Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006004.1 Hibiscus syriacus cultivar Beakdansim tig00014157_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: 33245
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:257 original size:24 final size:24
Alignment explanation
Indices: 220--281 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
210 AACCATATCA
*
220 GCAGACCATTGATCGCCTATTTAC
1 GCAGGCCATTGATCGCCTATTTAC
* *
244 GTAGGCCATTGATCGCCTATTTGC
1 GCAGGCCATTGATCGCCTATTTAC
*
268 GCAGGCAATTGATC
1 GCAGGCCATTGATC
282 AGCTGCTAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.29
Consensus pattern (24 bp):
GCAGGCCATTGATCGCCTATTTAC
Found at i:951 original size:60 final size:60
Alignment explanation
Indices: 876--1044 Score: 259
Period size: 60 Copynumber: 2.8 Consensus size: 60
866 TTCTTTCTCA
* *
876 TTTTAGCACACGAAGTGCCCTATTCGAGAATCCATACCATTAGTATGATTCATTTACCAT
1 TTTTAGCACATGAAGTGCCCTATTCGAGAATCCATACCATTAGTATGATCCATTTACCAT
* *
936 TTTTAGCATATGAAGTGCCCTATTCGAGAATCCATACCATTAGTATGATCCCTTTACCAT
1 TTTTAGCACATGAAGTGCCCTATTCGAGAATCCATACCATTAGTATGATCCATTTACCAT
* * *
996 TTTTAGCACATGAAATGCCCTATAT-GAAAATCCATACTATTAGTATGAT
1 TTTTAGCACATGAAGTGCCCTAT-TCGAGAATCCATACCATTAGTATGAT
1045 ATCCTTATAC
Statistics
Matches: 100, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
60 99 0.99
61 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.34
Consensus pattern (60 bp):
TTTTAGCACATGAAGTGCCCTATTCGAGAATCCATACCATTAGTATGATCCATTTACCAT
Found at i:1121 original size:59 final size:59
Alignment explanation
Indices: 1079--1299 Score: 266
Period size: 59 Copynumber: 3.7 Consensus size: 59
1069 GTGCTTTTTC
* * * * * *
1079 TGGAAATTCATACACTCAATATGATTCCCTTACCATTTTAGCACA-TATAATGC-CCTATC
1 TGGAAATCCATACACTCAATATGATTTCCTTATCATTTTAGCACACT-CAGTGCTCC-ATA
* * *
1138 TGGAAATCCATATATTCAATATGATTTTCTTATCATTTTAGCACACTCAGTGCTCCATA
1 TGGAAATCCATACACTCAATATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATA
* * * *
1197 TGGAAATCCATACACTCAGTCTGATTTTCTTATCATTTTAGCACACGCAGTGCTCCATA
1 TGGAAATCCATACACTCAATATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATA
* * *
1256 TGGAAATTCATACATTCAATATGATTTCCTTATAATTTTAGCAC
1 TGGAAATCCATACACTCAATATGATTTCCTTATCATTTTAGCAC
1300 GGATAGTGTC
Statistics
Matches: 140, Mismatches: 20, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
59 137 0.98
60 3 0.02
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.37
Consensus pattern (59 bp):
TGGAAATCCATACACTCAATATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATA
Found at i:1161 original size:118 final size:117
Alignment explanation
Indices: 979--1299 Score: 326
Period size: 118 Copynumber: 2.7 Consensus size: 117
969 ATACCATTAG
* *
979 TATGA-TCCCTTTACCATTTTTAGCACATGAAATGCCCTATATGAAAATCCATACTATT-AGTAT
1 TATGATTCCC-TTACCA-TTTTAGCACAT-AAATGCCCTATATGGAAATCCATA-TATTCAATAT
* * * * *** * *
1042 GATATCCTTATACTTGTAGCACCCTTAGTGCTTTTTCTGGAAATTCATACACTCAA
