Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009573.1 Corchorus capsularis cultivar CVL-1 contig09594, 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: 9102
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1046 original size:29 final size:30
Alignment explanation
Indices: 1014--1078 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 30
1004 GTTTAAGAGG
* *
1014 CAAAATGTCTAGAAT-TA-AAGTTCATGGGA
1 CAAAATGTCCA-AATCTACAAGTTCAGGGGA
1043 CAAAATGTCCAAATGCTACAAGTTCAGGGGA
1 CAAAATGTCCAAAT-CTACAAGTTCAGGGGA
1074 CAAAA
1 CAAAA
1079 AGGATCTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 3 0.10
29 10 0.32
30 2 0.06
31 16 0.52
ACGTcount: A:0.43, C:0.15, G:0.20, T:0.22
Consensus pattern (30 bp):
CAAAATGTCCAAATCTACAAGTTCAGGGGA
Found at i:2664 original size:202 final size:203
Alignment explanation
Indices: 2298--2673 Score: 641
Period size: 202 Copynumber: 1.9 Consensus size: 203
2288 GTGATTATAT
*
2298 GATACACCGGTGTTGTAAATTTTGGACTCCACAAGCGGGTTGTGGAGTTGACACATGTCCATTTT
1 GATACACCGGTGTTGTAAATTTTGGACTCCACAAGCGGGTTGTGAAGTTGACACATGTCCATTTT
*
2363 TTGAATTATTTAAGTTTTAAATATTTCAATCTAGTCCCTAAGGGACACATGTCACCCTTCAAGAC
66 TTGAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAAGGGACACATGTCACCCTTCAAGAC
*
2428 CCGCTTGTGTAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTGCCTATATATAAATGGT
131 CCGCTTGTGTAGTCTGCTAAACTCCACCGACGGTGTATTGTATAATTTGCCTATATATAAATGGT
2493 AATTATTC
196 AATTATTC
2501 GATACA-CGGCTG-TGTAAATTTTGGACTCCACAAGCGGGTTGTGAAGTTGACACATGTCCATTT
1 GATACACCGG-TGTTGTAAATTTTGGACTCCACAAGCGGGTTGTGAAGTTGACACATGTCCATTT
* * * *
2564 TTTTAATTAATTATGTTTTAAATATTTCAATCTAGTCCCT-AGATGACACATGTCACCCTTCAGG
65 TTTGAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAAG-GGACACATGTCACCCTTCAAG
*
2628 ACCCGCTTGTGTAGTCTGCTAAATTCCACCGACGGTGTATTGTATA
129 ACCCGCTTGTGTAGTCTGCTAAACTCCACCGACGGTGTATTGTATA
2674 TTTTCTTTAA
Statistics
Matches: 163, Mismatches: 8, Indels: 5
0.93 0.05 0.03
Matches are distributed among these distances:
201 2 0.01
202 153 0.94
203 8 0.05
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (203 bp):
GATACACCGGTGTTGTAAATTTTGGACTCCACAAGCGGGTTGTGAAGTTGACACATGTCCATTTT
TTGAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAAGGGACACATGTCACCCTTCAAGAC
CCGCTTGTGTAGTCTGCTAAACTCCACCGACGGTGTATTGTATAATTTGCCTATATATAAATGGT
AATTATTC
Found at i:2937 original size:32 final size:31
Alignment explanation
Indices: 2873--2939 Score: 91
Period size: 31 Copynumber: 2.1 Consensus size: 31
2863 AACTTTATGT
* *
2873 TTTCCGATTGTACCCTTATTTTCAAAACATA
1 TTTCCAATTGTACCCTTATTTTAAAAACATA
2904 TTTCCAATTGTACCCTT-TTTTAAAAAAACATA
1 TTTCCAATTGTACCCTTATTTT--AAAAACATA
2936 TTTC
1 TTTC
2940 TAAATTGCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
30 4 0.12
31 16 0.50
32 12 0.38
ACGTcount: A:0.31, C:0.21, G:0.04, T:0.43
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTATTTTAAAAACATA
Found at i:3136 original size:149 final size:147
Alignment explanation
Indices: 2845--3144 Score: 487
Period size: 148 Copynumber: 2.0 Consensus size: 147
2835 ACTATATATA
* * *
2845 AAAGTACGAATAAGGGGAAACTTTATGTTTTCCGATTGTACCCTTATTTTCAAAACATATTTCCA
1 AAAGTACGAATAAGGGGAAACTTTATATTTTCCAATTATACCCTTATTTTCAAAACATATTTCCA
*
2910 ATTGTACCCTTTTTTAAAAAAACATATTTCTAAATTGCCATTACTAAATAATATTTTAATTATTC
