Multiple sequence alignment - TraesCS4B01G375400

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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 TraesCS4B01G375400 chr4B 100.000 5292 0 0 1 5292 659501961 659496670 0.000000e+00 9773.0
1 TraesCS4B01G375400 chr4B 96.301 4542 98 17 594 5126 659485821 659481341 0.000000e+00 7393.0
2 TraesCS4B01G375400 chr4B 99.692 2273 1 1 170 2442 659514556 659512290 0.000000e+00 4154.0
3 TraesCS4B01G375400 chr4B 94.693 358 11 3 257 609 659486614 659486260 2.790000e-152 549.0
4 TraesCS4B01G375400 chr4B 100.000 168 0 0 1 168 659514824 659514657 1.430000e-80 311.0
5 TraesCS4B01G375400 chr4B 100.000 35 0 0 5123 5157 659481411 659481377 1.230000e-06 65.8
6 TraesCS4B01G375400 chr4B 100.000 35 0 0 5056 5090 659496839 659496805 1.230000e-06 65.8
7 TraesCS4B01G375400 chr4B 100.000 35 0 0 5123 5157 659496906 659496872 1.230000e-06 65.8
8 TraesCS4B01G375400 chrUn 97.409 3397 51 7 1501 4887 264518339 264521708 0.000000e+00 5751.0
9 TraesCS4B01G375400 chr5A 84.918 3355 388 65 1135 4420 704368590 704371895 0.000000e+00 3284.0
10 TraesCS4B01G375400 chr5A 86.098 1971 209 38 2499 4432 694577706 694579648 0.000000e+00 2061.0
11 TraesCS4B01G375400 chr5A 85.895 1971 213 39 2499 4432 694556175 694558117 0.000000e+00 2039.0
12 TraesCS4B01G375400 chr5A 85.791 1872 202 37 2598 4432 694535868 694537712 0.000000e+00 1925.0
13 TraesCS4B01G375400 chr5A 85.985 1320 157 16 1078 2395 694551705 694552998 0.000000e+00 1387.0
14 TraesCS4B01G375400 chr5A 85.909 1320 158 16 1078 2395 694531274 694532567 0.000000e+00 1382.0
15 TraesCS4B01G375400 chr5A 85.909 1320 158 16 1078 2395 694572076 694573369 0.000000e+00 1382.0
16 TraesCS4B01G375400 chr5A 79.130 1931 340 46 1083 2970 708848126 708850036 0.000000e+00 1275.0
17 TraesCS4B01G375400 chr5A 85.993 1078 125 16 2609 3674 704452042 704453105 0.000000e+00 1131.0
18 TraesCS4B01G375400 chr5A 91.940 335 22 2 324 658 400793466 400793795 1.040000e-126 464.0
19 TraesCS4B01G375400 chr5A 78.571 252 45 3 3979 4221 708850924 708851175 1.970000e-34 158.0
20 TraesCS4B01G375400 chr5A 84.868 152 22 1 4572 4722 694558579 694558730 9.180000e-33 152.0
21 TraesCS4B01G375400 chr5A 84.211 152 23 1 4572 4722 694538173 694538324 4.270000e-31 147.0
22 TraesCS4B01G375400 chr5A 82.895 152 25 1 4572 4722 694580110 694580261 9.240000e-28 135.0
23 TraesCS4B01G375400 chr5A 92.000 50 3 1 142 191 374902790 374902838 9.510000e-08 69.4
24 TraesCS4B01G375400 chr5A 94.595 37 1 1 203 239 692059699 692059734 7.400000e-04 56.5
25 TraesCS4B01G375400 chr4D 84.496 3425 401 59 1067 4420 508339587 508342952 0.000000e+00 3264.0
26 TraesCS4B01G375400 chr4D 88.010 1251 130 11 2502 3746 504520348 504521584 0.000000e+00 1461.0
27 TraesCS4B01G375400 chr4D 84.171 1333 180 19 1067 2395 504518216 504519521 0.000000e+00 1264.0
28 TraesCS4B01G375400 chr4D 89.323 384 36 5 3981 4360 504521788 504522170 1.330000e-130 477.0
29 TraesCS4B01G375400 chr2B 92.492 333 20 2 324 656 619961261 619961588 6.200000e-129 472.0
30 TraesCS4B01G375400 chr2B 80.114 352 47 18 327 666 523078658 523078318 1.900000e-59 241.0
