Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015254.1 Corchorus olitorius cultivar O-4 contig15287, 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: 65790
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Found at i:3828 original size:20 final size:22
Alignment explanation
Indices: 3788--3829 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3778 TATAAATTAT
*
3788 TATATATATGATAACTTATATA
1 TATATATATGATAACTGATATA
3810 TATATATAT-ATAA-TGATATA
1 TATATATATGATAACTGATATA
3830 ATAATCACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
21 4 0.21
22 9 0.47
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (22 bp):
TATATATATGATAACTGATATA
Found at i:5538 original size:16 final size:15
Alignment explanation
Indices: 5502--5541 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
5492 AGAAGTTCAA
*
5502 AGAAAGCAATTAAAC
1 AGAAAACAATTAAAC
*
5517 AGAAAACAATTATAC
1 AGAAAACAATTAAAC
5532 TAGAAAACAA
1 -AGAAAACAA
5542 AACAAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (15 bp):
AGAAAACAATTAAAC
Found at i:21067 original size:1 final size:1
Alignment explanation
Indices: 21061--21089 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
21051 ATTCATAGTT
21061 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
21090 CCTACAACCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:21794 original size:17 final size:16
Alignment explanation
Indices: 21758--21794 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
21748 GAGATTTATT
*
21758 AAGATTTTGAGAAGAG
1 AAGATTTTGAGAAAAG
21774 AAGATTTTGAGAATAAG
1 AAGATTTTGAGAA-AAG
21791 AAGA
1 AAGA
21795 GACAAAGGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (16 bp):
AAGATTTTGAGAAAAG
Found at i:40550 original size:17 final size:17
Alignment explanation
Indices: 40509--40556 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
40499 CACTTCTTCC
*
40509 TTTTTTTTTCTTTTCTT
1 TTTTTTTTTCATTTCTT
* *
40526 ATTCTTTTTCATTTCTT
1 TTTTTTTTTCATTTCTT
*
40543 TTTTTTTTTAATTT
1 TTTTTTTTTCATTT
40557 GGGTTGGGAC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.08, C:0.10, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTTTTTTCATTTCTT
Found at i:40627 original size:33 final size:33
Alignment explanation
Indices: 40590--40674 Score: 161
Period size: 33 Copynumber: 2.5 Consensus size: 33
40580 TTGAGCCCAA
40590 CTGCTGCCAGGCCCGCGCGCTGGCCCAAGCGGC
1 CTGCTGCCAGGCCCGCGCGCTGGCCCAAGCGGC
40623 CTGCTGCCAGGCCCGCGCGCTGGCCCAAGCGGC
1 CTGCTGCCAGGCCCGCGCGCTGGCCCAAGCGGC
40656 CTGCTGCGCAGGCCCGCGC
1 CTGCTGC-CAGGCCCGCGC
40675 AGCCTGGGCT
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 40 0.78
34 11 0.22
ACGTcount: A:0.08, C:0.46, G:0.36, T:0.09
Consensus pattern (33 bp):
CTGCTGCCAGGCCCGCGCGCTGGCCCAAGCGGC
Found at i:44293 original size:42 final size:42
Alignment explanation
Indices: 44234--44313 Score: 151
Period size: 42 Copynumber: 1.9 Consensus size: 42
44224 AGCAACAATT
*
44234 AATATTAGCTTTATTTTGATGAATTATCTAGAGATGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGTAG
44276 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGA
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGA
44314 ATACTAGAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.34, C:0.06, G:0.20, T:0.40
Consensus pattern (42 bp):
AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGTAG
Found at i:53003 original size:6 final size:6
Alignment explanation
Indices: 52992--53021 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
52982 GGCCCTGACC
52992 CCAAAG CCAAAG CCAAAG CCAAAG CCAAAG
1 CCAAAG CCAAAG CCAAAG CCAAAG CCAAAG
53022 ACTTTCTCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.33, G:0.17, T:0.00
Consensus pattern (6 bp):
CCAAAG
Found at i:53104 original size:6 final size:6
Alignment explanation
Indices: 53093--53117 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
53083 GCCCCCTTCT
53093 CTCTCA CTCTCA CTCTCA CTCTCA C
1 CTCTCA CTCTCA CTCTCA CTCTCA C
53118 ACTCCTCCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.52, G:0.00, T:0.32
Consensus pattern (6 bp):
CTCTCA
Found at i:57829 original size:23 final size:23
Alignment explanation
Indices: 57799--57846 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
57789 CGATTTTTAG
57799 TAGCCCAGGCCCTCGTTGTGAAC
1 TAGCCCAGGCCCTCGTTGTGAAC
57822 TAGCCCAGGCCCTCGTTGTGAAC
1 TAGCCCAGGCCCTCGTTGTGAAC
57845 TA
1 TA
57847 TGGACCTGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.19, C:0.33, G:0.25, T:0.23
Consensus pattern (23 bp):
TAGCCCAGGCCCTCGTTGTGAAC
