Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr13
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: 55873576
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1239791 characters in sequence are not A, C, G, or T
File 141 of 182
Found at i:43282073 original size:40 final size:40
Alignment explanation
Indices: 43282029--43282213 Score: 112
Period size: 40 Copynumber: 4.6 Consensus size: 40
43282019 TAAAATAAAA
43282029 TTATTTAAAAGTTTATATAATTATACAAATTAATTTTATT
1 TTATTTAAAAGTTTATATAATTATACAAATTAATTTTATT
** * ** * *
43282069 TTATTTAAAAGTAAAT-TAATTTTATTAA--AAGTTTATA
1 TTATTTAAAAGTTTATATAATTATACAAATTAATTTTATT
** * * * * * *
43282106 AAATTATACAAA-TTAATTTTATTTTATTTA-AAAGTAAATTAATT
1 TTATT-TA-AAAGTTTA-TATA-ATTA--TACAAATTAATTTTATT
*
43282150 TTA-TTAAAAGTTTATAAAATTATACAAATTAATTTTATT
1 TTATTTAAAAGTTTATATAATTATACAAATTAATTTTATT
*
43282189 TTATTTAAAAGTTTAATAAAATTAT
1 TTATTTAAAAGTTT-ATATAATTAT
43282214 TTTACTTTAG
Statistics
Matches: 107, Mismatches: 25, Indels: 25
0.68 0.16 0.16
Matches are distributed among these distances:
37 10 0.09
38 7 0.07
39 27 0.25
40 29 0.27
41 17 0.16
42 7 0.07
43 3 0.03
44 7 0.07
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (40 bp):
TTATTTAAAAGTTTATATAATTATACAAATTAATTTTATT
Found at i:43282098 original size:20 final size:20
Alignment explanation
Indices: 43282066--43282160 Score: 86
Period size: 20 Copynumber: 4.7 Consensus size: 20
43282056 AATTAATTTT
43282066 ATTTTATTTAAAAGTAAATTA
1 ATTTTA-TTAAAAGTAAATTA
**
43282087 ATTTTATTAAAAGTTTA-TA
1 ATTTTATTAAAAGTAAATTA
** * * *
43282106 AAATTA-TACAAATTAATTTT
1 ATTTTATTA-AAAGTAAATTA
43282126 ATTTTATTTAAAAGTAAATTA
1 ATTTTA-TTAAAAGTAAATTA
43282147 ATTTTATTAAAAGT
1 ATTTTATTAAAAGT
43282161 TTATAAAATT
Statistics
Matches: 56, Mismatches: 14, Indels: 9
0.71 0.18 0.11
Matches are distributed among these distances:
18 2 0.04
19 10 0.18
20 22 0.39
21 20 0.36
22 2 0.04
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.48
Consensus pattern (20 bp):
ATTTTATTAAAAGTAAATTA
Found at i:43282119 original size:60 final size:60
Alignment explanation
Indices: 43282033--43282200 Score: 327
Period size: 60 Copynumber: 2.8 Consensus size: 60
43282023 ATAAAATTAT
*
43282033 TTAAAAGTTTATATAATTATACAAATTAATTTTATTTTATTTAAAAGTAAATTAATTTTA
1 TTAAAAGTTTATAAAATTATACAAATTAATTTTATTTTATTTAAAAGTAAATTAATTTTA
43282093 TTAAAAGTTTATAAAATTATACAAATTAATTTTATTTTATTTAAAAGTAAATTAATTTTA
1 TTAAAAGTTTATAAAATTATACAAATTAATTTTATTTTATTTAAAAGTAAATTAATTTTA
43282153 TTAAAAGTTTATAAAATTATACAAATTAATTTTATTTTATTTAAAAGT
1 TTAAAAGTTTATAAAATTATACAAATTAATTTTATTTTATTTAAAAGT
43282201 TTAATAAAAT
Statistics
Matches: 107, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
60 107 1.00
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.49
Consensus pattern (60 bp):
TTAAAAGTTTATAAAATTATACAAATTAATTTTATTTTATTTAAAAGTAAATTAATTTTA
Found at i:43282121 original size:34 final size:34
Alignment explanation
Indices: 43282081--43282188 Score: 133
Period size: 34 Copynumber: 3.4 Consensus size: 34
43282071 ATTTAAAAGT
43282081 AAATTAATTTTATTAAAAGTTTATAAAATTATAC
1 AAATTAATTTTATTAAAAGTTTATAAAATTATAC
** *
43282115 AAATTAATTTTATT-TTA--TT-TAAAA--GT--
1 AAATTAATTTTATTAAAAGTTTATAAAATTATAC
43282141 AAATTAATTTTATTAAAAGTTTATAAAATTATAC
1 AAATTAATTTTATTAAAAGTTTATAAAATTATAC
43282175 AAATTAATTTTATT
1 AAATTAATTTTATT
43282189 TTATTTAAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
26 14 0.23
27 1 0.02
28 1 0.02
29 2 0.03
30 10 0.17
31 2 0.03
32 1 0.02
33 1 0.02
34 28 0.47
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (34 bp):
AAATTAATTTTATTAAAAGTTTATAAAATTATAC
Found at i:43282170 original size:21 final size:21
Alignment explanation
Indices: 43282066--43282211 Score: 60
Period size: 20 Copynumber: 7.1 Consensus size: 21
43282056 AATTAATTTT
* *
43282066 ATTTTATTTAAAAGTAAAT-TA
1 ATTTTA-TTAAAAGTTAATAAA
*
43282087 ATTTTATTAAAAGTTTATAAA
1 ATTTTATTAAAAGTTAATAAA
***
43282108 A--TTA-TACAAA-TTAATTTT
1 ATTTTATTA-AAAGTTAATAAA
* *
43282126 ATTTTATTTAAAAGTAAAT-TA
1 ATTTTA-TTAAAAGTTAATAAA
*
43282147 ATTTTATTAAAAGTTTATAAA
1 ATTTTATTAAAAGTTAATAAA
***
43282168 A--TTA-TACAAA-TTAATTTT
1 ATTTTATTA-AAAGTTAATAAA
43282186 ATTTTATTTAAAAGTTTAATAAA
1 ATTTTA-TTAAAAG-TTAATAAA
43282209 ATT
1 ATT
43282212 ATTTTACTTT
Statistics
Matches: 91, Mismatches: 19, Indels: 28
0.66 0.14 0.20
Matches are distributed among these distances:
18 14 0.15
19 12 0.13
20 26 0.29
21 23 0.25
22 8 0.09
23 8 0.09
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (21 bp):
ATTTTATTAAAAGTTAATAAA
Found at i:43282214 original size:60 final size:60
Alignment explanation
Indices: 43282019--43282214 Score: 304
Period size: 60 Copynumber: 3.2 Consensus size: 60
43282009 TACTTTTAAA
* *
43282019 TAAAATAAAATTATTTAAAAGTTTATATAATTATACAAATTAATTTTATTTTATTTAAAAG
1 TAAATTAAAATTA-TTAAAAGTTTATAAAATTATACAAATTAATTTTATTTTATTTAAAAG
**
43282080 TAAATTAATTTTATTAAAAGTTTATAAAATTATACAAATTAATTTTATTTTATTTAAAAG
1 TAAATTAAAATTATTAAAAGTTTATAAAATTATACAAATTAATTTTATTTTATTTAAAAG
**
43282140 TAAATTAATTTTATTAAAAGTTTATAAAATTATACAAATTAATTTTATTTTATTTAAAAG
1 TAAATTAAAATTATTAAAAGTTTATAAAATTATACAAATTAATTTTATTTTATTTAAAAG
*
43282200 TTTAA-TAAAATTATT
1 -TAAATTAAAATTATT
43282215 TTACTTTAGG
Statistics
Matches: 127, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
60 114 0.90
61 13 0.10
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (60 bp):
TAAATTAAAATTATTAAAAGTTTATAAAATTATACAAATTAATTTTATTTTATTTAAAAG
Found at i:43285129 original size:21 final size:20
Alignment explanation
Indices: 43285100--43285145 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 20
43285090 CACCAAATCA
43285100 AACACAAAATCAGAGAAACAAAG
1 AACA-AAAAT-AGA-AAACAAAG
*
43285123 AACAAAAATAGAAATCAAAG
1 AACAAAAATAGAAAACAAAG
43285143 AAC
1 AAC
43285146 GAAGGTGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 10 0.45
21 3 0.14
22 5 0.23
23 4 0.18
ACGTcount: A:0.67, C:0.15, G:0.11, T:0.07
Consensus pattern (20 bp):
AACAAAAATAGAAAACAAAG
Found at i:43285231 original size:8 final size:8
Alignment explanation
Indices: 43285212--43285249 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
43285202 TTATATATTT
43285212 TAAAACATA
1 TAAAA-ATA
43285221 TAAAAATA
1 TAAAAATA
*
43285229 TAATAATA
1 TAAAAATA
43285237 -AAAAATA
1 TAAAAATA
43285244 TAAAAA
1 TAAAAA
43285250 AATTTACCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
7 6 0.23
8 15 0.58
9 5 0.19
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (8 bp):
TAAAAATA
Found at i:43286720 original size:22 final size:21
Alignment explanation
Indices: 43286668--43286732 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 21
43286658 TTAAAGCCTT
* *
43286668 CTGATTATGGCTTTGTGTCAA
1 CTGATTATGGCTCTGTGCCAA
* *
43286689 CTTACATATGGCTCTGTGCCAA
1 CTGA-TTATGGCTCTGTGCCAA
*
43286711 CCTGATTATGGCTGTGTGCCAA
1 -CTGATTATGGCTCTGTGCCAA
43286733 ACGTATTTGC
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
21 3 0.09
22 29 0.83
23 3 0.09
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.35
Consensus pattern (21 bp):
CTGATTATGGCTCTGTGCCAA
Found at i:43286921 original size:27 final size:27
Alignment explanation
Indices: 43286891--43286992 Score: 134
Period size: 27 Copynumber: 3.8 Consensus size: 27
43286881 ATTCTGTTAA
* *
43286891 GTGGCTTTGCCACATTATCTGTTTCTG
1 GTGGCTCTGCCACAATATCTGTTTCTG
*
43286918 GTGGCTATGCCACAAATATCTG-TTCTG
1 GTGGCTCTGCCAC-AATATCTGTTTCTG
*
43286945 GTGGCTCTGCCACAATATCTGTATCTG
1 GTGGCTCTGCCACAATATCTGTTTCTG
* *
43286972 GTGACTCTGTCACAATATCTG
1 GTGGCTCTGCCACAATATCTG
43286993 ATAACTGAGC
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
26 8 0.12
27 52 0.78
28 7 0.10
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.36
Consensus pattern (27 bp):
GTGGCTCTGCCACAATATCTGTTTCTG
Found at i:43287167 original size:6 final size:6
Alignment explanation
Indices: 43287129--43287279 Score: 105
Period size: 6 Copynumber: 24.3 Consensus size: 6
43287119 TTGCATTCAC
* * *
43287129 ATTCTG ATTTTTG ATTCTG -TTACCTG ATACTG ATTCTG ATTTTG ATTCTG
1 ATTCTG A-TTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
* * *
43287179 -TTACCTG ATACTG ATTCTG ATTTTG ATTCTG -TTACCTG ATACTG ATTCTG
1 ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG
* *
43287229 ATTCTG ATTCTG -TCACCTA ATTCTG ATTCTG ATTCTG ATTCT- AGTTCTG
1 ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG A-TTCTG
43287278 AT
1 AT
43287280 AATGTTTCTT
Statistics
Matches: 114, Mismatches: 16, Indels: 30
0.71 0.10 0.19
Matches are distributed among these distances:
5 8 0.07
6 85 0.75
7 17 0.15
8 4 0.04
ACGTcount: A:0.19, C:0.17, G:0.15, T:0.48
Consensus pattern (6 bp):
ATTCTG
Found at i:43287193 original size:37 final size:31
Alignment explanation
Indices: 43287129--43287270 Score: 230
Period size: 31 Copynumber: 4.5 Consensus size: 31
43287119 TTGCATTCAC
43287129 ATTCTGATTTTTGATTCTGTTACCTGATACTG
1 ATTCTGA-TTTTGATTCTGTTACCTGATACTG
43287161 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
43287192 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
* * * *
43287223 ATTCTGATTCTGATTCTGTCACCTAATTCTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
*
43287254 ATTCTGATTCTGATTCT
1 ATTCTGATTTTGATTCT
43287271 AGTTCTGATA
Statistics
Matches: 106, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
31 99 0.93
32 7 0.07
ACGTcount: A:0.19, C:0.18, G:0.15, T:0.49
Consensus pattern (31 bp):
ATTCTGATTTTGATTCTGTTACCTGATACTG
Found at i:43287227 original size:62 final size:62
Alignment explanation
Indices: 43287129--43287295 Score: 230
Period size: 62 Copynumber: 2.7 Consensus size: 62
43287119 TTGCATTCAC
* * *
43287129 ATTCTGATTTTTGATTCTGTTACCTGATACTGATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGA-TTTTGATTCTGTTACCTGATACTGATTCTGATTCTGATTCTGTCACCTAATACTG
*
43287192 ATTCTGATTTTGATTCTGTTACCTGATACTGATTCTGATTCTGATTCTGTCACCTAATTCTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTGATTCTGATTCTGATTCTGTCACCTAATACTG
* * * *
43287254 ATTCTGATTCTGATTCTAGTT--CTGATAATGTTTCTTATTCTG
1 ATTCTGATTTTGATTCT-GTTACCTGATACTGATTCTGATTCTG
43287296 TAATGGGTTA
Statistics
Matches: 95, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
61 18 0.19
62 67 0.71
63 10 0.11
ACGTcount: A:0.19, C:0.17, G:0.15, T:0.49
Consensus pattern (62 bp):
ATTCTGATTTTGATTCTGTTACCTGATACTGATTCTGATTCTGATTCTGTCACCTAATACTG
Found at i:43289632 original size:13 final size:14
Alignment explanation
Indices: 43289614--43289645 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
43289604 GTATTATAAA
43289614 TAATTATAAT-GTT
1 TAATTATAATGGTT
43289627 TAATTATAATGGTT
1 TAATTATAATGGTT
43289641 TAATT
1 TAATT
43289646 TGTCGTTAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (14 bp):
TAATTATAATGGTT
Found at i:43290087 original size:21 final size:21
Alignment explanation
Indices: 43290058--43290109 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
43290048 TAGAGCGGAT
*
43290058 GCAGCAGCGACGGAGGCAGCG
1 GCAGCAGCGACGGAGGCAGAG
* * *
43290079 GCAGTAGCGAGGGAGGTAGAG
1 GCAGCAGCGACGGAGGCAGAG
43290100 GCAGCAGCGA
1 GCAGCAGCGA
43290110 TCGCAGCAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.21, G:0.48, T:0.04
Consensus pattern (21 bp):
GCAGCAGCGACGGAGGCAGAG
Found at i:43290385 original size:31 final size:31
Alignment explanation
Indices: 43290350--43290439 Score: 153
Period size: 31 Copynumber: 2.9 Consensus size: 31
43290340 TTTATGCTAC
*
43290350 ATTTGCTATTTTTGGTTGGATTTCATGTTAT
1 ATTTGCTGTTTTTGGTTGGATTTCATGTTAT
43290381 ATTTGCTGTTTTTGGTTGGATTTCATGTTAT
1 ATTTGCTGTTTTTGGTTGGATTTCATGTTAT
* *
