Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014904.1 Corchorus capsularis cultivar CVL-1 contig14925, 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: 31448
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:1086 original size:38 final size:37
Alignment explanation
Indices: 1043--1158 Score: 107
Period size: 38 Copynumber: 3.2 Consensus size: 37
1033 TAAATATATA
1043 AATAAAAGTAGAAAAAGTTAAAAGAAAGAAAGAGAGAG
1 AATAAAAGTAGAAAAAGTTAAAAGAAAGAAA-AGAGAG
* * *
1081 AATAAAAG-AG-AGAA-TTAGAA-AAAGAAAA-AAATG
1 AATAAAAGTAGAAAAAGTTAAAAGAAAGAAAAGAGA-G
** *
1114 GTTAGAAGTAGAAAAAGTTAAAAGAAAGAAAAAGAGAG
1 AATAAAAGTAGAAAAAGTTAAAAGAAAG-AAAAGAGAG
*
1152 AAAAAAA
1 AATAAAA
1159 AAGAGAGAAT
Statistics
Matches: 58, Mismatches: 13, Indels: 14
0.68 0.15 0.16
Matches are distributed among these distances:
32 2 0.03
33 7 0.12
34 9 0.16
35 8 0.14
36 8 0.14
37 6 0.10
38 16 0.28
39 2 0.03
ACGTcount: A:0.67, C:0.00, G:0.22, T:0.11
Consensus pattern (37 bp):
AATAAAAGTAGAAAAAGTTAAAAGAAAGAAAAGAGAG
Found at i:1177 original size:16 final size:14
Alignment explanation
Indices: 1136--1175 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
1126 AAAAGTTAAA
*
1136 AGAAAGAAAAAGAG
1 AGAAAAAAAAAGAG
1150 AGAAAAAAAAAGAG
1 AGAAAAAAAAAGAG
1164 AGAATAAAAAAA
1 AGAA-AAAAAAA
1176 AGGGTTAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 17 0.71
15 7 0.29
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.03
Consensus pattern (14 bp):
AGAAAAAAAAAGAG
Found at i:8575 original size:7 final size:7
Alignment explanation
Indices: 8565--8589 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
8555 AAAAACCAAA
8565 AAAATTC
1 AAAATTC
8572 AAAATTC
1 AAAATTC
8579 AAAATTC
1 AAAATTC
8586 AAAA
1 AAAA
8590 CAAAATTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (7 bp):
AAAATTC
Found at i:11646 original size:22 final size:22
Alignment explanation
Indices: 11597--11655 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
11587 TTAAAAATGA
* * * *
11597 TATATATATATATATGTTTTTT
1 TATACATATATATATGTATATG
*
11619 TGTACATATATATATGTATATG
1 TATACATATATATATGTATATG
*
11641 TATACACATATATAT
1 TATACATATATATAT
11656 TTGTACGGAA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (22 bp):
TATACATATATATATGTATATG
Found at i:13545 original size:28 final size:29
Alignment explanation
Indices: 13514--13570 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
13504 TATATATTGC
13514 TTTT-GGAACAAAATAATCCCTTACGTTT
1 TTTTCGGAACAAAATAATCCCTTACGTTT
* * *
13542 TTTTCGGGACAAATTAATCCCTTATGTTT
1 TTTTCGGAACAAAATAATCCCTTACGTTT
13571 AGTAAATGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 4 0.16
29 21 0.84
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.42
Consensus pattern (29 bp):
TTTTCGGAACAAAATAATCCCTTACGTTT
Found at i:13775 original size:33 final size:32
Alignment explanation
Indices: 13714--13807 Score: 133
Period size: 33 Copynumber: 3.0 Consensus size: 32
13704 AAGGGACTAA
*
13714 TTTGT-CCAAAA-AAAAACATAAGGG-ATTTT
1 TTTGTCCCAAAAGAAAAATATAAGGGAATTTT
13743 TTTGTCCCAAAAGAAAAATATAAGGGATATTTT
1 TTTGTCCCAAAAGAAAAATATAAGGGA-ATTTT
*
13776 TTTGTCCCAAAAG-AAAATATAAGGGACTTTT
1 TTTGTCCCAAAAGAAAAATATAAGGGAATTTT
13807 T
1 T
13808 AGTATTTAGT
Statistics
Matches: 59, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
29 5 0.08
30 6 0.10
31 17 0.29
32 13 0.22
33 18 0.31
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (32 bp):
TTTGTCCCAAAAGAAAAATATAAGGGAATTTT
Found at i:13776 original size:32 final size:32
Alignment explanation
Indices: 13714--13807 Score: 133
Period size: 31 Copynumber: 3.0 Consensus size: 32
13704 AAGGGACTAA
*
13714 TTTGT-CCAAAA-AAAAACATAAGGGA-TTTT
1 TTTGTCCCAAAAGAAAAATATAAGGGATTTTT
13743 TTTGTCCCAAAAGAAAAATATAAGGGATATTTT
