Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018486.1 Corchorus olitorius cultivar O-4 contig18519, 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: 53551
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.31
Found at i:1544 original size:18 final size:18
Alignment explanation
Indices: 1518--1577 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
1508 TACAAAATAT
*
1518 TGTTACACTGCCGCAGGA
1 TGTTCCACTGCCGCAGGA
* * *
1536 TGTTCCACTACTGCAGAA
1 TGTTCCACTGCCGCAGGA
* * *
1554 TGTTGCATTGCCGTAGGA
1 TGTTCCACTGCCGCAGGA
1572 TGTTCC
1 TGTTCC
1578 GCTACCGCAA
Statistics
Matches: 31, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.30
Consensus pattern (18 bp):
TGTTCCACTGCCGCAGGA
Found at i:9960 original size:11 final size:11
Alignment explanation
Indices: 9933--9981 Score: 50
Period size: 10 Copynumber: 4.6 Consensus size: 11
9923 TCTAATTTTT
9933 TATATTTATAAA
1 TATA-TTATAAA
9945 T-TATTATAAA
1 TATATTATAAA
9955 TATATTA-AAA
1 TATATTATAAA
* *
9965 -ACATTATATA
1 TATATTATAAA
9975 TATATTA
1 TATATTA
9982 GGCGGTCGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
9 5 0.16
10 13 0.42
11 12 0.39
12 1 0.03
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (11 bp):
TATATTATAAA
Found at i:15724 original size:22 final size:22
Alignment explanation
Indices: 15688--15769 Score: 96
Period size: 22 Copynumber: 3.7 Consensus size: 22
15678 TGAATATTTT
15688 TATGAAATTTTGATAACTACCC
1 TATGAAATTTTGATAACTACCC
* *
15710 TATTGAAA-TTTGATAACCACGC
1 TA-TGAAATTTTGATAACTACCC
*
15732 TATGAAATTTTGATAATTTA-CC
1 TATGAAATTTTGATAA-CTACCC
*
15754 TATGAAATTATGATAA
1 TATGAAATTTTGATAA
15770 ACTCCATATG
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
21 5 0.10
22 40 0.78
23 6 0.12
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACTACCC
Found at i:15779 original size:22 final size:22
Alignment explanation
Indices: 15688--15832 Score: 93
Period size: 22 Copynumber: 6.5 Consensus size: 22
15678 TGAATATTTT
15688 TATGAAATTTTGAT-AACTACCC
1 TATGAAATTTTGATAAACTA-CC
*
15710 TATTGAAA-TTTGAT-AACCACGC
1 TA-TGAAATTTTGATAAACTAC-C
**
15732 TATGAAATTTTGATAATTTACC
1 TATGAAATTTTGATAAACTACC
*
15754 TATGAAATTATGATAAACT-CC
1 TATGAAATTTTGATAAACTACC
** * *
15775 ATATGGGACTTTGA-AAACCTAAC
1 -TATGAAATTTTGATAAA-CTACC
* * * *
15798 TATGCAATTTTGATAAAATTTCT
1 TATGAAATTTTGAT-AAACTACC
15821 TATGAAATTTTG
1 TATGAAATTTTG
15833 TCACCTTCCT
Statistics
Matches: 94, Mismatches: 20, Indels: 17
0.72 0.15 0.13
Matches are distributed among these distances:
21 11 0.12
22 59 0.63
23 21 0.22
24 3 0.03
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAAACTACC
Found at i:18678 original size:28 final size:28
Alignment explanation
Indices: 18637--18726 Score: 128
Period size: 28 Copynumber: 3.2 Consensus size: 28
18627 ATTTATTTCT
*
18637 CATTTTGGTCATTTTGCACGTCCAGGGG
1 CATTTTGGTCATTTTGCATGTCCAGGGG
* *
18665 CATTTTGGTAATTTTGCATGTCTAGGGG
1 CATTTTGGTCATTTTGCATGTCCAGGGG
* *
18693 CATTTTGGTCATTTTACATGT-CAGGGT
1 CATTTTGGTCATTTTGCATGTCCAGGGG
18720 CATTTTG
1 CATTTTG
18727 CATGTCCAGG
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
27 11 0.20
28 44 0.80
ACGTcount: A:0.17, C:0.16, G:0.26, T:0.42
Consensus pattern (28 bp):
CATTTTGGTCATTTTGCATGTCCAGGGG
Found at i:18722 original size:18 final size:19
Alignment explanation
Indices: 18699--18745 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 19
18689 GGGGCATTTT
18699 GGTCATTTTACATGT-CAG
1 GGTCATTTTACATGTCCAG
*
18717 GGTCATTTTGCATGTCCAG
1 GGTCATTTTACATGTCCAG
*
18736 GGGCATTTTA
1 GGTCATTTTA
18746 GTCATTTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 14 0.56
19 11 0.44
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (19 bp):
GGTCATTTTACATGTCCAG
Found at i:29253 original size:17 final size:18
Alignment explanation
Indices: 29225--29261 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
29215 AACTTCAAAA
29225 GAAGATTAAAACATATAG
1 GAAGATTAAAACATATAG
29243 GAAGA-TAAAACATATAG
