Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024123.1 Corchorus olitorius cultivar O-4 contig24156, 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: 6829
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:2758 original size:14 final size:14
Alignment explanation
Indices: 2739--2799 Score: 52
Period size: 14 Copynumber: 4.4 Consensus size: 14
2729 TTTCAAAATA
*
2739 AAAAAACTTTTTTC
1 AAAAAACTATTTTC
**
2753 AAAAAAAGATTTTC
1 AAAAAACTATTTTC
* *
2767 AAGAAACTGTTTTC
1 AAAAAACTATTTTC
*
2781 AAAAAA-TGACTTTC
1 AAAAAACT-ATTTTC
2795 AAAAA
1 AAAAA
2800 TGAGTTTTCC
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
13 1 0.03
14 35 0.97
ACGTcount: A:0.51, C:0.11, G:0.07, T:0.31
Consensus pattern (14 bp):
AAAAAACTATTTTC
Found at i:2808 original size:28 final size:28
Alignment explanation
Indices: 2742--2796 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
2732 CAAAATAAAA
* *
2742 AAACTTTTTTCAAAAAAAGATTTTCAAG
1 AAACTGTTTTCAAAAAAAGACTTTCAAG
*
2770 AAACTGTTTTCAAAAAATGACTTTCAA
1 AAACTGTTTTCAAAAAAAGACTTTCAA
2797 AAATGAGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.45, C:0.13, G:0.07, T:0.35
Consensus pattern (28 bp):
AAACTGTTTTCAAAAAAAGACTTTCAAG
Found at i:3496 original size:4 final size:4
Alignment explanation
Indices: 3443--3516 Score: 66
Period size: 4 Copynumber: 18.8 Consensus size: 4
3433 GAAGCAATCT
* * *
3443 AAAG AAAA AAAG AAA- AAA- AGAG AAAG CAAAG AAA- AAAGTG AAAA AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG -AAAG AAAG AAA--G AAAG AAAG
3491 AAAG AAAG AAAG AAAG AAAG -AAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAA
3517 ATCAAAAGGA
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
3 11 0.19
4 40 0.69
5 4 0.07
6 3 0.05
ACGTcount: A:0.77, C:0.01, G:0.20, T:0.01
Consensus pattern (4 bp):
AAAG
Found at i:4682 original size:37 final size:37
Alignment explanation
Indices: 4620--5109 Score: 453
Period size: 37 Copynumber: 13.2 Consensus size: 37
4610 ATTGTTACTT
* * *
4620 ATCAAATCCTTACTTAAGGTCCCTGTTTAGGTGTCTC
1 ATCAAAACCTTATTTAAGATCCCTGTTTAGGTGTCTC
* * * * * *
4657 ATCAAAACCTTGTTCAAGATTCCTGTTTAGATTTCTT
1 ATCAAAACCTTATTTAAGATCCCTGTTTAGGTGTCTC
* * *
4694 ATCAAATCCTTATTTAAGGTCCCTATTTAGGTGTCTC
1 ATCAAAACCTTATTTAAGATCCCTGTTTAGGTGTCTC
* * *
4731 ATCAAAACCTT-TTTCAAGATTCCTGTTTAGGTTTCTT
1 ATCAAAACCTTATTT-AAGATCCCTGTTTAGGTGTCTC
* *
4768 ATCAAAATTCTTATTTAAGGTCCCTGTTTAGGTGTCTC
1 ATCAAAA-CCTTATTTAAGATCCCTGTTTAGGTGTCTC
* * * * *
4806 ATCAAAATCTTGTTCAAGATTCCTGTTTAGGTTTCTC
1 ATCAAAACCTTATTTAAGATCCCTGTTTAGGTGTCTC
* * *
4843 ATTAAATCCTTATTTAAGGTCCCTGTTTAGGTGTCTC
1 ATCAAAACCTTATTTAAGATCCCTGTTTAGGTGTCTC
* * * *
4880 ATCAAAATCTTGTTTAAGATCCCTGTTTAGGTTTCTT
