Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 111 of 279
Found at i:35073042 original size:18 final size:17
Alignment explanation
Indices: 35073021--35073055 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
35073011 TTATTATTAA
*
35073021 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
35073039 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
35073056 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:35073404 original size:18 final size:17
Alignment explanation
Indices: 35073383--35073417 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
35073373 TTATTATTAA
*
35073383 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
35073401 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
35073418 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:35073524 original size:18 final size:17
Alignment explanation
Indices: 35073503--35073537 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
35073493 TTATTATTAA
*
35073503 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
35073521 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
35073538 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:35073765 original size:18 final size:17
Alignment explanation
Indices: 35073744--35073778 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
35073734 TTATTATTAA
*
35073744 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
35073762 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
35073779 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:35073885 original size:18 final size:17
Alignment explanation
Indices: 35073864--35073898 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
35073854 TTATTATTAA
*
35073864 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
35073882 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
35073899 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:35074247 original size:18 final size:17
Alignment explanation
Indices: 35074226--35074260 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
35074216 TTATTATTAA
*
35074226 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
35074244 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
35074261 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:35074367 original size:18 final size:17
Alignment explanation
Indices: 35074346--35074380 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
35074336 TTATTATTAA
*
35074346 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
35074364 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
35074381 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:35074487 original size:18 final size:17
Alignment explanation
Indices: 35074466--35074500 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
35074456 TTATTATTAA
*
35074466 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
35074484 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
35074501 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:35074968 original size:18 final size:17
Alignment explanation
Indices: 35074947--35074981 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
35074937 TTATTATTAA
*
35074947 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
35074965 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
35074982 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:35075208 original size:18 final size:17
Alignment explanation
Indices: 35075187--35075221 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
35075177 TTATTATTAA
*
35075187 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
35075205 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
35075222 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:35075328 original size:18 final size:17
Alignment explanation
Indices: 35075307--35075341 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
35075297 TTATTATTAA
*
35075307 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
35075325 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
35075342 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:35078725 original size:76 final size:76
Alignment explanation
Indices: 35078599--35078861 Score: 526
Period size: 76 Copynumber: 3.5 Consensus size: 76
35078589 TAACATTTTC
35078599 ATCTTACCTATTTTTGCTACTTTCAGAGGACCAAATTACAACAGAACAAACAAACAAAAGAACTC
1 ATCTTACCTATTTTTGCTACTTTCAGAGGACCAAATTACAACAGAACAAACAAACAAAAGAACTC
35078664 GAACTGCAGAA
66 GAACTGCAGAA
35078675 ATCTTACCTATTTTTGCTACTTTCAGAGGACCAAATTACAACAGAACAAACAAACAAAAGAACTC
1 ATCTTACCTATTTTTGCTACTTTCAGAGGACCAAATTACAACAGAACAAACAAACAAAAGAACTC
35078740 GAACTGCAGAA
66 GAACTGCAGAA
35078751 ATCTTACCTATTTTTGCTACTTTCAGAGGACCAAATTACAACAGAACAAACAAACAAAAGAACTC
1 ATCTTACCTATTTTTGCTACTTTCAGAGGACCAAATTACAACAGAACAAACAAACAAAAGAACTC
35078816 GAACTGCAGAA
66 GAACTGCAGAA
35078827 ATCTTACCTATTTTTGCTACTTTCAGAGGACCAAA
1 ATCTTACCTATTTTTGCTACTTTCAGAGGACCAAA
35078862 AGAACTCAAT
Statistics
Matches: 187, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 187 1.00
ACGTcount: A:0.41, C:0.22, G:0.12, T:0.24
Consensus pattern (76 bp):
ATCTTACCTATTTTTGCTACTTTCAGAGGACCAAATTACAACAGAACAAACAAACAAAAGAACTC
GAACTGCAGAA
Found at i:35085343 original size:30 final size:30
Alignment explanation
Indices: 35085297--35085480 Score: 323
Period size: 30 Copynumber: 6.1 Consensus size: 30
35085287 TTTTATTATG
*
35085297 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
35085328 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
35085358 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
35085388 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
35085418 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* * *
35085448 CTATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
35085478 CCA
1 CCA
35085481 TAAATATGGA
Statistics
Matches: 148, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
30 141 0.95
31 7 0.05
ACGTcount: A:0.26, C:0.24, G:0.07, T:0.43
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:35090096 original size:30 final size:30
Alignment explanation
Indices: 35090050--35090143 Score: 143
Period size: 30 Copynumber: 3.1 Consensus size: 30
35090040 TTTTATTATG
*
35090050 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
35090081 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* * *
35090111 CTATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
35090141 CCA
1 CCA
35090144 TAAATATGGA
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
30 51 0.88
31 7 0.12
ACGTcount: A:0.26, C:0.24, G:0.06, T:0.44
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:35090105 original size:15 final size:15
Alignment explanation
Indices: 35090060--35090137 Score: 61
Period size: 15 Copynumber: 5.2 Consensus size: 15
35090050 CCAATATCTC
35090060 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
35090075 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
35090090 GATACCCATATCTTT
1 GATACCCATATCTTT
** * *
35090105 GACTTTCTAT-TATTT
1 GA-TACCCATATCTTT
35090120 GATACCCATATCTTT
1 GATACCCATATCTTT
35090135 GAT
1 GAT
35090138 TTTCCATAAA
Statistics
Matches: 45, Mismatches: 14, Indels: 8
0.67 0.21 0.12
Matches are distributed among these distances:
14 8 0.18
15 29 0.64
16 8 0.18
ACGTcount: A:0.26, C:0.22, G:0.08, T:0.45
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:35091587 original size:25 final size:24
Alignment explanation
Indices: 35091552--35091607 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
35091542 TAATTTCATT
* *
35091552 ATTTTTTAAAAAATATTTATTAAT
1 ATTTTTTAAAAAAGATTTATTAAA
*
35091576 TTTTTTTAAAAAAGATTTATTAAA
1 ATTTTTTAAAAAAGATTTATTAAA
35091600 ATTTTTTA
1 ATTTTTTA
35091608 TTTTTGAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (24 bp):
ATTTTTTAAAAAAGATTTATTAAA
Found at i:35092573 original size:30 final size:32
Alignment explanation
Indices: 35092509--35092574 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
35092499 TTGACCCTTT
* *
35092509 AAAAATAAAAAATAAGTATATTTAGTCTCTTC
1 AAAAATAAAAAATAAGTATATTTAATATCTTC
35092541 AAAAATAATAAAATAA-TAT-TTTAATATC-TC
1 AAAAATAA-AAAATAAGTATATTTAATATCTTC
35092571 AAAA
1 AAAA
35092575 TTTTATAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 6 0.19
31 7 0.23
32 11 0.35
33 7 0.23
ACGTcount: A:0.56, C:0.08, G:0.03, T:0.33
Consensus pattern (32 bp):
AAAAATAAAAAATAAGTATATTTAATATCTTC
Found at i:35101203 original size:31 final size:32
Alignment explanation
Indices: 35101136--35101207 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 32
35101126 TGAAAACCAT
* * *
35101136 AAAGTTTAGGCCCCAATGTAGGAATAATTGTC
1 AAAGTTTAGGCCCCAACGTAGGAACAACTGTC
* *
35101168 -AAGTTTAGGCCTCAACGTGGGAACAACTG-C
1 AAAGTTTAGGCCCCAACGTAGGAACAACTGTC
35101198 AAAGTTTAGG
1 AAAGTTTAGG
35101208 GATTAACTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
30 1 0.03
31 33 0.97
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (32 bp):
AAAGTTTAGGCCCCAACGTAGGAACAACTGTC
Found at i:35114144 original size:37 final size:37
Alignment explanation
Indices: 35114101--35114177 Score: 145
Period size: 37 Copynumber: 2.1 Consensus size: 37
35114091 AAAAATTCTT
35114101 TTTACAATTAATTAAATAAATTAACTTTTCTTAAGTA
1 TTTACAATTAATTAAATAAATTAACTTTTCTTAAGTA
*
35114138 TTTACAATTAATTAAATAAATTAATTTTTCTTAAGTA
1 TTTACAATTAATTAAATAAATTAACTTTTCTTAAGTA
35114175 TTT
1 TTT
35114178 CTATGTATCC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.49
Consensus pattern (37 bp):
TTTACAATTAATTAAATAAATTAACTTTTCTTAAGTA
Found at i:35125050 original size:17 final size:17
Alignment explanation
Indices: 35125028--35125066 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
35125018 AAATAATATT
*
35125028 ATTCATCACATATTAAA
1 ATTCATCAAATATTAAA
* *
35125045 ATTCATTAAATATTAGA
1 ATTCATCAAATATTAAA
35125062 ATTCA
1 ATTCA
35125067 ACTGTTTTCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.46, C:0.13, G:0.03, T:0.38
Consensus pattern (17 bp):
