Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007146.1 Hibiscus syriacus cultivar Beakdansim tig00018688_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: 87436
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:5130 original size:23 final size:23
Alignment explanation
Indices: 5112--5193 Score: 119
Period size: 23 Copynumber: 3.6 Consensus size: 23
5102 CTCGTATAAA
5112 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
5135 TACACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* **
5158 TGCATCGAAGTGCCGTGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
5181 TGCACCGTAGTGC
1 TGCACCGAAGTGC
5194 TATATAAGAT
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.28, C:0.24, G:0.27, T:0.21
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:5990 original size:19 final size:19
Alignment explanation
Indices: 5966--6013 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
5956 TTTTAAATTA
5966 GTGCATCGATGCACTTCAT
1 GTGCATCGATGCACTTCAT
5985 GTGCATCGATGCACTTCAT
1 GTGCATCGATGCACTTCAT
6004 GTGCATCGAT
1 GTGCATCGAT
6014 ACACCTTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.31
Consensus pattern (19 bp):
GTGCATCGATGCACTTCAT
Found at i:9860 original size:23 final size:23
Alignment explanation
Indices: 9834--9877 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
9824 CACCACAGCT
*
9834 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
9857 CGTAGAATTGCACCGTAGTGC
1 CGTAGAAATGCACCGAAGTGC
9878 TATATAAGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:21500 original size:23 final size:23
Alignment explanation
Indices: 21437--21500 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 23
21427 AGAGATGAAA
*
21437 AATATGTAACTGTATGATATGAG
1 AATATGTAACTGTATGTTATGAG
* * *
21460 AATATGTAAATATGTGTTATGA-
1 AATATGTAACTGTATGTTATGAG
*
21482 AAGTATGTAACTGCATGTT
1 AA-TATGTAACTGTATGTT
21501 TCATTAGTTC
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
22 2 0.06
23 30 0.94
ACGTcount: A:0.38, C:0.05, G:0.20, T:0.38
Consensus pattern (23 bp):
AATATGTAACTGTATGTTATGAG
Found at i:22129 original size:30 final size:30
Alignment explanation
Indices: 22095--22158 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
22085 GTTAACGTCG
* * *
22095 AGTGACTATTTTGTAAGAAACGATAATGTT
1 AGTGACCATTTTGTAACAAACGATAATATT
22125 AGTGACCATTTTGTAACAAACGATAATATT
1 AGTGACCATTTTGTAACAAACGATAATATT
22155 AGTG
1 AGTG
22159 TATGATTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.34
Consensus pattern (30 bp):
AGTGACCATTTTGTAACAAACGATAATATT
Found at i:23878 original size:14 final size:14
Alignment explanation
Indices: 23861--23910 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 14
23851 CGAAGCCATC
23861 CGACCGAGGGCATT
1 CGACCGAGGGCATT
*
23875 CGACCGAGGGCATC
1 CGACCGAGGGCATT
**
23889 CGACCGAGACCATT
1 CGACCGAGGGCATT
*
23903 CGAGCGAG
1 CGACCGAG
23911 CTATGCGAGG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.24, C:0.32, G:0.34, T:0.10
Consensus pattern (14 bp):
CGACCGAGGGCATT
Found at i:23890 original size:28 final size:28
Alignment explanation
Indices: 23857--23910 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
23847 CATCCGAAGC
**
23857 CATCCGACCGAGGGCATTCGACCGAGGG
1 CATCCGACCGAGACCATTCGACCGAGGG
*
23885 CATCCGACCGAGACCATTCGAGCGAG
1 CATCCGACCGAGACCATTCGACCGAG
23911 CTATGCGAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.24, C:0.33, G:0.31, T:0.11
Consensus pattern (28 bp):
CATCCGACCGAGACCATTCGACCGAGGG
Found at i:24841 original size:18 final size:18
Alignment explanation
Indices: 24818--24852 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
24808 CAAGCTGAAA
24818 AATA-TTAAAAACAATAAT
1 AATATTTAAAAA-AATAAT
24836 AATATTTAAAAAAATAA
1 AATATTTAAAAAAATAA
24853 GCATAAATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (18 bp):
AATATTTAAAAAAATAAT
Found at i:25327 original size:20 final size:20
Alignment explanation
