Multiple sequence alignment - TraesCS2B01G268800

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2B01G268800 chr2B 100.000 4081 0 0 1 4081 364133608 364137688 0.000000e+00 7537
1 TraesCS2B01G268800 chr2B 94.654 318 17 0 85 402 694533646 694533963 1.020000e-135 494
2 TraesCS2B01G268800 chr2B 83.005 559 67 14 866 1412 757706845 757707387 7.930000e-132 481
3 TraesCS2B01G268800 chr2B 95.402 87 4 0 2 88 783700181 783700267 5.500000e-29 139
4 TraesCS2B01G268800 chr2D 98.480 3684 43 6 400 4081 297601283 297597611 0.000000e+00 6481
5 TraesCS2B01G268800 chr2A 96.762 3212 57 14 400 3596 371047531 371044352 0.000000e+00 5312
6 TraesCS2B01G268800 chr2A 92.248 387 24 6 3696 4081 370967876 370967495 9.980000e-151 544
7 TraesCS2B01G268800 chr2A 98.701 77 1 0 3550 3626 371044351 371044275 1.980000e-28 137
8 TraesCS2B01G268800 chr5D 85.235 1043 107 28 827 1854 410193731 410194741 0.000000e+00 1029
9 TraesCS2B01G268800 chr3D 85.043 1043 108 27 827 1854 69648249 69649258 0.000000e+00 1018
10 TraesCS2B01G268800 chr4D 84.754 1056 110 28 827 1863 51308981 51310004 0.000000e+00 1011
11 TraesCS2B01G268800 chr6B 82.732 1054 131 34 837 1869 100636301 100637324 0.000000e+00 891
12 TraesCS2B01G268800 chr6B 93.210 324 20 2 81 402 562896890 562897213 3.690000e-130 475
13 TraesCS2B01G268800 chr6B 84.545 330 40 4 1021 1339 642321256 642321585 2.370000e-82 316
14 TraesCS2B01G268800 chr4B 85.027 561 54 13 866 1412 623068927 623068383 9.980000e-151 544
15 TraesCS2B01G268800 chr4B 94.025 318 19 0 85 402 567457396 567457713 2.210000e-132 483
16 TraesCS2B01G268800 chr4B 91.176 102 9 0 2 103 660181594 660181493 5.500000e-29 139
17 TraesCS2B01G268800 chr4A 90.594 404 35 3 2 403 697997071 697996669 2.160000e-147 532
18 TraesCS2B01G268800 chr1D 84.670 561 53 14 866 1412 60431220 60431761 2.790000e-146 529
19 TraesCS2B01G268800 chr5B 84.135 561 59 13 866 1412 536513085 536513629 2.170000e-142 516
20 TraesCS2B01G268800 chr5B 93.730 319 20 0 84 402 334971473 334971155 2.850000e-131 479
21 TraesCS2B01G268800 chr5B 95.455 88 4 0 2 89 137810291 137810378 1.530000e-29 141
22 TraesCS2B01G268800 chr5B 95.455 88 4 0 1 88 513988091 513988004 1.530000e-29 141
23 TraesCS2B01G268800 chr5B 93.478 92 6 0 4 95 388312644 388312735 1.980000e-28 137
24 TraesCS2B01G268800 chr7B 94.704 321 15 1 82 402 632555286 632554968 7.880000e-137 497
25 TraesCS2B01G268800 chr7B 83.333 330 43 4 1021 1339 709066469 709066141 1.110000e-75 294
26 TraesCS2B01G268800 chr7B 80.058 346 42 6 1021 1339 11441759 11442104 8.820000e-57 231
27 TraesCS2B01G268800 chr7B 94.565 92 4 1 2 92 251606115 251606206 1.530000e-29 141
28 TraesCS2B01G268800 chr7B 93.548 93 6 0 2 94 606367850 606367758 5.500000e-29 139
29 TraesCS2B01G268800 chr3B 94.340 318 18 0 85 402 559536453 559536770 4.740000e-134 488
30 TraesCS2B01G268800 chr3B 93.711 318 20 0 85 402 575219443 575219760 1.030000e-130 477
31 TraesCS2B01G268800 chr7A 91.740 339 27 1 69 406 110348235 110348573 1.720000e-128 470
32 TraesCS2B01G268800 chr7D 87.667 300 27 2 1050 1339 503810028 503810327 1.400000e-89 340
33 TraesCS2B01G268800 chr1B 83.735 332 40 6 1021 1339 2334638 2334968 6.630000e-78 302
34 TraesCS2B01G268800 chrUn 95.402 87 4 0 2 88 368222659 368222573 5.500000e-29 139
35 TraesCS2B01G268800 chr3A 97.368 76 2 0 1695 1770 146768485 146768410 3.310000e-26 130


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G268800 chr2B 364133608 364137688 4080 False 7537.0 7537 100.0000 1 4081 1 chr2B.!!$F1 4080
1 TraesCS2B01G268800 chr2B 757706845 757707387 542 False 481.0 481 83.0050 866 1412 1 chr2B.!!$F3 546
2 TraesCS2B01G268800 chr2D 297597611 297601283 3672 True 6481.0 6481 98.4800 400 4081 1 chr2D.!!$R1 3681
3 TraesCS2B01G268800 chr2A 371044275 371047531 3256 True 2724.5 5312 97.7315 400 3626 2 chr2A.!!$R2 3226
4 TraesCS2B01G268800 chr5D 410193731 410194741 1010 False 1029.0 1029 85.2350 827 1854 1 chr5D.!!$F1 1027
5 TraesCS2B01G268800 chr3D 69648249 69649258 1009 False 1018.0 1018 85.0430 827 1854 1 chr3D.!!$F1 1027
6 TraesCS2B01G268800 chr4D 51308981 51310004 1023 False 1011.0 1011 84.7540 827 1863 1 chr4D.!!$F1 1036
7 TraesCS2B01G268800 chr6B 100636301 100637324 1023 False 891.0 891 82.7320 837 1869 1 chr6B.!!$F1 1032
8 TraesCS2B01G268800 chr4B 623068383 623068927 544 True 544.0 544 85.0270 866 1412 1 chr4B.!!$R1 546
9 TraesCS2B01G268800 chr1D 60431220 60431761 541 False 529.0 529 84.6700 866 1412 1 chr1D.!!$F1 546
10 TraesCS2B01G268800 chr5B 536513085 536513629 544 False 516.0 516 84.1350 866 1412 1 chr5B.!!$F3 546

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
170 171 0.106918 TTTGCCAAACAGACCCGACT 60.107 50.0 0.00 0.00 0.00 4.18 F
247 248 0.399075 AGTCACCCCCTTTTACGTGG 59.601 55.0 0.00 0.00 0.00 4.94 F
248 249 0.607217 GTCACCCCCTTTTACGTGGG 60.607 60.0 0.00 0.55 44.03 4.61 F
265 266 0.912487 GGGTCCCACCACCTGTATGA 60.912 60.0 1.78 0.00 41.02 2.15 F
2257 2299 0.741221 GAAGATCAGGACCACACGGC 60.741 60.0 0.00 0.00 34.57 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1303 1323 1.533625 TGAGGGGAAATGCAAAGACG 58.466 50.000 0.00 0.00 0.00 4.18 R
2031 2073 1.941377 AGAAGGGCAATGGAAATGCA 58.059 45.000 0.00 0.00 45.60 3.96 R
2257 2299 5.282778 CGAAAATACTACAATTTGTGTGCGG 59.717 40.000 12.30 0.72 41.89 5.69 R
2534 2576 8.594550 AGGTCATTATGTAGTGAGTGTTAAACT 58.405 33.333 0.00 0.00 43.85 2.66 R
