Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold66
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: 4623749
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 850 characters in sequence are not A, C, G, or T
File 3 of 26
Found at i:403268 original size:19 final size:19
Alignment explanation
Indices: 403246--403293 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
403236 TATATAATAT
403246 ATAATATATTAAA-ATTTAG
1 ATAA-ATATTAAATATTTAG
*
403265 ATAAATATTAAATATTTAAA
1 ATAAATATTAAATATTT-AG
403285 ATAAATATT
1 ATAAATATT
403294 TAATGAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 8 0.31
19 8 0.31
20 10 0.38
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
ATAAATATTAAATATTTAG
Found at i:403288 original size:20 final size:18
Alignment explanation
Indices: 403246--403325 Score: 70
Period size: 18 Copynumber: 4.1 Consensus size: 18
403236 TATATAATAT
*
403246 ATAATATATTAAAATTTAG
1 ATAA-ATATTAAAATTTAA
403265 ATAAATATTAAATATTTAAA
1 ATAAATATTAAA-ATTT-AA
403285 ATAAATATTTAATGAATATTAA
1 ATAAATA-TTAA--AAT-TTAA
* *
403307 ATATATAATAAAATTTAA
1 ATAAATATTAAAATTTAA
403325 A
1 A
403326 AATATAAATA
Statistics
Matches: 52, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
18 13 0.25
19 11 0.21
20 8 0.15
21 7 0.13
22 10 0.19
23 3 0.06
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (18 bp):
ATAAATATTAAAATTTAA
Found at i:403303 original size:31 final size:30
Alignment explanation
Indices: 403255--403338 Score: 104
Period size: 31 Copynumber: 2.9 Consensus size: 30
403245 TATAATATAT
403255 TAAAATTTAGATAAATATTAAATATTTAAAA
1 TAAAATTTA-ATAAATATTAAATATTTAAAA
* *
403286 TAAATATTTAATGAATATTAAATA--TATAA
1 TAAA-ATTTAATAAATATTAAATATTTAAAA
403315 TAAAATTTAA-AAATA-TAAATATTT
1 TAAAATTTAATAAATATTAAATATTT
403339 TAATTATAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
26 6 0.13
27 4 0.09
28 7 0.15
29 8 0.17
31 17 0.36
32 5 0.11
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (30 bp):
TAAAATTTAATAAATATTAAATATTTAAAA
Found at i:407490 original size:3 final size:3
Alignment explanation
Indices: 407482--407511 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
407472 TGCATTTTCC
407482 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
407512 GTTTTGGGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:415057 original size:24 final size:22
Alignment explanation
Indices: 415004--415045 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
414994 TTGAATTATT
415004 TATATAAAAATATAAATATTAAA
1 TATA-AAAAATATAAATATTAAA
415027 TATAAAAAATAT-AATATTA
1 TATAAAAAATATAAATATTA
415046 TTTTAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 7 0.37
22 8 0.42
23 4 0.21
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
TATAAAAAATATAAATATTAAA
Found at i:415845 original size:2 final size:2
Alignment explanation
Indices: 415838--415875 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
415828 CTATGCCCAC
415838 CT CT CT CT CT 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 CT CT CT CT CT
415876 GTGTTTTCGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:416951 original size:2 final size:2
Alignment explanation
Indices: 416944--416973 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
416934 GAGAAGCTAC
416944 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
416974 CTTTGACATG
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:417707 original size:6 final size:6
Alignment explanation
Indices: 417696--417722 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
417686 TAGAGGTGAA
417696 AGAAAG AGAAAG AGAAAG AGAAAG AGA
1 AGAAAG AGAAAG AGAAAG AGAAAG AGA
417723 GACATTCGGA
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:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (6 bp):
AGAAAG
Found at i:418516 original size:37 final size:34
Alignment explanation
Indices: 418473--418552 Score: 117
Period size: 37 Copynumber: 2.3 Consensus size: 34
418463 TACCAATACG
*
418473 TTTAATAAAATAAAATAATTATAATAATTTAATTTAA
1 TTTAATAAAATAAAAT-ATTATAA-AATTTAAATT-A
418510 TTTAATAAAATAAAATATTATAAAATTTAAATTA
1 TTTAATAAAATAAAATATTATAAAATTTAAATTA
418544 -TTAATAAAA
1 TTTAATAAAA
418553 AATAACATTT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
33 9 0.21
34 1 0.02
35 9 0.21
36 7 0.17
37 16 0.38
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (34 bp):
TTTAATAAAATAAAATATTATAAAATTTAAATTA
Found at i:445232 original size:14 final size:14
Alignment explanation
Indices: 445213--445356 Score: 117
Period size: 14 Copynumber: 10.1 Consensus size: 14
445203 GATGAAGAAT
445213 TATATATATACATA
1 TATATATATACATA
* *
445227 TATATACATACATG
1 TATATATATACATA
* * * *
445241 TATACACACACACA
1 TATATATATACATA
*
445255 TATATATACACATACA
1 TATATATATACAT--A
* *
445271 CATATATATACACA
1 TATATATATACATA
* *
445285 CATTATATATACACA
1 TA-TATATATACATA
445300 TATATATATACATA
1 TATATATATACATA
* *
445314 CATATATATACAGA
1 TATATATATACATA
* *
445328 CATATATATATATA
1 TATATATATACATA
*
445342 TATATATATAGATA
1 TATATATATACATA
445356 T
1 T
445357 CCAGAAGGAT
Statistics
Matches: 107, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
14 83 0.78
15 13 0.12
16 11 0.10
ACGTcount: A:0.49, C:0.15, G:0.02, T:0.35
Consensus pattern (14 bp):
TATATATATACATA
Found at i:445264 original size:18 final size:18
Alignment explanation
Indices: 445241--445286 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
445231 TACATACATG
445241 TATACACACACACATATA
1 TATACACACACACATATA
*
445259 TATACACATACACATATA
1 TATACACACACACATATA
445277 TATACACACA
1 TATACACACA
445287 TTATATATAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (18 bp):
TATACACACACACATATA
Found at i:445293 original size:2 final size:2
Alignment explanation
Indices: 445288--445356 Score: 66
Period size: 2 Copynumber: 34.5 Consensus size: 2
445278 ATACACACAT
* * * * * * *
445288 TA TA TA TA CA CA TA TA TA TA TA CA TA CA TA TA TA TA CA GA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
445330 TA TA TA TA TA TA TA TA TA TA TA GA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
445357 CCAGAAGGAT
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.09, G:0.03, T:0.39
Consensus pattern (2 bp):
TA
Found at i:446780 original size:12 final size:12
Alignment explanation
Indices: 446749--446780 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
446739 TATTTACATT
446749 AAAATAT-ATTA
1 AAAATATAATTA
446760 AAAAT-TAATTA
1 AAAATATAATTA
446771 AAAATATAAT
1 AAAATATAAT
446781 ATATTAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 1 0.05
11 14 0.74
12 4 0.21
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
AAAATATAATTA
Found at i:468759 original size:34 final size:32
Alignment explanation
Indices: 468721--468783 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
468711 TTAAATCAAT
*
468721 TTAAATATGTTTATATTATTCTTT-TTTTAAAAAA
1 TTAAATAT-TTTAT-TT-TTATTTATTTTAAAAAA
468755 TTAAATATTTTATTTTTATTTATTTTAAA
1 TTAAATATTTTATTTTTATTTATTTTAAA
468784 TATTTTTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 5 0.19
32 9 0.33
33 5 0.19
34 8 0.30
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (32 bp):
TTAAATATTTTATTTTTATTTATTTTAAAAAA
Found at i:472513 original size:22 final size:22
Alignment explanation
Indices: 472460--472527 Score: 81
Period size: 22 Copynumber: 3.2 Consensus size: 22
472450 TCTAAAATAT
*
472460 AATAAATTTTTA-TATTT-TTA
1 AATATATTTTTATTATTTATTA
*
472480 AA-A-ATTTATATTATTTATTA
1 AATATATTTTTATTATTTATTA
472500 AATATATTTTTATTATTTATTA
1 AATATATTTTTATTATTTATTA
472522 TAATAT
1 -AATAT
472528 TTATATCATA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
18 6 0.15
19 6 0.15
20 7 0.17
21 1 0.02
22 16 0.39
23 5 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
