Multiple sequence alignment - TraesCS7B01G126100

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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 TraesCS7B01G126100 chr7B 100.000 2316 0 0 2161 4476 149613174 149610859 0.000000e+00 4277
1 TraesCS7B01G126100 chr7B 100.000 1766 0 0 1 1766 149615334 149613569 0.000000e+00 3262
2 TraesCS7B01G126100 chr7B 92.268 194 13 2 585 777 169374610 169374418 1.590000e-69 274
3 TraesCS7B01G126100 chr7B 93.514 185 10 2 595 777 598296402 598296218 1.590000e-69 274
4 TraesCS7B01G126100 chr7A 89.920 1627 93 39 2887 4476 190470873 190472465 0.000000e+00 2030
5 TraesCS7B01G126100 chr7A 97.030 909 22 4 857 1761 190469203 190470110 0.000000e+00 1524
6 TraesCS7B01G126100 chr7A 91.947 683 27 13 2188 2844 190470192 190470872 0.000000e+00 931
7 TraesCS7B01G126100 chr7A 89.494 257 13 2 12 255 190467533 190467788 3.360000e-81 313
8 TraesCS7B01G126100 chr7A 92.670 191 12 2 588 777 584381832 584381643 1.590000e-69 274
9 TraesCS7B01G126100 chr7D 96.293 998 31 5 771 1766 181608850 181607857 0.000000e+00 1633
10 TraesCS7B01G126100 chr7D 92.914 1002 52 13 2887 3881 181607152 181606163 0.000000e+00 1439
11 TraesCS7B01G126100 chr7D 95.646 666 16 2 2188 2844 181607814 181607153 0.000000e+00 1057
12 TraesCS7B01G126100 chr7D 96.768 495 15 1 3983 4476 181605866 181605372 0.000000e+00 824
13 TraesCS7B01G126100 chr7D 94.400 250 13 1 321 569 181610151 181609902 2.530000e-102 383
14 TraesCS7B01G126100 chr3B 95.187 187 8 1 592 777 627913631 627913817 1.220000e-75 294
15 TraesCS7B01G126100 chr2D 93.617 188 10 2 592 777 14087320 14087507 3.410000e-71 279
16 TraesCS7B01G126100 chr2D 92.268 194 12 3 583 774 37526607 37526799 5.710000e-69 272
17 TraesCS7B01G126100 chr5D 93.989 183 10 1 595 777 332918876 332918695 4.410000e-70 276
18 TraesCS7B01G126100 chr2B 92.268 194 13 2 586 777 166592381 166592188 1.590000e-69 274
19 TraesCS7B01G126100 chr4B 92.188 192 13 2 588 777 465476515 465476324 2.050000e-68 270


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 TraesCS7B01G126100 chr7B 149610859 149615334 4475 True 3769.5 4277 100.00000 1 4476 2 chr7B.!!$R3 4475
1 TraesCS7B01G126100 chr7A 190467533 190472465 4932 False 1199.5 2030 92.09775 12 4476 4 chr7A.!!$F1 4464
2 TraesCS7B01G126100 chr7D 181605372 181610151 4779 True 1067.2 1633 95.20420 321 4476 5 chr7D.!!$R1 4155

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
900 1994 0.033405 CCGTACTCTTCCCCTCTCCA 60.033 60.000 0.00 0.00 0.00 3.86 F
2865 4010 1.133668 AGCTTGGTAATCCATGGAGGC 60.134 52.381 21.33 12.02 43.91 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2884 4029 1.073025 AAGAATGACGTGCCAGGCA 59.927 52.632 11.22 11.22 35.6 4.75 R
4297 5672 0.663568 CCTCGATCGATACGTTGCCC 60.664 60.000 19.78 0.00 0.0 5.36 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
82 83 5.957796 CGTTCGTGCATATTTTTCCTAAGTC 59.042 40.000 0.00 0.00 0.00 3.01
83 84 5.712217 TCGTGCATATTTTTCCTAAGTCG 57.288 39.130 0.00 0.00 0.00 4.18
85 86 4.271687 GTGCATATTTTTCCTAAGTCGCG 58.728 43.478 0.00 0.00 0.00 5.87
147 148 9.005777 GTTCTGTTGGTTGAAGGTACAATAATA 57.994 33.333 0.00 0.00 32.36 0.98
167 168 9.994432 AATAATACATCTTCTTTTCTCTTTGCG 57.006 29.630 0.00 0.00 0.00 4.85
216 230 1.813337 CCACACACTGACACACGCA 60.813 57.895 0.00 0.00 0.00 5.24
229 243 2.167219 CACGCATCTCATCGCCGTT 61.167 57.895 0.00 0.00 0.00 4.44
230 244 2.167219 ACGCATCTCATCGCCGTTG 61.167 57.895 0.00 0.00 0.00 4.10
243 257 1.373570 GCCGTTGAGCTAAGAGCAAT 58.626 50.000 0.64 0.00 45.56 3.56