4052 4142 0.165944 CGACGGCCAAAAGATGTGTC 59.834 55.000 2.24 0.00 0.00 3.67 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 4.415881 TCTTCTTTAGTTGTCTGCCACA 57.584 40.909 0.00 0.00 0.00 4.17
23 24 4.973168 TCTTCTTTAGTTGTCTGCCACAT 58.027 39.130 0.00 0.00 33.90 3.21
24 25 6.109156 TCTTCTTTAGTTGTCTGCCACATA 57.891 37.500 0.00 0.00 33.90 2.29
25 26 6.530120 TCTTCTTTAGTTGTCTGCCACATAA 58.470 36.000 0.00 0.00 33.90 1.90
26 27 6.650807 TCTTCTTTAGTTGTCTGCCACATAAG 59.349 38.462 0.00 0.00 33.90 1.73
27 28 4.695455 TCTTTAGTTGTCTGCCACATAAGC 59.305 41.667 0.00 0.00 33.90 3.09
28 29 2.566833 AGTTGTCTGCCACATAAGCA 57.433 45.000 0.00 0.00 38.82 3.91
29 30 3.077484 AGTTGTCTGCCACATAAGCAT 57.923 42.857 0.00 0.00 40.04 3.79
30 31 2.751259 AGTTGTCTGCCACATAAGCATG 59.249 45.455 0.00 0.00 40.04 4.06
31 32 2.489329 GTTGTCTGCCACATAAGCATGT 59.511 45.455 0.00 0.00 46.58 3.21
32 33 2.794103 TGTCTGCCACATAAGCATGTT 58.206 42.857 0.00 0.00 42.98 2.71
33 34 3.156293 TGTCTGCCACATAAGCATGTTT 58.844 40.909 0.00 0.00 42.98 2.83
34 35 3.057386 TGTCTGCCACATAAGCATGTTTG 60.057 43.478 4.89 0.00 42.98 2.93
46 47 2.731217 GCATGTTTGCGAGTTTCAAGT 58.269 42.857 0.00 0.00 39.49 3.16
47 48 2.468777 GCATGTTTGCGAGTTTCAAGTG 59.531 45.455 0.00 0.00 39.49 3.16
48 49 2.187351 TGTTTGCGAGTTTCAAGTGC 57.813 45.000 0.00 0.00 0.00 4.40
49 50 1.470494 TGTTTGCGAGTTTCAAGTGCA 59.530 42.857 0.00 0.00 0.00 4.57
50 51 2.098934 TGTTTGCGAGTTTCAAGTGCAT 59.901 40.909 0.00 0.00 35.20 3.96
51 52 2.404265 TTGCGAGTTTCAAGTGCATG 57.596 45.000 0.00 0.00 35.20 4.06
52 53 1.592064 TGCGAGTTTCAAGTGCATGA 58.408 45.000 0.00 0.00 0.00 3.07
53 54 2.153645 TGCGAGTTTCAAGTGCATGAT 58.846 42.857 0.00 0.00 0.00 2.45
54 55 3.333804 TGCGAGTTTCAAGTGCATGATA 58.666 40.909 0.00 0.00 0.00 2.15
55 56 3.125146 TGCGAGTTTCAAGTGCATGATAC 59.875 43.478 0.00 0.00 33.21 2.24
56 57 3.372206 GCGAGTTTCAAGTGCATGATACT 59.628 43.478 11.67 11.67 42.06 2.12
57 58 4.566759 GCGAGTTTCAAGTGCATGATACTA 59.433 41.667 11.78 0.00 40.30 1.82
58 59 5.235186 GCGAGTTTCAAGTGCATGATACTAT 59.765 40.000 11.78 0.00 40.30 2.12
59 60 6.238211 GCGAGTTTCAAGTGCATGATACTATT 60.238 38.462 11.78 0.00 40.30 1.73
60 61 7.677276 GCGAGTTTCAAGTGCATGATACTATTT 60.677 37.037 11.78 0.00 40.30 1.40
61 62 8.817100 CGAGTTTCAAGTGCATGATACTATTTA 58.183 33.333 11.78 0.00 40.30 1.40
70 71 9.712305 AGTGCATGATACTATTTATGTTACTCC 57.288 33.333 0.00 0.00 0.00 3.85
71 72 8.936864 GTGCATGATACTATTTATGTTACTCCC 58.063 37.037 0.00 0.00 0.00 4.30
72 73 8.655901 TGCATGATACTATTTATGTTACTCCCA 58.344 33.333 0.00 0.00 0.00 4.37
73 74 8.936864 GCATGATACTATTTATGTTACTCCCAC 58.063 37.037 0.00 0.00 0.00 4.61
79 80 7.450903 ACTATTTATGTTACTCCCACTATGGC 58.549 38.462 0.00 0.00 35.79 4.40
80 81 4.699925 TTATGTTACTCCCACTATGGCC 57.300 45.455 0.00 0.00 35.79 5.36
81 82 1.959710 TGTTACTCCCACTATGGCCA 58.040 50.000 8.56 8.56 35.79 5.36
82 83 1.837439 TGTTACTCCCACTATGGCCAG 59.163 52.381 13.05 0.00 35.79 4.85
83 84 0.837272 TTACTCCCACTATGGCCAGC 59.163 55.000 13.05 0.00 35.79 4.85
84 85 1.054406 TACTCCCACTATGGCCAGCC 61.054 60.000 13.05 0.38 35.79 4.85
85 86 2.042762 TCCCACTATGGCCAGCCT 59.957 61.111 13.05 0.00 35.79 4.58
86 87 0.764369 CTCCCACTATGGCCAGCCTA 60.764 60.000 13.05 0.00 35.79 3.93
87 88 0.327095 TCCCACTATGGCCAGCCTAA 60.327 55.000 13.05 0.00 35.79 2.69
88 89 0.109342 CCCACTATGGCCAGCCTAAG 59.891 60.000 13.05 9.47 35.79 2.18
89 90 0.109342 CCACTATGGCCAGCCTAAGG 59.891 60.000 13.05 4.35 36.94 2.69
90 91 0.109342 CACTATGGCCAGCCTAAGGG 59.891 60.000 13.05 4.53 36.94 3.95
103 104 1.824852 CCTAAGGGCATGTTTGGTTCC 59.175 52.381 0.00 0.00 0.00 3.62
104 105 2.524306 CTAAGGGCATGTTTGGTTCCA 58.476 47.619 0.00 0.00 0.00 3.53
105 106 1.799933 AAGGGCATGTTTGGTTCCAA 58.200 45.000 0.00 0.00 0.00 3.53
106 107 1.799933 AGGGCATGTTTGGTTCCAAA 58.200 45.000 12.29 12.29 34.09 3.28
107 108 2.337849 AGGGCATGTTTGGTTCCAAAT 58.662 42.857 18.11 2.94 38.07 2.32
108 109 3.515562 AGGGCATGTTTGGTTCCAAATA 58.484 40.909 18.11 16.10 38.07 1.40
109 110 3.906846 AGGGCATGTTTGGTTCCAAATAA 59.093 39.130 18.11 11.31 38.07 1.40
110 111 4.020307 AGGGCATGTTTGGTTCCAAATAAG 60.020 41.667 18.11 13.93 38.07 1.73
111 112 4.262851 GGGCATGTTTGGTTCCAAATAAGT 60.263 41.667 18.11 1.70 38.07 2.24
112 113 4.929211 GGCATGTTTGGTTCCAAATAAGTC 59.071 41.667 18.11 11.50 38.07 3.01
113 114 5.510520 GGCATGTTTGGTTCCAAATAAGTCA 60.511 40.000 18.11 12.03 38.07 3.41
114 115 5.405269 GCATGTTTGGTTCCAAATAAGTCAC 59.595 40.000 18.11 6.79 38.07 3.67
115 116 5.523438 TGTTTGGTTCCAAATAAGTCACC 57.477 39.130 18.11 5.59 38.07 4.02
116 117 4.956700 TGTTTGGTTCCAAATAAGTCACCA 59.043 37.500 18.11 7.77 38.07 4.17
117 118 5.422331 TGTTTGGTTCCAAATAAGTCACCAA 59.578 36.000 18.11 0.00 41.48 3.67
118 119 5.523438 TTGGTTCCAAATAAGTCACCAAC 57.477 39.130 1.42 0.00 38.97 3.77
119 120 4.798882 TGGTTCCAAATAAGTCACCAACT 58.201 39.130 0.00 0.00 41.10 3.16
120 121 6.155393 TTTGGTTCCAAATAAGTCACCAACTT 59.845 34.615 12.29 0.00 42.59 2.66
133 134 7.653767 AGTCACCAACTTATAAGTCGAAAAG 57.346 36.000 18.28 7.33 38.57 2.27
134 135 7.215085 AGTCACCAACTTATAAGTCGAAAAGT 58.785 34.615 18.28 7.29 38.57 2.66
135 136 7.170998 AGTCACCAACTTATAAGTCGAAAAGTG 59.829 37.037 18.28 16.78 38.57 3.16
136 137 7.170320 GTCACCAACTTATAAGTCGAAAAGTGA 59.830 37.037 18.28 18.36 38.57 3.41
137 138 7.711772 TCACCAACTTATAAGTCGAAAAGTGAA 59.288 33.333 18.28 7.64 38.57 3.18
138 139 8.339714 CACCAACTTATAAGTCGAAAAGTGAAA 58.660 33.333 18.28 0.00 38.57 2.69
139 140 8.895737 ACCAACTTATAAGTCGAAAAGTGAAAA 58.104 29.630 18.28 0.00 38.57 2.29
