Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022521.1 Corchorus olitorius cultivar O-4 contig22554, 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: 31491
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:8513 original size:23 final size:23
Alignment explanation
Indices: 8499--8684 Score: 76
Period size: 22 Copynumber: 8.4 Consensus size: 23
8489 CCTTATAAAC
8499 TTTTGATAA-GATTCCTATGAAA
1 TTTTGATAACGATTCCTATGAAA
*
8521 TTTTGATAACGATT-CTATGCAA
1 TTTTGATAACGATTCCTATGAAA
* * * *
8543 TTTCGA-AA-AATTTCCAATCAAA
1 TTTTGATAACGA-TTCCTATGAAA
** *
8565 TTTCAAGAAC--TTCCCTATGAAA
1 TTTTGATAACGATT-CCTATGAAA
* *
8587 TTTTGTTAAC--CTCCTTAT-AGAA
1 TTTTGATAACGATTCC-TATGA-AA
* *
8609 TTTTGAAAAC-ATTACTATGAAA
1 TTTTGATAACGATTCCTATGAAA
* *
8631 TTTTGATGAC--CTCCTAATGAAA
1 TTTTGATAACGATTCCT-ATGAAA
* *
8653 TTTTGATAACCA-TCC-ACTTAAA
1 TTTTGATAACGATTCCTA-TGAAA
8675 TTTTGATAAC
1 TTTTGATAAC
8685 CGCACTATAA
Statistics
Matches: 126, Mismatches: 24, Indels: 28
0.71 0.13 0.16
Matches are distributed among these distances:
20 1 0.01
21 13 0.10
22 100 0.79
23 12 0.10
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (23 bp):
TTTTGATAACGATTCCTATGAAA
Found at i:8675 original size:22 final size:22
Alignment explanation
Indices: 8581--8710 Score: 97
Period size: 22 Copynumber: 5.9 Consensus size: 22
8571 GAACTTCCCT
* *
8581 ATGAAATTTTGTTAACCTCCTT
1 ATGAAATTTTGATAACCTCCTA
* * *
8603 AT-AGAATTTTGAAAACATTACT-
1 ATGA-AATTTTGATAAC-CTCCTA
*
8625 ATGAAATTTTGATGACCTCCTA
1 ATGAAATTTTGATAACCTCCTA
8647 ATGAAATTTTGATAACCATCC-A
1 ATGAAATTTTGATAACC-TCCTA
* * *
8669 CTTAAATTTTGATAACCGCACT-
1 ATGAAATTTTGATAACCTC-CTA
* *
8691 ATAAAATTTTGATAATCTCC
1 ATGAAATTTTGATAACCTCC
8711 ATGTAAAATG
Statistics
Matches: 85, Mismatches: 16, Indels: 15
0.73 0.14 0.13
Matches are distributed among these distances:
21 6 0.07
22 72 0.85
23 7 0.08
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (22 bp):
ATGAAATTTTGATAACCTCCTA
Found at i:8717 original size:22 final size:21
Alignment explanation
Indices: 8650--8719 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 21
8640 CCTCCTAATG
8650 AAATTTTGATAACCATCCACTT-
1 AAATTTTGATAA-C-TCCACTTA
8672 AAATTTTGATAAC-CGCACTATA
1 AAATTTTGATAACTC-CACT-TA
8694 AAATTTTGATAATCTCCA-TGTA
1 AAATTTTGATAA-CTCCACT-TA
8716 AAAT
1 AAAT
8720 GTTTTCTAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
19 1 0.02
20 4 0.10
21 2 0.05
22 31 0.74
23 3 0.07
24 1 0.02
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.36
Consensus pattern (21 bp):
AAATTTTGATAACTCCACTTA
Found at i:8933 original size:22 final size:22
Alignment explanation
Indices: 8875--8996 Score: 72
Period size: 22 Copynumber: 5.5 Consensus size: 22
8865 TGATAATCAC
* *
8875 AAATTTTGATAACCTCTCCCTATG
