Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 124041150
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: 124041150
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 335 characters in sequence are not A, C, G, or T
File 48 of 410
Found at i:12343320 original size:34 final size:34
Alignment explanation
Indices: 12343276--12343341 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
12343266 TGCTTTTTTA
*
12343276 ACTTTTTAAAAATA-TTATTGAGACAAAAAAAAAG
1 ACTTTATAAAAATACTTATTGA-ACAAAAAAAAAG
* *
12343310 ACTTTATAAAAATACTTTTTTAACAAAAAAAA
1 ACTTTATAAAAATACTTATTGAACAAAAAAAA
12343342 CAGAAGGATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 23 0.82
35 5 0.18
ACGTcount: A:0.56, C:0.08, G:0.05, T:0.32
Consensus pattern (34 bp):
ACTTTATAAAAATACTTATTGAACAAAAAAAAAG
Found at i:12344320 original size:24 final size:25
Alignment explanation
Indices: 12344271--12344327 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
12344261 GTCACATCAG
*
12344271 TTTTCAACAAGAAAAATGAATGTAA
1 TTTTTAACAAGAAAAATGAATGTAA
* *
12344296 TTTTTAACAA-AAAAATTAATTTAA
1 TTTTTAACAAGAAAAATGAATGTAA
*
12344320 TTATTAAC
1 TTTTTAAC
12344328 CCAACATATA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 19 0.68
25 9 0.32
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.37
Consensus pattern (25 bp):
TTTTTAACAAGAAAAATGAATGTAA
Found at i:12345409 original size:3 final size:3
Alignment explanation
Indices: 12345401--12345453 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
12345391 TTTTTACCCT
12345401 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
12345449 TAA TA
1 TAA TA
12345454 TACCATATCA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:12345921 original size:12 final size:13
Alignment explanation
Indices: 12345904--12345936 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
12345894 TAAGGTTTAA
12345904 GGTTTGAGTTT-G
1 GGTTTGAGTTTGG
*
12345916 GGTTTGGGTTTGG
1 GGTTTGAGTTTGG
12345929 GGTTTGAG
1 GGTTTGAG
12345937 GTTAAGTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 10 0.56
13 8 0.44
ACGTcount: A:0.06, C:0.00, G:0.48, T:0.45
Consensus pattern (13 bp):
GGTTTGAGTTTGG
Found at i:12346533 original size:14 final size:13
Alignment explanation
Indices: 12346510--12346557 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
12346500 AAACCTAACC
12346510 AAATTATAAACACT
1 AAATT-TAAACACT
*
12346524 AAATTCTAAACTCT
1 AAATT-TAAACACT
*
12346538 AAATATGAAACACT
1 AAAT-TTAAACACT
12346552 AAATTT
1 AAATTT
12346558 TACTCAAGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
13 1 0.04
14 26 0.93
15 1 0.04
ACGTcount: A:0.52, C:0.15, G:0.02, T:0.31
Consensus pattern (13 bp):
AAATTTAAACACT
Found at i:12347484 original size:20 final size:21
Alignment explanation
Indices: 12347459--12347502 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
12347449 AATTACTTAA
12347459 TTTTAAAAAATTAT-ATAATT
1 TTTTAAAAAATTATAATAATT
* *
12347479 TTTTAAATAATTTTAATAATT
1 TTTTAAAAAATTATAATAATT
12347500 TTT
1 TTT
12347503 ATATTTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTAAAAAATTATAATAATT
Found at i:12351567 original size:12 final size:12
Alignment explanation
Indices: 12351552--12351602 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 12
12351542 TTTTTAATAA
12351552 ATTTTTTTTGTT
1 ATTTTTTTTGTT
**
12351564 ATTTTTGCTGTT
1 ATTTTTTTTGTT
*
12351576 ATTTTTTTT-AT
1 ATTTTTTTTGTT
*
12351587 A-TTTTATTGTT
1 ATTTTTTTTGTT
12351598 ATTTT
1 ATTTT
12351603 CTCACTTTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
10 6 0.20
11 4 0.13
12 20 0.67
ACGTcount: A:0.14, C:0.02, G:0.08, T:0.76
Consensus pattern (12 bp):
ATTTTTTTTGTT
Found at i:12351568 original size:11 final size:11
Alignment explanation
Indices: 12351554--12351602 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
12351544 TTTAATAAAT
12351554 TTTTTTTGTTA
1 TTTTTTTGTTA
*
12351565 TTTTTGCTGTTA
1 TTTTT-TTGTTA
12351577 TTTTTTT-TATA
1 TTTTTTTGT-TA
*
12351588 TTTTATTGTTA
1 TTTTTTTGTTA
12351599 TTTT
1 TTTT
12351603 CTCACTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
10 1 0.03
11 20 0.62
12 11 0.34
ACGTcount: A:0.12, C:0.02, G:0.08, T:0.78
Consensus pattern (11 bp):
TTTTTTTGTTA
Found at i:12351580 original size:22 final size:22
Alignment explanation
Indices: 12351555--12351602 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
12351545 TTAATAAATT
*
12351555 TTTTTTGTTAT-TTTTGCTGTTA
1 TTTTTT-TTATATTTTACTGTTA
*
12351577 TTTTTTTTATATTTTATTGTTA
1 TTTTTTTTATATTTTACTGTTA
12351599 TTTT
1 TTTT
12351603 CTCACTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.12, C:0.02, G:0.08, T:0.77
Consensus pattern (22 bp):
TTTTTTTTATATTTTACTGTTA
Found at i:12351628 original size:11 final size:11
Alignment explanation
Indices: 12351574--12351645 Score: 53
Period size: 11 Copynumber: 6.9 Consensus size: 11
12351564 ATTTTTGCTG
12351574 TTATT-TTTT-
1 TTATTATTTTA
12351583 TTA-TATTTTA
1 TTATTATTTTA
* *
12351593 TTGTTATTTTC
1 TTATTATTTTA
* * *
12351604 TCACT-TTTTG
1 TTATTATTTTA
12351614 TTATTATTTTA
1 TTATTATTTTA
* *
12351625 TTATTATATTG
1 TTATTATTTTA
12351636 TTATTATTTT
1 TTATTATTTT
12351646 TTTTGTTAAT
Statistics
Matches: 47, Mismatches: 12, Indels: 6
0.72 0.18 0.09
Matches are distributed among these distances:
8 1 0.02
9 7 0.15
10 9 0.19
11 30 0.64
ACGTcount: A:0.19, C:0.04, G:0.04, T:0.72
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:12356250 original size:14 final size:15
Alignment explanation
Indices: 12356219--12356266 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
12356209 GTTCGGTTCG
12356219 TTTTTAAAATATATT
1 TTTTTAAAATATATT
*
12356234 TTTTTAAAATTTATT
1 TTTTTAAAATATATT
* **
12356249 TTTTGAACCTATATT
1 TTTTTAAAATATATT
12356264 TTT
1 TTT
12356267 ACCTTAATTC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.62
Consensus pattern (15 bp):
TTTTTAAAATATATT
Found at i:12356746 original size:30 final size:30
Alignment explanation
Indices: 12356701--12356762 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
12356691 CTTAACAAGT
*
12356701 AAATGCCTCTAAAATAATAAAAAAATTAAC
1 AAATACCTCTAAAATAATAAAAAAATTAAC
* *
12356731 AAATACCTTTAAAATAATAACAAAATTAAC
1 AAATACCTCTAAAATAATAAAAAAATTAAC
12356761 AA
1 AA
12356763 TAAAATAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.61, C:0.13, G:0.02, T:0.24
Consensus pattern (30 bp):
AAATACCTCTAAAATAATAAAAAAATTAAC
Found at i:12364683 original size:13 final size:13
Alignment explanation
Indices: 12364667--12364694 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
12364657 ACACGGCCAA
12364667 GTCACACGCCCGT
1 GTCACACGCCCGT
12364680 GTCACACGCCCGT
1 GTCACACGCCCGT
12364693 GT
1 GT
12364695 GCTAGGCCGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.43, G:0.25, T:0.18
Consensus pattern (13 bp):
GTCACACGCCCGT
Found at i:12365793 original size:43 final size:41
Alignment explanation
Indices: 12365730--12365883 Score: 191
Period size: 42 Copynumber: 3.7 Consensus size: 41
12365720 TACCATACCA
* * *
12365730 ATGCCATATCCCAGATATGGTCTTACATGTAATCTTATATCG
1 ATGCCATATCCTAGATATGGTCTTACATG-AATCTCATATTG
* *
12365772 ATGCCAATAGCCTAGCTATGGTCTTACATGAAATCTCATATTG
1 ATGCC-ATATCCTAGATATGGTCTTACATG-AATCTCATATTG
* * *
12365815 ATGTCATATCCCAGATATGGTCTTACACGAAGTCTCATATTG
1 ATGCCATATCCTAGATATGGTCTTACATGAA-TCTCATATTG
*
12365857 ATGCCATATCTTAGATATGGTCTTACA
1 ATGCCATATCCTAGATATGGTCTTACA
12365884 CATAGACTTA
Statistics
Matches: 96, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
41 2 0.02
42 59 0.61
43 35 0.36
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (41 bp):
ATGCCATATCCTAGATATGGTCTTACATGAATCTCATATTG
Found at i:12370846 original size:33 final size:33
Alignment explanation
Indices: 12370809--12370872 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
12370799 GCCCAGCGCT
*
12370809 AGTCGGATGAACCGACAATTTTTGCCCAGCATG
1 AGTCGGATGAACCGACAATTTGTGCCCAGCATG
12370842 AGTCGGATGAACCGACAATTTGTGCCCAGCA
1 AGTCGGATGAACCGACAATTTGTGCCCAGCA
12370873 CTGGGCAGAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.22
Consensus pattern (33 bp):
AGTCGGATGAACCGACAATTTGTGCCCAGCATG
Found at i:12374513 original size:32 final size:33
Alignment explanation
Indices: 12374477--12374552 Score: 86
Period size: 33 Copynumber: 2.3 Consensus size: 33
12374467 GCCCTGCCAC
* *
12374477 GGTCTTACACTC-GAGTGCCATAACCC-AGTTAT
1 GGTCTTACACTCAGAATGCCATAACCCAACTT-T
*
12374509 GGTCTTAC-CATCAGAATGCCATAGCCCAACTTT
1 GGTCTTACAC-TCAGAATGCCATAACCCAACTTT
12374542 GGTCTTACACT
1 GGTCTTACACT
12374553 TATACATATA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
31 1 0.03
32 10 0.27
33 22 0.59
34 4 0.11
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.29
Consensus pattern (33 bp):
GGTCTTACACTCAGAATGCCATAACCCAACTTT
Found at i:12377378 original size:24 final size:24
Alignment explanation
Indices: 12377332--12377378 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
12377322 ACATCCATTA
* *
12377332 TGAAATTTAATTAAAGAATATTTT
1 TGAAATTTAAATAAACAATATTTT
