Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr13
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: 55873576
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1239791 characters in sequence are not A, C, G, or T
File 64 of 182
Found at i:19544808 original size:14 final size:14
Alignment explanation
Indices: 19544791--19544825 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
19544781 TTTTTTAAAG
*
19544791 AATTTTAACTTTCA
1 AATTTTAACTTCCA
19544805 AATTTTAACTTCCA
1 AATTTTAACTTCCA
19544819 AATTTTA
1 AATTTTA
19544826 TTTGCACAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.37, C:0.14, G:0.00, T:0.49
Consensus pattern (14 bp):
AATTTTAACTTCCA
Found at i:19548190 original size:21 final size:21
Alignment explanation
Indices: 19548164--19548218 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
19548154 AACAGCGGTG
*
19548164 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGGTACTGTA
*
19548185 GCGGTGAGATTGGGTACTGTA
1 GCGGTGAGATTAGGTACTGTA
19548206 GCGGTGAGATTAG
1 GCGGTGAGATTAG
19548219 AAACAATGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.22, C:0.09, G:0.40, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGGTACTGTA
Found at i:19548531 original size:22 final size:22
Alignment explanation
Indices: 19548480--19548531 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 22
19548470 TTTTATAGTT
*
19548480 ATAATTAAATATTTTTTATAACA
1 ATAA-TAAATATTATTTATAACA
* *
19548503 ATGATAAATATTATTT-TCACAA
1 ATAATAAATATTATTTATAAC-A
19548525 ATAATAA
1 ATAATAA
19548532 CATTATACTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 3 0.12
22 18 0.75
23 3 0.12
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (22 bp):
ATAATAAATATTATTTATAACA
Found at i:19551886 original size:64 final size:64
Alignment explanation
Indices: 19551785--19551931 Score: 285
Period size: 64 Copynumber: 2.3 Consensus size: 64
19551775 ATGTTATATT
19551785 AGTTCGAATCCTCTAATTTTGATTGAATTAATAAGGTTAGAAATTTGAGAATTTTAAAATCTTA
1 AGTTCGAATCCTCTAATTTTGATTGAATTAATAAGGTTAGAAATTTGAGAATTTTAAAATCTTA
*
19551849 AGTTCGAATCCTTTAATTTTGATTGAATTAATAAGGTTAGAAATTTGAGAATTTTAAAATCTTA
1 AGTTCGAATCCTCTAATTTTGATTGAATTAATAAGGTTAGAAATTTGAGAATTTTAAAATCTTA
19551913 AGTTCGAATCCTCTAATTT
1 AGTTCGAATCCTCTAATTT
19551932 AAATACTATA
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 81 1.00
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.41
Consensus pattern (64 bp):
AGTTCGAATCCTCTAATTTTGATTGAATTAATAAGGTTAGAAATTTGAGAATTTTAAAATCTTA
Found at i:19552584 original size:15 final size:15
Alignment explanation
Indices: 19552564--19552595 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
19552554 TGTAAGTTTC
19552564 TTAGAAATAAAATGA
1 TTAGAAATAAAATGA
*
19552579 TTAGAAATAAGATGA
1 TTAGAAATAAAATGA
19552594 TT
1 TT
19552596 GGGGAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.31
Consensus pattern (15 bp):
TTAGAAATAAAATGA
Found at i:19553278 original size:379 final size:379
Alignment explanation
Indices: 19552579--19553323 Score: 1481
Period size: 379 Copynumber: 2.0 Consensus size: 379
19552569 AATAAAATGA
19552579 TTAGAAATAAGATGATTGGGGAAATTTGGGTCAAAATTGAGGAAAAAGCAGTGAAGATAATCCTG
1 TTAGAAATAAGATGATTGGGGAAATTTGGGTCAAAATTGAGGAAAAAGCAGTGAAGATAATCCTG
19552644 GGAAGTGAATGGGAAACTTCCCAATCCAGGTGTTGAATGCAACAGTTTTTTCCTTTGAAATGAAC
66 GGAAGTGAATGGGAAACTTCCCAATCCAGGTGTTGAATGCAACAGTTTTTTCCTTTGAAATGAAC
19552709 GACCGAAAGAGTGAGCTCTTTTTTTTCCTTCTTGTTGTTGATTTAATTTGTGCTTTCTTTGCTTC
131 GACCGAAAGAGTGAGCTCTTTTTTTTCCTTCTTGTTGTTGATTTAATTTGTGCTTTCTTTGCTTC
19552774 TTTTCATTTGGTTAACGAATCTCTGAATCTTTTCATTTGATTTAATTTGTGCTTTCTTCGCTTTT
196 TTTTCATTTGGTTAACGAATCTCTGAATCTTTTCATTTGATTTAATTTGTGCTTTCTTCGCTTTT
19552839 TTTCATTTGGTTTGATTTATCCTCTCCCTCTCTCTTTGTCTCACACATATGCACATCAACAGACG
261 TTTCATTTGGTTTGATTTATCCTCTCCCTCTCTCTTTGTCTCACACATATGCACATCAACAGACG
*
19552904 CAATTGTGTGTTCATCTCTTGTTTTCATTATAATTTATTGCATTTGTAAGTTTC
326 CAATTGTGTGTTCATCTCTTGTTCTCATTATAATTTATTGCATTTGTAAGTTTC
19552958 TTAGAAATAAGATGATTGGGGAAATTTGGGTCAAAATTGAGGAAAAAGCAGTGAAGATAATCCTG
1 TTAGAAATAAGATGATTGGGGAAATTTGGGTCAAAATTGAGGAAAAAGCAGTGAAGATAATCCTG
19553023 GGAAGTGAATGGGAAACTTCCCAATCCAGGTGTTGAATGCAACAGTTTTTTCCTTTGAAATGAAC
66 GGAAGTGAATGGGAAACTTCCCAATCCAGGTGTTGAATGCAACAGTTTTTTCCTTTGAAATGAAC
19553088 GACCGAAAGAGTGAGCTCTTTTTTTTCCTTCTTGTTGTTGATTTAATTTGTGCTTTCTTTGCTTC
131 GACCGAAAGAGTGAGCTCTTTTTTTTCCTTCTTGTTGTTGATTTAATTTGTGCTTTCTTTGCTTC
19553153 TTTTCATTTGGTTAACGAATCTCTGAATCTTTTCATTTGATTTAATTTGTGCTTTCTTCGCTTTT
196 TTTTCATTTGGTTAACGAATCTCTGAATCTTTTCATTTGATTTAATTTGTGCTTTCTTCGCTTTT
19553218 TTTCATTTGGTTTGATTTATCCTCTCCCTCTCTCTTTGTCTCACACATATGCACATCAACAGACG
261 TTTCATTTGGTTTGATTTATCCTCTCCCTCTCTCTTTGTCTCACACATATGCACATCAACAGACG
19553283 CAATTGTGTGTTCATCTCTTGTTCTCATTATAATTTATTGC
326 CAATTGTGTGTTCATCTCTTGTTCTCATTATAATTTATTGC
19553324 TATTGAATGC
Statistics
Matches: 365, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
379 365 1.00
ACGTcount: A:0.24, C:0.17, G:0.18, T:0.42
Consensus pattern (379 bp):
TTAGAAATAAGATGATTGGGGAAATTTGGGTCAAAATTGAGGAAAAAGCAGTGAAGATAATCCTG
GGAAGTGAATGGGAAACTTCCCAATCCAGGTGTTGAATGCAACAGTTTTTTCCTTTGAAATGAAC
GACCGAAAGAGTGAGCTCTTTTTTTTCCTTCTTGTTGTTGATTTAATTTGTGCTTTCTTTGCTTC
TTTTCATTTGGTTAACGAATCTCTGAATCTTTTCATTTGATTTAATTTGTGCTTTCTTCGCTTTT
TTTCATTTGGTTTGATTTATCCTCTCCCTCTCTCTTTGTCTCACACATATGCACATCAACAGACG
CAATTGTGTGTTCATCTCTTGTTCTCATTATAATTTATTGCATTTGTAAGTTTC
Found at i:19555647 original size:21 final size:21
Alignment explanation
Indices: 19555621--19555664 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
19555611 AAATAGAGCT
19555621 TCTTTGAGTCTGCTGTGAGTG
1 TCTTTGAGTCTGCTGTGAGTG
19555642 TCTTTGAGTCTGCTGTGAGTG
1 TCTTTGAGTCTGCTGTGAGTG
19555663 TC
1 TC
19555665 AATTGAAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.09, C:0.16, G:0.32, T:0.43
Consensus pattern (21 bp):
TCTTTGAGTCTGCTGTGAGTG
Found at i:19567289 original size:14 final size:14
Alignment explanation
Indices: 19567266--19567312 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
19567256 ATCATATTTA
*
19567266 AATATAATTATTATT
1 AATAT-ATTATAATT
19567281 AATATATTATAATT
1 AATATATTATAATT
*
19567295 AAAATA-TATAATTT
1 AATATATTATAA-TT
19567309 AATA
1 AATA
19567313 AAATTCTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 5 0.18
14 18 0.64
15 5 0.18
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AATATATTATAATT
Found at i:19567408 original size:120 final size:119
Alignment explanation
Indices: 19567261--19567687 Score: 481
Period size: 120 Copynumber: 3.5 Consensus size: 119
19567251 ATTTAATCAT
19567261 ATTTAAAT-ATAATTATTATTAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTAAATAATAATTATTA--AATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
* *
19567325 ATCAATATTCTTATATGAATTTACTCAAATCATTATATATGATACTATAAAATATA
64 ATCAATATTCTTATATGAATTTACTAAAATCATTATATATAATACTATAAAATATA
* **
19567381 ATTTAACATAATAATTATTAAATATATTATAATTAAAATATATAATTTAATATAATTAAAATATA
1 ATTTAA-ATAATAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT--CTTA-A
* * * * *
19567446 TAATTTAATAAAATTCTTAATAATTAATATT-CTTATATGAATT-TACTCA-AAT-C-ATAATAT
62 TAA-TCAAT---ATTCTT-AT-ATGAAT-TTACTAAAAT-CATTATA-T-ATAATACTATAA-A-
*
19567506 AGATA
115 ATATA
*
19567511 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
1 ATTTAA-ATAATAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
*
19567576 TCAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATA
65 TCAATATTCTTATATGAATTTACTAAAATCATTATATATAATACTATAAAATATA
* *
19567631 ATTTGAAATAATTAA-TATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATTT-AAATAA-TAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
19567688 TAAAATAATT
Statistics
Matches: 259, Mismatches: 24, Indels: 48
0.78 0.07 0.15
Matches are distributed among these distances:
119 1 0.00
120 102 0.39
121 20 0.08
122 18 0.07
123 10 0.04
124 4 0.02
126 4 0.02
127 10 0.04
128 8 0.03
129 14 0.05
130 67 0.26
131 1 0.00
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.44
Consensus pattern (119 bp):
ATTTAAATAATAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAT
CAATATTCTTATATGAATTTACTAAAATCATTATATATAATACTATAAAATATA
Found at i:19567424 original size:18 final size:19
Alignment explanation
Indices: 19567402--19567459 Score: 59
Period size: 23 Copynumber: 3.0 Consensus size: 19
19567392 TAATTATTAA
19567402 ATAT-ATTATAATTAAAAT
1 ATATAATTATAATTAAAAT
19567420 ATATAATTTAATATAATTAAAAT
1 ATATAA--T--TATAATTAAAAT
19567443 ATATAATT-TAA-TAAAAT
1 ATATAATTATAATTAAAAT
19567460 TCTTAATAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
17 6 0.17
18 7 0.20
19 2 0.06
21 2 0.06
23 18 0.51
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
ATATAATTATAATTAAAAT
Found at i:19567426 original size:13 final size:13
Alignment explanation
Indices: 19567397--19567450 Score: 60
Period size: 13 Copynumber: 4.2 Consensus size: 13
19567387 CATAATAATT
19567397 ATTAAATATATTATA
1 ATTAAA-ATA-TATA
19567412 ATTAAAATATATA
1 ATTAAAATATATA
*
19567425 ATT--TA-ATATA
1 ATTAAAATATATA
19567435 ATTAAAATATATA
1 ATTAAAATATATA
19567448 ATT
1 ATT
19567451 TAATAAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
10 8 0.24
11 1 0.03
12 1 0.03
13 15 0.44
14 3 0.09
15 6 0.18
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATTAAAATATATA
Found at i:19567428 original size:44 final size:43
Alignment explanation
Indices: 19567376--19567701 Score: 132
Period size: 44 Copynumber: 7.8 Consensus size: 43
19567366 ATACTATAAA
19567376 ATATAATTTAACATAATAATTATTAAATATATTATAATTAAAAT
1 ATATAATTTAA-ATAATAATTATTAAATATATTATAATTAAAAT
*
19567420 ATATAATTT-AAT-ATAATTA--AAATATATAATTTAA-TAAAAT
1 ATATAATTTAAATAATAATTATTAAATATAT--TATAATTAAAAT
* * * * *
19567460 -TCTTAA--TAATTAAT-ATTCTTATATGA-ATTTACTCAAATCATAATAT
1 AT-ATAATTTAAATAATAATTATTAAAT-ATA-TTA-T--AAT--TAAAAT
* *
19567506 AGATAATTTAACATAATTATTATTAAATATATTATAATTAAAAT
1 ATATAATTTAA-ATAATAATTATTAAATATATTATAATTAAAAT
* * **
19567550 ATATAATTT-AATAA-AATTCTT-AATA-ATCA-ATATT--CTT
1 ATATAATTTAAATAATAATTATTAAATATATTATA-ATTAAAAT
* * * *
19567587 ATATGAATTT-ACTAA-AATCA-T-AATATATAAT-ACTATAAA-
1 ATAT-AATTTAAATAATAATTATTAAATATATTATAATTA-AAAT
*
19567626 ATATAATTTGAAATAATTAA-TATTAAATATATTTTAATTAAAAT
1 ATATAATTT-AAATAA-TAATTATTAAATATATTATAATTAAAAT
* *
19567670 ATATGATTT-AATAA-AATT-TAAAATA-ATTATAA
1 ATATAATTTAAATAATAATTATTAAATATATTATAA
19567702 CTAACAAATT
Statistics
Matches: 211, Mismatches: 34, Indels: 79
0.65 0.10 0.24
Matches are distributed among these distances:
37 12 0.06
38 22 0.10
39 30 0.14
40 28 0.13
41 23 0.11
42 16 0.08
43 15 0.07
44 33 0.16
46 11 0.05
48 4 0.02
49 8 0.04
50 9 0.04
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (43 bp):
ATATAATTTAAATAATAATTATTAAATATATTATAATTAAAAT
Found at i:19567437 original size:23 final size:23
Alignment explanation
Indices: 19567408--19567460 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
19567398 TTAAATATAT
