Multiple sequence alignment - TraesCS3A01G191500

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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 TraesCS3A01G191500 chr3A 100.000 5264 0 0 1 5264 243872796 243878059 0.000000e+00 9721
1 TraesCS3A01G191500 chr3A 83.750 240 26 9 2076 2314 654354815 654355042 1.150000e-51 215
2 TraesCS3A01G191500 chr3D 94.631 2645 66 21 1754 4356 185072214 185074824 0.000000e+00 4028
3 TraesCS3A01G191500 chr3D 92.916 1468 55 19 314 1756 185070743 185072186 0.000000e+00 2089
4 TraesCS3A01G191500 chr3D 84.305 892 103 22 3409 4268 519318949 519318063 0.000000e+00 837
5 TraesCS3A01G191500 chr3D 78.775 947 148 38 2153 3072 519321498 519320578 2.110000e-163 586
6 TraesCS3A01G191500 chr3D 80.387 362 48 18 1563 1902 519277911 519278271 2.430000e-63 254
7 TraesCS3A01G191500 chr3D 98.148 108 2 0 12 119 185070266 185070373 6.960000e-44 189
8 TraesCS3A01G191500 chr3D 90.551 127 8 1 3160 3282 519319074 519318948 1.170000e-36 165
9 TraesCS3A01G191500 chr3D 96.875 64 2 0 1383 1446 519259801 519259864 2.000000e-19 108
10 TraesCS3A01G191500 chr3B 92.119 1383 59 26 1949 3298 263797884 263799249 0.000000e+00 1905
11 TraesCS3A01G191500 chr3B 85.887 1736 91 61 314 1962 263796195 263797863 0.000000e+00 1707
12 TraesCS3A01G191500 chr3B 94.258 714 29 4 3643 4355 263799959 263800661 0.000000e+00 1081
13 TraesCS3A01G191500 chr3B 84.516 620 71 12 3676 4272 683520166 683520783 1.630000e-164 590
14 TraesCS3A01G191500 chr3B 92.145 331 9 3 3297 3626 263799561 263799875 8.040000e-123 451
15 TraesCS3A01G191500 chr3B 96.629 89 1 1 34 120 263795807 263795895 4.250000e-31 147
16 TraesCS3A01G191500 chr3B 82.639 144 15 7 121 261 173123288 173123424 9.260000e-23 119
17 TraesCS3A01G191500 chr5D 92.665 927 50 5 4340 5264 500877978 500877068 0.000000e+00 1319
18 TraesCS3A01G191500 chr5D 90.601 915 73 2 4350 5264 507909565 507908664 0.000000e+00 1201
19 TraesCS3A01G191500 chr5D 86.842 152 10 6 121 264 386689122 386689271 1.520000e-35 161
20 TraesCS3A01G191500 chr5D 86.806 144 11 7 127 264 336413546 336413405 2.540000e-33 154
21 TraesCS3A01G191500 chr7A 92.484 918 55 3 4348 5264 591628898 591627994 0.000000e+00 1301
22 TraesCS3A01G191500 chr7A 91.547 698 45 3 4366 5063 167684061 167684744 0.000000e+00 950
23 TraesCS3A01G191500 chr7A 82.951 915 140 6 4351 5264 510616550 510617449 0.000000e+00 811
24 TraesCS3A01G191500 chr7A 82.683 872 118 18 3409 4265 16752703 16753556 0.000000e+00 743
25 TraesCS3A01G191500 chr7A 87.671 146 11 6 121 261 621568973 621569116 4.220000e-36 163
26 TraesCS3A01G191500 chr7A 74.640 347 55 21 1379 1722 16750839 16751155 7.160000e-24 122
27 TraesCS3A01G191500 chr7A 89.362 94 10 0 3163 3256 16752593 16752686 9.260000e-23 119
28 TraesCS3A01G191500 chr2D 89.198 898 84 4 4349 5246 509237465 509236581 0.000000e+00 1109
29 TraesCS3A01G191500 chr6D 88.706 912 90 4 4353 5264 105956291 105955393 0.000000e+00 1101
30 TraesCS3A01G191500 chr2A 87.946 896 95 4 4351 5246 712518963 712518081 0.000000e+00 1044
31 TraesCS3A01G191500 chr2A 84.314 153 12 8 121 264 216837877 216837728 7.110000e-29 139
