Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 95 of 125
Found at i:28562951 original size:29 final size:28
Alignment explanation
Indices: 28562817--28562952 Score: 107
Period size: 29 Copynumber: 4.7 Consensus size: 28
28562807 AGTCATTCGG
**
28562817 GGGT-AAAATGGTAATTTTTACAAGTTTTG
1 GGGTAAAAATGG-AATTTTTA-AAGTTTCA
*
28562846 GGGTCAAAAATGAAATTTTTTAAAG-TTCGA
1 GGGT-AAAAATGGAA-TTTTTAAAGTTTC-A
* *
28562876 GGGTAAAAATGGAATTTTTGGAAGTTTGA
1 GGGTAAAAATGGAATTTTT-AAAGTTTCA
**
28562905 GGGTAAAAATATAATTTTTAAAAGTTTCA
1 GGGTAAAAATGGAATTTTT-AAAGTTTCA
*
28562934 GGAGT-AAAATGGATTTTTT
1 GG-GTAAAAATGGAATTTTT
28562953 GGATAATTTA
Statistics
Matches: 86, Mismatches: 14, Indels: 14
0.75 0.12 0.12
Matches are distributed among these distances:
28 5 0.06
29 56 0.65
30 13 0.15
31 12 0.14
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.38
Consensus pattern (28 bp):
GGGTAAAAATGGAATTTTTAAAGTTTCA
Found at i:28563429 original size:15 final size:15
Alignment explanation
Indices: 28563409--28563437 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
28563399 GGTTTAAATA
28563409 CCCACACCAAAACGG
1 CCCACACCAAAACGG
28563424 CCCACACCAAAACG
1 CCCACACCAAAACG
28563438 CTTCCGTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.48, G:0.10, T:0.00
Consensus pattern (15 bp):
CCCACACCAAAACGG
Found at i:28564802 original size:19 final size:19
Alignment explanation
Indices: 28564764--28564801 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
28564754 AACTTAGACA
*
28564764 TGTAATTTGGACTTTCTTT
1 TGTAATTTGGACTCTCTTT
28564783 TGTAA-TTGGACTCTCTTT
1 TGTAATTTGGACTCTCTTT
28564801 T
1 T
28564802 TATTAAATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.16, C:0.13, G:0.16, T:0.55
Consensus pattern (19 bp):
TGTAATTTGGACTCTCTTT
Found at i:28565498 original size:134 final size:134
Alignment explanation
Indices: 28565250--28565539 Score: 544
Period size: 134 Copynumber: 2.2 Consensus size: 134
28565240 ACTTGGCCTT
28565250 CTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCTCAT
1 CTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCTCAT
* * *
28565315 CAGGAAGACGAATTTGGTCCACTTCTCAGTATCTTATCAGGAAGTTAACCATTTTATTGCTTCGA
66 CAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTGCTTCGA
28565380 CCTG
131 CCTG
*
28565384 CTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATTCGCTTCTCTGTATCTCAT
1 CTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCTCAT
28565449 CAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTGCTTCGA
66 CAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTGCTTCGA
28565514 CCTG
131 CCTG
28565518 CTTCTCAGTATCTCATCAGGAA
1 CTTCTCAGTATCTCATCAGGAA
28565540 ATTGGGGGTT
Statistics
Matches: 152, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
134 152 1.00
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (134 bp):
CTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCTCAT
CAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTGCTTCGA
CCTG
Found at i:28565739 original size:206 final size:206
Alignment explanation
Indices: 28565384--28565777 Score: 648
Period size: 206 Copynumber: 1.9 Consensus size: 206
28565374 CTTCGACCTG
*
28565384 CTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATTCGCTTCTCTGTATCTCAT
1 CTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCTCAT
*
28565449 CAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTGCTTCGA
66 CAGGAAGACAAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTGCTTCGA
* *
28565514 CCTGCTTCTCAGTATCTCATCAGGAA-ATTGGGGGTTCGAAGATTTGCTCACATCGAGCGTAGGT
131 CCTACTTCTCAGTATCTCATCAAGAAGA-T-GGGGTTCGAAGATTTGCTCACATCGAGCGTAGGT
28565578 TTGATTTGCTCTT
194 TTGATTTGCTCTT
* * *
28565591 CTTCTCAGTATCTGATCAGGAAGATGATCGCATCATTTGTTTCAATCCGCTTCT-TGTATCTCAT
1 CTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCTCAT
* * * *
28565655 CAGGAAGATAAATTTGGTCCACTTCTCAGTATCTTATTAGGAAGCTAACCATTTTATTGCTTCGA
66 CAGGAAGACAAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTGCTTCGA
*
28565720 CCTACTTCTCAGTATCTCATCAAGAAGATGGGGTTCGAAGATTTGCTCGCATCGAGCG
131 CCTACTTCTCAGTATCTCATCAAGAAGATGGGGTTCGAAGATTTGCTCACATCGAGCG
28565778 CTGAGTTGGT
Statistics
Matches: 174, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
205 28 0.16
206 95 0.55
207 51 0.29
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (206 bp):
CTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCTCAT
CAGGAAGACAAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTGCTTCGA
CCTACTTCTCAGTATCTCATCAAGAAGATGGGGTTCGAAGATTTGCTCACATCGAGCGTAGGTTT
GATTTGCTCTT
Found at i:28578004 original size:20 final size:20
Alignment explanation
Indices: 28577979--28578037 Score: 109
Period size: 20 Copynumber: 3.0 Consensus size: 20
28577969 GGATGCCCAG
28577979 GGGCAAAATGGTAATTTTGA
1 GGGCAAAATGGTAATTTTGA
28577999 GGGCAAAATGGTAATTTTGA
1 GGGCAAAATGGTAATTTTGA
*
28578019 GGGCAAAATGGTAAGTTTG
1 GGGCAAAATGGTAATTTTG
28578038 GAAAATTTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.34, C:0.05, G:0.32, T:0.29
Consensus pattern (20 bp):
GGGCAAAATGGTAATTTTGA
Found at i:28578197 original size:29 final size:29
Alignment explanation
Indices: 28578089--28578194 Score: 124
Period size: 30 Copynumber: 3.6 Consensus size: 29
28578079 GTAAAACGGT
*
28578089 AATTTTTAAAAGTTTCAA-GGTCAAAAATGA
1 AATTTTTAAAAGTTT-AAGGGT-AAAAATGG
* **
28578119 AATTTTTAGAAGTTCGAGGGTAAAAATGG
1 AATTTTTAAAAGTTTAAGGGTAAAAATGG
*
28578148 AATTTTTAGAAGTTTTAAGGGTAAAAATGG
1 AATTTTTAAAAG-TTTAAGGGTAAAAATGG
28578178 AATTTTTAAATAGTTTA
1 AATTTTTAAA-AGTTTA
28578195 GGGACCTCTA
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
29 20 0.30
30 44 0.67
31 2 0.03
ACGTcount: A:0.42, C:0.03, G:0.19, T:0.37
Consensus pattern (29 bp):
AATTTTTAAAAGTTTAAGGGTAAAAATGG
Found at i:28578726 original size:23 final size:25
Alignment explanation
Indices: 28578700--28578752 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 25
28578690 TCGTTTTCCC
28578700 TTCTCATTTT-AAAAAAA-TATTCT
1 TTCTCATTTTCAAAAAAACTATTCT
*
28578723 TTCT--TTTTCAAAAAAACTCTTCT
1 TTCTCATTTTCAAAAAAACTATTCT
*
28578746 CTCTCAT
1 TTCTCAT
28578753 CTCTCCATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
21 4 0.17
22 7 0.29
23 12 0.50
25 1 0.04
ACGTcount: A:0.32, C:0.21, G:0.00, T:0.47
Consensus pattern (25 bp):
TTCTCATTTTCAAAAAAACTATTCT
Found at i:28580003 original size:19 final size:19
Alignment explanation
Indices: 28579981--28580019 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
28579971 AACTTAGACA
28579981 TGTAATTTGGACTTTCTTT
1 TGTAATTTGGACTTTCTTT
28580000 TGTAATTTGGACTTTCTTT
1 TGTAATTTGGACTTTCTTT
28580019 T
1 T
28580020 TATTAAATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.10, G:0.15, T:0.59
Consensus pattern (19 bp):
TGTAATTTGGACTTTCTTT
Found at i:28580054 original size:18 final size:18
Alignment explanation
Indices: 28580033--28580068 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
28580023 TAAATTCAAT
*
28580033 TTTAAATTTAATCTTTAA
1 TTTAAATTTAAACTTTAA
28580051 TTTAAATTTAAACTTTAA
1 TTTAAATTTAAACTTTAA
28580069 AAGAAAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTAAATTTAAACTTTAA
Found at i:28583736 original size:24 final size:26
Alignment explanation
Indices: 28583694--28583741 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
28583684 TTATCCTGTT
*
28583694 TTTAACTTATATAA-TTTTATTAAAA
1 TTTAACTTATATAAGTTTAATTAAAA
*
28583719 TTTAA-TTATCTAAGTTTAATTAA
1 TTTAACTTATATAAGTTTAATTAA
28583742 TTTAAACAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (26 bp):
TTTAACTTATATAAGTTTAATTAAAA
Found at i:28592156 original size:2 final size:2
Alignment explanation
Indices: 28592149--28592182 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
28592139 TACCAGAGGA
28592149 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
28592183 GCAGGAAATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28596672 original size:2 final size:2
Alignment explanation
Indices: 28596667--28596694 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
28596657 AAAGAAAAGC
28596667 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
28596695 ACTTGGTAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:28597927 original size:17 final size:18
Alignment explanation
Indices: 28597890--28597936 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
28597880 TAAAATATTT
* *
28597890 ATATTAAAATATAATAAA
1 ATATTATAATATAAAAAA
28597908 ATATTATAATA-AAAAAA
1 ATATTATAATATAAAAAA
*
28597925 ATATTGTAATAT
1 ATATTATAATAT
28597937 TTAATTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 15 0.60
18 10 0.40
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (18 bp):
ATATTATAATATAAAAAA
Found at i:28598084 original size:26 final size:25
Alignment explanation
Indices: 28598020--28598093 Score: 69
Period size: 27 Copynumber: 2.8 Consensus size: 25
28598010 TTTTTTTGAG
*
28598020 AAAATAATATTTTTTATAAAATAAT
1 AAAATAATATTTTATATAAAATAAT
* *
28598045 AAAATACACAATTTTAT-TACAATAAT
1 AAAATA-A-TATTTTATATAAAATAAT
28598071 AAAAATATATATTTATATATAAA
1 -AAAATA-ATATTT-TATATAAA
28598094 TAACAAAGTA
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
25 6 0.16
26 13 0.34
27 16 0.42
28 3 0.08
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (25 bp):
AAAATAATATTTTATATAAAATAAT
Found at i:28598305 original size:20 final size:20
Alignment explanation
Indices: 28598280--28598321 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
28598270 AATCATAAAA
28598280 TATATATTTT-TATTAATATT
1 TATATATTTTATATTAA-ATT
28598300 TATATATTTTATATTAAATT
1 TATATATTTTATATTAAATT
28598320 TA
1 TA
28598322 AATAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TATATATTTTATATTAAATT
Found at i:28602634 original size:30 final size:31
Alignment explanation
Indices: 28602583--28602666 Score: 82
Period size: 31 Copynumber: 2.7 Consensus size: 31
