Multiple sequence alignment - TraesCS4B01G042200

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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 TraesCS4B01G042200 chr4B 100.000 6282 0 0 884 7165 28730489 28736770 0.000000e+00 11601.0
1 TraesCS4B01G042200 chr4B 97.151 351 10 0 1578 1928 28730826 28731176 1.720000e-165 593.0
2 TraesCS4B01G042200 chr4B 97.151 351 10 0 1221 1571 28731183 28731533 1.720000e-165 593.0
3 TraesCS4B01G042200 chr4B 100.000 301 0 0 1 301 28729606 28729906 2.260000e-154 556.0
4 TraesCS4B01G042200 chr4D 96.739 2177 65 4 2778 4949 16816044 16818219 0.000000e+00 3622.0
5 TraesCS4B01G042200 chr4D 93.337 1831 75 21 4988 6785 16818220 16820036 0.000000e+00 2662.0
6 TraesCS4B01G042200 chr4D 94.069 1568 55 18 1221 2786 16814484 16816015 0.000000e+00 2346.0
7 TraesCS4B01G042200 chr4D 96.008 1052 31 5 884 1928 16813786 16814833 0.000000e+00 1700.0
8 TraesCS4B01G042200 chr4D 96.726 336 9 2 1594 1928 16814143 16814477 6.280000e-155 558.0
9 TraesCS4B01G042200 chr4D 89.744 351 8 7 1221 1571 16814840 16815162 2.390000e-114 424.0
10 TraesCS4B01G042200 chr4D 91.611 298 15 4 4 301 16813378 16813665 3.110000e-108 403.0
11 TraesCS4B01G042200 chr4D 90.435 115 10 1 6961 7074 16820039 16820153 4.480000e-32 150.0
12 TraesCS4B01G042200 chr4A 91.061 2215 125 40 4968 7142 583703631 583701450 0.000000e+00 2926.0
13 TraesCS4B01G042200 chr4A 97.350 1283 29 3 2778 4057 583705926 583704646 0.000000e+00 2176.0
14 TraesCS4B01G042200 chr4A 93.990 1198 42 7 1591 2786 583707124 583705955 0.000000e+00 1786.0
15 TraesCS4B01G042200 chr4A 95.957 742 25 5 4236 4973 583704626 583703886 0.000000e+00 1199.0
16 TraesCS4B01G042200 chr4A 95.265 697 21 6 884 1571 583707481 583706788 0.000000e+00 1094.0
17 TraesCS4B01G042200 chr4A 90.033 301 16 5 4 301 583707908 583707619 1.890000e-100 377.0
18 TraesCS4B01G042200 chrUn 97.733 397 9 0 3273 3669 479066988 479067384 0.000000e+00 684.0
19 TraesCS4B01G042200 chrUn 93.617 47 3 0 6209 6255 452435306 452435352 3.590000e-08 71.3
20 TraesCS4B01G042200 chrUn 93.617 47 3 0 6209 6255 455046693 455046647 3.590000e-08 71.3
21 TraesCS4B01G042200 chrUn 93.617 47 3 0 6209 6255 456637954 456638000 3.590000e-08 71.3
22 TraesCS4B01G042200 chr5D 93.617 47 3 0 6209 6255 6182824 6182778 3.590000e-08 71.3
23 TraesCS4B01G042200 chr5D 93.617 47 3 0 6209 6255 503285422 503285468 3.590000e-08 71.3
24 TraesCS4B01G042200 chr3D 93.617 47 3 0 6209 6255 519674030 519673984 3.590000e-08 71.3
25 TraesCS4B01G042200 chr1D 93.617 47 3 0 6209 6255 254404235 254404281 3.590000e-08 71.3
26 TraesCS4B01G042200 chr5B 100.000 29 0 0 4245 4273 12334894 12334866 4.000000e-03 54.7
27 TraesCS4B01G042200 chr5B 100.000 28 0 0 4245 4272 398073748 398073775 1.300000e-02 52.8
28 TraesCS4B01G042200 chr2D 100.000 29 0 0 4245 4273 346087345 346087317 4.000000e-03 54.7
29 TraesCS4B01G042200 chr2A 100.000 29 0 0 4245 4273 459797751 459797723 4.000000e-03 54.7
30 TraesCS4B01G042200 chr7B 100.000 28 0 0 4245 4272 61605364 61605391 1.300000e-02 52.8
31 TraesCS4B01G042200 chr5A 100.000 28 0 0 4245 4272 439864809 439864836 1.300000e-02 52.8
32 TraesCS4B01G042200 chr5A 100.000 28 0 0 4245 4272 612226772 612226745 1.300000e-02 52.8


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 TraesCS4B01G042200 chr4B 28729606 28736770 7164 False 6078.500 11601 100.000000 1 7165 2 chr4B.!!$F1 7164
1 TraesCS4B01G042200 chr4B 28730826 28731533 707 False 593.000 593 97.151000 1221 1928 2 chr4B.!!$F2 707
2 TraesCS4B01G042200 chr4D 16813378 16820153 6775 False 1483.125 3622 93.583625 4 7074 8 chr4D.!!$F1 7070
3 TraesCS4B01G042200 chr4A 583701450 583707908 6458 True 1593.000 2926 93.942667 4 7142 6 chr4A.!!$R1 7138

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
178 182 0.391263 GGGTTCTACGACTGGGCTTG 60.391 60.000 0.00 0.00 0.00 4.01 F
1017 1021 1.691482 CCGATGGAGAGGAGGGGTAAA 60.691 57.143 0.00 0.00 0.00 2.01 F
2280 2636 0.770557 TTGTGGTAGGCCCTGTTCCT 60.771 55.000 0.00 0.00 37.72 3.36 F
2563 2919 1.064017 TCCAGGTTGCAAAAGGTGTCT 60.064 47.619 0.00 0.00 0.00 3.41 F
