Multiple sequence alignment - TraesCS2D01G068400

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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 TraesCS2D01G068400 chr2D 100.000 5298 0 0 1 5298 28755281 28760578 0.000000e+00 9784.0
1 TraesCS2D01G068400 chr2A 94.544 4637 168 23 2 4610 30560355 30564934 0.000000e+00 7083.0
2 TraesCS2D01G068400 chr2A 91.457 199 16 1 5101 5298 30565466 30565664 6.760000e-69 272.0
3 TraesCS2D01G068400 chr2A 92.913 127 9 0 4736 4862 30564996 30565122 9.060000e-43 185.0
4 TraesCS2D01G068400 chr2B 87.713 1880 172 30 2683 4554 46103483 46105311 0.000000e+00 2137.0
5 TraesCS2D01G068400 chr2B 93.139 1370 66 12 1289 2642 46101732 46103089 0.000000e+00 1984.0
6 TraesCS2D01G068400 chr2B 88.942 1266 115 12 2 1245 46100459 46101721 0.000000e+00 1539.0
7 TraesCS2D01G068400 chr2B 83.708 178 19 6 4877 5048 667259390 667259217 5.490000e-35 159.0
8 TraesCS2D01G068400 chr4D 83.883 273 28 10 5041 5298 9740736 9741007 4.100000e-61 246.0
9 TraesCS2D01G068400 chr1A 83.333 264 26 9 5050 5298 439690265 439690005 1.480000e-55 228.0
10 TraesCS2D01G068400 chr1A 82.707 266 27 14 5050 5298 515287886 515287623 8.930000e-53 219.0
11 TraesCS2D01G068400 chr3A 81.609 261 31 9 5052 5298 212746348 212746091 3.240000e-47 200.0
12 TraesCS2D01G068400 chr3A 83.616 177 21 4 4877 5048 176148039 176148212 5.490000e-35 159.0
13 TraesCS2D01G068400 chr3B 84.746 177 20 4 4877 5048 225173368 225173194 2.540000e-38 171.0
14 TraesCS2D01G068400 chr1B 84.746 177 18 6 4877 5048 26268924 26268752 9.130000e-38 169.0
15 TraesCS2D01G068400 chr6D 84.483 174 22 5 4877 5048 148175164 148175334 3.280000e-37 167.0
16 TraesCS2D01G068400 chr6A 82.915 199 18 10 5114 5298 158069726 158069922 1.180000e-36 165.0
17 TraesCS2D01G068400 chr6A 84.181 177 20 5 4877 5048 169514968 169514795 1.180000e-36 165.0
18 TraesCS2D01G068400 chr1D 84.181 177 21 6 4877 5048 397047586 397047760 1.180000e-36 165.0
19 TraesCS2D01G068400 chr5A 83.889 180 18 6 4877 5048 693649467 693649643 1.530000e-35 161.0
20 TraesCS2D01G068400 chr3D 83.616 177 22 4 4877 5048 153507194 153507020 5.490000e-35 159.0
21 TraesCS2D01G068400 chr7B 91.304 115 8 2 5044 5158 535497541 535497653 7.100000e-34 156.0
22 TraesCS2D01G068400 chr7B 86.420 81 7 2 5222 5298 179897796 179897876 9.450000e-13 86.1


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 TraesCS2D01G068400 chr2D 28755281 28760578 5297 False 9784.000000 9784 100.000000 1 5298 1 chr2D.!!$F1 5297
1 TraesCS2D01G068400 chr2A 30560355 30565664 5309 False 2513.333333 7083 92.971333 2 5298 3 chr2A.!!$F1 5296
2 TraesCS2D01G068400 chr2B 46100459 46105311 4852 False 1886.666667 2137 89.931333 2 4554 3 chr2B.!!$F1 4552

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
619 623 0.179936 CTGATGAGGGAGGCAGAACC 59.820 60.000 0.00 0.0 39.61 3.62 F
645 649 1.870580 CGGTGACTCAAAGCGGTGTAA 60.871 52.381 0.00 0.0 35.01 2.41 F
647 651 2.159627 GGTGACTCAAAGCGGTGTAATG 59.840 50.000 0.00 0.0 0.00 1.90 F
1277 1300 2.675658 TTTTAGGCCTTCCTGTGCTT 57.324 45.000 12.58 0.0 44.08 3.91 F
3142 3535 4.451435 GGACCAACAAACTTACTAGCACTC 59.549 45.833 0.00 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2112 2146 2.919229 CAGCGCAAAATTTCATCTCACC 59.081 45.455 11.47 0.0 0.00 4.02 R
2300 2335 7.500892 ACATAAAAGATAACATTATGGCCACGA 59.499 33.333 8.16 0.0 39.95 4.35 R
3142 3535 9.689976 TGTAATTTTCCAAAACTGTGATACATG 57.310 29.630 0.00 0.0 0.00 3.21 R
3686 4081 3.513462 TTCATTTATTACGGCGATGCG 57.487 42.857 16.62 0.0 0.00 4.73 R
4729 5136 0.105964 TCCGAATTCAGGTATGGCCG 59.894 55.000 6.22 0.0 43.70 6.13 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
29 30 3.129502 CACCGCCAGCCTCACATG 61.130 66.667 0.00 0.00 0.00 3.21
126 127 3.418913 CACCGCGGCATCGAACAA 61.419 61.111 28.58 0.00 39.00 2.83
167 168 0.992431 ATCAATCTGCAGGCCTCCCT 60.992 55.000 15.13 0.00 44.25 4.20
224 225 3.260100 CTTGACCCCCAGCCCACT 61.260 66.667 0.00 0.00 0.00 4.00
267 268 3.087031 CAGCTTCCAATTGACCAGACAT 58.913 45.455 7.12 0.00 0.00 3.06
296 298 3.612251 GCTTCAGCATGCCCACAT 58.388 55.556 15.66 0.00 41.59 3.21
393 396 1.728069 GCCGTAGCGATGAGAGTCA 59.272 57.895 0.00 0.00 0.00 3.41
431 434 1.478510 CTCCCAGTACGTCAGAGCATT 59.521 52.381 0.00 0.00 0.00 3.56
