Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016521.1 Corchorus capsularis cultivar CVL-1 contig16542, 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: 16446
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.29
Found at i:3741 original size:5 final size:5
Alignment explanation
Indices: 3731--3765 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
3721 TCTGGTCGAA
3731 ATTTT ATTTT ATTTT ATTTT ATTTT -TTTAT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTT-T ATTTT
3766 TCGATATAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 3 0.11
5 22 0.79
6 3 0.11
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:3867 original size:8 final size:8
Alignment explanation
Indices: 3839--3872 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
3829 GAATCGGCTA
3839 TGAATTTT
1 TGAATTTT
*
3847 TGAAGTTTC
1 TGAA-TTTT
3856 TGAATTTT
1 TGAATTTT
3864 TGAATTTT
1 TGAATTTT
3872 T
1 T
3873 CAAGAAGGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59
Consensus pattern (8 bp):
TGAATTTT
Found at i:6458 original size:21 final size:21
Alignment explanation
Indices: 6341--6589 Score: 224
Period size: 21 Copynumber: 11.7 Consensus size: 21
6331 AAAGGAGCAG
6341 AAAATAGTAATCAGTAAAAGAGT
1 AAAATAGTAATCAGT--AAGAGT
*
6364 AAAATAGTAATCAGTAGAAAGT
1 AAAATAGTAATCAGTA-AGAGT
* **
6386 AAGAA-GGTAATCAACAAGAGT
1 AA-AATAGTAATCAGTAAGAGT
* *
6407 AAAATAGTAGTCAGTAAAAAGT
1 AAAATAGTAATCAGT-AAGAGT
* *
6429 AAAA-GGTAATTAGTAAGAGT
1 AAAATAGTAATCAGTAAGAGT
* * *
6449 AAAATAGTAATCGGCAAAAAGT
1 AAAATAGTAATCAG-TAAGAGT
6471 -AAATAGTAATCAGTAAGAGT
1 AAAATAGTAATCAGTAAGAGT
*
6491 AAAATAGCAATCAGTAAGAAGT
1 AAAATAGTAATCAGTAAG-AGT
*
6513 AAAA-GGTAATCAGTAAGAGT
1 AAAATAGTAATCAGTAAGAGT
6533 AAAA-AGGTAATCAGTAAAGAGT
1 AAAATA-GTAATCAGT-AAGAGT
6555 AAAA-AGTTAATCAGTAAGAAGT
1 AAAATAG-TAATCAGTAAG-AGT
*
6577 AAAA-GGTAATCAG
1 AAAATAGTAATCAG
6590 CAAAAAGCAA
Statistics
Matches: 187, Mismatches: 27, Indels: 26
0.78 0.11 0.11
Matches are distributed among these distances:
20 23 0.12
21 85 0.45
22 62 0.33
23 17 0.09
ACGTcount: A:0.53, C:0.06, G:0.20, T:0.20
Consensus pattern (21 bp):
AAAATAGTAATCAGTAAGAGT
Found at i:6601 original size:21 final size:21
Alignment explanation
Indices: 6339--6644 Score: 152
Period size: 21 Copynumber: 14.3 Consensus size: 21
6329 AAAAAGGAGC
6339 AGAAAATA-GTAATCAGTAAAA
1 AGAAAA-AGGTAATCAGTAAAA
*
6360 GAGTAAAATA-GTAATCAGTAGAA
1 -AG-AAAA-AGGTAATCAGTAAAA
* *
6383 AGTAAGAAGGTAATCA--ACAAG
1 AG-AAAAAGGTAATCAGTA-AAA
*
6404 AGTAAAATA-GTAGTCAGTAAAA