62 GATTTCCTTATACTTTTAGCACACTCAGTGCTCCATATGGAAATCCATACACTCAA
*
1098 TATGATTCCCTTACCATTTTAGCACATATAATGCCCTATCTGGAAATCCATATATTCAATATGAT
1 TATGATTCCCTTACCATTTTAGCACATA-AATGCCCTATATGGAAATCCATATATTCAATATGAT
* *
1163 TTTCTTAT-CATTTTAGCACACTCAGTGCTCCATATGGAAATCCATACACTCAG
65 TTCCTTATAC-TTTTAGCACACTCAGTGCTCCATATGGAAATCCATACACTCAA
* ** * ** * * *
1216 TCTGATTTTCTTATCATTTTAGCACACGCAGTGCTCC-ATATGGAAATTCATACATTCAATATGA
1 TATGATTCCCTTACCATTTTAGCACA-TAAATGC-CCTATATGGAAATCCATATATTCAATATGA
*
1280 TTTCCTTATAATTTTAGCAC
64 TTTCCTTATACTTTTAGCAC
1300 GGATAGTGTC
Statistics
Matches: 169, Mismatches: 26, Indels: 15
0.80 0.12 0.07
Matches are distributed among these distances:
117 6 0.04
118 146 0.86
119 13 0.08
120 4 0.02
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (117 bp):
TATGATTCCCTTACCATTTTAGCACATAAATGCCCTATATGGAAATCCATATATTCAATATGATT
TCCTTATACTTTTAGCACACTCAGTGCTCCATATGGAAATCCATACACTCAA
Found at i:3865 original size:21 final size:21
Alignment explanation
Indices: 3835--3875 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3825 GTCGAGGGTT
* *
3835 TCATAGGTCATTCGGGACAAC
1 TCATACGTCATTCGAGACAAC
3856 TCATACGTCATTCGAGACAA
1 TCATACGTCATTCGAGACAA
3876 ATTCACAGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (21 bp):
TCATACGTCATTCGAGACAAC
Found at i:5986 original size:18 final size:18
Alignment explanation
Indices: 5955--5989 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5945 ACTTAGAATT
*
5955 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
*
5973 TGTCCTGAAGGACCACT
1 TGTCCCGAAGGACCACT
5990 CCTTAAGAAC
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:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:6688 original size:2 final size:2
Alignment explanation
Indices: 6681--6709 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6671 TTTTATTATC
6681 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6710 CATACCAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9580 original size:2 final size:2
Alignment explanation
Indices: 9573--9619 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
9563 TACAAAAATA
9573 AT AT AT AT AT AT AT AT AT AT AT 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 AT AT
9615 AT AT A
1 AT AT A
9620 AAACTTCTGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16811 original size:93 final size:93
Alignment explanation
Indices: 16626--16898 Score: 314
Period size: 93 Copynumber: 2.9 Consensus size: 93
16616 AATCTCATAT
* * *** * *
16626 ATCTATTTCCACTCATCCAACGATTCTAAATCTATGTAAAACTAAAGAGTTTTACACCGTGAAAG
1 ATCTATTTTCACTCATCCAACGATTTTAAATCTATGTAAAACTAAAGAGTTTTACATTATGTAAC
* * * * *
16691 T-AGATCTTATCCTATATGTATATAAGTC
66 TGA-ATCCTAACCCATATATATACAAGTC
* * *
16719 ATCTATTTTCACTCATTCGACGATTTTAAATCTGTGTAAAACTAAAGAGTTTTACATTATGTAAC
1 ATCTATTTTCACTCATCCAACGATTTTAAATCTATGTAAAACTAAAGAGTTTTACATTATGTAAC
*
16784 TGAATCCTAACCCATGTATATACAAGTC
66 TGAATCCTAACCCATATATATACAAGTC
