Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014018.1 Corchorus olitorius cultivar O-4 contig14051, 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: 18382
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:120 original size:22 final size:24
Alignment explanation
Indices: 85--143 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 24
75 ATAAATGTTG
* *
85 CTGATAA-TCTTCT-CTTTTATCT
1 CTGATAATTCTTCTCCATTTATCA
107 CTGATAATTC-TCTCCATTTATCA
1 CTGATAATTCTTCTCCATTTATCA
130 CTTGATAATATCTT
1 C-TGATAAT-TCTT
144 GCCAGATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
22 10 0.33
23 10 0.33
24 7 0.23
25 2 0.07
26 1 0.03
ACGTcount: A:0.24, C:0.22, G:0.05, T:0.49
Consensus pattern (24 bp):
CTGATAATTCTTCTCCATTTATCA
Found at i:4389 original size:65 final size:62
Alignment explanation
Indices: 4310--4522 Score: 241
Period size: 65 Copynumber: 3.4 Consensus size: 62
4300 GAAAGGTAAA
* * *
4310 ATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAATGTCTATTGGAAATTT
1 ATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAATATCAATT-GAAA--G
* *
4375 ATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAGTATCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAATATCAATTGAAAG
* * * * *** * * *
4437 ATCATGACAACTTATGGTGTCAATTG--CAAGATTATGACAACTTCTGGTGTCATTTGTAAG
1 ATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAATATCAATTGAAAG
*
4497 ACCATGACAACTTCTGGTGTCAATTG
1 ATCATGACAACTTCTGGTGTCAATTG
4523 TAAGACCATG
Statistics
Matches: 132, Mismatches: 16, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
60 50 0.38
62 25 0.19
64 3 0.02
65 54 0.41
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Consensus pattern (62 bp):
ATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAATATCAATTGAAAG
Found at i:4460 original size:30 final size:30
Alignment explanation
Indices: 4305--4556 Score: 216
Period size: 30 Copynumber: 8.2 Consensus size: 30
4295 ATTTTGAAAG
*
4305 GTAAAATCATGACAACTTCTGGTGTCAATT
1 GTAAGATCATGACAACTTCTGGTGTCAATT
* * * *** *
4335 GAATAAAATTATGACATCTTCAAATGTCTATT
1 G--TAAGATCATGACAACTTCTGGTGTCAATT
* *
4367 GGAAATTTATCATGACAACTTCTGGTGTCAATT
1 -GTAA--GATCATGACAACTTCTGGTGTCAATT
* * * ** *
4400 GAATAAAATTATGACATCTTCAAGTATCAATT
1 G--TAAGATCATGACAACTTCTGGTGTCAATT
* *
4432 GCAAGATCATGACAACTTATGGTGTCAATT
1 GTAAGATCATGACAACTTCTGGTGTCAATT
* * *
4462 GCAAGATTATGACAACTTCTGGTGTCATTT
1 GTAAGATCATGACAACTTCTGGTGTCAATT
*
4492 GTAAGACCATGACAACTTCTGGTGTCAATT
1 GTAAGATCATGACAACTTCTGGTGTCAATT
* * *
4522 GTAAGACCATGACAACTTCTAGTGTCATTT
1 GTAAGATCATGACAACTTCTGGTGTCAATT
4552 GTAAG
1 GTAAG
4557 TAGAATAAAT
Statistics
Matches: 177, Mismatches: 38, Indels: 14
0.77 0.17 0.06
Matches are distributed among these distances:
30 108 0.61
31 2 0.01
32 45 0.25
33 20 0.11
34 2 0.01
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Consensus pattern (30 bp):
GTAAGATCATGACAACTTCTGGTGTCAATT
Found at i:4508 original size:60 final size:60
Alignment explanation
Indices: 4312--4556 Score: 247
Period size: 60 Copynumber: 4.0 Consensus size: 60
4302 AAGGTAAAAT
