Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008222.1 Hibiscus syriacus cultivar Beakdansim tig00110854_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: 44157
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:2797 original size:22 final size:23
Alignment explanation
Indices: 2770--2813 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2760 CAAATTAATC
2770 TTTTTT-AAAAATCAGTAAATTT
1 TTTTTTCAAAAATCAGTAAATTT
* *
2792 TTTTTTCTAAAATCATTAAATT
1 TTTTTTCAAAAATCAGTAAATT
2814 ATATCAAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (23 bp):
TTTTTTCAAAAATCAGTAAATTT
Found at i:3583 original size:43 final size:44
Alignment explanation
Indices: 3512--3611 Score: 134
Period size: 43 Copynumber: 2.3 Consensus size: 44
3502 CGATACTTTA
*
3512 GCACCA-CGTCACACAGACATCAGATTACGTGCTAAGTAAC-A-C
1 GCACCACCGTCACAAAGACATCAGATTACGTGCTAAGT-ACTAGC
* * *
3554 GCACCACCATCACAAAGACGTCAGGTTACGTGCTAAGTACTAGC
1 GCACCACCGTCACAAAGACATCAGATTACGTGCTAAGTACTAGC
3598 GCACCACCGTCACA
1 GCACCACCGTCACA
3612 TGCGCGACGT
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
42 8 0.16
43 28 0.56
44 14 0.28
ACGTcount: A:0.33, C:0.33, G:0.18, T:0.16
Consensus pattern (44 bp):
GCACCACCGTCACAAAGACATCAGATTACGTGCTAAGTACTAGC
Found at i:8725 original size:21 final size:22
Alignment explanation
Indices: 8696--8741 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
8686 TGTCCAGACA
** *
8696 AGTAGTACTCCGCAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
8718 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
8739 AGT
1 AGT
8742 TTCAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:12169 original size:14 final size:13
Alignment explanation
Indices: 12133--12182 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 13
12123 TTTATATATA
12133 TTATATTTAGAGT
1 TTATATTTAGAGT
*
12146 TTAGAGTTTAGAGT
1 TTATA-TTTAGAGT
*
12160 TATATATTTAGGGT
1 T-TATATTTAGAGT
12174 TTAATATTT
1 TT-ATATTT
12183 TTATTAATCT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 5 0.16
14 23 0.74
15 3 0.10
ACGTcount: A:0.30, C:0.00, G:0.18, T:0.52
Consensus pattern (13 bp):
TTATATTTAGAGT
Found at i:12358 original size:7 final size:6
Alignment explanation
Indices: 12346--12418 Score: 51
Period size: 7 Copynumber: 11.0 Consensus size: 6
12336 GCAGGGTTTA
12346 AAATTT AAGATTT AACATTT ATAATTAT AAA--T AAATTAT AATATTT
1 AAATTT AA-ATTT AA-ATTT A-AATT-T AAATTT AAATT-T AA-ATTT
12392 AATATTT AAGATTT AGAATTT AAATTT
1 AA-ATTT AA-ATTT A-AATTT AAATTT
12419 TAAGTGTCAT
Statistics
Matches: 57, Mismatches: 2, Indels: 16
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.07
6 7 0.12
7 39 0.68
8 7 0.12
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (6 bp):
AAATTT
Found at i:23597 original size:2 final size:2
Alignment explanation
Indices: 23590--23622 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
23580 AAAGAAATCT
23590 TA TA TA 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 TA TA TA T
23623 TGAATTGATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:24451 original size:21 final size:21
Alignment explanation
Indices: 24425--24464 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
24415 CTATCTCGAA
24425 CTGAA-TCATTCAATAAAAATC
1 CTGAATTCATTCAA-AAAAATC
*
24446 CTGAATTCATTTAAAAAAA
1 CTGAATTCATTCAAAAAAA
24465 GTGCAGATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.50, C:0.15, G:0.05, T:0.30
Consensus pattern (21 bp):
CTGAATTCATTCAAAAAAATC
Found at i:24934 original size:18 final size:18
Alignment explanation
Indices: 24911--24945 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
24901 ATGAGTTATA
24911 ATATTAATTTTGTTAATC
1 ATATTAATTTTGTTAATC
*
24929 ATATTAATTTTTTTAAT
1 ATATTAATTTTGTTAAT
24946 TATCATGTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (18 bp):
ATATTAATTTTGTTAATC
Found at i:24950 original size:21 final size:20
Alignment explanation
Indices: 24906--24951 Score: 51
Period size: 18 Copynumber: 2.4 Consensus size: 20
24896 TAGGAATGAG
*
24906 TTATAATATTAATTTTGTTA
1 TTATCATATTAATTTTGTTA
*
24926 --ATCATATTAATTTTTTTAA
1 TTATCATATTAATTTTGTT-A
24945 TTATCAT
1 TTATCAT
24952 GTCAACTCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
18 15 0.71
19 1 0.05
21 5 0.24
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (20 bp):
TTATCATATTAATTTTGTTA
Done.