Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007704.1 Hibiscus syriacus cultivar Beakdansim tig00109919_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: 612835
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 3 of 3
Found at i:567903 original size:14 final size:14
Alignment explanation
Indices: 567854--567892 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
567844 AGTTTCATAA
*
567854 AAAAAGAAAAAAAT
1 AAAAAGAAAAAAAG
567868 AAAAAGAAAAAAAG
1 AAAAAGAAAAAAAG
567882 AAAAAGAAAAA
1 AAAAAGAAAAA
567893 GAAAGAAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.87, C:0.00, G:0.10, T:0.03
Consensus pattern (14 bp):
AAAAAGAAAAAAAG
Found at i:569649 original size:36 final size:38
Alignment explanation
Indices: 569602--569686 Score: 120
Period size: 38 Copynumber: 2.3 Consensus size: 38
569592 TATTTCATTT
* * *
569602 GAGATTGTTTTACTT-GAAACA-AATTTCGTCTCTCTA
1 GAGATTGTTTTACTTAAAAACATAATTTCGACTCACTA
*
569638 GAGATTGTTTTACTTAAAAACATAATTTCGACTCACTT
1 GAGATTGTTTTACTTAAAAACATAATTTCGACTCACTA
569676 GAGATTGTTTT
1 GAGATTGTTTT
569687 TCGACTTTGT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
36 15 0.35
37 5 0.12
38 23 0.53
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.42
Consensus pattern (38 bp):
GAGATTGTTTTACTTAAAAACATAATTTCGACTCACTA
Found at i:570203 original size:44 final size:44
Alignment explanation
Indices: 570125--570277 Score: 171
Period size: 44 Copynumber: 3.5 Consensus size: 44
570115 CATCCATCAT
* * **
570125 ATAAGGAGTTGGATCAACATCACCCTTTTTCTCGATTCAATTAC
1 ATAAGGAGTTGGATCAACATCATCATTTCGCTCGATTCAATTAC
* ** * *
570169 ATAAGGAGTTGGGTCATTATCATCATTTCGCTCGATTCCATCAC
1 ATAAGGAGTTGGATCAACATCATCATTTCGCTCGATTCAATTAC
* * * *
570213 ATAAGAAGTTTGATCAACATCATCTTTTCGCTCGATTCTATTAC
1 ATAAGGAGTTGGATCAACATCATCATTTCGCTCGATTCAATTAC
* *
570257 ATAAAGAGTTTGATCAACATC
1 ATAAGGAGTTGGATCAACATC
570278 GCCTTTTTAC
Statistics
Matches: 90, Mismatches: 19, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 90 1.00
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (44 bp):
ATAAGGAGTTGGATCAACATCATCATTTCGCTCGATTCAATTAC
Found at i:570284 original size:44 final size:44
Alignment explanation
Indices: 570125--570320 Score: 155
Period size: 44 Copynumber: 4.5 Consensus size: 44
570115 CATCCATCAT
* *
570125 ATAAGGAGTTGGATCAACATCACCCTTTT-TCTCGATTCAATTAC
1 ATAAAGAGTTGGATCAACATCA-CCTTTTCGCTCGATTCAATTAC
* * ** * * * *
570169 ATAAGGAGTTGGGTCATTATCATCATTTCGCTCGATTCCATCAC
1 ATAAAGAGTTGGATCAACATCACCTTTTCGCTCGATTCAATTAC
* * *
570213 AT-AAGAAGTTTGATCAACATCATCTTTTCGCTCGATTCTATTAC
1 ATAAAG-AGTTGGATCAACATCACCTTTTCGCTCGATTCAATTAC
* * ** * *
570257 ATAAAGAGTTTGATCAACATCGCCTTTTTACTCGATTCCATCAC
1 ATAAAGAGTTGGATCAACATCACCTTTTCGCTCGATTCAATTAC
* *
570301 A-AAATGAGGTGGATCGACAT
1 ATAAA-GAGTTGGATCAACAT
570321 TTCCAGTGGA
Statistics
Matches: 123, Mismatches: 25, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
43 9 0.07
44 111 0.90
45 3 0.02
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (44 bp):
ATAAAGAGTTGGATCAACATCACCTTTTCGCTCGATTCAATTAC
Found at i:570291 original size:88 final size:88
Alignment explanation
Indices: 570117--570301 Score: 210
Period size: 88 Copynumber: 2.1 Consensus size: 88
570107 CCTCGGCTCA
* * * * *
570117 TCCATCATATAAGGAGTTGGATCAACATCACCCTTTTTCTCGATTCAATTACATAAGGAGTTGGG
1 TCCATCACATAAGAAGTTGGATCAACATCACCCTTTTGCTCGATTCAATTACATAAAGAGTTGGA
** * *
570182 TCATTATCATCATTTCGCTCGAT
66 TCAACATCACCATTTCACTCGAT
* * * *
570205 TCCATCACATAAGAAGTTTGATCAACATCA-TCTTTTCGCTCGATTCTATTACATAAAGAGTTTG
1 TCCATCACATAAGAAGTTGGATCAACATCACCCTTTT-GCTCGATTCAATTACATAAAGAGTTGG
* * *
570269 ATCAACATCGCCTTTTTACTCGAT
65 ATCAACATCACCATTTCACTCGAT
570293 TCCATCACA
1 TCCATCACA
570302 AAATGAGGTG
Statistics
