Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018317.1 Corchorus olitorius cultivar O-4 contig18350, 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: 87837
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:210 original size:2 final size:2
Alignment explanation
Indices: 203--247 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
193 AATCAAGGTG
203 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
245 AT A
1 AT A
248 CTCTCTTGGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4359 original size:38 final size:37
Alignment explanation
Indices: 4294--4413 Score: 102
Period size: 38 Copynumber: 3.2 Consensus size: 37
4284 TTAAATATAA
*
4294 ATATATAAATTAT-TATGAAACATTAAAATTAAAAACTT
1 ATATATAAATTATATATTAAA-A-TAAAATTAAAAACTT
* * *
4332 ATATATAAATTATAAATTAAAACTAAAATTATTAATCTT
1 ATATATAAATTATATATTAAAA-TAAAATTA-AAAACTT
* * *
4371 -TAGATATATTATATA-TAAAATAAAATATAAAAATATT
1 ATATATAAATTATATATTAAAATAAAAT-TAAAAA-CTT
4408 ATATAT
1 ATATAT
4414 TTTATTAGCG
Statistics
Matches: 65, Mismatches: 12, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
36 8 0.12
37 9 0.14
38 38 0.58
39 10 0.15
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (37 bp):
ATATATAAATTATATATTAAAATAAAATTAAAAACTT
Found at i:4558 original size:14 final size:14
Alignment explanation
Indices: 4539--4565 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4529 CGGTGTTATA
4539 TCGGTTTCGGTCGG
1 TCGGTTTCGGTCGG
4553 TCGGTTTCGGTCG
1 TCGGTTTCGGTCG
4566 ATTTTAGGCC
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:0.00, C:0.22, G:0.41, T:0.37
Consensus pattern (14 bp):
TCGGTTTCGGTCGG
Found at i:5379 original size:2 final size:2
Alignment explanation
Indices: 5374--5403 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5364 TCGCACTATC
5374 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5404 TAAAACTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5587 original size:4 final size:4
Alignment explanation
Indices: 5578--5612 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
5568 ATGATATTAA
5578 ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATT
1 ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATT
5613 TGAATATCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
ATTG
Found at i:5608 original size:81 final size:80
Alignment explanation
Indices: 5513--5673 Score: 254
Period size: 81 Copynumber: 2.0 Consensus size: 80
5503 TATATATTAA
*
5513 ATTGATTGATTGATTTGA-AT-ATATTTTGATCCAATTAGAATCAATTAGTACTAAAATGATATT
1 ATTGATTGATTGA-TTGATATAATATCTTGATCCAATTAGAATCAATTAGTACT--AATGATATT
5576 AAATTGATTGATTGATTG
63 AAATTGATTGATTGATTG
*
5594 ATTGATTGATTGATTGATTTGAATATCTTGATCCAATTAGAATCAATTAGTACTAATGATATTAA
1 ATTGATTGATTGATTGATAT-AATATCTTGATCCAATTAGAATCAATTAGTACTAATGATATTAA
5659 ATTGATTGATTGATT
65 ATTGATTGATTGATT
5674 TGAATATTGA
Statistics
Matches: 75, Mismatches: 2, Indels: 6
0.90 0.02 0.07
Matches are distributed among these distances:
80 4 0.05
81 40 0.53
83 31 0.41
ACGTcount: A:0.36, C:0.06, G:0.15, T:0.43
Consensus pattern (80 bp):