* * * * * * *
16812 ATCTATTTTCACTCGTCCAACAATCTTAAATCTATATAAAATTAAAGAGTTTTACATTAAGTACC
1 ATCTATTTTCACTCATCCAACGATTTTAAATCTATGTAAAACTAAAGAGTTTTACATTATGTAAC
*
16877 TGGATCCTAACCCATATATATA
66 TGAATCCTAACCCATATATATA
16899 TATATATATA
Statistics
Matches: 151, Mismatches: 28, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
93 150 0.99
94 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.36
Consensus pattern (93 bp):
ATCTATTTTCACTCATCCAACGATTTTAAATCTATGTAAAACTAAAGAGTTTTACATTATGTAAC
TGAATCCTAACCCATATATATACAAGTC
Found at i:16897 original size:2 final size:2
Alignment explanation
Indices: 16890--16930 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
16880 ATCCTAACCC
16890 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16931 AGAATATTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:18574 original size:20 final size:21
Alignment explanation
Indices: 18536--18576 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
18526 CTTCGTTCCC
*
18536 AAATTAGAACCCCAGTTCCTA
1 AAATTAGAACCCCAATTCCTA
*
18557 AAATT-GAACCCTAATTCCTA
1 AAATTAGAACCCCAATTCCTA
18577 TATTATAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.39, C:0.27, G:0.07, T:0.27
Consensus pattern (21 bp):
AAATTAGAACCCCAATTCCTA
Found at i:23219 original size:83 final size:82
Alignment explanation
Indices: 23074--23333 Score: 272
Period size: 83 Copynumber: 3.1 Consensus size: 82
23064 CATCGCGACA
* * * * * * * * *
23074 TTTGTATAAAAATGCTGCTAAAGTACAACTCTATTGCGACGTTTTTTAAAAAAATGCCACTATAT
1 TTTGTATAAAAACGCCGCTAAAATACTACTCTATTACGGCATTTGTT-GAAAAATGCCACTATAT
23139 ATAAACCCTATTGTGGCG
65 ATAAACCCTATTGTGGCG
* * * *
23157 TTTATATAAAAACGCCGCTAAAATACTACTCTATTATGGCATTTGTTGAGAAAATGCTACTATAG
1 TTTGTATAAAAACGCCGCTAAAATACTACTCTATTACGGCATTTGTTGA-AAAATGCCACTATAT
* ** **
23222 ATGAACCCTATTACGGAAT
65 ATAAACCCTATTGTGG-CG
* * * *
23241 TTTGTATAAAAACGCCGCTAAAGTACTACTCTATTGCGGCATTTGTTGAAAAACGCCATTATATA
1 TTTGTATAAAAACGCCGCTAAAATACTACTCTATTACGGCATTTGTTGAAAAATGCCACTATATA
23306 TTAAA-CCTATTGTGGCG
66 -TAAACCCTATTGTGGCG
23323 TTTGT-TAAAAA
1 TTTGTATAAAAA
23334 ATATCACTAT
Statistics
Matches: 143, Mismatches: 31, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
81 6 0.04
82 6 0.04
83 83 0.58
84 48 0.34
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (82 bp):
TTTGTATAAAAACGCCGCTAAAATACTACTCTATTACGGCATTTGTTGAAAAATGCCACTATATA
TAAACCCTATTGTGGCG
Found at i:23275 original size:42 final size:41
Alignment explanation
Indices: 23164--23297 Score: 121
Period size: 42 Copynumber: 3.2 Consensus size: 41
23154 GCGTTTATAT
* *
23164 AAAAACGCCGCTAAAATACTACTCTATTATGGCATTTGTTG
1 AAAAACGCCGCTAAAGTACTACTCTATTACGGCATTTGTTG
* ** * * *
23205 AGAAAATGCTACTATAG-A-TGAACCCTATTACGGAATTTTGTAT-
1 A-AAAACGCCGCTAAAGTACT--ACTCTATTACGGCA-TTTGT-TG
*
23248 AAAAACGCCGCTAAAGTACTACTCTATTGCGGCATTTGTTG
1 AAAAACGCCGCTAAAGTACTACTCTATTACGGCATTTGTTG
23289 AAAAACGCC
1 AAAAACGCC
23298 ATTATATATT
Statistics
