Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002600.1 Hibiscus syriacus cultivar Beakdansim tig00005259_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: 67765
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:3113 original size:27 final size:27
Alignment explanation
Indices: 3075--3132 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
3065 ATAATAAAAT
*
3075 AATATATCATCGATGAATTTTTATTTA
1 AATATATCATCGATGAATTTTTATATA
*
3102 AATATATTATCGATGAATTTTTATATA
1 AATATATCATCGATGAATTTTTATATA
3129 AATA
1 AATA
3133 ATTTTTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.47
Consensus pattern (27 bp):
AATATATCATCGATGAATTTTTATATA
Found at i:5271 original size:14 final size:14
Alignment explanation
Indices: 5252--5279 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5242 CGCTGGGCAT
5252 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
5266 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
5280 AAGCATCTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.43, G:0.29, T:0.07
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:5296 original size:20 final size:19
Alignment explanation
Indices: 5266--5319 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
5256 GGCCATCCGA
5266 CCGAGGCCATCCGAAAGCAT
1 CCGA-GCCATCCGAAAGCAT
* *
5286 CTGATGCCATCCGAGAGCAT
1 CCGA-GCCATCCGAAAGCAT
*
5306 CCGAGGCATCCGAA
1 CCGAGCCATCCGAA
5320 CGAGCTATGT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 8 0.29
20 20 0.71
ACGTcount: A:0.28, C:0.33, G:0.26, T:0.13
Consensus pattern (19 bp):
CCGAGCCATCCGAAAGCAT
Found at i:5336 original size:23 final size:23
Alignment explanation
Indices: 5310--5364 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
5300 GAGCATCCGA
*
5310 GGCATCCGAACGAGCTATGTGAG
1 GGCATCCGAACGAGCTATGCGAG
*
5333 GGCATCCGAATGAGCTATGCGAG
1 GGCATCCGAACGAGCTATGCGAG
*
5356 GACATCCGA
1 GGCATCCGA
5365 GGGCAACCGA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.27, C:0.24, G:0.33, T:0.16
Consensus pattern (23 bp):
GGCATCCGAACGAGCTATGCGAG
Found at i:5381 original size:33 final size:33
Alignment explanation
Indices: 5330--5410 Score: 105
Period size: 33 Copynumber: 2.5 Consensus size: 33
5320 CGAGCTATGT
* **
5330 GAGGGCATCCGAATGAGCTATGCGA-GGACATCC
1 GAGGGCAACCGAGCGAGCTATGCGAGGGA-ATCC
5363 GAGGGCAACCGAGCGAGCTATGCGAGGGAATCC
1 GAGGGCAACCGAGCGAGCTATGCGAGGGAATCC
5396 GA--GCAACCGAGCGAG
1 GAGGGCAACCGAGCGAG
5411 GGTAGGTCGC
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
31 13 0.30
33 28 0.64
34 3 0.07
ACGTcount: A:0.28, C:0.25, G:0.37, T:0.10
Consensus pattern (33 bp):
GAGGGCAACCGAGCGAGCTATGCGAGGGAATCC
Found at i:5490 original size:33 final size:33
Alignment explanation
Indices: 5443--5526 Score: 116
Period size: 33 Copynumber: 2.6 Consensus size: 33
5433 GCGACCTACC
*
5443 CTCGCTC-GTTGCCCTCGGATTCCCTCGCATAG
1 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
*
5475 CTCGCTCGGTTGCCCTCCGATGCCCTCGCATAG
1 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
* * *
5508 CTCGTTCGGATGGCCTCGG
1 CTCGCTCGGTTGCCCTCGG
5527 TCGGATGGCC
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
32 7 0.16
33 38 0.84
ACGTcount: A:0.08, C:0.39, G:0.26, T:0.26
Consensus pattern (33 bp):
CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
Found at i:5530 original size:14 final size:14
Alignment explanation
Indices: 5508--5540 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
5498 CCTCGCATAG
*
5508 CTCGTTCGGATGGC
1 CTCGGTCGGATGGC
5522 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
5536 CTCGG
1 CTCGG
5541 ATGCCCAGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.30, G:0.39, T:0.24
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:5631 original size:29 final size:29
Alignment explanation
Indices: 5556--5631 Score: 134
Period size: 29 Copynumber: 2.6 Consensus size: 29
5546 CAGCGTGTTG
*
5556 GGGCGTGCATGGCGACCAGGTAGGTCGCT
1 GGGCGTGCATGGCGACCTGGTAGGTCGCT
*
5585 GGGCGTGCATGGCGACCTGGTAGGTCGTT
1 GGGCGTGCATGGCGACCTGGTAGGTCGCT
5614 GGGCGTGCATGGCGACCT
1 GGGCGTGCATGGCGACCT
5632 ACCCCCAGGG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.12, C:0.24, G:0.45, T:0.20
Consensus pattern (29 bp):
GGGCGTGCATGGCGACCTGGTAGGTCGCT
Found at i:16598 original size:21 final size:21
Alignment explanation
Indices: 16572--16647 Score: 61
Period size: 21 Copynumber: 3.6 Consensus size: 21
16562 TCTGCAATGA
16572 TGGCATCTGAAATAGTTACGG
1 TGGCATCTGAAATAGTTACGG
*
16593 TGGCATC-GAAA-ATGGTA--G
1 TGGCATCTGAAATA-GTTACGG
*
16611 TGGTTCTATCTGAAATAGTTACGA
1 TGG--C-ATCTGAAATAGTTACGG
*
16635 TGGCATCAGAAAT
1 TGGCATCTGAAAT
16648 GACTGCAGAA
Statistics
Matches: 43, Mismatches: 4, Indels: 16
0.68 0.06 0.25
Matches are distributed among these distances:
18 4 0.09
19 1 0.02
20 8 0.19
21 18 0.42
22 8 0.19
23 1 0.02
24 3 0.07
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (21 bp):
TGGCATCTGAAATAGTTACGG
Found at i:17417 original size:23 final size:23
Alignment explanation
Indices: 17373--17418 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
17363 TATTCAGTGT
* *
17373 AAAAATATTTCATTATATACTCA
1 AAAAATATTTCATTACAAACTCA
17396 AAAAATATTTACA-TACAAACTCA
1 AAAAATATTT-CATTACAAACTCA
17419 GTATTGAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (23 bp):
AAAAATATTTCATTACAAACTCA
Found at i:28698 original size:17 final size:17
Alignment explanation
Indices: 28678--28710 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
28668 AAATATTTTT
28678 TAAATTAAA-AAAATAAA
1 TAAA-TAAATAAAATAAA
28695 TAAATAAATAAAATAA
1 TAAATAAATAAAATAA
28711 TTTAAACTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
TAAATAAATAAAATAAA
Found at i:30869 original size:64 final size:62
Alignment explanation
Indices: 30789--31009 Score: 194
Period size: 64 Copynumber: 3.5 Consensus size: 62
30779 TTGAAGGTGT
**
30789 ATCGATGCATTGGTAGTGCATCGATGCACTCTTTTAA-AATAAAAACATCGAATGCAATTCATGC
1 ATCGATGCATAAGTAGTGCATCGATGCA-TC--TTAACAATAAAAACATCGAATGCAATTCATGC
* * **
30853 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAAT-GAAACATCGAATGCAATTGGTGC
1 ATCGATGCATAAGTAGTGCATCGATGCAT--C-TTAACAATAAAAACATCGAATGCAATTCATGC
* * * * ** * ** *
30917 ATCGATGCATAAGGAGGGCATTGATGTATCCCAACAATAATAATACATCGAATACCTTTTATGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCTTAACAATAA-AA-ACATCGAATGCAATTCATGC
* *
30981 ACCGATGCATCAGTAGTGCATCGATGCAT
1 ATCGATGCATAAGTAGTGCATCGATGCAT
31010 ACCTTCATTA
Statistics
Matches: 126, Mismatches: 25, Indels: 12