140 141 9.724839 CCAACTTATAAGTCGAAAAGTGAAAAA 57.275 29.630 18.28 0.00 38.57 1.94
161 162 7.913674 AAAAAGTGACTTATTTTGCCAAACA 57.086 28.000 0.00 0.00 0.00 2.83
162 163 7.538303 AAAAGTGACTTATTTTGCCAAACAG 57.462 32.000 0.00 0.00 0.00 3.16
163 164 6.463995 AAGTGACTTATTTTGCCAAACAGA 57.536 33.333 0.00 0.00 0.00 3.41
164 165 5.831997 AGTGACTTATTTTGCCAAACAGAC 58.168 37.500 0.00 0.00 0.00 3.51
165 166 4.982295 GTGACTTATTTTGCCAAACAGACC 59.018 41.667 0.00 0.00 0.00 3.85
166 167 4.038642 TGACTTATTTTGCCAAACAGACCC 59.961 41.667 0.00 0.00 0.00 4.46
167 168 3.005367 ACTTATTTTGCCAAACAGACCCG 59.995 43.478 0.00 0.00 0.00 5.28
168 169 1.698506 ATTTTGCCAAACAGACCCGA 58.301 45.000 0.00 0.00 0.00 5.14
169 170 0.741915 TTTTGCCAAACAGACCCGAC 59.258 50.000 0.00 0.00 0.00 4.79
170 171 0.106918 TTTGCCAAACAGACCCGACT 60.107 50.000 0.00 0.00 0.00 4.18
171 172 0.106918 TTGCCAAACAGACCCGACTT 60.107 50.000 0.00 0.00 0.00 3.01
172 173 0.759959 TGCCAAACAGACCCGACTTA 59.240 50.000 0.00 0.00 0.00 2.24
173 174 1.349688 TGCCAAACAGACCCGACTTAT 59.650 47.619 0.00 0.00 0.00 1.73
174 175 2.568062 TGCCAAACAGACCCGACTTATA 59.432 45.455 0.00 0.00 0.00 0.98
175 176 3.008157 TGCCAAACAGACCCGACTTATAA 59.992 43.478 0.00 0.00 0.00 0.98
176 177 3.621715 GCCAAACAGACCCGACTTATAAG 59.378 47.826 11.05 11.05 0.00 1.73
177 178 4.828829 CCAAACAGACCCGACTTATAAGT 58.171 43.478 18.05 18.05 43.16 2.24
196 197 5.836024 AAGTCACCCCAACTTATAAGTCA 57.164 39.130 18.28 0.00 38.57 3.41
197 198 6.388619 AAGTCACCCCAACTTATAAGTCAT 57.611 37.500 18.28 1.19 38.57 3.06
198 199 7.504926 AAGTCACCCCAACTTATAAGTCATA 57.495 36.000 18.28 0.00 38.57 2.15
199 200 7.504926 AGTCACCCCAACTTATAAGTCATAA 57.495 36.000 18.28 0.00 38.57 1.90
212 213 4.838904 AAGTCATAAGTTACTCCACCCC 57.161 45.455 0.00 0.00 0.00 4.95
213 214 3.798515 AGTCATAAGTTACTCCACCCCA 58.201 45.455 0.00 0.00 0.00 4.96
214 215 4.172807 AGTCATAAGTTACTCCACCCCAA 58.827 43.478 0.00 0.00 0.00 4.12
215 216 4.019591 AGTCATAAGTTACTCCACCCCAAC 60.020 45.833 0.00 0.00 0.00 3.77
216 217 4.019591 GTCATAAGTTACTCCACCCCAACT 60.020 45.833 0.00 0.00 32.73 3.16
217 218 4.600111 TCATAAGTTACTCCACCCCAACTT 59.400 41.667 4.24 4.24 42.32 2.66
218 219 5.786457 TCATAAGTTACTCCACCCCAACTTA 59.214 40.000 7.89 7.89 43.68 2.24
219 220 6.272792 TCATAAGTTACTCCACCCCAACTTAA 59.727 38.462 9.15 0.00 43.13 1.85
220 221 5.391577 AAGTTACTCCACCCCAACTTAAA 57.608 39.130 0.00 0.00 38.96 1.52
221 222 5.391577 AGTTACTCCACCCCAACTTAAAA 57.608 39.130 0.00 0.00 0.00 1.52
222 223 5.960704 AGTTACTCCACCCCAACTTAAAAT 58.039 37.500 0.00 0.00 0.00 1.82
223 224 6.378745 AGTTACTCCACCCCAACTTAAAATT 58.621 36.000 0.00 0.00 0.00 1.82
224 225 6.842280 AGTTACTCCACCCCAACTTAAAATTT 59.158 34.615 0.00 0.00 0.00 1.82
225 226 8.005976 AGTTACTCCACCCCAACTTAAAATTTA 58.994 33.333 0.00 0.00 0.00 1.40
226 227 8.809066 GTTACTCCACCCCAACTTAAAATTTAT 58.191 33.333 0.00 0.00 0.00 1.40
228 229 8.959676 ACTCCACCCCAACTTAAAATTTATAA 57.040 30.769 0.00 0.00 0.00 0.98
229 230 9.031537 ACTCCACCCCAACTTAAAATTTATAAG 57.968 33.333 13.80 13.80 36.62 1.73
230 231 8.959676 TCCACCCCAACTTAAAATTTATAAGT 57.040 30.769 14.66 14.66 43.57 2.24
231 232 9.027202 TCCACCCCAACTTAAAATTTATAAGTC 57.973 33.333 18.04 0.00 41.49 3.01
232 233 8.808092 CCACCCCAACTTAAAATTTATAAGTCA 58.192 33.333 18.04 0.00 41.49 3.41
233 234 9.634163 CACCCCAACTTAAAATTTATAAGTCAC 57.366 33.333 18.04 0.00 41.49 3.67
234 235 8.809066 ACCCCAACTTAAAATTTATAAGTCACC 58.191 33.333 18.04 0.00 41.49 4.02
235 236 8.255206 CCCCAACTTAAAATTTATAAGTCACCC 58.745 37.037 18.04 0.00 41.49 4.61
236 237 8.255206 CCCAACTTAAAATTTATAAGTCACCCC 58.745 37.037 18.04 0.00 41.49 4.95
237 238 8.255206 CCAACTTAAAATTTATAAGTCACCCCC 58.745 37.037 18.04 0.00 41.49 5.40
238 239 9.031537 CAACTTAAAATTTATAAGTCACCCCCT 57.968 33.333 18.04 6.19 41.49 4.79
239 240 9.610104 AACTTAAAATTTATAAGTCACCCCCTT 57.390 29.630 18.04 5.73 41.49 3.95
240 241 9.610104 ACTTAAAATTTATAAGTCACCCCCTTT 57.390 29.630 14.66 0.00 38.85 3.11
244 245 7.634671 AATTTATAAGTCACCCCCTTTTACG 57.365 36.000 0.00 0.00 0.00 3.18
245 246 5.760484 TTATAAGTCACCCCCTTTTACGT 57.240 39.130 0.00 0.00 0.00 3.57
246 247 2.265589 AAGTCACCCCCTTTTACGTG 57.734 50.000 0.00 0.00 0.00 4.49
247 248 0.399075 AGTCACCCCCTTTTACGTGG 59.601 55.000 0.00 0.00 0.00 4.94
248 249 0.607217 GTCACCCCCTTTTACGTGGG 60.607 60.000 0.00 0.55 44.03 4.61
249 250 4.006837 ACCCCCTTTTACGTGGGT 57.993 55.556 6.22 6.22 46.50 4.51
250 251 4.728409 CCCCCTTTTACGTGGGTC 57.272 61.111 7.83 0.00 41.82 4.46
251 252 1.001764 CCCCCTTTTACGTGGGTCC 60.002 63.158 7.83 0.00 41.82 4.46
252 253 1.001764 CCCCTTTTACGTGGGTCCC 60.002 63.158 0.00 0.00 41.82 4.46
253 254 1.762471 CCCTTTTACGTGGGTCCCA 59.238 57.895 6.47 6.47 38.65 4.37
262 263 2.621713 TGGGTCCCACCACCTGTA 59.378 61.111 6.47 0.00 41.02 2.74
263 264 1.162329 TGGGTCCCACCACCTGTAT 59.838 57.895 6.47 0.00 41.02 2.29
264 265 1.204786 TGGGTCCCACCACCTGTATG 61.205 60.000 6.47 0.00 41.02 2.39
265 266 0.912487 GGGTCCCACCACCTGTATGA 60.912 60.000 1.78 0.00 41.02 2.15
266 267 1.213296 GGTCCCACCACCTGTATGAT 58.787 55.000 0.00 0.00 38.42 2.45
267 268 1.134098 GGTCCCACCACCTGTATGATG 60.134 57.143 0.00 0.00 38.42 3.07
268 269 1.837439 GTCCCACCACCTGTATGATGA 59.163 52.381 0.00 0.00 0.00 2.92
269 270 2.439507 GTCCCACCACCTGTATGATGAT 59.560 50.000 0.00 0.00 0.00 2.45
270 271 2.439135 TCCCACCACCTGTATGATGATG 59.561 50.000 0.00 0.00 0.00 3.07
271 272 2.439135 CCCACCACCTGTATGATGATGA 59.561 50.000 0.00 0.00 0.00 2.92