32 TraesCS3A01G191500 chr2A 82.759 145 18 6 121 261 251253925 251254066 7.160000e-24 122
33 TraesCS3A01G191500 chr5A 85.419 919 115 9 4349 5264 549407622 549408524 0.000000e+00 937
34 TraesCS3A01G191500 chr4A 84.354 914 126 11 4352 5263 594204855 594203957 0.000000e+00 880
35 TraesCS3A01G191500 chr4A 81.264 870 131 20 3409 4268 716818142 716817295 0.000000e+00 675
36 TraesCS3A01G191500 chr4A 80.702 456 77 8 2095 2540 716819558 716819104 1.400000e-90 344
37 TraesCS3A01G191500 chr1B 84.048 909 129 8 4339 5245 476919624 476918730 0.000000e+00 861
38 TraesCS3A01G191500 chr6B 83.810 420 55 4 4351 4770 198447529 198447935 2.300000e-103 387
39 TraesCS3A01G191500 chr1D 84.564 149 13 8 121 264 6176893 6176750 7.110000e-29 139
40 TraesCS3A01G191500 chr2B 83.803 142 14 6 121 256 30164338 30164476 5.530000e-25 126
41 TraesCS3A01G191500 chr2B 83.803 142 14 6 121 256 30177733 30177871 5.530000e-25 126


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 TraesCS3A01G191500 chr3A 243872796 243878059 5263 False 9721.000000 9721 100.000000 1 5264 1 chr3A.!!$F1 5263
1 TraesCS3A01G191500 chr3D 185070266 185074824 4558 False 2102.000000 4028 95.231667 12 4356 3 chr3D.!!$F3 4344
2 TraesCS3A01G191500 chr3D 519318063 519321498 3435 True 529.333333 837 84.543667 2153 4268 3 chr3D.!!$R1 2115
3 TraesCS3A01G191500 chr3B 263795807 263800661 4854 False 1058.200000 1905 92.207600 34 4355 5 chr3B.!!$F3 4321
4 TraesCS3A01G191500 chr3B 683520166 683520783 617 False 590.000000 590 84.516000 3676 4272 1 chr3B.!!$F2 596
5 TraesCS3A01G191500 chr5D 500877068 500877978 910 True 1319.000000 1319 92.665000 4340 5264 1 chr5D.!!$R2 924
6 TraesCS3A01G191500 chr5D 507908664 507909565 901 True 1201.000000 1201 90.601000 4350 5264 1 chr5D.!!$R3 914
7 TraesCS3A01G191500 chr7A 591627994 591628898 904 True 1301.000000 1301 92.484000 4348 5264 1 chr7A.!!$R1 916
8 TraesCS3A01G191500 chr7A 167684061 167684744 683 False 950.000000 950 91.547000 4366 5063 1 chr7A.!!$F1 697
9 TraesCS3A01G191500 chr7A 510616550 510617449 899 False 811.000000 811 82.951000 4351 5264 1 chr7A.!!$F2 913
10 TraesCS3A01G191500 chr7A 16750839 16753556 2717 False 328.000000 743 82.228333 1379 4265 3 chr7A.!!$F4 2886
11 TraesCS3A01G191500 chr2D 509236581 509237465 884 True 1109.000000 1109 89.198000 4349 5246 1 chr2D.!!$R1 897
12 TraesCS3A01G191500 chr6D 105955393 105956291 898 True 1101.000000 1101 88.706000 4353 5264 1 chr6D.!!$R1 911
13 TraesCS3A01G191500 chr2A 712518081 712518963 882 True 1044.000000 1044 87.946000 4351 5246 1 chr2A.!!$R2 895
14 TraesCS3A01G191500 chr5A 549407622 549408524 902 False 937.000000 937 85.419000 4349 5264 1 chr5A.!!$F1 915
15 TraesCS3A01G191500 chr4A 594203957 594204855 898 True 880.000000 880 84.354000 4352 5263 1 chr4A.!!$R1 911
16 TraesCS3A01G191500 chr4A 716817295 716819558 2263 True 509.500000 675 80.983000 2095 4268 2 chr4A.!!$R2 2173
17 TraesCS3A01G191500 chr1B 476918730 476919624 894 True 861.000000 861 84.048000 4339 5245 1 chr1B.!!$R1 906

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
992 1251 1.276421 GCAGGAAACTAGGAGTGAGCA 59.724 52.381 0.0 0.0 40.21 4.26 F
