Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 256 of 290
Found at i:88290690 original size:53 final size:53
Alignment explanation
Indices: 88290610--88290716 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 53
88290600 TATGCATGTC
*
88290610 TGATTAATCCGTTTTCTGTATATAAGCTTGTTGTGTATGTTTAATCTGTTATT
1 TGATTAATCCATTTTCTGTATATAAGCTTGTTGTGTATGTTTAATCTGTTATT
88290663 TGATTAATCCATTTTCTGTATATAAGCTTGTTGTGTATGTTTAATCTGTTATT
1 TGATTAATCCATTTTCTGTATATAAGCTTGTTGTGTATGTTTAATCTGTTATT
88290716 T
1 T
88290717 ATGTATCTAT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.21, C:0.09, G:0.16, T:0.53
Consensus pattern (53 bp):
TGATTAATCCATTTTCTGTATATAAGCTTGTTGTGTATGTTTAATCTGTTATT
Found at i:88292611 original size:40 final size:40
Alignment explanation
Indices: 88292511--88292775 Score: 286
Period size: 40 Copynumber: 6.7 Consensus size: 40
88292501 GCTCCTCGTT
* * * *
88292511 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* **
88292551 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
88292590 CGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
88292630 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
88292670 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
88292710 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
88292751 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
88292776 CAGCATTCAA
Statistics
Matches: 197, Mismatches: 22, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
39 39 0.20
40 143 0.73
41 15 0.08
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:88292735 original size:80 final size:80
Alignment explanation
Indices: 88292478--88292775 Score: 263
Period size: 80 Copynumber: 3.7 Consensus size: 80
88292468 AAATCACGTA
* ** * * *
88292478 CCTTCGGGATTTAA-CCGGATATAGCTC-CTCGTTCAAATGCCTTCGGGACATAGCCCGG-TTTT
1 CCTTCGGGACTTAACCCGGATATAG-TCACTCGCACAAA-GCCTTCGGGACTTAACCCGGAATTT
* *
88292540 AGTAACTCACAC-AATG
64 AATAACTCGCACAAATG
* * * *
88292556 CCTTCGGGACATAACCCGGATTTA-ACAACTCGCACGAATGCCTTCGGGACTTAACCCGG-ATTT
1 CCTTCGGGACTTAACCCGGATATAGTC-ACTCGCAC-AAAGCCTTCGGGACTTAACCCGGAATTT
*
88292619 AATAACTCGCACGAATG
64 AATAACTCGCACAAATG
* *
88292636 CCTTCGGGACTTAACCCGGATTTAGT-ATCTCGCACAAAGGCCTTCGGGGCTTAACCCGGAATTT
1 CCTTCGGGACTTAACCCGGATATAGTCA-CTCGCACAAA-GCCTTCGGGACTTAACCCGGAATTT
* *
88292700 -GTATCTCGCACAAATG
64 AATAACTCGCACAAATG
** * * *
88292716 CCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 CCTTCGGGA-CTTAACCCGGATATAGTCAC-TCGCACAAAGCCTTCGGGACTTAACCCGGA
88292776 CAGCATTCAA
Statistics
Matches: 182, Mismatches: 26, Indels: 22
0.79 0.11 0.10
Matches are distributed among these distances:
77 1 0.01
78 12 0.07
79 50 0.27
80 106 0.58
81 13 0.07
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (80 bp):
CCTTCGGGACTTAACCCGGATATAGTCACTCGCACAAAGCCTTCGGGACTTAACCCGGAATTTAA
TAACTCGCACAAATG
Found at i:88292784 original size:41 final size:41
Alignment explanation
Indices: 88292707--88292784 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
88292697 TTTGTATCTC
* * *
88292707 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
88292748 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
88292785 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:88297762 original size:28 final size:29
Alignment explanation
Indices: 88297708--88297762 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
88297698 TATAGATCAA
*
88297708 GAAAAACAAAATTCGAATCTAGATCGAGG
1 GAAAAACAAAATTCCAATCTAGATCGAGG
*
88297737 GAAAAACAAAGTTCTCAA-CTA-ATCGA
1 GAAAAACAAAATTC-CAATCTAGATCGA
88297763 CTAGTTTAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 5 0.22
29 16 0.70
30 2 0.09
ACGTcount: A:0.49, C:0.16, G:0.16, T:0.18
Consensus pattern (29 bp):
GAAAAACAAAATTCCAATCTAGATCGAGG
Found at i:88299177 original size:28 final size:27
Alignment explanation
Indices: 88299111--88299431 Score: 148
Period size: 27 Copynumber: 11.9 Consensus size: 27
88299101 TACCCCCCCA
* ** *
88299111 ATTTATAAAATTACCCAAATATCCTCG
1 ATTTGTAAAATTACTAAAATACCCTCG
88299138 ATTTGTAAAATTACTAAAATAAACCCT-G
1 ATTTGTAAAATTACTAAAAT--ACCCTCG
* *
88299166 ATTTGTAAAATTATTGAAATACCCTCG
1 ATTTGTAAAATTACTAAAATACCCTCG
* * *
88299193 ACTTGTAAAATTACCAAAGTACCCTCG
1 ATTTGTAAAATTACTAAAATACCCTCG
* * **** * *
88299220 ATTTATAGAATTACTGTTTTACTCTTG
1 ATTTGTAAAATTACTAAAATACCCTCG
** * **** *
88299247 ATTTACAGAATTACTGTTTTATCCTCG
1 ATTTGTAAAATTACTAAAATACCCTCG
** ****
88299274 ATTTACAAAATTACTGTTTTACCCTCG
1 ATTTGTAAAATTACTAAAATACCCTCG
* * * *
88299301 A-TTGTGAAATTATTGAAATACCC-CT
1 ATTTGTAAAATTACTAAAATACCCTCG
* * * *
88299326 ATATGGTAGAATTACCAAAATA-CCTCT
1 AT-TTGTAAAATTACTAAAATACCCTCG
*
88299353 AGTTTGTAAAATTACCAAAATACCACT-G
1 A-TTTGTAAAATTACTAAAATACC-CTCG
* * ** *
88299381 GTTTGTGAAATTACCGAAATACCCTCA
1 ATTTGTAAAATTACTAAAATACCCTCG
*
88299408 ATTTGTAAAATTACCAAAATACCC
1 ATTTGTAAAATTACTAAAATACCC
88299432 CTAATTTACA
Statistics
Matches: 233, Mismatches: 51, Indels: 20
0.77 0.17 0.07
Matches are distributed among these distances:
25 2 0.01
26 24 0.10
27 180 0.77
28 21 0.09
29 6 0.03
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.35
Consensus pattern (27 bp):
ATTTGTAAAATTACTAAAATACCCTCG
Found at i:88299346 original size:27 final size:26
Alignment explanation
Indices: 88299316--88299458 Score: 135
Period size: 27 Copynumber: 5.3 Consensus size: 26
88299306 GAAATTATTG
* *
88299316 AAATACCCCTATATGGTAGAATTACCA
1 AAATACCCCTAT-TTGTAAAATTACCA
*
88299343 AAATACCTCTAGTTTGTAAAATTACCA
1 AAATACCCCTA-TTTGTAAAATTACCA
* * * *
88299370 AAATACCACTGGTTTGTGAAATTACCG
1 AAATACCCCT-ATTTGTAAAATTACCA
*
88299397 AAATACCCTCAATTTGTAAAATTACCA
1 AAATACCC-CTATTTGTAAAATTACCA
**
88299424 AAATACCCCTAATTTACAAAATTA-CA
1 AAATACCCCT-ATTTGTAAAATTACCA
88299450 GAAATACCC
1 -AAATACCC
88299459 TTGACTTTCT
Statistics
Matches: 96, Mismatches: 15, Indels: 10
0.79 0.12 0.08
Matches are distributed among these distances:
26 3 0.03
27 91 0.95
28 2 0.02
ACGTcount: A:0.42, C:0.22, G:0.08, T:0.28
Consensus pattern (26 bp):
AAATACCCCTATTTGTAAAATTACCA
Found at i:88299400 original size:81 final size:81
Alignment explanation
Indices: 88299302--88299457 Score: 199
Period size: 81 Copynumber: 1.9 Consensus size: 81
88299292 TTACCCTCGA
** * * * * **
88299302 TTGTGAAATTATTGAAATACCC-CTATATGGTAGAATTACCAAAATACCTCTAGTTTGTAAAATT
1 TTGTGAAATTACCGAAATACCCTCAAT-TGGTAAAATTACCAAAATACCCCTAATTTACAAAATT
88299366 ACCA-AAATACCACTGGT
65 A-CAGAAATACCACTGGT
*
88299383 TTGTGAAATTACCGAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTAATTTACAAAATTA
1 TTGTGAAATTACCGAAATACCCTCAATTGGTAAAATTACCAAAATACCCCTAATTTACAAAATTA
88299448 CAGAAATACC
66 CAGAAATACC
88299458 CTTGACTTTC
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
80 2 0.03
81 59 0.92
82 3 0.05
ACGTcount: A:0.41, C:0.19, G:0.10, T:0.30
Consensus pattern (81 bp):
TTGTGAAATTACCGAAATACCCTCAATTGGTAAAATTACCAAAATACCCCTAATTTACAAAATTA
CAGAAATACCACTGGT
Found at i:88299446 original size:54 final size:54
Alignment explanation
Indices: 88299335--88299513 Score: 173
Period size: 54 Copynumber: 3.3 Consensus size: 54
88299325 TATATGGTAG
* * * ***
88299335 AATTACCAAAATA-CCTCTAGTTTGTAAAATTACCAAAATACCACTGGTTTGTGA
1 AATTACCGAAATACCCTC-AATTTGTAAAATTACCAAAATACCACTAGTTTACAA
* *
88299389 AATTACCGAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTAATTTACAA
1 AATTACCGAAATACCCTCAATTTGTAAAATTACCAAAATACCACTAGTTTACAA
* * * * * *
88299443 AATTACAGAAATACCCTTGACTTTCTAAAAATTA-TAGAAATACCATTAGTTTACAA
1 AATTACCGAAATACCC-TCAATTTGT-AAAATTACCA-AAATACCACTAGTTTACAA
*
88299499 AATTACTGAAATACC
1 AATTACCGAAATACC
88299514 TTTGGTTTGT
Statistics
Matches: 104, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
54 56 0.54
55 11 0.11
56 37 0.36
ACGTcount: A:0.43, C:0.20, G:0.07, T:0.30
Consensus pattern (54 bp):
AATTACCGAAATACCCTCAATTTGTAAAATTACCAAAATACCACTAGTTTACAA
Found at i:88299509 original size:27 final size:28
Alignment explanation
Indices: 88299436--88299513 Score: 81
Period size: 29 Copynumber: 2.8 Consensus size: 28
88299426 ATACCCCTAA
* *
88299436 TTTACAAAATTACAGAAATACCCTTGAC
1 TTTACAAAATTACTGAAATACCATTGAC
*
88299464 TTT-CTAAAAATTA-TAGAAATACCATT-AG
1 TTTAC--AAAATTACT-GAAATACCATTGAC
88299492 TTTACAAAATTACTGAAATACC
1 TTTACAAAATTACTGAAATACC
88299514 TTTGGTTTGT
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
27 16 0.38
28 8 0.19
29 18 0.43
ACGTcount: A:0.45, C:0.17, G:0.06, T:0.32
Consensus pattern (28 bp):
TTTACAAAATTACTGAAATACCATTGAC
Found at i:88299521 original size:27 final size:27
Alignment explanation
Indices: 88299436--88299521 Score: 77
Period size: 27 Copynumber: 3.1 Consensus size: 27
88299426 ATACCCCTAA
* * *
88299436 TTTACAAAATTACAGAAATACCCTTGAC
1 TTTACAAAATTACTGAAATACCATTG-G
*
88299464 TTT-CTAAAAATTA-TAGAAATACCATTAG
1 TTTAC--AAAATTACT-GAAATACCATTGG
*
88299492 TTTACAAAATTACTGAAATACCTTTGG
1 TTTACAAAATTACTGAAATACCATTGG
88299519 TTT
1 TTT
88299522 GTAGATTTAC
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
27 22 0.47
28 7 0.15
29 18 0.38
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.36
Consensus pattern (27 bp):
TTTACAAAATTACTGAAATACCATTGG
Found at i:88299617 original size:27 final size:27
Alignment explanation
Indices: 88299562--88299639 Score: 70
Period size: 27 Copynumber: 2.9 Consensus size: 27
88299552 AAATGACTAC
* * *
88299562 AATACCCCTAATA-GGTAAAAAGACAGT
1 AATACCCCT-GTAGGGTAAAATGACCGT
*
88299589 AA-AGCCCCTGTAGGGTAAAGTGACCGT
1 AATA-CCCCTGTAGGGTAAAATGACCGT
* *
88299616 AATACCCTTGTATGGTAAAATGAC
1 AATACCCCTGTAGGGTAAAATGAC
88299640 GAATATGCCC
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
26 3 0.07
27 37 0.90
28 1 0.02
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (27 bp):
AATACCCCTGTAGGGTAAAATGACCGT
Found at i:88300292 original size:25 final size:25
Alignment explanation
Indices: 88300263--88300310 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
88300253 TTATAATGTG
*
88300263 AAAATAACTGTTTTGCCCCTAGGTA
1 AAAATAACTATTTTGCCCCTAGGTA
* *
88300288 AAAATGATTATTTTGCCCCTAGG
1 AAAATAACTATTTTGCCCCTAGG
88300311 GTTTAATTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (25 bp):
AAAATAACTATTTTGCCCCTAGGTA
Found at i:88300355 original size:14 final size:15
Alignment explanation
