Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006447.1 Hibiscus syriacus cultivar Beakdansim tig00015607_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: 56491
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:6133 original size:19 final size:19
Alignment explanation
Indices: 6109--6145 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
6099 CATGCATCAA
*
6109 CAACTCCTATTGACTAGGC
1 CAACTCCTATTAACTAGGC
6128 CAACTCCTATTAACTAGG
1 CAACTCCTATTAACTAGG
6146 AAACAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.27
Consensus pattern (19 bp):
CAACTCCTATTAACTAGGC
Found at i:6340 original size:67 final size:67
Alignment explanation
Indices: 6230--6356 Score: 236
Period size: 67 Copynumber: 1.9 Consensus size: 67
6220 TTTATTTAAC
* *
6230 AGTAAATGCATCCATTGCTAACTAATGCCTCACCATATGTGGTGCCTGTGTTATAAGACCACGCC
1 AGTAAATGCATCCACTGCTAACTAATGCCTCACCATATATGGTGCCTGTGTTATAAGACCACGCC
6295 TA
66 TA
6297 AGTAAATGCATCCACTGCTAACTAATGCCTCACCATATATGGTGCCTGTGTTATAAGACC
1 AGTAAATGCATCCACTGCTAACTAATGCCTCACCATATATGGTGCCTGTGTTATAAGACC
6357 GCAATATTTT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 58 1.00
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.28
Consensus pattern (67 bp):
AGTAAATGCATCCACTGCTAACTAATGCCTCACCATATATGGTGCCTGTGTTATAAGACCACGCC
TA
Found at i:11522 original size:28 final size:28
Alignment explanation
Indices: 11491--11569 Score: 79
Period size: 32 Copynumber: 2.7 Consensus size: 28
11481 AAAATTACGG
* *
11491 ATTCGGGTTGGGTTTTTTTAAGTTTGAT
1 ATTCGGGTTAGGTTTTTTTAAGTGTGAT
11519 ATTCTGGTCAGGTTAGG-TTTTTTAAGTGTGAT
1 ATTC--G---GGTTAGGTTTTTTTAAGTGTGAT
*
11551 ATTCGGGTTAAGTTTTTTT
1 ATTCGGGTTAGGTTTTTTT
11570 TAAAAAAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
27 6 0.14
28 10 0.24
30 2 0.05
32 18 0.43
33 6 0.14
ACGTcount: A:0.16, C:0.05, G:0.27, T:0.52
Consensus pattern (28 bp):
ATTCGGGTTAGGTTTTTTTAAGTGTGAT
Found at i:11671 original size:124 final size:124
Alignment explanation
Indices: 11424--11682 Score: 302
Period size: 124 Copynumber: 2.1 Consensus size: 124
11414 AATCTTTTGG
11424 TATTCGGGTTAGATCTTTTTAAAAAAAAATTCGGGATTCGATCGGAATTTTTTTTAAAAAATTAC
1 TATTCGGGTTAGATCTTTTTAAAAAAAAATTCGGGATTCGATCGGAATTTTTTTTAAAAAATTAC
11489 GGATTCGGGTTGGGTTTTTTTAAGTTTGATATTCTGGTCAGGTTAGGTTTTTTAAGTGTGA
66 GGATTCGGGTTGGGTTTTTTTAAGTTTGATATTC-GG-CAGGTTAGGTTTTTTAAGTGTGA
* * *
11550 TATTCGGGTTA-AGTTTTTTTTAAAAAAAA-TCGGGA-TCGGGTCGG-A-TTTTTTTAAAAAATT
1 TATTCGGGTTAGA-TCTTTTTAAAAAAAAATTCGGGATTC-GATCGGAATTTTTTTTAAAAAATT
* * *
11610 TCAGG-TTTGGGTTGGGTCGGGTTTTTTAAAGTTTGATATTC-G-A-GTTGAGTTTTTTTAAGTG
64 AC-GGATTCGGGTTGGGT----TTTTTT-AAGTTTGATATTCGGCAGGTT-AGGTTTTTTAAGTG
11671 TGA
122 TGA
11674 TATTCGGGT
1 TATTCGGGT
11683 CGGGTTTAGG
Statistics
Matches: 118, Mismatches: 6, Indels: 20
0.82 0.04 0.14
Matches are distributed among these distances:
123 30 0.25
124 31 0.26
125 12 0.10
126 26 0.22
127 6 0.05
128 13 0.11
ACGTcount: A:0.25, C:0.07, G:0.25, T:0.44