1534 1847 0.391130 GCGCCAGTGAGTTGATGGTA 60.391 55.000 0.0 0.0 36.43 3.25 F
2755 3227 1.162181 TCCGTCTCTCAACGTCACGT 61.162 55.000 0.0 0.0 43.97 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2875 3358 1.374125 CATCGAGTTCGTGCCCACA 60.374 57.895 1.07 0.0 40.80 4.17 R
3158 5067 0.036765 CCGTCGGATTCCTGAACCAA 60.037 55.000 4.91 0.0 0.00 3.67 R
4628 6962 0.175989 GCAAGGAGGTCGTAAGGAGG 59.824 60.000 0.00 0.0 38.47 4.30 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
159 203 7.093354 TCAGTCGATGCTATATTCCTTTGATC 58.907 38.462 0.00 0.00 0.00 2.92
167 211 6.208007 TGCTATATTCCTTTGATCTTGCATGG 59.792 38.462 0.00 0.00 0.00 3.66
173 217 5.266788 TCCTTTGATCTTGCATGGAGATTT 58.733 37.500 1.03 0.00 34.13 2.17
177 221 6.441093 TTGATCTTGCATGGAGATTTGTAC 57.559 37.500 1.03 0.00 34.13 2.90
264 374 3.440522 CAGTCGACTGAGACCATAGACAA 59.559 47.826 36.73 0.00 46.59 3.18
265 375 4.097135 CAGTCGACTGAGACCATAGACAAT 59.903 45.833 36.73 0.00 46.59 2.71
266 376 4.097135 AGTCGACTGAGACCATAGACAATG 59.903 45.833 19.30 0.00 41.83 2.82
267 377 4.017126 TCGACTGAGACCATAGACAATGT 58.983 43.478 0.00 0.00 33.34 2.71
268 378 4.108336 CGACTGAGACCATAGACAATGTG 58.892 47.826 0.00 0.00 33.34 3.21
269 379 4.437239 GACTGAGACCATAGACAATGTGG 58.563 47.826 0.00 0.00 45.45 4.17
278 388 6.910536 CCATAGACAATGTGGTTAAGTCTC 57.089 41.667 0.00 0.00 39.92 3.36
279 389 6.406370 CCATAGACAATGTGGTTAAGTCTCA 58.594 40.000 0.00 0.00 39.92 3.27
280 390 6.313905 CCATAGACAATGTGGTTAAGTCTCAC 59.686 42.308 0.00 0.00 39.92 3.51
281 391 5.552870 AGACAATGTGGTTAAGTCTCACT 57.447 39.130 0.00 0.00 34.71 3.41
282 392 5.542779 AGACAATGTGGTTAAGTCTCACTC 58.457 41.667 0.00 0.00 34.71 3.51
283 393 4.307432 ACAATGTGGTTAAGTCTCACTCG 58.693 43.478 0.00 0.00 33.04 4.18
284 394 4.038763 ACAATGTGGTTAAGTCTCACTCGA 59.961 41.667 0.00 0.00 33.04 4.04
285 395 3.637998 TGTGGTTAAGTCTCACTCGAC 57.362 47.619 0.00 0.00 33.04 4.20
286 396 3.220110 TGTGGTTAAGTCTCACTCGACT 58.780 45.455 0.00 0.00 45.73 4.18
287 397 3.004419 TGTGGTTAAGTCTCACTCGACTG 59.996 47.826 0.00 0.00 43.14 3.51
288 398 3.252701 GTGGTTAAGTCTCACTCGACTGA 59.747 47.826 0.00 0.00 43.14 3.41
289 399 3.502595 TGGTTAAGTCTCACTCGACTGAG 59.497 47.826 13.99 13.99 43.14 3.35
290 400 3.752222 GGTTAAGTCTCACTCGACTGAGA 59.248 47.826 17.60 17.60 45.57 3.27
294 404 2.498644 TCTCACTCGACTGAGACCAT 57.501 50.000 17.60 0.00 45.57 3.55
298 408 3.271729 TCACTCGACTGAGACCATAGAC 58.728 50.000 0.00 0.00 45.57 2.59
303 413 4.017126 TCGACTGAGACCATAGACAATGT 58.983 43.478 0.00 0.00 33.34 2.71
487 702 2.435372 AGCAACCACTGGTGAAGAAA 57.565 45.000 0.00 0.00 35.34 2.52
510 725 4.180057 CAGTAGAGTCCAAATGCTCACTC 58.820 47.826 0.00 0.00 36.32 3.51
604 829 2.857152 GAGAGAATCGCTGCAACAGTAG 59.143 50.000 0.00 0.00 42.67 2.57
699 929 1.742761 ACGATCTGTCAGCATTTGGG 58.257 50.000 0.00 0.00 0.00 4.12
743 980 1.648756 GATCAGCGACGACGACGAG 60.649 63.158 22.94 13.84 42.66 4.18
845 1088 6.093357 GCACCAGAGAAAAGGAAGATAAAGAG 59.907 42.308 0.00 0.00 0.00 2.85
861 1104 3.940209 AAGAGAGAGCAGTCAGAGTTG 57.060 47.619 0.00 0.00 0.00 3.16
927 1186 2.494445 GCTACAAATTGGGCCCGC 59.506 61.111 19.37 7.92 0.00 6.13
