Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009644.1 Corchorus olitorius cultivar O-4 contig09676, 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: 40008
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Found at i:54 original size:18 final size:20
Alignment explanation
Indices: 26--63 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
16 TTCAAAAAAA
26 TTTCAAAAAAAAT-ATTTTC
1 TTTCAAAAAAAATGATTTTC
45 TTTC-AAAAAAATGATTTTC
1 TTTCAAAAAAAATGATTTTC
64 ATTTTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.45, C:0.11, G:0.03, T:0.42
Consensus pattern (20 bp):
TTTCAAAAAAAATGATTTTC
Found at i:1422 original size:31 final size:31
Alignment explanation
Indices: 1384--1445 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
1374 GAGTTTTGTA
* * *
1384 AAACTTTTGAATCGCTTATTATACCCTTATT
1 AAACTTTTGAATCGCCTATCATAACCTTATT
*
1415 AAACTTTTGAATTGCCTATCATAACCTTATT
1 AAACTTTTGAATCGCCTATCATAACCTTATT
1446 TTTCAAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (31 bp):
AAACTTTTGAATCGCCTATCATAACCTTATT
Found at i:4953 original size:22 final size:21
Alignment explanation
Indices: 4902--5085 Score: 102
Period size: 22 Copynumber: 8.5 Consensus size: 21
4892 TGGATATTTT
* *
4902 TATGAAATTTTGATAACTATCT
1 TATGAAATTTTGATAACCA-CC
* *
4924 TTTTAAATTTTGATAACCACGC
1 TATGAAATTTTGATAACCAC-C
**
4946 TATGAAATTTTGATAATTACC
1 TATGAAATTTTGATAACCACC
** * *
4967 TATGAAATTGCGATAAACTCC
1 TATGAAATTTTGATAACCACC
* *
4988 ATATGAAACTTTGATAACCTAAC
1 -TATGAAATTTTGATAACC-ACC
* **
5011 TATGAAATTTTAATAAATCTTCC
1 TATGAAATTTTGAT-AA-CCACC
* *
5034 TATGAAATTTTG-TAACCTTCT
1 TATGAAATTTTGATAACC-ACC
* *
5055 TATG-ATTTTTGATAACCTCCC
1 TATGAAATTTTGATAACC-ACC
*
5076 TATGAGATTT
1 TATGAAATTT
5086 CGTTAATCTC
Statistics
Matches: 122, Mismatches: 32, Indels: 16
0.72 0.19 0.09
Matches are distributed among these distances:
20 7 0.06
21 37 0.30
22 62 0.51
23 15 0.12
24 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.41
Consensus pattern (21 bp):
TATGAAATTTTGATAACCACC
Found at i:5027 original size:44 final size:45
Alignment explanation
Indices: 4945--5051 Score: 123
Period size: 44 Copynumber: 2.4 Consensus size: 45
4935 GATAACCACG
* * *
4945 CTATGAAATTTTGATAA-TTACCTATGAAATTGCGATAAA-C-TC
1 CTATGAAATTTTGATAACCTAACTATGAAATTGCAATAAATCTTC
* **
4987 CATATGAAACTTTGATAACCTAACTATGAAATTTTAATAAATCTTC
1 C-TATGAAATTTTGATAACCTAACTATGAAATTGCAATAAATCTTC
5033 CTATGAAATTTTG-TAACCT
1 CTATGAAATTTTGATAACCT
5052 TCTTATGATT
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
42 1 0.02
43 15 0.28
44 23 0.43
45 12 0.22
46 3 0.06
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.37
Consensus pattern (45 bp):
CTATGAAATTTTGATAACCTAACTATGAAATTGCAATAAATCTTC
Found at i:5079 original size:21 final size:20
Alignment explanation
Indices: 5032--5085 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
5022 AATAAATCTT
*
5032 CCTATGAAATTTTGTAACCTT
1 CCTATG-AATTTTGTAACCTC
* *
5053 CTTATGATTTTTGATAACCTC
1 CCTATGAATTTTG-TAACCTC
5074 CCTATGAGATTT
1 CCTATGA-ATTT
5086 CGTTAATCTC
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 6 0.23
21 17 0.65
22 3 0.12
ACGTcount: A:0.26, C:0.19, G:0.11, T:0.44
