Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015865.1 Corchorus olitorius cultivar O-4 contig15898, 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: 24045
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:1053 original size:11 final size:11
Alignment explanation
Indices: 1039--1064 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1029 ATATGCTTAG
1039 TATATATACTT
1 TATATATACTT
1050 TATATATACTT
1 TATATATACTT
1061 TATA
1 TATA
1065 ATAATGGGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TATATATACTT
Found at i:6241 original size:89 final size:88
Alignment explanation
Indices: 6091--6260 Score: 331
Period size: 89 Copynumber: 1.9 Consensus size: 88
6081 GAAATCGGGT
6091 TGTCAAATTGGGTGACGTGGCGTGCTGGATTGGCGAATCAAACCAATTGCAAACAGTGCCACGGT
1 TGTCAAATTGGGTGACGTGGCGTGCTGGATTGGCGAATCAAACCAATTGCAAACAGTGCCACGGT
6156 TGGAGTCTTTAAATGTAGTAAGA
66 TGGAGTCTTTAAATGTAGTAAGA
6179 TGTCAAATTGGGTGACGTGGCGTGCCTGGATTGGCGAATCAAACCAATTGCAAACAGTGCCACGG
1 TGTCAAATTGGGTGACGTGGCGTG-CTGGATTGGCGAATCAAACCAATTGCAAACAGTGCCACGG
6244 TTGGAGTCTTTAAATGT
65 TTGGAGTCTTTAAATGT
6261 TGTATGTAAG
Statistics
Matches: 81, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
88 24 0.30
89 57 0.70
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.26
Consensus pattern (88 bp):
TGTCAAATTGGGTGACGTGGCGTGCTGGATTGGCGAATCAAACCAATTGCAAACAGTGCCACGGT
TGGAGTCTTTAAATGTAGTAAGA
Found at i:7201 original size:9 final size:9
Alignment explanation
Indices: 7183--7225 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
7173 TCCTAAATTG
*
7183 ATTATGGAA
1 ATTATAGAA
7192 ATTATAGAA
1 ATTATAGAA
7201 ATTATAGAAA
1 ATTATAG-AA
7211 ATTA-AGGAA
1 ATTATA-GAA
7220 ATTATA
1 ATTATA
7226 TTATTTTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
9 22 0.73
10 8 0.27
ACGTcount: A:0.53, C:0.00, G:0.14, T:0.33
Consensus pattern (9 bp):
ATTATAGAA
Found at i:8185 original size:21 final size:21
Alignment explanation
Indices: 8161--8205 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
8151 GCAAATCAAA
*
8161 TCAAGCTCCGTG-CTTTTACTC
1 TCAAGC-CCGTGACTTTCACTC
*
8182 TCAAGCCCTTGACTTTCACTC
1 TCAAGCCCGTGACTTTCACTC
8203 TCA
1 TCA
8206 TTTTTAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.18, C:0.36, G:0.11, T:0.36
Consensus pattern (21 bp):
TCAAGCCCGTGACTTTCACTC
Found at i:10706 original size:52 final size:52
Alignment explanation
Indices: 10623--10726 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
10613 TTGTGCTACA
10623 CATGATGCTTTATCAATCATGTTGGGATCGTTGTTACGTCGATTGAAGGAAG
1 CATGATGCTTTATCAATCATGTTGGGATCGTTGTTACGTCGATTGAAGGAAG
*
10675 CATGATGCTTTATCAATCATGTTGGGGTCGTTGTTACGTCGATTGAAGGAAG
1 CATGATGCTTTATCAATCATGTTGGGATCGTTGTTACGTCGATTGAAGGAAG
10727 TGAGTCCAGG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.24, C:0.13, G:0.28, T:0.35
Consensus pattern (52 bp):
CATGATGCTTTATCAATCATGTTGGGATCGTTGTTACGTCGATTGAAGGAAG
Found at i:11021 original size:37 final size:37
Alignment explanation
Indices: 10971--11044 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
10961 GAGATCGACA
10971 GGTGCATTTTCGAGAGTGACTGTTTGAGTGCGATGTT
1 GGTGCATTTTCGAGAGTGACTGTTTGAGTGCGATGTT
11008 GGTGCATTTTCGAGAGTGACTGTTTGAGTGCGATGTT
1 GGTGCATTTTCGAGAGTGACTGTTTGAGTGCGATGTT
