Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008503.1 Hibiscus syriacus cultivar Beakdansim tig00111355_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: 62977
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:4856 original size:30 final size:29
Alignment explanation
Indices: 4820--4897 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 29
4810 AATTTAAAAA
4820 ATTATAAAATACTTATTAAATTTAT-TAAAG
1 ATTATAAAATA-TTATTAAATTTATCT-AAG
* *
4850 ATTATAAAATTATTAATAAATTTATCTAAT
1 ATTATAAAA-TATTATTAAATTTATCTAAG
*
4880 ACTATAAAATAATTATTA
1 ATTATAAAAT-ATTATTA
4898 TACTATCGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
29 1 0.02
30 37 0.90
31 3 0.07
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (29 bp):
ATTATAAAATATTATTAAATTTATCTAAG
Found at i:12707 original size:23 final size:21
Alignment explanation
Indices: 12673--12748 Score: 86
Period size: 23 Copynumber: 3.5 Consensus size: 21
12663 ATTATATTGA
12673 TTTTAAT-TTTAATATTAATT
1 TTTTAATATTTAATATTAATT
12693 TTTTAAATATATTAAATATTAATT
1 TTTT-AATAT-TT-AATATTAATT
12717 TTTTAATATTATAGATATTAA--
1 TTTTAATATT-TA-ATATTAATT
12738 TTTTAATATTT
1 TTTTAATATTT
12749 TTTTTAAATA
Statistics
Matches: 50, Mismatches: 0, Indels: 12
0.81 0.00 0.19
Matches are distributed among these distances:
20 5 0.10
21 13 0.26
22 3 0.06
23 15 0.30
24 14 0.28
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (21 bp):
TTTTAATATTTAATATTAATT
Found at i:12712 original size:24 final size:23
Alignment explanation
Indices: 12683--12741 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 23
12673 TTTTAATTTT
12683 AATATTAATTTTTTAA-ATATATTA
1 AATATTAATTTTTTAATAT-TA-TA
12707 AATATTAATTTTTTAATATTATA
1 AATATTAATTTTTTAATATTATA
*
12730 GATATTAATTTT
1 AATATTAATTTT
12742 AATATTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
23 13 0.39
24 18 0.55
25 2 0.06
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
AATATTAATTTTTTAATATTATA
Found at i:12789 original size:61 final size:61
Alignment explanation
Indices: 12652--12863 Score: 292
Period size: 61 Copynumber: 3.5 Consensus size: 61
12642 TTATATTTAA
* * *
12652 TTTTATATTATATTATATTGATTTTAATTTTAATATTAATTTTTTAAATATATTAAATATTAAT
1 TTTTATATTATATTATA--GATATTAATTTTAATATT-ATTTTTTAAATAAATTAAATAGTAAT
12716 TTTT-TA--ATATTATAGATATTAATTTTAATATT-TTTTTTAAATAAATTAAATA-TAATT
1 TTTTATATTATATTATAGATATTAATTTTAATATTATTTTTTAAATAAATTAAATAGTAA-T
*
12773 TTTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTAAATAAATTAAATAGTAAT
1 TTTT-ATATTATATTATAGATATTAATTTTAATATTATTTTTTAAATAAATTAAATAGTAAT
12835 TTTTAATATTATATTATAGAT-TTAATTTT
1 TTTT-ATATTATATTATAGATATTAATTTT
12864 TTATATATAA
Statistics
Matches: 138, Mismatches: 3, Indels: 17
0.87 0.02 0.11
Matches are distributed among these distances:
56 3 0.02
57 24 0.17
59 19 0.14
61 42 0.30
62 41 0.30
63 5 0.04
64 4 0.03
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (61 bp):
TTTTATATTATATTATAGATATTAATTTTAATATTATTTTTTAAATAAATTAAATAGTAAT
Found at i:12815 original size:39 final size:37
Alignment explanation
Indices: 12764--12845 Score: 89
Period size: 36 Copynumber: 2.2 Consensus size: 37
12754 AAATAAATTA
* *
12764 AATA-TAATTTTTTAATATTATATTATAGATATTAA-TTTT
1 AATATTAATTTTTTAA-A-TAAATTA-A-ATAGTAATTTTT
12803 AATATTAA-TTTTTAAATAAATTAAATAGTAATTTTT
1 AATATTAATTTTTTAAATAAATTAAATAGTAATTTTT
12839 AATATTA
1 AATATTA
12846 TATTATAGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
35 6 0.15
36 12 0.31
37 6 0.15
38 1 0.03
39 11 0.28
40 3 0.08
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (37 bp):
