Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003641.1 Hibiscus syriacus cultivar Beakdansim tig00007722_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: 51461
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Found at i:1031 original size:3 final size:3
Alignment explanation
Indices: 1023--1053 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
1013 CTATAATTAG
1023 ATA ATA ATA ATA ATA ATA ATAA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA
1054 GTATTTTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:5638 original size:24 final size:23
Alignment explanation
Indices: 5611--5657 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
5601 TTATTTATAA
5611 ATTTCAATTTACATTTAAAATTTT
1 ATTTCAATTTA-ATTTAAAATTTT
** *
5635 ATTTGTATTTAATTTATAATTTT
1 ATTTCAATTTAATTTAAAATTTT
5658 TTTTTATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (23 bp):
ATTTCAATTTAATTTAAAATTTT
Found at i:5655 original size:23 final size:23
Alignment explanation
Indices: 5617--5666 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
5607 ATAAATTTCA
5617 ATTTACATTTAAAATTTTATTTGT
1 ATTTACATTTAAAATTTT-TTTGT
* *
5641 ATTTA-ATTTATAATTTTTTTTT
1 ATTTACATTTAAAATTTTTTTGT
5663 ATTT
1 ATTT
5667 TTATAATGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 8 0.33
23 11 0.46
24 5 0.21
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (23 bp):
ATTTACATTTAAAATTTTTTTGT
Found at i:7944 original size:20 final size:20
Alignment explanation
Indices: 7913--7968 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
7903 TGGTTCACGA
* * *
7913 AATATAAGATTACTAGTGTG
1 AATAAAAGATTACCAGTGGG
*
7933 AATAAAATATTACCAGTGGG
1 AATAAAAGATTACCAGTGGG
7953 AATAAAAGATTACCAG
1 AATAAAAGATTACCAG
7969 GGAATAGAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.46, C:0.09, G:0.18, T:0.27
Consensus pattern (20 bp):
AATAAAAGATTACCAGTGGG
Found at i:8196 original size:36 final size:36
Alignment explanation
Indices: 8125--8197 Score: 87
Period size: 36 Copynumber: 2.0 Consensus size: 36
8115 GTTTGAAAAT
* * *
8125 ATTTATGTATTTTCTTTAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAATTGAAAATCATAAA
8161 ATTTATATAATTTT-TTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTA-AAAATTGAAAATCATAAA
8197 A
1 A
8198 AGGTTTAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
36 17 0.53
37 15 0.47
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.47
Consensus pattern (36 bp):
ATTTATATATTTTCTTTAAAAATTGAAAATCATAAA
Found at i:10791 original size:18 final size:19
Alignment explanation
Indices: 10756--10792 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
10746 AACGGAATGT
10756 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
10776 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
10793 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:15088 original size:4 final size:4
Alignment explanation
Indices: 15079--15105 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
15069 CCTTGAAAGG
15079 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATA
15106 ACAACTCCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:15885 original size:2 final size:2
Alignment explanation
Indices: 15878--15915 Score: 60
Period size: 2 Copynumber: 19.0 Consensus size: 2
15868 ACTTAAATTA
15878 AT AT AT AT AT AT AT AT CA- 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
15916 TTGTTAAACC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 32 0.94
3 1 0.03
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:18567 original size:30 final size:30
Alignment explanation
