Multiple sequence alignment - TraesCS2A01G347200

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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 TraesCS2A01G347200 chr2A 100.000 6310 0 0 1 6310 585661383 585655074 0.000000e+00 11653
1 TraesCS2A01G347200 chr2B 97.496 4552 108 2 1125 5673 521330715 521326167 0.000000e+00 7769
2 TraesCS2A01G347200 chr2B 87.797 885 84 11 1 879 521332062 521331196 0.000000e+00 1014
3 TraesCS2A01G347200 chr2B 98.298 235 3 1 5934 6167 521322123 521321889 1.640000e-110 411
4 TraesCS2A01G347200 chr2B 96.622 148 4 1 6163 6310 521320044 521319898 1.760000e-60 244
5 TraesCS2A01G347200 chr2B 96.503 143 4 1 5795 5936 521326170 521326028 1.060000e-57 235
6 TraesCS2A01G347200 chr2B 96.667 120 2 2 918 1036 521331200 521331082 1.390000e-46 198
7 TraesCS2A01G347200 chr2D 97.694 4206 94 2 915 5117 441766192 441761987 0.000000e+00 7227
8 TraesCS2A01G347200 chr2D 97.402 1193 26 3 5114 6305 441761907 441760719 0.000000e+00 2026
9 TraesCS2A01G347200 chr2D 86.289 919 96 18 1 898 441767261 441766352 0.000000e+00 972
10 TraesCS2A01G347200 chr7B 84.536 291 42 3 1 289 655434114 655434403 1.040000e-72 285


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 TraesCS2A01G347200 chr2A 585655074 585661383 6309 True 11653.000000 11653 100.000000 1 6310 1 chr2A.!!$R1 6309
1 TraesCS2A01G347200 chr2B 521319898 521332062 12164 True 1645.166667 7769 95.563833 1 6310 6 chr2B.!!$R1 6309
2 TraesCS2A01G347200 chr2D 441760719 441767261 6542 True 3408.333333 7227 93.795000 1 6305 3 chr2D.!!$R1 6304

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
223 226 0.405198 TGGCACTGTTGGATCCATGT 59.595 50.000 17.06 12.18 0.00 3.21 F
1057 1221 0.745845 CTCTGCCTCCATTTCCACGG 60.746 60.000 0.00 0.00 0.00 4.94 F
1601 2042 0.830648 TTGGGGAGGATGATCGTGAC 59.169 55.000 0.00 0.00 0.00 3.67 F
2339 2780 0.179936 AGGAGATGCTGGTTGCTAGC 59.820 55.000 8.10 8.10 43.37 3.42 F
2342 2783 0.747283 AGATGCTGGTTGCTAGCTGC 60.747 55.000 17.23 19.05 44.14 5.25 F
2831 3272 1.218047 GGGCGAAATCCAAAAGGCC 59.782 57.895 0.00 0.00 40.27 5.19 F
3658 4099 0.457851 GACACAGCACCGATAGCTCT 59.542 55.000 0.00 0.00 41.14 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1778 2219 0.534412 CCGACATCTCCTTCTGCACT 59.466 55.000 0.00 0.00 0.00 4.40 R
2315 2756 1.804372 GCAACCAGCATCTCCTCGTAG 60.804 57.143 0.00 0.00 44.79 3.51 R
3369 3810 0.108138 CCAGCTTTCCCTAGTCCGTG 60.108 60.000 0.00 0.00 0.00 4.94 R
3571 4012 1.064758 TGCTGAAACCCTGAACTGTGT 60.065 47.619 0.00 0.00 0.00 3.72 R
3602 4043 2.951642 CTCCAACAAACCAAGAGAAGCA 59.048 45.455 0.00 0.00 0.00 3.91 R
4670 5114 2.691927 CTGCATGCAGTGTACTGAAGA 58.308 47.619 34.76 2.37 46.59 2.87 R
5633 6160 1.198408 CGTCAACACAATGATGCTGCT 59.802 47.619 0.00 0.00 30.20 4.24 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 85 4.639310 CAGCTGAAAATGCTAGACCAGAAT 59.361 41.667 8.42 0.00 38.92 2.40
104 107 6.790424 GAATGATGCATTAGCTTGCTAGCAAT 60.790 38.462 29.40 18.57 40.93 3.56
113 116 3.535561 GCTTGCTAGCAATTCCAGAGTA 58.464 45.455 29.40 4.40 46.95 2.59
120 123 5.277058 GCTAGCAATTCCAGAGTACAAATCG 60.277 44.000 10.63 0.00 0.00 3.34
122 125 3.126858 GCAATTCCAGAGTACAAATCGCA 59.873 43.478 0.00 0.00 0.00 5.10
123 126 4.728882 GCAATTCCAGAGTACAAATCGCAG 60.729 45.833 0.00 0.00 0.00 5.18
155 158 2.287788 GCAATGGTTCACACTTCACAGG 60.288 50.000 0.00 0.00 0.00 4.00
160 163 2.221169 GTTCACACTTCACAGGCATCA 58.779 47.619 0.00 0.00 0.00 3.07