255 269 2.123982 AGCAATGCTAGCAGCCCC 60.124 61.111 23.89 10.99 41.51 5.80
256 270 2.123982 GCAATGCTAGCAGCCCCT 60.124 61.111 23.89 2.25 41.51 4.79
258 272 1.890979 CAATGCTAGCAGCCCCTCG 60.891 63.158 23.89 2.24 41.51 4.63
284 299 4.540153 GCGCTAGCAGATTTCCCA 57.460 55.556 16.45 0.00 44.35 4.37
285 300 3.012560 GCGCTAGCAGATTTCCCAT 57.987 52.632 16.45 0.00 44.35 4.00
286 301 2.169832 GCGCTAGCAGATTTCCCATA 57.830 50.000 16.45 0.00 44.35 2.74
287 302 2.704572 GCGCTAGCAGATTTCCCATAT 58.295 47.619 16.45 0.00 44.35 1.78
288 303 2.675348 GCGCTAGCAGATTTCCCATATC 59.325 50.000 16.45 0.00 44.35 1.63
289 304 3.866066 GCGCTAGCAGATTTCCCATATCA 60.866 47.826 16.45 0.00 44.35 2.15
290 305 4.318332 CGCTAGCAGATTTCCCATATCAA 58.682 43.478 16.45 0.00 0.00 2.57
291 306 4.153117 CGCTAGCAGATTTCCCATATCAAC 59.847 45.833 16.45 0.00 0.00 3.18
292 307 5.065914 GCTAGCAGATTTCCCATATCAACA 58.934 41.667 10.63 0.00 0.00 3.33
293 308 5.532406 GCTAGCAGATTTCCCATATCAACAA 59.468 40.000 10.63 0.00 0.00 2.83
294 309 5.841957 AGCAGATTTCCCATATCAACAAC 57.158 39.130 0.00 0.00 0.00 3.32
295 310 4.646492 AGCAGATTTCCCATATCAACAACC 59.354 41.667 0.00 0.00 0.00 3.77
296 311 4.646492 GCAGATTTCCCATATCAACAACCT 59.354 41.667 0.00 0.00 0.00 3.50
297 312 5.221126 GCAGATTTCCCATATCAACAACCTC 60.221 44.000 0.00 0.00 0.00 3.85
298 313 5.008019 CAGATTTCCCATATCAACAACCTCG 59.992 44.000 0.00 0.00 0.00 4.63
299 314 4.561500 TTTCCCATATCAACAACCTCGA 57.438 40.909 0.00 0.00 0.00 4.04
300 315 4.561500 TTCCCATATCAACAACCTCGAA 57.438 40.909 0.00 0.00 0.00 3.71
301 316 4.561500 TCCCATATCAACAACCTCGAAA 57.438 40.909 0.00 0.00 0.00 3.46
302 317 4.258543 TCCCATATCAACAACCTCGAAAC 58.741 43.478 0.00 0.00 0.00 2.78
303 318 3.377172 CCCATATCAACAACCTCGAAACC 59.623 47.826 0.00 0.00 0.00 3.27
304 319 4.006989 CCATATCAACAACCTCGAAACCA 58.993 43.478 0.00 0.00 0.00 3.67
305 320 4.640201 CCATATCAACAACCTCGAAACCAT 59.360 41.667 0.00 0.00 0.00 3.55
306 321 5.125417 CCATATCAACAACCTCGAAACCATT 59.875 40.000 0.00 0.00 0.00 3.16
307 322 6.350110 CCATATCAACAACCTCGAAACCATTT 60.350 38.462 0.00 0.00 0.00 2.32
308 323 4.993029 TCAACAACCTCGAAACCATTTT 57.007 36.364 0.00 0.00 0.00 1.82
309 324 5.331876 TCAACAACCTCGAAACCATTTTT 57.668 34.783 0.00 0.00 0.00 1.94
310 325 5.105752 TCAACAACCTCGAAACCATTTTTG 58.894 37.500 0.00 0.00 0.00 2.44
311 326 4.993029 ACAACCTCGAAACCATTTTTGA 57.007 36.364 0.00 0.00 34.46 2.69
312 327 4.932146 ACAACCTCGAAACCATTTTTGAG 58.068 39.130 7.22 7.22 46.78 3.02
313 328 4.401202 ACAACCTCGAAACCATTTTTGAGT 59.599 37.500 11.65 0.94 46.18 3.41
314 329 5.105513 ACAACCTCGAAACCATTTTTGAGTT 60.106 36.000 11.65 5.54 46.18 3.01
315 330 5.183014 ACCTCGAAACCATTTTTGAGTTC 57.817 39.130 11.65 0.00 46.18 3.01
316 331 4.642885 ACCTCGAAACCATTTTTGAGTTCA 59.357 37.500 11.65 0.00 46.18 3.18
317 332 5.301805 ACCTCGAAACCATTTTTGAGTTCAT 59.698 36.000 11.65 0.00 46.18 2.57
318 333 6.183360 ACCTCGAAACCATTTTTGAGTTCATT 60.183 34.615 11.65 0.00 46.18 2.57
319 334 6.363357 CCTCGAAACCATTTTTGAGTTCATTC 59.637 38.462 11.65 0.00 46.18 2.67
334 349 5.787380 AGTTCATTCCAGAAAATTTGGAGC 58.213 37.500 0.00 0.00 45.00 4.70
354 370 2.048877 GCCAAGCTTGTGCGCAAT 60.049 55.556 24.35 0.00 45.42 3.56
422 438 9.884636 TCCATTCAAAAATTCTACTTCGATCTA 57.115 29.630 0.00 0.00 0.00 1.98
443 459 1.612726 GCACAGACTTTGGCAGGATCT 60.613 52.381 0.00 0.00 0.00 2.75
512 529 7.539034 ACAAGGGCAAAAGTTGTAGATTATT 57.461 32.000 0.00 0.00 32.63 1.40
592 637 9.137459 ACACTACTATACAAGATACTTGATGCT 57.863 33.333 16.65 0.00 0.00 3.79
