Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007618.1 Hibiscus syriacus cultivar Beakdansim tig00022827_pilon, 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: 89899
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.27
Found at i:21392 original size:17 final size:17
Alignment explanation
Indices: 21370--21405 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
21360 GGGAAGATAG
21370 AGAAAGAGAGACAAGAA
1 AGAAAGAGAGACAAGAA
* *
21387 AGAAAGAGATACAGGAA
1 AGAAAGAGAGACAAGAA
21404 AG
1 AG
21406 CTAAGGATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.61, C:0.06, G:0.31, T:0.03
Consensus pattern (17 bp):
AGAAAGAGAGACAAGAA
Found at i:22434 original size:46 final size:46
Alignment explanation
Indices: 22381--22474 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
22371 CAGAGAGCCT
22381 TCCCGCATCAGCCAACAGAGACTCCGCCTCTGGAGCCAGCATCCTG
1 TCCCGCATCAGCCAACAGAGACTCCGCCTCTGGAGCCAGCATCCTG
22427 TCCCGCATCAGCCAACAGAGACTCCGCCTCTGGAGCCAGCATCCTG
1 TCCCGCATCAGCCAACAGAGACTCCGCCTCTGGAGCCAGCATCCTG
22473 TC
1 TC
22475 ATGGAGCACC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.21, C:0.41, G:0.21, T:0.16
Consensus pattern (46 bp):
TCCCGCATCAGCCAACAGAGACTCCGCCTCTGGAGCCAGCATCCTG
Found at i:37318 original size:18 final size:18
Alignment explanation
Indices: 37295--37330 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
37285 GCGCATCCGT
37295 TTAGTCAGCCATAGAGTC
1 TTAGTCAGCCATAGAGTC
*
37313 TTAGTCTGCCATAGAGTC
1 TTAGTCAGCCATAGAGTC
37331 CGATTGTACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (18 bp):
TTAGTCAGCCATAGAGTC
Found at i:39434 original size:14 final size:14
Alignment explanation
Indices: 39415--39442 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
39405 ATGATTTCTC
39415 CTATGCTTTACGGA
1 CTATGCTTTACGGA
39429 CTATGCTTTACGGA
1 CTATGCTTTACGGA
39443 TCAGTTCGCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (14 bp):
CTATGCTTTACGGA
Found at i:62834 original size:17 final size:17
Alignment explanation
Indices: 62812--62847 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
62802 GGGAAGATAG
62812 AGAAAGAGAGACAAGAA
1 AGAAAGAGAGACAAGAA
* *
62829 AGAAAGAGATACAGGAA
1 AGAAAGAGAGACAAGAA
62846 AG
1 AG
62848 CTAAGGATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.61, C:0.06, G:0.31, T:0.03
Consensus pattern (17 bp):
AGAAAGAGAGACAAGAA
Found at i:63876 original size:46 final size:46
Alignment explanation
Indices: 63823--63916 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
63813 CAGAGAGCCT
63823 TCCCGCATCAGCCAACAGAGACTCCGCCTCTGGAGCCAGCATCCTG
1 TCCCGCATCAGCCAACAGAGACTCCGCCTCTGGAGCCAGCATCCTG
63869 TCCCGCATCAGCCAACAGAGACTCCGCCTCTGGAGCCAGCATCCTG
1 TCCCGCATCAGCCAACAGAGACTCCGCCTCTGGAGCCAGCATCCTG
63915 TC
1 TC
63917 ATGGAGCACC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.21, C:0.41, G:0.21, T:0.16
Consensus pattern (46 bp):
TCCCGCATCAGCCAACAGAGACTCCGCCTCTGGAGCCAGCATCCTG
Found at i:78754 original size:18 final size:18
Alignment explanation
Indices: 78731--78766 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
78721 GCGCATCCGT
78731 TTAGTCAGCCATAGAGTC
1 TTAGTCAGCCATAGAGTC
*
78749 TTAGTCTGCCATAGAGTC
1 TTAGTCAGCCATAGAGTC
78767 CGATTGTACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (18 bp):
TTAGTCAGCCATAGAGTC
Found at i:80869 original size:14 final size:14
Alignment explanation
Indices: 80850--80877 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
80840 ATGATTTCTC
80850 CTATGCTTTACGGA
1 CTATGCTTTACGGA
80864 CTATGCTTTACGGA
1 CTATGCTTTACGGA
80878 TCAGTTCGCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (14 bp):
CTATGCTTTACGGA
Done.