503 506 1.971357 AGGTGAATCTTGGACAGACGT 59.029 47.619 0.00 0.00 32.83 4.34
516 519 2.298610 ACAGACGTGTCACAGAGAGAA 58.701 47.619 3.42 0.00 26.76 2.87
531 535 1.002087 AGAGAAGCAACCCCAAGTACG 59.998 52.381 0.00 0.00 0.00 3.67
534 538 0.536460 AAGCAACCCCAAGTACGTGG 60.536 55.000 19.78 19.78 38.51 4.94
619 623 0.179936 CTGATGAGGGAGGCAGAACC 59.820 60.000 0.00 0.00 39.61 3.62
635 639 4.680237 CCCGCAGCGGTGACTCAA 62.680 66.667 31.68 0.00 46.80 3.02
636 640 2.664851 CCGCAGCGGTGACTCAAA 60.665 61.111 26.69 0.00 42.73 2.69
645 649 1.870580 CGGTGACTCAAAGCGGTGTAA 60.871 52.381 0.00 0.00 35.01 2.41
647 651 2.159627 GGTGACTCAAAGCGGTGTAATG 59.840 50.000 0.00 0.00 0.00 1.90
767 771 4.567195 TGGATCCACCAGACAGCT 57.433 55.556 11.44 0.00 44.64 4.24
816 827 3.303135 ACGCGGCCACTCTCTCAA 61.303 61.111 12.47 0.00 0.00 3.02
1184 1207 4.335647 CCCCAACTGTGAGCGCCT 62.336 66.667 2.29 0.00 0.00 5.52
1253 1276 4.676924 GTCTGCAAATCAAGTGCTTTGTAC 59.323 41.667 8.83 0.00 42.69 2.90
1254 1277 4.580167 TCTGCAAATCAAGTGCTTTGTACT 59.420 37.500 8.83 0.00 42.69 2.73
1255 1278 5.762711 TCTGCAAATCAAGTGCTTTGTACTA 59.237 36.000 8.83 0.00 42.69 1.82
1256 1279 6.000891 TGCAAATCAAGTGCTTTGTACTAG 57.999 37.500 8.83 0.00 42.69 2.57
1257 1280 5.762711 TGCAAATCAAGTGCTTTGTACTAGA 59.237 36.000 0.00 0.00 42.69 2.43
1277 1300 2.675658 TTTTAGGCCTTCCTGTGCTT 57.324 45.000 12.58 0.00 44.08 3.91
1297 1320 5.163663 TGCTTGTTGAGGTGTTTTAAGACTG 60.164 40.000 0.00 0.00 0.00 3.51
1300 1323 6.827586 TGTTGAGGTGTTTTAAGACTGTTT 57.172 33.333 0.00 0.00 0.00 2.83
1310 1333 7.805071 GTGTTTTAAGACTGTTTGATGATCCAG 59.195 37.037 0.00 0.00 0.00 3.86
1317 1340 6.013379 AGACTGTTTGATGATCCAGTTTAGGA 60.013 38.462 4.69 0.00 43.01 2.94
1448 1471 6.730960 AACAAATAGCAGCAATTGAATTGG 57.269 33.333 18.52 5.10 40.57 3.16
1497 1520 6.769512 ACTCACAATTCACTTTAGAGCCTTA 58.230 36.000 0.00 0.00 0.00 2.69
1498 1521 7.398024 ACTCACAATTCACTTTAGAGCCTTAT 58.602 34.615 0.00 0.00 0.00 1.73
1506 1529 6.753180 TCACTTTAGAGCCTTATAGATGCAG 58.247 40.000 0.00 0.00 0.00 4.41
1602 1625 4.938080 CACTCGTGCTTGATAGAATAGGT 58.062 43.478 0.00 0.00 0.00 3.08
1740 1774 8.499403 AAAGCTGGATAACACTCTAGATTTTC 57.501 34.615 0.00 0.00 38.63 2.29
1966 2000 6.828273 CCCAACTGTTGATTTACATATCCTGA 59.172 38.462 21.49 0.00 0.00 3.86
2069 2103 8.761575 ACCACAATTTTGTTTATCATGCTAAG 57.238 30.769 0.00 0.00 39.91 2.18
2168 2203 9.715119 AAGGCCTATAAATTTGAAGGAATAAGT 57.285 29.630 19.53 1.61 0.00 2.24
2671 2710 9.643693 CATTGTTCTAATTGCTTTACTCCATTT 57.356 29.630 0.00 0.00 0.00 2.32
2839 3231 7.228507 TCGAGGCTAATACAATATTGTTGCAAT 59.771 33.333 25.31 10.69 42.35 3.56
2852 3244 9.860898 AATATTGTTGCAATCTTTTAAGGAGAC 57.139 29.630 0.59 0.00 0.00 3.36
3142 3535 4.451435 GGACCAACAAACTTACTAGCACTC 59.549 45.833 0.00 0.00 0.00 3.51
3308 3703 9.039870 GGAGTCTTCATGAATGAAATACACTAG 57.960 37.037 8.96 0.00 45.26 2.57
3429 3824 7.616313 TGAAAACTTGATTAGTGTTTTGGGTT 58.384 30.769 7.63 0.00 41.89 4.11
3686 4081 5.705609 AGTTCACATTTTCACCCACATAC 57.294 39.130 0.00 0.00 0.00 2.39
3708 4103 4.081761 CGCATCGCCGTAATAAATGAATC 58.918 43.478 0.00 0.00 0.00 2.52
3905 4300 8.974060 TTACATAGAACACCAAAGAAGAAACT 57.026 30.769 0.00 0.00 0.00 2.66
4011 4406 1.067364 TGCATGACCTGTTTGTTGCTG 59.933 47.619 0.00 0.00 0.00 4.41
4013 4408 1.067364 CATGACCTGTTTGTTGCTGCA 59.933 47.619 0.00 0.00 0.00 4.41
4117 4513 0.953960 GGTGCCGTCCCTTGTTACAG 60.954 60.000 0.00 0.00 0.00 2.74
4149 4545 5.699915 GGAGTACTTTTTACAAGTCTGACCC 59.300 44.000 3.76 0.00 0.00 4.46
4240 4636 1.845143 AGGCAGATCAGAATGCTTCCT 59.155 47.619 10.05 0.00 42.19 3.36
4291 4687 1.491563 GAACGCAGCGGTTGTACTG 59.508 57.895 21.15 0.00 36.96 2.74
4334 4730 1.269166 CGTGCCTGTTCTTACTAGCG 58.731 55.000 0.00 0.00 0.00 4.26
4399 4795 0.802222 GATCGCGTTGCTAGCTCACA 60.802 55.000 17.23 0.00 0.00 3.58
4400 4796 0.179100 ATCGCGTTGCTAGCTCACAT 60.179 50.000 17.23 0.26 0.00 3.21
4401 4797 1.078201 TCGCGTTGCTAGCTCACATG 61.078 55.000 17.23 7.81 0.00 3.21
4402 4798 1.717937 GCGTTGCTAGCTCACATGG 59.282 57.895 17.23 2.00 0.00 3.66
4403 4799 1.709147 GCGTTGCTAGCTCACATGGG 61.709 60.000 17.23 0.00 0.00 4.00
4404 4800 0.391661 CGTTGCTAGCTCACATGGGT 60.392 55.000 17.23 0.00 0.00 4.51
4405 4801 1.134818 CGTTGCTAGCTCACATGGGTA 60.135 52.381 17.23 0.00 0.00 3.69
