Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011975.1 Corchorus capsularis cultivar CVL-1 contig11996, 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: 41568
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:618 original size:335 final size:332
Alignment explanation
Indices: 1--752 Score: 783
Period size: 335 Copynumber: 2.2 Consensus size: 332
* *
1 ATCCTTAAA-TCTAATGTGACTGAGATTTCGTTAGATGAATATAGATATTGCAATGAGTCTTGGC
1 ATCCTTAAATTC-AATGTGAGTGAGATTTCGTTAGATGAATATAGATATTTCAATGAGTCTTGGC
** * * * * **
65 GTCAAAAATCAAACAAAACTAATCCGGGTCCCCGGAAAGAGTTTTTAGCTAAAAAACGTGATGGT
65 GTCAAAAATCATGCAAAACAAAACCGGGGCCCC-GAAACAGTTTTTAGCTAAAAAACGTGATAAT
* *
130 TAGTACTCGATTTCGGCTAAAATTTTGCAAAAGTTTACCCGAAATAATTTTCCTCAATTTATGGC
129 TAGTACTCGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATAATTTTCCTCAATTTATGGC
*** * * * * *
195 CATGGAACTCATAAAAATATATATATAATTCAACACCAAAAAGATTGAAAGGCTTTTCACGCTTC
194 CACAAAACT-ATAAAAATATATACATAACTCAACACCAAAAAAATTGAAAGGCTTCTCACGATTC
* ** * * *
260 TTATATTTGTTTTCCTATTTTTTCTGAATTATTTTATAATTAAATTGAGACAT-GATTCATATGC
258 TTATATGTGTTTTCCTATTTTTTCCAAATTAATTTATAATTAAATCGA-A-ATCGATTCAGATGC
324 TCGTAAAAACAA
321 TCGTAAAAACAA
* * * *
336 ATCCTTAAATTCAATGTGAGTGAGTTTTGGTTAGATGGATATAGATATTTCAATGAGACTTGGCG
1 ATCCTTAAATTCAATGTGAGTGAGATTTCGTTAGATGAATATAGATATTTCAATGAGTCTTGGCG
* * **
401 TAAAAAATCATGCAAAGCAAAAGTGGGGCCCC-ATAACACGTTTTTAG-TAAAAAACTGTGATAA
66 TCAAAAATCATGCAAAACAAAACCGGGGCCCCGA-AACA-GTTTTTAGCTAAAAAAC-GTGATAA
*
464 TTAGTA-TACTG-TTTCGGCTAAAATTTTGCAAAAAAATTGATCCGAAA-AATTTTTCCTCAACT
128 TTAGTACT-C-GATTTCGGCTAAAATTTTGC--AAAAATTGACCCGAAATAA-TTTTCCTCAA-T
* ** * *
526 TT-TGGCCTACAAAAGT-TAAATTTATATACATAACTCAACGCCAAAAAAATTGAAGGGCTTCTC
187 TTATGGCC-ACAAAACTATAAAAATATATACATAACTCAACACCAAAAAAATTGAAAGGCTTCTC
* *
589 AC-ATTTTTAATATCGT-TTTTCCT-TTTTTTCCAAATTAATTTCTAATTAAATCGAAATCGGAT
251 ACGATTCTT-ATAT-GTGTTTTCCTATTTTTTCCAAATTAATTTATAATTAAATCGAAATC-GAT
* *
651 TGAGATGCTTGTAAAAACAA
313 TCAGATGCTCGTAAAAACAA
** * * * *
671 ATTTTTAAATCCAATGT-AGCTTAGATTTCGTTAGATGAATATAGATATTTCAATCAGTCTTTGC
1 ATCCTTAAATTCAATGTGAG-TGAGATTTCGTTAGATGAATATAGATATTTCAATGAGTCTTGGC
*
735 GCCAAAAATCATGCAAAA
65 GTCAAAAATCATGCAAAA
753 TTGAGCCGGG
Statistics
Matches: 344, Mismatches: 57, Indels: 32
0.79 0.13 0.07
Matches are distributed among these distances:
333 3 0.01
334 15 0.04
335 233 0.68
336 57 0.17
337 29 0.08
338 7 0.02
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (332 bp):
ATCCTTAAATTCAATGTGAGTGAGATTTCGTTAGATGAATATAGATATTTCAATGAGTCTTGGCG
TCAAAAATCATGCAAAACAAAACCGGGGCCCCGAAACAGTTTTTAGCTAAAAAACGTGATAATTA
GTACTCGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATAATTTTCCTCAATTTATGGCCA
CAAAACTATAAAAATATATACATAACTCAACACCAAAAAAATTGAAAGGCTTCTCACGATTCTTA
TATGTGTTTTCCTATTTTTTCCAAATTAATTTATAATTAAATCGAAATCGATTCAGATGCTCGTA
AAAACAA
Found at i:3995 original size:60 final size:60
Alignment explanation
Indices: 3900--4036 Score: 184
Period size: 60 Copynumber: 2.3 Consensus size: 60
3890 ACGACAGGTT
* * * * * *
