Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015685.1 Corchorus olitorius cultivar O-4 contig15718, 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: 74855
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:124 original size:2 final size:2
Alignment explanation
Indices: 117--160 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
107 CTTTAACTAG
117 TA TA TA TA 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 TA TA TA TA
159 TA
1 TA
161 GTTTACTTCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1498 original size:22 final size:23
Alignment explanation
Indices: 1473--1516 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
1463 CTATATATAT
1473 ATAGCT-AATTATATATAATTGA
1 ATAGCTCAATTATATATAATTGA
*
1495 ATAGCTGCTATTATATATAATT
1 ATAGCT-CAATTATATATAATT
1517 AATTTATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
24 13 0.68
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (23 bp):
ATAGCTCAATTATATATAATTGA
Found at i:5155 original size:18 final size:19
Alignment explanation
Indices: 5120--5157 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
5110 ATAATCCTTT
5120 AAGTATTTCACCTAAAAAAA
1 AAGTATTTCA-CTAAAAAAA
5140 AAGTATTTCA-TAAAAAAA
1 AAGTATTTCACTAAAAAAA
5158 TAAGAGAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
20 10 0.56
ACGTcount: A:0.58, C:0.11, G:0.05, T:0.26
Consensus pattern (19 bp):
AAGTATTTCACTAAAAAAA
Found at i:12068 original size:2 final size:2
Alignment explanation
Indices: 12030--12055 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12020 AATCCAAAAC
12030 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
12056 AGTTTATCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:17581 original size:3 final size:3
Alignment explanation
Indices: 17551--17595 Score: 56
Period size: 3 Copynumber: 14.7 Consensus size: 3
17541 TATTTTTATG
*
17551 ATA A-A ATA AAA ATA TATA ATA TATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA -ATA ATA -ATA ATA ATA ATA ATA ATA ATA AT
17596 GAAAAGTAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
2 2 0.05
3 29 0.78
4 6 0.16
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:18594 original size:13 final size:13
Alignment explanation
Indices: 18576--18606 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
18566 GCCAAGTCCT
18576 GAGTTTGTGTCAC
1 GAGTTTGTGTCAC
18589 GAGTTTGTGTCAC
1 GAGTTTGTGTCAC
18602 GAGTT
1 GAGTT
18607 GACTCGGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.16, C:0.13, G:0.32, T:0.39
Consensus pattern (13 bp):
GAGTTTGTGTCAC
Found at i:19212 original size:56 final size:56
Alignment explanation
Indices: 19123--19236 Score: 183
Period size: 56 Copynumber: 2.0 Consensus size: 56
19113 TATCCATTTC
* * *
19123 CTTTCATACAATAAATGTTATAATAAATTCTATCCCAATATCTCTACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCCTATCCCAATATCTCTACTTAACTATT
**
19179 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAACTATT
1 CTTTCACACAATAAATGTTATAATAAATCCTATCCCAATATCTCTACTTAACTATT
19235 CT
1 CT
19237 ATAAAATAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.35, C:0.23, G:0.02, T:0.40
Consensus pattern (56 bp):
CTTTCACACAATAAATGTTATAATAAATCCTATCCCAATATCTCTACTTAACTATT
Found at i:21264 original size:13 final size:13
Alignment explanation
Indices: 21241--21278 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
21231 TACTTTAATT
21241 ATTAGGAGGGTCAA
1 ATTA-GAGGGTCAA
21255 ATTAGAGGGTCAA
1 ATTAGAGGGTCAA
*
21268 ATTGGAGGGTC
1 ATTAGAGGGTC
21279 CAAAAGAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 19 0.83
14 4 0.17
ACGTcount: A:0.32, C:0.08, G:0.37, T:0.24
Consensus pattern (13 bp):
ATTAGAGGGTCAA
Found at i:24872 original size:69 final size:70
Alignment explanation
Indices: 24790--24932 Score: 261
Period size: 71 Copynumber: 2.0 Consensus size: 70
