 0.22
20 5 0.12
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTATTTTAAAATAAT
Found at i:19707282 original size:28 final size:27
Alignment explanation
Indices: 19707251--19707338 Score: 113
Period size: 28 Copynumber: 3.1 Consensus size: 27
19707241 AAAGCCATAT
19707251 AGGCGTCCTTAAACAAAGATAGCCACAA
1 AGGCGTCCTTAAACAAAG-TAGCCACAA
*
19707279 AGGCATCCTTAAACAAAGGTAGCCACAA
1 AGGCGTCCTTAAACAAA-GTAGCCACAA
* * *
19707307 ATGCGTCCTTAAATAGATGTAGCCACAA
1 AGGCGTCCTTAAACA-AAGTAGCCACAA
19707335 AGGC
1 AGGC
19707339 TCTCTTTTCG
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
28 50 0.96
29 2 0.04
ACGTcount: A:0.40, C:0.24, G:0.19, T:0.17
Consensus pattern (27 bp):
AGGCGTCCTTAAACAAAGTAGCCACAA
Found at i:19710756 original size:27 final size:27
Alignment explanation
Indices: 19710683--19710821 Score: 63
Period size: 27 Copynumber: 4.9 Consensus size: 27
19710673 AGAATAGACA
*
19710683 AAAATAAATAAGATAAAGAGATAAATAAT
1 AAAATAAATAAAATAAAGA-ATAAA-AAT
* * * **
19710712 -CAA-AGATAAATTTCAGAATAAAAAT
1 AAAATAAATAAAATAAAGAATAAAAAT
*
19710737 AAAATAAATAAAATAAAGAAGACTCATAAAT
1 AAAATAAATAAAATAAAG-A-A-T-AAAAAT
*
19710768 AAAATAAA-AACAACT-AACAATAAAAAT
1 AAAATAAATAA-AA-TAAAGAATAAAAAT
19710795 AAAAGTACAACTGAAAATAAA-AATAAA
1 AAAA-TA-AA-T-AAAATAAAGAATAAA
19710822 TAAAGTAGAA
Statistics
Matches: 82, Mismatches: 14, Indels: 27
0.67 0.11 0.22
Matches are distributed among these distances:
25 3 0.04
26 7 0.09
27 27 0.33
28 6 0.07
29 4 0.05
30 11 0.13
31 21 0.26
32 3 0.04
ACGTcount: A:0.68, C:0.06, G:0.06, T:0.19
Consensus pattern (27 bp):
AAAATAAATAAAATAAAGAATAAAAAT
Found at i:19710813 original size:24 final size:21
Alignment explanation
Indices: 19710764--19710821 Score: 73
Period size: 24 Copynumber: 2.6 Consensus size: 21
19710754 GAAGACTCAT
19710764 AAAT-AAAATAAAAACAACTA
1 AAATAAAAATAAAAACAACTA
19710784 ACAATAAAAATAAAAGTACAACTGA
1 A-AATAAAAATAAAA--ACAACT-A
19710809 AAATAAAAATAAA
1 AAATAAAAATAAA
19710822 TAAAGTAGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
20 1 0.03
21 3 0.09
22 9 0.27
24 18 0.55
25 2 0.06
ACGTcount: A:0.72, C:0.09, G:0.03, T:0.16
Consensus pattern (21 bp):
AAATAAAAATAAAAACAACTA
Found at i:19712245 original size:21 final size:21
Alignment explanation
Indices: 19712226--19712276 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
19712216 TATTTATTTG
19712226 TTTATATTAGTGTTTAATTTTA
1 TTTAT-TTAGTGTTTAATTTTA
* *
19712248 TTTATTTATTGTTT-ATTTATT
1 TTTATTTAGTGTTTAATTT-TA
19712269 TTTATTTA
1 TTTATTTA
19712277 CTTATATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 4 0.15
21 17 0.65
22 5 0.19
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (21 bp):
TTTATTTAGTGTTTAATTTTA
Found at i:19712274 original size:10 final size:10
Alignment explanation
Indices: 19712204--19712276 Score: 51
Period size: 10 Copynumber: 6.9 Consensus size: 10
19712194 TCCCTGTTAC
19712204 TTTTA-TTAT
1 TTTTATTTAT
*
19712213 TTGTATTTATT
1 TTTTATTTA-T
19712224 TGTTTATATTAGT
1 T-TTTAT-TTA-T
*
19712237 GTTTAATTT-T
1 -TTTTATTTAT
*
19712247 ATTTATTTAT
1 TTTTATTTAT
19712257 TGTTTATTTAT
1 T-TTTATTTAT
19712268 TTTTATTTA
1 TTTTATTTA
19712277 CTTATATATT
Statistics
Matches: 50, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
9 10 0.20
10 13 0.26
11 12 0.24
12 6 0.12
13 8 0.16
14 1 0.02
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.71
Consensus pattern (10 bp):
TTTTATTTAT
Found at i:19712286 original size:29 final size:30
Alignment explanation
Indices: 19712244--19712305 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
19712234 AGTGTTTAAT
* *
19712244 TTTATTTATTTATTGTT-TATTTATT-TTTA
1 TTTACTTATATATTGTTAT-TTTATTCTTTA
19712273 TTTACTTATATATTGTTATTTTATTCTTTA
1 TTTACTTATATATTGTTATTTTATTCTTTA
19712303 TTT
1 TTT
19712306 TTTTGCATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 21 0.72
30 8 0.28
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.73
Consensus pattern (30 bp):
TTTACTTATATATTGTTATTTTATTCTTTA
Found at i:19712526 original size:19 final size:21
Alignment explanation
Indices: 19712502--19712547 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
19712492 ATCATTATAA
*
19712502 TTATTTT-TAT-TGTTATTTT
1 TTATTTTGTATGTGTTATTTC
*
19712521 TTATTTTGTTTGTGTTATTTC
1 TTATTTTGTATGTGTTATTTC
19712542 TTATTT
1 TTATTT
19712548 ATGTTATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 7 0.30
20 2 0.09
21 14 0.61
ACGTcount: A:0.13, C:0.02, G:0.09, T:0.76
Consensus pattern (21 bp):
TTATTTTGTATGTGTTATTTC
Found at i:19712538 original size:21 final size:22
Alignment explanation
Indices: 19712512--19712552 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
19712502 TTATTTTTAT
*
19712512 TGTTATTTTTTATTT-TGTTTG
1 TGTTATTTCTTATTTATGTTTG
19712533 TGTTATTTCTTATTTATGTT
1 TGTTATTTCTTATTTATGTT
19712553 ATTTATCTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.12, C:0.02, G:0.12, T:0.73
Consensus pattern (22 bp):
TGTTATTTCTTATTTATGTTTG
Found at i:19728722 original size:15 final size:14
Alignment explanation
Indices: 19728704--19728748 Score: 58
Period size: 12 Copynumber: 3.3 Consensus size: 14
19728694 AAAAAGAGAA
19728704 AAGAGAAGAAGAAGG
1 AAGAGAAGAA-AAGG
19728719 AAGAGAAGAAAAGG
1 AAGAGAAGAAAAGG
*
19728733 AA-A-AAGAAAATG
1 AAGAGAAGAAAAGG
19728745 AAGA
1 AAGA
19728749 ATATTTTGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 10 0.36
13 2 0.07
14 6 0.21
15 10 0.36
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (14 bp):
AAGAGAAGAAAAGG
Found at i:19739519 original size:14 final size:13
Alignment explanation
Indices: 19739502--19739559 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
19739492 TTGCAATATA
19739502 TTTTTTTC-TTCT
1 TTTTTTTCTTTCT
19739514 CTTTTTTTC-TT-T
1 -TTTTTTTCTTTCT
* *
19739526 TTCTTTGCTTTCT
1 TTTTTTTCTTTCT
*
19739539 TTTTCTTCTTCTCT
1 TTTTTTTCTT-TCT
19739553 TTTTTTT
1 TTTTTTT
19739560 GTACGTGACT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
11 6 0.17
12 3 0.08
13 18 0.50
14 9 0.25
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (13 bp):
TTTTTTTCTTTCT
Found at i:19740161 original size:17 final size:17
Alignment explanation
Indices: 19740141--19740183 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
19740131 AAATGAACTA
* *
19740141 ACAAGTAAAATGCAACG
1 ACAACTAAAACGCAACG
*
19740158 ACAACTAAAACGCAATG
1 ACAACTAAAACGCAACG
*
19740175 ACAATTAAA
1 ACAACTAAA
19740184 TGAGATGCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.56, C:0.19, G:0.12, T:0.14
Consensus pattern (17 bp):
ACAACTAAAACGCAACG
Found at i:19740585 original size:15 final size:15
Alignment explanation
Indices: 19740567--19740617 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
19740557 CATCTACATC
19740567 CTCTTCATCCTTCTT
1 CTCTTCATCCTTCTT
* *
19740582 CTCTTCCTCCTTCTC
1 CTCTTCATCCTTCTT
*
19740597 CTCTTCAGTTCTT-TT
1 CTCTTCA-TCCTTCTT
19740612 CTCTTC
1 CTCTTC
19740618 CTCAAGGTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
15 26 0.87
16 4 0.13
ACGTcount: A:0.04, C:0.41, G:0.02, T:0.53
Consensus pattern (15 bp):
CTCTTCATCCTTCTT
Found at i:19744938 original size:43 final size:43
Alignment explanation
Indices: 19744889--19744984 Score: 147
Period size: 43 Copynumber: 2.2 Consensus size: 43
19744879 TTTGAAAAAG
* * *
19744889 CGCCGCTAAAGAACATGGTCTTCAGTGGCGCTTTTCCCACAAA
1 CGCCGCTAAAGAACATGGTCTTCAGCGACGCTTTCCCCACAAA
*
19744932 CGCCGCTAAAGAACATGGTCTTTAGCGACGCTTTCCCCACAAA
1 CGCCGCTAAAGAACATGGTCTTCAGCGACGCTTTCCCCACAAA
*
19744975 CGCCACTAAA
1 CGCCGCTAAA
19744985 ATTAACAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.28, C:0.32, G:0.19, T:0.21
Consensus pattern (43 bp):
CGCCGCTAAAGAACATGGTCTTCAGCGACGCTTTCCCCACAAA
Found at i:19746674 original size:19 final size:19
Alignment explanation
Indices: 19746620--19746681 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
19746610 TTTGTTAATT
*
19746620 TTTTTTATAATTTTTTATG-
1 TTTTTTATTA-TTTTTATGA
*
19746639 TTTTATGTA-TATATTTATGA
1 TTTT-T-TATTATTTTTATGA
*
19746659 TTTTTTATTATTTTTATAA
1 TTTTTTATTATTTTTATGA
19746678 TTTT
1 TTTT
19746682 CTCTATTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
18 2 0.06
19 25 0.71
20 6 0.17
21 2 0.06
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (19 bp):
TTTTTTATTATTTTTATGA
Found at i:19747696 original size:26 final size:26
Alignment explanation
Indices: 19747642--19747712 Score: 117
Period size: 26 Copynumber: 2.8 Consensus size: 26
19747632 AGATTTGACC
*
19747642 CTTGACCTTTCACCTACT-AAAAACT
1 CTTGATCTTTCACCTACTAAAAAACT
*
19747667 CTTGATCTTTCATCTACTAAAAAACT
1 CTTGATCTTTCACCTACTAAAAAACT
19747693 CTTGATCTTTCACCTACTAA
1 CTTGATCTTTCACCTACTAA
19747713 CTACTAAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
25 16 0.38
26 26 0.62
ACGTcount: A:0.31, C:0.28, G:0.04, T:0.37
Consensus pattern (26 bp):
CTTGATCTTTCACCTACTAAAAAACT
Found at i:19752077 original size:26 final size:26
Alignment explanation
Indices: 19752010--19752079 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 26
19752000 AGATTTGACC
* *
19752010 CTTGACCTTTCACCTGCT-AAAAACT
1 CTTGATCTTTCACCTACTAAAAAACT
**
19752035 CTT-ATCTTTCATATACTAAAAAACT
1 CTTGATCTTTCACCTACTAAAAAACT
*
19752060 CTTGATCTTCCACCTACTAA
1 CTTGATCTTTCACCTACTAA
19752080 CTACTAAATT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
24 10 0.28
25 13 0.36
26 13 0.36
ACGTcount: A:0.31, C:0.29, G:0.04, T:0.36
Consensus pattern (26 bp):
CTTGATCTTTCACCTACTAAAAAACT
Found at i:19756602 original size:41 final size:41
Alignment explanation
Indices: 19756540--19756650 Score: 177
Period size: 41 Copynumber: 2.7 Consensus size: 41
19756530 ATAAGCGCGA
* *
19756540 CGCTTTCCCATAAGCGCCGCTATTGCTCTGATCTTTAGCAT
1 CGCTTTCCCATAAGCGTCGCTATTGCTCTGATCTTTAGCAG
* *
19756581 TGCTTTCCCATAAGCGTCGCTATTGCTCTGATCTTTAGCGG
1 CGCTTTCCCATAAGCGTCGCTATTGCTCTGATCTTTAGCAG
*
19756622 CGCTTTTCCATAAGCGTCGCTATTGCTCT
1 CGCTTTCCCATAAGCGTCGCTATTGCTCT
19756651 ACCTTTTACG
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 64 1.00
ACGTcount: A:0.15, C:0.30, G:0.19, T:0.36
Consensus pattern (41 bp):
CGCTTTCCCATAAGCGTCGCTATTGCTCTGATCTTTAGCAG
Found at i:19765761 original size:90 final size:90
Alignment explanation
Indices: 19765608--19765788 Score: 353
Period size: 90 Copynumber: 2.0 Consensus size: 90