Matches: 80, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
87 5 0.06
88 75 0.94
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Consensus pattern (88 bp):
TCCATCACATAAGAAGTTGGATCAACATCACCCTTTTGCTCGATTCAATTACATAAAGAGTTGGA
TCAACATCACCATTTCACTCGAT
Found at i:571327 original size:40 final size:41
Alignment explanation
Indices: 571283--571375 Score: 104
Period size: 39 Copynumber: 2.3 Consensus size: 41
571273 TTTATAATAT
* **
571283 ATATATATATATAAATT-TTAT-GAATTTAAACTTTTTAAAA
1 ATATATATATATAAATTATAATAGAATTT-AACTAGTTAAAA
571323 ATATATATAT-T-AATTATAATAGAATTTAACTAGTTAAAA
1 ATATATATATATAAATTATAATAGAATTTAACTAGTTAAAA
* *
571362 AAATAAATATATAA
1 ATATATATATATAA
571376 TAAGGATAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
38 4 0.09
39 22 0.50
40 17 0.39
41 1 0.02
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (41 bp):
ATATATATATATAAATTATAATAGAATTTAACTAGTTAAAA
Found at i:577036 original size:33 final size:33
Alignment explanation
Indices: 576999--577065 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
576989 ACAGCCCCTT
*
576999 GTTTCGGGATTTGAACATCCTTTGAAGCAAGGA
1 GTTTCGGGATTTGAACATCCTCTGAAGCAAGGA
577032 GTTTCGGGATTTGAACATCCTCTGAAGCAAGGA
1 GTTTCGGGATTTGAACATCCTCTGAAGCAAGGA
577065 G
1 G
577066 GACTGAAGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.28
Consensus pattern (33 bp):
GTTTCGGGATTTGAACATCCTCTGAAGCAAGGA
Found at i:581196 original size:25 final size:25
Alignment explanation
Indices: 581152--581203 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
581142 ACACTCATAA
* *
581152 AACATCATTTAAAGATCATTCATGT
1 AACATCATTTAAAGACCATTAATGT
*
581177 AACATCATTTAAATACCATTAATGT
1 AACATCATTTAAAGACCATTAATGT
581202 AA
1 AA
581204 GAATTCAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.15, G:0.06, T:0.35
Consensus pattern (25 bp):
AACATCATTTAAAGACCATTAATGT
Found at i:584261 original size:20 final size:23
Alignment explanation
Indices: 584212--584270 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
584202 GTCGAAGGTT
584212 CTATGTGGTCCTTCGGGACAAAA
1 CTATGTGGTCCTTCGGGACAAAA
584235 CTATGTGGTCCTTC-GGAC-AAA
1 CTATGTGGTCCTTCGGGACAAAA
584256 -TATGTGG-CACTTCGG
1 CTATGTGGTC-CTTCGG
584271 TGCAAATTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
19 1 0.03
20 11 0.32
21 4 0.12
22 4 0.12
23 14 0.41
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (23 bp):
CTATGTGGTCCTTCGGGACAAAA
Found at i:585886 original size:13 final size:13
Alignment explanation
Indices: 585868--585915 Score: 78
Period size: 13 Copynumber: 3.7 Consensus size: 13
585858 ATCTATGGGT
*
585868 GCATTTATGACAC
1 GCATTTATGACGC
585881 GCATTTATGACGC
1 GCATTTATGACGC
*
585894 ACATTTATGACGC
1 GCATTTATGACGC
585907 GCATTTATG
1 GCATTTATG
585916 GCTTACATTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (13 bp):
GCATTTATGACGC
Found at i:586025 original size:85 final size:84
Alignment explanation
Indices: 585896--586060 Score: 240
Period size: 85 Copynumber: 2.0 Consensus size: 84
585886 TATGACGCAC
* * * *
585896 ATTTATGACGCGCATTTATGGCTTACATTGCGCGTCATTGAAGCCCCCGACATAAATGAAGATGA
1 ATTTATGACACGCATTTATGACTTACATTGCGCGTCATTAAAG-CCCCGACATAAATGAAAATGA
* *
585961 CACACGTTTGTGTGTCATAA
65 CACACATTCGTGTGTCATAA
* **
585981 ATTTATGACACGCATTTATGACTTACATTGCGTGTCATTAAAGCCCCTTCATAAATGAAAATGAC
1 ATTTATGACACGCATTTATGACTTACATTGCGCGTCATTAAAGCCCCGACATAAATGAAAATGAC
586046 ACACATTCGTGTGTC
66 ACACATTCGTGTGTC
586061 GTGATTGTAT
Statistics
Matches: 71, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
84 32 0.45
85 39 0.55
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (84 bp):
ATTTATGACACGCATTTATGACTTACATTGCGCGTCATTAAAGCCCCGACATAAATGAAAATGAC
ACACATTCGTGTGTCATAA
Found at i:588754 original size:24 final size:24