28602573 TTACAGTCAT
* * *
28602583 TTAATTAAAAATTTATAATTTAA-TAATTAAA
1 TTAATTAAAAGTTT-TTATTTAAGTAAGTAAA
* * *
28602614 TT-ATTCGAAAGTTTTTATTTAAGTCAGTATA
1 TTAATT-AAAAGTTTTTATTTAAGTAAGTAAA
28602645 TTAATTAAAAGTTTTTATTTAA
1 TTAATTAAAAGTTTTTATTTAA
28602667 ATGACTAGAC
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
30 10 0.23
31 30 0.70
32 3 0.07
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (31 bp):
TTAATTAAAAGTTTTTATTTAAGTAAGTAAA
Found at i:28607731 original size:19 final size:18
Alignment explanation
Indices: 28607692--28607733 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
28607682 TTATTAAATT
**
28607692 AATATTTTAATTTTAAAA
1 AATATTTTAATTGAAAAA
28607710 AATATTTTAATTGAATAAA
1 AATATTTTAATTGAA-AAA
28607729 AATAT
1 AATAT
28607734 AATTAATAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (18 bp):
AATATTTTAATTGAAAAA
Found at i:28617316 original size:22 final size:21
Alignment explanation
Indices: 28617292--28617351 Score: 93
Period size: 21 Copynumber: 2.8 Consensus size: 21
28617282 AATTACAAAA
28617292 AAAAAATTCAAAATAATTTTC
1 AAAAAATTCAAAATAATTTTC
* *
28617313 AAAAAATTTAAAATAGTTTTC
1 AAAAAATTCAAAATAATTTTC
28617334 AAAAAATTCTAAAATAAT
1 AAAAAATTC-AAAATAAT
28617352 AATTTTTGGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 27 0.79
22 7 0.21
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (21 bp):
AAAAAATTCAAAATAATTTTC
Found at i:28617320 original size:11 final size:12
Alignment explanation
Indices: 28617298--28617351 Score: 55
Period size: 11 Copynumber: 4.9 Consensus size: 12
28617288 AAAAAAAAAA
28617298 TTCAAAATAATT
1 TTCAAAATAATT
28617310 TTCAAAA-AA-T
1 TTCAAAATAATT
*
28617320 TT-AAAATAGTT
1 TTCAAAATAATT
28617331 TTCAAAA-AATT
1 TTCAAAATAATT
*
28617342 CT-AAAATAAT
1 TTCAAAATAAT
28617352 AATTTTTGGA
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
9 4 0.11
10 8 0.23
11 12 0.34
12 11 0.31
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (12 bp):
TTCAAAATAATT
Found at i:28620657 original size:12 final size:11
Alignment explanation
Indices: 28620625--28620663 Score: 55
Period size: 10 Copynumber: 3.6 Consensus size: 11
28620615 CTCTCTTAAC
28620625 AAAAATTAT-A
1 AAAAATTATCA
28620635 AAAAA-TATCA
1 AAAAATTATCA
28620645 AAATAATTATCA
1 AAA-AATTATCA
28620657 AAAAATT
1 AAAAATT
28620664 TAAAATGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 3 0.12
10 9 0.35
11 6 0.23
12 8 0.31
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (11 bp):
AAAAATTATCA
Found at i:28620734 original size:20 final size:18
Alignment explanation
Indices: 28620695--28620767 Score: 67
Period size: 19 Copynumber: 3.8 Consensus size: 18
28620685 AAATATTGAT
*
28620695 AAAATTCTAGAAAA-ATAA
1 AAAATT-TAAAAAATATAA
*
28620713 AAAATTTAAAGAATATATA
1 AAAATTTAAAAAATATA-A
*
28620732 AAAATGTTAAAAAATTTAA
1 AAAAT-TTAAAAAATATAA
28620751 AAAATTCTAAAATAATA
1 AAAATT-TAAAA-AATA
28620768 ATTTTTGGAC
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
17 5 0.11
18 10 0.22
19 17 0.38
20 13 0.29
ACGTcount: A:0.64, C:0.03, G:0.04, T:0.29
Consensus pattern (18 bp):
AAAATTTAAAAAATATAA
Found at i:28620754 original size:9 final size:9
Alignment explanation
Indices: 28620625--28620762 Score: 64
Period size: 9 Copynumber: 14.3 Consensus size: 9
28620615 CTCTCTTAAC
28620625 AAAAATTATA
1 AAAAATT-TA
*
28620635 AAAAATATCA
1 AAAAAT-TTA
28620645 AAATAATTATCA
1 AAA-AATT-T-A
28620657 AAAAATTTA
1 AAAAATTTA
* *
28620666 AAATGATTTT
1 AAA-AATTTA
* * *
28620676 TAGAATTCA
1 AAAAATTTA
* *
28620685 AAATATTGA
1 AAAAATTTA
*
28620694 TAAAATTCTA
1 AAAAATT-TA
28620704 GAAAAA--TA
1 -AAAAATTTA
28620712 AAAAATTTA
1 AAAAATTTA
* *
28620721 AAGAATATA
1 AAAAATTTA
28620730 TAAAAATGTTA
1 -AAAAAT-TTA
28620741 AAAAATTTA
1 AAAAATTTA
28620750 AAAAATTCTA
1 AAAAATT-TA
28620760 AAA
1 AAA
28620763 TAATAATTTT
Statistics
Matches: 95, Mismatches: 21, Indels: 24
0.68 0.15 0.17
Matches are distributed among these distances:
7 5 0.05
8 2 0.02
9 36 0.38
10 34 0.36
11 14 0.15
12 4 0.04
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.31
Consensus pattern (9 bp):
AAAAATTTA
Found at i:28632451 original size:23 final size:24
Alignment explanation
Indices: 28632424--28632479 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
28632414 TTTTCTTCTA
* *
28632424 GTTTTTATCTGT-CTTTGTGGCAC
1 GTTTTTATCTCTGCCTTGTGGCAC
*
28632447 GTTTTT-TCTCTGCCTTGTGGTAC
1 GTTTTTATCTCTGCCTTGTGGCAC
28632470 GTTTTTATCT
1 GTTTTTATCT
28632480 TATGGCACAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.14
23 21 0.75
24 3 0.11
ACGTcount: A:0.07, C:0.18, G:0.20, T:0.55
Consensus pattern (24 bp):
GTTTTTATCTCTGCCTTGTGGCAC
Found at i:28635128 original size:2 final size:2
Alignment explanation
Indices: 28635121--28635148 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
28635111 TAATCAGTAC
28635121 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
28635149 GCATGTACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28636112 original size:33 final size:31
Alignment explanation
Indices: 28636057--28636117 Score: 86
Period size: 33 Copynumber: 1.9 Consensus size: 31
28636047 TCAATTGAGC
28636057 CCTTAGACGTTAAAATTACAATAAATCAAGT
1 CCTTAGACGTTAAAATTACAATAAATCAAGT
* *
28636088 CCTTTGACGGTTAAAGTTAACAATAAATCA
1 CCTTAGAC-GTTAAAATT-ACAATAAATCA
28636118 TTACAGATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 7 0.27
32 8 0.31
33 11 0.42
ACGTcount: A:0.43, C:0.16, G:0.11, T:0.30
Consensus pattern (31 bp):
CCTTAGACGTTAAAATTACAATAAATCAAGT
Found at i:28636364 original size:20 final size:21
Alignment explanation
Indices: 28636334--28636384 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
28636324 CAAAATATTC
*
28636334 AAAAATAATAT-AAATTA-AA
1 AAAAATTATATAAAATTACAA
28636353 AATAAATTATATAAAATTACAA
1 AA-AAATTATATAAAATTACAA
28636375 AAAAA-TATAT
1 AAAAATTATAT
28636385 TTAGAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 2 0.07
20 13 0.46
21 9 0.32
22 4 0.14
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (21 bp):
AAAAATTATATAAAATTACAA
Found at i:28636396 original size:24 final size:25
Alignment explanation
Indices: 28636350--28636397 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
28636340 AATATAAATT
*
28636350 AAAAATAAATTATATAAAATTACAA
1 AAAAATAAATTATAGAAAATTACAA
* *
28636375 AAAAATATATT-TAGAAATTTACA
1 AAAAATAAATTATAGAAAATTACA
28636398 TATAATCTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.31
Consensus pattern (25 bp):
AAAAATAAATTATAGAAAATTACAA
Found at i:28636754 original size:2 final size:2
Alignment explanation
Indices: 28636747--28636787 Score: 57
Period size: 2 Copynumber: 20.5 Consensus size: 2
28636737 AATTATTACA
*
28636747 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT CAT TT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT A
28636788 ATTTTTTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 1 0.03
2 32 0.91
3 2 0.06
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28636927 original size:20 final size:19
Alignment explanation
Indices: 28636886--28636928 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
28636876 ACTTTAGTAT
* *
28636886 TTTTTATATTTTTTTATGA
1 TTTTTATATTTATTAATGA
*
28636905 TTTTTATAATTTATTAATTA
1 TTTTTAT-ATTTATTAATGA
28636925 TTTT
1 TTTT
28636929 AAATATAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (19 bp):
TTTTTATATTTATTAATGA
Found at i:28640352 original size:2 final size:2
Alignment explanation
Indices: 28640341--28640386 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
28640331 CCAAGATCTA
28640341 CT CT -T CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
28640382 CT CT C
1 CT CT C
28640387 AAAATCAAAG
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:28656963 original size:43 final size:43
Alignment explanation
Indices: 28656896--28657101 Score: 313
Period size: 43 Copynumber: 4.8 Consensus size: 43
28656886 GTGAATTCTT
28656896 AATGGAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTATA
1 AATGGAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTATA
* * *
28656939 AATGAAAGACTTATGTCTCAGTTAGAGCAAAAGATTGTTTATA
1 AATGGAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTATA
*
28656982 AATGGAAGACTTATGTCTCGATTAGAGCATAAGATTGTTTATA
1 AATGGAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTATA
* * * * *
28657025 AACGAAAGACTTATGTCTCGGCTAGAGCATAAGATTATTTGTA
1 AATGGAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTATA
*
28657068 AATGGAAGAACTTATGTCTCGGCTAGAGCATAAG
1 AATGGAAG-ACTTATGTCTCGGTTAGAGCATAAG
28657102 GTTAATTCAG
Statistics
Matches: 147, Mismatches: 15, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
43 122 0.83
44 25 0.17
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.32
Consensus pattern (43 bp):
AATGGAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTATA
Found at i:28661176 original size:22 final size:23
Alignment explanation
Indices: 28661148--28661190 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
28661138 AAGCGGACTT
28661148 TTAAATT-TGAAAAGTAAAAAGA
1 TTAAATTCTGAAAAGTAAAAAGA
*
28661170 TTAAATTCTTAAAAGTAAAAA
1 TTAAATTCTGAAAAGTAAAAA
28661191 TAAATGGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.58, C:0.02, G:0.09, T:0.30
Consensus pattern (23 bp):
TTAAATTCTGAAAAGTAAAAAGA
Found at i:28673892 original size:3 final size:3
Alignment explanation
Indices: 28673879--28673912 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
28673869 TTGAATGAAC
28673879 TAA TGAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
28673913 AGGAGGGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:28675003 original size:17 final size:17
Alignment explanation
Indices: 28674981--28675023 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
28674971 AAATCACATT
28674981 TATTTTTGAAAA-TTTTA
1 TATTTTT-AAAACTTTTA
28674998 TATTTTTAAAATCTTTTA
