Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007284.1 Corchorus capsularis cultivar CVL-1 contig07305, 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: 13763
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Found at i:1533 original size:48 final size:48
Alignment explanation
Indices: 1376--1649 Score: 340
Period size: 48 Copynumber: 5.7 Consensus size: 48
1366 GCTTTTCCCA
* * * * * * *
1376 AAAATGCCCTCCCCGGACGGAAGGCATTTA-TTTTACTTGTTTTTCCC
1 AAAACGCCCTTCCCGGACGGAAGGCACTGATTTTTACCTATTTTTCCT
*
1423 AACACGCCCTTCCCGGACGGAAGGCACTGA-TTTTACCTA-TTTTCCT
1 AAAACGCCCTTCCCGGACGGAAGGCACTGATTTTTACCTATTTTTCCT
1469 AAAACGCCCTTCCCGGACGGAAGGCACTGATTTTTACCTATTTTTCCT
1 AAAACGCCCTTCCCGGACGGAAGGCACTGATTTTTACCTATTTTTCCT
* *
1517 AAAACGCCCTTCCCGGACGGAGGGCACTGATTTTTACCTGTTTTTTCCT
1 AAAACGCCCTTCCCGGACGGAAGGCACTGATTTTTACCT-ATTTTTCCT
**
1566 AAAACGCCCTTCCCGGACGGAAGGCACCAATTTTTACTCGCT-TTTTTCCT
1 AAAACGCCCTTCCCGGACGGAAGGCACTGATTTTTA--C-CTATTTTTCCT
* * * *
1616 AAAACGCCATTCCCGGACGAAAGGCGCTAATTTT
1 AAAACGCCCTTCCCGGACGGAAGGCACTGATTTT
1650 ACTCGCTTTT
Statistics
Matches: 203, Mismatches: 18, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
46 35 0.17
47 41 0.20
48 45 0.22
49 41 0.20
50 38 0.19
51 1 0.00
52 2 0.01
ACGTcount: A:0.23, C:0.30, G:0.18, T:0.30
Consensus pattern (48 bp):
AAAACGCCCTTCCCGGACGGAAGGCACTGATTTTTACCTATTTTTCCT
Found at i:1599 original size:97 final size:93
Alignment explanation
Indices: 1376--1651 Score: 338
Period size: 94 Copynumber: 2.9 Consensus size: 93
1366 GCTTTTCCCA
* * * * * * *
1376 AAAATGCCCTCCCCGGACGGAAGGCATTTA-TTTTACTTGTTTTTCCCAACACGCCCTTCCCGGA
1 AAAACGCCCTTCCCGGACGGAAGGCACTAATTTTTACCT-TTTTTCCTAAAACGCCCTTCCCGGA
1440 CGGAAGGCACTGATTTTACCTATTTTCCT
65 CGGAAGGCACTGATTTTACCTATTTTCCT
*
1469 AAAACGCCCTTCCCGGACGGAAGGCACTGATTTTTACCTATTTTTCCTAAAACGCCCTTCCCGGA
1 AAAACGCCCTTCCCGGACGGAAGGCACTAATTTTTACCT-TTTTTCCTAAAACGCCCTTCCCGGA
* *
1534 CGGAGGGCACTGATTTTTACCTGTTTTTTCCT
65 CGGAAGGCACTGA-TTTTACC--TATTTTCCT
* *
1566 AAAACGCCCTTCCCGGACGGAAGGCACCAATTTTTACTCGCTTTTTTCCTAAAACGCCATTCCCG
1 AAAACGCCCTTCCCGGACGGAAGGCACTAATTTTTA--C-CTTTTTTCCTAAAACGCCCTTCCCG
* * *
1631 GACGAAAGGCGCTAATTTTAC
63 GACGGAAGGCACTGATTTTAC
1652 TCGCTTTTTC
Statistics
Matches: 159, Mismatches: 17, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
93 26 0.16
94 42 0.26
95 7 0.04
97 42 0.26
98 6 0.04
99 34 0.21
100 2 0.01
ACGTcount: A:0.23, C:0.30, G:0.18, T:0.30