24780 TTAAACGTTC
24790 CAATTGTCGAACTCGAACAG-GAGAAATCCCAAACCTTTCCCTCTTCCAGATTTTCCTTCACTTT
1 CAATTGTCGAACTCGAACAGAGAGAAATCCCAAACCTTTCCCTCTTCCAGATTTTCCTTCACTTT
24854 CTCTG
66 CTCTG
*
24859 CAATTGTCGAACTCGAACAGAAGAGAAATCCCAAACCTTTCCCTCTTTCAGATTTTCCTTCACTT
1 CAATTGTCGAACTCGAACAG-AGAGAAATCCCAAACCTTTCCCTCTTCCAGATTTTCCTTCACTT
24924 TCTCTG
65 TCTCTG
24930 CAA
1 CAA
24933 ATTTTCATTC
Statistics
Matches: 71, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
69 20 0.28
71 51 0.72
ACGTcount: A:0.27, C:0.31, G:0.11, T:0.31
Consensus pattern (70 bp):
CAATTGTCGAACTCGAACAGAGAGAAATCCCAAACCTTTCCCTCTTCCAGATTTTCCTTCACTTT
CTCTG
Found at i:28043 original size:19 final size:19
Alignment explanation
Indices: 28019--28057 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
28009 AAATCAAAGC
*
28019 TGTAAAACCATTAAGGCTT
1 TGTAAAACCATTAAGACTT
28038 TGTAAAACCATTAAGACTT
1 TGTAAAACCATTAAGACTT
28057 T
1 T
28058 AATAGACCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.33
Consensus pattern (19 bp):
TGTAAAACCATTAAGACTT
Found at i:29054 original size:21 final size:21
Alignment explanation
Indices: 29006--29054 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
28996 AGTAACAATA
29006 AAATAAA-TAAGCAAGAAAAT
1 AAATAAATTAAGCAAGAAAAT
* *
29026 -AATAAAATTAAGCAATAAGAT
1 AAAT-AAATTAAGCAAGAAAAT
29047 AAATAAAT
1 AAATAAAT
29055 ACTTCAATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
19 3 0.12
20 3 0.12
21 15 0.62
22 3 0.12
ACGTcount: A:0.67, C:0.04, G:0.08, T:0.20
Consensus pattern (21 bp):
AAATAAATTAAGCAAGAAAAT
Found at i:42106 original size:33 final size:32
Alignment explanation
Indices: 42064--42132 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 32
42054 CGGAATCTGA
* *
42064 TGAGAAATCAACCTACAAAAAGATGCCCAAGAT
1 TGAGAAATCAACCTACAAAAA-ATCCCCAAGAC
42097 TGAGAAATCAACCTACAAAAAATCCCCAAGAC
1 TGAGAAATCAACCTACAAAAAATCCCCAAGAC
42129 TGAG
1 TGAG
42133 TGATAGAGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 13 0.38
33 21 0.62
ACGTcount: A:0.48, C:0.23, G:0.14, T:0.14
Consensus pattern (32 bp):
TGAGAAATCAACCTACAAAAAATCCCCAAGAC
Found at i:50087 original size:7 final size:7
Alignment explanation
Indices: 50075--50105 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
50065 TCCTTTGTCC
50075 AAAAAAG
1 AAAAAAG
50082 AAAAAAG
1 AAAAAAG
50089 AAAAAAG
1 AAAAAAG
50096 AAAAAA-
1 AAAAAAG
50102 AAAA
1 AAAA
50106 GAAGTCCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.17
7 20 0.83
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:58926 original size:14 final size:14
Alignment explanation
Indices: 58907--58937 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
58897 GTCACTCCTT
*
58907 AAACCTCATCAACC
1 AAACCTCAGCAACC
58921 AAACCTCAGCAACC
1 AAACCTCAGCAACC
58935 AAA
1 AAA
58938 ACTGAACTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.39, G:0.03, T:0.10
Consensus pattern (14 bp):
AAACCTCAGCAACC
Found at i:65541 original size:20 final size:20
Alignment explanation
Indices: 65512--65550 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
65502 TGAGTTTGGT
* *
65512 TTAGTTTTTAGCATGTTTAA
1 TTAGTATTTAGCATATTTAA
65532 TTAGTATTTAGCATATTTA
1 TTAGTATTTAGCATATTTA
65551 GTCATTGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.05, G:0.13, T:0.54
Consensus pattern (20 bp):
TTAGTATTTAGCATATTTAA
Found at i:66425 original size:12 final size:12
Alignment explanation
Indices: 66389--66433 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
66379 GTTCCTGCTC
66389 TCTTTCTTTTGTT
1 TCTTTCTTTT-TT
66402 TCTTTCTTTTTT
1 TCTTTCTTTTTT
*
66414 TTTTTCTCTTTTT
1 TCTTTCT-TTTTT
*
66427 TCGTTCT
1 TCTTTCT
66434 GTTTGATCTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 8 0.29
13 20 0.71
ACGTcount: A:0.00, C:0.18, G:0.04, T:0.78
Consensus pattern (12 bp):
TCTTTCTTTTTT
Done.