Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016116.1 Corchorus olitorius cultivar O-4 contig16149, 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: 15654
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.28
Found at i:1803 original size:14 final size:14
Alignment explanation
Indices: 1778--1816 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
1768 AATTTGTCAT
1778 GAGAAA-TAAAAAA
1 GAGAAATTAAAAAA
*
1791 GATAAATTAAAAAA
1 GAGAAATTAAAAAA
*
1805 GAGAAATGAAAA
1 GAGAAATTAAAA
1817 TTTGTTTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 5 0.23
14 17 0.77
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.13
Consensus pattern (14 bp):
GAGAAATTAAAAAA
Found at i:13988 original size:38 final size:38
Alignment explanation
Indices: 13914--14025 Score: 138
Period size: 38 Copynumber: 2.9 Consensus size: 38
13904 TCTTTATCTT
* * *
13914 AGTAAACCTGCTTAGGTC-CCATTTAGAGT-TGCCATTTA
1 AGTAAACCTGCTTAGGTCTACGTTTAGAATCT--CATTTA
13952 AGTAAACCTGCTTAGGTCTACGTTTAGAATCTCATTTA
1 AGTAAACCTGCTTAGGTCTACGTTTAGAATCTCATTTA
* * *
13990 AGGAAACCTGTTTAGGTCTATGTTTAGAATCTCATT
1 AGTAAACCTGCTTAGGTCTACGTTTAGAATCTCATT
14026 AGAATTTTTG
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
38 57 0.86
39 8 0.12
40 1 0.02
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.37
Consensus pattern (38 bp):
AGTAAACCTGCTTAGGTCTACGTTTAGAATCTCATTTA
Found at i:14105 original size:38 final size:39
Alignment explanation
Indices: 14024--14173 Score: 194
Period size: 39 Copynumber: 3.9 Consensus size: 39
14014 TAGAATCTCA
** * * ** *
14024 TTAGAATTTTTGTTTAAGAAAACCTGCTTAGCTCCCCGC
1 TTAGAATTTCCGTTTAAGCAAACCTGCTTAGGTCCTTGT
* * **
14063 TTAGAATCT-CGTTTGATTAAACCTGCTTAGGTCCTTGT
1 TTAGAATTTCCGTTTAAGCAAACCTGCTTAGGTCCTTGT
14101 TTAGAATTTCCGTTTAAGCAAACCTGCTTAGGTCCTTGT
1 TTAGAATTTCCGTTTAAGCAAACCTGCTTAGGTCCTTGT
14140 TTAGAATTTCCGTTTAAGCAAACCTGCTTAGGTC
1 TTAGAATTTCCGTTTAAGCAAACCTGCTTAGGTC
14174 TCTGTTCCGT
Statistics
Matches: 97, Mismatches: 13, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
38 29 0.30
39 68 0.70
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (39 bp):
TTAGAATTTCCGTTTAAGCAAACCTGCTTAGGTCCTTGT
Found at i:14439 original size:39 final size:38
Alignment explanation
Indices: 14177--14669 Score: 245
Period size: 39 Copynumber: 12.9 Consensus size: 38
14167 TTAGGTCTCT
* * *
14177 GTTCCGTTTAAGTAAACCTGTTTAGGACTTCTGCTTT-GA
1 GTTCCATTTAAGTAAACCTGCTTAGGTC-TCTG-TTTAGA
** *
14216 GTT-CATTCGAGTAAACCTGCTTAGGTCT-TCGTTTAAAA
1 GTTCCATTTAAGTAAACCTGCTTAGGTCTCT-GTTT-AGA
* ** * * *
14254 GTTTCGCTTAA-TCAAACCCGCTTAGGTTTTTGTTTAGA
1 GTTCCATTTAAGT-AAACCTGCTTAGGTCTCTGTTTAGA
* ** * * * *
14292 ATTCCCGCTTAAGTGAACCTGCTTAAGTCTATGCTTAGA
1 GTT-CCATTTAAGTAAACCTGCTTAGGTCTCTGTTTAGA
* * * * * *
14331 GTTTCGTTCAA-TCAAACCTGCTTAGGTCCCTCTTTATA
1 GTTCCATTTAAGT-AAACCTGCTTAGGTCTCTGTTTAGA
* * * * * * **
14369 GTCTCGC-CTT-AGAAAAATCTGATCATGTCTCTACTTAGA
1 GT-TC-CATTTAAG-TAAACCTGCTTAGGTCTCTGTTTAGA
* *
14408 GTTCCATTTAAGAAAACCTGCTTAGGATCTCTGTCTAGA
1 GTTCCATTTAAGTAAACCTGCTTAGG-TCTCTGTTTAGA
* * * * * * *
14447 GTTTCGTTTAAGGAAACCTGCTTAGGTATTTATTTAAA
1 GTTCCATTTAAGTAAACCTGCTTAGGTCTCTGTTTAGA
* * *
14485 GTTCCACTT--G--AATCTACTTAGGTCTCTGTTTAGA
1 GTTCCATTTAAGTAAACCTGCTTAGGTCTCTGTTTAGA
* *
14519 GTTTCCAGTTAAGTAAACCTACTTAGGTCTCTGTTTAGA
1 G-TTCCATTTAAGTAAACCTGCTTAGGTCTCTGTTTAGA
* * ** * *
14558 ATTTCATTCGAGTAAACTTGCTTAGGTCTCTGCTTAGA
1 GTTCCATTTAAGTAAACCTGCTTAGGTCTCTGTTTAGA
* * * **
14596 GTTGCCATTTGAGAAAACTTGCTTAGGAATC-GTTTAGA
1 GTT-CCATTTAAGTAAACCTGCTTAGGTCTCTGTTTAGA
*
14634 GTTTCCATTTAAGTAAACCTACTTAGGTCTCTGTTT