Indices: 25294--25331 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
25284 TTTGGTTCAC
* *
25294 GGAATGTAAGATTACCAGTG
1 GGAATATAAAATTACCAGTG
25314 GGAATATAAAATTACCAG
1 GGAATATAAAATTACCAG
25332 GGAATAGGAT
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:0.42, C:0.11, G:0.24, T:0.24
Consensus pattern (20 bp):
GGAATATAAAATTACCAGTG
Found at i:25336 original size:18 final size:19
Alignment explanation
Indices: 25294--25337 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
25284 TTTGGTTCAC
* *
25294 GGAATGTAAGATTACCAGTG
1 GGAATATAAAATTACCAG-G
25314 GGAATATAAAATTACCA-G
1 GGAATATAAAATTACCAGG
25332 GGAATA
1 GGAATA
25338 GGATTACTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
20 15 0.68
ACGTcount: A:0.43, C:0.09, G:0.25, T:0.23
Consensus pattern (19 bp):
GGAATATAAAATTACCAGG
Found at i:26127 original size:21 final size:19
Alignment explanation
Indices: 26094--26162 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 19
26084 AAAATTTATG
*
26094 TTAAGGGATGAACTTAAAT
1 TTAAGGGATGAACTAAAAT
26113 TTAAGAGGAATGAACTAAAAT
1 TTAAG-GG-ATGAACTAAAAT
* *
26134 TTCAGGGGACGAACTAAAAT
1 TT-AAGGGATGAACTAAAAT
26154 TCTAAGGGA
1 T-TAAGGGA
26163 CGAAACATAT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
19 5 0.12
20 19 0.45
21 16 0.38
22 2 0.05
ACGTcount: A:0.43, C:0.09, G:0.23, T:0.25
Consensus pattern (19 bp):
TTAAGGGATGAACTAAAAT
Found at i:27553 original size:36 final size:36
Alignment explanation
Indices: 27513--27583 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 36
27503 AACACTTCTT
* * *
27513 TTAACCTTTAAAACAATTCTATAACTTTAATTATTA
1 TTAACCTCTAAAACAATTCAATAAATTTAATTATTA
**
27549 TTAACCTCTAAAATGATTCAATAAATTTAATTATT
1 TTAACCTCTAAAACAATTCAATAAATTTAATTATT
27584 CAATAAATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.42, C:0.13, G:0.01, T:0.44
Consensus pattern (36 bp):
TTAACCTCTAAAACAATTCAATAAATTTAATTATTA
Found at i:27586 original size:17 final size:17
Alignment explanation
Indices: 27564--27601 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
27554 CTCTAAAATG
27564 ATTCAATAAATTTAATT
1 ATTCAATAAATTTAATT
27581 ATTCAATAAATTTAATT
1 ATTCAATAAATTTAATT
27598 ATTC
1 ATTC
27602 TTACGTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (17 bp):
ATTCAATAAATTTAATT
Found at i:28777 original size:183 final size:184
Alignment explanation
Indices: 28419--28805 Score: 665
Period size: 183 Copynumber: 2.1 Consensus size: 184
28409 ATTAAATTTT
28419 AAATATTAAATATATTATATATAACATATGGGCTCAACCCAAATCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTCAACCCAAATCATTTAAAACCCAATTAATAA
* *
28484 TTTAATATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTATATAAATTTTT
66 TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTATATAAAATTTT
*
28549 TATTTTATAATTATATATTATTTAAATTAATTGTAAACTTTTTTTT-AATTAAA
131 TATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTTGAATTAAA
28602 AAATATTAAATATATTATATATAACATATGGGCT-AAGCCCAAATCATTTAAAACCCAATTAATA
1 AAATATTAAATATATTATATATAACATATGGGCTCAA-CCCAAATCATTTAAAACCCAATTAATA
* *
28666 ATTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAATTTTATCTAAAATT
65 ATTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAA-ATTATATAAAATT
28731 TTTATTTTATAATTATATATTATTTAAATTAATTATAAAC-TTTTTTTGAATTAAA
129 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTTGAATTAAA
* *
28786 AAATATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
28806 AATTAGAAAT
Statistics
Matches: 194, Mismatches: 7, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
182 2 0.01
183 126 0.65
184 66 0.34
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (184 bp):
AAATATTAAATATATTATATATAACATATGGGCTCAACCCAAATCATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTATATAAAATTTT
TATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTTGAATTAAA
Found at i:35546 original size:30 final size:30
Alignment explanation
Indices: 35512--35574 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
