Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr4
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: 31929104
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1434590 characters in sequence are not A, C, G, or T
File 3 of 82
Found at i:546202 original size:18 final size:18
Alignment explanation
Indices: 546179--546216 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
546169 GAAGAGAAAC
546179 AACAACA-ACATCATCAAG
1 AACAACAGA-ATCATCAAG
*
546197 AACAACAGAATCATCGAG
1 AACAACAGAATCATCAAG
546215 AA
1 AA
546217 GAAGAGCAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 17 0.94
19 1 0.06
ACGTcount: A:0.55, C:0.24, G:0.11, T:0.11
Consensus pattern (18 bp):
AACAACAGAATCATCAAG
Found at i:568777 original size:30 final size:30
Alignment explanation
Indices: 568743--568806 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
568733 AATTAAGTTT
* *
568743 TTATATTTTTATTTTGAGCCAAATAAGTCC
1 TTATACTTTTATTTTGAGCCAAATAAGTCA
*
568773 TTATACTTTTATTTTGAGTCAAATAAGTCA
1 TTATACTTTTATTTTGAGCCAAATAAGTCA
568803 TTAT
1 TTAT
568807 GACAAATGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.31, C:0.11, G:0.09, T:0.48
Consensus pattern (30 bp):
TTATACTTTTATTTTGAGCCAAATAAGTCA
Found at i:578220 original size:11 final size:12
Alignment explanation
Indices: 578204--578232 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
578194 GGCAGCCCAA
578204 AAAAAAT-AAAT
1 AAAAAATAAAAT
578215 AAAAAATAAAAT
1 AAAAAATAAAAT
578227 AAAAAA
1 AAAAAA
578233 GGTTGGGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 7 0.41
12 10 0.59
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (12 bp):
AAAAAATAAAAT
Found at i:591135 original size:12 final size:13
Alignment explanation
Indices: 591118--591148 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
591108 GAGCCGCCTA
591118 CTTTTTTTTTTC-
1 CTTTTTTTTTTCT
591130 CTTTTTTTTTTCT
1 CTTTTTTTTTTCT
591143 CTTTTT
1 CTTTTT
591149 GTCTTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
CTTTTTTTTTTCT
Found at i:591538 original size:22 final size:21
Alignment explanation
Indices: 591513--591565 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 21
591503 TAATTAAATC
591513 AATCATTATTTAAATTTAT-AAA
1 AATCATTATTT-AATTT-TGAAA
591535 AATCACTTAATTTAATTTTGAAA
1 AATCA-TT-ATTTAATTTTGAAA
*
591558 AATTATTA
1 AATCATTA
591566 GATAAGTGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
21 1 0.04
22 8 0.30
23 14 0.52
24 4 0.15
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (21 bp):
AATCATTATTTAATTTTGAAA
Found at i:591679 original size:15 final size:15
Alignment explanation
Indices: 591655--591685 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
591645 AAATAGATAT
591655 TGATTATAATTATAA
1 TGATTATAATTATAA
*
591670 TGATTGTAATTATAA
1 TGATTATAATTATAA
591685 T
1 T
591686 ATATGGTTGT
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:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (15 bp):
TGATTATAATTATAA
Found at i:591785 original size:31 final size:31
Alignment explanation
Indices: 591742--591800 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
591732 AATATCTTAT
*
591742 TTTATATCAAAATTG-AATATAATTATTAAAA
1 TTTATATAAAAATTGAAAT-TAATTATTAAAA
*
591773 TTTATATAAAAATTTAAATTAATTATTA
1 TTTATATAAAAATTGAAATTAATTATTA
591801 CTAATTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 22 0.88
32 3 0.12
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (31 bp):
TTTATATAAAAATTGAAATTAATTATTAAAA
Found at i:598760 original size:2 final size:2
Alignment explanation
Indices: 598753--598826 Score: 89
Period size: 2 Copynumber: 37.5 Consensus size: 2
598743 CCACCCTTAC
* *
598753 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
598795 GT CAT AT -T A- AT AT AT AT AT AT AT GT AT AT AT A
1 AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
598827 CACATAAGTA
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
1 2 0.03
2 58 0.95
3 1 0.02
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.50
Consensus pattern (2 bp):
AT
Found at i:616606 original size:1 final size:1
Alignment explanation
Indices: 616541--616586 Score: 65
Period size: 1 Copynumber: 46.0 Consensus size: 1
616531 GTACTTCAGT
* * *
616541 CCCCTCCCCCTCCCACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
616587 NNNNNNNNNN
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.02, C:0.93, G:0.00, T:0.04
Consensus pattern (1 bp):
C
Found at i:616607 original size:1 final size:1
Alignment explanation
Indices: 616599--616624 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
616589 NNNNNNNNNN
616599 CCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCC
616625 TCCAGCTACG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:617974 original size:24 final size:26
Alignment explanation
Indices: 617947--617994 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
617937 ATGAGTTTAC
*
617947 ATGAT-ATTTTTATTGG-AATTAAAT
1 ATGATAATTTGTATTGGAAATTAAAT
*
617971 ATGATAATTTGTCTTGGAAATTAA
1 ATGATAATTTGTATTGGAAATTAA
617995 TGTTTTGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 5 0.25
25 9 0.45
26 6 0.30
ACGTcount: A:0.38, C:0.02, G:0.15, T:0.46
Consensus pattern (26 bp):
ATGATAATTTGTATTGGAAATTAAAT
Found at i:622191 original size:5 final size:5
Alignment explanation
Indices: 622181--622205 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
622171 GTCGTAGTAC
622181 TTTAT TTTAT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT
622206 ACAATAAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTAT
Found at i:622942 original size:28 final size:29
Alignment explanation
Indices: 622902--622958 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
622892 TTATTTAAAA
**
622902 ATATTTAAAT-AAATTTTATTTTTTTATT
1 ATATTTAAATAAAATTTTACATTTTTATT
*
622930 ATATTTAATTAAAATTTTACATTTTTATT
1 ATATTTAAATAAAATTTTACATTTTTATT
622959 TTAAATCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 9 0.36
29 16 0.64
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (29 bp):
ATATTTAAATAAAATTTTACATTTTTATT
Found at i:632845 original size:9 final size:9
Alignment explanation
Indices: 632831--632856 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
632821 GTCCATTTCT
632831 TTCTTCTTG
1 TTCTTCTTG
632840 TTCTTCTTG
1 TTCTTCTTG
632849 TTCTTCTT
1 TTCTTCTT
632857 TTTTTTTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.23, G:0.08, T:0.69
Consensus pattern (9 bp):
TTCTTCTTG
Found at i:638613 original size:18 final size:19
Alignment explanation
Indices: 638592--638629 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
638582 ATTTAACACG
*
638592 ATTAACACG-TTTAATATA
1 ATTAACACGATTAAATATA
638610 ATTAACACGATTAAATATA
1 ATTAACACGATTAAATATA
638629 A
1 A
638630 ATATTTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.50, C:0.11, G:0.05, T:0.34
Consensus pattern (19 bp):
ATTAACACGATTAAATATA
Found at i:638614 original size:27 final size:30
Alignment explanation
Indices: 638566--638623 Score: 86
Period size: 27 Copynumber: 2.0 Consensus size: 30
638556 ATACGATACG
638566 ACACGATTAATAATACATTTAACACGATTA
1 ACACGATTAATAATACATTTAACACGATTA
*
638596 ACACGTTTAAT-ATA-A-TTAACACGATTA
1 ACACGATTAATAATACATTTAACACGATTA
638623 A
1 A
638624 ATATAAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 13 0.48
28 1 0.04
29 3 0.11
30 10 0.37
ACGTcount: A:0.47, C:0.16, G:0.07, T:0.31
Consensus pattern (30 bp):
ACACGATTAATAATACATTTAACACGATTA
Found at i:638675 original size:35 final size:36
Alignment explanation
Indices: 638620--638690 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 36
638610 ATTAACACGA
* *
638620 TTAAATATAAATATTTATAATTAAAAAAATTATTAT
1 TTAAATATAAATATCTATAATTAAAAAAATAATTAT
* *
638656 TTAAATTTAAA-ATCTATAATTATAAAAATAATTAT
1 TTAAATATAAATATCTATAATTAAAAAAATAATTAT
638691 AACAAACAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 21 0.68
36 10 0.32
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (36 bp):
TTAAATATAAATATCTATAATTAAAAAAATAATTAT
Found at i:641308 original size:3 final size:3
Alignment explanation
Indices: 641294--641336 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
641284 AGTCGTCTTT
* * *
641294 GAA GAG GAA GAA GAA GAA GAA GAA GAA GAA GGA GAC GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