3399 3794 0.684153 AATGGAGGTTTGCCATCCCG 60.684 55.000 0.00 0.00 45.11 5.14 F
3577 3972 0.743701 GATCTGGTGGCAGCAGTGAG 60.744 60.000 36.96 19.54 43.70 3.51 F
3999 4394 0.752658 AACTTTTGCCCTTCAGGTGC 59.247 50.000 0.00 0.00 38.26 5.01 F
4789 5186 0.978151 AATTGCATTGCCTCTTGCCA 59.022 45.000 6.12 0.00 40.16 4.92 F
6098 6762 0.535102 CCGAGGTTGCCAGACTTTGT 60.535 55.000 0.00 0.00 0.00 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1989 2338 6.352516 ACCACATAGGAATTTTGCAAAAACA 58.647 32.000 27.10 6.6 41.22 2.83 R
2413 2769 0.934496 GAGTTGCACGCTGTGTTGTA 59.066 50.000 9.76 0.0 35.75 2.41 R
3399 3794 0.548510 AGCAGATAACCCTTGGCCTC 59.451 55.000 3.32 0.0 0.00 4.70 R
3559 3954 1.298993 CTCACTGCTGCCACCAGAT 59.701 57.895 0.00 0.0 41.77 2.90 R
5233 5897 0.744414 TCTAGTAACCGACGTCCCCG 60.744 60.000 10.58 0.0 40.83 5.73 R
5387 6051 1.138859 TGCACTATCCGTTCCTCATGG 59.861 52.381 0.00 0.0 0.00 3.66 R
5510 6174 1.201647 CACGGTACCTGAGAATCACGT 59.798 52.381 10.90 0.0 42.56 4.49 R
6161 6825 0.179207 TCGACGCTACGCTGTGTTAG 60.179 55.000 0.00 0.0 0.00 2.34 R
7117 7821 0.526739 CATGGATGGCATTGTGCGTG 60.527 55.000 0.00 0.0 46.21 5.34 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
157 161 2.224621 CCTGACGGATGAAAGCCCATAT 60.225 50.000 0.00 0.00 41.45 1.78
158 162 3.007940 CCTGACGGATGAAAGCCCATATA 59.992 47.826 0.00 0.00 41.45 0.86
178 182 0.391263 GGGTTCTACGACTGGGCTTG 60.391 60.000 0.00 0.00 0.00 4.01
192 196 4.437587 CTTGGGCCTGCCAGGAGG 62.438 72.222 16.85 2.80 37.67 4.30
235 239 2.028733 GGCGGCATTTGTGGCAAAG 61.029 57.895 3.07 0.00 0.00 2.77
257 261 2.882927 AAAAAGGTTTTGCTCCGTCC 57.117 45.000 0.00 0.00 0.00 4.79
1017 1021 1.691482 CCGATGGAGAGGAGGGGTAAA 60.691 57.143 0.00 0.00 0.00 2.01
1167 1171 1.995646 GCGACCCTCTCGACTTCCTC 61.996 65.000 0.00 0.00 46.14 3.71
2017 2371 4.314121 TGCAAAATTCCTATGTGGTTTGC 58.686 39.130 11.02 11.02 46.66 3.68
2117 2471 7.036220 CGGAAGCTAGACTTTTCTTTAGATGA 58.964 38.462 0.00 0.00 39.29 2.92
2173 2527 8.196378 AGTCTAGACCTTTTCTTCACATACTT 57.804 34.615 19.38 0.00 35.55 2.24
2174 2528 8.652290 AGTCTAGACCTTTTCTTCACATACTTT 58.348 33.333 19.38 0.00 35.55 2.66
2175 2529 9.274206 GTCTAGACCTTTTCTTCACATACTTTT 57.726 33.333 12.13 0.00 35.55 2.27
2176 2530 9.847224 TCTAGACCTTTTCTTCACATACTTTTT 57.153 29.630 0.00 0.00 35.55 1.94
2246 2602 2.301577 AAGCTGAGTTATCGTCCTGC 57.698 50.000 0.00 0.00 0.00 4.85
2280 2636 0.770557 TTGTGGTAGGCCCTGTTCCT 60.771 55.000 0.00 0.00 37.72 3.36
2324 2680 4.714802 TGTCTTTCCGATTCTATTCCCTGA 59.285 41.667 0.00 0.00 0.00 3.86
2374 2730 6.642707 TCCAACCGAATTTGTCTAAAATGT 57.357 33.333 0.00 0.00 0.00 2.71
2404 2760 7.702348 GTCATCTTGTTTTAACTTGAACTTGCT 59.298 33.333 0.00 0.00 0.00 3.91
2413 2769 4.423625 ACTTGAACTTGCTTCAGGTACT 57.576 40.909 0.80 0.00 45.04 2.73
2414 2770 5.546621 ACTTGAACTTGCTTCAGGTACTA 57.453 39.130 0.80 0.00 45.04 1.82
2415 2771 5.298347 ACTTGAACTTGCTTCAGGTACTAC 58.702 41.667 0.80 0.00 45.04 2.73
2563 2919 1.064017 TCCAGGTTGCAAAAGGTGTCT 60.064 47.619 0.00 0.00 0.00 3.41
2627 2983 5.175491 GCATCAAATCAAAACGACATGTTGT 59.825 36.000 13.26 13.26 40.84 3.32
2656 3012 5.721960 ACCTTCCATGTTGAGTACTATCACT 59.278 40.000 0.00 0.00 0.00 3.41
2660 3016 8.533569 TTCCATGTTGAGTACTATCACTGATA 57.466 34.615 0.00 0.00 0.00 2.15
2661 3017 7.941919 TCCATGTTGAGTACTATCACTGATAC 58.058 38.462 0.00 0.00 0.00 2.24
2664 3020 5.298527 TGTTGAGTACTATCACTGATACCCG 59.701 44.000 0.00 0.00 0.00 5.28
2665 3021 3.819337 TGAGTACTATCACTGATACCCGC 59.181 47.826 0.00 0.00 0.00 6.13
2711 3067 4.643784 ACCAGCAGAAGAATGAAATGGATC 59.356 41.667 0.00 0.00 0.00 3.36
2720 3076 7.449395 AGAAGAATGAAATGGATCTGTTTGTGA 59.551 33.333 0.00 0.00 0.00 3.58
2752 3108 5.373981 AGTCGTCGTTAGATGTTTCTTCT 57.626 39.130 0.00 0.00 35.01 2.85
2754 3110 6.906659 AGTCGTCGTTAGATGTTTCTTCTTA 58.093 36.000 0.00 0.00 35.01 2.10
2756 3112 8.671921 AGTCGTCGTTAGATGTTTCTTCTTATA 58.328 33.333 0.00 0.00 35.01 0.98
2757 3113 9.282247 GTCGTCGTTAGATGTTTCTTCTTATAA 57.718 33.333 0.00 0.00 35.01 0.98
2878 3270 7.876068 CAGACCTGTTTCTGTATTTAGTTACCA 59.124 37.037 0.00 0.00 38.61 3.25
