Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002758.1 Hibiscus syriacus cultivar Beakdansim tig00005686_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: 70482
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:3237 original size:28 final size:29
Alignment explanation
Indices: 3200--3260 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
3190 TTAATTCACT
3200 AAAATAAAAATAAAAATTCAAG-AATTTA
1 AAAATAAAAATAAAAATTCAAGAAATTTA
* * *
3228 AAAATTAAAATATAAATTTAAGTAAATTTA
1 AAAATAAAAATAAAAATTCAAG-AAATTTA
3258 AAA
1 AAA
3261 GAATAATAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 19 0.68
30 9 0.32
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.30
Consensus pattern (29 bp):
AAAATAAAAATAAAAATTCAAGAAATTTA
Found at i:4072 original size:16 final size:15
Alignment explanation
Indices: 4034--4073 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
4024 TGCATATATA
*
4034 TATAATAATAATATT
1 TATAATAATAATACT
4049 TATAATAATATATACT
1 TATAATAATA-ATACT
*
4065 TCTAATAAT
1 TATAATAAT
4074 TACAATAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (15 bp):
TATAATAATAATACT
Found at i:6631 original size:11 final size:11
Alignment explanation
Indices: 6599--6632 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
6589 ACCTTTGCCA
*
6599 TCTTCTTCCTC
1 TCTTCTTCATC
6610 TCTTCTGTCATC
1 TCTTCT-TCATC
6622 TCTTCTTCATC
1 TCTTCTTCATC
6633 CTCAAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.06, C:0.38, G:0.03, T:0.53
Consensus pattern (11 bp):
TCTTCTTCATC
Found at i:7480 original size:19 final size:22
Alignment explanation
Indices: 7456--7504 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
7446 CTCAAACTGG
7456 TATCGATACCT-A-AGGCT-AA
1 TATCGATACCTGATAGGCTCAA
*
7475 TATCGAGA-CTGATAGGCTCAA
1 TATCGATACCTGATAGGCTCAA
7496 TATCGATAC
1 TATCGATAC
7505 TGACGTCATG
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 2 0.08
19 8 0.33
20 5 0.21
21 9 0.38
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (22 bp):
TATCGATACCTGATAGGCTCAA
Found at i:7499 original size:21 final size:20
Alignment explanation
Indices: 7468--7507 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
7458 TCGATACCTA
7468 AGGCTAATATCGAGACTGAT
1 AGGCTAATATCGAGACTGAT
*
7488 AGGCTCAATATCGATACTGA
1 AGGCT-AATATCGAGACTGA
7508 CGTCATGTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.25
Consensus pattern (20 bp):
AGGCTAATATCGAGACTGAT
Found at i:12907 original size:22 final size:21
Alignment explanation
Indices: 12874--12916 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
12864 TACGATGCAC
12874 TTTTGTACTAGTGCTAAGGCA
1 TTTTGTACTAGTGCTAAGGCA
*
12895 TTTTAGTATTAGTGCTAAGGCA
1 TTTT-GTACTAGTGCTAAGGCA
12917 CTTCCGCTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.40
Consensus pattern (21 bp):
TTTTGTACTAGTGCTAAGGCA
Found at i:17789 original size:136 final size:134
Alignment explanation
Indices: 17544--17951 Score: 460
Period size: 137 Copynumber: 3.0 Consensus size: 134
17534 CTGATTTAGT
* *
17544 CCTTGCTTTTGCTTAAGGTTCCATTTTGTTATTCGAACCAATAAATTGCTAAAATTGGTTAGGAT
1 CCTTGCTTTTGCCTAAGGTTCCATTTTGTTATTCGAACCAATAAATTGATAAAATTGGTTAGGAT
* * * * *
