Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005704.1 Hibiscus syriacus cultivar Beakdansim tig00013339_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: 232903
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
File 2 of 2
Found at i:198369 original size:63 final size:63
Alignment explanation
Indices: 198298--198437 Score: 187
Period size: 63 Copynumber: 2.2 Consensus size: 63
198288 CTTGGAATAA
* * *
198298 ATCGCAACGCGAACTTTG-ACT-ATCGCAACGAATTTGGAATAAATCGCAACGCGAACATGGACT
1 ATCGCAA-GCGAA-TTTGAAATAATCGCAACGAATTTAGAATAAATCGCAACGCGAACATCGACT
*
198361 ATCGCAA-CGAATTTGAAATAAATCGCAACGAATTTAGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAAGCGAATTTGAAAT-AATCGCAACGAATTTAGAATAAATCGCAACGCGAACATCGACT
198424 ATCGCAATGCGAAT
1 ATCGCAA-GCGAAT
198438 ATGTAAATCG
Statistics
Matches: 68, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
60 4 0.06
61 6 0.09
63 53 0.78
65 5 0.07
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (63 bp):
ATCGCAAGCGAATTTGAAATAATCGCAACGAATTTAGAATAAATCGCAACGCGAACATCGACT
Found at i:200519 original size:31 final size:31
Alignment explanation
Indices: 200484--200557 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
200474 ACACAAATGA
*
200484 TCCCTTAACTATAGCGTAATGTTTTATTAAG
1 TCCCTCAACTATAGCGTAATGTTTTATTAAG
* * *
200515 TCCCTCAACTCTAGGGTAATGTTTTATTATG
1 TCCCTCAACTATAGCGTAATGTTTTATTAAG
*
200546 TCCATCAACTAT
1 TCCCTCAACTAT
200558 TAAAAGTTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.41
Consensus pattern (31 bp):
TCCCTCAACTATAGCGTAATGTTTTATTAAG
Found at i:201932 original size:12 final size:11
Alignment explanation
Indices: 201915--201965 Score: 54
Period size: 10 Copynumber: 4.8 Consensus size: 11
201905 TTTGTATTAA
201915 TTATTTTGTTAT
1 TTATTTT-TTAT
201927 TTATTTTTT-T
1 TTATTTTTTAT
*
201937 TAATTTTTTAT
1 TTATTTTTTAT
*
201948 TTA-ATTTT-T
1 TTATTTTTTAT
201957 TTATTTTTT
1 TTATTTTTT
201966 TGCATTTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
9 4 0.12
10 17 0.52
11 5 0.15
12 7 0.21
ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80
Consensus pattern (11 bp):
TTATTTTTTAT
Found at i:201949 original size:21 final size:21
Alignment explanation
Indices: 201917--201966 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
201907 TGTATTAATT
*
201917 ATTTTGTTATTTATTTTTTTTA
1 ATTTT-TTATTTAATTTTTTTA
201939 ATTTTTTATTTAATTTTTTTA
1 ATTTTTTATTTAATTTTTTTA
*
201960 TTTTTTT
1 ATTTTTT
201967 GCATTTATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 21 0.81
22 5 0.19
ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80
Consensus pattern (21 bp):
ATTTTTTATTTAATTTTTTTA
Found at i:201958 original size:13 final size:12
Alignment explanation
Indices: 201917--201962 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 12
201907 TGTATTAATT
201917 ATTTTGTTATTT-
1 ATTTT-TTATTTA
201929 A-TTTTT-TTTA
1 ATTTTTTATTTA
201939 ATTTTTTATTTA
1 ATTTTTTATTTA
201951 ATTTTTTTATTT
1 A-TTTTTTATTT
201963 TTTTGCATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