1 TATTTTTAAAA-CTTTTA
28675016 TATTTTTA
1 TATTTTTA
28675024 TTTTTTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.17
17 7 0.29
18 13 0.54
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (17 bp):
TATTTTTAAAACTTTTA
Found at i:28675081 original size:21 final size:22
Alignment explanation
Indices: 28675043--28675083 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
28675033 TTGTAAAGAG
*
28675043 TTTTATTGTTTCATAATTTTGT
1 TTTTATTGTTTCAAAATTTTGT
*
28675065 TTTTATT-TTTTAAAATTTT
1 TTTTATTGTTTCAAAATTTT
28675084 TATGTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.71
Consensus pattern (22 bp):
TTTTATTGTTTCAAAATTTTGT
Found at i:28677510 original size:22 final size:22
Alignment explanation
Indices: 28677468--28677512 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
28677458 AACTCACCAT
*
28677468 TTTTGTAACTTACAAATCATAA
1 TTTTGTAACTTACAAACCATAA
*
28677490 TTTTGTAACTCTAC-AGCCATAA
1 TTTTGTAACT-TACAAACCATAA
28677512 T
1 T
28677513 ATTTTGTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.36, C:0.18, G:0.07, T:0.40
Consensus pattern (22 bp):
TTTTGTAACTTACAAACCATAA
Found at i:28679664 original size:16 final size:16
Alignment explanation
Indices: 28679643--28679673 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28679633 AATCAAATAT
*
28679643 TTTTTTATTTTTAAAG
1 TTTTTTAATTTTAAAG
28679659 TTTTTTAATTTTAAA
1 TTTTTTAATTTTAAA
28679674 AAAATGAAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (16 bp):
TTTTTTAATTTTAAAG
Found at i:28681209 original size:38 final size:41
Alignment explanation
Indices: 28681165--28681247 Score: 136
Period size: 41 Copynumber: 2.1 Consensus size: 41
28681155 TCACAAATTA
*
28681165 ACTTTTAAA-TT-TTTTTTT-TAAATAATACCTATATGTTT
1 ACTTTTAAAGTTGTTTTTTTCAAAATAATACCTATATGTTT
28681203 ACTTTTAAAGTTGTTTTTTTCAAAATAATACCTATATGTTT
1 ACTTTTAAAGTTGTTTTTTTCAAAATAATACCTATATGTTT
28681244 ACTT
1 ACTT
28681248 GTCTCATTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
38 9 0.22
39 2 0.05
40 7 0.17
41 23 0.56
ACGTcount: A:0.31, C:0.10, G:0.05, T:0.54
Consensus pattern (41 bp):
ACTTTTAAAGTTGTTTTTTTCAAAATAATACCTATATGTTT
Found at i:28682167 original size:8 final size:8
Alignment explanation
Indices: 28682154--28682178 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
28682144 CTTAAGTGAT
28682154 AAATGTTA
1 AAATGTTA
28682162 AAATGTTA
1 AAATGTTA
28682170 AAATGTTA
1 AAATGTTA
28682178 A
1 A
28682179 TTTAATTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.36
Consensus pattern (8 bp):
AAATGTTA
Found at i:28682818 original size:17 final size:17
Alignment explanation
Indices: 28682797--28682835 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
28682787 TAAAAGTAGG
28682797 GAAAAGACAAAAAAGAAA
1 GAAAAGA-AAAAAAGAAA
*
28682815 -AAAAGAAAAAAGGAAA
1 GAAAAGAAAAAAAGAAA
28682831 GAAAA
1 GAAAA
28682836 CCTACTTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (17 bp):
GAAAAGAAAAAAAGAAA
Found at i:28683232 original size:16 final size:17
Alignment explanation
Indices: 28683211--28683247 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
28683201 ATTAAATAAT
*
28683211 TAAAATAAATAAACAA-
1 TAAAATAAACAAACAAC
28683227 TAAAATAAACAAACAAC
1 TAAAATAAACAAACAAC
28683244 TAAA
1 TAAA
28683248 CAAATCAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.73, C:0.11, G:0.00, T:0.16
Consensus pattern (17 bp):
TAAAATAAACAAACAAC
Found at i:28684199 original size:16 final size:17
Alignment explanation
Indices: 28684175--28684207 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
28684165 TAGATAATGT
28684175 ACTACTATTAT-ATATA
1 ACTACTATTATAATATA
*
28684191 ACTATTATTATAATATA
1 ACTACTATTATAATATA
28684208 GGTTATAATA
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:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (17 bp):
ACTACTATTATAATATA
Found at i:28684412 original size:16 final size:17
Alignment explanation
Indices: 28684370--28684426 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
28684360 ATATTTCAAC
*
28684370 TAATATAA-TAATATATA
1 TAATATAACTACTAT-TA
*
28684387 TAATGT-ACTACTATTA
1 TAATATAACTACTATTA
*
28684403 T-ATATAACTATTATTA
1 TAATATAACTACTATTA
28684419 TAATATAA
1 TAATATAA
28684427 ATTATAATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
15 3 0.09
16 14 0.42
17 16 0.48
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (17 bp):
TAATATAACTACTATTA
Found at i:28684716 original size:19 final size:20
Alignment explanation
Indices: 28684692--28684731 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
28684682 TATAACGAAA
28684692 TAATATAT-TTTATAAATAT
1 TAATATATATTTATAAATAT
*
28684711 TAATATATATTTATAATTAT
1 TAATATATATTTATAAATAT
28684731 T
1 T
28684732 TTTATATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TAATATATATTTATAAATAT
Found at i:28695251 original size:21 final size:21
Alignment explanation
Indices: 28695222--28695263 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
28695212 TATGCTTTCA
* *
28695222 AATAATATATTAATTAATAAT
1 AATAATATAATAAATAATAAT
*
28695243 AATATTATAATAAATAATAAT
1 AATAATATAATAAATAATAAT
28695264 GTTTTAATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AATAATATAATAAATAATAAT
Found at i:28695271 original size:18 final size:18
Alignment explanation
Indices: 28695222--28695272 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
28695212 TATGCTTTCA
* *
28695222 AATAATATATTAATTAAT
1 AATAATATTTTAATAAAT
*
28695240 AATAATATTATAATAAAT
1 AATAATATTTTAATAAAT
*
28695258 AATAATGTTTTAATA
1 AATAATATTTTAATA
28695273 TTTATATTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
AATAATATTTTAATAAAT
Found at i:28696693 original size:15 final size:15
Alignment explanation
Indices: 28696673--28696702 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
28696663 TTATTGTGTG
28696673 AATTAAATTGATTAT
1 AATTAAATTGATTAT
28696688 AATTAAATTGATTAT
1 AATTAAATTGATTAT
28696703 GTGATTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (15 bp):
AATTAAATTGATTAT
Found at i:28703030 original size:58 final size:58
Alignment explanation
Indices: 28702968--28703275 Score: 381
Period size: 58 Copynumber: 5.3 Consensus size: 58
28702958 ACCCGGGGGC
** * *
28702968 AAAATGGTAA-TTTTAATGAAATTAGGGTTAAAAATGGAATTTTTGAGAGTTCGAGGGT
1 AAAATGGTAATTTTTGGTGAAATTAGGGTT-AAAATGGAATTTTGGAAAGTTCGAGGGT
* * * *
28703026 AAAATGGTAATTTTTGGTGAAATCAAGGTTAAAAATAGAATTTTGGAAAGTT-TACGGGT
1 AAAATGGTAATTTTTGGTGAAATTAGGGTT-AAAATGGAATTTTGGAAAGTTCGA-GGGT
* **
28703085 AAAATGGTAATTTTTGGTGAAA-TCGAGGTTAAAATGGAATTTTGGAAAGTTTAAGGGT
1 AAAATGGTAATTTTTGGTGAAATTAG-GGTTAAAATGGAATTTTGGAAAGTTCGAGGGT
* * * * *
28703143 AAAATGGTAA-TTTTGATGAAATTGGGGGTTAAAATGGAATTTTGGAGAGTTTGGGGGT
1 AAAATGGTAATTTTTGGTGAAATT-AGGGTTAAAATGGAATTTTGGAAAGTTCGAGGGT
* *
28703201 AAAATAGTAATTTTTGGTGAAATTAGGGTTAAAATGGAATTTTGGAAAGTTCGGGGGT
1 AAAATGGTAATTTTTGGTGAAATTAGGGTTAAAATGGAATTTTGGAAAGTTCGAGGGT
28703259 AAAATGGTAATTTTTGG
1 AAAATGGTAATTTTTGG
28703276 AAGTTTCGGG
Statistics
Matches: 219, Mismatches: 24, Indels: 14
0.85 0.09 0.05
Matches are distributed among these distances:
57 10 0.05
58 131 0.60
59 78 0.36
ACGTcount: A:0.36, C:0.02, G:0.28, T:0.35
Consensus pattern (58 bp):
AAAATGGTAATTTTTGGTGAAATTAGGGTTAAAATGGAATTTTGGAAAGTTCGAGGGT
Found at i:28703279 original size:29 final size:27
Alignment explanation
Indices: 28702998--28703286 Score: 127
Period size: 30 Copynumber: 9.9 Consensus size: 27
28702988 ATTAGGGTTA
* *
28702998 AAAATGGAATTTTTGAGAGTTCGAGGGT
1 AAAATGGAATTTTGGA-AGTTCGGGGGT
* ** *
28703026 AAAATGGTAATTTTTGGTGAA-ATCAAGGTT
1 AAAATGG-AA-TTTT-G-GAAGTTCGGGGGT
* ***
28703056 AAAAATAGAATTTTGGAAAGTTTACGGGT
1 -AAAATGGAATTTTGG-AAGTTCGGGGGT
* * *
28703085 AAAATGGTAATTTTTGGTGAA-ATCGAGGTT
1 AAAATGG-AA-TTTT-G-GAAGTTCGGGGGT
***
28703115 AAAATGGAATTTTGGAAAGTTTAAGGGT
1 AAAATGGAATTTTGG-AAGTTCGGGGGT
*
28703143 AAAATGGTAATTTTGATGAAATT-GGGGGTT
1 AAAATGG-AATTTTG--GAAGTTCGGGGG-T
*
28703173 AAAATGGAATTTTGGAGAGTTTGGGGGT
1 AAAATGGAATTTTGGA-AGTTCGGGGGT
* * * *
28703201 AAAATAGTAATTTTTGGTGAAATT-AGGGTT
1 AAAAT-GGAA-TTTT-G-GAAGTTCGGGGGT
28703231 AAAATGGAATTTTGGAAAGTTCGGGGGT
1 AAAATGGAATTTTGG-AAGTTCGGGGGT
28703259 AAAATGGTAATTTTTGGAAGTTTCGGGG
1 AAAATGG-AA-TTTTGGAAG-TTCGGGG
28703287 TCAGAATGTA
Statistics
Matches: 202, Mismatches: 31, Indels: 54
0.70 0.11 0.19
Matches are distributed among these distances:
26 2 0.01
27 11 0.05
28 56 0.28
29 48 0.24
30 65 0.32
31 15 0.07
32 5 0.02
ACGTcount: A:0.34, C:0.02, G:0.29, T:0.34
Consensus pattern (27 bp):
AAAATGGAATTTTGGAAGTTCGGGGGT
Found at i:28703287 original size:29 final size:28
Alignment explanation
Indices: 28703064--28703300 Score: 134
Period size: 30 Copynumber: 8.2 Consensus size: 28
28703054 TTAAAAATAG
28703064 AATTTTGGAAAGTTTAC-GGGTAAAATGGT
1 AATTTTGG-AAGTTT-CGGGGTAAAATGGT
* *
28703093 AATTTTTGGTGAA--ATCGAGGTTAAAATGG-
1 AA-TTTT-G-GAAGTTTCG-GGGTAAAATGGT
**
28703122 AATTTTGGAAAGTTTAAGGGTAAAATGGT
1 AATTTTGG-AAGTTTCGGGGTAAAATGGT
* *
28703151 AATTTTGATGAA-ATTGGGGGTTAAAATGG-
1 AATTTTG--GAAGTTTCGGGG-TAAAATGGT
* *
28703180 AATTTTGGAGAGTTTGGGGGTAAAATAGT
1 AATTTTGGA-AGTTTCGGGGTAAAATGGT
* * *
28703209 AATTTTTGGTGAA-ATTAGGGTTAAAATGG-
1 AA-TTTT-G-GAAGTTTCGGGGTAAAATGGT
28703238 AATTTTGGAAAG-TTCGGGGGTAAAATGGT
1 AATTTTGG-AAGTTTC-GGGGTAAAATGGT
*
28703267 AATTTTTGGAAGTTTCGGGGTCAGAAT-GT
1 AA-TTTTGGAAGTTTCGGGGT-AAAATGGT
28703296 AATTT
1 AATTT
28703301 CCTAAAATTT
Statistics
Matches: 165, Mismatches: 18, Indels: 51
0.71 0.08 0.22
Matches are distributed among these distances:
26 2 0.01
27 10 0.06
28 41 0.25
29 50 0.30
30 53 0.32
31 6 0.04
32 3 0.02
ACGTcount: A:0.33, C:0.02, G:0.30, T:0.35
Consensus pattern (28 bp):
AATTTTGGAAGTTTCGGGGTAAAATGGT
Found at i:28703316 original size:116 final size:113
Alignment explanation
Indices: 28702984--28703333 Score: 355
Period size: 116 Copynumber: 3.0 Consensus size: 113
