Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005769.1 Hibiscus syriacus cultivar Beakdansim tig00013503_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: 57813
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:816 original size:16 final size:16
Alignment explanation
Indices: 795--825 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
785 GGTTAGGGTA
795 GAAAGATAGAAGAAAT
1 GAAAGATAGAAGAAAT
*
811 GAAAGATAGTAGAAA
1 GAAAGATAGAAGAAA
826 GGATTTAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.26, T:0.13
Consensus pattern (16 bp):
GAAAGATAGAAGAAAT
Found at i:1070 original size:34 final size:32
Alignment explanation
Indices: 1013--1084 Score: 94
Period size: 34 Copynumber: 2.2 Consensus size: 32
1003 TTTGGCTTGC
*
1013 TTTC-TTTTTGAATTTCTTTTTCTTTTCT-TCT
1 TTTCTTTTTTGAATTTCTTCTTCTTTT-TGTCT
1044 TTTCTTTTTCTGAATTTTCTTCTTCTTTTTGTCT
1 TTTCTTTTT-TGAA-TTTCTTCTTCTTTTTGTCT
1078 TTTCTTT
1 TTTCTTT
1085 CTTTTTGTAC
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
31 4 0.11
32 4 0.11
33 5 0.14
34 23 0.64
ACGTcount: A:0.06, C:0.17, G:0.04, T:0.74
Consensus pattern (32 bp):
TTTCTTTTTTGAATTTCTTCTTCTTTTTGTCT
Found at i:1828 original size:19 final size:20
Alignment explanation
Indices: 1787--1837 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
1777 GAAACCCCTT
*
1787 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
1807 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
1826 TGAAGATACATG
1 TGAAAATACATG
1838 CTGTTGGCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:8753 original size:36 final size:36
Alignment explanation
Indices: 8705--8809 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
8695 GATTCAATCT
8705 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
8741 TTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
8777 GTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
8810 ACTTCTAAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 21 0.32
36 45 0.68
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:14368 original size:13 final size:12
Alignment explanation
Indices: 14349--14409 Score: 56
Period size: 13 Copynumber: 5.0 Consensus size: 12
14339 CACGCCTATA
14349 TCATCACCATAT
1 TCATCACCATAT
14361 TCCATCACC--AT
1 T-CATCACCATAT
*
14372 T-ATCACGCCTAT
1 TCATCAC-CATAT
14384 ATCATCACCATAT
1 -TCATCACCATAT
14397 TCCATCACCATAT
1 T-CATCACCATAT
14410 CACGCCTATA
Statistics
Matches: 41, Mismatches: 1, Indels: 13
0.75 0.02 0.24
Matches are distributed among these distances:
9 5 0.12
10 1 0.02
11 3 0.07
12 4 0.10
13 23 0.56
14 5 0.12
ACGTcount: A:0.31, C:0.36, G:0.02, T:0.31
Consensus pattern (12 bp):
TCATCACCATAT
Found at i:14375 original size:36 final size:36
Alignment explanation
Indices: 14328--14428 Score: 186
Period size: 36 Copynumber: 2.8 Consensus size: 36
14318 CAATCTGTCT
14328 ATCACCATTATCACGCCTATATCATCACCATATTCC
1 ATCACCATTATCACGCCTATATCATCACCATATTCC
14364 ATCACCATTATCACGCCTATATCATCACCATATTCC
1 ATCACCATTATCACGCCTATATCATCACCATATTCC
*
14400 ATCACCA-TATCACGCCTATATTATCACCA
1 ATCACCATTATCACGCCTATATCATCACCA
14429 ACTTCTAAAT
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
35 21 0.33
36 43 0.67
ACGTcount: A:0.32, C:0.36, G:0.03, T:0.30
Consensus pattern (36 bp):
ATCACCATTATCACGCCTATATCATCACCATATTCC
Found at i:15681 original size:30 final size:31
Alignment explanation
Indices: 15629--15688 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
15619 CTTAGCTTTA
**
15629 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
15659 TATTATGTTTGCATTTCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
15689 GGAAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:16622 original size:19 final size:20
Alignment explanation
Indices: 16598--16648 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
16588 CGGCCAAGAG
* *
16598 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
16617 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
16637 CATGTATTTTCA