9 3 0.10
10 3 0.10
11 8 0.27
12 6 0.20
13 10 0.33
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (12 bp):
ATTTTTTATTTA
Found at i:202231 original size:8 final size:8
Alignment explanation
Indices: 202215--202271 Score: 51
Period size: 8 Copynumber: 6.9 Consensus size: 8
202205 TTATAACTGC
*
202215 AAAAAAAT
1 AAAATAAT
202223 AAAATAAT
1 AAAATAAT
*
202231 AAAAAAAAT
1 -AAAATAAT
202240 AAAAATAAT
1 -AAAATAAT
*
202249 ATAATAAT
1 AAAATAAT
*
202257 ATAATAAT
1 AAAATAAT
*
202265 TAAATAA
1 AAAATAA
202272 AATACTAACA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
8 27 0.64
9 15 0.36
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (8 bp):
AAAATAAT
Found at i:202238 original size:18 final size:18
Alignment explanation
Indices: 202215--202249 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
202205 TTATAACTGC
202215 AAAAAAAT-AAAATAATA
1 AAAAAAATAAAAATAATA
202232 AAAAAAATAAAAATAATA
1 AAAAAAATAAAAATAATA
202250 TAATAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (18 bp):
AAAAAAATAAAAATAATA
Found at i:202268 original size:26 final size:25
Alignment explanation
Indices: 202215--202275 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 25
202205 TTATAACTGC
202215 AAAAAAATAAAATAATAAAAAAAAT
1 AAAAAAATAAAATAATAAAAAAAAT
* * * *
202240 AAAAATAATATAATAATATAATAATT
1 AAAAA-AATAAAATAATAAAAAAAAT
202266 AAATAAAATA
1 AAA-AAAATA
202276 CTAACAAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 5 0.17
26 23 0.77
27 2 0.07
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (25 bp):
AAAAAAATAAAATAATAAAAAAAAT
Found at i:205056 original size:23 final size:23
Alignment explanation
Indices: 205030--205079 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
205020 AATGAACGCC
*
205030 AAATGAACATGTTCGTGAACATT
1 AAATGAACATGTTCGTGAACAAT
*
205053 AAATGAACATGTTTGTGAACAAT
1 AAATGAACATGTTCGTGAACAAT
205076 AAAT
1 AAAT
205080 AAACGAACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.44, C:0.10, G:0.16, T:0.30
Consensus pattern (23 bp):
AAATGAACATGTTCGTGAACAAT
Found at i:207291 original size:2 final size:2
Alignment explanation
Indices: 207286--207343 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
207276 ATTTAAACTA
207286 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
207328 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
207344 TAAAACTATC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:210031 original size:187 final size:187
Alignment explanation
Indices: 209701--210462 Score: 1375
Period size: 187 Copynumber: 4.1 Consensus size: 187
209691 TCCACACGAA
*
209701 TTTGAAGCTATTGAGTGAAAATTGACGGCTTAGATTAACTCTTTGTTTTCTCGTGAATATCTTCT
1 TTTGAAGCTATTGAGTGAAAATTGACGGCTTAGATTAACTCTTTATTTTCTCGTGAATATCTTCT
*
209766 CATTT-C-AATCCCTAGGGTTAATCTCCATCTATTTACACTCATCCCACAATCCTAAATCTGTAC
66 CATTTCCTAATCCCTAGGGTTAATCTCAATCTATTTACACTCATCCCACAATCCTAAATCTGTAC
209829 ATTGTGTAATTGGATTCTATTCCCCGTATATATGTACATATATAAACAAAACTCGAC
131 ATTGTGTAATTGGATTCTATTCCCCGTATATATGTACATATATAAACAAAACTCGAC