641337 GAGAGGAAAG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.58, C:0.02, G:0.40, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:641337 original size:12 final size:12
Alignment explanation
Indices: 641302--641340 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
641292 TTGAAGAGGA
*
641302 AGAAGAAGAAGA
1 AGAAGAAGAAGG
641314 AGAAGAAGAAGG
1 AGAAGAAGAAGG
*
641326 AGACGAAGAAGG
1 AGAAGAAGAAGG
641338 AGA
1 AGA
641341 GGAAAGATCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.59, C:0.03, G:0.38, T:0.00
Consensus pattern (12 bp):
AGAAGAAGAAGG
Found at i:652324 original size:30 final size:31
Alignment explanation
Indices: 652262--652330 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
652252 AATTATAATT
* * *
652262 TTTTTAAAAAATAAAAAACAAAACTATAAAA
1 TTTTAAAAAAATAAAAAACAAAATTATTAAA
*
652293 TTTATAAAAAAAT-AAAGA-AAAATTATTAAA
1 TTT-TAAAAAAATAAAAAACAAAATTATTAAA
652323 TTTTAAAA
1 TTTTAAAA
652331 GTTTAAGAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 5 0.15
30 13 0.39
31 7 0.21
32 8 0.24
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.30
Consensus pattern (31 bp):
TTTTAAAAAAATAAAAAACAAAATTATTAAA
Found at i:652618 original size:12 final size:13
Alignment explanation
Indices: 652595--652623 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
652585 TTATTTTATA
652595 AAAATAAAAAATT
1 AAAATAAAAAATT
652608 AAAAT-AAAAATT
1 AAAATAAAAAATT
652620 AAAA
1 AAAA
652624 AAATTAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
AAAATAAAAAATT
Found at i:652632 original size:20 final size:19
Alignment explanation
Indices: 652592--652631 Score: 62
Period size: 21 Copynumber: 2.0 Consensus size: 19
652582 ACGTTATTTT
652592 ATAAAAATAAAAAATTAAA
1 ATAAAAATAAAAAATTAAA
652611 ATAAAAATTAAAAAAATTAAA
1 ATAAAAA-T-AAAAAATTAAA
652632 TGATAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.37
20 1 0.05
21 11 0.58
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.23
Consensus pattern (19 bp):
ATAAAAATAAAAAATTAAA
Found at i:652944 original size:11 final size:11
Alignment explanation
Indices: 652928--652954 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
652918 TATTATATAA
652928 TTTTATTAATT
1 TTTTATTAATT
652939 TTTTATTAATT
1 TTTTATTAATT
652950 TTTTA
1 TTTTA
652955 AAAAAACTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTATTAATT
Found at i:657926 original size:59 final size:59
Alignment explanation
Indices: 657862--657980 Score: 193
Period size: 59 Copynumber: 2.0 Consensus size: 59
657852 CATCAACTAA
*
657862 TGAGCTAAATGCTCTTAATCTAATTGAGTTGAATTTTATTATCATCAACTCATCATACC
1 TGAGCTAAATGCTCTTAATCTAATTGAGTTGAATTTTATTACCATCAACTCATCATACC
* * * *
657921 TGAGCTAAATGTTCTTAATCTAATTGAGTTGGATTTTATTGCCATCCACTCATCATACC
1 TGAGCTAAATGCTCTTAATCTAATTGAGTTGAATTTTATTACCATCAACTCATCATACC
657980 T
1 T
657981 AAGAGTGTAT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.39
Consensus pattern (59 bp):
TGAGCTAAATGCTCTTAATCTAATTGAGTTGAATTTTATTACCATCAACTCATCATACC
Found at i:659663 original size:18 final size:18
Alignment explanation
Indices: 659611--659656 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
659601 ACATGCTTAC
659611 TTAATCGTGTTATCGTGT
1 TTAATCGTGTTATCGTGT
*
659629 TTAATCATGTTATCGTGT
1 TTAATCGTGTTATCGTGT
*
659647 TTAAACGTGT
1 TTAATCGTGT
659657 ATACGTGACA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.22, C:0.11, G:0.20, T:0.48
Consensus pattern (18 bp):
TTAATCGTGTTATCGTGT
Found at i:661590 original size:21 final size:21
Alignment explanation
Indices: 661566--661621 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
661556 TGGATGGTTT
* *
661566 AGGATTGTTCTTTCGACTGTA
1 AGGATTGTTCTTTCAACTATA
*
661587 AGGATTGTTCTTTTAACTATA
1 AGGATTGTTCTTTCAACTATA
*
661608 AGCATTGTTCTTTC
1 AGGATTGTTCTTTC
661622 TCCTCCTCCT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.21, C:0.14, G:0.18, T:0.46
Consensus pattern (21 bp):
AGGATTGTTCTTTCAACTATA
Found at i:664882 original size:2 final size:2
Alignment explanation
Indices: 664870--664904 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
664860 AGCTGACATT
*
664870 GA GA GA AA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
664905 TGAGTAGTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:665150 original size:2 final size:2
Alignment explanation
Indices: 665143--665167 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
665133 TGAAGATGGT
665143 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
665168 GCTCCTTTTC
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:667586 original size:24 final size:24
Alignment explanation
Indices: 667555--667604 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
667545 GTTAAGCTGC
667555 GATGCCTGATCAGCTGAATTTTGG
1 GATGCCTGATCAGCTGAATTTTGG
*
667579 GATGCCTGATCAGCTGATTTTTGG
1 GATGCCTGATCAGCTGAATTTTGG
667603 GA
1 GA
667605 AGCCAATGAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.16, G:0.30, T:0.34
Consensus pattern (24 bp):
GATGCCTGATCAGCTGAATTTTGG
Found at i:678099 original size:25 final size:25
Alignment explanation
Indices: 678060--678126 Score: 118
Period size: 25 Copynumber: 2.7 Consensus size: 25
678050 CTCTTCCCAT
*
678060 CCTTC-TTCTTTCTCTCTAAAGAAA
1 CCTTCTTTCTTCCTCTCTAAAGAAA
678084 CCTTCTTTCTTCCTCTCTAAAGAAA
1 CCTTCTTTCTTCCTCTCTAAAGAAA
678109 CCTTCTTTCTTCCTCTCT
1 CCTTCTTTCTTCCTCTCT
678127 TAACAATGAT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
24 5 0.12
25 36 0.88
ACGTcount: A:0.18, C:0.34, G:0.03, T:0.45
Consensus pattern (25 bp):
CCTTCTTTCTTCCTCTCTAAAGAAA
Found at i:679815 original size:33 final size:33
Alignment explanation
Indices: 679772--679834 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
679762 AGTAGATCAT
* * *
679772 ATTATTATCAATTATGATATGTTAATATGTCAC
1 ATTATCATCAATTATGATACGTTAACATGTCAC
679805 ATTATCATCAATTATGATACGTTAACATGT
1 ATTATCATCAATTATGATACGTTAACATGT
679835 TACGTTAGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.37, C:0.11, G:0.10, T:0.43
Consensus pattern (33 bp):
ATTATCATCAATTATGATACGTTAACATGTCAC
Found at i:679888 original size:3 final size:3
Alignment explanation
Indices: 679880--679929 Score: 56
Period size: 3 Copynumber: 18.3 Consensus size: 3
679870 TTAAGTTAAT
*
679880 TAA TAA TAA TAA TAA TAA -AG T-A TAA -AA TAA -AA T-A TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
679923 TAA TAA T
1 TAA TAA T
679930 TTATTATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
2 8 0.20
3 32 0.80
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:679917 original size:31 final size:31
Alignment explanation
Indices: 679882--679955 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
679872 AAGTTAATTA
679882 ATAATAATAATAATAAAGTATAAAATAAAAT
1 ATAATAATAATAATAAAGTATAAAATAAAAT
** * *
679913 ATAATAATAATAATAATTTATTATATAAAAT
1 ATAATAATAATAATAAAGTATAAAATAAAAT
679944 ATAA-ATATAATA
1 ATAATA-ATAATA
679956 TAATTTATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
30 1 0.03
31 37 0.97
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (31 bp):
ATAATAATAATAATAAAGTATAAAATAAAAT
Found at i:680030 original size:3 final size:3
Alignment explanation
Indices: 680022--680070 Score: 56
Period size: 3 Copynumber: 18.3 Consensus size: 3
680012 TTAAGTTAAT
680022 TAA TAA TAA TAA TAA TAA -AA T-A TAA -AA TAA -AA TAA -AA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
680064 TAA TAA T
1 TAA TAA T
680071 TAATTATTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
2 12 0.30
3 28 0.70
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:680033 original size:6 final size:6
Alignment explanation
Indices: 680022--680070 Score: 56
Period size: 5 Copynumber: 9.2 Consensus size: 6
680012 TTAAGTTAAT
680022 TAATAA TAATAA TAATAA -AAT-A TAA-AA TAA-AA TAA-AA T-ATAA
1 TAATAA TAATAA TAATAA TAATAA TAATAA TAATAA TAATAA TAATAA
680064 TAATAA T
1 TAATAA T
680071 TAATTATTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
4 2 0.05
5 20 0.51
6 17 0.44
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
TAATAA
Found at i:680131 original size:29 final size:30
Alignment explanation
Indices: 680091--680159 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
680081 GTTAGTATAT
680091 AAAATAATAAGGGCTTA-TTGACTCAAAATA
