Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold418
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: 251372
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
File 1 of 2
Found at i:61 original size:17 final size:17
Alignment explanation
Indices: 39--81 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
29 TAAATTTAAA
39 TATTTAA-ATTTAATATT
1 TATTTAATATTTAATA-T
56 TATTTAAATATTTAATAT
1 TATTT-AATATTTAATAT
74 TATTTAAT
1 TATTTAAT
82 TATATATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.33
18 8 0.33
19 8 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATTTAATATTTAATAT
Found at i:542 original size:23 final size:24
Alignment explanation
Indices: 498--548 Score: 79
Period size: 23 Copynumber: 2.2 Consensus size: 24
488 TGAATATTTG
498 TTTT-TAATTTAAAATATATTTTA
1 TTTTGTAATTTAAAATATATTTTA
*
521 TTTTGTAATTTAAAAT-TTTTTTA
1 TTTTGTAATTTAAAATATATTTTA
544 TTTTG
1 TTTTG
549 AATATTATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 15 0.58
24 11 0.42
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (24 bp):
TTTTGTAATTTAAAATATATTTTA
Found at i:3204 original size:16 final size:16
Alignment explanation
Indices: 3183--3215 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3173 AACAACGGCC
3183 AAAGAAAAAAAAAACA
1 AAAGAAAAAAAAAACA
*
3199 AAAGAAAAAAGAAACA
1 AAAGAAAAAAAAAACA
3215 A
1 A
3216 TTAATCAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.85, C:0.06, G:0.09, T:0.00
Consensus pattern (16 bp):
AAAGAAAAAAAAAACA
Found at i:3430 original size:2 final size:2
Alignment explanation
Indices: 3423--3452 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3413 TGTATGGGTT
3423 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3453 AAGAGAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12021 original size:22 final size:22
Alignment explanation
Indices: 11996--12064 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 22
11986 TTTTAATCAT
11996 ATATAAATAAAATAAATATAAA
1 ATATAAATAAAATAAATATAAA
*
12018 ATATTAGA-AAAATAAATATAAA
1 ATA-TAAATAAAATAAATATAAA
*
12040 A-AT-TATAAGAA-AAATATATAA
1 ATATAAATAA-AATAAATATA-AA
12061 ATAT
1 ATAT
12065 TTTAGACATG
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
19 1 0.03
20 10 0.25
21 6 0.15
22 20 0.50
23 3 0.08
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (22 bp):
ATATAAATAAAATAAATATAAA
Found at i:12055 original size:24 final size:22
Alignment explanation
Indices: 11996--12055 Score: 77
Period size: 22 Copynumber: 2.6 Consensus size: 22
11986 TTTTAATCAT
11996 ATATAA-ATAAAATAAATATAAA
1 ATATAAGA-AAAATAAATATAAA
*
12018 ATATTAGAAAAATAAATATAAAA
1 ATATAAGAAAAATAAATAT-AAA
12041 ATTATAAGAAAAATA
1 A-TATAAGAAAAATA
12056 TATAAATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 16 0.48
23 5 0.15
24 12 0.36
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (22 bp):
ATATAAGAAAAATAAATATAAA
Found at i:12582 original size:21 final size:21
Alignment explanation
Indices: 12558--12602 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
12548 GGTAATCAAT
12558 TGTTCTCTACTGGCTGATTTG
1 TGTTCTCTACTGGCTGATTTG
*
12579 TGTTCTCTACTGGTTGATTTG
1 TGTTCTCTACTGGCTGATTTG
12600 TGT
1 TGT
12603 CGGCATAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.09, C:0.16, G:0.24, T:0.51
Consensus pattern (21 bp):
TGTTCTCTACTGGCTGATTTG
Found at i:14436 original size:17 final size:18
Alignment explanation
Indices: 14414--14452 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
14404 ATATACTGTA
14414 TTGTTCAT-TTGCTGGAC
1 TTGTTCATGTTGCTGGAC
*
14431 TTGTTCATGTTGCTTGAC
1 TTGTTCATGTTGCTGGAC
14449 TTGT
1 TTGT
14453 CTAATTACCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.10, C:0.15, G:0.23, T:0.51
Consensus pattern (18 bp):
TTGTTCATGTTGCTGGAC
Found at i:15421 original size:16 final size:16
Alignment explanation
Indices: 15400--15435 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
15390 GAAGTTCAAC
*
15400 GGTGTGTACTTCGTAT
1 GGTGTGTACCTCGTAT
*
15416 GGTGTGTACCTCGTGT
1 GGTGTGTACCTCGTAT
15432 GGTG
1 GGTG
15436 GCAGTGTGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.08, C:0.14, G:0.39, T:0.39
Consensus pattern (16 bp):
GGTGTGTACCTCGTAT
Found at i:20621 original size:4 final size:4
Alignment explanation
Indices: 20614--20644 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
20604 AAACTATATA
*
20614 TATG TATG TATG TATG TATT TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
20645 CTTTTCATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.26, C:0.00, G:0.19, T:0.55
Consensus pattern (4 bp):
TATG
Found at i:22581 original size:20 final size:20
Alignment explanation
Indices: 22556--22604 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
22546 AAATAGAGGC
22556 TCCCTCTTCCCTCTCAAGCA
1 TCCCTCTTCCCTCTCAAGCA
* ** *
22576 TCCCTCATCCCTCTCTTGTA
1 TCCCTCTTCCCTCTCAAGCA
22596 TCCCTCTTC
1 TCCCTCTTC
22605 AATTCTTTCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.10, C:0.49, G:0.04, T:0.37
Consensus pattern (20 bp):
TCCCTCTTCCCTCTCAAGCA
Found at i:26635 original size:20 final size:20
Alignment explanation
Indices: 26610--26658 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
26600 AAATAGAGGC
*
26610 TCCCTCTTCTCTCTCAAGCA
1 TCCCTCTTCCCTCTCAAGCA
* ** *
26630 TCCCTCATCCCTCTCTTGTA
1 TCCCTCTTCCCTCTCAAGCA
26650 TCCCTCTTC
1 TCCCTCTTC
26659 AATTCTTTCT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.10, C:0.47, G:0.04, T:0.39
Consensus pattern (20 bp):
TCCCTCTTCCCTCTCAAGCA
Found at i:27169 original size:11 final size:12
Alignment explanation
Indices: 27149--27177 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
27139 ATCTATTTAA
27149 ATATTTAATTAT
1 ATATTTAATTAT
27161 -TATTTAATTAT
1 ATATTTAATTAT
27172 ATATTT
1 ATATTT
27178 TTCAAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
ATATTTAATTAT
Found at i:27651 original size:23 final size:23
Alignment explanation
Indices: 27605--27662 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
27595 TAAAGGCATG
*
27605 AATA-TTTGTTTTTAATTTTAAA
1 AATATTTTATTTTTAATTTTAAA
27627 AATATTTTATTTTGTAATTTTAAA
1 AATATTTTATTTT-TAATTTTAAA
27651 AA-ATTTTATTTT
1 AATATTTTATTTT
27663 AAATATTATA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
22 4 0.12
23 17 0.52
24 12 0.36
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.60
Consensus pattern (23 bp):
AATATTTTATTTTTAATTTTAAA
Found at i:27674 original size:24 final size:24
Alignment explanation
Indices: 27618--27675 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 24
27608 ATTTGTTTTT
*
27618 AATTTTAAAAATATTTTATTTTGT
1 AATTTTAAAAATATTTTATTTTGA
27642 AATTTTAAAAA-ATTTTATTTT-A
1 AATTTTAAAAATATTTTATTTTGA
*
27664 AATATTATAAAA
1 AATTTTA-AAAA
27676 CAAACTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
22 6 0.19
23 14 0.45
24 11 0.35
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
AATTTTAAAAATATTTTATTTTGA
Found at i:27930 original size:16 final size:17
Alignment explanation
Indices: 27911--27950 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
27901 TATACTTTAT
27911 ATATATTTAATAAT-AA
1 ATATATTTAATAATAAA
* *
27927 ATATTTTTAGTAATAAA
1 ATATATTTAATAATAAA
27944 ATATATT
1 ATATATT
27951 ACTATTTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
ATATATTTAATAATAAA
Found at i:30285 original size:15 final size:16
Alignment explanation
Indices: 30267--30298 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
30257 AACAACGGCC
30267 AAAGAAAAAA-AAACA
1 AAAGAAAAAAGAAACA
30282 AAAGAAAAAAGAAACA
1 AAAGAAAAAAGAAACA
30298 A
1 A
30299 TTAATCAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.84, C:0.06, G:0.09, T:0.00
Consensus pattern (16 bp):
AAAGAAAAAAGAAACA
Found at i:31268 original size:15 final size:15
Alignment explanation
Indices: 31238--31266 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
31228 TTTTATAAAT
31238 TTTTTAAATTCAAAA
1 TTTTTAAATTCAAAA
31253 TTTTT-AATTCAAAA
1 TTTTTAAATTCAAAA
31267 ATAAATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (15 bp):
TTTTTAAATTCAAAA
Found at i:31930 original size:49 final size:49
Alignment explanation
Indices: 31858--31963 Score: 212
Period size: 49 Copynumber: 2.2 Consensus size: 49
31848 GAAATCAGAC
31858 TGTCTTGGTGGGTAATCTGTTTAAGATAGTCATCCATGCCAGCAATGAA
1 TGTCTTGGTGGGTAATCTGTTTAAGATAGTCATCCATGCCAGCAATGAA
31907 TGTCTTGGTGGGTAATCTGTTTAAGATAGTCATCCATGCCAGCAATGAA
1 TGTCTTGGTGGGTAATCTGTTTAAGATAGTCATCCATGCCAGCAATGAA
31956 TGTCTTGG
1 TGTCTTGG
