Multiple sequence alignment - TraesCS1B01G244700

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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 TraesCS1B01G244700 chr1B 100.000 5757 0 0 1 5757 434084585 434090341 0.000000e+00 10632.0
1 TraesCS1B01G244700 chr1D 95.028 3801 119 22 1415 5163 321259984 321263766 0.000000e+00 5908.0
2 TraesCS1B01G244700 chr1D 94.629 1415 57 7 1 1414 321258379 321259775 0.000000e+00 2174.0
3 TraesCS1B01G244700 chr1D 90.110 182 13 3 5535 5714 321263977 321264155 1.250000e-56 231.0
4 TraesCS1B01G244700 chr1D 93.750 128 8 0 1287 1414 321259804 321259931 5.890000e-45 193.0
5 TraesCS1B01G244700 chr1A 97.416 2206 54 3 1810 4014 401773539 401771336 0.000000e+00 3755.0
6 TraesCS1B01G244700 chr1A 95.336 1415 58 4 4 1414 401775522 401774112 0.000000e+00 2241.0
7 TraesCS1B01G244700 chr1A 92.292 960 43 6 4171 5103 401771334 401770379 0.000000e+00 1334.0
8 TraesCS1B01G244700 chr1A 95.262 401 17 2 1413 1812 401774061 401773662 8.140000e-178 634.0
9 TraesCS1B01G244700 chr1A 91.429 210 17 1 5500 5708 401770069 401769860 2.630000e-73 287.0
10 TraesCS1B01G244700 chr1A 100.000 28 0 0 5328 5355 401770269 401770242 1.000000e-02 52.8
11 TraesCS1B01G244700 chr4A 96.341 82 2 1 4282 4362 302680114 302680195 3.620000e-27 134.0
12 TraesCS1B01G244700 chr4A 86.747 83 7 4 4203 4281 266953899 266953981 7.950000e-14 89.8
13 TraesCS1B01G244700 chr4A 82.432 74 10 3 4203 4273 467527363 467527290 1.730000e-05 62.1
14 TraesCS1B01G244700 chr4A 100.000 28 0 0 427 454 551329955 551329982 1.000000e-02 52.8
15 TraesCS1B01G244700 chr7D 94.253 87 4 1 4281 4366 540843386 540843472 1.300000e-26 132.0
16 TraesCS1B01G244700 chr7A 94.253 87 4 1 4281 4366 552975462 552975548 1.300000e-26 132.0
17 TraesCS1B01G244700 chr5B 94.253 87 4 1 4281 4366 208438158 208438072 1.300000e-26 132.0
18 TraesCS1B01G244700 chrUn 93.103 87 5 1 4281 4366 55884309 55884395 6.060000e-25 126.0
19 TraesCS1B01G244700 chr7B 93.103 87 5 1 4281 4366 141816059 141816145 6.060000e-25 126.0
20 TraesCS1B01G244700 chr6A 92.135 89 6 1 4282 4369 63594962 63595050 2.180000e-24 124.0
21 TraesCS1B01G244700 chr3D 88.608 79 9 0 167 245 508170986 508171064 4.750000e-16 97.1
22 TraesCS1B01G244700 chr6B 87.952 83 6 4 4203 4281 47264055 47264137 1.710000e-15 95.3
23 TraesCS1B01G244700 chr4B 85.542 83 8 2 4203 4281 247563512 247563430 3.700000e-12 84.2
24 TraesCS1B01G244700 chr4B 83.562 73 10 2 4203 4273 167932496 167932424 3.720000e-07 67.6
25 TraesCS1B01G244700 chr4D 83.562 73 10 2 4203 4273 108862950 108863022 3.720000e-07 67.6


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 TraesCS1B01G244700 chr1B 434084585 434090341 5756 False 10632.000000 10632 100.000000 1 5757 1 chr1B.!!$F1 5756
1 TraesCS1B01G244700 chr1D 321258379 321264155 5776 False 2126.500000 5908 93.379250 1 5714 4 chr1D.!!$F1 5713
2 TraesCS1B01G244700 chr1A 401769860 401775522 5662 True 1383.966667 3755 95.289167 4 5708 6 chr1A.!!$R1 5704

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
539 544 1.470098 ACACTTTGCATCCTTGATCGC 59.530 47.619 0.00 0.00 0.0 4.58 F
1994 2364 1.075482 AAGGTGTGGGTCCATGCAG 59.925 57.895 0.00 0.00 0.0 4.41 F
2181 2553 1.068895 CATGGTTCAGGCTGCAAAACA 59.931 47.619 10.34 9.48 0.0 2.83 F
2184 2556 1.211743 GTTCAGGCTGCAAAACAAGC 58.788 50.000 10.34 0.00 0.0 4.01 F
3718 4091 1.470098 GCATCGGATTGTGATATGGGC 59.530 52.381 0.00 0.00 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2167 2539 1.042003 TGGCTTGTTTTGCAGCCTGA 61.042 50.000 12.97 0.00 46.77 3.86 R
3875 4248 2.344025 AGGCGGACGAATTAGTTTGTC 58.656 47.619 9.36 9.36 44.63 3.18 R
3892 4265 2.570135 CTCAAGCTCCTCCAAATAGGC 58.430 52.381 0.00 0.00 36.51 3.93 R
4119 4492 6.015688 GCATCAAATCCCATTAGTGATCATGT 60.016 38.462 0.00 0.00 0.00 3.21 R
5189 5625 0.036388 GGATCTCAGCCGTCCAACAA 60.036 55.000 0.00 0.00 32.23 2.83 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
27 32 6.790319 AGCGATGGGGGAATAGTAAATATTT 58.210 36.000 5.89 5.89 34.10 1.40
126 131 4.461431 TCGGATAGACTACTTTCTTGTGCA 59.539 41.667 0.00 0.00 0.00 4.57
133 138 6.000219 AGACTACTTTCTTGTGCACATCATT 59.000 36.000 22.39 5.93 0.00 2.57
266 271 7.553881 AACTACCGGTATCAAGAATGAAATG 57.446 36.000 16.25 0.21 39.49 2.32
407 412 5.445964 ACCTTTGTAATCCGCCAAAGATAT 58.554 37.500 12.36 0.00 46.65 1.63
432 437 4.284746 GCCACCTGCTTAGAATATACTCCT 59.715 45.833 0.00 0.00 36.87 3.69
476 481 4.101119 AGTTATGGAACGGAGGGAGTATTG 59.899 45.833 0.00 0.00 40.76 1.90
521 526 8.136563 TGTGGTAAAGTAGGTGACATATTACA 57.863 34.615 4.01 0.00 31.02 2.41