19567408 TATAATTAAAATATATAATTTAA
1 TATAATTAAAATATATAATTTAA
19567431 TATAATTAAAATATATAATTTAA
1 TATAATTAAAATATATAATTTAA
*
19567454 TAAAATT
1 TATAATT
19567461 CTTAATAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TATAATTAAAATATATAATTTAA
Found at i:19567551 original size:16 final size:16
Alignment explanation
Indices: 19567508--19567553 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
19567498 CATAATATAG
*
19567508 ATAATTTAACATA-ATT
1 ATAA-TTAAAATATATT
*
19567524 ATTATT-AAATATATT
1 ATAATTAAAATATATT
19567539 ATAATTAAAATATAT
1 ATAATTAAAATATAT
19567554 AATTTAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 4 0.16
15 10 0.40
16 11 0.44
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (16 bp):
ATAATTAAAATATATT
Found at i:19567560 original size:14 final size:15
Alignment explanation
Indices: 19567397--19567562 Score: 54
Period size: 15 Copynumber: 11.5 Consensus size: 15
19567387 CATAATAATT
19567397 ATTAAATATATTATA
1 ATTAAATATATTATA
19567412 ATTAAA-ATA-TATA
1 ATTAAATATATTATA
*
19567425 ATTTAATATAATTA-A
1 ATTAAATAT-ATTATA
* *
19567440 AATATATA-ATT-TA
1 ATTAAATATATTATA
* *
19567453 ATAAAAT-TCTTAATA
1 ATTAAATATATT-ATA
*
19567468 ATT-AATATTCTTAT-
1 ATTAAATA-TATTATA
* * *
19567482 A-TGAATTTACTCA-A
1 ATTAAATATA-TTATA
* *
19567496 ATCATAATATA-GATA
1 ATTA-AATATATTATA
*
19567511 ATTTAACATA-ATTATT
1 A-TTAA-ATATATTATA
19567527 ATTAAATATATTATA
1 ATTAAATATATTATA
19567542 ATTAAA-ATA-TATA
1 ATTAAATATATTATA
*
19567555 ATTTAATA
1 ATTAAATA
19567563 AAATTCTTAA
Statistics
Matches: 110, Mismatches: 21, Indels: 41
0.64 0.12 0.24
Matches are distributed among these distances:
13 30 0.27
14 23 0.21
15 38 0.35
16 19 0.17
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (15 bp):
ATTAAATATATTATA
Found at i:19567611 original size:37 final size:35
Alignment explanation
Indices: 19567442--19567611 Score: 100
Period size: 37 Copynumber: 4.7 Consensus size: 35
19567432 ATAATTAAAA
*
19567442 TATATAATTTAATAAAATTCTTAATAATTAATATTCT
1 TATATAATTTAATAAAA-TCATAATAATTAATATT-T
* *
19567479 TATATGAATTTACTCAAATCATAAT-A-TAGATAATTT
1 TATAT-AATTTAATAAAATCATAATAATTA-AT-ATTT
* * * * *
19567515 AACATAATTATTATTAAATAT-ATTATAATTAA-A--A
1 TATATAA-T-TTAATAAA-ATCATAATAATTAATATTT
* *
19567549 TATATAATTTAATAAAATTCTTAATAATCAATATTCT
1 TATATAATTTAATAAAA-TCATAATAATTAATATT-T
*
19567586 TATATGAATTTACTAAAATCATAATA
1 TATAT-AATTTAATAAAATCATAATA
19567612 TATAATACTA
Statistics
Matches: 100, Mismatches: 18, Indels: 30
0.68 0.12 0.20
Matches are distributed among these distances:
31 1 0.01
32 8 0.08
33 9 0.09
34 6 0.06
35 4 0.04
36 9 0.09
37 36 0.36
38 25 0.25
39 2 0.02
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (35 bp):
TATATAATTTAATAAAATCATAATAATTAATATTT
Found at i:19567664 original size:107 final size:107
Alignment explanation
Indices: 19567431--19567669 Score: 330
Period size: 107 Copynumber: 2.3 Consensus size: 107
19567421 TATAATTTAA
* *
19567431 TATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAA
1 TATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAA
* * * * *
19567496 ATCATAATATAGATAATTTAACATAATTATTATTAAATATAT
66 ATCATAATATAAATAATATAAAATAATAATTATGAAATATAT
19567538 TATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAA
1 TATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAA
*
19567603 ATCATAATATATAATACTATAAAAT-ATAATT-TGAAATA-AT
66 ATCATAATATA-AATAATATAAAATAATAATTATGAAATATAT
19567643 TA-ATATT-AAATATAT--TTTAATTAAAAT
1 TATA-ATTAAAATATATAATTTAA-TAAAAT
19567670 ATATGATTTA
Statistics
Matches: 121, Mismatches: 8, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
102 5 0.04
103 6 0.05
104 9 0.07
105 7 0.06
106 6 0.05
107 79 0.65
108 9 0.07
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (107 bp):
TATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAA
ATCATAATATAAATAATATAAAATAATAATTATGAAATATAT
Found at i:19569025 original size:17 final size:17
Alignment explanation
Indices: 19569003--19569036 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
19568993 GCACCTAATA
19569003 TAACTCATATTTCAAAT
1 TAACTCATATTTCAAAT
19569020 TAACTCATATTTCAAAT
1 TAACTCATATTTCAAAT
19569037 ACCACAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (17 bp):
TAACTCATATTTCAAAT
Found at i:19591712 original size:21 final size:20
Alignment explanation
Indices: 19591686--19591726 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
19591676 AAAGAAAGAA
19591686 AAAGAAATAGAAATAGAAAAG
1 AAAGAAA-AGAAATAGAAAAG
19591707 AAAG-AAAGAAATAGAGAAAG
1 AAAGAAAAGAAATAGA-AAAG
19591727 CCAAACGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 9 0.47
20 6 0.32
21 4 0.21
ACGTcount: A:0.71, C:0.00, G:0.22, T:0.07
Consensus pattern (20 bp):
AAAGAAAAGAAATAGAAAAG
Found at i:19591726 original size:43 final size:44
Alignment explanation
Indices: 19591678--19591761 Score: 100
Period size: 44 Copynumber: 1.9 Consensus size: 44
19591668 GAATAAAGAA
*
19591678 AGAAAG-AAAAAGAAATAGAAATAGAAAAGAAAG-AAAGAAATAG
1 AGAAAGCAAAAAGAAATAGAAAGA-AAAAGAAAGAAAAGAAATAG
* * **
19591721 AGAAAGCCAAACGAAATAGGGAGAAAAAGAAAGAAAAGAAA
1 AGAAAGCAAAAAGAAATAGAAAGAAAAAGAAAGAAAAGAAA
19591762 GAAGGAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
43 15 0.44
44 19 0.56
ACGTcount: A:0.69, C:0.04, G:0.23, T:0.05
Consensus pattern (44 bp):
AGAAAGCAAAAAGAAATAGAAAGAAAAAGAAAGAAAAGAAATAG
Found at i:19592454 original size:24 final size:24
Alignment explanation
Indices: 19592427--19592473 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
19592417 ATTGAAATGG
19592427 ATTG-ATTTAATATGTGA-TGAATTT
1 ATTGAATTT-ATAT-TGATTGAATTT
19592451 ATTGAATTTATATTGATTGAATT
1 ATTGAATTTATATTGATTGAATT
19592474 GGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 14 0.67
25 4 0.19
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (24 bp):
ATTGAATTTATATTGATTGAATTT
Found at i:19594533 original size:42 final size:42
Alignment explanation
Indices: 19594488--19594684 Score: 157
Period size: 42 Copynumber: 4.7 Consensus size: 42
19594478 CCGGAGGCTG
*
19594488 AACAGAAGCTCATGAA-AGCTAAACAGAAACCCATAAGGGTTG
1 AACAGAAGCTCAT-AAGAGCTAAACAGAAACCCATAAGGGTTA
* * * *
19594530 AACAGAAGCTCGTAAGAGCTGAAC-GAAAACCCATAAAGTTTA
1 AACAGAAGCTCATAAGAGCTAAACAG-AAACCCATAAGGGTTA
* * * * * *
19594572 AATAGAAGCTCA-AATGAGCTAAACGGAAACTCGTATGTGTTA
1 AACAGAAGCTCATAA-GAGCTAAACAGAAACCCATAAGGGTTA
* * * * * * * * *
19594614 AACAAAAGCTCAAAAAAGTTGAACGGAAACTCATATGAGTTA
1 AACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGTTA
*
19594656 AACAGAAGCTCGTAAGAGCTAAACAGAAA
1 AACAGAAGCTCATAAGAGCTAAACAGAAA
19594685 GTAAAACACG
Statistics
Matches: 122, Mismatches: 28, Indels: 10
0.76 0.17 0.06
Matches are distributed among these distances:
41 5 0.04
42 114 0.93
43 3 0.02
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (42 bp):
AACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGTTA
Found at i:19594552 original size:21 final size:21
Alignment explanation
Indices: 19594484--19594553 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
19594474 AAGCCCGGAG
19594484 GCTGAACAGAAGCTCATGAA-A
1 GCTGAACAGAAGCTCAT-AAGA
* * * *
19594505 GCTAAACAGAAACCCATAAGG
1 GCTGAACAGAAGCTCATAAGA
* *
19594526 GTTGAACAGAAGCTCGTAAGA
1 GCTGAACAGAAGCTCATAAGA
19594547 GCTGAAC
1 GCTGAAC
19594554 GAAAACCCAT
Statistics
Matches: 37, Mismatches: 11, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
20 2 0.05
21 35 0.95
ACGTcount: A:0.41, C:0.20, G:0.24, T:0.14
Consensus pattern (21 bp):
GCTGAACAGAAGCTCATAAGA
Found at i:19596097 original size:175 final size:175
Alignment explanation
Indices: 19595793--19596116 Score: 551
Period size: 175 Copynumber: 1.9 Consensus size: 175
19595783 CAATTTGGTC
19595793 CAACTCATCCATTTTTCTTAGTTTCTAGATCCTTCCACCCTTAAAATATTTACACTATTGGTCCT
1 CAACTCATCCATTTTTCTTAGTTTCTAGATCCTTCCACCCTTAAAATATTTACACTATTGGTCCT
* * * *
19595858 TCAAATTTTTTATATTTACACTTTAACCCTTCAAATTTTAAGTATTTACTTTTGGACCACAAAAC
66 TCAAATTTTTCATATTTACACTTTAACCCCTCAAATTTTAAGTATTTACTCTTGGACAACAAAAC
* *
19595923 TTTTCTCACTTTTTCAATTTAGTCCTTTCTTGAATTAATATATCA
131 CTTTCTCACTTTTACAATTTAGTCCTTTCTTGAATTAATATATCA
*
19595968 CAACTCATCCATTTTTCTTAGTTTCTAGATCCTTCCACCCTTAAAATATTTACACTATTGGTTCT
1 CAACTCATCCATTTTTCTTAGTTTCTAGATCCTTCCACCCTTAAAATATTTACACTATTGGTCCT
* *
19596033 TCAACTTTTTCATATTTACACTTTAACCCCTCAAATTTTGAGTATTTACTCTTGTG-CAACAAAA
66 TCAAATTTTTCATATTTACACTTTAACCCCTCAAATTTTAAGTATTTACTCTTG-GACAACAAAA
19596097 CCTTTCTCACTTTTACAATT
130 CCTTTCTCACTTTTACAATT
19596117 ATTAATATAT
Statistics
Matches: 139, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
175 138 0.99
176 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.05, T:0.44
Consensus pattern (175 bp):
CAACTCATCCATTTTTCTTAGTTTCTAGATCCTTCCACCCTTAAAATATTTACACTATTGGTCCT
TCAAATTTTTCATATTTACACTTTAACCCCTCAAATTTTAAGTATTTACTCTTGGACAACAAAAC
CTTTCTCACTTTTACAATTTAGTCCTTTCTTGAATTAATATATCA
Found at i:19599782 original size:40 final size:41
Alignment explanation
Indices: 19599717--19599799 Score: 114
Period size: 40 Copynumber: 2.0 Consensus size: 41
19599707 TACTGAACTG
* * *
19599717 AATATTGTTTCTGAGTACTGAATTGAATTGTGAAGTTACTA
1 AATATTGTTTATGAGTACTGAATTGAACTGTGAAATTACTA
* *
19599758 AATATTG-TTATGTGTACTGCATTGAACTGTGAAATTACTA
1 AATATTGTTTATGAGTACTGAATTGAACTGTGAAATTACTA
19599798 AA
1 AA
19599800 GTAATGAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
40 30 0.81
41 7 0.19
ACGTcount: A:0.34, C:0.08, G:0.18, T:0.40
Consensus pattern (41 bp):
AATATTGTTTATGAGTACTGAATTGAACTGTGAAATTACTA
Found at i:19604001 original size:32 final size:32
Alignment explanation
Indices: 19603957--19604023 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
19603947 CGTTACATTT
* *
19603957 CAGTCCGGTGCCGCCTTTGGCAGGCCCTCCAC
1 CAGTCCGATGCCGCCTGTGGCAGGCCCTCCAC
19603989 CAGTCCGATGCCGCCTGTGGCAGGCCCTCCAC
1 CAGTCCGATGCCGCCTGTGGCAGGCCCTCCAC
19604021 CAG
1 CAG
19604024 GCTGTCATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.12, C:0.43, G:0.28, T:0.16
Consensus pattern (32 bp):
CAGTCCGATGCCGCCTGTGGCAGGCCCTCCAC
Found at i:19608581 original size:44 final size:44
Alignment explanation
Indices: 19608314--19608943 Score: 258
Period size: 44 Copynumber: 14.4 Consensus size: 44
19608304 GATCTGTTCT
* * * * **
19608314 CTGCAACTTCA-GAAGGATAAGATCTAAGGTTTTAATCCACTCCA
1 CTGCAACTTCAGGGA-GATAAGATTTGAGGCTTTAATCTGCTCCA
* * *
19608358 CTGCAACTTCAGGGAGATAGGATTAT-CGGCTTTAATCTACTCCA
1 CTGCAACTTCAGGGAGATAAGATT-TGAGGCTTTAATCTGCTCCA
* * * *
19608402 CTGCAACTTTAGGGAGATAAGATTTGCCA-TCTTCAGTCTGC-CTCA
1 CTGCAACTTCAGGGAGATAAGATTTG--AGGCTTTAATCTGCTC-CA
* ** *
19608447 CTACAACTTCA-GGAGGATAAGGCTT---GCTTACGTAGTCTGCTCCA
1 CTGCAACTTCAGGGA-GATAAGATTTGAGGCTT---TAATCTGCTCCA
* * * * * * *
19608491 CTGCAACCTCAGGGAGATATGACTAGATGC---GATCTGCT-CT
1 CTGCAACTTCAGGGAGATAAGATTTGAGGCTTTAATCTGCTCCA
* * * * *
19608531 CTGCAACTTCAGAGAGGTACGATTTGAGGTTTTAATTTGCTCCA
1 CTGCAACTTCAGGGAGATAAGATTTGAGGCTTTAATCTGCTCCA
* *
19608575 CTGCAACTTCAGGGAGATAGGATTAT-CGGCTTTAATCTGCTCCA
