Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008568.1 Hibiscus syriacus cultivar Beakdansim tig00111492_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: 68128
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.30
Found at i:8245 original size:51 final size:51
Alignment explanation
Indices: 8156--8252 Score: 131
Period size: 51 Copynumber: 1.9 Consensus size: 51
8146 AATACTTCGC
* * * **
8156 TTAGGATGAAAACCCGAGAGGGCGTCCTAAGTTGAAAAAAAAAAAAAACTT
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATCAAAAAAAAAAAAAAACTT
* *
8207 TTAGGGTGAAAACCCGAAAGGGCGCCCTAAATCAAAAAAAGAAAAA
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATCAAAAAAAAAAAAA
8253 GAGGAAAAAG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 39 1.00
ACGTcount: A:0.48, C:0.15, G:0.22, T:0.14
Consensus pattern (51 bp):
TTAGGATGAAAACCCGAAAGGGCGCCCTAAATCAAAAAAAAAAAAAAACTT
Found at i:9249 original size:106 final size:106
Alignment explanation
Indices: 8989--9447 Score: 787
Period size: 106 Copynumber: 4.3 Consensus size: 106
8979 AGGTTTTACC
*
8989 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
9054 ACGAAGGGACCGCTGGTTGTCAACAAA-TATTTCTCAATGT
66 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
9094 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
9159 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
*
9200 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGATAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
9265 AAGAAGGGACCGCTGGTTGTCCACAAACAACTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
* *
9306 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAATGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
9371 ACGAAGGGACCGCTGGTTGTCAACAAACAATTTC-CAAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC-AATTT
*
9412 CGGAGCCAATTTCAACTTCACAACGAAGGATATTGG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
9448 CCTCGGAACA
Statistics
Matches: 337, Mismatches: 15, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
105 92 0.27
106 245 0.73
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (106 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
Found at i:10836 original size:20 final size:20
Alignment explanation
Indices: 10811--10848 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
10801 TTTTGTTTGT
*
10811 CCGCCGATGAACGACGGCCG
1 CCGCCGATCAACGACGGCCG
*
10831 CCGCCGATCAACGGCGGC
1 CCGCCGATCAACGACGGC
10849 GGTGAGGCGG
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:0.18, C:0.42, G:0.34, T:0.05
Consensus pattern (20 bp):
CCGCCGATCAACGACGGCCG
Found at i:11237 original size:24 final size:24
Alignment explanation
Indices: 11210--11255 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
11200 ATCATTATTG
11210 TTTTTATTATATATATATATTTCC
1 TTTTTATTATATATATATATTTCC
11234 TTTTTATTATATATATATATTT
1 TTTTTATTATATATATATATTT
11256 TATCCATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.65
Consensus pattern (24 bp):
TTTTTATTATATATATATATTTCC
Found at i:12895 original size:20 final size:21
Alignment explanation
Indices: 12858--12908 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 21
12848 TTTAAATTTT
12858 AAAA-TTATTATATATTTTA-A
1 AAAATTTA-TATATATTTTATA
*
12878 AAAATTTATATATTTTTTATTA
1 AAAATTTATATATATTTTA-TA
12900 AAAATTTAT
1 AAAATTTAT
12909 TTCGTTCGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 14 0.52