539 544 1.470098 ACACTTTGCATCCTTGATCGC 59.530 47.619 0.00 0.00 0.00 4.58
587 592 9.072375 TCCATTTCACACATTGTTTCATTACTA 57.928 29.630 0.00 0.00 0.00 1.82
588 593 9.689976 CCATTTCACACATTGTTTCATTACTAA 57.310 29.630 0.00 0.00 0.00 2.24
772 777 7.886629 TCTCTTTGGAATTTTCTCATATGGG 57.113 36.000 2.13 0.00 0.00 4.00
797 802 7.968405 GGACTATTTTGGCAACTATTTACAGTG 59.032 37.037 0.00 0.00 37.61 3.66
860 866 8.591940 TCACAAATTTACCATGGATGATTTCAA 58.408 29.630 21.47 5.98 0.00 2.69
981 987 9.102757 CTCTTAATTTAAGCAGAGCATACAGAA 57.897 33.333 10.71 0.00 35.76 3.02
1065 1071 2.367202 CCCAGATGGTGGTAGCGGT 61.367 63.158 0.00 0.00 46.37 5.68
1107 1113 2.124695 GAAGACCCCGATGCCACC 60.125 66.667 0.00 0.00 0.00 4.61
1358 1364 5.522456 TGTCAAATCATGTTTTCAGCAGTC 58.478 37.500 0.00 0.00 0.00 3.51
1398 1560 7.467623 AGACTCGAACAGAATGAAAATTATGC 58.532 34.615 0.00 0.00 39.69 3.14
1421 1635 7.051422 GCTAGAAGCAAAGTTACTGAGTTAC 57.949 40.000 0.00 0.00 41.89 2.50
1459 1673 2.802787 AATCGCTCTTATCTGGACGG 57.197 50.000 0.00 0.00 0.00 4.79
1506 1720 7.449704 AGCCAGAAAACTTCTTATCTTGAATGT 59.550 33.333 0.00 0.00 38.11 2.71
1558 1775 8.531146 ACTTAATATGCCAAGCAATTGTTAGTT 58.469 29.630 7.40 0.00 43.62 2.24
1611 1828 9.561270 GTTAGCCAGTGAGAAATTAAGAAATTC 57.439 33.333 0.00 0.00 34.12 2.17
1612 1829 9.520515 TTAGCCAGTGAGAAATTAAGAAATTCT 57.479 29.630 0.00 0.00 34.12 2.40
1725 1950 2.472695 TCAGTTCAGAACGGATTGGG 57.527 50.000 11.68 0.00 36.23 4.12
1812 2162 1.739466 CGCATGTGCAGTTCCTTGTAT 59.261 47.619 5.77 0.00 42.21 2.29
1847 2197 5.237996 TGCTATTAGTGCATGAGCTTGATTC 59.762 40.000 0.00 0.00 42.74 2.52
1853 2203 3.501445 GTGCATGAGCTTGATTCCCTATC 59.499 47.826 0.00 0.00 42.74 2.08
1994 2364 1.075482 AAGGTGTGGGTCCATGCAG 59.925 57.895 0.00 0.00 0.00 4.41
2167 2539 3.386932 AACCATATGAGCCACATGGTT 57.613 42.857 19.23 19.23 43.10 3.67
2181 2553 1.068895 CATGGTTCAGGCTGCAAAACA 59.931 47.619 10.34 9.48 0.00 2.83
2184 2556 1.211743 GTTCAGGCTGCAAAACAAGC 58.788 50.000 10.34 0.00 0.00 4.01
2357 2730 6.749118 GCTGGCTCTAGTTTGTGATATTTTTG 59.251 38.462 0.00 0.00 0.00 2.44
2504 2877 6.040391 TGTTTCTAGTTTTGTAGCAATGCCTT 59.960 34.615 0.00 0.00 0.00 4.35
2567 2940 3.408634 ACTATTAACTTGTGGCGCAACT 58.591 40.909 17.46 0.00 32.90 3.16
3091 3464 8.937884 TGCTTCATGATTTGAAAACAAATATGG 58.062 29.630 0.00 2.41 43.64 2.74
3175 3548 5.473039 AGTGCTTTTGTCCAGAAATAATGC 58.527 37.500 0.00 0.00 0.00 3.56
3226 3599 6.149308 CACTGTTGGTTGCATCTTGTATAGAA 59.851 38.462 0.00 0.00 36.22 2.10
3230 3603 7.446931 TGTTGGTTGCATCTTGTATAGAAGAAA 59.553 33.333 15.57 4.13 35.60 2.52
3414 3787 8.877808 TTTATATGTAGCAGATGAGTTCACAG 57.122 34.615 0.00 0.00 0.00 3.66
3625 3998 5.299279 CCTTAAAGTCAACACACAGGTCAAT 59.701 40.000 0.00 0.00 0.00 2.57
3673 4046 5.010012 ACATGGAAAAGGCAAAGTTACTGAG 59.990 40.000 0.00 0.00 0.00 3.35
3718 4091 1.470098 GCATCGGATTGTGATATGGGC 59.530 52.381 0.00 0.00 0.00 5.36
3837 4210 8.328758 AGATCCAGATAAAATTGGTGAACTACA 58.671 33.333 0.00 0.00 35.89 2.74
3875 4248 6.194463 CACAACTCTTTTATATCACGCCATG 58.806 40.000 0.00 0.00 0.00 3.66
3892 4265 3.485216 GCCATGACAAACTAATTCGTCCG 60.485 47.826 0.00 0.00 0.00 4.79
3983 4356 7.122055 ACAACAATGTTTCTGGTTAACTTCTCA 59.878 33.333 5.42 0.00 35.91 3.27
4043 4416 5.667539 TTGACAAACCTTGACATTTCCAA 57.332 34.783 0.00 0.00 35.43 3.53
4059 4432 3.737559 TCCAAGTGGCTAACAATCCAT 57.262 42.857 0.00 0.00 34.47 3.41
4097 4470 7.736893 AGTAGGTAAAGGCTAACAATGATAGG 58.263 38.462 0.00 0.00 0.00 2.57
4162 4535 5.919755 TGATGCGTACTAAATCATGGGTAA 58.080 37.500 0.00 0.00 0.00 2.85
4163 4536 5.989168 TGATGCGTACTAAATCATGGGTAAG 59.011 40.000 0.00 0.00 0.00 2.34
4164 4537 4.699637 TGCGTACTAAATCATGGGTAAGG 58.300 43.478 0.00 0.00 0.00 2.69
4250 4623 1.470285 GGGCGTAATCTTAGCGACACA 60.470 52.381 0.00 0.00 34.98 3.72
4283 4657 1.199789 CGGGTGTGGTGTCAAATGATG 59.800 52.381 0.00 0.00 0.00 3.07
4296 4670 6.808212 GTGTCAAATGATGTTATGGGTTTCAG 59.192 38.462 0.00 0.00 0.00 3.02
4331 4705 2.029918 CAGCTTGTTTGGGACTAAAGGC 60.030 50.000 0.00 0.00 0.00 4.35
4337 4711 4.027437 TGTTTGGGACTAAAGGCTTTGTT 58.973 39.130 22.32 8.73 0.00 2.83
4340 4714 3.637769 TGGGACTAAAGGCTTTGTTGTT 58.362 40.909 22.32 1.84 0.00 2.83
4349 4723 3.324993 AGGCTTTGTTGTTGTTGTTGTG 58.675 40.909 0.00 0.00 0.00 3.33
4355 4732 4.060038 TGTTGTTGTTGTTGTGGTTGTT 57.940 36.364 0.00 0.00 0.00 2.83
4359 4736 3.181475 TGTTGTTGTTGTGGTTGTTGTGT 60.181 39.130 0.00 0.00 0.00 3.72
4371 4748 4.116238 GGTTGTTGTGTTGGTGTATTTGG 58.884 43.478 0.00 0.00 0.00 3.28
4391 4768 3.578716 TGGAGGAGGTCAACTCTTTACTG 59.421 47.826 0.00 0.00 45.83 2.74
