Multiple sequence alignment - TraesCS3B01G114500

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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 TraesCS3B01G114500 chr3B 100.000 2300 0 0 1 2300 80656266 80658565 0.000000e+00 4248.0
1 TraesCS3B01G114500 chr3B 85.411 802 45 21 677 1442 59328308 59327543 0.000000e+00 767.0
2 TraesCS3B01G114500 chr3B 84.641 612 42 13 1144 1705 80199947 80200556 1.540000e-156 562.0
3 TraesCS3B01G114500 chr3B 87.624 404 32 6 1701 2100 59324803 59324414 9.690000e-124 453.0
4 TraesCS3B01G114500 chr3B 84.264 394 32 17 675 1044 80199544 80199931 7.810000e-95 357.0
5 TraesCS3B01G114500 chr3B 96.364 110 4 0 1543 1652 59327546 59327437 5.050000e-42 182.0
6 TraesCS3B01G114500 chr3B 83.417 199 19 7 2112 2300 59324357 59324163 3.040000e-39 172.0
7 TraesCS3B01G114500 chr3B 86.624 157 14 4 2149 2300 80200845 80200999 1.410000e-37 167.0
8 TraesCS3B01G114500 chr3A 85.244 1064 65 36 677 1677 47048600 47047566 0.000000e+00 1011.0
9 TraesCS3B01G114500 chr3A 88.832 197 12 4 2113 2300 47046986 47046791 1.370000e-57 233.0
10 TraesCS3B01G114500 chr3A 85.870 92 8 5 2212 2300 605240797 605240886 2.430000e-15 93.5
11 TraesCS3B01G114500 chr3D 84.689 1045 63 28 677 1677 36824966 36823975 0.000000e+00 953.0
12 TraesCS3B01G114500 chr3D 85.095 577 38 11 1167 1705 50655828 50656394 1.550000e-151 545.0
13 TraesCS3B01G114500 chr3D 83.553 456 37 7 1881 2300 36823235 36822782 2.140000e-105 392.0
14 TraesCS3B01G114500 chr3D 83.051 354 25 13 675 1005 50655451 50655792 2.890000e-74 289.0
15 TraesCS3B01G114500 chr3D 91.620 179 8 2 1701 1875 50657336 50657511 8.210000e-60 241.0
16 TraesCS3B01G114500 chr3D 94.268 157 5 1 1729 1881 36823533 36823377 1.060000e-58 237.0
17 TraesCS3B01G114500 chr3D 95.050 101 5 0 2112 2212 50657928 50658028 2.370000e-35 159.0
18 TraesCS3B01G114500 chr3D 96.296 54 2 0 2247 2300 50658038 50658091 3.150000e-14 89.8
19 TraesCS3B01G114500 chr3D 83.516 91 9 4 1701 1787 36592880 36592792 1.890000e-11 80.5
20 TraesCS3B01G114500 chr1D 80.594 876 66 47 675 1511 460995883 460995073 4.260000e-162 580.0
21 TraesCS3B01G114500 chr1D 80.527 873 61 43 684 1511 460982810 460982002 9.220000e-159 569.0
22 TraesCS3B01G114500 chr1B 80.449 890 64 45 675 1511 633260959 633260127 1.530000e-161 579.0
23 TraesCS3B01G114500 chr1B 96.610 59 1 1 2243 2300 620552137 620552079 1.880000e-16 97.1
24 TraesCS3B01G114500 chr1B 78.862 123 19 5 45 161 648107669 648107548 2.450000e-10 76.8
25 TraesCS3B01G114500 chr7A 78.795 797 93 37 666 1425 37937705 37938462 1.240000e-127 466.0
26 TraesCS3B01G114500 chr7A 81.481 189 17 10 1119 1302 37354543 37354368 3.080000e-29 139.0
27 TraesCS3B01G114500 chr7A 98.182 55 1 0 2246 2300 680264107 680264161 1.880000e-16 97.1
28 TraesCS3B01G114500 chr1A 78.935 826 58 49 684 1458 552119622 552118862 2.690000e-124 455.0
29 TraesCS3B01G114500 chr4A 78.684 760 76 37 709 1426 642186895 642186180 5.870000e-116 427.0
30 TraesCS3B01G114500 chr4A 79.964 554 81 22 879 1426 686579015 686579544 4.640000e-102 381.0
31 TraesCS3B01G114500 chr7D 76.289 679 72 45 674 1327 38203815 38204429 1.740000e-71 279.0
32 TraesCS3B01G114500 chr7D 88.764 89 6 1 728 816 38271290 38271374 3.130000e-19 106.0
33 TraesCS3B01G114500 chr6D 85.350 157 11 8 1564 1708 27758119 27757963 3.960000e-33 152.0
34 TraesCS3B01G114500 chrUn 94.915 59 3 0 2242 2300 69444039 69444097 2.430000e-15 93.5


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 TraesCS3B01G114500 chr3B 80656266 80658565 2299 False 4248.000000 4248 100.000000 1 2300 1 chr3B.!!$F1 2299
1 TraesCS3B01G114500 chr3B 59324163 59328308 4145 True 393.500000 767 88.204000 677 2300 4 chr3B.!!$R1 1623
2 TraesCS3B01G114500 chr3B 80199544 80200999 1455 False 362.000000 562 85.176333 675 2300 3 chr3B.!!$F2 1625
3 TraesCS3B01G114500 chr3A 47046791 47048600 1809 True 622.000000 1011 87.038000 677 2300 2 chr3A.!!$R1 1623
4 TraesCS3B01G114500 chr3D 36822782 36824966 2184 True 527.333333 953 87.503333 677 2300 3 chr3D.!!$R2 1623
5 TraesCS3B01G114500 chr3D 50655451 50658091 2640 False 264.760000 545 90.222400 675 2300 5 chr3D.!!$F1 1625
6 TraesCS3B01G114500 chr1D 460995073 460995883 810 True 580.000000 580 80.594000 675 1511 1 chr1D.!!$R2 836
7 TraesCS3B01G114500 chr1D 460982002 460982810 808 True 569.000000 569 80.527000 684 1511 1 chr1D.!!$R1 827
8 TraesCS3B01G114500 chr1B 633260127 633260959 832 True 579.000000 579 80.449000 675 1511 1 chr1B.!!$R2 836
9 TraesCS3B01G114500 chr7A 37937705 37938462 757 False 466.000000 466 78.795000 666 1425 1 chr7A.!!$F1 759
10 TraesCS3B01G114500 chr1A 552118862 552119622 760 True 455.000000 455 78.935000 684 1458 1 chr1A.!!$R1 774
11 TraesCS3B01G114500 chr4A 642186180 642186895 715 True 427.000000 427 78.684000 709 1426 1 chr4A.!!$R1 717
12 TraesCS3B01G114500 chr4A 686579015 686579544 529 False 381.000000 381 79.964000 879 1426 1 chr4A.!!$F1 547
13 TraesCS3B01G114500 chr7D 38203815 38204429 614 False 279.000000 279 76.289000 674 1327 1 chr7D.!!$F1 653

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
169 170 0.238289 CGAGCCAAATGACGTGCTTT 59.762 50.0 0.0 0.0 33.41 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1681 1902 0.315251 CTCTGCAGACAACGACTCCA 59.685 55.0 13.74 0.0 0.0 3.86 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 4.783764 AAAGGGCCAAAAGATACGAAAG 57.216 40.909 6.18 0.00 0.00 2.62
