Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017721.1 Corchorus olitorius cultivar O-4 contig17754, 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: 16779
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Found at i:6301 original size:19 final size:20
Alignment explanation
Indices: 6274--6311 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
6264 TACTATTATT
6274 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
6294 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
6312 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:6534 original size:22 final size:21
Alignment explanation
Indices: 6482--6708 Score: 96
Period size: 22 Copynumber: 10.2 Consensus size: 21
6472 CTGTATGGTA
*
6482 ATCAAAATTTTATTA-GATGGTT
1 ATCAAAATTTCA-TAGGA-GGTT
* *
6504 ATTATAATTTCATGAGGAGGTT
1 ATCAAAATTTCAT-AGGAGGTT
* *
6526 ATCAAAATTCCATAGTGTGGTT
1 ATCAAAATTTCATAG-GAGGTT
* * *
6548 ACCAAAATTTTATATGGAAGTT
1 ATCAAAATTTCATA-GGAGGTT
* * *
6570 ATAAAAATTTAATTGGAAGGTT
1 ATCAAAATTTCATAGG-AGGTT
* * *
6592 ATCAAAATTTCTTAATGTGGTT
1 ATCAAAATTTCAT-AGGAGGTT
*
6614 ACCAAAATTTCATAGGATCAGGTT
1 ATCAAAATTTCATAGG---AGGTT
** *
6638 ATTTAAATTTCTTAGGAAGGTT
1 ATCAAAATTTCATAGG-AGGTT
** * * *
6660 ATTGACATTTCATAGTGTGGTG
1 ATCAAAATTTCATAG-GAGGTT
* * *
6682 ATCACAATTTTATAGAAAGGTT
1 ATCAAAATTTCATAG-GAGGTT
6704 ATCAA
1 ATCAA
6709 GGAGATTATC
Statistics
Matches: 148, Mismatches: 47, Indels: 20
0.69 0.22 0.09
Matches are distributed among these distances:
21 7 0.05
22 120 0.81
23 5 0.03
24 16 0.11
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.39
Consensus pattern (21 bp):
ATCAAAATTTCATAGGAGGTT
Found at i:6679 original size:68 final size:66
Alignment explanation
Indices: 6521--6680 Score: 180
Period size: 66 Copynumber: 2.4 Consensus size: 66
6511 TTTCATGAGG
* *
6521 AGGTTATCAAAATTCCATAGTGTGGTTACCAAAATTTTATATGGAAGTTATAAAAATTTAATTGG
1 AGGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATATGGAAGTTATAAAAATTTAATTGG
6586 A
66 A
* * ** *
6587 AGGTTATCAAAATTTCTTAATGTGGTTACCAAAATTTCATA-GGATCAGGTTATTTAAATTT-CT
1 AGGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATATGGA--A-GTTATAAAAATTTAAT
6650 TAGGA
63 T-GGA
** *
6655 AGGTTATTGACATTTCATAGTGTGGT
1 AGGTTATCAAAATTTCATAGTGTGGT
6681 GATCACAATT
Statistics
Matches: 78, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
65 3 0.04
66 37 0.47
67 3 0.04
68 35 0.45
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.39
Consensus pattern (66 bp):
AGGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATATGGAAGTTATAAAAATTTAATTGG
A
Found at i:6739 original size:22 final size:22
Alignment explanation
Indices: 6714--7154 Score: 238
Period size: 22 Copynumber: 19.9 Consensus size: 22
6704 ATCAAGGAGA
* *
6714 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
*
6736 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGTGAGG
*
6758 TTAACAAAATTTCATA-TGAAGG
1 TTATCAAAATTTCATAGTG-AGG
* * *
6780 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCATAGTGAGG
*
6802 TTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
** * *
6824 TTATCAAAATTTTTTAGTGTGA
1 TTATCAAAATTTCATAGTGAGG
6846 TTATCAAAATTTCATA-TGAAGG
1 TTATCAAAATTTCATAGTG-AGG
* *
6868 TTAT-AAAAGTCTCAATTTCA-TAAGG