Indices: 88300338--88300371 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
88300328 ATACGTGGGG
88300338 TATGATAT-ACATGA
1 TATGATATCACATGA
88300352 TATGATATGCACATGA
1 TATGATAT-CACATGA
88300368 TATG
1 TATG
88300372 CATGATATGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
16 10 0.56
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (15 bp):
TATGATATCACATGA
Found at i:88300369 original size:11 final size:11
Alignment explanation
Indices: 88300353--88300408 Score: 66
Period size: 11 Copynumber: 5.5 Consensus size: 11
88300343 TATACATGAT
88300353 ATGATATGCAC
1 ATGATATGCAC
88300364 ATGATATG--C
1 ATGATATGCAC
88300373 ATGATATGCAC
1 ATGATATGCAC
*
88300384 ATGATATG--T
1 ATGATATGCAC
*
88300393 ATGAAATGCAC
1 ATGATATGCAC
88300404 ATGAT
1 ATGAT
88300409 GAATTCATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
9 16 0.43
11 21 0.57
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:88300378 original size:20 final size:20
Alignment explanation
Indices: 88300353--88300408 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
88300343 TATACATGAT
88300353 ATGATATGCACATGATATGC
1 ATGATATGCACATGATATGC
*
88300373 ATGATATGCACATGATATGT
1 ATGATATGCACATGATATGC
*
88300393 ATGAAATGCACATGAT
1 ATGATATGCACATGAT
88300409 GAATTCATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (20 bp):
ATGATATGCACATGATATGC
Found at i:88300555 original size:25 final size:26
Alignment explanation
Indices: 88300458--88300555 Score: 135
Period size: 26 Copynumber: 3.8 Consensus size: 26
88300448 GAGGAAGTGC
88300458 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
* * * **
88300484 AAAAAGACTTATGCCCTAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
88300510 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
88300536 AAAAGGGCTT-TGCCACAGTT
1 AAAAGGGCTTATGCCCCAGTT
88300556 ATTAAAGAGG
Statistics
Matches: 61, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
25 9 0.15
26 52 0.85
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:88300761 original size:42 final size:42
Alignment explanation
Indices: 88300702--88300791 Score: 162
Period size: 42 Copynumber: 2.1 Consensus size: 42
88300692 GTCTCTCCAG
*
88300702 ATGGGCTTGCATACATTCATTGGTATTTCATGTGATATTGAA
1 ATGGGCTTGCATACATTCATTGATATTTCATGTGATATTGAA
*
88300744 ATGGGCTTGCATACATTCATTGATATTTCATGTGTTATTGAA
1 ATGGGCTTGCATACATTCATTGATATTTCATGTGATATTGAA
88300786 ATGGGC
1 ATGGGC
88300792 CTATGGGCCA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.26, C:0.12, G:0.22, T:0.40
Consensus pattern (42 bp):
ATGGGCTTGCATACATTCATTGATATTTCATGTGATATTGAA
Found at i:88303435 original size:27 final size:27
Alignment explanation
Indices: 88303399--88303764 Score: 188
Period size: 27 Copynumber: 13.6 Consensus size: 27
88303389 AGAATACTTT
* *
88303399 TTACCCAAATATCCTCGATTTGTAAAA
1 TTACCAAAATACCCTCGATTTGTAAAA
* * *
88303426 TTACTAAAATACCCCCTGACTTGTAAAA
1 TTACCAAAATACCCTC-GATTTGTAAAA
*** *
88303454 TTATTGAAATACCCTCGACTTGTAAAA
1 TTACCAAAATACCCTCGATTTGTAAAA
* * *
88303481 TTACCAAAGTACCCTCGATTTATAGAA
1 TTACCAAAATACCCTCGATTTGTAAAA
***** ** * ** *
88303508 TTACTGTTTTATTCTTGATTTACAGAA
1 TTACCAAAATACCCTCGATTTGTAAAA
* *** * **
88303535 TTACTATTTTATCCTCGATTTACAAAA
1 TTACCAAAATACCCTCGATTTGTAAAA
*** *
88303562 TTACCATTTTACCCTCGA-TTGTGAAA
1 TTACCAAAATACCCTCGATTTGTAAAA
** * ** *
88303588 TTACTGAAATACCC-CTATAGGGTAGAA
1 TTACCAAAATACCCTCGAT-TTGTAAAA
*
88303615 TTACCAAAATACCC-CTAGTTTGTAAAA
1 TTACCAAAATACCCTCGA-TTTGTAAAA
*
88303642 TTACCAAAATACCC-CTAGTTTGTAAAA
1 TTACCAAAATACCCTCGA-TTTGTAAAA
* *
88303669 TTACCAAAATACCACT-GGTTTGTGAAA
1 TTACCAAAATACC-CTCGATTTGTAAAA
* *
88303696 TTACCGAAATACCCTCAATTTGTAAAA
1 TTACCAAAATACCCTCGATTTGTAAAA
**
88303723 TTACCAAAATACCC-CTGATTTACAAAA
1 TTACCAAAATACCCTC-GATTTGTAAAA
88303750 TTA-CAGAAATACCCT
1 TTACCA-AAATACCCT
88303765 TGACTTTCTA
Statistics
Matches: 270, Mismatches: 59, Indels: 19
0.78 0.17 0.05
Matches are distributed among these distances:
25 2 0.01
26 19 0.07
27 224 0.83
28 25 0.09
ACGTcount: A:0.37, C:0.21, G:0.09, T:0.33
Consensus pattern (27 bp):
TTACCAAAATACCCTCGATTTGTAAAA
Found at i:88303750 original size:81 final size:81
Alignment explanation
Indices: 88303613--88303762 Score: 216
Period size: 81 Copynumber: 1.9 Consensus size: 81
88303603 TATAGGGTAG
* **
88303613 AATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCA-AA
1 AATTACCAAAATACCCCTAATTTGTAAAATTACCAAAATACCCCTAGTTTACAAAATTA-CAGAA
88303677 ATACCACTGGTTTGTGA
65 ATACCACTGGTTTGTGA
*
88303694 AATTACCGAAATA-CCCTCAATTTGTAAAATTACCAAAATACCCCT-GATTTACAAAATTACAGA
1 AATTACCAAAATACCCCT-AATTTGTAAAATTACCAAAATACCCCTAG-TTTACAAAATTACAGA
88303757 AATACC
64 AATACC
88303763 CTTGACTTTC
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
80 7 0.11
81 55 0.89
ACGTcount: A:0.42, C:0.22, G:0.08, T:0.28
Consensus pattern (81 bp):
AATTACCAAAATACCCCTAATTTGTAAAATTACCAAAATACCCCTAGTTTACAAAATTACAGAAA
TACCACTGGTTTGTGA
Found at i:88303826 original size:27 final size:27
Alignment explanation
Indices: 88303719--88303826 Score: 94
Period size: 27 Copynumber: 3.9 Consensus size: 27
88303709 CTCAATTTGT
** * *
88303719 AAAATTACCAAAATACCCCTGATTTAC
1 AAAATTACTGAAATACCCTTGGTTTAC
* *
88303746 AAAATTACAGAAATACCCTTGACTTT-C
1 AAAATTACTGAAATACCCTTG-GTTTAC
* *
88303773 TAAAAATTA-TAGAAATACCATTAGTTTAC
1 --AAAATTACT-GAAATACCCTTGGTTTAC
88303802 AAAATTACTGAAATACCCTTGGTTT
1 AAAATTACTGAAATACCCTTGGTTT
88303827 GTAGATTTAC
Statistics
Matches: 65, Mismatches: 10, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
27 40 0.62
28 7 0.11
29 18 0.28
ACGTcount: A:0.43, C:0.19, G:0.07, T:0.31
Consensus pattern (27 bp):
AAAATTACTGAAATACCCTTGGTTTAC
Found at i:88304597 original size:25 final size:25
Alignment explanation
Indices: 88304568--88304615 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
88304558 TTATAATGTG
* *
88304568 AAAATGACTGTTTTGCCCCTAGGTA
1 AAAATGACAGTTGTGCCCCTAGGTA
88304593 AAAATGACAGTTGTGCCCCTAGG
1 AAAATGACAGTTGTGCCCCTAGG
88304616 GTTTAATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (25 bp):
AAAATGACAGTTGTGCCCCTAGGTA
Found at i:88304660 original size:14 final size:15
Alignment explanation
Indices: 88304643--88304676 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
88304633 ATACGTGGGG
88304643 TATGATAT-ACATGA
1 TATGATATCACATGA
88304657 TATGATATGCACATGA
1 TATGATAT-CACATGA
88304673 TATG
1 TATG
88304677 CATGATATGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
16 10 0.56
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (15 bp):
TATGATATCACATGA
Found at i:88304674 original size:11 final size:11
Alignment explanation
Indices: 88304658--88304713 Score: 66
Period size: 11 Copynumber: 5.5 Consensus size: 11
88304648 TATACATGAT
88304658 ATGATATGCAC
1 ATGATATGCAC
88304669 ATGATATG--C
1 ATGATATGCAC
88304678 ATGATATGCAC
1 ATGATATGCAC
*
88304689 ATGATATG--T
1 ATGATATGCAC
*
88304698 ATGAAATGCAC
1 ATGATATGCAC
88304709 ATGAT
1 ATGAT
88304714 GAATTCATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
9 16 0.43
11 21 0.57
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:88304683 original size:20 final size:20
Alignment explanation
Indices: 88304658--88304713 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
88304648 TATACATGAT
88304658 ATGATATGCACATGATATGC
1 ATGATATGCACATGATATGC
*
88304678 ATGATATGCACATGATATGT
1 ATGATATGCACATGATATGC
*
88304698 ATGAAATGCACATGAT
1 ATGATATGCACATGAT
88304714 GAATTCATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (20 bp):
ATGATATGCACATGATATGC
Found at i:88304886 original size:25 final size:26
Alignment explanation
Indices: 88304763--88304911 Score: 230
Period size: 26 Copynumber: 5.8 Consensus size: 26
88304753 GAGGAAGTGC
*
88304763 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATCG
* *
88304789 AAAAGGGCTTATGCCCCATTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATCG
*
88304815 AAAAGGGCTTATGCCCCAGTTTATGG
1 AAAAGGGCTTATGCCCCAGTTTATCG
*
88304841 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATCG
*
88304867 AAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATCG
88304892 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
88304912 ATTAAAGAGG
Statistics
Matches: 114, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
25 33 0.29
26 81 0.71
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATCG
Found at i:88305127 original size:42 final size:42
Alignment explanation
Indices: 88305062--88305147 Score: 138
Period size: 42 Copynumber: 2.0 Consensus size: 42
88305052 CTCCAGATGA
*
88305062 GCTTGCATACATTCATTAGTATTTCATGTGATATTGAAATGG
1 GCTTGCATACAGTCATTAGTATTTCATGTGATATTGAAATGG
*
88305104 GCTTGCATACAGTCATT-GATATTTCATGTGTTATTGAAATGG
1 GCTTGCATACAGTCATTAG-TATTTCATGTGATATTGAAATGG
88305146 GC
1 GC
88305148 CTATGGGCCA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
41 1 0.02
42 40 0.98
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.40
Consensus pattern (42 bp):
GCTTGCATACAGTCATTAGTATTTCATGTGATATTGAAATGG
Found at i:88307510 original size:27 final size:27
Alignment explanation
Indices: 88307470--88307582 Score: 102
Period size: 27 Copynumber: 4.1 Consensus size: 27
88307460 CCCCCCCCCA
* *
88307470 ATTTATAAAATTACCCAAATATCCTCG
1 ATTTGTAAAATTACCCAAATACCCTCG
* ** * *
88307497 ATTTGTAAACTTACTAAAATACCCCCTA
1 ATTTGTAAAATTACCCAAATACCCTC-G
**
88307525 ATTTGTAAAATTACTGAAATACCCTCG
1 ATTTGTAAAATTACCCAAATACCCTCG
* *
88307552 ACTTGTAAAATTA-CCAAAGTACCATCG
1 ATTTGTAAAATTACCCAAA-TACCCTCG
88307579 ATTT
1 ATTT
88307583 ATAGAATTTC
Statistics
Matches: 68, Mismatches: 16, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
26 3 0.04
27 42 0.62
28 23 0.34
ACGTcount: A:0.39, C:0.21, G:0.07, T:0.33
Consensus pattern (27 bp):
ATTTGTAAAATTACCCAAATACCCTCG
Found at i:88307528 original size:55 final size:55
Alignment explanation
Indices: 88307463--88307574 Score: 143
Period size: 55 Copynumber: 2.0 Consensus size: 55
88307453 CAAAGTACCC
* * * *
88307463 CCCCCCAATTTATAAAATTACCCAAATATCCTCGATTTGTAAACTTACTAAAATA
1 CCCCCCAATTTATAAAATTACCCAAATACCCTCGACTTGTAAAATTACCAAAATA
* * ** *
88307518 CCCCCTAATTTGTAAAATTACTGAAATACCCTCGACTTGTAAAATTACCAAAGTA
1 CCCCCCAATTTATAAAATTACCCAAATACCCTCGACTTGTAAAATTACCAAAATA
88307573 CC
1 CC
88307575 ATCGATTTAT