AATATTAATTTTTTAAATAAATTAAATAGTAATTTTT
Found at i:13389 original size:31 final size:31
Alignment explanation
Indices: 13352--13411 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
13342 TAGTTGTATG
* *
13352 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATCTCAGTATTGCAAAACTAA
13383 AATTATTTAAATCTCAGTATTGCAAAACT
1 AATTATTTAAATCTCAGTATTGCAAAACT
13412 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATCTCAGTATTGCAAAACTAA
Found at i:16333 original size:111 final size:112
Alignment explanation
Indices: 16154--16897 Score: 1008
Period size: 111 Copynumber: 6.6 Consensus size: 112
16144 AGAATTATGC
* * * * * *
16154 AAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTCTTCC-TCTTCAAATAAGTTCTTCTTATT
1 AAAGGTTGAACAA-TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
16218 ATGAACTTTCTCTGG-AAATGTTGATCCATCAAGTGAT-GATTTGAACA
65 ATGAACTTTCTCTGGCAAA-GCTGATCCATCAAGTGATGGATTTGAGCA
* * *
16265 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTT-TTCTTCATTATTCAGATGA-TTCTTCTCAT
1 AAAGGTTGAACAA-TTCTTCTCATTATGAA-TTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
**** *
16328 TATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCA
64 TATGAACTTTCTCTGGCAAAGCTGATCCATCAAGTGATGGATTTGAGCA
* *
16377 TAAGGTTGAACAAATTTCTTCTCATTATGAATTTCTTCTTCCTCCTTCAAGTAATGAGTTCTTCT
1 AAAGGTTGAAC-AA-TTCTTCTCATTATGAATTTCTTCTTCCTTCTTC-AG--ATGAGTTCTTCT
* * *
16442 CATTATGAACTCTAC-CTGGAAAAGCTGATCCATCAAATGATGGATTTGAGC-
61 CATTATGAACT-TTCTCTGGCAAAGCTGATCCATCAAGTGATGGATTTGAGCA
16493 AAAGGTTGAACAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA-TA
1 AAAGGTTGAACAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
*
16557 TGAACTTTCTCTGGCAAAGCTAATCCATCAAGTGATGGATTTGAGC-
66 TGAACTTTCTCTGGCAAAGCTGATCCATCAAGTGATGGATTTGAGCA
* *
16603 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCATATGAGTTCTTCTTATT
1 AAAGGTTGAAC-AATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * **
16668 ATGAACTTTCTCTGGCAAAGCTGATCCATCAAATGATGAATTCAAGCA
65 ATGAACTTTCTCTGGCAAAGCTGATCCATCAAGTGATGGATTTGAGCA
* *
16716 AAAGGTTGAACAAATCTTCTCATTATGAATTTCTTCTTCCTTCTTC--ATGAGTTTCTTCTTATT
1 AAAGGTTGAACAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAG-TTCTTCTCATT
*
16779 ATG-ACTTTCTCTGGCAAAGCTAATCCATCAAGTGATGGATTTGAGCA
65 ATGAACTTTCTCTGGCAAAGCTGATCCATCAAGTGATGGATTTGAGCA
16826 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAAC-AATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
16891 ATGAACT
65 ATGAACT
16898 CTAACTGACA
Statistics
Matches: 567, Mismatches: 46, Indels: 38
0.87 0.07 0.06
Matches are distributed among these distances:
109 2 0.00
110 107 0.19
111 182 0.32
112 124 0.22
113 49 0.09
114 34 0.06
115 2 0.00
116 14 0.02
117 53 0.09
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (112 bp):
AAAGGTTGAACAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
TGAACTTTCTCTGGCAAAGCTGATCCATCAAGTGATGGATTTGAGCA
Found at i:16654 original size:24 final size:23
Alignment explanation
Indices: 16619--16664 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
16609 TGAACAAATT
*
16619 CTTCTCATTATGAATTTCTTCTTC
1 CTTCTCATTATG-AGTTCTTCTTC
16643 CTTCTTCA-TATGAGTTCTTCTT
1 CTTC-TCATTATGAGTTCTTCTT
16665 ATTATGAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 9 0.45
24 8 0.40
25 3 0.15
ACGTcount: A:0.15, C:0.24, G:0.07, T:0.54
Consensus pattern (23 bp):
CTTCTCATTATGAGTTCTTCTTC
Found at i:16760 original size:223 final size:223
Alignment explanation
Indices: 16152--16897 Score: 1044
Period size: 223 Copynumber: 3.3 Consensus size: 223