ATTGATTGATTGATTGATATAATATCTTGATCCAATTAGAATCAATTAGTACTAATGATATTAAA
TTGATTGATTGATTG
Found at i:5683 original size:81 final size:84
Alignment explanation
Indices: 5513--5684 Score: 280
Period size: 83 Copynumber: 2.1 Consensus size: 84
5503 TATATATTAA
*
5513 ATTGATTGATTGATTTGAATATATTTTGATCCAATTAGAATCAATTAGTACTAAAATGATATTAA
1 ATTGATTGATTGATTTGAATATATCTTGATCCAATTAGAATCAATTAGTACT-AAATGATATTAA
*
5578 ATTGATTGATTGATTGATTG
65 ATTGATTGATTGATTGAATG
5598 ATTGATTGATTGATTTG-A-ATATCTTGATCCAATTAGAATCAATTAGTACT-AATGATATTAAA
1 ATTGATTGATTGATTTGAATATATCTTGATCCAATTAGAATCAATTAGTACTAAATGATATTAAA
5660 TTGATTGATTGATTTGAAT-
66 TTGATTGATTGA-TTGAATG
5679 ATTGAT
1 ATTGAT
5685 CAAATTAAAA
Statistics
Matches: 84, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
81 30 0.36
82 5 0.06
83 31 0.37
84 1 0.01
85 17 0.20
ACGTcount: A:0.36, C:0.05, G:0.15, T:0.44
Consensus pattern (84 bp):
ATTGATTGATTGATTTGAATATATCTTGATCCAATTAGAATCAATTAGTACTAAATGATATTAAA
TTGATTGATTGATTGAATG
Found at i:8540 original size:29 final size:28
Alignment explanation
Indices: 8496--8551 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 28
8486 TTCTTCAAAC
* *
8496 TTTCTAATTTCAAGAACGTTCAAGAACA
1 TTTCTAATTTCAAGAACGCTAAAGAACA
8524 TTTCTAATCTTCAAGAACGCTAAAGAAC
1 TTTCTAAT-TTCAAGAACGCTAAAGAAC
8552 GTGGAATAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 8 0.32
29 17 0.68
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (28 bp):
TTTCTAATTTCAAGAACGCTAAAGAACA
Found at i:10704 original size:284 final size:284
Alignment explanation
Indices: 10194--10720 Score: 1009
Period size: 284 Copynumber: 1.9 Consensus size: 284
10184 GATTCGGAAG
* *
10194 CAACACCACAATAACAACGCAAGCAACGGTAAGGTTGCTTCTCCTTCTTCCTATTATTATCTTTT
1 CAACACCACAATAACAACGCAAGCAAAGGTAAGGTTCCTTCTCCTTCTTCCTATTATTATCTTTT
* *
10259 TTTCCTTCGGAGCTTGCCTCTATTTTAGAACAGATCCTAATCAAAGTTTAAAGTTTAAACATTAG
66 TTTCCTTCGGAGCTGGCCTCTATTTTAGAACAGACCCTAATCAAAGTTTAAAGTTTAAACATTAG
10324 AATCCGACAAAGCTACCCAATCAAAGTTTAAACGTTATAGTATCCGATTTCTATCCGGCAGAGCT
131 AATCCGACAAAGCTACCCAATCAAAGTTTAAACGTTATAGTATCCGATTTCTATCCGGCAGAGCT
*
10389 ATCCAATCAAAGTTTAAAAGGCTAGTATCCGATTCTTATCCGATAAAGGAGTATTGATTTTTGTG
196 ATCCAATCAAAGTTTAAAAGGCTAGTATCCGATTCTTATCCGACAAAGGAGTATTGATTTTTGTG
10454 TTAGACAAGTTTGGTTCTTCTTCT
261 TTAGACAAGTTTGGTTCTTCTTCT
10478 CAACACCACAATAACAACGCAAGCAAAGGTAAGGTTCCTTCTCCTTCTTCCTATTATTATCTTTT
1 CAACACCACAATAACAACGCAAGCAAAGGTAAGGTTCCTTCTCCTTCTTCCTATTATTATCTTTT
10543 TTTCCTTCGGAGCTGGCCTCTATTTTAGAACAGACCCTAATCAAAGTTTAAAGTTTAAACATTAG
66 TTTCCTTCGGAGCTGGCCTCTATTTTAGAACAGACCCTAATCAAAGTTTAAAGTTTAAACATTAG
10608 AATCCGACAAAGCTACCCAATCAAAGTTTAAACGTTATAGTATCCGATTTCTATCCGGCAGAGCT
131 AATCCGACAAAGCTACCCAATCAAAGTTTAAACGTTATAGTATCCGATTTCTATCCGGCAGAGCT
10673 ATCCAATCAAAGTTTAAAAGGCTAGTATCCGATTCTTATCCGACAAAG
196 ATCCAATCAAAGTTTAAAAGGCTAGTATCCGATTCTTATCCGACAAAG
10721 CTACCCCATA
Statistics
Matches: 238, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
284 238 1.00
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.32
Consensus pattern (284 bp):
CAACACCACAATAACAACGCAAGCAAAGGTAAGGTTCCTTCTCCTTCTTCCTATTATTATCTTTT
