Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009875.1 Corchorus capsularis cultivar CVL-1 contig09896, 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: 33654
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:1634 original size:438 final size:434
Alignment explanation
Indices: 862--1922 Score: 1050
Period size: 438 Copynumber: 2.4 Consensus size: 434
852 GCGCGTTGCC
*
862 TTTTATTTTTGTATT-TTTTTTCTATTTGTCCGATTAA-ACTGATTCAAGTGTATATTAAAAGGT
1 TTTTATTTTTTTATTCTTTTTT-TATTTGTCCGATTAAGA-TGATTCAAGTGTATATTAAAAGGT
* * * * * * * * ** **
925 TATTTCATGATCTATAATTTTCATTAAGAACTCAAAAGTCAATTTTAATGTTTTGATTCTAAAAA
64 AATTTTATGATCTACAACTTTCATGAAGGACTCAAAAG-CAATTTTTATATTTCAATTAAAAAAA
* * * * *
990 ATGTTTCCGAAATTTTGTGGCTTTGATTGCCGATTAATTTAATATCGTATAATTTTTTGCCCACA
128 ATGCTTCCGAAATTTTGTCGCTTTGATTGCAGATTAATTTAATATCATATAATTTTTCGCCCACA
* * * * * * * * *
1055 TGTCCGATTGAAGTTATTGAAGTGTTGGTTAAAAGGTTATTGCATGATTTGCGACTTTCATGAAG
193 TGTCCAATTAAAGTTATTCAAGTGTCGATTAAAAGGTTACTGCATAATCTACGACTTTCATGAAG
* * * * *
1120 CACCCGAAAGCTAAATTTTATCTACGAGTTTCGTGAAGGGTTAAAAAATGAATTTTTATATTTCA
258 AACCCGAAAGCTAAATTTGATCTACGAGTTTCATGAAGGGTTAAAAAAGGAATTCTTATATTTCA
* ** * * **
1185 AAATCTCCATTAACAAACATATTCTTATTTGGATTATTTATTAAATGACTGTCATACTTTTCTAC
323 AAATCTCCATTAACAAACATATTCTTATTTGAATTAGATATCAAATCACCCTCATACTTTTCTAC
* * * * *
1250 TTTATACTATTTAGTTATTTACAAATTCTATCTTAATCTAATGTTTAA-G
388 TTTATACTACTTACTCATTGACAAATTCTATCTTAATC-AA--TTTAACA
* * * *
1299 TTTTATTTTTTTATTCTTTATTTTATTTGTCCGATTAAGTTGATTTATGTGTCTATTAAAAGGTA
1 TTTTATTTTTTTATTCTTT-TTTTATTTGTCCGATTAAGATGATTCAAGTGTATATTAAAAGGTA
1364 ATTTTATGATCTACAACTTTCATGAAGGACTCAAAAGCAAATTTTTATATTTCAATTAAAAAAAA
65 ATTTTATGATCTACAACTTTCATGAAGGACTCAAAAGC-AATTTTTATATTTCAATT-AAAAAAA
* * * *
1429 ATGCTTCCTAAA-TTTGTTCG-TTTCGATTGTAGGTCT-ATTTAATGA-CATATAA-TTTTCGAT
128 ATGCTTCCGAAATTTTG-TCGCTTT-GATTGCAGAT-TAATTTAAT-ATCATATAATTTTTCG-C
*
1489 CCACATGTCCAATTAAAGTTATTCAAGTGTCGATTAAAAGGTTACTGTATAATCTACGA-TATTC
188 CCACATGTCCAATTAAAGTTATTCAAGTGTCGATTAAAAGGTTACTGCATAATCTACGACT-TTC
* * * * *
1553 ATGATGAACCCGAAAG-TTAATTTGATCTATGAGTTTCATGAAGGGTTCAAAAGGGAATTCTTAT
252 ATGAAGAACCCGAAAGCTAAATTTGATCTACGAGTTTCATGAAGGGTTAAAAAAGGAATTCTTAT
* * * * *
1617 GTTTCAAGATCTCCATTAACAAATATTTTCTTATTTGAATTAGATATCAAATCACCCTCATAGTT
317 ATTTCAAAATCTCCATTAACAAACATATTCTTATTTGAATTAGATATCAAATCACCCTCATACTT
* * * * * *