Found at i:60369 original size:2 final size:2
Alignment explanation
Indices: 60364--60388 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
60354 AAAACAAAAA
60364 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
60389 GTAATTTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:62125 original size:2 final size:2
Alignment explanation
Indices: 62118--62147 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
62108 TGGAAAGATG
62118 AT AT AT AT AT AT AT AT AT AT AT ACT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A
62148 AGTCTAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:62858 original size:26 final size:27
Alignment explanation
Indices: 62829--62879 Score: 95
Period size: 26 Copynumber: 1.9 Consensus size: 27
62819 CAAATTAATT
62829 ATCATTAAATTTTAAACAC-TTAAAAA
1 ATCATTAAATTTTAAACACATTAAAAA
62855 ATCATTAAATTTTAAACACATTAAA
1 ATCATTAAATTTTAAACACATTAAA
62880 TTATAGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 19 0.79
27 5 0.21
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (27 bp):
ATCATTAAATTTTAAACACATTAAAAA
Found at i:62878 original size:16 final size:16
Alignment explanation
Indices: 62831--62881 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 16
62821 AATTAATTAT
62831 CATTAAATTTTAAACA
1 CATTAAATTTTAAACA
*
62847 C-TTAAA----AAA-T
1 CATTAAATTTTAAACA
62857 CATTAAATTTTAAACA
1 CATTAAATTTTAAACA
62873 CATTAAATT
1 CATTAAATT
62882 ATAGAAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 12
0.66 0.05 0.29
Matches are distributed among these distances:
10 1 0.04
11 8 0.30
15 8 0.30
16 10 0.37
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (16 bp):
CATTAAATTTTAAACA
Found at i:63711 original size:19 final size:18
Alignment explanation
Indices: 63687--63722 Score: 63
Period size: 18 Copynumber: 1.9 Consensus size: 18
63677 GGCCTAGCCC
63687 ATAAGAAATAAGAAAAAGA
1 ATAAGAAA-AAGAAAAAGA
63706 ATAAGAAAAAGAAAAAG
1 ATAAGAAAAAGAAAAAG
63723 GGCCTAGCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (18 bp):
ATAAGAAAAAGAAAAAGA
Found at i:63719 original size:6 final size:6
Alignment explanation
Indices: 63689--63722 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
63679 CCTAGCCCAT
*
63689 AAGAAA TAAGAAA AAGAAT AAGAAA AAGAAA AAG
1 AAGAAA -AAGAAA AAGAAA AAGAAA AAGAAA AAG
63723 GGCCTAGCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (6 bp):
AAGAAA
Found at i:63759 original size:9 final size:9
Alignment explanation
Indices: 63738--63787 Score: 50
Period size: 10 Copynumber: 5.4 Consensus size: 9
63728 AGCCCATAAC
63738 GAAGAAGAAA
1 GAAGAA-AAA
63748 GAAGAAAAA
1 GAAGAAAAA
63757 GAAGAAAGAA
1 GAAGAAA-AA
63767 -AAG-AAAA
1 GAAGAAAAA
*
63774 GAAAAGAAAA
1 GAAGA-AAAA
63784 GAAG
1 GAAG
63788 GAAATTTGGA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
7 2 0.06
8 4 0.12
9 13 0.38
10 15 0.44
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (9 bp):
GAAGAAAAA
Found at i:63760 original size:16 final size:17
Alignment explanation
Indices: 63739--63786 Score: 66
Period size: 16 Copynumber: 3.0 Consensus size: 17
63729 GCCCATAACG
*
63739 AAGAAGAAAGAAGA-AA
1 AAGAAGAAAGAAAAGAA
63755 AAGAAGAAAGAAAAGAA
1 AAGAAGAAAGAAAAGAA
63772 AAG-A-AAAGAAAAGAA
1 AAGAAGAAAGAAAAGAA
63787 GGAAATTTGG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 11 0.37
16 14 0.47
17 5 0.17
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (17 bp):
AAGAAGAAAGAAAAGAA
Found at i:63769 original size:47 final size:46
Alignment explanation
Indices: 63660--63768 Score: 150
Period size: 46 Copynumber: 2.3 Consensus size: 46
63650 TAAATAAAAC
*
63660 AAAAG-AAAAGAAAAAGGGGCCTAGCCCATAAGAAATAAGAAAAAGA
1 AAAAGAAAAAGAAAAA-GGGCCTAGCCCATAAGAAAGAAGAAAAAGA
*
63706 ATAAGAAAAAGAAAAAGGGCCTAGCCCATAACG-AAGAAGAAAGAAGA
1 AAAAGAAAAAGAAAAAGGGCCTAGCCCATAA-GAAAGAAGAAA-AAGA
63753 AAAAGAAGAAAGAAAA
1 AAAAGAA-AAAGAAAA
63769 GAAAAGAAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
46 27 0.48
47 21 0.38
48 8 0.14
ACGTcount: A:0.62, C:0.10, G:0.22, T:0.06
Consensus pattern (46 bp):
AAAAGAAAAAGAAAAAGGGCCTAGCCCATAAGAAAGAAGAAAAAGA
Found at i:63771 original size:5 final size:5
Alignment explanation
Indices: 63749--63786 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
63739 AAGAAGAAAG
*
63749 AAGAA AA-AG AAG-A AAGAA AAGAA AAGAA AAGAA AAGAA
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA
63787 GGAAATTTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 6 0.21
5 23 0.79
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (5 bp):
AAGAA
Done.