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
55 48 1.00
ACGTcount: A:0.38, C:0.26, G:0.06, T:0.29
Consensus pattern (55 bp):
CCCCCCAATTTATAAAATTACCCAAATACCCTCGACTTGTAAAATTACCAAAATA
Found at i:88307608 original size:27 final size:27
Alignment explanation
Indices: 88307571--88307662 Score: 103
Period size: 27 Copynumber: 3.4 Consensus size: 27
88307561 ATTACCAAAG
* * *
88307571 TACCATCGATTTATAGAATTTCTATTT
1 TACCCTCGATTTACAGAATTACTATTT
* * *
88307598 TACTCTTGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTATTT
* **
88307625 TACCCTCGATTTACAAAATTACCGTTT
1 TACCCTCGATTTACAGAATTACTATTT
88307652 TACCCTCGATT
1 TACCCTCGATT
88307663 GTGAAATTAC
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 55 1.00
ACGTcount: A:0.27, C:0.21, G:0.09, T:0.43
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACTATTT
Found at i:88307797 original size:27 final size:27
Alignment explanation
Indices: 88307694--88307831 Score: 118
Period size: 27 Copynumber: 5.1 Consensus size: 27
88307684 TATAGGGTAG
*
88307694 AATTACCAAAATACCTCT-AGTTTGTAA
1 AATTACCAAAATACCCCTGA-TTTGTAA
* * * * *
88307721 AATTTCCAAAGTACCACTGGTTTGTGA
1 AATTACCAAAATACCCCTGATTTGTAA
* * *
88307748 AATTACCGAAATACCCTTAATTTGTAA
1 AATTACCAAAATACCCCTGATTTGTAA
**
88307775 AATTACCAAAATACCCCTGATTTACAA
1 AATTACCAAAATACCCCTGATTTGTAA
* *
88307802 AATTA-CAGAAATACCCTTGACTTTTTAA
1 AATTACCA-AAATACCCCTGA-TTTGTAA
88307830 AA
1 AA
88307832 ATTATAGAAA
Statistics
Matches: 87, Mismatches: 21, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
26 2 0.02
27 78 0.90
28 7 0.08
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.32
Consensus pattern (27 bp):
AATTACCAAAATACCCCTGATTTGTAA
Found at i:88307805 original size:54 final size:54
Alignment explanation
Indices: 88307694--88307900 Score: 168
Period size: 54 Copynumber: 3.8 Consensus size: 54
88307684 TATAGGGTAG
* * * * * ***
88307694 AATTACCAAAATA-CCTCTAGTTTGTAAAATTTCCAAAGTACCACTGGTTTGTGA
1 AATTACCGAAATACCCT-TAGTTTGTAAAATTACCAAAATACCCCTGATTTACAA
*
88307748 AATTACCGAAATACCCTTAATTTGTAAAATTACCAAAATACCCCTGATTTACAA
1 AATTACCGAAATACCCTTAGTTTGTAAAATTACCAAAATACCCCTGATTTACAA
* * * * * *
88307802 AATTACAGAAATACCCTTGACTTTTTAAAAATTA-TAGAAATA-CCATTAGTTTACAA
1 AATTACCGAAATACCCTT-AGTTTGT-AAAATTACCA-AAATACCCCTGA-TTTACAA
* * * * *
88307858 AATTACTGAAATACCCTTGGTTTGTAGATTTACCAAAACACCC
1 AATTACCGAAATACCCTTAGTTTGTAAAATTACCAAAATACCC
88307901 TTGTAGGATG
Statistics
Matches: 123, Mismatches: 23, Indels: 13
0.77 0.14 0.08
Matches are distributed among these distances:
54 67 0.54
55 20 0.16
56 36 0.29
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.32
Consensus pattern (54 bp):
AATTACCGAAATACCCTTAGTTTGTAAAATTACCAAAATACCCCTGATTTACAA
Found at i:88307868 original size:27 final size:29
Alignment explanation
Indices: 88307795--88307872 Score: 83
Period size: 29 Copynumber: 2.8 Consensus size: 29
88307785 ATACCCCTGA
* * *
88307795 TTTACAAAATTACAGAAATACCCTTGACTT
1 TTTACAAAATTACTGAAATACCATTGAC-G
88307825 TTTA-AAAATTA-TAGAAATACCATT-A-G
1 TTTACAAAATTACT-GAAATACCATTGACG
88307851 TTTACAAAATTACTGAAATACC
1 TTTACAAAATTACTGAAATACC
88307873 CTTGGTTTGT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
26 4 0.10
27 15 0.36
28 2 0.05
29 17 0.40
30 4 0.10
ACGTcount: A:0.45, C:0.15, G:0.06, T:0.33
Consensus pattern (29 bp):
TTTACAAAATTACTGAAATACCATTGACG
Found at i:88307880 original size:27 final size:27
Alignment explanation
Indices: 88307747--88307876 Score: 120
Period size: 27 Copynumber: 4.7 Consensus size: 27
88307737 CTGGTTTGTG
* **
88307747 AAATTACCGAAATACCCTTAATTTGTA
1 AAATTACCGAAATACCCTTGATTTACA
* *
88307774 AAATTACCAAAATACCCCTGATTTACA
1 AAATTACCGAAATACCCTTGATTTACA
*
88307801 AAATTACAGAAATACCCTTGACTTTTTA-A
1 AAATTACCGAAATACCCTTGA---TTTACA
** *
88307830 AAATTATAGAAATACCATT-AGTTTACA
1 AAATTACCGAAATACCCTTGA-TTTACA
*
88307857 AAATTACTGAAATACCCTTG
1 AAATTACCGAAATACCCTTG
88307877 GTTTGTAGAT
Statistics
Matches: 84, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
26 4 0.05
27 57 0.68
28 1 0.01
29 18 0.21
30 4 0.05
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (27 bp):
AAATTACCGAAATACCCTTGATTTACA
Found at i:88308650 original size:25 final size:25
Alignment explanation
Indices: 88308621--88308668 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
88308611 TTATAATGTG
*
88308621 AAAATGATTGTTTTGCCCCTAGGTA
1 AAAATGACTGTTTTGCCCCTAGGTA
88308646 AAAATGACTGTTTTGCCCCTAGG
1 AAAATGACTGTTTTGCCCCTAGG
88308669 GTTTAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (25 bp):
AAAATGACTGTTTTGCCCCTAGGTA
Found at i:88308713 original size:14 final size:15
Alignment explanation
Indices: 88308696--88308729 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
88308686 ATACGTGGGG
88308696 TATGATAT-ACATGA
1 TATGATATCACATGA
88308710 TATGATATGCACATGA
1 TATGATAT-CACATGA
88308726 TATG
1 TATG
88308730 CATGATATGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
16 10 0.56
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (15 bp):
TATGATATCACATGA
Found at i:88308727 original size:11 final size:11
Alignment explanation
Indices: 88308711--88308766 Score: 66
Period size: 11 Copynumber: 5.5 Consensus size: 11
88308701 TATACATGAT
88308711 ATGATATGCAC
1 ATGATATGCAC
88308722 ATGATATG--C
1 ATGATATGCAC
88308731 ATGATATGCAC
1 ATGATATGCAC
*
88308742 ATGATATG--T
1 ATGATATGCAC
*
88308751 ATGAAATGCAC
1 ATGATATGCAC
88308762 ATGAT
1 ATGAT
88308767 GAATTCATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
9 16 0.43
11 21 0.57
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:88308736 original size:20 final size:20
Alignment explanation
Indices: 88308711--88308766 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
88308701 TATACATGAT
88308711 ATGATATGCACATGATATGC
1 ATGATATGCACATGATATGC
*
88308731 ATGATATGCACATGATATGT
1 ATGATATGCACATGATATGC
*
88308751 ATGAAATGCACATGAT
1 ATGATATGCACATGAT
88308767 GAATTCATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (20 bp):
ATGATATGCACATGATATGC
Found at i:88308894 original size:52 final size:51
Alignment explanation
Indices: 88308816--88308938 Score: 221
Period size: 52 Copynumber: 2.4 Consensus size: 51
88308806 GAGGAAGTGC
88308816 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTT-TGCCCCAGTTTACCG
88308868 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTTGCCCCAGTTTACCG
*
88308919 AAAAGGGCTT-TGCCCTAGTT
1 AAAAGGGCTTATGCCCCAGTT
88308939 ATTAAAGACA
Statistics
Matches: 70, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
50 9 0.13
51 25 0.36
52 36 0.51
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.28
Consensus pattern (51 bp):
AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTTGCCCCAGTTTACCG
Found at i:88308913 original size:25 final size:26
Alignment explanation
Indices: 88308816--88308938 Score: 187
Period size: 26 Copynumber: 4.8 Consensus size: 26
88308806 GAGGAAGTGC
**
88308816 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
88308842 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
**
88308868 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
88308894 AAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
*
88308919 AAAAGGGCTT-TGCCCTAGTT
1 AAAAGGGCTTATGCCCCAGTT
88308939 ATTAAAGACA
Statistics
Matches: 90, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
25 32 0.36
26 58 0.64
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.28
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACCG
Found at i:88309132 original size:42 final size:42
Alignment explanation
Indices: 88309085--88309174 Score: 153
Period size: 42 Copynumber: 2.1 Consensus size: 42
88309075 GTCTCTCTAG
*
88309085 ATGGGCTTGCATACATTCAATGGTATTTCATGTGATATTGAA
1 ATGGGCTTGCATACATTCAATGATATTTCATGTGATATTGAA
* *
88309127 ATGGGCTTGCATACATTCATTGATATTTCATGTGTTATTGAA
1 ATGGGCTTGCATACATTCAATGATATTTCATGTGATATTGAA
88309169 ATGGGC
1 ATGGGC
88309175 CTATGGGCCA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.39
Consensus pattern (42 bp):
ATGGGCTTGCATACATTCAATGATATTTCATGTGATATTGAA
Found at i:88311803 original size:31 final size:31
Alignment explanation
Indices: 88311761--88311823 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
88311751 GGAGTATGTT
*
88311761 TCTACTGAAGATATTGTGTGCAAACGGTTCG
1 TCTACTAAAGATATTGTGTGCAAACGGTTCG
88311792 TCTACTAAAGATATTGTGTGCAAACGGTTCG
1 TCTACTAAAGATATTGTGTGCAAACGGTTCG
88311823 T
1 T
88311824 TGATCGATTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (31 bp):
TCTACTAAAGATATTGTGTGCAAACGGTTCG
Found at i:88333681 original size:51 final size:51
Alignment explanation
Indices: 88333622--88333871 Score: 367
Period size: 51 Copynumber: 4.9 Consensus size: 51
88333612 CAGATACACG
* * ** *
88333622 GTGGCCTTCACATAGTACCACCCATGTAG-AGAAAGCTATTTTATTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGT-GTCCAAAGCTATTATATTCACAAA
**
88333673 GTGGCCTTCACATAGTACCACACTTGTGTTTAAAGCTATTATATTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTCACAAA
88333724 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTCACAAA
* * *
88333775 GTGACCTTGACATAGTACCACACTTGTGTCCAAAGCTATTATATTCAAAAA
1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTCACAAA
* * *
88333826 GTGGCCTTCATATAGTACCATACTTGTGTCCAAAGCTATTTTATTC
1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTC
88333872 CTAAGGTTCA
Statistics
Matches: 183, Mismatches: 15, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
50 1 0.01
51 182 0.99
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.32
Consensus pattern (51 bp):
GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTCACAAA
Found at i:88333934 original size:28 final size:28
Alignment explanation
Indices: 88333895--88333965 Score: 115
Period size: 28 Copynumber: 2.5 Consensus size: 28
88333885 GGGAAATTTC
* *
88333895 TCACTTATCACAATGCCATGGACTTATT
1 TCACTTAGCACAATGCCATGAACTTATT
*
88333923 TCACTTAGCACATTGCCATGAACTTATT
1 TCACTTAGCACAATGCCATGAACTTATT
88333951 TCACTTAGCACAATG
1 TCACTTAGCACAATG
88333966 TCATATCTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.34
Consensus pattern (28 bp):
TCACTTAGCACAATGCCATGAACTTATT
Found at i:88336623 original size:47 final size:48
Alignment explanation
Indices: 88336520--88336663 Score: 166
