Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011304.1 Corchorus capsularis cultivar CVL-1 contig11325, 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: 22328
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Found at i:5363 original size:3 final size:3
Alignment explanation
Indices: 5355--5439 Score: 111
Period size: 3 Copynumber: 28.3 Consensus size: 3
5345 ATAATTTGCC
5355 TAT TAT TAT TAT TAT TAT TAT TAAT T-T TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT
* * *
5400 TAT T-T TGAA GAA TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
5440 CATGTAAATA
Statistics
Matches: 74, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
2 4 0.05
3 67 0.91
4 3 0.04
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:5380 original size:30 final size:28
Alignment explanation
Indices: 5346--5434 Score: 94
Period size: 30 Copynumber: 3.1 Consensus size: 28
5336 GTGTATTGTA
5346 TAATTTGCCTATTATTATTATTATTATTAT
1 TAATTTG--TATTATTATTATTATTATTAT
5376 TAATTT-TATTATTATTATTATTATTAT
1 TAATTTGTATTATTATTATTATTATTAT
*
5403 T--TTGAAGAATATTATTATTATTATTATTAT
1 TAATT--TG--TATTATTATTATTATTATTAT
5433 TA
1 TA
5435 TTATTCATGT
Statistics
Matches: 52, Mismatches: 1, Indels: 11
0.81 0.02 0.17
Matches are distributed among these distances:
25 2 0.04
27 22 0.42
30 28 0.54
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (28 bp):
TAATTTGTATTATTATTATTATTATTAT
Found at i:6030 original size:85 final size:85
Alignment explanation
Indices: 5930--6097 Score: 309
Period size: 85 Copynumber: 2.0 Consensus size: 85
5920 GGAGTTTTAT
*
5930 TTTGATTATAATTCAATGTTCTAAATATTATTTATAAGTATTATTTGGAATTCTAAATATAAAAT
1 TTTGATTATAATTCAATGTTCTAAATATTATTTATAAATATTATTTGGAATTCTAAATATAAAAT
5995 AATATATATTGATTTTCTAC
66 AATATATATTGATTTTCTAC
*
6015 TTTGATTATAATTCAATGTTCTAAATATTATTTATAAATATTATTTGGAATTCTAAATATATAAT
1 TTTGATTATAATTCAATGTTCTAAATATTATTTATAAATATTATTTGGAATTCTAAATATAAAAT
*
6080 AATATATATTGGTTTTCT
66 AATATATATTGATTTTCT
6098 CTCAATTAAT
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
85 80 1.00
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.49
Consensus pattern (85 bp):
TTTGATTATAATTCAATGTTCTAAATATTATTTATAAATATTATTTGGAATTCTAAATATAAAAT
AATATATATTGATTTTCTAC
Found at i:6054 original size:13 final size:13
Alignment explanation
Indices: 6036--6060 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6026 TTCAATGTTC
6036 TAAATATTATTTA
1 TAAATATTATTTA
6049 TAAATATTATTT
1 TAAATATTATTT
6061 GGAATTCTAA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAAATATTATTTA
Found at i:6424 original size:2 final size:2
Alignment explanation
Indices: 6417--6448 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
6407 GATTGAGTGT
6417 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6449 CATGTGTGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11245 original size:5 final size:5
Alignment explanation
Indices: 11235--11282 Score: 52
Period size: 4 Copynumber: 10.6 Consensus size: 5
11225 AACTTTTAAC
*
11235 TTTGT TTTGT TTTGT TTTG- TTTG- TTTG- TTTG- TTTGT TTGGT TTT-T
1 TTTGT TTTGT TTTGT TTTGT TTTGT TTTGT TTTGT TTTGT TTTGT TTTGT
11280 TTT
1 TTT
11283 TTGGCATAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
4 20 0.50
5 20 0.50