16142 ATAGAATTAT
** * * * * *
16152 GCAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTCTTCC-TCTTCAAATAAGTTCTTCTTA
1 GCAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCATATGAGTTCTTCTCA
* * * * *
16216 TTATGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGATTTGAA-CAAAAGGTTAAACAAGT
66 TTATGAACTTTCTCTGGAAA-GCTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAA-T
* * ****
16280 TCTTCTCATTATGAACTTT-TTCTTCATTATTCAGATGA-TTCTTCTCATTATGAACTCGAACTG
129 TCTTCTCATTATGAA-TTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* *
16343 GAAAAGCTGATCCATCAAGTGATGGATTTGA
193 GCAAAGCTAATCCATCAAGTGATGGATTTGA
*
16374 GCATAAGGTTGAACAAATTTCTTCTCATTATGAATTTCTTCTTCCTCCTTCAAGTAATGAGTTCT
1 GCA-AAGGTTGAACAAA-TTCTTCTCATTATGAATTTCTTCTTCCTTCTTC-A-T-ATGAGTTCT
* * **
16439 TCTCATTATGAACTCTAC-CTGGAAAAGCTGATCCATCAAATGATGGATTTGAGC-AAAGGTTGA
61 TCTCATTATGAACT-TTCTCTGG-AAAGCTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGA
16502 ACAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA-TATGAACTTTC
124 ACAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTC
16566 TCTGGCAAAGCTAATCCATCAAGTGATGGATTTGA
189 TCTGGCAAAGCTAATCCATCAAGTGATGGATTTGA
*
16601 GCAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCATATGAGTTCTTCTTA
1 GCAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCATATGAGTTCTTCTCA
*
16666 TTATGAACTTTCTCTGGCAAAGCTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAAT
66 TTATGAACTTTCTCTGG-AAAGCTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAATT
*
16731 CTTCTCATTATGAATTTCTTCTTCCTTCTTC--ATGAGTTTCTTCTTATTATG-ACTTTCTCTGG
130 CTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAG-TTCTTCTCATTATGAACTTTCTCTGG
16793 CAAAGCTAATCCATCAAGTGATGGATTTGA
194 CAAAGCTAATCCATCAAGTGATGGATTTGA
*
16823 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GC-AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCATATGAGTTCTTCTC
16888 ATTATGAACT
65 ATTATGAACT
16898 CTAACTGACA
Statistics
Matches: 473, Mismatches: 35, Indels: 31
0.88 0.06 0.06
Matches are distributed among these distances:
221 7 0.01
222 108 0.23
223 132 0.28
224 25 0.05
225 36 0.08
226 17 0.04
227 76 0.16
228 66 0.14
229 6 0.01
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.38
Consensus pattern (223 bp):
GCAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCATATGAGTTCTTCTCA
TTATGAACTTTCTCTGGAAAGCTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAATTC
TTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGCA
AAGCTAATCCATCAAGTGATGGATTTGA
Found at i:17417 original size:94 final size:95
Alignment explanation
Indices: 17225--17423 Score: 391
Period size: 94 Copynumber: 2.1 Consensus size: 95
17215 TCATGCAACA
17225 TGATTCTGATAACAACTCATCTGATTATGAAGTGACCTTTCAAGATGATTTCACAGATATCGATA
1 TGATTCTGATAACAACTCATCTGATTATGAAGTGACCTTTCAAGATGATTTCACAGATATCGATA
17290 GTTCTTTTAATACCGAGAAATCTTGAATTC
66 GTTCTTTTAATACCGAGAAATCTTGAATTC
17320 TGATTCTGATAACAACTCATCTGATTATGAAGTGACCTTTCAAGATGA-TTCACAGATATCGATA
1 TGATTCTGATAACAACTCATCTGATTATGAAGTGACCTTTCAAGATGATTTCACAGATATCGATA
17384 GTTCTTTTAATACCGAGAAATCTTGAATTC
66 GTTCTTTTAATACCGAGAAATCTTGAATTC
17414 TGATTCTGAT
1 TGATTCTGAT
17424 GAAGAGAATA
Statistics
Matches: 104, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
94 56 0.54
95 48 0.46
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (95 bp):
TGATTCTGATAACAACTCATCTGATTATGAAGTGACCTTTCAAGATGATTTCACAGATATCGATA
GTTCTTTTAATACCGAGAAATCTTGAATTC
Found at i:18072 original size:164 final size:165
Alignment explanation