176 179 3.514645 GCATCAAGCATGTTAAAGTGGG 58.485 45.455 0.00 0.00 44.79 4.61
179 182 5.336372 GCATCAAGCATGTTAAAGTGGGTAA 60.336 40.000 0.00 0.00 44.79 2.85
181 184 6.079424 TCAAGCATGTTAAAGTGGGTAAAC 57.921 37.500 0.00 0.00 0.00 2.01
186 189 6.946009 AGCATGTTAAAGTGGGTAAACTGTAT 59.054 34.615 0.00 0.00 0.00 2.29
193 196 5.733620 AGTGGGTAAACTGTATCTTTCGA 57.266 39.130 0.00 0.00 0.00 3.71
196 199 5.697633 GTGGGTAAACTGTATCTTTCGACAA 59.302 40.000 0.00 0.00 0.00 3.18
197 200 6.370718 GTGGGTAAACTGTATCTTTCGACAAT 59.629 38.462 0.00 0.00 0.00 2.71
198 201 6.370442 TGGGTAAACTGTATCTTTCGACAATG 59.630 38.462 0.00 0.00 0.00 2.82
200 203 4.946784 AACTGTATCTTTCGACAATGGC 57.053 40.909 0.00 0.00 0.00 4.40
206 209 2.276201 TCTTTCGACAATGGCGTATGG 58.724 47.619 8.85 0.00 0.00 2.74
215 218 3.187058 GGCGTATGGCACTGTTGG 58.813 61.111 3.13 0.00 46.16 3.77
218 221 0.657840 GCGTATGGCACTGTTGGATC 59.342 55.000 0.00 0.00 42.87 3.36
223 226 0.405198 TGGCACTGTTGGATCCATGT 59.595 50.000 17.06 12.18 0.00 3.21
253 256 4.379186 GCACTCCAGATGTGACTCAATTTG 60.379 45.833 0.00 0.00 37.60 2.32
257 260 4.937620 TCCAGATGTGACTCAATTTGTAGC 59.062 41.667 0.00 0.00 0.00 3.58
259 262 6.070824 TCCAGATGTGACTCAATTTGTAGCTA 60.071 38.462 0.00 0.00 0.00 3.32
311 315 4.395854 TGTTTACATACATTCTGCAGCCAG 59.604 41.667 9.47 3.06 40.54 4.85
313 317 8.497730 ATGTTTACATACATTCTGCAGCCAGAA 61.498 37.037 9.47 7.71 46.31 3.02
318 322 4.905240 TCTGCAGCCAGAAAGCAA 57.095 50.000 9.47 0.00 44.79 3.91
358 362 4.997395 GCTGAAAAGCCTGATAATATCGGA 59.003 41.667 10.52 0.00 37.90 4.55
367 371 5.655488 CCTGATAATATCGGACAGCTAAGG 58.345 45.833 10.52 0.00 37.90 2.69
408 412 6.295236 CCAATTAACAGATCTGGCAAAAGGAA 60.295 38.462 26.08 8.56 34.19 3.36
409 413 5.705609 TTAACAGATCTGGCAAAAGGAAC 57.294 39.130 26.08 0.00 34.19 3.62
410 414 3.515602 ACAGATCTGGCAAAAGGAACT 57.484 42.857 26.08 0.00 35.38 3.01
437 441 1.217882 CGCAACAAGAACTTCCGACT 58.782 50.000 0.00 0.00 0.00 4.18
442 446 3.536956 ACAAGAACTTCCGACTGACAA 57.463 42.857 0.00 0.00 0.00 3.18
475 487 3.408634 TGCTAACACTTGACTAAAGCCC 58.591 45.455 0.00 0.00 39.76 5.19
478 490 2.632987 ACACTTGACTAAAGCCCGTT 57.367 45.000 0.00 0.00 39.76 4.44
515 527 5.541098 AACAGTAAGCGCTACCAAATAAC 57.459 39.130 12.05 0.00 0.00 1.89
516 528 4.571919 ACAGTAAGCGCTACCAAATAACA 58.428 39.130 12.05 0.00 0.00 2.41
518 530 5.121768 ACAGTAAGCGCTACCAAATAACAAG 59.878 40.000 12.05 0.00 0.00 3.16
521 533 1.404035 GCGCTACCAAATAACAAGGGG 59.596 52.381 0.00 0.00 0.00 4.79
545 560 4.524802 AACATGATTTGCCTCTGGGATA 57.475 40.909 0.00 0.00 33.58 2.59
563 578 5.070685 GGGATAAAGTTCAAACTCACCTGT 58.929 41.667 0.00 0.00 38.57 4.00
652 668 3.005791 CCACCCAGGAAATCAAGTGTTTC 59.994 47.826 0.00 0.00 41.22 2.78
747 768 2.611292 GAGATCAGGAGGCAACGAATTG 59.389 50.000 0.00 0.00 46.39 2.32
757 778 4.559153 AGGCAACGAATTGATGGAAAAAG 58.441 39.130 0.00 0.00 46.39 2.27
770 791 1.200252 GGAAAAAGGAAGAAGCGAGGC 59.800 52.381 0.00 0.00 0.00 4.70
771 792 2.155279 GAAAAAGGAAGAAGCGAGGCT 58.845 47.619 0.00 0.00 42.56 4.58
772 793 1.528129 AAAAGGAAGAAGCGAGGCTG 58.472 50.000 0.00 0.00 39.62 4.85
852 873 2.125673 GCGGGCTGCGACTTTCTA 60.126 61.111 0.81 0.00 0.00 2.10
854 875 2.158959 CGGGCTGCGACTTTCTACG 61.159 63.158 0.00 0.00 0.00 3.51
863 884 2.603892 GCGACTTTCTACGTCTGTGTGA 60.604 50.000 0.00 0.00 0.00 3.58
890 911 1.153489 CCACCGTCAGAGCCATGAG 60.153 63.158 0.00 0.00 0.00 2.90
891 912 1.812922 CACCGTCAGAGCCATGAGC 60.813 63.158 0.00 0.00 44.25 4.26