17609 TAATATTAGAGTCTTCATTATAGTTTTAATTTCACTTCCA-TCCTTTAATTTAGGAGACTTTCTA
66 TAATATTAGAG-CTT-ATTTTAGGTTTAATTTCACTT-TAGTCCTTTAATTTAGGAGAATTTTTA
17673 ATTTGGA
128 ATTTGGA
* *
17680 CCTTGCTTTTGCCCAAGGTTCCATTTTGGTTACTCGAACCAATAAATTGATAAAATTGGTTAGGA
1 CCTTGCTTTTGCCTAAGGTTCCATTTT-GTTATTCGAACCAATAAATTGATAAAATTGGTTAGGA
* *
17745 TTAATATTAGAGCATTATTTTAGGTTTAATTTAACTTTAGTCCTTTAATTTAGGAGAATTTTTGA
65 TTAATATTAGAGC-TTATTTTAGGTTTAATTTCACTTTAGTCCTTTAATTTAGGAGAATTTTTAA
*
17810 TTTGGT
129 TTTGGA
* * * * * * * * * *
17816 CCTCGTTTTTTTCCTGAGATTCTATTTTACTTATTTGAACCAATAAATTTGTTAAAATTGATTAG
1 CCTTG-CTTTTGCCTAAGGTTCCATTTT-GTTATTCGAACCAATAAA-TTGATAAAATTGGTTAG
** * * *
17881 CTTTTAATATTAGAGCCTCCA-TTTAGGTTTAATTGCACTTTAGTCCTTTAATTTAGGGGAATTT
63 -GATTAATATTAGAG-CT-TATTTTAGGTTTAATTTCACTTTAGTCCTTTAATTTAGGAGAATTT
17945 TTAATTT
125 TTAATTT
17952 ATTCCACTCC
Statistics
Matches: 232, Mismatches: 32, Indels: 13
0.84 0.12 0.05
Matches are distributed among these distances:
135 1 0.00
136 75 0.32
137 80 0.34
138 15 0.06
139 59 0.25
140 2 0.01
ACGTcount: A:0.27, C:0.13, G:0.14, T:0.45
Consensus pattern (134 bp):
CCTTGCTTTTGCCTAAGGTTCCATTTTGTTATTCGAACCAATAAATTGATAAAATTGGTTAGGAT
TAATATTAGAGCTTATTTTAGGTTTAATTTCACTTTAGTCCTTTAATTTAGGAGAATTTTTAATT
TGGA
Found at i:19612 original size:15 final size:15
Alignment explanation
Indices: 19588--19624 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
19578 GGTATTTAGT
*
19588 GGGCGAGCGGATGTG
1 GGGCGAGCGGATGTA
*
19603 GGGCGGGCGGATGTA
1 GGGCGAGCGGATGTA
19618 GGGCGAG
1 GGGCGAG
19625 TAAGGTCTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.14, C:0.14, G:0.62, T:0.11
Consensus pattern (15 bp):
GGGCGAGCGGATGTA
Found at i:28406 original size:270 final size:269
Alignment explanation
Indices: 27926--28527 Score: 832
Period size: 270 Copynumber: 2.2 Consensus size: 269
27916 GGATATCCAA
* *** * *
27926 TTCAAAGCTCAACTTCATAACGAAGGATTAACCTACGATTTTGACTTCACAACGAAGGATATCGT
1 TTCAAAGCTCAACTTCACAACGAAGGAGCCACCTATGATTTTGACTTCACAACGAAGGATATCAT
* * * * * *
27991 ACCCAATGATTGACCCAACTTCATGATGAATGAGTCATCTGTAACAAAACAATGAAAAACCAATT
66 ACCAAAAGATTGACCCAAATTCACGATCAAAGAGTCATCTGTAACAAAACAATGAAAAACCAATT
*
28056 TCATACCAAAGTATTCAGGTCAAATTTCAGCTTCACGACGAAGTATATTGGGCTATAAGACAATA
131 TCATACCAAAGTATTCAGGTCAAATTTCAGCTTCACGACGAAGTATATTGGGCTAGAAGACAATA
* * ** *
28121 CATGAGCGACTTTCCAATTCTTTGAGCCTTATTTTAACTTCACGACAAAGGATATAATGCTCAGG
196 CAGGAGCGACTTTCCAATGCTTTGAGCCCGATTTCAACTTCACGACAAAGGATATAATGCTCAGG
28186 ATTTTTCAG
261 ATTTTTCAG
* *
28195 TTCAAAGCTCAACATCACAACGAAGAAGCCACCTATGATTTTGACTTCACAACGAAGGATATCAT
1 TTCAAAGCTCAACTTCACAACGAAGGAGCCACCTATGATTTTGACTTCACAACGAAGGATATCAT
* * *
28260 ACCTAAAAGATTGACCTAAATTCACGA-CAAAGAAGTCATCTGTAACATAACAATGAAAAACCAG
66 ACC-AAAAGATTGACCCAAATTCACGATCAAAG-AGTCATCTGTAACAAAACAATGAAAAACCAA
* * *
28324 TTTCATACCAAAGTCTTCAGGTCAAATTTCAGCTTCACGATGAAGTATATTGGGCTAGAAGACGA
129 TTTCATACCAAAGTATTCAGGTCAAATTTCAGCTTCACGACGAAGTATATTGGGCTAGAAGACAA
* * * **
28389 TACAGGAGTGACTTTCCAATGCTTTGAGCCCGGTTTCAACTTCACGACGAAGGATATTGTGCTCA
194 TACAGGAGCGACTTTCCAATGCTTTGAGCCCGATTTCAACTTCACGACAAAGGATATAATGCTCA
28454 GGATTTTTCAG
259 GGATTTTTCAG
* ** *