11045 AGCGATTGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.16, C:0.11, G:0.35, T:0.38
Consensus pattern (37 bp):
GGTGCATTTTCGAGAGTGACTGTTTGAGTGCGATGTT
Found at i:13161 original size:15 final size:16
Alignment explanation
Indices: 13137--13171 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
13127 GCGTGTCTAA
13137 TGTT-TCGTGTAA-CG
1 TGTTATCGTGTAACCG
13151 TGTTATCGTGTAACCG
1 TGTTATCGTGTAACCG
13167 TGTTA
1 TGTTA
13172 ACACGAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.21
15 8 0.42
16 7 0.37
ACGTcount: A:0.17, C:0.14, G:0.26, T:0.43
Consensus pattern (16 bp):
TGTTATCGTGTAACCG
Found at i:14867 original size:31 final size:29
Alignment explanation
Indices: 14829--14912 Score: 98
Period size: 31 Copynumber: 2.8 Consensus size: 29
14819 ACAAGCTAAT
14829 TGCTCAATTTGGTCCTAAACCTTT-GACAGAA
1 TGCTCAATTTGGTCCTAAACCTTTAGAC---A
* *
14860 TGCTCAATTTGGTCCTAAAGCTTTAGACT
1 TGCTCAATTTGGTCCTAAACCTTTAGACA
* *
14889 TGCTCAAATCGGTCCTAAACCTTT
1 TGCTCAATTTGGTCCTAAACCTTT
14913 CAAAATCTGC
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
29 21 0.45
31 23 0.49
32 3 0.06
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (29 bp):
TGCTCAATTTGGTCCTAAACCTTTAGACA
Found at i:15441 original size:13 final size:13
Alignment explanation
Indices: 15423--15447 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15413 TTTTTTGATT
15423 AAAAAATATTTTA
1 AAAAAATATTTTA
15436 AAAAAATATTTT
1 AAAAAATATTTT
15448 TTTTTTTAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAAAATATTTTA
Found at i:15523 original size:30 final size:31
Alignment explanation
Indices: 15462--15538 Score: 104
Period size: 30 Copynumber: 2.5 Consensus size: 31
15452 TTTAAAAAAG
*
15462 TCAGGGACCCAATTGCTCAATTAACTTCACT
1 TCAGGGACCCAATTGCTCAACTAACTTCACT
*
15493 TCAGGGACTCAATTGCTC-ACT-ACGTTCACT
1 TCAGGGACCCAATTGCTCAACTAAC-TTCACT
*
15523 TCAGGGACCCATTTGC
1 TCAGGGACCCAATTGC
15539 ACATTTTCCC
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
29 2 0.05
30 22 0.54
31 17 0.41
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.29
Consensus pattern (31 bp):
TCAGGGACCCAATTGCTCAACTAACTTCACT
Found at i:18833 original size:29 final size:30
Alignment explanation
Indices: 18791--18870 Score: 101
Period size: 31 Copynumber: 2.6 Consensus size: 30
18781 ATTTTGAAAT
18791 GTTTAGGACTAAATTGAGCAGGTC-T-AAAG
1 GTTTAGGAC-AAATTGAGCAGGTCATCAAAG
**
18820 GTTTAGGATCAAATTGAGCATTTCATCAAAG
1 GTTTAGGA-CAAATTGAGCAGGTCATCAAAG
18851 GTTTAGGACCAAATTGAGCA
1 GTTTAGGA-CAAATTGAGCA
18871 ATTAGCCAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
29 20 0.44
30 2 0.04
31 23 0.51
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (30 bp):
GTTTAGGACAAATTGAGCAGGTCATCAAAG
Found at i:21012 original size:23 final size:23
Alignment explanation
Indices: 20979--21050 Score: 74
Period size: 23 Copynumber: 3.0 Consensus size: 23
20969 CCTTGTATCA
*
20979 ACAAGGGTGATGGAAAGTAAAAG
1 ACAAGGGTGATGAAAAGTAAAAG
* * *
21002 ACAAGGTTGATCACAACTTGTAAAA-
1 ACAAGGGTGATGA-AA--AGTAAAAG
21027 ACAAGGGTGATGAAAAGTAAAAG
1 ACAAGGGTGATGAAAAGTAAAAG
21050 A
1 A
21051 TAGGGTTGAT
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
22 6 0.16
23 11 0.29
24 4 0.11
25 11 0.29
26 6 0.16
ACGTcount: A:0.49, C:0.08, G:0.26, T:0.17
Consensus pattern (23 bp):
ACAAGGGTGATGAAAAGTAAAAG
Done.