1 AAATTTTGATAA-C-GTCACTATG
* * *
8899 -ATTTTTCGATAACTTCATTATG
1 AAATTTT-GATAACGTCACTATG
* *
8921 AAATTTTGTTAACGTCCCTATG
1 AAATTTTGATAACGTCACTATG
* *
8943 AAATTTTGATAAC--CCCTATA
1 AAATTTTGATAACGTCACTATG
* **
8963 AAATTTTGAAAAAC-AAACTATG
1 AAATTTTG-ATAACGTCACTATG
8985 AAATTTTGATAA
1 AAATTTTGATAA
8997 TCCCCCTTTA
Statistics
Matches: 78, Mismatches: 16, Indels: 11
0.74 0.15 0.10
Matches are distributed among these distances:
20 14 0.18
21 7 0.09
22 41 0.53
23 11 0.14
24 5 0.06
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.39
Consensus pattern (22 bp):
AAATTTTGATAACGTCACTATG
Found at i:9169 original size:22 final size:22
Alignment explanation
Indices: 9139--9236 Score: 92
Period size: 21 Copynumber: 4.5 Consensus size: 22
9129 CCAATGAAAT
*
9139 GTTATCAAAATTTCATAATTTG
1 GTTATCAAAATTTCATAATGTG
* * * *
9161 GTTA-CCAAATTTTATAAGGAG
1 GTTATCAAAATTTCATAATGTG
* * *
9182 GTTATAAAAATTT-ATACTATG
1 GTTATCAAAATTTCATAATGTG
* *
9203 GTTACCAAAATTTCATAAAGTG
1 GTTATCAAAATTTCATAATGTG
9225 GTTATCAAAATT
1 GTTATCAAAATT
9237 ATAGGGATTA
Statistics
Matches: 57, Mismatches: 17, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
21 31 0.54
22 26 0.46
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.39
Consensus pattern (22 bp):
GTTATCAAAATTTCATAATGTG
Found at i:9214 original size:43 final size:43
Alignment explanation
Indices: 9139--9236 Score: 126
Period size: 43 Copynumber: 2.3 Consensus size: 43
9129 CCAATGAAAT
* * *
9139 GTTATCAAAATTTCATAATTTGGTTACCAAATTTTATAAGGAG
1 GTTATCAAAATTTCATAATATGGTTACCAAATTTCATAAAGAG
* * *
9182 GTTATAAAAATTT-ATACTATGGTTACCAAAATTTCATAAAGTG
1 GTTATCAAAATTTCATAATATGGTTACC-AAATTTCATAAAGAG
9225 GTTATCAAAATT
1 GTTATCAAAATT
9237 ATAGGGATTA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
42 12 0.26
43 35 0.74
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.39
Consensus pattern (43 bp):
GTTATCAAAATTTCATAATATGGTTACCAAATTTCATAAAGAG
Found at i:19315 original size:65 final size:65
Alignment explanation
Indices: 19211--19342 Score: 255
Period size: 65 Copynumber: 2.0 Consensus size: 65
19201 ATAACAATGG
19211 CTCATACATATCTCTATAATCATCATTAAGGCTTGCCAATTTCTATCTAGACCTTATTTTATAGT
1 CTCATACATATCTCTATAATCATCATTAAGGCTTGCCAATTTCTATCTAGACCTTATTTTATAGT
*
19276 CTCATACGTATCTCTATAATCATCATTAAGGCTTGCCAATTTCTATCTAGACCTTATTTTATAGT
1 CTCATACATATCTCTATAATCATCATTAAGGCTTGCCAATTTCTATCTAGACCTTATTTTATAGT
19341 CT
1 CT
19343 TATATTAAGA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (65 bp):
CTCATACATATCTCTATAATCATCATTAAGGCTTGCCAATTTCTATCTAGACCTTATTTTATAGT
Found at i:19712 original size:2 final size:2
Alignment explanation
Indices: 19705--19744 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
19695 AGAAACAGAG
*