1 AG-AAAA-AGGTAATCAGTAAAA
* * *
6426 AGTAAAAGGTAATTAGT-AAG
1 AGAAAAAGGTAATCAGTAAAA
* *
6446 AGTAAAATA-GTAATCGGCAAAA
1 AG-AAAA-AGGTAATCAGTAAAA
* *
6468 AGTAAATA-GTAATCAGT-AAG
1 AG-AAAAAGGTAATCAGTAAAA
* *
6488 AGTAAAATA-GCAATCAGTAAGA
1 AG-AAAA-AGGTAATCAGTAAAA
* *
6510 AGTAAAAGGTAATCAGT-AAG
1 AGAAAAAGGTAATCAGTAAAA
*
6530 AGTAAAAAGGTAATCAGTAAAG
1 AG-AAAAAGGTAATCAGTAAAA
* *
6552 AGTAAAAAGTTAATCAGTAAGA
1 AG-AAAAAGGTAATCAGTAAAA
* *
6574 AGTAAAAGGTAATCAGCAAAA
1 AGAAAAAGGTAATCAGTAAAA
*
6595 AGCAAAAAGGCAATCAGTAAAAA
1 AG-AAAAAGGTAATCAGT-AAAA
*
6618 AGTAAAAGAGG-AATTAGTAAAA
1 AG-AAAA-AGGTAATCAGTAAAA
6640 A-AAAA
1 AGAAAA
6645 TGATAAAGAG
Statistics
Matches: 225, Mismatches: 41, Indels: 38
0.74 0.13 0.12
Matches are distributed among these distances:
20 22 0.10
21 92 0.41
22 73 0.32
23 35 0.16
24 3 0.01
ACGTcount: A:0.56, C:0.06, G:0.20, T:0.19
Consensus pattern (21 bp):
AGAAAAAGGTAATCAGTAAAA
Found at i:6602 original size:43 final size:43
Alignment explanation
Indices: 6347--6614 Score: 312
Period size: 42 Copynumber: 6.3 Consensus size: 43
6337 GCAGAAAATA
* *
6347 GTAATCAGTAAAAGAGTAAAATAGTAATCAGTAGAAAGTAAGAAG
1 GTAATCAGT--AAGAGTAAAATAGTAATCAGTAAAAAGTAAAAAG
** *
6392 GTAATCAACAAGAGTAAAATAGTAGTCAGTAAAAAGT-AAAAG
1 GTAATCAGTAAGAGTAAAATAGTAATCAGTAAAAAGTAAAAAG
* * * *
6434 GTAATTAGTAAGAGTAAAATAGTAATCGGCAAAAAGTAAATA-
1 GTAATCAGTAAGAGTAAAATAGTAATCAGTAAAAAGTAAAAAG
* *
6476 GTAATCAGTAAGAGTAAAATAGCAATCAGTAAGAAGT-AAAAG
1 GTAATCAGTAAGAGTAAAATAGTAATCAGTAAAAAGTAAAAAG
*
6518 GTAATCAGTAAGAGTAAAA-AGGTAATCAGTAAAGAGTAAAAAG
1 GTAATCAGTAAGAGTAAAATA-GTAATCAGTAAAAAGTAAAAAG
* * * *
6561 TTAATCAGTAAGAAGTAAAA-GGTAATCAGCAAAAAGCAAAAAG
1 GTAATCAGTAAG-AGTAAAATAGTAATCAGTAAAAAGTAAAAAG
*
6604 GCAATCAGTAA
1 GTAATCAGTAA
6615 AAAAGTAAAA
Statistics
Matches: 190, Mismatches: 28, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
41 4 0.02
42 99 0.52
43 73 0.38
44 7 0.04
45 7 0.04
ACGTcount: A:0.53, C:0.07, G:0.21, T:0.19
Consensus pattern (43 bp):
GTAATCAGTAAGAGTAAAATAGTAATCAGTAAAAAGTAAAAAG
Found at i:6624 original size:22 final size:21
Alignment explanation
Indices: 6347--6640 Score: 222
Period size: 22 Copynumber: 13.7 Consensus size: 21
6337 GCAGAAAATA
*
6347 GTAATCAGTAAAAGAGTAAAATA
1 GTAATCAGTAAAA-AGTAAAA-G
*
6370 GTAATCAGTAGAAAGTAAGAAG
1 GTAATCAGTAAAAAGTAA-AAG
* *
6392 GTAATCA--ACAAGAGTAAAATA
1 GTAATCAGTA-AAAAGTAAAA-G
*
6413 GTAGTCAGTAAAAAGTAAAAG
1 GTAATCAGTAAAAAGTAAAAG
* * *
6434 GTAATTAGT-AAGAGTAAAATA
1 GTAATCAGTAAAAAGTAAAA-G
* *
6455 GTAATCGGCAAAAAGTAAATA-
1 GTAATCAGTAAAAAGTAAA-AG