1 CTGCAACTTCAGGGAGATAAGATT-TGAGGCTTTAATCTGCTCCA
* * * * **
19608619 CTGTAACTTCAGGGAGATAAGATTTGCGATCTTCAGGCTGC-CTCA
1 CTGCAACTTCAGGGAGATAAGATTTGAG-GCTTTAATCTGCTC-CA
* * *
19608664 CTGTAACTTCA-GGAGGATAAGACTT---GCTTACGTAGTCTGCTCCA
1 CTGCAACTTCAGGGA-GATAAGATTTGAGGCTT---TAATCTGCTCCA
* * * ** *
19608708 CTGCAACCTCAGGGAGATATGACTAAATGCGATTT-A-CT-CT---
1 CTGCAACTTCAGGGAGATAAGATTTGA-G-GCTTTAATCTGCTCCA
* * * * *
19608748 CTGCAACTTCAGAGAGGTAAGATTTGAGGTTTTAATCCGTTCCA
1 CTGCAACTTCAGGGAGATAAGATTTGAGGCTTTAATCTGCTCCA
** * *
19608792 CTGCAACTTCAGAAAGATAGGATTAT-CGGCTTTAATCTGCTCCA
1 CTGCAACTTCAGGGAGATAAGATT-TGAGGCTTTAATCTGCTCCA
* * * *
19608836 CTGCAACTTCAGGGAGATAAGATTTGCCA-TCTTCAGTCTAC-CTCA
1 CTGCAACTTCAGGGAGATAAGATTTG--AGGCTTTAATCTGCTC-CA
* * *
19608881 CTGCAACTTCAGGGGGATAAGACTT---GCTTACATAGTCTGCTCCA
1 CTGCAACTTCAGGGAGATAAGATTTGAGGCTT---TAATCTGCTCCA
*
19608925 CTGCAACCTCAGGGAGATA
1 CTGCAACTTCAGGGAGATA
19608944 TGACTAGATG
Statistics
Matches: 445, Mismatches: 92, Indels: 98
0.70 0.14 0.15
Matches are distributed among these distances:
38 4 0.01
39 2 0.00
40 44 0.10
41 16 0.04
43 11 0.02
44 258 0.58
45 104 0.23
46 1 0.00
47 2 0.00
49 3 0.01
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (44 bp):
CTGCAACTTCAGGGAGATAAGATTTGAGGCTTTAATCTGCTCCA
Found at i:19608644 original size:217 final size:217
Alignment explanation
Indices: 19608262--19608972 Score: 1172
Period size: 217 Copynumber: 3.3 Consensus size: 217
19608252 TTTTCTATCT
* * *
19608262 TAGTCTACTCCACTGCAACCTCAGAGAGATATGACTAGATGCGATCTGTTCTCTGCAACTTCAGA
1 TAGTCTGCTCCACTGCAACCTCAGGGAGATATGACTAGATGCGATCTGCTCTCTGCAACTTCAGA
* * *
19608327 -AGGATAAGATCTAAGGTTTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTT
66 GAGG-TAAGATTTGAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTT
* * *
19608391 AATCTACTCCACTGCAACTTTAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTACAACTT
130 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTT
*
19608456 CAGGAGGATAAGGCTTGCTTACG
195 CAGGAGGATAAGACTTGCTTACG
19608479 TAGTCTGCTCCACTGCAACCTCAGGGAGATATGACTAGATGCGATCTGCTCTCTGCAACTTCAGA
1 TAGTCTGCTCCACTGCAACCTCAGGGAGATATGACTAGATGCGATCTGCTCTCTGCAACTTCAGA
* **
19608544 GAGGTACGATTTGAGGTTTTAATTTGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTA
66 GAGGTAAGATTTGAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTA
* * * *
19608609 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATTTGCGATCTTCAGGCTGCCTCACTGTAACTTC
131 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTC
19608674 AGGAGGATAAGACTTGCTTACG
196 AGGAGGATAAGACTTGCTTACG
* * *
19608696 TAGTCTGCTCCACTGCAACCTCAGGGAGATATGACTAAATGCGATTTACTCTCTGCAACTTCAGA
1 TAGTCTGCTCCACTGCAACCTCAGGGAGATATGACTAGATGCGATCTGCTCTCTGCAACTTCAGA
* **
19608761 GAGGTAAGATTTGAGGTTTTAATCCGTTCCACTGCAACTTCAGAAAGATAGGATTATCGGCTTTA
66 GAGGTAAGATTTGAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTA
*
19608826 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTACCTCACTGCAACTTC
131 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTC
* *
19608891 AGGGGGATAAGACTTGCTTACA
196 AGGAGGATAAGACTTGCTTACG
19608913 TAGTCTGCTCCACTGCAACCTCAGGGAGATATGACTAGATGCGATCTGCTCTCTGCAACT
1 TAGTCTGCTCCACTGCAACCTCAGGGAGATATGACTAGATGCGATCTGCTCTCTGCAACT
19608973 AGATATGACT
Statistics
Matches: 457, Mismatches: 36, Indels: 2
0.92 0.07 0.00
Matches are distributed among these distances:
217 454 0.99
218 3 0.01
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (217 bp):
TAGTCTGCTCCACTGCAACCTCAGGGAGATATGACTAGATGCGATCTGCTCTCTGCAACTTCAGA
GAGGTAAGATTTGAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTA
ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTC
AGGAGGATAAGACTTGCTTACG
Found at i:19611348 original size:23 final size:23
Alignment explanation
Indices: 19611322--19611419 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
19611312 ATAAGTGCCA
19611322 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
19611345 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
19611368 CACTG-GATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
19611390 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
19611413 CACTGAT
1 CACTGAT
19611420 CAATAACACT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
22 20 0.29
23 49 0.71
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:19611387 original size:45 final size:45
Alignment explanation
Indices: 19611329--19611417 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
19611319 CCACACTGAT
* *
19611329 ATGTAGCCGAAGCTACCACTGATATGTAGCCGAAGCTACCACTGG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
19611374 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
19611418 ATCAATAACA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.19
Consensus pattern (45 bp):
ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
Found at i:19625019 original size:27 final size:30
Alignment explanation
Indices: 19624964--19625020 Score: 75
Period size: 27 Copynumber: 2.0 Consensus size: 30
19624954 AAGGAGAAAA
*
19624964 AATACAAAATGAAAAAAATGAAAATTAATT
1 AATACAAAATGAAAAAAATGAAAACTAATT
*
19624994 AATA-AAAAT-AAAAAAA-GAGAACTAATT
1 AATACAAAATGAAAAAAATGAAAACTAATT
19625021 TGAACTATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 9 0.36
28 7 0.28
29 5 0.20
30 4 0.16
ACGTcount: A:0.68, C:0.04, G:0.07, T:0.21
Consensus pattern (30 bp):
AATACAAAATGAAAAAAATGAAAACTAATT
Found at i:19635353 original size:26 final size:26
Alignment explanation
Indices: 19635324--19635373 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
19635314 AAGTTAATAA
* *
19635324 ATTATCTTATTTAAATATATAATTTT
1 ATTAACTTATTTAAATATAAAATTTT
19635350 ATTAACTTATTTAAATATAAAATT
1 ATTAACTTATTTAAATATAAAATT
19635374 AATTAAACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (26 bp):
ATTAACTTATTTAAATATAAAATTTT
Found at i:19635383 original size:26 final size:26
Alignment explanation
Indices: 19635323--19635379 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
19635313 AAAGTTAATA
* *
19635323 AATTATCTTATTTAAATATATAATTT
1 AATTAACTTATTTAAATATATAAATT
*
19635349 TATTAACTTATTTAAATATA-AAATT
1 AATTAACTTATTTAAATATATAAATT
19635374 AATTAA
1 AATTAA
19635380 ACTTTATCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
25 9 0.33
26 18 0.67
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (26 bp):
AATTAACTTATTTAAATATATAAATT
Found at i:19638720 original size:9 final size:9
Alignment explanation
Indices: 19638702--19638747 Score: 76
Period size: 9 Copynumber: 5.2 Consensus size: 9
19638692 TTTGGTTAAA
*
19638702 AATTACCCG
1 AATTAACCG
19638711 AATTAACCG
1 AATTAACCG
19638720 AATTAACCG
1 AATTAACCG
19638729 AATTAACCG
1 AATTAACCG
19638738 AATT-ACCG
1 AATTAACCG
19638746 AA
1 AA
19638748 AAATACCTGA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
8 6 0.17
9 30 0.83
ACGTcount: A:0.43, C:0.24, G:0.11, T:0.22
Consensus pattern (9 bp):
AATTAACCG
Found at i:19638931 original size:13 final size:13
Alignment explanation
Indices: 19638910--19638943 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
19638900 TTTTAGTTTT
*
19638910 ATTGGGTTGGGTA
1 ATTGAGTTGGGTA
19638923 ATTGAGTTGGGTA
1 ATTGAGTTGGGTA
19638936 ATTGAGTT
1 ATTGAGTT
19638944 TGGGCTGGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.38, T:0.41
Consensus pattern (13 bp):
ATTGAGTTGGGTA
Found at i:19646465 original size:30 final size:31
Alignment explanation
Indices: 19646426--19646485 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
19646416 AGGGGTAGGA
19646426 TGGGAAGGGAATA-AAAGTTTTAGGGAAAAAG
1 TGGGAAGGGAATACAAA-TTTTAGGGAAAAAG
* *
19646457 TGGG-AGGGAGTACAAATTTTGGGGAAAAA
1 TGGGAAGGGAATACAAATTTTAGGGAAAAA
19646486 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 19 0.73
31 7 0.27
ACGTcount: A:0.42, C:0.02, G:0.37, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATACAAATTTTAGGGAAAAAG
Found at i:19654711 original size:111 final size:110
Alignment explanation
Indices: 19654546--19654869 Score: 454
Period size: 112 Copynumber: 2.9 Consensus size: 110
19654536 GGGCATTTAA
* *
19654546 AAAAAATAATTTTGGGTGCTGGTCAATAGATGGCCAGCACCAAGTACATTTTTCGGCTCCCAATG
1 AAAAAATAA-TTTGGGTGCTGGCCAGTAGATGGCCAGCACCAAGTACATTTTTCGGCTCCCAA-G
19654611 AACTTTTATTTTACTTTGGGACACTGATGGCCGGCACCAGTGTCATTT
64 AACTTTT-TTTTACTTTGGGACACTGATGGCCGGCACCAGTGTCATTT
* * *
19654659 AAAAAA-AATTTGGGTGCTGGCCAGTAGATGGTCAGCACCAAGTACATGTTTCGGCTCCCAAGGC
1 AAAAAATAATTTGGGTGCTGGCCAGTAGATGGCCAGCACCAAGTACATTTTTCGGCTCCCAA-GA
* *
19654723 ACTTTTTTTTACTTTGGTACACTGATGGCCGACACCAGTGTCATTT
65 ACTTTTTTTTACTTTGGGACACTGATGGCCGGCACCAGTGTCATTT
* * * *
19654769 AAAGAAATATTTTGGGTG-TCGGCCAGCAGATGGCCGGCACCAAGTACATTTTTCGGCTCCTAAG
1 AAA-AAATAATTTGGGTGCT-GGCCAGTAGATGGCCAGCACCAAGTACATTTTTCGGCTCCCAAG
* *
19654833 GACTTTTTTTTTACTTTGGGACACTGATGTCCGGCAC
64 AAC-TTTTTTTTACTTTGGGACACTGATGGCCGGCAC
19654870 TACCTTTTTT
Statistics
Matches: 189, Mismatches: 18, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
110 41 0.22
111 63 0.33
112 79 0.42
113 6 0.03
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (110 bp):
AAAAAATAATTTGGGTGCTGGCCAGTAGATGGCCAGCACCAAGTACATTTTTCGGCTCCCAAGAA
CTTTTTTTTACTTTGGGACACTGATGGCCGGCACCAGTGTCATTT
Found at i:19655702 original size:90 final size:90
Alignment explanation
Indices: 19655588--19655780 Score: 305
Period size: 90 Copynumber: 2.1 Consensus size: 90
19655578 TTTGTATCTG
* *
19655588 TAAATTTAATTTAGCCCGTATTATATGTAGTTTGAATTTAAAATTTTCGTGTATTAATTTTACCT
1 TAAATTTAATTTAGCCCGTATTATATGTAGTTTGAATTTAAAATTTTCGTGTATTAAATTTACCC
*
19655653 ATCTGTTTTTAGTTTGTTGGGTGTT
66 ATCTGTTTATAGTTTGTTGGGTGTT
*** * *
19655678 TAAATTTAATTTAGTTTGTGTTATATGTAGTTTGAATTTAAAATTTTTGTGTATTAAATTTACCC
1 TAAATTTAATTTAGCCCGTATTATATGTAGTTTGAATTTAAAATTTTCGTGTATTAAATTTACCC
*
19655743 ATCTGTTTATAGTTTTTTGGGTGTT
66 ATCTGTTTATAGTTTGTTGGGTGTT
19655768 TAAATTTAATTTA
1 TAAATTTAATTTA
19655781 ATGCGTATTA
Statistics
Matches: 94, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 94 1.00
ACGTcount: A:0.26, C:0.06, G:0.15, T:0.53
Consensus pattern (90 bp):
TAAATTTAATTTAGCCCGTATTATATGTAGTTTGAATTTAAAATTTTCGTGTATTAAATTTACCC
ATCTGTTTATAGTTTGTTGGGTGTT
Found at i:19658546 original size:22 final size:22
Alignment explanation
Indices: 19658505--19658561 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
19658495 TCCATTTCCA
*
19658505 TTTCATTTAAA-TTATCTTTTT
1 TTTCATTTAAATTTATATTTTT
19658526 TTTCTATTTAAATTTA-ATTTTT
1 TTTC-ATTTAAATTTATATTTTT
* *
19658548 TCTCATTTCAATTT
1 TTTCATTTAAATTT
19658562 TTTTCATATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 13 0.42
22 15 0.48
23 3 0.10
ACGTcount: A:0.25, C:0.11, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTCATTTAAATTTATATTTTT
Found at i:19658548 original size:20 final size:21
Alignment explanation
Indices: 19658523--19658561 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
19658513 AAATTATCTT
19658523 TTTTTTCT-ATTTAAATTTAA
1 TTTTTTCTCATTTAAATTTAA
