Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005412.1 Corchorus capsularis cultivar CVL-1 contig05430, 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: 6503
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Found at i:2881 original size:13 final size:13
Alignment explanation
Indices: 2863--2887 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2853 TAATAGTAAG
2863 TATAATAATAATA
1 TATAATAATAATA
2876 TATAATAATAAT
1 TATAATAATAAT
2888 TAAATTAAGT
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TATAATAATAATA
Found at i:4106 original size:315 final size:313
Alignment explanation
Indices: 3534--4644 Score: 1392
Period size: 314 Copynumber: 3.5 Consensus size: 313
3524 TGTTCGGGTT
* * * * *
3534 TTGTGACGCCCCAAGATCCTAGATTAAGAGGATGTGGTGATCTATTTTGTTTTATATAATAGAGA
1 TTGTGACGCCCCAAGATCCCACATCAAGAGGATGTGGTGATCTATTGTGGTTTATATAATAGAGA
* *
3599 TCTAACCCAAACTTGTGAGGCGCCTTTTGGGAAGGGCAAATCCGTGAGGCCTTTGGGCCAAAGTG
66 TCCAACCCAAACTTGTGAGGCGCCTTTTGGGAAGGGCAAATCCGTGAGGCCTTTGGGCCAAAGCG
* * * *
3664 GATAATACTTCGAAGGTTGGGCCGGGTCTCTATAGTTGGTATCAGAGCTTTAACCGACCGTGTAA
131 GACAATACTTCGAAGGTTGGGCCGGGTCTCTACAGTTGGTATCAGAGCTTTAACAGA-CGTGTAG
* *
3729 TGGGAGCTAAGTGCTACACAGTGGGAGTACGGTGGGAGCCACCTTTAGAATCCCGGCGCCCGGTT
195 TGGGAGCTAAGTGCTACACCGTGGGAGTGCGGTGGGAGCCACCTTTAGAATCCCGGCGCCCGGTT
* *
3794 GGTCCTGGTGATTGTGTGGGCATGTCGGGGACGACAAGTCTATAAGAGGAGTAGA
260 GGTCCTGGTGATTGTGTGGGCTTGTCGGGGACGACAAGCCTATAAGAGG-GTAGA
* * * *
3849 TTGTGACGTCCCAAGATCCCACAACATGAGGATGTGAG-GATCCATTGTGGTTTATAT-ATAGAG
1 TTGTGACGCCCCAAGATCCCACATCAAGAGGATGTG-GTGATCTATTGTGGTTTATATAATAGAG
* * * *
3912 ATCCAACCTAAACTTGTGAGGCGTCTTTTGGGAAGGGTAAATTCGTGAGGCCTTTTGGGCCAAAG
65 ATCCAACCCAAACTTGTGAGGCGCCTTTTGGGAAGGGCAAATCCGTGAGGCC-TTTGGGCCAAAG
** * * * * * *
3977 CAAACAATACTTCGCAGGTTGGGTCAGATCTCTACAGTTGGTATCAGAGCTTTCACTAGACGTCT
129 CGGACAATACTTCGAAGGTTGGGCCGGGTCTCTACAGTTGGTATCAGAGCTTTAAC-AGACGTGT
*** *
4042 AGCAAGAGCTAAGTGCTACACCGTGGGAGTGCGGTGGGAGCCACCTTTAAAATCCCGGCGCCCGG
193 AGTGGGAGCTAAGTGCTACACCGTGGGAGTGCGGTGGGAGCCACCTTTAGAATCCCGGCGCCCGG
* * *
4107 TGGGTCCTGGTGATTGTGTTGTAGGGCTTGTC-GGAACGACAAGCCTATAAAGGGGGTAGA
258 TTGGTCCTGGTGA-T-TG-TGT-GGGCTTGTCGGGGACGACAAGCCTAT-AAGAGGGTAGA
* * * *
4167 TTATGACGCCCCAAAATCCCACATCATGAGGATGTGAG-GATATATTGTGGTTTATAT-ATAGAG
1 TTGTGACGCCCCAAGATCCCACATCAAGAGGATGTG-GTGATCTATTGTGGTTTATATAATAGAG