Consensus pattern (124 bp):
TATTCGGGTTAGATCTTTTTAAAAAAAAATTCGGGATTCGATCGGAATTTTTTTTAAAAAATTAC
GGATTCGGGTTGGGTTTTTTTAAGTTTGATATTCGGCAGGTTAGGTTTTTTAAGTGTGA
Found at i:11689 original size:28 final size:28
Alignment explanation
Indices: 11623--11689 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
11613 GGTTTGGGTT
*
11623 GGGTCGGGTTTTTTAAAGTTTGATATTC
1 GGGTCGGGTTTTTTAAAGTGTGATATTC
* * * *
11651 GAGTTGAGTTTTTTTAAGTGTGATATTC
1 GGGTCGGGTTTTTTAAAGTGTGATATTC
11679 GGGTCGGGTTT
1 GGGTCGGGTTT
11690 AGGGTGAAAA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.16, C:0.06, G:0.31, T:0.46
Consensus pattern (28 bp):
GGGTCGGGTTTTTTAAAGTGTGATATTC
Found at i:12231 original size:16 final size:17
Alignment explanation
Indices: 12207--12255 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
12197 AGGTTTCAGA
*
12207 TTCAAATTCCAATTC-T
1 TTCAGATTCCAATTCAT
*
12223 TTCAGATTCAAATTCAT
1 TTCAGATTCCAATTCAT
*
12240 TCACAGATTCCAATTC
1 T-TCAGATTCCAATTC
12256 CCTCAGAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
16 13 0.48
17 2 0.07
18 12 0.44
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.39
Consensus pattern (17 bp):
TTCAGATTCCAATTCAT
Found at i:15463 original size:54 final size:54
Alignment explanation
Indices: 15070--15445 Score: 594
Period size: 54 Copynumber: 7.0 Consensus size: 54
15060 TTACCAAATG
* * * * *
15070 GGCACTATGTG-GCAACTTAAGAAATTCATAATGAGTTTATTAATTTTCATATT
1 GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
* *
15123 GGCACTGTGTGTGCAACTTAAGAATTTCATAATAAGTTTATAAATTTCCGTATT
1 GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
15177 GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
1 GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
*
15231 GGCACTGTGTGTGCAACTTAAGAAAATCATAATGAA-TTTATGAATTTCCGTATT
1 GGCACTGTGTGTGCAACTTAAGAAATTCATAAT-AAGTTTATGAATTTCCGTATT
*
15285 GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCTGTATT
1 GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
** *
15339 GGCACTGTGTGTATAACTTAAGAAATTCATAATAAGTTTATAAATTTCCGTATT
1 GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
* * *
15393 GGCATTGTGTGTACAACTTAAGAAATTCATAATGAGTTTATGAATTTCCGTAT
1 GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
15446 CGGTATTAAG
Statistics
Matches: 301, Mismatches: 19, Indels: 5
0.93 0.06 0.02
Matches are distributed among these distances:
53 12 0.04
54 287 0.95
55 2 0.01
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (54 bp):
GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
Found at i:15488 original size:54 final size:54
Alignment explanation
Indices: 15088--15491 Score: 295
Period size: 54 Copynumber: 7.5 Consensus size: 54
15078 GTGGCAACTT
* * * * * ** * **
15088 AAGAAATTCATAATGAGTTTATTAATTTTCATATTGGCACTGTGTGTGCAACTT
1 AAGAAATTCATAATGAGTTTATGAATTTCCGTATCGGCATTAAGTGTACAACCC
* * * * * ** * **
15142 AAGAATTTCATAATAAGTTTATAAATTTCCGTATTGGCACTGTGTGTGCAACTT