23 24 2.723273 AGGGCCAAAAGATACGAAAGG 58.277 47.619 6.18 0.00 0.00 3.11
24 25 1.134367 GGGCCAAAAGATACGAAAGGC 59.866 52.381 4.39 0.00 39.86 4.35
25 26 1.816224 GGCCAAAAGATACGAAAGGCA 59.184 47.619 0.00 0.00 42.26 4.75
26 27 2.230266 GGCCAAAAGATACGAAAGGCAA 59.770 45.455 0.00 0.00 42.26 4.52
27 28 3.501950 GCCAAAAGATACGAAAGGCAAG 58.498 45.455 0.00 0.00 40.29 4.01
28 29 3.673323 GCCAAAAGATACGAAAGGCAAGG 60.673 47.826 0.00 0.00 40.29 3.61
29 30 3.756434 CCAAAAGATACGAAAGGCAAGGA 59.244 43.478 0.00 0.00 0.00 3.36
30 31 4.217550 CCAAAAGATACGAAAGGCAAGGAA 59.782 41.667 0.00 0.00 0.00 3.36
31 32 5.278758 CCAAAAGATACGAAAGGCAAGGAAA 60.279 40.000 0.00 0.00 0.00 3.13
32 33 6.212955 CAAAAGATACGAAAGGCAAGGAAAA 58.787 36.000 0.00 0.00 0.00 2.29
33 34 5.372547 AAGATACGAAAGGCAAGGAAAAC 57.627 39.130 0.00 0.00 0.00 2.43
34 35 4.394729 AGATACGAAAGGCAAGGAAAACA 58.605 39.130 0.00 0.00 0.00 2.83
35 36 4.455877 AGATACGAAAGGCAAGGAAAACAG 59.544 41.667 0.00 0.00 0.00 3.16
36 37 2.650322 ACGAAAGGCAAGGAAAACAGA 58.350 42.857 0.00 0.00 0.00 3.41
37 38 3.020984 ACGAAAGGCAAGGAAAACAGAA 58.979 40.909 0.00 0.00 0.00 3.02
38 39 3.445805 ACGAAAGGCAAGGAAAACAGAAA 59.554 39.130 0.00 0.00 0.00 2.52
39 40 4.081917 ACGAAAGGCAAGGAAAACAGAAAA 60.082 37.500 0.00 0.00 0.00 2.29
40 41 4.504097 CGAAAGGCAAGGAAAACAGAAAAG 59.496 41.667 0.00 0.00 0.00 2.27
41 42 3.459232 AGGCAAGGAAAACAGAAAAGC 57.541 42.857 0.00 0.00 0.00 3.51
42 43 2.103094 AGGCAAGGAAAACAGAAAAGCC 59.897 45.455 0.00 0.00 39.82 4.35
43 44 2.127251 GCAAGGAAAACAGAAAAGCCG 58.873 47.619 0.00 0.00 0.00 5.52
44 45 2.223711 GCAAGGAAAACAGAAAAGCCGA 60.224 45.455 0.00 0.00 0.00 5.54
45 46 3.736740 GCAAGGAAAACAGAAAAGCCGAA 60.737 43.478 0.00 0.00 0.00 4.30
46 47 4.429108 CAAGGAAAACAGAAAAGCCGAAA 58.571 39.130 0.00 0.00 0.00 3.46
47 48 4.729227 AGGAAAACAGAAAAGCCGAAAA 57.271 36.364 0.00 0.00 0.00 2.29
48 49 5.079689 AGGAAAACAGAAAAGCCGAAAAA 57.920 34.783 0.00 0.00 0.00 1.94
82 83 8.593492 AAAATCATCTAAAAAGCCAGAAACAC 57.407 30.769 0.00 0.00 0.00 3.32
83 84 5.356882 TCATCTAAAAAGCCAGAAACACG 57.643 39.130 0.00 0.00 0.00 4.49
84 85 4.819630 TCATCTAAAAAGCCAGAAACACGT 59.180 37.500 0.00 0.00 0.00 4.49
85 86 4.545823 TCTAAAAAGCCAGAAACACGTG 57.454 40.909 15.48 15.48 0.00 4.49
86 87 1.921243 AAAAAGCCAGAAACACGTGC 58.079 45.000 17.22 0.00 0.00 5.34
87 88 0.814457 AAAAGCCAGAAACACGTGCA 59.186 45.000 17.22 0.00 0.00 4.57
88 89 0.814457 AAAGCCAGAAACACGTGCAA 59.186 45.000 17.22 0.00 0.00 4.08
89 90 0.814457 AAGCCAGAAACACGTGCAAA 59.186 45.000 17.22 0.00 0.00 3.68
90 91 0.814457 AGCCAGAAACACGTGCAAAA 59.186 45.000 17.22 0.00 0.00 2.44
91 92 1.203523 AGCCAGAAACACGTGCAAAAA 59.796 42.857 17.22 0.00 0.00 1.94
120 121 4.649088 AAAAATTACATAGGAAGCGCCC 57.351 40.909 2.29 0.00 37.37 6.13
121 122 3.290948 AAATTACATAGGAAGCGCCCA 57.709 42.857 2.29 0.00 37.37 5.36
122 123 2.550830 ATTACATAGGAAGCGCCCAG 57.449 50.000 2.29 0.00 37.37 4.45
123 124 1.491668 TTACATAGGAAGCGCCCAGA 58.508 50.000 2.29 0.00 37.37 3.86
124 125 1.040646 TACATAGGAAGCGCCCAGAG 58.959 55.000 2.29 0.00 37.37 3.35
125 126 1.596477 CATAGGAAGCGCCCAGAGC 60.596 63.158 2.29 0.00 37.37 4.09
159 160 4.215349 GCTGAGAGCGAGCCAAAT 57.785 55.556 0.00 0.00 0.00 2.32
160 161 1.720301 GCTGAGAGCGAGCCAAATG 59.280 57.895 0.00 0.00 0.00 2.32
161 162 0.742281 GCTGAGAGCGAGCCAAATGA 60.742 55.000 0.00 0.00 0.00 2.57
162 163 1.005340 CTGAGAGCGAGCCAAATGAC 58.995 55.000 0.00 0.00 0.00 3.06
163 164 0.737367 TGAGAGCGAGCCAAATGACG 60.737 55.000 0.00 0.00 0.00 4.35
164 165 0.737715 GAGAGCGAGCCAAATGACGT 60.738 55.000 0.00 0.00 0.00 4.34
165 166 1.016130 AGAGCGAGCCAAATGACGTG 61.016 55.000 0.00 0.00 0.00 4.49
166 167 2.202349 GCGAGCCAAATGACGTGC 60.202 61.111 0.00 0.00 0.00 5.34
167 168 2.680913 GCGAGCCAAATGACGTGCT 61.681 57.895 0.00 0.00 36.62 4.40
168 169 1.868997 CGAGCCAAATGACGTGCTT 59.131 52.632 0.00 0.00 33.41 3.91
169 170 0.238289 CGAGCCAAATGACGTGCTTT 59.762 50.000 0.00 0.00 33.41 3.51
170 171 1.334960 CGAGCCAAATGACGTGCTTTT 60.335 47.619 0.00 0.00 33.41 2.27
171 172 2.319472 GAGCCAAATGACGTGCTTTTC 58.681 47.619 0.00 0.00 33.41 2.29
172 173 1.956477 AGCCAAATGACGTGCTTTTCT 59.044 42.857 0.00 0.00 0.00 2.52
173 174 2.362077 AGCCAAATGACGTGCTTTTCTT 59.638 40.909 0.00 0.00 0.00 2.52
174 175 3.123050 GCCAAATGACGTGCTTTTCTTT 58.877 40.909 0.00 0.00 0.00 2.52
175 176 3.060339 GCCAAATGACGTGCTTTTCTTTG 60.060 43.478 0.00 0.00 0.00 2.77
176 177 4.111916 CCAAATGACGTGCTTTTCTTTGT 58.888 39.130 0.00 0.00 0.00 2.83
177 178 4.566360 CCAAATGACGTGCTTTTCTTTGTT 59.434 37.500 0.00 0.00 0.00 2.83
178 179 5.746245 CCAAATGACGTGCTTTTCTTTGTTA 59.254 36.000 0.00 0.00 0.00 2.41
179 180 6.420604 CCAAATGACGTGCTTTTCTTTGTTAT 59.579 34.615 0.00 0.00 0.00 1.89
180 181 7.593273 CCAAATGACGTGCTTTTCTTTGTTATA 59.407 33.333 0.00 0.00 0.00 0.98
181 182 8.963130 CAAATGACGTGCTTTTCTTTGTTATAA 58.037 29.630 0.00 0.00 0.00 0.98
182 183 9.522804 AAATGACGTGCTTTTCTTTGTTATAAA 57.477 25.926 0.00 0.00 0.00 1.40
183 184 9.691362 AATGACGTGCTTTTCTTTGTTATAAAT 57.309 25.926 0.00 0.00 0.00 1.40
184 185 9.691362 ATGACGTGCTTTTCTTTGTTATAAATT 57.309 25.926 0.00 0.00 0.00 1.82
