Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012309.1 Corchorus olitorius cultivar O-4 contig12342, 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: 22288
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.33
Found at i:5481 original size:16 final size:17
Alignment explanation
Indices: 5460--5505 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
5450 TTAAATTTAG
5460 TATTATTTATTATT-AT
1 TATTATTTATTATTGAT
*
5476 TATTATTGA-TATTGAT
1 TATTATTTATTATTGAT
* *
5492 TAGTATATATTATT
1 TATTATTTATTATT
5506 TTACTGATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
15 4 0.17
16 16 0.67
17 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.61
Consensus pattern (17 bp):
TATTATTTATTATTGAT
Found at i:9576 original size:6 final size:6
Alignment explanation
Indices: 9562--9597 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
9552 GTGGATTAAG
* *
9562 GTTTCA GTTTTA GTTTTA GTTTCA GTTTCA GTTTCA
1 GTTTCA GTTTCA GTTTCA GTTTCA GTTTCA GTTTCA
9598 TATCCCATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.17, C:0.11, G:0.17, T:0.56
Consensus pattern (6 bp):
GTTTCA
Found at i:21002 original size:22 final size:21
Alignment explanation
Indices: 20955--21075 Score: 75
Period size: 22 Copynumber: 5.6 Consensus size: 21
20945 TATTTTTATG
**
20955 AAATTTTGATAACTGTCCTACT-
1 AAATTTTGATAA-TCACCTA-TA
20977 AAATTTTGATAATCACCATATA
1 AAATTTTGATAATCACC-TATA
* *
20999 AAATTTCGATAATTACCTATA
1 AAATTTTGATAATCACCTATA
* * *
21020 AAATTGTGATAAACTCCGTA-A
1 AAATTTTGATAATCACC-TATA
* * *
21041 GAAACTTTGATAACCTAACTATA
1 -AAATTTTGATAATC-ACCTATA
*
21064 AAATTTTAATAA
1 AAATTTTGATAA
21076 ACTTTCCTAT
Statistics
Matches: 77, Mismatches: 16, Indels: 12
0.73 0.15 0.11
Matches are distributed among these distances:
21 21 0.27
22 54 0.70
23 2 0.03
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (21 bp):
AAATTTTGATAATCACCTATA
Found at i:21030 original size:21 final size:21
Alignment explanation
Indices: 20976--21031 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
20966 ACTGTCCTAC
*
20976 TAAATTTTGATAATCACCATA
1 TAAAATTTGATAATCACCATA
*
20997 TAAAATTTCGATAATTACC-TA
1 TAAAATTT-GATAATCACCATA
21018 TAAAATTGTGATAA
1 TAAAATT-TGATAA
21032 ACTCCGTAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 21 0.68
22 10 0.32
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.38
Consensus pattern (21 bp):
TAAAATTTGATAATCACCATA
Found at i:21982 original size:2 final size:2
Alignment explanation
Indices: 21975--22155 Score: 362
Period size: 2 Copynumber: 90.5 Consensus size: 2
21965 AAAGCCACAC
21975 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
22017 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
22059 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
22101 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
22143 TG TG TG TG TG TG T
1 TG TG TG TG TG TG T
22156 TATGCTTGCA
Statistics
Matches: 179, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 179 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Done.