Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01002356.1 Corchorus capsularis cultivar CVL-1 contig02362, 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, 625
Length: 1042
ACGTcount: A:0.28, C:0.28, G:0.25, T:0.19
Found at i:517 original size:13 final size:13
Alignment explanation
Indices: 499--571 Score: 82
Period size: 13 Copynumber: 5.6 Consensus size: 13
489 CATCCATCAG
499 CAAGTGCCGATGC
1 CAAGTGCCGATGC
512 CAAGTGCC-AT-C
1 CAAGTGCCGATGC
523 AGCAAGTGCCGATGC
1 --CAAGTGCCGATGC
538 CAAGTGCC-AT-C
1 CAAGTGCCGATGC
549 AGCAAGTGCCGATGC
1 --CAAGTGCCGATGC
564 CAAGTGCC
1 CAAGTGCC
572 ATCGGAGAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 16
0.76 0.00 0.24
Matches are distributed among these distances:
11 2 0.04
12 4 0.08
13 40 0.77
14 4 0.08
15 2 0.04
ACGTcount: A:0.26, C:0.32, G:0.27, T:0.15
Consensus pattern (13 bp):
CAAGTGCCGATGC
Found at i:585 original size:52 final size:51
Alignment explanation
Indices: 492--597 Score: 162
Period size: 52 Copynumber: 2.1 Consensus size: 51
482 CAAGTGCCAT
*
492 CCATCAGCAAGTGCCGATGCCAAGTGCCATCAGCAAGTGCCGATGCCAAGTG
1 CCATCAGCAAGTGCCGATGCCAAGTGCCATCAGCAAGTGCCGACGCCAAG-G
544 CCATCAGCAAGTGCCGATGCCAAGTGCCATCGGAG-AA-TGCCGACGCCAAGG
1 CCATCAGCAAGTGCCGATGCCAAGTGCCATC--AGCAAGTGCCGACGCCAAGG
595 CCA
1 CCA
598 AGATCCATCG
Statistics
Matches: 51, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
51 4 0.08
52 43 0.84
53 2 0.04
54 2 0.04
ACGTcount: A:0.27, C:0.32, G:0.27, T:0.13
Consensus pattern (51 bp):
CCATCAGCAAGTGCCGATGCCAAGTGCCATCAGCAAGTGCCGACGCCAAGG
Found at i:586 original size:26 final size:26
Alignment explanation
Indices: 492--574 Score: 166
Period size: 26 Copynumber: 3.2 Consensus size: 26
482 CAAGTGCCAT
492 CCATCAGCAAGTGCCGATGCCAAGTG
1 CCATCAGCAAGTGCCGATGCCAAGTG
518 CCATCAGCAAGTGCCGATGCCAAGTG
1 CCATCAGCAAGTGCCGATGCCAAGTG
544 CCATCAGCAAGTGCCGATGCCAAGTG
1 CCATCAGCAAGTGCCGATGCCAAGTG
570 CCATC
1 CCATC
575 GGAGAATGCC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 57 1.00
ACGTcount: A:0.27, C:0.33, G:0.25, T:0.16
Consensus pattern (26 bp):
CCATCAGCAAGTGCCGATGCCAAGTG
Found at i:591 original size:26 final size:26
Alignment explanation
Indices: 503--652 Score: 92
Period size: 26 Copynumber: 5.3 Consensus size: 26
493 CATCAGCAAG
*
503 TGCCGATGCCAAGTGCCATC--AGCAA
1 TGCCGACGCCAAGTGCCATCGGAG-AA
*
528 GTGCCGATGCCAAGTGCCATC--AGCAA
1 -TGCCGACGCCAAGTGCCATCGGAG-AA
*
554 GTGCCGATGCCAAGTGCCATCGGAGAA
1 -TGCCGACGCCAAGTGCCATCGGAGAA
*
581 TGCCGACGCCAAGGCCAAGATCCATCGGAGAA
1 TGCCGACGCCAA-G---TG--CCATCGGAGAA
613 TGCCGACGCCAAGGTCAAGTGCCATCGGAGAA
1 TGCCGACG-C-----CAAGTGCCATCGGAGAA
645 TGCCGACG
1 TGCCGACG
653 AAGGGCGTCC
Statistics
Matches: 107, Mismatches: 3, Indels: 22
0.81 0.02 0.17
Matches are distributed among these distances:
26 57 0.53
27 3 0.03
28 2 0.02
30 1 0.01
32 38 0.36
33 1 0.01
34 1 0.01
37 1 0.01
38 3 0.03
ACGTcount: A:0.27, C:0.30, G:0.29, T:0.13
Consensus pattern (26 bp):
TGCCGACGCCAAGTGCCATCGGAGAA
Found at i:598 original size:32 final size:32
Alignment explanation
Indices: 562--652 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 32
552 AAGTGCCGAT
562 GCCAAGTGCCATCGGAGAATGCCGACGCCAAG
1 GCCAAGTGCCATCGGAGAATGCCGACGCCAAG
594 GCCAAGAT-CCATCGGAGAATGCCGACGCCAAG
1 GCCAAG-TGCCATCGGAGAATGCCGACGCCAAG
*
626 GTCAAGTGCCATCGGAGAATGCCGACG
1 GCCAAGTGCCATCGGAGAATGCCGACG
653 AAGGGCGTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
31 1 0.02
32 54 0.96
33 1 0.02
ACGTcount: A:0.29, C:0.30, G:0.31, T:0.11
Consensus pattern (32 bp):
GCCAAGTGCCATCGGAGAATGCCGACGCCAAG
Found at i:1003 original size:77 final size:77
Alignment explanation
Indices: 871--1024 Score: 211
Period size: 77 Copynumber: 2.0 Consensus size: 77
861 AGGTGTTCGC
* **** *
871 TGAGTTTCGGGGGCAAAAAATGGCCAAAATGCATTAGGTTTTGTATCATGAGTTCCAGACCCAAA
1 TGAGCTTCGGGGGCAAAAAATGGCCAAAATGCATTAGGTTAACCATCAAGAGTTCCAGACCCAAA
936 AAATGGCCGAAA
66 AAATGGCCGAAA
* *
948 TGAGCTTCGGGGGCAAAAATTGGCCAAAATGCCA-TAGGTTAACCATCAAGAGTTCCGGACCCAA
1 TGAGCTTCGGGGGCAAAAAATGGCCAAAATG-CATTAGGTTAACCATCAAGAGTTCCAGACCCAA
*
1012 AAATTGGCCGAAA
65 AAAATGGCCGAAA
1025 AGCCCTAGGT
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
77 65 0.97
78 2 0.03
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.21
Consensus pattern (77 bp):
TGAGCTTCGGGGGCAAAAAATGGCCAAAATGCATTAGGTTAACCATCAAGAGTTCCAGACCCAAA
AAATGGCCGAAA
Done.