31 TraesCS4B01G375400 chr7B 91.369 336 22 5 324 656 734292054 734291723 2.250000e-123 453.0
32 TraesCS4B01G375400 chr7B 91.975 324 18 5 324 646 657081699 657081383 1.050000e-121 448.0
33 TraesCS4B01G375400 chr7B 91.304 46 4 0 137 182 31131710 31131755 4.420000e-06 63.9
34 TraesCS4B01G375400 chr7B 100.000 28 0 0 4435 4462 732277002 732277029 1.000000e-02 52.8
35 TraesCS4B01G375400 chr3D 92.284 324 16 6 324 647 21380694 21381008 8.080000e-123 451.0
36 TraesCS4B01G375400 chr1B 92.025 326 19 4 324 647 683036900 683037220 8.080000e-123 451.0
37 TraesCS4B01G375400 chr1B 98.551 138 2 0 5154 5291 26386863 26386726 1.470000e-60 244.0
38 TraesCS4B01G375400 chr1B 98.551 138 2 0 5154 5291 40630048 40629911 1.470000e-60 244.0
39 TraesCS4B01G375400 chr1B 98.551 138 2 0 5154 5291 50054170 50054307 1.470000e-60 244.0
40 TraesCS4B01G375400 chr1B 98.551 138 2 0 5154 5291 629611526 629611663 1.470000e-60 244.0
41 TraesCS4B01G375400 chr1B 89.796 49 5 0 135 183 503833133 503833181 4.420000e-06 63.9
42 TraesCS4B01G375400 chr6B 91.071 336 21 6 324 657 420771181 420770853 3.760000e-121 446.0
43 TraesCS4B01G375400 chr6B 98.551 138 2 0 5154 5291 4238783 4238920 1.470000e-60 244.0
44 TraesCS4B01G375400 chr6B 98.551 138 2 0 5154 5291 52965286 52965423 1.470000e-60 244.0
45 TraesCS4B01G375400 chr6B 98.551 138 2 0 5154 5291 642390956 642391093 1.470000e-60 244.0
46 TraesCS4B01G375400 chr6B 98.551 138 2 0 5154 5291 646156611 646156748 1.470000e-60 244.0
47 TraesCS4B01G375400 chr6B 98.551 138 2 0 5154 5291 671898041 671898178 1.470000e-60 244.0
48 TraesCS4B01G375400 chr7D 97.778 45 1 0 4435 4479 3181144 3181100 1.580000e-10 78.7
49 TraesCS4B01G375400 chr3B 95.556 45 2 0 4435 4479 793358238 793358282 7.350000e-09 73.1
50 TraesCS4B01G375400 chr4A 93.478 46 3 0 135 180 15772400 15772445 9.510000e-08 69.4
51 TraesCS4B01G375400 chr5D 93.333 45 3 0 4435 4479 25450891 25450935 3.420000e-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 TraesCS4B01G375400 chr4B 659496670 659501961 5291 True 9773.000000 9773 100.000000 1 5292 1 chr4B.!!$R4 5291
1 TraesCS4B01G375400 chr4B 659481341 659485821 4480 True 7393.000000 7393 96.301000 594 5126 1 chr4B.!!$R1 4532
2 TraesCS4B01G375400 chr4B 659512290 659514824 2534 True 2232.500000 4154 99.846000 1 2442 2 chr4B.!!$R6 2441
3 TraesCS4B01G375400 chrUn 264518339 264521708 3369 False 5751.000000 5751 97.409000 1501 4887 1 chrUn.!!$F1 3386
4 TraesCS4B01G375400 chr5A 704368590 704371895 3305 False 3284.000000 3284 84.918000 1135 4420 1 chr5A.!!$F5 3285
5 TraesCS4B01G375400 chr5A 694572076 694573369 1293 False 1382.000000 1382 85.909000 1078 2395 1 chr5A.!!$F4 1317
6 TraesCS4B01G375400 chr5A 694551705 694558730 7025 False 1192.666667 2039 85.582667 1078 4722 3 chr5A.!!$F8 3644
7 TraesCS4B01G375400 chr5A 694531274 694538324 7050 False 1151.333333 1925 85.303667 1078 4722 3 chr5A.!!$F7 3644
8 TraesCS4B01G375400 chr5A 704452042 704453105 1063 False 1131.000000 1131 85.993000 2609 3674 1 chr5A.!!$F6 1065
9 TraesCS4B01G375400 chr5A 694577706 694580261 2555 False 1098.000000 2061 84.496500 2499 4722 2 chr5A.!!$F9 2223