272 273 3.073503 CCCACCACCTGTATGATGATGAT 59.926 47.826 0.00 0.00 0.00 2.45
273 274 4.446745 CCCACCACCTGTATGATGATGATT 60.447 45.833 0.00 0.00 0.00 2.57
274 275 4.517832 CCACCACCTGTATGATGATGATTG 59.482 45.833 0.00 0.00 0.00 2.67
275 276 5.370679 CACCACCTGTATGATGATGATTGA 58.629 41.667 0.00 0.00 0.00 2.57
276 277 6.002082 CACCACCTGTATGATGATGATTGAT 58.998 40.000 0.00 0.00 0.00 2.57
277 278 6.002082 ACCACCTGTATGATGATGATTGATG 58.998 40.000 0.00 0.00 0.00 3.07
278 279 6.002082 CCACCTGTATGATGATGATTGATGT 58.998 40.000 0.00 0.00 0.00 3.06
279 280 6.072673 CCACCTGTATGATGATGATTGATGTG 60.073 42.308 0.00 0.00 0.00 3.21
280 281 6.002082 ACCTGTATGATGATGATTGATGTGG 58.998 40.000 0.00 0.00 0.00 4.17
281 282 6.183361 ACCTGTATGATGATGATTGATGTGGA 60.183 38.462 0.00 0.00 0.00 4.02
282 283 6.713450 CCTGTATGATGATGATTGATGTGGAA 59.287 38.462 0.00 0.00 0.00 3.53
283 284 7.229907 CCTGTATGATGATGATTGATGTGGAAA 59.770 37.037 0.00 0.00 0.00 3.13
284 285 8.161699 TGTATGATGATGATTGATGTGGAAAG 57.838 34.615 0.00 0.00 0.00 2.62
285 286 6.650427 ATGATGATGATTGATGTGGAAAGG 57.350 37.500 0.00 0.00 0.00 3.11
286 287 5.512298 TGATGATGATTGATGTGGAAAGGT 58.488 37.500 0.00 0.00 0.00 3.50
287 288 5.358725 TGATGATGATTGATGTGGAAAGGTG 59.641 40.000 0.00 0.00 0.00 4.00
288 289 4.665451 TGATGATTGATGTGGAAAGGTGT 58.335 39.130 0.00 0.00 0.00 4.16
289 290 4.460034 TGATGATTGATGTGGAAAGGTGTG 59.540 41.667 0.00 0.00 0.00 3.82
290 291 3.831323 TGATTGATGTGGAAAGGTGTGT 58.169 40.909 0.00 0.00 0.00 3.72
291 292 3.820467 TGATTGATGTGGAAAGGTGTGTC 59.180 43.478 0.00 0.00 0.00 3.67
292 293 3.289407 TTGATGTGGAAAGGTGTGTCA 57.711 42.857 0.00 0.00 0.00 3.58
293 294 2.849942 TGATGTGGAAAGGTGTGTCAG 58.150 47.619 0.00 0.00 0.00 3.51
294 295 2.154462 GATGTGGAAAGGTGTGTCAGG 58.846 52.381 0.00 0.00 0.00 3.86
295 296 0.916086 TGTGGAAAGGTGTGTCAGGT 59.084 50.000 0.00 0.00 0.00 4.00
296 297 1.308998 GTGGAAAGGTGTGTCAGGTG 58.691 55.000 0.00 0.00 0.00 4.00
297 298 1.134220 GTGGAAAGGTGTGTCAGGTGA 60.134 52.381 0.00 0.00 0.00 4.02
298 299 1.134220 TGGAAAGGTGTGTCAGGTGAC 60.134 52.381 2.99 2.99 44.97 3.67
299 300 1.141053 GGAAAGGTGTGTCAGGTGACT 59.859 52.381 11.31 0.00 44.99 3.41
300 301 2.421529 GGAAAGGTGTGTCAGGTGACTT 60.422 50.000 11.31 0.00 44.99 3.01
301 302 3.181458 GGAAAGGTGTGTCAGGTGACTTA 60.181 47.826 11.31 0.00 44.99 2.24
302 303 4.505039 GGAAAGGTGTGTCAGGTGACTTAT 60.505 45.833 11.31 0.00 44.99 1.73
303 304 5.279809 GGAAAGGTGTGTCAGGTGACTTATA 60.280 44.000 11.31 0.00 44.99 0.98
304 305 5.818678 AAGGTGTGTCAGGTGACTTATAA 57.181 39.130 11.31 0.00 44.99 0.98
305 306 5.407407 AGGTGTGTCAGGTGACTTATAAG 57.593 43.478 11.05 11.05 44.99 1.73
306 307 4.838986 AGGTGTGTCAGGTGACTTATAAGT 59.161 41.667 18.05 18.05 44.99 2.24
329 330 3.354089 GGTGACAACCAAACAGACATG 57.646 47.619 0.00 0.00 46.75 3.21
330 331 2.948979 GGTGACAACCAAACAGACATGA 59.051 45.455 0.00 0.00 46.75 3.07
331 332 3.243068 GGTGACAACCAAACAGACATGAC 60.243 47.826 0.00 0.00 46.75 3.06
332 333 3.627577 GTGACAACCAAACAGACATGACT 59.372 43.478 0.00 0.00 0.00 3.41
333 334 4.096382 GTGACAACCAAACAGACATGACTT 59.904 41.667 0.00 0.00 0.00 3.01
334 335 5.295787 GTGACAACCAAACAGACATGACTTA 59.704 40.000 0.00 0.00 0.00 2.24
335 336 6.017109 GTGACAACCAAACAGACATGACTTAT 60.017 38.462 0.00 0.00 0.00 1.73
336 337 7.172532 GTGACAACCAAACAGACATGACTTATA 59.827 37.037 0.00 0.00 0.00 0.98
337 338 7.717436 TGACAACCAAACAGACATGACTTATAA 59.283 33.333 0.00 0.00 0.00 0.98
338 339 8.099364 ACAACCAAACAGACATGACTTATAAG 57.901 34.615 11.05 11.05 0.00 1.73
339 340 7.719633 ACAACCAAACAGACATGACTTATAAGT 59.280 33.333 18.05 18.05 43.16 2.24
360 361 9.802039 ATAAGTCATTGGTTTTAAGTTACCTGA 57.198 29.630 0.00 0.00 35.41 3.86
361 362 8.706322 AAGTCATTGGTTTTAAGTTACCTGAT 57.294 30.769 0.00 0.00 35.41 2.90
362 363 8.706322 AGTCATTGGTTTTAAGTTACCTGATT 57.294 30.769 0.00 0.00 35.41 2.57
363 364 9.143155 AGTCATTGGTTTTAAGTTACCTGATTT 57.857 29.630 0.00 0.00 35.41 2.17
388 389 7.881775 ATAAGTCAGGTGATTTATTGGAACC 57.118 36.000 2.72 0.00 34.59 3.62
389 390 5.255397 AGTCAGGTGATTTATTGGAACCA 57.745 39.130 0.00 0.00 33.13 3.67
390 391 5.640147 AGTCAGGTGATTTATTGGAACCAA 58.360 37.500 8.75 8.75 40.47 3.67
391 392 6.074648 AGTCAGGTGATTTATTGGAACCAAA 58.925 36.000 10.36 0.00 39.55 3.28
392 393 6.015434 AGTCAGGTGATTTATTGGAACCAAAC 60.015 38.462 10.36 3.26 39.55 2.93
393 394 5.245075 TCAGGTGATTTATTGGAACCAAACC 59.755 40.000 10.36 11.52 39.55 3.27
394 395 5.245977 CAGGTGATTTATTGGAACCAAACCT 59.754 40.000 15.45 15.45 39.09 3.50
395 396 5.245977 AGGTGATTTATTGGAACCAAACCTG 59.754 40.000 18.63 0.00 37.90 4.00
396 397 4.929211 GTGATTTATTGGAACCAAACCTGC 59.071 41.667 10.36 2.16 39.55 4.85
397 398 4.020662 TGATTTATTGGAACCAAACCTGCC 60.021 41.667 10.36 0.64 39.55 4.85
398 399 1.931635 TATTGGAACCAAACCTGCCC 58.068 50.000 10.36 0.00 39.55 5.36
419 420 4.272504 CCCTAATAACATTAGCACCACACG 59.727 45.833 1.17 0.00 0.00 4.49
746 748 1.469308 GTCAGAACCACTCGATCTCGT 59.531 52.381 0.00 0.00 40.80 4.18
816 818 2.119029 GGGGGCGAATTTTCCTCCG 61.119 63.158 0.65 0.00 32.44 4.63
964 971 1.236616 TGCGGTCGACTCGGTTCTTA 61.237 55.000 22.10 0.00 0.00 2.10
974 981 5.357878 TCGACTCGGTTCTTAATAGGCTTAA 59.642 40.000 0.00 0.00 0.00 1.85
976 983 6.700520 CGACTCGGTTCTTAATAGGCTTAATT 59.299 38.462 0.00 0.00 0.00 1.40
1303 1323 1.743996 GGTGAGGACCATGCTTTCTC 58.256 55.000 0.00 0.00 42.59 2.87
1423 1444 8.356657 TGTTAGTTTGTTCATGGTAAGATTTGG 58.643 33.333 0.00 0.00 0.00 3.28
