Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012391.1 Corchorus olitorius cultivar O-4 contig12424, 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: 15073
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:4127 original size:13 final size:13
Alignment explanation
Indices: 4111--4137 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4101 TTAAAATTGT
4111 ACATTAAGTTATG
1 ACATTAAGTTATG
4124 ACATTAAGTTATG
1 ACATTAAGTTATG
4137 A
1 A
4138 AGTCATCACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (13 bp):
ACATTAAGTTATG
Found at i:4647 original size:15 final size:15
Alignment explanation
Indices: 4595--4648 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
4585 TTTAAAAGCT
* *
4595 TAAAACTTAATTTAA
1 TAAAATTTAATTTTA
*
4610 TCAAAATTTAATTTTT
1 T-AAAATTTAATTTTA
4626 TAAAATTTAATTTTA
1 TAAAATTTAATTTTA
*
4641 TATAATTT
1 TAAAATTT
4649 TTTTGTAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
15 21 0.64
16 12 0.36
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (15 bp):
TAAAATTTAATTTTA
Found at i:7189 original size:15 final size:15
Alignment explanation
Indices: 7169--7198 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
7159 ATCGATTTTG
7169 ACATATAAATCGACT
1 ACATATAAATCGACT
7184 ACATATAAATCGACT
1 ACATATAAATCGACT
7199 CTAACTTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.20, G:0.07, T:0.27
Consensus pattern (15 bp):
ACATATAAATCGACT
Found at i:10404 original size:21 final size:20
Alignment explanation
Indices: 10378--10486 Score: 118
Period size: 21 Copynumber: 5.4 Consensus size: 20
10368 TGCTAGAAGT
10378 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAG-AAGTTCCAAGC
10399 TCATTGGAGTAAGTTCCAAGC
1 TCATTGGAG-AAGTTCCAAGC
10420 TCATTGGAGCAAG-T---AGC
1 TCATTGGAG-AAGTTCCAAGC
*
10437 TCATTGGAGAAGGTTCCAAGT
1 TCATTGGAGAA-GTTCCAAGC
**
10458 TCATTGGAGAAGGTTCCAATA
1 TCATTGGAGAA-GTTCCAAGC
10479 TCATTGGA
1 TCATTGGA
10487 ATTGCCTAAG
Statistics
Matches: 78, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
16 2 0.03
17 13 0.17
18 1 0.01
20 1 0.01
21 61 0.78
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (20 bp):
TCATTGGAGAAGTTCCAAGC
Found at i:10453 original size:38 final size:40
Alignment explanation
Indices: 10378--10466 Score: 121
Period size: 38 Copynumber: 2.2 Consensus size: 40
10368 TGCTAGAAGT
10378 TCATTGGAGCAAGTTCCAAGCTCATTGGAGTAAGTTCCAAGC
1 TCATTGGAGCAAGTT-C-AGCTCATTGGAGTAAGTTCCAAGC
*
10420 TCATTGGAGCAAG-T-AGCTCATTGGAG-AAGGTTCCAAGT
1 TCATTGGAGCAAGTTCAGCTCATTGGAGTAA-GTTCCAAGC
10458 TCATTGGAG
1 TCATTGGAG
10467 AAGGTTCCAA
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
37 2 0.04
38 29 0.64
41 1 0.02
42 13 0.29
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (40 bp):
TCATTGGAGCAAGTTCAGCTCATTGGAGTAAGTTCCAAGC
Found at i:10895 original size:11 final size:11
