Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023841.1 Corchorus olitorius cultivar O-4 contig23874, 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: 36831
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:10976 original size:101 final size:100
Alignment explanation
Indices: 10801--11005 Score: 322
Period size: 101 Copynumber: 2.0 Consensus size: 100
10791 TGTAATAATT
* * *
10801 TATGGGTAATTATTTGATACATTGGTAGTGTAAATTTTGGACTCTACAAGCGGGTTATGGAGTTG
1 TATGGGTAATTATTTGATACACTGGCAGTGTAAATTTTGGACTCCACAAGCGGGTTATGGAGTTG
*
10866 ACATATGTCCA-TTTTCTGAATTAATTAAATTTTAAA
66 ACACATGTCCACTTTT-T-AATTAATTAAATTTTAAA
*
10902 TATGGGTAATTATTTGATACACTGGCGGTGTAAATTTTGGACTCCACAAGCGGGTTATGGAGTTG
1 TATGGGTAATTATTTGATACACTGGCAGTGTAAATTTTGGACTCCACAAGCGGGTTATGGAGTTG
*
10967 ACACATGTCCACCTTTTTAATTAATTAAGTTTTAAA
66 ACACATGTCCA-CTTTTTAATTAATTAAATTTTAAA
11003 TAT
1 TAT
11006 TTCAATCTAG
Statistics
Matches: 96, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
101 91 0.95
102 1 0.01
103 4 0.04
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (100 bp):
TATGGGTAATTATTTGATACACTGGCAGTGTAAATTTTGGACTCCACAAGCGGGTTATGGAGTTG
ACACATGTCCACTTTTTAATTAATTAAATTTTAAA
Found at i:11163 original size:101 final size:101
Alignment explanation
Indices: 10997--11191 Score: 282
Period size: 101 Copynumber: 1.9 Consensus size: 101
10987 TTAATTAAGT
* * * * ** *
10997 TTTAAATATTTCAATCTAGTTCTTAAAGGACACATGTCACCCTTCAGGACCCACTTGTGTAGTCT
1 TTTAAATATCTCAATCTAGTCCCTAAAGGACACATATCACCCTTCAAAACCCACTTGTGCAGTCT
* *
11062 GCTAAACTTCACCGTCGGTGTATTGTATAATTTACC
66 GCTAAACTTCACCGACGGTGTACTGTATAATTTACC
* *
11098 TTTAAATATCTCAATCTAGTCCCTAGAGGACACATATCACCCTTCAAAACCCGCTTGTGCAGTCT
1 TTTAAATATCTCAATCTAGTCCCTAAAGGACACATATCACCCTTCAAAACCCACTTGTGCAGTCT
*
11163 GCTAAACTTCACTGACGGTGTACTGTATA
66 GCTAAACTTCACCGACGGTGTACTGTATA
11192 TAAACCCATA
Statistics
Matches: 82, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
101 82 1.00
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.33
Consensus pattern (101 bp):
TTTAAATATCTCAATCTAGTCCCTAAAGGACACATATCACCCTTCAAAACCCACTTGTGCAGTCT
GCTAAACTTCACCGACGGTGTACTGTATAATTTACC
Found at i:11862 original size:22 final size:22
Alignment explanation
Indices: 11834--11875 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
11824 GTTTTTCATA
11834 TTTTTTTTGCACACACAAAATT
1 TTTTTTTTGCACACACAAAATT
11856 TTTTTTTTGCACACACAAAA
1 TTTTTTTTGCACACACAAAA
11876 GTGTTTTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.43
Consensus pattern (22 bp):
TTTTTTTTGCACACACAAAATT
Found at i:11882 original size:22 final size:22
Alignment explanation
Indices: 11835--11883 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
11825 TTTTTCATAT
* *
11835 TTTTTTTGCACACACAAAATTT
1 TTTTTTTGCACACACAAAAGTG
11857 TTTTTTTGCACACACAAAAGTG
1 TTTTTTTGCACACACAAAAGTG
11879 TTTTT
1 TTTTT
11884 CATATATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.16, G:0.08, T:0.47
Consensus pattern (22 bp):
TTTTTTTGCACACACAAAAGTG
Found at i:12197 original size:24 final size:22
Alignment explanation
Indices: 12141--12186 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
12131 ATATTAATTA
12141 AAGAAAAAAAAAGAGCTCATAT
1 AAGAAAAAAAAAGAGCTCATAT
12163 AAGAAAAAAAAAGAGCTCATAT
1 AAGAAAAAAAAAGAGCTCATAT
12185 AA
1 AA
12187 TAATTACAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.65, C:0.09, G:0.13, T:0.13
Consensus pattern (22 bp):
AAGAAAAAAAAAGAGCTCATAT
Found at i:22014 original size:25 final size:25
Alignment explanation
Indices: 21980--22028 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
21970 TAGCAACAAT
21980 ATGAATGAAAATGAATTATGAGGAA
1 ATGAATGAAAATGAATTATGAGGAA
22005 ATGAATGAAAATGAATTATGAGGA
1 ATGAATGAAAATGAATTATGAGGA
22029 GGAAAAGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.51, C:0.00, G:0.24, T:0.24
Consensus pattern (25 bp):
ATGAATGAAAATGAATTATGAGGAA
Found at i:22689 original size:3 final size:3
Alignment explanation
Indices: 22681--22752 Score: 144
Period size: 3 Copynumber: 24.0 Consensus size: 3
22671 TTTAATTGTC
22681 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
22729 TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT
22753 AACATATATG
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:23720 original size:22 final size:21
Alignment explanation
Indices: 23695--23738 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
23685 AGCTTTGATC
23695 TTCTGTTTTTCTTTCTTTCTTT
1 TTCTGTTTTTCTTTCTTT-TTT
* *
23717 TTCTTTTTTTTTTTCTTTTTT
1 TTCTGTTTTTCTTTCTTTTTT
23738 T
1 T
23739 CCTTCCAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84
Consensus pattern (21 bp):
TTCTGTTTTTCTTTCTTTTTT
Found at i:36801 original size:57 final size:57
Alignment explanation
Indices: 36699--36827 Score: 168
Period size: 57 Copynumber: 2.3 Consensus size: 57
36689 TGTAGGCTCT
* * * *
36699 TGGAGAGGGGTTGGAGAGCTTCCCTCTTTCAGAGACAGGACTTGCTAACGAATTTGA
1 TGGAAAGGGGTTCGAAAGCTTCCCTCCTTCAGAGACAGGACTTGCTAACGAATTTGA
* ** * * *
36756 TGGAAAGGGGTTCGAAAGCTTGCCTCCTTCAGAGATGGGATTTGCTGATGAATTTGA
1 TGGAAAGGGGTTCGAAAGCTTCCCTCCTTCAGAGACAGGACTTGCTAACGAATTTGA
36813 TGGAAAGGGGTTCGA
1 TGGAAAGGGGTTCGA
36828 GAGG
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
57 62 1.00
ACGTcount: A:0.25, C:0.15, G:0.33, T:0.27
Consensus pattern (57 bp):
TGGAAAGGGGTTCGAAAGCTTCCCTCCTTCAGAGACAGGACTTGCTAACGAATTTGA
Done.