1 AAAAT-ATAAGGGCTTATTTGACTCAAAATA
*
680121 AAAATATAAGGGCTTATTTGACTTAAAATA
1 AAAATATAAGGGCTTATTTGACTCAAAATA
*
680151 AAAGTATAA
1 AAAATATAA
680160 AAGCTTAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 11 0.31
30 25 0.69
ACGTcount: A:0.51, C:0.07, G:0.13, T:0.29
Consensus pattern (30 bp):
AAAATATAAGGGCTTATTTGACTCAAAATA
Found at i:680166 original size:30 final size:29
Alignment explanation
Indices: 680103--680190 Score: 88
Period size: 30 Copynumber: 3.0 Consensus size: 29
680093 AATAATAAGG
**
680103 GCTTATTGACTCAAAATAAAAATATAAGG
1 GCTTATTGACTCAAAATAAAAATATAAAA
* *
680132 GCTTATTTGACTTAAAATAAAAGTATAAAA
1 GCTTA-TTGACTCAAAATAAAAATATAAAA
* * *
680162 GCTTAAATGAAT-ATAATAAAAATATAAAA
1 GCTT-ATTGACTCAAAATAAAAATATAAAA
680191 AACTATTTAA
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
29 20 0.41
30 28 0.57
31 1 0.02
ACGTcount: A:0.53, C:0.07, G:0.10, T:0.30
Consensus pattern (29 bp):
GCTTATTGACTCAAAATAAAAATATAAAA
Found at i:687808 original size:2 final size:2
Alignment explanation
Indices: 687796--687828 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
687786 TTATAAGTNG
687796 TA TA CTA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
687829 TACGATGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 26 0.90
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:688551 original size:3 final size:3
Alignment explanation
Indices: 688543--688569 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
688533 TAATTTTTCC
688543 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
688570 CCAAAGTGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:694394 original size:19 final size:16
Alignment explanation
Indices: 694362--694415 Score: 65
Period size: 19 Copynumber: 3.2 Consensus size: 16
694352 ACATTCACAC
*
694362 TTTTATTTTATTTTTA
1 TTTTAATTTATTTTTA
694378 TTTAATAATTATATTTTTA
1 TTT--TAATT-TATTTTTA
694397 TTTTAATTTA-TTTTA
1 TTTTAATTTATTTTTA
694412 TTTT
1 TTTT
694416 TTAAGAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
15 9 0.26
16 5 0.15
17 5 0.15
18 4 0.12
19 11 0.32
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTAATTTATTTTTA
Found at i:696130 original size:33 final size:33
Alignment explanation
Indices: 696086--696158 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 33
696076 TAAAATATAT
* ** *
696086 AATATAAAAAATTATGTTAAGAAATGAAAACAA
1 AATATATAAAATTATAATAAGAAATAAAAACAA
*
696119 AATATATAAAATTATAATAAGAAATAAAAATAA
1 AATATATAAAATTATAATAAGAAATAAAAACAA
696152 AATATAT
1 AATATAT
696159 GAGATTAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.66, C:0.01, G:0.05, T:0.27
Consensus pattern (33 bp):
AATATATAAAATTATAATAAGAAATAAAAACAA
Found at i:704136 original size:18 final size:18
Alignment explanation
Indices: 704115--704156 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
704105 TCATCCTTTT
*
704115 TTTTTTTTTAATTTATGA
1 TTTTTTTTAAATTTATGA
* *
704133 TTTTTTTTAAATTTTTTA
1 TTTTTTTTAAATTTATGA
704151 TTTTTT
1 TTTTTT
704157 CAATTTTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (18 bp):
TTTTTTTTAAATTTATGA
Found at i:707103 original size:23 final size:23
Alignment explanation
Indices: 707077--707159 Score: 89
Period size: 23 Copynumber: 3.6 Consensus size: 23
707067 ACTTTACCTG
*
707077 AAGGTTTTGAAGATGATTATTCA
1 AAGGATTTGAAGATGATTATTCA
* *
707100 AAGGATTTGAAGATTATTA-TCTG
1 AAGGATTTGAAGATGATTATTC-A
* *
707123 AAGGATTTGAACATGATTAATTGA
1 AAGGATTTGAAGATGATT-ATTCA
707147 AA-GATTTGAAGAT
1 AAGGATTTGAAGAT
707160 ATTTTCCTGA
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
22 2 0.04
23 43 0.88
24 3 0.06
25 1 0.02
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.36
Consensus pattern (23 bp):
AAGGATTTGAAGATGATTATTCA
Found at i:707170 original size:46 final size:47
Alignment explanation
Indices: 707073--707179 Score: 130
Period size: 46 Copynumber: 2.3 Consensus size: 47
707063 AAAGACTTTA
* *
707073 CCTGAAGGTTTTGAAGATGATTATTCAAAGGATTTGAAGATTATTAT
1 CCTGAAGGATTTGAACATGATTATTCAAAGGATTTGAAGATTATTAT
* *
707120 -CTGAAGGATTTGAACATGATTAATTGAAA-GATTTGAAGA-TATTTT
1 CCTGAAGGATTTGAACATGATT-ATTCAAAGGATTTGAAGATTATTAT
* *
707165 CCTGAAAGACTTGAA
1 CCTGAAGGATTTGAA
707180 AATTTATACC
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
45 5 0.10
46 41 0.79
47 6 0.12
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (47 bp):
CCTGAAGGATTTGAACATGATTATTCAAAGGATTTGAAGATTATTAT
Found at i:709563 original size:60 final size:62
Alignment explanation
Indices: 709494--709617 Score: 216
Period size: 61 Copynumber: 2.0 Consensus size: 62
709484 CTCCAAAATC
709494 TCACAACCACCACCTATTG-TCTCTTTTCTTTTTACCAAATAGAAACAAAAAGT-TTTTTTT
1 TCACAACCACCACCTATTGTTCTCTTTTCTTTTTACCAAATAGAAACAAAAAGTCTTTTTTT
*
709554 TCACAACCACCACCTTTTGTTCTCTTTTCTTTTTACCAAATAGAAACAAAAAGTCCTTTTTTT
1 TCACAACCACCACCTATTGTTCTCTTTTCTTTTTACCAAATAGAAACAAAAAGT-CTTTTTTT
709617 T
1 T
709618 TTTGCTTACA
Statistics
Matches: 60, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
60 18 0.30
61 34 0.57
63 8 0.13
ACGTcount: A:0.30, C:0.24, G:0.05, T:0.41
Consensus pattern (62 bp):
TCACAACCACCACCTATTGTTCTCTTTTCTTTTTACCAAATAGAAACAAAAAGTCTTTTTTT
Found at i:711661 original size:280 final size:278
Alignment explanation
Indices: 711150--711871 Score: 923
Period size: 280 Copynumber: 2.6 Consensus size: 278
711140 CGACGTCGTT
* * *
711150 TTTGTAACGACCCAAGTCCAACCAATGACCTAGTAGCTTTTTGGGCCTAAA-CCATGCAGCCCTC
1 TTTGTAACGA-CCAAGTCCAACCACTGGCCTAGTAGCTTTTTGGACCTAAACCCATG--GCCCTC
* * *
711214 AAAAGCTTAAGTTCAAGTTACTAGTAGTGGTGGACTTGGATTGTTGTATAGGTCTTAACAATCAC
63 AAAAGCTTAAGCTCAAGTTGCTAATAGTGGTGGACTTGGATTGTTGTATAGGTCTTAACAATCAC
* * * * * * *
711279 ATTCACATCAAATGTGGGATGTTGGATATCACAATCTCATCCACTTAAATCCTTGATGTCTTCAT
128 ATTCACATCAGATGTGAGATGTTGGATATCATAATCCCACCCACTCAAATCCTTGATGTCCTCAT
* * * * *
711344 TAAGGCCACACATCACATCCACGGGATCAAAATCTCACCAGGGCAATGTGAAAGTTCACATC-AG
193 CAAGGCCACACATCACATCCACAGAACCAAAATCTCACCAGAGCAATGTGAAAGTTCACATCGA-
711408 ACTGGTGCATA-CTATGATACCA
257 ACTGGTGCA-AGCTATGATACCA
* * * * *
711430 TTTGTAACGATTCAAGTTCAACCACTGGCCTAGTAACTTTTTGGACCTAAACCACATGGTCCTAA
1 TTTGTAACGA-CCAAGTCCAACCACTGGCCTAGTAGCTTTTTGGACCTAAACC-CATGGCCCTCA
* * * * * ** *
711495 AAAACTTAAGCTAAAGTTGCTAATAGTGGTAGATTTAGATTGTTGTATAAATCTTAACAATTACA
64 AAAGCTTAAGCTCAAGTTGCTAATAGTGGTGGACTTGGATTGTTGTATAGGTCTTAACAATCACA
*
711560 TTCACATCAGATATGAGATGTTGGATATCATAATCCCACCCACTCAAATCCTTGATGTCCTCATC
129 TTCACATCAGATGTGAGATGTTGGATATCATAATCCCACCCACTCAAATCCTTGATGTCCTCATC
* * *
711625 AAGGTCACACATCACATCCACAGAACCAAGATCTCACCAGAGCAATGTGAAAGTTCACATCGAAT
194 AAGGCCACACATCACATCCACAGAACCAAAATCTCACCAGAGCAATGTGAAAGTTCACATCGAAC
*
711690 TGGTGCAAGCTTTGATACCA
259 TGGTGCAAGCTATGATACCA
* * ** *
711710 TTTGTAACGACCTAAGTCCAATCACT-GACTCAACAGCTTTTT-GAGCCTAAACCCCGTGGCCCT
1 TTTGTAACGACC-AAGTCCAACCACTGGCCT-AGTAGCTTTTTGGA-CCTAAA-CCCATGGCCCT
*
711773 CAAAAGCTTAAGCTCAAGTTGCTAATAGTGGTGGACTTGGATTGTTATATAGGTCTTAACAATCA
62 CAAAAGCTTAAGCTCAAGTTGCTAATAGTGGTGGACTTGGATTGTTGTATAGGTCTTAACAATCA
*
711838 CATTCACATCAGATGTAAGATGTTGGATATCATA
127 CATTCACATCAGATGTGAGATGTTGGATATCATA
711872 GTTTTAAGCA
Statistics
Matches: 376, Mismatches: 58, Indels: 16
0.84 0.13 0.04
Matches are distributed among these distances:
279 7 0.02
280 361 0.96
281 4 0.01
282 4 0.01
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (278 bp):
TTTGTAACGACCAAGTCCAACCACTGGCCTAGTAGCTTTTTGGACCTAAACCCATGGCCCTCAAA
AGCTTAAGCTCAAGTTGCTAATAGTGGTGGACTTGGATTGTTGTATAGGTCTTAACAATCACATT
CACATCAGATGTGAGATGTTGGATATCATAATCCCACCCACTCAAATCCTTGATGTCCTCATCAA
GGCCACACATCACATCCACAGAACCAAAATCTCACCAGAGCAATGTGAAAGTTCACATCGAACTG
GTGCAAGCTATGATACCA
Found at i:714510 original size:2 final size:2
Alignment explanation
Indices: 714503--714685 Score: 178
Period size: 2 Copynumber: 97.5 Consensus size: 2
714493 TAAGAGGTAC
714503 AT AT AT AT AT AT A- AT AT AT A- AT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
714542 AT AT A- AT AT AT -T AT A- 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 AT AT
* * ** ** * *
714580 AT AT AT A- AA AN NN NN AT -T AC AT AT AT AT AT AT TT AT AT AGT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
714621 -T AT AT AT AT AT AT AT AT AT AT -T AT -T AT A- AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