* *
6476 GTAATCAGT-AAGAGTAAAATA
1 GTAATCAGTAAAAAGTAAAA-G
* *
6497 GCAATCAGTAAGAAGTAAAAG
1 GTAATCAGTAAAAAGTAAAAG
*
6518 GTAATCAGT-AAGAGTAAAAAG
1 GTAATCAGTAAAAAGT-AAAAG
*
6539 GTAATCAGTAAAGAGTAAAAAG
1 GTAATCAGTAAAAAGT-AAAAG
* *
6561 TTAATCAGTAAGAAGTAAAAG
1 GTAATCAGTAAAAAGTAAAAG
* *
6582 GTAATCAGCAAAAAGCAAAAAG
1 GTAATCAGTAAAAAG-TAAAAG
*
6604 GCAATCAGTAAAAAAGTAAAAG
1 GTAATCAGT-AAAAAGTAAAAG
* *
6626 AGGAATTAGTAAAAA
1 -GTAATCAGTAAAAA
6641 AAAATGATAA
Statistics
Matches: 217, Mismatches: 38, Indels: 33
0.75 0.13 0.11
Matches are distributed among these distances:
19 1 0.00
20 24 0.11
21 79 0.36
22 84 0.39
23 29 0.13
ACGTcount: A:0.54, C:0.06, G:0.20, T:0.19
Consensus pattern (21 bp):
GTAATCAGTAAAAAGTAAAAG
Found at i:6660 original size:7 final size:7
Alignment explanation
Indices: 6648--6769 Score: 73
Period size: 7 Copynumber: 18.4 Consensus size: 7
6638 AAAAAAATGA
6648 TAAAGAG
1 TAAAGAG
6655 TAAAGAG
1 TAAAGAG
6662 T-AA-AG
1 TAAAGAG
6667 TAAAGAG
1 TAAAGAG
**
6674 TAATCAG
1 TAAAGAG
6681 TAAAGA-
1 TAAAGAG
* *
6687 AAAAAAG
1 TAAAGAG
* *
6694 TAAAATAA
1 T-AAAGAG
*
6702 TGAAGAG
1 TAAAGAG
6709 TAAAGA-
1 TAAAGAG
6715 -AAAGAG
1 TAAAGAG
**
6721 TAATCAG
1 TAAAGAG
6728 TAAAGA-
1 TAAAGAG
*
6734 -AAAGTGG
1 TAAAG-AG
6741 TAAAGAG
1 TAAAGAG
6748 TAAAGAG
1 TAAAGAG
6755 T--AGAG
1 TAAAGAG
6760 TAAAGAG
1 TAAAGAG
6767 TAA
1 TAA
6770 TCAGCAAAGG
Statistics
Matches: 85, Mismatches: 19, Indels: 22
0.67 0.15 0.17
Matches are distributed among these distances:
5 17 0.20
6 8 0.09
7 51 0.60
8 9 0.11
ACGTcount: A:0.58, C:0.02, G:0.24, T:0.16
Consensus pattern (7 bp):
TAAAGAG
Found at i:6667 original size:47 final size:46
Alignment explanation
Indices: 6616--6773 Score: 178
Period size: 46 Copynumber: 3.4 Consensus size: 46
6606 AATCAGTAAA
* *
6616 AAAGTAAAAGAGGAATTAGTAAAAAAAAATGATAAAGAGTAAAGAGT
1 AAAGTAAAAGAGTAATCAGTAAAAAAAAATG-TAAAGAGTAAAGAGT
* * * *
6663 AAAGT-AAAGAGTAATCAGTAAAGAAAAAAAGTAAAATAATGAAGAGT
1 AAAGTAAAAGAGTAATCAGTAAA-AAAAAATGT-AAAGAGTAAAGAGT
* *
6710 AAAG-AAAAGAGTAATCAGTAAAGAAAAGTGGTAAAGAGTAAAGAGT
1 AAAGTAAAAGAGTAATCAGTAAAAAAAAAT-GTAAAGAGTAAAGAGT
*
6756 AGAGT-AAAGAGTAATCAG
1 AAAGTAAAAGAGTAATCAG
6774 CAAAGGTAAA
Statistics
Matches: 93, Mismatches: 13, Indels: 11
0.79 0.11 0.09
Matches are distributed among these distances:
46 47 0.51
47 46 0.49
ACGTcount: A:0.59, C:0.02, G:0.23, T:0.16
Consensus pattern (46 bp):
AAAGTAAAAGAGTAATCAGTAAAAAAAAATGTAAAGAGTAAAGAGT
Found at i:6672 original size:19 final size:18
Alignment explanation
