Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023601.1 Corchorus olitorius cultivar O-4 contig23634, 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: 12806
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Found at i:320 original size:21 final size:21
Alignment explanation
Indices: 296--412 Score: 182
Period size: 21 Copynumber: 5.6 Consensus size: 21
286 CTTAGGCATT
* *
296 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAACTTGGAACCTTC
*
317 TCCAATGATCTTGGAACCTTC
1 TCCAATGAACTTGGAACCTTC
338 TCCAATGAACTTGGAACCTTC
1 TCCAATGAACTTGGAACCTTC
359 TCCAATGAACTTGGAACCTTC
1 TCCAATGAACTTGGAACCTTC
*
380 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAACTTGGAACCTT-C
401 TCCAATGAACTT
1 TCCAATGAACTT
413 CTAGCATCTT
Statistics
Matches: 90, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
20 3 0.03
21 87 0.97
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.30
Consensus pattern (21 bp):
TCCAATGAACTTGGAACCTTC
Found at i:1605 original size:29 final size:29
Alignment explanation
Indices: 1536--1746 Score: 257
Period size: 29 Copynumber: 7.4 Consensus size: 29
1526 TCGAGCATGC
*
1536 AAAATGACCAAAATGCTCCTGAATGTG-A
1 AAAATGACCAAAATGCCCCTGAATGTGCA
*
1564 AAAATGACCAAAATGCCCCTGAATGGGCA
1 AAAATGACCAAAATGCCCCTGAATGTGCA
* * * *
1593 AAAATTACCAAAATACCCATGAATATGCA
1 AAAATGACCAAAATGCCCCTGAATGTGCA
* *
1622 AAAATAACCAAAATGCCCCTGAATGTGTA
1 AAAATGACCAAAATGCCCCTGAATGTGCA
* * *
1651 AAATTAACTAAAATGCCCCTGAATGTGC-
1 AAAATGACCAAAATGCCCCTGAATGTGCA
* * * *
1679 -AAATGACCAAAATACCCTTGAATATGCT
1 AAAATGACCAAAATGCCCCTGAATGTGCA
*
1707 AAAATGACCAAAATGCCCCTGAGTGTGCA
1 AAAATGACCAAAATGCCCCTGAATGTGCA
1736 AAAATGACCAA
1 AAAATGACCAA
1747 TTAAGAAATA
Statistics
Matches: 154, Mismatches: 26, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
27 21 0.14
28 25 0.16
29 108 0.70
ACGTcount: A:0.44, C:0.21, G:0.15, T:0.20
Consensus pattern (29 bp):
AAAATGACCAAAATGCCCCTGAATGTGCA
Found at i:1717 original size:85 final size:84
Alignment explanation
Indices: 1532--1746 Score: 288
Period size: 85 Copynumber: 2.5 Consensus size: 84
1522 AAACTCGAGC
* *
1532 ATGCAAAATGACCAAAATGCTCCTGAATGTGAAAAATGACCAAAATGCCCCTGAATGGGCAAAAA
1 ATGCAAAATGACCAAAATGCCCCTGAATGTGAAAAATAACCAAAATGCCCCTGAATGGGC-AAAA
*
1597 TTACCAAAATACCCATGAAT
65 TGACCAAAATACCCATGAAT
* * * *
1617 ATGCAAAAATAACCAAAATGCCCCTGAATGTGTAAAATTAACTAAAATGCCCCTGAATGTGC-AA
1 ATGC-AAAATGACCAAAATGCCCCTGAATGTG-AAAAATAACCAAAATGCCCCTGAATGGGCAAA
*
1681 ATGACCAAAATACCCTTGAAT
64 ATGACCAAAATACCCATGAAT
* *
1702 ATGCTAAAATGACCAAAATGCCCCTGAGTGTGCAAAAATGACCAA
1 ATGC-AAAATGACCAAAATGCCCCTGAATGTG-AAAAATAACCAA
1747 TTAAGAAATA
Statistics
Matches: 113, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
85 63 0.56
86 25 0.22
87 25 0.22
ACGTcount: A:0.44, C:0.21, G:0.15, T:0.20
Consensus pattern (84 bp):
ATGCAAAATGACCAAAATGCCCCTGAATGTGAAAAATAACCAAAATGCCCCTGAATGGGCAAAAT
GACCAAAATACCCATGAAT
Found at i:2285 original size:59 final size:59
Alignment explanation
Indices: 2026--2664 Score: 768
Period size: 59 Copynumber: 10.8 Consensus size: 59
2016 TTTAAAAATA
* * * * * * **
2026 GAAAACTCTCTACCAGAGACCTCTAACAGGGTTTTAGAAGCAATATGAGATTTTGAATT
1 GAAAACTCTCTACCAGAGACCTCGATCAGGATTTTAAAAACAAGACAAGATTTTGAATT
** * * ***
2085 GGGAACTCTTCTACCAGAGACCTCGAACAGGATTTTAAAAGCAAGATGCGATTTTGAATT
1 GAAAACTC-TCTACCAGAGACCTCGATCAGGATTTTAAAAACAAGACAAGATTTTGAATT
* * * * **
2145 GAAAACTCTCTACCAAAGACCACAAACAACATTTAATTTAAAAACAAGACAAGATTTTGAATT
1 GAAAACTCTCTACCAGAGACCTCGATCAGGA--T--TTTAAAAACAAGACAAGATTTTGAATT
2208 GAAAACTCTCTACCAGAGACCTCGATCAGGA-TTTAAAACACAAGACAAGATTTTGAATT
