Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006832.1 Hibiscus syriacus cultivar Beakdansim tig00017368_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: 57493
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3567 original size:24 final size:24
Alignment explanation
Indices: 3531--3600 Score: 122
Period size: 24 Copynumber: 2.9 Consensus size: 24
3521 GGTGACGCTG
3531 ACATATCACCATAAGATAATATTA
1 ACATATCACCATAAGATAATATTA
* *
3555 ACATATCATCATAAGATAATATTG
1 ACATATCACCATAAGATAATATTA
3579 ACATATCACCATAAGATAATAT
1 ACATATCACCATAAGATAATAT
3601 CACATCATTA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.49, C:0.16, G:0.06, T:0.30
Consensus pattern (24 bp):
ACATATCACCATAAGATAATATTA
Found at i:3956 original size:27 final size:28
Alignment explanation
Indices: 3900--3957 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 28
3890 TCTTGGTCAC
*
3900 TTGTTAAAAAAAATCATTGACGTGACATT
1 TTGTTAAAAAAAATCAATGAC-TGACATT
* *
3929 TTGTTAAAAAAATTCAATGA-TGATATT
1 TTGTTAAAAAAAATCAATGACTGACATT
3956 TT
1 TT
3958 ATTGTCTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 8 0.31
29 18 0.69
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.40
Consensus pattern (28 bp):
TTGTTAAAAAAAATCAATGACTGACATT
Found at i:5325 original size:16 final size:17
Alignment explanation
Indices: 5303--5351 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 17
5293 TATATATATT
5303 TTTATATTTGTTATTAA
1 TTTATATTTGTTATTAA
5320 TTATATAATTTGTTATTAA
1 TT-TAT-ATTTGTTATTAA
*
5339 TTATATAATTGTT
1 TT-TATATTTGTT
5352 CATCTCTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 2 0.07
18 9 0.31
19 18 0.62
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (17 bp):
TTTATATTTGTTATTAA
Found at i:5330 original size:19 final size:19
Alignment explanation
Indices: 5308--5348 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
5298 ATATTTTTAT
5308 ATTTGTTATTAATTATATA
1 ATTTGTTATTAATTATATA
5327 ATTTGTTATTAATTATATA
1 ATTTGTTATTAATTATATA
5346 ATT
1 ATT
5349 GTTCATCTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (19 bp):
ATTTGTTATTAATTATATA
Found at i:8614 original size:16 final size:16
Alignment explanation
Indices: 8593--8623 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
8583 GATAACTTTT
8593 TTTATTATAATTATTG
1 TTTATTATAATTATTG
*
8609 TTTATTATGATTATT
1 TTTATTATAATTATT
8624 TGAAAAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (16 bp):
TTTATTATAATTATTG
Found at i:12076 original size:35 final size:34
Alignment explanation
Indices: 11991--12077 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
11981 AAAATAATTT
*
11991 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGG
* *
12025 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--G-TATTAAATGG
12063 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
12078 ACTGAAATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 4 0.09
38 11 0.24
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGG
Found at i:14445 original size:17 final size:18
Alignment explanation
Indices: 14404--14442 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
14394 ATTATATAAG
14404 TAAAATA-TTAAATAAAT
1 TAAAATACTTAAATAAAT
14421 TAAAATACTTAAATAAAT
1 TAAAATACTTAAATAAAT
14439 TAAA
1 TAAA
14443 TACAAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAAATACTTAAATAAAT
Found at i:42793 original size:29 final size:29
Alignment explanation
Indices: 42751--42830 Score: 97
Period size: 29 Copynumber: 2.7 Consensus size: 29
42741 TTGACCGATG
*
42751 ATATTCTGAGAATTAATTCGATTTTGGTA
1 ATATTCTGGGAATTAATTCGATTTTGGTA
** *
42780 ATATTCTGGGAATTAATTTAATTTTGGTG
1 ATATTCTGGGAATTAATTCGATTTTGGTA
* *
42809 CTATTTTGGGAATTTAATTCGA
1 ATATTCTGGGAA-TTAATTCGA
42831 AAAGGTGCCA
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 35 0.83
30 7 0.17
ACGTcount: A:0.29, C:0.06, G:0.19, T:0.46
Consensus pattern (29 bp):