Matches: 70, Mismatches: 15, Indels: 16
0.69 0.15 0.16
Matches are distributed among these distances:
40 2 0.03
41 16 0.23
42 43 0.61
43 7 0.10
44 2 0.03
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.29
Consensus pattern (41 bp):
AAAAACGCCGCTAAAGTACTACTCTATTACGGCATTTGTTG
Found at i:25004 original size:2 final size:2
Alignment explanation
Indices: 24997--25060 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
24987 CGGGTGGATG
24997 AT AT AT AT AT AT AT AT AT AT AT 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 AT AT
25039 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
25061 CGGGTCGGGT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26164 original size:36 final size:36
Alignment explanation
Indices: 26117--26187 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
26107 ACTGTTGATA
26117 ATGCTCAAATTA-AGTTATCCCACTAGTATTAGAAAT
1 ATGCTCAAATTAGA-TTATCCCACTAGTATTAGAAAT
* *
26153 ATGCTCAAATTAGATTATCTCACTAGTATTGGAAA
1 ATGCTCAAATTAGATTATCCCACTAGTATTAGAAA
26188 GACGATTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 31 0.97
37 1 0.03
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (36 bp):
ATGCTCAAATTAGATTATCCCACTAGTATTAGAAAT
Found at i:30973 original size:28 final size:28
Alignment explanation
Indices: 30924--30977 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
30914 AAGAGTTTGG
*
30924 GAGTTCCAAGTGAGGACATATTGAATGA
1 GAGTTCCAAGTGAGAACATATTGAATGA
* **
30952 GAGTTCCTAGTGAGAAGTTATTGAAT
1 GAGTTCCAAGTGAGAACATATTGAAT
30978 TCACGAATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.33, C:0.09, G:0.28, T:0.30
Consensus pattern (28 bp):
GAGTTCCAAGTGAGAACATATTGAATGA
Found at i:31574 original size:33 final size:34
Alignment explanation
Indices: 31526--31621 Score: 149
Period size: 33 Copynumber: 2.8 Consensus size: 34
31516 AATGTTGATA
31526 ATGCTCAAATTAGGTTATCCCACTAGTTAGAAAT
1 ATGCTCAAATTAGGTTATCCCACTAGTTAGAAAT
* *
31560 ATTCT-AAATTAGGTTATCCCATTAGTATTAGAAAT
1 ATGCTCAAATTAGGTTATCCCACTAG--TTAGAAAT
31595 ATGCTCAAATTAGGTTATCCCACTAGT
1 ATGCTCAAATTAGGTTATCCCACTAGT
31622 ATGGGAATGA
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
33 19 0.35
34 5 0.09
35 12 0.22
36 19 0.35
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (34 bp):
ATGCTCAAATTAGGTTATCCCACTAGTTAGAAAT
Found at i:31612 original size:36 final size:36
Alignment explanation
Indices: 31526--31623 Score: 157
Period size: 36 Copynumber: 2.8 Consensus size: 36
31516 AATGTTGATA
31526 ATGCTCAAATTAGGTTATCCCACTAG--TTAGAAAT
1 ATGCTCAAATTAGGTTATCCCACTAGTATTAGAAAT
* *
31560 ATTCT-AAATTAGGTTATCCCATTAGTATTAGAAAT
1 ATGCTCAAATTAGGTTATCCCACTAGTATTAGAAAT
31595 ATGCTCAAATTAGGTTATCCCACTAGTAT
1 ATGCTCAAATTAGGTTATCCCACTAGTAT
31624 GGGAATGACG
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
33 19 0.33
34 4 0.07
35 12 0.21
36 22 0.39
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (36 bp):
ATGCTCAAATTAGGTTATCCCACTAGTATTAGAAAT
Done.