1 GAAAACTCTCTACCAGAGACCTCGATCAGGATTTTAAAA-ACAAGACAAGATTTTGAATT
* *
2267 GAAAACTCTCTACTAGAGACCTCGATCAGGATTTTAAAAACAAGACAAGATTTAGAATT
1 GAAAACTCTCTACCAGAGACCTCGATCAGGATTTTAAAAACAAGACAAGATTTTGAATT
*
2326 GAAAACTCTCTACCAGAGACCTCGATCAGGATTTTAAAAACAAGACAAGATTTAGAATT
1 GAAAACTCTCTACCAGAGACCTCGATCAGGATTTTAAAAACAAGACAAGATTTTGAATT
* * ** *
2385 GAAATCTCTCTACCAGAGACCTCGATCAGGATTTTTAAAACAAGATGAGATTTAGAATT
1 GAAAACTCTCTACCAGAGACCTCGATCAGGATTTTAAAAACAAGACAAGATTTTGAATT
* * * *
2444 GAAAATTCTCTACCAGAGACCTCGAACAGGATTTTAAAAACAAGATAA-AATTTGAAATT
1 GAAAACTCTCTACCAGAGACCTCGATCAGGATTTTAAAAACAAGACAAGATTTTG-AATT
* *
2503 GAAAACTCTCTACCAGAGACCTCGATCAGGATTTTAAAAACAAGATAA-AATTTGAAATT
1 GAAAACTCTCTACCAGAGACCTCGATCAGGATTTTAAAAACAAGACAAGATTTTG-AATT
* * *
2562 GAAAACTTTCTACC-GAGACCTCGATTAGGATCTTAAAAACAAGATC-AGATTTAT-AATT
1 GAAAACTCTCTACCAGAGACCTCGATCAGGATTTTAAAAACAAGA-CAAGATTT-TGAATT
* * **
2620 GAAAGCTCTCTACCAGAGACCTTGAAAAGGATTTTAAAAACAAGA
1 GAAAACTCTCTACCAGAGACCTCGATCAGGATTTTAAAAACAAGA
2665 TAAAATTTGA
Statistics
Matches: 517, Mismatches: 51, Indels: 24
0.87 0.09 0.04
Matches are distributed among these distances:
58 56 0.11
59 352 0.68
60 60 0.12
61 1 0.00
63 48 0.09
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.26
Consensus pattern (59 bp):
GAAAACTCTCTACCAGAGACCTCGATCAGGATTTTAAAAACAAGACAAGATTTTGAATT
Found at i:3562 original size:38 final size:38
Alignment explanation
Indices: 3520--3618 Score: 141
Period size: 36 Copynumber: 2.7 Consensus size: 38
3510 TTTAGACATT
* *
3520 TTTCTATTTTAGGCCAAGTTTTTTTCTTTTTCGACCTC
1 TTTCTATTTTAGGCCAAGTTTTTTTCTTATCCGACCTC
3558 TTTCTATTTTAGGTCC-AG--TTTTTCTTATCCGACCTC
1 TTTCTATTTTAGG-CCAAGTTTTTTTCTTATCCGACCTC
*
3594 TTTCTATTTTAGGTCAAGTTTTTTT
1 TTTCTATTTTAGGCCAAGTTTTTTT
3619 TTTAGCTCCT
Statistics
Matches: 54, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
35 1 0.02
36 31 0.57
38 20 0.37
39 2 0.04
ACGTcount: A:0.14, C:0.19, G:0.11, T:0.56
Consensus pattern (38 bp):
TTTCTATTTTAGGCCAAGTTTTTTTCTTATCCGACCTC
Found at i:4457 original size:27 final size:27
Alignment explanation
Indices: 4419--4485 Score: 98
Period size: 27 Copynumber: 2.5 Consensus size: 27
4409 TTTACTTCTT
** *
4419 ATTTTGGTCATTTACATGTCCGGGGGC
1 ATTTTGGTCATTTACACATCCAGGGGC
*
4446 ATTTTGGTCATTTGCACATCCAGGGGC
1 ATTTTGGTCATTTACACATCCAGGGGC
4473 ATTTTGGTCATTT
1 ATTTTGGTCATTT
4486 CAAGTGCACT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.16, C:0.18, G:0.25, T:0.40
Consensus pattern (27 bp):
ATTTTGGTCATTTACACATCCAGGGGC
Found at i:4631 original size:27 final size:27
Alignment explanation
Indices: 4593--4659 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 27
4583 TTTACTTCTT
** **
4593 ATTTTGGTCATTTACATGTCTGGGGGC
1 ATTTTGGTCATTTACACATCCAGGGGC
*
4620 ATTTTGGTCATTTGCACATCCAGGGGC
1 ATTTTGGTCATTTACACATCCAGGGGC
4647 ATTTTGGTCATTT
1 ATTTTGGTCATTT
4660 CAAGTGCACT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.16, C:0.16, G:0.25, T:0.42
Consensus pattern (27 bp):
ATTTTGGTCATTTACACATCCAGGGGC
Found at i:6236 original size:28 final size:26
Alignment explanation
Indices: 6193--6282 Score: 144
Period size: 26 Copynumber: 3.4 Consensus size: 26
6183 GCACTCTCCC
*
6193 CTCTCCCATTCGAAAAAACTAGAAAGTT
1 CTCTCCCATTC--AAAAACCAGAAAGTT
6221 CTCTCCCATTCAAAAACCAGAAAGTT
1 CTCTCCCATTCAAAAACCAGAAAGTT
*
6247 CTCTCCCATTCAAAAACCAGAAGGTT
1 CTCTCCCATTCAAAAACCAGAAAGTT
6273 CTCTCCCATT
1 CTCTCCCATT
6283 TTTTTTCACC
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
26 49 0.82
28 11 0.18
ACGTcount: A:0.34, C:0.31, G:0.09, T:0.26
Consensus pattern (26 bp):
CTCTCCCATTCAAAAACCAGAAAGTT
Done.