Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009412.1 Hibiscus syriacus cultivar Beakdansim tig00113349_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: 47581
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:5174 original size:12 final size:12
Alignment explanation
Indices: 5159--5185 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
5149 CCAATTAATG
5159 TTAACATACTTC
1 TTAACATACTTC
5171 TTAACATACTTC
1 TTAACATACTTC
5183 TTA
1 TTA
5186 CAAGGGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.22, G:0.00, T:0.44
Consensus pattern (12 bp):
TTAACATACTTC
Found at i:5457 original size:16 final size:16
Alignment explanation
Indices: 5436--5469 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
5426 TAATCACTCC
5436 TAAATT-ATAAAACTTT
1 TAAATTGATAAAA-TTT
5452 TAAATTGATAAAATTT
1 TAAATTGATAAAATTT
5468 TA
1 TA
5470 TGGGAGCAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (16 bp):
TAAATTGATAAAATTT
Found at i:7828 original size:3 final size:3
Alignment explanation
Indices: 7820--7886 Score: 134
Period size: 3 Copynumber: 22.3 Consensus size: 3
7810 ATACCTAAAT
7820 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
7868 TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA T
7887 TCTAGAATCA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:10030 original size:14 final size:15
Alignment explanation
Indices: 10011--10041 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
10001 TCGACATAAA
10011 AACTTAAAA-TTTAT
1 AACTTAAAATTTTAT
10025 AACTTAAAATTTTAT
1 AACTTAAAATTTTAT
10040 AA
1 AA
10042 TACATAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (15 bp):
AACTTAAAATTTTAT
Found at i:10273 original size:3 final size:3
Alignment explanation
Indices: 10265--10297 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
10255 AAAGTCTAAT
10265 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
10298 ATAAAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:13842 original size:21 final size:22
Alignment explanation
Indices: 13801--13848 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
13791 GATTTTGTTG
13801 ACTAAT-TATAAAAAATATTAA
1 ACTAATATATAAAAAATATTAA
* *
13822 ACTAATATCTAAATAAT-TTAA
1 ACTAATATATAAAAAATATTAA
13843 A-TAATA
1 ACTAATA
13849 ATTTATTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 5 0.21
21 11 0.46
22 8 0.33
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (22 bp):
ACTAATATATAAAAAATATTAA
Found at i:14542 original size:32 final size:32
Alignment explanation
Indices: 14474--14561 Score: 99
Period size: 32 Copynumber: 2.8 Consensus size: 32
14464 AATACGACCT
* *
14474 TGACACT-TTCGTGTATTATCTGAATGCAATAT
1 TGACACTGTT-GTGCATTATCTGAATGCAATAC
* * *
14506 TGACATTGTTTTGCATTATCTGAATGCGACT-C
1 TGACACTGTTGTGCATTATCTGAATGC-AATAC
14538 TGACACTGTTGTGCATTATCTGAA
1 TGACACTGTTGTGCATTATCTGAA
14562 AATAGCATAC
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
32 43 0.91
33 4 0.09
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.40
Consensus pattern (32 bp):
TGACACTGTTGTGCATTATCTGAATGCAATAC
Found at i:18563 original size:14 final size:14
Alignment explanation
Indices: 18544--18571 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
18534 AGACCAAAAA
18544 CCATAGATCAGAAT
1 CCATAGATCAGAAT
18558 CCATAGATCAGAAT
1 CCATAGATCAGAAT
18572 TCAAATATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.21, G:0.14, T:0.21
Consensus pattern (14 bp):
CCATAGATCAGAAT
Found at i:21553 original size:20 final size:20
Alignment explanation
Indices: 21507--21553 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
21497 TGGGTAGGCT
* *
21507 CTTAGGCCCCAAGGTAGTCC
1 CTTAGGTCCCAAGATAGTCC
21527 CTTAGGTCCCAAGATAGTCC
1 CTTAGGTCCCAAGATAGTCC
21547 CTTAGGT
1 CTTAGGT
21554 AGGCTCTAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.26
Consensus pattern (20 bp):
CTTAGGTCCCAAGATAGTCC
Found at i:25054 original size:166 final size:167
Alignment explanation
Indices: 24382--25212 Score: 1375
Period size: 166 Copynumber: 5.0 Consensus size: 167
24372 ATTTCCATTC
* * *
24382 GCTAATAAAAATAATGGATGAAAGAAACTTTTTTTTTTTTAATTTCTGCATCTAGAGCAGTCAAT
1 GCTAATAAAAATAATGGATGAAAGAGAC-TTTTTTCTTTTAATTCCTGCATCTAGAGCAGTCAAT
