Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015093.1 Kokia drynarioides strain JFW-HI SEQ_130137, whole genome shotgun sequence
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: 636787
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 555 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:381236 original size:15 final size:15
Alignment explanation
Indices: 381216--381246 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
381206 AATATCGTGT
381216 GGTTATCCATACAAG
1 GGTTATCCATACAAG
381231 GGTTATCCATACAAG
1 GGTTATCCATACAAG
381246 G
1 G
381247 AGAAGTGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (15 bp):
GGTTATCCATACAAG
Found at i:381876 original size:20 final size:19
Alignment explanation
Indices: 381833--381876 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
381823 TGATCATTTT
*
381833 TTTTAATATTCAAAATATA
1 TTTTAATATTCAAAATAAA
* *
381852 GTTTATATATTCAAATTAAA
1 TTTTA-ATATTCAAAATAAA
381872 TTTTA
1 TTTTA
381877 CAAATAATTA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (19 bp):
TTTTAATATTCAAAATAAA
Found at i:383122 original size:32 final size:33
Alignment explanation
Indices: 383061--383136 Score: 104
Period size: 32 Copynumber: 2.3 Consensus size: 33
383051 CCTATTTACT
*
383061 TAAAATAA-ATAATTTCAGTCAAAATAAAATTAAG
1 TAAAATAACA-AATTTCAGTCAAAAAAAAATT-AG
383095 -AAAATAACAAATTT-AGTCAAAAAAAAATTAG
1 TAAAATAACAAATTTCAGTCAAAAAAAAATTAG
383126 TAAAATAACAA
1 TAAAATAACAA
383137 CTTTGAATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
31 2 0.05
32 24 0.62
33 12 0.31
34 1 0.03
ACGTcount: A:0.63, C:0.07, G:0.05, T:0.25
Consensus pattern (33 bp):
TAAAATAACAAATTTCAGTCAAAAAAAAATTAG
Found at i:393775 original size:14 final size:14
Alignment explanation
Indices: 393750--393806 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
393740 ATAAATAATT
393750 TTAGTCAAAATAAAA
1 TTAGT-AAAATAAAA
393765 TTAAG-AAAATAACAAA
1 TT-AGTAAAAT-A-AAA
393781 TTTAGTAAAA-AAAA
1 -TTAGTAAAATAAAA
393795 TTAGTAAAATAA
1 TTAGTAAAATAA
393807 CAACTTTGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 13
0.73 0.00 0.27
Matches are distributed among these distances:
13 9 0.25
14 10 0.28
15 4 0.11
16 7 0.19
17 6 0.17
ACGTcount: A:0.63, C:0.04, G:0.07, T:0.26
Consensus pattern (14 bp):
TTAGTAAAATAAAA
Found at i:393797 original size:30 final size:32
Alignment explanation
Indices: 393736--393809 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 32
393726 CTTATTTACT
393736 TAAAATAA-ATAATTTTAGTCAAAATAAAATTAAG
1 TAAAATAACA-AA-TTTAGTCAAAATAAAATT-AG
393770 -AAAATAACAAATTTAGT-AAAA-AAAATTAG
1 TAAAATAACAAATTTAGTCAAAATAAAATTAG
393799 TAAAATAACAA
1 TAAAATAACAA
393810 CTTTGAATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
29 2 0.05
30 16 0.42
31 4 0.11
32 6 0.16
33 9 0.24
34 1 0.03
ACGTcount: A:0.64, C:0.04, G:0.05, T:0.27
Consensus pattern (32 bp):
TAAAATAACAAATTTAGTCAAAATAAAATTAG
Found at i:395125 original size:40 final size:41
Alignment explanation
Indices: 395079--395168 Score: 155
Period size: 40 Copynumber: 2.2 Consensus size: 41
395069 TTAAAAATTA
*
395079 TTTTTAATACAATAAAATATTTATTATATTTATGGTAGTG-
1 TTTTTAATACAATAAAACATTTATTATATTTATGGTAGTGT
*
395119 TTTTTAATATAATAAAACATTTATTATATTTATGGTAGTGT
1 TTTTTAATACAATAAAACATTTATTATATTTATGGTAGTGT
395160 TTTTTAATA
1 TTTTTAATA
395169 TAAATATTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
40 38 0.81
41 9 0.19
ACGTcount: A:0.37, C:0.02, G:0.09, T:0.52
Consensus pattern (41 bp):
TTTTTAATACAATAAAACATTTATTATATTTATGGTAGTGT
Found at i:395835 original size:23 final size:25
Alignment explanation
Indices: 395788--395835 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
395778 TTTCTAATAT
*
395788 TTATTATTTTTTACTTTGACTCTAA
1 TTATTATTTTTTACTTTGACCCTAA
*
395813 TTATT-TTTTTTAC-TTGGCCCTAA
1 TTATTATTTTTTACTTTGACCCTAA
395836 ACTTTTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 8 0.38
24 8 0.38
25 5 0.24
ACGTcount: A:0.21, C:0.15, G:0.06, T:0.58
Consensus pattern (25 bp):
TTATTATTTTTTACTTTGACCCTAA
Found at i:396589 original size:21 final size:23
Alignment explanation
Indices: 396565--396615 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
396555 ATCAGTTTTT
396565 AAATTAATTT-GAAA-TCATATA
1 AAATTAATTTAGAAATTCATATA
* * *
396586 AAATAAATTTATAAATTTATATA
1 AAATTAATTTAGAAATTCATATA
396609 AAATTAA
1 AAATTAA
396616 AAATATATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 9 0.38
22 3 0.12
23 12 0.50
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (23 bp):
AAATTAATTTAGAAATTCATATA
Found at i:396634 original size:14 final size:16
Alignment explanation
Indices: 396603--396632 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
396593 TTTATAAATT
396603 TATATAAAATTAAAAA
1 TATATAAAATTAAAAA
396619 TATATAAAA-TAAAA
1 TATATAAAATTAAAA
396633 TAGGATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
TATATAAAATTAAAAA
Found at i:405626 original size:91 final size:91
Alignment explanation
Indices: 405459--405626 Score: 284
Period size: 92 Copynumber: 1.8 Consensus size: 91
405449 TGATCTCATT
* *
405459 CAATTAAAAAAAGATGCATCATATTTGATTTGGAAGTTTAGTCTAAATGTACATATGATGTAGAA
1 CAATTAAAAAAAGATGCATCATATTTGATTTGGAAGTTTAATCCAAATGTACATATGATGTAGAA
405524 AAAAAGATGATAAAGATGATCCCGTC
66 AAAAAGATGATAAAGATGATCCCGTC
* *
405550 CAATTAAAAAAAGATTGCATCATCTTTGATTTGGAAGTTTAATCCAAATGTACGTATGATGTAG-
1 CAATTAAAAAAAGA-TGCATCATATTTGATTTGGAAGTTTAATCCAAATGTACATATGATGTAGA
405614 AAAAAAGATGATA
65 AAAAAAGATGATA
405627 TGTCCTCTTT
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
91 27 0.38
92 45 0.62
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.30
Consensus pattern (91 bp):
CAATTAAAAAAAGATGCATCATATTTGATTTGGAAGTTTAATCCAAATGTACATATGATGTAGAA
AAAAAGATGATAAAGATGATCCCGTC
Found at i:405760 original size:28 final size:27
Alignment explanation
Indices: 405729--405799 Score: 79
Period size: 31 Copynumber: 2.4 Consensus size: 27
405719 TATTTTCAAC
*
405729 TATTTTATTTATCTTAAATAAGATTTTA
1 TATTTTATTTATATTAAATAA-ATTTTA
*
405757 TATTTTTATTGTTATATTAAATTAATTTTA
1 TA-TTTTA-T-TTATATTAAATAAATTTTA
405787 TATTTTAATTTAT
1 TATTTT-ATTTAT
405800 GAACTCAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
28 6 0.16
29 10 0.27
30 10 0.27
31 11 0.30
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (27 bp):
TATTTTATTTATATTAAATAAATTTTA
Found at i:410406 original size:105 final size:105
Alignment explanation
Indices: 410224--410433 Score: 377
Period size: 105 Copynumber: 2.0 Consensus size: 105
410214 AGTTACGAAA
* *
410224 ATATTAAAAGTAATATTATATTTGTAAAAGAAAATGATAATATTTCATTGAGACGTAAGGCTCCT
1 ATATTAAAAATAATATTATATTTGTAAAAGAAAATGATAATATTTCATTGAGACATAAGGCTCCT
*
410289 ATTAAATTCATTTTTTAGTTAAAAGTATGAA-ACGCTCTAT
66 ATTAAATTCATTTTTTAGTTAAAAATATGAACA-GCTCTAT
410329 ATATTAAAAATAATATTATATTTGTAAAAGAAAATGATAATATTTCATTGAGACATAAGGCTCCT
1 ATATTAAAAATAATATTATATTTGTAAAAGAAAATGATAATATTTCATTGAGACATAAGGCTCCT
410394 ATTAAATTCATTTTTTAGTTAAAAATATGAACAGCTCTAT
66 ATTAAATTCATTTTTTAGTTAAAAATATGAACAGCTCTAT
