Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023026.1 Corchorus olitorius cultivar O-4 contig23059, 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: 33871
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:1442 original size:72 final size:72
Alignment explanation
Indices: 1325--1468 Score: 279
Period size: 72 Copynumber: 2.0 Consensus size: 72
1315 TGATTAACTT
1325 ACAGCCAATGCAATATCTTCTTACTAACCAACTTAAACAACTACAAAAACTATAACCTTAATAAG
1 ACAGCCAATGCAATATCTTCTTACTAACCAACTTAAACAACTACAAAAACTATAACCTTAATAAG
1390 AAATTGA
66 AAATTGA
1397 ACAGCCAATGCAATATCTTCTTACTAACCAACTTAAACAACTACAAAAACTATAACCTTAATAAG
1 ACAGCCAATGCAATATCTTCTTACTAACCAACTTAAACAACTACAAAAACTATAACCTTAATAAG
*
1462 AAGTTGA
66 AAATTGA
1469 TTGCAGCGCA
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.47, C:0.22, G:0.06, T:0.25
Consensus pattern (72 bp):
ACAGCCAATGCAATATCTTCTTACTAACCAACTTAAACAACTACAAAAACTATAACCTTAATAAG
AAATTGA
Found at i:1815 original size:11 final size:11
Alignment explanation
Indices: 1799--1825 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1789 GTTACTCAGC
1799 TTTTATGACAA
1 TTTTATGACAA
1810 TTTTATGACAA
1 TTTTATGACAA
1821 TTTTA
1 TTTTA
1826 AAATATGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.52
Consensus pattern (11 bp):
TTTTATGACAA
Found at i:9613 original size:30 final size:30
Alignment explanation
Indices: 9574--9632 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
9564 AAGTTGGTTG
*
9574 AAAATATTATTAATGGGTATTTCCATCACA
1 AAAAAATTATTAATGGGTATTTCCATCACA
* *
9604 AAAAAATTATTAGTGGGTATTTTCATCAC
1 AAAAAATTATTAATGGGTATTTCCATCAC
9633 TAATATAGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (30 bp):
AAAAAATTATTAATGGGTATTTCCATCACA
Found at i:11846 original size:2 final size:2
Alignment explanation
Indices: 11834--11873 Score: 71
Period size: 2 Copynumber: 19.5 Consensus size: 2
11824 TGTATTCTCT
11834 TA TA GTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11874 TTTAATAGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12396 original size:31 final size:31
Alignment explanation
Indices: 12358--12432 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
12348 ACGATGACAG
*
12358 AACTGGTCATTCTCCAGTCTTGTCGCTGAAT
1 AACTGGTCATTCTCCAGTCTTGTCGCGGAAT
* *
12389 AACTGGTCATGT-TCCAGTCTTTTCGCGGCAT
1 AACTGGTCAT-TCTCCAGTCTTGTCGCGGAAT
*
12420 AATTGGTCCATTC
1 AACTGGT-CATTC
12433 CAGTTTTGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
31 33 0.89
32 4 0.11
ACGTcount: A:0.19, C:0.25, G:0.20, T:0.36
Consensus pattern (31 bp):
AACTGGTCATTCTCCAGTCTTGTCGCGGAAT
Found at i:15206 original size:25 final size:24
Alignment explanation
Indices: 15151--15205 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 24
15141 ATAGGTACGT
15151 AAAAAAGCTGTATTGGAATGTAGCA
1 AAAAAAGCTGTATTGGAATG-AGCA
15176 AAAAAAGCTGTATTGGATATG-GCA
1 AAAAAAGCTGTATTGGA-ATGAGCA
15200 AAAAAA
1 AAAAAA
15206 AAGGATTGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
24 9 0.31
25 17 0.59
26 3 0.10
ACGTcount: A:0.49, C:0.07, G:0.22, T:0.22
Consensus pattern (24 bp):
AAAAAAGCTGTATTGGAATGAGCA
Found at i:16889 original size:19 final size:19
Alignment explanation
Indices: 16865--16901 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
16855 ATAAAAAAAA