43290412 ATTTGCTGTTTTTGGTTGAATTTAATGT
1 ATTTGCTGTTTTTGGTTGGATTTCATGT
43290440 AGGAAGGGTT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 56 1.00
ACGTcount: A:0.16, C:0.06, G:0.21, T:0.58
Consensus pattern (31 bp):
ATTTGCTGTTTTTGGTTGGATTTCATGTTAT
Found at i:43295349 original size:22 final size:20
Alignment explanation
Indices: 43295321--43295373 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 20
43295311 GTTCGTGTAA
43295321 TTAAATTGTACATTTATATGTT
1 TTAAATTGTACA--TATATGTT
*
43295343 TTAAATTG-A-ATATTTGTT
1 TTAAATTGTACATATATGTT
43295361 TGTAAATTGTACA
1 T-TAAATTGTACA
43295374 ATTGCCATGA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
18 8 0.30
19 7 0.26
20 2 0.07
21 2 0.07
22 8 0.30
ACGTcount: A:0.34, C:0.04, G:0.11, T:0.51
Consensus pattern (20 bp):
TTAAATTGTACATATATGTT
Found at i:43295542 original size:25 final size:24
Alignment explanation
Indices: 43295514--43295572 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 24
43295504 TAGCTCAAAT
*
43295514 GAGCTTACCGTTACTCAACTAAGAG
1 GAGCTTACC-TTACTCAACTAAGAA
* * *
43295539 GAGCTTACTCTTATTCAGCTTAGAA
1 GAGCTTAC-CTTACTCAACTAAGAA
43295564 GAGCTTACC
1 GAGCTTACC
43295573 ATTTACAGCT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 1 0.03
25 27 0.93
26 1 0.03
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (24 bp):
GAGCTTACCTTACTCAACTAAGAA
Found at i:43298822 original size:21 final size:21
Alignment explanation
Indices: 43298797--43298865 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
43298787 TATAATGATT
43298797 ATTATTATGGTTTTATATTAA
1 ATTATTATGGTTTTATATTAA
**
43298818 ATTATTATAATTATTA-ATT-A
1 ATTATTATGGTT-TTATATTAA
* *
43298838 A-CATTATGGTTTTATATTAG
1 ATTATTATGGTTTTATATTAA
43298858 ATTATTAT
1 ATTATTAT
43298866 TATTAGCATT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
18 3 0.08
19 10 0.27
20 3 0.08
21 18 0.49
22 3 0.08
ACGTcount: A:0.36, C:0.01, G:0.07, T:0.55
Consensus pattern (21 bp):
ATTATTATGGTTTTATATTAA
Found at i:43298878 original size:15 final size:14
Alignment explanation
Indices: 43298852--43298882 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
43298842 TATGGTTTTA
43298852 TATTAGATTATTAT
1 TATTAGATTATTAT
43298866 TATTAGCATTATTAT
1 TATTAG-ATTATTAT
43298881 TA
1 TA
43298883 AATAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.55
Consensus pattern (14 bp):
TATTAGATTATTAT
Found at i:43299526 original size:23 final size:23
Alignment explanation
Indices: 43299498--43299554 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
43299488 CAATATTCCG
*
43299498 GGTGTGTTTGTGTTGGATATTCT
1 GGTGTGTTTGGGTTGGATATTCT
43299521 GGTGTGTTTGGGTTGGATATTCT
1 GGTGTGTTTGGGTTGGATATTCT
43299544 GGTGTGTTTGG
1 GGTGTGTTTGG
43299555 ATGGAATCCG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.07, C:0.04, G:0.40, T:0.49
Consensus pattern (23 bp):
GGTGTGTTTGGGTTGGATATTCT
Found at i:43310261 original size:43 final size:43
Alignment explanation
Indices: 43310196--43310286 Score: 128
Period size: 43 Copynumber: 2.1 Consensus size: 43
43310186 AATTTTGTTG
* * *
43310196 AAAAAACGCCGCTAAAGGCCAGGACTTTTAGCGGCGCTTATAT
1 AAAAAACGCCGCTAAAGACCAGGACTTATAGCAGCGCTTATAT
* * *
43310239 AAAAAACGCCGTTAAAGACCAGGACTTATAGCAGCGCTTTTTT
1 AAAAAACGCCGCTAAAGACCAGGACTTATAGCAGCGCTTATAT
43310282 AAAAA
1 AAAAA
43310287 CTAAAAGTCT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.22
Consensus pattern (43 bp):
AAAAAACGCCGCTAAAGACCAGGACTTATAGCAGCGCTTATAT
Found at i:43310381 original size:43 final size:43
Alignment explanation
Indices: 43310287--43310420 Score: 189
Period size: 43 Copynumber: 3.1 Consensus size: 43
43310277 TTTTTAAAAA
* * *
43310287 CTAAAAGTCTTGTTCTATAATGGCGTTTTATATAAAAAGCGCCG
1 CTAAAAGTCTTGTTCTTTAGTGGCGTTTTTTA-AAAAAGCGCCG
*
43310331 CTAAAAGTCTTGTTCTTTAGTGGCGTTTTTTAAAAAAGTGCCG
1 CTAAAAGTCTTGTTCTTTAGTGGCGTTTTTTAAAAAAGCGCCG
* *
43310374 CTAAAAGTCTTGGTCTTTAGCGGCGCTTTTTTAAAAAA-CGCCG
1 CTAAAAGTCTTGTTCTTTAGTGGCG-TTTTTTAAAAAAGCGCCG
43310417 CTAA
1 CTAA
43310421 TTTCCCAGTT
Statistics
Matches: 82, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
43 41 0.50
44 41 0.50
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.35
Consensus pattern (43 bp):
CTAAAAGTCTTGTTCTTTAGTGGCGTTTTTTAAAAAAGCGCCG
Found at i:43311258 original size:18 final size:18
Alignment explanation
Indices: 43311226--43311263 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
43311216 TACAATATAG
43311226 TAGTAAAAATATTATTTAA
1 TAGTAAAAATATTA-TTAA
*
43311245 TAGTAAAAA-GTTATTAA
1 TAGTAAAAATATTATTAA
43311262 TA
1 TA
43311264 CTTGATAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 3 0.17
19 9 0.50
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (18 bp):
TAGTAAAAATATTATTAA
Found at i:43318811 original size:37 final size:38
Alignment explanation
Indices: 43318731--43318844 Score: 117
Period size: 37 Copynumber: 3.0 Consensus size: 38
43318721 CTATGCAGCA
* * *
43318731 GATGCACGGGG-CGAAGGAGATGGAGGCCGAGATGGGTTAC
1 GATGAACGGGGACGAAGGCGATGGAGG--G-GATGGGTTGC
* *
43318771 GATGAAC-GGTACGAAGGCGATGGAGGGGATGGTTTGC
1 GATGAACGGGGACGAAGGCGATGGAGGGGATGGGTTGC
* *
43318808 GATGTACGGGGA-GAAGGCGATGGAGGAGATGGGTTGC
1 GATGAACGGGGACGAAGGCGATGGAGGGGATGGGTTGC
43318845 AATGCACAGG
Statistics
Matches: 63, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
37 37 0.59
38 4 0.06
39 2 0.03
40 20 0.32
ACGTcount: A:0.25, C:0.11, G:0.48, T:0.16
Consensus pattern (38 bp):
GATGAACGGGGACGAAGGCGATGGAGGGGATGGGTTGC
Found at i:43318857 original size:37 final size:37
Alignment explanation
Indices: 43318783--43318858 Score: 107
Period size: 37 Copynumber: 2.1 Consensus size: 37
43318773 TGAACGGTAC
* * * * *
43318783 GAAGGCGATGGAGGGGATGGTTTGCGATGTACGGGGA
1 GAAGGCGATGGAGGAGATGGGTTGCAATGCACAGGGA
43318820 GAAGGCGATGGAGGAGATGGGTTGCAATGCACAGGGA
1 GAAGGCGATGGAGGAGATGGGTTGCAATGCACAGGGA
43318857 GA
1 GA
43318859 TTTGGGGGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.26, C:0.09, G:0.49, T:0.16
Consensus pattern (37 bp):
GAAGGCGATGGAGGAGATGGGTTGCAATGCACAGGGA
Found at i:43319703 original size:15 final size:15
Alignment explanation
Indices: 43319680--43319711 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
43319670 AAATAATAAT
43319680 TTATATATATTTATC
1 TTATATATATTTATC
*
43319695 TTATTTATATTTATC
1 TTATATATATTTATC
43319710 TT
1 TT
43319712 CTAAATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (15 bp):
TTATATATATTTATC
Found at i:43319872 original size:18 final size:17
Alignment explanation
Indices: 43319846--43319879 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
43319836 CACTGTAACC
43319846 CCTAAACCAACCATAAAT
1 CCTAAACC-ACCATAAAT
*
43319864 CCTAGACCACCATAAA
1 CCTAAACCACCATAAA
43319880 GCCCAAACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.47, C:0.35, G:0.03, T:0.15
Consensus pattern (17 bp):
CCTAAACCACCATAAAT
Found at i:43320741 original size:40 final size:38
Alignment explanation
Indices: 43320650--43320741 Score: 87
Period size: 39 Copynumber: 2.3 Consensus size: 38
43320640 TCTGTTTGCT
* * *
43320650 TTTGCAGCGTTTTTATAAAAGCGCCGCTAATTCTGATA
1 TTTGCGGCGTTTTAATAAAAGCGCCACTAATTCTGATA
* * *
43320688 TATGGCGGTGTTTTAAGTAAAA-CGCCACTAATGTTTGATTA
1 T-TTGCGGCGTTTTAA-TAAAAGCGCCACTAAT-TCTGA-TA
43320729 TTTGCGGCGTTTT
1 TTTGCGGCGTTTT
43320742 TTCATAAGCG
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
38 1 0.02
39 19 0.45
40 19 0.45
41 3 0.07
ACGTcount: A:0.24, C:0.15, G:0.22, T:0.39
Consensus pattern (38 bp):
TTTGCGGCGTTTTAATAAAAGCGCCACTAATTCTGATA
Found at i:43328320 original size:253 final size:253
Alignment explanation
Indices: 43327872--43328377 Score: 985
Period size: 253 Copynumber: 2.0 Consensus size: 253
43327862 AATTGTAAAA
*
43327872 TTAATGTGTTAAATATTATTACACTTTAGATTCAAATATTATTGTGTGTATTTTTTAAATTTTAT
1 TTAATGTGTTAAATAGTATTACACTTTAGATTCAAATATTATTGTGTGTATTTTTTAAATTTTAT
43327937 ATGAAATAAAAAATTATTTTATAATAATATTGATAATTTTTCAAGAGTAGACACTTATCACACTA
66 ATGAAATAAAAAATTATTTTATAATAATATTGATAATTTTTCAAGAGTAGACACTTATCACACTA
43328002 ACTTAATAATCCATAGACTTATTTTTTTAAAATTTTATATAAAAATAAAAAATACAAAGTTGTTA
131 ACTTAATAATCCATAGACTTATTTTTTTAAAATTTTATATAAAAATAAAAAATACAAAGTTGTTA
43328067 TTTAGCAAAAATAAATTCTTGATTTCTTTAAAAAATAATATTTAATTAAAATTTAATT
196 TTTAGCAAAAATAAATTCTTGATTTCTTTAAAAAATAATATTTAATTAAAATTTAATT
* *
43328125 TTAATGTGTTAAATAGTATTGCATTTTAGATTCAAATATTATTGTGTGTATTTTTTAAATTTTAT
1 TTAATGTGTTAAATAGTATTACACTTTAGATTCAAATATTATTGTGTGTATTTTTTAAATTTTAT
43328190 ATGAAATAAAAAATTATTTTATAATAATATTGATAATTTTTCAAGAGTAGACACTTATCACACTA
66 ATGAAATAAAAAATTATTTTATAATAATATTGATAATTTTTCAAGAGTAGACACTTATCACACTA
43328255 ACTTAATAATCCATAGACTTATTTTTTTAAAATTTTATATAAAAATAAAAAATACAAAGTTGTTA
131 ACTTAATAATCCATAGACTTATTTTTTTAAAATTTTATATAAAAATAAAAAATACAAAGTTGTTA
43328320 TTTAGCAAAAATAAATTCTTGATTTCTTTAAAAAATAATATTTAATTAAAATTTAATT
196 TTTAGCAAAAATAAATTCTTGATTTCTTTAAAAAATAATATTTAATTAAAATTTAATT
43328378 AATGAATTCA
Statistics
Matches: 250, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
253 250 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.44
Consensus pattern (253 bp):
TTAATGTGTTAAATAGTATTACACTTTAGATTCAAATATTATTGTGTGTATTTTTTAAATTTTAT
ATGAAATAAAAAATTATTTTATAATAATATTGATAATTTTTCAAGAGTAGACACTTATCACACTA
ACTTAATAATCCATAGACTTATTTTTTTAAAATTTTATATAAAAATAAAAAATACAAAGTTGTTA
TTTAGCAAAAATAAATTCTTGATTTCTTTAAAAAATAATATTTAATTAAAATTTAATT
Found at i:43331579 original size:9 final size:9
Alignment explanation
Indices: 43331547--43331652 Score: 60
Period size: 10 Copynumber: 11.6 Consensus size: 9
43331537 TATTATTATT
43331547 ATTTTGTTAA
1 ATTTT-TTAA
*
43331557 ATTTTTATAT
1 ATTTTT-TAA
43331567 ATTTTTTAGA
1 ATTTTTTA-A
*
43331577 TTTTTTTAA
1 ATTTTTTAA
*
43331586 A-TTTAT-A
1 ATTTTTTAA
43331593 ATTTTTTAA
1 ATTTTTTAA
** *
43331602 A--AATAAA
1 ATTTTTTAA
43331609 ATTTTTTAA
1 ATTTTTTAA
43331618 A-TTTTTAA
1 ATTTTTTAA
43331626 ATTTTTTATAA
1 A-TTTTT-TAA
43331637 ATTATTTTCAA
1 ATT-TTTT-AA
43331648 ATTTT
1 ATTTT
43331653 GAAAATTACT
Statistics
Matches: 73, Mismatches: 12, Indels: 22
0.68 0.11 0.21
Matches are distributed among these distances:
7 6 0.08
8 16 0.22
9 10 0.14
10 29 0.40
11 12 0.16
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.61
Consensus pattern (9 bp):
ATTTTTTAA
Found at i:43331579 original size:19 final size:19
Alignment explanation
Indices: 43331542--43331581 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
43331532 GATTTTATTA
43331542 TTATTATTTTGTTAAATTT
1 TTATTATTTTGTTAAATTT
*
43331561 TTATATATTTT-TTAGATTT
1 TTAT-TATTTTGTTAAATTT
43331580 TT
1 TT
43331582 TTAAATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (19 bp):
TTATTATTTTGTTAAATTT
Found at i:43331579 original size:29 final size:26
Alignment explanation
Indices: 43331547--43331600 Score: 72
Period size: 29 Copynumber: 2.0 Consensus size: 26
43331537 TATTATTATT
43331547 ATTTTGTTAAATTTTTATATATTTTTTAG
1 ATTTTGTTAAA--TTTATA-ATTTTTTAG
*
43331576 ATTTTTTTAAATTTATAATTTTTTA
1 ATTTTGTTAAATTTATAATTTTTTA
43331601 AAAATAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 8 0.33
27 6 0.25
29 10 0.42
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.67
Consensus pattern (26 bp):
ATTTTGTTAAATTTATAATTTTTTAG
Found at i:43331589 original size:19 final size:20
Alignment explanation
Indices: 43331547--43331589 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
43331537 TATTATTATT
*
43331547 ATTTTGTTAAATTTTTATAT
1 ATTTTGTTAAATTTTTATAA
* *
43331567 ATTTT-TTAGATTTTTTTAA
1 ATTTTGTTAAATTTTTATAA
43331586 ATTT
1 ATTT
43331590 ATAATTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (20 bp):
ATTTTGTTAAATTTTTATAA