Alignment explanation
Indices: 588727--588775 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
588717 AGCGTGATGG
588727 CTCATCCAAGTCTGTGAACGTGGT
1 CTCATCCAAGTCTGTGAACGTGGT
588751 CTCATCCAAGTCTGTGAACGTGGT
1 CTCATCCAAGTCTGTGAACGTGGT
588775 C
1 C
588776 GAGGATGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.27, G:0.24, T:0.29
Consensus pattern (24 bp):
CTCATCCAAGTCTGTGAACGTGGT
Found at i:593027 original size:18 final size:18
Alignment explanation
Indices: 593004--593041 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
592994 TCTTGTAGTG
*
593004 ACTATCTGGGGTATCGAT
1 ACTATCTAGGGTATCGAT
593022 ACTATCTAGGGTATCGAT
1 ACTATCTAGGGTATCGAT
593040 AC
1 AC
593042 CAAATTTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (18 bp):
ACTATCTAGGGTATCGAT
Found at i:596746 original size:21 final size:21
Alignment explanation
Indices: 596720--596764 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
596710 CGTCATTTGC
*
596720 GCCTTTGCACGTTCTATTCGA
1 GCCTTTACACGTTCTATTCGA
*
596741 GCCTTTACGCGTTCTATTCGA
1 GCCTTTACACGTTCTATTCGA
596762 GCC
1 GCC
596765 GGCGCCACGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.13, C:0.31, G:0.20, T:0.36
Consensus pattern (21 bp):
GCCTTTACACGTTCTATTCGA
Found at i:601333 original size:18 final size:18
Alignment explanation
Indices: 601310--601372 Score: 67
Period size: 18 Copynumber: 3.6 Consensus size: 18
601300 ATGTTTACAA
601310 TTATCATATAATTTTCAG
1 TTATCATATAATTTTCAG
601328 TTATCATAT-ATTTAT-AG
1 TTATCATATAATTT-TCAG
* * * *
601345 TTATTAGATGATTTACAG
1 TTATCATATAATTTTCAG
601363 TTATCATATA
1 TTATCATATA
601373 TTACAAATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
17 13 0.36
18 23 0.64
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.49
Consensus pattern (18 bp):
TTATCATATAATTTTCAG
Found at i:601544 original size:41 final size:41
Alignment explanation
Indices: 601499--601580 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
601489 AAGTGAGTAC
*
601499 TTATCAGTTCAGCTTTGGTACATTCGTGTATCAATGTTCAG
1 TTATCAGTTCAGCTTTGGTACATTCATGTATCAATGTTCAG
601540 TTATCAGTTCAGCTTTGGTACATTCATGTATCAATGTTCAG
1 TTATCAGTTCAGCTTTGGTACATTCATGTATCAATGTTCAG
601581 CACCGTTGGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.41
Consensus pattern (41 bp):
TTATCAGTTCAGCTTTGGTACATTCATGTATCAATGTTCAG
Found at i:604756 original size:21 final size:21
Alignment explanation
Indices: 604712--604757 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
604702 CCTAGCTGCG
**
604712 GTGGCATCTGATATGGTTGCA
1 GTGGCATCTGATATGGAAGCA
*
604733 GTGGCATCTGATATGGAAGTA
1 GTGGCATCTGATATGGAAGCA
604754 GTGG
1 GTGG
604758 TGTCTGACTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.22, C:0.11, G:0.37, T:0.30
Consensus pattern (21 bp):
GTGGCATCTGATATGGAAGCA
Found at i:604801 original size:21 final size:21
Alignment explanation
Indices: 604777--604835 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
604767 TAGCGGTAGA
* *
604777 ATCTGAAATGGTTGTGGTACC
1 ATCTGAAACGGCTGTGGTACC
* **
604798 ATCTGATACGGCTACGGTACC
1 ATCTGAAACGGCTGTGGTACC
604819 ATCTGAAACGGCTGTGG
1 ATCTGAAACGGCTGTGG
604836 AATGTACATT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (21 bp):
ATCTGAAACGGCTGTGGTACC
Found at i:612442 original size:34 final size:35
Alignment explanation
Indices: 612382--612447 Score: 125
Period size: 35 Copynumber: 1.9 Consensus size: 35
612372 TCTTTGTGTA
612382 CTAGTACTGCTGCAACTTTGGAGTATCAGTTCTTG
1 CTAGTACTGCTGCAACTTTGGAGTATCAGTTCTTG
612417 CTAGTACTGCTGCAAC-TTGGAGTATCAGTTC
1 CTAGTACTGCTGCAACTTTGGAGTATCAGTTC
612448 CCGCTCCATA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 15 0.48
35 16 0.52
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (35 bp):
CTAGTACTGCTGCAACTTTGGAGTATCAGTTCTTG
Done.