Indices: 18532--18604 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
18522 CCCGAAGGAC
*
18532 CTATCCAGAGGTTATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
18562 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
18592 CTGTCCATAGGTC
1 CTATCCAGAGGTC
18605 CCGAAGAACC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:18628 original size:31 final size:31
Alignment explanation
Indices: 18590--18717 Score: 134
Period size: 31 Copynumber: 4.1 Consensus size: 31
18580 GATCCTCGGT
* *
18590 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* **
18621 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
*
18652 TAA-TGTCCATATGTCTCGAA-AGACATAGGTAA
1 -AACTGTCCATATGTCCCGAAGA-ACATAGGT-A
* * *
18684 AACTGTCCATATGTTCTGTAGAACATAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
18715 AAC
1 AAC
18718 CCTCGACTCT
Statistics
Matches: 79, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
30 1 0.01
31 53 0.67
32 24 0.30
33 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTCCCGAAGAACATAGGTA
Found at i:18698 original size:63 final size:62
Alignment explanation
Indices: 18593--18714 Score: 176
Period size: 63 Copynumber: 2.0 Consensus size: 62
18583 CCTCGGTAAC
*
18593 TGTCCATAGGTCCCGAAGAACCTAGGTAAACTGTCCATATGTTCCT-TAGAACATAGGTATAA
1 TGTCCATAGGTCCCGAAGAACATAGGTAAACTGTCCATATGTT-CTGTAGAACATAGGTATAA
* *
18655 TGTCCATATGTCTCGAA-AGACATAGGTAAAACTGTCCATATGTTCTGTAGAACATAGGTA
1 TGTCCATAGGTCCCGAAGA-ACATAGGT-AAACTGTCCATATGTTCTGTAGAACATAGGTA
18715 AACCCTCGAC
Statistics
Matches: 54, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
61 1 0.02
62 24 0.44
63 29 0.54
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.29
Consensus pattern (62 bp):
TGTCCATAGGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCTGTAGAACATAGGTATAA
Found at i:22252 original size:30 final size:30
Alignment explanation
Indices: 22217--22289 Score: 110
Period size: 30 Copynumber: 2.4 Consensus size: 30
22207 CCCGAAGGAC
* *
22217 CTATCCAGAGGTTATAAAGATCTTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
22247 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
22277 CTGTCCATAGGTC
1 CTATCCAGAGGTC
22290 CCGAAGAACC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:22313 original size:31 final size:31
Alignment explanation
Indices: 22275--22402 Score: 141
Period size: 31 Copynumber: 4.1 Consensus size: 31
22265 GATCCTCGGT
* *
22275 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* **
22306 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* *
22337 TACTGTCCATATGTCTCGAA-AGACATAGGTAA
1 AACTGTCCATATGTCCCGAAGA-ACATAGGT-A
* * *
22369 AACTGTCCATATGTTCTGTAGAACATAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
22400 AAC
1 AAC
22403 CCTCGACTCT
Statistics
Matches: 79, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
30 1 0.01
31 53 0.67
32 24 0.30
33 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTCCCGAAGAACATAGGTA
Found at i:22391 original size:63 final size:61
Alignment explanation
Indices: 22272--22400 Score: 181
Period size: 63 Copynumber: 2.1 Consensus size: 61
22262 AAAGATCCTC
*
22272 GGTAACTGTCCATAGGTCCCGAAGAACCTAGGTAAACTGTCCATATGTTCCTTAGAACATA
1 GGTAACTGTCCATAGGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCTTAGAACATA
* *
22333 GGTATACTGTCCATATGTCTCGAA-AGACATAGGTAAAACTGTCCATATGTT-CTGTAGAACATA
1 GGTA-ACTGTCCATAGGTCCCGAAGA-ACATAGGT-AAACTGTCCATATGTTCCT-TAGAACATA
22396 GGTAA
1 GGTAA
22401 ACCCTCGACT
Statistics
Matches: 61, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
61 5 0.08
62 27 0.44
63 29 0.48