Indices: 6648--6769 Score: 65
Period size: 19 Copynumber: 6.6 Consensus size: 18
6638 AAAAAAATGA
6648 TAAAGAGTAAAGAGTAAAG
1 TAAAGAGTAAAGA-TAAAG
6667 TAAAGAGTAATCAG-TAAAG
1 TAAAGAGTAA--AGATAAAG
* *
6686 AAAAAAAGTAAA-AT-AA-
1 -TAAAGAGTAAAGATAAAG
* *
6702 TGAAGAGTAAAGAAAAGAG
1 TAAAGAGTAAAGATAA-AG
**
6721 TAATCAGTAAAGA-AAAGTGG
1 TAAAGAGTAAAGATAAA---G
*
6741 TAAAGAGTAAAGAGTAGAG
1 TAAAGAGTAAAGA-TAAAG
6760 TAAAGAGTAA
1 TAAAGAGTAA
6770 TCAGCAAAGG
Statistics
Matches: 78, Mismatches: 12, Indels: 26
0.67 0.10 0.22
Matches are distributed among these distances:
15 8 0.10
16 1 0.01
17 4 0.05
18 5 0.06
19 36 0.46
20 20 0.26
21 2 0.03
22 2 0.03
ACGTcount: A:0.58, C:0.02, G:0.24, T:0.16
Consensus pattern (18 bp):
TAAAGAGTAAAGATAAAG
Found at i:6697 original size:27 final size:27
Alignment explanation
Indices: 6663--6750 Score: 73
Period size: 27 Copynumber: 3.5 Consensus size: 27
6653 AGTAAAGAGT
6663 AAAGTAAAGAGTAATCAGTAAAGAAAA
1 AAAGTAAAGAGTAATCAGTAAAGAAAA
**
6690 AAAGTAAA-A-TAAT--G--AAG-AGT
1 AAAGTAAAGAGTAATCAGTAAAGAAAA
*
6710 AAAGAAAAGAGTAATCAGTAAAGAAAA
1 AAAGTAAAGAGTAATCAGTAAAGAAAA
***
6737 GTGGTAAAGAGTAA
1 AAAGTAAAGAGTAA
6751 AGAGTAGAGT
Statistics
Matches: 45, Mismatches: 9, Indels: 14
0.66 0.13 0.21
Matches are distributed among these distances:
20 8 0.18
21 4 0.09
22 4 0.09
23 1 0.02
24 1 0.02
25 4 0.09
26 4 0.09
27 19 0.42
ACGTcount: A:0.60, C:0.02, G:0.22, T:0.16
Consensus pattern (27 bp):
AAAGTAAAGAGTAATCAGTAAAGAAAA
Found at i:6749 original size:20 final size:19
Alignment explanation
Indices: 6704--6769 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 19
6694 TAAAATAATG
6704 AAGAGTAAAGAAAAGAGTA
1 AAGAGTAAAGAAAAGAGTA
** *
6723 ATCAGTAAAGAAAAGTGGTA
1 AAGAGTAAAGAAAAG-AGTA
**
6743 AAGAGTAAAGAGTAGAGTA
1 AAGAGTAAAGAAAAGAGTA
6762 AAGAGTAA
1 AAGAGTAA
6770 TCAGCAAAGG
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
19 24 0.63
20 14 0.37
ACGTcount: A:0.56, C:0.02, G:0.27, T:0.15
Consensus pattern (19 bp):
AAGAGTAAAGAAAAGAGTA
Found at i:9748 original size:14 final size:14
Alignment explanation
Indices: 9703--9753 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
9693 TAAGAAACAT
9703 TTTTCAAAAATTGA-
1 TTTTCAAAAA-TGAG
*
9717 TTTT-AAGAAAAG-G
1 TTTTCAA-AAATGAG
9730 TTTTCAAAAATGAG
1 TTTTCAAAAATGAG
9744 TTTTCAAAAA
1 TTTTCAAAAA
9754 GGTTTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
13 11 0.35
14 20 0.65
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.37
Consensus pattern (14 bp):
TTTTCAAAAATGAG
Found at i:9753 original size:26 final size:27
