Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017260.1 Corchorus olitorius cultivar O-4 contig17293, 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: 14751
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:4948 original size:32 final size:32
Alignment explanation
Indices: 4907--5004 Score: 119
Period size: 32 Copynumber: 3.1 Consensus size: 32
4897 TCAGGTCGAC
4907 TTAAATTTGGGTCAGATTGATTCGGGTTCGGG
1 TTAAATTTGGGTCAGATTGATTCGGGTTCGGG
*
4939 TTAAATTTGGGTCA-AGTTGATTCAGGTTCGGG
1 TTAAATTTGGGTCAGA-TTGATTCGGGTTCGGG
* * * *
4971 TCAATTTTGGGTCATG-TTAATTCGGGTTCAGG
1 TTAAATTTGGGTCA-GATTGATTCGGGTTCGGG
5003 TT
1 TT
5005 CAGACTGGAT
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
31 1 0.02
32 55 0.98
ACGTcount: A:0.19, C:0.10, G:0.31, T:0.40
Consensus pattern (32 bp):
TTAAATTTGGGTCAGATTGATTCGGGTTCGGG
Found at i:5837 original size:22 final size:22
Alignment explanation
Indices: 5809--5871 Score: 90
Period size: 22 Copynumber: 2.9 Consensus size: 22
5799 TAGTATTGAA
*
5809 TTTGGGTTTTTTCAGGTTCGGG
1 TTTGGGTTTTTTCGGGTTCGGG
*
5831 TTTGGGTTTTTTTGGGTTCGGG
1 TTTGGGTTTTTTCGGGTTCGGG
* *
5853 TTTTGGATTTTTCGGGTTC
1 TTTGGGTTTTTTCGGGTTC
5872 TGATTTTTCG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.03, C:0.08, G:0.35, T:0.54
Consensus pattern (22 bp):
TTTGGGTTTTTTCGGGTTCGGG
Found at i:5866 original size:16 final size:15
Alignment explanation
Indices: 5847--5893 Score: 69
Period size: 15 Copynumber: 3.1 Consensus size: 15
5837 TTTTTTTGGG
5847 TTCGGGTTTTGGATTT
1 TTCGGGTTTT-GATTT
*
5863 TTCGGGTTCTGATTT
1 TTCGGGTTTTGATTT
5878 TTCGGG-TTTGATTT
1 TTCGGGTTTTGATTT
5892 TT
1 TT
5894 TTTTGTTCGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 9 0.31
15 11 0.38
16 9 0.31
ACGTcount: A:0.06, C:0.09, G:0.28, T:0.57
Consensus pattern (15 bp):
TTCGGGTTTTGATTT
Found at i:11013 original size:36 final size:36
Alignment explanation
Indices: 10966--11041 Score: 152
Period size: 36 Copynumber: 2.1 Consensus size: 36
10956 GAATAGGATA
10966 TTGCTGTCTCCATCTAACAGGGGATGCAGTTGAAAG
1 TTGCTGTCTCCATCTAACAGGGGATGCAGTTGAAAG
11002 TTGCTGTCTCCATCTAACAGGGGATGCAGTTGAAAG
1 TTGCTGTCTCCATCTAACAGGGGATGCAGTTGAAAG
11038 TTGC
1 TTGC
11042 GGTCAAATTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.29
Consensus pattern (36 bp):
TTGCTGTCTCCATCTAACAGGGGATGCAGTTGAAAG
Found at i:13044 original size:23 final size:23
Alignment explanation
Indices: 12991--13097 Score: 123
Period size: 23 Copynumber: 4.7 Consensus size: 23
12981 GATAATCACA
* *
12991 CTATGAAATTGTGAT-AA-CTTC
1 CTATAAAATTTTGATAAACCTTC
*
13012 GCTATGAAATTTTGATAAACCTTC
1 -CTATAAAATTTTGATAAACCTTC
*
13036 CTATAAAATTTTGATAAACCTCC
1 CTATAAAATTTTGATAAACCTTC
13059 CTATAAAATTTTGAT-AACC-TC
1 CTATAAAATTTTGATAAACCTTC
*
13080 CTTATAAAATCTTGATAA
