Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022933.1 Corchorus olitorius cultivar O-4 contig22966, 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: 66434
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:5956 original size:13 final size:12
Alignment explanation
Indices: 5938--5966 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
5928 CTTCAACTCG
5938 AAAAAAAAAAAC
1 AAAAAAAAAAAC
5950 AAAAAAAAAAAC
1 AAAAAAAAAAAC
5962 AAAAA
1 AAAAA
5967 CTTACCTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAC
Found at i:8914 original size:20 final size:20
Alignment explanation
Indices: 8883--8923 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
8873 TATCATTTTG
8883 TAAAAAATAAAAATTGTATTT
1 TAAAAAATAAAAATTG-ATTT
8904 TAAAAAA-AAAAATTGATTT
1 TAAAAAATAAAAATTGATTT
8923 T
1 T
8924 TCGTTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 5 0.25
20 8 0.40
21 7 0.35
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.37
Consensus pattern (20 bp):
TAAAAAATAAAAATTGATTT
Found at i:8924 original size:20 final size:21
Alignment explanation
Indices: 8877--8924 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
8867 GCCATGTATC
8877 ATTTTGTAAAAAATAAAAATTG
1 ATTTT-TAAAAAATAAAAATTG
8899 -TATTTTAAAAAA-AAAAATTG
1 AT-TTTTAAAAAATAAAAATTG
8919 ATTTTT
1 ATTTTT
8925 CGTTTTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
20 12 0.50
21 9 0.38
22 3 0.12
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (21 bp):
ATTTTTAAAAAATAAAAATTG
Found at i:15376 original size:435 final size:437
Alignment explanation
Indices: 14566--15459 Score: 1275
Period size: 435 Copynumber: 2.1 Consensus size: 437
14556 ATTTTTTTAA
* * * * *
14566 TTTTTTTATTTGTCTGATTAAGGTGATTCAGGTGTCTATTAAAACGTAATTGCATGATTTACAAC
1 TTTTTTTATTTATCCGATTAAGGTGATTCAGGCGTCGATTAAAACGTAATTGCATGATCTACAAC
** * ** *
14631 TTTCATGAAGGACTTAAAAGCCAATTTTTATGTTTCAATTCAAAAAAAAATGCTTCCGAAATTTG
66 TTTCATGAAAAACTCAAAAGCCAATTTTTACATTTCAATTCAAAAAAAAATGCTTCCCAAATTTG
* * *
14696 GTGATTTTGATTGCCGATTTATTTAATATATCATATAATTTTCAATCAACATGTCCGATTAATGT
131 GTGATTTTGATTGCCGATCTATTTAATATACCATATAATTTTCAATCAACATGTCCGATTAAAGT
* * *
14761 TTCTTAAGTGTCGATTAAAAGGTTATTGCATGATCTATGACTTTCATGAAGGACCCGAAAGTTAA
196 ATCTTAAGTGTCGATTAAAAGGTTATTGCATGATCTACGACTTTCATGAAGGACCCGAAAGCTAA
* * *
14826 ATTTGATCTACGAGTTTCATTAAGTGTTCAAAAGGGAATTTTTATGTTTCAAGATCTCCATCAAC
261 ATTTGATCTACAAGTTTCATGAAATGTTCAAAAGGGAATTTTTATGTTTCAAGATCTCCATCAAC
* *
14891 AAACATTTTTTATTTGGATTATTTATGAAATGACCCTCATATTTTTCTACTTTATACTACTTAGT
326 AAACATTTTTTATTTGGATTATTTATCAAATGACCCTCATACTTTTCTACTTTATACTACTTAGT
*
14956 CCATTACTAATTCTATCTTAATCGATTTAACGCTTAAGCTTTATTTT
391 CCATTACAAATTCTATCTTAATCGATTTAACGCTTAAGCTTTATTTT
* * *
