Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015253.1 Kokia drynarioides strain JFW-HI SEQ_130298, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 611692
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 551 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:93 original size:4 final size:4
Alignment explanation
Indices: 84--123 Score: 55
Period size: 4 Copynumber: 10.0 Consensus size: 4
74 CTTCTTCCTT
*
84 TTTC TTTC TTTC TTTC TTTC TCTTT TTTC TTTC TTT- TTTC
1 TTTC TTTC TTTC TTTC TTTC T-TTC TTTC TTTC TTTC TTTC
124 CTTTATTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 3 0.09
4 26 0.81
5 3 0.09
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:96 original size:18 final size:17
Alignment explanation
Indices: 75--121 Score: 67
Period size: 18 Copynumber: 2.7 Consensus size: 17
65 CTTCTTCTCC
*
75 TTCTTCCTTTTTCTTTCT
1 TTCTTTCTTTTTCTTT-T
*
93 TTCTTTCTTTCTCTTTT
1 TTCTTTCTTTTTCTTTT
110 TTCTTTCTTTTT
1 TTCTTTCTTTTT
122 TCCTTTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (17 bp):
TTCTTTCTTTTTCTTTT
Found at i:114 original size:21 final size:19
Alignment explanation
Indices: 88--127 Score: 62
Period size: 21 Copynumber: 2.0 Consensus size: 19
78 TTCCTTTTTC
88 TTTCTTTCTTTCTTTCTCTTT
1 TTTCTTTCTTT-TTTC-CTTT
109 TTTCTTTCTTTTTTCCTTT
1 TTTCTTTCTTTTTTCCTTT
128 ATTTTTCGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.21
20 4 0.21
21 11 0.58
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTCTTTCTTTTTTCCTTT
Found at i:127 original size:12 final size:11
Alignment explanation
Indices: 82--133 Score: 59
Period size: 12 Copynumber: 4.4 Consensus size: 11
72 TCCTTCTTCC
82 TTTTTCTTTCT
1 TTTTTCTTTCT
93 TTCTTTCTTTCTCT
1 TT-TTTC-TT-TCT
107 TTTTTCTTTCT
1 TTTTTCTTTCT
*
118 TTTTTCCTTTAT
1 TTTTT-CTTTCT
130 TTTT
1 TTTT
134 CGTTGGTCCC
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
11 10 0.28
12 15 0.42
13 6 0.17
14 5 0.14
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTTCTTTCT
Found at i:6334 original size:14 final size:14
Alignment explanation
Indices: 6315--6341 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6305 TTAGTTGCTT
6315 TAAGAAAAAGTTAG
1 TAAGAAAAAGTTAG
6329 TAAGAAAAAGTTA
1 TAAGAAAAAGTTA
6342 TAAAAACATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.19, T:0.22
Consensus pattern (14 bp):
TAAGAAAAAGTTAG
Found at i:7087 original size:27 final size:27
Alignment explanation
Indices: 7049--7128 Score: 142
Period size: 27 Copynumber: 3.0 Consensus size: 27
7039 CCATCAATGG
7049 ACTAGAGTTTGCTAGATTGATTACCAA
1 ACTAGAGTTTGCTAGATTGATTACCAA
7076 ACTAGAGTTTGCTAGATTGATTACCAA
1 ACTAGAGTTTGCTAGATTGATTACCAA
* *
7103 ACAAGAGTTTGCTAGATTCATTACCA
1 ACTAGAGTTTGCTAGATTGATTACCA
7129 TACAAGGAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 51 1.00
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (27 bp):
ACTAGAGTTTGCTAGATTGATTACCAA
Found at i:18312 original size:29 final size:27
Alignment explanation
Indices: 18267--18334 Score: 66
Period size: 29 Copynumber: 2.4 Consensus size: 27
18257 TTTACAAAGT
*
18267 AATCTTACATTTCATCAATAAAAT-AACAA
1 AATCTTA-ATTCCATC-ATAAAATCAA-AA
*
18296 AATCTTAATTCCAATCATCAAATCAAAA
1 AATCTTAATTCC-ATCATAAAATCAAAA
18324 AGATCTTAATT
1 A-ATCTTAATT
18335 AATTCGATAC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
28 13 0.38
29 21 0.62
ACGTcount: A:0.49, C:0.18, G:0.01, T:0.32
Consensus pattern (27 bp):
AATCTTAATTCCATCATAAAATCAAAA
Found at i:18923 original size:42 final size:42
Alignment explanation
Indices: 18862--19097 Score: 242
Period size: 42 Copynumber: 5.6 Consensus size: 42
18852 AGCTGAATCA
* * *
18862 TAGGACCGGTCCCGCCTTCTATAGTATCGATCATTAGGTGAG
1 TAGGAACGGTCCCGCCTTCTGTAGTATCGATCATCAGGTGAG
* *
18904 TAGGAACGATCCCACCTTCTGTAGTATCGATCATCAGGTGTA-
1 TAGGAACGGTCCCGCCTTCTGTAGTATCGATCATCAGGTG-AG
* *
18946 TAAGAACGGTCCCGCCTTCTGTAGTATAGATCATCAGGTGAG
1 TAGGAACGGTCCCGCCTTCTGTAGTATCGATCATCAGGTGAG
* * * * *
18988 TAGGAACGGTCCCGCCTGCGGTAGTAAC-AGTCATCAGGAGTG
1 TAGGAACGGTCCCGCCTTCTGTAGTATCGA-TCATCAGGTGAG
* * ** * * *
19030 TAAGATCTATCACGCCTTCTGTAGTATCGACCATCAGGAGAG
1 TAGGAACGGTCCCGCCTTCTGTAGTATCGATCATCAGGTGAG
* * *
19072 TAGGAACAGTCCCGTCTTCTATAGTA
1 TAGGAACGGTCCCGCCTTCTGTAGTA
19098 GTGGTCATCT
Statistics
Matches: 157, Mismatches: 33, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
41 2 0.01
42 153 0.97
43 2 0.01
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.26
Consensus pattern (42 bp):
TAGGAACGGTCCCGCCTTCTGTAGTATCGATCATCAGGTGAG
Found at i:19012 original size:84 final size:84
Alignment explanation
Indices: 18868--19085 Score: 267
Period size: 84 Copynumber: 2.6 Consensus size: 84
18858 ATCATAGGAC
* * * * * * *
18868 CGGTCCCGCCTTCTATAGTATCGATCATTAGGTGAGTAGGAACGATCCCACCTTCTGTAGTATC-
1 CGGTCCCGCCTTCTGTAGTATCGATCATCAGGTGAGTAGGAACGGTCCCGCCTGCGGTAGTAACA
*
18932 GATCATCAGGTGTATAAGAA
66 G-TCATCAGGAGTATAAGAA
*
18952 CGGTCCCGCCTTCTGTAGTATAGATCATCAGGTGAGTAGGAACGGTCCCGCCTGCGGTAGTAACA
1 CGGTCCCGCCTTCTGTAGTATCGATCATCAGGTGAGTAGGAACGGTCCCGCCTGCGGTAGTAACA
* *
19017 GTCATCAGGAGTGTAAGAT
66 GTCATCAGGAGTATAAGAA
** * * * *
19036 CTATCACGCCTTCTGTAGTATCGACCATCAGGAGAGTAGGAACAGTCCCG
1 CGGTCCCGCCTTCTGTAGTATCGATCATCAGGTGAGTAGGAACGGTCCCG
19086 TCTTCTATAG
Statistics
Matches: 115, Mismatches: 18, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
84 114 0.99
85 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (84 bp):
CGGTCCCGCCTTCTGTAGTATCGATCATCAGGTGAGTAGGAACGGTCCCGCCTGCGGTAGTAACA
GTCATCAGGAGTATAAGAA
Found at i:22495 original size:3 final size:3
Alignment explanation
Indices: 22487--22528 Score: 75
Period size: 3 Copynumber: 13.7 Consensus size: 3
22477 TTACTAAAAT
22487 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ACTA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA AT
22529 TTTGAACATT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:23427 original size:21 final size:23
Alignment explanation
Indices: 23400--23451 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 23
23390 TATTTTCTTT
23400 ATTATTATATATATTT-TTTATTTA
1 ATTATTA-A-ATATTTATTTATTTA
23424 ATTATTTAAATATTTGATTTATTTA
1 ATTA-TTAAATATTT-ATTTATTTA
23449 ATT
1 ATT
23452 TCTTTCTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
23 6 0.24
24 5 0.20
25 14 0.56
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (23 bp):
ATTATTAAATATTTATTTATTTA
Found at i:23444 original size:25 final size:24
Alignment explanation
Indices: 23392--23451 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 24
23382 CTTAATTTTA
* *
23392 TTTTCTTT-ATTATTATATATATT
1 TTTTATTTAATTATTATAAATATT
23415 TTTTATTTAATTATT-TAAATATT
1 TTTTATTTAATTATTATAAATATT
23438 TGATTTATTTAATT
1 T--TTTATTTAATT
23452 TCTTTCTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 15 0.47
24 6 0.19
25 11 0.34
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (24 bp):
TTTTATTTAATTATTATAAATATT
Found at i:23620 original size:6 final size:6
Alignment explanation
Indices: 23609--23637 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
23599 CTATCTCTCC
23609 CACATT CACATT CACATT CACATT CACAT
1 CACATT CACATT CACATT CACATT CACAT
23638 GTTCATTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.31
Consensus pattern (6 bp):
CACATT
Found at i:24587 original size:31 final size:31
Alignment explanation
Indices: 24549--24610 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
24539 TGGCCTTGTG
24549 GTTTTTCAGGAATAGTTTTGTTTTCTCCATC
1 GTTTTTCAGGAATAGTTTTGTTTTCTCCATC
24580 GTTTTTCAGGAATAGTTTTGTTTTCTCCATC
1 GTTTTTCAGGAATAGTTTTGTTTTCTCCATC
24611 TTGGATGGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.52
Consensus pattern (31 bp):
GTTTTTCAGGAATAGTTTTGTTTTCTCCATC
Found at i:25307 original size:16 final size:16
Alignment explanation
Indices: 25265--25331 Score: 55
Period size: 16 Copynumber: 4.1 Consensus size: 16
25255 AAGTCAACGG
*
25265 TTCAATATTAAATTAA
1 TTCAAAATTAAATTAA
*
25281 -TCGAAACTTAAATTAA
1 TTC-AAAATTAAATTAA
*
25297 TTCAAAATTAAAATTGA
1 TTCAAAATT-AAATTAA
* * *
25314 TACAAATTTAAAATAA
1 TTCAAAATTAAATTAA
25330 TT
1 TT
25332 TAATCTTAAA
Statistics
Matches: 39, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
15 2 0.05
16 22 0.56
17 15 0.38
ACGTcount: A:0.52, C:0.07, G:0.03, T:0.37
Consensus pattern (16 bp):
TTCAAAATTAAATTAA
Found at i:39453 original size:107 final size:107
Alignment explanation
Indices: 39267--39462 Score: 356
Period size: 107 Copynumber: 1.8 Consensus size: 107
39257 CTTTTATTTA
* *
39267 AAAAATTGACAAATTAATTTTTATAGATTAGATTAAAGAATGAATTAATTATTTTATTAAAAATT
1 AAAAATTGACAAATTAATTTTTATAGATTAGATTAAAGAATAAACTAATTATTTTATTAAAAATT
*
39332 CATTCATTTTTTTGTCAAAAAATAGTTTTTACACATCAGCAT
66 CATCCATTTTTTTGTCAAAAAATAGTTTTTACACATCAGCAT
39374 AAAAATTGACAAATTAATTTTTATAGATTAGATTAAAGAATAAACTAATTATTTTATTAAAAATT
1 AAAAATTGACAAATTAATTTTTATAGATTAGATTAAAGAATAAACTAATTATTTTATTAAAAATT
*
39439 CATCCTTTTTTTTGTCAAAAAATA
66 CATCCATTTTTTTGTCAAAAAATA
39463 AATTTTGATG
Statistics
Matches: 85, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
107 85 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (107 bp):
AAAAATTGACAAATTAATTTTTATAGATTAGATTAAAGAATAAACTAATTATTTTATTAAAAATT
CATCCATTTTTTTGTCAAAAAATAGTTTTTACACATCAGCAT
Found at i:40710 original size:19 final size:19
Alignment explanation
Indices: 40688--40724 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
40678 TGAAAAGAGA
*
40688 TCCATAATTACAAAATAAC
1 TCCATAACTACAAAATAAC
