Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007028.1 Hibiscus syriacus cultivar Beakdansim tig00018196_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: 78077
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1879 original size:25 final size:26
Alignment explanation
Indices: 1832--1882 Score: 86
Period size: 25 Copynumber: 2.0 Consensus size: 26
1822 GTTTCATAGT
1832 TAAAGAGAGGAAGGAAGAACTTAAAA
1 TAAAGAGAGGAAGGAAGAACTTAAAA
*
1858 TAAAGAGAGGGA-GAAGAACTTAAAA
1 TAAAGAGAGGAAGGAAGAACTTAAAA
1883 CCAAGTTCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 13 0.54
26 11 0.46
ACGTcount: A:0.57, C:0.04, G:0.27, T:0.12
Consensus pattern (26 bp):
TAAAGAGAGGAAGGAAGAACTTAAAA
Found at i:4998 original size:83 final size:83
Alignment explanation
Indices: 4856--5152 Score: 355
Period size: 83 Copynumber: 3.6 Consensus size: 83
4846 ATAAGTTTGA
** * * *
4856 GGCGTTTGTAAAAAAACGCCTACTATAGTGCTAA-TATATCGCGGCGTCTACTTAAAAAACACCA
1 GGCGTTTGTACGAAAACGCCT-CTATAGTGC-AACTCTATCGCGGCGTTTACTTAAAAAACGCCA
*
4920 CTACTGTCCAACTGTATAGC
64 CTACTGTCCAACTCTATAGC
* * ** *
4940 GACGTTTGTACGAAAATGCCTCTATAGTGCAACTCTATCGCAACGTTTACTTAAAAAACGCCATT
1 GGCGTTTGTACGAAAACGCCTCTATAGTGCAACTCTATCGCGGCGTTTACTTAAAAAACGCCACT
5005 ACTGTCCAACTCTATAGC
66 ACTGTCCAACTCTATAGC
* * * *
5023 GGCGTTTGTACGAAAACGCCTCTATAGTGTAACTCTATCGTGGCGTTTAC-TAAAAAATGCCACA
1 GGCGTTTGTACGAAAACGCCTCTATAGTGCAACTCTATCGCGGCGTTTACTTAAAAAACGCCACT
* *
5087 AATGTTCAACTCTATAGC
66 ACTGTCCAACTCTATAGC
** * * * *
5105 GGCGTTTGTACGAAAACAACTCTATAGTTCAACTATGTTGCGGCGTTT
1 GGCGTTTGTACGAAAACGCCTCTATAGTGCAACTCTATCGCGGCGTTT
5153 GTTGAAGAAA
Statistics
Matches: 182, Mismatches: 30, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
82 69 0.38
83 96 0.53
84 17 0.09
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.29
Consensus pattern (83 bp):
GGCGTTTGTACGAAAACGCCTCTATAGTGCAACTCTATCGCGGCGTTTACTTAAAAAACGCCACT
ACTGTCCAACTCTATAGC
Found at i:5068 original size:41 final size:41
Alignment explanation
Indices: 4928--5154 Score: 140
Period size: 41 Copynumber: 5.5 Consensus size: 41
4918 CACTACTGTC
* * * *
4928 CAACTGTATAGCGACGTTTGTACGAAAATGCCTCTATAGTG
1 CAACTCTATCGCGGCGTTTGTACGAAAACGCCTCTATAGTG
** * * *
4969 CAACTCTATCGCAACGTTTACTTA-AAAAACGCCAT-TACT-GTC
1 CAACTCTATCGCGGCGTTT--GTACGAAAACGCC-TCTA-TAGTG
*
5011 CAACTCTATAGCGGCGTTTGTACGAAAACGCCTCTATAGTG
1 CAACTCTATCGCGGCGTTTGTACGAAAACGCCTCTATAGTG
* * * * * * * *
5052 TAACTCTATCGTGGCGTTTACTA-AAAAATGCCAC-AAATGTT
1 CAACTCTATCGCGGCGTTT-GTACGAAAACGCCTCTATA-GTG
* ** *
5093 CAACTCTATAGCGGCGTTTGTACGAAAACAACTCTATAGTT
1 CAACTCTATCGCGGCGTTTGTACGAAAACGCCTCTATAGTG
* * *
5134 CAACTATGTTGCGGCGTTTGT
1 CAACTCTATCGCGGCGTTTGT
5155 TGAAGAAAAA
Statistics
Matches: 140, Mismatches: 35, Indels: 22
0.71 0.18 0.11
Matches are distributed among these distances:
40 8 0.06
41 97 0.69
42 31 0.22
43 4 0.03
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (41 bp):
CAACTCTATCGCGGCGTTTGTACGAAAACGCCTCTATAGTG
Found at i:9752 original size:16 final size:15
Alignment explanation
Indices: 9731--9760 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
9721 ATTTGATTAA
9731 AATTTAAATAATATTC
1 AATTTAAAT-ATATTC
9747 AATTTAAATATATT
1 AATTTAAATATATT
9761 GATTCTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTTAAATATATTC
Found at i:13738 original size:20 final size:20
Alignment explanation
Indices: 13715--13753 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
13705 TTTAAAGGTG
13715 TTAATATTCTTTTA-AAAATA
1 TTAAT-TTCTTTTATAAAATA
*
13735 TTAATTTTTTTTATAAAAT
1 TTAATTTCTTTTATAAAAT
13754 TTATATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (20 bp):
TTAATTTCTTTTATAAAATA
Found at i:14706 original size:32 final size:31
Alignment explanation
Indices: 14670--14746 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
14660 TGGGGCCACG
*
14670 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
14702 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
14733 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
14747 GTTACATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 24 0.65
32 13 0.35
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:25451 original size:20 final size:23
Alignment explanation
Indices: 25422--25480 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
25412 AGAACCCCAT
* *
25422 GGGGGTATCGATTCCC-CT-ACA
1 GGGGGAATCGATTCCCACTCAAA
*
25443 -GGGGAATCGATTCCCATTCAAA
1 GGGGGAATCGATTCCCACTCAAA
25465 GGGGGAATCGATTCCC
1 GGGGGAATCGATTCCC
25481 TTATGGGGGG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 14 0.44
21 1 0.03
22 2 0.06
23 15 0.47
ACGTcount: A:0.24, C:0.25, G:0.29, T:0.22
Consensus pattern (23 bp):
GGGGGAATCGATTCCCACTCAAA
Found at i:25473 original size:23 final size:21
Alignment explanation
Indices: 25422--25502 Score: 83
Period size: 21 Copynumber: 3.8 Consensus size: 21
25412 AGAACCCCAT
* * *
25422 GGGGGTATCGATTCCCCTACA
1 GGGGGAATCGATTCCCTTAAA
25443 -GGGGAATCGATTCCCATTCAAA
1 GGGGGAATCGATTCCC-TT-AAA
**
25465 GGGGGAATCGATTCCCTTATG
1 GGGGGAATCGATTCCCTTAAA
*
25486 GGGGGTATCGATTCCCT
1 GGGGGAATCGATTCCCT
25503 CTGCACCAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
20 14 0.27
21 18 0.35
22 4 0.08
23 15 0.29
ACGTcount: A:0.21, C:0.23, G:0.30, T:0.26
Consensus pattern (21 bp):
GGGGGAATCGATTCCCTTAAA
Found at i:33026 original size:19 final size:20
Alignment explanation
Indices: 32983--33020 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
32973 CCCCCTTTGA
*
32983 AGGGGAACCGATTCCCCCAT
1 AGGGGAACCGATACCCCCAT
*
33003 AGGGGAATCGATACCCCC
1 AGGGGAACCGATACCCCC
33021 CTGGGGTTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.34, G:0.26, T:0.13
Consensus pattern (20 bp):
AGGGGAACCGATACCCCCAT
Found at i:43192 original size:6 final size:7
Alignment explanation
Indices: 43169--43198 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
43159 CCATAAACAG
43169 AAATACAA
1 AAAT-CAA
43177 AAATCAA
1 AAATCAA
43184 AAATCAA
1 AAATCAA
43191 AAATCAA
1 AAATCAA
43198 A
1 A
43199 CCAGTAATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 18 0.82
8 4 0.18
ACGTcount: A:0.73, C:0.13, G:0.00, T:0.13
Consensus pattern (7 bp):
AAATCAA
Found at i:44108 original size:17 final size:17
Alignment explanation
Indices: 44086--44120 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
44076 ACCCGATCAA
44086 CGGTCAACGGGTCGGGT
1 CGGTCAACGGGTCGGGT
44103 CGGTCAACGGGTCGGGT
1 CGGTCAACGGGTCGGGT
44120 C
1 C
44121 ATAAACGGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.11, C:0.26, G:0.46, T:0.17
Consensus pattern (17 bp):
CGGTCAACGGGTCGGGT
