Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 123 of 199
Found at i:37322369 original size:16 final size:14
Alignment explanation
Indices: 37322344--37322423 Score: 60
Period size: 13 Copynumber: 5.7 Consensus size: 14
37322334 AATTGGAGTG
*
37322344 ATTAATTAAAACTAAA
1 ATTAACTAAAA-T-AA
*
37322360 ATTAACT-AAATTA
1 ATTAACTAAAATAA
37322373 ATTAACT-AAAT-A
1 ATTAACTAAAATAA
*
37322385 ATTAATTAAAACTAAA
1 ATTAACTAAAA-T-AA
*
37322401 ATTAACT-AAATTA
1 ATTAACTAAAATAA
37322414 ATTAACTAAA
1 ATTAACTAAA
37322424 TCAGGAAAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
12 7 0.13
13 23 0.43
14 5 0.09
15 6 0.11
16 13 0.24
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (14 bp):
ATTAACTAAAATAA
Found at i:37322377 original size:13 final size:13
Alignment explanation
Indices: 37322359--37322424 Score: 80
Period size: 13 Copynumber: 4.9 Consensus size: 13
37322349 TTAAAACTAA
37322359 AATTAACTAAATT
1 AATTAACTAAATT
37322372 AATTAACTAAA-T
1 AATTAACTAAATT
* *
37322384 AATTAATTAAAACTAA
1 AATTAACT-AAA-T-T
37322400 AATTAACTAAATT
1 AATTAACTAAATT
37322413 AATTAACTAAAT
1 AATTAACTAAAT
37322425 CAGGAAAATA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
12 8 0.18
13 26 0.58
14 1 0.02
15 3 0.07
16 7 0.16
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.35
Consensus pattern (13 bp):
AATTAACTAAATT
Found at i:37322396 original size:41 final size:41
Alignment explanation
Indices: 37322344--37322424 Score: 162
Period size: 41 Copynumber: 2.0 Consensus size: 41
37322334 AATTGGAGTG
37322344 ATTAATTAAAACTAAAATTAACTAAATTAATTAACTAAATA
1 ATTAATTAAAACTAAAATTAACTAAATTAATTAACTAAATA
37322385 ATTAATTAAAACTAAAATTAACTAAATTAATTAACTAAAT
1 ATTAATTAAAACTAAAATTAACTAAATTAATTAACTAAAT
37322425 CAGGAAAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (41 bp):
ATTAATTAAAACTAAAATTAACTAAATTAATTAACTAAATA
Found at i:37325431 original size:33 final size:33
Alignment explanation
Indices: 37325394--37325658 Score: 318
Period size: 33 Copynumber: 8.0 Consensus size: 33
37325384 TCAACATAAG
* * * *
37325394 TGATTGGAACATCTATCAAGGAAGCTTCATAAA
1 TGATTGGAACATCTATCAGGGCAGCTTCATCAT
* *
37325427 TGATTGGAACATCTATCATGGCAGTTTCATCAT
1 TGATTGGAACATCTATCAGGGCAGCTTCATCAT
* *
37325460 TGATTGGAACATCTATCAGGGCAACTTCATCAA
1 TGATTGGAACATCTATCAGGGCAGCTTCATCAT
* * *
37325493 TGATTGAAACATCTATCGGGGTAGCTTCATCAT
1 TGATTGGAACATCTATCAGGGCAGCTTCATCAT
*
37325526 TTATTGGAACATCTATC-GAGGCAGCTTCATCAT
1 TGATTGGAACATCTATCAG-GGCAGCTTCATCAT
* * * * * *
37325559 TGATTGGAAAATTTATCAGGGTAGCCTCGTCAA
1 TGATTGGAACATCTATCAGGGCAGCTTCATCAT
37325592 TGATTGGAACATCTATCAGGGCAGCTTCATCAT
1 TGATTGGAACATCTATCAGGGCAGCTTCATCAT
* *
37325625 TGATTGGATCATCTA-CTGGGGCAGCTTCATCAT
1 TGATTGGAACATCTATC-AGGGCAGCTTCATCAT
37325658 T
1 T
37325659 TTGTTCGATT
Statistics
Matches: 197, Mismatches: 32, Indels: 6
0.84 0.14 0.03
Matches are distributed among these distances:
32 2 0.01
33 194 0.98
34 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (33 bp):
TGATTGGAACATCTATCAGGGCAGCTTCATCAT
Found at i:37329654 original size:29 final size:29
Alignment explanation
Indices: 37329612--37329668 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
37329602 AATAATATTG
*
37329612 TACTCTTCTATCTACCAGCAATTGTGCTT
1 TACTCTTCTATCTACCAACAATTGTGCTT
37329641 TACTCTTCTATCTACCAACAATTGTGCT
1 TACTCTTCTATCTACCAACAATTGTGCT
37329669 AACTTATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.23, C:0.28, G:0.09, T:0.40
Consensus pattern (29 bp):
TACTCTTCTATCTACCAACAATTGTGCTT
Found at i:37331411 original size:5 final size:5
Alignment explanation
Indices: 37331401--37331434 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
37331391 TATCGTACTT
37331401 ACCTC ACCTC ACCTC ACCTC ACCTC ACCTC ACCT
1 ACCTC ACCTC ACCTC ACCTC ACCTC ACCTC ACCT
37331435 TGTGGCTCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.21, C:0.59, G:0.00, T:0.21
Consensus pattern (5 bp):
ACCTC
Found at i:37333850 original size:27 final size:26
Alignment explanation
Indices: 37333812--37333955 Score: 171
Period size: 27 Copynumber: 5.3 Consensus size: 26
37333802 CAGAAAGGTT
* * *
37333812 GGTAAAATGACCGAACTACCCTCGAAG
1 GGTAAAATTACCGAAATACCC-CGATG
* * *
37333839 GGTAAAATGACCGAATTACCCCTGAAG
1 GGTAAAATTACCGAAATACCCC-GATG
37333866 GGTAAAATTACCGAAATACCCTCGATG
1 GGTAAAATTACCGAAATACCC-CGATG
*
37333893 GGTAAAATTACTGAAATAACCCCGATG
1 GGTAAAATTACCGAAAT-ACCCCGATG
*
37333920 GGTAAAATTACTGAAATACCCCCGATG
1 GGTAAAATTACCGAAATA-CCCCGATG
37333947 GGTAAAATT
1 GGTAAAATT
37333956 GACTATTATG
Statistics
Matches: 108, Mismatches: 5, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
26 2 0.02
27 101 0.94
28 5 0.05
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (26 bp):
GGTAAAATTACCGAAATACCCCGATG
Found at i:37333955 original size:54 final size:54
Alignment explanation
Indices: 37333812--37333955 Score: 191
Period size: 54 Copynumber: 2.7 Consensus size: 54
37333802 CAGAAAGGTT
* * * * *
37333812 GGTAAAATGACCGAACTACCCTCGAAGGGTAAAATGACCGAATTACCCCTGAAG
1 GGTAAAATTACCGAAATACCCTCGATGGGTAAAATTACCGAATAACCCCTGAAG
* *
37333866 GGTAAAATTACCGAAATACCCTCGATGGGTAAAATTACTGAAATAACCCC-GATG
1 GGTAAAATTACCGAAATACCCTCGATGGGTAAAATTACCG-AATAACCCCTGAAG
* *
37333920 GGTAAAATTACTGAAATACCCCCGATGGGTAAAATT
1 GGTAAAATTACCGAAATACCCTCGATGGGTAAAATT
37333956 GACTATTATG
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
54 72 0.90
55 8 0.10
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (54 bp):
GGTAAAATTACCGAAATACCCTCGATGGGTAAAATTACCGAATAACCCCTGAAG
Found at i:37340346 original size:27 final size:27
Alignment explanation
Indices: 37340308--37340758 Score: 423
Period size: 27 Copynumber: 16.7 Consensus size: 27
37340298 ATTCGTGGGC
* *
37340308 AAATGATCGAAATACCCTCAAAAGGTA
1 AAATGACCGAAATACCCTCGAAAGGTA
*
37340335 AAATGACCGAAATACCCT-TAAAGGATA
1 AAATGACCGAAATACCCTCGAAAGG-TA
37340362 AAATGACCGAAATACCC-CTG-AAGGTTA
1 AAATGACCGAAATACCCTC-GAAAGG-TA
* * *
37340389 AAATGACAGAAATACCCCCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAAGGTA
* *
37340416 AAATGACCGAAATACCCTTGAAGGGTA
1 AAATGACCGAAATACCCTCGAAAGGTA
* *
37340443 AAATGATCGAAATACCC-CTAAAAGGTA
1 AAATGACCGAAATACCCTC-GAAAGGTA
*
37340470 AAATGATCGAAATACCCTC-AAAGGGTA
1 AAATGACCGAAATACCCTCGAAA-GGTA
* * *
37340497 AAATGACCAAAATACCC-CCAAAGGAAAA
1 AAATGACCGAAATACCCTCGAAAGG--TA
* *
37340525 AAATGACCAAAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAAGGTA
* *
37340552 AAATGATCGAAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAAGGTA
** * *
37340579 AAATGATTGAAATACCCCCGAATGGTA
1 AAATGACCGAAATACCCTCGAAAGGTA
***
37340606 AAATGATTAAAATACCC-CTGAAAGGTA
1 AAATGACCGAAATACCCTC-GAAAGGTA
* * *
37340633 AAATGACTGAAATACACTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAAGGTA
* * *
37340660 AAATAACCGAAATACCCCCAAAAGGTA
1 AAATGACCGAAATACCCTCGAAAGGTA
* * *
37340687 AAATGATCAAAATACCCCCGAAAGGTA
1 AAATGACCGAAATACCCTCGAAAGGTA
* *
37340714 AAATGATCGAAATACCCTC-ATAGGGTA
1 AAATGACCGAAATACCCTCGA-AAGGTA
* *
37340741 AAATGACTGATATACCCT
1 AAATGACCGAAATACCCT
37340759 TAGGAGTTGA
Statistics
Matches: 363, Mismatches: 46, Indels: 30
0.83 0.10 0.07
Matches are distributed among these distances:
26 13 0.04
27 321 0.88
28 24 0.07
29 5 0.01
ACGTcount: A:0.45, C:0.20, G:0.17, T:0.18
Consensus pattern (27 bp):
AAATGACCGAAATACCCTCGAAAGGTA
Found at i:37340445 original size:81 final size:80
Alignment explanation
Indices: 37340308--37340757 Score: 521
Period size: 81 Copynumber: 5.5 Consensus size: 80
37340298 ATTCGTGGGC
* * ** * * *
37340308 AAATGATCGAAATACCCTCAAAAGGTAAAATGACCGAAATACCCTTAAAGGATAAAATGACCGAA
1 AAATGATCGAAATACCCTCGAAGGGTAAAATGACCGAAATACCCCCAAAGGGTAAAATGATCAAA
37340373 ATACCCCTGAAGGTTA
66 ATACCCCTGAAGG-TA
* *** *
37340389 AAATGA-CAGAAATACCCCCGAAGGGTAAAATGACCGAAATACCCTTGAAGGGTAAAATGATCGA
1 AAATGATC-GAAATACCCTCGAAGGGTAAAATGACCGAAATACCCCCAAAGGGTAAAATGATCAA
*
37340453 AATACCCCTAAAAGGTA
65 AATACCCCT-GAAGGTA
* * ** *
37340470 AAATGATCGAAATACCCTCAAAGGGTAAAATGACCAAAATACCCCCAAAGGAAAAAAATGACCAA
1 AAATGATCGAAATACCCTCGAAGGGTAAAATGACCGAAATACCCCCAAAGG-GTAAAATGATCAA
37340535 AATA-CCCTCGAAGGGTA
65 AATACCCCT-GAA-GGTA
** * * *
37340552 AAATGATCGAAATACCCTCGAAGGGTAAAATGATTGAAATACCCCCGAATGGTAAAATGATTAAA
1 AAATGATCGAAATACCCTCGAAGGGTAAAATGACCGAAATACCCCCAAAGGGTAAAATGATCAAA
37340617 ATACCCCTGAAAGGTA
66 ATACCCCTG-AAGGTA
* * *
37340633 AAATGA-CTGAAATACACTCGAAGGGTAAAATAACCGAAATACCCCCAAAAGGTAAAATGATCAA
1 AAATGATC-GAAATACCCTCGAAGGGTAAAATGACCGAAATACCCCCAAAGGGTAAAATGATCAA
*
37340697 AATACCCCCGAAAGGTA
65 AATACCCCTG-AAGGTA
* *
37340714 AAATGATCGAAATACCCTC-ATAGGGTAAAATGACTGATATACCC
1 AAATGATCGAAATACCCTCGA-AGGGTAAAATGACCGAAATACCC
37340758 TTAGGAGTTG
Statistics
Matches: 318, Mismatches: 41, Indels: 20
0.84 0.11 0.05
Matches are distributed among these distances:
80 3 0.01
81 241 0.76
82 74 0.23
ACGTcount: A:0.46, C:0.20, G:0.17, T:0.17
Consensus pattern (80 bp):
AAATGATCGAAATACCCTCGAAGGGTAAAATGACCGAAATACCCCCAAAGGGTAAAATGATCAAA
ATACCCCTGAAGGTA
Found at i:37345892 original size:20 final size:20
Alignment explanation
Indices: 37345847--37345900 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
37345837 TGAACCCTTC
* *
37345847 CATTTACTTTCTTTTCGTAT
1 CATTTACTTACTTTTCATAT
*
37345867 CATTTACTTACTTTTCATTT
1 CATTTACTTACTTTTCATAT
*
37345887 CGTTTACTTACTTT
1 CATTTACTTACTTT
37345901 AGCTTAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.17, C:0.20, G:0.04, T:0.59
Consensus pattern (20 bp):
CATTTACTTACTTTTCATAT
Found at i:37346841 original size:138 final size:137
Alignment explanation
Indices: 37346589--37346857 Score: 337
Period size: 138 Copynumber: 2.0 Consensus size: 137
37346579 TAAATGGGTC
* * * *
37346589 TGCTCACACAAGTTGACGAACGGAATGTAGCTACACAATGTCGCTGACACAAGCTTACGAGTATC
1 TGCTCACACAAGTTGACGAACGGAATGTAGCTACACAATGCCCCTCACACAAGCTAACGAGTATC
* ** * * ***
37346654 GATAACAAATGTCAGAACTTAGCCATCAGTAGAACATTCATGACTAGCACCGTGAACATGGTAAC
66 GACAACAAATGTCAGAACACAGCCATCAGTAGAACATTCAAGACCAGCACCCAAAACATGGTAAC
37346719 CTAGATT
131 CTAGATT
*