* * * * * * * *
4312 CATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAATGTCTATTGGAAATTTAT
1 CATGACAACTTCTGGTGTCAATTG--TAAGATTATGACAACTTCTAGTGTC-ATTTGTAA--GAC
* * * * * * *
4377 CATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAGTATCAATTGCAAGAT
1 CATGACAACTTCTGGTGTCAATTG--TAAGATTATGACAACTTCTAGTGTCATTTGTAAGAC
* * *
4439 CATGACAACTTATGGTGTCAATTGCAAGATTATGACAACTTCTGGTGTCATTTGTAAGAC
1 CATGACAACTTCTGGTGTCAATTGTAAGATTATGACAACTTCTAGTGTCATTTGTAAGAC
**
4499 CATGACAACTTCTGGTGTCAATTGTAAGACCATGACAACTTCTAGTGTCATTTGTAAG
1 CATGACAACTTCTGGTGTCAATTGTAAGATTATGACAACTTCTAGTGTCATTTGTAAG
4557 TAGAATAAAT
Statistics
Matches: 159, Mismatches: 21, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
60 80 0.50
62 25 0.16
64 5 0.03
65 49 0.31
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (60 bp):
CATGACAACTTCTGGTGTCAATTGTAAGATTATGACAACTTCTAGTGTCATTTGTAAGAC
Found at i:5739 original size:22 final size:24
Alignment explanation
Indices: 5704--5762 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 24
5694 ATAAATGTTG
* *
5704 CTGATAA-TCTTCT-CTTTTATCT
1 CTGATAATTCTTCTCCATTTATCA
5726 CTGATAATTC-TCTCCATTTATCA
1 CTGATAATTCTTCTCCATTTATCA
5749 CTTGATAATATCTT
1 C-TGATAAT-TCTT
5763 GCCAGATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
22 10 0.33
23 10 0.33
24 7 0.23
25 2 0.07
26 1 0.03
ACGTcount: A:0.24, C:0.22, G:0.05, T:0.49
Consensus pattern (24 bp):
CTGATAATTCTTCTCCATTTATCA
Found at i:8823 original size:21 final size:21
Alignment explanation
Indices: 8768--8823 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 21
8758 AAAATACAAT
* **
8768 TTTTGAATTTTGACTTTTGTC
1 TTTTGAATTTTGAGTTTTGAA
***
8789 TTTTGAAGAATGAGTTTTGAA
1 TTTTGAATTTTGAGTTTTGAA
8810 TTTTGAATTTTGAG
1 TTTTGAATTTTGAG
8824 CAATGAAATG
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.23, C:0.04, G:0.20, T:0.54
Consensus pattern (21 bp):
TTTTGAATTTTGAGTTTTGAA
Found at i:9002 original size:33 final size:33
Alignment explanation
Indices: 8962--9036 Score: 114
Period size: 33 Copynumber: 2.3 Consensus size: 33
8952 AACTGTGGAT
* * *
8962 TTTGAACTTTGAGTTTTGATATGATATGCAAAA
1 TTTGAACTTTGAATTTTGAAATGAAATGCAAAA
*
8995 TTTGAACTTTGAATTTTGAAATGAAATGCAAAT
1 TTTGAACTTTGAATTTTGAAATGAAATGCAAAA
9028 TTTGAACTT
1 TTTGAACTT
9037 CTTAATTAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.35, C:0.07, G:0.16, T:0.43
Consensus pattern (33 bp):
TTTGAACTTTGAATTTTGAAATGAAATGCAAAA
Found at i:9200 original size:54 final size:54
Alignment explanation
Indices: 9140--9334 Score: 268
Period size: 54 Copynumber: 3.6 Consensus size: 54
9130 TGATCATCGT
* * * *
9140 AAACTTCT-TGGAATGACCACACTGGATCAACTTAAGATCAAATTAGATTTTTGA
1 AAACTTCTAT-GAAAGACCACACTGGATCAACTTAAGATCAACTTAGATCTCTGA
* * *
9194 AAACTTCTATGGAAGACCACACTGGGTCATCTTAAGATCAACTTAGATCTCTGA
1 AAACTTCTATGAAAGACCACACTGGATCAACTTAAGATCAACTTAGATCTCTGA
* *
9248 AAACTTCTATGAAAGACCACACT-AAGTCATCTTAAGATCAACTTAGATCTCTGA
1 AAACTTCTATGAAAGACCACACTGGA-TCAACTTAAGATCAACTTAGATCTCTGA
*
9302 AAACTTCTATGAAAGACCACACTAGATCAACTT
1 AAACTTCTATGAAAGACCACACTGGATCAACTT