12377356 TGAAATTTTAAATAAACAA-ATTT
1 TGAAA-TTTAAATAAACAATATTT
12377379 CTTAAGTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (24 bp):
TGAAATTTAAATAAACAATATTTT
Found at i:12378648 original size:20 final size:20
Alignment explanation
Indices: 12378619--12378656 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12378609 ATAATTATAT
* *
12378619 TAATTGTATATGTTAAATAA
1 TAATTATATATATTAAATAA
12378639 TAATTATATATATTAAAT
1 TAATTATATATATTAAAT
12378657 CATTAAGCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (20 bp):
TAATTATATATATTAAATAA
Found at i:12379386 original size:24 final size:24
Alignment explanation
Indices: 12379358--12379423 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
12379348 CATAATTTCT
12379358 TTTTTATATTAAAATATATATTTTG
1 TTTTT-TATTAAAATATATATTTTG
* *
12379383 TTTTTTAATAAAATAT-TATTTTT
1 TTTTTTATTAAAATATATATTTTG
12379406 TATTTTTATTAAAA-ATAT
1 T-TTTTTATTAAAATATAT
12379424 TTAAATTTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
23 9 0.25
24 22 0.61
25 5 0.14
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
TTTTTTATTAAAATATATATTTTG
Found at i:12379694 original size:13 final size:13
Alignment explanation
Indices: 12379676--12379734 Score: 51
Period size: 13 Copynumber: 5.0 Consensus size: 13
12379666 CACCCACCGG
12379676 AAGAGAGAAAGAA
1 AAGAGAGAAAGAA
12379689 AAGAGAGAAAG--
1 AAGAGAGAAAGAA
*
12379700 GAGA-AGAAA-AA
1 AAGAGAGAAAGAA
12379711 AAGA-AG-AAGAA
1 AAGAGAGAAAGAA
12379722 AA-AGAAGAAAGAA
1 AAGAG-AGAAAGAA
12379735 TAAAAAAAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
10 8 0.21
11 12 0.32
12 2 0.05
13 16 0.42
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (13 bp):
AAGAGAGAAAGAA
Found at i:12379708 original size:23 final size:24
Alignment explanation
Indices: 12379676--12379734 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 24
12379666 CACCCACCGG
12379676 AAGAGAGAAAGAAAAG-AG-AGAAA
1 AAGA-AGAAAGAAAAGAAGAAGAAA
*
12379699 GGAGAAGAAA-AAAAGAAGAAGAAA
1 -AAGAAGAAAGAAAAGAAGAAGAAA
12379723 AAGAAGAAAGAA
1 AAGAAGAAAGAA
12379735 TAAAAAAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
22 5 0.17
23 15 0.50
24 10 0.33
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (24 bp):
AAGAAGAAAGAAAAGAAGAAGAAA
Found at i:12379713 original size:14 final size:14
Alignment explanation
Indices: 12379683--12379747 Score: 60
Period size: 14 Copynumber: 4.5 Consensus size: 14
12379673 CGGAAGAGAG
* *
12379683 AAAGAA-AAGAGAG
1 AAAGAAGAAGAAAA
*
12379696 AAAGGAGAAGAAAA
1 AAAGAAGAAGAAAA
12379710 AAAGAAGAAGAAAA
1 AAAGAAGAAGAAAA
*
12379724 AGAAGAAAGAATAAAAA
1 A-AAG-AAGAA-GAAAA
12379741 AAAGAAG
1 AAAGAAG
12379748 GTAATGTATT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
13 5 0.12
14 19 0.44
15 6 0.14
16 8 0.19
17 5 0.12
ACGTcount: A:0.74, C:0.00, G:0.25, T:0.02
Consensus pattern (14 bp):
AAAGAAGAAGAAAA
Found at i:12379725 original size:12 final size:11
Alignment explanation
Indices: 12379701--12379731 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
12379691 GAGAGAAAGG
12379701 AGAAGAAAAAA
1 AGAAGAAAAAA
12379712 AGAAGAAGAAAA
1 AGAAGAA-AAAA
12379724 AGAAGAAA
1 AGAAGAAA
12379732 GAATAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (11 bp):
AGAAGAAAAAA
Found at i:12379734 original size:19 final size:19
Alignment explanation
Indices: 12379710--12379747 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
12379700 GAGAAGAAAA
*
12379710 AAAGAAGAAGAAAAAGAAG
1 AAAGAAGAAAAAAAAGAAG
*
12379729 AAAGAATAAAAAAAAGAAG
1 AAAGAAGAAAAAAAAGAAG
12379748 GTAATGTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (19 bp):
AAAGAAGAAAAAAAAGAAG
Found at i:12379984 original size:60 final size:61
Alignment explanation
Indices: 12379890--12380015 Score: 191
Period size: 60 Copynumber: 2.1 Consensus size: 61
12379880 TTTGTATGAA
* * * * *
12379890 TATAATTTTTTATTTTTTATAATTATTTTAAAATTAATTTGTTAGTAATTTAGGATTATGT
1 TATAATTTTTTAGTGTTTATAATCATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGT
*
12379951 TATAATTTTTT-GTGTTTGTAATCATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGT
1 TATAATTTTTTAGTGTTTATAATCATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGT
12380011 TATAA
1 TATAA
12380016 ATTGTTGCGT
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
60 48 0.81
61 11 0.19
ACGTcount: A:0.34, C:0.01, G:0.10, T:0.56
Consensus pattern (61 bp):
TATAATTTTTTAGTGTTTATAATCATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGT
Found at i:12382101 original size:33 final size:33
Alignment explanation
Indices: 12382061--12382209 Score: 163
Period size: 33 Copynumber: 4.5 Consensus size: 33
12382051 CTTGGCTCGT
* * *
12382061 TCCACCTCAGTACTCCGCTCCTTTCGGCCCGTA
1 TCCACCGCCGTACTCCACTCCTTTCGGCCCGTA
* ** * * *
12382094 TCCACCTCAATACTCCGCTCCTTTAGTCCCGTA
1 TCCACCGCCGTACTCCACTCCTTTCGGCCCGTA
*
12382127 TCCACCGCCGTACTCCACTCCTCTCGGCCCGTA
1 TCCACCGCCGTACTCCACTCCTTTCGGCCCGTA
* * * * *
12382160 TCCGCCACCGTATTCCACTCCTTCCAGCCCGTA
1 TCCACCGCCGTACTCCACTCCTTTCGGCCCGTA
12382193 TCCACCGCCGTACTCCA
1 TCCACCGCCGTACTCCA
12382210 TTCTTCTCGG
Statistics
Matches: 97, Mismatches: 19, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 97 1.00
ACGTcount: A:0.15, C:0.48, G:0.13, T:0.25
Consensus pattern (33 bp):
TCCACCGCCGTACTCCACTCCTTTCGGCCCGTA
Found at i:12382141 original size:66 final size:66
Alignment explanation
Indices: 12382061--12382220 Score: 187
Period size: 66 Copynumber: 2.4 Consensus size: 66
12382051 CTTGGCTCGT
* * * * * * *
12382061 TCCACCTCAGTACTCCGCTCCTTTCGGCCCGTATCCACCTCAATACTCCGCTCCTT-TAGTCCCG
1 TCCACCGCCGTACTCCACTCCTCTCGGCCCGTATCCACCACAATACTCCACTCCTTCCAG-CCCG
12382125 TA
65 TA
* ** *
12382127 TCCACCGCCGTACTCCACTCCTCTCGGCCCGTATCCGCCACCGTATTCCACTCCTTCCAGCCCGT
1 TCCACCGCCGTACTCCACTCCTCTCGGCCCGTATCCACCACAATACTCCACTCCTTCCAGCCCGT
12382192 A
66 A
* *
12382193 TCCACCGCCGTACTCCATTCTTCTCGGC
1 TCCACCGCCGTACTCCACTCCTCTCGGC
12382221 TCAAGTTCAT
Statistics
Matches: 80, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
66 78 0.98
67 2 0.03
ACGTcount: A:0.14, C:0.47, G:0.13, T:0.26
Consensus pattern (66 bp):
TCCACCGCCGTACTCCACTCCTCTCGGCCCGTATCCACCACAATACTCCACTCCTTCCAGCCCGT
A
Found at i:12383867 original size:20 final size:20
Alignment explanation
Indices: 12383842--12383887 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
12383832 GGTAAATACT
12383842 ATGGCACACCGGCACGCCTA
1 ATGGCACACCGGCACGCCTA
12383862 ATGGCACACCGGCACGCCTA
1 ATGGCACACCGGCACGCCTA
12383882 ATGGCA
1 ATGGCA
12383888 GCAATTAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.26, C:0.37, G:0.26, T:0.11
Consensus pattern (20 bp):
ATGGCACACCGGCACGCCTA
Found at i:12383979 original size:171 final size:171
Alignment explanation
Indices: 12383691--12384014 Score: 639
Period size: 171 Copynumber: 1.9 Consensus size: 171
12383681 ACGGATGTCC
12383691 ATGGCACACCGGCACGCCTAATGGCAGCAATTAATCTTTTCTCTCTATCGGAGATGATGCAAATA
1 ATGGCACACCGGCACGCCTAATGGCAGCAATTAATCTTTTCTCTCTATCGGAGATGATGCAAATA
*
12383756 TTATCGTTGCTAATAACATACTTCCGCAGGTTGGTAAGAAAGAATTCCATGATTCTATGTTCTCA
66 TTATCGTTGCTAATAACATACTTCCGCAGGTTGGTAAGAAAGAATCCCATGATTCTATGTTCTCA
12383821 TTATCGATAATGGTAAATACTATGGCACACCGGCACGCCTA
131 TTATCGATAATGGTAAATACTATGGCACACCGGCACGCCTA
12383862 ATGGCACACCGGCACGCCTAATGGCAGCAATTAATCTTTTCTCTCTATCGGAGATGATGCAAATA
1 ATGGCACACCGGCACGCCTAATGGCAGCAATTAATCTTTTCTCTCTATCGGAGATGATGCAAATA
12383927 TTATCGTTGCTAATAACATACTTCCGCAGGTTGGTAAGAAAGAATCCCATGATTCTATGTTCTCA
66 TTATCGTTGCTAATAACATACTTCCGCAGGTTGGTAAGAAAGAATCCCATGATTCTATGTTCTCA
12383992 TTATCGATAATGGTAAATACTAT
131 TTATCGATAATGGTAAATACTAT
12384015 TGGGAGCACG
Statistics
Matches: 152, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
171 152 1.00
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.30
Consensus pattern (171 bp):
ATGGCACACCGGCACGCCTAATGGCAGCAATTAATCTTTTCTCTCTATCGGAGATGATGCAAATA
TTATCGTTGCTAATAACATACTTCCGCAGGTTGGTAAGAAAGAATCCCATGATTCTATGTTCTCA
TTATCGATAATGGTAAATACTATGGCACACCGGCACGCCTA
Found at i:12387735 original size:34 final size:35
Alignment explanation
Indices: 12387692--12387765 Score: 141
Period size: 34 Copynumber: 2.1 Consensus size: 35
12387682 ACATAAAATT
12387692 AAGATAATTAGTATAGATTTAAATATGCAATTAGA
1 AAGATAATTAGTATAGATTTAAATATGCAATTAGA
12387727 AAGA-AATTAGTATAGATTTAAATATGCAATTAGA
1 AAGATAATTAGTATAGATTTAAATATGCAATTAGA
12387761 AAGAT
1 AAGAT
12387766 GAGTAAAAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
34 34 0.89
35 4 0.11
ACGTcount: A:0.50, C:0.03, G:0.15, T:0.32
Consensus pattern (35 bp):
AAGATAATTAGTATAGATTTAAATATGCAATTAGA
Found at i:12388124 original size:9 final size:9
Alignment explanation
Indices: 12388088--12388126 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
12388078 AACTGGTTCT
12388088 ATTAAAAAA
1 ATTAAAAAA
*
12388097 A-TATTAAAA
1 ATTA-AAAAA
12388106 ATTAAAAAA
1 ATTAAAAAA
12388115 ATTAAAAAA
1 ATTAAAAAA
12388124 ATT
1 ATT
12388127 CATTGCAACC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
8 2 0.08
9 22 0.85
10 2 0.08
