Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023986.1 Corchorus olitorius cultivar O-4 contig24019, 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: 40070
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Found at i:1162 original size:25 final size:25
Alignment explanation
Indices: 1128--1179 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
1118 GGACTCAATA
1128 CTGAGCCCAAAAGCAAATGTAACTT
1 CTGAGCCCAAAAGCAAATGTAACTT
1153 CTGAGCCCAAAAGCAAATGTAACTT
1 CTGAGCCCAAAAGCAAATGTAACTT
1178 CT
1 CT
1180 AATAATGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.38, C:0.25, G:0.15, T:0.21
Consensus pattern (25 bp):
CTGAGCCCAAAAGCAAATGTAACTT
Found at i:8274 original size:2 final size:2
Alignment explanation
Indices: 8269--8307 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
8259 GGATTTTTTG
8269 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
8308 AGAGTTTAGG
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:10549 original size:27 final size:27
Alignment explanation
Indices: 10488--10543 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
10478 TTTTTTTAAT
10488 CTCTCCCTCAAAACTTACCAACTAAAA
1 CTCTCCCTCAAAACTTACCAACTAAAA
*
10515 CTCTCCCTCAAAACTTACCAGCTAAAA
1 CTCTCCCTCAAAACTTACCAACTAAAA
10542 CT
1 CT
10544 ACCCCTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.38, C:0.38, G:0.02, T:0.23
Consensus pattern (27 bp):
CTCTCCCTCAAAACTTACCAACTAAAA
Found at i:10719 original size:18 final size:19
Alignment explanation
Indices: 10696--10732 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 19
10686 GTGCCCTTGG
10696 TTTGTTTTT-TTTGGCATT
1 TTTGTTTTTATTTGGCATT
10714 TTTGTTTTTAGTTTGGCAT
1 TTTGTTTTTA-TTTGGCAT
10733 GCTAGTTTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
20 8 0.47
ACGTcount: A:0.08, C:0.05, G:0.19, T:0.68
Consensus pattern (19 bp):
TTTGTTTTTATTTGGCATT
Found at i:12307 original size:15 final size:16
Alignment explanation
Indices: 12279--12315 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
12269 CTTTGAAGTT
12279 TTTTTATCTAATTATC
1 TTTTTATCTAATTATC
*
12295 TTTTTATCT-ATTATT
1 TTTTTATCTAATTATC
12310 TTTTTA
1 TTTTTA
12316 ATTTTAAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTTATCTAATTATC
Found at i:29218 original size:2 final size:2
Alignment explanation
Indices: 29213--29240 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
29203 TCTGTTCACC
29213 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
29241 TCCCTCAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:29901 original size:1 final size:1
Alignment explanation
Indices: 29897--29922 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
29887 TGTTTCCTTG
29897 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
29923 ATACCATTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.