4663 5040 1.202710 TGCTACACGGGCAAGAGAAAA 60.203 47.619 0.00 0.00 36.71 2.29
4798 5175 1.273838 ACACCCTATCCTCTGGCTTCA 60.274 52.381 0.00 0.00 0.00 3.02
4867 5267 8.324306 TCCTTCTATCTGACTGATGACATTTTT 58.676 33.333 5.16 0.00 36.65 1.94
4899 5300 5.251764 CAGAAGAGAGTGATGGAAAATGGT 58.748 41.667 0.00 0.00 0.00 3.55
4903 5304 3.350833 AGAGTGATGGAAAATGGTGCTC 58.649 45.455 0.00 0.00 0.00 4.26
4904 5305 3.009916 AGAGTGATGGAAAATGGTGCTCT 59.990 43.478 0.00 0.00 0.00 4.09
4953 5354 7.446769 TGTAAACCTAGCAATGTCTGTTTCTA 58.553 34.615 0.00 0.00 0.00 2.10
4958 5359 6.599638 ACCTAGCAATGTCTGTTTCTATTTCC 59.400 38.462 0.00 0.00 0.00 3.13
4959 5360 6.825721 CCTAGCAATGTCTGTTTCTATTTCCT 59.174 38.462 0.00 0.00 0.00 3.36
4975 5376 2.270275 TCCTTTGTTGTTGTTGCGTG 57.730 45.000 0.00 0.00 0.00 5.34
5047 5448 2.071540 GAAAAGGCTTTCCTGCAATGC 58.928 47.619 13.76 0.00 43.40 3.56
5050 5451 2.639327 GGCTTTCCTGCAATGCCGT 61.639 57.895 1.53 0.00 43.46 5.68
5089 5494 3.127533 GCGCGCCAACTCCTTGAT 61.128 61.111 23.24 0.00 0.00 2.57
5099 5504 4.393371 GCCAACTCCTTGATTCTACTGAAC 59.607 45.833 0.00 0.00 34.71 3.18
5103 5508 6.174720 ACTCCTTGATTCTACTGAACAACA 57.825 37.500 0.00 0.00 34.71 3.33
5104 5509 5.992217 ACTCCTTGATTCTACTGAACAACAC 59.008 40.000 0.00 0.00 34.71 3.32
5113 5518 5.587289 TCTACTGAACAACACATTTTTGCC 58.413 37.500 0.00 0.00 0.00 4.52
5138 5574 6.103330 TGCAGTTTAAAAGAAGAAAACCACC 58.897 36.000 0.00 0.00 34.39 4.61
5163 5599 7.255139 CCGAGTTCAGACTAATGGAAAACTTTT 60.255 37.037 0.00 0.00 35.88 2.27
5164 5600 7.798982 CGAGTTCAGACTAATGGAAAACTTTTC 59.201 37.037 5.78 5.78 35.88 2.29
5165 5601 7.639945 AGTTCAGACTAATGGAAAACTTTTCG 58.360 34.615 7.94 0.00 33.32 3.46
5166 5602 7.497909 AGTTCAGACTAATGGAAAACTTTTCGA 59.502 33.333 7.94 5.01 33.32 3.71
5167 5603 7.795482 TCAGACTAATGGAAAACTTTTCGAA 57.205 32.000 7.94 0.00 0.00 3.71
5172 5608 9.556030 GACTAATGGAAAACTTTTCGAAATAGG 57.444 33.333 12.12 7.82 0.00 2.57
5173 5609 9.292195 ACTAATGGAAAACTTTTCGAAATAGGA 57.708 29.630 12.12 0.00 0.00 2.94
5174 5610 9.774742 CTAATGGAAAACTTTTCGAAATAGGAG 57.225 33.333 12.12 8.54 0.00 3.69
5175 5611 7.996098 ATGGAAAACTTTTCGAAATAGGAGA 57.004 32.000 12.12 0.00 0.00 3.71
5176 5612 7.996098 TGGAAAACTTTTCGAAATAGGAGAT 57.004 32.000 12.12 0.00 0.00 2.75
5177 5613 7.816640 TGGAAAACTTTTCGAAATAGGAGATG 58.183 34.615 12.12 0.00 0.00 2.90
5178 5614 7.447238 TGGAAAACTTTTCGAAATAGGAGATGT 59.553 33.333 12.12 0.00 0.00 3.06
5179 5615 7.750903 GGAAAACTTTTCGAAATAGGAGATGTG 59.249 37.037 12.12 0.00 0.00 3.21
5180 5616 7.745620 AAACTTTTCGAAATAGGAGATGTGT 57.254 32.000 12.12 0.00 0.00 3.72
5181 5617 6.727824 ACTTTTCGAAATAGGAGATGTGTG 57.272 37.500 12.12 0.00 0.00 3.82
5182 5618 5.122396 ACTTTTCGAAATAGGAGATGTGTGC 59.878 40.000 12.12 0.00 0.00 4.57
5183 5619 3.885724 TCGAAATAGGAGATGTGTGCA 57.114 42.857 0.00 0.00 0.00 4.57
5184 5620 4.406648 TCGAAATAGGAGATGTGTGCAT 57.593 40.909 0.00 0.00 38.18 3.96
5185 5621 5.529581 TCGAAATAGGAGATGTGTGCATA 57.470 39.130 0.00 0.00 35.07 3.14
5187 5623 6.524734 TCGAAATAGGAGATGTGTGCATAAT 58.475 36.000 0.00 0.00 35.07 1.28
5188 5624 7.666623 TCGAAATAGGAGATGTGTGCATAATA 58.333 34.615 0.00 0.00 35.07 0.98
5189 5625 8.314021 TCGAAATAGGAGATGTGTGCATAATAT 58.686 33.333 0.00 0.00 35.07 1.28
5190 5626 8.939929 CGAAATAGGAGATGTGTGCATAATATT 58.060 33.333 0.00 0.00 35.07 1.28
5192 5628 9.578576 AAATAGGAGATGTGTGCATAATATTGT 57.421 29.630 0.00 0.00 35.07 2.71
5193 5629 9.578576 AATAGGAGATGTGTGCATAATATTGTT 57.421 29.630 0.00 0.00 35.07 2.83
5194 5630 7.268199 AGGAGATGTGTGCATAATATTGTTG 57.732 36.000 0.00 0.00 35.07 3.33
5195 5631 6.263842 AGGAGATGTGTGCATAATATTGTTGG 59.736 38.462 0.00 0.00 35.07 3.77
5197 5633 7.031226 AGATGTGTGCATAATATTGTTGGAC 57.969 36.000 14.11 14.11 35.07 4.02
5198 5634 5.228579 TGTGTGCATAATATTGTTGGACG 57.771 39.130 15.24 0.00 34.81 4.79
5199 5635 4.095632 TGTGTGCATAATATTGTTGGACGG 59.904 41.667 15.24 0.00 34.81 4.79
5201 5637 3.315191 GTGCATAATATTGTTGGACGGCT 59.685 43.478 0.00 0.00 0.00 5.52
5202 5638 3.314913 TGCATAATATTGTTGGACGGCTG 59.685 43.478 0.00 0.00 0.00 4.85
5203 5639 3.563808 GCATAATATTGTTGGACGGCTGA 59.436 43.478 0.00 0.00 0.00 4.26
5204 5640 4.319766 GCATAATATTGTTGGACGGCTGAG 60.320 45.833 0.00 0.00 0.00 3.35
5206 5642 3.845781 ATATTGTTGGACGGCTGAGAT 57.154 42.857 0.00 0.00 0.00 2.75
5208 5644 0.036388 TTGTTGGACGGCTGAGATCC 60.036 55.000 0.00 0.00 0.00 3.36
5209 5645 0.904865 TGTTGGACGGCTGAGATCCT 60.905 55.000 0.00 0.00 33.34 3.24
5212 5648 1.860641 TGGACGGCTGAGATCCTTAA 58.139 50.000 0.00 0.00 33.34 1.85