Consensus pattern (20 bp):
CCTATGAATTTTGTAACCTC
Found at i:5079 original size:65 final size:65
Alignment explanation
Indices: 4928--5085 Score: 158
Period size: 65 Copynumber: 2.4 Consensus size: 65
4918 CTATCTTTTT
* * *
4928 AAATTTTGATAACCACGCTATGAAATTTTGATAATTACCTATGAAATTGCGATAAACTCCATATG
1 AAATTTTGATAACCTCACTATGAAATTTTAATAATTACCTATGAAATTGCGATAAACTCCATATG
* * * ** * * *
4993 AAACTTTGATAACCTAACTATGAAATTTTAATAAATCTTCCTATGAAATTTTG-TAACCTTCTTA
1 AAATTTTGATAACCTCACTATGAAATTTTAAT-AAT-TACCTATGAAATTGCGATAAACTCCATA
5057 TG
64 TG
* * *
5059 -ATTTTTGATAACCTCCCTATGAGATTT
1 AAATTTTGATAACCTCACTATGAAATTT
5086 CGTTAATCTC
Statistics
Matches: 75, Mismatches: 16, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
65 49 0.65
66 13 0.17
67 13 0.17
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (65 bp):
AAATTTTGATAACCTCACTATGAAATTTTAATAATTACCTATGAAATTGCGATAAACTCCATATG
Found at i:8694 original size:14 final size:14
Alignment explanation
Indices: 8675--8706 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
8665 TAGGGATCTA
8675 TATGTATATTTTTC
1 TATGTATATTTTTC
*
8689 TATGTATATTTTTT
1 TATGTATATTTTTC
8703 TATG
1 TATG
8707 ATGGATGGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.22, C:0.03, G:0.09, T:0.66
Consensus pattern (14 bp):
TATGTATATTTTTC
Found at i:15203 original size:5 final size:5
Alignment explanation
Indices: 15193--15220 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
15183 TAAGAATATA
15193 TATCT TATCT TATCT TATCT TATCT TAT
1 TATCT TATCT TATCT TATCT TATCT TAT
15221 TGGAAAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.18, G:0.00, T:0.61
Consensus pattern (5 bp):
TATCT
Found at i:19676 original size:2 final size:2
Alignment explanation
Indices: 19669--19707 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
19659 AAACACGTAA
*
19669 AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19708 GACAAATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:24946 original size:14 final size:14
Alignment explanation
Indices: 24929--24956 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
24919 TCTTAAACCC
24929 TCACAAAGAAGAAA
1 TCACAAAGAAGAAA
24943 TCACAAAGAAGAAA
1 TCACAAAGAAGAAA
24957 AGCTTTTCTG
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:0.64, C:0.14, G:0.14, T:0.07
Consensus pattern (14 bp):
TCACAAAGAAGAAA
Found at i:35652 original size:28 final size:29
Alignment explanation
Indices: 35583--35653 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
35573 GCCATGTCGT
*
35583 CCTGCCACGTCATCCGTTGACCGAGTCAA
1 CCTGCCACGTCATTCGTTGACCGAGTCAA
*
35612 CCTGCCACATCATTCGTTGACC-AGTCAA
1 CCTGCCACGTCATTCGTTGACCGAGTCAA
*
35640 CCTGCCATGTCATT
1 CCTGCCACGTCATT
35654 TTGCCACATC
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
28 18 0.47
29 20 0.53
ACGTcount: A:0.21, C:0.37, G:0.17, T:0.25
Consensus pattern (29 bp):
CCTGCCACGTCATTCGTTGACCGAGTCAA
Found at i:35760 original size:13 final size:13
Alignment explanation
Indices: 35744--35779 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
35734 GCCACGTCAG
35744 CATTGACTTTGAC
1 CATTGACTTTGAC
35757 CATTGACTTTGAC
1 CATTGACTTTGAC
*
35770 TATTGACTTT