3900 CTTATTTGAGCATTTTGGCAAACTTTAGACCCTTATTTGGCCAAATTCAAAGATCGGGCC
1 CTTATTTGAGCATTTTGGAAAACGTTAGACACTTATTTGGCCAAATTAAAAAATCAGGCC
* * *
3960 TTTATTTGAGCATTTTGGAAAACGTTAGGCACTTATTTGGCCAAATTAAAAAATCATGCC
1 CTTATTTGAGCATTTTGGAAAACGTTAGACACTTATTTGGCCAAATTAAAAAATCAGGCC
*
4020 CTTATTTGAACATTTTG
1 CTTATTTGAGCATTTTG
4037 ACATACATTA
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 66 1.00
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (60 bp):
CTTATTTGAGCATTTTGGAAAACGTTAGACACTTATTTGGCCAAATTAAAAAATCAGGCC
Found at i:4055 original size:60 final size:60
Alignment explanation
Indices: 3900--4057 Score: 183
Period size: 60 Copynumber: 2.6 Consensus size: 60
3890 ACGACAGGTT
* * * * *
3900 CTTATTTGAGCATTTTGGCAAACTTTAGACCCTTATTTGGCCAAATTCAAAGATCGGGCC
1 CTTATTTGAGCATTTTGACAAACATTAGACCCTTATTTGGCCAAATTAAAAAATCAGGCC
* * * * *
3960 TTTATTTGAGCATTTTGGA-AAACGTTAGGCACTTATTTGGCCAAATTAAAAAATCATGCC
1 CTTATTTGAGCATTTT-GACAAACATTAGACCCTTATTTGGCCAAATTAAAAAATCAGGCC
* * *
4020 CTTATTTGAACATTTTGACATACATTAGATCCTTATTT
1 CTTATTTGAGCATTTTGACAAACATTAGACCCTTATTT
4058 AAGCAATGAG
Statistics
Matches: 80, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
59 2 0.03
60 77 0.96
61 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (60 bp):
CTTATTTGAGCATTTTGACAAACATTAGACCCTTATTTGGCCAAATTAAAAAATCAGGCC
Found at i:5323 original size:2 final size:2
Alignment explanation
Indices: 5316--5347 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5306 ACTACAATTA
5316 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5348 TCTTTGATTA
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):
AT
Found at i:5678 original size:3 final size:3
Alignment explanation
Indices: 5670--5703 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
5660 ACTTCCTTGC
* *
5670 AAG AAG AAG AAG AAG AAG AAG AAA AAG AAA AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
5704 CAAAAAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:5827 original size:15 final size:15
Alignment explanation
Indices: 5803--5854 Score: 86
Period size: 15 Copynumber: 3.5 Consensus size: 15
5793 TCGGACGAGT
* *
5803 ACGAGTACGAGCCCG
1 ACGAGGACGAGTCCG
5818 ACGAGGACGAGTCCG
1 ACGAGGACGAGTCCG
5833 ACGAGGACGAGTCCG
1 ACGAGGACGAGTCCG
5848 ACGAGGA
1 ACGAGGA
5855 GGTCAGTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.29, C:0.27, G:0.38, T:0.06
Consensus pattern (15 bp):
ACGAGGACGAGTCCG
Found at i:6049 original size:18 final size:18
Alignment explanation
Indices: 6038--6075 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
6028 AGAAGACTAC
6038 GAGGAGGAAGAAGAAGAA
1 GAGGAGGAAGAAGAAGAA
*
6056 GAGGAGGAAGGAGAAGAA
1 GAGGAGGAAGAAGAAGAA
6074 GA
1 GA
6076 TAATTATTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (18 bp):
GAGGAGGAAGAAGAAGAA
Found at i:6163 original size:18 final size:19
Alignment explanation
Indices: 6140--6182 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
6130 CTGGTGATGT
6140 TTAATAGATAATA-TAATA
1 TTAATAGATAATATTAATA
*
6158 TTAATA-TTAATATTAATA
1 TTAATAGATAATATTAATA
6176 TTAATAG