31964 CATGTGAAAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 57 1.00
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (49 bp):
TGTCTTGGTGGGTAATCTGTTTAAGATAGTCATCCATGCCAGCAATGAA
Found at i:39144 original size:22 final size:22
Alignment explanation
Indices: 39119--39187 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 22
39109 TTTTAATCAT
39119 ATATAAATAAAATAAATATAAA
1 ATATAAATAAAATAAATATAAA
*
39141 ATATTAGA-AAAATAAATATAAA
1 ATA-TAAATAAAATAAATATAAA
*
39163 A-AT-TATAAGAA-AAATATATAA
1 ATATAAATAA-AATAAATATA-AA
39184 ATAT
1 ATAT
39188 TTTAGACATG
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
19 1 0.03
20 10 0.25
21 6 0.15
22 20 0.50
23 3 0.08
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (22 bp):
ATATAAATAAAATAAATATAAA
Found at i:39178 original size:24 final size:22
Alignment explanation
Indices: 39119--39178 Score: 77
Period size: 22 Copynumber: 2.6 Consensus size: 22
39109 TTTTAATCAT
39119 ATATAA-ATAAAATAAATATAAA
1 ATATAAGA-AAAATAAATATAAA
*
39141 ATATTAGAAAAATAAATATAAAA
1 ATATAAGAAAAATAAATAT-AAA
39164 ATTATAAGAAAAATA
1 A-TATAAGAAAAATA
39179 TATAAATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 16 0.48
23 5 0.15
24 12 0.36
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (22 bp):
ATATAAGAAAAATAAATATAAA
Found at i:39701 original size:21 final size:21
Alignment explanation
Indices: 39677--39721 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
39667 GGTAATCAGT
39677 TGTTCTCTACTGGCTGATTTG
1 TGTTCTCTACTGGCTGATTTG
39698 TGTTCTCTACTGGCTGATTTG
1 TGTTCTCTACTGGCTGATTTG
39719 TGT
1 TGT
39722 CGGCATAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.09, C:0.18, G:0.24, T:0.49
Consensus pattern (21 bp):
TGTTCTCTACTGGCTGATTTG
Found at i:41542 original size:17 final size:18
Alignment explanation
Indices: 41520--41558 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
41510 ATATACTGTA
41520 TTGTTCAT-TTGCTGGAC
1 TTGTTCATGTTGCTGGAC
*
41537 TTGTTCATGTTGCTTGAC
1 TTGTTCATGTTGCTGGAC
41555 TTGT
1 TTGT
41559 CTAATTACCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.10, C:0.15, G:0.23, T:0.51
Consensus pattern (18 bp):
TTGTTCATGTTGCTGGAC
Found at i:41928 original size:2 final size:2
Alignment explanation
Indices: 41921--41957 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
41911 TATGTATGTG
41921 TA TA TA 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
41958 GTTGTTGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:47489 original size:4 final size:4
Alignment explanation
Indices: 47482--47512 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
47472 AAACTATATA
*
47482 TATG TATG TATG TATG TATT TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
47513 CTTTTCATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.26, C:0.00, G:0.19, T:0.55
Consensus pattern (4 bp):
TATG
Found at i:49449 original size:20 final size:20
Alignment explanation
Indices: 49424--49472 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
49414 AAATAGAGGC
49424 TCCCTCTTCCCTCTCAAGCA
1 TCCCTCTTCCCTCTCAAGCA
* ** *
49444 TCCCTCATCCCTCTCTTGTA
1 TCCCTCTTCCCTCTCAAGCA
49464 TCCCTCTTC
1 TCCCTCTTC
49473 AATTCTTTCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.10, C:0.49, G:0.04, T:0.37
Consensus pattern (20 bp):
TCCCTCTTCCCTCTCAAGCA
Found at i:53981 original size:20 final size:20
Alignment explanation
Indices: 53952--54004 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
53942 CTATAAATAG
53952 AAGC-TCCCTCTTCCCTCTC
1 AAGCATCCCTCTTCCCTCTC
*
53971 AAGCATCCCTCATCCCTCTC
1 AAGCATCCCTCTTCCCTCTC
** *
53991 TTGTATCCCTCTTC
1 AAGCATCCCTCTTC
54005 AATTCTTTCT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 4 0.14
20 24 0.86
ACGTcount: A:0.13, C:0.47, G:0.06, T:0.34
Consensus pattern (20 bp):
AAGCATCCCTCTTCCCTCTC
Found at i:54515 original size:11 final size:12
Alignment explanation
Indices: 54495--54523 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
54485 ATCTATTTAA
54495 ATATTTAATTAT
1 ATATTTAATTAT
54507 -TATTTAATTAT
1 ATATTTAATTAT
54518 ATATTT
1 ATATTT
54524 TTCAAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
ATATTTAATTAT
Found at i:54993 original size:24 final size:24
Alignment explanation
Indices: 54949--55008 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
54939 CAAAGGCATG
*
54949 AATA-TTTGTTTT-TAATTTTAAA
1 AATATTTTATTTTGTAATTTTAAA
54971 AATATTTTATTTTGTAATTTTAAA
1 AATATTTTATTTTGTAATTTTAAA
*
54995 AATTTTTTATTTTG
1 AATATTTTATTTTG
55009 AATATTATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
22 4 0.12
23 7 0.21
24 23 0.68
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (24 bp):
AATATTTTATTTTGTAATTTTAAA
Found at i:55020 original size:24 final size:24
Alignment explanation
Indices: 54949--55020 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 24
54939 CAAAGGCATG
* *
54949 AATA-TTTGTTTT-TAATTTTAAA
1 AATATTTTATTTTGTAATATTAAA
*
54971 AATATTTTATTTTGTAATTTTAAA
1 AATATTTTATTTTGTAATATTAAA
*
54995 AATTTTTTATTTTG-AATATTATAA
1 AATATTTTATTTTGTAATATTA-AA
55019 AA
1 AA
55021 CAAACTTATT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
22 4 0.09
23 13 0.30
24 27 0.61
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (24 bp):
AATATTTTATTTTGTAATATTAAA
Found at i:55546 original size:13 final size:13
Alignment explanation
Indices: 55528--55552 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55518 AATTTTTTTA
55528 TATATTTAATATT
1 TATATTTAATATT
55541 TATATTTAATAT
1 TATATTTAATAT
55553 ATAATTAGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TATATTTAATATT
Found at i:56986 original size:2 final size:2
Alignment explanation
Indices: 56979--57022 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
56969 GTTATCGGTC
*
56979 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT 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
57021 AT
1 AT
57023 GCATCATAGC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:63063 original size:22 final size:22
Alignment explanation
Indices: 63038--63106 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 22
63028 TTTTAATCAT
63038 ATATAAATAAAATAAATATAAA
1 ATATAAATAAAATAAATATAAA
*
63060 ATATTAGA-AAAATAAATATAAA
1 ATA-TAAATAAAATAAATATAAA
*
63082 A-AT-TATAAGAA-AAATATATAA
1 ATATAAATAA-AATAAATATA-AA
63103 ATAT
1 ATAT
63107 TTTAAACATG
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
19 1 0.03
20 10 0.25
21 6 0.15
22 20 0.50
23 3 0.08
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (22 bp):
ATATAAATAAAATAAATATAAA
Found at i:63097 original size:24 final size:22
Alignment explanation
Indices: 63038--63097 Score: 77
Period size: 22 Copynumber: 2.6 Consensus size: 22
63028 TTTTAATCAT
63038 ATATAA-ATAAAATAAATATAAA
1 ATATAAGA-AAAATAAATATAAA
*
63060 ATATTAGAAAAATAAATATAAAA
1 ATATAAGAAAAATAAATAT-AAA
63083 ATTATAAGAAAAATA
1 A-TATAAGAAAAATA
63098 TATAAATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 16 0.48
23 5 0.15
24 12 0.36
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (22 bp):
ATATAAGAAAAATAAATATAAA
Found at i:63623 original size:21 final size:21
Alignment explanation
Indices: 63599--63641 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
63589 TAATCAGTTT
63599 TTCTCTACTGGCTGATTTGTG
1 TTCTCTACTGGCTGATTTGTG
63620 TTCTCTACTGGCTGATTTGTG
1 TTCTCTACTGGCTGATTTGTG
63641 T
1 T
63642 CGGCATAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.09, C:0.19, G:0.23, T:0.49
Consensus pattern (21 bp):
TTCTCTACTGGCTGATTTGTG
Found at i:65480 original size:17 final size:18
Alignment explanation
Indices: 65458--65496 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
65448 ATATATTGAA
65458 TTGTTCAT-TTGCTGGAC
1 TTGTTCATGTTGCTGGAC
*
65475 TTGTTCATGTTGCTTGAC
1 TTGTTCATGTTGCTGGAC
65493 TTGT
1 TTGT
65497 CTAATTACCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.10, C:0.15, G:0.23, T:0.51
Consensus pattern (18 bp):
TTGTTCATGTTGCTGGAC
Found at i:65493 original size:18 final size:17
Alignment explanation
Indices: 65453--65496 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
65443 GATTCATATA
*
65453 TTGAATTGTTCATTTGC
1 TTGACTTGTTCATTTGC
*
65470 TGGACTTGTTCATGTTGC
1 TTGACTTGTTCAT-TTGC
65488 TTGACTTGT
1 TTGACTTGT
65497 CTAATTACCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.14, C:0.14, G:0.23, T:0.50
Consensus pattern (17 bp):
TTGACTTGTTCATTTGC
Found at i:77463 original size:11 final size:11
Alignment explanation
Indices: 77447--77490 Score: 54