906 927 5.226396 GCCATGAGCTACTACAGTAGATTG 58.774 45.833 18.46 9.29 46.01 2.67
907 928 5.221342 GCCATGAGCTACTACAGTAGATTGT 60.221 44.000 18.46 4.28 46.01 2.71
908 929 6.016192 GCCATGAGCTACTACAGTAGATTGTA 60.016 42.308 18.46 5.44 46.01 2.41
913 934 9.053840 TGAGCTACTACAGTAGATTGTATACAC 57.946 37.037 18.46 0.00 46.01 2.90
927 1090 9.817809 AGATTGTATACACATTACAGTTACAGG 57.182 33.333 4.68 0.00 33.76 4.00
936 1099 5.178809 ACATTACAGTTACAGGAGCGTTTTC 59.821 40.000 0.00 0.00 0.00 2.29
1057 1221 0.745845 CTCTGCCTCCATTTCCACGG 60.746 60.000 0.00 0.00 0.00 4.94
1262 1703 2.194271 CTCCACGACTTCGCCTTTATC 58.806 52.381 0.00 0.00 44.43 1.75
1367 1808 3.119096 GACTTCGACGGCAAGGCC 61.119 66.667 0.00 0.00 46.75 5.19
1601 2042 0.830648 TTGGGGAGGATGATCGTGAC 59.169 55.000 0.00 0.00 0.00 3.67
1636 2077 3.672447 CAATGTGCTGGTGCGGCA 61.672 61.111 0.00 0.00 44.04 5.69
1733 2174 1.359848 CGGTGACCTACAATGCACTC 58.640 55.000 0.00 0.00 0.00 3.51
1847 2288 2.439156 GGATCCTTTGCGCAGGCT 60.439 61.111 11.31 0.00 40.82 4.58
1862 2303 2.596851 GGCTCTGTGCAAGGAGGGA 61.597 63.158 15.87 0.00 45.15 4.20
1887 2328 1.026182 GGGCGATGCACTTGACATGA 61.026 55.000 0.00 0.00 0.00 3.07
1894 2335 4.680567 CGATGCACTTGACATGATAGAGAG 59.319 45.833 0.00 0.00 0.00 3.20
1910 2351 6.268847 TGATAGAGAGGGAGGATTTTAAGCTC 59.731 42.308 0.00 0.00 0.00 4.09
1916 2357 3.369576 GGGAGGATTTTAAGCTCGACACT 60.370 47.826 0.00 0.00 0.00 3.55
1988 2429 3.084039 TGAGGCCATGTCATTTCTTCAC 58.916 45.455 5.01 0.00 0.00 3.18
2027 2468 5.278610 CTCGTATATCCCGAATGTGGTAACA 60.279 44.000 0.00 0.00 41.58 2.41
2117 2558 2.885135 TGATGACAGAGGGTTGCAAT 57.115 45.000 0.59 0.00 0.00 3.56
2315 2756 3.569701 TGTTGGATTTGGCAGAGAAAGTC 59.430 43.478 0.00 0.00 0.00 3.01
2339 2780 0.179936 AGGAGATGCTGGTTGCTAGC 59.820 55.000 8.10 8.10 43.37 3.42
2342 2783 0.747283 AGATGCTGGTTGCTAGCTGC 60.747 55.000 17.23 19.05 44.14 5.25
2798 3239 7.568861 GCCGTTACATATAGTGCACTAATTGAC 60.569 40.741 30.77 22.42 31.39 3.18
2811 3252 3.767673 ACTAATTGACGGCCTCTGTAAGA 59.232 43.478 0.00 0.00 43.69 2.10
2831 3272 1.218047 GGGCGAAATCCAAAAGGCC 59.782 57.895 0.00 0.00 40.27 5.19
3080 3521 5.942826 TGGTTTTTGCAAAGTTGGAGAAATT 59.057 32.000 12.41 0.00 35.66 1.82
3093 3534 5.682234 TGGAGAAATTGATAGTGCTCAGA 57.318 39.130 0.00 0.00 0.00 3.27
3184 3625 2.507471 GGATGTTCAAGGATGGGAGACT 59.493 50.000 0.00 0.00 0.00 3.24
3369 3810 6.875195 TGTTGTAACTTACACTGCCCTAATAC 59.125 38.462 0.82 0.00 38.63 1.89
3568 4009 3.809832 CCAAAGTATCTGCAAGGATACCG 59.190 47.826 17.88 9.97 45.29 4.02
3571 4012 2.434336 AGTATCTGCAAGGATACCGCAA 59.566 45.455 17.88 0.00 45.29 4.85
3658 4099 0.457851 GACACAGCACCGATAGCTCT 59.542 55.000 0.00 0.00 41.14 4.09
3745 4186 4.699257 GCACAAAGAGATGATGGAAGTCTT 59.301 41.667 0.00 0.00 0.00 3.01
4060 4501 4.126437 TGTTGTCAGGCACATAATATCCG 58.874 43.478 0.00 0.00 33.90 4.18
4199 4640 7.847096 TCAAACTGAAGAGCACCTGTAATATA 58.153 34.615 0.00 0.00 0.00 0.86
4303 4744 5.731591 AGATACCAAAGTTACTTTCGGGAG 58.268 41.667 17.53 3.80 30.60 4.30
4343 4784 7.021790 GCTTAGTTTGTTGCATAGTTTAGTCC 58.978 38.462 0.00 0.00 0.00 3.85
4640 5081 2.923121 CTACATGTATGGGTGCTGCTT 58.077 47.619 5.91 0.00 0.00 3.91
4770 5214 6.318900 GTCAATAGTGGCAGCTAATTTAGGTT 59.681 38.462 5.41 0.00 33.57 3.50
4972 5416 7.288810 ACAAAGAAATTTCACTGGCTATCAA 57.711 32.000 19.99 0.00 0.00 2.57
5003 5447 8.938883 AGTCTTTGTATATAAGATGGTGATGGT 58.061 33.333 4.25 0.00 34.42 3.55