410434 TTCCTTTTAA
Statistics
Matches: 101, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
105 100 0.99
106 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.38
Consensus pattern (105 bp):
ATATTAAAAATAATATTATATTTGTAAAAGAAAATGATAATATTTCATTGAGACATAAGGCTCCT
ATTAAATTCATTTTTTAGTTAAAAATATGAACAGCTCTAT
Found at i:410585 original size:31 final size:31
Alignment explanation
Indices: 410548--410608 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
410538 TTATCTGGTC
*
410548 ATTAAATTATTTTAAAGTTTTCATTTAAGTT
1 ATTAAATTATTTAAAAGTTTTCATTTAAGTT
*
410579 ATTAAATTATTTAAAAGTTTTTATTTAAGT
1 ATTAAATTATTTAAAAGTTTTCATTTAAGT
410609 CGTCGAGCTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.54
Consensus pattern (31 bp):
ATTAAATTATTTAAAAGTTTTCATTTAAGTT
Found at i:412993 original size:19 final size:18
Alignment explanation
Indices: 412969--413016 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
412959 TTATTATTAA
412969 TTAATTTTAAATTATATAT
1 TTAATTTTAAATTATAT-T
*
412988 TTAATTATT-TATTATATT
1 TTAATT-TTAAATTATATT
*
413006 TTATTTTTAAA
1 TTAATTTTAAA
413017 AATAGATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
17 2 0.08
18 7 0.29
19 13 0.54
20 2 0.08
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTAATTTTAAATTATATT
Found at i:413268 original size:8 final size:8
Alignment explanation
Indices: 413255--413280 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
413245 GGCTGCAGAG
413255 AAAAAAGA
1 AAAAAAGA
413263 AAAAAAGA
1 AAAAAAGA
413271 AAAAAAGA
1 AAAAAAGA
413279 AA
1 AA
413281 TCCAGTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:417119 original size:39 final size:39
Alignment explanation
Indices: 417076--417152 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
417066 GTCAGTCAAC
* * *
417076 AAAATGCGAAATTTA-CTAGAATGCTTAGTGGGATTGAAG
1 AAAATG-GAAAATTATCCAGAATGCTTAGTGGGACTGAAG
*
417115 AAAATGGAAAATTATCCAGAATTCTTAGTGGGACTGAA
1 AAAATGGAAAATTATCCAGAATGCTTAGTGGGACTGAA
417153 AGGATTGGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 7 0.21
39 26 0.79
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.27
Consensus pattern (39 bp):
AAAATGGAAAATTATCCAGAATGCTTAGTGGGACTGAAG
Found at i:425179 original size:109 final size:109
Alignment explanation
Indices: 424986--425205 Score: 404
Period size: 109 Copynumber: 2.0 Consensus size: 109
424976 ACACAACTCT
* *
424986 ATATGGATTGAACATAAGAACCATTTTTATGAATGATGAAAACAATATATGAGAAATAGATTATA
1 ATATGGATTGAACATAAGAACCATATTTATGAATGATGAAAACAATATATGAGAAATAGATTACA
**
425051 CGGATTACTATCAGTAATAAATGCATTTTTCAAAGTAGCAAGAG
66 CGGATTACTATCAACAATAAATGCATTTTTCAAAGTAGCAAGAG
425095 ATATGGATTGAACATAAGAACCATATTTATGAATGATGAAAACAATATATGAGAAATAGATTACA
1 ATATGGATTGAACATAAGAACCATATTTATGAATGATGAAAACAATATATGAGAAATAGATTACA
425160 CGGATTACTATCAACAATAAATGCATTTTTCAAAGTAGCAAGAG
66 CGGATTACTATCAACAATAAATGCATTTTTCAAAGTAGCAAGAG
425204 AT
1 AT
425206 GACTTAAAAA
Statistics
Matches: 107, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
109 107 1.00
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.29
Consensus pattern (109 bp):
ATATGGATTGAACATAAGAACCATATTTATGAATGATGAAAACAATATATGAGAAATAGATTACA
CGGATTACTATCAACAATAAATGCATTTTTCAAAGTAGCAAGAG
Found at i:430495 original size:9 final size:9
Alignment explanation
Indices: 430441--430548 Score: 56
Period size: 9 Copynumber: 11.3 Consensus size: 9
430431 TTTCTATCTC
*
430441 TATATATTT
1 TATAAATTT
*
430450 TATAATTTT
1 TATAAATTT
* *
430459 TTTCAATTTT
1 TAT-AAATTT
**
430469 TATAAAAGT
1 TATAAATTT
*
430478 TACAAATTT
1 TATAAATTT
430487 TATAAATTTT
1 TATAAA-TTT
*
430497 TACAAATTTT
1 TATAAA-TTT
*
430507 TTTAAATTT
1 TATAAATTT
430516 T-TAATATTT
1 TATAA-ATTT
430525 TCATTAAAATTT
1 T-A-T-AAATTT
*
430537 AATAAATTT
1 TATAAATTT
430546 TAT
1 TAT
430549 TGATTTTTAT
Statistics
Matches: 76, Mismatches: 16, Indels: 14
0.72 0.15 0.13
Matches are distributed among these distances:
8 3 0.04
9 40 0.53
10 25 0.33
11 1 0.01
12 5 0.07
13 2 0.03
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.56
Consensus pattern (9 bp):
TATAAATTT
Found at i:430503 original size:10 final size:10
Alignment explanation
Indices: 430477--430518 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
430467 TTTATAAAAG
430477 TTACAAA-TT
1 TTACAAATTT
*
430486 TTATAAATTT
1 TTACAAATTT
430496 TTACAAATTT
1 TTACAAATTT
**
430506 TTTTAAATTT
1 TTACAAATTT
430516 TTA
1 TTA
430519 ATATTTTCAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
9 6 0.22
10 21 0.78
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (10 bp):
TTACAAATTT
Found at i:430516 original size:19 final size:19
Alignment explanation
Indices: 430463--430516 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
430453 AATTTTTTTC
**
430463 AATTTTTATAAAAGTTACA
1 AATTTTTATAAATTTTACA
430482 AA-TTTTATAAATTTTTACA
1 AATTTTTATAAA-TTTTACA
*
430501 AATTTTTTTAAATTTT
1 AATTTTTATAAATTTT
430517 TAATATTTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 9 0.30
19 13 0.43
20 8 0.27
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.54
Consensus pattern (19 bp):
AATTTTTATAAATTTTACA
Found at i:430531 original size:20 final size:20
Alignment explanation
Indices: 430477--430549 Score: 78
Period size: 20 Copynumber: 3.7 Consensus size: 20
430467 TTTATAAAAG
430477 TTACAAATTTTA-TAAATTT
1 TTACAAATTTTATTAAATTT
*
430496 TTACAAATTTTTTTAAATTT
1 TTACAAATTTTATTAAATTT
* *
430516 TTA-ATATTTTCATTAAAATT
1 TTACAAATTTT-ATTAAATTT
* *
430536 TAATAAATTTTATT
1 TTACAAATTTTATT
430550 GATTTTTATT
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
19 17 0.38
20 22 0.49
21 6 0.13
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (20 bp):
TTACAAATTTTATTAAATTT
Found at i:442438 original size:4 final size:4
Alignment explanation
Indices: 442429--442457 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
442419 CACTTAAAAA
442429 AATT AATT AATT AATT AATT AATT AATT A
1 AATT AATT AATT AATT AATT AATT AATT A
442458 TAATCTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:444620 original size:21 final size:22
Alignment explanation
Indices: 444580--444623 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
444570 GGCGGCATTC
* *
444580 AATAGAGAATTCCTATTTAAGT
1 AATAGAGAACTCCTACTTAAGT
444602 AATAGAG-ACTCCTACTTAAGT
1 AATAGAGAACTCCTACTTAAGT
444623 A
1 A
444624 GTGTTTTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.32
Consensus pattern (22 bp):
AATAGAGAACTCCTACTTAAGT
Found at i:456667 original size:91 final size:91
Alignment explanation
Indices: 456512--456694 Score: 330
Period size: 91 Copynumber: 2.0 Consensus size: 91
456502 CTTGTAAAAG
456512 CTTGACATGTGGCACCTCAAGACAAAGATTAACAGCAAATAAGGCTTAAAGCTCTTATAAAGCAA
1 CTTGACATGTGGCACCTCAAGACAAAGATTAACAGCAAATAAGGCTTAAAGCTCTTATAAAGCAA
*
456577 GGTGATCCTTTCTCTCTCTTCTCTCA
66 GGTGAACCTTTCTCTCTCTTCTCTCA
* * *
456603 CTTGACATGTGGCACCTCAAGACCAAGATTAAGAGCAAATAAGGCTTAAAGTTCTTATAAAGCAA
1 CTTGACATGTGGCACCTCAAGACAAAGATTAACAGCAAATAAGGCTTAAAGCTCTTATAAAGCAA