Alignment explanation
Indices: 9703--9759 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
9693 TAAGAAACAT
9703 TTTTCAAAAATTGATTTTAAGAAAAGG
1 TTTTCAAAAATTGATTTTAAGAAAAGG
*
9730 TTTTCAAAAA-TGAGTTTTCA-AAAAGG
1 TTTTCAAAAATTGA-TTTTAAGAAAAGG
9756 TTTT
1 TTTT
9760 AAGTTTTAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 13 0.46
27 15 0.54
ACGTcount: A:0.40, C:0.05, G:0.14, T:0.40
Consensus pattern (27 bp):
TTTTCAAAAATTGATTTTAAGAAAAGG
Found at i:10435 original size:16 final size:17
Alignment explanation
Indices: 10414--10446 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
10404 TCAAAGAAAG
10414 GAAGAAGAAAA-AAAAA
1 GAAGAAGAAAAGAAAAA
10430 GAAGAAGAAAAGAAAAA
1 GAAGAAGAAAAGAAAAA
10447 CCTCAGCCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (17 bp):
GAAGAAGAAAAGAAAAA
Found at i:11043 original size:15 final size:16
Alignment explanation
Indices: 11017--11056 Score: 64
Period size: 15 Copynumber: 2.5 Consensus size: 16
11007 TATAGTGCAT
11017 GAAAAGAAAGAAAAAA
1 GAAAAGAAAGAAAAAA
11033 GAAAA-AAAGAAAAAA
1 GAAAAGAAAGAAAAAA
11048 GAGAAAGAA
1 GA-AAAGAA
11057 GCTCTAGGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 12 0.55
16 8 0.36
17 2 0.09
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (16 bp):
GAAAAGAAAGAAAAAA
Found at i:12259 original size:55 final size:56
Alignment explanation
Indices: 12189--12446 Score: 301
Period size: 55 Copynumber: 4.6 Consensus size: 56
12179 AGTCGAATTC
* * *
12189 CAAAGTGATCTAGTGCGGTCAACCAAGAAATTTTCCAAT-GTTTCAAGTTTATCTT
1 CAAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAATGGTTTCAAGTTTATCTT
* * * *
12244 CAAAGTGATCCAGTGCGGTCAATCTAGACAGTTTCCAGTGGTCT-AAGTTTATCTT
1 CAAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAATGGTTTCAAGTTTATCTT
* ** *
12299 CAAAATGATCCAGTGCGGTCTGGCTGTTGAA-AAAGTTTCCAATGGTTT-AAGTTTATCTT
1 CAAAGTGATCCAGTGCGG--T--C-AATCAAGAAAGTTTCCAATGGTTTCAAGTTTATCTT
* * *
12358 CAAAGTGATCCAGCGCGGTCAATCAAGAAAGTTTCCAGTGGTTTTAAGTTTATCTT
1 CAAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAATGGTTTCAAGTTTATCTT
*
12414 C-AAGTGATCCAATGCGGTCAATCAAGAAAGTTT
1 CAAAGTGATCCAGTGCGGTCAATCAAGAAAGTTT
12447 ATCTTCAAGT
Statistics
Matches: 172, Mismatches: 23, Indels: 16
0.82 0.11 0.08
Matches are distributed among these distances:
54 3 0.02
55 108 0.63
56 15 0.09
57 2 0.01
59 42 0.24
60 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.33
Consensus pattern (56 bp):
CAAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAATGGTTTCAAGTTTATCTT
Found at i:12351 original size:114 final size:114
Alignment explanation
Indices: 12220--12432 Score: 340
Period size: 114 Copynumber: 1.9 Consensus size: 114
12210 ACCAAGAAAT
* * *
12220 TTTCCAATGTTTCAAGTTTATCTTCAAAGTGATCCAGTGCGGTCAATCTAGACAGTTTCCAGTGG
1 TTTCCAATGTTTCAAGTTTATCTTCAAAGTGATCCAGCGCGGTCAATCAAGAAAGTTTCCAGTGG
*
12285 -TCTAAGTTTATCTTCAAAATGATCCAGTGCGGTCTGGCTGTTGAAAAAG
66 TTCTAAGTTTATCTTC-AAATGATCCAATGCGGTCTGGCTGTTGAAAAAG
12334 TTTCCAATGGTTT-AAGTTTATCTTCAAAGTGATCCAGCGCGGTCAATCAAGAAAGTTTCCAGTG
1 TTTCCAAT-GTTTCAAGTTTATCTTCAAAGTGATCCAGCGCGGTCAATCAAGAAAGTTTCCAGTG
* *
12398 GTTTTAAGTTTATCTTCAAGTGATCCAATGCGGTC
65 GTTCTAAGTTTATCTTCAAATGATCCAATGCGGTC
12433 AATCAAGAAA
Statistics
Matches: 91, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
114 73 0.80
115 18 0.20
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (114 bp):
TTTCCAATGTTTCAAGTTTATCTTCAAAGTGATCCAGCGCGGTCAATCAAGAAAGTTTCCAGTGG
TTCTAAGTTTATCTTCAAATGATCCAATGCGGTCTGGCTGTTGAAAAAG
Found at i:12454 original size:38 final size:38
Alignment explanation
Indices: 12403--12485 Score: 148
Period size: 38 Copynumber: 2.2 Consensus size: 38
12393 CAGTGGTTTT
12403 AAGTTTATCTTCAAGTGATCCAATGCGGTCAATCAAGA
1 AAGTTTATCTTCAAGTGATCCAATGCGGTCAATCAAGA
* *
12441 AAGTTTATCTTCAAGTGATTCAGTGCGGTCAATCAAGA
1 AAGTTTATCTTCAAGTGATCCAATGCGGTCAATCAAGA
12479 AAGTTTA
1 AAGTTTA
12486 CAGTGGTATT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (38 bp):
AAGTTTATCTTCAAGTGATCCAATGCGGTCAATCAAGA
Found at i:12471 original size:93 final size:93
Alignment explanation
Indices: 12347--12637 Score: 388
Period size: 93 Copynumber: 3.0 Consensus size: 93
12337 CCAATGGTTT
* * *
12347 AAGTTTATCTTCAAAGTGATCCAGCGCGGTCAATCAAGAAAGTTTCCAGTGGTTTTAAGTTTATC
1 AAGTTTATCTTC-AAGTGATTCAGTGCGGTCAATCAAGAAAGTTTCCAGTGGTATTAAGTTTATC
*
12412 TTCAAGTGATCCAATGCGGTCAATCAAGA
65 TTCAAGTGATCCAGTGCGGTCAATCAAGA
* *
12441 AAGTTTATCTTCAAGTGATTCAGTGCGGTCAATCAAGAAAGTTTACAGTGGTATTAAGTTTACCT
1 AAGTTTATCTTCAAGTGATTCAGTGCGGTCAATCAAGAAAGTTTCCAGTGGTATTAAGTTTATCT
12506 TCAAGTGATCCAGTGCGGTCAATCAAGA
66 TCAAGTGATCCAGTGCGGTCAATCAAGA
* *
12534 AAGTTTATAATGGTATCTTCAAGT-AATCTAGTGCGGTCAATCAAGAAAGTTTCCAGTGG-CTTA
1 AAG----T--T--TATCTTCAAGTGATTC-AGTGCGGTCAATCAAGAAAGTTTCCAGTGGTATTA
* *
12597 AGTTTATCATCATGTGATCCAGTGCGGTCAATCAAGA
57 AGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGA
12634 AAGT
1 AAGT
12638 CTCAAGTGGT
Statistics
Matches: 176, Mismatches: 12, Indels: 16
0.86 0.06 0.08
Matches are distributed among these distances:
93 78 0.44
94 12 0.07
96 1 0.01
97 1 0.01
