Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011277.1 Corchorus capsularis cultivar CVL-1 contig11298, 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: 9051
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Found at i:1230 original size:26 final size:25
Alignment explanation
Indices: 1160--1230 Score: 65
Period size: 25 Copynumber: 2.8 Consensus size: 25
1150 GTGTTGGAGG
1160 TGTCCGTTGGAGGTCACGTGAGTAGT
1 TGTCCGTTGGA-GTCACGTGAGTAGT
* * *
1186 CGTACGATAGG-GTCACGTGAAG-AGT
1 TGTCCG-TTGGAGTCACGTG-AGTAGT
1211 TGTCCGTTGGAGATCACGTG
1 TGTCCGTTGGAG-TCACGTG
1231 TGGAGTGGTA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
24 3 0.09
25 16 0.46
26 13 0.37
27 3 0.09
ACGTcount: A:0.20, C:0.17, G:0.37, T:0.27
Consensus pattern (25 bp):
TGTCCGTTGGAGTCACGTGAGTAGT
Found at i:1329 original size:23 final size:23
Alignment explanation
Indices: 1303--1364 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
1293 TTATGGTCAT
1303 AAGTGGTCGAGT-GCCAGGCTTGG
1 AAGTGGTCG-GTCGCCAGGCTTGG
**
1326 AAGTGGTCGGTCGCTGGGCTTGG
1 AAGTGGTCGGTCGCCAGGCTTGG
*
1349 AAGTGGTCGGGCGCCA
1 AAGTGGTCGGTCGCCA
1365 AGCAATTGTG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
22 2 0.06
23 31 0.94
ACGTcount: A:0.15, C:0.19, G:0.45, T:0.21
Consensus pattern (23 bp):
AAGTGGTCGGTCGCCAGGCTTGG
Found at i:2767 original size:15 final size:16
Alignment explanation
Indices: 2746--2779 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2736 CTAAATCTAA
* *
2746 AAAAAAATCGAACCCG
1 AAAAAACTCAAACCCG
2762 AAAAAACTCAAACCCG
1 AAAAAACTCAAACCCG
2778 AA
1 AA
2780 CTTGAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.59, C:0.26, G:0.09, T:0.06
Consensus pattern (16 bp):
AAAAAACTCAAACCCG
Found at i:2780 original size:22 final size:22
Alignment explanation
Indices: 2754--2795 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2744 AAAAAAAAAT
*
2754 CGAACCCGAAAAAACTCAAACC
1 CGAACCCGAAAAAACCCAAACC
**
2776 CGAACTTGAAAAAACCCAAA
1 CGAACCCGAAAAAACCCAAA
2796 TTCAATACTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.52, C:0.31, G:0.10, T:0.07
Consensus pattern (22 bp):
CGAACCCGAAAAAACCCAAACC
Found at i:3000 original size:26 final size:26
Alignment explanation
Indices: 2971--3032 Score: 106
Period size: 26 Copynumber: 2.4 Consensus size: 26
2961 ACCCAACCCG
2971 AAACCGAATCAACCTGACTCAAATTT
1 AAACCGAATCAACCTGACTCAAATTT
*
2997 AAACCGAATAAACCTGACTCAAATTT
1 AAACCGAATCAACCTGACTCAAATTT
*
3023 AACCCGAATC
1 AAACCGAATC
3033 CGAATCAACC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.44, C:0.27, G:0.08, T:0.21
Consensus pattern (26 bp):
AAACCGAATCAACCTGACTCAAATTT
Found at i:3004 original size:32 final size:29
Alignment explanation
Indices: 2971--3063 Score: 102
Period size: 26 Copynumber: 3.2 Consensus size: 29
2961 ACCCAACCCG
2971 AAACCGAATCAACCTGACTCAAATTT---
1 AAACCGAATCAACCTGACTCAAATTTACC
*
2997 AAACCGAATAAACCTGACTCAAATTTAACCC
1 AAACCGAATCAACCTGACTCAAATTT-A-CC
* *
3028 GAATCCGAATCAACCTGACCCAAATTTAACC
1 -AAACCGAATCAACCTGACTCAAATTT-ACC
3059 AAACC
1 AAACC
3064 TAACTCAAGC
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
26 25 0.45
30 4 0.07
31 2 0.04
32 25 0.45
ACGTcount: A:0.43, C:0.30, G:0.08, T:0.19
Consensus pattern (29 bp):
