Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014562.1 Corchorus olitorius cultivar O-4 contig14595, 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: 2134
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Found at i:248 original size:56 final size:54
Alignment explanation
Indices: 80--256 Score: 150
Period size: 56 Copynumber: 3.2 Consensus size: 54
70 AAGAATGATG
* * **
80 GTCAAACCCTAAACTTCAATAGTCAAACCACAAAAAGCATTTCATTGTATAGGCATG
1 GTCAAACCC-AAAATTCAATAGTCAAACCACAAAAA--ATTTCATTGTATATGCACA
* * * * * *
137 GTCAAACCCAATATTTAATAGTC--CCCCCAAAACA--TCATTGCATAT--ACA
1 GTCAAACCCAAAATTCAATAGTCAAACCACAAAAAATTTCATTGTATATGCACA
185 TGATCAAACCTCAAAATTCAATAGTCAAACCACAAAAAATTTTCATTGTATATGCACA
1 -G-TCAAACC-CAAAATTCAATAGTCAAACCACAAAAAA-TTTCATTGTATATGCACA
243 GTCAAACCCCAAAA
1 GTCAAA-CCCAAAA
257 AACATCATTG
Statistics
Matches: 93, Mismatches: 16, Indels: 23
0.70 0.12 0.17
Matches are distributed among these distances:
48 1 0.01
49 1 0.01
50 16 0.17
51 13 0.14
52 1 0.01
53 8 0.09
54 7 0.08
56 31 0.33
57 12 0.13
58 3 0.03
ACGTcount: A:0.42, C:0.25, G:0.08, T:0.24
Consensus pattern (54 bp):
GTCAAACCCAAAATTCAATAGTCAAACCACAAAAAATTTCATTGTATATGCACA
Found at i:411 original size:54 final size:54
Alignment explanation
Indices: 242--411 Score: 173
Period size: 58 Copynumber: 3.1 Consensus size: 54
232 GTATATGCAC
* * *
242 AGTCAAACCCCAAAAAACATCATTGTGCGTGGATGGTCAAACCCC-AAAGTTCGAT
1 AGTCAAACCCC-AAAAACATCATTGTACATGCATGGTCAAACCCCAAAAGTT-GAT
* * * ** *
297 AGTCAAACCACAAAAAAACATTTCATAGTATATGCATGGTCAAACCCCAAATTTTAAT
1 AGTCAAACC-C-CAAAAACA--TCATTGTACATGCATGGTCAAACCCCAAAAGTTGAT
*
355 AGTCAAACCCCAAAAACATCATTGTACATGCATGG-CTAAACCCCAAAAGATGAT
1 AGTCAAACCCCAAAAACATCATTGTACATGCATGGTC-AAACCCCAAAAGTTGAT
409 AGT
1 AGT
412 TAAATCACAA
Statistics
Matches: 93, Mismatches: 16, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
53 1 0.01
54 31 0.33
55 9 0.10
56 15 0.16
57 1 0.01
58 32 0.34
59 4 0.04
ACGTcount: A:0.41, C:0.24, G:0.14, T:0.22
Consensus pattern (54 bp):
AGTCAAACCCCAAAAACATCATTGTACATGCATGGTCAAACCCCAAAAGTTGAT
Found at i:423 original size:54 final size:54
Alignment explanation
Indices: 242--423 Score: 170
Period size: 54 Copynumber: 3.3 Consensus size: 54
232 GTATATGCAC
* * * *
242 AGTCAAACCCCAAAAAACATCATTGTGCGTGGATGGTCAAACCCC-AAAGTTCGAT
1 AGTCAAACCAC-AAAAACATCATTGTACATGCATGGTCAAACCCCAAAAGTT-GAT
* * ** *
297 AGTCAAACCACAAAAAAACATTTCATAGTATATGCATGGTCAAACCCCAAATTTTAAT
1 AGTCAAACCAC--AAAAACA--TCATTGTACATGCATGGTCAAACCCCAAAAGTTGAT
* *
355 AGTCAAACCCCAAAAACATCATTGTACATGCATGG-CTAAACCCCAAAAGATGAT