19765598 TCATTGCTCA
19765608 CACCGAGAGGTGGAGTAGTGTATTTGAGTCGGGATTAAGTAGGGAGCTATTCTGGGTAAGAACTC
1 CACCGAGAGGTGGAGTAGTGTATTTGAGTCGGGATTAAGTAGGGAGCTATTCTGGGTAAGAACTC
*
19765673 AAAGGGACTTCATTGGAGTGACATT
66 AAAGGGACTTCATTGGAGCGACATT
19765698 CACCGAGAGGTGGAGTAGTGTATTTGAGTCGGGATTAAGTAGGGAGCTATTCTGGGTAAGAACTC
1 CACCGAGAGGTGGAGTAGTGTATTTGAGTCGGGATTAAGTAGGGAGCTATTCTGGGTAAGAACTC
19765763 AAAGGGACTTCATTGGAGCGACATT
66 AAAGGGACTTCATTGGAGCGACATT
19765788 C
1 C
19765789 CATCTATATT
Statistics
Matches: 90, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 90 1.00
ACGTcount: A:0.28, C:0.13, G:0.33, T:0.26
Consensus pattern (90 bp):
CACCGAGAGGTGGAGTAGTGTATTTGAGTCGGGATTAAGTAGGGAGCTATTCTGGGTAAGAACTC
AAAGGGACTTCATTGGAGCGACATT
Found at i:19767680 original size:24 final size:23
Alignment explanation
Indices: 19767643--19767689 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
19767633 AAGAGTTAGT
* *
19767643 TTGTCAACATAAATATAAAATAAA
1 TTGTCAAAAAAAAT-TAAAATAAA
*
19767667 TTGTCAAAAAAAATTAAGATAAA
1 TTGTCAAAAAAAATTAAAATAAA
19767690 ATGAATAGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.60, C:0.06, G:0.06, T:0.28
Consensus pattern (23 bp):
TTGTCAAAAAAAATTAAAATAAA
Found at i:19767847 original size:11 final size:11
Alignment explanation
Indices: 19767831--19767876 Score: 56
Period size: 11 Copynumber: 3.9 Consensus size: 11
19767821 CCTCAATCAC
19767831 ATATATAATAT
1 ATATATAATAT
19767842 ATATATAATAT
1 ATATATAATAT
*
19767853 ATATGTATATATT
1 ATATATA-ATA-T
19767866 ATTATATAATA
1 A-TATATAATA
19767877 AATGTTGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 17 0.57
12 3 0.10
13 5 0.17
14 5 0.17
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (11 bp):
ATATATAATAT
Found at i:19772989 original size:21 final size:21
Alignment explanation
Indices: 19772965--19773018 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
19772955 AACACCACAT
*
19772965 ACGCCCGTGTGTGATGGGCAC
1 ACGCCCGTGTGTGATGGGAAC
*
19772986 ACGCTCGTGTGTGATGGGAAC
1 ACGCCCGTGTGTGATGGGAAC
*
19773007 ATGCCCGTGTGT
1 ACGCCCGTGTGT
19773019 CACCCTACTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.15, C:0.24, G:0.37, T:0.24
Consensus pattern (21 bp):
ACGCCCGTGTGTGATGGGAAC
Found at i:19793372 original size:36 final size:36
Alignment explanation
Indices: 19793331--19793413 Score: 166
Period size: 36 Copynumber: 2.3 Consensus size: 36
19793321 CAATCTCAAC
19793331 CATTCATCCAAAAATAGAAGATACAACATTCAATCA
1 CATTCATCCAAAAATAGAAGATACAACATTCAATCA
19793367 CATTCATCCAAAAATAGAAGATACAACATTCAATCA
1 CATTCATCCAAAAATAGAAGATACAACATTCAATCA
19793403 CATTCATCCAA
1 CATTCATCCAA
19793414 TTCATTCATT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.48, C:0.24, G:0.05, T:0.23
Consensus pattern (36 bp):
CATTCATCCAAAAATAGAAGATACAACATTCAATCA
Found at i:19812351 original size:21 final size:21
Alignment explanation
Indices: 19812327--19812367 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
19812317 TTTATGCTAA
19812327 TGTTTAATTT-TATTTATTTAT
1 TGTTT-ATTTATATTTATTTAT
*
19812348 TGTTTATTTATTTTTATTTA
1 TGTTTATTTATATTTATTTA
19812368 CTTATATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.22, C:0.00, G:0.05, T:0.73
Consensus pattern (21 bp):
TGTTTATTTATATTTATTTAT
Found at i:19812410 original size:16 final size:17
Alignment explanation
Indices: 19812379--19812411 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
19812369 TTATATATTG
*
19812379 TTATTTTATGCTTTTTT
1 TTATTTCATGCTTTTTT
19812396 TTATTTCAT-CTTTTTT
1 TTATTTCATGCTTTTTT
19812412 ACCTTTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.12, C:0.09, G:0.03, T:0.76
Consensus pattern (17 bp):
TTATTTCATGCTTTTTT
Found at i:19812661 original size:21 final size:20
Alignment explanation
Indices: 19812608--19812663 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
19812598 ATTATAATTA
*
19812608 TTTTTATTTTATTTTTTATT
1 TTTTTATTTTATTTCTTATT
** *
19812628 TTGTTCGTGTTATTTCTTATT
1 TT-TTTATTTTATTTCTTATT
19812649 TATTTTATTTTATTT
1 T-TTTTATTTTATTT
19812664 ATCTTATATT
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
20 2 0.07
21 24 0.89
22 1 0.04
ACGTcount: A:0.14, C:0.04, G:0.05, T:0.77
Consensus pattern (20 bp):
TTTTTATTTTATTTCTTATT
Found at i:19815304 original size:19 final size:20
Alignment explanation
Indices: 19815280--19815319 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
19815270 ATAATCATGT
*
19815280 CAATGCACATATTGT-AAAA
1 CAATGCAAATATTGTGAAAA
*
19815299 CAATGCAAATTTTGTGAAAA
1 CAATGCAAATATTGTGAAAA
19815319 C
1 C
19815320 GGTCCAACCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (20 bp):
CAATGCAAATATTGTGAAAA
Found at i:19817927 original size:3 final size:3
Alignment explanation
Indices: 19817919--19817959 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
19817909 TGATAAGAAT
*
19817919 AAC AAC AAC AAC AAC AAC AAT AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
19817960 TAATAATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.68, C:0.29, G:0.00, T:0.02
Consensus pattern (3 bp):
AAC
Found at i:19817964 original size:3 final size:3
Alignment explanation
Indices: 19817958--19817983 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
19817948 CAACAACAAC
19817958 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
19817984 AGAAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:19820595 original size:10 final size:10
Alignment explanation
Indices: 19820580--19820626 Score: 58
Period size: 10 Copynumber: 4.5 Consensus size: 10
19820570 GTGTGGTCCC
19820580 TTTTTTCAAT
1 TTTTTTCAAT
*
19820590 TTTTTTGAAT
1 TTTTTTCAAT
*
19820600 TTTTTTGAATT
1 TTTTTTCAA-T
19820611 TTTTTTCTAAT
1 TTTTTTC-AAT
19820622 TTTTT
1 TTTTT
19820627 ATGATTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
10 18 0.55
11 13 0.39
12 2 0.06
ACGTcount: A:0.17, C:0.04, G:0.04, T:0.74
Consensus pattern (10 bp):
TTTTTTCAAT
Found at i:19820614 original size:22 final size:22
Alignment explanation
Indices: 19820589--19820637 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
19820579 CTTTTTTCAA
*
19820589 TTTTTTT-GAATTTTTT-TGAAT
1 TTTTTTTCTAATTTTTTATG-AT
19820610 TTTTTTTCTAATTTTTTATGAT
1 TTTTTTTCTAATTTTTTATGAT
19820632 TTTTTT
1 TTTTTT
19820638 AAGTAATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 7 0.28
22 16 0.64
23 2 0.08
ACGTcount: A:0.16, C:0.02, G:0.06, T:0.76
Consensus pattern (22 bp):
TTTTTTTCTAATTTTTTATGAT
Found at i:19820644 original size:23 final size:22
Alignment explanation
Indices: 19820580--19820638 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
19820570 GTGTGGTCCC
* *
19820580 TTTTTTCAATTTTTTT--GAAT
1 TTTTTTGAATTTTTTTACTAAT
*
19820600 TTTTTTGAATTTTTTTTCTAAT
1 TTTTTTGAATTTTTTTACTAAT
19820622 TTTTTATG-ATTTTTTTA
1 TTTTT-TGAATTTTTTTA
19820639 AGTAATAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 15 0.45
22 16 0.48
23 2 0.06
ACGTcount: A:0.19, C:0.03, G:0.05, T:0.73
Consensus pattern (22 bp):
TTTTTTGAATTTTTTTACTAAT
Found at i:19820713 original size:17 final size:20
Alignment explanation
Indices: 19820677--19820716 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 20
19820667 TTATTTTTTA
19820677 AAATAACATGAAAGTAAAAT
1 AAATAACATGAAAGTAAAAT
19820697 AAATAA-AT-AAA-TAAAAT
1 AAATAACATGAAAGTAAAAT
19820714 AAA
1 AAA
19820717 AAAAACTCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 9 0.45
18 3 0.15
19 2 0.10
20 6 0.30
ACGTcount: A:0.72, C:0.03, G:0.05, T:0.20
Consensus pattern (20 bp):
AAATAACATGAAAGTAAAAT
Found at i:19827867 original size:31 final size:31
Alignment explanation
Indices: 19827824--19827883 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
19827814 GATTTGATTT
*
19827824 GATTTTATTTTAAAATAATATTT-TTATTAA
1 GATTTAATTTTAAAATAATATTTATTATTAA
* *
19827854 GATTTAATATTTAAGATATTATTTATTATT
1 GATTTAAT-TTTAAAATAATATTTATTATT
19827884 TAAATTTGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 7 0.28
31 13 0.52
32 5 0.20
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (31 bp):
GATTTAATTTTAAAATAATATTTATTATTAA
Found at i:19827877 original size:19 final size:19
Alignment explanation
Indices: 19827855--19827899 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
19827845 TTTTATTAAG
19827855 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
19827874 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
19827893 ATTTAAT
1 ATTTAAT
19827900 TCATATTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:19827922 original size:14 final size:14
Alignment explanation
Indices: 19827903--19827929 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19827893 ATTTAATTCA
19827903 TATTTATCTTTTTG
1 TATTTATCTTTTTG
19827917 TATTTATCTTTTT
1 TATTTATCTTTTT
19827930 AGGGTTTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.07, G:0.04, T:0.74
Consensus pattern (14 bp):
TATTTATCTTTTTG
Found at i:19831066 original size:12 final size:12
Alignment explanation
Indices: 19831051--19831090 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
19831041 CTTAAACCCT
*
19831051 TTCTTCCCTTCC
1 TTCTTCACTTCC
19831063 TTCTTCACTTCC
1 TTCTTCACTTCC
* *
19831075 TTTTTGACTTCC
1 TTCTTCACTTCC
19831087 TTCT
1 TTCT
19831091 CCACCCCAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.05, C:0.38, G:0.03, T:0.55
Consensus pattern (12 bp):
TTCTTCACTTCC
Found at i:19842415 original size:62 final size:62
Alignment explanation
Indices: 19842318--19842459 Score: 196
Period size: 62 Copynumber: 2.3 Consensus size: 62
19842308 AATTTGAGGA
* * *
19842318 TTTAGGTTTTAAAAATTTTGGGATTTTCGAGATTTTTAGGGTTGTTGGGTTTGGGGAATTTGG
1 TTTAGG-TTTAAAAATTTGGGGATTTTCGAGATTTTTAGGGTTGTTGGGTTTGGAGAAATTGG
* *
19842381 TTTAGGTTTAAGAAATTTGGGGA-TTTCGGGATTTTTGGGGTTGTTGGGTTTGGAGAAATTGG
1 TTTAGGTTTAA-AAATTTGGGGATTTTCGAGATTTTTAGGGTTGTTGGGTTTGGAGAAATTGG
**
19842443 TTTAAATTTAAAAATTT
1 TTTAGGTTTAAAAATTT
19842460 TACGATTTTT
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
61 6 0.08
62 49 0.69
63 16 0.23
ACGTcount: A:0.23, C:0.01, G:0.30, T:0.46
Consensus pattern (62 bp):
TTTAGGTTTAAAAATTTGGGGATTTTCGAGATTTTTAGGGTTGTTGGGTTTGGAGAAATTGG
Found at i:19843688 original size:22 final size:22
Alignment explanation
Indices: 19843644--19843688 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
