Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005014.1 Hibiscus syriacus cultivar Beakdansim tig00011256_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: 49502
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:1926 original size:15 final size:16
Alignment explanation
Indices: 1886--1928 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
1876 AAAGTTTTAA
*
1886 TATAGTTATTTTCATC
1 TATAGTTATTATCATC
1902 TATA-TATATTAT-ATC
1 TATAGT-TATTATCATC
1917 TATAGTTATTAT
1 TATAGTTATTAT
1929 GATGATAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.56
Consensus pattern (16 bp):
TATAGTTATTATCATC
Found at i:4611 original size:13 final size:13
Alignment explanation
Indices: 4590--4632 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
4580 CTGCGGAATT
4590 GATGGTATTGATG
1 GATGGTATTGATG
*
4603 GATGTTATTGATG
1 GATGGTATTGATG
*
4616 G-TGGTAATGATG
1 GATGGTATTGATG
*
4628 AATGG
1 GATGG
4633 ATGGTGTTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
12 9 0.36
13 16 0.64
ACGTcount: A:0.26, C:0.00, G:0.37, T:0.37
Consensus pattern (13 bp):
GATGGTATTGATG
Found at i:5017 original size:19 final size:21
Alignment explanation
Indices: 4974--5025 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
4964 GAAACCCCTT
*
4974 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTGTAAA
4995 TGAAAATACATGA-TTGT-AA
1 TGAAAATACATGACTTGTAAA
*
5014 TGAAGATACATG
1 TGAAAATACATG
5026 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.45
20 3 0.10
21 13 0.45
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (21 bp):
TGAAAATACATGACTTGTAAA
Found at i:8281 original size:23 final size:22
Alignment explanation
Indices: 8234--8287 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 22
8224 TTGAACTTCA
8234 CTTTTTCTTTTCTTTCTTTCTT
1 CTTTTTCTTTTCTTTCTTTCTT
*
8256 CTTTCTTCTTTTCTGATTTTTCTCTT
1 CTTT-TTCTTTTCT--TTCTT-TCTT
8282 CTTTTT
1 CTTTTT
8288 GCACTCCAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 4 0.15
23 9 0.33
25 6 0.22
26 8 0.30
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.74
Consensus pattern (22 bp):
CTTTTTCTTTTCTTTCTTTCTT
Found at i:9030 original size:19 final size:21
Alignment explanation
Indices: 8988--9038 Score: 79
Period size: 19 Copynumber: 2.5 Consensus size: 21
8978 AAACCCCTTC
8988 GAAAATACATGACTTTTAAAT
1 GAAAATACATGACTTTTAAAT
9009 GAAAATACATGA-TTTT-AAT
1 GAAAATACATGACTTTTAAAT
*
9028 GAAGATACATG
1 GAAAATACATG
9039 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.45
20 4 0.14
21 12 0.41
ACGTcount: A:0.47, C:0.08, G:0.14, T:0.31
Consensus pattern (21 bp):
GAAAATACATGACTTTTAAAT
Found at i:15701 original size:19 final size:19
Alignment explanation
Indices: 15679--15726 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
15669 TTTTTTTTTT
*
15679 CTTTTTTTCTTTTTGAGTG
1 CTTTTTTTCTTTTTGAGGG
***
15698 CTTTCAATCTTTTTGAGGG
1 CTTTTTTTCTTTTTGAGGG
*
15717 CTTCTTTTCT
1 CTTTTTTTCT
15727 GATTTTTCTT
Statistics
Matches: 21, Mismatches: 8, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.08, C:0.17, G:0.15, T:0.60
Consensus pattern (19 bp):
CTTTTTTTCTTTTTGAGGG
Found at i:20100 original size:19 final size:17
Alignment explanation
Indices: 20053--20100 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
20043 ATCAGCAAAG
20053 AAAAA-AAGAAACACTC
1 AAAAAGAAGAAACACTC
*
20069 AAAAAGATTGAAAGCACTC
1 AAAAAGA-AGAAA-CACTC
20088 AAAAAAGAAGAAA
1 -AAAAAGAAGAAA
20101 AAGAAAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 5 0.19
17 1 0.04
18 4 0.15
19 9 0.35
20 7 0.27
ACGTcount: A:0.67, C:0.12, G:0.12, T:0.08
Consensus pattern (17 bp):
AAAAAGAAGAAACACTC
Found at i:24646 original size:19 final size:21
Alignment explanation
Indices: 24603--24654 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
24593 GAAACCCCTT
*
24603 TGAAAATTCATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
24624 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
24643 TGAAGATACATG
1 TGAAAATACATG
24655 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.45
20 4 0.14
21 12 0.41
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:28679 original size:22 final size:21
Alignment explanation
Indices: 28642--28683 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
28632 CCATCTCCAT
28642 TTCATCATCAACACCATCAAC
1 TTCATCATCAACACCATCAAC
*
28663 TTCATCCATCAAGACCATCAA
1 TTCAT-CATCAACACCATCAA
28684 TTCTGCAGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.38, C:0.36, G:0.02, T:0.24
Consensus pattern (21 bp):
TTCATCATCAACACCATCAAC
Found at i:30041 original size:25 final size:27