928 1187 3.076258 GCTACAAATTGGGCCCGCC 62.076 63.158 19.37 0.00 0.00 6.13
991 1250 1.552792 AGCAGGAAACTAGGAGTGAGC 59.447 52.381 0.00 0.00 40.21 4.26
992 1251 1.276421 GCAGGAAACTAGGAGTGAGCA 59.724 52.381 0.00 0.00 40.21 4.26
993 1252 2.676463 GCAGGAAACTAGGAGTGAGCAG 60.676 54.545 0.00 0.00 40.21 4.24
1029 1288 2.094659 CGCGCACTTCGTCATCCTT 61.095 57.895 8.75 0.00 41.07 3.36
1104 1369 4.081322 AGAGGTAGCTCTAGCAGTAGAC 57.919 50.000 22.67 0.00 45.16 2.59
1120 1385 8.770010 AGCAGTAGACTTATTCCTGTTATAGT 57.230 34.615 0.00 0.00 0.00 2.12
1121 1386 9.863650 AGCAGTAGACTTATTCCTGTTATAGTA 57.136 33.333 0.00 0.00 0.00 1.82
1122 1387 9.896263 GCAGTAGACTTATTCCTGTTATAGTAC 57.104 37.037 0.00 0.00 0.00 2.73
1158 1446 2.931512 CATGCATGCATGTGTCTGAA 57.068 45.000 40.30 10.77 46.20 3.02
1176 1469 3.149196 TGAACTCTGAACCCTGAAATGC 58.851 45.455 0.00 0.00 0.00 3.56
1184 1477 4.129380 TGAACCCTGAAATGCGATATCTG 58.871 43.478 0.34 0.00 0.00 2.90
1190 1483 4.212847 CCTGAAATGCGATATCTGAAGTGG 59.787 45.833 0.34 0.00 0.00 4.00
1369 1670 4.119363 GAGCAGGAGCCATGGCCA 62.119 66.667 33.14 8.56 43.56 5.36
1534 1847 0.391130 GCGCCAGTGAGTTGATGGTA 60.391 55.000 0.00 0.00 36.43 3.25
1991 2407 2.366167 AGGAAGCTCATCGGGGCT 60.366 61.111 0.00 0.00 40.85 5.19
2246 2668 3.151022 GGCGGGTGCTCTAGCTCT 61.151 66.667 3.26 0.00 42.66 4.09
2580 3028 2.708216 TGTTCTTGCAACCTGACTGA 57.292 45.000 0.00 0.00 0.00 3.41
2581 3029 2.288666 TGTTCTTGCAACCTGACTGAC 58.711 47.619 0.00 0.00 0.00 3.51
2666 3134 2.168666 GACCGGTTCCCTCTGGTGTC 62.169 65.000 9.42 0.00 45.86 3.67
2755 3227 1.162181 TCCGTCTCTCAACGTCACGT 61.162 55.000 0.00 0.00 43.97 4.49
2875 3358 1.403780 GCCGGAAAGATCGTAGTGTGT 60.404 52.381 5.05 0.00 0.00 3.72
2986 3469 1.445582 GAAGGACGTGCCGTTCGAT 60.446 57.895 2.38 0.00 40.73 3.59
3011 3494 2.124942 GCTTCGCCTTCTCCCAGG 60.125 66.667 0.00 0.00 36.95 4.45
3012 3495 2.960688 GCTTCGCCTTCTCCCAGGT 61.961 63.158 0.00 0.00 36.15 4.00
3111 4629 2.288729 AGTTTTTCCTTCCGTGTTACGC 59.711 45.455 0.00 0.00 40.91 4.42
3155 5064 5.254032 AGAAAGGAAGTATGGATGTTTCCCT 59.746 40.000 0.00 0.00 41.83 4.20
3156 5065 4.510167 AGGAAGTATGGATGTTTCCCTG 57.490 45.455 0.00 0.00 41.83 4.45
3157 5066 3.203040 AGGAAGTATGGATGTTTCCCTGG 59.797 47.826 0.00 0.00 41.83 4.45
3158 5067 3.053619 GGAAGTATGGATGTTTCCCTGGT 60.054 47.826 0.00 0.00 41.83 4.00
3351 5577 6.666678 AGAGAAAGATCCAATCTGGCATTTA 58.333 36.000 0.00 0.00 40.13 1.40
3352 5578 7.121382 AGAGAAAGATCCAATCTGGCATTTAA 58.879 34.615 0.00 0.00 40.13 1.52
3353 5579 7.783596 AGAGAAAGATCCAATCTGGCATTTAAT 59.216 33.333 0.00 0.00 40.13 1.40
3354 5580 8.315220 AGAAAGATCCAATCTGGCATTTAATT 57.685 30.769 0.00 0.00 40.13 1.40
3355 5581 8.765517 AGAAAGATCCAATCTGGCATTTAATTT 58.234 29.630 0.00 0.00 40.13 1.82
3356 5582 8.726870 AAAGATCCAATCTGGCATTTAATTTG 57.273 30.769 0.00 0.00 40.13 2.32
3357 5583 7.427989 AGATCCAATCTGGCATTTAATTTGT 57.572 32.000 0.00 0.00 38.44 2.83
3358 5584 8.537728 AGATCCAATCTGGCATTTAATTTGTA 57.462 30.769 0.00 0.00 38.44 2.41
3359 5585 8.636213 AGATCCAATCTGGCATTTAATTTGTAG 58.364 33.333 0.00 0.00 38.44 2.74
3360 5586 7.716799 TCCAATCTGGCATTTAATTTGTAGT 57.283 32.000 0.00 0.00 37.47 2.73