Indices: 17747--18215 Score: 734
Period size: 164 Copynumber: 2.8 Consensus size: 165
17737 GGTTTTATAT
* * * *
17747 CAAACCAAATCAGAGAACTC-AAGAATACTTCCAGAAGATGCTATTAGCACATTCCTCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCCAAA
* * *
17811 TTCAATAACTGGTTCTATGGTTCATACCAAACCAGATC-AGAACTCAAAGAAC-CTT-CAGAAGA
66 TTC---AA-TGATT-GAT--TT--TACCAAACCAGATCAATAACTCAAAGAACACTTCCAGAAGA
17873 TGCTATGAGCACATTCCTCTTCCAAATTCAATGATTGATTTTAC
122 TGCTATGAGCACATTCCTCTTCCAAATTCAATGATTGATTTTAC
17917 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCCAAA
17982 TTCAATGATTGATTTTACCAAACCAGATCAATAACTC-AAGAACACTTCCAGAAGATGCTATGAG
66 TTCAATGATTGATTTTACCAAACCAGATCAATAACTCAAAGAACACTTCCAGAAGATGCTATGAG
18046 CACATTCCTCTTCCAAATTCAATGATTGATTTTAC
131 CACATTCCTCTTCCAAATTCAATGATTGATTTTAC
18081 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCCAAA
*
18146 TTC-ATGATTGATTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTA
66 TTCAATGATTGATTTTACCAAACCAGATCA-ATAACTCAAAGAACACTTCCAGAAGATGCTATGA
18210 GCACAT
130 GCACAT
18216 GGCATTTGTT
Statistics
Matches: 285, Mismatches: 8, Indels: 17
0.92 0.03 0.05
Matches are distributed among these distances:
162 20 0.07
163 35 0.12
164 128 0.45
165 31 0.11
166 2 0.01
167 4 0.01
168 2 0.01
170 18 0.06
171 45 0.16
ACGTcount: A:0.38, C:0.24, G:0.12, T:0.26
Consensus pattern (165 bp):
CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCCAAA
TTCAATGATTGATTTTACCAAACCAGATCAATAACTCAAAGAACACTTCCAGAAGATGCTATGAG
CACATTCCTCTTCCAAATTCAATGATTGATTTTAC
Found at i:18073 original size:81 final size:83
Alignment explanation
Indices: 17835--18215 Score: 704
Period size: 83 Copynumber: 4.7 Consensus size: 83
17825 CTATGGTTCA
17835 TACCAAACCAGATCAG--AACTCAAAGAAC-CTT-CAGAAGATGCTATGAGCACATTCCTCTTCC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCC
17896 AAATTCAATGATTGATTT
66 AAATTCAATGATTGATTT
17914 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCC
17979 AAATTCAATGATTGATTT
66 AAATTCAATGATTGATTT
17997 TACCAAACCAGATCA-ATAACTC-AAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCC
18060 AAATTCAATGATTGATTT
66 AAATTCAATGATTGATTT
18078 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCC
18143 AAATTC-ATGATTGATTT
66 AAATTCAATGATTGATTT
*
18160 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCACAT
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACAT
18216 GGCATTTGTT
Statistics
Matches: 295, Mismatches: 1, Indels: 9
0.97 0.00 0.03
Matches are distributed among these distances:
79 16 0.05
81 86 0.29
82 83 0.28
83 110 0.37
ACGTcount: A:0.38, C:0.24, G:0.12, T:0.26
Consensus pattern (83 bp):
TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCC
AAATTCAATGATTGATTT
Found at i:26787 original size:15 final size:15
Alignment explanation
Indices: 26764--26795 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
26754 TGAAATGAAT
26764 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
26779 AATGCATGTATGCAA
1 AATGAATGTATGCAA
26794 AA
1 AA
26796 AGGTATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:30115 original size:24 final size:24
Alignment explanation
Indices: 30088--30137 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
30078 ATGAAATATT
30088 AATAATATATATAAATACT-ATAAA
1 AATAATATATATAAATA-TAATAAA
* *
30112 AATAATATGTATATATATAATAAA
1 AATAATATATATAAATATAATAAA
30136 AA
1 AA
30138 AGAATTATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 22 0.96
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (24 bp):
AATAATATATATAAATATAATAAA