456668 GGTGAACCTTTCTCTCTCTTCTCTCA
66 GGTGAACCTTTCTCTCTCTTCTCTCA
456694 C
1 C
456695 CTATTCTCAC
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
91 88 1.00
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (91 bp):
CTTGACATGTGGCACCTCAAGACAAAGATTAACAGCAAATAAGGCTTAAAGCTCTTATAAAGCAA
GGTGAACCTTTCTCTCTCTTCTCTCA
Found at i:459429 original size:367 final size:365
Alignment explanation
Indices: 458734--459415 Score: 901
Period size: 367 Copynumber: 1.9 Consensus size: 365
458724 TTTCTGGGTA
* * * *
458734 TATTGCATTTGTTTGTTTATGTGCTTTAGCTTGAAGGCAACTTGGTGCATTTTAATTTTGTTGAA
1 TATTGCATTTGTATGTCTATGTGCTTTAGCTTGAAGGCAACTTAGTGCATCTTAATTTTGTTGAA
* * *
458799 AAACCTAAATGCTAATTGTAATTAACAAAAAAAAAGTTGTGGTTAATATGTTGATTTTTTTTGTC
66 AAACCTAAATGATAACTGTAATTAACAAAAAAAAAGTTGTGGTTAATATGTTGATTTTTGTTG--
** * * *
458864 ATCTTGTAATTATTTCTAAGAGTGGAACTGGTTGGTGTGGGATGTTTAAACTCTTGGTGAGGTTC
129 ATCTTGTAATTATTTCTAAGAGTGGAACCAGTTGCTATGGGATGTTTAAACTCATGGTGAGGTTC
* * * *
458929 GAGTTGAGCTAATCTTTTGGTGAGCATTGATACATTTATAATAATGGTTTTCAAATCTACAAAAG
194 GAGTTGAGCTAATCTTTTGGTGAGCATTGATACATATATAAAAAAGGTTTTCAAATCAACAAAAG
* * * *
458994 AATTTCCTTTTTCCTTCTTAGGTTCAATACTCTCTTATTGCATTGCCTTATTTGTGAAAAATGAG
259 AACTTCCTTTTCCCTTCTTAGGCTCAATACTCTCTTATTGCATTGCCTTATTTGTGAAAAAGGAG
459059 GAGTTTTCAAATGTGTTTAGACATACTTTAGAAAAGCCAGAT
324 GAGTTTTCAAATGTGTTTAGACATACTTTAGAAAAGCCAGAT
* * * *
459101 TATTGCATTTGTATGTCTGTGTGGTTTAGCTTGAAGGC-AGTGTAGTGCATCTTAATTTTGTTTA
1 TATTGCATTTGTATGTCTATGTGCTTTAGCTTGAAGGCAACT-TAGTGCATCTTAATTTTGTTGA
* *
459165 GAAACCTAAATGATAACTGTAATTAACCAAAAAAAAAATGTTGTGGTTAGTATGTTGATTTGTTG
65 AAAACCTAAATGATAACTGTAATTAA-C-AAAAAAAAA-GTTGTGGTTAATATGTTGATTT-TTG
*
459230 TTG-TGTTGTAATTATTTCTAAGAGTGGAACCAGTTGCTACAT-GG-TGTTTAAACTCATGGTGA
126 TTGATCTTGTAATTATTTCTAAGAGTGGAACCAGTTGCT--ATGGGATGTTTAAACTCATGGTGA
* *
459292 GGTTCGGGTTGAGCTAATCTTTTGGTG-GCCATTGATGCATA-ATAAAAAAAGG-TTTCAAATCA
189 GGTTCGAGTTGAGCTAATCTTTTGGTGAG-CATTGATACATATAT-AAAAAAGGTTTTCAAATCA
* * * * * *
459354 ACGAAAGAACTTCCTTTTCCCTTCTTAGGCTCAGTGCTTTCTTATTGCATTTCCTTGTTTGT
252 ACAAAAGAACTTCCTTTTCCCTTCTTAGGCTCAATACTCTCTTATTGCATTGCCTTATTTGT
459416 TAACCCGGAG
Statistics
Matches: 272, Mismatches: 34, Indels: 18
0.84 0.10 0.06
Matches are distributed among these distances:
366 2 0.01
367 141 0.52
368 91 0.33
369 11 0.04
370 22 0.08
371 5 0.02
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.40
Consensus pattern (365 bp):
TATTGCATTTGTATGTCTATGTGCTTTAGCTTGAAGGCAACTTAGTGCATCTTAATTTTGTTGAA
AAACCTAAATGATAACTGTAATTAACAAAAAAAAAGTTGTGGTTAATATGTTGATTTTTGTTGAT
CTTGTAATTATTTCTAAGAGTGGAACCAGTTGCTATGGGATGTTTAAACTCATGGTGAGGTTCGA
GTTGAGCTAATCTTTTGGTGAGCATTGATACATATATAAAAAAGGTTTTCAAATCAACAAAAGAA
CTTCCTTTTCCCTTCTTAGGCTCAATACTCTCTTATTGCATTGCCTTATTTGTGAAAAAGGAGGA
GTTTTCAAATGTGTTTAGACATACTTTAGAAAAGCCAGAT
Found at i:469413 original size:136 final size:137
Alignment explanation
Indices: 469246--469522 Score: 384
Period size: 136 Copynumber: 2.0 Consensus size: 137
469236 ACATAGATAA
* * *
469246 AATTAATATATGAATTTGAGTTATACAAAATATTAATTGTATATATTTTGCCTAATTTATTAATA
1 AATTAATATATGAATTTGAGTTATACAAAATACTAATTGTATATATTTTACCAAATTTATTAATA
*
469311 TAAA-CATTATATTAATTAATTTCGGT-AATAA-AAAAAAGACATGAAAATTAATATTCCTTTGG
66 TAAATAATTATATTAATTAATTTCGGTCAA-AATAAAAAAGACATGAAAATTAATATT-CTTTGG
469373 AA-AGAATAT
129 AATA-AATAT
* *
469382 AATTAATATATGAATTTTA-TTCATACAAAATACTAGTTGTATATATTTTACCAAATTTATTAAT
1 AATTAATATATGAATTTGAGTT-ATACAAAATACTAATTGTATATATTTTACCAAATTTATTAAT
* * * * *
469446 ATAAATAATTATATTAATTACTTTTGGTCAAAATATAAAAGACATGATAATTAATATTGTTTGGA
65 ATAAATAATTATATTAATTAATTTCGGTCAAAATAAAAAAGACATGAAAATTAATATTCTTTGGA
469511 ATAAATAT
130 ATAAATAT
469519 AATT
1 AATT
469523 TCTTTTTCTA
Statistics
Matches: 125, Mismatches: 11, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
135 2 0.02
136 61 0.49
137 37 0.30
138 25 0.20
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (137 bp):
AATTAATATATGAATTTGAGTTATACAAAATACTAATTGTATATATTTTACCAAATTTATTAATA
TAAATAATTATATTAATTAATTTCGGTCAAAATAAAAAAGACATGAAAATTAATATTCTTTGGAA
TAAATAT
Found at i:473804 original size:40 final size:39
Alignment explanation
Indices: 473728--473817 Score: 114
Period size: 40 Copynumber: 2.3 Consensus size: 39
473718 GTCAACAAAT
*
473728 AATT-TTAAAATTATTAAAAGTCTTTTTTAAAGATATAA
1 AATTATTAAAATTATTAAAAGTCTTTTTTAAAAATATAA
473766 AATTATTAAAATTAATTTAAAA-T-TATTTTTAAAAATATAA
1 AATTATTAAAATT-A-TTAAAAGTCT-TTTTTAAAAATATAA
*
473806 AATTATGAAAAT
1 AATTATTAAAAT
473818 CATCGTCATC
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
38 4 0.09
39 9 0.20
40 27 0.59
41 6 0.13
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.43
Consensus pattern (39 bp):
AATTATTAAAATTATTAAAAGTCTTTTTTAAAAATATAA
Found at i:473806 original size:20 final size:20
Alignment explanation
Indices: 473751--473811 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
473741 TTAAAAGTCT
*
473751 TTTTTAAAGATATAAAATTA
1 TTTTTAAAAATATAAAATTA
* *
473771 --TTAAAATTAATTTAAAATTA
1 TTTTTAAA--AATATAAAATTA
473791 TTTTTAAAAATATAAAATTA
1 TTTTTAAAAATATAAAATTA
473811 T
1 T
473812 GAAAATCATC
Statistics
Matches: 32, Mismatches: 5, Indels: 8
0.71 0.11 0.18
Matches are distributed among these distances:
18 5 0.16
20 22 0.69
22 5 0.16
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (20 bp):
TTTTTAAAAATATAAAATTA
Found at i:474749 original size:28 final size:28
Alignment explanation
Indices: 474713--474787 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 28
474703 AAAATTATTT
**
474713 AATAATTTTAATAATTTTA-TATTTAAAA
1 AATAATTTTAATAATTTTACT-TCAAAAA
* *
474741 AATATTTTTAAAAATTTCTACTTCAAAAA
1 AATAATTTTAATAATTT-TACTTCAAAAA
474770 AATAATTTTAATAATTTT
1 AATAATTTTAATAATTTT
474788 CAAATCATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
28 16 0.41
29 22 0.56
30 1 0.03
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (28 bp):
AATAATTTTAATAATTTTACTTCAAAAA
Found at i:479560 original size:20 final size:18
Alignment explanation
Indices: 479532--479619 Score: 59
Period size: 20 Copynumber: 4.4 Consensus size: 18
479522 TCACATCAAC
*
479532 AAATGATTTTAAAATTATTA
1 AAATTATTTTAAAA-TA-TA
479552 AAATTATTTTTTAAAATATA
1 AAATTA--TTTTAAAATATA
*** *
479572 AAATTATGAAAATTAATTTA
1 AAATTATTTTAA--AATATA
479592 AAATTAATTTTTAAAATATA
1 AAATT-A-TTTTAAAATATA
479612 AAATTATT
1 AAATTATT
479620 AAAATCATCA
Statistics
Matches: 53, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
18 5 0.09
19 1 0.02
20 33 0.62
21 3 0.06
22 11 0.21
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (18 bp):
AAATTATTTTAAAATATA
Found at i:479595 original size:40 final size:38
Alignment explanation
Indices: 479542--479624 Score: 130
Period size: 40 Copynumber: 2.1 Consensus size: 38
479532 AAATGATTTT
*
479542 AAAATTATTAAAATTATTTTTTAAAATATAAAATTATG
1 AAAATTATTAAAATTAATTTTTAAAATATAAAATTATG
*
479580 AAAATTAATTTAAAATTAATTTTTAAAATATAAAATTATT
1 AAAATT-A-TTAAAATTAATTTTTAAAATATAAAATTATG
479620 AAAAT
1 AAAAT
479625 CATCATTATC