15003 TTTTTTCTATTTATCCGATTAAGGTGATTCAGGCGTCGATTAAAAGGTAATTTCATGATCTCCAA
1 TTTTTT-TATTTATCCGATTAAGGTGATTCAGGCGTCGATTAAAACGTAATTGCATGATCTACAA
*
15068 CTTTCATGAAAAACTCAAAAGCCAATTTTTACATTTCAATTCAAAGAAAAATGCTTCCCAAATTT
65 CTTTCATGAAAAACTCAAAAGCCAATTTTTACATTTCAATTCAAAAAAAAATGCTTCCCAAATTT
* * * * * *
15133 GGTGGTTTTGATTGTCGGTCTATTT-A-ATACCATATAATTTT-AGATCCATATGT-GGATTAAA
130 GGTGATTTTGATTGCCGATCTATTTAATATACCATATAATTTTCA-ATCAACATGTCCGATTAAA
* * *
15194 GTAAT-TTAAGTGTCGGTTAAAAGGTTATTGCGTGATCTACGACTTTCATGAAGTACCCGAAAGC
194 GT-ATCTTAAGTGTCGATTAAAAGGTTATTGCATGATCTACGACTTTCATGAAGGACCCGAAAGC
*
15258 TAAATTTGATCTACAAGTTTCATGAAATGTTCAAAAGGGAATTTTTATGTTT-AAGATCTCTATC
258 TAAATTTGATCTACAAGTTTCATGAAATGTTCAAAAGGGAATTTTTATGTTTCAAGATCTCCATC
15322 AACAAACATTTTCTTATTTGGATTATTTATCAAATGACCCTCATACTTTTCTACTTTATACTACT
323 AACAAACATTTT-TTATTTGGATTATTTATCAAATGACCCTCATACTTTTCTACTTTATACTACT
** * *
15387 TAGTCTTTTACAAATTCTATTTTACTCGATTTAACGCTTTAA--TTT-TTTT
387 TAGTCCATTACAAATTCTATCTTAATCGATTTAACGC-TTAAGCTTTATTTT
* *
15436 CTTTGTTTTATTTGTCCAATTAAG
1 -TTT-TTTTATTTATCCGATTAAG
15460 ATAATTCATG
Statistics
Matches: 407, Mismatches: 43, Indels: 17
0.87 0.09 0.04
Matches are distributed among these distances:
433 4 0.01
434 43 0.11
435 197 0.48
436 27 0.07
437 7 0.02
438 129 0.32
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (437 bp):
TTTTTTTATTTATCCGATTAAGGTGATTCAGGCGTCGATTAAAACGTAATTGCATGATCTACAAC
TTTCATGAAAAACTCAAAAGCCAATTTTTACATTTCAATTCAAAAAAAAATGCTTCCCAAATTTG
GTGATTTTGATTGCCGATCTATTTAATATACCATATAATTTTCAATCAACATGTCCGATTAAAGT
ATCTTAAGTGTCGATTAAAAGGTTATTGCATGATCTACGACTTTCATGAAGGACCCGAAAGCTAA
ATTTGATCTACAAGTTTCATGAAATGTTCAAAAGGGAATTTTTATGTTTCAAGATCTCCATCAAC
AAACATTTTTTATTTGGATTATTTATCAAATGACCCTCATACTTTTCTACTTTATACTACTTAGT
CCATTACAAATTCTATCTTAATCGATTTAACGCTTAAGCTTTATTTT
Found at i:17747 original size:14 final size:14
Alignment explanation
Indices: 17728--17762 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
17718 AATTAAGAGG
17728 CATGGCGCCGCTGA
1 CATGGCGCCGCTGA
17742 CATGGCGCCGCTGA
1 CATGGCGCCGCTGA
17756 CATGGCG
1 CATGGCG
17763 TCATATTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.14, C:0.34, G:0.37, T:0.14
Consensus pattern (14 bp):
CATGGCGCCGCTGA
Found at i:29001 original size:54 final size:54
Alignment explanation
Indices: 28919--29021 Score: 179
Period size: 54 Copynumber: 1.9 Consensus size: 54
28909 TTTGACACAG
* *
28919 ACTGCATACCAATATGCTAAAGTTGAAGCAGCGAGTCAAGCAATTTCCTATGGT
1 ACTGCATACCAATATGCTAAAGTCGAAGCAGCAAGTCAAGCAATTTCCTATGGT
*
28973 ACTGCATACCAATATGCTAAAGTCGAAGCAGCAAGTCAAGCACTTTCCT
1 ACTGCATACCAATATGCTAAAGTCGAAGCAGCAAGTCAAGCAATTTCCT
29022 TACTGTTAGT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.24
Consensus pattern (54 bp):
ACTGCATACCAATATGCTAAAGTCGAAGCAGCAAGTCAAGCAATTTCCTATGGT