Found at i:30138 original size:26 final size:24
Alignment explanation
Indices: 30088--30138 Score: 57
Period size: 26 Copynumber: 2.0 Consensus size: 24
30078 ATGAAATATT
* *
30088 AATAATATATATAAATACTATAAA
1 AATAATATATATAAATAATAAAAA
*
30112 AATAATATGTATATATATAATAAAAA
1 AATAATA--TATATAAATAATAAAAA
30138 A
1 A
30139 GAATTATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 7 0.32
26 15 0.68
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (24 bp):
AATAATATATATAAATAATAAAAA
Found at i:32253 original size:3 final size:3
Alignment explanation
Indices: 32224--32273 Score: 55
Period size: 3 Copynumber: 16.0 Consensus size: 3
32214 TTGGGTTTTG
* * *
32224 TAA TAT TAA TAAA TAA TATA TAT TAA TAA TAA TAA TAA TAA TTA TAA
1 TAA TAA TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
32271 TAA
1 TAA
32274 AAAAATGGGT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
3 33 0.85
4 6 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:32988 original size:2 final size:2
Alignment explanation
Indices: 32981--33016 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
32971 TCATTAATTA
32981 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
33017 CCTGAAAAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34114 original size:16 final size:18
Alignment explanation
Indices: 34093--34132 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
34083 TAATAGTTCC
34093 ATATATTT-ATA-TGATT
1 ATATATTTGATATTGATT
*
34109 ATATATTTGATATTTATT
1 ATATATTTGATATTGATT
34127 ATATAT
1 ATATAT
34133 ATATTATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.38
17 3 0.14
18 10 0.48
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (18 bp):
ATATATTTGATATTGATT
Found at i:34362 original size:21 final size:20
Alignment explanation
Indices: 34310--34363 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
34300 CCGGTAGAGC
34310 ACTACCTAAAATGTAATTTT
1 ACTACCTAAAATGTAATTTT
**
34330 TTTA-CTAGAAATGTTAATTTT
1 ACTACCTA-AAATG-TAATTTT
34351 ACTACCTAAAATG
1 ACTACCTAAAATG
34364 AATATTTCTG
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
19 3 0.11
20 7 0.26
21 14 0.52
22 3 0.11
ACGTcount: A:0.39, C:0.13, G:0.07, T:0.41
Consensus pattern (20 bp):
ACTACCTAAAATGTAATTTT
Found at i:38588 original size:2 final size:2
Alignment explanation
Indices: 38575--38604 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
38565 TGATTCAAAT
*
38575 TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38605 ATAAAGCTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:44093 original size:45 final size:45
Alignment explanation
Indices: 44033--44129 Score: 122
Period size: 45 Copynumber: 2.2 Consensus size: 45
44023 GGCTGGAGCC
* * *
44033 ATTTTGTGAGATGGTTCAACAGTGCTATTTGGTCTGACTGGAGTG
1 ATTTTGAGAGATGGTTCAACAGTGCTATTTGGTCCGACTGAAGTG
* * * * *
44078 ATTTTGAGAGCTGGTTCAGCAGTGTTGTTTGGTCCGGCTGAAGTG
1 ATTTTGAGAGATGGTTCAACAGTGCTATTTGGTCCGACTGAAGTG
44123 ATTTTGA
1 ATTTTGA
44130 TGGTTGTTTG
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.19, C:0.11, G:0.32, T:0.38
Consensus pattern (45 bp):
ATTTTGAGAGATGGTTCAACAGTGCTATTTGGTCCGACTGAAGTG
Found at i:45681 original size:15 final size:16
Alignment explanation
Indices: 45658--45707 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 16
45648 TGAAAATGAC
*
45658 ATATAAACTATGTGAT
1 ATATGAACTATGTGAT
*
45674 AT-TGAACTACGTGATT
1 ATATGAACTATGTGA-T
*
45690 ATATGAA-AATGTGAT
1 ATATGAACTATGTGAT
45705 ATA
1 ATA
45708 AGTTATGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
15 14 0.50
16 10 0.36
17 4 0.14