*
24447 ACACAGACATTGGCCTGGTAAG-CCCATGTTAGTTTTGAATGAAGAAAATTTGAGATGAAAAATA
65 ACGCAGACATTGGCCTGGTAAGCCCCATGTTAGTTTTGAATGAAGAAAATTTGAGATGAAAAATA
* *
24511 CAAACTTAGTTTTTGGTCAATGTATGGAAAATATTAAG
130 CAAACTTAGTTTTTGGTCAATGTATGGAAAAAAATAAG
* * *
24549 GCTAATAAAAATAATGGATGAAAGAGACTTTTTTCTTTTAACTCATGCATCTAAAGCAGTCAATA
1 GCTAATAAAAATAATGGATGAAAGAGACTTTTTTCTTTTAATTCCTGCATCTAGAGCAGTCAATA
* * *
24614 CGTAGACATTGGCCTGGTAAGCCCCGTGTTA-TTTCGGAATGAAGAAAATTTGAGATGAAAAATA
66 CGCAGACATTGGCCTGGTAAGCCCCATGTTAGTTT-TGAATGAAGAAAATTTGAGATGAAAAATA
*
24678 CAAACTTAGTTTTTGGTCAATGTATGGAAAAAAATTAAT
130 CAAACTTAGTTTTTGGTCAATGTATGGAAAAAAA-TAAG
24717 GCTAATAAAAATAATGGATGAAAGAGACTTTTTTCTTTTAATTCCTGCATCTAGAGCAGTCAATA
1 GCTAATAAAAATAATGGATGAAAGAGACTTTTTTCTTTTAATTCCTGCATCTAGAGCAGTCAATA
*
24782 CGCAGACATTGGCCTGGTAAGCCCCATGTTAGTATTGAATGAAGAAAATTTGAGATGAAAAATAC
66 CGCAGACATTGGCCTGGTAAGCCCCATGTTAGTTTTGAATGAAGAAAATTTGAGATGAAAAATAC
24847 AAACTTAGTTTTTGGTCAATGTATGGAAAAAAATAAG
131 AAACTTAGTTTTTGGTCAATGTATGGAAAAAAATAAG
* * *
24884 GCTAATACAATTAATGGATGAAAGAGACTTTTTTCTTTTAATTCCTGCATCTAGAGCAGTTAATA
1 GCTAATAAAAATAATGGATGAAAGAGACTTTTTTCTTTTAATTCCTGCATCTAGAGCAGTCAATA
24949 CGCAGACATTGGCCTGGTAAG-CCCATGTTAGTTTTGAATGAAGAAAATTTGAGATGAAAAATAC
66 CGCAGACATTGGCCTGGTAAGCCCCATGTTAGTTTTGAATGAAGAAAATTTGAGATGAAAAATAC
25013 AAACTTAGTTTTTGGTCAATGTATGGAAAAAAATAAG
131 AAACTTAGTTTTTGGTCAATGTATGGAAAAAAATAAG
*
25050 GCTAATACAAATAATGGATGAAAGAGACTTTTTTCTTTT-ATTCCTGCATCTAGAGCAGTCAATA
1 GCTAATAAAAATAATGGATGAAAGAGACTTTTTTCTTTTAATTCCTGCATCTAGAGCAGTCAATA
* * * *
25114 GGCAGACATTGGCTTGGTAAGCCCCATGTTA-TTTCGGAATGAAGAAAATTTGATATGAAAAATA
66 CGCAGACATTGGCCTGGTAAGCCCCATGTTAGTTT-TGAATGAAGAAAATTTGAGATGAAAAATA
* *
25178 AAAATTTAGTTTTTGGTCAATGTATGGAAAAAAAT
130 CAAACTTAGTTTTTGGTCAATGTATGGAAAAAAAT
25213 TAAGATTAAT
Statistics
Matches: 625, Mismatches: 33, Indels: 13
0.93 0.05 0.02
Matches are distributed among these distances:
165 46 0.07
166 240 0.38
167 181 0.29
168 156 0.25
169 2 0.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.32
Consensus pattern (167 bp):
GCTAATAAAAATAATGGATGAAAGAGACTTTTTTCTTTTAATTCCTGCATCTAGAGCAGTCAATA
CGCAGACATTGGCCTGGTAAGCCCCATGTTAGTTTTGAATGAAGAAAATTTGAGATGAAAAATAC
AAACTTAGTTTTTGGTCAATGTATGGAAAAAAATAAG
Found at i:30391 original size:90 final size:89
Alignment explanation
Indices: 30239--30403 Score: 251
Period size: 90 Copynumber: 1.8 Consensus size: 89
30229 CTAACACACC
* *
30239 CTTTTATAGCCAAGTTACCCTAAGCATATTAAGGTTTTATTATTTCAAATTATTTAAATCTATAT
1 CTTTTATAGCCAAGCTACCATAAGCATATTAAGGTTTTATTATTTCAAATTATTTAAATCTATAT
30304 TTAATTAATTGGAATTTAATAATT
66 TTAATTAATTGGAATTTAATAATT
* * * *
30328 CTTTTATATCCAAGCTACTATAATCATATTAGGGATTTTATTATTTCAAATTGA-TTAAATCTAT
1 CTTTTATAGCCAAGCTACCATAAGCATATTAAGG-TTTTATTATTTCAAATT-ATTTAAATCTAT
30392 ATTTAATTAATT
64 ATTTAATTAATT
30404 AAAATGAAAT
Statistics
Matches: 68, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
89 28 0.41
90 39 0.57
91 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.47
Consensus pattern (89 bp):
CTTTTATAGCCAAGCTACCATAAGCATATTAAGGTTTTATTATTTCAAATTATTTAAATCTATAT
TTAATTAATTGGAATTTAATAATT
Found at i:30444 original size:20 final size:21
Alignment explanation
Indices: 30376--30445 Score: 54
Period size: 20 Copynumber: 3.3 Consensus size: 21
30366 TATTATTTCA
* *
30376 AATTGATTAAATC-TATATTT
1 AATTAATTAAAACATATATTT
* *
30396 AATTAATTAAAATGAAATATTT
1 AATTAATTAAAA-CATATATTT
*
30418 GGGATT-ATTAAAACATATATTT
1 --AATTAATTAAAACATATATTT
30440 AATTAA
1 AATTAA
30446 CTCTAGATAT
Statistics
Matches: 37, Mismatches: 8, Indels: 9
0.69 0.15 0.17
Matches are distributed among these distances:
20 13 0.35
21 1 0.03
22 13 0.35
23 7 0.19
24 3 0.08
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (21 bp):
AATTAATTAAAACATATATTT
Found at i:32426 original size:17 final size:16
Alignment explanation
Indices: 32395--32428 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
32385 CACGTGAGGA
32395 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
32411 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
32428 T
1 T
32429 ACTATTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Done.