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
38 6 0.15
39 1 0.02
40 34 0.83
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (38 bp):
AAAATTATTAAAATTAATTTTTAAAATATAAAATTATG
Found at i:479604 original size:13 final size:13
Alignment explanation
Indices: 479544--479608 Score: 53
Period size: 13 Copynumber: 4.9 Consensus size: 13
479534 ATGATTTTAA
*
479544 AATTATTAAAATT
1 AATTTTTAAAATT
*
479557 ATTTTTTAAAATAT
1 AATTTTTAAAAT-T
* *
479571 AAAATTATGAAAATT
1 --AATTTTTAAAATT
479586 AA--TTTAAAATT
1 AATTTTTAAAATT
479597 AATTTTTAAAAT
1 AATTTTTAAAAT
479609 ATAAAATTAT
Statistics
Matches: 40, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
11 9 0.22
13 20 0.50
14 1 0.03
15 1 0.03
16 9 0.22
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (13 bp):
AATTTTTAAAATT
Found at i:482340 original size:17 final size:19
Alignment explanation
Indices: 482300--482340 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
482290 ATTTAAAAAG
482300 CATTATTAAATTTATTACAA
1 CATT-TTAAATTTATTACAA
482320 -ATTTTAAA-TTATTA-AA
1 CATTTTAAATTTATTACAA
482336 CATTT
1 CATTT
482341 AATTTTTAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
16 2 0.10
17 10 0.50
18 5 0.25
19 3 0.15
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (19 bp):
CATTTTAAATTTATTACAA
Found at i:483140 original size:42 final size:42
Alignment explanation
Indices: 483081--483165 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
483071 ACCCAGACTG
*
483081 TATAAAATTGGAGCCATCTATTTGTTGAAACTTGGCCACGCC
1 TATAAAATTGGAGCCATCTATTCGTTGAAACTTGGCCACGCC
* * *
483123 TATAAATTTTGAGCCATCTATTCGTTGAGACTTGGCCACGCC
1 TATAAAATTGGAGCCATCTATTCGTTGAAACTTGGCCACGCC
483165 T
1 T
483166 TATCCACACA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (42 bp):
TATAAAATTGGAGCCATCTATTCGTTGAAACTTGGCCACGCC
Found at i:485215 original size:3 final size:3
Alignment explanation
Indices: 485207--485231 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
485197 AAAGTAAGTT
485207 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
485232 AAATCAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:492463 original size:32 final size:32
Alignment explanation
Indices: 492400--492464 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
492390 ATGCATGACT
*
492400 ACTAATACATCTACTCAAAGTACATTAATTAA
1 ACTAATACATCTACTCAAAGTACATCAATTAA
** *
492432 ACTAGATACATCTACTTTAA-TACATCCATTAA
1 ACTA-ATACATCTACTCAAAGTACATCAATTAA
492464 A
1 A
492465 TATAAGTACA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 15 0.54
33 13 0.46
ACGTcount: A:0.45, C:0.20, G:0.03, T:0.32
Consensus pattern (32 bp):
ACTAATACATCTACTCAAAGTACATCAATTAA
Found at i:508476 original size:14 final size:14
Alignment explanation
Indices: 508457--508489 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
508447 TACAATATTC
508457 AAATAATAGCAACA
1 AAATAATAGCAACA
508471 AAATAATAGCAACA
1 AAATAATAGCAACA
*
508485 TAATA
1 AAATA
508490 GTGAAATGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.64, C:0.12, G:0.06, T:0.18
Consensus pattern (14 bp):
AAATAATAGCAACA
Found at i:512444 original size:11 final size:12
Alignment explanation
Indices: 512417--512449 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
512407 AACAGATAAA
*
512417 AAAAATATTTTG
1 AAAAATATTGTG
512429 AAAAATATTGTG
1 AAAAATATTGTG
512441 AAAAA-ATTG
1 AAAAATATTG
512450 ATTTTAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.55, C:0.00, G:0.12, T:0.33
Consensus pattern (12 bp):
AAAAATATTGTG
Found at i:512680 original size:16 final size:17
Alignment explanation
Indices: 512649--512680 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
512639 GTCTCAATTA
512649 TTATTAAATATTTTAAT
1 TTATTAAATATTTTAAT
512666 TTATTAAAT-TTTTAA
1 TTATTAAATATTTTAA
512681 AAAAAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTATTAAATATTTTAAT
Found at i:513202 original size:29 final size:30
Alignment explanation
Indices: 513138--513210 Score: 80
Period size: 29 Copynumber: 2.4 Consensus size: 30
513128 AATTATATAT
*
513138 AAATTTTAATTTAACGTACAATGTAATACATG
1 AAATTTTAATTT--TGTACAATGTAATACATG
513170 -AATTTTAATTTTGTACAATTGT-AT-CATG
1 AAATTTTAATTTTGTACAA-TGTAATACATG
*
513198 AAATTTTTATTTT
1 AAATTTTAATTTT
513211 AATTCAATCT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
28 4 0.11
29 19 0.51
30 3 0.08
31 11 0.30
ACGTcount: A:0.37, C:0.07, G:0.08, T:0.48
Consensus pattern (30 bp):
AAATTTTAATTTTGTACAATGTAATACATG
Found at i:515429 original size:16 final size:18
Alignment explanation
Indices: 515403--515443 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 18
515393 AAAGGAATTA
515403 AACATTATATAA-AAAAG
1 AACATTATATAATAAAAG
515420 AACA-TATATAATAAAA-
1 AACATTATATAATAAAAG
515436 AAC-TTATA
1 AACATTATA
515444 GTGAGATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.27
Consensus pattern (18 bp):
AACATTATATAATAAAAG
Found at i:515435 original size:19 final size:17
Alignment explanation
Indices: 515403--515437 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
515393 AAAGGAATTA
515403 AACATTATATAAAAAAG
1 AACATTATATAAAAAAG
515420 AACATATATAATAAAAAA
1 AACAT-TAT-ATAAAAAA
515438 CTTATAGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 3 0.19
19 8 0.50
ACGTcount: A:0.69, C:0.06, G:0.03, T:0.23
Consensus pattern (17 bp):
AACATTATATAAAAAAG
Found at i:516541 original size:30 final size:28
Alignment explanation
Indices: 516492--516563 Score: 81
Period size: 30 Copynumber: 2.5 Consensus size: 28
516482 ATCGAAGTTG
* * *
516492 AAAATGAGATTTTTGGATACCCGAGGGGGC
1 AAAATGATAATTTTAGATACCCGA--GGGC
* *
516522 AAAATGGTAATTTTAGATACTCGAGGGC
1 AAAATGATAATTTTAGATACCCGAGGGC
516550 AAAATGATAATTTT
1 AAAATGATAATTTT
516564 GGAAAAGTTC
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
28 17 0.47
30 19 0.53
ACGTcount: A:0.36, C:0.10, G:0.25, T:0.29
Consensus pattern (28 bp):
AAAATGATAATTTTAGATACCCGAGGGC
Found at i:516620 original size:29 final size:27
Alignment explanation
Indices: 516579--516682 Score: 97
Period size: 28 Copynumber: 3.7 Consensus size: 27
516569 AGTTCATGGT
* *
516579 TAAAAAGGGAATTTTTGGACATCCGAGGG
1 TAAAATGGTAATTTTTGGA-AT-CGAGGG
*
516608 TAAAATGGTAATTTTTGGAAAATAG-GGG
1 TAAAATGGTAATTTTTGG--AATCGAGGG
*
516636 TCAAATGG-AATTTTTGGAAGTTCGAGGG
1 TAAAATGGTAATTTTTGGAA--TCGAGGG
516664 TAAAATGGTAA-TTTTGGAA
1 TAAAATGGTAATTTTTGGAA
516683 AAAAAAAAAT
Statistics
Matches: 63, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
25 2 0.03
27 11 0.17
28 28 0.44
29 19 0.30
30 2 0.03
31 1 0.02
ACGTcount: A:0.36, C:0.05, G:0.29, T:0.31
Consensus pattern (27 bp):
TAAAATGGTAATTTTTGGAATCGAGGG
Found at i:516636 original size:28 final size:29
Alignment explanation
Indices: 516603--517043 Score: 107
Period size: 30 Copynumber: 14.9 Consensus size: 29
516593 TTGGACATCC
516603 GAGGGTAAAATGGTAATTTTTGGAAAATA
1 GAGGGTAAAATGGTAATTTTTGGAAAATA
* ** *
516632 G-GGGTCAAATGG-AATTTTTGGAAGTTC
1 GAGGGTAAAATGGTAATTTTTGGAAAATA
*
516659 GAGGGTAAAATGGTAA-TTTTGGAAAAAAAAA