40707 TCCATAACTACAAAATAA
1 TCCATAACTACAAAATAA
40725 AAATGTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.54, C:0.22, G:0.00, T:0.24
Consensus pattern (19 bp):
TCCATAACTACAAAATAAC
Found at i:45121 original size:31 final size:31
Alignment explanation
Indices: 45086--45144 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
45076 AGTAGCCCAA
*
45086 TGACTTAAAT-AAAAGCTTTCGAATAATTTAG
1 TGACTTAAATGAAAA-CTTTCAAATAATTTAG
*
45117 TGACTTAAATGAAAATTTTCAAATAATT
1 TGACTTAAATGAAAACTTTCAAATAATT
45145 CAGTATTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 21 0.84
32 4 0.16
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.37
Consensus pattern (31 bp):
TGACTTAAATGAAAACTTTCAAATAATTTAG
Found at i:52161 original size:30 final size:29
Alignment explanation
Indices: 52111--52167 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
52101 CTTATTCAAA
* * *
52111 AAAAAAAATCATTAACAGAAAGGAAAAGG
1 AAAAAAAATAATTAAAAGAAAAGAAAAGG
52140 AAAAAAAATAAGTTAAAAGAAAAGAAAA
1 AAAAAAAATAA-TTAAAAGAAAAGAAAA
52168 AAGAAGATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 10 0.42
30 14 0.58
ACGTcount: A:0.72, C:0.04, G:0.14, T:0.11
Consensus pattern (29 bp):
AAAAAAAATAATTAAAAGAAAAGAAAAGG
Found at i:59338 original size:20 final size:20
Alignment explanation
Indices: 59302--59339 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
59292 ATTTATGATT
*
59302 CCTTATTTCTATCTCATTAG
1 CCTTATTTCAATCTCATTAG
*
59322 CCTTATTTCAATTTCATT
1 CCTTATTTCAATCTCATT
59340 TCGTATTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.24, G:0.03, T:0.53
Consensus pattern (20 bp):
CCTTATTTCAATCTCATTAG
Found at i:59596 original size:16 final size:16
Alignment explanation
Indices: 59570--59609 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
59560 ATTCTATTAT
*
59570 ATATTTATATATTCTA
1 ATATATATATATTCTA
*
59586 TTATATATATATTCTA
1 ATATATATATATTCTA
59602 ATATATAT
1 ATATATAT
59610 TAGAATTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (16 bp):
ATATATATATATTCTA
Found at i:59629 original size:12 final size:12
Alignment explanation
Indices: 59571--59655 Score: 51
Period size: 12 Copynumber: 7.4 Consensus size: 12
59561 TTCTATTATA
59571 TATTTATATATT
1 TATTTATATATT
*
59583 CTA-TTATATATA
1 -TATTTATATATT
*
59595 TATTCTA-ATATA
1 TATT-TATATATT
*
59607 TA-TTAGA-ATT
1 TATTTATATATT
59617 TATTTATATATT
1 TATTTATATATT
59629 T-TATTA-AT-TT
1 TAT-TTATATATT
59639 T-TTTATATATTT
1 TATTTATATA-TT
59651 TATTT
1 TATTT
59656 CTAATATATT
Statistics
Matches: 59, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
9 3 0.05
10 12 0.20
11 11 0.19
12 26 0.44
13 7 0.12
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.62
Consensus pattern (12 bp):
TATTTATATATT
Found at i:59643 original size:21 final size:21
Alignment explanation
Indices: 59571--59654 Score: 80
Period size: 21 Copynumber: 3.8 Consensus size: 21
59561 TTCTATTATA
*
59571 TATTTATATATTCTATTATATAT
1 TATTTATATATTTTATTA-AT-T
* *
59594 ATATTCTAATATATATTA-GAATT
1 -TATT-T-ATATATTTTATTAATT
59617 TATTTATATATTTTATTAATT
1 TATTTATATATTTTATTAATT
*
59638 TTTTTATATATTTTATT
1 TATTTATATATTTTATT
59655 TCTAATATAT
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
20 9 0.18
21 21 0.41
22 4 0.08
23 1 0.02
24 6 0.12
25 2 0.04
26 8 0.16
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.62
Consensus pattern (21 bp):
TATTTATATATTTTATTAATT
Found at i:59704 original size:57 final size:56
Alignment explanation
Indices: 59604--59713 Score: 136
Period size: 57 Copynumber: 1.9 Consensus size: 56
59594 ATATTCTAAT
* *
59604 ATATATTAGAATTTATTTATATATTTTATTAATTTTTTTATATATTT-TATTTCTA
1 ATATATTAGAATTTATTTATATATTTTATTAATTTATTGATATATTTCTATTTCTA
*
59659 ATATATTAGAATATTATATTA-ATATTATT-TTTATATTATTGATATATTTCTATTT
1 ATATATTAGAAT-TTAT-TTATATATT-TTATTAAT-TTATTGATATATTTCTATTT
59714 TATTTATTTC
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
55 12 0.26
56 13 0.28
57 17 0.36
58 5 0.11
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.61
Consensus pattern (56 bp):
ATATATTAGAATTTATTTATATATTTTATTAATTTATTGATATATTTCTATTTCTA
Found at i:59729 original size:39 final size:39
Alignment explanation
Indices: 59686--59762 Score: 118
Period size: 39 Copynumber: 2.0 Consensus size: 39
59676 ATTAATATTA
*
59686 TTTTTATATTATTGATATATTTCTATTTTATTTATTTCC
1 TTTTTATATTATTGATATATTTCTATTTCATTTATTTCC
* * *
59725 TTTTTATATTATTTATCTATTTTTATTTCATTTATTTC
1 TTTTTATATTATTGATATATTTCTATTTCATTTATTTC
59763 ATTTGCATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.22, C:0.08, G:0.01, T:0.69
Consensus pattern (39 bp):
TTTTTATATTATTGATATATTTCTATTTCATTTATTTCC
Found at i:59766 original size:20 final size:19
Alignment explanation
Indices: 59685--59766 Score: 69
Period size: 19 Copynumber: 4.2 Consensus size: 19
59675 TATTAATATT
* *
59685 ATTTTTATATTATTGATAT-
1 ATTTTTAT-TTATTTATTTC
*
59704 ATTTCTATTTTATTTATTTC
1 ATTTTTA-TTTATTTATTTC
* *
59724 CTTTTTATATTATTTATCT-
1 ATTTTTAT-TTATTTATTTC
59743 ATTTTTATTTCATTTATTTC
1 ATTTTTATTT-ATTTATTTC
59763 ATTT
1 ATTT
59767 GCATTTAGAA
Statistics
Matches: 50, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
18 2 0.04
19 29 0.58
20 19 0.38
ACGTcount: A:0.23, C:0.07, G:0.01, T:0.68
Consensus pattern (19 bp):
ATTTTTATTTATTTATTTC
Found at i:60313 original size:2 final size:2
Alignment explanation
Indices: 60250--60295 Score: 76
Period size: 2 Copynumber: 23.0 Consensus size: 2
60240 NNNNNNNNNN
60250 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TCA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA
60292 TA TA
1 TA TA
60296 ATTTGATTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.02
2 39 0.93
3 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:61473 original size:2 final size:2
Alignment explanation
Indices: 61462--61497 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
61452 ATAGGCTATT
61462 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
61498 AATTTCAGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:80030 original size:30 final size:30
Alignment explanation
Indices: 79969--80033 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
79959 TTGAAATTAA
** * * *
79969 TTTATAATTTTTATGATAATAACTTATATT
1 TTTATAATTTTTAAAAGAATAAATTAAATT
*
79999 TTTATAATTTTTAAAAGATTAAATTAAATT
1 TTTATAATTTTTAAAAGAATAAATTAAATT
80029 TTTAT
1 TTTAT
80034 CCTTTCAAGA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (30 bp):
TTTATAATTTTTAAAAGAATAAATTAAATT
Found at i:81490 original size:15 final size:16
Alignment explanation
Indices: 81461--81490 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
81451 TTTTTCTGAT
81461 AATTTTTTAATAATTG
1 AATTTTTTAATAATTG
81477 AATTTTTTAA-AATT
1 AATTTTTTAATAATT
81491 TAAAATTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (16 bp):
AATTTTTTAATAATTG
Found at i:85164 original size:19 final size:19
Alignment explanation
Indices: 85139--85184 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
85129 ATTCAAAAAA
* *
85139 AAAAAAATTTATTTGTATTT
1 AAAAAAA-TTATTTATATTC
85159 AAAAAAATTATTTATATTC
1 AAAAAAATTATTTATATTC
85178 AAAAAAA
1 AAAAAAA
85185 AAAAAGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (19 bp):
AAAAAAATTATTTATATTC
Found at i:85185 original size:20 final size:20
Alignment explanation
Indices: 85138--85185 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
85128 TATTCAAAAA
*
85138 AAAAAAAATTTATTTGTATT
1 AAAAAAAATTTATTTATATT
*
85158 TAAAAAAA-TTATTTATATT
1 AAAAAAAATTTATTTATATT
85177 CAAAAAAAA
1 -AAAAAAAA
85186 AAAAGAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 10 0.42
20 14 0.58
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (20 bp):
AAAAAAAATTTATTTATATT
Found at i:86623 original size:3 final size:3
Alignment explanation
Indices: 86615--86641 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
86605 CATCAAAATA
86615 GCT GCT GCT GCT GCT GCT GCT GCT GCT
1 GCT GCT GCT GCT GCT GCT GCT GCT GCT
86642 ACTATAAAAT
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:0.00, C:0.33, G:0.33, T:0.33
Consensus pattern (3 bp):
GCT
Found at i:105262 original size:16 final size:16
Alignment explanation
Indices: 105238--105272 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
105228 ATATTAAAAT
*
105238 ATAATAAAATATTATA
1 ATAACAAAATATTATA
*
105254 ATAACAAAATATTGTA
1 ATAACAAAATATTATA
105270 ATA
1 ATA
105273 TTTAATTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (16 bp):
ATAACAAAATATTATA
Found at i:110507 original size:20 final size:20
Alignment explanation
Indices: 110482--110522 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
110472 ACTGATAGAA
110482 ATGTCAATGCTAATCGAGTT
1 ATGTCAATGCTAATCGAGTT
110502 ATGTCAATGCTAATCGAGTT
1 ATGTCAATGCTAATCGAGTT
110522 A
1 A
110523 AGACTCAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.34
Consensus pattern (20 bp):
ATGTCAATGCTAATCGAGTT
Found at i:112260 original size:7 final size:7
Alignment explanation
Indices: 112248--112297 Score: 73
Period size: 7 Copynumber: 7.0 Consensus size: 7
112238 AGAGCCAGAA
112248 ATTCTTG
1 ATTCTTG
112255 ATTCTTG
1 ATTCTTG
112262 ATTCTTG
1 ATTCTTG
112269 ATTCTTG
1 ATTCTTG
112276 ATTCTTG
1 ATTCTTG
*
112283 TTTTCTTG
1 -ATTCTTG
*
112291 CTTCTTG
1 ATTCTTG
112298 TTTTCTTTCT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
7 34 0.85
8 6 0.15
ACGTcount: A:0.10, C:0.16, G:0.14, T:0.60
Consensus pattern (7 bp):
ATTCTTG
Found at i:112290 original size:15 final size:15
Alignment explanation