10 TraesCS4B01G375400 chr5A 708848126 708851175 3049 False 716.500000 1275 78.850500 1083 4221 2 chr5A.!!$F10 3138
11 TraesCS4B01G375400 chr4D 508339587 508342952 3365 False 3264.000000 3264 84.496000 1067 4420 1 chr4D.!!$F1 3353
12 TraesCS4B01G375400 chr4D 504518216 504522170 3954 False 1067.333333 1461 87.168000 1067 4360 3 chr4D.!!$F2 3293

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
168 169 6.693315 AAAACGTTCTACATTATGGGATGG 57.307 37.5 0.00 0.00 0.00 3.51 F
3221 6951 5.700832 TGCAGTATTCATGAAGACGAAAAGT 59.299 36.0 23.52 6.14 37.58 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3311 7045 3.452755 TGTCAGTGACGATGTTTGACT 57.547 42.857 18.17 0.0 39.05 3.41 R
4678 8875 0.103208 GCGTGATGGATCTTCCGAGT 59.897 55.000 0.00 0.0 40.17 4.18 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
168 169 6.693315 AAAACGTTCTACATTATGGGATGG 57.307 37.500 0.00 0.00 0.00 3.51
2965 6671 5.847111 ATAAGGCAAGACGTATCTGTACA 57.153 39.130 0.00 0.00 34.48 2.90
3221 6951 5.700832 TGCAGTATTCATGAAGACGAAAAGT 59.299 36.000 23.52 6.14 37.58 2.66
3311 7045 7.701924 CACTTGTTGCAAAAATCTCTACTTTCA 59.298 33.333 1.65 0.00 0.00 2.69
4527 8712 5.839621 ACTTCTTTTACTTCTACGTGCTCA 58.160 37.500 0.00 0.00 0.00 4.26
4619 8816 2.076863 GACATGCACTTTTACGCCTCT 58.923 47.619 0.00 0.00 0.00 3.69
4692 8890 1.135139 CGACACACTCGGAAGATCCAT 59.865 52.381 0.00 0.00 40.84 3.41
4695 8893 2.093973 ACACACTCGGAAGATCCATCAC 60.094 50.000 0.00 0.00 40.84 3.06
4775 8973 3.357079 GGTTGGCACCGTGAGCAG 61.357 66.667 1.65 0.00 31.60 4.24
4883 9081 1.065854 ACGGAGCCCAGAATCTTGAAG 60.066 52.381 0.00 0.00 0.00 3.02
4910 9108 1.000145 GCTTCGTCGACCCTCAAATC 59.000 55.000 10.58 0.00 0.00 2.17
4950 9148 1.033202 AAGCGGTCCGGTTGTGTTTT 61.033 50.000 26.95 1.47 45.71 2.43
4982 9180 1.062587 CGGGTCTGCATCGATTTGTTC 59.937 52.381 0.00 0.00 0.00 3.18
5027 9225 1.070786 GCAAACCGGAGACAGACCA 59.929 57.895 9.46 0.00 0.00 4.02
5106 9304 2.224042 CCAAAAACACTCTTCCTTGCCC 60.224 50.000 0.00 0.00 0.00 5.36
5142 9340 4.526152 CGCCCACGTTTAGCAAAC 57.474 55.556 0.00 0.00 38.02 2.93
5149 9347 4.957266 GTTTAGCAAACGTGGCCC 57.043 55.556 0.00 0.00 0.00 5.80
5150 9348 2.034607 GTTTAGCAAACGTGGCCCA 58.965 52.632 0.00 0.00 0.00 5.36
5151 9349 0.601057 GTTTAGCAAACGTGGCCCAT 59.399 50.000 0.00 0.00 0.00 4.00
5152 9350 0.885196 TTTAGCAAACGTGGCCCATC 59.115 50.000 0.00 0.00 0.00 3.51
5153 9351 0.963355 TTAGCAAACGTGGCCCATCC 60.963 55.000 0.00 0.00 0.00 3.51
5154 9352 2.130821 TAGCAAACGTGGCCCATCCA 62.131 55.000 0.00 0.00 44.18 3.41
5163 9361 1.792115 TGGCCCATCCAAATTCATCC 58.208 50.000 0.00 0.00 43.21 3.51
5164 9362 1.008084 TGGCCCATCCAAATTCATCCA 59.992 47.619 0.00 0.00 43.21 3.41
5165 9363 2.332117 GGCCCATCCAAATTCATCCAT 58.668 47.619 0.00 0.00 34.01 3.41
5166 9364 2.301009 GGCCCATCCAAATTCATCCATC 59.699 50.000 0.00 0.00 34.01 3.51
5167 9365 2.029649 GCCCATCCAAATTCATCCATCG 60.030 50.000 0.00 0.00 0.00 3.84
5168 9366 2.029649 CCCATCCAAATTCATCCATCGC 60.030 50.000 0.00 0.00 0.00 4.58
5169 9367 2.351060 CCATCCAAATTCATCCATCGCG 60.351 50.000 0.00 0.00 0.00 5.87
5170 9368 0.662619 TCCAAATTCATCCATCGCGC 59.337 50.000 0.00 0.00 0.00 6.86