603 1656 2.427506 ACTTGATGCTTCCTCCGTTTC 58.572 47.619 0.00 0.00 0.00 2.78
609 1662 5.067273 TGATGCTTCCTCCGTTTCTTTTTA 58.933 37.500 0.00 0.00 0.00 1.52
610 1663 5.181245 TGATGCTTCCTCCGTTTCTTTTTAG 59.819 40.000 0.00 0.00 0.00 1.85
611 1664 4.457466 TGCTTCCTCCGTTTCTTTTTAGT 58.543 39.130 0.00 0.00 0.00 2.24
612 1665 4.514066 TGCTTCCTCCGTTTCTTTTTAGTC 59.486 41.667 0.00 0.00 0.00 2.59
613 1666 4.755629 GCTTCCTCCGTTTCTTTTTAGTCT 59.244 41.667 0.00 0.00 0.00 3.24
614 1667 5.334182 GCTTCCTCCGTTTCTTTTTAGTCTG 60.334 44.000 0.00 0.00 0.00 3.51
615 1668 4.062991 TCCTCCGTTTCTTTTTAGTCTGC 58.937 43.478 0.00 0.00 0.00 4.26
617 1670 4.455877 CCTCCGTTTCTTTTTAGTCTGCAT 59.544 41.667 0.00 0.00 0.00 3.96
618 1671 5.642063 CCTCCGTTTCTTTTTAGTCTGCATA 59.358 40.000 0.00 0.00 0.00 3.14
619 1672 6.316390 CCTCCGTTTCTTTTTAGTCTGCATAT 59.684 38.462 0.00 0.00 0.00 1.78
620 1673 7.494625 CCTCCGTTTCTTTTTAGTCTGCATATA 59.505 37.037 0.00 0.00 0.00 0.86
622 1675 8.879759 TCCGTTTCTTTTTAGTCTGCATATAAG 58.120 33.333 0.00 0.00 0.00 1.73
623 1676 8.879759 CCGTTTCTTTTTAGTCTGCATATAAGA 58.120 33.333 0.00 0.00 0.00 2.10
631 1684 9.679661 TTTTAGTCTGCATATAAGATTTGGTCA 57.320 29.630 0.00 0.00 0.00 4.02
632 1685 9.679661 TTTAGTCTGCATATAAGATTTGGTCAA 57.320 29.630 0.00 0.00 0.00 3.18
633 1686 9.679661 TTAGTCTGCATATAAGATTTGGTCAAA 57.320 29.630 0.00 0.00 34.46 2.69
634 1687 8.218338 AGTCTGCATATAAGATTTGGTCAAAG 57.782 34.615 2.55 0.00 33.32 2.77
635 1688 7.831193 AGTCTGCATATAAGATTTGGTCAAAGT 59.169 33.333 2.55 0.00 33.32 2.66
636 1689 8.462016 GTCTGCATATAAGATTTGGTCAAAGTT 58.538 33.333 2.55 1.84 33.32 2.66
637 1690 9.679661 TCTGCATATAAGATTTGGTCAAAGTTA 57.320 29.630 2.55 3.72 33.32 2.24
811 1865 2.375174 TGTTGTAAGCCCATCTGAGGTT 59.625 45.455 0.00 0.00 0.00 3.50
816 1870 5.826643 TGTAAGCCCATCTGAGGTTAAATT 58.173 37.500 0.00 0.00 0.00 1.82
836 1890 0.409484 ACATGGGCTGCTAAAGGGTT 59.591 50.000 0.00 0.00 0.00 4.11
837 1891 1.203174 ACATGGGCTGCTAAAGGGTTT 60.203 47.619 0.00 0.00 0.00 3.27
844 1898 2.491693 GCTGCTAAAGGGTTTATGTGCA 59.508 45.455 0.00 0.00 0.00 4.57
900 1994 0.033405 CCGTACTCTTCCCCTCTCCA 60.033 60.000 0.00 0.00 0.00 3.86
918 2012 2.529744 AACCTTTCTCGGCCCAGCT 61.530 57.895 0.00 0.00 0.00 4.24
930 2024 3.124921 CCAGCTGCCGTAAACCCG 61.125 66.667 8.66 0.00 0.00 5.28
1041 2135 1.364171 CCTCCTAACGGCATCTCGG 59.636 63.158 0.00 0.00 0.00 4.63
1415 2511 7.124901 AGGTATACAATGATCATAGAGCGGATT 59.875 37.037 9.04 0.00 0.00 3.01
1418 2514 5.862845 ACAATGATCATAGAGCGGATTTCT 58.137 37.500 9.04 0.00 0.00 2.52
1419 2515 6.294473 ACAATGATCATAGAGCGGATTTCTT 58.706 36.000 9.04 0.00 0.00 2.52
1661 2758 1.342174 AGCCAGTGCCAAAGACATTTG 59.658 47.619 0.00 0.00 44.53 2.32
1744 2841 7.718334 TTCACTAGTCATTGAAGAGTGGATA 57.282 36.000 20.75 10.13 38.43 2.59
2561 3706 4.608948 TTGTTGGTGTTGTGTTTCCTTT 57.391 36.364 0.00 0.00 0.00 3.11
2805 3950 9.841295 TGGTAACTTCTTTAGTTTGTGTCTATT 57.159 29.630 0.00 0.00 44.73 1.73
2862 4007 6.950842 CTGATATAGCTTGGTAATCCATGGA 58.049 40.000 18.88 18.88 43.91 3.41
2863 4008 6.950842 TGATATAGCTTGGTAATCCATGGAG 58.049 40.000 21.33 5.54 43.91 3.86
2864 4009 4.647564 ATAGCTTGGTAATCCATGGAGG 57.352 45.455 21.33 5.22 43.91 4.30
2865 4010 1.133668 AGCTTGGTAATCCATGGAGGC 60.134 52.381 21.33 12.02 43.91 4.70
2866 4011 1.133668 GCTTGGTAATCCATGGAGGCT 60.134 52.381 21.33 9.65 43.91 4.58
2867 4012 2.687914 GCTTGGTAATCCATGGAGGCTT 60.688 50.000 21.33 12.28 43.91 4.35
2868 4013 2.734755 TGGTAATCCATGGAGGCTTG 57.265 50.000 21.33 0.00 39.03 4.01
