Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold502
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: 762056
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 3 of 6
Found at i:376451 original size:16 final size:16
Alignment explanation
Indices: 376370--376451 Score: 51
Period size: 16 Copynumber: 4.9 Consensus size: 16
376360 AAACTTATTT
* *
376370 TTTATTATATTTAAAA
1 TTTAATATATTTATAA
*
376386 TATTATATATTTTATATAAA
1 T-TTA-ATATATT-TAT-AA
* *
376406 TTT-ATTTATTAATAA
1 TTTAATATATTTATAA
*
376421 TTT-ATATCATATATAA
1 TTTAATAT-ATTTATAA
376437 TTTAATATATTTATA
1 TTTAATATATTTATA
376452 TATTCTCATT
Statistics
Matches: 50, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
15 8 0.16
16 18 0.36
17 12 0.24
18 5 0.10
19 4 0.08
20 3 0.06
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTAATATATTTATAA
Found at i:378344 original size:24 final size:24
Alignment explanation
Indices: 378316--378361 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
378306 TATATTTTAT
* * *
378316 TTTATCATTTAATATTTTTAAAAA
1 TTTATAATTAAATATATTTAAAAA
378340 TTTATAATTAAATATATTTAAA
1 TTTATAATTAAATATATTTAAA
378362 TTTTATTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (24 bp):
TTTATAATTAAATATATTTAAAAA
Found at i:378940 original size:23 final size:23
Alignment explanation
Indices: 378922--379002 Score: 81
Period size: 23 Copynumber: 3.4 Consensus size: 23
378912 TAAATATTAG
378922 ATATAATTTAAATATAATAAAAA
1 ATATAATTTAAATATAATAAAAA
**
378945 ATATAATTTAAATATTTTAAAAA
1 ATATAATTTAAATATAATAAAAA
* * * *
378968 TTATGTAATATAAATATGATATAAAT
1 --ATATAATTTAAATATAATA-AAAA
378994 ATATAATTT
1 ATATAATTT
379003 GATAAATTTA
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
23 21 0.46
24 7 0.15
25 15 0.33
26 3 0.07
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
ATATAATTTAAATATAATAAAAA
Found at i:379205 original size:24 final size:25
Alignment explanation
Indices: 379174--379224 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 25
379164 TAATTAAATT
379174 AAATTTTA-TTTTAA-TAATATAAA
1 AAATTTTATTTTTAATTAATATAAA
*
379197 AAATATTTATTTTTAATTAATTTAAA
1 AAAT-TTTATTTTTAATTAATATAAA
379223 AA
1 AA
379225 TTATAAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 4 0.17
24 4 0.17
25 6 0.25
26 10 0.42
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
AAATTTTATTTTTAATTAATATAAA
Found at i:379733 original size:15 final size:15
Alignment explanation
Indices: 379692--379724 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
379682 TGGCGCCAAA
379692 AGCCGAGAAGAAGCC
1 AGCCGAGAAGAAGCC
379707 AGCCGAGAAGAAGCC
1 AGCCGAGAAGAAGCC
379722 AGC
1 AGC
379725 TGAGGAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.39, C:0.27, G:0.33, T:0.00
Consensus pattern (15 bp):
AGCCGAGAAGAAGCC
Found at i:380354 original size:21 final size:22
Alignment explanation
Indices: 380314--380364 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
380304 TTTACTTAAA
380314 TTAA-TAAAATAAAAATA-TTT
1 TTAATTAAAATAAAAATATTTT
*
380334 TTACATTAAAA-AAATATATTTT
1 TTA-ATTAAAATAAAAATATTTT
380356 TTAATTAAA
1 TTAATTAAA
380365 TTTAAATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 3 0.11
21 13 0.48
22 11 0.41
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
TTAATTAAAATAAAAATATTTT
Found at i:383125 original size:29 final size:29
Alignment explanation
Indices: 383083--383139 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
383073 TAACAGAATT
383083 TCAGTTTCGAGTCAGCTGGAATTTGCAGC
1 TCAGTTTCGAGTCAGCTGGAATTTGCAGC
383112 TCAGTTTCGAGTCAGCTGGAATTTGCAG
1 TCAGTTTCGAGTCAGCTGGAATTTGCAG
383140 ACCTGCTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (29 bp):
TCAGTTTCGAGTCAGCTGGAATTTGCAGC
Found at i:384672 original size:3 final size:3
Alignment explanation
Indices: 384664--384689 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
384654 CACCAATTAA
384664 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
384690 CATTAAAAAG
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:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:385116 original size:16 final size:16
Alignment explanation
Indices: 385087--385129 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
385077 TTTATAGAAA
385087 AATATATAATTATTCTT
1 AATATAT-ATTATTCTT
* *
385104 AATTTATATTATTTTT
1 AATATATATTATTCTT
385120 AATATATATT
1 AATATATATT
385130 TTAAAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 17 0.74
17 6 0.26
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (16 bp):
AATATATATTATTCTT
Found at i:389526 original size:15 final size:16
Alignment explanation
Indices: 389494--389544 Score: 63
Period size: 15 Copynumber: 3.4 Consensus size: 16
389484 AAATTATGTG
*
389494 ATAAATTTACATTTTT
1 ATAAATTTACAATTTT
389510 ATAAATTTA-AATTTT
1 ATAAATTTACAATTTT
*
389525 AT-AATTTATAATTTT
1 ATAAATTTACAATTTT
389540 -TAAAT
1 ATAAAT
389545 ATATAACCAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
14 7 0.22
15 16 0.50
16 9 0.28
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (16 bp):
ATAAATTTACAATTTT
Found at i:389549 original size:15 final size:16
Alignment explanation
Indices: 389504--389550 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 16
389494 ATAAATTTAC
*
389504 ATTTTTATAA-ATTTA
1 ATTTTTATAATATATA
* *
389519 AATTTTATAATTTATA
1 ATTTTTATAATATATA
389535 ATTTTTA-AATATATA
1 ATTTTTATAATATATA
389550 A
1 A
389551 CCATATTAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTTTTATAATATATA
Found at i:389549 original size:22 final size:22
Alignment explanation
Indices: 389507--389550 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
389497 AATTTACATT
*
389507 TTTATAAATTTAAATTTTATAA
1 TTTATAAATTTAAATTATATAA
*
389529 TTTATAATTTTTAAA-TATATAA
1 TTTATAA-ATTTAAATTATATAA
389551 CCATATTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTATAAATTTAAATTATATAA
Found at i:389859 original size:2 final size:2
Alignment explanation
Indices: 389852--389877 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
389842 TGAAAATTCC
389852 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
389878 ATCGATTCAA
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:390615 original size:14 final size:15
Alignment explanation
Indices: 390591--390649 Score: 59
Period size: 14 Copynumber: 4.1 Consensus size: 15
390581 TTTATAATTT
390591 TAAATATAATATAAA
1 TAAATATAATATAAA
390606 TAAA-ATAATATAAA
1 TAAATATAATATAAA
* **
390620 TATATATTTTA-AAA
1 TAAATATAATATAAA
**
390634 TTTATATAATATAAA
1 TAAATATAATATAAA
390649 T
1 T
390650 TATTAAATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
14 24 0.67
15 12 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TAAATATAATATAAA
Found at i:390619 original size:25 final size:25
Alignment explanation
Indices: 390591--390737 Score: 105
Period size: 25 Copynumber: 6.0 Consensus size: 25
390581 TTTATAATTT
*
390591 TAAATATAATATAAATAAAATAATA
1 TAAATATAATATAAATAAAATATTA
**
390616 TAAATAT-ATAT-TTTAAAAT-TTA
1 TAAATATAATATAAATAAAATATTA
* *
390638 TATAATATAA-AT-TATTAAATATTA
1 TA-AATATAATATAAATAAAATATTA
* *
390662 -AAAT-TCATATAAATATTAAATATTT
1 TAAATATAATATAAATA--AAATATTA
390687 TAAATATAAT-TATAATAAAATA-TA
1 TAAATATAATATA-AATAAAATATTA
* *
390711 TAAAAATAATATAAATATACATATTA
1 TAAATATAATATAAATA-AAATATTA
390737 T
1 T
390738 TAAAATTATA
Statistics
Matches: 96, Mismatches: 13, Indels: 25
0.72 0.10 0.19
Matches are distributed among these distances:
21 2 0.02
22 9 0.09
23 22 0.23
24 22 0.23
25 25 0.26
26 9 0.09
27 7 0.07
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (25 bp):
TAAATATAATATAAATAAAATATTA
Found at i:392949 original size:31 final size:31
Alignment explanation