99 1 0.01
100 43 0.24
101 40 0.23
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.31
Consensus pattern (93 bp):
AAGTTTATCTTCAAGTGATTCAGTGCGGTCAATCAAGAAAGTTTCCAGTGGTATTAAGTTTATCT
TCAAGTGATCCAGTGCGGTCAATCAAGA
Found at i:12500 original size:55 final size:54
Alignment explanation
Indices: 12441--12661 Score: 253
Period size: 55 Copynumber: 4.2 Consensus size: 54
12431 TCAATCAAGA
*
12441 AAGTTTATCTTCAAGTGATTCAGTGCGGTCAATCAAGAAAGTTTACAGTGGTATT
1 AAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTT-CAGTGGTATT
*
12496 AAGTTTACCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTT-A----TA--
1 AAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCAGTGGTATT
* * * * *
12543 ATG-GTATCTTCAAGTAATCTAGTGCGGTCAATCAAGAAAGTTTCCAGTGG-CTT
1 AAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTT-CAGTGGTATT
* * *
12596 AAGTTTATCATCATGTGATCCAGTGCGGTCAATCAAGAAAGTCTCAAGTGGTATT
1 AAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTC-AGTGGTATT
*
12651 AATTTTATCTT
1 AAGTTTATCTT
12662 TAAATGAACC
Statistics
Matches: 137, Mismatches: 18, Indels: 22
0.77 0.10 0.12
Matches are distributed among these distances:
46 36 0.26
47 2 0.01
48 1 0.01
49 2 0.01
53 4 0.03
54 39 0.28
55 53 0.39
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.33
Consensus pattern (54 bp):
AAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCAGTGGTATT
Found at i:12828 original size:35 final size:34
Alignment explanation
Indices: 12712--12829 Score: 141
Period size: 35 Copynumber: 3.4 Consensus size: 34
12702 TTTGGGGTTT
*
12712 ATCTTCAAAGTTGGATTCAGATGACTCGGT-ATAGC
1 ATCTTCAAAGTT-GAATCAGATGACTCGGTGA-AGC
* *
12747 ATCTTTAAAGATGAAATCAGATGACTCGGTGTAA-C
1 ATCTTCAAAGTTG-AATCAGATGACTCGGTG-AAGC
12782 ATCTTCAAAGTTAGAATCAGATGACTCGGTGAAGC
1 ATCTTCAAAGTT-GAATCAGATGACTCGGTGAAGC
*
12817 ATCTTCTAAGTTG
1 ATCTTCAAAGTTG
12830 GATTTGGTTA
Statistics
Matches: 72, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
34 4 0.06
35 65 0.90
36 2 0.03
37 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (34 bp):
ATCTTCAAAGTTGAATCAGATGACTCGGTGAAGC
Found at i:12844 original size:43 final size:42
Alignment explanation
Indices: 12796--12946 Score: 140
Period size: 43 Copynumber: 3.5 Consensus size: 42
12786 TCAAAGTTAG
* * *
12796 AATCAGATGACTCGGTGAAGCATCTTCTAAGTTGGATTTGGTT
1 AATCAGATGACTCGGTGTAGCATCTTC-AAGTTGGATTCGGTA
* * *
12839 AATCAGATGACTCGGTGTAGAATCCTCAAGCTGGATTCGGTA
1 AATCAGATGACTCGGTGTAGCATCTTCAAGTTGGATTCGGTA
* * * * * *
12881 AATTAGATGGCTCGATGTAGCATCTTCAAAATTGGATTCAGTG
