Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001128.1 Hibiscus syriacus cultivar Beakdansim tig00002231_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: 251207
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 2 of 2
Found at i:212639 original size:24 final size:25
Alignment explanation
Indices: 212607--212653 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
212597 CTATTCTTTC
212607 ACTTCAATCAAGC-TCGAATTTTAG
1 ACTTCAATCAAGCTTCGAATTTTAG
* *
212631 ACTTCAATCGAGCTTCTAATTTT
1 ACTTCAATCAAGCTTCGAATTTT
212654 TTTTTAGTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (25 bp):
ACTTCAATCAAGCTTCGAATTTTAG
Found at i:217491 original size:35 final size:37
Alignment explanation
Indices: 217420--217492 Score: 98
Period size: 35 Copynumber: 2.0 Consensus size: 37
217410 GTTGTAAAAT
*
217420 ATTTATATATTTTCTTTAAAAAAATTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
*
217457 ATTTATATATTTT-TTT-ACAAAATTGAAAAT-ATAAA
1 ATTTATATATTTTCTTTAAAAAAATT-AAAATCATAAA
217492 A
1 A
217493 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
35 13 0.39
36 7 0.21
37 13 0.39
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
Found at i:219149 original size:52 final size:52
Alignment explanation
Indices: 219087--219187 Score: 139
Period size: 52 Copynumber: 1.9 Consensus size: 52
219077 ATGTTTAAGA
* * *
219087 ACAATATCTTTTACTGTTCTTGACACGGTTACACGTATAATGCATTGTCTGG
1 ACAATATCTTTGACTGCTCTTCACACGGTTACACGTATAATGCATTGTCTGG
** * *
219139 ACAATATCTTTGACTGCTCTTCACACTTTTCCATGTATAATGCATTGTC
1 ACAATATCTTTGACTGCTCTTCACACGGTTACACGTATAATGCATTGTC
219188 CTCTTGTTGT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
52 42 1.00
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.40
Consensus pattern (52 bp):
ACAATATCTTTGACTGCTCTTCACACGGTTACACGTATAATGCATTGTCTGG
Found at i:223202 original size:2 final size:2
Alignment explanation
Indices: 223197--223241 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
223187 ATACACACGC
223197 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
223239 AT A
1 AT A
223242 GGTCATGATC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:223624 original size:2 final size:2
Alignment explanation
Indices: 223617--223672 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
223607 AATCCTTACC
223617 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
223659 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
223673 TGTAATTGGC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:229217 original size:19 final size:20
Alignment explanation
Indices: 229182--229220 Score: 62
Period size: 19 Copynumber: 1.9 Consensus size: 20
229172 TCTCAAATAT
229182 AAATATAAGTTTTTTAATTTA
1 AAATATAAG-TTTTTAATTTA
229203 AAATATAAG-TTTTAATTT
1 AAATATAAGTTTTTAATTT
229221 CATTATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
21 9 0.50
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (20 bp):
AAATATAAGTTTTTAATTTA
Found at i:229234 original size:19 final size:20
Alignment explanation
Indices: 229212--229252 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
229202 AAAATATAAG
**
229212 TTTTAATTTCATTAT-ATAT
1 TTTTAATTGAATTATGATAT
229231 TTTTAATTGAATTATGATAT
1 TTTTAATTGAATTATGATAT
229251 TT
1 TT
229253 CCTATTCTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (20 bp):
TTTTAATTGAATTATGATAT
Found at i:235308 original size:21 final size:22
Alignment explanation
Indices: 235278--235318 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
235268 AGTCATGTTT
*
235278 TCAACCATCATAGACTGTCATA
1 TCAACCATCATAGACCGTCATA
*
235300 TCAA-CATCATGGACCGTCA
1 TCAACCATCATAGACCGTCA
235319 CGTTGACACC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.34, C:0.29, G:0.12, T:0.24
Consensus pattern (22 bp):
TCAACCATCATAGACCGTCATA
Found at i:245292 original size:14 final size:14
Alignment explanation
Indices: 245273--245328 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
245263 CTATCTCTAA
245273 CTTAAACCCTAAAC
1 CTTAAACCCTAAAC
*
245287 CTTAAACCAT-AAC
1 CTTAAACCCTAAAC
*
245300 CCTATAACCTCTAAAC
1 CTTA-AACC-CTAAAC
* *
245316 CATAAATCCTAAA
1 CTTAAACCCTAAA
245329 TTATAAATCA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
13 6 0.18
14 18 0.53
15 4 0.12
16 6 0.18
ACGTcount: A:0.45, C:0.32, G:0.00, T:0.23
Consensus pattern (14 bp):
CTTAAACCCTAAAC
Found at i:245317 original size:22 final size:20
Alignment explanation
Indices: 245277--245320 Score: 70
Period size: 22 Copynumber: 2.1 Consensus size: 20
245267 CTCTAACTTA
245277 AACCCTAAACCTTAAACCAT
1 AACCCTAAACCTTAAACCAT
245297 AACCCTATAACCTCTAAACCAT
1 AACCCTA-AACCT-TAAACCAT
245319 AA
1 AA
245321 ATCCTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 7 0.32
21 5 0.23
22 10 0.45
ACGTcount: A:0.45, C:0.34, G:0.00, T:0.20
Consensus pattern (20 bp):
AACCCTAAACCTTAAACCAT
Found at i:245384 original size:14 final size:15
Alignment explanation
Indices: 245343--245411 Score: 67
Period size: 14 Copynumber: 4.9 Consensus size: 15
245333 AAATCATAAC
**
245343 TTAGA-GTTTATAAT
1 TTAGAGGTTTATGGT
*
245357 TTA-AGGTTAATGGT
1 TTAGAGGTTTATGGT
245371 TTAGAGGTTT-TGGT
1 TTAGAGGTTTATGGT
*
245385 TTAGA-GTTTATGAT
1 TTAGAGGTTTATGGT
245399 TTAGAGG-TTATGG
1 TTAGAGGTTTATGG
245412 GGTTATGATT
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
13 5 0.11
14 34 0.76
15 6 0.13
ACGTcount: A:0.26, C:0.00, G:0.28, T:0.46
Consensus pattern (15 bp):
TTAGAGGTTTATGGT
Done.