4406 4802 2.483714 CGTTGCTAGCTCACATGGGTAT 60.484 50.000 17.23 0.00 0.00 2.73
4407 4803 3.545703 GTTGCTAGCTCACATGGGTATT 58.454 45.455 17.23 0.00 0.00 1.89
4408 4804 3.475566 TGCTAGCTCACATGGGTATTC 57.524 47.619 17.23 0.00 0.00 1.75
4409 4805 3.041211 TGCTAGCTCACATGGGTATTCT 58.959 45.455 17.23 0.00 0.00 2.40
4410 4806 3.181462 TGCTAGCTCACATGGGTATTCTG 60.181 47.826 17.23 0.00 0.00 3.02
4411 4807 3.070159 GCTAGCTCACATGGGTATTCTGA 59.930 47.826 7.70 0.00 0.00 3.27
4514 4915 0.253044 TGCCACTCTGCCCTGTTATC 59.747 55.000 0.00 0.00 0.00 1.75
4530 4931 1.064003 TATCCCTGTTGCTGGTGTGT 58.936 50.000 0.00 0.00 0.00 3.72
4554 4960 8.946085 TGTTGAGAGTTGATGGTTAAATATGTC 58.054 33.333 0.00 0.00 0.00 3.06
4588 4995 0.716108 CGGCTGTCGTTCTGAATGAC 59.284 55.000 27.72 27.72 45.51 3.06
4591 4998 1.935300 GCTGTCGTTCTGAATGACCGT 60.935 52.381 29.91 0.00 44.87 4.83
4592 4999 2.670229 GCTGTCGTTCTGAATGACCGTA 60.670 50.000 29.91 16.69 44.87 4.02
4620 5027 3.431055 CTTGGGCAAGTCGCAACA 58.569 55.556 0.00 0.00 45.17 3.33
4621 5028 1.732917 CTTGGGCAAGTCGCAACAA 59.267 52.632 0.00 0.00 45.17 2.83
4622 5029 0.318107 CTTGGGCAAGTCGCAACAAG 60.318 55.000 6.41 6.41 44.95 3.16
4623 5030 1.034838 TTGGGCAAGTCGCAACAAGT 61.035 50.000 0.00 0.00 45.17 3.16
4624 5031 0.179043 TGGGCAAGTCGCAACAAGTA 60.179 50.000 0.00 0.00 45.17 2.24
4625 5032 0.237498 GGGCAAGTCGCAACAAGTAC 59.763 55.000 0.00 0.00 45.17 2.73
4626 5033 0.941542 GGCAAGTCGCAACAAGTACA 59.058 50.000 0.00 0.00 45.17 2.90
4627 5034 1.332375 GGCAAGTCGCAACAAGTACAA 59.668 47.619 0.00 0.00 45.17 2.41
4628 5035 2.223386 GGCAAGTCGCAACAAGTACAAA 60.223 45.455 0.00 0.00 45.17 2.83
4629 5036 3.550030 GGCAAGTCGCAACAAGTACAAAT 60.550 43.478 0.00 0.00 45.17 2.32
4630 5037 4.041723 GCAAGTCGCAACAAGTACAAATT 58.958 39.130 0.00 0.00 41.79 1.82
4648 5055 5.015072 ACAAATTTATTGGGGGAAAAGGCAT 59.985 36.000 0.00 0.00 0.00 4.40
4659 5066 1.467342 GAAAAGGCATCCGCGTAGTTT 59.533 47.619 4.92 0.00 39.92 2.66
4660 5067 1.084289 AAAGGCATCCGCGTAGTTTC 58.916 50.000 4.92 0.00 39.92 2.78
4661 5068 0.249398 AAGGCATCCGCGTAGTTTCT 59.751 50.000 4.92 0.00 39.92 2.52
4666 5073 3.125658 GGCATCCGCGTAGTTTCTTTTAA 59.874 43.478 4.92 0.00 39.92 1.52
4667 5074 4.378666 GGCATCCGCGTAGTTTCTTTTAAA 60.379 41.667 4.92 0.00 39.92 1.52
4668 5075 5.148568 GCATCCGCGTAGTTTCTTTTAAAA 58.851 37.500 4.92 0.00 0.00 1.52
4670 5077 6.183359 GCATCCGCGTAGTTTCTTTTAAAAAG 60.183 38.462 4.92 0.00 0.00 2.27
4673 5080 7.249858 TCCGCGTAGTTTCTTTTAAAAAGTTT 58.750 30.769 4.92 0.00 0.00 2.66
4675 5082 8.046132 CCGCGTAGTTTCTTTTAAAAAGTTTTC 58.954 33.333 4.92 0.00 0.00 2.29
4685 5092 7.592164 TCTTTTAAAAAGTTTTCCGAATAGGCG 59.408 33.333 0.32 0.00 40.77 5.52
4686 5093 4.841443 AAAAAGTTTTCCGAATAGGCGT 57.159 36.364 0.32 0.00 40.77 5.68
4687 5094 4.414999 AAAAGTTTTCCGAATAGGCGTC 57.585 40.909 0.00 0.00 40.77 5.19
4688 5095 3.329929 AAGTTTTCCGAATAGGCGTCT 57.670 42.857 0.00 0.00 40.77 4.18
4689 5096 2.618053 AGTTTTCCGAATAGGCGTCTG 58.382 47.619 0.00 0.00 40.77 3.51
4690 5097 1.062148 GTTTTCCGAATAGGCGTCTGC 59.938 52.381 0.00 0.00 40.77 4.26
4691 5098 0.248012 TTTCCGAATAGGCGTCTGCA 59.752 50.000 0.00 0.00 45.35 4.41
4694 5101 1.269723 TCCGAATAGGCGTCTGCATAG 59.730 52.381 0.00 0.00 41.20 2.23
4695 5102 1.000163 CCGAATAGGCGTCTGCATAGT 60.000 52.381 0.00 0.00 41.20 2.12
4722 5129 7.825627 CAACAAGTGCAAATTTATTGCTTTC 57.174 32.000 13.59 5.45 45.13 2.62
4723 5130 7.408123 CAACAAGTGCAAATTTATTGCTTTCA 58.592 30.769 13.59 0.00 45.13 2.69
4724 5131 7.551035 ACAAGTGCAAATTTATTGCTTTCAA 57.449 28.000 13.59 0.00 45.13 2.69
4725 5132 7.632721 ACAAGTGCAAATTTATTGCTTTCAAG 58.367 30.769 13.59 3.11 45.13 3.02
4726 5133 6.790285 AGTGCAAATTTATTGCTTTCAAGG 57.210 33.333 13.59 0.00 45.13 3.61
4727 5134 6.523840 AGTGCAAATTTATTGCTTTCAAGGA 58.476 32.000 13.59 0.00 45.13 3.36
4728 5135 6.647895 AGTGCAAATTTATTGCTTTCAAGGAG 59.352 34.615 13.59 0.00 45.13 3.69
4729 5136 5.409214 TGCAAATTTATTGCTTTCAAGGAGC 59.591 36.000 13.59 0.00 45.13 4.70
4730 5137 5.445010 GCAAATTTATTGCTTTCAAGGAGCG 60.445 40.000 5.94 0.00 43.02 5.03
4731 5138 3.848272 TTTATTGCTTTCAAGGAGCGG 57.152 42.857 0.00 0.00 43.02 5.52
4732 5139 1.094785 TATTGCTTTCAAGGAGCGGC 58.905 50.000 0.00 0.00 43.02 6.53