1 TTTGTCCCAAAAGAAAAATATAAGGGAT-TTTT
*
13776 TTTGTCCCAAAAG-AAAATATAAGGGACTTTT
1 TTTGTCCCAAAAGAAAAATATAAGGGATTTTT
13807 T
1 T
13808 AGTATTTAGT
Statistics
Matches: 59, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
29 5 0.08
30 6 0.10
31 18 0.31
32 13 0.22
33 17 0.29
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (32 bp):
TTTGTCCCAAAAGAAAAATATAAGGGATTTTT
Found at i:13862 original size:7 final size:7
Alignment explanation
Indices: 13852--13880 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
13842 AAATCAATTT
13852 TTTTTTC
1 TTTTTTC
13859 -TTTTTC
1 TTTTTTC
13865 TTTTTTC
1 TTTTTTC
13872 TTTTTTC
1 TTTTTTC
13879 TT
1 TT
13881 CTTCCTTCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTTC
Found at i:13870 original size:13 final size:13
Alignment explanation
Indices: 13852--13876 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13842 AAATCAATTT
13852 TTTTTTCTTTTTC
1 TTTTTTCTTTTTC
13865 TTTTTTCTTTTT
1 TTTTTTCTTTTT
13877 TCTTCTTCCT
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:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTCTTTTTC
Found at i:14121 original size:126 final size:127
Alignment explanation
Indices: 13971--14211 Score: 326
Period size: 126 Copynumber: 1.9 Consensus size: 127
13961 TAATTCCCTA
*
13971 AAAAGTGGTAAAGATAAAATAGTTATAAAAATATT-GAATTTAATTAAATAAAAATAGAATTTTT
1 AAAAGTGGTAAAAATAAAATAGTTATAAAAATATTAG-ATTTAATTAAATAAAAATAGAATTTTT
** *
14035 GGTAAAATAAAACTGTAAAAGTTTATATAAT-GTCATTTAAGAAATATATTTAATTAATATAGT
65 AATAAAATAAAACTGTAAAAGTTTAAATAATGGT-ATTTAAGAAATATATTTAATTAATATAGT
* * * *
14098 AAAA-TGGTAAAAATAAAATAGTTATAAATATATTAGATTTGATTAAATTAAAATAGAGTTTTTA
1 AAAAGTGGTAAAAATAAAATAGTTATAAAAATATTAGATTTAATTAAATAAAAATAGAATTTTTA
**** *
14162 ATTGTGTAAAATTGTAAAAGTTTAAATAATGGTATTTAAGAAATATATTT
66 ATAAAATAAAACTGTAAAAGTTTAAATAATGGTATTTAAGAAATATATTT
14212 GAAAAATAAG
Statistics
Matches: 99, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
126 92 0.93
127 7 0.07
ACGTcount: A:0.50, C:0.01, G:0.12, T:0.38
Consensus pattern (127 bp):
AAAAGTGGTAAAAATAAAATAGTTATAAAAATATTAGATTTAATTAAATAAAAATAGAATTTTTA
ATAAAATAAAACTGTAAAAGTTTAAATAATGGTATTTAAGAAATATATTTAATTAATATAGT
Found at i:15440 original size:11 final size:12
Alignment explanation
Indices: 15417--15462 Score: 55
Period size: 11 Copynumber: 4.2 Consensus size: 12
15407 ATATATAACA
15417 TATAATATATTT
1 TATAATATATTT
*
15429 TA-AATATTTTT
1 TATAATATATTT
15440 TATAATATA---
1 TATAATATATTT
15449 TATAATATATTT
1 TATAATATATTT
15461 TA
1 TA
15463 AATTTTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
9 9 0.32
11 10 0.36
12 9 0.32
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
TATAATATATTT
Found at i:15450 original size:39 final size:38
Alignment explanation
Indices: 15407--15525 Score: 100
Period size: 39 Copynumber: 3.0 Consensus size: 38
15397 TAATAAAAGC
*
15407 ATATATAACATATAATATATTTTAAATATTTTTTATAAT
1 ATATATAACATATAATATATTTTAAATATTATTTAT-AT
* ** *
15446 ATATATAATATATTTTAAATTTT--AT-TTATTTATAT
1 ATATATAACATATAATATATTTTAAATATTATTTATAT
*
15481 ATGATAAGAACATATATAATATATTTTAAATATATATATTATAT
1 AT-AT-ATAAC--ATATAATATATTTTAAATAT-TAT-TTATAT
15525 A
1 A
15526 AAATATCTAT
Statistics
Matches: 61, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
35 4 0.07
36 9 0.15
37 5 0.08
39 30 0.49
41 2 0.03
42 1 0.02
43 3 0.05
44 7 0.11
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (38 bp):
ATATATAACATATAATATATTTTAAATATTATTTATAT
Found at i:15457 original size:32 final size:31
Alignment explanation
Indices: 15416--15482 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 31
15406 CATATATAAC
15416 ATATAATATATTTTAAATATTT-TTTATAATAT
1 ATATAATATATTTTAAAT-TTTATTTAT-ATAT
*
15448 ATATAATATATTTTAAATTTTATTTATTTAT