19705 AT AT AT AT AT AT AT AT AA 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
19745 CAGAAAATCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:24030 original size:13 final size:13
Alignment explanation
Indices: 24012--24036 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24002 TTTAATTTTT
24012 ATAATATAATATA
1 ATAATATAATATA
24025 ATAATATAATAT
1 ATAATATAATAT
24037 TATCTTTATT
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
ATAATATAATATA
Found at i:26280 original size:22 final size:21
Alignment explanation
Indices: 26255--26313 Score: 82
Period size: 21 Copynumber: 2.7 Consensus size: 21
26245 TTTATAGTAT
26255 AGTTATCACAATTTCATGGGAA
1 AGTTATCA-AATTTCATGGGAA
*
26277 AGTTATCAAAATTCATGGGAA
1 AGTTATCAAATTTCATGGGAA
*
26298 GGTTATCATAATTTCA
1 AGTTATCA-AATTTCA
26314 CAGGGAGGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 19 0.58
22 14 0.42
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (21 bp):
AGTTATCAAATTTCATGGGAA
Found at i:26288 original size:44 final size:42
Alignment explanation
Indices: 26204--26427 Score: 132
Period size: 44 Copynumber: 5.1 Consensus size: 42
26194 AATACCTTTT
* * * * * *
26204 ATAGTGAAGTCATCAAAATTTTATGGGTAGGATATTAAAATTTT
1 ATAGT-AAGTTATCAAAATTTCATGGG-AAGTTATCAAAATTTC
*
26248 ATAGTATAGTTATCACAATTTCATGGGAAAGTTATCAAAA-TTC
1 ATAGTA-AGTTATCAAAATTTCATGGG-AAGTTATCAAAATTTC
* * * * *
26291 ATGGGAAGGTTATCATAATTTCACAGGGAGGTTA-CTAAAATTTC
1 ATAGTAA-GTTATCAAAATTTCA-TGGGAAGTTATC-AAAATTTC
* * * ** *
26335 ATACTCTAGTTATCAAAATTTCATAGGG-CGATTATTGAAATTTT
1 ATAGT-AAGTTATCAAAATTTCAT-GGGAAG-TTATCAAAATTTC
*
26379 ATA-TGAAGGTTATCAAAATTTCATAGGAAGATTATCAAAATTTC
1 ATAGT-AA-GTTATCAAAATTTCATGGGAAG-TTATCAAAATTTC
26423 ATAGT
1 ATAGT
26428 GTGCTTATAA
Statistics
Matches: 138, Mismatches: 30, Indels: 23
0.72 0.16 0.12
Matches are distributed among these distances:
42 2 0.01
43 35 0.25
44 99 0.72
45 2 0.01
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (42 bp):
ATAGTAAGTTATCAAAATTTCATGGGAAGTTATCAAAATTTC
Found at i:26369 original size:22 final size:22
Alignment explanation
Indices: 26240--26426 Score: 123
Period size: 22 Copynumber: 8.5 Consensus size: 22
26230 GTAGGATATT
* *
26240 AAAATTTTATAGTATAG-TTATC
1 AAAATTTCATAGGA-AGATTATC
* *
26262 ACAATTTCATGGGAA-AGTTATC
1 AAAATTTCATAGGAAGA-TTATC
* *
26284 AAAA-TTCATGGGAAGGTTATC
1 AAAATTTCATAGGAAGATTATC
* * * *
26305 ATAATTTCACAGGGAGGTTA-C
1 AAAATTTCATAGGAAGATTATC
***
26326 TAAAATTTCATACTCTAG-TTATC
1 -AAAATTTCATA-GGAAGATTATC
** *
26349 AAAATTTCATAGGGCGATTATT
1 AAAATTTCATAGGAAGATTATC
* * * *
26371 GAAATTTTATATGAAGGTTATC
1 AAAATTTCATAGGAAGATTATC
26393 AAAATTTCATAGGAAGATTATC
1 AAAATTTCATAGGAAGATTATC
26415 AAAATTTCATAG
1 AAAATTTCATAG
26427 TGTGCTTATA
Statistics
