Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A10
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: 110302803
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1825971 characters in sequence are not A, C, G, or T
File 22 of 343
Found at i:7439841 original size:15 final size:16
Alignment explanation
Indices: 7439807--7439845 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
7439797 ACAGAATAGG
7439807 GAAA-GAAAGAAAGAA
1 GAAAGGAAAGAAAGAA
*
7439822 AAAAGGAAAGAAA-AA
1 GAAAGGAAAGAAAGAA
7439837 GAAAGGAAA
1 GAAAGGAAA
7439846 AATAGGGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (16 bp):
GAAAGGAAAGAAAGAA
Found at i:7440313 original size:15 final size:15
Alignment explanation
Indices: 7440293--7440347 Score: 110
Period size: 15 Copynumber: 3.7 Consensus size: 15
7440283 TGTGTTGATG
7440293 ATTTTAAATGTTAAT
1 ATTTTAAATGTTAAT
7440308 ATTTTAAATGTTAAT
1 ATTTTAAATGTTAAT
7440323 ATTTTAAATGTTAAT
1 ATTTTAAATGTTAAT
7440338 ATTTTAAATG
1 ATTTTAAATG
7440348 AGTTTTTAAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 40 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (15 bp):
ATTTTAAATGTTAAT
Found at i:7440329 original size:8 final size:7
Alignment explanation
Indices: 7440293--7440346 Score: 54
Period size: 7 Copynumber: 7.3 Consensus size: 7
7440283 TGTGTTGATG
7440293 ATTTTAA
1 ATTTTAA
*
7440300 ATGTTAA
1 ATTTTAA
7440307 TATTTTAA
1 -ATTTTAA
*
7440315 ATGTTAA
1 ATTTTAA
7440322 TATTTTAA
1 -ATTTTAA
*
7440330 ATGTTAA
1 ATTTTAA
7440337 TATTTTAA
1 -ATTTTAA
7440345 AT
1 AT
7440347 GAGTTTTTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
7 20 0.53
8 18 0.47
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.54
Consensus pattern (7 bp):
ATTTTAA
Found at i:7440635 original size:12 final size:12
Alignment explanation
Indices: 7440618--7440650 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
7440608 TGTGTACCGG
7440618 TACTGTTACTAT
1 TACTGTTACTAT
7440630 TACTGTTACTAT
1 TACTGTTACTAT
7440642 TACTGTTAC
1 TACTGTTAC
7440651 GGTGTATTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.24, C:0.18, G:0.09, T:0.48
Consensus pattern (12 bp):
TACTGTTACTAT
Found at i:7441445 original size:27 final size:27
Alignment explanation
Indices: 7441407--7441461 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 27
7441397 GGCATTGGCA
*
7441407 CACAGGCGTGTGATCA-GACCGTGTGTC
1 CACAGACGTGTGAT-ATGACCGTGTGTC
7441434 CACAGACGTGTGATATGACCGTGTGTC
1 CACAGACGTGTGATATGACCGTGTGTC
7441461 C
1 C
7441462 CCTGCATCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 1 0.04
27 25 0.96
ACGTcount: A:0.20, C:0.25, G:0.31, T:0.24
Consensus pattern (27 bp):
CACAGACGTGTGATATGACCGTGTGTC
Found at i:7442677 original size:91 final size:91
Alignment explanation
Indices: 7442560--7442763 Score: 225
Period size: 91 Copynumber: 2.3 Consensus size: 91
7442550 TAGGTATTTA
* * * * *
7442560 AACTTTCACAATGCATGAAAAAGACCCTTAAACTTTTTTTAAAAAAAACAATTAAG-CCTCTG-C
1 AACTTTTAAAATGCATCAAAAAGACCCTCAAAC-TTTTTCAAAAAAAACAATTAAGCCCT-TGAC
* * *
7442623 CTTTTGTTTGCACTCAATTGAGTACTTG
64 CTTTTGTTTACACTCAATTAAGAACTTG
* * ** **
7442651 AACTTTTAAAATGCATTAAAATGACCCTCAAACTTTTTCAAAAAAAGTAATTAAGCCCTTGATTT
1 AACTTTTAAAATGCATCAAAAAGACCCTCAAACTTTTTCAAAAAAAACAATTAAGCCCTTGACCT
*
7442716 TTTTTTTACACTCAATTAAGAACTTG
66 TTTGTTTACACTCAATTAAGAACTTG
*
7442742 AA-TTGTAAAATGCATCAAAAAG
1 AACTTTTAAAATGCATCAAAAAG
7442764 GCTCTTTGAC
Statistics
Matches: 94, Mismatches: 17, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
90 38 0.40
91 56 0.60
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.34
Consensus pattern (91 bp):
AACTTTTAAAATGCATCAAAAAGACCCTCAAACTTTTTCAAAAAAAACAATTAAGCCCTTGACCT
TTTGTTTACACTCAATTAAGAACTTG
Found at i:7442880 original size:9 final size:9
Alignment explanation
Indices: 7442868--7442995 Score: 53
Period size: 10 Copynumber: 13.4 Consensus size: 9
7442858 CATGTGGCAA
7442868 AAAAATTAT
1 AAAAATTAT
*
7442877 AAAAA-AAT
1 AAAAATTAT
**
7442885 AAAAACCAAT
1 AAAAA-TTAT
*
7442895 AAAATTTAT
1 AAAAATTAT
*
7442904 AAAAATGATT
1 AAAAATTA-T
*
7442914 AAAATTTAAT
1 AAAAATT-AT
*
7442924 AAAAATAAT
1 AAAAATTAT
*
7442933 -AAAATTGT
1 AAAAATTAT
7442941 AAAAATATATAT
1 -AAAA-AT-TAT
*
7442953 AAAATATTGT
1 AAAA-ATTAT
**
7442963 AAATTTTTAT
1 AAA-AATTAT
*
7442973 AAAAATCAT
1 AAAAATTAT
7442982 AATAAATTAT
1 AA-AAATTAT
7442992 AAAA
1 AAAA
7442996 TGCATCAAAA
Statistics
Matches: 88, Mismatches: 21, Indels: 20
0.68 0.16 0.16
Matches are distributed among these distances:
8 13 0.15
9 22 0.25
10 41 0.47
11 10 0.11
12 2 0.02
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.32
Consensus pattern (9 bp):
AAAAATTAT
Found at i:7442905 original size:19 final size:19
Alignment explanation
Indices: 7442882--7442938 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
7442872 ATTATAAAAA
7442882 AATAAAAACCAATAAAATTT
1 AATAAAAA-CAATAAAATTT
* *
7442902 -ATAAAAATGATTAAAATTT
1 AATAAAAA-CAATAAAATTT
*
7442921 AATAAAAATAATAAAATT
1 AATAAAAACAATAAAATT
7442939 GTAAAAATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 24 0.77
20 7 0.23
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.30
Consensus pattern (19 bp):
AATAAAAACAATAAAATTT
Found at i:7442925 original size:20 final size:18
Alignment explanation
Indices: 7442892--7442957 Score: 71
Period size: 19 Copynumber: 3.4 Consensus size: 18
7442882 AATAAAAACC
7442892 AATAAAATTTATAAAAAT
1 AATAAAATTTATAAAAAT
*
7442910 GATTAAAATTTAATAAAAAT
1 -AATAAAATTT-ATAAAAAT
7442930 AATAAAATTGTA-AAAATAT
1 AATAAAATT-TATAAAA-AT
7442949 ATATAAAAT
1 A-ATAAAAT
7442958 ATTGTAAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
18 4 0.10
19 21 0.51
20 16 0.39
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (18 bp):
AATAAAATTTATAAAAAT
Found at i:7443234 original size:28 final size:29
Alignment explanation
Indices: 7443181--7443236 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
7443171 AGTACAATAA
*
7443181 TTTTTATAAATTTTTTACGAATTTTATAT
1 TTTTTATAAATTTTTTACGAACTTTATAT
*
7443210 TTTTTAT-AATTTTCTTATG-ACTTTATA
1 TTTTTATAAATTTT-TTACGAACTTTATA
7443237 AAAATTTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 13 0.54
29 11 0.46
ACGTcount: A:0.29, C:0.05, G:0.04, T:0.62
Consensus pattern (29 bp):
TTTTTATAAATTTTTTACGAACTTTATAT
Found at i:7443283 original size:38 final size:38
Alignment explanation
Indices: 7443200--7443283 Score: 102
Period size: 39 Copynumber: 2.2 Consensus size: 38
7443190 ATTTTTTACG
7443200 AATTTTATATTTTTTATAATTTTCTTATGACTTTATAA
1 AATTTTATATTTTTTATAATTTTCTTATGACTTTATAA
* *
7443238 AAATTTATAATTTTTTAT-ATATTTCTATAT-ATTTTAT-A
1 AATTTTAT-ATTTTTTATAAT-TTTCT-TATGACTTTATAA
7443276 AATTTTAT
1 AATTTTAT
7443284 TTTACCATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
38 17 0.43
39 20 0.50
40 3 0.08
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.61
Consensus pattern (38 bp):
AATTTTATATTTTTTATAATTTTCTTATGACTTTATAA
Found at i:7445732 original size:35 final size:37
Alignment explanation
Indices: 7445680--7445762 Score: 109
Period size: 35 Copynumber: 2.3 Consensus size: 37
7445670 TGAAAGAAAA
*
7445680 TCGGAGGGATT-AGCTCTTACGAGCAT-TGGTGTGTT
1 TCGGATGGATTGAGCTCTTACGAGCATCTGGTGTGTT
*
7445715 TCGGATGGATTGA-CTCTTATGAGCATCTGGTGTGTT
1 TCGGATGGATTGAGCTCTTACGAGCATCTGGTGTGTT
* *
7445751 TTGGTTGGATTG
1 TCGGATGGATTG
7445763 TCGATGTACT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
35 22 0.52
36 20 0.48
ACGTcount: A:0.16, C:0.12, G:0.34, T:0.39
Consensus pattern (37 bp):
TCGGATGGATTGAGCTCTTACGAGCATCTGGTGTGTT
Found at i:7447738 original size:14 final size:14
Alignment explanation
Indices: 7447719--7447747 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
7447709 ACTATGAGAT
7447719 AAAATAGGATCATA
1 AAAATAGGATCATA
7447733 AAAATAGGATCATA
1 AAAATAGGATCATA
7447747 A
1 A
7447748 TGGGAGAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.07, G:0.14, T:0.21
Consensus pattern (14 bp):
AAAATAGGATCATA
Found at i:7448339 original size:18 final size:20
Alignment explanation
Indices: 7448300--7448344 Score: 67
Period size: 18 Copynumber: 2.3 Consensus size: 20
7448290 TGGGTTGAGA
7448300 AATTTATTTAGTTTGAAAATT
1 AATTTATTTAGTTT-AAAATT
7448321 AATTTATTTA-TTT-AAATT
1 AATTTATTTAGTTTAAAATT
7448339 AATTTA
1 AATTTA
7448345 ATAATATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.46
20 3 0.12
21 10 0.42