TTTCCTTCGGAGCTGGCCTCTATTTTAGAACAGACCCTAATCAAAGTTTAAAGTTTAAACATTAG
AATCCGACAAAGCTACCCAATCAAAGTTTAAACGTTATAGTATCCGATTTCTATCCGGCAGAGCT
ATCCAATCAAAGTTTAAAAGGCTAGTATCCGATTCTTATCCGACAAAGGAGTATTGATTTTTGTG
TTAGACAAGTTTGGTTCTTCTTCT
Found at i:10723 original size:50 final size:51
Alignment explanation
Indices: 10609--10726 Score: 159
Period size: 51 Copynumber: 2.3 Consensus size: 51
10599 AAACATTAGA
* *
10609 ATCCGACAAAGCTACCCAATCAAAGTTTAAACGTTATAGTATCCGATTTCT
1 ATCCGACAAAGCTACCCAATCAAAGTTTAAAAGTGATAGTATCCGATTTCT
* * * *
10660 ATCCGGCAGAGCTATCCAATCAAAGTTTAAAAG-GCTAGTATCCGA-TTCTT
1 ATCCGACAAAGCTACCCAATCAAAGTTTAAAAGTGATAGTATCCGATTTC-T
10710 ATCCGACAAAGCTACCC
1 ATCCGACAAAGCTACCC
10727 CATATCCCAA
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
49 3 0.05
50 25 0.44
51 29 0.51
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.26
Consensus pattern (51 bp):
ATCCGACAAAGCTACCCAATCAAAGTTTAAAAGTGATAGTATCCGATTTCT
Found at i:11395 original size:14 final size:14
Alignment explanation
Indices: 11376--11404 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
11366 TATATACTAA
11376 ATAGTATTTGAAAG
1 ATAGTATTTGAAAG
11390 ATAGTATTTGAAAG
1 ATAGTATTTGAAAG
11404 A
1 A
11405 GAGATTCTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (14 bp):
ATAGTATTTGAAAG
Found at i:12902 original size:19 final size:19
Alignment explanation
Indices: 12862--12898 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
12852 AATTTTTAAG
12862 TAAAAATATAATATATAAA
1 TAAAAATATAATATATAAA
12881 TAAAAATATAATAT-TAAA
1 TAAAAATATAATATATAAA
12899 ATAATTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:15197 original size:27 final size:27
Alignment explanation
Indices: 15155--15208 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
15145 TACACCATTT
*
15155 CTTCTCGTCTTGAGTGCCATGGTAGCA
1 CTTCTCGTCTTAAGTGCCATGGTAGCA
* *
15182 CTTCTGGTCTTAAGTGGCATGGTAGCA
1 CTTCTCGTCTTAAGTGCCATGGTAGCA
15209 GGGACACCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.17, C:0.22, G:0.28, T:0.33
Consensus pattern (27 bp):
CTTCTCGTCTTAAGTGCCATGGTAGCA
Found at i:16335 original size:29 final size:29
Alignment explanation
Indices: 16293--16354 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
16283 TCATCTAATC
16293 TGGGTTTGTTGAGAAAAGTCTTAGAGATT
1 TGGGTTTGTTGAGAAAAGTCTTAGAGATT
16322 TGGGTTTGTTGAGAAAAGTCTTAGAGATT
1 TGGGTTTGTTGAGAAAAGTCTTAGAGATT
16351 TGGG
1 TGGG
16355 ATTTATAGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.26, C:0.03, G:0.34, T:0.37
Consensus pattern (29 bp):
TGGGTTTGTTGAGAAAAGTCTTAGAGATT
Found at i:16443 original size:14 final size:14
Alignment explanation
Indices: 16424--16452 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
16414 GAAGCATAAA
16424 CAAACCAGAATTGG
1 CAAACCAGAATTGG
16438 CAAACCAGAATTGG
1 CAAACCAGAATTGG
16452 C
1 C
16453 GGACTTAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.24, G:0.21, T:0.14
Consensus pattern (14 bp):
CAAACCAGAATTGG
Found at i:23194 original size:2 final size:2
Alignment explanation