Matches: 126, Mismatches: 31, Indels: 16
0.73 0.18 0.09
Matches are distributed among these distances:
21 21 0.17
22 102 0.81
23 3 0.02
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.36
Consensus pattern (22 bp):
AAAATTTCATAGGAAGATTATC
Found at i:26435 original size:22 final size:22
Alignment explanation
Indices: 26240--26454 Score: 104
Period size: 22 Copynumber: 9.8 Consensus size: 22
26230 GTAGGATATT
* *
26240 AAAATTTTATAGT-ATAGTTATC
1 AAAATTTCATAGTGAGA-TTATC
* * *
26262 ACAATTTCAT-GGGAAAGTTATC
1 AAAATTTCATAGTGAGA-TTATC
* *
26284 AAAA-TTCAT-GGGAAGGTTATC
1 AAAATTTCATAGTG-AGATTATC
* * * *
26305 ATAATTTCACAGGGAGGTTA-C
1 AAAATTTCATAGTGAGATTATC
* *
26326 TAAAATTTCATACTCTAG-TTATC
1 -AAAATTTCATAGT-GAGATTATC
* * *
26349 AAAATTTCATAGGGCGATTATT
1 AAAATTTCATAGTGAGATTATC
* * *
26371 GAAATTTTATA-TGAAGGTTATC
1 AAAATTTCATAGTG-AGATTATC
26393 AAAATTTCATAG-GAAGATTATC
1 AAAATTTCATAGTG-AGATTATC
* * *
26415 AAAATTTCATAGTGTGCTTATA
1 AAAATTTCATAGTGAGATTATC
*
26437 AAAATTACATAGTGAGAT
1 AAAATTTCATAGTGAGAT
26455 AGAGTGAAGT
Statistics
Matches: 148, Mismatches: 34, Indels: 22
0.73 0.17 0.11
Matches are distributed among these distances:
21 20 0.14
22 121 0.82
23 7 0.05
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.36
Consensus pattern (22 bp):
AAAATTTCATAGTGAGATTATC
Found at i:26441 original size:44 final size:42
Alignment explanation
Indices: 26256--26448 Score: 115
Period size: 44 Copynumber: 4.4 Consensus size: 42
26246 TTATAGTATA
* * *
26256 GTTATCACAATTTCATGGGAA-AGTTATCAAAA-TTCATGGGAAG-
1 GTTATCAAAATTTCATAGGAAGA-TTATCAAAATTTCAT---ATGT
* * * * *
26299 GTTATCATAATTTCACAGGGAGGTTA-CTAAAATTTCATACTCT
1 GTTATCAAAATTTCATAGGAAGATTATC-AAAATTTCATA-TGT
** ** * *
26342 AGTTATCAAAATTTCATAGGGCGATTATTGAAATTTTATATGAAG
1 -GTTATCAAAATTTCATAGGAAGATTATCAAAATTTCATATG--T
26387 GTTATCAAAATTTCATAGGAAGATTATCAAAATTTCATAGTGT
1 GTTATCAAAATTTCATAGGAAGATTATCAAAATTTCATA-TGT
* *
26430 GCTTATAAAAATTACATAG
1 G-TTATCAAAATTTCATAG
26449 TGAGATAGAG
Statistics
Matches: 115, Mismatches: 24, Indels: 21
0.72 0.15 0.13
Matches are distributed among these distances:
41 1 0.01
42 1 0.01
43 26 0.23
44 85 0.74
45 2 0.02
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (42 bp):
GTTATCAAAATTTCATAGGAAGATTATCAAAATTTCATATGT
Found at i:26695 original size:21 final size:22
Alignment explanation
Indices: 26650--26699 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
26640 TGTGGTAATT
* *
26650 AAAATTTCATAATGAGTTTATC
1 AAAATTTCATAATGAGATTAAC
*
26672 AAAATTT-ATAGTGAGATTAAC
1 AAAATTTCATAATGAGATTAAC
26693 AAAATTT
1 AAAATTT
26700 GACTTTGTGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 18 0.72
22 7 0.28
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.38
Consensus pattern (22 bp):