2869 4014 1.922447 TGGTAATCCATGGAGGCTTGT 59.078 47.619 21.33 0.00 39.03 3.16
2870 4015 3.119319 TGGTAATCCATGGAGGCTTGTA 58.881 45.455 21.33 2.61 39.03 2.41
2871 4016 3.118038 TGGTAATCCATGGAGGCTTGTAC 60.118 47.826 21.33 13.49 39.03 2.90
2872 4017 2.736670 AATCCATGGAGGCTTGTACC 57.263 50.000 21.33 0.00 37.29 3.34
2873 4018 1.595311 ATCCATGGAGGCTTGTACCA 58.405 50.000 21.33 0.00 37.29 3.25
2874 4019 1.595311 TCCATGGAGGCTTGTACCAT 58.405 50.000 11.44 0.00 43.97 3.55
2875 4020 1.922447 TCCATGGAGGCTTGTACCATT 59.078 47.619 11.44 0.00 41.68 3.16
2876 4021 2.311542 TCCATGGAGGCTTGTACCATTT 59.688 45.455 11.44 0.00 41.68 2.32
2877 4022 3.525609 TCCATGGAGGCTTGTACCATTTA 59.474 43.478 11.44 0.00 41.68 1.40
2878 4023 4.167892 TCCATGGAGGCTTGTACCATTTAT 59.832 41.667 11.44 0.00 41.68 1.40
2879 4024 4.279169 CCATGGAGGCTTGTACCATTTATG 59.721 45.833 5.56 0.00 41.68 1.90
2880 4025 4.853468 TGGAGGCTTGTACCATTTATGA 57.147 40.909 0.00 0.00 0.00 2.15
2881 4026 5.387113 TGGAGGCTTGTACCATTTATGAT 57.613 39.130 0.00 0.00 0.00 2.45
2882 4027 5.132502 TGGAGGCTTGTACCATTTATGATG 58.867 41.667 0.00 0.00 0.00 3.07
2883 4028 4.520492 GGAGGCTTGTACCATTTATGATGG 59.480 45.833 8.05 8.05 44.54 3.51
2951 4097 6.296026 TCACTTGCTTGAACTTATAAGTGGT 58.704 36.000 18.70 4.16 43.00 4.16
3003 4149 2.710096 TTGCCATACTCCACTTAGGC 57.290 50.000 0.00 0.00 42.32 3.93
3050 4203 7.122650 ACTTTGGTTCCTAACATAATCCACATG 59.877 37.037 0.00 0.00 0.00 3.21
3123 4276 2.882229 GCCATAACTTAGGTGTGGCCAA 60.882 50.000 24.74 0.00 44.89 4.52
3154 4307 3.319122 GCCAACTGAACACATCCTTCTTT 59.681 43.478 0.00 0.00 0.00 2.52
3182 4335 6.139671 TCTTTGTAGATAGATCCAGCCTTCT 58.860 40.000 0.00 0.00 0.00 2.85
3209 4362 5.784750 TCTTGTGCGAGTTCATATTCTTG 57.215 39.130 0.00 0.00 0.00 3.02
3264 4417 6.634436 GTCTTGTGATAACACTCTTTTTGCTG 59.366 38.462 4.65 0.00 46.07 4.41
3270 4423 3.360249 ACACTCTTTTTGCTGCATGAC 57.640 42.857 1.84 0.00 0.00 3.06
3407 4560 3.055312 TCTGAACCTAGACAGCGAGACTA 60.055 47.826 0.00 0.00 34.57 2.59
3409 4562 2.783609 ACCTAGACAGCGAGACTACA 57.216 50.000 0.00 0.00 0.00 2.74
3414 4567 1.403679 AGACAGCGAGACTACATCAGC 59.596 52.381 0.00 0.00 34.55 4.26
3500 4653 5.254115 GGGCTCTGTATTATGGGATAAACC 58.746 45.833 0.00 0.00 38.08 3.27
3534 4687 3.560025 CCTGTGATGTCTGGCCTTAGTTT 60.560 47.826 3.32 0.00 0.00 2.66
3569 4723 1.881973 GCAGACAGTTCAAAGCATCCA 59.118 47.619 0.00 0.00 0.00 3.41
3595 4749 3.306225 GCATGGAAGCCTGATGTTTCAAA 60.306 43.478 0.00 0.00 0.00 2.69
3610 4764 7.286546 TGATGTTTCAAACTTCCTATTGGTCAA 59.713 33.333 12.38 0.00 35.38 3.18
3660 4814 5.049543 GGAGCTGATATTCTTGCATCTGAAC 60.050 44.000 0.00 0.00 0.00 3.18
3749 4903 8.506168 TCTGTTCTACTTTCTTTTGTGATTGT 57.494 30.769 0.00 0.00 0.00 2.71
3812 4966 0.812549 GCATCATGTCATGTGCACCA 59.187 50.000 23.80 5.05 37.30 4.17
3839 4993 2.486592 CCGAAACACCCACCATAAAGTC 59.513 50.000 0.00 0.00 0.00 3.01
3841 4995 4.563993 CCGAAACACCCACCATAAAGTCTA 60.564 45.833 0.00 0.00 0.00 2.59
3842 4996 4.630069 CGAAACACCCACCATAAAGTCTAG 59.370 45.833 0.00 0.00 0.00 2.43
3844 4998 4.820894 ACACCCACCATAAAGTCTAGTC 57.179 45.455 0.00 0.00 0.00 2.59
3845 4999 4.164981 ACACCCACCATAAAGTCTAGTCA 58.835 43.478 0.00 0.00 0.00 3.41
3846 5000 4.595781 ACACCCACCATAAAGTCTAGTCAA 59.404 41.667 0.00 0.00 0.00 3.18
3847 5001 5.072600 ACACCCACCATAAAGTCTAGTCAAA 59.927 40.000 0.00 0.00 0.00 2.69
3848 5002 6.001460 CACCCACCATAAAGTCTAGTCAAAA 58.999 40.000 0.00 0.00 0.00 2.44
3849 5003 6.002082 ACCCACCATAAAGTCTAGTCAAAAC 58.998 40.000 0.00 0.00 0.00 2.43