ATATTCTGGGAATTAATTCGATTTTGGTA
Found at i:43607 original size:24 final size:24
Alignment explanation
Indices: 43581--43659 Score: 79
Period size: 24 Copynumber: 3.3 Consensus size: 24
43571 TATCTGATTT
*
43581 TTGACCTGGATTCTGATATGATAT
1 TTGACCTGGATTCTGATATGATAC
* * * *
43605 TTGACCTGAATTTTTATACGATAC
1 TTGACCTGGATTCTGATATGATAC
* * *
43629 TTGACATGGACTCTGATTTG-TAC
1 TTGACCTGGATTCTGATATGATAC
43652 TTGACCTG
1 TTGACCTG
43660 AATTATGTTT
Statistics
Matches: 42, Mismatches: 13, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
23 10 0.24
24 32 0.76
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.41
Consensus pattern (24 bp):
TTGACCTGGATTCTGATATGATAC
Found at i:50665 original size:16 final size:17
Alignment explanation
Indices: 50644--50682 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
50634 CCTTCGAACA
50644 TTATAA-ATAATAATAT
1 TTATAATATAATAATAT
*
50660 TTATAATATAATATTAT
1 TTATAATATAATAATAT
50677 TATATA
1 T-TATA
50683 TATTGACGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 6 0.30
17 10 0.50
18 4 0.20
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TTATAATATAATAATAT
Found at i:52170 original size:5 final size:5
Alignment explanation
Indices: 52160--52206 Score: 53
Period size: 5 Copynumber: 9.6 Consensus size: 5
52150 TGTTTAGAAA
* *
52160 AAAAT AAAAT AAAAT -AAAT CAAAAT AAAAT -AAAT AGAAT GAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT AAA
52207 GTCTACTACA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
4 8 0.23
5 23 0.66
6 4 0.11
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:52185 original size:15 final size:14
Alignment explanation
Indices: 52157--52206 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
52147 ATCTGTTTAG
52157 AAAA-AAATAAAAT
1 AAAATAAATAAAAT
52170 AAAATAAATCAAAAT
1 AAAATAAAT-AAAAT
*
52185 AAAATAAATAGAAT
1 AAAATAAATAAAAT
*
52199 GAAATAAA
1 AAAATAAA
52207 GTCTACTACA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
13 4 0.12
14 15 0.45
15 14 0.42
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.18
Consensus pattern (14 bp):
AAAATAAATAAAAT
Found at i:52189 original size:11 final size:11
Alignment explanation
Indices: 52160--52258 Score: 50
Period size: 11 Copynumber: 9.3 Consensus size: 11
52150 TGTTTAGAAA
52160 AAAATAAAAT-
1 AAAATAAAATC
52170 AAAAT-AAATC
1 AAAATAAAATC
52180 AAAATAAAAT-
1 AAAATAAAATC
*
52190 -AAATAGAAT-
1 AAAATAAAATC
* *
52199 GAAATAAAGTC
1 AAAATAAAATC
* *
52210 TACTACA-AAAATA
1 -A--AAATAAAATC
52223 AAAATAAAA-C
1 AAAATAAAATC
*
52233 GAAAATAAAATG
1 -AAAATAAAATC
*
52245 AAAATAAAAAC
1 AAAATAAAATC
52256 AAA
1 AAA
52259 GATATAACGA
Statistics
Matches: 67, Mismatches: 12, Indels: 19
0.68 0.12 0.19
Matches are distributed among these distances:
9 12 0.18
10 19 0.28
11 29 0.43
12 1 0.01
13 4 0.06
14 2 0.03
ACGTcount: A:0.72, C:0.06, G:0.05, T:0.17
Consensus pattern (11 bp):
AAAATAAAATC
Found at i:52270 original size:23 final size:22
Alignment explanation
Indices: 52223--52270 Score: 53
Period size: 23 Copynumber: 2.1 Consensus size: 22
52213 TACAAAAATA
*
52223 AAAATAAAACGAAAATAAAATG
1 AAAATAAAACGAAAATAAAACG
*
52245 AAAATAAAAAC-AAAGATATAACG
1 AAAAT-AAAACGAAA-ATAAAACG
52268 AAA
1 AAA
52271 TGGGTTACCT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.73, C:0.06, G:0.08, T:0.12
Consensus pattern (22 bp):
AAAATAAAACGAAAATAAAACG
Found at i:55307 original size:19 final size:19
Alignment explanation
Indices: 55285--55334 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
55275 GTTGTTTTTA
55285 AAATAAAAAAATAAGAATT
1 AAATAAAAAAATAAGAATT
*
55304 AAATAAAAGAAA-AATAATT
1 AAATAAAA-AAATAAGAATT
*
55323 AAATAAACAAAT
1 AAATAAAAAAAT
55335 TAAAGAGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 3 0.11
19 21 0.78
20 3 0.11
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.20
Consensus pattern (19 bp):
AAATAAAAAAATAAGAATT
Done.