Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013145.1 Corchorus olitorius cultivar O-4 contig13178, 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: 11066
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.30
Found at i:110 original size:68 final size:68
Alignment explanation
Indices: 1--282 Score: 449
Period size: 68 Copynumber: 4.1 Consensus size: 68
1 CATCCAAGCAGCAGAGGCTTTCTCACAAGCCAAACTCGTTTCCATACGAGCCAGTTAAGCCTTGG
1 CATCCAAGCAGCAGAGGCTTTCTCACAAGCCAAACTCGTTTCCATACGAGCCAGTTAAGCCTTGG
66 TTC
66 TTC
* * *
69 CATCCAAGCAGCAGGGGCTTTCTCGCAAGCCAAACTCGTTTCCATATGAGCCAGTTAAGCCTTGG
1 CATCCAAGCAGCAGAGGCTTTCTCACAAGCCAAACTCGTTTCCATACGAGCCAGTTAAGCCTTGG
134 TTC
66 TTC
* * *
137 CATCCAAGCAGCAGAGGCTTTCACACAAACCAAACTCGTTTCCATACGAGCTAGTTAAGCCTTGG
1 CATCCAAGCAGCAGAGGCTTTCTCACAAGCCAAACTCGTTTCCATACGAGCCAGTTAAGCCTTGG
202 TTC
66 TTC
* * ** *
205 CATCCAAGCAGCAGGGGCTTT-TCCACAAGTCAAACTCGTTTCCATACGAATCAGTTTAGCCTTG
1 CATCCAAGCAGCAGAGGCTTTCT-CACAAGCCAAACTCGTTTCCATACGAGCCAGTTAAGCCTTG
269 GTTC
65 GTTC
273 CATCCAAGCA
1 CATCCAAGCA
283 TCCAGGGGTT
Statistics
Matches: 196, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
68 196 1.00
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.24
Consensus pattern (68 bp):
CATCCAAGCAGCAGAGGCTTTCTCACAAGCCAAACTCGTTTCCATACGAGCCAGTTAAGCCTTGG
TTC
Found at i:454 original size:35 final size:35
Alignment explanation
Indices: 415--504 Score: 117
Period size: 39 Copynumber: 2.5 Consensus size: 35
405 TTCAAATCCT
415 CAGGTCACCTTTCAATTATCAAAGTTGACTGGAAA
1 CAGGTCACCTTTCAATTATCAAAGTTGACTGGAAA
*
450 CAGGTCATCTTTTCAGTAATTATCAAAGTTGACTGGAAA
1 CAGGTCA-CCTTTC---AATTATCAAAGTTGACTGGAAA
* *
489 CATGTCATCTTTCAAT
1 CAGGTCACCTTTCAAT
505 AGTTATCAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
35 10 0.21
36 5 0.11
38 4 0.09
39 28 0.60
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (35 bp):
CAGGTCACCTTTCAATTATCAAAGTTGACTGGAAA
Found at i:511 original size:38 final size:39
Alignment explanation
Indices: 428--516 Score: 144
Period size: 39 Copynumber: 2.3 Consensus size: 39
418 GTCACCTTTC
*
428 AATTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGT
1 AATTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAAT
*
467 AATTATCAAAGTTGACTGGAAACATGTCATC-TTTCAAT
1 AATTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAAT
*
505 AGTTATCAAAGT
1 AATTATCAAAGT
517 GTAGACACCC
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
38 17 0.36
39 30 0.64
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.34
Consensus pattern (39 bp):
AATTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAAT
Found at i:2897 original size:21 final size:22
Alignment explanation
Indices: 2873--2914 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
2863 TTTGCCTCAT
2873 GCATTCATTCAT-CATGCCATG
1 GCATTCATTCATGCATGCCATG
*
2894 GCATTCATTCATGCATTCCAT
1 GCATTCATTCATGCATGCCAT
2915 TAAAGCCTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.24, C:0.29, G:0.12, T:0.36
Consensus pattern (22 bp):
GCATTCATTCATGCATGCCATG
Found at i:5382 original size:12 final size:13