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (9 bp):
ATTAAAAAA
Found at i:12391656 original size:2 final size:2
Alignment explanation
Indices: 12391649--12391685 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
12391639 ACTCTTCTAC
12391649 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12391686 TCCTCCACCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12395963 original size:16 final size:16
Alignment explanation
Indices: 12395942--12395972 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12395932 TTCACTATTA
*
12395942 TGTCTTTTGTATTTTC
1 TGTCTTTTATATTTTC
12395958 TGTCTTTTATATTTT
1 TGTCTTTTATATTTT
12395973 GCATACAGAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.10, G:0.10, T:0.71
Consensus pattern (16 bp):
TGTCTTTTATATTTTC
Found at i:12399176 original size:20 final size:20
Alignment explanation
Indices: 12399151--12399190 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
12399141 CTCTTGAAAT
12399151 AGGGCACACA-CCCGTGTGGA
1 AGGGCA-ACAGCCCGTGTGGA
12399171 AGGGCAACATGCCCGTGTGG
1 AGGGCAACA-GCCCGTGTGG
12399191 TCATTATAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.17
20 6 0.33
21 9 0.50
ACGTcount: A:0.23, C:0.28, G:0.38, T:0.12
Consensus pattern (20 bp):
AGGGCAACAGCCCGTGTGGA
Found at i:12400413 original size:47 final size:49
Alignment explanation
Indices: 12400344--12400467 Score: 164
Period size: 47 Copynumber: 2.6 Consensus size: 49
12400334 ATAGGGTATA
* * ** *
12400344 ATGCCATGTCCCAGACATGGTCTTACATTGGCTCA-T-CCATT-AAGTCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGACT-ATTGAAATTGAAGCCG
*
12400391 ATGCCATGTCCCAGACATGGTCTTACACTGACTATTGAAATTGAGGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGACTATTGAAATTGAAGCCG
12400440 ATGCCATGTCCCAGACATGGTCTTACAC
1 ATGCCATGTCCCAGACATGGTCTTACAC
12400468 CAGCACTCAC
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
46 1 0.01
47 32 0.47
48 3 0.04
49 32 0.47
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.27
Consensus pattern (49 bp):
ATGCCATGTCCCAGACATGGTCTTACACTGACTATTGAAATTGAAGCCG
Found at i:12400461 original size:49 final size:47
Alignment explanation
Indices: 12400344--12400520 Score: 167
Period size: 50 Copynumber: 3.7 Consensus size: 47
12400334 ATAGGGTATA
* * ** *
12400344 ATGCCATGTCCCAGACATGGTCTTACATTGGCTCATCCATTAAGTCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGACTCATAAATTAAGCCG
*
12400391 ATGCCATGTCCCAGACATGGTCTTACACTGACT-ATTGAAATTGAGGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGACTCA-T-AAATT-AAGCCG
* * * ***
12400440 ATGCCATGTCCCAGACATGGTCTTACACCAGCACTCACATATCCGTGCCG
1 ATGCCATGTCCCAGACATGGTCTTACA-CTG-ACTCATAAAT-TAAGCCG
* *
12400490 ATGCCATGTACTAGACATGGTCTTACACTGA
1 ATGCCATGTCCCAGACATGGTCTTACACTGA
12400521 GATGTATGTC
Statistics
Matches: 108, Mismatches: 15, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
46 1 0.01
47 32 0.30
48 4 0.04
49 33 0.31
50 34 0.31
51 3 0.03
52 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (47 bp):
ATGCCATGTCCCAGACATGGTCTTACACTGACTCATAAATTAAGCCG
Found at i:12400596 original size:46 final size:46
Alignment explanation
Indices: 12400526--12400684 Score: 198
Period size: 46 Copynumber: 3.5 Consensus size: 46
12400516 ACTGAGATGT
*
12400526 ATGTCCCAGACATGTCTTACACTGGCTTATATCTAAAGGCCAATGC
1 ATGTCCCAAACATGTCTTACACTGGCTTATATCTAAAGGCCAATGC
* * * * *
12400572 ATATCCCAAACATGTCTTACACTGGC---TCTCGTAATGTGGCCGATAC
1 ATGTCCCAAACATGTCTTACACTGGCTTATATC-TAA--AGGCCAATGC
* *
12400618 ATGTCCCAGACATGTCTTACACTGGCTTATATCTAGAGGCCAATGC
1 ATGTCCCAAACATGTCTTACACTGGCTTATATCTAAAGGCCAATGC
12400664 ATGTCCCAAACATGTCTTACA
1 ATGTCCCAAACATGTCTTACA
12400685 TTAGCACATA
Statistics
Matches: 93, Mismatches: 14, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
43 3 0.03
44 3 0.03
46 82 0.88
48 2 0.02
49 3 0.03
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (46 bp):
ATGTCCCAAACATGTCTTACACTGGCTTATATCTAAAGGCCAATGC
Found at i:12411685 original size:43 final size:42
Alignment explanation
Indices: 12411638--12411767 Score: 127
Period size: 43 Copynumber: 3.0 Consensus size: 42
12411628 TTACATATTT
* * *
12411638 TCATATACCGATGCCAACGTCCCAGACGTGCTCTTACATGAAA
1 TCATATA-CGATGCCAATGTCCCAGACATGGTCTTACATGAAA
* * * * *
12411681 TCATATAATGATGTCAATGTCTCAAACATGGTCTTACA-CATAA
1 TCATAT-ACGATGCCAATGTCCCAGACATGGTCTTACATGA-AA
* *
12411724 TCACAATACAATGCCAATGTCCCAGACATGGTCTTACATGAAA
1 TCA-TATACGATGCCAATGTCCCAGACATGGTCTTACATGAAA
12411767 T
1 T
12411768 ATCATCTCGA
Statistics
Matches: 68, Mismatches: 15, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
42 1 0.01
43 63 0.93
44 4 0.06
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.27
Consensus pattern (42 bp):
TCATATACGATGCCAATGTCCCAGACATGGTCTTACATGAAA
Found at i:12424186 original size:12 final size:12
Alignment explanation
Indices: 12424169--12424194 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12424159 TCATAACATC
12424169 AAGATTAAGAGA
1 AAGATTAAGAGA
12424181 AAGATTAAGAGA
1 AAGATTAAGAGA
12424193 AA
1 AA
12424195 ACTTTGAGGG
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:0.62, C:0.00, G:0.23, T:0.15
Consensus pattern (12 bp):
AAGATTAAGAGA
Found at i:12426578 original size:31 final size:31
Alignment explanation
Indices: 12426540--12426618 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
12426530 TTTAACGGTT
12426540 ACTGGGCCGAAGCCTTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
* *
12426571 ACTGGGCCAAAGCCTTTTCATAAATCATTTC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
*
12426602 ACTAGGCCGAAGCCTTT
1 ACTGGGCCGAAGCCTTT
12426619 ACTGTAAACG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (31 bp):
ACTGGGCCGAAGCCTTTTCATAAATCATATC
Found at i:12426689 original size:42 final size:42
Alignment explanation
Indices: 12426642--12426733 Score: 130
Period size: 42 Copynumber: 2.2 Consensus size: 42
12426632 TGGCCCATAG
* ** *
12426642 GCCCATTTCAATATCACATGTAATGTCAATGGATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
* *
12426684 GCCCATTCCAATATCATATGAAATACCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
12426726 GCCCATTT
1 GCCCATTT
12426734 GGGGAGACTA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
Found at i:12426932 original size:26 final size:26
Alignment explanation
Indices: 12426866--12426977 Score: 156
Period size: 26 Copynumber: 4.3 Consensus size: 26
12426856 CTGGAGGCCT
* *
12426866 AGCCCTTTTCGGTAACCTGGGGCA-A
1 AGCCCTTTTCGATAAACTGGGGCATA
*
12426891 AGCCCTTTTCAATAAACTGGGGCATA
1 AGCCCTTTTCGATAAACTGGGGCATA
*
12426917 AGCCCCTTTT-GGTAAACTGGGGCATA
1 AG-CCCTTTTCGATAAACTGGGGCATA
*
12426943 AGCCCTTTTCAATAAACTGGGGCATA
1 AGCCCTTTTCGATAAACTGGGGCATA
12426969 AGCCCTTTT
1 AGCCCTTTT
12426978 GCACTTCCTC
Statistics
Matches: 77, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
25 28 0.36
26 42 0.55
27 7 0.09
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.28
Consensus pattern (26 bp):
AGCCCTTTTCGATAAACTGGGGCATA
Found at i:12426950 original size:52 final size:50
Alignment explanation
Indices: 12426866--12426978 Score: 190
Period size: 52 Copynumber: 2.2 Consensus size: 50
12426856 CTGGAGGCCT
*
12426866 AGCCCTTTTCGGTAACCTGGGGCAAAGCCCTTTTCAATAAACTGGGGCATA
1 AGCCCTTTT-GGTAAACTGGGGCAAAGCCCTTTTCAATAAACTGGGGCATA
12426917 AGCCCCTTTTGGTAAACTGGGGCATAAGCCCTTTTCAATAAACTGGGGCATA
1 AG-CCCTTTTGGTAAACTGGGGCA-AAGCCCTTTTCAATAAACTGGGGCATA
12426969 AGCCCTTTTG
1 AGCCCTTTTG
12426979 CACTTCCTCC
Statistics
Matches: 59, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
51 23 0.39
52 36 0.61
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (50 bp):
AGCCCTTTTGGTAAACTGGGGCAAAGCCCTTTTCAATAAACTGGGGCATA
Found at i:12427052 original size:20 final size:20
Alignment explanation
Indices: 12427027--12427093 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
12427017 TTATGAATAC
12427027 ATCATGTGCATTTCATACAA
1 ATCATGTGCATTTCATACAA
* *
12427047 ATCATGTGCATTTTATACAT
1 ATCATGTGCATTTCATACAA
* *
12427067 ATCAAGTGCATATCATATC-A
1 ATCATGTGCATTTCATA-CAA
12427087 ATCATGT
1 ATCATGT
12427094 ATATCATATC
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 38 0.97
21 1 0.03
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.37
Consensus pattern (20 bp):
ATCATGTGCATTTCATACAA
Found at i:12427948 original size:27 final size:27
Alignment explanation
Indices: 12427918--12428003 Score: 77
Period size: 27 Copynumber: 3.1 Consensus size: 27
12427908 GTAAATCTAC
12427918 AAACCAACGGTATTTCAGTAATTTTGT
1 AAACCAACGGTATTTCAGTAATTTTGT
* *
12427945 AAACCAATGGTATTTTTA-TAATTTT-T
1 AAACCAACGGTA-TTTCAGTAATTTTGT
* * *
12427971 AGAAAGTCAAGGGTATTTCTGTAATTTTGT
1 --AAA-CCAACGGTATTTCAGTAATTTTGT
12428001 AAA
1 AAA
12428004 TTAGGGGTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
26 1 0.02
27 18 0.38
28 13 0.28
29 14 0.30
30 1 0.02
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.41
Consensus pattern (27 bp):
AAACCAACGGTATTTCAGTAATTTTGT
Found at i:12428021 original size:27 final size:27
Alignment explanation