185 186 9.522804 TGACGTGCTTTTCTTTGTTATAAATTT 57.477 25.926 0.00 0.00 0.00 1.82
209 210 9.549078 TTTAGTTTTCTTTTGTTTTTCACTGGT 57.451 25.926 0.00 0.00 0.00 4.00
210 211 9.549078 TTAGTTTTCTTTTGTTTTTCACTGGTT 57.451 25.926 0.00 0.00 0.00 3.67
211 212 8.445275 AGTTTTCTTTTGTTTTTCACTGGTTT 57.555 26.923 0.00 0.00 0.00 3.27
212 213 8.898761 AGTTTTCTTTTGTTTTTCACTGGTTTT 58.101 25.926 0.00 0.00 0.00 2.43
245 246 7.575332 TTTCTTTGTTCCTTTGTTTTCTTCG 57.425 32.000 0.00 0.00 0.00 3.79
246 247 6.262193 TCTTTGTTCCTTTGTTTTCTTCGT 57.738 33.333 0.00 0.00 0.00 3.85
247 248 6.319399 TCTTTGTTCCTTTGTTTTCTTCGTC 58.681 36.000 0.00 0.00 0.00 4.20
248 249 5.890424 TTGTTCCTTTGTTTTCTTCGTCT 57.110 34.783 0.00 0.00 0.00 4.18
249 250 5.890424 TGTTCCTTTGTTTTCTTCGTCTT 57.110 34.783 0.00 0.00 0.00 3.01
250 251 6.262193 TGTTCCTTTGTTTTCTTCGTCTTT 57.738 33.333 0.00 0.00 0.00 2.52
251 252 7.380431 TGTTCCTTTGTTTTCTTCGTCTTTA 57.620 32.000 0.00 0.00 0.00 1.85
252 253 7.992008 TGTTCCTTTGTTTTCTTCGTCTTTAT 58.008 30.769 0.00 0.00 0.00 1.40
253 254 8.463607 TGTTCCTTTGTTTTCTTCGTCTTTATT 58.536 29.630 0.00 0.00 0.00 1.40
254 255 9.297586 GTTCCTTTGTTTTCTTCGTCTTTATTT 57.702 29.630 0.00 0.00 0.00 1.40
255 256 8.850454 TCCTTTGTTTTCTTCGTCTTTATTTG 57.150 30.769 0.00 0.00 0.00 2.32
256 257 8.463607 TCCTTTGTTTTCTTCGTCTTTATTTGT 58.536 29.630 0.00 0.00 0.00 2.83
257 258 8.531530 CCTTTGTTTTCTTCGTCTTTATTTGTG 58.468 33.333 0.00 0.00 0.00 3.33
258 259 8.973835 TTTGTTTTCTTCGTCTTTATTTGTGT 57.026 26.923 0.00 0.00 0.00 3.72
259 260 8.973835 TTGTTTTCTTCGTCTTTATTTGTGTT 57.026 26.923 0.00 0.00 0.00 3.32
260 261 8.973835 TGTTTTCTTCGTCTTTATTTGTGTTT 57.026 26.923 0.00 0.00 0.00 2.83
261 262 8.855279 TGTTTTCTTCGTCTTTATTTGTGTTTG 58.145 29.630 0.00 0.00 0.00 2.93
262 263 8.856247 GTTTTCTTCGTCTTTATTTGTGTTTGT 58.144 29.630 0.00 0.00 0.00 2.83
263 264 8.973835 TTTCTTCGTCTTTATTTGTGTTTGTT 57.026 26.923 0.00 0.00 0.00 2.83
264 265 8.973835 TTCTTCGTCTTTATTTGTGTTTGTTT 57.026 26.923 0.00 0.00 0.00 2.83
265 266 8.388319 TCTTCGTCTTTATTTGTGTTTGTTTG 57.612 30.769 0.00 0.00 0.00 2.93
266 267 8.024285 TCTTCGTCTTTATTTGTGTTTGTTTGT 58.976 29.630 0.00 0.00 0.00 2.83
267 268 8.522178 TTCGTCTTTATTTGTGTTTGTTTGTT 57.478 26.923 0.00 0.00 0.00 2.83
268 269 7.943952 TCGTCTTTATTTGTGTTTGTTTGTTG 58.056 30.769 0.00 0.00 0.00 3.33
269 270 7.808381 TCGTCTTTATTTGTGTTTGTTTGTTGA 59.192 29.630 0.00 0.00 0.00 3.18
270 271 8.591312 CGTCTTTATTTGTGTTTGTTTGTTGAT 58.409 29.630 0.00 0.00 0.00 2.57
385 386 9.326413 AGACCATTACTTTAATGATCTAAACGG 57.674 33.333 1.51 0.00 45.10 4.44
386 387 9.106070 GACCATTACTTTAATGATCTAAACGGT 57.894 33.333 7.38 0.00 46.52 4.83
387 388 9.106070 ACCATTACTTTAATGATCTAAACGGTC 57.894 33.333 7.38 0.00 46.52 4.79
388 389 9.326413 CCATTACTTTAATGATCTAAACGGTCT 57.674 33.333 7.38 0.00 46.52 3.85
415 416 2.018542 TTTTATGGAGGGAGTTCGCG 57.981 50.000 0.00 0.00 0.00 5.87
416 417 0.899720 TTTATGGAGGGAGTTCGCGT 59.100 50.000 5.77 0.00 0.00 6.01
417 418 0.899720 TTATGGAGGGAGTTCGCGTT 59.100 50.000 5.77 0.00 0.00 4.84
418 419 1.766494 TATGGAGGGAGTTCGCGTTA 58.234 50.000 5.77 0.00 0.00 3.18
419 420 0.899720 ATGGAGGGAGTTCGCGTTAA 59.100 50.000 5.77 0.00 0.00 2.01
420 421 0.680618 TGGAGGGAGTTCGCGTTAAA 59.319 50.000 5.77 0.00 0.00 1.52
421 422 1.073964 GGAGGGAGTTCGCGTTAAAC 58.926 55.000 5.77 3.08 0.00 2.01
422 423 1.606224 GGAGGGAGTTCGCGTTAAACA 60.606 52.381 5.77 0.00 0.00 2.83
423 424 2.344025 GAGGGAGTTCGCGTTAAACAT 58.656 47.619 5.77 0.00 0.00 2.71
424 425 2.740447 GAGGGAGTTCGCGTTAAACATT 59.260 45.455 5.77 0.00 0.00 2.71
425 426 3.143728 AGGGAGTTCGCGTTAAACATTT 58.856 40.909 5.77 0.00 0.00 2.32
426 427 3.187842 AGGGAGTTCGCGTTAAACATTTC 59.812 43.478 5.77 0.00 0.00 2.17
427 428 3.187842 GGGAGTTCGCGTTAAACATTTCT 59.812 43.478 5.77 0.00 0.00 2.52
428 429 4.319984 GGGAGTTCGCGTTAAACATTTCTT 60.320 41.667 5.77 0.00 0.00 2.52
429 430 5.106987 GGGAGTTCGCGTTAAACATTTCTTA 60.107 40.000 5.77 0.00 0.00 2.10
430 431 6.365050 GGAGTTCGCGTTAAACATTTCTTAA 58.635 36.000 5.77 0.00 0.00 1.85
431 432 6.852345 GGAGTTCGCGTTAAACATTTCTTAAA 59.148 34.615 5.77 0.00 0.00 1.52
432 433 7.536281 GGAGTTCGCGTTAAACATTTCTTAAAT 59.464 33.333 5.77 0.00 0.00 1.40
433 434 9.532697 GAGTTCGCGTTAAACATTTCTTAAATA 57.467 29.630 5.77 0.00 0.00 1.40
434 435 9.321590 AGTTCGCGTTAAACATTTCTTAAATAC 57.678 29.630 5.77 0.00 0.00 1.89
435 436 9.105206 GTTCGCGTTAAACATTTCTTAAATACA 57.895 29.630 5.77 0.00 0.00 2.29
436 437 9.828852 TTCGCGTTAAACATTTCTTAAATACAT 57.171 25.926 5.77 0.00 0.00 2.29
437 438 9.268255 TCGCGTTAAACATTTCTTAAATACATG 57.732 29.630 5.77 0.00 0.00 3.21
438 439 9.268255 CGCGTTAAACATTTCTTAAATACATGA 57.732 29.630 0.00 0.00 0.00 3.07
491 492 3.297391 TTTTTGAAACATGGCGCCC 57.703 47.368 26.77 7.71 0.00 6.13
492 493 0.250081 TTTTTGAAACATGGCGCCCC 60.250 50.000 26.77 6.54 0.00 5.80
493 494 2.427540 TTTTGAAACATGGCGCCCCG 62.428 55.000 26.77 17.82 0.00 5.73
510 511 4.265056 GGGCCAGGGTGTCGTGTT 62.265 66.667 4.39 0.00 0.00 3.32
511 512 2.668550 GGCCAGGGTGTCGTGTTC 60.669 66.667 0.00 0.00 0.00 3.18
512 513 2.426023 GCCAGGGTGTCGTGTTCT 59.574 61.111 0.00 0.00 0.00 3.01
513 514 1.668151 GCCAGGGTGTCGTGTTCTC 60.668 63.158 0.00 0.00 0.00 2.87
514 515 2.050269 CCAGGGTGTCGTGTTCTCT 58.950 57.895 0.00 0.00 0.00 3.10