5213 5649 1.480954 TGGACGGCTGAGATCCTTAAC 59.519 52.381 0.00 0.00 33.34 2.01
5215 5651 2.482142 GGACGGCTGAGATCCTTAACAG 60.482 54.545 0.00 0.00 0.00 3.16
5217 5653 2.567615 ACGGCTGAGATCCTTAACAGTT 59.432 45.455 0.00 0.00 33.57 3.16
5218 5654 2.932614 CGGCTGAGATCCTTAACAGTTG 59.067 50.000 0.00 0.00 33.57 3.16
5220 5656 4.187694 GGCTGAGATCCTTAACAGTTGAG 58.812 47.826 0.00 0.00 33.57 3.02
5221 5657 4.323104 GGCTGAGATCCTTAACAGTTGAGT 60.323 45.833 4.48 0.00 33.57 3.41
5224 5660 6.174720 TGAGATCCTTAACAGTTGAGTTGT 57.825 37.500 4.48 0.00 33.07 3.32
5225 5661 5.991606 TGAGATCCTTAACAGTTGAGTTGTG 59.008 40.000 4.48 0.00 33.07 3.33
5227 5663 6.357367 AGATCCTTAACAGTTGAGTTGTGTT 58.643 36.000 4.48 0.00 38.04 3.32
5228 5664 5.811399 TCCTTAACAGTTGAGTTGTGTTG 57.189 39.130 4.48 0.00 35.95 3.33
5229 5665 5.250200 TCCTTAACAGTTGAGTTGTGTTGT 58.750 37.500 4.48 0.00 35.95 3.32
5230 5666 5.708230 TCCTTAACAGTTGAGTTGTGTTGTT 59.292 36.000 4.48 0.00 35.95 2.83
5231 5667 5.799936 CCTTAACAGTTGAGTTGTGTTGTTG 59.200 40.000 4.48 0.00 35.95 3.33
5232 5668 3.216147 ACAGTTGAGTTGTGTTGTTGC 57.784 42.857 0.00 0.00 0.00 4.17
5233 5669 2.556189 ACAGTTGAGTTGTGTTGTTGCA 59.444 40.909 0.00 0.00 0.00 4.08
5234 5670 3.193267 ACAGTTGAGTTGTGTTGTTGCAT 59.807 39.130 0.00 0.00 0.00 3.96
5237 5673 2.538437 TGAGTTGTGTTGTTGCATTGC 58.462 42.857 0.46 0.46 0.00 3.56
5238 5674 2.094338 TGAGTTGTGTTGTTGCATTGCA 60.094 40.909 7.38 7.38 36.47 4.08
5239 5675 3.125316 GAGTTGTGTTGTTGCATTGCAT 58.875 40.909 12.95 0.00 38.76 3.96
5241 5677 3.310227 AGTTGTGTTGTTGCATTGCATTG 59.690 39.130 12.95 4.20 38.76 2.82
5242 5678 2.210961 TGTGTTGTTGCATTGCATTGG 58.789 42.857 12.95 0.00 38.76 3.16
5243 5679 2.159000 TGTGTTGTTGCATTGCATTGGA 60.159 40.909 12.95 4.71 38.76 3.53
5244 5680 2.477375 GTGTTGTTGCATTGCATTGGAG 59.523 45.455 12.95 0.00 38.76 3.86
5245 5681 2.102757 TGTTGTTGCATTGCATTGGAGT 59.897 40.909 12.95 0.00 38.76 3.85
5246 5682 3.132925 GTTGTTGCATTGCATTGGAGTT 58.867 40.909 12.95 0.00 38.76 3.01
5247 5683 2.756829 TGTTGCATTGCATTGGAGTTG 58.243 42.857 12.95 0.00 38.76 3.16
5249 5685 1.630223 TGCATTGCATTGGAGTTGGA 58.370 45.000 7.38 0.00 31.71 3.53
5250 5686 1.546923 TGCATTGCATTGGAGTTGGAG 59.453 47.619 7.38 0.00 31.71 3.86
5251 5687 1.134907 GCATTGCATTGGAGTTGGAGG 60.135 52.381 10.41 0.00 0.00 4.30
5252 5688 1.479323 CATTGCATTGGAGTTGGAGGG 59.521 52.381 0.47 0.00 0.00 4.30
5253 5689 0.776810 TTGCATTGGAGTTGGAGGGA 59.223 50.000 0.00 0.00 0.00 4.20
5255 5691 1.272092 TGCATTGGAGTTGGAGGGAAG 60.272 52.381 0.00 0.00 0.00 3.46
5259 5699 1.289160 TGGAGTTGGAGGGAAGATGG 58.711 55.000 0.00 0.00 0.00 3.51
5289 5729 3.999001 CAGTGCTCTGAAAACATAGCTCA 59.001 43.478 10.27 0.00 43.76 4.26
5304 5744 5.775701 ACATAGCTCATTTCCTCCGTATAGT 59.224 40.000 0.00 0.00 0.00 2.12
5305 5745 4.592485 AGCTCATTTCCTCCGTATAGTG 57.408 45.455 0.00 0.00 0.00 2.74
5386 5826 1.414919 ACAGGGAGCAACGAAGTGTTA 59.585 47.619 0.00 0.00 45.00 2.41
5395 5835 5.548406 AGCAACGAAGTGTTATAGGAACTT 58.452 37.500 0.00 0.00 45.00 2.66
5396 5836 5.995897 AGCAACGAAGTGTTATAGGAACTTT 59.004 36.000 0.00 0.00 45.00 2.66
5397 5837 6.073222 AGCAACGAAGTGTTATAGGAACTTTG 60.073 38.462 0.00 8.75 45.00 2.77
5399 5839 5.861727 ACGAAGTGTTATAGGAACTTTGGT 58.138 37.500 12.54 6.41 42.51 3.67
5402 5899 6.312180 CGAAGTGTTATAGGAACTTTGGTACC 59.688 42.308 4.43 4.43 41.75 3.34
5423 5920 5.663456 ACCGACAGGAAAATTTATAGCGTA 58.337 37.500 0.00 0.00 41.02 4.42
5446 5943 3.323758 GACATGCTACGGGGGCACA 62.324 63.158 0.00 0.00 42.69 4.57
5451 5948 2.106332 CTACGGGGGCACATCGAC 59.894 66.667 7.93 0.00 0.00 4.20
5468 5965 4.939368 CCCGTTCCGTGGCAACCA 62.939 66.667 0.00 0.00 0.00 3.67
5477 5974 3.756802 TGGCAACCACACGATTGG 58.243 55.556 5.63 5.63 43.04 3.16
5478 5975 1.149401 TGGCAACCACACGATTGGA 59.851 52.632 13.07 0.00 39.24 3.53
5479 5976 0.888736 TGGCAACCACACGATTGGAG 60.889 55.000 13.07 6.89 39.24 3.86
5480 5977 0.605319 GGCAACCACACGATTGGAGA 60.605 55.000 13.07 0.00 39.24 3.71
5481 5978 1.234821 GCAACCACACGATTGGAGAA 58.765 50.000 13.07 0.00 39.24 2.87
5482 5979 1.606668 GCAACCACACGATTGGAGAAA 59.393 47.619 13.07 0.00 39.24 2.52
5483 5980 2.228822 GCAACCACACGATTGGAGAAAT 59.771 45.455 13.07 0.00 39.24 2.17
5484 5981 3.825308 CAACCACACGATTGGAGAAATG 58.175 45.455 13.07 2.24 39.24 2.32
5485 5982 3.140325 ACCACACGATTGGAGAAATGT 57.860 42.857 13.07 0.00 39.24 2.71
5486 5983 3.486383 ACCACACGATTGGAGAAATGTT 58.514 40.909 13.07 0.00 39.24 2.71
5487 5984 3.888930 ACCACACGATTGGAGAAATGTTT 59.111 39.130 13.07 0.00 39.24 2.83
5488 5985 4.340950 ACCACACGATTGGAGAAATGTTTT 59.659 37.500 13.07 0.00 39.24 2.43