28702974 GTAATTTTAA
* * *
28702984 TGAAATTAGGGTTAAAAATGGAATTTTTGAGAGTTCGAGGGTAAAATGGTAATTTTTGGTGAAAT
1 TGAAATTAGGGTT-AAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTT-GTGAATT
* * *
28703049 CAAGGTTAAAAATAGAATTTTGGAAAGTTTACGGGTAAAATGGTAATTTTTGG
64 C-GGGGTAAAAAT-GAATTTTGGAAAGTTTAGGGGTAAAAT-GTAATTTTTGG
* **
28703102 TGAAA-TCGAGGTTAAAATGGAATTTTGGAAAGTTTAAGGGTAAAATGGTAA-TTTTGATGAAAT
1 TGAAATTAG-GGTTAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTG-TG-AAT
* * * *
28703165 TGGGGGTTAAAATGGAATTTTGGAGAGTTTGGGGGTAAAATAGTAATTTTTGG
63 TCGGGGTAAAAAT-GAATTTTGGAAAGTTTAGGGGTAAAAT-GTAATTTTTGG
*
28703218 TGAAATTAGGGTTAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTG-GAAGTTT
1 TGAAATTAGGGTTAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGTGAA--TT
* * *** * * *
28703282 CGGGGTCAGAATGTAATTTCCTAAAATTTTGGGGTCAAAATGCAATTTTTGG
64 CGGGGTAAAAATG-AATTTTGGAAAGTTTAGGGGT-AAAATGTAATTTTTGG
28703334 ACTATTTGGG
Statistics
Matches: 194, Mismatches: 29, Indels: 20
0.80 0.12 0.08
Matches are distributed among these distances:
114 2 0.01
115 3 0.02
116 129 0.66
117 51 0.26
118 9 0.05
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.35
Consensus pattern (113 bp):
TGAAATTAGGGTTAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGTGAATTCG
GGGTAAAAATGAATTTTGGAAAGTTTAGGGGTAAAATGTAATTTTTGG
Found at i:28705235 original size:6 final size:6
Alignment explanation
Indices: 28705226--28705325 Score: 75
Period size: 6 Copynumber: 16.8 Consensus size: 6
28705216 TTGAATTTGA
* * *
28705226 TTAAAT TTAAAT CTAAA- ATAAAT TTAAAT AAGTAAAT TTAAAT TTAAGA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT --TTAAAT TTAAAT TTAA-AT
** *
28705275 -TAAAT TTAAAT TTAAAT TTAAA- ACAAAT TTAAAA TT-AAT TTAAACT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA-T
28705321 TTAAA
1 TTAAA
28705326 AGCCCAAGCC
Statistics
Matches: 74, Mismatches: 11, Indels: 17
0.73 0.11 0.17
Matches are distributed among these distances:
4 1 0.01
5 14 0.19
6 47 0.64
7 7 0.09
8 5 0.07
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (6 bp):
TTAAAT
Found at i:28705247 original size:17 final size:17
Alignment explanation
Indices: 28705227--28705326 Score: 91
Period size: 17 Copynumber: 6.0 Consensus size: 17
28705217 TGAATTTGAT
*
28705227 TAAATTTAAATCTAAAA
1 TAAATTTAAATTTAAAA
*
28705244 TAAATTTAAA--T-AAG
1 TAAATTTAAATTTAAAA
*
28705258 TAAATTTAAATTTAAGA
1 TAAATTTAAATTTAAAA
*
28705275 TAAATTTAAATTTAAATT
1 TAAATTTAAATTTAAA-A
**
28705293 TAAA-ACAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
28705309 TTAATTTAAACTTTAAAA
1 TAAATTTAAA-TTTAAAA
28705327 GCCCAAGCCC
Statistics
Matches: 66, Mismatches: 11, Indels: 11
0.75 0.12 0.12
Matches are distributed among these distances:
14 12 0.18
15 1 0.02
16 4 0.06
17 38 0.58
18 11 0.17
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:28705253 original size:11 final size:11
Alignment explanation
Indices: 28705233--28705318 Score: 70
Period size: 11 Copynumber: 7.9 Consensus size: 11
28705223 TGATTAAATT
*
28705233 TAAATCTAAAA
1 TAAATTTAAAA
28705244 TAAATTT-AAA
1 TAAATTTAAAA
* *
28705254 T-AA-GTAAATT
1 TAAATTTAAA-A
*
28705264 TAAATTTAAGA
1 TAAATTTAAAA
*
28705275 TAAATTTAAATT
1 TAAATTTAAA-A
28705287 TAAATTTAAAA
1 TAAATTTAAAA
*
28705298 CAAATTTAAAA
1 TAAATTTAAAA
*
28705309 TTAATTTAAA
1 TAAATTTAAA
28705319 CTTTAAAAGC
Statistics
Matches: 58, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
8 1 0.02
9 4 0.07
10 5 0.09
11 35 0.60
12 13 0.22
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:28705262 original size:31 final size:31
Alignment explanation
Indices: 28705227--28705285 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
28705217 TGAATTTGAT
28705227 TAAATTTAAATCTAAAATAAATTTAAATAAG
1 TAAATTTAAATCTAAAATAAATTTAAATAAG
* *
28705258 TAAATTTAAATTTAAGATAAATTTAAAT
1 TAAATTTAAATCTAAAATAAATTTAAAT
28705286 TTAAATTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (31 bp):
TAAATTTAAATCTAAAATAAATTTAAATAAG
Found at i:28705288 original size:23 final size:23
Alignment explanation
Indices: 28705258--28705318 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
28705248 TTTAAATAAG
* *
28705258 TAAATTTAAATTTAAGATAAATT
1 TAAATTTAAATTTAAAACAAATT
28705281 TAAATTTAAATTTAAAACAAATT
1 TAAATTTAAATTTAAAACAAATT
*
28705304 TAAAATT-AATTTAAA
1 TAAATTTAAATTTAAA
28705319 CTTTAAAAGC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
22 8 0.23
23 27 0.77
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (23 bp):
TAAATTTAAATTTAAAACAAATT
Found at i:28705670 original size:38 final size:37
Alignment explanation
Indices: 28705619--28705972 Score: 153
Period size: 38 Copynumber: 9.4 Consensus size: 37
28705609 CTATCCAACT
28705619 TTACTTCAATTTCAAGAGGATGGGAAACGATCTTGCTC
1 TTACTTCAATTTCAAGAGGAT-GGAAACGATCTTGCTC
* ***
28705657 TTACTTCAATTTC-AGA-GAT-TAAGACTTGTTATCCAACTC
1 TTACTTCAATTTCAAGAGGATGGAA-AC--G--ATCTTGCTC
* *
28705696 -TACTTCAATTTCAAGAGGATATGAAATGATCTTGCTC
1 TTACTTCAATTTCAAGAGGAT-GGAAACGATCTTGCTC
** ***
28705733 TTACTTCAATTTC-AGA-GATAAAAACTTGTTATCCAACTC
1 TTACTTCAATTTCAAGAGGATGGAAAC--G--ATCTTGCTC
* * *
28705772 -TACTTCAATTTCAAGCGAATAGGAAAAGATCTTGCTC
1 TTACTTCAATTTCAAGAGGAT-GGAAACGATCTTGCTC
* * * * *
28705809 TTACTTTAATTTC-AGA-GAT-AAAGACG-TGTTATCCAC
1 TTACTTCAATTTCAAGAGGATGGAA-ACGAT-CT-TGCTC
* *
28705845 TCTACTTCAATTTCAAGCGGATAGGAAAAGATCTTGCTC
1 T-TACTTCAATTTCAAGAGGAT-GGAAACGATCTTGCTC
* * * *
28705884 TTACTTCAATTTC-AGA-GAT-AAATACG-TGTTATCCAC
1 TTACTTCAATTTCAAGAGGATGGAA-ACGAT-CT-TGCTC
* *
28705920 TCTACTTCAATTTCAAGCGGATAGGAAAAGATCTTGCTC
1 T-TACTTCAATTTCAAGAGGAT-GGAAACGATCTTGCTC
*
28705959 TTACTTTAATTTCA
1 TTACTTCAATTTCA
28705973 GAGATAAATA
Statistics
Matches: 229, Mismatches: 51, Indels: 72
0.65 0.14 0.20
Matches are distributed among these distances:
34 8 0.03
35 11 0.05
36 19 0.08
37 47 0.21
38 88 0.38
39 33 0.14
40 11 0.05
41 10 0.04
42 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (37 bp):
TTACTTCAATTTCAAGAGGATGGAAACGATCTTGCTC
Found at i:28705883 original size:75 final size:76
Alignment explanation
Indices: 28705594--28706031 Score: 673
Period size: 76 Copynumber: 5.8 Consensus size: 76
28705584 TGCTCTACAG
* * * * *
28705594 AGAGATAAAGACTTGCTATCCAACTTTACTTCAATTTCAAGAGGATGGGAAACGATCTTGCTCTT
1 AGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
28705659 ACTTCAATTTC
66 ACTTCAATTTC
* * * *
28705670 AGAGATTAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATATGAAATGATCTTGCTCTT
1 AGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
28705735 ACTTCAATTTC
66 ACTTCAATTTC
* * * *
28705746 AGAGATAAAAACTTGTTATCCAACTCTACTTCAATTTCAAGCGAATAGGAAAAGATCTTGCTCTT
1 AGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
*
28705811 ACTTTAATTTC
66 ACTTCAATTTC
*
28705822 AGAGATAAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGCGGATAGGAAAAGATCTTGCTCTT
1 AGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
28705886 ACTTCAATTTC
66 ACTTCAATTTC
* *
28705897 AGAGATAAATACGTGTTATCC-ACTCTACTTCAATTTCAAGCGGATAGGAAAAGATCTTGCTCTT
1 AGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
*
28705961 ACTTTAATTTC
66 ACTTCAATTTC
* * *
28705972 AGAGATAAATACGTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGGAATGATCTTG
1 AGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTG
28706032 TTGCGGTCTG
Statistics
Matches: 339, Mismatches: 22, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
75 146 0.43
76 193 0.57
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (76 bp):
AGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
ACTTCAATTTC
Found at i:28705998 original size:151 final size:152
Alignment explanation
Indices: 28705594--28706031 Score: 709
Period size: 151 Copynumber: 2.9 Consensus size: 152
28705584 TGCTCTACAG
* * * * * *
28705594 AGAGATAAAGACTTGCTATCCAACTTTACTTCAATTTCAAGAGGATGGGAAACGATCTTGCTCTT
1 AGAGATAAAAACTTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAAAGATCTTGCTCTT
* * * *
28705659 ACTTCAATTTCAGAGATTAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATATGAAATG
66 ACTTTAATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAATG
28705724 ATCTTGCTCTTACTTCAATTTC
131 ATCTTGCTCTTACTTCAATTTC
*
28705746 AGAGATAAAAACTTGTTATCCAACTCTACTTCAATTTCAAGCGAATAGGAAAAGATCTTGCTCTT
1 AGAGATAAAAACTTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAAAGATCTTGCTCTT
* *
28705811 ACTTTAATTTCAGAGATAAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGCGGATAGGAAAAG
66 ACTTTAATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAATG
28705875 ATCTTGCTCTTACTTCAATTTC
131 ATCTTGCTCTTACTTCAATTTC
* *
28705897 AGAGATAAATACGTGTTATCC-ACTCTACTTCAATTTCAAGCGGATAGGAAAAGATCTTGCTCTT
1 AGAGATAAAAACTTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAAAGATCTTGCTCTT
* *
28705961 ACTTTAATTTCAGAGATAAATACGTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGGAATG
66 ACTTTAATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAATG
28706026 ATCTTG
131 ATCTTG
28706032 TTGCGGTCTG
Statistics
Matches: 265, Mismatches: 20, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
150 73 0.28
151 105 0.40
152 87 0.33
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (152 bp):
AGAGATAAAAACTTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAAAGATCTTGCTCTT
ACTTTAATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAATG
ATCTTGCTCTTACTTCAATTTC
Found at i:28718083 original size:28 final size:27
Alignment explanation
Indices: 28718033--28718200 Score: 122
Period size: 29 Copynumber: 5.8 Consensus size: 27
28718023 AACGATAGAA
* *
28718033 TCGGGGTTAAAAATGGAACTTTTGGATAC
1 TCGGGGGT-AAAATGGAA-TTTTGGAAAC
* *
28718062 CCGGGGGTAAAATGGTAATTTTGGTAAAA
1 TCGGGGGTAAAATGG-AATTTTGG-AAAC
*
28718091 TCGGGGTTAAAAATGGAATTTTGGAAAC
1 TCGGGGGT-AAAATGGAATTTTGGAAAC
*
28718119 TTCGAGGGTAAAATGGTAATTTTTGGTGAAA-