1 ATCAAAACCTTATTTAAGATCCCTGTTTAGGTGTCTC
* * * *
4917 ATCAAATCCTTATTTAAGATGCCTGTTTAGGTTTCTTG
1 ATCAAAACCTTATTTAAGATCCCTGTTTAGGTGTC-TC
** * * * *
4955 A-CAAAATTTTTGTTTAAGATCACTGTTTAGGTTTCTT
1 ATCAAAA-CCTTATTTAAGATCCCTGTTTAGGTGTCTC
* *
4992 ATCAAATCCTTATTTAAGGTCCCTGTTTAGGTGTCTC
1 ATCAAAACCTTATTTAAGATCCCTGTTTAGGTGTCTC
* * * * * * *
5029 ATCAAAATCTTGTTCAAAATTCCTGTTTAGGTTTCTT
1 ATCAAAACCTTATTTAAGATCCCTGTTTAGGTGTCTC
* * * *
5066 ATTAAATCCTTATTTAAGGTACCTGTTTAGGTGTCTC
1 ATCAAAACCTTATTTAAGATCCCTGTTTAGGTGTCTC
*
5103 TTCAAAA
1 ATCAAAA
5110 TCCCAGTTTA
Statistics
Matches: 356, Mismatches: 91, Indels: 12
0.78 0.20 0.03
Matches are distributed among these distances:
36 3 0.01
37 293 0.82
38 57 0.16
39 3 0.01
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.43
Consensus pattern (37 bp):
ATCAAAACCTTATTTAAGATCCCTGTTTAGGTGTCTC
Found at i:4717 original size:74 final size:74
Alignment explanation
Indices: 4580--5111 Score: 775
Period size: 74 Copynumber: 7.2 Consensus size: 74
4570 ACGAAATTCA
* * * * *
4580 GTCTCATCAAAACCTTGTTCAAGATTTCTGATT--GTTACTTATCAAATCCTTACTTAAGGTCCC
1 GTCTCATCAAAATCTTGTTCAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTCCC
4643 TGTTTAGGT
66 TGTTTAGGT
* *
4652 GTCTCATCAAAACCTTGTTCAAGATTCCTGTTTAGATTTCTTATCAAATCCTTATTTAAGGTCCC
1 GTCTCATCAAAATCTTGTTCAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTCCC
*
4717 TATTTAGGT
66 TGTTTAGGT
* * *
4726 GTCTCATCAAAACCTTTTTCAAGATTCCTGTTTAGGTTTCTTATCAAAATTCTTATTTAAGGTCC
1 GTCTCATCAAAATCTTGTTCAAGATTCCTGTTTAGGTTTCTTATC-AAATCCTTATTTAAGGTCC
4791 CTGTTTAGGT
65 CTGTTTAGGT
* *
4801 GTCTCATCAAAATCTTGTTCAAGATTCCTGTTTAGGTTTCTCATTAAATCCTTATTTAAGGTCCC
1 GTCTCATCAAAATCTTGTTCAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTCCC
4866 TGTTTAGGT
66 TGTTTAGGT
* * * *
4875 GTCTCATCAAAATCTTGTTTAAGATCCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGATGCC
1 GTCTCATCAAAATCTTGTTCAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTCCC
4940 TGTTTAGGT
66 TGTTTAGGT
* * * *
4949 TTCTTGA-CAAAATTTTTGTTTAAGA-TCACTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGT
1 GTC-TCATCAAAA-TCTTGTTCAAGATTC-CTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGT
5012 CCCTGTTTAGGT
63 CCCTGTTTAGGT
* * *
5024 GTCTCATCAAAATCTTGTTCAAAATTCCTGTTTAGGTTTCTTATTAAATCCTTATTTAAGGTACC
1 GTCTCATCAAAATCTTGTTCAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTCCC
5089 TGTTTAGGT
66 TGTTTAGGT
*
5098 GTCTCTTCAAAATC
1 GTCTCATCAAAATC
5112 CCAGTTTAGG
Statistics
Matches: 417, Mismatches: 35, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
72 31 0.07
74 251 0.60
75 135 0.32
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.43
Consensus pattern (74 bp):
GTCTCATCAAAATCTTGTTCAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTCCC
TGTTTAGGT
Found at i:4850 original size:149 final size:148
Alignment explanation
Indices: 4580--5111 Score: 775
Period size: 149 Copynumber: 3.6 Consensus size: 148
4570 ACGAAATTCA
* * * *
4580 GTCTCATCAAAACCTTGTTCAAGATTTCTGATT--GTTACTTATCAAATCCTTACTTAAGGTCCC
1 GTCTCATCAAAACCTTGTTCAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTCCC
* *
4643 TGTTTAGGTGTCTCATCAAAACCTTGTTCAAGATTCCTGTTTAGATTTCTTATCAAATCCTTATT
66 TGTTTAGGTGTCTCATCAAAATCTTGTTCAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTATT
*
4708 TAAGGTCCCTATTTAGGT
131 TAAGGTCCCTGTTTAGGT
* *
4726 GTCTCATCAAAACCTTTTTCAAGATTCCTGTTTAGGTTTCTTATCAAAATTCTTATTTAAGGTCC
1 GTCTCATCAAAACCTTGTTCAAGATTCCTGTTTAGGTTTCTTATC-AAATCCTTATTTAAGGTCC
* *
4791 CTGTTTAGGTGTCTCATCAAAATCTTGTTCAAGATTCCTGTTTAGGTTTCTCATTAAATCCTTAT
65 CTGTTTAGGTGTCTCATCAAAATCTTGTTCAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTAT
4856 TTAAGGTCCCTGTTTAGGT
130 TTAAGGTCCCTGTTTAGGT
* * * * *
4875 GTCTCATCAAAATCTTGTTTAAGATCCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGATGCC
1 GTCTCATCAAAACCTTGTTCAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTCCC
* * * *
4940 TGTTTAGGTTTCTTGA-CAAAATTTTTGTTTAAGA-TCACTGTTTAGGTTTCTTATCAAATCCTT
66 TGTTTAGGTGTC-TCATCAAAA-TCTTGTTCAAGATTC-CTGTTTAGGTTTCTTATCAAATCCTT
5003 ATTTAAGGTCCCTGTTTAGGT
128 ATTTAAGGTCCCTGTTTAGGT
* * * *
5024 GTCTCATCAAAATCTTGTTCAAAATTCCTGTTTAGGTTTCTTATTAAATCCTTATTTAAGGTACC
1 GTCTCATCAAAACCTTGTTCAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTCCC
*
5089 TGTTTAGGTGTCTCTTCAAAATC
66 TGTTTAGGTGTCTCATCAAAATC
5112 CCAGTTTAGG
Statistics
Matches: 345, Mismatches: 34, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
146 30 0.09
148 46 0.13
149 269 0.78
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.43
Consensus pattern (148 bp):
GTCTCATCAAAACCTTGTTCAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTCCC
TGTTTAGGTGTCTCATCAAAATCTTGTTCAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTATT
TAAGGTCCCTGTTTAGGT
Found at i:5353 original size:54 final size:54
Alignment explanation
Indices: 5206--5472 Score: 329
Period size: 54 Copynumber: 4.8 Consensus size: 54
5196 TCTCTCTGGA
* * * *
5206 AAGTTGATCTTAAGTTGATCCAATGTGGTCTTTCATAGAAGTTTTCAGAGATTT
1 AAGTTGATCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCT
5260 AAGTTGATCTTAAGATGACCCAGTGCCGGTGTGGTCTTTCATAGAAGTTTTCAGAGATCT
1 AAGTTGATCTTAAGATGACCCA------GTGTGGTCTTTCATAGAAGTTTTCAGAGATCT
*
5320 AAGTTGATCTTAAGATGACCCAATGTGGTCTTTCATAGAAGTTTTCAGAGATCT
1 AAGTTGATCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCT
* * * * * *
5374 AAGTTGATCTTCAGACGACCCTGTGTGGTCTTCCATAGAAGTTTTCAAAAATCT