515 516 1.254026 CCAGGGTGTCGTGTTCTCTA 58.746 55.000 0.00 0.00 0.00 2.43
516 517 1.202582 CCAGGGTGTCGTGTTCTCTAG 59.797 57.143 0.00 0.00 0.00 2.43
517 518 0.889306 AGGGTGTCGTGTTCTCTAGC 59.111 55.000 0.00 0.00 0.00 3.42
518 519 0.601558 GGGTGTCGTGTTCTCTAGCA 59.398 55.000 0.00 0.00 0.00 3.49
519 520 1.204941 GGGTGTCGTGTTCTCTAGCAT 59.795 52.381 0.00 0.00 0.00 3.79
520 521 2.263077 GGTGTCGTGTTCTCTAGCATG 58.737 52.381 0.00 0.00 0.00 4.06
521 522 2.263077 GTGTCGTGTTCTCTAGCATGG 58.737 52.381 0.00 0.00 0.00 3.66
522 523 1.893137 TGTCGTGTTCTCTAGCATGGT 59.107 47.619 1.62 1.62 0.00 3.55
523 524 2.263077 GTCGTGTTCTCTAGCATGGTG 58.737 52.381 7.89 0.00 0.00 4.17
524 525 1.002366 CGTGTTCTCTAGCATGGTGC 58.998 55.000 7.89 0.00 45.46 5.01
525 526 1.373570 GTGTTCTCTAGCATGGTGCC 58.626 55.000 7.89 0.00 46.52 5.01
526 527 0.253044 TGTTCTCTAGCATGGTGCCC 59.747 55.000 7.89 0.00 46.52 5.36
527 528 0.464554 GTTCTCTAGCATGGTGCCCC 60.465 60.000 7.89 0.00 46.52 5.80
528 529 1.635817 TTCTCTAGCATGGTGCCCCC 61.636 60.000 7.89 0.00 46.52 5.40
529 530 3.466791 CTCTAGCATGGTGCCCCCG 62.467 68.421 7.89 0.00 46.52 5.73
542 543 4.047125 CCCCGCCCAAGGTGTCAT 62.047 66.667 0.00 0.00 0.00 3.06
543 544 2.751436 CCCGCCCAAGGTGTCATG 60.751 66.667 0.00 0.00 0.00 3.07
544 545 3.443045 CCGCCCAAGGTGTCATGC 61.443 66.667 0.00 0.00 0.00 4.06
545 546 2.360350 CGCCCAAGGTGTCATGCT 60.360 61.111 0.00 0.00 0.00 3.79
546 547 1.078497 CGCCCAAGGTGTCATGCTA 60.078 57.895 0.00 0.00 0.00 3.49
547 548 0.464373 CGCCCAAGGTGTCATGCTAT 60.464 55.000 0.00 0.00 0.00 2.97
548 549 1.767759 GCCCAAGGTGTCATGCTATT 58.232 50.000 0.00 0.00 0.00 1.73
549 550 2.744823 CGCCCAAGGTGTCATGCTATTA 60.745 50.000 0.00 0.00 0.00 0.98
550 551 2.618709 GCCCAAGGTGTCATGCTATTAC 59.381 50.000 0.00 0.00 0.00 1.89
551 552 3.884895 CCCAAGGTGTCATGCTATTACA 58.115 45.455 0.00 0.00 0.00 2.41
552 553 4.464008 CCCAAGGTGTCATGCTATTACAT 58.536 43.478 0.00 0.00 0.00 2.29
554 555 4.276678 CCAAGGTGTCATGCTATTACATGG 59.723 45.833 0.00 0.00 46.08 3.66
555 556 4.090761 AGGTGTCATGCTATTACATGGG 57.909 45.455 0.00 0.00 46.08 4.00
556 557 3.716353 AGGTGTCATGCTATTACATGGGA 59.284 43.478 0.00 0.00 46.08 4.37
557 558 4.165950 AGGTGTCATGCTATTACATGGGAA 59.834 41.667 0.00 0.00 46.08 3.97
558 559 4.275936 GGTGTCATGCTATTACATGGGAAC 59.724 45.833 0.00 1.93 46.08 3.62
595 596 7.790823 AAACTTCATGGAAAATCAAGTTTGG 57.209 32.000 14.75 0.00 42.76 3.28
596 597 6.729690 ACTTCATGGAAAATCAAGTTTGGA 57.270 33.333 0.00 0.00 0.00 3.53
597 598 7.123355 ACTTCATGGAAAATCAAGTTTGGAA 57.877 32.000 0.00 0.00 0.00 3.53
598 599 7.212274 ACTTCATGGAAAATCAAGTTTGGAAG 58.788 34.615 0.00 0.00 34.58 3.46
599 600 6.729690 TCATGGAAAATCAAGTTTGGAAGT 57.270 33.333 0.00 0.00 0.00 3.01
600 601 7.123355 TCATGGAAAATCAAGTTTGGAAGTT 57.877 32.000 0.00 0.00 0.00 2.66
601 602 7.563906 TCATGGAAAATCAAGTTTGGAAGTTT 58.436 30.769 0.00 0.00 0.00 2.66
602 603 7.710475 TCATGGAAAATCAAGTTTGGAAGTTTC 59.290 33.333 0.00 0.00 0.00 2.78
639 640 8.541899 AAAAAGGTAAAATGTTAAGAGGGTGA 57.458 30.769 0.00 0.00 0.00 4.02
640 641 8.721133 AAAAGGTAAAATGTTAAGAGGGTGAT 57.279 30.769 0.00 0.00 0.00 3.06
641 642 9.816787 AAAAGGTAAAATGTTAAGAGGGTGATA 57.183 29.630 0.00 0.00 0.00 2.15
642 643 8.803397 AAGGTAAAATGTTAAGAGGGTGATAC 57.197 34.615 0.00 0.00 0.00 2.24
643 644 8.159229 AGGTAAAATGTTAAGAGGGTGATACT 57.841 34.615 0.00 0.00 0.00 2.12
644 645 8.612145 AGGTAAAATGTTAAGAGGGTGATACTT 58.388 33.333 0.00 0.00 0.00 2.24
645 646 9.239551 GGTAAAATGTTAAGAGGGTGATACTTT 57.760 33.333 0.00 0.00 0.00 2.66
650 651 7.859325 TGTTAAGAGGGTGATACTTTAATGC 57.141 36.000 0.00 0.00 0.00 3.56
651 652 6.826741 TGTTAAGAGGGTGATACTTTAATGCC 59.173 38.462 0.00 0.00 0.00 4.40
652 653 5.450818 AAGAGGGTGATACTTTAATGCCA 57.549 39.130 0.00 0.00 0.00 4.92
653 654 5.653255 AGAGGGTGATACTTTAATGCCAT 57.347 39.130 0.00 0.00 0.00 4.40
654 655 5.380043 AGAGGGTGATACTTTAATGCCATG 58.620 41.667 0.00 0.00 0.00 3.66
655 656 5.103940 AGAGGGTGATACTTTAATGCCATGT 60.104 40.000 0.00 0.00 0.00 3.21
656 657 4.889409 AGGGTGATACTTTAATGCCATGTG 59.111 41.667 0.00 0.00 0.00 3.21
657 658 4.887071 GGGTGATACTTTAATGCCATGTGA 59.113 41.667 0.00 0.00 0.00 3.58
658 659 5.359576 GGGTGATACTTTAATGCCATGTGAA 59.640 40.000 0.00 0.00 0.00 3.18
659 660 6.460123 GGGTGATACTTTAATGCCATGTGAAG 60.460 42.308 0.00 0.00 0.00 3.02
660 661 6.460123 GGTGATACTTTAATGCCATGTGAAGG 60.460 42.308 0.00 0.00 0.00 3.46
670 671 2.192711 TGTGAAGGCAGCACAGCA 59.807 55.556 8.14 0.00 41.00 4.41
671 672 1.895231 TGTGAAGGCAGCACAGCAG 60.895 57.895 8.14 0.00 41.00 4.24
672 673 2.281970 TGAAGGCAGCACAGCAGG 60.282 61.111 0.00 0.00 35.83 4.85
673 674 2.033141 GAAGGCAGCACAGCAGGA 59.967 61.111 0.00 0.00 35.83 3.86
692 693 2.254703 AAAACACGCGCGAAACCACA 62.255 50.000 39.36 0.00 0.00 4.17
694 695 3.334751 CACGCGCGAAACCACAGA 61.335 61.111 39.36 0.00 0.00 3.41
755 772 2.650116 GCTCGCTGGTTCTCCCTCA 61.650 63.158 0.00 0.00 0.00 3.86
883 924 1.674057 CGCTCTCCCTTCACCAAGT 59.326 57.895 0.00 0.00 0.00 3.16
902 994 5.048083 CCAAGTAAGCAAAGCCAGTTGATTA 60.048 40.000 9.19 0.46 38.10 1.75
951 1052 4.445545 GCAAGAAAGCGTCGGCCG 62.446 66.667 22.12 22.12 41.24 6.13
1122 1246 3.478274 GGGAGGAGGCTGCAGGAG 61.478 72.222 17.12 0.00 0.00 3.69
1164 1290 1.304962 TAGAGCAGGGCAAGACGGA 60.305 57.895 0.00 0.00 0.00 4.69