AATATATTTTTATTATTTATTA
Found at i:473861 original size:19 final size:17
Alignment explanation
Indices: 473827--473869 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
473817 TTGATTTAAA
*
473827 ATTTTATTTTATTATTT
1 ATTTTATTTAATTATTT
473844 ATTTTATATTAATATATTT
1 ATTTTAT-TTAAT-TATTT
473863 ATATTTA
1 AT-TTTA
473870 AATAAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 7 0.32
18 4 0.18
19 7 0.32
20 4 0.18
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
ATTTTATTTAATTATTT
Found at i:473880 original size:20 final size:19
Alignment explanation
Indices: 473839--473886 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
473829 TTTATTTTAT
* * *
473839 TATTTATTTTATATTAATA
1 TATTTATTTTAAATAAAAA
473858 TATTTATATTTAAATAAAAA
1 TATTTAT-TTTAAATAAAAA
473878 TA-TTATTTT
1 TATTTATTTT
473887 TATCATTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 3 0.12
19 11 0.44
20 11 0.44
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATTTATTTTAAATAAAAA
Found at i:474575 original size:2 final size:2
Alignment explanation
Indices: 474568--474606 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
474558 ATCTTTTTCC
474568 AT AT 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 AT AT A
474607 GCCATATAGC
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:476555 original size:31 final size:31
Alignment explanation
Indices: 476515--476575 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 31
476505 ATATATGAAT
*
476515 ATATTAAAATTTATATA-ATAAAATTATTAAC
1 ATATAAAAATTTATATATATAAAA-TATTAAC
476546 ATATAAAAATTTATATATTATAAAATATTA
1 ATATAAAAATTTATATA-TATAAAATATTA
476576 TAAATTTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 16 0.59
32 5 0.19
33 6 0.22
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (31 bp):
ATATAAAAATTTATATATATAAAATATTAAC
Found at i:476576 original size:17 final size:16
Alignment explanation
Indices: 476513--476624 Score: 60
Period size: 15 Copynumber: 7.3 Consensus size: 16
476503 GAATATATGA
476513 ATATAT-TAAAAT-TT
1 ATATATATAAAATATT
476527 ATATA-ATAAAATTATT
1 ATATATATAAAA-TATT
*
476543 A-ACATATAAAA-ATTT
1 ATATATATAAAATA-TT
476558 ATATATTATAAAATATT
1 ATATA-TATAAAATATT
* * * *
476575 ATAAAT-TTAATTATG
1 ATATATATAAAATATT
*
476590 ATAT-GATAAAATA-T
1 ATATATATAAAATATT
* * *
476604 ATAAATATAATATAAT
1 ATATATATAAAATATT
476620 ATATA
1 ATATA
476625 AATTATCAAA
Statistics
Matches: 72, Mismatches: 15, Indels: 20
0.67 0.14 0.19
Matches are distributed among these distances:
14 14 0.19
15 27 0.38
16 17 0.24
17 13 0.18
18 1 0.01
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.42
Consensus pattern (16 bp):
ATATATATAAAATATT
Found at i:476580 original size:25 final size:25
Alignment explanation
Indices: 476552--476635 Score: 64
Period size: 25 Copynumber: 3.2 Consensus size: 25
476542 TAACATATAA
476552 AAATTTATATATTATAAAATATTAT
1 AAATTTATATATTATAAAATATTAT
476577 AAATTTAATTATGATATGATAAAATA-TAT
1 AAATTT-A-TAT-AT-T-ATAAAATATTAT
* * *
476606 AAATATAATATAATATATAA-ATTAT
1 AAAT-TTATATATTATAAAATATTAT
476631 CAAAT
1 -AAAT
476636 CTTAAATCAA
Statistics
Matches: 48, Mismatches: 3, Indels: 15
0.73 0.05 0.23
Matches are distributed among these distances:
24 1 0.02
25 14 0.29
26 6 0.12
27 4 0.08
28 5 0.10
29 9 0.19
30 9 0.19
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.42
Consensus pattern (25 bp):
AAATTTATATATTATAAAATATTAT
Found at i:476601 original size:30 final size:27
Alignment explanation
Indices: 476556--476626 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 27
476546 ATATAAAAAT
*
476556 TTATATATTATAAAATATTATAAATTTAA
1 TTATATA-TATAAAATA-TATAAATATAA
476585 TTATGATATGATAAAATATATAAATATAA
1 TTAT-ATAT-ATAAAATATATAAATATAA
476614 -TATAATATATAAA
1 TTAT-ATATATAAA
476627 TTATCAAATC
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.13
28 7 0.18
29 15 0.39
30 11 0.29
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (27 bp):
TTATATATATAAAATATATAAATATAA
Found at i:480572 original size:24 final size:23
Alignment explanation
Indices: 480535--480593 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 23
480525 AGATATTAAT
480535 TTTATAATTT-AAAT-AAATTATTA
1 TTTA-AATTTAAAATAAAATT-TTA
480558 TTTAAATATTAAAATAAAAATTTTA
1 TTTAAAT-TTAAAAT-AAAATTTTA
480583 TTTAAATTTAA
1 TTTAAATTTAA
480594 TTATAAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
22 3 0.09
23 6 0.19
24 8 0.25
25 10 0.31
26 5 0.16
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TTTAAATTTAAAATAAAATTTTA
Found at i:480588 original size:25 final size:26
Alignment explanation
Indices: 480549--480603 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 26
480539 TAATTTAAAT
480549 AAATTATTATTTAAATATTAA-AATAA
1 AAATTATTATTTAAAT-TTAATAATAA
*
480575 AAATT-TTATTTAAATTTAATTATAA
1 AAATTATTATTTAAATTTAATAATAA
480600 AAAT
1 AAAT
480604 AAATTTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 4 0.15
25 18 0.67
26 5 0.19
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
AAATTATTATTTAAATTTAATAATAA
Found at i:487100 original size:2 final size:2
Alignment explanation
Indices: 487093--487128 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
487083 CCATGAAACG
*
487093 AT AT AT AT AT AT A- AT AT AA 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 AT A
487129 ATACCAAGAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:489299 original size:19 final size:19
Alignment explanation
Indices: 489277--489319 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
489267 ATATAAATAT
* *
489277 ATTTAATTTTTTTAAAAAA
1 ATTTAATGTATTTAAAAAA
489296 ATTT-ATGTATTTAAAAAA
1 ATTTAATGTATTTAAAAAA
489314 ATTTAA
1 ATTTAA
489320 AAAAATTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
ATTTAATGTATTTAAAAAA
Found at i:490580 original size:105 final size:105
Alignment explanation
Indices: 490431--490744 Score: 556
Period size: 105 Copynumber: 3.0 Consensus size: 105
490421 TCTCCTCAAG
*
490431 CAACCGATCGTACTCAAGAAGAAAATCTTCAGATTGTTTCCTTAAAGCAACTGCATTAGCTTCTG
1 CAACCGATCATACTCAAGAAGAAAATCTTCAGATTGTTTCCTTAAAGCAACTGCATTAGCTTCTG
490496 CAGCATTCAACTCTTTTGTCTTTGTCTCAAGATCAGACTT
66 CAGCATTCAACTCTTTTGTCTTTGTCTCAAGATCAGACTT
* *
490536 TAACCGATCATACTCAAGAAGAAAATCTTCAAATTGTTTCCTTAAAGCAACTGCATTAGCTTCTG
1 CAACCGATCATACTCAAGAAGAAAATCTTCAGATTGTTTCCTTAAAGCAACTGCATTAGCTTCTG
490601 CAGCATTCAACTCTTTTGTCTTTGTCTCAAGATCAGACTT
66 CAGCATTCAACTCTTTTGTCTTTGTCTCAAGATCAGACTT
* *
490641 CAGCCGATCATACTCAAGAAGAAAATCTTCAGATTGTTTCCTTAAAGCAACTACATTAGCTTCTG
1 CAACCGATCATACTCAAGAAGAAAATCTTCAGATTGTTTCCTTAAAGCAACTGCATTAGCTTCTG
* * *
490706 CAGCATTCATCTCCTTTGTCTTAGTCTCAAGATCAGACT
66 CAGCATTCAACTCTTTTGTCTTTGTCTCAAGATCAGACT
490745 CAAGCTGCTT
Statistics
Matches: 199, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
105 199 1.00
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.33
Consensus pattern (105 bp):
CAACCGATCATACTCAAGAAGAAAATCTTCAGATTGTTTCCTTAAAGCAACTGCATTAGCTTCTG
CAGCATTCAACTCTTTTGTCTTTGTCTCAAGATCAGACTT
Found at i:492566 original size:18 final size:17
Alignment explanation
Indices: 492510--492566 Score: 50
Period size: 18 Copynumber: 3.5 Consensus size: 17
492500 AGTTTAATCT
492510 AAATTTTAAA--TAA-A
1 AAATTTTAAATTTAATA
* *
492524 AAA-TTTAAATTTAGTT
1 AAATTTTAAATTTAATA
492540 AAATATTTAAATATTAATA
1 AAAT-TTTAAAT-TTAATA
492559 AAATTTTA
1 AAATTTTA
492567 TTTAATTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
13 6 0.18
14 3 0.09
15 2 0.06
16 3 0.09
18 11 0.33
19 8 0.24
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (17 bp):
AAATTTTAAATTTAATA
Found at i:500386 original size:4 final size:4
Alignment explanation
Indices: 500377--500426 Score: 64
Period size: 4 Copynumber: 12.5 Consensus size: 4
500367 TGAAAATTAT
* * * *