66 ATTGTA-CCTTTTTAAAAAAAACATATTTCTAAATTGCCATTACTAAATAATATTTTAATTATTC
2975 CATTATTTTTTTAATCAT
130 CATTATTTTTTTAATCAT
*
2993 AAAGTACGAATAAGGGGAAACTTTATATTTTCCAATTATACCCTTATTTTTAAAACATATTTCCA
1 AAAGTACGAATAAGGGGAAACTTTATATTTTCCAATTATACCCTTATTTTCAAAACATATTTCCA
*
3058 ATTGTA-CTTTTTAAAAAAAAAATGATATTTCTAAATTG-CACTTACTAAATAATATTTTAATTA
66 ATTGTACCTTTTT--AAAAAAAA-CATATTTCTAAATTGCCA-TTACTAAATAATATTTTAATTA
3121 TTCCATTATTTTTTTAATCAT
127 TTCCATTATTTTTTTAATCAT
3142 AAA
1 AAA
3145 TTATTCCATT
Statistics
Matches: 142, Mismatches: 6, Indels: 7
0.92 0.04 0.05
Matches are distributed among these distances:
146 6 0.04
148 76 0.54
149 60 0.42
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.42
Consensus pattern (147 bp):
AAAGTACGAATAAGGGGAAACTTTATATTTTCCAATTATACCCTTATTTTCAAAACATATTTCCA
ATTGTACCTTTTTAAAAAAAACATATTTCTAAATTGCCATTACTAAATAATATTTTAATTATTCC
ATTATTTTTTTAATCAT
Found at i:4301 original size:121 final size:116
Alignment explanation
Indices: 4135--4371 Score: 307
Period size: 121 Copynumber: 2.0 Consensus size: 116
4125 AGTACGAATA
* * *
4135 ATGGAAAACGTTATGTTTTCCGATTGTACCATTTTTTCAATTATATTTCTAAATTGAC-ATTATT
1 ATGGAAAACGTTATGTTTTCCGATTGAACCATTTTTCCAAATATATTTCTAAATT-ACTATTATT
* *
4199 AAAATTTATTACTTAAAACTTAATTATAAAATTTCAATTTAGATCGAATTATAAGTT
65 ---ATTTATTACTTAAAAATTAA-T-TAAAATTTCAATTTAGACCGAATTATAAGTT
* * * *
4256 ATGGGAAACTTTATG-TTTCCGATTGCAACTATTTTTCCAAATATATTTCTAAATTTCTATTATT
1 ATGGAAAACGTTATGTTTTCCGATTG-AACCATTTTTCCAAATATATTTCTAAATTACTATTATT
*
4320 ATTTATTATTTAAAAATTAATTAAAATTTCAATTTAGACCGAATTATAAGTT
65 ATTTATTACTTAAAAATTAATTAAAATTTCAATTTAGACCGAATTATAAGTT
4372 TGTCAAATTG
Statistics
Matches: 104, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
116 30 0.29
117 1 0.01
118 18 0.17
120 11 0.11
121 44 0.42
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.45
Consensus pattern (116 bp):
ATGGAAAACGTTATGTTTTCCGATTGAACCATTTTTCCAAATATATTTCTAAATTACTATTATTA
TTTATTACTTAAAAATTAATTAAAATTTCAATTTAGACCGAATTATAAGTT
Found at i:4437 original size:19 final size:19
Alignment explanation
Indices: 4423--4459 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
4413 ACTATTATTT
4423 TTTTAATTTAATATTTTAC
1 TTTTAATTTAATATTTTAC
4442 TTTTAATTTCAAT-TTTTA
1 TTTTAATTT-AATATTTTA
4460 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTAATTTAATATTTTAC
Found at i:4578 original size:22 final size:22
Alignment explanation
Indices: 4552--4756 Score: 175
Period size: 22 Copynumber: 9.3 Consensus size: 22
4542 TTAGTTGATG
*
4552 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAGGA
* *
4574 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AGGA
*
4597 -GGTTATCAAAATTCCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
* *
4618 TGGTTACCAAAATTTCATATGA
1 TGGTTATCAAAATTTCATAGGA
** *
4640 AAGTTATCAAAATTTCATATG-
1 TGGTTATCAAAATTTCATAGGA
*
4661 TGGTTACCAAAATTTCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
* *
4683 TGTTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAGGA
* * *
4705 TCAGGTTATTAAAATTTCTTAGGT
1 T--GGTTATCAAAATTTCATAGGA
** *
4729 TGGTTATTGAAATTTCATAGGG
1 TGGTTATCAAAATTTCATAGGA
4751 TGGTTA
1 TGGTTA
4757 ATTATCACAA
Statistics
Matches: 150, Mismatches: 25, Indels: 16
0.79 0.13 0.08
Matches are distributed among these distances:
21 20 0.13
22 110 0.73
23 3 0.02
24 17 0.11
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.39
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGGA
Found at i:5107 original size:44 final size:44
Alignment explanation
Indices: 5058--5206 Score: 129
Period size: 44 Copynumber: 3.3 Consensus size: 44
5048 CATAGTGTTG
* *
5058 TTATCAAAATTTCAAAGCGAGGTTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCAAAGAGAGGTTATCAAAATTACAAAATGTGA
* * * * * * ** *
5102 TTATCAGAATTTCATAGAGGGGTCAACAAAATTTTAAAAAAAAATGG
1 TTATCAAAATTTCAAAGAGAGGTTATCAAAA--TT-ACAAAATGTGA
* *
5149 TTATCAAAATTTCATAA-AGAGGTTATCAAATTTGCAAAATGTGA
1 TTATCAAAATTTCA-AAGAGAGGTTATCAAAATTACAAAATGTGA
*
5193 TTATAAAAATTTCA
1 TTATCAAAATTTCA
5207 TAGTGGTATT
Statistics
Matches: 78, Mismatches: 23, Indels: 8
0.72 0.21 0.07
Matches are distributed among these distances:
44 44 0.56
45 2 0.03
46 2 0.03
47 29 0.37
48 1 0.01
ACGTcount: A:0.45, C:0.09, G:0.13, T:0.32
Consensus pattern (44 bp):
TTATCAAAATTTCAAAGAGAGGTTATCAAAATTACAAAATGTGA
Found at i:5175 original size:22 final size:22
Alignment explanation
Indices: 4990--5208 Score: 90
Period size: 22 Copynumber: 9.7 Consensus size: 22
4980 CATAGAGTTA
* *
4990 TTATCGAAATTTCATAGAGATCGG
1 TTATCAAAATTTCATAAAGA--GG
5014 ATTATCAAAATTT-ATAGGAAGA--
1 -TTATCAAAATTTCATA--AAGAGG
* ** **
5036 TTATCATAATTTCATAGTGTTG
1 TTATCAAAATTTCATAAAGAGG
*
5058 TTATCAAAATTTCA-AAGCGAGG
1 TTATCAAAATTTCATAA-AGAGG
* * * *
5080 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAAAGAGG
* * *
5102 TTATCAGAATTTCATAGAGGGG
1 TTATCAAAATTTCATAAAGAGG
* * * * *
5124 TCAACAAAATTTTAAAAAAAAATGG
1 TTATCAAAA-TTT-CATAAAGA-GG
5149 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAAAGAGG
* *
5171 TTATC-AAATTTGCA-AAATGTGA
1 TTATCAAAATTT-CATAAA-GAGG
*
5193 TTATAAAAATTTCATA
1 TTATCAAAATTTCATA
5209 GTGGTATTTC
Statistics
Matches: 143, Mismatches: 37, Indels: 30
0.68 0.18 0.14
Matches are distributed among these distances:
20 1 0.01
21 21 0.15
22 72 0.50
23 17 0.12
24 9 0.06
25 20 0.14
26 3 0.02
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.34
Consensus pattern (22 bp):
TTATCAAAATTTCATAAAGAGG
Found at i:5316 original size:20 final size:20
Alignment explanation
Indices: 5291--5342 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
5281 TTATGGAGTA
5291 ATCAAAATTTCAGACAAGAT
1 ATCAAAATTTCAGACAAGAT
** *
5311 ATCAAAATTTCAGGGAGGAT
1 ATCAAAATTTCAGACAAGAT
5331 ATCAAAATTTCA
1 ATCAAAATTTCA
5343 TATGAAGGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.27
Consensus pattern (20 bp):
ATCAAAATTTCAGACAAGAT
Found at i:5487 original size:23 final size:22
Alignment explanation
Indices: 5310--5829 Score: 191
Period size: 22 Copynumber: 23.7 Consensus size: 22
5300 TCAGACAAGA
*
5310 TATCAAAATTTC--AGGGAGGA
1 TATCAAAATTTCATAGGGAGGT
* *
5330 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATAGGGAGGT
* ****
5352 TGTCAAAATTTCATAGTTTTGT
1 TATCAAAATTTCATAGGGAGGT
* *
5374 TTTCAAAATTTCATA-AGAGGGT
1 TATCAAAATTTCATAGGGA-GGT
* *
5396 TATCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATAGGGAGGT
* * *
5417 AGATCAAAATTTCGTAGGGAGAT
1 -TATCAAAATTTCATAGGGAGGT
* * **
5440 TAACAAAATTCCATAATGAGGT
1 TATCAAAATTTCATAGGGAGGT
**
5462 TATCAAAAAATCATAGGGAGGTT
1 TATCAAAATTTCATAGGGAGG-T
* * *