4733 5140 1.598701 ATTGCTTTCAAGGAGCGGCC 61.599 55.000 0.00 0.00 43.02 6.13
4734 5141 2.672996 GCTTTCAAGGAGCGGCCA 60.673 61.111 2.24 0.00 40.02 5.36
4735 5142 2.048603 GCTTTCAAGGAGCGGCCAT 61.049 57.895 2.24 0.00 40.02 4.40
4736 5143 0.748005 GCTTTCAAGGAGCGGCCATA 60.748 55.000 2.24 0.00 40.02 2.74
4737 5144 1.017387 CTTTCAAGGAGCGGCCATAC 58.983 55.000 2.24 0.00 40.02 2.39
4738 5145 0.393808 TTTCAAGGAGCGGCCATACC 60.394 55.000 2.24 1.73 40.02 2.73
4739 5146 1.271840 TTCAAGGAGCGGCCATACCT 61.272 55.000 2.24 4.48 40.02 3.08
4740 5147 1.524621 CAAGGAGCGGCCATACCTG 60.525 63.158 2.24 0.00 40.02 4.00
4741 5148 1.689233 AAGGAGCGGCCATACCTGA 60.689 57.895 2.24 0.00 40.02 3.86
4742 5149 1.271840 AAGGAGCGGCCATACCTGAA 61.272 55.000 2.24 0.00 40.02 3.02
4743 5150 1.056700 AGGAGCGGCCATACCTGAAT 61.057 55.000 2.24 0.00 40.02 2.57
4744 5151 0.179018 GGAGCGGCCATACCTGAATT 60.179 55.000 2.24 0.00 36.34 2.17
4750 5157 1.594331 GCCATACCTGAATTCGGACC 58.406 55.000 16.17 0.00 0.00 4.46
4791 5198 3.961477 TCCGCATTCGTATTCAAATGG 57.039 42.857 0.00 0.00 34.22 3.16
4831 5238 9.926751 CATTTACAGTCATACTAGCATTTTCAG 57.073 33.333 0.00 0.00 0.00 3.02
4840 5247 4.327680 ACTAGCATTTTCAGGAGTTGGTC 58.672 43.478 0.00 0.00 0.00 4.02
4846 5253 0.531974 TTCAGGAGTTGGTCGTGCAC 60.532 55.000 6.82 6.82 40.32 4.57
4862 5269 7.081976 GGTCGTGCACATTTTCTTACTTTTAT 58.918 34.615 18.64 0.00 0.00 1.40
4863 5270 8.231837 GGTCGTGCACATTTTCTTACTTTTATA 58.768 33.333 18.64 0.00 0.00 0.98
4864 5271 9.601971 GTCGTGCACATTTTCTTACTTTTATAA 57.398 29.630 18.64 0.00 0.00 0.98
4875 5282 9.590451 TTTCTTACTTTTATAATCCATCGACGT 57.410 29.630 0.00 0.00 0.00 4.34
4876 5283 8.570096 TCTTACTTTTATAATCCATCGACGTG 57.430 34.615 0.00 0.00 0.00 4.49
4877 5284 8.192774 TCTTACTTTTATAATCCATCGACGTGT 58.807 33.333 0.00 0.00 0.00 4.49
4878 5285 9.454585 CTTACTTTTATAATCCATCGACGTGTA 57.545 33.333 0.00 0.00 0.00 2.90
4879 5286 9.800433 TTACTTTTATAATCCATCGACGTGTAA 57.200 29.630 0.00 0.00 0.00 2.41
4880 5287 8.123445 ACTTTTATAATCCATCGACGTGTAAC 57.877 34.615 0.00 0.00 0.00 2.50
4881 5288 7.760794 ACTTTTATAATCCATCGACGTGTAACA 59.239 33.333 0.00 0.00 35.74 2.41
4882 5289 8.651391 TTTTATAATCCATCGACGTGTAACAT 57.349 30.769 0.00 0.00 35.74 2.71
4883 5290 7.862741 TTATAATCCATCGACGTGTAACATC 57.137 36.000 0.00 0.00 35.74 3.06
4884 5291 2.182904 TCCATCGACGTGTAACATCG 57.817 50.000 0.00 0.00 35.74 3.84
4885 5292 0.570734 CCATCGACGTGTAACATCGC 59.429 55.000 0.00 0.00 35.74 4.58
4886 5293 0.570734 CATCGACGTGTAACATCGCC 59.429 55.000 0.00 0.00 35.74 5.54
4887 5294 0.526954 ATCGACGTGTAACATCGCCC 60.527 55.000 0.00 0.00 35.74 6.13
4892 5299 0.389296 CGTGTAACATCGCCCTGACA 60.389 55.000 0.00 0.00 35.74 3.58
4893 5300 1.803334 GTGTAACATCGCCCTGACAA 58.197 50.000 0.00 0.00 36.32 3.18
4911 5318 7.169140 CCCTGACAATTTTTACACTAAAGTTGC 59.831 37.037 0.00 0.00 32.80 4.17
4958 5373 6.738114 TGAAAGTTGCTATCCAAACAGAAAG 58.262 36.000 0.00 0.00 34.68 2.62
4964 5379 3.255642 GCTATCCAAACAGAAAGTTGCCA 59.744 43.478 0.00 0.00 41.19 4.92
4980 5395 4.367450 GTTGCCATGCTTCACAACTAAAA 58.633 39.130 0.00 0.00 39.39 1.52
4983 5398 5.229423 TGCCATGCTTCACAACTAAAATTC 58.771 37.500 0.00 0.00 0.00 2.17
4990 5405 5.185828 GCTTCACAACTAAAATTCCCATCCT 59.814 40.000 0.00 0.00 0.00 3.24
4991 5406 6.625960 GCTTCACAACTAAAATTCCCATCCTC 60.626 42.308 0.00 0.00 0.00 3.71
4992 5407 4.941263 TCACAACTAAAATTCCCATCCTCG 59.059 41.667 0.00 0.00 0.00 4.63
4993 5408 4.096382 CACAACTAAAATTCCCATCCTCGG 59.904 45.833 0.00 0.00 0.00 4.63
5051 5552 2.031163 GCTTCGTGCCACACCTCT 59.969 61.111 0.00 0.00 35.15 3.69
5060 5561 0.879090 GCCACACCTCTTTTTACCGG 59.121 55.000 0.00 0.00 0.00 5.28
5064 5565 2.551032 CACACCTCTTTTTACCGGTTCC 59.449 50.000 15.04 0.00 0.00 3.62
5088 5589 2.747396 TGTACCGGTACAACATCCAC 57.253 50.000 38.70 17.27 42.49 4.02
5095 5596 2.151202 GGTACAACATCCACCACACAG 58.849 52.381 0.00 0.00 32.32 3.66
5102 5648 0.185901 ATCCACCACACAGTGCCTTT 59.814 50.000 0.00 0.00 36.38 3.11
5106 5652 2.034558 CCACCACACAGTGCCTTTTAAG 59.965 50.000 0.00 0.00 36.38 1.85
5116 5662 5.587844 ACAGTGCCTTTTAAGATCTATGCAG 59.412 40.000 0.00 0.00 0.00 4.41
5120 5666 5.163622 TGCCTTTTAAGATCTATGCAGTTGC 60.164 40.000 0.00 0.00 42.50 4.17
5131 5677 1.185618 TGCAGTTGCGGTCCTACTCT 61.186 55.000 0.00 0.00 45.83 3.24
