Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015406.1 Corchorus capsularis cultivar CVL-1 contig15427, 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: 13798
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:2837 original size:14 final size:14
Alignment explanation
Indices: 2827--2853 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2817 TTTTTTTTTT
2827 AAATATTTTTTAAA
1 AAATATTTTTTAAA
2841 AAATATTTTTTAA
1 AAATATTTTTTAA
2854 TCAAAAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
AAATATTTTTTAAA
Found at i:3896 original size:26 final size:26
Alignment explanation
Indices: 3860--3924 Score: 103
Period size: 26 Copynumber: 2.5 Consensus size: 26
3850 CACGCGCGAT
** *
3860 GTCACGTGTGGAGGTGTCCGTTGGAG
1 GTCACGTGTGGAGCCGTACGTTGGAG
3886 GTCACGTGTGGAGCCGTACGTTGGAG
1 GTCACGTGTGGAGCCGTACGTTGGAG
3912 GTCACGTGTGGAG
1 GTCACGTGTGGAG
3925 TGCCAGCTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.14, C:0.17, G:0.45, T:0.25
Consensus pattern (26 bp):
GTCACGTGTGGAGCCGTACGTTGGAG
Found at i:3897 original size:13 final size:14
Alignment explanation
Indices: 3860--3924 Score: 61
Period size: 13 Copynumber: 4.9 Consensus size: 14
3850 CACGCGCGAT
*
3860 GTCACGTGTGGAGGT
1 GTCACGTGTGGA-GC
3875 GTC-CGT-TGGAG-
1 GTCACGTGTGGAGC
3886 GTCACGTGTGGAGCC
1 GTCACGTGTGGAG-C
3901 GT-ACGT-TGGAG-
1 GTCACGTGTGGAGC
3912 GTCACGTGTGGAG
1 GTCACGTGTGGAG
3925 TGCCAGCTGG
Statistics
Matches: 44, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
11 5 0.11
12 8 0.18
13 19 0.43
14 7 0.16
15 5 0.11
ACGTcount: A:0.14, C:0.17, G:0.45, T:0.25
Consensus pattern (14 bp):
GTCACGTGTGGAGC
Found at i:4044 original size:23 final size:23
Alignment explanation
Indices: 3986--4044 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 23
3976 TCGCCGAGCA
* *
3986 TGGAAGTGGTCGGTCGCTGAGCC
1 TGGAAGTGATCGGTCGCTAAGCC
* * *
4009 TGAAAATGATCGGTCGCTAAGCT
1 TGGAAGTGATCGGTCGCTAAGCC
*
4032 TGGAAGTGTTCGG
1 TGGAAGTGATCGG
4045 GTGCCAAACA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.20, C:0.17, G:0.37, T:0.25
Consensus pattern (23 bp):
TGGAAGTGATCGGTCGCTAAGCC
Found at i:9970 original size:18 final size:18
Alignment explanation
Indices: 9944--9997 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
9934 GCTGTTATAT
* *
9944 TATAATATAATAATAATA
1 TATATTATATTAATAATA
9962 TATATTATATTAATAAT-
1 TATATTATATTAATAATA
*
9979 TAATATAATATTAATAATA
1 T-ATATTATATTAATAATA
9998 GGGTTACATT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 1 0.03
18 30 0.97
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TATATTATATTAATAATA
Found at i:11217 original size:22 final size:22
Alignment explanation
Indices: 11159--11223 Score: 67
Period size: 23 Copynumber: 2.9 Consensus size: 22
11149 GAAGACATCA
*
11159 ATATGAAATTTTGATAACCAAC
1 ATATGAAATATTGATAACCAAC
* * **
11181 ACTATGAGATGTTGATAACCTCC
1 A-TATGAAATATTGATAACCAAC
*
11204 ATATGATATATTGATAACCA
1 ATATGAAATATTGATAACCA
11224 CGTTATGAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
22 17 0.49
23 18 0.51
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.32
Consensus pattern (22 bp):
ATATGAAATATTGATAACCAAC
Found at i:11230 original size:22 final size:22
Alignment explanation
Indices: 11157--11330 Score: 66
Period size: 22 Copynumber: 7.9 Consensus size: 22