Indices: 23187--23215 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
23177 AAATAAATAA
23187 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
23216 AGATAAGGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:36909 original size:1 final size:1
Alignment explanation
Indices: 36905--36937 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
36895 CCTTTTTAGG
36905 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
36938 CAGAAATACG
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:37339 original size:26 final size:26
Alignment explanation
Indices: 37298--37347 Score: 84
Period size: 26 Copynumber: 1.9 Consensus size: 26
37288 CAGCCTTTTC
37298 ATTACAACAACTGATTATTTTATCGG
1 ATTACAACAACTGATTATTTTATCGG
37324 ATTACAACAA-TGGATTATTTTATC
1 ATTACAACAACT-GATTATTTTATC
37348 AGATCGAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 1 0.04
26 22 0.96
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (26 bp):
ATTACAACAACTGATTATTTTATCGG
Found at i:38026 original size:21 final size:20
Alignment explanation
Indices: 37987--38026 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
37977 TTTGGATGAT
* *
37987 GTTGGAAAACCAGCTTTGCA
1 GTTGGAAAACAACCTTTGCA
38007 GTTGGAAAAGCAACCTTTGC
1 GTTGGAAAA-CAACCTTTGC
38027 TCGAATCTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (20 bp):
GTTGGAAAACAACCTTTGCA
Found at i:42620 original size:9 final size:9
Alignment explanation
Indices: 42608--42633 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
42598 TCGGTTCGGT
42608 CGGTTTTGG
1 CGGTTTTGG
42617 CGGTTTTGG
1 CGGTTTTGG
42626 CGGTTTTG
1 CGGTTTTG
42634 ACAGTTTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.12, G:0.42, T:0.46
Consensus pattern (9 bp):
CGGTTTTGG
Found at i:45743 original size:2 final size:2
Alignment explanation
Indices: 45738--45767 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
45728 TAATTACAGA
45738 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45768 TCATGTGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45945 original size:9 final size:9
Alignment explanation
Indices: 45933--45968 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
45923 CATATTTCAT
45933 TCATCAATA
1 TCATCAATA
45942 TCATCAATCA
1 TCATCAAT-A
*
45952 CCATCAATA
1 TCATCAATA
45961 TCATCAAT
1 TCATCAAT
45969 CATTTACTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.31
Consensus pattern (9 bp):
TCATCAATA
Found at i:45958 original size:19 final size:19
Alignment explanation
Indices: 45934--45970 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
45924 ATATTTCATT
45934 CATCAATATCATCAATCAC
1 CATCAATATCATCAATCAC
45953 CATCAATATCATCAATCA
1 CATCAATATCATCAATCA
45971 TTTACTTAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.43, C:0.30, G:0.00, T:0.27
Consensus pattern (19 bp):
CATCAATATCATCAATCAC
Found at i:63522 original size:3 final size:3
Alignment explanation
Indices: 63516--63541 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
63506 AATTTTTGAA
63516 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