Found at i:43331597 original size:16 final size:16
Alignment explanation
Indices: 43331578--43331633 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
43331568 TTTTTTAGAT
43331578 TTTTTTAAATTTATAA
1 TTTTTTAAATTTATAA
** *
43331594 TTTTTTAAAAATAAAA
1 TTTTTTAAATTTATAA
*
43331610 TTTTTTAAATTTTTAAA
1 TTTTTTAAATTTAT-AA
43331627 TTTTTTA
1 TTTTTTA
43331634 TAAATTATTT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
16 23 0.72
17 9 0.28
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTTTAAATTTATAA
Found at i:43350207 original size:53 final size:53
Alignment explanation
Indices: 43350126--43350276 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
43350116 CTTACACGGT
* *
43350126 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
43350181 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
43350234 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
43350277 GCACACTTAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:43352066 original size:27 final size:27
Alignment explanation
Indices: 43352035--43352097 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 27
43352025 TTTATTAAAC
* *
43352035 TACCCCTAAGTATG-AAAATTACCGTTT
1 TACCCCTAAG-ATGCAAAATGACCGTTA
*
43352062 TACCCCT-AGGTGCAAAATGACCGTTA
1 TACCCCTAAGATGCAAAATGACCGTTA
43352088 TACCCCTAAG
1 TACCCCTAAG
43352098 GTTAATTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
25 2 0.06
26 20 0.65
27 9 0.29
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.27
Consensus pattern (27 bp):
TACCCCTAAGATGCAAAATGACCGTTA
Found at i:43354907 original size:46 final size:46
Alignment explanation
Indices: 43354796--43354971 Score: 228
Period size: 46 Copynumber: 3.7 Consensus size: 46
43354786 TTATCTTTGA
* * * * *
43354796 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTTTCTGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTC-TTTTC---CTGT
*
43354846 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCCTGT
* *
43354892 CACGTTGCCATGGTATCTTTCAACCATGGTCTTATT-TATTTCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCT-TTTCCTGT
43354938 CATGTTGCCATGGTATCTTTCAACCATGGTCTTA
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTA
43354972 CACATTTCAT
Statistics
Matches: 115, Mismatches: 10, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
45 1 0.01
46 77 0.67
49 5 0.04
50 32 0.28
ACGTcount: A:0.18, C:0.23, G:0.15, T:0.43
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCCTGT
Found at i:43355086 original size:54 final size:54
Alignment explanation
Indices: 43355020--43355317 Score: 533
Period size: 54 Copynumber: 5.4 Consensus size: 54
43355010 TCCTTACAGT
43355020 GGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTC
1 GGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTC
43355074 GGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTC
1 GGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTC
43355128 GGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTC
1 GGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTC
43355182 GGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTC
1 GGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTC
43355236 GGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTAAGCTTGGATC
1 GGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGT-A--TT-G-TC
* *
43355295 TGAATTACCAGTCCAGGCTAAAT
1 GGGATTACCAGTCCAGGCTAAAT
43355318 TCAGACCCTA
Statistics
Matches: 237, Mismatches: 2, Indels: 5
0.97 0.01 0.02
Matches are distributed among these distances:
54 210 0.89
55 1 0.00
57 2 0.01
58 1 0.00
59 23 0.10
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (54 bp):
GGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTC
Found at i:43356708 original size:18 final size:20
Alignment explanation
Indices: 43356693--43356729 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
43356683 TAATAATAAA
*
43356693 ATATCTCATTAAAATAATAT
1 ATATCTAATTAAAATAATAT
43356713 ATATCTAATT-AAATAAT
1 ATATCTAATTAAAATAAT
43356730 CATAAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (20 bp):
ATATCTAATTAAAATAATAT
Found at i:43357890 original size:17 final size:18
Alignment explanation
Indices: 43357851--43357897 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
43357841 TGCTGTTATA
* *
43357851 TTTTCTTTTATTTATTTAT
1 TTTTCTTCT-TTTATTTAC
43357870 TTTTCTTCTTTT-TTTAC
1 TTTTCTTCTTTTATTTAC
43357887 TTTTCTTCTTT
1 TTTTCTTCTTT
43357898 CCAAAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 15 0.58
18 3 0.12
19 8 0.31
ACGTcount: A:0.09, C:0.13, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTCTTCTTTTATTTAC
Found at i:43358856 original size:18 final size:18
Alignment explanation
Indices: 43358835--43358916 Score: 53
Period size: 18 Copynumber: 4.3 Consensus size: 18
43358825 AAATCCTTTT
43358835 ATTATTGTAAATCTTTGG
1 ATTATTGTAAATCTTTGG
* *
43358853 ATTATTATATAT-TTTAAGG
1 ATTATTGTAAATCTTT--GG
*
43358872 -TTAATTGTTTTAAATCCTTT-T
1 ATT-ATTG---TAAAT-CTTTGG
43358893 ATTATTGTAAATCTTTGG
1 ATTATTGTAAATCTTTGG
43358911 ATTATT
1 ATTATT
43358917 ATATATTTTA
Statistics
Matches: 48, Mismatches: 6, Indels: 20
0.65 0.08 0.27
Matches are distributed among these distances:
17 7 0.15
18 23 0.48
19 5 0.10
21 4 0.08
22 6 0.12
24 3 0.06
ACGTcount: A:0.29, C:0.05, G:0.11, T:0.55
Consensus pattern (18 bp):
ATTATTGTAAATCTTTGG
Found at i:43358886 original size:58 final size:58
Alignment explanation
Indices: 43358816--43358931 Score: 232
Period size: 58 Copynumber: 2.0 Consensus size: 58
43358806 TTCACATGTA
43358816 AATTGTTTTAAATCCTTTTATTATTGTAAATCTTTGGATTATTATATATTTTAAGGTT
1 AATTGTTTTAAATCCTTTTATTATTGTAAATCTTTGGATTATTATATATTTTAAGGTT
43358874 AATTGTTTTAAATCCTTTTATTATTGTAAATCTTTGGATTATTATATATTTTAAGGTT
1 AATTGTTTTAAATCCTTTTATTATTGTAAATCTTTGGATTATTATATATTTTAAGGTT
43358932 TCATATATTA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.29, C:0.05, G:0.10, T:0.55
Consensus pattern (58 bp):
AATTGTTTTAAATCCTTTTATTATTGTAAATCTTTGGATTATTATATATTTTAAGGTT
Found at i:43385214 original size:32 final size:32
Alignment explanation
Indices: 43385175--43385334 Score: 239
Period size: 32 Copynumber: 5.0 Consensus size: 32
43385165 CATAAAAAAT
*
43385175 ATCATACATTAGGTTTACATATAAAAAAGTAG
1 ATCATACATTAGTTTTACATATAAAAAAGTAG
*
43385207 ATCATACATTAGTTTTGCATATAAAAAAGTAG
1 ATCATACATTAGTTTTACATATAAAAAAGTAG
* * *
43385239 ATCATACATTAGGTTCACATATAAAAAAGTAT
1 ATCATACATTAGTTTTACATATAAAAAAGTAG
* *
43385271 ATCATACATTAGTTTTGCATATGAAAAAGTAG
1 ATCATACATTAGTTTTACATATAAAAAAGTAG
* *
43385303 ATCATATATTAGTTTTATATATAAAAAAGTAG
1 ATCATACATTAGTTTTACATATAAAAAAGTAG
43385335 CATAGTTATA
Statistics
Matches: 113, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 113 1.00
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.34
Consensus pattern (32 bp):
ATCATACATTAGTTTTACATATAAAAAAGTAG
Found at i:43385248 original size:64 final size:64
Alignment explanation
Indices: 43385175--43385334 Score: 266
Period size: 64 Copynumber: 2.5 Consensus size: 64
43385165 CATAAAAAAT
43385175 ATCATACATTAGGTTTACATATAAAAAAGTAGATCATACATTAGTTTTGCATATAAAAAAGTAG
1 ATCATACATTAGGTTTACATATAAAAAAGTAGATCATACATTAGTTTTGCATATAAAAAAGTAG
* * *
43385239 ATCATACATTAGGTTCACATATAAAAAAGTATATCATACATTAGTTTTGCATATGAAAAAGTAG
1 ATCATACATTAGGTTTACATATAAAAAAGTAGATCATACATTAGTTTTGCATATAAAAAAGTAG
* * *
43385303 ATCATATATTAGTTTTATATATAAAAAAGTAG
1 ATCATACATTAGGTTTACATATAAAAAAGTAG
43385335 CATAGTTATA
Statistics
Matches: 88, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 88 1.00
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.34
Consensus pattern (64 bp):
ATCATACATTAGGTTTACATATAAAAAAGTAGATCATACATTAGTTTTGCATATAAAAAAGTAG
Found at i:43415535 original size:74 final size:74
Alignment explanation
Indices: 43415439--43415641 Score: 259
Period size: 74 Copynumber: 2.7 Consensus size: 74
43415429 TGTTCCAAAG
** * * * *
43415439 ATCAACTCATAGGGCGAAAGGTGAGTTGAGCCTCAGGACATGCTAAGGTATTTTCAAATTC-TT-
1 ATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTC-AA-TCGTTG
43415502 TTT-TCAAAAAA
64 TTTGTC-AAAAA
* * * *
43415513 ATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGGCACGGTGAGGTATTTTCAATCGTTGTT
1 ATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATCGTTGTT
43415578 TGTCAAAAA
66 TGTCAAAAA
*
43415587 ATCAACTCATACTGCCAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTC
1 ATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTC
43415642 GATTTCCGCT
Statistics
Matches: 112, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
72 2 0.02
73 4 0.04
74 104 0.93
75 2 0.02
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.29
Consensus pattern (74 bp):
ATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATCGTTGTT
TGTCAAAAA
Found at i:43415822 original size:14 final size:14
Alignment explanation
Indices: 43415803--43415831 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
43415793 AGCTGAGGTC
43415803 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
43415817 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
43415831 T
1 T
43415832 CGTCAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.14, G:0.07, T:0.66
Consensus pattern (14 bp):
TTTTCAATTTCTGT
Found at i:43415931 original size:91 final size:91
Alignment explanation
Indices: 43415747--43416268 Score: 863
Period size: 91 Copynumber: 5.7 Consensus size: 91
43415737 TCTGTTTGTC
* * * *
43415747 AAAAATCAACTCATATCGCGAGAGGTGAGTTGAGCCTC--GGCTCACAAGCTGAGGTCTTTTCAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGG----CATGCTGAGGTATTTTCGA
* * * *
43415810 TTTCTGTTTTTCAATTTCTGTTCGTC--AA
62 TTTCTGCTTTCCAATTTCTGCTCTTCAAAA
43415838 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGGCATGCTGAGGTATTTTCGATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGGCATGCTGAGGTATTTTCGATTTC
43415903 TGCTTTCCAATTTCTGCTCTTCAAAA
66 TGCTTTCCAATTTCTGCTCTTCAAAA
43415929 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGGCATGCTGAGGTATTTTCGATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGGCATGCTGAGGTATTTTCGATTTC
43415994 TGCTTTCCAATTTCTGCTCTTCAAAA
66 TGCTTTCCAATTTCTGCTCTTCAAAA
43416020 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGGCATGCTGAGGTATTTTCGATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGGCATGCTGAGGTATTTTCGATTTC
43416085 TGCTTTCCAATTTCTGCTCTTCAAAA
66 TGCTTTCCAATTTCTGCTCTTCAAAA
43416111 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGGCATGCTGAGGTATTTTCGATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGGCATGCTGAGGTATTTTCGATTTC
43416176 TGCTTTCCAATTTCTGCTCTTCAAAA
66 TGCTTTCCAATTTCTGCTCTTCAAAA
* * * * *
43416202 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTAAGACACGCTGAGGTCTTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGGCATGCTGAGGTATTTTCGATTTC
43416267 TG
66 TG
43416269 TTTGTCAAAA
Statistics
Matches: 414, Mismatches: 13, Indels: 8
0.95 0.03 0.02
Matches are distributed among these distances:
89 38 0.09
91 374 0.90
93 2 0.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (91 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGGCATGCTGAGGTATTTTCGATTTC
TGCTTTCCAATTTCTGCTCTTCAAAA
Found at i:43416342 original size:75 final size:72
Alignment explanation
Indices: 43416202--43416410 Score: 278
Period size: 73 Copynumber: 2.9 Consensus size: 72
43416192 CTCTTCAAAA
* **
43416202 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTAAGACACGCTGAGGTCTTTTCAATTTC
1 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCC-TCGGACACGCTGAGGTCTTTTCAATTTC
*
43416267 TGTTTGTC
65 TGTTCGTC
* *
43416275 AAAAATCAACTCATATCGCAAGAGGTGAGTTGAGCCTCGGCTCACATGCTGAGGTCTTTTCAATT
