Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016729.1 Corchorus olitorius cultivar O-4 contig16762, 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: 55869
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:2628 original size:15 final size:16
Alignment explanation
Indices: 2608--2643 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
2598 GTTTGAAACT
2608 AACAATTAAA-AAGAA
1 AACAATTAAACAAGAA
*
2623 AACAATTAAACTAGAA
1 AACAATTAAACAAGAA
2639 AACAA
1 AACAA
2644 AGCAAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.69, C:0.11, G:0.06, T:0.14
Consensus pattern (16 bp):
AACAATTAAACAAGAA
Found at i:10005 original size:14 final size:14
Alignment explanation
Indices: 9986--10013 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
9976 ATTCTTAATT
9986 TTGGAGTTAAAAAC
1 TTGGAGTTAAAAAC
10000 TTGGAGTTAAAAAC
1 TTGGAGTTAAAAAC
10014 CCAATTTTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.21, T:0.29
Consensus pattern (14 bp):
TTGGAGTTAAAAAC
Found at i:12198 original size:30 final size:30
Alignment explanation
Indices: 12162--12224 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
12152 TCTTCAAGGG
12162 GGAGGGAATGATGCGCCCAAGG-CTTATCAT
1 GGAGGGAATGATGCG-CCAAGGACTTATCAT
* *
12192 GGAGGGAATGATGTGCCAAGGAGTTATCAT
1 GGAGGGAATGATGCGCCAAGGACTTATCAT
12222 GGA
1 GGA
12225 CTTGAAGATG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 6 0.20
30 24 0.80
ACGTcount: A:0.29, C:0.14, G:0.37, T:0.21
Consensus pattern (30 bp):
GGAGGGAATGATGCGCCAAGGACTTATCAT
Found at i:32206 original size:18 final size:18
Alignment explanation
Indices: 32179--32213 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
32169 ATATATATAA
32179 TTATGATATTTAGCATAC
1 TTATGATATTTAGCATAC
*
32197 TTATGGTATTTAGCATA
1 TTATGATATTTAGCATA
32214 TAATTATGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (18 bp):
TTATGATATTTAGCATAC
Found at i:35593 original size:23 final size:24
Alignment explanation
Indices: 35539--35594 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
35529 TTAAATAAAT
* *
35539 ATTATATATATTAATATATATTTG
1 ATTATATATATAAATATATATTTA
35563 A-TATTATATATAAAT-TATATTTA
1 ATTA-TATATATAAATATATATTTA
35586 ATTATATAT
1 ATTATATAT
35595 TAATAAACGG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
23 15 0.54
24 13 0.46
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (24 bp):
ATTATATATATAAATATATATTTA
Found at i:39895 original size:24 final size:23
Alignment explanation
Indices: 39868--39925 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
39858 CTACTTGCAA
*
39868 TGCAGTGCCCTCACTATTAGCATC
1 TGCAATGCCC-CACTATTAGCATC
*
39892 TGCAATTCCCCACTATTAGCATC
1 TGCAATGCCCCACTATTAGCATC
*
39915 TGCAATTCCCC
1 TGCAATGCCCC
39926 TAGATAGAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 24 0.75
24 8 0.25
ACGTcount: A:0.22, C:0.36, G:0.12, T:0.29
Consensus pattern (23 bp):
TGCAATGCCCCACTATTAGCATC
Found at i:39905 original size:23 final size:23
Alignment explanation
Indices: 39879--39925 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
39869 GCAGTGCCCT
39879 CACTATTAGCATCTGCAATTCCC
1 CACTATTAGCATCTGCAATTCCC
39902 CACTATTAGCATCTGCAATTCCC
1 CACTATTAGCATCTGCAATTCCC
39925 C