Period size: 48 Copynumber: 3.0 Consensus size: 48
88336510 TCATTAGGGA
* * * *
88336520 ATTCATTGATTTGGCTTCGGGACATGATATTGGTACTTTGAGTGCAAG
1 ATTCATTGATTTGGCTTCGGGACATGATATTGGCACTTAGGGTGCGAG
* * * * *
88336568 -TTAAATTGATGTGGCTCCGGG-CATGATATTGGCACTTCGGGTGTGAG
1 ATT-CATTGATTTGGCTTCGGGACATGATATTGGCACTTAGGGTGCGAG
* *
88336615 ATTCATTGATTTAGCTTCGGGCCATGATATTGGCACTTAGGGTGCGAG
1 ATTCATTGATTTGGCTTCGGGACATGATATTGGCACTTAGGGTGCGAG
88336663 A
1 A
88336664 CTCCCAAGTA
Statistics
Matches: 79, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
47 37 0.47
48 42 0.53
ACGTcount: A:0.22, C:0.15, G:0.30, T:0.34
Consensus pattern (48 bp):
ATTCATTGATTTGGCTTCGGGACATGATATTGGCACTTAGGGTGCGAG
Found at i:88341891 original size:26 final size:26
Alignment explanation
Indices: 88341862--88341917 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
88341852 TGATACAAAT
88341862 TGATAATGGGTTAGGTAAA-GTTCCCA
1 TGATAATGGGTTAGGTAAATGTT-CCA
*
88341888 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
88341914 TGAT
1 TGAT
88341918 GGGAATTTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
26 25 0.89
27 3 0.11
ACGTcount: A:0.30, C:0.09, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:88343637 original size:27 final size:27
Alignment explanation
Indices: 88343540--88343644 Score: 135
Period size: 27 Copynumber: 3.9 Consensus size: 27
88343530 AGGAAGCGTC
*
88343540 CTGGTGGCTATGCCACAATTATCTG-AT
1 CTGGTGGCTCTGCCACAA-TATCTGTAT
88343567 CTGGTGGCTCTGCCACATATATCTGT-T
1 CTGGTGGCTCTGCCACA-ATATCTGTAT
88343594 CTGGTGGCTCTGCCACAATATCTGTAT
1 CTGGTGGCTCTGCCACAATATCTGTAT
* *
88343621 CTGGTGACT-TCGTCACAATATCTG
1 CTGGTGGCTCT-GCCACAATATCTG
88343645 GCAGCCTCGC
Statistics
Matches: 71, Mismatches: 3, Indels: 8
0.87 0.04 0.10
Matches are distributed among these distances:
26 9 0.13
27 61 0.86
28 1 0.01
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATATCTGTAT
Found at i:88345416 original size:18 final size:19
Alignment explanation
Indices: 88345393--88345428 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
88345383 TAAATCAAGT
*
88345393 TACAAAGAT-ATTAAAAAA
1 TACAAAAATCATTAAAAAA
88345411 TACAAAAATCATTAAAAA
1 TACAAAAATCATTAAAAA
88345429 CGGGGCAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.67, C:0.08, G:0.03, T:0.22
Consensus pattern (19 bp):
TACAAAAATCATTAAAAAA
Found at i:88347847 original size:43 final size:43
Alignment explanation
Indices: 88347791--88348068 Score: 218
Period size: 43 Copynumber: 6.5 Consensus size: 43
88347781 AAAAAAATGG
* * *
88347791 CACTAAAGGTCATGATCTTTAGCGGCGCTTTTCCCAAAAACGC
1 CACTAAAGATCATGACCTTTAGCGGCGCTTTTCCCACAAACGC
* **
88347834 CACTAAAGATCATGACCTTTAGCAGCATTTTTCCCACAAACGC
1 CACTAAAGATCATGACCTTTAGCGGCGCTTTTCCCACAAACGC
* * ** *
88347877 CGCTAAAGGTCATGTTCTCTAGCGGCGCTTTTCCCACAAACGC
1 CACTAAAGATCATGACCTTTAGCGGCGCTTTTCCCACAAACGC
** * * * * **
88347920 TGCTAAAGAACATGACCTTTAGCGACGCTTCTCTCACAAACAT
1 CACTAAAGATCATGACCTTTAGCGGCGCTTTTCCCACAAACGC
* * * * * * *
88347963 CGCTAAAGAACATGACTTTTAACGGCACTTTTACCACAAATGC
1 CACTAAAGATCATGACCTTTAGCGGCGCTTTTCCCACAAACGC
* * * * *
88348006 CGCTATAA-AACAT-ACCTTTAGCGGCACTTTTCTCACAAACAC
1 CACTA-AAGATCATGACCTTTAGCGGCGCTTTTCCCACAAACGC
* * **
88348048 CGCTAAAAAAGATGACCTTTA
1 CACTAAAGATCATGACCTTTA
88348069 AAAATATATT
Statistics
Matches: 189, Mismatches: 43, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
41 2 0.01
42 32 0.17
43 153 0.81
44 2 0.01
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (43 bp):
CACTAAAGATCATGACCTTTAGCGGCGCTTTTCCCACAAACGC
Found at i:88347958 original size:86 final size:85
Alignment explanation
Indices: 88347793--88348054 Score: 273
Period size: 86 Copynumber: 3.1 Consensus size: 85
88347783 AAAAATGGCA
* * * *
88347793 CTAAAGGTCATGATCTTTAGCGGCGCTTTTCCCAAAAACGCCACTAAAGATCATGACCTTTAGC-
1 CTAAAGGTCATGTTC-TTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAACATGACCTTTAGCG
* *
88347857 A-GCATTTTTCCCACAAACGCCG
65 ACGC--TTTTCTCACAAACACCG
*
88347879 CTAAAGGTCATGTTCTCTAGCGGCGCTTTTCCCACAAACGCTGCTAAAGAACATGACCTTTAGCG
1 CTAAAGGTCATGTTCT-TAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAACATGACCTTTAGCG
* *
88347944 ACGCTTCTCTCACAAACATCG
65 ACGCTTTTCTCACAAACACCG
** * * * *
88347965 CTAAAGAACATGACTT-TTAACGGCACTTTTACCACAAATGCCGCTATAA-AACAT-ACCTTTAG
1 CTAAAGGTCATG--TTCTTAGCGGCGCTTTTCCCACAAACGCCGCTA-AAGAACATGACCTTTAG
* *
88348027 CGGCACTTTTCTCACAAACACCG
63 CGACGCTTTTCTCACAAACACCG
88348050 CTAAA
1 CTAAA
88348055 AAAGATGACC
Statistics
Matches: 150, Mismatches: 20, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
85 33 0.22
86 109 0.73
87 4 0.03
88 4 0.03
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.26
Consensus pattern (85 bp):
CTAAAGGTCATGTTCTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAACATGACCTTTAGCGA
CGCTTTTCTCACAAACACCG
Found at i:88349785 original size:20 final size:22
Alignment explanation
Indices: 88349746--88349785 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
88349736 TGCTTGTAGT
*
88349746 AAGAAAACTATAGTAAGGAACC
1 AAGAAAACTATAGGAAGGAACC
88349768 AAGAAAA-T-TAGGAAGGAA
1 AAGAAAACTATAGGAAGGAA
88349786 AATATTCTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 1 0.06
22 7 0.41
ACGTcount: A:0.57, C:0.07, G:0.23, T:0.12
Consensus pattern (22 bp):
AAGAAAACTATAGGAAGGAACC
Found at i:88352175 original size:41 final size:41
Alignment explanation
Indices: 88352083--88352197 Score: 140
Period size: 41 Copynumber: 2.8 Consensus size: 41
88352073 TATTGTTGCG
* **
88352083 TTTTCACCAAAAACGCCATTATAGCTCAATTTTTTACGGTG
1 TTTTGACCAAAAACGCCATTATAGCTCAATTTTTTACGGCA
* * * **
88352124 TTTTTACCAAAAATGCCACTATAGCTCAATTTTTTGTGGCA
1 TTTTGACCAAAAACGCCATTATAGCTCAATTTTTTACGGCA
* *
88352165 TTTTGCCCAAAAACGCCATTATTGCTCAATTTT
1 TTTTGACCAAAAACGCCATTATAGCTCAATTTT
88352198 AATTTTTTTC
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 62 1.00
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.38
Consensus pattern (41 bp):
TTTTGACCAAAAACGCCATTATAGCTCAATTTTTTACGGCA
Found at i:88352326 original size:7 final size:7
Alignment explanation
Indices: 88352298--88352370 Score: 83
Period size: 7 Copynumber: 10.0 Consensus size: 7
88352288 ATATGGACTA
*
88352298 AAATATT
1 AAATTTT
*
88352305 AAATATTA
1 AAAT-TTT
88352313 AAATTTT
1 AAATTTT
*
88352320 AAGTTTTT
1 AA-ATTTT
*
88352328 AATTTTTT
1 AA-ATTTT
88352336 AAATTTT
1 AAATTTT
88352343 AAATTTT
1 AAATTTT
88352350 AAATTTT
1 AAATTTT
88352357 AAATTTT
1 AAATTTT
88352364 AAATTTT
1 AAATTTT
88352371 TTTGAAGATT
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
7 40 0.69
8 18 0.31
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.56
Consensus pattern (7 bp):
AAATTTT
Found at i:88352856 original size:21 final size:21
Alignment explanation
Indices: 88352832--88352877 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
88352822 CCAAACATCG
*
88352832 AACCCCAAATCCTAGATCATA
1 AACCCCAAATCCTAGACCATA
* *
88352853 AACCCTAAATCTTAGACCATA
1 AACCCCAAATCCTAGACCATA
88352874 AACC
1 AACC
88352878 TACACCCTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.43, C:0.33, G:0.04, T:0.20
Consensus pattern (21 bp):
AACCCCAAATCCTAGACCATA
Found at i:88353087 original size:21 final size:21
Alignment explanation
Indices: 88353063--88353104 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
88353053 TATAAAACAA
*
88353063 TAAATCATAAACCCCAAACTC
1 TAAACCATAAACCCCAAACTC
*
88353084 TAAACCATAAACCCTAAACTC
1 TAAACCATAAACCCCAAACTC
88353105 AAAAATTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.48, C:0.33, G:0.00, T:0.19
Consensus pattern (21 bp):
TAAACCATAAACCCCAAACTC
Found at i:88353436 original size:40 final size:40
Alignment explanation
Indices: 88353381--88353496 Score: 162
Period size: 40 Copynumber: 2.9 Consensus size: 40
88353371 GCATTTCCTG
* * *
88353381 AAAAGCGTCGCTAATGGC-CAACCTATAGTGGCGTTTTTTA
1 AAAAGCGTCGCTAAT-GCTCAATCTATAGCGGCGTTTTTAA
* * *
88353421 AAAAGCGCCGGTAATGCTCGATCTATAGCGGCGTTTTTAA
1 AAAAGCGTCGCTAATGCTCAATCTATAGCGGCGTTTTTAA
88353461 AAAAGCGTCGCTAATGCTCAATCTATAGCGGCGTTT
1 AAAAGCGTCGCTAATGCTCAATCTATAGCGGCGTTT
88353497 GTTATCCAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
39 2 0.03
40 64 0.97
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (40 bp):
AAAAGCGTCGCTAATGCTCAATCTATAGCGGCGTTTTTAA
Found at i:88365358 original size:27 final size:27
Alignment explanation
Indices: 88365328--88365505 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
88365318 ATATTGAGTC
* * * *
88365328 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
88365355 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
88365382 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
88365410 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
88365437 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
88365464 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
88365491 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
88365506 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:88365467 original size:82 final size:81
Alignment explanation
Indices: 88365349--88365504 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
88365339 TGCTATATAA
* *
88365349 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
88365414 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
88365431 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
88365495 CACTTAGTGC
65 CACTTAGTGC
88365505 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:88372484 original size:17 final size:17
Alignment explanation
Indices: 88372462--88372500 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
88372452 CCATATTGCG
88372462 GGCCCACATACCCGTGT
1 GGCCCACATACCCGTGT
88372479 GGCCCACATACCCGTGT
1 GGCCCACATACCCGTGT
88372496 GGCCC
1 GGCCC
88372501 GTTTAGCCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.15, C:0.44, G:0.26, T:0.15
Consensus pattern (17 bp):
GGCCCACATACCCGTGT
Found at i:88378222 original size:27 final size:27
Alignment explanation
Indices: 88378205--88378550 Score: 312
Period size: 27 Copynumber: 12.9 Consensus size: 27
88378195 ATGCCCTCAA
*
88378205 TTTGTAAAATTACTAAAATACCCCTAG
1 TTTGTAAAATTACCAAAATACCCCTAG
* ** *
88378232 TTTATAAAATTA-CATAAATACCTTTGG