Indices: 12427981--12428131 Score: 180
Period size: 27 Copynumber: 5.6 Consensus size: 27
12427971 AGAAAGTCAA
** *
12427981 GGGTATTTCT-GTAATTTTGTAAATTAG
1 GGGTATTT-TGGTAATTTTACAAACTAG
*
12428008 GGGTATTTTGGTAATTTTACAAA-TTG
1 GGGTATTTTGGTAATTTTACAAACTAG
* * * *
12428034 AGAGTATTTCGGTAATTTCACAAACCAG
1 -GGGTATTTTGGTAATTTTACAAACTAG
* *
12428062 TGGTATTTCGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACTAG
12428089 GGGTATTTTGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACTAG
12428116 GGGTATTTTGGTAATT
1 GGGTATTTTGGTAATT
12428132 CTATCTTACA
Statistics
Matches: 107, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
26 3 0.03
27 103 0.96
28 1 0.01
ACGTcount: A:0.28, C:0.08, G:0.22, T:0.42
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAACTAG
Found at i:12428067 original size:54 final size:54
Alignment explanation
Indices: 12428006--12428164 Score: 178
Period size: 54 Copynumber: 2.9 Consensus size: 54
12427996 TTTGTAAATT
*
12428006 AGGGGTATTTTGGTAATTTTACAAA-TTGAGAGTATTTCGGTAATTTCACAAACC
1 AGGGGTATTTTGGTAATTTTACAAACTAG-GAGTATTTCGGTAATTTCACAAACC
* * * * * *
12428060 AGTGGTATTTCGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAACT
1 AGGGGTATTTTGGTAATTTTACAAACTAGGAGTATTTCGGTAATTTCACAAACC
* ** * *
12428114 AGGGGTATTTTGGTAATTCTATCTTAC-AGGGGTATTTCAGTAATTTCACAA
1 AGGGGTATTTTGGTAATTTTA-CAAACTAGGAGTATTTCGGTAATTTCACAA
12428165 TCGAGGGTAA
Statistics
Matches: 88, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
54 83 0.94
55 5 0.06
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.39
Consensus pattern (54 bp):
AGGGGTATTTTGGTAATTTTACAAACTAGGAGTATTTCGGTAATTTCACAAACC
Found at i:12428122 original size:81 final size:81
Alignment explanation
Indices: 12427982--12428131 Score: 221
Period size: 81 Copynumber: 1.9 Consensus size: 81
12427972 GAAAGTCAAG
* ** * *
12427982 GGTATTTCTGTAATTTTGTAAATTAGGGGTATTTTGGTAATTTTACAAATTGAGAGTATTTCGGT
1 GGTATTTCGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAATAGAGAGTATTTCGGT
12428047 AATTTCACAAACCAGT
66 AATTTCACAAACCAGT
* *
12428063 GGTATTTCGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAACTAG-GGGTATTTTGG
1 GGTATTTCGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAA-TAGAGAGTATTTCGG
12428127 TAATT
65 TAATT
12428132 CTATCTTACA
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
81 59 0.97
82 2 0.03
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.42
Consensus pattern (81 bp):
GGTATTTCGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAATAGAGAGTATTTCGGT
AATTTCACAAACCAGT
Found at i:12428148 original size:81 final size:81
Alignment explanation
Indices: 12427981--12428164 Score: 212
Period size: 81 Copynumber: 2.3 Consensus size: 81
12427971 AGAAAGTCAA
* ** * *
12427981 GGGTATTTCTGTAATTTTGTAAATTAGGGGTATTTTGGTAATTTTACAAATTGAGAGTATTTCGG
1 GGGTATTTCAGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAATAGAGAGTATTTCGG
12428046 TAATTTCACAAACCAG
66 TAATTTCACAAACCAG
* * * *
12428062 TGGTATTTCGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAACTAG-GGGTATTTTG
1 GGGTATTTCAGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAA-TAGAGAGTATTTCG
**
12428126 GTAA-TTCTATCTTA-CAG
65 GTAATTTC-A-CAAACCAG
*
12428143 GGGTATTTCAGTAATTTCACAA
1 GGGTATTTCAGTAATTTTACAA
12428165 TCGAGGGTAA
Statistics
Matches: 87, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
80 3 0.03
81 80 0.92
82 4 0.05
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.41
Consensus pattern (81 bp):
GGGTATTTCAGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAATAGAGAGTATTTCGG
TAATTTCACAAACCAG
Found at i:12428171 original size:27 final size:27
Alignment explanation
Indices: 12428006--12428171 Score: 140
Period size: 27 Copynumber: 6.1 Consensus size: 27
12427996 TTTGTAAATT
* * *
12428006 AGGGGTATTTTGGTAATTTTACAAATTG
1 AGGGGTATTTCGGTAATTTCACAAA-CG
* *
12428034 A-GAGTATTTCGGTAATTTCACAAACC
1 AGGGGTATTTCGGTAATTTCACAAACG
* * *
12428060 AGTGGTATTTCGGTAATTTTACAAACT
1 AGGGGTATTTCGGTAATTTCACAAACG
* * *
12428087 AGGGGTATTTTGGTAATTTTACAAACT
1 AGGGGTATTTCGGTAATTTCACAAACG
* **
12428114 AGGGGTATTTTGGTAA-TTCTATCTTAC-
1 AGGGGTATTTCGGTAATTTC-A-CAAACG
* *
12428141 AGGGGTATTTCAGTAATTTCACAATCG
1 AGGGGTATTTCGGTAATTTCACAAACG
12428168 AGGG
1 AGGG
12428172 TAAAACAGTA
Statistics
Matches: 114, Mismatches: 19, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
26 5 0.04
27 102 0.89
28 7 0.06
ACGTcount: A:0.29, C:0.11, G:0.22, T:0.38
Consensus pattern (27 bp):
AGGGGTATTTCGGTAATTTCACAAACG
Found at i:12428209 original size:27 final size:27
Alignment explanation
Indices: 12428163--12428360 Score: 218
Period size: 27 Copynumber: 7.3 Consensus size: 27
12428153 GTAATTTCAC
** *
12428163 AATCGAGGGTAAAACAGTAATTTTGTA
1 AATCGAGGGTAAAATGGTAATTCTGTA
* * *
12428190 AATTGAAGGTAAAATGGTAATTTTGTA
1 AATCGAGGGTAAAATGGTAATTCTGTA
* * *
12428217 AATCGAGAGTAAAACGGTAACTCTGTA
1 AATCGAGGGTAAAATGGTAATTCTGTA
*
12428244 AATCGAGGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAATGGTAATTCTGTA
* *
12428271 AATCGAGGGTAAAACT-ATAATTTTGTA
1 AATCGAGGGTAAAA-TGGTAATTCTGTA
* ** *
12428298 AATCGAGGGTGAAACAGTAATTCTATA
1 AATCGAGGGTAAAATGGTAATTCTGTA
**
12428325 AATCGAGGGTAAAATGGTAATTCTACA
1 AATCGAGGGTAAAATGGTAATTCTGTA
12428352 AATCGAGGG
1 AATCGAGGG
12428361 CATTGCAGTA
Statistics
Matches: 143, Mismatches: 26, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
27 142 0.99
28 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.28
Consensus pattern (27 bp):
AATCGAGGGTAAAATGGTAATTCTGTA
Found at i:12428346 original size:54 final size:54
Alignment explanation
Indices: 12428163--12428360 Score: 243
Period size: 54 Copynumber: 3.7 Consensus size: 54
12428153 GTAATTTCAC
* * * * * *
12428163 AATCGAGGGTAAAACAGTAATTTTGTAAATTGAAGGTAAAATGGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTATA
* *
12428217 AATCGAGAGTAAAACGGTAACTCTGTAAATCGAGGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTATA
** * * **
12428271 AATCGAGGGTAAAACTATAATTTTGTAAATCGAGGGTGAAACAGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTATA
* **
12428325 AATCGAGGGTAAAATGGTAATTCTACAAATCGAGGG
1 AATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGG
12428361 CATTGCAGTA
Statistics
Matches: 122, Mismatches: 22, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 122 1.00
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.28
Consensus pattern (54 bp):
AATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTATA
Found at i:12428358 original size:81 final size:81
Alignment explanation
Indices: 12428163--12428360 Score: 263
Period size: 81 Copynumber: 2.4 Consensus size: 81
12428153 GTAATTTCAC
** * * * * *
12428163 AATCGAGGGTAAAACAGTAATTTTGTAAATTGAAGGTAAAATGGTAATTTTGTAAATCGAGAGTA
1 AATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAATGATAATTTTGTAAATCGAGAGTA
* *
12428228 AAACGGTAACTCTGTA
66 AAACAGTAACTCTATA
*
12428244 AATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAACT-ATAATTTTGTAAATCGAGGGT
1 AATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAA-TGATAATTTTGTAAATCGAGAGT
* *
12428308 GAAACAGTAATTCTATA
65 AAAACAGTAACTCTATA
*
12428325 AATCGAGGGTAAAATGGTAATTCTACAAATCGAGGG
1 AATCGAGGGTAAAATGGTAATTCTATAAATCGAGGG
12428361 CATTGCAGTA
Statistics
Matches: 103, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
81 102 0.99
82 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.28
Consensus pattern (81 bp):
AATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAATGATAATTTTGTAAATCGAGAGTA
AAACAGTAACTCTATA
Found at i:12431887 original size:3 final size:3
Alignment explanation
Indices: 12431877--12431908 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
12431867 TTTTTTCTAA
12431877 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
12431909 ATTTTAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:12432228 original size:17 final size:17
Alignment explanation
Indices: 12432185--12432239 Score: 60
Period size: 16 Copynumber: 3.2 Consensus size: 17
12432175 TTAGTAAATT
12432185 TTTATAATTATTT-TAAA
1 TTTA-AATTATTTGTAAA
*
12432202 ATTAAATTATTTGT-AA
1 TTTAAATTATTTGTAAA
12432218 TTTAGAATTATTTGATAAA
1 TTTA-AATTATTTG-TAAA
12432237 TTT
1 TTT
12432240 TTGTGTTAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
16 13 0.41
17 13 0.41
18 1 0.03
19 5 0.16
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (17 bp):
TTTAAATTATTTGTAAA
Found at i:12434730 original size:18 final size:18
Alignment explanation
Indices: 12434693--12434732 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
12434683 GGTAGACCTA
* *
12434693 GAGCCAAAGTCGGAGCCG
1 GAGCCAAAGCCAGAGCCG
*
12434711 GAGCCAAAGCCAGAGTCG
1 GAGCCAAAGCCAGAGCCG
12434729 GAGC
1 GAGC
12434733 TACACTCCGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.38, T:0.05
Consensus pattern (18 bp):
GAGCCAAAGCCAGAGCCG
Found at i:12435047 original size:20 final size:21
Alignment explanation
Indices: 12435007--12435056 Score: 93
Period size: 20 Copynumber: 2.4 Consensus size: 21