1 GAGGGTAAAATGGTAATTTTTGG---AAAATA
* ** *
516690 AATCGGGATCAAAAATGG-AATTTTTGGAAGCTT
1 GA--GGG-T--AAAATGGTAATTTTTGGAAAATA
** * * * *
516723 G-GGGTTAAAAACG-AATTTTTTTGACATTC
1 GAGGG-TAAAATGGTAA-TTTTTGGAAAATA
*
516752 G-GGGTTAAAATGGTAATTTTTTGGAAAAATC
1 GAGGG-TAAAATGGTAA-TTTTTGG-AAAATA
* **
516783 GA-GGTCAAAAATAG-AATTTTTGGAAGTTTA
1 GAGGGT--AAAATGGTAATTTTTGGAA-AATA
*
516813 G-GGGTAAAAATGGTAATTTTGGGAAAA-A
1 GAGGGT-AAAATGGTAATTTTTGGAAAATA
**
516841 -ATGGGATAAAAATGG-AATTTTTGGAAGTTTA
1 GA-GGG-T-AAAATGGTAATTTTTGGAA-AATA
* *
516872 GA-GGTAAAATGGT-ATTTTTTGAAAAAA
1 GAGGGTAAAATGGTAATTTTTGGAAAATA
* * * *
516899 TCATGGTCAAAAATGG-AA-TTTTGGAAAGTTT
1 -GAGGGT--AAAATGGTAATTTTTGGAAA-ATA
* * *
516930 GAGGGTAAAATTGTAATTTCTGGGAAAATC
1 GAGGGTAAAATGGTAATTT-TTGGAAAATA
* * *
516960 GA-TGTCAAAAATGG-AA-TTTTGGAAAGTTT
1 GAGGGT--AAAATGGTAATTTTTGGAAA-ATA
* *
516989 GGGGGTAAAAAT-GTAATTTTTGGAAAAATTT
1 GAGGGT-AAAATGGTAATTTTTGG-AAAA-TA
*
517020 GAGGTTAAAATGG-AATTTTTGGAA
1 GAGGGTAAAATGGTAATTTTTGGAA
517044 GTTCGGGGGT
Statistics
Matches: 303, Mismatches: 64, Indels: 90
0.66 0.14 0.20
Matches are distributed among these distances:
27 14 0.05
28 64 0.21
29 66 0.22
30 88 0.29
31 43 0.14
32 7 0.02
33 5 0.02
34 1 0.00
35 2 0.01
36 13 0.04
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.32
Consensus pattern (29 bp):
GAGGGTAAAATGGTAATTTTTGGAAAATA
Found at i:516803 original size:59 final size:59
Alignment explanation
Indices: 516752--517067 Score: 312
Period size: 59 Copynumber: 5.3 Consensus size: 59
516742 TTTGACATTC
* *
516752 GGGGTTAAAATGGTAATTTTTTGGAAAAATCGAGGTCAAAAATAGAATTTTTGGAAGTTTA
1 GGGGTAAAAATGGTAA-TTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTGGAAG-TTA
*
516813 GGGGTAAAAATGGTAATTTTGGGAAAAAAT-G-GGAT-AAAAATGGAATTTTTGGAAGTTTA
1 GGGGTAAAAATGGTAATTTTTGG-AAAAATCGAGG-TCAAAAATGGAATTTTTGGAAG-TTA
* * * *
516872 GAGGT-AAAATGGTATTTTTTGAAAAAATC-ATGGTCAAAAATGGAA-TTTTGGAAAGTTT
1 GGGGTAAAAATGGTAATTTTTGGAAAAATCGA-GGTCAAAAATGGAATTTTTGG-AAGTTA
* * * * *
516930 GAGGGT-AAAATTGTAATTTCTGGGAAAATCGATGTCAAAAATGGAA-TTTTGGAAAGTTTG
1 G-GGGTAAAAATGGTAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTGG-AAG-TTA
* * *
516990 GGGGTAAAAAT-GTAATTTTTGGAAAAATTTGAGGT-TAAAATGGAATTTTTGGAAGTTCG
1 GGGGTAAAAATGGTAATTTTTGGAAAAA-TCGAGGTCAAAAATGGAATTTTTGGAAGTT-A
517049 GGGGTAAAAAT-GTAATTTT
1 GGGGTAAAAATGGTAATTTT
517068 CAAAAAGTTC
Statistics
Matches: 220, Mismatches: 21, Indels: 30
0.81 0.08 0.11
Matches are distributed among these distances:
57 6 0.03
58 26 0.12
59 139 0.63
60 28 0.13
61 21 0.10
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.34
Consensus pattern (59 bp):
GGGGTAAAAATGGTAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTTA
Found at i:516805 original size:30 final size:29
Alignment explanation
Indices: 516758--517043 Score: 161
Period size: 30 Copynumber: 9.6 Consensus size: 29
516748 ATTCGGGGTT
516758 AAAATGGTAATTTTTTGGAAAAATCGAGGTCA
1 AAAATGG-AA-TTTTTGGAAAAATCGAGGT-A
* *** * *
516790 AAAATAGAATTTTTGGAAGTTTAGGGGTA
1 AAAATGGAATTTTTGGAAAAATCGAGGTA
*
516819 AAAATGGTAATTTTGGGAAAAAAT-G-GGATA
1 AAAATGG-AATTTTTGG-AAAAATCGAGG-TA
*** *
516849 AAAATGGAATTTTTGGAAGTTTAGAGGT-
1 AAAATGGAATTTTTGGAAAAATCGAGGTA
* *
516877 AAAATGGTATTTTTTGAAAAAATC-ATGGTCA
1 AAAATGG-AATTTTTGGAAAAATCGA-GGT-A
** *
516908 AAAATGGAA-TTTTGGAAAGTTTGAGGGTA
1 AAAATGGAATTTTTGGAAAAATCGA-GGTA
* * * * *
516937 AAATTGTAATTTCTGGGAAAATCGATGTCA
1 AAAATGGAATTTTTGGAAAAATCGAGGT-A
** * *
516967 AAAATGGAA-TTTTGGAAAGTTTGGGGGTA
1 AAAATGGAATTTTTGGAAA-AATCGAGGTA
* * *
516996 AAAATGTAATTTTTGGAAAAATTTGAGGTT
1 AAAATGGAATTTTTGGAAAAA-TCGAGGTA
517026 AAAATGGAATTTTTGGAA
1 AAAATGGAATTTTTGGAA
517044 GTTCGGGGGT
Statistics
Matches: 188, Mismatches: 51, Indels: 32
0.69 0.19 0.12
Matches are distributed among these distances:
28 11 0.06
29 67 0.36
30 92 0.49
31 12 0.06
32 6 0.03
ACGTcount: A:0.40, C:0.02, G:0.25, T:0.33
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAAAATCGAGGTA
Found at i:517078 original size:30 final size:28
Alignment explanation
Indices: 516966--517123 Score: 95
Period size: 29 Copynumber: 5.5 Consensus size: 28
516956 AATCGATGTC
* **
516966 AAAAATGGAATTTTGGAAAGTTTGGGGGT
1 AAAAATGTAATTTTAAAAAG-TTGGGGGT
* *
516995 AAAAATGTAATTTTTGGAAAAA-TTTGAGGT
1 AAAAATGTAA-TTTT--AAAAAGTTGGGGGT
* * ***
517025 TAAAATGGAATTTTTGGAAGTTCGGGGGT
1 AAAAATGTAATTTTAAAAAGTT-GGGGGT
* **
517054 AAAAATGTAATTTTCAAAAAGTTCGGTAT
1 AAAAATGTAATTTT-AAAAAGTTGGGGGT
* * *
517083 CAAAATGGAATTTTAGAAAA-TTTGGGGT
1 AAAAATGTAATTTTA-AAAAGTTGGGGGT
517111 AAAAATGTAATTT
1 AAAAATGTAATTT
517124 CTTGATAGTT
Statistics
Matches: 95, Mismatches: 27, Indels: 15
0.69 0.20 0.11
Matches are distributed among these distances:
27 2 0.02
28 19 0.20
29 48 0.51
30 23 0.24
32 3 0.03
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.34
Consensus pattern (28 bp):
AAAAATGTAATTTTAAAAAGTTGGGGGT
Found at i:517086 original size:118 final size:117
Alignment explanation
Indices: 516752--517123 Score: 379
Period size: 118 Copynumber: 3.2 Consensus size: 117
516742 TTTGACATTC
* * * *
516752 GGGGTTAAAATGGTAATTTTTTGGAAAAATCGAGGTCAAAAATAGAATTTTTGGAAGTTTAGGGG
1 GGGGTAAAAATGGTAA-TTTTTGGAAAAATTGAGGTCAAAAATGGAATTTTTGGAAGTTTGGGGG
*
516817 TAAAAATGGTAATTTTGGGAAAAAAT-GGGAT-AAAAATGGAATTTTTGG-AAGTTT
65 TAAAAAT-GTAATTTT-GG-AAAAATCGGTATCAAAAATGGAA-TTTTGGAAAGTTT
* * * * *
516871 AGAGGT-AAAATGGT-ATTTTTTGAAAAAATCATGGTCAAAAATGGAA-TTTTGGAAAGTTTGAG
1 -GGGGTAAAAATGGTAATTTTTGGAAAAATTGA-GGTCAAAAATGGAATTTTTGG-AAGTTTGGG
* * * *
516933 GGTAAAATTGTAATTTCTGGGAAAATCGATGTCAAAAATGGAATTTTGGAAAGTTT
63 GGTAAAAATGTAATTT-TGGAAAAATCGGTATCAAAAATGGAATTTTGGAAAGTTT
* *
516989 GGGGGTAAAAAT-GTAATTTTTGGAAAAATTTGAGGT-TAAAATGGAATTTTTGGAAGTTCGGGG
1 -GGGGTAAAAATGGTAATTTTTGGAAAAA-TTGAGGTCAAAAATGGAATTTTTGGAAGTTTGGGG
* * *
517052 GTAAAAATGTAATTTT-CAAAAAGTTCGGTATC-AAAATGGAATTTTAGAAAATTT
64 GTAAAAATGTAATTTTGGAAAAA--TCGGTATCAAAAATGGAATTTTGGAAAGTTT
517106 GGGGTAAAAAT-GTAATTT
1 GGGGTAAAAATGGTAATTT
517124 CTTGATAGTT
Statistics
Matches: 212, Mismatches: 28, Indels: 28
0.79 0.10 0.10
Matches are distributed among these distances:
116 27 0.13
117 56 0.26
118 89 0.42
119 34 0.16
120 6 0.03
ACGTcount: A:0.39, C:0.03, G:0.25, T:0.33
Consensus pattern (117 bp):
GGGGTAAAAATGGTAATTTTTGGAAAAATTGAGGTCAAAAATGGAATTTTTGGAAGTTTGGGGGT
AAAAATGTAATTTTGGAAAAATCGGTATCAAAAATGGAATTTTGGAAAGTTT
Found at i:518161 original size:3 final size:3
Alignment explanation
Indices: 518141--518205 Score: 76
Period size: 3 Copynumber: 21.3 Consensus size: 3
518131 TTTTGTTAAA
* * *
518141 ATT AAT ATT ATT AAT ATT ATT ATT ATT ATT ATT GTT ATTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT
* *
518187 ATT AAT ATT ATC ATT ATT A
1 ATT ATT ATT ATT ATT ATT A
518206 ATAATAATGT
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
3 48 0.94
4 3 0.06
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:518941 original size:17 final size:17
Alignment explanation
Indices: 518919--518988 Score: 61