1 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGG---ACACGCTGAGGTCTTTTCAATT
43416340 TCTGTTCGTC
63 TCTGTTCGTC
* * *
43416350 --AAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGAGGCACGCTGAGGTATTCTCAATT
1 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCG-GACACGCTGAGGTCTTTTCAATT
43416411 AATGTTTTTT
Statistics
Matches: 121, Mismatches: 11, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
71 18 0.15
72 2 0.02
73 70 0.58
74 1 0.01
75 30 0.25
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.30
Consensus pattern (72 bp):
AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGACACGCTGAGGTCTTTTCAATTTCT
GTTCGTC
Found at i:43417076 original size:53 final size:53
Alignment explanation
Indices: 43416996--43417106 Score: 204
Period size: 53 Copynumber: 2.1 Consensus size: 53
43416986 GCAAGACCAG
*
43416996 GCAAAATTGGCCTCTCTTTATGTCTTTGCTCTATTCCCGTTATACGATAATGA
1 GCAAAATTGACCTCTCTTTATGTCTTTGCTCTATTCCCGTTATACGATAATGA
*
43417049 GCAAAATTGACCTCTCTTTATGTCTTTGCTCTATTCTCGTTATACGATAATGA
1 GCAAAATTGACCTCTCTTTATGTCTTTGCTCTATTCCCGTTATACGATAATGA
43417102 GCAAA
1 GCAAA
43417107 GAGGGGCAGC
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
53 56 1.00
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (53 bp):
GCAAAATTGACCTCTCTTTATGTCTTTGCTCTATTCCCGTTATACGATAATGA
Found at i:43420236 original size:19 final size:19
Alignment explanation
Indices: 43420212--43420250 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
43420202 TCATTTACAT
43420212 ACATTTGGGTGCCTACCAA
1 ACATTTGGGTGCCTACCAA
*
43420231 ACATTTGGGTGCCTATCAA
1 ACATTTGGGTGCCTACCAA
43420250 A
1 A
43420251 GGTTGAACCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (19 bp):
ACATTTGGGTGCCTACCAA
Found at i:43420344 original size:25 final size:25
Alignment explanation
Indices: 43420313--43420370 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
43420303 TACAAACTGT
* *
43420313 GAATATGGTCGCAAGAAGAACCAGA
1 GAATATGGTAGCAAGAAGAAACAGA
*
43420338 GATTATGGTAGCAAGAAGAAACAGA
1 GAATATGGTAGCAAGAAGAAACAGA
43420363 GAATATGG
1 GAATATGG
43420371 GAATGAAAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.45, C:0.10, G:0.29, T:0.16
Consensus pattern (25 bp):
GAATATGGTAGCAAGAAGAAACAGA
Found at i:43421050 original size:18 final size:18
Alignment explanation
Indices: 43421027--43421061 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
43421017 ATCGAAGGGT
43421027 AAGGTTAAACCCACAACC
1 AAGGTTAAACCCACAACC
43421045 AAGGTTAAACCCACAAC
1 AAGGTTAAACCCACAAC
43421062 TGACTGCCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.31, G:0.11, T:0.11
Consensus pattern (18 bp):
AAGGTTAAACCCACAACC
Found at i:43425079 original size:13 final size:14
Alignment explanation
Indices: 43425055--43425087 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
43425045 ATGGGGATAG
*
43425055 GATTCTGTATATCT
1 GATTCTGCATATCT
43425069 G-TTCTGCATATCT
1 GATTCTGCATATCT
43425082 GATTCT
1 GATTCT
43425088 ATTATCTGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.18, C:0.18, G:0.15, T:0.48
Consensus pattern (14 bp):
GATTCTGCATATCT
Found at i:43435195 original size:43 final size:43
Alignment explanation
Indices: 43435131--43435218 Score: 133
Period size: 43 Copynumber: 2.0 Consensus size: 43
43435121 GTGTTAAATT
43435131 AAATTGCACAAGCCCTGCTTTGTGCAACAATACTAGAAGAATG
1 AAATTGCACAAGCCCTGCTTTGTGCAACAATACTAGAAGAATG
* * *
43435174 AAATTGC-CGAAGTCCTTCTTTGTGCACCAATACTAGAAGAATG
1 AAATTGCAC-AAGCCCTGCTTTGTGCAACAATACTAGAAGAATG
43435217 AA
1 AA
43435219 GGCTCTCCCT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
42 1 0.02
43 40 0.98
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.25
Consensus pattern (43 bp):
AAATTGCACAAGCCCTGCTTTGTGCAACAATACTAGAAGAATG
Found at i:43438250 original size:28 final size:28
Alignment explanation
Indices: 43438209--43438262 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
43438199 TTAGAAAAAG
43438209 TTAAATAATTTTTTATTAAAAATATTAA
1 TTAAATAATTTTTTATTAAAAATATTAA
* *
43438237 TTAAA-AATTATTTTTTTAATAATATT
1 TTAAATAATT-TTTTATTAAAAATATT
43438263 CGCGTAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
TTAAATAATTTTTTATTAAAAATATTAA
Found at i:43444026 original size:13 final size:13
Alignment explanation
Indices: 43444004--43444028 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43443994 CGAAATAATT
43444004 TTTTGAAAATTTA
1 TTTTGAAAATTTA
43444017 TTTTGAAAATTT
1 TTTTGAAAATTT
43444029 TGACGTTTGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (13 bp):
TTTTGAAAATTTA
Found at i:43445336 original size:42 final size:42
Alignment explanation
Indices: 43445236--43445336 Score: 103
Period size: 42 Copynumber: 2.4 Consensus size: 42
43445226 TCTGGGATAT
* * *
43445236 GACATCGGTATCGATATGTGATTTCATGTAAAACCGTATCTAG
1 GACAT-GGCATCGATATGAGATTTCATGTAAAACCATATCTAG
* * * * * * *
43445279 GATATGGCGTTGATATGAGATTTCATGTAAGACCATGTTTGG
1 GACATGGCATCGATATGAGATTTCATGTAAAACCATATCTAG
43445321 GACATGGCATCGATAT
1 GACATGGCATCGATAT
43445337 ATGGTCCCGT
Statistics
Matches: 45, Mismatches: 13, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
42 41 0.91
43 4 0.09
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.33
Consensus pattern (42 bp):
GACATGGCATCGATATGAGATTTCATGTAAAACCATATCTAG
Found at i:43445434 original size:48 final size:48
Alignment explanation
Indices: 43445394--43445516 Score: 158
Period size: 48 Copynumber: 2.6 Consensus size: 48
43445384 TGAGACTTCG
*
43445394 TGTAAGACCATATCTGGGATATGGCATTGGCATC-AGTATGAGATCCCA
1 TGTAAGACCATATCTGGGATATGGCATTAGCATCGA-TATGAGATCCCA
* * *
43445442 TGTAAGCCCATATCTGGGATATGGCATTAGCATCGATATGAGGTCCCG
1 TGTAAGACCATATCTGGGATATGGCATTAGCATCGATATGAGATCCCA
* * * *
43445490 TATAAGGCCATGTCTGGGACATGGCAT
1 TGTAAGACCATATCTGGGATATGGCAT
43445517 CGGCACCGTT
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
48 65 0.98
49 1 0.02
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (48 bp):
TGTAAGACCATATCTGGGATATGGCATTAGCATCGATATGAGATCCCA
Found at i:43459153 original size:46 final size:46
Alignment explanation
Indices: 43459086--43459178 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
43459076 AGTCCCTAAC
43459086 TTACTTCTACATTCACCGGGGTGACTTCTTCCACAATGTTGACACT
1 TTACTTCTACATTCACCGGGGTGACTTCTTCCACAATGTTGACACT
43459132 TTACTTCTACATTCACCGGGGTGACTTCTTCCACAATGTTGACACT
1 TTACTTCTACATTCACCGGGGTGACTTCTTCCACAATGTTGACACT
43459178 T
1 T
43459179 AGGCCTTTGG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.22, C:0.28, G:0.15, T:0.35
Consensus pattern (46 bp):
TTACTTCTACATTCACCGGGGTGACTTCTTCCACAATGTTGACACT
Found at i:43461587 original size:53 final size:53
Alignment explanation
Indices: 43461506--43461656 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
43461496 CTTACACGGT
* *
43461506 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
43461561 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
43461614 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
43461657 GCACACTTAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:43477170 original size:10 final size:9
Alignment explanation
Indices: 43477159--43477213 Score: 53
Period size: 10 Copynumber: 6.0 Consensus size: 9
43477149 TTTCAATTTA
43477159 ATAATTTTT
1 ATAATTTTT
43477168 AATATATTTTT
1 -ATA-ATTTTT
43477179 AT-A-TTTT
1 ATAATTTTT
43477186 AT-ATTTTGT
1 ATAATTTT-T
43477195 ATAATATTTT
1 ATAAT-TTTT
43477205 ATAATTTTT
1 ATAATTTTT
43477214 TGTTTTATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
7 7 0.17
8 4 0.10
9 7 0.17
10 13 0.32
11 9 0.22
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (9 bp):
ATAATTTTT
Found at i:43482347 original size:20 final size:21
Alignment explanation
Indices: 43482322--43482360 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
43482312 TAAATTTTCC
43482322 TTTTCTT-TTTCTTTCCCTTT
1 TTTTCTTATTTCTTTCCCTTT
43482342 TTTTCTTATTTCTTTCCCT
1 TTTTCTTATTTCTTTCCCT
43482361 GCTATTCCTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTTCTTATTTCTTTCCCTTT
Found at i:43482425 original size:9 final size:9
Alignment explanation
Indices: 43482413--43482437 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
43482403 TTATTTTATT
43482413 TATTATAAC
1 TATTATAAC
43482422 TATTATAAC
1 TATTATAAC
43482431 TATTATA
1 TATTATA
43482438 TTATTATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (9 bp):
TATTATAAC
Found at i:43483076 original size:12 final size:12
Alignment explanation
Indices: 43483059--43483083 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43483049 TAATTGAGAT
43483059 AAACTTTAAAAC
1 AAACTTTAAAAC
43483071 AAACTTTAAAAC
1 AAACTTTAAAAC
43483083 A
1 A
43483084 TTATAATGAT
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:0.60, C:0.16, G:0.00, T:0.24
Consensus pattern (12 bp):
AAACTTTAAAAC
Found at i:43483313 original size:23 final size:22
Alignment explanation
Indices: 43483285--43483329 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 22
43483275 AACATTGGGT
43483285 AAAATTAAATATATTATATTATA
1 AAAATTAAATATATTA-ATTATA
43483308 AAAATTAAATATATTAATTATA
1 AAAATTAAATATATTAATTATA
43483330 TATTTAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
AAAATTAAATATATTAATTATA
Found at i:43483338 original size:27 final size:23
Alignment explanation
Indices: 43483284--43483356 Score: 74
Period size: 23 Copynumber: 3.0 Consensus size: 23
43483274 AAACATTGGG
43483284 TAAAATTAAATATATTATATTAT
1 TAAAATTAAATATATTATATTAT
*
43483307 AAAAATTAAATATATTAATTATATATT
1 TAAAATTAAATATATT-A-TAT-TA-T
* *
43483334 TAAAATTATATCTATTTATATTA
1 TAAAATTAAATATA-TTATATTA
43483357 AATCACTAAC
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
23 15 0.37
24 1 0.02
25 5 0.12
26 5 0.12
27 13 0.32
28 2 0.05
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (23 bp):
TAAAATTAAATATATTATATTAT
Found at i:43483356 original size:29 final size:28
Alignment explanation
Indices: 43483294--43483356 Score: 67
Period size: 27 Copynumber: 2.2 Consensus size: 28
43483284 TAAAATTAAA
43483294 TATATTATATTATAAAAATTAAATATAT
1 TATATTATATTATAAAAATTAAATATAT
* * *
43483322 TA-ATTATA-TATTTAAAATTATATCTATT
1 TATATTATATTA-TAAAAATTAAATATA-T
43483350 TATATTA
1 TATATTA
43483357 AATCACTAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
26 2 0.07
27 18 0.62
28 5 0.17
29 4 0.14
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (28 bp):
TATATTATATTATAAAAATTAAATATAT
Found at i:43492507 original size:28 final size:29
Alignment explanation
Indices: 43492476--43492538 Score: 87
Period size: 28 Copynumber: 2.2 Consensus size: 29
43492466 CCAAAATATA
*
43492476 TTATATTA-TAAATATTAATTATAT-TAAT
1 TTATATTATTAAATAATAATTATATCT-AT
43492504 TTATA-TATTAAATAATAATTATATCTAT
1 TTATATTATTAAATAATAATTATATCTAT
43492532 TTATATT
1 TTATATT
43492539 GAATCACTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
27 2 0.06
28 27 0.87
29 2 0.06
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (29 bp):
TTATATTATTAAATAATAATTATATCTAT
Found at i:43494515 original size:3 final size:3
Alignment explanation
Indices: 43494507--43494634 Score: 68
Period size: 3 Copynumber: 43.0 Consensus size: 3
43494497 TTTTATTAAT
* * *
43494507 TTA TTA TTA TTA TGT- TTG TTA ATA TT- TTT TGTA TTA TTA TT- TCTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA T-TA TTA TTA TTA T-TA
* * * * *
43494552 TTA TTA CTA TCA CTA TTA TT- TTAA TTA GTA TTG TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA
* * * * *
43494597 GTA GTA TTA CTA CTA TTA TTA TTA TTA TCA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
43494635 AATTAATTAG
Statistics
Matches: 96, Mismatches: 20, Indels: 18