12434997 GGTTTTGTAT
12435007 TGTAAATTACTTTATTTTTTA
1 TGTAAATTACTTTATTTTTTA
12435028 TGTAAATTACTTTA-TTTTTA
1 TGTAAATTACTTTATTTTTTA
12435048 TGTAAATTA
1 TGTAAATTA
12435057 TTTTTTGCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.32, C:0.04, G:0.06, T:0.58
Consensus pattern (21 bp):
TGTAAATTACTTTATTTTTTA
Found at i:12438328 original size:27 final size:27
Alignment explanation
Indices: 12438271--12438328 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
12438261 CCTACCTGAC
* *
12438271 AGGCGCGACATGTTGAGCTTGTCAGGT
1 AGGCGCGACATGTGGAGCTTCTCAGGT
*
12438298 AGGCGCGACATGTGGTGCCTTCTCAGG-
1 AGGCGCGACATGTGGAG-CTTCTCAGGT
12438325 AGGC
1 AGGC
12438329 TCAACCCGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 19 0.70
28 8 0.30
ACGTcount: A:0.17, C:0.22, G:0.38, T:0.22
Consensus pattern (27 bp):
AGGCGCGACATGTGGAGCTTCTCAGGT
Found at i:12439032 original size:3 final size:3
Alignment explanation
Indices: 12439026--12439057 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
12439016 TTTTTAAAAT
12439026 ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
12439058 TTAGAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:12439125 original size:17 final size:17
Alignment explanation
Indices: 12439103--12439155 Score: 97
Period size: 17 Copynumber: 3.1 Consensus size: 17
12439093 CCTGTCAGGT
12439103 AGGCACGACTAAGAAAA
1 AGGCACGACTAAGAAAA
12439120 AGGCACGACTAAGAAAA
1 AGGCACGACTAAGAAAA
*
12439137 AGGCACGACTAAAAAAA
1 AGGCACGACTAAGAAAA
12439154 AG
1 AG
12439156 TAACCTATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 35 1.00
ACGTcount: A:0.55, C:0.17, G:0.23, T:0.06
Consensus pattern (17 bp):
AGGCACGACTAAGAAAA
Found at i:12453037 original size:12 final size:12
Alignment explanation
Indices: 12453020--12453052 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
12453010 CGTCCCGCCC
12453020 ATATTAATTTTT
1 ATATTAATTTTT
12453032 ATATT-ATTTTT
1 ATATTAATTTTT
12453043 ATA-TAATTTT
1 ATATTAATTTT
12453053 AAAATACATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:12453213 original size:30 final size:30
Alignment explanation
Indices: 12453177--12453238 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
12453167 CTTAACAAGC
12453177 AAATGTCTCTAAAATAATAACAAAATTAAT
1 AAATGTCTCTAAAATAATAACAAAATTAAT
*
12453207 AAATGTCTTTAAAATAATAACAAAATTAAT
1 AAATGTCTCTAAAATAATAACAAAATTAAT
12453237 AA
1 AA
12453239 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.58, C:0.08, G:0.03, T:0.31
Consensus pattern (30 bp):
AAATGTCTCTAAAATAATAACAAAATTAAT
Found at i:12453644 original size:7 final size:7
Alignment explanation
Indices: 12453632--12453670 Score: 78
Period size: 7 Copynumber: 5.6 Consensus size: 7
12453622 CCTAAATTCC
12453632 CAATCCT
1 CAATCCT
12453639 CAATCCT
1 CAATCCT
12453646 CAATCCT
1 CAATCCT
12453653 CAATCCT
1 CAATCCT
12453660 CAATCCT
1 CAATCCT
12453667 CAAT
1 CAAT
12453671 TTCCAATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.31, C:0.41, G:0.00, T:0.28
Consensus pattern (7 bp):
CAATCCT
Found at i:12453677 original size:21 final size:21
Alignment explanation
Indices: 12453621--12453677 Score: 80
Period size: 21 Copynumber: 2.7 Consensus size: 21
12453611 CATTCTTATG
*
12453621 TCCTAAATTCCCAATCCTCAA
1 TCCTCAATTCCCAATCCTCAA
12453642 TCCTCAA-TCCTCAATCCTCAA
1 TCCTCAATTCC-CAATCCTCAA
*
12453663 TCCTCAATTTCCAAT
1 TCCTCAATTCCCAAT
12453678 TTTGAATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 3 0.09
21 27 0.84
22 2 0.06
ACGTcount: A:0.30, C:0.39, G:0.00, T:0.32
Consensus pattern (21 bp):
TCCTCAATTCCCAATCCTCAA
Found at i:12453699 original size:14 final size:14
Alignment explanation
Indices: 12453621--12453699 Score: 70
Period size: 14 Copynumber: 5.6 Consensus size: 14
12453611 CATTCTTATG
* *
12453621 TCCTAAATTCCCAA
1 TCCTCAATTCTCAA
*
12453635 TCCTCAATCCTCAA
1 TCCTCAATTCTCAA
*
12453649 TCCTCAATCCTCAA
1 TCCTCAATTCTCAA
12453663 TCCTCAATT-TCCAA
1 TCCTCAATTCT-CAA
** * *
12453677 TTTTGAATTTTCAA
1 TCCTCAATTCTCAA
12453691 TCCTCAATT
1 TCCTCAATT
12453700 ATTTTTAAAA
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
13 1 0.02
14 51 0.96
15 1 0.02
ACGTcount: A:0.29, C:0.33, G:0.01, T:0.37
Consensus pattern (14 bp):
TCCTCAATTCTCAA
Found at i:12462323 original size:30 final size:30
Alignment explanation
Indices: 12462289--12462357 Score: 138
Period size: 30 Copynumber: 2.3 Consensus size: 30
12462279 CCATGTCCTA
12462289 AGGCCGTGTCCTCCACACGGCATGAGACAC
1 AGGCCGTGTCCTCCACACGGCATGAGACAC
12462319 AGGCCGTGTCCTCCACACGGCATGAGACAC
1 AGGCCGTGTCCTCCACACGGCATGAGACAC
12462349 AGGCCGTGT
1 AGGCCGTGT
12462358 TTCTCCTTGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.22, C:0.35, G:0.29, T:0.14
Consensus pattern (30 bp):
AGGCCGTGTCCTCCACACGGCATGAGACAC
Found at i:12463463 original size:2 final size:2
Alignment explanation
Indices: 12463456--12463500 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
12463446 AATCACAGCT
12463456 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12463498 TA T
1 TA T
12463501 CGAACTATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12470051 original size:19 final size:18
Alignment explanation
Indices: 12470028--12470087 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 18
12470018 AATAAAATCA
12470028 ATAAAATTTATAAAAATT
1 ATAAAATTTATAAAAATT
*
12470046 ATTAAATTTTAATAAAAA-T
1 A-TAAAATTT-ATAAAAATT
*
12470065 ATAAAATAT-TAAAAATT
1 ATAAAATTTATAAAAATT
*
12470082 AGAAAA
1 ATAAAA
12470088 AAAATTATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
16 6 0.17
17 6 0.17
18 7 0.20
19 9 0.26
20 7 0.20
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (18 bp):
ATAAAATTTATAAAAATT
Found at i:12470314 original size:28 final size:26
Alignment explanation
Indices: 12470274--12470325 Score: 77
Period size: 28 Copynumber: 1.9 Consensus size: 26
12470264 TAATACGATA
*
12470274 ATTTTTTTTATTTTTTATGAATTTTAT
1 ATTTTTTATATTTTTTAT-AATTTTAT
12470301 ATTTCTTTATATTTTTTATAATTTT
1 ATTT-TTTATATTTTTTATAATTTT
12470326 CATGACTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 10 0.43
28 13 0.57
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (26 bp):
ATTTTTTATATTTTTTATAATTTTAT
Found at i:12470317 original size:19 final size:19
Alignment explanation
Indices: 12470274--12470330 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 19
12470264 TAATACGATA
*
12470274 ATTTTTTTTATTTTTTATG
1 ATTTTTTATATTTTTTATG
*
12470293 A-ATTTTATATTTCTTTAT-
1 ATTTTTTATATTT-TTTATG
* *
12470311 ATTTTTTATAATTTTCATG
1 ATTTTTTATATTTTTTATG
12470330 A
1 A
12470331 CTTTATAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
18 14 0.47
19 16 0.53
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.68
Consensus pattern (19 bp):
ATTTTTTATATTTTTTATG
Found at i:12470318 original size:9 final size:9
Alignment explanation
Indices: 12470274--12470325 Score: 52
Period size: 9 Copynumber: 5.6 Consensus size: 9
12470264 TAATACGATA
*
12470274 ATTTTTTTT
1 ATTTTTTAT
12470283 ATTTTTTAT
1 ATTTTTTAT
*
12470292 GA-ATTTTAT
1 -ATTTTTTAT
12470301 ATTTCTTTAT
1 ATTT-TTTAT
12470311 ATTTTTTAT
1 ATTTTTTAT
12470320 AATTTT
1 -ATTTT
12470326 CATGACTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
8 1 0.03
9 20 0.56
10 15 0.42
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (9 bp):
ATTTTTTAT
Found at i:12470334 original size:26 final size:28
Alignment explanation
Indices: 12470282--12470337 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
12470272 TAATTTTTTT
* **
12470282 TATTTTTTATGAATTTTATATTTCTTTA
1 TATTTTTTATGAATTTTACATGACTTTA
12470310 TATTTTTTAT-AATTTT-CATGACTTTA
1 TATTTTTTATGAATTTTACATGACTTTA
12470336 TA
1 TA
12470338 AAATTTTACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 9 0.36
27 6 0.24
28 10 0.40
ACGTcount: A:0.27, C:0.05, G:0.04, T:0.64
Consensus pattern (28 bp):
TATTTTTTATGAATTTTACATGACTTTA
Found at i:12470393 original size:20 final size:20
Alignment explanation
Indices: 12470341--12470385 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
12470331 CTTTATAAAA
*
12470341 TTTTACAATTTTTTTTAATTT
1 TTTTACAA-TTTTTCTAATTT
*
12470362 TTTTACGATTTTTCTAATTT
1 TTTTACAATTTTTCTAATTT
12470382 TTTT
1 TTTT
12470386 CTAATTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.20, C:0.07, G:0.02, T:0.71
Consensus pattern (20 bp):
TTTTACAATTTTTCTAATTT
Found at i:12470450 original size:18 final size:19
Alignment explanation
Indices: 12470402--12470450 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 19
12470392 TTAAGCATAT
12470402 ATTTA-TATTTTTATTAAA
1 ATTTATTATTTTTATTAAA
*
12470420 ATTTAGTCA-TTTTA-TAAA
1 ATTTA-TTATTTTTATTAAA
*
12470438 TTTTATTATTTTT
1 ATTTATTATTTTT
12470451 TATTTTTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
17 2 0.08
18 17 0.68
19 5 0.20
20 1 0.04
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (19 bp):
ATTTATTATTTTTATTAAA
Found at i:12475244 original size:21 final size:21
Alignment explanation
Indices: 12475220--12475260 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