Period size: 17 Copynumber: 4.1 Consensus size: 17
518909 AATATTAAGT
*
518919 TTTTAAATCAATATAAA
1 TTTTAAATAAATATAAA
* *
518936 TTTTAATTAAATTTAAA
1 TTTTAAATAAATATAAA
*
518953 -TTTAAGATAAATTTAAA
1 TTTTAA-ATAAATATAAA
* *
518970 TTTAAAAATAAATTTAAA
1 TTT-TAAATAAATATAAA
518988 T
1 T
518989 CAATTTAAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
16 5 0.11
17 24 0.53
18 14 0.31
19 2 0.04
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (17 bp):
TTTTAAATAAATATAAA
Found at i:518948 original size:11 final size:11
Alignment explanation
Indices: 518932--518997 Score: 53
Period size: 11 Copynumber: 5.9 Consensus size: 11
518922 TAAATCAATA
*
518932 TAAATTTTAAT
1 TAAATTTAAAT
518943 TAAATTTAAAT
1 TAAATTTAAAT
* **
518954 TTAAGATAAATT
1 TAAATTTAAA-T
*
518966 TAAATTTAAAAA
1 TAAATTT-AAAT
518978 TAAATTTAAA-
1 TAAATTTAAAT
*
518988 TCAATTTAAA
1 TAAATTTAAA
518998 CCCAACTTAA
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
10 9 0.20
11 20 0.45
12 12 0.27
13 3 0.07
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (11 bp):
TAAATTTAAAT
Found at i:518951 original size:6 final size:6
Alignment explanation
Indices: 518932--518988 Score: 57
Period size: 6 Copynumber: 9.8 Consensus size: 6
518922 TAAATCAATA
* **
518932 TAAATT TTAA-T TAAATT TAAATT TAAGA-- TAAATT TAAATT TAAAAA
1 TAAATT TAAATT TAAATT TAAATT TAA-ATT TAAATT TAAATT TAAATT
518978 TAAATT TAAAT
1 TAAATT TAAAT
518989 CAATTTAAAC
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
4 1 0.02
5 7 0.17
6 32 0.78
7 1 0.02
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (6 bp):
TAAATT
Found at i:518982 original size:18 final size:17
Alignment explanation
Indices: 518932--518988 Score: 78
Period size: 17 Copynumber: 3.3 Consensus size: 17
518922 TAAATCAATA
* *
518932 TAAATTTTAATTAAATT
1 TAAATTTAAAATAAATT
*
518949 TAAATTTAAGATAAATT
1 TAAATTTAAAATAAATT
518966 TAAATTTAAAAATAAATT
1 TAAATTT-AAAATAAATT
518984 TAAAT
1 TAAAT
518989 CAATTTAAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
17 21 0.60
18 14 0.40
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (17 bp):
TAAATTTAAAATAAATT
Found at i:518995 original size:28 final size:31
Alignment explanation
Indices: 518920--518997 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 31
518910 ATATTAAGTT
*
518920 TTTAAATCAATATAAATTTTAATTAAATTTAAA
1 TTTAAATCAATTTAAATTTTAA-TAAA-TTAAA
*
518953 TTTAAGATAAATTTAAA-TTTAA-AAA-TAAA
1 TTTAA-ATCAATTTAAATTTTAATAAATTAAA
518982 TTTAAATCAATTTAAA
1 TTTAAATCAATTTAAA
518998 CCCAACTTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
28 10 0.24
29 9 0.22
31 3 0.07
33 10 0.24
34 9 0.22
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (31 bp):
TTTAAATCAATTTAAATTTTAATAAATTAAA
Found at i:523316 original size:66 final size:66
Alignment explanation
Indices: 523210--523335 Score: 207
Period size: 66 Copynumber: 1.9 Consensus size: 66
523200 TGAAAGTTAG
* *
523210 AACTTTGAAGAGTGCTTTAGGATGCATTGATGTAGGTTGACTAAGACCAAAACTGAATAAATGTG
1 AACTTAGAAGAGTGCTTTAGGATGCATGGATGTAGGTTGACTAAGACCAAAACTGAATAAATGTG
523275 A
66 A
* * *
523276 AACTTAGAAGAGTGCTTTAGGATTCATGGATGTAGTTTGACTAGGACCAAAACTGAATAA
1 AACTTAGAAGAGTGCTTTAGGATGCATGGATGTAGGTTGACTAAGACCAAAACTGAATAA
523336 TAGGATGTAA
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 55 1.00
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.29
Consensus pattern (66 bp):
AACTTAGAAGAGTGCTTTAGGATGCATGGATGTAGGTTGACTAAGACCAAAACTGAATAAATGTG
A
Found at i:526733 original size:13 final size:13
Alignment explanation
Indices: 526715--526741 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
526705 TATTAAATTC
526715 ATAAAAATAAAAA
1 ATAAAAATAAAAA
526728 ATAAAAATAAAAA
1 ATAAAAATAAAAA
526741 A
1 A
526742 AGAAAGAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
ATAAAAATAAAAA
Found at i:526964 original size:6 final size:6
Alignment explanation
Indices: 526953--526983 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
526943 AAAACAAAAT
526953 CCCATC CCCATC CCCATC CCCATC CCCATC C
1 CCCATC CCCATC CCCATC CCCATC CCCATC C
526984 TCAACACCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.68, G:0.00, T:0.16
Consensus pattern (6 bp):
CCCATC
Found at i:527229 original size:2 final size:2
Alignment explanation
Indices: 527222--527247 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
527212 CTACGAAACA
527222 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
527248 TCTATCTGCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:529283 original size:30 final size:30
Alignment explanation
Indices: 529234--529307 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 30
529224 AAAAATTCAA
* *
529234 AAAAATTAT-GAAAACTATTTATAAAAATT
1 AAAAATTATAAAAAAATATTTATAAAAATT
* * *
529263 AAAAATTATAAAAAAATATTTGTAATATTT
1 AAAAATTATAAAAAAATATTTATAAAAATT
* *
529293 TAAAATTCTAAAAAA
1 AAAAATTATAAAAAA
529308 TTAATTAAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 9 0.24
30 28 0.76
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (30 bp):
AAAAATTATAAAAAAATATTTATAAAAATT
Found at i:533014 original size:20 final size:21
Alignment explanation
Indices: 532976--533024 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
532966 AATTATGTAC
* * *
532976 TTTGAATTTATAAATTTTATG
1 TTTGGATTTATAAACTTTATA
532997 TTTGGATTT-TAAACTTTATA
1 TTTGGATTTATAAACTTTATA
533017 TTTGGATT
1 TTTGGATT
533025 ATGCTATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.57
Consensus pattern (21 bp):
TTTGGATTTATAAACTTTATA
Found at i:533531 original size:4 final size:4
Alignment explanation
Indices: 533522--533554 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
533512 TAGAGTATTA
*
533522 TTAT TTAT TTAT TTAT TTAT TTAT TTAT ATAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT T
533555 GTCTTGTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
TTAT
Found at i:553619 original size:175 final size:175
Alignment explanation
Indices: 553275--553638 Score: 447
Period size: 175 Copynumber: 2.1 Consensus size: 175
553265 AATTAGGAGC
*
553275 CAAAATGTAATTTTGGAAAAATATGGGCGTTAAAATGCAATTTTAGGAAAGTTTGGGGATCAAAA
1 CAAAATGTAATTTTGGAAAAATATAGGCGTTAAAATGCAATTTTAGGAAAGTTTGGGGATCAAAA
* * *
553340 TGTAATTTTTGAAAAGTTTAGAGTCAGAATGCAATTTTGGGAAGTTTGGGATTAAAATATGATTT
66 TGTAATTTTTGAAAAGTTTAGAGTCAAAATGCAATTTTGGGAAGTTTGGGATCAAAATATGATAT
* *
553405 TAAGAAAGTTTGGGGTCAAAATATAATTTTGGAAAAGTTTAGGGGT
131 TAAGAAAGTTTAGGGTCAAAATATAATTTTGGAAAAGTTTA-AGGT
** *
553451 CAAAATGTAATTTTGGGAAAAATCA-AGG-GTTAAAATGTGATTTTAGG-AAGTTTAGGGG-TTA
1 CAAAATGTAATTTT-GGAAAAAT-ATAGGCGTTAAAATGCAATTTTAGGAAAGTTT-GGGGATCA
* * * * *
553512 AAATGTAATTTTTGAAAAGTTTGGTGTCAAAATGTAATTTTTGGAAGTTTAGGG-TCAAAATGT-
63 AAATGTAATTTTTGAAAAGTTTAGAGTCAAAATGCAATTTTGGGAAGTTT-GGGATCAAAATATG
* *
553575 A-ATT-AGAAAAGTTTAAGGGTCAAAATGTAATTTTTGAGAAAGTTTAAGGT
127 ATATTAAG-AAAGTTT-AGGGTCAAAATATAATTTTGGA-AAAGTTTAAGGT
*
553625 TAAAATGTAATTTT
1 CAAAATGTAATTTT
553639 AAAAAAGTTT
Statistics
Matches: 164, Mismatches: 17, Indels: 16