37346726 TGCTCACACAAGTTGAC-AGTCGGAATGTAAGCTACACAATGCCCCTCACACAAGCTAACGAGTA
1 TGCTCACACAAGTTGACGA-ACGGAATGT-AGCTACACAATGCCCCTCACACAAGCTAACGAGTA
* **
37346790 TCTG-CAACAAATGTC-GAACCACAGCCATCATTAGGGCATTCAAGACCAGCACCCAAAACATGG
64 TC-GACAACAAATGTCAGAA-CACAGCCATCAGTAGAACATTCAAGACCAGCACCCAAAACATGG
37346853 TAACC
127 TAACC
37346858 CTAATGACAT
Statistics
Matches: 112, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
136 1 0.01
137 28 0.25
138 82 0.73
139 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (137 bp):
TGCTCACACAAGTTGACGAACGGAATGTAGCTACACAATGCCCCTCACACAAGCTAACGAGTATC
GACAACAAATGTCAGAACACAGCCATCAGTAGAACATTCAAGACCAGCACCCAAAACATGGTAAC
CTAGATT
Found at i:37349739 original size:23 final size:23
Alignment explanation
Indices: 37349708--37349758 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
37349698 ACCTACTTTC
* *
37349708 TTACTGTAGCAATTTTCGGGGTA
1 TTACAGTAGCAATTTTCGGGATA
*
37349731 TTACAGTAGTAATTTTCGGGATA
1 TTACAGTAGCAATTTTCGGGATA
37349754 TTACA
1 TTACA
37349759 TAACCAGCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.39
Consensus pattern (23 bp):
TTACAGTAGCAATTTTCGGGATA
Found at i:37352087 original size:27 final size:26
Alignment explanation
Indices: 37352045--37352104 Score: 84
Period size: 27 Copynumber: 2.3 Consensus size: 26
37352035 CTAATAGATG
37352045 AAAATGACCGTAATGCCCATGTAGGGT
1 AAAATGACCGTAATGCCCATGTA-GGT
* * *
37352072 AAAATGATCGTGATGCCCCTGTAGGT
1 AAAATGACCGTAATGCCCATGTAGGT
37352098 AAAATGA
1 AAAATGA
37352105 ATGTAATACC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 10 0.33
27 20 0.67
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (26 bp):
AAAATGACCGTAATGCCCATGTAGGT
Found at i:37352234 original size:24 final size:24
Alignment explanation
Indices: 37352177--37352226 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
37352167 CCCCTCGAGG
**
37352177 TTAAATGTTTGATTTGTCCGTGAT
1 TTAAATGACTGATTTGTCCGTGAT
37352201 TTAAATGACTGATTTG-CCTGTGAT
1 TTAAATGACTGATTTGTCC-GTGAT
37352225 TT
1 TT
37352227 GTATGACTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 2 0.09
24 21 0.91
ACGTcount: A:0.22, C:0.10, G:0.20, T:0.48
Consensus pattern (24 bp):
TTAAATGACTGATTTGTCCGTGAT
Found at i:37352407 original size:26 final size:26
Alignment explanation
Indices: 37352372--37352474 Score: 136
Period size: 26 Copynumber: 4.0 Consensus size: 26
37352362 CTTGCCACGT
37352372 ATACTGTTACTGGCAGCTTTGCTGCG
1 ATACTGTTACTGGCAGCTTTGCTGCG
* *
37352398 ATACTGTTACTGGCAGTTTTGTTGCG
1 ATACTGTTACTGGCAGCTTTGCTGCG
*
37352424 TTACTGTTACTGGCAGCTTTGCTGCG
1 ATACTGTTACTGGCAGCTTTGCTGCG
* * *
37352450 -TCATTATCACTGGCAGCTTTGCTGC
1 AT-ACTGTTACTGGCAGCTTTGCTGC
37352475 AATATTGGTG
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
25 1 0.01
26 67 0.99
ACGTcount: A:0.15, C:0.22, G:0.25, T:0.38
Consensus pattern (26 bp):
ATACTGTTACTGGCAGCTTTGCTGCG
Found at i:37358633 original size:67 final size:67
Alignment explanation
Indices: 37358516--37358653 Score: 195
Period size: 67 Copynumber: 2.1 Consensus size: 67
37358506 CAAGTAGGTA
* * * * *
37358516 CACACGGCCGTGTCCCAACCCGTGTCTGTGCCTATGTAACTCACTGACTTGGGTCACACAGACAA
1 CACAAGGCCGTGTCCCAACCCATGTCCGTGCCCATGTAACTCACTAACTTGGGTCACACAGACAA
37358581 GC
66 GC
* * * *
37358583 CACAAGGCCGTGTCCCAGCCCATGTCCGTGCCCGTGTAACTCACTAACTTGGGTCACACGGCCAA
1 CACAAGGCCGTGTCCCAACCCATGTCCGTGCCCATGTAACTCACTAACTTGGGTCACACAGACAA
37358648 GC
66 GC
37358650 CACA
1 CACA
37358654 CACCCGTGTG
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
67 62 1.00
ACGTcount: A:0.22, C:0.36, G:0.22, T:0.19
Consensus pattern (67 bp):
CACAAGGCCGTGTCCCAACCCATGTCCGTGCCCATGTAACTCACTAACTTGGGTCACACAGACAA
GC
Found at i:37358661 original size:67 final size:67
Alignment explanation
Indices: 37358523--37358674 Score: 189
Period size: 67 Copynumber: 2.3 Consensus size: 67
37358513 GTACACACGG
* * * * *
37358523 CCGTGTCCCAACCCGTGTCTGTGCCTATGTAACTCACTGACTTGGGTCACACAGACAAGCCACAA
1 CCGTGTCCCAGCCCATGTCCGTGCCCATGTAACTCACTAACTTGGGTCACACAGACAAGCCACAA
*
37358588 GG
66 GC
* * *
37358590 CCGTGTCCCAGCCCATGTCCGTGCCCGTGTAACTCACTAACTTGGGTCACACGGCCAAGCCACAC
1 CCGTGTCCCAGCCCATGTCCGTGCCCATGTAACTCACTAACTTGGGTCACACAGACAAGCCACA-
37358655 A-C
65 AGC
* *
37358657 CCGTGTGCCAGGCCATGT
1 CCGTGTCCCAGCCCATGT
37358675 GCCCGTGTAA
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
67 72 0.99
68 1 0.01
ACGTcount: A:0.21, C:0.36, G:0.23, T:0.20
Consensus pattern (67 bp):
CCGTGTCCCAGCCCATGTCCGTGCCCATGTAACTCACTAACTTGGGTCACACAGACAAGCCACAA
GC
Found at i:37361839 original size:20 final size:19
Alignment explanation
Indices: 37361812--37361853 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
37361802 CTTTCCAAAT
37361812 TTTCTTACTTT-CAGTTGCA
1 TTTCTTACTTTCCA-TTGCA
37361831 TTTCATTACTTTCCATTGCA
1 TTTC-TTACTTTCCATTGCA
37361851 TTT
1 TTT
37361854 ACTTTCTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 15 0.71
21 2 0.10
ACGTcount: A:0.17, C:0.21, G:0.07, T:0.55
Consensus pattern (19 bp):
TTTCTTACTTTCCATTGCA
Found at i:37363388 original size:20 final size:19
Alignment explanation
Indices: 37363361--37363402 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
37363351 CTTTACAAAT
37363361 TTTCTTACTTT-CATTTGCA
1 TTTCTTACTTTCCA-TTGCA
37363380 TTTCATTACTTTCCATTGCA
1 TTTC-TTACTTTCCATTGCA
37363400 TTT
1 TTT
37363403 ACTTTCTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 15 0.71
21 2 0.10
ACGTcount: A:0.17, C:0.21, G:0.05, T:0.57
Consensus pattern (19 bp):
TTTCTTACTTTCCATTGCA
Found at i:37364936 original size:20 final size:20
Alignment explanation
Indices: 37364907--37364950 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
37364897 CCCTCTCCAA
*
37364907 ATTTCGTTACTTT-CATTTGC
1 ATTTCATTACTTTCCA-TTGC
37364927 ATTTCATTACTTTCCATTGC
1 ATTTCATTACTTTCCATTGC
37364947 ATTT
1 ATTT
37364951 ACTTTCTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.18, C:0.20, G:0.07, T:0.55
Consensus pattern (20 bp):
ATTTCATTACTTTCCATTGC
Found at i:37365968 original size:23 final size:23
Alignment explanation
Indices: 37365925--37365969 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
37365915 ATTTAATACA
* *
37365925 TAATCACATATTAACATTTCATT
1 TAATCACAAATTAACAGTTCATT
37365948 TAATCA-AAATTATACAGTTCAT
1 TAATCACAAATTA-ACAGTTCAT
37365970 ACGAACTTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.42, C:0.16, G:0.02, T:0.40
Consensus pattern (23 bp):
TAATCACAAATTAACAGTTCATT
Found at i:37366533 original size:20 final size:19
Alignment explanation
Indices: 37366506--37366547 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
37366496 CTTTCCAAAT
37366506 TTTCTTACTTT-CATTTGCA
1 TTTCTTACTTTCCA-TTGCA
37366525 TTTCATTACTTTCCATTGCA
1 TTTC-TTACTTTCCATTGCA
37366545 TTT
1 TTT
37366548 ACTTTCTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 15 0.71
21 2 0.10
ACGTcount: A:0.17, C:0.21, G:0.05, T:0.57
Consensus pattern (19 bp):
TTTCTTACTTTCCATTGCA
Found at i:37368141 original size:20 final size:20
Alignment explanation
Indices: 37368118--37368155 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
37368108 CCAAATTTTT
37368118 TTACTTTCAT-TTGCATTTCA
1 TTACTTTC-TGTTGCATTTCA
37368138 TTACTTTCTGTTGCATTT
1 TTACTTTCTGTTGCATTT
37368156 ACTTTCTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.16, C:0.18, G:0.08, T:0.58
Consensus pattern (20 bp):
TTACTTTCTGTTGCATTTCA
Found at i:37369627 original size:17 final size:18
Alignment explanation
Indices: 37369595--37369628 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
37369585 CGTTGGGCCG
37369595 AAATGGATCATGTGGGCT
1 AAATGGATCATGTGGGCT
*
37369613 AAATGGA-CTTGTGGGC
1 AAATGGATCATGTGGGC
37369629 CCCACACTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.26, C:0.12, G:0.35, T:0.26
Consensus pattern (18 bp):
AAATGGATCATGTGGGCT
Found at i:37369816 original size:27 final size:27
Alignment explanation
Indices: 37369778--37370184 Score: 449
Period size: 27 Copynumber: 15.1 Consensus size: 27
37369768 TTACGATACT
**
37369778 ATGACCGAAATACCCTTATAGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
** * *
37369805 ATGATTGAAATACCCCCATATGATAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
*
37369832 ATGACTGAAATACCCCCATAGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* * *
37369859 ATGAACGAAATACCCCCTTAGGGTAGA
1 ATGACCGAAATACCCCCATAGGGTAAA
* *
37369886 ATGATCGAAATACCCCCATAGGGTAGA
1 ATGACCGAAATACCCCCATAGGGTAAA
* *
37369913 ATGACCGAAATA-CCCCATAGGTTGAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* *
37369939 ATGACCGAAACACCCCCATAAGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* * * * * *
37369966 ATAACTGAAACACCTCCACA-GGAAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
*
37369992 ATGACCGAAATACCCCTATAGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
** *
37370019 ATGATTGAAATACCCCTATAGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
*
37370046 ATGACCGAAATACCCCCGTAGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* * ** *
37370073 ATGACTGAAATATCCTAATAGGGTAGA
1 ATGACCGAAATACCCCCATAGGGTAAA
*
37370100 ATGATCGAAATACCCCCATAGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* * * * * *
37370127 ATGACCAAAACACCCCTACAAGGTAGA
1 ATGACCGAAATACCCCCATAGGGTAAA
37370154 ATGACCGAAATACCCCCATAGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
37370181 ATGA
1 ATGA
37370185 TTGTTATATC
Statistics
Matches: 312, Mismatches: 66, Indels: 4
0.82 0.17 0.01
Matches are distributed among these distances:
26 41 0.13
27 271 0.87
ACGTcount: A:0.41, C:0.22, G:0.18, T:0.18
Consensus pattern (27 bp):
ATGACCGAAATACCCCCATAGGGTAAA
Found at i:37372390 original size:12 final size:12
Alignment explanation
Indices: 37372352--37372393 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
37372342 ATTCGTCATA
37372352 GAGAGATTTGAG
1 GAGAGATTTGAG
* *
37372364 GAGGGATATT-TG
1 GAGAGAT-TTGAG
37372376 GAGAGATTTGAG
1 GAGAGATTTGAG
37372388 GAGAGA
1 GAGAGA
37372394 ATACTGGGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
11 2 0.08
12 20 0.83
13 2 0.08
ACGTcount: A:0.33, C:0.00, G:0.43, T:0.24