16865 ACCTCATTTGTTTTTATGC
1 ACCTCATTTGTTTTTATGC
16884 ACCTCATTTGTTTTTATG
1 ACCTCATTTGTTTTTATG
16902 TACACAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.16, C:0.19, G:0.11, T:0.54
Consensus pattern (19 bp):
ACCTCATTTGTTTTTATGC
Found at i:17298 original size:4 final size:4
Alignment explanation
Indices: 17289--17323 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
17279 CTGTTATTAG
17289 TTCT TTCT TTCT TTCT TT-T TT-T TTCT TTCT TTCT T
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT T
17324 CTATGTATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 6 0.20
4 24 0.80
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (4 bp):
TTCT
Found at i:20764 original size:34 final size:32
Alignment explanation
Indices: 20711--20779 Score: 111
Period size: 34 Copynumber: 2.1 Consensus size: 32
20701 GTGAAAAATG
20711 AAATGGGAAATCAAGTAGATAGCAAAAGAGAA
1 AAATGGGAAATCAAGTAGATAGCAAAAGAGAA
*
20743 AAATGTGGAAAATTAAGTAGATAGCAAAAGAGAA
1 AAATG-GG-AAATCAAGTAGATAGCAAAAGAGAA
20777 AAA
1 AAA
20780 GAAAAAGGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
32 5 0.15
33 2 0.06
34 27 0.79
ACGTcount: A:0.58, C:0.04, G:0.23, T:0.14
Consensus pattern (32 bp):
AAATGGGAAATCAAGTAGATAGCAAAAGAGAA
Found at i:21992 original size:16 final size:16
Alignment explanation
Indices: 21971--22003 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
21961 AACAAGGCTT
21971 TACTGGTACTACGAGA
1 TACTGGTACTACGAGA
*
21987 TACTGGTACTATGAGA
1 TACTGGTACTACGAGA
22003 T
1 T
22004 TTTAATGGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.30
Consensus pattern (16 bp):
TACTGGTACTACGAGA
Found at i:23505 original size:36 final size:33
Alignment explanation
Indices: 23430--23506 Score: 84
Period size: 33 Copynumber: 2.2 Consensus size: 33
23420 GAGCAGTTGC
*
23430 AGAGGGAGAGAGAGGCTGAGGCTGCTCGGATTT
1 AGAGGGAGAGAGAGGCTGAGGCTGCTCAGATTT
* *
23463 ATAGGGAGAGGGAGGCTGATGCTGCTGCTCAGAGTTT
1 AGAGGGAGAGAGAGGCTGA-G--GCTGCTCAGA-TTT
23500 -GAGGGAG
1 AGAGGGAG
23507 CAAACGGAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
33 17 0.47
34 1 0.03
36 15 0.42
37 3 0.08
ACGTcount: A:0.23, C:0.12, G:0.45, T:0.19
Consensus pattern (33 bp):
AGAGGGAGAGAGAGGCTGAGGCTGCTCAGATTT
Found at i:30995 original size:12 final size:12
Alignment explanation
Indices: 30978--31012 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
30968 ATATATCAGC
*
30978 TGCTGTTGCTGT
1 TGCTGTTGCGGT
30990 TGCTGTTGCGGT
1 TGCTGTTGCGGT
*
31002 TGCGGTTGCGG
1 TGCTGTTGCGG
31013 AAGAAGCTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.00, C:0.17, G:0.43, T:0.40
Consensus pattern (12 bp):
TGCTGTTGCGGT
Found at i:33463 original size:41 final size:41
Alignment explanation
Indices: 33416--33516 Score: 202
Period size: 41 Copynumber: 2.5 Consensus size: 41
33406 TAAGTCTTTG
33416 ATAAATGGGCCGGGCTTGGACAAAAGTTTGAGGCCCGTTTT
1 ATAAATGGGCCGGGCTTGGACAAAAGTTTGAGGCCCGTTTT
33457 ATAAATGGGCCGGGCTTGGACAAAAGTTTGAGGCCCGTTTT
1 ATAAATGGGCCGGGCTTGGACAAAAGTTTGAGGCCCGTTTT
33498 ATAAATGGGCCGGGCTTGG
1 ATAAATGGGCCGGGCTTGG
33517 GCAACACTAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 60 1.00
ACGTcount: A:0.24, C:0.17, G:0.34, T:0.26
Consensus pattern (41 bp):
ATAAATGGGCCGGGCTTGGACAAAAGTTTGAGGCCCGTTTT
Done.