Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014003.1 Corchorus olitorius cultivar O-4 contig14036, 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: 30837
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Found at i:1329 original size:28 final size:28
Alignment explanation
Indices: 1288--1362 Score: 73
Period size: 28 Copynumber: 2.7 Consensus size: 28
1278 TTAAGATGTC
** *
1288 AAAATTACTGTTTTGCCCTTGGTCGGCT
1 AAAATTACCATTTTGCCCTTGGTCGACT
* * *
1316 AAAATTACCATTTTACCCATGGTTGACT
1 AAAATTACCATTTTGCCCTTGGTCGACT
1344 -AAATTA-CAGTTTTGCCCTT
1 AAAATTACCA-TTTTGCCCTT
1363 AAATGCCGGA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.05
27 14 0.37
28 22 0.58
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (28 bp):
AAAATTACCATTTTGCCCTTGGTCGACT
Found at i:18471 original size:23 final size:23
Alignment explanation
Indices: 18441--18491 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
18431 TGAAATCAAC
*
18441 ATTCAATTTAAAGGAACAAAGCA
1 ATTCAATTTAAAGCAACAAAGCA
* *
18464 ATTCAATTTCAAGCAATAAAGCA
1 ATTCAATTTAAAGCAACAAAGCA
18487 ATTCA
1 ATTCA
18492 TATCATATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.49, C:0.16, G:0.10, T:0.25
Consensus pattern (23 bp):
ATTCAATTTAAAGCAACAAAGCA
Found at i:24579 original size:24 final size:24
Alignment explanation
Indices: 24552--24599 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
24542 TAAGAAGATC
*
24552 AAAACACAATTTATTACATAGTTT
1 AAAACACAATTTATTACAAAGTTT
24576 AAAACACAATTTATTACAAAGTTT
1 AAAACACAATTTATTACAAAGTTT
24600 TGACGAGCGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.48, C:0.12, G:0.04, T:0.35
Consensus pattern (24 bp):
AAAACACAATTTATTACAAAGTTT
Found at i:27696 original size:15 final size:15
Alignment explanation
Indices: 27656--27697 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
27646 ATAACTGGTC
27656 CTCATCATCTTCGTA
1 CTCATCATCTTCGTA
* *
27671 CTCTTCGTCTTC-TA
1 CTCATCATCTTCGTA
27685 CGTCATCATCTTC
1 C-TCATCATCTTC
27698 CTCGTCTCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 3 0.14
15 19 0.86
ACGTcount: A:0.14, C:0.36, G:0.07, T:0.43
Consensus pattern (15 bp):
CTCATCATCTTCGTA
Found at i:29216 original size:23 final size:23
Alignment explanation
Indices: 29173--29216 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
29163 TAAGTTTTTT
*
29173 AATAAAATTAGTAAAATGATAAA
1 AATAAAATTAGTAAAAGGATAAA
*
29196 AATAAAA-TAGGTATAAGGATA
1 AATAAAATTA-GTAAAAGGATA
29217 TTATATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 16 0.89
ACGTcount: A:0.61, C:0.00, G:0.14, T:0.25
Consensus pattern (23 bp):
AATAAAATTAGTAAAAGGATAAA
Found at i:29352 original size:97 final size:99
Alignment explanation
Indices: 29175--29364 Score: 278
Period size: 97 Copynumber: 1.9 Consensus size: 99
29165 AGTTTTTTAA
* * *
29175 TAAAATTAGTAAAATGATAAAAATAAAATAGGTATAAGGATATTATATTTAATTAAATAAAAGTA
1 TAAAATTAGTAAAATGATAAAAATAAAATAGGTAT----ATATTAGATTTAATCAAATAAAAATA
29240 GAGTTTTTAGTTGAGTAAAACTATAAAAGTATTTTCAT
62 GAGTTTTTAGTTGAGTAAAACTATAAAAGTATTTTCAT
*
29278 TAAAA-TAGTAAAATGGTAAAAATAAAATA-GTACT-TATTAGATTTAATCAAATAAAAATAGAG
1 TAAAATTAGTAAAATGATAAAAATAAAATAGGTA-TATATTAGATTTAATCAAATAAAAATAGAG
29340 TTTTTAGTTGAGTAAAACTATAAAA
65 TTTTTAGTTGAGTAAAACTATAAAA
29365 ATTTAAGCAA
Statistics
Matches: 82, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
97 50 0.61
101 3 0.04
102 24 0.29
103 5 0.06
ACGTcount: A:0.51, C:0.03, G:0.12, T:0.34
Consensus pattern (99 bp):
TAAAATTAGTAAAATGATAAAAATAAAATAGGTATATATTAGATTTAATCAAATAAAAATAGAGT
TTTTAGTTGAGTAAAACTATAAAAGTATTTTCAT
Done.