Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011727.1 Corchorus capsularis cultivar CVL-1 contig11748, 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: 29998
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Found at i:2176 original size:32 final size:33
Alignment explanation
Indices: 2140--2205 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
2130 AGTTCTTTTG
2140 GGTGG-TTGAATATATCTTACCTCCACTTTCTT
1 GGTGGTTTGAATATATCTTACCTCCACTTTCTT
*
2172 GGTGGTTTGAATATATCTTACCTCCATTTTCTT
1 GGTGGTTTGAATATATCTTACCTCCACTTTCTT
2205 G
1 G
2206 ATGAGGCTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 5 0.16
33 27 0.84
ACGTcount: A:0.18, C:0.20, G:0.17, T:0.45
Consensus pattern (33 bp):
GGTGGTTTGAATATATCTTACCTCCACTTTCTT
Found at i:3178 original size:13 final size:13
Alignment explanation
Indices: 3160--3186 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3150 GGCAGCATGC
3160 TGGATTATAATGT
1 TGGATTATAATGT
3173 TGGATTATAATGT
1 TGGATTATAATGT
3186 T
1 T
3187 TTGATGATGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.48
Consensus pattern (13 bp):
TGGATTATAATGT
Found at i:8151 original size:15 final size:15
Alignment explanation
Indices: 8067--8162 Score: 72
Period size: 15 Copynumber: 6.6 Consensus size: 15
8057 TCCAGATTCT
*
8067 CCTCCACCACCCCCA
1 CCTCCACCACCTCCA
** *
8082 CCTTTACCACCTTCA
1 CCTCCACCACCTCCA
* * *
8097 CCCCCACCCCCACCA
1 CCTCCACCACCTCCA
* *
8112 CCTCCATCATCTCCA
1 CCTCCACCACCTCCA
8127 --T-CACCACCTCCA
1 CCTCCACCACCTCCA
*
8139 CCTCCACCTCCTCCA
1 CCTCCACCACCTCCA
*
8154 CCTCTACCA
1 CCTCCACCA
8163 GCACAACCAC
Statistics
Matches: 58, Mismatches: 20, Indels: 6
0.69 0.24 0.07
Matches are distributed among these distances:
12 9 0.16
13 1 0.02
14 1 0.02
15 47 0.81
ACGTcount: A:0.20, C:0.62, G:0.00, T:0.18
Consensus pattern (15 bp):
CCTCCACCACCTCCA
Found at i:19597 original size:31 final size:31
Alignment explanation
Indices: 19559--19693 Score: 143
Period size: 31 Copynumber: 4.4 Consensus size: 31
19549 AAATGACACC
19559 AGGCCCTTATTTGAGCATTTTCGATAACGTT
1 AGGCCCTTATTTGAGCATTTTCGATAACGTT
19590 AGGCCCTTATTTGAGCATTTTCGATAACGTT
1 AGGCCCTTATTTGAGCATTTTCGATAACGTT
* ** * **
19621 AGACCCTTATTTG-GCCAAATT--A-AAAGACC
1 AGGCCCTTATTTGAG-CATTTTCGATAACG-TT
*
19650 AGGCCCTTATTTGAGCATTTTCGATAATGTT
1 AGGCCCTTATTTGAGCATTTTCGATAACGTT
**
19681 AAACCCTTATTTG
1 AGGCCCTTATTTG
19694 GCTAGATTAA
Statistics
Matches: 84, Mismatches: 14, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
28 3 0.04
29 17 0.20
30 2 0.02
31 59 0.70
32 3 0.04
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (31 bp):
AGGCCCTTATTTGAGCATTTTCGATAACGTT
Found at i:19659 original size:60 final size:60
Alignment explanation
Indices: 19590--19753 Score: 240
Period size: 60 Copynumber: 2.7 Consensus size: 60
19580 CGATAACGTT
19590 AGGCCCTTATTTGAGCATTTTCGATAACGTTAGACCCTTATTTGGCCAAATTAAAAGACC
1 AGGCCCTTATTTGAGCATTTTCGATAACGTTAGACCCTTATTTGGCCAAATTAAAAGACC
* * * * *
19650 AGGCCCTTATTTGAGCATTTTCGATAATGTTAAACCCTTATTTGGCTAGATTAAAAGATC
1 AGGCCCTTATTTGAGCATTTTCGATAACGTTAGACCCTTATTTGGCCAAATTAAAAGACC
* * *
19710 GGGCCCTTATTTGAGCATTTT-GACAAACATTAGACCCTTATTTG
1 AGGCCCTTATTTGAGCATTTTCGA-TAACGTTAGACCCTTATTTG
19754 AGCAATTAGC
Statistics
Matches: 93, Mismatches: 10, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
59 2 0.02
60 91 0.98
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.35
Consensus pattern (60 bp):
AGGCCCTTATTTGAGCATTTTCGATAACGTTAGACCCTTATTTGGCCAAATTAAAAGACC
Found at i:19751 original size:31 final size:31
Alignment explanation
Indices: 19562--19757 Score: 127
Period size: 31 Copynumber: 6.5 Consensus size: 31
19552 TGACACCAGG
* * *
19562 CCCTTATTTGAGCATTTTCGATAACGTTAGG
1 CCCTTATTTGAGCATTTTCGAAAACATTAGA
* *
19593 CCCTTATTTGAGCATTTTCGATAACGTTAGA
1 CCCTTATTTGAGCATTTTCGAAAACATTAGA
** * ** *
19624 CCCTTATTTG-GCCAAATT--AAAAGACCAGG
1 CCCTTATTTGAG-CATTTTCGAAAACATTAGA
* ** *
19653 CCCTTATTTGAGCATTTTCGATAATGTTAAA
1 CCCTTATTTGAGCATTTTCGAAAACATTAGA
** * ** *
19684 CCCTTATTTG-GCTAGATT--AAAAGATCGGG
1 CCCTTATTTGAGC-ATTTTCGAAAACATTAGA
19713 CCCTTATTTGAGCATTTT-GACAAACATTAGA
1 CCCTTATTTGAGCATTTTCGA-AAACATTAGA
19744 CCCTTATTTGAGCA
1 CCCTTATTTGAGCA
19758 ATTAGCCTAA
Statistics
Matches: 124, Mismatches: 33, Indels: 16
0.72 0.19 0.09
Matches are distributed among these distances:
29 36 0.29
30 7 0.06
31 81 0.65
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (31 bp):
CCCTTATTTGAGCATTTTCGAAAACATTAGA
Found at i:25651 original size:18 final size:18
Alignment explanation
Indices: 25628--25662 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
25618 ATCCATGGTT
*
25628 CAAGCTATCCGATCCCTC
1 CAAGCTATCAGATCCCTC
25646 CAAGCTATCAGATCCCT
1 CAAGCTATCAGATCCCT
25663 TCCCAAAGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.40, G:0.11, T:0.23
Consensus pattern (18 bp):
CAAGCTATCAGATCCCTC
Found at i:28045 original size:12 final size:12
Alignment explanation
Indices: 28028--28062 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
28018 TATAAGAAAA
28028 TATTTTCCTTGG
1 TATTTTCCTTGG
* *
28040 TATTTTCCATAG
1 TATTTTCCTTGG
28052 TATTTTCCTTG
1 TATTTTCCTTG
28063 ACACCAAACA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.14, C:0.17, G:0.11, T:0.57
Consensus pattern (12 bp):
TATTTTCCTTGG
Done.