63542 CCATATATGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:67448 original size:21 final size:21
Alignment explanation
Indices: 67422--67466 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
67412 ATGATACTTC
67422 AAACTCGATGCCTTTCACTAG
1 AAACTCGATGCCTTTCACTAG
67443 AAACTCGATGCCTTTCACTAG
1 AAACTCGATGCCTTTCACTAG
67464 AAA
1 AAA
67467 TTTCAAGTTC
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:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (21 bp):
AAACTCGATGCCTTTCACTAG
Found at i:71772 original size:31 final size:31
Alignment explanation
Indices: 71737--71811 Score: 134
Period size: 30 Copynumber: 2.5 Consensus size: 31
71727 AGACCGAAAT
71737 TGGAGTAATAATTTTTTGATAAATAAAAAAC
1 TGGAGTAATAATTTTTTGATAAATAAAAAAC
*
71768 TGGAGTAATAA-TTTTTGATAAATAAAAAGC
1 TGGAGTAATAATTTTTTGATAAATAAAAAAC
71798 TGGAGTAATAATTT
1 TGGAGTAATAATTT
71812 GATTAATTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
30 29 0.69
31 13 0.31
ACGTcount: A:0.45, C:0.03, G:0.16, T:0.36
Consensus pattern (31 bp):
TGGAGTAATAATTTTTTGATAAATAAAAAAC
Found at i:71876 original size:15 final size:15
Alignment explanation
Indices: 71858--71894 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
71848 GTAGAGGATT
71858 ATTTTGATTAATCTG
1 ATTTTGATTAATCTG
71873 ATTTTGATTAATCTG
1 ATTTTGATTAATCTG
*
71888 AATTTGA
1 ATTTTGA
71895 CTTGCATCGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.30, C:0.05, G:0.14, T:0.51
Consensus pattern (15 bp):
ATTTTGATTAATCTG
Found at i:73887 original size:10 final size:10
Alignment explanation
Indices: 73872--73909 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
73862 CCGTTTAATA
73872 ATTATATATT
1 ATTATATATT
73882 ATTATATA-T
1 ATTATATATT
73891 ATCTA-ATATT
1 AT-TATATATT
73901 ATTATATAT
1 ATTATATAT
73910 AAAATAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
9 8 0.32
10 17 0.68
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (10 bp):
ATTATATATT
Found at i:73919 original size:21 final size:19
Alignment explanation
Indices: 73877--73938 Score: 61
Period size: 19 Copynumber: 3.1 Consensus size: 19
73867 TAATAATTAT
**
73877 ATATTATTATATATATCTA
1 ATATTATTATATATAAATA
73896 ATATTATTATATATAAAATAA
1 ATATTATTATATAT-AAAT-A
*
73917 ATATTTAATTATATATTAATA
1 ATA-TT-ATTATATATAAATA
73938 A
1 A
73939 ACGATCGGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
19 14 0.39
20 2 0.06
21 6 0.17
22 5 0.14
23 9 0.25
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (19 bp):
ATATTATTATATATAAATA
Found at i:78285 original size:7 final size:7
Alignment explanation
Indices: 78273--78297 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
78263 TCCCATACTA
78273 TATATAG
1 TATATAG
78280 TATATAG
1 TATATAG
78287 TATATAG
1 TATATAG
78294 TATA
1 TATA
78298 ATATAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (7 bp):
TATATAG
Found at i:86879 original size:24 final size:24
Alignment explanation
Indices: 86826--86887 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 24
86816 GGCGCGTTGT
* * *
86826 CACTTCGGATGGGGGGTGTGCTCC
1 CACTTCCGATGGTGGGTGCGCTCC