1 TTAATAG
6183 TGAGGGTGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (19 bp):
TTAATAGATAATATTAATA
Found at i:6164 original size:6 final size:6
Alignment explanation
Indices: 6148--6181 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
6138 GTTTAATAGA
6148 TAATA- TAATAT TAATAT TAATAT TAATAT TAATA
1 TAATAT TAATAT TAATAT TAATAT TAATAT TAATA
6182 GTGAGGGTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.18
6 23 0.82
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
TAATAT
Found at i:11035 original size:63 final size:63
Alignment explanation
Indices: 10936--11062 Score: 236
Period size: 63 Copynumber: 2.0 Consensus size: 63
10926 AGGAAACCGT
*
10936 ATATACACTATGATCTGTGTTTCTTGATAGCAAATAGTTTTTTAAACCAAAATTCTAAAATTA
1 ATATACACTATGATCTGTCTTTCTTGATAGCAAATAGTTTTTTAAACCAAAATTCTAAAATTA
*
10999 ATATACACTATGCTCTGTCTTTCTTGATAGCAAATAGTTTTTTAAACCAAAATTCTAAAATTA
1 ATATACACTATGATCTGTCTTTCTTGATAGCAAATAGTTTTTTAAACCAAAATTCTAAAATTA
11062 A
1 A
11063 ACATTAAACT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (63 bp):
ATATACACTATGATCTGTCTTTCTTGATAGCAAATAGTTTTTTAAACCAAAATTCTAAAATTA
Found at i:12574 original size:11 final size:11
Alignment explanation
Indices: 12536--12576 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
12526 AATATACATG
12536 TATAATTAATT
1 TATAATTAATT
**
12547 TATAACAAATT
1 TATAATTAATT
12558 TATAATTAATT
1 TATAATTAATT
12569 TATAATTA
1 TATAATTA
12577 TTTGATTAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (11 bp):
TATAATTAATT
Found at i:13464 original size:33 final size:33
Alignment explanation
Indices: 13427--13516 Score: 162
Period size: 33 Copynumber: 2.7 Consensus size: 33
13417 GACGGCTCAA
13427 CCATGGCGGAGCCGCCCCACTAGGATGAATCAG
1 CCATGGCGGAGCCGCCCCACTAGGATGAATCAG
* *
13460 CCATGGCGGAGCCGCCCCATTAGGATGACTCAG
1 CCATGGCGGAGCCGCCCCACTAGGATGAATCAG
13493 CCATGGCGGAGCCGCCCCACTAGG
1 CCATGGCGGAGCCGCCCCACTAGG
13517 GCGGCTAAAC
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.21, C:0.36, G:0.31, T:0.12
Consensus pattern (33 bp):
CCATGGCGGAGCCGCCCCACTAGGATGAATCAG
Found at i:13961 original size:2 final size:2
Alignment explanation
Indices: 13950--13983 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
13940 TTAGCTATTG
13950 TA TA -A TA TA TA 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 TA
13984 ATGATAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:14614 original size:15 final size:15
Alignment explanation
Indices: 14596--14625 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
14586 CTAATCTCAT
14596 CTCATCAAATAAAAA
1 CTCATCAAATAAAAA
14611 CTCATCAAATAAAAA
1 CTCATCAAATAAAAA
14626 GAAAACAGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.20, G:0.00, T:0.20
Consensus pattern (15 bp):
CTCATCAAATAAAAA
Found at i:21003 original size:15 final size:15
Alignment explanation
Indices: 20983--21012 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
20973 CTTTTAGAAC
20983 GTGAGACAATTAAAA
1 GTGAGACAATTAAAA
20998 GTGAGACAATTAAAA
1 GTGAGACAATTAAAA