5485 TATCAAAATTTTATAGGAAGATT
1 TATCAAAATTTCATAGGGAG-GT
*
5508 TATCAAAATTTCATAGCGAGGT
1 TATCAAAATTTCATAGGGAGGT
* * *
5530 TATCACAATTTCATAGTGTA-AT
1 TATCAAAATTTCATAG-GGAGGT
* * * * *
5552 TATAAAAATTTCAGAGTGTGAT
1 TATCAAAATTTCATAGGGAGGT
* *
5574 TA-CTAACAA-TTCATATGGAAGT
1 TATC-AA-AATTTCATAGGGAGGT
* * * ** * *
5596 TTTTAAATTTTCATAACGTGAT
1 TATCAAAATTTCATAGGGAGGT
* * *
5618 TATCAATATATCATATGGAGGT
1 TATCAAAATTTCATAGGGAGGT
* * **
5640 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATAG-GGAGGT
** *
5663 TATCAAAATTTCATATCGTGGT
1 TATCAAAATTTCATAGGGAGGT
* *
5685 CT-TCAAAA-TTCTTTAGGGAAGT
1 -TATCAAAATTTC-ATAGGGAGGT
* * *
5707 TAACAAAATTT-ATAAGAAGGT
1 TATCAAAATTTCATAGGGAGGT
** * ***
5728 TAAAAAAAATT-ATAAAAAGGT
1 TATCAAAATTTCATAGGGAGGT
* * * * **
5749 TCTCGAAATTCCATA-GTATCAT
1 TATCAAAATTTCATAGGGA-GGT
* *
5771 TATTAAAATTTCATAGGAAGGT
1 TATCAAAATTTCATAGGGAGGT
* *
5793 AATCAAAATTTCATAGGAAGGT
1 TATCAAAATTTCATAGGGAGGT
*
5815 AATCAAAATTTCATA
1 TATCAAAATTTCATA
5830 ATGGGATCAT
Statistics
Matches: 358, Mismatches: 121, Indels: 40
0.69 0.23 0.08
Matches are distributed among these distances:
20 12 0.03
21 37 0.10
22 246 0.69
23 63 0.18
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (22 bp):
TATCAAAATTTCATAGGGAGGT
Found at i:5642 original size:22 final size:22
Alignment explanation
Indices: 5617--5678 Score: 61
Period size: 23 Copynumber: 2.8 Consensus size: 22
5607 CATAACGTGA
*
5617 TTATCAATATATCATATGGAGG
1 TTATCAAAATATCATATGGAGG
* * **
5639 TTATCAACATCTCATAGTGTTGG
1 TTATCAAAATATCATA-TGGAGG
*
5662 TTATCAAAATTTCATAT
1 TTATCAAAATATCATAT
5679 CGTGGTCTTC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
22 15 0.45
23 18 0.55
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (22 bp):
TTATCAAAATATCATATGGAGG
Found at i:5735 original size:21 final size:21
Alignment explanation
Indices: 5705--5749 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
5695 CTTTAGGGAA
* * *
5705 GTTAACAAAATTTATAAGAAG
1 GTTAAAAAAAATTATAAAAAG
5726 GTTAAAAAAAATTATAAAAAG
1 GTTAAAAAAAATTATAAAAAG
5747 GTT
1 GTT
5750 CTCGAAATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.56, C:0.02, G:0.13, T:0.29
Consensus pattern (21 bp):
GTTAAAAAAAATTATAAAAAG
Found at i:6450 original size:51 final size:51
Alignment explanation
Indices: 6387--6541 Score: 301
Period size: 51 Copynumber: 3.0 Consensus size: 51
6377 ATTGCTGCTG
*
6387 TTTCATCTAGCAATCATGATGACACTAATGTGAAATATCTTCCAATTATTA
1 TTTCATCTAGCAATCATGATGGCACTAATGTGAAATATCTTCCAATTATTA
6438 TTTCATCTAGCAATCATGATGGCACTAATGTGAAATATCTTCCAATTATTA
1 TTTCATCTAGCAATCATGATGGCACTAATGTGAAATATCTTCCAATTATTA
6489 TTTCATCTAGCAATCATGATGGCACTAATGTGAAATATCTTCCAATTATTA
1 TTTCATCTAGCAATCATGATGGCACTAATGTGAAATATCTTCCAATTATTA
6540 TT
1 TT
6542 AAATGCAGGT
Statistics
Matches: 103, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
51 103 1.00
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (51 bp):
TTTCATCTAGCAATCATGATGGCACTAATGTGAAATATCTTCCAATTATTA
Found at i:9059 original size:2 final size:2
Alignment explanation
Indices: 9054--9102 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
9044 ATATTGCTGG
9054 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
9096 GA GA GA G
1 GA GA GA G
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Done.