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (20 bp):
AATTTATTTAGTTTAAAATT
Found at i:7449824 original size:42 final size:42
Alignment explanation
Indices: 7449777--7449861 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
7449767 TAGAACTGGG
7449777 CCAGAAAAACAAATGTGATTAATTTGAGTAATTATTTTATAA
1 CCAGAAAAACAAATGTGATTAATTTGAGTAATTATTTTATAA
7449819 CCAGAAAAACAAATGTGATTAATTTGAGTAATTATTTTATAA
1 CCAGAAAAACAAATGTGATTAATTTGAGTAATTATTTTATAA
7449861 C
1 C
7449862 TTTCTATAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.35
Consensus pattern (42 bp):
CCAGAAAAACAAATGTGATTAATTTGAGTAATTATTTTATAA
Found at i:7449936 original size:35 final size:35
Alignment explanation
Indices: 7449890--7449958 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
7449880 AAAAAAGAAG
* *
7449890 TTTAAACATAATTGGAAAGCTATTGATATAATTTT
1 TTTAAACATAATTGGAAAGCTACTGACATAATTTT
7449925 TTTAAACATAATTGGAAAGCTACTGACATAATTT
1 TTTAAACATAATTGGAAAGCTACTGACATAATTT
7449959 ATCCTCTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.39
Consensus pattern (35 bp):
TTTAAACATAATTGGAAAGCTACTGACATAATTTT
Found at i:7450568 original size:29 final size:29
Alignment explanation
Indices: 7450500--7450569 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 29
7450490 TTACAATTTA
* *
7450500 AACTTATTTGATTCTTTTAATAATATAAG
1 AACTAATTTGATTCTTTTAATAATAGAAG
* * * *
7450529 GATTAAATTGATT-TATTTAATAATAGATG
1 AACTAATTTGATTCT-TTTAATAATAGAAG
7450558 AACTAATTTGAT
1 AACTAATTTGAT
7450570 CTAATCCCTA
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
28 1 0.03
29 30 0.97
ACGTcount: A:0.40, C:0.04, G:0.10, T:0.46
Consensus pattern (29 bp):
AACTAATTTGATTCTTTTAATAATAGAAG
Found at i:7461464 original size:32 final size:32
Alignment explanation
Indices: 7461401--7461466 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
7461391 ACACCATCAC
*
7461401 CACCCACAAATACTGAACCACATATTGAACCA
1 CACCCACAAATACTGAACCACATATTAAACCA
*
7461433 CACCCATAAATACTGAACCACATGA-TAAACCA
1 CACCCACAAATACTGAACCACAT-ATTAAACCA
7461465 CA
1 CA
7461467 TATTGAACCA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 30 0.97
33 1 0.03
ACGTcount: A:0.45, C:0.33, G:0.06, T:0.15
Consensus pattern (32 bp):
CACCCACAAATACTGAACCACATATTAAACCA
Found at i:7469447 original size:21 final size:21
Alignment explanation
Indices: 7469415--7469455 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
7469405 AGGCTCGAGG
7469415 GGCCTGTTTTAGGCC-ATACAA
1 GGCCTGTTTTA-GCCTATACAA
7469436 GGCCT-TTCTTAGCCTATACA
1 GGCCTGTT-TTAGCCTATACA
7469456 CCAATTGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.32
Consensus pattern (21 bp):
GGCCTGTTTTAGCCTATACAA
Found at i:7474773 original size:24 final size:24
Alignment explanation
Indices: 7474725--7474773 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
7474715 AATATATATT
* **
7474725 CAATGATCAAATTTTGTTTGTATA
1 CAATGATCAAATTTTGATTCAATA
*
7474749 CAATGATCAAGTTTTGATTCAATA
1 CAATGATCAAATTTTGATTCAATA
7474773 C
1 C
7474774 GGTATTCTCG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (24 bp):
CAATGATCAAATTTTGATTCAATA
Found at i:7486594 original size:26 final size:26
Alignment explanation
Indices: 7486557--7486640 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
7486547 TGATACAAAT
* *
7486557 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
7486583 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
7486609 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
7486635 TGATAA
1 TGATAA
7486641 GAATTTCATG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:7488670 original size:137 final size:137
Alignment explanation
Indices: 7488424--7488710 Score: 529
Period size: 137 Copynumber: 2.1 Consensus size: 137
7488414 GAGTAGTCTC
*
7488424 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTGGAAATGGGCCTATGGGCCATAC
*
7488489 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGCCCCAGTACC
7488554 ACTGTTA
131 ACTGTTA
7488561 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTGGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTGGAAATGGGCCTATGGGCCATAC
*
7488626 TGTTATCTGAATAAGGGGCTAAGGCCCATTTTATTGTAATCTGAAAAGGGCTCTGCCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGCCCCAGTACC
7488691 ACTGTTA
131 ACTGTTA
**
7488698 CCTGAATGGGCTT
1 CCCAAATGGGCTT
7488711 AGGCCCAATA
Statistics
Matches: 145, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
137 145 1.00
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (137 bp):
CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTGGAAATGGGCCTATGGGCCATAC
TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGCCCCAGTACC
ACTGTTA
Found at i:7489893 original size:20 final size:20
Alignment explanation
Indices: 7489850--7489895 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
7489840 ACTGTTTTGT
7489850 TATGGGCCAACTGTATTGAA
1 TATGGGCCAACTGTATTGAA
*
7489870 -ATGGGCTCAACTGTGTT-AA
1 TATGGGC-CAACTGTATTGAA
7489889 TATGGGC
1 TATGGGC
7489896 AAAGCCCAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.30
Consensus pattern (20 bp):
TATGGGCCAACTGTATTGAA
Found at i:7490036 original size:27 final size:28
Alignment explanation
Indices: 7489924--7490029 Score: 81
Period size: 28 Copynumber: 3.7 Consensus size: 28
7489914 ACTTGTAATA
* * *
7489924 GGGCTACGGCCCAGATTGACACTGATAT
1 GGGCTAAGGCCCAGATTAATACTGATAT
* * *
7489952 GGGCT-AGGCCCAGTATACTCTGATACTGAAAG
1 GGGCTAAGGCCCAG---A-T-TAATACTGATAT
* *
7489984 GGGCTATGGCCCAGATTAATATTGATAT
1 GGGCTAAGGCCCAGATTAATACTGATAT
7490012 GGGCTAAGGCCCA-ATTAA
1 GGGCTAAGGCCCAGATTAA
7490030 CTCTGATTTC
Statistics
Matches: 62, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
27 12 0.19
28 25 0.40
29 1 0.02
30 2 0.03
31 1 0.02
32 14 0.23
33 7 0.11
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.24
Consensus pattern (28 bp):
GGGCTAAGGCCCAGATTAATACTGATAT
Found at i:7494329 original size:23 final size:22
Alignment explanation
Indices: 7494303--7494346 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
7494293 GTGATGAGGT
7494303 TATCTT-ATAAATATGTATGAATC
1 TATCTTGA-AAATATGT-TGAATC
7494326 TATCTTGAAAATATGTTGAAT
1 TATCTTGAAAATATGTTGAAT
7494347 TGGATTGGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 5 0.25
23 14 0.70
24 1 0.05
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.43
Consensus pattern (22 bp):
TATCTTGAAAATATGTTGAATC
Found at i:7495754 original size:39 final size:39
Alignment explanation
Indices: 7495711--7495788 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
7495701 ACATTTTCAG
7495711 ATAATTCGTGTAAATTACAATTCATTAACTGAGATTTAT
1 ATAATTCGTGTAAATTACAATTCATTAACTGAGATTTAT
7495750 ATAATTCGTGTAAATTACAATTCATTAACTGAGATTTAT
1 ATAATTCGTGTAAATTACAATTCATTAACTGAGATTTAT
7495789 TCATAACGTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.41
Consensus pattern (39 bp):
ATAATTCGTGTAAATTACAATTCATTAACTGAGATTTAT
Found at i:7498027 original size:16 final size:17
Alignment explanation
Indices: 7497996--7498028 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
7497986 TTCATAAGTA
7497996 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
7498013 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
7498029 GCACCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:7498420 original size:46 final size:46
Alignment explanation
Indices: 7498314--7498673 Score: 465
Period size: 46 Copynumber: 7.8 Consensus size: 46
7498304 TTTGACATGA
* * * * *
7498314 TGCCATAGTGTCTTTCAACTATGGTCTTATTTATCTT--TGTCACGC
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCAT-TTCATGTCACGT
* *
7498359 TGCCATGGTACCTTTCAACCATGGTCTTATTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTTCATGTCACGT
*
7498405 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGC
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGT
** * *
7498451 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCCGTTATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGT
*
7498497 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGT
** * *
7498543 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGT
* ** * *
7498589 TGTCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGT
**
7498635 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCAT
7498674 ATCAAAGAGC
Statistics
Matches: 287, Mismatches: 25, Indels: 5
0.91 0.08 0.02
Matches are distributed among these distances:
45 34 0.12
46 253 0.88
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.41