ACGTcount: A:0.42, C:0.06, G:0.16, T:0.36
Consensus pattern (16 bp):
ATATGAACTATGTGAT
Found at i:45692 original size:45 final size:44
Alignment explanation
Indices: 45642--45735 Score: 116
Period size: 45 Copynumber: 2.1 Consensus size: 44
45632 GATCTATGTA
*
45642 ATTATATGAAAATGACATATAAACTATGTGATATTGAACTACGTG
1 ATTATATGAAAATGACATATAAACTATGTGACA-TGAACTACGTG
** ** * *
45687 ATTATATGAAAATGTGATATAAGTTATGTGACATGATCTATGTG
1 ATTATATGAAAATGACATATAAACTATGTGACATGAACTACGTG
45731 ATTAT
1 ATTAT
45736 TTGTCTATGT
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
44 14 0.33
45 28 0.67
ACGTcount: A:0.39, C:0.06, G:0.17, T:0.37
Consensus pattern (44 bp):
ATTATATGAAAATGACATATAAACTATGTGACATGAACTACGTG
Found at i:52974 original size:46 final size:46
Alignment explanation
Indices: 52922--53016 Score: 120
Period size: 46 Copynumber: 2.1 Consensus size: 46
52912 AGAGTCGAGG
* * * *
52922 TTTCTACGCGGTTCTTCGGGATAAT-TCTACGTGGTCTTTCGGGACA
1 TTTCTACGCGGTCCTTCGAGA-AATATCTACATGGTCATTCGGGACA
* *
52968 TTTCTACGCGGTCCTTCGAGACATATCTATATGGTCATTCGGGACA
1 TTTCTACGCGGTCCTTCGAGAAATATCTACATGGTCATTCGGGACA
53014 TTT
1 TTT
53017 TTACATGGCA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
45 2 0.05
46 40 0.95
ACGTcount: A:0.18, C:0.22, G:0.23, T:0.37
Consensus pattern (46 bp):
TTTCTACGCGGTCCTTCGAGAAATATCTACATGGTCATTCGGGACA
Found at i:52991 original size:23 final size:23
Alignment explanation
Indices: 52922--53016 Score: 91
Period size: 23 Copynumber: 4.1 Consensus size: 23
52912 AGAGTCGAGG
* *
52922 TTTCTACGCGGTTCTTCGGGATA
1 TTTCTACGCGGTCCTTCGGGACA
* * *
52945 ATTCTACGTGGTCTTTCGGGACA
1 TTTCTACGCGGTCCTTCGGGACA
*
52968 TTTCTACGCGGTCCTTCGAGACA
1 TTTCTACGCGGTCCTTCGGGACA
* *** *
52991 TATCTATATGGTCATTCGGGACA
1 TTTCTACGCGGTCCTTCGGGACA
53014 TTT
1 TTT
53017 TTACATGGCA
Statistics
Matches: 56, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 56 1.00
ACGTcount: A:0.18, C:0.22, G:0.23, T:0.37
Consensus pattern (23 bp):
TTTCTACGCGGTCCTTCGGGACA
Found at i:53024 original size:23 final size:23
Alignment explanation
Indices: 52936--53032 Score: 79
Period size: 23 Copynumber: 4.2 Consensus size: 23
52926 TACGCGGTTC
* * * *
52936 TTCGGGATAATTCTACGTGGTCT
1 TTCGGGACATTTCTACATGGTCA
** *
52959 TTCGGGACATTTCTACGCGGTCC
1 TTCGGGACATTTCTACATGGTCA
* * *
52982 TTCGAGACATATCTATATGGTCA
1 TTCGGGACATTTCTACATGGTCA
*
53005 TTCGGGACATTTTTACATGG-CA
1 TTCGGGACATTTCTACATGGTCA
53027 CTTCGG
1 -TTCGG
53033 TGCAATTTAT
Statistics
Matches: 59, Mismatches: 14, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
22 2 0.03
23 57 0.97
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.35
Consensus pattern (23 bp):
TTCGGGACATTTCTACATGGTCA
Found at i:53164 original size:2 final size:2
Alignment explanation
Indices: 53157--53184 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
53147 GTGTATGATG
53157 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
53185 GTATGATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55801 original size:21 final size:21
Alignment explanation
Indices: 55733--55808 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
55723 TTGATGCATG
* * *
55733 GGGTATCGATACCTGTATGAA
1 GGGTATCGATACCTATGTGGA
** *
55754 TAGTATCGATACCATATGGTTGA
1 GGGTATCGATACC-TAT-GTGGA
55777 -GGTATCGATACCTATGTGGA
1 GGGTATCGATACCTATGTGGA
55797 GGGTATCGATAC
1 GGGTATCGATAC
55809 ACGGGGAACT
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
20 4 0.09
21 25 0.57
22 13 0.30
23 2 0.05
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (21 bp):
GGGTATCGATACCTATGTGGA
Done.