Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013843.1 Corchorus olitorius cultivar O-4 contig13876, 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: 48917
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:4736 original size:15 final size:15
Alignment explanation
Indices: 4713--4751 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
4703 AGGATAGAAA
*
4713 ATTGTTTGTTTTTGG
1 ATTGATTGTTTTTGG
4728 ATTGATTGTTTTTGG
1 ATTGATTGTTTTTGG
4743 ATTGATTGT
1 ATTGATTGT
4752 CCCCCAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.13, C:0.00, G:0.26, T:0.62
Consensus pattern (15 bp):
ATTGATTGTTTTTGG
Found at i:12918 original size:25 final size:25
Alignment explanation
Indices: 12888--12936 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
12878 GTTGCTGCAA
*
12888 AAAGTGGCACAGGGCCTGAGAGAAG
1 AAAGTGGCACAGGGCATGAGAGAAG
**
12913 AAAGTGGTGCAGGGCATGAGAGAA
1 AAAGTGGCACAGGGCATGAGAGAA
12937 AATAAGCACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.37, C:0.12, G:0.41, T:0.10
Consensus pattern (25 bp):
AAAGTGGCACAGGGCATGAGAGAAG
Found at i:19123 original size:15 final size:17
Alignment explanation
Indices: 19090--19126 Score: 51
Period size: 15 Copynumber: 2.2 Consensus size: 17
19080 GTGATCTTCT
19090 TTTTTTATGTGTGATTGA
1 TTTTTTATGTGTGA-TGA
19108 TTTTTT-TGTGTG-TGA
1 TTTTTTATGTGTGATGA
19123 TTTT
1 TTTT
19127 GTGTGTGAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
17 6 0.32
18 6 0.32
ACGTcount: A:0.11, C:0.00, G:0.22, T:0.68
Consensus pattern (17 bp):
TTTTTTATGTGTGATGA
Found at i:22683 original size:29 final size:26
Alignment explanation
Indices: 22639--22704 Score: 78
Period size: 29 Copynumber: 2.4 Consensus size: 26
22629 TAAGGGACCC
* *
22639 ATGACCAAAATGCCCCTCTAAATACACAA
1 ATGACCAAAATACCCCT-GAAAT--ACAA
*
22668 ATGACCAAAATACCCCTGAAGTACAA
1 ATGACCAAAATACCCCTGAAATACAA
22694 ATGACCAAAAT
1 ATGACCAAAAT
22705 GCTAAATAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 15 0.44
28 3 0.09
29 16 0.47
ACGTcount: A:0.47, C:0.27, G:0.09, T:0.17
Consensus pattern (26 bp):
ATGACCAAAATACCCCTGAAATACAA
Found at i:23832 original size:41 final size:40
Alignment explanation
Indices: 23751--23833 Score: 103
Period size: 41 Copynumber: 2.0 Consensus size: 40
23741 TCCATATACG
** * * *
23751 TTGTGAAATATTGCATGAAAGAATGGCAATCATTGTTGCC
1 TTGTGAAATATTGCAAAAAAAAAAGACAATCATTGTTGCC
*
23791 TTGTGAAATATTGCGAAAAAAAAAAGACAATCATTTTTGCC
1 TTGTGAAATATTGC-AAAAAAAAAAGACAATCATTGTTGCC
23832 TT
1 TT
23834 ATACTGAAGA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
40 14 0.39
41 22 0.61
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (40 bp):
TTGTGAAATATTGCAAAAAAAAAAGACAATCATTGTTGCC
Found at i:23892 original size:46 final size:46
Alignment explanation
Indices: 23790--23892 Score: 102
Period size: 46 Copynumber: 2.2 Consensus size: 46
23780 TCATTGTTGC
* *
23790 CTTGTGAAATATTGCGAAAAAAAAAAGACAATCATTTTTGCCTTATA
1 CTTGTGAAATATTGC-AAAAAAAAAAGACAATAATTTTTGCCATATA
* ** * *
23837 C-TGAAGAAATATTGC-AGGAAAAAAGGCAATTAATTTTTGTCATATA
1 CTTG-TGAAATATTGCAAAAAAAAAAGACAA-TAATTTTTGCCATATA
23883 CTTGTGAAAT
1 CTTGTGAAAT
23893 TTTGTTAAGT
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
45 11 0.24
46 21 0.47
47 13 0.29
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.32
Consensus pattern (46 bp):
CTTGTGAAATATTGCAAAAAAAAAAGACAATAATTTTTGCCATATA
Found at i:24293 original size:2 final size:2
Alignment explanation
Indices: 24286--24319 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
24276 AGGTATTGAC
24286 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
24320 AGTTAAGCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:29100 original size:17 final size:18
Alignment explanation