Indices: 112256--112304 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
112246 AAATTCTTGA
*
112256 TTCTTGATTCTTG-A
1 TTCTTGATTCTTGTT
112270 TTCTTGATTCTTGTT
1 TTCTTGATTCTTGTT
*
112285 TTCTTGCTTCTTGTT
1 TTCTTGATTCTTGTT
112300 TTCTT
1 TTCTT
112305 TCTCAAATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
14 13 0.41
15 19 0.59
ACGTcount: A:0.06, C:0.16, G:0.12, T:0.65
Consensus pattern (15 bp):
TTCTTGATTCTTGTT
Found at i:117295 original size:290 final size:290
Alignment explanation
Indices: 116775--117354 Score: 1088
Period size: 290 Copynumber: 2.0 Consensus size: 290
116765 TTCAAAACAA
116775 CATTGATAACCCATTCATTAAGGACACATAGATATACCATTTGTACATGTCATTTTACCTTTAAA
1 CATTGATAACCCATTCATTAAGGACACATAGATATACCATTTGTACATGTCATTTTACCTTTAAA
*
116840 TAAAGTACTTAAGCTTGAAGTCTTCCAAGAGTGATGTGATGAGAGGTCCCTTGGCTTGATTCTAT
66 TAAAGTACTTAAGCTTGAAGTCTTCCAAGAGTGATGTGATGAGAGATCCCTTGGCTTGATTCTAT
*
116905 CCTCACTTAGCCTTTGTACCTACGCGTTAAGCCGGTGAAGGCTTAGTAAGTACTACAAGTGTCAT
131 CCTCACTTAGCCTTTGTACCTACGCGTTAAGCCAGTGAAGGCTTAGTAAGTACTACAAGTGTCAT
116970 TAATCATTCATCTTTTAATCACTCATTTCAAACTCATTCATATAATTGTTTATTCATGTAAAATA
196 TAATCATTCATCTTTTAATCACTCATTTCAAACTCATTCATATAATTGTTTATTCATGTAAAATA
117035 CATACCTTTTATGTATATAACATTTAACTT
261 CATACCTTTTATGTATATAACATTTAACTT
* * *
117065 CATTGATAACCCATTCATTAAGGACATATAGCTGTACCATTTGTACATGTCATTTTACCTTTAAA
1 CATTGATAACCCATTCATTAAGGACACATAGATATACCATTTGTACATGTCATTTTACCTTTAAA
* *
117130 TAAAGTACTTAAGCTTGAAGTCTTCCAAGAGTGATGTGATGAGAGATCCTTTGGCTTGATTTTAT
66 TAAAGTACTTAAGCTTGAAGTCTTCCAAGAGTGATGTGATGAGAGATCCCTTGGCTTGATTCTAT
*
117195 CCTCTCTTAGCCTTTGTACCTACGCGTTAAGCCAGTGAAGGCTTAGTAAGTACTACAAGTGTCAT
131 CCTCACTTAGCCTTTGTACCTACGCGTTAAGCCAGTGAAGGCTTAGTAAGTACTACAAGTGTCAT
117260 TAATCATTCATCTTTTAATCACTCATTTCAAACTCATTCATATAATTGTTTATTCATGTAAAATA
196 TAATCATTCATCTTTTAATCACTCATTTCAAACTCATTCATATAATTGTTTATTCATGTAAAATA
117325 CATACCTTTTATGTATATAACATTTAACTT
261 CATACCTTTTATGTATATAACATTTAACTT
117355 ACAGTAGTGT
Statistics
Matches: 282, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
290 282 1.00
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.38
Consensus pattern (290 bp):
CATTGATAACCCATTCATTAAGGACACATAGATATACCATTTGTACATGTCATTTTACCTTTAAA
TAAAGTACTTAAGCTTGAAGTCTTCCAAGAGTGATGTGATGAGAGATCCCTTGGCTTGATTCTAT
CCTCACTTAGCCTTTGTACCTACGCGTTAAGCCAGTGAAGGCTTAGTAAGTACTACAAGTGTCAT
TAATCATTCATCTTTTAATCACTCATTTCAAACTCATTCATATAATTGTTTATTCATGTAAAATA
CATACCTTTTATGTATATAACATTTAACTT
Found at i:117730 original size:23 final size:23
Alignment explanation
Indices: 117679--117731 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
117669 GTGCTGGGGA
117679 AACAGTAGGCACACACAGTGCAT
1 AACAGTAGGCACACACAGTGCAT
**
117702 TTCAGTAGGCACACACAGTGC-T
1 AACAGTAGGCACACACAGTGCAT
117724 GAACAGTA
1 -AACAGTA
117732 AGCGCGCTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 1 0.04
23 24 0.96
ACGTcount: A:0.36, C:0.25, G:0.23, T:0.17
Consensus pattern (23 bp):
AACAGTAGGCACACACAGTGCAT
Found at i:120881 original size:20 final size:20
Alignment explanation
Indices: 120858--120900 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
120848 TAAAATTTTA
*
120858 AATAT-AAACAACTAAAAAAT
1 AATATGAAACAAAT-AAAAAT
*
120878 AATATGAAATAAATAAAAAT
1 AATATGAAACAAATAAAAAT
120898 AAT
1 AAT
120901 TATTTTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (20 bp):
AATATGAAACAAATAAAAAT
Found at i:133636 original size:23 final size:25
Alignment explanation
Indices: 133610--133655 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
133600 CCAATTAGGG
133610 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
133633 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
133656 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:134658 original size:21 final size:21
Alignment explanation
Indices: 134632--134672 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
134622 CTGCATCAAG
134632 TTTTTTTGCAGTTTTTTAAAT
1 TTTTTTTGCAGTTTTTTAAAT
* *
134653 TTTTTTTTCATTTTTTTAAA
1 TTTTTTTGCAGTTTTTTAAA
134673 AAAACATGAA
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:0.20, C:0.05, G:0.05, T:0.71
Consensus pattern (21 bp):
TTTTTTTGCAGTTTTTTAAAT
Found at i:135859 original size:22 final size:22
Alignment explanation
Indices: 135802--135861 Score: 88
Period size: 21 Copynumber: 2.8 Consensus size: 22
135792 AAATTACAAA
135802 AAAAAATTC-AAAATAATTTTC
1 AAAAAATTCTAAAATAATTTTC
*
135823 AAAAAATT-TAAAATAGTTTTC
1 AAAAAATTCTAAAATAATTTTC
*
135844 AAGAAATTCTAAAATAAT
1 AAAAAATTCTAAAATAAT
135862 AATTTTTGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 26 0.76
22 8 0.24
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (22 bp):
AAAAAATTCTAAAATAATTTTC
Found at i:138965 original size:19 final size:18
Alignment explanation
Indices: 138924--138974 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
138914 AAATATTTAC
138924 AAAAATTCTAAAAAAAATA
1 AAAAATT-TAAAAAAAATA
* *
138943 AAAAATTTAAAGAATATA
1 AAAAATTTAAAAAAAATA
*
138961 TAAAAAGTTAAAAA
1 -AAAAATTTAAAAA
138975 TTCTAAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 9 0.33
19 18 0.67
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.24
Consensus pattern (18 bp):
AAAAATTTAAAAAAAATA
Found at i:151876 original size:30 final size:29
Alignment explanation
Indices: 151812--151876 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
151802 TTTTAAAATA
* *
151812 TAAAAAAGTATTAAAAATATAGAAAAGTG
1 TAAAAAAATATAAAAAATATAGAAAAGTG
* * *
151841 CAAAAAAATATAAAAATATATAGAAAATTT
1 TAAAAAAATATAAAAA-ATATAGAAAAGTG
151871 TAAAAA
1 TAAAAA
151877 TGTTATTACA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
29 13 0.45
30 16 0.55
ACGTcount: A:0.66, C:0.02, G:0.08, T:0.25
Consensus pattern (29 bp):
TAAAAAAATATAAAAAATATAGAAAAGTG
Found at i:170433 original size:43 final size:43
Alignment explanation
Indices: 170323--170559 Score: 375
Period size: 43 Copynumber: 5.5 Consensus size: 43
170313 GTGAATTCTT
170323 AATGGAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTATA
1 AATGGAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTATA
*
170366 AATGGAAAGACTTATGTCTCGGTTAGAGCATTAGATTGTTTATA
1 AATGG-AAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTATA
*
170410 AATGGAAGACTTATGTCTCGGTTAGAGCATTAGATTGTTTATA
1 AATGGAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTATA
*
170453 AATGAAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTATA
1 AATGGAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTATA
** * * *
170496 AATGGAAGACTTATGTCTCGACTAGAGCATAATATTATTTGTA
1 AATGGAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTATA
*
170539 AATGGAAGAACTTATGACTCG
1 AATGGAAG-ACTTATGTCTCG
170560 AACAGAGCAT
Statistics
Matches: 182, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
43 129 0.71
44 53 0.29
ACGTcount: A:0.33, C:0.10, G:0.22, T:0.35
Consensus pattern (43 bp):
AATGGAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTATA
Found at i:170567 original size:130 final size:130
Alignment explanation
Indices: 170323--170569 Score: 379
Period size: 130 Copynumber: 1.9 Consensus size: 130
170313 GTGAATTCTT
* *
170323 AATGGAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTATAAATGGAAAGACTTATGTCTCGG
1 AATGAAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTATAAATGGAAAGACTTATGTCTCGA
* * * * ***
170388 TTAGAGCATTAGATTGTTTATAAATGGAAGACTTATGTCTCGGTTAGAGCATTAGATTGTTTATA
66 CTAGAGCATAAGATTATTTATAAATGGAAGACTTATGACTCGAACAGAGCATTAGATTGTTTATA
170453 AATGAAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTATAAATGG-AAGACTTATGTCTCGA
1 AATGAAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTATAAATGGAAAGACTTATGTCTCGA
* *
170517 CTAGAGCATAATATTATTTGTAAATGGAAGAACTTATGACTCGAACAGAGCAT
66 CTAGAGCATAAGATTATTTATAAATGGAAG-ACTTATGACTCGAACAGAGCAT
170570 AAGGTTAATT
Statistics
Matches: 105, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
129 40 0.38
130 65 0.62
ACGTcount: A:0.34, C:0.11, G:0.22, T:0.34
Consensus pattern (130 bp):
AATGAAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTATAAATGGAAAGACTTATGTCTCGA
CTAGAGCATAAGATTATTTATAAATGGAAGACTTATGACTCGAACAGAGCATTAGATTGTTTATA
Found at i:174602 original size:28 final size:31
Alignment explanation
Indices: 174566--174630 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 31
174556 TCGAAGAGTA
174566 GAAA-GATTAAATTCTTAAA-A-ATAAAA-GT
1 GAAAGGATTAAATTC-TAAACATATAAAATGT
174594 -AAAGGATTAAATTCTAAACATATAAAATGT
1 GAAAGGATTAAATTCTAAACATATAAAATGT
174624 GAAAGGA
1 GAAAGGA
174631 CTTAGAGTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
27 7 0.22
28 11 0.34
29 6 0.19
30 2 0.06
31 6 0.19
ACGTcount: A:0.55, C:0.05, G:0.14, T:0.26
Consensus pattern (31 bp):
GAAAGGATTAAATTCTAAACATATAAAATGT
Found at i:175424 original size:7 final size:7
Alignment explanation
Indices: 175412--175448 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
175402 AATATTTATG
175412 TATTTTC
1 TATTTTC
175419 TATTTTC
1 TATTTTC
175426 TATTTTC
1 TATTTTC
175433 TATTTTC
1 TATTTTC
175440 TATTTTC
1 TATTTTC
175447 TA
1 TA
175449 GTCGCAGCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.16, C:0.14, G:0.00, T:0.70
Consensus pattern (7 bp):
TATTTTC
Found at i:187380 original size:3 final size:3
Alignment explanation
Indices: 187372--187396 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
187362 TTAAATGAAT
187372 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