5140 5686 7.389884 CAGTTGCGGTCCTACTCTATAAGTATA 59.610 40.741 0.00 0.00 39.73 1.47
5146 5692 9.537192 CGGTCCTACTCTATAAGTATATCTCTG 57.463 40.741 0.00 0.00 39.73 3.35
5203 5749 7.227512 CACTTAAGTCAAATAGTGATCCCATCC 59.772 40.741 4.77 0.00 40.24 3.51
5206 5752 2.437651 TCAAATAGTGATCCCATCCGCA 59.562 45.455 0.00 0.00 0.00 5.69
5210 5756 0.179037 AGTGATCCCATCCGCACATG 60.179 55.000 0.00 0.00 33.85 3.21
5211 5757 0.464373 GTGATCCCATCCGCACATGT 60.464 55.000 0.00 0.00 0.00 3.21
5235 5781 4.219115 TGACACATATTCTCTCTCCTCCC 58.781 47.826 0.00 0.00 0.00 4.30
5249 5795 1.303236 CTCCCAACAATGGCACGGA 60.303 57.895 0.00 0.00 46.09 4.69
5252 5798 1.250154 CCCAACAATGGCACGGACAT 61.250 55.000 0.00 0.00 46.09 3.06
5256 5802 3.489059 CCAACAATGGCACGGACATAATC 60.489 47.826 0.00 0.00 40.58 1.75
5261 5807 1.548973 GGCACGGACATAATCGCTCG 61.549 60.000 0.00 0.00 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.857854 GCGGTGCGATGTCAGCTG 61.858 66.667 7.63 7.63 35.28 4.24
116 117 1.330080 GCGTGTGCTTTGTTCGATGC 61.330 55.000 0.00 0.00 38.39 3.91
126 127 1.376424 CCTCATGAGGCGTGTGCTT 60.376 57.895 28.45 0.00 42.44 3.91
167 168 1.239296 GCATGAGTGTGCAAGCCTCA 61.239 55.000 12.10 12.10 44.43 3.86
176 177 3.684305 TCGTATGAAAAGGCATGAGTGTG 59.316 43.478 0.00 0.00 0.00 3.82
177 178 3.937814 TCGTATGAAAAGGCATGAGTGT 58.062 40.909 0.00 0.00 0.00 3.55
224 225 2.434185 GCACGCCGATGGAGTTCA 60.434 61.111 0.00 0.00 32.34 3.18
230 231 3.326889 CTGGTTTGCACGCCGATGG 62.327 63.158 0.00 0.00 0.00 3.51
267 268 2.078452 CTGAAGCAAAGGGGGAGGA 58.922 57.895 0.00 0.00 0.00 3.71
364 367 1.300233 GCTACGGCGATCTTCCCTG 60.300 63.158 16.62 0.00 0.00 4.45
393 396 4.105697 TGGGAGGTTGGTTCTGATTAACTT 59.894 41.667 0.00 0.00 0.00 2.66
431 434 1.377202 GCCGATGTGGAAAGCCTCA 60.377 57.895 0.00 0.00 42.00 3.86
457 460 0.107897 GTATGTGGATCGTGGTGCCA 60.108 55.000 0.00 0.00 0.00 4.92
503 506 1.070758 GGGTTGCTTCTCTCTGTGACA 59.929 52.381 0.00 0.00 0.00 3.58
516 519 1.072505 CCACGTACTTGGGGTTGCT 59.927 57.895 10.54 0.00 32.35 3.91
531 535 1.405105 TGTGCTCAACTTTCTTGCCAC 59.595 47.619 0.00 0.00 0.00 5.01
534 538 2.669364 CCATGTGCTCAACTTTCTTGC 58.331 47.619 0.00 0.00 0.00 4.01
577 581 3.649277 GATGAGGTCACCGCTGCGT 62.649 63.158 21.59 6.30 0.00 5.24
634 638 3.552068 GCAAAGGTTCATTACACCGCTTT 60.552 43.478 0.00 0.00 39.56 3.51
635 639 2.030274 GCAAAGGTTCATTACACCGCTT 60.030 45.455 0.00 0.00 39.56 4.68
636 640 1.539827 GCAAAGGTTCATTACACCGCT 59.460 47.619 0.00 0.00 39.56 5.52
645 649 3.747976 GGCGCGGCAAAGGTTCAT 61.748 61.111 29.32 0.00 0.00 2.57
647 651 3.683587 GATGGCGCGGCAAAGGTTC 62.684 63.158 39.24 26.74 0.00 3.62
708 712 1.885049 CTGGGATCCTTCTTCCTCCA 58.115 55.000 12.58 0.00 33.53 3.86
760 764 0.779997 ATGGTTTTCCCCAGCTGTCT 59.220 50.000 13.81 0.00 38.07 3.41
767 771 1.828979 GCGAGTAATGGTTTTCCCCA 58.171 50.000 0.00 0.00 39.73 4.96
923 946 1.221021 CTTAGGGTTGGAGGCGGTC 59.779 63.158 0.00 0.00 0.00 4.79
1183 1206 0.758685 AGCAGGAAGGGGATCGAGAG 60.759 60.000 0.00 0.00 0.00 3.20
1184 1207 1.045350 CAGCAGGAAGGGGATCGAGA 61.045 60.000 0.00 0.00 0.00 4.04
1253 1276 3.879892 GCACAGGAAGGCCTAAAATCTAG 59.120 47.826 5.16 0.00 44.80 2.43
1254 1277 3.523564 AGCACAGGAAGGCCTAAAATCTA 59.476 43.478 5.16 0.00 44.80 1.98
1255 1278 2.310052 AGCACAGGAAGGCCTAAAATCT 59.690 45.455 5.16 0.00 44.80 2.40
1256 1279 2.728007 AGCACAGGAAGGCCTAAAATC 58.272 47.619 5.16 0.00 44.80 2.17
1257 1280 2.827921 CAAGCACAGGAAGGCCTAAAAT 59.172 45.455 5.16 0.00 44.80 1.82
1277 1300 6.431543 TCAAACAGTCTTAAAACACCTCAACA 59.568 34.615 0.00 0.00 0.00 3.33
1297 1320 7.556844 TCTAGTCCTAAACTGGATCATCAAAC 58.443 38.462 0.00 0.00 40.26 2.93
1300 1323 7.400339 AGTTTCTAGTCCTAAACTGGATCATCA 59.600 37.037 6.51 0.00 44.07 3.07
1310 1333 6.202379 GTCACCACAAGTTTCTAGTCCTAAAC 59.798 42.308 0.00 0.00 36.13 2.01
1317 1340 6.069331 TCTCTAGTCACCACAAGTTTCTAGT 58.931 40.000 0.00 0.00 33.93 2.57
1386 1409 1.035932 ATGTGCAAGCTCCCAGCATC 61.036 55.000 6.41 2.72 45.56 3.91
1497 1520 5.649265 TCAGGAGGAAGTATCTGCATCTAT 58.351 41.667 0.00 0.00 0.00 1.98
1498 1521 5.066913 TCAGGAGGAAGTATCTGCATCTA 57.933 43.478 0.00 0.00 0.00 1.98
1506 1529 6.825721 ACAATGATGTTTCAGGAGGAAGTATC 59.174 38.462 0.00 0.00 35.91 2.24
1558 1581 8.177119 AGTGCAGAACCAAATTTTATTCTACA 57.823 30.769 11.57 10.18 30.28 2.74