1171 1297 2.563427 GGCAAGACGGAAAGCAGC 59.437 61.111 0.00 0.00 0.00 5.25
1237 1363 3.598715 AGTCACCGCCGACGTTGA 61.599 61.111 3.74 0.00 38.49 3.18
1353 1509 6.420903 TGTGTGAGACTAATTCTTTCTTCGTG 59.579 38.462 0.00 0.00 33.22 4.35
1417 1597 0.179225 GCCGCGTGTTGTACAGAATG 60.179 55.000 4.92 0.00 46.00 2.67
1461 1646 6.713762 TTTCGCCATGATTATTTGGAGATT 57.286 33.333 0.00 0.00 40.76 2.40
1504 1694 0.171455 GTCGTGACGGAGCAGAGATT 59.829 55.000 4.70 0.00 0.00 2.40
1575 1792 4.451096 TCAAAGCCATCGAACTGAGTTTAC 59.549 41.667 0.00 0.00 0.00 2.01
1627 1844 3.521727 ACTGAAATAGACTCACCACCCT 58.478 45.455 0.00 0.00 0.00 4.34
1630 1847 4.422057 TGAAATAGACTCACCACCCTACA 58.578 43.478 0.00 0.00 0.00 2.74
1681 1902 2.039084 AGAGAAACATCTCTGCCGGTTT 59.961 45.455 1.90 0.00 44.63 3.27
1705 1926 3.062763 AGTCGTTGTCTGCAGAGATTTG 58.937 45.455 18.89 8.83 0.00 2.32
1730 4890 3.751518 ACCATGTACTCCCAAGAACAAC 58.248 45.455 0.00 0.00 0.00 3.32
1731 4891 3.137544 ACCATGTACTCCCAAGAACAACA 59.862 43.478 0.00 0.00 0.00 3.33
1732 4892 4.141287 CCATGTACTCCCAAGAACAACAA 58.859 43.478 0.00 0.00 0.00 2.83
1733 4893 4.766891 CCATGTACTCCCAAGAACAACAAT 59.233 41.667 0.00 0.00 0.00 2.71
1734 4894 5.335897 CCATGTACTCCCAAGAACAACAATG 60.336 44.000 0.00 0.00 0.00 2.82
1735 4895 4.787551 TGTACTCCCAAGAACAACAATGT 58.212 39.130 0.00 0.00 43.14 2.71
1736 4896 4.578516 TGTACTCCCAAGAACAACAATGTG 59.421 41.667 0.00 0.00 40.46 3.21
1817 4977 4.613570 GCACAAGAAAAGTTTATGTGCG 57.386 40.909 25.36 8.91 45.51 5.34
1846 5006 7.061054 TCTCTAAATAAACATCCTCTCCTCGA 58.939 38.462 0.00 0.00 0.00 4.04
1881 5045 2.882927 TCCATTAACCTCACGATCCG 57.117 50.000 0.00 0.00 0.00 4.18
1882 5046 2.104967 TCCATTAACCTCACGATCCGT 58.895 47.619 0.00 0.00 42.36 4.69
1883 5047 2.498481 TCCATTAACCTCACGATCCGTT 59.502 45.455 0.00 0.00 38.32 4.44
1956 5274 7.604164 TGAAACTGAGTTTGTCTGAAGATATCC 59.396 37.037 16.25 0.00 35.77 2.59
1960 5278 6.768483 TGAGTTTGTCTGAAGATATCCACAA 58.232 36.000 0.00 0.00 31.39 3.33
1993 5321 2.949644 ACTGAAACAGGGCACTAAACAC 59.050 45.455 0.00 0.00 35.51 3.32
2245 5647 3.249999 CGGACGACGTGCCAAATT 58.750 55.556 14.16 0.00 37.93 1.82
2268 5670 0.105964 CGGAGGTGAACTTGGTGACA 59.894 55.000 0.00 0.00 39.83 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.723273 CCTTTCGTATCTTTTGGCCCT 58.277 47.619 0.00 0.00 0.00 5.19
4 5 1.134367 GCCTTTCGTATCTTTTGGCCC 59.866 52.381 0.00 0.00 33.45 5.80
5 6 1.816224 TGCCTTTCGTATCTTTTGGCC 59.184 47.619 0.00 0.00 38.23 5.36
13 14 4.454504 TCTGTTTTCCTTGCCTTTCGTATC 59.545 41.667 0.00 0.00 0.00 2.24
14 15 4.394729 TCTGTTTTCCTTGCCTTTCGTAT 58.605 39.130 0.00 0.00 0.00 3.06
15 16 3.811083 TCTGTTTTCCTTGCCTTTCGTA 58.189 40.909 0.00 0.00 0.00 3.43
16 17 2.650322 TCTGTTTTCCTTGCCTTTCGT 58.350 42.857 0.00 0.00 0.00 3.85
17 18 3.708563 TTCTGTTTTCCTTGCCTTTCG 57.291 42.857 0.00 0.00 0.00 3.46
18 19 4.271049 GCTTTTCTGTTTTCCTTGCCTTTC 59.729 41.667 0.00 0.00 0.00 2.62
19 20 4.191544 GCTTTTCTGTTTTCCTTGCCTTT 58.808 39.130 0.00 0.00 0.00 3.11
20 21 3.432186 GGCTTTTCTGTTTTCCTTGCCTT 60.432 43.478 0.00 0.00 35.44 4.35
21 22 2.103094 GGCTTTTCTGTTTTCCTTGCCT 59.897 45.455 0.00 0.00 35.44 4.75
22 23 2.483876 GGCTTTTCTGTTTTCCTTGCC 58.516 47.619 0.00 0.00 0.00 4.52
23 24 2.127251 CGGCTTTTCTGTTTTCCTTGC 58.873 47.619 0.00 0.00 0.00 4.01
24 25 3.708563 TCGGCTTTTCTGTTTTCCTTG 57.291 42.857 0.00 0.00 0.00 3.61
25 26 4.729227 TTTCGGCTTTTCTGTTTTCCTT 57.271 36.364 0.00 0.00 0.00 3.36
26 27 4.729227 TTTTCGGCTTTTCTGTTTTCCT 57.271 36.364 0.00 0.00 0.00 3.36
56 57 9.045223 GTGTTTCTGGCTTTTTAGATGATTTTT 57.955 29.630 0.00 0.00 0.00 1.94
57 58 7.382218 CGTGTTTCTGGCTTTTTAGATGATTTT 59.618 33.333 0.00 0.00 0.00 1.82
58 59 6.863126 CGTGTTTCTGGCTTTTTAGATGATTT 59.137 34.615 0.00 0.00 0.00 2.17
59 60 6.016276 ACGTGTTTCTGGCTTTTTAGATGATT 60.016 34.615 0.00 0.00 0.00 2.57
60 61 5.473504 ACGTGTTTCTGGCTTTTTAGATGAT 59.526 36.000 0.00 0.00 0.00 2.45
61 62 4.819630 ACGTGTTTCTGGCTTTTTAGATGA 59.180 37.500 0.00 0.00 0.00 2.92
62 63 4.911610 CACGTGTTTCTGGCTTTTTAGATG 59.088 41.667 7.58 0.00 0.00 2.90
63 64 4.556699 GCACGTGTTTCTGGCTTTTTAGAT 60.557 41.667 18.38 0.00 0.00 1.98
64 65 3.242936 GCACGTGTTTCTGGCTTTTTAGA 60.243 43.478 18.38 0.00 0.00 2.10
65 66 3.042887 GCACGTGTTTCTGGCTTTTTAG 58.957 45.455 18.38 0.00 0.00 1.85
66 67 2.423892 TGCACGTGTTTCTGGCTTTTTA 59.576 40.909 18.38 0.00 0.00 1.52
67 68 1.203523 TGCACGTGTTTCTGGCTTTTT 59.796 42.857 18.38 0.00 0.00 1.94
68 69 0.814457 TGCACGTGTTTCTGGCTTTT 59.186 45.000 18.38 0.00 0.00 2.27
69 70 0.814457 TTGCACGTGTTTCTGGCTTT 59.186 45.000 18.38 0.00 0.00 3.51
70 71 0.814457 TTTGCACGTGTTTCTGGCTT 59.186 45.000 18.38 0.00 0.00 4.35
71 72 0.814457 TTTTGCACGTGTTTCTGGCT 59.186 45.000 18.38 0.00 0.00 4.75
72 73 1.634702 TTTTTGCACGTGTTTCTGGC 58.365 45.000 18.38 0.47 0.00 4.85
99 100 4.020543 TGGGCGCTTCCTATGTAATTTTT 58.979 39.130 7.64 0.00 34.39 1.94
100 101 3.626930 TGGGCGCTTCCTATGTAATTTT 58.373 40.909 7.64 0.00 34.39 1.82
101 102 3.118038 TCTGGGCGCTTCCTATGTAATTT 60.118 43.478 7.64 0.00 34.39 1.82
102 103 2.438021 TCTGGGCGCTTCCTATGTAATT 59.562 45.455 7.64 0.00 34.39 1.40
103 104 2.037772 CTCTGGGCGCTTCCTATGTAAT 59.962 50.000 7.64 0.00 34.39 1.89
104 105 1.412710 CTCTGGGCGCTTCCTATGTAA 59.587 52.381 7.64 0.00 34.39 2.41
