Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014199.1 Corchorus capsularis cultivar CVL-1 contig14220, 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: 25864
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Found at i:4270 original size:40 final size:38
Alignment explanation
Indices: 4215--4317 Score: 170
Period size: 40 Copynumber: 2.7 Consensus size: 38
4205 CTGTTTAAGC
*
4215 AATTCCAAGAGAAGACTTTTGGAAAATGAAAGTTTTTAG
1 AATTCCAAGAGAAGACTTTTGGAAAATAAAAG-TTTTAG
4254 TAATTCCAAGAGAAGACTTTTGGAAAATAAAAGTTTTAG
1 -AATTCCAAGAGAAGACTTTTGGAAAATAAAAGTTTTAG
*
4293 AAATCCAAGAGAAGACTTTTGGAAA
1 AATTCCAAGAGAAGACTTTTGGAAA
4318 TTAATAAAAT
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
38 24 0.39
39 6 0.10
40 31 0.51
ACGTcount: A:0.44, C:0.09, G:0.19, T:0.28
Consensus pattern (38 bp):
AATTCCAAGAGAAGACTTTTGGAAAATAAAAGTTTTAG
Found at i:5790 original size:28 final size:26
Alignment explanation
Indices: 5735--5784 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
5725 CATGATTAGG
* *
5735 GGTTACTAACTCCCTTTTTCTTTTGA
1 GGTTACTAACACCATTTTTCTTTTGA
5761 GGTTACTAACACTCATTTTT-TTTT
1 GGTTACTAACAC-CATTTTTCTTTT
5785 CAGAGGGACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 15 0.71
27 6 0.29
ACGTcount: A:0.18, C:0.20, G:0.10, T:0.52
Consensus pattern (26 bp):
GGTTACTAACACCATTTTTCTTTTGA
Found at i:6750 original size:33 final size:33
Alignment explanation
Indices: 6713--6819 Score: 126
Period size: 33 Copynumber: 3.2 Consensus size: 33
6703 GCCCAATCGA
* *
6713 TGGCCGGTTG-TGGCCGGACATGTCCATGTCGCG
1 TGGCCGG-TGATGGCCGGGCATCTCCATGTCGCG
* **
6746 TGGCCAGTGATGGCCGGGCATCTCCGGGTCGCG
1 TGGCCGGTGATGGCCGGGCATCTCCATGTCGCG
* * *
6779 TGGCCGGTGTTGGCCGGGCTTCTCCATGTCGCA
1 TGGCCGGTGATGGCCGGGCATCTCCATGTCGCG
6812 TGGCCGGT
1 TGGCCGGT
6820 CACTCGCGCC
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
32 2 0.03
33 60 0.97
ACGTcount: A:0.07, C:0.29, G:0.40, T:0.23
Consensus pattern (33 bp):
TGGCCGGTGATGGCCGGGCATCTCCATGTCGCG
Found at i:11712 original size:10 final size:9
Alignment explanation
Indices: 11692--11726 Score: 52
Period size: 10 Copynumber: 3.7 Consensus size: 9
11682 CTGGTCGAAA
11692 ATTTTTTTT
1 ATTTTTTTT
11701 ATTTTATTTT
1 ATTTT-TTTT
11711 ATTTTTTTAT
1 ATTTTTTT-T
11721 ATTTTT
1 ATTTTT
11727 CGATATAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:11824 original size:17 final size:17
Alignment explanation
Indices: 11799--11832 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
11789 GAATTGGCTA
11799 TGAAGTTTTGAAGTTTC
1 TGAAGTTTTGAAGTTTC
* *
11816 TGAATTTTTGAATTTTC
1 TGAAGTTTTGAAGTTTC
11833 AAGAAGGGTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.06, G:0.18, T:0.53
Consensus pattern (17 bp):
TGAAGTTTTGAAGTTTC
Found at i:12857 original size:33 final size:33
Alignment explanation
Indices: 12789--12895 Score: 108
Period size: 33 Copynumber: 3.2 Consensus size: 33
12779 CGCCAAGCGA
** * * *
12789 TGGCCGGTTG-TGGCCGAACATGTCCATGTCCCG
1 TGGCCGG-TGATGGCCGGGCATCTCCAAGTCGCG
**
12822 TGGCCGGTGATGGCCGGGCATCTCCGGGTCGCG
1 TGGCCGGTGATGGCCGGGCATCTCCAAGTCGCG
* * *
12855 TGGCCGGTGTTGGCCGGGCGTCTCCAAGTCGCA
1 TGGCCGGTGATGGCCGGGCATCTCCAAGTCGCG
12888 TGGCCGGT
1 TGGCCGGT
12896 CACTCGCGCC
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