1 AAGAAATTCATAATGAGTTTATGAATTTCCGTATCGGCATTAAGTGTACAACCC
* * * ** * **
15196 AAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTGTGTGTGCAACTT
1 AAGAAATTCATAATGAGTTTATGAATTTCCGTATCGGCATTAAGTGTACAACCC
* * * * ** * **
15250 AAGAAAATCATAATGAATTTATGAATTTCCGTATTGGCACTGTGTGTGCAACTT
1 AAGAAATTCATAATGAGTTTATGAATTTCCGTATCGGCATTAAGTGTACAACCC
* * * * ** * **
15304 AAGAAATTCATAATAAGTTTATGAATTTCTGTATTGGCACTGTGTGTATAACTT
1 AAGAAATTCATAATGAGTTTATGAATTTCCGTATCGGCATTAAGTGTACAACCC
* * * ** **
15358 AAGAAATTCATAATAAGTTTATAAATTTCCGTATTGGCATTGTGTGTACAACTT
1 AAGAAATTCATAATGAGTTTATGAATTTCCGTATCGGCATTAAGTGTACAACCC
*
15412 AAGAAATTCATAATGAGTTTATGAATTTCCGTATCGGTATTAAGTGTACAACCC
1 AAGAAATTCATAATGAGTTTATGAATTTCCGTATCGGCATTAAGTGTACAACCC
* * *
15466 ATGAAATTTATAATGAGATTATGAAT
1 AAGAAATTCATAATGAGTTTATGAAT
15492 ATTGTATCGA
Statistics
Matches: 319, Mismatches: 31, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 319 1.00
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (54 bp):
AAGAAATTCATAATGAGTTTATGAATTTCCGTATCGGCATTAAGTGTACAACCC
Found at i:18022 original size:23 final size:23
Alignment explanation
Indices: 17995--18042 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
17985 AATATATGTA
17995 ACTATTCATCATGAAT-GAATATG
1 ACTATTCATCATGAATAG-ATATG
*
18018 ACTATTCATGATGAATAGATATG
1 ACTATTCATCATGAATAGATATG
18041 AC
1 AC
18043 CATGTAGATG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 22 0.96
24 1 0.04
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (23 bp):
ACTATTCATCATGAATAGATATG
Found at i:20231 original size:18 final size:18
Alignment explanation
Indices: 20208--20251 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
20198 TGACCGGTCA
*
20208 CGACCCGACCCATTTACC
1 CGACCCGACCCATTGACC
*
20226 CGACCCGACCCGTTGACC
1 CGACCCGACCCATTGACC
20244 CGACCCGA
1 CGACCCGA
20252 TCGTTGATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.20, C:0.50, G:0.18, T:0.11
Consensus pattern (18 bp):
CGACCCGACCCATTGACC
Found at i:20315 original size:29 final size:29
Alignment explanation
Indices: 20268--20378 Score: 177
Period size: 29 Copynumber: 3.8 Consensus size: 29
20258 ATCGTTGACC
* *
20268 GGTGTTATTCTGGTAAATAATTCAGTTTT
1 GGTGCTATTCTGGTAAATAATTCGGTTTT
* *
20297 TGTGCTATTCTGGTAAATAATTTGGTTTT
1 GGTGCTATTCTGGTAAATAATTCGGTTTT
20326 GGTGCTATTCTGGTAAATAATTCGGTTTT
1 GGTGCTATTCTGGTAAATAATTCGGTTTT
*
20355 GGTGCTATTCTGGTAATTAATTCG
1 GGTGCTATTCTGGTAAATAATTCG
20379 AAATGGGTAC
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 75 1.00
ACGTcount: A:0.22, C:0.09, G:0.23, T:0.47
Consensus pattern (29 bp):
GGTGCTATTCTGGTAAATAATTCGGTTTT
Found at i:20391 original size:29 final size:29
Alignment explanation
Indices: 20301--20402 Score: 87
Period size: 29 Copynumber: 3.5 Consensus size: 29
20291 AGTTTTTGTG
* *** * *
20301 CTATTCTGGTAAATAATTTGGTTTTGGTG
1 CTATTCTGGTAAATAATTCGAAATGGGTA
*** * *
20330 CTATTCTGGTAAATAATTCGGTTTTGGTG
1 CTATTCTGGTAAATAATTCGAAATGGGTA
*