28465 TTCAAAGCTCAACTTCACAACAAAGGAGCCA-CTCATGATTTCAACTTCACGAA-GAATGATATC
1 TTCAAAGCTCAACTTCACAACGAAGGAGCCACCT-ATGATTTTGACTTCAC-AACGAAGGATATC
28528 GTCTGAATGA
Statistics
Matches: 292, Mismatches: 37, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
269 65 0.22
270 225 0.77
271 2 0.01
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (269 bp):
TTCAAAGCTCAACTTCACAACGAAGGAGCCACCTATGATTTTGACTTCACAACGAAGGATATCAT
ACCAAAAGATTGACCCAAATTCACGATCAAAGAGTCATCTGTAACAAAACAATGAAAAACCAATT
TCATACCAAAGTATTCAGGTCAAATTTCAGCTTCACGACGAAGTATATTGGGCTAGAAGACAATA
CAGGAGCGACTTTCCAATGCTTTGAGCCCGATTTCAACTTCACGACAAAGGATATAATGCTCAGG
ATTTTTCAG
Found at i:29355 original size:18 final size:18
Alignment explanation
Indices: 29332--29374 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
29322 TTTTAGATTA
29332 TTTATTTAATTCTTATAT
1 TTTATTTAATTCTTATAT
*
29350 TTTATTTAATTCTTATCT
1 TTTATTTAATTCTTATAT
29368 TTTATTT
1 TTTATTT
29375 TAAAAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTATTTAATTCTTATAT
Found at i:29527 original size:6 final size:5
Alignment explanation
Indices: 29502--29531 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
29492 AAATTTAACT
29502 TTTTA TTTTA TTTTA TTTTA TCTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA T-TTTA TTTT
29532 CCCACTTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:29547 original size:36 final size:36
Alignment explanation
Indices: 29499--29568 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 36
29489 TTAAAATTTA
29499 ACTTTTTATTTTATTTTATTTTATCTTTATTTTCCC
1 ACTTTTTATTTTATTTTATTTTATCTTTATTTTCCC
* *
29535 ACTTCTTT-TTTTATTTTGTTTTATTTTTATTTTC
1 ACTT-TTTATTTTATTTTATTTTATCTTTATTTTC
29569 TCTTTTAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 28 0.90
37 3 0.10
ACGTcount: A:0.14, C:0.11, G:0.01, T:0.73
Consensus pattern (36 bp):
ACTTTTTATTTTATTTTATTTTATCTTTATTTTCCC
Found at i:34895 original size:32 final size:32
Alignment explanation
Indices: 34859--34927 Score: 93
Period size: 32 Copynumber: 2.2 Consensus size: 32
34849 AATCCAACTT
* * * *
34859 AAGGGAGTGCCTTGGGGCCTTAGAGCCTACCC
1 AAGGGAGTACCTTGAGGCCTAAGAGCCAACCC
*
34891 AAGGGAGTACTTTGAGGCCTAAGAGCCAACCC
1 AAGGGAGTACCTTGAGGCCTAAGAGCCAACCC
34923 AAGGG
1 AAGGG
34928 TCACCTTAGG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.26, C:0.25, G:0.33, T:0.16
Consensus pattern (32 bp):
AAGGGAGTACCTTGAGGCCTAAGAGCCAACCC
Found at i:36245 original size:2 final size:2
Alignment explanation
Indices: 36238--36310 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
36228 TTGTGTACCA
36238 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36280 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
36311 ATCGTACCGA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:37752 original size:20 final size:21
Alignment explanation
Indices: 37707--37764 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
37697 CAGAAACTTT
**
37707 GGGATCGATCCTTTTTGGTTAA
1 GGGATCGATCCTTTTT-GAAAA
37729 GGGATCGATCCTTTTT-AAAA
1 GGGATCGATCCTTTTTGAAAA
*
37749 GGGATCAATCCTTTTT
1 GGGATCGATCCTTTTT
37765 CTGGAAAACT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 17 0.52
22 16 0.48