AAAATTTCATAATGAGATTAAC
Found at i:26865 original size:44 final size:44
Alignment explanation
Indices: 26801--26902 Score: 125
Period size: 44 Copynumber: 2.3 Consensus size: 44
26791 AATAGTGTTC
** * *
26801 TTATCAAAATTTCGTAGGAGGTTATAAAAAATTTATATGGATG-
1 TTATCAAAATTTCAAAGGAGGTTATAAAAAATTTATAGGGAGGT
* *
26844 TTATCAAAATTTCAAATGGAGGTTATCAAAACTTTATAGGGAGGT
1 TTATCAAAATTTCAAA-GGAGGTTATAAAAAATTTATAGGGAGGT
*
26889 TTATAAAAATTTCA
1 TTATCAAAATTTCA
26903 TAGTAAGGTA
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
43 14 0.28
44 23 0.46
45 13 0.26
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.36
Consensus pattern (44 bp):
TTATCAAAATTTCAAAGGAGGTTATAAAAAATTTATAGGGAGGT
Found at i:26945 original size:22 final size:20
Alignment explanation
Indices: 26801--26945 Score: 87
Period size: 22 Copynumber: 6.7 Consensus size: 20
26791 AATAGTGTTC
*
26801 TTATCAAAATTTCGTAGGAGG
1 TTATCAAAATTTCAT-GGAGG
* * *
26822 TTATAAAAAATTTATATGGATG
1 TTAT-CAAAATTT-CATGGAGG
26844 TTATCAAAATTTCAAATGGAGG
1 TTATCAAAATTTC--ATGGAGG
26866 TTATCAAAACTTT-ATAGGGAGG
1 TTATCAAAA-TTTCAT--GGAGG
* *
26888 TTTATAAAAATTTCATAGTAAGG
1 -TTATCAAAATTTCAT-G-GAGG
* *
26911 -TATTACAATTTCATGGTATGG
1 TTATCAAAATTTCATGG-A-GG
26932 TTATCAAAATTTCA
1 TTATCAAAATTTCA
26946 CAATGTGATT
Statistics
Matches: 96, Mismatches: 15, Indels: 25
0.71 0.11 0.18
Matches are distributed among these distances:
20 4 0.04
21 25 0.26
22 50 0.52
23 17 0.18
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.37
Consensus pattern (20 bp):
TTATCAAAATTTCATGGAGG
Found at i:27047 original size:22 final size:22
Alignment explanation
Indices: 27022--27077 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
27012 TATTGGGAGG
27022 TTATCAAAATTTCA-TAGGATGA
1 TTATCAAAATTTCATTA-GATGA
* *
27044 TTATCAAATTTTCATTAGATGG
1 TTATCAAAATTTCATTAGATGA
*
27066 TTATTAAAATTT
1 TTATCAAAATTT
27078 TTATAGGTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 27 0.93
23 2 0.07
ACGTcount: A:0.38, C:0.07, G:0.11, T:0.45
Consensus pattern (22 bp):
TTATCAAAATTTCATTAGATGA
Found at i:27396 original size:20 final size:20
Alignment explanation
Indices: 27371--27410 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
27361 ACGTTTCATT
27371 AAAACGTCATTAGGATCAAA
1 AAAACGTCATTAGGATCAAA
27391 AAAACGTCATTAGGATCAAA
1 AAAACGTCATTAGGATCAAA
27411 CTTCTAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.15, G:0.15, T:0.20
Consensus pattern (20 bp):
AAAACGTCATTAGGATCAAA
Found at i:27452 original size:2 final size:2
Alignment explanation
Indices: 27445--27469 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
27435 CCTTGCAAAA
27445 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
27470 ATTAAGTTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.