105 106 1.040646 CTCTGGGCGCTTCCTATGTA 58.959 55.000 7.64 0.00 34.39 2.29
106 107 1.826024 CTCTGGGCGCTTCCTATGT 59.174 57.895 7.64 0.00 34.39 2.29
107 108 1.596477 GCTCTGGGCGCTTCCTATG 60.596 63.158 7.64 0.00 34.39 2.23
108 109 2.825264 GCTCTGGGCGCTTCCTAT 59.175 61.111 7.64 0.00 34.39 2.57
142 143 0.742281 TCATTTGGCTCGCTCTCAGC 60.742 55.000 0.00 0.00 38.02 4.26
143 144 1.005340 GTCATTTGGCTCGCTCTCAG 58.995 55.000 0.00 0.00 0.00 3.35
144 145 0.737367 CGTCATTTGGCTCGCTCTCA 60.737 55.000 0.00 0.00 0.00 3.27
145 146 0.737715 ACGTCATTTGGCTCGCTCTC 60.738 55.000 0.00 0.00 0.00 3.20
146 147 1.016130 CACGTCATTTGGCTCGCTCT 61.016 55.000 0.00 0.00 0.00 4.09
147 148 1.421485 CACGTCATTTGGCTCGCTC 59.579 57.895 0.00 0.00 0.00 5.03
148 149 2.680913 GCACGTCATTTGGCTCGCT 61.681 57.895 0.00 0.00 0.00 4.93
149 150 2.187599 AAGCACGTCATTTGGCTCGC 62.188 55.000 0.00 0.00 35.11 5.03
150 151 0.238289 AAAGCACGTCATTTGGCTCG 59.762 50.000 0.00 0.00 35.11 5.03
151 152 2.030805 AGAAAAGCACGTCATTTGGCTC 60.031 45.455 0.00 0.00 35.11 4.70
152 153 1.956477 AGAAAAGCACGTCATTTGGCT 59.044 42.857 0.00 0.00 38.45 4.75
153 154 2.422276 AGAAAAGCACGTCATTTGGC 57.578 45.000 0.00 0.00 0.00 4.52
154 155 4.111916 ACAAAGAAAAGCACGTCATTTGG 58.888 39.130 0.00 0.00 32.01 3.28
155 156 5.701029 AACAAAGAAAAGCACGTCATTTG 57.299 34.783 0.00 0.00 33.53 2.32
156 157 9.522804 TTTATAACAAAGAAAAGCACGTCATTT 57.477 25.926 0.00 0.00 0.00 2.32
157 158 9.691362 ATTTATAACAAAGAAAAGCACGTCATT 57.309 25.926 0.00 0.00 0.00 2.57
158 159 9.691362 AATTTATAACAAAGAAAAGCACGTCAT 57.309 25.926 0.00 0.00 0.00 3.06
159 160 9.522804 AAATTTATAACAAAGAAAAGCACGTCA 57.477 25.926 0.00 0.00 0.00 4.35
183 184 9.549078 ACCAGTGAAAAACAAAAGAAAACTAAA 57.451 25.926 0.00 0.00 0.00 1.85
184 185 9.549078 AACCAGTGAAAAACAAAAGAAAACTAA 57.451 25.926 0.00 0.00 0.00 2.24
185 186 9.549078 AAACCAGTGAAAAACAAAAGAAAACTA 57.451 25.926 0.00 0.00 0.00 2.24
186 187 8.445275 AAACCAGTGAAAAACAAAAGAAAACT 57.555 26.923 0.00 0.00 0.00 2.66
219 220 9.296400 CGAAGAAAACAAAGGAACAAAGAAATA 57.704 29.630 0.00 0.00 0.00 1.40
220 221 7.817478 ACGAAGAAAACAAAGGAACAAAGAAAT 59.183 29.630 0.00 0.00 0.00 2.17
221 222 7.149307 ACGAAGAAAACAAAGGAACAAAGAAA 58.851 30.769 0.00 0.00 0.00 2.52
222 223 6.683715 ACGAAGAAAACAAAGGAACAAAGAA 58.316 32.000 0.00 0.00 0.00 2.52
223 224 6.150474 AGACGAAGAAAACAAAGGAACAAAGA 59.850 34.615 0.00 0.00 0.00 2.52
224 225 6.322491 AGACGAAGAAAACAAAGGAACAAAG 58.678 36.000 0.00 0.00 0.00 2.77
225 226 6.262193 AGACGAAGAAAACAAAGGAACAAA 57.738 33.333 0.00 0.00 0.00 2.83
226 227 5.890424 AGACGAAGAAAACAAAGGAACAA 57.110 34.783 0.00 0.00 0.00 2.83
227 228 5.890424 AAGACGAAGAAAACAAAGGAACA 57.110 34.783 0.00 0.00 0.00 3.18
228 229 8.851960 AATAAAGACGAAGAAAACAAAGGAAC 57.148 30.769 0.00 0.00 0.00 3.62
229 230 9.296400 CAAATAAAGACGAAGAAAACAAAGGAA 57.704 29.630 0.00 0.00 0.00 3.36
230 231 8.463607 ACAAATAAAGACGAAGAAAACAAAGGA 58.536 29.630 0.00 0.00 0.00 3.36
231 232 8.531530 CACAAATAAAGACGAAGAAAACAAAGG 58.468 33.333 0.00 0.00 0.00 3.11
232 233 9.072294 ACACAAATAAAGACGAAGAAAACAAAG 57.928 29.630 0.00 0.00 0.00 2.77
233 234 8.973835 ACACAAATAAAGACGAAGAAAACAAA 57.026 26.923 0.00 0.00 0.00 2.83
234 235 8.973835 AACACAAATAAAGACGAAGAAAACAA 57.026 26.923 0.00 0.00 0.00 2.83
235 236 8.855279 CAAACACAAATAAAGACGAAGAAAACA 58.145 29.630 0.00 0.00 0.00 2.83
236 237 8.856247 ACAAACACAAATAAAGACGAAGAAAAC 58.144 29.630 0.00 0.00 0.00 2.43
237 238 8.973835 ACAAACACAAATAAAGACGAAGAAAA 57.026 26.923 0.00 0.00 0.00 2.29
238 239 8.973835 AACAAACACAAATAAAGACGAAGAAA 57.026 26.923 0.00 0.00 0.00 2.52
239 240 8.855279 CAAACAAACACAAATAAAGACGAAGAA 58.145 29.630 0.00 0.00 0.00 2.52
240 241 8.024285 ACAAACAAACACAAATAAAGACGAAGA 58.976 29.630 0.00 0.00 0.00 2.87
241 242 8.168681 ACAAACAAACACAAATAAAGACGAAG 57.831 30.769 0.00 0.00 0.00 3.79
242 243 8.428536 CAACAAACAAACACAAATAAAGACGAA 58.571 29.630 0.00 0.00 0.00 3.85
243 244 7.808381 TCAACAAACAAACACAAATAAAGACGA 59.192 29.630 0.00 0.00 0.00 4.20
244 245 7.943952 TCAACAAACAAACACAAATAAAGACG 58.056 30.769 0.00 0.00 0.00 4.18
361 362 9.106070 GACCGTTTAGATCATTAAAGTAATGGT 57.894 33.333 7.87 0.00 44.33 3.55
362 363 9.326413 AGACCGTTTAGATCATTAAAGTAATGG 57.674 33.333 7.87 0.00 44.33 3.16
395 396 2.289819 ACGCGAACTCCCTCCATAAAAA 60.290 45.455 15.93 0.00 0.00 1.94
396 397 1.276989 ACGCGAACTCCCTCCATAAAA 59.723 47.619 15.93 0.00 0.00 1.52
397 398 0.899720 ACGCGAACTCCCTCCATAAA 59.100 50.000 15.93 0.00 0.00 1.40
398 399 0.899720 AACGCGAACTCCCTCCATAA 59.100 50.000 15.93 0.00 0.00 1.90
399 400 1.766494 TAACGCGAACTCCCTCCATA 58.234 50.000 15.93 0.00 0.00 2.74
400 401 0.899720 TTAACGCGAACTCCCTCCAT 59.100 50.000 15.93 0.00 0.00 3.41
401 402 0.680618 TTTAACGCGAACTCCCTCCA 59.319 50.000 15.93 0.00 0.00 3.86
402 403 1.073964 GTTTAACGCGAACTCCCTCC 58.926 55.000 15.93 0.00 0.00 4.30
403 404 1.787012 TGTTTAACGCGAACTCCCTC 58.213 50.000 15.93 0.00 0.00 4.30
404 405 2.467566 ATGTTTAACGCGAACTCCCT 57.532 45.000 15.93 0.00 0.00 4.20
405 406 3.187842 AGAAATGTTTAACGCGAACTCCC 59.812 43.478 15.93 0.00 0.00 4.30
406 407 4.400036 AGAAATGTTTAACGCGAACTCC 57.600 40.909 15.93 0.00 0.00 3.85
407 408 7.825627 TTTAAGAAATGTTTAACGCGAACTC 57.174 32.000 15.93 0.80 0.00 3.01
