Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012068.1 Corchorus capsularis cultivar CVL-1 contig12089, 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: 31266
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Found at i:2733 original size:13 final size:14
Alignment explanation
Indices: 2715--2743 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
2705 ATAATCAGAC
2715 TTTGCATCCAT-CA
1 TTTGCATCCATGCA
2728 TTTGCATCCATGCA
1 TTTGCATCCATGCA
2742 TT
1 TT
2744 AAAGTAGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.21, C:0.28, G:0.10, T:0.41
Consensus pattern (14 bp):
TTTGCATCCATGCA
Found at i:3036 original size:37 final size:40
Alignment explanation
Indices: 2942--3044 Score: 149
Period size: 40 Copynumber: 2.6 Consensus size: 40
2932 TTTTTTTAAG
* **
2942 CAACTCCAAAAGAAGACTTTTGGAAAATAAATGTTTTTTA
1 CAACTCCAAAAGAAGACTTTTGGAAAATAAAAGTTTTGGA
2982 CAACTCCAAAAGAAGACTTTTGGAAAATAAAAG-TTTGGA
1 CAACTCCAAAAGAAGACTTTTGGAAAATAAAAGTTTTGGA
*
3021 -AA-TCCAAGAGAAGACTTTTGGAAA
1 CAACTCCAAAAGAAGACTTTTGGAAA
3045 TTAATAAAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
37 21 0.36
38 2 0.03
39 4 0.07
40 32 0.54
ACGTcount: A:0.45, C:0.13, G:0.17, T:0.26
Consensus pattern (40 bp):
CAACTCCAAAAGAAGACTTTTGGAAAATAAAAGTTTTGGA
Found at i:5569 original size:16 final size:18
Alignment explanation
Indices: 5536--5576 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 18
5526 TCAATGATAA
5536 AATAAGAAAAAGTCTTTTC
1 AATAA-AAAAAGTCTTTTC
*
5555 AATAAAAAAA-T-TTTTG
1 AATAAAAAAAGTCTTTTC
5571 AATAAA
1 AATAAA
5577 TGAAAGGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 10 0.48
17 1 0.05
18 5 0.24
19 5 0.24
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.32
Consensus pattern (18 bp):
AATAAAAAAAGTCTTTTC
Found at i:6082 original size:14 final size:13
Alignment explanation
Indices: 6030--6085 Score: 58
Period size: 14 Copynumber: 4.2 Consensus size: 13
6020 TCAAAATAAG
*
6030 AAATGTTTTTCAA
1 AAATGGTTTTCAA
*
6043 AAATTGTTTTCAA
1 AAATGGTTTTCAA
* *
6056 GAAAAGGTATTCAA
1 -AAATGGTTTTCAA
6070 AAATGGATTTTCAA
1 AAATGG-TTTTCAA
6084 AA
1 AA
6086 GGTTTTTGAG
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
13 16 0.47
14 18 0.53
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.36
Consensus pattern (13 bp):
AAATGGTTTTCAA
Found at i:6729 original size:12 final size:13
Alignment explanation
Indices: 6712--6744 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
6702 AGAAGACAAC
*
6712 AAAAAAAAA-ATG
1 AAAAAAAAAGAAG
6724 AAAAAAAAAGAAG
1 AAAAAAAAAGAAG
6737 AAAAAAAA
1 AAAAAAAA
6745 CTTGGCCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.88, C:0.00, G:0.09, T:0.03
Consensus pattern (13 bp):
AAAAAAAAAGAAG
Found at i:9365 original size:65 final size:65
Alignment explanation
Indices: 9241--9441 Score: 303
Period size: 65 Copynumber: 3.1 Consensus size: 65
9231 TTGCATTTGG
* ** * * * * *
9241 TAAGCCCTCCGGGCGTGACATCAGAAACCTCCTGGTAGCAATTCTGATAGCCCCCGGGCATGTTA
