Multiple sequence alignment - TraesCS1A01G103900

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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 TraesCS1A01G103900 chr1A 100.000 5075 0 0 1 5075 99872106 99867032 0.000000e+00 9372.0
1 TraesCS1A01G103900 chr5D 93.503 3694 180 28 579 4245 11953110 11949450 0.000000e+00 5437.0
2 TraesCS1A01G103900 chr5D 87.188 601 52 17 1 586 11953832 11953242 0.000000e+00 660.0
3 TraesCS1A01G103900 chr5D 87.952 249 22 5 4358 4598 11949399 11949151 2.310000e-73 287.0
4 TraesCS1A01G103900 chr5B 92.387 3704 206 29 579 4249 11774905 11771245 0.000000e+00 5208.0
5 TraesCS1A01G103900 chr5B 84.692 601 72 11 1 586 11775632 11775037 2.630000e-162 582.0
6 TraesCS1A01G103900 chr5B 84.429 289 24 9 4684 4958 11770655 11770374 1.080000e-66 265.0
7 TraesCS1A01G103900 chr5B 84.921 126 14 4 4478 4598 11770886 11770761 6.900000e-24 122.0
8 TraesCS1A01G103900 chr5B 95.122 41 2 0 4257 4297 412774186 412774146 1.180000e-06 65.8
9 TraesCS1A01G103900 chr4D 84.483 116 13 3 3698 3809 397094309 397094195 5.370000e-20 110.0
10 TraesCS1A01G103900 chr7D 84.545 110 13 4 3670 3777 407071755 407071648 6.950000e-19 106.0
11 TraesCS1A01G103900 chr7B 84.545 110 13 4 3670 3777 418049155 418049048 6.950000e-19 106.0
12 TraesCS1A01G103900 chr7A 84.545 110 13 4 3670 3777 464572761 464572654 6.950000e-19 106.0
13 TraesCS1A01G103900 chr1B 86.458 96 9 4 3698 3791 687276772 687276679 8.990000e-18 102.0
14 TraesCS1A01G103900 chr4A 82.759 116 15 5 3698 3809 54107181 54107067 1.160000e-16 99.0
15 TraesCS1A01G103900 chr4A 81.356 118 18 4 3698 3813 532796847 532796962 5.410000e-15 93.5
16 TraesCS1A01G103900 chr4A 87.500 56 7 0 4259 4314 725496823 725496878 1.180000e-06 65.8
17 TraesCS1A01G103900 chr5A 92.982 57 4 0 4258 4314 440703775 440703719 3.260000e-12 84.2
18 TraesCS1A01G103900 chr5A 91.071 56 5 0 4259 4314 411087308 411087363 5.450000e-10 76.8
19 TraesCS1A01G103900 chr3A 94.444 54 3 0 4261 4314 380471464 380471411 3.260000e-12 84.2
20 TraesCS1A01G103900 chr2A 94.444 54 3 0 4261 4314 420169694 420169747 3.260000e-12 84.2
21 TraesCS1A01G103900 chr1D 94.444 54 3 0 4261 4314 363585040 363584987 3.260000e-12 84.2
22 TraesCS1A01G103900 chr2B 92.593 54 4 0 4261 4314 840793 840846 1.510000e-10 78.7
23 TraesCS1A01G103900 chr3B 100.000 37 0 0 4261 4297 773021333 773021297 9.120000e-08 69.4


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 TraesCS1A01G103900 chr1A 99867032 99872106 5074 True 9372.00 9372 100.000000 1 5075 1 chr1A.!!$R1 5074
1 TraesCS1A01G103900 chr5D 11949151 11953832 4681 True 2128.00 5437 89.547667 1 4598 3 chr5D.!!$R1 4597
2 TraesCS1A01G103900 chr5B 11770374 11775632 5258 True 1544.25 5208 86.607250 1 4958 4 chr5B.!!$R2 4957

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
909 1072 0.116541 ACAGTACAGTAGTGGGGCCT 59.883 55.0 18.05 0.00 33.39 5.19 F
1149 1312 0.394899 CCCTCATGGCCTTCAAGTCC 60.395 60.0 3.32 0.00 0.00 3.85 F
2169 2332 0.744874 AGAATCGATTCTCCGGCGAA 59.255 50.0 30.53 9.72 43.27 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2356 2519 0.538746 AATTTGTTCCCGGCGAGGTT 60.539 50.0 9.3 0.0 38.74 3.50 R
2928 3091 0.676466 TGATGAAAATCGCCACGCCT 60.676 50.0 0.0 0.0 0.00 5.52 R
4101 4267 0.400213 ACGGACCCAAAATGCTCAGA 59.600 50.0 0.0 0.0 0.00 3.27 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
110 111 2.434702 AGACGAACAAAAGTCCTGAGGT 59.565 45.455 0.00 0.00 38.08 3.85
146 147 2.743636 GTGGATCTCACCTTCGAACA 57.256 50.000 0.00 0.00 40.39 3.18
160 161 4.440802 CCTTCGAACACTCCCTATTGAGAG 60.441 50.000 0.00 0.00 36.22 3.20
171 172 4.220821 TCCCTATTGAGAGTGTGAAGTCAC 59.779 45.833 4.43 4.43 46.59 3.67
182 183 1.292223 GAAGTCACGGTGCTAGCCA 59.708 57.895 13.29 0.00 0.00 4.75
229 231 0.179089 CTCTCGCCTTGGATCACAGG 60.179 60.000 5.24 5.24 0.00 4.00
262 264 0.176680 CCGCCTCACTAAGAGCACAT 59.823 55.000 0.00 0.00 43.31 3.21
272 274 7.404671 TCACTAAGAGCACATATGAACACTA 57.595 36.000 10.38 0.00 0.00 2.74
285 287 7.557358 ACATATGAACACTAGATTGGCAATCAA 59.443 33.333 34.54 14.36 40.42 2.57
286 288 6.839124 ATGAACACTAGATTGGCAATCAAA 57.161 33.333 34.54 23.37 40.42 2.69
287 289 6.839124 TGAACACTAGATTGGCAATCAAAT 57.161 33.333 34.54 20.66 40.42 2.32
288 290 6.855836 TGAACACTAGATTGGCAATCAAATC 58.144 36.000 34.54 23.63 40.42 2.17
289 291 6.433716 TGAACACTAGATTGGCAATCAAATCA 59.566 34.615 34.54 25.34 40.42 2.57
290 292 6.839124 ACACTAGATTGGCAATCAAATCAA 57.161 33.333 34.54 15.70 40.42 2.57
296 298 6.864342 AGATTGGCAATCAAATCAAGAGAAG 58.136 36.000 34.54 0.00 40.42 2.85
329 337 2.293399 CACCACACTAAGCAAACTTCCC 59.707 50.000 0.00 0.00 37.33 3.97
355 363 2.361610 AAGCCATCGCCCCACAAG 60.362 61.111 0.00 0.00 34.57 3.16
381 389 6.088483 CACAATCCAAATTTGATTCGACACTG 59.912 38.462 19.86 8.76 0.00 3.66
397 407 4.631377 CGACACTGAGAGGCAAATCATTAA 59.369 41.667 0.00 0.00 0.00 1.40
435 445 5.358298 AAGGCAAGTCACTAAAAATCGTC 57.642 39.130 0.00 0.00 0.00 4.20
437 447 4.691216 AGGCAAGTCACTAAAAATCGTCTC 59.309 41.667 0.00 0.00 0.00 3.36
438 448 4.451096 GGCAAGTCACTAAAAATCGTCTCA 59.549 41.667 0.00 0.00 0.00 3.27