500377 TACA TACA TACA TACA TATA TACA TATA TACA TATA TACA TATA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
500425 TA
1 TA
500427 TACATATATA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (4 bp):
TACA
Found at i:500390 original size:8 final size:8
Alignment explanation
Indices: 500380--500441 Score: 92
Period size: 8 Copynumber: 8.0 Consensus size: 8
500370 AAATTATTAC
*
500380 ATACATAC
1 ATACATAT
500388 ATACATAT
1 ATACATAT
500396 ATACATAT
1 ATACATAT
500404 ATACATAT
1 ATACATAT
500412 ATACATAT
1 ATACATAT
500420 ATAC--AT
1 ATACATAT
500426 ATACATAT
1 ATACATAT
*
500434 ATATATAT
1 ATACATAT
500442 CTTGTTCAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
6 6 0.12
8 44 0.88
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (8 bp):
ATACATAT
Found at i:500441 original size:6 final size:6
Alignment explanation
Indices: 500392--500441 Score: 55
Period size: 6 Copynumber: 8.3 Consensus size: 6
500382 ACATACATAC
* * * * *
500392 ATATAT ACATAT ATACAT ATATAC ATATAT ACATAT ACATAT ATATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
500440 AT
1 AT
500442 CTTGTTCAAT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (6 bp):
ATATAT
Found at i:500769 original size:21 final size:22
Alignment explanation
Indices: 500743--500784 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
500733 ATAAAAATAA
*
500743 TATTTTTATT-AATTAAATTAT
1 TATTTTTATTGAAGTAAATTAT
500764 TATTTTTATTGAAGTAAATTA
1 TATTTTTATTGAAGTAAATTA
500785 AATTTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (22 bp):
TATTTTTATTGAAGTAAATTAT
Found at i:500789 original size:21 final size:21
Alignment explanation
Indices: 500744--500789 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
500734 TAAAAATAAT
* *
500744 ATTTTTATTAATTAAATTATT
1 ATTTTTATTAAGTAAATTATA
500765 ATTTTTATTGAAGTAAATTA-A
1 ATTTTTATT-AAGTAAATTATA
500786 ATTT
1 ATTT
500790 AAATTAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (21 bp):
ATTTTTATTAAGTAAATTATA
Found at i:500825 original size:36 final size:37
Alignment explanation
Indices: 500753--500833 Score: 92
Period size: 36 Copynumber: 2.2 Consensus size: 37
500743 TATTTTTATT
* * *
500753 AATTAAATTATTATTTTTATTGAAGTAAATTAAATTTA
1 AATTAAAATATTA-TTTTATTAAACTAAATTAAATTTA
* *
500791 AATTAAAATATTA-TTTATTAAACTCAATTTAATTTA
1 AATTAAAATATTATTTTATTAAACTAAATTAAATTTA
500827 ATATTAA
1 A-ATTAA
500834 TAGATTATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
36 20 0.54
37 5 0.14
38 12 0.32
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.48
Consensus pattern (37 bp):
AATTAAAATATTATTTTATTAAACTAAATTAAATTTA
Found at i:501018 original size:18 final size:19
Alignment explanation
Indices: 500979--501017 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
500969 TCTTAAATAT
500979 AATAAAAAAATTAATTAAA
1 AATAAAAAAATTAATTAAA
500998 AATAAAAAATATT-ATTAAA
1 AATAAAAAA-ATTAATTAAA
501017 A
1 A
501018 TTTTAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 16 0.84
20 3 0.16
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (19 bp):
AATAAAAAAATTAATTAAA
Found at i:507400 original size:13 final size:14
Alignment explanation
Indices: 507370--507401 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
507360 TGATAGCCGT
507370 TAGATAAAGTGTAG
1 TAGATAAAGTGTAG
507384 -AGATAAAGTG-AG
1 TAGATAAAGTGTAG
507396 TAGATA
1 TAGATA
507402 GGAGAAACAG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 2 0.12
13 15 0.88
ACGTcount: A:0.47, C:0.00, G:0.28, T:0.25
Consensus pattern (14 bp):
TAGATAAAGTGTAG
Found at i:510519 original size:2 final size:2
Alignment explanation
Indices: 510512--510537 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
510502 AATAAATGAA
510512 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
510538 TCGTTTTAAT
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:515175 original size:17 final size:16
Alignment explanation
Indices: 515137--515179 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
515127 ACCTTAAATT
* *
515137 TAAAAATTAAATTTAA
1 TAAAATTTAAATTGAA
*
515153 TTAAATTTAAACTTGAA
1 TAAAATTTAAA-TTGAA
515170 TAAAATTTAA
1 TAAAATTTAA
515180 CTGAATTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (16 bp):
TAAAATTTAAATTGAA
Found at i:515191 original size:16 final size:17
Alignment explanation
Indices: 515151--515193 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
515141 AATTAAATTT
515151 AATTAAATTTAAACTTG
1 AATTAAATTTAAACTTG
*
515168 AATAAAATTT-AAC-TG
1 AATTAAATTTAAACTTG
515183 AATTTAAATTT
1 AA-TTAAATTT
515194 GATAAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 4 0.17
16 10 0.43
17 9 0.39
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.42
Consensus pattern (17 bp):
AATTAAATTTAAACTTG
Found at i:515201 original size:27 final size:27
Alignment explanation
Indices: 515145--515200 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
515135 TTTAAAAATT
*
515145 AAATTTAATTAAATTTAAACTTGAATA
1 AAATTTAACTAAATTTAAACTTGAATA
* *
515172 AAATTTAACTGAATTTAAATTTG-ATA
1 AAATTTAACTAAATTTAAACTTGAATA
515198 AAA
1 AAA
515201 AATAGAATGG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 6 0.23
27 20 0.77
ACGTcount: A:0.52, C:0.04, G:0.05, T:0.39
Consensus pattern (27 bp):
AAATTTAACTAAATTTAAACTTGAATA
Found at i:516116 original size:15 final size:15
Alignment explanation
Indices: 516096--516126 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
516086 CCTTTCCCCG
516096 CACCACCCCCACCTC
1 CACCACCCCCACCTC
*
516111 CACCACCGCCACCTC
1 CACCACCCCCACCTC
516126 C
1 C
516127 GCCCCCCTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.71, G:0.03, T:0.06
Consensus pattern (15 bp):
CACCACCCCCACCTC
Found at i:516238 original size:18 final size:18
Alignment explanation
Indices: 516215--516255 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
516205 ATAACCATTG
516215 CCACCTCCACCACC-CTCT
1 CCACCTCCACCACCTC-CT
516233 CCACCTCCACCACCTCCT
1 CCACCTCCACCACCTCCT
516251 CCACC
1 CCACC
516256 AGTCCCAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 21 0.95
19 1 0.05
ACGTcount: A:0.17, C:0.68, G:0.00, T:0.15
Consensus pattern (18 bp):
CCACCTCCACCACCTCCT
Found at i:517181 original size:3 final size:3
Alignment explanation
Indices: 517170--517219 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
517160 ATAATATTAC
*
517170 ATT AGT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
517218 AT
1 AT
517220 AAAAGACACA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:517612 original size:13 final size:13
Alignment explanation
Indices: 517594--517632 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
517584 TAATTTTTTA
517594 AATATTTATATTT
1 AATATTTATATTT
*
517607 AATATTTATTTTT
1 AATATTTATATTT
517620 ATATATTTCATAT
1 A-ATATTT-ATAT
517633 ATAAATATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 13 0.59
14 6 0.27
15 3 0.14
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (13 bp):
AATATTTATATTT
Found at i:517625 original size:14 final size:13
Alignment explanation
Indices: 517588--517627 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
517578 ATTTTTTAAT
517588 TTTTTAAATATTTA
1 TTTTT-AATATTTA
*
517602 TATTTAATATTTA
1 TTTTTAATATTTA
517615 TTTTTATATATTT
1 TTTTTA-ATATTT
517628 CATATATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 13 0.57
14 10 0.43
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTTTAATATTTA
Found at i:518695 original size:2 final size:2
Alignment explanation
Indices: 518684--518717 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
518674 AGTCAGTATC
518684 TA TA TA -A 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 T
518718 TTATGCAATG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:519068 original size:22 final size:21
