Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022703.1 Corchorus olitorius cultivar O-4 contig22736, 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: 12396
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Found at i:981 original size:15 final size:15
Alignment explanation
Indices: 951--992 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
941 TTACTTTGTT
951 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
967 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
982 TTGCTTTCTGT
1 TTGTTTTCTGT
993 CAATCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:6543 original size:21 final size:21
Alignment explanation
Indices: 6519--6568 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
6509 GGAATGGTAA
**
6519 TGGCACGGGCATGGCCGGTGG
1 TGGCACGGGCATAACCGGTGG
*
6540 TGGCACGGGCTTAACCGGTGG
1 TGGCACGGGCATAACCGGTGG
6561 TGGCACGG
1 TGGCACGG
6569 TGAATGGGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.12, C:0.24, G:0.48, T:0.16
Consensus pattern (21 bp):
TGGCACGGGCATAACCGGTGG
Found at i:7629 original size:21 final size:21
Alignment explanation
Indices: 7605--7654 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
7595 GGAATGGTAA
* **
7605 TGGCACTGGCATGGCCGGTGG
1 TGGCACGGGCATAACCGGTGG
*
7626 TGGCACGGGCTTAACCGGTGG
1 TGGCACGGGCATAACCGGTGG
7647 TGGCACGG
1 TGGCACGG
7655 TGAATGGGCG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.12, C:0.24, G:0.46, T:0.18
Consensus pattern (21 bp):
TGGCACGGGCATAACCGGTGG
Found at i:7905 original size:21 final size:21
Alignment explanation
Indices: 7867--7906 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
7857 GCATTTGGCT
* *
7867 CGGATGGCGCGGAAGAAGGCG
1 CGGATGACGCAGAAGAAGGCG
*
7888 CGGATGACGCAGAGGAAGG
1 CGGATGACGCAGAAGAAGG
7907 TACGGCTAGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.17, G:0.50, T:0.05
Consensus pattern (21 bp):
CGGATGACGCAGAAGAAGGCG
Found at i:9340 original size:32 final size:32
Alignment explanation
Indices: 9293--9438 Score: 213
Period size: 32 Copynumber: 4.5 Consensus size: 32
9283 AAAAAACAGT
9293 TAAATATAGCGGCGTTTTGTTTTGAAGACGCCGC
1 TAAATA-AG-GGCGTTTTGTTTTGAAGACGCCGC
9327 TAAATAAGGGCGTTTTGTTTTGAAGACGCCGC
1 TAAATAAGGGCGTTTTGTTTTGAAGACGCCGC
* * *
9359 TAAATAAGGGCGTTTTGATCTGTAGACGCCGC
1 TAAATAAGGGCGTTTTGTTTTGAAGACGCCGC
*
9391 TAAATAAGGGCGTTTTG-TTTCATAGACGCCGC
1 TAAATAAGGGCGTTTTGTTTTGA-AGACGCCGC
*
9423 TAAATAAGAGCGTTTT
1 TAAATAAGGGCGTTTT
9439 CTATTCACAC
Statistics
Matches: 104, Mismatches: 7, Indels: 4
0.90 0.06 0.03
Matches are distributed among these distances:
31 2 0.02
32 94 0.90
33 2 0.02
34 6 0.06
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (32 bp):
TAAATAAGGGCGTTTTGTTTTGAAGACGCCGC
Found at i:10980 original size:17 final size:17
Alignment explanation
Indices: 10955--10989 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
10945 TGGATAATGT
10955 TAATATACCAACAAGAA
1 TAATATACCAACAAGAA
*
10972 TAATGTACCAACAAGAA
1 TAATATACCAACAAGAA
10989 T
1 T
10990 GCACTTTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.54, C:0.17, G:0.09, T:0.20
Consensus pattern (17 bp):
TAATATACCAACAAGAA
Found at i:11615 original size:13 final size:13
Alignment explanation
Indices: 11597--11622 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11587 ATGAGTTAGT
11597 AAATTATAAAAAA
1 AAATTATAAAAAA
11610 AAATTATAAAAAA
1 AAATTATAAAAAA
11623 TTGGAAGTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AAATTATAAAAAA
Found at i:11827 original size:27 final size:27
Alignment explanation
Indices: 11789--11890 Score: 195
Period size: 27 Copynumber: 3.8 Consensus size: 27
11779 CGACCCGAGG
11789 CGAAGTGGGAGGATCCACTGCTGGGGT
1 CGAAGTGGGAGGATCCACTGCTGGGGT
11816 CGAAGTGGGAGGATCCACTGCTGGGGT
1 CGAAGTGGGAGGATCCACTGCTGGGGT
*
11843 CGAAGTGGGAGGATCCACTGCTGTGGT
1 CGAAGTGGGAGGATCCACTGCTGGGGT
11870 CGAAGTGGGAGGATCCACTGC
1 CGAAGTGGGAGGATCCACTGC
11891 GGCAACCGTC
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
27 74 1.00
ACGTcount: A:0.20, C:0.20, G:0.42, T:0.19
Consensus pattern (27 bp):
CGAAGTGGGAGGATCCACTGCTGGGGT
Done.