1 -TCGGGGGTAAAATGG-AA-TTTT-G-GAAAC
* * * *
28718150 TTGAGGTTAAAATGGAATTTTGGAAAGT
1 TCGGGGGTAAAATGGAATTTTGGAAA-C
*
28718178 TTGGGGGTAAAATGGTAATTTTG
1 TCGGGGGTAAAATGG-AATTTTG
28718201 ATGAAATTAA
Statistics
Matches: 115, Mismatches: 13, Indels: 22
0.77 0.09 0.15
Matches are distributed among these distances:
26 4 0.03
27 1 0.01
28 40 0.35
29 41 0.36
30 24 0.21
31 1 0.01
32 4 0.03
ACGTcount: A:0.33, C:0.05, G:0.30, T:0.33
Consensus pattern (27 bp):
TCGGGGGTAAAATGGAATTTTGGAAAC
Found at i:28718095 original size:29 final size:29
Alignment explanation
Indices: 28718032--28718200 Score: 125
Period size: 28 Copynumber: 5.8 Consensus size: 29
28718022 AAACGATAGA
* *
28718032 ATCGGGGTTAAAAATGG-AACTTTTGGATAC
1 ATCGGGGGT-AAAATGGTAA-TTTTGGAAAC
*
28718062 -CCGGGGGTAAAATGGTAATTTTGGTAAA-
1 ATCGGGGGTAAAATGGTAATTTTGG-AAAC
*
28718090 ATCGGGGTTAAAAATGG-AATTTTGGAAAC
1 ATCGGGGGT-AAAATGGTAATTTTGGAAAC
* * *
28718119 TTCGAGGGTAAAATGGTAATTTTTGGTGAA-
1 ATCGGGGGTAAAATGGTAA-TTTTGG-AAAC
* * * *
28718149 ATTGAGGTTAAAATGG-AATTTTGGAAAG
1 ATCGGGGGTAAAATGGTAATTTTGGAAAC
* *
28718177 TTTGGGGGTAAAATGGTAATTTTG
1 ATCGGGGGTAAAATGGTAATTTTG
28718201 ATGAAATTAA
Statistics
Matches: 113, Mismatches: 16, Indels: 21
0.75 0.11 0.14
Matches are distributed among these distances:
27 2 0.02
28 42 0.37
29 41 0.36
30 26 0.23
31 2 0.02
ACGTcount: A:0.33, C:0.05, G:0.30, T:0.33
Consensus pattern (29 bp):
ATCGGGGGTAAAATGGTAATTTTGGAAAC
Found at i:28718217 original size:29 final size:28
Alignment explanation
Indices: 28718069--28718288 Score: 153
Period size: 29 Copynumber: 7.5 Consensus size: 28
28718059 TACCCGGGGG
* * * *
28718069 TAAAATGGTAATTTTGGTAAAATCGGGGT
1 TAAAATGG-AATTTTGATGAAATTGAGGT
*
28718098 TAAAAATGGAATTTTG--GAAACTTCGAGGG
1 T-AAAATGGAATTTTGATGAAA-TT-GAGGT
*
28718127 TAAAATGGTAATTTTTGGTGAAATTGAGGT
1 TAAAATGG-AA-TTTTGATGAAATTGAGGT
* *
28718157 TAAAATGGAATTTTG--GAAAGTTTGGGGG
1 TAAAATGGAATTTTGATGAAA--TTGAGGT
*
28718185 TAAAATGGTAATTTTGATGAAATTAAGGT
1 TAAAATGG-AATTTTGATGAAATTGAGGT
** * *
28718214 TAAAAATGGAATTTTAGA-GAGTTTGGGGG
1 T-AAAATGGAATTTT-GATGAAATTGAGGT
*
28718243 TAAAATGGTAATTTTTGATGAAATCGAGGT
1 TAAAATGG-AA-TTTTGATGAAATTGAGGT
28718273 TAAAAATGGAATTTTG
1 T-AAAATGGAATTTTG
28718289 GAAGTTTCGG
Statistics
Matches: 153, Mismatches: 20, Indels: 36
0.73 0.10 0.17
Matches are distributed among these distances:
26 4 0.03
27 3 0.02
28 33 0.22
29 50 0.33
30 46 0.30
31 13 0.08
32 4 0.03
ACGTcount: A:0.36, C:0.02, G:0.27, T:0.35
Consensus pattern (28 bp):
TAAAATGGAATTTTGATGAAATTGAGGT
Found at i:28718295 original size:58 final size:58
Alignment explanation
Indices: 28718031--28718314 Score: 335
Period size: 58 Copynumber: 4.9 Consensus size: 58
28718021 GAAACGATAG
* *** * *
28718031 AATCGGGGTTAAAAATGGAACTTTTGGATA-CCCGGGGGTAAAATGGTAA-TTTTGGTAA
1 AATCGAGGTTAAAAATGGAA-TTTTGGA-AGTTTGGGGGTAAAATGGTAATTTTTGATGA
* * * * *
28718089 AATCGGGGTTAAAAATGGAATTTTGGAAACTTCGAGGGTAAAATGGTAATTTTTGGTGA
1 AATCGAGGTTAAAAATGGAATTTTGG-AAGTTTGGGGGTAAAATGGTAATTTTTGATGA
*
28718148 AATTGAGGTT-AAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGTAA-TTTTGATGA
1 AATCGAGGTTAAAAATGGAATTTTGG-AAGTTTGGGGGTAAAATGGTAATTTTTGATGA
** *
28718205 AATTAAGGTTAAAAATGGAATTTTAGAGAGTTTGGGGGTAAAATGGTAATTTTTGATGA
1 AATCGAGGTTAAAAATGGAATTTTGGA-AGTTTGGGGGTAAAATGGTAATTTTTGATGA
*
28718264 AATCGAGGTTAAAAATGGAATTTTGGAAGTTTCGGGGTCAAAAT-GTAATTT
1 AATCGAGGTTAAAAATGGAATTTTGGAAGTTTGGGGGT-AAAATGGTAATTT
28718315 CTTAAAATTT
Statistics
Matches: 203, Mismatches: 16, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
57 25 0.12
58 124 0.61
59 54 0.27
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.33
Consensus pattern (58 bp):
AATCGAGGTTAAAAATGGAATTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTGATGA
Found at i:28718306 original size:29 final size:27
Alignment explanation
Indices: 28718065--28718314 Score: 123
Period size: 29 Copynumber: 8.6 Consensus size: 27
28718055 TGGATACCCG
*
28718065 GGGGTAAAATGGTAATTTTGGTAA-AATC
1 GGGGTAAAATGG-AATTTTGG-AAGATTC
28718093 GGGGTTAAAAATGGAATTTTGGAA-ACTTC
1 GGGG-T-AAAATGGAATTTTGGAAGA-TTC
28718122 GAGGGTAAAATGGTAATTTTTGGTGAA-ATT-
1 G-GGGTAAAATGG-AA-TTTT-G-GAAGATTC
* * *
28718152 GAGGTTAAAATGGAATTTTGGAAAGTTTG
1 G-GGGTAAAATGGAATTTTGG-AAGATTC
*
28718181 GGGGTAAAATGGTAATTTTGATGAA-ATTA
1 GGGGTAAAATGG-AATTTTG--GAAGATTC
* * * * *
28718210 AGGTTAAAAATGGAATTTTAGAGAGTTTG
1 GGGGT-AAAATGGAATTTTGGA-AGATTC
* * *
28718239 GGGGTAAAATGGTAATTTTTGATGAAATC
1 GGGGTAAAATGG-AATTTTGGAAG-ATTC
* *
28718268 GAGGTTAAAAATGGAATTTTGGAAGTTTC
1 G-GGGT-AAAATGGAATTTTGGAAGATTC
*
28718297 GGGGTCAAAATGTAATTT
1 GGGGT-AAAATGGAATTT
28718315 CTTAAAATTT
Statistics
Matches: 175, Mismatches: 26, Indels: 42
0.72 0.11 0.17
Matches are distributed among these distances:
26 1 0.01
27 5 0.03
28 53 0.30
29 54 0.31
30 47 0.27
31 11 0.06
32 4 0.02
ACGTcount: A:0.35, C:0.02, G:0.28, T:0.34
Consensus pattern (27 bp):
GGGGTAAAATGGAATTTTGGAAGATTC
Found at i:28718336 original size:116 final size:115
Alignment explanation
Indices: 28718065--28718343 Score: 341
Period size: 116 Copynumber: 2.4 Consensus size: 115
28718055 TGGATACCCG
* ** *
28718065 GGGGTAAAATGGTAATTTTGGTAAAATCGGGGTTAAAAATGGAATTTTGGAAACTTCGAGGGTAA
1 GGGGTAAAATGGTAATTTT-ATAAAATTAGGGTTAAAAATGGAATTTTAGAAACTTCGAGGGTAA
* * *
28718130 AATGGTAATTTTTGGTGAAATTGAGGTTAAAATGGAATTTTGGAAAGTTTG
65 AATGGTAATTTTTGATGAAATCGAGGTTAAAATGGAATTTTGGAAAGTTTC
* * * * * *
28718181 GGGGTAAAATGGTAATTTTGATGAAATTAAGGTTAAAAATGGAATTTTAGAGAGTTTGGGGGTAA
1 GGGGTAAAATGGTAATTTT-ATAAAATTAGGGTTAAAAATGGAATTTTAGAAACTTCGAGGGTAA
28718246 AATGGTAATTTTTGATGAAATCGAGGTTAAAAATGGAATTTTGG-AAGTTTC
65 AATGGTAATTTTTGATGAAATCGAGGTT-AAAATGGAATTTTGGAAAGTTTC
*
28718297 GGGGTCAAAAT-GTAATTTCT-TAAAATTTTAGGGTT-AAAATGTAATTT
1 GGGGT-AAAATGGTAATTT-TATAAAA--TTAGGGTTAAAAATGGAATTT
28718344 CTGGACTATT
Statistics
Matches: 142, Mismatches: 16, Indels: 10
0.85 0.10 0.06
Matches are distributed among these distances:
115 4 0.03
116 110 0.77
117 28 0.20
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (115 bp):
GGGGTAAAATGGTAATTTTATAAAATTAGGGTTAAAAATGGAATTTTAGAAACTTCGAGGGTAAA
ATGGTAATTTTTGATGAAATCGAGGTTAAAATGGAATTTTGGAAAGTTTC
Found at i:28720262 original size:6 final size:6
Alignment explanation
Indices: 28720253--28720329 Score: 61
Period size: 6 Copynumber: 12.8 Consensus size: 6
28720243 TTGAATTTGA
* * *
28720253 TTAAAT TTAAAT CTAAA- ATAAAT TTAAAT AAGTAAAT TTAAAT TTAAA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT --TTAAAT TTAAAT TTAAAT
* *
28720301 ATAAAT TTAAAA TT-AAT TTAAACT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAA-T TTAAA
28720330 AGCCCAAGCC
Statistics
Matches: 56, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
5 12 0.21
6 33 0.59
7 6 0.11
8 5 0.09
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (6 bp):
TTAAAT
Found at i:28720274 original size:17 final size:16
Alignment explanation
Indices: 28720254--28720316 Score: 76
Period size: 17 Copynumber: 3.9 Consensus size: 16
28720244 TGAATTTGAT
28720254 TAAATTTAAATCTAAAA
1 TAAATTTAAAT-TAAAA
*
28720271 TAAATTTAAA-T-AAG
1 TAAATTTAAATTAAAA
28720285 TAAATTTAAATTTAAAA
1 TAAATTTAAA-TTAAAA
28720302 TAAATTTAAAATTAA
1 TAAATTT-AAATTAA
28720317 TTTAAACTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
14 12 0.30
15 1 0.03
16 1 0.03
17 23 0.57
18 3 0.08
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (16 bp):
TAAATTTAAATTAAAA
Found at i:28720280 original size:11 final size:11
Alignment explanation
Indices: 28720260--28720322 Score: 60
Period size: 11 Copynumber: 5.9 Consensus size: 11
28720250 TGATTAAATT
*
28720260 TAAATCTAAAA
1 TAAATTTAAAA
28720271 TAAATTT-AAA
1 TAAATTTAAAA
* *
28720281 T-AA-GTAAATT
1 TAAATTTAAA-A
28720291 TAAATTTAAAA
1 TAAATTTAAAA
28720302 TAAATTTAAAA
1 TAAATTTAAAA
*
28720313 TTAATTTAAA
1 TAAATTTAAA
28720323 CTTTAAAAGC
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
8 1 0.02
9 4 0.10
10 5 0.12
11 28 0.67
12 4 0.10
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:28720322 original size:17 final size:17
Alignment explanation
Indices: 28720254--28720330 Score: 72
Period size: 17 Copynumber: 4.6 Consensus size: 17
28720244 TGAATTTGAT
28720254 TAAATTT-AAATCTAAAA
1 TAAATTTAAAAT-TAAAA
*
28720271 TAAATTT-AAA-T-AAG
1 TAAATTTAAAATTAAAA
*
28720285 TAAATTTAAATTTAAAA
1 TAAATTTAAAATTAAAA
**
28720302 TAAATTTAAAATTAATT
1 TAAATTTAAAATTAAAA
28720319 TAAACTTTAAAA
1 TAAA-TTTAAAA
28720331 GCCCAAGCCC
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
14 9 0.18
15 3 0.06
16 1 0.02
17 30 0.60
18 7 0.14
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (17 bp):
TAAATTTAAAATTAAAA
Found at i:28720815 original size:17 final size:17
Alignment explanation
Indices: 28720780--28720822 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
28720770 CTCCTTTTAC
* *
28720780 CTTTAACCTTCCATCTT
1 CTTTAACTTTCCATATT
*
28720797 CTTTAACTTTTCATATT
1 CTTTAACTTTCCATATT
28720814 CTTGTAACT
1 CTT-TAACT
28720823 ACTTTTTCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.21, C:0.26, G:0.02, T:0.51
Consensus pattern (17 bp):
CTTTAACTTTCCATATT
Found at i:28722251 original size:29 final size:29
Alignment explanation
Indices: 28722202--28722277 Score: 100
Period size: 29 Copynumber: 2.7 Consensus size: 29
28722192 TTCTAAACTC
*
28722202 TAAATTCTC-ATTTTTTTATTTTTAATTG
1 TAAATTCTCAATTTTTTTATTTTAAATTG
* ** *
28722230 TCAATTCTTGATTTTTTTATTTTAAATTT
1 TAAATTCTCAATTTTTTTATTTTAAATTG
28722259 TAAATTCTCAATTTTTTTA
1 TAAATTCTCAATTTTTTTA
28722278 AAATTTTGTC
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
28 7 0.17
29 33 0.82
ACGTcount: A:0.26, C:0.08, G:0.03, T:0.63
Consensus pattern (29 bp):
TAAATTCTCAATTTTTTTATTTTAAATTG
Found at i:28725625 original size:19 final size:19
Alignment explanation