Found at i:37127 original size:33 final size:33
Alignment explanation
Indices: 37090--37159 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
37080 CTCGCACGCG
* *
37090 GGTCGCAACCGGACCATGGTCAGGTCGCGATTC
1 GGTCGCAACCGGACCATGCTCAGGTCGCGATCC
**
37123 GGTCGGGACCGGACCATGCTCAGGTCGCGATCC
1 GGTCGCAACCGGACCATGCTCAGGTCGCGATCC
37156 GGTC
1 GGTC
37160 ACGACCCGCC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.16, C:0.31, G:0.36, T:0.17
Consensus pattern (33 bp):
GGTCGCAACCGGACCATGCTCAGGTCGCGATCC
Found at i:42050 original size:19 final size:20
Alignment explanation
Indices: 42026--42074 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
42016 ATATTATTAT
*
42026 ATATTTAGAA-TTCTAAATA
1 ATATTTAGAATTTATAAATA
*
42045 ATATTTATAATTTATAAATA
1 ATATTTAGAATTTATAAATA
*
42065 ATTTTTAGAA
1 ATATTTAGAA
42075 CATTGAATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (20 bp):
ATATTTAGAATTTATAAATA
Found at i:45584 original size:19 final size:18
Alignment explanation
Indices: 45550--45592 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
45540 TTTTAAGAAG
45550 GAAAA-GGAAAAAGAAAA
1 GAAAAGGGAAAAAGAAAA
*
45567 TAAAAGGGAAAGAAGAAAA
1 GAAAAGGGAAA-AAGAAAA
45586 GAAAAGG
1 GAAAAGG
45593 AAGAGGAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 4 0.18
18 5 0.23
19 13 0.59
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.02
Consensus pattern (18 bp):
GAAAAGGGAAAAAGAAAA
Found at i:47504 original size:436 final size:434
Alignment explanation
Indices: 46696--47705 Score: 1271
Period size: 436 Copynumber: 2.3 Consensus size: 434
46686 CGCGTTGTGT
* *
46696 TTTATTTTTGTATT-TTTTTTCTATTTGTTCGATTAAGATAATTCAAGTGTCTATTAAAAGGTAA
1 TTTATTTTT-TATTCTTTGTTCTATTTGTCCGATTAAGATAATTCAAGTGTCTATTAAAAGGTAA
* * **
46760 TTTCATGATCTACAATTTTCATTTTCATTAAGAACTCAAAAGTCAATTTTAATGTTTTGATTCTA
65 TTTCATGATCTACAA----C--TTTCATTAAGGACTCAAAAG-CAATTTTTATGTTTCAATTCTA
* * * *
46825 AAAAATGCTTCCGAAATTTTGTGGTTTTGATTGTCGGTTAATTTAATATCGTATAATTTTTTGCC
123 AAAAATGCTTCCGAAATTTTGTGGTTTCGATTGTCGGTTAATTTAATACCATATAATTTTTCGCC
* * * * * *
46890 CACACGTCCGATTGAAGTTATTGAAGTGTCGGTTAAAAGGTTATTGCATGATTTACGACTTTCAT
188 CACACGTCCAATTAAAGTTATTCAAGTGTCGGTTAAAAGGTTATTGCATAATCTACAACTTTCAT
* * *
46955 GAAGGACCCGAAAGCTAAATTTGATCTACGAGTTTCGTGAAGGGTTCAAAAGGGAATTTTTATGT
253 GAAGAACCCGAAAGCTAAATTTGATCTACGAGTTTCATGAACGGTTCAAAAGGGAATTTTTATGT
* *
47020 TTCAAGATCTCCATTAACAAACATTTTCTTATTTGGATTATTTATCAAATGACCCTCATACTTTT
318 TTCAAGATCTCCATTAACAAACATTTTCTTATTTGAATTATTTATCAAATCACCCTCATACTTTT
**
47085 CTACTTTATACTACTTAGTCCTTTACAAATTCTATCTTAATCTAACG-TTCAA-GG
383 CTACTTTATACTACTTAGTCCTTTACAAATTCTATCTT-A-CT--CGATTCAATAC
* * * *
47139 TTTATTTTTTATTCTTTGTTCTATTTGTCCGTTTAAGTTGATTCATGTGTCTATTAAAAGGTAAT