439 449 5.122396 GGCAAGTCACTAAAAATCGTCTCAT 59.878 40.000 0.00 0.00 0.00 2.90
503 524 6.932901 ACGTGCAAACATTTAATGAATGAG 57.067 33.333 12.28 7.51 46.59 2.90
544 566 3.627395 TCACAAATCCATAACCGCTCT 57.373 42.857 0.00 0.00 0.00 4.09
561 583 4.065789 CGCTCTCTTGTAACCTTCCTTTT 58.934 43.478 0.00 0.00 0.00 2.27
573 595 5.993748 ACCTTCCTTTTCAGAAAAACACA 57.006 34.783 9.63 0.00 31.23 3.72
577 599 5.730296 TCCTTTTCAGAAAAACACACCAA 57.270 34.783 9.63 0.00 31.23 3.67
593 753 0.251916 CCAATAAGTGGCACTCCCGA 59.748 55.000 22.31 7.28 41.72 5.14
613 773 3.625764 CGAAGGTCTTTCAGGTTTGTTGA 59.374 43.478 0.00 0.00 35.43 3.18
630 790 6.844097 TTGTTGACCAAGGTTAAAACTTCT 57.156 33.333 0.00 0.00 0.00 2.85
631 791 6.202516 TGTTGACCAAGGTTAAAACTTCTG 57.797 37.500 0.00 0.00 0.00 3.02
632 792 5.126384 TGTTGACCAAGGTTAAAACTTCTGG 59.874 40.000 0.00 3.33 0.00 3.86
635 795 6.424883 TGACCAAGGTTAAAACTTCTGGTAA 58.575 36.000 8.71 1.29 33.26 2.85
643 803 9.865321 AGGTTAAAACTTCTGGTAAAAGAAAAC 57.135 29.630 0.00 0.00 35.79 2.43
662 822 9.750125 AAGAAAACTTATGAACCTCATTGAAAC 57.250 29.630 0.00 0.00 38.26 2.78
700 860 6.091034 TGGTGATTTTCAATGAATTGCAATCG 59.909 34.615 13.38 0.00 38.57 3.34
744 904 7.607991 AGTTAGTCTTATTCTGACCCACAATTG 59.392 37.037 3.24 3.24 35.21 2.32
780 940 9.804758 AAACCACTGAAAATTCGTTAACATTTA 57.195 25.926 6.39 0.00 0.00 1.40
811 973 7.595819 ATCACAGAAAACAGTTTATTCCCAA 57.404 32.000 0.00 0.00 0.00 4.12
812 974 6.801575 TCACAGAAAACAGTTTATTCCCAAC 58.198 36.000 0.00 0.00 0.00 3.77
825 987 8.088365 AGTTTATTCCCAACAAAAATCTAGTGC 58.912 33.333 0.00 0.00 0.00 4.40
847 1009 7.039923 AGTGCATCTTTCATGAATCAAAGAGTT 60.040 33.333 9.40 0.00 40.96 3.01
853 1016 9.745018 TCTTTCATGAATCAAAGAGTTCCTAAT 57.255 29.630 9.40 0.00 34.39 1.73
862 1025 6.407202 TCAAAGAGTTCCTAATCTAAGCACC 58.593 40.000 0.00 0.00 0.00 5.01
897 1060 5.567430 ACTATCACAGTGTAGGACAGTACA 58.433 41.667 0.00 0.00 35.62 2.90
900 1063 4.976864 TCACAGTGTAGGACAGTACAGTA 58.023 43.478 0.00 0.00 34.86 2.74
906 1069 2.233305 AGGACAGTACAGTAGTGGGG 57.767 55.000 18.05 0.00 33.39 4.96
909 1072 0.116541 ACAGTACAGTAGTGGGGCCT 59.883 55.000 18.05 0.00 33.39 5.19
933 1096 1.339929 AGCCAACCGCAACCTTAAAAG 59.660 47.619 0.00 0.00 41.38 2.27
963 1126 1.956170 AGCAGCGAGTCCAAACACG 60.956 57.895 0.00 0.00 41.63 4.49
1149 1312 0.394899 CCCTCATGGCCTTCAAGTCC 60.395 60.000 3.32 0.00 0.00 3.85
1275 1438 2.576317 GCGCTCTCCGTACACGAC 60.576 66.667 0.00 0.00 43.02 4.34
1278 1441 1.428620 GCTCTCCGTACACGACCTC 59.571 63.158 2.76 0.00 43.02 3.85
1443 1606 0.966920 TCAACTCCTTCTCCGGTGAC 59.033 55.000 5.53 0.00 0.00 3.67
1603 1766 2.351276 CCACCAAGTCCTTCCCGG 59.649 66.667 0.00 0.00 0.00 5.73
1607 1770 4.016706 CAAGTCCTTCCCGGCCGT 62.017 66.667 26.12 0.00 0.00 5.68
1697 1860 4.776322 CATCGGCCGGCTCACCAA 62.776 66.667 28.56 2.60 34.57 3.67
1728 1891 4.373116 GAGCTCGCCGACAACCCA 62.373 66.667 0.00 0.00 0.00 4.51
1860 2023 3.016474 GCTGCAGTTCTTCGACGCC 62.016 63.158 16.64 0.00 0.00 5.68
1960 2123 4.316823 TCTCCGGTGAGGTGCCCT 62.317 66.667 0.00 0.00 41.99 5.19
2142 2305 1.801332 CACCATGCTGAAGCTGCTC 59.199 57.895 1.00 0.00 42.66 4.26
2169 2332 0.744874 AGAATCGATTCTCCGGCGAA 59.255 50.000 30.53 9.72 43.27 4.70
2356 2519 2.954611 CGTCGCTCACCAGTCTCA 59.045 61.111 0.00 0.00 0.00 3.27
2486 2649 2.270205 CATCGGCAAGCTGGTCCT 59.730 61.111 0.37 0.00 0.00 3.85
2625 2788 4.694233 ACTGAGCTGCGTGGCCTG 62.694 66.667 3.32 0.00 0.00 4.85
2928 3091 3.138798 GTCCTGCTCGCCGTCCTA 61.139 66.667 0.00 0.00 0.00 2.94
2940 3103 2.499685 GTCCTAGGCGTGGCGATT 59.500 61.111 2.96 0.00 0.00 3.34
3021 3184 1.740664 GTTCGCGAAGAAGGGGTCC 60.741 63.158 24.13 2.86 39.95 4.46
3180 3343 1.003839 GAAGCACATCACCCGGACA 60.004 57.895 0.73 0.00 0.00 4.02
3555 3718 1.728971 GTCAAGTCGAGCAACATCCTG 59.271 52.381 0.00 0.00 0.00 3.86
4010 4176 4.899239 GATGCTGGAGGACGCGGG 62.899 72.222 12.47 0.00 0.00 6.13
4101 4267 7.307989 CCGTTCAAAGTTATTTCAGTGTCTGAT 60.308 37.037 0.24 0.00 40.39 2.90
4115 4281 3.128242 GTGTCTGATCTGAGCATTTTGGG 59.872 47.826 2.02 0.00 0.00 4.12
4157 4332 3.532155 GCCGAGATCTGAGCCGGT 61.532 66.667 18.62 0.00 43.51 5.28
4162 4345 2.125512 GATCTGAGCCGGTGCGTT 60.126 61.111 1.90 0.00 44.33 4.84
4163 4346 1.141019 GATCTGAGCCGGTGCGTTA 59.859 57.895 1.90 0.00 44.33 3.18
4189 4372 2.587956 GCATGTAGCATGTGTTGTGTG 58.412 47.619 10.31 0.00 44.79 3.82
4190 4373 2.030893 GCATGTAGCATGTGTTGTGTGT 60.031 45.455 10.31 0.00 44.79 3.72
4206 4395 7.428183 GTGTTGTGTGTGTAGTAAAGATTGTTG 59.572 37.037 0.00 0.00 0.00 3.33
4245 4434 3.004315 CCAACCAATCTTGTGTGTGTACC 59.996 47.826 0.00 0.00 0.00 3.34
4246 4435 3.569194 ACCAATCTTGTGTGTGTACCA 57.431 42.857 0.00 0.00 0.00 3.25
4247 4436 3.892284 ACCAATCTTGTGTGTGTACCAA 58.108 40.909 0.00 0.00 0.00 3.67
4262 4451 8.407064 TGTGTGTACCAAACCAAAGTTAATTAG 58.593 33.333 0.00 0.00 34.19 1.73
4265 4454 9.882996 GTGTACCAAACCAAAGTTAATTAGTAC 57.117 33.333 0.00 0.00 34.19 2.73
4269 4458 7.449395 ACCAAACCAAAGTTAATTAGTACTCCC 59.551 37.037 0.00 0.00 34.19 4.30
4270 4459 7.668469 CCAAACCAAAGTTAATTAGTACTCCCT 59.332 37.037 0.00 0.00 34.19 4.20
4271 4460 8.727910 CAAACCAAAGTTAATTAGTACTCCCTC 58.272 37.037 0.00 0.00 34.19 4.30