20359 CTATTCTGGTAATTAATTCGAAATGGGTA
1 CTATTCTGGTAAATAATTCGAAATGGGTA
*
20388 CTATTTTGGTAAATA
1 CTATTCTGGTAAATA
20403 TTTTAAAAAG
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 64 1.00
ACGTcount: A:0.25, C:0.09, G:0.22, T:0.44
Consensus pattern (29 bp):
CTATTCTGGTAAATAATTCGAAATGGGTA
Found at i:20392 original size:58 final size:58
Alignment explanation
Indices: 20273--20402 Score: 170
Period size: 58 Copynumber: 2.2 Consensus size: 58
20263 TGACCGGTGT
* * *** * *
20273 TATTCTGGTAAATAATTCAGTTTTTGTGCTATTCTGGTAAATAATTTGGTTTTGGTGC
1 TATTCTGGTAAATAATTCAGTTTTGGTGCTATTCTGGTAAATAATTCGAAATGGGTAC
* *
20331 TATTCTGGTAAATAATTCGGTTTTGGTGCTATTCTGGTAATTAATTCGAAATGGGTAC
1 TATTCTGGTAAATAATTCAGTTTTGGTGCTATTCTGGTAAATAATTCGAAATGGGTAC
*
20389 TATTTTGGTAAATA
1 TATTCTGGTAAATA
20403 TTTTAAAAAG
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
58 62 1.00
ACGTcount: A:0.25, C:0.08, G:0.21, T:0.45
Consensus pattern (58 bp):
TATTCTGGTAAATAATTCAGTTTTGGTGCTATTCTGGTAAATAATTCGAAATGGGTAC
Found at i:28152 original size:3 final size:3
Alignment explanation
Indices: 28144--28177 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
28134 CTTGATTTAT
28144 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
28178 AAGGATAGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:28703 original size:116 final size:116
Alignment explanation
Indices: 28495--28827 Score: 361
Period size: 116 Copynumber: 2.9 Consensus size: 116
28485 TATGAACTTC
* * * *
28495 GCTTCCACCTAT-TTAAAAAGAGTAGACGAGCTCTCTTATATAAGCTCTC-TATTCTCTCATAAA
1 GCTTCCTCCTATATGAAAAA-AGTAGACGAGCTCTCCTATATAAGCTC-CATATTCTCCCATAAA
* * * *
28558 -GTCCATGTTGAGGTCAAACAATCTTTCCTATATGAAGTTCTTCTCCCTTGATT
64 GGT-CATGTTGAGGTCGAACAAGCTCTCCTATATGAACTTCTTCTCCCTTGATT
28611 GCTTCCTCCTATATGAAAAAAGTAGACGAGCTCTCCTATATAAGCTCCATATTCTCCCATAAAGG
1 GCTTCCTCCTATATGAAAAAAGTAGACGAGCTCTCCTATATAAGCTCCATATTCTCCCATAAAGG
* *
28676 TCATGTTGAGGTCGAACAAGCTCTCCTATATTAACTTCTTCTCCTTTGATT
66 TCATGTTGAGGTCGAACAAGCTCTCCTATATGAACTTCTTCTCCCTTGATT
* ** * * * * * * *
28727 GCCTCCTTATATATGGAAATAGTAGATGTGCTCTCCTATATAAACCCCATATTCAT-CCAAAAAG
1 GCTTCCTCCTATATGAAAAAAGTAGACGAGCTCTCCTATATAAGCTCCATATTC-TCCCATAAAG
* * * * *
28791 GTCATGGTT-TGGTCGAACGAGTTCTCTTATATAAACT
65 GTCAT-GTTGAGGTCGAACAAGCTCTCCTATATGAACT
28828 CATTATTCAC
Statistics
Matches: 187, Mismatches: 25, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
115 1 0.01
116 174 0.93
117 12 0.06
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (116 bp):
GCTTCCTCCTATATGAAAAAAGTAGACGAGCTCTCCTATATAAGCTCCATATTCTCCCATAAAGG
TCATGTTGAGGTCGAACAAGCTCTCCTATATGAACTTCTTCTCCCTTGATT
Found at i:29129 original size:44 final size:44
Alignment explanation
Indices: 29062--29207 Score: 125
Period size: 44 Copynumber: 3.3 Consensus size: 44
29052 GTGAAATATA
* * *
29062 ATGTTGATCCACCT-ACTTCTGTGATGGAATCAAACTAAATATCG
1 ATGTTGATCTACCTCA-TTATGTGATAGAATCAAACTAAATATCG
* * **
29106 ATGTTGATCTACCTCATTATGTGATAGAATCAAGCAAAATAAGG