11147 TTGAAGACAT
*
11157 CAATATGAAATTTTGATAACCAA
1 CAATATGAAATATTGATAACC-A
* * * *
11180 CACTATGAGATGTTGATAACCT
1 CAATATGAAATATTGATAACCA
* *
11202 CCATATGATATATTGATAACCA
1 CAATATGAAATATTGATAACCA
** * * * *
11224 CGTTATGAAA-ATTTAAAAATCT
1 CAATATGAAATA-TTGATAACCA
* * * *
11246 CCATATGAATTGTT-AGTAATCA
1 CAATATGAAATATTGA-TAACCA
* * * *
11268 CACTCTGAAATTTTGATAATCA
1 CAATATGAAATATTGATAACCA
*
11290 CACTATGAAAT-TGTGATAACCA
1 CAATATGAAATAT-TGATAACCA
** *
11312 CGCTATGAAATTTTGATAA
1 CAATATGAAATATTGATAA
11331 ATCTTCCTAT
Statistics
Matches: 115, Mismatches: 30, Indels: 13
0.73 0.19 0.08
Matches are distributed among these distances:
21 3 0.03
22 92 0.80
23 20 0.17
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (22 bp):
CAATATGAAATATTGATAACCA
Found at i:11395 original size:22 final size:22
Alignment explanation
Indices: 11273--11510 Score: 117
Period size: 22 Copynumber: 10.7 Consensus size: 22
11263 AATCACACTC
**
11273 TGAAATTTTGATAA-TCACACTA
1 TGAAATTTTGATAACTTTC-CTA
* **
11295 TGAAATTGTGATAAC-CACGCTA
1 TGAAATTTTGATAACTTTC-CTA
*
11317 TGAAATTTTGATAAATCTTCCTA
1 TGAAATTTTGATAACT-TTCCTA
* * *
11340 TAAAATTTTGATAAACCTCCCTA
1 TGAAATTTTGAT-AACTTTCCTA
* *
11363 TCAAATTTTGATAACTTTCTTA
1 TGAAATTTTGATAACTTTCCTA
* * *
11385 TGAAATCTTGATAACCTCCCTA
1 TGAAATTTTGATAACTTTCCTA
** * *
11407 TGATTTTTTGATAAC-CTCATTA
1 TGAAATTTTGATAACTTTC-CTA
* * *
11429 TGAAATTTCGTTAA-TCTCCATA
1 TGAAATTTTGATAACTTTCC-TA
* * * *
11451 TGAAATTTTAATCTAC-ATACTA
1 TGAAATTTTGAT-AACTTTCCTA
** *
11473 TGAAATTTTGATAACCCTCTTA
1 TGAAATTTTGATAACTTTCCTA
*
11495 TGAAATTTTGAAAACT
1 TGAAATTTTGATAACT
11511 AAAGTATGAA
Statistics
Matches: 163, Mismatches: 43, Indels: 20
0.72 0.19 0.09
Matches are distributed among these distances:
21 3 0.02
22 124 0.76
23 33 0.20
24 3 0.02
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.39
Consensus pattern (22 bp):
TGAAATTTTGATAACTTTCCTA
Found at i:11416 original size:44 final size:43
Alignment explanation
Indices: 11293--11548 Score: 171
Period size: 44 Copynumber: 5.8 Consensus size: 43
11283 ATAATCACAC
* * * *
11293 TATGAAATTGTGATAACCACGCTATGAAATTTTGATAAATCTTCC
1 TATGAAATT-TGATAACCTCCCTATGAAATTTTGATAACT-TTCT
* *
11338 TATAAAATTTTGATAAACCTCCCTATCAAATTTTGATAACTTTCT
1 TATGAAA-TTTGAT-AACCTCCCTATGAAATTTTGATAACTTTCT
** *
11383 TATGAAATCTTGATAACCTCCCTATGATTTTTTGATAAC-CTCAT
1 TATGAAAT-TTGATAACCTCCCTATGAAATTTTGATAACTTTC-T
* * * * * * *
11427 TATGAAATTTCGTTAATCTCCATATGAAATTTTAATCTACATAC-
1 TATGAAATTT-GATAACCTCCCTATGAAATTTTGAT-AACTTTCT
* * ****
11471 TATGAAATTTTGATAACC-CTCTTATGAAATTTTGAAAACTAAAG
1 TATGAAA-TTTGATAACCTC-CCTATGAAATTTTGATAACTTTCT
*
11515 TATGAAAATTTGATATCCTCCC--TGAAATTTTGAT
1 TATG-AAATTTGATAACCTCCCTATGAAATTTTGAT
11549 GACTCCATAG
Statistics
Matches: 167, Mismatches: 32, Indels: 27
0.74 0.14 0.12
Matches are distributed among these distances:
42 11 0.07
43 8 0.05
44 90 0.54
45 33 0.20
46 25 0.15
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.39
Consensus pattern (43 bp):
TATGAAATTTGATAACCTCCCTATGAAATTTTGATAACTTTCT
Found at i:11688 original size:22 final size:22
Alignment explanation
Indices: 11656--11778 Score: 108
Period size: 22 Copynumber: 5.6 Consensus size: 22
11646 TCACATTTTG
11656 AAAA-TTTGATAACCTCTTTAT
1 AAAATTTTGATAACCTCTTTAT
*
11677 AAAATTTTGATAACCTCTTTAC