Indices: 28725594--28725630 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
28725584 GACAATTAAC
28725594 AAAGACAATGGTTGAAGAG
1 AAAGACAATGGTTGAAGAG
28725613 AAAGAACAA-GGTTGAAGA
1 AAAG-ACAATGGTTGAAGA
28725631 CAATGAGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.51, C:0.05, G:0.30, T:0.14
Consensus pattern (19 bp):
AAAGACAATGGTTGAAGAG
Found at i:28728010 original size:17 final size:18
Alignment explanation
Indices: 28727983--28728018 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
28727973 TATGTTTTAA
28727983 TTTTATCATTTATAATAG
1 TTTTATCATTTATAATAG
*
28728001 TTTT-TCATTTATATTAG
1 TTTTATCATTTATAATAG
28728018 T
1 T
28728019 AACATGCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.61
Consensus pattern (18 bp):
TTTTATCATTTATAATAG
Found at i:28739967 original size:29 final size:27
Alignment explanation
Indices: 28739907--28739969 Score: 74
Period size: 29 Copynumber: 2.3 Consensus size: 27
28739897 AACGAATTAG
*
28739907 ATCAAATTAATTTTTATTATTAAATAT
1 ATCAAATTAATTTTTATTATTAAAAAT
*
28739934 ATCAATTTAATTTATATATTATTAAAAA-
1 ATCAAATTAATTT-T-TATTATTAAAAAT
28739962 ATTCAAAT
1 A-TCAAAT
28739970 AAGGTTTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 12 0.40
28 2 0.07
29 16 0.53
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (27 bp):
ATCAAATTAATTTTTATTATTAAAAAT
Found at i:28740482 original size:10 final size:10
Alignment explanation
Indices: 28740449--28740502 Score: 51
Period size: 9 Copynumber: 5.5 Consensus size: 10
28740439 ATATTATAAA
28740449 TAAAAAATA-
1 TAAAAAATAT
*
28740458 TAAAAATATTCT
1 TAAAAA-A-TAT
28740470 TAAAAAATAT
1 TAAAAAATAT
28740480 T-AAAAAT-T
1 TAAAAAATAT
*
28740488 TAAATAATAT
1 TAAAAAATAT
28740498 TAAAA
1 TAAAA
28740503 TTCAAAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
8 2 0.06
9 17 0.47
10 9 0.25
11 2 0.06
12 6 0.17
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (10 bp):
TAAAAAATAT
Found at i:28740514 original size:18 final size:18
Alignment explanation
Indices: 28740471--28740516 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
28740461 AAATATTCTT
*
28740471 AAAAAATATTAAAAATTT
1 AAAAAATATTAAAAATTA
*
28740489 AAATAATATT-AAAATTCA
1 AAAAAATATTAAAAATT-A
28740507 AAAAAATATT
1 AAAAAATATT
28740517 TTAATTATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 6 0.25
18 18 0.75
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAAAATATTAAAAATTA
Found at i:28740527 original size:29 final size:28
Alignment explanation
Indices: 28740481--28740539 Score: 82
Period size: 29 Copynumber: 2.1 Consensus size: 28
28740471 AAAAAATATT
28740481 AAAAATTTAAATAATATTAAAATTCAAA
1 AAAAATTTAAATAATATTAAAATTCAAA
* * *
28740509 AAAATATTTTAATTATATTAAAATTCCAA
1 AAAA-ATTTAAATAATATTAAAATTCAAA
28740538 AA
1 AA
28740540 TTCAATGTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 4 0.15
29 23 0.85
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (28 bp):
AAAAATTTAAATAATATTAAAATTCAAA
Found at i:28741022 original size:24 final size:23
Alignment explanation
Indices: 28740988--28741066 Score: 79
Period size: 23 Copynumber: 3.4 Consensus size: 23
28740978 TTGTTGTTTA
28740988 TTTTTTAATTTTAAAGTTTTTATT
1 TTTTTTAATTTTAAA-TTTTTATT
* * **
28741012 TTTTTTCATTTTATATTTTTAAA
1 TTTTTTAATTTTAAATTTTTATT
** *
28741035 AATTATAATTTTAAATTTTTA-T
1 TTTTTTAATTTTAAATTTTTATT
28741057 TTTTTTAATT
1 TTTTTTAATT
28741067 GACAAAAAAA
Statistics
Matches: 42, Mismatches: 13, Indels: 2
0.74 0.23 0.04
Matches are distributed among these distances:
22 7 0.17
23 22 0.52
24 13 0.31
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.68
Consensus pattern (23 bp):
TTTTTTAATTTTAAATTTTTATT
Found at i:28746777 original size:10 final size:10
Alignment explanation
Indices: 28746742--28746813 Score: 64
Period size: 10 Copynumber: 7.6 Consensus size: 10
28746732 TAGAAAGATT
*
28746742 TAAAATTTTA
1 TAAAATATTA
* *
28746752 TAAAAAATCA
1 TAAAATATTA
28746762 TAAAATATTA
1 TAAAATATTA
28746772 TAAAATA-TA
1 TAAAATATTA
28746781 TAGAAATA--A
1 TA-AAATATTA
28746790 -AAAA-ATTA
1 TAAAATATTA
*
28746798 TAAAATTTTA
1 TAAAATATTA
28746808 TAAAAT
1 TAAAAT
28746814 CATAAGAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
6 1 0.02
7 3 0.06
8 2 0.04
9 9 0.18
10 36 0.71
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (10 bp):
TAAAATATTA
Found at i:28746793 original size:36 final size:36
Alignment explanation
Indices: 28746753--28746822 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 36
28746743 AAAATTTTAT
28746753 AAAAAATCATAAAATATTATAAAAT-ATATAGAAATA
1 AAAAAATCATAAAATATTATAAAATCATA-AGAAATA
* *
28746789 AAAAAATTATAAAATTTTATAAAATCATAAGAAA
1 AAAAAATCATAAAATATTATAAAATCATAAGAAA
28746823 ATTATAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 28 0.90
37 3 0.10
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (36 bp):
AAAAAATCATAAAATATTATAAAATCATAAGAAATA
Found at i:28746823 original size:29 final size:28
Alignment explanation
Indices: 28746742--28746831 Score: 105
Period size: 26 Copynumber: 3.2 Consensus size: 28
28746732 TAGAAAGATT
*
28746742 TAAAATTTTATAAAAAATCATAAAATATTA
1 TAAAATTTTAT--AAAATCATAAAAAATTA
*
28746772 TAAAA-TATATAGAAAT-A-AAAAAATTA
1 TAAAATTTTATA-AAATCATAAAAAATTA
28746798 TAAAATTTTATAAAATCATAAGAAAATTA
1 TAAAATTTTATAAAATCATAA-AAAATTA
28746827 TAAAA
1 TAAAA
28746832 AAGGTAAAGA
Statistics
Matches: 52, Mismatches: 3, Indels: 11
0.79 0.05 0.17
Matches are distributed among these distances:
26 17 0.33
27 8 0.15
28 6 0.12
29 16 0.31
30 5 0.10
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.32
Consensus pattern (28 bp):
TAAAATTTTATAAAATCATAAAAAATTA
Found at i:28746844 original size:20 final size:20
Alignment explanation
Indices: 28746820--28746871 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
28746810 AAATCATAAG
*
28746820 AAAATTATAAAAAAGGTAAA
1 AAAATTATAAAAAACGTAAA
* **
28746840 GAAA-TATAAAATTCGTAAA
1 AAAATTATAAAAAACGTAAA
28746859 AAAATTATAAAAA
1 AAAATTATAAAAA
28746872 TTATCGTACC
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.67, C:0.02, G:0.08, T:0.23
Consensus pattern (20 bp):
AAAATTATAAAAAACGTAAA
Found at i:28749052 original size:20 final size:20
Alignment explanation
Indices: 28749006--28749044 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
28748996 AAATTTATTA
28749006 TATTTTTAAAAATATTTTTG
1 TATTTTTAAAAATATTTTTG
* *
28749026 TATTTTTATATATATTTTT
1 TATTTTTAAAAATATTTTT
28749045 TAATTTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (20 bp):
TATTTTTAAAAATATTTTTG
Found at i:28750784 original size:22 final size:22
Alignment explanation
Indices: 28750750--28750817 Score: 82
Period size: 22 Copynumber: 3.0 Consensus size: 22
28750740 AATTTAATAA
28750750 ACTATGAAAATAATTTTTAATT
1 ACTATGAAAATAATTTTTAATT
* * **
28750772 ATTATTAAAATAAAATTTAATT
1 ACTATGAAAATAATTTTTAATT
*
28750794 AACTATGAAAATCATTTTTAATT
1 -ACTATGAAAATAATTTTTAATT
28750817 A
1 A
28750818 ACATATCTAC
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
22 19 0.53
23 17 0.47
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.44
Consensus pattern (22 bp):
ACTATGAAAATAATTTTTAATT
Found at i:28750816 original size:23 final size:23
Alignment explanation
Indices: 28750742--28750819 Score: 95
Period size: 23 Copynumber: 3.4 Consensus size: 23
28750732 AATAATAAAA
*
28750742 TTTAATAAACTATGAAAATAATT
1 TTTAATTAACTATGAAAATAATT
* * **
28750765 TTTAATT-ATTATTAAAATAAAA
1 TTTAATTAACTATGAAAATAATT
*
28750787 TTTAATTAACTATGAAAATCATT
1 TTTAATTAACTATGAAAATAATT
28750810 TTTAATTAAC
1 TTTAATTAAC
28750820 ATATCTACCC
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
22 18 0.41
23 26 0.59
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (23 bp):
TTTAATTAACTATGAAAATAATT
Found at i:28761307 original size:21 final size:22
Alignment explanation
Indices: 28761282--28761336 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
28761272 ATTTATCTAA
28761282 TAACAAATTTAATC-TAAATGT
1 TAACAAATTTAATCTTAAATGT
* *
28761303 TAACAAGTTTAATCTTTAATGT
1 TAACAAATTTAATCTTAAATGT
*
28761325 TTACAAATTTAA
1 TAACAAATTTAA
28761337 AAATAAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 13 0.45
22 16 0.55
ACGTcount: A:0.44, C:0.09, G:0.05, T:0.42
Consensus pattern (22 bp):
TAACAAATTTAATCTTAAATGT
Found at i:28762540 original size:20 final size:18
Alignment explanation
Indices: 28762511--28762558 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
28762501 CTAAATTTTT
28762511 TTTAAAAAAATTCAAAATA
1 TTTAAAAAAATT-AAAATA
*
28762530 TTTATAAAAAATTAAAAAA
1 TTTA-AAAAAATTAAAATA
*
28762549 TATAAAAAAA
1 TTTAAAAAAA
28762559 CTACATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 6 0.23
19 12 0.46
20 8 0.31
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (18 bp):
TTTAAAAAAATTAAAATA
Found at i:28762548 original size:21 final size:19
Alignment explanation
Indices: 28762511--28762558 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
28762501 CTAAATTTTT
*
28762511 TTTAAAAAAATTCAAAATA
1 TTTAAAAAAATTAAAAATA
28762530 TTTATAAAAAATTAAAAA-A
1 TTTA-AAAAAATTAAAAATA
*
28762549 TATAAAAAAA
1 TTTAAAAAAA
28762559 CTACATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 6 0.23
19 8 0.31
20 12 0.46
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (19 bp):
TTTAAAAAAATTAAAAATA
Found at i:28762701 original size:10 final size:10
Alignment explanation
Indices: 28762686--28762732 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
28762676 TTAATTCCTC
28762686 TAAAAAATTT
1 TAAAAAATTT
28762696 TAAAAAA-TT
1 TAAAAAATTT
*
28762705 TAAAATA-TT
1 TAAAAAATTT
28762714 TATAAAAATTT
1 TA-AAAAATTT
*
28762725 AAAAAAAT
1 TAAAAAAT
28762733 AAAAAATTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
9 12 0.38
10 17 0.53
11 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
TAAAAAATTT
Found at i:28762706 original size:9 final size:9
Alignment explanation
Indices: 28762686--28762740 Score: 67