Alignment explanation
Indices: 5358--5413 Score: 58
Period size: 15 Copynumber: 3.9 Consensus size: 13
5348 CTCCATCAAG
5358 AAATTCAAAAAAA
1 AAATTCAAAAAAA
5371 AAATTCAAAAAAAAA
1 AAATTC--AAAAAAA
5386 GAAATTCAAAAAAA
1 -AAATTCAAAAAAA
*
5400 TCAAAATCAAAAAA
1 --AAATTCAAAAAA
5414 TCAAATCAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
13 6 0.16
14 7 0.19
15 18 0.49
16 6 0.16
ACGTcount: A:0.75, C:0.09, G:0.02, T:0.14
Consensus pattern (13 bp):
AAATTCAAAAAAA
Found at i:5385 original size:16 final size:16
Alignment explanation
Indices: 5364--5413 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
5354 CAAGAAATTC
5364 AAAAAAAAAATTCAAA
1 AAAAAAAAAATTCAAA
*
5380 AAAAAAGAAATTCAAA
1 AAAAAAAAAATTCAAA
**
5396 AAAATCAAAA-TCAAA
1 AAAAAAAAAATTCAAA
5411 AAA
1 AAA
5414 TCAAATCAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.78, C:0.08, G:0.02, T:0.12
Consensus pattern (16 bp):
AAAAAAAAAATTCAAA
Found at i:5397 original size:29 final size:30
Alignment explanation
Indices: 5355--5413 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
5345 CCACTCCATC
*
5355 AAGAAATTCAAAAAAA-AAATTCAAAAAAA
1 AAGAAATTCAAAAAAACAAAATCAAAAAAA
5384 AAGAAATTCAAAAAAATCAAAATCAAAAAA
1 AAGAAATTCAAAAAAA-CAAAATCAAAAAA
5414 TCAAATCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 16 0.59
31 11 0.41
ACGTcount: A:0.75, C:0.08, G:0.03, T:0.14
Consensus pattern (30 bp):
AAGAAATTCAAAAAAACAAAATCAAAAAAA
Found at i:5419 original size:13 final size:14
Alignment explanation
Indices: 5394--5423 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
5384 AAGAAATTCA
5394 AAAAAATCAAAATC
1 AAAAAATCAAAATC
5408 AAAAAATC-AAATC
1 AAAAAATCAAAATC
5421 AAA
1 AAA
5424 GTCAATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.73, C:0.13, G:0.00, T:0.13
Consensus pattern (14 bp):
AAAAAATCAAAATC
Found at i:5438 original size:19 final size:18
Alignment explanation
Indices: 5393--5439 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
5383 AAAGAAATTC
5393 AAAAAAATCAAAATCAAA
1 AAAAAAATCAAAATCAAA
* *
5411 AAATCAAATCAAAGTCAATA
1 AAA-AAAATCAAAATCAA-A
5431 AAAAAAATC
1 AAAAAAATC
5440 GAATCAAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 3 0.12
19 17 0.71
20 4 0.17
ACGTcount: A:0.70, C:0.13, G:0.02, T:0.15
Consensus pattern (18 bp):
AAAAAAATCAAAATCAAA
Found at i:6171 original size:50 final size:50
Alignment explanation
Indices: 6092--6238 Score: 267
Period size: 50 Copynumber: 2.9 Consensus size: 50
6082 AGTTTTACAA
6092 TAAAATTGCTTTCCATTTATGAGTCCAAGATCAAAATTCGCTTTTCAGAG
1 TAAAATTGCTTTCCATTTATGAGTCCAAGATCAAAATTCGCTTTTCAGAG
*
6142 TAAAATTGCTTTCCATTTATGAGTTCAAGATCAAAATTCGCTTTTCAGAG
1 TAAAATTGCTTTCCATTTATGAGTCCAAGATCAAAATTCGCTTTTCAGAG
* *
6192 TAAAATTGCTTTCCATTTGTAAGTCCAAGATCAAAATTCGCTTTTCA
1 TAAAATTGCTTTCCATTTATGAGTCCAAGATCAAAATTCGCTTTTCA
6239 AAGGGCATTT
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 93 1.00
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (50 bp):
TAAAATTGCTTTCCATTTATGAGTCCAAGATCAAAATTCGCTTTTCAGAG
Found at i:6805 original size:91 final size:91
Alignment explanation