1 CATTGACTTT
35780 TGAGAGTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.22, C:0.19, G:0.14, T:0.44
Consensus pattern (13 bp):
CATTGACTTTGAC
Found at i:35963 original size:18 final size:18
Alignment explanation
Indices: 35939--35981 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
35929 ATGTTTTCTG
35939 CCTGTTTGACCTCTT-GGT
1 CCTGTTTGACCT-TTCGGT
*
35957 TCTGTTTGACCTTTCGGT
1 CCTGTTTGACCTTTCGGT
35975 CCTGTTT
1 CCTGTTT
35982 TCTGCATGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 2 0.09
18 20 0.91
ACGTcount: A:0.05, C:0.26, G:0.21, T:0.49
Consensus pattern (18 bp):
CCTGTTTGACCTTTCGGT
Found at i:35983 original size:47 final size:47
Alignment explanation
Indices: 35914--36104 Score: 269
Period size: 47 Copynumber: 4.1 Consensus size: 47
35904 ATTCCGCTTT
* *
35914 TTTGACATTTCGGTCATGTTTTCTGCCTGTTTGACCTCTTGGTTCTG
1 TTTGACATTTCGGTCCTGTTTTCTGCCTGTTTGACCTCTTGGTCCTG
* * *
35961 TTTGACCTTTCGGTCCTGTTTTCTGCATGTTTGACCTTTTGGTCCTG
1 TTTGACATTTCGGTCCTGTTTTCTGCCTGTTTGACCTCTTGGTCCTG
* *
36008 TTTGACCATTT-GATCCTGTTTTCTACCTGTTTGACCTCTTGGTCCTG
1 TTTGA-CATTTCGGTCCTGTTTTCTGCCTGTTTGACCTCTTGGTCCTG
* *
36055 TTTGACATTTCGGTCCTATTTTCTGCCTGATTGACCT-TTCGGTCCTG
1 TTTGACATTTCGGTCCTGTTTTCTGCCTGTTTGACCTCTT-GGTCCTG
36102 TTT
1 TTT
36105 TTAGCCCTTA
Statistics
Matches: 127, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
46 7 0.06
47 116 0.91
48 4 0.03
ACGTcount: A:0.09, C:0.24, G:0.19, T:0.48
Consensus pattern (47 bp):
TTTGACATTTCGGTCCTGTTTTCTGCCTGTTTGACCTCTTGGTCCTG
Found at i:36009 original size:18 final size:18
Alignment explanation
Indices: 35988--36028 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
35978 GTTTTCTGCA
* *
35988 TGTTTGACCTTTTGGTCC
1 TGTTTGACCATTTGATCC
36006 TGTTTGACCATTTGATCC
1 TGTTTGACCATTTGATCC
36024 TGTTT
1 TGTTT
36029 TCTACCTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.10, C:0.20, G:0.20, T:0.51
Consensus pattern (18 bp):
TGTTTGACCATTTGATCC
Found at i:36069 original size:18 final size:18
Alignment explanation
Indices: 36033--36071 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
36023 CTGTTTTCTA
*
36033 CCTGTTTGACCTCTTGGT
1 CCTGTTTGACATCTTGGT
36051 CCTGTTTGACAT-TTCGGT
1 CCTGTTTGACATCTT-GGT
36069 CCT
1 CCT
36072 ATTTTCTGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 2 0.11
18 17 0.89
ACGTcount: A:0.08, C:0.28, G:0.21, T:0.44
Consensus pattern (18 bp):
CCTGTTTGACATCTTGGT
Found at i:36894 original size:47 final size:47
Alignment explanation
Indices: 36825--36958 Score: 160
Period size: 47 Copynumber: 2.9 Consensus size: 47
36815 ATGGCCCAGT
* * * *
36825 AGGACCTTGCTACTACTGCATCTCTCATAAAGGGCCAAAAGCACACA
1 AGGACCTTGCTACTGCTGCATCTCTCATAAAGGCCCAAAAACACAAA
* *
36872 AGGACCTTGCTACTGCTGCATCTCTCACAAAGCCCCAAAAACACAAA
1 AGGACCTTGCTACTGCTGCATCTCTCATAAAGGCCCAAAAACACAAA
* * ** * *
36919 AGGGCCTTGCTATTGCCACACCTCTCATGAAGGCCCAAAA
1 AGGACCTTGCTACTGCTGCATCTCTCATAAAGGCCCAAAA
36959 CACGCAAAGG
Statistics
Matches: 73, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
47 73 1.00
ACGTcount: A:0.33, C:0.32, G:0.16, T:0.19
Consensus pattern (47 bp):
AGGACCTTGCTACTGCTGCATCTCTCATAAAGGCCCAAAAACACAAA
Done.