1522 1545 1.098869 TCCTGCGTTGCACTTTTTGA 58.901 45.000 0.00 0.00 33.79 2.69
1888 1930 7.414873 CCAGGAGTGAGATCAATTGTACATTTG 60.415 40.741 19.73 19.73 0.00 2.32
2031 2073 4.582656 TCGGACATTTTGAGGTGTCATTTT 59.417 37.500 7.67 0.00 44.99 1.82
2257 2299 0.741221 GAAGATCAGGACCACACGGC 60.741 60.000 0.00 0.00 34.57 5.68
2848 2890 3.542648 TCTCTCGGAGTGACACGATATT 58.457 45.455 4.69 0.00 38.56 1.28
3464 3507 1.372582 TGCATCGATTTGGCAGTCTC 58.627 50.000 4.89 0.00 32.95 3.36
3607 3697 1.003839 CTGTACTTGAAGGGGCGCA 60.004 57.895 10.83 0.00 0.00 6.09
3638 3728 5.704515 TGTGCCATTGATATTTTGGGTTTTG 59.295 36.000 0.00 0.00 0.00 2.44
3676 3766 7.875327 TCCTCTGGTTTAAAATATAAGGTGC 57.125 36.000 0.00 0.00 0.00 5.01
3742 3832 7.623999 TCTTCTTAGGCTCAATAATCTGGAT 57.376 36.000 0.00 0.00 0.00 3.41
3749 3839 6.706295 AGGCTCAATAATCTGGATACTAAGC 58.294 40.000 0.00 0.00 37.61 3.09
3827 3917 7.538575 GCTTTCTTAGCCATGAATTTAGAACA 58.461 34.615 0.00 0.00 44.48 3.18
3900 3990 1.695242 ACGGCCATATTATCAACCCGA 59.305 47.619 2.24 0.00 37.76 5.14
3995 4085 7.451566 ACAACATTCTTTTAGGTTAGGAGCAAT 59.548 33.333 0.00 0.00 0.00 3.56
4047 4137 5.700722 AAAACAAGTATTTCTCCCGTTCC 57.299 39.130 0.00 0.00 0.00 3.62
4048 4138 4.635699 AACAAGTATTTCTCCCGTTCCT 57.364 40.909 0.00 0.00 0.00 3.36
4050 4140 5.082251 ACAAGTATTTCTCCCGTTCCTAC 57.918 43.478 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 6.621596 GCTTATGTGGCAGACAACTAAAGAAG 60.622 42.308 0.00 0.00 38.36 2.85
3 4 5.181245 GCTTATGTGGCAGACAACTAAAGAA 59.819 40.000 0.00 0.00 38.36 2.52
5 6 4.455533 TGCTTATGTGGCAGACAACTAAAG 59.544 41.667 0.00 0.00 38.36 1.85
7 8 4.014569 TGCTTATGTGGCAGACAACTAA 57.985 40.909 0.00 0.00 38.36 2.24
8 9 3.694043 TGCTTATGTGGCAGACAACTA 57.306 42.857 0.00 0.00 38.36 2.24
9 10 2.566833 TGCTTATGTGGCAGACAACT 57.433 45.000 0.00 0.00 38.36 3.16
10 11 2.489329 ACATGCTTATGTGGCAGACAAC 59.511 45.455 0.00 0.00 43.15 3.32
11 12 2.794103 ACATGCTTATGTGGCAGACAA 58.206 42.857 0.00 0.00 43.15 3.18
12 13 2.495155 ACATGCTTATGTGGCAGACA 57.505 45.000 0.00 0.00 43.15 3.41
13 14 3.504863 CAAACATGCTTATGTGGCAGAC 58.495 45.455 0.00 0.00 43.15 3.51
14 15 2.094597 GCAAACATGCTTATGTGGCAGA 60.095 45.455 10.53 0.00 43.15 4.26
15 16 2.264813 GCAAACATGCTTATGTGGCAG 58.735 47.619 10.53 0.00 43.15 4.85
16 17 1.402588 CGCAAACATGCTTATGTGGCA 60.403 47.619 13.85 0.00 44.05 4.92
17 18 1.135431 TCGCAAACATGCTTATGTGGC 60.135 47.619 0.00 0.00 34.56 5.01
18 19 2.162208 ACTCGCAAACATGCTTATGTGG 59.838 45.455 0.00 0.00 34.56 4.17
19 20 3.476295 ACTCGCAAACATGCTTATGTG 57.524 42.857 0.00 0.00 34.56 3.21
20 21 4.023279 TGAAACTCGCAAACATGCTTATGT 60.023 37.500 0.00 0.00 36.10 2.29
21 22 4.475028 TGAAACTCGCAAACATGCTTATG 58.525 39.130 0.00 0.00 0.00 1.90
22 23 4.764679 TGAAACTCGCAAACATGCTTAT 57.235 36.364 0.00 0.00 0.00 1.73
23 24 4.036262 ACTTGAAACTCGCAAACATGCTTA 59.964 37.500 0.00 0.00 0.00 3.09
24 25 3.181487 ACTTGAAACTCGCAAACATGCTT 60.181 39.130 0.00 0.00 0.00 3.91
25 26 2.358898 ACTTGAAACTCGCAAACATGCT 59.641 40.909 0.00 0.00 0.00 3.79
26 27 2.468777 CACTTGAAACTCGCAAACATGC 59.531 45.455 0.00 0.00 0.00 4.06
27 28 2.468777 GCACTTGAAACTCGCAAACATG 59.531 45.455 0.00 0.00 0.00 3.21
28 29 2.098934 TGCACTTGAAACTCGCAAACAT 59.901 40.909 0.00 0.00 0.00 2.71
29 30 1.470494 TGCACTTGAAACTCGCAAACA 59.530 42.857 0.00 0.00 0.00 2.83
30 31 2.187351 TGCACTTGAAACTCGCAAAC 57.813 45.000 0.00 0.00 0.00 2.93
31 32 2.357323 TCATGCACTTGAAACTCGCAAA 59.643 40.909 0.00 0.00 35.98 3.68
32 33 1.946081 TCATGCACTTGAAACTCGCAA 59.054 42.857 0.00 0.00 35.98 4.85
33 34 1.592064 TCATGCACTTGAAACTCGCA 58.408 45.000 0.00 0.00 36.95 5.10
34 35 2.907910 ATCATGCACTTGAAACTCGC 57.092 45.000 0.00 0.00 0.00 5.03
35 36 6.834959 ATAGTATCATGCACTTGAAACTCG 57.165 37.500 5.29 0.00 0.00 4.18
44 45 9.712305 GGAGTAACATAAATAGTATCATGCACT 57.288 33.333 0.00 5.31 0.00 4.40
45 46 8.936864 GGGAGTAACATAAATAGTATCATGCAC 58.063 37.037 0.00 0.00 0.00 4.57
46 47 8.655901 TGGGAGTAACATAAATAGTATCATGCA 58.344 33.333 0.00 0.00 0.00 3.96
47 48 8.936864 GTGGGAGTAACATAAATAGTATCATGC 58.063 37.037 5.13 0.00 0.00 4.06
53 54 8.591072 GCCATAGTGGGAGTAACATAAATAGTA 58.409 37.037 0.00 0.00 38.19 1.82
54 55 7.450903 GCCATAGTGGGAGTAACATAAATAGT 58.549 38.462 0.00 0.00 38.19 2.12
55 56 6.879458 GGCCATAGTGGGAGTAACATAAATAG 59.121 42.308 0.00 0.00 38.19 1.73
56 57 6.330514 TGGCCATAGTGGGAGTAACATAAATA 59.669 38.462 0.00 0.00 38.19 1.40
57 58 5.133660 TGGCCATAGTGGGAGTAACATAAAT 59.866 40.000 0.00 0.00 38.19 1.40
58 59 4.475381 TGGCCATAGTGGGAGTAACATAAA 59.525 41.667 0.00 0.00 38.19 1.40
59 60 4.041464 TGGCCATAGTGGGAGTAACATAA 58.959 43.478 0.00 0.00 38.19 1.90
60 61 3.646162 CTGGCCATAGTGGGAGTAACATA 59.354 47.826 5.51 0.00 38.19 2.29
61 62 2.439507 CTGGCCATAGTGGGAGTAACAT 59.560 50.000 5.51 0.00 38.19 2.71
62 63 1.837439 CTGGCCATAGTGGGAGTAACA 59.163 52.381 5.51 0.00 38.19 2.41
63 64 1.475213 GCTGGCCATAGTGGGAGTAAC 60.475 57.143 5.51 0.00 38.19 2.50
64 65 0.837272 GCTGGCCATAGTGGGAGTAA 59.163 55.000 5.51 0.00 38.19 2.24
65 66 1.054406 GGCTGGCCATAGTGGGAGTA 61.054 60.000 5.51 0.00 38.19 2.59
66 67 2.378634 GGCTGGCCATAGTGGGAGT 61.379 63.158 5.51 0.00 38.19 3.85
67 68 0.764369 TAGGCTGGCCATAGTGGGAG 60.764 60.000 5.51 0.00 38.19 4.30
68 69 0.327095 TTAGGCTGGCCATAGTGGGA 60.327 55.000 5.51 0.00 38.19 4.37
69 70 0.109342 CTTAGGCTGGCCATAGTGGG 59.891 60.000 5.51 0.00 38.19 4.61
70 71 0.109342 CCTTAGGCTGGCCATAGTGG 59.891 60.000 5.51 0.02 41.55 4.00
71 72 0.109342 CCCTTAGGCTGGCCATAGTG 59.891 60.000 5.51 0.00 38.92 2.74
