Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015067.1 Corchorus olitorius cultivar O-4 contig15100, 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: 7566
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Found at i:684 original size:25 final size:24
Alignment explanation
Indices: 650--696 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
640 ACATTTGCAC
650 AAATACCTAAGAATTTGAATTAAAA
1 AAATACCTAAGAATTT-AATTAAAA
675 AAATACCTAAGAATTTAATTAA
1 AAATACCTAAGAATTTAATTAA
697 TGTAAGTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30
Consensus pattern (24 bp):
AAATACCTAAGAATTTAATTAAAA
Found at i:742 original size:39 final size:40
Alignment explanation
Indices: 687--767 Score: 128
Period size: 39 Copynumber: 2.0 Consensus size: 40
677 ATACCTAAGA
*
687 ATTTAATTAATGTAAGTATTTCAGTTATTA-TAATATTAC
1 ATTTAATTAATATAAGTATTTCAGTTATTATTAATATTAC
* *
726 ATTTAATTAATATAAGTATTTTAGTTATTATTTATATTAC
1 ATTTAATTAATATAAGTATTTCAGTTATTATTAATATTAC
766 AT
1 AT
768 CAGAATTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 28 0.74
40 10 0.26
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.52
Consensus pattern (40 bp):
ATTTAATTAATATAAGTATTTCAGTTATTATTAATATTAC
Found at i:1022 original size:2 final size:2
Alignment explanation
Indices: 1011--1058 Score: 53
Period size: 2 Copynumber: 24.5 Consensus size: 2
1001 AGTTTAGACT
* * * *
1011 TA TA TA -A TA TA TA GA TA TA GA TA TA GA TA GA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1052 TA TA TA T
1 TA TA TA T
1059 TGTACCCAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (2 bp):
TA
Found at i:1623 original size:12 final size:12
Alignment explanation
Indices: 1597--1632 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
1587 CTTTCTTTAG
1597 AATATATAA-AT
1 AATATATAATAT
1608 -ATATATAATAT
1 AATATATAATAT
1619 AATATATAATAT
1 AATATATAATAT
1631 AA
1 AA
1633 ACTAAGGCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 8 0.35
11 2 0.09
12 13 0.57
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
AATATATAATAT
Found at i:2075 original size:23 final size:24
Alignment explanation
Indices: 2041--2085 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
2031 TATGAGTTGA
*
2041 AATTTAAACTCATATT-AGACCTT
1 AATTTAAACTCAAATTCAGACCTT
*
2064 AATTTAATCTCAAATTCAGACC
1 AATTTAAACTCAAATTCAGACC
2086 ATTCTGTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.40, C:0.20, G:0.04, T:0.36
Consensus pattern (24 bp):
AATTTAAACTCAAATTCAGACCTT
Found at i:4999 original size:7 final size:7
Alignment explanation
Indices: 4987--5017 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
4977 TCCCGTCTTT
4987 TTTTTTC
1 TTTTTTC
4994 TTTTTTTC
1 -TTTTTTC
5002 TTTTTTC
1 TTTTTTC
5009 TTTTTTC
1 TTTTTTC
5016 TT
1 TT
5018 GTTATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 16 0.70
8 7 0.30
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTTTC