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGT
Found at i:7502126 original size:15 final size:16
Alignment explanation
Indices: 7502094--7502131 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
7502084 AATTTTTTTC
7502094 TTATCATTTAATTAAA
1 TTATCATTTAATTAAA
7502110 TTATCATTTAA-TAAA
1 TTATCATTTAATTAAA
*
7502125 TTTTCAT
1 TTATCAT
7502132 CTTTCCAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (16 bp):
TTATCATTTAATTAAA
Found at i:7506571 original size:21 final size:21
Alignment explanation
Indices: 7506545--7506585 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
7506535 TGGGTGGATA
*
7506545 AGCTCTTAAGAGCTTCTGTTC
1 AGCTCTCAAGAGCTTCTGTTC
* *
7506566 AGCTCTCACGAGCTTTTGTT
1 AGCTCTCAAGAGCTTCTGTT
7506586 GGCGTGTTCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.39
Consensus pattern (21 bp):
AGCTCTCAAGAGCTTCTGTTC
Found at i:7511867 original size:15 final size:15
Alignment explanation
Indices: 7511847--7511924 Score: 70
Period size: 15 Copynumber: 5.2 Consensus size: 15
7511837 TTTATGGAAA
7511847 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* **
7511862 ATCAAATA-ATGGAA
1 ATCAAAGATATGGGT
7511876 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
7511892 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
7511906 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
7511922 ATC
1 ATC
7511925 GAGATATTGG
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
14 9 0.19
15 29 0.62
16 9 0.19
ACGTcount: A:0.44, C:0.08, G:0.23, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:7511876 original size:30 final size:30
Alignment explanation
Indices: 7511840--7511924 Score: 152
Period size: 30 Copynumber: 2.8 Consensus size: 30
7511830 ATCCATATTT
*
7511840 ATGGAAAATCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
7511870 ATGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
7511900 TTGGAAAGTCAAAGATATGGGTATC
1 ATGGAAAGTCAAAGATATGGGTATC
7511925 GAGATATTGG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.45, C:0.07, G:0.24, T:0.25
Consensus pattern (30 bp):
ATGGAAAGTCAAAGATATGGGTATCAAATA
Found at i:7516517 original size:15 final size:15
Alignment explanation
Indices: 7516497--7516574 Score: 70
Period size: 15 Copynumber: 5.2 Consensus size: 15
7516487 TTTATGGAAA
7516497 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* **
7516512 ATCAAATA-ATGGAA
1 ATCAAAGATATGGGT
7516526 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
7516542 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
7516556 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
7516572 ATC
1 ATC
7516575 GAGATATTGG
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
14 9 0.19
15 29 0.62
16 9 0.19
ACGTcount: A:0.44, C:0.08, G:0.23, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:7516526 original size:30 final size:30
Alignment explanation
Indices: 7516490--7516574 Score: 152
Period size: 30 Copynumber: 2.8 Consensus size: 30
7516480 ATCCATATTT
*
7516490 ATGGAAAATCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
7516520 ATGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
7516550 TTGGAAAGTCAAAGATATGGGTATC
1 ATGGAAAGTCAAAGATATGGGTATC
7516575 GAGATATTGG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.45, C:0.07, G:0.24, T:0.25
Consensus pattern (30 bp):
ATGGAAAGTCAAAGATATGGGTATCAAATA
Found at i:7520596 original size:2 final size:2
Alignment explanation
Indices: 7520589--7520623 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
7520579 CAATAATTAA
* *
7520589 AT AT AT AT AT CT AT AT AT AT CT 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 A
7520624 AAATTTTAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:7520605 original size:10 final size:10
Alignment explanation
Indices: 7520590--7520623 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
7520580 AATAATTAAA
7520590 TATATATATC
1 TATATATATC
7520600 TATATATATC
1 TATATATATC
*
7520610 TATATATATA
1 TATATATATC
7520620 TATA
1 TATA
7520624 AAATTTTAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (10 bp):
TATATATATC
Found at i:7528741 original size:15 final size:17
Alignment explanation
Indices: 7528716--7528748 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
7528706 CTTGACTTGT
7528716 TTTTAATTTTATA-ATA
1 TTTTAATTTTATATATA
7528732 TTTT-ATTTTATATATA
1 TTTTAATTTTATATATA
7528748 T
1 T
7528749 ATATTTTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTAATTTTATATATA
Found at i:7528863 original size:26 final size:28
Alignment explanation
Indices: 7528834--7528887 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 28
7528824 TAAGATGATT
*
7528834 ATATAAAAAAATT-CAAT-AAATAAAAA
1 ATATAAAAAAATTAAAATAAAATAAAAA
* *
7528860 ATATTAAAATATTAAAATAAAATAAAAA
1 ATATAAAAAAATTAAAATAAAATAAAAA
7528888 TAATTTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 11 0.48
27 3 0.13
28 9 0.39
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (28 bp):
ATATAAAAAAATTAAAATAAAATAAAAA
Found at i:7528915 original size:12 final size:12
Alignment explanation
Indices: 7528867--7528921 Score: 51
Period size: 12 Copynumber: 4.5 Consensus size: 12
7528857 AAAATATTAA
7528867 AATATT-AAAAT
1 AATATTAAAAAT
*
7528878 AA-AATAAAAAT
1 AATATTAAAAAT
*
7528889 AATTTTTTAAAAAAT
1 AA--TATT-AAAAAT
7528904 AATATTAAAAAT
1 AATATTAAAAAT
7528916 AATATT
1 AATATT
7528922 GATGGACATA
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
10 2 0.06
11 9 0.26
12 12 0.34
13 3 0.09
14 1 0.03
15 8 0.23
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
AATATTAAAAAT
Found at i:7529656 original size:21 final size:20
Alignment explanation
Indices: 7529630--7529677 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
7529620 TACTTCTTTA
7529630 ATAATTTTTATA-AATAATTTT
1 ATAATTTTT-TAGAAT-ATTTT
7529651 ATAATTTTTTAGAATATTTT
1 ATAATTTTTTAGAATATTTT
7529671 A-AATTTT
1 ATAATTTT
7529678 AAAAAATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.23
20 8 0.31
21 12 0.46
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (20 bp):
ATAATTTTTTAGAATATTTT
Found at i:7544609 original size:19 final size:19
Alignment explanation
Indices: 7544585--7544623 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
7544575 AATACTTATT
*
7544585 TATTATT-TATACATGTGTA
1 TATTATTAT-TACATATGTA
7544604 TATTATTATTACATATGTA
1 TATTATTATTACATATGTA
7544623 T
1 T
7544624 CCATAAATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 17 0.94
20 1 0.06
ACGTcount: A:0.33, C:0.05, G:0.08, T:0.54
Consensus pattern (19 bp):
TATTATTATTACATATGTA
Found at i:7544720 original size:20 final size:21
Alignment explanation
Indices: 7544697--7544736 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
7544687 ATTATTTAAT
*
7544697 TAATAAATA-CTTTTTATAAA
1 TAATAAATATCTTTTAATAAA
*
7544717 TAATAATTATCTTTTAATAA
1 TAATAAATATCTTTTAATAA
7544737 TTAAATACGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (21 bp):
TAATAAATATCTTTTAATAAA
Found at i:7552309 original size:25 final size:24
Alignment explanation
Indices: 7552272--7552349 Score: 77
Period size: 25 Copynumber: 3.2 Consensus size: 24
7552262 CATACAAGCA
*
7552272 CATA-AACAAGAAGCTCATTCGAGC
1 CATATAACGAGAAGCTCATT-GAGC
* *
7552296 CATATAATGGGAAGCTCATGTGAGC
1 CATATAACGAGAAGCTCAT-TGAGC
* *
7552321 CATGTAACGAGAAGCTCATGAGAGC
1 CATATAACGAGAAGCTCAT-TGAGC
7552346 CATA
1 CATA
7552350 ATCGGGAAAC
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
24 4 0.09
25 39 0.89
26 1 0.02
ACGTcount: A:0.37, C:0.21, G:0.23, T:0.19
Consensus pattern (24 bp):
CATATAACGAGAAGCTCATTGAGC
Found at i:7555173 original size:22 final size:23
Alignment explanation
Indices: 7555139--7555200 Score: 63
Period size: 27 Copynumber: 2.6 Consensus size: 23
7555129 ACATACCATA
* *
7555139 CATAATATCCATAT-TAGTATAT
1 CATAAAATACATATATAGTATAT
7555161 CATAAAATACATAACATACTAGTATAT
1 CATAAAATACAT---ATA-TAGTATAT
7555188 CATAAAATACATA
1 CATAAAATACATA
7555201 ACATACATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
22 10 0.30
24 1 0.03
25 2 0.06
27 20 0.61
ACGTcount: A:0.50, C:0.15, G:0.03, T:0.32
Consensus pattern (23 bp):
CATAAAATACATATATAGTATAT
Found at i:7555178 original size:27 final size:27
Alignment explanation
Indices: 7555148--7555206 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
7555138 ACATAATATC
*
7555148 CATATTAGTATATCATAAAATACATAA