1599 1622 5.047802 CACAAAGCCAACAATCTATTGACCT 60.048 40.000 9.60 0.00 40.14 3.85
1600 1623 5.163513 CACAAAGCCAACAATCTATTGACC 58.836 41.667 9.60 0.00 40.14 4.02
1601 1624 5.772521 ACACAAAGCCAACAATCTATTGAC 58.227 37.500 9.60 0.00 40.14 3.18
1602 1625 5.769662 AGACACAAAGCCAACAATCTATTGA 59.230 36.000 9.60 0.00 40.14 2.57
1740 1774 5.454232 ACTTGTTTCGCTAATGTCAAAAACG 59.546 36.000 0.00 0.00 31.06 3.60
1933 1967 8.141298 TGTAAATCAACAGTTGGGAGTCTATA 57.859 34.615 13.52 0.00 0.00 1.31
1941 1975 6.828273 TCAGGATATGTAAATCAACAGTTGGG 59.172 38.462 13.52 0.00 31.70 4.12
1966 2000 9.034800 TCCAAACCTTATCATTTAGAAGCATTT 57.965 29.630 0.00 0.00 0.00 2.32
2112 2146 2.919229 CAGCGCAAAATTTCATCTCACC 59.081 45.455 11.47 0.00 0.00 4.02
2300 2335 7.500892 ACATAAAAGATAACATTATGGCCACGA 59.499 33.333 8.16 0.00 39.95 4.35
3142 3535 9.689976 TGTAATTTTCCAAAACTGTGATACATG 57.310 29.630 0.00 0.00 0.00 3.21
3187 3580 7.422399 GGACTTTTACAAACTGTGCTAAATCA 58.578 34.615 0.00 0.00 0.00 2.57
3429 3824 9.781633 TGCCTGTTCTAAAACATTAGTAAACTA 57.218 29.630 0.00 0.00 44.18 2.24
3569 3964 9.049050 TGAAGTTTATGACCCTTGGTAATACTA 57.951 33.333 0.00 0.00 35.25 1.82
3686 4081 3.513462 TTCATTTATTACGGCGATGCG 57.487 42.857 16.62 0.00 0.00 4.73
3708 4103 8.777865 ATACGATTGTCATATCATTAGGGTTG 57.222 34.615 0.00 0.00 0.00 3.77
4013 4408 3.879998 TGTAACCAATGACGGCATGTAT 58.120 40.909 3.39 0.00 34.26 2.29
4026 4421 6.765403 AGTGCTACTGAAACTATGTAACCAA 58.235 36.000 0.00 0.00 0.00 3.67
4066 4462 6.626623 GCAACCAAAAATGCTCTGTATCAGAT 60.627 38.462 0.00 0.00 39.92 2.90
4067 4463 5.335897 GCAACCAAAAATGCTCTGTATCAGA 60.336 40.000 0.00 0.00 39.46 3.27
4117 4513 6.709397 ACTTGTAAAAAGTACTCCCTAACAGC 59.291 38.462 0.00 0.00 0.00 4.40
4149 4545 2.094545 GGTGCCTGCATGAAGGTAAAAG 60.095 50.000 21.55 0.00 39.75 2.27
4216 4612 2.641305 AGCATTCTGATCTGCCTGAAC 58.359 47.619 8.57 0.00 39.22 3.18
4240 4636 3.698040 GGTACCTCTGGACGTATTCTTCA 59.302 47.826 4.06 0.00 0.00 3.02
4291 4687 1.228657 GGCGGGGATCTTGTTATCGC 61.229 60.000 0.00 0.00 40.77 4.58
4334 4730 2.611292 CAGATCAAAGAGCGGGACATTC 59.389 50.000 0.00 0.00 0.00 2.67
4399 4795 8.095452 AGTTCTTCTACATTCAGAATACCCAT 57.905 34.615 0.00 0.00 34.14 4.00
4400 4796 7.496346 AGTTCTTCTACATTCAGAATACCCA 57.504 36.000 0.00 0.00 34.14 4.51
4401 4797 8.145122 CCTAGTTCTTCTACATTCAGAATACCC 58.855 40.741 0.00 0.00 34.14 3.69
4402 4798 7.654116 GCCTAGTTCTTCTACATTCAGAATACC 59.346 40.741 0.00 0.00 34.14 2.73
4403 4799 8.417884 AGCCTAGTTCTTCTACATTCAGAATAC 58.582 37.037 0.00 0.00 34.14 1.89
4404 4800 8.540507 AGCCTAGTTCTTCTACATTCAGAATA 57.459 34.615 0.00 0.00 34.14 1.75
4405 4801 7.430760 AGCCTAGTTCTTCTACATTCAGAAT 57.569 36.000 0.00 0.00 34.14 2.40
4406 4802 6.859112 AGCCTAGTTCTTCTACATTCAGAA 57.141 37.500 0.00 0.00 33.55 3.02
4407 4803 7.067615 CAGTAGCCTAGTTCTTCTACATTCAGA 59.932 40.741 0.00 0.00 35.19 3.27
4408 4804 7.067615 TCAGTAGCCTAGTTCTTCTACATTCAG 59.932 40.741 0.00 0.00 35.19 3.02
4409 4805 6.890268 TCAGTAGCCTAGTTCTTCTACATTCA 59.110 38.462 0.00 0.00 35.19 2.57
4410 4806 7.336161 TCAGTAGCCTAGTTCTTCTACATTC 57.664 40.000 0.00 0.00 35.19 2.67
4411 4807 7.363968 GGTTCAGTAGCCTAGTTCTTCTACATT 60.364 40.741 0.00 0.00 35.19 2.71
4514 4915 0.751277 TCAACACACCAGCAACAGGG 60.751 55.000 0.00 0.00 0.00 4.45
4530 4931 7.822334 ACGACATATTTAACCATCAACTCTCAA 59.178 33.333 0.00 0.00 0.00 3.02
4588 4995 1.202533 CCCAAGTGCCAGTATCTACGG 60.203 57.143 0.00 0.00 0.00 4.02
4591 4998 1.578897 TGCCCAAGTGCCAGTATCTA 58.421 50.000 0.00 0.00 0.00 1.98
4592 4999 0.698238 TTGCCCAAGTGCCAGTATCT 59.302 50.000 0.00 0.00 0.00 1.98
4610 5017 7.381139 CCAATAAATTTGTACTTGTTGCGACTT 59.619 33.333 5.50 0.00 0.00 3.01
4612 5019 6.088883 CCCAATAAATTTGTACTTGTTGCGAC 59.911 38.462 0.00 0.00 0.00 5.19
4613 5020 6.153067 CCCAATAAATTTGTACTTGTTGCGA 58.847 36.000 0.00 0.00 0.00 5.10
4614 5021 5.347364 CCCCAATAAATTTGTACTTGTTGCG 59.653 40.000 0.00 0.00 0.00 4.85
4615 5022 5.641636 CCCCCAATAAATTTGTACTTGTTGC 59.358 40.000 0.00 0.00 0.00 4.17
4616 5023 6.998802 TCCCCCAATAAATTTGTACTTGTTG 58.001 36.000 0.00 0.00 0.00 3.33
4617 5024 7.619512 TTCCCCCAATAAATTTGTACTTGTT 57.380 32.000 0.00 0.00 0.00 2.83
4618 5025 7.619512 TTTCCCCCAATAAATTTGTACTTGT 57.380 32.000 0.00 0.00 0.00 3.16