Alignment explanation
Indices: 519022--519068 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
519012 TTTCTAAAAT
* *
519022 TTTTAAAAATAATTTTTTATC
1 TTTTAAAAATAATTATTGATC
519043 TTTTAAAAATAATTATTGATC
1 TTTTAAAAATAATTATTGATC
519064 ATTTT
1 -TTTT
519069 TCATTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.55
Consensus pattern (21 bp):
TTTTAAAAATAATTATTGATC
Found at i:521386 original size:2 final size:2
Alignment explanation
Indices: 521379--521419 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
521369 ATTAGCGCAA
521379 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
521420 TCATTACGGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:522187 original size:3 final size:3
Alignment explanation
Indices: 522173--522206 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
522163 ACAAATTTAT
522173 TTA TTAA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA
522207 CTTTTTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:522649 original size:3 final size:3
Alignment explanation
Indices: 522641--522675 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
522631 TGATCGTCCA
*
522641 AAG AAG AAG AAG AAG AAG AAG AAG AAG ATG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
522676 CACCCTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.66, C:0.00, G:0.31, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:529716 original size:17 final size:17
Alignment explanation
Indices: 529696--529751 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
529686 ATTCACTTCC
529696 TATAATAATTATTTTAT
1 TATAATAATTATTTTAT
*
529713 TATAAATTAATT-TATTTAA
1 TAT-AA-TAATTAT-TTTAT
*
529732 TAAAATAATTATTTTAT
1 TATAATAATTATTTTAT
529749 TAT
1 TAT
529752 GACCTTATTC
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
17 14 0.45
18 6 0.19
19 11 0.35
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TATAATAATTATTTTAT
Found at i:529724 original size:36 final size:36
Alignment explanation
Indices: 529650--529751 Score: 98
Period size: 36 Copynumber: 2.8 Consensus size: 36
529640 TTTGATTGAC
* * *
529650 TTCACTGTAATAATTATAA-TATTTCATTACAAACTAA
1 TTCACT-TAATAA-AATAATTATTTTATTATAAACTAA
** * *
529687 TTCACTTCCTATAATAATTATTTTATTATAAATTAA
1 TTCACTTAATAAAATAATTATTTTATTATAAACTAA
* *
529723 TTTATTTAATAAAATAATTATTTTATTAT
1 TTCACTTAATAAAATAATTATTTTATTAT
529752 GACCTTATTC
Statistics
Matches: 52, Mismatches: 12, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
35 4 0.08
36 42 0.81
37 6 0.12
ACGTcount: A:0.41, C:0.09, G:0.01, T:0.49
Consensus pattern (36 bp):
TTCACTTAATAAAATAATTATTTTATTATAAACTAA
Found at i:533718 original size:33 final size:33
Alignment explanation
Indices: 533679--533743 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
533669 GTAAAATATA
* ** *
533679 TATTAATATTTTTTAATTTATATAAATATAAAT
1 TATTAATATATTAAAATTTAAATAAATATAAAT
533712 TATTAATATATTAAAATTTAAATAAATATAAA
1 TATTAATATATTAAAATTTAAATAAATATAAA
533744 AATATGATGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (33 bp):
TATTAATATATTAAAATTTAAATAAATATAAAT
Found at i:534652 original size:2 final size:2
Alignment explanation
Indices: 534645--534672 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
534635 TAAAATCTCT
534645 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
534673 AAAGAACTAT
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):
TA
Found at i:535305 original size:11 final size:13
Alignment explanation
Indices: 535289--535317 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
535279 AATTTTTATG
535289 AAAAAA-ATTTAA
1 AAAAAATATTTAA
535301 AAAAAATATTTAA
1 AAAAAATATTTAA
535314 AAAA
1 AAAA
535318 TTAGTTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAAAATATTTAA
Found at i:535483 original size:25 final size:26
Alignment explanation
Indices: 535455--535505 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
535445 TAAAATATAC
535455 ATATAAAATTT-AAAAATTAAATAAA
1 ATATAAAATTTAAAAAATTAAATAAA
* * *
535480 ATATTATATTTAAAAAATTACATAAA
1 ATATAAAATTTAAAAAATTAAATAAA
535506 CTATTTAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (26 bp):
ATATAAAATTTAAAAAATTAAATAAA
Found at i:535510 original size:26 final size:25
Alignment explanation
Indices: 535462--535510 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
535452 TACATATAAA
535462 ATTTAAAAATTAAATAAAATATTAT
1 ATTTAAAAATTAAATAAAATATTAT
* *
535487 ATTTAAAAAATTACATAAACTATT
1 ATTT-AAAAATTAAATAAAATATT
535511 TAAATAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (25 bp):
ATTTAAAAATTAAATAAAATATTAT
Found at i:535578 original size:44 final size:43
Alignment explanation
Indices: 535476--535578 Score: 115
Period size: 44 Copynumber: 2.3 Consensus size: 43
535466 AAAAATTAAA
*
535476 TAAAATATTATATTTAAAAAATTACATAAACTATTTAAATAAATT
1 TAAAATATTATATTTAAAAAATTAAATAAAC--TTTAAATAAATT
535521 T-AAATGATT-TATTTACAAAAATATAAATAAAC-TTAAATAAAATT
1 TAAAAT-ATTATATTTA-AAAAAT-TAAATAAACTTTAAAT-AAATT
535565 TAAAAT-TTATATTT
1 TAAAATATTATATTT
535579 TAGATTATAA
Statistics
Matches: 51, Mismatches: 1, Indels: 13
0.78 0.02 0.20
Matches are distributed among these distances:
43 8 0.16
44 21 0.41
45 14 0.27
46 8 0.16
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (43 bp):
TAAAATATTATATTTAAAAAATTAAATAAACTTTAAATAAATT
Found at i:548383 original size:2 final size:2
Alignment explanation
Indices: 548376--548405 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
548366 TCACAATCTG
548376 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
548406 TAAGGCCATT
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:548525 original size:2 final size:2
Alignment explanation
Indices: 548520--548566 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
548510 ATATATATAT
* *
548520 AG AG AG AG AG AG AG AG GG AG AG AG AG AG AG AG AG AG AG AG AA
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
548562 AG AG A
1 AG AG A
548567 ACTGGGGAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:550867 original size:20 final size:20
Alignment explanation
Indices: 550830--550867 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
550820 AATTTTTGAT
*
550830 TTTAAAAAAATAACTACTCG
1 TTTAAAAAAATAAATACTCG
550850 TTTAAAAATAA-AAATACT
1 TTTAAAAA-AATAAATACT
550868 ACTTATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.88
21 2 0.12
ACGTcount: A:0.55, C:0.11, G:0.03, T:0.32
Consensus pattern (20 bp):
TTTAAAAAAATAAATACTCG
Found at i:550881 original size:24 final size:24
Alignment explanation
Indices: 550835--550880 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
550825 TTGATTTTAA
*
550835 AAAAATAACTACTCGTTTAAAAAT
1 AAAAATAACTACTCATTTAAAAAT
*
550859 AAAAAT-ACTACTTATTTAAAAA
1 AAAAATAACTACTCATTTAAAAA
550881 AATTAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.30
Consensus pattern (24 bp):
AAAAATAACTACTCATTTAAAAAT
Found at i:551191 original size:5 final size:5
Alignment explanation
Indices: 551174--551235 Score: 56
Period size: 5 Copynumber: 12.0 Consensus size: 5
551164 TCAATAATAT
* *
551174 TATTA TA-TA TATTA TATTA TATGTA T-TTCG TATAA TATTA TTATATA
1 TATTA TATTA TATTA TATTA TAT-TA TATT-A TATTA TATTA -TAT-TA
551221 TATTA TATTA TATTA
1 TATTA TATTA TATTA
551236 ATAAATTAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
4 5 0.11
5 30 0.64
6 10 0.21
7 2 0.04
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (5 bp):
TATTA
Found at i:551193 original size:14 final size:13
Alignment explanation
Indices: 551173--551233 Score: 63
Period size: 14 Copynumber: 4.7 Consensus size: 13
551163 TTCAATAATA
551173 TTATTATATATAT
1 TTATTATATATAT
*
551186 TATATTATATGTAT
1 T-TATTATATATAT
**
551200 TTCGTATA-ATA-
1 TTATTATATATAT
551211 TTATTATATATAT
1 TTATTATATATAT
551224 TATATTATAT
