Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005684.1 Corchorus capsularis cultivar CVL-1 contig05702, 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: 8396
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Found at i:572 original size:159 final size:160
Alignment explanation
Indices: 379--695 Score: 564
Period size: 160 Copynumber: 2.0 Consensus size: 160
369 AGAATTAAAT
379 AATTATAAAATATTGAATTTAATTAAAAGAAAATAGAGTTTTCGGTAGAATAAAACTGTATA-TA
1 AATTATAAAATATTGAATTTAATTAAAAGAAAATAGAGTTTTCGGTAGAATAAAACTGTATATTA
* *
443 AAAATTTTAATATATCCAATTTTTATTGAAAAATAGTAAAATGATAAAAATAAATAAATTATAAA
66 AAAATTTTAATATATCCAATTTTTATTCAAAAATAGTAAAATGATAAAAATAAAGAAATTATAAA
*
508 GAAATTAGATTTAATATTTGAATAAAAACA
131 GAAATTAGATTTAATAATTGAATAAAAACA
* *
538 AATTATAAAATATTGAATTTAATTAAATGAAAATAGAGTTTTTGGTAGAATAAAACTGTATATTA
1 AATTATAAAATATTGAATTTAATTAAAAGAAAATAGAGTTTTCGGTAGAATAAAACTGTATATTA
* *
603 AAAATTTTAATATATCCAATTTTTATTCAAAAATAGTAAAATGGTAAAAATAAAGAAATTATAAT
66 AAAATTTTAATATATCCAATTTTTATTCAAAAATAGTAAAATGATAAAAATAAAGAAATTATAAA
668 GAAATTAGATTTAATAATTGAATAAAAA
131 GAAATTAGATTTAATAATTGAATAAAAA
696 TAGAGTTTTT
Statistics
Matches: 150, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
159 60 0.40
160 90 0.60
ACGTcount: A:0.53, C:0.03, G:0.09, T:0.35
Consensus pattern (160 bp):
AATTATAAAATATTGAATTTAATTAAAAGAAAATAGAGTTTTCGGTAGAATAAAACTGTATATTA
AAAATTTTAATATATCCAATTTTTATTCAAAAATAGTAAAATGATAAAAATAAAGAAATTATAAA
GAAATTAGATTTAATAATTGAATAAAAACA
Found at i:3500 original size:78 final size:78
Alignment explanation
Indices: 3258--3502 Score: 196
Period size: 78 Copynumber: 3.1 Consensus size: 78
3248 AATTATAAAA
* * *
3258 TATTGAATTTAATTAAAAGAAAATAGAGTTTTCGGTAGAATAAAACTGTATATTAAAAATTTTAA
1 TATTGAATTTAATTAAATGAAAATAGAGTTTTTGGTAGAATAAATCTGTATATTAAAAATTTTAA
3323 TATATCCAATTTT
66 TATATCCAATTTT
** * * * ** * * * *
3336 TATTGAAAAATAGTAAAATGATAAAAATA-AATAAATT-ATA-AAGAAATTTG-AT-TTAATAA-
1 TATTG-AATTTAATTAAATG---AAAATAGAGT-TTTTGGTAGAATAAATCTGTATATTAAAAAT
* * * *
3395 TTAAATAAAAACTAATTATT
61 TTTAAT-ATATCCAATT-TT
3415 AAATATTGAATTTAATTAAATGAAAATAGAGTTTTTGGTAGAATAAATCTGTATATTAAAAATTT
1 ---TATTGAATTTAATTAAATGAAAATAGAGTTTTTGGTAGAATAAATCTGTATATTAAAAATTT
3480 TAATATATCCAATTTT
63 TAATATATCCAATTTT
3496 TATTGAA
1 TATTGAA
3503 AAATAGTAAA
Statistics
Matches: 118, Mismatches: 33, Indels: 32
0.64 0.18 0.17
Matches are distributed among these distances:
77 5 0.04
78 33 0.28
79 17 0.14
80 15 0.13
81 18 0.15
82 25 0.21
83 5 0.04
ACGTcount: A:0.49, C:0.03, G:0.09, T:0.39
Consensus pattern (78 bp):
TATTGAATTTAATTAAATGAAAATAGAGTTTTTGGTAGAATAAATCTGTATATTAAAAATTTTAA
TATATCCAATTTT
Found at i:3540 original size:149 final size:153
Alignment explanation
Indices: 3247--3554 Score: 462