714658 AT AT AT AT AT AGT AT AT AT AT AT AT AT A
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT A
714686 ACATGGCGTA
Statistics
Matches: 157, Mismatches: 8, Indels: 32
0.80 0.04 0.16
Matches are distributed among these distances:
1 14 0.09
2 140 0.89
3 3 0.02
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.46
Consensus pattern (2 bp):
AT
Found at i:714666 original size:97 final size:94
Alignment explanation
Indices: 714500--714686 Score: 247
Period size: 97 Copynumber: 2.0 Consensus size: 94
714490 GTTTAAGAGG
*
714500 TACATATATATATATAATATATAATATATATATATATATAATATATAATATATTATAATATATAT
1 TACATATATATATATAATATATAATATATATATATATATAATATATAATATAATATAATATATAT
714565 ATATATA-TATATATA-ATATATAAAANNNNNAT
66 ATATATAGTATATATATATATATAAAA-----AT
* * *
714597 TACATATATATATAT-TTATATAGT-TATATATATATATATATATATTATTATAATATAATATAT
1 TACATATATATATATAATATATAATATATATATATATATA-ATATA-TAATATAATATAATATAT
714660 ATATATATAGTATATATATATATATAA
64 ATATATATAGTATATATATATATATAA
714687 CATGGCGTAA
Statistics
Matches: 82, Mismatches: 4, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
95 14 0.17
96 12 0.15
97 40 0.49
98 8 0.10
99 8 0.10
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.45
Consensus pattern (94 bp):
TACATATATATATATAATATATAATATATATATATATATAATATATAATATAATATAATATATAT
ATATATAGTATATATATATATATAAAAAT
Found at i:721712 original size:19 final size:19
Alignment explanation
Indices: 721688--721741 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
721678 TGACACGTTA
721688 AGATACGAAAATTTTTTAT
1 AGATACGAAAATTTTTTAT
*
721707 AGATACGAAAAATTTTTAT
1 AGATACGAAAATTTTTTAT
** *
721726 AGCCATGAAAATTTTT
1 AGATACGAAAATTTTT
721742 AATTAAACAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (19 bp):
AGATACGAAAATTTTTTAT
Found at i:724842 original size:26 final size:25
Alignment explanation
Indices: 724781--724854 Score: 77
Period size: 26 Copynumber: 3.1 Consensus size: 25
724771 ATAAACAATA
724781 TTATT-AATAATTAAAT-TATTAA-
1 TTATTAAATAATTAAATATATTAAT
* *
724803 TT-TTACATAGTTAAATATATTAAT
1 TTATTAAATAATTAAATATATTAAT
724827 TTATTAAATTAATTAAA-ATTATTAAT
1 TTATTAAA-TAATTAAATA-TATTAAT
724853 TT
1 TT
724855 TTTTTACCTA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
21 2 0.05
22 11 0.26
23 6 0.14
24 2 0.05
25 5 0.12
26 16 0.38
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (25 bp):
TTATTAAATAATTAAATATATTAAT
Found at i:727191 original size:2 final size:2
Alignment explanation
Indices: 727184--727214 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
727174 ATTTAACACG
727184 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 T
727215 TTATTATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:728266 original size:8 final size:7
Alignment explanation
Indices: 728256--728282 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
728246 TAAATTATAT
728256 TTTTATC
1 TTTTATC
728263 TTTTATC
1 TTTTATC
728270 TTTTATC
1 TTTTATC
728277 TTTTAT
1 TTTTAT
728283 AAATTTAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.11, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTTATC
Found at i:733058 original size:91 final size:92
Alignment explanation
Indices: 732931--733104 Score: 244
Period size: 91 Copynumber: 1.9 Consensus size: 92
732921 CATGACTTGG
*
732931 AATAAAAGGAGAACAACATTCAGCACAGAAAAGAAAAAAGAGGAGAGATTTGG-TTAAATTAAGG
1 AATAAAAGGAGAACAACATTCAGCACAGAAAAG-AAAAAGAGGAGAGATTAGGTTTAAATTAAGG
*
732995 CTTTCTTTTAAATT-TTGCATGGCTTAT
65 CTTTCTTTAAAATTATTGCATGGCTTAT
*** * * * *
733022 AATAAAAGGAGAATGGCGTTCAGCGCAGAAAAGAAAAGGAGGAGAGATTAGGTTTAAGTTAAGGC
1 AATAAAAGGAGAACAACATTCAGCACAGAAAAGAAAAAGAGGAGAGATTAGGTTTAAATTAAGGC
733087 TTTCTTTAAAATTATTGC
66 TTTCTTTAAAATTATTGC
733105 GAAGGTTTTA
Statistics
Matches: 72, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
90 17 0.24
91 51 0.71
92 4 0.06
ACGTcount: A:0.41, C:0.09, G:0.23, T:0.26
Consensus pattern (92 bp):
AATAAAAGGAGAACAACATTCAGCACAGAAAAGAAAAAGAGGAGAGATTAGGTTTAAATTAAGGC
TTTCTTTAAAATTATTGCATGGCTTAT
Found at i:740131 original size:41 final size:41
Alignment explanation
Indices: 740069--740188 Score: 158
Period size: 41 Copynumber: 3.0 Consensus size: 41
740059 ACATTAGACT
* *
740069 TACAAGTTGAAAGTCCCAAATACTAACTCTTAAGGTGGCTC
1 TACAGGTTGAAAGTCCCAAATACTAACTGTTAAGGTGGCTC
*
740110 TACAGGTTGAAAGGCCCAAATACTAACTGTTAAGGTGGCT-
1 TACAGGTTGAAAGTCCCAAATACTAACTGTTAAGGTGGCTC
* *
740150 T-CTTGG-T-AAAGTCTCAAATACTAACTGTTAAGGTGGCTC
1 TAC-AGGTTGAAAGTCCCAAATACTAACTGTTAAGGTGGCTC
740189 CTTGGTGATA
Statistics
Matches: 71, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
38 29 0.41
39 2 0.03
40 3 0.04
41 37 0.52
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (41 bp):
TACAGGTTGAAAGTCCCAAATACTAACTGTTAAGGTGGCTC
Found at i:740177 original size:38 final size:39
Alignment explanation
Indices: 740076--740196 Score: 156
Period size: 38 Copynumber: 3.1 Consensus size: 39
740066 ACTTACAAGT
* *
740076 TGAAAGTCCCAAATACTAACTCTTAAGGTGGC-TCTACAGG
1 TGAAAGTCCCAAATACTAACTGTTAAGGTGGCTTCT--TGG
*
740116 TTGAAAGGCCCAAATACTAACTGTTAAGGTGGCTTCTTGG
1 -TGAAAGTCCCAAATACTAACTGTTAAGGTGGCTTCTTGG
* *
740156 T-AAAGTCTCAAATACTAACTGTTAAGGTGGCTCCTTGG
1 TGAAAGTCCCAAATACTAACTGTTAAGGTGGCTTCTTGG
740194 TGA
1 TGA
740197 TACATATAGC
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
38 35 0.49
39 2 0.03
40 2 0.03
41 30 0.42
42 3 0.04
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (39 bp):
TGAAAGTCCCAAATACTAACTGTTAAGGTGGCTTCTTGG
Found at i:743160 original size:30 final size:29
Alignment explanation
Indices: 743106--743166 Score: 86
Period size: 30 Copynumber: 2.1 Consensus size: 29
743096 AATCAAGCTC
743106 TTATATTTTTATTTTAAGCCAAATAAATCT
1 TTATATTTTTATTTTAAGCCAAATAAA-CT
* **
743136 TTATATTTTTATTTTGAGTTAAATAAACT
1 TTATATTTTTATTTTAAGCCAAATAAACT
743165 TT
1 TT
743167 TATAACTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 4 0.14
30 24 0.86
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.54
Consensus pattern (29 bp):
TTATATTTTTATTTTAAGCCAAATAAACT
Found at i:743493 original size:28 final size:26
Alignment explanation
Indices: 743437--743502 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 26
743427 ATAAACACTT
743437 ATTTAATTCAAAATAAAAAAAATAAAA
1 ATTTAATT-AAAATAAAAAAAATAAAA
*
743464 ATTTAATTAAACGTAATAAAAAATAAAA
1 ATTTAATTAAA-ATAA-AAAAAATAAAA
*
743492 ATTTATTTAAA
1 ATTTAATTAAA
743503 TATTTTTACC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
26 3 0.09
27 11 0.31
28 21 0.60
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.32
Consensus pattern (26 bp):
ATTTAATTAAAATAAAAAAAATAAAA
Found at i:749108 original size:40 final size:43
Alignment explanation
Indices: 749059--749139 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 43
749049 AAATTAACTT
749059 GGAAAAATATTTAA-AAA-T-CCTAACA-ATTAAAAAAAATAAA
1 GGAAAAATATTTAAGAAAGTCCCTAA-ATATTAAAAAAAATAAA
*
749099 GGAATAATATTTAAGAAAGTCCCTAAATTATTAAAAAAAAT
1 GGAAAAATATTTAAGAAAGTCCCTAAA-TATTAAAAAAAAT
749140 TCAAATAAGC
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
40 13 0.37
41 3 0.09
42 2 0.06
43 5 0.14
44 12 0.34
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.26
Consensus pattern (43 bp):
GGAAAAATATTTAAGAAAGTCCCTAAATATTAAAAAAAATAAA
Found at i:751968 original size:286 final size:286
Alignment explanation
Indices: 751447--752014 Score: 971
Period size: 286 Copynumber: 2.0 Consensus size: 286
751437 TGTTGATTGA
*
751447 AAATAAGAAAAATAAGTGAGAAAAAAATAGTTATTGGAGATGATTAAATACATATGACCGTTAGT
1 AAATAAGAAAAATAAGTGAGAAAAAAATAGTTATTGGAGATGATTAAATACATATGACCGTTAAT
* * *
751512 TGATTGGAAATAATATAGTATTCTAGAAATTAAAAAGTGATAGAAAATTGAGATTTATTAAACAT
66 TGATTGAAAATAATATAGCATTCTAGAAATTAAAAAGTGATAGAAAATTGAGATTTATTAAACAC
751577 ATAATTAAGAAAATGAGAAAATAAGTAATTTTATTAATTATTTTTATTTTTATTATATTTTTTAT
131 ATAATTAAGAAAATGAGAAAATAAGTAATTTTATTAATTATTTTTATTTTTATTATATTTTTTAT
* *
751642 ATAATTAATTATATTATAAAATTATAGGACTTTCCCAAATTGGGGACCTATAGCCCTCGTTTGGG
196 ATAATTAATTATATTATAAAATTATAGGACTTTCCCAAATTGGGGACCTAAAGCCCTCGCTTGGG
* *
751707 TG-GCTTCACCTAAGGGTCGGCCTTGG
261 -GCGCTTCACCCAAGGGCCGGCCTTGG
* **
751733 AAATAAGAAAAATAAGTGAGAAAAAAATAGTTGTTGGAGATGATTAAATATTTATGACCGTTAAT
1 AAATAAGAAAAATAAGTGAGAAAAAAATAGTTATTGGAGATGATTAAATACATATGACCGTTAAT