19843634 TGTTTAATAA
*
19843644 TGTTTAATCGATGTTTCTATTT
1 TGTTTAATCGATGTTGCTATTT
*
19843666 TGTTTAATCGATGTTGCTGTTT
1 TGTTTAATCGATGTTGCTATTT
19843688 T
1 T
19843689 ACCGAGAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.16, C:0.09, G:0.18, T:0.58
Consensus pattern (22 bp):
TGTTTAATCGATGTTGCTATTT
Found at i:19845568 original size:162 final size:161
Alignment explanation
Indices: 19845234--19845617 Score: 608
Period size: 162 Copynumber: 2.4 Consensus size: 161
19845224 TTAAATTTAA
* * * * *
19845234 ATAATTTGGAATTGACAATGAGAAAGTGTTTACGAGATACCTGTGATCCAGTTGTGTTAGACTGA
1 ATAATTTGGAATTGACAATGAGAAAGTGTTTACAATATACCTGTGTTCCCGTTGTGTTAGGCTGA
*
19845299 ATGCATGGTGATGTTCTGTCGTTCTTTCTTTGGGTTGTAGTTCTCGTACTCGTACCAGACTAAGA
66 ATGCATGGTGATGTTCTGTCGTTCTTTCTTTAGGTTGTAGTTCTCGTACTCGTACCAGACTAAGA
19845364 CACAAAAAATCAAAACGAAAATTAGATTATT
131 CACAAAAAATCAAAACGAAAATTAGATTATT
19845395 ATAATTTGGAATTGACAATGAGAAAGTGTTTACAATATACCTGTGTTCCCGTTGTGTTAGGCTGA
1 ATAATTTGGAATTGACAATGAGAAAGTGTTTACAATATACCTGTGTTCCCGTTGTGTTAGGCTGA
* * * *
19845460 TTGCATGGTGGTGTTCTGTCGTTATTTTTTTTAGGTTGTAGTTCTCGTACTCGTACCAGACTAAG
66 ATGCATGGTGATGTTCTGTCGTT-CTTTCTTTAGGTTGTAGTTCTCGTACTCGTACCAGACTAAG
*
19845525 ACATAAAAAATCAAAACTG-AAATTAGATTATT
130 ACACAAAAAATCAAAAC-GAAAATTAGATTATT
* * **
19845557 ATAATTTGGAATTGACAATGAGAAAGTGTTTACAGTATACCTATGTTTTCGTTGTGTTAGG
1 ATAATTTGGAATTGACAATGAGAAAGTGTTTACAATATACCTGTGTTCCCGTTGTGTTAGG
19845618 ATCTTGTTTG
Statistics
Matches: 206, Mismatches: 15, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
161 81 0.39
162 124 0.60
163 1 0.00
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (161 bp):
ATAATTTGGAATTGACAATGAGAAAGTGTTTACAATATACCTGTGTTCCCGTTGTGTTAGGCTGA
ATGCATGGTGATGTTCTGTCGTTCTTTCTTTAGGTTGTAGTTCTCGTACTCGTACCAGACTAAGA
CACAAAAAATCAAAACGAAAATTAGATTATT
Found at i:19846584 original size:36 final size:36
Alignment explanation
Indices: 19846541--19846625 Score: 134
Period size: 36 Copynumber: 2.4 Consensus size: 36
19846531 GACCCTGCAA
19846541 TTTAAATTAAAAAACATAAGTAAGTATGCTATCAAT
1 TTTAAATTAAAAAACATAAGTAAGTATGCTATCAAT
* * * *
19846577 TTTAAATTTAAAAACATAAGTACGTCTGCTGTCAAT
1 TTTAAATTAAAAAACATAAGTAAGTATGCTATCAAT
19846613 TTTAAATTAAAAA
1 TTTAAATTAAAAA
19846626 CAGAACACTA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.35
Consensus pattern (36 bp):
TTTAAATTAAAAAACATAAGTAAGTATGCTATCAAT
Found at i:19849026 original size:9 final size:9
Alignment explanation
Indices: 19849014--19849044 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
19849004 CCACCTCCTT
19849014 CACCCTCAA
1 CACCCTCAA
19849023 CACCCTCAA
1 CACCCTCAA
*
19849032 CATCCTCAA
1 CACCCTCAA
19849041 CACC
1 CACC
19849045 TTCACTAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.32, C:0.55, G:0.00, T:0.13
Consensus pattern (9 bp):
CACCCTCAA
Found at i:19849072 original size:72 final size:72
Alignment explanation
Indices: 19848955--19849098 Score: 216
Period size: 72 Copynumber: 2.0 Consensus size: 72
19848945 CACCCTGACA
* * * * *
19848955 CTCAACACCCTCAACACCTTCAATAACAGTACCTTTACCTGAACCCTTACCACCTCCTTCACCCT
1 CTCAACACCCTCAACACCTTCAATAACAGCACCCTTACCCGAACCCTCACCACCTCCCTCACCCT
19849020 CAACACC
66 CAACACC
* * *
19849027 CTCAACATCCTCAACACCTTCACTAATAGCACCCTTACCCGAACCCTCACCACCTCCCTCACCCT
1 CTCAACACCCTCAACACCTTCAATAACAGCACCCTTACCCGAACCCTCACCACCTCCCTCACCCT
19849092 CAACACC
66 CAACACC
19849099 TTCACTAACA
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
72 64 1.00
ACGTcount: A:0.28, C:0.49, G:0.03, T:0.20
Consensus pattern (72 bp):
CTCAACACCCTCAACACCTTCAATAACAGCACCCTTACCCGAACCCTCACCACCTCCCTCACCCT
CAACACC
Found at i:19849073 original size:54 final size:52
Alignment explanation
Indices: 19849015--19849170 Score: 190
Period size: 54 Copynumber: 2.9 Consensus size: 52
19849005 CACCTCCTTC
*
19849015 ACCCTCAACACCCTCAACATCCTCAACACCTTCACTAATAGCACCCTTACCCGA
1 ACCCTCAACACCCTC-ACA-CCTCAACACCTTCACTAACAGCACCCTTACCCGA
*
19849069 ACCCTCACCACCTCCCTCAC-CCTCAACACCTTCACTAACAGCACCCTTACCCGA
1 ACCCTCA--A-CACCCTCACACCTCAACACCTTCACTAACAGCACCCTTACCCGA
* *
19849123 ACCCTCACCACTTCCCTCAC-CCTCAACACCTTCACTAACAGTACCCTT
1 ACCCTCA--AC-ACCCTCACACCTCAACACCTTCACTAACAGCACCCTT
19849171 GCCCTTACCC
Statistics
Matches: 95, Mismatches: 3, Indels: 8
0.90 0.03 0.08
Matches are distributed among these distances:
53 1 0.01
54 85 0.89
56 3 0.03
57 6 0.06
ACGTcount: A:0.28, C:0.50, G:0.03, T:0.19
Consensus pattern (52 bp):
ACCCTCAACACCCTCACACCTCAACACCTTCACTAACAGCACCCTTACCCGA
Found at i:19849181 original size:6 final size:6
Alignment explanation
Indices: 19849172--19849205 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
19849162 AGTACCCTTG
*
19849172 CCCTTA CCCTCA CCCTCA CCCTCA CCCTCA CCCT
1 CCCTCA CCCTCA CCCTCA CCCTCA CCCTCA CCCT
19849206 TACCACCTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.15, C:0.65, G:0.00, T:0.21
Consensus pattern (6 bp):
CCCTCA
Found at i:19849181 original size:54 final size:54
Alignment explanation
Indices: 19849035--19849201 Score: 255
Period size: 54 Copynumber: 3.1 Consensus size: 54
19849025 CCCTCAACAT
* *
19849035 CCTCAACACCTTCACTAATAGCACCCTTACCCGAACCCTCACCACCTCCCTCAC
1 CCTCAACACCTTCACTAACAGCACCCTTACCCGAACCCTCACCACTTCCCTCAC
19849089 CCTCAACACCTTCACTAACAGCACCCTTACCCGAACCCTCACCACTTCCCTCAC
1 CCTCAACACCTTCACTAACAGCACCCTTACCCGAACCCTCACCACTTCCCTCAC
* * ** *
19849143 CCTCAACACCTTCACTAACAGTACCCTTGCCCTTACCCTCACC-CTCACCCTCAC
1 CCTCAACACCTTCACTAACAGCACCCTTACCCGAACCCTCACCACT-TCCCTCAC
19849197 CCTCA
1 CCTCA
19849202 CCCTTACCAC
Statistics
Matches: 105, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
53 2 0.02
54 103 0.98
ACGTcount: A:0.25, C:0.52, G:0.04, T:0.20
Consensus pattern (54 bp):
CCTCAACACCTTCACTAACAGCACCCTTACCCGAACCCTCACCACTTCCCTCAC
Found at i:19849968 original size:57 final size:57
Alignment explanation
Indices: 19849875--19850002 Score: 220
Period size: 57 Copynumber: 2.2 Consensus size: 57
19849865 CAACCAGCAG
19849875 ACATGTCAAATATATAAATTACCAAGTTTTAAATTAATACAATTCAATAAATTATCA
1 ACATGTCAAATATATAAATTACCAAGTTTTAAATTAATACAATTCAATAAATTATCA
* * *
19849932 ACATATCAAATATATAAATTACCAATTTTTAAATTAATACGATTCAATAAATTATCA
1 ACATGTCAAATATATAAATTACCAAGTTTTAAATTAATACAATTCAATAAATTATCA
*
19849989 ACACGTCAAATATA
1 ACATGTCAAATATA
19850003 AATTATAGCA
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 66 1.00
ACGTcount: A:0.49, C:0.13, G:0.03, T:0.34
Consensus pattern (57 bp):
ACATGTCAAATATATAAATTACCAAGTTTTAAATTAATACAATTCAATAAATTATCA
Found at i:19850003 original size:22 final size:24
Alignment explanation
Indices: 19849978--19850026 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 24
19849968 ATACGATTCA
19849978 ATAAATTAT-CA-ACACGTCAAAT
1 ATAAATTATACAGACACGTCAAAT
*
19850000 ATAAATTATAGCAGACATGTCAAAT
1 ATAAATTATA-CAGACACGTCAAAT
19850025 AT
1 AT
19850027 TTAAATTACC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 9 0.39
24 2 0.09
25 12 0.52
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.29
Consensus pattern (24 bp):
ATAAATTATACAGACACGTCAAAT
Found at i:19850079 original size:82 final size:79
Alignment explanation
Indices: 19849921--19850084 Score: 256
Period size: 82 Copynumber: 2.0 Consensus size: 79
19849911 ATACAATTCA
* *
19849921 ATAAATTATCAACATATCAAATATATAAATTACCAATTTTTAAATTAATACGATTCAATAAATTA
1 ATAAATTATCAACATATCAAATATATAAATTACCAAGTTTTAAATTAATACAATTCAATAAATTA
19849986 TCAACACGTCAAAT
66 TCAACACGTCAAAT
* *
19850000 ATAAATTATAGCAGACATGTCAAATATTTAAATTACCAAGTTTTAAATTAATACAATTCAATAAA
1 ATAAATTAT--CA-ACATATCAAATATATAAATTACCAAGTTTTAAATTAATACAATTCAATAAA
*
19850065 TTATCAACATGTCAAAT
63 TTATCAACACGTCAAAT
19850082 ATA
1 ATA
19850085 TAAATTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
79 9 0.12
81 2 0.03
82 66 0.86
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.34
Consensus pattern (79 bp):
ATAAATTATCAACATATCAAATATATAAATTACCAAGTTTTAAATTAATACAATTCAATAAATTA
TCAACACGTCAAAT
Found at i:19850091 original size:57 final size:57
Alignment explanation
Indices: 19850000--19850142 Score: 232
Period size: 57 Copynumber: 2.5 Consensus size: 57
19849990 CACGTCAAAT
* *
19850000 ATAAATTATAGCAGACATGTCAAATATTTAAATTACCAAGTTTTAAATTAATACAATTCA
1 ATAAATTAT--CA-ACATGTCAAATATATAAATTACCAAGTTTAAAATTAATACAATTCA
*
19850060 ATAAATTATCAACATGTCAAATATATAAATTACCAAGTTTAAAATTAATACGATTCA
1 ATAAATTATCAACATGTCAAATATATAAATTACCAAGTTTAAAATTAATACAATTCA
19850117 ATAAATTATCAACATGTCAAATATAT
1 ATAAATTATCAACATGTCAAATATAT
19850143 TTTCTAGAAA
Statistics
Matches: 80, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
57 69 0.86
58 2 0.03
60 9 0.11
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.34
Consensus pattern (57 bp):
ATAAATTATCAACATGTCAAATATATAAATTACCAAGTTTAAAATTAATACAATTCA
Found at i:19850120 original size:139 final size:139
Alignment explanation
Indices: 19849870--19850141 Score: 499
Period size: 139 Copynumber: 2.0 Consensus size: 139
19849860 AACAACAACC
19849870 AGCAGACATGTCAAATATATAAATTACCAAGTTTTAAATTAATACAATTCAATAAATTATCAACA
1 AGCAGACATGTCAAATATATAAATTACCAAGTTTTAAATTAATACAATTCAATAAATTATCAACA
* *
19849935 TATCAAATATATAAATTACCAATTTTTAAATTAATACGATTCAATAAATTATCAACACGTCAAAT
66 TATCAAATATATAAATTACCAAGTTTAAAATTAATACGATTCAATAAATTATCAACACGTCAAAT
19850000 ATAAATTAT
131 ATAAATTAT
*
19850009 AGCAGACATGTCAAATATTTAAATTACCAAGTTTTAAATTAATACAATTCAATAAATTATCAACA
1 AGCAGACATGTCAAATATATAAATTACCAAGTTTTAAATTAATACAATTCAATAAATTATCAACA
* *
19850074 TGTCAAATATATAAATTACCAAGTTTAAAATTAATACGATTCAATAAATTATCAACATGTCAAAT
66 TATCAAATATATAAATTACCAAGTTTAAAATTAATACGATTCAATAAATTATCAACACGTCAAAT
19850139 ATA
131 ATA
19850142 TTTTCTAGAA
Statistics
Matches: 128, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
139 128 1.00
ACGTcount: A:0.49, C:0.13, G:0.05, T:0.33
Consensus pattern (139 bp):
AGCAGACATGTCAAATATATAAATTACCAAGTTTTAAATTAATACAATTCAATAAATTATCAACA
TATCAAATATATAAATTACCAAGTTTAAAATTAATACGATTCAATAAATTATCAACACGTCAAAT
ATAAATTAT
Found at i:19851718 original size:62 final size:63
Alignment explanation
Indices: 19851627--19851782 Score: 262
Period size: 62 Copynumber: 2.5 Consensus size: 63
19851617 ACTTAAGTCC
*
19851627 CAAAAATCCCTAAATTTTTAAAACTTAAATCAAATTCCCCAAACCCAACAACCCCAAAAATCT