1 ATGTTGATCTACCTCATTATGTGATAGAATCAAACTAAATATCG
* * * * * *
29150 TTATGTTTATTCAACTTC-TTTTGTGATTGAATCAAATTAAATATCG
1 --ATGTTGA-TCTACCTCATTATGTGATAGAATCAAACTAAATATCG
29196 ATGTTGATCTAC
1 ATGTTGATCTAC
29208 ATCTTTCTAT
Statistics
Matches: 79, Mismatches: 19, Indels: 9
0.74 0.18 0.08
Matches are distributed among these distances:
43 4 0.05
44 41 0.52
45 1 0.01
46 27 0.34
47 6 0.08
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (44 bp):
ATGTTGATCTACCTCATTATGTGATAGAATCAAACTAAATATCG
Found at i:29136 original size:87 final size:89
Alignment explanation
Indices: 29025--29207 Score: 208
Period size: 90 Copynumber: 2.1 Consensus size: 89
29015 AGTGACGCTA
* * * * ** *
29025 ATCTAACTCATTTTGTCATGGAATCGAGTGAAAT-A-TAATGTTGATCCACCTACTTCTGTGATG
1 ATCTACCTCATTATGTCATAGAATCAAGCAAAATAAGTAATGTTGATCCAACTACTTCTGTGATG
29088 GAATCAAACTAAATATCGATGTTG
66 GAATCAAACTAAATATCGATGTTG
* * * * * *
29112 ATCTACCTCATTATGTGATAGAATCAAGCAAAATAAGGTTATGTTTATTCAACTTCTTTTGTGAT
1 ATCTACCTCATTATGTCATAGAATCAAGCAAAATAA-GTAATGTTGATCCAACTACTTCTGTGAT
* *
29177 TGAATCAAATTAAATATCGATGTTG
65 GGAATCAAACTAAATATCGATGTTG
29202 ATCTAC
1 ATCTAC
29208 ATCTTTCTAT
Statistics
Matches: 78, Mismatches: 15, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
87 27 0.35
88 1 0.01
90 50 0.64
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (89 bp):
ATCTACCTCATTATGTCATAGAATCAAGCAAAATAAGTAATGTTGATCCAACTACTTCTGTGATG
GAATCAAACTAAATATCGATGTTG
Found at i:30813 original size:24 final size:24
Alignment explanation
Indices: 30786--30831 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
30776 ATAAATGGAG
30786 ATATCAGAAATCAAAACAGAATTC
1 ATATCAGAAATCAAAACAGAATTC
* * *
30810 ATATCATATATCAGAACAGAAT
1 ATATCAGAAATCAAAACAGAAT
30832 CCAGAACAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.52, C:0.15, G:0.09, T:0.24
Consensus pattern (24 bp):
ATATCAGAAATCAAAACAGAATTC
Found at i:30838 original size:12 final size:12
Alignment explanation
Indices: 30821--30854 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
30811 TATCATATAT
30821 CAGAACAGAATC
1 CAGAACAGAATC
*
30833 CAGAACAGAATT
1 CAGAACAGAATC
*
30845 CAGATCAGAA
1 CAGAACAGAA
30855 ATTAGATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.50, C:0.21, G:0.18, T:0.12
Consensus pattern (12 bp):
CAGAACAGAATC
Found at i:37270 original size:24 final size:24
Alignment explanation
Indices: 37238--37285 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
37228 CCTCTGTGGC
37238 CGTACATAGTTTATATAATTAGGT
1 CGTACATAGTTTATATAATTAGGT
*
37262 CGTACATAGTTTATGTAATTAGGT
1 CGTACATAGTTTATATAATTAGGT
37286 TGTCCCTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.08, G:0.19, T:0.42
Consensus pattern (24 bp):
CGTACATAGTTTATATAATTAGGT
Found at i:40194 original size:41 final size:41
Alignment explanation
Indices: 40134--40217 Score: 141
Period size: 41 Copynumber: 2.0 Consensus size: 41
40124 CCCCAAAATC
*
40134 CCGTGTTTGTTTCATGTAATTCATTTTCCGGAAAATATTTT
