Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006777.1 Hibiscus syriacus cultivar Beakdansim tig00017140_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: 63718
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:10973 original size:16 final size:16
Alignment explanation
Indices: 10952--10984 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
10942 TTCTGCCACC
10952 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
10968 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
10984 T
1 T
10985 GAGCTAACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.33
Consensus pattern (16 bp):
TATGTTAGAATGCAAA
Found at i:15157 original size:15 final size:17
Alignment explanation
Indices: 15132--15165 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
15122 TAAAGGTCCT
15132 AAATAACTAATAAA-TA
1 AAATAACTAATAAACTA
15148 AAATAA-TAATAAACTA
1 AAATAACTAATAAACTA
15164 AA
1 AA
15166 CATATCTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAACTAATAAACTA
Found at i:19021 original size:14 final size:14
Alignment explanation
Indices: 19004--19037 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
18994 TTGTTTTGAA
19004 ATTTTTATTT-TTTT
1 ATTTTT-TTTGTTTT
19018 ATTTTTTTTGTTTT
1 ATTTTTTTTGTTTT
19032 ATTTTT
1 ATTTTT
19038 GCCTTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 3 0.16
14 16 0.84
ACGTcount: A:0.12, C:0.00, G:0.03, T:0.85
Consensus pattern (14 bp):
ATTTTTTTTGTTTT
Found at i:19053 original size:22 final size:21
Alignment explanation
Indices: 19005--19053 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
18995 TGTTTTGAAA
**
19005 TTTTTATTTTTTTATTTTTTT
1 TTTTTATTTTTGCATTTTTTT
*
19026 TGTTTTATTTTTGCCTTTTTTT
1 T-TTTTATTTTTGCATTTTTTT
19048 CTTTTT
1 -TTTTT
19054 TTGAAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 21 0.91
23 1 0.04
ACGTcount: A:0.06, C:0.06, G:0.04, T:0.84
Consensus pattern (21 bp):
TTTTTATTTTTGCATTTTTTT
Found at i:31035 original size:24 final size:24
Alignment explanation
Indices: 31008--31066 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
30998 TGTGAATCAC
31008 CAAAAGTCATGGCTATTGGTTTTT
1 CAAAAGTCATGGCTATTGGTTTTT
*** *
31032 CAAAAGTCACATCTTTTGGTTTTT
1 CAAAAGTCATGGCTATTGGTTTTT
*
31056 CAAAAGCCATG
1 CAAAAGTCATG
31067 ATTTTTGAAT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (24 bp):
CAAAAGTCATGGCTATTGGTTTTT
Found at i:32741 original size:22 final size:21
Alignment explanation
Indices: 32713--32753 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
32703 GATGTGGAAT
32713 TGATGGTCTTGATGGATGAAGA
1 TGATGGTCTTGAT-GATGAAGA
*
32735 TGATGGTGTTGATGATGAA
1 TGATGGTCTTGATGATGAA
32754 ATGGAGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.27, C:0.02, G:0.37, T:0.34
Consensus pattern (21 bp):
TGATGGTCTTGATGATGAAGA
Found at i:39789 original size:22 final size:19
Alignment explanation
Indices: 39759--39801 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 19
39749 TGCCACGTTT
39759 GTTTATGGCAATGTGAGCTAA
1 GTTTATGGCAA--TGAGCTAA
*
39780 GTTTGATGGCCATGAGCTAA
1 GTTT-ATGGCAATGAGCTAA
39800 GT
1 GT
39802 ACATCATCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 10 0.50
21 4 0.20
22 6 0.30
ACGTcount: A:0.26, C:0.12, G:0.30, T:0.33
Consensus pattern (19 bp):
GTTTATGGCAATGAGCTAA
Found at i:56975 original size:24 final size:22
Alignment explanation
Indices: 56941--56985 Score: 54
Period size: 24 Copynumber: 2.0 Consensus size: 22
56931 TGCACAAGAT
* *
56941 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGAAATTTAAAAGG
56963 ATGTACCTCTTGAAATTTAAAAG
1 ATGT-CCT-TTGAAATTTAAAAG
56986 AATGAGCCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 3 0.16
24 12 0.63
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (22 bp):
ATGTCCTTTGAAATTTAAAAGG
Done.