ACGTcount: A:0.00, C:0.00, G:0.21, T:0.79
Consensus pattern (5 bp):
TTTGT
Found at i:11464 original size:19 final size:19
Alignment explanation
Indices: 11431--11491 Score: 83
Period size: 19 Copynumber: 3.4 Consensus size: 19
11421 ATTGCTAATG
11431 GCTGCTGG--TAT-ATATT
1 GCTGCTGGTATATAATATT
11447 GCTGCTGGTATATAATATT
1 GCTGCTGGTATATAATATT
* *
11466 GTTGTTGGTATATAATATT
1 GCTGCTGGTATATAATATT
11485 GCTGCTG
1 GCTGCTG
11492 CTTGCTGCCT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
16 8 0.21
18 3 0.08
19 27 0.71
ACGTcount: A:0.21, C:0.10, G:0.25, T:0.44
Consensus pattern (19 bp):
GCTGCTGGTATATAATATT
Found at i:11584 original size:58 final size:58
Alignment explanation
Indices: 11455--11573 Score: 229
Period size: 58 Copynumber: 2.1 Consensus size: 58
11445 TTGCTGCTGG
11455 TATATAATATTGTTGTTGGTATATAATATTGCTGCTGCTTGCTGCCTGTTAAATTAGC
1 TATATAATATTGTTGTTGGTATATAATATTGCTGCTGCTTGCTGCCTGTTAAATTAGC
*
11513 TATATAATATTGTTGTTGGTATATAATATTGTTGCTGCTTGCTGCCTGTTAAATTAGC
1 TATATAATATTGTTGTTGGTATATAATATTGCTGCTGCTTGCTGCCTGTTAAATTAGC
11571 TAT
1 TAT
11574 GGTTTTTTGT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 60 1.00
ACGTcount: A:0.24, C:0.11, G:0.18, T:0.46
Consensus pattern (58 bp):
TATATAATATTGTTGTTGGTATATAATATTGCTGCTGCTTGCTGCCTGTTAAATTAGC
Found at i:12425 original size:25 final size:26
Alignment explanation
Indices: 12371--12426 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
12361 AACGTGCAAT
* *
12371 TAATTCTTTTGACTTATAATTAATTT
1 TAATTCTTTTGAATTATAATTAATTA
12397 TAATTCTTTT-AA-TATATATTAATTA
1 TAATTCTTTTGAATTATA-ATTAATTA
12422 TAATT
1 TAATT
12427 TAAACATGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 4 0.15
25 13 0.48
26 10 0.37
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (26 bp):
TAATTCTTTTGAATTATAATTAATTA
Found at i:13483 original size:2 final size:2
Alignment explanation
Indices: 13476--13506 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
13466 AAATGGTGGG
13476 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
13507 CCCCACTTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:15221 original size:22 final size:22
Alignment explanation
Indices: 15152--15337 Score: 104
Period size: 22 Copynumber: 8.5 Consensus size: 22
15142 TAAAAGTCTC
* *
15152 AATTTCATA-AG-GAGTACCAA
1 AATTTCATAGAGTGATTATCAA
* **
15172 AATTTAATAGAAAG-TTATC-A
1 AATTTCATAGAGTGATTATCAA
* *
15192 AATCTCATAGAGTGATTATCGA
1 AATTTCATAGAGTGATTATCAA
15214 AATTTCATAGAGATCAGATTATCAA
1 AATTTCATAGAG-T--GATTATCAA
*
15239 AATTT-ATACGA-AGATTATCAA
1 AATTTCATA-GAGTGATTATCAA
15260 AATTTCATA-ATGTTG-TTATCAA
1 AATTTCATAGA-G-TGATTATCAA
* * * *
15282 AATCTCA-ACGCGAGGTTATCAA
1 AATTTCATA-GAGTGATTATCAA
* *
15304 AATTACATA-ATGTGATTATCAT
1 AATTTCATAGA-GTGATTATCAA
15326 AATTTCATAGAG
1 AATTTCATAGAG
15338 GGGTCAACGT
Statistics
Matches: 126, Mismatches: 22, Indels: 34
0.69 0.12 0.19
Matches are distributed among these distances:
20 20 0.16
21 25 0.20
22 59 0.47
23 4 0.03
24 3 0.02
25 15 0.12
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (22 bp):
AATTTCATAGAGTGATTATCAA
Found at i:15613 original size:22 final size:22
Alignment explanation
Indices: 15486--16001 Score: 182
Period size: 22 Copynumber: 23.6 Consensus size: 22
15476 TTATGGAGTA
*
