Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012330.1 Corchorus olitorius cultivar O-4 contig12363, 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: 28925
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:2407 original size:21 final size:20
Alignment explanation
Indices: 2361--2403 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2351 CTCTCACAAG
* *
2361 TTTCTAGCCGTTGGAGCTCT
1 TTTCTAGCCGTTAGAGCACT
*
2381 TTTCTAGCCGTTATAGCACT
1 TTTCTAGCCGTTAGAGCACT
2401 TTT
1 TTT
2404 TCTACTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (20 bp):
TTTCTAGCCGTTAGAGCACT
Found at i:8737 original size:22 final size:22
Alignment explanation
Indices: 8712--8759 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
8702 ATGGAATTAT
*
8712 GATAATCACACTATGAAATTTC
1 GATAACCACACTATGAAATTTC
* * *
8734 GATAACCTCCCTATGAAATTTT
1 GATAACCACACTATGAAATTTC
8756 GATA
1 GATA
8760 GTTTTTTTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (22 bp):
GATAACCACACTATGAAATTTC
Found at i:11791 original size:22 final size:21
Alignment explanation
Indices: 11749--11791 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
11739 TTAATAACCA
*
11749 AATTTTTTTGGGGTAGCCAAT
1 AATTTTTTTGGGGTAGACAAT
11770 AATTTTTTCTAGGGGTA-ACAAT
1 AATTTTTT-T-GGGGTAGACAAT
11792 TTCTAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 8 0.42
22 5 0.26
23 6 0.32
ACGTcount: A:0.28, C:0.09, G:0.21, T:0.42
Consensus pattern (21 bp):
AATTTTTTTGGGGTAGACAAT
Found at i:13695 original size:24 final size:24
Alignment explanation
Indices: 13667--13716 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
13657 AAAATTAAGC
*
13667 TAAACATCTTATCATTATAATTAT
1 TAAACATCTTATCATTATAATAAT
* *
13691 TAAACTTCTTATTATTATAATAAT
1 TAAACATCTTATCATTATAATAAT
13715 TA
1 TA
13717 TTAGTAGTAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (24 bp):
TAAACATCTTATCATTATAATAAT
Found at i:13920 original size:18 final size:18
Alignment explanation
Indices: 13877--13940 Score: 67
Period size: 18 Copynumber: 3.6 Consensus size: 18
13867 TTAACATCAT
* *
13877 ATTATTATAATTATTAAA
1 ATTATTATTATTAGTAAA
* *
13895 CTTCTTATTATTA-TAATA
1 ATTATTATTATTAGTAA-A
*
13913 ATTATTATTAGTAGTAAA
1 ATTATTATTATTAGTAAA
13931 ATTATTATTA
1 ATTATTATTA
13941 GTTATATTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
17 3 0.08
18 32 0.84
19 3 0.08
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (18 bp):
ATTATTATTATTAGTAAA
Found at i:13949 original size:15 final size:15
Alignment explanation
Indices: 13900--13955 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
13890 TTAAACTTCT
*
13900 TATTATTA-TAATAA
1 TATTATTATTAGTAA
*
13914 TTATTATTAGTAGTAA
1 -TATTATTATTAGTAA
* *
13930 AATTATTATTAGTTA
1 TATTATTATTAGTAA
*
13945 TATTATCATTA
1 TATTATTATTA
13956 TGTTTTGCTT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
15 29 0.85
16 5 0.15
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (15 bp):
TATTATTATTAGTAA
Found at i:16368 original size:18 final size:19
Alignment explanation
Indices: 16329--16368 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
16319 GTGCTCCCGT
16329 TGTGATGCTCCCACTTTTCAA
1 TGTGATGCTCCCA--TTTCAA
16350 TGTGATGCTCCCA-TTCAA
1 TGTGATGCTCCCATTTCAA
16368 T
1 T
16369 TATGACCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
21 13 0.68
ACGTcount: A:0.20, C:0.28, G:0.15, T:0.38
Consensus pattern (19 bp):
TGTGATGCTCCCATTTCAA