*
19658543 TTTTTTCTCATTTCAATTT
1 TTTTTTCTCATTTAAATTT
19658562 TTTTCATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTTTCTCATTTAAATTTAA
Found at i:19658622 original size:18 final size:17
Alignment explanation
Indices: 19658596--19658629 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
19658586 CAGATATTAA
19658596 TTTTTTTTTCATTTCAG
1 TTTTTTTTTCATTTCAG
19658613 TTTTTGTTTTCATTTCA
1 TTTTT-TTTTCATTTCA
19658630 ATTTATAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.12, C:0.12, G:0.06, T:0.71
Consensus pattern (17 bp):
TTTTTTTTTCATTTCAG
Found at i:19658693 original size:5 final size:5
Alignment explanation
Indices: 19658655--19658754 Score: 65
Period size: 5 Copynumber: 18.4 Consensus size: 5
19658645 TCTTTTAAAC
* * * *
19658655 TTTCA TTCCA TTTCA TAATCA TTACAA ATTCA TTTCA TTTCA TTTCA TATTCA
1 TTTCA TTTCA TTTCA T-TTCA TTTC-A TTTCA TTTCA TTTCA TTTCA T-TTCA
* * *
19658708 TTACAAA TTACA TTTCA TTTCA TATTCA TTTAATA TTTCA TTTCA TT
1 TTTC--A TTTCA TTTCA TTTCA T-TTCA TTT--CA TTTCA TTTCA TT
19658755 AATTTTTTTT
Statistics
Matches: 75, Mismatches: 12, Indels: 16
0.73 0.12 0.16
Matches are distributed among these distances:
5 49 0.65
6 17 0.23
7 9 0.12
ACGTcount: A:0.31, C:0.18, G:0.00, T:0.51
Consensus pattern (5 bp):
TTTCA
Found at i:19658699 original size:32 final size:33
Alignment explanation
Indices: 19658655--19658736 Score: 130
Period size: 32 Copynumber: 2.5 Consensus size: 33
19658645 TCTTTTAAAC
*
19658655 TTTCATTCCATTTCATAATCATTACAAATT-CA
1 TTTCATTTCATTTCATAATCATTACAAATTACA
*
19658687 TTTCATTTCATTTCATATTCATTACAAATTACA
1 TTTCATTTCATTTCATAATCATTACAAATTACA
19658720 TTTCATTTCATATTCAT
1 TTTCATTTCAT-TTCAT
19658737 TTAATATTTC
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
32 28 0.61
33 13 0.28
34 5 0.11
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.49
Consensus pattern (33 bp):
TTTCATTTCATTTCATAATCATTACAAATTACA
Found at i:19658724 original size:28 final size:28
Alignment explanation
Indices: 19658658--19658754 Score: 106
Period size: 28 Copynumber: 3.3 Consensus size: 28
19658648 TTTAAACTTT
* *
19658658 CATTCCATTTCATAATCATTACAAATTCA
1 CATTTCATTTCATATTCATTACAAATT-A
19658687 TTTCATTTCATTTCATATTCATTACAAATTA
1 ---CATTTCATTTCATATTCATTACAAATTA
* *
19658718 CATTTCATTTCATATTCATTTA-ATATTT
1 CATTTCATTTCATATTCA-TTACAAATTA
19658746 CATTTCATT
1 CATTTCATT
19658755 AATTTTTTTT
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
28 31 0.52
29 3 0.05
31 1 0.02
32 25 0.42
ACGTcount: A:0.32, C:0.19, G:0.00, T:0.49
Consensus pattern (28 bp):
CATTTCATTTCATATTCATTACAAATTA
Found at i:19658737 original size:11 final size:11
Alignment explanation
Indices: 19658663--19658753 Score: 77
Period size: 11 Copynumber: 8.7 Consensus size: 11
19658653 ACTTTCATTC
*
19658663 CATTTCATAAT
1 CATTTCATATT
* *
19658674 CATTACAAATT
1 CATTTCATATT
19658685 CATTTCAT-TT
1 CATTTCATATT
19658695 CATTTCATATT
1 CATTTCATATT
*
19658706 CATTACA-A--
1 CATTTCATATT
*
19658714 -ATTACAT-TT
1 CATTTCATATT
19658723 CATTTCATATT
1 CATTTCATATT
*
19658734 CATTTAATATTT
1 CATTTCATA-TT
19658746 CATTTCAT
1 CATTTCAT
19658754 TAATTTTTTT
Statistics
Matches: 64, Mismatches: 9, Indels: 13
0.74 0.10 0.15
Matches are distributed among these distances:
7 6 0.09
10 17 0.27
11 32 0.50
12 9 0.14
ACGTcount: A:0.33, C:0.18, G:0.00, T:0.49
Consensus pattern (11 bp):
CATTTCATATT
Found at i:19659230 original size:17 final size:17
Alignment explanation
Indices: 19659208--19659249 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
19659198 TTCTATTTAA
19659208 ATTTAATTTTTTTTCTC
1 ATTTAATTTTTTTTCTC
19659225 ATTTAA-TTTTTTTCTC
1 ATTTAATTTTTTTTCTC
*
19659241 ATTTCATTT
1 ATTTAATTT
19659250 AAGTTGTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 15 0.65
17 8 0.35
ACGTcount: A:0.19, C:0.12, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTTAATTTTTTTTCTC
Found at i:19659297 original size:20 final size:20
Alignment explanation
Indices: 19659260--19659298 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
19659250 AAGTTGTCTT
*
19659260 TTTTTCCATTTTAATTTATG
1 TTTTTCCATATTAATTTATG
19659280 TTTTTCCATATTAATTTAT
1 TTTTTCCATATTAATTTAT
19659299 ATATTTCATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.10, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTTTCCATATTAATTTATG
Found at i:19659305 original size:20 final size:20
Alignment explanation
Indices: 19659262--19659305 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
19659252 GTTGTCTTTT
* * *
19659262 TTTCCATTTTAATTTATGTT
1 TTTCCATATTAATTTATATA
19659282 TTTCCATATTAATTTATATA
1 TTTCCATATTAATTTATATA
19659302 TTTC
1 TTTC
19659306 ATCTTTTTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.25, C:0.11, G:0.02, T:0.61
Consensus pattern (20 bp):
TTTCCATATTAATTTATATA
Found at i:19659425 original size:29 final size:29
Alignment explanation
Indices: 19659367--19659441 Score: 75
Period size: 28 Copynumber: 2.6 Consensus size: 29
19659357 ATTAAATTTG
*
19659367 AATTTCA-TTTCATTTCATTCCCTTATTTT
1 AATTTCATTTTCATTTCATT-CCTTACTTT
*
19659396 AATTTCATTTTCATTTCACTT-TTTACTTT
1 AATTTCATTTTCATTTCA-TTCCTTACTTT
* *
19659425 -ATTTGATTTTCAGTTCA
1 AATTTCATTTTCATTTCA
19659442 ATTAATATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
28 15 0.38
29 13 0.32
30 10 0.25
31 2 0.05
ACGTcount: A:0.21, C:0.17, G:0.03, T:0.59
Consensus pattern (29 bp):
AATTTCATTTTCATTTCATTCCTTACTTT
Found at i:19659514 original size:22 final size:22
Alignment explanation
Indices: 19659447--19659514 Score: 59
Period size: 22 Copynumber: 3.1 Consensus size: 22
19659437 GTTCAATTAA
*
19659447 TATAATTTAATGTGTTTTAAAA
1 TATAATTTAATGTGTTTTAAAT
* * **
19659469 TA-AATATGT-ATGTATATTGTAT
1 TATAAT-T-TAATGTGTTTTAAAT
19659491 TATAATTTAATGTGTTTTAAAT
1 TATAATTTAATGTGTTTTAAAT
19659513 TA
1 TA
19659515 GGAATAAGAA
Statistics
Matches: 33, Mismatches: 9, Indels: 8
0.66 0.18 0.16
Matches are distributed among these distances:
21 4 0.12
22 25 0.76
23 4 0.12
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.51
Consensus pattern (22 bp):
TATAATTTAATGTGTTTTAAAT
Found at i:19662771 original size:113 final size:111
Alignment explanation
Indices: 19662640--19662965 Score: 393
Period size: 113 Copynumber: 2.9 Consensus size: 111
19662630 GAAAAAGGTG
* * ** * * * *
19662640 GTGCGGGCCATCAATGTCCCAAAGTAAAAAAAATGCCTTAAGAGCTGAAAGATGGACTTGGTGTC
1 GTGCAGGCCATCAGTGTCCCAAAGTAAAAAAAATGCCTTGGGAGCCGAAAAATGTACTTGGTGCC
*
19662705 GACCATTTACTGGCCAGCACCAAGAAAAAAAAATTTAAAATGACACTA
66 GACCATCTACTGGCCAGCACC-A-AAAAAAAAATTTAAAATGACACTA
* * *
19662753 GTGCTGGCCATCAGTGTCCCAAAGTAAAAAAAATGCATTGGGAACCGAAAAATGTACTTGGTGCC
1 GTGCAGGCCATCAGTGTCCCAAAGTAAAAAAAATGCCTTGGGAGCCGAAAAATGTACTTGGTGCC
* * * ** *
19662818 GACCATCTACTCGCTAGCACC-CAAAAAACTTTTTAAATGACACTA
66 GACCATCTACTGGCCAGCACCAAAAAAAAAATTTAAAATGACACTA
* ** *
19662863 GTGCAGGCCGTCAGTGTCCCAAAGTAAAAAAAAGTTTCTTGGGAGCCGAAAAATGTACTTGGTAC
1 GTGCAGGCCATCAGTGTCCCAAAGTAAAAAAAA-TGCCTTGGGAGCCGAAAAATGTACTTGGTGC
* * *
19662928 CGGCCATCTATTGGCCAGCATCAAAAAAAAAATTTAAA
65 CGACCATCTACTGGCCAGCACCAAAAAAAAAATTTAAA
19662966 TGCCTCTGGT
Statistics
Matches: 178, Mismatches: 33, Indels: 5
0.82 0.15 0.02
Matches are distributed among these distances:
110 51 0.29
111 43 0.24
112 11 0.06
113 73 0.41
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.22
Consensus pattern (111 bp):
GTGCAGGCCATCAGTGTCCCAAAGTAAAAAAAATGCCTTGGGAGCCGAAAAATGTACTTGGTGCC
GACCATCTACTGGCCAGCACCAAAAAAAAAATTTAAAATGACACTA
Found at i:19662993 original size:50 final size:51
Alignment explanation
Indices: 19662922--19663017 Score: 115
Period size: 50 Copynumber: 1.9 Consensus size: 51
19662912 AAAATGTACT
* ** * *
19662922 TGGTACCGGCCATCTATTGGCCAGCATC-AAAAAAAAAATTTAAATGCCTC
1 TGGTACCGGCCATCTAATGGCCAAAACCGAAAAAAAAAATTCAAATGCCTC
*
19662972 TGGTGCCGGCCAT-TACATGGCCAAAACCGAAAAAAAAAATTCAAAT
1 TGGTACCGGCCATCTA-ATGGCCAAAACCGAAAAAAAAAATTCAAAT
19663018 ACTAGTATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
49 2 0.05
50 20 0.53
51 16 0.42
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.21
Consensus pattern (51 bp):
TGGTACCGGCCATCTAATGGCCAAAACCGAAAAAAAAAATTCAAATGCCTC
Found at i:19667840 original size:28 final size:28
Alignment explanation
Indices: 19667808--19667865 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
19667798 ATATAGAGGA
*
19667808 AAGAAAGGCTTTCATGTAAAAACATTTT
1 AAGAAAGGATTTCATGTAAAAACATTTT
19667836 AAGAAAGGATTTCATGTAAAAACATTTT
1 AAGAAAGGATTTCATGTAAAAACATTTT
19667864 AA
1 AA
19667866 CCCCCTACAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.47, C:0.09, G:0.14, T:0.31
Consensus pattern (28 bp):
AAGAAAGGATTTCATGTAAAAACATTTT
Found at i:19669625 original size:191 final size:194
Alignment explanation
Indices: 19669299--19669690 Score: 646
Period size: 191 Copynumber: 2.0 Consensus size: 194
19669289 GACAAATGGA
19669299 ATCCCTGAAATTGGCCATCTGGAATTTTAAACACCCAAGTGCACTTAATGCTCAGGGTCAGGAGC
1 ATCCCTGAAATTGGCCATCTGGAATTTTAAACACCCAAGTGCACTTAATGCTCAGGGTCAGGAGC
* * *
19669364 TGCTTAAGAACCGGCAAGTGAAGTTGCTTCTGTAAAAGAACCAACATGTCCTTCTCAAGACACCA
66 TGCTTAAGAAACAGCAAGTGAAGTTGCTTCTGTAAAAGAACCAACATGCCCTTCTCAAGACACCA
*
19669429 CCATTTAAGTAAGC-A-T-TATGCAAGTTTTGGTGTACTCAAATGCTAGAATTAAATAGCTTTT
131 CCATTTAAGTAAGCTACTATATGCAAGTTTTGGTGTACTCAAATGCTAGAATTAAATAACTTTT
*
19669490 ATCCCTGAAATTGGCCATCTGGAGTTTTAAACACCCAAGTGCACTTAATGCTCAGGGTCAGGAGC
1 ATCCCTGAAATTGGCCATCTGGAATTTTAAACACCCAAGTGCACTTAATGCTCAGGGTCAGGAGC
* *
19669555 TGCTTAAGAAACAGTAAGTGAAGTTGCTTCTGTAAAAGAACCAACATGCCCTTCTCAAGACACTA
66 TGCTTAAGAAACAGCAAGTGAAGTTGCTTCTGTAAAAGAACCAACATGCCCTTCTCAAGACACCA
*
19669620 CCATTTAAGTAATCATTTAACTAGTATGCAAGTTTTGGTGTACTCAAATGCTAGAATTAAATAAC
131 CCATTTAAGTAAGC---T-ACTA-TATGCAAGTTTTGGTGTACTCAAATGCTAGAATTAAATAAC
19669685 TTTT
191 TTTT
19669689 AT
1 AT
19669691 AATCTAAATA
Statistics
Matches: 185, Mismatches: 8, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
191 137 0.74
196 1 0.01
197 1 0.01
199 46 0.25
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (194 bp):
ATCCCTGAAATTGGCCATCTGGAATTTTAAACACCCAAGTGCACTTAATGCTCAGGGTCAGGAGC
TGCTTAAGAAACAGCAAGTGAAGTTGCTTCTGTAAAAGAACCAACATGCCCTTCTCAAGACACCA
CCATTTAAGTAAGCTACTATATGCAAGTTTTGGTGTACTCAAATGCTAGAATTAAATAACTTTT
Found at i:19688334 original size:85 final size:83
Alignment explanation
Indices: 19688213--19688376 Score: 211
Period size: 85 Copynumber: 2.0 Consensus size: 83
19688203 TTGTTTTTTC
* * * **
19688213 TTTTTGCACTCATTTGGGTATTTAAACTTTCAAAATGCATAAAAAAAACTCTCAAACCTTTTCAA
1 TTTTTGCACTCAATTGGGTACTTAAACTTTCAAAATGCATAAAAAAAACCCTCAAA--TTTAAAA
19688278 AAAAGCAATTAAGCCCATTT
64 AAAAGCAATTAAGCCCATTT
* * * * * *
19688298 TTTTTGCACTCAATTGGGTACTTGAATTTTTAAAATGTATCAAAAAGACCCTCAAATTTAAAAAA
1 TTTTTGCACTCAATTGGGTACTTAAACTTTCAAAATGCATAAAAAAAACCCTCAAATTTAAAAAA
19688363 AAGCAATTAAGCCC
66 AAGCAATTAAGCCC
19688377 CTGCTTTTAT
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
83 21 0.31
85 47 0.69