1 TTATCAAAA-TTTC-A--T-AGTGAGG
* * * *
6893 AGTACCAAAATTTGATAG-AAGG
1 -TTATCAAAATTTCATAGTGAGG
* * * *
6915 TTATC-AAATCTCATAGAGTGA
1 TTATCAAAATTTCATAGTGAGG
* *
6936 TTATCGAAATTTCATAGAGATCGG
1 TTATCAAAATTTCATAGTGA--GG
*
6960 ATTATCAAAATTT-ATAG-GAAGA
1 -TTATCAAAATTTCATAGTG-AGG
**
6982 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAGTGAGG
*
7004 TTATCAAAATTTCA-AATCGAGG
1 TTATCAAAATTTCATAGT-GAGG
* * * *
7026 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAGTGAGG
* *
7048 TTATCAAAATTTCATAGAGGGG
1 TTATCAAAATTTCATAGTGAGG
* * * *
7070 TCAACAAAATTTTATAGAGAGG
1 TTATCAAAATTTCATAGTGAGG
*** *
7092 TTATCAAAATTTCATAAAAAAG
1 TTATCAAAATTTCATAGTGAGG
* * * * *
7114 TTATCAAATTTTCAAAATGTGA
1 TTATCAAAATTTCATAGTGAGG
*
7136 TTACCAAAATTTCATAGTG
1 TTATCAAAATTTCATAGTG
7155 GTATTTCTGG
Statistics
Matches: 322, Mismatches: 72, Indels: 50
0.73 0.16 0.11
Matches are distributed among these distances:
20 9 0.03
21 34 0.11
22 236 0.73
23 11 0.03
24 6 0.02
25 16 0.05
26 6 0.02
27 4 0.01
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:7281 original size:22 final size:22
Alignment explanation
Indices: 7253--7872 Score: 191
Period size: 22 Copynumber: 28.4 Consensus size: 22
7243 TCAGGGAGGA
*
7253 TATCAAAATTTCTTATGAAGGT
1 TATCAAAATTTCATATGAAGGT
**
7275 TATCAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* *
7297 TTTCAAAATTTCATAAGAAGGT
1 TATCAAAATTTCATATGAAGGT
*
7319 TATCAAAATTTCATAT--ATGT
1 TATCAAAATTTCATATGAAGGT
* * * * *
7339 AGATCAAATTTTCATAGGGAGAT
1 -TATCAAAATTTCATATGAAGGT
* *
7362 TAACAAAATTTCATAAT-TAGGT
1 TATCAAAATTTCAT-ATGAAGGT
* *
7384 TATCAAACA-TTCATAGGGAGGT
1 TATCAAA-ATTTCATATGAAGGT
*
7406 TATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * * *
7422 TATCAAGATTTCATAAGGATGT
1 TATCAAAATTTCATATGAAGGT
* * *
7444 TATCAAAATTTTATAAGGAGGTT
1 TATCAAAATTTCATATGAAGG-T
* *
7467 TATCAAAATTTTATAGGAAGGTT
1 TATCAAAATTTCATATGAAGG-T
*
7490 TATCAAAATTTCATA-GCGAGGTT
1 TATCAAAATTTCATATG-AAGG-T
* * *
7513 TATCAAAATTTTATAGGAAGTTT
1 TATCAAAATTTCATATGAAG-GT
* *
7536 TATCAAAATTCCATA-GCGAGGT
1 TATCAAAATTTCATATG-AAGGT
* * *
7558 TATCACAATTTCATA-GTATGAT
1 TATCAAAATTTCATATG-AAGGT
* *
7580 TATCAAAATTTCAGAGTGTAA--C
1 TATCAAAATTTCATA-TG-AAGGT
*
7602 TA-CTAACAA-TTCATATGGAGGT
1 TATC-AA-AATTTCATATGAAGGT
* * *
7624 T-TTAAAATTTTCATAACG-TGGT
1 TATCAAAA-TTTCAT-ATGAAGGT
* *
7646 TATCAATATATT-ATATGGAGGT
1 TATCAAAAT-TTCATATGAAGGT
* * **
7668 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATA-TGAAGGT
* * *
7691 CATCAAGATTTCATTAGGAA-GT
1 TATCAAAATTTCA-TATGAAGGT
7713 TATCAAAATTTCATAGTG-AGGT
1 TATCAAAATTTCATA-TGAAGGT
* * *
7735 CT-TCAAAA-TTCCTCAGGGAGGT
1 -TATCAAAATTTCAT-ATGAAGGT
*
7757 TAAT-AAAATTTCATAAGAAGGT
1 T-ATCAAAATTTCATATGAAGGT
* * ** **
7779 TA-AAAAAATT-ATAAAAATAT
1 TATCAAAATTTCATATGAAGGT
** * **
7799 TATTGAAATTCCATA-GTATCGT
1 TATCAAAATTTCATATG-AAGGT
* *
7821 TATTAAAATTTCATAGGAAGGT
1 TATCAAAATTTCATATGAAGGT
* *
7843 TATCAAAATTTCATAAGGAGGT
1 TATCAAAATTTCATATGAAGGT
*
7865 CATCAAAA
1 TATCAAAA
7873 ATAGTGTAAT
Statistics
Matches: 449, Mismatches: 101, Indels: 96
0.70 0.16 0.15
Matches are distributed among these distances:
16 9 0.02
17 2 0.00
18 2 0.00
20 17 0.04
21 46 0.10
22 255 0.57
23 112 0.25
24 6 0.01
