Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007249.1 Hibiscus syriacus cultivar Beakdansim tig00019206_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: 46462
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:4180 original size:23 final size:24
Alignment explanation
Indices: 4123--4199 Score: 75
Period size: 24 Copynumber: 3.2 Consensus size: 24
4113 TGTTAAAATG
* * *
4123 ATAAACGAACACGAATGAAAGAAAC
1 ATAAACGAACACAAACGAACG-AAC
* * *
4148 GTAAACGAACAC-AACGAATGAAT
1 ATAAACGAACACAAACGAACGAAC
*
4171 ATAAATGAACACAAACGAACGAAC
1 ATAAACGAACACAAACGAACGAAC
4195 ATAAA
1 ATAAA
4200 ATTAATTGGT
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
23 12 0.28
24 20 0.47
25 11 0.26
ACGTcount: A:0.58, C:0.17, G:0.14, T:0.10
Consensus pattern (24 bp):
ATAAACGAACACAAACGAACGAAC
Found at i:4392 original size:14 final size:14
Alignment explanation
Indices: 4373--4403 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
4363 CGGGTTTGGA
4373 GAACATAAATAAAC
1 GAACATAAATAAAC
*
4387 GAACATAAATGAAC
1 GAACATAAATAAAC
4401 GAA
1 GAA
4404 TCACCTAACG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.13, G:0.13, T:0.13
Consensus pattern (14 bp):
GAACATAAATAAAC
Found at i:7701 original size:22 final size:23
Alignment explanation
Indices: 7676--7722 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
7666 TAATTTCATT
*
7676 TTTATCATCATT-CGTTAAAAAA
1 TTTATCACCATTCCGTTAAAAAA
*
7698 TTTATCACCTTTCCGTTAAAAAA
1 TTTATCACCATTCCGTTAAAAAA
7721 TT
1 TT
7723 AATGGTGATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.36, C:0.17, G:0.04, T:0.43
Consensus pattern (23 bp):
TTTATCACCATTCCGTTAAAAAA
Found at i:8462 original size:60 final size:59
Alignment explanation
Indices: 8365--8497 Score: 155
Period size: 60 Copynumber: 2.2 Consensus size: 59
8355 TCATATGATG
* * *
8365 ATTTTGTAACTTTTAATAGTCAAAGGACTCAATAAAGCAATATCC-TATAATCAAGGGACC
1 ATTTTGTAACTTTTAATAGTC-AAGGACTCAAAAAAGCAACA-CCTTATAATAAAGGGACC
* *
8425 ATTTTGTAACTTTTAATAGTC-GGGTACTCAAAAAAAGCAACACCTTATAGTAAAGGGACC
1 ATTTTGTAACTTTTAATAGTCAAGG-ACTC-AAAAAAGCAACACCTTATAATAAAGGGACC
8485 ATTTGTGT-ACTTT
1 ATTT-TGTAACTTT
8498 ACTCTTTTTT
Statistics
Matches: 64, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
58 2 0.03
59 6 0.09
60 53 0.83
61 3 0.05
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (59 bp):
ATTTTGTAACTTTTAATAGTCAAGGACTCAAAAAAGCAACACCTTATAATAAAGGGACC
Found at i:23694 original size:13 final size:13
Alignment explanation
Indices: 23676--23701 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
23666 TCTTTGCGAC
23676 GTTTGTATTTAAT
1 GTTTGTATTTAAT
23689 GTTTGTATTTAAT
1 GTTTGTATTTAAT
23702 TTTTTTAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.15, T:0.62
Consensus pattern (13 bp):
GTTTGTATTTAAT
Found at i:23754 original size:25 final size:24
Alignment explanation
Indices: 23685--23755 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 24
23675 CGTTTGTATT
*
23685 TAATGTTTGTATTTAA-TTTTTT-
1 TAATGTTTTTATTTAATTTTTTTG
* *
23707 TAAT-TTTTTAATT-ATTTAGTTTG