12475210 TTTCTTTCGT
*
12475220 AATCTTTATTCTT-TTTAATTC
1 AATCTTT-CTCTTCTTTAATTC
12475241 AATCTTTCTCTTCTTTAATT
1 AATCTTTCTCTTCTTTAATT
12475261 GTTTTTTCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.22, C:0.17, G:0.00, T:0.61
Consensus pattern (21 bp):
AATCTTTCTCTTCTTTAATTC
Found at i:12487899 original size:18 final size:19
Alignment explanation
Indices: 12487862--12487902 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
12487852 TTATCCAAAT
12487862 CAAATAAAGAAAAAAGAAA
1 CAAATAAAGAAAAAAGAAA
12487881 CAAATAAA-AAAAATA-AAA
1 CAAATAAAGAAAAA-AGAAA
12487899 CAAA
1 CAAA
12487903 GAAACTCATG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.80, C:0.07, G:0.05, T:0.07
Consensus pattern (19 bp):
CAAATAAAGAAAAAAGAAA
Found at i:12489962 original size:23 final size:24
Alignment explanation
Indices: 12489920--12489970 Score: 79
Period size: 23 Copynumber: 2.2 Consensus size: 24
12489910 CGCAATTATC
12489920 AAGT-TGGCATAGTATAAAATATT
1 AAGTCTGGCATAGTATAAAATATT
*
12489943 AAGTCTGGCATAGTA-CAAATATT
1 AAGTCTGGCATAGTATAAAATATT
12489966 AAGTC
1 AAGTC
12489971 AAAAATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 16 0.62
24 10 0.38
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.31
Consensus pattern (24 bp):
AAGTCTGGCATAGTATAAAATATT
Found at i:12497494 original size:2 final size:2
Alignment explanation
Indices: 12497487--12497525 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
12497477 TGTTGGTAGA
12497487 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12497526 AGTGAAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12499853 original size:23 final size:25
Alignment explanation
Indices: 12499797--12499844 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
12499787 GAGTAACATC
12499797 ATAATATTTTATATAAATAAATATA
1 ATAATATTTTATATAAATAAATATA
12499822 ATAATATTTTATATAAATAAATA
1 ATAATATTTTATATAAATAAATA
12499845 ATGTTATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
ATAATATTTTATATAAATAAATATA
Found at i:12501972 original size:20 final size:20
Alignment explanation
Indices: 12501936--12501990 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
12501926 TTTATTTCTA
*
12501936 TTAATTTAACCATTTTTATTT
1 TTAATTTAA-TATTTTTATTT
* *
12501957 TTACTTTAATATTTTTGTTT
1 TTAATTTAATATTTTTATTT
12501977 TTAATTTAAT-TTTT
1 TTAATTTAATATTTT
12501991 ACATTCTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 4 0.13
20 18 0.60
21 8 0.27
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.67
Consensus pattern (20 bp):
TTAATTTAATATTTTTATTT
Found at i:12507948 original size:40 final size:40
Alignment explanation
Indices: 12507883--12508048 Score: 160
Period size: 40 Copynumber: 4.2 Consensus size: 40
12507873 AAATTGAATG
* * *
12507883 ATATCC-GGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
12507921 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
*
12507961 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
12508001 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
12508041 ATATCCGG
1 ATATCCGG
12508049 TTATATTCCG
Statistics
Matches: 104, Mismatches: 18, Indels: 10
0.79 0.14 0.08
Matches are distributed among these distances:
38 6 0.06
39 9 0.09
40 87 0.84
41 2 0.02
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:12512058 original size:17 final size:17
Alignment explanation
Indices: 12512036--12512070 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
12512026 GGTATCATCG
12512036 GGTATTCGAGTCGACCC
1 GGTATTCGAGTCGACCC
12512053 GGTATTCGAGTCGACCC
1 GGTATTCGAGTCGACCC
12512070 G
1 G
12512071 AATAAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.29, G:0.31, T:0.23
Consensus pattern (17 bp):
GGTATTCGAGTCGACCC
Found at i:12514281 original size:40 final size:40
Alignment explanation
Indices: 12514222--12514390 Score: 173
Period size: 40 Copynumber: 4.2 Consensus size: 40
12514212 CGGGACTTTA
* * *
12514222 CCCGGATATCACGATTTGCACAAATGCCTTCGGGTCTTAG
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* *
12514262 CCCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAG
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* * * * *
12514302 CCCGGATATAGCTACTAGCACAATTGCCTTCGGGTCTTAA
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* * *
12514342 CCCGGATAT-A-AA-TTTCAGCATAATTGTCTTCGGGGCTTAG
1 CCCGGATATAACAACTTGCA-CA-AA-TGCCTTCGGGTCTTAG
12514382 CCCGGATAT
1 CCCGGATAT
12514391 CATTCAATTT
Statistics
Matches: 106, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
37 3 0.03
38 3 0.03
39 1 0.01
40 99 0.93
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (40 bp):
CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
Found at i:12519666 original size:20 final size:20
Alignment explanation
Indices: 12519641--12519681 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
12519631 TAAAGTGTCG
12519641 GCCGATCCACACTTATAGCA
1 GCCGATCCACACTTATAGCA
12519661 GCCGATCCACACTTATAGCA
1 GCCGATCCACACTTATAGCA
12519681 G
1 G
12519682 GAGATCACGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.34, G:0.17, T:0.20
Consensus pattern (20 bp):
GCCGATCCACACTTATAGCA
Found at i:12519687 original size:20 final size:20
Alignment explanation
Indices: 12519644--12519687 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
12519634 AGTGTCGGCC
*
12519644 GATCCACACTTATAGCAGCC
1 GATCCACACTTATAGCAGCA
*
12519664 GATCCACACTTATAGCAGGA
1 GATCCACACTTATAGCAGCA
12519684 GATC
1 GATC
12519688 ACGAAACCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.32, C:0.30, G:0.18, T:0.20
Consensus pattern (20 bp):
GATCCACACTTATAGCAGCA
Found at i:12522744 original size:25 final size:25
Alignment explanation
Indices: 12522716--12522763 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
12522706 CCCTTATAAT
* * *
12522716 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
12522741 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
12522764 GTTTATGTAT
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:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:12522832 original size:20 final size:20
Alignment explanation
Indices: 12522807--12522865 Score: 109
Period size: 20 Copynumber: 3.0 Consensus size: 20
12522797 TAAATATGGT
12522807 ATGTATGATATGCACATGAC
1 ATGTATGATATGCACATGAC
*
12522827 ATGTATGATATGCACATGAT
1 ATGTATGATATGCACATGAC
12522847 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
12522866 GTAATCATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (20 bp):
ATGTATGATATGCACATGAC
Found at i:12522847 original size:11 final size:11
Alignment explanation
Indices: 12522811--12522865 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
12522801 TATGGTATGT
12522811 ATGATATGCAC
1 ATGATATGCAC
* *
12522822 ATGACATG--T
1 ATGATATGCAC
12522831 ATGATATGCAC
1 ATGATATGCAC
*
12522842 ATGATATG--T
1 ATGATATGCAC
12522851 ATGATATGCAC
1 ATGATATGCAC
12522862 ATGA
1 ATGA
12522866 GTAATCATAA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:12522945 original size:23 final size:24
Alignment explanation
Indices: 12522915--12523056 Score: 200
Period size: 24 Copynumber: 6.0 Consensus size: 24
12522905 GAGGAAGTGA
12522915 AAAAGGGCTTATG-CCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
12522938 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
12522962 AAAAGGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
12522985 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
* * *
12523009 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
12523033 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
12523057 ATGATAAAGC
Statistics
Matches: 110, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
23 36 0.33
24 63 0.57
25 11 0.10
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:12522989 original size:47 final size:47
Alignment explanation
Indices: 12522915--12523056 Score: 198
Period size: 47 Copynumber: 3.0 Consensus size: 47
12522905 GAGGAAGTGA
12522915 AAAAGGGCTTATG-CCCAGTTATCAAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATC
*
12522962 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
* * *
12523009 GAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTA-TAAAAG-GGCTTATGCC-CCAGTTAT
12523057 ATGATAAAGC
Statistics
Matches: 87, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
47 56 0.64
48 20 0.23
49 11 0.13
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
Found at i:12523308 original size:30 final size:31
Alignment explanation
Indices: 12523248--12523311 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
12523238 CGTTTACAGT
12523248 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
12523279 AAAGGCTTCGGCCCAGTGTTATG-AATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
12523309 AAA
1 AAA
12523312 TGAAAAGGGC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 10 0.32
31 21 0.68
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:12530829 original size:25 final size:25
Alignment explanation