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (61 bp):
GGTAACTGTCCATAGGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCTTAGAACATA
Found at i:23778 original size:21 final size:20
Alignment explanation
Indices: 23735--23774 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
23725 TTTTGTTCGT
* *
23735 TTGAAGGGGTATCGGTTCCC
1 TTGAAGGGGTACCGATTCCC
*
23755 TTGAATGGGTACCGATTCCC
1 TTGAAGGGGTACCGATTCCC
23775 CTTGCCCAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.17, C:0.23, G:0.30, T:0.30
Consensus pattern (20 bp):
TTGAAGGGGTACCGATTCCC
Found at i:27732 original size:18 final size:17
Alignment explanation
Indices: 27704--27738 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
27694 CATATTACAT
27704 ATAAAAAATATAAATAA
1 ATAAAAAATATAAATAA
*
27721 ATAAATAAATATATATAA
1 ATAAA-AAATATAAATAA
27739 TATATGATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAAAATATAAATAA
Found at i:31988 original size:87 final size:83
Alignment explanation
Indices: 31832--32000 Score: 198
Period size: 87 Copynumber: 2.0 Consensus size: 83
31822 TAATCTCAAT
* *
31832 CATTTGACAATAAACGCTCAATCACCCTTGCAGTCGCTGACGCTCAAACCTGTGACCTCTAAAAT
1 CATTTGACAATAAACGCTCAATCACCCTTGCAGT--CTGACCCTCAAACCTATGACCTCTAAAAT
31897 CAACAACATTTCATTTAACAAC
64 CAAC-A-ATTTCATTTAACAAC
* * *
31919 CATTTGACAATAAATGCTCAATCACCCTTGCAGT-TGACCCTTGACACC-ATGACCTCTAGAAAT
1 CATTTGACAATAAACGCTCAATCACCCTTGCAGTCTGACCC-TCAAACCTATGACCTCTA-AAAT
*
31982 AACAACATTTTCATTTAAC
64 --CAACAATTTCATTTAAC
32001 TACTAGGTTA
Statistics
Matches: 72, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
84 14 0.19
85 20 0.28
86 1 0.01
87 37 0.51
ACGTcount: A:0.34, C:0.28, G:0.10, T:0.27
Consensus pattern (83 bp):
CATTTGACAATAAACGCTCAATCACCCTTGCAGTCTGACCCTCAAACCTATGACCTCTAAAATCA
ACAATTTCATTTAACAAC
Found at i:34788 original size:2 final size:2
Alignment explanation
Indices: 34781--34829 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
34771 TAGACAGATA
34781 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
34823 AG AG AG A
1 AG AG AG A
34830 CCCAACACAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:38211 original size:19 final size:19
Alignment explanation
Indices: 38187--38238 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
38177 TCATTCAAAA
38187 AATAAATCTAAATAATA-AT
1 AATAAAT-TAAATAATAGAT
* *
38206 AATAAATTTATTAATAGAT
1 AATAAATTAAATAATAGAT
38225 AATAAA--AAATAATA
1 AATAAATTAAATAATA
38239 AGTTAACTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 6 0.21
18 7 0.25
19 15 0.54
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (19 bp):
AATAAATTAAATAATAGAT
Found at i:43030 original size:19 final size:18
Alignment explanation
Indices: 43006--43051 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
42996 AATAATAAGT
43006 AATATTATTATATATATAC
1 AATATTATTATA-ATATAC
* *
43025 AATATTAATATAATATTC
1 AATATTATTATAATATAC
43043 AAGTATTAT
1 AA-TATTAT
43052 CTTTTAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (18 bp):
AATATTATTATAATATAC
Found at i:47496 original size:30 final size:32
Alignment explanation
Indices: 47462--47529 Score: 81
Period size: 30 Copynumber: 2.2 Consensus size: 32
47452 ATCTAAATTA
*
47462 AAAATATT-AAATTGA-TCTCTAAAC-TTAAAT
1 AAAATATTCAAATTCATTCT-TAAACTTTAAAT
*
47492 AAAAT-TTCAATTTCATTCTTAAACTTTAAAT
1 AAAATATTCAAATTCATTCTTAAACTTTAAAT
47523 AAAATAT
1 AAAATAT
47530 CAATTTAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
29 2 0.06
30 15 0.47
31 14 0.44
32 1 0.03
ACGTcount: A:0.49, C:0.10, G:0.01, T:0.40
Consensus pattern (32 bp):
AAAATATTCAAATTCATTCTTAAACTTTAAAT
Done.