Alignment explanation
Indices: 10855--10888 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
10845 AGGAGTAGGG
10855 TCCTTCCTAGC
1 TCCTTCCTAGC
10866 TCCTTCCTAGC
1 TCCTTCCTAGC
10877 TCCTTCCTAGC
1 TCCTTCCTAGC
10888 T
1 T
10889 TTTTCCTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.09, C:0.44, G:0.09, T:0.38
Consensus pattern (11 bp):
TCCTTCCTAGC
Found at i:13051 original size:33 final size:33
Alignment explanation
Indices: 12968--13094 Score: 105
Period size: 33 Copynumber: 3.8 Consensus size: 33
12958 AGTAATTCTG
* ** *
12968 AACCTAATTTGAGTGTTGTTTGCAATGACACGA
1 AACCTAATTTAAGTGTTGTTTGTGATGACACTA
* * * *
13001 AA--TATGTTTTAGATGTTGTTAGTGATGATACTA
1 AACCTA-ATTTAAG-TGTTGTTTGTGATGACACTA
*
13034 AACCTAATTTAAGTGTTGTTTGTGATGACAGTA
1 AACCTAATTTAAGTGTTGTTTGTGATGACACTA
* ** *
13067 AATCTGTTTTAGGTGTTGTTTGTGATGA
1 AACCTAATTTAAGTGTTGTTTGTGATGA
13095 AAAAAATTAT
Statistics
Matches: 74, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
31 2 0.03
32 5 0.07
33 60 0.81
34 5 0.07
35 2 0.03
ACGTcount: A:0.28, C:0.08, G:0.23, T:0.42
Consensus pattern (33 bp):
AACCTAATTTAAGTGTTGTTTGTGATGACACTA
Found at i:13051 original size:66 final size:66
Alignment explanation
Indices: 12968--13094 Score: 184
Period size: 66 Copynumber: 1.9 Consensus size: 66
12958 AGTAATTCTG
*
12968 AACCTAATTTGAGTGTTGTTTGCAATGACACG-AAATATGTTTTAGATGTTGTTAGTGATGATAC
1 AACCTAATTTAAGTGTTGTTTGCAATGACA-GTAAATATGTTTTAGATGTTGTTAGTGATGATAC
13032 TA
65 TA
** * * *
13034 AACCTAATTTAAGTGTTGTTTGTGATGACAGTAAATCTGTTTTAGGTGTTGTTTGTGATGA
1 AACCTAATTTAAGTGTTGTTTGCAATGACAGTAAATATGTTTTAGATGTTGTTAGTGATGA
13095 AAAAAATTAT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
65 1 0.02
66 53 0.98
ACGTcount: A:0.28, C:0.08, G:0.23, T:0.42
Consensus pattern (66 bp):
AACCTAATTTAAGTGTTGTTTGCAATGACAGTAAATATGTTTTAGATGTTGTTAGTGATGATACT
A
Found at i:13108 original size:33 final size:33
Alignment explanation
Indices: 12979--13109 Score: 86
Period size: 33 Copynumber: 4.0 Consensus size: 33
12969 ACCTAATTTG
** **
12979 AGTGTTGTTTGCAATGACACGAAATATGTTTT-
1 AGTGTTGTTTGTGATGACAAAAAATATGTTTTA
* * ** ** **
13011 AGATGTTGTTAGTGATGATACTAAACCTAATTTA
1 AG-TGTTGTTTGTGATGACAAAAAATATGTTTTA
** *
13045 AGTGTTGTTTGTGATGACAGTAAATCTGTTTTA
1 AGTGTTGTTTGTGATGACAAAAAATATGTTTTA
*
13078 GGTGTTGTTTGTGATGA-AAAAAATTATGTTTT
1 AGTGTTGTTTGTGATGACAAAAAA-TATGTTTT
13110 GGATGCTAAT
Statistics
Matches: 77, Mismatches: 19, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
32 6 0.08
33 69 0.90
34 2 0.03
ACGTcount: A:0.29, C:0.06, G:0.22, T:0.43
Consensus pattern (33 bp):
AGTGTTGTTTGTGATGACAAAAAATATGTTTTA
Found at i:14954 original size:21 final size:21
Alignment explanation
Indices: 14885--15040 Score: 167
Period size: 21 Copynumber: 7.4 Consensus size: 21
