Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000811.1 Hibiscus syriacus cultivar Beakdansim tig00001571_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: 47508
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3581 original size:18 final size:18
Alignment explanation
Indices: 3544--3582 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
3534 AATTCAGACT
*
3544 TAATTTAAATATACTGAA
1 TAATTTAAATATACTAAA
* *
3562 TAATTTACATATATTAAA
1 TAATTTAAATATACTAAA
3580 TAA
1 TAA
3583 AAAAGTTTAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (18 bp):
TAATTTAAATATACTAAA
Found at i:4209 original size:23 final size:23
Alignment explanation
Indices: 4166--4235 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
4156 CATATAAAAT
* *
4166 TGTCCCGAAGGACCGCGTAGATA
1 TGTCCCGAAGGACCACATAGATA
*
4189 TGTCCCGAAGGACCACATAGATT
1 TGTCCCGAAGGACCACATAGATA
* ** *
4212 TCTCCTTAAGGACCACATATATA
1 TGTCCCGAAGGACCACATAGATA
4235 T
1 T
4236 TCCAATTGAC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (23 bp):
TGTCCCGAAGGACCACATAGATA
Found at i:12202 original size:18 final size:18
Alignment explanation
Indices: 12168--12202 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12158 GAACAGCACG
*
12168 AGGAACAAGCTCCACCAA
1 AGGAACAAGCACCACCAA
*
12186 AGGAACAAGCACGACCA
1 AGGAACAAGCACCACCA
12203 GAAGATCAGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.31, G:0.20, T:0.03
Consensus pattern (18 bp):
AGGAACAAGCACCACCAA
Found at i:23637 original size:29 final size:29
Alignment explanation
Indices: 23560--23637 Score: 68
Period size: 29 Copynumber: 2.6 Consensus size: 29
23550 TTAATATTTT
* * *
23560 AATAATTAAAACAAATATAATATATAAATTA
1 AATAATT-AAA-AAATATTATACAAAAATTA
* **
23591 AA-CATTATCAAATGATTATACAAAAATTA
1 AATAATTAAAAAAT-ATTATACAAAAATTA
23620 AATAATTAAAAAATATTA
1 AATAATTAAAAAATATTA
23638 ACACAATATT
Statistics
Matches: 36, Mismatches: 9, Indels: 6
0.71 0.18 0.12
Matches are distributed among these distances:
28 4 0.11
29 19 0.53
30 11 0.31
31 2 0.06
ACGTcount: A:0.62, C:0.05, G:0.01, T:0.32
Consensus pattern (29 bp):
AATAATTAAAAAATATTATACAAAAATTA
Found at i:23815 original size:17 final size:17
Alignment explanation
Indices: 23793--23829 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
23783 AAAATACTCT
23793 CTTATTCTTTCATGCTC
1 CTTATTCTTTCATGCTC
23810 CTTATTCTTTCATGCTC
1 CTTATTCTTTCATGCTC
23827 CTT
1 CTT
23830 TTTGGTGTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.11, C:0.30, G:0.05, T:0.54
Consensus pattern (17 bp):
CTTATTCTTTCATGCTC
Found at i:26330 original size:20 final size:19
Alignment explanation
Indices: 26301--26351 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
26291 CGCCATAGGG
26301 AGTATCGATACTGCAGGGGC
1 AGTATCGATACT-CAGGGGC
*
26321 AGTATGGATACTCAGGGTGAC
1 AGTATCGATACTCAGGG-G-C
*
26342 AATATCGATA
1 AGTATCGATA
26352 TTGGGGCCTC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 5 0.19
20 12 0.46
21 9 0.35
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (19 bp):
AGTATCGATACTCAGGGGC
Found at i:29537 original size:21 final size:20
Alignment explanation
Indices: 29513--29552 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
29503 GTTCCAAAGG
29513 GAGTATCGATAATGCTAGGGT
1 GAGTATCGATAATGC-AGGGT
*
29534 GAGTATCGATATTGCAGGG
1 GAGTATCGATAATGCAGGG
29553 ACAATATCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.28, C:0.10, G:0.35, T:0.28
Consensus pattern (20 bp):
GAGTATCGATAATGCAGGGT
Found at i:30871 original size:32 final size:32
Alignment explanation
Indices: 30797--30864 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
30787 GCATATGAGT
* * *
30797 CACAACAGAGTTAGTATTATATTCATATAATG
1 CACAACAGAGTTAGCATGATATTCAGATAATG
*
30829 CACAACAGAGTTAGCATGATATTTAGATAATG
1 CACAACAGAGTTAGCATGATATTCAGATAATG
30861 CACA
1 CACA
30865 GTAGAGTCAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (32 bp):
CACAACAGAGTTAGCATGATATTCAGATAATG
Found at i:33732 original size:5 final size:5
Alignment explanation
Indices: 33722--33748 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
33712 CATACTATGA
33722 AATGC AATGC AATGC AATGC AATGC AA
1 AATGC AATGC AATGC AATGC AATGC AA
33749 GGTACCTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
AATGC
Found at i:42929 original size:15 final size:16
Alignment explanation
Indices: 42895--42936 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
42885 GGAATTATGA
42895 TTTAGTTTTATATCAAT
1 TTTA-TTTTATATCAAT
*
42912 TTTATTTTATA-GAAT
1 TTTATTTTATATCAAT
*
42927 TTTATATTAT
1 TTTATTTTAT
42937 TAAGTTTAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 12 0.52
16 7 0.30
17 4 0.17
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (16 bp):
TTTATTTTATATCAAT
Found at i:44959 original size:14 final size:14
Alignment explanation
Indices: 44942--44968 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
44932 ATCATTTATA
44942 AAATAAAACTTTGC
1 AAATAAAACTTTGC
44956 AAATAAAACTTTG
1 AAATAAAACTTTG
44969 TAAAACGTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.11, G:0.07, T:0.30
Consensus pattern (14 bp):
AAATAAAACTTTGC
Found at i:45247 original size:41 final size:41
Alignment explanation
Indices: 45190--45269 Score: 142
Period size: 41 Copynumber: 2.0 Consensus size: 41
45180 AATATACAAG
*
45190 AACTTAAATTAGAGACTCCACTTAAGTGATATCAAATTAAA
1 AACTTAAATTAGAGACTCCACTTAAATGATATCAAATTAAA
*
45231 AACTTAAATTTGAGACTCCACTTAAATGATATCAAATTA
1 AACTTAAATTAGAGACTCCACTTAAATGATATCAAATTA
45270 TTTAACCCTC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (41 bp):
AACTTAAATTAGAGACTCCACTTAAATGATATCAAATTAAA
Done.