0.72 0.15 0.13
Matches are distributed among these distances:
2 7 0.07
3 83 0.86
4 6 0.06
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:43496468 original size:36 final size:36
Alignment explanation
Indices: 43496422--43496493 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
43496412 AGGCTGATAG
*
43496422 TTCATGGAGGAAAATAAGACTTTACCTAAGGATTCA
1 TTCATAGAGGAAAATAAGACTTTACCTAAGGATTCA
*
43496458 TTCATAGAGGAAAATAAGACTTTACCTGAGGATTCA
1 TTCATAGAGGAAAATAAGACTTTACCTAAGGATTCA
43496494 AGTCGATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (36 bp):
TTCATAGAGGAAAATAAGACTTTACCTAAGGATTCA
Found at i:43496818 original size:19 final size:19
Alignment explanation
Indices: 43496777--43496818 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
43496767 TACTTTCTTT
*
43496777 TGCATTCATTCCATGCATT
1 TGCATTCATTCCATGCATG
*
43496796 TGCATTGCATTGCAT-CATG
1 TGCATT-CATTCCATGCATG
43496815 TGCA
1 TGCA
43496819 CTAAACTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.38
Consensus pattern (19 bp):
TGCATTCATTCCATGCATG
Found at i:43501514 original size:44 final size:44
Alignment explanation
Indices: 43501458--43501870 Score: 143
Period size: 44 Copynumber: 9.4 Consensus size: 44
43501448 CACCCTATCT
* *
43501458 CCCTAAGCAGTAGTGGAGTAGGTTGAAGACGGTGAGCCTTAACC
1 CCCTAAGCAGTAGTGGAATAGGTCGAAGACGGTGAGCCTTAACC
* *** * * *
43501502 CCCTAAGCAGTAG-GGAAATAGGCTAGAA-ATCACAGA-TCTTATCT
1 CCCTAAGCAGTAGTGG-AATAGG-TCGAAGA-CGGTGAGCCTTAACC
* * *
43501546 CCCTAAGCAGTAGTGGAATAGATCAAATACGGTGAGCCTTAACC
1 CCCTAAGCAGTAGTGGAATAGGTCGAAGACGGTGAGCCTTAACC
* * *** * * *
43501590 CCCTAAGCAGTAG-GGCAACAGG-CTGAAAATTAT-AGATCTTATCT
1 CCCTAAGCAGTAGTGG-AATAGGTC-GAAGACGGTGAG-CCTTAACC
** *
43501634 CCCTAAGCAGTAGTGGAGCAGATCGAAGACGGTGAGCCTTAACC
1 CCCTAAGCAGTAGTGGAATAGGTCGAAGACGGTGAGCCTTAACC
* * * * * *** * * *
43501678 GCCTAAGTACTAG-GGAAACAGGCTAGAA-ATCACAGA-TCTTATCT
1 CCCTAAGCAGTAGTGG-AATAGG-TCGAAGA-CGGTGAGCCTTAACC
* * *
43501722 CCCTAAGCAGTAGT-GAAGTAGATCAAATACGGTGAGCCTTAACC
1 CCCTAAGCAGTAGTGGAA-TAGGTCGAAGACGGTGAGCCTTAACC
* * * * * * * * * *
43501766 CCTTAAGCAGTAGAGCAACAGGCTAGAA-A--TTACAGATCTTATCT
1 CCCTAAGCAGTAGTGGAATAGG-TCGAAGACGGT-GAG-CCTTAACC
* ** *
43501810 CCCTAAGCAGTAGTGGAGTAAATCGAAGACGGTGAACCTTAACC
1 CCCTAAGCAGTAGTGGAATAGGTCGAAGACGGTGAGCCTTAACC
*
43501854 CCTTAAGCAGTAG-GGAA
1 CCCTAAGCAGTAGTGGAA
43501871 ACAGGCTGAA
Statistics
Matches: 254, Mismatches: 89, Indels: 53
0.64 0.22 0.13
Matches are distributed among these distances:
42 1 0.00
43 32 0.13
44 193 0.76
45 27 0.11
46 1 0.00
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.21
Consensus pattern (44 bp):
CCCTAAGCAGTAGTGGAATAGGTCGAAGACGGTGAGCCTTAACC
Found at i:43502467 original size:88 final size:88
Alignment explanation
Indices: 43501401--43502448 Score: 1404
Period size: 88 Copynumber: 11.9 Consensus size: 88
43501391 TGAATTCACT
* * * *
43501401 AGCCTTATCCCCCTAAGCAGTAGGGAAACAGGCT-GAAAATGACAGACCACCCTATCTCCCTAAG
1 AGCCTTAACCCCCTAAGCAGTAGGGAAACAGGCTAG-AAATTACAG---ATCTTATCTCCCTAAG
* * *
43501465 CAGTAGTGGAGTAGGTTGAAGACGGTG
62 CAGTAGTGGAGCAGATCGAAGACGGTG
* *
43501492 AGCCTTAACCCCCTAAGCAGTAGGGAAATAGGCTAGAAATCACAGATCTTATCTCCCTAAGCAGT
1 AGCCTTAACCCCCTAAGCAGTAGGGAAACAGGCTAGAAATTACAGATCTTATCTCCCTAAGCAGT
** * *
43501557 AGTGGAATAGATCAAATACGGTG
66 AGTGGAGCAGATCGAAGACGGTG
* *
43501580 AGCCTTAACCCCCTAAGCAGTAGGGCAACAGGCT-GAAAATTATAGATCTTATCTCCCTAAGCAG
1 AGCCTTAACCCCCTAAGCAGTAGGGAAACAGGCTAG-AAATTACAGATCTTATCTCCCTAAGCAG
43501644 TAGTGGAGCAGATCGAAGACGGTG
65 TAGTGGAGCAGATCGAAGACGGTG
* * * *
43501668 AGCCTTAACCGCCTAAGTACTAGGGAAACAGGCTAGAAATCACAGATCTTATCTCCCTAAGCAGT
1 AGCCTTAACCCCCTAAGCAGTAGGGAAACAGGCTAGAAATTACAGATCTTATCTCCCTAAGCAGT
* * * *
43501733 AGTGAAGTAGATCAAATACGGTG
66 AGTGGAGCAGATCGAAGACGGTG
* * *
43501756 AGCCTTAACCCCTTAAGCAGTAGAGCAACAGGCTAGAAATTACAGATCTTATCTCCCTAAGCAGT
1 AGCCTTAACCCCCTAAGCAGTAGGGAAACAGGCTAGAAATTACAGATCTTATCTCCCTAAGCAGT
* *
43501821 AGTGGAGTAAATCGAAGACGGTG
66 AGTGGAGCAGATCGAAGACGGTG
* * *
43501844 AACCTTAACCCCTTAAGCAGTAGGGAAACAGGCT-GAAAATTACAGATCTTATCTCCCTAAGTAG
1 AGCCTTAACCCCCTAAGCAGTAGGGAAACAGGCTAG-AAATTACAGATCTTATCTCCCTAAGCAG
* * *
43501908 TAGTGGAGTAGATCAAATACGGTG
65 TAGTGGAGCAGATCGAAGACGGTG
* * * * * *
43501932 AGCTTTAACCCCCTAAGCAGTAGGGCAACATGCT-GAAAATTATAGATTTTATCTCCTTAAGCAG
1 AGCCTTAACCCCCTAAGCAGTAGGGAAACAGGCTAG-AAATTACAGATCTTATCTCCCTAAGCAG
* *
43501996 TAGTGGAGCAGATCGAATACAGTG
65 TAGTGGAGCAGATCGAAGACGGTG
* **
43502020 AGCCTTAACCCCC-AAGCAGTAGGGAAACAGGCTAGAAATCACAGATCTTATCTCCCTAAATAGT
1 AGCCTTAACCCCCTAAGCAGTAGGGAAACAGGCTAGAAATTACAGATCTTATCTCCCTAAGCAGT
* * *
43502084 AGTGGAGTAGATCAAATACGGTG
66 AGTGGAGCAGATCGAAGACGGTG
* *
43502107 AGCCTTAACCCCCTAAGCAGTAGGGCAACAGGCTGGAAATTACAGATCTTATCTCCCTAAGCAGT
1 AGCCTTAACCCCCTAAGCAGTAGGGAAACAGGCTAGAAATTACAGATCTTATCTCCCTAAGCAGT
43502172 AGTGGAGCAGATCGAAGACGGTG
66 AGTGGAGCAGATCGAAGACGGTG
* * * * *
43502195 AGCCTTAACCCTCTAAGCAGTAGGGCAACAGGCTAAAAATTACAGATTTTATCTCCCTAAGCAAT
1 AGCCTTAACCCCCTAAGCAGTAGGGAAACAGGCTAGAAATTACAGATCTTATCTCCCTAAGCAGT
*
43502260 AGTGGAGCAGATCGAAGATGGTG
66 AGTGGAGCAGATCGAAGACGGTG
* * * *
43502283 AACCTGAACCCCCTAAGCAGTAGGGAAATAGGCTGGAAATTACAGATCTTATCTCCCTAAGCAGT
1 AGCCTTAACCCCCTAAGCAGTAGGGAAACAGGCTAGAAATTACAGATCTTATCTCCCTAAGCAGT
*
43502348 GGTGGAGCAGATCGAAGACGGTG
66 AGTGGAGCAGATCGAAGACGGTG
* * * *
43502371 AGCCTTATCCCCCTAAGTAGTAGGGAAACAGGCTAGAAATTACAAATCTTATCTCCCTAAGTAGT
1 AGCCTTAACCCCCTAAGCAGTAGGGAAACAGGCTAGAAATTACAGATCTTATCTCCCTAAGCAGT
*
43502436 AATGGAGCAGATC
66 AGTGGAGCAGATC
43502449 AAGGACAGTA
Statistics
Matches: 846, Mismatches: 105, Indels: 15
0.88 0.11 0.02
Matches are distributed among these distances:
87 76 0.09
88 728 0.86
89 1 0.00
91 40 0.05
92 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.22
Consensus pattern (88 bp):
AGCCTTAACCCCCTAAGCAGTAGGGAAACAGGCTAGAAATTACAGATCTTATCTCCCTAAGCAGT
AGTGGAGCAGATCGAAGACGGTG
Found at i:43503857 original size:3 final size:3
Alignment explanation
Indices: 43503849--43503976 Score: 50
Period size: 3 Copynumber: 43.0 Consensus size: 3
43503839 TTTTATTAAT
* * *
43503849 TTA TTA TTA TTA TGT- TTG TTA ATA TT- TTT TGTA TTA TTA TT- TCTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA T-TA TTA TTA TTA T-TA
* * * * * *
43503894 TTA TTA CTA TCA CTA TTA TT- TTAA TTA GTA TTG TTA TTA TTA GTA
1 TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA
* * * * * *
43503939 GTA GTA TTA CTA CTA CTA TTA TTA TTA TCA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
43503977 AATTAATTAG
Statistics
Matches: 96, Mismatches: 20, Indels: 18
0.72 0.15 0.13
Matches are distributed among these distances:
2 7 0.07
3 83 0.86
4 6 0.06
ACGTcount: A:0.30, C:0.06, G:0.06, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:43503898 original size:15 final size:15
Alignment explanation
Indices: 43503880--43503976 Score: 70
Period size: 15 Copynumber: 6.3 Consensus size: 15
43503870 ATATTTTTTG
*
43503880 TATTATTATTTCTAT
1 TATTATTATTACTAT
* *
43503895 TATTACTATCACTAT
1 TATTATTATTACTAT
*
43503910 TATT-TTAATTAGTAT
1 TATTATT-ATTACTAT
* * *
43503925 TGTTATTATTAGTAG
1 TATTATTATTACTAT
* * *
43503940 TAGTATTACTACTAC
1 TATTATTATTACTAT
43503955 TATTATTATTATCATAT
1 TATTATTATTA-C-TAT
43503972 TATTA
1 TATTA
43503977 AATTAATTAG
Statistics
Matches: 62, Mismatches: 16, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
14 1 0.02
15 51 0.82
16 3 0.05
17 7 0.11
ACGTcount: A:0.32, C:0.08, G:0.05, T:0.55
Consensus pattern (15 bp):
TATTATTATTACTAT
Found at i:43506177 original size:29 final size:28
Alignment explanation
Indices: 43506123--43506182 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
43506113 TAATTTGAGA
* *
43506123 TTTTTTTATATTTTGTGGTTATAGAATT
1 TTTTTTTATATTTTGTGGTTAAAGAAGT
*
43506151 TTTTTTTGTA-TTTGTGCGTATAAAGAAGT
1 TTTTTTTATATTTTGTG-GT-TAAAGAAGT
43506180 TTT
1 TTT
43506183 ATGATAATGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 6 0.22
28 11 0.41
29 10 0.37
ACGTcount: A:0.22, C:0.02, G:0.17, T:0.60
Consensus pattern (28 bp):
TTTTTTTATATTTTGTGGTTAAAGAAGT
Found at i:43520679 original size:217 final size:213
Alignment explanation
Indices: 43520298--43520731 Score: 796
Period size: 217 Copynumber: 2.0 Consensus size: 213
43520288 TTGTTAAACA
*
43520298 CTTATCATTATTATTAAAATTTCAGATTTGTTGAGAGCAGAATTTTCTTTGAGTTTTCTCTAAGA
1 CTTATCATTATTATTAAAATTTCAGATTTGTTGAGAGCAGAATTTTCTTTGAGTTTTCTCCAAGA
43520363 TTTCTCTCTTGAGTTTTCTTTAGAAGTTTTAACAATCTTTTTGATTGTGGGAGCCATCTTCAACC
66 TTTCTCTCTTGAGTTTTCTTTAGAAGTTTTAACAATCTTTTTGATTGTGGGAGCCATCTTCAACC
*
43520428 TTCTTCTTGCCATTGATATTCTTTGGCGGGGAGATTAGAGCCGTTTGAAGGCAGTTGTGAGATCT
131 TTCTTCTTGCCATTGATATTCTTTGGAGGGGAGATTAGAGCCGTTTGAAGGCAGTTGTGAGATCT
43520493 TTCGAGATTTCAAGGCTTT
196 TTCGAGATTTCAAGGC-TT
43520512 CTTATCATTATTATTAAAATTTCAGATTTGTTGAGAGCAGAATTTTCTTTGAGTTTTCTCCAAGA
1 CTTATCATTATTATTAAAATTTCAGATTTGTTGAGAGCAGAATTTTCTTTGAGTTTTCTCCAAGA
*
43520577 TTTCTCTCTTGAGTTTTCTTTAGAAGTTGTTTTAACAATCTTTTTTATTGTGGGAGCCATCTTCA
66 TTTCTCTCTTGAGTTTTCTTTAGAA---GTTTTAACAATCTTTTTGATTGTGGGAGCCATCTTCA
*
43520642 ACCTTCTTCTTGCCATTGATATTCTTTGGAGGGGAGATTAGAGCCGTTTGAAGGGAGTTGTGAGA
128 ACCTTCTTCTTGCCATTGATATTCTTTGGAGGGGAGATTAGAGCCGTTTGAAGGCAGTTGTGAGA
43520707 TCTTTCGAGATTTCAAGGCTT
193 TCTTTCGAGATTTCAAGGCTT
43520728 CTTA
1 CTTA
43520732 GGACTTATCT
Statistics
Matches: 213, Mismatches: 4, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
214 89 0.42
216 6 0.03
217 118 0.55
ACGTcount: A:0.23, C:0.15, G:0.20, T:0.43
Consensus pattern (213 bp):
CTTATCATTATTATTAAAATTTCAGATTTGTTGAGAGCAGAATTTTCTTTGAGTTTTCTCCAAGA
TTTCTCTCTTGAGTTTTCTTTAGAAGTTTTAACAATCTTTTTGATTGTGGGAGCCATCTTCAACC
TTCTTCTTGCCATTGATATTCTTTGGAGGGGAGATTAGAGCCGTTTGAAGGCAGTTGTGAGATCT
TTCGAGATTTCAAGGCTT
Found at i:43526348 original size:20 final size:18
Alignment explanation
Indices: 43526301--43526392 Score: 58
Period size: 17 Copynumber: 5.4 Consensus size: 18
43526291 CAAGATAAAC
43526301 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
43526318 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
*
43526338 ATTAAATTAATA--AAAT
1 ATTAAATTAATATTTAAT
*
43526354 ACT--ATTAATA--TAAGT
1 ATTAAATTAATATTTAA-T
*
43526369 ATTAAACTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
43526386 ATTAAAT
1 ATTAAAT
43526393 CTATTAAAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 9 0.15
15 3 0.05
16 6 0.10
17 19 0.32
18 4 0.07
19 3 0.05
20 15 0.25
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.41
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:43527892 original size:11 final size:11
Alignment explanation
Indices: 43527873--43527901 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
43527863 TATTTTGTGA
43527873 AAAAT-AAAAT
1 AAAATAAAAAT
43527883 AAAATAAAAAT
1 AAAATAAAAAT
43527894 AAAATAAA
1 AAAATAAA
43527902 GAACACACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.28
11 13 0.72
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:43532777 original size:19 final size:19
Alignment explanation
Indices: 43532749--43532802 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 19
43532739 CAGAAATAAA
43532749 AAAAAT-TAAAATTATTTT
1 AAAAATATAAAATTATTTT
*
43532767 AAAAATAT-AAATTAATTT
1 AAAAATATAAAATTATTTT
* *
43532785 AAAAAAATATAATT-TTTT
1 AAAAATATAAAATTATTTT
43532803 TGGACAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
18 25 0.83
19 5 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AAAAATATAAAATTATTTT
Found at i:43534052 original size:2 final size:2
Alignment explanation
Indices: 43534015--43534040 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