15486 ATCAAAATTT--TAGGGAGGAT
1 ATCAAAATTTCATAGGGAGGTT
**
15506 ATCAAAATTTCATAGTTCA-GTT
1 ATCAAAATTTCATAG-GGAGGTT
* **
15528 TTCAAAATTTCATA-AAAGGGTT
1 ATCAAAATTTCATAGGGA-GGTT
*
15550 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATAGGGAGGTT
* **
15572 AACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
** *
15594 ATCAAAAAATCATAGGGAGGTG
1 ATCAAAATTTCATAGGGAGGTT
* *
15616 ATTAAAA-TT--T--GTA-GTT
1 ATCAAAATTTCATAGGGAGGTT
* *** *
15632 ATCAAGATTTCATAAAAAAGTT
1 ATCAAAATTTCATAGGGAGGTT
*
15654 ATCAAAATTTTATAGGGAGGTTTAT
1 ATCAAAATTTCATAGGGAGG--T-T
* * * *
15679 ATTAAAATTTTATAGGAAGATTT
1 ATCAAAATTTCATAGGGAG-GTT
* *
15702 ATTAAAATTTCATAGCGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * * *
15724 ATCATAATTTCATAGTGTGATT
1 ATCAAAATTTCATAGGGAGGTT
* * * *
15746 ATCAAAATTTTAGAGTGTGGTT
1 ATCAAAATTTCATAGGGAGGTT
15768 AGT-AACAA-TTCATAGGGAGGTT
1 A-TCAA-AATTTCATAGGGAGGTT
* * * * ** *
15790 TTTATATTTTCATAACGTGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * *
15812 ATCAATATATCATATGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * **
15834 AT-AACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATAG-GGAGGTT
*
15856 ATCAAAATTTCATATTGG-GGTGT
1 ATCAAAATTTCATA-GGGAGGT-T
**
15879 -TCAAAATTTTTTAGGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * *
15900 AACAAAATTTCATAAGAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
** * ***
15922 AAAAAAATTTTATAAAAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * * * **
15944 CTCGAAATTTCAGA-GTATCATT
1 ATCAAAATTTCATAGGGA-GGTT
* * *
15966 ATTAAAATTTCATAGGAATGTT
1 ATCAAAATTTCATAGGGAGGTT
15988 ATCAAAATTTCATA
1 ATCAAAATTTCATA
16002 ATGAGATCAT
Statistics
Matches: 361, Mismatches: 107, Indels: 54
0.69 0.20 0.10
Matches are distributed among these distances:
16 7 0.02
17 4 0.01
19 2 0.01
20 11 0.03
21 17 0.05
22 265 0.73
23 35 0.10
24 2 0.01
25 18 0.05
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.37
Consensus pattern (22 bp):
ATCAAAATTTCATAGGGAGGTT
Found at i:15685 original size:25 final size:24
Alignment explanation
Indices: 15652--15723 Score: 83
Period size: 23 Copynumber: 3.0 Consensus size: 24
15642 CATAAAAAAG
*
15652 TTATCAAAATTTTATAGGGAGGTT
1 TTATTAAAATTTTATAGGGAGGTT
* *
15676 TATATTAAAATTTTATA-GGAAGAT
1 T-TATTAAAATTTTATAGGGAGGTT
* *
15700 TTATTAAAATTTCATAGCGAGGTT
1 TTATTAAAATTTTATAGGGAGGTT
15724 ATCATAATTT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
23 14 0.36
24 11 0.28
25 14 0.36
ACGTcount: A:0.38, C:0.04, G:0.17, T:0.42
Consensus pattern (24 bp):
TTATTAAAATTTTATAGGGAGGTT
Found at i:16319 original size:12 final size:12
Alignment explanation
Indices: 16302--16326 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16292 TTTGCACTGG
16302 AGCGTTTGACTC
1 AGCGTTTGACTC
16314 AGCGTTTGACTC
1 AGCGTTTGACTC
16326 A
1 A
16327 AATAGTTTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.32
Consensus pattern (12 bp):
AGCGTTTGACTC
Found at i:18296 original size:32 final size:33
Alignment explanation
Indices: 18228--18298 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 33
18218 TGGCTATGGT
*
18228 GAGGCGCATGGGTAATACGCCCCGCCATATGGC
1 GAGGCGCATGGGTAATACGCCCCGCCATATGAC
*
18261 GAGGCGCAT-GGT-A-ACGCACCCTGTCATATGAC
1 GAGGCGCATGGGTAATACGC-CCC-GCCATATGAC