5171 9369 0.318107 CCAAATTCATCCATCGCGCC 60.318 55.000 0.00 0.00 0.00 6.53
5172 9370 0.381445 CAAATTCATCCATCGCGCCA 59.619 50.000 0.00 0.00 0.00 5.69
5173 9371 1.001048 CAAATTCATCCATCGCGCCAT 60.001 47.619 0.00 0.00 0.00 4.40
5174 9372 2.183478 AATTCATCCATCGCGCCATA 57.817 45.000 0.00 0.00 0.00 2.74
5175 9373 2.183478 ATTCATCCATCGCGCCATAA 57.817 45.000 0.00 0.00 0.00 1.90
5176 9374 2.183478 TTCATCCATCGCGCCATAAT 57.817 45.000 0.00 0.00 0.00 1.28
5177 9375 1.441738 TCATCCATCGCGCCATAATG 58.558 50.000 0.00 2.44 0.00 1.90
5178 9376 1.159285 CATCCATCGCGCCATAATGT 58.841 50.000 0.00 0.00 0.00 2.71
5179 9377 1.135888 CATCCATCGCGCCATAATGTG 60.136 52.381 0.00 0.00 0.00 3.21
5191 9389 4.987408 CCATAATGTGGCAATGTTGAGA 57.013 40.909 0.00 0.00 42.12 3.27
5192 9390 4.675510 CCATAATGTGGCAATGTTGAGAC 58.324 43.478 0.00 0.00 42.12 3.36
5193 9391 4.400251 CCATAATGTGGCAATGTTGAGACT 59.600 41.667 0.00 0.00 42.12 3.24
5194 9392 5.449588 CCATAATGTGGCAATGTTGAGACTC 60.450 44.000 0.00 0.00 42.12 3.36
5195 9393 1.896220 TGTGGCAATGTTGAGACTCC 58.104 50.000 0.00 0.00 0.00 3.85
5196 9394 0.798776 GTGGCAATGTTGAGACTCCG 59.201 55.000 0.00 0.00 0.00 4.63
5197 9395 0.396435 TGGCAATGTTGAGACTCCGT 59.604 50.000 0.00 0.00 0.00 4.69
5198 9396 0.798776 GGCAATGTTGAGACTCCGTG 59.201 55.000 0.00 0.00 0.00 4.94
5199 9397 1.608025 GGCAATGTTGAGACTCCGTGA 60.608 52.381 0.00 0.00 0.00 4.35
5200 9398 2.350522 GCAATGTTGAGACTCCGTGAT 58.649 47.619 0.00 0.00 0.00 3.06
5201 9399 3.521560 GCAATGTTGAGACTCCGTGATA 58.478 45.455 0.00 0.00 0.00 2.15
5202 9400 3.553511 GCAATGTTGAGACTCCGTGATAG 59.446 47.826 0.00 0.00 0.00 2.08
5203 9401 2.941453 TGTTGAGACTCCGTGATAGC 57.059 50.000 0.00 0.00 0.00 2.97
5204 9402 2.167662 TGTTGAGACTCCGTGATAGCA 58.832 47.619 0.00 0.00 0.00 3.49
5205 9403 2.760650 TGTTGAGACTCCGTGATAGCAT 59.239 45.455 0.00 0.00 0.00 3.79
5206 9404 3.181486 TGTTGAGACTCCGTGATAGCATC 60.181 47.826 0.00 0.00 0.00 3.91
5207 9405 1.957177 TGAGACTCCGTGATAGCATCC 59.043 52.381 0.00 0.00 0.00 3.51
5208 9406 1.957177 GAGACTCCGTGATAGCATCCA 59.043 52.381 0.00 0.00 0.00 3.41
5209 9407 1.683917 AGACTCCGTGATAGCATCCAC 59.316 52.381 0.00 0.00 0.00 4.02
5216 9414 3.238108 GTGATAGCATCCACGGGATAG 57.762 52.381 5.27 2.82 40.98 2.08
5217 9415 1.550524 TGATAGCATCCACGGGATAGC 59.449 52.381 5.27 10.52 40.98 2.97
5218 9416 1.827969 GATAGCATCCACGGGATAGCT 59.172 52.381 21.30 21.30 40.98 3.32
5219 9417 0.969149 TAGCATCCACGGGATAGCTG 59.031 55.000 23.62 10.91 40.98 4.24
5220 9418 1.302033 GCATCCACGGGATAGCTGG 60.302 63.158 0.00 0.00 40.98 4.85
5221 9419 1.302033 CATCCACGGGATAGCTGGC 60.302 63.158 0.00 0.00 40.98 4.85
5222 9420 1.766059 ATCCACGGGATAGCTGGCA 60.766 57.895 0.00 0.00 41.16 4.92
5223 9421 1.762522 ATCCACGGGATAGCTGGCAG 61.763 60.000 10.94 10.94 41.16 4.85
5224 9422 2.109799 CACGGGATAGCTGGCAGG 59.890 66.667 17.64 0.00 0.00 4.85
5225 9423 2.041922 ACGGGATAGCTGGCAGGA 60.042 61.111 17.64 0.00 0.00 3.86
5226 9424 2.136878 ACGGGATAGCTGGCAGGAG 61.137 63.158 17.64 0.00 0.00 3.69
5227 9425 2.429494 GGGATAGCTGGCAGGAGC 59.571 66.667 17.64 2.33 39.46 4.70
5237 9435 2.343758 GCAGGAGCCGTCAAGACA 59.656 61.111 0.72 0.00 33.58 3.41