*
751798 TGATTGAAAATAATATAGCATTCTAGAAATTAGAAAGTGATAGAAAATTGAGATTTATTAAACAC
66 TGATTGAAAATAATATAGCATTCTAGAAATTAAAAAGTGATAGAAAATTGAGATTTATTAAACAC
751863 ATAATTAAGAAAATGAGAAAATAAGTAATTTTATTAATTATTTTTTATTTTTA-TATATTTTTTA
131 ATAATTAAGAAAATGAGAAAATAAGTAATTTTATTAATTA-TTTTTATTTTTATTATATTTTTTA
*
751927 TATAATTAATTATATTATAAAATTATAGGACCTTT-CCAAATTGGGGGCCTAAAGCCCTCGCTTG
195 TATAATTAATTATATTATAAAATTATAGGA-CTTTCCCAAATTGGGGACCTAAAGCCCTCGCTTG
751991 GGGCGCTTCACCCAAGGGCCGGCC
259 GGGCGCTTCACCCAAGGGCCGGCC
752015 CTGCTTGGAA
Statistics
Matches: 266, Mismatches: 13, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
285 1 0.00
286 249 0.94
287 16 0.06
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (286 bp):
AAATAAGAAAAATAAGTGAGAAAAAAATAGTTATTGGAGATGATTAAATACATATGACCGTTAAT
TGATTGAAAATAATATAGCATTCTAGAAATTAAAAAGTGATAGAAAATTGAGATTTATTAAACAC
ATAATTAAGAAAATGAGAAAATAAGTAATTTTATTAATTATTTTTATTTTTATTATATTTTTTAT
ATAATTAATTATATTATAAAATTATAGGACTTTCCCAAATTGGGGACCTAAAGCCCTCGCTTGGG
GCGCTTCACCCAAGGGCCGGCCTTGG
Found at i:767808 original size:25 final size:24
Alignment explanation
Indices: 767780--767828 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
767770 GCCTGTTTGT
*
767780 TGGCCAGTGCGCCCAGTCTGCTTGC
1 TGGCCAGTGCACCCA-TCTGCTTGC
* *
767805 TGGCCTGTGCACTCATCTGCTTGC
1 TGGCCAGTGCACCCATCTGCTTGC
767829 GGGTGCCGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.08, C:0.35, G:0.29, T:0.29
Consensus pattern (24 bp):
TGGCCAGTGCACCCATCTGCTTGC
Found at i:771456 original size:29 final size:29
Alignment explanation
Indices: 771326--771486 Score: 117
Period size: 29 Copynumber: 5.8 Consensus size: 29
771316 ATGCTTAGGA
*
771326 TGTTACACGCCATGTTGAAAAAAATACTGT
1 TGTTACACGTCATGTT-AAAAAAATACTGT
* * *
771356 TGTTACATGTCATG-T-ACAAAA-AC--A
1 TGTTACACGTCATGTTAAAAAAATACTGT
*
771380 TATTACACGTCATGGTT--AAAAA-A--GT
1 TGTTACACGTCAT-GTTAAAAAAATACTGT
* *
771405 TGTTACATGCCATGTTGAAAAAAAATACTGT
1 TGTTACACGTCATGTT--AAAAAAATACTGT
* *
771436 TGTTACACGTCATGTTAAAAAAATATTAT
1 TGTTACACGTCATGTTAAAAAAATACTGT
* *
771465 TGTTACACGTCATATTCAAAAA
1 TGTTACACGTCATGTTAAAAAA
771487 CATTTTGTTA
Statistics
Matches: 104, Mismatches: 17, Indels: 21
0.73 0.12 0.15
Matches are distributed among these distances:
24 14 0.13
25 16 0.15
26 3 0.03
27 5 0.05
28 5 0.05
29 33 0.32
30 12 0.12
31 16 0.15
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (29 bp):
TGTTACACGTCATGTTAAAAAAATACTGT
Found at i:771507 original size:28 final size:28
Alignment explanation
Indices: 771435--771525 Score: 69
Period size: 28 Copynumber: 3.2 Consensus size: 28
771425 AAAAATACTG
* * * *
771435 TTGTTACACGTCATGTTAAAAAAATATTA
1 TTGTTACACGTAATATT-CAAAAACATTA
*
771464 TTGTTACACGTCATATTCAAAAACATT-
1 TTGTTACACGTAATATTCAAAAACATTA
* * **
771491 TTGTTACACTTTAATA-TCTAAAATGTTA
1 TTGTTACAC-GTAATATTCAAAAACATTA
771519 TTGTTAC
1 TTGTTAC
771526 TTACGAACCA
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
27 17 0.33
28 19 0.37
29 16 0.31
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (28 bp):
TTGTTACACGTAATATTCAAAAACATTA
Found at i:773959 original size:31 final size:31
Alignment explanation
Indices: 773921--773983 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
773911 GTTTGGTATT
773921 ATACATCAATTAATAGTGTCTTATAGCTCTC
1 ATACATCAATTAATAGTGTCTTATAGCTCTC
773952 ATACATCAATTAATAGTGTCTTATAGCTCTC
1 ATACATCAATTAATAGTGTCTTATAGCTCTC
773983 A
1 A
773984 GTAAAATGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.38
Consensus pattern (31 bp):
ATACATCAATTAATAGTGTCTTATAGCTCTC
Found at i:775236 original size:12 final size:12
Alignment explanation
Indices: 775219--775243 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
775209 TTTGATTCAG
775219 TTTTAAAAATTT
1 TTTTAAAAATTT
775231 TTTTAAAAATTT
1 TTTTAAAAATTT
775243 T
1 T
775244 CAATTTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTTAAAAATTT
Found at i:775269 original size:18 final size:19
Alignment explanation
Indices: 775241--775289 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
775231 TTTTAAAAAT
*
775241 TTTCAATTTATATTA-TTA
1 TTTCTATTTATATTATTTA
*
775259 TTTTTATTTAT-TTATTTA
1 TTTCTATTTATATTATTTA
775277 TTTCTATTT-TATT
1 TTTCTATTTATATT
775290 TACTCATATG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 4 0.15
18 22 0.85
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTCTATTTATATTATTTA
Found at i:778183 original size:36 final size:36
Alignment explanation
Indices: 778136--778247 Score: 154
Period size: 36 Copynumber: 3.1 Consensus size: 36
778126 TCAACTCAGC
*
778136 TCATGTGCACTCCCACATCACACAT-AGCAAATACCG
1 TCATGTGCACTCCCACATCACACATGA-CAAATACCA
* *
778172 TCATGTGCACTCCCACATCGCACATGACAAATATCA
1 TCATGTGCACTCCCACATCACACATGACAAATACCA
* * *
778208 TCATGTGCACTCCCACACCGCACATGACAAATATCA
1 TCATGTGCACTCCCACATCACACATGACAAATACCA
778244 TCAT
1 TCAT
778248 CTCGAGCTCC
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
36 70 0.99
37 1 0.01
ACGTcount: A:0.33, C:0.35, G:0.11, T:0.21
Consensus pattern (36 bp):
TCATGTGCACTCCCACATCACACATGACAAATACCA
Found at i:779298 original size:10 final size:10
Alignment explanation
Indices: 779272--779317 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
779262 ATGAAGAAGT
*
779272 AAGAAAAGAA
1 AAGAAAGGAA
779282 AAGGAAAGGAA
1 AA-GAAAGGAA
779293 AAGAAAGGAA
1 AAGAAAGGAA
779303 GAA-AAA-GAA
1 -AAGAAAGGAA
779312 AAGAAA
1 AAGAAA
779318 TTGATTTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
8 2 0.06
9 6 0.19
10 13 0.41
11 11 0.34
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (10 bp):
AAGAAAGGAA
Found at i:783172 original size:30 final size:30
Alignment explanation
Indices: 783138--783219 Score: 96
Period size: 30 Copynumber: 2.7 Consensus size: 30
783128 CCCTTATATG
*
783138 TTTTATTTTGAGTCAAATAAG-TTTTTATA
1 TTTTATTTTGAGTCAAATAAGCTTTGTATA
**
783167 CTTTTATTTTGAACCAAATAAGCCTTTGTATA
1 -TTTTATTTTGAGTCAAATAAG-CTTTGTATA
*
783199 -TTTATTTTAAGTCAAATAAGC
1 TTTTATTTTGAGTCAAATAAGC
783220 CCTTATCACT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
29 1 0.02
30 36 0.82
32 7 0.16
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.48
Consensus pattern (30 bp):
TTTTATTTTGAGTCAAATAAGCTTTGTATA
Found at i:783203 original size:60 final size:60
Alignment explanation
Indices: 783090--783218 Score: 152
Period size: 60 Copynumber: 2.1 Consensus size: 60
783080 TTCAAAAAAT
** * * *
783090 TCAAATAAGTCTTTATACTTTTATTGTGTTCAATTAAACCCTTATATGTTTTATTTTGAG
1 TCAAATAAGTCTTTATACTTTTATTGTGACCAAATAAACCCTTATATGATTTATTTTAAG
* * * * *
783150 TCAAATAAGTTTTTATACTTTTATTTTGAACCAAATAAGCCTTTGTAT-ATTTATTTTAAG
1 TCAAATAAGTCTTTATACTTTTATTGTG-ACCAAATAAACCCTTATATGATTTATTTTAAG
783210 TCAAATAAG
1 TCAAATAAG
783219 CCCTTATCAC
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
60 45 0.78
61 13 0.22
ACGTcount: A:0.33, C:0.11, G:0.09, T:0.47
Consensus pattern (60 bp):
TCAAATAAGTCTTTATACTTTTATTGTGACCAAATAAACCCTTATATGATTTATTTTAAG
Found at i:784839 original size:51 final size:51
Alignment explanation
Indices: 784734--784871 Score: 192
Period size: 51 Copynumber: 2.7 Consensus size: 51
784724 AATTCTAATT
* *
784734 ATAATTTTACCACCATAAGTGGAT-AATAATTTTACCATCAGAATCTAAGA
1 ATAATTTTACCACCAAAAGTGGATGGATAATTTTACCATCAGAATCTAAGA
* *
784784 ATAATTTTACCACCAAAAGTGGATGGATAATTTTACTATTAGAATCTAA-A
1 ATAATTTTACCACCAAAAGTGGATGGATAATTTTACCATCAGAATCTAAGA
* *
784834 GATAATTTTGCCACCAGAAGTGGATGGATAA-TTTACCA
1 -ATAATTTTACCACCAAAAGTGGATGGATAATTTTACCA
784872 CCAAAAGTAG
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
50 30 0.38
51 49 0.62
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (51 bp):
ATAATTTTACCACCAAAAGTGGATGGATAATTTTACCATCAGAATCTAAGA
Found at i:784872 original size:25 final size:26
Alignment explanation
Indices: 784734--784884 Score: 112
Period size: 25 Copynumber: 6.0 Consensus size: 26
784724 AATTCTAATT
* *
784734 ATAATTTTACCACCATAAGTGGAT-A
1 ATAATTTTACCACCAGAAGTGGATGG
* ** * *
784759 ATAATTTTACCATCAGAA-TCTAAGA
1 ATAATTTTACCACCAGAAGTGGATGG
*
784784 ATAATTTTACCACCAAAAGTGGATGG
1 ATAATTTTACCACCAGAAGTGGATGG
* ** ** **
784810 ATAATTTTACTATTAGAA-TCTAAAG
1 ATAATTTTACCACCAGAAGTGGATGG
*
784835 ATAATTTTGCCACCAGAAGTGGATGG
1 ATAATTTTACCACCAGAAGTGGATGG
* *
784861 ATAA-TTTACCACCAAAAGTAGATG
