Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013133.1 Corchorus olitorius cultivar O-4 contig13166, 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: 31414
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.30
Found at i:4927 original size:121 final size:121
Alignment explanation
Indices: 4798--5039 Score: 412
Period size: 121 Copynumber: 2.0 Consensus size: 121
4788 ATTTTATTTG
* * * * *
4798 TTTGTTTTAAGAAAAAGAATAATAATCTTTCTTTCTATGGGATCGACCCCTACTTGCCCTAGCTA
1 TTTGTTTTAAGAAAAAGAATAATAACCTATCTCTCTATGGGATCGACCCCTACTTGACCTAACTA
*
4863 TATTTAGTTAGTAATTGTTGGGATTTTTATTTTTATGATTTGCTGACGACCGATCA
66 TATTTAGTTAGTAATTGTTGGGAATTTTATTTTTATGATTTGCTGACGACCGATCA
*
4919 TTTGTTTTAAGAAAAAGAATAATAACCTATCTCTCTGTGGGATCGACCCCTACTTGACCTAACTA
1 TTTGTTTTAAGAAAAAGAATAATAACCTATCTCTCTATGGGATCGACCCCTACTTGACCTAACTA
*
4984 TCTTTAGTTAGTAATTGTTGGGAATTTTATTTTTATGATTTGCTGACGACCGATCA
66 TATTTAGTTAGTAATTGTTGGGAATTTTATTTTTATGATTTGCTGACGACCGATCA
5040 CTCAGCCTGA
Statistics
Matches: 113, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
121 113 1.00
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (121 bp):
TTTGTTTTAAGAAAAAGAATAATAACCTATCTCTCTATGGGATCGACCCCTACTTGACCTAACTA
TATTTAGTTAGTAATTGTTGGGAATTTTATTTTTATGATTTGCTGACGACCGATCA
Found at i:5780 original size:130 final size:130
Alignment explanation
Indices: 5540--5796 Score: 487
Period size: 130 Copynumber: 2.0 Consensus size: 130
5530 CAACAATTAA
5540 ATTAACTTGAAATCCAAAAATGTAGAGTTTGACATTTGACAAATTGCCATCTTAAAAACTATTCT
1 ATTAACTTGAAATCCAAAAATGTAGAGTTTGACATTTGACAAATTGCCATCTTAAAAACTATTCT
*
5605 TCCACGTGGTCTTCAGGAGACTTTGGTGGAGGGAATATCTTAGGGAGTTGTGTCTTGATCAACAT
66 TCCACGTGGTCTTCAGGAGACTTTGGTGGAGGGAATATCTCAGGGAGTTGTGTCTTGATCAACAT
5670 ATTAACTTGAAATCCAAAAATGTAGAGTTTGACATTTGACAAATTGCCATCTTAAAAACTATTCT
1 ATTAACTTGAAATCCAAAAATGTAGAGTTTGACATTTGACAAATTGCCATCTTAAAAACTATTCT
* *
5735 TCCACGTGTTCTTCAGGAGACTTTGGTGGAGGGAATGTCTCAGGGAGTTGTGTCTTGATCAA
66 TCCACGTGGTCTTCAGGAGACTTTGGTGGAGGGAATATCTCAGGGAGTTGTGTCTTGATCAA
5797 AATAAATTTC
Statistics
Matches: 124, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
130 124 1.00
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (130 bp):
ATTAACTTGAAATCCAAAAATGTAGAGTTTGACATTTGACAAATTGCCATCTTAAAAACTATTCT
TCCACGTGGTCTTCAGGAGACTTTGGTGGAGGGAATATCTCAGGGAGTTGTGTCTTGATCAACAT
Found at i:8365 original size:29 final size:30
Alignment explanation
Indices: 8326--8386 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
8316 TATAAATAAT
* *
8326 ATAATATAATT-AACTAA-TTATATTTATAC
1 ATAATAAAATTGAA-TAATTTATATGTATAC
8355 ATAATAAAATTGAATAATTTATATGTATAC
1 ATAATAAAATTGAATAATTTATATGTATAC
8385 AT
1 AT
8387 TAATTAGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 13 0.46
30 15 0.54
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (30 bp):
ATAATAAAATTGAATAATTTATATGTATAC
Found at i:8416 original size:19 final size:20
Alignment explanation
Indices: 8378--8416 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
8368 ATAATTTATA
* *
8378 TGTATACATTAATTAGAATT
1 TGTAAACATTAATTAAAATT
8398 TGTAAACATT-ATTAAAATT
1 TGTAAACATTAATTAAAATT
8417 AATTTTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.44
Consensus pattern (20 bp):
TGTAAACATTAATTAAAATT
Found at i:9715 original size:16 final size:15
Alignment explanation
Indices: 9683--9719 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
9673 CTGACTTTAA
9683 TAATTAAAATTACTT
1 TAATTAAAATTACTT
*
9698 TAATTAATAATTAGTT
1 TAATTAA-AATTACTT
9714 TAATTA
1 TAATTA
9720 TCCCAGACAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (15 bp):
TAATTAAAATTACTT
Found at i:11184 original size:38 final size:38
Alignment explanation
Indices: 11133--11209 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
11123 GACAATGTAA
11133 CTAAGGCACTAACGGTCCAAACAAACGCCTTAGGCATC
1 CTAAGGCACTAACGGTCCAAACAAACGCCTTAGGCATC
*
11171 CTAAGGCACTAACGGTCCAAACAAACGCCTTAGTCATC
1 CTAAGGCACTAACGGTCCAAACAAACGCCTTAGGCATC
11209 C
1 C
11210 CCATACACAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (38 bp):
CTAAGGCACTAACGGTCCAAACAAACGCCTTAGGCATC
Found at i:26740 original size:51 final size:52
Alignment explanation
Indices: 26639--26740 Score: 120
Period size: 51 Copynumber: 2.0 Consensus size: 52
26629 GTTCATCATA
* **
26639 TTCTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCTTTTAGTGTTT
1 TTCTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGTTT
* *
26691 TTCT-CTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGTT
1 TTCTCCTTGTTT-AGATCTTGTCTCAGGACAAACAAACACTCGTACA-GTGTT
26741 CTTCATTCAG
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
50 2 0.05
51 36 0.84
52 5 0.12
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.40
Consensus pattern (52 bp):
TTCTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGTTT
Found at i:28544 original size:11 final size:11
Alignment explanation
Indices: 28528--28575 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 11
28518 GAAGTTCGTG
28528 TTTGAAGACCA
1 TTTGAAGACCA
**
28539 TTTGAAGATAA
1 TTTGAAGACCA
28550 TTTGAAGA-C-
1 TTTGAAGACCA
28559 -TTGAAGACCA
1 TTTGAAGACCA
28569 -TTGAAGA
1 TTTGAAGA
28576 TTTATTTCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
8 7 0.22
9 1 0.03
10 7 0.22
11 17 0.53
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (11 bp):
TTTGAAGACCA
Done.