32 2 0.03
33 60 0.97
ACGTcount: A:0.08, C:0.30, G:0.40, T:0.21
Consensus pattern (33 bp):
TGGCCGGTGATGGCCGGGCATCTCCAAGTCGCG
Found at i:14449 original size:299 final size:299
Alignment explanation
Indices: 13911--14505 Score: 1118
Period size: 299 Copynumber: 2.0 Consensus size: 299
13901 GGTCCATGTA
* *
13911 AACTCTCATCTCACTTCTATGTTGCCTCATCTTTCGAACCATAAGTTGTTGGATCTGTCGCATAG
1 AACTCTCATCTCACTTCTATGTTGCCTCATCTCTCGAACCATAAGTTGTTGGATCTATCGCATAG
13976 GAAGCTCTTGGAAATTCTCTTCATCAACTTCCAAGGGTGGTTGTCCTTCCACATGTGGTTGCTCA
66 GAAGCTCTTGGAAATTCTCTTCATCAACTTCCAAGGGTGGTTGTCCTTCCACATGTGGTTGCTCA
* *
14041 AGTCCTTGCTCATAAGTCCTACGATGTACATTGTACCAATGTGCACTATTGGGAATGACTCGTCT
131 AGTCCTTGCTCATAAGTCCTACGATGTACATTGTACCAATGCGCACTATTGGCAATGACTCGTCT
*
14106 CTTGATACCCAAATGACTCAAACAATCTACATCCTAGAAAGTAACAACCTAGCCATTGGTATTCC
196 CTTGATACCCAAATGACTCAAACAATCTACATCCTAGAAAGTAACAACCTAGACATTGGTATTCC
14171 ATTACAATGGCCTAATCCATGATAAATCTTATCCACAAC
261 ATTACAATGGCCTAATCCATGATAAATCTTATCCACAAC
14210 AACTCTCATCTCACTTCTATGTTGCCTCATCTCTCGAACCATAAGTTGTTGGATCTATCGCATAG
1 AACTCTCATCTCACTTCTATGTTGCCTCATCTCTCGAACCATAAGTTGTTGGATCTATCGCATAG
*
14275 GAAGCTCTTGGAAATTCTCTTCATCAACTTCCAAGGGTGGTTGTCCTTCCACATGTGGTTGTTCA
66 GAAGCTCTTGGAAATTCTCTTCATCAACTTCCAAGGGTGGTTGTCCTTCCACATGTGGTTGCTCA
*
14340 AGTCCTTGCTCATAAGTCCTACGATGTACATTGTACCAATGCGCACTATTGTCAATGACTCGTCT
131 AGTCCTTGCTCATAAGTCCTACGATGTACATTGTACCAATGCGCACTATTGGCAATGACTCGTCT
*
14405 CTTGATACCCAAATGACTCAAAGAATCTACATCCTAGAAAGTAACAACCTAGACATTGGTATTCC
196 CTTGATACCCAAATGACTCAAACAATCTACATCCTAGAAAGTAACAACCTAGACATTGGTATTCC
14470 ATTACAATGGCCTAATCCATGATAAATCTTATCCAC
261 ATTACAATGGCCTAATCCATGATAAATCTTATCCAC
14506 CACATAGAAA
Statistics
Matches: 288, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
299 288 1.00
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (299 bp):
AACTCTCATCTCACTTCTATGTTGCCTCATCTCTCGAACCATAAGTTGTTGGATCTATCGCATAG
GAAGCTCTTGGAAATTCTCTTCATCAACTTCCAAGGGTGGTTGTCCTTCCACATGTGGTTGCTCA
AGTCCTTGCTCATAAGTCCTACGATGTACATTGTACCAATGCGCACTATTGGCAATGACTCGTCT
CTTGATACCCAAATGACTCAAACAATCTACATCCTAGAAAGTAACAACCTAGACATTGGTATTCC
ATTACAATGGCCTAATCCATGATAAATCTTATCCACAAC
Found at i:17203 original size:17 final size:16
Alignment explanation
Indices: 17173--17206 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
17163 ATAAAACGAA
*
17173 AAATAAAAATAAAAAG
1 AAATAAAAAGAAAAAG
17189 AAATGAAAAAGAAAAAG
1 AAAT-AAAAAGAAAAAG
17206 A
1 A
17207 TAAGGGTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (16 bp):
AAATAAAAAGAAAAAG
Found at i:20283 original size:41 final size:40
Alignment explanation
Indices: 20184--20370 Score: 227
Period size: 41 Copynumber: 4.6 Consensus size: 40
20174 AATGTAGACT
* *
20184 TAAAAAACACCTTCCGGTGAGGAAGGGCAAACTGGGAAAC
1 TAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAAAC
20224 T--A-AACACCTTCCGGTGGGGAAGGGCAAACTGGGAAATC
1 TAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAAA-C
* * *
20262 TAAACAACACCATCTGGTGGGGAAGGGCAAATTGGGAAATC
1 TAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAAA-C
* * *
20303 TAAACGACAACTTCCGGTGAGGAGGAAGGGCAAACTGAGAAAC
1 TAAACAACACCTTCCGGT--GG-GGAAGGGCAAACTGGGAAAC
*
20346 TAAACAACACCTTCCGGTGAGGAAG
1 TAAACAACACCTTCCGGTGGGGAAG
20371 TGAAACGAAT