1 ATAATTTTACCACCAGAAGTGGATG
784885 AATGTCGTAA
Statistics
Matches: 93, Mismatches: 30, Indels: 6
0.72 0.23 0.05
Matches are distributed among these distances:
24 2 0.02
25 67 0.72
26 24 0.26
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (26 bp):
ATAATTTTACCACCAGAAGTGGATGG
Found at i:789084 original size:15 final size:16
Alignment explanation
Indices: 789064--789098 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
789054 TTCACTAAAA
*
789064 TTTTTTCC-CATGAGG
1 TTTTTTCCTAATGAGG
789079 TTTTTTCCTAATGAGG
1 TTTTTTCCTAATGAGG
789095 TTTT
1 TTTT
789099 AAAGAAGCAT
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:0.14, C:0.14, G:0.17, T:0.54
Consensus pattern (16 bp):
TTTTTTCCTAATGAGG
Found at i:789671 original size:22 final size:23
Alignment explanation
Indices: 789646--789688 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
789636 TCTTGAAAAG
789646 GAAAAAAG-AAAAGAAATATAAA
1 GAAAAAAGTAAAAGAAATATAAA
* *
789668 GAAAATAGTAAAAGAATTATA
1 GAAAAAAGTAAAAGAAATATA
789689 TTTGTTTTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.70, C:0.00, G:0.14, T:0.16
Consensus pattern (23 bp):
GAAAAAAGTAAAAGAAATATAAA
Found at i:792366 original size:15 final size:15
Alignment explanation
Indices: 792305--792366 Score: 56
Period size: 15 Copynumber: 4.1 Consensus size: 15
792295 TTCTTACATA
792305 TAATATTTAAAAT-AT
1 TAAT-TTTAAAATAAT
*
792320 TAATGTTAAAA-AAT
1 TAATTTTAAAATAAT
** *
792334 TAATTATTAACTTTAT
1 TAATT-TTAAAATAAT
792350 TAATTTTAAAATAAT
1 TAATTTTAAAATAAT
792365 TA
1 TA
792367 CAATTTTAAG
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
14 12 0.33
15 17 0.47
16 7 0.19
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
TAATTTTAAAATAAT
Found at i:797105 original size:16 final size:16
Alignment explanation
Indices: 797065--797128 Score: 51
Period size: 15 Copynumber: 4.1 Consensus size: 16
797055 TTTTTAAATT
* *
797065 AATAATTATAAAA-AT
1 AATAATAATAAAATAA
*
797080 AATTATAATAAAATAA
1 AATAATAATAAAATAA
* *
797096 AATAATAATAACATCA
1 AATAATAATAAAATAA
* *
797112 AAT-ATAACAAAACAA
1 AATAATAATAAAATAA
797127 AA
1 AA
797129 AGTTCAAAAT
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
15 21 0.55
16 17 0.45
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (16 bp):
AATAATAATAAAATAA
Found at i:799413 original size:2 final size:2
Alignment explanation
Indices: 799406--799441 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
799396 ATCTTAATTT
*
799406 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
799442 GTTGAATGCC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:800981 original size:19 final size:19
Alignment explanation
Indices: 800954--800992 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
800944 TTACTAAAAA
*
800954 TCATTAAATTACAAATTAT
1 TCATGAAATTACAAATTAT
*
800973 TCATGAAATTATAAATTAT
1 TCATGAAATTACAAATTAT
800992 T
1 T
800993 TTAAAAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.44
Consensus pattern (19 bp):
TCATGAAATTACAAATTAT
Found at i:802802 original size:30 final size:30
Alignment explanation
Indices: 802768--802835 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
802758 ATTTTGAGTT
* *
802768 AAATAAGCTTTTATACT-TTTATTTTAAACC
1 AAATAAGCCTTTATA-TATTTATTTCAAACC
**
802798 AAATAAGCCTTTATATATTTATTTCAAGTC
1 AAATAAGCCTTTATATATTTATTTCAAACC
802828 AAATAAGC
1 AAATAAGC
802836 ACTTATCACT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 1 0.03
30 32 0.97
ACGTcount: A:0.40, C:0.13, G:0.06, T:0.41
Consensus pattern (30 bp):
AAATAAGCCTTTATATATTTATTTCAAACC
Found at i:808742 original size:67 final size:66
Alignment explanation
Indices: 808635--808768 Score: 232
Period size: 67 Copynumber: 2.0 Consensus size: 66
808625 CTGCGATGAA
* *
808635 ATGCCTTGGTGGGGGTCAAGTGTTGTGATGGAAACACTTAGACAGACGTACAGCTGAAGTAAAGG
1 ATGCCTTGGTGGGAGTCAAGTGTTGTGATGGAAACACTTAGAAAGACGTACAGCTGAAGTAAAGG
808700 G
66 G
*
808701 ATGCCTTGGTGGGAGTCAAAGTGTTGTGATGGAAACGCTTAGAAAGACGTACAGCTGAAGTAAAG
1 ATGCCTTGGTGGGAGTC-AAGTGTTGTGATGGAAACACTTAGAAAGACGTACAGCTGAAGTAAAG
808766 GG
65 GG
808768 A
1 A
808769 GGTTTTGTAA
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
66 16 0.25
67 48 0.75
ACGTcount: A:0.31, C:0.13, G:0.34, T:0.22
Consensus pattern (66 bp):
ATGCCTTGGTGGGAGTCAAGTGTTGTGATGGAAACACTTAGAAAGACGTACAGCTGAAGTAAAGG
G
Found at i:809744 original size:42 final size:42
Alignment explanation
Indices: 809676--809763 Score: 158
Period size: 42 Copynumber: 2.1 Consensus size: 42
809666 TTGATCAATC
*
809676 GTTGTAATTATAGTTGGATCACTCAACTTGAAAACCATCTTT
1 GTTGCAATTATAGTTGGATCACTCAACTTGAAAACCATCTTT
*
809718 GTTGCAATTATAGTTGGATCATTCAACTTGAAAACCATCTTT
1 GTTGCAATTATAGTTGGATCACTCAACTTGAAAACCATCTTT
809760 GTTG
1 GTTG
809764 GTTTAGGAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.39
Consensus pattern (42 bp):
GTTGCAATTATAGTTGGATCACTCAACTTGAAAACCATCTTT
Found at i:810211 original size:19 final size:19
Alignment explanation
Indices: 810187--810231 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
810177 TGGCACATTT
*
810187 TGATGACCTAGCGTCGACA
1 TGATGACCTAGCATCGACA
** *
810206 TGATGATGTGGCATCGACA
1 TGATGACCTAGCATCGACA
810225 TGATGAC
1 TGATGAC
810232 GTGGTAGTGC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (19 bp):
TGATGACCTAGCATCGACA
Found at i:818035 original size:2 final size:2
Alignment explanation
Indices: 818028--818062 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
818018 ATACGAAAAT
818028 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 T
818063 TTACATGCTC
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:821689 original size:55 final size:55
Alignment explanation
Indices: 821615--821725 Score: 195
Period size: 55 Copynumber: 2.0 Consensus size: 55
821605 CGATATCGCG
* *
821615 CGAACGAATTGACAAATCGAACGATCTGCATTGTAGAAATTAAGGTATCGAACGA
1 CGAACGAATTGACAAATCGAACGATCTGCAGTGTAGAAATTAAGGAATCGAACGA
*
821670 CGAAGGAATTGACAAATCGAACGATCTGCAGTGTAGAAATTAAGGAATCGAACGA
1 CGAACGAATTGACAAATCGAACGATCTGCAGTGTAGAAATTAAGGAATCGAACGA
821725 C
1 C
821726 TAATTAATAA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.41, C:0.16, G:0.23, T:0.20
Consensus pattern (55 bp):
CGAACGAATTGACAAATCGAACGATCTGCAGTGTAGAAATTAAGGAATCGAACGA
Found at i:822987 original size:145 final size:145
Alignment explanation
Indices: 822818--823113 Score: 477
Period size: 145 Copynumber: 2.0 Consensus size: 145
822808 ATATAACACG
*
822818 ACAT-AACACGTTTAATAAATTTATTAAATACGTCAATATAGGACACAACACTATTAAATAAAAA
1 ACATCAACACGTTTAATAAATTTATTAAATACGTCAATATAAGACACAACACTATTAAATAAAAA
* * * *
822882 TATTTAAAATTAAATATAATTTTATTATTTTTTAAAATCAATAATTATAAAAATAATTATAATAA
66 TATTTAAAATTAAATATAATTTTATTACTTTTTAAAATAAAAAATTATAAAAATAATTATAACAA
*
822947 AGTAAAATAATAATA
131 AGCAAAATAATAATA
* ** *
822962 ACATCAACACGTTTAATAAGTTTATTAAATGTGTCAATATAAGACACAATACTATTAAATAAAAA
1 ACATCAACACGTTTAATAAATTTATTAAATACGTCAATATAAGACACAACACTATTAAATAAAAA
* *
823027 TATTTATAATTAAATATAATTTTATTGCTTTTTAAAATAAAAAATTATAAAAATAATTATAACAA
66 TATTTAAAATTAAATATAATTTTATTACTTTTTAAAATAAAAAATTATAAAAATAATTATAACAA
823092 AGCAAAATAATAATA
131 AGCAAAATAATAATA
823107 ACATCAA
1 ACATCAA
823114 ATGTAACAAA
Statistics
Matches: 139, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
144 4 0.03
145 135 0.97
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.35
Consensus pattern (145 bp):
ACATCAACACGTTTAATAAATTTATTAAATACGTCAATATAAGACACAACACTATTAAATAAAAA
TATTTAAAATTAAATATAATTTTATTACTTTTTAAAATAAAAAATTATAAAAATAATTATAACAA
AGCAAAATAATAATA
Found at i:830516 original size:2 final size:2
Alignment explanation
Indices: 830509--830543 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
830499 TTTTCCACTT
830509 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
830544 TTCCCAATGT
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:844026 original size:19 final size:18
Alignment explanation
Indices: 843998--844039 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
843988 AATAATAATT
843998 TTTA-ATATTAAATTTTAA
1 TTTATATATT-AATTTTAA
* *
844016 TTTATATATTATTTTTTA
1 TTTATATATTAATTTTAA
844034 TTTATA
1 TTTATA
844040 AATTTTTTAT
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTATATATTAATTTTAA
Found at i:844031 original size:18 final size:17
Alignment explanation