Found at i:17048 original size:32 final size:33
Alignment explanation
Indices: 17001--17064 Score: 85
Period size: 32 Copynumber: 1.9 Consensus size: 33
16991 GTGGAAAACG
*
17001 GAGAAGAAAAGAATAAA-AAATAAAAAAAGTTT
1 GAGAAAAAAAGAATAAACAAATAAAAAAAGTTT
* *
17033 GAGAAAAAAATAATAAATCAAGTAAAAAAAGT
1 GAGAAAAAAAGAATAAA-CAAATAAAAAAAGT
17065 AGTTGATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 15 0.56
34 12 0.44
ACGTcount: A:0.69, C:0.02, G:0.14, T:0.16
Consensus pattern (33 bp):
GAGAAAAAAAGAATAAACAAATAAAAAAAGTTT
Found at i:17682 original size:110 final size:110
Alignment explanation
Indices: 17536--17757 Score: 435
Period size: 110 Copynumber: 2.0 Consensus size: 110
17526 ATGATTAAGG
17536 TAACAAATTAATTATAGGGTTAACCCCTAGTTACAAATAAGGAGAATTTACAGGGTAAATCCATT
1 TAACAAATTAATTATAGGGTTAACCCCTAGTTACAAATAAGGAGAATTTACAGGGTAAATCCATT
17601 GATTTTTTTTGAGGTAAAATCCATTGATTTTATGGTATTATTGAA
66 GATTTTTTTTGAGGTAAAATCCATTGATTTTATGGTATTATTGAA
*
17646 TAACAAATTAATTATAGGGTTAACCCCTAGTTACAAATAAGGAGAATTTATAGGGTAAATCCATT
1 TAACAAATTAATTATAGGGTTAACCCCTAGTTACAAATAAGGAGAATTTACAGGGTAAATCCATT
17711 GATTTTTTTTGAGGTAAAATCCATTGATTTTATGGTATTATTGAA
66 GATTTTTTTTGAGGTAAAATCCATTGATTTTATGGTATTATTGAA
17756 TA
1 TA
17758 GGATTTTAAA
Statistics
Matches: 111, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
110 111 1.00
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.38
Consensus pattern (110 bp):
TAACAAATTAATTATAGGGTTAACCCCTAGTTACAAATAAGGAGAATTTACAGGGTAAATCCATT
GATTTTTTTTGAGGTAAAATCCATTGATTTTATGGTATTATTGAA
Found at i:18869 original size:22 final size:22
Alignment explanation
Indices: 18841--18920 Score: 110
Period size: 22 Copynumber: 3.7 Consensus size: 22
18831 ATTATGCTAT
18841 TATATATAAAATATATTTATGA
1 TATATATAAAATATATTTATGA
* *
18863 TATATATAGAATATATGTA--A
1 TATATATAAAATATATTTATGA
* *
18883 AATATATAAATTATATTTATGA
1 TATATATAAAATATATTTATGA
18905 TATATATAAAATATAT
1 TATATATAAAATATAT
18921 ATAACAAATT
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 16 0.33
22 32 0.67
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (22 bp):
TATATATAAAATATATTTATGA
Found at i:18898 original size:31 final size:31
Alignment explanation
Indices: 18841--18921 Score: 83
Period size: 33 Copynumber: 2.5 Consensus size: 31
18831 ATTATGCTAT
** *
18841 TATATATAAAATATATTTATGATATATATAGA
1 TATATATAAAATATATAAATTATATATAT-GA
* *
18873 -ATATATGTAAAATATATAAATTATATTTATGA
1 TATATAT-AAAA-TATATAAATTATATATATGA
18905 TATATATAAAATATATA
1 TATATATAAAATATATA
18922 TAACAAATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
31 12 0.30
32 8 0.20
33 20 0.50
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (31 bp):
TATATATAAAATATATAAATTATATATATGA
Found at i:18929 original size:13 final size:11
Alignment explanation
Indices: 18841--18924 Score: 73
Period size: 11 Copynumber: 7.8 Consensus size: 11
18831 ATTATGCTAT
18841 TATATATAAAA
1 TATATATAAAA
* **
18852 TATATTTATGA
1 TATATATAAAA
*
18863 TATATATAGAA
1 TATATATAAAA
*
18874 TATATGT-AAA
1 TATATATAAAA
*
18884 -ATATATAAAT
1 TATATATAAAA
* **
18894 TATATTTATGA
1 TATATATAAAA
18905 TATATATAAAA
1 TATATATAAAA
18916 TATATATAA
1 TATATATAA
18925 CAAATTTTTT
Statistics
Matches: 54, Mismatches: 17, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
9 5 0.09
10 4 0.07
11 45 0.83
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (11 bp):
TATATATAAAA
Found at i:19879 original size:31 final size:31