35502 GTAAATTATT
35512 ACAACATCTAGAGAGATTGCTCCAAGTTAA
1 ACAACATCTAGAGAGATTGCTCCAAGTTAA
35542 ACAACATCTAGAGAGATTGCTCCAAGTTAA
1 ACAACATCTAGAGAGATTGCTCCAAGTTAA
35572 ACA
1 ACA
35575 TTATGTATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.22
Consensus pattern (30 bp):
ACAACATCTAGAGAGATTGCTCCAAGTTAA
Found at i:46812 original size:21 final size:20
Alignment explanation
Indices: 46763--46813 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
46753 ATTCAATTCA
*
46763 AAAAATTAAAATGTCAATTTG
1 AAAAATT-AAATGCCAATTTG
**
46784 AATTATTAAATGACCAATTTG
1 AAAAATTAAATG-CCAATTTG
46805 AAAAATTAA
1 AAAAATTAA
46814 TGAGCATATT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
20 5 0.21
21 19 0.79
ACGTcount: A:0.53, C:0.06, G:0.08, T:0.33
Consensus pattern (20 bp):
AAAAATTAAATGCCAATTTG
Found at i:52840 original size:20 final size:20
Alignment explanation
Indices: 52815--52860 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
52805 TTTTGAGTAA
52815 TTAAAACATGTTTAAAG-TGT
1 TTAAAACATGTTTAAAGCT-T
**
52835 TTAAAATGTGTTTAAAGCTT
1 TTAAAACATGTTTAAAGCTT
52855 TTAAAA
1 TTAAAA
52861 TATTAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.41, C:0.04, G:0.13, T:0.41
Consensus pattern (20 bp):
TTAAAACATGTTTAAAGCTT
Found at i:52861 original size:20 final size:20
Alignment explanation
Indices: 52823--52861 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
52813 AATTAAAACA
52823 TGTTTAAAGTGTTTAAAATG
1 TGTTTAAAGTGTTTAAAATG
52843 TGTTTAAAGCT-TTTAAAAT
1 TGTTTAAAG-TGTTTAAAAT
52862 ATTAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.36, C:0.03, G:0.15, T:0.46
Consensus pattern (20 bp):
TGTTTAAAGTGTTTAAAATG
Found at i:54082 original size:19 final size:18
Alignment explanation
Indices: 54066--54100 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
54056 GTTCGAACTG
*
54066 GTTTGACCGGTCTGAACC
1 GTTTGAACGGTCTGAACC
54084 GTTTGAACGGTCT-AACC
1 GTTTGAACGGTCTGAACC
54101 CGACCCAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.29
Consensus pattern (18 bp):
GTTTGAACGGTCTGAACC
Found at i:54155 original size:7 final size:7
Alignment explanation
Indices: 54130--54162 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
54120 CGACCCGACT
54130 GTTGACC
1 GTTGACC
*
54137 GTTAACC
1 GTTGACC
54144 G-TGACC
1 GTTGACC
54150 GTTGACC
1 GTTGACC
54157 GTTGAC
1 GTTGAC
54163 TTCCTTTGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.27
Consensus pattern (7 bp):
GTTGACC
Found at i:61321 original size:19 final size:18
Alignment explanation
Indices: 61278--61336 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 18
61268 GAAACCGGTT
61278 AACCGGTTTCGACCGGT-TCG
1 AACCGGTTT-GA-CGGTCT-G
61298 AACCGGTTTGACTGGTCTG
1 AACCGGTTTGAC-GGTCTG
*
61317 AACCGATTTGAACGGTCTG
1 AACCGGTTTG-ACGGTCTG
61336 A
1 A
61337 CCTGACCCGA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
18 1 0.03
19 22 0.63
20 12 0.34
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (18 bp):
AACCGGTTTGACGGTCTG
Found at i:61364 original size:19 final size:19
Alignment explanation
Indices: 61340--61381 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
61330 GGTCTGACCT
61340 GACCCGACTGACCCAACCC
1 GACCCGACTGACCCAACCC
*
61359 GACCCGACTGACCCGACCC
1 GACCCGACTGACCCAACCC
61378 GACC
1 GACC
61382 GTTGACCGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.24, C:0.52, G:0.19, T:0.05
Consensus pattern (19 bp):
GACCCGACTGACCCAACCC
Found at i:61390 original size:7 final size:7
Alignment explanation
Indices: 61378--61414 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
61368 GACCCGACCC
61378 GACCGTT
1 GACCGTT
61385 GACCGTT
1 GACCGTT
61392 GACCG-T
1 GACCGTT
61398 GACCGTT
1 GACCGTT
*
61405 GACCCTT
1 GACCGTT
61412 GAC
1 GAC
61415 TTCCTTTGAC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
6 6 0.21
7 22 0.79
ACGTcount: A:0.16, C:0.32, G:0.27, T:0.24
Consensus pattern (7 bp):
GACCGTT
Found at i:61402 original size:13 final size:14
