Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019094.1 Corchorus olitorius cultivar O-4 contig19127, 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: 13752
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.37
Found at i:1104 original size:18 final size:18
Alignment explanation
Indices: 1083--1117 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1073 AAGGTGATTT
1083 GGTGCCACAACATCATTA
1 GGTGCCACAACATCATTA
* *
1101 GGTGCCATATCATCATT
1 GGTGCCACAACATCATT
1118 GCTGACAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.29
Consensus pattern (18 bp):
GGTGCCACAACATCATTA
Found at i:1992 original size:23 final size:25
Alignment explanation
Indices: 1953--2001 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
1943 TATTTTGGCC
*
1953 TTTTATGGTGTATG-TTTAATAATT
1 TTTTATGGTGTACGTTTTAATAATT
*
1977 TTTTATGGTGT-CGTTTTACTAATT
1 TTTTATGGTGTACGTTTTAATAATT
2001 T
1 T
2002 ATGTTATATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 21 0.95
ACGTcount: A:0.20, C:0.04, G:0.16, T:0.59
Consensus pattern (25 bp):
TTTTATGGTGTACGTTTTAATAATT
Found at i:5311 original size:29 final size:28
Alignment explanation
Indices: 5268--5330 Score: 108
Period size: 29 Copynumber: 2.2 Consensus size: 28
5258 TTTCGAATAT
*
5268 ATATATATATATATATATATATATTAGA
1 ATATATATATATATATAAATATATTAGA
5296 ATTATATATATATATATAAATATATTAGA
1 A-TATATATATATATATAAATATATTAGA
5325 ATATAT
1 ATATAT
5331 TAGAATTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
28 6 0.18
29 27 0.82
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (28 bp):
ATATATATATATATATAAATATATTAGA
Found at i:5327 original size:10 final size:10
Alignment explanation
Indices: 5286--5336 Score: 54
Period size: 10 Copynumber: 5.2 Consensus size: 10
5276 ATATATATAT
5286 ATATATTAGA
1 ATATATTAGA
*
5296 AT-TATATA-T
1 ATATAT-TAGA
5305 ATATATATA-A
1 ATATAT-TAGA
5315 ATATATTAGA
1 ATATATTAGA
5325 ATATATTAGA
1 ATATATTAGA
5335 AT
1 AT
5337 TTTTAAATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
9 7 0.19
10 29 0.81
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (10 bp):
ATATATTAGA
Found at i:5330 original size:2 final size:2
Alignment explanation
Indices: 5264--5320 Score: 75
Period size: 2 Copynumber: 30.0 Consensus size: 2
5254 GGTTTTTCGA
*
5264 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AG A- AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
5303 AT AT AT AT AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT
5321 TAGAATATAT
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
1 3 0.06
2 46 0.94
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:6887 original size:4 final size:4
Alignment explanation
Indices: 6870--6921 Score: 68
Period size: 4 Copynumber: 13.0 Consensus size: 4
6860 ATCGAACAAC
* * * *
6870 ATAT ATAA ATAT ATAT ATAT ATAA ATAT ATAT ATAT ATAT ACAT ACAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
6918 ATAT
1 ATAT
6922 TTTGTAAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (4 bp):
ATAT
Found at i:6921 original size:16 final size:16
Alignment explanation
Indices: 6870--6908 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
6860 ATCGAACAAC
6870 ATATATAAATATATAT
1 ATATATAAATATATAT
6886 ATATATAAATATATAT
1 ATATATAAATATATAT
6902 ATATATA
1 ATATATA
6909 TACATACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATATATAAATATATAT
Found at i:8362 original size:31 final size:31
Alignment explanation
Indices: 8267--8363 Score: 74
Period size: 31 Copynumber: 3.1 Consensus size: 31
8257 TATATATGCG
8267 AATTATTTGTTTCGATGTATGAGTTTCTCCT
1 AATTATTTGTTTCGATGTATGAGTTTCTCCT
** * * ** * *
8298 AATTGATTAACTTACCATCAATGCA--ATAT-CT
1 AATT-ATT-TGTTTCGATGTATG-AGTTTCTCCT
8329 AATTATTTGTTTCGATGTATGAGTTTCTCCT
1 AATTATTTGTTTCGATGTATGAGTTTCTCCT
8360 AATT
1 AATT
8364 GATTAACTTA
Statistics
Matches: 44, Mismatches: 16, Indels: 12
0.61 0.22 0.17
Matches are distributed among these distances:
28 1 0.02
29 8 0.18
30 5 0.11
31 16 0.36
32 5 0.11
33 8 0.18
34 1 0.02
ACGTcount: A:0.27, C:0.14, G:0.12, T:0.46
Consensus pattern (31 bp):
AATTATTTGTTTCGATGTATGAGTTTCTCCT
Found at i:8364 original size:62 final size:62
Alignment explanation
Indices: 8267--8390 Score: 223
Period size: 62 Copynumber: 2.0 Consensus size: 62
8257 TATATATGCG
8267 AATTATTTGTTTCGATGTATGAGTTTCTCCTAATTGATTAACTTACCA-TCAATGCAATATCT
1 AATTATTTGTTTCGATGTATGAGTTTCTCCTAATTGATTAACTTA-CAGTCAATGCAATATCT
*
8329 AATTATTTGTTTCGATGTATGAGTTTCTCCTAATTGATTAACTTACAGTTAATGCAATATCT
1 AATTATTTGTTTCGATGTATGAGTTTCTCCTAATTGATTAACTTACAGTCAATGCAATATCT
8391 TCTTACTAAC
Statistics
Matches: 60, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
61 2 0.03
62 58 0.97
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (62 bp):
AATTATTTGTTTCGATGTATGAGTTTCTCCTAATTGATTAACTTACAGTCAATGCAATATCT
Found at i:9377 original size:21 final size:20
Alignment explanation
Indices: 9335--9378 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
9325 TCTTGTAATC
*
9335 TAAAATTACTAAAAAAGTTA
1 TAAAATTACTAAAAAAGCTA
* *
9355 TAAAAGTTATTAAAATAGCTA
1 TAAAA-TTACTAAAAAAGCTA
9376 TAA
1 TAA
9379 TGCTTTCCAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.32
Consensus pattern (20 bp):
TAAAATTACTAAAAAAGCTA
Done.