Multiple sequence alignment - TraesCS2B01G007500

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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 TraesCS2B01G007500 chr2B 100.000 2930 0 0 1 2930 4641754 4644683 0 5411
1 TraesCS2B01G007500 chr2B 82.200 2000 329 22 935 2925 727685996 727687977 0 1696
2 TraesCS2B01G007500 chr2D 90.657 2130 180 12 810 2930 7969941 7972060 0 2813
3 TraesCS2B01G007500 chr2D 88.291 1785 161 22 52 1819 8276531 8278284 0 2095
4 TraesCS2B01G007500 chr2D 82.350 2000 328 21 935 2925 598814038 598816021 0 1714
5 TraesCS2B01G007500 chrUn 90.427 2131 183 14 810 2930 11753812 11751693 0 2785
6 TraesCS2B01G007500 chr2A 82.473 2054 333 24 887 2930 733087692 733089728 0 1773
7 TraesCS2B01G007500 chr7D 82.473 2014 329 21 904 2913 20442389 20444382 0 1742
8 TraesCS2B01G007500 chr7D 82.517 2002 331 19 935 2930 555196430 555194442 0 1740
9 TraesCS2B01G007500 chr7D 82.217 1985 332 14 953 2930 20404284 20406254 0 1690
10 TraesCS2B01G007500 chr7B 81.936 2004 336 25 936 2930 601114429 601116415 0 1672


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 TraesCS2B01G007500 chr2B 4641754 4644683 2929 False 5411 5411 100.000 1 2930 1 chr2B.!!$F1 2929
1 TraesCS2B01G007500 chr2B 727685996 727687977 1981 False 1696 1696 82.200 935 2925 1 chr2B.!!$F2 1990
2 TraesCS2B01G007500 chr2D 7969941 7972060 2119 False 2813 2813 90.657 810 2930 1 chr2D.!!$F1 2120
3 TraesCS2B01G007500 chr2D 8276531 8278284 1753 False 2095 2095 88.291 52 1819 1 chr2D.!!$F2 1767
4 TraesCS2B01G007500 chr2D 598814038 598816021 1983 False 1714 1714 82.350 935 2925 1 chr2D.!!$F3 1990
5 TraesCS2B01G007500 chrUn 11751693 11753812 2119 True 2785 2785 90.427 810 2930 1 chrUn.!!$R1 2120
6 TraesCS2B01G007500 chr2A 733087692 733089728 2036 False 1773 1773 82.473 887 2930 1 chr2A.!!$F1 2043
7 TraesCS2B01G007500 chr7D 20442389 20444382 1993 False 1742 1742 82.473 904 2913 1 chr7D.!!$F2 2009
8 TraesCS2B01G007500 chr7D 555194442 555196430 1988 True 1740 1740 82.517 935 2930 1 chr7D.!!$R1 1995
9 TraesCS2B01G007500 chr7D 20404284 20406254 1970 False 1690 1690 82.217 953 2930 1 chr7D.!!$F1 1977
10 TraesCS2B01G007500 chr7B 601114429 601116415 1986 False 1672 1672 81.936 936 2930 1 chr7B.!!$F1 1994

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
111 112 0.036577 CTCACCTTCACCTCAGCCTG 60.037 60.0 0.00 0.0 0.00 4.85 F