Indices: 392914--392979 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
392904 TATTTTTCTA
* *
392914 AATACTCATATCTGATACATATCTTGATAAG
1 AATACTCATATCTAACACATATCTTGATAAG
*
392945 AATACTCATGTCTAACACATATCTTGATAAG
1 AATACTCATATCTAACACATATCTTGATAAG
392976 AATA
1 AATA
392980 AGAGATTTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.33
Consensus pattern (31 bp):
AATACTCATATCTAACACATATCTTGATAAG
Found at i:396557 original size:19 final size:21
Alignment explanation
Indices: 396533--396574 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
396523 TTTAAAAAAT
396533 TTTACATTT-A-TTATTTAAA
1 TTTACATTTAATTTATTTAAA
396552 TTTACATTTAATTTATTTAAA
1 TTTACATTTAATTTATTTAAA
396573 TT
1 TT
396575 ATTTAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 9 0.43
20 1 0.05
21 11 0.52
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTACATTTAATTTATTTAAA
Found at i:396578 original size:24 final size:20
Alignment explanation
Indices: 396528--396593 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 20
396518 AATAATTTAA
396528 AAAATTTTACATTTATTATTT
1 AAAA-TTTACATTTATTATTT
396549 -AAATTTACATTTAATTTATTT
1 AAAATTTACATTT-A-TTATTT
*
396570 AAATTATTTAAATTTTATTATTT
1 AAA--ATTTACA-TTTATTATTT
396593 A
1 A
396594 TTATTAATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
19 9 0.24
20 4 0.11
21 6 0.16
22 2 0.05
23 7 0.18
24 7 0.18
25 3 0.08
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (20 bp):
AAAATTTACATTTATTATTT
Found at i:396662 original size:23 final size:21
Alignment explanation
Indices: 396619--396662 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
396609 TAAAAATTAT
*
396619 TTTATATTAATATTAATAAAA
1 TTTATATTAAAATTAATAAAA
396640 TTTATAATTAAAATATAATAAAA
1 TTTAT-ATTAAAAT-TAATAAAA
396663 AATATTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 5 0.25
22 7 0.35
23 8 0.40
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TTTATATTAAAATTAATAAAA
Found at i:397115 original size:19 final size:17
Alignment explanation
Indices: 397087--397122 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 17
397077 TTTTTTACTC
397087 AAAATATTTTTTAATTAT
1 AAAATA-TTTTTAATTAT
397105 AAAACTATTTTTAATTAT
1 AAAA-TATTTTTAATTAT
397123 TATTAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.88
19 2 0.12
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
AAAATATTTTTAATTAT
Found at i:397144 original size:16 final size:16
Alignment explanation
Indices: 397123--397166 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 16
397113 TTTTAATTAT
397123 TATTAATTTAAAATAA
1 TATTAATTTAAAATAA
*
397139 TATTAAATATAAAAATAA
1 TATT-AAT-TTAAAATAA
397157 TA-TAATTTAA
1 TATTAATTTAA
397167 TGTAAACCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
15 3 0.12
16 7 0.29
17 4 0.17
18 10 0.42
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TATTAATTTAAAATAA
Found at i:397400 original size:20 final size:20
Alignment explanation
Indices: 397364--397402 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
397354 TTTTGTATTC
*
397364 ATATATATATTTATAAATAG
1 ATATATATATCTATAAATAG
397384 ATATATTATATCT-TAAATA
1 ATATA-TATATCTATAAATA
397403 TAATTATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (20 bp):
ATATATATATCTATAAATAG
Found at i:397413 original size:11 final size:11
Alignment explanation
Indices: 397399--397437 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
397389 TTATATCTTA
*
397399 AATATAATTAT
1 AATATAAATAT
*
397410 AATATAAAAAAT
1 AATAT-AAATAT
397422 AATATAAATAT
1 AATATAAATAT
397433 AATAT
1 AATAT
397438 GATGTATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 15 0.62
12 9 0.38
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
AATATAAATAT
Found at i:400084 original size:14 final size:14
Alignment explanation
Indices: 400061--400113 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 14
400051 TATATCAAAA
400061 AAAAATTAATATGAT
1 AAAAA-TAATATGAT
**
400076 AAAAATAATTAAAAT
1 AAAAATAA-TATGAT
* *
400091 AAAATTAATATGTT
1 AAAAATAATATGAT
400105 AAAAATAAT
1 AAAAATAAT
400114 TAAATTGTGA
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
14 14 0.47
15 16 0.53
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (14 bp):
AAAAATAATATGAT
Found at i:400099 original size:29 final size:29
Alignment explanation
Indices: 400057--400117 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
400047 ATTATATATC
400057 AAAAAAAAATTAATATGATAAAAATAATT
1 AAAAAAAAATTAATATGATAAAAATAATT
* *
400086 AAAATAAAATTAATATGTTAAAAATAATT
1 AAAAAAAAATTAATATGATAAAAATAATT
400115 AAA
1 AAA
400118 TTGTGAGATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (29 bp):
AAAAAAAAATTAATATGATAAAAATAATT
Found at i:400872 original size:29 final size:29
Alignment explanation
Indices: 400840--400905 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
400830 TTATTATCAT
*
400840 ATTTAAATAAAATT-TTAAGT-TTTAATTTC
1 ATTTAAAT-AAATTATTAA-TATTTAATTTA
400869 ATTTAAATAAATTATTAATATTTAATTTA
1 ATTTAAATAAATTATTAATATTTAATTTA
400898 ATTTAAAT
1 ATTTAAAT
400906 TTAAATACAC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
28 6 0.18
29 28 0.82
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (29 bp):
ATTTAAATAAATTATTAATATTTAATTTA
Found at i:400965 original size:17 final size:18
Alignment explanation
Indices: 400918--400966 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 18
400908 AAATACACTC
* *
400918 TTAATATAAAT-TAATAT
1 TTAATTTAAATATAAAAT
400935 TTAATTTAAA-ATAAAAT
1 TTAATTTAAATATAAAAT
400952 TT-ATTTAAATATAAA
1 TTAATTTAAATATAAA
400967 TTAAAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 7 0.25
17 21 0.75
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TTAATTTAAATATAAAAT
Found at i:400966 original size:22 final size:21
Alignment explanation
Indices: 400932--400972 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
400922 TATAAATTAA
*
400932 TATTTAATTTAAAATAAAATT
1 TATTTAATATAAAATAAAATT
*
400953 TATTTAAATATAAATTAAAA
1 TATTT-AATATAAAATAAAA
400973 AATAAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TATTTAATATAAAATAAAATT
Found at i:401210 original size:22 final size:19
Alignment explanation
Indices: 401179--401220 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
401169 TATTTTTATT
401179 TAAATTTAATTATAAAATATA
1 TAAATTTAA-TATAAAA-ATA
401200 TAAATATTAATATAAAAATA
1 TAAAT-TTAATATAAAAATA
401220 T
1 T
401221 TTTTAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 12 0.60
22 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAATTTAATATAAAAATA
Found at i:401269 original size:16 final size:15
Alignment explanation
Indices: 401248--401279 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
401238 ATATAAATAA
401248 TAAATTTAAATTAAAT
1 TAAATTTAAA-TAAAT
401264 TAAATTTAAATAAAT
1 TAAATTTAAATAAAT
401279 T
1 T
401280 TTTAAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TAAATTTAAATAAAT
Found at i:401660 original size:23 final size:22
Alignment explanation
Indices: 401607--401660 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
401597 TTAAATTTTG
*
401607 TTTTAAAAAATTAAATTTAAAT
1 TTTTAATAAATTAAATTTAAAT
* *
401629 TATTGAATAAGTTAAATTTAAAT
1 T-TTTAATAAATTAAATTTAAAT
401652 ATTTTAATA
1 -TTTTAATA
401661 TTTGATGGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 1 0.04
23 24 0.92
24 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (22 bp):
TTTTAATAAATTAAATTTAAAT
Found at i:407640 original size:12 final size:12
Alignment explanation
Indices: 407623--407654 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
407613 GAAAACAAAG
407623 GCTGCCAACTGT
1 GCTGCCAACTGT
407635 GCTGCCAACTGT
1 GCTGCCAACTGT
*
407647 GCCGCCAA