1682 TTCTATTTTATGCTACTTACTCCTTGCCAAATTCTATCTTACTCGATTTAACA
382 TTCTACTTTATACTACTTACTCATTGACAAATTCTATCTTAATCAATTTAACA
* * * * * * * *
1735 CTTCATTTTTTTATTTTCTTTGTTCTATTTGTCCAATTAAGATAATTCAGGTGTTTGTTAAAAGG
1 TTTTATTTTTTTA--TTCTTT-TTTTATTTGTCCGATTAAGATGATTCAAGTGTATATTAAAAGG
* * * **
1800 TAATTTTATAATCTACAACTCTCATGAAAGACTCAAAAGCTAATTTTTATATTTCAATTCTAAAA
63 TAATTTTATGATCTACAACTTTCATGAAGGACTCAAAAGC-AATTTTTATATTTCAATTAAAAAA
* ** * *
1865 ATTGCTTTTGAAATTTTGT-GATTTCGATTGACA-ATCT-ATTTAATATCATATTATTTTT
127 AATGCTTCCGAAATTTTGTCGCTTT-GATTG-CAGAT-TAATTTAATATCATATAATTTTT
1923 GATCCAGATG
Statistics
Matches: 512, Mismatches: 93, Indels: 37
0.80 0.14 0.06
Matches are distributed among these distances:
435 5 0.01
436 13 0.03
437 55 0.11
438 331 0.65
439 106 0.21
440 2 0.00
ACGTcount: A:0.31, C:0.13, G:0.12, T:0.44
Consensus pattern (434 bp):
TTTTATTTTTTTATTCTTTTTTTATTTGTCCGATTAAGATGATTCAAGTGTATATTAAAAGGTAA
TTTTATGATCTACAACTTTCATGAAGGACTCAAAAGCAATTTTTATATTTCAATTAAAAAAAATG
CTTCCGAAATTTTGTCGCTTTGATTGCAGATTAATTTAATATCATATAATTTTTCGCCCACATGT
CCAATTAAAGTTATTCAAGTGTCGATTAAAAGGTTACTGCATAATCTACGACTTTCATGAAGAAC
CCGAAAGCTAAATTTGATCTACGAGTTTCATGAAGGGTTAAAAAAGGAATTCTTATATTTCAAAA
TCTCCATTAACAAACATATTCTTATTTGAATTAGATATCAAATCACCCTCATACTTTTCTACTTT
ATACTACTTACTCATTGACAAATTCTATCTTAATCAATTTAACA
Found at i:2214 original size:2 final size:2
Alignment explanation
Indices: 2207--2245 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
2197 TTAGCTTCTT
2207 TA TA TA TA TA TA TA TA TA TA -A T- TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2246 GTAGCTTTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5811 original size:19 final size:19
Alignment explanation
Indices: 5791--5827 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5781 AATTAATTAT
5791 TTTA-ATATTAAATTTTTA
1 TTTATATATTAAATTTTTA
*
5809 TTTATATATTATATTTTTA
1 TTTATATATTAAATTTTTA
5828 CTTAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTATATATTAAATTTTTA
Found at i:30220 original size:17 final size:17
Alignment explanation
Indices: 30184--30221 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
30174 CATAGTACCC
*
30184 AGGTAGTATGAGCTGCT
1 AGGTAGTATGAGCTGAT
*
30201 AGGTAGTATGAGGTGAT
1 AGGTAGTATGAGCTGAT
30218 AGGT
1 AGGT
30222 TGCATCTGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.26, C:0.05, G:0.39, T:0.29
Consensus pattern (17 bp):
AGGTAGTATGAGCTGAT
Done.