4619 5026 7.606073 CCTTTTCCCCCAATAAATTTGTACTTG 59.394 37.037 0.00 0.05 0.00 3.16
4620 5027 7.685481 CCTTTTCCCCCAATAAATTTGTACTT 58.315 34.615 0.00 0.00 0.00 2.24
4621 5028 6.296202 GCCTTTTCCCCCAATAAATTTGTACT 60.296 38.462 0.00 0.00 0.00 2.73
4622 5029 5.878116 GCCTTTTCCCCCAATAAATTTGTAC 59.122 40.000 0.00 0.00 0.00 2.90
4623 5030 5.548056 TGCCTTTTCCCCCAATAAATTTGTA 59.452 36.000 0.00 0.00 0.00 2.41
4624 5031 4.352298 TGCCTTTTCCCCCAATAAATTTGT 59.648 37.500 0.00 0.00 0.00 2.83
4625 5032 4.916183 TGCCTTTTCCCCCAATAAATTTG 58.084 39.130 0.00 0.00 0.00 2.32
4626 5033 5.339944 GGATGCCTTTTCCCCCAATAAATTT 60.340 40.000 0.00 0.00 0.00 1.82
4627 5034 4.165950 GGATGCCTTTTCCCCCAATAAATT 59.834 41.667 0.00 0.00 0.00 1.82
4628 5035 3.716353 GGATGCCTTTTCCCCCAATAAAT 59.284 43.478 0.00 0.00 0.00 1.40
4629 5036 3.111484 GGATGCCTTTTCCCCCAATAAA 58.889 45.455 0.00 0.00 0.00 1.40
4630 5037 2.758130 GGATGCCTTTTCCCCCAATAA 58.242 47.619 0.00 0.00 0.00 1.40
4648 5055 6.362210 ACTTTTTAAAAGAAACTACGCGGA 57.638 33.333 22.31 0.00 0.00 5.54
4659 5066 7.592164 CGCCTATTCGGAAAACTTTTTAAAAGA 59.408 33.333 22.31 0.00 33.16 2.52
4660 5067 7.380333 ACGCCTATTCGGAAAACTTTTTAAAAG 59.620 33.333 15.03 15.03 33.16 2.27
4661 5068 7.201835 ACGCCTATTCGGAAAACTTTTTAAAA 58.798 30.769 0.00 0.00 33.16 1.52
4666 5073 4.070009 AGACGCCTATTCGGAAAACTTTT 58.930 39.130 0.00 0.00 33.16 2.27
4667 5074 3.435671 CAGACGCCTATTCGGAAAACTTT 59.564 43.478 0.00 0.00 33.16 2.66
4668 5075 3.000727 CAGACGCCTATTCGGAAAACTT 58.999 45.455 0.00 0.00 33.16 2.66
4670 5077 1.062148 GCAGACGCCTATTCGGAAAAC 59.938 52.381 0.00 0.00 33.16 2.43
4673 5080 0.464036 ATGCAGACGCCTATTCGGAA 59.536 50.000 0.00 0.00 37.32 4.30
4675 5082 1.000163 ACTATGCAGACGCCTATTCGG 60.000 52.381 0.00 0.00 37.32 4.30
4706 5113 5.445010 CGCTCCTTGAAAGCAATAAATTTGC 60.445 40.000 0.00 2.17 45.22 3.68
4707 5114 5.062558 CCGCTCCTTGAAAGCAATAAATTTG 59.937 40.000 0.00 0.00 39.81 2.32
4708 5115 5.170748 CCGCTCCTTGAAAGCAATAAATTT 58.829 37.500 0.00 0.00 39.81 1.82
4709 5116 4.747810 CCGCTCCTTGAAAGCAATAAATT 58.252 39.130 0.00 0.00 39.81 1.82
4710 5117 3.429410 GCCGCTCCTTGAAAGCAATAAAT 60.429 43.478 0.00 0.00 39.81 1.40
4711 5118 2.094752 GCCGCTCCTTGAAAGCAATAAA 60.095 45.455 0.00 0.00 39.81 1.40
4712 5119 1.472480 GCCGCTCCTTGAAAGCAATAA 59.528 47.619 0.00 0.00 39.81 1.40
4713 5120 1.094785 GCCGCTCCTTGAAAGCAATA 58.905 50.000 0.00 0.00 39.81 1.90
4714 5121 1.598701 GGCCGCTCCTTGAAAGCAAT 61.599 55.000 0.00 0.00 39.81 3.56
4715 5122 2.268076 GGCCGCTCCTTGAAAGCAA 61.268 57.895 0.00 0.00 39.81 3.91
4716 5123 2.672996 GGCCGCTCCTTGAAAGCA 60.673 61.111 0.00 0.00 39.81 3.91
4717 5124 0.748005 TATGGCCGCTCCTTGAAAGC 60.748 55.000 0.00 0.00 36.38 3.51
4718 5125 1.017387 GTATGGCCGCTCCTTGAAAG 58.983 55.000 0.00 0.00 35.26 2.62
4719 5126 0.393808 GGTATGGCCGCTCCTTGAAA 60.394 55.000 0.00 0.00 35.26 2.69
4720 5127 1.223487 GGTATGGCCGCTCCTTGAA 59.777 57.895 0.00 0.00 35.26 2.69
4721 5128 1.689233 AGGTATGGCCGCTCCTTGA 60.689 57.895 0.00 0.00 43.70 3.02
4722 5129 1.524621 CAGGTATGGCCGCTCCTTG 60.525 63.158 9.28 3.38 43.70 3.61
4723 5130 1.271840 TTCAGGTATGGCCGCTCCTT 61.272 55.000 9.28 0.00 43.70 3.36
4724 5131 1.056700 ATTCAGGTATGGCCGCTCCT 61.057 55.000 0.00 1.97 43.70 3.69
4725 5132 0.179018 AATTCAGGTATGGCCGCTCC 60.179 55.000 0.00 0.00 43.70 4.70
4726 5133 1.230324 GAATTCAGGTATGGCCGCTC 58.770 55.000 0.00 0.00 43.70 5.03
4727 5134 0.532862 CGAATTCAGGTATGGCCGCT 60.533 55.000 6.22 0.00 43.70 5.52
4728 5135 1.507141 CCGAATTCAGGTATGGCCGC 61.507 60.000 6.22 0.00 43.70 6.53
4729 5136 0.105964 TCCGAATTCAGGTATGGCCG 59.894 55.000 6.22 0.00 43.70 6.13
4730 5137 1.594331 GTCCGAATTCAGGTATGGCC 58.406 55.000 6.22 0.00 37.58 5.36
4731 5138 1.594331 GGTCCGAATTCAGGTATGGC 58.406 55.000 6.22 0.00 0.00 4.40
4732 5139 1.411246 TCGGTCCGAATTCAGGTATGG 59.589 52.381 12.68 0.00 31.06 2.74
4733 5140 2.882927 TCGGTCCGAATTCAGGTATG 57.117 50.000 12.68 3.13 31.06 2.39
4734 5141 2.102588 CCTTCGGTCCGAATTCAGGTAT 59.897 50.000 26.30 0.00 44.85 2.73
4735 5142 1.479323 CCTTCGGTCCGAATTCAGGTA 59.521 52.381 26.30 2.40 44.85 3.08
4736 5143 0.249398 CCTTCGGTCCGAATTCAGGT 59.751 55.000 26.30 0.00 44.85 4.00
4737 5144 0.535335 TCCTTCGGTCCGAATTCAGG 59.465 55.000 26.30 22.67 44.85 3.86