1 CAAAAATCCCTAAATTTTTAAAACCTAAATCAAATTCCCCAAACCCAACAACCCCAAAAATCT
* *
19851690 C-GAAATCCCTAAATTTCTT-AAACCTAAATCAAATTCCCCAAACCCAACAACCCTAAAAATCT
1 CAAAAATCCCTAAATTT-TTAAAACCTAAATCAAATTCCCCAAACCCAACAACCCCAAAAATCT
19851752 CAAAAATCCCTAAATTTTTAAAACCTAAATC
1 CAAAAATCCCTAAATTTTTAAAACCTAAATC
19851783 CCCAAATTCC
Statistics
Matches: 86, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
62 58 0.67
63 28 0.33
ACGTcount: A:0.46, C:0.29, G:0.01, T:0.24
Consensus pattern (63 bp):
CAAAAATCCCTAAATTTTTAAAACCTAAATCAAATTCCCCAAACCCAACAACCCCAAAAATCT
Found at i:19851835 original size:32 final size:32
Alignment explanation
Indices: 19851755--19851836 Score: 85
Period size: 32 Copynumber: 2.6 Consensus size: 32
19851745 AAAATCTCAA
* *
19851755 AAAT-CCCTAAATTTTTAAAACCTAAATCCCC
1 AAATACCCAAAATTTTTAAAACCTAAAACCCC
* * * *
19851786 AAATTCCCAAAAATTTTAAAATCTAAAACCCG
1 AAATACCCAAAATTTTTAAAACCTAAAACCCC
* *
19851818 AAATACCCACATTTTTTAA
1 AAATACCCAAAATTTTTAA
19851837 CCTAAACCAA
Statistics
Matches: 41, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 4 0.10
32 37 0.90
ACGTcount: A:0.45, C:0.24, G:0.01, T:0.29
Consensus pattern (32 bp):
AAATACCCAAAATTTTTAAAACCTAAAACCCC
Found at i:19854180 original size:40 final size:39
Alignment explanation
Indices: 19854119--19854220 Score: 141
Period size: 40 Copynumber: 2.5 Consensus size: 39
19854109 ATACTAGAGA
*
19854119 TTAGCAGGCTTTAAGTCGGTGATGTGATTCAAGCTACGGC
1 TTAGCAGGCTTTAAG-CGGTGATGTAATTCAAGCTACGGC
* * *
19854159 TTAGCAAGCTTTGAGCAGGTGATGTAATTCAAGCTACTGC
1 TTAGCAGGCTTTAAGC-GGTGATGTAATTCAAGCTACGGC
19854199 TTAGCAGGCTTTAAGCCGGTGA
1 TTAGCAGGCTTTAAG-CGGTGA
19854221 GAAGATTCAA
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
39 1 0.02
40 52 0.96
41 1 0.02
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (39 bp):
TTAGCAGGCTTTAAGCGGTGATGTAATTCAAGCTACGGC
Found at i:19859636 original size:35 final size:36
Alignment explanation
Indices: 19859548--19859638 Score: 132
Period size: 36 Copynumber: 2.6 Consensus size: 36
19859538 TGGCTTAAAT
*
19859548 TTATTGGGAATCTTGAAGAGCTCGTATGAGTTGAAA
1 TTATTGGGAAACTTGAAGAGCTCGTATGAGTTGAAA
* *
19859584 TTACTT-GGAAACTTGAAGGGCTCGTATGAGTTG-GA
1 TTA-TTGGGAAACTTGAAGAGCTCGTATGAGTTGAAA
19859619 TTATTGGGAAACTTGAAGAG
1 TTATTGGGAAACTTGAAGAG
19859639 ATCATTGAGA
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
34 2 0.04
35 17 0.35
36 28 0.57
37 2 0.04
ACGTcount: A:0.30, C:0.09, G:0.30, T:0.32
Consensus pattern (36 bp):
TTATTGGGAAACTTGAAGAGCTCGTATGAGTTGAAA
Found at i:19866645 original size:36 final size:36
Alignment explanation
Indices: 19866603--19866703 Score: 125
Period size: 36 Copynumber: 2.8 Consensus size: 36
19866593 AATATTATTG
* *
19866603 GGAATCTTGAAGAACTCGTATGAGTT-AAATTTACTA
1 GGAATCTTGAAGAGCTCGTATGAGTTGAAA-CTACTA
*
19866639 GGAATCTTGAAGAGCTCGTATAAGTTGAAACTACTA
1 GGAATCTTGAAGAGCTCGTATGAGTTGAAACTACTA
* *
19866675 GG-ATACTTGAAGGGCTCGTATGAGATGAA
1 GGAAT-CTTGAAGAGCTCGTATGAGTTGAA
19866704 TTATTGGGAA
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
35 2 0.04
36 52 0.91
37 3 0.05
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.29
Consensus pattern (36 bp):
GGAATCTTGAAGAGCTCGTATGAGTTGAAACTACTA
Found at i:19871999 original size:7 final size:8
Alignment explanation
Indices: 19871974--19872003 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
19871964 AAAGTAGAAA
19871974 AAAATAAT
1 AAAATAAT
19871982 AAAATAAT
1 AAAATAAT
19871990 AAAA-AAT
1 AAAATAAT
19871997 AAAATAA
1 AAAATAA
19872004 AAGTGTTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (8 bp):
AAAATAAT
Found at i:19871999 original size:15 final size:16
Alignment explanation
Indices: 19871974--19872003 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
19871964 AAAGTAGAAA
19871974 AAAATAATAAAATAAT
1 AAAATAATAAAATAAT
19871990 AAAA-AATAAAATAA
1 AAAATAATAAAATAA
19872004 AAGTGTTAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (16 bp):
AAAATAATAAAATAAT
Found at i:19876131 original size:19 final size:19
Alignment explanation
Indices: 19876109--19876146 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
19876099 TGGCTCACAA
*
19876109 GAGCGATATACTGTACTGG
1 GAGCAATATACTGTACTGG
*
19876128 GAGCAATATATTGTACTGG
1 GAGCAATATACTGTACTGG
19876147 CTTGTAAGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.29, C:0.13, G:0.29, T:0.29
Consensus pattern (19 bp):
GAGCAATATACTGTACTGG
Found at i:19876325 original size:35 final size:35
Alignment explanation
Indices: 19876189--19876335 Score: 145
Period size: 36 Copynumber: 4.1 Consensus size: 35
19876179 TATATTGACT
** *
19876189 GAGCTCGTATGA-ACAAATTATTACTGGGAATCTTGAA
1 GAGCTCGTATGAGTTAAATTATTA---GGAAACTTGAA
* *
19876226 GAACTCGTATGAGTTAAATTTATT-GAGAATCTTGAA
1 GAGCTCGTATGAGTTAAA-TTATTAG-GAAACTTGAA
*
19876262 GAGCTCGTATGAGTTAAAATTACTAGGAAACTTGAA
1 GAGCTCGTATGAGTT-AAATTATTAGGAAACTTGAA
* * *
19876298 GGGCTCGTATGAGCTGAATTATTAGGAAACTTGAA
1 GAGCTCGTATGAGTTAAATTATTAGGAAACTTGAA
19876333 GAG
1 GAG
19876336 ATCATTGAGA
Statistics
Matches: 94, Mismatches: 11, Indels: 12
0.80 0.09 0.10
Matches are distributed among these distances:
35 21 0.22
36 50 0.53
37 15 0.16
38 3 0.03
39 5 0.05
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.30
Consensus pattern (35 bp):
GAGCTCGTATGAGTTAAATTATTAGGAAACTTGAA
Found at i:19891111 original size:19 final size:19
Alignment explanation
Indices: 19891075--19891112 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
19891065 ATGGCTGATT
*
19891075 TTATATTTATTTGAACATA
1 TTATATTTATTTAAACATA
19891094 TTATATTT-TTTAAGACATA
1 TTATATTTATTTAA-ACATA
19891113 AAGTGGACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (19 bp):
TTATATTTATTTAAACATA
Found at i:19911171 original size:40 final size:40
Alignment explanation
Indices: 19911108--19911329 Score: 345
Period size: 40 Copynumber: 5.5 Consensus size: 40
19911098 ATACTAGAGA
* * *
19911108 TTAGTAGGCTTTGAGCCGATGATGTAATTCAAGCTACGGC
1 TTAGCAGGCTTTGAGCCGGTGATGTGATTCAAGCTACGGC
* *
19911148 TTAGCAGGCTTTGAGCCGGTGATGTAATTTAAGCTACGGC
1 TTAGCAGGCTTTGAGCCGGTGATGTGATTCAAGCTACGGC
* * *
19911188 TTAGCAGGCTTTGACCCGTTGATGTGATTCAAGCTACGAC
1 TTAGCAGGCTTTGAGCCGGTGATGTGATTCAAGCTACGGC
**
19911228 TTAGCAGGCTTTGAGCCATTGATGTGATTCAAGCTACGGC
1 TTAGCAGGCTTTGAGCCGGTGATGTGATTCAAGCTACGGC
19911268 TTAGCAGGCTTTGAGCCGGTGATGTGATTCAAGCTACGGC
1 TTAGCAGGCTTTGAGCCGGTGATGTGATTCAAGCTACGGC
*
19911308 TTAGCAGGCTTTAAGCCGGTGA
1 TTAGCAGGCTTTGAGCCGGTGA
19911330 GAAGATTCAG
Statistics
Matches: 168, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 168 1.00
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.29
Consensus pattern (40 bp):
TTAGCAGGCTTTGAGCCGGTGATGTGATTCAAGCTACGGC
Found at i:19911337 original size:120 final size:120
Alignment explanation
Indices: 19911108--19911364 Score: 358
Period size: 120 Copynumber: 2.1 Consensus size: 120
19911098 ATACTAGAGA
*
19911108 TTAGTAGGCTTTGAGCCGATGATGTAATTCAAGCTACGGCTTAGCAGGCTTTGAGCCGGTGATGT
1 TTAGCAGGCTTTGAGCCGATGATGTAATTCAAGCTACGGCTTAGCAGGCTTTGAGCCGGTGATGT
* * * *
19911173 AATTTAAGCTACGGCTTAGCAGGCTTTGACCCGTTGATGTGATTCAAGCTACGAC
66 AATTCAAGCTACGGCTTAGCAGGCTTTAACCCGGTGATGAGATTCAAGCTACGAC
*
19911228 TTAGCAGGCTTTGAGCC-ATTGATGTGATTCAAGCTACGGCTTAGCAGGCTTTGAGCCGGTGATG
1 TTAGCAGGCTTTGAGCCGA-TGATGTAATTCAAGCTACGGCTTAGCAGGCTTTGAGCCGGTGATG
* * * * *
19911292 TGATTCAAGCTACGGCTTAGCAGGCTTTAAGCCGGTGA-GAAGATTCAGGTTATGAC
65 TAATTCAAGCTACGGCTTAGCAGGCTTTAACCCGGTGATG-AGATTCAAGCTACGAC
* *
19911348 CTAGTAGGCTTT-AGCCG
1 TTAGCAGGCTTTGAGCCG
19911365 GTGTAATTGA
Statistics
Matches: 121, Mismatches: 13, Indels: 6
0.86 0.09 0.04
Matches are distributed among these distances:
119 6 0.05
120 115 0.95
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.29
Consensus pattern (120 bp):
TTAGCAGGCTTTGAGCCGATGATGTAATTCAAGCTACGGCTTAGCAGGCTTTGAGCCGGTGATGT
AATTCAAGCTACGGCTTAGCAGGCTTTAACCCGGTGATGAGATTCAAGCTACGAC
Found at i:19912537 original size:35 final size:35
Alignment explanation
Indices: 19912498--19912591 Score: 80
Period size: 40 Copynumber: 2.5 Consensus size: 35
19912488 GGTTTAGCTG
*
19912498 ACTAGCGCTGGGCGCAAACATCGTTGGTTTATCCA
1 ACTAGCGCTGGGCGCAAACATCGTCGGTTTATCCA
* * * * *
19912533 ACTAGAGTTGGGCTCACATTTAATATCGTCGGTTTATCCG
1 ACTAGCGCTGGG--CGCA---AACATCGTCGGTTTATCCA
*
19912573 ACTAGCGCTGGGTGCAAAC
1 ACTAGCGCTGGGCGCAAAC
19912592 TCTTTCGCGA
Statistics
Matches: 43, Mismatches: 11, Indels: 10
0.67 0.17 0.16
Matches are distributed among these distances:
35 12 0.28
37 3 0.07
38 2 0.05
40 26 0.60
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (35 bp):
ACTAGCGCTGGGCGCAAACATCGTCGGTTTATCCA
Found at i:19913727 original size:16 final size:17
Alignment explanation
Indices: 19913706--19913738 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
19913696 CCTTTCTTAA
19913706 TTTAATGAATA-ATATG
1 TTTAATGAATATATATG
*
19913722 TTTAATGTATATATATG
1 TTTAATGAATATATATG
19913739 AGTGTGATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (17 bp):
TTTAATGAATATATATG
Found at i:19914031 original size:16 final size:16
Alignment explanation
Indices: 19914014--19914043 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19914004 CCATACTTTA
19914014 AAAT-TTTATTTATTT
1 AAATGTTTATTTATTT
19914029 AAATGTTTATTTATT
1 AAATGTTTATTTATT
19914044 GTTGCTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (16 bp):
AAATGTTTATTTATTT
Found at i:19914416 original size:23 final size:23
Alignment explanation
Indices: 19914367--19914417 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
19914357 ATTATACTAC
* *
19914367 AAATTGAAGTGTTTAAATGTTGT
1 AAATTGAAGTGTTTAAATGCTGG
**
19914390 AAATTGAAGTGTTTAGTTGCTGG
1 AAATTGAAGTGTTTAAATGCTGG
19914413 AAATT
1 AAATT
19914418 TGATGCTAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.33, C:0.02, G:0.24, T:0.41
Consensus pattern (23 bp):
AAATTGAAGTGTTTAAATGCTGG
Found at i:19917184 original size:40 final size:40
Alignment explanation
Indices: 19917121--19917297 Score: 228
Period size: 40 Copynumber: 4.4 Consensus size: 40
19917111 CTTACACGGT
* * * * *
19917121 TTAGCAGGTTTTTAGTCGGTGATGTAATTCAAGCTACGAC
1 TTAGCAGGCTTTGAGCCAGTGATGTGATTCAAGCTACGAC
*
19917161 TTAGCAGGCTTTGAGCCATTGATGTGATTCAAGCTACGAC
1 TTAGCAGGCTTTGAGCCAGTGATGTGATTCAAGCTACGAC
* * *