72 73 2.544768 CCCTTAGGCTGGCCATAGT 58.455 57.895 5.51 0.00 38.92 2.12
83 84 1.824852 GGAACCAAACATGCCCTTAGG 59.175 52.381 0.00 0.00 0.00 2.69
84 85 2.524306 TGGAACCAAACATGCCCTTAG 58.476 47.619 0.00 0.00 0.00 2.18
85 86 2.685106 TGGAACCAAACATGCCCTTA 57.315 45.000 0.00 0.00 0.00 2.69
86 87 1.799933 TTGGAACCAAACATGCCCTT 58.200 45.000 3.62 0.00 32.44 3.95
87 88 1.799933 TTTGGAACCAAACATGCCCT 58.200 45.000 14.02 0.00 40.51 5.19
88 89 2.857186 ATTTGGAACCAAACATGCCC 57.143 45.000 19.23 0.00 46.80 5.36
89 90 4.893608 ACTTATTTGGAACCAAACATGCC 58.106 39.130 19.23 0.00 46.80 4.40
90 91 5.405269 GTGACTTATTTGGAACCAAACATGC 59.595 40.000 19.23 9.92 46.80 4.06
91 92 5.925969 GGTGACTTATTTGGAACCAAACATG 59.074 40.000 19.23 13.30 46.80 3.21
92 93 5.600484 TGGTGACTTATTTGGAACCAAACAT 59.400 36.000 19.23 8.93 46.80 2.71
93 94 4.956700 TGGTGACTTATTTGGAACCAAACA 59.043 37.500 19.23 7.15 46.80 2.83
94 95 5.523438 TGGTGACTTATTTGGAACCAAAC 57.477 39.130 19.23 8.57 46.80 2.93
95 96 5.659079 AGTTGGTGACTTATTTGGAACCAAA 59.341 36.000 19.15 19.15 46.21 3.28
96 97 5.205056 AGTTGGTGACTTATTTGGAACCAA 58.795 37.500 1.83 1.83 43.50 3.67
97 98 4.798882 AGTTGGTGACTTATTTGGAACCA 58.201 39.130 0.00 0.00 33.92 3.67
98 99 5.784578 AAGTTGGTGACTTATTTGGAACC 57.215 39.130 0.00 0.00 46.61 3.62
109 110 7.170998 CACTTTTCGACTTATAAGTTGGTGACT 59.829 37.037 25.99 9.24 39.88 3.41
110 111 7.170320 TCACTTTTCGACTTATAAGTTGGTGAC 59.830 37.037 25.99 10.35 39.88 3.67
111 112 7.211573 TCACTTTTCGACTTATAAGTTGGTGA 58.788 34.615 25.99 25.09 39.88 4.02
112 113 7.416154 TCACTTTTCGACTTATAAGTTGGTG 57.584 36.000 25.99 23.76 39.88 4.17
113 114 8.441312 TTTCACTTTTCGACTTATAAGTTGGT 57.559 30.769 25.99 16.17 39.88 3.67
114 115 9.724839 TTTTTCACTTTTCGACTTATAAGTTGG 57.275 29.630 25.99 17.93 39.88 3.77
137 138 7.821846 TCTGTTTGGCAAAATAAGTCACTTTTT 59.178 29.630 15.29 0.00 0.00 1.94
138 139 7.277760 GTCTGTTTGGCAAAATAAGTCACTTTT 59.722 33.333 15.29 0.00 0.00 2.27
139 140 6.756542 GTCTGTTTGGCAAAATAAGTCACTTT 59.243 34.615 15.29 0.00 0.00 2.66
140 141 6.273071 GTCTGTTTGGCAAAATAAGTCACTT 58.727 36.000 15.29 0.00 0.00 3.16
141 142 5.221244 GGTCTGTTTGGCAAAATAAGTCACT 60.221 40.000 15.29 0.00 0.00 3.41
142 143 4.982295 GGTCTGTTTGGCAAAATAAGTCAC 59.018 41.667 15.29 7.77 0.00 3.67
143 144 4.038642 GGGTCTGTTTGGCAAAATAAGTCA 59.961 41.667 15.29 6.39 0.00 3.41
144 145 4.556233 GGGTCTGTTTGGCAAAATAAGTC 58.444 43.478 15.29 10.05 0.00 3.01
145 146 3.005367 CGGGTCTGTTTGGCAAAATAAGT 59.995 43.478 15.29 0.00 0.00 2.24
146 147 3.254657 TCGGGTCTGTTTGGCAAAATAAG 59.745 43.478 15.29 12.47 0.00 1.73
147 148 3.004944 GTCGGGTCTGTTTGGCAAAATAA 59.995 43.478 15.29 2.73 0.00 1.40
148 149 2.554893 GTCGGGTCTGTTTGGCAAAATA 59.445 45.455 15.29 6.13 0.00 1.40
149 150 1.339929 GTCGGGTCTGTTTGGCAAAAT 59.660 47.619 15.29 0.00 0.00 1.82
150 151 0.741915 GTCGGGTCTGTTTGGCAAAA 59.258 50.000 15.29 4.59 0.00 2.44
151 152 0.106918 AGTCGGGTCTGTTTGGCAAA 60.107 50.000 8.93 8.93 0.00 3.68
152 153 0.106918 AAGTCGGGTCTGTTTGGCAA 60.107 50.000 0.00 0.00 0.00 4.52
153 154 0.759959 TAAGTCGGGTCTGTTTGGCA 59.240 50.000 0.00 0.00 0.00 4.92
154 155 2.109425 ATAAGTCGGGTCTGTTTGGC 57.891 50.000 0.00 0.00 0.00 4.52
155 156 4.828829 ACTTATAAGTCGGGTCTGTTTGG 58.171 43.478 12.50 0.00 32.86 3.28
171 172 8.612486 TGACTTATAAGTTGGGGTGACTTATA 57.388 34.615 18.96 10.90 44.36 0.98
172 173 7.504926 TGACTTATAAGTTGGGGTGACTTAT 57.495 36.000 18.96 12.48 46.52 1.73
173 174 6.938698 TGACTTATAAGTTGGGGTGACTTA 57.061 37.500 18.96 0.00 42.07 2.24
174 175 5.836024 TGACTTATAAGTTGGGGTGACTT 57.164 39.130 18.96 0.00 39.88 3.01
175 176 7.504926 TTATGACTTATAAGTTGGGGTGACT 57.495 36.000 18.96 0.00 39.88 3.41
176 177 7.787725 CTTATGACTTATAAGTTGGGGTGAC 57.212 40.000 18.96 4.87 42.11 3.67
187 188 7.624478 TGGGGTGGAGTAACTTATGACTTATAA 59.376 37.037 0.00 0.00 0.00 0.98
188 189 7.134162 TGGGGTGGAGTAACTTATGACTTATA 58.866 38.462 0.00 0.00 0.00 0.98
189 190 5.968167 TGGGGTGGAGTAACTTATGACTTAT 59.032 40.000 0.00 0.00 0.00 1.73
190 191 5.343715 TGGGGTGGAGTAACTTATGACTTA 58.656 41.667 0.00 0.00 0.00 2.24
191 192 4.172807 TGGGGTGGAGTAACTTATGACTT 58.827 43.478 0.00 0.00 0.00 3.01
192 193 3.798515 TGGGGTGGAGTAACTTATGACT 58.201 45.455 0.00 0.00 0.00 3.41
193 194 4.019591 AGTTGGGGTGGAGTAACTTATGAC 60.020 45.833 0.00 0.00 29.65 3.06
194 195 4.172807 AGTTGGGGTGGAGTAACTTATGA 58.827 43.478 0.00 0.00 29.65 2.15
195 196 4.569719 AGTTGGGGTGGAGTAACTTATG 57.430 45.455 0.00 0.00 29.65 1.90
196 197 6.707273 TTAAGTTGGGGTGGAGTAACTTAT 57.293 37.500 0.00 0.00 42.08 1.73
197 198 6.512514 TTTAAGTTGGGGTGGAGTAACTTA 57.487 37.500 0.00 0.00 41.84 2.24
198 199 5.391577 TTTAAGTTGGGGTGGAGTAACTT 57.608 39.130 0.00 0.00 43.48 2.66
199 200 5.391577 TTTTAAGTTGGGGTGGAGTAACT 57.608 39.130 0.00 0.00 35.06 2.24
200 201 6.659745 AATTTTAAGTTGGGGTGGAGTAAC 57.340 37.500 0.00 0.00 0.00 2.50
201 202 8.959676 ATAAATTTTAAGTTGGGGTGGAGTAA 57.040 30.769 0.00 0.00 0.00 2.24
203 204 8.959676 TTATAAATTTTAAGTTGGGGTGGAGT 57.040 30.769 0.00 0.00 0.00 3.85
204 205 9.031537 ACTTATAAATTTTAAGTTGGGGTGGAG 57.968 33.333 14.66 0.00 36.70 3.86
205 206 8.959676 ACTTATAAATTTTAAGTTGGGGTGGA 57.040 30.769 14.66 0.00 36.70 4.02
206 207 8.808092 TGACTTATAAATTTTAAGTTGGGGTGG 58.192 33.333 18.46 1.33 39.40 4.61
207 208 9.634163 GTGACTTATAAATTTTAAGTTGGGGTG 57.366 33.333 18.46 1.79 39.40 4.61
208 209 8.809066 GGTGACTTATAAATTTTAAGTTGGGGT 58.191 33.333 18.46 4.82 39.40 4.95