18293 GAGGCG
1 GAGGCG
18299 GTTTCATCCC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 4 0.12
31 4 0.12
32 17 0.50
33 9 0.26
ACGTcount: A:0.23, C:0.28, G:0.34, T:0.15
Consensus pattern (33 bp):
GAGGCGCATGGGTAATACGCCCCGCCATATGAC
Found at i:18873 original size:2 final size:2
Alignment explanation
Indices: 18868--18900 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
18858 TTTACCAAAA
*
18868 AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18901 CTAGTCCTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20154 original size:225 final size:224
Alignment explanation
Indices: 19717--20166 Score: 810
Period size: 225 Copynumber: 2.0 Consensus size: 224
19707 CAAATAAAAA
* *
19717 AAAGAATTAAAGCTGAAACATTCAATCGTCGAACCCATAATTGTAAAGGATTAAATAGCATAAAA
1 AAAGAATTAAAGCCGAAACATTCAATCGTCCAACCCATAATTGTAAAGGATTAAATAGCATAAAA
* *
19782 CATAAAAGTATGAGGATCATTTGATAAATAATCCAACAGAAAAAAGATTTGTTTATTGCGTGTGG
66 CATAAAAGTATGAGGATCATTTGATAAATAATCCAACAAAAAAAAGATTTGTTTATTGCGTATGG
* *
19847 GATCCAACAAATAGTAACTTTATCCTAAAGTTACTAAAACACCCTCAACAATCAACAATAATAAC
131 GACCCAACAAATAGTAACTTTATCCTAAAGTTACCAAAACACCCTCAACAATCAACAATAATAAC
19912 GAAAATACTGAGCATGAAAGTACCGAAAT
196 GAAAATACTGAGCATGAAAGTACCGAAAT
19941 AAAGAATTAAAGCCGAAACATTCAATCGTCCAACCCATAATTGTAAAGGATTAAATAGCATAAAA
1 AAAGAATTAAAGCCGAAACATTCAATCGTCCAACCCATAATTGTAAAGGATTAAATAGCATAAAA
*
20006 CATAAAATTATGAGGATCATTTGATAAATAATCCAACAAAAAAAAAGATTTGTTTATTGCGTATG
66 CATAAAAGTATGAGGATCATTTGATAAATAATCCAAC-AAAAAAAAGATTTGTTTATTGCGTATG
20071 GGACCCAACAAATAGTAACTTTATCCTAAAGTTACCAAAACACCCTCAACAATCAACAATAATAA
130 GGACCCAACAAATAGTAACTTTATCCTAAAGTTACCAAAACACCCTCAACAATCAACAATAATAA
* *
20136 CGAATATACTGAGCATGAATGTACCGAAAT
195 CGAAAATACTGAGCATGAAAGTACCGAAAT
20166 A
1 A
20167 CCCTTGACAA
Statistics
Matches: 216, Mismatches: 9, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
224 99 0.46
225 117 0.54
ACGTcount: A:0.46, C:0.16, G:0.13, T:0.24
Consensus pattern (224 bp):
AAAGAATTAAAGCCGAAACATTCAATCGTCCAACCCATAATTGTAAAGGATTAAATAGCATAAAA
CATAAAAGTATGAGGATCATTTGATAAATAATCCAACAAAAAAAAGATTTGTTTATTGCGTATGG
GACCCAACAAATAGTAACTTTATCCTAAAGTTACCAAAACACCCTCAACAATCAACAATAATAAC
GAAAATACTGAGCATGAAAGTACCGAAAT
Found at i:20506 original size:4 final size:4
Alignment explanation
Indices: 20497--20523 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
20487 ACACAAATGA
20497 TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TAT
20524 ATTTGATGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:20897 original size:22 final size:22
Alignment explanation
Indices: 20872--20921 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
20862 ACTCATATGT
*
20872 TCAAAATATGTCTTCTGTTTGA
1 TCAAAATATGTCTTCTATTTGA
20894 TCAAAATATGTCTTCTATTTGA
1 TCAAAATATGTCTTCTATTTGA
*
20916 CCAAAA
1 TCAAAA
20922 ATTTGTTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (22 bp):
TCAAAATATGTCTTCTATTTGA
Found at i:21168 original size:14 final size:14
Alignment explanation
Indices: 21149--21176 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
21139 AATTAGTCAT
21149 GGTCAATGTAATTA
1 GGTCAATGTAATTA
21163 GGTCAATGTAATTA
1 GGTCAATGTAATTA
21177 CGGGATATCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (14 bp):
GGTCAATGTAATTA
Done.