Consensus pattern (12 bp):
GAGAGATTTGAG
Found at i:37373043 original size:27 final size:27
Alignment explanation
Indices: 37373008--37373470 Score: 410
Period size: 27 Copynumber: 17.2 Consensus size: 27
37372998 TTACACTATT
*
37373008 ATGACCGAAATACCCCCAGAGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* * **
37373035 ATAATCGAAATACCCCCATAGAATAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* ** *
37373062 ATGACCAAAATATTCCCATAAGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* *
37373089 ATGACCAAAATACCCCCATAGGGTAGA
1 ATGACCGAAATACCCCCATAGGGTAAA
** *
37373116 ATGACCGAAATACCCTTATAGGGTAGA
1 ATGACCGAAATACCCCCATAGGGTAAA
* * *
37373143 ATGACCAAAATA-CCCCATAAGATAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
*** *
37373169 ATGACCGAAATACCAATATGGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* * *
37373196 ATAACCGAAATACCCTCC-CAGGGAAAA
1 ATGACCGAAATACCC-CCATAGGGTAAA
* * * *
37373223 ATGATCAAAATGCCCCAATAGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* *
37373250 ATGATCGAAATACCCCCATAGGTTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* ** *
37373277 ACGACTAAAATACCCCTATAGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* * * *
37373304 ATGATCGAAATATCCCCATAGGATAGA
1 ATGACCGAAATACCCCCATAGGGTAAA
*
37373331 ATGACCGAAATACCCTCATAGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
** * *
37373358 ATGACTAAAATACCCCCACAGGGTAGA
1 ATGACCGAAATACCCCCATAGGGTAAA
* * ** *
37373385 ATGA-CTAACATACCCCCACAATGTAGA
1 ATGACCGAA-ATACCCCCATAGGGTAAA
* * ** *
37373412 ATGTCTGAAATACCCTTATAAGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
37373439 ATGACCGAAATACCCCCATAGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
37373466 ATGAC
1 ATGAC
37373471 TGTTATATCC
Statistics
Matches: 339, Mismatches: 92, Indels: 10
0.77 0.21 0.02
Matches are distributed among these distances:
26 23 0.07
27 314 0.93
28 2 0.01
ACGTcount: A:0.43, C:0.22, G:0.16, T:0.18
Consensus pattern (27 bp):
ATGACCGAAATACCCCCATAGGGTAAA
Found at i:37373903 original size:29 final size:32
Alignment explanation
Indices: 37373871--37373930 Score: 90
Period size: 29 Copynumber: 2.0 Consensus size: 32
37373861 TATATGCACT
*
37373871 GATTAATGAT-TT-TATACTGTT-ACTGCATC
1 GATTAATGATATTACATACTGTTCACTGCATC
37373900 GATTAATGATATTACATACTGTTCACTGCAT
1 GATTAATGATATTACATACTGTTCACTGCAT
37373931 GACTGATATC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 10 0.37
30 2 0.07
31 8 0.30
32 7 0.26
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (32 bp):
GATTAATGATATTACATACTGTTCACTGCATC
Found at i:37375087 original size:8 final size:8
Alignment explanation
Indices: 37375074--37375098 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
37375064 ACCCAAAACC
37375074 AAAGTCCA
1 AAAGTCCA
37375082 AAAGTCCA
1 AAAGTCCA
37375090 AAAGTCCA
1 AAAGTCCA
37375098 A
1 A
37375099 TTACAACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.24, G:0.12, T:0.12
Consensus pattern (8 bp):
AAAGTCCA
Found at i:37379250 original size:20 final size:19
Alignment explanation
Indices: 37379223--37379264 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
37379213 CTTTACAAAT
37379223 TTTCTTACTTT-CATTTGCA
1 TTTCTTACTTTCCA-TTGCA
37379242 TTTCATTACTTTCCATTGCA
1 TTTC-TTACTTTCCATTGCA
37379262 TTT
1 TTT
37379265 ACTTTCTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 15 0.71
21 2 0.10
ACGTcount: A:0.17, C:0.21, G:0.05, T:0.57
Consensus pattern (19 bp):
TTTCTTACTTTCCATTGCA
Found at i:37380165 original size:2 final size:2
Alignment explanation
Indices: 37380160--37380198 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
37380150 ACACACACAC
37380160 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
37380199 GATTTAGTAA
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:37384997 original size:16 final size:16
Alignment explanation
Indices: 37384928--37384997 Score: 59
Period size: 16 Copynumber: 4.3 Consensus size: 16
37384918 TTTAGATTTG
*
37384928 AAACTAAAGACTGTGA
1 AAACTATAGACTGTGA
* * *
37384944 AAACTGTAGATTATGAA
1 AAACTATAGACTGTG-A
* * *
37384961 AAACAATAGATTGAGA
1 AAACTATAGACTGTGA
*
37384977 CAACTATAGACTGTGA
1 AAACTATAGACTGTGA
37384993 AAACT
1 AAACT
37384998 CTAAATAGTG
Statistics
Matches: 40, Mismatches: 13, Indels: 2
0.73 0.24 0.04
Matches are distributed among these distances:
16 28 0.70
17 12 0.30
ACGTcount: A:0.49, C:0.11, G:0.17, T:0.23
Consensus pattern (16 bp):
AAACTATAGACTGTGA
Found at i:37386937 original size:15 final size:16
Alignment explanation
Indices: 37386917--37386946 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
37386907 CTCTTTGTTA
37386917 TTTCTTT-TCATTTTT
1 TTTCTTTATCATTTTT
37386932 TTTCTTTATCATTTT
1 TTTCTTTATCATTTT
37386947 ATTATGCTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTCTTTATCATTTTT
Found at i:37391155 original size:45 final size:45
Alignment explanation
Indices: 37391018--37391156 Score: 143
Period size: 45 Copynumber: 3.1 Consensus size: 45
37391008 TCGGAATGGG
* * * * *
37391018 CCGAATATCATTGGAAATATAGGTGGATGTTATGTGCTGATTCCA
1 CCGAATACCAATGAAAATATAGGTGGTTGTTATGTGCTGATTTCA
* ** * * *
37391063 CCCAATATTAATGAAAATAAAGGTGGTTGCTATGTGTTGATTTCA
1 CCGAATACCAATGAAAATATAGGTGGTTGTTATGTGCTGATTTCA
* ***
37391108 CCGGATACCAATGGTTATATAGGTGGTTGTTATGTGCTGATTTCA
1 CCGAATACCAATGAAAATATAGGTGGTTGTTATGTGCTGATTTCA
37391153 CCGA
1 CCGA
37391157 GTACTATTGA
Statistics
Matches: 74, Mismatches: 20, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
45 74 1.00
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.35
Consensus pattern (45 bp):
CCGAATACCAATGAAAATATAGGTGGTTGTTATGTGCTGATTTCA
Found at i:37400230 original size:41 final size:41
Alignment explanation
Indices: 37400185--37400266 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
37400175 GCATGTCATA
37400185 TCTGTATATTGCATTACATTGGGTTGGGGAATTATAATGTT
1 TCTGTATATTGCATTACATTGGGTTGGGGAATTATAATGTT
37400226 TCTGTATATTGCATTACATTGGGTTGGGGAATTATAATGTT
1 TCTGTATATTGCATTACATTGGGTTGGGGAATTATAATGTT
37400267 CAGAGGAAGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.24, C:0.07, G:0.24, T:0.44
Consensus pattern (41 bp):
TCTGTATATTGCATTACATTGGGTTGGGGAATTATAATGTT
Found at i:37400980 original size:18 final size:18
Alignment explanation
Indices: 37400946--37401003 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
37400936 CAATAAGTGC
*
37400946 CGTTTTGAAAATTAATAA
1 CGTTTTGAAAATGAATAA
37400964 CGTTTTGAAAGA-GAATAA
1 CGTTTTGAAA-ATGAATAA
* * *
37400982 C-TTTTGAATACGAATCA
1 CGTTTTGAAAATGAATAA
37400999 CGTTT
1 CGTTT
37401004 AAATTGATCG
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
16 1 0.03
17 13 0.38
18 19 0.56
19 1 0.03
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (18 bp):
CGTTTTGAAAATGAATAA
Found at i:37405904 original size:12 final size:12
Alignment explanation
Indices: 37405887--37405928 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
37405877 AAAATAAAAC
37405887 AATAAAAAGAAA
1 AATAAAAAGAAA
*
37405899 AAT-AAAAGCAA
1 AATAAAAAGAAA
*
37405910 AAGAAAAAGAAA
1 AATAAAAAGAAA
37405922 AAGTAAA
1 AA-TAAA
37405929 CAAAATGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
11 9 0.38
12 12 0.50
13 3 0.12
ACGTcount: A:0.79, C:0.02, G:0.12, T:0.07
Consensus pattern (12 bp):
AATAAAAAGAAA
Found at i:37408862 original size:13 final size:13
Alignment explanation
Indices: 37408844--37408868 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
37408834 TTGACAAAGG
37408844 CAAGTGCACCTAT
1 CAAGTGCACCTAT
37408857 CAAGTGCACCTA
1 CAAGTGCACCTA
37408869 AAAATTTGAC
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:0.32, C:0.32, G:0.16, T:0.20
Consensus pattern (13 bp):
CAAGTGCACCTAT
Found at i:37411928 original size:11 final size:11
Alignment explanation
Indices: 37411914--37411942 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
37411904 TTTAATTTTT
37411914 TAATTTTAAAA
1 TAATTTTAAAA
37411925 TAATTTTAAAA
1 TAATTTTAAAA
37411936 TAATTTT
1 TAATTTT
37411943 TTTTATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
TAATTTTAAAA
Found at i:37412607 original size:17 final size:18
Alignment explanation
Indices: 37412570--37412616 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
37412560 TCAGTTTTAG
*
37412570 CAAC-TCTTCTTCAGCAT
1 CAACTTCTTCTTCAGCAA
37412587 CAACTTCTTCTTC-GCAA
1 CAACTTCTTCTTCAGCAA
*
37412604 CAACTTCTACTTC
1 CAACTTCTTCTTC
37412617 TGCAGCATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 19 0.70
18 8 0.30
ACGTcount: A:0.23, C:0.36, G:0.04, T:0.36
Consensus pattern (18 bp):
CAACTTCTTCTTCAGCAA
Found at i:37417402 original size:63 final size:63
Alignment explanation
Indices: 37417303--37417428 Score: 243
Period size: 63 Copynumber: 2.0 Consensus size: 63
37417293 CTTCAATAGA
37417303 TGGTTTGAAAATTAAGGTTGTTCAATTAGCTAGGTCTAAGGATTCAATCTGCCATCCATGTTT
1 TGGTTTGAAAATTAAGGTTGTTCAATTAGCTAGGTCTAAGGATTCAATCTGCCATCCATGTTT
*
37417366 TGGTTTGAAAATTAGGGTTGTTCAATTAGCTAGGTCTAAGGATTCAATCTGCCATCCATGTTT
1 TGGTTTGAAAATTAAGGTTGTTCAATTAGCTAGGTCTAAGGATTCAATCTGCCATCCATGTTT
37417429 GAGTTTAAGA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.38
Consensus pattern (63 bp):
TGGTTTGAAAATTAAGGTTGTTCAATTAGCTAGGTCTAAGGATTCAATCTGCCATCCATGTTT
Found at i:37423226 original size:24 final size:26
Alignment explanation
Indices: 37423190--37423237 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
37423180 CCTCATATTC
37423190 TTTTCCAAATTAAACTCTG-TTATCT
1 TTTTCCAAATTAAACTCTGATTATCT
*
37423215 TTTTCC-AGTTAAACTCTGATTAT
1 TTTTCCAAATTAAACTCTGATTAT
37423238 TCCAGGGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.27, C:0.19, G:0.06, T:0.48
Consensus pattern (26 bp):
TTTTCCAAATTAAACTCTGATTATCT
Found at i:37426889 original size:27 final size:27
Alignment explanation
Indices: 37426859--37426912 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
37426849 TCTCCTATAT
*
37426859 GTATAACAGTCATTTTACCCTATGGGG
1 GTATAACAGTCATTCTACCCTATGGGG
** *
37426886 GTATTTCGGTCATTCTACCCTATGGGG
1 GTATAACAGTCATTCTACCCTATGGGG