3078 3470 4.497006 GGATGTCAAGTATGATGCAGCAAC 60.497 45.833 9.54 8.93 38.01 4.17
3157 3552 1.138069 TGCTCTGTCGTTGGTTCTTCA 59.862 47.619 0.00 0.00 0.00 3.02
3213 3608 2.557056 CACGAGTTCCTCAGAGTAACCA 59.443 50.000 2.33 0.00 0.00 3.67
3342 3737 4.461081 TGGTGATTGGAATCCTAAAAACCG 59.539 41.667 0.00 0.00 34.50 4.44
3361 3756 4.196626 CCGTCAGGTTCCTAATACAACA 57.803 45.455 0.00 0.00 0.00 3.33
3399 3794 0.684153 AATGGAGGTTTGCCATCCCG 60.684 55.000 0.00 0.00 45.11 5.14
3532 3927 5.240844 ACATTTCTTTAAGGTGAACGGGAAG 59.759 40.000 0.00 0.00 27.87 3.46
3577 3972 0.743701 GATCTGGTGGCAGCAGTGAG 60.744 60.000 36.96 19.54 43.70 3.51
3610 4005 6.959361 AGTTATATCAATGGAACGTGCAATC 58.041 36.000 0.00 0.00 0.00 2.67
3835 4230 5.869888 AGTTATCGGACTCATTTTCTGTGTC 59.130 40.000 0.00 0.00 44.15 3.67
3859 4254 8.691797 GTCCTGGGAGTATTTTATTAAATGCAA 58.308 33.333 7.79 0.00 38.40 4.08
3999 4394 0.752658 AACTTTTGCCCTTCAGGTGC 59.247 50.000 0.00 0.00 38.26 5.01
4010 4405 1.129251 CTTCAGGTGCACGCATAACAG 59.871 52.381 11.45 0.00 0.00 3.16
4034 4429 7.544566 CAGAATCATGTCCTTTGAAATTTCCAG 59.455 37.037 15.48 10.88 0.00 3.86
4092 4487 2.440409 AGGCTAGCACCAATGAAACTG 58.560 47.619 18.24 0.00 0.00 3.16
4205 4601 5.008613 GTCTTGCTGTGTGAAACCTGATTAA 59.991 40.000 0.00 0.00 34.36 1.40
4209 4605 5.008613 TGCTGTGTGAAACCTGATTAAGAAC 59.991 40.000 0.00 0.00 34.36 3.01
4214 4610 7.771361 TGTGTGAAACCTGATTAAGAACAACTA 59.229 33.333 0.00 0.00 34.36 2.24
4397 4793 2.510382 AGAAGGTCCTATCTCACCTCGA 59.490 50.000 0.00 0.00 42.61 4.04
4421 4817 8.288208 CGAGATGGAAAAATTAAGGATGATCAG 58.712 37.037 0.09 0.00 0.00 2.90
4493 4889 2.175202 GCTCAGAAGTGGAAGGAGAGA 58.825 52.381 0.00 0.00 0.00 3.10
4495 4891 3.368323 GCTCAGAAGTGGAAGGAGAGAAG 60.368 52.174 0.00 0.00 0.00 2.85
4565 4961 7.066525 TGGCAGGTAACCTTTATTTAATTCGAG 59.933 37.037 0.00 0.00 37.17 4.04
4789 5186 0.978151 AATTGCATTGCCTCTTGCCA 59.022 45.000 6.12 0.00 40.16 4.92
4872 5269 5.501413 CGCATTCTATTGAGTTACTGTGCTG 60.501 44.000 0.00 0.00 0.00 4.41
4892 5289 6.017357 GTGCTGTTAAAGTTTGTACTAAGCCT 60.017 38.462 0.00 0.00 33.17 4.58
4956 5353 8.410141 ACTGATAGAGCTGAAAGTAATGTAGTC 58.590 37.037 0.00 0.00 35.30 2.59
5005 5662 7.074507 TGGCATGTGCAAAATTTTAATCATC 57.925 32.000 2.44 3.83 44.36 2.92
5050 5707 2.679082 ACATATACTTGCTCCGTCCCT 58.321 47.619 0.00 0.00 0.00 4.20
5051 5708 2.365617 ACATATACTTGCTCCGTCCCTG 59.634 50.000 0.00 0.00 0.00 4.45
5052 5709 2.447408 TATACTTGCTCCGTCCCTGA 57.553 50.000 0.00 0.00 0.00 3.86
5068 5725 5.488341 GTCCCTGAATGTAATGTGTAGTGT 58.512 41.667 0.00 0.00 0.00 3.55
5069 5726 5.351465 GTCCCTGAATGTAATGTGTAGTGTG 59.649 44.000 0.00 0.00 0.00 3.82
5070 5727 5.247337 TCCCTGAATGTAATGTGTAGTGTGA 59.753 40.000 0.00 0.00 0.00 3.58
5071 5728 6.070251 TCCCTGAATGTAATGTGTAGTGTGAT 60.070 38.462 0.00 0.00 0.00 3.06
5072 5729 6.599244 CCCTGAATGTAATGTGTAGTGTGATT 59.401 38.462 0.00 0.00 0.00 2.57
5073 5730 7.201644 CCCTGAATGTAATGTGTAGTGTGATTC 60.202 40.741 0.00 0.00 0.00 2.52
5074 5731 7.334171 CCTGAATGTAATGTGTAGTGTGATTCA 59.666 37.037 0.00 0.00 0.00 2.57
5075 5732 8.791327 TGAATGTAATGTGTAGTGTGATTCAT 57.209 30.769 0.00 0.00 0.00 2.57
5076 5733 8.667463 TGAATGTAATGTGTAGTGTGATTCATG 58.333 33.333 0.00 0.00 0.00 3.07
5077 5734 8.791327 AATGTAATGTGTAGTGTGATTCATGA 57.209 30.769 0.00 0.00 0.00 3.07
5078 5735 7.832503 TGTAATGTGTAGTGTGATTCATGAG 57.167 36.000 0.00 0.00 0.00 2.90
5079 5736 7.610865 TGTAATGTGTAGTGTGATTCATGAGA 58.389 34.615 0.00 0.00 0.00 3.27
5080 5737 6.974932 AATGTGTAGTGTGATTCATGAGAC 57.025 37.500 0.00 0.00 0.00 3.36
5081 5738 4.485163 TGTGTAGTGTGATTCATGAGACG 58.515 43.478 0.00 0.00 0.00 4.18
5232 5896 6.586082 ACGAATCAAAATACACCTTGCATTTC 59.414 34.615 0.00 0.00 0.00 2.17
5233 5897 6.034898 CGAATCAAAATACACCTTGCATTTCC 59.965 38.462 0.00 0.00 0.00 3.13
5355 6019 7.224557 CCTTCTCAAATTTACCTTGTTTTGTGG 59.775 37.037 0.00 0.00 32.33 4.17
5551 6215 2.340337 GGATGCAATTTGCTTTCGCTT 58.660 42.857 21.19 0.00 45.31 4.68
5564 6228 3.980775 GCTTTCGCTTGTTTATTTCTGCA 59.019 39.130 0.00 0.00 0.00 4.41