5191 5718 1.733912 GCTCTGTGATCGCATGAACAA 59.266 47.619 9.87 0.00 0.00 2.83
5224 5751 0.537828 TCACCCTTTTGTTACCGGGC 60.538 55.000 6.32 0.00 40.45 6.13
5310 5837 6.903516 TCCATCATAGTGGAACATTTCATCT 58.096 36.000 0.00 0.00 45.03 2.90
5311 5838 6.769341 TCCATCATAGTGGAACATTTCATCTG 59.231 38.462 0.00 0.00 45.03 2.90
5409 5936 6.767902 TCTCAGCTTGTTTCTGACATTTAGTT 59.232 34.615 0.00 0.00 38.26 2.24
5536 6063 2.886862 TGCAACCAATTGTGTTGAGG 57.113 45.000 28.84 13.57 44.57 3.86
5633 6160 4.907269 TGGAGGCATATTCTATGTCAGGAA 59.093 41.667 1.99 0.00 0.00 3.36
5634 6161 5.012458 TGGAGGCATATTCTATGTCAGGAAG 59.988 44.000 1.99 0.00 0.00 3.46
5635 6162 4.904241 AGGCATATTCTATGTCAGGAAGC 58.096 43.478 1.99 0.00 0.00 3.86
5644 6171 2.502142 TGTCAGGAAGCAGCATCATT 57.498 45.000 0.00 0.00 0.00 2.57
5673 6325 1.802365 GGCTCAAAATTTGCCAAGCTG 59.198 47.619 14.65 0.00 45.46 4.24
5674 6326 1.196127 GCTCAAAATTTGCCAAGCTGC 59.804 47.619 9.70 0.00 0.00 5.25
5675 6327 2.485903 CTCAAAATTTGCCAAGCTGCA 58.514 42.857 1.02 0.00 40.07 4.41
5676 6328 3.071479 CTCAAAATTTGCCAAGCTGCAT 58.929 40.909 1.02 0.00 41.70 3.96
5677 6329 2.809119 TCAAAATTTGCCAAGCTGCATG 59.191 40.909 1.02 0.00 41.70 4.06
5678 6330 1.816074 AAATTTGCCAAGCTGCATGG 58.184 45.000 18.99 18.99 41.70 3.66
5679 6331 0.688487 AATTTGCCAAGCTGCATGGT 59.312 45.000 23.20 2.47 41.70 3.55
5680 6332 0.688487 ATTTGCCAAGCTGCATGGTT 59.312 45.000 23.20 5.56 41.70 3.67
5681 6333 0.469070 TTTGCCAAGCTGCATGGTTT 59.531 45.000 23.20 0.00 41.70 3.27
5682 6334 0.033781 TTGCCAAGCTGCATGGTTTC 59.966 50.000 23.20 9.06 41.70 2.78
5683 6335 0.828762 TGCCAAGCTGCATGGTTTCT 60.829 50.000 23.20 0.00 40.23 2.52
5684 6336 0.319405 GCCAAGCTGCATGGTTTCTT 59.681 50.000 23.20 0.00 40.23 2.52
5685 6337 1.270465 GCCAAGCTGCATGGTTTCTTT 60.270 47.619 23.20 0.00 40.23 2.52
5686 6338 2.409975 CCAAGCTGCATGGTTTCTTTG 58.590 47.619 15.42 0.96 33.63 2.77
5687 6339 2.036217 CCAAGCTGCATGGTTTCTTTGA 59.964 45.455 15.42 0.00 33.63 2.69
5688 6340 3.493002 CCAAGCTGCATGGTTTCTTTGAA 60.493 43.478 15.42 0.00 33.63 2.69
5689 6341 4.312443 CAAGCTGCATGGTTTCTTTGAAT 58.688 39.130 1.02 0.00 33.63 2.57
5690 6342 4.612264 AGCTGCATGGTTTCTTTGAATT 57.388 36.364 1.02 0.00 0.00 2.17
5691 6343 4.964593 AGCTGCATGGTTTCTTTGAATTT 58.035 34.783 1.02 0.00 0.00 1.82
5692 6344 5.370679 AGCTGCATGGTTTCTTTGAATTTT 58.629 33.333 1.02 0.00 0.00 1.82
5693 6345 5.824097 AGCTGCATGGTTTCTTTGAATTTTT 59.176 32.000 1.02 0.00 0.00 1.94
5694 6346 6.991531 AGCTGCATGGTTTCTTTGAATTTTTA 59.008 30.769 1.02 0.00 0.00 1.52
5695 6347 7.172019 AGCTGCATGGTTTCTTTGAATTTTTAG 59.828 33.333 1.02 0.00 0.00 1.85
5696 6348 7.171337 GCTGCATGGTTTCTTTGAATTTTTAGA 59.829 33.333 0.00 0.00 0.00 2.10
5697 6349 8.364129 TGCATGGTTTCTTTGAATTTTTAGAC 57.636 30.769 0.00 0.00 0.00 2.59
5698 6350 7.984050 TGCATGGTTTCTTTGAATTTTTAGACA 59.016 29.630 0.00 0.00 0.00 3.41
5699 6351 8.992073 GCATGGTTTCTTTGAATTTTTAGACAT 58.008 29.630 0.00 0.00 0.00 3.06
5751 6403 8.743085 ATGACTCAAGCAATATGTTTGTATCT 57.257 30.769 6.79 0.00 39.23 1.98
5752 6404 8.201554 TGACTCAAGCAATATGTTTGTATCTC 57.798 34.615 6.79 0.46 39.23 2.75
5753 6405 8.043113 TGACTCAAGCAATATGTTTGTATCTCT 58.957 33.333 6.79 0.00 39.23 3.10
5754 6406 8.206325 ACTCAAGCAATATGTTTGTATCTCTG 57.794 34.615 6.79 0.00 39.23 3.35
5755 6407 7.019774 TCAAGCAATATGTTTGTATCTCTGC 57.980 36.000 6.79 0.00 39.23 4.26
5756 6408 6.598850 TCAAGCAATATGTTTGTATCTCTGCA 59.401 34.615 6.79 0.00 39.23 4.41
5757 6409 6.369059 AGCAATATGTTTGTATCTCTGCAC 57.631 37.500 0.00 0.00 0.00 4.57