Period size: 11 Copynumber: 3.8 Consensus size: 11
77437 CTTCTCTTCA
77447 AAAAAAAAAGC
1 AAAAAAAAAGC
77458 AAAAAAAAAAAGC
1 --AAAAAAAAAGC
77471 AAAAAAAAA-C
1 AAAAAAAAAGC
77481 AAAACAAAAA
1 AAAA-AAAAA
77491 AACAAAACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 5 0.17
11 14 0.47
13 11 0.37
ACGTcount: A:0.86, C:0.09, G:0.05, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGC
Found at i:77464 original size:13 final size:13
Alignment explanation
Indices: 77446--77507 Score: 72
Period size: 14 Copynumber: 4.5 Consensus size: 13
77436 CCTTCTCTTC
77446 AAAAAAAAAAGCA
1 AAAAAAAAAAGCA
77459 AAAAAAAAAAGCAA
1 AAAAAAAAAAGC-A
*
77473 AAAAAAACAAAACA
1 AAAAAAA-AAAGCA
77487 AAAAAACAAAA-CA
1 AAAAAA-AAAAGCA
77500 AAGAAAAA
1 AA-AAAAA
77508 GAGAGAAAAG
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
13 17 0.39
14 22 0.50
15 5 0.11
ACGTcount: A:0.85, C:0.10, G:0.05, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAGCA
Found at i:77477 original size:23 final size:22
Alignment explanation
Indices: 77448--77507 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 22
77438 TTCTCTTCAA
77448 AAAAAAAAGCAAAAAAAAAAAGC
1 AAAAAAAAGCAAAAAAAAAAA-C
*
77471 AAAAAAAAACAAAACAAAAAAAC
1 AAAAAAAAGCAAAA-AAAAAAAC
*
77494 AAAACAAAG-AAAAA
1 AAAAAAAAGCAAAAA
77508 GAGAGAAAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 1 0.03
22 4 0.12
23 21 0.64
24 7 0.21
ACGTcount: A:0.85, C:0.10, G:0.05, T:0.00
Consensus pattern (22 bp):
AAAAAAAAGCAAAAAAAAAAAC
Found at i:77488 original size:28 final size:27
Alignment explanation
Indices: 77446--77507 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 27
77436 CCTTCTCTTC
*
77446 AAAAAAAAAAGCAAAAAAA-AAAAGCAA
1 AAAAAAAAAAACAAAAAAACAAAA-CAA
77473 AAAAAAACAAAACAAAAAAACAAAACAA
1 AAAAAAA-AAAACAAAAAAACAAAACAA
*
77501 AGAAAAA
1 AAAAAAA
77508 GAGAGAAAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
27 7 0.23
28 20 0.65
29 4 0.13
ACGTcount: A:0.85, C:0.10, G:0.05, T:0.00
Consensus pattern (27 bp):
AAAAAAAAAAACAAAAAAACAAAACAA
Found at i:78637 original size:59 final size:59
Alignment explanation
Indices: 78487--79265 Score: 891
Period size: 59 Copynumber: 13.4 Consensus size: 59
78477 CCTTCCGCTT
* * * *
78487 TTTAGTCCTCAGAGAGCAGGATGCCTTTTCCTTTTAAAAGCCCCCACAAGTTGGTGGCA-T
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTT-CTTTT-AAAGCCCACACAAGTTGGTGGCACC
* *
78547 TTTCCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGTCCACCCAAGTTGGTGGCACC
1 TTT--AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * * * *
78608 TTTAGTCCTCAAAGAGCAAGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGATGGTACC
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTCTTTT-AAAGCCCACACAAGTTGGTGGCACC
* * *
78668 TTTCAGTCCCCAAAGAGCAGGAC-AC----CTTTTAAAGCCCACACAAGTTGGTGGCA-T
1 TTT-AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
* *
78722 TTTCCAGTCCTCAAAGAGCAGGACACC---TC--TCAAAGCCCACACAAGTTGGTGGCACC
1 TTT--AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
* *
78778 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * * * *
78837 TTCAGCCCTCAAAGAGCGGGACACATTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
* *
78896 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * * *
78955 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTCAAAGCCCACACAAGTTGGTAGCACC
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
* **
79014 TTTCAGTCCTCAAAGAGCAGGACACC-TTTC----AAAGCCCACACAAGTTGGTGGCATT
1 TTT-AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
* *
79069 TTTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACCCAAGTTGGTGGCACC
1 TTT-AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * * *
79129 TTCAGTCCTCAAAGAGCAGGATGCTTTTTTTTTTCAAAGCCCACACAAGTTGGTGGCACC
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTCTTTT-AAAGCCCACACAAGTTGGTGGCACC
* * * *
79189 TTTTAGTCCCCAAAGAGCAGGACACC-TTTC----AAAGCCCACACGAGTTGGTGGCACTT
1 -TTTAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCAC-C
* *
79245 TTTACTCCTCAATGAGCAGGA
1 TTTAGTCCTCAAAGAGCAGGA
79266 TACACTTTAT
Statistics
Matches: 631, Mismatches: 65, Indels: 51
0.84 0.09 0.07
Matches are distributed among these distances:
54 23 0.04
55 151 0.24
56 12 0.02
57 3 0.00
59 256 0.41
60 118 0.19
61 44 0.07
62 24 0.04
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (59 bp):
TTTAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
Found at i:79256 original size:175 final size:174
Alignment explanation
Indices: 78523--79265 Score: 1054
Period size: 175 Copynumber: 4.3 Consensus size: 174
78513 TTTCCTTTTA
* *
78523 AAAGCCCCCACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGT
1 AAAGCCCACACAAGTTGGTGGCATTTT-CAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGC
* * * *
78588 CCACCCAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAAGATGCTTTTTCTTTTCAAAGCCCACA
65 CCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCTTTTTCTTTTCAAAGCCCACA
* * *
78653 CAAGTTGATGGTACCTTTCAGTCCCCAAAGAGCAGGACACCTTTT
130 CAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTTTC
* *
78698 AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACC---TC--TCAAAGC
1 AAAGCCCACACAAGTTGGTGGCATTTT-CAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGC
* *
78758 CCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTT-AAAGCCCACA
65 CCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCTTTTTCTTTTCAAAGCCCACA
* *
78822 CAAGTTGGTGGCACC-TTCAG-CCCTCAAAGAGCGGGACACATTTTCTTTT
130 CAAGTTGGTGGCACCTTTCAGTCCC-CAAAGAGCAGGACAC-----CTTTC
** *
78871 AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCC
1 AAAGCCCACACAAGTTGGTGGCATTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCC
* *
78936 CACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACGCCTTTTC-TTTCAAAGCCCACAC
66 CACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCTTTTTCTTTTCAAAGCCCACAC
* *
79000 AAGTTGGTAGCACCTTTCAGTCCTCAAAGAGCAGGACACCTTTC
131 AAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTTTC
*
79044 AAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGC
1 AAAGCCCACACAAGTTGGTGGCA-TTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGC
* * *
79109 CCACCCAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGATGCTTTTTTTTTTCAAAGCCCACA
65 CCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCTTTTTCTTTTCAAAGCCCACA
*
79174 CAAGTTGGTGGCACCTTTTAGTCCCCAAAGAGCAGGACACCTTTC
130 CAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTTTC
* * * *
79219 AAAGCCCACACGAGTTGGTGGCACTTTTTACTCCTCAATGAGCAGGA
1 AAAGCCCACACAAGTTGGTGGCA-TTTTCAGTCCTCAAAGAGCAGGA
79266 TACACTTTAT
Statistics
Matches: 514, Mismatches: 38, Indels: 32
0.88 0.07 0.05
Matches are distributed among these distances:
167 3 0.01
168 19 0.04
169 23 0.04
170 53 0.10
172 23 0.04
173 57 0.11
174 84 0.16
175 148 0.29
176 3 0.01
177 80 0.16
178 19 0.04
179 2 0.00
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.25
Consensus pattern (174 bp):
AAAGCCCACACAAGTTGGTGGCATTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCC
CACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCTTTTTCTTTTCAAAGCCCACAC
AAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTTTC
Found at i:80117 original size:19 final size:19
Alignment explanation
Indices: 80093--80160 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
80083 AATTCAACAA
80093 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
80112 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
80127 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
80144 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
80161 TTAGCTACTA
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:80132 original size:13 final size:13
Alignment explanation
Indices: 80114--80138 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
80104 ACATAAGTTT
80114 TGTATCGATACAA
1 TGTATCGATACAA
80127 TGTATCGATACA
1 TGTATCGATACA
80139 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:80132 original size:32 final size:32
Alignment explanation
Indices: 80095--80157 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
80085 TTCAACAATT
*
80095 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
80127 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
80158 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:80218 original size:13 final size:13
Alignment explanation
Indices: 80200--80225 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
80190 CATTTTTCTG
