Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004905.1 Corchorus capsularis cultivar CVL-1 contig04923, 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: 23376
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Found at i:726 original size:16 final size:16
Alignment explanation
Indices: 694--769 Score: 55
Period size: 16 Copynumber: 4.8 Consensus size: 16
684 GTCGGGTTGA
* *
694 TCGGGTTCTGGTCATT
1 TCGGGTTCGGGTAATT
* *
710 TTGGGTTTGGGTAATT
1 TCGGGTTCGGGTAATT
**
726 TCGGGTTCGGGTTGTT
1 TCGGGTTCGGGTAATT
* * *
742 T-GGATTTGGGTCATT
1 TCGGGTTCGGGTAATT
*
757 TCAGGTTCGGGTA
1 TCGGGTTCGGGTA
770 CCCAAAAAAT
Statistics
Matches: 43, Mismatches: 16, Indels: 2
0.70 0.26 0.03
Matches are distributed among these distances:
15 11 0.26
16 32 0.74
ACGTcount: A:0.09, C:0.11, G:0.37, T:0.43
Consensus pattern (16 bp):
TCGGGTTCGGGTAATT
Found at i:750 original size:31 final size:31
Alignment explanation
Indices: 709--768 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
699 TTCTGGTCAT
* *
709 TTTGGGTTTGGGTAATTTCGGGTTCGGGTTG
1 TTTGGATTTGGGTAATTTCAGGTTCGGGTTG
*
740 TTTGGATTTGGGTCATTTCAGGTTCGGGT
1 TTTGGATTTGGGTAATTTCAGGTTCGGGT
769 ACCCAAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.08, C:0.08, G:0.38, T:0.45
Consensus pattern (31 bp):
TTTGGATTTGGGTAATTTCAGGTTCGGGTTG
Found at i:1061 original size:12 final size:12
Alignment explanation
Indices: 1029--1067 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
1019 ATGGAATTAA
1029 ATATCCGTCG--
1 ATATCCGTCGAT
1039 ATA-CC-TCGAT
1 ATATCCGTCGAT
1049 ATATCCGTCGAT
1 ATATCCGTCGAT
1061 ATATCCG
1 ATATCCG
1068 ATATCTGTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
8 3 0.12
9 2 0.08
10 6 0.24
11 2 0.08
12 12 0.48
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.31
Consensus pattern (12 bp):
ATATCCGTCGAT
Found at i:3047 original size:12 final size:12
Alignment explanation
Indices: 3030--3084 Score: 92
Period size: 12 Copynumber: 4.5 Consensus size: 12
3020 CATCGATACC
*
3030 TCGATATATCCA
1 TCGATATATCCG
3042 TCGATATATCCG
1 TCGATATATCCG
3054 TCGATATATCCG
1 TCGATATATCCG
3066 TTCGATATATCCG
1 -TCGATATATCCG
3079 TCGATA
1 TCGATA
3085 CCTGTATTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
12 29 0.71
13 12 0.29
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.35
Consensus pattern (12 bp):
TCGATATATCCG
Found at i:3076 original size:25 final size:24
Alignment explanation
Indices: 3030--3084 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 24
3020 CATCGATACC
3030 TCGATATATCCATCGATATATCCG
1 TCGATATATCCATCGATATATCCG
*
3054 TCGATATATCCGTTCGATATATCCG
1 TCGATATATCC-ATCGATATATCCG
3079 TCGATA
1 TCGATA
3085 CCTGTATTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 11 0.38
25 18 0.62
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.35
Consensus pattern (24 bp):
TCGATATATCCATCGATATATCCG
Found at i:3880 original size:18 final size:18
Alignment explanation
Indices: 3854--3898 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
3844 GCTGCATCGC
* **
3854 CTTCTTCATCAGCTTTGT
1 CTTCATCATCAGCTTCAT
*
3872 CTTCATCATCATCTTCAT
1 CTTCATCATCAGCTTCAT
3890 CTTCATCAT
1 CTTCATCAT
3899 TGTCTTCGTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.18, C:0.31, G:0.04, T:0.47
Consensus pattern (18 bp):
CTTCATCATCAGCTTCAT
Found at i:11191 original size:18 final size:17
Alignment explanation
Indices: 11155--11197 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
11145 CGGAGTAAAA
*
11155 TATTATTTTATAGAGAT
1 TATTAATTTATAGAGAT
*
11172 TATTAATTTATCGAG--
1 TATTAATTTATAGAGAT
11187 TATTAATTTAT
1 TATTAATTTAT
11198 GAAAGTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 11 0.46
17 13 0.54
ACGTcount: A:0.35, C:0.02, G:0.09, T:0.53
Consensus pattern (17 bp):
TATTAATTTATAGAGAT
Found at i:20198 original size:2 final size:2
Alignment explanation
Indices: 20187--20245 Score: 84
Period size: 2 Copynumber: 30.0 Consensus size: 2
20177 TTTAAGGGTG
* *
20187 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA TA GA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
20228 TA TA GA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
20246 AATTGATGGA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (2 bp):
TA
Found at i:22188 original size:21 final size:24
Alignment explanation
Indices: 22159--22209 Score: 63
Period size: 22 Copynumber: 2.2 Consensus size: 24
22149 TTTTGGATTC
22159 ATTATT-TATTATTCAA-AATATAT
1 ATTATTAT-TTATTCAATAATATAT
*
22182 -TTATTATTTATTTAATAATATAT
1 ATTATTATTTATTCAATAATATAT
22205 ATTAT
1 ATTAT
22210 ATCTAAGATA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
22 12 0.50
23 8 0.33
24 4 0.17
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (24 bp):
ATTATTATTTATTCAATAATATAT
Found at i:22204 original size:25 final size:25
Alignment explanation
Indices: 22159--22207 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
22149 TTTTGGATTC
*
22159 ATTATTTATTATTCAAAATATATTT
1 ATTATTTATTAATCAAAATATATTT
*
22184 ATTATTTATTTAAT-AATATATATT
1 ATTATTTA-TTAATCAAAATATATT
22208 ATATCTAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (25 bp):
ATTATTTATTAATCAAAATATATTT
Found at i:22815 original size:10 final size:10
Alignment explanation
Indices: 22802--22828 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
22792 ACCGACCTAA
22802 GTCGGTTTCG
1 GTCGGTTTCG
22812 GTCGGTTTCG
1 GTCGGTTTCG
22822 GTCGGTT
1 GTCGGTT
22829 AATGCCTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.00, C:0.19, G:0.41, T:0.41
Consensus pattern (10 bp):
GTCGGTTTCG
Done.