255 263 0.311165 ACGATAGCACCGATTCCTCG 59.689 55.0 0.00 0.0 42.20 4.63 F
864 883 2.036958 TGGCACGTGCTTGCTATTAT 57.963 45.0 36.84 0.0 42.56 1.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1287 1309 0.837272 ACCCAGTATCATGTTCCCGG 59.163 55.000 0.0 0.0 0.0 5.73 R
1569 1591 1.351017 ACATCGTCACTTCCCAACCAT 59.649 47.619 0.0 0.0 0.0 3.55 R
2607 2629 1.062428 ACCAATCTCCGTCCATCCCTA 60.062 52.381 0.0 0.0 0.0 3.53 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
20 21 3.166489 GGTACCTCTGACAAATCCGAG 57.834 52.381 4.06 0.00 36.28 4.63
21 22 2.758979 GGTACCTCTGACAAATCCGAGA 59.241 50.000 4.06 0.00 38.19 4.04
22 23 3.194968 GGTACCTCTGACAAATCCGAGAA 59.805 47.826 4.06 0.00 38.19 2.87
23 24 3.601443 ACCTCTGACAAATCCGAGAAG 57.399 47.619 0.00 0.00 38.19 2.85
24 25 3.165875 ACCTCTGACAAATCCGAGAAGA 58.834 45.455 0.00 0.00 38.19 2.87
25 26 3.056465 ACCTCTGACAAATCCGAGAAGAC 60.056 47.826 0.00 0.00 38.19 3.01
26 27 3.194542 CCTCTGACAAATCCGAGAAGACT 59.805 47.826 0.00 0.00 38.19 3.24
27 28 4.172505 CTCTGACAAATCCGAGAAGACTG 58.827 47.826 0.00 0.00 38.19 3.51
28 29 2.670414 CTGACAAATCCGAGAAGACTGC 59.330 50.000 0.00 0.00 0.00 4.40
29 30 1.656095 GACAAATCCGAGAAGACTGCG 59.344 52.381 0.00 0.00 0.00 5.18
30 31 1.272490 ACAAATCCGAGAAGACTGCGA 59.728 47.619 0.00 0.00 0.00 5.10
31 32 2.288825 ACAAATCCGAGAAGACTGCGAA 60.289 45.455 0.00 0.00 0.00 4.70
32 33 2.285827 AATCCGAGAAGACTGCGAAG 57.714 50.000 0.00 0.00 0.00 3.79
33 34 1.178276 ATCCGAGAAGACTGCGAAGT 58.822 50.000 0.00 0.00 0.00 3.01
34 35 0.522180 TCCGAGAAGACTGCGAAGTC 59.478 55.000 16.38 16.38 39.00 3.01
35 36 0.794981 CCGAGAAGACTGCGAAGTCG 60.795 60.000 17.99 6.25 43.15 4.18
36 37 0.166161 CGAGAAGACTGCGAAGTCGA 59.834 55.000 17.99 0.00 43.15 4.20
37 38 1.608822 GAGAAGACTGCGAAGTCGAC 58.391 55.000 17.99 15.05 43.15 4.20
38 39 0.110147 AGAAGACTGCGAAGTCGACG 60.110 55.000 17.99 0.00 43.15 5.12
39 40 0.385723 GAAGACTGCGAAGTCGACGT 60.386 55.000 17.99 6.85 43.15 4.34
40 41 0.660595 AAGACTGCGAAGTCGACGTG 60.661 55.000 17.99 4.48 43.15 4.49
41 42 1.370172 GACTGCGAAGTCGACGTGT 60.370 57.895 8.06 0.00 43.02 4.49
42 43 1.328685 GACTGCGAAGTCGACGTGTC 61.329 60.000 8.06 6.34 43.02 3.67
43 44 2.050714 TGCGAAGTCGACGTGTCC 60.051 61.111 9.23 4.08 43.02 4.02
44 45 2.804090 GCGAAGTCGACGTGTCCC 60.804 66.667 9.23 0.00 43.02 4.46
