Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020309.1 Corchorus olitorius cultivar O-4 contig20342, 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: 17093
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:694 original size:13 final size:13
Alignment explanation
Indices: 676--700 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
666 TTGGAATTTC
676 AAATGATATTTAT
1 AAATGATATTTAT
689 AAATGATATTTA
1 AAATGATATTTA
701 GAATATTAAA
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:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (13 bp):
AAATGATATTTAT
Found at i:757 original size:14 final size:14
Alignment explanation
Indices: 738--765 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
728 CTACAATTTC
738 TTTTTTCAATAGAT
1 TTTTTTCAATAGAT
752 TTTTTTCAATAGAT
1 TTTTTTCAATAGAT
766 AATTATTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.57
Consensus pattern (14 bp):
TTTTTTCAATAGAT
Found at i:7119 original size:438 final size:426
Alignment explanation
Indices: 6359--7353 Score: 1196
Period size: 438 Copynumber: 2.3 Consensus size: 426
6349 GTTGTATTTT
* * * * * *
6359 ATTTTTATGTATTTTTTTTCTGTTTGTCTGATTAAAGTGATTC-TAGTGTCTATTAAAAGGTAAT
1 ATTTTTTTTTATTTTTTTTCTATATGTCCGATT-AAGTGATTCAT-GTGTTTATTAAAAGGTAAT
* * * **
6423 TTCATGATCTACAATTTTCATGAACA-ACTCAAAAGTCAATTTTAATGTTTTGATT--TTAAAAA
64 TTCATGATCTACAACTTTCATGAA-AGACTCAAAA-ACAATTTTAATGTTTTAATTCAAAAAAAA
* * * * *
6485 TGCTTCCGAAATTTTGTGGTTTTGATTGCCGGTCAATTTAATATCGTATAATATTTTGTCCACAT
127 TGCTTCCGAAATTTGGTCGTTTTGATTGCCGGTCAATTTAATAGCATATAATATTTCGTCCACAT
* * * * * *
6550 GTCTGATTAAAGTTATTGAAGTGTCAGTTAAAAGGTTATTGCATGATTTACGACTTTCATGAAGG
192 GTCCGATTAAAGTTATTCAAGTGTCAGTTAAAAAGTTACTGCATGATCTACGACTTTCATGAAGA
*
6615 ACCCGAAAGCTAAATTTGATCTACGAGTTTCATGAAAGGTTCAAAAGGGAATTTTTATGCTTCAA
257 ACCCGAAAGCTAAATTTGATCTACGAATTTCATGAAAGGTTCAAAAGGGAATTTTTATGCTTCAA
* * *
6680 GATCTCCATTAACAAACATTTTCTTATTTGAATTATTTATCAAATGA-CTCATATTTTTCTACTT
322 GATATCCATTAACAAACATTTTCTTATTTGAATTAGTTATCAAATGACCTCATACTTTTCTACTT
* *
6744 TATACTACTTAGTCCTTCACAAATTCTATCTTAATCTAACGTTTAAG
387 TATACTACTTAGTCATTCACAAATTCTATCTTAA-C--AC--TT--C
*
6791 ATTTATTTTGTTATTTTTTGTTCTATCTGTCCGATTAAGTTGATTCATGTGTTTATTAAAAGGTA
1 ATTT-TTTT-TTATTTTTT-TTCTATATGTCCGATTAAG-TGATTCATGTGTTTATTAAAAGGTA
* * *
6856 ATTTCATGATCCACAACTTTCATGAAGGACTCAAAAACAAATTTTTATGTTTTAATTCAAAAAAA
62 ATTTCATGATCTACAACTTTCATGAAAGACTCAAAAAC-AATTTTAATGTTTTAATTC-AAAAAA
* ** *
6921 AATGCTTCCTAAATTTGGTCGTTTTGATTGTTGGTCTATTTAATAGCATATAAT-TTTCGATCCA
125 AATGCTTCCGAAATTTGGTCGTTTTGATTGCCGGTCAATTTAATAGCATATAATATTTCG-TCCA
** *
6985 CATGTCCGATTAAAGTTATTCAAGTGTTGGTTAAAAAGTTACTGTATGATCTACGACTTTCATGA
189 CATGTCCGATTAAAGTTATTCAAGTGTCAGTTAAAAAGTTACTGCATGATCTACGACTTTCATGA
* * * *
7050 AGAACCCGAAAG-TTAATTTGATCTAAC-AATTTCATTAAGGGTTCAAAAGGGAATTTTTATGTT
254 AGAACCCGAAAGCTAAATTTGATCT-ACGAATTTCATGAAAGGTTCAAAAGGGAATTTTTATG-C
* *
7113 TTCAAGATATCCATTAAGAAATATTTTCTTATTTGAATTAGTTATCAAATGACCCTCATACTTTT
317 TTCAAGATATCCATTAACAAACATTTTCTTATTTGAATTAGTTATCAAATGA-CCTCATACTTTT
* * * *
7178 CTATTTTATGCTACTTAGTCATTTACAAATTTTATCTTAACACTTC
381 CTACTTTATACTACTTAGTCATTCACAAATTCTATCTTAACACTTC
* * *
7224 ATTTTTTTTTATTTTCTTTATTCTATATGTCCAATTAAGGTAATTCAGGTGTTTATTAAAAGGTA
1 ATTTTTTTTTA-TTT-TTT-TTCTATATGTCCGATTAA-GTGATTCATGTGTTTATTAAAAGGTA
* * * *
7289 ATTTTATGATCTACAACTTTCATGAAAGACTCAAAAACTAATTTTCATGTTTCAATTCTAAAAAA
62 ATTTCATGATCTACAACTTTCATGAAAGACTCAAAAAC-AATTTTAATGTTTTAATTCAAAAAAA