ATTCATCAAATATTAAA
Found at i:35126355 original size:16 final size:16
Alignment explanation
Indices: 35126326--35126379 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
35126316 TTTGGTTCGC
*
35126326 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
* *
35126342 CGTAATGGAATAGAGG
1 TGTAATGGATTAGAGG
35126358 TGTAATGGATTAGAGG
1 TGTAATGGATTAGAGG
35126374 TGTAAT
1 TGTAAT
35126380 AGCAAATCAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.31, C:0.02, G:0.35, T:0.31
Consensus pattern (16 bp):
TGTAATGGATTAGAGG
Found at i:35126424 original size:45 final size:44
Alignment explanation
Indices: 35126358--35126448 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 44
35126348 GGAATAGAGG
* *
35126358 TGTAATGGATTAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAG-AAATCAACTGTTTGGTTGAA
* ***
35126403 TGTAATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
35126447 TG
1 TG
35126449 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 18 0.45
45 22 0.55
ACGTcount: A:0.31, C:0.05, G:0.29, T:0.35
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
Found at i:35126628 original size:16 final size:17
Alignment explanation
Indices: 35126591--35126628 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
35126581 ATTTAATCAT
35126591 ATTTAAACATAATTATA
1 ATTTAAACATAATTATA
*
35126608 A-TTAAATAT-ATTATA
1 ATTTAAACATAATTATA
35126623 ATTTAA
1 ATTTAA
35126629 TAAAATTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 7 0.37
16 11 0.58
17 1 0.05
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
ATTTAAACATAATTATA
Found at i:35126664 original size:22 final size:21
Alignment explanation
Indices: 35126574--35126860 Score: 92
Period size: 22 Copynumber: 14.0 Consensus size: 21
35126564 ATTATCAATA
* *
35126574 ATAA-ATAATTTAATCATATT
1 ATAATATAATTTAATAAAATT
* *
35126594 -TAAACATAATTATAATTAAA-T
1 AT-AATATAATT-TAATAAAATT
*
35126615 ATATTATAATTTAATAAAATT
1 ATAATATAATTTAATAAAATT
* * *
35126636 CTTATATGAATTTACTAAAATT
1 ATAATAT-AATTTAATAAAATT
**
35126658 ATAATAT-A--TAATAGTA-T
1 ATAATATAATTTAATAAAATT
*
35126675 AAAATATAATTTAAAATAATAATT
1 ATAATATAATTT--AATAA-AATT
35126699 ATTAAATATAATTTAATAAAA--
1 A-T-AATATAATTTAATAAAATT
35126720 A-AATATAATTTAATAAAATT
1 ATAATATAATTTAATAAAATT
* * *
35126740 CTTA-AT-A-TTAA-AATATT
1 ATAATATAATTTAATAAAATT
* * * *
35126757 CTTATATGAATTTACTAAAATC
1 ATAATAT-AATTTAATAAAATT
*
35126779 ATAATAT-ATAATACTATAAAA-T
1 ATAATATAAT-TTA--ATAAAATT
* ** **
35126801 ATAATCTAAAATAATTATTATT
1 ATAATATAATTTAA-TAAAATT
*
35126823 A-AATATAATTTAATATAA--
1 ATAATATAATTTAATAAAATT
35126841 AT-ATATAATTTAATAAAATT
1 ATAATATAATTTAATAAAATT
35126861 CTTAGTATTA
Statistics
Matches: 197, Mismatches: 38, Indels: 64
0.66 0.13 0.21
Matches are distributed among these distances:
17 16 0.08
18 45 0.23
19 2 0.01
20 21 0.11
21 38 0.19
22 49 0.25
23 9 0.05
24 7 0.04
26 10 0.05
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (21 bp):
ATAATATAATTTAATAAAATT
Found at i:35126698 original size:13 final size:12
Alignment explanation
Indices: 35126674--35126714 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 12
35126664 TATAATAGTA
35126674 TAAAATATAATT
1 TAAAATATAATT
35126686 TAAAATAATAATT
1 TAAAAT-ATAATT
*
35126699 ATTAAATATAATT
1 -TAAAATATAATT
35126712 TAA
1 TAA
35126715 TAAAAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 8 0.32
13 12 0.48
14 5 0.20
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TAAAATATAATT
Found at i:35126723 original size:18 final size:18
Alignment explanation
Indices: 35126702--35126737 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
35126692 AATAATTATT
35126702 AAATATAATTTAATAAAA
1 AAATATAATTTAATAAAA
35126720 AAATATAATTTAATAAAA
1 AAATATAATTTAATAAAA
35126738 TTCTTAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATATAATTTAATAAAA
Found at i:35126848 original size:18 final size:17
Alignment explanation
Indices: 35126825--35126859 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
35126815 TTATTATTAA
35126825 ATATAATTTAATATAAAT
1 ATATAATTTAATA-AAAT
35126843 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
35126860 TCTTAGTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:35126918 original size:61 final size:60
Alignment explanation
Indices: 35126629--35126920 Score: 192
Period size: 59 Copynumber: 4.8 Consensus size: 60
35126619 TATAATTTAA
* * *
35126629 TAAA-ATTCTTATATGAATTTACTAAAATTATAATATATAATAGTATAAAA-T-ATAAT-T
1 TAAATATTCTTATA-GAATTTACTAAAATCATAATATATAATACTATAAAATTCTTAATAT
** * * ** * * * *
35126686 TAAAATAATAATTATTA-AATATAATTTAATAAAAAAATATAAT-TTAATAAAATTCTTAATAT
1 T-AAAT-ATTCTTA-TAGAATTTACTAAAATCATAATATATAATACT-ATAAAATTCTTAATAT
* *
35126748 TAAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAA-T-ATAATCT
1 T-AAATATTCTTATA-GAATTTACTAAAATCATAATATATAATACTATAAAATTCTTAATAT
* * * * ** * *
35126808 AAAATAATTATTATTA-AATATAATTTAAT-ATAAATATATAAT-TTAATAAAATTCTTAGTAT
1 TAAAT-ATTCTTA-TAGAATTTACTAAAATCAT-AATATATAATACT-ATAAAATTCTTAATAT
35126869 TAAATATTCTTATACGAATTTACTAAAATCATAATATATAATACTATAAAAT
1 TAAATATTCTTATA-GAATTTACTAAAATCATAATATATAATACTATAAAAT
35126921 ATAATCTAAA
Statistics
Matches: 174, Mismatches: 40, Indels: 38
0.69 0.16 0.15
Matches are distributed among these distances:
57 1 0.01
58 7 0.04
59 56 0.32
60 26 0.15
61 48 0.28
62 35 0.20
63 1 0.01
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (60 bp):
TAAATATTCTTATAGAATTTACTAAAATCATAATATATAATACTATAAAATTCTTAATAT
Found at i:35126957 original size:121 final size:120
Alignment explanation
Indices: 35126629--35126936 Score: 528
Period size: 121 Copynumber: 2.6 Consensus size: 120
35126619 TATAATTTAA
* * *
35126629 TAAA-ATTCTTATATGAATTTACTAAAATTATAATATATAATAGTATAAAATATAATTTAAAATA
1 TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATCTAAAATA
*
35126693 ATAATTATTAAATATAATTTAATAAAAAAATATAATTTAATAAAATTCTTAATAT
66 ATTATTATTAAATATAATTTAATAAAAAAATATAATTTAATAAAATTCTTAATAT
35126748 TAAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATCTAAAAT
1 T-AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATCTAAAAT
* * *
35126813 AATTATTATTAAATATAATTTAATATAAATATATAATTTAATAAAATTCTTAGTAT
65 AATTATTATTAAATATAATTTAATAAAAAAATATAATTTAATAAAATTCTTAATAT
*
35126869 TAAATATTCTTATACGAATTTACTAAAATCATAATATATAATACTATAAAATATAATCTAAAATA
1 TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATCTAAAATA
35126934 ATT
66 ATT
35126937 GATTTTGTGG
Statistics
Matches: 179, Mismatches: 8, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
119 1 0.01
120 69 0.39
121 109 0.61
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.41
Consensus pattern (120 bp):
TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATCTAAAATA
ATTATTATTAAATATAATTTAATAAAAAAATATAATTTAATAAAATTCTTAATAT
Found at i:35128437 original size:13 final size:13
Alignment explanation
Indices: 35128421--35128450 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
35128411 TAGACCAAGC
35128421 TTTTCAAAAGCAT
1 TTTTCAAAAGCAT
*
35128434 TTTTCATAAGCAT
1 TTTTCAAAAGCAT
35128447 TTTT
1 TTTT
35128451 TTGCAGCACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.13, G:0.07, T:0.50
Consensus pattern (13 bp):
TTTTCAAAAGCAT
Found at i:35132196 original size:18 final size:18
Alignment explanation
Indices: 35132168--35132250 Score: 80
Period size: 18 Copynumber: 4.5 Consensus size: 18
35132158 ATATTTTTCC
*
35132168 TATAAAGATA-TTAAAAA
1 TATAAAAATATTTAAAAA
35132185 TCATAAAAATATTTAAAAA
1 T-ATAAAAATATTTAAAAA
* *
35132204 TATACAAAT-TATTAAATA
1 TATAAAAATAT-TTAAAAA
*
35132222 TTTAAAAATATTTAAAAAAA
1 TATAAAAATATTT--AAAAA
35132242 TATAAAAAT
1 TATAAAAAT
35132251 TGATATCAAG
Statistics
Matches: 53, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
17 2 0.04
18 30 0.57
19 9 0.17
20 12 0.23
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.34
Consensus pattern (18 bp):
TATAAAAATATTTAAAAA
Found at i:35132242 original size:12 final size:10
Alignment explanation
Indices: 35132188--35132250 Score: 55
Period size: 10 Copynumber: 6.7 Consensus size: 10
35132178 TTAAAAATCA
35132188 TAAAAATATT
1 TAAAAATATT
35132198 TAAAAATA--
1 TAAAAATATT
*
35132206 TACAAAT-TAT
1 TAAAAATAT-T
35132216 T--AAATATT
1 TAAAAATATT
35132224 TAAAAATATT
1 TAAAAATATT
* *
35132234 TAAAAAAATA
1 TAAAAATATT
35132244 TAAAAAT
1 TAAAAAT
35132251 TGATATCAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
8 12 0.28
9 1 0.02
10 30 0.70
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (10 bp):
TAAAAATATT
Found at i:35132308 original size:17 final size:17
Alignment explanation
Indices: 35132288--35132329 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
35132278 AATAAAAAAA
35132288 TCTAA-AAATTTATAAAT
1 TCTAATAAA-TTATAAAT
*
35132305 TCTAATAAATTATAAAA
1 TCTAATAAATTATAAAT
35132322 T-TAATAAA
1 TCTAATAAA
35132330 AACATATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 7 0.30
17 13 0.57
18 3 0.13
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (17 bp):
TCTAATAAATTATAAAT
Found at i:35134457 original size:4 final size:4
Alignment explanation
Indices: 35134441--35134474 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
35134431 TTAACTCTTT
* *
35134441 TGTA TGTA CGTA TGTA TGTA TGTA TGAA TGTA TG
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG
35134475 ACTTTGGGCT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.26, C:0.03, G:0.26, T:0.44
Consensus pattern (4 bp):
TGTA
Found at i:35135602 original size:17 final size:17
Alignment explanation
Indices: 35135554--35135603 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 17
35135544 TTTTAAATTA
*
35135554 TTAAT-TTTATA-AAAT
1 TTAATATTTATATATAT
35135569 TT-ATAATTTAT-TATAT
1 TTAAT-ATTTATATATAT
35135585 TTAATATTTATATATAT
1 TTAATATTTATATATAT
35135602 TT
1 TT
35135604 TTATAAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
14 2 0.07
15 2 0.07
16 16 0.55
17 9 0.31
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTAATATTTATATATAT
Found at i:35138004 original size:30 final size:32
Alignment explanation
Indices: 35137969--35138040 Score: 87
Period size: 31 Copynumber: 2.3 Consensus size: 32
35137959 CTTAATTTTT
*
35137969 AATTCAGTCATTTAAT-TT-TAAAAAAATAAC
1 AATTCAATCATTTAATGTTATAAAAAAATAAC
* * *
35137999 GATTCAATTA-TTAATGTTATCAAAAAATAAC
1 AATTCAATCATTTAATGTTATAAAAAAATAAC
35138030 AATTCAATCAT
1 AATTCAATCAT
35138041 CCACTAACAC
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
29 5 0.15
30 9 0.27
31 19 0.58
ACGTcount: A:0.49, C:0.11, G:0.04, T:0.36
Consensus pattern (32 bp):
AATTCAATCATTTAATGTTATAAAAAAATAAC
Found at i:35147677 original size:25 final size:25
Alignment explanation
Indices: 35147630--35147679 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
35147620 TTCCTTATAA
**
35147630 ACTTTAAATTAGGAATTCTATTAGG
1 ACTTTAAATTAGGAATTAGATTAGG
35147655 ACTTTAAATTAGGAATTAGATTAGG
1 ACTTTAAATTAGGAATTAGATTAGG
35147680 TTTTTCCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.38
Consensus pattern (25 bp):
ACTTTAAATTAGGAATTAGATTAGG
Found at i:35152341 original size:25 final size:25
Alignment explanation
Indices: 35152304--35152354 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
35152294 TTCCTTATAA
* **
35152304 ACTTTAAATTAGGAATTCTATTAGG
1 ACTTTAAACTAGGAATTAGATTAGG
35152329 ACTTTAAACTAGGAATTAGATTAGG
1 ACTTTAAACTAGGAATTAGATTAGG
35152354 A
1 A
35152355 TTTTTCTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.35
Consensus pattern (25 bp):
ACTTTAAACTAGGAATTAGATTAGG
Found at i:35152945 original size:7 final size:7
Alignment explanation
Indices: 35152933--35152963 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
35152923 TATATATGCA
35152933 TAGGCCG
1 TAGGCCG
35152940 TAGGCCG
1 TAGGCCG
35152947 TAGGCCG
1 TAGGCCG
35152954 TAGGCCG
1 TAGGCCG
35152961 TAG
1 TAG
35152964 AGAGATTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.26, G:0.42, T:0.16
Consensus pattern (7 bp):
TAGGCCG
Found at i:35155338 original size:32 final size:32
Alignment explanation
Indices: 35155271--35155429 Score: 239
Period size: 32 Copynumber: 5.0 Consensus size: 32
35155261 CATAAAAAAT
* *
35155271 ATCATACATTAGGTTTACCTAT-AAAAAGTAG
1 ATCATACATTAGTTTTACATATAAAAAAGTAG
* *
35155302 ATCATACATTAGTTTTGCATATAAAAAAGTAT
1 ATCATACATTAGTTTTACATATAAAAAAGTAG
* *
35155334 ATCATACATTAGGTTCACATATAAAAAAGTAG
1 ATCATACATTAGTTTTACATATAAAAAAGTAG
* *
35155366 ATCATACATTAGTTTTGCATATGAAAAAGTAG
1 ATCATACATTAGTTTTACATATAAAAAAGTAG
35155398 ATCATACATTAGTTTTACATATAAAAAAGTAG
1 ATCATACATTAGTTTTACATATAAAAAAGTAG
35155430 CATAGTTATA
Statistics
Matches: 113, Mismatches: 14, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
31 19 0.17
32 94 0.83
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (32 bp):
ATCATACATTAGTTTTACATATAAAAAAGTAG
Found at i:35155381 original size:64 final size:64
Alignment explanation
Indices: 35155269--35155429 Score: 270
Period size: 64 Copynumber: 2.5 Consensus size: 64
35155259 AACATAAAAA
*
35155269 ATATCATACATTAGGTTTACCTAT-AAAAAGTAGATCATACATTAGTTTTGCATATAAAAAAGT
1 ATATCATACATTAGGTTTACATATAAAAAAGTAGATCATACATTAGTTTTGCATATAAAAAAGT
* *
35155332 ATATCATACATTAGGTTCACATATAAAAAAGTAGATCATACATTAGTTTTGCATATGAAAAAGT
1 ATATCATACATTAGGTTTACATATAAAAAAGTAGATCATACATTAGTTTTGCATATAAAAAAGT
* *
35155396 AGATCATACATTAGTTTTACATATAAAAAAGTAG
1 ATATCATACATTAGGTTTACATATAAAAAAGTAG
35155430 CATAGTTATA
Statistics
Matches: 91, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
63 22 0.24
64 69 0.76
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.34
Consensus pattern (64 bp):
ATATCATACATTAGGTTTACATATAAAAAAGTAGATCATACATTAGTTTTGCATATAAAAAAGT
Found at i:35168381 original size:16 final size:15
Alignment explanation
Indices: 35168357--35168400 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
35168347 TGTAAAACTA
35168357 ATGTATGGTATTTTTT
1 ATGTATGGT-TTTTTT
*
35168373 ATGTTTGGTTTTTTT
1 ATGTATGGTTTTTTT
*
35168388 ATGCTATGCTTTT
1 ATG-TATGGTTTT
35168401 ATTCAAGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 9 0.38
16 15 0.62
ACGTcount: A:0.14, C:0.05, G:0.18, T:0.64
Consensus pattern (15 bp):
ATGTATGGTTTTTTT
Found at i:35168387 original size:15 final size:16
Alignment explanation
Indices: 35168357--35168395 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
35168347 TGTAAAACTA
35168357 ATGTATGGTATTTTTT
1 ATGTATGGTATTTTTT
*
35168373 ATGTTTGGT-TTTTTT
1 ATGTATGGTATTTTTT
35168388 ATGCTATG
1 ATG-TATG
35168396 CTTTTATTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.15, C:0.03, G:0.21, T:0.62
Consensus pattern (16 bp):
ATGTATGGTATTTTTT
Found at i:35170380 original size:21 final size:21
Alignment explanation
Indices: 35170354--35170407 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
35170344 ACCATTGTTT
*
35170354 CTAATCTCACCGCTATAGT-A
1 CTAATCTCACCGCTACAGTAA
* *
35170374 TTCAATCTCACCACTACAGTAA
1 CT-AATCTCACCGCTACAGTAA
35170396 CTAATCTCACCG
1 CTAATCTCACCG
35170408 TCAGCACTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
20 1 0.04
21 24 0.89
22 2 0.07
ACGTcount: A:0.31, C:0.33, G:0.07, T:0.28
Consensus pattern (21 bp):
CTAATCTCACCGCTACAGTAA
Found at i:35171871 original size:21 final size:21
Alignment explanation
Indices: 35171845--35171900 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
35171835 AACAGCGGTG
*
35171845 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
*
35171866 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
35171887 GCGGTGAGATTAGA
1 GCGGTGAGATTAGA
35171901 AACAGCGATA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.25, C:0.09, G:0.38, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:35179478 original size:22 final size:23
Alignment explanation
Indices: 35179452--35179497 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
35179442 CAACCAAACC
35179452 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
35179474 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
35179497 A
1 A
35179498 CATCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:35183367 original size:36 final size:36
Alignment explanation
Indices: 35183326--35183396 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 36
35183316 CACCCTACAC
* *
35183326 TGGTCGGTATAACCGACAAATAGATGTGCCCAACAT
1 TGGTCGATACAACCGACAAATAGATGTGCCCAACAT
* * *
35183362 TGGTCGATACAATCGACAAATGGGTGTGCCCAACA
1 TGGTCGATACAACCGACAAATAGATGTGCCCAACA
35183397 CTCCCCGACA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.21
Consensus pattern (36 bp):
TGGTCGATACAACCGACAAATAGATGTGCCCAACAT
Found at i:35196696 original size:18 final size:17
Alignment explanation
Indices: 35196675--35196728 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 17
35196665 CAGTCACTCT
*
35196675 TTAATAGTCAGTTATTCA
1 TTAATA-TCAATTATTCA
*
35196693 TTAACTATAAATTATTCA
1 TTAA-TATCAATTATTCA
*
35196711 GTAATAATCAATTATTCA
1 TTAAT-ATCAATTATTCA
35196729 GTAACAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
17 1 0.03
18 27 0.90
19 2 0.07
ACGTcount: A:0.41, C:0.11, G:0.06, T:0.43
Consensus pattern (17 bp):
TTAATATCAATTATTCA
Found at i:35196791 original size:18 final size:18
Alignment explanation
Indices: 35196746--35196804 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
35196736 ATTTTTTACG
* * *
35196746 CAGTAGCAATCAGTGATC
1 CAGTAGCAGTCAGTTATT
* *
35196764 CAATAACAGTCAGTTATT
1 CAGTAGCAGTCAGTTATT
35196782 CAGTAGCAGTCCA-TTATT
1 CAGTAGCAGT-CAGTTATT
35196800 CAGTA
1 CAGTA
35196805 CCTTTATTTA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
18 31 0.94
19 2 0.06
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (18 bp):
CAGTAGCAGTCAGTTATT
Found at i:35198255 original size:14 final size:15
Alignment explanation
Indices: 35198236--35198264 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
35198226 TATGGTAATA
35198236 TATATT-TTAAAAAT
1 TATATTATTAAAAAT
35198250 TATATTATTAAAAAT
1 TATATTATTAAAAAT
35198265 GATCTTAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TATATTATTAAAAAT
Found at i:35198391 original size:23 final size:23
Alignment explanation
Indices: 35198354--35198422 Score: 75
Period size: 25 Copynumber: 2.9 Consensus size: 23
35198344 CTCATCTCTA
* *
35198354 CCCTCTACTGATTCTTTGTTCTG
1 CCCTCTGCTGGTTCTTTGTTCTG
*
35198377 TCCTCTGCTGGTTCTTTGTCCTCTG
1 CCCTCTGCTGGTTCTTTGT--TCTG
* *
35198402 CCCTGTGCCGGTTCTTTGTTC
1 CCCTCTGCTGGTTCTTTGTTC
35198423 CTCTTCTCCA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
23 18 0.47
25 20 0.53
ACGTcount: A:0.03, C:0.32, G:0.19, T:0.46
Consensus pattern (23 bp):
CCCTCTGCTGGTTCTTTGTTCTG
Found at i:35200123 original size:28 final size:28
Alignment explanation
Indices: 35200083--35201204 Score: 2016
Period size: 28 Copynumber: 40.1 Consensus size: 28
35200073 ACAGAGTCTT
*
35200083 ATACATACATACATACATACATACATAC
1 ATACATACATACATACATACATACACAC
35200111 ATACATACATACATACATACATACACAC
1 ATACATACATACATACATACATACACAC
35200139 ATACATACATACATACATACATACACAC
1 ATACATACATACATACATACATACACAC
35200167 ATACATACATACATACATACATACACAC
1 ATACATACATACATACATACATACACAC
35200195 ATACATACATACATACATACATACACAC
1 ATACATACATACATACATACATACACAC
35200223 ATACATACATACATACATACATACACAC
1 ATACATACATACATACATACATACACAC
35200251 ATACATACATACATACATACATACACAC
1 ATACATACATACATACATACATACACAC
35200279 ATACATACATACATACATACATACACAC
1 ATACATACATACATACATACATACACAC
35200307 ATACATACATACATACATACATACACAC
1 ATACATACATACATACATACATACACAC
35200335 ATACATACATACATACATACATACACAC
1 ATACATACATACATACATACATACACAC
35200363 ATACATACATACATACATACATACACAC
1 ATACATACATACATACATACATACACAC
35200391 ATACATACATACATACATACATACACAC
1 ATACATACATACATACATACATACACAC
35200419 ATACATACATACATACATACATACACAC
1 ATACATACATACATACATACATACACAC
35200447 ATACATACATACATACATACATACACAC
1 ATACATACATACATACATACATACACAC
35200475 ATACATACATACATACATACATACACAC
1 ATACATACATACATACATACATACACAC
35200503 ATACATACATACATACATACATACACAC
1 ATACATACATACATACATACATACACAC
35200531 ATACATACATACATACATACATACACAC