Found at i:48150 original size:22 final size:22
Alignment explanation
Indices: 48109--48152 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
48099 TATTTAGTCA
48109 TTTAATTATTTTCGTAATTTTAT
1 TTTAATTATTTTCG-AATTTTAT
48132 TTTAATTATTTATCG-ATTTTA
1 TTTAATTATTT-TCGAATTTTA
48153 AAAAAAATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 6 0.30
23 11 0.55
24 3 0.15
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.64
Consensus pattern (22 bp):
TTTAATTATTTTCGAATTTTAT
Found at i:49064 original size:31 final size:31
Alignment explanation
Indices: 49028--49125 Score: 110
Period size: 31 Copynumber: 3.2 Consensus size: 31
49018 TTAAAAAATA
*
49028 AAAATAAGTATTAAATTTATTAATTGATTAT
1 AAAATAATTATTAAATTTATTAATTGATTAT
* * * *
49059 AAAATAATTATCATACTTATTAAATT-ACTAT
1 AAAATAATTATTAAATTTATT-AATTGATTAT
* *
49090 AAAATAATTATTAAATTTATTCATTG-TCAT
1 AAAATAATTATTAAATTTATTAATTGATTAT
49120 AAAATA
1 AAAATA
49126 GTCATAATAT
Statistics
Matches: 54, Mismatches: 11, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
30 11 0.20
31 39 0.72
32 4 0.07
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (31 bp):
AAAATAATTATTAAATTTATTAATTGATTAT
Found at i:49182 original size:76 final size:78
Alignment explanation
Indices: 49091--49252 Score: 265
Period size: 76 Copynumber: 2.1 Consensus size: 78
49081 AATTACTATA
* *
49091 AAATAATTATTAAATTTATTCATTGTCATAAAATAGTCATAATATTTATATTTTTCACG-AAG-C
1 AAATATTTATTAAATTTATTCATTGTAATAAAATAGTCATAATATTTATATTTTTCACGAAAGTC
49154 TTTTTTTATTGAG
66 TTTTTTTATTGAG
49167 AAATATTTATTAAATTTATTCATTGTAATAAAATAGTCATAATATTTATATTTTTCACGAAAGTT
1 AAATATTTATTAAATTTATTCATTGTAATAAAATAGTCATAATATTTATATTTTTCACGAAAG-T
* *
49232 TTTTTTTTTTTGAG
65 CTTTTTTTATTGAG
49246 AAATATT
1 AAATATT
49253 GCTTCCAGCT
Statistics
Matches: 79, Mismatches: 4, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
76 57 0.72
77 3 0.04
79 19 0.24
ACGTcount: A:0.37, C:0.06, G:0.07, T:0.49
Consensus pattern (78 bp):
AAATATTTATTAAATTTATTCATTGTAATAAAATAGTCATAATATTTATATTTTTCACGAAAGTC
TTTTTTTATTGAG
Found at i:50842 original size:15 final size:16
Alignment explanation
Indices: 50817--50849 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
50807 TGAGTTCGAG
*
50817 GATTAGTATCGGTACT
1 GATTAGTATCGATACT
50833 GATT-GTATCGATACT
1 GATTAGTATCGATACT
50848 GA
1 GA
50850 AATGGGGGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.36
Consensus pattern (16 bp):
GATTAGTATCGATACT
Found at i:54920 original size:19 final size:19
Alignment explanation
Indices: 54896--54943 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
54886 TGTAAAATAA
*
54896 TGTACCGATGTACCCCTAG
1 TGTACCGATGGACCCCTAG
54915 TGTACCGATGGACCCCTAG
1 TGTACCGATGGACCCCTAG
*
54934 TGTACTGATG
1 TGTACCGATG
54944 CACTAAGTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.21, C:0.27, G:0.25, T:0.27
Consensus pattern (19 bp):
TGTACCGATGGACCCCTAG
Found at i:58383 original size:20 final size:21
Alignment explanation
Indices: 58344--58383 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
58334 TAACCTTTAA
* *
58344 GATCATCTATTTTCTTTTGAT
1 GATCATCTATTTACTCTTGAT
58365 GATCATC-ATTTACTCTTGA
1 GATCATCTATTTACTCTTGA
58384 AAGTAAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.23, C:0.17, G:0.10, T:0.50
Consensus pattern (21 bp):