45 46 2.952245 CGAAGTCGACGTGTCCCT 59.048 61.111 9.23 0.00 43.02 4.20
46 47 1.285023 CGAAGTCGACGTGTCCCTT 59.715 57.895 9.23 0.00 43.02 3.95
47 48 0.728466 CGAAGTCGACGTGTCCCTTC 60.728 60.000 9.23 5.08 43.02 3.46
48 49 0.597072 GAAGTCGACGTGTCCCTTCT 59.403 55.000 9.23 0.00 34.18 2.85
49 50 0.597072 AAGTCGACGTGTCCCTTCTC 59.403 55.000 10.46 0.00 0.00 2.87
50 51 1.212229 GTCGACGTGTCCCTTCTCC 59.788 63.158 0.00 0.00 0.00 3.71
68 69 2.873288 GCTTCGCCTCCTGCAAAG 59.127 61.111 0.00 0.00 41.33 2.77
69 70 1.968540 GCTTCGCCTCCTGCAAAGT 60.969 57.895 0.00 0.00 41.33 2.66
102 103 1.623542 ATACCCCGCCTCACCTTCAC 61.624 60.000 0.00 0.00 0.00 3.18
107 108 1.079543 CGCCTCACCTTCACCTCAG 60.080 63.158 0.00 0.00 0.00 3.35
110 111 1.197430 CCTCACCTTCACCTCAGCCT 61.197 60.000 0.00 0.00 0.00 4.58
111 112 0.036577 CTCACCTTCACCTCAGCCTG 60.037 60.000 0.00 0.00 0.00 4.85
112 113 0.764369 TCACCTTCACCTCAGCCTGT 60.764 55.000 0.00 0.00 0.00 4.00
121 122 3.596066 CTCAGCCTGTCACCCGTGG 62.596 68.421 0.00 0.00 0.00 4.94
125 126 4.248842 CCTGTCACCCGTGGCACA 62.249 66.667 19.09 0.00 40.71 4.57
126 127 2.666190 CTGTCACCCGTGGCACAG 60.666 66.667 19.09 10.77 40.71 3.66
148 156 4.468153 AGGAGAAGGTAGGATCTTGTGTTC 59.532 45.833 0.00 0.00 0.00 3.18
156 164 3.960571 AGGATCTTGTGTTCCCATTCTG 58.039 45.455 0.00 0.00 33.59 3.02
160 168 5.011023 GGATCTTGTGTTCCCATTCTGTTTT 59.989 40.000 0.00 0.00 0.00 2.43
171 179 6.077322 TCCCATTCTGTTTTGAAAGAAGGAT 58.923 36.000 0.00 0.00 36.55 3.24
172 180 7.237982 TCCCATTCTGTTTTGAAAGAAGGATA 58.762 34.615 0.00 0.00 36.55 2.59
173 181 7.895429 TCCCATTCTGTTTTGAAAGAAGGATAT 59.105 33.333 0.00 0.00 36.55 1.63
202 210 6.326375 ACTCTAGCTAGTTGTTGAAATCTCG 58.674 40.000 20.10 0.00 0.00 4.04
211 219 9.831737 CTAGTTGTTGAAATCTCGAATTTTGAT 57.168 29.630 6.91 0.00 0.00 2.57
224 232 6.184068 TCGAATTTTGATGGTTGATTCCCTA 58.816 36.000 0.00 0.00 0.00 3.53
225 233 6.661377 TCGAATTTTGATGGTTGATTCCCTAA 59.339 34.615 0.00 0.00 0.00 2.69
235 243 6.252233 TGGTTGATTCCCTAATGATGTTGAA 58.748 36.000 0.00 0.00 0.00 2.69
237 245 7.035612 GGTTGATTCCCTAATGATGTTGAAAC 58.964 38.462 0.00 0.00 0.00 2.78
255 263 0.311165 ACGATAGCACCGATTCCTCG 59.689 55.000 0.00 0.00 42.20 4.63
274 282 4.702131 CCTCGGAATTTCACCTTCAAATCT 59.298 41.667 0.00 0.00 0.00 2.40
275 283 5.163713 CCTCGGAATTTCACCTTCAAATCTC 60.164 44.000 0.00 0.00 0.00 2.75
276 284 4.700213 TCGGAATTTCACCTTCAAATCTCC 59.300 41.667 0.00 0.00 0.00 3.71