5758 6410 5.882000 AGCAATATGTTTGTATCTCTGCACA 59.118 36.000 0.00 0.00 0.00 4.57
5759 6411 6.544931 AGCAATATGTTTGTATCTCTGCACAT 59.455 34.615 0.00 0.00 0.00 3.21
5760 6412 6.854892 GCAATATGTTTGTATCTCTGCACATC 59.145 38.462 0.00 0.00 0.00 3.06
5761 6413 7.255035 GCAATATGTTTGTATCTCTGCACATCT 60.255 37.037 0.00 0.00 0.00 2.90
5762 6414 9.264719 CAATATGTTTGTATCTCTGCACATCTA 57.735 33.333 0.00 0.00 0.00 1.98
5766 6418 8.877808 TGTTTGTATCTCTGCACATCTATAAG 57.122 34.615 0.00 0.00 0.00 1.73
5767 6419 8.695456 TGTTTGTATCTCTGCACATCTATAAGA 58.305 33.333 0.00 0.00 0.00 2.10
5768 6420 9.534565 GTTTGTATCTCTGCACATCTATAAGAA 57.465 33.333 0.00 0.00 0.00 2.52
5796 6448 9.883142 ATATCTTATACCTTTTCTAGATGCAGC 57.117 33.333 0.00 0.00 0.00 5.25
5797 6449 7.366847 TCTTATACCTTTTCTAGATGCAGCT 57.633 36.000 10.44 10.44 0.00 4.24
5824 6476 6.201044 CCATATCCGAAGCACTAGTTACTTTG 59.799 42.308 12.84 12.84 0.00 2.77
6002 10562 5.654650 AGCATAGGAGGATGTGCTATAGTAC 59.345 44.000 13.52 13.52 44.66 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 5.793030 AGTAGGATCTCCAAGGAAATACG 57.207 43.478 0.00 0.00 38.89 3.06
40 41 6.374333 TCAGCTGTTGGAAATCTTTGGTATAC 59.626 38.462 14.67 0.00 0.00 1.47
49 50 4.282703 AGCATTTTCAGCTGTTGGAAATCT 59.717 37.500 14.67 11.44 42.02 2.40
50 51 4.563061 AGCATTTTCAGCTGTTGGAAATC 58.437 39.130 14.67 9.84 42.02 2.17
104 107 2.354704 CCCTGCGATTTGTACTCTGGAA 60.355 50.000 0.00 0.00 0.00 3.53
113 116 0.110486 AGTGTTCCCCTGCGATTTGT 59.890 50.000 0.00 0.00 0.00 2.83
120 123 0.037975 CATTGCAAGTGTTCCCCTGC 60.038 55.000 4.94 0.00 0.00 4.85
122 125 0.188342 ACCATTGCAAGTGTTCCCCT 59.812 50.000 4.94 0.00 0.00 4.79
123 126 1.000843 GAACCATTGCAAGTGTTCCCC 59.999 52.381 23.46 8.24 32.83 4.81
155 158 3.056607 ACCCACTTTAACATGCTTGATGC 60.057 43.478 6.60 0.00 43.25 3.91
160 163 5.596772 ACAGTTTACCCACTTTAACATGCTT 59.403 36.000 0.00 0.00 0.00 3.91
172 175 5.232463 TGTCGAAAGATACAGTTTACCCAC 58.768 41.667 0.00 0.00 45.19 4.61
176 179 6.248631 GCCATTGTCGAAAGATACAGTTTAC 58.751 40.000 0.00 0.00 45.19 2.01
179 182 3.370978 CGCCATTGTCGAAAGATACAGTT 59.629 43.478 0.00 0.00 45.19 3.16
181 184 2.930040 ACGCCATTGTCGAAAGATACAG 59.070 45.455 0.00 0.00 45.19 2.74
186 189 2.276201 CCATACGCCATTGTCGAAAGA 58.724 47.619 0.00 0.00 38.16 2.52
193 196 0.322456 ACAGTGCCATACGCCATTGT 60.322 50.000 0.00 0.00 36.24 2.71
196 199 1.031571 CCAACAGTGCCATACGCCAT 61.032 55.000 0.00 0.00 36.24 4.40
197 200 1.673993 CCAACAGTGCCATACGCCA 60.674 57.895 0.00 0.00 36.24 5.69
198 201 0.748005 ATCCAACAGTGCCATACGCC 60.748 55.000 0.00 0.00 36.24 5.68
200 203 1.299541 GGATCCAACAGTGCCATACG 58.700 55.000 6.95 0.00 0.00 3.06
206 209 3.081061 TGTTACATGGATCCAACAGTGC 58.919 45.455 20.67 14.35 0.00 4.40
209 212 3.127548 GCAGTGTTACATGGATCCAACAG 59.872 47.826 20.67 14.21 31.92 3.16
210 213 3.081061 GCAGTGTTACATGGATCCAACA 58.919 45.455 20.67 15.75 0.00 3.33
214 217 2.939103 GAGTGCAGTGTTACATGGATCC 59.061 50.000 4.20 4.20 0.00 3.36
215 218 2.939103 GGAGTGCAGTGTTACATGGATC 59.061 50.000 0.00 0.00 0.00 3.36
218 221 2.079158 CTGGAGTGCAGTGTTACATGG 58.921 52.381 0.00 0.00 0.00 3.66
223 226 2.632512 TCACATCTGGAGTGCAGTGTTA 59.367 45.455 11.78 4.67 36.93 2.41
238 241 9.703892 ATAGATAGCTACAAATTGAGTCACATC 57.296 33.333 0.00 0.00 0.00 3.06
311 315 1.244019 ATCGCTGTGGGGTTGCTTTC 61.244 55.000 0.00 0.00 0.00 2.62
313 317 0.827507 AAATCGCTGTGGGGTTGCTT 60.828 50.000 0.00 0.00 0.00 3.91