Alignment explanation
Indices: 29991--30043 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 27
29981 CTAAAGGACC
29991 CAACAAGAGAGAATTGAGAGGAAAAAGG
1 CAACAAGAGAGAATTGAGA-GAAAAAGG
30019 CAAC-AGAGAG-ATTGAGA-ACAAAAGG
1 CAACAAGAGAGAATTGAGAGA-AAAAGG
30044 GGATAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
24 1 0.04
25 6 0.25
26 7 0.29
27 6 0.25
28 4 0.17
ACGTcount: A:0.53, C:0.09, G:0.30, T:0.08
Consensus pattern (27 bp):
CAACAAGAGAGAATTGAGAGAAAAAGG
Found at i:35276 original size:11 final size:13
Alignment explanation
Indices: 35244--35273 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
35234 TGGCCAAAGA
35244 TGAAAAGGTATGT
1 TGAAAAGGTATGT
35257 TGAAAAGGTATG-
1 TGAAAAGGTATGT
35269 TGAAA
1 TGAAA
35274 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:40383 original size:36 final size:36
Alignment explanation
Indices: 40331--40430 Score: 157
Period size: 36 Copynumber: 2.8 Consensus size: 36
40321 GATACTATTT
* *
40331 TCATGACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
40367 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
40403 TCATCACCATATTCCATCACCA-TATCAC
1 TCATCACCATAATCCATCACCATTATCAC
40431 CCAATAACAT
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
35 6 0.10
36 54 0.90
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.29
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:40386 original size:13 final size:11
Alignment explanation
Indices: 40364--40429 Score: 62
Period size: 13 Copynumber: 5.5 Consensus size: 11
40354 TATCACGCCT
40364 ATATCATCACC
1 ATATCATCACC
40375 ATAGTCCATCACC
1 ATA-T-CATCACC
*
40388 ATTATCA-CGCC
1 A-TATCATCACC
40399 TATATCATCACC
1 -ATATCATCACC
40411 ATATTCCATCACC
1 ATA-T-CATCACC
40424 ATATCA
1 ATATCA
40430 CCCAATAACA
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
11 16 0.35
12 9 0.20
13 19 0.41
14 2 0.04
ACGTcount: A:0.33, C:0.35, G:0.03, T:0.29
Consensus pattern (11 bp):
ATATCATCACC
Found at i:40457 original size:32 final size:33
Alignment explanation
Indices: 40414--40481 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 33
40404 CATCACCATA
40414 TTCCATCACCATATCA-C-CCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
40446 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
40479 TTC
1 TTC
40482 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 14 0.45
33 11 0.35
34 6 0.19
ACGTcount: A:0.31, C:0.37, G:0.00, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:40850 original size:5 final size:5
Alignment explanation
Indices: 40833--40874 Score: 50
Period size: 5 Copynumber: 8.2 Consensus size: 5
40823 AAAAGCAACA
*
40833 AAAAG AAAA- AAAAG AAAAA AAAAG AAAGAAG AAAAG AAAAG A
1 AAAAG AAAAG AAAAG AAAAG AAAAG -AA-AAG AAAAG AAAAG A
40875 CTCCTACAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
4 4 0.12
5 21 0.66
6 4 0.12
7 3 0.09
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:40872 original size:17 final size:16
Alignment explanation
Indices: 40833--40874 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
40823 AAAAGCAACA
40833 AAAAG-AAA-AAAAAG
1 AAAAGAAAAGAAAAAG
*
40847 AAAAAAAAAGAAAGAAG
1 AAAAGAAAAGAAA-AAG
40864 AAAAGAAAAGA
1 AAAAGAAAAGA
40875 CTCCTACAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 4 0.17
15 3 0.13
16 3 0.13
17 13 0.57
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAGAAAAAG
Found at i:46118 original size:34 final size:35
Alignment explanation
Indices: 46009--46106 Score: 128
Period size: 36 Copynumber: 2.8 Consensus size: 35
45999 GATACTATTT
*
46009 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCC-ATA
* * *
46045 TCATCACCGTAGTCCATCACAATTATCACGCC-TA
1 TCATCACCATAATCCATCACCATTATCACGCCATA
*
46079 TCATCACCATATTCCATCACCA-TATCAC
1 TCATCACCATAATCCATCACCATTATCAC
46107 ACCAAAACAT
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
33 6 0.11
34 21 0.38
36 28 0.51
ACGTcount: A:0.31, C:0.37, G:0.04, T:0.29
Consensus pattern (35 bp):
TCATCACCATAATCCATCACCATTATCACGCCATA
Found at i:46133 original size:32 final size:32
Alignment explanation
Indices: 46090--46156 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
46080 CATCACCATA
46090 TTCCATCACCATATCA-CACCA-AAACATCATCC
1 TTCCATCACCAT-TCATCACCATAAA-ATCATCC
* *
46122 TTCCATTACCATTCATCACCATTAAATCATCC
1 TTCCATCACCATTCATCACCATAAAATCATCC
46154 TTC
1 TTC
46157 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 3 0.10
32 26 0.84
33 2 0.06
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (32 bp):
TTCCATCACCATTCATCACCATAAAATCATCC
Done.