1 ATACATACATACATACATACATACACAC
35200559 ATACATACATACATACATACATACACAC
1 ATACATACATACATACATACATACACAC
35200587 ATACATACATACATACATACATACACAC
1 ATACATACATACATACATACATACACAC
35200615 ATACATACATACATACATACATACACAC
1 ATACATACATACATACATACATACACAC
35200643 ATACATACATACATACATACATACACAC
1 ATACATACATACATACATACATACACAC
35200671 ATACATACATACATACATACATACACAC
1 ATACATACATACATACATACATACACAC
35200699 ATACATACATACATACATACATACACAC
1 ATACATACATACATACATACATACACAC
35200727 ATACATACATACATACATACATACACAC
1 ATACATACATACATACATACATACACAC
35200755 ATACATACATACATACATACATACACAC
1 ATACATACATACATACATACATACACAC
35200783 ATACATACATACATACATACATACACAC
1 ATACATACATACATACATACATACACAC
35200811 ATACATACATACATACATACATACACAC
1 ATACATACATACATACATACATACACAC
35200839 ATACATACATACATACATACATACACAC
1 ATACATACATACATACATACATACACAC
35200867 ATACATACATACATACATACATACACAC
1 ATACATACATACATACATACATACACAC
35200895 ATACATACATACATACATACATACACAC
1 ATACATACATACATACATACATACACAC
35200923 ATACATACATACATACATACATACACAC
1 ATACATACATACATACATACATACACAC
*
35200951 ATACATACATACATACATACATACATAC
1 ATACATACATACATACATACATACACAC
*
35200979 ATACATACATACATACATACATACATAC
1 ATACATACATACATACATACATACACAC
*
35201007 ATACATACATACATACATACATACATAC
1 ATACATACATACATACATACATACACAC
* * *
35201035 ATCCATACATACATACATACATCCATAC
1 ATACATACATACATACATACATACACAC
* *
35201063 ATCCATACATACATCCATACATACATC-C
1 ATACATACATACATACATACATACA-CAC
* *
35201091 ATACATACATACATACATCCATCCATC-C
1 ATACATACATACATACATACATACA-CAC
* * *
35201119 ATCCATACAGACATCCATACATACATC-C
1 ATACATACATACATACATACATACA-CAC
* * * *
35201147 ATACATACATACATCCATCCATACATAA
1 ATACATACATACATACATACATACACAC
* *
35201175 ATACATACATACATACATGCATACATAC
1 ATACATACATACATACATACATACACAC
35201203 AT
1 AT
35201205 TGAAAGCTAA
Statistics
Matches: 1068, Mismatches: 24, Indels: 4
0.97 0.02 0.00
Matches are distributed among these distances:
28 1068 1.00
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.22
Consensus pattern (28 bp):
ATACATACATACATACATACATACACAC
Found at i:35201850 original size:71 final size:71
Alignment explanation
Indices: 35201734--35201987 Score: 508
Period size: 71 Copynumber: 3.6 Consensus size: 71
35201724 TTGTGAAAAC
35201734 CTTATCACAGAATTATCTAGTACGTGTCTTGAAGTTTAATTTCTGGAATATTTGGATCTAGAAGT
1 CTTATCACAGAATTATCTAGTACGTGTCTTGAAGTTTAATTTCTGGAATATTTGGATCTAGAAGT
35201799 ATTAAA
66 ATTAAA
35201805 CTTATCACAGAATTATCTAGTACGTGTCTTGAAGTTTAATTTCTGGAATATTTGGATCTAGAAGT
1 CTTATCACAGAATTATCTAGTACGTGTCTTGAAGTTTAATTTCTGGAATATTTGGATCTAGAAGT
35201870 ATTAAA
66 ATTAAA
35201876 CTTATCACAGAATTATCTAGTACGTGTCTTGAAGTTTAATTTCTGGAATATTTGGATCTAGAAGT
1 CTTATCACAGAATTATCTAGTACGTGTCTTGAAGTTTAATTTCTGGAATATTTGGATCTAGAAGT
35201941 ATTAAA
66 ATTAAA
35201947 CTTATCACAGAATTATCTAGTACGTGTCTTGAAGTTTAATT
1 CTTATCACAGAATTATCTAGTACGTGTCTTGAAGTTTAATT
35201988 GTTTGCTCGC
Statistics
Matches: 183, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 183 1.00
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.40
Consensus pattern (71 bp):
CTTATCACAGAATTATCTAGTACGTGTCTTGAAGTTTAATTTCTGGAATATTTGGATCTAGAAGT
ATTAAA
Found at i:35201864 original size:41 final size:41
Alignment explanation
Indices: 35201819--35201936 Score: 96
Period size: 41 Copynumber: 3.1 Consensus size: 41
35201809 TCACAGAATT
35201819 ATCTAGTACGTGTCTTGAAGTTTAATTTCTGGAATATTTGG
1 ATCTAGTACGTGTCTTGAAGTTTAATTTCTGGAATATTTGG
* * ** ** *
35201860 ATCTAG-A--AGTATT-AAACTT-ATCAC-AG-A-A-TT--
1 ATCTAGTACGTGTCTTGAAGTTTAATTTCTGGAATATTTGG
35201890 ATCTAGTACGTGTCTTGAAGTTTAATTTCTGGAATATTTGG
1 ATCTAGTACGTGTCTTGAAGTTTAATTTCTGGAATATTTGG
35201931 ATCTAG
1 ATCTAG
35201937 AAGTATTAAA
Statistics
Matches: 52, Mismatches: 14, Indels: 22
0.59 0.16 0.25
Matches are distributed among these distances:
30 6 0.12
31 1 0.02
32 2 0.04
33 5 0.10
34 5 0.10
35 4 0.08
36 4 0.08
37 5 0.10
38 5 0.10
39 2 0.04
40 1 0.02
41 12 0.23
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.41
Consensus pattern (41 bp):
ATCTAGTACGTGTCTTGAAGTTTAATTTCTGGAATATTTGG
Found at i:35204249 original size:167 final size:168
Alignment explanation
Indices: 35203973--35204275 Score: 473
Period size: 167 Copynumber: 1.8 Consensus size: 168
35203963 TGCTTGAAAG
* * *
35203973 ATTGGGTAAAAAATGAAAGTTATTGTTCTTGAACTAGCAGCTGTTAATTACACAATCATTCATTG
1 ATTGGGTAAAAAATGAAAGTCATTGTTCTTGAACTAGCACCTGTTAATTACACAATCATTCATTC
* * * * *
35204038 ATCTGTATTGGAATTGGAACTTCATTAAATTGCTGAAATGAAACATTGATGAATATTGAAC-AGT
66 ATCTGTATTGGAACTGGAACTTCATTAAATAGCTGAAATGAAACAGTGATGAATACTGAACAACT
35204102 TTTCTTTGTTTACAAATTGCTGAAATGAAACGTTAAAT
131 TTTCTTTGTTTACAAATTGCTGAAATGAAACGTTAAAT
* * * *
35204140 ATTGGGTAATAATTGGAAGTCATTGTTCTTGAACTAGCACCTGTTAATTAGACAATCATTCATTC
1 ATTGGGTAAAAAATGAAAGTCATTGTTCTTGAACTAGCACCTGTTAATTACACAATCATTCATTC
* *
35204205 ATCTGTGTTGGAACTGGAACTTCATTAGATAGCTGAAATGAAACAGTGATGAATACTGAACAACT
66 ATCTGTATTGGAACTGGAACTTCATTAAATAGCTGAAATGAAACAGTGATGAATACTGAACAACT
35204270 TTTCTT
131 TTTCTT
35204276 GATTATCTAT
Statistics
Matches: 121, Mismatches: 14, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
167 113 0.93
168 8 0.07
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (168 bp):
ATTGGGTAAAAAATGAAAGTCATTGTTCTTGAACTAGCACCTGTTAATTACACAATCATTCATTC
ATCTGTATTGGAACTGGAACTTCATTAAATAGCTGAAATGAAACAGTGATGAATACTGAACAACT
TTTCTTTGTTTACAAATTGCTGAAATGAAACGTTAAAT
Found at i:35211023 original size:19 final size:20
Alignment explanation
Indices: 35211001--35211044 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
35210991 AATTAATCTT
*
35211001 TAAAAAGTAAATT-AGTGAC
1 TAAAAAGGAAATTGAGTGAC
*
35211020 TAAAATGGAAATTGAGTGAC
1 TAAAAAGGAAATTGAGTGAC
35211040 TAAAA
1 TAAAA
35211045 TAAGTGACCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.52, C:0.05, G:0.18, T:0.25
Consensus pattern (20 bp):
TAAAAAGGAAATTGAGTGAC
Found at i:35222163 original size:16 final size:16
Alignment explanation
Indices: 35222142--35222174 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
35222132 GATACAATAT
*
35222142 AACAAAGGATAAGCAA
1 AACAAAGGATAACCAA
35222158 AACAAAGGATAACCAA
1 AACAAAGGATAACCAA
35222174 A
1 A
35222175 GTAACATGAA
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:0.64, C:0.15, G:0.15, T:0.06
Consensus pattern (16 bp):
AACAAAGGATAACCAA
Found at i:35229689 original size:16 final size:15
Alignment explanation
Indices: 35229662--35229714 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 15
35229652 AATTAGAATT
35229662 AATTACATAAATATTA
1 AATTA-ATAAATATTA
35229678 AATTAATAAAATATT-
1 AATTAAT-AAATATTA
35229693 -ATCTAGATAAATATTA
1 AAT-TA-ATAAATATTA
35229709 AATTAA
1 AATTAA
35229715 ATTTAATATC
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
14 2 0.06
15 12 0.38
16 16 0.50
17 2 0.06
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.38
Consensus pattern (15 bp):
AATTAATAAATATTA
Found at i:35235608 original size:23 final size:23
Alignment explanation
Indices: 35235578--35235625 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
35235568 ATTTTCATAA
35235578 AAGGATTGCAAATAATAGGTTCC
1 AAGGATTGCAAATAATAGGTTCC
35235601 AAGGATTGCAAATAATAGGTTCC
1 AAGGATTGCAAATAATAGGTTCC
35235624 AA
1 AA
35235626 CTTCAAACCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.25
Consensus pattern (23 bp):
AAGGATTGCAAATAATAGGTTCC
Found at i:35237842 original size:7 final size:7
Alignment explanation
Indices: 35237830--35237855 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
35237820 AACCTCAAGG
35237830 TTTAAGA
1 TTTAAGA
35237837 TTTAAGA
1 TTTAAGA
35237844 TTTAAGA
1 TTTAAGA
35237851 TTTAA
1 TTTAA
35237856 TATTCGAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (7 bp):
TTTAAGA
Found at i:35238220 original size:21 final size:22
Alignment explanation
Indices: 35238187--35238235 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
35238177 AGATGATACT
* *
35238187 AATATAATTTATT-CAATTTTA
1 AATATAATATATTACAATTTAA
* *
35238208 AATATAGTATATTAGAATTTAA
1 AATATAATATATTACAATTTAA
35238230 AATATA
1 AATATA
35238236 CTAACTAGTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (22 bp):
AATATAATATATTACAATTTAA
Found at i:35242648 original size:17 final size:17
Alignment explanation
Indices: 35242622--35242659 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
35242612 CATTTTTATC
35242622 AAAA-AGAAAAAAGAAA
1 AAAATAGAAAAAAGAAA
* *
35242638 AAAATAGAAAATATAAA
1 AAAATAGAAAAAAGAAA
35242655 AAAAT
1 AAAAT
35242660 TAAACTTAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.82, C:0.00, G:0.08, T:0.11
Consensus pattern (17 bp):
AAAATAGAAAAAAGAAA
Found at i:35253416 original size:73 final size:73
Alignment explanation
Indices: 35253297--35253442 Score: 283
Period size: 73 Copynumber: 2.0 Consensus size: 73
35253287 GTAACAAAAA
*
35253297 TCTAAGATTTTCTTAGACATTTATTATTGTTTAATTAGTTAATATTATTATTAAGCTATAAATTA
1 TCTAAGAGTTTCTTAGACATTTATTATTGTTTAATTAGTTAATATTATTATTAAGCTATAAATTA
35253362 TATTAATT
66 TATTAATT
35253370 TCTAAGAGTTTCTTAGACATTTATTATTGTTTAATTAGTTAATATTATTATTAAGCTATAAATTA
1 TCTAAGAGTTTCTTAGACATTTATTATTGTTTAATTAGTTAATATTATTATTAAGCTATAAATTA
35253435 TATTAATT
66 TATTAATT
35253443 ATTATATTAT
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.36, C:0.05, G:0.08, T:0.51
Consensus pattern (73 bp):
TCTAAGAGTTTCTTAGACATTTATTATTGTTTAATTAGTTAATATTATTATTAAGCTATAAATTA
TATTAATT
Found at i:35253567 original size:32 final size:32
Alignment explanation
Indices: 35253519--35253593 Score: 93
Period size: 32 Copynumber: 2.3 Consensus size: 32
35253509 TTAAATAAGT
35253519 ATATTTGTATTATTTATGTA-TAATTAGCGAAAA-
1 ATATTT-TATTATTTAT-TATTAATTAG-GAAAAG
*
35253552 ATATTTTATTATTTATTATTAATTAGTAAAAG
1 ATATTTTATTATTTATTATTAATTAGGAAAAG
35253584 ATA-TTTATTA
1 ATATTTTATTA
35253594 GATGATTATT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
31 13 0.33
32 20 0.51
33 6 0.15
ACGTcount: A:0.40, C:0.01, G:0.08, T:0.51
Consensus pattern (32 bp):
ATATTTTATTATTTATTATTAATTAGGAAAAG
Found at i:35253760 original size:15 final size:16