318 322 2.046314 CCGAAATCGCTGTGGGGT 60.046 61.111 0.00 0.00 38.18 4.95
367 371 2.897350 GGGGATAGTGTGCGCTGC 60.897 66.667 9.73 1.68 0.00 5.25
408 412 5.135508 AGTTCTTGTTGCGTGATAGTAGT 57.864 39.130 0.00 0.00 0.00 2.73
409 413 5.062308 GGAAGTTCTTGTTGCGTGATAGTAG 59.938 44.000 2.25 0.00 0.00 2.57
410 414 4.927425 GGAAGTTCTTGTTGCGTGATAGTA 59.073 41.667 2.25 0.00 0.00 1.82
437 441 7.763528 AGTGTTAGCAAATTCATTGTTTTGTCA 59.236 29.630 12.83 7.59 41.32 3.58
442 446 7.981225 AGTCAAGTGTTAGCAAATTCATTGTTT 59.019 29.630 0.00 0.00 41.32 2.83
515 527 3.008266 AGGCAAATCATGTTTTCCCCTTG 59.992 43.478 5.71 0.00 0.00 3.61
516 528 3.250617 AGGCAAATCATGTTTTCCCCTT 58.749 40.909 5.71 0.00 0.00 3.95
518 530 2.833943 AGAGGCAAATCATGTTTTCCCC 59.166 45.455 5.71 6.51 0.00 4.81
521 533 3.511146 TCCCAGAGGCAAATCATGTTTTC 59.489 43.478 0.00 0.00 0.00 2.29
545 560 3.356290 AGCACAGGTGAGTTTGAACTTT 58.644 40.909 3.10 0.00 39.88 2.66
612 628 3.109547 TTGTAGTTCGCGCGCCAG 61.110 61.111 27.95 13.23 0.00 4.85
623 639 2.714250 TGATTTCCTGGGTGGTTGTAGT 59.286 45.455 0.00 0.00 37.07 2.73
625 641 3.139397 ACTTGATTTCCTGGGTGGTTGTA 59.861 43.478 0.00 0.00 37.07 2.41
652 668 2.099652 TTGTCGACTCACCTGCCCTG 62.100 60.000 17.92 0.00 0.00 4.45
747 768 3.127721 CCTCGCTTCTTCCTTTTTCCATC 59.872 47.826 0.00 0.00 0.00 3.51
757 778 0.459411 GTCTCAGCCTCGCTTCTTCC 60.459 60.000 0.00 0.00 36.40 3.46
770 791 3.055167 TCCTCTCTCAGTCTCAGTCTCAG 60.055 52.174 0.00 0.00 0.00 3.35
771 792 2.909662 TCCTCTCTCAGTCTCAGTCTCA 59.090 50.000 0.00 0.00 0.00 3.27
772 793 3.627395 TCCTCTCTCAGTCTCAGTCTC 57.373 52.381 0.00 0.00 0.00 3.36
854 875 4.699522 GGCCCCGGTCACACAGAC 62.700 72.222 0.00 0.00 46.83 3.51
901 922 9.817809 CCTGTAACTGTAATGTGTATACAATCT 57.182 33.333 7.25 0.00 40.84 2.40
902 923 9.811995 TCCTGTAACTGTAATGTGTATACAATC 57.188 33.333 7.25 0.00 40.84 2.67
903 924 9.817809 CTCCTGTAACTGTAATGTGTATACAAT 57.182 33.333 7.25 1.19 40.84 2.71
904 925 7.762615 GCTCCTGTAACTGTAATGTGTATACAA 59.237 37.037 7.25 0.00 40.84 2.41
906 927 6.417044 CGCTCCTGTAACTGTAATGTGTATAC 59.583 42.308 0.00 0.00 0.00 1.47
907 928 6.095860 ACGCTCCTGTAACTGTAATGTGTATA 59.904 38.462 0.00 0.00 0.00 1.47
908 929 5.105473 ACGCTCCTGTAACTGTAATGTGTAT 60.105 40.000 0.00 0.00 0.00 2.29
911 932 3.585862 ACGCTCCTGTAACTGTAATGTG 58.414 45.455 0.00 0.00 0.00 3.21
913 934 5.408604 AGAAAACGCTCCTGTAACTGTAATG 59.591 40.000 0.00 0.00 0.00 1.90
927 1090 5.791974 GGTATTTCGGTAAAAGAAAACGCTC 59.208 40.000 0.00 0.00 40.44 5.03
936 1099 2.610833 GCGGAGGGTATTTCGGTAAAAG 59.389 50.000 0.00 0.00 0.00 2.27
1236 1677 1.507174 CGAAGTCGTGGAGGGAGAC 59.493 63.158 0.00 0.00 35.30 3.36
1312 1753 1.667154 CGCCTTGGAGATCAGGACGA 61.667 60.000 1.03 0.00 0.00 4.20
1481 1922 1.303317 GTGGCTGTAACCCACCTGG 60.303 63.158 0.00 0.00 45.51 4.45
1562 2003 0.753479 TCTCCCTAAGCAGCCTCTCG 60.753 60.000 0.00 0.00 0.00 4.04
1601 2042 2.806856 GAGCAATCTGCCGAGCACG 61.807 63.158 0.00 0.00 46.52 5.34
1670 2111 2.123632 AGCCTCCCAAGCTCCTCA 59.876 61.111 0.00 0.00 34.91 3.86
1733 2174 4.081030 CTCGCAAGCACCTGCACG 62.081 66.667 0.00 0.87 42.77 5.34
1754 2195 2.364186 CCCATTTCCACCTGCCCC 60.364 66.667 0.00 0.00 0.00 5.80
1778 2219 0.534412 CCGACATCTCCTTCTGCACT 59.466 55.000 0.00 0.00 0.00 4.40
1847 2288 1.407656 AACGTCCCTCCTTGCACAGA 61.408 55.000 0.00 0.00 0.00 3.41
1862 2303 3.842925 AAGTGCATCGCCCCAACGT 62.843 57.895 0.00 0.00 0.00 3.99
1887 2328 5.245075 CGAGCTTAAAATCCTCCCTCTCTAT 59.755 44.000 0.00 0.00 0.00 1.98
