Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015519.1 Corchorus capsularis cultivar CVL-1 contig15540, 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: 13806
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Found at i:4595 original size:20 final size:20
Alignment explanation
Indices: 4570--4615 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
4560 AAGGGACAGG
4570 GGAAGCAGAAAGGGAACTAA
1 GGAAGCAGAAAGGGAACTAA
*
4590 GGAAGCAGAAGGGGAACTAA
1 GGAAGCAGAAAGGGAACTAA
4610 GGAAGC
1 GGAAGC
4616 GAGAGGAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.46, C:0.11, G:0.39, T:0.04
Consensus pattern (20 bp):
GGAAGCAGAAAGGGAACTAA
Found at i:5204 original size:14 final size:14
Alignment explanation
Indices: 5185--5223 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
5175 TCTATTATTG
5185 TTTTTATTTATTTA
1 TTTTTATTTATTTA
5199 TTTTTA-TT-TTTA
1 TTTTTATTTATTTA
5211 TATTTTATTTATT
1 T-TTTTATTTATT
5224 ATTCAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 5 0.23
13 7 0.32
14 8 0.36
15 2 0.09
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTTATTTATTTA
Found at i:5225 original size:14 final size:14
Alignment explanation
Indices: 5186--5263 Score: 63
Period size: 13 Copynumber: 5.4 Consensus size: 14
5176 CTATTATTGT
5186 TTTTATTTATT-TA
1 TTTTATTTATTATA
5199 TTTTTATTT-TTATA
1 -TTTTATTTATTATA
5213 TTTTATTTATTATTCAA
1 TTTTATTTATTA-T--A
* *
5230 TTTTAATAATTA-A
1 TTTTATTTATTATA
*
5243 TTTTATTTATAATA
1 TTTTATTTATTATA
5257 TATTTAT
1 T-TTTAT
5264 ATATATACAC
Statistics
Matches: 52, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
13 20 0.38
14 15 0.29
15 6 0.12
17 11 0.21
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTTATTTATTATA
Found at i:5286 original size:33 final size:36
Alignment explanation
Indices: 5249--5322 Score: 109
Period size: 37 Copynumber: 2.1 Consensus size: 36
5239 TTAATTTTAT
5249 TTATAATATA-TT-TA-TATATATACACATAAATTG
1 TTATAATATATTTCTATTATATATACACATAAATTG
*
5282 TTATAATATATTTCTATTTATATATATACATAAATTG
1 TTATAATATATTTCTA-TTATATATACACATAAATTG
5319 TTAT
1 TTAT
5323 CCGTGACATA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
33 10 0.28
34 2 0.06
35 2 0.06
37 22 0.61
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (36 bp):
TTATAATATATTTCTATTATATATACACATAAATTG
Found at i:7795 original size:25 final size:25
Alignment explanation
Indices: 7742--7796 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
7732 TGATAATAAC
* * * *
7742 TTTTAAACACTATACACTTAATGTT
1 TTTTTAACAATATACACTTAATATA
*
7767 TTTTTAACAATATACACTTCATATA
1 TTTTTAACAATATACACTTAATATA
7792 TTTTT
1 TTTTT
7797 TTTATGAGCC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.35, C:0.15, G:0.02, T:0.49
Consensus pattern (25 bp):
TTTTTAACAATATACACTTAATATA
Found at i:10343 original size:22 final size:22
Alignment explanation
Indices: 10318--10895 Score: 200
Period size: 22 Copynumber: 26.6 Consensus size: 22
10308 ATGATCCCAT
10318 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* ** *
10340 TATGAAATTTTAATAACGATAC
1 TATGAAATTTTGATAACCTTCC
* * * * **
10362 TATGGAATTTCGAAAACTTTTT
1 TATGAAATTTTGATAACCTTCC
** *
10384 TAT-AAATTTTTTTAA---TCT
1 TATGAAATTTTGATAACCTTCC
*
10402 TATGAAATTTTGTTAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* * **** *
10424 TAAGGAATTTTGATTTTTTTCAA
1 TATGAAATTTTGATAACCTTC-C
10447 TATGAAATTTTGATAA-CTTCC
1 TATGAAATTTTGATAACCTTCC
* **
10468 CAGTGAAATTTTGATAACCAACAC
1 TA-TGAAATTTTGATAACCTTC-C
* *
10492 TATGAGATGTTGATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * * *
10513 ATATGATATATTGATAACC-ACGT
1 -TATGAAATTTTGATAACCTTC-C
* *
10536 TATGAAAATTTGAAAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* *
10557 ATATG-AATTGTT-AGTAATC-ACAC
1 -TATGAAATT-TTGA-TAACCTTC-C
* * * * *
10580 TCTCAAATTTTCATAATC-ACAC
1 TATGAAATTTTGATAACCTTC-C
*
10602 TATGAAATTGTGATAA-CTTCGC
1 TATGAAATTTTGATAACCTTC-C
*
10624 TATGAAATTTTGATAAATCTTCC
1 TATGAAATTTTGAT-AACCTTCC
* * *
10647 TATAAAATTTCGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTTCC
* * *
10670 TATAAAATTTTGATAACTTTCT
1 TATGAAATTTTGATAACCTTCC
*
10692 TATGAAATCTTGATAA-----C
1 TATGAAATTTTGATAACCTTCC
*
10709 TA-CAAATTTTGATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
** *
10729 TTATGAGTTTTTGATAACC-TCAT
1 -TATGAAATTTTGATAACCTTC-C
* * *
10752 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTTCC
* * *
10774 AATGAAATTTTGAT--CTATATAC
1 TATGAAATTTTGATAAC-CT-TCC
* *
10796 TACGAAATTTTGATAACCCTCC
1 TATGAAATTTTGATAACCTTCC
* * **
10818 TATAAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-TCC
* *
10840 TATTAAATTTTGATAACCTTCA
1 TATGAAATTTTGATAACCTTCC
*
10862 TATGAAATTTTGATATCC-TCC
1 TATGAAATTTTGATAACCTTCC
*
10883 -CTGAAATTTTGAT
1 TATGAAATTTTGAT
10896 TACTCCATAA
Statistics
Matches: 410, Mismatches: 113, Indels: 68
0.69 0.19 0.12
Matches are distributed among these distances:
16 11 0.03
17 2 0.00
18 5 0.01
19 11 0.03
20 13 0.03
21 22 0.05
22 265 0.65
23 74 0.18
24 7 0.02
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:10649 original size:23 final size:23
Alignment explanation
Indices: 10601--10707 Score: 103
Period size: 23 Copynumber: 4.7 Consensus size: 23
10591 CATAATCACA
*
10601 CTATGAAATTGTGAT-AA-CTTC
1 CTATGAAATTTTGATAAATCTTC
10622 GCTATGAAATTTTGATAAATCTTC
1 -CTATGAAATTTTGATAAATCTTC
* * * *
10646 CTATAAAATTTCGATAAACCTCC
1 CTATGAAATTTTGATAAATCTTC
* *
10669 CTATAAAATTTTGATAACT-TTC
1 CTATGAAATTTTGATAAATCTTC
* *
10691 TTATGAAATCTTGATAA
1 CTATGAAATTTTGATAA
10708 CTACAAATTT
Statistics
Matches: 71, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
22 30 0.42
23 37 0.52
24 4 0.06
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.39
Consensus pattern (23 bp):
CTATGAAATTTTGATAAATCTTC
Found at i:11072 original size:22 final size:22
Alignment explanation
Indices: 11001--11391 Score: 133
Period size: 22 Copynumber: 17.6 Consensus size: 22
10991 AATCACATTT
* * *
11001 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCCCTCTA
* *
11023 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCCCTCTA
* * *
11045 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCCCTCTA
* * * *
11067 TGAAATTCTGATAA-TCATATTA
1 TGAAATTTTGATAACCCCT-CTA
* * * * *
11089 TG-TAGTTTGATAACCTCGCTT
1 TGAAATTTTGATAACCCCTCTA
** *
11110 TGAAATTTTGATAACAACACTA
1 TGAAATTTTGATAACCCCTCTA
* *
11132 TGAAATTTTGATAA-TCTTCCTA
1 TGAAATTTTGATAACCCCT-CTA
* *
11154 T-AAGTTTTGATAATCCGTTCTCTA
1 TGAAATTTTGATAA-CC--CCTCTA
* * *
11178 TGAAATTTCGATAAACACTCTA
1 TGAAATTTTGATAACCCCTCTA
* *
11200 TGAGA-TTTGATAA-CCTTCTA
1 TGAAATTTTGATAACCCCTCTA
* * *
11220 TCAAATTTTGGT-ACTCCT-TA
1 TGAAATTTTGATAACCCCTCTA
* *
11240 TGAAATTGAGACTTTTATAA-CCTTCATA
1 TGAAA-T-----TTTGATAACCCCTC-TA
* *
11268 TGAAATTTTGATAACCACACTA
1 TGAAATTTTGATAACCCCTCTA
* *
11290 TAAAATTTTGATAACCTCC-CCA
1 TGAAATTTTGATAACC-CCTCTA
* *
11312 TGAAATATT-AGTAACCTCCT-AA
1 TGAAATTTTGA-TAACC-CCTCTA
* * *
11334 TGAAATTTTGTTAACCACACTA
1 TGAAATTTTGATAACCCCTCTA
* *
11356 TGAAATTCTT-ATAACCTCGCTA
1 TGAAATT-TTGATAACCCCTCTA
*
11378 TGACATTTTGATAA
1 TGAAATTTTGATAA
11392 TCTCTTTGAT
Statistics