1 GCTGCCAA
407655 TTTTGAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.38, G:0.25, T:0.19
Consensus pattern (12 bp):
GCTGCCAACTGT
Found at i:407671 original size:12 final size:12
Alignment explanation
Indices: 407656--407701 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
407646 TGCCGCCAAT
407656 TTTGAAATTCAA
1 TTTGAAATTCAA
*
407668 TTTGAAATAGTAAA
1 TTTGAAAT--TCAA
407682 TGTTGAAATTCAA
1 T-TTGAAATTCAA
407695 TTTGAAA
1 TTTGAAA
407702 CAGTGAAGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 14 0.48
13 4 0.14
14 4 0.14
15 7 0.24
ACGTcount: A:0.43, C:0.04, G:0.13, T:0.39
Consensus pattern (12 bp):
TTTGAAATTCAA
Found at i:414153 original size:2 final size:2
Alignment explanation
Indices: 414146--414181 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
414136 AGTCAGCCTT
414146 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
414182 AAAGATAATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:419346 original size:26 final size:26
Alignment explanation
Indices: 419287--419347 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 26
419277 GAGACGATGT
*
419287 TACGAATATGATAAAAAATAATTAAAT
1 TACG-ATATGATAAAAAATAATTAAAG
*
419314 TATGATATGATATTAAAAATAA-T-AAG
1 TACGATATGATA--AAAAATAATTAAAG
419340 TACGATAT
1 TACGATAT
419348 AAATATATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
26 17 0.59
27 4 0.14
28 8 0.28
ACGTcount: A:0.54, C:0.03, G:0.10, T:0.33
Consensus pattern (26 bp):
TACGATATGATAAAAAATAATTAAAG
Found at i:419417 original size:27 final size:27
Alignment explanation
Indices: 419344--419425 Score: 76
Period size: 31 Copynumber: 2.8 Consensus size: 27
419334 AATAAGTACG
419344 ATATAAATATATAAATATATTAAAATTAA
1 ATATAAATAT-T-AATATATTAAAATTAA
*
419373 ATTATACGAATTATTAATATATTAAAATT-T
1 A-TATA--AA-TATTAATATATTAAAATTAA
*
419403 ATATAAATATGTAATATTTTAAA
1 ATATAAATAT-TAATATATTAAA
419426 TACGAATTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
26 3 0.07
27 13 0.28
29 5 0.11
30 5 0.11
31 14 0.30
32 3 0.07
33 3 0.07
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43
Consensus pattern (27 bp):
ATATAAATATTAATATATTAAAATTAA
Found at i:420721 original size:67 final size:68
Alignment explanation
Indices: 420585--420721 Score: 170
Period size: 68 Copynumber: 2.0 Consensus size: 68
420575 CATTTTGGGT
* * * *
420585 TTTGATCATTTTTAATTCTAATCATTTTTAAGTTGTTAACTTTTCTGATAAAATCATGTTAATTC
1 TTTGATCATTCTAAATTCTAATCATTTTTAAATTATTAACTTTTCTGATAAAATCATGTTAATTC
420650 GAA
66 GAA
* * * *
420653 TTTGATCATTCTAAATT-TAAATTATTTTTAAATTATT-ATTTTTTTGATCAAATCATGTTAATT
1 TTTGATCATTCTAAATTCT-AATCATTTTTAAATTATTAACTTTTCTGATAAAATCATGTTAATT
*
420716 TGAA
65 CGAA
420720 TT
1 TT
420722 GAAATTTGGA
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
67 29 0.49
68 30 0.51
ACGTcount: A:0.32, C:0.08, G:0.07, T:0.53
Consensus pattern (68 bp):
TTTGATCATTCTAAATTCTAATCATTTTTAAATTATTAACTTTTCTGATAAAATCATGTTAATTC
GAA
Found at i:421399 original size:25 final size:24
Alignment explanation
Indices: 421357--421403 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
421347 ATATAAATTT
** *
421357 ATATTTTATTAATGAATTATTAATA
1 ATATTTTACAAATAAATT-TTAATA
421382 ATATTTTACAAATAAATTTTAA
1 ATATTTTACAAATAAATTTTAA
421404 ATTTAAATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 4 0.21
25 15 0.79
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (24 bp):
ATATTTTACAAATAAATTTTAATA
Found at i:423581 original size:16 final size:16
Alignment explanation
Indices: 423536--423590 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
423526 ATTTATTTAT
*
423536 TTATATGAATTTT-AA
1 TTATATAAATTTTAAA
*
423551 -TATATTAATAATTTAAA
1 TTATA-TAA-ATTTTAAA
423568 TTATATAAATTTTAAA
1 TTATATAAATTTTAAA
*
423584 ATATATA
1 TTATATA
423591 TTCATATCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
14 4 0.12
15 2 0.06
16 17 0.53
17 5 0.16
18 4 0.12
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (16 bp):
TTATATAAATTTTAAA
Found at i:424269 original size:22 final size:21
Alignment explanation
Indices: 424243--424292 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
424233 TATTAAAAAT
*
424243 TATTTTTA-AATTAATATTT-G
1 TATTTTTATAATTAA-ATTTAA
424263 TATATTTTATAATTAAATTTAA
1 TAT-TTTTATAATTAAATTTAA
424285 TATTTTTA
1 TATTTTTA
424293 CTATTCAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 3 0.12
21 14 0.54
22 9 0.35
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
TATTTTTATAATTAAATTTAA
Found at i:424458 original size:16 final size:16
Alignment explanation
Indices: 424437--424487 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
424427 CGATATCAAA
424437 TAATTATATTAAATTT
1 TAATTATATTAAATTT
*
424453 TAATTAT-TATAAAATT
1 TAATTATAT-TAAATTT
* *
424469 AAATTAAATTAAATTT
1 TAATTATATTAAATTT
424485 TAA
1 TAA
424488 ATATTTTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 1 0.04
16 26 0.93
17 1 0.04
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TAATTATATTAAATTT
Found at i:424815 original size:3 final size:3
Alignment explanation
Indices: 424809--424850 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
424799 TATTTAAAAG
424809 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
424851 CATTTATTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:429906 original size:2 final size:2
Alignment explanation
Indices: 429901--429943 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
429891 CGTGTGTATG
*
429901 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
429943 T
1 T
429944 TTCTAAACCA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:431113 original size:39 final size:39
Alignment explanation
Indices: 431059--431137 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
431049 GTGACAGGTG
431059 AATCACTCTTTCCCCATTTCACCCCCTTCAAATTCCCTT
1 AATCACTCTTTCCCCATTTCACCCCCTTCAAATTCCCTT
431098 AATCACTCTTTCCCCATTTCACCCCCTTCAAATTCCCTT
1 AATCACTCTTTCCCCATTTCACCCCCTTCAAATTCCCTT
431137 A
1 A
431138 CTCCGATTCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.22, C:0.43, G:0.00, T:0.35
Consensus pattern (39 bp):
AATCACTCTTTCCCCATTTCACCCCCTTCAAATTCCCTT
Found at i:433532 original size:2 final size:2
Alignment explanation
Indices: 433525--433554 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
433515 CGTCACTTGA
433525 AT AT 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 AT AT
433555 TGACTTCTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:435471 original size:14 final size:14
Alignment explanation
Indices: 435442--435479 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
435432 TTTTAAATTT
*
435442 TTTAAATT-TGATA
1 TTTAAATTATCATA
435455 TTTAAATTATCATA
1 TTTAAATTATCATA
*
435469 TTTGAATTATC
1 TTTAAATTATC
435480 GAGTTCAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 8 0.36
14 14 0.64
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (14 bp):
TTTAAATTATCATA
Found at i:436999 original size:15 final size:14
Alignment explanation
Indices: 436952--437003 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 14
436942 AATAGAATAT
436952 ATTTGATTTAATTTTA
1 ATTT-ATTTAA-TTTA
*
436968 ATTTATGTAATAATTA
1 ATTTATTTAAT--TTA
436984 ATTATATTTAATTTA
1 ATT-TATTTAATTTA
436999 ATTTA
1 ATTTA
437004 ATTTTAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
14 3 0.10
15 11 0.35
16 10 0.32
17 7 0.23
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (14 bp):
ATTTATTTAATTTA
Found at i:437223 original size:20 final size:21
Alignment explanation
Indices: 437195--437245 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
437185 AATCAACAAA
*
437195 TTTAAATTAAATTAAT-TAAT
1 TTTATATTAAATTAATCTAAT
*
437215 TTTATATT-ATTTAATCTAAT