5238 9436 1.078848 GCAGGAGCCGTCAAGACAT 60.079 57.895 0.72 0.00 33.58 3.06
5239 9437 1.364626 GCAGGAGCCGTCAAGACATG 61.365 60.000 0.72 0.00 33.58 3.21
5240 9438 1.078848 AGGAGCCGTCAAGACATGC 60.079 57.895 0.00 2.66 0.00 4.06
5241 9439 1.078848 GGAGCCGTCAAGACATGCT 60.079 57.895 12.34 12.34 40.38 3.79
5242 9440 1.086634 GGAGCCGTCAAGACATGCTC 61.087 60.000 23.11 23.11 46.48 4.26
5243 9441 1.078848 AGCCGTCAAGACATGCTCC 60.079 57.895 8.03 0.00 35.09 4.70
5244 9442 2.456119 GCCGTCAAGACATGCTCCG 61.456 63.158 0.00 0.00 0.00 4.63
5245 9443 1.811266 CCGTCAAGACATGCTCCGG 60.811 63.158 0.00 0.00 0.00 5.14
5246 9444 2.456119 CGTCAAGACATGCTCCGGC 61.456 63.158 0.00 0.00 39.26 6.13
5247 9445 1.078848 GTCAAGACATGCTCCGGCT 60.079 57.895 0.00 0.00 39.59 5.52
5248 9446 1.078918 TCAAGACATGCTCCGGCTG 60.079 57.895 0.00 0.00 39.59 4.85
5249 9447 1.078918 CAAGACATGCTCCGGCTGA 60.079 57.895 0.00 0.00 39.59 4.26
5250 9448 0.674581 CAAGACATGCTCCGGCTGAA 60.675 55.000 0.00 0.00 39.59 3.02
5251 9449 0.392193 AAGACATGCTCCGGCTGAAG 60.392 55.000 0.00 0.00 39.59 3.02
5252 9450 2.437359 ACATGCTCCGGCTGAAGC 60.437 61.111 0.00 0.00 39.59 3.86
5253 9451 2.437180 CATGCTCCGGCTGAAGCA 60.437 61.111 9.60 9.60 44.36 3.91
5254 9452 2.042259 CATGCTCCGGCTGAAGCAA 61.042 57.895 11.66 0.00 44.36 3.91
5255 9453 2.042831 ATGCTCCGGCTGAAGCAAC 61.043 57.895 11.66 0.00 44.36 4.17
5256 9454 2.359230 GCTCCGGCTGAAGCAACT 60.359 61.111 0.00 0.00 44.36 3.16
5257 9455 2.394563 GCTCCGGCTGAAGCAACTC 61.395 63.158 0.00 0.00 44.36 3.01
5258 9456 1.004560 CTCCGGCTGAAGCAACTCA 60.005 57.895 4.43 0.00 44.36 3.41
5259 9457 1.004560 TCCGGCTGAAGCAACTCAG 60.005 57.895 4.43 6.20 44.82 3.35
5260 9458 1.302033 CCGGCTGAAGCAACTCAGT 60.302 57.895 4.43 0.00 44.04 3.41
5261 9459 1.572085 CCGGCTGAAGCAACTCAGTG 61.572 60.000 4.43 5.56 44.04 3.66
5262 9460 1.572085 CGGCTGAAGCAACTCAGTGG 61.572 60.000 4.43 0.00 44.04 4.00
5263 9461 0.250467 GGCTGAAGCAACTCAGTGGA 60.250 55.000 4.43 0.00 44.04 4.02
5264 9462 1.597742 GCTGAAGCAACTCAGTGGAA 58.402 50.000 10.91 0.00 44.04 3.53
5265 9463 1.534595 GCTGAAGCAACTCAGTGGAAG 59.465 52.381 10.91 0.00 44.04 3.46
5266 9464 1.534595 CTGAAGCAACTCAGTGGAAGC 59.465 52.381 0.00 0.00 38.43 3.86
5267 9465 0.877743 GAAGCAACTCAGTGGAAGCC 59.122 55.000 0.00 0.00 0.00 4.35
5268 9466 0.183492 AAGCAACTCAGTGGAAGCCA 59.817 50.000 0.00 0.00 0.00 4.75
5281 9479 4.749310 AGCCACGCTGCTTCTCCG 62.749 66.667 0.00 0.00 38.85 4.63
5283 9481 4.749310 CCACGCTGCTTCTCCGCT 62.749 66.667 0.00 0.00 0.00 5.52
5284 9482 3.485431 CACGCTGCTTCTCCGCTG 61.485 66.667 0.00 0.00 0.00 5.18
5285 9483 3.684990 ACGCTGCTTCTCCGCTGA 61.685 61.111 0.00 0.00 0.00 4.26
5286 9484 2.884685 CGCTGCTTCTCCGCTGAG 60.885 66.667 0.00 0.00 40.17 3.35
5287 9485 2.575993 GCTGCTTCTCCGCTGAGA 59.424 61.111 3.40 3.40 45.90 3.27
5288 9486 1.143620 GCTGCTTCTCCGCTGAGAT 59.856 57.895 8.79 0.00 46.75 2.75
5289 9487 1.152989 GCTGCTTCTCCGCTGAGATG 61.153 60.000 8.79 12.01 46.75 2.90
5290 9488 0.530211 CTGCTTCTCCGCTGAGATGG 60.530 60.000 18.48 11.73 46.75 3.51
5291 9489 1.260538 TGCTTCTCCGCTGAGATGGT 61.261 55.000 18.48 0.00 46.75 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