Found at i:4999 original size:8 final size:8
Alignment explanation
Indices: 4986--5014 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
4976 CTCCCGTCTT
4986 TTTTTTTC
1 TTTTTTTC
4994 TTTTTTTC
1 TTTTTTTC
5002 -TTTTTTC
1 TTTTTTTC
5009 TTTTTT
1 TTTTTT
5015 CTTGTTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTTTC
Found at i:5126 original size:22 final size:22
Alignment explanation
Indices: 5100--5175 Score: 68
Period size: 22 Copynumber: 3.5 Consensus size: 22
5090 AATTCATATT
5100 AAATTTTGATAATCACACTATA
1 AAATTTTGATAATCACACTATA
*
5122 AAA-TTT--TAATGACATCTATA
1 AAATTTTGATAATCACA-CTATA
* *
5142 TGTAATTTTGATAATCACACTATG
1 --AAATTTTGATAATCACACTATA
*
5166 AAATTCTGAT
1 AAATTTTGAT
5176 TACGACATCA
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
19 7 0.17
20 5 0.12
21 3 0.07
22 13 0.31
23 3 0.07
24 4 0.10
25 7 0.17
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39
Consensus pattern (22 bp):
AAATTTTGATAATCACACTATA
Found at i:5581 original size:42 final size:44
Alignment explanation
Indices: 5405--5547 Score: 286
Period size: 44 Copynumber: 3.2 Consensus size: 44
5395 CTCCATGTGG
5405 AATGTTGGTAAGCACACTACGAAATTTTGATCACCTTCCTATAA
1 AATGTTGGTAAGCACACTACGAAATTTTGATCACCTTCCTATAA
5449 AATGTTGGTAAGCACACTACGAAATTTTGATCACCTTCCTATAA
1 AATGTTGGTAAGCACACTACGAAATTTTGATCACCTTCCTATAA
5493 AATGTTGGTAAGCACACTACGAAATTTTGATCACCTTCCTATAA
1 AATGTTGGTAAGCACACTACGAAATTTTGATCACCTTCCTATAA
5537 AATGTTGGTAA
1 AATGTTGGTAA
5548 TCACTGTCAA
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 99 1.00
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (44 bp):
AATGTTGGTAAGCACACTACGAAATTTTGATCACCTTCCTATAA
Found at i:5609 original size:43 final size:40
Alignment explanation
Indices: 5556--5699 Score: 128
Period size: 43 Copynumber: 3.4 Consensus size: 40
5546 AATCACTGTC
* *
5556 AAATTGTGATAACCTCATTATAAAATTTTGATAAACCTCTG
1 AAATTTTGATAACCTC-TTATGAAATTTTGATAAACCTCTG
* *
5597 TAAAATTTTGATAACCCTCTTTTGAAATTTTGAT-AATCTCATG
1 --AAATTTTGATAA-CCTCTTATGAAATTTTGATAAACCTC-TG
* * * *
5640 AAATTTCGATAACCACCTAATGAAATTTTGATAACTAACCTATG
1 AAATTTTGATAACC-TCTTATGAAATTTTGAT-A--AACCTCTG
5684 AAATTTTGATAACCTC
1 AAATTTTGATAACCTC
5700 CCTATGAATA
Statistics
Matches: 82, Mismatches: 12, Indels: 14
0.76 0.11 0.13
Matches are distributed among these distances:
40 2 0.02
41 25 0.30
42 5 0.06
43 27 0.33
44 19 0.23
45 4 0.05
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (40 bp):
AAATTTTGATAACCTCTTATGAAATTTTGATAAACCTCTG
Found at i:5703 original size:22 final size:22
Alignment explanation
Indices: 5425--5829 Score: 145
Period size: 22 Copynumber: 18.7 Consensus size: 22
5415 AGCACACTAC
* *
5425 GAAATTTTGATCACCTTCCTAT
1 GAAATTTTGATAACCTCCCTAT
* * * * * * *
5447 AAAATGTTGGTAAGCACACTAC
1 GAAATTTTGATAACCTCCCTAT
* *
5469 GAAATTTTGATCACCTTCCTAT
1 GAAATTTTGATAACCTCCCTAT
* * * * * * *