Indices: 6648--6864 Score: 362
Period size: 91 Copynumber: 2.4 Consensus size: 91
6638 CAACCCAGAG
* **
6648 GTTTTCAGTTACAACATCAGACTCAGAGTTATCTTTCAAGTTCTCTTTCAAGTTGACTGCAAATT
1 GTTTTCAGTTACAACATCAGACTCAGAGTTATTTTTCAAGTTCTCTTTCAAGTTGACCACAAATT
6713 GGTCCTCTTTCATCATCAATCAAGAA
66 GGTCCTCTTTCATCATCAATCAAGAA
* * *
6739 GTTTTCAGTTACAACATCAGACTCAGAGTTATTTTTCAAGTTGTTTTTCAAGTTGACCACACATT
1 GTTTTCAGTTACAACATCAGACTCAGAGTTATTTTTCAAGTTCTCTTTCAAGTTGACCACAAATT
*
6804 GGTCCTTTTTCATCATCAATCAAGAA
66 GGTCCTCTTTCATCATCAATCAAGAA
*
6830 GTTTTCAGTTACAACATCAGATTCAGAGTTATTTT
1 GTTTTCAGTTACAACATCAGACTCAGAGTTATTTT
6865 CCAAAGGTAT
Statistics
Matches: 118, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
91 118 1.00
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (91 bp):
GTTTTCAGTTACAACATCAGACTCAGAGTTATTTTTCAAGTTCTCTTTCAAGTTGACCACAAATT
GGTCCTCTTTCATCATCAATCAAGAA
Found at i:7168 original size:50 final size:50
Alignment explanation
Indices: 7040--7274 Score: 373
Period size: 50 Copynumber: 4.7 Consensus size: 50
7030 CGGTGCATTA
*
7040 CCTTTTAAGATTGCATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGT
1 CCTTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGT
* *
7090 CCTTTTTAAGGTTGAATTGGTAGACAGTTCAAAGGATAAGCTGAAGACGGT
1 CC-TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGT
7141 CCTTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGT
1 CCTTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGT
* *
7191 CCTTTTAAGATTGAATTGGTAGACGGTTCAATGGATAAGCGGAAGACGGT
1 CCTTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGT
* *
7241 CCTTTTTAATATT-AGATTGGAAGACAGTTCAAAG
1 CC-TTTTAAGATTGA-ATTGGTAGACAGTTCAAAG
7275 AAGTTGATCG
Statistics
Matches: 171, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
50 99 0.58
51 72 0.42
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.29
Consensus pattern (50 bp):
CCTTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGT
Found at i:7248 original size:101 final size:101
Alignment explanation
Indices: 7040--7274 Score: 375
Period size: 101 Copynumber: 2.3 Consensus size: 101
7030 CGGTGCATTA
* *
7040 CCTTTTAAGATTGCATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTTAAGGTTGA
1 CCTTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTTAAGATTGA
*
7105 ATTGGTAGACAGTTCAAAGGATAAGCTGAAGACGGT
66 ATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGT
7141 CCTTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC-TTTTAAGATTGA
1 CCTTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTTAAGATTGA
* *
7205 ATTGGTAGACGGTTCAATGGATAAGCGGAAGACGGT
66 ATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGT
* *
7241 CCTTTTTAATATT-AGATTGGAAGACAGTTCAAAG
1 CC-TTTTAAGATTGA-ATTGGTAGACAGTTCAAAG
7275 AAGTTGATCG
Statistics
Matches: 125, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
100 47 0.38
101 78 0.62
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.29
Consensus pattern (101 bp):
CCTTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTTAAGATTGA
ATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGT
Done.