4272 4461 6.955364 ACCAAAGTTAATTAGTACTCCCTCC 58.045 40.000 0.00 0.00 0.00 4.30
4274 4463 6.351626 CCAAAGTTAATTAGTACTCCCTCCGT 60.352 42.308 0.00 0.00 0.00 4.69
4275 4464 6.864151 AAGTTAATTAGTACTCCCTCCGTT 57.136 37.500 0.00 0.00 0.00 4.44
4276 4465 6.864151 AGTTAATTAGTACTCCCTCCGTTT 57.136 37.500 0.00 0.00 0.00 3.60
4277 4466 7.250032 AGTTAATTAGTACTCCCTCCGTTTT 57.750 36.000 0.00 0.00 0.00 2.43
4279 4468 8.815912 AGTTAATTAGTACTCCCTCCGTTTTTA 58.184 33.333 0.00 0.00 0.00 1.52
4280 4469 9.605275 GTTAATTAGTACTCCCTCCGTTTTTAT 57.395 33.333 0.00 0.00 0.00 1.40
4284 4473 9.605275 ATTAGTACTCCCTCCGTTTTTATTTAC 57.395 33.333 0.00 0.00 0.00 2.01
4286 4475 7.683578 AGTACTCCCTCCGTTTTTATTTACTT 58.316 34.615 0.00 0.00 0.00 2.24
4287 4476 8.159447 AGTACTCCCTCCGTTTTTATTTACTTT 58.841 33.333 0.00 0.00 0.00 2.66
4288 4477 9.435688 GTACTCCCTCCGTTTTTATTTACTTTA 57.564 33.333 0.00 0.00 0.00 1.85
4289 4478 8.327941 ACTCCCTCCGTTTTTATTTACTTTAC 57.672 34.615 0.00 0.00 0.00 2.01
4290 4479 7.938490 ACTCCCTCCGTTTTTATTTACTTTACA 59.062 33.333 0.00 0.00 0.00 2.41
4291 4480 8.866970 TCCCTCCGTTTTTATTTACTTTACAT 57.133 30.769 0.00 0.00 0.00 2.29
4317 4506 7.969536 TTAGAATTGACTGAAGTGAAAGAGG 57.030 36.000 0.00 0.00 0.00 3.69
4318 4507 6.179906 AGAATTGACTGAAGTGAAAGAGGA 57.820 37.500 0.00 0.00 0.00 3.71
4319 4508 6.229733 AGAATTGACTGAAGTGAAAGAGGAG 58.770 40.000 0.00 0.00 0.00 3.69
4320 4509 3.393089 TGACTGAAGTGAAAGAGGAGC 57.607 47.619 0.00 0.00 0.00 4.70
4321 4510 2.700371 TGACTGAAGTGAAAGAGGAGCA 59.300 45.455 0.00 0.00 0.00 4.26
4350 4539 8.863086 CCATATTTTGGTTGGTAGATCAATCAT 58.137 33.333 0.00 0.00 40.99 2.45
4353 4542 5.581126 TTGGTTGGTAGATCAATCATTGC 57.419 39.130 0.00 0.00 37.56 3.56
4354 4543 3.953612 TGGTTGGTAGATCAATCATTGCC 59.046 43.478 0.00 0.00 33.34 4.52
4355 4544 3.953612 GGTTGGTAGATCAATCATTGCCA 59.046 43.478 0.00 0.00 0.00 4.92
4356 4545 4.202050 GGTTGGTAGATCAATCATTGCCAC 60.202 45.833 0.00 0.00 0.00 5.01
4385 4574 5.301805 CAGGTCAAACTACCCAGTGAAAAAT 59.698 40.000 0.00 0.00 40.71 1.82
4389 4578 7.812669 GGTCAAACTACCCAGTGAAAAATAATG 59.187 37.037 0.00 0.00 34.36 1.90
4486 4831 9.683069 AAAACATACTAAGAGCAAAAATGAGTG 57.317 29.630 0.00 0.00 0.00 3.51
4499 4844 5.534207 AAAATGAGTGTCTCCATTTTGCA 57.466 34.783 10.95 0.00 33.97 4.08
4501 4846 4.713824 ATGAGTGTCTCCATTTTGCATG 57.286 40.909 0.00 0.00 0.00 4.06
4509 4854 5.419788 TGTCTCCATTTTGCATGCTAAATCT 59.580 36.000 29.26 14.21 31.20 2.40
4512 4857 7.806960 GTCTCCATTTTGCATGCTAAATCTATC 59.193 37.037 29.26 17.80 31.20 2.08
4513 4858 7.503230 TCTCCATTTTGCATGCTAAATCTATCA 59.497 33.333 29.26 14.52 31.20 2.15
4528 4879 7.756395 AAATCTATCATTAATCAGGCAGGTG 57.244 36.000 0.00 0.00 0.00 4.00
4593 4944 2.499289 TCTCTGACTGCCTGGATTTCTC 59.501 50.000 0.00 0.00 0.00 2.87
4594 4945 2.235650 CTCTGACTGCCTGGATTTCTCA 59.764 50.000 0.00 0.00 0.00 3.27
4599 4950 2.641815 ACTGCCTGGATTTCTCAAGAGT 59.358 45.455 0.00 0.00 0.00 3.24
4600 4951 3.073650 ACTGCCTGGATTTCTCAAGAGTT 59.926 43.478 0.00 0.00 0.00 3.01
4601 4952 3.415212 TGCCTGGATTTCTCAAGAGTTG 58.585 45.455 0.00 0.00 0.00 3.16
4602 4953 3.072915 TGCCTGGATTTCTCAAGAGTTGA 59.927 43.478 0.00 0.00 38.17 3.18
4629 5027 2.752354 AGAGAGAGAGATGTGTTGTCCG 59.248 50.000 0.00 0.00 0.00 4.79
4634 5032 1.639298 GAGATGTGTTGTCCGGCTGC 61.639 60.000 0.00 0.00 0.00 5.25
4635 5033 1.965930 GATGTGTTGTCCGGCTGCA 60.966 57.895 0.50 0.00 0.00 4.41
4636 5034 2.187599 GATGTGTTGTCCGGCTGCAC 62.188 60.000 0.50 3.89 0.00 4.57
4637 5035 2.899838 GTGTTGTCCGGCTGCACA 60.900 61.111 0.50 0.00 0.00 4.57
4638 5036 2.899838 TGTTGTCCGGCTGCACAC 60.900 61.111 0.50 0.00 0.00 3.82
4639 5037 2.899838 GTTGTCCGGCTGCACACA 60.900 61.111 0.50 0.00 0.00 3.72
4640 5038 2.899838 TTGTCCGGCTGCACACAC 60.900 61.111 0.50 0.00 0.00 3.82
4641 5039 3.689002 TTGTCCGGCTGCACACACA 62.689 57.895 0.50 0.00 0.00 3.72
4642 5040 2.899838 GTCCGGCTGCACACACAA 60.900 61.111 0.50 0.00 0.00 3.33
4643 5041 2.124529 TCCGGCTGCACACACAAA 60.125 55.556 0.50 0.00 0.00 2.83
4644 5042 2.026014 CCGGCTGCACACACAAAC 59.974 61.111 0.50 0.00 0.00 2.93
4645 5043 2.769539 CCGGCTGCACACACAAACA 61.770 57.895 0.50 0.00 0.00 2.83
4646 5044 1.586042 CGGCTGCACACACAAACAC 60.586 57.895 0.50 0.00 0.00 3.32
4658 5056 2.556189 ACACAAACACACACACACATGT 59.444 40.909 0.00 0.00 40.80 3.21
4661 5059 1.013596 AACACACACACACATGTCCG 58.986 50.000 0.00 0.00 36.72 4.79
4662 5060 0.813610 ACACACACACACATGTCCGG 60.814 55.000 0.00 0.00 36.72 5.14
4663 5061 1.227823 ACACACACACATGTCCGGG 60.228 57.895 0.00 0.00 36.72 5.73
4664 5062 1.070615 CACACACACATGTCCGGGA 59.929 57.895 0.00 0.00 36.72 5.14
4665 5063 0.950555 CACACACACATGTCCGGGAG 60.951 60.000 0.00 0.00 36.72 4.30
4688 5086 4.187694 GGATGCTTCCAAACAAACAAACA 58.812 39.130 13.60 0.00 42.12 2.83
4691 5089 5.349824 TGCTTCCAAACAAACAAACAAAC 57.650 34.783 0.00 0.00 0.00 2.93
4692 5090 4.816385 TGCTTCCAAACAAACAAACAAACA 59.184 33.333 0.00 0.00 0.00 2.83
4693 5091 5.296780 TGCTTCCAAACAAACAAACAAACAA 59.703 32.000 0.00 0.00 0.00 2.83
4694 5092 6.183360 TGCTTCCAAACAAACAAACAAACAAA 60.183 30.769 0.00 0.00 0.00 2.83