9335 TCTAGAGAGA
Statistics
Matches: 126, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
54 124 0.98
55 2 0.02
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.28
Consensus pattern (54 bp):
AAACTTCTATGAAAGACCACACTGGATCAACTTAAGATCAACTTAGATCTCTGA
Found at i:9252 original size:108 final size:109
Alignment explanation
Indices: 9089--9326 Score: 283
Period size: 108 Copynumber: 2.2 Consensus size: 109
9079 ATGGAAACCT
* *
9089 TTCT-TGGAATGACCGCACTAGGTCAGTTTAGAGATCAACTCTGATCATCGTAAACTTCT-TGGA
1 TTCTATGGAA-GACCACACTAGGTCAGTTTAGAGATCAACTCTGATCATCGAAAACTTCTAT-GA
* * * *
9152 ATGACCACACT-GGATCAACTTAAGATCAAATTAGATTTTTGAAAAC
64 AAGACCACACTAAG-TCAACTTAAGATCAAATTAGATCTCTGAAAAC
*
9198 TTCTATGGAAGACCACACTGGGTCA-TCTTA-AGATCAACT-TAGATC-TCTGAAAACTTCTATG
1 TTCTATGGAAGACCACACTAGGTCAGT-TTAGAGATCAACTCT-GATCATC-GAAAACTTCTATG
* *
9259 AAAGACCACACTAAGTCATCTTAAGATCAACTTAGATCTCTGAAAAC
63 AAAGACCACACTAAGTCAACTTAAGATCAAATTAGATCTCTGAAAAC
*
9306 TTCTATGAAAGACCACACTAG
1 TTCTATGGAAGACCACACTAG
9327 ATCAACTTTC
Statistics
Matches: 112, Mismatches: 11, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
107 3 0.03
108 82 0.73
109 22 0.20
110 5 0.04
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.29
Consensus pattern (109 bp):
TTCTATGGAAGACCACACTAGGTCAGTTTAGAGATCAACTCTGATCATCGAAAACTTCTATGAAA
GACCACACTAAGTCAACTTAAGATCAAATTAGATCTCTGAAAAC
Found at i:9487 original size:37 final size:37
Alignment explanation
Indices: 9441--9973 Score: 479
Period size: 37 Copynumber: 14.4 Consensus size: 37
9431 GATTTTGAAT
* * * *
9441 AGACACCTAAACATGTACCTTTAATAAGGATTTAATA
1 AGACACCTAAACAGGGACCTTAAATAAGGATTTGATA
* * ** * * *
9478 AGAAACCTAAACAGGAATTTTGAACAA-GATTTTGATG
1 AGACACCTAAACAGGGACCTTAAATAAGGA-TTTGATA
9515 AGACACCTAAACAGGGACCTTAAATAAGGATTTGATA
1 AGACACCTAAACAGGGACCTTAAATAAGGATTTGATA
* * * * *
9552 AGAAACCTAAACAGGGATCTTAAACAA-AACTTTTGACA
1 AGACACCTAAACAGGGACCTTAAATAAGGA--TTTGATA
* * *
9590 AGAAACCTAAACATGCACCTTAAATAAGGATTTGATA
1 AGACACCTAAACAGGGACCTTAAATAAGGATTTGATA
* * * * *
9627 AGAAACCTAAACAAGGATCTTAAACAA-GATTTTGATG
1 AGACACCTAAACAGGGACCTTAAATAAGGA-TTTGATA
* * *
9664 AGACACCTAAATAGGGACCTTAAATAAAGATTTAATA
1 AGACACCTAAACAGGGACCTTAAATAAGGATTTGATA
* * * * * **
9701 AGAAACCTAAACAGGAATCTTGAACAA-GATTTTGACG
1 AGACACCTAAACAGGGACCTTAAATAAGGA-TTTGATA
* * * ** *
9738 GGACACCTAAACAGGGATCTTGAACCA-GATTTCGATG
1 AGACACCTAAACAGGGACCTTAAATAAGGATTT-GATA
*
9775 AGACACCTAAACAAGGACCTTAAATAAGGATTTGATA
1 AGACACCTAAACAGGGACCTTAAATAAGGATTTGATA
*
9812 AGACACCTAAACAGGGACCTTAAATAAGGATTTAATA
1 AGACACCTAAACAGGGACCTTAAATAAGGATTTGATA
*
9849 AGACACCTAAACATGGACCTTAAACT-AGGATTTGATA
1 AGACACCTAAACAGGGACCTTAAA-TAAGGATTTGATA
* * * * * *
9886 AGACACCTAAATAGGAATCTTGAACAA-TATTTTGATGA
1 AGACACCTAAACAGGGACCTTAAATAAGGA-TTTGAT-A
*
9924 A-ACACCTAAACAGAGACCTTAAATAAGGATTTGATA
1 AGACACCTAAACAGGGACCTTAAATAAGGATTTGATA
9960 AGACACCTAAACAG
1 AGACACCTAAACAG
9974 AAATCTTGAA
Statistics
Matches: 402, Mismatches: 78, Indels: 32
0.79 0.15 0.06
Matches are distributed among these distances:
36 13 0.03
37 346 0.86
38 42 0.10
