Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021426.1 Corchorus olitorius cultivar O-4 contig21459, 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: 41656
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Found at i:1373 original size:19 final size:19
Alignment explanation
Indices: 1345--1383 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1335 TAACAATCTA
* *
1345 ATTGGTGGAAGTGGAAATG
1 ATTGGAGGAAGTGAAAATG
*
1364 ATTGGAGGAATTGAAAATG
1 ATTGGAGGAAGTGAAAATG
1383 A
1 A
1384 ACAAGGAGTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.36, T:0.26
Consensus pattern (19 bp):
ATTGGAGGAAGTGAAAATG
Found at i:3250 original size:2 final size:2
Alignment explanation
Indices: 3245--3305 Score: 95
Period size: 2 Copynumber: 30.5 Consensus size: 2
3235 TGTGTGTGTG
* *
3245 TA TA TA TA TA TA TA TA CA TA TA TG 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 TA TA TA TA
*
3287 CA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
3306 TAGAAGCTTA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5876 original size:13 final size:13
Alignment explanation
Indices: 5858--5882 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5848 TTTTTACCAC
5858 CTTAAAATTATTG
1 CTTAAAATTATTG
5871 CTTAAAATTATT
1 CTTAAAATTATT
5883 TTTTGGCAAA
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:0.04, T:0.48
Consensus pattern (13 bp):
CTTAAAATTATTG
Found at i:10576 original size:25 final size:27
Alignment explanation
Indices: 10526--10576 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 27
10516 ATATCATAAT
*
10526 TTTCGGCTAGAATGAATTTTTGTATTA
1 TTTCGGCTAGAATCAATTTTTGTATTA
10553 TTTCGGCTA-AATCAA-TTTTGTATT
1 TTTCGGCTAGAATCAATTTTTGTATT
10577 TTAACCCTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 9 0.39
26 5 0.22
27 9 0.39
ACGTcount: A:0.25, C:0.10, G:0.16, T:0.49
Consensus pattern (27 bp):
TTTCGGCTAGAATCAATTTTTGTATTA
Found at i:11055 original size:10 final size:11
Alignment explanation
Indices: 11040--11105 Score: 70
Period size: 10 Copynumber: 6.4 Consensus size: 11
11030 TAACAATTTA
11040 AATTAAT-AAT
1 AATTAATAAAT
11050 AATTAATAAAT
1 AATTAATAAAT
11061 AA-TAATTAAAT
1 AATTAA-TAAAT
11072 AATTAAT-AAT
1 AATTAATAAAT
11082 AATTAA-AAA-
1 AATTAATAAAT
* *
11091 AATAAAAAAAT
1 AATTAATAAAT
11102 AATT
1 AATT
11106 GGTGCCGTCC
Statistics
Matches: 48, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
9 5 0.10
10 24 0.50
11 16 0.33
12 3 0.06
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AATTAATAAAT
Found at i:11058 original size:7 final size:7
Alignment explanation
Indices: 11046--11081 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
11036 TTTAAATTAA
11046 TAATAAT
1 TAATAAT
*
11053 TAATAAA
1 TAATAAT
11060 TAATAAT
1 TAATAAT
11067 TAAATAAT
1 T-AATAAT
11075 TAATAAT
1 TAATAAT
11082 AATTAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
7 19 0.73
8 7 0.27
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (7 bp):
TAATAAT
Found at i:11074 original size:18 final size:18
Alignment explanation
Indices: 11038--11088 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
11028 AATAACAATT
*