277 285 4.142381 CGGAATTTCACCTTCAAATCTCCC 60.142 45.833 0.00 0.00 0.00 4.30
280 288 6.095580 GGAATTTCACCTTCAAATCTCCCTAC 59.904 42.308 0.00 0.00 0.00 3.18
285 293 5.104776 TCACCTTCAAATCTCCCTACTCATG 60.105 44.000 0.00 0.00 0.00 3.07
294 302 4.965814 TCTCCCTACTCATGCATCAATTC 58.034 43.478 0.00 0.00 0.00 2.17
352 360 5.284079 AGCACATGATTTGTTGAGTGTTTC 58.716 37.500 0.00 0.00 36.00 2.78
400 408 9.500785 GATCAAAATTAGAAACCCAATCCAAAA 57.499 29.630 0.00 0.00 0.00 2.44
407 415 2.857186 ACCCAATCCAAAACCAATGC 57.143 45.000 0.00 0.00 0.00 3.56
416 424 5.752036 TCCAAAACCAATGCCATCAATTA 57.248 34.783 0.00 0.00 0.00 1.40
438 446 5.975988 AAATGAGAGGCTACCAATCCTAA 57.024 39.130 0.00 0.00 31.71 2.69
447 455 4.503469 GGCTACCAATCCTAAGGAGCTTAC 60.503 50.000 0.00 0.00 34.05 2.34
487 499 2.216898 GCAGTAGTCCCATGAAGATGC 58.783 52.381 0.00 0.00 0.00 3.91
500 512 8.946085 TCCCATGAAGATGCGAATAATTAATAC 58.054 33.333 0.00 0.00 0.00 1.89
544 556 6.785191 ACTACGGATTCATTAGCATTTGTTG 58.215 36.000 0.00 0.00 0.00 3.33
554 566 2.114616 AGCATTTGTTGTGGGGAACAA 58.885 42.857 0.00 0.00 46.66 2.83
568 580 7.846066 TGTGGGGAACAAATTAATTAGGATTG 58.154 34.615 0.01 0.00 35.24 2.67
583 595 8.930846 AATTAGGATTGATTACAGATGGAAGG 57.069 34.615 0.00 0.00 0.00 3.46
600 612 3.756963 GGAAGGACAAATCTACCACAACC 59.243 47.826 0.00 0.00 0.00 3.77
603 619 3.394606 AGGACAAATCTACCACAACCAGT 59.605 43.478 0.00 0.00 0.00 4.00
610 626 4.431416 TCTACCACAACCAGTCATTGTT 57.569 40.909 0.00 0.00 38.22 2.83
619 635 7.807907 CCACAACCAGTCATTGTTAGAAAATAC 59.192 37.037 0.00 0.00 38.22 1.89
633 649 9.896263 TGTTAGAAAATACGAAATTACCAAACC 57.104 29.630 0.00 0.00 0.00 3.27
643 659 5.321927 GAAATTACCAAACCCTCCTTGAGA 58.678 41.667 0.00 0.00 0.00 3.27
660 676 3.020984 TGAGACAAACTTTGGGTCCAAC 58.979 45.455 1.33 0.00 35.46 3.77
661 677 3.020984 GAGACAAACTTTGGGTCCAACA 58.979 45.455 1.33 0.00 35.46 3.33
662 678 3.636764 GAGACAAACTTTGGGTCCAACAT 59.363 43.478 1.33 0.00 35.46 2.71
663 679 4.798882 AGACAAACTTTGGGTCCAACATA 58.201 39.130 1.33 0.00 35.46 2.29
664 680 5.205056 AGACAAACTTTGGGTCCAACATAA 58.795 37.500 1.33 0.00 35.46 1.90
665 681 5.838521 AGACAAACTTTGGGTCCAACATAAT 59.161 36.000 1.33 0.00 35.46 1.28
666 682 6.326323 AGACAAACTTTGGGTCCAACATAATT 59.674 34.615 1.33 0.00 35.46 1.40
667 683 7.507616 AGACAAACTTTGGGTCCAACATAATTA 59.492 33.333 1.33 0.00 35.46 1.40
