Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006984.1 Corchorus capsularis cultivar CVL-1 contig07005, 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: 21458
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--29 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
30 TTCTAGTACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10738 original size:30 final size:30
Alignment explanation
Indices: 10680--10738 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
10670 TGTCTTCAAG
*
10680 TCCATAATAAGTCCTTGGTGCATAATTCCT
1 TCCATAATAAGTCCTTGGCGCATAATTCCT
* *
10710 TCCATGATAAG-CCTTGGGCGCATCATTCC
1 TCCATAATAAGTCCTT-GGCGCATAATTCC
10739 CTCCCCCTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 4 0.16
30 21 0.84
ACGTcount: A:0.24, C:0.27, G:0.17, T:0.32
Consensus pattern (30 bp):
TCCATAATAAGTCCTTGGCGCATAATTCCT
Found at i:11147 original size:33 final size:33
Alignment explanation
Indices: 11080--11225 Score: 208
Period size: 33 Copynumber: 4.5 Consensus size: 33
11070 TTCTTTTCAT
* *
11080 CCAAAACAGAATTATTTTCAATGC---CATCAA
1 CCAAAACAGAATTATTTCCAATGCTATGATCAA
*
11110 CCAAAACAGAATTATTTCCAGTGCTATGATCAA
1 CCAAAACAGAATTATTTCCAATGCTATGATCAA
*
11143 CCAAAACAGAATTATTTTCAATGCTATGATCAA
1 CCAAAACAGAATTATTTCCAATGCTATGATCAA
* *
11176 CCAAAACAGAATTATTTGCTATGCTATGATCAA
1 CCAAAACAGAATTATTTCCAATGCTATGATCAA
*
11209 CCAAAACAGATTTATTT
1 CCAAAACAGAATTATTT
11226 TCATCACAAA
Statistics
Matches: 105, Mismatches: 8, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
30 22 0.21
33 83 0.79
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (33 bp):
CCAAAACAGAATTATTTCCAATGCTATGATCAA
Found at i:11252 original size:33 final size:33
Alignment explanation
Indices: 11215--11345 Score: 138
Period size: 33 Copynumber: 4.0 Consensus size: 33
11205 TCAACCAAAA
* *
11215 CAGATTTATTTTCATCACAAACAACACCTAAAT
1 CAGATTTAGTGTCATCACAAACAACACCTAAAT
* * *
11248 CAGATTTAGTGTCATCACAAACATCACTTAAAA
1 CAGATTTAGTGTCATCACAAACAACACCTAAAT
**
11281 CAGATTTAGTGTCATTGCAAACAACA-CTCAAAT
1 CAGATTTAGTGTCATCACAAACAACACCT-AAAT
* * * * *
11314 TAGGTTTAGTATCATCGCAAACAACATCTAAA
1 CAGATTTAGTGTCATCACAAACAACACCTAAA
11346 AGACTCTTTT
Statistics
Matches: 82, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
32 1 0.01
33 79 0.96
34 2 0.02
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.28
Consensus pattern (33 bp):
CAGATTTAGTGTCATCACAAACAACACCTAAAT
Found at i:11281 original size:66 final size:66
Alignment explanation
Indices: 11211--11336 Score: 164
Period size: 66 Copynumber: 1.9 Consensus size: 66
11201 ATGATCAACC
* * *
11211 AAAACAGATTTATTTTCATCACAAACAACAC-CTAAATCAGATTTAGTGTCATCACAAACATCAC
1 AAAACAGATTTAGTGTCATCACAAACAACACTC-AAATCAGATTTAGTATCATCACAAACATCAC
11275 TT
65 TT
** * * *
11277 AAAACAGATTTAGTGTCATTGCAAACAACACTCAAATTAGGTTTAGTATCATCGCAAACA
1 AAAACAGATTTAGTGTCATCACAAACAACACTCAAATCAGATTTAGTATCATCACAAACA
11337 ACATCTAAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
66 50 0.98
67 1 0.02
ACGTcount: A:0.42, C:0.21, G:0.10, T:0.28
Consensus pattern (66 bp):
AAAACAGATTTAGTGTCATCACAAACAACACTCAAATCAGATTTAGTATCATCACAAACATCACT
T
Found at i:12854 original size:8 final size:8
Alignment explanation
Indices: 12826--12859 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
12816 GAATCATCTA
12826 TGAATTTT
1 TGAATTTT
*
12834 TGAAGTTTC
1 TGAA-TTTT
12843 TGAATTTT
1 TGAATTTT
12851 TGAATTTT
1 TGAATTTT
12859 T
1 T
12860 CAAGAAGGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59
Consensus pattern (8 bp):
TGAATTTT
Found at i:18210 original size:33 final size:32
Alignment explanation
Indices: 18140--18257 Score: 121
Period size: 33 Copynumber: 3.5 Consensus size: 32
18130 AAAGGATCAT
* * **
18140 GTGGCCGGTTGTGGACGGGCATGGCCGAGTCAT
1 GTGGCCGGTTGTGGCCGGGCATGTCC-AGTCGC
18173 GTGGCCGGTTGTGGCCGGGCATGTCCATGTCGC
1 GTGGCCGGTTGTGGCCGGGCATGTCCA-GTCGC
* *
18206 GTGGCCGG-TGATGTCCGGGCATCTCCAAGTCGC
1 GTGGCCGGTTG-TGGCCGGGCATGTCC-AGTCGC
18239 GTGGCCGGTCTTGTGGCCG
1 GTGGCCGG--TTGTGGCCG
18258 ATGTTGCGCG
Statistics
Matches: 72, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
32 3 0.04
33 61 0.85
34 1 0.01
35 5 0.07
36 2 0.03
ACGTcount: A:0.08, C:0.26, G:0.42, T:0.23
Consensus pattern (32 bp):
GTGGCCGGTTGTGGCCGGGCATGTCCAGTCGC
Done.