5489 5986 5.163457 ACCACACGATTGGAGAAATGTTTTT 60.163 36.000 13.07 0.00 39.24 1.94
5520 6017 7.487509 GGGAAACAATTGGAAAAATGTTTGTTG 59.512 33.333 10.83 0.00 44.53 3.33
5528 6025 8.558973 TTGGAAAAATGTTTGTTGAACTGATT 57.441 26.923 0.00 0.00 39.08 2.57
5533 6030 6.774354 AATGTTTGTTGAACTGATTCATGC 57.226 33.333 0.00 0.00 44.36 4.06
5570 6067 4.290155 ACATGAAAACGTGAAACATGAGC 58.710 39.130 22.43 0.00 40.13 4.26
5574 6071 3.609103 AAACGTGAAACATGAGCAGTC 57.391 42.857 0.00 0.00 35.74 3.51
5699 6197 1.103398 ATAATGCAGGACTTGGGCGC 61.103 55.000 0.00 0.00 0.00 6.53
5703 6201 3.423154 CAGGACTTGGGCGCGAAC 61.423 66.667 12.10 0.74 0.00 3.95
5709 6207 1.198178 GACTTGGGCGCGAACAAATTA 59.802 47.619 12.10 0.00 0.00 1.40
5710 6208 1.816224 ACTTGGGCGCGAACAAATTAT 59.184 42.857 12.10 0.00 0.00 1.28
5711 6209 2.230266 ACTTGGGCGCGAACAAATTATT 59.770 40.909 12.10 0.00 0.00 1.40
5712 6210 3.440872 ACTTGGGCGCGAACAAATTATTA 59.559 39.130 12.10 0.00 0.00 0.98
5713 6211 3.408288 TGGGCGCGAACAAATTATTAC 57.592 42.857 12.10 0.00 0.00 1.89
5714 6212 2.747989 TGGGCGCGAACAAATTATTACA 59.252 40.909 12.10 0.00 0.00 2.41
5715 6213 3.378742 TGGGCGCGAACAAATTATTACAT 59.621 39.130 12.10 0.00 0.00 2.29
5716 6214 4.575236 TGGGCGCGAACAAATTATTACATA 59.425 37.500 12.10 0.00 0.00 2.29
5717 6215 5.239744 TGGGCGCGAACAAATTATTACATAT 59.760 36.000 12.10 0.00 0.00 1.78
5718 6216 5.567534 GGGCGCGAACAAATTATTACATATG 59.432 40.000 12.10 0.00 0.00 1.78
5719 6217 5.567534 GGCGCGAACAAATTATTACATATGG 59.432 40.000 12.10 0.00 0.00 2.74
5720 6218 5.567534 GCGCGAACAAATTATTACATATGGG 59.432 40.000 12.10 0.00 0.00 4.00
5721 6219 6.664515 CGCGAACAAATTATTACATATGGGT 58.335 36.000 0.00 0.00 0.00 4.51
5722 6220 6.577055 CGCGAACAAATTATTACATATGGGTG 59.423 38.462 0.00 0.00 0.00 4.61
5723 6221 6.362283 GCGAACAAATTATTACATATGGGTGC 59.638 38.462 7.80 0.00 0.00 5.01
5724 6222 6.577055 CGAACAAATTATTACATATGGGTGCG 59.423 38.462 7.80 0.00 0.00 5.34
5725 6223 5.768317 ACAAATTATTACATATGGGTGCGC 58.232 37.500 7.80 0.00 0.00 6.09
5726 6224 5.300539 ACAAATTATTACATATGGGTGCGCA 59.699 36.000 5.66 5.66 0.00 6.09
5727 6225 6.183360 ACAAATTATTACATATGGGTGCGCAA 60.183 34.615 14.00 0.00 0.00 4.85
5728 6226 5.627499 ATTATTACATATGGGTGCGCAAG 57.373 39.130 14.00 0.00 43.44 4.01
5747 6245 3.883997 CTCTCCGGCTTAGAGCATC 57.116 57.895 5.77 0.00 44.75 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 32 2.264480 CGCCTCGTGGGAATGTGA 59.736 61.111 5.54 0.00 37.23 3.58
266 271 4.582240 GGGTTTCCTCCATGAGATTCATTC 59.418 45.833 0.00 0.00 34.28 2.67
336 341 4.142708 TGCTGCAGAAAATTATACACCACG 60.143 41.667 20.43 0.00 0.00 4.94
378 383 1.132453 GCGGATTACAAAGGTTGCCTC 59.868 52.381 0.00 0.00 30.89 4.70
432 437 7.931578 AACTGACAATAATTATGGAACGGAA 57.068 32.000 6.86 0.00 0.00 4.30
476 481 7.593825 ACCACAAGAGCAAATAACTGATAAAC 58.406 34.615 0.00 0.00 0.00 2.01
521 526 1.741706 CTGCGATCAAGGATGCAAAGT 59.258 47.619 0.00 0.00 36.82 2.66
539 544 1.986882 AAGTTCAGCCAAAGACCCTG 58.013 50.000 0.00 0.00 0.00 4.45
627 632 7.201670 CGAAGGTACCACTTTCAAAAAGTAACT 60.202 37.037 15.94 0.00 34.30 2.24
628 633 6.908820 CGAAGGTACCACTTTCAAAAAGTAAC 59.091 38.462 15.94 4.66 34.30 2.50
739 744 3.967467 ATTCCAAAGAGATGGCCAGAT 57.033 42.857 13.05 0.66 40.46 2.90
741 746 4.465305 AGAAAATTCCAAAGAGATGGCCAG 59.535 41.667 13.05 0.00 40.46 4.85
772 777 7.484959 GCACTGTAAATAGTTGCCAAAATAGTC 59.515 37.037 0.00 0.00 0.00 2.59
797 802 5.048083 TGTTCAGAACCCAAATGATAAGTGC 60.048 40.000 10.93 0.00 0.00 4.40
875 881 7.732315 TGCATTGCATGAGGAAAAACAATTTTC 60.732 33.333 7.38 5.66 42.48 2.29
879 885 4.453136 GTGCATTGCATGAGGAAAAACAAT 59.547 37.500 15.49 0.00 41.91 2.71
981 987 6.434340 CCTCCATTTTAAGGTTGACTTTAGCT 59.566 38.462 0.00 0.00 40.64 3.32
1358 1364 2.410902 CGAGTCTATCACGAGATGAGCG 60.411 54.545 5.53 4.92 41.91 5.03
1421 1635 6.865726 AGCGATTACAGCTCAAATGAGTATAG 59.134 38.462 11.77 3.02 41.83 1.31
1482 1696 9.007901 AGACATTCAAGATAAGAAGTTTTCTGG 57.992 33.333 0.00 0.00 40.59 3.86
1506 1720 6.942005 ACCACAAATTCATGTCTCACATTAGA 59.058 34.615 0.00 0.00 36.53 2.10
1528 1745 6.379703 ACAATTGCTTGGCATATTAAGTACCA 59.620 34.615 5.05 0.00 38.76 3.25
1529 1746 6.805713 ACAATTGCTTGGCATATTAAGTACC 58.194 36.000 5.05 0.00 38.76 3.34
1558 1775 4.776349 TGCTCCTTTCAAACTGTAGACAA 58.224 39.130 0.00 0.00 0.00 3.18
1725 1950 1.834263 AGTTCCTCAGGGTATGCACTC 59.166 52.381 0.00 0.00 0.00 3.51
1768 1993 7.326063 GCGAACTTCAACTGCAAATTACTAATT 59.674 33.333 0.00 0.00 0.00 1.40
1886 2236 9.915629 GAAAAGATGAAGTCTAGAAACTAGTCA 57.084 33.333 0.00 0.00 35.67 3.41
1911 2261 3.878103 GGAGTACGAATGCTCTGACTAGA 59.122 47.826 0.00 0.00 37.68 2.43