**
86850 TGCTTCCGATGGTGGGTGCGCTCC
1 CACTTCCGATGGTGGGTGCGCTCC
*
86874 CACTTCTGATGGTG
1 CACTTCCGATGGTG
86888 AGCATTCCAC
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.08, C:0.26, G:0.37, T:0.29
Consensus pattern (24 bp):
CACTTCCGATGGTGGGTGCGCTCC
Found at i:87168 original size:28 final size:28
Alignment explanation
Indices: 87137--87791 Score: 566
Period size: 28 Copynumber: 23.4 Consensus size: 28
87127 TTGTCTTCGA
*
87137 GAGCGTACTACCTCTTCGCGATCTTTGG
1 GAGCGTACTACCGCTTCGCGATCTTTGG
* *
87165 GAGCGTACTACCGCTTCGCGGTCGTTGG
1 GAGCGTACTACCGCTTCGCGATCTTTGG
*
87193 GAGCGTACTACCGCTTCGCGGTCTTTGG
1 GAGCGTACTACCGCTTCGCGATCTTTGG
* * *
87221 GAGTGTACTACCGCTTCGCGATCCTTGA
1 GAGCGTACTACCGCTTCGCGATCTTTGG
* * * * *
87249 GAGCGTACTACCACCTCGAGAGCTTGGAGG
1 GAGCGTACTACCGCTTCGCGATCTT--TGG
* * ** *
87279 GGGCGTTCTACCAATTCGCGAGCTTTGG
1 GAGCGTACTACCGCTTCGCGATCTTTGG
*
87307 GAGCGTACTACCGCTTCGCGCTCTTTGG
1 GAGCGTACTACCGCTTCGCGATCTTTGG
*** * *
87335 GAGCGTACTA-CGCATTTTTG-TCTTCGA
1 GAGCGTACTACCGC-TTCGCGATCTTTGG
*
87362 GAGCGTACTACCTCTTCGCGATCTTTGG
1 GAGCGTACTACCGCTTCGCGATCTTTGG
* * *
87390 GAGCGTACTACTGCTTCGCGATCCTTGA
1 GAGCGTACTACCGCTTCGCGATCTTTGG
* *
87418 GAGCGTACTACCGCTTCGCGGTCGTTGG
1 GAGCGTACTACCGCTTCGCGATCTTTGG
* *
87446 GAGTGTACTACCGCTTCGCGCTCTTTGG
1 GAGCGTACTACCGCTTCGCGATCTTTGG
* * *
87474 GAGCGTACTACAGCTTCACGCTCTTTGG
1 GAGCGTACTACCGCTTCGCGATCTTTGG
* * *
87502 GAGCGTACTACAGCTTCACGCTCTTTGG
1 GAGCGTACTACCGCTTCGCGATCTTTGG
* * * *
87530 GAGCGTACTACCACCTCGAGAGC-TTGG
1 GAGCGTACTACCGCTTCGCGATCTTTGG
* ** * *
87557 AGGGCGTACTACCATTTCGTGATCTTTGA
1 -GAGCGTACTACCGCTTCGCGATCTTTGG
* * * *
87586 G-GCGTACTACCACTTTGCGATCCTTGA
1 GAGCGTACTACCGCTTCGCGATCTTTGG
* * * *
87613 GAGCGTACTACCGCTTTGTGGTCGTTGG
1 GAGCGTACTACCGCTTCGCGATCTTTGG
*
87641 GAGCGTACTACCGCTTCGCGCTCTTTGG
1 GAGCGTACTACCGCTTCGCGATCTTTGG
* * *
87669 GAGCGTACTATCGCTTCACGCTCTTTGG
1 GAGCGTACTACCGCTTCGCGATCTTTGG
* * * * *
87697 GAACGTACTACCACCTCGAGAGC-TTGG
1 GAGCGTACTACCGCTTCGCGATCTTTGG
* ** * * *
87724 AGGGCGTACTACCATTTCGTGAACTTTGA
1 -GAGCGTACTACCGCTTCGCGATCTTTGG
* * * *
87753 G-GCGTACTACCACTTTGCGATCCTTGA
1 GAGCGTACTACCGCTTCGCGATCTTTGG
87780 GAGCGTACTACC
1 GAGCGTACTACC
87792 ACCTCGGGAG
Statistics
Matches: 515, Mismatches: 101, Indels: 22
0.81 0.16 0.03
Matches are distributed among these distances:
27 74 0.14
28 414 0.80
29 6 0.01
30 21 0.04
ACGTcount: A:0.16, C:0.28, G:0.28, T:0.28
Consensus pattern (28 bp):
GAGCGTACTACCGCTTCGCGATCTTTGG
Found at i:87593 original size:167 final size:166
Alignment explanation
Indices: 87137--87791 Score: 690
Period size: 167 Copynumber: 3.9 Consensus size: 166
87127 TTGTCTTCGA
* * * * *
87137 GAGCGTACTACCTCTTCGCGATCTTTGGGAGCGTACTACCGCTTCGCGGTCGTTGGGAGCGTACT
1 GAGCGTACTACCGCTTCGCGCTCTTTGGGAGCGTACTA-CGCTTCACGCTCTTTGGGAGCGTACT
* * * * * ** * * *
87202 ACCGCTTCGCG-GTCTTTGG-GAGTGTACTACCGCTTCGCGATCCTTGAGAGCGTACTACCACCT
65 ACCACCTCGAGAG-C-TTGGAGGGCGTACTACCATTTCGTGATCTTTGAG-GCGTACTACCACTT
* * * * * ** **
87265 CGAGA-GCTTGGAGGGGGCGTTCTACCAATTCGCGAGCTTTGG
127 TGCGATCCTT-GA--GAGCGTACTACCGCTTCGCGCTCTTTGG