187397 GGAGGGTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:187542 original size:20 final size:21
Alignment explanation
Indices: 187505--187544 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
187495 TTGACTGGTT
* *
187505 GGGGGCAAATGGGCTTTGGGA
1 GGGGGCAAATGAGATTTGGGA
187526 GGGGGC-AATGAGATTTGGG
1 GGGGGCAAATGAGATTTGGG
187545 CTTTGAGGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.20, C:0.07, G:0.53, T:0.20
Consensus pattern (21 bp):
GGGGGCAAATGAGATTTGGGA
Found at i:188578 original size:22 final size:22
Alignment explanation
Indices: 188550--188592 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
188540 TTGTAAAGAG
*
188550 TTTTATTGTTTCATAATTTTTT
1 TTTTATTGTTTCAAAATTTTTT
* *
188572 TTTTATTTTTTTAAAATTTTT
1 TTTTATTGTTTCAAAATTTTT
188593 ATGTTTTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTATTGTTTCAAAATTTTTT
Found at i:190756 original size:11 final size:11
Alignment explanation
Indices: 190730--190781 Score: 54
Period size: 11 Copynumber: 4.9 Consensus size: 11
190720 TTATTTTTCG
*
190730 ATAAAAATA-C
1 ATAAAAATATT
* *
190740 ATAAAATTTTT
1 ATAAAAATATT
190751 ATAAAAATATT
1 ATAAAAATATT
*
190762 ATAAAAATA-C
1 ATAAAAATATT
190772 ATAAAAATAT
1 ATAAAAATAT
190782 ATGCAAAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
10 16 0.47
11 18 0.53
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (11 bp):
ATAAAAATATT
Found at i:196922 original size:19 final size:20
Alignment explanation
Indices: 196898--196937 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
196888 TATAACGAAA
196898 TAATATAT-TTTATAAATAT
1 TAATATATATTTATAAATAT
*
196917 TAATATATATTTATAATTAT
1 TAATATATATTTATAAATAT
196937 T
1 T
196938 TTTATATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TAATATATATTTATAAATAT
Found at i:201368 original size:1 final size:1
Alignment explanation
Indices: 201362--201394 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
201352 TGATTTTAGC
201362 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
201395 NNNNNNNNNN
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:204844 original size:5 final size:6
Alignment explanation
Indices: 204813--204841 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
204803 GTCTTTTAGA
204813 AAGGGG AAGGGG AAGGGG AAGGGG AAGGG
1 AAGGGG AAGGGG AAGGGG AAGGGG AAGGG
204842 AAGTCACTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (6 bp):
AAGGGG
Found at i:205167 original size:16 final size:18
Alignment explanation
Indices: 205143--205179 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
205133 AATTTTATTA
*
205143 TTATTAATT-TAAA-ATT
1 TTATAAATTATAAAGATT
205159 TTATAAATTATAAAGATT
1 TTATAAATTATAAAGATT
205177 TTA
1 TTA
205180 AATAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 8 0.44
17 4 0.22
18 6 0.33
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
TTATAAATTATAAAGATT
Found at i:205404 original size:3 final size:3
Alignment explanation
Indices: 205396--205440 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
205386 CATTTTGGCT
205396 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
205441 CAAGATAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:205602 original size:22 final size:22
Alignment explanation
Indices: 205576--205628 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
205566 AGGTTTTCTA
205576 TTAAAATTATTATTTTAACATT
1 TTAAAATTATTATTTTAACATT
205598 TTAAAATTATTATTTTAACATT
1 TTAAAATTATTATTTTAACATT
205620 TTAAAATTA
1 TTAAAATTA
205629 AAAGAAATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (22 bp):
TTAAAATTATTATTTTAACATT
Found at i:206842 original size:7 final size:7
Alignment explanation
Indices: 206830--206872 Score: 59
Period size: 7 Copynumber: 6.1 Consensus size: 7
206820 TTTCTAACTT
206830 AATTCTC
1 AATTCTC
206837 AATTCTC
1 AATTCTC
206844 AATTCTC
1 AATTCTC
*
206851 AATTCTA
1 AATTCTC
* *
206858 AACTCTA
1 AATTCTC
206865 AATTCTC
1 AATTCTC
206872 A
1 A
206873 CTGTTTTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.35, C:0.26, G:0.00, T:0.40
Consensus pattern (7 bp):
AATTCTC
Found at i:206914 original size:31 final size:31
Alignment explanation
Indices: 206876--206949 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 31
206866 ATTCTCACTG
* * *
206876 TTTTATTTTTAATTGTCAATTCTCAATTTTT
1 TTTTATTTTAAATTCTAAATTCTCAATTTTT
206907 TTTTATTTTAAATTCTAAATTCTCAA-TTTT
1 TTTTATTTTAAATTCTAAATTCTCAATTTTT
206937 TTTT-TTTTAAATT
1 TTTTATTTTAAATT
206950 TTGTCTCTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 9 0.22
30 8 0.20
31 23 0.57
ACGTcount: A:0.26, C:0.08, G:0.01, T:0.65
Consensus pattern (31 bp):
TTTTATTTTAAATTCTAAATTCTCAATTTTT
Found at i:209333 original size:28 final size:29
Alignment explanation
Indices: 209301--209373 Score: 89
Period size: 28 Copynumber: 2.6 Consensus size: 29
209291 ATAAAATGTT
209301 TAAATTTTATATAAAAGT-AT-ATTAATCA
1 TAAATTTTATATAAAA-TAATCATTAATCA
* * *
209329 TAAATTTTAAATGAAATAATCCTTAATCA
1 TAAATTTTATATAAAATAATCATTAATCA
209358 TAAATTTTAT-TAAAAT
1 TAAATTTTATATAAAAT
209374 TATGATCTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
27 1 0.03
28 21 0.55
29 16 0.42
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.42
Consensus pattern (29 bp):
TAAATTTTATATAAAATAATCATTAATCA
Found at i:212105 original size:18 final size:18
Alignment explanation
Indices: 212078--212116 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
212068 AGGAGACTTT
*
212078 GGGCAAAGGAGCAGTCTC
1 GGGCAAAGGAACAGTCTC
*
212096 GGGCAGAGGAACAGTCTC
1 GGGCAAAGGAACAGTCTC
212114 GGG
1 GGG
212117 TGCCGAGGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.44, T:0.10
Consensus pattern (18 bp):
GGGCAAAGGAACAGTCTC
Found at i:215276 original size:19 final size:19
Alignment explanation
Indices: 215254--215298 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
215244 TTATATTAGG
215254 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
215273 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
215292 ATTTAAT
1 ATTTAAT
215299 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:216123 original size:22 final size:22
Alignment explanation
Indices: 216096--216138 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
216086 TGGTCTTCCC
216096 TATTTTCTATTT-CTTTTAATTT
1 TATTTTCT-TTTACTTTTAATTT
*
216118 TATTTTCTTTTATTTTTAATT
1 TATTTTCTTTTACTTTTAATT
216139 CTGTTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (22 bp):
TATTTTCTTTTACTTTTAATTT
Found at i:216126 original size:16 final size:16
Alignment explanation
Indices: 216105--216154 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
216095 CTATTTTCTA
216105 TTTCTTTTAATTTTAT
1 TTTCTTTTAATTTTAT
*
216121 TTTCTTTTATTTTTA-
1 TTTCTTTTAATTTTAT
*
216136 ATTCTGTTT-ATTTTAT
1 TTTCT-TTTAATTTTAT
216152 TTT
1 TTT
216155 TCCTTAGATC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 9 0.32
16 19 0.68
ACGTcount: A:0.16, C:0.06, G:0.02, T:0.76
Consensus pattern (16 bp):
TTTCTTTTAATTTTAT
Found at i:221166 original size:19 final size:18
Alignment explanation
Indices: 221119--221166 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
221109 AAAATATTCT
**
221119 AAAAAATCATTAAAATTTT
1 AAAAAAT-ATTAAAATTAA
*
221138 AAATAATATTAAAATTCAA
1 AAAAAATATTAAAATT-AA
221157 AAAAAATATT
1 AAAAAATATT
221167 TTAATTATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAAAATATTAAAATTAA
Found at i:221716 original size:15 final size:15
Alignment explanation
Indices: 221677--221708 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
221667 TTTTTTCATT
*
221677 TTATATTTTTAAAAA
1 TTATAATTTTAAAAA
221692 TTATAATTTTAAAAA
1 TTATAATTTTAAAAA
221707 TT
1 TT
221709 TTTATTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTATAATTTTAAAAA
Found at i:221717 original size:16 final size:16
Alignment explanation
Indices: 221674--221717 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
221664 TATTTTTTTC
221674 ATTTTATATTTTTAAAA
1 ATTTT-TATTTTTAAAA
* *
221691 A-TTATAATTTTAAAA
1 ATTTTTATTTTTAAAA
221706 ATTTTTATTTTT
1 ATTTTTATTTTT
221718 TTAATCGACA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
15 11 0.50
16 10 0.45
17 1 0.05
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTTTATTTTTAAAA
Found at i:227474 original size:10 final size:10
Alignment explanation
Indices: 227446--227533 Score: 58
Period size: 10 Copynumber: 9.0 Consensus size: 10
227436 ATTTAAAATT
227446 TTATAAAAAA
1 TTATAAAAAA
*
227456 TCATAAAAAAA
1 TTAT-AAAAAA
*
227467 TTATAAAATA
1 TTATAAAAAA
*
227477 -TAT-AGAAA
1 TTATAAAAAA
* *
227485 TAAAAAAAAA
1 TTATAAAAAA
227495 TTAT--AAAA
1 TTATAAAAAA
* *
227503 TTTTATAAAA
1 TTATAAAAAA
*
227513 TCATAAGAAAA
1 TTATAA-AAAA
227524 TTATAAAAAA
1 TTATAAAAAA
227534 GGTAAAGAAA
Statistics
Matches: 57, Mismatches: 15, Indels: 12
0.68 0.18 0.14
Matches are distributed among these distances:
8 10 0.18
9 4 0.07
10 25 0.44
11 18 0.32
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (10 bp):
TTATAAAAAA
Found at i:227478 original size:28 final size:29
Alignment explanation
Indices: 227446--227531 Score: 104
Period size: 28 Copynumber: 3.0 Consensus size: 29
227436 ATTTAAAATT
227446 TTATAAAAAATCATAAAAAAATTATAAAA
1 TTATAAAAAATCATAAAAAAATTATAAAA
* *
227475 -TATATAGAAAT-AAAAAAAAATTATAAAA
1 TTATA-AAAAATCATAAAAAAATTATAAAA
* * *
227503 TTTTATAAAATCATAAGAAAATTATAAAA
1 TTATAAAAAATCATAAAAAAATTATAAAA
227532 AAGGTAAAGA
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
28 24 0.51
29 23 0.49
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.29