1894 2335 2.937149 GTGTCGAGCTTAAAATCCTCCC 59.063 50.000 0.00 0.00 0.00 4.30
1988 2429 2.743752 CGAGTTGCACCGCATCCTG 61.744 63.158 0.00 0.00 38.76 3.86
2027 2468 2.166829 CCTGAGAGCAGCGTCCTATAT 58.833 52.381 0.00 0.00 40.91 0.86
2117 2558 7.015487 AGTGAATTGAACAATGAAGGATTTGGA 59.985 33.333 0.69 0.00 0.00 3.53
2315 2756 1.804372 GCAACCAGCATCTCCTCGTAG 60.804 57.143 0.00 0.00 44.79 3.51
2339 2780 5.408604 AGTGTTAACCTTATTGAGAACGCAG 59.591 40.000 2.48 0.00 31.40 5.18
2342 2783 5.390567 GGCAGTGTTAACCTTATTGAGAACG 60.391 44.000 2.48 0.00 0.00 3.95
2798 3239 2.494918 CCCGTCTTACAGAGGCCG 59.505 66.667 0.00 0.00 0.00 6.13
2811 3252 1.873270 GCCTTTTGGATTTCGCCCGT 61.873 55.000 0.00 0.00 44.07 5.28
2831 3272 5.484173 TTAATTTGGCATAGACTTCGCAG 57.516 39.130 0.00 0.00 0.00 5.18
2945 3386 3.221771 AGCTTTGCACAAACCATCTACA 58.778 40.909 0.00 0.00 0.00 2.74
3080 3521 6.798427 AGAAATACCTTCTGAGCACTATCA 57.202 37.500 0.00 0.00 43.09 2.15
3093 3534 3.914426 AGTCATCCGCAGAAATACCTT 57.086 42.857 0.00 0.00 0.00 3.50
3184 3625 7.267128 AGACAAAACTTTCATTGCAAGATCAA 58.733 30.769 4.94 0.00 0.00 2.57
3239 3680 3.366985 CCATAGCTGTGTAAGTGACGACA 60.367 47.826 9.80 0.00 0.00 4.35
3369 3810 0.108138 CCAGCTTTCCCTAGTCCGTG 60.108 60.000 0.00 0.00 0.00 4.94
3568 4009 1.748493 TGAAACCCTGAACTGTGTTGC 59.252 47.619 0.00 0.00 0.00 4.17
3571 4012 1.064758 TGCTGAAACCCTGAACTGTGT 60.065 47.619 0.00 0.00 0.00 3.72
3602 4043 2.951642 CTCCAACAAACCAAGAGAAGCA 59.048 45.455 0.00 0.00 0.00 3.91
3658 4099 7.062322 ACTATCAATGAGCATCCCATAAACAA 58.938 34.615 0.00 0.00 0.00 2.83
3745 4186 3.498481 GCTGGCCATATTTAGGGATGACA 60.498 47.826 5.51 0.00 0.00 3.58
4028 4469 3.433615 GTGCCTGACAACAGTTCATCTAC 59.566 47.826 0.00 0.00 42.05 2.59
4199 4640 4.976540 AACTGTAGAGGCTGTTTAAGGT 57.023 40.909 0.00 0.00 0.00 3.50
4303 4744 8.451908 ACAAACTAAGCATTGGATATAACTCC 57.548 34.615 0.00 0.00 35.74 3.85
4640 5081 5.865085 TCAATCATCATGATCATCAGCAGA 58.135 37.500 4.86 0.00 35.76 4.26
4670 5114 2.691927 CTGCATGCAGTGTACTGAAGA 58.308 47.619 34.76 2.37 46.59 2.87
4770 5214 4.409718 TGTCACAGTTAAGCAGGTAACA 57.590 40.909 7.45 0.00 36.59 2.41
5003 5447 2.438021 ACCACCAGCAAGACTTCTGTAA 59.562 45.455 11.34 0.00 0.00 2.41
5120 5647 6.786959 AGAACATGAAGGAGCTAGAAGGATAT 59.213 38.462 0.00 0.00 0.00 1.63
5310 5837 8.783093 AGATATTTTGATGTCGAAACAGAAACA 58.217 29.630 0.00 0.00 39.20 2.83
5311 5838 9.055248 CAGATATTTTGATGTCGAAACAGAAAC 57.945 33.333 0.00 0.00 39.20 2.78
5409 5936 8.616942 TCTTCATACGAAAACAAATGAAACAGA 58.383 29.630 0.00 0.00 37.76 3.41
5523 6050 2.816087 CCCAGAGTCCTCAACACAATTG 59.184 50.000 3.24 3.24 0.00 2.32
5525 6052 2.338809 TCCCAGAGTCCTCAACACAAT 58.661 47.619 0.00 0.00 0.00 2.71
5536 6063 1.271597 ACATGCCAAGTTCCCAGAGTC 60.272 52.381 0.00 0.00 0.00 3.36
5633 6160 1.198408 CGTCAACACAATGATGCTGCT 59.802 47.619 0.00 0.00 30.20 4.24
5634 6161 1.609932 CGTCAACACAATGATGCTGC 58.390 50.000 0.00 0.00 30.20 5.25
5635 6162 1.730121 GCCGTCAACACAATGATGCTG 60.730 52.381 0.00 0.00 35.44 4.41
5644 6171 3.443037 CAAATTTTGAGCCGTCAACACA 58.557 40.909 2.88 0.00 42.60 3.72
5673 6325 8.364129 TGTCTAAAAATTCAAAGAAACCATGC 57.636 30.769 0.00 0.00 0.00 4.06
5725 6377 9.182214 AGATACAAACATATTGCTTGAGTCATT 57.818 29.630 0.00 0.00 28.90 2.57
5726 6378 8.743085 AGATACAAACATATTGCTTGAGTCAT 57.257 30.769 0.00 0.00 28.90 3.06
5727 6379 8.043113 AGAGATACAAACATATTGCTTGAGTCA 58.957 33.333 0.00 0.00 28.90 3.41
