Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007574.1 Corchorus capsularis cultivar CVL-1 contig07595, 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: 7926
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:2394 original size:17 final size:17
Alignment explanation
Indices: 2365--2432 Score: 93
Period size: 17 Copynumber: 4.1 Consensus size: 17
2355 TCCTCCTCAT
* *
2365 GGTACCAGGTAGCATAA
1 GGTACTAGGTAGCATGA
*
2382 GGTACTAGATAGCATGA
1 GGTACTAGGTAGCATGA
*
2399 GGTACCAGGTAGCATGA
1 GGTACTAGGTAGCATGA
2416 -GTACTAGGTAGCATGA
1 GGTACTAGGTAGCATGA
2432 G
1 G
2433 CTGCAGTCTC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
16 15 0.34
17 29 0.66
ACGTcount: A:0.32, C:0.15, G:0.32, T:0.21
Consensus pattern (17 bp):
GGTACTAGGTAGCATGA
Found at i:2428 original size:33 final size:34
Alignment explanation
Indices: 2365--2432 Score: 111
Period size: 33 Copynumber: 2.0 Consensus size: 34
2355 TCCTCCTCAT
2365 GGTACCAGGTAGCATAAGGTACTAGATAGCATGA
1 GGTACCAGGTAGCATAAGGTACTAGATAGCATGA
* *
2399 GGTACCAGGTAGCATGA-GTACTAGGTAGCATGA
1 GGTACCAGGTAGCATAAGGTACTAGATAGCATGA
2432 G
1 G
2433 CTGCAGTCTC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 16 0.50
34 16 0.50
ACGTcount: A:0.32, C:0.15, G:0.32, T:0.21
Consensus pattern (34 bp):
GGTACCAGGTAGCATAAGGTACTAGATAGCATGA
Found at i:3107 original size:156 final size:154
Alignment explanation
Indices: 2750--3278 Score: 577
Period size: 156 Copynumber: 3.4 Consensus size: 154
2740 GGTGAACCTA
* *
2750 GGTTTCACATCCCAAACTGTCCTTAAATGAAAAACTTGCATAAGTTTTTCA-CCTTAAGTCTGAT
1 GGTTTCACACCCCAAACTGTCCTTAAATGAAAAACTTGCATAAGTTTTTCATCC-TAAGTC-CAT
* * *
2814 TG-AGATGAAACTTTGCCA-AGGGACTTAGATTCTTTCCA-CAAGACTATGG-AAAAATTCTAAG
64 TGAAGATGAAACTTCGCCAGA-GG-CTTAGATT-ATTCCATAAAG-CTATGGAAAAAATTCTAAG
* * * *
2875 TAAAACCGAGCTCCCCTTG-ATGGTGAACTT
125 TAAAACCGAACT-CCCTAGCATAGTGAAGTT
* * * * *** * *
2905 CGTTTCTCTCCCTAGGTTGTCCTTAAATGAAAAACTTGCATAAGTTTTTCATTCTAAGTCCAATG
1 GGTTTCACACCCCAAACTGTCCTTAAATGAAAAACTTGCATAAGTTTTTCATCCTAAGTCCATTG
* * * * *
2970 AAGCTAAAACTCCACCAGTAGGCTTATATTATCTCCATAAAGCTATGGAAAAAATTCTAAGTAAA
66 AAGATGAAACTTCGCCAG-AGGCTTAGATTAT-TCCATAAAGCTATGGAAAAAATTCTAAGTAAA
* *
3035 ACCGAACTCTCTAGCATAGAGAAGTT
129 ACCGAACTCCCTAGCATAGTGAAGTT
*
3061 GGTTTCACACCCCAAACTGTCCTTAAATGAAAAACTTGCATAAGTTTTTCATACTAAGT-CATTG
1 GGTTTCACACCCCAAACTGTCCTTAAATGAAAAACTTGCATAAGTTTTTCATCCTAAGTCCATTG
* * * *
3125 AGAGATGAAACTTGGCCACGAGACTTAGAATATTCCCATAAGGCTATGGAAAAAAATTCTAAGTA
66 A-AGATGAAACTTCGCCA-GAGGCTTAGATTATT-CCATAAAGCTATGG-AAAAAATTCTAAGTA
* *
3190 AAATCGAACTCCCTATCATAGTGAAGTT
127 AAACCGAACTCCCTAGCATAGTGAAGTT
* *
3218 GGTTTCACACCCCTAAACTATCCTTAACTGAAAAACTTGCATAAGTTTTTCATCCTAAGTC
1 GGTTTCACACCCC-AAACTGTCCTTAAATGAAAAACTTGCATAAGTTTTTCATCCTAAGTC
3279 TGTTTGAGAT
Statistics
Matches: 310, Mismatches: 50, Indels: 24
0.81 0.13 0.06
Matches are distributed among these distances:
154 4 0.01
155 87 0.28
156 122 0.39
157 54 0.17
158 43 0.14
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (154 bp):
GGTTTCACACCCCAAACTGTCCTTAAATGAAAAACTTGCATAAGTTTTTCATCCTAAGTCCATTG
AAGATGAAACTTCGCCAGAGGCTTAGATTATTCCATAAAGCTATGGAAAAAATTCTAAGTAAAAC
CGAACTCCCTAGCATAGTGAAGTT
Found at i:4115 original size:21 final size:21
Alignment explanation
Indices: 4091--4135 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
4081 CTTTCTATGG
*
4091 TTTGGGTAATATCCGTAAAAC
1 TTTGGCTAATATCCGTAAAAC
*
4112 TTT-GCTATTATCCGTAAAAC
1 TTTGGCTAATATCCGTAAAAC
4132 TTTG
1 TTTG
4136 CTATTCCCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.40
Consensus pattern (21 bp):
TTTGGCTAATATCCGTAAAAC
Found at i:4125 original size:20 final size:20
Alignment explanation
Indices: 4100--4140 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
4090 GTTTGGGTAA
4100 TATCCGTAAAACTTTGCTAT
1 TATCCGTAAAACTTTGCTAT
4120 TATCCGTAAAACTTTGCTAT
1 TATCCGTAAAACTTTGCTAT
4140 T
1 T
4141 CCCTCGTGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.20, G:0.10, T:0.41
Consensus pattern (20 bp):
TATCCGTAAAACTTTGCTAT
Found at i:7891 original size:1 final size:1
Alignment explanation
Indices: 7885--7915 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
7875 CTAAATATTT
7885 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
7916 CCATATTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Done.