Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012502.1 Corchorus capsularis cultivar CVL-1 contig12523, 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: 10868
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Found at i:1287 original size:21 final size:21
Alignment explanation
Indices: 1261--1305 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1251 TTGAATTGGA
1261 TTGCTAAACACCGCCCCATTT
1 TTGCTAAACACCGCCCCATTT
**
1282 TTGCTATTCACCGCCCCATTT
1 TTGCTAAACACCGCCCCATTT
1303 TTG
1 TTG
1306 ACGCTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.18, C:0.36, G:0.11, T:0.36
Consensus pattern (21 bp):
TTGCTAAACACCGCCCCATTT
Found at i:1613 original size:33 final size:32
Alignment explanation
Indices: 1521--1690 Score: 137
Period size: 32 Copynumber: 5.2 Consensus size: 32
1511 CCGTGGCGAA
** * * *
1521 GCCGCCCCACTTAGGAGGCTTCGCCACGGCAA
1 GCCGCCCCACTGGGGTGGCTTCGCCAGGGCAG
* * *
1553 GCCGCCCTCA-TGGGGTAGTTTCACCATGGGCAG
1 GCCGCCC-CACTGGGGTGGCTTCGCCA-GGGCAG
* ***
1586 GCCGCCCCA-TGAGGGTGGCTTCCCCATGAAAAG
1 GCCGCCCCACTG-GGGTGGCTTCGCCA-GGGCAG
*
1619 GCCGCCCCACTGGGGTGGCTTAGCCAGGGCAG
1 GCCGCCCCACTGGGGTGGCTTCGCCAGGGCAG
* * * *
1651 GCCGTCCCAGTGGGGCGGCTTCGCCACGGCAG
1 GCCGCCCCACTGGGGTGGCTTCGCCAGGGCAG
1683 GCCGCCCC
1 GCCGCCCC
1691 GATGGGGCGG
Statistics
Matches: 109, Mismatches: 25, Indels: 8
0.77 0.18 0.06
Matches are distributed among these distances:
32 58 0.53
33 49 0.45
34 2 0.02
ACGTcount: A:0.15, C:0.37, G:0.34, T:0.14
Consensus pattern (32 bp):
GCCGCCCCACTGGGGTGGCTTCGCCAGGGCAG
Found at i:1665 original size:32 final size:32
Alignment explanation
Indices: 1617--1702 Score: 111
Period size: 32 Copynumber: 2.7 Consensus size: 32
1607 CCCCATGAAA
* *
1617 AGGCCGCCCCACTGGGGTGGCTTAGCCAGGGC
1 AGGCCGCCCCACTGGGGCGGCTTAGCCACGGC
* * *
1649 AGGCCGTCCCAGTGGGGCGGCTTCGCCACGGC
1 AGGCCGCCCCACTGGGGCGGCTTAGCCACGGC
1681 AGGCCGCCCCGA-TGGGGCGGCT
1 AGGCCGCCCC-ACTGGGGCGGCT
1703 CGGCTATTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
32 46 0.98
33 1 0.02
ACGTcount: A:0.10, C:0.36, G:0.42, T:0.12
Consensus pattern (32 bp):
AGGCCGCCCCACTGGGGCGGCTTAGCCACGGC
Found at i:1863 original size:33 final size:31
Alignment explanation
Indices: 1769--1886 Score: 112
Period size: 33 Copynumber: 3.6 Consensus size: 31
1759 CCCCACCGGT
* *
1769 GCCGTCCCCCTGGGGCGG-CTGAGCCATGACCAA
1 GCCG-CCCCCTGGGGCGGCCT-A-CCATGGCCAG
1802 GCCGCCCTCCTGGGGCGGCACTACCATGGCCAG
1 GCCGCCC-CCTGGGGCGGC-CTACCATGGCCAG
**
1835 GCCGCCTCCCTGGGGCGGCCCTACCATGGATAG
1 GCCGCC-CCCTGGGGCGG-CCTACCATGGCCAG
*
1868 ACCGCCCCCCTGGGGCGGC
1 GCCG-CCCCCTGGGGCGGC
1887 ACCGGTACTA
Statistics
Matches: 74, Mismatches: 5, Indels: 13
0.80 0.05 0.14
Matches are distributed among these distances:
32 4 0.05
33 63 0.85
34 5 0.07
35 2 0.03
ACGTcount: A:0.12, C:0.42, G:0.34, T:0.12
Consensus pattern (31 bp):
GCCGCCCCCTGGGGCGGCCTACCATGGCCAG
Found at i:5666 original size:13 final size:13
Alignment explanation
Indices: 5650--5682 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
5640 AAATTAAGTC
5650 TTAAAAATAATTA
1 TTAAAAATAATTA
5663 TTAAAAATAATTA
1 TTAAAAATAATTA
*
5676 TGAAAAA
1 TTAAAAA
5683 ACATATTCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (13 bp):
TTAAAAATAATTA
Found at i:7744 original size:21 final size:20
Alignment explanation
Indices: 7719--7767 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
7709 CTTAATTCTA
* *
7719 AAATATAAAAATATGTAAACT
1 AAATATAAAAAAAAGT-AACT
*
7740 AAATAAAAAAAAAAGTAACT
1 AAATATAAAAAAAAGTAACT
7760 AAAGTATA
1 AAA-TATA
7768 TTCGATTCTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.67, C:0.04, G:0.06, T:0.22
Consensus pattern (20 bp):
AAATATAAAAAAAAGTAACT
Found at i:8389 original size:32 final size:33
Alignment explanation
Indices: 8334--8422 Score: 126
Period size: 32 Copynumber: 2.7 Consensus size: 33
8324 ATGCCGTGGT
*
8334 CAGGCCGCCCCCCTAGGGCGGCACTACCAAGGC
1 CAGGCCGCCCCCCTGGGGCGGCACTACCAAGGC
* ** *
8367 CAGGCCG-CCCCCTGGGGTGGCACTACCGTGGT
1 CAGGCCGCCCCCCTGGGGCGGCACTACCAAGGC
8399 CAGGCCGCCCCCCTGGGGCGGCAC
1 CAGGCCGCCCCCCTGGGGCGGCAC
8423 CAACCCTAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
32 27 0.55
33 22 0.45
ACGTcount: A:0.12, C:0.44, G:0.35, T:0.09
Consensus pattern (33 bp):
CAGGCCGCCCCCCTGGGGCGGCACTACCAAGGC
Done.