37426913 TATTTCGATC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.35
Consensus pattern (27 bp):
GTATAACAGTCATTCTACCCTATGGGG
Found at i:37426950 original size:27 final size:27
Alignment explanation
Indices: 37426868--37427079 Score: 264
Period size: 27 Copynumber: 7.9 Consensus size: 27
37426858 TGTATAACAG
* *
37426868 TCATTTTACCCTATGGGGGTATTTCGG
1 TCATTTTACCCTATAGGGGTATTTCGA
*
37426895 TCATTCTACCCTAT-GGGGTATTTCGA
1 TCATTTTACCCTATAGGGGTATTTCGA
* * *
37426921 TCATTTTACCCAATAGAGGTATTTCAA
1 TCATTTTACCCTATAGGGGTATTTCGA
* * * *
37426948 TCATTTTACCCCATATGGATATTTTGA
1 TCATTTTACCCTATAGGGGTATTTCGA
*
37426975 TCATTTTACCCTATAGGGGTATTTTCGG
1 TCATTTTACCCTATAGGGGTA-TTTCGA
* * *
37427003 TCATTCTATCCTATGGGGGTATTTCGA
1 TCATTTTACCCTATAGGGGTATTTCGA
* *
37427030 TCATTTTACCTTATAGGGGTAATTCGA
1 TCATTTTACCCTATAGGGGTATTTCGA
37427057 TCATTTTACCCTATAGGGGTATT
1 TCATTTTACCCTATAGGGGTATT
37427080 CTTGTTATTT
Statistics
Matches: 155, Mismatches: 28, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
26 23 0.15
27 110 0.71
28 22 0.14
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.41
Consensus pattern (27 bp):
TCATTTTACCCTATAGGGGTATTTCGA
Found at i:37427034 original size:82 final size:82
Alignment explanation
Indices: 37426868--37427079 Score: 266
Period size: 82 Copynumber: 2.6 Consensus size: 82
37426858 TGTATAACAG
* * * *
37426868 TCATTTTACCCTATGGGGGTATTTCGGTCATTCTACCCTAT-GGGGTA-TTTCGATCATTTTACC
1 TCATTTTACCCTATAGGGGTATTTCGATCATTTTACCCTATAGGGGTATTTTCGATCATTCTACC
37426931 CAATAGAGGTATTTCAA
66 CAATAGAGGTATTTCAA
* * * * * *
37426948 TCATTTTACCCCATATGGATATTTTGATCATTTTACCCTATAGGGGTATTTTCGGTCATTCTATC
1 TCATTTTACCCTATAGGGGTATTTCGATCATTTTACCCTATAGGGGTATTTTCGATCATTCTACC
* * * *
37427013 CTATGGGGGTATTTCGA
66 CAATAGAGGTATTTCAA
* *
37427030 TCATTTTACCTTATAGGGGTAATTCGATCATTTTACCCTATAGGGGTATT
1 TCATTTTACCCTATAGGGGTATTTCGATCATTTTACCCTATAGGGGTATT
37427080 CTTGTTATTT
Statistics
Matches: 110, Mismatches: 20, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
80 34 0.31
81 6 0.05
82 70 0.64
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.41
Consensus pattern (82 bp):
TCATTTTACCCTATAGGGGTATTTCGATCATTTTACCCTATAGGGGTATTTTCGATCATTCTACC
CAATAGAGGTATTTCAA
Found at i:37436009 original size:21 final size:20
Alignment explanation
Indices: 37435975--37436013 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
37435965 GAATATACGC
37435975 CTGTTTGTCAGAACATTTTGT
1 CTGTTTGTCAGAAC-TTTTGT
**
37435996 CTGTTTGTGTGAACTTTT
1 CTGTTTGTCAGAACTTTT
37436014 CGTTATTGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.15, C:0.13, G:0.21, T:0.51
Consensus pattern (20 bp):
CTGTTTGTCAGAACTTTTGT
Found at i:37436190 original size:10 final size:10
Alignment explanation
Indices: 37436175--37436200 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
37436165 TTGTGTCACT
37436175 CCATCTTTTG
1 CCATCTTTTG
37436185 CCATCTTTTG
1 CCATCTTTTG
37436195 CCATCT
1 CCATCT
37436201 GGTCATCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.12, C:0.35, G:0.08, T:0.46
Consensus pattern (10 bp):
CCATCTTTTG
Found at i:37457253 original size:35 final size:35
Alignment explanation
Indices: 37457202--37457272 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
37457192 AAGAGTTACC
37457202 TGAATTACTGCCGGTCAGAGAGGTTGAGTATGCTA
1 TGAATTACTGCCGGTCAGAGAGGTTGAGTATGCTA
*
37457237 TGAATTACTGCTGGTCAGAGAGGTTGAGTATGCTA
1 TGAATTACTGCCGGTCAGAGAGGTTGAGTATGCTA
37457272 T
1 T
37457273 CTTATACCGG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.25, C:0.13, G:0.31, T:0.31
Consensus pattern (35 bp):
TGAATTACTGCCGGTCAGAGAGGTTGAGTATGCTA
Found at i:37461280 original size:25 final size:24
Alignment explanation
Indices: 37461216--37461288 Score: 65
Period size: 25 Copynumber: 2.9 Consensus size: 24
37461206 ATTACATTGC
* *
37461216 AGCTCGTGGGAGCTTACCAATTCTT
1 AGCTCGT-AGAGCTTACCATTTCTT
* * *
37461241 CGCTTGTGAGCGCTTACCATTTCTT
1 AGCTCGT-AGAGCTTACCATTTCTT
37461266 AGCTCGTATGAGCTTACCGATTT
1 AGCTCGTA-GAGCTTACC-ATTT
37461289 ATATCTCGTG
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
24 1 0.03
25 33 0.87
26 4 0.11
ACGTcount: A:0.18, C:0.25, G:0.22, T:0.36
Consensus pattern (24 bp):
AGCTCGTAGAGCTTACCATTTCTT
Found at i:37461296 original size:25 final size:25
Alignment explanation
Indices: 37461265--37461332 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 25
37461255 TACCATTTCT
* *
37461265 TAGCTCGTATGAGCTTACCGATTTA
1 TAGCTCGTATGAGCATACCGATTCA
* *
37461290 TATCTCGTGA-GAGCATATCGATTCA
1 TAGCTCGT-ATGAGCATACCGATTCA
*
37461315 TAGCTCGTATAAGCATAC
1 TAGCTCGTATGAGCATAC
37461333 ATATACAGGA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
24 1 0.03
25 32 0.94
26 1 0.03
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (25 bp):
TAGCTCGTATGAGCATACCGATTCA
Found at i:37469905 original size:19 final size:19
Alignment explanation
Indices: 37469874--37469922 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
37469864 TAGTTTAGAT
37469874 TTCAAAAAT-TATAAAAAA
1 TTCAAAAATATATAAAAAA
* *
37469892 TTGAAAAATATATAAACAA
1 TTCAAAAATATATAAAAAA
37469911 TTCAAAACATAT
1 TTCAAAA-ATAT
37469923 GTTAAGAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 8 0.31
19 14 0.54
20 4 0.15
ACGTcount: A:0.61, C:0.08, G:0.02, T:0.29
Consensus pattern (19 bp):
TTCAAAAATATATAAAAAA
Found at i:37469922 original size:18 final size:17
Alignment explanation
Indices: 37469874--37469922 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 17
37469864 TAGTTTAGAT
37469874 TTCAAAAATTATAAAAAA
1 TTCAAAAA-TATAAAAAA
*
37469892 TTGAAAAATATATAAACAA
1 TTCAAAAATATA-AAA-AA
37469911 TTCAAAACATAT
1 TTCAAAA-ATAT
37469923 GTTAAGAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 4 0.15
18 10 0.38
19 8 0.31
20 4 0.15
ACGTcount: A:0.61, C:0.08, G:0.02, T:0.29
Consensus pattern (17 bp):
TTCAAAAATATAAAAAA
Found at i:37470177 original size:18 final size:18
Alignment explanation
Indices: 37470128--37470238 Score: 64
Period size: 19 Copynumber: 5.7 Consensus size: 18
37470118 AAATTTTTGC
37470128 TTTTTGAATTTTAAAAATAT
1 TTTTTGAATTTT--AAATAT
*
37470148 TTTTT-ATTTTTTAAATAT
1 TTTTTGA-ATTTTAAATAT
37470166 TTTTTGAATTTTTATAAT-T
1 TTTTTGAA-TTTTA-AATAT
* ** *
37470185 TTCTAAAATTTTAACTAT
1 TTTTTGAATTTTAAATAT
37470203 ATTTTTGAATTTATCTAAATAT
1 -TTTTTGAA-TT-T-TAAATAT
*
37470225 TTTGTGAATCTTTA
1 TTTTTGAAT-TTTA
37470239 TATTTCGTGT
Statistics
Matches: 70, Mismatches: 11, Indels: 21
0.69 0.11 0.21
Matches are distributed among these distances:
17 2 0.03
18 17 0.24
19 20 0.29
20 16 0.23
21 9 0.13
22 6 0.09
ACGTcount: A:0.32, C:0.04, G:0.05, T:0.59
Consensus pattern (18 bp):
TTTTTGAATTTTAAATAT
Found at i:37470177 original size:19 final size:19
Alignment explanation
Indices: 37470128--37470238 Score: 91
Period size: 18 Copynumber: 5.7 Consensus size: 19
37470118 AAATTTTTGC
*
37470128 TTTTTGAATTTTAAAAATAT
1 TTTTTGAATTTT-TAAATAT
*
37470148 TTTTT-ATTTTTTAAATAT
1 TTTTTGAATTTTTAAATAT
*
37470166 TTTTTGAATTTTTATA-AT
1 TTTTTGAATTTTTAAATAT
* * * *
37470184 TTTCTAAAATTTTAACTAT
1 TTTTTGAATTTTTAAATAT
37470203 ATTTTTGAATTTATCTAAATAT
1 -TTTTTGAATTT-T-TAAATAT
* *
37470225 TTTGTGAATCTTTA
1 TTTTTGAATTTTTA
37470239 TATTTCGTGT
Statistics
Matches: 71, Mismatches: 15, Indels: 11
0.73 0.15 0.11
Matches are distributed among these distances:
18 24 0.34
19 17 0.24
20 14 0.20
21 10 0.14
22 6 0.08
ACGTcount: A:0.32, C:0.04, G:0.05, T:0.59
Consensus pattern (19 bp):
TTTTTGAATTTTTAAATAT
Found at i:37475933 original size:21 final size:21
Alignment explanation
Indices: 37475907--37475961 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
37475897 AACAGCGGTG
*
37475907 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGGTACTGTA
*
37475928 GCGGTGAGATTGGGTACTGTA
1 GCGGTGAGATTAGGTACTGTA
37475949 GCGGTGAGATTAG
1 GCGGTGAGATTAG
37475962 AAATAATGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.22, C:0.09, G:0.40, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGGTACTGTA
Found at i:37482251 original size:19 final size:19
Alignment explanation
Indices: 37482224--37482260 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
37482214 AAACTGGCAA
*
37482224 AAACGAGGGACAAACCAGT
1 AAACAAGGGACAAACCAGT
*
37482243 AAACAAGGGAGAAACCAG
1 AAACAAGGGACAAACCAG
37482261 CAAGAACGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.19, G:0.27, T:0.03
Consensus pattern (19 bp):
AAACAAGGGACAAACCAGT
Found at i:37484207 original size:29 final size:28
Alignment explanation
Indices: 37484170--37484234 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
37484160 AAACGACTCA
37484170 TTTTATAATTAATCTAAATTTTATACTAT
1 TTTTATAATTAAT-TAAATTTTATACTAT
* *
37484199 TTTTATAATTAATTAATTTTTATATTAT
1 TTTTATAATTAATTAAATTTTATACTAT
*
37484227 TTTAATAA
1 TTTTATAA
37484235 AAAATCGGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 20 0.61
29 13 0.39
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.58
Consensus pattern (28 bp):
TTTTATAATTAATTAAATTTTATACTAT
Found at i:37484623 original size:21 final size:23
Alignment explanation
Indices: 37484592--37484638 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 23
37484582 CCGGCCTGAA
*
37484592 TTATATTTTAAATATATATAT-T
1 TTATATTTTAAATAAATATATAT
*
37484614 TTAT-TTTTAATTAAATATATAT
1 TTATATTTTAAATAAATATATAT
37484636 TTA
1 TTA
37484639 ATATGGATCG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
TTATATTTTAAATAAATATATAT
Found at i:37485185 original size:17 final size:16
Alignment explanation
Indices: 37485163--37485205 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
37485153 TTTCAAAAAG
37485163 AAATAAATTATATTAAA
1 AAATAAATTA-ATTAAA
*
37485180 AAATAAA-TAATTCAA
1 AAATAAATTAATTAAA
*
37485195 AAACAAATTAA
1 AAATAAATTAA
37485206 AAGAATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 11 0.48
16 5 0.22
17 7 0.30
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (16 bp):
AAATAAATTAATTAAA
Found at i:37487018 original size:23 final size:23
Alignment explanation
Indices: 37486985--37487064 Score: 115