1 G-TTCCATTTAAGTAAACCTGCTTAGGTCTCTGTTT
14670 CGAACTTTCG
Statistics
Matches: 338, Mismatches: 92, Indels: 48
0.71 0.19 0.10
Matches are distributed among these distances:
34 19 0.06
35 7 0.02
36 5 0.01
37 5 0.01
38 141 0.42
39 158 0.47
40 3 0.01
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.38
Consensus pattern (38 bp):
GTTCCATTTAAGTAAACCTGCTTAGGTCTCTGTTTAGA
Found at i:14596 original size:77 final size:77
Alignment explanation
Indices: 14498--14666 Score: 196
Period size: 77 Copynumber: 2.2 Consensus size: 77
14488 CCACTTGAAT
* * * **
14498 CTACTTAGGTCTCTGTTTAGAGTTTCCAGTTAAGTAAACCTACTTAGGTCTCTGTTTAGAATTT-
1 CTACTTAGGTCTCTGCTTAGAGTTGCCAGTTAAGAAAACCTACTTAGGAATC-GTTTAGAATTTC
*
14562 CATTCGAGTAAAC
65 CATTCAAGTAAAC
* * * * * * *
14575 TTGCTTAGGTCTCTGCTTAGAGTTGCCATTTGAGAAAACTTGCTTAGGAATCGTTTAGAGTTTCC
1 CTACTTAGGTCTCTGCTTAGAGTTGCCAGTTAAGAAAACCTACTTAGGAATCGTTTAGAATTTCC
*
14640 ATTTAAGTAAAC
66 ATTCAAGTAAAC
14652 CTACTTAGGTCTCTG
1 CTACTTAGGTCTCTG
14667 TTTCGAACTT
Statistics
Matches: 75, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
76 10 0.13
77 65 0.87
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (77 bp):
CTACTTAGGTCTCTGCTTAGAGTTGCCAGTTAAGAAAACCTACTTAGGAATCGTTTAGAATTTCC
ATTCAAGTAAAC
Found at i:14684 original size:25 final size:25
Alignment explanation
Indices: 14656--14708 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
14646 GTAAACCTAC
*
14656 TTAGGTCTCTGTTTCGAACTTTCGT
1 TTAGGTCTCTGTTTAGAACTTTCGT
**
14681 TTAGGTCTCTGTTTAGAGTTTTCGT
1 TTAGGTCTCTGTTTAGAACTTTCGT
14706 TTA
1 TTA
14709 AGTTAACCTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.13, C:0.15, G:0.21, T:0.51
Consensus pattern (25 bp):
TTAGGTCTCTGTTTAGAACTTTCGT
Found at i:14696 original size:64 final size:64
Alignment explanation
Indices: 14627--14747 Score: 163
Period size: 64 Copynumber: 1.9 Consensus size: 64
14617 CTTAGGAATC
* * *
14627 GTTTAGAGTTTCCATTTAAGTAAACCTACTTAGGTCTCTGTTTCGAACTTT-CGTTTAGGTCTCT
1 GTTTAGAGTTTCCATTTAAGTAAACCTACTTAAGTCTCTATTTAGAA-TTTCCGTTTAGGTCTCT
* * * *
14691 GTTTAGAGTTTTCGTTTAAGTTAACCTGCTTAAGTCTCTATTTAGAATTTCCGTTTA
1 GTTTAGAGTTTCCATTTAAGTAAACCTACTTAAGTCTCTATTTAGAATTTCCGTTTA
14748 AGTGAACATG
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
63 3 0.06
64 46 0.94
ACGTcount: A:0.21, C:0.17, G:0.17, T:0.45
Consensus pattern (64 bp):
GTTTAGAGTTTCCATTTAAGTAAACCTACTTAAGTCTCTATTTAGAATTTCCGTTTAGGTCTCT
Found at i:14767 original size:39 final size:38
Alignment explanation
Indices: 14681--14785 Score: 115
Period size: 39 Copynumber: 2.7 Consensus size: 38
14671 GAACTTTCGT
* * *
14681 TTAGGTCTCTGTTTAGAGTTTTCGTTTAAGTTAACCTGC
1 TTAGGTCTCTATTTAGAG-TTTCGTTTAAGTGAACATGC
* *
14720 TTAAGTCTCTATTTAGAATTTCCGTTTAAGTGAACATG-
1 TTAGGTCTCTATTTAGAGTTT-CGTTTAAGTGAACATGC
14758 TGTAGGTCTCTGA-TTAGAGTTTCGTTTA
1 T-TAGGTCTCT-ATTTAGAGTTTCGTTTA
14786 GAAACTTGTG
Statistics
Matches: 56, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
38 10 0.18
39 45 0.80
40 1 0.02
ACGTcount: A:0.22, C:0.13, G:0.20, T:0.45
Consensus pattern (38 bp):
TTAGGTCTCTATTTAGAGTTTCGTTTAAGTGAACATGC
Found at i:14874 original size:34 final size:34
Alignment explanation
Indices: 14828--14893 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
14818 CATTTTGGGA
*
14828 AAACCTGTTTAGGTCTCTGTTTAGAGCTTCGTAT
1 AAACCTGCTTAGGTCTCTGTTTAGAGCTTCGTAT
* *
14862 AAACCTGCTTAGGTCTTTGTTTAGAGTTTCGT
1 AAACCTGCTTAGGTCTCTGTTTAGAGCTTCGT
14894 TCAGAAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.20, C:0.17, G:0.21, T:0.42
Consensus pattern (34 bp):
AAACCTGCTTAGGTCTCTGTTTAGAGCTTCGTAT
Done.