1 CATGTATTTTCA
16649 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:17364 original size:18 final size:18
Alignment explanation
Indices: 17343--17377 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17333 GGAGTGCAAA
17343 AAAAAAAAAGAAAAAGAC
1 AAAAAAAAAGAAAAAGAC
* *
17361 AAAAGAAAATAAAAAGA
1 AAAAAAAAAGAAAAAGA
17378 TAAAGCAAGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.83, C:0.03, G:0.11, T:0.03
Consensus pattern (18 bp):
AAAAAAAAAGAAAAAGAC
Found at i:20649 original size:19 final size:20
Alignment explanation
Indices: 20625--20675 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
20615 CGGCCAAGAG
* *
20625 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
20644 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
20664 CATGTATTTTCA
1 CATGTATTTTCA
20676 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:23369 original size:30 final size:31
Alignment explanation
Indices: 23317--23376 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
23307 CTTAGCTGTA
**
23317 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
23347 TATTATGTTTGCATTTCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
23377 GGCAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:24310 original size:19 final size:20
Alignment explanation
Indices: 24286--24336 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
24276 CGGCCAAGAG
*
24286 CATGTATCTTCAT-AAAAAT
1 CATGTATTTTCATCAAAAAT
24305 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
24325 CATGTATTTTCA
1 CATGTATTTTCA
24337 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.37, C:0.16, G:0.06, T:0.41
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:24776 original size:19 final size:19
Alignment explanation
Indices: 24739--24789 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
24729 GCCATCTCTA
* *
24739 TCATTTCTT-TATTTTATT
1 TCATTACTTATATTTCATT
24757 TCATT-CTTAATATTTCATT
1 TCATTACTT-ATATTTCATT
24776 TCATTACTTATATT
1 TCATTACTTATATT
24790 ATTATCCCCT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 3 0.10
18 5 0.17
19 18 0.62
20 3 0.10
ACGTcount: A:0.24, C:0.14, G:0.00, T:0.63
Consensus pattern (19 bp):
TCATTACTTATATTTCATT
Found at i:27727 original size:11 final size:12
Alignment explanation
Indices: 27706--27790 Score: 65
Period size: 13 Copynumber: 7.2 Consensus size: 12
27696 TTTATAAGTT
*
27706 GGTGATAATATA
1 GGTGATGATATA
27718 GGTG-TGATAT-
1 GGTGATGATATA
27728 GGTGATGGA-ATA
1 GGTGAT-GATATA
27740 TGGTGATGATATA
1 -GGTGATGATATA
*
27753 GGCG-TGATA-A
1 GGTGATGATATA
27763 TGGTGATGGAT-TA
1 -GGTGAT-GATATA
27776 TGGTGATGATATA
1 -GGTGATGATATA
27789 GG
1 GG
27791 CGTGATAATG
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
10 5 0.08
11 16 0.27
12 17 0.28
13 22 0.37
ACGTcount: A:0.29, C:0.01, G:0.36, T:0.33
Consensus pattern (12 bp):
GGTGATGATATA
Found at i:27742 original size:13 final size:12
Alignment explanation
Indices: 27723--27808 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
27713 ATATAGGTGT
27723 GATATGGTGATG
1 GATATGGTGATG
27735 GAATATGGTGAT-
1 G-ATATGGTGATG
*
27747 GATATAGGCG-T-
1 GATAT-GGTGATG
27758 GATAATGGTGATG
1 GAT-ATGGTGATG
27771 GATTATGGTGAT-
1 GA-TATGGTGATG
*
27783 GATATAGGCG-T-
1 GATAT-GGTGATG
27794 GATAATGGTGATG
1 GAT-ATGGTGATG
27807 GA
1 GA
27809 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.02, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:27778 original size:36 final size:36
Alignment explanation
Indices: 27705--27808 Score: 174
Period size: 36 Copynumber: 2.9 Consensus size: 36
27695 ATTTATAAGT
* *
27705 TGGTGATAATATAGGTGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
27740 TGGTGATGATATAGGCGTGATAATGGTGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
27776 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGA
27809 CAGATTGTAT
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 19 0.29
36 46 0.71
ACGTcount: A:0.29, C:0.02, G:0.37, T:0.33
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