4695 5093 6.141527 GCTTCCAAACAAACAAACAAACAAAC 59.858 34.615 0.00 0.00 0.00 2.93
4696 5094 6.677781 TCCAAACAAACAAACAAACAAACA 57.322 29.167 0.00 0.00 0.00 2.83
4697 5095 7.083875 TCCAAACAAACAAACAAACAAACAA 57.916 28.000 0.00 0.00 0.00 2.83
4698 5096 7.189512 TCCAAACAAACAAACAAACAAACAAG 58.810 30.769 0.00 0.00 0.00 3.16
4707 5105 2.344521 AAACAAACAAGCCGTCGCCC 62.345 55.000 0.00 0.00 34.57 6.13
4727 5125 0.607217 GAAATCGGTTCGGGGTTGGT 60.607 55.000 0.00 0.00 0.00 3.67
4728 5126 0.178984 AAATCGGTTCGGGGTTGGTT 60.179 50.000 0.00 0.00 0.00 3.67
4729 5127 0.607217 AATCGGTTCGGGGTTGGTTC 60.607 55.000 0.00 0.00 0.00 3.62
4732 5130 1.962822 GGTTCGGGGTTGGTTCGTC 60.963 63.158 0.00 0.00 0.00 4.20
4733 5131 2.029369 TTCGGGGTTGGTTCGTCG 59.971 61.111 0.00 0.00 0.00 5.12
4734 5132 2.795110 TTCGGGGTTGGTTCGTCGT 61.795 57.895 0.00 0.00 0.00 4.34
4735 5133 2.280321 CGGGGTTGGTTCGTCGTT 60.280 61.111 0.00 0.00 0.00 3.85
4738 5136 1.096967 GGGGTTGGTTCGTCGTTTGT 61.097 55.000 0.00 0.00 0.00 2.83
4740 5138 1.261354 GGGTTGGTTCGTCGTTTGTAC 59.739 52.381 0.00 0.00 0.00 2.90
4771 5169 3.562232 GGGGTTGGGTGACGGACA 61.562 66.667 0.00 0.00 0.00 4.02
4794 5192 2.993899 CAACTATATGTCCGGGAATCGC 59.006 50.000 0.00 0.00 37.59 4.58
4799 5197 2.892425 GTCCGGGAATCGCTGCTG 60.892 66.667 0.00 0.00 37.59 4.41
4807 5205 0.813210 GAATCGCTGCTGAGGAAGGG 60.813 60.000 0.00 0.00 32.84 3.95
4811 5209 2.125350 CTGCTGAGGAAGGGCGAC 60.125 66.667 0.00 0.00 0.00 5.19
4832 5230 2.885502 GCCACGTTTTTCAGGCAAG 58.114 52.632 7.41 0.00 46.26 4.01
4835 5233 0.934436 CACGTTTTTCAGGCAAGCGG 60.934 55.000 0.00 0.00 32.68 5.52
4845 5243 0.321653 AGGCAAGCGGGTAGACTTTG 60.322 55.000 0.00 0.00 0.00 2.77
4855 5253 2.286772 GGGTAGACTTTGTTGCACGTTG 60.287 50.000 0.00 0.00 0.00 4.10
4878 5282 4.374702 GCGTCGCCACTGTTGCTG 62.375 66.667 5.75 0.00 0.00 4.41
4909 5318 2.842462 TGCCTCGTGTGACCTGGT 60.842 61.111 0.00 0.00 0.00 4.00
4911 5320 1.215647 GCCTCGTGTGACCTGGTAG 59.784 63.158 0.00 0.00 0.00 3.18
4924 5333 4.527038 TGACCTGGTAGTTTTGTCTCCTAG 59.473 45.833 0.00 0.00 0.00 3.02
4926 5335 5.648247 ACCTGGTAGTTTTGTCTCCTAGTA 58.352 41.667 0.00 0.00 0.00 1.82
4930 5339 5.163581 TGGTAGTTTTGTCTCCTAGTATCGC 60.164 44.000 0.00 0.00 0.00 4.58
4958 5367 3.705051 TCTTGTCCACCGACCTACTAAT 58.295 45.455 0.00 0.00 38.32 1.73
4959 5368 3.446161 TCTTGTCCACCGACCTACTAATG 59.554 47.826 0.00 0.00 38.32 1.90
4960 5369 2.104967 TGTCCACCGACCTACTAATGG 58.895 52.381 0.00 0.00 38.32 3.16
4961 5370 1.117150 TCCACCGACCTACTAATGGC 58.883 55.000 0.00 0.00 0.00 4.40
4962 5371 0.106149 CCACCGACCTACTAATGGCC 59.894 60.000 0.00 0.00 0.00 5.36
4963 5372 1.120530 CACCGACCTACTAATGGCCT 58.879 55.000 3.32 0.00 0.00 5.19
4964 5373 1.120530 ACCGACCTACTAATGGCCTG 58.879 55.000 3.32 0.00 0.00 4.85
4965 5374 0.393077 CCGACCTACTAATGGCCTGG 59.607 60.000 3.32 0.00 0.00 4.45
4966 5375 0.249911 CGACCTACTAATGGCCTGGC 60.250 60.000 11.05 11.05 0.00 4.85
4967 5376 1.132500 GACCTACTAATGGCCTGGCT 58.868 55.000 19.68 0.70 0.00 4.75
4968 5377 0.839946 ACCTACTAATGGCCTGGCTG 59.160 55.000 19.68 6.63 0.00 4.85
4969 5378 1.131638 CCTACTAATGGCCTGGCTGA 58.868 55.000 19.68 5.99 0.00 4.26
4970 5379 1.701847 CCTACTAATGGCCTGGCTGAT 59.298 52.381 19.68 8.26 0.00 2.90
4971 5380 2.551721 CCTACTAATGGCCTGGCTGATG 60.552 54.545 19.68 8.01 0.00 3.07
4972 5381 0.466922 ACTAATGGCCTGGCTGATGC 60.467 55.000 19.68 1.35 38.76 3.91
4973 5382 0.466739 CTAATGGCCTGGCTGATGCA 60.467 55.000 19.68 7.89 41.91 3.96
4974 5383 0.752743 TAATGGCCTGGCTGATGCAC 60.753 55.000 19.68 0.00 41.91 4.57
4975 5384 4.746309 TGGCCTGGCTGATGCACC 62.746 66.667 19.68 0.00 41.91 5.01
4978 5387 2.360350 CCTGGCTGATGCACCGTT 60.360 61.111 0.00 0.00 41.91 4.44
4979 5388 2.401766 CCTGGCTGATGCACCGTTC 61.402 63.158 0.00 0.00 41.91 3.95
4980 5389 1.376424 CTGGCTGATGCACCGTTCT 60.376 57.895 0.00 0.00 41.91 3.01
4981 5390 1.364626 CTGGCTGATGCACCGTTCTC 61.365 60.000 0.00 0.00 41.91 2.87
4982 5391 2.109126 GGCTGATGCACCGTTCTCC 61.109 63.158 0.00 0.00 41.91 3.71
4983 5392 2.456119 GCTGATGCACCGTTCTCCG 61.456 63.158 0.00 0.00 39.41 4.63
4999 5408 4.833811 CGGCTGTCGGATGATTCA 57.166 55.556 0.00 0.00 34.75 2.57
5000 5409 3.295734 CGGCTGTCGGATGATTCAT 57.704 52.632 0.00 0.00 34.75 2.57
5001 5410 1.586422 CGGCTGTCGGATGATTCATT 58.414 50.000 0.00 0.00 34.75 2.57
5002 5411 1.528586 CGGCTGTCGGATGATTCATTC 59.471 52.381 0.00 0.00 34.75 2.67
5003 5412 2.804572 CGGCTGTCGGATGATTCATTCT 60.805 50.000 0.00 0.00 34.75 2.40
5004 5413 3.552890 CGGCTGTCGGATGATTCATTCTA 60.553 47.826 0.00 0.00 34.75 2.10
5005 5414 4.573900 GGCTGTCGGATGATTCATTCTAT 58.426 43.478 0.00 0.00 0.00 1.98
5006 5415 4.999950 GGCTGTCGGATGATTCATTCTATT 59.000 41.667 0.00 0.00 0.00 1.73
5007 5416 5.121454 GGCTGTCGGATGATTCATTCTATTC 59.879 44.000 0.00 0.00 0.00 1.75
5008 5417 5.931146 GCTGTCGGATGATTCATTCTATTCT 59.069 40.000 0.00 0.00 0.00 2.40
5009 5418 6.426328 GCTGTCGGATGATTCATTCTATTCTT 59.574 38.462 0.00 0.00 0.00 2.52
5010 5419 7.041508 GCTGTCGGATGATTCATTCTATTCTTT 60.042 37.037 0.00 0.00 0.00 2.52
5011 5420 8.737168 TGTCGGATGATTCATTCTATTCTTTT 57.263 30.769 0.00 0.00 0.00 2.27