1981 2351 1.959042 CTATGTCTGCATGGACCCAC 58.041 55.000 3.85 0.00 35.88 4.61
2015 2385 4.407365 CCTTTACAACAAGGGGAGACAAT 58.593 43.478 0.00 0.00 39.95 2.71
2167 2539 1.042003 TGGCTTGTTTTGCAGCCTGA 61.042 50.000 12.97 0.00 46.77 3.86
2181 2553 3.669939 ATATAAAGTGGCACCTGGCTT 57.330 42.857 15.27 0.00 44.01 4.35
2184 2556 7.039993 GGGTATTAAATATAAAGTGGCACCTGG 60.040 40.741 15.27 0.00 0.00 4.45
2357 2730 9.840427 TCAGCTTTAATCAATTTACTTGCTTAC 57.160 29.630 0.00 0.00 34.66 2.34
2465 2838 7.715265 AACTAGAAACATACACACAACTGAG 57.285 36.000 0.00 0.00 0.00 3.35
2504 2877 7.092444 ACACCACAGATAGGAATCCAAGAAATA 60.092 37.037 0.61 0.00 31.98 1.40
3091 3464 4.246458 AGCATTTTAGGTGTTCGAGAGAC 58.754 43.478 0.00 0.00 41.84 3.36
3175 3548 5.966636 TTGTGCTCTATAAGTATGCAACG 57.033 39.130 0.00 0.00 35.34 4.10
3230 3603 7.681939 TTATCGTAAGCAGGAAATGAGTTTT 57.318 32.000 0.00 0.00 37.18 2.43
3298 3671 5.889853 ACTGACCTTGACATGCAATTATGAT 59.110 36.000 0.00 0.00 35.59 2.45
3673 4046 5.371526 TCTTGAGGTGATATTTCAGGCATC 58.628 41.667 0.00 0.00 30.85 3.91
3875 4248 2.344025 AGGCGGACGAATTAGTTTGTC 58.656 47.619 9.36 9.36 44.63 3.18
3892 4265 2.570135 CTCAAGCTCCTCCAAATAGGC 58.430 52.381 0.00 0.00 36.51 3.93
4059 4432 6.877322 GCCTTTACCTACTCAATTCACTAACA 59.123 38.462 0.00 0.00 0.00 2.41
4070 4443 6.614694 TCATTGTTAGCCTTTACCTACTCA 57.385 37.500 0.00 0.00 0.00 3.41
4071 4444 7.873505 CCTATCATTGTTAGCCTTTACCTACTC 59.126 40.741 0.00 0.00 0.00 2.59
4119 4492 6.015688 GCATCAAATCCCATTAGTGATCATGT 60.016 38.462 0.00 0.00 0.00 3.21
4162 4535 7.505258 TCTTTAAAATTGCCACTTTTAAGCCT 58.495 30.769 11.12 0.00 38.54 4.58
4163 4536 7.722795 TCTTTAAAATTGCCACTTTTAAGCC 57.277 32.000 11.12 0.00 38.54 4.35
4164 4537 8.826710 AGTTCTTTAAAATTGCCACTTTTAAGC 58.173 29.630 11.12 5.80 38.54 3.09
4250 4623 0.996583 ACACCCGGTTCCAATATGGT 59.003 50.000 0.00 0.00 39.03 3.55
4283 4657 3.118223 AGGCTAGAGCTGAAACCCATAAC 60.118 47.826 0.00 0.00 41.70 1.89
4296 4670 1.051556 AAGCTGGGGTAGGCTAGAGC 61.052 60.000 0.00 0.53 37.87 4.09
4331 4705 4.509600 ACAACCACAACAACAACAACAAAG 59.490 37.500 0.00 0.00 0.00 2.77
4337 4711 3.181475 ACACAACAACCACAACAACAACA 60.181 39.130 0.00 0.00 0.00 3.33
4340 4714 3.384668 CAACACAACAACCACAACAACA 58.615 40.909 0.00 0.00 0.00 3.33
4349 4723 4.116238 CCAAATACACCAACACAACAACC 58.884 43.478 0.00 0.00 0.00 3.77
4355 4732 3.497763 CCTCCTCCAAATACACCAACACA 60.498 47.826 0.00 0.00 0.00 3.72
4359 4736 2.983192 TGACCTCCTCCAAATACACCAA 59.017 45.455 0.00 0.00 0.00 3.67
4371 4748 4.875561 ACAGTAAAGAGTTGACCTCCTC 57.124 45.455 0.00 0.00 41.47 3.71
4391 4768 6.487689 AGTCTGTAAGCAAAGCAAGATAAC 57.512 37.500 0.00 0.00 0.00 1.89
4663 5040 1.003573 AATCTTCGGCCTCCTCCCT 59.996 57.895 0.00 0.00 0.00 4.20
4798 5175 7.331026 TCATCATCTAATCAAACGGAAGAACT 58.669 34.615 0.00 0.00 0.00 3.01
4867 5267 2.361230 TCTCTTCTGGCTCCGCGA 60.361 61.111 8.23 0.00 0.00 5.87
4953 5354 3.616379 CACGCAACAACAACAAAGGAAAT 59.384 39.130 0.00 0.00 0.00 2.17
4958 5359 1.653114 CCACACGCAACAACAACAAAG 59.347 47.619 0.00 0.00 0.00 2.77
4959 5360 1.000163 ACCACACGCAACAACAACAAA 60.000 42.857 0.00 0.00 0.00 2.83
4975 5376 4.876107 TGACTCTTTCAGAACAAAGACCAC 59.124 41.667 0.00 0.00 37.45 4.16
4998 5399 7.888424 AGTTACACTGTAACAACCAAAGTTTT 58.112 30.769 26.62 5.79 32.45 2.43
4999 5400 7.457024 AGTTACACTGTAACAACCAAAGTTT 57.543 32.000 26.62 6.20 32.45 2.66
5048 5449 3.058501 AGTGCCCGTCTGAAAATAAAACG 60.059 43.478 0.00 0.00 0.00 3.60
5050 5451 4.794655 GCAAGTGCCCGTCTGAAAATAAAA 60.795 41.667 0.00 0.00 34.31 1.52
5089 5494 6.039616 GGCAAAAATGTGTTGTTCAGTAGAA 58.960 36.000 0.00 0.00 0.00 2.10
5099 5504 2.553086 ACTGCAGGCAAAAATGTGTTG 58.447 42.857 19.93 0.00 0.00 3.33
5103 5508 6.112058 TCTTTTAAACTGCAGGCAAAAATGT 58.888 32.000 19.93 0.00 0.00 2.71
5104 5509 6.601741 TCTTTTAAACTGCAGGCAAAAATG 57.398 33.333 19.93 13.65 0.00 2.32
5113 5518 6.255670 GGTGGTTTTCTTCTTTTAAACTGCAG 59.744 38.462 13.48 13.48 33.44 4.41
5138 5574 6.787085 AAGTTTTCCATTAGTCTGAACTCG 57.213 37.500 0.00 0.00 36.92 4.18
5163 5599 3.885724 TGCACACATCTCCTATTTCGA 57.114 42.857 0.00 0.00 0.00 3.71
5164 5600 6.791887 ATTATGCACACATCTCCTATTTCG 57.208 37.500 0.00 0.00 37.74 3.46
5166 5602 9.578576 ACAATATTATGCACACATCTCCTATTT 57.421 29.630 0.00 0.00 37.74 1.40
5167 5603 9.578576 AACAATATTATGCACACATCTCCTATT 57.421 29.630 0.00 0.00 37.74 1.73
5170 5606 6.263842 CCAACAATATTATGCACACATCTCCT 59.736 38.462 0.00 0.00 37.74 3.69
5171 5607 6.262944 TCCAACAATATTATGCACACATCTCC 59.737 38.462 0.00 0.00 37.74 3.71