Alignment explanation
Indices: 35253730--35253763 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
35253720 TTTATTAATT
35253730 AATTAAATAGAAAACA
1 AATTAAATAGAAAACA
*
35253746 AATTAAA-ATAAAACA
1 AATTAAATAGAAAACA
35253761 AAT
1 AAT
35253764 AGATATGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.71, C:0.06, G:0.03, T:0.21
Consensus pattern (16 bp):
AATTAAATAGAAAACA
Found at i:35254943 original size:25 final size:25
Alignment explanation
Indices: 35254915--35254965 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
35254905 TTCGGATAGA
35254915 TTCGATGAGGTACTGGGTACCGCTT
1 TTCGATGAGGTACTGGGTACCGCTT
35254940 TTCGATGAGGTACTGGGTACCGCTT
1 TTCGATGAGGTACTGGGTACCGCTT
35254965 T
1 T
35254966 ACTTCGGCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.16, C:0.20, G:0.31, T:0.33
Consensus pattern (25 bp):
TTCGATGAGGTACTGGGTACCGCTT
Found at i:35257718 original size:21 final size:21
Alignment explanation
Indices: 35257693--35257761 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
35257683 TATAATGATT
35257693 ATTATTATGGTTTTATATTAA
1 ATTATTATGGTTTTATATTAA
**
35257714 ATTATTATAATTATTA-ATT-A
1 ATTATTATGGTT-TTATATTAA
* *
35257734 A-CATTATGGTTTTATATTAG
1 ATTATTATGGTTTTATATTAA
35257754 ATTATTAT
1 ATTATTAT
35257762 TATTAGCATT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
18 3 0.08
19 10 0.27
20 3 0.08
21 18 0.49
22 3 0.08
ACGTcount: A:0.36, C:0.01, G:0.07, T:0.55
Consensus pattern (21 bp):
ATTATTATGGTTTTATATTAA
Found at i:35257774 original size:15 final size:14
Alignment explanation
Indices: 35257748--35257778 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
35257738 TATGGTTTTA
35257748 TATTAGATTATTAT
1 TATTAGATTATTAT
35257762 TATTAGCATTATTAT
1 TATTAG-ATTATTAT
35257777 TA
1 TA
35257779 AATAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.55
Consensus pattern (14 bp):
TATTAGATTATTAT
Found at i:35263538 original size:19 final size:19
Alignment explanation
Indices: 35263511--35263561 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
35263501 TATCAATAAT
* *
35263511 TTCAGATCGAGATCCTCGG
1 TTCACATCGAGATCCTCAG
35263530 TTCACATCGAGATCCTCAG
1 TTCACATCGAGATCCTCAG
35263549 TTCACATCGAGAT
1 TTCACATCGAGAT
35263562 TTTGGAGACA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.27
Consensus pattern (19 bp):
TTCACATCGAGATCCTCAG
Found at i:35270436 original size:33 final size:32
Alignment explanation
Indices: 35270394--35270467 Score: 98
Period size: 33 Copynumber: 2.3 Consensus size: 32
35270384 AAATAAGCAC
*
35270394 ATTTGTATTATTTATGTA-TAATTAGTGAAAAGAT
1 ATTT-TATTATTTAT-TATTAATTAAT-AAAAGAT
35270428 ATTTTATTATTTATTATTAATTAATAAAAGAT
1 ATTTTATTATTTATTATTAATTAATAAAAGAT
35270460 A-TTTATTA
1 ATTTTATTA
35270468 GATGATTATT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
31 7 0.18
32 10 0.26
33 17 0.45
34 4 0.11
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (32 bp):
ATTTTATTATTTATTATTAATTAATAAAAGAT
Found at i:35270487 original size:31 final size:32
Alignment explanation
Indices: 35270412--35270487 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 32
35270402 TATTTATGTA
* * *
35270412 TAATTAGTGAAAAGATATTTTATTATTTATTAT
1 TAATTAAT-AAAAGATATTTTATTAATGATTAT
35270445 TAATTAATAAAAGATA-TTTATTAGATGATTAT
1 TAATTAATAAAAGATATTTTATTA-ATGATTAT
*
35270477 T-ATTATTAAAA
1 TAATTAATAAAA
35270488 TTATTAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
31 16 0.42
32 15 0.39
33 7 0.18
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (32 bp):
TAATTAATAAAAGATATTTTATTAATGATTAT
Found at i:35272921 original size:41 final size:39
Alignment explanation
Indices: 35272807--35272929 Score: 119
Period size: 37 Copynumber: 3.1 Consensus size: 39
35272797 TACCCAATAC
*
35272807 CTCATCAGA-TAATTCGAAGTAATAAGTTGACACCCAGTGT
1 CTCATC-GACTAATCCGAAGTAATAA-TTGACACCCAGTGT
* * * *
35272847 CTCATCGGCTAAACCGAAGT--TAGTTGGCACCCAGTG-
1 CTCATCGACTAATCCGAAGTAATAATTGACACCCAGTGT
*
35272883 CTTCATCGAATTAATCCGAAGTAAATAATTGACACCCAGTGT
1 C-TCATCG-ACTAATCCGAAGT-AATAATTGACACCCAGTGT
35272925 CTCAT
1 CTCAT
35272930 TAACTCGAGG
Statistics
Matches: 66, Mismatches: 10, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
36 1 0.02
37 18 0.27
38 12 0.18
39 1 0.02
40 15 0.23
41 18 0.27
42 1 0.02
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.27
Consensus pattern (39 bp):
CTCATCGACTAATCCGAAGTAATAATTGACACCCAGTGT
Found at i:35273866 original size:5 final size:5
Alignment explanation
Indices: 35273856--35274012 Score: 314
Period size: 5 Copynumber: 31.4 Consensus size: 5
35273846 AGTTATTATA
35273856 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
35273906 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
35273956 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
35274006 ATAAT AT
1 ATAAT AT
35274013 TAATTATTCA
Statistics
Matches: 152, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 152 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:35274029 original size:11 final size:10
Alignment explanation
Indices: 35273848--35274036 Score: 60
Period size: 10 Copynumber: 19.0 Consensus size: 10
35273838 ATTCTTTTAG
35273848 TTATTATAATA
1 TTATTAT-ATA
* *
35273859 ATATAATATA
1 TTATTATATA
* *
35273869 ATATAATATA
1 TTATTATATA
* *
35273879 ATATAATATA
1 TTATTATATA
* *
35273889 ATATAATATA
1 TTATTATATA
* *
35273899 ATATAATATA
1 TTATTATATA
* *
35273909 ATATAATATA
1 TTATTATATA
* *
35273919 ATATAATATA
1 TTATTATATA
* *
35273929 ATATAATATA
1 TTATTATATA
* *
35273939 ATATAATATA
1 TTATTATATA
* *
35273949 ATATAATATA
1 TTATTATATA
* *
35273959 ATATAATATA
1 TTATTATATA
* *
35273969 ATATAATATA
1 TTATTATATA
* *
35273979 ATATAATATA
1 TTATTATATA
* *
35273989 ATATAATATA
1 TTATTATATA
* *
35273999 ATATAATATA
1 TTATTATATA
*
35274009 ATA-T-TA-A
1 TTATTATATA
35274016 TTATTCATATA
1 TTATT-ATATA
35274027 TTATTATATA
1 TTATTATATA
35274037 CATATGTATA
Statistics
Matches: 170, Mismatches: 4, Indels: 9
0.93 0.02 0.05
Matches are distributed among these distances:
7 3 0.02
8 3 0.02
10 153 0.90
11 11 0.06
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.43
Consensus pattern (10 bp):
TTATTATATA
Found at i:35274062 original size:19 final size:20
Alignment explanation
Indices: 35274023--35274065 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
35274013 TAATTATTCA
*
35274023 TATATTATTATATACATATG
1 TATATTATTATATACACATG
*
35274043 TATATTATT-TGTACACATG
1 TATATTATTATATACACATG
35274062 TATA
1 TATA
35274066 CACAATCACC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.49
Consensus pattern (20 bp):
TATATTATTATATACACATG
Found at i:35278466 original size:13 final size:14
Alignment explanation
Indices: 35278424--35278468 Score: 51
Period size: 13 Copynumber: 3.3 Consensus size: 14
35278414 TAATAATGAT
35278424 TAAAGTATATTATAA
1 TAAAGTA-ATTATAA
35278439 TAATA-TAA-TATAA
1 TAA-AGTAATTATAA
35278452 TAAAGTAATTA-AA
1 TAAAGTAATTATAA
35278465 TAAA
1 TAAA
35278469 AAAATAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
12 1 0.04
13 17 0.63
14 3 0.11
15 5 0.19
16 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (14 bp):
TAAAGTAATTATAA
Found at i:35278537 original size:12 final size:12
Alignment explanation
Indices: 35278507--35278544 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
35278497 GAAACAGAGC
35278507 AGGGAAAGAAAGA
1 AGGGAAAGAAA-A
*
35278520 A-AGAAAGAAAA
1 AGGGAAAGAAAA
35278531 AGGGAAAGAAAA
1 AGGGAAAGAAAA
35278543 AG
1 AG
35278545 AAAAGGAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
11 2 0.09
12 19 0.86
13 1 0.05
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (12 bp):
AGGGAAAGAAAA
Found at i:35281334 original size:5 final size:5
Alignment explanation
Indices: 35281313--35281361 Score: 54
Period size: 5 Copynumber: 10.8 Consensus size: 5
35281303 TGTTTTTCTT
*
35281313 TTTCA TTTC- TTTTA TTTCA TTT-A TTTCA TTT-A TTTC- TTT-A TTTCA
1 TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA
35281358 TTTC
1 TTTC
35281362 TTTATTTTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
4 17 0.46
5 20 0.54
ACGTcount: A:0.16, C:0.14, G:0.00, T:0.69
Consensus pattern (5 bp):
TTTCA
Found at i:35281335 original size:9 final size:9
Alignment explanation
Indices: 35281317--35281360 Score: 72
Period size: 9 Copynumber: 5.0 Consensus size: 9
35281307 TTTCTTTTTC
*
35281317 ATTTCTTTT
1 ATTTCATTT
35281326 ATTTCATTT
1 ATTTCATTT
35281335 ATTTCATTT
1 ATTTCATTT
35281344 ATTTC-TTT
1 ATTTCATTT
35281352 ATTTCATTT
1 ATTTCATTT
35281361 CTTTATTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
8 8 0.24
9 25 0.76
ACGTcount: A:0.18, C:0.11, G:0.00, T:0.70
Consensus pattern (9 bp):
ATTTCATTT
Found at i:35281360 original size:13 final size:13
Alignment explanation
Indices: 35281313--35281368 Score: 78
Period size: 13 Copynumber: 4.2 Consensus size: 13
35281303 TGTTTTTCTT
35281313 TTTCATTTCTTTTA
1 TTTCATTTC-TTTA
*
35281327 TTTCATTTATTTCA
1 TTTCATTTCTTT-A
35281341 TTT-ATTTCTTTA
1 TTTCATTTCTTTA
35281353 TTTCATTTCTTTA
1 TTTCATTTCTTTA
35281366 TTT
1 TTT
35281369 TATTATTAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
12 4 0.11
13 22 0.58
14 12 0.32
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTCATTTCTTTA
Found at i:35284307 original size:24 final size:25
Alignment explanation
Indices: 35284280--35284328 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
35284270 TGCAAGTCAA
*
35284280 TAATAGG-TAGCTCCGAAAAGCCAT
1 TAATAGGAAAGCTCCGAAAAGCCAT
* *
35284304 TAATTGGAAAGCTCCGAATAGCCAT
1 TAATAGGAAAGCTCCGAAAAGCCAT
35284329 ATATCGAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.22
Consensus pattern (25 bp):
TAATAGGAAAGCTCCGAAAAGCCAT
Found at i:35284339 original size:25 final size:25
Alignment explanation
Indices: 35284288--35284339 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
35284278 AATAATAGGT
* *
35284288 AGCTCCGAAAAGCCATTAATTGGAA
1 AGCTCCGAAAAGCCATTAATCGAAA
*
35284313 AGCTCCGAATAGCCA-TATATCGAAA