Indices: 12530801--12530848 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
12530791 TTATACCATG
* * *
12530801 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
12530826 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
12530849 GTTTATGTTG
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:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:12530950 original size:20 final size:20
Alignment explanation
Indices: 12530890--12530950 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
12530880 ATAAATATGG
*
12530890 TATGTATGAGATGCACATGA
1 TATGTATGATATGCACATGA
*
12530910 CATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
12530930 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
12530950 T
1 T
12530951 GTAATCATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.33
Consensus pattern (20 bp):
TATGTATGATATGCACATGA
Found at i:12531027 original size:24 final size:24
Alignment explanation
Indices: 12531000--12531141 Score: 200
Period size: 24 Copynumber: 6.0 Consensus size: 24
12530990 GAGGAAGTGA
12531000 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
12531024 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
12531048 AAAAGGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
12531071 AAAA-GGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
* * *
12531094 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
12531118 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
12531142 ATGATAAAGC
Statistics
Matches: 109, Mismatches: 5, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
22 18 0.17
23 7 0.06
24 73 0.67
25 11 0.10
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:12531099 original size:46 final size:46
Alignment explanation
Indices: 12531000--12531122 Score: 192
Period size: 46 Copynumber: 2.6 Consensus size: 46
12530990 GAGGAAGTGA
12531000 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTAT-AAAA-GGCTTATGCCCCAGTTATC
*
12531048 AAAAGGGCTTATGCCCCAGTTATAAAAGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATAAAAGGCTTATGCCCCAGTTATC
* *
12531094 GAAAGGGCTTTTGCCCCAGTTATTAAAAG
1 AAAAGGGCTTATGCCCCAGTTA-TAAAAG
12531123 AGGCTAGGCC
Statistics
Matches: 71, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
46 38 0.54
47 10 0.14
48 23 0.32
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (46 bp):
AAAAGGGCTTATGCCCCAGTTATAAAAGGCTTATGCCCCAGTTATC
Found at i:12531122 original size:70 final size:72
Alignment explanation
Indices: 12531000--12531142 Score: 211
Period size: 70 Copynumber: 2.0 Consensus size: 72
12530990 GAGGAAGTGA
*
12531000 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAG-GGCTTATGCC-
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGC-TAGGCCT
12531063 CCAGTTAT
65 CCAGTTAT
** * *
12531071 AAAA-GGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGCTAGGCCTC
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
12531135 CAGTTAT
66 CAGTTAT
12531142 A
1 A
12531143 TGATAAAGCA
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
70 49 0.75
71 16 0.25
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (72 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
CAGTTAT
Found at i:12531357 original size:31 final size:31
Alignment explanation
Indices: 12531322--12531385 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
12531312 CGTTTACAGT
12531322 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
** *
12531353 AAAGGCTTCGGCCCAGTGTTATGGAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
12531384 AA
1 AA
12531386 CATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:12536867 original size:38 final size:35
Alignment explanation
Indices: 12536808--12536925 Score: 135
Period size: 31 Copynumber: 3.5 Consensus size: 35
12536798 TCAATCATGC
*
12536808 ACTGGGCCGTAGCCCTTTTCATATTTCATATTTCATAAT
1 ACTGGGCCGAAG-CCTTTTCATATTTCATATTT-AT--T
12536847 ACTGGGCCGAAGCCTTTTCATATTTC--A--TATT
1 ACTGGGCCGAAGCCTTTTCATATTTCATATTTATT
12536878 ACTGGGCCGAAGCCTTTTCATATTTC--A--TATT
1 ACTGGGCCGAAGCCTTTTCATATTTCATATTTATT
12536909 ACTGGGCCGAAGCCTTT
1 ACTGGGCCGAAGCCTTT
12536926 ACTGTAAACG
Statistics
Matches: 78, Mismatches: 1, Indels: 8
0.90 0.01 0.09
Matches are distributed among these distances:
31 49 0.63
33 2 0.03
34 1 0.01
36 1 0.01
38 14 0.18
39 11 0.14
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (35 bp):
ACTGGGCCGAAGCCTTTTCATATTTCATATTTATT
Found at i:12536869 original size:31 final size:31
Alignment explanation
Indices: 12536831--12536925 Score: 181
Period size: 31 Copynumber: 3.1 Consensus size: 31
12536821 CCTTTTCATA
*
12536831 TTTCATATTTCATAATACTGGGCCGAAGCCT
1 TTTCATATTTCATATTACTGGGCCGAAGCCT
12536862 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATATTACTGGGCCGAAGCCT
12536893 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATATTACTGGGCCGAAGCCT
12536924 TT
1 TT
12536926 ACTGTAAACG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 63 1.00
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.39
Consensus pattern (31 bp):
TTTCATATTTCATATTACTGGGCCGAAGCCT
Found at i:12537168 original size:24 final size:24
Alignment explanation
Indices: 12537117--12537259 Score: 209
Period size: 24 Copynumber: 6.0 Consensus size: 24
12537107 GCTTTATCAT
*
12537117 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
12537142 ATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGGGGCATAAGCCCTTTTA
12537166 ATAACTGGGGCATAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTA
*
12537189 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
12537213 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
12537237 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
12537260 TCACTTCCTC
Statistics
Matches: 111, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
23 23 0.21
24 76 0.68
25 12 0.11
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:12537196 original size:47 final size:48
Alignment explanation
Indices: 12537117--12537258 Score: 207
Period size: 47 Copynumber: 3.0 Consensus size: 48
12537107 GCTTTATCAT
* *
12537117 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCATAAGCCCTTTCA
**
12537166 ATAACTGGGGCATAAGCCCTTTT-ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTCA
*
12537213 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTT
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTT
12537259 TTCACTTCCT
Statistics
Matches: 87, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
47 44 0.51
48 31 0.36
49 12 0.14
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.28
Consensus pattern (48 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTCA
Found at i:12537217 original size:71 final size:72
Alignment explanation
Indices: 12537116--12537259 Score: 220
Period size: 71 Copynumber: 2.0 Consensus size: 72
12537106 TGCTTTATCA
*
12537116 TATAACTGGAGGCCTAGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAA
1 TATAACTGGAGGCATAGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAA
12537181 GCCCTTT
66 GCCCTTT
* * **
12537188 TATAACTGG-GGCATAAGCC-CTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATA
1 TATAACTGGAGGCAT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATA
12537251 AGCCCTTT
65 AGCCCTTT
12537259 T
1 T
12537260 TCACTTCCTC
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
71 53 0.80
72 13 0.20
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (72 bp):
TATAACTGGAGGCATAGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAA
GCCCTTT
Found at i:12537335 original size:20 final size:20
Alignment explanation
Indices: 12537310--12537369 Score: 111
Period size: 20 Copynumber: 3.0 Consensus size: 20
12537300 TATGATTACC
12537310 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
*
12537330 TCATGTGCATATCATACATT
1 TCATGTGCATATCATACATA
12537350 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
12537370 CCATATTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (20 bp):
TCATGTGCATATCATACATA
Found at i:12537340 original size:11 final size:11
Alignment explanation
Indices: 12537310--12537364 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
12537300 TATGATTACC
12537310 TCATGTGCATA
1 TCATGTGCATA
*
12537321 TCA--TACATA
1 TCATGTGCATA
12537330 TCATGTGCATA
1 TCATGTGCATA
* *
12537341 TCA--TACATT
1 TCATGTGCATA
12537350 TCATGTGCATA
1 TCATGTGCATA
12537361 TCAT
1 TCAT
12537365 ACATACCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (11 bp):
TCATGTGCATA
Found at i:12537444 original size:25 final size:25
Alignment explanation
Indices: 12537412--12537459 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
12537402 ATACATAAAC
* * *
12537412 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
12537437 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
12537460 CATATTATAA
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:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:12544991 original size:38 final size:35
Alignment explanation
Indices: 12544932--12545049 Score: 135