209886 TTTGAAGCTATTGAGTGAAAATTGACGGCTTAGATTAACTCTTTATTTTCTCGTGAATATCTTCT
1 TTTGAAGCTATTGAGTGAAAATTGACGGCTTAGATTAACTCTTTATTTTCTCGTGAATATCTTCT
209951 CATTTCCTAATCCCTAGGGTTAATCTCAATCTATTTACACTCATCCCACAATCCTAAATCTGTAC
66 CATTTCCTAATCCCTAGGGTTAATCTCAATCTATTTACACTCATCCCACAATCCTAAATCTGTAC
*
210016 ATTGTGTAGTTGGATTCTATTCCCCGTATATATGTACATATATAAACAAAACTCGAC
131 ATTGTGTAATTGGATTCTATTCCCCGTATATATGTACATATATAAACAAAACTCGAC
*
210073 TTTGAAGCTATTGAGTGAAAATTGACGGCTTAGATTAACTCTTTGTTTTCTCGTGAATATCTTCT
1 TTTGAAGCTATTGAGTGAAAATTGACGGCTTAGATTAACTCTTTATTTTCTCGTGAATATCTTCT
* * * * *
210138 CATTTCTTAATCCCTAGAGTTAATCTCAATCTATTTACATTCATCCCACAATCTTAAATCTGTAT
66 CATTTCCTAATCCCTAGGGTTAATCTCAATCTATTTACACTCATCCCACAATCCTAAATCTGTAC
210203 ATTGTGTAATTGGATTCTATTCCCCGTATATATGTACATATATAAACAAAACTCGAC
131 ATTGTGTAATTGGATTCTATTCCCCGTATATATGTACATATATAAACAAAACTCGAC
210260 TTTGAAGCTATTGAGTGAAAATTGACGGCTTAGATTAACTCTTTATTTTCTCGTGAATATCTTCT
1 TTTGAAGCTATTGAGTGAAAATTGACGGCTTAGATTAACTCTTTATTTTCTCGTGAATATCTTCT
* * * * *
210325 CATTTTCTAATCTCTAGGGTTAATCTCAATCTATTTATATTCATCCCACAATCTTAAATCTGTAC
66 CATTTCCTAATCCCTAGGGTTAATCTCAATCTATTTACACTCATCCCACAATCCTAAATCTGTAC
*
210390 ATTGTGTAATTGGATTCTATTCCCCGTATATATGTACACATATAAACAAAACTCGAC
131 ATTGTGTAATTGGATTCTATTCCCCGTATATATGTACATATATAAACAAAACTCGAC
210447 TTTGAAGCTATTGAGT
1 TTTGAAGCTATTGAGT
210463 ACTTGCCCAT
Statistics
Matches: 557, Mismatches: 18, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
185 69 0.12
186 1 0.00
187 487 0.87
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.39
Consensus pattern (187 bp):
TTTGAAGCTATTGAGTGAAAATTGACGGCTTAGATTAACTCTTTATTTTCTCGTGAATATCTTCT
CATTTCCTAATCCCTAGGGTTAATCTCAATCTATTTACACTCATCCCACAATCCTAAATCTGTAC
ATTGTGTAATTGGATTCTATTCCCCGTATATATGTACATATATAAACAAAACTCGAC
Found at i:215406 original size:23 final size:23
Alignment explanation
Indices: 215376--215427 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
215366 GCAGATAGAG
*
215376 GTTGCTCTCCTTCAAAAGCTTAT
1 GTTGCTCTCCTTCAAAAGCTAAT
215399 GTTGCTCTCCTTCAAAAGCTAAT
1 GTTGCTCTCCTTCAAAAGCTAAT
215422 GTTGCT
1 GTTGCT
215428 GCATGTTGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.21, C:0.25, G:0.15, T:0.38
Consensus pattern (23 bp):
GTTGCTCTCCTTCAAAAGCTAAT
Found at i:218941 original size:31 final size:31
Alignment explanation
Indices: 218896--218973 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
218886 TTGTAAAATT
* *
218896 TTTGATAAAATTTAATGATTATTTTGTAA-CA
1 TTTGAT-AAATTTAATGATCAATTTGTAATCA
218927 GTTTGATAAATTTAATGATCAATTTGTAATCA
1 -TTTGATAAATTTAATGATCAATTTGTAATCA
*
218959 TTTGATAACTTTAAT
1 TTTGATAAATTTAAT
218974 CATTTTGTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
31 34 0.81
32 8 0.19
ACGTcount: A:0.37, C:0.05, G:0.10, T:0.47
Consensus pattern (31 bp):
TTTGATAAATTTAATGATCAATTTGTAATCA
Found at i:218990 original size:18 final size:17
Alignment explanation
Indices: 218953--218987 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
218943 GATCAATTTG
218953 TAATCATTTGATAACTT