1 AGCTCCGAAAAGCCATTA-ATCGAAA
35284338 AG
1 AG
35284340 TTAAAGTGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 2 0.09
25 21 0.91
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.19
Consensus pattern (25 bp):
AGCTCCGAAAAGCCATTAATCGAAA
Found at i:35285621 original size:21 final size:18
Alignment explanation
Indices: 35285584--35285624 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 18
35285574 CTAAAGTTAA
35285584 AATGTATTATAATATTAT
1 AATGTATTATAATATTAT
35285602 AATGATATTATATTATATTAT
1 AATG-TATTATA--ATATTAT
35285623 AA
1 AA
35285625 AAACAAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 7 0.35
21 9 0.45
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (18 bp):
AATGTATTATAATATTAT
Found at i:35285708 original size:13 final size:12
Alignment explanation
Indices: 35285679--35285719 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
35285669 ATAAACAGGG
*
35285679 GAGAAAG-AAAG
1 GAGAAAGAAAAA
35285690 GAGAAACGAAAAA
1 GAGAAA-GAAAAA
35285703 GAGAAAGAAAAA
1 GAGAAAGAAAAA
35285715 G-GAAA
1 GAGAAA
35285720 AACTAAAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
11 10 0.37
12 8 0.30
13 9 0.33
ACGTcount: A:0.68, C:0.02, G:0.29, T:0.00
Consensus pattern (12 bp):
GAGAAAGAAAAA
Found at i:35285721 original size:19 final size:19
Alignment explanation
Indices: 35285697--35285739 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
35285687 AAGGAGAAAC
35285697 GAAAAAGAGAAAGAAAAA-G
1 GAAAAA-AGAAAGAAAAAGG
**
35285716 GAAAAACTAAAGAAAAAGG
1 GAAAAAAGAAAGAAAAAGG
35285735 GAAAA
1 GAAAA
35285740 CTAAGGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.72, C:0.02, G:0.23, T:0.02
Consensus pattern (19 bp):
GAAAAAAGAAAGAAAAAGG
Found at i:35285740 original size:18 final size:18
Alignment explanation
Indices: 35285706--35285743 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
35285696 CGAAAAAGAG
35285706 AAAGAAAAAGGAAAAACT
1 AAAGAAAAAGGAAAAACT
*
35285724 AAAGAAAAAGGGAAAACT
1 AAAGAAAAAGGAAAAACT
35285742 AA
1 AA
35285744 GGTTTTCAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.71, C:0.05, G:0.18, T:0.05
Consensus pattern (18 bp):
AAAGAAAAAGGAAAAACT
Found at i:35286641 original size:25 final size:25
Alignment explanation
Indices: 35286596--35286683 Score: 122
Period size: 25 Copynumber: 3.4 Consensus size: 25
35286586 TTAAGGAACT
*
35286596 TTAGTGCGGTCTCTGATTATTAGCACG
1 TTAGTGC--TCTCCGATTATTAGCACG
* *
35286623 TTAGTGCTCTTCGATTATTAGCATG
1 TTAGTGCTCTCCGATTATTAGCACG
*
35286648 TTAGTGCTCTCCGATTATTAGCACT
1 TTAGTGCTCTCCGATTATTAGCACG
35286673 TTAGTGCTCTC
1 TTAGTGCTCTC
35286684 TGTTTAGCAC
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
25 48 0.87
27 7 0.13
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.41
Consensus pattern (25 bp):
TTAGTGCTCTCCGATTATTAGCACG
Found at i:35286693 original size:22 final size:22
Alignment explanation
Indices: 35286665--35286728 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
35286655 TCTCCGATTA
35286665 TTAGCACTTTAGTGCTCTCTGT
1 TTAGCACTTTAGTGCTCTCTGT
* * *
35286687 TTAGCACATTCGTGCTCGCTGT
1 TTAGCACTTTAGTGCTCTCTGT
* *
35286709 ATATCACTTTAGTGCTCTCT
1 TTAGCACTTTAGTGCTCTCT
35286729 ATTCATTAGT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.16, C:0.25, G:0.17, T:0.42
Consensus pattern (22 bp):
TTAGCACTTTAGTGCTCTCTGT
Found at i:35290462 original size:21 final size:21
Alignment explanation
Indices: 35290433--35290563 Score: 176
Period size: 21 Copynumber: 6.3 Consensus size: 21
35290423 TTATTCTACT
*
35290433 TTCTGTTCAGCTCTTATGAGC
1 TTCTGTTCAGCTCTTACGAGC
* * * *
35290454 TTCTATTCAACTCTTATGAGT
1 TTCTGTTCAGCTCTTACGAGC
*
35290475 TTCTGTTTAGCTCTTACGAGC
1 TTCTGTTCAGCTCTTACGAGC
35290496 TTCTGTTCAGCT-TT-CGAGC
1 TTCTGTTCAGCTCTTACGAGC
* *
35290515 TTCTGTTCAGCTCTTATGAGT
1 TTCTGTTCAGCTCTTACGAGC
35290536 TTCTGTTCAGCTCTTACGAGC
1 TTCTGTTCAGCTCTTACGAGC
35290557 TTCTGTT
1 TTCTGTT
35290564 GGTGTATTCA
Statistics
Matches: 95, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
19 17 0.18
20 4 0.04
21 74 0.78
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.45
Consensus pattern (21 bp):
TTCTGTTCAGCTCTTACGAGC
Found at i:35290529 original size:61 final size:63
Alignment explanation
Indices: 35290433--35290563 Score: 212
Period size: 61 Copynumber: 2.1 Consensus size: 63
35290423 TTATTCTACT
* *
35290433 TTCTGTTCAGCTCTTATGAGCTTCTATTCAACTCTTATGAGTTTCTGTTTAGCTCTTACGAGC
1 TTCTGTTCAGCTCTTACGAGCTTCTATTCAACTCTTATGAGTTTCTGTTCAGCTCTTACGAGC
* *
35290496 TTCTGTTCAGCT-TT-CGAGCTTCTGTTCAGCTCTTATGAGTTTCTGTTCAGCTCTTACGAGC
1 TTCTGTTCAGCTCTTACGAGCTTCTATTCAACTCTTATGAGTTTCTGTTCAGCTCTTACGAGC
35290557 TTCTGTT
1 TTCTGTT
35290564 GGTGTATTCA
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
61 50 0.78
62 2 0.03
63 12 0.19
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.45
Consensus pattern (63 bp):
TTCTGTTCAGCTCTTACGAGCTTCTATTCAACTCTTATGAGTTTCTGTTCAGCTCTTACGAGC
Found at i:35290763 original size:21 final size:20
Alignment explanation
Indices: 35290736--35290784 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
35290726 AATAGAAGTT
*
35290736 ATGAATGACAGGAAATTGTC
1 ATGAATGACAGGAAATTGAC
*
35290756 AGTGAATGACAGGGAATTGAC
1 A-TGAATGACAGGAAATTGAC
35290777 ATGAATGA
1 ATGAATGA
35290785 TTTTATTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 8 0.31
21 18 0.69
ACGTcount: A:0.41, C:0.08, G:0.29, T:0.22
Consensus pattern (20 bp):
ATGAATGACAGGAAATTGAC
Found at i:35295229 original size:9 final size:9
Alignment explanation
Indices: 35295215--35295243 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
35295205 GTATGAGGTT
35295215 GTGATGCAG
1 GTGATGCAG
35295224 GTGATGCAG
1 GTGATGCAG
35295233 GTGATGCAG
1 GTGATGCAG
35295242 GT
1 GT
35295244 TTGTCATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.21, C:0.10, G:0.45, T:0.24
Consensus pattern (9 bp):
GTGATGCAG
Found at i:35310348 original size:29 final size:29
Alignment explanation
Indices: 35310316--35310380 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
35310306 TTTAATGTGA
*
35310316 TTAATATAAAGTAATAT-TATTCAAAAAAT
1 TTAATATAAAGTAAAATATATT-AAAAAAT
* * *
35310345 TTAATATAAATTAAAATATATTAACAATT
1 TTAATATAAAGTAAAATATATTAAAAAAT
35310374 TTAATAT
1 TTAATAT
35310381 TAAAAAATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 27 0.87
30 4 0.13
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.42
Consensus pattern (29 bp):
TTAATATAAAGTAAAATATATTAAAAAAT
Found at i:35312405 original size:25 final size:25
Alignment explanation
Indices: 35312344--35312407 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 25
35312334 TTTTATCACT
*
35312344 CCACTTCAATTTTATATTAAATTTTG
1 CCACTT-AATTTTATATTAAATTTTA
*
35312370 CCACTTGATTTT-TGATTAAATTTTA
1 CCACTTAATTTTAT-ATTAAATTTTA
* *
35312395 CTATTTAATTTTA
1 CCACTTAATTTTA
35312408 ATTTTAATTA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
24 1 0.03
25 24 0.77
26 6 0.19
ACGTcount: A:0.30, C:0.12, G:0.05, T:0.53
Consensus pattern (25 bp):
CCACTTAATTTTATATTAAATTTTA
Found at i:35315872 original size:44 final size:45
Alignment explanation
Indices: 35315805--35315912 Score: 137
Period size: 44 Copynumber: 2.4 Consensus size: 45
35315795 TATCTTTGAC
** * * *
35315805 ATAGACTTACATGAATTATTCCTGTCTCCAATGCCATA-TATAAT
1 ATAGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTATAAT
* *
35315849 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATAGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA-TTATAAT
35315895 ATAGACTTACATGGCTCA
1 ATAGACTTACATGGCTCA
35315913 TTTCTGTTCT
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
44 32 0.59
46 22 0.41
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.33
Consensus pattern (45 bp):
ATAGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTATAAT
Found at i:35325684 original size:28 final size:28
Alignment explanation
Indices: 35325644--35325699 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
35325634 GAGACCCAGA
*
35325644 TGCAATCTATATGTTGAAGTTTCTCTTT
1 TGCAATCGATATGTTGAAGTTTCTCTTT
35325672 TGCAATCGATATGTTGAAGTTTCTCTTT
1 TGCAATCGATATGTTGAAGTTTCTCTTT
35325700 CACTCCTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.21, C:0.14, G:0.16, T:0.48
Consensus pattern (28 bp):
TGCAATCGATATGTTGAAGTTTCTCTTT
Found at i:35328067 original size:29 final size:29
Alignment explanation
Indices: 35328010--35328067 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
35328000 TAAAAAATTA
*
35328010 AATAAATTTTAAATATAAAATTATTCGTT
1 AATAAATTTTAAATATAAAATTATACGTT
*
35328039 AATAAATTTTACAA-ATAAAATTCTACGTT
1 AATAAATTTTA-AATATAAAATTATACGTT
35328068 TTAACAAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 24 0.92
30 2 0.08
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.41
Consensus pattern (29 bp):
AATAAATTTTAAATATAAAATTATACGTT
Found at i:35328865 original size:23 final size:25
Alignment explanation
Indices: 35328814--35328870 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
35328804 CAAAAATAGT
* *
35328814 TATATTTATATTAATATAATTGAGT
1 TATATTTATATTAATATAATTAAGA
*
35328839 TATATTTATATTTATAT-A-TAAGA
1 TATATTTATATTAATATAATTAAGA
35328862 TATATTTAT
1 TATATTTAT
35328871 TAGAAAAACT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 12 0.41
24 1 0.03
25 16 0.55
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.54
Consensus pattern (25 bp):
TATATTTATATTAATATAATTAAGA
Found at i:35332191 original size:103 final size:104
Alignment explanation
Indices: 35332004--35332212 Score: 375
Period size: 103 Copynumber: 2.0 Consensus size: 104
35331994 GTTTTTCCCT
* *
35332004 CAAGCCTTCAAACGGCGTCGTTTAATCACCATAAAAGCAGAAAAAAAAAAGAACTCTTTCTGCAG
1 CAAGCCTTCAAACAGCGCCGTTTAATCACCATAAAAGCAG--AAAAAAAAGAACTCTTTCTGCAG
35332069 TTTCATTTTCTTGCAGAGAACGCACAAAAAATAAATAAAAC
64 TTTCATTTTCTTGCAGAGAACGCACAAAAAATAAATAAAAC
35332110 CAAGCCTTCAAACAGCGCCGTTTAATCACCATAAAAGCAG-AAAAAAAGAACTCTTTCTGCAGTT
1 CAAGCCTTCAAACAGCGCCGTTTAATCACCATAAAAGCAGAAAAAAAAGAACTCTTTCTGCAGTT