1 TTTATATTAAATTAATCTAAT
437235 TTT-TA-TAAATT
1 TTTATATTAAATT
437246 TAAAATATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 1 0.04
19 11 0.42
20 14 0.54
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTATATTAAATTAATCTAAT
Found at i:438045 original size:23 final size:22
Alignment explanation
Indices: 438019--438070 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
438009 TGTCCAAAAA
438019 TAAAATTAAAAATAAATTATATT
1 TAAAATTAAAAATAAA-TATATT
* * * *
438042 TAAAAATAATATTTAATATATT
1 TAAAATTAAAAATAAATATATT
438064 TAAAATT
1 TAAAATT
438071 TAGATTTTGT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 12 0.50
23 12 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TAAAATTAAAAATAAATATATT
Found at i:438077 original size:22 final size:22
Alignment explanation
Indices: 438036--438077 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
438026 AAAAATAAAT
*
438036 TATATTTAAAAATAATATTTAA
1 TATATTTAAAAATAAGATTTAA
* *
438058 TATATTTAAAATTTAGATTT
1 TATATTTAAAAATAAGATTT
438078 TGTACCTAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
TATATTTAAAAATAAGATTTAA
Found at i:438537 original size:16 final size:16
Alignment explanation
Indices: 438518--438673 Score: 111
Period size: 16 Copynumber: 9.7 Consensus size: 16
438508 ATCGAGTTAA
*
438518 TTTAAATTTATATTAT
1 TTTAAATTTAAATTAT
*
438534 TTTAATTTTAAATTAT
1 TTTAAATTTAAATTAT
* *
438550 TTTAAGTTTAAATGGA-
1 TTTAAATTTAAAT-TAT
* * *
438566 ATTGAATTGAAATTAT
1 TTTAAATTTAAATTAT
* **
438582 TTT-ATTTTTTATTAT
1 TTTAAATTTAAATTAT
* *
438597 TTTAGATTTAAATTTTTT
1 TTTAAATTTAAA--TTAT
438615 ATTTAAATTTAAATTAT
1 -TTTAAATTTAAATTAT
* *
438632 TTTAAATTTGAGTTAT
1 TTTAAATTTAAATTAT
*
438648 TTTAAATTTAGATTA-
1 TTTAAATTTAAATTAT
*
438663 ATTAAATTTAA
1 TTTAAATTTAA
438674 TATTTAAATT
Statistics
Matches: 106, Mismatches: 28, Indels: 13
0.72 0.19 0.09
Matches are distributed among these distances:
15 21 0.20
16 67 0.63
17 4 0.04
18 3 0.03
19 11 0.10
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (16 bp):
TTTAAATTTAAATTAT
Found at i:438624 original size:19 final size:20
Alignment explanation
Indices: 438597--438635 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
438587 TTTTTATTAT
*
438597 TTTAGATTTAAATT-TTTTA
1 TTTAAATTTAAATTATTTTA
438616 TTTAAATTTAAATTATTTTA
1 TTTAAATTTAAATTATTTTA
438636 AATTTGAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (20 bp):
TTTAAATTTAAATTATTTTA
Found at i:438779 original size:39 final size:38
Alignment explanation
Indices: 438726--438802 Score: 100
Period size: 39 Copynumber: 2.0 Consensus size: 38
438716 AAGTTTTTAA
* *
438726 ATTTAATTATTTTGAGTTTAAATCATTTTAAATTAAAT
1 ATTTAATTAATTTGAGTATAAATCATTTTAAATTAAAT
* * *
438764 ATTTAAGTTAATTTGAGTATGAATTATTTTAAGTTAAAT
1 ATTTAA-TTAATTTGAGTATAAATCATTTTAAATTAAAT
438803 TGATTAATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
38 6 0.18
39 27 0.82
ACGTcount: A:0.39, C:0.01, G:0.09, T:0.51
Consensus pattern (38 bp):
ATTTAATTAATTTGAGTATAAATCATTTTAAATTAAAT
Found at i:438822 original size:14 final size:15
Alignment explanation
Indices: 438797--438825 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
438787 TTATTTTAAG
438797 TTAAATTGATTAATT
1 TTAAATTGATTAATT
438812 TTAAATT-ATTAATT
1 TTAAATTGATTAATT
438826 ATTTTTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
TTAAATTGATTAATT
Found at i:440373 original size:32 final size:32
Alignment explanation
Indices: 440313--440374 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
440303 TATTATAATT
* **
440313 ATATTTTATAATTTTAATTTTTTCAATTATTG
1 ATATTTAATAATTTTAATTTTTAAAATTATTG
* *
440345 ATATTTAATATTTTTTATTTTTAAAATTAT
1 ATATTTAATAATTTTAATTTTTAAAATTAT
440375 AATAAACACA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (32 bp):
ATATTTAATAATTTTAATTTTTAAAATTATTG
Found at i:441524 original size:13 final size:13
Alignment explanation
Indices: 441502--441532 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
441492 TTTTCTTTCT
*
441502 CTTCTTTTCTATC
1 CTTCTGTTCTATC
441515 CTTCTGTTCTATC
1 CTTCTGTTCTATC
441528 CTTCT
1 CTTCT
441533 TCTTCTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.06, C:0.32, G:0.03, T:0.58
Consensus pattern (13 bp):
CTTCTGTTCTATC
Found at i:441536 original size:3 final size:3
Alignment explanation
Indices: 441528--441563 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
441518 CTGTTCTATC
*
441528 CTT CTT CTT CTT CTT CTT CTT CTT CTT -AT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
441564 CCTCTTGTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 1 0.03
3 29 0.97
ACGTcount: A:0.03, C:0.33, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:441750 original size:3 final size:3
Alignment explanation
Indices: 441742--441778 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
441732 TGAGAGGAAG
441742 ATT ATT ATT ATT ATT ATT ATT ATT ATT -TT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
441779 AAGGTTTGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:442038 original size:26 final size:26
Alignment explanation
Indices: 441990--442066 Score: 70
Period size: 26 Copynumber: 3.0 Consensus size: 26
441980 ATTAACTTTA
*
441990 AAATTATTGTT-AATTACTATTAAATT
1 AAATTATTGTTAAATTA-TTTTAAATT
* *
442016 AAATTTTTGTTAAATTATTTTAATTT
1 AAATTATTGTTAAATTATTTTAAATT
* *
442042 ATATCCA-TGTTAAA-TATTTTAAATT
1 AAAT-TATTGTTAAATTATTTTAAATT
442067 TATTTTTAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
25 10 0.24
26 27 0.64
27 5 0.12
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (26 bp):
AAATTATTGTTAAATTATTTTAAATT
Found at i:443059 original size:28 final size:27
Alignment explanation
Indices: 443007--443067 Score: 88
Period size: 27 Copynumber: 2.2 Consensus size: 27
442997 ATTCGATAAA
443007 AATATAATATAAAAATAATTAAAATAT
1 AATATAATATAAAAATAATTAAAATAT
443034 AATATAATATAAAAATTAATGT-AAATAT
1 AATATAATATAAAAA-TAAT-TAAAATAT
*
443062 TATATA
1 AATATA
443068 TTAAATTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
27 15 0.48
28 15 0.48
29 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (27 bp):
AATATAATATAAAAATAATTAAAATAT
Found at i:443078 original size:14 final size:14
Alignment explanation
Indices: 443055--443113 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
443045 AAAATTAATG
*
443055 TAAATATTATATAT
1 TAAATTTTATATAT
*
443069 TAAATTTTATATAA
1 TAAATTTTATATAT
443083 TACGAATTATTAATATAT
1 TA--AATT-TT-ATATAT
*
443101 TAAAATTTATATA
1 TAAATTTTATATA
443114 AGTATATAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
14 19 0.51
15 2 0.05
16 7 0.19
17 2 0.05
18 7 0.19
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (14 bp):
TAAATTTTATATAT
Found at i:443376 original size:8 final size:8
Alignment explanation
Indices: 443358--443453 Score: 58
Period size: 8 Copynumber: 11.5 Consensus size: 8
443348 TAAAAATAAA
443358 ATAAA-AT
1 ATAAATAT
443365 ATAAATAT
1 ATAAATAT
443373 ATAAATAT
1 ATAAATAT
*
443381 ATTAAAATTT
1 A-T-AAATAT
443391 ATAAA-ACT
1 ATAAATA-T
443399 -TAAAT-T
1 ATAAATAT
443405 ATTAATATATT
1 A-TAA-ATA-T
*
443416 AATAACTAT
1 -ATAAATAT
443425 ATAAATAT
1 ATAAATAT
443433 AT-AATAT
1 ATAAATAT
443440 ATTAAATAT
1 A-TAAATAT
443449 GATAA
1 -ATAA
443454 TAATTAATTT
Statistics
Matches: 71, Mismatches: 4, Indels: 26
0.70 0.04 0.26
Matches are distributed among these distances:
6 1 0.01
7 15 0.21
8 28 0.39
9 13 0.18
10 9 0.13
11 4 0.06
12 1 0.01
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (8 bp):
ATAAATAT
Found at i:443386 original size:24 final size:25
Alignment explanation
Indices: 443359--443434 Score: 70
Period size: 26 Copynumber: 3.0 Consensus size: 25
443349 AAAAATAAAA