*** * *
87307 GAGCGTACTACCGCTTCGCGCTCTTTGGGAGCGTACTACGCATTTTTG-TCTTCGAGAGCGTACT
1 GAGCGTACTACCGCTTCGCGCTCTTTGGGAGCGTACTACGC-TTCACGCTCTTTGGGAGCGTACT
* * * * * *** * * * *
87371 ACCTCTTCGCGATCTTTGG-GAGCGTACTACTGCTTCGCGATCCTTGAGAGCGTACTACCGCTTC
65 ACCACCTCGAGAGC-TTGGAGGGCGTACTACCATTTCGTGATCTTTGAG-GCGTACTACCACTTT
* * * *
87435 GCGGTCGTTGGGAGTGTACTACCGCTTCGCGCTCTTTGG
128 GCGATCCTTGAGAGCGTACTACCGCTTCGCGCTCTTTGG
* *
87474 GAGCGTACTACAGCTTCACGCTCTTTGGGAGCGTACTACAGCTTCACGCTCTTTGGGAGCGTACT
1 GAGCGTACTACCGCTTCGCGCTCTTTGGGAGCGTACTAC-GCTTCACGCTCTTTGGGAGCGTACT
87539 ACCACCTCGAGAGCTTGGAGGGCGTACTACCATTTCGTGATCTTTGAGGCGTACTACCACTTTGC
65 ACCACCTCGAGAGCTTGGAGGGCGTACTACCATTTCGTGATCTTTGAGGCGTACTACCACTTTGC
* * * *
87604 GATCCTTGAGAGCGTACTACCGCTTTGTGGTCGTTGG
130 GATCCTTGAGAGCGTACTACCGCTTCGCGCTCTTTGG
*
87641 GAGCGTACTACCGCTTCGCGCTCTTTGGGAGCGTACTATCGCTTCACGCTCTTTGGGAACGTACT
1 GAGCGTACTACCGCTTCGCGCTCTTTGGGAGCGTACTA-CGCTTCACGCTCTTTGGGAGCGTACT
*
87706 ACCACCTCGAGAGCTTGGAGGGCGTACTACCATTTCGTGAACTTTGAGGCGTACTACCACTTTGC
65 ACCACCTCGAGAGCTTGGAGGGCGTACTACCATTTCGTGATCTTTGAGGCGTACTACCACTTTGC
87771 GATCCTTGAGAGCGTACTACC
130 GATCCTTGAGAGCGTACTACC
87792 ACCTCGGGAG
Statistics
Matches: 421, Mismatches: 57, Indels: 17
0.85 0.12 0.03
Matches are distributed among these distances:
167 254 0.60
168 50 0.12
169 76 0.18
170 41 0.10
ACGTcount: A:0.16, C:0.28, G:0.28, T:0.28
Consensus pattern (166 bp):
GAGCGTACTACCGCTTCGCGCTCTTTGGGAGCGTACTACGCTTCACGCTCTTTGGGAGCGTACTA
CCACCTCGAGAGCTTGGAGGGCGTACTACCATTTCGTGATCTTTGAGGCGTACTACCACTTTGCG
ATCCTTGAGAGCGTACTACCGCTTCGCGCTCTTTGG
Found at i:87595 original size:195 final size:195
Alignment explanation
Indices: 87165--87707 Score: 608
Period size: 195 Copynumber: 2.8 Consensus size: 195
87155 CGATCTTTGG
* * * * * * * * *
87165 GAGCGTACTACCGCTTCGCGGTCGTTGGGAGCGTACTACCGCTTCGCGGTCTTTGGGAGTGTACT
1 GAGCGTACTACCTCTTCGCGATCTTTGAGAGCGTACTACCACTTCGCGATCCTTGAGAGCGTACT
* * * * * * ** * * * * **
87230 ACCGCTTCGCGATCCTTGAGAGCGTACTACCACCTCGAGAGCTTGGAGGGGGCGTTCTACCAATT
66 ACCGCTTCGCGGTCGTTGGGAGCGTACTACCGCTTCGCGCTCTT--TGGGAGCGTACTATCGCTT
* ** * * * *** *
87295 CGCGAGCTTTGGGAGCGTACTACCGCTTCGCGCTCTTTGGGAGCGTACTACGCATTTTTGTCTTC
129 CACGCTCTTTGGGAGCGTACTACAGCTTCACGCTCTTTGGGAGCGTACTACGCACTCGAGGCTTC
87360 GA
194 GA
* **
87362 GAGCGTACTACCTCTTCGCGATCTTTGGGAGCGTACTACTGCTTCGCGATCCTTGAGAGCGTACT
1 GAGCGTACTACCTCTTCGCGATCTTTGAGAGCGTACTACCACTTCGCGATCCTTGAGAGCGTACT
*
87427 ACCGCTTCGCGGTCGTTGGGAGTGTACTACCGCTTCGCGCTCTTTGGGAGCGTACTA-CAGCTTC
66 ACCGCTTCGCGGTCGTTGGGAGCGTACTACCGCTTCGCGCTCTTTGGGAGCGTACTATC-GCTTC
87491 ACGCTCTTTGGGAGCGTACTACAGCTTCACGCTCTTTGGGAGCGTACTAC-CACCTCGAGAGCTT
130 ACGCTCTTTGGGAGCGTACTACAGCTTCACGCTCTTTGGGAGCGTACTACGCA-CTCGAG-GCTT
*
87555 GGA
193 CGA
* * *
87558 GGGCGTACTACCAT-TTCGTGATCTTTGAG-GCGTACTACCACTTTGCGATCCTTGAGAGCGTAC
1 GAGCGTACTACC-TCTTCGCGATCTTTGAGAGCGTACTACCACTTCGCGATCCTTGAGAGCGTAC
* *
87621 TACCGCTTTGTGGTCGTTGGGAGCGTACTACCGCTTCGCGCTCTTTGGGAGCGTACTATCGCTTC
65 TACCGCTTCGCGGTCGTTGGGAGCGTACTACCGCTTCGCGCTCTTTGGGAGCGTACTATCGCTTC
*