Alignment explanation
Indices: 19841--19922 Score: 146
Period size: 31 Copynumber: 2.6 Consensus size: 31
19831 ACAAGTGGCT
*
19841 TTTCAAAATTTTGTCATTTTACCCTTTAAAA
1 TTTCAAAATTTTGTCATTTTACCCCTTAAAA
19872 TTTCAAAATTTTGTCATTTTACCCCTTAAAA
1 TTTCAAAATTTTGTCATTTTACCCCTTAAAA
*
19903 TTTCAAATTTTTGTCATTTT
1 TTTCAAAATTTTGTCATTTT
19923 TTTGCTCCTT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 49 1.00
ACGTcount: A:0.29, C:0.16, G:0.04, T:0.51
Consensus pattern (31 bp):
TTTCAAAATTTTGTCATTTTACCCCTTAAAA
Found at i:23834 original size:15 final size:14
Alignment explanation
Indices: 23814--23850 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 14
23804 TGATCTTCAT
23814 TCTCCTCCTCCTACC
1 TCTCCTCCTCCT-CC
23829 TCTCCTCCTCCTCC
1 TCTCCTCCTCCTCC
23843 TCATCCTC
1 TC-TCCTC
23851 TACTTCATCG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 4 0.19
15 17 0.81
ACGTcount: A:0.05, C:0.59, G:0.00, T:0.35
Consensus pattern (14 bp):
TCTCCTCCTCCTCC
Found at i:25502 original size:31 final size:29
Alignment explanation
Indices: 25450--25538 Score: 90
Period size: 29 Copynumber: 3.0 Consensus size: 29
25440 AAAAATGGAT
* * *
25450 ACATGTCATTTTT-AACACGTGGTGTGCC
1 ACATGTCCTTTTTGTACACGTGGCGTGCC
* *
25478 ACATGTCCTTTTTTTGTACACGTGGCATGCT
1 ACATGTCC--TTTTTGTACACGTGGCGTGCC
**
25509 ATGTGTCCTTTTTGTACACGTGGCGTGCC
1 ACATGTCCTTTTTGTACACGTGGCGTGCC
25538 A
1 A
25539 TCGGTCGCCG
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
28 7 0.14
29 20 0.41
30 5 0.10
31 17 0.35
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (29 bp):
ACATGTCCTTTTTGTACACGTGGCGTGCC
Found at i:27389 original size:107 final size:107
Alignment explanation
Indices: 27203--27416 Score: 401
Period size: 107 Copynumber: 2.0 Consensus size: 107
27193 GTGAAGGCGC
*
27203 GTTTGACTTCTGATTAAGGCGATTTTAGCGGTGTTTCAAAGATCTCGATGAGAAGAATATAATAG
1 GTTTGACTTCTGATTAAGCCGATTTTAGCGGTGTTTCAAAGATCTCGATGAGAAGAATATAATAG
*
27268 TTTCTTTTTGCTACTAAGTCTCTTGGCTCAATGGTAGTTGTA
66 CTTCTTTTTGCTACTAAGTCTCTTGGCTCAATGGTAGTTGTA
*
27310 GTTTGACTTCTGATTAAGCCGATTTTAGCGGTGTTTCAAAGATCTCGATGAGTAGAATATAATAG
1 GTTTGACTTCTGATTAAGCCGATTTTAGCGGTGTTTCAAAGATCTCGATGAGAAGAATATAATAG
27375 CTTCTTTTTGCTACTAAGTCTCTTGGCTCAATGGTAGTTGTA
66 CTTCTTTTTGCTACTAAGTCTCTTGGCTCAATGGTAGTTGTA
27417 TACTAATAGT
Statistics
Matches: 104, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
107 104 1.00
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.39
Consensus pattern (107 bp):
GTTTGACTTCTGATTAAGCCGATTTTAGCGGTGTTTCAAAGATCTCGATGAGAAGAATATAATAG
CTTCTTTTTGCTACTAAGTCTCTTGGCTCAATGGTAGTTGTA
Found at i:28127 original size:26 final size:26
Alignment explanation
Indices: 28098--28175 Score: 156
Period size: 26 Copynumber: 3.0 Consensus size: 26
28088 TGCCTTAAAA
28098 CATGCTATTGTAGAAAATAAAAGTTT
1 CATGCTATTGTAGAAAATAAAAGTTT
28124 CATGCTATTGTAGAAAATAAAAGTTT
1 CATGCTATTGTAGAAAATAAAAGTTT
28150 CATGCTATTGTAGAAAATAAAAGTTT
1 CATGCTATTGTAGAAAATAAAAGTTT
28176 TCGTAGTTGG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 52 1.00
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (26 bp):
CATGCTATTGTAGAAAATAAAAGTTT
Found at i:28898 original size:2 final size:2
Alignment explanation
Indices: 28891--28924 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
28881 ATATGTAGTG
28891 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28925 G
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.