443359 TAAAA-TATAAATATATAAATATAT
1 TAAAATTATAAATATATAAATATAT
443383 TAAAATTTATAAA-ACT-TAAAT-TAT
1 TAAAA-TTATAAATA-TATAAATATAT
*
443407 TAATATATTAATAACTATATAAATATAT
1 TAA-A-ATT-ATAAATATATAAATATAT
443435 AATATATTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 14
0.74 0.02 0.25
Matches are distributed among these distances:
24 11 0.26
25 9 0.21
26 13 0.31
27 6 0.14
28 3 0.07
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (25 bp):
TAAAATTATAAATATATAAATATAT
Found at i:443459 original size:16 final size:16
Alignment explanation
Indices: 443366--443460 Score: 64
Period size: 16 Copynumber: 6.2 Consensus size: 16
443356 AAATAAAATA
443366 TAAATATATAAATATAT
1 TAAATATAT-AATATAT
*
443383 TAAAATTTATAA-A-ACT
1 T-AAATATATAATATA-T
443399 TAAAT-TATTAATATAT
1 TAAATATA-TAATATAT
*
443415 T--A-ATA-ACTATA-
1 TAAATATATAATATAT
443426 TAAATATATAATATAT
1 TAAATATATAATATAT
443442 TAAATATGATAATA-AT
1 TAAATAT-ATAATATAT
443458 TAA
1 TAA
443461 TTTATATCGA
Statistics
Matches: 63, Mismatches: 3, Indels: 25
0.69 0.03 0.27
Matches are distributed among these distances:
11 1 0.02
12 5 0.08
13 1 0.02
14 8 0.13
15 13 0.21
16 18 0.29
17 10 0.16
18 7 0.11
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (16 bp):
TAAATATATAATATAT
Found at i:443738 original size:18 final size:18
Alignment explanation
Indices: 443703--443740 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
443693 AATAAAATAT
*
443703 AAATTATTAATATGTAAA
1 AAATTATTAATATATAAA
443721 AAATTATATAAT-TATAAA
1 AAATTAT-TAATATATAAA
443739 AA
1 AA
443741 TAACTTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (18 bp):
AAATTATTAATATATAAA
Found at i:444397 original size:22 final size:21
Alignment explanation
Indices: 444372--444412 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
444362 AACATTTTTT
444372 ATAAA-TAAAATCATAAAAATTA
1 ATAAATTAAAAT-A-AAAAATTA
444394 ATAAATTAAAATAAAAAAT
1 ATAAATTAAAATAAAAAAT
444413 ATCTTACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.33
22 6 0.33
23 6 0.33
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (21 bp):
ATAAATTAAAATAAAAAATTA
Found at i:444691 original size:22 final size:22
Alignment explanation
Indices: 444666--444769 Score: 65
Period size: 22 Copynumber: 4.7 Consensus size: 22
444656 TAATTTAGAG
444666 TATTATATATTTTAATAATTTA
1 TATTATATATTTTAATAATTTA
* *
444688 TATTATATAAATGTTAATAAATTGA
1 TATTATAT--ATTTTAAT-AATTTA
*
444713 TA-TAT-T-TTTAAATAATATTA
1 TATTATATATTTTAATAAT-TTA
* **
444733 TATTTTAT-TTTTTTTAATTTTA
1 TATTATATATTTTAATAA-TTTA
*
444755 TATT-TATATTATAAT
1 TATTATATATTTTAAT
444770 CAAAATTATT
Statistics
Matches: 62, Mismatches: 12, Indels: 16
0.69 0.13 0.18
Matches are distributed among these distances:
19 3 0.05
20 9 0.15
21 5 0.08
22 26 0.42
23 2 0.03
24 10 0.16
25 7 0.11
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (22 bp):
TATTATATATTTTAATAATTTA
Found at i:444735 original size:20 final size:20
Alignment explanation
Indices: 444666--444735 Score: 54
Period size: 20 Copynumber: 3.4 Consensus size: 20
444656 TAATTTAGAG
* *
444666 TATTATATATTTTAATAATTTA
1 TATTATATATTTT--TAAATAA
* *
444688 TATTATATAAATGTT-AATAA
1 TATTATAT-ATTTTTAAATAA
444708 -ATTGATATATTTTTAAATAA
1 TATT-ATATATTTTTAAATAA
444728 TATTATAT
1 TATTATAT
444736 TTTATTTTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
19 7 0.18
20 16 0.42
21 4 0.11
22 8 0.21
23 3 0.08
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
TATTATATATTTTTAAATAA
Found at i:445357 original size:16 final size:18
Alignment explanation
Indices: 445331--445364 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
445321 AAAAAATAAA
445331 AAAAATATAAA-TAATTT
1 AAAAATATAAATTAATTT
445348 AAAAAT-TAAATTAATTT
1 AAAAATATAAATTAATTT
445365 TTTAACATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAAATATAAATTAATTT
Found at i:446011 original size:16 final size:16
Alignment explanation
Indices: 445990--446105 Score: 78
Period size: 16 Copynumber: 7.4 Consensus size: 16
445980 TGATCCGAAT
445990 CTAAAATGACTTGAAA
1 CTAAAATGACTTGAAA
* *
446006 CTAAAATGA-TCCGAAC
1 CTAAAATGACT-TGAAA
446022 CTAAAATGACTTGAAA
1 CTAAAATGACTTGAAA
*
446038 TTAAAATGACTT-AAA
1 CTAAAATGACTTGAAA
* * *
446053 ATCAAATAAAC-TGAAA
1 CTAAAAT-GACTTGAAA
* * * *
446069 TTGAAATTATTTGAAA
1 CTAAAATGACTTGAAA
* *
446085 TTAAAATGATTTG-AA
1 CTAAAATGACTTGAAA
446100 CTAAAA
1 CTAAAA
446106 AATATCTAAA
Statistics
Matches: 80, Mismatches: 15, Indels: 11
0.75 0.14 0.10
Matches are distributed among these distances:
15 18 0.22
16 61 0.76
17 1 0.01
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.28
Consensus pattern (16 bp):
CTAAAATGACTTGAAA
Found at i:446016 original size:32 final size:32
Alignment explanation
Indices: 445980--446046 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
445970 TAAACCTGAT
*
445980 TGATCCGAATCTAAAATGACTTGAAACTAAAA
1 TGATCCGAACCTAAAATGACTTGAAACTAAAA
*
446012 TGATCCGAACCTAAAATGACTTGAAATTAAAA
1 TGATCCGAACCTAAAATGACTTGAAACTAAAA
446044 TGA
1 TGA
446047 CTTAAAATCA
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:0.46, C:0.15, G:0.13, T:0.25
Consensus pattern (32 bp):
TGATCCGAACCTAAAATGACTTGAAACTAAAA
Found at i:447368 original size:15 final size:16
Alignment explanation
Indices: 447336--447370 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
447326 TTTATCTATT
447336 TTTATAATTAATAAAA
1 TTTATAATTAATAAAA
*
447352 TTTATATTTAA-AAAA
1 TTTATAATTAATAAAA
447367 TTTA
1 TTTA
447371 ATTCAAACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TTTATAATTAATAAAA
Found at i:447413 original size:37 final size:38
Alignment explanation
Indices: 447340--447428 Score: 112
Period size: 37 Copynumber: 2.3 Consensus size: 38
447330 TCTATTTTTA
*
447340 TAATTAATAAAATTTATATTTAAAAAATTTAATTCAAAC
1 TAATTAATAAAATTTATATTT-AAAAATTCAATTCAAAC
447379 TAATTAA-AAAATTTTATATTT-AAAATTCAATTCAAAC
1 TAATTAATAAAA-TTTATATTTAAAAATTCAATTCAAAC
*
447416 -AGATTAATTAAAT
1 TA-ATTAATAAAAT
447429 AACTCGATTC
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
36 1 0.02
37 21 0.47
38 7 0.16
39 16 0.36
ACGTcount: A:0.53, C:0.06, G:0.01, T:0.40
Consensus pattern (38 bp):
TAATTAATAAAATTTATATTTAAAAATTCAATTCAAAC
Found at i:448683 original size:19 final size:20
Alignment explanation
Indices: 448642--448683 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
448632 GATTCATTTA
*
448642 AATTTTTATATAAAATAAGT
1 AATTTTTATATAAAAAAAGT
* *
448662 AATTTTTGT-TAAAAAAATT
1 AATTTTTATATAAAAAAAGT
448681 AAT
1 AAT
448684 CATTCTTGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (20 bp):
AATTTTTATATAAAAAAAGT
Found at i:452518 original size:2 final size:2
Alignment explanation
Indices: 452511--452545 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
452501 CCTCCTGAGA
452511 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
452546 ATGTTTTGGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:452897 original size:2 final size:2
Alignment explanation
Indices: 452890--452922 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
452880 TAGAAATTGA
*
452890 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
452923 AACATTGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:454232 original size:11 final size:11
Alignment explanation
Indices: 454190--454242 Score: 56
Period size: 11 Copynumber: 5.0 Consensus size: 11
454180 ATATTTTTAC
454190 ATATTTATA-T
1 ATATTTATATT
454200 ATATTT-TATT
1 ATATTTATATT
* *
454210 ATATTAAAATT
1 ATATTTATATT
454221 ATATTTATATT
1 ATATTTATATT
* *
454232 AGATATATATT
1 ATATTTATATT
454243 TAATATTTGA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
9 2 0.06
10 12 0.34
11 21 0.60