5012 5421 9.177608 TGTCGGATGATTCATTCTATTCTTTTT 57.822 29.630 0.00 0.00 0.00 1.94
5029 5438 3.320673 TTTTTCCTTGCAACGGTTGTT 57.679 38.095 20.92 0.00 39.43 2.83
5030 5439 4.451629 TTTTTCCTTGCAACGGTTGTTA 57.548 36.364 20.92 8.96 36.28 2.41
5031 5440 4.657436 TTTTCCTTGCAACGGTTGTTAT 57.343 36.364 20.92 0.00 36.28 1.89
5032 5441 3.634568 TTCCTTGCAACGGTTGTTATG 57.365 42.857 20.92 12.45 36.28 1.90
5033 5442 1.883275 TCCTTGCAACGGTTGTTATGG 59.117 47.619 20.92 19.03 36.28 2.74
5034 5443 1.668628 CCTTGCAACGGTTGTTATGGC 60.669 52.381 20.92 7.15 36.28 4.40
5035 5444 0.315568 TTGCAACGGTTGTTATGGCC 59.684 50.000 20.92 0.00 36.28 5.36
5036 5445 0.823769 TGCAACGGTTGTTATGGCCA 60.824 50.000 20.92 8.56 36.28 5.36
5037 5446 0.530288 GCAACGGTTGTTATGGCCAT 59.470 50.000 24.45 24.45 36.28 4.40
5038 5447 1.067213 GCAACGGTTGTTATGGCCATT 60.067 47.619 26.37 8.31 36.28 3.16
5039 5448 2.874849 CAACGGTTGTTATGGCCATTC 58.125 47.619 26.37 17.69 36.28 2.67
5040 5449 2.208132 ACGGTTGTTATGGCCATTCA 57.792 45.000 26.37 20.11 0.00 2.57
5041 5450 2.733956 ACGGTTGTTATGGCCATTCAT 58.266 42.857 26.37 1.70 0.00 2.57
5042 5451 3.892284 ACGGTTGTTATGGCCATTCATA 58.108 40.909 26.37 6.76 0.00 2.15
5043 5452 4.469657 ACGGTTGTTATGGCCATTCATAT 58.530 39.130 26.37 0.29 30.69 1.78
5044 5453 4.518970 ACGGTTGTTATGGCCATTCATATC 59.481 41.667 26.37 15.05 30.69 1.63
5045 5454 4.761739 CGGTTGTTATGGCCATTCATATCT 59.238 41.667 26.37 0.00 30.69 1.98
5046 5455 5.106555 CGGTTGTTATGGCCATTCATATCTC 60.107 44.000 26.37 7.33 30.69 2.75
5047 5456 5.106555 GGTTGTTATGGCCATTCATATCTCG 60.107 44.000 26.37 0.00 30.69 4.04
5048 5457 4.578871 TGTTATGGCCATTCATATCTCGG 58.421 43.478 26.37 0.00 30.69 4.63
5049 5458 2.795231 ATGGCCATTCATATCTCGGG 57.205 50.000 14.09 0.00 0.00 5.14
5050 5459 0.036732 TGGCCATTCATATCTCGGGC 59.963 55.000 0.00 0.00 42.38 6.13
5051 5460 0.036732 GGCCATTCATATCTCGGGCA 59.963 55.000 0.00 0.00 43.09 5.36
5052 5461 1.340405 GGCCATTCATATCTCGGGCAT 60.340 52.381 0.00 0.00 43.09 4.40
5053 5462 2.092968 GGCCATTCATATCTCGGGCATA 60.093 50.000 0.00 0.00 43.09 3.14
5054 5463 2.939103 GCCATTCATATCTCGGGCATAC 59.061 50.000 0.00 0.00 41.02 2.39
5055 5464 3.535561 CCATTCATATCTCGGGCATACC 58.464 50.000 0.00 0.00 0.00 2.73
5064 5473 4.910585 GGGCATACCGTGGAGGCG 62.911 72.222 0.00 0.00 46.52 5.52
5073 5482 4.373116 GTGGAGGCGGTCGAGCAA 62.373 66.667 15.89 0.00 39.27 3.91
5074 5483 3.621805 TGGAGGCGGTCGAGCAAA 61.622 61.111 15.89 0.00 39.27 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 8.375506 CCTCTCAGTTTGTGGCCTATATATTAA 58.624 37.037 3.32 0.00 0.00 1.40
17 18 4.040461 GCCTCTCAGTTTGTGGCCTATATA 59.960 45.833 3.32 0.00 37.81 0.86
18 19 3.181450 GCCTCTCAGTTTGTGGCCTATAT 60.181 47.826 3.32 0.00 37.81 0.86
19 20 2.170607 GCCTCTCAGTTTGTGGCCTATA 59.829 50.000 3.32 0.00 37.81 1.31
20 21 1.065126 GCCTCTCAGTTTGTGGCCTAT 60.065 52.381 3.32 0.00 37.81 2.57
25 26 1.593196 TTTCGCCTCTCAGTTTGTGG 58.407 50.000 0.00 0.00 0.00 4.17
72 73 2.417787 CGTCTCCATTGTGAGCTCATCA 60.418 50.000 21.47 16.40 34.79 3.07
73 74 2.159184 TCGTCTCCATTGTGAGCTCATC 60.159 50.000 21.47 13.93 32.22 2.92
110 111 4.100084 CTCCGGTGGCATGGCTCA 62.100 66.667 21.08 0.00 0.00 4.26
146 147 4.421131 ACTTCACACTCTCAATAGGGAGT 58.579 43.478 0.00 0.00 42.67 3.85
160 161 1.419374 CTAGCACCGTGACTTCACAC 58.581 55.000 9.94 0.00 46.75 3.82
171 172 3.390521 TGGAGGTGGCTAGCACCG 61.391 66.667 22.49 0.00 46.77 4.94
182 183 4.443934 CTCTTCGGAGGTGGAGGT 57.556 61.111 0.00 0.00 38.36 3.85
201 202 2.294078 AAGGCGAGAGTGAAGGGGG 61.294 63.158 0.00 0.00 0.00 5.40
250 252 7.646548 TCTAGTGTTCATATGTGCTCTTAGT 57.353 36.000 1.90 0.00 0.00 2.24
262 264 7.936496 TTTGATTGCCAATCTAGTGTTCATA 57.064 32.000 17.73 0.00 38.72 2.15
272 274 6.127423 CCTTCTCTTGATTTGATTGCCAATCT 60.127 38.462 17.73 0.00 38.72 2.40
285 287 2.557056 TCGTCGTGTCCTTCTCTTGATT 59.443 45.455 0.00 0.00 0.00 2.57
286 288 2.095161 GTCGTCGTGTCCTTCTCTTGAT 60.095 50.000 0.00 0.00 0.00 2.57
287 289 1.266175 GTCGTCGTGTCCTTCTCTTGA 59.734 52.381 0.00 0.00 0.00 3.02
288 290 1.666311 GGTCGTCGTGTCCTTCTCTTG 60.666 57.143 0.00 0.00 0.00 3.02
289 291 0.597072 GGTCGTCGTGTCCTTCTCTT 59.403 55.000 0.00 0.00 0.00 2.85
290 292 0.536687 TGGTCGTCGTGTCCTTCTCT 60.537 55.000 0.00 0.00 0.00 3.10
296 298 2.355481 GTGGTGGTCGTCGTGTCC 60.355 66.667 0.00 0.00 0.00 4.02
329 337 2.202932 CGATGGCTTGGGTCCTCG 60.203 66.667 0.00 0.00 0.00 4.63
355 363 4.922692 TGTCGAATCAAATTTGGATTGTGC 59.077 37.500 17.90 9.00 35.23 4.57
381 389 9.736023 AATACGATTTTTAATGATTTGCCTCTC 57.264 29.630 0.00 0.00 0.00 3.20
397 407 7.708752 TGACTTGCCTTTTTGAAATACGATTTT 59.291 29.630 0.00 0.00 0.00 1.82
461 473 7.518161 TGCACGTATATATCTTTTAAGCATGC 58.482 34.615 10.51 10.51 0.00 4.06
464 476 8.884726 TGTTTGCACGTATATATCTTTTAAGCA 58.115 29.630 0.00 0.00 0.00 3.91
516 538 6.204688 GCGGTTATGGATTTGTGATTATGAGA 59.795 38.462 0.00 0.00 0.00 3.27
539 561 3.320673 AAGGAAGGTTACAAGAGAGCG 57.679 47.619 0.00 0.00 0.00 5.03
544 566 7.948034 TTTTCTGAAAAGGAAGGTTACAAGA 57.052 32.000 11.33 0.00 0.00 3.02
561 583 6.142818 CCACTTATTGGTGTGTTTTTCTGA 57.857 37.500 0.00 0.00 41.10 3.27
577 599 0.541863 CCTTCGGGAGTGCCACTTAT 59.458 55.000 0.00 0.00 37.25 1.73