1 T-TATTATAT
551234 TAATAAATTA
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
11 6 0.16
12 5 0.13
13 7 0.18
14 20 0.53
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (13 bp):
TTATTATATATAT
Found at i:551218 original size:38 final size:40
Alignment explanation
Indices: 551153--551233 Score: 139
Period size: 38 Copynumber: 2.0 Consensus size: 40
551143 ACTGGAAATA
551153 ATGTATTTCGTTCAATAATATTATTATATATATTATATTAT
1 ATGTATTTCGTT-AATAATATTATTATATATATTATATTAT
551194 ATGTATTTCG-T-ATAATATTATTATATATATTATATTAT
1 ATGTATTTCGTTAATAATATTATTATATATATTATATTAT
551232 AT
1 AT
551234 TAATAAATTA
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
38 29 0.73
40 1 0.03
41 10 0.25
ACGTcount: A:0.37, C:0.04, G:0.05, T:0.54
Consensus pattern (40 bp):
ATGTATTTCGTTAATAATATTATTATATATATTATATTAT
Found at i:551569 original size:12 final size:12
Alignment explanation
Indices: 551546--551596 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
551536 GGAGTTTGGG
551546 TAAATGATAATAT
1 TAAAT-ATAATAT
551559 TAAATATAATAT
1 TAAATATAATAT
*
551571 TAAAAAT-A-AT
1 TAAATATAATAT
551581 T-AATATATATAT
1 TAAATATA-ATAT
551593 TAAA
1 TAAA
551597 AATGATACTA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
9 4 0.12
10 3 0.09
11 2 0.06
12 16 0.50
13 7 0.22
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (12 bp):
TAAATATAATAT
Found at i:551574 original size:25 final size:26
Alignment explanation
Indices: 551546--551618 Score: 66
Period size: 22 Copynumber: 2.9 Consensus size: 26
551536 GGAGTTTGGG
551546 TAAATGATAATATTAAATATA-ATAT
1 TAAATGATAATATTAAATATATATAT
*
551571 TAAA-AAT-A-ATT-AATATATATAT
1 TAAATGATAATATTAAATATATATAT
*
551593 TAAAAATGATACTATATAAATATATA
1 T--AAATGATAATAT-TAAATATATA
551619 AATAATTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
21 6 0.16
22 8 0.22
23 1 0.03
24 5 0.14
25 6 0.16
27 2 0.05
28 1 0.03
29 8 0.22
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (26 bp):
TAAATGATAATATTAAATATATATAT
Found at i:551608 original size:21 final size:22
Alignment explanation
Indices: 551561--551663 Score: 72
Period size: 22 Copynumber: 4.7 Consensus size: 22
551551 GATAATATTA
551561 AATATA-ATATTAAAAATAATT
1 AATATATATATTAAAAATAATT
*
551582 AATATATATATTAAAAATGA-T
1 AATATATATATTAAAAATAATT
* * *
551603 ACTATATAAATATATAAATAATTT
1 AATATATATAT-TAAAAATAA-TT
* * *
551627 AA-A-ATTTATGTAATATTATATT
1 AATATATATAT-TAAAAATA-ATT
551649 AATA-ATATATTAAAA
1 AATATATATATTAAAA
551664 TTTATATATA
Statistics
Matches: 62, Mismatches: 14, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
21 16 0.26
22 36 0.58
23 8 0.13
24 2 0.03
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (22 bp):
AATATATATATTAAAAATAATT
Found at i:551672 original size:16 final size:16
Alignment explanation
Indices: 551584--551680 Score: 56
Period size: 16 Copynumber: 5.9 Consensus size: 16
551574 AAATAATTAA
*
551584 TATATATATTAAAAAT
1 TATATATATTAAAATT
* *
551600 GATACTATA-T-AAATA
1 TATA-TATATTAAAATT
*
551615 TATAAATAATTTAAAATT
1 TATATAT-A-TTAAAATT
* *
551633 TATGTAATATT-ATATT
1 TATAT-ATATTAAAATT
*
551649 AATAATATATTAAAATT
1 TAT-ATATATTAAAATT
*
551666 TATATATAATAAAAT
1 TATATATATTAAAAT
551681 AAAATATTTT
Statistics
Matches: 59, Mismatches: 14, Indels: 16
0.66 0.16 0.18
Matches are distributed among these distances:
14 2 0.03
15 7 0.12
16 26 0.44
17 14 0.24
18 8 0.14
19 2 0.03
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43
Consensus pattern (16 bp):
TATATATATTAAAATT
Found at i:551904 original size:2 final size:2
Alignment explanation
Indices: 551897--551928 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
551887 TGCACTGCCA
*
551897 CT CT CT CT GT 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 CT CT
551929 ATTTTCTGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.47, G:0.03, T:0.50
Consensus pattern (2 bp):
CT
Found at i:552120 original size:30 final size:31
Alignment explanation
Indices: 552084--552152 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 31
552074 TTTAAATTTT
* *
552084 AATTTTAATATTTTTATTAT-AATTTTTAAA
1 AATTTTAATATTTTTATTATAAAATTTAAAA
* *
552114 GATTTT-ATTTTTTTATTATAAAATTTAAAA
1 AATTTTAATATTTTTATTATAAAATTTAAAA
552144 AATTTTAAT
1 AATTTTAAT
552153 TTAATTAATG
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
29 12 0.38
30 18 0.56
31 2 0.06
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (31 bp):
AATTTTAATATTTTTATTATAAAATTTAAAA
Found at i:552140 original size:29 final size:30
Alignment explanation
Indices: 552085--552152 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 30
552075 TTAAATTTTA
**
552085 ATTTTAATATTTTTATTATAATTTTTAAAG
1 ATTTTAATATTTTTATTATAAAATTTAAAG
* *
552115 ATTTT-ATTTTTTTATTATAAAATTTAAAAA
1 ATTTTAATATTTTTATTATAAAATTT-AAAG
552145 ATTTTAAT
1 ATTTTAAT
552153 TTAATTAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 17 0.53
30 13 0.41
31 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (30 bp):
ATTTTAATATTTTTATTATAAAATTTAAAG
Found at i:552384 original size:24 final size:24
Alignment explanation
Indices: 552342--552400 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
552332 TATATATTTA
* *
552342 TTTTATTTATAATAATTTTGAAATT
1 TTTTATTT-TTATAATTTTGAAAAT
* *
552367 TTTTATTTTTATACTTTTTAAAAT
1 TTTTATTTTTATAATTTTGAAAAT
*
552391 TTTAATTTTT
1 TTTTATTTTT
552401 GATCTGATCT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 21 0.72
25 8 0.28
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (24 bp):
TTTTATTTTTATAATTTTGAAAAT
Found at i:552874 original size:83 final size:83
Alignment explanation
Indices: 552776--552939 Score: 301
Period size: 83 Copynumber: 2.0 Consensus size: 83
552766 TAAACATTAT
552776 CTATTAGTAAGATTACTTACCAAACTCACAAATTTTATTTTATTTTAATCATATCTTGAACAAGA
1 CTATTAGTAAGATTACTTACCAAACTCACAAATTTTATTTTATTTTAATCATATCTTGAACAAGA
552841 TTTTTATACTAAAACTAG
66 TTTTTATACTAAAACTAG
* **
552859 CTATTAGTAAGATTACTTACTAAACTCGTAAATTTTATTTTATTTTAATCATATCTTGAACAAGA
1 CTATTAGTAAGATTACTTACCAAACTCACAAATTTTATTTTATTTTAATCATATCTTGAACAAGA
552924 TTTTTATACTAAAACT
66 TTTTTATACTAAAACT
552940 TACTTGATTA
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 78 1.00
ACGTcount: A:0.38, C:0.13, G:0.06, T:0.43
Consensus pattern (83 bp):
CTATTAGTAAGATTACTTACCAAACTCACAAATTTTATTTTATTTTAATCATATCTTGAACAAGA
TTTTTATACTAAAACTAG
Found at i:553486 original size:29 final size:30
Alignment explanation
Indices: 553431--553492 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 30
553421 AATTGGACTA
* *
553431 AAATTTTTAAAATTATATAATAAAAAAATT
1 AAATTTATAAAAATATATAATAAAAAAATT
*
553461 AAATTTATAAAAAT-TATAGTAAAAAAATT
1 AAATTTATAAAAATATATAATAAAAAAATT
553490 AAA
1 AAA
553493 CTTCAAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 17 0.59
30 12 0.41
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (30 bp):
AAATTTATAAAAATATATAATAAAAAAATT
Found at i:558045 original size:56 final size:56
Alignment explanation
Indices: 557959--558071 Score: 226
Period size: 56 Copynumber: 2.0 Consensus size: 56
557949 AAGAATGTAA
557959 AATGGGTTAGAAGACATCATTGCTGGTTTGATGAATCTAGTTTAGAGGATGAAACT
1 AATGGGTTAGAAGACATCATTGCTGGTTTGATGAATCTAGTTTAGAGGATGAAACT
558015 AATGGGTTAGAAGACATCATTGCTGGTTTGATGAATCTAGTTTAGAGGATGAAACT
1 AATGGGTTAGAAGACATCATTGCTGGTTTGATGAATCTAGTTTAGAGGATGAAACT
558071 A
1 A
558072 TCTCGAGGAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.33, C:0.09, G:0.27, T:0.32
Consensus pattern (56 bp):
AATGGGTTAGAAGACATCATTGCTGGTTTGATGAATCTAGTTTAGAGGATGAAACT
Found at i:559443 original size:2 final size:2
Alignment explanation
Indices: 559436--559476 Score: 64
Period size: 2 Copynumber: 19.5 Consensus size: 2
559426 CATTACGTTG
559436 TA TA TA TA TA TA TA TA TGA TA TA TA TA TA TA TA TGA TA TA T
