Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021603.1 Corchorus olitorius cultivar O-4 contig21636, 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: 15885
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Found at i:1027 original size:25 final size:25
Alignment explanation
Indices: 997--1044 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
987 ATGCAATGTC
997 AAATTAGATTTGAGCTACATGAATG
1 AAATTAGATTTGAGCTACATGAATG
*
1022 AAATTAGCTTTGAGCTACATGAA
1 AAATTAGATTTGAGCTACATGAA
1045 CGCAAAATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (25 bp):
AAATTAGATTTGAGCTACATGAATG
Found at i:1958 original size:21 final size:21
Alignment explanation
Indices: 1920--1963 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1910 GGAGATTCCA
* * *
1920 AAGATATCATTTGATCCATTG
1 AAGATACCATTAGATCCAATG
*
1941 AAGATACCATTAGGTCCAATG
1 AAGATACCATTAGATCCAATG
1962 AA
1 AA
1964 AAGAGCAAGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.30
Consensus pattern (21 bp):
AAGATACCATTAGATCCAATG
Found at i:2176 original size:19 final size:19
Alignment explanation
Indices: 2146--2213 Score: 127
Period size: 19 Copynumber: 3.5 Consensus size: 19
2136 TTTATGAGGC
2146 TACCCAGGGGCAGGTAGGGG
1 TACCC-GGGGCAGGTAGGGG
2166 TACCCGGGGCAGGTAGGGG
1 TACCCGGGGCAGGTAGGGG
2185 TACCCGGGGCAGGTAGGGG
1 TACCCGGGGCAGGTAGGGG
2204 TACCCGGGGC
1 TACCCGGGGC
2214 CGGGTCACCC
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
19 43 0.90
20 5 0.10
ACGTcount: A:0.16, C:0.24, G:0.50, T:0.10
Consensus pattern (19 bp):
TACCCGGGGCAGGTAGGGG
Found at i:3555 original size:26 final size:26
Alignment explanation
Indices: 3526--3646 Score: 91
Period size: 26 Copynumber: 4.2 Consensus size: 26
3516 TACTTCTTGA
*
3526 TTACTGATTACCATTTTTTACTCTTT
1 TTACTAATTACCATTTTTTACTCTTT
*
3552 TTACTAATTACCAGTTTTTACTCTTT
1 TTACTAATTACCATTTTTTACTCTTT
*
3578 CTACTTAAATTACTGATCACATTTTTCTTACTCTTTCT
1 TTAC-T-AA-T--T-A-C-CA-TTTT-TTACTC-TT-T
*
3616 TTACTGATTACCA-TTTTTACTCTTT
1 TTACTAATTACCATTTTTTACTCTTT
3641 TTACTA
1 TTACTA
3647 TTTTCTTACT
Statistics
Matches: 76, Mismatches: 7, Indels: 25
0.70 0.06 0.23
Matches are distributed among these distances:
25 6 0.08
26 29 0.38
27 7 0.09
28 5 0.07
29 1 0.01
30 2 0.03
31 2 0.03
32 2 0.03
33 2 0.03
34 2 0.03
35 4 0.05
36 7 0.09
37 3 0.04
38 4 0.05
ACGTcount: A:0.22, C:0.21, G:0.03, T:0.54
Consensus pattern (26 bp):
TTACTAATTACCATTTTTTACTCTTT
Found at i:3806 original size:21 final size:21
Alignment explanation
Indices: 3781--3945 Score: 160
Period size: 21 Copynumber: 7.9 Consensus size: 21
3771 ACCATTACCA
*
3781 TACTGACTACTTTTTACTCTT
1 TACTGATTACTTTTTACTCTT
*
3802 TACTGATTAC-TATTACTCTTT
1 TACTGATTACTTTTTACTC-TT
*
3823 TACTGATTACTCTTTACTCCTT
1 TACTGATTACTTTTTACT-CTT
*
3845 TACTGATTAC-TATTACTCTT
1 TACTGATTACTTTTTACTCTT
*
3865 T-CTTGATTACTCTTTACTCTT
1 TAC-TGATTACTTTTTACTCTT
* *
3886 TACTGACTA-TTATTACTCTT
1 TACTGATTACTTTTTACTCTT
* * *
3906 T-CTTGATCACTCTTCACTCTT
1 TAC-TGATTACTTTTTACTCTT
3927 TACTGATTACTATTTTACT
1 TACTGATTACT-TTTTACT
3946 GATTGCTCTC
Statistics