AAACCGAATCAACCTGACTCAAATTTACC
Found at i:4381 original size:22 final size:21
Alignment explanation
Indices: 4353--4429 Score: 77
Period size: 22 Copynumber: 3.5 Consensus size: 21
4343 CAATGGTTGG
4353 AAAATTTCATAAGAGAGTTATC
1 AAAATTTCAT-AGAGAGTTATC
4375 AAAATTTCATAGTATGTAG--ATC
1 AAAATTTCATAG-A-G-AGTTATC
* *
4397 AAAATTTCATAGGGAGATTAAC
1 AAAATTTCATAGAGAG-TTATC
4419 AAAATTTCATA
1 AAAATTTCATA
4430 ATGAGATAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
19 2 0.04
20 1 0.02
21 2 0.04
22 39 0.83
23 1 0.02
24 2 0.04
ACGTcount: A:0.45, C:0.09, G:0.13, T:0.32
Consensus pattern (21 bp):
AAAATTTCATAGAGAGTTATC
Found at i:4435 original size:22 final size:21
Alignment explanation
Indices: 4353--4444 Score: 73
Period size: 22 Copynumber: 4.2 Consensus size: 21
4343 CAATGGTTGG
*
4353 AAAATTTCATAA-GAGAGTTATC
1 AAAATTTCATAATGAGA--TAAC
4375 AAAATTTCATAGTATGTAGAT--C
1 AAAATTTCATA--ATG-AGATAAC
**
4397 AAAATTTCATAGGGAGATTAAC
1 AAAATTTCATAATGAGA-TAAC
4419 AAAATTTCATAATGAGATAATC
1 AAAATTTCATAATGAGATAA-C
4441 AAAA
1 AAAA
4445 AAACTAAACT
Statistics
Matches: 58, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
19 3 0.05
20 2 0.03
21 3 0.05
22 44 0.76
24 2 0.03
25 1 0.02
26 3 0.05
ACGTcount: A:0.48, C:0.09, G:0.13, T:0.30
Consensus pattern (21 bp):
AAAATTTCATAATGAGATAAC
Found at i:4553 original size:19 final size:19
Alignment explanation
Indices: 4481--4547 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
4471 CTTCATATGA
*
4481 AATTTTGATATCCTCACTG
1 AATTTTGATATCCTCCCTG
* *
4500 AATTTCGATATCCTCCTTG
1 AATTTTGATATCCTCCCTG
*
4519 AATTTTGGTATCCTCCCTG
1 AATTTTGATATCCTCCCTG
4538 AAATTTTGAT
1 -AATTTTGAT
4548 TACTCCATCA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 32 0.80
20 8 0.20
ACGTcount: A:0.24, C:0.21, G:0.12, T:0.43
Consensus pattern (19 bp):
AATTTTGATATCCTCCCTG
Found at i:4682 original size:22 final size:22
Alignment explanation
Indices: 4651--4858 Score: 143
Period size: 22 Copynumber: 9.4 Consensus size: 22
4641 GTAATCATTT
*
4651 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
*
4673 TGAAATTTTGATAACATCTTTA
1 TGAAATTTTGATAACCTCTTTA
* * * * *
4695 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTTTA
* * * *
4717 TAAAATTTTGATAATCACATTA
1 TGAAATTTTGATAACCTCTTTA
* *
4739 TGTAATTTTGATAACCTCGCTT-
1 TGAAATTTTGATAACCTC-TTTA
** **
4761 TGAAATTTTGATAACAACACTA
1 TGAAATTTTGATAACCTCTTTA
4783 TGAAATTTTGATAATCCTATCTTTA
1 TGAAATTTTGATAA-CC--TCTTTA
* * * *
4808 TGAAATTTCGATAATCACTCTA
1 TGAAATTTTGATAACCTCTTTA
* *
4830 TGAGA-TTTGATAACCT-TCTA
1 TGAAATTTTGATAACCTCTTTA
*
4850 TCAAATTTT
1 TGAAATTTT
4859 TCCGGTACTC
Statistics
Matches: 142, Mismatches: 38, Indels: 13
0.74 0.20 0.07
Matches are distributed among these distances:
20 7 0.05
21 12 0.08
22 103 0.73
23 3 0.02
24 1 0.01
25 16 0.11
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTTTA
Found at i:4914 original size:22 final size:22
Alignment explanation
Indices: 4885--4995 Score: 79
Period size: 22 Copynumber: 5.1 Consensus size: 22
4875 AAATTGAGAC
*
4885 TTTT-ATAACCTTCATATGAAA
1 TTTTGATAACCTACATATGAAA
*
4906 TTTTGATAACC-ACACTATAAAA
1 TTTTGATAACCTACA-TATGAAA
* **
4928 TTTTGATAACCTCCCGATGAAA
1 TTTTGATAACCTACATATGAAA
