Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015043.1 Corchorus capsularis cultivar CVL-1 contig15064, 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: 45864
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:2160 original size:13 final size:14
Alignment explanation
Indices: 2144--2182 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
2134 ACCAAAATAA
2144 AAACCGAAAAACC-
1 AAACCGAAAAACCG
2157 AAACCGAAAAAACCG
1 AAACCG-AAAAACCG
*
2172 ACACCGAAAAA
1 AAACCGAAAAA
2183 TGAGCAGCCC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 6 0.26
14 12 0.52
15 5 0.22
ACGTcount: A:0.62, C:0.28, G:0.10, T:0.00
Consensus pattern (14 bp):
AAACCGAAAAACCG
Found at i:2167 original size:14 final size:15
Alignment explanation
Indices: 2144--2182 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
2134 ACCAAAATAA
2144 AAACCG-AAAAACC-
1 AAACCGAAAAAACCG
2157 AAACCGAAAAAACCG
1 AAACCGAAAAAACCG
*
2172 ACACCGAAAAA
1 AAACCGAAAAA
2183 TGAGCAGCCC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 6 0.26
14 7 0.30
15 10 0.43
ACGTcount: A:0.62, C:0.28, G:0.10, T:0.00
Consensus pattern (15 bp):
AAACCGAAAAAACCG
Found at i:5962 original size:71 final size:71
Alignment explanation
Indices: 5846--5977 Score: 264
Period size: 71 Copynumber: 1.9 Consensus size: 71
5836 AGGTGCCTTT
5846 TGTGATTATAATCAAACTTTTTTTTAATGATATTTTGGAAGTTGTAGCGGGTCTTAATTTATCTT
1 TGTGATTATAATCAAACTTTTTTTTAATGATATTTTGGAAGTTGTAGCGGGTCTTAATTTATCTT
5911 GTGAGG
66 GTGAGG
5917 TGTGATTATAATCAAACTTTTTTTTAATGATATTTTGGAAGTTGTAGCGGGTCTTAATTTA
1 TGTGATTATAATCAAACTTTTTTTTAATGATATTTTGGAAGTTGTAGCGGGTCTTAATTTA
5978 AAAAATTAAT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 61 1.00
ACGTcount: A:0.27, C:0.07, G:0.20, T:0.47
Consensus pattern (71 bp):
TGTGATTATAATCAAACTTTTTTTTAATGATATTTTGGAAGTTGTAGCGGGTCTTAATTTATCTT
GTGAGG
Found at i:6036 original size:29 final size:28
Alignment explanation
Indices: 5984--6059 Score: 118
Period size: 29 Copynumber: 2.7 Consensus size: 28
5974 TTTAAAAAAT
*
5984 TAATAAATAG-TTTTTGTTTTGGCCAAC
1 TAATAAATAGTTTTTTTTTTTGGCCAAC
6011 TAATAAATAGTTTTTTTTTCTTGGCCAAC
1 TAATAAATAGTTTTTTTTT-TTGGCCAAC
*
6040 TAAGAAATAGTTTTTTTTTT
1 TAATAAATAGTTTTTTTTTT
6060 CATAAAACTA
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
27 10 0.22
28 8 0.18
29 27 0.60
ACGTcount: A:0.29, C:0.09, G:0.12, T:0.50
Consensus pattern (28 bp):
TAATAAATAGTTTTTTTTTTTGGCCAAC
Found at i:13636 original size:51 final size:51
Alignment explanation
Indices: 13580--13684 Score: 210
Period size: 51 Copynumber: 2.1 Consensus size: 51
13570 CAAGTTAATA
13580 ATTAGAAGTTGTTTGAGTCGATCCTTTTTTGCACTTAATCAAAATACTATC
1 ATTAGAAGTTGTTTGAGTCGATCCTTTTTTGCACTTAATCAAAATACTATC
13631 ATTAGAAGTTGTTTGAGTCGATCCTTTTTTGCACTTAATCAAAATACTATC
1 ATTAGAAGTTGTTTGAGTCGATCCTTTTTTGCACTTAATCAAAATACTATC
13682 ATT
1 ATT
13685 TCACTTACAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (51 bp):
ATTAGAAGTTGTTTGAGTCGATCCTTTTTTGCACTTAATCAAAATACTATC
Found at i:14890 original size:42 final size:43
Alignment explanation
Indices: 14831--14916 Score: 165
Period size: 42 Copynumber: 2.0 Consensus size: 43
14821 CCAGTTCAAT
14831 ATTTATTTGCTTAGACTAATCAG-CCCATCCAAGTGAAGAAAC
1 ATTTATTTGCTTAGACTAATCAGCCCCATCCAAGTGAAGAAAC
14873 ATTTATTTGCTTAGACTAATCAGCCCCATCCAAGTGAAGAAAC
1 ATTTATTTGCTTAGACTAATCAGCCCCATCCAAGTGAAGAAAC
14916 A
1 A
14917 GTCTCTAGTA
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 23 0.53
43 20 0.47
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (43 bp):
ATTTATTTGCTTAGACTAATCAGCCCCATCCAAGTGAAGAAAC
Found at i:15151 original size:28 final size:28
Alignment explanation
Indices: 15118--15173 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
15108 AAGACGATAT
*
15118 CCCCTCAATAAGACGACCTTCATATGAA
1 CCCCTCAATAAGACGACCTCCATATGAA
15146 CCCCTCAATAAGACGACCTCCATATGAA
1 CCCCTCAATAAGACGACCTCCATATGAA
15174 ATGAAATTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.36, C:0.34, G:0.11, T:0.20
Consensus pattern (28 bp):
CCCCTCAATAAGACGACCTCCATATGAA
Found at i:21937 original size:7 final size:8
Alignment explanation
Indices: 21921--21945 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
21911 ACTTAAACCC
21921 AAAATAAA
1 AAAATAAA
21929 AAAATAAA
1 AAAATAAA
21937 AAAATAAA
1 AAAATAAA
21945 A
1 A
21946 TGAAAATGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAATAAA
Found at i:23630 original size:35 final size:35
Alignment explanation
Indices: 23584--23653 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