43534005 GATTGAATGA
43534015 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
43534041 GAAGAGATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43543717 original size:38 final size:38
Alignment explanation
Indices: 43543620--43543727 Score: 144
Period size: 38 Copynumber: 2.8 Consensus size: 38
43543610 GGCTTAAAGA
** * *
43543620 CCCGCAGGCTTCGTGCTGGTAAAATATCTGGGTTAAAT
1 CCCGCAGGCTTCGTGCTGGTATTATATCCGGGATAAAT
*
43543658 CCCGCAGGCTTCGTGCTGGTATTATATCCGGGATAATT
1 CCCGCAGGCTTCGTGCTGGTATTATATCCGGGATAAAT
* * *
43543696 CCCGCAGGCCTAGTGCTGGTATTATATTCGGG
1 CCCGCAGGCTTCGTGCTGGTATTATATCCGGG
43543728 CCTTCGTGCC
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 62 1.00
ACGTcount: A:0.19, C:0.23, G:0.28, T:0.30
Consensus pattern (38 bp):
CCCGCAGGCTTCGTGCTGGTATTATATCCGGGATAAAT
Found at i:43543768 original size:43 final size:43
Alignment explanation
Indices: 43543720--43544562 Score: 1668
Period size: 43 Copynumber: 19.6 Consensus size: 43
43543710 GCTGGTATTA
* *
43543720 TATTCGGGCCTTCGTGCCTAGCAGGCTTCATGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTG
43543763 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTG
43543806 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTG
43543849 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTG
43543892 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTG
43543935 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTG
43543978 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTG
43544021 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTG
43544064 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTG
43544107 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTG
43544150 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTG
43544193 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTG
43544236 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTG
43544279 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTG
43544322 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTG
43544365 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTG
43544408 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTG
43544451 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTG
43544494 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTG
43544537 TATTCGGGCCTTCGTGCCTAGCAGGC
1 TATTCGGGCCTTCGTGCCTAGCAGGC
43544563 GTAATGCCGG
Statistics
Matches: 798, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 798 1.00
ACGTcount: A:0.12, C:0.26, G:0.33, T:0.30
Consensus pattern (43 bp):
TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTG
Found at i:43546187 original size:48 final size:48
Alignment explanation
Indices: 43546093--43546196 Score: 122
Period size: 48 Copynumber: 2.2 Consensus size: 48
43546083 TGTGCTAAGC
* * *
43546093 GTAAGACCTATCTGGGATAGGCATCGGCACAGCCCAGTGAGTGCTAGT
1 GTAAGACCTATCTGGGATAGGCATCAGCACAGCCCAGAGAGAGCTAGT
**
43546141 GTAAGACCTATC-GGGAATAGGCATCAGCAC-GGTCAGAGCAGAGCTAGT
1 GTAAGACCTATCTGGG-ATAGGCATCAGCACAGCCCAGAG-AGAGCTAGT
*
43546189 ATAAGACC
1 GTAAGACC
43546197 ATAGTTGGAC
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
47 8 0.17
48 40 0.83
ACGTcount: A:0.30, C:0.22, G:0.30, T:0.18
Consensus pattern (48 bp):
GTAAGACCTATCTGGGATAGGCATCAGCACAGCCCAGAGAGAGCTAGT
Found at i:43548125 original size:46 final size:45
Alignment explanation
Indices: 43548058--43548232 Score: 181
Period size: 46 Copynumber: 3.8 Consensus size: 45
43548048 TGTAACCCGC
*
43548058 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGC-TTCGCAT
* * * *
43548104 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCAGATGCCTAG-TT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTC-G-GGCTTCGCAT
* *** * **
43548150 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGAACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGGC-TTCGCAT
*
43548197 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
43548233 ATGCCCAAAT
Statistics
Matches: 104, Mismatches: 20, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
45 1 0.01
46 68 0.65
47 33 0.32
48 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCTTCGCAT
Found at i:43548177 original size:93 final size:93
Alignment explanation
Indices: 43548065--43548237 Score: 292
Period size: 93 Copynumber: 1.9 Consensus size: 93
43548055 CGCCCATAAG
** *
43548065 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
43548130 ACGAGCTCAGATGCCTAGTTACATCTCT
66 ACGAGCTCAGATGCCTAGTTACATCTCT
*
43548158 CGAACTCGGACTCAACTCAACGAGTTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
* *
43548223 ACGAGTTCGGATGCC
66 ACGAGCTCAGATGCC
43548238 CAAATATCCC
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.28, C:0.31, G:0.20, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGCTCAGATGCCTAGTTACATCTCT
Found at i:43550072 original size:43 final size:43
Alignment explanation
Indices: 43550011--43550094 Score: 150
Period size: 43 Copynumber: 2.0 Consensus size: 43
43550001 GTGACAGCCC
43550011 TAATTTGGCCCTAGTCGGAAAGTGGTTTCGGGATCAAAAAACT
1 TAATTTGGCCCTAGTCGGAAAGTGGTTTCGGGATCAAAAAACT
* *
43550054 TAATTTGGTCCTAGTCGGAAAGTGGTTTCGGGATCACAAAA
1 TAATTTGGCCCTAGTCGGAAAGTGGTTTCGGGATCAAAAAA
43550095 TCGAGTCACA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (43 bp):
TAATTTGGCCCTAGTCGGAAAGTGGTTTCGGGATCAAAAAACT
Found at i:43551043 original size:117 final size:117
Alignment explanation
Indices: 43550859--43551184 Score: 559
Period size: 117 Copynumber: 2.8 Consensus size: 117
43550849 AGGATATTCG
* * * *
43550859 AATACTTAAATCGAAT--AAAAAATGAAACTCAGTACGGTAGGGCAC-ATTTTTTAAAACGATTA
1 AATACTTAAATCGAATAAAAAAAACG-AACCCAATACGGTAGGGCACTTTTTTTTAAAACGATTA
43550921 AGTATAGAAAATTGCTTTTATTAAAAACTATTTGGGAACAAAATGTTGAATAA
65 AGTATAGAAAATTGCTTTTATTAAAAACTATTTGGGAACAAAATGTTGAATAA
43550974 AATACTTAAATCGAATAAAAAAAACGAACCCAATACGGTAGGGCACTTTTTTTTAAAACGATTAA
1 AATACTTAAATCGAATAAAAAAAACGAACCCAATACGGTAGGGCACTTTTTTTTAAAACGATTAA
43551039 GTATAGAAAATTGCTTTTATTAAAAACTATTTGGGAACAAAATGTTGAATAA
66 GTATAGAAAATTGCTTTTATTAAAAACTATTTGGGAACAAAATGTTGAATAA
43551091 AATACTTAAATCGAATAAAAAAAACGAACCCAATACGGTAGGGCACTTTTTTTTAAAACGATTAA
1 AATACTTAAATCGAATAAAAAAAACGAACCCAATACGGTAGGGCACTTTTTTTTAAAACGATTAA
*
43551156 GTATAGAAAATTGTTTTTATGTTAAAAAC
66 GTATAGAAAATTGCTTTTA--TTAAAAAC
43551185 AAGTTGAGAA
Statistics
Matches: 201, Mismatches: 5, Indels: 6
0.95 0.02 0.03
Matches are distributed among these distances:
115 16 0.08
116 18 0.09
117 159 0.79
119 8 0.04
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.30
Consensus pattern (117 bp):
AATACTTAAATCGAATAAAAAAAACGAACCCAATACGGTAGGGCACTTTTTTTTAAAACGATTAA
GTATAGAAAATTGCTTTTATTAAAAACTATTTGGGAACAAAATGTTGAATAA
Found at i:43554814 original size:52 final size:49
Alignment explanation
Indices: 43554631--43554823 Score: 200
Period size: 47 Copynumber: 4.0 Consensus size: 49
43554621 TGCACATAGT
* ** * *
43554631 CACATATCACA-TACCGAGGCCATAGCCCAGCCATGGTCTTACACGG-AT
1 CACATATCACACT-CCGATGCCATAGCCCAGATATGGTCTTATACGGAAG
* * *
43554679 CACATATCACACT--GATGCCATATCCCAGATATGGTCTTATACAGTAG
1 CACATATCACACTCCGATGCCATAGCCCAGATATGGTCTTATACGGAAG
* *
43554726 CACATATCACA--CCGATGCCATATCCCGGATATGGTCTTATACGGAAG
1 CACATATCACACTCCGATGCCATAGCCCAGATATGGTCTTATACGGAAG
* *
43554773 CACATATCACATTTCTCCGAAGCCATAGCCCAGCTATGGTCTTATACGGAA
1 CACATATCACA---CTCCGATGCCATAGCCCAGATATGGTCTTATACGGAA
43554824 ATCACATTTC
Statistics
Matches: 122, Mismatches: 14, Indels: 14
0.81 0.09 0.09
Matches are distributed among these distances:
46 25 0.20
47 54 0.44
48 11 0.09
49 1 0.01
52 31 0.25
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (49 bp):
CACATATCACACTCCGATGCCATAGCCCAGATATGGTCTTATACGGAAG
Found at i:43555549 original size:45 final size:45
Alignment explanation
Indices: 43555499--43555588 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
43555489 CATCATAAAA
43555499 TGCCCTTACTCAGCCAGGGAAACTTCCAATTTCATCCACCAAATC
1 TGCCCTTACTCAGCCAGGGAAACTTCCAATTTCATCCACCAAATC
*
43555544 TGCCCTTACTCAGCCAGGGGAACTTCCAATTTCATCCACCAAATC
1 TGCCCTTACTCAGCCAGGGAAACTTCCAATTTCATCCACCAAATC
43555589 AAAAACTAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.28, C:0.36, G:0.12, T:0.24
Consensus pattern (45 bp):
TGCCCTTACTCAGCCAGGGAAACTTCCAATTTCATCCACCAAATC
Found at i:43556874 original size:44 final size:43
Alignment explanation
Indices: 43556767--43556877 Score: 109
Period size: 44 Copynumber: 2.6 Consensus size: 43
43556757 TTCAACCTGT
* * *
43556767 TCCACTACTGCTTAGGGACACAAGGTTTGTATCTTCAACTTGC
1 TCCACTACTGCTTAGGGAGATAAGGTTTGTATCTTCAACTTAC
* * ** *
43556810 T-CTCTGCAACTTCAGAGAGATAAGGTTTGCTATCTTCAA-TCTAC
1 TCCACTACTGCTT-AGGGAGATAAGGTTTG-TATCTTCAACT-TAC
43556854 TCCACTACTGCTTAGGGAGATAAG
1 TCCACTACTGCTTAGGGAGATAAG
43556878 ATCTTGTAAT
Statistics
Matches: 51, Mismatches: 13, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
42 7 0.14
43 15 0.29
44 22 0.43
45 7 0.14
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (43 bp):
TCCACTACTGCTTAGGGAGATAAGGTTTGTATCTTCAACTTAC
Found at i:43557211 original size:90 final size:88
Alignment explanation
Indices: 43556841--43557246 Score: 294
Period size: 90 Copynumber: 4.6 Consensus size: 88
43556831 AAGGTTTGCT
* * ** ** *
43556841 ATCTTCAATCTACTCCACTACTGCTTAGGGAGATAAGATCTTGTAATCCTC-CAGCCTTTTACCC
1 ATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATC-TGTAATTTTCTC-GTATATTACCC
* **
43556905 TACTGCTTAGGGAGTTAAAGCCTGCTCATT
64 TACTGCTTAGGG-GTT-AAG---ACTCACC
* * * *
43556935 ATCTTCGATCTGCTCCACTGCTGCTTAGGGAGATAAGATCTGTAATCTTC-AGCT-TGCTCTA--
1 ATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCTCG-TAT-AT-TACC
* * * **
43556996 CTGCTGCTCAGGGAGATAA-AGCTTTCC
63 CTACTGCTTAGGG-GTTAAGA-CTCACC
* * * * * * * *
43557023 ATTTTCGATCCGCTCCATTATTGCTTAGGGAAATAGGATCTG---TTTTC-AGTCA-GTTACCCT
1 ATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCTCGT-ATATTACCCT
*
43557083 ATTGCTTAGGGGTTAAGACTCACC
65 ACTGCTTAGGGGTTAAGACTCACC
* * *
43557107 ATCTTTGATCTGCTCCACTATTGCTTAGGGAGATAAAGATCTGTCATTTTCTCGTATATTACCCT
1 ATCTTCGATCTGCTCCACTACTGCTTAGGGAGAT-AAGATCTGTAATTTTCTCGTATATTACCCT
* *
43557172 ACTGCTTAGGGGGTTAAGGCTCATC
65 ACTGCTTA-GGGGTTAAGACTCACC
*
43557197 GTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTC
1 ATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTC
43557247 GATCCACTCC
Statistics
Matches: 251, Mismatches: 45, Indels: 37
0.75 0.14 0.11
Matches are distributed among these distances:
83 2 0.01
84 39 0.16
85 24 0.10
88 43 0.17
89 31 0.12
90 45 0.18
91 2 0.01
92 16 0.06
93 10 0.04
94 39 0.16
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.34
Consensus pattern (88 bp):
ATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCTCGTATATTACCCTA
CTGCTTAGGGGTTAAGACTCACC
Found at i:43557248 original size:44 final size:44
Alignment explanation
Indices: 43556848--43557282 Score: 175
Period size: 44 Copynumber: 9.8 Consensus size: 44
43556838 GCTATCTTCA
* ** *
43556848 ATCTACTCCACTACTGCTTAGGGAGATAAGATCTTGTAATCCTCC
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATC-TGTAATTTTCG
* ** * * *
43556893 AGCCTTTTACC-CTACTGCTTAGGGAGTTAA-AGCCTGCTCATTATCTTCG
1 A-TCTGCT-CCACTACTGCTTAGGGAGATAAGA-TCTG-T-A--ATTTTCG
* *
43556942 ATCTGCTCCACTGCTGCTTAGGGAGATAAGATCTGTAATCTTC-
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCG
* * * * * * *
43556985 AGCTTGCTCTACTGCTGCTCAGGGAGATAA-AGCTTTCCATTTTCG
1 ATC-TGCTCCACTACTGCTTAGGGAGATAAGATCTGT-AATTTTCG
* * * * *
43557030 ATCCGCTCCATTATTGCTTAGGGAAATAGGATCTG---TTTTC-
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCG
* * * * *