14875 GCTATGGAGA
*
14885 TCATTGGAGGAA-GTGTGCAAGC
1 TCATTGGA-GAAGGT-TCCAAGC
*
14907 TGCATTGGAGAAGCGTTGCAGAGC
1 T-CATTGGAGAAG-GTTCCA-AGC
14931 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
14952 TCATTGGAGAAAGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
* *
14973 TCATT-G-GAA-GTGCCAAGA
1 TCATTGGAGAAGGTTCCAAGC
* *
14991 TCATTGGAGAAGATTCCAAGA
1 TCATTGGAGAAGGTTCCAAGC
*
15012 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
15033 TCATTGGA
1 TCATTGGA
15041 AATGCCTAAG
Statistics
Matches: 118, Mismatches: 9, Indels: 15
0.83 0.06 0.11
Matches are distributed among these distances:
18 12 0.10
19 4 0.03
20 4 0.03
21 61 0.52
22 9 0.08
23 22 0.19
24 6 0.05
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.24
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:14988 original size:18 final size:18
Alignment explanation
Indices: 14946--14998 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
14936 GGAGAAGGTT
*
14946 CCAAGCTCATTGGAGAAAGTT
1 CCAAGCTCATT-G-G-AAGTG
14967 CCAAGCTCATTGGAAGTG
1 CCAAGCTCATTGGAAGTG
*
14985 CCAAGATCATTGGA
1 CCAAGCTCATTGGA
14999 GAAGATTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
18 17 0.57
19 1 0.03
20 1 0.03
21 11 0.37
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.23
Consensus pattern (18 bp):
CCAAGCTCATTGGAAGTG
Found at i:14996 original size:39 final size:40
Alignment explanation
Indices: 14909--15019 Score: 118
Period size: 39 Copynumber: 2.7 Consensus size: 40
14899 GTGCAAGCTG
* * * *
14909 CATTGGAGAAGCGTTGCAGAGCTCATTGGAGAAGGTTCCAAGCT
1 CATTGGAGAA-AGTTCCA-AGCTCATT-G-GAAGGTGCCAAGAT
14953 CATTGGAGAAAGTTCCAAGCTCATTGGAA-GTGCCAAGAT
1 CATTGGAGAAAGTTCCAAGCTCATTGGAAGGTGCCAAGAT
*
14992 CATTGGAG-AAGATTCCAAGATCATTGGA
1 CATTGGAGAAAG-TTCCAAGCTCATTGGA
15020 GAAGGTTTCA
Statistics
Matches: 61, Mismatches: 5, Indels: 7
0.84 0.07 0.10
Matches are distributed among these distances:
38 3 0.05
39 31 0.51
40 3 0.05
41 1 0.02
42 8 0.13
43 5 0.08
44 10 0.16
ACGTcount: A:0.32, C:0.17, G:0.28, T:0.23
Consensus pattern (40 bp):
CATTGGAGAAAGTTCCAAGCTCATTGGAAGGTGCCAAGAT
Found at i:15008 original size:60 final size:61
Alignment explanation
Indices: 14931--15052 Score: 192
Period size: 60 Copynumber: 2.0 Consensus size: 61
14921 GTTGCAGAGC
* * *
14931 TCATTGGAGAAGGTTCCAAGCTCATTGGAGAAAGTTCCAAGCTCATTGGAAGTGCC-AAGA
1 TCATTGGAGAAGATTCCAAGATCATTGGAGAAAGTTCCAAGCTCATTGGAAATGCCTAAGA
* *
14991 TCATTGGAGAAGATTCCAAGATCATTGGAGAAGGTTTCAAGCTCATTGGAAATGCCTAAGA
1 TCATTGGAGAAGATTCCAAGATCATTGGAGAAAGTTCCAAGCTCATTGGAAATGCCTAAGA
15052 T
1 T
15053 GCCATTTGAT
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
60 51 0.91
61 5 0.09
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.25
Consensus pattern (61 bp):
TCATTGGAGAAGATTCCAAGATCATTGGAGAAAGTTCCAAGCTCATTGGAAATGCCTAAGA
Done.