5172 5608 7.134815 GTCCAACAATATTATGCACACATCTC 58.865 38.462 0.00 0.00 37.74 2.75
5173 5609 6.238456 CGTCCAACAATATTATGCACACATCT 60.238 38.462 0.00 0.00 37.74 2.90
5174 5610 5.909054 CGTCCAACAATATTATGCACACATC 59.091 40.000 0.00 0.00 37.74 3.06
5175 5611 5.221028 CCGTCCAACAATATTATGCACACAT 60.221 40.000 0.00 0.00 40.49 3.21
5176 5612 4.095632 CCGTCCAACAATATTATGCACACA 59.904 41.667 0.00 0.00 0.00 3.72
5177 5613 4.597079 CCGTCCAACAATATTATGCACAC 58.403 43.478 0.00 0.00 0.00 3.82
5178 5614 3.066064 GCCGTCCAACAATATTATGCACA 59.934 43.478 0.00 0.00 0.00 4.57
5179 5615 3.315191 AGCCGTCCAACAATATTATGCAC 59.685 43.478 0.00 0.00 0.00 4.57
5180 5616 3.314913 CAGCCGTCCAACAATATTATGCA 59.685 43.478 0.00 0.00 0.00 3.96
5181 5617 3.563808 TCAGCCGTCCAACAATATTATGC 59.436 43.478 0.00 0.00 0.00 3.14
5182 5618 5.056480 TCTCAGCCGTCCAACAATATTATG 58.944 41.667 0.00 0.00 0.00 1.90
5183 5619 5.290493 TCTCAGCCGTCCAACAATATTAT 57.710 39.130 0.00 0.00 0.00 1.28
5184 5620 4.746535 TCTCAGCCGTCCAACAATATTA 57.253 40.909 0.00 0.00 0.00 0.98
5185 5621 3.627395 TCTCAGCCGTCCAACAATATT 57.373 42.857 0.00 0.00 0.00 1.28
5187 5623 2.158957 GGATCTCAGCCGTCCAACAATA 60.159 50.000 0.00 0.00 32.23 1.90
5188 5624 1.407437 GGATCTCAGCCGTCCAACAAT 60.407 52.381 0.00 0.00 32.23 2.71
5189 5625 0.036388 GGATCTCAGCCGTCCAACAA 60.036 55.000 0.00 0.00 32.23 2.83
5190 5626 0.904865 AGGATCTCAGCCGTCCAACA 60.905 55.000 0.00 0.00 34.42 3.33
5191 5627 0.250513 AAGGATCTCAGCCGTCCAAC 59.749 55.000 0.00 0.00 34.42 3.77
5192 5628 1.860641 TAAGGATCTCAGCCGTCCAA 58.139 50.000 0.00 0.00 34.42 3.53
5193 5629 1.480954 GTTAAGGATCTCAGCCGTCCA 59.519 52.381 0.00 0.00 34.42 4.02
5194 5630 1.480954 TGTTAAGGATCTCAGCCGTCC 59.519 52.381 0.00 0.00 0.00 4.79
5195 5631 2.166664 ACTGTTAAGGATCTCAGCCGTC 59.833 50.000 0.00 0.00 0.00 4.79
5197 5633 2.932614 CAACTGTTAAGGATCTCAGCCG 59.067 50.000 0.00 0.00 0.00 5.52
5198 5634 4.187694 CTCAACTGTTAAGGATCTCAGCC 58.812 47.826 0.00 0.00 0.00 4.85
5199 5635 4.826556 ACTCAACTGTTAAGGATCTCAGC 58.173 43.478 0.00 0.00 0.00 4.26
5201 5637 5.991606 CACAACTCAACTGTTAAGGATCTCA 59.008 40.000 0.00 0.00 0.00 3.27
5202 5638 5.992217 ACACAACTCAACTGTTAAGGATCTC 59.008 40.000 0.00 0.00 0.00 2.75
5203 5639 5.930135 ACACAACTCAACTGTTAAGGATCT 58.070 37.500 0.00 0.00 0.00 2.75
5204 5640 6.038271 ACAACACAACTCAACTGTTAAGGATC 59.962 38.462 0.00 0.00 0.00 3.36
5206 5642 5.250200 ACAACACAACTCAACTGTTAAGGA 58.750 37.500 0.00 0.00 0.00 3.36
5208 5644 5.286082 GCAACAACACAACTCAACTGTTAAG 59.714 40.000 0.00 0.00 0.00 1.85
5209 5645 5.157781 GCAACAACACAACTCAACTGTTAA 58.842 37.500 0.00 0.00 0.00 2.01
5212 5648 2.556189 TGCAACAACACAACTCAACTGT 59.444 40.909 0.00 0.00 0.00 3.55
5213 5649 3.214697 TGCAACAACACAACTCAACTG 57.785 42.857 0.00 0.00 0.00 3.16
5215 5651 3.242059 GCAATGCAACAACACAACTCAAC 60.242 43.478 0.00 0.00 0.00 3.18
5217 5653 2.094338 TGCAATGCAACAACACAACTCA 60.094 40.909 5.01 0.00 34.76 3.41
5218 5654 2.538437 TGCAATGCAACAACACAACTC 58.462 42.857 5.01 0.00 34.76 3.01
5220 5656 3.546417 CCAATGCAATGCAACAACACAAC 60.546 43.478 13.45 0.00 43.62 3.32
5221 5657 2.612672 CCAATGCAATGCAACAACACAA 59.387 40.909 13.45 0.00 43.62 3.33
5224 5660 2.102757 ACTCCAATGCAATGCAACAACA 59.897 40.909 13.45 0.00 43.62 3.33
5225 5661 2.758009 ACTCCAATGCAATGCAACAAC 58.242 42.857 13.45 0.00 43.62 3.32
5227 5663 2.548280 CCAACTCCAATGCAATGCAACA 60.548 45.455 13.45 0.00 43.62 3.33
5228 5664 2.070783 CCAACTCCAATGCAATGCAAC 58.929 47.619 13.45 0.00 43.62 4.17
5229 5665 1.969208 TCCAACTCCAATGCAATGCAA 59.031 42.857 13.45 0.00 43.62 4.08
5230 5666 1.546923 CTCCAACTCCAATGCAATGCA 59.453 47.619 11.44 11.44 44.86 3.96
5231 5667 1.134907 CCTCCAACTCCAATGCAATGC 60.135 52.381 0.00 0.00 0.00 3.56
5232 5668 1.479323 CCCTCCAACTCCAATGCAATG 59.521 52.381 0.00 0.00 0.00 2.82
5233 5669 1.358787 TCCCTCCAACTCCAATGCAAT 59.641 47.619 0.00 0.00 0.00 3.56
5234 5670 0.776810 TCCCTCCAACTCCAATGCAA 59.223 50.000 0.00 0.00 0.00 4.08
5237 5673 3.285484 CATCTTCCCTCCAACTCCAATG 58.715 50.000 0.00 0.00 0.00 2.82
5238 5674 2.243221 CCATCTTCCCTCCAACTCCAAT 59.757 50.000 0.00 0.00 0.00 3.16
5239 5675 1.635487 CCATCTTCCCTCCAACTCCAA 59.365 52.381 0.00 0.00 0.00 3.53
5241 5677 0.106967 GCCATCTTCCCTCCAACTCC 60.107 60.000 0.00 0.00 0.00 3.85
5242 5678 0.106967 GGCCATCTTCCCTCCAACTC 60.107 60.000 0.00 0.00 0.00 3.01
5243 5679 0.846427 TGGCCATCTTCCCTCCAACT 60.846 55.000 0.00 0.00 0.00 3.16
5244 5680 0.394899 CTGGCCATCTTCCCTCCAAC 60.395 60.000 5.51 0.00 0.00 3.77
5245 5681 2.001803 CTGGCCATCTTCCCTCCAA 58.998 57.895 5.51 0.00 0.00 3.53
5246 5682 2.683465 GCTGGCCATCTTCCCTCCA 61.683 63.158 5.51 0.00 0.00 3.86