Matches: 115, Mismatches: 19, Indels: 19
0.75 0.12 0.12
Matches are distributed among these distances:
19 2 0.02
20 32 0.28
21 56 0.49
22 24 0.21
23 1 0.01
ACGTcount: A:0.21, C:0.23, G:0.05, T:0.52
Consensus pattern (21 bp):
TACTGATTACTTTTTACTCTT
Found at i:3833 original size:15 final size:14
Alignment explanation
Indices: 3808--3837 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
3798 TCTTTACTGA
3808 TTACTATTACTCTT
1 TTACTATTACTCTT
3822 TTACTGATTACTCTT
1 TTACT-ATTACTCTT
3837 T
1 T
3838 ACTCCTTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.20, C:0.20, G:0.03, T:0.57
Consensus pattern (14 bp):
TTACTATTACTCTT
Found at i:3845 original size:8 final size:7
Alignment explanation
Indices: 3788--3889 Score: 59
Period size: 7 Copynumber: 14.6 Consensus size: 7
3778 CCATACTGAC
*
3788 TACTTTT
1 TACTCTT
3795 TACTCTT
1 TACTCTT
**
3802 TACTGAT
1 TACTCTT
*
3809 TACT-AT
1 TACTCTT
3815 TACTCTTT
1 TACTC-TT
**
3823 TACTGAT
1 TACTCTT
3830 TACTCTT
1 TACTCTT
3837 TACTCCTT
1 TACT-CTT
**
3845 TACTGAT
1 TACTCTT
*
3852 TACT-AT
1 TACTCTT
3858 TACTCTT
1 TACTCTT
3865 T-CT-TGAT
1 TACTCT--T
3872 TACTCTT
1 TACTCTT
3879 TACTCTT
1 TACTCTT
3886 TACT
1 TACT
3890 GACTATTATT
Statistics
Matches: 76, Mismatches: 11, Indels: 16
0.74 0.11 0.16
Matches are distributed among these distances:
5 1 0.01
6 14 0.18
7 46 0.61
8 14 0.18
9 1 0.01
ACGTcount: A:0.20, C:0.23, G:0.04, T:0.54
Consensus pattern (7 bp):
TACTCTT
Found at i:3900 original size:41 final size:41
Alignment explanation
Indices: 3762--3979 Score: 236
Period size: 41 Copynumber: 5.4 Consensus size: 41
3752 TGAATTTTAA
* * * * *
3762 TTACTGATTACCATTAC-CATAC-TGACTACTTTTTACTCT
1 TTACTGATTACTATTACTCTTTCTTGATTACTCTTTACTCT
3801 TTACTGATTACTATTACTCTTT-TACTGATTACTCTTTACTCCT
1 TTACTGATTACTATTACTCTTTCT--TGATTACTCTTTACT-CT
3844 TTACTGATTACTATTACTCTTTCTTGATTACTCTTTACTCT
1 TTACTGATTACTATTACTCTTTCTTGATTACTCTTTACTCT
* * * *
3885 TTACTGACTATTATTACTCTTTCTTGATCACTCTTCACTCT
1 TTACTGATTACTATTACTCTTTCTTGATTACTCTTTACTCT
* * *
3926 TTACTGATTACTA-T--T-TTAC-TGATTGCTCTCTTATTCT
1 TTACTGATTACTATTACTCTTTCTTGATTACTCT-TTACTCT
3963 TTACTGATTACTATTAC
1 TTACTGATTACTATTAC
3980 CATTGTGCCG
Statistics
Matches: 153, Mismatches: 16, Indels: 19
0.81 0.09 0.10
Matches are distributed among these distances:
36 8 0.05
37 21 0.14
38 2 0.01
39 16 0.10
40 3 0.02
41 50 0.33
42 28 0.18
43 24 0.16
44 1 0.01
ACGTcount: A:0.22, C:0.23, G:0.06, T:0.50
Consensus pattern (41 bp):
TTACTGATTACTATTACTCTTTCTTGATTACTCTTTACTCT
Found at i:4464 original size:19 final size:19
Alignment explanation
Indices: 4440--4476 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
4430 AACATGATAA
4440 TAACAACAGTTTATAAAAT
1 TAACAACAGTTTATAAAAT
4459 TAACAACAGTTTATAAAA
1 TAACAACAGTTTATAAAA
4477 ATAAATATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.54, C:0.11, G:0.05, T:0.30
Consensus pattern (19 bp):
TAACAACAGTTTATAAAAT
Found at i:7142 original size:40 final size:40
Alignment explanation
Indices: 7083--7160 Score: 138
Period size: 40 Copynumber: 1.9 Consensus size: 40
7073 GATGGTATTA