3854 5008 9.796120 CACCATAAAGTCTAGTCAAAACAAAAA 57.204 29.630 0.00 0.00 0.00 1.94
3856 5010 8.953990 CCATAAAGTCTAGTCAAAACAAAAACG 58.046 33.333 0.00 0.00 0.00 3.60
3881 5035 1.154225 GCGGACGTCAATTGCCTTG 60.154 57.895 18.91 0.00 36.09 3.61
3882 5036 1.501741 CGGACGTCAATTGCCTTGG 59.498 57.895 18.91 0.00 35.43 3.61
3883 5037 1.883021 GGACGTCAATTGCCTTGGG 59.117 57.895 18.91 0.00 35.43 4.12
3917 5104 0.883833 CAAATGGTGTCTGAGGGCAC 59.116 55.000 0.00 0.00 35.07 5.01
3927 5114 4.023963 GTGTCTGAGGGCACTTTTAAGTTC 60.024 45.833 0.00 0.00 37.08 3.01
4103 5454 0.591170 CCACCACTTAACAAGGCACG 59.409 55.000 0.00 0.00 0.00 5.34
4135 5486 6.452494 TGGTCAGCAACTAACTAGTAGATC 57.548 41.667 3.59 0.00 34.99 2.75
4219 5570 3.208692 ACTCTCCTCCCCACTATGATCTT 59.791 47.826 0.00 0.00 0.00 2.40
4233 5584 8.915057 CACTATGATCTTCCAGTGGAAAATAT 57.085 34.615 24.59 17.50 41.54 1.28
4274 5625 7.255942 CCTCAAAACCAAGGTAACATCAGAAAT 60.256 37.037 0.00 0.00 41.41 2.17
4297 5672 0.318699 TTGCTTCTCAGGACGTGACG 60.319 55.000 2.24 2.24 0.00 4.35
4335 5711 4.660168 GAGGTACGGGGATATCTACAGAA 58.340 47.826 2.05 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.271379 GCCCAGAAGCTCAACAACCTA 60.271 52.381 0.00 0.00 0.00 3.08
1 2 0.538287 GCCCAGAAGCTCAACAACCT 60.538 55.000 0.00 0.00 0.00 3.50
2 3 0.538287 AGCCCAGAAGCTCAACAACC 60.538 55.000 0.00 0.00 39.48 3.77
3 4 1.322442 AAGCCCAGAAGCTCAACAAC 58.678 50.000 0.00 0.00 44.11 3.32
4 5 2.071778 AAAGCCCAGAAGCTCAACAA 57.928 45.000 0.00 0.00 44.11 2.83
5 6 1.682854 CAAAAGCCCAGAAGCTCAACA 59.317 47.619 0.00 0.00 44.11 3.33
6 7 1.000171 CCAAAAGCCCAGAAGCTCAAC 60.000 52.381 0.00 0.00 44.11 3.18
7 8 1.331214 CCAAAAGCCCAGAAGCTCAA 58.669 50.000 0.00 0.00 44.11 3.02
8 9 1.181098 GCCAAAAGCCCAGAAGCTCA 61.181 55.000 0.00 0.00 44.11 4.26
9 10 0.897401 AGCCAAAAGCCCAGAAGCTC 60.897 55.000 0.00 0.00 44.11 4.09
17 18 5.109210 GTTCATAACAATAGCCAAAAGCCC 58.891 41.667 0.00 0.00 45.47 5.19
46 47 0.661020 CACGAACGCTTGAAAACCCT 59.339 50.000 0.00 0.00 0.00 4.34
82 83 0.863957 AAACCGCAAGAAAACACGCG 60.864 50.000 3.53 3.53 46.96 6.01
83 84 2.108178 TAAACCGCAAGAAAACACGC 57.892 45.000 0.00 0.00 43.02 5.34
85 86 7.136772 ACTTCTTATAAACCGCAAGAAAACAC 58.863 34.615 0.00 0.00 37.72 3.32
119 120 4.590918 TGTACCTTCAACCAACAGAACAA 58.409 39.130 0.00 0.00 0.00 2.83
124 125 8.330466 TGTATTATTGTACCTTCAACCAACAG 57.670 34.615 0.00 0.00 0.00 3.16
127 128 9.747898 AAGATGTATTATTGTACCTTCAACCAA 57.252 29.630 0.00 0.00 0.00 3.67
147 148 4.137543 ACCGCAAAGAGAAAAGAAGATGT 58.862 39.130 0.00 0.00 0.00 3.06
167 168 4.086457 TGAAATTCCTTGGCCTTTCTACC 58.914 43.478 3.32 0.00 0.00 3.18
216 230 1.032794 TAGCTCAACGGCGATGAGAT 58.967 50.000 39.72 36.77 45.74 2.75
229 243 2.169144 TGCTAGCATTGCTCTTAGCTCA 59.831 45.455 24.76 9.62 42.97 4.26
230 244 2.801679 CTGCTAGCATTGCTCTTAGCTC 59.198 50.000 24.76 5.81 42.97 4.09
260 274 2.876368 AATCTGCTAGCGCCACCACC 62.876 60.000 10.77 0.00 34.43 4.61
261 275 1.026718 AAATCTGCTAGCGCCACCAC 61.027 55.000 10.77 0.00 34.43 4.16
262 276 0.744414 GAAATCTGCTAGCGCCACCA 60.744 55.000 10.77 0.00 34.43 4.17
263 277 1.440145 GGAAATCTGCTAGCGCCACC 61.440 60.000 10.77 5.08 34.43 4.61
264 278 1.440145 GGGAAATCTGCTAGCGCCAC 61.440 60.000 10.77 0.00 34.43 5.01
265 279 1.153168 GGGAAATCTGCTAGCGCCA 60.153 57.895 10.77 0.00 34.43 5.69
266 280 0.536006 ATGGGAAATCTGCTAGCGCC 60.536 55.000 10.77 4.29 34.43 6.53
267 281 2.169832 TATGGGAAATCTGCTAGCGC 57.830 50.000 10.77 0.00 0.00 5.92