209 210 8.255206 GGGTGACTTATAAATTTTAAGTTGGGG 58.745 37.037 18.46 2.71 39.40 4.96
210 211 8.255206 GGGGTGACTTATAAATTTTAAGTTGGG 58.745 37.037 18.46 3.17 39.40 4.12
211 212 8.255206 GGGGGTGACTTATAAATTTTAAGTTGG 58.745 37.037 18.46 3.41 39.40 3.77
212 213 9.031537 AGGGGGTGACTTATAAATTTTAAGTTG 57.968 33.333 18.46 2.51 39.40 3.16
213 214 9.610104 AAGGGGGTGACTTATAAATTTTAAGTT 57.390 29.630 18.46 9.15 39.40 2.66
214 215 9.610104 AAAGGGGGTGACTTATAAATTTTAAGT 57.390 29.630 17.91 17.91 41.41 2.24
218 219 8.525316 CGTAAAAGGGGGTGACTTATAAATTTT 58.475 33.333 0.00 0.00 0.00 1.82
219 220 7.670979 ACGTAAAAGGGGGTGACTTATAAATTT 59.329 33.333 0.00 0.00 0.00 1.82
220 221 7.121611 CACGTAAAAGGGGGTGACTTATAAATT 59.878 37.037 0.00 0.00 32.23 1.82
221 222 6.600427 CACGTAAAAGGGGGTGACTTATAAAT 59.400 38.462 0.00 0.00 32.23 1.40
222 223 5.939296 CACGTAAAAGGGGGTGACTTATAAA 59.061 40.000 0.00 0.00 32.23 1.40
223 224 5.490159 CACGTAAAAGGGGGTGACTTATAA 58.510 41.667 0.00 0.00 32.23 0.98
224 225 4.080975 CCACGTAAAAGGGGGTGACTTATA 60.081 45.833 0.00 0.00 32.23 0.98
225 226 3.307904 CCACGTAAAAGGGGGTGACTTAT 60.308 47.826 0.00 0.00 32.23 1.73
226 227 2.038820 CCACGTAAAAGGGGGTGACTTA 59.961 50.000 0.00 0.00 32.23 2.24
227 228 1.202842 CCACGTAAAAGGGGGTGACTT 60.203 52.381 0.00 0.00 32.23 3.01
228 229 0.399075 CCACGTAAAAGGGGGTGACT 59.601 55.000 0.00 0.00 32.23 3.41
229 230 2.936928 CCACGTAAAAGGGGGTGAC 58.063 57.895 0.00 0.00 32.23 3.67
236 237 2.936928 GTGGGACCCACGTAAAAGG 58.063 57.895 27.79 0.00 44.95 3.11
245 246 1.162329 ATACAGGTGGTGGGACCCA 59.838 57.895 9.95 9.95 37.50 4.51
246 247 0.912487 TCATACAGGTGGTGGGACCC 60.912 60.000 2.45 2.45 37.50 4.46
247 248 1.134098 CATCATACAGGTGGTGGGACC 60.134 57.143 0.00 0.00 39.22 4.46
248 249 1.837439 TCATCATACAGGTGGTGGGAC 59.163 52.381 0.00 0.00 31.09 4.46
249 250 2.262266 TCATCATACAGGTGGTGGGA 57.738 50.000 0.00 0.00 31.09 4.37
250 251 2.439135 TCATCATCATACAGGTGGTGGG 59.561 50.000 0.00 0.00 31.09 4.61
251 252 3.843893 TCATCATCATACAGGTGGTGG 57.156 47.619 0.00 0.00 31.09 4.61
252 253 5.370679 TCAATCATCATCATACAGGTGGTG 58.629 41.667 0.00 0.00 0.00 4.17
253 254 5.635278 TCAATCATCATCATACAGGTGGT 57.365 39.130 0.00 0.00 0.00 4.16
254 255 6.002082 ACATCAATCATCATCATACAGGTGG 58.998 40.000 0.00 0.00 0.00 4.61
255 256 6.072673 CCACATCAATCATCATCATACAGGTG 60.073 42.308 0.00 0.00 0.00 4.00
256 257 6.002082 CCACATCAATCATCATCATACAGGT 58.998 40.000 0.00 0.00 0.00 4.00
257 258 6.235664 TCCACATCAATCATCATCATACAGG 58.764 40.000 0.00 0.00 0.00 4.00
258 259 7.739498 TTCCACATCAATCATCATCATACAG 57.261 36.000 0.00 0.00 0.00 2.74
259 260 7.229907 CCTTTCCACATCAATCATCATCATACA 59.770 37.037 0.00 0.00 0.00 2.29
260 261 7.230108 ACCTTTCCACATCAATCATCATCATAC 59.770 37.037 0.00 0.00 0.00 2.39
261 262 7.229907 CACCTTTCCACATCAATCATCATCATA 59.770 37.037 0.00 0.00 0.00 2.15
262 263 6.040504 CACCTTTCCACATCAATCATCATCAT 59.959 38.462 0.00 0.00 0.00 2.45
263 264 5.358725 CACCTTTCCACATCAATCATCATCA 59.641 40.000 0.00 0.00 0.00 3.07
264 265 5.359009 ACACCTTTCCACATCAATCATCATC 59.641 40.000 0.00 0.00 0.00 2.92
265 266 5.126545 CACACCTTTCCACATCAATCATCAT 59.873 40.000 0.00 0.00 0.00 2.45
266 267 4.460034 CACACCTTTCCACATCAATCATCA 59.540 41.667 0.00 0.00 0.00 3.07
267 268 4.460382 ACACACCTTTCCACATCAATCATC 59.540 41.667 0.00 0.00 0.00 2.92
268 269 4.410099 ACACACCTTTCCACATCAATCAT 58.590 39.130 0.00 0.00 0.00 2.45
269 270 3.820467 GACACACCTTTCCACATCAATCA 59.180 43.478 0.00 0.00 0.00 2.57
270 271 3.820467 TGACACACCTTTCCACATCAATC 59.180 43.478 0.00 0.00 0.00 2.67
271 272 3.822735 CTGACACACCTTTCCACATCAAT 59.177 43.478 0.00 0.00 0.00 2.57
272 273 3.213506 CTGACACACCTTTCCACATCAA 58.786 45.455 0.00 0.00 0.00 2.57
273 274 2.487086 CCTGACACACCTTTCCACATCA 60.487 50.000 0.00 0.00 0.00 3.07
274 275 2.154462 CCTGACACACCTTTCCACATC 58.846 52.381 0.00 0.00 0.00 3.06
275 276 1.494721 ACCTGACACACCTTTCCACAT 59.505 47.619 0.00 0.00 0.00 3.21
276 277 0.916086 ACCTGACACACCTTTCCACA 59.084 50.000 0.00 0.00 0.00 4.17
277 278 1.134220 TCACCTGACACACCTTTCCAC 60.134 52.381 0.00 0.00 0.00 4.02
278 279 1.134220 GTCACCTGACACACCTTTCCA 60.134 52.381 0.31 0.00 44.18 3.53
279 280 1.594331 GTCACCTGACACACCTTTCC 58.406 55.000 0.31 0.00 44.18 3.13
296 297 5.790593 TGGTTGTCACCTGACTTATAAGTC 58.209 41.667 30.61 30.61 46.58 3.01
297 298 5.818678 TGGTTGTCACCTGACTTATAAGT 57.181 39.130 18.05 18.05 44.61 2.24
298 299 6.485313 TGTTTGGTTGTCACCTGACTTATAAG 59.515 38.462 11.05 11.05 44.61 1.73
299 300 6.358178 TGTTTGGTTGTCACCTGACTTATAA 58.642 36.000 6.97 0.00 44.61 0.98
300 301 5.931294 TGTTTGGTTGTCACCTGACTTATA 58.069 37.500 6.97 0.00 44.61 0.98
301 302 4.787551 TGTTTGGTTGTCACCTGACTTAT 58.212 39.130 6.97 0.00 44.61 1.73
302 303 4.080807 TCTGTTTGGTTGTCACCTGACTTA 60.081 41.667 6.97 0.00 44.61 2.24
303 304 3.016736 CTGTTTGGTTGTCACCTGACTT 58.983 45.455 6.97 0.00 44.61 3.01
304 305 2.238646 TCTGTTTGGTTGTCACCTGACT 59.761 45.455 6.97 0.00 44.61 3.41
305 306 2.354821 GTCTGTTTGGTTGTCACCTGAC 59.645 50.000 0.00 0.00 44.61 3.51
306 307 2.026729 TGTCTGTTTGGTTGTCACCTGA 60.027 45.455 0.00 0.00 44.61 3.86
307 308 2.364632 TGTCTGTTTGGTTGTCACCTG 58.635 47.619 0.00 0.00 44.61 4.00
308 309 2.799126 TGTCTGTTTGGTTGTCACCT 57.201 45.000 0.00 0.00 44.61 4.00
309 310 2.948979 TCATGTCTGTTTGGTTGTCACC 59.051 45.455 0.00 0.00 44.56 4.02
310 311 3.627577 AGTCATGTCTGTTTGGTTGTCAC 59.372 43.478 0.00 0.00 0.00 3.67
311 312 3.884895 AGTCATGTCTGTTTGGTTGTCA 58.115 40.909 0.00 0.00 0.00 3.58