1 TTTATTTTTTATTCTTTGTTCTATTTGTCCGATTAAGATAATTCAAGTGTCTATTAAAAGGTAAT
*
47204 TTCATGATCTACAACTTTCATGAAGGACTCAAAAGCAAATTTTTATGTTTCAATTC-AAAAAAGT
66 TTCATGATCTACAACTTTCATTAAGGACTCAAAAGC-AATTTTTATGTTTCAATTCTAAAAAA-T
* * * *
47268 GCTTCCTAAA-TTTGTTTGTTTCGATTGTTGGTCT-ATTTAATACCATATAA-TTTTCGATCCAC
129 GCTTCCGAAATTTTG-TGGTTTCGATTGTCGGT-TAATTTAATACCATATAATTTTTCG-CCCAC
** * *
47330 GTGTCCAATTAAAGTTATTCAAGTGTCGGTTAAAAGGTTATTGTATAATCTATAACTTTCATGAA
191 ACGTCCAATTAAAGTTATTCAAGTGTCGGTTAAAAGGTTATTGCATAATCTACAACTTTCATGAA
*
47395 GAACCCGAAAG-TTAATTTGATCTACGAGTTTCATGAACGGTTCAAAAGGGAATTTTTATGTTTC
256 GAACCCGAAAGCTAAATTTGATCTACGAGTTTCATGAACGGTTCAAAAGGGAATTTTTATGTTTC
* * *
47459 AAGATCTCCATTAATAAATATTTTCTTATTTGAATTATTTATCAAATCACCTTCATACTTTTCTA
321 AAGATCTCCATTAACAAACATTTTCTTATTTGAATTATTTATCAAATCACCCTCATACTTTTCTA
* * * * * *
47524 TTTTATGCTACTTAGTCCTTTCCAATTTTTATCTTACTCGATTTAATAC
386 CTTTATACTACTTAGTCCTTTACAAATTCTATCTTACTCGATTCAATAC
* * * *
47573 TTCATTTTTTTTATTTCCTTTGTTCTATTTGTCCAATTAAGGTAATTCAGGTGTCTATTAAAAGG
1 TT--TATTTTTTA-TT-CTTTGTTCTATTTGTCCGATTAAGATAATTCAAGTGTCTATTAAAAGG
* * * * *
47638 TAATTTTATAATCTACAACTTTCATTAAAGACTCAAAAGCTAATTTTTATATTTCAATTCTAGAA
62 TAATTTCATGATCTACAACTTTCATTAAGGACTCAAAAGC-AATTTTTATGTTTCAATTCTAAAA
47703 AAT
126 AAT
47706 ACGTTTGAAA
Statistics
Matches: 495, Mismatches: 59, Indels: 31
0.85 0.10 0.05
Matches are distributed among these distances:
432 2 0.00
433 4 0.01
434 4 0.01
435 1 0.00
436 164 0.33
437 143 0.29
438 99 0.20
439 6 0.01
442 4 0.01
443 68 0.14
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.43
Consensus pattern (434 bp):
TTTATTTTTTATTCTTTGTTCTATTTGTCCGATTAAGATAATTCAAGTGTCTATTAAAAGGTAAT
TTCATGATCTACAACTTTCATTAAGGACTCAAAAGCAATTTTTATGTTTCAATTCTAAAAAATGC
TTCCGAAATTTTGTGGTTTCGATTGTCGGTTAATTTAATACCATATAATTTTTCGCCCACACGTC
CAATTAAAGTTATTCAAGTGTCGGTTAAAAGGTTATTGCATAATCTACAACTTTCATGAAGAACC
CGAAAGCTAAATTTGATCTACGAGTTTCATGAACGGTTCAAAAGGGAATTTTTATGTTTCAAGAT
CTCCATTAACAAACATTTTCTTATTTGAATTATTTATCAAATCACCCTCATACTTTTCTACTTTA
TACTACTTAGTCCTTTACAAATTCTATCTTACTCGATTCAATAC
Found at i:56470 original size:61 final size:61
Alignment explanation
Indices: 56375--56498 Score: 212
Period size: 61 Copynumber: 2.0 Consensus size: 61
56365 TGTCTAAATC
* *
56375 TTTATGTATTTCACCTAAATTTTCATTAGGATCAAGTTACTCTGTTGATCCAAATCCATTA
1 TTTATGTATTTCACCCAAATTTTCAGTAGGATCAAGTTACTCTGTTGATCCAAATCCATTA
* *
56436 TTTATGTTTTTCACCCAAATTTTCAGTAGGATCAAGTTACTTTGTTGATCCAAATCCATTA
1 TTTATGTATTTCACCCAAATTTTCAGTAGGATCAAGTTACTCTGTTGATCCAAATCCATTA
56497 TT
1 TT
56499 AATTTCCCCT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.28, C:0.18, G:0.10, T:0.44
Consensus pattern (61 bp):
TTTATGTATTTCACCCAAATTTTCAGTAGGATCAAGTTACTCTGTTGATCCAAATCCATTA
Done.