275 290 5.104527 TCGAGGTTGTTGATATGGGAAATCT 60.105 40.000 0.00 0.00 0.00 2.40
280 295 4.258543 GTTTCGAGGTTGTTGATATGGGA 58.741 43.478 0.00 0.00 0.00 4.37
281 296 3.377172 GGTTTCGAGGTTGTTGATATGGG 59.623 47.826 0.00 0.00 0.00 4.00
282 297 4.006989 TGGTTTCGAGGTTGTTGATATGG 58.993 43.478 0.00 0.00 0.00 2.74
283 298 5.818136 ATGGTTTCGAGGTTGTTGATATG 57.182 39.130 0.00 0.00 0.00 1.78
284 299 6.834168 AAATGGTTTCGAGGTTGTTGATAT 57.166 33.333 0.00 0.00 0.00 1.63
285 300 6.642707 AAAATGGTTTCGAGGTTGTTGATA 57.357 33.333 0.00 0.00 0.00 2.15
286 301 5.529581 AAAATGGTTTCGAGGTTGTTGAT 57.470 34.783 0.00 0.00 0.00 2.57
287 302 4.993029 AAAATGGTTTCGAGGTTGTTGA 57.007 36.364 0.00 0.00 0.00 3.18
288 303 5.105752 TCAAAAATGGTTTCGAGGTTGTTG 58.894 37.500 0.00 0.00 0.00 3.33
289 304 5.105513 ACTCAAAAATGGTTTCGAGGTTGTT 60.106 36.000 0.00 0.00 0.00 2.83
290 305 4.401202 ACTCAAAAATGGTTTCGAGGTTGT 59.599 37.500 0.00 0.00 0.00 3.32
291 306 4.932146 ACTCAAAAATGGTTTCGAGGTTG 58.068 39.130 0.00 0.00 0.00 3.77
292 307 5.126384 TGAACTCAAAAATGGTTTCGAGGTT 59.874 36.000 0.00 0.00 0.00 3.50
293 308 4.642885 TGAACTCAAAAATGGTTTCGAGGT 59.357 37.500 0.00 0.00 0.00 3.85
294 309 5.181690 TGAACTCAAAAATGGTTTCGAGG 57.818 39.130 0.00 0.00 0.00 4.63
295 310 6.363357 GGAATGAACTCAAAAATGGTTTCGAG 59.637 38.462 0.00 0.00 0.00 4.04
296 311 6.183360 TGGAATGAACTCAAAAATGGTTTCGA 60.183 34.615 0.00 0.00 0.00 3.71
297 312 5.982516 TGGAATGAACTCAAAAATGGTTTCG 59.017 36.000 0.00 0.00 0.00 3.46
298 313 7.209475 TCTGGAATGAACTCAAAAATGGTTTC 58.791 34.615 0.00 0.00 0.00 2.78
299 314 7.123355 TCTGGAATGAACTCAAAAATGGTTT 57.877 32.000 0.00 0.00 0.00 3.27
300 315 6.729690 TCTGGAATGAACTCAAAAATGGTT 57.270 33.333 0.00 0.00 0.00 3.67
301 316 6.729690 TTCTGGAATGAACTCAAAAATGGT 57.270 33.333 0.00 0.00 0.00 3.55
302 317 8.611654 ATTTTCTGGAATGAACTCAAAAATGG 57.388 30.769 0.00 0.00 0.00 3.16
305 320 8.891720 CCAAATTTTCTGGAATGAACTCAAAAA 58.108 29.630 0.00 0.00 35.85 1.94
306 321 8.263640 TCCAAATTTTCTGGAATGAACTCAAAA 58.736 29.630 0.00 0.00 40.08 2.44
307 322 7.790027 TCCAAATTTTCTGGAATGAACTCAAA 58.210 30.769 0.00 0.00 40.08 2.69
308 323 7.358770 TCCAAATTTTCTGGAATGAACTCAA 57.641 32.000 0.00 0.00 40.08 3.02
309 324 6.517194 GCTCCAAATTTTCTGGAATGAACTCA 60.517 38.462 0.00 0.00 42.43 3.41
310 325 5.866092 GCTCCAAATTTTCTGGAATGAACTC 59.134 40.000 0.00 0.00 42.43 3.01
311 326 5.279657 GGCTCCAAATTTTCTGGAATGAACT 60.280 40.000 0.00 0.00 42.43 3.01
312 327 4.931601 GGCTCCAAATTTTCTGGAATGAAC 59.068 41.667 0.00 0.00 42.43 3.18
313 328 4.840115 AGGCTCCAAATTTTCTGGAATGAA 59.160 37.500 0.00 0.00 42.43 2.57
314 329 4.221262 CAGGCTCCAAATTTTCTGGAATGA 59.779 41.667 0.00 0.00 42.43 2.57
315 330 4.501071 CAGGCTCCAAATTTTCTGGAATG 58.499 43.478 0.00 0.00 42.43 2.67
316 331 3.055602 GCAGGCTCCAAATTTTCTGGAAT 60.056 43.478 0.00 0.00 42.43 3.01
317 332 2.299867 GCAGGCTCCAAATTTTCTGGAA 59.700 45.455 0.00 0.00 42.43 3.53
318 333 1.895131 GCAGGCTCCAAATTTTCTGGA 59.105 47.619 0.00 0.00 40.77 3.86
319 334 1.066645 GGCAGGCTCCAAATTTTCTGG 60.067 52.381 0.00 0.00 35.05 3.86
334 349 4.712425 GCGCACAAGCTTGGCAGG 62.712 66.667 29.18 17.39 39.10 4.85
354 370 3.068024 GCTGTGGTTTGGACAATCTGAAA 59.932 43.478 0.00 0.00 0.00 2.69
422 438 0.403271 ATCCTGCCAAAGTCTGTGCT 59.597 50.000 0.00 0.00 0.00 4.40
443 459 6.416455 GCACTGTTGTTCAATTTTTCGATGTA 59.584 34.615 0.00 0.00 0.00 2.29
486 503 6.575162 AATCTACAACTTTTGCCCTTGTAG 57.425 37.500 9.54 9.54 44.59 2.74
512 529 6.758886 TGACGCAACATGTATGTATAATGTCA 59.241 34.615 0.00 6.26 40.80 3.58