0.77 0.15 0.07
Matches are distributed among these distances:
61 5 0.04
62 1 0.01
63 3 0.02
64 113 0.90
65 4 0.03
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (62 bp):
ATCGATGCATAAGTAGTGCATCGATGCATCTTAACAATAAAAACATCGAATGCAATTCATGC
Found at i:36995 original size:3 final size:3
Alignment explanation
Indices: 36987--37019 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
36977 TCCAGAGTTC
36987 TCT TCT TCT TCT TCT TCT TCT TCT TCTT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC-T TCT TC
37020 CTTGTGCGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:37628 original size:64 final size:64
Alignment explanation
Indices: 37548--37768 Score: 248
Period size: 64 Copynumber: 3.5 Consensus size: 64
37538 TTGAAGGTGT
** **
37548 ATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAAAACATCGAATGCAATTCATG
1 ATCGATGCATAAGTAGTGCATCGATGCATC-CCATTAATAAT-AAAACATCGAATGCAATTCATG
37611 C
64 C
* **
37612 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTGGTGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGC
* ** * * ** *
37676 ATCGATGCATAAGGAGTGCATCGATGCATCCCAACAATAATAATACATCGAATACCTTTTATGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGC
* * *
37740 ACCGATGCATCAGCAGTGCATCGATGCAT
1 ATCGATGCATAAGTAGTGCATCGATGCAT
37769 ACCTTCATTA
Statistics
Matches: 135, Mismatches: 20, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
64 131 0.97
65 4 0.03
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.27
Consensus pattern (64 bp):
ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGC
Found at i:38094 original size:12 final size:12
Alignment explanation
Indices: 38076--38111 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
38066 TATATATGTT
38076 CATGTGATATGA
1 CATGTGATATGA
*
38088 TATGTGATATGA
1 CATGTGATATGA
38100 CATGTGATATGA
1 CATGTGATATGA
38112 GAAAATGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (12 bp):
CATGTGATATGA
Found at i:38277 original size:15 final size:15
Alignment explanation
Indices: 38259--38287 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
38249 GGTATAATAG
38259 TCCTTCGGGATGTAA
1 TCCTTCGGGATGTAA
38274 TCCTTCGGGATGTA
1 TCCTTCGGGATGTA
38288 GTGGTCCTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.21, G:0.28, T:0.34
Consensus pattern (15 bp):
TCCTTCGGGATGTAA
Found at i:45417 original size:51 final size:52
Alignment explanation
Indices: 45358--45480 Score: 203
Period size: 51 Copynumber: 2.4 Consensus size: 52
45348 AATAGTAGAT
*
45358 TTGGGATATCTCGGCGTCTTCAGGGTTGAACCAGATTTTTTTTTG-TCTTGC
1 TTGGGATATCTCGGCGTCTTCAGGGTTGAACCAGATTTTTTTTCGATCTTGC
*
45409 TTGGGATATCTCGGCGTCTTCAGGGTTGAATCAGATTTTTTTTCGATCTTGC
1 TTGGGATATCTCGGCGTCTTCAGGGTTGAACCAGATTTTTTTTCGATCTTGC
* *
45461 TTGGGATCTCCCGGCGTCTT
1 TTGGGATATCTCGGCGTCTT
45481 TAAGGTGTTT
Statistics
Matches: 67, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
51 43 0.64
52 24 0.36
ACGTcount: A:0.13, C:0.20, G:0.26, T:0.41
Consensus pattern (52 bp):
TTGGGATATCTCGGCGTCTTCAGGGTTGAACCAGATTTTTTTTCGATCTTGC
Found at i:45958 original size:13 final size:13
Alignment explanation
Indices: 45942--46001 Score: 79
Period size: 13 Copynumber: 4.8 Consensus size: 13
45932 TAACTGTAAA
