Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024454.1 Corchorus olitorius cultivar O-4 contig24487, 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: 17800
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Found at i:2373 original size:6 final size:6
Alignment explanation
Indices: 2354--2390 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
2344 GTATTTTTTT
*
2354 TTTATA TTT-T- TTTATA TTTAAA TTTATA TTTATA TTT
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTT
2391 TTCTCATCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
4 3 0.11
5 2 0.07
6 22 0.81
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTATA
Found at i:9278 original size:23 final size:23
Alignment explanation
Indices: 9251--9317 Score: 64
Period size: 23 Copynumber: 2.9 Consensus size: 23
9241 GTTTCTTTTG
9251 ACCCTCGAAAACCCTCGATTTCA
1 ACCCTCGAAAACCCTCGATTTCA
* * * * *
9274 ACCCTCCAAAGCCTTTGATTTTA
1 ACCCTCGAAAACCCTCGATTTCA
*
9297 ACCC-CAGAAATCCCTCGATTT
1 ACCCTC-GAAAACCCTCGATTT
9318 TAAACCCTTA
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
22 1 0.03
23 33 0.97
ACGTcount: A:0.28, C:0.36, G:0.09, T:0.27
Consensus pattern (23 bp):
ACCCTCGAAAACCCTCGATTTCA
Found at i:13024 original size:18 final size:18
Alignment explanation
Indices: 13001--13051 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 18
12991 GGAGCTGGTT
13001 TTTAAGATGAGTGATATC
1 TTTAAGATGAGTGATATC
*
13019 TTTAAGA-GA-TGGT-T-
1 TTTAAGATGAGTGATATC
*
13033 TTTGAGATGAGTGATATC
1 TTTAAGATGAGTGATATC
13051 T
1 T
13052 GATTTAAGCC
Statistics
Matches: 26, Mismatches: 3, Indels: 8
0.70 0.08 0.22
Matches are distributed among these distances:
14 6 0.23
15 3 0.12
16 6 0.23
17 3 0.12
18 8 0.31
ACGTcount: A:0.29, C:0.04, G:0.25, T:0.41
Consensus pattern (18 bp):
TTTAAGATGAGTGATATC
Found at i:15397 original size:11 final size:11
Alignment explanation
Indices: 15383--15416 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
15373 TAAAGGAAAA
15383 AGCTAGGAAGG
1 AGCTAGGAAGG
15394 AGCTAGGAAGG
1 AGCTAGGAAGG
15405 AGCTAGGAAGG
1 AGCTAGGAAGG
15416 A
1 A
15417 TCCTACTCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.38, C:0.09, G:0.44, T:0.09
Consensus pattern (11 bp):
AGCTAGGAAGG
Found at i:16256 original size:154 final size:154
Alignment explanation
Indices: 15975--17739 Score: 2757
Period size: 154 Copynumber: 11.5 Consensus size: 154
15965 GGCCAAAAAT
* * * * *
15975 CCAAAATGATTATAGTTAGTCCATAAACAATGAAAAGAAAAGC-TTAAGGGTTTGCCGAATTGAA
1 CCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA-GGTTTGCCAAATCGAA
** *
16039 GACGATTCAAAACGTCACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTA
65 GACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTA
16104 AAAACTTCACAGTGGACTAATCTCA
130 AAAACTTCACAGTGGACTAATCTCA
* *
16129 CCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCTAAATCGAAG
1 CCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAG
* * ** * * * *
16194 ACGATTCAATATGTCACAAATAGGCCCCGATAGGCCTAAAATAACAAGTGTTCCAAACGAGCTAA
66 ACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAA
16259 AAACTTCACAGTGGACTAATCTCA
131 AAACTTCACAGTGGACTAATCTCA
*
16283 CCAAAATGATTATAGTTAGGCCATAAACACTGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAG
1 CCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAG
*
16348 ACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAACGAGCTAA
66 ACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAA
16413 AAACTTCACAGTGGACTAATCTCA
131 AAACTTCACAGTGGACTAATCTCA
* *
16437 CCAAAATGATTATAGTTAGGCCATAAACACTGGAAAGAAAGGCATTGAGGTTTGCCAAATCGAAG
1 CCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAG
* * ** *
16502 ACGATTCAAAACGGAACTAATGGGCTCCGAAAGGCTTAAAATAACAAGTGTCCCAAATGAGCTAA
66 ACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAA
* *
16567 GAACTGCACAGTGGACTAATCTCA
131 AAACTTCACAGTGGACTAATCTCA