1 TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA T-A TA TA T
559477 GCTAATCTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 33 0.89
3 4 0.11
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
TA
Found at i:559459 original size:15 final size:14
Alignment explanation
Indices: 559436--559476 Score: 64
Period size: 15 Copynumber: 2.8 Consensus size: 14
559426 CATTACGTTG
559436 TATATATATATATA
1 TATATATATATATA
559450 TATGATATATATATA
1 TAT-ATATATATATA
559465 TATATGATATAT
1 TATAT-ATATAT
559477 GCTAATCTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.20
15 20 0.80
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (14 bp):
TATATATATATATA
Found at i:559459 original size:17 final size:17
Alignment explanation
Indices: 559437--559476 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
559427 ATTACGTTGT
559437 ATATATATATATATATG
1 ATATATATATATATATG
559454 ATATATATATATATATG
1 ATATATATATATATATG
559471 ATATAT
1 ATATAT
559477 GCTAATCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (17 bp):
ATATATATATATATATG
Found at i:559550 original size:2 final size:2
Alignment explanation
Indices: 559543--559574 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
559533 ATCTATGCAG
559543 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
559575 ATCTAGTAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:560556 original size:103 final size:103
Alignment explanation
Indices: 560375--560564 Score: 290
Period size: 103 Copynumber: 1.8 Consensus size: 103
560365 AGTTAAACTC
* * *
560375 AGAACAATAAATTAGTTGATTTAATGTAAGTTCAAGTTAAACTTGAACAATTAATGGGTTAGTTT
1 AGAACAATAAATTAGTTGATTTAATGAAAGTTCAACTTAAACTTGAACAATAAATGGGTTAGTTT
* *
560440 AGTCTATAGATGGGACTTAATAAGTATATGGATATTAT
66 AATCTATACATGGGACTTAATAAGTATATGGATATTAT
* * *
560478 AGAACAATAAATTGGTTGATTTAATGAAAGTTGAACTTGAACTTGAACAATAAATGGGTTAGTTT
1 AGAACAATAAATTAGTTGATTTAATGAAAGTTCAACTTAAACTTGAACAATAAATGGGTTAGTTT
* *
560543 AATGTATACATGGGGCTTAATA
66 AATCTATACATGGGACTTAATA
560565 GTTGAGGATA
Statistics
Matches: 77, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
103 77 1.00
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.35
Consensus pattern (103 bp):
AGAACAATAAATTAGTTGATTTAATGAAAGTTCAACTTAAACTTGAACAATAAATGGGTTAGTTT
AATCTATACATGGGACTTAATAAGTATATGGATATTAT
Found at i:560819 original size:28 final size:28
Alignment explanation
Indices: 560782--560836 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
560772 TGTTATTTAT
* *
560782 TAAAAATTTATTGAGGCTAAGTTGAAAC
1 TAAAAATTTATTAAGGCTAAGTAGAAAC
*
560810 TAAAATTTTATTAAGGCTAAGTAGAAA
1 TAAAAATTTATTAAGGCTAAGTAGAAA
560837 AATAAACACA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.45, C:0.05, G:0.16, T:0.33
Consensus pattern (28 bp):
TAAAAATTTATTAAGGCTAAGTAGAAAC
Found at i:561243 original size:14 final size:15
Alignment explanation
Indices: 561214--561268 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
561204 TTTTATTTAT
*
561214 TTTATATATGTCATA
1 TTTATATATATCATA
561229 TTTATATA-ATCATA
1 TTTATATATATCATA
* * *
561243 TTTAAATTTATTATA
1 TTTATATATATCATA
561258 TATTA-ATATAT
1 T-TTATATATAT
561269 TTAGAGGAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
14 11 0.33
15 19 0.58
16 3 0.09
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.55
Consensus pattern (15 bp):
TTTATATATATCATA
Found at i:561829 original size:2 final size:2
Alignment explanation
Indices: 561774--561815 Score: 52
Period size: 2 Copynumber: 21.5 Consensus size: 2
561764 ATAAAACAGT
*
561774 TA TA T- TA TA TA TA TA TA TA TA TA TT TA TA CTA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
561815 T
1 T
561816 TCAAAAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
1 2 0.06
2 31 0.89
3 2 0.06
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:562187 original size:24 final size:24
Alignment explanation
Indices: 562160--562205 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
562150 TTCGATTTTT
*
562160 AATTTTTAATTTAATACTTAAAAA
1 AATTATTAATTTAATACTTAAAAA
*
562184 AATTATTAATTTAATATTTAAA
1 AATTATTAATTTAATACTTAAA
562206 TTTTTATTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
AATTATTAATTTAATACTTAAAAA
Found at i:562501 original size:12 final size:12
Alignment explanation
Indices: 562486--562515 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
562476 CAATATTTTT
*
562486 TTAAATATTAAA
1 TTAAAAATTAAA
562498 TTAAAAATTAAA
1 TTAAAAATTAAA
562510 TTAAAA
1 TTAAAA
562516 TGTAAGACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
TTAAAAATTAAA
Found at i:562774 original size:2 final size:2
Alignment explanation
Indices: 562769--562797 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
562759 ATATATATAT
562769 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
562798 ATAATGTAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:564352 original size:17 final size:18
Alignment explanation
Indices: 564327--564360 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
564317 TAAAAAAAAT
564327 AATTGAAAAAAAATATAA
1 AATTGAAAAAAAATATAA
*
564345 AATT-AAAACAAATATA
1 AATTGAAAAAAAATATA
564361 TTCTAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (18 bp):
AATTGAAAAAAAATATAA
Found at i:564941 original size:2 final size:2
Alignment explanation
Indices: 564934--564974 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
564924 TAAATCTTCC
* *
564934 AT AT AT AT AT AT AT AT AT AT AT A- AG AT AT AT A- AG AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
564974 A
1 A
564975 GTATTAATGC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (2 bp):
AT
Found at i:564964 original size:9 final size:9
Alignment explanation
Indices: 564940--564974 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
564930 TTCCATATAT
*
564940 ATATATATAT
1 ATATATA-AG
564950 ATATATAAG
1 ATATATAAG
564959 ATATATAAG
1 ATATATAAG
564968 ATATATA
1 ATATATA
564975 GTATTAATGC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 17 0.71
10 7 0.29
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (9 bp):
ATATATAAG
Found at i:566211 original size:18 final size:18
Alignment explanation
Indices: 566172--566213 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
566162 TTTATTTAAA
566172 TTTAAT-TATAAATATAT
1 TTTAATATATAAATATAT
*
566189 ATTAATATA-AAATAATAT
1 TTTAATATATAAAT-ATAT
566207 TTTAATA
1 TTTAATA
566214 ATATTATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TTTAATATATAAATATAT
Found at i:566226 original size:23 final size:22
Alignment explanation
Indices: 566191--566235 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
566181 AAATATATAT
*
566191 TAATATAAAAT-AATATTTTAA
1 TAATATAAAATAAAAATTTTAA
566212 TAATATTATAAATAAAAATTTTAA
1 TAATA-TA-AAATAAAAATTTTAA
566236 ATCAATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 2 0.10
23 4 0.20
24 9 0.45
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TAATATAAAATAAAAATTTTAA
Found at i:577355 original size:2 final size:2
Alignment explanation
Indices: 577348--577377 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
577338 ATTAATTTGA
577348 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
577378 TAACAAGGAA
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:583835 original size:9 final size:9
Alignment explanation
Indices: 583821--583853 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
583811 AATGCAAAAT
583821 AAAAAATAA
1 AAAAAATAA
583830 AAAAAATAA
1 AAAAAATAA
583839 AAAAAA-AA
1 AAAAAATAA
583847 AAGAAAA
1 AA-AAAA
583854 AAGAAGACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 4 0.17
9 19 0.83
ACGTcount: A:0.91, C:0.00, G:0.03, T:0.06
Consensus pattern (9 bp):
AAAAAATAA
Found at i:583837 original size:16 final size:15
Alignment explanation
