Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012086.1 Corchorus olitorius cultivar O-4 contig12119, 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: 22230
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.36
Found at i:2088 original size:20 final size:20
Alignment explanation
Indices: 2060--2113 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
2050 GTGGCTTTTT
*
2060 TTTTCCTTTTCTTCTTTTTCA
1 TTTT-CTTTTCCTCTTTTTCA
*
2081 TTTTCTTTTCCT-TTTTTCC
1 TTTTCTTTTCCTCTTTTTCA
2100 TTTT-TTTTCCTCTT
1 TTTTCTTTTCCTCTT
2114 CTCCTTCTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 7 0.23
19 12 0.40
20 7 0.23
21 4 0.13
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTCTTTTCCTCTTTTTCA
Found at i:2091 original size:26 final size:26
Alignment explanation
Indices: 2055--2104 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
2045 CTGACGTGGC
*
2055 TTTTTTTTTCCTTTTCTT-CTTTTTCA
1 TTTTCTTTTCCTTTT-TTCCTTTTTCA
2081 TTTTCTTTTCCTTTTTTCCTTTTT
1 TTTTCTTTTCCTTTTTTCCTTTTT
2105 TTTCCTCTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 2 0.09
26 20 0.91
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (26 bp):
TTTTCTTTTCCTTTTTTCCTTTTTCA
Found at i:2113 original size:26 final size:25
Alignment explanation
Indices: 2055--2126 Score: 67
Period size: 26 Copynumber: 2.8 Consensus size: 25
2045 CTGACGTGGC
*
2055 TTTTTTTTTCCTTTTCTT-CTTTTTCA
1 TTTTCTTTTCCTTTT-TTCCTTTTT-A
2081 TTTTCTTTTCCTTTTTTCCTTTTT-
1 TTTTCTTTTCCTTTTTTCCTTTTTA
* *
2105 TTTCCTCTTCTCCTTCTTTCCT
1 TTT--TCTTTTCCTTTTTTCCT
2127 AACCTGAAAC
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
24 3 0.08
25 2 0.05
26 35 0.88
ACGTcount: A:0.01, C:0.26, G:0.00, T:0.72
Consensus pattern (25 bp):
TTTTCTTTTCCTTTTTTCCTTTTTA
Found at i:2118 original size:18 final size:19
Alignment explanation
Indices: 2081--2119 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
2071 TTCTTTTTCA
* *
2081 TTTTCTTTTCCTTTTTTCC
1 TTTTCTTTTCCTCTTCTCC
2100 TTTT-TTTTCCTCTTCTCC
1 TTTTCTTTTCCTCTTCTCC
2118 TT
1 TT
2120 CTTTCCTAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTCTTTTCCTCTTCTCC
Found at i:3548 original size:26 final size:26
Alignment explanation
Indices: 3519--3568 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
3509 GATACTGTAG
3519 AAATTAAAATTTTCTAAATAAAATTA
1 AAATTAAAATTTTCTAAATAAAATTA
* *
3545 AAATTGAATTTTTCTAAATAAAAT
1 AAATTAAAATTTTCTAAATAAAAT
3569 ATTTTAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (26 bp):
AAATTAAAATTTTCTAAATAAAATTA
Found at i:6233 original size:2 final size:2
Alignment explanation
Indices: 6226--6264 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
6216 AATGGGTAGG
6226 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6265 AAGTGATTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12923 original size:14 final size:15
Alignment explanation
Indices: 12898--12926 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
12888 GGTATGGTAG
12898 AAATAGAAATTTTAT
1 AAATAGAAATTTTAT
12913 AAATA-AAATTTTAT
1 AAATAGAAATTTTAT
12927 GTTGTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.41
Consensus pattern (15 bp):
AAATAGAAATTTTAT
Found at i:15919 original size:13 final size:13
Alignment explanation
Indices: 15901--15926 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
15891 ATTAGTGTCA
15901 AATGTGTTATAAT
1 AATGTGTTATAAT
15914 AATGTGTTATAAT
1 AATGTGTTATAAT
15927 TCATTCTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (13 bp):
AATGTGTTATAAT
Found at i:18318 original size:25 final size:25
Alignment explanation
Indices: 18284--18334 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
18274 TGCTACTATT
18284 TTACTTTGCAAAATTACCTCTTCAA
1 TTACTTTGCAAAATTACCTCTTCAA
*
18309 TTACTTTGCAAAATTATCTCTTCAA
1 TTACTTTGCAAAATTACCTCTTCAA
18334 T
1 T
18335 AATAAGATCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.31, C:0.22, G:0.04, T:0.43
Consensus pattern (25 bp):
TTACTTTGCAAAATTACCTCTTCAA
Found at i:18786 original size:40 final size:39
Alignment explanation
Indices: 18717--18797 Score: 101
Period size: 40 Copynumber: 2.1 Consensus size: 39
18707 TGAGAGAAAG
*
18717 TTCGAGCAAAGGTTCTCTGCAAATTAAATGGTTCTCCAAA
1 TTCGAGCAAAGGTTCTCTGCAAATCAAATGG-TCTCCAAA
** *
18757 TTCGAGCAAAGGTTCATC-GCCGATCAAATGGTCTGCAAA
1 TTCGAGCAAAGGTTC-TCTGCAAATCAAATGGTCTCCAAA
18796 TT
1 TT
18798 AAAGGTTAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
39 9 0.25
40 25 0.69
41 2 0.06
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (39 bp):
TTCGAGCAAAGGTTCTCTGCAAATCAAATGGTCTCCAAA
Done.