1 CATACTAGTATATCATAAAATACATAA
7555175 CATACTAGTATATCATAAAATACATAA
1 CATACTAGTATATCATAAAATACATAA
7555202 CATAC
1 CATAC
7555207 ATAATATACA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.51, C:0.15, G:0.03, T:0.31
Consensus pattern (27 bp):
CATACTAGTATATCATAAAATACATAA
Found at i:7555179 original size:9 final size:9
Alignment explanation
Indices: 7555161--7555216 Score: 51
Period size: 9 Copynumber: 6.2 Consensus size: 9
7555151 ATTAGTATAT
7555161 CATAAAATA
1 CATAAAATA
*
7555170 CATAACATA
1 CATAAAATA
**
7555179 C-TAGTATA
1 CATAAAATA
7555187 TCATAAAATA
1 -CATAAAATA
*
7555197 CATAACATA
1 CATAAAATA
*
7555206 CATAATATA
1 CATAAAATA
7555215 CA
1 CA
7555217 CACTAATATA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
8 5 0.13
9 28 0.74
10 5 0.13
ACGTcount: A:0.55, C:0.16, G:0.02, T:0.27
Consensus pattern (9 bp):
CATAAAATA
Found at i:7555254 original size:67 final size:66
Alignment explanation
Indices: 7555129--7555258 Score: 163
Period size: 67 Copynumber: 1.9 Consensus size: 66
7555119 AGGGTCTAAC
* * * * * *
7555129 ACATACCATACATAATATCCATATTAGTATATCATAAAATACATAACATACTAGTATATCATAAA
1 ACATAACATACATAATATACACACTAATATATCATAAAATA-ATAACATACTAATATATCATAAA
7555194 AT
65 AT
*
7555196 ACATAACATACATAATATACACACTAATATATCATAACAT-ATAACATACACTAATATATCATA
1 ACATAACATACATAATATACACACTAATATATCATAAAATAATAACAT--ACTAATATATCATA
7555259 TCATTTTTTA
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
65 7 0.13
67 47 0.87
ACGTcount: A:0.51, C:0.18, G:0.02, T:0.30
Consensus pattern (66 bp):
ACATAACATACATAATATACACACTAATATATCATAAAATAATAACATACTAATATATCATAAAA
T
Found at i:7570604 original size:17 final size:19
Alignment explanation
Indices: 7570580--7570616 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
7570570 GTAGTACTCG
7570580 ATTTTTTT-TGTCCACTAT
1 ATTTTTTTCTGTCCACTAT
7570598 ATTTTTTTCTGTCCACTAT
1 ATTTTTTTCTGTCCACTAT
7570617 TTTGATACCG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.16, C:0.19, G:0.05, T:0.59
Consensus pattern (19 bp):
ATTTTTTTCTGTCCACTAT
Found at i:7570617 original size:17 final size:17
Alignment explanation
Indices: 7570580--7570619 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
7570570 GTAGTACTCG
7570580 ATTTTTTTTGTCCACTAT
1 ATTTTTTTTGTCCAC-AT
7570598 ATTTTTTTCTGTCCAC-T
1 ATTTTTTT-TGTCCACAT
7570615 ATTTT
1 ATTTT
7570620 GATACCGAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 6 0.29
18 8 0.38
19 7 0.33
ACGTcount: A:0.15, C:0.17, G:0.05, T:0.62
Consensus pattern (17 bp):
ATTTTTTTTGTCCACAT
Found at i:7570802 original size:15 final size:15
Alignment explanation
Indices: 7570782--7570810 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
7570772 CCTTTCACCA
7570782 TTGTCTTCTACCTCT
1 TTGTCTTCTACCTCT
7570797 TTGTCTTCTACCTC
1 TTGTCTTCTACCTC
7570811 ACTTATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.34, G:0.07, T:0.52
Consensus pattern (15 bp):
TTGTCTTCTACCTCT
Found at i:7571884 original size:18 final size:18
Alignment explanation
Indices: 7571863--7571897 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
7571853 TGGCATGGTA
*
7571863 GAAGGAGTTGGTCGTGTT
1 GAAGGAGCTGGTCGTGTT
*
7571881 GAAGGAGCTGGTGGTGT
1 GAAGGAGCTGGTCGTGT
7571898 CTGTAATAGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.06, G:0.49, T:0.29
Consensus pattern (18 bp):
GAAGGAGCTGGTCGTGTT
Found at i:7573185 original size:30 final size:31
Alignment explanation
Indices: 7573136--7573199 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 31
7573126 ACTTATTTTA
*
7573136 TTGTTAATTTTTTTTATTATTTTAAAGACAT
1 TTGTTAATTTTTGTTATTATTTTAAAGACAT
* *
7573167 TTGTTAA-TTTTGTTATTATTTTAGAGACTT
1 TTGTTAATTTTTGTTATTATTTTAAAGACAT
7573197 TTG
1 TTG
7573200 CTTATTAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 23 0.77
31 7 0.23
ACGTcount: A:0.25, C:0.03, G:0.11, T:0.61
Consensus pattern (31 bp):
TTGTTAATTTTTGTTATTATTTTAAAGACAT
Found at i:7573353 original size:12 final size:12
Alignment explanation
Indices: 7573323--7573355 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
7573313 TATATATTTT
7573323 AAAATT-ATATA
1 AAAATTAATATA
7573334 AAAA-TAATATA
1 AAAATTAATATA
7573345 AAAATTAATAT
1 AAAATTAATAT
7573356 GGGCGGGCCG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:7574566 original size:3 final size:3
Alignment explanation
Indices: 7574558--7574588 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
7574548 ATTAACATGT
*
7574558 ATA ATA ATA ATA AGA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
7574589 AAGAAATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:7577721 original size:18 final size:18
Alignment explanation
Indices: 7577700--7577759 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
7577690 AATCGATTAA
*
7577700 TCAGTAATATTCATTTAT
1 TCAGTAATAGTCATTTAT
*
7577718 TCAGT-ATCAGTCGTTTAT
1 TCAGTAAT-AGTCATTTAT
* * *
7577736 TCTGTAAAAGTCAATTAT
1 TCAGTAATAGTCATTTAT
7577754 TCAGTA
1 TCAGTA
7577760 GCAGACAGTC
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
17 2 0.06
18 30 0.91
19 1 0.03
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (18 bp):
TCAGTAATAGTCATTTAT
Found at i:7589008 original size:19 final size:20
Alignment explanation
Indices: 7588984--7589022 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
7588974 TCTTATTTTT
7588984 TATTTGTTTTT-TGTTTTAA
1 TATTTGTTTTTATGTTTTAA
7589003 TATTTGTTTTTATGTTTTAA
1 TATTTGTTTTTATGTTTTAA
7589023 ATGTATTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.18, C:0.00, G:0.10, T:0.72
Consensus pattern (20 bp):
TATTTGTTTTTATGTTTTAA
Found at i:7589040 original size:25 final size:23
Alignment explanation
Indices: 7588984--7589048 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 23
7588974 TCTTATTTTT
*
7588984 TATTTGTTTTT-TGTTTT-AA--
1 TATTTGTTTTTATATTTTAAATG
*
7589003 TATTTGTTTTTATGTTTTAAATG
1 TATTTGTTTTTATATTTTAAATG
7589026 TATTTGATTTATTATATTTTAAA
1 TATTTG-TTT-TTATATTTTAAA
7589049 GTTTTTTATT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
19 11 0.28
20 6 0.15
21 2 0.05
23 6 0.15
24 3 0.08
25 11 0.28
ACGTcount: A:0.25, C:0.00, G:0.09, T:0.66
Consensus pattern (23 bp):
TATTTGTTTTTATATTTTAAATG
Found at i:7589297 original size:46 final size:47
Alignment explanation
Indices: 7589227--7589382 Score: 153
Period size: 46 Copynumber: 3.4 Consensus size: 47
7589217 TGCACACTTC
* *
7589227 TAGGTTAAACCTACACCAAT--TGGATAATAGTGCCTGGTCACCCGT
1 TAGGTTGAACCTACACAAATCATGGATAATAGTGCCTGGTCACCCGT
* ** * **
7589272 TAAGGTTGAATCTACATGAA-C-TGGATAATAGTGTCTAATCACCCGT
1 T-AGGTTGAACCTACACAAATCATGGATAATAGTGCCTGGTCACCCGT
*
7589318 TAGAGTTGAACCTACACAAATCAT--ATAATAATGCCTGGTCACCCGT
1 TAG-GTTGAACCTACACAAATCATGGATAATAGTGCCTGGTCACCCGT
*
7589364 TGGGGTTGAACCTACACAA
1 T-AGGTTGAACCTACACAA
7589383 CAAATAGCCT
Statistics
Matches: 90, Mismatches: 15, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
45 3 0.03
46 84 0.93
47 2 0.02
48 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (47 bp):
TAGGTTGAACCTACACAAATCATGGATAATAGTGCCTGGTCACCCGT
Found at i:7604742 original size:17 final size:17
Alignment explanation
Indices: 7604720--7604753 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
7604710 ATCCACTAAT
*
7604720 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
7604737 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
7604754 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:7609381 original size:17 final size:17
Alignment explanation
Indices: 7609359--7609392 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
7609349 ATCCACTAAT
*
7609359 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
7609376 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
7609393 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:7609838 original size:31 final size:31
Alignment explanation
Indices: 7609795--7609856 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
7609785 ACATTCTTGA
7609795 GGTTATTTCAGATTATTGATCACCAAAACTT
1 GGTTATTTCAGATTATTGATCACCAAAACTT
* * *
7609826 GGTTCTTTCAGATTCTTGATCATCAAAACTT
1 GGTTATTTCAGATTATTGATCACCAAAACTT
7609857 TTGTTATGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (31 bp):
GGTTATTTCAGATTATTGATCACCAAAACTT
Found at i:7611295 original size:27 final size:27
Alignment explanation
Indices: 7611265--7611324 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
7611255 CCAGGAAAGA
* * *
7611265 AAACATGGGGTAATTCGCCGAGACAGT
