Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012400.1 Corchorus olitorius cultivar O-4 contig12433, 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: 35646
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.32
Found at i:2255 original size:38 final size:38
Alignment explanation
Indices: 2159--2306 Score: 235
Period size: 38 Copynumber: 3.9 Consensus size: 38
2149 GGCTGTGCAT
*
2159 AGTGGACCCGTACCTCAGGGGGTTAAACTGATGGTAAAG
1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGT-AAG
* *
2198 AGTGGACCCATACCACAGGGGGTTAAACTGTTGGTAAG
1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGTAAG
*
2236 AGTGGACCCGTACCTCAGGGAGTTAAACTGTTGGTAAG
1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGTAAG
*
2274 AGTGGACCCGTGCCTCAGGGGGTT-AACTGTTGG
1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGG
2307 CTAGACTCGA
Statistics
Matches: 101, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
37 9 0.09
38 60 0.59
39 32 0.32
ACGTcount: A:0.25, C:0.19, G:0.34, T:0.22
Consensus pattern (38 bp):
AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGTAAG
Found at i:5802 original size:38 final size:38
Alignment explanation
Indices: 5704--5853 Score: 212
Period size: 38 Copynumber: 3.9 Consensus size: 38
5694 GGCTGTGCAT
*
5704 AGTGGACCCGTACCTCAGGGGGGGTTAAACTGATGGTAAAG
1 AGTGGACCCGTACCTCA--GGGGGTTAAACTGTTGGT-AAG
* * *
5745 AGTGGACTCATACCACAGGGGGTTAAACTGTTGGTAAG
1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGTAAG
*
5783 AGTGGACCCGTACCTCAGGGAGTTAAACTGTTGGTAAG
1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGTAAG
*
5821 AGTGGACCCGTGCCTCAGGGGGTT-AACTGTTGG
1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGG
5854 CTAGACTCGA
Statistics
Matches: 99, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
37 9 0.09
38 59 0.60
39 17 0.17
41 14 0.14
ACGTcount: A:0.25, C:0.18, G:0.35, T:0.23
Consensus pattern (38 bp):
AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGTAAG
Found at i:9294 original size:39 final size:38
Alignment explanation
Indices: 9250--9397 Score: 208
Period size: 38 Copynumber: 3.9 Consensus size: 38
9240 GGCTGTGCAT
*
9250 AGTGGACCCGTACCTCAGGGGGTTAAACTGATGGTAAAG
1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGT-AAG
* * *
9289 AGTGGACCCATACCACAGGGGGTTAAACTGTTGGCAAG
1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGTAAG
* * *
9327 AGTGGACCCGTGCCTCAGGGAGTTAAACCGTTGGTAAG
1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGTAAG
*
9365 AGTGGACCCGTGCCTCAGGGGGTT-AACTGTTGG
1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGG
9398 CTAGACTCGA
Statistics
Matches: 97, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
37 8 0.08
38 58 0.60
39 31 0.32
ACGTcount: A:0.24, C:0.20, G:0.34, T:0.21
Consensus pattern (38 bp):
AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGTAAG
Found at i:11959 original size:38 final size:38
Alignment explanation
Indices: 11863--12010 Score: 235
Period size: 38 Copynumber: 3.9 Consensus size: 38
11853 GGCTGTGCAT
*
11863 AGTGGACCCGTACCTCAGGGGGTTAAACTGATGGTAAAG
1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGT-AAG
* *
11902 AGTGGACCCATACCACAGGGGGTTAAACTGTTGGTAAG
1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGTAAG
*
11940 AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGGTAAG
1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGTAAG
*
11978 AGTGGACCCGTGCCTCAGGGGGTT-AACTGTTGG
1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGG
12011 CTAGACTCGA
Statistics
Matches: 103, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
37 9 0.09
38 62 0.60
39 32 0.31
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (38 bp):
AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGTAAG
Found at i:12050 original size:6 final size:6
Alignment explanation
Indices: 12040--12095 Score: 94
Period size: 6 Copynumber: 9.3 Consensus size: 6
12030 CGTTAACGGA
* *
12040 TGATTA TGATTG TGATTG TGATTG TGATTG TGATTG TGATTG TGATTA
1 TGATTG TGATTG TGATTG TGATTG TGATTG TGATTG TGATTG TGATTG
12088 TGATTG TG
1 TGATTG TG
12096 GTGCAGCCTG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.20, C:0.00, G:0.30, T:0.50
Consensus pattern (6 bp):
TGATTG
Found at i:14915 original size:17 final size:17
Alignment explanation
Indices: 14886--14924 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
14876 GTTTGGTTCC
*
14886 CTTTTCTTTCATG-TTT
1 CTTTTCTTGCATGTTTT
14902 CTTTGTCTTGCATGTTTT
1 CTTT-TCTTGCATGTTTT
14920 CTTTT
1 CTTTT
14925 ATTTGTTTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 4 0.20
17 9 0.45
18 7 0.35
ACGTcount: A:0.05, C:0.18, G:0.10, T:0.67
Consensus pattern (17 bp):
CTTTTCTTGCATGTTTT
Found at i:17494 original size:21 final size:21
Alignment explanation
Indices: 17465--17506 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
17455 TCCTTTGCTT
*
17465 ATGATCTCCGAT-GCTCTTCAA
1 ATGAACTCCGATGGC-CTTCAA
17486 ATGAACTCCGATGGCCTTCAA
1 ATGAACTCCGATGGCCTTCAA
17507 GTCTTCAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGAACTCCGATGGCCTTCAA
Found at i:18891 original size:21 final size:21
Alignment explanation
Indices: 18865--18909 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
18855 TCCAATCAAC
*
18865 CAAGAACTCTAATTTTGAACT
1 CAAGAACCCTAATTTTGAACT
*
18886 CAAGAACCCTAATTTTGAATT
1 CAAGAACCCTAATTTTGAACT
18907 CAA
1 CAA
18910 TGAGCTCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (21 bp):
CAAGAACCCTAATTTTGAACT
Found at i:20277 original size:21 final size:21
Alignment explanation
Indices: 20251--20292 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
20241 CGATATCTCC
20251 ATGATCTTCATGCTTCTCCAT
1 ATGATCTTCATGCTTCTCCAT
20272 ATGATCTTCATGCTTCTCCAT
1 ATGATCTTCATGCTTCTCCAT
20293 TCTTCCTTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.29, G:0.10, T:0.43
Consensus pattern (21 bp):
ATGATCTTCATGCTTCTCCAT
Found at i:26927 original size:17 final size:17
Alignment explanation
Indices: 26905--26939 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
26895 ATGCTGAGTC
26905 AGAGTTAGACGTGGATA
1 AGAGTTAGACGTGGATA
26922 AGAGTTAGACGTGGATA
1 AGAGTTAGACGTGGATA
26939 A
1 A
26940 CACGTGTGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.37, C:0.06, G:0.34, T:0.23
Consensus pattern (17 bp):
AGAGTTAGACGTGGATA
Found at i:33523 original size:17 final size:17
Alignment explanation
Indices: 33493--33530 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
33483 CTTATCAACA
*
33493 GCAAATACAAAGTCAAG
1 GCAAACACAAAGTCAAG
*
33510 GCAAACACAGAGTCAAG
1 GCAAACACAAAGTCAAG
33527 GCAA
1 GCAA
33531 GTCAAGTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.21, G:0.21, T:0.08
Consensus pattern (17 bp):
GCAAACACAAAGTCAAG
Done.