7083 CTGTTTACTTTGAAAGCATAATGCCTTGTCCATATGGATG
1 CTGTTTACTTTGAAAGCATAATGCCTTGTCCATATGGATG
* *
7123 CTGTTTACTTTGAATGCATAATGCCTTGTTCATATGGA
1 CTGTTTACTTTGAAAGCATAATGCCTTGTCCATATGGA
7161 AATGCAATGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.40
Consensus pattern (40 bp):
CTGTTTACTTTGAAAGCATAATGCCTTGTCCATATGGATG
Found at i:7806 original size:16 final size:16
Alignment explanation
Indices: 7785--7851 Score: 55
Period size: 16 Copynumber: 3.9 Consensus size: 16
7775 AAGTAGCAAA
7785 GACTAAAAAGTAAATG
1 GACTAAAAAGTAAATG
*
7801 GACTAAACACAAGTAGCAA-A
1 GACT-AA-A-AAGTA--AATG
7821 GACTAAAAAGTAAATG
1 GACTAAAAAGTAAATG
*
7837 GACCAAAAAGATAAA
1 GACTAAAAAG-TAAA
7852 AGGAAATGGA
Statistics
Matches: 41, Mismatches: 3, Indels: 13
0.72 0.05 0.23
Matches are distributed among these distances:
15 2 0.05
16 13 0.32
17 11 0.27
18 2 0.05
19 7 0.17
20 4 0.10
21 2 0.05
ACGTcount: A:0.58, C:0.12, G:0.16, T:0.13
Consensus pattern (16 bp):
GACTAAAAAGTAAATG
Found at i:7815 original size:36 final size:36
Alignment explanation
Indices: 7768--7839 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
7758 GGCCAATTGA
7768 TAAACACAAGTAGCAAAGACTAAAAAGTAAATGGAC
1 TAAACACAAGTAGCAAAGACTAAAAAGTAAATGGAC
7804 TAAACACAAGTAGCAAAGACTAAAAAGTAAATGGAC
1 TAAACACAAGTAGCAAAGACTAAAAAGTAAATGGAC
7840 CAAAAAGATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.56, C:0.14, G:0.17, T:0.14
Consensus pattern (36 bp):
TAAACACAAGTAGCAAAGACTAAAAAGTAAATGGAC
Found at i:7826 original size:20 final size:20
Alignment explanation
Indices: 7768--7827 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
7758 GGCCAATTGA
7768 TAAACACAAGTAGCAAAGAC
1 TAAACACAAGTAGCAAAGAC
*
7788 T-AA-A-AAGTA--AATGGAC
1 TAAACACAAGTAGCAA-AGAC
7804 TAAACACAAGTAGCAAAGAC
1 TAAACACAAGTAGCAAAGAC
7824 TAAA
1 TAAA
7828 AAGTAAATGG
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
15 2 0.06
16 4 0.12
17 7 0.22
18 2 0.06
19 7 0.22
20 8 0.25
21 2 0.06
ACGTcount: A:0.57, C:0.15, G:0.15, T:0.13
Consensus pattern (20 bp):
TAAACACAAGTAGCAAAGAC
Found at i:12677 original size:15 final size:15
Alignment explanation
Indices: 12647--12688 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
12637 TTACTTTGTT
12647 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
12663 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
12678 TTGCTTTCTGT
1 TTGTTTTCTGT
12689 CAATCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:12964 original size:29 final size:29
Alignment explanation
Indices: 12861--12962 Score: 168
Period size: 29 Copynumber: 3.4 Consensus size: 29
12851 TTTGGCGCCG
12861 TTGCCGGGGAAGGGTAACTTTTTCTGGTAT
1 TTGCCGGGGAAGGG-AACTTTTTCTGGTAT
*
12891 TTGCCGGGGAAGGGAACTATTTCTGGTAT
1 TTGCCGGGGAAGGGAACTTTTTCTGGTAT
*
12920 TTGCCGGGGAAGGGAACTTTTTCTGGTTT
1 TTGCCGGGGAAGGGAACTTTTTCTGGTAT
12949 TTGCCAGGGGAAGG
1 TTGCC-GGGGAAGG
12963 AAAATAGACT
Statistics
Matches: 68, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
29 46 0.68
30 22 0.32
ACGTcount: A:0.18, C:0.14, G:0.36, T:0.32
Consensus pattern (29 bp):
TTGCCGGGGAAGGGAACTTTTTCTGGTAT
Done.