45942 AAATAAAATAATT
1 AAATAAAATAATT
45955 AAATAAAATAATT
1 AAATAAAATAATT
* *
45968 AAATAATACAA-T
1 AAATAAAATAATT
*
45980 -AATTAAATAATT
1 AAATAAAATAATT
45992 AAATAAAATA
1 AAATAAAATA
46002 CTAACAAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
11 7 0.18
12 2 0.05
13 30 0.77
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (13 bp):
AAATAAAATAATT
Found at i:45960 original size:8 final size:8
Alignment explanation
Indices: 45947--45997 Score: 65
Period size: 8 Copynumber: 6.8 Consensus size: 8
45937 GTAAAAAATA
45947 AAATAATT
1 AAATAATT
45955 AAAT-A--
1 AAATAATT
45960 AAATAATT
1 AAATAATT
45968 AAATAA-T
1 AAATAATT
45975 ACAATAATT
1 A-AATAATT
45984 AAATAATT
1 AAATAATT
45992 AAATAA
1 AAATAA
45998 AATACTAACA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
5 4 0.11
6 1 0.03
7 3 0.08
8 28 0.74
9 2 0.05
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (8 bp):
AAATAATT
Found at i:45975 original size:16 final size:16
Alignment explanation
Indices: 45938--45997 Score: 72
Period size: 16 Copynumber: 3.9 Consensus size: 16
45928 TTTATAACTG
*
45938 TAAAAAATAAAATAAT
1 TAAATAATAAAATAAT
45954 T--A-AATAAAATAAT
1 TAAATAATAAAATAAT
*
45967 TAAATAATACAATAAT
1 TAAATAATAAAATAAT
*
45983 TAAATAATTAAATAA
1 TAAATAATAAAATAA
45998 AATACTAACA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
13 12 0.32
14 1 0.03
15 1 0.03
16 24 0.63
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (16 bp):
TAAATAATAAAATAAT
Found at i:46011 original size:24 final size:24
Alignment explanation
Indices: 45959--46012 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
45949 ATAATTAAAT
* *
45959 AAAATAATTAAATAATACAATAAT
1 AAAATAATTAAATAAAACAATAAC
* * *
45983 TAAATAATTAAATAAAATACTAAC
1 AAAATAATTAAATAAAACAATAAC
46007 AAAATA
1 AAAATA
46013 TGATTGATTT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.28
Consensus pattern (24 bp):
AAAATAATTAAATAAAACAATAAC
Found at i:53816 original size:14 final size:14
Alignment explanation
Indices: 53797--53823 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
53787 TATGTTTTAA
53797 AATTAGAAATTTTG
1 AATTAGAAATTTTG
53811 AATTAGAAATTTT
1 AATTAGAAATTTT
53824 ATTTAATGTA
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:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (14 bp):
AATTAGAAATTTTG
Found at i:54847 original size:13 final size:14
Alignment explanation
Indices: 54815--54850 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
54805 AAACAAGCAA
54815 AAAATTAAATACTG
1 AAAATTAAATACTG
*
54829 AAAATTAATTACT-
1 AAAATTAAATACTG
54842 AAAATTAAA
1 AAAATTAAA
54851 ATGAGGGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.31
Consensus pattern (14 bp):
AAAATTAAATACTG
Found at i:61912 original size:21 final size:22
Alignment explanation
Indices: 61863--61922 Score: 86
Period size: 21 Copynumber: 2.8 Consensus size: 22
61853 ATGAAATTTA
*
61863 TCCCGAAGGACCTGTGAGTATG
1 TCCCGAAGGACCTATGAGTATG
*
61885 TCTCGAAGGACCTATGAGT-TG
1 TCCCGAAGGACCTATGAGTATG
*
61906 TCCCGAAGAACCTATGA
1 TCCCGAAGGACCTATGA
61923 AACCCTCGAC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 17 0.50
22 17 0.50
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (22 bp):
TCCCGAAGGACCTATGAGTATG
Done.