Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023342.1 Corchorus olitorius cultivar O-4 contig23375, 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: 3669
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Found at i:327 original size:14 final size:14
Alignment explanation
Indices: 310--358 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
300 AGGGATAAGG
*
310 AAGAAAGAGAAAAA
1 AAGAAAAAGAAAAA
324 AAGAAAAAGAAAAA
1 AAGAAAAAGAAAAA
* * * *
338 AATACAAATAGAAA
1 AAGAAAAAGAAAAA
352 AAGAAAA
1 AAGAAAA
359 TCTTTTAAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.80, C:0.02, G:0.14, T:0.04
Consensus pattern (14 bp):
AAGAAAAAGAAAAA
Found at i:1050 original size:19 final size:19
Alignment explanation
Indices: 996--1058 Score: 63
Period size: 19 Copynumber: 3.1 Consensus size: 19
986 CACAATTGCT
996 TGGCGCCCGACCACTTCCAAA
1 TGGCGCCCGACCACTTCC--A
** *
1017 CCTGGCGATCAACCACTTCCA
1 --TGGCGCCCGACCACTTCCA
1038 TGGCGCCCGACCACTTCCA
1 TGGCGCCCGACCACTTCCA
1057 TG
1 TG
1059 ACGCGACGCT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
19 18 0.53
21 1 0.03
23 15 0.44
ACGTcount: A:0.21, C:0.43, G:0.19, T:0.17
Consensus pattern (19 bp):
TGGCGCCCGACCACTTCCA
Found at i:1226 original size:26 final size:26
Alignment explanation
Indices: 1159--1226 Score: 84
Period size: 27 Copynumber: 2.6 Consensus size: 26
1149 AACCAGCTGG
*
1159 CACCCCACACGTGACCTCCAAACGTA
1 CACCCCACACGTGACCTCCAAACGGA
*
1185 CGACCCCACACGTGACCTCC-AATGGA
1 C-ACCCCACACGTGACCTCCAAACGGA
*
1211 CACCTCCACATGTGAC
1 CACC-CCACACGTGAC
1227 ATCGCGCGTG
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
25 3 0.08
26 16 0.43
27 18 0.49
ACGTcount: A:0.28, C:0.44, G:0.15, T:0.13
Consensus pattern (26 bp):
CACCCCACACGTGACCTCCAAACGGA
Found at i:3585 original size:39 final size:40
Alignment explanation
Indices: 3529--3609 Score: 128
Period size: 39 Copynumber: 2.0 Consensus size: 40
3519 TTTAATTCCT
3529 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* * *
3569 ATGTAATA-CTATAATAACTGAAATACTTATATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
3608 AT
1 AT
3610 TCTTAGGTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 30 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.38
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:3599 original size:18 final size:18
Alignment explanation
Indices: 3539--3599 Score: 52
Period size: 17 Copynumber: 3.2 Consensus size: 18
3529 ATGTAATATA
*
3539 TATAATAACTAAAATACT
1 TATAATAACTGAAATACT
* *
3557 TACATTAATTAAATGTAATAC-
1 T--A-TAA-TAACTGAAATACT
3578 TATAATAACTGAAATACT
1 TATAATAACTGAAATACT
3596 TATA
1 TATA
3600 TTAATTAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 10
0.69 0.10 0.21
Matches are distributed among these distances:
17 10 0.30
18 8 0.24
19 1 0.03
20 1 0.03
21 4 0.12
22 9 0.27
ACGTcount: A:0.51, C:0.10, G:0.03, T:0.36
Consensus pattern (18 bp):
TATAATAACTGAAATACT
Found at i:3636 original size:25 final size:24
Alignment explanation
Indices: 3600--3646 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
3590 AATACTTATA
3600 TTAATTAAATTCTTAGGTATTTTT
1 TTAATTAAATTCTTAGGTATTTTT
3624 TTAATTCAAATTCTTAGGTATTT
1 TTAATT-AAATTCTTAGGTATTT
3647 GTGCAAACGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (24 bp):
TTAATTAAATTCTTAGGTATTTTT
Done.