21 3 0.11
22 10 0.37
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
AAAATTTATATATATTTTATA
Found at i:12936 original size:20 final size:21
Alignment explanation
Indices: 12913--12954 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
12903 ATTTATTTCG
12913 TTCG-TTAAAATTTTAATTTA
1 TTCGCTTAAAATTTTAATTTA
* *
12933 TTCGCTTAAGATTTTAGTTTA
1 TTCGCTTAAAATTTTAATTTA
12954 T
1 T
12955 CATCTTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.29, C:0.07, G:0.10, T:0.55
Consensus pattern (21 bp):
TTCGCTTAAAATTTTAATTTA
Found at i:15334 original size:11 final size:11
Alignment explanation
Indices: 15320--15363 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
15310 ATTTCTTAAA
15320 TTTATTATTAT
1 TTTATTATTAT
15331 TTTATTA-TA-
1 TTTATTATTAT
*
15340 TTTAATATTTAT
1 TTTATTA-TTAT
15352 TTTATTATTAT
1 TTTATTATTAT
15363 T
1 T
15364 AAAATTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
9 6 0.21
10 2 0.07
11 14 0.50
12 6 0.21
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTATTATTAT
Found at i:15353 original size:21 final size:20
Alignment explanation
Indices: 15319--15359 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
15309 TATTTCTTAA
*
15319 ATTTATTATTATTTTATTAT
1 ATTTAATATTATTTTATTAT
15339 ATTTAATATTTATTTTATTAT
1 ATTTAATA-TTATTTTATTAT
15360 TATTAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
ATTTAATATTATTTTATTAT
Found at i:15365 original size:21 final size:21
Alignment explanation
Indices: 15327--15370 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
15317 AAATTTATTA
*
15327 TTATTTTATTATATTTAATAT
1 TTATTTTATTATATTTAAAAT
15348 TTATTTTATTAT-TATTAAAAT
1 TTATTTTATTATAT-TTAAAAT
15369 TT
1 TT
15371 TAATAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
TTATTTTATTATATTTAAAAT
Found at i:16394 original size:155 final size:152
Alignment explanation
Indices: 16197--16568 Score: 417
Period size: 155 Copynumber: 2.4 Consensus size: 152
16187 AAAAAATAAC
* * * * * *
16197 AATT-AAAGTTACATATGTATTTTATTGTAGTATATGATCATGTGATTCAAATTTGGTAAAAA-T
1 AATTGAAAG-TACACATGTA-TTTATTGTGGTTTAGGAGCATGTGATTCAAATTTGGTAAAAAGA
** * *
16260 GACTTAAAATAAATCACAAATTGAAGGCATAAGGAGATTATGAAAAATTGAA-GACTAAATTGAA
64 GACTTAAAATAAATCACAAATTGAAGAAATAAAGAGATTATGAAAAATTAAATGACTAAATTG--
* *
16324 AAATAAAAAATTTGTTATCAAAAAGATT
127 AAA-AAAAAA-TTGTTATCAAAAAAATG
* *
16352 AATTGAAAGTACACATGTATTATATTGTGGTTTAGGAGCATGTGACTCAAATTTAGTAAAAAAAG
1 AATTGAAAGTACACATGTATT-TATTGTGGTTTAGGAGCATGTGATTCAAATTTGGT--AAAAAG
* ** *
16417 AGACTTAAAATAAATGATGAATTGAAGAAATAAAGAGATTATGAAAAATTAAATGATTAAATTGA
63 AGACTTAAAATAAATCACAAATTGAAGAAATAAAGAGATTATGAAAAATTAAATGACTAAATTGA
16482 AAAAAAAATTGTTATCAAAAAAATG
128 AAAAAAAATTGTTATCAAAAAAATG
* * * * * *
16507 AATTGAAAGTACACATGTATTTGAGTATGATTTAGAAGCATGTGGTTCAAATTTGATAAAAA
1 AATTGAAAGTACACATGTATTT-ATTGTGGTTTAGGAGCATGTGATTCAAATTTGGTAAAAA
16569 AAAAATGGGC
Statistics
Matches: 184, Mismatches: 26, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
153 5 0.03
154 3 0.02
155 104 0.57
156 10 0.05
157 8 0.04
158 45 0.24
159 9 0.05
ACGTcount: A:0.47, C:0.05, G:0.16, T:0.31
Consensus pattern (152 bp):
AATTGAAAGTACACATGTATTTATTGTGGTTTAGGAGCATGTGATTCAAATTTGGTAAAAAGAGA
CTTAAAATAAATCACAAATTGAAGAAATAAAGAGATTATGAAAAATTAAATGACTAAATTGAAAA
AAAAATTGTTATCAAAAAAATG
Found at i:16569 original size:155 final size:156