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (11 bp):
ATATTTATATT
Found at i:455171 original size:10 final size:10
Alignment explanation
Indices: 455156--455180 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
455146 CTATAAATTA
455156 AAAAAAAAAG
1 AAAAAAAAAG
455166 AAAAAAAAAG
1 AAAAAAAAAG
455176 AAAAA
1 AAAAA
455181 TTTATATGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:455483 original size:25 final size:23
Alignment explanation
Indices: 455455--455527 Score: 64
Period size: 25 Copynumber: 3.1 Consensus size: 23
455445 TTAGATAGAA
455455 TATTTAATATAATATTATA-TAAATT
1 TATTTAATA-AA-ATTA-AGTAAATT
455480 TATTT-A-AAAATTAAGTAAATT
1 TATTTAATAAAATTAAGTAAATT
455501 TATTTAATTTAAAA-TAAGTTAAATT
1 TATTTAA--TAAAATTAAG-TAAATT
455526 TA
1 TA
455528 AATTTTTTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
20 1 0.02
21 15 0.36
22 3 0.07
23 1 0.02
24 5 0.12
25 17 0.40
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (23 bp):
TATTTAATAAAATTAAGTAAATT
Found at i:455536 original size:25 final size:26
Alignment explanation
Indices: 455474--455536 Score: 71
Period size: 25 Copynumber: 2.5 Consensus size: 26
455464 TAATATTATA
455474 TAAATTTATTTAAAAATTAAGTAAATT
1 TAAATTTATTT-AAAATTAAGTAAATT
455501 T--ATTTAATTTAAAA-TAAGTTAAATT
1 TAAATTT-ATTTAAAATTAAG-TAAATT
455526 TAAATTT-TTTA
1 TAAATTTATTTA
455537 TTAAGATTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
24 4 0.12
25 19 0.59
26 4 0.12
27 5 0.16
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (26 bp):
TAAATTTATTTAAAATTAAGTAAATT
Found at i:455669 original size:28 final size:28
Alignment explanation
Indices: 455575--455669 Score: 65
Period size: 28 Copynumber: 3.5 Consensus size: 28
455565 TTATTTAATA
455575 AAATAATAATTT-TTATTTTAAA--TTT
1 AAATAATAATTTATTATTTTAAATTTTT
* * * **
455600 AATGATAA-AATATATAGATATT-AATTTAA
1 AA--ATAATAATTTAT-TATTTTAAATTTTT
**
455629 AAATAATTTTTTATTATTTTAAATTTTT
1 AAATAATAATTTATTATTTTAAATTTTT
455657 AAATAATAATTTA
1 AAATAATAATTTA
455670 AACTTACAAA
Statistics
Matches: 48, Mismatches: 14, Indels: 13
0.64 0.19 0.17
Matches are distributed among these distances:
25 2 0.04
26 4 0.08
27 15 0.31
28 24 0.50
29 3 0.06
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (28 bp):
AAATAATAATTTATTATTTTAAATTTTT
Found at i:455849 original size:2 final size:2
Alignment explanation
Indices: 455842--455885 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
455832 TATCTCCATG
455842 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
455884 TA
1 TA
455886 ATCGGTCACT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:456272 original size:10 final size:10
Alignment explanation
Indices: 456245--456299 Score: 56
Period size: 10 Copynumber: 5.5 Consensus size: 10
456235 CACTTAGCTC
456245 ATATTAATTT
1 ATATTAATTT
* *
456255 GTAATAATTT
1 ATATTAATTT
*
456265 ATATTAATTA
1 ATATTAATTT
* **
456275 ATATCAATAC
1 ATATTAATTT
456285 ATATTAATTT
1 ATATTAATTT
456295 ATATT
1 ATATT
456300 GATTGATATA
Statistics
Matches: 34, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
10 34 1.00
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (10 bp):
ATATTAATTT
Found at i:456991 original size:3 final size:3
Alignment explanation
Indices: 456983--457020 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
456973 CTGAAAAATC
456983 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
457021 CATTTGCCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:460974 original size:6 final size:7
Alignment explanation
Indices: 460949--460973 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
460939 ACTCAACTCA
460949 AAAAATT
1 AAAAATT
460956 AAAAATT
1 AAAAATT
460963 AAAAATT
1 AAAAATT
460970 AAAA
1 AAAA
460974 TGAAGAACAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
AAAAATT
Found at i:461533 original size:14 final size:14
Alignment explanation
Indices: 461516--461557 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 14
461506 TTTAATATTT
461516 ATTTTTTAAATAAA
1 ATTTTTTAAATAAA
*
461530 A--TTTTAAATTTAA
1 ATTTTTTAAA-TAAA
461543 ATTTTTTAAATAAA
1 ATTTTTTAAATAAA
461557 A
1 A
461558 AAATCATCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
12 7 0.30
13 4 0.17
14 5 0.22
15 7 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTTTTTAAATAAA
Found at i:461742 original size:5 final size:5
Alignment explanation
Indices: 461734--461764 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
461724 TAAAATTTTC
*
461734 AATTA AATTA AATTA AATTA AATTA ATTTA A
1 AATTA AATTA AATTA AATTA AATTA AATTA A
461765 GTTACATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
AATTA
Found at i:462046 original size:40 final size:38
Alignment explanation
Indices: 462001--462083 Score: 112
Period size: 41 Copynumber: 2.1 Consensus size: 38
461991 TTAAATCAAT
* *
462001 TTTTTTATGTTTTATATTTATTATTTAATTATAAAATATAA
1 TTTTTTATATTTTATA-TTATTATTTAA-CAT-AAATATAA
*
462042 TTTTTTATATTTTTTATTATTATTTAACATAAATATAA
1 TTTTTTATATTTTATATTATTATTTAACATAAATATAA
462080 TTTT
1 TTTT
462084 AACATATATG
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
38 12 0.31
39 2 0.05
40 11 0.28
41 14 0.36
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (38 bp):
TTTTTTATATTTTATATTATTATTTAACATAAATATAA
Found at i:462057 original size:43 final size:37
Alignment explanation
Indices: 461998--462083 Score: 100
Period size: 38 Copynumber: 2.2 Consensus size: 37
461988 GTTTTAAATC
*
461998 AATTTTTTTATGTTTTATATTTATTATTTAATTATAAAATAT
1 AATTTTTTTA-GTTTT-TA-TTATTATTTAA-CAT-AAATAT
*
462040 AATTTTTTATATTTTTTATTATTATTTAACATAAATAT
1 AATTTTTT-TAGTTTTTATTATTATTTAACATAAATAT
462078 AATTTT
1 AATTTT
462084 AACATATATG
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
38 12 0.29
39 2 0.05
40 11 0.27
41 2 0.05
42 12 0.29
43 2 0.05
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (37 bp):
AATTTTTTTAGTTTTTATTATTATTTAACATAAATAT
Found at i:462528 original size:2 final size:2
Alignment explanation
Indices: 462521--462548 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
462511 GCATGAGATA
462521 AT 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 AT
462549 TGCAAAACCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:465117 original size:2 final size:2
Alignment explanation
Indices: 465110--465148 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
465100 ACCCTAATTT
465110 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
465149 CCAACATTTC
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:466562 original size:33 final size:34
Alignment explanation
Indices: 466524--466621 Score: 101
Period size: 33 Copynumber: 2.8 Consensus size: 34
466514 TTTTAATGAC
466524 AATAATTAAAATAATATTTTTTAAAAAATAAAAT
1 AATAATTAAAATAATATTTTTTAAAAAATAAAAT
* * *
466558 -ATAATTAATATATTATTTTTTAATTCAAATAAAAT
1 AATAATTAAAATAATATTTTTTAA--AAAATAAAAT
*
466593 AATACATT-AAATATATAATTTTTTTAAAA
1 AATA-ATTAAAATA-AT-ATTTTTTAAAAA
466622 TAGTTATATA
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
33 21 0.41
35 9 0.18
36 9 0.18
37 4 0.08
38 8 0.16
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (34 bp):
AATAATTAAAATAATATTTTTTAAAAAATAAAAT
Found at i:466623 original size:35 final size:32
Alignment explanation
Indices: 466525--466623 Score: 85
Period size: 35 Copynumber: 2.9 Consensus size: 32
466515 TTTAATGACA
466525 ATAATTAA-A-ATAATATTTTTTAAAAAATAAAAT
1 ATAATTAATATATAAT-TTTTTT--AAAATAAAAT
* *
466558 ATAATTAATATATTATTTTTTAATTCAAATAAAAT
1 ATAATTAATATA-TAATTTTT--TTAAAATAAAAT
466593 AATACATTAAATATATAATTTTTTTAAAATA
1 -ATA-ATT-AATATATAATTTTTTTAAAATA
466624 GTTATATAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 14
0.75 0.06 0.19