1 AGTCAAACCACAAAAACATCATTGTACATGCATGGTC-AAACCCCAAAAGTTGAT
* *
409 AGTTAAATCACAAAA
1 AGTCAAACCACAAAA
424 CTCGATAGTC
Statistics
Matches: 103, Mismatches: 19, Indels: 11
0.77 0.14 0.08
Matches are distributed among these distances:
53 1 0.01
54 40 0.39
55 10 0.10
56 15 0.15
58 33 0.32
59 4 0.04
ACGTcount: A:0.43, C:0.23, G:0.13, T:0.21
Consensus pattern (54 bp):
AGTCAAACCACAAAAACATCATTGTACATGCATGGTCAAACCCCAAAAGTTGAT
Found at i:540 original size:133 final size:131
Alignment explanation
Indices: 292--629 Score: 358
Period size: 133 Copynumber: 2.5 Consensus size: 131
282 ACCCCAAAGT
*
292 TCGATAGTCAAACCACAAAAAAACATTTCATAGTATATGCATGGTCAAACCCCAAATTTTAATAG
1 TCGATAGTCAAACCAC-AAAAAACATTTCATAGTATATGCATGATCAAACCCCAAATTTTAATAG
* * *
357 TCAAACCCCAAAAACATCATTGTACATGCATGGCTAAACCCCAAAAGATGATAGTTAAA-TCACA
65 TCAAACCCAAAAAACATCATTATACATACATGGCTAAACCCCAAAAGATGATAGTTAAACTC-C-
421 AAAC
128 AAAC
* ** *
425 TCGATAGTCAAACCACATAAAGTATTTCATTA-TATATGCATGATTAAACCCCAAATTTTAATAG
1 TCGATAGTCAAACCACAAAAAACATTTCA-TAGTATATGCATGATCAAACCCCAAATTTTAATAG
* * * ** * *
489 TCGAATCTCAAAAAACATCATTATACATACAT-GATCAAATTCCAAAGGATGATGGTTAAACTCC
65 TC-AAACCCAAAAAACATCATTATACATACATGGCT-AAACCCCAAAAGATGATAGTTAAACTCC
*
553 AAAG
128 AAAC
* * * * * * ** *
557 TCCGATTGTCAAACCACACAAAACATTTAATTGCATATGCATGGTCAAACAACAAATTTTGATAG
1 T-CGATAGTCAAACCACAAAAAACATTTCATAGTATATGCATGATCAAACCCCAAATTTTAATAG
*
622 TTAAACCC
65 TCAAACCC
630 TAAAGTTTGA
Statistics
Matches: 168, Mismatches: 31, Indels: 13
0.79 0.15 0.06
Matches are distributed among these distances:
132 53 0.32
133 113 0.67
134 2 0.01
ACGTcount: A:0.43, C:0.21, G:0.11, T:0.26
Consensus pattern (131 bp):
TCGATAGTCAAACCACAAAAAACATTTCATAGTATATGCATGATCAAACCCCAAATTTTAATAGT
CAAACCCAAAAAACATCATTATACATACATGGCTAAACCCCAAAAGATGATAGTTAAACTCCAAA
C
Found at i:1297 original size:13 final size:13
Alignment explanation
Indices: 1279--1304 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1269 TTGCACACCC
1279 TTATATATTAGAG
1 TTATATATTAGAG
1292 TTATATATTAGAG
1 TTATATATTAGAG
1305 ATATGAGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (13 bp):
TTATATATTAGAG
Found at i:1830 original size:16 final size:16
Alignment explanation
Indices: 1805--1838 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1795 ATCTTGATTT
*
1805 TTCAGGGCTTTTCTGC
1 TTCAGAGCTTTTCTGC
*
1821 TTCAGAGCTTTTTTGC
1 TTCAGAGCTTTTCTGC
1837 TT
1 TT
1839 TGTAGAGCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.09, C:0.21, G:0.21, T:0.50
Consensus pattern (16 bp):
TTCAGAGCTTTTCTGC
Done.