Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000632.1 Hibiscus syriacus cultivar Beakdansim tig00001228_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: 71068
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:1217 original size:19 final size:18
Alignment explanation
Indices: 1139--1219 Score: 76
Period size: 18 Copynumber: 4.4 Consensus size: 18
1129 TCAAAGTCAA
1139 CGGGTCAGGTCAAACAGTT
1 CGGGTC-GGTCAAACAGTT
1158 C-GGTCGGGTCAAACAGTT
1 CGGGTC-GGTCAAACAGTT
* * *
1176 TGAGTCTGGTC-AATAGTT
1 CGGGTC-GGTCAAACAGTT
*
1194 TGGGTCGGATCAAACAGTT
1 CGGGTCGG-TCAAACAGTT
1213 CGGGTCG
1 CGGGTCG
1220 AGTGGGACCG
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
17 2 0.04
18 29 0.57
19 20 0.39
ACGTcount: A:0.22, C:0.19, G:0.33, T:0.26
Consensus pattern (18 bp):
CGGGTCGGTCAAACAGTT
Found at i:11246 original size:21 final size:18
Alignment explanation
Indices: 11220--11275 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 18
11210 ATGTTGTTCG
11220 AAAAAAAGGAAAAAACATGCA
1 AAAAAAAGGAAAAAA-A--CA
*
11241 AAAAAATGGAAAAGAAACA
1 AAAAAAAGGAAAA-AAACA
11260 ACAAAAAAGGAAAAAA
1 A-AAAAAAGGAAAAAA
11276 TGCAGTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
19 5 0.16
20 11 0.35
21 13 0.42
22 2 0.06
ACGTcount: A:0.75, C:0.07, G:0.14, T:0.04
Consensus pattern (18 bp):
AAAAAAAGGAAAAAAACA
Found at i:16477 original size:36 final size:37
Alignment explanation
Indices: 16431--16502 Score: 112
Period size: 36 Copynumber: 2.0 Consensus size: 37
16421 TCAAAGTTAA
*
16431 AGGTCGGGTCAAACAGTTC-GGTTGGGTCAAACAGTTT
1 AGGTCGGGTC-AACAGTTCGGGTTGGATCAAACAGTTT
16468 AGGTC-GGTCAACAGTTCGGGTTGGATCAAACAGTT
1 AGGTCGGGTCAACAGTTCGGGTTGGATCAAACAGTT
16503 CGGGTCGAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
35 8 0.24
36 20 0.61
37 5 0.15
ACGTcount: A:0.25, C:0.17, G:0.32, T:0.26
Consensus pattern (37 bp):
AGGTCGGGTCAACAGTTCGGGTTGGATCAAACAGTTT
Found at i:16501 original size:19 final size:18
Alignment explanation
Indices: 16437--16507 Score: 83
Period size: 18 Copynumber: 3.9 Consensus size: 18
16427 TTAAAGGTCG
16437 GGTCAAACAGTTC-GGTT
1 GGTCAAACAGTTCGGGTT
** *
16454 GGGTCAAACAGTTTAGGTC
1 -GGTCAAACAGTTCGGGTT
16473 GGTC-AACAGTTCGGGTT
1 GGTCAAACAGTTCGGGTT
16490 GGATCAAACAGTTCGGGT
1 GG-TCAAACAGTTCGGGT
16508 CGAGTGGGAC
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
17 12 0.27
18 18 0.40
19 15 0.33
ACGTcount: A:0.24, C:0.17, G:0.32, T:0.27
Consensus pattern (18 bp):
GGTCAAACAGTTCGGGTT
Found at i:38723 original size:21 final size:21
Alignment explanation
Indices: 38697--38736 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
38687 CAGAACCCCA
*
38697 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
38718 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
38737 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:47159 original size:20 final size:20
Alignment explanation
Indices: 47134--47179 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
47124 GACCAAAGTT
*
47134 GAAAGAGGCGCCAAAATATG
1 GAAAGAGGCACCAAAATATG
47154 GAAAGAGGCACCAAAATATG
1 GAAAGAGGCACCAAAATATG
47174 GAAAGA
1 GAAAGA
47180 AAAAGAAAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.50, C:0.13, G:0.28, T:0.09
Consensus pattern (20 bp):
GAAAGAGGCACCAAAATATG
Found at i:47382 original size:6 final size:6
Alignment explanation
Indices: 47371--47395 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
47361 ATTTGGTTTT
47371 ACTGCA ACTGCA ACTGCA ACTGCA A
1 ACTGCA ACTGCA ACTGCA ACTGCA A
47396 AACGAATTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.32, G:0.16, T:0.16
Consensus pattern (6 bp):
ACTGCA
Found at i:54903 original size:2 final size:2
Alignment explanation
Indices: 54896--54921 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
54886 TAAAGGCGAT
54896 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
54922 CAATAAAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:56995 original size:3 final size:3
Alignment explanation
Indices: 56987--57015 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
56977 TCTCACTACT
56987 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
57016 GAACTCTGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:65635 original size:19 final size:20
Alignment explanation
Indices: 65613--65656 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
65603 GAGAAAAGGT
65613 AAAAGTTAA-AATGAAAGAG
1 AAAAGTTAATAATGAAAGAG
* *
65632 AAAAATTAATAATGAAAGAT
1 AAAAGTTAATAATGAAAGAG
65652 AAAAG
1 AAAAG
65657 AAAAGTTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.18
Consensus pattern (20 bp):
AAAAGTTAATAATGAAAGAG
Done.