4738 5145 2.271800 CTTCCTTCGGTCCGAATTCAG 58.728 52.381 26.30 17.16 44.85 3.02
4739 5146 1.066430 CCTTCCTTCGGTCCGAATTCA 60.066 52.381 26.30 10.90 44.85 2.57
4740 5147 1.206371 TCCTTCCTTCGGTCCGAATTC 59.794 52.381 26.30 0.00 44.85 2.17
4741 5148 1.272807 TCCTTCCTTCGGTCCGAATT 58.727 50.000 26.30 0.00 44.85 2.17
4742 5149 1.272807 TTCCTTCCTTCGGTCCGAAT 58.727 50.000 26.30 0.00 44.85 3.34
4743 5150 1.272807 ATTCCTTCCTTCGGTCCGAA 58.727 50.000 24.71 24.71 43.75 4.30
4744 5151 1.272807 AATTCCTTCCTTCGGTCCGA 58.727 50.000 10.71 10.71 0.00 4.55
4750 5157 5.408604 CGGATTATGGTAATTCCTTCCTTCG 59.591 44.000 0.00 0.00 37.07 3.79
4820 5227 3.244422 ACGACCAACTCCTGAAAATGCTA 60.244 43.478 0.00 0.00 0.00 3.49
4831 5238 0.951558 AAATGTGCACGACCAACTCC 59.048 50.000 13.13 0.00 0.00 3.85
4871 5278 0.108992 TCAGGGCGATGTTACACGTC 60.109 55.000 8.52 6.37 0.00 4.34
4872 5279 0.389426 GTCAGGGCGATGTTACACGT 60.389 55.000 8.52 0.00 0.00 4.49
4873 5280 0.389296 TGTCAGGGCGATGTTACACG 60.389 55.000 0.00 0.00 0.00 4.49
4874 5281 1.803334 TTGTCAGGGCGATGTTACAC 58.197 50.000 0.00 0.00 0.00 2.90
4875 5282 2.779755 ATTGTCAGGGCGATGTTACA 57.220 45.000 0.00 0.00 0.00 2.41
4876 5283 4.434713 AAAATTGTCAGGGCGATGTTAC 57.565 40.909 0.00 0.00 0.00 2.50
4877 5284 5.473846 TGTAAAAATTGTCAGGGCGATGTTA 59.526 36.000 0.00 0.00 0.00 2.41
4878 5285 4.279671 TGTAAAAATTGTCAGGGCGATGTT 59.720 37.500 0.00 0.00 0.00 2.71
4879 5286 3.823873 TGTAAAAATTGTCAGGGCGATGT 59.176 39.130 0.00 0.00 0.00 3.06
4880 5287 4.082787 AGTGTAAAAATTGTCAGGGCGATG 60.083 41.667 0.00 0.00 0.00 3.84
4881 5288 4.079253 AGTGTAAAAATTGTCAGGGCGAT 58.921 39.130 0.00 0.00 0.00 4.58
4882 5289 3.482436 AGTGTAAAAATTGTCAGGGCGA 58.518 40.909 0.00 0.00 0.00 5.54
4883 5290 3.915437 AGTGTAAAAATTGTCAGGGCG 57.085 42.857 0.00 0.00 0.00 6.13
4884 5291 6.745116 ACTTTAGTGTAAAAATTGTCAGGGC 58.255 36.000 0.00 0.00 0.00 5.19
4885 5292 7.169140 GCAACTTTAGTGTAAAAATTGTCAGGG 59.831 37.037 0.00 0.00 31.48 4.45
4886 5293 7.169140 GGCAACTTTAGTGTAAAAATTGTCAGG 59.831 37.037 0.00 0.00 32.74 3.86
4887 5294 7.704472 TGGCAACTTTAGTGTAAAAATTGTCAG 59.296 33.333 6.39 0.00 35.38 3.51
4929 5344 7.231317 TCTGTTTGGATAGCAACTTTCATCTTT 59.769 33.333 0.00 0.00 0.00 2.52
4932 5347 6.500684 TCTGTTTGGATAGCAACTTTCATC 57.499 37.500 0.00 0.00 0.00 2.92
4935 5350 6.739112 ACTTTCTGTTTGGATAGCAACTTTC 58.261 36.000 0.00 0.00 0.00 2.62
4939 5354 4.681483 GCAACTTTCTGTTTGGATAGCAAC 59.319 41.667 0.00 0.00 36.63 4.17
4944 5359 4.321899 GCATGGCAACTTTCTGTTTGGATA 60.322 41.667 0.00 0.00 36.63 2.59
4948 5363 3.102052 AGCATGGCAACTTTCTGTTTG 57.898 42.857 0.00 0.00 36.63 2.93
4958 5373 3.641437 TTAGTTGTGAAGCATGGCAAC 57.359 42.857 0.00 0.00 40.83 4.17
4964 5379 6.351286 GGATGGGAATTTTAGTTGTGAAGCAT 60.351 38.462 0.00 0.00 0.00 3.79
4990 5405 2.279935 ATGCAAGTTTGGTTACCCGA 57.720 45.000 0.00 0.00 0.00 5.14
4991 5406 4.506886 TTTATGCAAGTTTGGTTACCCG 57.493 40.909 0.00 0.00 0.00 5.28
5075 5576 2.151202 CTGTGTGGTGGATGTTGTACC 58.849 52.381 0.00 0.00 35.05 3.34
5088 5589 4.074970 AGATCTTAAAAGGCACTGTGTGG 58.925 43.478 9.86 0.00 40.86 4.17
5095 5596 6.261118 CAACTGCATAGATCTTAAAAGGCAC 58.739 40.000 0.00 0.00 0.00 5.01
5102 5648 4.119862 GACCGCAACTGCATAGATCTTAA 58.880 43.478 0.00 0.00 42.21 1.85
5106 5652 1.202580 AGGACCGCAACTGCATAGATC 60.203 52.381 2.12 0.00 42.21 2.75
5116 5662 4.915158 ACTTATAGAGTAGGACCGCAAC 57.085 45.455 0.00 0.00 36.65 4.17
5120 5666 9.537192 CAGAGATATACTTATAGAGTAGGACCG 57.463 40.741 0.00 0.00 43.79 4.79
5140 5686 9.965902 AAAATAGAAGTTGGACAATACAGAGAT 57.034 29.630 0.00 0.00 0.00 2.75
5210 5756 6.071616 GGGAGGAGAGAGAATATGTGTCATAC 60.072 46.154 0.00 0.00 0.00 2.39
5211 5757 6.013379 GGGAGGAGAGAGAATATGTGTCATA 58.987 44.000 0.00 0.00 0.00 2.15
5235 5781 3.694734 GATTATGTCCGTGCCATTGTTG 58.305 45.455 0.00 0.00 0.00 3.33
5243 5789 1.846648 CGAGCGATTATGTCCGTGC 59.153 57.895 0.00 0.00 0.00 5.34
5249 5795 2.352225 GGAGAGATGCGAGCGATTATGT 60.352 50.000 0.00 0.00 0.00 2.29
5252 5798 0.598562 GGGAGAGATGCGAGCGATTA 59.401 55.000 0.00 0.00 0.00 1.75
5256 5802 2.334653 GAGGGAGAGATGCGAGCG 59.665 66.667 0.00 0.00 0.00 5.03
5261 5807 5.028549 TGAATTTAGTGAGGGAGAGATGC 57.971 43.478 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.