39 1 0.00
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.23
Consensus pattern (37 bp):
AGACACCTAAACAGGGACCTTAAATAAGGATTTGATA
Found at i:11110 original size:17 final size:18
Alignment explanation
Indices: 11044--11110 Score: 59
Period size: 17 Copynumber: 3.8 Consensus size: 18
11034 CATTTTGATT
*
11044 TTTTCTTTCTTTCTTTTTC
1 TTTTCTTT-TCTCTTTTTC
*
11063 TTTT-TTTTCACTTTTTC
1 TTTTCTTTTCTCTTTTTC
* *
11080 TTTGC-TTTCGCTTTTT-
1 TTTTCTTTTCTCTTTTTC
*
11096 TTTTCTTTTTTCTTT
1 TTTTCTTTTCTCTTT
11111 AGATTGCTTC
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
16 4 0.10
17 28 0.72
18 3 0.08
19 4 0.10
ACGTcount: A:0.01, C:0.18, G:0.03, T:0.78
Consensus pattern (18 bp):
TTTTCTTTTCTCTTTTTC
Found at i:11497 original size:6 final size:6
Alignment explanation
Indices: 11481--11538 Score: 84
Period size: 6 Copynumber: 10.0 Consensus size: 6
11471 AACAATCTTA
* *
11481 TTTTTC CTTTTC TTTTTC TTTTTC TTTTT- TTCTT- TTTTTC TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
11527 TTTTTC TTTTTC
1 TTTTTC TTTTTC
11539 CCATTTTTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
5 8 0.17
6 39 0.83
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTC
Found at i:11512 original size:8 final size:8
Alignment explanation
Indices: 11476--11525 Score: 57
Period size: 8 Copynumber: 5.9 Consensus size: 8
11466 TTAAGAACAA
11476 TCTTATTTT
1 TCTT-TTTT
11485 TCCTTTTCTT
1 T-CTTTT-TT
11495 T-TTCTTTT
1 TCTT-TTTT
11503 TCTTTTTT
1 TCTTTTTT
11511 TCTTTTTT
1 TCTTTTTT
11519 TCTTTTT
1 TCTTTTT
11526 CTTTTTCTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
8 24 0.65
9 7 0.19
10 6 0.16
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (8 bp):
TCTTTTTT
Found at i:11545 original size:20 final size:20
Alignment explanation
Indices: 11507--11545 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
11497 TCTTTTTCTT
** *
11507 TTTTTCTTTTTTTCTTTTTC
1 TTTTTCTTTTTCCCATTTTC
11527 TTTTTCTTTTTCCCATTTT
1 TTTTTCTTTTTCCCATTTT
11546 TTTAATTCAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTTCTTTTTCCCATTTTC
Found at i:11545 original size:28 final size:28
Alignment explanation
Indices: 11488--11547 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
11478 TTATTTTTCC
** *
11488 TTTTCTTTTTCTTTTTCTTTTTTTCTTT
1 TTTTCTTTTTCTTTTTCTTTTTCCCATT
11516 TTTTCTTTTTCTTTTTCTTTTTCCCATT
1 TTTTCTTTTTCTTTTTCTTTTTCCCATT
11544 TTTT
1 TTTT
11548 TAATTCACAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.82
Consensus pattern (28 bp):
TTTTCTTTTTCTTTTTCTTTTTCCCATT
Found at i:11829 original size:14 final size:13
Alignment explanation
Indices: 11765--11828 Score: 85
Period size: 14 Copynumber: 4.7 Consensus size: 13
11755 TAAGATGATC
11765 TTTTGAAAACTCAT
1 TTTTGAAAA-TCAT
11779 TTTTGAAAATCAT
1 TTTTGAAAATCAT
11792 TTCTTGAAAA-CAGT
1 TT-TTGAAAATCA-T
11806 TTCTTGAAAATCAT
1 TT-TTGAAAATCAT
11820 TTTTGAAAA
1 TTTTGAAAA
11829 ACGTCCTTTA
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
13 15 0.32
14 30 0.64
15 2 0.04
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (13 bp):
TTTTGAAAATCAT
Done.