Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020918.1 Corchorus olitorius cultivar O-4 contig20951, 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: 14659
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:207 original size:46 final size:42
Alignment explanation
Indices: 130--224 Score: 111
Period size: 46 Copynumber: 2.2 Consensus size: 42
120 AATCAACAAT
* *
130 AATATTAGCTTTATTTTGAAGAATTATCTAGAGATAGAGGAGTAG
1 AATATTAGCTTAATTTTGAAGAATTACCTAGAGAT---GGAGTAG
* *
175 AATATTAGCTCTAATTTTGATGTATTACCTAGAGATGGAGTAG
1 AATATTAGCT-TAATTTTGAAGAATTACCTAGAGATGGAGTAG
218 AAT-TTAG
1 AATATTAG
225 GTAATGCACT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
42 4 0.09
43 10 0.22
45 10 0.22
46 21 0.47
ACGTcount: A:0.36, C:0.06, G:0.21, T:0.37
Consensus pattern (42 bp):
AATATTAGCTTAATTTTGAAGAATTACCTAGAGATGGAGTAG
Found at i:607 original size:30 final size:30
Alignment explanation
Indices: 571--631 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
561 GAAGTTCGTG
* *
571 ATTGAAGATTTATTGAA-TATAATTTCAAGA
1 ATTGAAGA-CTATTGAAGAATAATTTCAAGA
*
601 ATTGAAGACTATTGAAGAATTATTTCAAGA
1 ATTGAAGACTATTGAAGAATAATTTCAAGA
631 A
1 A
632 GCAAGAATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 7 0.26
30 20 0.74
ACGTcount: A:0.44, C:0.05, G:0.15, T:0.36
Consensus pattern (30 bp):
ATTGAAGACTATTGAAGAATAATTTCAAGA
Found at i:1778 original size:16 final size:17
Alignment explanation
Indices: 1757--1789 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1747 CTATGCTTTA
1757 TTTTAATTGCT-TTCTT
1 TTTTAATTGCTATTCTT
1773 TTTTAATTGCTATTCTT
1 TTTTAATTGCTATTCTT
1790 AATCCCCTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.15, C:0.12, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTTAATTGCTATTCTT
Found at i:2070 original size:24 final size:25
Alignment explanation
Indices: 2020--2070 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
2010 TTTGTATTTT
*
2020 TTAAAAAAAATTCTCTTTCTTTGCG
1 TTAAAAAAAATTCTCTTTCTTTCCG
2045 TTAAAAAAAATT-TCTTAT-TTTCCG
1 TTAAAAAAAATTCTCTT-TCTTTCCG
2069 TT
1 TT
2071 TTTAACTACT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 11 0.46
25 13 0.54
ACGTcount: A:0.33, C:0.14, G:0.06, T:0.47
Consensus pattern (25 bp):
TTAAAAAAAATTCTCTTTCTTTCCG
Found at i:4769 original size:21 final size:21
Alignment explanation
Indices: 4739--4779 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
4729 GGCCGACTAT
*
4739 GGCCTGGCCATCCGCACACCA
1 GGCCTAGCCATCCGCACACCA
*
4760 GGCCTAGCCATCCGCGCACC
1 GGCCTAGCCATCCGCACACC
4780 TTGCCCGACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.49, G:0.24, T:0.10
Consensus pattern (21 bp):
GGCCTAGCCATCCGCACACCA
Found at i:4947 original size:21 final size:20
Alignment explanation
Indices: 4897--4947 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
4887 GCCGAGACAG
*
4897 GACCGGCCATGTCCGCACCA
1 GACCAGCCATGTCCGCACCA
* *
4917 GTCCATGCCATGTCCGCGCCAA
1 GACCA-GCCATGTCCGCACC-A
4939 GACCAGCCA
1 GACCAGCCA
4948 CCACCGGCCA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 3 0.12
21 17 0.68
22 5 0.20
ACGTcount: A:0.22, C:0.43, G:0.24, T:0.12
Consensus pattern (20 bp):
GACCAGCCATGTCCGCACCA
Found at i:8831 original size:78 final size:78
Alignment explanation
Indices: 8696--8851 Score: 240
Period size: 78 Copynumber: 2.0 Consensus size: 78
8686 TTTTTTCCAG
* * *
8696 CACAAAAATCTCAACCAACTCACTTCACTTCCCTATGAATACCGTACTACACCAGACCTCAAATC
1 CACAAAAATCTCAACCAACTAACTTCACTTCACTATGAATACCCTACTACACCAGACCTCAAATC
8761 ACACCTCAAACAA
66 ACACCTCAAACAA
* * * * *
8774 CACATAAATCTCAACCGACTAACTTCACTTCACTATGAATACCCTACTGCACTAGACCTCTAATC
1 CACAAAAATCTCAACCAACTAACTTCACTTCACTATGAATACCCTACTACACCAGACCTCAAATC
8839 ACACCTCAAACAA
66 ACACCTCAAACAA
8852 TCATTTCTTC
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
78 70 1.00
ACGTcount: A:0.38, C:0.36, G:0.04, T:0.21
Consensus pattern (78 bp):
CACAAAAATCTCAACCAACTAACTTCACTTCACTATGAATACCCTACTACACCAGACCTCAAATC
ACACCTCAAACAA
Done.