21013 CGTCACTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.07, G:0.20, T:0.20
Consensus pattern (15 bp):
GTGAGACAATTAAAA
Found at i:24530 original size:6 final size:6
Alignment explanation
Indices: 24519--24544 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
24509 GGATCGGTCA
24519 AGTCCC AGTCCC AGTCCC AGTCCC AG
1 AGTCCC AGTCCC AGTCCC AGTCCC AG
24545 CAACATCATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.46, G:0.19, T:0.15
Consensus pattern (6 bp):
AGTCCC
Found at i:25831 original size:15 final size:14
Alignment explanation
Indices: 25813--25884 Score: 53
Period size: 15 Copynumber: 5.1 Consensus size: 14
25803 AGCAGAGACT
25813 GAAGAAGCAAGGAGA
1 GAAGAAG-AAGGAGA
*
25828 GAAG-AGAAAGAGA
1 GAAGAAGAAGGAGA
25841 -AAGATAAGAAGGA-A
1 GAAG--AAGAAGGAGA
*
25855 GAAGATGAA-GAGGA
1 GAAGAAGAAGGA-GA
25869 GAGAGAAGAAGGAGA
1 GA-AGAAGAAGGAGA
25884 G
1 G
25885 GAGGAAGAGA
Statistics
Matches: 45, Mismatches: 4, Indels: 16
0.69 0.06 0.25
Matches are distributed among these distances:
12 5 0.11
13 10 0.22
14 6 0.13
15 22 0.49
16 2 0.04
ACGTcount: A:0.56, C:0.01, G:0.40, T:0.03
Consensus pattern (14 bp):
GAAGAAGAAGGAGA
Found at i:25877 original size:28 final size:28
Alignment explanation
Indices: 25815--25896 Score: 82
Period size: 28 Copynumber: 3.0 Consensus size: 28
25805 CAGAGACTGA
25815 AGAAGCAAGGAGAGAAGAGAAAGAGAAAG
1 AGAAG-AAGGAGAGAAGAGAAAGAGAAAG
* *
25844 ATAAGAAGGA-AGAAGATG-AAGAGGAGAG
1 AGAAGAAGGAGAGAAGA-GAAAGA-GAAAG
*
25872 AGAAGAAGGAGAG--GAGGAAGAGAAA
1 AGAAGAAGGAGAGAAGAGAAAGAGAAA
25897 TTTGACTTGG
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
26 4 0.09
27 16 0.36
28 19 0.42
29 6 0.13
ACGTcount: A:0.56, C:0.01, G:0.40, T:0.02
Consensus pattern (28 bp):
AGAAGAAGGAGAGAAGAGAAAGAGAAAG
Found at i:31193 original size:18 final size:18
Alignment explanation
Indices: 31170--31213 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
31160 TCCACCACCA
* **
31170 TGATGATGGTGGTGGTGG
1 TGATGATGGTGATGGCCG
31188 TGATGATGGTGATGGCCG
1 TGATGATGGTGATGGCCG
31206 TGATGATG
1 TGATGATG
31214 ACTCTGCTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.05, G:0.48, T:0.32
Consensus pattern (18 bp):
TGATGATGGTGATGGCCG
Found at i:35946 original size:16 final size:16
Alignment explanation
Indices: 35905--35946 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
35895 CATTTTACTT
*
35905 TTATT-TTATTATATA
1 TTATTATTAATATATA
35920 TTA-TATATAATATATA
1 TTATTAT-TAATATATA
35936 TTATTATTAAT
1 TTATTATTAAT
35947 TAATACAACC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
14 1 0.04
15 4 0.17
16 15 0.65
17 3 0.13
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTATTATTAATATATA
Found at i:38320 original size:6 final size:6
Alignment explanation
Indices: 38311--38340 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
38301 ATTGGAAGGT
*
38311 CTAGCA CTAGCA CTAGCA CTAACA CTAGCA
1 CTAGCA CTAGCA CTAGCA CTAGCA CTAGCA
38341 GATGGATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.37, C:0.33, G:0.13, T:0.17
Consensus pattern (6 bp):
CTAGCA
Done.