Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010524.1 Corchorus capsularis cultivar CVL-1 contig10545, 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: 37246
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:184 original size:22 final size:20
Alignment explanation
Indices: 142--183 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
132 TTACACACAT
142 ATATATATTACATATTAATA
1 ATATATATTACATATTAATA
*
162 ATATATATTATATATTAA-A
1 ATATATATTACATATTAATA
181 ATA
1 ATA
184 AAATTTTTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
ATATATATTACATATTAATA
Found at i:270 original size:17 final size:18
Alignment explanation
Indices: 234--271 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
224 ATATATATAT
*
234 ATATTCTTATTTAATAAA
1 ATATTCTTACTTAATAAA
*
252 ATATT-TTACTTATTAAA
1 ATATTCTTACTTAATAAA
269 ATA
1 ATA
272 AAATAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (18 bp):
ATATTCTTACTTAATAAA
Found at i:467 original size:18 final size:18
Alignment explanation
Indices: 444--478 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
434 CCGACTTCAC
*
444 AAACCGAATCACCCGACA
1 AAACCGAATCAACCGACA
*
462 AAACCGACTCAACCGAC
1 AAACCGAATCAACCGAC
479 CCATTTCACC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.40, G:0.11, T:0.06
Consensus pattern (18 bp):
AAACCGAATCAACCGACA
Found at i:22131 original size:21 final size:21
Alignment explanation
Indices: 22105--22151 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
22095 GAGCCACTGC
* * *
22105 TGTTGCTGTTGCTGCTGCTGT
1 TGTTGCTGGTGATGATGCTGT
22126 TGTTGCTGGTGATGATGCTGT
1 TGTTGCTGGTGATGATGCTGT
22147 TGTTG
1 TGTTG
22152 TTGCTGGTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.04, C:0.13, G:0.36, T:0.47
Consensus pattern (21 bp):
TGTTGCTGGTGATGATGCTGT
Found at i:22168 original size:24 final size:25
Alignment explanation
Indices: 22116--22175 Score: 79
Period size: 24 Copynumber: 2.4 Consensus size: 25
22106 GTTGCTGTTG
* *
22116 CTGCTGCTGTTGTTGCTGGTGATGA
1 CTGCTGTTGTTGTTGCTGGTGATAA
22141 -TGCTGTTGTTGTTGCTGGTGA-AA
1 CTGCTGTTGTTGTTGCTGGTGATAA
22164 CTGCTGGTTGTT
1 CTGCT-GTTGTT
22176 CTGCATCATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 1 0.03
24 24 0.77
25 6 0.19
ACGTcount: A:0.08, C:0.13, G:0.35, T:0.43
Consensus pattern (25 bp):
CTGCTGTTGTTGTTGCTGGTGATAA
Found at i:27849 original size:21 final size:21
Alignment explanation
Indices: 27825--27869 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
27815 AAAAACTAGA
27825 TTGCTAAATACCGCCCCATTT
1 TTGCTAAATACCGCCCCATTT
** * *
27846 TTGCTATTTATCGTCCCATTT
1 TTGCTAAATACCGCCCCATTT
27867 TTG
1 TTG
27870 ACGTTTTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.18, C:0.27, G:0.11, T:0.44
Consensus pattern (21 bp):
TTGCTAAATACCGCCCCATTT
Found at i:28276 original size:32 final size:32
Alignment explanation
Indices: 28203--28277 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 32
28193 CCGCCCCACC
* * *
28203 AGGGCGCCCTGCCGTGGCAAAGCCACCCCATG
1 AGGGCGGCCTGTCTTGGCAAAGCCACCCCATG
*
28235 AGGGCGGCCTGTCTTGGCAAAGCCGCCCCAGTG
1 AGGGCGGCCTGTCTTGGCAAAGCCACCCCA-TG
*
28268 -GGGTGGCCTG
1 AGGGCGGCCTG
28278 CCCATGGTGA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 35 0.95
33 2 0.05
ACGTcount: A:0.15, C:0.35, G:0.37, T:0.13
Consensus pattern (32 bp):
AGGGCGGCCTGTCTTGGCAAAGCCACCCCATG
Found at i:28421 original size:21 final size:21
Alignment explanation
Indices: 28397--28437 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
28387 AAAAATGGGG
* *
28397 CGGTATTTAGCAAAACTAGGA
1 CGGTACTTAACAAAACTAGGA
28418 CGGTACTTAACAAAACTAGG
1 CGGTACTTAACAAAACTAGG
28438 GCGTTAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (21 bp):
CGGTACTTAACAAAACTAGGA
Done.