Period size: 31 Copynumber: 3.5 Consensus size: 35
12544922 TCAATCATGC
*
12544932 ACTGGGCCGTAGCCCTTTTCATATTTCATATTTCATAAT
1 ACTGGGCCGAAG-CCTTTTCATATTTCATATTT-AT--T
12544971 ACTGGGCCGAAGCCTTTTCATATTTC--A--TATT
1 ACTGGGCCGAAGCCTTTTCATATTTCATATTTATT
12545002 ACTGGGCCGAAGCCTTTTCATATTTC--A--TATT
1 ACTGGGCCGAAGCCTTTTCATATTTCATATTTATT
12545033 ACTGGGCCGAAGCCTTT
1 ACTGGGCCGAAGCCTTT
12545050 ACTGTAAACG
Statistics
Matches: 78, Mismatches: 1, Indels: 8
0.90 0.01 0.09
Matches are distributed among these distances:
31 49 0.63
33 2 0.03
34 1 0.01
36 1 0.01
38 14 0.18
39 11 0.14
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (35 bp):
ACTGGGCCGAAGCCTTTTCATATTTCATATTTATT
Found at i:12544993 original size:31 final size:31
Alignment explanation
Indices: 12544955--12545049 Score: 181
Period size: 31 Copynumber: 3.1 Consensus size: 31
12544945 CCTTTTCATA
*
12544955 TTTCATATTTCATAATACTGGGCCGAAGCCT
1 TTTCATATTTCATATTACTGGGCCGAAGCCT
12544986 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATATTACTGGGCCGAAGCCT
12545017 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATATTACTGGGCCGAAGCCT
12545048 TT
1 TT
12545050 ACTGTAAACG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 63 1.00
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.39
Consensus pattern (31 bp):
TTTCATATTTCATATTACTGGGCCGAAGCCT
Found at i:12545292 original size:24 final size:24
Alignment explanation
Indices: 12545241--12545383 Score: 209
Period size: 24 Copynumber: 6.0 Consensus size: 24
12545231 GCTTTATCAT
*
12545241 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
12545266 ATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGGGGCATAAGCCCTTTTA
12545290 ATAACTGGGGCATAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTA
*
12545313 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
12545337 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
12545361 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
12545384 TCACTTCCTC
Statistics
Matches: 111, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
23 23 0.21
24 76 0.68
25 12 0.11
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:12545320 original size:47 final size:48
Alignment explanation
Indices: 12545241--12545382 Score: 207
Period size: 47 Copynumber: 3.0 Consensus size: 48
12545231 GCTTTATCAT
* *
12545241 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCATAAGCCCTTTCA
**
12545290 ATAACTGGGGCATAAGCCCTTTT-ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTCA
*
12545337 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTT
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTT
12545383 TTCACTTCCT
Statistics
Matches: 87, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
47 44 0.51
48 31 0.36
49 12 0.14
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.28
Consensus pattern (48 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTCA
Found at i:12545341 original size:71 final size:72
Alignment explanation
Indices: 12545240--12545383 Score: 220
Period size: 71 Copynumber: 2.0 Consensus size: 72
12545230 TGCTTTATCA
*
12545240 TATAACTGGAGGCCTAGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAA
1 TATAACTGGAGGCATAGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAA
12545305 GCCCTTT
66 GCCCTTT
* * **
12545312 TATAACTGG-GGCATAAGCC-CTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATA
1 TATAACTGGAGGCAT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATA
12545375 AGCCCTTT
65 AGCCCTTT
12545383 T
1 T
12545384 TCACTTCCTC
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
71 53 0.80
72 13 0.20
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (72 bp):
TATAACTGGAGGCATAGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAA
GCCCTTT
Found at i:12545459 original size:20 final size:20
Alignment explanation
Indices: 12545434--12545493 Score: 111
Period size: 20 Copynumber: 3.0 Consensus size: 20
12545424 TATGATTACC
12545434 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
*
12545454 TCATGTGCATATCATACATT
1 TCATGTGCATATCATACATA
12545474 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
12545494 CCATATTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (20 bp):
TCATGTGCATATCATACATA
Found at i:12545464 original size:11 final size:11
Alignment explanation
Indices: 12545434--12545488 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
12545424 TATGATTACC
12545434 TCATGTGCATA
1 TCATGTGCATA
*
12545445 TCA--TACATA
1 TCATGTGCATA
12545454 TCATGTGCATA
1 TCATGTGCATA
* *
12545465 TCA--TACATT
1 TCATGTGCATA
12545474 TCATGTGCATA
1 TCATGTGCATA
12545485 TCAT
1 TCAT
12545489 ACATACCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (11 bp):
TCATGTGCATA
Found at i:12545568 original size:25 final size:25
Alignment explanation
Indices: 12545536--12545583 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
12545526 ATACATAAAC
* * *
12545536 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
12545561 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
12545584 CATATTATAA
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:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:12549051 original size:21 final size:21
Alignment explanation
Indices: 12549026--12549068 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
12549016 ATAGGTTAAT
* *
12549026 TTTATCTTATTACAGAGCATA
1 TTTATCATATTACAGAACATA
*
12549047 TTTATCATATTATAGAACATA
1 TTTATCATATTACAGAACATA
12549068 T
1 T
12549069 ATAGCATACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (21 bp):
TTTATCATATTACAGAACATA
Found at i:12549076 original size:21 final size:21
Alignment explanation
Indices: 12549033--12549076 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
12549023 AATTTTATCT
* * *
12549033 TATTACAGAGCATATTTATCA
1 TATTACAGAACATATATAGCA
*
12549054 TATTATAGAACATATATAGCA
1 TATTACAGAACATATATAGCA
12549075 TA
1 TA
12549077 CAACATGATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.36
Consensus pattern (21 bp):
TATTACAGAACATATATAGCA
Found at i:12552536 original size:21 final size:22
Alignment explanation
Indices: 12552497--12552537 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
12552487 GTTGAAATGT
12552497 CACACGGGCGTGTTGCCCCTCC
1 CACACGGGCGTGTTGCCCCTCC
12552519 CACACGGGCGTG-TGCCCCT
1 CACACGGGCGTGTTGCCCCT
12552538 GTGTTAAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.10, C:0.44, G:0.29, T:0.17
Consensus pattern (22 bp):
CACACGGGCGTGTTGCCCCTCC
Found at i:12560025 original size:40 final size:42
Alignment explanation
Indices: 12559981--12560059 Score: 110
Period size: 41 Copynumber: 1.9 Consensus size: 42
12559971 AGGTTTTTGC
*
12559981 ACACGGGCTAG-GACACAGGCGTGTCTT-A-GCCGTGTGAGGG
1 ACACGGGCCAGAGACACAGGCGTGT-TTCAGGCCGTGTGAGGG
*
12560021 ACACGGGCCAGAGACACCGGCGTGTTTCAGGCCGTGTGA
1 ACACGGGCCAGAGACACAGGCGTGTTTCAGGCCGTGTGA
12560060 AAACCTATGT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
40 12 0.35
41 13 0.38
42 9 0.26
ACGTcount: A:0.20, C:0.25, G:0.38, T:0.16
Consensus pattern (42 bp):
ACACGGGCCAGAGACACAGGCGTGTTTCAGGCCGTGTGAGGG
Found at i:12561166 original size:44 final size:44
Alignment explanation
Indices: 12561117--12561201 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 44
12561107 TGTTCAGGGA
*
12561117 TACTTCGACCTT-GAGTCGATGAGGCACTATAAGTGTCGTACGGT
1 TACTTCGA-CTTCGAGTCGATGAGGCACCATAAGTGTCGTACGGT
* **
12561161 TACTTCGACTTCGAGTTGATGAGGCACCATGTGTGTCGTAC
1 TACTTCGACTTCGAGTCGATGAGGCACCATAAGTGTCGTAC
12561202 TGCTACTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
43 3 0.08
44 33 0.92
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.31
Consensus pattern (44 bp):
TACTTCGACTTCGAGTCGATGAGGCACCATAAGTGTCGTACGGT
Found at i:12564228 original size:8 final size:8
Alignment explanation
Indices: 12564215--12564244 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
12564205 AGATCGGCAC
12564215 AAGCCGAA
1 AAGCCGAA
12564223 AAGCCGAA
1 AAGCCGAA
*
12564231 ATGCCGAA
1 AAGCCGAA
12564239 AAGCCG
1 AAGCCG
12564245 GTATTTTGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.43, C:0.27, G:0.27, T:0.03
Consensus pattern (8 bp):
AAGCCGAA
Found at i:12564675 original size:27 final size:27
Alignment explanation
Indices: 12564637--12564774 Score: 176
Period size: 27 Copynumber: 5.1 Consensus size: 27
12564627 AAGCGTCCTA
*
12564637 GTGGCTATGCCACAATTATCTGATCTG
1 GTGGCTCTGCCACAATTATCTGATCTG
12564664 GTGGCTCTGCCAC-ATATATCTG-TCCTG
1 GTGGCTCTGCCACAAT-TATCTGAT-CTG
*
12564691 GTGGCTATGCCACAATTATCTGATCTG
1 GTGGCTCTGCCACAATTATCTGATCTG
* *
12564718 GTGGCTCTACCAC-ATATATCTGTTCTG
1 GTGGCTCTGCCACAAT-TATCTGATCTG
12564745 GTGGCTCTGCCACAA-TATCTGTATCTG
1 GTGGCTCTGCCACAATTATCTG-ATCTG
12564772 GTG
1 GTG
12564775 ACTTCGTCAC
Statistics
Matches: 97, Mismatches: 7, Indels: 14
0.82 0.06 0.12
Matches are distributed among these distances:
26 11 0.11
27 82 0.85
28 4 0.04
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (27 bp):
GTGGCTCTGCCACAATTATCTGATCTG
Done.