668 684 7.438564 ACAAACTTTGGGTCCAACATAATTAC 58.561 34.615 1.33 0.00 35.46 1.89
669 685 7.289084 ACAAACTTTGGGTCCAACATAATTACT 59.711 33.333 1.33 0.00 35.46 2.24
670 686 8.798402 CAAACTTTGGGTCCAACATAATTACTA 58.202 33.333 1.33 0.00 35.46 1.82
671 687 9.541884 AAACTTTGGGTCCAACATAATTACTAT 57.458 29.630 1.33 0.00 35.46 2.12
672 688 9.541884 AACTTTGGGTCCAACATAATTACTATT 57.458 29.630 1.33 0.00 35.46 1.73
673 689 8.966868 ACTTTGGGTCCAACATAATTACTATTG 58.033 33.333 1.33 0.00 35.46 1.90
674 690 7.889873 TTGGGTCCAACATAATTACTATTGG 57.110 36.000 14.16 14.16 41.04 3.16
675 691 7.214460 TGGGTCCAACATAATTACTATTGGA 57.786 36.000 17.17 17.17 45.07 3.53
799 815 6.775629 TGAAGTAAGAGGGTTGCTTAATTTGT 59.224 34.615 0.00 0.00 36.59 2.83
833 849 7.203218 ACTTAATTTCACTTTTCAGCTGTTCC 58.797 34.615 14.67 0.00 0.00 3.62
838 854 2.099592 CACTTTTCAGCTGTTCCTGCAA 59.900 45.455 14.67 0.00 32.87 4.08
850 869 2.307934 TCCTGCAAAGTTTTTGGCAC 57.692 45.000 3.97 0.00 38.32 5.01
864 883 2.036958 TGGCACGTGCTTGCTATTAT 57.963 45.000 36.84 0.00 42.56 1.28
865 884 2.364632 TGGCACGTGCTTGCTATTATT 58.635 42.857 36.84 0.00 42.56 1.40
906 925 7.707104 AGTTAAATTAATGCAGCTATCGCTTT 58.293 30.769 0.00 0.00 46.47 3.51
957 978 2.785857 AGGAAAATATGCACCTAGGCCT 59.214 45.455 11.78 11.78 0.00 5.19
1014 1035 7.530426 AGAGAAAGTAATGGCTGAAATTGTT 57.470 32.000 0.00 0.00 0.00 2.83
1040 1062 8.378565 TCTTCTTCTAGTCATTGAAAAGATGGT 58.621 33.333 10.21 0.00 0.00 3.55
1048 1070 4.035091 TCATTGAAAAGATGGTAATCGCCG 59.965 41.667 0.00 0.00 37.92 6.46
1287 1309 5.237344 GGATGAGTACATGTATCAAGTTGGC 59.763 44.000 9.18 0.00 36.82 4.52
1314 1336 3.347216 ACATGATACTGGGTGTTGCTTC 58.653 45.455 0.00 0.00 0.00 3.86
1423 1445 3.244665 TGCACACCTGTCAGAGATGAAAT 60.245 43.478 0.00 0.00 0.00 2.17
1569 1591 7.581213 TGAAAATAGAGGAAAACTTGAGCAA 57.419 32.000 0.00 0.00 0.00 3.91
1629 1651 0.846015 TGATAGGAATGGGTGGGCTG 59.154 55.000 0.00 0.00 0.00 4.85
1647 1669 1.340889 CTGGGCAAAACAGCTTTAGCA 59.659 47.619 4.33 0.00 45.16 3.49
1800 1822 2.093890 TCAAACATTGCAGCGATGGAT 58.906 42.857 24.17 11.59 30.00 3.41
1830 1852 3.688673 GCCTTGAAGAGACATTGAAGAGG 59.311 47.826 0.00 0.00 0.00 3.69
1927 1949 6.362248 AGGTCACTTGTTTGTAATGGTAAGT 58.638 36.000 0.00 0.00 0.00 2.24
2323 2345 1.266989 GTTGTTTCCTGTACTGCAGCC 59.733 52.381 15.27 5.21 43.71 4.85