1 AATCAGATGACTCGGTGTAGCATCTTC-AAGTTGGATTCGGTA
* * *
12924 AACCAGGTGAGCTCGGTGCAGCA
1 AATCAGATGA-CTCGGTGTAGCA
12947 AATTTTCAAA
Statistics
Matches: 85, Mismatches: 21, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
42 34 0.40
43 41 0.48
44 10 0.12
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.28
Consensus pattern (42 bp):
AATCAGATGACTCGGTGTAGCATCTTCAAGTTGGATTCGGTA
Found at i:12889 original size:42 final size:42
Alignment explanation
Indices: 12796--12909 Score: 138
Period size: 42 Copynumber: 2.7 Consensus size: 42
12786 TCAAAGTTAG
* * * *
12796 AATCAGATGACTCGGTGAAGCATCTTCTAAGTTGGATTTGGTT
1 AATCAGATGACTCGGTGTAGCATCTTC-AAGCTGGATTCGGTA
* *
12839 AATCAGATGACTCGGTGTAGAATCCTCAAGCTGGATTCGGTA
1 AATCAGATGACTCGGTGTAGCATCTTCAAGCTGGATTCGGTA
* * *
12881 AATTAGATGGCTCGATGTAGCATCTTCAA
1 AATCAGATGACTCGGTGTAGCATCTTCAA
12910 AATTGGATTC
Statistics
Matches: 60, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
42 36 0.60
43 24 0.40
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.31
Consensus pattern (42 bp):
AATCAGATGACTCGGTGTAGCATCTTCAAGCTGGATTCGGTA
Found at i:13141 original size:90 final size:89
Alignment explanation
Indices: 12929--13293 Score: 421
Period size: 90 Copynumber: 4.1 Consensus size: 89
12919 CAGTGAACCA
* *
12929 GGTGAGCTCGGTGCAGCAAATTTTCAAACAGTTCATGGTGATTCGGTGAATCAAGTTAATGTGGT
1 GGTGAGCTCGGTGCAGCAAATTTTCAAACAGTTCATGATGATTCGGTGAATCAAGTTAATGCGGT
* *
12994 GCAT-TTAC-TCAGAGATTGGATTC
66 GCATATTTCTTCA-AGATTGGACTC
* * *
13017 GGTGAGCTCGGTGCAGCAAATTTTCAAACAGTTCATGATGATTCAGTGAATCAAGTTGATGCGAT
1 GGTGAGCTCGGTGCAGCAAATTTTCAAACAGTTCATGATGATTCGGTGAATCAAGTTAATGCGGT
13082 GCAGTATTTCTTCAAGATTGGACTC
66 GCA-TATTTCTTCAAGATTGGACTC
* ** ** * * *
13107 GGTGAGCTCGGTACAGCACTTTTTCAGGCAGTTCAGGATGATGCGGTGAATCAAGTTGA-GACGG
1 GGTGAGCTCGGTGCAGCAAATTTTCAAACAGTTCATGATGATTCGGTGAATCAAGTTAATG-CGG
* * *
13171 TGCCTTATTTCGTCAAGATTGGATTC
65 TG-CATATTTCTTCAAGATTGGACTC
* * * * *
13197 AGTGAGCTCGGTGCAGCACATTTTCAAACAGTTCAAAGTTTGATTCGGTGGATCAAGTTAATGCG
1 GGTGAGCTCGGTGCAGCAAATTTTCAAACAGTTC-ATG-ATGATTCGGTGAATCAAGTTAATGCG
* *
13262 GTGCAATATTTCTTCAAAATTTGACTC
64 GTGC-ATATTTCTTCAAGATTGGACTC
13289 GGTGA
1 GGTGA
13294 ATCAAATATT
Statistics
Matches: 233, Mismatches: 35, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
88 63 0.27
89 2 0.01
90 116 0.50
91 7 0.03
92 44 0.19
93 1 0.00
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.31
Consensus pattern (89 bp):
GGTGAGCTCGGTGCAGCAAATTTTCAAACAGTTCATGATGATTCGGTGAATCAAGTTAATGCGGT
GCATATTTCTTCAAGATTGGACTC
Done.