Alignment explanation
Indices: 61378--61414 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
61368 GACCCGACCC
61378 GACCGTTGACCGTT
1 GACCGTTGACCGTT
61392 GACCG-TGACCGTT
1 GACCGTTGACCGTT
*
61405 GACCCTTGAC
1 GACCGTTGAC
61415 TTCCTTTGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.16, C:0.32, G:0.27, T:0.24
Consensus pattern (14 bp):
GACCGTTGACCGTT
Found at i:73441 original size:23 final size:24
Alignment explanation
Indices: 73415--73466 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
73405 TCTAACAAAC
* * *
73415 TAAAAATCCTAATTAATAA-ATAT
1 TAAAAATCATAAATAATAATAAAT
73438 TAAAAATCATAAATAATAATAAAT
1 TAAAAATCATAAATAATAATAAAT
73462 TAAAA
1 TAAAA
73467 TTTCTATGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 17 0.68
24 8 0.32
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (24 bp):
TAAAAATCATAAATAATAATAAAT
Found at i:75348 original size:24 final size:24
Alignment explanation
Indices: 75296--75349 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
75286 AAATTAAATT
* *
75296 GAAAATAAATTTGAATCAAATAAA
1 GAAAATAAATATGAATAAAATAAA
*
75320 AAAAATAAATAT-AATAAAATAAGA
1 GAAAATAAATATGAATAAAATAA-A
75344 GAAAAT
1 GAAAAT
75350 GGGTTGTCTC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.69, C:0.02, G:0.07, T:0.22
Consensus pattern (24 bp):
GAAAATAAATATGAATAAAATAAA
Found at i:78282 original size:25 final size:26
Alignment explanation
Indices: 78254--78308 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 26
78244 AAGGGGGTTT
*
78254 ATAAAAATCAAGTAAATA-AAATA-AA
1 ATAAAAATAAAGTAAA-AGAAATATAA
78279 ATAAAAATAAAGTAAAAGAAATATAA
1 ATAAAAATAAAGTAAAAGAAATATAA
78305 ATAA
1 ATAA
78309 GAAAGATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 1 0.04
25 20 0.74
26 6 0.22
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (26 bp):
ATAAAAATAAAGTAAAAGAAATATAA
Found at i:78288 original size:16 final size:16
Alignment explanation
Indices: 78267--78305 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
78257 AAAATCAAGT
*
78267 AAATAAAATAAAATAA
1 AAATAAAATAAAAGAA
*
78283 AAATAAAGTAAAAGAA
1 AAATAAAATAAAAGAA
*
78299 ATATAAA
1 AAATAAA
78306 TAAGAAAGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (16 bp):
AAATAAAATAAAAGAA
Found at i:84581 original size:81 final size:81
Alignment explanation
Indices: 84351--84762 Score: 505
Period size: 81 Copynumber: 5.1 Consensus size: 81
84341 TGTTCTAAAA
* * * ** * *
84351 TAAAAAATTAATGGCCTCGCTGTGCATTTGGTAGAAAAAATGTCAATA-TTGCAGTTAGATGAAA
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAG-AAATGTGCCAATATTTCCAGTTAGATGAAA
84415 GGCTAAATGCCTTTGAG
65 GGCTAAATGCCTTTGAG
* * * * *
84432 T-ATAGATT-ATGGCCTAGCTGTGCA-TTGGCATAAAGGTGCCAAT-TTTGTCAATTAGATGAAA
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAATGTGCCAATATTT-CCAGTTAGATGAAA
84493 GGCTAAATGCCTTTGAG
65 GGCTAAATGCCTTTGAG
* *
84510 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAATGTACCAATATTTCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAATGTGCCAATATTTCCAGTTAGATGAAAG
* *
84575 GCTAAATGTCTTTTAG
66 GCTAAATGCCTTTGAG
* * * * * *
84591 TAAAAGATTAATGGTCTAGATGTGCATTTAGCAGTAATGTGCCAATATTGCCAGTTAGATAAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAATGTGCCAATATTTCCAGTTAGATGAAAG
84656 GCTAAATGCCTTTGAG
66 GCTAAATGCCTTTGAG
* * * *
84672 TAAAAGATTAATGGCCTAG-TAGTGCATTTGGGAGAAAGGTGCCAATA-TTGCAGTTCGATGAAA
1 TAAAAGATTAATGGCCTAGCT-GTGCATTTGGCAGAAATGTGCCAATATTTCCAGTTAGATGAAA
*
84735 GGCTAAATGCCTTTGAC
65 GGCTAAATGCCTTTGAG
84752 TAAAAGATTAA
1 TAAAAGATTAA
84763 ATGCTTAATA
Statistics
Matches: 286, Mismatches: 38, Indels: 15
0.84 0.11 0.04
Matches are distributed among these distances:
77 11 0.04
78 35 0.12
79 21 0.07
80 60 0.21
81 156 0.55
82 3 0.01
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.31
Consensus pattern (81 bp):
TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAATGTGCCAATATTTCCAGTTAGATGAAAG
GCTAAATGCCTTTGAG
Done.