5565 6229 4.089065 GCTTTCGCTTGTTTATTTCTGCAG 59.911 41.667 7.63 7.63 0.00 4.41
5616 6280 8.321353 AGAATATTACTGACCAGTCACATCAAA 58.679 33.333 5.87 0.00 42.54 2.69
5693 6357 5.307196 AGGAACACTTAACTACATGTCACCT 59.693 40.000 0.00 0.00 31.45 4.00
5774 6438 4.444022 CCAACTGATATCTGGTCTCTTGGG 60.444 50.000 13.48 0.66 0.00 4.12
5783 6447 4.942944 TCTGGTCTCTTGGGTGTATTCTA 58.057 43.478 0.00 0.00 0.00 2.10
5912 6576 5.376625 GACAACCCATGGCTTATTGATCTA 58.623 41.667 17.94 0.00 32.61 1.98
5945 6609 3.827898 GCCTGGGACCGAGACGAG 61.828 72.222 4.84 0.00 0.00 4.18
5954 6618 4.180946 CGAGACGAGCGGTGGAGG 62.181 72.222 2.87 0.00 0.00 4.30
6006 6670 2.124983 CTCTGGTGCCACGGGATG 60.125 66.667 0.00 0.00 0.00 3.51
6098 6762 0.535102 CCGAGGTTGCCAGACTTTGT 60.535 55.000 0.00 0.00 0.00 2.83
6161 6825 1.678101 AGCAGTCAAAGCACTGAAACC 59.322 47.619 6.12 0.00 45.92 3.27
6189 6853 1.804326 GTAGCGTCGACGGCATGTT 60.804 57.895 36.13 16.11 40.23 2.71
6225 6909 3.552684 GCCATCTTCTCCTCGAGATCAAG 60.553 52.174 15.71 11.89 38.56 3.02
6234 6918 4.124970 TCCTCGAGATCAAGCATCAATTG 58.875 43.478 15.71 0.00 33.29 2.32
6308 6992 1.673626 GGCTGACCGTCACCGATTTTA 60.674 52.381 0.00 0.00 35.63 1.52
6309 6993 2.277084 GCTGACCGTCACCGATTTTAT 58.723 47.619 0.00 0.00 35.63 1.40
6310 6994 2.030457 GCTGACCGTCACCGATTTTATG 59.970 50.000 0.00 0.00 35.63 1.90
6312 6996 1.329599 GACCGTCACCGATTTTATGGC 59.670 52.381 0.00 0.00 35.63 4.40
6313 6997 1.065709 ACCGTCACCGATTTTATGGCT 60.066 47.619 0.00 0.00 35.63 4.75
6314 6998 1.597663 CCGTCACCGATTTTATGGCTC 59.402 52.381 0.00 0.00 35.63 4.70
6315 6999 2.276201 CGTCACCGATTTTATGGCTCA 58.724 47.619 0.00 0.00 35.63 4.26
6326 7010 6.365789 CGATTTTATGGCTCAATTGTGTTGTT 59.634 34.615 5.13 0.00 0.00 2.83
6334 7018 4.217754 TCAATTGTGTTGTTACGGAAGC 57.782 40.909 5.13 0.00 0.00 3.86
6352 7036 1.627329 AGCTCAGCACTTCATTGAGGA 59.373 47.619 0.00 0.00 38.94 3.71
6391 7076 0.594602 CTGAGGTCGTCGTTGGTGTA 59.405 55.000 0.00 0.00 0.00 2.90
6472 7158 1.542547 GGACCATTTGTGACACGAGGT 60.543 52.381 6.48 6.48 0.00 3.85
6516 7206 3.961408 TCCTGTTAGATGAGGAACTAGGC 59.039 47.826 0.00 0.00 41.55 3.93
6540 7230 3.997681 GGTGGTGCTTTAGTCTCTTCTTC 59.002 47.826 0.00 0.00 0.00 2.87
6567 7257 4.522789 TGTTTGGTCCTTCTGAATTTAGGC 59.477 41.667 0.00 0.00 0.00 3.93
6571 7261 2.603560 GTCCTTCTGAATTTAGGCGACG 59.396 50.000 0.00 0.00 0.00 5.12
6592 7282 4.096833 ACGGCGTCTGTTGTAATCTGTATA 59.903 41.667 6.77 0.00 0.00 1.47
6593 7283 5.220381 CGGCGTCTGTTGTAATCTGTATAT 58.780 41.667 0.00 0.00 0.00 0.86
6733 7431 1.802960 GCAGGACTGACACTGATGTTG 59.197 52.381 3.00 0.00 39.95 3.33
6734 7432 2.548707 GCAGGACTGACACTGATGTTGA 60.549 50.000 3.00 0.00 39.95 3.18
6777 7475 0.392998 ATGTTAGTTGGGCGCAGGAG 60.393 55.000 10.83 0.00 0.00 3.69
6789 7487 1.153005 GCAGGAGGCATCTTCCCTG 60.153 63.158 0.00 0.00 46.67 4.45
6797 7495 3.717294 ATCTTCCCTGGCCGCGTT 61.717 61.111 4.92 0.00 0.00 4.84
6811 7509 1.208259 CGCGTTTGATGATGATCCGA 58.792 50.000 0.00 0.00 0.00 4.55
6819 7517 0.875908 ATGATGATCCGACGGCGTTG 60.876 55.000 20.27 20.27 35.23 4.10
6821 7519 2.901051 GATGATCCGACGGCGTTGGT 62.901 60.000 37.71 27.40 38.23 3.67
6822 7520 2.433664 GATCCGACGGCGTTGGTT 60.434 61.111 37.71 31.99 38.23 3.67
6823 7521 2.030958 GATCCGACGGCGTTGGTTT 61.031 57.895 37.71 28.33 38.23 3.27
6825 7523 1.167781 ATCCGACGGCGTTGGTTTTT 61.168 50.000 37.71 22.03 38.23 1.94
6826 7524 1.369568 CCGACGGCGTTGGTTTTTC 60.370 57.895 33.32 9.47 32.65 2.29
6827 7525 1.644913 CGACGGCGTTGGTTTTTCT 59.355 52.632 19.51 0.00 0.00 2.52
6828 7526 0.656205 CGACGGCGTTGGTTTTTCTG 60.656 55.000 19.51 0.00 0.00 3.02
6829 7527 0.379316 GACGGCGTTGGTTTTTCTGT 59.621 50.000 16.19 0.00 0.00 3.41
6830 7528 0.812549 ACGGCGTTGGTTTTTCTGTT 59.187 45.000 6.77 0.00 0.00 3.16
6831 7529 1.196200 CGGCGTTGGTTTTTCTGTTG 58.804 50.000 0.00 0.00 0.00 3.33
6832 7530 1.202200 CGGCGTTGGTTTTTCTGTTGA 60.202 47.619 0.00 0.00 0.00 3.18
6833 7531 2.459934 GGCGTTGGTTTTTCTGTTGAG 58.540 47.619 0.00 0.00 0.00 3.02
6834 7532 2.098443 GGCGTTGGTTTTTCTGTTGAGA 59.902 45.455 0.00 0.00 0.00 3.27