Consensus pattern (29 bp):
TTATAAAAAATCATAAAAAAATTATAAAA
Found at i:227524 original size:29 final size:29
Alignment explanation
Indices: 227439--227531 Score: 118
Period size: 29 Copynumber: 3.2 Consensus size: 29
227429 TAGAAAGATT
227439 TAAAATTTTATAAAAAATCATAAAAAAATTA
1 TAAAATTTTAT--AAAATCATAAAAAAATTA
* *
227470 TAAAA-TATATAGAAAT-AAAAAAAAATTA
1 TAAAATTTTATA-AAATCATAAAAAAATTA
*
227498 TAAAATTTTATAAAATCATAAGAAAATTA
1 TAAAATTTTATAAAATCATAAAAAAATTA
227527 TAAAA
1 TAAAA
227532 AAGGTAAAGA
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
28 21 0.39
29 24 0.44
30 4 0.07
31 5 0.09
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (29 bp):
TAAAATTTTATAAAATCATAAAAAAATTA
Found at i:227543 original size:59 final size:58
Alignment explanation
Indices: 227439--227550 Score: 154
Period size: 59 Copynumber: 1.9 Consensus size: 58
227429 TAGAAAGATT
* *
227439 TAAAATTTTATAAAAAATCATAAAAAAATTATAAAATATATAGAAATAAAAAAAAATTA
1 TAAAATTTTAT-AAAAATCATAAAAAAATTATAAAAAATAAAGAAATAAAAAAAAATTA
* *
227498 TAAAATTTTAT-AAAATCATAAGAAAATTATAAAAAAGGTAAAGAAATATAAAA
1 TAAAATTTTATAAAAATCATAAAAAAATTATAAAAAA--TAAAGAAATAAAAAA
227551 TTCGTAAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
57 23 0.49
59 24 0.51
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.28
Consensus pattern (58 bp):
TAAAATTTTATAAAAATCATAAAAAAATTATAAAAAATAAAGAAATAAAAAAAAATTA
Found at i:229233 original size:27 final size:29
Alignment explanation
Indices: 229182--229237 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
229172 ACCGCTTCAA
229182 ATTTTTATATTAATATAACTAATATAATT
1 ATTTTTATATTAATATAACTAATATAATT
229211 ATTTTTAT-TTAATATTAA-T-ATATAATT
1 ATTTTTATATTAATA-TAACTAATATAATT
229238 TAAATTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 8 0.31
28 7 0.27
29 11 0.42
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (29 bp):
ATTTTTATATTAATATAACTAATATAATT
Found at i:234343 original size:23 final size:24
Alignment explanation
Indices: 234292--234343 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
234282 GATGAGTCAA
* *
234292 AATT-AAATTATAATTTTTACGAT
1 AATTAAAAATATAATTTTTACAAT
234315 AA-TAAAAATATAATTTTTA-AAT
1 AATTAAAAATATAATTTTTACAAT
234337 AATTAAA
1 AATTAAA
234344 TCAAAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
22 5 0.20
23 20 0.80
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (24 bp):
AATTAAAAATATAATTTTTACAAT
Found at i:241381 original size:22 final size:22
Alignment explanation
Indices: 241353--241399 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
241343 TCTAATAACG
241353 ATTTAATCTAAAATGTTGACAA
1 ATTTAATCTAAAATGTTGACAA
** *
241375 ATTTAATCTTTAATGTTTACAA
1 ATTTAATCTAAAATGTTGACAA
241397 ATT
1 ATT
241400 CAAAGATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.45
Consensus pattern (22 bp):
ATTTAATCTAAAATGTTGACAA
Found at i:242625 original size:20 final size:19
Alignment explanation
Indices: 242596--242642 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
242586 TTCATCTCTC
242596 TAAAAAATTTA-AAAGAAAT
1 TAAAAAATTTATAAA-AAAT
*
242615 TCAAAATATTTATAAAAAAT
1 T-AAAAAATTTATAAAAAAT
242635 TAAAAAAT
1 TAAAAAAT
242643 ATCAAAAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 7 0.29
20 14 0.58
21 3 0.12
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (19 bp):
TAAAAAATTTATAAAAAAT
Found at i:242868 original size:188 final size:184
Alignment explanation
Indices: 242535--242911 Score: 480
Period size: 188 Copynumber: 2.0 Consensus size: 184
242525 CAGGATTCAC
* * *
242535 TTGAATAATTTAAATAATTCGGGTATTTTTCAATTTTAAAAAATAAACAAATTCATCTCTCTAAA
1 TTGAATAATTTAAATAATTCAGATATTTTTCAATTTTAAAAAATAAACAAATTAATCTCTCTAAA
*
242600 AAATTTAAAAGAAATTCAAAATATTTATAAAAAATTAAAAAATATCAAAAACTACATAAAATTCT
66 AAATTTAAAAGAAATTCAAAATATTTATAAAAAATTAAAAAAAATCAAAAACTACATAAAATTCT
* *
242665 TAAAAGTTATAGAAATTATAAATA-TATTTTT-AAAAAATACAAAATGATAACT
131 TAAAAGTTATAGAAATTATAAATATTATTTTTAAAAAAATAAAAAATGATAAAT
* **
242717 TTGAATAATTTAAATAATTCAGATATCTTTTTCTATTTT-AAAAATAAGTAAATTAATC-CATCT
1 TTGAATAATTTAAATAATTCAGATA--TTTTTCAATTTTAAAAAATAAACAAATTAATCTC-TCT
** *
242780 AAAATTTTTTTAAAA-AAATTCAAAATATTTAT-AAAAATTAAAAAAAAAAAAATCAAAAATTAC
63 AAAA--AATTTAAAAGAAATTCAAAATATTTATAAAAAATT-----AAAAAAAATCAAAAACTAC
*
242843 ATAAAATTCTTACAAAG-TATAGAAATTATAAATATTTTTTTTTAAAAAAATAAAAAATGATAAA
121 ATAAAATTCTTA-AAAGTTATAGAAATTATAAATA-TTATTTTTAAAAAAATAAAAAATGATAAA
242907 T
184 T
242908 TTGA
1 TTGA
242912 GTCATATTAT
Statistics
Matches: 168, Mismatches: 13, Indels: 19
0.84 0.06 0.09
Matches are distributed among these distances:
182 24 0.14
183 30 0.18
184 28 0.17
185 7 0.04
188 46 0.27
189 4 0.02
190 6 0.04
191 23 0.14
ACGTcount: A:0.53, C:0.07, G:0.04, T:0.36
Consensus pattern (184 bp):
TTGAATAATTTAAATAATTCAGATATTTTTCAATTTTAAAAAATAAACAAATTAATCTCTCTAAA
AAATTTAAAAGAAATTCAAAATATTTATAAAAAATTAAAAAAAATCAAAAACTACATAAAATTCT
TAAAAGTTATAGAAATTATAAATATTATTTTTAAAAAAATAAAAAATGATAAAT
Found at i:243554 original size:12 final size:12
Alignment explanation
Indices: 243537--243561 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
243527 AACAAATAAT
243537 TATATTTATTTA
1 TATATTTATTTA
243549 TATATTTATTTA
1 TATATTTATTTA
243561 T
1 T
243562 TTAAATGTAC
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TATATTTATTTA
Found at i:244734 original size:5 final size:5
Alignment explanation
Indices: 244693--244732 Score: 73
Period size: 5 Copynumber: 8.2 Consensus size: 5
244683 ATGGTGTATC
244693 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A-AAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A
244733 AAGGAGTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.11
5 31 0.89
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
ATAAA
Found at i:248069 original size:32 final size:31
Alignment explanation
Indices: 248003--248069 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
247993 TATATTTTGA
*
248003 GTGAACAAAATGAAAGTGACTTAAAAGTTAG
1 GTGAACAAAATGAAAATGACTTAAAAGTTAG
* * * *
248034 GTGATCAAAATGAAAATGCCTTTGAAAGTTGG
1 GTGAACAAAATGAAAATGAC-TTAAAAGTTAG
248066 GTGA
1 GTGA
248070 CCAACTAAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 17 0.57
32 13 0.43
ACGTcount: A:0.42, C:0.07, G:0.25, T:0.25
Consensus pattern (31 bp):
GTGAACAAAATGAAAATGACTTAAAAGTTAG
Found at i:257262 original size:5 final size:5
Alignment explanation
Indices: 257252--257283 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
257242 AAAGAGAACG
257252 AAAA- AAAA- AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
257284 GGTGATGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 8 0.30
5 19 0.70
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (5 bp):
AAAAT
Found at i:268588 original size:6 final size:6
Alignment explanation
Indices: 268577--268608 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
268567 GAGAGAGGAA
268577 GGGTCG GGGTCG GGGTCG GGGTCG GGGTCG GG
1 GGGTCG GGGTCG GGGTCG GGGTCG GGGTCG GG
268609 TCCGAACGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.16, G:0.69, T:0.16
Consensus pattern (6 bp):
GGGTCG
Found at i:284796 original size:22 final size:22
Alignment explanation
Indices: 284763--284814 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
284753 ATGGTTGACA
*
284763 TGGCAATGACGTAGCGCTGATG
1 TGGCGATGACGTAGCGCTGATG
* * * *
284785 TGGTGATGACGTGGTGTTGATG
1 TGGCGATGACGTAGCGCTGATG
284807 TGGCGATG
1 TGGCGATG
284815 CTGACGTGGC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.17, C:0.12, G:0.42, T:0.29
Consensus pattern (22 bp):
TGGCGATGACGTAGCGCTGATG
Found at i:287396 original size:26 final size:26
Alignment explanation
Indices: 287367--287424 Score: 116
Period size: 26 Copynumber: 2.2 Consensus size: 26
287357 CCTCATATGA
287367 GGCCAATAGTAACATTCCTCCAAAAG
1 GGCCAATAGTAACATTCCTCCAAAAG
287393 GGCCAATAGTAACATTCCTCCAAAAG
1 GGCCAATAGTAACATTCCTCCAAAAG
287419 GGCCAA
1 GGCCAA
287425 CGTATGGTGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.38, C:0.28, G:0.17, T:0.17
Consensus pattern (26 bp):
GGCCAATAGTAACATTCCTCCAAAAG
Found at i:301988 original size:31 final size:28
Alignment explanation
Indices: 301944--302001 Score: 71
Period size: 31 Copynumber: 2.0 Consensus size: 28
301934 TTGTCCTTTG
*
301944 TTTGTTATCTTTCTGCTACATTTTAATTTCA
1 TTTGTAATCTTTCT-CT--ATTTTAATTTCA
*
301975 TTTGTAATGTTTCTCTATTTTAATTTC
1 TTTGTAATCTTTCTCTATTTTAATTTC
302002 TAATAAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 11 0.44
30 2 0.08
31 12 0.48
ACGTcount: A:0.19, C:0.14, G:0.07, T:0.60
Consensus pattern (28 bp):
TTTGTAATCTTTCTCTATTTTAATTTCA
Found at i:307471 original size:58 final size:58
Alignment explanation
Indices: 307409--307544 Score: 141
Period size: 59 Copynumber: 2.3 Consensus size: 58
307399 CTCGGGGAGC
* * * * *
307409 AAAATGGTAATTTTGGGAAAATTTGGTG-TTAAAAA-TGACATTTTAGACATCCGACGGT
1 AAAATGGTAATTTTAGAAAAAATCGG-GATTAAAAACAGA-ATTTTAGACATCCGACGGT
* * * *
307467 AAAATGATAATTTTTAGAAAAAATCGGGATTAAAAACAGAATTTTGGACTTCCGAGGGT
1 AAAATGGTAA-TTTTAGAAAAAATCGGGATTAAAAACAGAATTTTAGACATCCGACGGT
*
307526 AAAATGGTAATTTTTGAAA
1 AAAATGGTAATTTTAGAAA
307545 GTTTCGGGTC
Statistics
Matches: 64, Mismatches: 11, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
58 18 0.28
59 44 0.69
60 2 0.03
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.32
Consensus pattern (58 bp):
AAAATGGTAATTTTAGAAAAAATCGGGATTAAAAACAGAATTTTAGACATCCGACGGT
Found at i:307558 original size:29 final size:29
