Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005649.1 Hibiscus syriacus cultivar Beakdansim tig00013197_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: 70998
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:3382 original size:28 final size:30
Alignment explanation
Indices: 3316--3386 Score: 128
Period size: 28 Copynumber: 2.4 Consensus size: 30
3306 TCTCAGGCAC
3316 AATGAAATGAATGCTCCTTTCTAGTAAAAT
1 AATGAAATGAATGCTCCTTTCTAGTAAAAT
3346 AATGAAATGAATGCTCC-TTCTAGT-AAAT
1 AATGAAATGAATGCTCCTTTCTAGTAAAAT
3374 AATGAAATGAATG
1 AATGAAATGAATG
3387 TTAGTCGCAG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
28 17 0.41
29 7 0.17
30 17 0.41
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.31
Consensus pattern (30 bp):
AATGAAATGAATGCTCCTTTCTAGTAAAAT
Found at i:21481 original size:6 final size:6
Alignment explanation
Indices: 21470--21500 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
21460 TCAACTCACA
21470 GGAACC GGAACC GGAACC GGAACC GGAACC G
1 GGAACC GGAACC GGAACC GGAACC GGAACC G
21501 CGGAGAGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.32, G:0.35, T:0.00
Consensus pattern (6 bp):
GGAACC
Found at i:24532 original size:10 final size:10
Alignment explanation
Indices: 24517--24544 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
24507 TGTTTAAATA
24517 CTTCGATTTC
1 CTTCGATTTC
24527 CTTCGATTTC
1 CTTCGATTTC
24537 CTTCGATT
1 CTTCGATT
24545 ATTGTCTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.11, C:0.29, G:0.11, T:0.50
Consensus pattern (10 bp):
CTTCGATTTC
Found at i:28788 original size:14 final size:14
Alignment explanation
Indices: 28771--28797 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28761 TTTTTTTAAC
28771 CCCTTTTCCCTTTG
1 CCCTTTTCCCTTTG
28785 CCCTTTTCCCTTT
1 CCCTTTTCCCTTT
28798 TTTTTTCTTT
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:0.00, C:0.44, G:0.04, T:0.52
Consensus pattern (14 bp):
CCCTTTTCCCTTTG
Found at i:38474 original size:22 final size:20
Alignment explanation
Indices: 38448--38487 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
38438 AATTTCGTCC
38448 TTATATTATACAATATATATAT
1 TTATATTATA-AAT-TATATAT
38470 TTATATTATAAATTATAT
1 TTATATTATAAATTATAT
38488 TTACATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 3 0.17
22 10 0.56
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (20 bp):
TTATATTATAAATTATATAT
Found at i:39799 original size:20 final size:20
Alignment explanation
Indices: 39774--39811 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
39764 ACTTTCGTTT
39774 TTTTATTTT-TATATTATTTA
1 TTTTATTTTAT-TATTATTTA
39794 TTTTATTTTATTATTATT
1 TTTTATTTTATTATTATT
39812 ATATATACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTATTTTATTATTATTTA
Found at i:39895 original size:21 final size:22
Alignment explanation
Indices: 39844--39886 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
39834 ATCTAATTTC
39844 TTTTAT-TTT-TATTCTCCATT
1 TTTTATCTTTCTATTCTCCATT
39864 TTTTATCTTTCTATTCTCC-TT
1 TTTTATCTTTCTATTCTCCATT
39885 TT
1 TT
39887 GTTTGTTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.29
21 7 0.33
22 8 0.38
ACGTcount: A:0.12, C:0.19, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTTATCTTTCTATTCTCCATT
Found at i:40951 original size:10 final size:10
Alignment explanation
Indices: 40938--40969 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
40928 TTATTTCTTG
40938 TTATTTTTAT
1 TTATTTTTAT
*
40948 TTATTTTCAT
1 TTATTTTTAT
40958 TTATTTTTAT
1 TTATTTTTAT
40968 TT
1 TT
40970 TACTAACCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (10 bp):
TTATTTTTAT
Found at i:50409 original size:16 final size:16
Alignment explanation
Indices: 50384--50427 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