Period size: 23 Copynumber: 3.4 Consensus size: 23
37486975 ACAAACTCAA
* *
37486985 CTACCAATTTGTTTTATTACCAG
1 CTACCATTTTGTTTCATTACCAG
*
37487008 CTACCATTTTGTTTCGTTACCAG
1 CTACCATTTTGTTTCATTACCAG
*
37487031 CTACCATTTTGTTTCATTACCAA
1 CTACCATTTTGTTTCATTACCAG
37487054 CTACCAATTTT
1 CTACC-ATTTT
37487065 TTTTTAAAGT
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
23 46 0.90
24 5 0.10
ACGTcount: A:0.24, C:0.25, G:0.07, T:0.44
Consensus pattern (23 bp):
CTACCATTTTGTTTCATTACCAG
Found at i:37487284 original size:9 final size:9
Alignment explanation
Indices: 37487270--37487319 Score: 73
Period size: 9 Copynumber: 5.6 Consensus size: 9
37487260 TTTGGTTAAA
37487270 AATTAACCG
1 AATTAACCG
37487279 AATTAACCG
1 AATTAACCG
*
37487288 AATTAACCA
1 AATTAACCG
*
37487297 AATTACCCG
1 AATTAACCG
*
37487306 AATTATCCG
1 AATTAACCG
37487315 AATTA
1 AATTA
37487320 CCTGAATTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 37 1.00
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:37487320 original size:18 final size:18
Alignment explanation
Indices: 37487270--37487327 Score: 80
Period size: 18 Copynumber: 3.2 Consensus size: 18
37487260 TTTGGTTAAA
*
37487270 AATTAACCGAATTAACCG
1 AATTAACCGAATTACCCG
*
37487288 AATTAACCAAATTACCCG
1 AATTAACCGAATTACCCG
* *
37487306 AATTATCCGAATTACCTG
1 AATTAACCGAATTACCCG
37487324 AATT
1 AATT
37487328 GAATCACTAC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.28
Consensus pattern (18 bp):
AATTAACCGAATTACCCG
Found at i:37487326 original size:9 final size:8
Alignment explanation
Indices: 37487270--37487327 Score: 53
Period size: 9 Copynumber: 6.5 Consensus size: 8
37487260 TTTGGTTAAA
37487270 AATTAACCG
1 AATT-ACCG
37487279 AATTAACCG
1 AATT-ACCG
*
37487288 AATTAACCA
1 AATT-ACCG
37487297 AATTACCCG
1 AATTA-CCG
37487306 AATTATCCG
1 AATTA-CCG
37487315 AATTACCTG
1 AATTACC-G
37487324 AATT
1 AATT
37487328 GAATCACTAC
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
8 3 0.07
9 41 0.93
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.28
Consensus pattern (8 bp):
AATTACCG
Found at i:37487583 original size:38 final size:39
Alignment explanation
Indices: 37487532--37487607 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 39
37487522 ACTTAAGAGT
* *
37487532 TAGACTTTTGTTTTATTTTTATTAGG-TTGGTAATTGGA
1 TAGACTTTAGTTTTAGTTTTATTAGGTTTGGTAATTGGA
37487570 TAGACTTTAGTTTTAGTTTTATTAGGTTTGGTAATTGG
1 TAGACTTTAGTTTTAGTTTTATTAGGTTTGGTAATTGG
37487608 GTTGGGTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
38 24 0.69
39 11 0.31
ACGTcount: A:0.21, C:0.03, G:0.22, T:0.54
Consensus pattern (39 bp):
TAGACTTTAGTTTTAGTTTTATTAGGTTTGGTAATTGGA
Found at i:37487619 original size:52 final size:52
Alignment explanation
Indices: 37487556--37487666 Score: 188
Period size: 52 Copynumber: 2.2 Consensus size: 52
37487546 ATTTTTATTA
*
37487556 GGTT-GGTAATTGGATAGACTTTAGTTTTAGTTTTATTAGGTTTGGTAATTG
1 GGTTGGGTAATTGGATAGACTTTAGTTTTAGTTTTATTAGGTTGGGTAATTG
* *
37487607 GGTTGGGTAATTGGGTAGACTTTAGTTTTAGTTTTATTTGGTTGGGTAATTG
1 GGTTGGGTAATTGGATAGACTTTAGTTTTAGTTTTATTAGGTTGGGTAATTG
37487659 GGTTGGGT
1 GGTTGGGT
37487667 TGGTAATTGG
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
51 4 0.07
52 52 0.93
ACGTcount: A:0.18, C:0.02, G:0.32, T:0.48
Consensus pattern (52 bp):
GGTTGGGTAATTGGATAGACTTTAGTTTTAGTTTTATTAGGTTGGGTAATTG
Found at i:37487671 original size:17 final size:18
Alignment explanation
Indices: 37487646--37487681 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
37487636 AGTTTTATTT
37487646 GGTTGGGTAATTGGGTTG
1 GGTTGGGTAATTGGGTTG
37487664 GGTT-GGTAATTGGGTTG
1 GGTTGGGTAATTGGGTTG
37487681 G
1 G
37487682 TAATTAGGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.11, C:0.00, G:0.50, T:0.39
Consensus pattern (18 bp):
GGTTGGGTAATTGGGTTG
Found at i:37487676 original size:12 final size:12
Alignment explanation
Indices: 37487661--37487693 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
37487651 GGTAATTGGG
37487661 TTGGGTTGGTAA
1 TTGGGTTGGTAA
37487673 TTGGGTTGGTAA
1 TTGGGTTGGTAA
*
37487685 TTAGGTTGG
1 TTGGGTTGG
37487694 GTTAGATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.42, T:0.42
Consensus pattern (12 bp):
TTGGGTTGGTAA
Found at i:37489057 original size:35 final size:35
Alignment explanation
Indices: 37488973--37489348 Score: 287
Period size: 35 Copynumber: 10.4 Consensus size: 35
37488963 CAGAACTTTA
*
37488973 AAAAAGTTTGGGATAGACCTAGTC-AAGGCCAACCTTT
1 AAAAAGGTTGGGATAGACC-AGTCTAAGG-CAACC-TT
*
37489010 GAAAAAGGTTGGGATAAACCAGTCTAAGGCAACCTT
1 -AAAAAGGTTGGGATAGACCAGTCTAAGGCAACCTT
**
37489046 AAAAAGGTTGGGATAGACCAGTCTAAGATAACCTTT
1 AAAAAGGTTGGGATAGACCAGTCTAAGGCAACC-TT
** * * *** **
37489082 AAAAAAATTTGGGATATACCTCA-TTTAAAAAAATTTT
1 -AAAAAGGTTGGGATAGA-C-CAGTCTAAGGCAACCTT
* * * *
37489119 AAAATATGTTGAGATAGACCTGTTTAAGGCAACCTT
1 AAAA-AGGTTGGGATAGACCAGTCTAAGGCAACCTT
* *
37489155 AAAAAGGTTAGGATAGACTC-GTTTAAGGCAA-CTT
1 AAAAAGGTTGGGATAGAC-CAGTCTAAGGCAACCTT
* * * *
37489189 TAAAATGTTGGGATAGACCTTGTCTAAGACAACCCTT
1 AAAAAGGTTGGGATAGACC-AGTCTAAGGCAA-CCTT
* *
37489226 AAAAAAGGTTGGGATAGACCAGTCTAAAGCAACCCT
1 -AAAAAGGTTGGGATAGACCAGTCTAAGGCAACCTT
*
37489262 AAAAAGGTTGAGATAGACCTTA-TCTAAGGCAACCTTT
1 AAAAAGGTTGGGATAGACC--AGTCTAAGGCAACC-TT
* * **
37489299 AAAAAGGTTGAGATAGAGTC-GTCTAATACAACCTT
1 AAAAAGGTTGGGATAGA-CCAGTCTAAGGCAACCTT
37489334 AAAAAGGTTGGGATA
1 AAAAAGGTTGGGATA
37489349 TACCTTACAA
Statistics
Matches: 276, Mismatches: 44, Indels: 39
0.77 0.12 0.11
Matches are distributed among these distances:
33 1 0.00
34 18 0.07
35 96 0.35
36 47 0.17
37 65 0.24
38 47 0.17
39 2 0.01
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (35 bp):
AAAAAGGTTGGGATAGACCAGTCTAAGGCAACCTT
Found at i:37489238 original size:144 final size:143
Alignment explanation
Indices: 37488973--37489354 Score: 391
Period size: 144 Copynumber: 2.6 Consensus size: 143
37488963 CAGAACTTTA
* * * *
37488973 AAAAAGTTTGGGATAGACCTAG-TCAAGGCCAACCTTTGAAAAAGGTTGGGATAAAC-CAGTCTA
1 AAAAAGGTTGAGATAGACCT-GTTTAAGG-CAACCTTT-AAAAAGGTT-GGATAGACTC-GTCTA
* * * * *
37489036 AGGCAACCTTAAAAAGGTTGGGATAGACC-AGTCTAAGATAACCTTTAAAAAAATTTGGGATATA
61 AGGCAACCTTAAAAAGGTTGGGATAGACCTTGTCTAAGACAACCCTTAAAAAAAGTTGGGATAGA
* ***
37489100 CCTCA-TTTAAAAAAATTTT
126 -C-CAGTCTAAAAAAACCCT
* *
37489119 AAAATATGTTGAGATAGACCTGTTTAAGGCAACC-TTAAAAAGGTTAGGATAGACTCGTTTAAGG
1 AAAA-AGGTTGAGATAGACCTGTTTAAGGCAACCTTTAAAAAGGTT-GGATAGACTCGTCTAAGG
* * *
37489183 CAA-CTTTAAAATGTTGGGATAGACCTTGTCTAAGACAACCCTTAAAAAAGGTTGGGATAGACCA
64 CAACCTTAAAAAGGTTGGGATAGACCTTGTCTAAGACAACCCTTAAAAAAAGTTGGGATAGACCA
**
37489247 GTCTAAAGCAACCCT
129 GTCTAAAAAAACCCT
* *
37489262 AAAAAGGTTGAGATAGACCT-TATCTAAGGCAACCTTTAAAAAGGTTGAGATAGAGTCGTCTAAT
1 AAAAAGGTTGAGATAGACCTGT-T-TAAGGCAACCTTTAAAAAGGTTG-GATAGACTCGTCTAAG
* *
37489326 ACAACCTTAAAAAGGTTGGGATATACCTT
63 GCAACCTTAAAAAGGTTGGGATAGACCTT
37489355 ACAAAATCTT
Statistics
Matches: 197, Mismatches: 29, Indels: 21
0.80 0.12 0.09
Matches are distributed among these distances:
141 1 0.01
142 18 0.09
143 44 0.22
144 82 0.42
145 24 0.12
146 10 0.05
147 18 0.09
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (143 bp):
AAAAAGGTTGAGATAGACCTGTTTAAGGCAACCTTTAAAAAGGTTGGATAGACTCGTCTAAGGCA
ACCTTAAAAAGGTTGGGATAGACCTTGTCTAAGACAACCCTTAAAAAAAGTTGGGATAGACCAGT
CTAAAAAAACCCT
Found at i:37489258 original size:72 final size:73
Alignment explanation
Indices: 37488973--37489354 Score: 309
Period size: 72 Copynumber: 5.3 Consensus size: 73
37488963 CAGAACTTTA
* * * * * *
37488973 AAAAAGTTTGGGATAGACCTAGTC-AAGGCCAACCTTTGAAAAAGGTTGGGATAAACCAGTCTAA
1 AAAAAGGTTGGGATAGACCTTGTCTAA-GACAACCCTTAAAAAAGGTTGGGATAGACCAGTCTAA
*
37489037 GGCAACCTT
65 AGCAACCTT
* * * ** * *
37489046 AAAAAGGTTGGGATAGACC-AGTCTAAGATAACCTTTAAAAAAATTTGGGATATACCTCA-TTTA
1 AAAAAGGTTGGGATAGACCTTGTCTAAGACAACCCTTAAAAAAGGTTGGGATAGA-C-CAGTCTA
** **
37489109 AAAAAATTTT
64 AAGCAACCTT
* * * * * *
37489119 AAAATATGTTGAGATAGACC-TGTTTAAGGCAA-CCTT-AAAAAGGTTAGGATAGACTC-GTTTA
1 AAAA-AGGTTGGGATAGACCTTGTCTAAGACAACCCTTAAAAAAGGTTGGGATAGAC-CAGTCTA
*
37489180 AGGCAA-CTT
64 AAGCAACCTT
* *
37489189 TAAAATGTTGGGATAGACCTTGTCTAAGACAACCCTTAAAAAAGGTTGGGATAGACCAGTCTAAA
1 AAAAAGGTTGGGATAGACCTTGTCTAAGACAACCCTTAAAAAAGGTTGGGATAGACCAGTCTAAA
*
37489254 GCAACCCT
66 GCAACCTT
* * * * * *
37489262 AAAAAGGTTGAGATAGACCTTATCTAAGGCAA-CCTTTAAAAAGGTTGAGATAGAGTC-GTCTAA
1 AAAAAGGTTGGGATAGACCTTGTCTAAGACAACCCTTAAAAAAGGTTGGGATAGA-CCAGTCTAA
37489325 TA-CAACCTT
65 -AGCAACCTT
*
37489334 AAAAAGGTTGGGATATACCTT
1 AAAAAGGTTGGGATAGACCTT
37489355 ACAAAATCTT
Statistics
Matches: 250, Mismatches: 47, Indels: 25
0.78 0.15 0.08
Matches are distributed among these distances:
69 14 0.06
70 15 0.06
71 15 0.06
72 116 0.46
73 67 0.27
74 23 0.09
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (73 bp):
AAAAAGGTTGGGATAGACCTTGTCTAAGACAACCCTTAAAAAAGGTTGGGATAGACCAGTCTAAA
GCAACCTT
Found at i:37489835 original size:23 final size:24
Alignment explanation
Indices: 37489787--37489837 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
37489777 AATCAAAGTC
*
37489787 AAATATATCATGCTAATAAATACT
1 AAATATATCATACTAATAAATACT
* *
37489811 AAATATATTATACTCAT-AATACT
1 AAATATATCATACTAATAAATACT
37489834 AAAT
1 AAAT
37489838 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 10 0.42
24 14 0.58
ACGTcount: A:0.51, C:0.12, G:0.02, T:0.35
Consensus pattern (24 bp):
AAATATATCATACTAATAAATACT
Found at i:37495297 original size:24 final size:24
Alignment explanation
Indices: 37495262--37495309 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
37495252 TGAGATATCA
* *
37495262 ACCTTTTTATTGTTATCCTTTTCG
1 ACCTTTTCATTGATATCCTTTTCG
*
37495286 ACCTTTTCATTGATATCTTTTTCG
1 ACCTTTTCATTGATATCCTTTTCG
37495310 GATAACATCC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.15, C:0.21, G:0.08, T:0.56
Consensus pattern (24 bp):
ACCTTTTCATTGATATCCTTTTCG
Found at i:37495355 original size:41 final size:40
Alignment explanation
Indices: 37495276--37495417 Score: 189