80200 TGTATCGATACAT
1 TGTATCGATACAT
80213 TGTATCGATACAT
1 TGTATCGATACAT
80226 GAATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:80222 original size:33 final size:33
Alignment explanation
Indices: 80180--80246 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
80170 ACCAAGGAAA
***
80180 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGAATCTGTGTATCGATACAT
*
80213 TGTATCGATACATGAATCTTTGTATCGATACAT
1 TGTATCGATACATGAATCTGTGTATCGATACAT
80246 T
1 T
80247 TAGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGAATCTGTGTATCGATACAT
Found at i:82729 original size:28 final size:28
Alignment explanation
Indices: 82697--82768 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
82687 TCACAGTCAA
** * **
82697 GGATACTCCAACCTTGTTATTTCATCGG
1 GGATACTCCAACCCCGTTACTTCAGAGG
*
82725 GGATACTCCAACCCCGTTACTTCCGAGG
1 GGATACTCCAACCCCGTTACTTCAGAGG
82753 GGATACTCCAACCCCG
1 GGATACTCCAACCCCG
82769 GCTTTATTCC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.22, C:0.33, G:0.19, T:0.25
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTACTTCAGAGG
Found at i:82901 original size:78 final size:78
Alignment explanation
Indices: 82722--82925 Score: 230
Period size: 78 Copynumber: 2.6 Consensus size: 78
82712 GTTATTTCAT
* * *
82722 CGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCC-GATTTATTCCCAAAATAT
* * *
82787 TGATTTCTCATAAT
65 CGATTTCTCACAAC
* * * ** *
82801 TGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAATCCCGATTTTTTTTC-TAATCAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTATTCCCAAAAT-AT
*
82865 CGATTTCTTACAAC
65 CGATTTCTCACAAC
* * * *
82879 CGGGGATACTCCAGCCCCGTTATTTTCAAGGGAACACTCCAACCCCG
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCG
82926 TTATTATCTC
Statistics
Matches: 105, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
77 3 0.03
78 60 0.57
79 42 0.40
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.29
Consensus pattern (78 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTATTCCCAAAATATC
GATTTCTCACAAC
Found at i:86099 original size:24 final size:24
Alignment explanation
Indices: 86067--86122 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
86057 ATATTTTTTT
*
86067 ATAA-ATTTTTAAAATTTTATAAA
1 ATAATATTTTTAAAAATTTATAAA
*
86090 TTAATATTTTTAAAAATTTATAAA
1 ATAATATTTTTAAAAATTTATAAA
86114 ATAATATTT
1 ATAATATTT
86123 CAAGTGGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 3 0.10
24 26 0.90
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
ATAATATTTTTAAAAATTTATAAA
Found at i:86836 original size:13 final size:13
Alignment explanation
Indices: 86818--86844 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
86808 TCACCTAAAC
86818 AATCATCAAGCAG
1 AATCATCAAGCAG
86831 AATCATCAAGCAG
1 AATCATCAAGCAG
86844 A
1 A
86845 GGCTACGGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.22, G:0.15, T:0.15
Consensus pattern (13 bp):
AATCATCAAGCAG
Found at i:91874 original size:15 final size:14
Alignment explanation
Indices: 91849--91891 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
91839 AAGAAAAAAA
91849 AAAGTTTTTATTTT
1 AAAGTTTTTATTTT
* *
91863 AATGTATTTTATGTT
1 AAAGT-TTTTATTTT
91878 AAAGTTTTTATTTT
1 AAAGTTTTTATTTT
91892 TTATAAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.63
Consensus pattern (14 bp):
AAAGTTTTTATTTT
Found at i:92061 original size:19 final size:19
Alignment explanation
Indices: 92037--92090 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
92027 TGAACGTATG
*
92037 ATAAAAGGCTAATTTTATC
1 ATAAAAAGCTAATTTTATC
* * *
92056 ATAAAAAGCCAATGTAATC
1 ATAAAAAGCTAATTTTATC
92075 ATAAAAAGCTAATTTT
1 ATAAAAAGCTAATTTT
92091 TTAAGAATTT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.48, C:0.11, G:0.09, T:0.31
Consensus pattern (19 bp):
ATAAAAAGCTAATTTTATC
Found at i:94173 original size:31 final size:30
Alignment explanation
Indices: 94133--94225 Score: 89
Period size: 31 Copynumber: 3.0 Consensus size: 30
94123 TTTAATTCAT
94133 AATCAAAATTGAAAGATAAAATTCAATCAAA
1 AATCAAAATT-AAAGATAAAATTCAATCAAA
* * *
94164 AATCCAAATT-AGGTCATAAAATTCAATCAAC
1 AATCAAAATTAAAG--ATAAAATTCAATCAAA
** *
94195 AATCAAAATATAATTATATAATTCAATCAAA
1 AATCAAAAT-TAAAGATAAAATTCAATCAAA
94226 TAAAAAAATA
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
29 2 0.04
31 46 0.92
32 1 0.02
33 1 0.02
ACGTcount: A:0.56, C:0.13, G:0.04, T:0.27
Consensus pattern (30 bp):
AATCAAAATTAAAGATAAAATTCAATCAAA
Found at i:97301 original size:2 final size:2
Alignment explanation
Indices: 97294--97322 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
97284 CAATCCCTTT
97294 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
97323 TAAATATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:97488 original size:2 final size:2
Alignment explanation
Indices: 97481--97519 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
97471 GATTGTCGTG
97481 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
97520 TAGAAAAAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:98263 original size:27 final size:27
Alignment explanation
Indices: 98204--98263 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
98194 AAAGAGAAAA
*
98204 TGAAGAAAATATCATTTCTTTAAGATAC
1 TGAA-AAAATATCATTTCTTTAAGACAC
* * *
98232 AGAAAAAATATCATTTCTTTAAGGCAT
1 TGAAAAAATATCATTTCTTTAAGACAC
98259 TGAAA
1 TGAAA
98264 TTAAAATGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 24 0.89
28 3 0.11
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (27 bp):
TGAAAAAATATCATTTCTTTAAGACAC
Found at i:104040 original size:19 final size:19
Alignment explanation
Indices: 104016--104056 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
104006 ATTTATATTT
104016 ATATAAAAA-ATAAAATATA
1 ATATAAAAATAT-AAATATA
*
104035 ATATAAATATATAAATATA
1 ATATAAAAATATAAATATA
104054 ATA
1 ATA
104057 AATTTTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
ATATAAAAATATAAATATA
Found at i:104053 original size:33 final size:32
Alignment explanation
Indices: 104016--104085 Score: 77
Period size: 33 Copynumber: 2.2 Consensus size: 32
104006 ATTTATATTT
*
104016 ATATAAAAAATAAAATATAATATAAATATATAA
1 ATATAAAAAATAAAATATAAAATAAAT-TATAA
* *** *
104049 ATATAATAAATTTTATATAAAATAAATTATTA
1 ATATAAAAAATAAAATATAAAATAAATTATAA
104081 ATATA
1 ATATA
104086 TCAAAATTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
32 9 0.29
33 22 0.71
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (32 bp):
ATATAAAAAATAAAATATAAAATAAATTATAA
Found at i:104104 original size:33 final size:33
Alignment explanation
Indices: 104030--104157 Score: 97
Period size: 32 Copynumber: 3.9 Consensus size: 33
104020 AAAAAATAAA
* *
104030 ATATAATATAAATATATAAATATAATAAATTTT
1 ATATAAAATAAATATATAAATATAATAAAATTT
*
104063 ATATAAAATAAAT-TATTAATAT-ATCAAAATTT
1 ATATAAAATAAATATATAAATATAAT-AAAATTT
** *
104095 ATAT--AA-AAATATAT-AATATTTTAAATATAATG
1 ATATAAAATAAATATATAAATATAATAAA-AT--TT
* *
104127 ATATAATATATAACATATAAATATAATAAAA
1 ATATAAAATA-AATATATAAATATAATAAAA
104158 ATATATGTAT
Statistics
Matches: 75, Mismatches: 9, Indels: 19
0.73 0.09 0.18
Matches are distributed among these distances:
29 12 0.16
30 8 0.11
31 2 0.03
32 23 0.31
33 12 0.16
34 1 0.01
35 1 0.01
36 7 0.09
37 9 0.12
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.39
Consensus pattern (33 bp):
ATATAAAATAAATATATAAATATAATAAAATTT
Found at i:104107 original size:40 final size:38
Alignment explanation
Indices: 104012--104163 Score: 93
Period size: 40 Copynumber: 3.9 Consensus size: 38
104002 ATGCATTTAT
104012 ATTTATATAAAAA-ATAAAATATAATATAAATATATAA
1 ATTTATATAAAAATATAAAATATAATATAAATATATAA
* * *
104049 ATATA-ATAAATTTTATATAAAATA-AATTATTAATATATCAAA
1 ATTTATATAAA---AATATAAAATATAA-TATAAATATAT--AA
* * *
104091 ATTTATATAAAAATATATAATAT--TTTAAATATA-ATG
1 ATTTATATAAAAATATAAAATATAATATAAATATATA-A
* * *
104127 ATATAATATATAACATAT-AAATATAATAAAAATATAT
1 AT-TTATATA-AAAATATAAAATATAATATAAATATAT
104164 GTATTAAAAA
Statistics
Matches: 86, Mismatches: 14, Indels: 27
0.68 0.11 0.21
Matches are distributed among these distances:
35 1 0.01
36 7 0.08
37 15 0.17
38 14 0.16
39 11 0.13
40 27 0.31
42 6 0.07
43 5 0.06
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (38 bp):
ATTTATATAAAAATATAAAATATAATATAAATATATAA
Found at i:104144 original size:22 final size:20
Alignment explanation
Indices: 104105--104154 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 20
104095 ATATAAAAAT
*
104105 ATATAATATTTTAAATATAA
1 ATATAATATTATAAATATAA