1 C-TATAAAATTTTGATAA
13098 CTACAAATTT
Statistics
Matches: 76, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
21 2 0.03
22 31 0.41
23 39 0.51
24 4 0.05
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.37
Consensus pattern (23 bp):
CTATAAAATTTTGATAAACCTTC
Found at i:13078 original size:45 final size:44
Alignment explanation
Indices: 12974--13097 Score: 133
Period size: 45 Copynumber: 2.8 Consensus size: 44
12964 TTACACTTTG
* * * * * * *
12974 AAATTTTGATAATCACACTATGAAATTGTGAT-AACTTCGCTATG
1 AAATTTTGATAACCTC-CTATAAAATTTTGATAAACCTCCCTATA
13018 AAATTTTGATAAACCTTCCTATAAAATTTTGATAAACCTCCCTATA
1 AAATTTTGAT-AACC-TCCTATAAAATTTTGATAAACCTCCCTATA
*
13064 AAATTTTGATAACCTCCTTATAAAATCTTGATAA
1 AAATTTTGATAACCTCC-TATAAAATTTTGATAA
13098 CTACAAATTT
Statistics
Matches: 68, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
44 13 0.19
45 35 0.51
46 20 0.29
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (44 bp):
AAATTTTGATAACCTCCTATAAAATTTTGATAAACCTCCCTATA
Found at i:13080 original size:22 final size:22
Alignment explanation
Indices: 12791--13198 Score: 226
Period size: 22 Copynumber: 18.6 Consensus size: 22
12781 TTTTTAACCT
*
12791 TATGAAATTTTGTTAACCTCTCCC
1 TATGAAATTTTGATAA-C-CTCCC
* * *
12815 TAAGGAATTTTGA-AGACCTCAC
1 TATGAAATTTTGATA-ACCTCCC
* * **
12837 TATGAAATTTTGTTTATTTCCC
1 TATGAAATTTTGATAACCTCCC
* * * *
12859 AATGAAATTTCGATAACCAACAC
1 TATGAAATTTTGATAACC-TCCC
* *
12882 TATGAAATATTGATAACCTCCA
1 TATGAAATTTTGATAACCTCCC
* * * **
12904 TATGATATATTGATAACCACGT
1 TATGAAATTTTGATAACCTCCC
* * * *
12926 TATGAAAATTTAAAAACCTCCA
1 TATGAAATTTTGATAACCTCCC
* *
12948 TATG-AATTGTT-AGTAA-TTACAC
1 TATGAAATT-TTGA-TAACCT-CCC
* * * *
12970 TTTGAAATTTTGATAATCACAC
1 TATGAAATTTTGATAACCTCCC
* * *
12992 TATGAAATTGTGATAACTTCGC
1 TATGAAATTTTGATAACCTCCC
*
13014 TATGAAATTTTGATAAACCTTCC
1 TATGAAATTTTGAT-AACCTCCC
*
13037 TATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTCCC
* *
13060 TATAAAATTTTGATAACCTCCT
1 TATGAAATTTTGATAACCTCCC
* *
13082 TATAAAATCTTGATAA-----C
1 TATGAAATTTTGATAACCTCCC
*
13099 TA-CAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTCCC
** ***
13120 TATGATTTTTTGATAACCTTAT
1 TATGAAATTTTGATAACCTCCC
* *
13142 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTCCC
*
13164 TATGAAATTTTGATAACC-CTCT
1 TATGAAATTTTGATAACCTC-CC
13186 TATGAAATTTTGA
1 TATGAAATTTTGA
13199 AAACTAAACT
Statistics
Matches: 289, Mismatches: 78, Indels: 36
0.72 0.19 0.09
Matches are distributed among these distances:
16 11 0.04
17 2 0.01
21 9 0.03
22 192 0.66
23 64 0.22
24 11 0.04
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCC
Found at i:13314 original size:22 final size:22
Alignment explanation
Indices: 13284--13448 Score: 131
Period size: 22 Copynumber: 7.5 Consensus size: 22