* *
4950 TATT-AGTAACCTTC-TAATGAAA
1 TTTTGA-TAACCTACAT-ATGAAA
*
4972 TTTTGTTAACC-ACAATATGAAA
1 TTTTGATAACCTAC-ATATGAAA
4994 TT
1 TT
4996 CGTATAACCT
Statistics
Matches: 70, Mismatches: 12, Indels: 15
0.72 0.12 0.15
Matches are distributed among these distances:
21 8 0.11
22 60 0.86
23 2 0.03
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (22 bp):
TTTTGATAACCTACATATGAAA
Found at i:5121 original size:24 final size:22
Alignment explanation
Indices: 5060--5196 Score: 82
Period size: 22 Copynumber: 6.1 Consensus size: 22
5050 TTGTGATAAT
* *
5060 TAACCACCCTATGAAATTTCAA
1 TAACCAACCTATGAAATTTTAA
*
5082 TAACCAACCTAAGAAATTTTAA
1 TAACCAACCTATGAAATTTTAA
* * **
5104 TTACCTGATCCTATGAAATTTTGG
1 TAACC--AACCTATGAAATTTTAA
**
5128 TAACC-ACTCTATGAAATTTTGG
1 TAACCAAC-CTATGAAATTTTAA
* **
5150 TAA-CTACACTATGAAATTTTGG
1 TAACCAAC-CTATGAAATTTTAA
* *
5172 TAACC-ACACTATGGAATTTTGA
1 TAACCAAC-CTATGAAATTTTAA
5194 TAA
1 TAA
5197 ACTTCTCATG
Statistics
Matches: 97, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
21 2 0.02
22 77 0.79
23 1 0.01
24 17 0.18
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTTAA
Found at i:5132 original size:46 final size:44
Alignment explanation
Indices: 5067--5177 Score: 109
Period size: 46 Copynumber: 2.5 Consensus size: 44
5057 AATTAACCAC
*** * *
5067 CCTATGAAATTTCAATAACCAAC-CTAAGAAATTTTAATTACCTGA
1 CCTATGAAATTTTGGTAACCAACTCTAAGAAATTTT-AGTAACT-A
* *
5112 TCCTATGAAATTTTGGTAACC-ACTCTATGAAATTTTGGTAACTA
1 -CCTATGAAATTTTGGTAACCAACTCTAAGAAATTTTAGTAACTA
5156 CACTATGAAATTTTGGTAACCA
1 C-CTATGAAATTTTGGTAACCA
5178 CACTATGGAA
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
43 1 0.02
44 20 0.36
45 6 0.11
46 28 0.51
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (44 bp):
CCTATGAAATTTTGGTAACCAACTCTAAGAAATTTTAGTAACTA
Found at i:5207 original size:22 final size:22
Alignment explanation
Indices: 5182--5240 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
5172 TAACCACACT
*
5182 ATGGAATTTTGATAAACTTCTC
1 ATGGAATTTTGATAAACATCTC
* * * *
5204 ATGGAATTATAATAATCATCTT
1 ATGGAATTTTGATAAACATCTC
5226 ATGGAATTTTGATAA
1 ATGGAATTTTGATAA
5241 CCAGATAGAG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.41
Consensus pattern (22 bp):
ATGGAATTTTGATAAACATCTC
Found at i:5550 original size:31 final size:31
Alignment explanation
Indices: 5514--5584 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
5504 TGACAATTTA
* *
5514 GAAATATGTTTTAAAAAAAAAGGTACAATTG
1 GAAATATATTTTAAAAAAAAAGGTACAATCG
* *
5545 GAAATATATTTTAAAAATAAGGGTACAATCG
1 GAAATATATTTTAAAAAAAAAGGTACAATCG
5576 GAAAATATA
1 G-AAATATA
5585 AAGTTTCCCC
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
31 28 0.80
32 7 0.20
ACGTcount: A:0.52, C:0.04, G:0.15, T:0.28
Consensus pattern (31 bp):
GAAATATATTTTAAAAAAAAAGGTACAATCG
Found at i:7853 original size:3 final size:3
Alignment explanation
Indices: 7845--7878 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
7835 CTTTGTTGCT
7845 TTA TTA TTA TTTA TTA TTA TTA TTA -TA TTA TTA T
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA T
7879 ATATATAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 24 0.83
4 3 0.10
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Done.