Period size: 160 Copynumber: 2.0 Consensus size: 153
3237 AAAAATTAAA
3247 TAATTATAAAATATTGAATTTAATTAAAAGAAAATAGAGTTTTCGGTAGAATAAAACTGTATATT
1 TAATTATAAAATATTGAATTTAATTAAAAGAAAATAGAGTTTTCGGTAGAATAAAACTGTATATT
3312 AAAAATTTTAATATATCCAATTTTTATTGAAAAATAGTAAAATGATAAAAATAAATAAATTATAA
66 AAAAATTTTAATATATCCAATTTTTATTGAAAAATAGTAAAATG-----AAT-AATAAA-TATAA
*
3377 AGAAATTTGATTTAATAATTAAATAAAAAC
124 AGAAATTAGATTTAATAATTAAATAAAAAC
* * * *
3407 TAATTATTAAATATTGAATTTAATTAAATGAAAATAGAGTTTTTGGTAGAATAAATCTGTATATT
1 TAATTATAAAATATTGAATTTAATTAAAAGAAAATAGAGTTTTCGGTAGAATAAAACTGTATATT
*
3472 AAAAATTTTAATATATCCAATTTTTATTGAAAAATAGTAAAATG-GT-A-AAA-ATAAAGAAATT
66 AAAAATTTTAATATATCCAATTTTTATTGAAAAATAGTAAAATGAATAATAAATATAAAGAAATT
*
3533 AGATTTAATAATTGAATAAAAA
131 AGATTTAATAATTAAATAAAAA
3555 TAGAGTTTTT
Statistics
Matches: 141, Mismatches: 7, Indels: 11
0.89 0.04 0.07
Matches are distributed among these distances:
149 31 0.22
151 3 0.02
152 1 0.01
154 1 0.01
160 105 0.74
ACGTcount: A:0.52, C:0.03, G:0.09, T:0.37
Consensus pattern (153 bp):
TAATTATAAAATATTGAATTTAATTAAAAGAAAATAGAGTTTTCGGTAGAATAAAACTGTATATT
AAAAATTTTAATATATCCAATTTTTATTGAAAAATAGTAAAATGAATAATAAATATAAAGAAATT
AGATTTAATAATTAAATAAAAAC
Found at i:7141 original size:14 final size:14
Alignment explanation
Indices: 7122--7148 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
7112 CACAGCCCTC
7122 TTTTTATTTTTTTA
1 TTTTTATTTTTTTA
7136 TTTTTATTTTTTT
1 TTTTTATTTTTTT
7149 TCTTCTTCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (14 bp):
TTTTTATTTTTTTA
Found at i:8101 original size:160 final size:160
Alignment explanation
Indices: 7897--8196 Score: 530
Period size: 159 Copynumber: 1.9 Consensus size: 160
7887 TGGTCTTATA
7897 TTAATTAAAAGAAAATAGAGTTTTTTGGTAGAATAAAACTGTATATTAAAAATTTTAATATATCC
1 TTAATTAAAAGAAAATAGAGTTTTTTGGTAGAATAAAACTGTATATTAAAAATTTTAATATATCC
*
7962 AATTTTTATTGAAAAATAGTAAAATGATAAAAATAAATAAATTATAAAGAAATTAGACTTAATAA
66 AATTTTTATT-AAAAATAGTAAAATGATAAAAATAAAGAAATTATAAAGAAATTAGACTTAATAA
8027 TTGAATAAAAACTAATTATAAAATATTGAAT
130 TTGAATAAAAACTAATTATAAAATATTGAAT
* *
8058 TTAATTAAATGAAAATAGA-TTTTTTGGTAGAATAAAGCTGTATATTAAAAATTTTAATATATCC
1 TTAATTAAAAGAAAATAGAGTTTTTTGGTAGAATAAAACTGTATATTAAAAATTTTAATATATCC
* * *
8122 AATTTTTATTAAAAATAGTAAAATGGTAAAAATAAAGAAATTATAAGGAAATTAGATTTAATAAT
66 AATTTTTATTAAAAATAGTAAAATGATAAAAATAAAGAAATTATAAAGAAATTAGACTTAATAAT
8187 TGAATAAAAA
131 TGAATAAAAA
8197 TAGAGTTTTT
Statistics
Matches: 133, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
159 61 0.46
160 54 0.41
161 18 0.14
ACGTcount: A:0.52, C:0.03, G:0.10, T:0.36
Consensus pattern (160 bp):
TTAATTAAAAGAAAATAGAGTTTTTTGGTAGAATAAAACTGTATATTAAAAATTTTAATATATCC
AATTTTTATTAAAAATAGTAAAATGATAAAAATAAAGAAATTATAAAGAAATTAGACTTAATAAT
TGAATAAAAACTAATTATAAAATATTGAAT
Done.