1 TTTGTAAAATTACCA-AAATACCCCTAG
88378259 TTTGTAAAATTACCAAAATACCCCTAG
1 TTTGTAAAATTACCAAAATACCCCTAG
* *
88378286 TTTGTGAAATTACCAAAATA-CCCTCG
1 TTTGTAAAATTACCAAAATACCCCTAG
** *
88378312 ATCAGTAAAATTACCAAAATACCCCTGG
1 -TTTGTAAAATTACCAAAATACCCCTAG
*
88378340 TTTGTAAAATTACTAAAATACCCCTAG
1 TTTGTAAAATTACCAAAATACCCCTAG
88378367 TTTGTAAAATTACCAAAATACCCCTAG
1 TTTGTAAAATTACCAAAATACCCCTAG
*
88378394 CTTGTAAAATTACCAAAATACCCCT-G
1 TTTGTAAAATTACCAAAATACCCCTAG
* * ** * *
88378420 ATTTGTGAAATTATCGGAATA-CTCTTG
1 -TTTGTAAAATTACCAAAATACCCCTAG
*
88378447 ATTTGTAAAA-TATCAAAATACCCCT-G
1 -TTTGTAAAATTACCAAAATACCCCTAG
** * *
88378473 TAAGGTAGAATTATCAAAATACCCCT-G
1 T-TTGTAAAATTACCAAAATACCCCTAG
** *
88378500 TAGGATAGAATTACCAAAATACCCCT-G
1 TTTG-TAAAATTACCAAAATACCCCTAG
** *
88378527 TAGGGTAGAATTACCAAAATACCC
1 T-TTGTAAAATTACCAAAATACCC
88378551 TAATAGGGTA
Statistics
Matches: 272, Mismatches: 36, Indels: 22
0.82 0.11 0.07
Matches are distributed among these distances:
25 1 0.00
26 27 0.10
27 235 0.86
28 9 0.03
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.30
Consensus pattern (27 bp):
TTTGTAAAATTACCAAAATACCCCTAG
Found at i:88378563 original size:54 final size:53
Alignment explanation
Indices: 88378460--88378623 Score: 202
Period size: 54 Copynumber: 3.0 Consensus size: 53
88378450 TGTAAAATAT
* * *
88378460 CAAAATACCCCTGTAAGGTAGAATTATCAAAATACCCCTGTAGGATAGAATTAC
1 CAAAATACCCCTGTAGGGTAGAATTATCAAAATA-CCCTATAGGGTAGAATTAC
* *
88378514 CAAAATACCCCTGTAGGGTAGAATTACCAAAATACCCTAATAGGGTAGAAATAC
1 CAAAATACCCCTGTAGGGTAGAATTATCAAAATACCCT-ATAGGGTAGAATTAC
** * * * *
88378568 TGAAATACCCCTGTAGGGTAGAATTATCGAGATACCCTTATGGGGTAAAATTAC
1 CAAAATACCCCTGTAGGGTAGAATTATCAAAATACCC-TATAGGGTAGAATTAC
88378622 CA
1 CA
88378624 TTTTGCCCCT
Statistics
Matches: 93, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
53 4 0.04
54 88 0.95
55 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.24
Consensus pattern (53 bp):
CAAAATACCCCTGTAGGGTAGAATTATCAAAATACCCTATAGGGTAGAATTAC
Found at i:88378604 original size:27 final size:27
Alignment explanation
Indices: 88378460--88378593 Score: 189
Period size: 27 Copynumber: 5.0 Consensus size: 27
88378450 TGTAAAATAT
* *
88378460 CAAAATACCCCTGTAAGGTAGAATTAT
1 CAAAATACCCCTGTAGGGTAGAATTAC
*
88378487 CAAAATACCCCTGTAGGATAGAATTAC
1 CAAAATACCCCTGTAGGGTAGAATTAC
88378514 CAAAATACCCCTGTAGGGTAGAATTAC
1 CAAAATACCCCTGTAGGGTAGAATTAC
* *
88378541 CAAAATA-CCCTAATAGGGTAGAAATAC
1 CAAAATACCCCT-GTAGGGTAGAATTAC
**
88378568 TGAAATACCCCTGTAGGGTAGAATTA
1 CAAAATACCCCTGTAGGGTAGAATTA
88378594 TCGAGATACC
Statistics
Matches: 95, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
26 4 0.04
27 87 0.92
28 4 0.04
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.23
Consensus pattern (27 bp):
CAAAATACCCCTGTAGGGTAGAATTAC
Found at i:88378613 original size:27 final size:26
Alignment explanation
Indices: 88378462--88378621 Score: 113
Period size: 27 Copynumber: 6.0 Consensus size: 26
88378452 TAAAATATCA
* * * *
88378462 AAATACCCCTGTAAGGTAGAATTATCA
1 AAATACCCTTATAGGGTAGAATTA-CG
* * * *
88378489 AAATACCCCTGTAGGATAGAATTACCA
1 AAATACCCTTATAGGGTAGAATTA-CG
* * *
88378516 AAATACCCCTGTAGGGTAGAATTACCA
1 AAATACCCTTATAGGGTAGAATTA-CG
* *
88378543 AAATACCCTAATAGGGTAGAAATACTG
1 AAATACCCTTATAGGGTAGAATTAC-G
* *
88378570 AAATACCCCTGTAGGGTAGAATTATCG
1 AAATACCCTTATAGGGTAGAATTA-CG
* * *
88378597 AGATACCCTTATGGGGTAAAATTAC
1 AAATACCCTTATAGGGTAGAATTAC
88378622 CATTTTGCCC
Statistics
Matches: 113, Mismatches: 18, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
26 2 0.02
27 110 0.97
28 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Consensus pattern (26 bp):
AAATACCCTTATAGGGTAGAATTACG
Found at i:88380817 original size:28 final size:28
Alignment explanation
Indices: 88380769--88380859 Score: 139
Period size: 28 Copynumber: 3.2 Consensus size: 28
88380759 GTGACAGAGT
*
88380769 CACCAGATACAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATAATTTGTGGCAGTGC
*
88380798 CACCAGAACAGATAATTTGTGGCAGGGC
1 CACCAGAACAGATAATTTGTGGCAGTGC
88380826 CACCAGAACAGATAATTTGTGGCA-TAGC
1 CACCAGAACAGATAATTTGTGGCAGT-GC
88380854 CACCAG
1 CACCAG
88380860 GATGCTTCCT
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
28 51 0.88
29 7 0.12
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.21
Consensus pattern (28 bp):
CACCAGAACAGATAATTTGTGGCAGTGC
Found at i:88381013 original size:28 final size:28
Alignment explanation
Indices: 88380967--88381030 Score: 101
Period size: 28 Copynumber: 2.3 Consensus size: 28
88380957 ATTAACCCTA
*
88380967 AGGGGTATAAAGGTTATTTTGCACACAT
1 AGGGGTATAAAGGTAATTTTGCACACAT
* *
88380995 AGGGGTATAATGGTAATTTTGCATACAT
1 AGGGGTATAAAGGTAATTTTGCACACAT
88381023 AGGGGTAT
1 AGGGGTAT
88381031 TCTAGTAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.31, C:0.08, G:0.28, T:0.33
Consensus pattern (28 bp):
AGGGGTATAAAGGTAATTTTGCACACAT
Found at i:88385998 original size:43 final size:43
Alignment explanation
Indices: 88385951--88386061 Score: 125
Period size: 43 Copynumber: 2.6 Consensus size: 43
88385941 TCCTAGATAT
* * *
88385951 GGTCTTACATGTTATAACATATCGATGCCACTATCCCACACAG
1 GGTCTTACATGTAATCACATATCGATGCCAATATCCCACACAG
* * * * * *
88385994 GGTCTTACACGAAATCACA-ATACAATGCCAATGTCCCAGACAT
1 GGTCTTACATGTAATCACATAT-CGATGCCAATATCCCACACAG
88386037 GGTCTTACATGTAATCACATATCGA
1 GGTCTTACATGTAATCACATATCGA
88386062 GTCGATGCCA
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
42 2 0.04
43 50 0.93
44 2 0.04
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.26
Consensus pattern (43 bp):
GGTCTTACATGTAATCACATATCGATGCCAATATCCCACACAG
Found at i:88386139 original size:50 final size:49
Alignment explanation
Indices: 88386018--88386239 Score: 183
Period size: 50 Copynumber: 4.6 Consensus size: 49
88386008 TCACAATACA
* * * *
88386018 ATGCCAATGTCCCAGACATGGTCTTACA-TGTAATCAC--ATATCGAGTCG
1 ATGCC-ATGTCCTAGACATGGTCTTACACTG-ACTCTCTTATATCGAGGCG
*
88386066 ATGCCATGTCCCAGACATGGTCTTACACTGACTCTCTTATATCGAGGCAG
1 ATGCCATGTCCTAGACATGGTCTTACACTGACTCTCTTATATCGAGGC-G
* * * * *
88386116 ATGCCGTATCCTAGACATGGTCTTACACTGCCTCTCCTCT-TTTC-ACGCCG
1 ATGCCATGTCCTAGACATGGTCTTACACTGACTCT-CT-TATATCGA-GGCG
* * * *
88386166 ATGCCATGTCCTAGACATGGTCTTACACTGA--CAC--ATATCAAGCCA
1 ATGCCATGTCCTAGACATGGTCTTACACTGACTCTCTTATATCGAGGCG
* *
88386211 ATTCCATGTCCCAGACATGGTCTTACACT
1 ATGCCATGTCCTAGACATGGTCTTACACT
88386240 AGCTCACATG
Statistics
Matches: 148, Mismatches: 17, Indels: 21
0.80 0.09 0.11
Matches are distributed among these distances:
45 33 0.22
46 1 0.01
47 27 0.18
48 8 0.05
49 9 0.06
50 62 0.42
51 7 0.05
52 1 0.01
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.28
Consensus pattern (49 bp):
ATGCCATGTCCTAGACATGGTCTTACACTGACTCTCTTATATCGAGGCG
Found at i:88395357 original size:32 final size:31
Alignment explanation
Indices: 88395283--88395364 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 31
88395273 GGACCCACAT
* * * * *
88395283 GCCCGTGTGGGCCCACACGTCCAGATTGGCCTT
1 GCCCGTGT-GG-CCACATGCCCAAATTAGCCTA
88395316 GCCCGTGTGGCCTACATGCCCAAATTAGCCTA
1 GCCCGTGTGGCC-ACATGCCCAAATTAGCCTA
88395348 GCCCGTGTGGCCACATG
1 GCCCGTGTGGCCACATG
88395365 GCCATACTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
31 7 0.16
32 28 0.65
33 8 0.19
ACGTcount: A:0.16, C:0.35, G:0.28, T:0.21
Consensus pattern (31 bp):
GCCCGTGTGGCCACATGCCCAAATTAGCCTA
Found at i:88398212 original size:42 final size:42
Alignment explanation
Indices: 88398103--88398265 Score: 206
Period size: 42 Copynumber: 3.9 Consensus size: 42
88398093 CTTGTATAAA
* * *
88398103 ACACCGGCA-CAGAGCCTACTAGGTAATAAACCTGAT-TCAAT
1 ACACCGGCATCAAAGCCTACTAGGCAATAAGCCTGATATC-AT
* * *
88398144 ACATCGGCAT-AAAGCCTGCTAGGCAATAAGCCTGGTATCAT
1 ACACCGGCATCAAAGCCTACTAGGCAATAAGCCTGATATCAT
88398185 ACACCGGCATCAAAGCCTACTAGGCAATAAGCCTGATATCAT
1 ACACCGGCATCAAAGCCTACTAGGCAATAAGCCTGATATCAT
* * **
88398227 ACATCGGCATCAAAGGCTGTTAGGCAATAAGCCTGATAT
1 ACACCGGCATCAAAGCCTACTAGGCAATAAGCCTGATAT
88398266 ATCACTGTTA
Statistics
Matches: 106, Mismatches: 13, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
41 40 0.38
42 66 0.62
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.21
Consensus pattern (42 bp):
ACACCGGCATCAAAGCCTACTAGGCAATAAGCCTGATATCAT
Found at i:88398229 original size:83 final size:83
Alignment explanation
Indices: 88398081--88398266 Score: 243
Period size: 83 Copynumber: 2.2 Consensus size: 83
88398071 TAAAATTCAT
* * *
88398081 TAGGC-ATAAAGCCTTGTATAAAACACCGGCACAGAGCCTACTAGGTAATAAACCTGATTCAATA
1 TAGGCAAT-AAGCCTGGTATAAAACACCGGCACAAAGCCTACTAGGCAATAAACCTGATTCAATA
88398145 CATCGGCAT-AAAGCCTGC
65 CATCGGCATCAAAGCCTGC
* * *
88398163 TAGGCAATAAGCCTGGTATCATACACCGGCATCAAAGCCTACTAGGCAATAAGCCTGATATC-AT
1 TAGGCAATAAGCCTGGTATAAAACACCGGCA-CAAAGCCTACTAGGCAATAAACCTGAT-TCAAT
* *
88398227 ACATCGGCATCAAAGGCTGT
64 ACATCGGCATCAAAGCCTGC
*
88398247 TAGGCAATAAGCCTGATATA
1 TAGGCAATAAGCCTGGTATA
88398267 TCACTGTTAC
Statistics
Matches: 90, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
82 25 0.28
83 38 0.42
84 27 0.30
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (83 bp):
TAGGCAATAAGCCTGGTATAAAACACCGGCACAAAGCCTACTAGGCAATAAACCTGATTCAATAC
ATCGGCATCAAAGCCTGC
Found at i:88401900 original size:26 final size:25
Alignment explanation
Indices: 88401870--88401922 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 25
88401860 ACCAACACAC
88401870 TAATATCGCAACAAAGCTACCAGTAA
1 TAATATCGCAACAAAGCTACCAG-AA
* * *
88401896 TAATATCGCAGCATAGCTGCCAGAA
1 TAATATCGCAACAAAGCTACCAGAA
88401921 TA
1 TA
88401923 GTAAACGTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 4 0.17
26 20 0.83
ACGTcount: A:0.42, C:0.23, G:0.15, T:0.21
Consensus pattern (25 bp):
TAATATCGCAACAAAGCTACCAGAA
Found at i:88401973 original size:27 final size:26
Alignment explanation
Indices: 88401929--88402005 Score: 75
Period size: 27 Copynumber: 2.9 Consensus size: 26
88401919 AATAGTAAAC
* *
88401929 GTGGCAAAGCTACCAGTAACAGTAATT
1 GTGGCATAGCCACCAGTAACAGTAA-T
* *
88401956 GTGGCATAGCCACTAGTAATAGTGAAT
1 GTGGCATAGCCACCAGTAACAGT-AAT
* *
88401983 GTGACATAGTCACCAGT-ACAGTA
1 GTGGCATAGCCACCAGTAACAGTA
88402006 CTTCCACCAT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
25 1 0.02
26 4 0.10
27 34 0.83
28 2 0.05