1 TAAGGCCTCCGGGCACGACGTCAGAAACCTCCAGGTAGCAATTTTAATAGCCTCCGGGCATGTTA
* *
9306 TAAGGCCTCCGGGCACGACGTCAGAAACCTCCAGGTAGCAATTTTAATGGCCTCTGGGCATGTTA
1 TAAGGCCTCCGGGCACGACGTCAGAAACCTCCAGGTAGCAATTTTAATAGCCTCCGGGCATGTTA
*
9371 TAAGGCCTCCGGGCACGACGTCAGAAACCTCCGGGTAGCAATTTTAATAGCCTCCGGGCATGTTA
1 TAAGGCCTCCGGGCACGACGTCAGAAACCTCCAGGTAGCAATTTTAATAGCCTCCGGGCATGTTA
9436 TAAGGC
1 TAAGGC
9442 AATTCTGATA
Statistics
Matches: 123, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
65 123 1.00
ACGTcount: A:0.24, C:0.28, G:0.26, T:0.22
Consensus pattern (65 bp):
TAAGGCCTCCGGGCACGACGTCAGAAACCTCCAGGTAGCAATTTTAATAGCCTCCGGGCATGTTA
Found at i:9625 original size:36 final size:36
Alignment explanation
Indices: 9578--9654 Score: 111
Period size: 36 Copynumber: 2.1 Consensus size: 36
9568 GATGGATCTA
*
9578 AAGACAGTTCCTGAAAGATATTTGAGAACGGAGT-TG
1 AAGACAGTTCCTGAAAGATATTTAAGAA-GGAGTATG
* *
9614 AAGACAGTTCCTGAAAGGTATTTAAGAATGAGTATG
1 AAGACAGTTCCTGAAAGATATTTAAGAAGGAGTATG
9650 AAGAC
1 AAGAC
9655 GGCTCATAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 4 0.11
36 33 0.89
ACGTcount: A:0.39, C:0.10, G:0.26, T:0.25
Consensus pattern (36 bp):
AAGACAGTTCCTGAAAGATATTTAAGAAGGAGTATG
Found at i:9773 original size:32 final size:32
Alignment explanation
Indices: 9732--9870 Score: 114
Period size: 32 Copynumber: 4.5 Consensus size: 32
9722 GAAGATGGGT
9732 TCTGAAGACAGTTCCACAATGGTATAGACGGA
1 TCTGAAGACAGTTCCACAATGGTATAGACGGA
** * **
9764 TCTGAAGACAGTTCCTGAAAGGTATTTAAGAATGA
1 TCTGAAGACAGTTCCACAATGGTA--T-AGACGGA
* * *
9799 GTATGAAGACAGCT-CA-AA--G-AT-G--GGT
1 -TCTGAAGACAGTTCCACAATGGTATAGACGGA
9824 TCTGAAGACAGTTCCACAATGGTATAGACGGA
1 TCTGAAGACAGTTCCACAATGGTATAGACGGA
9856 TCTGAAGACAGTTCC
1 TCTGAAGACAGTTCC
9871 TGAAAGGTAT
Statistics
Matches: 82, Mismatches: 13, Indels: 24
0.69 0.11 0.20
Matches are distributed among these distances:
24 11 0.13
25 3 0.04
26 2 0.02
27 1 0.01
28 1 0.01
29 3 0.04
30 1 0.01
31 1 0.01
32 39 0.48
34 3 0.04
35 6 0.07
36 11 0.13
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.24
Consensus pattern (32 bp):
TCTGAAGACAGTTCCACAATGGTATAGACGGA
Found at i:9833 original size:92 final size:92
Alignment explanation
Indices: 9723--9940 Score: 409
Period size: 92 Copynumber: 2.4 Consensus size: 92
9713 ATAGTTCACG
9723 AAGATGGGTTCTGAAGACAGTTCCACAATGGTATAGACGGATCTGAAGACAGTTCCTGAAAGGTA
1 AAGATGGGTTCTGAAGACAGTTCCACAATGGTATAGACGGATCTGAAGACAGTTCCTGAAAGGTA
9788 TTTAAGAATGAGTATGAAGACAGCTCA
66 TTTAAGAATGAGTATGAAGACAGCTCA
9815 AAGATGGGTTCTGAAGACAGTTCCACAATGGTATAGACGGATCTGAAGACAGTTCCTGAAAGGTA
1 AAGATGGGTTCTGAAGACAGTTCCACAATGGTATAGACGGATCTGAAGACAGTTCCTGAAAGGTA
9880 TTTAAGAATGAGTATGAAGACAGCTCA
66 TTTAAGAATGAGTATGAAGACAGCTCA
* * *
9907 AAGATGGCTTCTGAAGATAGTTCCTCAATGGTAT
1 AAGATGGGTTCTGAAGACAGTTCCACAATGGTAT
9941 TTAAGAATGA
Statistics
Matches: 123, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
92 123 1.00
ACGTcount: A:0.35, C:0.14, G:0.26, T:0.25