Found at i:40109 original size:24 final size:21
Alignment explanation
Indices: 40075--40117 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
40065 TCCACAAGAT
*
40075 ATGTCCTTTGACATCTCAAAGG
1 ATGTCCTTTGAAAT-TCAAAGG
40097 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
40118 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 8 0.44
24 6 0.33
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.33
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:41658 original size:36 final size:36
Alignment explanation
Indices: 41618--41700 Score: 148
Period size: 36 Copynumber: 2.3 Consensus size: 36
41608 GGTAATAGAA
*
41618 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TATGGTGATGATATAGGCGTGATAATGGAGATGGAC
*
41654 TATGGTGATGATATAGGCGTGATAATGGAGATGGAT
1 TATGGTGATGATATAGGCGTGATAATGGAGATGGAC
41690 TATGGTGATGA
1 TATGGTGATGA
41701 AAATAGTATC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.29, C:0.04, G:0.36, T:0.31
Consensus pattern (36 bp):
TATGGTGATGATATAGGCGTGATAATGGAGATGGAC
Found at i:42086 original size:19 final size:20
Alignment explanation
Indices: 42039--42089 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
42029 GAAATCCCTT
**
42039 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
42059 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
42078 TGAAGATACATG
1 TGAAAATACATG
42090 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:45561 original size:23 final size:24
Alignment explanation
Indices: 45518--45566 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
45508 AAAGGTTATG
*
45518 AAAGATGATAAGGTAATGAAAAGA
1 AAAGATGATAAGATAATGAAAAGA
*
45542 AAAGATGA-AAGAATAA-GAAATGA
1 AAAGATGATAAG-ATAATGAAAAGA
45565 AA
1 AA
45567 TAGTAAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.63, C:0.00, G:0.22, T:0.14
Consensus pattern (24 bp):
AAAGATGATAAGATAATGAAAAGA
Found at i:45824 original size:19 final size:20
Alignment explanation
Indices: 45784--45825 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
45774 TGTAGGAGTC
*
45784 TTTTTCTTTTCTCTTTTGTT
1 TTTTTCTTTTCTCTGTTGTT
45804 TTTTTC-TTTCT-TGTTGCTT
1 TTTTTCTTTTCTCTGTTG-TT
45823 TTT
1 TTT
45826 GTTGTAGCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 4 0.20
19 10 0.50
20 6 0.30
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (20 bp):
TTTTTCTTTTCTCTGTTGTT
Found at i:46238 original size:36 final size:36
Alignment explanation
Indices: 46191--46286 Score: 138
Period size: 36 Copynumber: 2.7 Consensus size: 36
46181 ATGGTGATGA
*
46191 AATGGTAATGGAATATGGTGATGATATAGGCGTGAT
1 AATGGTGATGGAATATGGTGATGATATAGGCGTGAT
* *
46227 AATGGTGATGGACTATGGTGATGATATAGGTGTGAT
1 AATGGTGATGGAATATGGTGATGATATAGGCGTGAT
* * *
46263 AACGGAGATGGATTATGGTGATGA
1 AATGGTGATGGAATATGGTGATGA
46287 AAATAGTATC
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.31, C:0.03, G:0.35, T:0.30
Consensus pattern (36 bp):
AATGGTGATGGAATATGGTGATGATATAGGCGTGAT
Found at i:54044 original size:11 final size:13
Alignment explanation
Indices: 54012--54041 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
54002 TGGCCAAAGA
54012 TGAAAAGGTATGT
1 TGAAAAGGTATGT
54025 TGAAAAGGTATG-
1 TGAAAAGGTATGT
54037 TGAAA
1 TGAAA
54042 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:55353 original size:15 final size:15
Alignment explanation
Indices: 55318--55346 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
55308 CTGCTTCAAC
55318 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
55332 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
55347 CTTTTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:56217 original size:24 final size:21
Alignment explanation
Indices: 56183--56225 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
56173 TCCACAAGAC
*
56183 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
56205 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
56226 AGAATGCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Done.