6835 7533 3.243401 GGCGTTGGTTTTTCTGTTGAGAT 60.243 43.478 0.00 0.00 0.00 2.75
6836 7534 4.023536 GGCGTTGGTTTTTCTGTTGAGATA 60.024 41.667 0.00 0.00 0.00 1.98
6837 7535 4.909880 GCGTTGGTTTTTCTGTTGAGATAC 59.090 41.667 0.00 0.00 0.00 2.24
6894 7592 1.077140 TGCTGGTTGTGGCTTGTGA 60.077 52.632 0.00 0.00 0.00 3.58
6910 7608 2.554142 TGTGAGCACAGTTCTCTTGTG 58.446 47.619 1.70 1.21 36.21 3.33
6922 7620 2.771089 TCTCTTGTGTGTGCTCCAATC 58.229 47.619 0.00 0.00 0.00 2.67
6943 7641 9.889128 CCAATCTGGGTTGATTATTATGTTTTT 57.111 29.630 0.00 0.00 35.18 1.94
6972 7670 2.704725 GTACGTACGACTGAACCCAA 57.295 50.000 24.41 0.00 0.00 4.12
7007 7705 2.000447 GCACCTTATCGACTGTCCAAC 59.000 52.381 1.55 0.00 0.00 3.77
7014 7712 0.528901 TCGACTGTCCAACCACGTTG 60.529 55.000 1.55 0.00 42.49 4.10
7062 7760 3.733443 GAAAGTGTTGGTGCTTTCCAT 57.267 42.857 5.92 0.00 42.62 3.41
7063 7761 3.642705 GAAAGTGTTGGTGCTTTCCATC 58.357 45.455 5.92 0.00 42.62 3.51
7065 7763 2.233271 AGTGTTGGTGCTTTCCATCTG 58.767 47.619 0.00 0.00 37.33 2.90
7066 7764 0.961019 TGTTGGTGCTTTCCATCTGC 59.039 50.000 0.00 0.00 37.33 4.26
7067 7765 0.961019 GTTGGTGCTTTCCATCTGCA 59.039 50.000 0.00 0.00 37.33 4.41
7068 7766 1.068055 GTTGGTGCTTTCCATCTGCAG 60.068 52.381 7.63 7.63 37.39 4.41
7069 7767 0.401356 TGGTGCTTTCCATCTGCAGA 59.599 50.000 20.79 20.79 37.39 4.26
7070 7768 1.005097 TGGTGCTTTCCATCTGCAGAT 59.995 47.619 23.75 23.75 37.39 2.90
7098 7798 4.096984 AGCACAGGCATTATCTTTTGTAGC 59.903 41.667 0.00 0.00 44.61 3.58
7099 7799 4.734695 GCACAGGCATTATCTTTTGTAGCC 60.735 45.833 0.00 0.00 40.72 3.93
7129 7833 2.089936 CACATGCACGCACAATGCC 61.090 57.895 0.00 0.00 41.12 4.40
7133 7837 2.202650 GCACGCACAATGCCATCC 60.203 61.111 0.00 0.00 41.12 3.51
7142 7846 1.064240 ACAATGCCATCCATGCTCAGA 60.064 47.619 0.00 0.00 33.49 3.27
7143 7847 1.609072 CAATGCCATCCATGCTCAGAG 59.391 52.381 0.00 0.00 33.49 3.35
7144 7848 0.537600 ATGCCATCCATGCTCAGAGC 60.538 55.000 16.21 16.21 42.82 4.09
7155 7859 2.985406 GCTCAGAGCAAACTCCAAAG 57.015 50.000 18.17 0.00 44.65 2.77
7156 7860 1.538950 GCTCAGAGCAAACTCCAAAGG 59.461 52.381 18.17 0.00 44.65 3.11
7157 7861 2.157738 CTCAGAGCAAACTCCAAAGGG 58.842 52.381 0.00 0.00 44.65 3.95
7158 7862 1.202927 TCAGAGCAAACTCCAAAGGGG 60.203 52.381 0.00 0.00 44.65 4.79
7159 7863 0.540597 AGAGCAAACTCCAAAGGGGC 60.541 55.000 0.00 0.00 44.65 5.80
7160 7864 1.866853 GAGCAAACTCCAAAGGGGCG 61.867 60.000 0.00 0.00 36.90 6.13
7161 7865 1.901464 GCAAACTCCAAAGGGGCGA 60.901 57.895 0.00 0.00 36.21 5.54
7162 7866 1.956802 CAAACTCCAAAGGGGCGAC 59.043 57.895 0.00 0.00 36.21 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
100 104 1.134877 GGTTAAGTCGGCCTCACTACC 60.135 57.143 0.00 4.60 0.00 3.18
133 137 1.653151 GGCTTTCATCCGTCAGGTAC 58.347 55.000 0.00 0.00 39.05 3.34
157 161 0.333993 AGCCCAGTCGTAGAACCCTA 59.666 55.000 0.00 0.00 39.69 3.53
158 162 0.544595 AAGCCCAGTCGTAGAACCCT 60.545 55.000 0.00 0.00 39.69 4.34
185 189 4.176752 GCTAACGGGGCCTCCTGG 62.177 72.222 0.84 0.00 43.79 4.45
186 190 4.176752 GGCTAACGGGGCCTCCTG 62.177 72.222 0.84 0.00 45.57 3.86
192 196 4.354162 TGGTTGGGCTAACGGGGC 62.354 66.667 7.68 0.00 40.28 5.80
193 197 2.045340 CTGGTTGGGCTAACGGGG 60.045 66.667 7.68 0.00 40.28 5.73
195 199 2.033448 TGCTGGTTGGGCTAACGG 59.967 61.111 7.68 4.54 40.28 4.44
196 200 2.677003 CGTGCTGGTTGGGCTAACG 61.677 63.158 7.68 0.00 40.28 3.18
197 201 2.332654 CCGTGCTGGTTGGGCTAAC 61.333 63.158 5.00 5.00 38.60 2.34
198 202 2.033448 CCGTGCTGGTTGGGCTAA 59.967 61.111 0.00 0.00 0.00 3.09
257 261 4.218578 ATGCCGAGCGAGCAGGAG 62.219 66.667 12.49 0.00 44.90 3.69
273 277 3.592877 AGCCCCCAAATTTTGAAATGGAT 59.407 39.130 10.72 1.73 0.00 3.41
909 913 1.689582 CCCTAGGGTTCCGGAGCTT 60.690 63.158 20.88 9.40 0.00 3.74
1986 2335 8.186821 CCACATAGGAATTTTGCAAAAACAAAA 58.813 29.630 27.10 13.91 45.55 2.44
1987 2336 7.337942 ACCACATAGGAATTTTGCAAAAACAAA 59.662 29.630 27.10 15.33 41.22 2.83
1988 2337 6.825721 ACCACATAGGAATTTTGCAAAAACAA 59.174 30.769 27.10 15.62 41.22 2.83
1989 2338 6.352516 ACCACATAGGAATTTTGCAAAAACA 58.647 32.000 27.10 6.60 41.22 2.83