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:7473 original size:23 final size:22
Alignment explanation
Indices: 7421--7590 Score: 164
Period size: 23 Copynumber: 7.5 Consensus size: 22
7411 AAATTTGTAG
* * *
7421 TTATCAAGATTTCATAAGGATG-
1 TTATCAAAATTTTAT-AGGAGGT
7443 TTATCAAAATTTTATAAGGAGGT
1 TTATCAAAATTTTAT-AGGAGGT
7466 TTATCAAAATTTTATAGGAAGGT
1 TTATCAAAATTTTATAGG-AGGT
*
7489 TTATCAAAATTTCATAGCGAGGT
1 TTATCAAAATTTTATAG-GAGGT
*
7512 TTATCAAAATTTTATAGGAAGTT
1 TTATCAAAATTTTATAGG-AGGT
**
7535 TTATCAAAATTCCATAGCGAGG-
1 TTATCAAAATTTTATAG-GAGGT
* * * * *
7557 TTATCACAATTTCATAGTATGA
1 TTATCAAAATTTTATAGGAGGT
7579 TTATCAAAATTT
1 TTATCAAAATTT
7591 CAGAGTGTAA
Statistics
Matches: 128, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
21 2 0.02
22 49 0.38
23 75 0.59
24 2 0.02
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTTTATAGGAGGT
Found at i:7495 original size:46 final size:46
Alignment explanation
Indices: 7443--7592 Score: 198
Period size: 46 Copynumber: 3.3 Consensus size: 46
7433 CATAAGGATG
*
7443 TTATCAAAATTTTATAAG-GAGGTTTATCAAAATTTTATAGGAAGGT
1 TTATCAAAATTTCAT-AGCGAGGTTTATCAAAATTTTATAGGAAGGT
*
7489 TTATCAAAATTTCATAGCGAGGTTTATCAAAATTTTATAGGAAGTT
1 TTATCAAAATTTCATAGCGAGGTTTATCAAAATTTTATAGGAAGGT
* * * * * *
7535 TTATCAAAATTCCATAGCGAGG-TTATCACAATTTCATA-GTATGA
1 TTATCAAAATTTCATAGCGAGGTTTATCAAAATTTTATAGGAAGGT
7579 TTATCAAAATTTCA
1 TTATCAAAATTTCA
7593 GAGTGTAACT
Statistics
Matches: 93, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
44 15 0.16
45 16 0.17
46 62 0.67
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (46 bp):
TTATCAAAATTTCATAGCGAGGTTTATCAAAATTTTATAGGAAGGT
Found at i:12776 original size:22 final size:22
Alignment explanation
Indices: 12733--12784 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
12723 TCTTTGTTTG
* *
12733 CAAAATTTCATAATATGGTTAT
1 CAAAATTTCATAATAAGCTTAT
12755 CAAAATTTCAT-ATAAAGCTTAT
1 CAAAATTTCATAAT-AAGCTTAT
*
12777 AAAAATTT
1 CAAAATTT
12785 TATAGGGAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 2 0.08
22 24 0.92
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.38
Consensus pattern (22 bp):
CAAAATTTCATAATAAGCTTAT
Found at i:13704 original size:22 final size:22
Alignment explanation
Indices: 13675--13739 Score: 94
Period size: 22 Copynumber: 3.0 Consensus size: 22
13665 TGAATATTTT
13675 TATGAAATTTTGATAACTACCC
1 TATGAAATTTTGATAACTACCC
* *
13697 TATTAAATTTTGATAACCACCC
1 TATGAAATTTTGATAACTACCC
* *
13719 TATGAAAATTTGATAATTACC
1 TATGAAATTTTGATAACTACC
13740 TATCATTATC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.37
Consensus pattern (22 bp):
TATGAAATTTTGATAACTACCC
Found at i:13921 original size:43 final size:42
Alignment explanation
Indices: 13840--13925 Score: 102
Period size: 43 Copynumber: 2.0 Consensus size: 42
13830 AGTCGTACAA
* * * *
13840 ACATATATAATTCATATTGAACTCCTCCCTTTGATAGTATAT
1 ACATATACAATTCAAATTGAACTCATCCCTTCGATAGTATAT
*
13882 ACATATACATATTCAAATTGAACTCATCCAC-TCGGTAGTATAT
1 ACATATACA-ATTCAAATTGAACTCATCC-CTTCGATAGTATAT
13925 A
1 A
13926 GAGCACGTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
42 8 0.22
43 28 0.76
44 1 0.03
ACGTcount: A:0.36, C:0.20, G:0.08, T:0.36
Consensus pattern (42 bp):
ACATATACAATTCAAATTGAACTCATCCCTTCGATAGTATAT
Done.