Alignment explanation
Indices: 307522--307728 Score: 213
Period size: 30 Copynumber: 7.0 Consensus size: 29
307512 GGACTTCCGA
* *
307522 GGGT-AAAATGGTAATTTTTGAAAGTTT-C
1 GGGTAAAAAT-GTAATTTTTGGAAGTTTAG
* *
307550 GGGTCAAAAATGGAATTTTTGGAATTTTAAG
1 GGGT-AAAAATGTAATTTTTGGAAGTTT-AG
* * *
307581 GGGT-AAAATAGTAATTTTCGGAAATTTTG
1 GGGTAAAAAT-GTAATTTTTGGAAGTTTAG
* * *
307610 GTGTCAAAATTTGAATTTTTGGAAGTTTGAG
1 GGGTAAAAATGT-AATTTTTGGAAGTTT-AG
307641 GGGTAAAAATGTAATTTTTGGAAGTTTTAG
1 GGGTAAAAATGTAATTTTTGGAAG-TTTAG
* *
307671 GGTTAAAAATGGAATTTTTGGAAGTTTAG
1 GGGTAAAAATGTAATTTTTGGAAGTTTAG
307700 GGGTAAAAATGTAATTTTTGGATAGTTTA
1 GGGTAAAAATGTAATTTTTGGA-AGTTTA
307729 AGGACCTCCA
Statistics
Matches: 149, Mismatches: 20, Indels: 18
0.80 0.11 0.10
Matches are distributed among these distances:
28 4 0.03
29 49 0.33
30 79 0.53
31 17 0.11
ACGTcount: A:0.33, C:0.02, G:0.26, T:0.39
Consensus pattern (29 bp):
GGGTAAAAATGTAATTTTTGGAAGTTTAG
Found at i:307727 original size:60 final size:59
Alignment explanation
Indices: 307522--307727 Score: 256
Period size: 60 Copynumber: 3.5 Consensus size: 59
307512 GGACTTCCGA
* * * *
307522 GGGTAAAATGGTAATTTTTGAAAGTTTCGGGTCAAAAATGGAATTTTTGGAATTTTAAG
1 GGGTAAAATAGTAATTTTTGGAAGTTTTGGGTCAAAAATGGAATTTTTGGAAGTTTAAG
* * * * *
307581 GGGTAAAATAGTAATTTTCGGAAATTTTGGTGTCAAAATTTGAATTTTTGGAAGTTTGAG
1 GGGTAAAATAGTAATTTTTGGAAGTTTTGG-GTCAAAAATGGAATTTTTGGAAGTTTAAG
*
307641 GGGTAAAA-ATGTAATTTTTGGAAGTTTTAGGGTTAAAAATGGAATTTTTGGAAGTTT-AG
1 GGGTAAAATA-GTAATTTTTGGAAGTTTT-GGGTCAAAAATGGAATTTTTGGAAGTTTAAG
307700 GGGTAAAA-ATGTAATTTTTGGATAGTTT
1 GGGTAAAATA-GTAATTTTTGGA-AGTTT
307728 AAGGACCTCC
Statistics
Matches: 129, Mismatches: 14, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
59 50 0.39
60 77 0.60
61 2 0.02
ACGTcount: A:0.33, C:0.02, G:0.26, T:0.39
Consensus pattern (59 bp):
GGGTAAAATAGTAATTTTTGGAAGTTTTGGGTCAAAAATGGAATTTTTGGAAGTTTAAG
Found at i:325978 original size:27 final size:26
Alignment explanation
Indices: 325948--325999 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
325938 TCAATTAATG
**
325948 ATTGTTTCCTTTGATCCTCCTTTTAAA
1 ATTGTTTCCTCCGATCCT-CTTTTAAA
325975 ATTGTTTCCTCCGATCCTCTTTTAA
1 ATTGTTTCCTCCGATCCTCTTTTAA
326000 TAAAATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.17, C:0.25, G:0.08, T:0.50
Consensus pattern (26 bp):
ATTGTTTCCTCCGATCCTCTTTTAAA
Found at i:326846 original size:200 final size:198
Alignment explanation
Indices: 326543--327128 Score: 860
Period size: 196 Copynumber: 2.9 Consensus size: 198
326533 TTAGACCTAC
* * * * * *
326543 GCTC-AAAGCGAGCGAAATCTTCAAACCCCAGCTTCCTGATGAGATACCGAGAAGCAGGTCGAAG
1 GCTCGAAA-CGAGCGAAACCTTTAAAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTGGAAG
326607 CAATAAATGGTTAGCTTCCTGATGAGATA-TGGAGAAGTGAACCTAATTCATCTTCCTGATGAGA
65 CAATAAATGGTTAGCTTCCTGATGAGATACTGG-GAAGTGAACC-AATTC-TCTTCCTGATGAGA
* *
326671 TACAGAGAAGCAGATTGAAACGGTGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAGATCC
127 TACAGAGAAGCAGATTGAAACAGTGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAGACCC
326736 AAACGAG
192 AAACGAG
*
326743 GCTCGAAACGAGCGAAACCTTTAAAACCCAGCTTCTTGATGAGACACTGAGAAGCAGGTGGAAGC
1 GCTCGAAACGAGCGAAACCTTTAAAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTGGAAGC
* * * * *
326808 AATAAATGGTTAGCTTCCTAATGAGATACTAGGAAGTGAACCAAAT-TCGT-CTGATGAGATATA
66 AATAAATGGTTAGCTTCCTGATGAGATACTGGGAAGTGAACCAATTCTCTTCCTGATGAGATACA
* *
326871 GAGAAGCGGATTGAAACAGTGATGGGATCATCTTCCTGATGAGACATTGAGAAGAAGACCCAAAC
131 GAGAAGCAGATTGAAACAGTGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAAC
326936 GAG
196 GAG
* *
326939 GCTCGAAACGAGCGAAACCTTTAAAACCCAGCTTCCTAATGAGACACTGAGAAGCAGGTGAAAGC
1 GCTCGAAACGAGCGAAACCTTTAAAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTGGAAGC
327004 AATAAATGGTTAGCTTCCTGATGAGATACTGGGAAGTGAACCAAATTCGTCTTCCTGATGAGATA
66 AATAAATGGTTAGCTTCCTGATGAGATACTGGGAAGTGAACC-AATTC-TCTTCCTGATGAGATA
* * *
327069 CAGAGAAGCAGATTGAAACAAGCGACGCGG-TCAT-TCTCCTGATGAGATACTGAGAAGAAG
129 CAGAGAAGCAGATTGAAAC-AGTGATG-GGATCATCT-TCCTGATGAGACACTGAGAAGAAG
327129 GCCAAGTCAA
Statistics
Matches: 348, Mismatches: 29, Indels: 17
0.88 0.07 0.04
Matches are distributed among these distances:
196 178 0.51
197 6 0.02
199 6 0.02
200 120 0.34
201 36 0.10
202 2 0.01
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.21
Consensus pattern (198 bp):
GCTCGAAACGAGCGAAACCTTTAAAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTGGAAGC
AATAAATGGTTAGCTTCCTGATGAGATACTGGGAAGTGAACCAATTCTCTTCCTGATGAGATACA
GAGAAGCAGATTGAAACAGTGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAAC
GAG
Found at i:327462 original size:17 final size:17
Alignment explanation
Indices: 327440--327510 Score: 70
Period size: 17 Copynumber: 4.1 Consensus size: 17
327430 CATACTCCCT
327440 TTAAATTTATTTTAAAA
1 TTAAATTTATTTTAAAA
* *
327457 TTAAATTTGTTTAAAAA
1 TTAAATTTATTTTAAAA
* **
327474 TTTAAATTTAATTTAAGT
1 -TTAAATTTATTTTAAAA
* *
327492 TTAAAATTATTTTCAAA
1 TTAAATTTATTTTAAAA
327509 TT
1 TT
327511 TAGAGTTTAA
Statistics
Matches: 41, Mismatches: 12, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
17 29 0.71
18 12 0.29
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Found at i:327510 original size:35 final size:35
Alignment explanation
Indices: 327439--327512 Score: 85
Period size: 35 Copynumber: 2.1 Consensus size: 35
327429 CCATACTCCC
* * *
327439 TTTAAATTTATTTTAAAATTAAATTTGTTTAAAAA
1 TTTAAATTTAATTTAAAATTAAAATTATTTAAAAA
** **
327474 TTTAAATTTAATTTAAGTTTAAAATTATTTTCAAA
1 TTTAAATTTAATTTAAAATTAAAATTATTTAAAAA
327509 TTTA
1 TTTA
327513 GAGTTTAAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (35 bp):
TTTAAATTTAATTTAAAATTAAAATTATTTAAAAA
Found at i:328190 original size:18 final size:19
Alignment explanation
Indices: 328156--328197 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
328146 AAAACGTTTC
*
328156 AATAACTTTTATTAATATT
1 AATAACTGTTATTAATATT
328175 AATAACTGTT-TTAATATT
1 AATAACTGTTATTAATATT
328193 AATAA
1 AATAA
328198 TAATACTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (19 bp):
AATAACTGTTATTAATATT
Found at i:328296 original size:7 final size:7
Alignment explanation
Indices: 328265--328305 Score: 52
Period size: 7 Copynumber: 6.3 Consensus size: 7
328255 AATGTTTTGA
328265 TAATAA-
1 TAATAAT
328271 TAATAA-
1 TAATAAT
328277 TAAT-AT
1 TAATAAT
328283 TAATAAT
1 TAATAAT
*
328290 TATTAAT
1 TAATAAT
328297 TAATAAT
1 TAATAAT
328304 TA
1 TA
328306 CTAAAAAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
5 1 0.03
6 14 0.45
7 16 0.52
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TAATAAT
Found at i:328699 original size:21 final size:23
Alignment explanation
Indices: 328670--328712 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
328660 AGGAAAAATC
*
328670 GTTTAGATCTAGGC-TAGATCTG
1 GTTTAGATCTAGCCTTAGATCTG
328692 GTTT-GATCTAGCCTTAGATCT
1 GTTTAGATCTAGCCTTAGATCT
328713 ATTTTTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.21, C:0.16, G:0.23, T:0.40
Consensus pattern (23 bp):
GTTTAGATCTAGCCTTAGATCTG
Found at i:329556 original size:29 final size:28
Alignment explanation
Indices: 329514--329927 Score: 316
Period size: 29 Copynumber: 14.0 Consensus size: 28
329504 GAGGTCCCTA
329514 AACTATCCAAAAATTACCATTTTACCCACG
1 AACT-TCCAAAAATTACCATTTTACCC-CG
* *
329544 AACTTCGAAAAATT-CCATTTTTGACCTCG
1 AACTTCCAAAAATTACCA-TTTT-ACCCCG
*
329573 AACCTTCCAAAAATTACTATTTTACCCCTG
1 AA-CTTCCAAAAATTACCATTTTACCCC-G
329603 AACTTCCAAAAATTACCATTTTACCCTCG
1 AACTTCCAAAAATTACCATTTTACCC-CG
*
329632 AACTTCCAAAAA-TCCCATTTTGACCCCG
1 AACTTCCAAAAATTACCATTTT-ACCCCG
* *
329660 AACCTTCCAAAATTTACTATTTTACCCCCG
1 AA-CTTCCAAAAATTACCATTTTA-CCCCG
** *
329690 AACTTCC-AAAGGTCCCATTTTTTTACCCCG
1 AACTTCCAAAAATTACCA---TTTTACCCCG
*
329720 AACCTTCGAAAAATTACCATTTTACCCTCG
1 AA-CTTCCAAAAATTACCATTTTACCC-CG
* * * *
329750 AACTTTCAAAAA-TCCCATTTTTGACTCTG
1 AACTTCCAAAAATTACCA-TTTT-ACCCCG
*
329779 AACCTTCCAAGAATTACCATTTTACCCCCG
1 AA-CTTCCAAAAATTACCATTTTA-CCCCG
* * *
329809 AACTTCC-AAAAGTCCCATTTTTGATCCCG
1 AACTTCCAAAAATTACCA-TTTT-ACCCCG
*
329838 AACCTTCCAAAAAATACCATTTTACCCCCTCG
1 AA-CTTCCAAAAATTACCATTTTA--CCC-CG
* * **
329870 AACTTCCAAAAAATCCCATTTTTAACCCTA
1 AACTTCCAAAAATTACCA-TTTT-ACCCCG
* *
329900 AACCTTCCAAAAAATACCCTTTTACCCC
1 AA-CTTCCAAAAATTACCATTTTACCCC
329928 CGAATGTTTG
Statistics
Matches: 312, Mismatches: 41, Indels: 63
0.75 0.10 0.15
Matches are distributed among these distances:
28 32 0.10
29 120 0.38
30 87 0.28
31 57 0.18
32 15 0.05
33 1 0.00
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (28 bp):
AACTTCCAAAAATTACCATTTTACCCCG
Found at i:329614 original size:59 final size:57
Alignment explanation
Indices: 329514--329931 Score: 344
Period size: 59 Copynumber: 7.0 Consensus size: 57
329504 GAGGTCCCTA
*
329514 AACTATCCAAAAATTACCATTTTACCCACGAACTTCGAAAAATT-CCATTTTTGA-CCTCG
1 AACT-TCCAAAAATTACCATTTTACCC-CGAACTTCCAAAAATTACCA-TTTT-ACCCTCG
*
329573 AACCTTCCAAAAATTACTATTTTACCCCTGAACTTCCAAAAATTACCATTTTACCCTCG
1 AA-CTTCCAAAAATTACCATTTTACCCC-GAACTTCCAAAAATTACCATTTTACCCTCG
* * * *
329632 AACTTCCAAAAA-TCCCATTTTGACCCCGAACCTTCCAAAATTTACTATTTTACCCCCG
1 AACTTCCAAAAATTACCATTTT-ACCCCGAA-CTTCCAAAAATTACCATTTTACCCTCG
** * *
329690 AACTTCC-AAAGGTCCCATTTTTTTACCCCGAACCTTCGAAAAATTACCATTTTACCCTCG
1 AACTTCCAAAAATTACCA---TTTTACCCCGAA-CTTCCAAAAATTACCATTTTACCCTCG
* * * * * *
329750 AACTTTCAAAAA-TCCCATTTTTGACTCTGAACCTTCCAAGAATTACCATTTTACCCCCG