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.23
Consensus pattern (26 bp):
GTGGCATAGCCACCAGTAACAGTAAT
Found at i:88402172 original size:27 final size:27
Alignment explanation
Indices: 88402141--88402221 Score: 90
Period size: 27 Copynumber: 3.0 Consensus size: 27
88402131 GGGCATAATC
* *
88402141 GTCATATTACCATACAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGTATTACG
* * * *
88402168 GTCATTTTACCCTACAAGAGCATTACA
1 GTCATTTTACCCTACAGGGGTATTACG
* *
88402195 TTCATTTTACCCTATAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGTATTACG
88402222 TGTAACACCC
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.33
Consensus pattern (27 bp):
GTCATTTTACCCTACAGGGGTATTACG
Found at i:88402990 original size:27 final size:26
Alignment explanation
Indices: 88402942--88402993 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
88402932 GCGAGGCTGC
*
88402942 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
88402968 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
88402994 TTGCAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:88403091 original size:85 final size:85
Alignment explanation
Indices: 88402997--88403166 Score: 295
Period size: 85 Copynumber: 2.0 Consensus size: 85
88402987 CACCAGATTG
*
88402997 CAGCGAGGCTGCCAGAACGCTTCCTCCATCAATATAAACCCATATCCCATGCAACAGAAATAATA
1 CAGCGAGGCTACCAGAACGCTTCCTCCATCAATATAAACCCATATCCCATGCAACAGAAATAATA
*
88403062 TGTCATGGCATACGTATACA
66 TGTCACGGCATACGTATACA
* * *
88403082 CAGCGAGGCTACCAGAACGCTTCCTCCATCAATGTAAACCCATGTCTCATGCAACAGAAATAATA
1 CAGCGAGGCTACCAGAACGCTTCCTCCATCAATATAAACCCATATCCCATGCAACAGAAATAATA
88403147 TGTCACGGCATACGTATACA
66 TGTCACGGCATACGTATACA
88403167 GAAACAGAAC
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
85 80 1.00
ACGTcount: A:0.35, C:0.28, G:0.16, T:0.21
Consensus pattern (85 bp):
CAGCGAGGCTACCAGAACGCTTCCTCCATCAATATAAACCCATATCCCATGCAACAGAAATAATA
TGTCACGGCATACGTATACA
Found at i:88403705 original size:26 final size:27
Alignment explanation
Indices: 88403676--88403729 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
88403666 TCACACAAGT
*
88403676 TAGTCATTT-ACGCACG-AGGGGCAAAA
1 TAGTCATTTAACAC-CGTAGGGGCAAAA
88403702 TAGTCATTTAACACCGTAGGGGCAAAA
1 TAGTCATTTAACACCGTAGGGGCAAAA
88403729 T
1 T
88403730 GGTAATTACC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 11 0.44
27 14 0.56
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.22
Consensus pattern (27 bp):
TAGTCATTTAACACCGTAGGGGCAAAA
Found at i:88403728 original size:27 final size:26
Alignment explanation
Indices: 88403676--88403729 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 26
88403666 TCACACAAGT
*
88403676 TAGTCATTTACGCACGAGGGGCAAAA
1 TAGTCATTTACACACGAGGGGCAAAA
88403702 TAGTCATTTA-ACACCGTAGGGGCAAAA
1 TAGTCATTTACACA-CG-AGGGGCAAAA
88403729 T
1 T
88403730 GGTAATTACC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 2 0.08
26 12 0.48
27 11 0.44
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.22
Consensus pattern (26 bp):
TAGTCATTTACACACGAGGGGCAAAA
Found at i:88403772 original size:27 final size:27
Alignment explanation
Indices: 88403736--88403792 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
88403726 AAATGGTAAT
88403736 TACCCCACAAGGGTATCTCGGTAATTC
1 TACCCCACAAGGGTATCTCGGTAATTC
* * *
88403763 TACCCTACAAGGGTATTTTGGTAATTC
1 TACCCCACAAGGGTATCTCGGTAATTC
88403790 TAC
1 TAC
88403793 AACTTATCCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.32
Consensus pattern (27 bp):
TACCCCACAAGGGTATCTCGGTAATTC
Found at i:88404657 original size:27 final size:27
Alignment explanation
Indices: 88404619--88404746 Score: 186
Period size: 27 Copynumber: 4.7 Consensus size: 27
88404609 GGGGCGTTAC
* *
88404619 ATTACGGTCATTTTACCCTATAGGGGT
1 ATTACGATCATTTTACCCTACAGGGGT
*
88404646 ATTACGATCATTTTATCCTACAGGGGT
1 ATTACGATCATTTTACCCTACAGGGGT
*
88404673 ATTACAATCATTTTACCCTACAGGGGT
1 ATTACGATCATTTTACCCTACAGGGGT
88404700 ATTAC-AGTCATTTTACCCTACAGGGGT
1 ATTACGA-TCATTTTACCCTACAGGGGT
* *
88404727 ATTACGGTTATTTTACCCTA
1 ATTACGATCATTTTACCCTA
88404747 GATAACAACC
Statistics
Matches: 92, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
26 1 0.01
27 91 0.99
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (27 bp):
ATTACGATCATTTTACCCTACAGGGGT
Found at i:88408707 original size:27 final size:27
Alignment explanation
Indices: 88408677--88408818 Score: 160
Period size: 27 Copynumber: 5.3 Consensus size: 27
88408667 TAAGTTGTAG
* *
88408677 AATTACCAAAATACCCCTGTAAGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAA
* * *
88408704 AATTACTGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAA
* *
88408731 AATTATCGAAATACCCTTGTAGGGTAGA
1 AATTACCGAAATACCCCTGTAGGGTA-A
* *
88408759 AA-TACCGAAATACCCCTGTAGGATAG
1 AATTACCGAAATACCCCTGTAGGGTAA
* * *
88408785 AATTACCGAGATACCCTTGTGGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAA
88408812 AATTACC
1 AATTACC
88408819 ATTTTGCCCC
Statistics
Matches: 94, Mismatches: 19, Indels: 4
0.80 0.16 0.03
Matches are distributed among these distances:
26 2 0.02
27 90 0.96
28 2 0.02
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAA
Found at i:88408769 original size:54 final size:53
Alignment explanation
Indices: 88408673--88408814 Score: 185
Period size: 54 Copynumber: 2.6 Consensus size: 53
88408663 TGAATAAGTT
* * * *
88408673 GTAGAATTACCAAAATACCCCTGTAAGGTAAAATTACTGAAATACCCCTATAGG
1 GTAGAATTACCGAAATACCCTTGTAGGGTAAAA-TACCGAAATACCCCTATAGG
* *
88408727 GTAGAATTATCGAAATACCCTTGTAGGGTAGAAATACCGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCTTGTAGGGTA-AAATACCGAAATACCCCTATAGG
* * *
88408781 ATAGAATTACCGAGATACCCTTGTGGGGTAAAAT
1 GTAGAATTACCGAAATACCCTTGTAGGGTAAAAT
88408815 TACCATTTTG
Statistics
Matches: 77, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
53 4 0.05
54 70 0.91
55 3 0.04
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (53 bp):
GTAGAATTACCGAAATACCCTTGTAGGGTAAAATACCGAAATACCCCTATAGG
Found at i:88409530 original size:27 final size:27
Alignment explanation
Indices: 88409490--88409549 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
88409480 GCATATATAT
* *
88409490 ATATCT-TTTCTGGTGGCCTAGCCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
* * *
88409516 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
88409543 ATATCTG
1 ATATCTG
88409550 GCAGCCTCGC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 6 0.21
27 22 0.79
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.37
Consensus pattern (27 bp):
ATATCTGTATCTGGTGACCTAGCCACA
Found at i:88417132 original size:27 final size:26
Alignment explanation
Indices: 88417115--88417184 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 26
88417105 ATATTAAGTC
88417115 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATAT-ATCAACT
*
88417142 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATAT-ATC-AACT
*
88417170 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
88417185 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (26 bp):
CGCACACTCAGTGCTATATATCAACT
Found at i:88417178 original size:28 final size:28
Alignment explanation
Indices: 88417115--88417212 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
88417105 ATATTAAGTC
*
88417115 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
88417142 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
88417170 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
88417199 CGCACACTTAGTGC
1 CGCACACTTAGTGC
88417213 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:88420406 original size:43 final size:43
Alignment explanation
Indices: 88420358--88420510 Score: 184
Period size: 43 Copynumber: 3.6 Consensus size: 43
88420348 TGTGTGTGCA
* *
88420358 TGTAAGACCACATCTGGGATGTTGGCATCAATATGTGATTACG
1 TGTAAGACCACGTCTGGGACGTTGGCATCAATATGTGATTACG
* ** *
88420401 TGTAAGACTACGTCCAGGACGTTGGCATCTATATGTGATTACG
1 TGTAAGACCACGTCTGGGACGTTGGCATCAATATGTGATTACG
* * *
88420444 TGTAAGACC-CTGTTTGGGACAG-TGGCATCGATATGTGATTACA
1 TGTAAGACCAC-GTCTGGGAC-GTTGGCATCAATATGTGATTACG
*
88420487 TGTAAGACCATGTCTGGGACGTTG
1 TGTAAGACCACGTCTGGGACGTTG
88420511 TCATTGTACG
Statistics
Matches: 92, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
42 2 0.02
43 89 0.97
44 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.30
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCAATATGTGATTACG
Found at i:88443509 original size:54 final size:54
Alignment explanation
Indices: 88443439--88443594 Score: 185
Period size: 54 Copynumber: 2.9 Consensus size: 54
88443429 CCCCTACAGG
* *
88443439 GTAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCA-AAATAACCCT-AGTTC
1 GTAAAATTACCAAAATACCCCTAGGTTGTAAAATTA-CAGAAAT-ACCCTCAATTC
* * * *
88443493 GTAAAATTACCGAAATACCACTAGGTTGTGAAATTACAGAAATACCCTCAATTT
1 GTAAAATTACCAAAATACCCCTAGGTTGTAAAATTACAGAAATACCCTCAATTC
*
88443547 GTAAAATTACCAAAATACCCCT-GATT-TACAAAATTACAGAAATACCCT
1 GTAAAATTACCAAAATACCCCTAGGTTGT--AAAATTACAGAAATACCCT
88443595 TGACTTTCTA
Statistics
Matches: 88, Mismatches: 10, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
52 1 0.01
53 10 0.11
54 77 0.88
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.27
Consensus pattern (54 bp):
GTAAAATTACCAAAATACCCCTAGGTTGTAAAATTACAGAAATACCCTCAATTC
Found at i:88443573 original size:27 final size:27
Alignment explanation
Indices: 88443439--88443593 Score: 165
Period size: 27 Copynumber: 5.7 Consensus size: 27
88443429 CCCCTACAGG
88443439 GTAAAATTACCAAAATACCCCTAGTTT
1 GTAAAATTACCAAAATACCCCTAGTTT
* *
88443466 GTAAAATTACCAAAATAACCCTAGTTC
1 GTAAAATTACCAAAATACCCCTAGTTT
* * *
88443493 GTAAAATTACCGAAATACCACTAGGTT
1 GTAAAATTACCAAAATACCCCTAGTTT
* *
88443520 GTGAAATTA-CAGAAATA-CCCTCAATTT
1 GTAAAATTACCA-AAATACCCCT-AGTTT
88443547 GTAAAATTACCAAAATACCCCT-GATTT
1 GTAAAATTACCAAAATACCCCTAG-TTT
**
88443574 ACAAAATTA-CAGAAATACCC
1 GTAAAATTACCA-AAATACCC
88443594 TTGACTTTCT
Statistics
Matches: 106, Mismatches: 16, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
26 6 0.06
27 94 0.89
28 6 0.06
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.26
Consensus pattern (27 bp):
GTAAAATTACCAAAATACCCCTAGTTT
Found at i:88443580 original size:81 final size:80
Alignment explanation
Indices: 88443442--88443592 Score: 200