Period size: 9 Copynumber: 6.0 Consensus size: 9
28762676 TTAATTCCTC
28762686 TAAAAAATTT
1 TAAAAAA-TT
28762696 TAAAAAATT
1 TAAAAAATT
*
28762705 TAAAATATT
1 TAAAAAATT
28762714 TATAAAAATT
1 TA-AAAAATT
*
28762724 TAAAAAA-A
1 TAAAAAATT
28762732 TAAAAAATT
1 TAAAAAATT
28762741 ACATAAAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
8 7 0.18
9 17 0.44
10 15 0.38
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
TAAAAAATT
Found at i:28762708 original size:19 final size:19
Alignment explanation
Indices: 28762686--28762730 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
28762676 TTAATTCCTC
28762686 TAAAAAATTT-TAAAAAATT
1 TAAAAAATTTAT-AAAAATT
*
28762705 TAAAATATTTATAAAAATT
1 TAAAAAATTTATAAAAATT
28762724 TAAAAAA
1 TAAAAAA
28762731 ATAAAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 22 0.96
20 1 0.04
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
TAAAAAATTTATAAAAATT
Found at i:28767995 original size:31 final size:31
Alignment explanation
Indices: 28767957--28768030 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
28767947 GATTTAATGC
** *
28767957 TTGGGTGATTAAAATGAAAGCACCCTAAAAG
1 TTGGGTGACCAAAATGAAAACACCCTAAAAG
* * *
28767988 TTGGGTGACCAAAATGAAAACGCCGTGAAAG
1 TTGGGTGACCAAAATGAAAACACCCTAAAAG
28768019 TTGGGTGACCAA
1 TTGGGTGACCAA
28768031 CTAAGTAGTT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.38, C:0.15, G:0.27, T:0.20
Consensus pattern (31 bp):
TTGGGTGACCAAAATGAAAACACCCTAAAAG
Found at i:28777684 original size:21 final size:21
Alignment explanation
Indices: 28777658--28777704 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
28777648 TTAGTTATGA
28777658 ATTTAGGGTTCGTGAATTT-AG
1 ATTTAGGGTT-GTGAATTTGAG
*
28777679 ATTTAGGGTTTTGAATTTGAG
1 ATTTAGGGTTGTGAATTTGAG
28777700 ATTTA
1 ATTTA
28777705 AGGTAAAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.26, C:0.02, G:0.26, T:0.47
Consensus pattern (21 bp):
ATTTAGGGTTGTGAATTTGAG
Found at i:28782079 original size:2 final size:2
Alignment explanation
Indices: 28782072--28782113 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
28782062 GATAGAAATA
28782072 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
28782114 TCAATTATTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28784132 original size:28 final size:27
Alignment explanation
Indices: 28784095--28784181 Score: 77
Period size: 28 Copynumber: 3.0 Consensus size: 27
28784085 TTAAGATGAT
28784095 TATATAAATTTTTTTAATAAATTAAAAA
1 TATATAAATTTTTTTAA-AAATTAAAAA
* *
28784123 TATATAAA-TTTATTAAATATTAAAATAATA
1 TATATAAATTTTTTTAAAAATT--AA-AA-A
*
28784153 TAATATAAATATTTTTAAAAAATTAAAAA
1 T-ATATAAAT-TTTTTTAAAAATTAAAAA
28784182 ATAATATAGG
Statistics
Matches: 47, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
26 4 0.09
27 7 0.15
28 10 0.21
29 3 0.06
30 4 0.09
31 9 0.19
33 10 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (27 bp):
TATATAAATTTTTTTAAAAATTAAAAA
Found at i:28784139 original size:24 final size:26
Alignment explanation
Indices: 28784107--28784155 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 26
28784097 TATAAATTTT
28784107 TTTAATAAAT-TAAAAAT-ATATAAA
1 TTTAATAAATATAAAAATAATATAAA
* *
28784131 TTTATTAAATATTAAAATAATATAA
1 TTTAATAAATATAAAAATAATATAA
28784156 TATAAATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 9 0.43
25 6 0.29
26 6 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
TTTAATAAATATAAAAATAATATAAA
Found at i:28784158 original size:33 final size:32
Alignment explanation
Indices: 28784096--28784184 Score: 82
Period size: 32 Copynumber: 2.9 Consensus size: 32
28784086 TAAGATGATT
* *
28784096 ATATAAATTTTTTTAATAAATT--AAAA-AT-
1 ATATAAATATTTTTAAAAAATTAAAAAATATA
* * *
28784124 ATATAAAT-TTATT-AAATATTAAAATAATATA
1 ATATAAATATTTTTAAAAAATT-AAAAAATATA
28784155 ATATAAATATTTTTAAAAAATTAAAAAATA
1 ATATAAATATTTTTAAAAAATTAAAAAATA
28784185 ATATAGGCAT
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
26 5 0.11
27 4 0.09
28 8 0.17
29 3 0.06
30 2 0.04
31 8 0.17
32 11 0.23
33 6 0.13
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (32 bp):
ATATAAATATTTTTAAAAAATTAAAAAATATA
Found at i:28791664 original size:6 final size:6
Alignment explanation
Indices: 28791653--28791680 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
28791643 GCGTATAATA
28791653 GCAGAT GCAGAT GCAGAT GCAGAT GCAG
1 GCAGAT GCAGAT GCAGAT GCAGAT GCAG
28791681 TGTAGTGGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.18, G:0.36, T:0.14
Consensus pattern (6 bp):
GCAGAT
Found at i:28799047 original size:37 final size:38
Alignment explanation
Indices: 28798957--28799048 Score: 98
Period size: 38 Copynumber: 2.4 Consensus size: 38
28798947 AAAAACAATA
* *
28798957 GACATG-ATTAACATGTATTCAGTTCAACACCAACAGTT
1 GACATGCA-TAACATGTATTCAATTCAACACCAACAGAT
* * * *
28798995 GACATGCTTATCATGTATTCAATTCAACACTAGCA-AT
1 GACATGCATAACATGTATTCAATTCAACACCAACAGAT
*
28799032 GTCATGCATAACATGTA
1 GACATGCATAACATGTA
28799049 CTCAGTAAGG
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
37 15 0.34
38 29 0.66
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.30
Consensus pattern (38 bp):
GACATGCATAACATGTATTCAATTCAACACCAACAGAT
Found at i:28799983 original size:2 final size:2
Alignment explanation
Indices: 28799976--28800014 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
28799966 AGATTATTCA
28799976 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28800015 GAGAGAGAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28800019 original size:2 final size:2
Alignment explanation
Indices: 28800014--28800077 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
28800004 ATATATATAT
28800014 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
28800056 AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG
28800078 CTCAACATAA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:28802579 original size:6 final size:6
Alignment explanation
Indices: 28802568--28802600 Score: 57
Period size: 6 Copynumber: 5.3 Consensus size: 6
28802558 AATTTGTGTG
28802568 TTTTCT TTTTCT TTTTCT TTTTCT TTTTACT TT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTT-CT TT
28802601 GCGCCGTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 22 0.85
7 4 0.15
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTCT
Found at i:28803608 original size:30 final size:30
Alignment explanation
Indices: 28803572--28803642 Score: 142
Period size: 30 Copynumber: 2.4 Consensus size: 30
28803562 TTTGTCATAT
28803572 AACAATTATATAGCTTAGCGATTATTAAAA
1 AACAATTATATAGCTTAGCGATTATTAAAA
28803602 AACAATTATATAGCTTAGCGATTATTAAAA
1 AACAATTATATAGCTTAGCGATTATTAAAA
28803632 AACAATTATAT
1 AACAATTATAT
28803643 GGAGTAATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.48, C:0.10, G:0.08, T:0.34
Consensus pattern (30 bp):
AACAATTATATAGCTTAGCGATTATTAAAA
Found at i:28804154 original size:22 final size:24
Alignment explanation
Indices: 28804120--28804163 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
28804110 AGTTCTTGAA
*
28804120 TTTTGGCGAAAAATCA-ATTAAGT
1 TTTTAGCGAAAAATCATATTAAGT
28804143 TTTTAGCG-AAAATCATATTAA
1 TTTTAGCGAAAAATCATATTAA
28804164 TTTAAATTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (24 bp):
TTTTAGCGAAAAATCATATTAAGT
Found at i:28804464 original size:21 final size:18
Alignment explanation
Indices: 28804440--28804491 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
28804430 TAAATCATTG
28804440 AAATTTATAAAAATATCAAA
1 AAATTTATAAAAA-AT-AAA
*
28804460 TAAATTT-CAAAAAATAAA
1 -AAATTTATAAAAAATAAA
*
28804478 AAATTAATAAAAAA
1 AAATTTATAAAAAA
28804492 AACTATTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
17 5 0.19
18 9 0.33
19 2 0.07
20 5 0.19
21 6 0.22
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (18 bp):
AAATTTATAAAAAATAAA
Found at i:28813932 original size:6 final size:6
Alignment explanation
Indices: 28813923--28813955 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
28813913 CTGTATACAT
28813923 ATACTC ATACTC ATACTC ATACTC ATAC-C ATAC
1 ATACTC ATACTC ATACTC ATACTC ATACTC ATAC
28813956 AATCATTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.30
Consensus pattern (6 bp):
ATACTC
Found at i:28818187 original size:49 final size:49
Alignment explanation
Indices: 28818124--28818586 Score: 234
Period size: 49 Copynumber: 9.4 Consensus size: 49
28818114 TGAAGACATG
* *
28818124 AAGGGAAAGATTTAAGCCGCAATGGCGAATCCAATACCATAAGGATATA
1 AAGGGAAAGATTTAAGTCGCAATGGCGAATCCAGTACCATAAGGATATA
* * * * * * * *
28818173 AAGGGAAGGGTTTAAGTCGCAACGGCGAA-CCTTGTACC-TCAGAAACATG
1 AAGGGAAAGATTTAAGTCGCAATGGCGAATCC-AGTACCATAAG-GATATA
* *
28818222 AAGGGAAAGATTTAAGTCGTAATGGCGAATCCAGTACCACAAGGATATA
1 AAGGGAAAGATTTAAGTCGCAATGGCGAATCCAGTACCATAAGGATATA
* * * * * * *
28818271 AAGGGAAGGGTTTAAGTCGCAATGGCGAA-CCTTGTACC-TCAGAAACATG
1 AAGGGAAAGATTTAAGTCGCAATGGCGAATCC-AGTACCATAAG-GATATA
* * * * * * * **
28818320 AAGGGAATGATTTAAGCCGCAACGACAAATCCTGTACCACGAA-GATACG
1 AAGGGAAAGATTTAAGTCGCAATGGCGAATCCAGTACCA-TAAGGATATA
* * * * *
28818369 GAGGGAAATATTTAAGTCGCAATGGCGAA-CCTTA-TACC-TCAGAAGTATG
1 AAGGGAAAGATTTAAGTCGCAATGGCGAATCC--AGTACCATAAGGA-TATA
* * * *
28818418 AAGGGAAAGATTTAAGCCGCAATGACGAATCCTGTACCATGAA-GATAATG
1 AAGGGAAAGATTTAAGTCGCAATGGCGAATCCAGTACCAT-AAGGAT-ATA
* * * * * * *
28818468 GAGGGAAAGGTTTCAGTCGCAATGACGAA-CCTTGTACTTCA-AA--AGATG
1 AAGGGAAAGATTTAAGTCGCAATGGCGAATCC-AGTAC--CATAAGGATATA
* * * * *
28818516 AAGGGAAAGATTTAAGCCGCAATGGCAAATCTAGTACCATGAA-GATGTC
1 AAGGGAAAGATTTAAGTCGCAATGGCGAATCCAGTACCAT-AAGGATATA
* * *
28818565 AAGGGAACGGTCTAAGTCGCAA
1 AAGGGAAAGATTTAAGTCGCAA
28818587 CGGCAAGCCT
Statistics
Matches: 310, Mismatches: 79, Indels: 50
0.71 0.18 0.11
Matches are distributed among these distances:
46 2 0.01
47 1 0.00
48 44 0.14
49 214 0.69
50 45 0.15
51 2 0.01
52 2 0.01