19917201 TTAGCAGGCTTTGAGCTAGTGATATGATTCAAGCTACGGC
1 TTAGCAGGCTTTGAGCCAGTGATGTGATTCAAGCTACGAC
* * *
19917241 TTAGCAGGCTTTGAGCTAGTGATGTGATTCAAGCTATGGC
1 TTAGCAGGCTTTGAGCCAGTGATGTGATTCAAGCTACGAC
* *
19917281 TTAACAGGCTTTAAGCC
1 TTAGCAGGCTTTGAGCC
19917298 GATGAGAAGA
Statistics
Matches: 122, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 122 1.00
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.32
Consensus pattern (40 bp):
TTAGCAGGCTTTGAGCCAGTGATGTGATTCAAGCTACGAC
Found at i:19917310 original size:80 final size:80
Alignment explanation
Indices: 19917147--19917340 Score: 230
Period size: 80 Copynumber: 2.4 Consensus size: 80
19917137 CGGTGATGTA
* *
19917147 ATTCAAGCTACGACTTAGCAGGCTTTGAGCCATTGATGTGATTCAAGCTACGACTTAGCAGGCTT
1 ATTCAAGCTACGACTTAGCAGGCTTTGAGCCAGTGATGTGATTCAAGCTACGACTTAACAGGCTT
* * * *
19917212 TGAGCTAGTGATATG
66 TAAGCGAGTGAGAAG
* * * *
19917227 ATTCAAGCTACGGCTTAGCAGGCTTTGAGCTAGTGATGTGATTCAAGCTATGGCTTAACAGGCTT
1 ATTCAAGCTACGACTTAGCAGGCTTTGAGCCAGTGATGTGATTCAAGCTACGACTTAACAGGCTT
19917292 TAAGCCGA-TGAGAAG
66 TAAG-CGAGTGAGAAG
* * * * *
19917307 ATTCAGGTTATGACCTGGCAGGCTTT-AGCCAGTG
1 ATTCAAGCTACGACTTAGCAGGCTTTGAGCCAGTG
19917341 TAATTGATAT
Statistics
Matches: 96, Mismatches: 17, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
79 7 0.07
80 87 0.91
81 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.29
Consensus pattern (80 bp):
ATTCAAGCTACGACTTAGCAGGCTTTGAGCCAGTGATGTGATTCAAGCTACGACTTAACAGGCTT
TAAGCGAGTGAGAAG
Found at i:19917311 original size:40 final size:40
Alignment explanation
Indices: 19917139--19917292 Score: 236
Period size: 40 Copynumber: 3.9 Consensus size: 40
19917129 TTTTTAGTCG
* *
19917139 GTGATGTAATTCAAGCTACGACTTAGCAGGCTTTGAGCCA
1 GTGATGTGATTCAAGCTACGACTTAGCAGGCTTTGAGCTA
*
19917179 TTGATGTGATTCAAGCTACGACTTAGCAGGCTTTGAGCTA
1 GTGATGTGATTCAAGCTACGACTTAGCAGGCTTTGAGCTA
* *
19917219 GTGATATGATTCAAGCTACGGCTTAGCAGGCTTTGAGCTA
1 GTGATGTGATTCAAGCTACGACTTAGCAGGCTTTGAGCTA
* * *
19917259 GTGATGTGATTCAAGCTATGGCTTAACAGGCTTT
1 GTGATGTGATTCAAGCTACGACTTAGCAGGCTTT
19917293 AAGCCGATGA
Statistics
Matches: 105, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 105 1.00
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (40 bp):
GTGATGTGATTCAAGCTACGACTTAGCAGGCTTTGAGCTA
Found at i:19924961 original size:27 final size:26
Alignment explanation
Indices: 19924921--19925079 Score: 105
Period size: 25 Copynumber: 6.1 Consensus size: 26
19924911 TAAGGAGTAA
* *
19924921 TCTGATTCTAGCTCGAAGAAGCGTTAT
1 TCTGATTCTGGCTCGAAG-AGCGATAT
* * *
19924948 TCTGATTATGGCTCATAAGAGCAATAT
1 TCTGATTCTGGCTC-GAAGAGCGATAT
*
19924975 TCTGATTCTGACTCGTAAGAGCGATAT
1 TCTGATTCTGGCTCG-AAGAGCGATAT
* *
19925002 TCTGA--CTAGCTCGTAAGAGTGATAT
1 TCTGATTCTGGCTCG-AAGAGCGATAT
* **
19925027 TCT-ATT-TGGCTTGTAAGAGAAATAT
1 TCTGATTCTGGCTCG-AAGAGCGATAT
* *
19925052 TCTG--TCCGGCTCGTAAGAGCAATAT
1 TCTGATTCTGGCTCG-AAGAGCGATAT
19925077 TCT
1 TCT
19925080 TTTTGAGCTC
Statistics
Matches: 107, Mismatches: 19, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
24 2 0.02
25 57 0.53
27 45 0.42
28 3 0.03
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (26 bp):
TCTGATTCTGGCTCGAAGAGCGATAT
Found at i:19925053 original size:50 final size:50
Alignment explanation
Indices: 19924958--19925097 Score: 145
Period size: 50 Copynumber: 2.7 Consensus size: 50
19924948 TCTGATTATG
* ** *
19924958 GCTCATAAGAGCAATATTCTGATTCTGACTCGTAAGAGCGATATTCTGACTA
1 GCTCGTAAGAGCAATATTCT-ATT-TGACTCGTAAGAGAAATATTCTGACCA
** * * * *
19925010 GCTCGTAAGAGTGATATTCTATTTGGCTTGTAAGAGAAATATTCTGTCCG
1 GCTCGTAAGAGCAATATTCTATTTGACTCGTAAGAGAAATATTCTGACCA
* *
19925060 GCTCGTAAGAGCAATATTCTTTTTGAGCTCGTATGAGA
1 GCTCGTAAGAGCAATATTCTATTTGA-CTCGTAAGAGA
19925098 TAAATTTTTG
Statistics
Matches: 71, Mismatches: 16, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
50 42 0.59
51 12 0.17
52 17 0.24
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (50 bp):
GCTCGTAAGAGCAATATTCTATTTGACTCGTAAGAGAAATATTCTGACCA
Found at i:19927707 original size:42 final size:42
Alignment explanation
Indices: 19927655--19927737 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
19927645 GTCGCTATAG
* * *
19927655 AACATGGTCTTTAGCGGCCCTTATCCCACAAGTGCCGCTAAA
1 AACATGGTCTTTAGCAGCCCTTATCCCACAAATGCCACTAAA
* *
19927697 AACATGGTCTTTAGCAGCGCTTTTCCCACAAATGCCACTAA
1 AACATGGTCTTTAGCAGCCCTTATCCCACAAATGCCACTAA
19927738 CATTAACAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.25
Consensus pattern (42 bp):
AACATGGTCTTTAGCAGCCCTTATCCCACAAATGCCACTAAA
Found at i:19933468 original size:82 final size:82
Alignment explanation
Indices: 19933331--19933525 Score: 250
Period size: 82 Copynumber: 2.4 Consensus size: 82
19933321 CTTTAACCAA
* * *
19933331 AAGCGCGGCTATTGCTCTGACCTTTAGCGACGCTTGCCAAAAAGCCCTGCTATTGCTCTGACCTT
1 AAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTGCCAAAAAGCCCTGCTATTGCTCTAACCTT
19933396 TAGCTACGCTTGCCCAT
66 TAGCTACGCTTGCCCAT
* * * * *
19933413 AAGCGCCGCTATTGTTCTGACCTTTAGCGGCGCTTGCCCATAAG-CGTCGCTATTGCTTTAACCT
1 AAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTGCCAAAAAGCCCT-GCTATTGCTCTAACCT
* * *
19933477 TTAGCTGCGTTTTCCCAT
65 TTAGCTACGCTTGCCCAT
* *
19933495 AAGCGTCGCTATTGCTCT-ACCTTTTGCGGCG
1 AAGCGCCGCTATTGCTCTGACCTTTAGCGGCG
19933526 TTTATATAAA
Statistics
Matches: 98, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
81 14 0.14
82 84 0.86
ACGTcount: A:0.17, C:0.30, G:0.22, T:0.31
Consensus pattern (82 bp):
AAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTGCCAAAAAGCCCTGCTATTGCTCTAACCTT
TAGCTACGCTTGCCCAT
Found at i:19933494 original size:41 final size:41
Alignment explanation
Indices: 19933338--19933525 Score: 227
Period size: 41 Copynumber: 4.6 Consensus size: 41
19933328 CAAAAGCGCG
* * * *
19933338 GCTATTGCTCTGACCTTTAGCGACGCTTGCCAAAAAGC-CC
1 GCTATTGCTCTGACCTTTAGCGGCGCTTGCCCATAAGCGTC
** *
19933378 TGCTATTGCTCTGACCTTTAGCTACGCTTGCCCATAAGCGCC
1 -GCTATTGCTCTGACCTTTAGCGGCGCTTGCCCATAAGCGTC
*
19933420 GCTATTGTTCTGACCTTTAGCGGCGCTTGCCCATAAGCGTC
1 GCTATTGCTCTGACCTTTAGCGGCGCTTGCCCATAAGCGTC
* * * * *
19933461 GCTATTGCTTTAACCTTTAGCTGCGTTTTCCCATAAGCGTC
1 GCTATTGCTCTGACCTTTAGCGGCGCTTGCCCATAAGCGTC
*
19933502 GCTATTGCTCT-ACCTTTTGCGGCG
1 GCTATTGCTCTGACCTTTAGCGGCG
19933526 TTTATATAAA
Statistics
Matches: 130, Mismatches: 16, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
40 11 0.08
41 117 0.90
42 2 0.02
ACGTcount: A:0.16, C:0.30, G:0.21, T:0.32
Consensus pattern (41 bp):
GCTATTGCTCTGACCTTTAGCGGCGCTTGCCCATAAGCGTC
Found at i:19933545 original size:40 final size:41
Alignment explanation
Indices: 19933501--19933586 Score: 120
Period size: 40 Copynumber: 2.1 Consensus size: 41
19933491 CCATAAGCGT
19933501 CGCTATTGCTCTACCTTTTGCGGCG-TTTATATAAAAACGC
1 CGCTATTGCTCTACCTTTTGCGGCGTTTTATATAAAAACGC
* * * **
19933541 CGCTATTGCTTTATCTTTTGCGGCGTTTTCTATCCAAACGC
1 CGCTATTGCTCTACCTTTTGCGGCGTTTTATATAAAAACGC
19933582 CGCTA
1 CGCTA
19933587 AAAGTGCCGC
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 23 0.57
41 17 0.43
ACGTcount: A:0.19, C:0.27, G:0.17, T:0.37
Consensus pattern (41 bp):
CGCTATTGCTCTACCTTTTGCGGCGTTTTATATAAAAACGC
Found at i:19935202 original size:25 final size:25
Alignment explanation
Indices: 19935168--19935236 Score: 102
Period size: 25 Copynumber: 2.8 Consensus size: 25
19935158 GCTTTTTCGA
* * *
19935168 ATAATTCACCATAAGGGCTTTACAG
1 ATAACTCACCACAAAGGCTTTACAG
19935193 ATAACTCACCACAAAGGCTTTACAG
1 ATAACTCACCACAAAGGCTTTACAG
*
19935218 ATAACTCGCCACAAAGGCT
1 ATAACTCACCACAAAGGCT
19935237 CTATTTCGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.38, C:0.26, G:0.14, T:0.22
Consensus pattern (25 bp):
ATAACTCACCACAAAGGCTTTACAG
Found at i:19939664 original size:11 final size:11
Alignment explanation
Indices: 19939650--19939691 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
19939640 ATTATTAAAT
19939650 ATAATTTAATA
1 ATAATTTAATA
*
19939661 ATAA-ATAATAA
1 ATAATTTAAT-A
19939672 ATAATTTAATA
1 ATAATTTAATA
*
19939683 ATATTTTAA
1 ATAATTTAA
19939692 CATAATTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 4 0.15
11 18 0.69
12 4 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
ATAATTTAATA
Found at i:19946634 original size:22 final size:22
Alignment explanation
Indices: 19946604--19946649 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
19946594 CTCAAGATAG
19946604 GGAGCGAGGTAGGAAGCAACCA
1 GGAGCGAGGTAGGAAGCAACCA
*
19946626 GGAGTGAGGTAGGAAGCAACCA
1 GGAGCGAGGTAGGAAGCAACCA
19946648 GG
1 GG
19946650 CTCAATAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.35, C:0.15, G:0.43, T:0.07
Consensus pattern (22 bp):
GGAGCGAGGTAGGAAGCAACCA
Found at i:19948088 original size:13 final size:13
Alignment explanation
Indices: 19948065--19948143 Score: 59
Period size: 13 Copynumber: 5.9 Consensus size: 13
19948055 TCATTGACTT
*
19948065 TGACTCGTTGACC
1 TGACCCGTTGACC
* **
19948078 CGACCCGTTGAATT
1 TGACCCGTTG-ACC
*
19948092 TGAACCGTTGACC
1 TGACCCGTTGACC
*
19948105 TGACCCGTTGACTT
1 TGACCCGTTGAC-C
* * *
19948119 TTAACCGTTAACC
1 TGACCCGTTGACC
19948132 TGACCCGTTGAC
1 TGACCCGTTGAC
19948144 TTTGATCCAT
Statistics
Matches: 47, Mismatches: 17, Indels: 4
0.69 0.25 0.06
Matches are distributed among these distances:
13 29 0.62
14 18 0.38
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.29
Consensus pattern (13 bp):
TGACCCGTTGACC
Found at i:19948088 original size:27 final size:26
Alignment explanation
Indices: 19948058--19948185 Score: 132
Period size: 27 Copynumber: 4.8 Consensus size: 26
19948048 GATCCGATCA
19948058 TTGACTTTGACTCGTTGACCCGACCCG
1 TTGACTTTGAC-CGTTGACCCGACCCG
* *
19948085 TTGAATTTGAACCGTTGACCTGACCCG
1 TTGACTTTG-ACCGTTGACCCGACCCG
* * *
19948112 TTGACTTTTAACCGTTAACCTGACCCG
1 TTGAC-TTTGACCGTTGACCCGACCCG
* * * *
19948139 TTGACTTTGATCCATTGACTCGACTCA
1 TTGACTTTGA-CCGTTGACCCGACCCG
19948166 TTGACTTTGACC-TTGACCCG
1 TTGACTTTGACCGTTGACCCG
19948186 TTGACTGTTG
Statistics
Matches: 85, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
25 7 0.08
26 6 0.07
27 67 0.79
28 5 0.06
ACGTcount: A:0.20, C:0.29, G:0.19, T:0.33
Consensus pattern (26 bp):
TTGACTTTGACCGTTGACCCGACCCG
Found at i:19949936 original size:12 final size:12
Alignment explanation