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.33
Consensus pattern (83 bp):
TTTTTGCACTCAATTGGGTACTTAAACTTTCAAAATGCATAAAAAAAACCCTCAAATTTAAAAAA
AAGCAATTAAGCCCATTT
Found at i:19688411 original size:19 final size:19
Alignment explanation
Indices: 19688387--19688560 Score: 74
Period size: 19 Copynumber: 9.3 Consensus size: 19
19688377 CTGCTTTTAT
19688387 TAAAAATTATAAAAAATTA
1 TAAAAATTATAAAAAATTA
*
19688406 TAAAAAATTA-AAATAA--A
1 T-AAAAATTATAAAAAATTA
** *
19688423 TAAAAGCTAT-AAATATTA
1 TAAAAATTATAAAAAATTA
* *
19688441 T-TAAATTTTAATAAAA-TA
1 TAAAAATTATAA-AAAATTA
* ***
19688459 TTAAAA-TATTAAAGTTTTA
1 TAAAAATTA-TAAAAAATTA
* * *
19688478 TTAAAATTAGAAAAAAATA
1 TAAAAATTATAAAAAATTA
**
19688497 TAAAAATCGTAAAAAATATA
1 TAAAAATTATAAAAAAT-TA
* * **
19688517 AAAAAATTGTAAAATTTTA
1 TAAAAATTATAAAAAATTA
*
19688536 TAAAAATCATAAAAAAATTA
1 TAAAAATTAT-AAAAAATTA
19688556 TAAAA
1 TAAAA
19688561 TTTTATAAAG
Statistics
Matches: 109, Mismatches: 34, Indels: 23
0.66 0.20 0.14
Matches are distributed among these distances:
16 9 0.08
17 6 0.06
18 8 0.07
19 49 0.45
20 37 0.34
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (19 bp):
TAAAAATTATAAAAAATTA
Found at i:19688423 original size:10 final size:10
Alignment explanation
Indices: 19688383--19688415 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
19688373 GCCCCTGCTT
*
19688383 TTATTAAAAA
1 TTATAAAAAA
19688393 TTATAAAAAA
1 TTATAAAAAA
19688403 TTATAAAAAA
1 TTATAAAAAA
19688413 TTA
1 TTA
19688416 AAATAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
TTATAAAAAA
Found at i:19688556 original size:20 final size:19
Alignment explanation
Indices: 19688488--19688560 Score: 74
Period size: 20 Copynumber: 3.7 Consensus size: 19
19688478 TTAAAATTAG
*
19688488 AAAAAAATATAAAAATCGT
1 AAAAAATTATAAAAATCGT
* *
19688507 AAAAAATATAAAAAAATTGT
1 AAAAAAT-TATAAAAATCGT
** *
19688527 AAAATTTTATAAAAATCAT
1 AAAAAATTATAAAAATCGT
19688546 AAAAAAATTATAAAA
1 -AAAAAATTATAAAA
19688561 TTTTATAAAG
Statistics
Matches: 42, Mismatches: 10, Indels: 3
0.76 0.18 0.05
Matches are distributed among these distances:
19 15 0.36
20 27 0.64
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (19 bp):
AAAAAATTATAAAAATCGT
Found at i:19688574 original size:29 final size:30
Alignment explanation
Indices: 19688468--19688586 Score: 120
Period size: 29 Copynumber: 4.1 Consensus size: 30
19688458 ATTAAAATAT
* * * *
19688468 TAAAGTTTTATTAAAATTAGAAAAAAA-TA
1 TAAAATTTTATAAAAATCATAAAAAAATTA
** *
19688497 TAAAAATCGTA-AAAAAT-ATAAAAAAATTG
1 T-AAAATTTTATAAAAATCATAAAAAAATTA
19688526 TAAAATTTTATAAAAATCATAAAAAAATTA
1 TAAAATTTTATAAAAATCATAAAAAAATTA
* *
19688556 TAAAATTTTAT-AAAGTCATAAGAAAATTA
1 TAAAATTTTATAAAAATCATAAAAAAATTA
19688585 TA
1 TA
19688587 CAAAATGTAA
Statistics
Matches: 75, Mismatches: 11, Indels: 8
0.80 0.12 0.09
Matches are distributed among these distances:
28 15 0.20
29 32 0.43
30 28 0.37
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.32
Consensus pattern (30 bp):
TAAAATTTTATAAAAATCATAAAAAAATTA
Found at i:19688827 original size:18 final size:18
Alignment explanation
Indices: 19688806--19688862 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
19688796 TTTTATGATT
19688806 TTTATAAAAAATTTATAA
1 TTTATAAAAAATTTATAA
*
19688824 TTTAT-AATAATTTAT-A
1 TTTATAAAAAATTTATAA
* *
19688840 TTTTTATTAAAATTTAATAA
1 TTTATA-AAAAATTT-ATAA
19688860 TTT
1 TTT
19688863 TTCTAAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
16 5 0.16
17 9 0.29
18 11 0.35
19 2 0.06
20 4 0.13
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTATAAAAAATTTATAA
Found at i:19688838 original size:37 final size:37
Alignment explanation
Indices: 19688760--19688888 Score: 120
Period size: 37 Copynumber: 3.5 Consensus size: 37
19688750 TCGTTATTTT
* * * * **
19688760 TTTATGATTTTTATAAAATTTTACAATTTTTTTATTT
1 TTTATGATTTTTATAAAAATTTATAATTTTATAATAA
19688797 TTTATGATTTTTATAAAAAATTTATAA-TTTATAATAA
1 TTTATGATTTTTAT-AAAAATTTATAATTTTATAATAA
* *
19688834 TTTAT-ATTTTTATTAAAATTTAATAATTTTTCTAA-AA
1 TTTATGATTTTTATAAAAATTT-ATAA-TTTTATAATAA
*
19688871 TTTATTATTTTTTATAAA
1 TTTATGA-TTTTTATAAA
19688889 TTTTTTTCTA
Statistics
Matches: 77, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
35 7 0.09
36 12 0.16
37 32 0.42
38 17 0.22
39 9 0.12
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (37 bp):
TTTATGATTTTTATAAAAATTTATAATTTTATAATAA
Found at i:19688874 original size:19 final size:17
Alignment explanation
Indices: 19688813--19688891 Score: 79
Period size: 18 Copynumber: 4.4 Consensus size: 17
19688803 ATTTTTATAA
*
19688813 AAAATTTATAA-TTTAT
1 AAAATTTATAATTTTTT
*
19688829 AATAATTTATATTTTTATT
1 AA-AATTTATAATTTT-TT
19688848 AAAATTTAATAATTTTTCT
1 AAAATTT-ATAATTTTT-T
*
19688867 AAAATTTATTATTTTTT
1 AAAATTTATAATTTTTT
19688884 ATAAATTT
1 A-AAATTT
19688892 TTTTCTAATT
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
16 2 0.04
17 10 0.19
18 23 0.43
19 18 0.34
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (17 bp):
AAAATTTATAATTTTTT
Found at i:19695754 original size:29 final size:29
Alignment explanation
Indices: 19695712--19695770 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
19695702 AAGCATAAAC
19695712 ATATTAGGCCATTTATGCAAAAAAT-GAAA
1 ATATTAGGCCATTTAT-CAAAAAATAGAAA
* *
19695741 ATATTGGGCCATTTATTAAAAAATAGAAA
1 ATATTAGGCCATTTATCAAAAAATAGAAA
19695770 A
1 A
19695771 GGAAGGACGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 7 0.26
29 20 0.74
ACGTcount: A:0.49, C:0.08, G:0.14, T:0.29
Consensus pattern (29 bp):
ATATTAGGCCATTTATCAAAAAATAGAAA
Found at i:19699690 original size:262 final size:264
Alignment explanation
Indices: 19699197--19699723 Score: 995
Period size: 262 Copynumber: 2.0 Consensus size: 264
19699187 GTGGCAAATG
19699197 GACCACATGAGGTATCAACATTTAGCTAAGAGGAACCAAACATGTGGGATATCTTCAACTAATAC
1 GACCACATGAGGTATCAACATTTAGCTAAGAGGAACCAAACATGTGGGATATCTTCAACTAATAC
*
19699262 TTCAATTATTCAGATGCTAACTCTGTTTCCATCTTAATGTCATATTATTACTTGTTCCATTGGTC
66 TTCAATTATTCAGATGCTAACTCTGTTTCCATCTTAATGTCATATTATTA-TTGTTCCATTGGCC
*
19699327 CCACTTGGTTTTTTTGGCCTTTTCCTTCCTTAGTTTATCCAAATAAAGAATAACCCACTTTTTAA
130 CCACTTGGTTTTTTTGGCCTTTTCCTACCTTAGTTTATCCAAATAAAGAATAACCCACTTTTTAA
*
19699392 CACCCACCTTCCAATTCATATTATGCTATGAGTTGAAGATGGAATTTTGTGATGAAAATTATATT
195 CACCCACCTTCCAATTCATATTATGCAATGAGTTGAAGATGGAATTTTGTGATGAAAATTATATT
19699457 AAAAA
260 AAAAA
*
19699462 GACCACATGGGGTATCAACATTTAGCTAAGAGGAACCAAACATGTGGGATATCTTCAACTAATAC
1 GACCACATGAGGTATCAACATTTAGCTAAGAGGAACCAAACATGTGGGATATCTTCAACTAATAC
19699527 TTCAATTATTCAGATGCTAACTCTGTTTCCATCTTAATGTCATATTA-T-TTGTTCCATTGGCCC
66 TTCAATTATTCAGATGCTAACTCTGTTTCCATCTTAATGTCATATTATTATTGTTCCATTGGCCC
19699590 CACTTGGTTTTTTTGGCCTTTTCCTACCTTAGTTTATCCAAATAAAGAATAACCCACTTTTTAAC
131 CACTTGGTTTTTTTGGCCTTTTCCTACCTTAGTTTATCCAAATAAAGAATAACCCACTTTTTAAC
19699655 ACCCACCTTCCAATTCATATTATGCAATGAGTTGAAGATGGAATTTTGTGATGAAAATTATATTA
196 ACCCACCTTCCAATTCATATTATGCAATGAGTTGAAGATGGAATTTTGTGATGAAAATTATATTA
19699720 AAAA
261 AAAA
19699724 ATAAATTAAA
Statistics
Matches: 258, Mismatches: 4, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
262 146 0.57
264 1 0.00
265 111 0.43
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.36
Consensus pattern (264 bp):
GACCACATGAGGTATCAACATTTAGCTAAGAGGAACCAAACATGTGGGATATCTTCAACTAATAC
TTCAATTATTCAGATGCTAACTCTGTTTCCATCTTAATGTCATATTATTATTGTTCCATTGGCCC
CACTTGGTTTTTTTGGCCTTTTCCTACCTTAGTTTATCCAAATAAAGAATAACCCACTTTTTAAC
ACCCACCTTCCAATTCATATTATGCAATGAGTTGAAGATGGAATTTTGTGATGAAAATTATATTA
AAAA
Found at i:19707042 original size:23 final size:23
Alignment explanation
Indices: 19707013--19707060 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
19707003 TTATATACTA
* *
19707013 TTAAAATATAAT-TATATTAAGAT
1 TTAAAATAAAATGT-TACTAAGAT
19707036 TTAAAATAAAATGTTACTAAGAT
1 TTAAAATAAAATGTTACTAAGAT
19707059 TT
1 TT
19707061 CATCGTTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 21 0.95
24 1 0.05
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.42
Consensus pattern (23 bp):
TTAAAATAAAATGTTACTAAGAT
Found at i:19708867 original size:23 final size:27
Alignment explanation
Indices: 19708839--19708890 Score: 76
Period size: 23 Copynumber: 2.1 Consensus size: 27
19708829 CCCTTAAAAT
19708839 TTACAAAGT-AAT-TT-TTTTTTC-AA
1 TTACAAAGTAAATGTTATTTTTTCGAA
19708862 TTACAAAGTAAATGTTATTTTTTCGAA
1 TTACAAAGTAAATGTTATTTTTTCGAA
19708889 TT
1 TT
19708891 GATACACATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 9 0.36
24 3 0.12
25 2 0.08
26 7 0.28
27 4 0.16
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.50
Consensus pattern (27 bp):
TTACAAAGTAAATGTTATTTTTTCGAA
Found at i:19711140 original size:30 final size:29
Alignment explanation
Indices: 19711070--19711163 Score: 179
Period size: 29 Copynumber: 3.2 Consensus size: 29
19711060 GCTTCAATAA
19711070 AAAAAATATATGTAGTGTATTTTAAAAAT
1 AAAAAATATATGTAGTGTATTTTAAAAAT
19711099 AAAAAATATATGTAGTGTATTTTAAAAAT
1 AAAAAATATATGTAGTGTATTTTAAAAAT
19711128 AAAAATATATATGTAGTGTATTTTAAAAAT
1 AAAAA-ATATATGTAGTGTATTTTAAAAAT
19711158 AAAAAA
1 AAAAAA
19711164 AATTAATCTG
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
29 35 0.55
30 29 0.45
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.36
Consensus pattern (29 bp):
AAAAAATATATGTAGTGTATTTTAAAAAT
Found at i:19711910 original size:21 final size:21
Alignment explanation
Indices: 19711884--19711936 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
19711874 CCATTGTTCT
* *
19711884 AATCTCACCGTTACAATATCC
1 AATCTCACCGCTACAATAACC
*
19711905 AATCTCACCGCTACAATAACT
1 AATCTCACCGCTACAATAACC
19711926 AATCTCACCGC
1 AATCTCACCGC
19711937 CACCGTTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.34, C:0.36, G:0.06, T:0.25
Consensus pattern (21 bp):
AATCTCACCGCTACAATAACC
Found at i:19727468 original size:19 final size:19
Alignment explanation
Indices: 19727444--19727487 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
19727434 GTAACTAAAA
19727444 TATTTTCTGAAAAATAATT
1 TATTTTCTGAAAAATAATT
* * *
19727463 TATTTTTTTAAAAATGATT
1 TATTTTCTGAAAAATAATT
19727482 TATTTT
1 TATTTT
19727488 TCTAGTCTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (19 bp):
TATTTTCTGAAAAATAATT
Found at i:19728704 original size:48 final size:48
Alignment explanation
Indices: 19728633--19728725 Score: 186
Period size: 48 Copynumber: 1.9 Consensus size: 48
19728623 TTGAAAGTAT
19728633 TAGAAGGCTTATTTCCTCTCTTGGCCTCCTCTGCTAGAATTTCAAAAA
1 TAGAAGGCTTATTTCCTCTCTTGGCCTCCTCTGCTAGAATTTCAAAAA
19728681 TAGAAGGCTTATTTCCTCTCTTGGCCTCCTCTGCTAGAATTTCAA
1 TAGAAGGCTTATTTCCTCTCTTGGCCTCCTCTGCTAGAATTTCAA
19728726 GAAAAAGAGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.37
Consensus pattern (48 bp):
TAGAAGGCTTATTTCCTCTCTTGGCCTCCTCTGCTAGAATTTCAAAAA
Found at i:19728867 original size:32 final size:32
Alignment explanation
Indices: 19728826--19728898 Score: 137
Period size: 32 Copynumber: 2.3 Consensus size: 32