1 AACTTCCAAAAATTACCA-TTTT-ACCCCGAA-CTTCCAAAAATTACCATTTTACCCTCG
* * * *
329809 AACTTCC-AAAAGTCCCATTTTTGATCCCGAACCTTCCAAAAAATACCATTTTACCCCCTCG
1 AACTTCCAAAAATTACCA-TTTT-ACCCCGAA-CTTCCAAAAATTACCATTTTA--CCCTCG
* * ** * * *
329870 AACTTCCAAAAAATCCCATTTTTAACCCTAAACCTTCCAAAAAATACCCTTTTACCCCCG
1 AACTTCCAAAAATTACCA-TTTT-ACCCCGAA-CTTCCAAAAATTACCATTTTACCCTCG
329930 AA
1 AA
329932 TGTTTGAAAT
Statistics
Matches: 310, Mismatches: 33, Indels: 31
0.83 0.09 0.08
Matches are distributed among these distances:
57 13 0.04
58 62 0.20
59 121 0.39
60 55 0.18
61 19 0.06
62 40 0.13
ACGTcount: A:0.33, C:0.32, G:0.06, T:0.30
Consensus pattern (57 bp):
AACTTCCAAAAATTACCATTTTACCCCGAACTTCCAAAAATTACCATTTTACCCTCG
Found at i:329739 original size:118 final size:117
Alignment explanation
Indices: 329592--329931 Score: 477
Period size: 118 Copynumber: 2.9 Consensus size: 117
329582 AAAATTACTA
329592 TTTTACCCCTGAA-CTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCA-TTTTGA
1 TTTTACCCC-GAACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
* * *
329655 CCCCGAACCTTCCAAAATTTACTATTTTACCCCCGAACTTCCAAAGGTCCCATTT
65 CCCTGAACCTTCCAAAA-TTACCATTTTACCCCCGAACTTCCAAAAGTCCCA-TT
* *
329710 TTTTACCCCGAACCTTCGAAAAATTACCATTTTACCCTCGAACTTTCAAAAATCCCATTTTTGAC
1 TTTTACCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGAC
*
329775 TCTGAACCTTCCAAGAATTACCATTTTACCCCCGAACTTCCAAAAGTCCCATT
66 CCTGAACCTTCCAA-AATTACCATTTTACCCCCGAACTTCCAAAAGTCCCATT
* * *
329828 TTTGATCCCGAACCTTCCAAAAAATACCATTTTACCCCCTCGAACTTCCAAAAAATCCCATTTTT
1 TTTTACCCCGAACCTTCCAAAAATTACCATTTTA--CCCTCGAACTTCC-AAAAATCCCATTTTT
* * * *
329893 AACCCTAAACCTTCCAAAAAATACCCTTTTACCCCCGAA
63 GACCCTGAACCTTCC-AAAATTACCATTTTACCCCCGAA
329932 TGTTTGAAAT
Statistics
Matches: 199, Mismatches: 16, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
117 3 0.02
118 83 0.42
119 51 0.26
120 14 0.07
121 46 0.23
122 2 0.01
ACGTcount: A:0.31, C:0.33, G:0.06, T:0.30
Consensus pattern (117 bp):
TTTTACCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGAC
CCTGAACCTTCCAAAATTACCATTTTACCCCCGAACTTCCAAAAGTCCCATT
Found at i:335086 original size:2 final size:2
Alignment explanation
Indices: 335079--335111 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
335069 TGCTGTTCTT
335079 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 T
335112 TTCCCATAGT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:351253 original size:3 final size:3
Alignment explanation
Indices: 351245--351281 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
351235 ACTGAGTGAC
351245 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
351282 AAGAACATGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:360271 original size:14 final size:13
Alignment explanation
Indices: 360238--360275 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 13
360228 TATTTAATTT
360238 TTTTAAA-AT-TA
1 TTTTAAATATATA
360249 TTTTAAATATATA
1 TTTTAAATATATA
360262 TTTTATAATATATA
1 TTTTA-AATATATA
360276 AGTTGGTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 7 0.29
12 2 0.08
13 7 0.29
14 8 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TTTTAAATATATA
Found at i:362099 original size:10 final size:10
Alignment explanation
Indices: 362080--362116 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
362070 ATTTCCATTC
362080 TTTCATTTGA
1 TTTCATTTGA
*
362090 TTTGATTTGA
1 TTTCATTTGA
*
362100 TTTCATTTCA
1 TTTCATTTGA
362110 TTTCATT
1 TTTCATT
362117 CATTGATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.19, C:0.11, G:0.08, T:0.62
Consensus pattern (10 bp):
TTTCATTTGA
Found at i:366122 original size:12 final size:11
Alignment explanation
Indices: 366099--366132 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
366089 AAAATATATA
*
366099 CTTTTTTTTTT
1 CTTTCTTTTTT
366110 CTTTCTATTTTT
1 CTTTCT-TTTTT
366122 CTTTCTTTTTT
1 CTTTCTTTTTT
366133 ATGTGTGAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (11 bp):
CTTTCTTTTTT
Found at i:367507 original size:17 final size:19
Alignment explanation
Indices: 367473--367512 Score: 66
Period size: 17 Copynumber: 2.2 Consensus size: 19
367463 TGTTTTCTAG
367473 TTATATTGTATATTATATA
1 TTATATTGTATATTATATA
367492 TTATATT-TAT-TTATATA
1 TTATATTGTATATTATATA
367509 TTAT
1 TTAT
367513 GTAATTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 11 0.52
18 3 0.14
19 7 0.33
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (19 bp):
TTATATTGTATATTATATA
Found at i:367985 original size:18 final size:18
Alignment explanation
Indices: 367945--367986 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
367935 TTATCACTAC
*
367945 ACTAG-TGAATAATTGAA
1 ACTAGTTGAATAATGGAA
* *
367962 ATTAGTTGAATAATGGTA
1 ACTAGTTGAATAATGGAA
367980 ACTAGTT
1 ACTAGTT
367987 TATAATTAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.36
Consensus pattern (18 bp):
ACTAGTTGAATAATGGAA
Found at i:368734 original size:108 final size:106
Alignment explanation
Indices: 368578--368933 Score: 422
Period size: 108 Copynumber: 3.4 Consensus size: 106
368568 GAAGTTATCA
** * *
368578 AAGGGAGGGCCTACTCCACCAGCTGCCCCTGGAAAAGGTGGAAATCAAGTTCCACCACCATCTAA
1 AAGGGAGGGCCTGTTCCACCATCTTCCCCTGGAAAAGGTGG-AATCAAGTTCCACCACCATCTAA
* * * * *
368643 ACTAAGTCAAGTTGATGGTAGTTTAAACTTTGGGATATTACCG
65 ACTAAGTCAAGATGGTCGT-GTTTGAACGTTGGGATATTACCG
* **
368686 AAGGGAGGGCCGGTTCCACCATCTTCCCCTGGAAAAGGTGGAAGTCAAGTTCCACCACCATCTCC
1 AAGGGAGGGCCTGTTCCACCATCTTCCCCTGGAAAAGGTGGAA-TCAAGTTCCACCACCATCTAA
* * * *
368751 ATTAAGTCAAGCTGGTTGTGTTTTGAACGTTGAGATATTACCG
65 ACTAAGTCAAGATGGTCGTG-TTTGAACGTTGGGATATTACCG
* *
368794 AAGGGAGGGCCTGTTCCACCATCTTCCCCTGGAAAAGGTGG-A--AA--T---CCACCATTTAAT
1 AAGGGAGGGCCTGTTCCACCATCTTCCCCTGGAAAAGGTGGAATCAAGTTCCACCACCATCTAAA
* * *
368851 GTAAGTGAAGATGGTCCTGGTTTGAACGTTGGGATATTACCG
66 CTAAGTCAAGATGGTCGT-GTTTGAACGTTGGGATATTACCG
368893 AAGGGAGGGCCTGTTCCACCATCTTCCCCTGGAAAAGGTGG
1 AAGGGAGGGCCTGTTCCACCATCTTCCCCTGGAAAAGGTGG
368934 TGGAAATCCA
Statistics
Matches: 220, Mismatches: 25, Indels: 15
0.85 0.10 0.06
Matches are distributed among these distances:
99 83 0.38
100 1 0.00
102 1 0.00
104 2 0.01
107 4 0.02
108 129 0.59
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.24
Consensus pattern (106 bp):
AAGGGAGGGCCTGTTCCACCATCTTCCCCTGGAAAAGGTGGAATCAAGTTCCACCACCATCTAAA
CTAAGTCAAGATGGTCGTGTTTGAACGTTGGGATATTACCG
Found at i:368895 original size:99 final size:100
Alignment explanation
Indices: 368772--368968 Score: 351
Period size: 99 Copynumber: 2.0 Consensus size: 100
368762 CTGGTTGTGT
368772 TTTGAACGTTGAGATATTACCGAAGGGAGGGCCTGTTCCACCATCTTCCCCTGGAAAA-GGTGGA
1 TTTGAACGTTGAGATATTACCGAAGGGAGGGCCTGTTCCACCATCTTCCCCTGGAAAAGGGTGGA
*
368836 AATCCACCATTTAATGTAAGTGAAGATGGTCCTGG
66 AATCCACCATTTAATGTAAGTAAAGATGGTCCTGG
*
368871 TTTGAACGTTGGGATATTACCGAAGGGAGGGCCTGTTCCACCATCTTCCCCTGGAAAAGGTGGTG
1 TTTGAACGTTGAGATATTACCGAAGGGAGGGCCTGTTCCACCATCTTCCCCTGGAAAA-G-GGTG
368936 GAAATCCACCATTTAATGTAAGTAAAGATGGTC
64 GAAATCCACCATTTAATGTAAGTAAAGATGGTC
368969 GGAGGGCCTG
Statistics
Matches: 93, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
99 57 0.61
102 36 0.39
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.26
Consensus pattern (100 bp):
TTTGAACGTTGAGATATTACCGAAGGGAGGGCCTGTTCCACCATCTTCCCCTGGAAAAGGGTGGA
AATCCACCATTTAATGTAAGTAAAGATGGTCCTGG
Found at i:368988 original size:172 final size:169
Alignment explanation
Indices: 368797--369134 Score: 615
Period size: 172 Copynumber: 2.0 Consensus size: 169
368787 ATTACCGAAG
*
368797 GGAGGGCCTGTTCCACCATCTTCCCCTGGAAAAGGTGGAAATCCACCATTTAATGTAAGTGAAGA
1 GGAGGGCCTGTTCCACCATCTTCCCCTGGAAAAGGTGGAAATCCACCATTTAATGTAAGTAAAGA
368862 TGGTCCTGGTTTGAACGTTGGGATATTACCGAAGGGAGGGC-CTGTTCCACCATCTTCCCCTGGA
66 TGGTCCTGGTTTGAACGTTGGGATATTACCGAAGGGAGGGCTC-GTTCCACCATCTTCCCCTGGA
368926 AAAGGTGGTGGAAATCCACCATTTAATGTAAGTAAAGATGGTC
130 AAA---GGTGGAAATCCACCATTTAATGTAAGTAAAGATGGTC
368969 GGAGGGCCTGTTCCACCATCTTCCCCTGGAAAAGGTGGAAATCCACCATTTAATGTAAGTAAAGA
1 GGAGGGCCTGTTCCACCATCTTCCCCTGGAAAAGGTGGAAATCCACCATTTAATGTAAGTAAAGA
369034 TGGTCCTGGTTTGAACGTTGGGATATTACCGAAGGGAGGGCTCGTTCCACCATCTTCCCCTGGAA
66 TGGTCCTGGTTTGAACGTTGGGATATTACCGAAGGGAGGGCTCGTTCCACCATCTTCCCCTGGAA
*
369099 AAGGTGGAAATCCACCATTTAATGTAAGTCAAGATG
131 AAGGTGGAAATCCACCATTTAATGTAAGTAAAGATG
369135 ATCCTGGTTT
Statistics
Matches: 163, Mismatches: 2, Indels: 5
0.96 0.01 0.03
Matches are distributed among these distances:
169 33 0.20
172 129 0.79
173 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.25
Consensus pattern (169 bp):
GGAGGGCCTGTTCCACCATCTTCCCCTGGAAAAGGTGGAAATCCACCATTTAATGTAAGTAAAGA
TGGTCCTGGTTTGAACGTTGGGATATTACCGAAGGGAGGGCTCGTTCCACCATCTTCCCCTGGAA
AAGGTGGAAATCCACCATTTAATGTAAGTAAAGATGGTC
Found at i:369140 original size:99 final size:99
Alignment explanation
Indices: 368969--369321 Score: 402
Period size: 99 Copynumber: 3.5 Consensus size: 99
368959 AAAGATGGTC
** * *
368969 GGAGGGCCTGTTCCACCATCTTCCCCTGGAAAAGGTGGAAATCCACCATTTAATGTAAGTAAAGA
1 GGAGGGCCCATTCCACCATCTTCCCCTGGAAAACGTGGAAATCCACCATTTAATGTAAGTCAAGA
*
369034 TGGTCCTGGTTTGAACGTTGGGATATTACCGAAG
66 TGGTCCTGGTTTGAACATTGGGATATTACCGAAG
* * *
369068 GGAGGGCTCGTTCCACCATCTTCCCCTGGAAAAGGTGGAAATCCACCATTTAATGTAAGTCAAGA
1 GGAGGGCCCATTCCACCATCTTCCCCTGGAAAACGTGGAAATCCACCATTTAATGTAAGTCAAGA
* *
369133 TGATCCTGGTTTGAACATTGGGATATTACCGAAT
66 TGGTCCTGGTTTGAACATTGGGATATTACCGAAG
* * * * * *
369167 GGAGAGCCCACTCCATCATCATCCCCTGGAAAACGTGGAAATCAAGTTTCGCCACAATCTCAA-G