1 AAACACGGGGTAATTCGCCGAAACAAT
*
7611292 AAACACGGGGTAGTTCGCCGAAACAAT
1 AAACACGGGGTAATTCGCCGAAACAAT
7611319 AAACAC
1 AAACAC
7611325 AGGAGGTGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.38, C:0.22, G:0.25, T:0.15
Consensus pattern (27 bp):
AAACACGGGGTAATTCGCCGAAACAAT
Found at i:7613581 original size:16 final size:16
Alignment explanation
Indices: 7613562--7613597 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
7613552 TATATAAATT
* *
7613562 AAACTGAAGATAATAA
1 AAACTGAAAACAATAA
7613578 AAACTGAAAACAATAA
1 AAACTGAAAACAATAA
7613594 AAAC
1 AAAC
7613598 ACTCGTCGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.67, C:0.11, G:0.08, T:0.14
Consensus pattern (16 bp):
AAACTGAAAACAATAA
Found at i:7614391 original size:9 final size:10
Alignment explanation
Indices: 7614377--7614419 Score: 56
Period size: 9 Copynumber: 4.6 Consensus size: 10
7614367 AATTATGAAG
7614377 AAAATTTTA-
1 AAAATTTTAT
7614386 AAAA-TTTAT
1 AAAATTTTAT
*
7614395 AAAATTATAT
1 AAAATTTTAT
7614405 AAAATTTTA-
1 AAAATTTTAT
7614414 AAAATT
1 AAAATT
7614420 CAAAAGGTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
8 4 0.13
9 14 0.47
10 12 0.40
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
AAAATTTTAT
Found at i:7614430 original size:28 final size:27
Alignment explanation
Indices: 7614377--7614434 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
7614367 AATTATGAAG
*
7614377 AAAATTTTAAAAATTTATAAAATTATAT
1 AAAATTTTAAAAATTCATAAAATTAT-T
*
7614405 AAAATTTTAAAAATTCA-AAAGGTTATT
1 AAAATTTTAAAAATTCATAAA-ATTATT
7614432 AAA
1 AAA
7614435 CAAAAATAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 7 0.26
28 20 0.74
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (27 bp):
AAAATTTTAAAAATTCATAAAATTATT
Found at i:7615988 original size:17 final size:19
Alignment explanation
Indices: 7615954--7615988 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
7615944 GTTATTGTTA
7615954 TATATAAATAAGAGAAAAT
1 TATATAAATAAGAGAAAAT
7615973 TATATAAA-AAGA-AAAA
1 TATATAAATAAGAGAAAA
7615989 GAGATAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 4 0.25
19 8 0.50
ACGTcount: A:0.69, C:0.00, G:0.09, T:0.23
Consensus pattern (19 bp):
TATATAAATAAGAGAAAAT
Found at i:7618682 original size:43 final size:44
Alignment explanation
Indices: 7618595--7618684 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 44
7618585 TATTCCATCA
**
7618595 AACCAAATACAAGAATATTATTATAATTCTATTTTATTCAATTC
1 AACCAAATACAAGAATATTATTATAATTCTATTCCATTCAATTC
*
7618639 AACCAAATACAAGAATATT-TTATAACTT-TATTCCATTCTATTC
1 AACCAAATACAAGAATATTATTATAA-TTCTATTCCATTCAATTC
7618682 AAC
1 AAC
7618685 TAAACAATTA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
43 21 0.50
44 21 0.50
ACGTcount: A:0.42, C:0.17, G:0.02, T:0.39
Consensus pattern (44 bp):
AACCAAATACAAGAATATTATTATAATTCTATTCCATTCAATTC
Found at i:7618724 original size:16 final size:16
Alignment explanation
Indices: 7618703--7618753 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
7618693 TAAATTACTG
*
7618703 ATTACAGTTTTATTCT
1 ATTACAATTTTATTCT
*
7618719 ATTACAATTTTATTCC
1 ATTACAATTTTATTCT
* **
7618735 ATTTCAATCATATTCT
1 ATTACAATTTTATTCT
7618751 ATT
1 ATT
7618754 CCAGTAAACC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.29, C:0.16, G:0.02, T:0.53
Consensus pattern (16 bp):
ATTACAATTTTATTCT
Found at i:7631451 original size:31 final size:31
Alignment explanation
Indices: 7631416--7631496 Score: 96
Period size: 31 Copynumber: 2.6 Consensus size: 31
7631406 ATGATGCTAG
*
7631416 AGATATTTTGA-TATTTTATAAT-TATTTAATT
1 AGATATTTT-ATTATTTTATAATAT-TTTAATA
*
7631447 AGATA-ATTATTATTTTATTAATATTTTAATA
1 AGATATTTTATTATTTTA-TAATATTTTAATA
7631478 AGATATTTTATTATTTTAT
1 AGATATTTTATTATTTTAT
7631497 TAGTATACAA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
29 1 0.02
30 9 0.21
31 21 0.49
32 12 0.28
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (31 bp):
AGATATTTTATTATTTTATAATATTTTAATA
Found at i:7634865 original size:104 final size:104
Alignment explanation
Indices: 7634743--7634966 Score: 369
Period size: 104 Copynumber: 2.2 Consensus size: 104
7634733 AATGGATATC
7634743 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
7634808 GGAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCA
66 GGATCA-CGCACATAGCACCACCAATAAACCGGGGAATCA
7634847 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
7634912 GGATCACGCACATAGCACCACCCATAAATCGGGGAATCA
66 GGATCACGCACATAGCACCACCAATAAACCGGGGAATCA
* **
7634951 GAACACAGCAACCCCT
1 GCACTTAGCAACCCCT
7634967 TTTATATACA
Statistics
Matches: 112, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
104 111 0.99
105 1 0.01
ACGTcount: A:0.32, C:0.31, G:0.19, T:0.18
Consensus pattern (104 bp):
GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
GGATCACGCACATAGCACCACCAATAAACCGGGGAATCA
Found at i:7635328 original size:29 final size:29
Alignment explanation
Indices: 7635295--7635358 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
7635285 TAATCCACCA
7635295 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
7635324 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
7635354 CCCAA
1 CCCAA
7635359 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:7635332 original size:30 final size:30
Alignment explanation
Indices: 7635302--7635358 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
7635292 CCACCCAACT
7635302 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
7635331 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
7635359 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:7636368 original size:46 final size:47
Alignment explanation
Indices: 7636172--7636358 Score: 238
Period size: 46 Copynumber: 4.1 Consensus size: 47
7636162 GGGCTGTTAC
* * *
7636172 AGATACCATGGCAACATGAC-GGTAAATGAATAAGATCATGGTTGAA
1 AGATACCATGGCAACATGACATGAAAATGAATAAGACCATGGTTGAA
* * * * **
7636218 AGATACCATGGTAGCGTGATATG-AAATGTGTAAGACCATGGTTGAA
1 AGATACCATGGCAACATGACATGAAAATGAATAAGACCATGGTTGAA
*
7636264 AGATACCATGGCAACGTGACATGAAAA-GAATAAGACCATGGTTGAA
1 AGATACCATGGCAACATGACATGAAAATGAATAAGACCATGGTTGAA
* *
7636310 AGATACCATGGCAACATGACA-GAAAATGAGTAAGACCATAGTTGAA
1 AGATACCATGGCAACATGACATGAAAATGAATAAGACCATGGTTGAA
7636356 AGA
1 AGA
7636359 CATTATGGCA
Statistics
Matches: 122, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
45 5 0.04
46 113 0.93
47 4 0.03
ACGTcount: A:0.42, C:0.13, G:0.25, T:0.20
Consensus pattern (47 bp):
AGATACCATGGCAACATGACATGAAAATGAATAAGACCATGGTTGAA
Found at i:7636944 original size:23 final size:23
Alignment explanation
Indices: 7636918--7636963 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
7636908 TAATTGAATG
7636918 GTAATATATTTATTTATATGATA
1 GTAATATATTTATTTATATGATA
7636941 GTAATATATTTATTTATATGATA
1 GTAATATATTTATTTATATGATA
7636964 CACTGAATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (23 bp):
GTAATATATTTATTTATATGATA
Found at i:7640118 original size:16 final size:16
Alignment explanation
Indices: 7640097--7640129 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
7640087 AAGGAAAAAC
7640097 AGAAAAAAAAAGAAGA
1 AGAAAAAAAAAGAAGA
*
7640113 AGAAAAAAAAAGTAGA
1 AGAAAAAAAAAGAAGA
7640129 A
1 A
7640130 TCTTTACCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (16 bp):
AGAAAAAAAAAGAAGA
Found at i:7640531 original size:20 final size:20
Alignment explanation
Indices: 7640506--7640696 Score: 103
Period size: 20 Copynumber: 9.6 Consensus size: 20
7640496 TTCTTTAGAT
*
7640506 TTTTTGGTATTCCCTCGTAA
1 TTTTTGGTATTCCCTCATAA
* **
7640526 TTTTTGGTATTTCCTCATGT
1 TTTTTGGTATTCCCTCATAA
* *
7640546 TTTTTAGTATATCCTTCGAT--
1 TTTTTGGTAT-TCCCTC-ATAA
*
7640566 TTTTTGGTATTCTCC-AATATA
1 TTTTTGGTATTC-CCTCATA-A
7640587 TTTTTGGTATTCCCTCATAA
1 TTTTTGGTATTCCCTCATAA
*
7640607 TTTTTGATGCATT--CTCATAA
1 TTTTTG--GTATTCCCTCATAA
* *
7640627 TTTTTTGTACTT-TCTCATAA
1 TTTTTGGTA-TTCCCTCATAA
* * * *
7640647 TTTTT-TTATTCTCTCGTAG
1 TTTTTGGTATTCCCTCATAA
*
7640666 TTTTTGATACTT-CCTCATAA
1 TTTTTGGTA-TTCCCTCATAA
7640686 TTATTT-GTATT
1 TT-TTTGGTATT
7640697 GTTTCGAAAA
Statistics
Matches: 134, Mismatches: 22, Indels: 31
0.72 0.12 0.17
Matches are distributed among these distances:
18 6 0.04
19 19 0.14
20 79 0.59
21 24 0.18
22 6 0.04
ACGTcount: A:0.19, C:0.16, G:0.10, T:0.55
Consensus pattern (20 bp):
TTTTTGGTATTCCCTCATAA
Found at i:7640804 original size:20 final size:21