Indices: 844010--844053 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
844000 TAATATTAAA
*
844010 TTTTAATTTATATATTAT
1 TTTTAATTTATAAATT-T
*
844028 TTTTTATTTATAAATTT
1 TTTTAATTTATAAATTT
844045 TTTATAATT
1 TTT-TAATT
844054 AATGTAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTAATTTATAAATTT
Found at i:851893 original size:8 final size:9
Alignment explanation
Indices: 851873--851902 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
851863 AATGGCTGCA
851873 TTTTT-TTC
1 TTTTTCTTC
851881 TTTTTCTTC
1 TTTTTCTTC
851890 TTTTTCTTC
1 TTTTTCTTC
851899 TTTT
1 TTTT
851903 GGGTCATGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 5 0.24
9 16 0.76
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTTTCTTC
Found at i:858575 original size:30 final size:29
Alignment explanation
Indices: 858539--858614 Score: 93
Period size: 30 Copynumber: 2.6 Consensus size: 29
858529 AATCATTAAT
*
858539 TATAAAAATTTATTTAACTCAAAATAAAAA
1 TATAAAAATTTATTTAAAT-AAAATAAAAA
*
858569 TATAAAAATTTGA-TTAAATATAATAAAAA
1 TATAAAAATTT-ATTTAAATAAAATAAAAA
*
858598 -ATAAAATTTTATTTAAA
1 TATAAAAATTTATTTAAA
858615 ACTTTTTGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
27 1 0.02
28 14 0.34
29 9 0.22
30 16 0.39
31 1 0.02
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (29 bp):
TATAAAAATTTATTTAAATAAAATAAAAA
Found at i:859801 original size:6 final size:6
Alignment explanation
Indices: 859790--859814 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
859780 TTTTTTGAAT
859790 AAAGAA AAAGAA AAAGAA AAAGAA A
1 AAAGAA AAAGAA AAAGAA AAAGAA A
859815 TGTATACCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:871922 original size:30 final size:31
Alignment explanation
Indices: 871888--871950 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 31
871878 TCTTTAGACC
*
871888 AAATCCAAACTAGAAATAATAAGCAAT-ACA
1 AAATCCAAACTAGAAATAAGAAGCAATGACA
871918 AAATCCAAACTAGAAATAAGAAGCAATGACA
1 AAATCCAAACTAGAAATAAGAAGCAATGACA
871949 AA
1 AA
871951 GTGCTCCTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 26 0.84
31 5 0.16
ACGTcount: A:0.60, C:0.16, G:0.10, T:0.14
Consensus pattern (31 bp):
AAATCCAAACTAGAAATAAGAAGCAATGACA
Found at i:878936 original size:15 final size:15
Alignment explanation
Indices: 878916--878948 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
878906 CTTAAGAGAG
878916 AGAAAGGAAGAAA-GA
1 AGAAAGGAA-AAAGGA
878931 AGAAAGGAAAAAGGA
1 AGAAAGGAAAAAGGA
878946 AGA
1 AGA
878949 GAAAAGCTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.18
15 14 0.82
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (15 bp):
AGAAAGGAAAAAGGA
Found at i:878943 original size:7 final size:8
Alignment explanation
Indices: 878916--878948 Score: 52
Period size: 7 Copynumber: 4.4 Consensus size: 8
878906 CTTAAGAGAG
878916 AGAAAGGA
1 AGAAAGGA
878924 AGAAA-GA
1 AGAAAGGA
878931 AGAAAGGA
1 AGAAAGGA
878939 A-AAAGGA
1 AGAAAGGA
878946 AGA
1 AGA
878949 GAAAAGCTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 14 0.61
8 9 0.39
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (8 bp):
AGAAAGGA
Found at i:880106 original size:39 final size:39
Alignment explanation
Indices: 880063--880155 Score: 114
Period size: 39 Copynumber: 2.4 Consensus size: 39
880053 ATAGCGTGTG
* *
880063 GTGTGGGAGAGCACACGCCGATGATATATGCCATGTGCA
1 GTGTGGGAGAGCACACGACGATGATAAATGCCATGTGCA
* * * **
880102 GTGTGGGAGAGCATATGATGATGATAAATGCCATGTGTG
1 GTGTGGGAGAGCACACGACGATGATAAATGCCATGTGCA
*
880141 GTGTGGGAGTGCACA
1 GTGTGGGAGAGCACA
880156 TGAGGATGTT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.26, C:0.14, G:0.37, T:0.24
Consensus pattern (39 bp):
GTGTGGGAGAGCACACGACGATGATAAATGCCATGTGCA
Found at i:882372 original size:20 final size:20
Alignment explanation
Indices: 882328--882366 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
882318 TTATACAATT
*
882328 ATTACTGACGAAATTCATCC
1 ATTACTGAAGAAATTCATCC
882348 ATTACTGAAGAAATTCATC
1 ATTACTGAAGAAATTCATC
882367 AGTTACCACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (20 bp):
ATTACTGAAGAAATTCATCC
Found at i:885910 original size:15 final size:15
Alignment explanation
Indices: 885890--885936 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
885880 CTTACAAAGC
*
885890 AATGTGATTATAGGA
1 AATGTGATTACAGGA
* *
885905 AATGTGATTGCAGGT
1 AATGTGATTACAGGA
*
885920 AATGTGATTGCAGGA
1 AATGTGATTACAGGA
885935 AA
1 AA
885937 AATAACATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.36, C:0.04, G:0.30, T:0.30
Consensus pattern (15 bp):
AATGTGATTACAGGA
Found at i:886291 original size:25 final size:27
Alignment explanation
Indices: 886221--886329 Score: 78
Period size: 30 Copynumber: 3.7 Consensus size: 27
886211 ATTTTTTGTA
*
886221 TTATATATTTTATTTTAATTTCTTTTACC
1 TTAT-TATTTTATTTTAATTTCTTATA-C
** *
886250 TTATTATATAAATTTTTAATTTCTTATATT
1 TTATTAT-TTTA-TTTTAATTTCTTATA-C
886280 TTATTTTATTTTGATTTCTAA-TTCTTATA-
1 TTA--TTATTTT-ATTT-TAATTTCTTATAC
886309 TTATATATTTTATTTTAATTT
1 TTAT-TATTTTATTTTAATTT
886330 TTTTATTAAT
Statistics
Matches: 65, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
26 3 0.05
27 7 0.11
28 9 0.14
29 9 0.14
30 17 0.26
31 12 0.18
32 8 0.12
ACGTcount: A:0.28, C:0.06, G:0.01, T:0.66
Consensus pattern (27 bp):
TTATTATTTTATTTTAATTTCTTATAC
Found at i:889713 original size:1 final size:1
Alignment explanation
Indices: 889702--889735 Score: 50
Period size: 1 Copynumber: 34.0 Consensus size: 1
889692 CTCTCTCTCT
* *
889702 CCCCACCCCCCCCCCCCCCCNCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
889736 TTTTCTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.03, C:0.94, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:889726 original size:16 final size:16
Alignment explanation
Indices: 889702--889735 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
889692 CTCTCTCTCT
889702 CCCCACCCCCCCCCCC
1 CCCCACCCCCCCCCCC
*
889718 CCCCNCCCCCCCCCCC
1 CCCCACCCCCCCCCCC
889734 CC
1 CC
889736 TTTTCTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.03, C:0.94, G:0.00, T:0.00
Consensus pattern (16 bp):
CCCCACCCCCCCCCCC
Found at i:893681 original size:22 final size:22
Alignment explanation
Indices: 893653--893696 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
893643 TTATTAATAT
893653 ATATGCACATCATATTAGTTGC
1 ATATGCACATCATATTAGTTGC
893675 ATATGCACATCATATTAGTTGC
1 ATATGCACATCATATTAGTTGC
893697 TTCATCCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (22 bp):
ATATGCACATCATATTAGTTGC
Found at i:898937 original size:20 final size:20
Alignment explanation
Indices: 898914--898951 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
898904 ATCTAGTAAA
898914 TAAATAAAAAAAATACAATT
1 TAAATAAAAAAAATACAATT
*
898934 TAAATTAAAAAAATACAA
1 TAAATAAAAAAAATACAA
898952 GTAATAAGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (20 bp):
TAAATAAAAAAAATACAATT
Found at i:898992 original size:2 final size:2
Alignment explanation
Indices: 898985--899020 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
898975 AGAATAAAAG
* *
898985 AT AT AT AT AT AT AT AT AT AT AT AT AC AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
899021 TTGCATGCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:903483 original size:22 final size:23
Alignment explanation
Indices: 903458--903503 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
903448 TAATTATTTA
*
903458 TTAGGTATTGTATTACT-AGTTT
1 TTAGGCATTGTATTACTAAGTTT
*
903480 TTAGGCATTGTGTTACTAAGTTT
1 TTAGGCATTGTATTACTAAGTTT
903503 T
1 T
903504 AAGCACTACG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.22, C:0.07, G:0.20, T:0.52
Consensus pattern (23 bp):
TTAGGCATTGTATTACTAAGTTT
Found at i:912207 original size:29 final size:30
Alignment explanation
Indices: 912156--912231 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 30
912146 TTAAAAAAAT
** *
912156 TCAAATAAGTTTTTA-ATTTTTTATTGT-AT
1 TCAAATAAACTTTTATA-TTTTTATTGTGAG
* *
912185 TCAATTAAACTTTTATATTTTTATTTTGAG
1 TCAAATAAACTTTTATATTTTTATTGTGAG
912215 TCAAATAAACTTTTATA
1 TCAAATAAACTTTTATA
912232 ACTAATTATT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
29 21 0.54
30 18 0.46
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.54
Consensus pattern (30 bp):
TCAAATAAACTTTTATATTTTTATTGTGAG
