Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008099.1 Corchorus capsularis cultivar CVL-1 contig08120, 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: 68637
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:723 original size:19 final size:19
Alignment explanation
Indices: 699--736 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
689 TGGGTTGCTC
699 CTATTCCCAGATAGGATAA
1 CTATTCCCAGATAGGATAA
**
718 CTATTCCCATCTAGGATAA
1 CTATTCCCAGATAGGATAA
737 AAATAACAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.34, C:0.24, G:0.13, T:0.29
Consensus pattern (19 bp):
CTATTCCCAGATAGGATAA
Found at i:15468 original size:10 final size:10
Alignment explanation
Indices: 15455--15490 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
15445 AAATCTCGAT
15455 ATATCCGTAA
1 ATATCCGTAA
15465 ATATCCGTAA
1 ATATCCGTAA
*
15475 ATATCCATAA
1 ATATCCGTAA
15485 ATATCC
1 ATATCC
15491 ATATTAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.42, C:0.22, G:0.06, T:0.31
Consensus pattern (10 bp):
ATATCCGTAA
Found at i:16093 original size:3 final size:3
Alignment explanation
Indices: 16081--16122 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
16071 GCTCACGGAA
16081 GAT G-T GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
16123 GGGAAATGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.31, C:0.00, G:0.36, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:17221 original size:13 final size:12
Alignment explanation
Indices: 17191--17233 Score: 68
Period size: 12 Copynumber: 3.5 Consensus size: 12
17181 CATCGATACC
*
17191 TCGATATATTCG
1 TCGATATATCCG
17203 TCGATATATCCG
1 TCGATATATCCG
17215 TTCGATATATCCG
1 -TCGATATATCCG
17228 TCGATA
1 TCGATA
17234 CCTGTATTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 17 0.59
13 12 0.41
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (12 bp):
TCGATATATCCG
Found at i:27366 original size:4 final size:4
Alignment explanation
Indices: 27357--27385 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
27347 GAAGAAGGAG
27357 AAAT AAAT AAA- AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
27386 TGAACCTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:27373 original size:11 final size:12
Alignment explanation
Indices: 27357--27385 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
27347 GAAGAAGGAG
27357 AAATAAATAAA-
1 AAATAAATAAAT
27368 AAATAAATAAAT
1 AAATAAATAAAT
27380 AAATAA
1 AAATAA
27386 TGAACCTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (12 bp):
AAATAAATAAAT
Found at i:28274 original size:14 final size:13
Alignment explanation
Indices: 28243--28307 Score: 58
Period size: 13 Copynumber: 4.8 Consensus size: 13
28233 AATATATTAA
*
28243 AAATAAATATAAAT
1 AAATAAATA-AAAG
28257 AAATAAATAAAACG
1 AAATAAATAAAA-G
*
28271 AAATTAAAAAAAAG
1 AAA-TAAATAAAAG
* * *
28285 AAAGAAATACAAT
1 AAATAAATAAAAG
28298 AAATAAATAA
1 AAATAAATAA
28308 CGCTGAATTT
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
13 17 0.41
14 16 0.39
15 8 0.20
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.18
Consensus pattern (13 bp):
AAATAAATAAAAG
Found at i:35548 original size:11 final size:11
Alignment explanation
Indices: 35532--35556 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
35522 TCACTTCAAG
35532 TAATGATATTT
1 TAATGATATTT
35543 TAATGATATTT
1 TAATGATATTT
35554 TAA
1 TAA
35557 GGTTCCCAAG
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:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (11 bp):
TAATGATATTT
Found at i:39091 original size:2 final size:2
Alignment explanation
Indices: 39084--39109 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
39074 AGCAAGGATG
39084 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
39110 GCTTTGATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57126 original size:182 final size:182
Alignment explanation
Indices: 56901--57264 Score: 613
Period size: 182 Copynumber: 2.0 Consensus size: 182
56891 ACCAAAACAA
*
56901 TTTTTTAACATATTCAGGGTGGCATTAGATGAAGTCTTAGAAAACATGTGCAACTACATATTGCA
1 TTTTTTAACATATTCAGGGTGGCATTAGATGAAGTCTTAGAAAACATGTGCAACTACAAATTGCA
* *
56966 CAGAATCAGCATTCGAACAAAAGAAC-AGGCTAATGAAAAAGCAATCAACGTTCTAGGAAGTCAC
66 CAGAATCAGCATCCAAACAAAAGAACTA-GCTAATGAAAAAGCAATCAACGTTCTAGGAAGTCAC
* *
57030 CCTACAATGCTTCATAGTCAACATCAGACTGTAACACAAACATCTGTTTCTAG
130 CCTACAATGCTTCATAGTCAACATCAGACTGCAACACAAACATCTATTTCTAG
57083 TTTTTTAACATATTCAGGGTGGCATTAGATGAAGTCTTAGAAAACATGTGCAACTACAAATTGCA
1 TTTTTTAACATATTCAGGGTGGCATTAGATGAAGTCTTAGAAAACATGTGCAACTACAAATTGCA
* *
57148 CAGAATCAGCATCCAAACAAAAGAACTAGCTAATGAAATAGCAATCAACGTTCTAGGAAGTTACC
66 CAGAATCAGCATCCAAACAAAAGAACTAGCTAATGAAAAAGCAATCAACGTTCTAGGAAGTCACC
* * * *
57213 CTACAATGCTTCATAGTTAATATCAGATTGCAGCACAAACATCTATTTCTAG
131 CTACAATGCTTCATAGTCAACATCAGACTGCAACACAAACATCTATTTCTAG
57265 GCCAACTCAT
Statistics
Matches: 170, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
182 169 0.99
183 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.27
Consensus pattern (182 bp):
TTTTTTAACATATTCAGGGTGGCATTAGATGAAGTCTTAGAAAACATGTGCAACTACAAATTGCA
CAGAATCAGCATCCAAACAAAAGAACTAGCTAATGAAAAAGCAATCAACGTTCTAGGAAGTCACC
CTACAATGCTTCATAGTCAACATCAGACTGCAACACAAACATCTATTTCTAG
Found at i:66510 original size:16 final size:17
Alignment explanation
Indices: 66489--66520 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
66479 TTTTTTTTCT
66489 TTATTATATA-ATAATA
1 TTATTATATATATAATA
66505 TTATTATATATATAAT
1 TTATTATATATATAAT
66521 GGGTAGACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTATTATATATATAATA
Done.