Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017653.1 Corchorus olitorius cultivar O-4 contig17686, 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: 17317
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:274 original size:30 final size:29
Alignment explanation
Indices: 192--275 Score: 91
Period size: 30 Copynumber: 2.8 Consensus size: 29
182 TTAATACCTT
192 TTTTGCCCC-TGAACTTGTACGATTTTGACG
1 TTTTGCCCCATGAACTTGTA--ATTTTGACG
* *
222 TTTTACCCCCATAAACTT-TAATTTTGGACG
1 TTTT-GCCCCATGAACTTGTAATTTT-GACG
*
252 TTTTGCCCCATGAATTTGTAATTT
1 TTTTGCCCCATGAACTTGTAATTT
276 AGAGCCACGT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
29 15 0.33
30 18 0.40
31 6 0.13
32 6 0.13
ACGTcount: A:0.21, C:0.21, G:0.14, T:0.43
Consensus pattern (29 bp):
TTTTGCCCCATGAACTTGTAATTTTGACG
Found at i:4280 original size:19 final size:19
Alignment explanation
Indices: 4256--4293 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
4246 CAGGCTCCGT
*
4256 TTAGAAAAACTTGGAAAAA
1 TTAGAAAAACTTAGAAAAA
4275 TTAGAAAAACTTAGAAAAA
1 TTAGAAAAACTTAGAAAAA
4294 CCCAATAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.61, C:0.05, G:0.13, T:0.21
Consensus pattern (19 bp):
TTAGAAAAACTTAGAAAAA
Found at i:4281 original size:9 final size:10
Alignment explanation
Indices: 4256--4294 Score: 62
Period size: 10 Copynumber: 4.0 Consensus size: 10
4246 CAGGCTCCGT
4256 TTAGAAAAAC
1 TTAGAAAAAC
*
4266 TTGGAAAAA-
1 TTAGAAAAAC
4275 TTAGAAAAAC
1 TTAGAAAAAC
4285 TTAGAAAAAC
1 TTAGAAAAAC
4295 CCAATAAGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
9 8 0.31
10 18 0.69
ACGTcount: A:0.59, C:0.08, G:0.13, T:0.21
Consensus pattern (10 bp):
TTAGAAAAAC
Found at i:4500 original size:17 final size:17
Alignment explanation
Indices: 4474--4506 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4464 ATAAGAAATC
*
4474 ACAAATATTCAAATAAA
1 ACAAACATTCAAATAAA
4491 ACAAACATTCAAATAA
1 ACAAACATTCAAATAA
4507 TAATAATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.64, C:0.15, G:0.00, T:0.21
Consensus pattern (17 bp):
ACAAACATTCAAATAAA
Found at i:5370 original size:29 final size:29
Alignment explanation
Indices: 5308--5376 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 29
5298 ATTTTATTAG
** *
5308 AAATATTTA-TTAATATGTAATAAATATT
1 AAATATTTATTTAATATACAATAAATACT
*
5336 AGAATATTTATTTAATATACAATATATACT
1 A-AATATTTATTTAATATACAATAAATACT
5366 AAATA-TTATTT
1 AAATATTTATTT
5377 TTAGTGACAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
28 7 0.20
29 12 0.34
30 16 0.46
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (29 bp):
AAATATTTATTTAATATACAATAAATACT
Found at i:13850 original size:21 final size:21
Alignment explanation
Indices: 13826--13876 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
13816 CTGGTCCTAT
13826 CCGGGCCATGTGCAAGGATGG
1 CCGGGCCATGTGCAAGGATGG
13847 CCGGGCCATGTGCAAGGATGG
1 CCGGGCCATGTGCAAGGATGG
13868 CCGGGCCAT
1 CCGGGCCAT
13877 AGCCGGGTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.18, C:0.27, G:0.41, T:0.14
Consensus pattern (21 bp):
CCGGGCCATGTGCAAGGATGG
Found at i:16037 original size:26 final size:24
Alignment explanation
Indices: 15999--16109 Score: 93