168 169 3.487120 AACCACAACAAGTACTCCCTC 57.513 47.619 0.00 0.00 0.00 4.30
3311 7045 3.452755 TGTCAGTGACGATGTTTGACT 57.547 42.857 18.17 0.00 39.05 3.41
4426 8251 1.217244 GGACACTCGGCGGTTACAT 59.783 57.895 7.21 0.00 0.00 2.29
4519 8701 1.227089 GGATCGCATCTGAGCACGT 60.227 57.895 0.00 0.00 0.00 4.49
4527 8712 0.471191 TGCAAGGATGGATCGCATCT 59.529 50.000 18.04 7.01 0.00 2.90
4574 8771 1.973515 TGATCGATCAATCTGGGAGGG 59.026 52.381 25.44 0.00 33.08 4.30
4619 8816 0.173935 TATCGGCTCGCCTCGAAAAA 59.826 50.000 6.35 0.00 38.92 1.94
4663 8860 3.493830 GAGTGTGTCGCCACCGTCA 62.494 63.158 0.00 0.00 41.09 4.35
4678 8875 0.103208 GCGTGATGGATCTTCCGAGT 59.897 55.000 0.00 0.00 40.17 4.18
4758 8956 3.357079 CTGCTCACGGTGCCAACC 61.357 66.667 2.51 0.00 43.76 3.77
4759 8957 4.030452 GCTGCTCACGGTGCCAAC 62.030 66.667 2.51 0.00 0.00 3.77
4767 8965 4.504916 CTCCCTCCGCTGCTCACG 62.505 72.222 0.00 0.00 0.00 4.35
4768 8966 4.828925 GCTCCCTCCGCTGCTCAC 62.829 72.222 0.00 0.00 0.00 3.51
4769 8967 3.662117 TAGCTCCCTCCGCTGCTCA 62.662 63.158 0.00 0.00 38.38 4.26
4770 8968 2.835431 TAGCTCCCTCCGCTGCTC 60.835 66.667 0.00 0.00 38.38 4.26
4771 8969 3.151022 GTAGCTCCCTCCGCTGCT 61.151 66.667 0.00 0.00 38.38 4.24
4772 8970 3.461773 TGTAGCTCCCTCCGCTGC 61.462 66.667 0.00 0.00 40.01 5.25
4773 8971 2.496817 GTGTAGCTCCCTCCGCTG 59.503 66.667 0.00 0.00 38.38 5.18
4774 8972 3.141488 CGTGTAGCTCCCTCCGCT 61.141 66.667 0.00 0.00 41.35 5.52
4775 8973 3.138798 TCGTGTAGCTCCCTCCGC 61.139 66.667 0.00 0.00 0.00 5.54
4816 9014 3.427503 GGGCATCACGAAATAACCAACAG 60.428 47.826 0.00 0.00 0.00 3.16
4883 9081 1.282930 GGTCGACGAAGCAGTTGTCC 61.283 60.000 9.92 0.00 0.00 4.02
4910 9108 1.012486 GTCTGGACAGTTTACGGGCG 61.012 60.000 0.00 0.00 0.00 6.13
4950 9148 1.685765 AGACCCGTGCTAGATGGCA 60.686 57.895 0.00 0.00 40.15 4.92
4982 9180 2.042104 AGTTACGTCTCGAAACACCG 57.958 50.000 0.00 0.00 0.00 4.94
5027 9225 2.604382 AATGCCCGCAAAGCCCTT 60.604 55.556 0.00 0.00 0.00 3.95
5132 9330 0.601057 ATGGGCCACGTTTGCTAAAC 59.399 50.000 9.28 0.00 38.02 2.01
5133 9331 0.885196 GATGGGCCACGTTTGCTAAA 59.115 50.000 9.28 0.00 0.00 1.85
5134 9332 0.963355 GGATGGGCCACGTTTGCTAA 60.963 55.000 9.28 0.00 36.34 3.09
5135 9333 1.377987 GGATGGGCCACGTTTGCTA 60.378 57.895 9.28 0.00 36.34 3.49
5136 9334 2.676471 GGATGGGCCACGTTTGCT 60.676 61.111 9.28 0.00 36.34 3.91
5137 9335 2.988684 TGGATGGGCCACGTTTGC 60.989 61.111 9.28 0.00 43.33 3.68
5145 9343 1.792115 TGGATGAATTTGGATGGGCC 58.208 50.000 0.00 0.00 37.10 5.80
5146 9344 2.029649 CGATGGATGAATTTGGATGGGC 60.030 50.000 0.00 0.00 0.00 5.36
5147 9345 2.029649 GCGATGGATGAATTTGGATGGG 60.030 50.000 0.00 0.00 0.00 4.00
5148 9346 2.351060 CGCGATGGATGAATTTGGATGG 60.351 50.000 0.00 0.00 0.00 3.51
5149 9347 2.919387 GCGCGATGGATGAATTTGGATG 60.919 50.000 12.10 0.00 0.00 3.51
5150 9348 1.267806 GCGCGATGGATGAATTTGGAT 59.732 47.619 12.10 0.00 0.00 3.41
5151 9349 0.662619 GCGCGATGGATGAATTTGGA 59.337 50.000 12.10 0.00 0.00 3.53
5152 9350 0.318107 GGCGCGATGGATGAATTTGG 60.318 55.000 12.10 0.00 0.00 3.28
5153 9351 0.381445 TGGCGCGATGGATGAATTTG 59.619 50.000 12.10 0.00 0.00 2.32