591 751 3.625764 TCAACAAACCTGAAAGACCTTCG 59.374 43.478 0.00 0.00 36.78 3.79
593 753 3.699538 GGTCAACAAACCTGAAAGACCTT 59.300 43.478 0.00 0.00 37.81 3.50
611 771 4.862371 ACCAGAAGTTTTAACCTTGGTCA 58.138 39.130 7.20 0.00 34.38 4.02
613 773 7.616542 TCTTTTACCAGAAGTTTTAACCTTGGT 59.383 33.333 13.96 13.96 39.31 3.67
630 790 8.754991 TGAGGTTCATAAGTTTTCTTTTACCA 57.245 30.769 0.00 0.00 40.91 3.25
670 830 9.281371 TGCAATTCATTGAAAATCACCATTAAA 57.719 25.926 2.68 0.00 40.14 1.52
672 832 8.843885 TTGCAATTCATTGAAAATCACCATTA 57.156 26.923 2.68 0.00 40.14 1.90
676 836 6.310956 TCGATTGCAATTCATTGAAAATCACC 59.689 34.615 14.33 0.00 38.71 4.02
681 841 8.771766 TCAAATTCGATTGCAATTCATTGAAAA 58.228 25.926 14.33 0.58 38.71 2.29
685 845 8.994881 CAATTCAAATTCGATTGCAATTCATTG 58.005 29.630 14.33 13.84 40.66 2.82
723 883 5.567138 CCAATTGTGGGTCAGAATAAGAC 57.433 43.478 4.43 0.00 41.77 3.01
787 949 7.069331 TGTTGGGAATAAACTGTTTTCTGTGAT 59.931 33.333 11.48 0.00 32.46 3.06
811 973 8.114331 TCATGAAAGATGCACTAGATTTTTGT 57.886 30.769 0.00 0.00 0.00 2.83
812 974 8.975410 TTCATGAAAGATGCACTAGATTTTTG 57.025 30.769 5.45 0.00 0.00 2.44
825 987 8.053026 AGGAACTCTTTGATTCATGAAAGATG 57.947 34.615 13.09 7.32 38.86 2.90
847 1009 6.055588 GCTAACAATGGTGCTTAGATTAGGA 58.944 40.000 0.00 0.00 0.00 2.94
853 1016 3.751175 GTGTGCTAACAATGGTGCTTAGA 59.249 43.478 0.00 0.00 38.27 2.10
897 1060 1.689582 GCTGGTAGGCCCCACTACT 60.690 63.158 0.00 0.00 42.29 2.57
906 1069 4.715523 TGCGGTTGGCTGGTAGGC 62.716 66.667 0.00 0.00 44.05 3.93
909 1072 2.281900 GGTTGCGGTTGGCTGGTA 60.282 61.111 0.00 0.00 44.05 3.25
916 1079 1.404477 CGCTTTTAAGGTTGCGGTTG 58.596 50.000 0.00 0.00 43.97 3.77
963 1126 2.225467 AGGAAGCTTCTTTGTGTCAGC 58.775 47.619 25.05 5.26 0.00 4.26
1028 1191 2.283966 CGAGGTGGAGGTGGAGGT 60.284 66.667 0.00 0.00 0.00 3.85
1029 1192 3.775654 GCGAGGTGGAGGTGGAGG 61.776 72.222 0.00 0.00 0.00 4.30
1072 1235 3.519930 GACGGCGGAGAGGAGGAC 61.520 72.222 13.24 0.00 0.00 3.85
1073 1236 4.816984 GGACGGCGGAGAGGAGGA 62.817 72.222 13.24 0.00 0.00 3.71
1074 1237 4.824515 AGGACGGCGGAGAGGAGG 62.825 72.222 13.24 0.00 0.00 4.30
1075 1238 3.213402 GAGGACGGCGGAGAGGAG 61.213 72.222 13.24 0.00 0.00 3.69
1076 1239 4.816984 GGAGGACGGCGGAGAGGA 62.817 72.222 13.24 0.00 0.00 3.71
1078 1241 2.835431 ATGGAGGACGGCGGAGAG 60.835 66.667 13.24 0.00 0.00 3.20
1079 1242 3.147595 CATGGAGGACGGCGGAGA 61.148 66.667 13.24 0.00 0.00 3.71
1080 1243 4.899239 GCATGGAGGACGGCGGAG 62.899 72.222 13.24 0.00 0.00 4.63
1149 1312 3.237741 GGAGGGATGGCGAGGGAG 61.238 72.222 0.00 0.00 0.00 4.30
1443 1606 3.917760 GGCGAGAGGTCGGGGATG 61.918 72.222 0.00 0.00 46.91 3.51
1576 1739 2.358737 CTTGGTGGGCGTGAGGTC 60.359 66.667 0.00 0.00 0.00 3.85
1603 1766 2.512515 GAGCCTGGTGATCACGGC 60.513 66.667 27.92 27.92 38.84 5.68
1607 1770 0.036732 GTTGGTGAGCCTGGTGATCA 59.963 55.000 0.00 0.00 35.27 2.92
1728 1891 2.125961 GGGTATCTCGCCGGTGAGT 61.126 63.158 37.02 27.49 37.28 3.41
1860 2023 1.298014 GGTGAGCTGGTTCTGGGAG 59.702 63.158 0.00 0.00 0.00 4.30
2038 2201 3.003173 CTCCGACCAGCTCCCCAA 61.003 66.667 0.00 0.00 0.00 4.12
2076 2239 2.432628 CCCGTGAGCGAGTTGGTC 60.433 66.667 2.37 2.37 45.46 4.02
2356 2519 0.538746 AATTTGTTCCCGGCGAGGTT 60.539 50.000 9.30 0.00 38.74 3.50
2439 2602 4.116328 TCGCCGGAGAGCTCGTTG 62.116 66.667 5.05 1.45 0.00 4.10
2486 2649 0.976641 AATGTCCAGGCTGTCGAGAA 59.023 50.000 14.43 0.00 0.00 2.87
2625 2788 1.225745 CAACGAATTCAGCCGCGTC 60.226 57.895 4.92 0.00 35.74 5.19
2694 2857 1.189752 TCAGGTAGCTCAGCTTCAGG 58.810 55.000 3.31 0.00 40.44 3.86
2769 2932 1.226717 CTGGAAGCTCTCGCCGTAC 60.227 63.158 0.00 0.00 36.60 3.67
2844 3007 1.516386 CGAATGTCCACCGTCTCCG 60.516 63.158 0.00 0.00 0.00 4.63
2928 3091 0.676466 TGATGAAAATCGCCACGCCT 60.676 50.000 0.00 0.00 0.00 5.52
2940 3103 1.922135 GCCGGCGCTTCTTGATGAAA 61.922 55.000 12.58 0.00 33.79 2.69
3555 3718 1.807573 CTTGAAGGCCTCGTCGAGC 60.808 63.158 17.02 11.78 0.00 5.03
3714 3880 0.456995 CGCTCTTCTCCGTCACCTTC 60.457 60.000 0.00 0.00 0.00 3.46
4101 4267 0.400213 ACGGACCCAAAATGCTCAGA 59.600 50.000 0.00 0.00 0.00 3.27
4134 4309 2.044352 TCAGATCTCGGCCGTCCA 60.044 61.111 27.15 10.65 0.00 4.02
4157 4332 2.425668 TGCTACATGCTCTACTAACGCA 59.574 45.455 0.00 0.00 43.37 5.24
4162 4345 5.105351 ACAACACATGCTACATGCTCTACTA 60.105 40.000 7.46 0.00 43.37 1.82
4163 4346 4.186926 CAACACATGCTACATGCTCTACT 58.813 43.478 7.46 0.00 43.37 2.57
4189 4372 6.261381 TCACCAACCAACAATCTTTACTACAC 59.739 38.462 0.00 0.00 0.00 2.90
4190 4373 6.358178 TCACCAACCAACAATCTTTACTACA 58.642 36.000 0.00 0.00 0.00 2.74
4245 4434 8.631480 AGGGAGTACTAATTAACTTTGGTTTG 57.369 34.615 0.00 0.00 36.92 2.93
4246 4435 7.886970 GGAGGGAGTACTAATTAACTTTGGTTT 59.113 37.037 0.00 0.00 36.92 3.27
4247 4436 7.400439 GGAGGGAGTACTAATTAACTTTGGTT 58.600 38.462 0.00 0.00 39.26 3.67
4262 4451 7.912056 AAGTAAATAAAAACGGAGGGAGTAC 57.088 36.000 0.00 0.00 0.00 2.73
4265 4454 8.326680 TGTAAAGTAAATAAAAACGGAGGGAG 57.673 34.615 0.00 0.00 0.00 4.30
4291 4480 9.658799 CCTCTTTCACTTCAGTCAATTCTAATA 57.341 33.333 0.00 0.00 0.00 0.98
