Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011440.1 Corchorus olitorius cultivar O-4 contig11473, 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: 30967
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:128 original size:3 final size:3
Alignment explanation
Indices: 120--166 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
110 GTTACTAACC
120 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
167 TTAAAAGAGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5223 original size:27 final size:27
Alignment explanation
Indices: 5182--5290 Score: 193
Period size: 27 Copynumber: 4.1 Consensus size: 27
5172 ACCTAGAGCA
5182 TGCA-AAATGACCAAAATGCCCCTGAG
1 TGCATAAATGACCAAAATGCCCCTGAG
* *
5208 TGCACACATGACCAAAATGCCCCTGAG
1 TGCATAAATGACCAAAATGCCCCTGAG
5235 TGCATAAATGACCAAAATGCCCCTGAG
1 TGCATAAATGACCAAAATGCCCCTGAG
5262 TGCATAAATGACCAAAATGCCCCTGAG
1 TGCATAAATGACCAAAATGCCCCTGAG
5289 TG
1 TG
5291 TGCAAATGAC
Statistics
Matches: 79, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
26 4 0.05
27 75 0.95
ACGTcount: A:0.36, C:0.28, G:0.19, T:0.17
Consensus pattern (27 bp):
TGCATAAATGACCAAAATGCCCCTGAG
Found at i:5297 original size:27 final size:27
Alignment explanation
Indices: 5182--5303 Score: 192
Period size: 27 Copynumber: 4.6 Consensus size: 27
5172 ACCTAGAGCA
5182 TGCA-AAATGACCAAAATGCCCCTGAG
1 TGCACAAATGACCAAAATGCCCCTGAG
*
5208 TGCACACATGACCAAAATGCCCCTGAG
1 TGCACAAATGACCAAAATGCCCCTGAG
*
5235 TGCATAAATGACCAAAATGCCCCTGAG
1 TGCACAAATGACCAAAATGCCCCTGAG
*
5262 TGCATAAATGACCAAAATGCCCCTGAG
1 TGCACAAATGACCAAAATGCCCCTGAG
**
5289 TGTGCAAATGACCAA
1 TGCACAAATGACCAA
5304 TTAAGAAACA
Statistics
Matches: 89, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
26 4 0.04
27 85 0.96
ACGTcount: A:0.37, C:0.27, G:0.19, T:0.17
Consensus pattern (27 bp):
TGCACAAATGACCAAAATGCCCCTGAG
Found at i:22275 original size:23 final size:23
Alignment explanation
Indices: 22249--22294 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
22239 GCATAAAGAT
22249 CCAAAACCCAAATGGACTAAAAG
1 CCAAAACCCAAATGGACTAAAAG
*
22272 CCAAAACCTAAATGGACTAAAAG
1 CCAAAACCCAAATGGACTAAAAG
22295 GAAGAAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.52, C:0.24, G:0.13, T:0.11
Consensus pattern (23 bp):
CCAAAACCCAAATGGACTAAAAG
Found at i:22636 original size:20 final size:21
Alignment explanation
Indices: 22584--22659 Score: 91
Period size: 21 Copynumber: 3.6 Consensus size: 21
22574 ATATGTCTAC
* * *
22584 ACCCCAAAATTTGACAGTGAA
1 ACCCCAAATTTTGATAGTCAA
*
22605 ACCCCAAAATTTGAT-GATCAA
1 ACCCCAAATTTTGATAG-TCAA
22626 ACCCCAAATTTTGATAGTCAA
1 ACCCCAAATTTTGATAGTCAA
22647 ACCCCAAAGTTTT
1 ACCCCAAA-TTTT
22660 ATATATCAAG
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.02
21 43 0.88
22 5 0.10
ACGTcount: A:0.39, C:0.25, G:0.11, T:0.25
Consensus pattern (21 bp):
ACCCCAAATTTTGATAGTCAA
Found at i:22668 original size:22 final size:20
Alignment explanation
Indices: 22603--22668 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 20
22593 TTTGACAGTG
* *
22603 AAACCCCAAAATTTGATGATC
1 AAACCCC-AAATTTTATAATC
*
22624 AAACCCCAAATTTTGATAGTC
1 AAACCCCAAATTTT-ATAATC
22645 AAACCCCAAAGTTTTATATATC
1 AAACCCCAAA-TTTTATA-ATC
22667 AA
1 AA
22669 GTAAGGAACT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
20 6 0.16
21 24 0.63
22 8 0.21
ACGTcount: A:0.42, C:0.23, G:0.08, T:0.27
Consensus pattern (20 bp):
AAACCCCAAATTTTATAATC
Found at i:29731 original size:14 final size:13
Alignment explanation
Indices: 29712--29750 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
29702 AAATTGTAAA
29712 ATTTAAAAAATTT
1 ATTTAAAAAATTT
* *
29725 CATTTAAGAAATAT
1 -ATTTAAAAAATTT
29739 ATTTAAAAAATT
1 ATTTAAAAAATT
29751 CTAATATATA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (13 bp):
ATTTAAAAAATTT
Found at i:29979 original size:124 final size:127
Alignment explanation
Indices: 29736--29992 Score: 421
Period size: 124 Copynumber: 2.0 Consensus size: 127
29726 ATTTAAGAAA
29736 TATATTTAAAAAATTCTAATATATATAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAA
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTTAATTAAAATAGTAAAATGGT---AATAAA
*
29801 ATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAA
63 AT--GTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAA
29866 AG
126 AG
*
29868 TATATTTAAAAAATTCTAATATATATACGTTTTTTTAATTAAAATAGTAAAATGGT-A-AAAAT-
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTTAATTAAAATAGTAAAATGGTAATAAAATG
*
29930 TATAATGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
66 TATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
29992 T
1 T
29993 TTAAACAATG
Statistics
Matches: 122, Mismatches: 3, Indels: 8
0.92 0.02 0.06
Matches are distributed among these distances:
124 61 0.50
127 5 0.04
128 1 0.01
132 55 0.45
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.39
Consensus pattern (127 bp):
TATATTTAAAAAATTCTAATATATATAAGTTTTTTTAATTAAAATAGTAAAATGGTAATAAAATG
TATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
Done.