19728816 TGTCAATCAT
19728826 TTCAATATCCAACAAACTTAAAACATAATAAA
1 TTCAATATCCAACAAACTTAAAACATAATAAA
*
19728858 TTCAATATCCAACAAGCTTAAAACATAATAAA
1 TTCAATATCCAACAAACTTAAAACATAATAAA
19728890 TTCAATATC
1 TTCAATATC
19728899 TAATATCATT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.52, C:0.19, G:0.01, T:0.27
Consensus pattern (32 bp):
TTCAATATCCAACAAACTTAAAACATAATAAA
Found at i:19734596 original size:30 final size:30
Alignment explanation
Indices: 19734561--19734619 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
19734551 TATTTTATTG
19734561 TTAATTTTGTTATTATTTTAAAGACATTTA
1 TTAATTTTGTTATTATTTTAAAGACATTTA
* *
19734591 TTAATTTTGTTATTATTTTAGAGGCATTT
1 TTAATTTTGTTATTATTTTAAAGACATTT
19734620 GCTTGTTAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.29, C:0.03, G:0.10, T:0.58
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGACATTTA
Found at i:19738390 original size:5 final size:5
Alignment explanation
Indices: 19738375--19738408 Score: 59
Period size: 5 Copynumber: 6.6 Consensus size: 5
19738365 ATAAGTTAGG
19738375 AAATAA AAATA AAATA AAATA AAATA AAATA AAA
1 AAAT-A AAATA AAATA AAATA AAATA AAATA AAA
19738409 ACATATGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 24 0.86
6 4 0.14
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:19738913 original size:12 final size:12
Alignment explanation
Indices: 19738896--19738920 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19738886 CAAAAAGAAC
19738896 ATATGTTCTTTT
1 ATATGTTCTTTT
19738908 ATATGTTCTTTT
1 ATATGTTCTTTT
19738920 A
1 A
19738921 GGGCTTCTCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.08, G:0.08, T:0.64
Consensus pattern (12 bp):
ATATGTTCTTTT
Found at i:19742547 original size:24 final size:21
Alignment explanation
Indices: 19742509--19742555 Score: 58
Period size: 24 Copynumber: 2.1 Consensus size: 21
19742499 TATATTTGAA
*
19742509 ATTAATATATTGAATTTAATC
1 ATTAATATATTGAATTGAATC
19742530 ATTATATATATTAAGAATTGAATC
1 ATTA-ATATATT--GAATTGAATC
19742554 AT
1 AT
19742556 ATAGAGAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 4 0.18
22 7 0.32
24 11 0.50
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (21 bp):
ATTAATATATTGAATTGAATC
Found at i:19746113 original size:29 final size:29
Alignment explanation
Indices: 19746037--19746113 Score: 136
Period size: 29 Copynumber: 2.7 Consensus size: 29
19746027 AATGATAACG
*
19746037 TAAGTGACTAAAACGTAACATTTCAAACA
1 TAAGTGACTAAAACGTAATATTTCAAACA
19746066 TAAGTGACTAAAACGTAATATTTCAAACA
1 TAAGTGACTAAAACGTAATATTTCAAACA
*
19746095 TAAGTGACTAAAATGTAAT
1 TAAGTGACTAAAACGTAAT
19746114 CTGAGGCAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.48, C:0.13, G:0.12, T:0.27
Consensus pattern (29 bp):
TAAGTGACTAAAACGTAATATTTCAAACA
Found at i:19751340 original size:56 final size:56
Alignment explanation
Indices: 19751259--19751374 Score: 232
Period size: 56 Copynumber: 2.1 Consensus size: 56
19751249 TATTGTTTAT
19751259 TCAAGGAGTACTTTACCTTATTTGTTAGTGTTATTTAATATATGGCCTTTGTATTG
1 TCAAGGAGTACTTTACCTTATTTGTTAGTGTTATTTAATATATGGCCTTTGTATTG
19751315 TCAAGGAGTACTTTACCTTATTTGTTAGTGTTATTTAATATATGGCCTTTGTATTG
1 TCAAGGAGTACTTTACCTTATTTGTTAGTGTTATTTAATATATGGCCTTTGTATTG
19751371 TCAA
1 TCAA
19751375 TTATAACAGG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 60 1.00
ACGTcount: A:0.24, C:0.11, G:0.17, T:0.47
Consensus pattern (56 bp):
TCAAGGAGTACTTTACCTTATTTGTTAGTGTTATTTAATATATGGCCTTTGTATTG
Found at i:19756994 original size:15 final size:15
Alignment explanation
Indices: 19756950--19756988 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
19756940 CCCTCAAATT
*
19756950 AAAAAAAACCTTTTA
1 AAAAAAAACCTTTAA
19756965 AAAAAAAACCTTTAA
1 AAAAAAAACCTTTAA
19756980 AAAAAAAAC
1 AAAAAAAAC
19756989 AATTAAGCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.69, C:0.13, G:0.00, T:0.18
Consensus pattern (15 bp):
AAAAAAAACCTTTAA
Found at i:19757211 original size:19 final size:18
Alignment explanation
Indices: 19757189--19757232 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
19757179 AAAATTTATC
19757189 AAAAATTACAAAAAAATA
1 AAAAATTACAAAAAAATA
***
19757207 TAAAAATCGTAAAAAAATA
1 -AAAAATTACAAAAAAATA
19757226 AAAAATT
1 AAAAATT
19757233 GTAAAATTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.73, C:0.05, G:0.02, T:0.20
Consensus pattern (18 bp):
AAAAATTACAAAAAAATA
Found at i:19757230 original size:37 final size:37
Alignment explanation
Indices: 19757189--19757268 Score: 97
Period size: 37 Copynumber: 2.2 Consensus size: 37
19757179 AAAATTTATC
19757189 AAAAATTACAAAAAAATATAAAAATCGTAAAAAAATA
1 AAAAATTACAAAAAAATATAAAAATCGTAAAAAAATA
** *** *
19757226 AAAAATTGTAAAATTTTATAAAAATCGTAAAAAATTA
1 AAAAATTACAAAAAAATATAAAAATCGTAAAAAAATA
*
19757263 TAAAAT
1 AAAAAT
19757269 ATATAGAAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.66, C:0.04, G:0.04, T:0.26
Consensus pattern (37 bp):
AAAAATTACAAAAAAATATAAAAATCGTAAAAAAATA
Found at i:19757247 original size:28 final size:28
Alignment explanation
Indices: 19757146--19757303 Score: 101
Period size: 27 Copynumber: 5.6 Consensus size: 28
19757136 ATCTATAAAT
* * * *
19757146 ATTATTAAATTTTAATAAAAAATTTAAAT
1 ATTATAAAATTTT-ATAAAAAAGTAAAAA
* *
19757175 ATTA-AAAA-TTTATCAAAAATTACAAAAA
1 ATTATAAAATTTTATAAAAAAGT--AAAAA
* **
19757203 AATATAAAAATCGTA-AAAAAA-TAAAAA
1 ATTAT-AAAATTTTATAAAAAAGTAAAAA
* *
19757230 ATTGTAAAATTTTATAAAAATCGTAAAAA
1 ATTATAAAATTTTATAAAAA-AGTAAAAA
* * *
19757259 ATTATAAAA-TATATAGAAATGTAAAAA
1 ATTATAAAATTTTATAAAAAAGTAAAAA
*
19757286 AATATAAAATTTTATAAA
1 ATTATAAAATTTTATAAA
19757304 TTCATAAGAA
Statistics
Matches: 100, Mismatches: 20, Indels: 19
0.72 0.14 0.14
Matches are distributed among these distances:
26 16 0.16
27 31 0.31
28 23 0.23
29 19 0.19
30 9 0.09
31 2 0.02
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (28 bp):
ATTATAAAATTTTATAAAAAAGTAAAAA
Found at i:19757248 original size:19 final size:19
Alignment explanation
Indices: 19757198--19757364 Score: 103
Period size: 19 Copynumber: 8.8 Consensus size: 19
19757188 CAAAAATTAC
*
19757198 AAAAAAATATAAAAATCGT
1 AAAAAATTATAAAAATCGT
* *
19757217 AAAAAAATA-AAAAATTGT
1 AAAAAATTATAAAAATCGT
**
19757235 AAAATTTTATAAAAATCGT
1 AAAAAATTATAAAAATCGT
*
19757254 AAAAAATTAT-AAAAT-AT
1 AAAAAATTATAAAAATCGT
* * *
19757271 ATAGAAATGTAAAAAAAT-AT
1 A-AAAAAT-TATAAAAATCGT
** * *
19757291 AAAATTTTAT-AAATTCAT
1 AAAAAATTATAAAAATCGT
19757309 AAGAAAATTATACAAAAT-GT
1 AA-AAAATTATA-AAAATCGT
* **
19757329 AAAAAAATATAAATTTCGT
1 AAAAAATTATAAAAATCGT
19757348 AAAAAAATTATAAAAAT
1 -AAAAAATTATAAAAAT
19757365 TATCGTACGA
Statistics
Matches: 113, Mismatches: 25, Indels: 19
0.72 0.16 0.12
Matches are distributed among these distances:
17 6 0.05
18 33 0.29
19 46 0.41
20 24 0.21
21 4 0.04
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (19 bp):
AAAAAATTATAAAAATCGT
Found at i:19757249 original size:56 final size:55
Alignment explanation
Indices: 19757177--19757366 Score: 143
Period size: 56 Copynumber: 3.3 Consensus size: 55
19757167 ATTTAAATAT
19757177 TAAAAATTTATCAAAAATTACAAAAAAATATAAAAATCGTAAAAAAATAAAAAATTG
1 TAAAAATTTAT-AAAAATTACAAAAAAATATAAAAAT-GTAAAAAAATAAAAAATTG
* *** * * * ** * *
19757234 TAAAATTTTATAAAAATCGTAAAAAATTATAAAATATATAGAAATGTAAAAAAATA
1 TAAAAATTTATAAAAATTACAAAAAAATATAAAA-ATGTAAAAAAATAAAAAATTG
* * *
19757290 T-AAAATTT-TATAAATT-CATAAGAAAATTATACAAAATGTAAAAAAATATAAATTTCG
1 TAAAAATTTATAAAAATTACA-AA-AAAA-TATA-AAAATGTAAAAAAATAAAAAATT-G
*
19757347 TAAAAAAATTATAAAAATTA
1 T-AAAAATTTATAAAAATTA
19757367 TCGTACGAAA
Statistics
Matches: 97, Mismatches: 26, Indels: 16
0.70 0.19 0.12
Matches are distributed among these distances:
53 1 0.01
54 8 0.08
55 9 0.09
56 50 0.52
57 16 0.16
59 6 0.06
60 7 0.07
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (55 bp):
TAAAAATTTATAAAAATTACAAAAAAATATAAAAATGTAAAAAAATAAAAAATTG
Found at i:19757266 original size:10 final size:10
Alignment explanation
Indices: 19757177--19757341 Score: 59
Period size: 10 Copynumber: 17.4 Consensus size: 10
19757167 ATTTAAATAT
*
19757177 TAAAAATTTA
1 TAAAAAATTA
*
19757187 TCAAAAATTA
1 TAAAAAATTA
* *
19757197 CAAAAAAATA
1 TAAAAAATTA
**
19757207 T-AAAAATCG
1 TAAAAAATTA
19757216 TAAAAAA--A
1 TAAAAAATTA
*
19757224 TAAAAAATTG
1 TAAAAAATTA
**
19757234 TAAAATTTTA
1 TAAAAAATTA
**
19757244 T-AAAAATCG
1 TAAAAAATTA
19757253 TAAAAAATTA
1 TAAAAAATTA
*
19757263 TAAAATA-TA
1 TAAAAAATTA
*
19757272 T-AGAAATGTA
1 TAAAAAAT-TA
19757282 -AAAAAA-TA
1 TAAAAAATTA
19757290 T--AAAATT-
1 TAAAAAATTA
* *
19757297 TTATAAATTCA
1 TAAAAAATT-A
19757308 TAAGAAAATTA
1 TAA-AAAATTA
*
19757319 TACAAAATGTA
1 TAAAAAAT-TA
19757330 -AAAAAA-TA
1 TAAAAAATTA
19757338 TAAA
1 TAAA
19757342 TTTCGTAAAA
Statistics
Matches: 110, Mismatches: 29, Indels: 33
0.64 0.17 0.19
Matches are distributed among these distances:
7 5 0.05
8 15 0.14
9 22 0.20
10 56 0.51
11 7 0.06
12 5 0.05
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.28
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:19757286 original size:37 final size:37
Alignment explanation
Indices: 19757205--19757288 Score: 98
Period size: 37 Copynumber: 2.2 Consensus size: 37
19757195 TACAAAAAAA
* *
19757205 TATAAAAATCGTAAAAAAATAAAAAATTGTAAAATTT
1 TATAAAAATCGTAAAAAAATAAAAAATTATAAAATTG
* *
19757242 TATAAAAATCGTAAAAAATTATAAAATATATAGAAA-TG
1 TATAAAAATCGTAAAAAAATAAAAAAT-TATA-AAATTG
*
19757280 TAAAAAAAT
1 TATAAAAAT
19757289 ATAAAATTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
37 25 0.62
38 12 0.30
39 3 0.08
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (37 bp):
TATAAAAATCGTAAAAAAATAAAAAATTATAAAATTG
Found at i:19757315 original size:28 final size:27
Alignment explanation
Indices: 19757223--19757316 Score: 75
Period size: 29 Copynumber: 3.3 Consensus size: 27
19757213 TCGTAAAAAA
* *
19757223 ATAAAAAATTGTAAAATTTTATAAAAATC
1 ATAAAAAA-TATAAAATTTTAT-AAATTC
* * *
19757252 GTAAAAAATTATAAAATATATAGAAATGT-
1 ATAAAAAA-TATAAAAT-TTTATAAAT-TC
19757281 A-AAAAAATATAAAATTTTATAAATTC
1 ATAAAAAATATAAAATTTTATAAATTC
19757307 ATAAGAAAAT
1 ATAA-AAAAT
19757317 TATACAAAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 11
0.73 0.11 0.15
Matches are distributed among these distances:
25 1 0.02
26 8 0.15
27 10 0.19
28 11 0.21
29 18 0.35
30 4 0.08
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (27 bp):
ATAAAAAATATAAAATTTTATAAATTC
Found at i:19757364 original size:48 final size:47
Alignment explanation
Indices: 19757242--19757367 Score: 129
Period size: 48 Copynumber: 2.7 Consensus size: 47
19757232 TGTAAAATTT
* *
19757242 TATAAAA-ATCGTAAAAAATTAT-AAAATATATAGAAATGTAAAAAAA
1 TATAAAATTTCGTAAAAAATTATAAAAAT-TATAAAAATGTAAAAAAA
*
19757288 TATAAAATTT--T-ATAAATTCATAAGAAAATTATACAAAATGTAAAAAAA
1 TATAAAATTTCGTAAAAAATT-AT-A-AAAATTATA-AAAATGTAAAAAAA
19757336 TAT-AAATTTCGTAAAAAAATTATAAAAATTAT
1 TATAAAATTTCGT-AAAAAATTATAAAAATTAT
19757368 CGTACGAAAA
Statistics
Matches: 66, Mismatches: 4, Indels: 18
