Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023943.1 Corchorus olitorius cultivar O-4 contig23976, 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: 6405
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Found at i:1560 original size:69 final size:69
Alignment explanation
Indices: 1464--1668 Score: 263
Period size: 69 Copynumber: 2.9 Consensus size: 69
1454 AATCAACCCA
* *
1464 ATCTATTCGAAGATTTGCTGCACCGAGCCCACTGAGTCCATATTGAAGATGCTACACCGAGTCAT
1 ATCTATTTGAAGATTTGCTGCACCGAGCCCACCGAGT-CATATTGAAGATGCTACACCGAGTCAT
1529 CCT-G
65 CCTGG
* *
1533 ATCTATTTGAAGACTTGCTGCACCGAG-CCATCCGAGATCATTTTTGAAGATGCTACACCGAGTC
1 ATCTATTTGAAGATTTGCTGCACCGAGCCCA-CCGAG-TCA-TATTGAAGATGCTACACCGAGTC
1597 AT-CTGG
63 ATCCTGG
* * * * *
1603 ATCTATTTGAAGGTTTGTTACACTGAGCTCACCGAGTTCATATTGAAGATGCTACACCGAGTCAT
1 ATCTATTTGAAGATTTGCTGCACCGAGCCCACCGAG-TCATATTGAAGATGCTACACCGAGTCAT
1668 C
65 C
1669 TGAATTCATC
Statistics
Matches: 118, Mismatches: 12, Indels: 11
0.84 0.09 0.08
Matches are distributed among these distances:
68 3 0.03
69 57 0.48
70 56 0.47
71 2 0.02
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.29
Consensus pattern (69 bp):
ATCTATTTGAAGATTTGCTGCACCGAGCCCACCGAGTCATATTGAAGATGCTACACCGAGTCATC
CTGG
Found at i:2019 original size:35 final size:35
Alignment explanation
Indices: 1506--2020 Score: 527
Period size: 35 Copynumber: 14.7 Consensus size: 35
1496 TGAGTCCATA
*
1506 TTGAAGATGCTACACCGAGTCATCCT-GA-TCTA-T
1 TTGAAGATGCTACACCGAGTCAT-CTGGATTCAACT
* * * **
1539 TTGAAGACTTGCTGCACCGAGCCATCCGAGA-TCATTT
1 TTGAAGA--TGCTACACCGAGTCATCTG-GATTCAACT
*
1576 TTGAAGATGCTACACCGAGTCATCTGGA-TCTA-T
1 TTGAAGATGCTACACCGAGTCATCTGGATTCAACT
* * * *
1609 TTGAAGGTTTGTTACACTGAGCTCA-C-CGAGTTC-A-T
1 TTGAA-G-ATGCTACACCGAG-TCATCTGGA-TTCAACT
* *
1644 ATTGAAGATGCTACACCGAGTCATCTGAATTCATCT
1 -TTGAAGATGCTACACCGAGTCATCTGGATTCAACT
* *
1680 TTGAAGATGCTACACCGAGTCATCCGAGATT-ATCT
1 TTGAAGATGCTACACCGAGTCATCTG-GATTCAACT
* *
1715 TTGAAGATGCTATAACGAGTCATCTGGATTCAACT
1 TTGAAGATGCTACACCGAGTCATCTGGATTCAACT
* * *
1750 TTGAGGATGCTATACCGAGTCATCT-GAGTTCAATT
1 TTGAAGATGCTACACCGAGTCATCTGGA-TTCAACT
* * *
1785 TTGAAGATGCTGCATCGAGTCATCT-GAGTTCAATT
1 TTGAAGATGCTACACCGAGTCATCTGGA-TTCAACT
*
1820 TTGAAGATGCTACACCGAGTCATCTGGATTCAATT
1 TTGAAGATGCTACACCGAGTCATCTGGATTCAACT
* *
1855 TTGAAGATGCTGCACCGAGTCATCT-GAGTTCATCT
1 TTGAAGATGCTACACCGAGTCATCTGGA-TTCAACT
* *
1890 TTGAAGATGCTGCACCGAGTCATCTGGATTCGACT
1 TTGAAGATGCTACACCGAGTCATCTGGATTCAACT
* * *
1925 TTAAAGATGCTACACCGAGTCATCTAGAATCAACT
1 TTGAAGATGCTACACCGAGTCATCTGGATTCAACT
*
1960 TTGAAGATGCTTCACCGAGTCATCTGGATTCAACT
1 TTGAAGATGCTACACCGAGTCATCTGGATTCAACT
1995 TTGAAGATGCTACACCGAGTCATCTG
1 TTGAAGATGCTACACCGAGTCATCTG
2021 AAGATGGTAA
Statistics
Matches: 411, Mismatches: 50, Indels: 40
0.82 0.10 0.08
Matches are distributed among these distances:
33 16 0.04
34 30 0.07
35 335 0.82
36 22 0.05
37 8 0.02
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (35 bp):
TTGAAGATGCTACACCGAGTCATCTGGATTCAACT
Found at i:2193 original size:105 final size:105
Alignment explanation
Indices: 2038--2332 Score: 446
Period size: 105 Copynumber: 2.8 Consensus size: 105
2028 TAATGCACCG
* * ** * **
2038 TATGGAAACGAACTATGGCTTGTGGAAAAGCCTATGTGGCTTGGACGGAACCAAGGTTTGAACTG
1 TATGGAAATGAACT-TGGCTTATGGAAAAGCCCCTGTTGCTTGGGTGGAACCAAGGTTTGAACTG
*
2103 ACTCGCATGGAAACGAGTTTAGTCTTGGAAGACTGAATTCA
65 ACTCGTATGGAAACGAGTTTAGTCTTGGAAGACTGAATTCA
* *
2144 TATGGAAATGAACTTGGCTTATGGGAAAGCCCCCGTTGCTTGGGTGGAACCAAGGTTTGAACTGA
1 TATGGAAATGAACTTGGCTTATGGAAAAGCCCCTGTTGCTTGGGTGGAACCAAGGTTTGAACTGA
2209 CTCGTATGGAAACGAGTTTAGTCTTGGAAGACTGAATTCA
66 CTCGTATGGAAACGAGTTTAGTCTTGGAAGACTGAATTCA
* * * *
2249 TATGGAAATGAGCTTGGCTTATGGAAAAGCCCCTGTTGCTTGGGTGGAAGCAAGGCTTCAACTGA
1 TATGGAAATGAACTTGGCTTATGGAAAAGCCCCTGTTGCTTGGGTGGAACCAAGGTTTGAACTGA
*
2314 CTCATATGGAAACGAGTTT
66 CTCGTATGGAAACGAGTTT
2333 GGCTTATGGA
Statistics
Matches: 172, Mismatches: 17, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
105 159 0.92
106 13 0.08
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.27
Consensus pattern (105 bp):
TATGGAAATGAACTTGGCTTATGGAAAAGCCCCTGTTGCTTGGGTGGAACCAAGGTTTGAACTGA
CTCGTATGGAAACGAGTTTAGTCTTGGAAGACTGAATTCA
Found at i:3240 original size:33 final size:33
Alignment explanation
Indices: 3145--3244 Score: 173
Period size: 33 Copynumber: 3.0 Consensus size: 33
3135 CAAATGGAAA
* **
3145 GCAATCTTGTTTTGAAAAGCGAATTTTGACCTT
1 GCAAACTTGTTTTGAAAAGCGAATTTTGATTTT
3178 GCAAACTTGTTTTGAAAAGCGAATTTTGATTTT
1 GCAAACTTGTTTTGAAAAGCGAATTTTGATTTT
3211 GCAAACTTGTTTTGAAAAGCGAATTTTGATTTT
1 GCAAACTTGTTTTGAAAAGCGAATTTTGATTTT
3244 G
1 G
3245 AACTCACAAA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 64 1.00
ACGTcount: A:0.29, C:0.11, G:0.19, T:0.41
Consensus pattern (33 bp):
GCAAACTTGTTTTGAAAAGCGAATTTTGATTTT
Found at i:3591 original size:8 final size:8
Alignment explanation
Indices: 3558--3582 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
3548 TCTCTTTTCA
3558 TCATTTTT
1 TCATTTTT
3566 TCATTTTT
1 TCATTTTT
3574 TCATTTTT
1 TCATTTTT
3582 T
1 T
3583 TGATTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (8 bp):
TCATTTTT
Found at i:4843 original size:19 final size:20
Alignment explanation
Indices: 4798--4845 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
4788 GATCTCATCT
*
4798 CATCTTTTTTGTTCAAAACA
1 CATCTTGTTTGTTCAAAACA
* *
4818 CA-ATTGTTTGTTCAAAAGA
1 CATCTTGTTTGTTCAAAACA
4837 -ATCTTGTTT
1 CATCTTGTTT
4846 TTATTTTTTC
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 1 0.04
19 20 0.87
20 2 0.09
ACGTcount: A:0.29, C:0.15, G:0.10, T:0.46
Consensus pattern (20 bp):
CATCTTGTTTGTTCAAAACA
Done.