5154 9352 1.321474 ATGGCGCGATGGATGAATTT 58.679 45.000 12.10 0.00 0.00 1.82
5155 9353 2.183478 TATGGCGCGATGGATGAATT 57.817 45.000 15.78 0.00 0.00 2.17
5156 9354 2.183478 TTATGGCGCGATGGATGAAT 57.817 45.000 15.78 0.00 0.00 2.57
5157 9355 1.805943 CATTATGGCGCGATGGATGAA 59.194 47.619 15.78 0.80 0.00 2.57
5158 9356 1.270785 ACATTATGGCGCGATGGATGA 60.271 47.619 25.75 3.21 0.00 2.92
5159 9357 1.135888 CACATTATGGCGCGATGGATG 60.136 52.381 15.78 18.91 0.00 3.51
5160 9358 1.159285 CACATTATGGCGCGATGGAT 58.841 50.000 15.78 6.24 0.00 3.41
5161 9359 0.884259 CCACATTATGGCGCGATGGA 60.884 55.000 15.78 3.96 43.24 3.41
5162 9360 1.575922 CCACATTATGGCGCGATGG 59.424 57.895 15.78 4.79 43.24 3.51
5171 9369 5.449588 GGAGTCTCAACATTGCCACATTATG 60.450 44.000 1.47 0.00 0.00 1.90
5172 9370 4.641989 GGAGTCTCAACATTGCCACATTAT 59.358 41.667 1.47 0.00 0.00 1.28
5173 9371 4.009675 GGAGTCTCAACATTGCCACATTA 58.990 43.478 1.47 0.00 0.00 1.90
5174 9372 2.821969 GGAGTCTCAACATTGCCACATT 59.178 45.455 1.47 0.00 0.00 2.71
5175 9373 2.440409 GGAGTCTCAACATTGCCACAT 58.560 47.619 1.47 0.00 0.00 3.21
5176 9374 1.877680 CGGAGTCTCAACATTGCCACA 60.878 52.381 1.47 0.00 0.00 4.17
5177 9375 0.798776 CGGAGTCTCAACATTGCCAC 59.201 55.000 1.47 0.00 0.00 5.01
5178 9376 0.396435 ACGGAGTCTCAACATTGCCA 59.604 50.000 1.47 0.00 29.74 4.92
5179 9377 0.798776 CACGGAGTCTCAACATTGCC 59.201 55.000 1.47 0.00 41.61 4.52
5180 9378 1.795768 TCACGGAGTCTCAACATTGC 58.204 50.000 1.47 0.00 41.61 3.56
5181 9379 3.553511 GCTATCACGGAGTCTCAACATTG 59.446 47.826 1.47 0.00 41.61 2.82
5182 9380 3.195610 TGCTATCACGGAGTCTCAACATT 59.804 43.478 1.47 0.00 41.61 2.71
5183 9381 2.760650 TGCTATCACGGAGTCTCAACAT 59.239 45.455 1.47 0.00 41.61 2.71
5184 9382 2.167662 TGCTATCACGGAGTCTCAACA 58.832 47.619 1.47 0.00 41.61 3.33
5185 9383 2.941453 TGCTATCACGGAGTCTCAAC 57.059 50.000 1.47 0.00 41.61 3.18
5186 9384 2.362397 GGATGCTATCACGGAGTCTCAA 59.638 50.000 1.47 0.00 41.61 3.02
5187 9385 1.957177 GGATGCTATCACGGAGTCTCA 59.043 52.381 1.47 0.00 41.61 3.27
5188 9386 1.957177 TGGATGCTATCACGGAGTCTC 59.043 52.381 0.00 0.00 41.61 3.36
5189 9387 1.683917 GTGGATGCTATCACGGAGTCT 59.316 52.381 0.00 0.00 41.61 3.24
5190 9388 2.141535 GTGGATGCTATCACGGAGTC 57.858 55.000 0.00 0.00 41.61 3.36
5196 9394 2.675317 GCTATCCCGTGGATGCTATCAC 60.675 54.545 13.77 0.00 43.06 3.06
5197 9395 1.550524 GCTATCCCGTGGATGCTATCA 59.449 52.381 13.77 0.00 43.06 2.15
5198 9396 1.827969 AGCTATCCCGTGGATGCTATC 59.172 52.381 18.69 0.00 43.06 2.08
5199 9397 1.552337 CAGCTATCCCGTGGATGCTAT 59.448 52.381 19.21 6.49 43.06 2.97
5200 9398 0.969149 CAGCTATCCCGTGGATGCTA 59.031 55.000 19.21 3.25 43.06 3.49
5201 9399 1.750930 CAGCTATCCCGTGGATGCT 59.249 57.895 13.77 15.34 43.06 3.79
5202 9400 1.302033 CCAGCTATCCCGTGGATGC 60.302 63.158 13.77 13.85 43.06 3.91
5203 9401 1.302033 GCCAGCTATCCCGTGGATG 60.302 63.158 13.77 6.78 43.06 3.51
5204 9402 1.762522 CTGCCAGCTATCCCGTGGAT 61.763 60.000 9.89 9.89 45.40 3.41
5205 9403 2.364973 TGCCAGCTATCCCGTGGA 60.365 61.111 0.00 0.00 35.55 4.02
5206 9404 2.109799 CTGCCAGCTATCCCGTGG 59.890 66.667 0.00 0.00 0.00 4.94