0.75 0.05 0.20
Matches are distributed among these distances:
44 6 0.09
45 3 0.05
46 7 0.11
47 11 0.17
48 29 0.44
49 2 0.03
50 2 0.03
51 6 0.09
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.31
Consensus pattern (47 bp):
TATAAAATTTCGTAAAAAATTATAAAAATTATAAAAATGTAAAAAAA
Found at i:19757429 original size:12 final size:12
Alignment explanation
Indices: 19757404--19757441 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
19757394 TTTCTACAAC
19757404 TTTTATTGATTTT
1 TTTTATT-ATTTT
19757417 TATTT-TTATTTT
1 T-TTTATTATTTT
19757429 TTTTATTATTTT
1 TTTTATTATTTT
19757441 T
1 T
19757442 CACCACATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
11 3 0.13
12 14 0.61
13 3 0.13
14 3 0.13
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.82
Consensus pattern (12 bp):
TTTTATTATTTT
Found at i:19757700 original size:18 final size:19
Alignment explanation
Indices: 19757672--19757726 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 19
19757662 TTTATAATTT
*
19757672 TTTTATGATTTTTATAAAC
1 TTTTACGATTTTTATAAAC
* * **
19757691 TTTTAC-ATTTTTTTTATT
1 TTTTACGATTTTTATAAAC
19757709 TTTTACGATTTTTATAAA
1 TTTTACGATTTTTATAAA
19757727 AAAAATTCTA
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
18 14 0.52
19 13 0.48
ACGTcount: A:0.27, C:0.05, G:0.04, T:0.64
Consensus pattern (19 bp):
TTTTACGATTTTTATAAAC
Found at i:19757967 original size:91 final size:91
Alignment explanation
Indices: 19757842--19758058 Score: 244
Period size: 91 Copynumber: 2.4 Consensus size: 91
19757832 AAGCAGGGGA
** * *
19757842 TTAATTGC--TTTTTTGAAGATTTTTTAGGGTCTTTTTGATGCATTTTGAAAG-TTCAAGCACCC
1 TTAATTGCTTTTTTTTGAAGAAGTTTGAGGGCCTTTTTGATGCATTTTGAAAGATT-AAGCACCC
* *
19757904 AATTGAATGGAAAAAAAAACAATGACT
65 AATTGAATGCAAAAAAAAACAAGGACT
* ** *
19757931 TT-ATTGGTTTTTTTTGGAAGAAGTTTGAGGGCCTTTTTGATGCATTTTGAAAGATTAAGTGCTC
1 TTAATTGCTTTTTTTT-GAAGAAGTTTGAGGGCCTTTTTGATGCATTTTGAAAGATTAAGCACCC
* * ** *
19757995 AATTGAGTGCAAAAAAAGATGAGGGCT
65 AATTGAATGCAAAAAAAAACAAGGACT
*
19758022 TTAATTGCTTTTTTTTGAAAAAGTTTGAGGGCCTTTT
1 TTAATTGCTTTTTTTTGAAGAAGTTTGAGGGCCTTTT
19758059 ACACCTTTAA
Statistics
Matches: 106, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
88 4 0.04
89 2 0.02
90 6 0.06
91 80 0.75
92 14 0.13
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.40
Consensus pattern (91 bp):
TTAATTGCTTTTTTTTGAAGAAGTTTGAGGGCCTTTTTGATGCATTTTGAAAGATTAAGCACCCA
ATTGAATGCAAAAAAAAACAAGGACT
Found at i:19759073 original size:18 final size:19
Alignment explanation
Indices: 19759048--19759088 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
19759038 TTTTGAAAAC
*
19759048 TTTCCTTTCTTTGGA-TATT
1 TTTCTTTTCTTT-GATTATT
19759067 TTTCTTTTCTTTGATTATT
1 TTTCTTTTCTTTGATTATT
19759086 TTT
1 TTT
19759089 TAAAATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 2 0.10
19 18 0.90
ACGTcount: A:0.10, C:0.12, G:0.07, T:0.71
Consensus pattern (19 bp):
TTTCTTTTCTTTGATTATT
Found at i:19761213 original size:14 final size:14
Alignment explanation
Indices: 19761194--19761229 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
19761184 GAAAAGTAAG
19761194 TCATTTTCCAGAAA
1 TCATTTTCCAGAAA
19761208 TCATTTTCCAGAAA
1 TCATTTTCCAGAAA
*
19761222 CCATTTTC
1 TCATTTTC
19761230 AGTGAAACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.39
Consensus pattern (14 bp):
TCATTTTCCAGAAA
Found at i:19761925 original size:20 final size:21
Alignment explanation
Indices: 19761897--19761935 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
19761887 ATATTCATAT
19761897 TATTCAATAAA-ATAGTAAAA
1 TATTCAATAAATATAGTAAAA
*
19761917 TATTTAATAAATATAGTAA
1 TATTCAATAAATATAGTAA
19761936 TTTTTAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.36
Consensus pattern (21 bp):
TATTCAATAAATATAGTAAAA
Found at i:19764378 original size:43 final size:43
Alignment explanation
Indices: 19764325--19764408 Score: 105
Period size: 43 Copynumber: 2.0 Consensus size: 43
19764315 CAAGTTCGTG
* * * *
19764325 AGGTACACTATAAGGTCCGTGAAGCCCATTACATAAGGTATCA
1 AGGTACACTATAAAGTCCGCGAAGCACATTACACAAGGTATCA
* * *
19764368 AGGTGCACTATAAAGTTCGCGAAGCATATTACACAAGGTAT
1 AGGTACACTATAAAGTCCGCGAAGCACATTACACAAGGTAT
19764409 AACAAGCAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (43 bp):
AGGTACACTATAAAGTCCGCGAAGCACATTACACAAGGTATCA
Found at i:19768354 original size:12 final size:12
Alignment explanation
Indices: 19768337--19768364 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
19768327 TTAATTTCAT
19768337 ATTCATCCTTTA
1 ATTCATCCTTTA
19768349 ATTCATCCTTTA
1 ATTCATCCTTTA
19768361 ATTC
1 ATTC
19768365 GATCTCTACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (12 bp):
ATTCATCCTTTA
Found at i:19769941 original size:14 final size:14
Alignment explanation
Indices: 19769922--19769948 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19769912 TTCTCTTGCA
19769922 CACTTGTATTTTAC
1 CACTTGTATTTTAC
19769936 CACTTGTATTTTA
1 CACTTGTATTTTA
19769949 TTTTATCATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.19, G:0.07, T:0.52
Consensus pattern (14 bp):
CACTTGTATTTTAC
Found at i:19771310 original size:139 final size:139
Alignment explanation
Indices: 19771060--19771351 Score: 512
Period size: 139 Copynumber: 2.1 Consensus size: 139
19771050 GTGCAGAGGA
* *
19771060 CACACGCCCATGTGGTTCACACAGCCAAGAGACACGCCCATGTCTCAGGCCGTGTGGGCATTCAA
1 CACACGCCCGTGTGGTTCACACAGCCAAGAGACACGCCCATGTCTCAGGCCATGTGGGCATTCAA
*
19771125 AATAGGGCACACGGCCGTGTCCCAGCCTGTGTTGGTACCCATCTAACTCTCTGACTTAAGTCACA
66 AATAGGGCACACGGCCGTGTCCCAGCCTGTGTTGGTACCCATCTAACTCTCTAACTTAAGTCACA
*
19771190 TAGCCAAGC
131 CAGCCAAGC
* *
19771199 CACACGCCCGTGTGGTTCACACGGCCAAGAGACATGCCCATGTCTCAGGCCATGTGGGCATTCAA
1 CACACGCCCGTGTGGTTCACACAGCCAAGAGACACGCCCATGTCTCAGGCCATGTGGGCATTCAA
* *
19771264 AATAGGGCACACGGCCGTGTCCCAGCCTGTGTTGGTACCCATCTAACTCTTTAACTTAGGTCACA
66 AATAGGGCACACGGCCGTGTCCCAGCCTGTGTTGGTACCCATCTAACTCTCTAACTTAAGTCACA
19771329 CAGCCAAGC
131 CAGCCAAGC
19771338 CACACGCCCGTGTG
1 CACACGCCCGTGTG
19771352 CTAGTGTAAC
Statistics
Matches: 145, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
139 145 1.00
ACGTcount: A:0.24, C:0.33, G:0.24, T:0.20
Consensus pattern (139 bp):
CACACGCCCGTGTGGTTCACACAGCCAAGAGACACGCCCATGTCTCAGGCCATGTGGGCATTCAA
AATAGGGCACACGGCCGTGTCCCAGCCTGTGTTGGTACCCATCTAACTCTCTAACTTAAGTCACA
CAGCCAAGC
Found at i:19775367 original size:25 final size:25
Alignment explanation
Indices: 19775289--19775371 Score: 87
Period size: 25 Copynumber: 3.3 Consensus size: 25
19775279 GCTCTCTTTC
*
19775289 GAGCTATATAACGAGAAGCTTA-AA
1 GAGCTATATAACGGGAAGCTTATAA
* * * **
19775313 TGAGCCATGTAACGGGAAACTTATCC
1 -GAGCTATATAACGGGAAGCTTATAA
*
19775339 GAGCTATATAACGGGAAGCTCATAA
1 GAGCTATATAACGGGAAGCTTATAA
19775364 GAGCTATA
1 GAGCTATA
19775372 ATCAGGAAAC
Statistics
Matches: 45, Mismatches: 12, Indels: 2
0.76 0.20 0.03
Matches are distributed among these distances:
25 45 1.00
ACGTcount: A:0.39, C:0.17, G:0.23, T:0.22
Consensus pattern (25 bp):
GAGCTATATAACGGGAAGCTTATAA
Found at i:19775391 original size:24 final size:25
Alignment explanation
Indices: 19775322--19775391 Score: 61
Period size: 25 Copynumber: 2.8 Consensus size: 25
19775312 ATGAGCCATG
* * *
19775322 TAACGGGAAACTTATCCGAGCTATA
1 TAACAGGAAACTCATACGAGCTATA
* * *
19775347 TAACGGGAAGCTCATAAGAGCTATA
1 TAACAGGAAACTCATACGAGCTATA
* *
19775372 -ATCAGGAAACTCATGCGAGC
1 TAACAGGAAACTCATACGAGC
19775392 CAATAACGGG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
24 15 0.42
25 21 0.58
ACGTcount: A:0.37, C:0.20, G:0.23, T:0.20
Consensus pattern (25 bp):
TAACAGGAAACTCATACGAGCTATA
Found at i:19775423 original size:49 final size:50
Alignment explanation
Indices: 19775288--19775431 Score: 143
Period size: 49 Copynumber: 2.9 Consensus size: 50
19775278 AGCTCTCTTT
* * * * *
19775288 CGAGCTATATAACGAGAAGCTTA-AATGAGCCATGTAA-CGGGAAACTTATC
1 CGAGCCATATAACGGGAAGCTCAGAA-GAGCCAT-TAATCAGGAAACTCATC
* * * *
19775338 CGAGCTATATAACGGGAAGCTCATAAGAGCTA-TAATCAGGAAACTCATG
1 CGAGCCATATAACGGGAAGCTCAGAAGAGCCATTAATCAGGAAACTCATC
* *
19775387 CGAGCCA-ATAACGGGTAGCTCCGAAGAGCCATTAATCAGGAAACT
1 CGAGCCATATAACGGGAAGCTCAGAAGAGCCATTAATCAGGAAACT
19775432 TTAGATAGCC
Statistics
Matches: 80, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
48 23 0.29
49 29 0.36
50 26 0.32
51 2 0.03
ACGTcount: A:0.38, C:0.20, G:0.23, T:0.19
Consensus pattern (50 bp):
CGAGCCATATAACGGGAAGCTCAGAAGAGCCATTAATCAGGAAACTCATC
Found at i:19775442 original size:49 final size:49
Alignment explanation
Indices: 19775339--19775454 Score: 119
Period size: 49 Copynumber: 2.4 Consensus size: 49
19775329 AAACTTATCC
* * * *
19775339 GAGCTATATAACGGGAAGCTCATAAGAGCTATAATCAGGAAACTCATGC
1 GAGCCATATAACGGGAAGCTCAGAAGAGCCATAATCAGGAAACTCATGA
* * *
19775388 GAGCCA-ATAACGGGTAGCTCCGAAGAGCCATTAATCAGGAAACT-TTAGA
1 GAGCCATATAACGGGAAGCTCAGAAGAGCCA-TAATCAGGAAACTCAT-GA
* *
19775437 TAGCCATATATCGGGAAG
1 GAGCCATATAACGGGAAG
19775455 TTCAAGCGAG
Statistics
Matches: 54, Mismatches: 10, Indels: 5
0.78 0.14 0.07
Matches are distributed among these distances:
48 21 0.39
49 24 0.44
50 9 0.17
ACGTcount: A:0.37, C:0.19, G:0.24, T:0.20
Consensus pattern (49 bp):
GAGCCATATAACGGGAAGCTCAGAAGAGCCATAATCAGGAAACTCATGA
Found at i:19775503 original size:25 final size:26
Alignment explanation
Indices: 19775472--19775543 Score: 83
Period size: 26 Copynumber: 2.8 Consensus size: 26
19775462 GAGCCATATC
19775472 GGGAAGCTC-CGAAGAGCCATTAATT
1 GGGAAGCTCACGAAGAGCCATTAATT
** * * *
19775497 GGGAAGCTCAAAAATAACCTTTAATT
1 GGGAAGCTCACGAAGAGCCATTAATT
*
19775523 AGGAAGCTCACGAAGAGCCAT
1 GGGAAGCTCACGAAGAGCCAT
19775544 ATACCGGGAC
Statistics
Matches: 35, Mismatches: 11, Indels: 1
0.74 0.23 0.02
Matches are distributed among these distances:
25 9 0.26
26 26 0.74
ACGTcount: A:0.38, C:0.19, G:0.24, T:0.19
Consensus pattern (26 bp):
GGGAAGCTCACGAAGAGCCATTAATT
Found at i:19776002 original size:21 final size:21
Alignment explanation
Indices: 19775978--19776019 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
19775968 TAAATTTAGC
* *
19775978 TCAATTTAGTACAATTCATAT
1 TCAATTCAATACAATTCATAT
*
19775999 TCAATTCAATCCAATTCATAT
1 TCAATTCAATACAATTCATAT
19776020 ATTAGGCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.19, G:0.02, T:0.40
Consensus pattern (21 bp):
TCAATTCAATACAATTCATAT
Found at i:19788453 original size:15 final size:15
Alignment explanation
Indices: 19788430--19788473 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
19788420 ATGTATGGTA
19788430 TTTTGATGATTAAAT
1 TTTTGATGATTAAAT
*
19788445 TTTTTATGATTAAAT
1 TTTTGATGATTAAAT
* *
19788460 TATTG-TTATTAAAT
1 TTTTGATGATTAAAT
19788474 ATGCTTGAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
14 8 0.32
15 17 0.68
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (15 bp):
TTTTGATGATTAAAT
Found at i:19788476 original size:24 final size:24
Alignment explanation
Indices: 19788449--19788494 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