104125 TGATATAATA-TATAACATATAA
1 --ATATAATATTATAA-ATATAA
104147 ATATAATA
1 ATATAATA
104155 AAAATATATG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 8 0.31
21 4 0.15
22 14 0.54
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (20 bp):
ATATAATATTATAAATATAA
Found at i:104457 original size:11 final size:11
Alignment explanation
Indices: 104441--104495 Score: 62
Period size: 11 Copynumber: 5.3 Consensus size: 11
104431 TACATTTACG
104441 TATTTATATTA
1 TATTTATATTA
104452 TATTTATA-TA
1 TATTTATATTA
*
104462 TTTTTATATTA
1 TATTTATATTA
*
104473 TAATTATATT-
1 TATTTATATTA
*
104483 TA-ATATATTA
1 TATTTATATTA
104493 TAT
1 TAT
104496 ATTTATATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
9 6 0.16
10 13 0.35
11 18 0.49
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TATTTATATTA
Found at i:104461 original size:8 final size:8
Alignment explanation
Indices: 104450--104504 Score: 58
Period size: 8 Copynumber: 6.5 Consensus size: 8
104440 GTATTTATAT
104450 TATATTTA
1 TATATTTA
*
104458 TATATTTT
1 TATATTTA
104466 TATATTATAA
1 TATATT-T-A
104476 TTATATTTA
1 -TATATTTA
104485 -ATATATTA
1 TATAT-TTA
104493 TATATTTA
1 TATATTTA
104501 TATA
1 TATA
104505 AATTTTAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
7 4 0.10
8 23 0.57
9 6 0.15
10 1 0.03
11 6 0.15
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
TATATTTA
Found at i:104469 original size:10 final size:10
Alignment explanation
Indices: 104441--104509 Score: 57
Period size: 11 Copynumber: 6.5 Consensus size: 10
104431 TACATTTACG
104441 TATTTATATTA
1 TATTTATA-TA
104452 TATTTATATA
1 TATTTATATA
*
104462 TTTTTATATTA
1 TATTTATA-TA
* *
104473 TAATTATATT
1 TATTTATATA
*
104483 TAATATATTATA
1 T-ATTTA-TATA
104495 TATTTATATA
1 TATTTATATA
*
104505 AATTT
1 TATTT
104510 TAATACATTA
Statistics
Matches: 46, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
10 19 0.41
11 23 0.50
12 4 0.09
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (10 bp):
TATTTATATA
Found at i:104471 original size:27 final size:27
Alignment explanation
Indices: 104441--104525 Score: 86
Period size: 27 Copynumber: 3.1 Consensus size: 27
104431 TACATTTACG
*
104441 TATTTATATTATATTT-ATATATT-TT
1 TATTTATATTATATTTAATATATTATA
104466 TATATTATAATTATATTTAATATATTATA
1 TAT-TTAT-ATTATATTTAATATATTATA
* *
104495 TATTTATA-TAAATTTTAATACATTAATA
1 TATTTATATTATA-TTTAATATATT-ATA
104523 TAT
1 TAT
104526 AATATCATAT
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
25 3 0.06
26 7 0.14
27 20 0.39
28 17 0.33
29 4 0.08
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (27 bp):
TATTTATATTATATTTAATATATTATA
Found at i:108701 original size:14 final size:15
Alignment explanation
Indices: 108660--108690 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
108650 AATAATCTTT
*
108660 AATATTAATATTTTA
1 AATAGTAATATTTTA
108675 AATAGTAATATTTTA
1 AATAGTAATATTTTA
108690 A
1 A
108691 TGATAATATT
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:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (15 bp):
AATAGTAATATTTTA
Found at i:109046 original size:18 final size:19
Alignment explanation
Indices: 109023--109063 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
109013 CTTATTTTTA
109023 TTTATTAAT-AAATTATTT
1 TTTATTAATCAAATTATTT
109041 TTTATTAATCAAATTATTT
1 TTTATTAATCAAATTATTT
109060 TTTA
1 TTTA
109064 CTAAACAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTATTAATCAAATTATTT
Found at i:109072 original size:19 final size:19
Alignment explanation
Indices: 109032--109072 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
109022 ATTTATTAAT
* *
109032 AAATTATTTTTTATTAATC
1 AAATTATTTTTTACTAAAC
109051 AAATTATTTTTTACTAAAC
1 AAATTATTTTTTACTAAAC
109070 AAA
1 AAA
109073 CATAAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (19 bp):
AAATTATTTTTTACTAAAC
Found at i:109421 original size:23 final size:22
Alignment explanation
Indices: 109395--109437 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
109385 ATTCAATATG
*
109395 ATATATAAAATATGAAAAATTTA
1 ATATATAAAATA-AAAAAATTTA
*
109418 ATATATTAAATAAAAAAATT
1 ATATATAAAATAAAAAAATT
109438 AAAAAAAACT
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:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATATAAAATAAAAAAATTTA
Found at i:112268 original size:13 final size:13
Alignment explanation
Indices: 112250--112274 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
112240 TTAATGAATG
112250 TTTATTAATTTTA
1 TTTATTAATTTTA
112263 TTTATTAATTTT
1 TTTATTAATTTT
112275 GATCCAATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTATTAATTTTA
Found at i:113266 original size:20 final size:21
Alignment explanation
Indices: 113243--113283 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
113233 ATTTATCTAA
113243 TATTTATTT-AATA-TTAAAAT
1 TATTT-TTTAAATATTTAAAAT
113263 TATTTTTTAAATATTTAAAAT
1 TATTTTTTAAATATTTAAAAT
113284 GATATTATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.16
20 9 0.47
21 7 0.37
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TATTTTTTAAATATTTAAAAT
Found at i:113626 original size:16 final size:16
Alignment explanation
Indices: 113605--113637 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
113595 TTTAAAATTT
113605 ATATGCATATTAATGG
1 ATATGCATATTAATGG
113621 ATATGCATATTAATGG
1 ATATGCATATTAATGG
113637 A
1 A
113638 ACTGAAGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.36
Consensus pattern (16 bp):
ATATGCATATTAATGG
Found at i:117419 original size:24 final size:25
Alignment explanation
Indices: 117372--117420 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
117362 ATTTGAATAT
*
117372 ATAAATATATAATATTAATTTTTTA
1 ATAAATATATAATATTAATATTTTA
117397 ATAAATA-ATAAT-TTAAGTATTTTA
1 ATAAATATATAATATTAA-TATTTTA
117421 GACTCATTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 4 0.18
24 11 0.50
25 7 0.32
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (25 bp):
ATAAATATATAATATTAATATTTTA
Found at i:118746 original size:14 final size:15
Alignment explanation
Indices: 118696--118749 Score: 51
Period size: 14 Copynumber: 3.8 Consensus size: 15
118686 TAAATTACAT
* *
118696 TATATAAT-TTTTAT
1 TATATAATATTATAA
* *
118710 TATATAAAAATA-AA
1 TATATAATATTATAA
118724 TATATAATATTATAA
1 TATATAATATTATAA
118739 TATA-AATATTA
1 TATATAATATTA
118750 AAAAAATAAG
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
14 25 0.78
15 7 0.22
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
TATATAATATTATAA
Found at i:118799 original size:33 final size:34
Alignment explanation
Indices: 118761--118825 Score: 89
Period size: 33 Copynumber: 1.9 Consensus size: 34
118751 AAAAATAAGT
* *
118761 AAAAATATT-CATGTTTTAAA-ACTTAATAAAAGA
1 AAAAATATTAAAT-TTTTAAACACTAAATAAAAGA
118794 AAAAATATTAAATTTTTAAACACTAAATAAAA
1 AAAAATATTAAATTTTTAAACACTAAATAAAA
118826 ATAATTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 16 0.57
34 12 0.43
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.32
Consensus pattern (34 bp):
AAAAATATTAAATTTTTAAACACTAAATAAAAGA
Found at i:119233 original size:31 final size:31
Alignment explanation
Indices: 119198--119272 Score: 75
Period size: 33 Copynumber: 2.4 Consensus size: 31
119188 TTTAAAATTT
*
119198 TATTTTATTATTTATAA-T-ATTATTAAATTAA
1 TATTTTATTATTTATAATTAAAT-TTAAA-TAA
*
119229 TATTTATATATTTTTATAATTAAATTTAAATAA
1 TATTT-TAT-TATTTATAATTAAATTTAAATAA
119262 T-TTTTATTATT
1 TATTTTATTATT
119273 AAATAATAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
30 3 0.08
31 8 0.22
32 6 0.16
33 12 0.32
34 6 0.16
35 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (31 bp):
TATTTTATTATTTATAATTAAATTTAAATAA
Found at i:119275 original size:23 final size:22
Alignment explanation
Indices: 119207--119276 Score: 79
Period size: 23 Copynumber: 3.1 Consensus size: 22
119197 TTATTTTATT
*
119207 ATTTATAATATTATTA-AATTAA
1 ATTTA-AATATTTTTATAATTAA
*
119229 TATTTATATATTTTTATAATTAA
1 -ATTTAAATATTTTTATAATTAA
*
119252 ATTTAAATAATTTTTATTATTAA
1 ATTTAAAT-ATTTTTATAATTAA
119275 AT
1 AT
119277 AATAATTCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
22 15 0.37
23 26 0.63
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
ATTTAAATATTTTTATAATTAA
Found at i:120209 original size:29 final size:30
Alignment explanation
Indices: 120140--120212 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 30
120130 TTATATTATA
* *
120140 TTAATATATTTTATTAAATAATTAATATAT
1 TTAAAATATTTTATTAAATAATTAAAATAT