1 AAAATTTTGATAACCTCTTTAT
* *
11699 AAAATTTTGTTGACC-CTTCTAT
1 AAAATTTTGATAACCTCTT-TAT
* * * *
11721 GAAATTTTGATAATCACATTAT
1 AAAATTTTGATAACCTCTTTAT
** *
11743 GTAATTTTGTTAACCTCGTTT-T
1 AAAATTTTGATAACCTC-TTTAT
*
11765 GAAATTTTGATAAC
1 AAAATTTTGATAAC
11779 AACACTATGA
Statistics
Matches: 82, Mismatches: 16, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
21 7 0.09
22 71 0.87
23 4 0.05
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (22 bp):
AAAATTTTGATAACCTCTTTAT
Found at i:11749 original size:44 final size:44
Alignment explanation
Indices: 11630--11795 Score: 160
Period size: 44 Copynumber: 3.8 Consensus size: 44
11620 GAAATACCAC
* * *
11630 TATGAAATTTTTG-TAATCACATTTTGAAAATTTGATAACCTCTT
1 TATGAAA-TTTTGATAATCACATTATGAAATTTTGTTAACCTCTT
* * * * ** *
11674 TATAAAATTTTGATAACCTCTTTACAAAATTTTGTTGACC-CTT
1 TATGAAATTTTGATAATCACATTATGAAATTTTGTTAACCTCTT
*
11717 CTATGAAATTTTGATAATCACATTATGTAATTTTGTTAACCTCGTT
1 -TATGAAATTTTGATAATCACATTATGAAATTTTGTTAACCTC-TT
*
11763 T-TGAAATTTTGATAA-CAACACTATGAAATTTTG
1 TATGAAATTTTGATAATC-ACATTATGAAATTTTG
11796 ATAATATGAT
Statistics
Matches: 97, Mismatches: 20, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
43 9 0.09
44 84 0.87
45 2 0.02
46 2 0.02
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.44
Consensus pattern (44 bp):
TATGAAATTTTGATAATCACATTATGAAATTTTGTTAACCTCTT
Found at i:11789 original size:22 final size:21
Alignment explanation
Indices: 11717--11799 Score: 78
Period size: 22 Copynumber: 3.8 Consensus size: 21
11707 GTTGACCCTT
11717 CTATGAAATTTTGATAATCACA
1 CTATGAAATTTTGATAA-CACA
* * * *
11739 TTATGTAATTTTGTTAAC-CT
1 CTATGAAATTTTGATAACACA
*
11759 CGTTTTGAAATTTTGATAACAACA
1 C--TATGAAATTTTGATAAC-ACA
11783 CTATGAAATTTTGATAA
1 CTATGAAATTTTGATAA
11800 TATGATCTCT
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 43 0.91
24 2 0.04
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (21 bp):
CTATGAAATTTTGATAACACA
Found at i:11792 original size:88 final size:88
Alignment explanation
Indices: 11629--11795 Score: 203
Period size: 88 Copynumber: 1.9 Consensus size: 88
11619 AGAAATACCA
* **
11629 CTATGAAATTTTTGTAATCACATTTTGAAAATTTGATAACCTCTTTATAAAATTTTGATAACCTC
1 CTATGAAATTTTTGTAATCACATTATGAAAATTTGATAACCTCTTTATAAAATTTTGATAACAAC
**
11694 TTTACAAAATTTTGTTGACCCTT
66 ACTACAAAATTTTGTTGACCCTT
* * * *
11717 CTATGAAA-TTTTGATAATCACATTATGTAATTTTGTTAACCTCGTTT-TGAAATTTTGATAACA
1 CTATGAAATTTTTG-TAATCACATTATGAAAATTTGATAACCTC-TTTATAAAATTTTGATAACA
**
11780 ACACTATGAAATTTTG
64 ACACTACAAAATTTTG
11796 ATAATATGAT
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
87 5 0.08
88 58 0.88
89 3 0.05
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.44
Consensus pattern (88 bp):
CTATGAAATTTTTGTAATCACATTATGAAAATTTGATAACCTCTTTATAAAATTTTGATAACAAC
ACTACAAAATTTTGTTGACCCTT
Found at i:11834 original size:22 final size:22
Alignment explanation
Indices: 11716--11840 Score: 76
Period size: 22 Copynumber: 5.5 Consensus size: 22
11706 TGTTGACCCT
* *
11716 TCTATGAAATTTTGATAATCAC
1 TCTATGAAATTTTGATTATAAC
* *
11738 AT-TATGTAATTTTG-TTA-ACC
1 -TCTATGAAATTTTGATTATAAC
* * *
11758 TCGTTTTGAAATTTTGATAACAAC
1 TC--TATGAAATTTTGATTATAAC
* *
11782 ACTATGAAATTTTGATAATATGATC
1 TCTATGAAATTTTGAT--TAT-AAC
*
11807 TCTATGAAATTTCGATTATAAC
1 TCTATGAAATTTTGATTATAAC
