Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012630.1 Corchorus olitorius cultivar O-4 contig12663, 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: 17004
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Found at i:1727 original size:19 final size:19
Alignment explanation
Indices: 1677--1727 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
1667 TGTAGGGTTT
1677 TTAATAA-TAATTATTCAA
1 TTAATAATTAATTATTCAA
* *
1695 TAAAATAATT-ATTATTTAA
1 T-TAATAATTAATTATTCAA
1714 TTAATAATTAATTA
1 TTAATAATTAATTA
1728 ATTTCAGCCA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 8 0.30
19 18 0.67
20 1 0.04
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
TTAATAATTAATTATTCAA
Found at i:1961 original size:31 final size:31
Alignment explanation
Indices: 1923--1984 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
1913 GAGCTTTGTA
* *
1923 AAACTTTTGAATCGCCTATTATACCCTTATT
1 AAACTTTTGAATCACCTATTATACACTTATT
1954 AAACTTTTGAATCACCTATTATACACTTATT
1 AAACTTTTGAATCACCTATTATACACTTATT
1985 TTTTTAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.32, C:0.21, G:0.05, T:0.42
Consensus pattern (31 bp):
AAACTTTTGAATCACCTATTATACACTTATT
Found at i:2131 original size:93 final size:93
Alignment explanation
Indices: 2020--2189 Score: 295
Period size: 93 Copynumber: 1.8 Consensus size: 93
2010 TTGTTTAAAT
* *
2020 TTTTATAGTTTTAGTCAACTAAAAACTATATTTTTATTTAATTAAATCTAATATCCTTATAACTA
1 TTTTATAGTCTTACTCAACTAAAAACTATATTTTTATTTAATTAAATCTAATATCCTTATAACTA
2085 TTCTATTTTTACCATTTTACTATTTTAC
66 TTCTATTTTTACCATTTTACTATTTTAC
* *
2113 TTTTATAGTCTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACCTA
1 TTTTATAGTCTTACTCAACTAAAAACTATATTTTTATTTAATTAAATCTAATATCCTTATAACTA
*
2178 TTTTATTTTTAC
66 TTCTATTTTTAC
2190 GGTGTTACTA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.33, C:0.14, G:0.02, T:0.51
Consensus pattern (93 bp):
TTTTATAGTCTTACTCAACTAAAAACTATATTTTTATTTAATTAAATCTAATATCCTTATAACTA
TTCTATTTTTACCATTTTACTATTTTAC
Found at i:2994 original size:17 final size:17
Alignment explanation
Indices: 2972--3004 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2962 TCATTATATC
2972 AATTAA-AATTATAAATT
1 AATTAATAA-TATAAATT
2989 AATTAATAATATAAAT
1 AATTAATAATATAAAT
3005 ATCCATAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AATTAATAATATAAATT
Found at i:10729 original size:21 final size:21
Alignment explanation
Indices: 10699--10738 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
10689 AACAGACCAT
* *
10699 GTCCTGGGCAGGAGTTGTCGA
1 GTCCTAGGCAGGACTTGTCGA
10720 GTCCTAGGCAGGACTTGTC
1 GTCCTAGGCAGGACTTGTC
10739 CTGTTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.23, G:0.38, T:0.25
Consensus pattern (21 bp):
GTCCTAGGCAGGACTTGTCGA
Found at i:16021 original size:21 final size:20
Alignment explanation
Indices: 15986--16025 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
15976 TATGGGGAGC
15986 TTTAAATTCTAGTTTTTAGT
1 TTTAAATTCTAGTTTTTAGT
*
16006 TTTAAGTTCTTAGTTTTTAG
1 TTTAAATTC-TAGTTTTTAG
16026 GTTTGAACGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.23, C:0.05, G:0.12, T:0.60
Consensus pattern (20 bp):
TTTAAATTCTAGTTTTTAGT
Found at i:16748 original size:29 final size:30
Alignment explanation
Indices: 16694--16767 Score: 105
Period size: 29 Copynumber: 2.5 Consensus size: 30
16684 TACCCAGAAA
*
16694 AATCCCTTATGTTTTGCTTTTGGGACAAAAT
1 AATCCCTTATGTTTT-CTTTCGGGACAAAAT
*
16725 AATCCCTTATGTTTT-TTTCGGGACAAATT
1 AATCCCTTATGTTTTCTTTCGGGACAAAAT
*
16754 AATCCCTTACGTTT
1 AATCCCTTATGTTT
16768 AAAAAGTGAG
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 25 0.62
31 15 0.38
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.43
Consensus pattern (30 bp):
AATCCCTTATGTTTTCTTTCGGGACAAAAT
Found at i:16934 original size:29 final size:31
Alignment explanation
Indices: 16901--16966 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
16891 CCACGTCAGC
16901 AAGGGACTAATTGGT-CCAAAA-AAAAACAT
1 AAGGGACTAATTGGTCCCAAAAGAAAAACAT
* ** *
16930 AAGGGATTTTTTTGTCCCAAAAGAAAAACAT
1 AAGGGACTAATTGGTCCCAAAAGAAAAACAT
16961 AAGGGA
1 AAGGGA
16967 TTTTTTTACC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 11 0.35
30 6 0.19
31 14 0.45
ACGTcount: A:0.47, C:0.12, G:0.20, T:0.21
Consensus pattern (31 bp):
AAGGGACTAATTGGTCCCAAAAGAAAAACAT
Found at i:16986 original size:28 final size:31
Alignment explanation
Indices: 16916--17000 Score: 124
Period size: 31 Copynumber: 2.9 Consensus size: 31
16906 ACTAATTGGT
*
16916 CCAAAA-AAAAACATAAGGGATTTTTTTGTC
1 CCAAAAGAAAAACATAAGGGATTTTTTTGAC
16946 CCAAAAGAAAAACATAAGGGATTTTTTT-AC
1 CCAAAAGAAAAACATAAGGGATTTTTTTGAC
*
16976 CC-AAAG-AAAACATTAGGGATTTTTT
1 CCAAAAGAAAAACATAAGGGATTTTTT
17001 AGTA
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
28 18 0.35
29 4 0.08
30 9 0.17
31 21 0.40
ACGTcount: A:0.44, C:0.13, G:0.14, T:0.29
Consensus pattern (31 bp):
CCAAAAGAAAAACATAAGGGATTTTTTTGAC
Done.