19788439 TTAAATTTTT
*
19788449 TATGATT-AAATTATTGTTATTAAA
1 TATGATTGAAATTACTG-TATTAAA
*
19788473 TATGCTTGAAATTACTGTATTA
1 TATGATTGAAATTACTGTATTA
19788495 TATTTTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.37, C:0.04, G:0.11, T:0.48
Consensus pattern (24 bp):
TATGATTGAAATTACTGTATTAAA
Found at i:19795560 original size:36 final size:36
Alignment explanation
Indices: 19795513--19795703 Score: 229
Period size: 36 Copynumber: 5.0 Consensus size: 36
19795503 GCTAAACTAC
*
19795513 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
*
19795549 CACTTATCACTTTTTCACTTGATCAGATAAGTATAA
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
*
19795585 CACTTATTACTTTTTCACTTGATCAGATAAGTGTAGCTAAAG
1 CACTTATCACTTTTTCACTTGATCAGATAA--GTA--T--AG
* * *
19795627 CTACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
1 ----CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
*
19795667 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
19795703 C
1 C
19795704 TAAAGCTACC
Statistics
Matches: 135, Mismatches: 10, Indels: 20
0.82 0.06 0.12
Matches are distributed among these distances:
36 98 0.73
38 3 0.02
40 3 0.02
42 2 0.01
44 2 0.01
46 27 0.20
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (36 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
Found at i:19795637 original size:46 final size:46
Alignment explanation
Indices: 19795585--19795739 Score: 195
Period size: 46 Copynumber: 3.6 Consensus size: 46
19795575 ATAAGTATAA
*
19795585 CACTTATTACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
19795631 CACTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T--AG----
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
19795667 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
19795713 CACTTATCACTTTATCTCTTGATCAGA
1 CACTTATCACTTTTTCACTTGATCAGA
19795740 AGTACTCAAA
Statistics
Matches: 92, Mismatches: 7, Indels: 20
0.77 0.06 0.17
Matches are distributed among these distances:
36 28 0.30
38 2 0.02
39 1 0.01
40 3 0.03
42 3 0.03
43 1 0.01
44 2 0.02
46 52 0.57
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.37
Consensus pattern (46 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:19795643 original size:82 final size:82
Alignment explanation
Indices: 19795549--19795739 Score: 328
Period size: 82 Copynumber: 2.3 Consensus size: 82
19795539 ATAAGTATAG
* * *
19795549 CACTTATCACTTTTTCACTTGATCAGATAAGTATAACACTTATTACTTTTTCACTTGATCAGATA
1 CACTTATCACTTTATCTCTTGATCAGATAAGTATAACACTTATCACTTTTTCACTTGATCAGATA
19795614 AGTGTAGCTAAAGCTAC
66 AGTGTAGCTAAAGCTAC
* * *
19795631 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCACTTATCACTTTTTCACTTGATCAGATA
1 CACTTATCACTTTATCTCTTGATCAGATAAGTATAACACTTATCACTTTTTCACTTGATCAGATA
19795696 AGTGTAGCTAAAGCTAC
66 AGTGTAGCTAAAGCTAC
19795713 CACTTATCACTTTATCTCTTGATCAGA
1 CACTTATCACTTTATCTCTTGATCAGA
19795740 AGTACTCAAA
Statistics
Matches: 103, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
82 103 1.00
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (82 bp):
CACTTATCACTTTATCTCTTGATCAGATAAGTATAACACTTATCACTTTTTCACTTGATCAGATA
AGTGTAGCTAAAGCTAC
Found at i:19795652 original size:118 final size:117
Alignment explanation
Indices: 19795487--19795698 Score: 397
Period size: 118 Copynumber: 1.8 Consensus size: 117
19795477 CATTTGTCCC
19795487 TGATCAGATAAGTGTAGCTAAACTACCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCAC
1 TGATCAGATAAGTGTAGCTAAACTACCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCAC
19795552 TTATCACTTTTTCACTTGATCAGATAAGTATAACACTTATTACTTTTTCACT
66 TTATCACTTTTTCACTTGATCAGATAAGTATAACACTTATTACTTTTTCACT
* *
19795604 TGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCA
1 TGATCAGATAAGTGTAGCTAAA-CTACCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCA
19795669 CTTATCACTTTTTCACTTGATCAGATAAGT
65 CTTATCACTTTTTCACTTGATCAGATAAGT
19795699 GTAGCTAAAG
Statistics
Matches: 92, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
117 22 0.24
118 70 0.76
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (117 bp):
TGATCAGATAAGTGTAGCTAAACTACCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCAC
TTATCACTTTTTCACTTGATCAGATAAGTATAACACTTATTACTTTTTCACT
Found at i:19802452 original size:18 final size:19
Alignment explanation
Indices: 19802425--19802470 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
19802415 ATAATATTAA
19802425 TTAA-TAAAATATTAGCAC
1 TTAATTAAAATATTAGCAC
**
19802443 TT-ATTAAAATATTATTAC
1 TTAATTAAAATATTAGCAC
19802461 TTAATTAAAA
1 TTAATTAAAA
19802471 AAATAATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 1 0.04
18 16 0.67
19 7 0.29
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (19 bp):
TTAATTAAAATATTAGCAC
Found at i:19802472 original size:21 final size:21
Alignment explanation
Indices: 19802421--19802472 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 21
19802411 TATTATAATA
19802421 TTAATTAATAAAATATTAGCAC
1 TTAATTAA-AAAATATTAGCAC
**
19802443 TT-ATT--AAAATATTATTAC
1 TTAATTAAAAAATATTAGCAC
19802461 TTAATTAAAAAA
1 TTAATTAAAAAA
19802473 ATAATTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
18 13 0.52
19 3 0.12
21 7 0.28
22 2 0.08
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (21 bp):
TTAATTAAAAAATATTAGCAC
Found at i:19802770 original size:2 final size:2
Alignment explanation
Indices: 19802763--19802801 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
19802753 CCATAAATAT
19802763 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
19802802 TAAAGTAGGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:19805055 original size:25 final size:25
Alignment explanation
Indices: 19804985--19805062 Score: 77
Period size: 25 Copynumber: 3.2 Consensus size: 25
19804975 ATACATCACA
* * *
19804985 GCTCTCACGAGCTTGTCGTTATTTA
1 GCTCTCACGAGCTTCTCGATATTTG
* * * *
19805010 GCTCTTATGAGCATCCCGATATTTG
1 GCTCTCACGAGCTTCTCGATATTTG
*
19805035 GCTCTCACGAGCTTCTTGATA-TTG
1 GCTCTCACGAGCTTCTCGATATTTG
19805059 GCTC
1 GCTC
19805063 GCTTGAACTT
Statistics
Matches: 41, Mismatches: 12, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
24 7 0.17
25 34 0.83
ACGTcount: A:0.17, C:0.26, G:0.21, T:0.37
Consensus pattern (25 bp):
GCTCTCACGAGCTTCTCGATATTTG
Found at i:19805084 original size:24 final size:24
Alignment explanation
Indices: 19805052--19805112 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
19805042 CGAGCTTCTT
*
19805052 GATAT-TGGCTCGCTTGAACTTCCC
1 GATATATGGCTCG-ATGAACTTCCC
*
19805076 GAT-TATGGCTCGATGAGCTTCCC
1 GATATATGGCTCGATGAACTTCCC
*
19805099 GTTATATGGCTCGA
1 GATATATGGCTCGA
19805113 AAGAGCTTCC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 12 0.38
24 20 0.62
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.33
Consensus pattern (24 bp):
GATATATGGCTCGATGAACTTCCC
Found at i:19805124 original size:25 final size:23
Alignment explanation
Indices: 19805070--19805128 Score: 82
Period size: 25 Copynumber: 2.5 Consensus size: 23
19805060 CTCGCTTGAA
* *
19805070 CTTCCCGATTATGGCTCGATGAG
1 CTTCCCGTTTATGGCTCGAAGAG
19805093 CTTCCCGTTATATGGCTCGAAAGAG
1 CTTCCCGTT-TATGGCTCG-AAGAG
19805118 CTTCCCGTTTA
1 CTTCCCGTTTA
19805129 CATGTTTGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
23 8 0.25
24 11 0.34
25 13 0.41
ACGTcount: A:0.19, C:0.27, G:0.22, T:0.32
Consensus pattern (23 bp):
CTTCCCGTTTATGGCTCGAAGAG
Found at i:19806490 original size:76 final size:76
Alignment explanation
Indices: 19806374--19806521 Score: 219
Period size: 76 Copynumber: 1.9 Consensus size: 76
19806364 TTTAGTCTCG
19806374 ACTTTTTTCTAATGTATATTTTGGGCCTCGAGAGTTCATATAAGGGACCACATGA-TTAGTTTTG
1 ACTTTTTTCTAATGTATATTTTGGGCCTCGAGAGTTCATATAAGGGACCACATGATTTA-TTTTG
19806438 TTTGGTTTCCCA
65 TTTGGTTTCCCA
* * * * *
19806450 ACTTATTTT-TAATGTGTATTTTGGGCCTTGAGGGTTCATATAAGGGACTATATGATTTATTTTG
1 ACTT-TTTTCTAATGTATATTTTGGGCCTCGAGAGTTCATATAAGGGACCACATGATTTATTTTG
19806514 TTTGGTTT
65 TTTGGTTT
19806522 ATGATATGAA
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
76 58 0.89
77 7 0.11
ACGTcount: A:0.22, C:0.11, G:0.21, T:0.46
Consensus pattern (76 bp):
ACTTTTTTCTAATGTATATTTTGGGCCTCGAGAGTTCATATAAGGGACCACATGATTTATTTTGT
TTGGTTTCCCA
Found at i:19806856 original size:79 final size:79
Alignment explanation
Indices: 19806717--19807032 Score: 384
Period size: 79 Copynumber: 4.0 Consensus size: 79
19806707 CAGTTAGATC
* * * *
19806717 GAGACAACTTCCGAGAAACAAGAGGAACACCAAAGTACCTCACTAGCAGCTTACCAACTTTAAAC
1 GAGACATCTTCCAAGAAACAAGAGGAACACCAAGGTACCTCACTAGCAGCCTACCAACTTTAAAC
**
19806782 CTTGTATAAGAAGT
66 CTTGTGCAAGAAGT
*
19806796 GAGACATCTTCCAAGAAACAAGAGGAACACCGAA-GTACCTCACTAGCAGCCTACCGACTTTAAA
1 GAGACATCTTCCAAGAAACAAGAGGAACACC-AAGGTACCTCACTAGCAGCCTACCAACTTTAAA
19806860 CCTTGTGCAAGAAGT
65 CCTTGTGCAAGAAGT
* ** * * * *
19806875 GAGACAGCTTCCAAGAAACAAGAGGTGCACCAAGGTACCTCATTGGTAGCTTACCAACTTTAAAC
1 GAGACATCTTCCAAGAAACAAGAGGAACACCAAGGTACCTCACTAGCAGCCTACCAACTTTAAAC
19806940 CTTGTGCAAGAAGT
66 CTTGTGCAAGAAGT
* * * * * * * * *
19806954 GAGA-TTGCTTTCGAGAAACAAAAGGAGCACCAATGTACCTCATTGGCAACCTACCAACTTTAAA
1 GAGACAT-CTTCCAAGAAACAAGAGGAACACCAAGGTACCTCACTAGCAGCCTACCAACTTTAAA
*
19807018 CCTTGTGCAAAAAGT
65 CCTTGTGCAAGAAGT
19807033 CATGAGAGCC
Statistics
Matches: 209, Mismatches: 25, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
78 2 0.01
79 205 0.98
80 2 0.01
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (79 bp):
GAGACATCTTCCAAGAAACAAGAGGAACACCAAGGTACCTCACTAGCAGCCTACCAACTTTAAAC
CTTGTGCAAGAAGT
Found at i:19809602 original size:5 final size:5
Alignment explanation
Indices: 19809592--19809627 Score: 72
Period size: 5 Copynumber: 7.2 Consensus size: 5
19809582 TGGTGGGGTA
19809592 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG A
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG A
19809628 GCAAACCTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:19812728 original size:43 final size:43
Alignment explanation
Indices: 19812669--19812751 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
19812659 TTTCAGTAGA
* * * *
19812669 TTTCTCGATTGTGATTTTATTTTAATTGATTTCTTTCCTTAGG
1 TTTCTCGATTGCGATTTCACTTTAATTGATTTCTGTCCTTAGG
* *
19812712 TTTCTCTATTGCGATTTCACTTTAGTTGATTTCTGTCCTT
1 TTTCTCGATTGCGATTTCACTTTAATTGATTTCTGTCCTT
19812752 TCTAGAATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.14, C:0.16, G:0.13, T:0.57
Consensus pattern (43 bp):
TTTCTCGATTGCGATTTCACTTTAATTGATTTCTGTCCTTAGG
Found at i:19819661 original size:24 final size:25
Alignment explanation
Indices: 19819628--19819681 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
19819618 CCGTTAACTT
19819628 AAAATAAAAATA-AAAAATATTTAA
1 AAAATAAAAATATAAAAATATTTAA
* * * *
19819652 AAAATCAAAATATTAATATTTTTAA
1 AAAATAAAAATATAAAAATATTTAA
19819677 AAAAT
1 AAAAT
19819682 TATTATATCA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 11 0.44
25 14 0.56
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (25 bp):
AAAATAAAAATATAAAAATATTTAA
Done.