Indices: 19949919--19949943 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19949909 TGTTGTTATG
19949919 ATGAATGCTATT
1 ATGAATGCTATT
19949931 ATGAATGCTATT
1 ATGAATGCTATT
19949943 A
1 A
19949944 ATTATTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (12 bp):
ATGAATGCTATT
Found at i:19950674 original size:15 final size:16
Alignment explanation
Indices: 19950637--19950674 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
19950627 ATATGAATAC
*
19950637 AATTTAGTCTTAGTTT
1 AATTTAGTCTTAATTT
*
19950653 AACTTAGT-TTAATTT
1 AATTTAGTCTTAATTT
19950668 AATTTAG
1 AATTTAG
19950675 ATACTTTAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.53
Consensus pattern (16 bp):
AATTTAGTCTTAATTT
Found at i:19951225 original size:36 final size:36
Alignment explanation
Indices: 19951183--19951255 Score: 87
Period size: 36 Copynumber: 2.0 Consensus size: 36
19951173 TTTTTAGTCA
19951183 TTTTCAT-TTATTAT-TCATTATGAATTATTTTGGGAT
1 TTTTCATATTATTATGTCATTA--AATTATTTTGGGAT
* * *
19951219 TTTTCATATTGTTGTGTTATTAAATTATTTTGGGAT
1 TTTTCATATTATTATGTCATTAAATTATTTTGGGAT
19951255 T
1 T
19951256 GTGATATTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
36 22 0.69
37 5 0.16
38 5 0.16
ACGTcount: A:0.23, C:0.04, G:0.14, T:0.59
Consensus pattern (36 bp):
TTTTCATATTATTATGTCATTAAATTATTTTGGGAT
Found at i:19952071 original size:22 final size:22
Alignment explanation
Indices: 19952030--19952103 Score: 114
Period size: 22 Copynumber: 3.4 Consensus size: 22
19952020 AGTGTGTTCC
* *
19952030 GTTCTTTTAT-TTCACAAACAA
1 GTTCGTTTATGTTCACGAACAA
19952051 GTTCGTTTATGTTCACGAACAA
1 GTTCGTTTATGTTCACGAACAA
19952073 GTTCGTTTATGTTCACGAACAA
1 GTTCGTTTATGTTCACGAACAA
*
19952095 ATTCGTTTA
1 GTTCGTTTA
19952104 AAAGTTCGTT
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
21 9 0.18
22 40 0.82
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.41
Consensus pattern (22 bp):
GTTCGTTTATGTTCACGAACAA
Found at i:19952298 original size:23 final size:23
Alignment explanation
Indices: 19952242--19952311 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
19952232 CCATTAACAT
* *
19952242 TGTTCGTGATCATGTTCAATTATA
1 TGTTCGTGAACATGTTCGATTA-A
* *
19952266 TGTTCATGAACATGTTCGTTTAA
1 TGTTCGTGAACATGTTCGATTAA
*
19952289 TGTTCGTGAACATATTCGATTAA
1 TGTTCGTGAACATGTTCGATTAA
19952312 ATTAAATGAA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 21 0.54
24 18 0.46
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.43
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCGATTAA
Found at i:19952338 original size:23 final size:23
Alignment explanation
Indices: 19952295--19952341 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
19952285 TTAATGTTCG
*
19952295 TGAACATATTCGATTAAATTAAA
1 TGAACATATTCGATGAAATTAAA
*
19952318 TGAACATGTTCG-TGAACATTAAA
1 TGAACATATTCGATGAA-ATTAAA
19952341 T
1 T
19952342 AAACGAACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.34
Consensus pattern (23 bp):
TGAACATATTCGATGAAATTAAA
Found at i:19955005 original size:26 final size:26
Alignment explanation
Indices: 19954906--19955073 Score: 110
Period size: 26 Copynumber: 6.4 Consensus size: 26
19954896 CCTTTGATTG
* *
19954906 TGCCACAAAGACGTTCCTTTATAGAT
1 TGCCACAAAGACTTTCCTTTATAGAA
* * *
19954932 TAGCCAAAAAGGCTTTCCTTTCATA-TA
1 T-GCCACAAAGACTTTCCTTT-ATAGAA
**
19954959 TGCCACAAAGAC-AACCTTTTATAGAA
1 TGCCACAAAGACTTTCC-TTTATAGAA
* * *
19954985 TGCCACAAAGATTTTCCTTTACAGAT
1 TGCCACAAAGACTTTCCTTTATAGAA
* * *
19955011 TAGCCAAAAAGGCTTTCCTTTCATA-TA
1 T-GCCACAAAGACTTTCCTTT-ATAGAA
** *
19955038 TGCCACAAAGAC-GACCTTTTACAGAA
1 TGCCACAAAGACTTTCC-TTTATAGAA
19955064 TGCCACAAAG
1 TGCCACAAAG
19955074 GTTTTCCTAT
Statistics
Matches: 106, Mismatches: 27, Indels: 18
0.70 0.18 0.12
Matches are distributed among these distances:
25 9 0.08
26 56 0.53
27 36 0.34
28 5 0.05
ACGTcount: A:0.35, C:0.24, G:0.13, T:0.28
Consensus pattern (26 bp):
TGCCACAAAGACTTTCCTTTATAGAA
Found at i:19955079 original size:79 final size:79
Alignment explanation
Indices: 19954906--19955081 Score: 298
Period size: 79 Copynumber: 2.2 Consensus size: 79
19954896 CCTTTGATTG
** *
19954906 TGCCACAAAGACGTTCCTTTATAGATTAGCCAAAAAGGCTTTCCTTTCATATATGCCACAAAGAC
1 TGCCACAAAGATTTTCCTTTACAGATTAGCCAAAAAGGCTTTCCTTTCATATATGCCACAAAGAC
*
19954971 AACCTTTTATAGAA
66 AACCTTTTACAGAA
19954985 TGCCACAAAGATTTTCCTTTACAGATTAGCCAAAAAGGCTTTCCTTTCATATATGCCACAAAGAC
1 TGCCACAAAGATTTTCCTTTACAGATTAGCCAAAAAGGCTTTCCTTTCATATATGCCACAAAGAC
*
19955050 GACCTTTTACAGAA
66 AACCTTTTACAGAA
*
19955064 TGCCACAAAGGTTTTCCT
1 TGCCACAAAGATTTTCCT
19955082 ATTAAGAGTT
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
79 91 1.00
ACGTcount: A:0.34, C:0.24, G:0.13, T:0.30
Consensus pattern (79 bp):
TGCCACAAAGATTTTCCTTTACAGATTAGCCAAAAAGGCTTTCCTTTCATATATGCCACAAAGAC
AACCTTTTACAGAA
Found at i:19964995 original size:7 final size:7
Alignment explanation
Indices: 19964983--19965055 Score: 51
Period size: 7 Copynumber: 10.7 Consensus size: 7
19964973 TTCGAAAAAA
19964983 GTCAACG
1 GTCAACG
*
19964990 GTCAACA
1 GTCAACG
* *
19964997 ATCAA-A
1 GTCAACG
19965003 GTCAACG
1 GTCAACG
*
19965010 ATCAACG
1 GTCAACG
19965017 GTCAAC-
1 GTCAACG
**
19965023 GTCAATT
1 GTCAACG
*
19965030 GTCAATG
1 GTCAACG
*
19965037 GTCAATG
1 GTCAACG
*
19965044 GTCAATG
1 GTCAACG
19965051 GTCAA
1 GTCAA
19965056 AGTCAACAGT
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
6 10 0.18
7 46 0.82
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.22
Consensus pattern (7 bp):
GTCAACG
Found at i:19965040 original size:14 final size:14
Alignment explanation
Indices: 19965023--19965055 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
19965013 AACGGTCAAC
*
19965023 GTCAATTGTCAATG
1 GTCAATGGTCAATG
19965037 GTCAATGGTCAATG
1 GTCAATGGTCAATG
19965051 GTCAA
1 GTCAA
19965056 AGTCAACAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.30
Consensus pattern (14 bp):
GTCAATGGTCAATG
Found at i:19965041 original size:27 final size:27
Alignment explanation
Indices: 19964983--19965062 Score: 72
Period size: 27 Copynumber: 3.0 Consensus size: 27
19964973 TTCGAAAAAA
19964983 GTCAACGGTCAACAATCAAAGTCAACG
1 GTCAACGGTCAACAATCAAAGTCAACG
* * * *
19965010 ATCAACGGTCAAC-GTCAATTGTCAATG
1 GTCAACGGTCAACAATCAA-AGTCAACG
* ***
19965037 GTCAATGGTCAATGGTCAAAGTCAAC
1 GTCAACGGTCAACAATCAAAGTCAAC
19965063 AGTCGATCAA
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
26 4 0.10
27 33 0.79
28 5 0.12
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (27 bp):
GTCAACGGTCAACAATCAAAGTCAACG
Found at i:19965060 original size:20 final size:20
Alignment explanation
Indices: 19964980--19965055 Score: 62
Period size: 20 Copynumber: 3.8 Consensus size: 20
19964970 TTTTTCGAAA
* **
19964980 AAAGTCAACGGTCAACAATC
1 AAAGTCAATGGTCAACGGTC
* *
19965000 AAAGTCAACGATCAACGGTC
1 AAAGTCAATGGTCAACGGTC
* * *
19965020 AACGTCAATTGTCAATGGTC
1 AAAGTCAATGGTCAACGGTC
*
19965040 AATGGTCAATGGTCAA
1 AA-AGTCAATGGTCAA
19965056 AGTCAACAGT
Statistics
Matches: 45, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
20 34 0.76
21 11 0.24
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (20 bp):
AAAGTCAATGGTCAACGGTC
Found at i:19965082 original size:22 final size:22
Alignment explanation
Indices: 19965057--19965127 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 22
19965047 AATGGTCAAA
*
19965057 GTCAACAGTCGATCAACGGCCT
1 GTCAACAGTCGATCAACGGCCG
* *
19965079 GTCAATAGTCGATTAACGGCCG
1 GTCAACAGTCGATCAACGGCCG
* * * *
19965101 GTCAACGGTCGGTTAACAGCCG
1 GTCAACAGTCGATCAACGGCCG
19965123 GTCAA
1 GTCAA
19965128 TGGTTTGACT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (22 bp):
GTCAACAGTCGATCAACGGCCG
Found at i:19968030 original size:33 final size:29
Alignment explanation
Indices: 19967983--19968071 Score: 90
Period size: 29 Copynumber: 2.9 Consensus size: 29
19967973 GATCCTTCTG
* *
19967983 CAATTTTAAGGGTTTTAATTTAGTCCTTTTT
1 CAATTTTTATGGTTTTAATTTAGTCC--TTT
*
19968014 GCATTTTTTATAGGTTTTAATTTAG-CCTTT
1 -CAATTTTTAT-GGTTTTAATTTAGTCCTTT
19968044 CAATTTTTATGTGTTTATAATTTAGTCC
1 CAATTTTTATG-GTTT-TAATTTAGTCC
19968072 CTAATTCTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
28 1 0.02
29 13 0.27
30 11 0.22
31 2 0.04
32 9 0.18
33 13 0.27
ACGTcount: A:0.22, C:0.10, G:0.12, T:0.55
Consensus pattern (29 bp):
CAATTTTTATGGTTTTAATTTAGTCCTTT
Found at i:19976318 original size:49 final size:51
Alignment explanation
Indices: 19976257--19976364 Score: 184
Period size: 49 Copynumber: 2.2 Consensus size: 51
19976247 ATTTTGCCTA
*
19976257 AAAAAAAATCAAAATCCAAAAGTTTGAGTTGAAAACCTGAAA-GGCGGCT-
1 AAAAAAAATCAAAATCCAAAAGTTTAAGTTGAAAACCTGAAAGGGCGGCTC
*
19976306 AAAAAAAATCAAAATCCAAAAGTTTAAGTTGAAAACCTGAAAGGGCGGTTC
1 AAAAAAAATCAAAATCCAAAAGTTTAAGTTGAAAACCTGAAAGGGCGGCTC
19976357 AAAAAAAA
1 AAAAAAAA
19976365 GGGAGAGGCC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
49 41 0.75
50 6 0.11
51 8 0.15
ACGTcount: A:0.53, C:0.13, G:0.17, T:0.18
Consensus pattern (51 bp):
AAAAAAAATCAAAATCCAAAAGTTTAAGTTGAAAACCTGAAAGGGCGGCTC
Found at i:19977703 original size:147 final size:146
Alignment explanation
Indices: 19977552--19978371 Score: 793
Period size: 147 Copynumber: 5.6 Consensus size: 146
19977542 GGTGGATCTT
* * * * * *
19977552 ACACCTTAAAA-CTGAAGAGGGATAGGTTGAAGTCATAATGGTAGACCTAACACCCTAAAATCGA
1 ACACCTTAAAATC-AAAGAGGGATAGATTGAAGCCATAATGGTGGATCTAACACCCTAAAACCGA
* * * *
19977616 AGAGGAAAAGATTGAAGTCGCAACAAT-GACTTTTACACTTTAAAACCGAAGAGGGATAGGTTGA
65 AGAGGAAAAGATTGAAGTCGCAACGATGGA-TCTTACACCTTAAAATCGAAGAGGGATAGGTTGA
*
19977680 AGCCGCAGCAGTGAACCTA
129 AGCCGTA-CAGTGAACCTA
* * * * *
19977699 ACACCTTAAAATCGAAGAGGGATAGATTGAAGCCGTAATAGTGGGTCTAACACCTTAAAACC-AA
1 ACACCTTAAAATCAAAGAGGGATAGATTGAAGCCATAATGGTGGATCTAACACCCTAAAACCGAA
* * * * * *
19977763 AAAGAGAAAGATTGAAGTCGTAACGATAGATCTTACACCTTAAAATTGAAGAGGGATAGGTTAAA
66 GAGGA-AAAGATTGAAGTCGCAACGATGGATCTTACACCTTAAAATCGAAGAGGGATAGGTTGAA
*
19977828 GCCGTA-A-TGGCAGACATA
130 GCCGTACAGT-G-A-ACCTA
* * * * * *
19977846 ACACCTTAAAATCAAAGAGGAATAGATTAAAGTCGTAATGGCGAATCTAACACCCTAAAACCGAA
1 ACACCTTAAAATCAAAGAGGGATAGATTGAAGCCATAATGGTGGATCTAACACCCTAAAACCGAA
* * * * * * *
19977911 AAGGGAAAGATTAAAGTCGTAACGATGGATTTTACACCTTAAAATCGAAAAAGGATAGGTTGAAG