4294 4483 7.303182 TCCTCTTTCACTTCAGTCAATTCTA 57.697 36.000 0.00 0.00 0.00 2.10
4295 4484 6.179906 TCCTCTTTCACTTCAGTCAATTCT 57.820 37.500 0.00 0.00 0.00 2.40
4297 4486 4.759183 GCTCCTCTTTCACTTCAGTCAATT 59.241 41.667 0.00 0.00 0.00 2.32
4298 4487 4.202398 TGCTCCTCTTTCACTTCAGTCAAT 60.202 41.667 0.00 0.00 0.00 2.57
4299 4488 3.134623 TGCTCCTCTTTCACTTCAGTCAA 59.865 43.478 0.00 0.00 0.00 3.18
4300 4489 2.700371 TGCTCCTCTTTCACTTCAGTCA 59.300 45.455 0.00 0.00 0.00 3.41
4301 4490 3.063485 GTGCTCCTCTTTCACTTCAGTC 58.937 50.000 0.00 0.00 0.00 3.51
4302 4491 2.703007 AGTGCTCCTCTTTCACTTCAGT 59.297 45.455 0.00 0.00 37.78 3.41
4303 4492 3.324993 GAGTGCTCCTCTTTCACTTCAG 58.675 50.000 0.00 0.00 40.74 3.02
4304 4493 2.037772 GGAGTGCTCCTCTTTCACTTCA 59.962 50.000 10.80 0.00 46.16 3.02
4305 4494 2.694213 GGAGTGCTCCTCTTTCACTTC 58.306 52.381 10.80 0.00 46.16 3.01
4306 4495 2.849294 GGAGTGCTCCTCTTTCACTT 57.151 50.000 10.80 0.00 46.16 3.16
4327 4516 8.196771 GCAATGATTGATCTACCAACCAAAATA 58.803 33.333 9.76 0.00 0.00 1.40
4331 4520 4.402155 GGCAATGATTGATCTACCAACCAA 59.598 41.667 9.76 0.00 0.00 3.67
4334 4523 4.641989 AGTGGCAATGATTGATCTACCAAC 59.358 41.667 9.76 2.27 0.00 3.77
4353 4542 1.880027 GTAGTTTGACCTGCCAAGTGG 59.120 52.381 0.00 0.00 38.53 4.00
4354 4543 1.880027 GGTAGTTTGACCTGCCAAGTG 59.120 52.381 0.00 0.00 37.20 3.16
4355 4544 1.202891 GGGTAGTTTGACCTGCCAAGT 60.203 52.381 0.00 0.00 38.82 3.16
4356 4545 1.202879 TGGGTAGTTTGACCTGCCAAG 60.203 52.381 0.00 0.00 38.82 3.61
4385 4574 4.769488 TGTTTGGCCAAGAATACTGCATTA 59.231 37.500 19.48 0.00 0.00 1.90
4389 4578 3.874392 ATGTTTGGCCAAGAATACTGC 57.126 42.857 19.48 3.75 0.00 4.40
4439 4679 1.609208 TTTCTCTGCAGAAACCCAGC 58.391 50.000 18.85 0.00 42.66 4.85
4461 4701 8.850156 ACACTCATTTTTGCTCTTAGTATGTTT 58.150 29.630 0.00 0.00 0.00 2.83
4463 4703 7.880195 AGACACTCATTTTTGCTCTTAGTATGT 59.120 33.333 0.00 0.00 0.00 2.29
4464 4704 8.261492 AGACACTCATTTTTGCTCTTAGTATG 57.739 34.615 0.00 0.00 0.00 2.39
4465 4705 7.550906 GGAGACACTCATTTTTGCTCTTAGTAT 59.449 37.037 0.00 0.00 31.08 2.12
4486 4831 5.899299 AGATTTAGCATGCAAAATGGAGAC 58.101 37.500 21.98 0.66 0.00 3.36
4499 4844 9.175312 CTGCCTGATTAATGATAGATTTAGCAT 57.825 33.333 0.00 0.00 37.50 3.79
4501 4846 7.609532 ACCTGCCTGATTAATGATAGATTTAGC 59.390 37.037 0.00 0.00 0.00 3.09
4509 4854 5.532406 GCTTTCACCTGCCTGATTAATGATA 59.468 40.000 0.00 0.00 0.00 2.15
4512 4857 3.444742 TGCTTTCACCTGCCTGATTAATG 59.555 43.478 0.00 0.00 0.00 1.90
4513 4858 3.700538 TGCTTTCACCTGCCTGATTAAT 58.299 40.909 0.00 0.00 0.00 1.40
4517 4862 1.891150 CTTTGCTTTCACCTGCCTGAT 59.109 47.619 0.00 0.00 0.00 2.90
4593 4944 5.491070 TCTCTCTCTCTCTCTCAACTCTTG 58.509 45.833 0.00 0.00 0.00 3.02
4594 4945 5.485353 TCTCTCTCTCTCTCTCTCAACTCTT 59.515 44.000 0.00 0.00 0.00 2.85
4599 4950 5.045651 ACACATCTCTCTCTCTCTCTCTCAA 60.046 44.000 0.00 0.00 0.00 3.02
4600 4951 4.471025 ACACATCTCTCTCTCTCTCTCTCA 59.529 45.833 0.00 0.00 0.00 3.27
4601 4952 5.028549 ACACATCTCTCTCTCTCTCTCTC 57.971 47.826 0.00 0.00 0.00 3.20
4602 4953 5.188434 CAACACATCTCTCTCTCTCTCTCT 58.812 45.833 0.00 0.00 0.00 3.10
4603 4954 4.943705 ACAACACATCTCTCTCTCTCTCTC 59.056 45.833 0.00 0.00 0.00 3.20
4604 4955 4.922206 ACAACACATCTCTCTCTCTCTCT 58.078 43.478 0.00 0.00 0.00 3.10
4610 5008 1.821753 CCGGACAACACATCTCTCTCT 59.178 52.381 0.00 0.00 0.00 3.10
4613 5011 0.247736 AGCCGGACAACACATCTCTC 59.752 55.000 5.05 0.00 0.00 3.20
4629 5027 0.801836 GTGTGTTTGTGTGTGCAGCC 60.802 55.000 0.00 0.00 0.00 4.85
4634 5032 2.287248 TGTGTGTGTGTGTTTGTGTGTG 60.287 45.455 0.00 0.00 0.00 3.82
4635 5033 1.950216 TGTGTGTGTGTGTTTGTGTGT 59.050 42.857 0.00 0.00 0.00 3.72
4636 5034 2.695613 TGTGTGTGTGTGTTTGTGTG 57.304 45.000 0.00 0.00 0.00 3.82
4637 5035 2.556189 ACATGTGTGTGTGTGTTTGTGT 59.444 40.909 0.00 0.00 37.14 3.72
4638 5036 3.170505 GACATGTGTGTGTGTGTTTGTG 58.829 45.455 1.15 0.00 39.09 3.33
4639 5037 2.163412 GGACATGTGTGTGTGTGTTTGT 59.837 45.455 1.15 0.00 39.09 2.83
4640 5038 2.790812 CGGACATGTGTGTGTGTGTTTG 60.791 50.000 1.15 0.00 39.09 2.93
4641 5039 1.400142 CGGACATGTGTGTGTGTGTTT 59.600 47.619 1.15 0.00 39.09 2.83
4642 5040 1.013596 CGGACATGTGTGTGTGTGTT 58.986 50.000 1.15 0.00 39.09 3.32
4643 5041 0.813610 CCGGACATGTGTGTGTGTGT 60.814 55.000 1.15 0.00 39.09 3.72
4644 5042 1.506309 CCCGGACATGTGTGTGTGTG 61.506 60.000 1.15 0.00 39.09 3.82
4645 5043 1.227823 CCCGGACATGTGTGTGTGT 60.228 57.895 1.15 0.00 39.09 3.72
4646 5044 0.950555 CTCCCGGACATGTGTGTGTG 60.951 60.000 1.15 0.00 39.09 3.82
4658 5056 3.634157 TGGAAGCATCCCTCCCGGA 62.634 63.158 0.73 0.00 45.95 5.14
4661 5059 0.039618 TGTTTGGAAGCATCCCTCCC 59.960 55.000 5.34 0.00 45.95 4.30
4662 5060 1.923356 TTGTTTGGAAGCATCCCTCC 58.077 50.000 5.34 0.00 45.95 4.30
4663 5061 2.627699 TGTTTGTTTGGAAGCATCCCTC 59.372 45.455 5.34 0.00 45.95 4.30
4664 5062 2.676748 TGTTTGTTTGGAAGCATCCCT 58.323 42.857 5.34 0.00 45.95 4.20
4665 5063 3.467374 TTGTTTGTTTGGAAGCATCCC 57.533 42.857 5.34 0.00 45.95 3.85
4688 5086 1.065109 GGCGACGGCTTGTTTGTTT 59.935 52.632 15.00 0.00 39.81 2.83
4691 5089 4.383602 CGGGCGACGGCTTGTTTG 62.384 66.667 21.48 1.11 39.81 2.93