559 576 8.937884 AGTATCTTGTATAGTAGTGTATGCTCG 58.062 37.037 0.00 0.00 0.00 5.03
590 635 4.755629 AGACTAAAAAGAAACGGAGGAAGC 59.244 41.667 0.00 0.00 0.00 3.86
591 636 5.334182 GCAGACTAAAAAGAAACGGAGGAAG 60.334 44.000 0.00 0.00 0.00 3.46
592 637 4.514066 GCAGACTAAAAAGAAACGGAGGAA 59.486 41.667 0.00 0.00 0.00 3.36
594 639 3.813166 TGCAGACTAAAAAGAAACGGAGG 59.187 43.478 0.00 0.00 0.00 4.30
609 1662 7.831193 ACTTTGACCAAATCTTATATGCAGACT 59.169 33.333 0.00 0.00 0.00 3.24
610 1663 7.989826 ACTTTGACCAAATCTTATATGCAGAC 58.010 34.615 0.00 0.00 0.00 3.51
611 1664 8.579850 AACTTTGACCAAATCTTATATGCAGA 57.420 30.769 0.00 0.00 0.00 4.26
811 1865 4.892934 CCCTTTAGCAGCCCATGTAATTTA 59.107 41.667 0.00 0.00 0.00 1.40
816 1870 1.295020 ACCCTTTAGCAGCCCATGTA 58.705 50.000 0.00 0.00 0.00 2.29
836 1890 1.009078 GAGTGAGCGCATGCACATAA 58.991 50.000 23.54 0.00 43.58 1.90
837 1891 0.108233 TGAGTGAGCGCATGCACATA 60.108 50.000 23.54 12.83 43.58 2.29
844 1898 0.322975 AAGAAGGTGAGTGAGCGCAT 59.677 50.000 11.47 0.00 0.00 4.73
900 1994 2.034221 GCTGGGCCGAGAAAGGTT 59.966 61.111 20.35 0.00 0.00 3.50
918 2012 3.285523 CTCGGTCGGGTTTACGGCA 62.286 63.158 0.00 0.00 40.90 5.69
930 2024 4.222847 GCGGTGGGATCCTCGGTC 62.223 72.222 12.58 0.00 0.00 4.79
1041 2135 2.308722 TGGGGTTGAGGAGATGCCC 61.309 63.158 0.00 0.00 37.37 5.36
1438 2534 1.647545 GCCGCACTAGCAAAGCATGA 61.648 55.000 0.00 0.00 42.27 3.07
1567 2664 0.391661 ACTTGGCCAGTATGTGCTCG 60.392 55.000 5.11 0.00 31.97 5.03
1661 2758 1.760192 TAGACCCGAGTTACCTCAGC 58.240 55.000 0.00 0.00 37.59 4.26
1674 2771 3.320626 GACAGTTACAACGGTTAGACCC 58.679 50.000 0.00 0.00 37.45 4.46
2193 3303 7.393216 AGCTGATCCTCTTACATTGATATTCC 58.607 38.462 0.00 0.00 0.00 3.01
2561 3706 7.153315 TGTAATTTGCAGCAATCTGATTTTCA 58.847 30.769 9.12 6.28 42.95 2.69
2709 3854 2.562738 GCCCTGCCAAGTAACAAAATCT 59.437 45.455 0.00 0.00 0.00 2.40
2808 3953 3.494626 GCATCTCACTTTTTCACTCGTGA 59.505 43.478 0.00 0.00 37.91 4.35
2850 3995 2.736670 ACAAGCCTCCATGGATTACC 57.263 50.000 16.63 3.98 43.52 2.85
2851 3996 3.118038 TGGTACAAGCCTCCATGGATTAC 60.118 47.826 16.63 7.81 43.52 1.89
2852 3997 3.119319 TGGTACAAGCCTCCATGGATTA 58.881 45.455 16.63 0.00 43.52 1.75
2853 3998 1.922447 TGGTACAAGCCTCCATGGATT 59.078 47.619 16.63 3.75 46.81 3.01
2854 3999 1.595311 TGGTACAAGCCTCCATGGAT 58.405 50.000 16.63 1.02 33.53 3.41
2855 4000 3.096852 TGGTACAAGCCTCCATGGA 57.903 52.632 15.27 15.27 33.53 3.41
2871 4016 1.342174 GCCAGGCACCATCATAAATGG 59.658 52.381 6.55 2.52 44.54 3.16
2872 4017 2.033372 TGCCAGGCACCATCATAAATG 58.967 47.619 11.22 0.00 31.71 2.32
2873 4018 2.457813 TGCCAGGCACCATCATAAAT 57.542 45.000 11.22 0.00 31.71 1.40
2874 4019 3.996361 TGCCAGGCACCATCATAAA 57.004 47.368 11.22 0.00 31.71 1.40
2884 4029 1.073025 AAGAATGACGTGCCAGGCA 59.927 52.632 11.22 11.22 35.60 4.75
2885 4030 1.237285 ACAAGAATGACGTGCCAGGC 61.237 55.000 3.66 3.66 0.00 4.85
2951 4097 3.523157 TGGAGCAATCAGGATTTGGAGTA 59.477 43.478 0.00 0.00 0.00 2.59
3021 4167 6.657541 TGGATTATGTTAGGAACCAAAGTCAC 59.342 38.462 0.00 0.00 0.00 3.67
3024 4170 6.548321 TGTGGATTATGTTAGGAACCAAAGT 58.452 36.000 0.00 0.00 0.00 2.66
3025 4171 7.122650 ACATGTGGATTATGTTAGGAACCAAAG 59.877 37.037 0.00 0.00 35.32 2.77
3050 4203 6.149474 AGTCTTGGTAAAAGCATATGTGTGAC 59.851 38.462 4.29 0.00 0.00 3.67
3106 4259 2.440253 ACAGTTGGCCACACCTAAGTTA 59.560 45.455 3.88 0.00 40.22 2.24
3123 4276 1.488812 TGTTCAGTTGGCTACCACAGT 59.511 47.619 0.00 0.00 30.78 3.55
3137 4290 5.312079 AGAGGAAAAGAAGGATGTGTTCAG 58.688 41.667 0.00 0.00 0.00 3.02