66 GAGGAAAAGATTGAAGTCGCAACGATGGATCTTACACCTTAAAATCGAAGAGGGATAGGTTGAAG
19977976 CCGTA-A-TGACGGACCTA
131 CCGTACAGTGA---ACCTA
* * * ** * *
19977993 ATACCCTAAAATCAAAGAGGGATAGATTGAAGCCACAATGACGGATCTAACACCCTAAAAGCAAA
1 ACACCTTAAAATCAAAGAGGGATAGATTGAAGCCATAATGGTGGATCTAACACCCTAAAACCGAA
* * * *
19978058 GAGGGAAATATTGAAGTCGAAACGGTGGATCTTACACCTTAAAA-CTGAAGAGGGATAGGTTGAA
66 GAGGAAAAGATTGAAGTCGCAACGATGGATCTTACACCTTAAAATC-GAAGAGGGATAGGTTGAA
* *
19978122 GCCGTAACGGTGGACCTA
130 GCCGT-ACAGTGAACCTA
* * *
19978140 ACA-CTCTAAAATC---GAGGGATATG-TTGAAGCCGTAATGATGGATCTAACACCCTAAAACCA
1 ACACCT-TAAAATCAAAGAGGGATA-GATTGAAGCCATAATGGTGGATCTAACACCCTAAAACCG
** * *
19978200 AAGAGGAAAAGATTGAAGTTACAACGGTGAATCTTACACCTTAAAATCGAAGAGGGATAGGTTGA
64 AAGAGGAAAAGATTGAAGTCGCAACGATGGATCTTACACCTTAAAATCGAAGAGGGATAGGTTGA
* * * * *
19978265 AGTCATAACGGTGGACATA
129 AGCCGT-ACAGTGAACCTA
* * * * **
19978284 ACACCTTAAAACCAAAGAGGGATAGATTGTAGTCATAACGGTGGATCTAACACCCTAAAATTGAA
1 ACACCTTAAAATCAAAGAGGGATAGATTGAAGCCATAATGGTGGATCTAACACCCTAAAACCGAA
*
19978349 GAGGGAACAGATTGAAGTCGCAA
66 GA-GGAAAAGATTGAAGTCGCAA
19978372 TAGCGAATCT
Statistics
Matches: 564, Mismatches: 87, Indels: 43
0.81 0.13 0.06
Matches are distributed among these distances:
144 124 0.22
145 7 0.01
146 10 0.02
147 395 0.70
148 26 0.05
150 2 0.00
ACGTcount: A:0.41, C:0.17, G:0.23, T:0.20
Consensus pattern (146 bp):
ACACCTTAAAATCAAAGAGGGATAGATTGAAGCCATAATGGTGGATCTAACACCCTAAAACCGAA
GAGGAAAAGATTGAAGTCGCAACGATGGATCTTACACCTTAAAATCGAAGAGGGATAGGTTGAAG
CCGTACAGTGAACCTA
Found at i:19978215 original size:193 final size:193
Alignment explanation
Indices: 19977844--19978344 Score: 472
Period size: 193 Copynumber: 2.6 Consensus size: 193
19977834 ATGGCAGACA
* * * * * * * *
19977844 TAACACCTTAAAATCAAAGA-GGAATAGATTAAAGTCGTAATGGCGAATC-TAACACCCTAAAAC
1 TAACACCCTAAAAGCAAAGAGGGAA-AGATTGAAGTCATAACGGTGGA-CATAACACCTTAAAAC
* * * * * ** * * *
19977907 CGAAA-AGGGAAAGATTAAAGTCGTAACGATGGATTTTACACCTTAAAATCGAAAAAGGATAGGT
64 C-AAAGAGGGATAGATTGAAGCCATAACGGTGGACCTAACACCCTAAAATCG---AGGGATAGGT
* * * * *
19977971 TGAAGCCGTAATGACGGACCTAATACCCTAAAATCAAAGAGGGATAGATTGAAGCCACAATGACG
125 TGAAGCCGTAATGACGGACCTAACACCCTAAAACCAAAGAGGAAAAGATTGAAGCCACAACGACG
*
19978036 GATC
190 AATC
* *
19978040 TAACACCCTAAAAGCAAAGAGGGAAATATTGAAGTCGA-AACGGTGGATC-TTACACCTTAAAAC
1 TAACACCCTAAAAGCAAAGAGGGAAAGATTGAAGTC-ATAACGGTGGA-CATAACACCTTAAAAC
** * * * *
19978103 TGAAGAGGGATAGGTTGAAGCCGTAACGGTGGACCTAACACTCTAAAATCGAGGGATATGTTGAA
64 CAAAGAGGGATAGATTGAAGCCATAACGGTGGACCTAACACCCTAAAATCGAGGGATAGGTTGAA
* * ** **
19978168 GCCGTAATGATGGATCTAACACCCTAAAACCAAAGAGGAAAAGATTGAAGTTACAACGGTGAATC
129 GCCGTAATGACGGACCTAACACCCTAAAACCAAAGAGGAAAAGATTGAAGCCACAACGACGAATC
* * * * * *
19978233 TTACACCTTAAAATCGAAGAGGGATAGGTTGAAGTCATAACGGTGGACATAACACCTTAAAACCA
1 TAACACCCTAAAAGCAAAGAGGGAAAGATTGAAGTCATAACGGTGGACATAACACCTTAAAACCA
* * *
19978298 AAGAGGGATAGATTGTAGTCATAACGGTGGATCTAACACCCTAAAAT
66 AAGAGGGATAGATTGAAGCCATAACGGTGGACCTAACACCCTAAAAT
19978345 TGAAGAGGGA
Statistics
Matches: 248, Mismatches: 52, Indels: 13
0.79 0.17 0.04
Matches are distributed among these distances:
192 2 0.01
193 157 0.63
195 2 0.01
196 83 0.33
197 4 0.02
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (193 bp):
TAACACCCTAAAAGCAAAGAGGGAAAGATTGAAGTCATAACGGTGGACATAACACCTTAAAACCA
AAGAGGGATAGATTGAAGCCATAACGGTGGACCTAACACCCTAAAATCGAGGGATAGGTTGAAGC
CGTAATGACGGACCTAACACCCTAAAACCAAAGAGGAAAAGATTGAAGCCACAACGACGAATC
Found at i:19978351 original size:49 final size:49
Alignment explanation
Indices: 19977418--19978368 Score: 607
Period size: 49 Copynumber: 19.4 Consensus size: 49
19977408 TCCTAGAGTT
* * * * *
19977418 GAAGAGGGATAGGTTGAAG-CTGTAACGATGGACCTAACACCCTAAAACC
1 GAAGAGGGATAGATTGAAGTC-GTAACGGTGGATCTAACACCTTAAAATC
* * * * ** *
19977467 AAAAAGGGATAAATTGAAG-C-TACAATGGCAGATCTAACACCTTAAAATT
1 GAAGAGGGATAGATTGAAGTCGT--AACGGTGGATCTAACACCTTAAAATC
* * * * *
19977516 AAAGAAGGAAAGATTGAAG-CTGCAACGGTGGATCTTACACCTTAAAA-C
1 GAAGAGGGATAGATTGAAGTC-GTAACGGTGGATCTAACACCTTAAAATC
* * * * * *
19977564 TGAAGAGGGATAGGTTGAAGTCATAATGGTAGACCTAACACCCTAAAATC
1 -GAAGAGGGATAGATTGAAGTCGTAACGGTGGATCTAACACCTTAAAATC
* * * ** * * * *
19977614 GAAGAGGAAAAGATTGAAGTCGCAACAAT-GACTTTTACACTTTAAAACC
1 GAAGAGGGATAGATTGAAGTCGTAACGGTGGA-TCTAACACCTTAAAATC
* * * * * * *
19977663 GAAGAGGGATAGGTTGAAGCCGCAGCAGTGAACCTAACACCTTAAAATC
1 GAAGAGGGATAGATTGAAGTCGTAACGGTGGATCTAACACCTTAAAATC
* ** * *
19977712 GAAGAGGGATAGATTGAAGCCGTAATAGTGGGTCTAACACCTTAAAACC
1 GAAGAGGGATAGATTGAAGTCGTAACGGTGGATCTAACACCTTAAAATC
* * * * * * * *
19977761 AAAAAGAGAAAGATTGAAGTCGTAACGATAGATCTTACACCTTAAAATT
1 GAAGAGGGATAGATTGAAGTCGTAACGGTGGATCTAACACCTTAAAATC
* * * * **
19977810 GAAGAGGGATAGGTTAAAGCCGTAATGGCAGA-CATAACACCTTAAAATC
1 GAAGAGGGATAGATTGAAGTCGTAACGGTGGATC-TAACACCTTAAAATC
* * * * * * * *
19977859 AAAGAGGAATAGATTAAAGTCGTAATGGCGAATCTAACACCCTAAAACC
1 GAAGAGGGATAGATTGAAGTCGTAACGGTGGATCTAACACCTTAAAATC
* * * * * *
19977908 GAAAAGGGAAAGATTAAAGTCGTAACGATGGATTTTACACCTTAAAATC
1 GAAGAGGGATAGATTGAAGTCGTAACGGTGGATCTAACACCTTAAAATC
* * * * * ** * * *
19977957 GAAAAAGGATAGGTTGAAGCCGTAATGACGGACCTAATACCCTAAAATC
1 GAAGAGGGATAGATTGAAGTCGTAACGGTGGATCTAACACCTTAAAATC
* * ** * ** * *
19978006 AAAGAGGGATAGATTGAAGCCACAATGACGGATCTAACACCCTAAAAGC
1 GAAGAGGGATAGATTGAAGTCGTAACGGTGGATCTAACACCTTAAAATC
* * * * *
19978055 AAAGAGGGAAATATTGAAGTCGAAACGGTGGATCTTACACCTTAAAA-C
1 GAAGAGGGATAGATTGAAGTCGTAACGGTGGATCTAACACCTTAAAATC
* * *
19978103 TGAAGAGGGATAGGTTGAAGCCGTAACGGTGGACCTAACA-CTCTAAAATC
1 -GAAGAGGGATAGATTGAAGTCGTAACGGTGGATCTAACACCT-TAAAATC
* * * * *
19978153 ---GAGGGATATG-TTGAAGCCGTAATGATGGATCTAACACCCTAAAACC
1 GAAGAGGGATA-GATTGAAGTCGTAACGGTGGATCTAACACCTTAAAATC
* * * *** * *
19978199 AAAGAGGAAAAGATTGAAGTTACAACGGTGAATCTTACACCTTAAAATC
1 GAAGAGGGATAGATTGAAGTCGTAACGGTGGATCTAACACCTTAAAATC
* * *
19978248 GAAGAGGGATAGGTTGAAGTCATAACGGTGGA-CATAACACCTTAAAACC
1 GAAGAGGGATAGATTGAAGTCGTAACGGTGGATC-TAACACCTTAAAATC
* * * * *
19978297 AAAGAGGGATAGATTGTAGTCATAACGGTGGATCTAACACCCTAAAATT
1 GAAGAGGGATAGATTGAAGTCGTAACGGTGGATCTAACACCTTAAAATC
*
19978346 GAAGAGGGAACAGATTGAAGTCG
1 GAAGAGGG-ATAGATTGAAGTCG
19978369 CAATAGCGAA
Statistics
Matches: 692, Mismatches: 187, Indels: 45
0.75 0.20 0.05
Matches are distributed among these distances:
46 37 0.05
47 3 0.00
48 8 0.01
49 627 0.91
50 17 0.02
ACGTcount: A:0.41, C:0.16, G:0.23, T:0.20
Consensus pattern (49 bp):
GAAGAGGGATAGATTGAAGTCGTAACGGTGGATCTAACACCTTAAAATC
Found at i:19979016 original size:25 final size:26
Alignment explanation
Indices: 19978988--19979039 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
19978978 ATCAATAGGA
19978988 AAAT-TGAATAAAAAGATCGTAA-ATC
1 AAATCTGAA-AAAAAGATCGTAATATC
* *
19979013 AAATCTGCAAAAAAGATTGTAATATC
1 AAATCTGAAAAAAAGATCGTAATATC
19979039 A
1 A
19979040 TGTATATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.54, C:0.10, G:0.12, T:0.25
Consensus pattern (26 bp):
AAATCTGAAAAAAAGATCGTAATATC
Found at i:19985718 original size:17 final size:16
Alignment explanation
Indices: 19985696--19985736 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
19985686 TATTTTTTCT
19985696 TTTCTTATTTCCTCTTC
1 TTTCTTATTTCCTC-TC
*
19985713 TTTCTT-TTTCTTCTC
1 TTTCTTATTTCCTCTC
19985728 TTT-TTATTT
1 TTTCTTATTT
19985737 TATAAGTGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 2 0.09
15 8 0.36
16 6 0.27
17 6 0.27
ACGTcount: A:0.05, C:0.22, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTCTTATTTCCTCTC
Found at i:19986295 original size:17 final size:18
Alignment explanation
Indices: 19986273--19986323 Score: 63
Period size: 17 Copynumber: 2.9 Consensus size: 18
19986263 ACTATACATA
19986273 TAACAATGGAAATGCAAC
1 TAACAATGGAAATGCAAC
*
19986291 T-ACAATGCAAATGC-AC
1 TAACAATGGAAATGCAAC
19986307 TAACAAAT-GAAATGCAA
1 TAAC-AATGGAAATGCAA
19986324 TGACAACTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
16 3 0.11
17 20 0.71
18 5 0.18
ACGTcount: A:0.51, C:0.18, G:0.14, T:0.18
Consensus pattern (18 bp):
TAACAATGGAAATGCAAC
Found at i:20007321 original size:17 final size:17
Alignment explanation
Indices: 20007299--20007332 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
20007289 TGTGTGTGTG
*
20007299 TTTTAAAAATATTTATT
1 TTTTAAAAATATATATT
20007316 TTTTAAAAATATATATT
1 TTTTAAAAATATATATT
20007333 AAATTCATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTAAAAATATATATT
Found at i:20007370 original size:21 final size:20
Alignment explanation
Indices: 20007346--20007410 Score: 69
Period size: 23 Copynumber: 3.1 Consensus size: 20
20007336 TTCATATTCA
20007346 ATTTTTCATAATTTAATTTAT
1 ATTTTT-ATAATTTAATTTAT
*
20007367 ATTTTTTTATAATTAAAATTTAT
1 A--TTTTTATAATT-TAATTTAT
*
20007390 -TTTATATAATTTAATTTAT
1 ATTTTTATAATTTAATTTAT
20007409 AT
1 AT
20007411 ATACATTAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
19 7 0.19
20 11 0.30
21 1 0.03
22 6 0.16
23 12 0.32
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTTTTATAATTTAATTTAT
Found at i:20007386 original size:23 final size:22
Alignment explanation
Indices: 20007347--20007410 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
20007337 TCATATTCAA
*
20007347 TTTTTCATAATTTAATTTATAT
1 TTTTTCATAATTAAATTTATAT
* *
20007369 TTTTTTATAATTAAAATT-TAT
1 TTTTTCATAATTAAATTTATAT
* *
20007390 TTTAT-ATAATTTAATTTATAT
1 TTTTTCATAATTAAATTTATAT
20007411 ATACATTAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
20 10 0.29
21 10 0.29
22 15 0.43
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTTTCATAATTAAATTTATAT
Found at i:20008070 original size:11 final size:11
Alignment explanation
Indices: 20008034--20008127 Score: 59
Period size: 11 Copynumber: 8.4 Consensus size: 11
20008024 TTCAAATCTC
* *
20008034 ATTTAATTTGA
1 ATTTCATTTCA
*
20008045 ATTTCCA-TTCC
1 ATTT-CATTTCA
20008056 ATTTCATTTCA
1 ATTTCATTTCA
20008067 ATTTCAACTTTC-
1 ATTTC-A-TTTCA
*
20008079 ATTTAATTTCA
1 ATTTCATTTCA
* *
20008090 ACTTCTATTTAA
1 ATTTC-ATTTCA
20008102 ATTTCATTTTC-
1 ATTTCA-TTTCA
*
20008113 ATTTCATTTAA
1 ATTTCATTTCA
20008124 ATTT
1 ATTT
20008128 AAACTTTTAA
Statistics
Matches: 64, Mismatches: 11, Indels: 16
0.70 0.12 0.18
Matches are distributed among these distances:
10 9 0.14
11 33 0.52