0.83 0.09 0.08
Matches are distributed among these distances:
172 2 0.01
173 9 0.05
174 36 0.22
175 68 0.41
176 38 0.23
177 10 0.06
178 1 0.01
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.35
Consensus pattern (175 bp):
CAAAATGTAATTTTGGAAAAATATAGGCGTTAAAATGCAATTTTAGGAAAGTTTGGGGATCAAAA
TGTAATTTTTGAAAAGTTTAGAGTCAAAATGCAATTTTGGGAAGTTTGGGATCAAAATATGATAT
TAAGAAAGTTTAGGGTCAAAATATAATTTTGGAAAAGTTTAAGGT
Found at i:553655 original size:30 final size:29
Alignment explanation
Indices: 553275--553679 Score: 304
Period size: 30 Copynumber: 13.9 Consensus size: 29
553265 AATTAGGAGC
* * * *
553275 CAAAATGTAATTTTGGAAAAATATGGGCGT
1 CAAAATGTAATTTTAGAAAAGTTTAGG-GT
* * * *
553305 TAAAATGCAATTTTAGGAAAGTTTGGGGAT
1 CAAAATGTAATTTTAGAAAAGTTTAGGG-T
* *
553335 CAAAATGTAATTTTTGAAAAGTTTAGAGT
1 CAAAATGTAATTTTAGAAAAGTTTAGGGT
* * **
553364 CAGAATGCAATTTT-GGGAAGTTT-GGGAT
1 CAAAATGTAATTTTAGAAAAGTTTAGGG-T
* * * *
553392 TAAAATATGATTTTA-AGAAAGTTTGGGGT
1 CAAAATGTAATTTTAGA-AAAGTTTAGGGT
* *
553421 CAAAATATAATTTTGGAAAAGTTTAGGGGT
1 CAAAATGTAATTTTAGAAAAGTTTA-GGGT
* * **
553451 CAAAATGTAATTTTGGGAAAAATCAAGGGT
1 CAAAATGTAATTTT-AGAAAAGTTTAGGGT
* * *
553481 TAAAATGTGATTTTAG-GAAGTTTAGGGGT
1 CAAAATGTAATTTTAGAAAAGTTTA-GGGT
* *
553510 TAAAATGTAATTTTTGAAAAGTTT-GGTGT
1 CAAAATGTAATTTTAGAAAAGTTTAGG-GT
* *
553539 CAAAATGTAATTTTTG-GAAGTTTAGGGT
1 CAAAATGTAATTTTAGAAAAGTTTAGGGT
553567 CAAAATGTAA--TTAGAAAAGTTTAAGGGT
1 CAAAATGTAATTTTAGAAAAGTTT-AGGGT
* *
553595 CAAAATGTAATTTTTGAGAAAGTTTAAGGT
1 CAAAATGTAATTTTAGA-AAAGTTTAGGGT
* *
553625 TAAAATGTAATTTTAAAAAAGTTTAGAGGT
1 CAAAATGTAATTTTAGAAAAGTTTAG-GGT
* * * *
553655 TAAAATATATTTTTAGAAGAGTTTA
1 CAAAATGTAATTTTAGAAAAGTTTA
553680 AGGGCTCTTT
Statistics
Matches: 301, Mismatches: 56, Indels: 36
0.77 0.14 0.09
Matches are distributed among these distances:
26 3 0.01
27 8 0.03
28 56 0.19
29 86 0.29
30 133 0.44
31 15 0.05
ACGTcount: A:0.39, C:0.03, G:0.23, T:0.36
Consensus pattern (29 bp):
CAAAATGTAATTTTAGAAAAGTTTAGGGT
Found at i:555732 original size:55 final size:55
Alignment explanation
Indices: 555672--555776 Score: 149
Period size: 55 Copynumber: 1.9 Consensus size: 55
555662 ACAAAATTGA
* *
555672 ATAGTT-GGGGGATCATTTTGTTACTTTTCATAGTTGGGTGACCAAAAAAAAAAAC
1 ATAGTTAGGGGG-TCATTTTGTAAATTTTCATAGTTGGGTGACCAAAAAAAAAAAC
* * *
555727 ATAGTTAGGTGGTGATTTTGTAAATTTTCATAGTTGGGTGATCAAAAAAA
1 ATAGTTAGGGGGTCATTTTGTAAATTTTCATAGTTGGGTGACCAAAAAAA
555777 GAAAGAAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
55 40 0.91
56 4 0.09
ACGTcount: A:0.34, C:0.08, G:0.23, T:0.35
Consensus pattern (55 bp):
ATAGTTAGGGGGTCATTTTGTAAATTTTCATAGTTGGGTGACCAAAAAAAAAAAC
Found at i:558875 original size:91 final size:91
Alignment explanation
Indices: 558720--558901 Score: 364
Period size: 91 Copynumber: 2.0 Consensus size: 91
558710 CAAAAGAAAA
558720 GAAAACTTTTTCTAGATATGTGTTTTGATTCAATTTATTCAAATCCACACTCGAAGCAGTTCGTG
1 GAAAACTTTTTCTAGATATGTGTTTTGATTCAATTTATTCAAATCCACACTCGAAGCAGTTCGTG
558785 GTACGAAAATAGCAAAGAAGATCATT
66 GTACGAAAATAGCAAAGAAGATCATT
558811 GAAAACTTTTTCTAGATATGTGTTTTGATTCAATTTATTCAAATCCACACTCGAAGCAGTTCGTG
1 GAAAACTTTTTCTAGATATGTGTTTTGATTCAATTTATTCAAATCCACACTCGAAGCAGTTCGTG
558876 GTACGAAAATAGCAAAGAAGATCATT
66 GTACGAAAATAGCAAAGAAGATCATT
558902 TGGTTGAAAG
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 91 1.00
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.33
Consensus pattern (91 bp):
GAAAACTTTTTCTAGATATGTGTTTTGATTCAATTTATTCAAATCCACACTCGAAGCAGTTCGTG
GTACGAAAATAGCAAAGAAGATCATT
Found at i:563157 original size:22 final size:24
Alignment explanation
Indices: 563130--563174 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
563120 TTTAAAATTT
*
563130 TAAATT-T-AATTATAAATATATA
1 TAAATTATAAATTACAAATATATA
563152 TAAATTATAAATTACAAATATAT
1 TAAATTATAAATTACAAATATAT
563175 TTTTTAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 6 0.30
23 1 0.05
24 13 0.65
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (24 bp):
TAAATTATAAATTACAAATATATA
Found at i:572548 original size:20 final size:21
Alignment explanation
Indices: 572523--572562 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
572513 TTTTCAATGA
572523 ATTTTTATTTATA-AAATTAG
1 ATTTTTATTTATATAAATTAG
*
572543 ATTTTTATTTTTATAAATTA
1 ATTTTTATTTATATAAATTA
572563 AATAAAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (21 bp):
ATTTTTATTTATATAAATTAG
Found at i:573429 original size:24 final size:24
Alignment explanation
Indices: 573401--573468 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
573391 AGAAATAATC
* *
573401 TTTCAGTTAAATTCTGT-TTATTTG
1 TTTCAATTAAACTCT-TATTATTTG
573425 TTTCAATTAAACTCTTATTATTTG
1 TTTCAATTAAACTCTTATTATTTG
* * *
573449 TTTGAGTCAAACTCTTATTA
1 TTTCAATTAAACTCTTATTA
573469 GTCTAGATTA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
23 1 0.03
24 37 0.97
ACGTcount: A:0.26, C:0.12, G:0.09, T:0.53
Consensus pattern (24 bp):
TTTCAATTAAACTCTTATTATTTG
Found at i:588995 original size:14 final size:15
Alignment explanation
Indices: 588976--589023 Score: 55
Period size: 14 Copynumber: 3.2 Consensus size: 15
588966 TTGAAAAAAT
588976 ATAAATAATTA-ATA
1 ATAAATAATTATATA
588990 ATAAAT-ATTATATA
1 ATAAATAATTATATA
*
589004 ATTTAAATAATTATTTA
1 A--TAAATAATTATATA
589021 ATA
1 ATA
589024 GGCTAAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
13 4 0.14
14 10 0.34
15 2 0.07
16 5 0.17
17 8 0.28
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAAATAATTATATA
Found at i:589424 original size:16 final size:14
Alignment explanation
Indices: 589391--589430 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 14
589381 AATATTTTTA
589391 AAAATATTAAAAATT
1 AAAA-ATTAAAAATT
589406 AAAAATTAAAAAGTAT
1 AAAAATTAAAAA-T-T
589422 AAAAATTAA
1 AAAAATTAA
589431 CTAATTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.35
15 5 0.22
16 10 0.43
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (14 bp):
AAAAATTAAAAATT
Found at i:589426 original size:9 final size:7
Alignment explanation
Indices: 589391--589430 Score: 53
Period size: 7 Copynumber: 5.3 Consensus size: 7
589381 AATATTTTTA
589391 AAAATATT
1 AAAA-ATT
589399 AAAAATT
1 AAAAATT
589406 AAAAATT
1 AAAAATT
589413 AAAAAGTAT
1 AAAAA-T-T
589422 AAAAATT
1 AAAAATT
589429 AA
1 AA
589431 CTAATTATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
7 18 0.60
8 6 0.20
9 6 0.20
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (7 bp):
AAAAATT
Found at i:589593 original size:15 final size:17
Alignment explanation
Indices: 589570--589610 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
589560 AAAATAAAAT
*
589570 AAATCATTATA-TT-AA
1 AAATTATTATACTTAAA
589585 AAATTATTATAGCTTAAA
1 AAATTATTATA-CTTAAA
589603 AAATTATT
1 AAATTATT
589611 TTTTACATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 10 0.45
17 2 0.09
18 10 0.45
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.41
Consensus pattern (17 bp):
AAATTATTATACTTAAA
Found at i:593994 original size:11 final size:12