5491 AAAATGTTGGTAAGCACACTAC
1 GAAATTTTGATAACCTCCCTAT
* *
5513 GAAATTTTGATCACCTTCCTAT
1 GAAATTTTGATAACCTCCCTAT
* * * * *
5535 AAAATGTTGGTAA--TCACTGT
1 GAAATTTTGATAACCTCCCTAT
* * **
5555 CAAATTGTGATAACCTCATTAT
1 GAAATTTTGATAACCTCCCTAT
* *
5577 AAAATTTTGATAAACCT--CTGT
1 GAAATTTTGAT-AACCTCCCTAT
* * *
5598 AAAATTTTGATAACC-CTCTTTT
1 GAAATTTTGATAACCTC-CCTAT
*
5620 GAAATTTTGATAA--TCTC-AT
1 GAAATTTTGATAACCTCCCTAT
* *
5639 GAAATTTCGATAACC-ACCTAAT
1 GAAATTTTGATAACCTCCCT-AT
*
5661 GAAATTTTGATAA-CTAACCTAT
1 GAAATTTTGATAACCT-CCCTAT
5683 GAAATTTTGATAACCTCCCTAT
1 GAAATTTTGATAACCTCCCTAT
* * * *
5705 G-AATATTCGATAACATCCTTAC
1 GAAAT-TTTGATAACCTCCCTAT
* * ** *
5727 GGAATTTTGTTAATTTTCCC-AC
1 GAAATTTTGATAA-CCTCCCTAT
* *
5749 GAAATTTTGAAAACCAT-ACTAT
1 GAAATTTTGATAACC-TCCCTAT
* *
5771 TAAATTTTGATAA-CTACACTAT
1 GAAATTTTGATAACCT-CCCTAT
** *
5793 GAAATTACGATAACTTCCCTAT
1 GAAATTTTGATAACCTCCCTAT
*
5815 GTAATTTTGATAACC
1 GAAATTTTGATAACC
5830 AAACTATCAA
Statistics
Matches: 270, Mismatches: 91, Indels: 44
0.67 0.22 0.11
Matches are distributed among these distances:
19 13 0.05
20 19 0.07
21 20 0.07
22 200 0.74
23 18 0.07
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.36
Consensus pattern (22 bp):
GAAATTTTGATAACCTCCCTAT
Found at i:5821 original size:88 final size:88
Alignment explanation
Indices: 5661--5823 Score: 206
Period size: 88 Copynumber: 1.9 Consensus size: 88
5651 ACCACCTAAT
* * * *
5661 GAAATTTTGATAACTAACCTATGAAATTTTGATAACCTCCCTATGAATATTCGATAACATCCTTA
1 GAAATTTTGAAAACCAACCTATGAAATTTTGATAACCTCACTATGAATATTCGATAACATCCCTA
5726 CGGAATTTTGTTAATTTTCCCAC
66 CGGAATTTTGTTAATTTTCCCAC
* *
5749 GAAATTTTGAAAACCATA-CTATTAAATTTTGATAA-CTACACTATGAA-ATTACGATAACTTCC
1 GAAATTTTGAAAACCA-ACCTATGAAATTTTGATAACCT-CACTATGAATATT-CGATAACATCC
* *
5811 CTATGTAATTTTG
63 CTACGGAATTTTG
5824 ATAACCAAAC
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
87 5 0.08
88 58 0.91
89 1 0.02
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (88 bp):
GAAATTTTGAAAACCAACCTATGAAATTTTGATAACCTCACTATGAATATTCGATAACATCCCTA
CGGAATTTTGTTAATTTTCCCAC
Found at i:5935 original size:22 final size:22
Alignment explanation
Indices: 5903--5969 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
5893 ATAACATCCC
*
5903 TCTTAAAAACCACACTATAAAA
1 TCTTAATAACCACACTATAAAA
* *
5925 TCTTAATAACCACATTATGAAA
1 TCTTAATAACCACACTATAAAA
* * *
5947 TCTTGATAATCACACAATAAAA
1 TCTTAATAACCACACTATAAAA
5969 T
1 T
5970 TTAGATCATC
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.49, C:0.19, G:0.03, T:0.28
Consensus pattern (22 bp):
TCTTAATAACCACACTATAAAA
Found at i:7543 original size:2 final size:2
Alignment explanation
Indices: 7536--7564 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
7526 CCGTAAAGTG
7536 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
7565 CT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.