1990 2339 6.859420 ACCACATAGGAATTTTGCAAAAAC 57.141 33.333 27.10 21.82 41.22 2.43
1991 2340 7.701445 CAAACCACATAGGAATTTTGCAAAAA 58.299 30.769 27.10 11.87 41.22 1.94
1992 2341 7.256756 CAAACCACATAGGAATTTTGCAAAA 57.743 32.000 25.76 25.76 41.22 2.44
2017 2371 7.163001 TCCATATAGACGGAAATCTGAGATG 57.837 40.000 0.00 0.00 0.00 2.90
2255 2611 2.247358 CAGGGCCTACCACAAAAATGT 58.753 47.619 5.28 0.00 43.89 2.71
2300 2656 5.053145 CAGGGAATAGAATCGGAAAGACAG 58.947 45.833 0.00 0.00 0.00 3.51
2324 2680 2.093235 GCATCTTTCTCTGTAGCAGGGT 60.093 50.000 0.00 0.00 33.01 4.34
2374 2730 8.519526 AGTTCAAGTTAAAACAAGATGACAACA 58.480 29.630 0.00 0.00 0.00 3.33
2404 2760 2.363038 ACGCTGTGTTGTAGTACCTGAA 59.637 45.455 0.00 0.00 0.00 3.02
2413 2769 0.934496 GAGTTGCACGCTGTGTTGTA 59.066 50.000 9.76 0.00 35.75 2.41
2414 2770 1.721487 GAGTTGCACGCTGTGTTGT 59.279 52.632 9.76 0.00 35.75 3.32
2415 2771 1.368019 CGAGTTGCACGCTGTGTTG 60.368 57.895 9.76 0.00 35.75 3.33
2502 2858 2.305009 GCTTCTGCATAGCCATTCCTT 58.695 47.619 9.25 0.00 39.41 3.36
2563 2919 4.394920 GCGTTAACATCCTTTTGATCAGGA 59.605 41.667 6.39 4.76 44.86 3.86
2627 2983 5.084519 AGTACTCAACATGGAAGGTGTAGA 58.915 41.667 0.00 0.00 0.00 2.59
2656 3012 2.158769 AGCATTCTGATTGCGGGTATCA 60.159 45.455 16.20 0.00 44.82 2.15
2660 3016 1.033746 CCAGCATTCTGATTGCGGGT 61.034 55.000 25.53 7.10 46.37 5.28
2661 3017 1.731700 CCAGCATTCTGATTGCGGG 59.268 57.895 22.62 22.62 46.35 6.13
2664 3020 3.581024 TTTGACCAGCATTCTGATTGC 57.419 42.857 14.85 14.85 42.95 3.56
2665 3021 3.916172 CGTTTTGACCAGCATTCTGATTG 59.084 43.478 0.00 0.00 42.95 2.67
2720 3076 5.633830 TCTAACGACGACTTATTCCTGTT 57.366 39.130 0.00 0.00 0.00 3.16
2752 3108 8.837788 ATGCATTTCGAGATGTGATCTTATAA 57.162 30.769 16.44 0.00 40.38 0.98
2754 3110 6.932960 TGATGCATTTCGAGATGTGATCTTAT 59.067 34.615 16.44 2.14 40.38 1.73
2756 3112 5.121105 TGATGCATTTCGAGATGTGATCTT 58.879 37.500 16.44 0.00 40.38 2.40
2757 3113 4.700700 TGATGCATTTCGAGATGTGATCT 58.299 39.130 16.44 0.00 43.70 2.75
2834 3226 8.254508 ACAGGTCTGCATTTAACTTTACAAAAA 58.745 29.630 0.00 0.00 0.00 1.94
2878 3270 5.072741 ACATTCTCACCTGCAATGTAAACT 58.927 37.500 0.00 0.00 38.65 2.66
3078 3470 4.605640 TCAATCCCTTTTTGAGGCAAAG 57.394 40.909 0.00 0.00 44.85 2.77
3157 3552 7.170393 TGAATGTAGTGATACAGCAGTAACT 57.830 36.000 0.00 0.00 33.13 2.24
3342 3737 5.790593 TGTCTGTTGTATTAGGAACCTGAC 58.209 41.667 3.36 0.26 0.00 3.51
3361 3756 2.437897 CCAGGGGCAGCTTTGTCT 59.562 61.111 0.00 0.00 0.00 3.41
3399 3794 0.548510 AGCAGATAACCCTTGGCCTC 59.451 55.000 3.32 0.00 0.00 4.70
3532 3927 8.925700 CCAATTTTACCAAGTTTCTGATAAAGC 58.074 33.333 0.00 0.00 0.00 3.51
3556 3951 2.226315 ACTGCTGCCACCAGATCCA 61.226 57.895 0.00 0.00 41.77 3.41
3559 3954 1.298993 CTCACTGCTGCCACCAGAT 59.701 57.895 0.00 0.00 41.77 2.90
3577 3972 7.696453 CGTTCCATTGATATAACTTTGTGAACC 59.304 37.037 0.00 0.00 0.00 3.62
3610 4005 4.636206 AGCTTTATCTTTTTCAGGGCGTAG 59.364 41.667 0.00 0.00 0.00 3.51
3835 4230 9.533253 CTTTGCATTTAATAAAATACTCCCAGG 57.467 33.333 0.00 0.00 33.45 4.45
3838 4233 8.700973 TCCCTTTGCATTTAATAAAATACTCCC 58.299 33.333 0.00 0.00 33.45 4.30
3893 4288 7.174253 ACAATAGAAGTTAATTTTCTGCACGGA 59.826 33.333 12.79 0.00 36.38 4.69
3927 4322 1.777272 AGGGAACAAGAAGCTTCCAGT 59.223 47.619 22.81 17.86 38.18 4.00
3999 4394 3.873361 AGGACATGATTCTGTTATGCGTG 59.127 43.478 0.00 0.00 0.00 5.34
4010 4405 7.330208 CACTGGAAATTTCAAAGGACATGATTC 59.670 37.037 19.49 0.00 0.00 2.52
4421 4817 7.305474 CAAACTCAAGGACCATGTAAATGTAC 58.695 38.462 0.00 0.00 0.00 2.90
4693 5090 1.880027 ACAAGATTTGGTTCACCGAGC 59.120 47.619 0.00 0.00 39.43 5.03
4754 5151 7.534918 GCAATGCAATTAAAAATCTGGAACAAC 59.465 33.333 0.00 0.00 32.39 3.32
4789 5186 6.581712 ACAATGGAAAATTGTGTAGCAGTTT 58.418 32.000 3.03 0.00 40.37 2.66
4892 5289 6.539826 CCTACATTGCACAGAAGATGTATTGA 59.460 38.462 7.03 0.00 41.41 2.57
4969 5366 5.866159 TGCACATGCCAATAATTATGGAA 57.134 34.783 14.50 7.33 40.56 3.53
4971 5368 6.922247 TTTTGCACATGCCAATAATTATGG 57.078 33.333 0.00 4.41 41.18 2.74
5005 5662 4.789012 ACAGAGCCAAATAAACACATGG 57.211 40.909 0.00 0.00 36.00 3.66