Matches are distributed among these distances:
33 8 0.15
34 1 0.02
35 21 0.39
36 6 0.11
37 12 0.22
38 6 0.11
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (32 bp):
ATAATTAATATATAATTTTTTTAAAATAAAAT
Found at i:466855 original size:21 final size:23
Alignment explanation
Indices: 466830--466874 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
466820 ATTTTTTATT
466830 TAAAT-TTAAT-TATAAAAAATA
1 TAAATATTAATATATAAAAAATA
*
466851 TAAATATTAATATATAAATAATA
1 TAAATATTAATATATAAAAAATA
466874 T
1 T
466875 TTTAATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.24
22 5 0.24
23 11 0.52
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
TAAATATTAATATATAAAAAATA
Found at i:467127 original size:17 final size:17
Alignment explanation
Indices: 467105--467162 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 17
467095 GTTTTAAAGA
467105 TATTTTAAAATAATATT
1 TATTTTAAAATAATATT
*
467122 TATTTT--AATATTATT
1 TATTTTAAAATAATATT
* *
467137 AAATTTAAAATAATATT
1 TATTTTAAAATAATATT
467154 TATTCTTAA
1 TATT-TTAA
467163 TATATTAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
15 12 0.38
17 16 0.50
18 4 0.12
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (17 bp):
TATTTTAAAATAATATT
Found at i:467136 original size:15 final size:15
Alignment explanation
Indices: 467113--467168 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 15
467103 GATATTTTAA
467113 AATAATATTTATTTT
1 AATAATATTTATTTT
* * *
467128 AATATTATTAAATTTAA
1 AATAATATT-TATTT-T
467145 AATAATATTTATTCTT
1 AATAATATTTATT-TT
467161 AAT-ATATT
1 AATAATATT
467169 AAATTTAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
15 13 0.41
16 10 0.31
17 9 0.28
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (15 bp):
AATAATATTTATTTT
Found at i:467149 original size:32 final size:32
Alignment explanation
Indices: 467108--467181 Score: 132
Period size: 32 Copynumber: 2.3 Consensus size: 32
467098 TTAAAGATAT
467108 TTTAAAATAATATTTATT-TTAATATTATTAAA
1 TTTAAAATAATATTTATTCTTAATA-TATTAAA
467140 TTTAAAATAATATTTATTCTTAATATATTAAA
1 TTTAAAATAATATTTATTCTTAATATATTAAA
467172 TTTAAAATAA
1 TTTAAAATAA
467182 AAATATTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
32 35 0.85
33 6 0.15
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (32 bp):
TTTAAAATAATATTTATTCTTAATATATTAAA
Found at i:467620 original size:21 final size:20
Alignment explanation
Indices: 467594--467636 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
467584 AATTATTTTA
467594 TTTAAATAAAAAT-TTAAATAT
1 TTTAAA-AAAAATATT-AATAT
*
467615 TTTAAAAATAATATTAATAT
1 TTTAAAAAAAATATTAATAT
467635 TT
1 TT
467637 AATAATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TTTAAAAAAAATATTAATAT
Found at i:467969 original size:22 final size:23
Alignment explanation
Indices: 467928--467996 Score: 68
Period size: 22 Copynumber: 2.9 Consensus size: 23
467918 TTATATAAAT
*
467928 ATATAAAATTTTTAACATAATTATA
1 ATATAAAA-TATTAA-ATAATTATA
*
467953 ATATAAAA-ATTAAATAAATATA
1 ATATAAAATATTAAATAATTATA
* *
467975 ATTTAAAATATATAAATTATTA
1 ATATAAAATAT-TAAATAATTA
467997 AAGTTACTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
22 15 0.41
23 6 0.16
24 8 0.22
25 8 0.22
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (23 bp):
ATATAAAATATTAAATAATTATA
Found at i:468291 original size:30 final size:31
Alignment explanation
Indices: 468250--468332 Score: 93
Period size: 30 Copynumber: 2.6 Consensus size: 31
468240 ATAAATTAAA
468250 ATAT-AATATAAATATTTAATTTA-AAAA-T
1 ATATAAATATAAATATTTAATTTATAAAATT
468278 ATATAATATATAAAT-TATTAATTTATTAAAATTT
1 ATATAA-ATATAAATAT-TTAATTTA-TAAAA-TT
468312 ATATAAATATAAAATATTTAA
1 ATATAAATAT-AAATATTTAA
468333 ATATACTTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
28 4 0.09
29 2 0.04
30 16 0.35
32 4 0.09
33 4 0.09
34 15 0.33
35 1 0.02
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (31 bp):
ATATAAATATAAATATTTAATTTATAAAATT
Found at i:468328 original size:7 final size:8
Alignment explanation
Indices: 468219--468392 Score: 56
Period size: 8 Copynumber: 21.0 Consensus size: 8
468209 GTAATTTTAA
*
468219 ATATAATT
1 ATATAAAT
468227 ATATAAAGAT
1 ATAT-AA-AT
468237 AATATAAAT
1 -ATATAAAT
*
468246 -TAAAATAT
1 ATATAA-AT
468254 AATATAAAT
1 -ATATAAAT
*
468263 AT-TTAAT
1 ATATAAAT
* *
468270 TTAAAAAT
1 ATATAAAT
468278 ATAT-AAT
1 ATATAAAT
468285 ATATAAAT
1 ATATAAAT
*
468293 -TATTAAT
1 ATATAAAT
*
468300 TTATTAAAATTT
1 ATA-T-AAA--T
468312 ATATAAAT
1 ATATAAAT
468320 ATA-AAAT
1 ATATAAAT
*
468327 ATTTAAAT
1 ATATAAAT
* *
468335 ATACTTATT
1 ATA-TAAAT
*
468344 ATATAAAAA
1 ATAT-AAAT
468353 ATATAAAT
1 ATATAAAT
*
468361 A-A-ACAT
1 ATATAAAT
*
468367 GCATATATAT
1 --ATATAAAT
*
468377 ATATATAT
1 ATATAAAT
468385 ATATAAAT
1 ATATAAAT
468393 TTGGCGATCT
Statistics
Matches: 123, Mismatches: 23, Indels: 40
0.66 0.12 0.22
Matches are distributed among these distances:
6 3 0.02
7 29 0.24
8 49 0.40
9 19 0.15
10 15 0.12
11 5 0.04
12 3 0.02
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (8 bp):
ATATAAAT
Found at i:469049 original size:16 final size:16
Alignment explanation
Indices: 469025--469055 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
469015 TGTGTTAATT
469025 ATTTAGATCATTTTAA
1 ATTTAGATCATTTTAA
*
469041 ATTTTGATCATTTTA
1 ATTTAGATCATTTTA
469056 GACTTGATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.55
Consensus pattern (16 bp):
ATTTAGATCATTTTAA
Found at i:469151 original size:5 final size:5
Alignment explanation
Indices: 469141--469205 Score: 66
Period size: 5 Copynumber: 13.2 Consensus size: 5
469131 AAAAATTTTT
*
469141 AATTA AATTA AATTA AATTAA AATT- AATT- AATT- AATTA AATT- TATTA
1 AATTA AATTA AATTA AATT-A AATTA AATTA AATTA AATTA AATTA AATTA
469188 AATTAA AATTAA AATTA A
1 AATT-A AATT-A AATTA A
469206 TAAATATATA
Statistics
Matches: 54, Mismatches: 2, Indels: 8
0.84 0.03 0.12
Matches are distributed among these distances:
4 15 0.28
5 23 0.43
6 16 0.30
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
AATTA
Found at i:469166 original size:6 final size:6
Alignment explanation
Indices: 469141--469205 Score: 50
Period size: 6 Copynumber: 11.0 Consensus size: 6
469131 AAAAATTTTT
*
469141 AATT-A AATT-A AATT-A AATTAA AATT-- AATTAA TTAATTAA ATTTATTA
1 AATTAA AATTAA AATTAA AATTAA AATTAA AATTAA --AATTAA AATTA--A
469188 AATTAA AATTAA AATTAA
1 AATTAA AATTAA AATTAA
469206 TAAATATATA
Statistics
Matches: 51, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
4 4 0.08
5 14 0.27
6 22 0.43
8 11 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (6 bp):
AATTAA
Found at i:469472 original size:8 final size:8
Alignment explanation
Indices: 469461--469485 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
469451 TAAAAATATT
469461 AAAAATAA
1 AAAAATAA
469469 AAAAATAA
1 AAAAATAA
469477 AAAAATAA
1 AAAAATAA
469485 A
1 A
469486 TTATCTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAATAA
Found at i:469936 original size:11 final size:11
Alignment explanation
Indices: 469906--469947 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
469896 TAATTTTATT
469906 AATTAAATTT-
1 AATTAAATTTA
**
469916 AATTTGATTTA
1 AATTAAATTTA
469927 AATTAAATTTA
1 AATTAAATTTA
*
469938 AATTACATTT
1 AATTAAATTT
469948 TTTTAACATC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
10 8 0.31
11 18 0.69
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (11 bp):
AATTAAATTTA
Found at i:470367 original size:2 final size:2
Alignment explanation
Indices: 470360--470387 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
470350 CAGCCGTCAA
470360 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