Alignment explanation
Indices: 7640779--7640819 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
7640769 TTGGTACACC
7640779 CTCATAA-TTTTCTGTATGGT
1 CTCATAATTTTTCTGTATGGT
*
7640799 CTCATAATTTTTTTGTATGGT
1 CTCATAATTTTTCTGTATGGT
7640820 TTTGAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.20, C:0.12, G:0.15, T:0.54
Consensus pattern (21 bp):
CTCATAATTTTTCTGTATGGT
Found at i:7641248 original size:19 final size:20
Alignment explanation
Indices: 7641207--7641249 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
7641197 GCTAAAACTT
*
7641207 AATTTTGAAAGCATATCAAA
1 AATTCTGAAAGCATATCAAA
7641227 AATTCTGAAAGCATAT-AAA
1 AATTCTGAAAGCATATCAAA
7641246 AATT
1 AATT
7641250 ATGTGAGAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.30
Consensus pattern (20 bp):
AATTCTGAAAGCATATCAAA
Found at i:7641309 original size:20 final size:20
Alignment explanation
Indices: 7641286--7641347 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
7641276 GATTGTGAAT
7641286 AATTATAAAGGAATACCAAA
1 AATTATAAAGGAATACCAAA
*
7641306 AATTAT-TAGAGAATACCAAA
1 AATTATAAAG-GAATACCAAA
* * *
7641326 AATAATAAAGGAGTACTAAA
1 AATTATAAAGGAATACCAAA
7641346 AA
1 AA
7641348 CATGGGGTAC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 2 0.06
20 31 0.89
21 2 0.06
ACGTcount: A:0.60, C:0.08, G:0.11, T:0.21
Consensus pattern (20 bp):
AATTATAAAGGAATACCAAA
Found at i:7641478 original size:20 final size:20
Alignment explanation
Indices: 7641295--7641483 Score: 56
Period size: 20 Copynumber: 9.8 Consensus size: 20
7641285 TAATTATAAA
*
7641295 GGAATACCAAAAATTATTAG
1 GGAATACCAAAAATTATGAG
* * * *
7641315 AGAATACCAAAAATAATAAA
1 GGAATACCAAAAATTATGAG
* * *
7641335 GGAGTACTAAAAA-CATG-G
1 GGAATACCAAAAATTATGAG
**
7641353 GG--TACCAAAAATTAAAAG
1 GGAATACCAAAAATTATGAG
** * *
7641371 GGAATGTCAATAATTATAAG
1 GGAATACCAAAAATTATGAG
* *
7641391 GTGAGTACCAAAAAGCT-TG-G
1 G-GAATACCAAAAA-TTATGAG
* * *
7641411 GAAAGTACCTAAAATTATGAA
1 GGAA-TACCAAAAATTATGAG
* * *
7641432 GTAA-A--AAAAA-AAAGAG
1 GGAATACCAAAAATTATGAG
*
7641448 GGAATATCAAAAATTATGAG
1 GGAATACCAAAAATTATGAG
* *
7641468 GGACTACCAAATATTA
1 GGAATACCAAAAATTA
7641484 GTTCATCTTA
Statistics
Matches: 116, Mismatches: 40, Indels: 26
0.64 0.22 0.14
Matches are distributed among these distances:
16 14 0.12
17 6 0.05
18 5 0.04
19 10 0.09
20 68 0.59
21 12 0.10
22 1 0.01
ACGTcount: A:0.52, C:0.10, G:0.18, T:0.21
Consensus pattern (20 bp):
GGAATACCAAAAATTATGAG
Found at i:7645113 original size:33 final size:33
Alignment explanation
Indices: 7645076--7645204 Score: 125
Period size: 33 Copynumber: 3.9 Consensus size: 33
7645066 ATAAATACAA
*
7645076 AATAGAGATAGTCCACTAGGACTGTAAACATAG
1 AATAGAGATAGTCCACTAGGACAGTAAACATAG
* ** * * * *
7645109 AATAGAGAAAGTCCGTTGGGACAGTAAAAACAA
1 AATAGAGATAGTCCACTAGGACAGTAAACATAG
* *
7645142 AATAGAGATAGCCCGCTAGGACAGTAAACATAG
1 AATAGAGATAGTCCACTAGGACAGTAAACATAG
* * *
7645175 -ATAAGAGATAGTCCATTGGGACAATAAACA
1 AAT-AGAGATAGTCCACTAGGACAGTAAACA
7645205 CAAATAAAGT
Statistics
Matches: 75, Mismatches: 20, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
32 2 0.03
33 73 0.97
ACGTcount: A:0.45, C:0.15, G:0.22, T:0.18
Consensus pattern (33 bp):
AATAGAGATAGTCCACTAGGACAGTAAACATAG
Found at i:7645144 original size:66 final size:65
Alignment explanation
Indices: 7645044--7645208 Score: 204
Period size: 66 Copynumber: 2.5 Consensus size: 65
7645034 TATGATATCC
* * * * * * *
7645044 ATAGAGAAATTTCGCTGGAACAATAAATACAAAATAGAGATAGTCCACTAGGACTGTAAACATAG
1 ATAGAGAAAGTCCGTTGGGACAATAAAAACAAAATAGAGATAGCCCACTAGGACAGTAAACATAG
* *
7645109 AATAGAGAAAGTCCGTTGGGACAGTAAAAACAAAATAGAGATAGCCCGCTAGGACAGTAAACATA
1 -ATAGAGAAAGTCCGTTGGGACAATAAAAACAAAATAGAGATAGCCCACTAGGACAGTAAACATA
7645174 G
65 G
* * *
7645175 ATAAGAGATAGTCCATTGGGACAATAAACACAAA
1 AT-AGAGAAAGTCCGTTGGGACAATAAAAACAAA
7645209 TAAAGTTCAT
Statistics
Matches: 85, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
65 2 0.02
66 83 0.98
ACGTcount: A:0.47, C:0.15, G:0.21, T:0.18
Consensus pattern (65 bp):
ATAGAGAAAGTCCGTTGGGACAATAAAAACAAAATAGAGATAGCCCACTAGGACAGTAAACATAG
Found at i:7645235 original size:28 final size:28
Alignment explanation
Indices: 7645193--7645261 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 28
7645183 TAGTCCATTG
* * *
7645193 GGACAATAAACACAAATAAAGTTCATCA
1 GGACAGTAAACACAAATAAAGCTCACCA
* * *
7645221 GGACAGTAAATACAAGTTAAGCTCACCA
1 GGACAGTAAACACAAATAAAGCTCACCA
*
7645249 GGAAAGTAAACAC
1 GGACAGTAAACAC
7645262 GAGGTAAGTT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.49, C:0.19, G:0.16, T:0.16
Consensus pattern (28 bp):
GGACAGTAAACACAAATAAAGCTCACCA
Found at i:7647575 original size:43 final size:43
Alignment explanation
Indices: 7647511--7647632 Score: 201
Period size: 43 Copynumber: 2.9 Consensus size: 43
7647501 TCTAAATTCA
* *
7647511 TTCACCGGGATT-TCGCCTGCTAGGCTCGAAGCCCGATATTAT
1 TTCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCGATATTAT
* *
7647553 TTCACCGGTATTATAGCCTGCTAGGCTCGAGGCCCGATATTAT
1 TTCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCGATATTAT
7647596 TTCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCGA
1 TTCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCGA
7647633 ATGGTACCAT
Statistics
Matches: 74, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
42 11 0.15
43 63 0.85
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.27
Consensus pattern (43 bp):
TTCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCGATATTAT
Found at i:7650986 original size:22 final size:21
Alignment explanation
Indices: 7650951--7650995 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
7650941 AGATTGAATG
*
7650951 TGAAATCAATGGTTATATTTA
1 TGAAATCAATGGTTATATGTA
* *
7650972 TGAAATGCTATGGTTTTATGTA
1 TGAAAT-CAATGGTTATATGTA
7650994 TG
1 TG
7650996 CTTGGATGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.31, C:0.04, G:0.20, T:0.44
Consensus pattern (21 bp):
TGAAATCAATGGTTATATGTA
Found at i:7652779 original size:23 final size:23
Alignment explanation
Indices: 7652745--7652790 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
7652735 GTAACATCAT
7652745 TTACTTTAGATATTGAAA-AAAAA
1 TTACTTTAGATATT-AAAGAAAAA
*
7652768 TTACTTTGGATATTAAAGAAAAA
1 TTACTTTAGATATTAAAGAAAAA
7652791 CATAATTTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.50, C:0.04, G:0.11, T:0.35
Consensus pattern (23 bp):
TTACTTTAGATATTAAAGAAAAA
Found at i:7653918 original size:5 final size:5
Alignment explanation
Indices: 7653908--7653946 Score: 78
Period size: 5 Copynumber: 7.8 Consensus size: 5
7653898 AAAAGTAGAT
7653908 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAA
1 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAA
7653947 TTGGAAATCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TTAAA
Found at i:7655473 original size:2 final size:2
Alignment explanation
Indices: 7655466--7655490 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
7655456 AACCTCTACC
7655466 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 A
7655491 ATTCTAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7661083 original size:40 final size:39
Alignment explanation
Indices: 7660997--7661110 Score: 120
Period size: 40 Copynumber: 2.8 Consensus size: 39
7660987 AGCTATAGAG
* * **
7660997 GCATTAGCGACATTTTTTGTAAAACGCCGCAATATATTGA
1 GCATTAGCGGC-TTTTTTGTAAAACGCCGCAAAATATCAA
* * *
7661037 GAATTAGCGGCGTTTGTTGTAAAACGCCGCAAAATGTCAA
1 GCATTAGCGGC-TTTTTTGTAAAACGCCGCAAAATATCAA
* *
7661077 TCATTAGCGGCTTTTTTGTTAAAACACCGCAAAA
1 GCATTAGCGGCTTTTTTG-TAAAACGCCGCAAAA
7661111 AAAATATGTT
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
39 6 0.10
40 55 0.90
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.30
Consensus pattern (39 bp):
GCATTAGCGGCTTTTTTGTAAAACGCCGCAAAATATCAA
Found at i:7661236 original size:27 final size:29
Alignment explanation
Indices: 7661206--7661261 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
7661196 TGTTTATTAT
7661206 TTTGGGTTAT-GGGTTTA-TGTTTTAGAG
1 TTTGGGTTATGGGGTTTATTGTTTTAGAG
*
7661233 TTTGGGTTTTGGGGTTTATTGTTTTAGAG
1 TTTGGGTTATGGGGTTTATTGTTTTAGAG
7661262 ATTAGGGTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 9 0.35
28 7 0.27
29 10 0.38
ACGTcount: A:0.12, C:0.00, G:0.34, T:0.54
Consensus pattern (29 bp):
TTTGGGTTATGGGGTTTATTGTTTTAGAG
Found at i:7661798 original size:14 final size:14
Alignment explanation