Consensus pattern (93 bp):
AAAACGCCCTTCCCGGACGGAAGGCACTAATTTTTACCTTTTTTCCTAAAACGCCCTTCCCGGAC
GGAAGGCACTGATTTTACCTATTTTCCT
Found at i:1632 original size:50 final size:49
Alignment explanation
Indices: 1376--1660 Score: 320
Period size: 49 Copynumber: 5.9 Consensus size: 49
1366 GCTTTTCCCA
* * * * * *
1376 AAAATGCCCTCCCCGGACGGAAGGCATTTA-TTTTA-C-TTGTTTTTCCC
1 AAAACGCCCTTCCCGGACGGAAGGCACTGATTTTTACCGCT-TTTTTCCT
* *
1423 AACACGCCCTTCCCGGACGGAAGGCACTGA-TTTTA-C-CTATTTTCCT
1 AAAACGCCCTTCCCGGACGGAAGGCACTGATTTTTACCGCTTTTTTCCT
1469 AAAACGCCCTTCCCGGACGGAAGGCACTGATTTTTA-C-CTATTTTTCCT
1 AAAACGCCCTTCCCGGACGGAAGGCACTGATTTTTACCGCT-TTTTTCCT
*
1517 AAAACGCCCTTCCCGGACGGAGGGCACTGATTTTTACCTG-TTTTTTCCT
1 AAAACGCCCTTCCCGGACGGAAGGCACTGATTTTTACC-GCTTTTTTCCT
**
1566 AAAACGCCCTTCCCGGACGGAAGGCACCAATTTTTACTCGCTTTTTTCCT
1 AAAACGCCCTTCCCGGACGGAAGGCACTGATTTTTAC-CGCTTTTTTCCT
* * * *
1616 AAAACGCCATTCCCGGACGAAAGGCGCT-AATTTTACTCGCTTTTT
1 AAAACGCCCTTCCCGGACGGAAGGCACTGATTTTTAC-CGCTTTTT
1661 CTTGAAGTGC
Statistics
Matches: 212, Mismatches: 19, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
46 35 0.17
47 40 0.19
48 42 0.20
49 60 0.28
50 35 0.17
ACGTcount: A:0.22, C:0.29, G:0.18, T:0.31
Consensus pattern (49 bp):
AAAACGCCCTTCCCGGACGGAAGGCACTGATTTTTACCGCTTTTTTCCT
Found at i:1683 original size:48 final size:50
Alignment explanation
Indices: 1415--1689 Score: 257
Period size: 48 Copynumber: 5.7 Consensus size: 50
1405 ATTTTACTTG
* * * **
1415 TTTTTCCCAACACGCCCTTCCCGGACGGAAGGCACTGA-TTTTA--C-CT
1 TTTTTCCTAAAACGCCCTTCCCGGACGAAAGGCACCAATTTTTACTCGCT
* * **
1461 ATTTTCCTAAAACGCCCTTCCCGGACGGAAGGCACTGATTTTTA--C-CT
1 TTTTTCCTAAAACGCCCTTCCCGGACGAAAGGCACCAATTTTTACTCGCT
* * **
1508 ATTTTTCCTAAAACGCCCTTCCCGGACGGAGGGCACTGATTTTTAC-CTG-T
1 -TTTTTCCTAAAACGCCCTTCCCGGACGAAAGGCACCAATTTTTACTC-GCT
*
1558 TTTTTCCTAAAACGCCCTTCCCGGACGGAAGGCACCAATTTTTACTCGCT
1 TTTTTCCTAAAACGCCCTTCCCGGACGAAAGGCACCAATTTTTACTCGCT
* * *
1608 TTTTTCCTAAAACGCCATTCCCGGACGAAAGGCGCTAA-TTTTACTCGC-
1 TTTTTCCTAAAACGCCCTTCCCGGACGAAAGGCACCAATTTTTACTCGCT
* * ** *
1656 TTTTTCTTGAAGTGCCCTTTCCGGACGAAAGGCA
1 TTTTTCCTAAAACGCCCTTCCCGGACGAAAGGCA
1690 AGTTCATTTT
Statistics
Matches: 203, Mismatches: 19, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
46 35 0.17
47 8 0.04
48 69 0.34
49 54 0.27
50 37 0.18
ACGTcount: A:0.22, C:0.30, G:0.18, T:0.30
Consensus pattern (50 bp):
TTTTTCCTAAAACGCCCTTCCCGGACGAAAGGCACCAATTTTTACTCGCT
Done.