5207 9405 2.109799 CCTGCCAGCTATCCCGTG 59.890 66.667 0.00 0.00 0.00 4.94
5208 9406 2.041922 TCCTGCCAGCTATCCCGT 60.042 61.111 0.00 0.00 0.00 5.28
5209 9407 2.739784 CTCCTGCCAGCTATCCCG 59.260 66.667 0.00 0.00 0.00 5.14
5210 9408 2.429494 GCTCCTGCCAGCTATCCC 59.571 66.667 0.00 0.00 36.38 3.85
5220 9418 1.078848 ATGTCTTGACGGCTCCTGC 60.079 57.895 0.00 0.00 38.76 4.85
5221 9419 1.364626 GCATGTCTTGACGGCTCCTG 61.365 60.000 9.09 0.00 0.00 3.86
5222 9420 1.078848 GCATGTCTTGACGGCTCCT 60.079 57.895 9.09 0.00 0.00 3.69
5223 9421 1.078848 AGCATGTCTTGACGGCTCC 60.079 57.895 11.99 0.00 0.00 4.70
5224 9422 2.378028 GAGCATGTCTTGACGGCTC 58.622 57.895 22.06 22.06 43.41 4.70
5225 9423 1.078848 GGAGCATGTCTTGACGGCT 60.079 57.895 15.97 15.97 37.56 5.52
5226 9424 2.456119 CGGAGCATGTCTTGACGGC 61.456 63.158 8.52 8.52 0.00 5.68
5227 9425 1.811266 CCGGAGCATGTCTTGACGG 60.811 63.158 0.00 4.85 33.12 4.79
5228 9426 2.456119 GCCGGAGCATGTCTTGACG 61.456 63.158 5.05 0.00 39.53 4.35
5229 9427 1.078848 AGCCGGAGCATGTCTTGAC 60.079 57.895 5.05 0.00 43.56 3.18
5230 9428 1.078918 CAGCCGGAGCATGTCTTGA 60.079 57.895 5.05 0.00 43.56 3.02
5231 9429 0.674581 TTCAGCCGGAGCATGTCTTG 60.675 55.000 5.05 0.00 43.56 3.02
5232 9430 0.392193 CTTCAGCCGGAGCATGTCTT 60.392 55.000 5.05 0.00 43.56 3.01
5233 9431 1.220206 CTTCAGCCGGAGCATGTCT 59.780 57.895 5.05 0.00 43.56 3.41
5234 9432 2.467826 GCTTCAGCCGGAGCATGTC 61.468 63.158 5.05 0.00 43.56 3.06
5235 9433 2.437359 GCTTCAGCCGGAGCATGT 60.437 61.111 5.05 0.00 43.56 3.21
5236 9434 2.042259 TTGCTTCAGCCGGAGCATG 61.042 57.895 15.54 3.44 43.56 4.06
5237 9435 2.042831 GTTGCTTCAGCCGGAGCAT 61.043 57.895 15.54 0.00 43.56 3.79
5238 9436 2.669569 GTTGCTTCAGCCGGAGCA 60.670 61.111 11.28 11.28 43.56 4.26
5239 9437 2.359230 AGTTGCTTCAGCCGGAGC 60.359 61.111 5.05 5.60 41.18 4.70
5240 9438 1.004560 TGAGTTGCTTCAGCCGGAG 60.005 57.895 5.05 0.00 41.18 4.63
5241 9439 1.004560 CTGAGTTGCTTCAGCCGGA 60.005 57.895 5.05 0.00 38.28 5.14
5242 9440 1.302033 ACTGAGTTGCTTCAGCCGG 60.302 57.895 0.00 0.00 46.77 6.13
5243 9441 1.572085 CCACTGAGTTGCTTCAGCCG 61.572 60.000 11.64 5.43 46.77 5.52
5244 9442 0.250467 TCCACTGAGTTGCTTCAGCC 60.250 55.000 11.64 0.00 46.77 4.85
5245 9443 1.534595 CTTCCACTGAGTTGCTTCAGC 59.465 52.381 11.64 0.00 46.77 4.26
5247 9445 1.597742 GCTTCCACTGAGTTGCTTCA 58.402 50.000 0.00 0.00 0.00 3.02
5248 9446 0.877743 GGCTTCCACTGAGTTGCTTC 59.122 55.000 0.00 0.00 0.00 3.86
5249 9447 0.183492 TGGCTTCCACTGAGTTGCTT 59.817 50.000 0.00 0.00 0.00 3.91
5250 9448 1.839191 TGGCTTCCACTGAGTTGCT 59.161 52.632 0.00 0.00 0.00 3.91
5251 9449 4.481195 TGGCTTCCACTGAGTTGC 57.519 55.556 0.00 0.00 0.00 4.17
5266 9464 4.749310 AGCGGAGAAGCAGCGTGG 62.749 66.667 0.00 0.00 42.89 4.94
5267 9465 3.485431 CAGCGGAGAAGCAGCGTG 61.485 66.667 0.00 0.00 42.89 5.34
5268 9466 3.639541 CTCAGCGGAGAAGCAGCGT 62.640 63.158 8.31 0.00 44.26 5.07
5269 9467 2.884685 CTCAGCGGAGAAGCAGCG 60.885 66.667 8.31 0.00 44.26 5.18
5270 9468 2.575993 TCTCAGCGGAGAAGCAGC 59.424 61.111 14.55 0.00 46.94 5.25


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

AutoCloner maintained by Alex Coulton.