1 TAATGTTTTTATTTAATTT-TTTTG
23730 TAATGTTTTTATTTAATTTTCTTTG
1 TAATGTTTTTATTTAATTTT-TTTG
23755 T
1 T
23756 TTCTTAATGT
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
20 1 0.03
21 9 0.24
22 7 0.18
23 4 0.11
24 8 0.21
25 9 0.24
ACGTcount: A:0.23, C:0.01, G:0.08, T:0.68
Consensus pattern (24 bp):
TAATGTTTTTATTTAATTTTTTTG
Found at i:26332 original size:102 final size:102
Alignment explanation
Indices: 26160--26349 Score: 231
Period size: 102 Copynumber: 1.9 Consensus size: 102
26150 AAGCTAGTAG
* * * * * *
26160 TTGAATGTATTCCCCTTGAACTTGAAGGCATCGTGTCATACGGGTCATGAACTGAGTGTTGTGTT
1 TTGAATGCATTCCCCTTGAACTTGAAGGCATCATGTCAAACGGGTCATAAACAGAGTGTTGTGTC
* * * *
26225 GAAGGCTTCTCTATATTGAGGTCGAAGAAGCTCACAT
66 AAAGGCATCTCCATATTCAGGTCGAAGAAGCTCACAT
* * *
26262 TTGAATGCA-TCCCCTTGGAACTTGAAGGCATCATGTCAAATGGGT-ATTAAACAGATTGTTTTG
1 TTGAATGCATTCCCCTT-GAACTTGAAGGCATCATGTCAAACGGGTCA-TAAACAGAGTGTTGTG
26325 TCAAAGGCATCTCCATATTCAGGTC
64 TCAAAGGCATCTCCATATTCAGGTC
26350 AAAAAAATTG
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
101 8 0.11
102 65 0.89
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.32
Consensus pattern (102 bp):
TTGAATGCATTCCCCTTGAACTTGAAGGCATCATGTCAAACGGGTCATAAACAGAGTGTTGTGTC
AAAGGCATCTCCATATTCAGGTCGAAGAAGCTCACAT
Found at i:27643 original size:31 final size:31
Alignment explanation
Indices: 27572--27631 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
27562 AAGCATAAGG
* *
27572 GATTAAAATCGAACTGAACGATAATGTTAGA
1 GATTAAAATCGAACTGAACAATAACGTTAGA
*
27603 GATTAAAATCGAACTGATCAATAACGTTA
1 GATTAAAATCGAACTGAACAATAACGTTA
27632 TGAACTTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.27
Consensus pattern (31 bp):
GATTAAAATCGAACTGAACAATAACGTTAGA
Found at i:32076 original size:394 final size:394
Alignment explanation
Indices: 31408--32192 Score: 1491
Period size: 394 Copynumber: 2.0 Consensus size: 394
31398 TATGATCTGC
31408 CACATAAGGGGTTTTGTGTTTGACTGATGTAACAATGAAAATGGGCCCAAATCCCACCGCTTTAG
1 CACATAAGGGGTTTTGTGTTTGACTGATGTAACAATGAAAATGGGCCCAAATCCCACCGCTTTAG
31473 GCCTTTCATCACGAGCTTTAGGGAGTGAGAGCAAGATGCGACGCTGACACTGAACCTTCTTATGC
66 GCCTTTCATCACGAGCTTTAGGGAGTGAGAGCAAGATGCGACGCTGACACTGAACCTTCTTATGC
31538 CAGCTTTATAAATTCGATGACTTGAGATATGACCGAAATCTTAATCAGATCTAATCCATTGTCAT
131 CAGCTTTATAAATTCGATGACTTGAGATATGACCGAAATCTTAATCAGATCTAATCCATTGTCAT
* * *
31603 CCTTTCATTTATGTGTCTAACGTTATAAACGTTATCATTTTAGGTGTCTAAGTTATAACGATTGT
196 CCTTTCATTTATCTGTCTAACGTTATAAACGTTATCATTTTAGGTGTCTAAATCATAACGATTGT
* *
31668 TAAATTTCTCCGTTAAGCGACACTTGTCACATTAAGATAATTCTGAAAATTTTATTTAAATTTTA
261 TAAATTTCTCCGTTAAACGACACTTATCACATTAAGATAATTCTGAAAATTTTATTTAAATTTTA
31733 AAAAATCTTAAAATTACATTTTTTTAATAAAACCACAAAAATATTCAAAAATATTTTTTTAAAAA
326 AAAAATCTTAAAATTACATTTTTTTAATAAAACCACAAAAATATTCAAAAATATTTTTTTAAAAA
31798 AAAT
391 AAAT
31802 CACATAAGGGGTTTTGTGTTTGACTGATGTAACAATGAAAATGGGCCCAAATCCCACCGCTTTAG
1 CACATAAGGGGTTTTGTGTTTGACTGATGTAACAATGAAAATGGGCCCAAATCCCACCGCTTTAG
31867 GCCTTTCATCACGAGCTTTAGGGAGTGAGAGCAAGATGCGACGCTGACACTGAACCTTCTTATGC