312 313 4.900635 AAGTCATGTCTGTTTGGTTGTC 57.099 40.909 0.00 0.00 0.00 3.18
313 314 7.719633 ACTTATAAGTCATGTCTGTTTGGTTGT 59.280 33.333 12.50 0.00 32.86 3.32
314 315 8.099364 ACTTATAAGTCATGTCTGTTTGGTTG 57.901 34.615 12.50 0.00 32.86 3.77
362 363 9.403583 GGTTCCAATAAATCACCTGACTTATAA 57.596 33.333 0.00 0.00 27.86 0.98
363 364 8.553153 TGGTTCCAATAAATCACCTGACTTATA 58.447 33.333 0.00 0.00 27.86 0.98
364 365 7.410174 TGGTTCCAATAAATCACCTGACTTAT 58.590 34.615 0.00 0.00 28.87 1.73
365 366 6.785076 TGGTTCCAATAAATCACCTGACTTA 58.215 36.000 0.00 0.00 0.00 2.24
366 367 5.640147 TGGTTCCAATAAATCACCTGACTT 58.360 37.500 0.00 0.00 0.00 3.01
367 368 5.255397 TGGTTCCAATAAATCACCTGACT 57.745 39.130 0.00 0.00 0.00 3.41
368 369 5.975693 TTGGTTCCAATAAATCACCTGAC 57.024 39.130 0.00 0.00 0.00 3.51
369 370 5.245075 GGTTTGGTTCCAATAAATCACCTGA 59.755 40.000 5.06 0.00 0.00 3.86
370 371 5.245977 AGGTTTGGTTCCAATAAATCACCTG 59.754 40.000 17.37 0.00 32.06 4.00
371 372 5.245977 CAGGTTTGGTTCCAATAAATCACCT 59.754 40.000 14.14 14.14 32.91 4.00
372 373 5.478407 CAGGTTTGGTTCCAATAAATCACC 58.522 41.667 5.06 8.56 0.00 4.02
373 374 4.929211 GCAGGTTTGGTTCCAATAAATCAC 59.071 41.667 5.06 0.00 0.00 3.06
374 375 4.020662 GGCAGGTTTGGTTCCAATAAATCA 60.021 41.667 5.06 0.00 0.00 2.57
375 376 4.503910 GGCAGGTTTGGTTCCAATAAATC 58.496 43.478 5.06 0.00 0.00 2.17
376 377 3.263170 GGGCAGGTTTGGTTCCAATAAAT 59.737 43.478 5.06 0.00 0.00 1.40
377 378 2.635427 GGGCAGGTTTGGTTCCAATAAA 59.365 45.455 5.06 0.00 0.00 1.40
378 379 2.158234 AGGGCAGGTTTGGTTCCAATAA 60.158 45.455 5.06 0.00 0.00 1.40
379 380 1.431243 AGGGCAGGTTTGGTTCCAATA 59.569 47.619 5.06 0.00 0.00 1.90
380 381 0.190815 AGGGCAGGTTTGGTTCCAAT 59.809 50.000 5.06 0.00 0.00 3.16
381 382 0.854218 TAGGGCAGGTTTGGTTCCAA 59.146 50.000 0.00 0.00 0.00 3.53
382 383 0.854218 TTAGGGCAGGTTTGGTTCCA 59.146 50.000 0.00 0.00 0.00 3.53
383 384 2.231716 ATTAGGGCAGGTTTGGTTCC 57.768 50.000 0.00 0.00 0.00 3.62
384 385 4.083565 TGTTATTAGGGCAGGTTTGGTTC 58.916 43.478 0.00 0.00 0.00 3.62
385 386 4.120946 TGTTATTAGGGCAGGTTTGGTT 57.879 40.909 0.00 0.00 0.00 3.67
386 387 3.818295 TGTTATTAGGGCAGGTTTGGT 57.182 42.857 0.00 0.00 0.00 3.67
387 388 5.221244 GCTAATGTTATTAGGGCAGGTTTGG 60.221 44.000 9.80 0.00 0.00 3.28
388 389 5.359576 TGCTAATGTTATTAGGGCAGGTTTG 59.640 40.000 9.80 0.00 0.00 2.93
389 390 5.359860 GTGCTAATGTTATTAGGGCAGGTTT 59.640 40.000 9.80 0.00 0.00 3.27
390 391 4.887655 GTGCTAATGTTATTAGGGCAGGTT 59.112 41.667 9.80 0.00 0.00 3.50
391 392 4.461198 GTGCTAATGTTATTAGGGCAGGT 58.539 43.478 9.80 0.00 0.00 4.00
392 393 3.821033 GGTGCTAATGTTATTAGGGCAGG 59.179 47.826 9.80 0.00 0.00 4.85
393 394 4.275936 GTGGTGCTAATGTTATTAGGGCAG 59.724 45.833 9.80 0.00 0.00 4.85
394 395 4.204012 GTGGTGCTAATGTTATTAGGGCA 58.796 43.478 9.80 2.25 0.00 5.36
395 396 4.036380 GTGTGGTGCTAATGTTATTAGGGC 59.964 45.833 9.80 0.02 0.00 5.19
396 397 4.272504 CGTGTGGTGCTAATGTTATTAGGG 59.727 45.833 9.80 0.00 0.00 3.53
397 398 4.272504 CCGTGTGGTGCTAATGTTATTAGG 59.727 45.833 9.80 0.00 0.00 2.69
398 399 5.403897 CCGTGTGGTGCTAATGTTATTAG 57.596 43.478 4.60 4.60 0.00 1.73
431 433 4.609018 CGCCATACGGAGCAGGGG 62.609 72.222 0.00 0.00 38.44 4.79
746 748 4.695455 CCCAAGATTAACAAAGCGAGAGAA 59.305 41.667 0.00 0.00 0.00 2.87
842 844 2.947652 CAAGCAATCGAGGTCATTCCAT 59.052 45.455 0.00 0.00 39.02 3.41
964 971 7.202139 CCTCCCTCTCTGTTAATTAAGCCTATT 60.202 40.741 0.00 0.00 0.00 1.73
974 981 2.360854 CCCTCCCTCCCTCTCTGTTAAT 60.361 54.545 0.00 0.00 0.00 1.40
976 983 0.637195 CCCTCCCTCCCTCTCTGTTA 59.363 60.000 0.00 0.00 0.00 2.41
1303 1323 1.533625 TGAGGGGAAATGCAAAGACG 58.466 50.000 0.00 0.00 0.00 4.18
1423 1444 6.199908 ACTCTCGAATCAATTCATCGATGTTC 59.800 38.462 24.09 17.23 43.75 3.18
1522 1545 2.504367 CAGAACAACAAATCCTCCGGT 58.496 47.619 0.00 0.00 0.00 5.28
1888 1930 7.387948 TCAAGAATTTAAGTGAGACTTGGCTAC 59.612 37.037 0.00 0.00 39.11 3.58
2031 2073 1.941377 AGAAGGGCAATGGAAATGCA 58.059 45.000 0.00 0.00 45.60 3.96
2257 2299 5.282778 CGAAAATACTACAATTTGTGTGCGG 59.717 40.000 12.30 0.72 41.89 5.69
2534 2576 8.594550 AGGTCATTATGTAGTGAGTGTTAAACT 58.405 33.333 0.00 0.00 43.85 2.66
2848 2890 3.007290 CCTCACATCAGAACCAAGACTCA 59.993 47.826 0.00 0.00 0.00 3.41
2918 2960 0.038744 TCCCGTCCCTCGTTTCTAGT 59.961 55.000 0.00 0.00 37.94 2.57
3706 3796 7.913789 TGAGCCTAAGAAGAAAATACACCTTA 58.086 34.615 0.00 0.00 0.00 2.69
3742 3832 7.317390 TCAGATTAATTGACACACGCTTAGTA 58.683 34.615 0.00 0.00 0.00 1.82
3749 3839 5.290885 TCCGATTCAGATTAATTGACACACG 59.709 40.000 0.00 0.00 0.00 4.49
3827 3917 7.667557 CAAAATCATGAGCCTCCATATTTGAT 58.332 34.615 0.09 0.00 32.05 2.57
3900 3990 7.066525 TGTTTACTTGGACAAAGAAAAGATCGT 59.933 33.333 0.00 0.00 39.38 3.73
4047 4137 1.737793 GGCCAAAAGATGTGTCCGTAG 59.262 52.381 0.00 0.00 0.00 3.51
4048 4138 1.816074 GGCCAAAAGATGTGTCCGTA 58.184 50.000 0.00 0.00 0.00 4.02
4050 4140 1.234615 ACGGCCAAAAGATGTGTCCG 61.235 55.000 2.24 0.00 40.98 4.79
4051 4141 0.521735 GACGGCCAAAAGATGTGTCC 59.478 55.000 2.24 0.00 0.00 4.02
4052 4142 0.165944 CGACGGCCAAAAGATGTGTC 59.834 55.000 2.24 0.00 0.00 3.67
4053 4143 1.234615 CCGACGGCCAAAAGATGTGT 61.235 55.000 2.24 0.00 0.00 3.72
4054 4144 1.501741 CCGACGGCCAAAAGATGTG 59.498 57.895 2.24 0.00 0.00 3.21
4055 4145 2.332654 GCCGACGGCCAAAAGATGT 61.333 57.895 28.74 0.00 44.06 3.06
4056 4146 2.485122 GCCGACGGCCAAAAGATG 59.515 61.111 28.74 0.00 44.06 2.90


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.