Alignment explanation
Indices: 16235--16571 Score: 418
Period size: 155 Copynumber: 2.2 Consensus size: 156
16225 AGTATATGAT
* * ** *
16235 CATGTGATTCAAATTTGGT--AAAAATGACTTAAAATAAATCACAAATTGAAGGCATAAGGAGAT
1 CATGTGATTCAAATTTGATAAAAAAAAGACTTAAAATAAATCACAAATTGAAGAAATAAAGAGAT
* * *
16298 TATGAAAAATTGAAGACTAAATTGAAAAATAAAAAATTTGTTATCAAAAAGATTAATTGAAAGTA
66 TATGAAAAATTAAAGACTAAATTG-AAAATAAAAAATTTGTTATCAAAAAAATGAATTGAAAGTA
* * * *
16363 CACATGTATTATATTGTGGTTTAGGAG
130 CACATGTATTATAGTATGATTTAGAAG
* * **
16390 CATGTGACTCAAATTT-AGTAAAAAAAGAGACTTAAAATAAATGATGAATTGAAGAAATAAAGAG
1 CATGTGATTCAAATTTGA-TAAAAAAA-AGACTTAAAATAAATCACAAATTGAAGAAATAAAGAG
*
16454 ATTATGAAAAATTAAATGATTAAATTG-AAA-AAAAAA-TTGTTATCAAAAAAATGAATTGAAAG
64 ATTATGAAAAATTAAA-GACTAAATTGAAAATAAAAAATTTGTTATCAAAAAAATGAATTGAAAG
16516 TACACATGTATT-TGAGTATGATTTAGAAG
128 TACACATGTATTAT-AGTATGATTTAGAAG
*
16545 CATGTGGTTCAAATTTGATAAAAAAAA
1 CATGTGATTCAAATTTGATAAAAAAAA
16572 AATGGGCTTA
Statistics
Matches: 156, Mismatches: 19, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
154 2 0.01
155 85 0.54
156 7 0.04
157 8 0.05
158 45 0.29
159 9 0.06
ACGTcount: A:0.49, C:0.06, G:0.16, T:0.29
Consensus pattern (156 bp):
CATGTGATTCAAATTTGATAAAAAAAAGACTTAAAATAAATCACAAATTGAAGAAATAAAGAGAT
TATGAAAAATTAAAGACTAAATTGAAAATAAAAAATTTGTTATCAAAAAAATGAATTGAAAGTAC
ACATGTATTATAGTATGATTTAGAAG
Found at i:16625 original size:155 final size:153
Alignment explanation
Indices: 16328--16625 Score: 345
Period size: 155 Copynumber: 1.9 Consensus size: 153
16318 ATTGAAAAAT
* * * * * * *
16328 AAAAAATTTGTTATCAAAAAGATTAATTGAAAGTACACATGTATTATATTGTGGTTTAGGAGCAT
1 AAAAAAATTGTTATCAAAAAAATGAATTGAAAGTACACATGTATTATAGTATGATTTAGAAGCAT
* *
16393 GTGACTCAAATTTAGTAAAAAAAGAGACTTAAAATAAATGATGAATTGAAGAAATAAAGAGATTA
66 GTGACTCAAATTTAGTAAAAAAAAAGACTTAAAATAAATGATGAATTGAAGAAATAAAGAAATTA
*
16458 TGAAAAATTAAATGATTAAATTGAA
131 T--AAAACTAAATGATTAAATTGAA
16483 AAAAAAATTGTTATCAAAAAAATGAATTGAAAGTACACATGTATT-TGAGTATGATTTAGAAGCA
1 AAAAAAATTGTTATCAAAAAAATGAATTGAAAGTACACATGTATTAT-AGTATGATTTAGAAGCA
** * *
16547 TGTGGTTCAAATTT-GATAAAAAAAAAATGGGCTTAAAATGAAA-GA-GAATTTGAAGAAATAAT
65 TGTGACTCAAATTTAG-T-AAAAAAAAA--GACTTAAAAT-AAATGATGAA-TTGAAGAAATAAA
*
16609 GAAATTAT-ATACTAAAT
124 GAAATTATAAAACTAAAT
16626 CGTAAAACTG
Statistics
Matches: 121, Mismatches: 15, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
154 2 0.02
155 75 0.62
156 8 0.07
157 3 0.02
158 30 0.25
159 3 0.02
ACGTcount: A:0.49, C:0.05, G:0.16, T:0.30
Consensus pattern (153 bp):
AAAAAAATTGTTATCAAAAAAATGAATTGAAAGTACACATGTATTATAGTATGATTTAGAAGCAT
GTGACTCAAATTTAGTAAAAAAAAAGACTTAAAATAAATGATGAATTGAAGAAATAAAGAAATTA
TAAAACTAAATGATTAAATTGAA
Found at i:17884 original size:3 final size:3
Alignment explanation
Indices: 17876--17916 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
17866 AATTAATTAA
17876 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
17917 ACTGCAGTGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:26796 original size:28 final size:28
Alignment explanation
Indices: 26765--26823 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
26755 ATATATTTAA
26765 AAGT-AATCAATAAAACAAATATAGTAGC
1 AAGTAAAT-AATAAAACAAATATAGTAGC
* *
26793 AAGTAAATAATAAAACAGATATATTAGC
1 AAGTAAATAATAAAACAAATATAGTAGC
26821 AAG
1 AAG
26824 AAAAGATACA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 25 0.89