* * * * * *
4230 ATCCAACCCAAACTTGTGAGGGGCCTTTTAGGAAAGGCAAATCCGTGAGACTTTTGGGACAAAGC
65 ATCCAACCCAAACTTGTGAGGCGCCTTTTGGGAAGGGCAAATCCGTGAGGCCTTTGGGCCAAAGC
* * * * *
4295 GGACAATACCTCGTAGGTTGGGCCGGGTCTCTACAGTTAGTATCAGAGCTTTAACCGGGCGTGTA
130 GGACAATACTTCGAAGGTTGGGCCGGGTCTCTACAGTTGGTATCAGAGCTTTAA-CAGACGTGTA
* *
4360 GTGGGAGCTAAGTGCTACACCGTGGGAGTGCGGTGGGAGCCACCTCTAGAATTCCGGCGCCCGGT
194 GTGGGAGCTAAGTGCTACACCGTGGGAGTGCGGTGGGAGCCACCTTTAGAATCCCGGCGCCCGGT
* *
4425 TGGTCCTGATGATTGTGTGGACTTGTCGGGGACGACAA-CCATATAACGAGGGTAGA
259 TGGTCCTGGTGATTGTGTGGGCTTGTCGGGGACGACAAGCC-TATAA-GAGGGTAGA
* * * ** *
4481 TTGTGACGCCCCAAGAT-CCAGATCAAGAGGATATGGTGATCTATTCTGAATTATATAATTGAGA
1 TTGTGACGCCCCAAGATCCCACATCAAGAGGATGTGGTGATCTATTGTGGTTTATATAATAGAGA
* * **
4545 TCTAACCCAAACTTGTGAGGCGCCTTTTGGGAAGGGCAAATCCGTGAAGCCTTTGGGCCAAAATG
66 TCCAACCCAAACTTGTGAGGCGCCTTTTGGGAAGGGCAAATCCGTGAGGCCTTTGGGCCAAAGCG
* * * *
4610 GACAATAGC-TCGCATGTTGGGCTGGATCTCTACAG
131 GACAATA-CTTCGAAGGTTGGGCCGGGTCTCTACAG
4645 GTTTTTAAGC
Statistics
Matches: 680, Mismatches: 101, Indels: 31
0.84 0.12 0.04
Matches are distributed among these distances:
312 1 0.00
313 42 0.06
314 181 0.27
315 181 0.27
316 5 0.01
317 134 0.20
318 123 0.18
319 13 0.02
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (313 bp):
TTGTGACGCCCCAAGATCCCACATCAAGAGGATGTGGTGATCTATTGTGGTTTATATAATAGAGA
TCCAACCCAAACTTGTGAGGCGCCTTTTGGGAAGGGCAAATCCGTGAGGCCTTTGGGCCAAAGCG
GACAATACTTCGAAGGTTGGGCCGGGTCTCTACAGTTGGTATCAGAGCTTTAACAGACGTGTAGT
GGGAGCTAAGTGCTACACCGTGGGAGTGCGGTGGGAGCCACCTTTAGAATCCCGGCGCCCGGTTG
GTCCTGGTGATTGTGTGGGCTTGTCGGGGACGACAAGCCTATAAGAGGGTAGA
Found at i:4801 original size:31 final size:31
Alignment explanation
Indices: 4763--4824 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
4753 TTTAAAAATG
4763 CTCTTAAAGGATGTTGTCCAAACCAAACTCA
1 CTCTTAAAGGATGTTGTCCAAACCAAACTCA
4794 CTCTTAAAGGATGTTGTCCAAACCAAACTCA
1 CTCTTAAAGGATGTTGTCCAAACCAAACTCA
4825 GAACCCCTGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.35, C:0.26, G:0.13, T:0.26
Consensus pattern (31 bp):
CTCTTAAAGGATGTTGTCCAAACCAAACTCA
Found at i:6485 original size:2 final size:2
Alignment explanation
Indices: 6478--6503 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6468 TAACGGACAC
6478 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.