408 409 9.321590 GTATTTAAGAAATGTTTAACGCGAACT 57.678 29.630 15.93 0.00 32.38 3.01
409 410 9.105206 TGTATTTAAGAAATGTTTAACGCGAAC 57.895 29.630 15.93 7.81 32.38 3.95
410 411 9.828852 ATGTATTTAAGAAATGTTTAACGCGAA 57.171 25.926 15.93 0.00 32.38 4.70
411 412 9.268255 CATGTATTTAAGAAATGTTTAACGCGA 57.732 29.630 15.93 0.00 32.38 5.87
412 413 9.268255 TCATGTATTTAAGAAATGTTTAACGCG 57.732 29.630 3.53 3.53 32.38 6.01
473 474 0.250081 GGGGCGCCATGTTTCAAAAA 60.250 50.000 30.85 0.00 0.00 1.94
474 475 1.369321 GGGGCGCCATGTTTCAAAA 59.631 52.632 30.85 0.00 0.00 2.44
475 476 2.925262 CGGGGCGCCATGTTTCAAA 61.925 57.895 30.85 0.00 0.00 2.69
476 477 3.369400 CGGGGCGCCATGTTTCAA 61.369 61.111 30.85 0.00 0.00 2.69
493 494 4.265056 AACACGACACCCTGGCCC 62.265 66.667 0.00 0.00 0.00 5.80
494 495 2.668550 GAACACGACACCCTGGCC 60.669 66.667 0.00 0.00 0.00 5.36
495 496 1.668151 GAGAACACGACACCCTGGC 60.668 63.158 0.00 0.00 0.00 4.85
496 497 1.202582 CTAGAGAACACGACACCCTGG 59.797 57.143 0.00 0.00 0.00 4.45
497 498 1.402984 GCTAGAGAACACGACACCCTG 60.403 57.143 0.00 0.00 0.00 4.45
498 499 0.889306 GCTAGAGAACACGACACCCT 59.111 55.000 0.00 0.00 0.00 4.34
499 500 0.601558 TGCTAGAGAACACGACACCC 59.398 55.000 0.00 0.00 0.00 4.61
500 501 2.263077 CATGCTAGAGAACACGACACC 58.737 52.381 0.00 0.00 0.00 4.16
501 502 2.263077 CCATGCTAGAGAACACGACAC 58.737 52.381 0.00 0.00 0.00 3.67
502 503 1.893137 ACCATGCTAGAGAACACGACA 59.107 47.619 0.00 0.00 0.00 4.35
503 504 2.263077 CACCATGCTAGAGAACACGAC 58.737 52.381 0.00 0.00 0.00 4.34
504 505 1.404181 GCACCATGCTAGAGAACACGA 60.404 52.381 0.00 0.00 40.96 4.35
505 506 1.002366 GCACCATGCTAGAGAACACG 58.998 55.000 0.00 0.00 40.96 4.49
506 507 1.373570 GGCACCATGCTAGAGAACAC 58.626 55.000 0.00 0.00 44.28 3.32
507 508 3.861341 GGCACCATGCTAGAGAACA 57.139 52.632 0.00 0.00 44.28 3.18
525 526 4.047125 ATGACACCTTGGGCGGGG 62.047 66.667 0.00 0.00 0.00 5.73
526 527 2.751436 CATGACACCTTGGGCGGG 60.751 66.667 0.00 0.00 0.00 6.13
527 528 2.535485 TAGCATGACACCTTGGGCGG 62.535 60.000 0.00 0.00 0.00 6.13
528 529 0.464373 ATAGCATGACACCTTGGGCG 60.464 55.000 0.00 0.00 0.00 6.13
529 530 1.767759 AATAGCATGACACCTTGGGC 58.232 50.000 0.00 0.00 0.00 5.36
530 531 3.884895 TGTAATAGCATGACACCTTGGG 58.115 45.455 0.00 0.00 0.00 4.12
531 532 4.276678 CCATGTAATAGCATGACACCTTGG 59.723 45.833 0.00 0.00 46.65 3.61
532 533 4.276678 CCCATGTAATAGCATGACACCTTG 59.723 45.833 0.00 0.00 46.65 3.61
533 534 4.165950 TCCCATGTAATAGCATGACACCTT 59.834 41.667 0.00 0.00 46.65 3.50
534 535 3.716353 TCCCATGTAATAGCATGACACCT 59.284 43.478 0.00 0.00 46.65 4.00
535 536 4.085357 TCCCATGTAATAGCATGACACC 57.915 45.455 0.00 0.00 46.65 4.16
536 537 4.275936 GGTTCCCATGTAATAGCATGACAC 59.724 45.833 0.00 2.03 46.65 3.67
537 538 4.080072 TGGTTCCCATGTAATAGCATGACA 60.080 41.667 0.00 0.00 46.65 3.58
538 539 4.460263 TGGTTCCCATGTAATAGCATGAC 58.540 43.478 0.00 0.00 46.65 3.06
539 540 4.787135 TGGTTCCCATGTAATAGCATGA 57.213 40.909 0.00 0.00 46.65 3.07
540 541 4.644234 TGTTGGTTCCCATGTAATAGCATG 59.356 41.667 0.00 0.00 44.18 4.06
541 542 4.865905 TGTTGGTTCCCATGTAATAGCAT 58.134 39.130 0.00 0.00 31.53 3.79
542 543 4.308526 TGTTGGTTCCCATGTAATAGCA 57.691 40.909 0.00 0.00 31.53 3.49
543 544 5.852282 AATGTTGGTTCCCATGTAATAGC 57.148 39.130 0.00 0.00 31.53 2.97
569 570 8.676401 CCAAACTTGATTTTCCATGAAGTTTTT 58.324 29.630 13.51 0.00 41.71 1.94
570 571 8.046107 TCCAAACTTGATTTTCCATGAAGTTTT 58.954 29.630 13.51 1.87 41.71 2.43
571 572 7.563906 TCCAAACTTGATTTTCCATGAAGTTT 58.436 30.769 11.38 11.38 43.99 2.66
572 573 7.123355 TCCAAACTTGATTTTCCATGAAGTT 57.877 32.000 0.00 0.00 38.25 2.66
573 574 6.729690 TCCAAACTTGATTTTCCATGAAGT 57.270 33.333 0.00 0.00 0.00 3.01
574 575 7.212274 ACTTCCAAACTTGATTTTCCATGAAG 58.788 34.615 0.00 0.00 0.00 3.02
575 576 7.123355 ACTTCCAAACTTGATTTTCCATGAA 57.877 32.000 0.00 0.00 0.00 2.57
576 577 6.729690 ACTTCCAAACTTGATTTTCCATGA 57.270 33.333 0.00 0.00 0.00 3.07
577 578 7.041848 GGAAACTTCCAAACTTGATTTTCCATG 60.042 37.037 3.50 0.00 46.76 3.66
578 579 6.992123 GGAAACTTCCAAACTTGATTTTCCAT 59.008 34.615 3.50 0.00 46.76 3.41
579 580 6.345298 GGAAACTTCCAAACTTGATTTTCCA 58.655 36.000 3.50 0.00 46.76 3.53
580 581 6.844696 GGAAACTTCCAAACTTGATTTTCC 57.155 37.500 3.50 0.00 46.76 3.13
614 615 8.541899 TCACCCTCTTAACATTTTACCTTTTT 57.458 30.769 0.00 0.00 0.00 1.94
615 616 8.721133 ATCACCCTCTTAACATTTTACCTTTT 57.279 30.769 0.00 0.00 0.00 2.27
616 617 9.239551 GTATCACCCTCTTAACATTTTACCTTT 57.760 33.333 0.00 0.00 0.00 3.11
617 618 8.612145 AGTATCACCCTCTTAACATTTTACCTT 58.388 33.333 0.00 0.00 0.00 3.50
618 619 8.159229 AGTATCACCCTCTTAACATTTTACCT 57.841 34.615 0.00 0.00 0.00 3.08
619 620 8.803397 AAGTATCACCCTCTTAACATTTTACC 57.197 34.615 0.00 0.00 0.00 2.85
624 625 8.903820 GCATTAAAGTATCACCCTCTTAACATT 58.096 33.333 0.00 0.00 0.00 2.71
625 626 7.502561 GGCATTAAAGTATCACCCTCTTAACAT 59.497 37.037 0.00 0.00 0.00 2.71
626 627 6.826741 GGCATTAAAGTATCACCCTCTTAACA 59.173 38.462 0.00 0.00 0.00 2.41
627 628 6.826741 TGGCATTAAAGTATCACCCTCTTAAC 59.173 38.462 0.00 0.00 0.00 2.01
628 629 6.964464 TGGCATTAAAGTATCACCCTCTTAA 58.036 36.000 0.00 0.00 0.00 1.85
629 630 6.569127 TGGCATTAAAGTATCACCCTCTTA 57.431 37.500 0.00 0.00 0.00 2.10
630 631 5.450818 TGGCATTAAAGTATCACCCTCTT 57.549 39.130 0.00 0.00 0.00 2.85