3154 4307 5.305644 GGCTGGATCTATCTACAAAGAGGAA 59.694 44.000 0.00 0.00 34.49 3.36
3182 4335 8.492673 AGAATATGAACTCGCACAAGAAATAA 57.507 30.769 0.00 0.00 0.00 1.40
3209 4362 8.647143 AACATAACAGCATACATTATTTTGGC 57.353 30.769 0.00 0.00 0.00 4.52
3222 4375 6.262944 TCACAAGACAAGAAACATAACAGCAT 59.737 34.615 0.00 0.00 0.00 3.79
3223 4376 5.588246 TCACAAGACAAGAAACATAACAGCA 59.412 36.000 0.00 0.00 0.00 4.41
3264 4417 4.035558 CCACAACACCTACATATGTCATGC 59.964 45.833 12.68 0.00 0.00 4.06
3270 4423 2.092429 AGCCCCACAACACCTACATATG 60.092 50.000 0.00 0.00 0.00 1.78
3407 4560 1.023513 GCTCTTTCAGCCGCTGATGT 61.024 55.000 23.48 0.00 43.17 3.06
3409 4562 4.215349 GCTCTTTCAGCCGCTGAT 57.785 55.556 23.48 0.00 43.17 2.90
3435 4588 1.959085 CAGCCAGGTTTGCGACAAT 59.041 52.632 0.00 0.00 0.00 2.71
3456 4609 2.354821 CCTTATGGCGCTTTACAAGTCC 59.645 50.000 7.64 0.00 0.00 3.85
3457 4610 2.354821 CCCTTATGGCGCTTTACAAGTC 59.645 50.000 7.64 0.00 0.00 3.01
3477 4630 5.014228 AGGTTTATCCCATAATACAGAGCCC 59.986 44.000 0.00 0.00 36.75 5.19
3487 4640 7.620491 GGGTTTAGGAAAAGGTTTATCCCATAA 59.380 37.037 0.00 0.00 36.75 1.90
3500 4653 5.182001 CAGACATCACAGGGTTTAGGAAAAG 59.818 44.000 0.00 0.00 0.00 2.27
3534 4687 7.121020 TGAACTGTCTGCATAGCAAATCAAATA 59.879 33.333 0.00 0.00 38.41 1.40
3595 4749 9.533831 ACTTCAATAAATTGACCAATAGGAAGT 57.466 29.630 4.89 14.43 45.63 3.01
3749 4903 7.658525 AAAGCAATGGTGTCATCCAAATATA 57.341 32.000 0.00 0.00 41.09 0.86
3812 4966 2.852075 TGGGTGTTTCGGGGCTCT 60.852 61.111 0.00 0.00 0.00 4.09
3839 4993 7.164204 GCAAGTTTCGTTTTTGTTTTGACTAG 58.836 34.615 0.00 0.00 0.00 2.57
3841 4995 5.387958 CGCAAGTTTCGTTTTTGTTTTGACT 60.388 36.000 0.00 0.00 0.00 3.41
3842 4996 4.774054 CGCAAGTTTCGTTTTTGTTTTGAC 59.226 37.500 0.00 0.00 0.00 3.18
3844 4998 4.078346 CCGCAAGTTTCGTTTTTGTTTTG 58.922 39.130 0.00 0.00 0.00 2.44
3845 4999 3.988517 TCCGCAAGTTTCGTTTTTGTTTT 59.011 34.783 0.00 0.00 0.00 2.43
3846 5000 3.365520 GTCCGCAAGTTTCGTTTTTGTTT 59.634 39.130 0.00 0.00 0.00 2.83
3847 5001 2.918600 GTCCGCAAGTTTCGTTTTTGTT 59.081 40.909 0.00 0.00 0.00 2.83
3848 5002 2.521996 GTCCGCAAGTTTCGTTTTTGT 58.478 42.857 0.00 0.00 0.00 2.83
3849 5003 1.511147 CGTCCGCAAGTTTCGTTTTTG 59.489 47.619 0.00 0.00 0.00 2.44
3854 5008 0.806884 TTGACGTCCGCAAGTTTCGT 60.807 50.000 14.12 0.00 38.30 3.85
3856 5010 2.307049 CAATTGACGTCCGCAAGTTTC 58.693 47.619 14.12 0.00 0.00 2.78
3881 5035 3.569250 TTTGCTAGATTTCGTTTGCCC 57.431 42.857 0.00 0.00 0.00 5.36
3882 5036 3.859386 CCATTTGCTAGATTTCGTTTGCC 59.141 43.478 0.00 0.00 0.00 4.52
3883 5037 4.324402 CACCATTTGCTAGATTTCGTTTGC 59.676 41.667 0.00 0.00 0.00 3.68
3884 5038 5.460646 ACACCATTTGCTAGATTTCGTTTG 58.539 37.500 0.00 0.00 0.00 2.93
3895 5082 1.340017 GCCCTCAGACACCATTTGCTA 60.340 52.381 0.00 0.00 0.00 3.49
4003 5352 8.995220 CAATTTTAGGTTGTGCTAACTACTACA 58.005 33.333 4.78 0.00 33.23 2.74
4004 5353 9.211485 TCAATTTTAGGTTGTGCTAACTACTAC 57.789 33.333 4.78 0.00 33.23 2.73
4103 5454 3.801114 AGTTGCTGACCAAGGAAAAAC 57.199 42.857 0.00 0.00 38.05 2.43
4135 5486 6.312426 ACTTGAGATCGAATTACTGAAGCAAG 59.688 38.462 0.00 0.00 35.33 4.01
4233 5584 6.547880 TGGTTTTGAGGCTGTATTGTTTCTTA 59.452 34.615 0.00 0.00 0.00 2.10
4274 5625 1.289066 CGTCCTGAGAAGCAACCGA 59.711 57.895 0.00 0.00 0.00 4.69
4297 5672 0.663568 CCTCGATCGATACGTTGCCC 60.664 60.000 19.78 0.00 0.00 5.36
4335 5711 9.220767 GATTAGTTGAAGATGGTCTAGTTTTGT 57.779 33.333 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.