13274 ACCTTCCTAA
* *
13284 TTTGGTAACCATACTATGAAAT
1 TTTGATAACCATCCTATGAAAT
* *
13306 TTTGATAACCTTCCCATGAAAT
1 TTTGATAACCATCCTATGAAAT
*
13328 TTTGATAA-CTTCCATATGAAAT
1 TTTGATAACCATCC-TATGAAAT
* *
13350 TTTGCTAA-CTTCCATATGAAAT
1 TTTGATAACCATCC-TATGAAAT
* * *
13372 CTTGGTAACCA-CACTATGGAAT
1 TTTGATAACCATC-CTATGAAAT
*
13394 TTTGATAACC-TCCTCATGAGAT
1 TTTGATAACCATCCT-ATGAAAT
** * *
13416 CATAATAACCATCTTATGAAAT
1 TTTGATAACCATCCTATGAAAT
13438 TTTGATAACCA
1 TTTGATAACCA
13449 CACAGAGACA
Statistics
Matches: 115, Mismatches: 22, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
21 7 0.06
22 103 0.90
23 5 0.04
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.36
Consensus pattern (22 bp):
TTTGATAACCATCCTATGAAAT
Found at i:13346 original size:44 final size:43
Alignment explanation
Indices: 13215--13447 Score: 139
Period size: 44 Copynumber: 5.5 Consensus size: 43
13205 AACTAATCTT
* *
13215 CATATGAAATTTTGATATCC-TCCC-TGAAATTTTGATTACTC
1 CATATGAAATTTTGATAACCTTCCCATGAAATTTTGATAACTC
* * * *
13256 CATAATAAAAGTTTAATAACCTT-CC-T--AA-TTTGGTAAC-C
1 CAT-ATGAAATTTTGATAACCTTCCCATGAAATTTTGATAACTC
*
13294 ATACTATGAAATTTTGATAACCTTCCCATGAAATTTTGATAACTTC
1 -CA-TATGAAATTTTGATAACCTTCCCATGAAATTTTGATAAC-TC
* * * *
13340 CATATGAAATTTTGCTAA-CTTCCATATGAAATCTTGGTAAC-C
1 CATATGAAATTTTGATAACCTTCC-CATGAAATTTTGATAACTC
* * ** *
13382 ACACTATGGAATTTTGATAACC-TCCTCATGAGATCATAATAAC-C
1 -CA-TATGAAATTTTGATAACCTTCC-CATGAAATTTTGATAACTC
*
13426 ATCTTATGAAATTTTGATAACC
1 --CATATGAAATTTTGATAACC
13448 ACACAGAGAC
Statistics
Matches: 149, Mismatches: 27, Indels: 29
0.73 0.13 0.14
Matches are distributed among these distances:
38 1 0.01
39 24 0.16
40 5 0.03
41 4 0.03
42 17 0.11
43 10 0.07
44 84 0.56
45 3 0.02
46 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.36
Consensus pattern (43 bp):
CATATGAAATTTTGATAACCTTCCCATGAAATTTTGATAACTC
Found at i:13652 original size:20 final size:20
Alignment explanation
Indices: 13614--13652 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
13604 TATTGACATT
13614 TAAAAAATTGAAATTAAAAG
1 TAAAAAATTGAAATTAAAAG
*
13634 TAAAATATT-AAATTCAAAA
1 TAAAAAATTGAAATT-AAAA
13653 AATAATAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (20 bp):
TAAAAAATTGAAATTAAAAG
Found at i:13947 original size:30 final size:27
Alignment explanation
Indices: 13893--13947 Score: 65
Period size: 30 Copynumber: 1.9 Consensus size: 27
13883 GTCTAAATTG
**
13893 AAATTTTATAATTAATTTTTAAATAAT
1 AAATTTTATAATTAATTTAGAAATAAT
13920 AAATTTTAATAATGTTAATTTAGAAATA
1 AAATTTT-ATAA--TTAATTTAGAAATA
13948 TATTTGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 7 0.30
28 4 0.17
30 12 0.52
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (27 bp):
AAATTTTATAATTAATTTAGAAATAAT
Done.