Period size: 40 Copynumber: 3.5 Consensus size: 40
37495266 TTTTATTGTT
* * *
37495276 ATCCTTTTCGACCTTTTCATTGATAT-CTTTTTCGGATAAC
1 ATCCTTTTCAACCTTTTCATTTATATCCTTTTT-TGATAAC
37495316 ATCCTTTTCAACCTTTTCATTTTATATCCTTTTTTGATAAC
1 ATCCTTTTCAACCTTTTCA-TTTATATCCTTTTTTGATAAC
*
37495357 ATCATTTTCAACCTTTTCATTTATATCCTTTTTTGATAAC
1 ATCCTTTTCAACCTTTTCATTTATATCCTTTTTTGATAAC
* *
37495397 -GCCATTTTCAACCTGTTCATT
1 ATCC-TTTTCAACCTTTTCATT
37495418 GATTCAGAAA
Statistics
Matches: 92, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
39 1 0.01
40 55 0.60
41 30 0.33
42 6 0.07
ACGTcount: A:0.22, C:0.23, G:0.06, T:0.50
Consensus pattern (40 bp):
ATCCTTTTCAACCTTTTCATTTATATCCTTTTTTGATAAC
Found at i:37498470 original size:12 final size:12
Alignment explanation
Indices: 37498453--37498518 Score: 78
Period size: 12 Copynumber: 5.5 Consensus size: 12
37498443 TTTAAGGTGT
37498453 ACACGGCCTGGG
1 ACACGGCCTGGG
* **
37498465 ACACGGGCTGTC
1 ACACGGCCTGGG
37498477 ACACGGCCTGGG
1 ACACGGCCTGGG
* **
37498489 ACACGGGCTGTC
1 ACACGGCCTGGG
37498501 ACACGGCCTGGG
1 ACACGGCCTGGG
37498513 ACACGG
1 ACACGG
37498519 GCTGTCACAT
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 42 1.00
ACGTcount: A:0.18, C:0.33, G:0.38, T:0.11
Consensus pattern (12 bp):
ACACGGCCTGGG
Found at i:37498535 original size:24 final size:24
Alignment explanation
Indices: 37498453--37498527 Score: 150
Period size: 24 Copynumber: 3.1 Consensus size: 24
37498443 TTTAAGGTGT
37498453 ACACGGCCTGGGACACGGGCTGTC
1 ACACGGCCTGGGACACGGGCTGTC
37498477 ACACGGCCTGGGACACGGGCTGTC
1 ACACGGCCTGGGACACGGGCTGTC
37498501 ACACGGCCTGGGACACGGGCTGTC
1 ACACGGCCTGGGACACGGGCTGTC
37498525 ACA
1 ACA
37498528 TAGCCTGGCC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.19, C:0.33, G:0.36, T:0.12
Consensus pattern (24 bp):
ACACGGCCTGGGACACGGGCTGTC
Found at i:37500437 original size:11 final size:11
Alignment explanation
Indices: 37500423--37500459 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
37500413 TCTTTATATT
37500423 TTTTTTTTGAA
1 TTTTTTTTGAA
37500434 TTTTTTTTGAA
1 TTTTTTTTGAA
*
37500445 TTTTTTAT-AA
1 TTTTTTTTGAA
37500455 TTTTT
1 TTTTT
37500460 ATATGTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
10 7 0.28
11 18 0.72
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.76
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:37500736 original size:52 final size:52
Alignment explanation
Indices: 37500667--37500772 Score: 185
Period size: 52 Copynumber: 2.0 Consensus size: 52
37500657 CATTGTAAAT
*
37500667 AAGTATACATTTTAGATGAAAAACAAAGTATATAAAAAATTACAAAATTACA
1 AAGTATACATTTCAGATGAAAAACAAAGTATATAAAAAATTACAAAATTACA
* *
37500719 AAGTATACGTTTCAGATGTAAAACAAAGTATATAAAAAATTACAAAATTACA
1 AAGTATACATTTCAGATGAAAAACAAAGTATATAAAAAATTACAAAATTACA
37500771 AA
1 AA
37500773 ATAATGTAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.57, C:0.08, G:0.08, T:0.26
Consensus pattern (52 bp):
AAGTATACATTTCAGATGAAAAACAAAGTATATAAAAAATTACAAAATTACA
Found at i:37501334 original size:63 final size:63
Alignment explanation
Indices: 37501204--37501335 Score: 138
Period size: 63 Copynumber: 2.1 Consensus size: 63
37501194 GTAGGTGTTG
* * * ** * * * * * *
37501204 ATGCAGGGAATGATTGCGCGTGTTGTGATGCTTGTTTTAAATAAATTAGTACTGAATGTGCTG
1 ATGCAGAGAATGATTGCGCGTGTTGTGATGCTTGTGTAAAATAAACCAGAACGGAAGGCGATA
* * *
37501267 ATGCAGAGAATGATTGTGCGTGTTGTGGTGGTTGTGTAAAATAAACCAGAACGGAAGGCGATA
1 ATGCAGAGAATGATTGCGCGTGTTGTGATGCTTGTGTAAAATAAACCAGAACGGAAGGCGATA
37501330 ATGCAG
1 ATGCAG
37501336 GGAGTGAGTG
Statistics
Matches: 55, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
63 55 1.00
ACGTcount: A:0.29, C:0.10, G:0.31, T:0.30
Consensus pattern (63 bp):
ATGCAGAGAATGATTGCGCGTGTTGTGATGCTTGTGTAAAATAAACCAGAACGGAAGGCGATA
Found at i:37503259 original size:25 final size:25
Alignment explanation
Indices: 37503239--37503301 Score: 90
Period size: 25 Copynumber: 2.5 Consensus size: 25
37503229 ATGAGCTCTG
* *
37503239 AATCGGTATGCTCTCTCGAGCTGAA
1 AATCGGTATGCTCTCACGAGCTGTA
*
37503264 AATCGATATGCTCTCACGAGCTGTA
1 AATCGGTATGCTCTCACGAGCTGTA
*
37503289 AATCGGTAAGCTC
1 AATCGGTATGCTC
37503302 ATATGAGCTA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (25 bp):
AATCGGTATGCTCTCACGAGCTGTA
Found at i:37503309 original size:25 final size:24
Alignment explanation
Indices: 37503219--37503310 Score: 85
Period size: 25 Copynumber: 3.7 Consensus size: 24
37503209 TCCTATACAT
* *
37503219 GTATGCTCATATGAGCTCTGAATCG
1 GTATGCTC-TATGAGCTGTAAATCG
* *
37503244 GTATGCTCTCTCGAGCTGAAAATCG
1 GTATGCTCTAT-GAGCTGTAAATCG
* *
37503269 ATATGCTCTCACGAGCTGTAAATCG
1 GTATGCTCT-ATGAGCTGTAAATCG
*
37503294 GTAAGCTCATATGAGCT
1 GTATGCTC-TATGAGCT
37503311 ATGGTGTGTC
Statistics
Matches: 53, Mismatches: 11, Indels: 6
0.76 0.16 0.09
Matches are distributed among these distances:
24 2 0.04
25 50 0.94
26 1 0.02
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (24 bp):
GTATGCTCTATGAGCTGTAAATCG
Found at i:37505906 original size:15 final size:15
Alignment explanation
Indices: 37505886--37505915 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
37505876 AAAATTATAA
37505886 GAAGAGAATAAAATT
1 GAAGAGAATAAAATT
*
37505901 GAAGAGGATAAAATT
1 GAAGAGAATAAAATT
37505916 CAAAAAAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.23, T:0.20
Consensus pattern (15 bp):
GAAGAGAATAAAATT
Found at i:37505957 original size:22 final size:22
Alignment explanation
Indices: 37505932--37505981 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
37505922 AAATTGAGGA
* *
37505932 TTGAAAATTTAAAATTTAAAAT
1 TTGAAAATTAAAAATATAAAAT
* *
37505954 TTGAAGATTAAAAATATAAAGT
1 TTGAAAATTAAAAATATAAAAT
37505976 TTGAAA
1 TTGAAA
37505982 TTGGGGATTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.36
Consensus pattern (22 bp):
TTGAAAATTAAAAATATAAAAT
Found at i:37505997 original size:7 final size:7
Alignment explanation
Indices: 37505987--37506027 Score: 64
Period size: 7 Copynumber: 5.9 Consensus size: 7
37505977 TGAAATTGGG
*
37505987 GATTGAA
1 GATTGAT
*
37505994 GATTGAA
1 GATTGAT
37506001 GATTGAT
1 GATTGAT
37506008 GATTGAT
1 GATTGAT
37506015 GATTGAT
1 GATTGAT
37506022 GATTGA
1 GATTGA
37506028 GAATTTAGGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (7 bp):
GATTGAT
Found at i:37506481 original size:12 final size:12
Alignment explanation
Indices: 37506464--37506498 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
37506454 TAATTTCACC
37506464 TTTTCTTTTCTT
1 TTTTCTTTTCTT
*
37506476 TTTTCTTTTTTT
1 TTTTCTTTTCTT
37506488 TTTATCTTTTC
1 TTT-TCTTTTC
37506499 CTAGATTAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 14 0.70
13 6 0.30
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (12 bp):
TTTTCTTTTCTT
Found at i:37507140 original size:40 final size:40
Alignment explanation
Indices: 37507096--37507197 Score: 177
Period size: 40 Copynumber: 2.5 Consensus size: 40
37507086 TGGACTTAAA
* *
37507096 ATCTCAATCCATGATGACAAGCCCATGTGGAAGATGTAAC
1 ATCTCAATCCATGATGACAAGCCCATATGGAAGATATAAC
*
37507136 ATCTCAATCCATGATGGCAAGCCCATATGGAAGATATAAC
1 ATCTCAATCCATGATGACAAGCCCATATGGAAGATATAAC
37507176 ATCTCAATCCATGATGACAAGC
1 ATCTCAATCCATGATGACAAGC
37507198 TCACATGTCT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 58 1.00
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.23
Consensus pattern (40 bp):
ATCTCAATCCATGATGACAAGCCCATATGGAAGATATAAC
Found at i:37507772 original size:27 final size:28
Alignment explanation
Indices: 37507736--37507788 Score: 83
Period size: 26 Copynumber: 1.9 Consensus size: 28
37507726 AGTTAATAAA
37507736 TTCTCTTTGAGTTTTTCTTTTA-AAGAAT
1 TTCTCTTTGAG-TTTTCTTTTAGAAGAAT
37507764 TTCTC-TTGAGTTTTCTTTTAGAAGA
1 TTCTCTTTGAGTTTTCTTTTAGAAGA
37507789 GTTTTAACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 10 0.42
27 9 0.38
28 5 0.21
ACGTcount: A:0.21, C:0.11, G:0.13, T:0.55
Consensus pattern (28 bp):
TTCTCTTTGAGTTTTCTTTTAGAAGAAT
Found at i:37508485 original size:19 final size:19
Alignment explanation
Indices: 37508444--37508486 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
37508434 ATATTATGTA
**
37508444 TAATTTTAAGATTTATTTC
1 TAATTTTAAGATTTAAGTC
* *
37508463 TAATTTTAAGTTTTAAGTG
1 TAATTTTAAGATTTAAGTC
37508482 TAATT
1 TAATT
37508487 AATATATTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.02, G:0.09, T:0.56
Consensus pattern (19 bp):
TAATTTTAAGATTTAAGTC
Found at i:37512631 original size:19 final size:19
Alignment explanation
Indices: 37512607--37512648 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
37512597 AGTTTATTTT
*
37512607 TTTTTTAAATTTTTCAAAA
1 TTTTTTAAATTTCTCAAAA
* *
37512626 TTTTTTTAATTTCTCATAA
1 TTTTTTAAATTTCTCAAAA
37512645 TTTT
1 TTTT
37512649 AATTTATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTTTAAATTTCTCAAAA
Found at i:37512752 original size:23 final size:23
Alignment explanation
Indices: 37512708--37512758 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
37512698 CAAAAATTAA
*
37512708 TTTTA-TTTATTATAATATATAT
1 TTTTATTTTATTATAATAAATAT
* *
37512730 TTTTATTTTATTTTATTAAATAT
1 TTTTATTTTATTATAATAAATAT
*
37512753 ATTTAT
1 TTTTAT
37512759 AGTTTTTTAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTTATTTTATTATAATAAATAT
Found at i:37513945 original size:3 final size:3
Alignment explanation
Indices: 37513937--37513965 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
37513927 ATTTGATCTT
37513937 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
37513966 TAAAAGATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:37516904 original size:40 final size:40
Alignment explanation
Indices: 37516857--37516954 Score: 160
Period size: 40 Copynumber: 2.5 Consensus size: 40
37516847 TTTCGTACAT
* *
37516857 CGGCATTAAACCTGCTAGACGTATAGTCTGAATATTTCAC
1 CGGCATTAAGCCTGCTAGACGTATAGTCTAAATATTTCAC
*
37516897 CGGCATTACGCCTGCTAGACGTATAGTCTAAATATTTCAC
1 CGGCATTAAGCCTGCTAGACGTATAGTCTAAATATTTCAC
*
37516937 CGGTATTAAGCCTGCTAG
1 CGGCATTAAGCCTGCTAG
37516955 GCAAAAGCCT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 53 1.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (40 bp):