Indices: 7661758--7661802 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
7661748 GGTGTTTTGT
7661758 GGTTTAAGGTTTAG
1 GGTTTAAGGTTTAG
** * *
7661772 AATTCAAGATTTAG
1 GGTTTAAGGTTTAG
7661786 GGTTTAAGGTTTAG
1 GGTTTAAGGTTTAG
7661800 GGT
1 GGT
7661803 ATAATTTTGG
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.27, C:0.02, G:0.31, T:0.40
Consensus pattern (14 bp):
GGTTTAAGGTTTAG
Found at i:7666554 original size:28 final size:28
Alignment explanation
Indices: 7666491--7666588 Score: 128
Period size: 27 Copynumber: 3.5 Consensus size: 28
7666481 ATATTAAGTC
*
7666491 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
7666518 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * *
7666546 CGCACACTTAGTGCTGA-ACAATTTAAACC
1 CGCACACTTAGTGCT-ATATAA-TCAAACT
7666575 CGCACACTTAGTGC
1 CGCACACTTAGTGC
7666589 CAATCTCATG
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
27 22 0.34
28 22 0.34
29 20 0.31
ACGTcount: A:0.33, C:0.29, G:0.13, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:7670421 original size:9 final size:9
Alignment explanation
Indices: 7670407--7670494 Score: 93
Period size: 9 Copynumber: 10.7 Consensus size: 9
7670397 CCAGCAACTC
7670407 ACATAATTT
1 ACATAATTT
7670416 ACATAATTT
1 ACATAATTT
7670425 ACATAATTT
1 ACATAATTT
7670434 ACATAA--T
1 ACATAATTT
*
7670441 ACATAACTT
1 ACATAATTT
*
7670450 ATATAATTT
1 ACATAATTT
7670459 A-AT-A-TT
1 ACATAATTT
7670465 -CA-AATTT
1 ACATAATTT
*
7670472 -CATAACTT
1 ACATAATTT
7670480 ACATAATTT
1 ACATAATTT
7670489 ACATAA
1 ACATAA
7670495 ATATATATCA
Statistics
Matches: 68, Mismatches: 4, Indels: 14
0.79 0.05 0.16
Matches are distributed among these distances:
6 4 0.06
7 12 0.18
8 6 0.09
9 46 0.68
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (9 bp):
ACATAATTT
Found at i:7670446 original size:25 final size:25
Alignment explanation
Indices: 7670415--7670486 Score: 80
Period size: 25 Copynumber: 3.0 Consensus size: 25
7670405 TCACATAATT
7670415 TACATAATTTACATAATTTACATAA
1 TACATAATTTACATAATTTACATAA
* *
7670440 TACATAACTTATATAATTTA-AT-A
1 TACATAATTTACATAATTTACATAA
* *
7670463 TTCA-AATTT-CATAACTTACATAA
1 TACATAATTTACATAATTTACATAA
7670486 T
1 T
7670487 TTACATAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
21 7 0.18
22 6 0.15
23 6 0.15
24 2 0.05
25 18 0.46
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (25 bp):
TACATAATTTACATAATTTACATAA
Found at i:7672261 original size:12 final size:12
Alignment explanation
Indices: 7672244--7672269 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
7672234 AAGATCGAGG
7672244 GATGAATCTGAT
1 GATGAATCTGAT
7672256 GATGAATCTGAT
1 GATGAATCTGAT
7672268 GA
1 GA
7672270 AGAGGATGAT
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:0.35, C:0.08, G:0.27, T:0.31
Consensus pattern (12 bp):
GATGAATCTGAT
Found at i:7673799 original size:21 final size:21
Alignment explanation
Indices: 7673775--7673817 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
7673765 AAATTGTGGA
7673775 ATAGTTGTTAATTCTTCAATT
1 ATAGTTGTTAATTCTTCAATT
7673796 ATAGTTGTTAATTCTTCAATT
1 ATAGTTGTTAATTCTTCAATT
7673817 A
1 A
7673818 CAAGTTATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.51
Consensus pattern (21 bp):
ATAGTTGTTAATTCTTCAATT
Found at i:7676069 original size:33 final size:33
Alignment explanation
Indices: 7676027--7676107 Score: 103
Period size: 31 Copynumber: 2.5 Consensus size: 33
7676017 TTAGATTTAA
* * *
7676027 TGTTTTTGGTTGTATTTTTTATGCTACATTTGC
1 TGTTTTTGGTTGCATTTTTCATGCCACATTTGC
* *
7676060 TGTTTTTGGTTGGA--TTTCATGCCATATTTGC
1 TGTTTTTGGTTGCATTTTTCATGCCACATTTGC
7676091 TGTTTTTGGTTGCATTT
1 TGTTTTTGGTTGCATTT
7676108 AATGCAGGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
31 27 0.66
33 14 0.34
ACGTcount: A:0.11, C:0.10, G:0.21, T:0.58
Consensus pattern (33 bp):
TGTTTTTGGTTGCATTTTTCATGCCACATTTGC
Found at i:7676279 original size:43 final size:42
Alignment explanation
Indices: 7676230--7676328 Score: 128
Period size: 43 Copynumber: 2.3 Consensus size: 42
7676220 AAAAGCACTA
*
7676230 CTAAAAGCCATGACTTTTAGCGAAGC-TTCTCCCACAAACGTCG
1 CTAAAAGCCATGACTTTTAGC--AGCATTCTCCCACAAACGCCG
* *
7676273 CTAAAAGCCATGACTTTTAGCAGCAATTTTCCCATAAACGCCG
1 CTAAAAGCCATGACTTTTAGCAGC-ATTCTCCCACAAACGCCG
*
7676316 CTAAAAGTCATGA
1 CTAAAAGCCATGA
7676329 TCATTTGCGG
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
41 3 0.06
43 47 0.94
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.24
Consensus pattern (42 bp):
CTAAAAGCCATGACTTTTAGCAGCATTCTCCCACAAACGCCG
Found at i:7683341 original size:27 final size:27
Alignment explanation
Indices: 7683311--7683364 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
7683301 GGAATGATGG
*
7683311 GTTCATCATAGATCTATTTAAAGTTAA
1 GTTCATCACAGATCTATTTAAAGTTAA
7683338 GTTCATCACAGATCTATTTAAAGTTAA
1 GTTCATCACAGATCTATTTAAAGTTAA
7683365 CATATCATAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (27 bp):
GTTCATCACAGATCTATTTAAAGTTAA
Found at i:7685737 original size:2 final size:2
Alignment explanation
Indices: 7685730--7685754 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
7685720 AAAAACGATG
7685730 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 A
7685755 AACTATAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7690057 original size:40 final size:40
Alignment explanation
Indices: 7690021--7690099 Score: 115
Period size: 39 Copynumber: 2.0 Consensus size: 40
7690011 CACTAAAGAT
*
7690021 TGAGCATTAGTGGCGTTTAT-AAAAAAATGCCGCTAAAAA
1 TGAGCATTAGCGGCGTTTATCAAAAAAATGCCGCTAAAAA
* * *
7690060 TGAGCATTAGCGGCGTTTTTCAAAAAAACGCCGCAAAAAA
1 TGAGCATTAGCGGCGTTTATCAAAAAAATGCCGCTAAAAA
7690100 CCTTAGCCCA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
39 18 0.51
40 17 0.49
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (40 bp):
TGAGCATTAGCGGCGTTTATCAAAAAAATGCCGCTAAAAA
Found at i:7690075 original size:39 final size:39
Alignment explanation
Indices: 7689946--7690099 Score: 130
Period size: 40 Copynumber: 3.8 Consensus size: 39
7689936 AGCGGCACTT
** * *
7689946 TTAGCGGCGTTTGGACAAAAAACGCCGGTAAAAATCAAGCA
1 TTAGCGGCGTTTATA-AAAAAACGCCGCTAAAAAT-GAGCA
* ** * * *
7689987 TTAGCGGCGCTTTCT-GGAAATCGCCACTAAAGATTGAGCA
1 TTAGCGGCG-TTTATAAAAAAACGCCGCTAAA-AATGAGCA
* *
7690027 TTAGTGGCGTTTATAAAAAAATGCCGCTAAAAATGAGCA
1 TTAGCGGCGTTTATAAAAAAACGCCGCTAAAAATGAGCA
* *
7690066 TTAGCGGCGTTTTTCAAAAAAACGCCGCAAAAAA
1 TTAGCGGCGTTTAT-AAAAAAACGCCGCTAAAAA
7690100 CCTTAGCCCA
Statistics
Matches: 88, Mismatches: 21, Indels: 9
0.75 0.18 0.08
Matches are distributed among these distances:
39 23 0.26
40 51 0.58
41 11 0.12
42 3 0.03
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (39 bp):
TTAGCGGCGTTTATAAAAAAACGCCGCTAAAAATGAGCA
Found at i:7690200 original size:41 final size:41
Alignment explanation
Indices: 7690135--7690246 Score: 158
Period size: 41 Copynumber: 2.7 Consensus size: 41
7690125 AACATTTCGT
7690135 GGCTTTAGCGGCGTTTTTCA-AAAAGCGCCGCTAATGCCT-GG
1 GGCTTTAGCGGCGTTTTT-AGAAAAGCGCCGCTAATG-CTAGG
* *
7690176 GTCTTTAGCGGCGTTTTTAGAAAAGCGCCGCTAATGGTAGG
1 GGCTTTAGCGGCGTTTTTAGAAAAGCGCCGCTAATGCTAGG
7690217 GGCTTTAGCGGCGTTTTT-GATAAAGCGCCG
1 GGCTTTAGCGGCGTTTTTAGA-AAAGCGCCG
7690247 TTAAAAACAT
Statistics
Matches: 65, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
40 4 0.06
41 61 0.94
ACGTcount: A:0.20, C:0.21, G:0.31, T:0.29
Consensus pattern (41 bp):
GGCTTTAGCGGCGTTTTTAGAAAAGCGCCGCTAATGCTAGG
Found at i:7690493 original size:22 final size:22
Alignment explanation
Indices: 7690468--7690542 Score: 75
Period size: 21 Copynumber: 3.5 Consensus size: 22
7690458 GAGTTACTGT
7690468 TTTAAGGTTTATGGAGTATGGA
1 TTTAAGGTTTATGGAGTATGGA
* * *
7690490 TTTAAGGATTATGGATTAGGGA
1 TTTAAGGTTTATGGAGTATGGA
* *
7690512 -TTATGGTTTAAGG-GT-TGAGA
1 TTTAAGGTTTATGGAGTATG-GA
7690532 TTTAAGGTTTA
1 TTTAAGGTTTA
7690543 GGGGTTAGTG
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
19 1 0.02
20 3 0.07
21 19 0.45
22 19 0.45
ACGTcount: A:0.28, C:0.00, G:0.31, T:0.41
Consensus pattern (22 bp):
TTTAAGGTTTATGGAGTATGGA
Found at i:7690514 original size:14 final size:15
Alignment explanation
Indices: 7690484--7690524 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
7690474 GTTTATGGAG
7690484 TATGGATTTAAGGAT
1 TATGGATTTAAGGAT
*
7690499 TATGGA-TTAGGGAT
1 TATGGATTTAAGGAT
7690513 TATGG-TTTAAGG
1 TATGGATTTAAGG
7690525 GTTGAGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 17 0.74