29 3 0.11
ACGTcount: A:0.58, C:0.08, G:0.12, T:0.22
Consensus pattern (28 bp):
AAGTAAATAATAAAACAAATATAGTAGC
Found at i:29902 original size:162 final size:162
Alignment explanation
Indices: 29635--29958 Score: 639
Period size: 162 Copynumber: 2.0 Consensus size: 162
29625 CAAAGATACG
29635 CAGAAAAATGAAACATTCCATTGAGAATAACGTCTAACCTCAAAAGAACTCAATAACCTTCATAA
1 CAGAAAAATGAAACATTCCATTGAGAATAACGTCTAACCTCAAAAGAACTCAATAACCTTCATAA
29700 AATTCATTGTCTCTATAGAATAAGACATTTTATGAAGTGGTAAAGGAGTGGTGAGCGAACCAAAC
66 AATTCATTGTCTCTATAGAATAAGACATTTTATGAAGTGGTAAAGGAGTGGTGAGCGAACCAAAC
29765 AATATGACAGATTGTTTTGCTACACAATTCTA
131 AATATGACAGATTGTTTTGCTACACAATTCTA
*
29797 CAGAAAAATGAAACATTCCATTGAGAATAACGTCTAACCTCAAAAGAACTCAGTAACCTTCATAA
1 CAGAAAAATGAAACATTCCATTGAGAATAACGTCTAACCTCAAAAGAACTCAATAACCTTCATAA
29862 AATTCATTGTCTCTATAGAATAAGACATTTTATGAAGTGGTAAAGGAGTGGTGAGCGAACCAAAC
66 AATTCATTGTCTCTATAGAATAAGACATTTTATGAAGTGGTAAAGGAGTGGTGAGCGAACCAAAC
29927 AATATGACAGATTGTTTTGCTACACAATTCTA
131 AATATGACAGATTGTTTTGCTACACAATTCTA
29959 ATTATATCGA
Statistics
Matches: 161, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
162 161 1.00
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.27
Consensus pattern (162 bp):
CAGAAAAATGAAACATTCCATTGAGAATAACGTCTAACCTCAAAAGAACTCAATAACCTTCATAA
AATTCATTGTCTCTATAGAATAAGACATTTTATGAAGTGGTAAAGGAGTGGTGAGCGAACCAAAC
AATATGACAGATTGTTTTGCTACACAATTCTA
Found at i:31218 original size:23 final size:22
Alignment explanation
Indices: 31176--31218 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
31166 AAACATAAGA
*
31176 TATATGATATGATATGTATGAT
1 TATATGATATGATATATATGAT
31198 TATATGCATATG-TGATATATG
1 TATATG-ATATGAT-ATATATG
31219 CAATGAGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.35, C:0.02, G:0.19, T:0.44
Consensus pattern (22 bp):
TATATGATATGATATATATGAT
Found at i:37571 original size:35 final size:36
Alignment explanation
Indices: 37513--37583 Score: 135
Period size: 35 Copynumber: 2.0 Consensus size: 36
37503 GTATTTGCAG
37513 GGGAACAGATTCCCCCCTGGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCCTGGGGGGTATCGATTCCCC
37549 GGGAACAGATT-CCCCCTGGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCCTGGGGGGTATCGATTCCCC
37584 CCTAAATGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 24 0.69
36 11 0.31
ACGTcount: A:0.17, C:0.32, G:0.31, T:0.20
Consensus pattern (36 bp):
GGGAACAGATTCCCCCCTGGGGGGTATCGATTCCCC
Found at i:38210 original size:15 final size:15
Alignment explanation
Indices: 38192--38221 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
38182 CGAGGGTATT
38192 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
38207 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
38222 ATATATAGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:45060 original size:15 final size:15
Alignment explanation
Indices: 45042--45071 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
45032 TCGAGGGTAT
45042 TGTAGTCCTTCGGGA
1 TGTAGTCCTTCGGGA
45057 TGTAGTCCTTCGGGA
1 TGTAGTCCTTCGGGA
45072 CGAATACTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.20, G:0.33, T:0.33
Consensus pattern (15 bp):
TGTAGTCCTTCGGGA
Found at i:48146 original size:2 final size:2
Alignment explanation
Indices: 48139--48179 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
48129 CACGTGGATG
* *