Period size: 28 Copynumber: 4.3 Consensus size: 24
15989 AGAAATTTTT
15999 TTTTTTATATATGACGCAAAAAAAAA
1 TTTTTT-T-TATGACGCAAAAAAAAA
16025 CCTTTTTTTTATGACGCAGAAACAAAAA
1 --TTTTTTTTATGACGCA-AAA-AAAAA
*
16053 -TTTTTTTATGACGC--AAAAATA
1 TTTTTTTTATGACGCAAAAAAAAA
*
16074 TTTTTTTTTTCGACGCAAAACACAAAA
1 TTTTTTTTAT-GACGCAAAA-A-AAAA
16101 CTTTTTTTT
1 -TTTTTTTT
16110 TCTTTGACGC
Statistics
Matches: 71, Mismatches: 3, Indels: 18
0.77 0.03 0.20
Matches are distributed among these distances:
21 4 0.06
22 10 0.14
23 5 0.07
25 16 0.23
26 10 0.14
27 7 0.10
28 19 0.27
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.41
Consensus pattern (24 bp):
TTTTTTTTATGACGCAAAAAAAAA
Found at i:16062 original size:25 final size:24
Alignment explanation
Indices: 16008--16108 Score: 91
Period size: 25 Copynumber: 4.0 Consensus size: 24
15998 TTTTTTTATA
16008 TATGACGCAAAA-AAAAACCTTTTTTT
1 TATGACGCAAAACAAAAA---TTTTTT
16034 TATGACGCAGAAACAAAAATTTTTT
1 TATGACGCA-AAACAAAAATTTTTT
* *
16059 TATGACGC-AAA-AATATTTTTTT
1 TATGACGCAAAACAAAAATTTTTT
*
16081 TTTCGACGCAAAACACAAAACTTTTTT
1 TAT-GACGCAAAACA-AAAA-TTTTTT
16108 T
1 T
16109 TTCTTTGACG
Statistics
Matches: 63, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
22 11 0.17
23 8 0.13
24 3 0.05
25 15 0.24
26 11 0.17
27 10 0.16
28 5 0.08
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.37
Consensus pattern (24 bp):
TATGACGCAAAACAAAAATTTTTT
Found at i:16100 original size:30 final size:30
Alignment explanation
Indices: 16066--16131 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
16056 TTTTATGACG
16066 CAAAAATATTTTTTTT-TTCGACGCAAAACA
1 CAAAAAT-TTTTTTTTCTTCGACGCAAAACA
* * * *
16096 CAAAACTTTTTTTTTCTTTGACGCAAGACT
1 CAAAAATTTTTTTTTCTTCGACGCAAAACA
16126 CAAAAA
1 CAAAAA
16132 AATTAAAAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 8 0.27
30 22 0.73
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (30 bp):
CAAAAATTTTTTTTTCTTCGACGCAAAACA
Found at i:16109 original size:78 final size:78
Alignment explanation
Indices: 15975--16120 Score: 176
Period size: 78 Copynumber: 1.9 Consensus size: 78
15965 ACAAGAAATT
* * *
15975 TTTTTTTATGACGCAGAAATTTTTTTTTTTATATATGACGCAAAAAAAAACCTTTTTT-TTATGA
1 TTTTTTTATGACGCAGAAAATATTTTTTTTATATACGACGCAAAAAAAAACCTTTTTTCTT-TGA
16039 CGCAGAAACAAAAA
65 CGCAGAAACAAAAA
*
16053 TTTTTTTATGACGCA-AAAATATTTTTTTT-T-T-CGACGCAAAACACAAAACTTTTTTTTTCTT
1 TTTTTTTATGACGCAGAAAATATTTTTTTTATATACGACGCAAAA-A-AAAAC--CTTTTTTCTT
16114 TGACGCA
62 TGACGCA
16121 AGACTCAAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
74 9 0.15
75 2 0.03
76 6 0.10
77 12 0.20
78 28 0.47
79 2 0.03
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (78 bp):
TTTTTTTATGACGCAGAAAATATTTTTTTTATATACGACGCAAAAAAAAACCTTTTTTCTTTGAC
GCAGAAACAAAAA
Found at i:16561 original size:16 final size:15
Alignment explanation
Indices: 16523--16564 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
16513 ACAGAGGTTG
16523 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
16538 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
16553 ACTAGAAAACAA
1 AC-AGAAAACAA
16565 AACAAAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Done.