Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009917.1 Corchorus capsularis cultivar CVL-1 contig09938, 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: 7818
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Found at i:411 original size:18 final size:19
Alignment explanation
Indices: 374--411 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
364 TTCATGATAA
374 CTTTGCAGACCATTATTTTTT
1 CTTTGCAGACC--TATTTTTT
395 CTTTGCAGACC-ATTTTT
1 CTTTGCAGACCTATTTTT
412 ACTCTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.35
21 11 0.65
ACGTcount: A:0.18, C:0.21, G:0.11, T:0.50
Consensus pattern (19 bp):
CTTTGCAGACCTATTTTTT
Found at i:4552 original size:116 final size:116
Alignment explanation
Indices: 4198--4561 Score: 373
Period size: 116 Copynumber: 3.0 Consensus size: 116
4188 ATAATACATT
*
4198 AAACTATCAAATAGAATATGTCAATCACAATAACCTTTTAAATTAAAATGGTAAAAATAAAATAA
1 AAACTATCAAATAGAATATGTCAATCACAATAATCTTTTAAATTAAAATGGTAAAAATAAAATAA
* *
4263 TTATAAAATATATTAAATTTAATTAAATGAAAATAGAGTTTTTATTAGAATA
66 TTAT-AAAGATATTAAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATA
* * * * * * * *
4315 AAATTGT-ATATTA-AAAATTTTAAT-A-TATCCAATTTTTATTAAAAAAATAGTAAAATGGTAA
1 AAACTATCA-AATAGAATATGTCAATCACAAT--AA-TCTT-TT----AAAT--TAAAATGGTAA
* * * *
4376 AAATAAAGA-AATTATAAAGATATTAGATTTAATAATTGAATAAAAAAAGAGTTTTTAGTAGAAT
55 AAATAAA-ATAATTATAAAGATATTA-AATT--TAATTAAATGAAAATAGAGTTTTTAGTAG-A-
4440 ATA
114 ATA
4443 AAACTATCAAATAGAATATGTCAATCACAATAATCTTTTAAATTAAAATGGTAAAAA-AAAATAA
1 AAACTATCAAATAGAATATGTCAATCACAATAATCTTTTAAATTAAAATGGTAAAAATAAAATAA
*
4507 TTATAAA-ATATTAAATTTAATTAAATGAAAATAGAGTTTTTAGTAGGATA
66 TTATAAAGATATTAAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATA
4557 AAACT
1 AAACT
4562 GTATATTAAA
Statistics
Matches: 197, Mismatches: 28, Indels: 47
0.72 0.10 0.17
Matches are distributed among these distances:
114 10 0.05
115 1 0.01
116 37 0.19
117 10 0.05
118 5 0.03
119 7 0.04
120 12 0.06
121 14 0.07
122 4 0.02
123 13 0.07
124 27 0.14
125 1 0.01
126 25 0.13
127 3 0.02
128 14 0.07
129 11 0.06
130 1 0.01
131 2 0.01
ACGTcount: A:0.53, C:0.04, G:0.08, T:0.34
Consensus pattern (116 bp):
AAACTATCAAATAGAATATGTCAATCACAATAATCTTTTAAATTAAAATGGTAAAAATAAAATAA
TTATAAAGATATTAAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATA
Found at i:4684 original size:124 final size:123
Alignment explanation
Indices: 4241--4684 Score: 481
Period size: 124 Copynumber: 3.6 Consensus size: 123
4231 CCTTTTAAAT
* *
4241 TAAAATGGTAAAAATAAA-ATAATTATAAAATATATTAAATTTAATTAAATGAAAATAGAGTTTT
1 TAAAATGGTAAAAATAAAGATAATTAT-AAAGATATTAAATTTAATTAAATAAAAATAGAGTTTT
* *
4305 TATTAGAATAAAATTGTATATTAAAAATTTTAATATATCCAATTTTTATTAAAAAAATAG
65 TAGTAGAATAAAACTGTATATTAAAAATTTTAATATATCCAATTTTTATT-AAAAAATAG
* * *
4365 TAAAATGGTAAAAATAAAGA-AATTATAAAGATATTAGATTTAATAATTGAATAAAAAAAGAGTT
1 TAAAATGGTAAAAATAAAGATAATTATAAAGATATTA-AATT--TAATTAAATAAAAATAGAGTT
* * * * * * *
4429 TTTAGTAGAATATAAAACTATCA-AATAGAATATGTCAAT-CA--CAATAATCTT-TT---AAAT
63 TTTAGTAG-A-ATAAAACTGT-ATATTA-AAAATTTTAATATATCCAAT--TTTTATTAAAAAAT
4486 --
122 AG
*
4486 TAAAATGGTAAAAA-AAA-ATAATTATAAA-ATATTAAATTTAATTAAATGAAAATAGAGTTTTT
1 TAAAATGGTAAAAATAAAGATAATTATAAAGATATTAAATTTAATTAAATAAAAATAGAGTTTTT
*
4548 AGTAGGATAAAACTGTATATTAAAAATTTTAATATATCCAATTTTTATTAAAAAATAG
66 AGTAGAATAAAACTGTATATTAAAAATTTTAATATATCCAATTTTTATTAAAAAATAG
* *
4606 TAAAATGGT-AAAATAAAGAT-ATTATAAAGATATTAGATTTAATAATTAATTAAAAATAGAGTT
1 TAAAATGGTAAAAATAAAGATAATTATAAAGATATTA-AATT--TAATTAAATAAAAATAGAGTT
4669 TTTAGTAGAATAAAAC
63 TTTAGTAGAATAAAAC
4685 GATTATAGTT
Statistics
Matches: 263, Mismatches: 30, Indels: 54
0.76 0.09 0.16
Matches are distributed among these distances:
113 9 0.03
114 16 0.06
115 2 0.01
116 30 0.11
118 7 0.03
119 11 0.04
120 32 0.12
121 22 0.08
122 3 0.01
123 13 0.05
124 61 0.23
125 1 0.00
126 29 0.11
127 3 0.01
128 15 0.06
129 9 0.03
ACGTcount: A:0.53, C:0.03, G:0.09, T:0.36
Consensus pattern (123 bp):
TAAAATGGTAAAAATAAAGATAATTATAAAGATATTAAATTTAATTAAATAAAAATAGAGTTTTT
AGTAGAATAAAACTGTATATTAAAAATTTTAATATATCCAATTTTTATTAAAAAATAG
Done.