43557070 AGTCAGTTACC-CTATTGCTTAGGG-GTTAAGA-CT-CACCATCTTT-G
1 A-TCTGCT-CCACTACTGCTTAGGGAGATAAGATCTGTA--AT-TTTCG
* *
43557114 ATCTGCTCCACTATTGCTTAGGGAGATAAAGATCTGTCATTTTCTCG
1 ATCTGCTCCACTACTGCTTAGGGAGAT-AAGATCTGT-AATTT-TCG
* * * * * ** *
43557161 TATAT--TACC-CTACTGCTTAGGGGGTTAAG-GCTCATCGTCTTCG
1 -ATCTGCT-CCACTACTGCTTAGGGAGATAAGATCT-GTAATTTTCG
43557204 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCG
** * *
43557248 ATCCACTCCACTATTGCTTAGGGAGATAGGATCTG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTG
43557283 CCGATATTTA
Statistics
Matches: 290, Mismatches: 63, Indels: 75
0.68 0.15 0.18
Matches are distributed among these distances:
39 2 0.01
40 5 0.02
41 21 0.07
42 7 0.02
43 29 0.10
44 119 0.41
45 21 0.07
46 43 0.15
47 9 0.03
48 27 0.09
49 7 0.02
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.34
Consensus pattern (44 bp):
ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCG
Found at i:43564292 original size:52 final size:53
Alignment explanation
Indices: 43564214--43564347 Score: 184
Period size: 52 Copynumber: 2.6 Consensus size: 53
43564204 GACGAAAAAT
* *
43564214 ATGTGATAAGTGTG-C-CCGTTTAAGACCATAGCTGGACTATAGCATCGGTGCA
1 ATGTGATAA-TGTGACTCCGTATAAGACCATAGCTGGACTATAGCATCGGTACA
* * *
43564266 ATGTGATAATGTGACTCC-TATAAGACCATAGCTGGGCTATGGCATCGGTATA
1 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGACTATAGCATCGGTACA
*
43564318 ATGTGATAATGTGATTCCGTATAAGACCAT
1 ATGTGATAATGTGACTCCGTATAAGACCAT
43564348 GTCTGGGATA
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
51 4 0.05
52 56 0.77
53 13 0.18
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (53 bp):
ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGACTATAGCATCGGTACA
Found at i:43564367 original size:53 final size:53
Alignment explanation
Indices: 43564234--43564378 Score: 174
Period size: 52 Copynumber: 2.7 Consensus size: 53
43564224 TGTGCCCGTT
*
43564234 TAAGACCATAGCT-GGACTATAGCATCGG--TGCAATGTGATAATGTGACTCCTA
1 TAAGACCATAGCTGGGA-TATGGCATCGGTATG-AATGTGATAATGTGACTCCTA
* *
43564286 TAAGACCATAGCTGGGCTATGGCATCGGTAT-AATGTGATAATGTGATTCCGTA
1 TAAGACCATAGCTGGGATATGGCATCGGTATGAATGTGATAATGTGACTCC-TA
*
43564339 TAAGACCAT-GTCTGGGATATGGCTTCGGTATGATATGTGA
1 TAAGACCATAG-CTGGGATATGGCATCGGTATGA-ATGTGA
43564379 ACCGTGTAAG
Statistics
Matches: 81, Mismatches: 5, Indels: 11
0.84 0.05 0.11
Matches are distributed among these distances:
52 42 0.52
53 31 0.38
54 2 0.02
55 6 0.07
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (53 bp):
TAAGACCATAGCTGGGATATGGCATCGGTATGAATGTGATAATGTGACTCCTA
Found at i:43577979 original size:45 final size:45
Alignment explanation
Indices: 43577928--43578018 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 45
43577918 CTTCTGCTGG
* *
43577928 ACTCGAGCCATAACCCACTACTCACTCATCCCGGTAATATTCATC
1 ACTCGAGCCACAACCCACTACTCACTCATCCCAGTAATATTCATC
* *
43577973 ACTCGAGCCACAACCCACTGCTCACTTATCCCAGTAATATTCATC
1 ACTCGAGCCACAACCCACTACTCACTCATCCCAGTAATATTCATC
43578018 A
1 A
43578019 ATCTCTTGAC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.30, C:0.37, G:0.09, T:0.24
Consensus pattern (45 bp):
ACTCGAGCCACAACCCACTACTCACTCATCCCAGTAATATTCATC
Found at i:43582137 original size:54 final size:52
Alignment explanation
Indices: 43582079--43582189 Score: 118
Period size: 53 Copynumber: 2.1 Consensus size: 52
43582069 CCAAGCCCTT
43582079 CAAAAAAAATTTCTTTTACTTTGCCCCCAAATA-TTTTACTTCCTCC-AAATCCCC
1 CAAAAAAAATTTCTTTTACTTT-CCCCCAAA-ACTTTTACTTCCTCCTAAA--CCC
* ** ** *
43582133 CAAAATATTTTTCTTTTTGTTTTCCCCAAAACTTTTACTTCCTCCTAAACCC
1 CAAAAAAAATTTCTTTTACTTTCCCCCAAAACTTTTACTTCCTCCTAAACCC
43582185 CAAAA
1 CAAAA
43582190 TTTTTTTCAA
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
52 9 0.18
53 20 0.41
54 20 0.41
ACGTcount: A:0.31, C:0.30, G:0.02, T:0.38
Consensus pattern (52 bp):
CAAAAAAAATTTCTTTTACTTTCCCCCAAAACTTTTACTTCCTCCTAAACCC
Found at i:43582569 original size:19 final size:19
Alignment explanation
Indices: 43582545--43582582 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
43582535 AAAGTTAATA
43582545 ACAAATTTGATTACGGTGG
1 ACAAATTTGATTACGGTGG
*
43582564 ACAAATTTTATTACGGTGG
1 ACAAATTTGATTACGGTGG
43582583 GTGGTAGTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.34
Consensus pattern (19 bp):
ACAAATTTGATTACGGTGG
Found at i:43585069 original size:42 final size:45
Alignment explanation
Indices: 43585007--43585169 Score: 156
Period size: 49 Copynumber: 3.6 Consensus size: 45
43584997 TCGTTTTCTT
** *
43585007 GATGCCATAGCCCAAATATGGTCTTACAC-AT-AT-TCATATATC
1 GATGCCATAGCCCAGCTATGGTCTTACACAATCATATCACATATC
*
43585049 GATGCCATAGCCTAGCTATGGTCTTACACGTAATCACATATCACATATC
1 GATGCCATAGCCCAGCTATGGTCTTACAC--AAT--CATATCACATATC
* *
43585098 GATGCCATAGCCCAGCTATGGTCTTACACGAATCACATATCTCA-CT-
1 GATGCCATAGCCCAGCTATGGTCTTACAC-AAT--CATATCACATATC
* *
43585144 GATGCCATATCCCAGATATGGTCTTA
1 GATGCCATAGCCCAGCTATGGTCTTA
43585170 TACGGTAGCA
Statistics
Matches: 104, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
42 26 0.25
45 2 0.02
46 24 0.23
47 1 0.01
48 15 0.14
49 36 0.35
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (45 bp):
GATGCCATAGCCCAGCTATGGTCTTACACAATCATATCACATATC
Found at i:43585106 original size:49 final size:48
Alignment explanation
Indices: 43585033--43585169 Score: 188
Period size: 49 Copynumber: 2.9 Consensus size: 48
43585023 TATGGTCTTA
* *
43585033 CACATATTCATATATCGATGCCATAGCCTAGCTATGGTCTTACACGTAAT
1 CACATA-TCACATATCGATGCCATAGCCCAGCTATGGTCTTACACG-AAT
43585083 CACATATCACATATCGATGCCATAGCCCAGCTATGGTCTTACACGAAT
1 CACATATCACATATCGATGCCATAGCCCAGCTATGGTCTTACACGAAT
* * * *
43585131 CACATATCTCA-CT-GATGCCATATCCCAGATATGGTCTTA
1 CACATATCACATATCGATGCCATAGCCCAGCTATGGTCTTA
43585170 TACGGTAGCA
Statistics
Matches: 81, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
46 24 0.30
47 1 0.01
48 13 0.16
49 37 0.46
50 6 0.07
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (48 bp):
CACATATCACATATCGATGCCATAGCCCAGCTATGGTCTTACACGAAT
Found at i:43585188 original size:95 final size:91
Alignment explanation
Indices: 43585007--43585216 Score: 221
Period size: 95 Copynumber: 2.3 Consensus size: 91
43584997 TCGTTTTCTT
* * *
43585007 GATGCCATAGCCCAAATATGGTCTTACACATATTCATATATCGATGCCATAGCCTAGCTATGGTC
1 GATGCCATAGCCCAAATATGGTCTTACACATATACATATATCGATGCCATAGCCCAGATATGGTC
*
43585072 TTACACGTAATCACATATCACATATC
66 TTACACGTAAGCACATATCACATATC
** * *
43585098 GATGCCATAGCCCAGCTATGGTCTTACACGA-ATCACATATCTCACTGATGCCATATCCCAGATA
1 GATGCCATAGCCCAAATATGGTCTTACAC-ATAT-ACATATAT--C-GATGCCATAGCCCAGATA
* * *
43585162 TGGTCTTATACGGT-AGCATATATCACA-CT-
61 TGGTCTTACAC-GTAAGCACATATCACATATC
* *
43585191 GATGCCATATCCCTAATATGGTCTTA
1 GATGCCATAGCCCAAATATGGTCTTA
43585217 TACGGAAATC
Statistics
Matches: 98, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
91 29 0.30
92 7 0.07
93 22 0.22
94 2 0.02
95 36 0.37
96 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.30
Consensus pattern (91 bp):
GATGCCATAGCCCAAATATGGTCTTACACATATACATATATCGATGCCATAGCCCAGATATGGTC
TTACACGTAAGCACATATCACATATC
Found at i:43585198 original size:47 final size:46
Alignment explanation
Indices: 43585049--43585216 Score: 185
Period size: 47 Copynumber: 3.6 Consensus size: 46
43585039 TTCATATATC
* * *
43585049 GATGCCATAGCCTAGCTATGGTCTTACACGTAATCACATATCACATAT
1 GATGCCATAGCCCAGATATGGTCTTACACGT-ATCACATATCACA-CT
* * *
43585097 CGATGCCATAGCCCAGCTATGGTCTTACACGAATCACATATCTCACT
1 -GATGCCATAGCCCAGATATGGTCTTACACGTATCACATATCACACT
* * * *
43585144 GATGCCATATCCCAGATATGGTCTTATACGGTAGCATATATCACACT
1 GATGCCATAGCCCAGATATGGTCTTACAC-GTATCACATATCACACT
*
43585191 GATGCCATATCCCTA-ATATGGTCTTA
1 GATGCCATAGCCC-AGATATGGTCTTA
43585217 TACGGAAATC
Statistics
Matches: 106, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
46 26 0.25
47 38 0.36
48 13 0.12
49 29 0.27
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.29
Consensus pattern (46 bp):
GATGCCATAGCCCAGATATGGTCTTACACGTATCACATATCACACT
Found at i:43585288 original size:31 final size:31
Alignment explanation
Indices: 43585252--43585393 Score: 214
Period size: 31 Copynumber: 4.6 Consensus size: 31
43585242 CTTATAGACA
43585252 AAGCTACCA-TTATTCACTGATCAGGTAGCCG
1 AAGCTACCACTT-TTCACTGATCAGGTAGCCG
* *
43585283 GAGCTACCATTTTTCACTGATCAGGTAGCCG
1 AAGCTACCACTTTTCACTGATCAGGTAGCCG
* * *
43585314 GAGCTACCACTTTTCACTGATCATGTAGCAG
1 AAGCTACCACTTTTCACTGATCAGGTAGCCG
*
43585345 AAGCTACAACTTTTCACTGATCAGGTAGCCG
1 AAGCTACCACTTTTCACTGATCAGGTAGCCG
43585376 AAGCTACCACTTTTCACT
1 AAGCTACCACTTTTCACT
43585394 TGTCATTTGT
Statistics
Matches: 101, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
31 99 0.98
32 2 0.02
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (31 bp):
AAGCTACCACTTTTCACTGATCAGGTAGCCG
Found at i:43588604 original size:47 final size:48
Alignment explanation
Indices: 43588535--43588630 Score: 131
Period size: 47 Copynumber: 2.0 Consensus size: 48
43588525 TCATTAGGGA
* * * *
43588535 ATACATTGATTTGGCTTCGGGCCATGATTTTGG-ACTTCGGGTGCGAG
1 ATACATTAAGTTGGCTTCGGGCCATGATATTGGCACTTAGGGTGCGAG
* *
43588582 ATACATTAAGTTGGCTTTGGGCCATTATATTGGCACTTAGGGTGCGAG
1 ATACATTAAGTTGGCTTCGGGCCATGATATTGGCACTTAGGGTGCGAG
43588630 A
1 A
43588631 CTCCCGAGTA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
47 28 0.67
48 14 0.33
ACGTcount: A:0.21, C:0.16, G:0.30, T:0.33
Consensus pattern (48 bp):
ATACATTAAGTTGGCTTCGGGCCATGATATTGGCACTTAGGGTGCGAG
Found at i:43593148 original size:23 final size:23
Alignment explanation
Indices: 43593118--43593169 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
43593108 TGGGGGGGTT
43593118 GAAGCACTATCGATGGTATCATA
1 GAAGCACTATCGATGGTATCATA
43593141 GAAGCACTATCGATGGTATCATA
1 GAAGCACTATCGATGGTATCATA
43593164 GAAGCA
1 GAAGCA
43593170 TATGTATAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (23 bp):
GAAGCACTATCGATGGTATCATA
Found at i:43598642 original size:24 final size:24
Alignment explanation
Indices: 43598594--43598646 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
43598584 CTTGGTCCCA
* **
43598594 CAGGCTTCTTTGGTTGCTAACCAG
1 CAGGCTTCTTTGGATAATAACCAG
*
43598618 CAGGCTTCTTTGGATAATAATCAG
1 CAGGCTTCTTTGGATAATAACCAG
43598642 CAGGC
1 CAGGC
43598647 CTCTAGTAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.30
Consensus pattern (24 bp):
CAGGCTTCTTTGGATAATAACCAG
Found at i:43599335 original size:15 final size:16
Alignment explanation
Indices: 43599305--43599343 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
43599295 TGCAATTTTG
43599305 TAAA-TAAATGGAAGT
1 TAAATTAAATGGAAGT
*
43599320 TTAATTAAAT-GAAGT
1 TAAATTAAATGGAAGT
43599335 TAAATTAAA
1 TAAATTAAA
43599344 GAATGAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 16 0.76
16 5 0.24
ACGTcount: A:0.54, C:0.00, G:0.13, T:0.33
Consensus pattern (16 bp):
TAAATTAAATGGAAGT
Found at i:43602032 original size:261 final size:263
Alignment explanation
Indices: 43601652--43602164 Score: 708
Period size: 261 Copynumber: 2.0 Consensus size: 263
43601642 GAGAGTATGA
* * * * *
43601652 GTGAAATTCTAAAGGAATCTTCGATCATTTTGGACAAACAGGAAATTGCAACCTAGCACGATAGA
1 GTGAAATTCTAAAGGAATATTCAATCATTTTGAACAAACAGGAAATCGCAACCCAGCACGATAGA
* * *
43601717 GCACGATTCCCCGAATTGCCAAACATCGAAAATTACCTTCGTTTTGAAGAGTTTTTAGAAAACGT
66 GCACGATTCCCCGAATTACCAAACATCGAAAATTACCTTCGTTTTAAAGAGTTTTTAGAAAACAT
* * * * *
43601782 GAGTGAAATTCAAAAGGGACCTTAGATTATTTTGAACCAATGAGAAATTGTAACCCAACACGATA
131 GAATGAAATTCAAAAGGGACATTAGATTATTTTGAACAAACGAGAAATTGCAACCCAACACGATA
* *
43601847 GGGCACAATTTCGCGAATTGCCAAATATCGAACATCGCCTTCG-CTTAAAGAATTTTTAAAGACA
196 GGGCACAATTCCGCGAATTGCCAAATATCAAACATCGCCTTCGTCTTAAAGAATTTTTAAAGACA