1 GGAGGGCCCATTCCACCATCTTCCCCTGGAAAACGTGG--A--AA---T--CCACCAT-TTAATG
* * *
369231 TAAGTCAAGTTGGTCCTGATTTGAACATTGAGATATTACCGAAG
56 TAAGTCAAGATGGTCCTGGTTTGAACATTGGGATATTACCGAAG
* * * *
369275 GGAGTGCCCATTCCACCATCTGCCCCTGGAAGACGTGGAAATTCACC
1 GGAGGGCCCATTCCACCATCTTCCCCTGGAAAACGTGGAAATCCACC
369322 GACTCCATCA
Statistics
Matches: 216, Mismatches: 28, Indels: 20
0.82 0.11 0.08
Matches are distributed among these distances:
99 127 0.59
101 2 0.01
103 2 0.01
104 2 0.01
106 2 0.01
108 78 0.36
109 3 0.01
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.25
Consensus pattern (99 bp):
GGAGGGCCCATTCCACCATCTTCCCCTGGAAAACGTGGAAATCCACCATTTAATGTAAGTCAAGA
TGGTCCTGGTTTGAACATTGGGATATTACCGAAG
Found at i:369284 original size:108 final size:108
Alignment explanation
Indices: 369122--369316 Score: 293
Period size: 108 Copynumber: 1.8 Consensus size: 108
369112 ACCATTTAAT
* * * *
369122 GTAAGTCAAGATGATCCTGGTTTGAACATTGGGATATTACCGAATGGAGAGCCCACTCCATCATC
1 GTAAGTCAAGATGATCCTGATTTGAACATTGAGATATTACCGAAGGGAGAGCCCACTCCACCATC
369187 AT-CCCCTGGAAAACGTGGAAATCAAGTTTCGCCACAATCTCAA
66 -TGCCCCTGGAAAACGTGGAAATCAAGTTTCGCCACAATCTCAA
* * * *
369230 GTAAGTCAAGTTGGTCCTGATTTGAACATTGAGATATTACCGAAGGGAGTGCCCATTCCACCATC
1 GTAAGTCAAGATGATCCTGATTTGAACATTGAGATATTACCGAAGGGAGAGCCCACTCCACCATC
*
369295 TGCCCCTGGAAGACGTGGAAAT
66 TGCCCCTGGAAAACGTGGAAAT
369317 TCACCGACTC
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
107 1 0.01
108 76 0.99
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (108 bp):
GTAAGTCAAGATGATCCTGATTTGAACATTGAGATATTACCGAAGGGAGAGCCCACTCCACCATC
TGCCCCTGGAAAACGTGGAAATCAAGTTTCGCCACAATCTCAA
Found at i:369445 original size:146 final size:147
Alignment explanation
Indices: 369195--369462 Score: 369
Period size: 146 Copynumber: 1.8 Consensus size: 147
369185 TCATCCCCTG
* ** *
369195 GAAAACGTGGAAATCAAGTTTCGCCACAATCTCAAGTAAGTCAAGTTGGTCCTGATTTGAACATT
1 GAAAACGTGGAAATCAAGTTTCGCAACAATCTCAAACAAGTCAAGTTGATCCTGATTTGAACATT
* * * * *
369260 GAGATATTACCGAAGGGAGTGCCCATTCCACCATCTGCCCCTGGAAGACGTGGAAATTCACCGAC
66 GAGATACTACCGAAAGGAGGGCCCACTCCACCATCTGCCCCTGGAAAACGTGGAAATTCACCGAC
369325 TCCATCATTTGCCCTTA
131 TCCATCATTTGCCCTTA
* * *
369342 GAAAAGGTGGAAATC-AGTTTCGCAACCATCTCAAACAAGTCAAGTTGATCCTGGTTTGAACATT
1 GAAAACGTGGAAATCAAGTTTCGCAACAATCTCAAACAAGTCAAGTTGATCCTGATTTGAACATT
* * * *
369406 -AGAGTACTACCGAAAGGAGGGCTCACTCCACCATTTGCCCTTGGAAAAGGTGGAAAT
66 GAGA-TACTACCGAAAGGAGGGCCCACTCCACCATCTGCCCCTGGAAAACGTGGAAAT
369463 CAAGTTCCGC
Statistics
Matches: 104, Mismatches: 16, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
145 3 0.03
146 87 0.84
147 14 0.13
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (147 bp):
GAAAACGTGGAAATCAAGTTTCGCAACAATCTCAAACAAGTCAAGTTGATCCTGATTTGAACATT
GAGATACTACCGAAAGGAGGGCCCACTCCACCATCTGCCCCTGGAAAACGTGGAAATTCACCGAC
TCCATCATTTGCCCTTA
Found at i:381577 original size:149 final size:148
Alignment explanation
Indices: 381308--381587 Score: 366
Period size: 149 Copynumber: 1.9 Consensus size: 148
381298 AATCATATTT
* **
381308 TTCCTCTTGATTTTTAGTATTTTTAGTTGGATTTGTATTCTTAAAGAGGAAAAAATTAAAAATCA
1 TTCCTCTTGATTTTTAGCATTTTTAGTTGGATTTAAATTCTTAAAGAGGAAAAAATTAAAAATCA
** * ** ** *
381373 GGAGAAAAAATCTGATTTGTCATTCTCTTATTGGAAAGGGATAGAGATGACATGAAATCATAATT
66 AAAGAAAAAATCTGATTTGTCATTCTCCTATTAAAAAGAAATAGAGATGACATGAAATCACAATT
381438 TTATACAATATTTTCTCA
131 TTATACAATATTTTCTCA
* * * **
381456 TTCCTCTTGGTTTTTAGCATTTTTAGTTTGATTTAAATTTTTTCAG-GAGAAAAAATTCAAAAAT
1 TTCCTCTTGATTTTTAGCATTTTTAGTTGGATTTAAATTCTTAAAGAG-GAAAAAATT-AAAAAT
*
381520 CAAAAGAAAAAATTTGATTTGTCATTCTCCTATTAAAAAGAAATA-AGGATGACATGAAATCACA
64 CAAAAGAAAAAATCTGATTTGTCATTCTCCTATTAAAAAGAAATAGA-GATGACATGAAATCACA
381584 ATTT
128 ATTT
381588 CATGCGATCA
Statistics
Matches: 112, Mismatches: 17, Indels: 5
0.84 0.13 0.04
Matches are distributed among these distances:
147 1 0.01
148 48 0.43
149 63 0.56
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.39
Consensus pattern (148 bp):
TTCCTCTTGATTTTTAGCATTTTTAGTTGGATTTAAATTCTTAAAGAGGAAAAAATTAAAAATCA
AAAGAAAAAATCTGATTTGTCATTCTCCTATTAAAAAGAAATAGAGATGACATGAAATCACAATT
TTATACAATATTTTCTCA
Found at i:382054 original size:31 final size:31
Alignment explanation
Indices: 382019--382083 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
382009 AAGAAAACTT
382019 AATAGTCCAATGACTTAAAT-AAAGACTTTCA
1 AATAGTCCAATGACTTAAATGAAA-ACTTTCA
* * *
382050 AATAGTTCGATGACTTAAATGAAAACTTTTA
1 AATAGTCCAATGACTTAAATGAAAACTTTCA
382081 AAT
1 AAT
382084 TCAACGATCA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 27 0.90
32 3 0.10
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.32
Consensus pattern (31 bp):
AATAGTCCAATGACTTAAATGAAAACTTTCA
Found at i:389228 original size:3 final size:3
Alignment explanation
Indices: 389222--389358 Score: 96
Period size: 3 Copynumber: 45.3 Consensus size: 3
389212 ATTATACTAT
* * * *
389222 TTA TTA TTA TTA -AA TAA TTCA TTA TTA CTA TTA TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * * * * * * * * *
389267 ATA TTA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
389315 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTAA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA T
389359 CATCAATGCC
Statistics
Matches: 121, Mismatches: 10, Indels: 6
0.88 0.07 0.04
Matches are distributed among these distances:
2 1 0.01
3 114 0.94
4 6 0.05
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.53
Consensus pattern (3 bp):
TTA
Found at i:389257 original size:12 final size:12
Alignment explanation
Indices: 389223--389355 Score: 110
Period size: 12 Copynumber: 11.1 Consensus size: 12
389213 TTATACTATT
389223 TATTATTATTAAA
1 TATTATTATT-AA
*
389236 TAATTCATTATTAC
1 T-ATT-ATTATTAA
389250 TATTATTATTAA
1 TATTATTATTAA
*
389262 TATTAATATTAA
1 TATTATTATTAA
*
389274 TA--A-TAATAA
1 TATTATTATTAA
* * *
389283 TAATAATAATAA
1 TATTATTATTAA
* * *
389295 TAATAATAATAA
1 TATTATTATTAA
*
389307 TATTATTATTAT
1 TATTATTATTAA
*
389319 TATTATTATTAT
1 TATTATTATTAA
*
389331 TATTATTATTAT
1 TATTATTATTAA
389343 TATTATTATTAA
1 TATTATTATTAA
389355 T
1 T
389356 TATCATCAAT
Statistics
Matches: 106, Mismatches: 9, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
9 7 0.07
10 1 0.01
11 1 0.01
12 82 0.77
13 4 0.04
14 5 0.05
15 6 0.06
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (12 bp):
TATTATTATTAA
Found at i:390005 original size:17 final size:17
Alignment explanation
Indices: 389983--390019 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
389973 TAATATTAAG
389983 TTTTAAATAAATTAAAA
1 TTTTAAATAAATTAAAA
* *
390000 TTTTAATTAAATTTAAA
1 TTTTAAATAAATTAAAA
390017 TTT
1 TTT
390020 AAAGAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTTAAATAAATTAAAA
Found at i:390028 original size:17 final size:18
Alignment explanation
Indices: 389989--390089 Score: 100
Period size: 17 Copynumber: 5.7 Consensus size: 18
389979 TAAGTTTTAA
* *
389989 ATAAATTAAAATTTTAA-
1 ATAAATTTAAATTTAAAG
*
390006 TTAAATTTAAATTTAAAG
1 ATAAATTTAAATTTAAAG
*
390024 A-AAATTTAAATTAAAAAAG
1 ATAAATTTAAATT--TAAAG
* *
390043 ATAAATTTGAATTT-ATG
1 ATAAATTTAAATTTAAAG
*
390060 ATAAATTTAAATTTAAAA
1 ATAAATTTAAATTTAAAG
390078 ATAAATTTAAAT
1 ATAAATTTAAAT
390090 CAATTTAAAC
Statistics
Matches: 68, Mismatches: 11, Indels: 9
0.77 0.12 0.10
Matches are distributed among these distances:
17 40 0.59
18 13 0.19
19 5 0.07
20 10 0.15
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (18 bp):
ATAAATTTAAATTTAAAG
Found at i:390056 original size:37 final size:35
Alignment explanation
Indices: 390007--390089 Score: 105
Period size: 37 Copynumber: 2.3 Consensus size: 35
389997 AAATTTTAAT
390007 TAAATTTAAATTTAAAGA-AAATTTAAATTAAAAAAGA
1 TAAATTTAAATTT-AAGATAAATTTAAATT-AAAAA-A
* * *
390044 TAAATTTGAATTTATGATAAATTTAAATTTAAAAA
1 TAAATTTAAATTTAAGATAAATTTAAATTAAAAAA
390079 TAAATTTAAAT
1 TAAATTTAAAT
390090 CAATTTAAAC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
35 11 0.27
36 7 0.17
37 23 0.56
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.39
Consensus pattern (35 bp):
TAAATTTAAATTTAAGATAAATTTAAATTAAAAAA
Found at i:390627 original size:49 final size:48
Alignment explanation
Indices: 390556--390889 Score: 194
Period size: 50 Copynumber: 6.8 Consensus size: 48
390546 ACCATCGTGA
* * *
390556 CTTAAATCCTTCCCCTT-GTGTCTTTGCGGTACTGGATCCACTGTTGCGG
1 CTTAAAT-CTTTCCCTTCGTGTCTTTGAGGTACTGGATCC-CCGTTGCGG
* * * * * * * ** *
390605 CGTAGATCTTTCCCTTCATGTCTCTAAGGTTCAGGATTTACCATTGCGG
1 CTTAAATCTTTCCCTTCGTGTCTTTGAGGTACTGGA-TCCCCGTTGCGG
* * *
390654 CTTAAATC-TTCCCTT-GTGTCTTCGTGGTACTGGATTCGCCGTTGCGG
1 CTTAAATCTTTCCCTTCGTGTCTTTGAGGTACTGGA-TCCCCGTTGCGG
* * * * *
390701 CTCAAATATTTCCCTTCGTGTCTTTTGAGGTACACGG-TCCGTCGTTGCGA
1 CTTAAATCTTTCCCTTCGTGTC-TTTGAGGTAC-TGGATCC-CCGTTGCGG
* * * * *
390751 CTTAGACCTTTCCCTTTTGTCTCTTTGCA-GTACTGGATCCGCCGTTGCGAT
1 CTTAAATCTTTCCC-TTCGTGTCTTTG-AGGTACTGGATCC-CCGTTGCG-G
* * * ** *
390802 CTTAGATCTTTCCCTTCATGT-TTCTGAGATACTGGATTCGTCGTTACGG
1 CTTAAATCTTTCCCTTCGTGTCTT-TGAGGTACTGGA-TCCCCGTTGCGG
* *
390851 CTTAAATCTTTCCCTTCTGTGTCTTTGGGGTACTAGATC
1 CTTAAATCTTTCCCTTC-GTGTCTTTGAGGTACTGGATC
390890 TGCCATTGTG
Statistics
Matches: 213, Mismatches: 56, Indels: 32
0.71 0.19 0.11
Matches are distributed among these distances:
47 28 0.13
48 22 0.10
49 61 0.29
50 76 0.36
51 26 0.12
ACGTcount: A:0.14, C:0.26, G:0.21, T:0.39
Consensus pattern (48 bp):
CTTAAATCTTTCCCTTCGTGTCTTTGAGGTACTGGATCCCCGTTGCGG
Done.