Consensus pattern (92 bp):
AAGATGGGTTCTGAAGACAGTTCCACAATGGTATAGACGGATCTGAAGACAGTTCCTGAAAGGTA
TTTAAGAATGAGTATGAAGACAGCTCA
Found at i:9949 original size:60 final size:59
Alignment explanation
Indices: 9853--9990 Score: 222
Period size: 60 Copynumber: 2.3 Consensus size: 59
9843 TGGTATAGAC
*
9853 GGATCTGAAGACAGTTCCTGAAAGGTATTTAAGAATGAGTATGAAGACAGCTCAAAGAT
1 GGATCTGAAGACAGTTCCTCAAAGGTATTTAAGAATGAGTATGAAGACAGCTCAAAGAT
* * * *
9912 GGCTTCTGAAGATAGTTCCTCAATGGTATTTAAGAATGAGTATGAAGACAGCTCATAGAT
1 GG-ATCTGAAGACAGTTCCTCAAAGGTATTTAAGAATGAGTATGAAGACAGCTCAAAGAT
9972 GGATCTGAAGACAGTTCCT
1 GGATCTGAAGACAGTTCCT
9991 GGAAGTTTTT
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
59 17 0.24
60 54 0.76
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.27
Consensus pattern (59 bp):
GGATCTGAAGACAGTTCCTCAAAGGTATTTAAGAATGAGTATGAAGACAGCTCAAAGAT
Found at i:10109 original size:56 final size:56
Alignment explanation
Indices: 10044--10159 Score: 164
Period size: 56 Copynumber: 2.1 Consensus size: 56
10034 TTTTCAACTG
10044 TTTTAAGTAGTTACTCAAGTTGATCG-AGGACGATCATCTTTCTCAG-TTTCCAGCAA
1 TTTTAAGTAGTTACTCAAGTTGATCGCA-GACGATCATCTTTCTCAGATTT-CAGCAA
* * * *
10100 TTTTTAGTAGTTACTCAAGTTGGTCGCAGACGATCATTTTTCTTAGATTTCAGCAA
1 TTTTAAGTAGTTACTCAAGTTGATCGCAGACGATCATCTTTCTCAGATTTCAGCAA
10156 TTTT
1 TTTT
10160 CCGTGCAGAC
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
56 50 0.93
57 4 0.07
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.41
Consensus pattern (56 bp):
TTTTAAGTAGTTACTCAAGTTGATCGCAGACGATCATCTTTCTCAGATTTCAGCAA
Found at i:13640 original size:13 final size:14
Alignment explanation
Indices: 13622--13650 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
13612 ATAATCAGAC
13622 TTTGCATCCAT-CA
1 TTTGCATCCATGCA
13635 TTTGCATCCATGCA
1 TTTGCATCCATGCA
13649 TT
1 TT
13651 AAAGTAGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.21, C:0.28, G:0.10, T:0.41
Consensus pattern (14 bp):
TTTGCATCCATGCA
Found at i:13945 original size:37 final size:40
Alignment explanation
Indices: 13854--13953 Score: 143
Period size: 40 Copynumber: 2.6 Consensus size: 40
13844 TTTAAAGCAT
* **
13854 CTCCAAAAGAAGACTTTTGGAAAATAAATGTTTTTTACAA
1 CTCCAAAAGAAGACTTTTGGAAAATAAAAGTTTTGGACAA
13894 CTCCAAAAGAAGACTTTTGGAAAATAAAAG-TTTGGA-AA
1 CTCCAAAAGAAGACTTTTGGAAAATAAAAGTTTTGGACAA
*
13932 -TCCAAGAGAAGACTTTTGGAAA
1 CTCCAAAAGAAGACTTTTGGAAA
13954 TTAATAAAAT
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
37 21 0.38
38 2 0.04
39 4 0.07
40 29 0.52
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.27
Consensus pattern (40 bp):
CTCCAAAAGAAGACTTTTGGAAAATAAAAGTTTTGGACAA
Found at i:21666 original size:21 final size:20
Alignment explanation
Indices: 21636--21689 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 20
21626 TTACAAAAGA
21636 AAAACTAAATAGAAAGATACCG
1 AAAAC-AAATAGAAAGATA-CG
*
21658 AGAACAAATAGAAAGATACG
1 AAAACAAATAGAAAGATACG
21678 AAAACAAA-AGAA