Indices: 583816--583848 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
583806 AGCAAAATGC
583816 AAAATAAAAAATAAAA
1 AAAATAAAAAA-AAAA
583832 AAAATAAAAAAAAAA
1 AAAATAAAAAAAAAA
583847 AA
1 AA
583849 GAAAAAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.91, C:0.00, G:0.00, T:0.09
Consensus pattern (15 bp):
AAAATAAAAAAAAAA
Found at i:597378 original size:2 final size:2
Alignment explanation
Indices: 597371--597397 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
597361 AATACTTTAA
597371 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 A
597398 AAGTTCGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:597688 original size:2 final size:2
Alignment explanation
Indices: 597681--597705 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
597671 TAAAATGGAA
597681 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
597706 AATTCAGTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:598778 original size:20 final size:21
Alignment explanation
Indices: 598745--598790 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
598735 TATGCCTTTT
**
598745 TTTTTAAATTATTTTT-TATA
1 TTTTTAAAAAATTTTTATATA
*
598765 TTTTTAAAAAATTTTTATTTA
1 TTTTTAAAAAATTTTTATATA
598786 TTTTT
1 TTTTT
598791 CTCAATCTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTTAAAAAATTTTTATATA
Found at i:607416 original size:5 final size:5
Alignment explanation
Indices: 607400--607433 Score: 59
Period size: 5 Copynumber: 6.6 Consensus size: 5
607390 TAAATTTTGA
607400 TTAAT TTAAAT TTAAT TTAAT TTAAT TTAAT TTA
1 TTAAT TT-AAT TTAAT TTAAT TTAAT TTAAT TTA
607434 TAAAATCTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 23 0.82
6 5 0.18
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TTAAT
Found at i:612301 original size:12 final size:14
Alignment explanation
Indices: 612262--612312 Score: 56
Period size: 12 Copynumber: 3.9 Consensus size: 14
612252 TGAACATATA
612262 TTTAAAAATA-AA-
1 TTTAAAAATATAAT
*
612274 TATAAAAATATAAT
1 TTTAAAAATATAAT
612288 TTTAAAAA-AT-AT
1 TTTAAAAATATAAT
*
612300 TTTAAATATATAA
1 TTTAAAAATATAA
612313 AAAAATTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
12 18 0.56
13 6 0.19
14 8 0.25
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TTTAAAAATATAAT
Found at i:612330 original size:26 final size:27
Alignment explanation
Indices: 612262--612341 Score: 69
Period size: 32 Copynumber: 2.9 Consensus size: 27
612252 TGAACATATA
612262 TTTAAAAA-TAAATATAAAAATATAAT
1 TTTAAAAATTAAATATAAAAATATAAT
612288 TTTAAAAAATATTTTAAATATATAAAA-A-AAT
1 TTT--AAAA-A--TTAAATATA-AAAATATAAT
*
612319 TTTAAAAATTAAA-ATAATAATAT
1 TTTAAAAATTAAATATAAAAATAT
612342 TATACACGTA
Statistics
Matches: 44, Mismatches: 1, Indels: 18
0.70 0.02 0.29
Matches are distributed among these distances:
24 3 0.07
25 4 0.09
26 8 0.18
28 5 0.11
29 5 0.11
31 6 0.14
32 9 0.20
33 4 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (27 bp):
TTTAAAAATTAAATATAAAAATATAAT
Found at i:620112 original size:14 final size:12
Alignment explanation
Indices: 620068--620109 Score: 50
Period size: 14 Copynumber: 3.3 Consensus size: 12
620058 TTTCACCATT
620068 AAAAAAAACAA-
1 AAAAAAAACAAG
620079 AAAAAAAATCAAG
1 AAAAAAAA-CAAG
620092 AAAAGAAAAGCAAG
1 AAAA-AAAA-CAAG
620106 AAAA
1 AAAA
620110 GAAGAAGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 8 0.30
12 3 0.11
13 4 0.15
14 12 0.44
ACGTcount: A:0.81, C:0.07, G:0.10, T:0.02
Consensus pattern (12 bp):
AAAAAAAACAAG
Found at i:625197 original size:2 final size:2
Alignment explanation
Indices: 625190--625218 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
625180 TGTTTGAGTG
625190 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 T
625219 GAATATAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:627377 original size:34 final size:33
Alignment explanation
Indices: 627313--627533 Score: 235
Period size: 34 Copynumber: 6.5 Consensus size: 33
627303 TGGTAAAAAC
** *
627313 CACCATTTAATCAACAATGACAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAAGCTACCAAAT
* ** *
627346 CTACCATTTAGTCAGTAATGGTAAGCCACCAAAT
1 C-ACCATTTAATCAACAATGGTAAGCTACCAAAT
*
627380 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAAGCTACCAAAT
** *
627414 TTCTCATTTAATCAACAATGATAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAAGCTACCAAAT
* * * * *
627448 CTCTCATTTAGTCAACAATGGCAAACCACCAAAT
1 CAC-CATTTAATCAACAATGGTAAGCTACCAAAT
* *
627482 CACCCATTTAATCAACAATTGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAAGCTACCAAAT
627516 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
627534 TCTCCCACTT
Statistics
Matches: 159, Mismatches: 25, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
33 19 0.12
34 139 0.87
35 1 0.01
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.26
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAAGCTACCAAAT
Found at i:627457 original size:102 final size:101
Alignment explanation
Indices: 627313--627533 Score: 318
Period size: 102 Copynumber: 2.2 Consensus size: 101
627303 TGGTAAAAAC
** * *
627313 CACCATTTAATCAACAATGACAACCTACCAAATCTACCATTTAGTCAGTAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGACAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
* *
627378 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
** * *
627414 TTCTCATTTAATCAACAATGATAAGCTACCAAATCT-CTCATTTAGTCAACAATGGCAAACCACC
1 CAC-CATTTAATCAACAATGACAACCTACCAAATCTAC-CATTTAGTCAACAATGGCAAACCACC
*
627478 AAATCACCCATTTAATCAACAATTGTAAACTACCAAAT
64 AAATCACCCATTTAATCAACAATGGTAAACTACCAAAT
627516 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
627534 TCTCCCACTT
Statistics
Matches: 105, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
101 17 0.16
102 88 0.84
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.26
Consensus pattern (101 bp):
CACCATTTAATCAACAATGACAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:631988 original size:34 final size:33
Alignment explanation
Indices: 631940--632152 Score: 231
Period size: 34 Copynumber: 6.4 Consensus size: 33
631930 TGGTAAAAAC
*
631940 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
631973 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
632007 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** *
632041 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* *
632075 CTCCCATTTAGT---CAA-GGTAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATGGT-AACCTACCAAAT
*
632105 CACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
632139 CACCATTTAATCAA
1 CACCATTTAATCAA
632153 TAGTATGTCA
Statistics
Matches: 152, Mismatches: 15, Indels: 26
0.79 0.08 0.13
Matches are distributed among these distances:
30 19 0.12
31 6 0.04
33 22 0.14
34 102 0.67
35 3 0.02
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.25
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:632056 original size:68 final size:67
Alignment explanation
Indices: 631942--632154 Score: 256
Period size: 68 Copynumber: 3.2 Consensus size: 67
631932 GTAAAAACCA
* * * * *
631942 CCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAATAATGGTAAACTACCAAAT-TACCATTTAATCAACAATGGTAAGCTACCAAAT
632007 CAC
65 CAC
* *
632010 CCATTTAATCAATAATGGTAAGCTACCAAATTTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAATAATGGTAAACTACCAAATTAC-CATTTAATCAACAATGGTAAGCTACCAAAT
*
632075 CTC
65 CAC
* * * *
632078 CCATTTAGTC---AA-GGTAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CCATTTAATCAATAATGGTAAACTACCAAATTA-CCATTTAATCAACAATGGTAAGCTACCAAAT
632139 CA-
65 CAC
632141 CCATTTAATCAATA
1 CCATTTAATCAATA
632155 GTATGTCAAT
Statistics
Matches: 125, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
63 9 0.07
64 43 0.34
65 3 0.02
66 1 0.01
67 2 0.02
68 67 0.54
