Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020276.1 Corchorus olitorius cultivar O-4 contig20309, 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: 13576
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:350 original size:36 final size:36
Alignment explanation
Indices: 303--372 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
293 GAGATTTTGG
* *
303 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA
*
339 AGAAATATGATAACCAAAATCACAAAAGATGTAA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAA
373 GGTTATTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATCACAAAAAATGTAATA
Found at i:1733 original size:57 final size:57
Alignment explanation
Indices: 1635--1744 Score: 177
Period size: 57 Copynumber: 1.9 Consensus size: 57
1625 GCATCATGCA
*
1635 TCGGTCCTAAAACGTCTTTTTTTAGGCATCTAATAAAAACATGTCACTCGATAAGTC
1 TCGGTCCGAAAACGTCTTTTTTTAGGCATCTAATAAAAACATGTCACTCGATAAGTC
* *
1692 TCGGTCCGAAAACGTC-TTTTTTATGCATCTAATAAAGAACATGTCACTTGATA
1 TCGGTCCGAAAACGTCTTTTTTTAGGCATCTAATAAA-AACATGTCACTCGATA
1745 TTTGATTAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
56 19 0.39
57 30 0.61
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.34
Consensus pattern (57 bp):
TCGGTCCGAAAACGTCTTTTTTTAGGCATCTAATAAAAACATGTCACTCGATAAGTC
Found at i:8319 original size:25 final size:26
Alignment explanation
Indices: 8276--8325 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 26
8266 GGTACTGTAC
8276 AAATTGAATATTTCTAAATAAAATAA
1 AAATTGAATATTTCTAAATAAAATAA
8302 AAATTGAAT-TTTCTAAATAAAATA
1 AAATTGAATATTTCTAAATAAAATA
8326 TTTTAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 15 0.62
26 9 0.38
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.36
Consensus pattern (26 bp):
AAATTGAATATTTCTAAATAAAATAA
Found at i:8501 original size:25 final size:27
Alignment explanation
Indices: 8450--8515 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
8440 AAAAGTACAC
*
8450 AAAATTATATTTTAATAGTGGCATAA-TT
1 AAAA-TATATTTTAATAATGG-ATAATTT
*
8478 AAAATATTTTTTAATAATGG-TAATTT
1 AAAATATATTTTAATAATGGATAATTT
8504 AGAAATATATTT
1 A-AAATATATTT
8516 GAAAAAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
25 3 0.09
26 3 0.09
27 23 0.70
28 4 0.12
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.45
Consensus pattern (27 bp):
AAAATATATTTTAATAATGGATAATTT
Found at i:10171 original size:9 final size:10
Alignment explanation
Indices: 10157--10195 Score: 55
Period size: 9 Copynumber: 4.0 Consensus size: 10
10147 TGATGAGATG
10157 AATAATAA-T
1 AATAATAATT
10166 AATAATAATT
1 AATAATAATT
10176 AATAA-AATT
1 AATAATAATT
10185 AATAATTAATT
1 AATAA-TAATT
10196 TTTTTGGCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 17 0.63
10 6 0.22
11 4 0.15
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
AATAATAATT
Found at i:10178 original size:16 final size:16
Alignment explanation
Indices: 10159--10194 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
10149 ATGAGATGAA
10159 TAATAATAA-TAATAAT
1 TAATAA-AATTAATAAT
10175 TAATAAAATTAATAAT
1 TAATAAAATTAATAAT
10191 TAAT
1 TAAT
10195 TTTTTTGGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 2 0.11
16 17 0.89
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAATAAAATTAATAAT
Done.