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.40
Consensus pattern (21 bp):
GGGATCGATCCTTTTTGAAAA
Found at i:39829 original size:17 final size:19
Alignment explanation
Indices: 39807--39844 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
39797 AAATCAAGAC
*
39807 ATTAATT-AACTCTTA-AA
1 ATTAATTGAAATCTTAGAA
39824 ATTAATTGAAATCTTAGAA
1 ATTAATTGAAATCTTAGAA
39843 AT
1 AT
39845 CATTTCAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 7 0.39
19 4 0.22
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.39
Consensus pattern (19 bp):
ATTAATTGAAATCTTAGAA
Found at i:52894 original size:24 final size:25
Alignment explanation
Indices: 52867--52920 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
52857 GAATATTTTA
*
52867 TCTGATA-TCTGTTCTGATTTCTGC
1 TCTGATATTCTGTTATGATTTCTGC
*
52891 TCTGA-ATTCTGTTATGATTTTTGC
1 TCTGATATTCTGTTATGATTTCTGC
52915 TCTGAT
1 TCTGAT
52921 TACTGATTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 1 0.04
24 25 0.96
ACGTcount: A:0.15, C:0.17, G:0.17, T:0.52
Consensus pattern (25 bp):
TCTGATATTCTGTTATGATTTCTGC
Found at i:52920 original size:12 final size:12
Alignment explanation
Indices: 52867--52921 Score: 56
Period size: 12 Copynumber: 4.6 Consensus size: 12
52857 GAATATTTTA
* *
52867 TCTGATATCTGT
1 TCTGATTTCTGC
52879 TCTGATTTCTGC
1 TCTGATTTCTGC
* *
52891 TCTGAATTCTGT
1 TCTGATTTCTGC
* *
52903 TATGATTTTTGC
1 TCTGATTTCTGC
52915 TCTGATT
1 TCTGATT
52922 ACTGATTTCT
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.15, C:0.16, G:0.16, T:0.53
Consensus pattern (12 bp):
TCTGATTTCTGC
Found at i:53132 original size:32 final size:32
Alignment explanation
Indices: 53067--53140 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 32
53057 CTAAGGTGAC
* * *
53067 CTTGGGTAGG-CTATGCGGCCCTGAGATTTTT
1 CTTGGGTAGGCCTATGCGGCCCCGAGAATATT
* *
53098 CTTGGGTAGGCCTCTGTGGCCCCGAGAATATT
1 CTTGGGTAGGCCTATGCGGCCCCGAGAATATT
53130 CTTGGGTAGGC
1 CTTGGGTAGGC
53141 TCACAGGCCC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
31 10 0.27
32 27 0.73
ACGTcount: A:0.14, C:0.22, G:0.34, T:0.31
Consensus pattern (32 bp):
CTTGGGTAGGCCTATGCGGCCCCGAGAATATT
Found at i:54777 original size:32 final size:33
Alignment explanation
Indices: 54706--54778 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 33
54696 ATGACTGTAA
* **
54706 CTGCTATGCATTATCTAAATGTGACATTGACAT
1 CTGCTATGCATTAACTAAATGCAACATTGACAT
* *
54739 -TACTATGCATTAACTGAATGCAACATTGAC-T
1 CTGCTATGCATTAACTAAATGCAACATTGACAT
54770 CTGCTATGC
1 CTGCTATGC
54779 TAGTATCTAC
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
31 1 0.03
32 32 0.97
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (33 bp):
CTGCTATGCATTAACTAAATGCAACATTGACAT
Found at i:62805 original size:21 final size:21
Alignment explanation
Indices: 62779--62830 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
62769 CAAGGTGCGT
62779 TATTACAAAGCAAAACAACTC
1 TATTACAAAGCAAAACAACTC
* *
62800 TATTACAAAGTAAAGCAACTC
1 TATTACAAAGCAAAACAACTC
62821 TATTACAAAG
1 TATTACAAAG
62831 AGTGTTAGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.50, C:0.19, G:0.08, T:0.23
Consensus pattern (21 bp):
TATTACAAAGCAAAACAACTC
Done.