Period size: 81 Copynumber: 1.9 Consensus size: 80
88443432 CTACAGGGTA
* *
88443442 AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATAACCCTAGTTCGTAAAATTACCGAA
1 AAATTACCAAAATACCCCTAATTTGTAAAATTACCAAAATAACCCTAGTTCG-AAAATTACAGAA
88443507 ATACCACTAGGTTGTG
65 ATACCACTAGGTTGTG
* *
88443523 AAATTA-CAGAAATA-CCCTCAATTTGTAAAATTACCAAAATACCCCTGATTTAC-AAAATTACA
1 AAATTACCA-AAATACCCCT-AATTTGTAAAATTACCAAAATAACCCT-AGTT-CGAAAATTACA
88443585 GAAATACC
62 GAAATACC
88443593 CTTGACTTTC
Statistics
Matches: 62, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
80 6 0.10
81 52 0.84
82 3 0.05
83 1 0.02
ACGTcount: A:0.44, C:0.21, G:0.09, T:0.26
Consensus pattern (80 bp):
AAATTACCAAAATACCCCTAATTTGTAAAATTACCAAAATAACCCTAGTTCGAAAATTACAGAAA
TACCACTAGGTTGTG
Found at i:88443631 original size:56 final size:55
Alignment explanation
Indices: 88443440--88443652 Score: 156
Period size: 54 Copynumber: 3.9 Consensus size: 55
88443430 CCCTACAGGG
* ** *
88443440 TAAAATTACCAAAATACCCCT-AGTTTGTAAAATTACCA-AAATAACCC-T--AGTTC
1 TAAAATTACCAAAATACCACTGA-TTTACAAAATTA-CAGAAAT-ACCCTTGAATTTC
* * * * *
88443493 GTAAAATTACCGAAATACCACTAGGTTGT--GAAATTACAGAAATACCC-TCAATTTG
1 -TAAAATTACCAAAATACCACT-GATT-TACAAAATTACAGAAATACCCTTGAATTTC
* *
88443548 TAAAATTACCAAAATACCCCTGATTTACAAAATTACAGAAATACCCTTGACTTTC
1 TAAAATTACCAAAATACCACTGATTTACAAAATTACAGAAATACCCTTGAATTTC
* * * *
88443603 TAAAAATTA-TAGAAATACCATTGGTTTACAAAATTACTGAAATACCCTTG
1 T-AAAATTACCA-AAATACCACTGATTTACAAAATTACAGAAATACCCTTG
88443653 GTTTGTAGAT
Statistics
Matches: 130, Mismatches: 18, Indels: 20
0.77 0.11 0.12
Matches are distributed among these distances:
52 1 0.01
53 10 0.08
54 65 0.50
55 12 0.09
56 42 0.32
ACGTcount: A:0.42, C:0.20, G:0.09, T:0.29
Consensus pattern (55 bp):
TAAAATTACCAAAATACCACTGATTTACAAAATTACAGAAATACCCTTGAATTTC
Found at i:88443644 original size:27 final size:27
Alignment explanation
Indices: 88443549--88443656 Score: 103
Period size: 27 Copynumber: 3.9 Consensus size: 27
88443539 CTCAATTTGT
** * *
88443549 AAAATTACCAAAATACCCCTGATTTAC
1 AAAATTACTGAAATACCCTTGGTTTAC
* *
88443576 AAAATTACAGAAATACCCTTGACTTT-C
1 AAAATTACTGAAATACCCTTG-GTTTAC
*
88443603 TAAAAATTA-TAGAAATACCATTGGTTTAC
1 --AAAATTACT-GAAATACCCTTGGTTTAC
88443632 AAAATTACTGAAATACCCTTGGTTT
1 AAAATTACTGAAATACCCTTGGTTT
88443657 GTAGATTTAC
Statistics
Matches: 67, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
27 41 0.61
28 7 0.10
29 19 0.28
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (27 bp):
AAAATTACTGAAATACCCTTGGTTTAC
Found at i:88443740 original size:27 final size:27
Alignment explanation
Indices: 88443697--88443770 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 27
88443687 AAATGACTAA
*
88443697 AATACCCCTAATA-GGTAAAAAGACCGT
1 AATACCCCT-GTAGGGTAAAAAGACCGT
**
88443724 AA-AGCCCCTGTAGGGTAAAGTGACCGT
1 AATA-CCCCTGTAGGGTAAAAAGACCGT
* *
88443751 AATACCCTTGTATGGTAAAA
1 AATACCCCTGTAGGGTAAAA
88443771 TGACGAATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
26 3 0.08
27 34 0.89
28 1 0.03
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (27 bp):
AATACCCCTGTAGGGTAAAAAGACCGT
Found at i:88443774 original size:27 final size:27
Alignment explanation
Indices: 88443710--88443774 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
88443700 ACCCCTAATA
*
88443710 GGTAAAAAGACCGTAAAGCCCCTGTAG
1 GGTAAAATGACCGTAAAGCCCCTGTAG
* * *
88443737 GGTAAAGTGACCGTAATA-CCCTTGTAT
1 GGTAAAATGACCGTAA-AGCCCCTGTAG
88443764 GGTAAAATGAC
1 GGTAAAATGAC
88443775 GAATATGCCC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 31 0.97
28 1 0.03
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (27 bp):
GGTAAAATGACCGTAAAGCCCCTGTAG
Found at i:88444507 original size:20 final size:20
Alignment explanation
Indices: 88444482--88444548 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
88444472 GATATGATAT
*
88444482 ACATGAT-TGATATGATATGC
1 ACATGATATG-TATGAAATGC
* *
88444502 ACATGATATGTATAAAACGC
1 ACATGATATGTATGAAATGC
88444522 ACATGATATGTATGAAATGC
1 ACATGATATGTATGAAATGC
88444542 ACATGAT
1 ACATGAT
88444549 GTATTCATAA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
20 39 0.95
21 2 0.05
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (20 bp):
ACATGATATGTATGAAATGC
Found at i:88444627 original size:26 final size:26
Alignment explanation
Indices: 88444598--88444733 Score: 181
Period size: 26 Copynumber: 5.3 Consensus size: 26
88444588 GAGGAAGTGC
88444598 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
***
88444624 AAAAGGGCTTATGCCCCAGTTTACCA
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
88444650 AAAAGGGCTTATGCCCCAGCTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
**
88444676 AAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
88444701 AAAAGGGCTT-TGCCCCAG-TTATT-
1 AAAAGGGCTTATGCCCCAGTTTATTG
88444724 AAAAGAGGCT
1 AAAAG-GGCT
88444734 AGGCCTCCAG
Statistics
Matches: 97, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
23 5 0.05
24 7 0.07
25 30 0.31
26 55 0.57
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.26
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:88444674 original size:52 final size:50
Alignment explanation
Indices: 88444598--88444733 Score: 213
Period size: 52 Copynumber: 2.7 Consensus size: 50
88444588 GAGGAAGTGC
88444598 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCA
1 AAAAGGGCTTATGCCCCAG-TTATTGAAAAGGGCTT-TGCCCCAGTTTACCA
*
88444650 AAAAGGGCTTATGCCCCAGCTTATTGAAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAG-TTATTGAAAAGGGCTTTGCCCCAGTTTACCA
88444701 AAAAGGGCTT-TGCCCCAGTTATT-AAAAGAGGCT
1 AAAAGGGCTTATGCCCCAGTTATTGAAAAG-GGCT
88444734 AGGCCTCCAG
Statistics
Matches: 81, Mismatches: 2, Indels: 5
0.92 0.02 0.06
Matches are distributed among these distances:
48 5 0.06
49 9 0.11
50 8 0.10
51 24 0.30
52 35 0.43
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.26
Consensus pattern (50 bp):
AAAAGGGCTTATGCCCCAGTTATTGAAAAGGGCTTTGCCCCAGTTTACCA
Found at i:88455089 original size:15 final size:16
Alignment explanation
Indices: 88455064--88455111 Score: 75
Period size: 15 Copynumber: 3.2 Consensus size: 16
88455054 TTAGTAGCCT
88455064 TAAATTAAATAAAATA
1 TAAATTAAATAAAATA
88455080 TAAA-TAAATAAAATA
1 TAAATTAAATAAAATA
88455095 -AAATTAAATAAAA-A
1 TAAATTAAATAAAATA
88455109 TAA
1 TAA
88455112 CTAAAACTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
14 4 0.13
15 22 0.73
16 4 0.13
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
TAAATTAAATAAAATA
Found at i:88455093 original size:25 final size:25
Alignment explanation
Indices: 88455065--88455117 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
88455055 TAGTAGCCTT
* *
88455065 AAATTAAATAAAATATAAATAAATA
1 AAATAAAATAAAATAAAAATAAATA
* *
88455090 AAATAAAATTAAATAAAAATAACTA
1 AAATAAAATAAAATAAAAATAAATA
88455115 AAA
1 AAA
88455118 CTGAAATTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.25
Consensus pattern (25 bp):
AAATAAAATAAAATAAAAATAAATA
Found at i:88455102 original size:6 final size:5
Alignment explanation
Indices: 88455065--88455107 Score: 52
Period size: 5 Copynumber: 8.6 Consensus size: 5
88455055 TAGTAGCCTT
* *
88455065 AAATT AAATA AAATA TAAAT- AAATA AAATA AAATT AAATA AAA
1 AAATA AAATA AAATA -AAATA AAATA AAATA AAATA AAATA AAA
88455108 ATAACTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
4 4 0.12
5 25 0.76
6 4 0.12
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (5 bp):
AAATA
Found at i:88455117 original size:10 final size:10
Alignment explanation
Indices: 88455069--88455117 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
88455059 AGCCTTAAAT
88455069 TAAATAAAATA
1 TAAATAAAA-A
*
88455080 TAAATAAATA
1 TAAATAAAAA
*
88455090 -AAATAAAAT
1 TAAATAAAAA
88455099 TAAATAAAAA
1 TAAATAAAAA
*
88455109 TAACTAAAA
1 TAAATAAAA
88455118 CTGAAATTCA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
9 7 0.22
10 17 0.53
11 8 0.25
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (10 bp):
TAAATAAAAA
Found at i:88473805 original size:38 final size:38
Alignment explanation
Indices: 88473725--88473805 Score: 101
Period size: 38 Copynumber: 2.1 Consensus size: 38
88473715 CGCGTGATTT
* * **
88473725 AATAAGCATATTATTCATGTTACTATTTTTAGTGATTT
1 AATAAGCATATTATTCATGTTACTATTGTTAGTCATGA
*
88473763 AATAAGCATATTATTCATGTTATTATTGTTA-TACATGA
1 AATAAGCATATTATTCATGTTACTATTGTTAGT-CATGA
88473801 AATAA
1 AATAA
88473806 TTTTACTATG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 1 0.03
38 36 0.97
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.46
Consensus pattern (38 bp):
AATAAGCATATTATTCATGTTACTATTGTTAGTCATGA
Found at i:88490281 original size:42 final size:43
Alignment explanation
Indices: 88490212--88490325 Score: 106
Period size: 43 Copynumber: 2.7 Consensus size: 43
88490202 CATCGACTTA
* * *
88490212 TGATTTACGTGTAAGACCATTTATGGGACA-TCAGCATC-CTATT
1 TGATTT-CATGTAAGACCATGTATGGGACAGTCA-CATCGATATT
* * * *
88490255 TGATTTCATGTAAGACCCTGTCTGGGATAGTGACATCGATATT
1 TGATTTCATGTAAGACCATGTATGGGACAGTCACATCGATATT
* * *
88490298 TGATTACATGTAAGACCACGTTTGGGAC
1 TGATTTCATGTAAGACCATGTATGGGAC
88490326 GTTGGCATTG
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
42 22 0.39
43 35 0.61
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (43 bp):
TGATTTCATGTAAGACCATGTATGGGACAGTCACATCGATATT
Found at i:88491066 original size:12 final size:11
Alignment explanation
Indices: 88491045--88491087 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 11
88491035 TAATGAATCT
88491045 TATGTTTTGGG
1 TATGTTTTGGG
*
88491056 TATGATTTTGGAT
1 TATG-TTTTGG-G
88491069 TATGTTTT-GG
1 TATGTTTTGGG
88491079 TATGTTTTG
1 TATGTTTTG
88491088 ATTTAGATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
10 8 0.30
11 5 0.19
12 10 0.37
13 4 0.15
ACGTcount: A:0.14, C:0.00, G:0.28, T:0.58
Consensus pattern (11 bp):
TATGTTTTGGG
Found at i:88491071 original size:24 final size:22
Alignment explanation
Indices: 88491044--88491087 Score: 70
Period size: 24 Copynumber: 1.9 Consensus size: 22
88491034 GTAATGAATC
88491044 TTATGTTTTGGGTATGATTTTGGA
1 TTATGTTTT-GGTATG-TTTTGGA
88491068 TTATGTTTTGGTATGTTTTG
1 TTATGTTTTGGTATGTTTTG
88491088 ATTTAGATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 5 0.25