50374 TCCTAAGTTG
50384 AAAAAA-AAAAAAAAA
1 AAAAAAGAAAAAAAAA
50399 AAAAAAGAAAAAAAAA
1 AAAAAAGAAAAAAAAA
*
50415 AAAAAGGAAAAAA
1 AAAAAAGAAAAAA
50428 CGTTTGGGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
15 6 0.22
16 21 0.78
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (16 bp):
AAAAAAGAAAAAAAAA
Found at i:50420 original size:15 final size:15
Alignment explanation
Indices: 50384--50427 Score: 72
Period size: 15 Copynumber: 2.9 Consensus size: 15
50374 TCCTAAGTTG
50384 AAAAAAA-AAAAAAA
1 AAAAAAAGAAAAAAA
50398 AAAAAAAGAAAAAAA
1 AAAAAAAGAAAAAAA
50413 AAAAAAAGGAAAAAA
1 AAAAAAA-GAAAAAA
50428 CGTTTGGGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.25
15 14 0.50
16 7 0.25
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (15 bp):
AAAAAAAGAAAAAAA
Found at i:50427 original size:1 final size:1
Alignment explanation
Indices: 50384--50419 Score: 63
Period size: 1 Copynumber: 36.0 Consensus size: 1
50374 TCCTAAGTTG
*
50384 AAAAAAAAAAAAAAAAAAAAAGAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
50420 GGAAAAAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:51527 original size:105 final size:105
Alignment explanation
Indices: 51226--51859 Score: 1178
Period size: 105 Copynumber: 6.0 Consensus size: 105
51216 AGGTTTTACC
51226 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
51291 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
51331 CAGAGCCAATTTCAAACTTCACAACGAAGGATATTGGGCTCCAGACAACGTAAGTTCAACTTCAC
1 CAGAGCCAATTTC-AACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
51396 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
65 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
51437 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
*
51502 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
51542 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGGCAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
*
51607 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
51647 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
*
51712 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
51752 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGGCAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
*
51817 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
51857 CAG
1 CAG
51860 CTCCACAACG
Statistics
Matches: 513, Mismatches: 15, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
105 409 0.80
106 104 0.20
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:51955 original size:20 final size:20
Alignment explanation
Indices: 51917--51957 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
51907 CCAGAACTCT
*
51917 GAGTTCGATTTCAGCTTCAC
1 GAGTTCGATTTCAACTTCAC
* *
51937 GAGTTTGATTTCAATTTCAC
1 GAGTTCGATTTCAACTTCAC
51957 G
1 G
51958 TCGAAGGATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.39
Consensus pattern (20 bp):
GAGTTCGATTTCAACTTCAC
Found at i:52203 original size:22 final size:20
Alignment explanation
Indices: 52177--52216 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
52167 AATTTCGTCC
52177 TTATATTATACAATATATATAT
1 TTATATTATA-AAT-TATATAT
52199 TTATATTATAAATTATAT
1 TTATATTATAAATTATAT
52217 TTACATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 3 0.17
22 10 0.56
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (20 bp):
TTATATTATAAATTATATAT
Found at i:53527 original size:20 final size:20
Alignment explanation
Indices: 53502--53539 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
53492 ACTTTCGTTT
53502 TTTTATTTT-TATATTATTTA
1 TTTTATTTTAT-TATTATTTA
53522 TTTTATTTTATTATTATT
1 TTTTATTTTATTATTATT
53540 ATATATACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTATTTTATTATTATTTA
Found at i:53623 original size:21 final size:22
Alignment explanation
Indices: 53572--53614 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
53562 ATCTAATTTC
53572 TTTTAT-TTT-TATTCTCCATT
1 TTTTATCTTTCTATTCTCCATT
53592 TTTTATCTTTCTATTCTCC-TT
1 TTTTATCTTTCTATTCTCCATT
53613 TT
1 TT
53615 GTTTGTTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.29
21 7 0.33
22 8 0.38
ACGTcount: A:0.12, C:0.19, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTTATCTTTCTATTCTCCATT
Found at i:56932 original size:60 final size:60
Alignment explanation
Indices: 56868--56981 Score: 174
Period size: 60 Copynumber: 1.9 Consensus size: 60
56858 TATAAGATAC
* * *
56868 TACTTTGTTGAGTCCCTCAACTATTAAAAGTTACAAAATAATCCCCTGATTATTGAAAGT
1 TACTTTGTTGAGTCCCTCAACTATTAAAAATTACAAAATAATCACCTGACTATTGAAAGT
* * *
56928 TACTTTGTTGAGTCCCTCGACTATTAAAAATTATAAAATGATCACCTGACTATT
1 TACTTTGTTGAGTCCCTCAACTATTAAAAATTACAAAATAATCACCTGACTATT
56982 TATCATATTC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.36
Consensus pattern (60 bp):
TACTTTGTTGAGTCCCTCAACTATTAAAAATTACAAAATAATCACCTGACTATTGAAAGT
Found at i:60158 original size:24 final size:24
Alignment explanation
Indices: 60131--60186 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
60121 GTTCATTTAT
* * *
60131 GTTTGTGAACGTTCGGTTATGTTC
1 GTTTATGAACGTCCAGTTATGTTC
**
60155 GTTTATGTTCGTCCAGTTATGTTC
1 GTTTATGAACGTCCAGTTATGTTC
60179 GTTTATGA
1 GTTTATGA
60187 TCATTCATTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.14, C:0.12, G:0.25, T:0.48
Consensus pattern (24 bp):
GTTTATGAACGTCCAGTTATGTTC
Found at i:60198 original size:24 final size:24
Alignment explanation
Indices: 60146--60201 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
60136 TGAACGTTCG
* *
60146 GTTATGTTCGTTTATGTTCGTCCA
1 GTTATGTTCGTTTATGATCATCCA
*
60170 GTTATGTTCGTTTATGATCATTCA
1 GTTATGTTCGTTTATGATCATCCA
*
60194 TTTATGTT
1 GTTATGTT
60202 TAACCCAATC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.16, C:0.12, G:0.18, T:0.54
Consensus pattern (24 bp):
GTTATGTTCGTTTATGATCATCCA
Found at i:61260 original size:64 final size:63
Alignment explanation
Indices: 61183--61315 Score: 148
Period size: 64 Copynumber: 2.1 Consensus size: 63
61173 CAATGTGTAC
** *
61183 CGATGC-ACTCTTAAATAATGAACATTGAATGCCA-TTAGTGCA-TCGATGCATAAGG-AGTGCA
1 CGATGCAACTCTTAAATAACAAACATCGAATGCCATTTA-TGCACT-GATGCAT-AGGAAGTGCA
61244 T
63 T
* **
61245 CGATGCAACTGCTTAAATTACAAACATCGAATGGGATTTATGCACTGATGCATAGGAAGTGCAT
1 CGATGCAACT-CTTAAATAACAAACATCGAATGCCATTTATGCACTGATGCATAGGAAGTGCAT
61309 CGATGCA
1 CGATGCA
61316 CCCGTCAAGG
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
62 6 0.10
63 6 0.10
64 44 0.73
65 4 0.07
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (63 bp):
CGATGCAACTCTTAAATAACAAACATCGAATGCCATTTATGCACTGATGCATAGGAAGTGCAT
Found at i:61953 original size:18 final size:18
Alignment explanation
Indices: 61886--61956 Score: 65
Period size: 18 Copynumber: 3.8 Consensus size: 18
61876 AGGGATTATC
61886 AGTGGTTCTTT-GGGACAT
1 AGTGG-TCTTTCGGGACAT
*
61904 AGTGGT-TCTTCGGAACAAT
1 AGTGGTCT-TTCGGGAC-AT
* *
61923 CAGTGATCATTCGGGACAT
1 -AGTGGTCTTTCGGGACAT
61942 AGTGGTCTTTCGGGA
1 AGTGGTCTTTCGGGA
61957 AAAATATTCA
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
16 1 0.02
17 3 0.07
18 22 0.52
19 4 0.10
20 12 0.29
ACGTcount: A:0.21, C:0.15, G:0.31, T:0.32
Consensus pattern (18 bp):
AGTGGTCTTTCGGGACAT
Found at i:70213 original size:2 final size:2
Alignment explanation
Indices: 70206--70235 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
70196 ATTATTAACA
70206 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
70236 TCAAGTTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.