CGGCATTAAGCCTGCTAGACGTATAGTCTAAATATTTCAC
Found at i:37519126 original size:24 final size:24
Alignment explanation
Indices: 37519073--37519138 Score: 69
Period size: 24 Copynumber: 2.8 Consensus size: 24
37519063 TGAACACTTT
* *
37519073 TAAAATACCCTAATCCTAAAAAAA
1 TAAAAAACCCTAACCCTAAAAAAA
** *
37519097 CCAAAAACCCTAACCCTACAAAAA
1 TAAAAAACCCTAACCCTAAAAAAA
* *
37519121 TAAAAAGCTCTAACCCTA
1 TAAAAAACCCTAACCCTA
37519139 GAAAGAGAAA
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.53, C:0.29, G:0.02, T:0.17
Consensus pattern (24 bp):
TAAAAAACCCTAACCCTAAAAAAA
Found at i:37532783 original size:30 final size:30
Alignment explanation
Indices: 37532749--37532808 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
37532739 AAGATAAATG
37532749 CAAATGCCTCTAAAACAATAACAAAATTAA
1 CAAATGCCTCTAAAACAATAACAAAATTAA
* *
37532779 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAACAATAACAAAATTAA
37532809 TAATAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.57, C:0.17, G:0.03, T:0.23
Consensus pattern (30 bp):
CAAATGCCTCTAAAACAATAACAAAATTAA
Found at i:37557632 original size:17 final size:18
Alignment explanation
Indices: 37557610--37557645 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
37557600 TTTTAATGTC
*
37557610 ATTA-TTTTTCTTTTGTA
1 ATTATTTTTTATTTTGTA
37557627 ATTATTTTTTATTTTGTA
1 ATTATTTTTTATTTTGTA
37557645 A
1 A
37557646 AATTCCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.22, C:0.03, G:0.06, T:0.69
Consensus pattern (18 bp):
ATTATTTTTTATTTTGTA
Found at i:37562281 original size:12 final size:13
Alignment explanation
Indices: 37562258--37562292 Score: 54
Period size: 12 Copynumber: 2.7 Consensus size: 13
37562248 TGATAGTCGT
37562258 AATTTGGAAATTGA
1 AATTT-GAAATTGA
37562272 AA-TTGAAATTGA
1 AATTTGAAATTGA
37562284 AATTTGAAA
1 AATTTGAAA
37562293 GAGTGTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 10 0.50
13 8 0.40
14 2 0.10
ACGTcount: A:0.49, C:0.00, G:0.17, T:0.34
Consensus pattern (13 bp):
AATTTGAAATTGA
Found at i:37562318 original size:159 final size:154
Alignment explanation
Indices: 37562005--37562318 Score: 459
Period size: 159 Copynumber: 2.0 Consensus size: 154
37561995 ATAGGGAGAG
* * * *
37562005 TTTAAAGAGTTCAACTATGATTAAACTTAATCACTTTAATATTAAATTGATTGTCTCGAGGACCT
1 TTTAAAGAGTTCAACTATGATTAAACCTAATAACTTTAATATGAAATTAATTGTCTCGAGGACCT
*
37562070 GAGGATGGAAGTTGTAATGTGATAGTCGTAATTTGGAAATTGAAATTGAAATTTGAAATAGTGTT
66 GAGGATGGAAGTTGTAATGTGATAGTCGTAATTTGGAAATTGAAATTGAAATTTGAAAGAGTGTT
37562135 TAATTAAAATTTTTGAAAAGGAAAATAAC
131 TAATTAAAATTTTT----A-GAAAATAAC
**
37562164 TTTAAAGAGTTCAACTATGATTAAACCTAATAACTTTAATATGAAATTAATTGTCTCGAGGATTT
1 TTTAAAGAGTTCAACTATGATTAAACCTAATAACTTTAATATGAAATTAATTGTCTCGAGGACCT
37562229 GAGGATGGAAGTTGTAATGTGATAGTCGTAATTTGGAAATTGAAATTGAAATTGAAATTTGAAAG
66 GAGGATGGAAGTTGTAATGTGATAGTCGTAATTT-G-----GAAATTGAAATTGAAATTTGAAAG
37562294 AGTGTTTAATTAAAATTTTT-GAAAA
125 AGTGTTTAATTAAAATTTTTAGAAAA
37562319 GGAAAATAAC
Statistics
Matches: 142, Mismatches: 7, Indels: 12
0.88 0.04 0.07
Matches are distributed among these distances:
159 98 0.69
160 1 0.01
165 43 0.30
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.36
Consensus pattern (154 bp):
TTTAAAGAGTTCAACTATGATTAAACCTAATAACTTTAATATGAAATTAATTGTCTCGAGGACCT
GAGGATGGAAGTTGTAATGTGATAGTCGTAATTTGGAAATTGAAATTGAAATTTGAAAGAGTGTT
TAATTAAAATTTTTAGAAAATAAC
Found at i:37563268 original size:15 final size:16
Alignment explanation
Indices: 37563248--37563296 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
37563238 AAGTAATATG
37563248 TAAAATAAATTT-AAA
1 TAAAATAAATTTAAAA
37563263 TAAAAT-AATTTGAAAA
1 TAAAATAAATTT-AAAA
37563279 TAAAA-AAATTTTAAAA
1 TAAAATAAA-TTTAAAA
37563295 TA
1 TA
37563297 GCATATGTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
14 5 0.17
15 6 0.20
16 16 0.53
17 3 0.10
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (16 bp):
TAAAATAAATTTAAAA
Found at i:37563704 original size:15 final size:15
Alignment explanation
Indices: 37563684--37563720 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
37563674 AAATGCGATT
37563684 AAAATAAAATTAAAA
1 AAAATAAAATTAAAA
*
37563699 AAAATAGAATTAAAA
1 AAAATAAAATTAAAA
*
37563714 TAAATAA
1 AAAATAA
37563721 CAAGGACTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.22
Consensus pattern (15 bp):
AAAATAAAATTAAAA
Found at i:37568569 original size:26 final size:26
Alignment explanation
Indices: 37568540--37568616 Score: 118
Period size: 26 Copynumber: 3.0 Consensus size: 26
37568530 ATACCAATAT
*
37568540 CGCAGCAAAGCTGTCAGTAATAGTAA
1 CGCAGCAAAGCTGCCAGTAATAGTAA
* *
37568566 CGCAGCAAAGTTGCCAGTAATAATAA
1 CGCAGCAAAGCTGCCAGTAATAGTAA
*
37568592 CGCAGCAAAGCTGCCAGTAACAGTA
1 CGCAGCAAAGCTGCCAGTAATAGTA
37568617 TATGTGGCAG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 45 1.00
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.17
Consensus pattern (26 bp):
CGCAGCAAAGCTGCCAGTAATAGTAA
Found at i:37568787 original size:27 final size:27
Alignment explanation
Indices: 37568757--37568815 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
37568747 ATCTCCTAGA
37568757 GGTATAACAATCATTTTACCCTATGGG
1 GGTATAACAATCATTTTACCCTATGGG
** **
37568784 GGTATTTCGGTCATTTTACCCTATGGG
1 GGTATAACAATCATTTTACCCTATGGG
*
37568811 AGTAT
1 GGTAT
37568816 TTCGGTTATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (27 bp):
GGTATAACAATCATTTTACCCTATGGG
Found at i:37568816 original size:27 final size:27
Alignment explanation
Indices: 37568767--37568826 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
37568757 GGTATAACAA
*
37568767 TCATTTTACCCTATGGGGGTATTTCGG
1 TCATTTTACCCTATGGGAGTATTTCGG
37568794 TCATTTTACCCTATGGGAGTATTTCGG
1 TCATTTTACCCTATGGGAGTATTTCGG
*
37568821 TTATTT
1 TCATTT
37568827 ATTGATCGCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.17, C:0.17, G:0.22, T:0.45
Consensus pattern (27 bp):
TCATTTTACCCTATGGGAGTATTTCGG
Found at i:37569068 original size:20 final size:20
Alignment explanation
Indices: 37569043--37569097 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
37569033 GGGCCCACGA
37569043 GCCCATTTCGGCCTAACGTG
1 GCCCATTTCGGCCTAACGTG
37569063 GCCCATTTCGGCCTAACGTG
1 GCCCATTTCGGCCTAACGTG
*
37569083 GCCCATTACGGCCTA
1 GCCCATTTCGGCCTA
37569098 CGCTCATGGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.16, C:0.36, G:0.24, T:0.24
Consensus pattern (20 bp):
GCCCATTTCGGCCTAACGTG
Found at i:37571278 original size:20 final size:20
Alignment explanation
Indices: 37571253--37571290 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
37571243 AAAGGTTAAC
37571253 TTAGTAAAATAATAATAATG
1 TTAGTAAAATAATAATAATG
* *
37571273 TTAGTATAATGATAATAA
1 TTAGTAAAATAATAATAA
37571291 AATAAAACAC
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:0.53, C:0.00, G:0.11, T:0.37
Consensus pattern (20 bp):
TTAGTAAAATAATAATAATG
Found at i:37573079 original size:23 final size:23
Alignment explanation
Indices: 37573043--37573414 Score: 321
Period size: 23 Copynumber: 15.7 Consensus size: 23
37573033 TTCGATTCAA
* *
37573043 GTCCAATTTTGGTGTAAAAATGCT
1 GTCCAA-TTTGGTGTATATATGCT
* *
37573067 GCCCAATTTGGTGTCTATATGCT
1 GTCCAATTTGGTGTATATATGCT
* *
37573090 GCCCAATTTGGTGTCTATATGCT
1 GTCCAATTTGGTGTATATATGCT
* *
37573113 GTCCAATTTTGGTGTAAAAATGCT
1 GTCCAA-TTTGGTGTATATATGCT
* * *
37573137 GCCCAATTTGGTGTCTATATGTT
1 GTCCAATTTGGTGTATATATGCT
* * *
37573160 GTTCAATTTGCTGTCTATATGCT
1 GTCCAATTTGGTGTATATATGCT
* *
37573183 GTCCAATTTTTGGTGTAAAAATGCT
1 GTCCAA--TTTGGTGTATATATGCT
* *
37573208 GCCCAATTTGGTGTCTATATGCT
1 GTCCAATTTGGTGTATATATGCT
* *
37573231 GTCCAATTTTGGTGTAAAAATGCT
1 GTCCAA-TTTGGTGTATATATGCT
* *
37573255 GTCCAATTTGATATATATATGCT
1 GTCCAATTTGGTGTATATATGCT
* *
37573278 GCCCAATTTGGTGTATATTTGCT
1 GTCCAATTTGGTGTATATATGCT
* * * *
37573301 GTCAAATTTTGGTGTAAAAAAAATGTT
1 GTCCAA-TTTGGTGT---ATATATGCT
* * *
37573328 GTTCAATTTGATATATATATGCT
1 GTCCAATTTGGTGTATATATGCT
* * * *
37573351 GCCCAAATTAGTGTATAAATGCT
1 GTCCAATTTGGTGTATATATGCT
*
37573374 GTCCAATTTTGGTGTATAAATGCT
1 GTCCAA-TTTGGTGTATATATGCT
*
37573398 GTCCAATTTGATGTATA
1 GTCCAATTTGGTGTATA
37573415 AGAGCTGTAC
Statistics
Matches: 277, Mismatches: 62, Indels: 19
0.77 0.17 0.05
Matches are distributed among these distances:
23 171 0.62
24 73 0.26
25 18 0.06
26 6 0.02
27 9 0.03
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.40
Consensus pattern (23 bp):
GTCCAATTTGGTGTATATATGCT
Found at i:37573156 original size:70 final size:71
Alignment explanation
Indices: 37573043--37573406 Score: 403
Period size: 70 Copynumber: 5.1 Consensus size: 71
37573033 TTCGATTCAA
*
37573043 GTCCAATTTTGGTGTAAAAATGCTGCCCAATTTGGTGTCTATATGCTGCCCAA-TTTGGTGTCTA
1 GTCCAATTTTGGTGTAAAAATGCTGCCCAATTTGGTGTCTATATGCTGTCCAATTTTGGTGTCTA
37573107 TATGCT
66 TATGCT
* * *
37573113 GTCCAATTTTGGTGTAAAAATGCTGCCCAATTTGGTGTCTATATGTTGTTCAA-TTTGCTGTCTA
1 GTCCAATTTTGGTGTAAAAATGCTGCCCAATTTGGTGTCTATATGCTGTCCAATTTTGGTGTCTA
37573177 TATGCT
66 TATGCT
**
37573183 GTCCAATTTTTGGTGTAAAAATGCTGCCCAATTTGGTGTCTATATGCTGTCCAATTTTGGTGTAA
1 GTCCAA-TTTTGGTGTAAAAATGCTGCCCAATTTGGTGTCTATATGCTGTCCAATTTTGGTGTCT
*
37573248 AAATGCT
65 ATATGCT
* * * * * * *
37573255 GTCCAA-TTTGATATATATATGCTGCCCAATTTGGTGTATATTTGCTGTCAAATTTTGGTGTAAA
1 GTCCAATTTTGGTGTAAAAATGCTGCCCAATTTGGTGTCTATATGCTGTCCAATTTTGGTGT---
** * *
37573319 AAAAATGTT
63 CTATATGCT
* * * * * * * * * *
37573328 GTTCAA-TTTGATATATATATGCTGCCCAAATTAGTGTATAAATGCTGTCCAATTTTGGTGTATA
1 GTCCAATTTTGGTGTAAAAATGCTGCCCAATTTGGTGTCTATATGCTGTCCAATTTTGGTGTCTA
*
37573392 AATGCT
66 TATGCT
37573398 GTCCAATTT
1 GTCCAATTT
37573407 GATGTATAAG
Statistics
Matches: 261, Mismatches: 27, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
70 132 0.51
71 47 0.18
72 19 0.07
73 63 0.24
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.40
Consensus pattern (71 bp):
GTCCAATTTTGGTGTAAAAATGCTGCCCAATTTGGTGTCTATATGCTGTCCAATTTTGGTGTCTA
TATGCT
Found at i:37573207 original size:118 final size:117
Alignment explanation