1 ATATAATATATTTTAAATTTTATTTATATAT
15479 ATAT
1 ATAT
15483 GATAAGAACA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
31 10 0.30
32 23 0.70
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (31 bp):
ATATAATATATTTTAAATTTTATTTATATAT
Found at i:15458 original size:23 final size:23
Alignment explanation
Indices: 15417--15461 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
15407 ATATATAACA
*
15417 TATAATATATTTTAAATATTTTT
1 TATAATATATTATAAATATTTTT
15440 TATAATATA-TATAATATATTTT
1 TATAATATATTATAA-ATATTTT
15462 AAATTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
TATAATATATTATAAATATTTTT
Found at i:16033 original size:22 final size:22
Alignment explanation
Indices: 16008--16049 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
15998 GAATGACCCA
*
16008 TAACCCGAGTGACCCGAGAAGT
1 TAACCCGAATGACCCGAGAAGT
*
16030 TAACCCGAATGATCCGAGAA
1 TAACCCGAATGACCCGAGAA
16050 TATTATAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.36, C:0.26, G:0.24, T:0.14
Consensus pattern (22 bp):
TAACCCGAATGACCCGAGAAGT
Found at i:17853 original size:43 final size:43
Alignment explanation
Indices: 17805--17915 Score: 138
Period size: 31 Copynumber: 2.9 Consensus size: 43
17795 CATGCGACTT
17805 TTTGTCAATTGAGAAATGACCAAAAAGTTTAGTTATTGAGTCA
1 TTTGTCAATTGAGAAATGACCAAAAAGTTTAGTTATTGAGTCA
17848 TTTGTCAATTGAGAAATGA-C--------T--TT-TTGAGTCA
1 TTTGTCAATTGAGAAATGACCAAAAAGTTTAGTTATTGAGTCA
17879 TTTGTCAATTGAGAAATGACCAAAAAGTTTAGTTATT
1 TTTGTCAATTGAGAAATGACCAAAAAGTTTAGTTATT
17916 TAATCCACTC
Statistics
Matches: 56, Mismatches: 0, Indels: 24
0.70 0.00 0.30
Matches are distributed among these distances:
31 27 0.48
32 3 0.05
34 1 0.02
40 1 0.02
42 3 0.05
43 21 0.38
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (43 bp):
TTTGTCAATTGAGAAATGACCAAAAAGTTTAGTTATTGAGTCA
Found at i:18273 original size:66 final size:66
Alignment explanation
Indices: 18167--18300 Score: 223
Period size: 66 Copynumber: 2.0 Consensus size: 66
18157 CTAACTCCAA
* * *
18167 AAGCAAGGCTTGGTAGGGATCTTTTAGTAATCCCACTACTCTATTAAAGTCAATTGAGAAATGAC
1 AAGCAAGCCTTCGTAGGGATCTTTTAGTAATCACACTACTCTATTAAAGTCAATTGAGAAATGAC
18232 C
66 C
* *
18233 AAGCAAGCCTTCGTAGGGATCTTTTAGTAATTACACTACTCTATTAAAGTTAATTGAGAAATGAC
1 AAGCAAGCCTTCGTAGGGATCTTTTAGTAATCACACTACTCTATTAAAGTCAATTGAGAAATGAC
18298 C
66 C
18299 AA
1 AA
18301 AAAGTCTAAT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (66 bp):
AAGCAAGCCTTCGTAGGGATCTTTTAGTAATCACACTACTCTATTAAAGTCAATTGAGAAATGAC
C
Found at i:24832 original size:22 final size:22
Alignment explanation
Indices: 24807--24851 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
24797 AACCACTATG
24807 TGGCCGAATCTCACGGCCACCA
1 TGGCCGAATCTCACGGCCACCA
*
24829 TGGCCGAATCTCACGGTCACCA
1 TGGCCGAATCTCACGGCCACCA
24851 T
1 T
24852 CTCAAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.22, C:0.38, G:0.22, T:0.18
Consensus pattern (22 bp):
TGGCCGAATCTCACGGCCACCA
Found at i:27436 original size:31 final size:31
Alignment explanation
Indices: 27393--27451 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
27383 TTAGGAATGG
27393 TGTGGTTAATCTTTAGAAGCAAAATAGAACA
1 TGTGGTTAATCTTTAGAAGCAAAATAGAACA
* *
27424 TGTGGTTCATCTTTAGAAGCAGAATAGA
1 TGTGGTTAATCTTTAGAAGCAAAATAGA
27452 TTAATATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.31
Consensus pattern (31 bp):
TGTGGTTAATCTTTAGAAGCAAAATAGAACA
Found at i:29371 original size:11 final size:11
Alignment explanation
Indices: 29355--29379 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
29345 TTTAAGTAAA
29355 AAATTTCAAAT
1 AAATTTCAAAT
29366 AAATTTCAAAT
1 AAATTTCAAAT
29377 AAA
1 AAA
29380 AAATGCTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (11 bp):
AAATTTCAAAT
Done.