2346 2368 8.332487 AGCCTATTTCCAGAAGACTATCTTTTT 58.668 33.333 0.00 0.00 36.73 1.94
2348 2370 8.821894 CCTATTTCCAGAAGACTATCTTTTTCG 58.178 37.037 0.00 0.00 36.73 3.46
2357 2379 8.070769 AGAAGACTATCTTTTTCGCAGAAAAAC 58.929 33.333 18.62 11.61 38.28 2.43
2358 2380 7.497925 AGACTATCTTTTTCGCAGAAAAACT 57.502 32.000 18.62 13.00 45.90 2.66
2405 2427 0.544357 TTCATCGTGGAGAGGGGTGT 60.544 55.000 0.00 0.00 0.00 4.16
2433 2455 4.042187 ACATTAGAAGAAGTGGCAGAAGGT 59.958 41.667 0.00 0.00 0.00 3.50
2457 2479 4.351874 TCTGAAGGAGTTGGTTAACAGG 57.648 45.455 8.10 0.00 39.30 4.00
2476 2498 4.275936 ACAGGAACATGCTACAACTTGTTC 59.724 41.667 12.36 12.36 46.26 3.18
2478 2500 2.969443 ACATGCTACAACTTGTTCGC 57.031 45.000 0.00 4.57 0.00 4.70
2485 2507 3.667960 GCTACAACTTGTTCGCAGGAATG 60.668 47.826 0.00 0.00 34.05 2.67
2556 2578 2.397549 GCAGTTGATTTGTGCCAGAAC 58.602 47.619 0.00 0.00 0.00 3.01
2557 2579 2.035066 GCAGTTGATTTGTGCCAGAACT 59.965 45.455 0.00 0.00 0.00 3.01
2573 2595 6.548441 CCAGAACTATCGTTTTGGTGTTAA 57.452 37.500 10.59 0.00 45.54 2.01
2576 2598 7.749126 CCAGAACTATCGTTTTGGTGTTAAATC 59.251 37.037 10.59 0.00 45.54 2.17
2584 2606 6.488683 TCGTTTTGGTGTTAAATCTGAGGATT 59.511 34.615 0.00 0.00 43.26 3.01
2599 2621 4.886163 TGAGGATTATATATGCGGGGGTA 58.114 43.478 0.00 0.00 0.00 3.69
2607 2629 2.097110 TATGCGGGGGTACTCTTCAT 57.903 50.000 0.00 0.00 0.00 2.57
2619 2641 2.320781 ACTCTTCATAGGGATGGACGG 58.679 52.381 0.00 0.00 33.49 4.79
2620 2642 2.091278 ACTCTTCATAGGGATGGACGGA 60.091 50.000 0.00 0.00 33.49 4.69
2655 2677 8.462016 GTGCACAAACTAAAGAAGGATATTCAT 58.538 33.333 13.17 0.00 0.00 2.57
2715 2737 0.387622 CACTGGACAAAAGCATGCCG 60.388 55.000 15.66 3.07 0.00 5.69
2716 2738 1.444895 CTGGACAAAAGCATGCCGC 60.445 57.895 15.66 0.00 42.91 6.53
2721 2743 0.894141 ACAAAAGCATGCCGCCATTA 59.106 45.000 15.66 0.00 44.04 1.90
2724 2746 0.175531 AAAGCATGCCGCCATTAACC 59.824 50.000 15.66 0.00 44.04 2.85
2727 2749 1.735360 CATGCCGCCATTAACCCTG 59.265 57.895 0.00 0.00 0.00 4.45
2737 2759 3.135895 GCCATTAACCCTGCTACCTCTAA 59.864 47.826 0.00 0.00 0.00 2.10
2748 2770 6.667414 CCCTGCTACCTCTAATATCTGAGAAT 59.333 42.308 6.52 0.00 32.44 2.40
2802 2824 3.193903 GCCTACCTATCGAGAAGATTCCC 59.806 52.174 0.00 0.00 40.66 3.97
2861 2883 2.669391 GCTTGCGGGATTCAAAAGTGAG 60.669 50.000 0.00 0.00 34.49 3.51
2863 2885 1.202879 TGCGGGATTCAAAAGTGAGGT 60.203 47.619 0.00 0.00 34.49 3.85