* ** * * *
16591 TCAAAATGATTATAACTAGGCCATAAACAACT-TAAAGAAAAACTTTGAGGTTTGCCAAATCGAA
1 CCAAAATGATTATAGTTAGGCCATAAACAA-TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAA
*** * *
16655 GACGATTCAAAACATCAGTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGTTA
65 GACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTA
* *
16720 AAAACTTGACAGTGGACTAATCACA
130 AAAACTTCACAGTGGACTAATCTCA
* * * *
16745 CCAATATGATTATAGTTAGTCCATAAACAATGAAAAGAAAAGCATT-AGGGTTTGCCGAATCGAA
1 CCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA-GGTTTGCCAAATCGAA
** * * *
16809 GACGATTCAAAACGTCACTAATGGGCCTCGATAGG-CCAAATTAACAAGTGTTCCAAATGAG-TT
65 GACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTA
16872 AAAACTTCACAGTGGACTAATCTCA
130 AAAACTTCACAGTGGACTAATCTCA
*
16897 CCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAG
1 CCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAG
* * ** * *
16962 ACGATTCAATATGTCACAAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAACGAGCTAA
66 ACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAA
*
17027 AAACTTCACAGTGTACTAATCTCA
131 AAACTTCACAGTGGACTAATCTCA
* *
17051 CCAAAATGATTATAGTTAGGCCATAAACACTGGAAAGAAAGGCATTGAGGTTTGCCAAATCGAAG
1 CCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAG
17116 ACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAA
66 ACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAA
* *
17181 AAACTTCACAGTAGACTAGTCTCA
131 AAACTTCACAGTGGACTAATCTCA
* * *
17205 CTAAAATGATTATAGTTAGGCCATAAACAATGGAATGAAAAGCTTTGAGGTTTGCCAAATCGAAG
1 CCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAG
*
17270 ACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCGAATGAGCTAA
66 ACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAA
17335 AAACTTCACAGTGGACTAATCTCA
131 AAACTTCACAGTGGACTAATCTCA
* *
17359 CCAAAATGATTATAGTTTGGCCATAAACAATGGAAAGAAAAGAATTGAGGTTTGCCAAATCGAAG
1 CCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAG
* * *
17424 ATGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAGCAAGCGTTCCAAATGAGCTAA
66 ACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAA
* *
17489 AAAGTTCACAGTGGACTAATGTCA
131 AAACTTCACAGTGGACTAATCTCA
*
17513 CCGAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAG
1 CCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAG
*
17578 ACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGCTCCAAATGAGCTAA
66 ACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAA
*
17643 AAAGTTCACAGTGGACTAATCTCA
131 AAACTTCACAGTGGACTAATCTCA
* *
17667 CCAAAATGATTATAGTTTGGCCATAAACAATGGAAAGAAAAGCATTGAGGTCTGCCAAATCGAAG
1 CCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAG
17732 ACGATTCA
66 ACGATTCA
17740 CCAAAATGAT
Statistics
Matches: 1482, Mismatches: 122, Indels: 14
0.92 0.08 0.01
Matches are distributed among these distances:
152 114 0.08
153 52 0.04
154 1312 0.89
155 4 0.00
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.21
Consensus pattern (154 bp):
CCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAG
ACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAA
AAACTTCACAGTGGACTAATCTCA
Found at i:17783 original size:73 final size:73
Alignment explanation
Indices: 17664--17800 Score: 247
Period size: 73 Copynumber: 1.9 Consensus size: 73
17654 TGGACTAATC
*
17664 TCACCAAAATGATTATAGTTTGGCCATAAACAATGGAAAGAAAAGCATTGAGGTCTGCCAAATCG
1 TCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTCTGCCAAATCG
17729 AAGACGAT
66 AAGACGAT
* *
17737 TCACCAAAATGATTATAGTTAGGCCATAAAGAATGGAAAGAAAAGCATTGAGGTTTGCCAAATC
1 TCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTCTGCCAAATC
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
73 61 1.00
ACGTcount: A:0.42, C:0.15, G:0.20, T:0.23
Consensus pattern (73 bp):
TCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTCTGCCAAATCG
AAGACGAT
Done.