5728 6380 8.333908 CAGAGATACAAACATATTGCTTGAGTC 58.666 37.037 0.00 0.00 28.90 3.36
5729 6381 7.201679 GCAGAGATACAAACATATTGCTTGAGT 60.202 37.037 0.00 0.00 28.90 3.41
5730 6382 7.130917 GCAGAGATACAAACATATTGCTTGAG 58.869 38.462 0.00 0.00 28.90 3.02
5731 6383 6.598850 TGCAGAGATACAAACATATTGCTTGA 59.401 34.615 0.00 0.00 28.90 3.02
5732 6384 6.690098 GTGCAGAGATACAAACATATTGCTTG 59.310 38.462 0.00 0.00 30.36 4.01
5733 6385 6.375174 TGTGCAGAGATACAAACATATTGCTT 59.625 34.615 0.00 0.00 0.00 3.91
5734 6386 5.882000 TGTGCAGAGATACAAACATATTGCT 59.118 36.000 0.00 0.00 0.00 3.91
5735 6387 6.122850 TGTGCAGAGATACAAACATATTGC 57.877 37.500 0.00 0.00 0.00 3.56
5736 6388 8.151141 AGATGTGCAGAGATACAAACATATTG 57.849 34.615 0.00 0.00 0.00 1.90
5740 6392 9.486497 CTTATAGATGTGCAGAGATACAAACAT 57.514 33.333 0.00 0.00 0.00 2.71
5741 6393 8.695456 TCTTATAGATGTGCAGAGATACAAACA 58.305 33.333 0.00 0.00 0.00 2.83
5742 6394 9.534565 TTCTTATAGATGTGCAGAGATACAAAC 57.465 33.333 0.00 0.00 0.00 2.93
5770 6422 9.883142 GCTGCATCTAGAAAAGGTATAAGATAT 57.117 33.333 0.00 0.00 0.00 1.63
5771 6423 9.094578 AGCTGCATCTAGAAAAGGTATAAGATA 57.905 33.333 1.02 0.00 0.00 1.98
5772 6424 7.972301 AGCTGCATCTAGAAAAGGTATAAGAT 58.028 34.615 1.02 0.00 0.00 2.40
5773 6425 7.366847 AGCTGCATCTAGAAAAGGTATAAGA 57.633 36.000 1.02 0.00 0.00 2.10
5774 6426 7.600752 GGTAGCTGCATCTAGAAAAGGTATAAG 59.399 40.741 3.61 0.00 0.00 1.73
5775 6427 7.070696 TGGTAGCTGCATCTAGAAAAGGTATAA 59.929 37.037 3.61 4.72 0.00 0.98
5776 6428 6.553476 TGGTAGCTGCATCTAGAAAAGGTATA 59.447 38.462 3.61 5.48 0.00 1.47
5777 6429 5.366768 TGGTAGCTGCATCTAGAAAAGGTAT 59.633 40.000 3.61 0.00 0.00 2.73
5778 6430 4.714802 TGGTAGCTGCATCTAGAAAAGGTA 59.285 41.667 3.61 2.19 0.00 3.08
5779 6431 3.519510 TGGTAGCTGCATCTAGAAAAGGT 59.480 43.478 3.61 3.19 0.00 3.50
5780 6432 4.142609 TGGTAGCTGCATCTAGAAAAGG 57.857 45.455 3.61 0.00 0.00 3.11
5781 6433 6.593382 GGATATGGTAGCTGCATCTAGAAAAG 59.407 42.308 3.61 0.00 0.00 2.27
5782 6434 6.467677 GGATATGGTAGCTGCATCTAGAAAA 58.532 40.000 3.61 0.00 0.00 2.29
5783 6435 5.336770 CGGATATGGTAGCTGCATCTAGAAA 60.337 44.000 3.61 0.00 0.00 2.52
5784 6436 4.158579 CGGATATGGTAGCTGCATCTAGAA 59.841 45.833 3.61 0.00 0.00 2.10
5785 6437 3.696548 CGGATATGGTAGCTGCATCTAGA 59.303 47.826 3.61 0.00 0.00 2.43
5786 6438 3.696548 TCGGATATGGTAGCTGCATCTAG 59.303 47.826 3.61 0.00 0.00 2.43
5787 6439 3.697166 TCGGATATGGTAGCTGCATCTA 58.303 45.455 3.61 0.00 0.00 1.98
5788 6440 2.529632 TCGGATATGGTAGCTGCATCT 58.470 47.619 3.61 0.00 0.00 2.90
5789 6441 3.257393 CTTCGGATATGGTAGCTGCATC 58.743 50.000 3.61 0.00 0.00 3.91
5790 6442 2.613977 GCTTCGGATATGGTAGCTGCAT 60.614 50.000 3.61 0.00 0.00 3.96
5791 6443 1.270305 GCTTCGGATATGGTAGCTGCA 60.270 52.381 3.61 0.00 0.00 4.41
5792 6444 1.270305 TGCTTCGGATATGGTAGCTGC 60.270 52.381 0.00 0.00 33.15 5.25
5793 6445 2.036475 AGTGCTTCGGATATGGTAGCTG 59.964 50.000 0.00 0.00 33.15 4.24
5794 6446 2.320781 AGTGCTTCGGATATGGTAGCT 58.679 47.619 0.00 0.00 33.15 3.32
5795 6447 2.821991 AGTGCTTCGGATATGGTAGC 57.178 50.000 0.00 0.00 0.00 3.58
5796 6448 5.455056 AACTAGTGCTTCGGATATGGTAG 57.545 43.478 0.00 0.00 0.00 3.18
5797 6449 6.066690 AGTAACTAGTGCTTCGGATATGGTA 58.933 40.000 0.00 0.00 0.00 3.25
5824 6476 6.073657 TCCAAATACTAACGCAAACACAGTAC 60.074 38.462 0.00 0.00 0.00 2.73
6002 10562 7.976175 GCAAGGTATCCTCTTTCCAATAAAAAG 59.024 37.037 0.00 0.00 35.49 2.27


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

AutoCloner maintained by Alex Coulton.