Indices: 29071--29104 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
29061 AACCTTAATT
29071 ATTAAACGCATTGAAAAA
1 ATTAAACGCATTGAAAAA
29089 ATTAAA-GCATTGAAAA
1 ATTAAACGCATTGAAAA
29105 TTTTCATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.56, C:0.09, G:0.12, T:0.24
Consensus pattern (18 bp):
ATTAAACGCATTGAAAAA
Found at i:29925 original size:21 final size:21
Alignment explanation
Indices: 29901--29948 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
29891 GTAGCAAAGT
29901 TCTTTTCAAAATGCACTCTTC
1 TCTTTTCAAAATGCACTCTTC
29922 TCTTTTCAAAATGCACTCTTC
1 TCTTTTCAAAATGCACTCTTC
*
29943 TTTTTT
1 TCTTTT
29949 GGGTATATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.21, C:0.25, G:0.04, T:0.50
Consensus pattern (21 bp):
TCTTTTCAAAATGCACTCTTC
Found at i:45671 original size:27 final size:28
Alignment explanation
Indices: 45629--45691 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 28
45619 TTTTGGTACT
45629 TGTTG-AAGAACAC-TTTTTTTCACAAA
1 TGTTGAAAGAACACTTTTTTTTCACAAA
45655 TGTTGAAAGAACACTTTTTTTTTTCACAAA
1 TGTTGAAAGAACAC--TTTTTTTTCACAAA
45685 TGTTGAA
1 TGTTGAA
45692 GACAATGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
26 5 0.15
27 8 0.24
30 20 0.61
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (28 bp):
TGTTGAAAGAACACTTTTTTTTCACAAA
Found at i:45702 original size:29 final size:30
Alignment explanation
Indices: 45642--45703 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
45632 TGAAGAACAC
*
45642 TTTTTTTCACAAATGTTGAAAGAACACTTT
1 TTTTTTTCACAAATGTTGAAAGAACAATTT
*
45672 TTTTTTTCACAAATGTTG-AAG-ACAATGT
1 TTTTTTTCACAAATGTTGAAAGAACAATTT
45700 TTTT
1 TTTT
45704 ATAATCGGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 9 0.30
29 3 0.10
30 18 0.60
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.47
Consensus pattern (30 bp):
TTTTTTTCACAAATGTTGAAAGAACAATTT
Found at i:45934 original size:34 final size:34
Alignment explanation
Indices: 45895--45962 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
45885 CATTTTTTTC
45895 AAATACAAGTCATGAGTTCAAAACCCATAACCCA
1 AAATACAAGTCATGAGTTCAAAACCCATAACCCA
45929 AAATACAAGTCATGAGTTCAAAACCCATAACCCA
1 AAATACAAGTCATGAGTTCAAAACCCATAACCCA
45963 CAAGATATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.47, C:0.26, G:0.09, T:0.18
Consensus pattern (34 bp):
AAATACAAGTCATGAGTTCAAAACCCATAACCCA
Found at i:46223 original size:4 final size:4
Alignment explanation
Indices: 46214--46242 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
46204 AAACCCTTCT
46214 TTTA TTTA TTTA -TTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
46243 CTTTGATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:46234 original size:15 final size:15
Alignment explanation
Indices: 46214--46242 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
46204 AAACCCTTCT
46214 TTTATTTATTTATTA
1 TTTATTTATTTATTA
46229 TTTATTTATTTATT
1 TTTATTTATTTATT
46243 CTTTGATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTATTTATTTATTA
Found at i:46882 original size:17 final size:17
Alignment explanation
Indices: 46862--46905 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
46852 TTTGCTATGG
*
46862 TGAACTTCTCCCAGCAA
1 TGAACTTCTCCCAACAA
* *
46879 TGAACCTCTGCCAACAA
1 TGAACTTCTCCCAACAA
*
46896 CGAACTTCTC
1 TGAACTTCTC
46906 TGCTTTCCCC
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.30, C:0.36, G:0.11, T:0.23
Consensus pattern (17 bp):
TGAACTTCTCCCAACAA
Found at i:48868 original size:2 final size:2
Alignment explanation
Indices: 48861--48913 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
48851 TATTGGAAAA
48861 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
48903 AG AG AG AG AG A
1 AG AG AG AG AG A
48914 TCGC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Done.