1 AAAACAAATAGAA
21690 TAAAAACCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 4 0.13
20 9 0.30
21 13 0.43
22 4 0.13
ACGTcount: A:0.65, C:0.11, G:0.15, T:0.09
Consensus pattern (20 bp):
AAAACAAATAGAAAGATACG
Found at i:22365 original size:13 final size:15
Alignment explanation
Indices: 22337--22369 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
22327 AAACCCTAAC
22337 ATATATATCATATAT
1 ATATATATCATATAT
*
22352 ATATATATCTTATAT
1 ATATATATCATATAT
22367 ATA
1 ATA
22370 AACTAAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (15 bp):
ATATATATCATATAT
Found at i:27229 original size:167 final size:163
Alignment explanation
Indices: 26732--27231 Score: 576
Period size: 167 Copynumber: 3.0 Consensus size: 163
26722 TGAGTCATTT
* * *
26732 GTCAATTGAGAAATGAACAAAAATTTTAGTTATTTAATTCCCTCAAGAATCATAAGTTAGGACAT
1 GTCAATTGAGAAATGACCAAAAA-GTTAGTTATTTAA-TCCCTCAAGAATCAAAAGTTAGGACAT
* * * *
26797 TTAAGTAATCTGCCAAGTAGGTAAATACGAAAAAAATTAGTTCTCTAGCTCATCATCAATCCTTG
64 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAGCTCCTCGTCAATCCTTG
* * * *
26862 ATGGGGATCTTTTATTAATTCCACTACTCTATTCAAA
129 GT-AGGATCTTTTAGTAATTCCACTACTTTATT-AAA
* * *
26899 -TCCATTGAGAAATGACCAAAAAGATTACTTATTTAATCCCCTCAAGAATCAAAAGTTAAGACAT
1 GTCAATTGAGAAATGACCAAAAAG-TTAGTTATTTAAT-CCCTCAAGAATCAAAAGTTAGGACAT
* * * ** *
26963 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATAAGTTATCTAACTCCAAAAG-CAAACCT
64 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAGCTCC--TCGTCAATCCT
27027 TGGTAAGGATCTTTTAGTAATTCCACTACTTTATTAAA
127 TGGT-AGGATCTTTTAGTAATTCCACTACTTTATTAAA
* *
27065 GTCAATTGTGAAATGACCAAAAAGTCTAGTTATTTAATCACCTCAAGAATCAAAAGTTAGGGCAT
1 GTCAATTGAGAAATGACCAAAAAGT-TAGTTATTTAATC-CCTCAAGAATCAAAAGTTAGGACAT
* * * * **
27130 TTAAGTAATCGGTCAAGT-GTGAAAAGACGAAAAAAATTAGTTCTCTCGCTCCTCGTTAATCCGG
64 TTAAGTAATCTGCCAAGTAG-GAAAAGACGAAAAAAATTAGTTCTCTAGCTCCTCGTCAATCCTT
*
27194 GGTAGGAATCTTTTAGTAATTTCCA-TATGTTTATTAAA
128 GGTAGG-ATCTTTTAGTAA-TTCCACTA-CTTTATTAAA
27232 ATAATAAGTA
Statistics
Matches: 282, Mismatches: 39, Indels: 24
0.82 0.11 0.07
Matches are distributed among these distances:
165 5 0.02
166 128 0.45
167 149 0.53
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (163 bp):
GTCAATTGAGAAATGACCAAAAAGTTAGTTATTTAATCCCTCAAGAATCAAAAGTTAGGACATTT
AAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAGCTCCTCGTCAATCCTTGGT
AGGATCTTTTAGTAATTCCACTACTTTATTAAA
Found at i:29827 original size:39 final size:39
Alignment explanation
Indices: 29773--29849 Score: 145
Period size: 39 Copynumber: 2.0 Consensus size: 39
29763 CATCAATATA
*
29773 TCATGCAATATATCATATGTTCTATCAACTCCAAAGTGT
1 TCATGCAATATATCATATGTTCAATCAACTCCAAAGTGT
29812 TCATGCAATATATCATATGTTCAATCAACTCCAAAGTG
1 TCATGCAATATATCATATGTTCAATCAACTCCAAAGTG
29850 ACCCATTAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.35, C:0.21, G:0.10, T:0.34
Consensus pattern (39 bp):
TCATGCAATATATCATATGTTCAATCAACTCCAAAGTGT
Done.