15 6 0.26
ACGTcount: A:0.29, C:0.00, G:0.32, T:0.39
Consensus pattern (15 bp):
TATGGATTTAAGGAT
Found at i:7690563 original size:22 final size:22
Alignment explanation
Indices: 7690537--7690599 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
7690527 TGAGATTTAA
*
7690537 GGTTTAGGGGTT-AGTGGTTAGG
1 GGTTTAGGGGTTAAG-AGTTAGG
7690559 GGTTTAGGGGTTAAGAGTTAGG
1 GGTTTAGGGGTTAAGAGTTAGG
* * *
7690581 GATTTAGGGTTTATGAGTT
1 GGTTTAGGGGTTAAGAGTT
7690600 CATGGGTCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
22 34 0.94
23 2 0.06
ACGTcount: A:0.19, C:0.00, G:0.43, T:0.38
Consensus pattern (22 bp):
GGTTTAGGGGTTAAGAGTTAGG
Found at i:7690651 original size:12 final size:12
Alignment explanation
Indices: 7690630--7690672 Score: 54
Period size: 11 Copynumber: 3.8 Consensus size: 12
7690620 TGGGTTTAGA
7690630 TTAA-TTATTTT
1 TTAATTTATTTT
7690641 TTAATTTATTTT
1 TTAATTTATTTT
* *
7690653 TAAATAT-TTTT
1 TTAATTTATTTT
7690664 TTAATTTAT
1 TTAATTTAT
7690673 ATATTAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
11 13 0.50
12 13 0.50
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TTAATTTATTTT
Found at i:7690667 original size:23 final size:24
Alignment explanation
Indices: 7690629--7690682 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 24
7690619 TTGGGTTTAG
*
7690629 ATTAATTA-TTTTTTAATTTAT-T
1 ATTAAATATTTTTTTAATTTATAT
*
7690651 TTTAAATATTTTTTTAATTTATAT
1 ATTAAATATTTTTTTAATTTATAT
7690675 ATTAAATA
1 ATTAAATA
7690683 ATTTCATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 6 0.22
23 13 0.48
24 8 0.30
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (24 bp):
ATTAAATATTTTTTTAATTTATAT
Found at i:7690875 original size:14 final size:15
Alignment explanation
Indices: 7690858--7690918 Score: 67
Period size: 14 Copynumber: 4.3 Consensus size: 15
7690848 GGGATTATAG
*
7690858 TTTAAGTGTTA-GGA
1 TTTAAGAGTTAGGGA
7690872 TTTAAG-GTTTAGGGA
1 TTTAAGAG-TTAGGGA
7690887 -TTAAGAGTTAGGG-
1 TTTAAGAGTTAGGGA
*
7690900 GTTAAGAGTTAGGGA
1 TTTAAGAGTTAGGGA
7690915 TTTA
1 TTTA
7690919 GGGTTTCAAG
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
13 1 0.02
14 33 0.80
15 7 0.17
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.38
Consensus pattern (15 bp):
TTTAAGAGTTAGGGA
Found at i:7695601 original size:85 final size:86
Alignment explanation
Indices: 7695500--7695676 Score: 223
Period size: 85 Copynumber: 2.1 Consensus size: 86
7695490 AAAAATGTCG
* *
7695500 CTAAAAGTCATGATCTATAGTGGCGTTTATAAAAAAAGCGCCGCTAAAGG-TCTTGATCTATAGC
1 CTAAAGGTCATGATCTATAGCGGCGTTTATAAAAAAAGCGCCGCTAAAGGTTC-TGATCTATAGC
*
7695564 GGCGTTTGT-GTAAAAGTGCCA
65 GGCGTTTGTGGGAAAAGTGCCA
* * *** * * *
7695585 CTAAAGGTCCTGATCTATAGCGGCGTTTGTGGGAAAAGTGTCGCTAAAGGTTCTGATTTATAGCG
1 CTAAAGGTCATGATCTATAGCGGCGTTTATAAAAAAAGCGCCGCTAAAGGTTCTGATCTATAGCG
*
7695650 GCGTTTGTGGGAAAAGTGCCG
66 GCGTTTGTGGGAAAAGTGCCA
7695671 CTAAAG
1 CTAAAG
7695677 TTAGCGACGT
Statistics
Matches: 78, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
85 60 0.77
86 18 0.23
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (86 bp):
CTAAAGGTCATGATCTATAGCGGCGTTTATAAAAAAAGCGCCGCTAAAGGTTCTGATCTATAGCG
GCGTTTGTGGGAAAAGTGCCA
Found at i:7695656 original size:43 final size:43
Alignment explanation
Indices: 7695474--7695676 Score: 221
Period size: 43 Copynumber: 4.7 Consensus size: 43
7695464 ATGGCACTTT
* * * * *
7695474 TAGCGGCGTTTGCGAAAAAAATGTCGCTAAAAGTCATGATCTA
1 TAGCGGCGTTTGTGGAAAAAGTGCCGCTAAAGGTCATGATCTA
* * ** * *
7695517 TAGTGGCGTTTATAAAAAAAGCGCCGCTAAAGGTCTTGATCTA
1 TAGCGGCGTTTGTGGAAAAAGTGCCGCTAAAGGTCATGATCTA
* * *
7695560 TAGCGGCGTTTGT-GTAAAAGTGCCACTAAAGGTCCTGATCTA
1 TAGCGGCGTTTGTGGAAAAAGTGCCGCTAAAGGTCATGATCTA
* * *
7695602 TAGCGGCGTTTGTGGGAAAAGTGTCGCTAAAGGTTC-TGATTTA
1 TAGCGGCGTTTGTGGAAAAAGTGCCGCTAAAGG-TCATGATCTA
*
7695645 TAGCGGCGTTTGTGGGAAAAGTGCCGCTAAAG
1 TAGCGGCGTTTGTGGAAAAAGTGCCGCTAAAG
7695677 TTAGCGACGT
Statistics
Matches: 137, Mismatches: 21, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
42 37 0.27
43 98 0.72
44 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.28
Consensus pattern (43 bp):
TAGCGGCGTTTGTGGAAAAAGTGCCGCTAAAGGTCATGATCTA
Found at i:7695760 original size:22 final size:22
Alignment explanation
Indices: 7695732--7695774 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
7695722 CAGCGGCGCT
*
7695732 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
7695754 AAAAAGCGCCGCTAAAAGCCT
1 AAAAAGCGCCGCTAAAAGCCT
7695775 TTTTGGTGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.28, G:0.21, T:0.09
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAAGCCTA
Found at i:7698835 original size:9 final size:9
Alignment explanation
Indices: 7698821--7698853 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
7698811 ATAGCTTAAT
7698821 AATAAAATA
1 AATAAAATA
*
7698830 AATAAAAGA
1 AATAAAATA
7698839 AATAAAAT-
1 AATAAAATA
7698847 AATAAAA
1 AATAAAA
7698854 AACATAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (9 bp):
AATAAAATA
Found at i:7700137 original size:16 final size:17
Alignment explanation
Indices: 7700118--7700152 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
7700108 ATGATTTTTG
*
7700118 TTATAAATGTT-TAAAA
1 TTATAAATATTGTAAAA
7700134 TTATAAATATTGTAAAA
1 TTATAAATATTGTAAAA
7700151 TT
1 TT
7700153 CTTGTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (17 bp):
TTATAAATATTGTAAAA
Found at i:7706269 original size:28 final size:26
Alignment explanation
Indices: 7706238--7706324 Score: 68
Period size: 28 Copynumber: 3.1 Consensus size: 26
7706228 TAATATACAT
7706238 ATATTTATTTATATTAAATACATACTTA
1 ATATTTATTTATATTAAATA-ATA-TTA
* *
7706266 ATATTTAAGTATATATAAAATAATATTA
1 ATATTT-A-TTTATATTAAATAATATTA
* *
7706294 TTATATTATATTATATTATAATAGT-TTA
1 ATAT-TTAT-TTATATTA-AATAATATTA
7706322 ATA
1 ATA
7706325 ATAAAATAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
27 1 0.02
28 24 0.51
29 11 0.23
30 11 0.23
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (26 bp):
ATATTTATTTATATTAAATAATATTA
Found at i:7706309 original size:30 final size:32
Alignment explanation
Indices: 7706236--7706314 Score: 80
Period size: 30 Copynumber: 2.6 Consensus size: 32
7706226 TATAATATAC
*
7706236 ATATATT-TATT-TATATTAAATACATACTTA
1 ATATATTATATTATATATAAAATACATACTTA
*
7706266 ATAT-TTA-AGTATATATAAAATA-ATA-TTA
1 ATATATTATATTATATATAAAATACATACTTA
*
7706294 TTATATTATATTATATTATAA
1 ATATATTATATTATA-TATAA
7706315 TAGTTTAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
28 6 0.15
29 10 0.25
30 19 0.47
31 5 0.12
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (32 bp):
ATATATTATATTATATATAAAATACATACTTA
Found at i:7707051 original size:15 final size:15
Alignment explanation
Indices: 7707031--7707064 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
7707021 GAGTATTGGT
7707031 ATTAAATTGAATTGA
1 ATTAAATTGAATTGA
7707046 ATTAAATTGAATTGA
1 ATTAAATTGAATTGA
7707061 ATTA
1 ATTA
7707065 TGAGTATATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (15 bp):
ATTAAATTGAATTGA
Found at i:7707657 original size:16 final size:17
Alignment explanation
Indices: 7707638--7707672 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
7707628 ATGATTTTTG
*
7707638 TTATAAATGTT-TAAAA
1 TTATAAATATTGTAAAA
7707654 TTATAAATATTGTAAAA
1 TTATAAATATTGTAAAA
7707671 TT
1 TT
7707673 CTTGTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (17 bp):
TTATAAATATTGTAAAA
Found at i:7709745 original size:34 final size:34
Alignment explanation
Indices: 7709702--7709771 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
7709692 GCATGACTGC
7709702 TACTAATACTGTGATGGGCTAAGGCCCTAATGCA
1 TACTAATACTGTGATGGGCTAAGGCCCTAATGCA
*
7709736 TACTAATACTGTGATGGGCTAAGGCCCTACTGCA
1 TACTAATACTGTGATGGGCTAAGGCCCTAATGCA
7709770 TA
1 TA
7709772 TTTGATACTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (34 bp):
TACTAATACTGTGATGGGCTAAGGCCCTAATGCA
Found at i:7710746 original size:21 final size:21
Alignment explanation
Indices: 7710722--7710764 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
7710712 CATGTCTTAG
*
7710722 GGTCACATGGGCGTGTCCCTT
1 GGTCACATAGGCGTGTCCCTT
7710743 GGTCACATAGGCGTGTCCCTT
1 GGTCACATAGGCGTGTCCCTT
7710764 G
1 G
7710765 TCCATACAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.12, C:0.28, G:0.33, T:0.28
Consensus pattern (21 bp):
GGTCACATAGGCGTGTCCCTT
Done.