23 6 0.30
24 9 0.45
ACGTcount: A:0.14, C:0.00, G:0.27, T:0.59
Consensus pattern (22 bp):
TTATGTTTTGGTATGTTTTGGA
Found at i:88495761 original size:14 final size:15
Alignment explanation
Indices: 88495738--88495767 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
88495728 AAGAGAATGG
88495738 AAATGAACAGAGGGA
1 AAATGAACAGAGGGA
88495753 AAATG-ACAGAGGGA
1 AAATGAACAGAGGGA
88495767 A
1 A
88495768 TTTACAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.53, C:0.07, G:0.33, T:0.07
Consensus pattern (15 bp):
AAATGAACAGAGGGA
Found at i:88495808 original size:13 final size:13
Alignment explanation
Indices: 88495790--88495814 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
88495780 TTAAACACAA
88495790 GGGAAATGAACAT
1 GGGAAATGAACAT
88495803 GGGAAATGAACA
1 GGGAAATGAACA
88495815 AGTTTACAAA
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:0.48, C:0.08, G:0.32, T:0.12
Consensus pattern (13 bp):
GGGAAATGAACAT
Found at i:88497067 original size:2 final size:2
Alignment explanation
Indices: 88497060--88497093 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
88497050 CATTCTGAAG
* *
88497060 TA TA TA TA TA TA TA TA CA TA TA TA TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
88497094 CACAAGTATG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:88497103 original size:18 final size:18
Alignment explanation
Indices: 88497061--88497097 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
88497051 ATTCTGAAGT
* *
88497061 ATATATATATATATACAT
1 ATATATGTATATATACAC
88497079 ATATATGTATATATACAC
1 ATATATGTATATATACAC
88497097 A
1 A
88497098 AGTATGCCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.41
Consensus pattern (18 bp):
ATATATGTATATATACAC
Found at i:88497686 original size:28 final size:28
Alignment explanation
Indices: 88497545--88497836 Score: 308
Period size: 28 Copynumber: 10.5 Consensus size: 28
88497535 CATGAGATTG
* * *
88497545 GCACTAAGTGTGCGGGTTTAAAT-TGTACA
1 GCACTAAGTGTGCGAGTTTGACTATGT--A
*
88497574 GCACTAAGTGTGCGA-TTTGACTATGTT
1 GCACTAAGTGTGCGAGTTTGACTATGTA
** *
88497601 GCACTAAGTGTGCGA-AATGAATATG-A
1 GCACTAAGTGTGCGAGTTTGACTATGTA
* * **
88497627 TGCACTAAGTGTGCGA-ATTGACCATGCG
1 -GCACTAAGTGTGCGAGTTTGACTATGTA
88497655 GCACTAAGTGTGCGAGTTTGACTATGTA
1 GCACTAAGTGTGCGAGTTTGACTATGTA
* *
88497683 GCACTAAGTGTGCGAGCTTGATTATGTA
1 GCACTAAGTGTGCGAGTTTGACTATGTA
* *
88497711 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGACTATGTA
* * *
88497739 GCACTAAGTGTGCAAGTTTGATTATGTT
1 GCACTAAGTGTGCGAGTTTGACTATGTA
* * *
88497767 TCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGACTATGTA
*
88497795 GCACTAAGTGTGCGAGTTCGACTAT-TAA
1 GCACTAAGTGTGCGAGTTTGACTATGT-A
88497823 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
88497837 GGCTTATTAT
Statistics
Matches: 228, Mismatches: 30, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
27 60 0.26
28 151 0.66
29 17 0.07
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGACTATGTA
Found at i:88497765 original size:84 final size:84
Alignment explanation
Indices: 88497545--88497836 Score: 342
Period size: 84 Copynumber: 3.5 Consensus size: 84
88497535 CATGAGATTG
* * * *
88497545 GCACTAAGTGTGCGGGTTTAAATTGTACAGCACTAAGTGTGCGA-TTTGACTATGTTGCACTAAG
1 GCACTAAGTGTGCGAGTTT-GACTATACAGCACTAAGTGTGCGAGTTTGACTATGTTGCACTAAG
* *
88497609 TGTGCGA-AATGAATATG-A
65 TGTGCGAGATTGATTATGTA
* * * * *
88497627 TGCACTAAGTGTGCGA-ATTGACCATGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAG
1 -GCACTAAGTGTGCGAGTTTGACTATACAGCACTAAGTGTGCGAGTTTGACTATGTTGCACTAAG
*
88497691 TGTGCGAGCTTGATTATGTA
65 TGTGCGAGATTGATTATGTA
* * * * *
88497711 GCACTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCAAGTTTGATTATGTTTCACTAAGT
1 GCACTAAGTGTGCGAGTTTGACTATACAGCACTAAGTGTGCGAGTTTGACTATGTTGCACTAAGT
* *
88497776 GTGCGAGTTTGATTATATA
66 GTGCGAGATTGATTATGTA
*
88497795 GCACTAAGTGTGCGAGTTCGACTATTA-AGCACTAAGTGTGCG
1 GCACTAAGTGTGCGAGTTTGACTA-TACAGCACTAAGTGTGCG
88497837 GGCTTATTAT
Statistics
Matches: 177, Mismatches: 27, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
81 18 0.10
82 28 0.16
83 36 0.20
84 93 0.53
85 2 0.01
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32
Consensus pattern (84 bp):
GCACTAAGTGTGCGAGTTTGACTATACAGCACTAAGTGTGCGAGTTTGACTATGTTGCACTAAGT
GTGCGAGATTGATTATGTA
Found at i:88507940 original size:93 final size:93
Alignment explanation
Indices: 88507828--88507998 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
88507818 GCCCATAAGT
* *
88507828 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
88507893 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
*
88507921 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
88507986 CGAGTTCGGATGC
66 CGAGCTCGGATGC
88507999 TCAACCATCC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:88507995 original size:46 final size:46
Alignment explanation
Indices: 88507820--88507995 Score: 214
Period size: 46 Copynumber: 3.8 Consensus size: 46
88507810 TGTAACCCGC
* *
88507820 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
88507866 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T
* *** *
88507912 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
88507959 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
88507996 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
46 70 0.63
47 32 0.29
49 4 0.04
50 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:88510430 original size:30 final size:30
Alignment explanation
Indices: 88510386--88510474 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
88510376 CAAAGATAAC
88510386 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* *
88510415 GAGAAACCCAGAATAAAGAAATCC-AGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * * *
88510445 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
88510475 CGATACTATG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
29 9 0.18
30 39 0.78
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Found at i:88510434 original size:15 final size:15
Alignment explanation
Indices: 88510386--88510465 Score: 92
Period size: 15 Copynumber: 5.4 Consensus size: 15
88510376 CAAAGATAAC
*
88510386 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
88510400 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
88510415 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
88510430 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
88510445 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
88510460 AAGAAA
1 AAGAAA
88510466 CCCAAGATAC
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
14 9 0.16
15 45 0.82
16 1 0.02
ACGTcount: A:0.59, C:0.14, G:0.17, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:88510474 original size:15 final size:15
Alignment explanation
Indices: 88510397--88510474 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 15
88510387 AGAAAACCGA
88510397 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
88510412 ATAGAGAAA-CCCAG
1 ATAAAGAAATCCAAG
88510426 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
88510441 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
88510457 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
88510472 ATA
1 ATA
88510475 CGATACTATG
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
14 4 0.08
15 45 0.87
16 3 0.06
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:88513554 original size:93 final size:93
Alignment explanation
Indices: 88513442--88513612 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
88513432 GCCCATAAGT
* *
88513442 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
88513507 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
88513535 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
88513600 CGAGTTCGGATGC
66 CGAGTTCGGATGC
88513613 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:88513609 original size:46 final size:46
Alignment explanation
Indices: 88513434--88513609 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
88513424 TGTAACCCGC
* * *
88513434 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
88513480 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
88513530 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
88513573 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
88513610 TGCTCAACCA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 64 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:88516071 original size:22 final size:21
Alignment explanation
Indices: 88516046--88516086 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
88516036 GATAACCCCA
*
88516046 TCCAACCCTGCACTTGCCTGCG
1 TCCAACCCTACACTT-CCTGCG
*
88516068 TCCATCCCTACACTTCCTG
1 TCCAACCCTACACTTCCTG
88516087 TGGGGAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.15, C:0.46, G:0.12, T:0.27
Consensus pattern (21 bp):
TCCAACCCTACACTTCCTGCG
Found at i:88517428 original size:14 final size:14
Alignment explanation
Indices: 88517403--88517445 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
88517393 GCTATAGGGG
*
88517403 AGAA-AAGAAAAACA
1 AGAAGAAGAAAAA-T
88517417 AGAAGAAGAAAAAT
1 AGAAGAAGAAAAAT
88517431 AGAAGAAGAGAAAAT
1 AGAAGAAGA-AAAAT
88517446 GAAAAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 13 0.50
15 13 0.50
ACGTcount: A:0.72, C:0.02, G:0.21, T:0.05
Consensus pattern (14 bp):
AGAAGAAGAAAAAT
Found at i:88518755 original size:19 final size:18
Alignment explanation
Indices: 88518718--88518761 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
88518708 ATACATGCAG
88518718 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
88518735 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTAATAA
*
88518754 TACTAATT
1 TAATAATT
88518762 AAAATTTCGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 14 0.61
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:88518783 original size:18 final size:19
Alignment explanation
Indices: 88518760--88518796 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
88518750 ATAATACTAA
*
88518760 TTAAAAT-TTCGTAAAAAT
1 TTAAAATATCCGTAAAAAT
88518778 TTAAAATATCCGTAAAAAT
1 TTAAAATATCCGTAAAAAT
88518797 AAATACAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.35
Consensus pattern (19 bp):
TTAAAATATCCGTAAAAAT
Done.