4692 5090 4.612412 TCGGGCGACGGCTTGTTT 62.612 61.111 21.48 0.00 44.45 2.83
4693 5091 4.612412 TTCGGGCGACGGCTTGTT 62.612 61.111 21.48 0.00 44.45 2.83
4694 5092 3.894547 ATTTCGGGCGACGGCTTGT 62.895 57.895 21.48 0.72 44.45 3.16
4695 5093 3.095898 GATTTCGGGCGACGGCTTG 62.096 63.158 21.48 13.91 44.45 4.01
4696 5094 2.818274 GATTTCGGGCGACGGCTT 60.818 61.111 21.48 1.45 44.45 4.35
4771 5169 3.006537 CGATTCCCGGACATATAGTTGGT 59.993 47.826 0.73 0.00 33.91 3.67
4773 5171 2.993899 GCGATTCCCGGACATATAGTTG 59.006 50.000 0.73 0.00 39.04 3.16
4777 5175 1.067142 GCAGCGATTCCCGGACATATA 60.067 52.381 0.73 0.00 39.04 0.86
4778 5176 0.320771 GCAGCGATTCCCGGACATAT 60.321 55.000 0.73 0.00 39.04 1.78
4779 5177 1.069090 GCAGCGATTCCCGGACATA 59.931 57.895 0.73 0.00 39.04 2.29
4780 5178 2.203070 GCAGCGATTCCCGGACAT 60.203 61.111 0.73 0.00 39.04 3.06
4794 5192 2.125350 GTCGCCCTTCCTCAGCAG 60.125 66.667 0.00 0.00 0.00 4.24
4811 5209 2.642700 CCTGAAAAACGTGGCGGG 59.357 61.111 0.00 0.00 0.00 6.13
4832 5230 0.237498 GTGCAACAAAGTCTACCCGC 59.763 55.000 0.00 0.00 36.32 6.13
4835 5233 2.286772 CCAACGTGCAACAAAGTCTACC 60.287 50.000 0.00 0.00 35.74 3.18
4845 5243 1.654137 CGCTGTTCCAACGTGCAAC 60.654 57.895 0.00 0.00 32.88 4.17
4861 5259 4.374702 CAGCAACAGTGGCGACGC 62.375 66.667 12.43 12.43 42.66 5.19
4863 5261 2.974698 AGCAGCAACAGTGGCGAC 60.975 61.111 0.00 0.00 36.08 5.19
4866 5264 4.695231 CGCAGCAGCAACAGTGGC 62.695 66.667 0.82 0.00 42.27 5.01
4909 5318 6.546403 AGATGCGATACTAGGAGACAAAACTA 59.454 38.462 0.00 0.00 0.00 2.24
4911 5320 5.593010 AGATGCGATACTAGGAGACAAAAC 58.407 41.667 0.00 0.00 0.00 2.43
4924 5333 4.686554 GGTGGACAAGATAAGATGCGATAC 59.313 45.833 0.00 0.00 0.00 2.24
4926 5335 3.733337 GGTGGACAAGATAAGATGCGAT 58.267 45.455 0.00 0.00 0.00 4.58
4930 5339 3.133003 AGGTCGGTGGACAAGATAAGATG 59.867 47.826 0.00 0.00 45.28 2.90
4958 5367 4.746309 GGTGCATCAGCCAGGCCA 62.746 66.667 8.22 0.00 41.13 5.36
4961 5370 2.360350 AACGGTGCATCAGCCAGG 60.360 61.111 0.00 0.00 41.13 4.45
4962 5371 1.364626 GAGAACGGTGCATCAGCCAG 61.365 60.000 0.00 0.00 41.13 4.85
4963 5372 1.375908 GAGAACGGTGCATCAGCCA 60.376 57.895 0.00 0.00 41.13 4.75
4964 5373 2.109126 GGAGAACGGTGCATCAGCC 61.109 63.158 0.00 0.00 41.13 4.85
4965 5374 2.456119 CGGAGAACGGTGCATCAGC 61.456 63.158 0.00 0.00 39.42 4.26
4966 5375 3.786101 CGGAGAACGGTGCATCAG 58.214 61.111 0.00 0.00 39.42 2.90
4982 5391 1.528586 GAATGAATCATCCGACAGCCG 59.471 52.381 0.00 0.00 38.18 5.52
4983 5392 2.843701 AGAATGAATCATCCGACAGCC 58.156 47.619 0.00 0.00 0.00 4.85
4984 5393 5.931146 AGAATAGAATGAATCATCCGACAGC 59.069 40.000 0.00 0.00 0.00 4.40
4985 5394 7.959689 AAGAATAGAATGAATCATCCGACAG 57.040 36.000 0.00 0.00 0.00 3.51
4986 5395 8.737168 AAAAGAATAGAATGAATCATCCGACA 57.263 30.769 0.00 0.00 0.00 4.35
5009 5418 3.320673 AACAACCGTTGCAAGGAAAAA 57.679 38.095 20.29 0.00 32.81 1.94
5010 5419 4.363999 CATAACAACCGTTGCAAGGAAAA 58.636 39.130 20.29 0.65 36.52 2.29
5011 5420 3.243569 CCATAACAACCGTTGCAAGGAAA 60.244 43.478 20.29 0.00 36.52 3.13
5012 5421 2.294791 CCATAACAACCGTTGCAAGGAA 59.705 45.455 20.29 0.00 36.52 3.36
5013 5422 1.883275 CCATAACAACCGTTGCAAGGA 59.117 47.619 20.29 0.00 36.52 3.36
5014 5423 1.668628 GCCATAACAACCGTTGCAAGG 60.669 52.381 12.17 12.17 36.52 3.61
5015 5424 1.668628 GGCCATAACAACCGTTGCAAG 60.669 52.381 11.29 0.00 36.52 4.01
5016 5425 0.315568 GGCCATAACAACCGTTGCAA 59.684 50.000 11.29 0.00 36.52 4.08
5017 5426 0.823769 TGGCCATAACAACCGTTGCA 60.824 50.000 11.29 0.00 36.52 4.08
5018 5427 0.530288 ATGGCCATAACAACCGTTGC 59.470 50.000 19.18 0.00 36.52 4.17
5019 5428 2.230025 TGAATGGCCATAACAACCGTTG 59.770 45.455 21.15 9.80 36.52 4.10
5020 5429 2.520069 TGAATGGCCATAACAACCGTT 58.480 42.857 21.15 0.00 39.24 4.44
5021 5430 2.208132 TGAATGGCCATAACAACCGT 57.792 45.000 21.15 0.00 0.00 4.83
5022 5431 4.761739 AGATATGAATGGCCATAACAACCG 59.238 41.667 21.15 0.00 33.28 4.44
5023 5432 5.106555 CGAGATATGAATGGCCATAACAACC 60.107 44.000 21.15 14.24 33.28 3.77
5024 5433 5.106555 CCGAGATATGAATGGCCATAACAAC 60.107 44.000 21.15 16.12 33.28 3.32
5025 5434 5.003160 CCGAGATATGAATGGCCATAACAA 58.997 41.667 21.15 12.82 33.28 2.83
5026 5435 4.565444 CCCGAGATATGAATGGCCATAACA 60.565 45.833 21.15 21.72 33.28 2.41
5027 5436 3.941483 CCCGAGATATGAATGGCCATAAC 59.059 47.826 21.15 16.65 33.28 1.89
5028 5437 3.622206 GCCCGAGATATGAATGGCCATAA 60.622 47.826 21.15 11.38 33.28 1.90
5029 5438 2.092968 GCCCGAGATATGAATGGCCATA 60.093 50.000 21.15 4.23 33.98 2.74
5030 5439 1.340405 GCCCGAGATATGAATGGCCAT 60.340 52.381 14.09 14.09 32.74 4.40
5031 5440 0.036732 GCCCGAGATATGAATGGCCA 59.963 55.000 8.56 8.56 32.74 5.36
5032 5441 0.036732 TGCCCGAGATATGAATGGCC 59.963 55.000 0.00 0.00 38.10 5.36
5033 5442 2.119801 ATGCCCGAGATATGAATGGC 57.880 50.000 0.00 0.00 39.33 4.40
5034 5443 3.535561 GGTATGCCCGAGATATGAATGG 58.464 50.000 0.00 0.00 0.00 3.16
5047 5456 4.910585 CGCCTCCACGGTATGCCC 62.911 72.222 0.00 0.00 34.25 5.36
5056 5465 3.876589 TTTGCTCGACCGCCTCCAC 62.877 63.158 0.00 0.00 0.00 4.02
5057 5466 3.621805 TTTGCTCGACCGCCTCCA 61.622 61.111 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.