12 18 0.28
13 4 0.06
ACGTcount: A:0.29, C:0.16, G:0.01, T:0.54
Consensus pattern (11 bp):
ATTTCATTTCA
Found at i:20008072 original size:6 final size:6
Alignment explanation
Indices: 20008015--20008127 Score: 62
Period size: 6 Copynumber: 19.8 Consensus size: 6
20008005 AAAACTTTGA
* * * * *
20008015 AATTTA AATTTC AAATCTC -ATTT- AATTTG AATTTC CA-TTC CATTTC
1 AATTTC AATTTC -AATTTC AATTTC AATTTC AATTTC AATTTC AATTTC
* * *
20008061 -ATTTC AATTTC AACTTTC -ATTT- AATTTC AACTTC TATTTA AATTTC
1 AATTTC AATTTC AA-TTTC AATTTC AATTTC AATTTC AATTTC AATTTC
* *
20008107 ATTTTC -ATTTC -ATTTA AATTT
1 AATTTC AATTTC AATTTC AATTT
20008128 AAACTTTTAA
Statistics
Matches: 84, Mismatches: 14, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
5 32 0.38
6 43 0.51
7 9 0.11
ACGTcount: A:0.31, C:0.16, G:0.01, T:0.52
Consensus pattern (6 bp):
AATTTC
Found at i:20008088 original size:17 final size:18
Alignment explanation
Indices: 20008057--20008116 Score: 72
Period size: 17 Copynumber: 3.4 Consensus size: 18
20008047 TTCCATTCCA
*
20008057 TTTCATTTCAATTTCAAC
1 TTTCATTTAAATTTCAAC
20008075 TTTCATTT-AATTTCAAC
1 TTTCATTTAAATTTCAAC
*
20008092 -TTCTATTTAAATTTC-AT
1 TTTC-ATTTAAATTTCAAC
20008109 TTTCATTT
1 TTTCATTT
20008117 CATTTAAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
16 3 0.08
17 18 0.47
18 17 0.45
ACGTcount: A:0.27, C:0.17, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTCATTTAAATTTCAAC
Found at i:20008088 original size:23 final size:22
Alignment explanation
Indices: 20008015--20008123 Score: 84
Period size: 23 Copynumber: 5.1 Consensus size: 22
20008005 AAAACTTTGA
* *
20008015 AATTTAAATTTCAAATCTCATTT
1 AATTTCAATTTC-AATTTCATTT
* * *
20008038 AATTTGAATTTCCATTCCATTT
1 AATTTCAATTTCAATTTCATTT
*
20008060 CATTTCAATTTCAACTTTCATTT
1 AATTTCAATTTCAA-TTTCATTT
* *
20008083 AATTTCAACTTCTATTT-A---
1 AATTTCAATTTCAATTTCATTT
*
20008101 AATTTCATTTTC-ATTTCATTT
1 AATTTCAATTTCAATTTCATTT
20008122 AA
1 AA
20008124 ATTTAAACTT
Statistics
Matches: 68, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
17 4 0.06
18 11 0.16
21 3 0.04
22 21 0.31
23 29 0.43
ACGTcount: A:0.31, C:0.17, G:0.01, T:0.51
Consensus pattern (22 bp):
AATTTCAATTTCAATTTCATTT
Found at i:20008375 original size:23 final size:22
Alignment explanation
Indices: 20008349--20008408 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 22
20008339 TTTATTTGCT
*
20008349 TTTGTGGGACGCTTTTCCTCTA
1 TTTGTGGCACGCTTTTCCTCTA
20008371 CTTTGTGGCACGCTTTTCCTCTA
1 -TTTGTGGCACGCTTTTCCTCTA
20008394 TCTTGTGGCACGCTT
1 T-TTGTGGCACGCTT
20008409 CTGCCTTGTG
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
22 1 0.03
23 34 0.97
ACGTcount: A:0.08, C:0.27, G:0.22, T:0.43
Consensus pattern (22 bp):
TTTGTGGCACGCTTTTCCTCTA
Found at i:20008980 original size:36 final size:36
Alignment explanation
Indices: 20008938--20009015 Score: 138
Period size: 36 Copynumber: 2.2 Consensus size: 36
20008928 TTGATATTTT
*
20008938 AATTAAATTCCATTGTTTAAATTCAAAAGCATGGAC
1 AATTAAATTCCAGTGTTTAAATTCAAAAGCATGGAC
*
20008974 AATTAAATTTCAGTGTTTAAATTCAAAAGCATGGAC
1 AATTAAATTCCAGTGTTTAAATTCAAAAGCATGGAC
20009010 AATTAA
1 AATTAA
20009016 TAAATAAGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.33
Consensus pattern (36 bp):
AATTAAATTCCAGTGTTTAAATTCAAAAGCATGGAC
Found at i:20020446 original size:42 final size:42
Alignment explanation
Indices: 20020386--20020670 Score: 300
Period size: 42 Copynumber: 6.9 Consensus size: 42
20020376 TTACATCATC
* * *
20020386 CCATCCAATCTTTCACCCTAACAAGAAGGTAGATTGAAGACA
1 CCATCCAATCTTTTACCCTAACAAGAGGGCAGATTGAAGACA
20020428 CCATCCAATCTTTTACCCTAACAAGAGGGCAGATTGAAGACA
1 CCATCCAATCTTTTACCCTAACAAGAGGGCAGATTGAAGACA
* * * * * *
20020470 CCATCCAATCTCTGACCCCAACCATG-GAGCAAATTGAAG---
1 CCATCCAATCTTTTACCCTAA-CAAGAGGGCAGATTGAAGACA
* * *
20020509 TCATCCAATCTTTTACCCTAACTAA-AGGGCAAATTGAAAACA
1 CCATCCAATCTTTTACCCTAAC-AAGAGGGCAGATTGAAGACA
* * * * *
20020551 CCATCTAATCTCTTACCCCAACCATG-GGGTAGATTGAAG---
1 CCATCCAATCTTTTACCCTAA-CAAGAGGGCAGATTGAAGACA
*
20020590 TCATCCAATCTTTTACCCTAACAAGAGGGCAGATTGAAGACA
1 CCATCCAATCTTTTACCCTAACAAGAGGGCAGATTGAAGACA
* *
20020632 CCATCCAATCTTTTACCCTAACCAGAGGGTAGATTGAAG
1 CCATCCAATCTTTTACCCTAACAAGAGGGCAGATTGAAG
20020671 TTACAACACC
Statistics
Matches: 198, Mismatches: 33, Indels: 24
0.78 0.13 0.09
Matches are distributed among these distances:
38 4 0.02
39 58 0.29
42 132 0.67
43 4 0.02
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.23
Consensus pattern (42 bp):
CCATCCAATCTTTTACCCTAACAAGAGGGCAGATTGAAGACA
Found at i:20020648 original size:81 final size:81
Alignment explanation
Indices: 20020429--20020671 Score: 373
Period size: 81 Copynumber: 3.0 Consensus size: 81
20020419 TTGAAGACAC
*
20020429 CATCCAATCTTTTACCCTAACAAGAGGGCAGATTGAAGACACCATCCAATCTCTGACCCCAACCA
1 CATCCAATCTTTTACCCTAACAAGAGGGCAGATTGAAGACACCATCCAATCTCTTACCCCAACCA
* * *
20020494 TGGAGCAAATTGAAGT
66 TGGGGTAGATTGAAGT
* * *
20020510 CATCCAATCTTTTACCCTAACTAA-AGGGCAAATTGAAAACACCATCTAATCTCTTACCCCAACC
1 CATCCAATCTTTTACCCTAAC-AAGAGGGCAGATTGAAGACACCATCCAATCTCTTACCCCAACC
20020574 ATGGGGTAGATTGAAGT
65 ATGGGGTAGATTGAAGT
* *
20020591 CATCCAATCTTTTACCCTAACAAGAGGGCAGATTGAAGACACCATCCAATCTTTTACCCTAACCA
1 CATCCAATCTTTTACCCTAACAAGAGGGCAGATTGAAGACACCATCCAATCTCTTACCCCAACCA
20020656 -GAGGGTAGATTGAAGT
66 TG-GGGTAGATTGAAGT
20020672 TACAACACCA
Statistics
Matches: 147, Mismatches: 12, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
80 3 0.02
81 142 0.97
82 2 0.01
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (81 bp):
CATCCAATCTTTTACCCTAACAAGAGGGCAGATTGAAGACACCATCCAATCTCTTACCCCAACCA
TGGGGTAGATTGAAGT
Found at i:20020668 original size:123 final size:121
Alignment explanation
Indices: 20020386--20020669 Score: 297
Period size: 123 Copynumber: 2.3 Consensus size: 121
20020376 TTACATCATC
* * * * *
20020386 CCATCCAATCTTTCACCCTAACAAGAAGGTAGATTGAAGACACCATCCAATCTTTTACCCTAACA
1 CCATCCAATCTTTTACCCTAACAAGAGGGTAGATTGAAAACACCATCCAATCTCTTACCCCAACA
*
20020451 AGAGGGCAGATTGAAGACACCATCCAATCTCTGACCCCAACCATGGAGCAAATTGAAG
66 AGAGGGCAGATTGAAG--ACCATCCAATCTCTGACCCCAACCAAGGAGCAAATTGAAG
* * * *
20020509 TCATCCAATCTTTTACCCTAACTAA-AGGGCAAATTGAAAACACCATCTAATCTCTTACCCCAAC
1 CCATCCAATCTTTTACCCTAAC-AAGAGGGTAGATTGAAAACACCATCCAATCTCTTACCCCAA-
* * * * * * * *
20020573 CATG-GGGTAGATTGAAG-TCATCCAATCTTTTACCCTAA-CAAGAGGGCAGATTGAAG
64 CAAGAGGGCAGATTGAAGACCATCCAATCTCTGACCCCAACCAAG-GAGCAAATTGAAG
*
20020629 ACACCATCCAATCTTTTACCCTAACCAGAGGGTAGATTGAA
1 ---CCATCCAATCTTTTACCCTAACAAGAGGGTAGATTGAA
20020670 GTTACAACAC
Statistics
Matches: 132, Mismatches: 22, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
119 3 0.02
120 28 0.21
122 1 0.01
123 95 0.72
124 5 0.04
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.23
Consensus pattern (121 bp):
CCATCCAATCTTTTACCCTAACAAGAGGGTAGATTGAAAACACCATCCAATCTCTTACCCCAACA
AGAGGGCAGATTGAAGACCATCCAATCTCTGACCCCAACCAAGGAGCAAATTGAAG
Found at i:20021130 original size:22 final size:24
Alignment explanation
Indices: 20021091--20021137 Score: 71
Period size: 22 Copynumber: 2.0 Consensus size: 24
20021081 TTAAGAGGGG
20021091 GGATTTTTTTGTATTTTGTTCAGA
1 GGATTTTTTTGTATTTTGTTCAGA
*
20021115 GGATTTTTTT-TA-TTTGTTTAGA
1 GGATTTTTTTGTATTTTGTTCAGA
20021137 G
1 G
20021138 AGAAGTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 10 0.45
23 2 0.09
24 10 0.45
ACGTcount: A:0.17, C:0.02, G:0.21, T:0.60
Consensus pattern (24 bp):
GGATTTTTTTGTATTTTGTTCAGA
Found at i:20021963 original size:9 final size:9
Alignment explanation
Indices: 20021926--20022015 Score: 51
Period size: 10 Copynumber: 9.7 Consensus size: 9
20021916 ATTTTAGTTC
20021926 AAATTATAAA
1 AAATT-TAAA
*
20021936 AAATATTTAA
1 AAAT-TTAAA
*
20021946 AATTCTTAAA
1 AAAT-TTAAA
20021956 AAATTT-AA
1 AAATTTAAA
*
20021964 AAATTATATA
1 AAATT-TAAA
*
20021974 AATTATTAAA
1 AAAT-TTAAA
20021984 AAA-TT-AA
1 AAATTTAAA
20021991 AAATTTAAA
1 AAATTTAAA
* *
20022000 AAGTATAAA
1 AAATTTAAA
20022009 AATATTT
1 AA-ATTT
20022016 TTAAGATTTT
Statistics
Matches: 60, Mismatches: 13, Indels: 14
0.69 0.15 0.16
Matches are distributed among these distances:
7 5 0.08
8 11 0.18
9 14 0.23
10 28 0.47
11 2 0.03
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (9 bp):
AAATTTAAA
Found at i:20021967 original size:8 final size:8
Alignment explanation
Indices: 20021935--20022011 Score: 55
Period size: 8 Copynumber: 8.8 Consensus size: 8
20021925 CAAATTATAA
20021935 AAAATATTT
1 AAAA-ATTT
*
20021944 AAAATTCTT
1 AAAAAT-TT
20021953 AAAAAATTT
1 -AAAAATTT
20021962 AAAAATTAT
1 AAAAATT-T
*
20021971 ATAAATTATT
1 A-AAAAT-TT
*
20021981 AAAAAATT
1 AAAAATTT
20021989 AAAAATTT
1 AAAAATTT
*
20021997 AAAAAGTAT
1 AAAAA-TTT
20022006 AAAAAT
1 AAAAAT
20022012 ATTTTTAAGA
Statistics
Matches: 55, Mismatches: 7, Indels: 13
0.73 0.09 0.17
Matches are distributed among these distances:
8 23 0.42
9 20 0.36
10 11 0.20
11 1 0.02
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (8 bp):
AAAAATTT
Found at i:20021976 original size:28 final size:29
Alignment explanation
Indices: 20021926--20022015 Score: 91
Period size: 28 Copynumber: 3.2 Consensus size: 29
20021916 ATTTTAGTTC
* * *
20021926 AAATTATAAAAAATATTTAAAATTCTTAAA
1 AAATT-TAAAAATTATATAAAATTATTAAA
20021956 AAATTTAAAAATTATAT-AAATTATTAAA
1 AAATTTAAAAATTATATAAAATTATTAAA
*
20021984 AAA-TTAAAAATT-TA-AAAAGTA-TAAA
1 AAATTTAAAAATTATATAAAATTATTAAA
20022009 AATATTT
1 AA-ATTT
20022016 TTAAGATTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
25 6 0.11
26 8 0.15
27 11 0.21
28 13 0.25
29 10 0.19
30 5 0.09
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (29 bp):
AAATTTAAAAATTATATAAAATTATTAAA
Found at i:20022856 original size:31 final size:31
Alignment explanation
Indices: 20022807--20022871 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
20022797 ACAATTTTGA
* * *
20022807 TCACTGAATTATTTAAAAATT-TTCATTTAAG
1 TCACTAAACTATTCAAAAATTCTT-ATTTAAG
*
20022838 TCACTAAACTATTCAAAAATTCTTATTTGAG
1 TCACTAAACTATTCAAAAATTCTTATTTAAG
20022869 TCA
1 TCA
20022872 TTGGATTGTC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 27 0.93
32 2 0.07
ACGTcount: A:0.38, C:0.14, G:0.06, T:0.42
Consensus pattern (31 bp):
TCACTAAACTATTCAAAAATTCTTATTTAAG
Done.