1 CCGTGTTTGTTTCACGTAATTCATTTTCCGGAAAATATTTT
* *
40175 CCGTGTTTGTTTCACGTAATTCATTTTCTGGAAAATGTTTT
1 CCGTGTTTGTTTCACGTAATTCATTTTCCGGAAAATATTTT
40216 CC
1 CC
40218 AGGGTTTAGT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.48
Consensus pattern (41 bp):
CCGTGTTTGTTTCACGTAATTCATTTTCCGGAAAATATTTT
Found at i:40487 original size:22 final size:22
Alignment explanation
Indices: 40459--40507 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
40449 AAATATTTAT
40459 TAATATTTATAATAGTATAATA
1 TAATATTTATAATAGTATAATA
* *
40481 TAATATTTTTAATATTATAATA
1 TAATATTTATAATAGTATAATA
*
40503 AAATA
1 TAATA
40508 ATCAATTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
TAATATTTATAATAGTATAATA
Found at i:40509 original size:30 final size:32
Alignment explanation
Indices: 40450--40509 Score: 88
Period size: 30 Copynumber: 1.9 Consensus size: 32
40440 ATATTTAAAA
**
40450 AATATTTATTAATATTTATAATAGTATAATAT
1 AATATTTATTAATATTTATAATAAAATAATAT
40482 AATATTT-TTAATA-TTATAATAAAATAAT
1 AATATTTATTAATATTTATAATAAAATAAT
40510 CAATTATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 13 0.50
31 6 0.23
32 7 0.27
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (32 bp):
AATATTTATTAATATTTATAATAAAATAATAT
Found at i:40522 original size:23 final size:23
Alignment explanation
Indices: 40492--40550 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
40482 AATATTTTTA
40492 ATATTATAATAAAATAATCA-ATT
1 ATATTATAATAAAATAA-CATATT
* *
40515 ATATTATAATAATATAAGATATT
1 ATATTATAATAAAATAACATATT
*
40538 ATATTTTAATAAA
1 ATATTATAATAAA
40551 TATATAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 1 0.03
23 30 0.97
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
ATATTATAATAAAATAACATATT
Found at i:40571 original size:30 final size:31
Alignment explanation
Indices: 40536--40638 Score: 101
Period size: 28 Copynumber: 3.5 Consensus size: 31
40526 ATATAAGATA
*
40536 TTATAT-TTTAATAA-ATATATAATAATTTTT
1 TTATATATTTAATAATA-ATATAATAATTTAT
*
40566 TTATATATTTAATAATGA-ATAAT-A-TTAT
1 TTATATATTTAATAATAATATAATAATTTAT
* * *
40594 TTATATATTTAATATTAATATAATAATCTAA
1 TTATATATTTAATAATAATATAATAATTTAT
*
40625 TAATAT-TTTAATAA
1 TTATATATTTAATAA
40639 ATATATTTAA
Statistics
Matches: 60, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
28 19 0.32
29 6 0.10
30 19 0.32
31 16 0.27
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (31 bp):
TTATATATTTAATAATAATATAATAATTTAT
Found at i:40636 original size:19 final size:18
Alignment explanation
Indices: 40568--40638 Score: 52
Period size: 19 Copynumber: 3.7 Consensus size: 18
40558 TAATTTTTTT
*
40568 ATATATTTAATAATGAATA
1 ATAT-TTTAATAATTAATA
*
40587 ATATTATTTATATATTTAATA
1 ATA-T-TTTA-ATAATTAATA
* * *
40608 TTAATATAATAATCTAATA
1 ATATTTTAATAAT-TAATA
40627 ATATTTTAATAA
1 ATATTTTAATAA
40639 ATATATTTAA
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
18 4 0.10
19 20 0.50
20 6 0.15
21 10 0.25
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (18 bp):