1 AAGTTGATCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCT
* * *
5428 AAGTTGATCTTAAAGTTGATCCAGTGTGGTCATTCCA-AGAAGTTT
1 AAGTTGATCTT-AAGATGACCCAGTGTGGTC-TTTCATAGAAGTTT
5473 ACGATGATCA
Statistics
Matches: 188, Mismatches: 17, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
54 109 0.58
55 22 0.12
56 5 0.03
60 52 0.28
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (54 bp):
AAGTTGATCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCT
Found at i:5618 original size:33 final size:33
Alignment explanation
Indices: 5576--5653 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
5566 ATTAATTAGG
* * * *
5576 AAGTTCAAAATTTGCATTTCATTTCAAAATTCA
1 AAGTTCAAAATCTGCATATCATATCAAAACTCA
5609 AAGTTCAAAATCTGCATATCATATCAAAACTCA
1 AAGTTCAAAATCTGCATATCATATCAAAACTCA
5642 AAGTTCAAAATC
1 AAGTTCAAAATC
5654 CACAGTTTCT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.44, C:0.18, G:0.06, T:0.32
Consensus pattern (33 bp):
AAGTTCAAAATCTGCATATCATATCAAAACTCA
Found at i:5820 original size:7 final size:7
Alignment explanation
Indices: 5811--5888 Score: 129
Period size: 7 Copynumber: 10.9 Consensus size: 7
5801 AATAGGCAAT
*
5811 TCAAAAT
1 TCAAAAC
5818 TCAAAAC
1 TCAAAAC
5825 TCAAAAC
1 TCAAAAC
5832 TCAAAAC
1 TCAAAAC
5839 TCAAAAC
1 TCAAAAC
5846 TCAAAAC
1 TCAAAAC
5853 TCAAAAC
1 TCAAAAC
5860 TACAAAAC
1 T-CAAAAC
5868 TCAAAAC
1 TCAAAAC
5875 TCAAAAC
1 TCAAAAC
5882 TACAAAA
1 T-CAAAA
5889 TTCATGGCTA
Statistics
Matches: 68, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
7 56 0.82
8 12 0.18
ACGTcount: A:0.59, C:0.26, G:0.00, T:0.15
Consensus pattern (7 bp):
TCAAAAC
Found at i:5868 original size:22 final size:22
Alignment explanation
Indices: 5819--5888 Score: 133
Period size: 22 Copynumber: 3.2 Consensus size: 22
5809 ATTCAAAATT
5819 CAAAACTCAAAACTCAAAACT-
1 CAAAACTCAAAACTCAAAACTA
5840 CAAAACTCAAAACTCAAAACTA
1 CAAAACTCAAAACTCAAAACTA
5862 CAAAACTCAAAACTCAAAACTA
1 CAAAACTCAAAACTCAAAACTA
5884 CAAAA
1 CAAAA
5889 TTCATGGCTA
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
21 21 0.44
22 27 0.56
ACGTcount: A:0.60, C:0.27, G:0.00, T:0.13
Consensus pattern (22 bp):
CAAAACTCAAAACTCAAAACTA
Found at i:5999 original size:27 final size:28
Alignment explanation
Indices: 5948--6014 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 28
5938 TCCTCAAAAG
* *
5948 TCAAAATTC-AAAATTTGCATTTCAT-T
1 TCAAAACTCAAAAATTTGCATGTCATGT
5974 TCAAAACTCAAAAATTTGCATGTCATGT
1 TCAAAACTCAAAAATTTGCATGTCATGT
*
6002 TCGAAACTCAAAA
1 TCAAAACTCAAAA
6015 TCCAGAGTCT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
26 8 0.22
27 15 0.42
28 13 0.36
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.33
Consensus pattern (28 bp):
TCAAAACTCAAAAATTTGCATGTCATGT
Done.