Matches: 268, Mismatches: 73, Indels: 56
0.68 0.18 0.14
Matches are distributed among these distances:
20 15 0.06
21 43 0.16
22 174 0.65
23 5 0.02
24 5 0.02
25 11 0.04
26 6 0.02
27 2 0.01
28 7 0.03
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.39
Consensus pattern (22 bp):
TGAAATTTTGATAACCCCTCTA
Found at i:11491 original size:24 final size:22
Alignment explanation
Indices: 11427--11611 Score: 83
Period size: 22 Copynumber: 8.3 Consensus size: 22
11417 TTGTGATAAT
* *
11427 TAACCACCCTATGAAATTTCAA
1 TAACCAACCTATGAAATTTTAA
*
11449 TAACCAACCTAAGAAATTTTAA
1 TAACCAACCTATGAAATTTTAA
* * **
11471 TAACCTGATCTTATGAAATTTTGG
1 TAACC--AACCTATGAAATTTTAA
* *
11495 TAAACC-ACACTTTGAAATTTTGA
1 T-AACCAAC-CTATGAAATTTTAA
** **
11518 TAA-CTTCCATATGAAATTTTGG
1 TAACCAACC-TATGAAATTTTAA
* * *
11540 TAACC-ACAATATGGAATTTTGA
1 TAACCAAC-CTATGAAATTTTAA
* *
11562 TAACC-TCCTCATGAAATTATAA
1 TAACCAACCT-ATGAAATTTTAA
* *
11584 TAA-CAATCTTATGAAATTTTGA
1 TAACCAA-CCTATGAAATTTTAA
11606 TAACCA
1 TAACCA
11612 CATAGAGACA
Statistics
Matches: 123, Mismatches: 28, Indels: 23
0.71 0.16 0.13
Matches are distributed among these distances:
21 4 0.03
22 85 0.69
23 17 0.14
24 13 0.11
25 4 0.03
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.34
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTTAA
Found at i:11535 original size:22 final size:22
Alignment explanation
Indices: 11507--11610 Score: 95
Period size: 22 Copynumber: 4.7 Consensus size: 22
11497 AACCACACTT
*
11507 TGAAATTTTGATAACTTCCATA
1 TGAAATTTTGATAACCTCCATA
* * *
11529 TGAAATTTTGGTAACCACAATA
1 TGAAATTTTGATAACCTCCATA
*
11551 TGGAATTTTGATAACCTCC-TCA
1 TGAAATTTTGATAACCTCCAT-A
* * * *
11573 TGAAATTATAATAACAAT-CTTA
1 TGAAATTTTGATAAC-CTCCATA
11595 TGAAATTTTGATAACC
1 TGAAATTTTGATAACC
11611 ACATAGAGAC
Statistics
Matches: 64, Mismatches: 15, Indels: 7
0.74 0.17 0.08
Matches are distributed among these distances:
21 1 0.02
22 61 0.95
23 2 0.03
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCCATA
Found at i:11560 original size:44 final size:44
Alignment explanation
Indices: 11482--11579 Score: 135
Period size: 44 Copynumber: 2.2 Consensus size: 44
11472 AACCTGATCT
* * *
11482 TATGAAATTTTGGTAAACCACACTTTGAAATTTTGATAACTTCC
1 TATGAAATTTTGGTAAACCACAATATGAAATTTTGATAACCTCC
*
11526 ATATGAAATTTTGGT-AACCACAATATGGAATTTTGATAACCTCC
1 -TATGAAATTTTGGTAAACCACAATATGAAATTTTGATAACCTCC
11570 TCATGAAATT
1 T-ATGAAATT
11580 ATAATAACAA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
43 1 0.02
44 33 0.69
45 14 0.29
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (44 bp):
TATGAAATTTTGGTAAACCACAATATGAAATTTTGATAACCTCC
Found at i:11804 original size:19 final size:20
Alignment explanation
Indices: 11773--11810 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
11763 TATTGACATT
11773 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
11792 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
11811 AATAATAGTA
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:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:11940 original size:25 final size:25
Alignment explanation
Indices: 11884--11933 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
11874 GTCTAAATTG
* *
11884 AAAATTTTAACTAATTTTTAAGTAAT
1 AAAATTAT-ACTAAATTTTAAGTAAT
11910 AAAATTATACTAAATTTTAA-TAAT
1 AAAATTATACTAAATTTTAAGTAAT
11934 GGAAATTTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 4 0.18
25 11 0.50
26 7 0.32
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (25 bp):
AAAATTATACTAAATTTTAAGTAAT
Done.