1 GAAGATTAAAACATATAG
29260 GA
1 GA
29262 CATAAAGAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.57, C:0.05, G:0.19, T:0.19
Consensus pattern (18 bp):
GAAGATTAAAACATATAG
Found at i:29700 original size:18 final size:18
Alignment explanation
Indices: 29679--29717 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
29669 ATAGCCAAAA
*
29679 CCACAACCACGGCCACGT
1 CCACAACCACGACCACGT
**
29697 CCACGTCCACGACCACGT
1 CCACAACCACGACCACGT
29715 CCA
1 CCA
29718 TAATTATAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.26, C:0.51, G:0.15, T:0.08
Consensus pattern (18 bp):
CCACAACCACGACCACGT
Found at i:29714 original size:12 final size:12
Alignment explanation
Indices: 29679--29717 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
29669 ATAGCCAAAA
* *
29679 CCACAACCACGG
1 CCACGACCACGT
*
29691 CCACGTCCACGT
1 CCACGACCACGT
29703 CCACGACCACGT
1 CCACGACCACGT
29715 CCA
1 CCA
29718 TAATTATAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.26, C:0.51, G:0.15, T:0.08
Consensus pattern (12 bp):
CCACGACCACGT
Found at i:30691 original size:30 final size:32
Alignment explanation
Indices: 30657--30722 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
30647 TTTAATAATA
*
30657 AAAGAAAGGTAG-G-AGGAGATTATGCATGAT
1 AAAGAAAGGTAGAGAAGGAGATCATGCATGAT
30687 AAAGAAAGGTAGAAGAAGGAGATCATGCATGAT
1 AAAGAAAGGTAG-AGAAGGAGATCATGCATGAT
30720 AAA
1 AAA
30723 TAAACTTTCT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 12 0.38
32 1 0.03
33 19 0.59
ACGTcount: A:0.48, C:0.05, G:0.30, T:0.17
Consensus pattern (32 bp):
AAAGAAAGGTAGAGAAGGAGATCATGCATGAT
Found at i:31458 original size:2 final size:2
Alignment explanation
Indices: 31451--31481 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
31441 AACAAATTAT
*
31451 TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
31482 TGAATATGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:35501 original size:19 final size:18
Alignment explanation
Indices: 35468--35503 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
35458 TCGAGATAAT
35468 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
35486 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
35504 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:36377 original size:17 final size:18
Alignment explanation
Indices: 36342--36378 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
36332 CTCCTCTATC
*
36342 ATGAAAACACTTCTTTTT
1 ATGAAAACAATTCTTTTT
36360 ATGAAAACAATT-TTTTT
1 ATGAAAACAATTCTTTTT
36377 AT
1 AT
36379 TACCCTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (18 bp):
ATGAAAACAATTCTTTTT
Found at i:37079 original size:30 final size:30
Alignment explanation
Indices: 37040--37098 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
37030 GTTTATTAAT
37040 GAAACTTGAAAATTAAAGACATAAAATAAAG
1 GAAACTTGAAAATTAAAG-CATAAAATAAAG
*
37071 GAAA-TTGAAAATTAAAGCATAAATTAAA
1 GAAACTTGAAAATTAAAGCATAAAATAAA
37099 TAACTAATCC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 10 0.37
30 13 0.48
31 4 0.15
ACGTcount: A:0.61, C:0.05, G:0.12, T:0.22
Consensus pattern (30 bp):
GAAACTTGAAAATTAAAGCATAAAATAAAG
Found at i:42124 original size:19 final size:18
Alignment explanation
Indices: 42091--42126 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
42081 TCGAGATAAT
42091 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
42109 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
42127 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:53435 original size:22 final size:22
Alignment explanation
Indices: 53405--53451 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
53395 GACGTTAAAA
*
53405 CAAAA-TTTTTTTT-TATGACG
1 CAAAATTTTTTTTTCTTTGACG
53425 CAAAATTTTTTTTTCTTTGACG
1 CAAAATTTTTTTTTCTTTGACG
53447 CAAAA
1 CAAAA
53452 CACAAAAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 5 0.21
21 8 0.33
22 11 0.46
ACGTcount: A:0.32, C:0.13, G:0.09, T:0.47
Consensus pattern (22 bp):
CAAAATTTTTTTTTCTTTGACG
Done.