Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022982.1 Corchorus olitorius cultivar O-4 contig23015, 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: 12504
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Found at i:4897 original size:46 final size:46
Alignment explanation
Indices: 4820--4917 Score: 151
Period size: 46 Copynumber: 2.1 Consensus size: 46
4810 GGGGGAGTAG
* * *
4820 GAAAAGACTTTCCATGGAAAGTACTCTCTTGGGAATCACTCTCCTT
1 GAAAAGACTCTCCATGGAAAGTAATCTCTTGGAAATCACTCTCCTT
*
4866 GAAATGACTCTCCATGGAAAGTAATCTCTTGGAAATCACTCTCCTT
1 GAAAAGACTCTCCATGGAAAGTAATCTCTTGGAAATCACTCTCCTT
*
4912 GGAAAG
1 GAAAAG
4918 TAATATCTTC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (46 bp):
GAAAAGACTCTCCATGGAAAGTAATCTCTTGGAAATCACTCTCCTT
Found at i:4900 original size:15 final size:15
Alignment explanation
Indices: 4880--4935 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 15
4870 TGACTCTCCA
4880 TGGAAAGTAATCTCT
1 TGGAAAGTAATCTCT
*
4895 TGGAAA-TCACTCTCCT
1 TGGAAAGT-AATCT-CT
*
4911 TGGAAAGTAATATCT
1 TGGAAAGTAATCTCT
4926 TCGGAAAGTA
1 T-GGAAAGTA
4936 CCAAACGGCT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
14 1 0.03
15 13 0.38
16 19 0.56
17 1 0.03
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (15 bp):
TGGAAAGTAATCTCT
Found at i:4907 original size:31 final size:32
Alignment explanation
Indices: 4866--4932 Score: 100
Period size: 31 Copynumber: 2.1 Consensus size: 32
4856 CACTCTCCTT
* *
4866 GAAATGACTCTCCATGGAAAGTAATCTCTT-G
1 GAAATCACTCTCCATGGAAAGTAATATCTTCG
*
4897 GAAATCACTCTCCTTGGAAAGTAATATCTTCG
1 GAAATCACTCTCCATGGAAAGTAATATCTTCG
4929 GAAA
1 GAAA
4933 GTACCAAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
31 27 0.84
32 5 0.16
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.28
Consensus pattern (32 bp):
GAAATCACTCTCCATGGAAAGTAATATCTTCG
Found at i:5835 original size:21 final size:19
Alignment explanation
Indices: 5810--5867 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
5800 GTTGCTCTAA
*
5810 TAATCTCATATGTACAGTACC
1 TAATCTCATCTGTACAGT--C
* *
5831 TAATCTAATCTGTACAGTG
1 TAATCTCATCTGTACAGTC
5850 TAATCTCATCTGTACAGT
1 TAATCTCATCTGTACAGT
5868 TGCTAAACAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 17 0.52
21 16 0.48
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (19 bp):
TAATCTCATCTGTACAGTC
Found at i:6712 original size:87 final size:87
Alignment explanation
Indices: 6560--7368 Score: 1354
Period size: 87 Copynumber: 9.3 Consensus size: 87
6550 CCAAAATTAA
*
6560 TTTCAGGATGTTGCCTAAGAGCACACCTGTTCCTCCATCCGCACCTGGCAAAGGTGGAGATCCAT
1 TTTCA-GATGTTGCCTAAGAGCACACCCGTTCCTCCATCCGCACCTGGCAAAGGTGGAGATCCAT
* *
6625 CGCCTCCCCATGCTACCCTGAAG
65 CGCCTCCCCATACTGCCCTGAAG