3361 5587 8.815565 TCCAATCTGGCATTTAATTTGTAGTA 57.184 30.769 0.00 0.00 37.47 1.82
3362 5588 8.682710 TCCAATCTGGCATTTAATTTGTAGTAC 58.317 33.333 0.00 0.00 37.47 2.73
3363 5589 8.686334 CCAATCTGGCATTTAATTTGTAGTACT 58.314 33.333 0.00 0.00 0.00 2.73
3364 5590 9.507280 CAATCTGGCATTTAATTTGTAGTACTG 57.493 33.333 5.39 0.00 0.00 2.74
3365 5591 8.807948 ATCTGGCATTTAATTTGTAGTACTGT 57.192 30.769 5.39 0.00 0.00 3.55
3366 5592 9.899661 ATCTGGCATTTAATTTGTAGTACTGTA 57.100 29.630 5.39 0.00 0.00 2.74
3626 5853 1.002888 CAGCTCTCATGACCACAGGTT 59.997 52.381 0.00 0.00 35.25 3.50
3633 5860 3.820467 CTCATGACCACAGGTTTAAGCAA 59.180 43.478 0.00 0.00 35.25 3.91
3636 5863 2.360801 TGACCACAGGTTTAAGCAAAGC 59.639 45.455 0.00 0.00 41.48 3.51
4174 6504 1.154580 GTGAGTTTTGCGAGCGCTC 60.155 57.895 27.64 27.64 42.51 5.03
4317 6651 5.046663 TGTGTTTGCCTCTTCCTTTTCTTTT 60.047 36.000 0.00 0.00 0.00 2.27
4318 6652 5.291858 GTGTTTGCCTCTTCCTTTTCTTTTG 59.708 40.000 0.00 0.00 0.00 2.44
4319 6653 5.046663 TGTTTGCCTCTTCCTTTTCTTTTGT 60.047 36.000 0.00 0.00 0.00 2.83
4320 6654 4.654091 TGCCTCTTCCTTTTCTTTTGTG 57.346 40.909 0.00 0.00 0.00 3.33
4389 6723 7.168219 TCAGTCACATCTTTATTTAAGCACCT 58.832 34.615 0.00 0.00 33.66 4.00
4392 6726 7.831193 AGTCACATCTTTATTTAAGCACCTCAT 59.169 33.333 0.00 0.00 33.66 2.90
4498 6832 1.679032 CCCTAGCTAACAAGTGGGCAC 60.679 57.143 0.82 0.00 0.00 5.01
4541 6875 2.616510 CCCACGAAATCTTCCAGCTCTT 60.617 50.000 0.00 0.00 0.00 2.85
4580 6914 0.105194 TTGACCTCCTCCACCACAGA 60.105 55.000 0.00 0.00 0.00 3.41
4588 6922 3.569210 CCACCACAGACCCCAGCA 61.569 66.667 0.00 0.00 0.00 4.41
4623 6957 2.226330 TGCGTGCCTTGAAGTTTACAT 58.774 42.857 0.00 0.00 0.00 2.29
4624 6958 3.403968 TGCGTGCCTTGAAGTTTACATA 58.596 40.909 0.00 0.00 0.00 2.29
4625 6959 3.187637 TGCGTGCCTTGAAGTTTACATAC 59.812 43.478 0.00 0.00 0.00 2.39
4626 6960 3.425758 GCGTGCCTTGAAGTTTACATACC 60.426 47.826 0.00 0.00 0.00 2.73
4627 6961 3.749088 CGTGCCTTGAAGTTTACATACCA 59.251 43.478 0.00 0.00 0.00 3.25
4628 6962 4.378046 CGTGCCTTGAAGTTTACATACCAC 60.378 45.833 0.00 0.00 0.00 4.16
4629 6963 4.076394 TGCCTTGAAGTTTACATACCACC 58.924 43.478 0.00 0.00 0.00 4.61
4630 6964 4.202524 TGCCTTGAAGTTTACATACCACCT 60.203 41.667 0.00 0.00 0.00 4.00
4631 6965 4.395231 GCCTTGAAGTTTACATACCACCTC 59.605 45.833 0.00 0.00 0.00 3.85
4632 6966 4.941873 CCTTGAAGTTTACATACCACCTCC 59.058 45.833 0.00 0.00 0.00 4.30
4633 6967 5.280521 CCTTGAAGTTTACATACCACCTCCT 60.281 44.000 0.00 0.00 0.00 3.69
4639 6973 4.989279 TTACATACCACCTCCTTACGAC 57.011 45.455 0.00 0.00 0.00 4.34
4824 7158 4.394712 CGGCTCCACCACTGTCCC 62.395 72.222 0.00 0.00 39.03 4.46
4864 7199 1.600164 CCGTCGACGTTTACCTTCACA 60.600 52.381 33.49 0.00 37.74 3.58
4896 7231 0.990818 AGGGGCCTCCATTTCTCCTC 60.991 60.000 0.00 0.00 38.24 3.71
4900 7235 0.620556 GCCTCCATTTCTCCTCCACA 59.379 55.000 0.00 0.00 0.00 4.17
4998 7334 0.187117 ATCTCTGCCTCCTCGATCCA 59.813 55.000 0.00 0.00 0.00 3.41
5126 7462 0.522180 CGACAACGCACTCTAGGAGT 59.478 55.000 0.00 0.00 44.44 3.85
5199 7535 9.770097 CATTATCTTCCAGAACTTAGCAGAATA 57.230 33.333 0.00 0.00 0.00 1.75