87686 ACGCTCTTTGGGAACGTACTAC
130 ACGCTCTTTGGGAGCGTACTAC
87708 CACCTCGAGA
Statistics
Matches: 298, Mismatches: 43, Indels: 12
0.84 0.12 0.03
Matches are distributed among these distances:
194 3 0.01
195 172 0.58
196 30 0.10
197 93 0.31
ACGTcount: A:0.16, C:0.28, G:0.28, T:0.28
Consensus pattern (195 bp):
GAGCGTACTACCTCTTCGCGATCTTTGAGAGCGTACTACCACTTCGCGATCCTTGAGAGCGTACT
ACCGCTTCGCGGTCGTTGGGAGCGTACTACCGCTTCGCGCTCTTTGGGAGCGTACTATCGCTTCA
CGCTCTTTGGGAGCGTACTACAGCTTCACGCTCTTTGGGAGCGTACTACGCACTCGAGGCTTCGA
Found at i:87792 original size:83 final size:83
Alignment explanation
Indices: 87530--87837 Score: 359
Period size: 83 Copynumber: 3.7 Consensus size: 83
87520 CGCTCTTTGG
* *
87530 GAGCGTACTACCACCTCGAGAGCTTGGAGGGCGTACTACCATTTCGTGATCTTTGAGGCGTACTA
1 GAGCGTACTACCACCTCGAGAGCTTGGAGGGCGTACTACCATTTCGCGAACTTTGAGGCGTACTA
87595 CCACTTTGCGATCCTTGA
66 CCACTTTGCGATCCTTGA
* * * * * ** ** *
87613 GAGCGTACTACCGCTTTGTG-GTCGTTGG-GAGCGTACTACCGCTTCGCGCTCTTTGGGAGCGTA
1 GAGCGTACTACCACCTCGAGAG-C-TTGGAGGGCGTACTACCATTTCGCGAACTTTGAG-GCGTA
* * ** * * *
87676 CTATCGCTTCACGCTCTTTGG
63 CTACCACTTTGCGATCCTTGA
* *
87697 GAACGTACTACCACCTCGAGAGCTTGGAGGGCGTACTACCATTTCGTGAACTTTGAGGCGTACTA
1 GAGCGTACTACCACCTCGAGAGCTTGGAGGGCGTACTACCATTTCGCGAACTTTGAGGCGTACTA
87762 CCACTTTGCGATCCTTGA
66 CCACTTTGCGATCCTTGA
* * *
87780 GAGCGTACTACCACCTCGGGAGCTTGGAGGGAGTACTACTATTTCGCGAACTTTGAGG
1 GAGCGTACTACCACCTCGAGAGCTTGGAGGGCGTACTACCATTTCGCGAACTTTGAGG
Statistics
Matches: 179, Mismatches: 41, Indels: 10
0.78 0.18 0.04
Matches are distributed among these distances:
82 1 0.01
83 116 0.65
84 61 0.34
85 1 0.01
ACGTcount: A:0.19, C:0.26, G:0.27, T:0.28
Consensus pattern (83 bp):
GAGCGTACTACCACCTCGAGAGCTTGGAGGGCGTACTACCATTTCGCGAACTTTGAGGCGTACTA
CCACTTTGCGATCCTTGA
Found at i:87837 original size:28 final size:28
Alignment explanation
Indices: 87524--87837 Score: 124
Period size: 28 Copynumber: 11.3 Consensus size: 28
87514 GCTTCACGCT
** * *
87524 CTTTG-GGAGCGTACTACCACCTCGAGAG
1 CTTTGAGG-GCGTACTACCATTTCGCGAA
* * *
87552 CTTGGAGGGCGTACTACCATTTCGTGAT
1 CTTTGAGGGCGTACTACCATTTCGCGAA
*
87580 CTTTGA-GGCGTACTACCACTTT-GCGAT
1 CTTTGAGGGCGTACTACCA-TTTCGCGAA
* * * * **
87607 CCTTGAGAGCGTACTACCGCTTT-GTGGT
1 CTTTGAGGGCGTACTACC-ATTTCGCGAA
* ** **
87635 CGTTG-GGAGCGTACTACCGCTTCGCGCT
1 CTTTGAGG-GCGTACTACCATTTCGCGAA
* ** * **
87663 CTTTG-GGAGCGTACTATCGCTTCACGCT
1 CTTTGAGG-GCGTACTACCATTTCGCGAA
* ** * *
87691 CTTTG-GGAACGTACTACCACCTCGAGAG
1 CTTTGAGG-GCGTACTACCATTTCGCGAA
* *
87719 CTTGGAGGGCGTACTACCATTTCGTGAA
1 CTTTGAGGGCGTACTACCATTTCGCGAA
*
87747 CTTTGA-GGCGTACTACCACTTT-GCGAT
1 CTTTGAGGGCGTACTACCA-TTTCGCGAA
* * ** * *
87774 CCTTGAGAGCGTACTACCACCTCGGGAG
1 CTTTGAGGGCGTACTACCATTTCGCGAA
* * *
87802 CTTGGAGGGAGTACTACTATTTCGCGAA
1 CTTTGAGGGCGTACTACCATTTCGCGAA
87830 CTTTGAGG
1 CTTTGAGG
Statistics
Matches: 222, Mismatches: 54, Indels: 20
0.75 0.18 0.07
Matches are distributed among these distances:
27 45 0.20
28 173 0.78
29 4 0.02
ACGTcount: A:0.19, C:0.26, G:0.27, T:0.28
Consensus pattern (28 bp):
CTTTGAGGGCGTACTACCATTTCGCGAA
Done.