2864 2886 2.039216 TGCGGGATTCAAAAGTGAGGTA 59.961 45.455 0.00 0.00 34.49 3.08
2871 2893 5.339200 GGATTCAAAAGTGAGGTATCTCCCA 60.339 44.000 0.00 0.00 39.23 4.37
2877 2899 4.779993 AGTGAGGTATCTCCCAAAATCC 57.220 45.455 0.00 0.00 39.23 3.01
2880 2902 5.066593 GTGAGGTATCTCCCAAAATCCATC 58.933 45.833 0.00 0.00 39.23 3.51
2891 2913 4.082026 CCCAAAATCCATCGAGAAGCTTTT 60.082 41.667 0.00 0.00 0.00 2.27
2896 2918 5.747951 ATCCATCGAGAAGCTTTTGAATC 57.252 39.130 0.00 0.00 0.00 2.52
2913 2935 3.244215 TGAATCTGTTGACACTGGACCTC 60.244 47.826 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.758979 TCTCGGATTTGTCAGAGGTACC 59.241 50.000 2.73 2.73 33.71 3.34
1 2 4.158025 TCTTCTCGGATTTGTCAGAGGTAC 59.842 45.833 5.90 0.00 33.71 3.34
4 5 3.194542 AGTCTTCTCGGATTTGTCAGAGG 59.805 47.826 5.90 0.00 33.71 3.69
5 6 4.172505 CAGTCTTCTCGGATTTGTCAGAG 58.827 47.826 0.07 0.07 34.09 3.35
6 7 3.615110 GCAGTCTTCTCGGATTTGTCAGA 60.615 47.826 0.00 0.00 0.00 3.27
7 8 2.670414 GCAGTCTTCTCGGATTTGTCAG 59.330 50.000 0.00 0.00 0.00 3.51
8 9 2.688507 GCAGTCTTCTCGGATTTGTCA 58.311 47.619 0.00 0.00 0.00 3.58
9 10 1.656095 CGCAGTCTTCTCGGATTTGTC 59.344 52.381 0.00 0.00 0.00 3.18
10 11 1.272490 TCGCAGTCTTCTCGGATTTGT 59.728 47.619 0.00 0.00 0.00 2.83
11 12 1.996292 TCGCAGTCTTCTCGGATTTG 58.004 50.000 0.00 0.00 0.00 2.32
12 13 2.028930 ACTTCGCAGTCTTCTCGGATTT 60.029 45.455 0.00 0.00 0.00 2.17
13 14 1.546476 ACTTCGCAGTCTTCTCGGATT 59.454 47.619 0.00 0.00 0.00 3.01
14 15 1.133407 GACTTCGCAGTCTTCTCGGAT 59.867 52.381 8.03 0.00 45.54 4.18
15 16 0.522180 GACTTCGCAGTCTTCTCGGA 59.478 55.000 8.03 0.00 45.54 4.55
16 17 0.794981 CGACTTCGCAGTCTTCTCGG 60.795 60.000 13.31 0.00 46.67 4.63
17 18 0.166161 TCGACTTCGCAGTCTTCTCG 59.834 55.000 13.31 0.42 46.67 4.04
18 19 1.608822 GTCGACTTCGCAGTCTTCTC 58.391 55.000 13.31 0.00 46.67 2.87
19 20 0.110147 CGTCGACTTCGCAGTCTTCT 60.110 55.000 14.70 0.00 46.67 2.85
20 21 0.385723 ACGTCGACTTCGCAGTCTTC 60.386 55.000 14.70 5.27 46.67 2.87
21 22 0.660595 CACGTCGACTTCGCAGTCTT 60.661 55.000 14.70 0.00 46.67 3.01
22 23 1.082038 CACGTCGACTTCGCAGTCT 60.082 57.895 14.70 0.00 46.67 3.24
23 24 1.328685 GACACGTCGACTTCGCAGTC 61.329 60.000 14.70 5.02 45.54 3.51
24 25 1.370172 GACACGTCGACTTCGCAGT 60.370 57.895 14.70 3.27 39.60 4.40
25 26 2.081212 GGACACGTCGACTTCGCAG 61.081 63.158 14.70 0.00 39.60 5.18
26 27 2.050714 GGACACGTCGACTTCGCA 60.051 61.111 14.70 0.00 39.60 5.10