7354 TTGTTTTTGG
Statistics
Matches: 485, Mismatches: 60, Indels: 36
0.83 0.10 0.06
Matches are distributed among these distances:
431 3 0.01
432 17 0.04
433 101 0.21
434 13 0.03
435 85 0.18
436 1 0.00
437 48 0.10
438 171 0.35
439 1 0.00
440 45 0.09
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (426 bp):
ATTTTTTTTTATTTTTTTTCTATATGTCCGATTAAGTGATTCATGTGTTTATTAAAAGGTAATTT
CATGATCTACAACTTTCATGAAAGACTCAAAAACAATTTTAATGTTTTAATTCAAAAAAAATGCT
TCCGAAATTTGGTCGTTTTGATTGCCGGTCAATTTAATAGCATATAATATTTCGTCCACATGTCC
GATTAAAGTTATTCAAGTGTCAGTTAAAAAGTTACTGCATGATCTACGACTTTCATGAAGAACCC
GAAAGCTAAATTTGATCTACGAATTTCATGAAAGGTTCAAAAGGGAATTTTTATGCTTCAAGATA
TCCATTAACAAACATTTTCTTATTTGAATTAGTTATCAAATGACCTCATACTTTTCTACTTTATA
CTACTTAGTCATTCACAAATTCTATCTTAACACTTC
Found at i:9440 original size:42 final size:42
Alignment explanation
Indices: 9393--9501 Score: 218
Period size: 42 Copynumber: 2.6 Consensus size: 42
9383 AAAAGAAGCA
9393 ATTTCATATTAGACTCAAATAAAAAAAAAACATTTCACTATG
1 ATTTCATATTAGACTCAAATAAAAAAAAAACATTTCACTATG
9435 ATTTCATATTAGACTCAAATAAAAAAAAAACATTTCACTATG
1 ATTTCATATTAGACTCAAATAAAAAAAAAACATTTCACTATG
9477 ATTTCATATTAGACTCAAATAAAAA
1 ATTTCATATTAGACTCAAATAAAAA
9502 CATTTTAATC
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 67 1.00
ACGTcount: A:0.50, C:0.14, G:0.05, T:0.31
Consensus pattern (42 bp):
ATTTCATATTAGACTCAAATAAAAAAAAAACATTTCACTATG
Found at i:12293 original size:75 final size:75
Alignment explanation
Indices: 12166--12311 Score: 240
Period size: 75 Copynumber: 1.9 Consensus size: 75
12156 CTAAATTGAT
* **
12166 AAAAGACCAAAACGGGGCGAAAAGGTTCTCCCACGTTAAAAGTTGATGGGAGCTATTGGTAATTT
1 AAAAGACCAAAACGGGGCGAAAAGGTTCTCCCACGTTAAAAGTTGATGGGAGCAATCAGTAATTT
12231 CCAGAGTGAG
66 CCAGAGTGAG
*
12241 AAAAGACCAAAACGGGGCGAAAAGGTT-TACCCACGTTAAAAGTTGATTGGAGCAATCAGTAATT
1 AAAAGACCAAAACGGGGCGAAAAGGTTCT-CCCACGTTAAAAGTTGATGGGAGCAATCAGTAATT
12305 TCCAGAG
65 TCCAGAG
12312 GGTATTCAAA
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
74 1 0.02
75 65 0.98
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.21
Consensus pattern (75 bp):
AAAAGACCAAAACGGGGCGAAAAGGTTCTCCCACGTTAAAAGTTGATGGGAGCAATCAGTAATTT
CCAGAGTGAG
Found at i:15647 original size:16 final size:16
Alignment explanation
Indices: 15622--15660 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
15612 GTTGCTTAAT
*
15622 TTTA-TTATTTTCTTG
1 TTTATTTATTTTATTG
15637 TTTATTTATTTTATTG
1 TTTATTTATTTTATTG
*
15653 TTTCTTTA
1 TTTATTTA
15661 ATTCAAAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.15, C:0.05, G:0.05, T:0.74
Consensus pattern (16 bp):
TTTATTTATTTTATTG
Found at i:15647 original size:24 final size:25
Alignment explanation
Indices: 15601--15651 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
15591 ATTGGAGTAT
*
15601 TTATTTATCTTGTTGCTTAATTTTA
1 TTATTTATCTTGTTGATTAATTTTA
* *
15626 TTATTT-TCTTGTTTATTTATTTTA
1 TTATTTATCTTGTTGATTAATTTTA
15650 TT
1 TT
15652 GTTTCTTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.71
Consensus pattern (25 bp):
TTATTTATCTTGTTGATTAATTTTA
Found at i:16498 original size:22 final size:22
Alignment explanation
Indices: 16468--16513 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
16458 AAAATCTCCT
16468 AATTCAACC-TCTGGAGAGGTCG
1 AATTCAACCTTC-GGAGAGGTCG
* *
16490 AATTTAACCTTCGTAGAGGTCG
1 AATTCAACCTTCGGAGAGGTCG
16512 AA
1 AA
16514 ACAACAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (22 bp):
AATTCAACCTTCGGAGAGGTCG
Done.