5202 7538 8.900983 ATCTTCCAGAACTTAGCAGAATAATC 57.099 34.615 0.00 0.00 0.00 1.75
5238 7574 6.442541 TCTATGGTAGTTTGTTTCTTCCCA 57.557 37.500 0.00 0.00 0.00 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.183969 TCCTTCTTGCTTTCAGATCATCAG 58.816 41.667 0.00 0.00 0.00 2.90
3 4 6.906157 TTTTCCTTCTTGCTTTCAGATCAT 57.094 33.333 0.00 0.00 0.00 2.45
5 6 7.972832 CCTATTTTTCCTTCTTGCTTTCAGATC 59.027 37.037 0.00 0.00 0.00 2.75
8 9 5.866092 GCCTATTTTTCCTTCTTGCTTTCAG 59.134 40.000 0.00 0.00 0.00 3.02
9 10 5.304101 TGCCTATTTTTCCTTCTTGCTTTCA 59.696 36.000 0.00 0.00 0.00 2.69
10 11 5.783111 TGCCTATTTTTCCTTCTTGCTTTC 58.217 37.500 0.00 0.00 0.00 2.62
15 16 4.219288 AGCACTGCCTATTTTTCCTTCTTG 59.781 41.667 0.00 0.00 0.00 3.02
218 264 6.092955 AGACTTAACCGTCAAGTGACATTA 57.907 37.500 11.77 6.65 44.99 1.90
220 266 4.038763 TGAGACTTAACCGTCAAGTGACAT 59.961 41.667 11.77 0.36 44.99 3.06
224 270 3.978687 ACTGAGACTTAACCGTCAAGTG 58.021 45.455 0.00 0.00 36.38 3.16
226 272 3.058432 TCGACTGAGACTTAACCGTCAAG 60.058 47.826 0.00 0.00 36.38 3.02
229 275 2.849110 GTCGACTGAGACTTAACCGTC 58.151 52.381 8.70 0.00 38.09 4.79
264 374 4.175787 GTCGAGTGAGACTTAACCACAT 57.824 45.455 0.00 0.00 38.09 3.21
265 375 3.637998 GTCGAGTGAGACTTAACCACA 57.362 47.619 0.00 0.00 38.09 4.17
276 386 3.311322 GTCTATGGTCTCAGTCGAGTGAG 59.689 52.174 34.80 34.80 44.71 3.51
277 387 3.271729 GTCTATGGTCTCAGTCGAGTGA 58.728 50.000 21.32 21.32 40.44 3.41
278 388 3.010420 TGTCTATGGTCTCAGTCGAGTG 58.990 50.000 14.33 14.33 40.44 3.51
279 389 3.351794 TGTCTATGGTCTCAGTCGAGT 57.648 47.619 0.00 0.00 40.44 4.18
280 390 4.097135 ACATTGTCTATGGTCTCAGTCGAG 59.903 45.833 0.00 0.00 38.64 4.04
281 391 4.017126 ACATTGTCTATGGTCTCAGTCGA 58.983 43.478 0.00 0.00 38.64 4.20
282 392 4.108336 CACATTGTCTATGGTCTCAGTCG 58.892 47.826 0.00 0.00 38.64 4.18
283 393 5.078411 ACACATTGTCTATGGTCTCAGTC 57.922 43.478 0.00 0.00 38.64 3.51
284 394 5.078411 GACACATTGTCTATGGTCTCAGT 57.922 43.478 0.00 0.00 43.73 3.41
298 408 6.417635 GTGTTGGACAATACAAAGACACATTG 59.582 38.462 7.00 0.00 33.39 2.82
303 413 5.995282 CCTAGTGTTGGACAATACAAAGACA 59.005 40.000 13.20 0.00 35.27 3.41
309 419 3.868369 GCTGCCTAGTGTTGGACAATACA 60.868 47.826 13.20 0.00 35.27 2.29
357 572 0.179200 CCGCACATGTCGTTAAAGCC 60.179 55.000 13.90 0.00 0.00 4.35
487 702 3.580458 AGTGAGCATTTGGACTCTACTGT 59.420 43.478 0.00 0.00 33.92 3.55
510 725 1.202568 TGCCCATGATTAGAGCTGACG 60.203 52.381 0.00 0.00 0.00 4.35
604 829 0.179062 CTATGACACTCAGCCAGCCC 60.179 60.000 0.00 0.00 0.00 5.19
682 911 4.454678 TGATACCCAAATGCTGACAGATC 58.545 43.478 6.65 0.00 0.00 2.75
699 929 2.036475 ACATGGCCGTCTGAGATGATAC 59.964 50.000 2.61 0.00 0.00 2.24
743 980 3.679389 TCTCATGGAAACTGCTTTCTCC 58.321 45.455 0.00 0.00 36.71 3.71
845 1088 3.443329 TCATCTCAACTCTGACTGCTCTC 59.557 47.826 0.00 0.00 0.00 3.20
991 1250 1.382522 CGGTTCACCATTGATCCCTG 58.617 55.000 0.00 0.00 38.09 4.45
992 1251 0.394352 GCGGTTCACCATTGATCCCT 60.394 55.000 0.00 0.00 38.09 4.20
993 1252 1.714899 CGCGGTTCACCATTGATCCC 61.715 60.000 0.00 0.00 38.09 3.85
1104 1369 9.970243 CGATCTACGTACTATAACAGGAATAAG 57.030 37.037 0.00 0.00 37.22 1.73