Statistics
Matches: 127, Mismatches: 13, Indels: 14
0.82 0.08 0.09
Matches are distributed among these distances:
37 33 0.26
38 3 0.02
40 7 0.06
41 48 0.38
43 19 0.15
44 17 0.13
ACGTcount: A:0.37, C:0.20, G:0.29, T:0.14
Consensus pattern (40 bp):
TAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAAAC
Found at i:20298 original size:78 final size:82
Alignment explanation
Indices: 20184--20370 Score: 258
Period size: 78 Copynumber: 2.3 Consensus size: 82
20174 AATGTAGACT
*
20184 TAAAAAACACCTTCCGGTGAGGAAGGGCAAACTGGGAAA-CTAAAC-AC-CTTCCGGT-GG-GGA
1 TAAACAACACCTTCCGGTGAGGAAGGGCAAACTGGGAAATCTAAACGACACTTCCGGTAGGAGGA
*
20244 AGGGCAAACTGGGAAATC
66 AGGGCAAACTGAGAAA-C
* * * *
20262 TAAACAACACCATCTGGTGGGGAAGGGCAAATTGGGAAATCTAAACGACAACTTCCGGTGAGGAG
1 TAAACAACACCTTCCGGTGAGGAAGGGCAAACTGGGAAATCTAAACGAC-ACTTCCGGT-AGGAG
20327 GAAGGGCAAACTGAGAAAC
64 GAAGGGCAAACTGAGAAAC
20346 TAAACAACACCTTCCGGTGAGGAAG
1 TAAACAACACCTTCCGGTGAGGAAG
20371 TGAAACGAAT
Statistics
Matches: 93, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
78 34 0.37
79 6 0.06
80 2 0.02
82 8 0.09
84 25 0.27
85 18 0.19
ACGTcount: A:0.37, C:0.20, G:0.29, T:0.14
Consensus pattern (82 bp):
TAAACAACACCTTCCGGTGAGGAAGGGCAAACTGGGAAATCTAAACGACACTTCCGGTAGGAGGA
AGGGCAAACTGAGAAAC
Found at i:24486 original size:33 final size:33
Alignment explanation
Indices: 24448--24527 Score: 106
Period size: 33 Copynumber: 2.4 Consensus size: 33
24438 GGCGCGAGTG
* *
24448 ACCGGCCATGCGACTTGGAGAAGACCAGCCAAC
1 ACCGGCCACGCGACTCGGAGAAGACCAGCCAAC
* * * *
24481 ACCGGCCACGCGACTCGGAGATGCCCGGCCATC
1 ACCGGCCACGCGACTCGGAGAAGACCAGCCAAC
24514 ACCGGCCACGCGAC
1 ACCGGCCACGCGAC
24528 ATTGACATGT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.24, C:0.40, G:0.29, T:0.07
Consensus pattern (33 bp):
ACCGGCCACGCGACTCGGAGAAGACCAGCCAAC
Found at i:24542 original size:33 final size:32
Alignment explanation
Indices: 24479--24554 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 32
24469 AGACCAGCCA
*
24479 ACACCGGCCACGCGACTCGGAGATGCCCGGCC
1 ACACCGGCCACGCGACTCGGACATGCCCGGCC
* *
24511 ATCACCGGCCACGCGACAT-TGACATGTCCGGCC
1 A-CACCGGCCACGCGAC-TCGGACATGCCCGGCC
24544 ACAACCGGCCA
1 AC-ACCGGCCA
24555 TCGCTTGGCG
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
32 2 0.05
33 35 0.92
34 1 0.03
ACGTcount: A:0.22, C:0.42, G:0.26, T:0.09
Consensus pattern (32 bp):
ACACCGGCCACGCGACTCGGACATGCCCGGCC
Found at i:25542 original size:17 final size:17
Alignment explanation
Indices: 25517--25550 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
25507 CACCCTTTTT
25517 GAAAATTCAAAAATTCA
1 GAAAATTCAAAAATTCA
*
25534 GAAACTTCAAAAATTCA
1 GAAAATTCAAAAATTCA
25551 TAGCCAATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.15, G:0.06, T:0.24
Consensus pattern (17 bp):
GAAAATTCAAAAATTCA
Found at i:25656 original size:9 final size:9
Alignment explanation
Indices: 25624--25657 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
25614 AGTTATATCG
25624 AAAAATATAA
1 AAAAATA-AA
25634 AAAAATAAA
1 AAAAATAAA
*
25643 TAAAATAAA
1 AAAAATAAA
25652 AAAAAT
1 AAAAAT
25658 TTTCGACCAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 15 0.68
10 7 0.32
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (9 bp):
AAAAATAAA
Done.