11038 TAAATTAATAA-TAATTAA
1 TAAA-TAATAATTAAATAA
11056 TAAATAATAATTAAATAA
1 TAAATAATAATTAAATAA
*
11074 TTAATAATAATTAAA
1 TAAATAATAATTAAA
11089 AAAATAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.20
18 24 0.80
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TAAATAATAATTAAATAA
Found at i:11093 original size:22 final size:22
Alignment explanation
Indices: 11047--11095 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
11037 TTAAATTAAT
**
11047 AATAATTAATAAATAATAATTA
1 AATAATTAATAAATAATAAAAA
11069 AATAATTAAT-AATAATTAAAAA
1 AATAATTAATAAATAA-TAAAAA
11091 AATAA
1 AATAA
11096 AAAAATAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 5 0.21
22 19 0.79
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
AATAATTAATAAATAATAAAAA
Found at i:14613 original size:39 final size:40
Alignment explanation
Indices: 14558--14634 Score: 111
Period size: 39 Copynumber: 1.9 Consensus size: 40
14548 CGTTTTCTTT
* **
14558 TCCCTTCTTCGTTCTCTACTGTATCCTTCTCCCTCTATTC
1 TCCCTTCTTCATTCTCTACCATATCCTTCTCCCTCTATTC
*
14598 TCCCTT-TTCATTCTCTACCATATCCTTCTCCTTCTAT
1 TCCCTTCTTCATTCTCTACCATATCCTTCTCCCTCTAT
14635 GCCCCGCTCG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
39 27 0.82
40 6 0.18
ACGTcount: A:0.10, C:0.39, G:0.03, T:0.48
Consensus pattern (40 bp):
TCCCTTCTTCATTCTCTACCATATCCTTCTCCCTCTATTC
Found at i:17501 original size:27 final size:27
Alignment explanation
Indices: 17470--17528 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
17460 GGATCCTTCC
* *
17470 TTTTCCTGGTAGGCTTATTCAAATCTT
1 TTTTCCTGGTAGGCTTATCCAAACCTT
* * *
17497 TTTTCTTTGTAGGCTTGTCCAAACCTT
1 TTTTCCTGGTAGGCTTATCCAAACCTT
17524 TTTTC
1 TTTTC
17529 TTTGAAGTCT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.15, C:0.20, G:0.14, T:0.51
Consensus pattern (27 bp):
TTTTCCTGGTAGGCTTATCCAAACCTT
Found at i:17529 original size:27 final size:27
Alignment explanation
Indices: 17478--17532 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
17468 CCTTTTCCTG
* *
17478 GTAGGCTTATTCAAATCTTTTTTCTTT
1 GTAGGCTTATCCAAACCTTTTTTCTTT
*
17505 GTAGGCTTGTCCAAACCTTTTTTCTTT
1 GTAGGCTTATCCAAACCTTTTTTCTTT
17532 G
1 G
17533 AAGTCTTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.16, C:0.18, G:0.15, T:0.51
Consensus pattern (27 bp):
GTAGGCTTATCCAAACCTTTTTTCTTT
Found at i:25937 original size:199 final size:199
Alignment explanation
Indices: 25597--25998 Score: 696
Period size: 199 Copynumber: 2.0 Consensus size: 199
25587 AAAGCCAAAT
*
25597 GAAGAAATTACATCATAAAATTTCAAATACCACTGACGGGAGGCTTGTTTCAATCTATATATGAA
1 GAAGAAATTACATCATAAAATTTCAAATACCACTGACGGGAGGCTTGTTTCAATCCATATATGAA
* * ** *
25662 TTTCTTGGGCTTGCATACTAGATGCTCACCGTCACTAGAGGAGAATCCTTCTGGTTGTTTCATAT
66 TTTCTTGAGCTTGCATACTAGATGCTCACCATCACTAGAAAAAAATCCTTCTGGTTGTTTCATAT
25727 AAACCTCCTCCTCTAAGGCTCCATTGAGGAATGCCGTTTTCACATCCATTTGATATGCAATTCCA
131 AAACCTCCTCCTCTAAGGCTCCATTGAGGAATGCCGTTTTCACATCCATTTGATATGCAATTCCA
25792 TATC
196 TATC
*
25796 GAAGAAATTACATCATGAAATTTCAAATACCACTGACGGGAGGCTTGTTTCAATCCATATATGAA
1 GAAGAAATTACATCATAAAATTTCAAATACCACTGACGGGAGGCTTGTTTCAATCCATATATGAA
* * *