120170 TTAAAATATTTTATGTAAAT-A-TAAAAT-T
1 TTAAAATATTTTAT-TAAATAATTAAAATAT
120198 TTAAAAATATTTTAT
1 TT-AAAATATTTTAT
120213 ATTATATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
28 3 0.08
29 17 0.44
30 14 0.36
31 5 0.13
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (30 bp):
TTAAAATATTTTATTAAATAATTAAAATAT
Found at i:120219 original size:5 final size:5
Alignment explanation
Indices: 120209--120321 Score: 80
Period size: 5 Copynumber: 23.2 Consensus size: 5
120199 TAAAAATATT
* *
120209 TTATA TTATA TTTTAA TT-T- TTATA ATATA TTATA TTATA TTATA TTTATAA
1 TTATA TTATA TTAT-A TTATA TTATA TTATA TTATA TTATA TTATA -TTAT-A
* *
120260 TTA-A ATAAA TTAT- TTATA -TAT- TTATA TTATA TTAATA TTAT- TT-TA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TT-ATA TTATA TTATA
*
120305 TAATA TTATAA TTATA T
1 TTATA TTAT-A TTATA T
120322 ATAAATTTTA
Statistics
Matches: 87, Mismatches: 8, Indels: 26
0.72 0.07 0.21
Matches are distributed among these distances:
3 3 0.03
4 17 0.20
5 46 0.53
6 20 0.23
7 1 0.01
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TTATA
Found at i:120226 original size:29 final size:29
Alignment explanation
Indices: 120194--120283 Score: 85
Period size: 29 Copynumber: 3.0 Consensus size: 29
120184 GTAAATATAA
*
120194 AATTTTAAAAATATTTTATATTATATTTT
1 AATTTTAAAAATATATTATATTATATTTT
* * *
120223 AATTTTTATAATATATTATATTATATTAT
1 AATTTTAAAAATATATTATATTATATTTT
*
120252 -ATTTATAATTAAATAAATTAT-TTATATATTT
1 AATTT-TAA--AAATATATTATATTATAT-TTT
120283 A
1 A
120284 TATTATATTA
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
28 4 0.08
29 27 0.56
30 6 0.12
31 11 0.23
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (29 bp):
AATTTTAAAAATATATTATATTATATTTT
Found at i:120290 original size:32 final size:33
Alignment explanation
Indices: 120228--120371 Score: 91
Period size: 32 Copynumber: 4.6 Consensus size: 33
120218 ATTTTAATTT
* *
120228 TTATAATATATTATAT-TATA-TTATATTTATAA
1 TTATAATAAATTATTTATATATTTATA-TTATAA
120260 TTA-AATAAATTATTTATATATTTATATTAT-A
1 TTATAATAAATTATTTATATATTTATATTATAA
120291 -T-TAAT--ATTATTT-TATA---ATATTATAA
1 TTATAATAAATTATTTATATATTTATATTATAA
* * *
120316 TTATATATAAA-T-TTTATTTATTTAAATTTTAA
1 TTATA-ATAAATTATTTATATATTTATATTATAA
*
120348 TATATTAATAATTTATTTTATATA
1 T-TA-TAATAAATTA-TTTATATA
120372 AAATTATATA
Statistics
Matches: 87, Mismatches: 7, Indels: 32
0.69 0.06 0.25
Matches are distributed among these distances:
24 7 0.08
25 1 0.01
26 1 0.01
27 6 0.07
28 12 0.14
29 4 0.05
30 5 0.06
31 11 0.13
32 19 0.22
33 11 0.13
34 3 0.03
36 7 0.08
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (33 bp):
TTATAATAAATTATTTATATATTTATATTATAA
Found at i:120292 original size:19 final size:19
Alignment explanation
Indices: 120204--120384 Score: 80
Period size: 17 Copynumber: 10.4 Consensus size: 19
120194 AATTTTAAAA
*
120204 ATAT-TTTATATTATATTT
1 ATATATTTATATAATATTT
* *
120222 -TA-ATTTTTATAATATAT
1 ATATATTTATATAATATTT
*
120239 -TATA-TTATATTATATTT
1 ATATATTTATATAATATTT
*
120256 ATA-A-TTAAATAAATTATTT
1 ATATATTTATAT-AA-TATTT
* *
120275 ATATATTTATATTATATTA
1 ATATATTTATATAATATTT
120294 ATATTATTT-TATAATA-TT
1 ATA-TATTTATATAATATTT
120312 ATA-ATTATATATAA-A-TT
1 ATATATT-TATATAATATTT
*
120329 -T-TATTTATTTAA-ATTT
1 ATATATTTATATAATATTT
* *
120345 -TA-ATATAT-TAATAATT
1 ATATATTTATATAATATTT
*
120361 -TAT-TTTATATAA-AATT
1 ATATATTTATATAATATTT
120377 ATATATTT
1 ATATATTT
120385 TATTAATTTT
Statistics
Matches: 128, Mismatches: 17, Indels: 36
0.71 0.09 0.20
Matches are distributed among these distances:
15 10 0.08
16 28 0.22
17 41 0.32
18 16 0.12
19 21 0.16
20 7 0.05
21 5 0.04
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
ATATATTTATATAATATTT
Found at i:120351 original size:72 final size:72
Alignment explanation
Indices: 120129--120353 Score: 183
Period size: 73 Copynumber: 3.0 Consensus size: 72
120119 ATCAGTATTT
* * * * *
120129 TTTATATTATATTAATATATTTTATTAA-ATAATTAATATATTTAAAATATTTTATGTAAATATA
1 TTTATATTATATTAATATATTTTA-TAATATTATTAAT-TATATATAA-ATTTTAT-T-TAT-TT
*
120193 AAATTTTAAAAATA
60 AAATTTT-AATATA
* * * **
120207 TTTTATATTATATT-TTA-ATTTTTATAATA-TATTATATTATAT-TATATTTATAATTAAATAA
1 -TTTATATTATATTAATATA-TTTTATAATATTATTA-ATTATATATAAATTT-TATTTATTTAA
*
120268 ATTATTTATATA
62 ATT-TTAATATA
120280 TTTATATTATATTAATATTATTTTATAATATTA-TAATTATATATAAATTTTATTTATTTAAATT
1 TTTATATTATATTAATA-TATTTTATAATATTATTAATTATATATAAATTTTATTTATTTAAATT
120344 TTAATATA
65 TTAATATA
120352 TT
1 TT
120354 AATAATTTAT
Statistics
Matches: 118, Mismatches: 18, Indels: 27
0.72 0.11 0.17
Matches are distributed among these distances:
72 22 0.19
73 29 0.25
74 21 0.18
75 8 0.07
76 3 0.03
77 12 0.10
78 10 0.08
79 13 0.11
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (72 bp):
TTTATATTATATTAATATATTTTATAATATTATTAATTATATATAAATTTTATTTATTTAAATTT
TAATATA
Found at i:120392 original size:32 final size:32
Alignment explanation
Indices: 120282--120393 Score: 81
Period size: 32 Copynumber: 3.5 Consensus size: 32
120272 TTTATATATT
* *
120282 TATATTATATTAATATTA-TTT-TATAATATTA
1 TATATTTTATTAAT-TTATTTTATATAAAATTA
* * *
120313 TA-ATTATATATAAATTT-TATTTAT-TTAAATTT
1 TATATT-T-TATTAATTTAT-TTTATATAAAATTA
* *
120345 TAATATATTAATAATTTATTTTATATAAAATTA
1 T-ATATTTTATTAATTTATTTTATATAAAATTA
120378 TATATTTTATTAATTT
1 TATATTTTATTAATTT
120394 TAAGTATTTT
Statistics
Matches: 60, Mismatches: 12, Indels: 17
0.67 0.13 0.19
Matches are distributed among these distances:
30 3 0.05
31 4 0.07
32 40 0.67
33 11 0.18
34 2 0.03
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (32 bp):
TATATTTTATTAATTTATTTTATATAAAATTA
Found at i:121153 original size:18 final size:19
Alignment explanation
Indices: 121119--121154 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
121109 ACAATGATAT
*
121119 ATTTTTAAAAAATTAATAG
1 ATTTATAAAAAATTAATAG
121138 ATTTATAAAAAA-TAATA
1 ATTTATAAAAAATTAATA
121155 ATAATGATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (19 bp):
ATTTATAAAAAATTAATAG
Found at i:121911 original size:3 final size:3
Alignment explanation
Indices: 121903--121947 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
121893 TTTGACTTGG
121903 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
121948 GTAAACAAAA
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:122581 original size:27 final size:27
Alignment explanation
Indices: 122549--122600 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 27
122539 AAAAATAAAA
122549 ATAAA-TTA-TAAATATTAAATTTTAATT
1 ATAAATTTATTAAATA-T-AATTTTAATT
122576 ATAAATTTATTAAATATAATTTTAA
1 ATAAATTTATTAAATATAATTTTAA
122601 AAAATCTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
27 13 0.57
28 4 0.17
29 6 0.26
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
ATAAATTTATTAAATATAATTTTAATT
Found at i:122810 original size:18 final size:18
Alignment explanation
Indices: 122789--122957 Score: 82
Period size: 18 Copynumber: 9.8 Consensus size: 18
122779 GGTAAAAACT
122789 TTAAATTTTATATTTATA
1 TTAAATTTTATATTTATA
122807 TTAAATTTTTATATTT-TA
1 TTAAA-TTTTATATTTATA
* *
122825 TT--ATATTATAATTATA
1 TTAAATTTTATATTTATA
122841 TTTAAAATATTTTATATTTATA
1 -TT--AA-ATTTTATATTTATA
122863 -TAAATTTTA-A--TATA
1 TTAAATTTTATATTTATA
* *
122877 TTAATAATTTATA-TAATA
1 TTAA-ATTTTATATTTATA
*
122895 -TAAATTTTA-A--AATA
1 TTAAATTTTATATTTATA
*
122909 -TATATTTATATATTT-T-
1 TTAAATTT-TATATTTATA
122925 TTAAATATTT-TATTTATA
1 TTAAAT-TTTATATTTATA
* *
122943 TTATATTTAATATTT
1 TTAAATTTTATATTT
122958 TTTTCTTTTT
Statistics
Matches: 118, Mismatches: 12, Indels: 42
0.69 0.07 0.24
Matches are distributed among these distances:
14 14 0.12
15 14 0.12
16 20 0.17
17 21 0.18
18 26 0.22
19 10 0.08
20 1 0.01
22 12 0.10
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTAAATTTTATATTTATA
Found at i:122861 original size:56 final size:55
Alignment explanation
Indices: 122793--122957 Score: 158
Period size: 56 Copynumber: 2.9 Consensus size: 55
122783 AAAACTTTAA
122793 ATTTTATATTTATATTAAATTTTTATATTTTATTATATTATAATTATATTTAAAAT
1 ATTTTATATTTATA-TAAATTTTTATATTTTATTATATTATAATTATATTTAAAAT
* * * * *
122849 ATTTTATATTTATATAAATTTTAATATATTAATAATTTATATAATATAAATTTTAAAAT
1 ATTTTATATTTATATAAATTTTTATAT-TTTATTATAT-TATAAT-TATA-TTTAAAAT
* *
122908 A---TATATTTATAT-ATTTTTTAAATATTTTATTTATATTATATTTAATATTT
1 ATTTTATATTTATATAAATTTTT--ATATTTTA-TTATATTATAATT-ATATTT
122958 TTTTCTTTTT
Statistics
Matches: 89, Mismatches: 12, Indels: 17
0.75 0.10 0.14
Matches are distributed among these distances:
55 21 0.24
56 42 0.47
57 14 0.16
58 3 0.03
59 9 0.10
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (55 bp):
ATTTTATATTTATATAAATTTTTATATTTTATTATATTATAATTATATTTAAAAT
Found at i:122866 original size:20 final size:20
Alignment explanation
Indices: 122793--122866 Score: 68
Period size: 20 Copynumber: 3.9 Consensus size: 20
122783 AAAACTTTAA
*
122793 ATTTTATATTTATATTAAAT
1 ATTTTATATTTATATAAAAT
*
122813 -TTTTATATTT-TAT--TAT
1 ATTTTATATTTATATAAAAT
* *
122829 ATTATA-ATTATATTTAAAAT
1 ATTTTATATT-TATATAAAAT
122849 ATTTTATATTTATATAAA
1 ATTTTATATTTATATAAA
122867 TTTTAATATA
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
16 5 0.12
17 5 0.12
18 5 0.12
19 10 0.24
20 14 0.33
21 3 0.07
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTTTATATTTATATAAAAT
Found at i:122888 original size:33 final size:32
Alignment explanation
Indices: 122846--122920 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
122836 TTATATTTAA
* * *
122846 AATATTTTATATTTATATAAATTTTAATATATT
1 AATAATTTATA-TAATATAAATTTTAAAATATT
122879 AATAATTTATATAATATAAATTTTAAAATA-T
1 AATAATTTATATAATATAAATTTTAAAATATT
122910 -AT-ATTTATATA
1 AATAATTTATATA
122921 TTTTTTAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 9 0.23
30 2 0.05
31 1 0.03
32 17 0.44
33 10 0.26
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (32 bp):
AATAATTTATATAATATAAATTTTAAAATATT
Found at i:122919 original size:24 final size:24
Alignment explanation
Indices: 122892--122952 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
122882 AATTTATATA
122892 ATATAAATTTTAAAATA-TATATTT
1 ATAT-AATTTTAAAATATTATATTT
* * *
122916 ATATATTTTTTAAATATTTTATTT
1 ATATAATTTTAAAATATTATATTT
*
122940 ATATTATATTTAA
1 ATATAAT-TTTAA
122953 TATTTTTTTC
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
23 10 0.34
24 15 0.52
25 4 0.14
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
ATATAATTTTAAAATATTATATTT
Found at i:122943 original size:11 final size:12
Alignment explanation
Indices: 122911--122958 Score: 55
Period size: 11 Copynumber: 4.1 Consensus size: 12
122901 TTAAAATATA
122911 TATTTATATATTT
1 TATTTA-ATATTT
*
122924 T-TTAAATATTT
1 TATTTAATATTT
*
122935 TATTT-ATATTA
1 TATTTAATATTT
122946 TATTTAATATTT
1 TATTTAATATTT
122958 T
1 T
122959 TTTCTTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
11 17 0.59
12 11 0.38
13 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TATTTAATATTT
Found at i:122959 original size:24 final size:24
Alignment explanation
Indices: 122911--122958 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
122901 TTAAAATATA
*
122911 TATTTATATATTTTTTAAATATTT
1 TATTTATATATTATTTAAATATTT
122935 TATTTATAT-TATATTT-AATATTT
1 TATTTATATAT-TATTTAAATATTT
122958 T
1 T
122959 TTTCTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (24 bp):
TATTTATATATTATTTAAATATTT
Found at i:124389 original size:16 final size:17
Alignment explanation
Indices: 124367--124407 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
124357 AAATGATACT
124367 AATTCAATAAA-AAAAA
1 AATTCAATAAATAAAAA
*
124383 TATTCAA-AAATAAAAA
1 AATTCAATAAATAAAAA
124399 AATT-AATAA
1 AATTCAATAA
124408 TATTAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
15 5 0.24
16 16 0.76
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (17 bp):
AATTCAATAAATAAAAA
Found at i:126289 original size:20 final size:21
Alignment explanation
Indices: 126247--126290 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
126237 TTCATTCTTA
* *
126247 AATTTTTAAAGATAATTTTTT
1 AATTTTTAAAGATAAGTTATT
126268 AATTTTTAAAGAT-AGTTATT
1 AATTTTTAAAGATAAGTTATT
126288 AAT
1 AAT
126291 CGTTTTTTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (21 bp):
AATTTTTAAAGATAAGTTATT
Found at i:130589 original size:2 final size:2
Alignment explanation
Indices: 130582--130615 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
130572 CTAATCTTCC
130582 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
130616 TTTTGTACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:130633 original size:2 final size:2
Alignment explanation
Indices: 130628--130671 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
130618 TTGTACAAGA
* *
130628 AT AT AT AA AT AT AT AT AA 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
130670 AT
1 AT
130672 GAGAAATGCT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:141692 original size:24 final size:24
Alignment explanation
Indices: 141613--141680 Score: 81
Period size: 24 Copynumber: 2.9 Consensus size: 24
141603 ACACATGATA
141613 AAATATA-TATATATATATTT-TAA-
1 AAATATATTAT-TAT-TATTTATAAT
141636 AAATATTATTATTATTATTTATAAT
1 AAATA-TATTATTATTATTTATAAT
141661 AAATATATTATTATT-TTTAT
1 AAATATATTATTATTATTTAT
141681 GGTAAGTCAT
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
23 15 0.37
24 18 0.44
25 8 0.20
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
AAATATATTATTATTATTTATAAT
Found at i:141917 original size:5 final size:5
Alignment explanation
Indices: 141902--141934 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
141892 ATATTCCTTG
141902 AAATAA AAATA AAATA AAATA AAATA AAATA AA
1 AAAT-A AAATA AAATA AAATA AAATA AAATA AA
141935 TGCATGTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 23 0.85
6 4 0.15
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:142341 original size:29 final size:29
Alignment explanation
Indices: 142305--142366 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 29
142295 TTTTAAAATT
*
142305 TAATA-TTTAAATTAATTAATTAAT-TTAAA
1 TAATATTTTAAAATAATT--TTAATATTAAA
142334 TAATATTTTAAAATAATTTTAATATTAAA
1 TAATATTTTAAAATAATTTTAATATTAAA
142363 TAAT
1 TAAT
142367 TAATAAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 5 0.17
29 14 0.47
30 11 0.37
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
TAATATTTTAAAATAATTTTAATATTAAA
Found at i:142392 original size:131 final size:132
Alignment explanation
Indices: 142172--142532 Score: 505
Period size: 132 Copynumber: 2.8 Consensus size: 132
142162 AGTTTACGCG
*
142172 ATTTAATAGTTAAATTAATTTGTTCATTTAAATAATATTTT-AAATAATTTTAATATTAAATAAT
1 ATTTAATACTTAAATTAATTTGTTCATTTAAATAATATTTTAAAATAATTTTAATATTAAATAAT
* * * *
142236 TAATAAAAATGTTAAAAAGTATCAAAATTATTTTAAAAAGTAATGTTTTAAATTTTGAT-TTTTA
66 TAATAAAAATATTAAAAAGTATCAAAATTATATTAAAAAGTAATATTTCAAATTTT-ATATTTTA
142300 -AA
130 GAA
* ** *
142302 ATTTAATATTTAAATTAATTAATTAATTTAAATAATATTTTAAAATAATTTTAATATTAAATAAT
1 ATTTAATACTTAAATTAATTTGTTCATTTAAATAATATTTTAAAATAATTTTAATATTAAATAAT
* * *
142367 TAATAAAAATATT-AAAGGATATCAAAATTATATTAAAAAGTAATATTTCAGATTTTTTATTTTA
66 TAATAAAAATATTAAAAAG-TATCAAAATTATATTAAAAAGTAATATTTCAAATTTTATATTTTA
**
142431 GTG
130 GAA
* *
142434 ACTTAATACTTAAATTAATTTGTTCATTTAAATAATGTTTTAAAATAATTTTAATATTAAATAAT
1 ATTTAATACTTAAATTAATTTGTTCATTTAAATAATATTTTAAAATAATTTTAATATTAAATAAT
* **
142499 TAATAAAAATATTAAAAAATATCTTAATTATATT
66 TAATAAAAATATTAAAAAGTATCAAAATTATATT
142533 TAAGATTATT
Statistics
Matches: 203, Mismatches: 23, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
130 42 0.21
131 73 0.36
132 85 0.42
133 3 0.01
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (132 bp):
ATTTAATACTTAAATTAATTTGTTCATTTAAATAATATTTTAAAATAATTTTAATATTAAATAAT
TAATAAAAATATTAAAAAGTATCAAAATTATATTAAAAAGTAATATTTCAAATTTTATATTTTAG
AA
Found at i:142647 original size:21 final size:22
Alignment explanation
Indices: 142571--142723 Score: 83
Period size: 21 Copynumber: 7.3 Consensus size: 22
142561 TCAAATCATA
* *
142571 TAAAAATTATCAAAATTAAATC
1 TAAAACTTATCAAAATTATATC
*
142593 -AAATA-TTA-CAAAAATTAT-TT
1 TAAA-ACTTATC-AAAATTATATC
** *
142613 TAAAGGTTAACAAAATTATATC
1 TAAAACTTATCAAAATTATATC
* *
142635 TAAAA-TTCTCAAAATCATAT-
1 TAAAACTTATCAAAATTATATC
* * *
142655 TAAAAGTTTTTAAAATTATAT-
1 TAAAACTTATCAAAATTATATC
142676 TAAAACTTAT-AAAATTATATC
1 TAAAACTTATCAAAATTATATC
* * *
142697 -GAAAGTTATTAAAATTTATATC
1 TAAAACTTATCAAAA-TTATATC
142719 -AAAAC
1 TAAAAC
142724 CTAATTAAAT
Statistics
Matches: 104, Mismatches: 17, Indels: 20
0.74 0.12 0.14
Matches are distributed among these distances:
20 24 0.23
21 63 0.61
22 17 0.16
ACGTcount: A:0.52, C:0.08, G:0.03, T:0.37
Consensus pattern (22 bp):
TAAAACTTATCAAAATTATATC
Found at i:142649 original size:42 final size:41
Alignment explanation
Indices: 142551--142723 Score: 100
Period size: 42 Copynumber: 4.2 Consensus size: 41
142541 TTATTAATAG
* * * * * *
142551 TTAAAAGTTATCAAATCATA-TAAAAATTATCAAAATTAAA
1 TTAAAACTTATAAAATTATATTAAAAGTTAACAAAATTATA