Alignment explanation
Indices: 593971--594002 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
593961 AGTAAAACTT
593971 TAAAATAAT-TA
1 TAAAATAATATA
593982 TAAAA-AATATA
1 TAAAATAATATA
593993 TAAAATAATA
1 TAAAATAATA
594003 AATGTTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 3 0.16
11 12 0.63
12 4 0.21
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
TAAAATAATATA
Found at i:594756 original size:6 final size:6
Alignment explanation
Indices: 594745--594771 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
594735 CTTATTGTAA
594745 TAATTT TAATTT TAATTT TAATTT TAA
1 TAATTT TAATTT TAATTT TAATTT TAA
594772 ATATAATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (6 bp):
TAATTT
Found at i:595926 original size:15 final size:17
Alignment explanation
Indices: 595895--595927 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
595885 GTTTTCTTAA
595895 ATACAATATAATAATTT
1 ATACAATATAATAATTT
595912 ATACAATA-AAT-ATTT
1 ATACAATATAATAATTT
595927 A
1 A
595928 ATTTATTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 3 0.19
17 8 0.50
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (17 bp):
ATACAATATAATAATTT
Found at i:598117 original size:10 final size:12
Alignment explanation
Indices: 598085--598123 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
598075 TATTGATATG
598085 AAGAAAGAGAGA
1 AAGAAAGAGAGA
598097 AAGAAAGAGAGA
1 AAGAAAGAGAGA
*
598109 AAGAAAGAGAAA
1 AAGAAAGAGAGA
598121 AAG
1 AAG
598124 CTGTTCATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (12 bp):
AAGAAAGAGAGA
Found at i:602167 original size:27 final size:28
Alignment explanation
Indices: 602120--602174 Score: 94
Period size: 27 Copynumber: 2.0 Consensus size: 28
602110 AAACAAACAA
*
602120 CAAAATTCAAAATAAATGATAACACCAG
1 CAAAATTCAAAATAAAGGATAACACCAG
602148 CAAAATTC-AAATAAAGGATAACACCAG
1 CAAAATTCAAAATAAAGGATAACACCAG
602175 AAAGTTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 18 0.69
28 8 0.31
ACGTcount: A:0.56, C:0.18, G:0.09, T:0.16
Consensus pattern (28 bp):
CAAAATTCAAAATAAAGGATAACACCAG
Found at i:602966 original size:27 final size:27
Alignment explanation
Indices: 602931--602994 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
602921 CAAACAACAA
*
602931 AAATTCAAAACAAAGGAAAACAGCAGC
1 AAATTCAAAACAAAGGAAAACACCAGC
* **
602958 AAATTCAAAACAAATGCTAACACCAGC
1 AAATTCAAAACAAAGGAAAACACCAGC
602985 AAATTTCAAA
1 AAA-TTCAAA
602995 TAAAGGATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 26 0.81
28 6 0.19
ACGTcount: A:0.56, C:0.20, G:0.09, T:0.14
Consensus pattern (27 bp):
AAATTCAAAACAAAGGAAAACACCAGC
Found at i:603768 original size:22 final size:22
Alignment explanation
Indices: 603738--603781 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
603728 GAAATTATCT
* *
603738 AAAATCCTAAGCACATTGATTA
1 AAAACCCTAAGCAAATTGATTA
603760 AAAACCCTAAGCAAATTGATTA
1 AAAACCCTAAGCAAATTGATTA
603782 CAAAGGATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.48, C:0.18, G:0.09, T:0.25
Consensus pattern (22 bp):
AAAACCCTAAGCAAATTGATTA
Found at i:604970 original size:18 final size:18
Alignment explanation
Indices: 604933--604970 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
604923 GTTGACGAGA
*
604933 AGAAAGAAAGAAATAGAG
1 AGAAAGAAAGAAATAAAG
604951 AGAAAGAAAGAGAA-AAAG
1 AGAAAGAAAGA-AATAAAG
604969 AG
1 AG
604971 CTGTTCTTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (18 bp):
AGAAAGAAAGAAATAAAG
Found at i:607721 original size:30 final size:30
Alignment explanation
Indices: 607687--607754 Score: 127
Period size: 30 Copynumber: 2.3 Consensus size: 30
607677 ATATGTGGAA
607687 GGAGGTGATGCTGATGATGATGATAGAAGT
1 GGAGGTGATGCTGATGATGATGATAGAAGT
607717 GGAGGTGATGCTGATGATGATGATAGAAGT
1 GGAGGTGATGCTGATGATGATGATAGAAGT
*
607747 GAAGGTGA
1 GGAGGTGA
607755 AGGCCGTAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.31, C:0.03, G:0.41, T:0.25
Consensus pattern (30 bp):
GGAGGTGATGCTGATGATGATGATAGAAGT
Found at i:610753 original size:3 final size:3
Alignment explanation
Indices: 610745--610770 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
610735 TCAAAAATAA
610745 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
610771 CTTCCCTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:626070 original size:31 final size:30
Alignment explanation
Indices: 625965--626072 Score: 85
Period size: 31 Copynumber: 3.5 Consensus size: 30
625955 TGGGTCTAAG
* *
625965 TTAAGTCTTAAATTTGGCAATTGTTCCTACA
1 TTAAGGCTTAAACTTGGCAATTGTTCC-ACA
* * ** *
625996 TTAAGACGTGGACTTGGTAACTT-TTCACACA
1 TTAAGGCTTAAACTTGGCAA-TTGTTC-CACA
*
626027 TT-AGGACCTAAACTTGGCAATTGTTCTCACA
1 TTAAGG-CTTAAACTTGGCAATTGTTC-CACA
626058 TTAAGGCTTAAACTT
1 TTAAGGCTTAAACTT
626073 TAGGGTTTTC
Statistics
Matches: 59, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
30 4 0.07
31 49 0.83
32 6 0.10
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.36
Consensus pattern (30 bp):
TTAAGGCTTAAACTTGGCAATTGTTCCACA
Found at i:626533 original size:24 final size:24
Alignment explanation
Indices: 626506--626572 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 24
626496 AGTTTGACTC
626506 AAACAAAGTTTAATTGAAACAAAT
1 AAACAAAGTTTAATTGAAACAAAT
* * *
626530 AAACAAAGTTTAATTTAAATAATT
1 AAACAAAGTTTAATTGAAACAAAT
* * *
626554 AAACAGATTTTAACTGAAA
1 AAACAAAGTTTAATTGAAA
626573 GATTATTTCT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.30
Consensus pattern (24 bp):
AAACAAAGTTTAATTGAAACAAAT
Found at i:628484 original size:24 final size:25
Alignment explanation
Indices: 628456--628517 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 25
628446 ATTCAGACAA
628456 AGTTTAATTGAAACAAA-TAAACAG
1 AGTTTAATTGAAACAAATTAAACAG
* * *
628480 AGTTTATTTGATACAAATTAAATAG
1 AGTTTAATTGAAACAAATTAAACAG
* *
628505 AATTTAACTGAAA
1 AGTTTAATTGAAA
628518 GATTATTTCT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
24 15 0.50
25 15 0.50
ACGTcount: A:0.50, C:0.06, G:0.11, T:0.32
Consensus pattern (25 bp):
AGTTTAATTGAAACAAATTAAACAG
Found at i:628510 original size:25 final size:24
Alignment explanation
Indices: 628458--628517 Score: 66
Period size: 25 Copynumber: 2.5 Consensus size: 24
628448 TCAGACAAAG
*
628458 TTTAATTGAAACAAATAAACAGAG
1 TTTAATTGAAACAAATAAACAGAA
* * *
628482 TTTATTTGATACAAATTAAATAGAA
1 TTTAATTGAAACAAA-TAAACAGAA
*
628507 TTTAACTGAAA
1 TTTAATTGAAA
628518 GATTATTTCT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
24 13 0.46
25 15 0.54
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (24 bp):
TTTAATTGAAACAAATAAACAGAA
Found at i:632337 original size:22 final size:22
Alignment explanation
Indices: 632295--632339 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
632285 ATTTTGAACC
* *
632295 AATCTAATATTTTTATCATATT
1 AATCTAAAATTTATATCATATT
632317 AATCTAAAATATTATAT-ATATT
1 AATCTAAAAT-TTATATCATATT
632339 A
1 A
632340 CTATTTATCG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (22 bp):
AATCTAAAATTTATATCATATT
Done.