Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015918.1 Corchorus olitorius cultivar O-4 contig15951, 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: 30831
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:230 original size:27 final size:27
Alignment explanation
Indices: 190--242 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
180 AAGAATCATC
* *
190 AATCAATTAGAACTTTGATTGGAAAAG
1 AATCAATTACAACTTTAATTGGAAAAG
217 AATCAATTACAACTTTAATTGGAAAA
1 AATCAATTACAACTTTAATTGGAAAA
243 TTTTACTAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.30
Consensus pattern (27 bp):
AATCAATTACAACTTTAATTGGAAAAG
Found at i:424 original size:21 final size:22
Alignment explanation
Indices: 400--450 Score: 68
Period size: 24 Copynumber: 2.3 Consensus size: 22
390 AATGACATGT
*
400 TCAATTTT-TTTTATTACTAAA
1 TCAATTTTCGTTTATTACTAAA
421 TCAATAGTTTCGTTTATTACTAAA
1 TCAAT--TTTCGTTTATTACTAAA
445 TCAATT
1 TCAATT
451 ATATCTTTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 5 0.19
22 1 0.04
23 3 0.12
24 17 0.65
ACGTcount: A:0.33, C:0.12, G:0.04, T:0.51
Consensus pattern (22 bp):
TCAATTTTCGTTTATTACTAAA
Found at i:1478 original size:2 final size:2
Alignment explanation
Indices: 1471--1511 Score: 73
Period size: 2 Copynumber: 20.0 Consensus size: 2
1461 TACAGTTTTA
1471 AT AT AT AT AT AT AT AT AT AT AT CAT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT
1512 GATTCTTAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 36 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3022 original size:106 final size:106
Alignment explanation
Indices: 2837--3051 Score: 403
Period size: 106 Copynumber: 2.0 Consensus size: 106
2827 AAGACACGCT
2837 TCATTCTTCCCTTTTTGTCTCGTTTCTGAATGAGGTTAAGTCAGCCCTGGGTTGTTTGCTGCACC
1 TCATTCTTCCCTTTTTGTCTCGTTTCTGAATGAGGTTAAGTCAGCCCTGGGTTGTTTGCTGCACC
*
2902 AACCACTCCAAAGCTGCAGCACAAAGTCAACAGGCACAAAA
66 AACCACTCCAAAGCTGCAGCACAAAGCCAACAGGCACAAAA
* *
2943 TCATTCTTCCCTTTTTGTCTCGTTTCTGAATGTGGTTAAGTCAGCCCTGGGTTGTTTGTTGCACC
1 TCATTCTTCCCTTTTTGTCTCGTTTCTGAATGAGGTTAAGTCAGCCCTGGGTTGTTTGCTGCACC
3008 AACCACTCCAAAGCTGCAGCACAAAGCCAACAGGCACAAAA
66 AACCACTCCAAAGCTGCAGCACAAAGCCAACAGGCACAAAA
3049 TCA
1 TCA
3052 AGCAGTGAGA
Statistics
Matches: 106, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
106 106 1.00
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (106 bp):
TCATTCTTCCCTTTTTGTCTCGTTTCTGAATGAGGTTAAGTCAGCCCTGGGTTGTTTGCTGCACC
AACCACTCCAAAGCTGCAGCACAAAGCCAACAGGCACAAAA
Found at i:18535 original size:27 final size:27
Alignment explanation
Indices: 18505--18575 Score: 133
Period size: 27 Copynumber: 2.6 Consensus size: 27
18495 GATCAACTAA
*
18505 GGGCATTTTGGTCATTTGCATGTCCAG
1 GGGCATTTTGGTCATTTGCACGTCCAG
18532 GGGCATTTTGGTCATTTGCACGTCCAG
1 GGGCATTTTGGTCATTTGCACGTCCAG
18559 GGGCATTTTGGTCATTT
1 GGGCATTTTGGTCATTT
18576 TAAGTTCACA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.14, C:0.18, G:0.30, T:0.38
Consensus pattern (27 bp):
GGGCATTTTGGTCATTTGCACGTCCAG
Found at i:26859 original size:18 final size:19
Alignment explanation
Indices: 26820--26859 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
26810 GTGCTCCCGT
26820 TGTGATGCACCCACTTTTCAA
1 TGTGATGCACCCA--TTTCAA
26841 TGTGATGCACCCA-TTCAA
1 TGTGATGCACCCATTTCAA
26859 T
1 T
26860 TTTGACCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
21 13 0.68
ACGTcount: A:0.25, C:0.28, G:0.15, T:0.33
Consensus pattern (19 bp):
TGTGATGCACCCATTTCAA
Found at i:27356 original size:21 final size:21
Alignment explanation
Indices: 27317--27356 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
27307 CAGAATTGAA
**
27317 TGGGTGCATCACATTGAAAAG
1 TGGGTGCATCACAACGAAAAG
*
27338 TGGGTGCATTACAACGAAA
1 TGGGTGCATCACAACGAAA
27357 GCACCGAAGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.15, G:0.28, T:0.23
Consensus pattern (21 bp):
TGGGTGCATCACAACGAAAAG
Done.