ATATTTTAATAATTAATA
Found at i:40642 original size:34 final size:35
Alignment explanation
Indices: 40604--40683 Score: 87
Period size: 35 Copynumber: 2.3 Consensus size: 35
40594 TTATATATTT
*
40604 AATATTAATATAATA-AT-CTAA-TAATATTTTAATA
1 AATA-TAATATAAAATATACTAATTAATATTTTAA-A
* *
40638 AATAT-ATTTAAAATATACTAATTAATATTTTTAA
1 AATATAATATAAAATATACTAATTAATATTTTAAA
40672 AATATAATATAA
1 AATATAATATAA
40684 CACTATCACT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
32 6 0.16
33 3 0.08
34 14 0.37
35 15 0.39
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (35 bp):
AATATAATATAAAATATACTAATTAATATTTTAAA
Found at i:40652 original size:23 final size:23
Alignment explanation
Indices: 40605--40677 Score: 76
Period size: 23 Copynumber: 3.1 Consensus size: 23
40595 TATATATTTA
*
40605 ATATTAATATAATA-ATCTAATAAT
1 ATATTAATA-AATATATTTAA-AAT
*
40629 ATTTTAATAAATATATTTAAAAT
1 ATATTAATAAATATATTTAAAAT
* * *
40652 ATACTAATTAATATTTTTAAAAT
1 ATATTAATAAATATATTTAAAAT
40675 ATA
1 ATA
40678 ATATAACACT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
23 29 0.69
24 13 0.31
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (23 bp):
ATATTAATAAATATATTTAAAAT
Found at i:40756 original size:92 final size:88
Alignment explanation
Indices: 40646--40816 Score: 204
Period size: 90 Copynumber: 1.9 Consensus size: 88
40636 TAAATATATT
* * * * *
40646 TAAAATATACTAATTAATATTTTTA-AAATATAA-TATAACACT-ATCACTTTAATAAATAATTA
1 TAAAATATACCAATTAATATTTTTATAAATAAAATTATAAAAATAAT-A-TTTAAT-AATAAATA
40708 ATATAATTTATAATATTTTTTATTTCAC
63 A-ATAATTT-TAATATTTTTTATTTCAC
*
40736 TAAAATATACCAATAATAATATTTTTATTAATAAAATTATAAAAATAATATTTAATAATAAATAA
1 TAAAATATACCAAT--TAATATTTTTATAAATAAAATTATAAAAATAATATTTAATAATAAATAA
40801 ATAATTTTAATATTTT
64 ATAATTTTAATATTTT
40817 AAAATAATAA
Statistics
Matches: 70, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
90 22 0.31
91 7 0.10
92 19 0.27
93 12 0.17
94 8 0.11
95 2 0.03
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.44
Consensus pattern (88 bp):
TAAAATATACCAATTAATATTTTTATAAATAAAATTATAAAAATAATATTTAATAATAAATAAAT
AATTTTAATATTTTTTATTTCAC
Found at i:41025 original size:14 final size:15
Alignment explanation
Indices: 41009--41074 Score: 71
Period size: 15 Copynumber: 4.5 Consensus size: 15
40999 TCCAGAAATA
*
41009 TAATCCATTTTCCA-
1 TAATTCATTTTCCAG
**
41023 TAATTCAAATTCCAG
1 TAATTCATTTTCCAG
41038 TAATTCATTTTCCAG
1 TAATTCATTTTCCAG
* **
41053 TAATTTAAATTCCAG
1 TAATTCATTTTCCAG
41068 TAATTCA
1 TAATTCA
41075 AATTCCAGAA
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
14 11 0.26
15 31 0.74
ACGTcount: A:0.35, C:0.20, G:0.05, T:0.41
Consensus pattern (15 bp):
TAATTCATTTTCCAG
Found at i:41051 original size:29 final size:30
Alignment explanation
Indices: 41009--41074 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 30
40999 TCCAGAAATA
*
41009 TAATCCATTTTCCA-TAATTCAAATTCCAG
1 TAATTCATTTTCCAGTAATTCAAATTCCAG
*
41038 TAATTCATTTTCCAGTAATTTAAATTCCAG
