Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013216.1 Corchorus capsularis cultivar CVL-1 contig13237, 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: 23827
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Found at i:623 original size:16 final size:16
Alignment explanation
Indices: 604--707 Score: 106
Period size: 16 Copynumber: 6.6 Consensus size: 16
594 TCCAACCCGA
604 GACCCGAGACCCGAAT
1 GACCCGAGACCCGAAT
*
620 GACCCG-GAACCCGTAT
1 GACCCGAG-ACCCGAAT
*
636 GACCCGAGGCCCGAAT
1 GACCCGAGACCCGAAT
* **
652 GACCCGAAACCCGTGT
1 GACCCGAGACCCGAAT
*
668 GACCCGAGAACCGAAT
1 GACCCGAGACCCGAAT
*
684 AACCCGA-ACCC-AGAT
1 GACCCGAGACCCGA-AT
699 GACCCGAGA
1 GACCCGAGA
708 AAACTGCCTG
Statistics
Matches: 70, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
14 1 0.01
15 12 0.17
16 56 0.80
17 1 0.01
ACGTcount: A:0.31, C:0.37, G:0.25, T:0.08
Consensus pattern (16 bp):
GACCCGAGACCCGAAT
Found at i:640 original size:32 final size:31
Alignment explanation
Indices: 597--707 Score: 136
Period size: 32 Copynumber: 3.5 Consensus size: 31
587 GAACCCGTCC
597 AACCCGA-GACCCGAGACCCGAATGACCCGG
1 AACCCGATGACCCGAGACCCGAATGACCCGG
* *
627 AACCCGTATGACCCGAGGCCCGAATGACCCGA
1 AACCCG-ATGACCCGAGACCCGAATGACCCGG
* * *
659 AACCCGTGTGACCCGAGAACCGAATAACCC-G
1 AACCCG-ATGACCCGAGACCCGAATGACCCGG
690 AACCCAGATGACCCGAGA
1 AACCC-GATGACCCGAGA
708 AAACTGCCTG
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
30 6 0.09
31 16 0.23
32 48 0.69
ACGTcount: A:0.32, C:0.37, G:0.24, T:0.07
Consensus pattern (31 bp):
AACCCGATGACCCGAGACCCGAATGACCCGG
Found at i:16596 original size:26 final size:27
Alignment explanation
Indices: 16563--16627 Score: 73
Period size: 26 Copynumber: 2.4 Consensus size: 27
16553 ATAATTTTAG
16563 TTTTAATTTATAAT-TTATAT-ATAAGT
1 TTTTAATTTATAATATTATATAATAA-T
*
16589 TTTTAATTT-TAATATTTTATAATAAT
1 TTTTAATTTATAATATTATATAATAAT
*
16615 TTATATATTTATA
1 TTTTA-ATTTATA
16628 CTTAACATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
25 4 0.12
26 19 0.58
27 8 0.24
28 2 0.06
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (27 bp):
TTTTAATTTATAATATTATATAATAAT
Found at i:19072 original size:33 final size:33
Alignment explanation
Indices: 18993--19073 Score: 90
Period size: 33 Copynumber: 2.5 Consensus size: 33
18983 CATGGTCGCG
*
18993 CGCGGCTCGGACGCGCACGACTAACGACCAAGC
1 CGCGGCTCGGTCGCGCACGACTAACGACCAAGC
* ** * * *
19026 CACGAATCGGTCGCGCGCGGCTCACGACCAAGC
1 CGCGGCTCGGTCGCGCACGACTAACGACCAAGC
*
19059 CGCGGCTCTGTCGCG
1 CGCGGCTCGGTCGCG
19074 ATCTGCGCAT
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.19, C:0.40, G:0.32, T:0.10
Consensus pattern (33 bp):
CGCGGCTCGGTCGCGCACGACTAACGACCAAGC
Found at i:19169 original size:27 final size:26
Alignment explanation
Indices: 19121--19174 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
19111 GCATATTTTC
**
19121 TATTTTTTTAAATTAATAATTAGTTAT
1 TATTTTTAAAAATTAATAATTA-TTAT
* *
19148 TATTTTTAAAAATTAGTTATTATTAT
1 TATTTTTAAAAATTAATAATTATTAT
19174 T
1 T
19175 TTATATGATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (26 bp):
TATTTTTAAAAATTAATAATTATTAT
Found at i:19185 original size:23 final size:20
Alignment explanation
Indices: 19133--19171 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
19123 TTTTTTTAAA
*
19133 TTAATAATTAGTTATTATTT
1 TTAAAAATTAGTTATTATTT
19153 TTAAAAATTAGTTATTATT
1 TTAAAAATTAGTTATTATT
19172 ATTTTATATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (20 bp):
TTAAAAATTAGTTATTATTT
Done.