1120 1385 2.837883 GCCGGGTGCGATCTACGTA 61.838 63.158 2.18 0.00 44.60 3.57
1121 1386 4.203076 GCCGGGTGCGATCTACGT 62.203 66.667 2.18 0.00 44.60 3.57
1122 1387 4.944372 GGCCGGGTGCGATCTACG 62.944 72.222 2.18 0.00 42.61 3.51
1123 1388 3.165160 ATGGCCGGGTGCGATCTAC 62.165 63.158 2.18 0.00 42.61 2.59
1151 1416 2.677914 TCAGGGTTCAGAGTTCAGACA 58.322 47.619 0.00 0.00 0.00 3.41
1152 1417 3.753294 TTCAGGGTTCAGAGTTCAGAC 57.247 47.619 0.00 0.00 0.00 3.51
1156 1444 2.160417 CGCATTTCAGGGTTCAGAGTTC 59.840 50.000 0.00 0.00 0.00 3.01
1158 1446 1.347707 TCGCATTTCAGGGTTCAGAGT 59.652 47.619 0.00 0.00 0.00 3.24
1176 1469 5.299531 TCAACTCCTACCACTTCAGATATCG 59.700 44.000 0.00 0.00 0.00 2.92
1184 1477 4.657436 ATCGATCAACTCCTACCACTTC 57.343 45.455 0.00 0.00 0.00 3.01
1190 1483 3.309954 GGCAACAATCGATCAACTCCTAC 59.690 47.826 0.00 0.00 0.00 3.18
1369 1670 4.796231 GTCAGCGACGGCGTGGAT 62.796 66.667 26.19 17.55 46.35 3.41
1534 1847 6.419116 GTGCAACAACCAAACAAAACAAAATT 59.581 30.769 0.00 0.00 36.32 1.82
1991 2407 1.731433 GCTGGATGCCGTAGTACCGA 61.731 60.000 0.00 0.00 35.15 4.69
2246 2668 1.659622 CGATGGCCTTGAGCAATGCA 61.660 55.000 8.35 0.00 46.50 3.96
2282 2704 2.571757 GAGATCACGTCCACGCCA 59.428 61.111 0.00 0.00 44.43 5.69
2755 3227 3.145286 TCAAAATTCATCCGTCTGCACA 58.855 40.909 0.00 0.00 0.00 4.57
2875 3358 1.374125 CATCGAGTTCGTGCCCACA 60.374 57.895 1.07 0.00 40.80 4.17
3111 4629 2.755655 CTGGTCAGTGGTCACTACTAGG 59.244 54.545 3.06 0.00 40.20 3.02
3155 5064 1.060729 TCGGATTCCTGAACCAACCA 58.939 50.000 0.30 0.00 0.00 3.67
3156 5065 1.450025 GTCGGATTCCTGAACCAACC 58.550 55.000 0.30 0.00 0.00 3.77
3157 5066 1.076332 CGTCGGATTCCTGAACCAAC 58.924 55.000 0.30 0.00 0.00 3.77
3158 5067 0.036765 CCGTCGGATTCCTGAACCAA 60.037 55.000 4.91 0.00 0.00 3.67
3351 5577 7.383687 TGCAAGCTACTACAGTACTACAAATT 58.616 34.615 0.00 0.00 0.00 1.82
3352 5578 6.931838 TGCAAGCTACTACAGTACTACAAAT 58.068 36.000 0.00 0.00 0.00 2.32
3353 5579 6.335471 TGCAAGCTACTACAGTACTACAAA 57.665 37.500 0.00 0.00 0.00 2.83
3354 5580 5.970317 TGCAAGCTACTACAGTACTACAA 57.030 39.130 0.00 0.00 0.00 2.41
3355 5581 6.377429 AGAATGCAAGCTACTACAGTACTACA 59.623 38.462 0.00 0.00 0.00 2.74
3356 5582 6.693545 CAGAATGCAAGCTACTACAGTACTAC 59.306 42.308 0.00 0.00 0.00 2.73
3357 5583 6.602009 TCAGAATGCAAGCTACTACAGTACTA 59.398 38.462 0.00 0.00 34.76 1.82
3358 5584 5.419155 TCAGAATGCAAGCTACTACAGTACT 59.581 40.000 0.00 0.00 34.76 2.73
3359 5585 5.517054 GTCAGAATGCAAGCTACTACAGTAC 59.483 44.000 0.00 0.00 34.76 2.73
3360 5586 5.185056 TGTCAGAATGCAAGCTACTACAGTA 59.815 40.000 0.00 0.00 34.76 2.74
3361 5587 4.021104 TGTCAGAATGCAAGCTACTACAGT 60.021 41.667 0.00 0.00 34.76 3.55
3362 5588 4.498241 TGTCAGAATGCAAGCTACTACAG 58.502 43.478 0.00 0.00 34.76 2.74
3363 5589 4.498241 CTGTCAGAATGCAAGCTACTACA 58.502 43.478 0.00 0.00 34.76 2.74
3364 5590 3.868077 CCTGTCAGAATGCAAGCTACTAC 59.132 47.826 0.00 0.00 34.76 2.73
3365 5591 3.769300 TCCTGTCAGAATGCAAGCTACTA 59.231 43.478 0.00 0.00 34.76 1.82
3366 5592 2.568956 TCCTGTCAGAATGCAAGCTACT 59.431 45.455 0.00 0.00 34.76 2.57
3633 5860 9.141400 CTTAAATTTGTCGAGACTACTAAGCTT 57.859 33.333 3.48 3.48 0.00 3.74