Indices: 37573085--37573414 Score: 365
Period size: 118 Copynumber: 2.8 Consensus size: 117
37573075 TGGTGTCTAT
* *
37573085 ATGCTGCCCAATTTGGTGTCTATATGCTGTCCAATTTTGGTGTAAAAATGCTGCCCAATTTGGTG
1 ATGCTGCCCAATTTGGTGTCTATATGCTGTCCAATTTTGGTGTAAAAATGCTGCCCAATTTGATA
* * ** * *
37573150 TCTATATGTTGTTCAATTTGCTGTCTATATGCTGTCCAATTTTTGGTGTAAAA
66 TATATATGCTGCCCAATTTGCTGTATATATGCTGT-CAAATTTTGGTGTAAAA
*
37573203 ATGCTGCCCAATTTGGTGTCTATATGCTGTCCAATTTTGGTGTAAAAATGCTGTCCAATTTGATA
1 ATGCTGCCCAATTTGGTGTCTATATGCTGTCCAATTTTGGTGTAAAAATGCTGCCCAATTTGATA
* *
37573268 TATATATGCTGCCCAATTTGGTGTATATTTGCTGTCAAATTTTGGTGTAAAAAAA
66 TATATATGCTGCCCAATTTGCTGTATATATGCTGTCAAATTTTGGTGT---AAAA
* ** * * * * * * * * *
37573323 ATGTTGTTCAATTTGATATATATATGCTGCCCAA-ATTAGTGTATAAATGCTGTCCAATTTTGGT
1 ATGCTGCCCAATTTGGTGTCTATATGCTGTCCAATTTTGGTGTAAAAATGCTGCCCAA-TTTGAT
* * * *
37573387 GTATAAATGCTGTCCAATTTGATGTATA
65 ATATATATGCTGCCCAATTTGCTGTATA
37573415 AGAGCTGTAC
Statistics
Matches: 182, Mismatches: 26, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
117 12 0.07
118 90 0.49
119 20 0.11
120 60 0.33
ACGTcount: A:0.26, C:0.14, G:0.19, T:0.41
Consensus pattern (117 bp):
ATGCTGCCCAATTTGGTGTCTATATGCTGTCCAATTTTGGTGTAAAAATGCTGCCCAATTTGATA
TATATATGCTGCCCAATTTGCTGTATATATGCTGTCAAATTTTGGTGTAAAA
Found at i:37573413 original size:47 final size:46
Alignment explanation
Indices: 37573043--37573415 Score: 314
Period size: 47 Copynumber: 7.9 Consensus size: 46
37573033 TTCGATTCAA
* * * *
37573043 GTCCAATTTTGGTGTAAAAATGCTGCCCAATTTGGTGTCTATATGCT
1 GTCCAA-TTTGGTGTATAAATGCTGTCCAATTTGGTGTATAAATGCT
* * * *
37573090 GCCCAATTTGGTGTCTATATGCTGTCCAATTTTGGTGTAAAAATGCT
1 GTCCAATTTGGTGTATAAATGCTGTCCAA-TTTGGTGTATAAATGCT
* * * * * * * *
37573137 GCCCAATTTGGTGTCTATATGTTGTTCAATTTGCTGTCTATATGCT
1 GTCCAATTTGGTGTATAAATGCTGTCCAATTTGGTGTATAAATGCT
* * * *
37573183 GTCCAATTTTTGGTGTAAAAATGCTGCCCAATTTGGTGTCTATATGCT
1 GTCCAA--TTTGGTGTATAAATGCTGTCCAATTTGGTGTATAAATGCT
* * * *
37573231 GTCCAATTTTGGTGTAAAAATGCTGTCCAATTTGATATATATATGCT
1 GTCCAA-TTTGGTGTATAAATGCTGTCCAATTTGGTGTATAAATGCT
* ** * * *
37573278 GCCCAATTTGGTGTATATTTGCTGTCAAATTTTGGTGTAAAAAAAATGTT
1 GTCCAATTTGGTGTATAAATGCTGTCCAA-TTTGGTGT---ATAAATGCT
* * * * * * *
37573328 GTTCAATTTGATATATATATGCTGCCCAAATTAGTGTATAAATGCT
1 GTCCAATTTGGTGTATAAATGCTGTCCAATTTGGTGTATAAATGCT
*
37573374 GTCCAATTTTGGTGTATAAATGCTGTCCAATTTGATGTATAA
1 GTCCAA-TTTGGTGTATAAATGCTGTCCAATTTGGTGTATAA
37573416 GAGCTGTACA
Statistics
Matches: 263, Mismatches: 55, Indels: 16
0.79 0.16 0.05
Matches are distributed among these distances:
46 68 0.26
47 122 0.46
48 39 0.15
49 6 0.02
50 28 0.11
ACGTcount: A:0.26, C:0.14, G:0.19, T:0.40
Consensus pattern (46 bp):
GTCCAATTTGGTGTATAAATGCTGTCCAATTTGGTGTATAAATGCT
Found at i:37573691 original size:2 final size:2
Alignment explanation
Indices: 37573684--37573730 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
37573674 ATTATGTGCT
37573684 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
37573726 TA TA T
1 TA TA T
37573731 GAGATGACTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:37575738 original size:15 final size:12
Alignment explanation
Indices: 37575707--37575732 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
37575697 TGTTTTCAGC
37575707 TAGTTCTTTTTT
1 TAGTTCTTTTTT
37575719 TAGTTCTTTTTT
1 TAGTTCTTTTTT
37575731 TA
1 TA
37575733 TCAGTTGACT
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:0.12, C:0.08, G:0.08, T:0.73
Consensus pattern (12 bp):
TAGTTCTTTTTT
Found at i:37577813 original size:37 final size:38
Alignment explanation
Indices: 37577714--37577826 Score: 105
Period size: 37 Copynumber: 3.1 Consensus size: 38
37577704 ATCTACAATA
37577714 TAAATATTAAATTTAAT-TT-AA-TATTAAGAT-AGTCACT
1 TAAATATT-AATTTAATATTAAACTATTAAGATAAGT-A-T
* * *
37577751 TTAATATTAAATTAATA-AAATACTATTAAGATAAGTAT
1 TAAATATTAATTTAATATTAA-ACTATTAAGATAAGTAT
*
37577789 TAAAT-TTAATTTAATATTAAACTATTAAAATAA-TAT
1 TAAATATTAATTTAATATTAAACTATTAAGATAAGTAT
37577825 TA
1 TA
37577827 TTTTTAGAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
36 12 0.19
37 30 0.48
38 8 0.13
39 10 0.16
40 3 0.05
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (38 bp):
TAAATATTAATTTAATATTAAACTATTAAGATAAGTAT
Found at i:37581093 original size:23 final size:22
Alignment explanation
Indices: 37581051--37581094 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
37581041 CATATCATTT
37581051 TGAATTTTTATTATTATTTATA
1 TGAATTTTTATTATTATTTATA
* *
37581073 TGAATTGTTTGTTATTTTTTAT
1 TGAATT-TTTATTATTATTTAT
37581095 TTAATGTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.25, C:0.00, G:0.09, T:0.66
Consensus pattern (22 bp):
TGAATTTTTATTATTATTTATA
Found at i:37588840 original size:10 final size:9
Alignment explanation
Indices: 37588776--37588840 Score: 51
Period size: 9 Copynumber: 6.9 Consensus size: 9
37588766 TAAAATATAT
37588776 ATTA-TAAA
1 ATTATTAAA
* *
37588784 AATAATAAA
1 ATTATTAAA
37588793 ATTATTATAA
1 ATTATTA-AA
37588803 ATTATTAATAA
1 ATTATT-A-AA
*
37588814 ATTATAAAA
1 ATTATTAAA
*
37588823 ACTATTAAA
1 ATTATTAAA
37588832 ATTTATTAA
1 A-TTATTAA
37588841 TTTTTATAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
8 3 0.07
9 19 0.41
10 15 0.33
11 9 0.20
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (9 bp):
ATTATTAAA
Found at i:37588850 original size:9 final size:9
Alignment explanation
Indices: 37588833--37588872 Score: 53
Period size: 9 Copynumber: 4.2 Consensus size: 9
37588823 ACTATTAAAA
37588833 TTTATTAATT
1 TTTA-TAATT
37588843 TTTATAATGT
1 TTTATAAT-T
*
37588853 TTCATAATT
1 TTTATAATT
37588862 TTTATAATT
1 TTTATAATT
37588871 TT
1 TT
37588873 AATATTCTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
9 15 0.56
10 12 0.44
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (9 bp):
TTTATAATT
Found at i:37590536 original size:18 final size:17
Alignment explanation
Indices: 37590509--37590542 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
37590499 CAACTAAATC
*
37590509 ATTTTAAAAAACATAAA
1 ATTTTAAAAAAAATAAA
37590526 ATTTATAAAAAAAATAA
1 ATTT-TAAAAAAAATAA
37590543 TTATAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
ATTTTAAAAAAAATAAA
Found at i:37592006 original size:19 final size:19
Alignment explanation
Indices: 37591971--37592012 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
37591961 TAATTCATGA
37591971 TATTAATATCAAATAATAT
1 TATTAATATCAAATAATAT
*
37591990 TATTGAATAT-AATTAATA-
1 TATT-AATATCAAATAATAT
37592008 TATTA
1 TATTA
37592013 TATTAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 1 0.05
18 4 0.19
19 11 0.52
20 5 0.24
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (19 bp):
TATTAATATCAAATAATAT
Found at i:37594770 original size:34 final size:35
Alignment explanation
Indices: 37594715--37594781 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
37594705 CAAACACCAG
*
37594715 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
37594750 AAAACATTTTCCCG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
37594782 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:37598011 original size:68 final size:68
Alignment explanation
Indices: 37597900--37598155 Score: 289
Period size: 68 Copynumber: 3.8 Consensus size: 68
37597890 TTTTTGGCTC
* ** * **
37597900 ACTGTCTTGGTGGACTTTATATGTTAACATAACCCAACTATGGTCTTACACTACGTGGTGCCATG
1 ACTGTCCTGGTGGACTTTATATGTTGCCATAGCCCAACTATGGTCTTACACTATATGGTGCCATG
37597965 TTT
66 TTT
* * * * *
37597968 ACTGTCCTGGCGGACTTTGTATGTTGCCATTGCCCAACAATGGTCTTACTCTATATGGTGCCATG
1 ACTGTCCTGGTGGACTTTATATGTTGCCATAGCCCAACTATGGTCTTACACTATATGGTGCCATG
37598033 TTT
66 TTT
* * *
37598036 ACTATCCTAGTGGACTTTATATGTTGCCATAGCCCAACTACGGTCTTACACTATATGGTGCCATG
1 ACTGTCCTGGTGGACTTTATATGTTGCCATAGCCCAACTATGGTCTTACACTATATGGTGCCATG
37598101 TTT
66 TTT
* * *** * * * *
37598104 ATTGT-CTTGACAAATTTCATATGTTACCATAACCCAACTATGATCTTACACT
1 ACTGTCCTGGTGGACTTT-ATATGTTGCCATAGCCCAACTATGGTCTTACACT
37598156 CTTATAAGCT
Statistics
Matches: 157, Mismatches: 30, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
67 7 0.04
68 150 0.96
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.36
Consensus pattern (68 bp):
ACTGTCCTGGTGGACTTTATATGTTGCCATAGCCCAACTATGGTCTTACACTATATGGTGCCATG
TTT
Found at i:37598277 original size:122 final size:122
Alignment explanation
Indices: 37598060--37598330 Score: 400
Period size: 122 Copynumber: 2.2 Consensus size: 122
37598050 CTTTATATGT
* * * *
37598060 TGCCATAGCCCAACTACGGTCTTACACTATATGGTGCCATGTTTATTGTCTTGACAAATTTCATA
1 TGCCATGGCCCAACTATGGTCTTACACTATATGGTGCCATGTTTATTGTCATGACAAACTTCATA
*
37598125 TGTTACCATAACCCAACTATGATCTTACACTCTTATAAGCTTAGAGCCTCCAACCGG
66 TGTTACCATAACCCAACTATGATCTTACACTCTTATAAGCTTAGAGCCTCCAACCGA
* *
37598182 TGCCATGGCCCAGCTATGGTCTTACACTATATGGTGCCATGTTTATTGTCATGA-AGGACTTCAT
1 TGCCATGGCCCAACTATGGTCTTACACTATATGGTGCCATGTTTATTGTCATGACA-AACTTCAT
* * * * **
37598246 ATGTTACCATAGCCCAGCTATGATCTTACACTTTTATAGGCTTAGAGCCTCCAATTGA
65 ATGTTACCATAACCCAACTATGATCTTACACTCTTATAAGCTTAGAGCCTCCAACCGA
*
37598304 TGCCATGACCCAACTATGGTCTTACAC
1 TGCCATGGCCCAACTATGGTCTTACAC
37598331 ATCATTCCCG
Statistics
Matches: 133, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
121 1 0.01
122 132 0.99
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.32
Consensus pattern (122 bp):
TGCCATGGCCCAACTATGGTCTTACACTATATGGTGCCATGTTTATTGTCATGACAAACTTCATA
TGTTACCATAACCCAACTATGATCTTACACTCTTATAAGCTTAGAGCCTCCAACCGA
Found at i:37598802 original size:38 final size:38
Alignment explanation
Indices: 37598751--37598831 Score: 144
Period size: 38 Copynumber: 2.1 Consensus size: 38
37598741 ATCATTTCAT
*
37598751 ACACAACAGCAGGTTCTGACAACTTAGAACAAACACTA
1 ACACAACAGCAGGTTCTGACAACTCAGAACAAACACTA
*
37598789 ACACAATAGCAGGTTCTGACAACTCAGAACAAACACTA
1 ACACAACAGCAGGTTCTGACAACTCAGAACAAACACTA
37598827 ACACA
1 ACACA
37598832 GACCATTCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.46, C:0.27, G:0.12, T:0.15
Consensus pattern (38 bp):
ACACAACAGCAGGTTCTGACAACTCAGAACAAACACTA
Done.