25861 TTTCTTGAGCTTGCATACTAGATGTTCATCATCATTAGAAAAAAATCCTTCTGGTTGTTTCATAT
66 TTTCTTGAGCTTGCATACTAGATGCTCACCATCACTAGAAAAAAATCCTTCTGGTTGTTTCATAT
* *
25926 AAACCTCCTCCTCTAAGTCTCCATTGAGGAATGTCGTTTTCACATCCATTTGATATGCAATTCCA
131 AAACCTCCTCCTCTAAGGCTCCATTGAGGAATGCCGTTTTCACATCCATTTGATATGCAATTCCA
25991 TATC
196 TATC
25995 GAAG
1 GAAG
25999 TGTGCAACTA
Statistics
Matches: 191, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
199 191 1.00
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (199 bp):
GAAGAAATTACATCATAAAATTTCAAATACCACTGACGGGAGGCTTGTTTCAATCCATATATGAA
TTTCTTGAGCTTGCATACTAGATGCTCACCATCACTAGAAAAAAATCCTTCTGGTTGTTTCATAT
AAACCTCCTCCTCTAAGGCTCCATTGAGGAATGCCGTTTTCACATCCATTTGATATGCAATTCCA
TATC
Found at i:28702 original size:18 final size:19
Alignment explanation
Indices: 28669--28705 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
28659 GAAGTTCATG
28669 TTTGAAGACTTATTGAAGA
1 TTTGAAGACTTATTGAAGA
28688 TTTGAAGAC-TATTGAAGA
1 TTTGAAGACTTATTGAAGA
28706 ATTATTTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.38, C:0.05, G:0.22, T:0.35
Consensus pattern (19 bp):
TTTGAAGACTTATTGAAGA
Found at i:32421 original size:29 final size:29
Alignment explanation
Indices: 32338--32474 Score: 98
Period size: 29 Copynumber: 4.6 Consensus size: 29
32328 CACAAACGAT
32338 CAAAATGCCCCT-GAATTGTGCAAAAATGAC
1 CAAAATGCCCCTAG-A-TGTGCAAAAATGAC
* * * *
32368 CAAAATGACACTAGATATGCGAAAATGAC
1 CAAAATGCCCCTAGATGTGCAAAAATGAC
*
32397 CAAAATGCCCCTAGACGTGCAAAAAAATGAC
1 CAAAATGCCCCTAGATGTGC--AAAAATGAC
* ** **
32428 AAAAAT-ATCCTAGATGTAAAAAAATATGAC
1 CAAAATGCCCCTAGATGT-GCAAAA-ATGAC
* *
32458 CAAAATGACACTAGATG
1 CAAAATGCCCCTAGATG
32475 ACCCTAATGC
Statistics
Matches: 83, Mismatches: 18, Indels: 11
0.74 0.16 0.10
Matches are distributed among these distances:
29 32 0.39
30 29 0.35
31 22 0.27
ACGTcount: A:0.47, C:0.19, G:0.15, T:0.18
Consensus pattern (29 bp):
CAAAATGCCCCTAGATGTGCAAAAATGAC
Found at i:32440 original size:30 final size:30
Alignment explanation
Indices: 32406--32463 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
32396 CCAAAATGCC
*
32406 CCTAGACGTGCAAAAAA-ATGACAAAAATAT
1 CCTAGACGT-AAAAAAATATGACAAAAATAT
* *
32436 CCTAGATGTAAAAAAATATGACCAAAAT
1 CCTAGACGTAAAAAAATATGACAAAAAT
32464 GACACTAGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 6 0.25
30 18 0.75
ACGTcount: A:0.53, C:0.16, G:0.12, T:0.19
Consensus pattern (30 bp):
CCTAGACGTAAAAAAATATGACAAAAATAT
Found at i:32729 original size:51 final size:51
Alignment explanation
Indices: 32646--32773 Score: 229
Period size: 51 Copynumber: 2.5 Consensus size: 51
32636 ACACCCGTCC
*
32646 TATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGACCGTCTTCCGCT
1 TATCCTTTGAACTGTCTTCCAATTCAACCTTAAAAAGGACCGTCTTCCGCT
*
32697 TATCTTTTGAACTGTCTTCCAATTCAACCTTAAAAAGGACCGTCTTCCGCT
1 TATCCTTTGAACTGTCTTCCAATTCAACCTTAAAAAGGACCGTCTTCCGCT
*
32748 TATCCTTTGAATTGTCTTCCAATTCA
1 TATCCTTTGAACTGTCTTCCAATTCA
32774 CTCTTCTGTA
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 73 1.00
ACGTcount: A:0.25, C:0.27, G:0.11, T:0.38
Consensus pattern (51 bp):
TATCCTTTGAACTGTCTTCCAATTCAACCTTAAAAAGGACCGTCTTCCGCT
Done.