470388 ATATATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:479356 original size:17 final size:15
Alignment explanation
Indices: 479324--479372 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
479314 ATTATAAATA
**
479324 AAAATTAAAATTTTT
1 AAAATTAAAAAATTT
479339 AAATATTAAAAAAATTT
1 AAA-ATT-AAAAAATTT
*
479356 AAAATTTAAAAATTT
1 AAAATTAAAAAATTT
479371 AA
1 AA
479373 GTATAGTCAC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 13 0.45
16 6 0.21
17 10 0.34
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAAATTAAAAAATTT
Found at i:479366 original size:16 final size:16
Alignment explanation
Indices: 479322--479372 Score: 50
Period size: 17 Copynumber: 3.2 Consensus size: 16
479312 ATATTATAAA
* **
479322 TAAAAATTAAAATTTT
1 TAAAATTTAAAAAATT
*
479338 TAAATATTAAAAAAATT
1 TAAA-ATTTAAAAAATT
479355 TAAAATTT-AAAAATT
1 TAAAATTTAAAAAATT
479370 TAA
1 TAA
479373 GTATAGTCAC
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
15 10 0.34
16 7 0.24
17 12 0.41
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAAAATTTAAAAAATT
Found at i:489800 original size:18 final size:17
Alignment explanation
Indices: 489772--489819 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
489762 ATATTAAATT
489772 AAATTATATATATAATA
1 AAATTATATATATAATA
* *
489789 AATATTAAATAT-TATTA
1 AA-ATTATATATATAATA
489806 AAATTATATATATA
1 AAATTATATATATA
489820 TTGAATGATA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 8 0.31
17 10 0.38
18 8 0.31
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATTATATATATAATA
Found at i:489878 original size:29 final size:28
Alignment explanation
Indices: 489750--489893 Score: 77
Period size: 29 Copynumber: 5.1 Consensus size: 28
489740 AAAATAAAAG
489750 TAATTATT-AAAA-ATATTAA-ATTAAA
1 TAATTATTAAAAATATATTAATATTAAA
* * *
489775 TTATATATATAATAAATAT-TAAATATT-AT
1 TAAT-TAT-TAA-AAATATATTAATATTAAA
* * * *
489804 TAA-AATTATATATATATTGAATGATAAAA
1 TAATTATTAAAAATATATT-AAT-ATTAAA
* *
489833 T-ATAAATTAAAAATATATTAATAATTAAT
1 TAAT-TATTAAAAATATATTAAT-ATTAAA
* *
489862 TAATTATTAAAATTATATTTATATTAAA
1 TAATTATTAAAAATATATTAATATTAAA
489890 TAAT
1 TAAT
489894 AAAATATATA
Statistics
Matches: 87, Mismatches: 19, Indels: 23
0.67 0.15 0.18
Matches are distributed among these distances:
25 8 0.09
26 6 0.07
27 6 0.07
28 13 0.15
29 34 0.39
30 20 0.23
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (28 bp):
TAATTATTAAAAATATATTAATATTAAA
Found at i:489915 original size:38 final size:34
Alignment explanation
Indices: 489768--489971 Score: 143
Period size: 34 Copynumber: 6.0 Consensus size: 34
489758 AAAAATATTA
* * *
489768 AATT-AAATTATATATATAATAAATATTAA-ATAT
1 AATTAAAATTATATTTATATTAAATAATAATA-AT
* * * *
489801 TATTAAAATTATATATATATTGAATGATAA-AAT
1 AATTAAAATTATATTTATATTAAATAATAATAAT
* **
489834 -A-T-AAATTAAAAATATATT-AATAATTAATTAAT
1 AATTAAAATTATATTTATATTAAATAA-TAA-TAAT
*
489866 TATTAAAATTATATTTATATTAAATAATAAAATATAT
1 AATTAAAATTATATTTATATTAAATAAT--AATA-AT
*
489903 AAATTAAAATTATATTTATTTTAAATAATAATAAT
1 -AATTAAAATTATATTTATATTAAATAATAATAAT
** * *
489938 AATTATTATTATATTTACATTAAAATAAAAATAA
1 AATTAAAATTATATTTATATT-AAATAATAATAA
489972 ATAAAAATAA
Statistics
Matches: 140, Mismatches: 18, Indels: 24
0.77 0.10 0.13
Matches are distributed among these distances:
29 4 0.03
30 17 0.12
31 1 0.01
32 4 0.03
33 6 0.04
34 40 0.29
35 27 0.19
36 11 0.08
37 4 0.03
38 26 0.19
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (34 bp):
AATTAAAATTATATTTATATTAAATAATAATAAT
Found at i:489916 original size:15 final size:15
Alignment explanation
Indices: 489832--489917 Score: 50
Period size: 15 Copynumber: 5.3 Consensus size: 15
489822 GAATGATAAA
*
489832 ATATAAATTAAAAAT
1 ATATAAATTAAAATT
489847 ATATTAATAATTAATTAATT
1 ATA-T-A-AATTAA--AATT
* *
489867 AT-TAAAATTATATTT
1 ATAT-AAATTAAAATT
489882 ATATTAAATAATAAAA-T
1 ATA-TAAAT--TAAAATT
489899 ATATAAATTAAAATT
1 ATATAAATTAAAATT
489914 ATAT
1 ATAT
489918 TTATTTTAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 20
0.69 0.06 0.25
Matches are distributed among these distances:
14 5 0.09
15 13 0.23
16 10 0.18
17 11 0.20
18 12 0.21
20 5 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATATAAATTAAAATT
Found at i:489949 original size:34 final size:37
Alignment explanation
Indices: 489867--489976 Score: 129
Period size: 38 Copynumber: 3.0 Consensus size: 37
489857 TTAATTAATT
489867 ATTAAAATTATATTTATATTAAATAATAAAATATATAA
1 ATTAAAATTATATTTATATTAAATAAT-AAATATATAA
*
489905 ATTAAAATTATATTTATTTTAAATAAT-AATA-AT-A
1 ATTAAAATTATATTTATATTAAATAATAAATATATAA
** * *
489939 ATTATTATTATATTTACATTAAAATAA-AAATAAATAA
1 ATTAAAATTATATTTATATT-AAATAATAAATATATAA
489976 A
1 A
489977 AATAATTTTA
Statistics
Matches: 63, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
34 17 0.27
35 12 0.19
36 6 0.10
37 2 0.03
38 26 0.41
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (37 bp):
ATTAAAATTATATTTATATTAAATAATAAATATATAA
Found at i:491013 original size:24 final size:22
Alignment explanation
Indices: 490986--491044 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 22
490976 TATCAATAAT
490986 AAATTTTTTATTTAAATTTCTTAA
1 AAATTTTTTATTTAAATTT-TT-A
*
491010 AAATTTTTATTTTTTAAATTTTTA
1 AAA-TTTT-TTATTTAAATTTTTA
491034 AAATTTTTTAT
1 AAATTTTTTAT
491045 AATTACGTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
22 3 0.10
23 4 0.13
24 7 0.23
25 6 0.19
26 11 0.35
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.63
Consensus pattern (22 bp):
AAATTTTTTATTTAAATTTTTA
Found at i:491034 original size:25 final size:26
Alignment explanation
Indices: 490996--491044 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
490986 AAATTTTTTA
490996 TTTAAATTTCTTAAAAATTTTTATTT
1 TTTAAATTTCTTAAAAATTTTTATTT
*
491022 TTTAAATTT-TTAAAATTTTTTAT
1 TTTAAATTTCTTAAAAATTTTTAT
491045 AATTACGTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (26 bp):
TTTAAATTTCTTAAAAATTTTTATTT
Found at i:492530 original size:19 final size:20
Alignment explanation
Indices: 492508--492557 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
492498 TTATTTTACC
*
492508 TATTAAAT-TTTATTTAAAA
1 TATTAAATATTTATATAAAA
*
492527 TATTATATATTTATATAAAA
1 TATTAAATATTTATATAAAA
492547 T-TTAATATATT
1 TATTAA-ATATT
492558 AATAATTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TATTAAATATTTATATAAAA
Found at i:492760 original size:19 final size:17
Alignment explanation
Indices: 492751--492792 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
492741 ATATTTTATT
*
492751 ATAATTATAATTTTTTAC
1 ATAATAATAA-TTTTTAC
492769 ATAATAATAATTTTTA-
1 ATAATAATAATTTTTAC
492785 ATAATAAT
1 ATAATAAT
492793 TTATATTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.35
17 6 0.26
18 9 0.39
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (17 bp):
ATAATAATAATTTTTAC
Found at i:492788 original size:13 final size:13
Alignment explanation
Indices: 492770--492794 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
492760 ATTTTTTACA
492770 TAATAATAATTTT
1 TAATAATAATTTT
492783 TAATAATAATTT
1 TAATAATAATTT
492795 ATATTATATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TAATAATAATTTT
Found at i:492788 original size:16 final size:16
Alignment explanation
Indices: 492738--492792 Score: 58
Period size: 18 Copynumber: 3.3 Consensus size: 16
492728 TTATATCAAC
*
492738 ATAAT-ATTTTATTATA
1 ATAATAATTTT-TAATA
*
492754 ATTATAATTTTTTACATA
1 ATAATAA-TTTTTA-ATA
492772 ATAATAATTTTTAATA
1 ATAATAATTTTTAATA
492788 ATAAT
1 ATAAT
492793 TTATATTATA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
16 12 0.36
17 8 0.24
18 13 0.39
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (16 bp):
ATAATAATTTTTAATA
Done.