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.20
Consensus pattern (49 bp):
AAGGGAAAGATTTAAGTCGCAATGGCGAATCCAGTACCATAAGGATATA
Found at i:28818288 original size:98 final size:97
Alignment explanation
Indices: 28818119--28818651 Score: 577
Period size: 98 Copynumber: 5.5 Consensus size: 97
28818109 TACCATGAAG
* * *
28818119 ACATGAAGGGAAAGATTTAAGCCGCAATGGCGAATCCAATACCATAAGGATATAAAGGGAAGGGT
1 ACATGAAGGGAAAGATTTAAGCCGCAATGGCGAATCCAGTACCACAA-GATATAAAGGGAAAGGT
*
28818184 TTAAGTCGCAACGGCGAACCTTGTACCTCAGAA
65 TTAAGTCGCAATGGCGAACCTTGTACCTCAGAA
* * *
28818217 ACATGAAGGGAAAGATTTAAGTCGTAATGGCGAATCCAGTACCACAAGGATATAAAGGGAAGGGT
1 ACATGAAGGGAAAGATTTAAGCCGCAATGGCGAATCCAGTACCACAA-GATATAAAGGGAAAGGT
28818282 TTAAGTCGCAATGGCGAACCTTGTACCTCAGAA
65 TTAAGTCGCAATGGCGAACCTTGTACCTCAGAA
* * * * * *** **
28818315 ACATGAAGGGAATGATTTAAGCCGCAACGACAAATCCTGTACCACGAAGATACGGAGGGAAATAT
1 ACATGAAGGGAAAGATTTAAGCCGCAATGGCGAATCCAGTACCAC-AAGATATAAAGGGAAAGGT
*
28818380 TTAAGTCGCAATGGCGAACCTTATACCTCAGAA
65 TTAAGTCGCAATGGCGAACCTTGTACCTCAGAA
** * * * **
28818413 GTATGAAGGGAAAGATTTAAGCCGCAATGACGAATCCTGTACCATGAAGATAATGGAGGGAAAGG
1 ACATGAAGGGAAAGATTTAAGCCGCAATGGCGAATCCAGTACCA-CAAGAT-ATAAAGGGAAAGG
* * *
28818478 TTTCAGTCGCAATGACGAACCTTGTACTTCA-AA
64 TTTAAGTCGCAATGGCGAACCTTGTACCTCAGAA
* * * * * * *
28818511 AGATGAAGGGAAAGATTTAAGCCGCAATGGCAAATCTAGTACCATGAAGATGTCAAGGGAACGGT
1 ACATGAAGGGAAAGATTTAAGCCGCAATGGCGAATCCAGTACCA-CAAGATATAAAGGGAAAGGT
* * * *
28818576 CTAAGTCGCAACGGC-AAGCCTTATACCTCGGAA
65 TTAAGTCGCAATGGCGAA-CCTTGTACCTCAGAA
* * * * **
28818609 GCATGAAAGGAAA-ATTTAAGCCGTAACGGCGAATTTAGTACCA
1 ACATGAAGGGAAAGATTTAAGCCGCAATGGCGAATCCAGTACCA
28818652 TGCAAAATGA
Statistics
Matches: 374, Mismatches: 56, Indels: 11
0.85 0.13 0.02
Matches are distributed among these distances:
96 2 0.01
97 56 0.15
98 277 0.74
99 39 0.10
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.20
Consensus pattern (97 bp):
ACATGAAGGGAAAGATTTAAGCCGCAATGGCGAATCCAGTACCACAAGATATAAAGGGAAAGGTT
TAAGTCGCAATGGCGAACCTTGTACCTCAGAA
Found at i:28826288 original size:31 final size:31
Alignment explanation
Indices: 28826250--28826315 Score: 132
Period size: 31 Copynumber: 2.1 Consensus size: 31
28826240 CTATATATAC
28826250 CTTAATTAGTAATGTCATTAAGCTTAATTAA
1 CTTAATTAGTAATGTCATTAAGCTTAATTAA
28826281 CTTAATTAGTAATGTCATTAAGCTTAATTAA
1 CTTAATTAGTAATGTCATTAAGCTTAATTAA
28826312 CTTA
1 CTTA
28826316 TCGTTTTAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (31 bp):
CTTAATTAGTAATGTCATTAAGCTTAATTAA
Found at i:28827171 original size:43 final size:43
Alignment explanation
Indices: 28827123--28827209 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
28827113 ATTTTATGGA
28827123 TGATTTTGTTGTTGTCCTCTCTAGTTTGGTGAATGCTCAATTC
1 TGATTTTGTTGTTGTCCTCTCTAGTTTGGTGAATGCTCAATTC
28827166 TGATTTTGTTGTTGTCCTCTCTAGTTTGGTGAATGCTCAATTC
1 TGATTTTGTTGTTGTCCTCTCTAGTTTGGTGAATGCTCAATTC
28827209 T
1 T
28827210 TTTGTCGATT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.14, C:0.16, G:0.21, T:0.49
Consensus pattern (43 bp):
TGATTTTGTTGTTGTCCTCTCTAGTTTGGTGAATGCTCAATTC
Found at i:28835985 original size:1 final size:1
Alignment explanation
Indices: 28835979--28836005 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
28835969 CTGTTATGGA
28835979 GGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGG
28836006 CGTCTAGTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:28837889 original size:16 final size:16
Alignment explanation
Indices: 28837868--28837900 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
28837858 GTTAATAACC
28837868 TTAATATTTTAAGGGT
1 TTAATATTTTAAGGGT
28837884 TTAATATTTTAAGGGT
1 TTAATATTTTAAGGGT
28837900 T
1 T
28837901 GACATGTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.18, T:0.52
Consensus pattern (16 bp):
TTAATATTTTAAGGGT
Found at i:28848178 original size:17 final size:17
Alignment explanation
Indices: 28848148--28848224 Score: 77
Period size: 17 Copynumber: 4.4 Consensus size: 17
28848138 TTAAATTGAT
28848148 TTTAAATTTA-TTTAAA
1 TTTAAATTTATTTTAAA
*
28848164 TTTAGATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
28848181 TTTTAAATTAAATATTTAAA
1 -TTTAAATT-TAT-TTTAAA
*
28848201 TTT-AATTTGAATTTAAA
1 TTTAAATTT-ATTTTAAA
28848218 TTTAAAT
1 TTTAAAT
28848225 AAAAATTAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
16 9 0.18
17 15 0.30
18 15 0.30
19 5 0.10
20 6 0.12
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:28848202 original size:37 final size:34
Alignment explanation
Indices: 28848156--28848247 Score: 103
Period size: 37 Copynumber: 2.5 Consensus size: 34
28848146 ATTTTAAATT
*
28848156 TATTTAAATTTAGATTTATTTTAAATTTTAAATTAAA
1 TATTTAAATTTA-ATTTAATTTAAA-TTTAAA-TAAA
28848193 TATTTAAATTTAATTTGAATTTAAATTTAAATAAA
1 TATTTAAATTTAATTT-AATTTAAATTTAAATAAA
* *
28848228 AATTAAAATATTAAATTTAA
1 TATTTAAAT-TT-AATTTAA
28848248 CATTTAAAAG
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
35 11 0.22
36 14 0.29
37 24 0.49
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (34 bp):
TATTTAAATTTAATTTAATTTAAATTTAAATAAA
Found at i:28848213 original size:11 final size:11
Alignment explanation
Indices: 28848138--28848224 Score: 61
Period size: 11 Copynumber: 7.5 Consensus size: 11
28848128 GACTTTTGAG
* *
28848138 TTAAATTGATT
1 TTAAATTTAAT
28848149 TTAAATTT-AT
1 TTAAATTTAAT
28848159 TTAAATTTAGAT
1 TTAAATTTA-AT
*
28848171 TT-ATTTTAAATT
1 TTAAATTT-AA-T
*
28848183 TTAAATTAAATAT
1 TTAAATT-TA-AT
28848196 TTAAATTTAAT
1 TTAAATTTAAT
*
28848207 TTGAATTTAAAT
1 TTAAATTT-AAT
28848219 TTAAAT
1 TTAAAT
28848225 AAAAATTAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 15
0.72 0.10 0.18
Matches are distributed among these distances:
10 9 0.15
11 21 0.35
12 17 0.28
13 12 0.20
14 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:28848252 original size:7 final size:6
Alignment explanation
Indices: 28848148--28848255 Score: 89
Period size: 6 Copynumber: 18.0 Consensus size: 6
28848138 TTAAATTGAT
* * *
28848148 TTTAAA TTT--A TTTAAA TTTAGA TTT-AT TTTAAA TTTTAAA TTAAATA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA TTTAA-A
* ** *
28848195 TTTAAA TTT-AA TTTGAA TTTAAA TTTAAA TAAAAA TTAAAA TATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA
28848243 TTTAACA TTTAAA
1 TTTAA-A TTTAAA
28848256 AGTCCAAATG
Statistics
Matches: 83, Mismatches: 11, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
4 4 0.05
5 8 0.10
6 49 0.59
7 22 0.27
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (6 bp):
TTTAAA
Found at i:28849948 original size:161 final size:163
Alignment explanation
Indices: 28849773--28850085 Score: 472
Period size: 162 Copynumber: 1.9 Consensus size: 163
28849763 TTTATAATTT
* * *
28849773 AGTCCTTTGACTGTTTGACTGTACCATAGACTGCCACGTGTCA-CTTTTTGGATCATTTCTGCAT
1 AGTCCTTTGACTGTTTGACTGCACCAGAGACTGCCACATGTCATCTTTTTGGATCATTTCTGCAT
* *
28849837 TTAGTCCTTTTTATTTTTTATTTGTTTTAATTTAATCC-CAAATCAAC-TTTATTTTAATTACGA
66 TTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTTTA-TTTAATTACAA
*
28849900 AATTGG-CCTAATAATTTTTCAAGGTTTATAAACC
130 AATTGGTCC-AAAAATTTTTCAAGGTTTATAAACC
** * *
28849934 AGTCCTTTGACTGTTTGACTGCACCAGAGGTTGCCACATGTCATCTTTTTGGATTATTTCTGTAT
1 AGTCCTTTGACTGTTTGACTGCACCAGAGACTGCCACATGTCATCTTTTTGGATCATTTCTGCAT
* *
28849999 TTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCTTAAATCGACTTTTATTTAATTACAAA
66 TTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTTTATTTAATTACAAA
28850064 ATTGGTCCAAAAATTTTTCAAG
131 ATTGGTCCAAAAATTTTTCAAG
28850086 ATTTTCAAAT
Statistics
Matches: 136, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
161 38 0.28
162 56 0.41
163 36 0.26
164 6 0.04
ACGTcount: A:0.26, C:0.16, G:0.12, T:0.46
Consensus pattern (163 bp):
AGTCCTTTGACTGTTTGACTGCACCAGAGACTGCCACATGTCATCTTTTTGGATCATTTCTGCAT
TTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTTTATTTAATTACAAA
ATTGGTCCAAAAATTTTTCAAGGTTTATAAACC
Found at i:28850216 original size:30 final size:28
Alignment explanation
Indices: 28850166--28850289 Score: 140
Period size: 30 Copynumber: 4.2 Consensus size: 28
28850156 TGCTTTGTAA
* *
28850166 ACCCTAAATTGTCCAGAAATTACATTTTG
1 ACCCCAAATTTTCCA-AAATTACATTTTG
28850195 ACCCCACAATTTTCCCAAAATTACATTTTG
1 ACCCCA-AATTTT-CCAAAATTACATTTTG
* *
28850225 ACCTCGAAACTTTACCAAAATTACATTTTG
1 ACC-CCAAA-TTTTCCAAAATTACATTTTG
*
28850255 ACCCCAAAACTTTTCCAAAATTACATTTTT
1 ACCCC-AAA-TTTTCCAAAATTACATTTTG
28850285 ACCCC
1 ACCCC
28850290 GATTTCACCG
Statistics
Matches: 83, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
29 6 0.07
30 69 0.83
31 8 0.10
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.33
Consensus pattern (28 bp):
ACCCCAAATTTTCCAAAATTACATTTTG
Found at i:28850446 original size:30 final size:29
Alignment explanation
Indices: 28850335--28850564 Score: 119
Period size: 30 Copynumber: 7.7 Consensus size: 29
28850325 CCGAATCTCT
28850335 AAAATTCCATTTTAACCCCGATTTCACCA
1 AAAATTCCATTTTAACCCCGATTTCACCA
** ** *
28850364 AAAATTACCATTTTAACCACCCCGA-AGCTTCT
1 AAAATT-CCATTTT-A--ACCCCGATTTCACCA
*
28850396 AAAATTCCATTTTTAACCCCGATTTCACCG
1 AAAATTCCA-TTTTAACCCCGATTTCACCA
* * ****
28850426 AAAATTACCATTTTACCCCCGA-ATCTTTT
1 AAAATT-CCATTTTAACCCCGATTTCACCA
* * *
28850455 AAAATTCCGTTTTTAACCCTGATTTCACACC
1 AAAATTCC-ATTTTAACCCCGATTTCAC-CA
** ** *
28850486 AAAATTACCATTTT--CCCCGA-AGCTTCT
1 AAAATT-CCATTTTAACCCCGATTTCACCA
* *
28850513 AAAATTCCGTTTTTAACCCCGATTTTACCA
1 AAAATTCC-ATTTTAACCCCGATTTCACCA
*
28850543 AAAATTGCCATTTTACCCCCGA
1 AAAATT-CCATTTTAACCCCGA
28850565 ATCTTTTAAA
Statistics
Matches: 145, Mismatches: 40, Indels: 31
0.67 0.19 0.14
Matches are distributed among these distances:
26 2 0.01
27 11 0.08
28 3 0.02
29 42 0.29
30 46 0.32
31 20 0.14
32 14 0.10
33 7 0.05
ACGTcount: A:0.31, C:0.30, G:0.06, T:0.33
Consensus pattern (29 bp):
AAAATTCCATTTTAACCCCGATTTCACCA
Done.