43601911 TGG
261 TGG
** * *
43601914 GTGAAATT-TCAAAGGAATATTCAATTGTTTTGAACGAACGGGAAATCGCAACCCAGCACGATAG
1 GTGAAATTCT-AAAGGAATATTCAATCATTTTGAACAAACAGGAAATCGCAACCCAGCACGATAG
* * ** *
43601978 GGCACGATT-CTCGAATTACCAAACATCGAGTATTACCTTTGTTTTAAAGAGTTTTTAGAAAACA
65 AGCACGATTCCCCGAATTACCAAACATCGAAAATTACCTTCGTTTTAAAGAGTTTTTAGAAAACA
* * * * *
43602042 TGAATGAAGTTCCAAAGGGACATTCGATTATTTTGAGCAAACGAGAAATTGCAACCCAACACGTT
130 TGAATGAAATTCAAAAGGGACATTAGATTATTTTGAACAAACGAGAAATTGCAACCCAACACGAT
* * *
43602107 AGGGCACGATTCCGCGAATTGTCAAATATCAAACATCGCCTTCGTTTTAAAGAATTTT
195 AGGGCACAATTCCGCGAATTGCCAAATATCAAACATCGCCTTCGTCTTAAAGAATTTT
43602165 CTTTAAAAAA
Statistics
Matches: 217, Mismatches: 32, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
261 144 0.66
262 73 0.34
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.27
Consensus pattern (263 bp):
GTGAAATTCTAAAGGAATATTCAATCATTTTGAACAAACAGGAAATCGCAACCCAGCACGATAGA
GCACGATTCCCCGAATTACCAAACATCGAAAATTACCTTCGTTTTAAAGAGTTTTTAGAAAACAT
GAATGAAATTCAAAAGGGACATTAGATTATTTTGAACAAACGAGAAATTGCAACCCAACACGATA
GGGCACAATTCCGCGAATTGCCAAATATCAAACATCGCCTTCGTCTTAAAGAATTTTTAAAGACA
TGG
Found at i:43602098 original size:131 final size:131
Alignment explanation
Indices: 43601648--43602164 Score: 513
Period size: 132 Copynumber: 3.9 Consensus size: 131
43601638 TTTAGAGAGT
* * * * * *
43601648 ATGAGTGAAATTCTAAAGGAATC-TTCGATCATTTTGGACAAAC-AGGAAATTGCAACCTAGCAC
1 ATGAGTGAAATTCCAAAGGGA-CATTCGATTATTTTGAACAAACGA-GAAATTGCAACCCAACAC
* *
43601711 GATAGAGCACGATTCCCCGAATTGCCAAACATCGAAAATTACCTTCGTTTTGAAGAGTTTTTAGA
64 GATAGGGCACGATT-CCCGAATTGCCAAACATCGAAAATTACCTTCGTTTTAAAGAGTTTTTAGA
43601776 AAAC
128 AAAC
* * * * * * *
43601780 GTGAGTGAAATTCAAAAGGGACCTTAGATTATTTTGAACCAATGAGAAATTGTAACCCAACACGA
1 ATGAGTGAAATTCCAAAGGGACATTCGATTATTTTGAACAAACGAGAAATTGCAACCCAACACGA
* * * * ** * * *
43601845 TAGGGCACAATTTCGCGAATTGCCAAATATCGAACATCGCCTTCG-CTTAAAGAATTTTTA-AAG
66 TAGGGCACGA-TTCCCGAATTGCCAAACATCGAAAATTACCTTCGTTTTAAAGAGTTTTTAGAAA
43601908 AC
130 AC
* * * * * * * * * *
43601910 ATGGGTGAAATTTCAAAGGAATATTCAATTGTTTTGAACGAACGGGAAATCGCAACCCAGCACGA
1 ATGAGTGAAATTCCAAAGGGACATTCGATTATTTTGAACAAACGAGAAATTGCAACCCAACACGA
* * ** *
43601975 TAGGGCACGATTCTCGAATTACCAAACATCGAGTATTACCTTTGTTTTAAAGAGTTTTTAGAAAA
66 TAGGGCACGATTCCCGAATTGCCAAACATCGAAAATTACCTTCGTTTTAAAGAGTTTTTAGAAAA
43602040 C
131 C
* * * *
43602041 ATGAATGAAGTTCCAAAGGGACATTCGATTATTTTGAGCAAACGAGAAATTGCAACCCAACACGT
1 ATGAGTGAAATTCCAAAGGGACATTCGATTATTTTGAACAAACGAGAAATTGCAACCCAACACGA
* * ** *
43602106 TAGGGCACGATTCCGCGAATTGTCAAATATC-AAACATCGCCTTCGTTTTAAAGAATTTT
66 TAGGGCACGATTCC-CGAATTGCCAAACATCGAAA-ATTACCTTCGTTTTAAAGAGTTTT
43602165 CTTTAAAAAA
Statistics
Matches: 304, Mismatches: 74, Indels: 14
0.78 0.19 0.04
Matches are distributed among these distances:
129 26 0.09
130 75 0.25
131 82 0.27
132 118 0.39
133 3 0.01
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (131 bp):
ATGAGTGAAATTCCAAAGGGACATTCGATTATTTTGAACAAACGAGAAATTGCAACCCAACACGA
TAGGGCACGATTCCCGAATTGCCAAACATCGAAAATTACCTTCGTTTTAAAGAGTTTTTAGAAAA
C
Found at i:43603239 original size:12 final size:12
Alignment explanation
Indices: 43603222--43603247 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
43603212 TACTATAAAG
43603222 TACATATATATA
1 TACATATATATA
43603234 TACATATATATA
1 TACATATATATA
43603246 TA
1 TA
43603248 TATGGTAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (12 bp):
TACATATATATA
Found at i:43606355 original size:8 final size:8
Alignment explanation
Indices: 43606313--43606337 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
43606303 ATATAGACTA
43606313 AATAAAAT
1 AATAAAAT
43606321 AATAAAAT
1 AATAAAAT
43606329 AATAAAAT
1 AATAAAAT
43606337 A
1 A
43606338 TATTATTAAA
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAAAAT
Found at i:43606645 original size:30 final size:30
Alignment explanation
Indices: 43606591--43606659 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
43606581 CACCCTTAAA
* *
43606591 ATATTTGCACTATTAATCATTCAAAATTTTC
1 ATATTTACACTATTAATCACTC-AAATTTTC
* *
43606622 ATATTTACACT-TTAATCCCTCAAATTTTG
1 ATATTTACACTATTAATCACTCAAATTTTC
43606651 AGTATTTAC
1 A-TATTTAC
43606660 TATTGTGCCA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.24
30 15 0.45
31 10 0.30
ACGTcount: A:0.33, C:0.17, G:0.04, T:0.45
Consensus pattern (30 bp):
ATATTTACACTATTAATCACTCAAATTTTC
Found at i:43612238 original size:411 final size:411
Alignment explanation
Indices: 43611476--43612709 Score: 2252
Period size: 411 Copynumber: 3.0 Consensus size: 411
43611466 TGTGATTAGT
*
43611476 GTAGATGGTACACTTCTCTCTATACAGATAATGTCTCAAAATCTTTAATGCAAAGACCACTGCAG
1 GTAGATGGTACACTTCTCTCCATACAGATAATGTCTCAAAATCTTTAATGCAAAGACCACTGCAG
*
43611541 CCAGCTCCAAATCATATGTCAAATAATTAGCCTCGTGAGTCTTAAGCTGTCGAGACGCATAAGCA
66 CCAGCTCCAAATCATACGTCAAATAATTAGCCTCGTGAGTCTTAAGCTGTCGAGACGCATAAGCA
*
43611606 ACTACTTACCGTCTTACATCAAGACGCAACCCAAACCCACATGTGACGCATCACTGTAAACCACG
131 ACTACTTACCGTCTTGCATCAAGACGCAACCCAAACCCACATGTGACGCATCACTGTAAACCACG
* *
43611671 AAGTCCTTACCAGGCTCAGGTTGTATCAGAACTGGAGCCTGAGCTGTTGATGTACGTAATAATTT
196 AAGTCCTTACCAGGCTCAGGCTGTATCAGAACTGGAGCCTGAGCTGTTGATGTACGTGATAATTT
*
43611736 TTATATTTATGATTGATCGTATTTGAAAGCTAACTATTATCACAATAAAGGCGAGCGCACCTATC
261 TTATATTTATGATTGATCGTATTTGAAAGCTAACTATTATCACAATAAAGGCAAGCGCACCTATC
43611801 AAATAGTAGTATAGCTTATAGCAAGACTGGAATGTCGAACCCACAGGAACTAAAAGTACTAGTAT
326 AAATAGTAGTATAGCTTATAGCAAGACTGGAATGTCGAACCCACAGGAACTAAAAGTACTAGTAT
43611866 TAACCTTCTTTTTATTATCTA
391 TAACCTTCTTTTTATTATCTA
*
43611887 GTAGATGGTACACTTCTCTCCATACAGATAATGTCTCAAAATCTTTGATGCAAAGACCACTGCAG
1 GTAGATGGTACACTTCTCTCCATACAGATAATGTCTCAAAATCTTTAATGCAAAGACCACTGCAG
* *
43611952 CCAACTCCAAATCATACGTCAAATAATTAGCCTCGTGAGTCTTAAGCTGTTGAGACGCATAAGCA
66 CCAGCTCCAAATCATACGTCAAATAATTAGCCTCGTGAGTCTTAAGCTGTCGAGACGCATAAGCA
*
43612017 ACTACTTACCATCTTGCATCAAGACGCAACCCAAACCCACATGTGACGCATCACTGTAAACCACG
131 ACTACTTACCGTCTTGCATCAAGACGCAACCCAAACCCACATGTGACGCATCACTGTAAACCACG
* *
43612082 AAGTCCTTACCAGGCTCAGGCTGTATCAGAACTGGAGCCTGCGCTGTTGATGTTCGTGATAATTT
196 AAGTCCTTACCAGGCTCAGGCTGTATCAGAACTGGAGCCTGAGCTGTTGATGTACGTGATAATTT
*
43612147 TTATATTTATGATTGATCGTATTTGAAAGCTAACTATTATCACAATAAAGGCAAGCGCCCCTATC
261 TTATATTTATGATTGATCGTATTTGAAAGCTAACTATTATCACAATAAAGGCAAGCGCACCTATC
* * *
43612212 AAATAGTAGTATAGCTTATAGCAAGACTGGTATGTTGAACCCACAGGAACTAAAAGAACTAGTAT
326 AAATAGTAGTATAGCTTATAGCAAGACTGGAATGTCGAACCCACAGGAACTAAAAGTACTAGTAT
*
43612277 AAACCTTCTTTTTATTATCTA
391 TAACCTTCTTTTTATTATCTA
43612298 GTAGATGGTACACTTCTCTCCATACAGATAATGTCTCAAAATCTTTAATGCAAAGACCACTGCAG
1 GTAGATGGTACACTTCTCTCCATACAGATAATGTCTCAAAATCTTTAATGCAAAGACCACTGCAG
* *
43612363 CTAGCTCCAAATCAGACGTCAAATAATTAGCCTCGTGAGTCTTAAGCTGTCGAGACGCATAAGCA
66 CCAGCTCCAAATCATACGTCAAATAATTAGCCTCGTGAGTCTTAAGCTGTCGAGACGCATAAGCA
*
43612428 ACTACTTACCGTCTTGCATCAAGACGCAACCTAAACCCACATGTGACGCATCACTGTAAACCACG
131 ACTACTTACCGTCTTGCATCAAGACGCAACCCAAACCCACATGTGACGCATCACTGTAAACCACG
*
43612493 AAGTCCTTACCAGGCTCAGGCTGTTTCAGAACTGGAGCCTGAGCTGTTGATGTACGTGATAATTT
196 AAGTCCTTACCAGGCTCAGGCTGTATCAGAACTGGAGCCTGAGCTGTTGATGTACGTGATAATTT
*
43612558 TTATATTTATGATTGATCGTACTTGAAAGCTAACTATTATCACAATAAAGGCAAGCGCACCTATC
261 TTATATTTATGATTGATCGTATTTGAAAGCTAACTATTATCACAATAAAGGCAAGCGCACCTATC
* *
43612623 GAATAGTAGTATAGCTTATAGCAAGACTGGAATGTCGATCCCACAGGAACTAAAAGTACTAGTAT
326 AAATAGTAGTATAGCTTATAGCAAGACTGGAATGTCGAACCCACAGGAACTAAAAGTACTAGTAT
43612688 TAACCTTCTTTTTATTATCTA
391 TAACCTTCTTTTTATTATCTA
43612709 G
1 G
43612710 CCTAAAAATA
Statistics
Matches: 788, Mismatches: 35, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
411 788 1.00
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (411 bp):
GTAGATGGTACACTTCTCTCCATACAGATAATGTCTCAAAATCTTTAATGCAAAGACCACTGCAG
CCAGCTCCAAATCATACGTCAAATAATTAGCCTCGTGAGTCTTAAGCTGTCGAGACGCATAAGCA
ACTACTTACCGTCTTGCATCAAGACGCAACCCAAACCCACATGTGACGCATCACTGTAAACCACG
AAGTCCTTACCAGGCTCAGGCTGTATCAGAACTGGAGCCTGAGCTGTTGATGTACGTGATAATTT
TTATATTTATGATTGATCGTATTTGAAAGCTAACTATTATCACAATAAAGGCAAGCGCACCTATC
AAATAGTAGTATAGCTTATAGCAAGACTGGAATGTCGAACCCACAGGAACTAAAAGTACTAGTAT
TAACCTTCTTTTTATTATCTA
Found at i:43616229 original size:14 final size:14
Alignment explanation
Indices: 43616212--43616250 Score: 78
Period size: 14 Copynumber: 2.8 Consensus size: 14
43616202 TCAAAACAAG
43616212 AATTAAGAACACAT
1 AATTAAGAACACAT
43616226 AATTAAGAACACAT
1 AATTAAGAACACAT
43616240 AATTAAGAACA
1 AATTAAGAACA
43616251 AGTCAAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.59, C:0.13, G:0.08, T:0.21
Consensus pattern (14 bp):
AATTAAGAACACAT
Found at i:43617108 original size:7 final size:7
Alignment explanation
Indices: 43617079--43617122 Score: 63
Period size: 7 Copynumber: 6.3 Consensus size: 7
43617069 TAAAAAGATA
43617079 AATAAAT
1 AATAAAT
*
43617086 ATATAAGT
1 A-ATAAAT
43617094 AA-AAAT
1 AATAAAT
43617100 AATAAAT
1 AATAAAT
43617107 AATAAAT
1 AATAAAT
43617114 AATAAAT
1 AATAAAT
43617121 AA
1 AA
43617123 AAGTCTTCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 5 0.15
7 22 0.67
8 6 0.18
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.27
Consensus pattern (7 bp):
AATAAAT
Found at i:43618638 original size:33 final size:33
Alignment explanation
Indices: 43618601--43618663 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
43618591 ATGCATATGG
43618601 GAATGATAATATGGAATATGGTGTGGGTAATGA
1 GAATGATAATATGGAATATGGTGTGGGTAATGA
43618634 GAATGATAATATGGAATATGGTGTGGGTAA
1 GAATGATAATATGGAATATGGTGTGGGTAA
43618664 GGCATGAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.37, C:0.00, G:0.33, T:0.30
Consensus pattern (33 bp):
GAATGATAATATGGAATATGGTGTGGGTAATGA
Found at i:43621581 original size:30 final size:31
Alignment explanation
Indices: 43621557--43621615 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
43621547 GTAAATACTC
* *
43621557 AAAATTTGAGGGATTAA-AGTGTAAATATAA
1 AAAATTTGAAGGACTAACAGTGTAAATATAA
*
43621587 AAAATTTGAAGGACTAACAGTGCAAATAT
1 AAAATTTGAAGGACTAACAGTGTAAATAT
43621616 TTTAAGGGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.49, C:0.05, G:0.19, T:0.27
Consensus pattern (31 bp):
AAAATTTGAAGGACTAACAGTGTAAATATAA
Found at i:43627273 original size:27 final size:26
Alignment explanation
Indices: 43627236--43627350 Score: 115
Period size: 27 Copynumber: 4.3 Consensus size: 26
43627226 AGCATGGCTG
* *
43627236 CCAGAACAGATAATGTGATAGAGTCA
1 CCAGAACAGATAATGTGACAGAGCCA
*
43627262 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGACAGAGCCA
*
43627290 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGACAGAGCCA
* * *
43627317 CCA-AATCAGATATTTGTGGCATAGCCA
1 CCAGAA-CAGATA-ATGTGACAGAGCCA
43627344 CCAGAAC
1 CCAGAAC
43627351 GCTTCCTCCA
Statistics
Matches: 79, Mismatches: 5, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
26 7 0.09
27 54 0.68
28 18 0.23
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGACAGAGCCA
Found at i:43627295 original size:54 final size:54
Alignment explanation
Indices: 43627236--43627350 Score: 151
Period size: 54 Copynumber: 2.1 Consensus size: 54
43627226 AGCATGGCTG
* * *
43627236 CCAGAACAGATA-ATGTGATAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAAAT-CAGATAATCGTGGCAGAGCCA
* * * *
43627290 CCAGAACAGATATATGTGGCAGAGCCACCAAATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAAATCAGATAATCGTGGCAGAGCCA
43627344 CCAGAAC
1 CCAGAAC
43627351 GCTTCCTCCA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
54 37 0.70
55 16 0.30
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAAATCAGATAATCGTGGCAGAGCCA
Done.