1 TAATTCATTTTCCAGTAATTCAAATTCCAG
41068 TAATTCA
1 TAATTCA
41075 AATTCCAGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
29 13 0.38
30 21 0.62
ACGTcount: A:0.35, C:0.20, G:0.05, T:0.41
Consensus pattern (30 bp):
TAATTCATTTTCCAGTAATTCAAATTCCAG
Found at i:41090 original size:15 final size:15
Alignment explanation
Indices: 41018--41082 Score: 96
Period size: 15 Copynumber: 4.4 Consensus size: 15
41008 ATAATCCATT
41018 TTCCA-TAATTCAAA
1 TTCCAGTAATTCAAA
**
41032 TTCCAGTAATTCATT
1 TTCCAGTAATTCAAA
*
41047 TTCCAGTAATTTAAA
1 TTCCAGTAATTCAAA
41062 TTCCAGTAATTCAAA
1 TTCCAGTAATTCAAA
41077 TTCCAG
1 TTCCAG
41083 AAAATCAATT
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
14 5 0.11
15 39 0.89
ACGTcount: A:0.35, C:0.20, G:0.06, T:0.38
Consensus pattern (15 bp):
TTCCAGTAATTCAAA
Found at i:44046 original size:21 final size:22
Alignment explanation
Indices: 44008--44051 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
43998 GACGTTATCT
*
44008 TGGTGGAGAAAATGGATGAAAA
1 TGGTGAAGAAAATGGATGAAAA
*
44030 TGGTGAAG-AAATTGATGAAAA
1 TGGTGAAGAAAATGGATGAAAA
44051 T
1 T
44052 TTGAGAGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.45, C:0.00, G:0.32, T:0.23
Consensus pattern (22 bp):
TGGTGAAGAAAATGGATGAAAA
Found at i:45030 original size:64 final size:64
Alignment explanation
Indices: 44958--45105 Score: 219
Period size: 64 Copynumber: 2.3 Consensus size: 64
44948 ACACACCATT
* * * *
44958 TCGAATGCATTTTATGCATCGATGCACTG-TCATACATGGATGCACTCAGG-TTTTTATGAAAAC
1 TCGAATGCATTTTATGCATCGATGCACAGACCATACATCGATGCACTCAGGCTTGTT-TG-AAAC
45021 A
64 A
*
45022 TCGAATGCATTTTATGCATCGATGCACAGACCATGCATCGATGCACTCAGGCTTGTTTGAAACA
1 TCGAATGCATTTTATGCATCGATGCACAGACCATACATCGATGCACTCAGGCTTGTTTGAAACA
45086 TCGAATGCATTTTATGCATC
1 TCGAATGCATTTTATGCATC
45106 AATTCACCCT
Statistics
Matches: 77, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
64 53 0.69
65 20 0.26
66 4 0.05
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (64 bp):
TCGAATGCATTTTATGCATCGATGCACAGACCATACATCGATGCACTCAGGCTTGTTTGAAACA
Found at i:47076 original size:21 final size:21
Alignment explanation
Indices: 47051--47090 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
47041 AAGACTCTAT
47051 TTTCAAAA-TACAAAAATGATA
1 TTTCAAAATTA-AAAAATGATA
47072 TTTCAAAATTAAAAAATGA
1 TTTCAAAATTAAAAAATGA
47091 AAACAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.30
Consensus pattern (21 bp):
TTTCAAAATTAAAAAATGATA
Found at i:55396 original size:15 final size:15
Alignment explanation
Indices: 55376--55422 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
55366 ATATAAACGT
55376 TTAATAATAAATAAA
1 TTAATAATAAATAAA
*
55391 TTAATAATAGACTAAAA
1 TTAATAATA-AAT-AAA
55408 TGTAATAA-AAATAAA
1 T-TAATAATAAATAAA
55423 CATAAGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
15 12 0.44
16 4 0.15
17 5 0.19
18 6 0.22
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (15 bp):
TTAATAATAAATAAA
Done.