Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016315.1 Corchorus capsularis cultivar CVL-1 contig16336, 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: 6078
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:463 original size:6 final size:6
Alignment explanation
Indices: 452--478 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
442 AAAGCAAAGC
452 AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAA
479 GCAGAATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Found at i:1432 original size:10 final size:10
Alignment explanation
Indices: 1417--1442 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1407 GAGGACTCTA
1417 GAATTTTCTG
1 GAATTTTCTG
1427 GAATTTTCTG
1 GAATTTTCTG
1437 GAATTT
1 GAATTT
1443 GTCAGCAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.19, T:0.50
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:2194 original size:33 final size:33
Alignment explanation
Indices: 2106--2194 Score: 106
Period size: 33 Copynumber: 2.7 Consensus size: 33
2096 GTGTTTTAGA
* * *
2106 TGTTGTTTGCCATGATACTAAACCTAATTTGAG
1 TGTTGTTTGCAATGATACTAAATCTAATTTAAG
* **
2139 TGTTGTTTGCAATGACACTAAATCTGCTTTAAG
1 TGTTGTTTGCAATGATACTAAATCTAATTTAAG
**
2172 TGTTGTTTGTGATGATACTAAAT
1 TGTTGTTTGCAATGATACTAAAT
2195 TTGTTTTGGA
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.42
Consensus pattern (33 bp):
TGTTGTTTGCAATGATACTAAATCTAATTTAAG
Found at i:2298 original size:33 final size:32
Alignment explanation
Indices: 2228--2306 Score: 113
Period size: 32 Copynumber: 2.4 Consensus size: 32
2218 GAAAACAAAT
* *
2228 CTGTTTTGGTTGAACATAGCATTAAAATAATT
1 CTGTTTTGGTTGATCATAGCATTAAAATAATC
* *
2260 TTGTTTTGGTTGATCATAGCATTGCAAATAATC
1 CTGTTTTGGTTGATCATAGCATT-AAAATAATC
2293 CTGTTTTGGTTGAT
1 CTGTTTTGGTTGAT
2307 GACATTGAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
32 21 0.51
33 20 0.49
ACGTcount: A:0.27, C:0.10, G:0.19, T:0.44
Consensus pattern (32 bp):
CTGTTTTGGTTGATCATAGCATTAAAATAATC
Found at i:2319 original size:30 final size:32
Alignment explanation
Indices: 2228--2320 Score: 93
Period size: 33 Copynumber: 2.9 Consensus size: 32
2218 GAAAACAAAT
* * *
2228 CTGTTTTGGTTGAACATAGCATT-AAAATAATT
1 CTGTTTTGGTTG-ATAGAGCATTGAAAATAATC
* * *
2260 TTGTTTTGGTTGATCATAGCATTGCAAATAATC
1 CTGTTTTGGTTGAT-AGAGCATTGAAAATAATC
2293 CTGTTTTGGTTGAT-GA-CATTGAAAATAA
1 CTGTTTTGGTTGATAGAGCATTGAAAATAA
2321 ATTTGTTTTG
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
30 11 0.21
31 2 0.04
32 19 0.37
33 20 0.38
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41
Consensus pattern (32 bp):
CTGTTTTGGTTGATAGAGCATTGAAAATAATC
Found at i:2328 original size:30 final size:32
Alignment explanation
Indices: 2217--2331 Score: 103
Period size: 32 Copynumber: 3.6 Consensus size: 32
2207 CTAATTGTGA
* * * *
2217 TGAAAACAAATCTGTTTTGGTTGAACATAGCAT
1 TGAAAATAAATTTGTTTTGGTTG-ATAGAGCAT
* *
2250 T-AAAATAATTTTGTTTTGGTTGATCATAGCAT
1 TGAAAATAAATTTGTTTTGGTTGAT-AGAGCAT
* *
2282 TGCAAAT-AATCCTGTTTTGGTTGAT-GA-CAT
1 TGAAAATAAAT-TTGTTTTGGTTGATAGAGCAT
2312 TGAAAATAAATTTGTTTTGG
1 TGAAAATAAATTTGTTTTGG
2332 GTGAAAAGAA
Statistics
Matches: 68, Mismatches: 10, Indels: 11
0.76 0.11 0.12
Matches are distributed among these distances:
30 17 0.25
31 5 0.07
32 28 0.41
33 18 0.26
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.41
Consensus pattern (32 bp):
TGAAAATAAATTTGTTTTGGTTGATAGAGCAT
Found at i:4150 original size:12 final size:13
Alignment explanation
Indices: 4128--4191 Score: 52
Period size: 12 Copynumber: 5.5 Consensus size: 13
4118 CGCGCAACAC
*
4128 CGGCTACATGACT
1 CGGCCACATGACT
4141 -GGCCACATGACT
1 CGGCCACATGACT
*
4153 CGG-C-CATG-CC
1 CGGCCACATGACT
*
4163 CGGCTACA--AC-
1 CGGCCACATGACT
4173 CGGCCACATGACT
1 CGGCCACATGACT
4186 CGGCCA
1 CGGCCA
4192 TGCCCGGCCA
Statistics
Matches: 40, Mismatches: 4, Indels: 14
0.69 0.07 0.24
Matches are distributed among these distances:
10 11 0.28
11 5 0.12
12 16 0.40
13 8 0.20
ACGTcount: A:0.22, C:0.39, G:0.25, T:0.14
Consensus pattern (13 bp):
CGGCCACATGACT
Done.