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (67 bp):
CCATTTAATCAATAATGGTAAACTACCAAATTACCATTTAATCAACAATGGTAAGCTACCAAATC
AC
Found at i:632134 original size:98 final size:99
Alignment explanation
Indices: 631940--632152 Score: 313
Period size: 98 Copynumber: 2.1 Consensus size: 99
631930 TGGTAAAAAC
*
631940 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGT--ACAATGGTAAACCACCAA
* *
632005 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
64 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
** * * *
632041 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGT-CAA-GGTAAACCACCAAA
1 CAC-CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTACAATGGTAAACCACCAAA
632104 TCACCCATTTAATCAACAATGGTAAACTACCAAAT
65 TCACCCATTTAATCAACAATGGTAAACTACCAAAT
632139 CACCATTTAATCAA
1 CACCATTTAATCAA
632153 TAGTATGTCA
Statistics
Matches: 101, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
97 11 0.11
98 47 0.47
99 3 0.03
101 1 0.01
102 39 0.39
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.25
Consensus pattern (99 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTACAATGGTAAACCACCAAAT
CACCCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:636367 original size:2 final size:2
Alignment explanation
Indices: 636360--636392 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
636350 GATCCCATAC
636360 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 A
636393 ATGCTAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:636900 original size:2 final size:2
Alignment explanation
Indices: 636893--636926 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
636883 AAATTTGAGA
* *
636893 AT AT AT AT AT AT AT AT AT AT GT AT CT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
636927 GGGACCAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:637347 original size:2 final size:2
Alignment explanation
Indices: 637334--637377 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
637324 ATCTGTGGTT
*
637334 TA TA TT 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
637376 TA
1 TA
637378 AGGCATTGAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:638048 original size:24 final size:24
Alignment explanation
Indices: 638021--638071 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
638011 AATACAAAAA
* * *
638021 TATTTATATAAAATAATATTATTT
1 TATTTATAAAAAATAAAATAATTT
*
638045 TATTTTTAAAAAATAAAATAATTT
1 TATTTATAAAAAATAAAATAATTT
638069 TAT
1 TAT
638072 GGATAAAATC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TATTTATAAAAAATAAAATAATTT
Found at i:638715 original size:108 final size:110
Alignment explanation
Indices: 638596--638844 Score: 272
Period size: 111 Copynumber: 2.3 Consensus size: 110
638586 GCTCTTTTGG
* * *
638596 CCCATTTAAGGTTTA-TTTGGATTATAAGTATATATTATTGGG-TTTTAACGTCCGAAGGGC-TA
1 CCCATTCAAGGTTTACTTTGGATTATAAGTAAAAATTATTGGGTTTTTAACGTCCGAAGGGCGT-
*
638658 TGCTAGATCTTGGGCAGAGATTTCAAAGGCCCAAATCCTAACTCGA
65 TGCTAGATCTTGGGCAGAGATTTCAAAGGCCCAAAGCCTAACTCGA
* * * **
638704 CCCATTCAAGG-TTAGTTTGGATTATAAGGTTAAAAATTATTGGGTTTTTAAGGTCTGACTGGCG
1 CCCATTCAAGGTTTACTTTGGATTATAA-G-TAAAAATTATTGGGTTTTTAACGTCCGAAGGGCG
* * * ** * **
638768 TTGTTAGATCTTGGGCGGAGATTTCAAAGGCCTACGGGCTCGCTCGA
64 TTGCTAGATCTTGGGCAGAGATTTCAAAGGCCCAAAGCCTAACTCGA
* *
638815 CCCATGCAAGGTTTACTTTGAATTATAAGT
1 CCCATTCAAGGTTTACTTTGGATTATAAGT
638845 TTATTAAACA
Statistics
Matches: 116, Mismatches: 19, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
107 3 0.03
108 22 0.19
109 1 0.01
110 13 0.11
111 62 0.53
112 15 0.13
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.34
Consensus pattern (110 bp):
CCCATTCAAGGTTTACTTTGGATTATAAGTAAAAATTATTGGGTTTTTAACGTCCGAAGGGCGTT
GCTAGATCTTGGGCAGAGATTTCAAAGGCCCAAAGCCTAACTCGA
Found at i:645621 original size:15 final size:13
Alignment explanation
Indices: 645588--645612 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
645578 TTAATATATA
645588 TTAAAATATAAAT
1 TTAAAATATAAAT
645601 TTAAAATATAAA
1 TTAAAATATAAA
645613 ATTTTAAAAA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TTAAAATATAAAT
Found at i:647917 original size:123 final size:124
Alignment explanation
Indices: 647693--647948 Score: 471
Period size: 123 Copynumber: 2.1 Consensus size: 124
647683 TCCAATAACT
* *
647693 AATTTACAGAGTACTGAAATCAGCAGCCAGATACCATCATGCATAAGATTTTATTGGTTATGGAG
1 AATTCACAGAGTACTGAAATCAGCAGCCACATACCATCATGCATAAGATTTTATTGGTTATGGAG
647758 CAATTCTAATTACTTGACATTGAACTTAGACTGCTAAAACCTTAAGGAAAGATCA-ACG
66 CAATTCTAATTACTTGACATTGAACTTAGACTGCTAAAACCTTAAGGAAAGATCAGACG
647816 AATTCACAGAGTACTGAAATCAGCAGCCACATACCATCATGCATAAGA-TTTATTGGTTATGGAG
1 AATTCACAGAGTACTGAAATCAGCAGCCACATACCATCATGCATAAGATTTTATTGGTTATGGAG
647880 CAATTCTAATTACTTGACATTGAACTTAAGACTGCTAAAACCTTAAGGAAAGATCAGACG
66 CAATTCTAATTACTTGACATTGAACTT-AGACTGCTAAAACCTTAAGGAAAGATCAGACG
647940 AATTCACAG
1 AATTCACAG
647949 CAATACTTCC
Statistics
Matches: 129, Mismatches: 2, Indels: 3
0.96 0.01 0.02
Matches are distributed among these distances:
122 43 0.33
123 74 0.57
124 12 0.09
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (124 bp):
AATTCACAGAGTACTGAAATCAGCAGCCACATACCATCATGCATAAGATTTTATTGGTTATGGAG
CAATTCTAATTACTTGACATTGAACTTAGACTGCTAAAACCTTAAGGAAAGATCAGACG
Found at i:648454 original size:20 final size:20
Alignment explanation
Indices: 648429--648495 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 20
648419 ATCTAAGACA
648429 TAAATATAAATATAATTTTT
1 TAAATATAAATATAATTTTT
* * *
648449 TAAATATATATAAAATTTTA
1 TAAATATAAATATAATTTTT
* *
648469 AAAATTTAAATAT-ATTTATAT
1 TAAATATAAATATAATTT-T-T
648490 TAAATA
1 TAAATA
648496 CATATTAATA
Statistics
Matches: 35, Mismatches: 10, Indels: 3
0.73 0.21 0.06
Matches are distributed among these distances:
19 4 0.11
20 27 0.77
21 4 0.11
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TAAATATAAATATAATTTTT
Found at i:649564 original size:21 final size:21
Alignment explanation
Indices: 649525--649565 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
649515 TAGGTTACTC
**
649525 AGATTTGGGTTTTGGGTGTCA
1 AGATTTGGGTTTTACGTGTCA
649546 AGATTTGGGTTTTACGTGTC
1 AGATTTGGGTTTTACGTGTC
649566 GATATTAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.07, G:0.34, T:0.44
Consensus pattern (21 bp):
AGATTTGGGTTTTACGTGTCA
Found at i:652361 original size:17 final size:17
Alignment explanation
Indices: 652323--652361 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
652313 CTTGGCCGAG
*
652323 CTTTAAAATTAACTTTT
1 CTTTAAAAATAACTTTT
652340 C-TTAAAAATAACTTTT
1 CTTTAAAAATAACTTTT
652356 CTTTAA
1 CTTTAA
652362 GTGAATTCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (17 bp):
CTTTAAAAATAACTTTT
Found at i:655962 original size:21 final size:20
Alignment explanation
Indices: 655927--655965 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
655917 ATAAAATATT
655927 AATTATTTTAAAATTTTAAA
1 AATTATTTTAAAATTTTAAA
*
655947 AATTATTTTTATAATTTTA
1 AATTA-TTTTAAAATTTTA
655966 TTTAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
AATTATTTTAAAATTTTAAA
Found at i:656732 original size:18 final size:17
Alignment explanation
Indices: 656698--656794 Score: 76
Period size: 18 Copynumber: 5.8 Consensus size: 17
656688 ATATAAATAT
*
656698 AATATAAAAAATAATTAA
1 AATATAAATAAT-ATTAA
656716 AATATAATATAATATTAA
1 AATATAA-ATAATATTAA
* *
656734 TATATAAAT--TTTTAA
1 AATATAAATAATATTAA
* *
656749 AATTTATATAATA-TAA
1 AATATAAATAATATTAA
*
656765 AATATTAAT-ATATTAA
1 AATATAAATAATATTAA
*
656781 AATTTAATATAATA
1 AATATAA-ATAATA
656795 ATAATACTAA
Statistics
Matches: 61, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
15 14 0.23
16 17 0.28
17 5 0.08
18 21 0.34
19 4 0.07
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AATATAAATAATATTAA
Done.