Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020408.1 Corchorus olitorius cultivar O-4 contig20441, 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: 20532
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.33
Found at i:9358 original size:2 final size:2
Alignment explanation
Indices: 9351--9377 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
9341 TTATTTTAAT
9351 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
9378 CAAAAACCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15513 original size:2 final size:2
Alignment explanation
Indices: 15506--15545 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
15496 TGTATAATGT
15506 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
15546 CCTTGGTGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:16113 original size:30 final size:30
Alignment explanation
Indices: 16077--16133 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
16067 TAAATTTTCA
16077 TTTTTGAAGCAATAAAAAGATCCAAAATTT
1 TTTTTGAAGCAATAAAAAGATCCAAAATTT
16107 TTTTTGAAGCAATAAAAAGATCCAAAA
1 TTTTTGAAGCAATAAAAAGATCCAAAA
16134 AATACCAGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.30
Consensus pattern (30 bp):
TTTTTGAAGCAATAAAAAGATCCAAAATTT
Found at i:16954 original size:2 final size:2
Alignment explanation
Indices: 16947--16971 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16937 ATGTAGTAGA
16947 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 A
16972 CTACATATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17995 original size:2 final size:2
Alignment explanation
Indices: 17982--18033 Score: 51
Period size: 2 Copynumber: 28.0 Consensus size: 2
17972 ATTAAAAATA
*
17982 AT AT AT AGT AT AT AT -T AT -T A- AT AT -T AT AG A- AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18020 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
18034 GTTATGGCCA
Statistics
Matches: 43, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
1 5 0.12
2 36 0.84
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18030 original size:21 final size:20
Alignment explanation
Indices: 17980--18032 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
17970 TAATTAAAAA
*
17980 TAATATATAGTATATATTAT
1 TAATATATAGAATATATTAT
18000 TAATATTATAGAATATATATAT
1 TAATA-TATAGAATATAT-TAT
18022 ATATATATATA
1 -TA-ATATATA
18033 TGTTATGGCC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 5 0.18
21 11 0.39
22 3 0.11
23 6 0.21
24 3 0.11
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (20 bp):
TAATATATAGAATATATTAT
Done.