5247 5683 2.194326 GCTGGCCATCTTCCCTCC 59.806 66.667 5.51 0.00 0.00 4.30
5249 5685 3.004951 CTGCTGGCCATCTTCCCT 58.995 61.111 5.51 0.00 0.00 4.20
5250 5686 2.832201 GCTGCTGGCCATCTTCCC 60.832 66.667 5.51 0.00 34.27 3.97
5251 5687 2.044650 TGCTGCTGGCCATCTTCC 60.045 61.111 5.51 0.00 40.92 3.46
5252 5688 1.378250 ACTGCTGCTGGCCATCTTC 60.378 57.895 5.51 0.00 40.92 2.87
5253 5689 1.677966 CACTGCTGCTGGCCATCTT 60.678 57.895 5.51 0.00 40.92 2.40
5255 5691 3.823330 GCACTGCTGCTGGCCATC 61.823 66.667 5.51 1.26 40.63 3.51
5283 5723 4.523173 CCACTATACGGAGGAAATGAGCTA 59.477 45.833 0.00 0.00 0.00 3.32
5289 5729 2.224305 GCTGCCACTATACGGAGGAAAT 60.224 50.000 0.00 0.00 0.00 2.17
5361 5801 3.726517 CGTTGCTCCCTGTTGGCG 61.727 66.667 0.00 0.00 0.00 5.69
5386 5826 3.197116 CCTGTCGGTACCAAAGTTCCTAT 59.803 47.826 13.54 0.00 31.44 2.57
5395 5835 6.316890 GCTATAAATTTTCCTGTCGGTACCAA 59.683 38.462 13.54 0.00 0.00 3.67
5396 5836 5.818857 GCTATAAATTTTCCTGTCGGTACCA 59.181 40.000 13.54 0.00 0.00 3.25
5397 5837 5.050567 CGCTATAAATTTTCCTGTCGGTACC 60.051 44.000 0.16 0.16 0.00 3.34
5399 5839 5.663456 ACGCTATAAATTTTCCTGTCGGTA 58.337 37.500 0.00 0.00 0.00 4.02
5402 5899 6.590357 CCATACGCTATAAATTTTCCTGTCG 58.410 40.000 0.00 0.00 0.00 4.35
5423 5920 2.108976 CCCGTAGCATGTCGCCAT 59.891 61.111 0.00 0.00 44.04 4.40
5433 5930 3.845259 TCGATGTGCCCCCGTAGC 61.845 66.667 0.00 0.00 0.00 3.58
5488 5985 9.467796 ACATTTTTCCAATTGTTTCCCTAAAAA 57.532 25.926 4.43 6.20 0.00 1.94
5489 5986 9.467796 AACATTTTTCCAATTGTTTCCCTAAAA 57.532 25.926 4.43 1.49 34.31 1.52
5490 5987 9.467796 AAACATTTTTCCAATTGTTTCCCTAAA 57.532 25.926 4.43 0.00 40.20 1.85
5491 5988 8.897752 CAAACATTTTTCCAATTGTTTCCCTAA 58.102 29.630 4.43 0.00 41.38 2.69
5492 5989 8.049721 ACAAACATTTTTCCAATTGTTTCCCTA 58.950 29.630 4.43 0.00 41.38 3.53
5493 5990 6.889177 ACAAACATTTTTCCAATTGTTTCCCT 59.111 30.769 4.43 0.00 41.38 4.20
5494 5991 7.094508 ACAAACATTTTTCCAATTGTTTCCC 57.905 32.000 4.43 0.00 41.38 3.97
5495 5992 8.239998 TCAACAAACATTTTTCCAATTGTTTCC 58.760 29.630 4.43 0.00 41.38 3.13
5496 5993 9.617975 TTCAACAAACATTTTTCCAATTGTTTC 57.382 25.926 4.43 0.00 41.38 2.78
5497 5994 9.404348 GTTCAACAAACATTTTTCCAATTGTTT 57.596 25.926 4.43 0.00 42.89 2.83
5498 5995 8.791675 AGTTCAACAAACATTTTTCCAATTGTT 58.208 25.926 4.43 0.00 40.49 2.83
5520 6017 3.076621 TGTGTCCAGCATGAATCAGTTC 58.923 45.455 0.00 0.00 39.69 3.01
5528 6025 0.320683 CCGTTCTGTGTCCAGCATGA 60.321 55.000 0.00 0.00 39.69 3.07
5533 6030 1.000843 TCATGTCCGTTCTGTGTCCAG 59.999 52.381 0.00 0.00 40.25 3.86
5570 6067 5.506483 CGTACTGGACTGGATGAATAGACTG 60.506 48.000 0.00 0.00 0.00 3.51
5574 6071 3.553096 GCCGTACTGGACTGGATGAATAG 60.553 52.174 7.77 0.00 42.00 1.73
5618 6116 3.123804 CAGACACGTTGCAGTACTCTTT 58.876 45.455 0.00 0.00 0.00 2.52
5621 6119 0.784778 GCAGACACGTTGCAGTACTC 59.215 55.000 5.84 0.00 41.17 2.59
5623 6121 0.600255 AGGCAGACACGTTGCAGTAC 60.600 55.000 12.42 0.00 43.28 2.73
5671 6169 5.345702 CAAGTCCTGCATTATTTCCATGTG 58.654 41.667 0.00 0.00 0.00 3.21
5699 6197 6.577055 CGCACCCATATGTAATAATTTGTTCG 59.423 38.462 1.24 0.00 29.06 3.95
5703 6201 5.767269 TGCGCACCCATATGTAATAATTTG 58.233 37.500 5.66 0.00 29.06 2.32
5709 6207 1.608590 GCTTGCGCACCCATATGTAAT 59.391 47.619 11.12 0.00 35.78 1.89
5710 6208 1.021202 GCTTGCGCACCCATATGTAA 58.979 50.000 11.12 0.00 35.78 2.41
5711 6209 0.180171 AGCTTGCGCACCCATATGTA 59.820 50.000 11.12 0.00 39.10 2.29
5712 6210 1.077501 AGCTTGCGCACCCATATGT 60.078 52.632 11.12 0.00 39.10 2.29
5713 6211 0.816825 AGAGCTTGCGCACCCATATG 60.817 55.000 11.12 0.00 39.10 1.78
5714 6212 0.533755 GAGAGCTTGCGCACCCATAT 60.534 55.000 11.12 0.00 39.10 1.78
5715 6213 1.153369 GAGAGCTTGCGCACCCATA 60.153 57.895 11.12 0.00 39.10 2.74
5716 6214 2.437359 GAGAGCTTGCGCACCCAT 60.437 61.111 11.12 0.00 39.10 4.00
5717 6215 4.704833 GGAGAGCTTGCGCACCCA 62.705 66.667 11.12 0.00 39.10 4.51
5729 6227 1.327303 AGATGCTCTAAGCCGGAGAG 58.673 55.000 5.05 10.33 41.51 3.20
5730 6228 2.658807 TAGATGCTCTAAGCCGGAGA 57.341 50.000 5.05 0.00 41.51 3.71
5731 6229 4.381079 GGTTATAGATGCTCTAAGCCGGAG 60.381 50.000 5.05 0.00 41.51 4.63
5732 6230 3.510360 GGTTATAGATGCTCTAAGCCGGA 59.490 47.826 5.05 0.00 41.51 5.14
5733 6231 3.673594 CGGTTATAGATGCTCTAAGCCGG 60.674 52.174 0.00 0.00 41.51 6.13
5734 6232 3.502920 CGGTTATAGATGCTCTAAGCCG 58.497 50.000 13.25 13.25 41.51 5.52
5735 6233 3.851098 CCGGTTATAGATGCTCTAAGCC 58.149 50.000 0.00 0.00 41.51 4.35


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

AutoCloner maintained by Alex Coulton.