23574 TAAGCAATTT
23584 ATAACTTCGTCAATTAAGGTTGCCTTTGATAACTA
1 ATAACTTCGTCAATTAAGGTTGCCTTTGATAACTA
23619 ATAACTTCGTCAATTAAGGTTGCCTTTGATAACTA
1 ATAACTTCGTCAATTAAGGTTGCCTTTGATAACTA
23654 TGTGTGTTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.37
Consensus pattern (35 bp):
ATAACTTCGTCAATTAAGGTTGCCTTTGATAACTA
Found at i:24408 original size:17 final size:17
Alignment explanation
Indices: 24356--24412 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
24346 AACCCATGTA
*
24356 ATCTTTGATCAC-CGGTG
1 ATCTTAGATCACTC-GTG
24373 ATCTT-GCATCACT-GATG
1 ATCTTAG-ATCACTCG-TG
24390 ATCTTAGATCACTCGTG
1 ATCTTAGATCACTCGTG
24407 AT-TTAG
1 ATCTTAG
24413 GGGGTGATCC
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
16 6 0.17
17 27 0.77
18 2 0.06
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (17 bp):
ATCTTAGATCACTCGTG
Found at i:26639 original size:8 final size:9
Alignment explanation
Indices: 26607--26638 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
26597 TTTTTTTAAA
26607 AAAAAATTT
1 AAAAAATTT
26616 AAAAAATTT
1 AAAAAATTT
26625 AAAAAATTT
1 AAAAAATTT
26634 AAAAA
1 AAAAA
26639 TGGCCTAGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (9 bp):
AAAAAATTT
Found at i:26830 original size:26 final size:26
Alignment explanation
Indices: 26801--26868 Score: 118
Period size: 26 Copynumber: 2.6 Consensus size: 26
26791 TACTTAGTTT
*
26801 ATTAGTTTATGTTTAATTAATATTTA
1 ATTAGTTTATGATTAATTAATATTTA
*
26827 ATTAGTTTATGATTAATTAGTATTTA
1 ATTAGTTTATGATTAATTAATATTTA
26853 ATTAGTTTATGATTAA
1 ATTAGTTTATGATTAA
26869 AATGAAGGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.54
Consensus pattern (26 bp):
ATTAGTTTATGATTAATTAATATTTA
Found at i:26844 original size:15 final size:15
Alignment explanation
Indices: 26824--26868 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
26814 TAATTAATAT
26824 TTAATTAGTTTATGA
1 TTAATTAGTTTATGA
26839 TTAATTAG--TAT--
1 TTAATTAGTTTATGA
26850 TTAATTAGTTTATGA
1 TTAATTAGTTTATGA
26865 TTAA
1 TTAA
26869 AATGAAGGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
11 8 0.31
13 6 0.23
15 12 0.46
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (15 bp):
TTAATTAGTTTATGA
Found at i:26920 original size:10 final size:10
Alignment explanation
Indices: 26905--26930 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
26895 TGTTAGAAAT
26905 GAAGTTTGAA
1 GAAGTTTGAA
26915 GAAGTTTGAA
1 GAAGTTTGAA
26925 GAAGTT
1 GAAGTT
26931 GTTAGAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (10 bp):
GAAGTTTGAA
Found at i:27041 original size:21 final size:21
Alignment explanation
Indices: 27017--27060 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
27007 CAAAACTGTA
*
27017 AAAAGGGGGGCGGTATTTAGC
1 AAAAGGAGGGCGGTATTTAGC
*
27038 AAAAGGAGGGCGGTGTTTAGC
1 AAAAGGAGGGCGGTATTTAGC
27059 AA
1 AA
27061 TCCAGTTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.32, C:0.09, G:0.41, T:0.18
Consensus pattern (21 bp):
AAAAGGAGGGCGGTATTTAGC
Found at i:42090 original size:1 final size:1
Alignment explanation
Indices: 42084--42125 Score: 84
Period size: 1 Copynumber: 42.0 Consensus size: 1
42074 ACCAAATGGG
42084 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
42126 GCTTATATTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:43782 original size:1 final size:1
Alignment explanation
Indices: 43778--43803 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
43768 TGAAAAATGG
43778 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
43804 CTGAAGTACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:44435 original size:27 final size:27
Alignment explanation
Indices: 44405--44456 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
44395 TTGCCACTGT
* *
44405 ACTAAATGCAGAGCCAGTAAGGTTAGC
1 ACTAAATGCAGACCCAATAAGGTTAGC
* *
44432 ACTATATGTAGACCCAATAAGGTTA
1 ACTAAATGCAGACCCAATAAGGTTA
44457 ACCTGTGGTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.23
Consensus pattern (27 bp):
ACTAAATGCAGACCCAATAAGGTTAGC
Found at i:45497 original size:27 final size:27
Alignment explanation
Indices: 45462--45517 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
45452 GTAATACTTT
*
45462 TTTTTGAGGTAATCAAAATTATTATAC
1 TTTTTGAGGAAATCAAAATTATTATAC
45489 TTTTTGAGGAAATCAAAATTATTATAC
1 TTTTTGAGGAAATCAAAATTATTATAC
45516 TT
1 TT
45518 GAATGCATGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.38, C:0.07, G:0.11, T:0.45
Consensus pattern (27 bp):
TTTTTGAGGAAATCAAAATTATTATAC
Done.