66 GCCTTTCATCACGAGCTTTAGGGAGTGAGAGCAAGATGCGACGCTGACACTGAACCTTCTTATGC
31932 CAGCTTTATAAATTCGATGACTTGAGATATGACCGAAATCTTAATCAGATCTAATCCATTGTCAT
131 CAGCTTTATAAATTCGATGACTTGAGATATGACCGAAATCTTAATCAGATCTAATCCATTGTCAT
31997 CCTTTCATTTATCTGTCTAACGTTATAAACGTTATCATTTTAGGTGT-TCAAATCATAACGATTG
196 CCTTTCATTTATCTGTCTAACGTTATAAACGTTATCATTTTAGGTGTCT-AAATCATAACGATTG
* *
32061 TTAAATTTCTCCGTTAAATGGCACTTATCACATTAAGATAATTCTGAAAATTTTATTTAAATTTT
260 TTAAATTTCTCCGTTAAACGACACTTATCACATTAAGATAATTCTGAAAATTTTATTTAAATTTT
32126 AAAAAATCTTAAAATTACATTTTTTTAATAAAACCACAAAAATATTCAAAAATATTTTTTTAAAA
325 AAAAAATCTTAAAATTACATTTTTTTAATAAAACCACAAAAATATTCAAAAATATTTTTTTAAAA
32191 AA
390 AA
32193 TCATACTTAA
Statistics
Matches: 383, Mismatches: 7, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
393 1 0.00
394 382 1.00
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (394 bp):
CACATAAGGGGTTTTGTGTTTGACTGATGTAACAATGAAAATGGGCCCAAATCCCACCGCTTTAG
GCCTTTCATCACGAGCTTTAGGGAGTGAGAGCAAGATGCGACGCTGACACTGAACCTTCTTATGC
CAGCTTTATAAATTCGATGACTTGAGATATGACCGAAATCTTAATCAGATCTAATCCATTGTCAT
CCTTTCATTTATCTGTCTAACGTTATAAACGTTATCATTTTAGGTGTCTAAATCATAACGATTGT
TAAATTTCTCCGTTAAACGACACTTATCACATTAAGATAATTCTGAAAATTTTATTTAAATTTTA
AAAAATCTTAAAATTACATTTTTTTAATAAAACCACAAAAATATTCAAAAATATTTTTTTAAAAA
AAAT
Found at i:37149 original size:35 final size:37
Alignment explanation
Indices: 37077--37149 Score: 87
Period size: 35 Copynumber: 2.0 Consensus size: 37
37067 TACTATAATT
***
37077 AATTTATATATTTTCTTTAAAAAAATTAAATTTATAA
1 AATTTATATATTTTCTTTAAAAAAATTAAAAAGATAA
* *
37114 AATTTATA-ATTTT-TTTTACAAAATTAAAAAGATAA
1 AATTTATATATTTTCTTTAAAAAAATTAAAAAGATAA
37149 A
1 A
37150 TAGGTTTAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
35 18 0.58
36 5 0.16
37 8 0.26
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (37 bp):
AATTTATATATTTTCTTTAAAAAAATTAAAAAGATAA
Found at i:42694 original size:28 final size:28
Alignment explanation
Indices: 42646--42713 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 28
42636 TTTTTTCATT
** *
42646 TAAAGTATTTTTTGGTCAAAATATGTACC
1 TAAAGTA-TTTTACGTCAAAATAGGTACC
*
42675 TAAAGTATTTTACGTCAAAATAGGTATC
1 TAAAGTATTTTACGTCAAAATAGGTACC
42703 TAAAGT-TTTTA
1 TAAAGTATTTTA
42714 AACTTTTTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 5 0.14
28 23 0.66
29 7 0.20
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.41
Consensus pattern (28 bp):
TAAAGTATTTTACGTCAAAATAGGTACC
Found at i:42871 original size:29 final size:29
Alignment explanation
Indices: 42794--42871 Score: 86
Period size: 31 Copynumber: 2.6 Consensus size: 29
42784 GAAAATTTGA
*
42794 ATACTTTAGGTATCTATTTTAACCAAAAAG
1 ATACTTTAGGTAT-TATTTTAACCAAAAAC
* *
42824 ATAACTTTAGGTACTTATTTTGATC-AAAAC
1 AT-ACTTTAGGTA-TTATTTTAACCAAAAAC
42854 ATACTTTAGGTATGTATT
1 ATACTTTAGGTAT-TATT
42872 ACTTTTTTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
28 1 0.02
29 14 0.33
30 8 0.19
31 18 0.43
32 1 0.02
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.41
Consensus pattern (29 bp):
ATACTTTAGGTATTATTTTAACCAAAAAC
Done.