Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021260.1 Corchorus olitorius cultivar O-4 contig21293, 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: 23232
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:2400 original size:17 final size:17
Alignment explanation
Indices: 2380--2415 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
2370 AATAAGATCC
*
2380 AACAAAACATAAAAACA
1 AACAAAACACAAAAACA
2397 AACAAAACACAAAAACA
1 AACAAAACACAAAAACA
2414 AA
1 AA
2416 ATAAAGTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.78, C:0.19, G:0.00, T:0.03
Consensus pattern (17 bp):
AACAAAACACAAAAACA
Found at i:11538 original size:13 final size:13
Alignment explanation
Indices: 11520--11544 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11510 ATAGGCCTAA
11520 TAAGAGTAACTTG
1 TAAGAGTAACTTG
11533 TAAGAGTAACTT
1 TAAGAGTAACTT
11545 CTTTCTTCTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (13 bp):
TAAGAGTAACTTG
Found at i:12795 original size:119 final size:119
Alignment explanation
Indices: 12662--12899 Score: 413
Period size: 119 Copynumber: 2.0 Consensus size: 119
12652 TAAAAAGGGG
12662 GGGGGTCGATGCCTTTATATAGGCAAAGGATCGACCTAAACTATCCAAAAATAAGCCCTCTAGGC
1 GGGGGTCGATGCCTTTATATAGGCAAAGGATCGACCTAAACTATCCAAAAATAAGCCCTCTAGGC
*
12727 GGTTTACAATGCCCTGGGCGGCACACATAAGGAAAAGACAAGGAAATAGCCTAA
66 AGTTTACAATGCCCTGGGCGGCACACATAAGGAAAAGACAAGGAAATAGCCTAA
* * * *
12781 GGGGGTCGATGCCTTTATATAGGGAGAGTATCTACCTAAACTATCCAAAAATAAGCCCTCTAGGC
1 GGGGGTCGATGCCTTTATATAGGCAAAGGATCGACCTAAACTATCCAAAAATAAGCCCTCTAGGC
* *
12846 AGTTTACAATGCCTTGGGTGGCACACATAAGGAAAAGACAAGGAAATAGCCTAA
66 AGTTTACAATGCCCTGGGCGGCACACATAAGGAAAAGACAAGGAAATAGCCTAA
12900 TTCCAAGTCC
Statistics
Matches: 112, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
119 112 1.00
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.20
Consensus pattern (119 bp):
GGGGGTCGATGCCTTTATATAGGCAAAGGATCGACCTAAACTATCCAAAAATAAGCCCTCTAGGC
AGTTTACAATGCCCTGGGCGGCACACATAAGGAAAAGACAAGGAAATAGCCTAA
Found at i:12939 original size:14 final size:15
Alignment explanation
Indices: 12920--12949 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
12910 AACTAGGAAA
12920 AATAAAT-AACAAGG
1 AATAAATAAACAAGG
12934 AATAAATAAACAAGG
1 AATAAATAAACAAGG
12949 A
1 A
12950 TTGGACTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.67, C:0.07, G:0.13, T:0.13
Consensus pattern (15 bp):
AATAAATAAACAAGG
Found at i:18364 original size:43 final size:43
Alignment explanation
Indices: 18308--18596 Score: 409
Period size: 43 Copynumber: 6.6 Consensus size: 43
18298 TTTCAGTATC
*
18308 TTTTTATTT-CAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTG
1 TTTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTG
* ** *
18350 TTTTCATTTCCAAAAATACCCCTTTATGGTTGGAAGGTCCCTA
1 TTTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTG
* * *
18393 TTTTCATTTCCAGAAATGCCCCTTCCTAGTTGGAAGGTCCTTG
1 TTTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTG
18436 TTTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTG
1 TTTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTG
* *
18479 TTTTCATTTCCAAAAATGCCCCTTCCTGGCTGGAAGGTCCTTG
1 TTTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTG
* *
18522 TTTTCTTATTTTCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCCGTC
1 TTTTC--ATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGT-CCC-TG
*
18569 TTCTTCATTACCAAAAATGCCCCTTCCT
1 TT-TTCATTTCCAAAAATGCCCCTTCCT
18597 AGCCTGAAGG
Statistics
Matches: 218, Mismatches: 23, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
42 8 0.04
43 151 0.69
45 31 0.14
46 22 0.10
47 3 0.01
48 3 0.01
ACGTcount: A:0.20, C:0.27, G:0.16, T:0.37
Consensus pattern (43 bp):
TTTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTG
Found at i:19209 original size:55 final size:55
Alignment explanation
Indices: 19125--19239 Score: 160
Period size: 55 Copynumber: 2.1 Consensus size: 55
19115 AATTAAATCT
* * * *
19125 TTTGATTCAATCTCCTGGAGAAGTCTTCGAGGACTTGACATCTTGATCTTGATGA
1 TTTGATTCAATCTCCTAGAGAAGTCTTCGAGGACTTGACAGCTTGATCTCGATAA
* *
19180 TTTGATTCGATCTCCTAGA-AATGTTTTCGAGGACTTGACAGCTTGATCTCGATAA
1 TTTGATTCAATCTCCTAGAGAA-GTCTTCGAGGACTTGACAGCTTGATCTCGATAA
19235 TTTGA
1 TTTGA
19240 AAGGATTGGC
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
54 2 0.04
55 51 0.96
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.37
Consensus pattern (55 bp):
TTTGATTCAATCTCCTAGAGAAGTCTTCGAGGACTTGACAGCTTGATCTCGATAA
Found at i:19985 original size:2 final size:2
Alignment explanation
Indices: 19978--20002 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19968 TTAGCCGCCT
19978 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
20003 AACTTTCTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:21369 original size:31 final size:30
Alignment explanation
Indices: 21334--21393 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
21324 AAGTTCGTGT
*
21334 TTGAAGACCATTTGAAGAATAATTTGAAGAC
1 TTGAAGA-CATTTGAAGAATAATTTCAAGAC
** *
21365 TTGAAGATTTTTGAAGAATTATTTCAAGA
1 TTGAAGACATTTGAAGAATAATTTCAAGA
21394 GGAAAGAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 18 0.72
31 7 0.28
ACGTcount: A:0.40, C:0.07, G:0.18, T:0.35
Consensus pattern (30 bp):
TTGAAGACATTTGAAGAATAATTTCAAGAC
Found at i:22472 original size:15 final size:15
Alignment explanation
Indices: 22448--22481 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
22438 CTCTAAATTT
*
22448 TTTTTTATTTTTGCG
1 TTTTTAATTTTTGCG
*
22463 TTTTTAATTTTTGTG
1 TTTTTAATTTTTGCG
22478 TTTT
1 TTTT
22482 GCGTTTTTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.03, G:0.12, T:0.76
Consensus pattern (15 bp):
TTTTTAATTTTTGCG
Done.