* * * *
142591 TCAAATA-TTACAAAAATTATTTTAAAGGTTAACAAAATTATA
1 TTAAA-ACTTA-TAAAATTATATTAAAAGTTAACAAAATTATA
* * ***
142633 TCTAAAA-TTCTCAAAATCATATTAAAAGTTTTTAAAATTATA
1 T-TAAAACTTAT-AAAATTATATTAAAAGTTAACAAAATTATA
** **
142675 TTAAAACTTATAAAATTATATCGAAAGTTATTAAAATTTATA
1 TTAAAACTTATAAAATTATATTAAAAGTTAACAAAA-TTATA
*
142717 TCAAAAC
1 TTAAAAC
142724 CTAATTAAAT
Statistics
Matches: 102, Mismatches: 24, Indels: 12
0.74 0.17 0.09
Matches are distributed among these distances:
40 7 0.07
41 33 0.32
42 59 0.58
43 3 0.03
ACGTcount: A:0.52, C:0.08, G:0.03, T:0.36
Consensus pattern (41 bp):
TTAAAACTTATAAAATTATATTAAAAGTTAACAAAATTATA
Found at i:142854 original size:21 final size:21
Alignment explanation
Indices: 142830--142870 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
142820 AATATTAATC
*
142830 AAAATTATAATAAAAGTTATT
1 AAAATTATAATAAAAATTATT
*
142851 AAAATTATATTAAAAATTAT
1 AAAATTATAATAAAAATTAT
142871 CTATAATTTA
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:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
AAAATTATAATAAAAATTATT
Found at i:144869 original size:21 final size:21
Alignment explanation
Indices: 144843--144882 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
144833 AAAAATATTT
144843 TTGAATGAAATG-ATGCATTAG
1 TTGAATGAAA-GAATGCATTAG
144864 TTGAATGAAAGAATGCATT
1 TTGAATGAAAGAATGCATT
144883 TTTTAGATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.40, C:0.05, G:0.23, T:0.33
Consensus pattern (21 bp):
TTGAATGAAAGAATGCATTAG
Found at i:148294 original size:21 final size:22
Alignment explanation
Indices: 148261--148301 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
148251 GAATGAAATG
148261 ATGCATTGGTTGGA-TAAAAGA
1 ATGCATTGGTTGGATTAAAAGA
**
148282 ATGCATTTTTTGGATTAAAA
1 ATGCATTGGTTGGATTAAAA
148302 AATATAACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.37, C:0.05, G:0.22, T:0.37
Consensus pattern (22 bp):
ATGCATTGGTTGGATTAAAAGA
Found at i:148383 original size:12 final size:12
Alignment explanation
Indices: 148366--148394 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
148356 TGGGATATTT
148366 TCTTTGATTGTG
1 TCTTTGATTGTG
148378 TCTTTGATTGTG
1 TCTTTGATTGTG
148390 TCTTT
1 TCTTT
148395 TGTTAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.10, G:0.21, T:0.62
Consensus pattern (12 bp):
TCTTTGATTGTG
Found at i:153814 original size:22 final size:21
Alignment explanation
Indices: 153783--153841 Score: 55
Period size: 23 Copynumber: 2.6 Consensus size: 21
153773 ACTTATACAC
153783 ATTTATTTATAATAAAATAATTA
1 ATTT-TTTATAATAAAATAA-TA
* *
153806 ATTTTTTATTATGTAAATAATA
1 ATTTTTTATAAT-AAAATAATA
*
153828 ATTTTATAATAATA
1 ATTTT-TTATAATA
153842 TTAAAATGTA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
22 14 0.48
23 15 0.52
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
ATTTTTTATAATAAAATAATA
Found at i:158689 original size:29 final size:32
Alignment explanation
Indices: 158613--158690 Score: 76
Period size: 29 Copynumber: 2.6 Consensus size: 32
158603 GGTTAGGGGG
*
158613 AGAA-AGAGAAAGGAAAAAAATAAAGAGCAAA
1 AGAAGAGAGAAAGGAAAGAAATAAAGAGCAAA
* * * *
158644 A-AAGAAAGCATGAAAAGAAAT-AAG-G-AAA
1 AGAAGAGAGAAAGGAAAGAAATAAAGAGCAAA
158672 AGAAGAGAGAAAGGAAAGA
1 AGAAGAGAGAAAGGAAAGA
158691 GAAAAAATTG
Statistics
Matches: 36, Mismatches: 9, Indels: 6
0.71 0.18 0.12
Matches are distributed among these distances:
28 4 0.11
29 14 0.39
30 5 0.14
31 13 0.36
ACGTcount: A:0.68, C:0.03, G:0.26, T:0.04
Consensus pattern (32 bp):
AGAAGAGAGAAAGGAAAGAAATAAAGAGCAAA
Found at i:159715 original size:13 final size:13
Alignment explanation
Indices: 159694--159727 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
159684 ACTTAATAAA
159694 ATTAAAATTAATT
1 ATTAAAATTAATT
*
159707 ATTACAATTAATT
1 ATTAAAATTAATT
159720 AATTAAAA
1 -ATTAAAA
159728 ATTATAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (13 bp):
ATTAAAATTAATT
Found at i:159897 original size:12 final size:13
Alignment explanation
Indices: 159882--159911 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
159872 TTGTATTATA
159882 TTTTAA-TTATTT
1 TTTTAAGTTATTT
159894 TTTTAAGTTATTT
1 TTTTAAGTTATTT
159907 TTTTA
1 TTTTA
159912 TCTTAGCTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.73
Consensus pattern (13 bp):
TTTTAAGTTATTT
Found at i:162792 original size:16 final size:16
Alignment explanation
Indices: 162773--162818 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
162763 AAAATTATAT
162773 ATTTATATAAATTTTA
1 ATTTATATAAATTTTA
162789 ATTTATA-ATAA-TTT-
1 ATTTATATA-AATTTTA
*
162803 ATTTATATAGATTTTA
1 ATTTATATAAATTTTA
162819 TATGTTTGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
14 8 0.32
15 8 0.32
16 9 0.36
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (16 bp):
ATTTATATAAATTTTA
Found at i:162878 original size:22 final size:20
Alignment explanation
Indices: 162839--162904 Score: 80
Period size: 22 Copynumber: 3.2 Consensus size: 20
162829 TCTTTATGTT
162839 ATATTTATTTATTTTATATC
1 ATATTTATTTATTTTATATC
*
162859 ATATTTATTTATTTTTTATATT
1 ATATTTATTTA--TTTTATATC
* *
162881 ATATTTATATAATTTA-ATC
1 ATATTTATTTATTTTATATC
162900 ATATT
1 ATATT
162905 AAATCTAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
19 7 0.17
20 15 0.38
22 18 0.45
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (20 bp):
ATATTTATTTATTTTATATC
Found at i:162896 original size:9 final size:11
Alignment explanation
Indices: 162831--162890 Score: 63
Period size: 11 Copynumber: 5.6 Consensus size: 11
162821 TGTTTGTATC
*
162831 TTTATGTTATA
1 TTTATATTATA
162842 TTTAT-TTAT-
1 TTTATATTATA
*
162851 TTTATATCATA
1 TTTATATTATA
*
162862 TTTAT-TTATTT
1 TTTATATTA-TA
162873 TTTATATTATA
1 TTTATATTATA
162884 TTTATAT
1 TTTATAT
162891 AATTTAATCA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
9 5 0.12
10 9 0.22
11 24 0.59
12 3 0.07
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (11 bp):
TTTATATTATA
Found at i:166654 original size:17 final size:17
Alignment explanation
Indices: 166618--166655 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
166608 TGATACAATG
*
166618 AATAATGTATCGATACA
1 AATAATGTATCGAAACA
*
166635 AATAATGTATCGAAATA
1 AATAATGTATCGAAACA
166652 AATA
1 AATA
166656 GTAAATGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.53, C:0.08, G:0.11, T:0.29
Consensus pattern (17 bp):
AATAATGTATCGAAACA
Found at i:167527 original size:52 final size:52
Alignment explanation
Indices: 167456--167586 Score: 149
Period size: 52 Copynumber: 2.5 Consensus size: 52
167446 TTAAAGATAG
* *
167456 TAAAGATGAGAAGGGTGCCAATGTGCTAATTCATAG-CCAGTGACATTAAACT
1 TAAAGATGAGAAGAGTGCCAATGTGCTAATTCA-AGACCAGCGACATTAAACT
* * ** *
167508 TAAAGATGAGAAGAATGCCAATGTGTTGGTTCAAGACCAGCGACATTAGACT
1 TAAAGATGAGAAGAGTGCCAATGTGCTAATTCAAGACCAGCGACATTAAACT
* *
167560 TAAAAATGACAA-AGGTGCCAATGTGCT
1 TAAAGATGAGAAGA-GTGCCAATGTGCT
167587 GATTTAAGGC
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
51 3 0.05
52 63 0.95
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.24
Consensus pattern (52 bp):
TAAAGATGAGAAGAGTGCCAATGTGCTAATTCAAGACCAGCGACATTAAACT
Found at i:167758 original size:52 final size:52
Alignment explanation
Indices: 167680--167992 Score: 199
Period size: 52 Copynumber: 6.1 Consensus size: 52
167670 ATAATAAGGG
* * * * *
167680 TGAGAAGAGTGCTAATGTGCTGATTCACGACTAGTGACATTAGACTTGAAGA
1 TGAGAAGAATGCTAATGTGCTGATTCAAGGCTAGTGACATTAGACTTAAAAA
* * *
167732 TGAGAAGAATGCTAATGTGTTGATTCAAGGCTAGCGACATTGGACTTAAAAA
1 TGAGAAGAATGCTAATGTGCTGATTCAAGGCTAGTGACATTAGACTTAAAAA
** * * * * ** *
167784 TTTGAAGAATACCAATGTGCTGATTCAAGGCTAGTGACATTGGGCTTAGGAT
1 TGAGAAGAATGCTAATGTGCTGATTCAAGGCTAGTGACATTAGACTTAAAAA
* * * * * * * * * *
167836 TGATAAAAATGCCAATATGTTGATTCAAAGTTAGTGATA-TCGAACTTAAAGA
1 TGAGAAGAATGCTAATGTGCTGATTCAAGGCTAGTGACATTAG-ACTTAAAAA
* * * * * * *
167888 TGACAA-AGGTGCCAATATGTTGATTCAAGGCTAGCGATATTAGACTTAAGAAA
1 TGAGAAGA-ATGCTAATGTGCTGATTCAAGGCTAGTGACATTAGACTTAA-AAA
* * * * *
167941 --A-AA-AATGCCAATGTGCTGATTCAATGCTAGCGACATTGGACTTAGAAA
1 TGAGAAGAATGCTAATGTGCTGATTCAAGGCTAGTGACATTAGACTTAAAAA
167989 -GAGA
1 TGAGA
167993 TAGTTTAACA
Statistics
Matches: 207, Mismatches: 48, Indels: 14
0.77 0.18 0.05
Matches are distributed among these distances:
48 3 0.01
49 35 0.17
50 4 0.02
51 4 0.02
52 157 0.76
53 4 0.02
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (52 bp):
TGAGAAGAATGCTAATGTGCTGATTCAAGGCTAGTGACATTAGACTTAAAAA
Done.