5050 5707 8.667463 CATGAATCACACTACACATTACATTCA 58.333 33.333 0.00 0.00 33.50 2.57
5051 5708 8.882736 TCATGAATCACACTACACATTACATTC 58.117 33.333 0.00 0.00 0.00 2.67
5052 5709 8.791327 TCATGAATCACACTACACATTACATT 57.209 30.769 0.00 0.00 0.00 2.71
5068 5725 3.055891 TCAAAGCCTCGTCTCATGAATCA 60.056 43.478 0.00 0.00 0.00 2.57
5069 5726 3.308323 GTCAAAGCCTCGTCTCATGAATC 59.692 47.826 0.00 0.00 0.00 2.52
5070 5727 3.265791 GTCAAAGCCTCGTCTCATGAAT 58.734 45.455 0.00 0.00 0.00 2.57
5071 5728 2.612972 GGTCAAAGCCTCGTCTCATGAA 60.613 50.000 0.00 0.00 0.00 2.57
5072 5729 1.066858 GGTCAAAGCCTCGTCTCATGA 60.067 52.381 0.00 0.00 0.00 3.07
5073 5730 1.338105 TGGTCAAAGCCTCGTCTCATG 60.338 52.381 0.00 0.00 0.00 3.07
5074 5731 0.976641 TGGTCAAAGCCTCGTCTCAT 59.023 50.000 0.00 0.00 0.00 2.90
5075 5732 0.756294 TTGGTCAAAGCCTCGTCTCA 59.244 50.000 0.00 0.00 0.00 3.27
5076 5733 2.100605 ATTGGTCAAAGCCTCGTCTC 57.899 50.000 0.00 0.00 0.00 3.36
5077 5734 3.695830 TTATTGGTCAAAGCCTCGTCT 57.304 42.857 0.00 0.00 0.00 4.18
5078 5735 4.965119 AATTATTGGTCAAAGCCTCGTC 57.035 40.909 0.00 0.00 0.00 4.20
5079 5736 7.122055 TCAATTAATTATTGGTCAAAGCCTCGT 59.878 33.333 0.00 0.00 43.19 4.18
5080 5737 7.479980 TCAATTAATTATTGGTCAAAGCCTCG 58.520 34.615 0.00 0.00 43.19 4.63
5081 5738 9.822185 AATCAATTAATTATTGGTCAAAGCCTC 57.178 29.630 0.00 0.00 43.19 4.70
5162 5822 5.689383 AAGACATGTGGTTTATGTGACAC 57.311 39.130 1.15 0.00 38.78 3.67
5233 5897 0.744414 TCTAGTAACCGACGTCCCCG 60.744 60.000 10.58 0.00 40.83 5.73
5272 5936 8.644318 ACCACTTATCTGAACGTATTCATTAC 57.356 34.615 0.00 0.00 43.92 1.89
5327 5991 5.468540 AACAAGGTAAATTTGAGAAGGCC 57.531 39.130 0.00 0.00 0.00 5.19
5387 6051 1.138859 TGCACTATCCGTTCCTCATGG 59.861 52.381 0.00 0.00 0.00 3.66
5510 6174 1.201647 CACGGTACCTGAGAATCACGT 59.798 52.381 10.90 0.00 42.56 4.49
5616 6280 6.528537 TTAGCATGCCAGATACAACAAATT 57.471 33.333 15.66 0.00 0.00 1.82
5774 6438 9.809096 CCATACACCATCTGATATAGAATACAC 57.191 37.037 0.00 0.00 39.30 2.90
5783 6447 7.671302 GTGTCTTACCATACACCATCTGATAT 58.329 38.462 0.00 0.00 40.07 1.63
5874 6538 1.387756 GTTGTCGACCGGTTCATAACG 59.612 52.381 9.42 6.67 0.00 3.18
5954 6618 3.437049 GGTGTTGAAGCAACTGAGGTATC 59.563 47.826 11.11 0.00 43.85 2.24
6006 6670 1.379044 CAGGGTTGATGGGAGGCAC 60.379 63.158 0.00 0.00 0.00 5.01
6050 6714 0.470833 AGTGTGGTCTGACCTGCTCT 60.471 55.000 26.03 19.83 39.58 4.09
6053 6717 1.302033 CCAGTGTGGTCTGACCTGC 60.302 63.158 26.03 18.71 39.58 4.85
6098 6762 3.371063 ACGCCTCGAAGCTCGGAA 61.371 61.111 4.21 0.00 40.88 4.30
6132 6796 2.555325 TGCTTTGACTGCTTTGATCCTG 59.445 45.455 0.00 0.00 0.00 3.86
6161 6825 0.179207 TCGACGCTACGCTGTGTTAG 60.179 55.000 0.00 0.00 0.00 2.34
6234 6918 2.464865 AGCTGTCTATCGAATCGTTGC 58.535 47.619 1.52 0.00 0.00 4.17
6258 6942 1.970114 CCAAGACCTGCAGTGCCTG 60.970 63.158 13.72 6.02 34.12 4.85
6272 6956 3.204827 CCGCGGATCTTGCCCAAG 61.205 66.667 24.07 1.62 39.71 3.61
6308 6992 3.057596 CCGTAACAACACAATTGAGCCAT 60.058 43.478 13.59 0.00 0.00 4.40
6309 6993 2.292016 CCGTAACAACACAATTGAGCCA 59.708 45.455 13.59 0.00 0.00 4.75
6310 6994 2.550606 TCCGTAACAACACAATTGAGCC 59.449 45.455 13.59 0.00 0.00 4.70
6312 6996 4.024048 AGCTTCCGTAACAACACAATTGAG 60.024 41.667 13.59 6.93 0.00 3.02
6313 6997 3.880490 AGCTTCCGTAACAACACAATTGA 59.120 39.130 13.59 0.00 0.00 2.57
6314 6998 4.219033 GAGCTTCCGTAACAACACAATTG 58.781 43.478 3.24 3.24 0.00 2.32
6315 6999 3.880490 TGAGCTTCCGTAACAACACAATT 59.120 39.130 0.00 0.00 0.00 2.32
6326 7010 0.966179 TGAAGTGCTGAGCTTCCGTA 59.034 50.000 5.83 0.00 41.03 4.02
6334 7018 4.096081 GGAATTCCTCAATGAAGTGCTGAG 59.904 45.833 17.73 0.00 37.03 3.35
6352 7036 4.081142 TCAGGACGACACATACATGGAATT 60.081 41.667 0.00 0.00 0.00 2.17
6391 7076 3.259374 CGAAGAGGAGGGCATACATACAT 59.741 47.826 0.00 0.00 0.00 2.29
6457 7143 3.551846 AGGAAAACCTCGTGTCACAAAT 58.448 40.909 3.42 0.00 0.00 2.32
6488 7174 5.620738 TTCCTCATCTAACAGGAAGATGG 57.379 43.478 11.92 4.61 46.81 3.51
6516 7206 3.007398 AGAAGAGACTAAAGCACCACCTG 59.993 47.826 0.00 0.00 0.00 4.00
6540 7230 2.526304 TCAGAAGGACCAAACAGACG 57.474 50.000 0.00 0.00 0.00 4.18