6648 TTTCAGATGTTGCCTAAGAGCACACCCGTTCCTCCATCCGCACCTGGCAAAGGTGGAGATCCATC
1 TTTCAGATGTTGCCTAAGAGCACACCCGTTCCTCCATCCGCACCTGGCAAAGGTGGAGATCCATC
*
6713 GCCTCCCCATACTGCCTTGAAG
66 GCCTCCCCATACTGCCCTGAAG
*
6735 TTTCAGATGTTGCCTAAGAGCACACCCGTTCCTCCATCTGCACCTGGCAAAGGTGGAGATCCATC
1 TTTCAGATGTTGCCTAAGAGCACACCCGTTCCTCCATCCGCACCTGGCAAAGGTGGAGATCCATC
6800 GCCTCCCCATACTGCCCTGAAG
66 GCCTCCCCATACTGCCCTGAAG
*
6822 TTTCAGATGTTGCCTAAGAGCACACCCGTTCCTCCATCCGCACCTGGAAAAGGTGGAGATCCATC
1 TTTCAGATGTTGCCTAAGAGCACACCCGTTCCTCCATCCGCACCTGGCAAAGGTGGAGATCCATC
* *
6887 GCCTCCCCACA-TGGCCTTGAAG
66 GCCTCCCCATACT-GCCCTGAAG
*
6909 TTTCAGATGTTGCCTAAGAGCACACCTGTTCCTCCATCCGCACCTGGCAAAGGTGGAGATCCATC
1 TTTCAGATGTTGCCTAAGAGCACACCCGTTCCTCCATCCGCACCTGGCAAAGGTGGAGATCCATC
*
6974 GCCTCCCCATACTGCCTTGAAG
66 GCCTCCCCATACTGCCCTGAAG
* * *
6996 TTTCAGATGTTGCCTAAGAGCACACCTGTTCCTCCATTCGCACCTGGAAAAGGTGGAGATCCATC
1 TTTCAGATGTTGCCTAAGAGCACACCCGTTCCTCCATCCGCACCTGGCAAAGGTGGAGATCCATC
7061 GCCTCCCCATACTGCCCTGAAG
66 GCCTCCCCATACTGCCCTGAAG
*
7083 TTTCAGATGTTGCCTAAGAGCACACCCACTTCCTCCATCCGCACCTGGCAAAGGTGGAGATCCAT
1 TTTCAGATGTTGCCTAAGAGCACACCC-GTTCCTCCATCCGCACCTGGCAAAGGTGGAGATCCAT
7148 CGCCTCCCCATACTGCCCTGAAG
65 CGCCTCCCCATACTGCCCTGAAG
*
7171 TTTCAGATGTTGCCTAAGAGCACACCCGTTCCTCCATCTGCACCTGGCAAAGGTGGAGATCCATC
1 TTTCAGATGTTGCCTAAGAGCACACCCGTTCCTCCATCCGCACCTGGCAAAGGTGGAGATCCATC
*
7236 GCCTCCCCAAACTGCCCTGAAG
66 GCCTCCCCATACTGCCCTGAAG
* *
7258 TTTCAGATGTTGCCTAAGAGCACACCTGTTCCTCCATCCGCACCTGGGAAAGGTGGAGATCCATC
1 TTTCAGATGTTGCCTAAGAGCACACCCGTTCCTCCATCCGCACCTGGCAAAGGTGGAGATCCATC
* * * *
7323 GCCTCCCCATAATGCCTTTAAT
66 GCCTCCCCATACTGCCCTGAAG
* *
7345 TTTC-G-TATTGCCTAAGAACACACC
1 TTTCAGATGTTGCCTAAGAGCACACC
7369 TATTCCACCG
Statistics
Matches: 685, Mismatches: 33, Indels: 9
0.94 0.05 0.01
Matches are distributed among these distances:
85 17 0.02
86 2 0.00
87 576 0.84
88 90 0.13
ACGTcount: A:0.23, C:0.34, G:0.20, T:0.23
Consensus pattern (87 bp):
TTTCAGATGTTGCCTAAGAGCACACCCGTTCCTCCATCCGCACCTGGCAAAGGTGGAGATCCATC
GCCTCCCCATACTGCCCTGAAG
Found at i:8139 original size:51 final size:51
Alignment explanation
Indices: 8066--8168 Score: 118
Period size: 51 Copynumber: 2.0 Consensus size: 51
8056 GTTATTTCTG
* * **
8066 AAAGAGAAACACGAATACAGTGTTTTTATGTCCGGAGACAAGAT-TGAAACA
1 AAAGAGAAACAAGAAAACAGTGTTTGGATGTCCGGAGACAAGATCT-AAACA
* * * *
8117 AAAGAGAAACAATAAAAGAGTGTTTGGGTGTCCTGAGACAAGATCTAAACA
1 AAAGAGAAACAAGAAAACAGTGTTTGGATGTCCGGAGACAAGATCTAAACA
8168 A
1 A
8169 GAAAAATATG
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
51 42 0.98
52 1 0.02
ACGTcount: A:0.45, C:0.13, G:0.22, T:0.20
Consensus pattern (51 bp):
AAAGAGAAACAAGAAAACAGTGTTTGGATGTCCGGAGACAAGATCTAAACA
Done.