3636 5863 8.462143 TGCTTAAATTTGTCGAGACTACTAAG 57.538 34.615 0.00 5.73 0.00 2.18
3638 5865 8.821147 TTTGCTTAAATTTGTCGAGACTACTA 57.179 30.769 0.00 0.00 0.00 1.82
3639 5866 7.441458 ACTTTGCTTAAATTTGTCGAGACTACT 59.559 33.333 0.00 0.00 0.00 2.57
3640 5867 7.573627 ACTTTGCTTAAATTTGTCGAGACTAC 58.426 34.615 0.00 0.00 0.00 2.73
4048 6372 3.408020 CGTGTACGTGGCGTTGGG 61.408 66.667 0.00 0.00 41.54 4.12
4174 6504 4.796495 GTACCCCTTGCTGGCCCG 62.796 72.222 0.00 0.00 0.00 6.13
4241 6571 2.070783 ACACGACATTAACCGCGAAAT 58.929 42.857 8.23 0.97 0.00 2.17
4317 6651 5.123227 CCTGAAAAAGTTCCAGTAGACACA 58.877 41.667 0.00 0.00 32.28 3.72
4318 6652 4.515567 CCCTGAAAAAGTTCCAGTAGACAC 59.484 45.833 0.00 0.00 32.28 3.67
4319 6653 4.165372 ACCCTGAAAAAGTTCCAGTAGACA 59.835 41.667 0.00 0.00 32.28 3.41
4320 6654 4.715713 ACCCTGAAAAAGTTCCAGTAGAC 58.284 43.478 0.00 0.00 32.28 2.59
4392 6726 3.899052 ATTTCAGACGAAATCCCCGTA 57.101 42.857 0.00 0.00 46.69 4.02
4414 6748 6.098266 GTGCCCCCAGATTTTATTTTACAGAT 59.902 38.462 0.00 0.00 0.00 2.90
4498 6832 4.213482 GGTTAGGCGTGATGCTAATAAAGG 59.787 45.833 0.00 0.00 45.43 3.11
4541 6875 2.725312 CGCCTGCTAGCCTCAAGGA 61.725 63.158 20.16 0.00 37.39 3.36
4580 6914 1.484444 GGACTTCTCACTGCTGGGGT 61.484 60.000 0.00 0.00 0.00 4.95
4588 6922 2.213499 CACGCAAAAGGACTTCTCACT 58.787 47.619 0.00 0.00 0.00 3.41
4623 6957 1.341383 GGAGGTCGTAAGGAGGTGGTA 60.341 57.143 0.00 0.00 38.47 3.25
4624 6958 0.614134 GGAGGTCGTAAGGAGGTGGT 60.614 60.000 0.00 0.00 38.47 4.16
4625 6959 0.324460 AGGAGGTCGTAAGGAGGTGG 60.324 60.000 0.00 0.00 38.47 4.61
4626 6960 1.204941 CAAGGAGGTCGTAAGGAGGTG 59.795 57.143 0.00 0.00 38.47 4.00
4627 6961 1.558233 CAAGGAGGTCGTAAGGAGGT 58.442 55.000 0.00 0.00 38.47 3.85
4628 6962 0.175989 GCAAGGAGGTCGTAAGGAGG 59.824 60.000 0.00 0.00 38.47 4.30
4629 6963 0.895530 TGCAAGGAGGTCGTAAGGAG 59.104 55.000 0.00 0.00 38.47 3.69
4630 6964 0.895530 CTGCAAGGAGGTCGTAAGGA 59.104 55.000 0.00 0.00 38.47 3.36
4631 6965 0.608640 ACTGCAAGGAGGTCGTAAGG 59.391 55.000 0.00 0.00 39.30 2.69
4632 6966 1.404315 GGACTGCAAGGAGGTCGTAAG 60.404 57.143 0.00 0.00 39.30 2.34
4633 6967 0.606604 GGACTGCAAGGAGGTCGTAA 59.393 55.000 0.00 0.00 39.30 3.18
4639 6973 0.179089 CGAGATGGACTGCAAGGAGG 60.179 60.000 0.00 0.00 39.30 4.30
4714 7048 0.318441 CGCAAGGACTGAACTCCTGA 59.682 55.000 0.00 0.00 40.04 3.86
4900 7235 1.734388 GCAAGGAAAACACACCGGCT 61.734 55.000 0.00 0.00 0.00 5.52
4914 7249 0.962356 ACATGGCCGAAAGAGCAAGG 60.962 55.000 0.00 0.00 0.00 3.61
4973 7309 2.107378 TCGAGGAGGCAGAGATGATAGT 59.893 50.000 0.00 0.00 0.00 2.12
5011 7347 1.569479 GGCTCGCGAGGAATAATGCC 61.569 60.000 35.10 24.73 0.00 4.40
5069 7405 4.647615 CGCGGAGGCTACGGATGG 62.648 72.222 22.54 0.00 36.88 3.51
5126 7462 3.458163 CCCGCCGGAGTCAGCTTA 61.458 66.667 5.05 0.00 0.00 3.09
5154 7490 0.182775 GCAGTCGGAATTGGGGGTAT 59.817 55.000 0.00 0.00 0.00 2.73
5199 7535 3.480470 CATAGATTCTGGGGTTGCGATT 58.520 45.455 0.00 0.00 0.00 3.34
5202 7538 1.134098 ACCATAGATTCTGGGGTTGCG 60.134 52.381 10.02 0.00 38.14 4.85


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

AutoCloner maintained by Alex Coulton.