48139 TC TC TC TC TC TC TA TC TC TC TC TA TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
48180 TCCCCAGGAG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.05, C:0.44, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:48805 original size:22 final size:21
Alignment explanation
Indices: 48766--48806 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
48756 GGTGAAAAAA
**
48766 CCGGATCGATTTTTATCCGGT
1 CCGGATCGATTTAAATCCGGT
48787 CCGGATCGGATTTAAATCCG
1 CCGGATC-GATTTAAATCCG
48807 ACTTTGTGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.32
Consensus pattern (21 bp):
CCGGATCGATTTAAATCCGGT
Found at i:52584 original size:3 final size:3
Alignment explanation
Indices: 52576--52600 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
52566 GAATTGGGTT
52576 TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG T
52601 ATTCTCCAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:56210 original size:19 final size:19
Alignment explanation
Indices: 56186--56242 Score: 55
Period size: 19 Copynumber: 3.0 Consensus size: 19
56176 ATAATATATC
56186 TATATAAAAAATACAATTT
1 TATATAAAAAATACAATTT
***
56205 TATATAATCTATA-ATATTT
1 TATATAAAAAATACA-ATTT
56224 T-TATATAAAAATACAATTT
1 TATATA-AAAAATACAATTT
56243 GTTAAATAGT
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
18 5 0.17
19 23 0.79
20 1 0.03
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (19 bp):
TATATAAAAAATACAATTT
Found at i:56211 original size:39 final size:38
Alignment explanation
Indices: 56168--56242 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 38
56158 ATTATTTATC
56168 TATAATCTATAATATATCTATATAAAAAATACAATTTTA
1 TATAATCTATAATATATCTATAT-AAAAATACAATTTTA
* *
56207 TATAATCTATAATATTTTTATATAAAAATACAATTT
1 TATAATCTATAATATATCTATATAAAAATACAATTT
56243 GTTAAATAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
38 13 0.38
39 21 0.62
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (38 bp):
TATAATCTATAATATATCTATATAAAAATACAATTTTA
Found at i:56661 original size:23 final size:23
Alignment explanation
Indices: 56631--56681 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
56621 TTGTTGCACA
*
56631 TTTTCATCGACTTTTATGATATG
1 TTTTCATCGACTTTTATGACATG
* *
56654 TTTTCATCGATTTTTATGGCATG
1 TTTTCATCGACTTTTATGACATG
56677 TTTTC
1 TTTTC
56682 TTATGTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.18, C:0.14, G:0.14, T:0.55
Consensus pattern (23 bp):
TTTTCATCGACTTTTATGACATG
Found at i:66495 original size:21 final size:21
Alignment explanation
Indices: 66462--66511 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
66452 TTGACGTTTA
66462 ATGCTGA--TAACACTTCACG
1 ATGCTGATGTAACACTTCACG
66481 ATGCTGATGTAACACTTCACG
1 ATGCTGATGTAACACTTCACG
*
66502 ATACTGATGT
1 ATGCTGATGT
66512 GGAGATCTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 7 0.25
21 21 0.75
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (21 bp):
ATGCTGATGTAACACTTCACG
Found at i:66704 original size:18 final size:19
Alignment explanation
Indices: 66678--66716 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
66668 TTTTAAATTC
66678 AAACATAAAAATAT-TCAA
1 AAACATAAAAATATATCAA
* *
66696 AAACTTAAATATATATCAA
1 AAACATAAAAATATATCAA
66715 AA
1 AA
66717 TAAAAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.64, C:0.10, G:0.00, T:0.26
Consensus pattern (19 bp):
AAACATAAAAATATATCAA
Done.