Found at i:912315 original size:25 final size:26
Alignment explanation
Indices: 912287--912336 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
912277 CATAGCATGC
912287 TGACATGTT-ATAATGG-ATGATGACG
1 TGACATGTTGAT-ATGGTATGATGACG
912312 TGACATGTTGATATGGTATGATGAC
1 TGACATGTTGATATGGTATGATGAC
912337 ATAATCAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.30, C:0.08, G:0.28, T:0.34
Consensus pattern (26 bp):
TGACATGTTGATATGGTATGATGACG
Found at i:916330 original size:2 final size:2
Alignment explanation
Indices: 916325--916376 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
916315 CTAAAAAAAA
916325 AT AT AT AT AT AT 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 AT AT AT AT AT AT
916367 AT AT AT AT AT
1 AT AT AT AT AT
916377 GAAACCTTTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:916626 original size:23 final size:25
Alignment explanation
Indices: 916572--916621 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
916562 TGTGAGACAA
*
916572 TAATTAATATAAAAATATAGTTATT
1 TAATTAATATAAAAATAAAGTTATT
*
916597 TAATTAATA-AAAAATAAATTTATT
1 TAATTAATATAAAAATAAAGTTATT
916621 T
1 T
916622 TTTAAAGGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (25 bp):
TAATTAATATAAAAATAAAGTTATT
Found at i:925505 original size:3 final size:3
Alignment explanation
Indices: 925497--925524 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
925487 TATTTAACAA
925497 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
925525 CAAGTGGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:934786 original size:40 final size:40
Alignment explanation
Indices: 934731--934808 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 40
934721 ATTTATGTGG
*
934731 AATCAATAGTCATTTCTTTTTTGTATAATGCTGTATTGGC
1 AATCAATAGTCATTTCTTTTTTGTATAATGCTGCATTGGC
* *
934771 AATCAATTGTCATTTCTTTTTTGTGTAATGCTGCATTG
1 AATCAATAGTCATTTCTTTTTTGTATAATGCTGCATTG
934809 ACTATGGGTG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.23, C:0.13, G:0.15, T:0.49
Consensus pattern (40 bp):
AATCAATAGTCATTTCTTTTTTGTATAATGCTGCATTGGC
Found at i:962724 original size:18 final size:20
Alignment explanation
Indices: 962687--962725 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
962677 TTACCCATAT
962687 TCAACATGACGTGAAATTTAA
1 TCAACATGACGT-AAATTTAA
962708 TCAACATGAC-T-AATTTAA
1 TCAACATGACGTAAATTTAA
962726 GAAACAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
20 1 0.06
21 10 0.56
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (20 bp):
TCAACATGACGTAAATTTAA
Found at i:964654 original size:11 final size:11
Alignment explanation
Indices: 964627--964665 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
964617 AATAGATATT
964627 TTAATTAATTA
1 TTAATTAATTA
*
964638 -TAATTAACTA
1 TTAATTAATTA
*
964648 TTAATTAATTG
1 TTAATTAATTA
964659 TTAATTA
1 TTAATTA
964666 TAAATTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (11 bp):
TTAATTAATTA
Found at i:967671 original size:137 final size:136
Alignment explanation
Indices: 967425--967691 Score: 507
Period size: 137 Copynumber: 2.0 Consensus size: 136
967415 AATATTTTTC
967425 TTAGGCGATGATTCACTTTTAGTACTACAGAGACATACAATGATAATTAATTATTAATTGATTAG
1 TTAGGCGATGATTCACTTTTAGTACTACAGAGACATACAATGATAATTAATTATTAATTGATTAG
967490 TAATTATAAAAATTTATTTAAATTTAATACAATAAAAAATAAAAACTTATTTAAAATTTTTAAAA
66 TAATTATAAAAATTTATTTAAATTTAATACAATAAAAAATAAAAACTTATTTAAAATTTTTAAAA
967555 ATATTT
131 ATATTT
967561 NTTAGGCGATGATTCACTTTTAGTACTACAGAGACATACAATGATAATTAATTATTAATTGATTA
1 -TTAGGCGATGATTCACTTTTAGTACTACAGAGACATACAATGATAATTAATTATTAATTGATTA
* *
967626 GTAATTATAAAAATTTATTTAAATTTAATACAATAAAAAATAAAAACTTATTTGAATTTTTTAAA
65 GTAATTATAAAAATTTATTTAAATTTAATACAATAAAAAATAAAAACTTATTTAAAATTTTTAAA
967691 A
130 A
967692 TAATTTAAGA
Statistics
Matches: 128, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
137 128 1.00
ACGTcount: A:0.46, C:0.07, G:0.08, T:0.39
Consensus pattern (136 bp):
TTAGGCGATGATTCACTTTTAGTACTACAGAGACATACAATGATAATTAATTATTAATTGATTAG
TAATTATAAAAATTTATTTAAATTTAATACAATAAAAAATAAAAACTTATTTAAAATTTTTAAAA
ATATTT
Found at i:967694 original size:33 final size:33
Alignment explanation
Indices: 967632--967694 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 33
967622 ATTAGTAATT
* *
967632 ATAAAAATTTATTTAAATTTAATACAATAAAAA
1 ATAAAAACTTATTTAAATTTAATAAAATAAAAA
* **
967665 ATAAAAACTTATTTGAATTTTTTAAAATAA
1 ATAAAAACTTATTTAAATTTAATAAAATAA
967695 TTTAAGAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 25 1.00
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.40
Consensus pattern (33 bp):
ATAAAAACTTATTTAAATTTAATAAAATAAAAA
Found at i:968007 original size:14 final size:14
Alignment explanation
Indices: 967984--968014 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
967974 TACAGTGAAA
967984 ATTTTCATTTTTTT
1 ATTTTCATTTTTTT
*
967998 ATTTTTATTTTTTT
1 ATTTTCATTTTTTT
968012 ATT
1 ATT
968015 AAGTTCAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (14 bp):
ATTTTCATTTTTTT
Found at i:969213 original size:31 final size:31
Alignment explanation
Indices: 969176--969235 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
969166 CAAACTCTTA
* *
969176 TACTTTTATTTTGAGTCAAATAATTTTTTTT
1 TACTTTTATTTTGAATCAAATAAATTTTTTT
969207 TACTTTTATTTTGAATCAAATAAATTTTT
1 TACTTTTATTTTGAATCAAATAAATTTTT
969236 ATAACTAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.30, C:0.07, G:0.05, T:0.58
Consensus pattern (31 bp):
TACTTTTATTTTGAATCAAATAAATTTTTTT
Found at i:980099 original size:2 final size:2
Alignment explanation
Indices: 980092--980166 Score: 84
Period size: 2 Copynumber: 38.5 Consensus size: 2
980082 CATCAAATGC
**
980092 TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA T- TA -A NNN
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
**
980132 NC 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 T
980167 TAATGGGGAT
Statistics
Matches: 65, Mismatches: 4, Indels: 8
0.84 0.05 0.10
Matches are distributed among these distances:
1 3 0.05
2 62 0.95
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:984829 original size:2 final size:2
Alignment explanation
Indices: 984822--984852 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
984812 AAATTAATAA
984822 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
984853 GGTACTAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:998763 original size:129 final size:130
Alignment explanation
Indices: 998530--998766 Score: 336
Period size: 129 Copynumber: 1.8 Consensus size: 130
998520 TGCTTAAGAA
*
998530 CGATTGACTACCTAACTAAATTTTTTTTCTAATGAGGAACTAAGTTTGACTGAGTTTACTAAAAA
1 CGATTGACTACCTAACTAAATTTTTTTTCTAATGAGG-A-TAAGCTTGACTGAGTTTACTAAAAA
* * *
998595 AAATCGATTTCGATCTATGAAACAAGTTCGGAAGTAGTTATGTGTGAGGAAGCTATTAGCACCGT
64 AAATAGATATCGATCTACGAAACAAGTTCGGAAGTAGTTATGTGTGAGGAAGCTATTAGCACCGT
998660 CG
129 CG
* * *
998662 CGATTGATTACCTAACTAAATTTTTTTTTCTAATGAGG-T-AGCTTGACTTAGTTTATTAAAGAA
1 CGATTGACTACCTAACTAAA-TTTTTTTTCTAATGAGGATAAGCTTGACTGAGTTTACTAAA-AA
* *
998725 AATTAG-TATCGATCTACGAAACAAGTTTGGAAGTAGTTATGT
64 AAATAGATATCGATCTACGAAACAAGTTCGGAAGTAGTTATGT
998767 ATGAAAAAGA
Statistics
Matches: 94, Mismatches: 9, Indels: 7
0.85 0.08 0.06
Matches are distributed among these distances:
129 51 0.54
130 7 0.07
132 19 0.20
133 17 0.18
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (130 bp):
CGATTGACTACCTAACTAAATTTTTTTTCTAATGAGGATAAGCTTGACTGAGTTTACTAAAAAAA
ATAGATATCGATCTACGAAACAAGTTCGGAAGTAGTTATGTGTGAGGAAGCTATTAGCACCGTCG
Found at i:999679 original size:3 final size:3
Alignment explanation
Indices: 999671--999700 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
999661 TTACAAATAT
999671 TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
999701 GTTTATACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:1000875 original size:24 final size:24
Alignment explanation
Indices: 1000842--1000891 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
1000832 CTTTACTTAA
* *
1000842 ATTTATTAAAAAGAATAGGTTCAG
1 ATTTACTAAAAAGAATAGATTCAG
* *
1000866 ATTTACTAAATAGACTAGATTCAG
1 ATTTACTAAAAAGAATAGATTCAG
1000890 AT
1 AT
1000892 GTACAGTTAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.34
Consensus pattern (24 bp):
ATTTACTAAAAAGAATAGATTCAG
Done.