*
11829 TCTATGAGATTT
1 TCTATGAAATTT
11841 GATAACCTTC
Statistics
Matches: 77, Mismatches: 17, Indels: 17
0.69 0.15 0.15
Matches are distributed among these distances:
19 1 0.01
20 1 0.01
21 2 0.03
22 47 0.61
23 6 0.08
24 4 0.05
25 16 0.21
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.43
Consensus pattern (22 bp):
TCTATGAAATTTTGATTATAAC
Found at i:11950 original size:22 final size:23
Alignment explanation
Indices: 11925--11976 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 23
11915 CCACTCTGTA
11925 AAATTTTGA-TAACCTCCCCAA-G
1 AAATTTTGAGTAACCT-CCCAATG
* *
11947 AAATATT-AGTAACCTCCTAATG
1 AAATTTTGAGTAACCTCCCAATG
11969 AAATTTTG
1 AAATTTTG
11977 TTAATCATAC
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
21 5 0.21
22 19 0.79
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (23 bp):
AAATTTTGAGTAACCTCCCAATG
Found at i:12121 original size:24 final size:22
Alignment explanation
Indices: 12060--12108 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
12050 TTGTGATAAT
* *
12060 TAACCACCCAAAGAAATTTCAA
1 TAACCAACCTAAGAAATTTCAA
*
12082 TAACCAACCTAAGAAATTTTAA
1 TAACCAACCTAAGAAATTTCAA
12104 TAACC
1 TAACC
12109 TAATCCTATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.49, C:0.24, G:0.04, T:0.22
Consensus pattern (22 bp):
TAACCAACCTAAGAAATTTCAA
Found at i:12148 original size:22 final size:22
Alignment explanation
Indices: 12114--12233 Score: 100
Period size: 22 Copynumber: 5.5 Consensus size: 22
12104 TAACCTAATC
* *
12114 CTATGAAAATTTGGTAACCACG
1 CTATGAAATTTTGGTAACCACA
* *
12136 TTATGATATTTTGGTAACCACA
1 CTATGAAATTTTGGTAACCACA
* **
12158 CTATGAAATTTTGATAACTTTCA
1 CTATGAAATTTTGGTAAC-CACA
* *
12181 -TATAAAATTTTGGTAACCATA
1 CTATGAAATTTTGGTAACCACA
* * *
12202 CTATGGAATTTTGATAACCTC-
1 CTATGAAATTTTGGTAACCACA
12223 CTCATGAAATT
1 CT-ATGAAATT
12234 ATAATAGCCA
Statistics
Matches: 75, Mismatches: 20, Indels: 6
0.74 0.20 0.06
Matches are distributed among these distances:
21 3 0.04
22 70 0.93
23 2 0.03
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (22 bp):
CTATGAAATTTTGGTAACCACA
Found at i:12233 original size:44 final size:43
Alignment explanation
Indices: 12114--12269 Score: 134
Period size: 44 Copynumber: 3.6 Consensus size: 43
12104 TAACCTAATC
* * * * * *
12114 CTATGAAAATTTGGTAACCACGTTATGATATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCTC-ATATGAAATTTTGGTAACCATA
* *
12158 CTATGAAATTTTGATAACTTTCATATAAAATTTTGGTAACCATA
1 CTATGAAATTTTGATAAC-CTCATATGAAATTTTGGTAACCATA
* * * ** *
12202 CTATGGAATTTTGATAACCTCCTCATGAAATTATAATAGCCAT-
1 CTATGAAATTTTGATAACCTCAT-ATGAAATTTTGGTAACCATA
*
12245 CTGATGAAATTTTGATAACCACATA
1 CT-ATGAAATTTTGATAACCTCATA
12270 GAGACAAGAA
Statistics
Matches: 90, Mismatches: 19, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
43 6 0.07
44 83 0.92
45 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (43 bp):
CTATGAAATTTTGATAACCTCATATGAAATTTTGGTAACCATA
Found at i:13226 original size:2 final size:2
Alignment explanation
Indices: 13219--13252 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
13209 TTCGTACTTT
13219 TA TA TA TA GTA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
13253 AAATATACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 27 0.90
3 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Done.