631 632 5.103940 ACATGGCATTAAAGTATCACCCTCT 60.104 40.000 0.00 0.00 0.00 3.69
632 633 5.009010 CACATGGCATTAAAGTATCACCCTC 59.991 44.000 0.00 0.00 0.00 4.30
633 634 4.889409 CACATGGCATTAAAGTATCACCCT 59.111 41.667 0.00 0.00 0.00 4.34
634 635 4.887071 TCACATGGCATTAAAGTATCACCC 59.113 41.667 0.00 0.00 0.00 4.61
635 636 6.449635 TTCACATGGCATTAAAGTATCACC 57.550 37.500 0.00 0.00 0.00 4.02
636 637 6.498304 CCTTCACATGGCATTAAAGTATCAC 58.502 40.000 0.00 0.00 0.00 3.06
637 638 6.698008 CCTTCACATGGCATTAAAGTATCA 57.302 37.500 0.00 0.00 0.00 2.15
650 651 1.880894 CTGTGCTGCCTTCACATGG 59.119 57.895 0.00 0.00 42.74 3.66
651 652 1.211969 GCTGTGCTGCCTTCACATG 59.788 57.895 0.00 0.00 42.74 3.21
652 653 1.228337 TGCTGTGCTGCCTTCACAT 60.228 52.632 0.00 0.00 42.74 3.21
653 654 1.895231 CTGCTGTGCTGCCTTCACA 60.895 57.895 0.00 3.36 41.62 3.58
654 655 2.623915 CCTGCTGTGCTGCCTTCAC 61.624 63.158 0.00 0.00 35.14 3.18
655 656 2.281970 CCTGCTGTGCTGCCTTCA 60.282 61.111 0.00 0.00 0.00 3.02
656 657 1.174712 TTTCCTGCTGTGCTGCCTTC 61.175 55.000 0.00 0.00 0.00 3.46
657 658 0.756442 TTTTCCTGCTGTGCTGCCTT 60.756 50.000 0.00 0.00 0.00 4.35
658 659 1.152694 TTTTCCTGCTGTGCTGCCT 60.153 52.632 0.00 0.00 0.00 4.75
659 660 1.006922 GTTTTCCTGCTGTGCTGCC 60.007 57.895 0.00 0.00 0.00 4.85
660 661 0.595825 GTGTTTTCCTGCTGTGCTGC 60.596 55.000 0.00 0.00 0.00 5.25
661 662 0.317269 CGTGTTTTCCTGCTGTGCTG 60.317 55.000 0.00 0.00 0.00 4.41
662 663 2.024918 CGTGTTTTCCTGCTGTGCT 58.975 52.632 0.00 0.00 0.00 4.40
663 664 1.658409 GCGTGTTTTCCTGCTGTGC 60.658 57.895 0.00 0.00 0.00 4.57
664 665 1.369209 CGCGTGTTTTCCTGCTGTG 60.369 57.895 0.00 0.00 0.00 3.66
665 666 3.022287 CGCGTGTTTTCCTGCTGT 58.978 55.556 0.00 0.00 0.00 4.40
666 667 2.427410 GCGCGTGTTTTCCTGCTG 60.427 61.111 8.43 0.00 0.00 4.41
667 668 4.012895 CGCGCGTGTTTTCCTGCT 62.013 61.111 24.19 0.00 0.00 4.24
668 669 2.975167 TTTCGCGCGTGTTTTCCTGC 62.975 55.000 30.98 0.00 0.00 4.85
669 670 1.010574 TTTCGCGCGTGTTTTCCTG 60.011 52.632 30.98 0.00 0.00 3.86
670 671 1.010462 GTTTCGCGCGTGTTTTCCT 60.010 52.632 30.98 0.00 0.00 3.36
671 672 2.007114 GGTTTCGCGCGTGTTTTCC 61.007 57.895 30.98 19.14 0.00 3.13
672 673 1.297745 TGGTTTCGCGCGTGTTTTC 60.298 52.632 30.98 15.45 0.00 2.29
673 674 1.584225 GTGGTTTCGCGCGTGTTTT 60.584 52.632 30.98 0.00 0.00 2.43
883 924 7.225784 TCAATTAATCAACTGGCTTTGCTTA 57.774 32.000 0.00 0.00 0.00 3.09
902 994 3.304257 CGCTCTGTGACTTTGCTTCAATT 60.304 43.478 0.00 0.00 0.00 2.32
1072 1187 4.400961 GAGCCGAGCCCAGCTGTT 62.401 66.667 13.81 0.00 39.88 3.16
1074 1189 4.527583 GAGAGCCGAGCCCAGCTG 62.528 72.222 6.78 6.78 39.88 4.24
1077 1192 3.847602 CAGGAGAGCCGAGCCCAG 61.848 72.222 0.00 0.00 39.96 4.45
1121 1245 4.406173 CGTCGTCGTCCTGCTGCT 62.406 66.667 0.00 0.00 0.00 4.24
1122 1246 4.400109 TCGTCGTCGTCCTGCTGC 62.400 66.667 1.33 0.00 38.33 5.25
1123 1247 2.502080 GTCGTCGTCGTCCTGCTG 60.502 66.667 1.33 0.00 38.33 4.41
1124 1248 3.735029 GGTCGTCGTCGTCCTGCT 61.735 66.667 10.58 0.00 40.85 4.24
1125 1249 3.948086 CTGGTCGTCGTCGTCCTGC 62.948 68.421 17.27 0.00 43.48 4.85
1126 1250 2.176055 CTGGTCGTCGTCGTCCTG 59.824 66.667 17.27 13.55 43.48 3.86
1127 1251 3.054503 CCTGGTCGTCGTCGTCCT 61.055 66.667 17.27 0.00 43.48 3.85
1128 1252 4.773117 GCCTGGTCGTCGTCGTCC 62.773 72.222 10.88 10.88 43.41 4.79
1129 1253 2.307137 CTAGCCTGGTCGTCGTCGTC 62.307 65.000 1.33 0.00 38.33 4.20
1363 1532 4.085619 GCACAAGTTAACAGCAAATGAACG 60.086 41.667 8.61 0.00 0.00 3.95
1417 1597 5.635417 AATTGGTTTCTTTCTAGCTCTGC 57.365 39.130 0.00 0.00 0.00 4.26
1461 1646 5.918011 CGTCAAGCATTAAAAACCAAAGCTA 59.082 36.000 0.00 0.00 0.00 3.32
1540 1737 1.168714 GGCTTTGATCGCCTGAAACT 58.831 50.000 3.09 0.00 44.17 2.66
1575 1792 3.489180 AAGTGTCGGTATCTTCAGACG 57.511 47.619 0.00 0.00 35.82 4.18
1627 1844 4.040339 TGAACTCTGAACTTGCAGGATGTA 59.960 41.667 1.40 0.00 39.31 2.29
1630 1847 3.777106 TGAACTCTGAACTTGCAGGAT 57.223 42.857 1.40 0.00 36.55 3.24
1681 1902 0.315251 CTCTGCAGACAACGACTCCA 59.685 55.000 13.74 0.00 0.00 3.86
1705 1926 3.838244 TCTTGGGAGTACATGGTATGC 57.162 47.619 0.00 0.00 0.00 3.14
1733 4893 9.632807 GCCACTTTTTGTAATAATGTAATCACA 57.367 29.630 0.00 0.00 39.52 3.58
1734 4894 8.794406 CGCCACTTTTTGTAATAATGTAATCAC 58.206 33.333 0.00 0.00 0.00 3.06
1735 4895 8.731605 TCGCCACTTTTTGTAATAATGTAATCA 58.268 29.630 0.00 0.00 0.00 2.57
1736 4896 9.562583 TTCGCCACTTTTTGTAATAATGTAATC 57.437 29.630 0.00 0.00 0.00 1.75
1817 4977 8.700973 AGGAGAGGATGTTTATTTAGAGAAGAC 58.299 37.037 0.00 0.00 0.00 3.01
1846 5006 4.851639 AATGGATCAGGCTTGTTCTAGT 57.148 40.909 6.82 0.00 0.00 2.57
1881 5045 1.152673 GGCCATGATCCCCCAGAAC 60.153 63.158 0.00 0.00 0.00 3.01
1882 5046 1.000590 ATGGCCATGATCCCCCAGAA 61.001 55.000 20.04 0.00 0.00 3.02
1883 5047 1.000590 AATGGCCATGATCCCCCAGA 61.001 55.000 21.63 0.00 0.00 3.86
1926 5238 6.481313 TCTTCAGACAAACTCAGTTTCATCTG 59.519 38.462 23.97 23.97 41.83 2.90
1929 5247 9.160496 GATATCTTCAGACAAACTCAGTTTCAT 57.840 33.333 0.00 0.00 33.10 2.57
1993 5321 8.633408 CAATTCTTAATTTCAGTTTCAGCGAAG 58.367 33.333 0.00 0.00 0.00 3.79
2245 5647 0.834687 ACCAAGTTCACCTCCGCCTA 60.835 55.000 0.00 0.00 0.00 3.93


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

AutoCloner maintained by Alex Coulton.