6567 7257 0.638746 GATTACAACAGACGCCGTCG 59.361 55.000 12.13 9.40 37.67 5.12
6571 7261 5.983720 ACATATACAGATTACAACAGACGCC 59.016 40.000 0.00 0.00 0.00 5.68
6592 7282 5.379187 TCATCATGCAGGTGCTATTTACAT 58.621 37.500 3.18 0.00 42.66 2.29
6593 7283 4.779696 TCATCATGCAGGTGCTATTTACA 58.220 39.130 3.18 0.00 42.66 2.41
6789 7487 0.040958 GATCATCATCAAACGCGGCC 60.041 55.000 12.47 0.00 0.00 6.13
6797 7495 0.597377 CGCCGTCGGATCATCATCAA 60.597 55.000 17.49 0.00 0.00 2.57
6811 7509 0.812549 AACAGAAAAACCAACGCCGT 59.187 45.000 0.00 0.00 0.00 5.68
6819 7517 6.912591 CACAACAGTATCTCAACAGAAAAACC 59.087 38.462 0.00 0.00 30.24 3.27
6821 7519 7.857734 TCACAACAGTATCTCAACAGAAAAA 57.142 32.000 0.00 0.00 30.24 1.94
6822 7520 7.714813 TGATCACAACAGTATCTCAACAGAAAA 59.285 33.333 0.00 0.00 30.24 2.29
6823 7521 7.216494 TGATCACAACAGTATCTCAACAGAAA 58.784 34.615 0.00 0.00 30.24 2.52
6825 7523 6.345096 TGATCACAACAGTATCTCAACAGA 57.655 37.500 0.00 0.00 0.00 3.41
6826 7524 7.293745 GTTTGATCACAACAGTATCTCAACAG 58.706 38.462 0.00 0.00 35.63 3.16
6827 7525 6.204688 GGTTTGATCACAACAGTATCTCAACA 59.795 38.462 17.03 0.00 35.63 3.33
6828 7526 6.204688 TGGTTTGATCACAACAGTATCTCAAC 59.795 38.462 17.03 6.39 35.63 3.18
6829 7527 6.295249 TGGTTTGATCACAACAGTATCTCAA 58.705 36.000 17.03 0.00 35.63 3.02
6830 7528 5.863965 TGGTTTGATCACAACAGTATCTCA 58.136 37.500 17.03 6.42 35.63 3.27
6831 7529 6.348540 GGTTGGTTTGATCACAACAGTATCTC 60.349 42.308 22.11 6.22 44.61 2.75
6832 7530 5.473504 GGTTGGTTTGATCACAACAGTATCT 59.526 40.000 22.11 0.00 44.61 1.98
6833 7531 5.616866 CGGTTGGTTTGATCACAACAGTATC 60.617 44.000 22.11 9.16 44.61 2.24
6834 7532 4.215399 CGGTTGGTTTGATCACAACAGTAT 59.785 41.667 22.11 0.00 44.61 2.12
6835 7533 3.562141 CGGTTGGTTTGATCACAACAGTA 59.438 43.478 22.11 0.00 44.61 2.74
6836 7534 2.357637 CGGTTGGTTTGATCACAACAGT 59.642 45.455 22.11 0.00 44.61 3.55
6837 7535 2.858260 GCGGTTGGTTTGATCACAACAG 60.858 50.000 22.11 19.84 44.61 3.16
6894 7592 2.283298 CACACACAAGAGAACTGTGCT 58.717 47.619 2.96 0.00 37.08 4.40
6910 7608 0.883833 CAACCCAGATTGGAGCACAC 59.116 55.000 0.00 0.00 40.96 3.82
6957 7655 0.598158 TGCGTTGGGTTCAGTCGTAC 60.598 55.000 0.00 0.00 0.00 3.67
6958 7656 0.598158 GTGCGTTGGGTTCAGTCGTA 60.598 55.000 0.00 0.00 0.00 3.43
6959 7657 1.885850 GTGCGTTGGGTTCAGTCGT 60.886 57.895 0.00 0.00 0.00 4.34
6963 7661 2.954753 GCTCGTGCGTTGGGTTCAG 61.955 63.158 0.00 0.00 0.00 3.02
7007 7705 3.571571 TCGTCTATCTGAAACAACGTGG 58.428 45.455 0.00 0.00 0.00 4.94
7014 7712 1.480954 TGGGGCTCGTCTATCTGAAAC 59.519 52.381 0.00 0.00 0.00 2.78
7065 7763 2.875485 CCTGTGCTGTGCATCTGC 59.125 61.111 0.00 0.09 41.91 4.26
7066 7764 1.313091 ATGCCTGTGCTGTGCATCTG 61.313 55.000 0.00 0.00 41.68 2.90
7067 7765 0.611062 AATGCCTGTGCTGTGCATCT 60.611 50.000 0.00 0.00 44.49 2.90
7068 7766 1.097232 TAATGCCTGTGCTGTGCATC 58.903 50.000 0.00 0.00 44.49 3.91
7070 7768 1.097232 GATAATGCCTGTGCTGTGCA 58.903 50.000 0.00 0.00 39.68 4.57
7071 7769 1.386533 AGATAATGCCTGTGCTGTGC 58.613 50.000 0.00 0.00 38.71 4.57
7072 7770 4.171005 CAAAAGATAATGCCTGTGCTGTG 58.829 43.478 0.00 0.00 38.71 3.66
7073 7771 3.828451 ACAAAAGATAATGCCTGTGCTGT 59.172 39.130 0.00 0.00 38.71 4.40
7081 7781 5.278022 GCACTAGGCTACAAAAGATAATGCC 60.278 44.000 0.00 0.00 40.25 4.40
7117 7821 0.526739 CATGGATGGCATTGTGCGTG 60.527 55.000 0.00 0.00 46.21 5.34
7121 7825 1.067060 CTGAGCATGGATGGCATTGTG 59.933 52.381 0.00 2.40 0.00 3.33
7123 7827 1.609072 CTCTGAGCATGGATGGCATTG 59.391 52.381 0.00 0.00 0.00 2.82
7142 7846 1.903404 CGCCCCTTTGGAGTTTGCT 60.903 57.895 0.00 0.00 35.39 3.91
7143 7847 1.901464 TCGCCCCTTTGGAGTTTGC 60.901 57.895 0.00 0.00 35.07 3.68
7144 7848 1.524008 GGTCGCCCCTTTGGAGTTTG 61.524 60.000 0.00 0.00 35.07 2.93
7145 7849 1.228459 GGTCGCCCCTTTGGAGTTT 60.228 57.895 0.00 0.00 35.07 2.66
7146 7850 2.154074 AGGTCGCCCCTTTGGAGTT 61.154 57.895 0.00 0.00 42.73 3.01
7147 7851 2.529389 AGGTCGCCCCTTTGGAGT 60.529 61.111 0.00 0.00 42.73 3.85


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

AutoCloner maintained by Alex Coulton.