1 TAATCATTTGATAACTT
218970 TAATCATTTTG-TAACTT
1 TAATCA-TTTGATAACTT
218987 T
1 T
218988 TAAAAGTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.31, C:0.11, G:0.06, T:0.51
Consensus pattern (17 bp):
TAATCATTTGATAACTT
Found at i:221489 original size:18 final size:19
Alignment explanation
Indices: 221458--221502 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
221448 ATACGAAAGT
221458 TTTA-AAAAATTTAA-AAA
1 TTTATAAAAATTTAATAAA
*
221475 TTTATTAAAAA-TTAATACA
1 TTTA-TAAAAATTTAATAAA
221494 TTTATAAAA
1 TTTATAAAA
221503 TTGTCACTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 4 0.17
18 9 0.38
19 11 0.46
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
TTTATAAAAATTTAATAAA
Found at i:222636 original size:3 final size:3
Alignment explanation
Indices: 222623--222658 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
222613 ATGGTAAGTG
222623 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
222659 TATTATTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:223786 original size:27 final size:27
Alignment explanation
Indices: 223739--223812 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 27
223729 ATTTTGTATA
*
223739 TATTAACTT-A-TTAAATATATTTTAT
1 TATTAACTTAATTTAAAAATATTTTAT
223764 TATTAACTTAATTTAAAAATATTTTAT
1 TATTAACTTAATTTAAAAATATTTTAT
*
223791 T-TTAATTTTAATTTAAAAATAT
1 TATTAA-CTTAATTTAAAAATAT
223813 AGATTTTATT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
25 9 0.20
26 5 0.11
27 30 0.68
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (27 bp):
TATTAACTTAATTTAAAAATATTTTAT
Found at i:226176 original size:30 final size:30
Alignment explanation
Indices: 226142--226232 Score: 79
Period size: 30 Copynumber: 3.2 Consensus size: 30
226132 TTCAAATAAT
226142 ATTATTTTGTATTAATCTACACCTTTAAAA
1 ATTATTTTGTATTAATCTACACCTTTAAAA
* * *
226172 ATTATTCTGT-TT-A--TAAAAC--TAATAA
1 ATTATTTTGTATTAATCTACACCTTTAA-AA
*
226197 A-TATTATTATATTAATCTACACCTTTAAAA
1 ATTATT-TTGTATTAATCTACACCTTTAAAA
226227 ATTATT
1 ATTATT
226233 CCATTCATAA
Statistics
Matches: 45, Mismatches: 7, Indels: 17
0.65 0.10 0.25
Matches are distributed among these distances:
24 7 0.16
25 5 0.11
26 6 0.13
27 1 0.02
28 1 0.02
29 6 0.13
30 12 0.27
31 7 0.16
ACGTcount: A:0.41, C:0.11, G:0.02, T:0.46
Consensus pattern (30 bp):
ATTATTTTGTATTAATCTACACCTTTAAAA
Found at i:226230 original size:28 final size:28
Alignment explanation
Indices: 226151--226232 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 28
226141 TATTATTTTG
*
226151 TATTAATCTACACCTTTAAAAATTATTC
1 TATTAATCTACACCTTTAAAAATTATTA
* * * * * *
226179 TGTT--TATAAAACTAATAAATATTATTA
1 TATTAATCTACACCT-TTAAAAATTATTA
226206 TATTAATCTACACCTTTAAAAATTATT
1 TATTAATCTACACCTTTAAAAATTATT
226233 CCATTCATAA
Statistics
Matches: 38, Mismatches: 13, Indels: 6
0.67 0.23 0.11
Matches are distributed among these distances:
26 6 0.16
27 13 0.34
28 13 0.34
29 6 0.16
ACGTcount: A:0.43, C:0.12, G:0.01, T:0.44
Consensus pattern (28 bp):
TATTAATCTACACCTTTAAAAATTATTA
Done.