1 C
39926 TAGATAGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.26, C:0.36, G:0.09, T:0.30
Consensus pattern (23 bp):
CACTATTAGCATCTGCAATTCCC
Found at i:40828 original size:30 final size:30
Alignment explanation
Indices: 40793--40853 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
40783 ACACCACCCC
40793 GGAGGATCTGTTTCTTGATGAGCAGGAGCA
1 GGAGGATCTGTTTCTTGATGAGCAGGAGCA
40823 GGAGGATCTGTTTCTTGATGAGCAGGAGCA
1 GGAGGATCTGTTTCTTGATGAGCAGGAGCA
40853 G
1 G
40854 TGGTTTGTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.23, C:0.13, G:0.38, T:0.26
Consensus pattern (30 bp):
GGAGGATCTGTTTCTTGATGAGCAGGAGCA
Found at i:41061 original size:30 final size:32
Alignment explanation
Indices: 40997--41074 Score: 90
Period size: 34 Copynumber: 2.5 Consensus size: 32
40987 AAAAAGAATC
*
40997 AAGAAAGAAAGAAGAAATTGACAGACATGTAAAA
1 AAGAAAGAAAGAAGAAACTGACAGA-ATGT-AAA
*
41031 AAGAAAAAAAGAAGAAACTGACAG-A-G-AAA
1 AAGAAAGAAAGAAGAAACTGACAGAATGTAAA
*
41060 AAGAAGGAAAGAAGA
1 AAGAAAGAAAGAAGA
41075 TAAAAAAGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
29 16 0.40
31 1 0.03
32 1 0.03
34 22 0.55
ACGTcount: A:0.65, C:0.05, G:0.23, T:0.06
Consensus pattern (32 bp):
AAGAAAGAAAGAAGAAACTGACAGAATGTAAA
Found at i:42906 original size:18 final size:18
Alignment explanation
Indices: 42883--42918 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
42873 TCCTAGCAAC
42883 ATTGTCCAAACAATTCTG
1 ATTGTCCAAACAATTCTG
42901 ATTGTCCAAACAATTCTG
1 ATTGTCCAAACAATTCTG
42919 GTCGTTCCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.33
Consensus pattern (18 bp):
ATTGTCCAAACAATTCTG
Found at i:47811 original size:23 final size:23
Alignment explanation
Indices: 47785--47830 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
47775 GTTGATGAAT
47785 AATTCTTCCTTCTTCCTATCACA
1 AATTCTTCCTTCTTCCTATCACA
47808 AATTCTTCCTTCTTCCTATCACA
1 AATTCTTCCTTCTTCCTATCACA
47831 CATCAGCATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.35, G:0.00, T:0.43
Consensus pattern (23 bp):
AATTCTTCCTTCTTCCTATCACA
Found at i:55769 original size:13 final size:14
Alignment explanation
Indices: 55740--55770 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
55730 AATAGGTATG
55740 TGTTTTATTTAATT
1 TGTTTTATTTAATT
55754 TGTTTTATTT-ATT
1 TGTTTTATTTAATT
55767 TGTT
1 TGTT
55771 GAGCTTTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.16, C:0.00, G:0.10, T:0.74
Consensus pattern (14 bp):
TGTTTTATTTAATT
Found at i:55779 original size:24 final size:24
Alignment explanation
Indices: 55752--55806 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
55742 TTTTATTTAA
* *
55752 TTTGTTTTATTTATTT-GTTGAGCT
1 TTTGTTTT-GTTATTTACTTGAGCT
* *
55776 TTTGTCTTGTTATTTACTTGGGCT
1 TTTGTTTTGTTATTTACTTGAGCT
55800 TTTGTTT
1 TTTGTTT
55807 CTTATTATGT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
23 6 0.24
24 19 0.76
ACGTcount: A:0.09, C:0.07, G:0.18, T:0.65
Consensus pattern (24 bp):
TTTGTTTTGTTATTTACTTGAGCT
Found at i:55843 original size:2 final size:2
Alignment explanation
Indices: 55836--55869 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
55826 TTATGTATGC
55836 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.