35332174 TCATTTTCTTGCAGAGAACGCACAAAAAATAAATAAAAC
66 TCATTTTCTTGCAGAGAACGCACAAAAAATAAATAAAAC
35332213 AAAAGGGAGG
Statistics
Matches: 101, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
103 63 0.62
106 38 0.38
ACGTcount: A:0.43, C:0.22, G:0.13, T:0.22
Consensus pattern (104 bp):
CAAGCCTTCAAACAGCGCCGTTTAATCACCATAAAAGCAGAAAAAAAAGAACTCTTTCTGCAGTT
TCATTTTCTTGCAGAGAACGCACAAAAAATAAATAAAAC
Found at i:35332586 original size:5 final size:5
Alignment explanation
Indices: 35332576--35332604 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
35332566 GATTTGCAAT
35332576 AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
35332605 CTATGAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:35333416 original size:45 final size:45
Alignment explanation
Indices: 35333356--35333515 Score: 126
Period size: 45 Copynumber: 3.4 Consensus size: 45
35333346 GATCTGTAAT
* *
35333356 CTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGG
1 CTTCAATCTACTCCACTGCCAAATACAGGGAGATAGAGTTATCGA
* * * * * * *
35333401 CTTCAATGTACTCCACTG--TAGTCACATGGAGGTAAAATCTGCCATATTCGA
1 CTTCAATCTACTCCACTGCCAAAT-ACAGGGAGAT-AGA---G--TTA-TCGA
*
35333452 TCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGA
1 -CTTCAATCTACTCCACTGCCAAATACAGGGAGATAGAGTTATCGA
*
35333498 CTTCAATGTACTCCACTG
1 CTTCAATCTACTCCACTG
35333516 TAGTCAGGGA
Statistics
Matches: 85, Mismatches: 19, Indels: 22
0.67 0.15 0.17
Matches are distributed among these distances:
43 2 0.02
44 8 0.09
45 34 0.40
46 4 0.05
47 2 0.02
48 1 0.01
49 1 0.01
50 2 0.02
51 3 0.04
52 18 0.21
53 8 0.09
54 2 0.02
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (45 bp):
CTTCAATCTACTCCACTGCCAAATACAGGGAGATAGAGTTATCGA
Found at i:35333520 original size:97 final size:95
Alignment explanation
Indices: 35333354--35333583 Score: 406
Period size: 97 Copynumber: 2.4 Consensus size: 95
35333344 AAGATCTGTA
*
35333354 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGACTTCAATGTACTCCACTG
*
35333419 TAGTCACATGGAGGTAAAATCTGCCATATTCG
66 TAGT--CAGGGAGGTAAAATCTGCCATATTCG
35333451 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGACTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGACTTCAATGTACTCCACTG
* *
35333516 TAGTCAGGGAGGTAAAATCTGCCATCTTTG
66 TAGTCAGGGAGGTAAAATCTGCCATATTCG
35333546 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAG
35333584 GATCTGTTTT
Statistics
Matches: 129, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
95 61 0.47
97 68 0.53
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (95 bp):
ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGACTTCAATGTACTCCACTG
TAGTCAGGGAGGTAAAATCTGCCATATTCG
Found at i:35333656 original size:44 final size:44
Alignment explanation
Indices: 35333608--35334206 Score: 466
Period size: 44 Copynumber: 13.6 Consensus size: 44
35333598 TCCACTTCCT
*
35333608 ACCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCAC
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * *
35333652 ACCAATATATGAATACAAGATCTGCTTTCTTCGATCTACTTCACC
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCA-C
* * * *
35333697 ACCAGTATGGGAAGACAAGATCTGC-ATCTTGGATCCACTTC-C
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * * *
35333739 TATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCAC
1 -ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * ** * *
35333784 GCCAATACATAAAGACAAGATCTGCTTTCTGCGATCTACTTCATC
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCA-C
** * * * * *
35333829 TGTCAAGCA-AGATGAAG--TAGATCTGCTTTCTGCGATCTACTTCGCC
1 -ACCAA-TATAG--GAAGACAAGATCTGCTATCTTCGATCTACTTC-AC
* * * *
35333875 ACCATTATGGGAAGACAAGATCTGC-ATCTTGGATCCACTTC-C
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * * * *
35333917 TATCAATATAGGAAGATAGGACCTGTTATCTTCGATCTACTTCAC
1 -ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * * * * *
35333962 GCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCC
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTC-AC
* *
35334007 ACCAATAT-GAGAAGACAAGATCTGC-ATCTTGGATCCACTTC-C
1 ACCAATATAG-GAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * * *
35334049 TATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCAC
1 -ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * * * * *
35334094 GCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCC
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTC-AC
* * * *
35334139 ACCAATATGGGAATACAAGATCTGC-ATCTTCGATCCACTTCAT
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * *
35334182 GCCAATACATG-AGACAAGATCTGCT
1 ACCAATATAGGAAGACAAGATCTGCT
35334207 TTAATGACTT
Statistics
Matches: 428, Mismatches: 103, Indels: 49
0.74 0.18 0.08
Matches are distributed among these distances:
42 15 0.04
43 67 0.16
44 231 0.54
45 80 0.19
46 31 0.07
47 1 0.00
48 3 0.01
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (44 bp):
ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
Found at i:35333923 original size:178 final size:178
Alignment explanation
Indices: 35333669--35334003 Score: 625
Period size: 178 Copynumber: 1.9 Consensus size: 178
35333659 TATGAATACA
*
35333669 AGATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCATCTTGGATCCA
1 AGATCTGCTTTCTGCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCATCTTGGATCCA
35333734 CTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATAAAGA
66 CTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATAAAGA
35333799 CAAGATCTGCTTTCTGCGATCTACTTCATCTGTCAAGCAAGATGAAGT
131 CAAGATCTGCTTTCTGCGATCTACTTCATCTGTCAAGCAAGATGAAGT
* *
35333847 AGATCTGCTTTCTGCGATCTACTTCGCCACCATTATGGGAAGACAAGATCTGCATCTTGGATCCA
1 AGATCTGCTTTCTGCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCATCTTGGATCCA
* *
35333912 CTTCCTATCAATATAGGAAGATAGGACCTGTTATCTTCGATCTACTTCACGCCAATACATGAAGA
66 CTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATAAAGA
35333977 CAAGATCTGCTTTCTGCGATCTACTTC
131 CAAGATCTGCTTTCTGCGATCTACTTC
35334004 GCCACCAATA
Statistics
Matches: 152, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
178 152 1.00
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (178 bp):
AGATCTGCTTTCTGCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCATCTTGGATCCA
CTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATAAAGA
CAAGATCTGCTTTCTGCGATCTACTTCATCTGTCAAGCAAGATGAAGT
Found at i:35334005 original size:132 final size:132
Alignment explanation
Indices: 35333847--35334179 Score: 621
Period size: 132 Copynumber: 2.5 Consensus size: 132
35333837 AAGATGAAGT
*
35333847 AGATCTGCTTTCTGCGATCTACTTCGCCACCATTATGGGAAGACAAGATCTGCATCTTGGATCCA
1 AGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTGGATCCA
*
35333912 CTTCCTATCAATATAGGAAGATAGGACCTGTTATCTTCGATCTACTTCACGCCAATACATGAAGA
66 CTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGA
35333977 CA
131 CA
*
35333979 AGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGAGAAGACAAGATCTGCATCTTGGATCCA
1 AGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTGGATCCA
35334044 CTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGA
66 CTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGA
35334109 CA
131 CA
* *
35334111 AGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAATACAAGATCTGCATCTTCGATCCA
1 AGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTGGATCCA
35334176 CTTC
66 CTTC
35334180 ATGCCAATAC
Statistics
Matches: 195, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
132 195 1.00
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.29
Consensus pattern (132 bp):
AGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTGGATCCA
CTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGA
CA
Found at i:35334188 original size:132 final size:133
Alignment explanation
Indices: 35333608--35334206 Score: 611
Period size: 132 Copynumber: 4.5 Consensus size: 133
35333598 TCCACTTCCT
* * * * * * *
35333608 ACCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACACCAATATATGAATACAAGAT
1 ACCAATATGGGAAGACAAGATCTGC-ATCTTCGATCCACTTCATACCAATATAGGAAGACAAGAC
* * * *** * *
35333673 CTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGC-ATCTTG-GATCCACT
65 CTGCTATCTTCGATCTACTTCACCGCCAATACATGAAGACAAGATCTGCTTTC-TGCGATCTACT
*
35333736 TC-CT
129 TCGCC
* * * * * * ** * ** *
35333740 ATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATAAAGACAAGAT
1 ACCAATATGGGAAGACAAGATCTGC-ATCTTCGATCCACTTCATACCAATATAGGAAGACAAGAC
* * * * * * *
35333805 CTGCTTTCTGCGATCTACTTCATCTGTCAAGCAAGATGAAG--TAGATCTGCTTTCTGCGATCTA
65 CTGCTATCTTCGATCTACTTCA-CCGCCAA--TACATGAAGACAAGATCTGCTTTCTGCGATCTA
35333868 CTTCGCC
127 CTTCGCC
* * * * * *
35333875 ACCATTATGGGAAGACAAGATCTGCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACC
1 ACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCATACCAATATAGGAAGACAAGACC
*
35333940 TGTTATCTTCGATCTACTTCA-CGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTC
66 TGCTATCTTCGATCTACTTCACCGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTC
35334004 GCC
131 GCC
* * * * * *
35334007 ACCAATATGAGAAGACAAGATCTGCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACC
1 ACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCATACCAATATAGGAAGACAAGACC
35334072 TGCTATCTTCGATCTACTTCA-CGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTC
66 TGCTATCTTCGATCTACTTCACCGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTC
35334136 GCC
131 GCC
* * * * *
35334139 ACCAATATGGGAATACAAGATCTGCATCTTCGATCCACTTCATGCCAATACATG-AGACAAGATC
1 ACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCATACCAATATAGGAAGACAAGACC
35334203 TGCT
66 TGCT
35334207 TTAATGACTT
Statistics
Matches: 399, Mismatches: 60, Indels: 17
0.84 0.13 0.04
Matches are distributed among these distances:
130 7 0.02
131 11 0.03
132 286 0.72
133 13 0.03
134 57 0.14
135 25 0.06
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (133 bp):
ACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCATACCAATATAGGAAGACAAGACC
TGCTATCTTCGATCTACTTCACCGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTC
GCC
Found at i:35345577 original size:75 final size:75
Alignment explanation
Indices: 35345454--35345602 Score: 280
Period size: 75 Copynumber: 2.0 Consensus size: 75
35345444 TATGAAATTA
35345454 AAAAAAACGGGTTCGGGAGTCGGTTACGCACGAGGAAGGATTAGCACCCTCGATACGCCCAAAAT
1 AAAAAAACGGGTTCGGGAGTCGGTTACGCACGAGGAAGGATTAGCACCCTCGATACGCCCAAAAT
*
35345519 TGGTACCTAC
66 TAGTACCTAC
*
35345529 AAAAAAAGGGGTTCGGGAGTCGGTTACGCACGAGGAAGGATTAGCACCCTCGATACGCCCAAAAT
1 AAAAAAACGGGTTCGGGAGTCGGTTACGCACGAGGAAGGATTAGCACCCTCGATACGCCCAAAAT
35345594 TAGTACCTA
66 TAGTACCTA
35345603 GTTGATTAAT
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 72 1.00
ACGTcount: A:0.33, C:0.23, G:0.27, T:0.17
Consensus pattern (75 bp):
AAAAAAACGGGTTCGGGAGTCGGTTACGCACGAGGAAGGATTAGCACCCTCGATACGCCCAAAAT
TAGTACCTAC
Found at i:35345752 original size:197 final size:197
Alignment explanation
Indices: 35345529--35345921 Score: 759
Period size: 197 Copynumber: 2.0 Consensus size: 197
35345519 TGGTACCTAC
*
35345529 AAAAAAAGGGGTTCGGGAGTCGGTTACGCACGAGGAAGGATTAGCACCCTCGATACGCCCAAAAT
1 AAAAAAACGGGTTCGGGAGTCGGTTACGCACGAGGAAGGATTAGCACCCTCGATACGCCCAAAAT
35345594 TAGTACCTAGTTGATTAATTAGTGTCTTAGTGTCGAAAATTGAAAATTTGAAGAGTTTTAAAAAT
66 TAGTACCTAGTTGATTAATTAGTGTCTTAGTGTCGAAAATTGAAAATTTGAAGAGTTTTAAAAAT
35345659 ACGATCCTTAAAAGAAACTCTGATAACGTGAATTGAAATATAAGATTCTCTTGTTCCGAAGGAAT
131 ACGATCCTTAAAAGAAACTCTGATAACGTGAATTGAAATATAAGATTCTCTTGTTCCGAAGGAAT
35345724 AA
196 AA
35345726 AAAAAAACGGGTTCGGGAGTCGGTTACGCACGAGGAAGGATTAGCACCCTCGATACGCCCAAAAT
1 AAAAAAACGGGTTCGGGAGTCGGTTACGCACGAGGAAGGATTAGCACCCTCGATACGCCCAAAAT
*
35345791 TGGTACCTAGTTGATTAATTAGTGTCTTAGTGTCGAAAATTGAAAATTTGAAGAGTTTTAAAAAT
66 TAGTACCTAGTTGATTAATTAGTGTCTTAGTGTCGAAAATTGAAAATTTGAAGAGTTTTAAAAAT
*
35345856 ACGGTCCTTAAAAGAAACTCTGATAACGTGAATTGAAATATAAGATTCTCTTGTTCCGAAGGAAT
131 ACGATCCTTAAAAGAAACTCTGATAACGTGAATTGAAATATAAGATTCTCTTGTTCCGAAGGAAT
35345921 A
196 A
35345922 TCACATCCAG
Statistics
Matches: 193, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
197 193 1.00
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (197 bp):
AAAAAAACGGGTTCGGGAGTCGGTTACGCACGAGGAAGGATTAGCACCCTCGATACGCCCAAAAT
TAGTACCTAGTTGATTAATTAGTGTCTTAGTGTCGAAAATTGAAAATTTGAAGAGTTTTAAAAAT
ACGATCCTTAAAAGAAACTCTGATAACGTGAATTGAAATATAAGATTCTCTTGTTCCGAAGGAAT
AA
Found at i:35346256 original size:140 final size:140
Alignment explanation
Indices: 35346004--35346283 Score: 542
Period size: 140 Copynumber: 2.0 Consensus size: 140
35345994 ATACTTTGAA
35346004 GCTTTAAGAGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGT
1 GCTTTAAGAGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGT
*
35346069 TTTCTCGATTTTTCAAACGCGAAATATTGCCTTATTTAGAAAAATTTTCCTTTTGATGTTTGGTG
66 TTTCTCGATTTTCCAAACGCGAAATATTGCCTTATTTAGAAAAATTTTCCTTTTGATGTTTGGTG
35346134 TTAATGCTTG
131 TTAATGCTTG
*
35346144 GCTTTAAGAGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCATGT
1 GCTTTAAGAGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGT
35346209 TTTCTCGATTTTCCAAACGCGAAATATTGCCTTATTTAGAAAAATTTTCCTTTTGATGTTTGGTG
66 TTTCTCGATTTTCCAAACGCGAAATATTGCCTTATTTAGAAAAATTTTCCTTTTGATGTTTGGTG
35346274 TTAATGCTTG
131 TTAATGCTTG
35346284 ACAAAACAAT
Statistics
Matches: 138, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
140 138 1.00
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (140 bp):
GCTTTAAGAGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGT
TTTCTCGATTTTCCAAACGCGAAATATTGCCTTATTTAGAAAAATTTTCCTTTTGATGTTTGGTG
TTAATGCTTG
Found at i:35346767 original size:38 final size:38
Alignment explanation
Indices: 35346708--35346813 Score: 105
Period size: 37 Copynumber: 2.8 Consensus size: 38
35346698 CATTTTTAAG
*
35346708 AATAT-AAAGAATATATATAAGTATGTATATG-ATGTA-A
1 AATATGAAA-AATATATATAAGTATGTATAAGAAT-TAGA
* *
35346745 AATATGCATAAATATATGTAAGTA--TATAAGAATTATGA
1 AATATG-AAAAATATATATAAGTATGTATAAGAATTA-GA
*
35346783 AATATGAAAAATATATTTAAGTATGTATAAG
1 AATATGAAAAATATATATAAGTATGTATAAG
35346814 TACGTATATA
Statistics
Matches: 57, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
36 7 0.12
37 22 0.39
38 20 0.35
39 8 0.14
ACGTcount: A:0.51, C:0.01, G:0.13, T:0.35
Consensus pattern (38 bp):
AATATGAAAAATATATATAAGTATGTATAAGAATTAGA
Found at i:35349096 original size:79 final size:79
Alignment explanation
Indices: 35349008--35349164 Score: 233
Period size: 79 Copynumber: 2.0 Consensus size: 79
35348998 TGATTTGATA
* * * * * *
35349008 AAAGTTAATTGCTGATACTACTAGATTTGAATTTTTCATGATTTTGTAGAATATATTTAGTGCTG
1 AAAGTTAATTGCTAATACTACTAGACTTGAATTTTTCATGATTTTGAAAAATAAATTTAGTACTG
*
35349073 ATTGTGAATTTATG
66 ATTGCGAATTTATG
* *
35349087 AAAGTTAATTGCTAATACTACTAGGCTTGAATTTTTCATGATTTTGAAAAATAAATTTAGTATTG
1 AAAGTTAATTGCTAATACTACTAGACTTGAATTTTTCATGATTTTGAAAAATAAATTTAGTACTG
35349152 ATTGCGAATTTAT
66 ATTGCGAATTTAT
35349165 TTAATTTTGC
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
79 69 1.00
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.44
Consensus pattern (79 bp):
AAAGTTAATTGCTAATACTACTAGACTTGAATTTTTCATGATTTTGAAAAATAAATTTAGTACTG
ATTGCGAATTTATG
Found at i:35355065 original size:20 final size:20
Alignment explanation
Indices: 35355036--35355080 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
35355026 TTATTATTTC
* * *
35355036 ATTTTTTTATTTTTTTTGTT
1 ATTTTATTATTTCTTTTATT
35355056 ATTTTATTATTTCTTTTATT
1 ATTTTATTATTTCTTTTATT
35355076 ATTTT
1 ATTTT
35355081 TGGAACTTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.80
Consensus pattern (20 bp):
ATTTTATTATTTCTTTTATT
Found at i:35357046 original size:6 final size:6
Alignment explanation
Indices: 35357037--35357093 Score: 57
Period size: 6 Copynumber: 9.7 Consensus size: 6
35357027 ATACTACAAC
* *
35357037 AAAAAG AAAAAG AAAAAG AAAAA- AAAGAA- AATAAG AGAAAAG AAAATG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAA-AAG AAAAAG A-AAAAG AAAAAG
35357085 -AAAAG AAAA
1 AAAAAG AAAA
35357094 CCTAAACTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
5 9 0.21
6 29 0.67
7 5 0.12
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.04
Consensus pattern (6 bp):
AAAAAG
Found at i:35357052 original size:5 final size:5
Alignment explanation
Indices: 35357038--35357093 Score: 60
Period size: 5 Copynumber: 10.8 Consensus size: 5
35357028 TACTACAACA
* *
35357038 AAAAG AAAAAG AAAAAG AAAA- AAAAG AAAAT AAGAG AAAAG AAAATG
1 AAAAG -AAAAG -AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA-G
35357085 AAAAG AAAA
1 AAAAG AAAA
35357094 CCTAAACTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
4 4 0.09
5 24 0.55
6 16 0.36
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (5 bp):
AAAAG
Found at i:35357271 original size:20 final size:21
Alignment explanation
Indices: 35357246--35357288 Score: 79
Period size: 20 Copynumber: 2.1 Consensus size: 21
35357236 ATGTAAAATT
35357246 GTCTATGTAGTTTTTT-AACC
1 GTCTATGTAGTTTTTTCAACC
35357266 GTCTATGTAGTTTTTTCAACC
1 GTCTATGTAGTTTTTTCAACC
35357287 GT
1 GT
35357289 TAGGCAGCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.19, C:0.16, G:0.16, T:0.49
Consensus pattern (21 bp):
GTCTATGTAGTTTTTTCAACC
Found at i:35359937 original size:55 final size:55
Alignment explanation
Indices: 35359853--35359962 Score: 202
Period size: 55 Copynumber: 2.0 Consensus size: 55
35359843 TTTTTTTTAG
*
35359853 AAATGTTGATTTTATAGCATTGCAAAACGGCGCCGTTTTGGGCCGGATGTTGAAC
1 AAATGTTGATTTTATAGCATTGCAAAACGGCACCGTTTTGGGCCGGATGTTGAAC
*
35359908 AAATGTTGATTTTATAGCATTGCAAAACGGCACCGTTTTGGGCTGGATGTTGAAC
1 AAATGTTGATTTTATAGCATTGCAAAACGGCACCGTTTTGGGCCGGATGTTGAAC
35359963 GTCCAAACGA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.32
Consensus pattern (55 bp):
AAATGTTGATTTTATAGCATTGCAAAACGGCACCGTTTTGGGCCGGATGTTGAAC
Found at i:35360448 original size:23 final size:24
Alignment explanation
Indices: 35360394--35360448 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
35360384 ATTGTTATGT
* *
35360394 TTTTATTTGTTTATTCATATATCC
1 TTTTATTTATTTATTCATATATAC
* * *
35360418 ATTCATTTATTT-TTCTTATATAC
1 TTTTATTTATTTATTCATATATAC
35360441 TTTTATTT
1 TTTTATTT
35360449 TGTATTTAAA
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.22, C:0.11, G:0.02, T:0.65
Consensus pattern (24 bp):
TTTTATTTATTTATTCATATATAC
Found at i:35360578 original size:3 final size:3
Alignment explanation
Indices: 35360570--35360634 Score: 69
Period size: 3 Copynumber: 21.3 Consensus size: 3
35360560 TTTGCATTGG
* *
35360570 TTA TTA TTA TTA ATA TTA TTA TTA TTA GTA TTA TTA TTA TTCA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA
* *
35360615 CTA TTA TTT TTA TTA CTTA T
1 TTA TTA TTA TTA TTA -TTA T
35360635 CTCATCGCTT
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
2 1 0.02
3 47 0.90
4 4 0.08
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:35360590 original size:15 final size:15
Alignment explanation
Indices: 35360570--35360622 Score: 79
Period size: 15 Copynumber: 3.5 Consensus size: 15
35360560 TTTGCATTGG
35360570 TTATTATTATTAATA
1 TTATTATTATTAATA
*
35360585 TTATTATTATTAGTA
1 TTATTATTATTAATA
*
35360600 TTATTATTATTCATA
1 TTATTATTATTAATA
*
35360615 CTATTATT
1 TTATTATT
35360623 TTTATTACTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (15 bp):
TTATTATTATTAATA
Found at i:35376845 original size:25 final size:24
Alignment explanation
Indices: 35376817--35376884 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 24
35376807 ATAAATGGGG
35376817 TTTAAAATAAGGTATATAAAAT-AA
1 TTTAAAATAA-GTATATAAAATCAA
*
35376841 TTTTAAAATAAGTAATATATAAGTCAA
1 -TTTAAAATAAGT-ATATA-AAATCAA
35376868 TTTAAAATAA-TATATAA
1 TTTAAAATAAGTATATAA
35376885 CAAGTTTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
23 1 0.03
24 7 0.18
25 16 0.41
26 13 0.33
27 2 0.05
ACGTcount: A:0.56, C:0.01, G:0.06, T:0.37
Consensus pattern (24 bp):
TTTAAAATAAGTATATAAAATCAA
Done.