GATCATCTATTTACTCTTGAT
Found at i:59354 original size:129 final size:128
Alignment explanation
Indices: 59124--59381 Score: 455
Period size: 129 Copynumber: 2.0 Consensus size: 128
59114 TCGATGATCG
*
59124 TCGTCTTCTTTGATTTCCAAGATTTTGGAAGAGAATAAACTAACTTCCTCACAAGCTTCCCGTTT
1 TCGTCTTCTTTGATTGCCAAGATTTTGGAAGAGAATAAACTAACTTCCTCACAAGCTTCCCGTTT
* *
59189 GGAATGATCTCTCCATATGATTTGAGACCATTGACAATCGTGGAAAATTTTATCCGTCATAGCT
66 GAAATGATCTCTCCATATGATTTGAGACCATTGACAATCGTGGAAAA-TATATCCGTCATAGCT
*
59253 TCGTCTTCTTTGATTGCCAAGATTTTGGAAGA-AAGTAAACTAACTTCCTCACAAGCTTCTCGTT
1 TCGTCTTCTTTGATTGCCAAGATTTTGGAAGAGAA-TAAACTAACTTCCTCACAAGCTTCCCGTT
59317 TGAAATGATCTCTCCATATGATTTGAGACCATTGACAATCGTGGAAAATATATCCGTCATAGCT
65 TGAAATGATCTCTCCATATGATTTGAGACCATTGACAATCGTGGAAAATATATCCGTCATAGCT
59381 T
1 T
59382 TGATATCTTC
Statistics
Matches: 124, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
128 18 0.15
129 106 0.85
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (128 bp):
TCGTCTTCTTTGATTGCCAAGATTTTGGAAGAGAATAAACTAACTTCCTCACAAGCTTCCCGTTT
GAAATGATCTCTCCATATGATTTGAGACCATTGACAATCGTGGAAAATATATCCGTCATAGCT
Found at i:63782 original size:18 final size:19
Alignment explanation
Indices: 63752--63794 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
63742 TATTCTCTTA
63752 TTTT-TTTACTTTAATCGC
1 TTTTATTTACTTTAATCGC
*
63770 TTTTATTTA-TTTAATCGT
1 TTTTATTTACTTTAATCGC
63788 TTTTATT
1 TTTTATT
63795 ACTACTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.19, C:0.09, G:0.05, T:0.67
Consensus pattern (19 bp):
TTTTATTTACTTTAATCGC
Found at i:67151 original size:23 final size:23
Alignment explanation
Indices: 67121--67183 Score: 126
Period size: 23 Copynumber: 2.7 Consensus size: 23
67111 CCAGAACCCC
67121 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTCAA
67144 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTCAA
67167 AGGGGGAATCGGTTCCC
1 AGGGGGAATCGGTTCCC
67184 TCACGGGGGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.21, C:0.25, G:0.33, T:0.21
Consensus pattern (23 bp):
AGGGGGAATCGGTTCCCCTTCAA
Found at i:71045 original size:22 final size:21
Alignment explanation
Indices: 71003--71042 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
70993 GAGTTTATTT
*
71003 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
71024 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
71043 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:71206 original size:15 final size:15
Alignment explanation
Indices: 71186--71224 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
71176 TTCTTGTTCC
71186 TCTTCATCGGAACCT
1 TCTTCATCGGAACCT
71201 TCTTCATCGGAACCT
1 TCTTCATCGGAACCT
71216 TCTTCATCG
1 TCTTCATCG
71225 CTCCATGTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.18, C:0.33, G:0.13, T:0.36
Consensus pattern (15 bp):
TCTTCATCGGAACCT
Found at i:77302 original size:20 final size:19
Alignment explanation
Indices: 77279--77326 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
77269 TGAATGCGAG
77279 AAAAAAAATAGTTCGAACGA
1 AAAAAAAATAGTTCGAA-GA
** *
77299 AAAAAAGGTTGTTCGAAGA
1 AAAAAAAATAGTTCGAAGA
77318 AAAGAAAAA
1 AAA-AAAAA
77327 AAAGATTGAA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.60, C:0.06, G:0.19, T:0.15
Consensus pattern (19 bp):
AAAAAAAATAGTTCGAAGA
Done.