27 28 2.744307 AAGGGACACGTCGACTTCGC 62.744 60.000 14.70 14.38 39.60 4.70
28 29 0.728466 GAAGGGACACGTCGACTTCG 60.728 60.000 14.70 2.83 35.85 3.79
29 30 0.597072 AGAAGGGACACGTCGACTTC 59.403 55.000 14.70 18.18 40.95 3.01
30 31 0.597072 GAGAAGGGACACGTCGACTT 59.403 55.000 14.70 0.03 32.45 3.01
31 32 1.242665 GGAGAAGGGACACGTCGACT 61.243 60.000 14.70 0.00 32.45 4.18
32 33 1.212229 GGAGAAGGGACACGTCGAC 59.788 63.158 5.18 5.18 32.45 4.20
33 34 2.330372 CGGAGAAGGGACACGTCGA 61.330 63.158 0.00 0.00 32.45 4.20
34 35 2.178521 CGGAGAAGGGACACGTCG 59.821 66.667 0.00 0.00 32.45 5.12
35 36 2.126031 GCGGAGAAGGGACACGTC 60.126 66.667 0.00 0.00 0.00 4.34
36 37 2.156051 GAAGCGGAGAAGGGACACGT 62.156 60.000 0.00 0.00 0.00 4.49
37 38 1.446272 GAAGCGGAGAAGGGACACG 60.446 63.158 0.00 0.00 0.00 4.49
38 39 1.446272 CGAAGCGGAGAAGGGACAC 60.446 63.158 0.00 0.00 0.00 3.67
39 40 2.970639 CGAAGCGGAGAAGGGACA 59.029 61.111 0.00 0.00 0.00 4.02
102 103 3.314331 ACGGGTGACAGGCTGAGG 61.314 66.667 23.66 5.66 0.00 3.86
110 111 4.248842 CCTGTGCCACGGGTGACA 62.249 66.667 14.90 0.00 39.82 3.58
111 112 3.883744 CTCCTGTGCCACGGGTGAC 62.884 68.421 21.86 0.00 45.01 3.67
112 113 3.625897 CTCCTGTGCCACGGGTGA 61.626 66.667 21.86 3.21 45.01 4.02
121 122 2.393646 AGATCCTACCTTCTCCTGTGC 58.606 52.381 0.00 0.00 0.00 4.57
122 123 3.772025 ACAAGATCCTACCTTCTCCTGTG 59.228 47.826 0.00 0.00 0.00 3.66
123 124 3.772025 CACAAGATCCTACCTTCTCCTGT 59.228 47.826 0.00 0.00 0.00 4.00
125 126 4.067944 ACACAAGATCCTACCTTCTCCT 57.932 45.455 0.00 0.00 0.00 3.69
126 127 4.383226 GGAACACAAGATCCTACCTTCTCC 60.383 50.000 0.00 0.00 34.10 3.71
128 129 3.519913 GGGAACACAAGATCCTACCTTCT 59.480 47.826 0.00 0.00 36.94 2.85
129 130 3.263425 TGGGAACACAAGATCCTACCTTC 59.737 47.826 0.00 0.00 36.94 3.46
148 156 5.789643 TCCTTCTTTCAAAACAGAATGGG 57.210 39.130 0.00 0.00 43.62 4.00
202 210 8.477256 TCATTAGGGAATCAACCATCAAAATTC 58.523 33.333 0.00 0.00 0.00 2.17
211 219 5.825532 TCAACATCATTAGGGAATCAACCA 58.174 37.500 0.00 0.00 0.00 3.67
224 232 4.201812 CGGTGCTATCGTTTCAACATCATT 60.202 41.667 0.00 0.00 0.00 2.57
225 233 3.309682 CGGTGCTATCGTTTCAACATCAT 59.690 43.478 0.00 0.00 0.00 2.45
235 243 1.269102 CGAGGAATCGGTGCTATCGTT 60.269 52.381 0.00 0.00 0.00 3.85
237 245 3.093566 CGAGGAATCGGTGCTATCG 57.906 57.895 0.00 0.00 0.00 2.92
255 263 5.019470 AGGGAGATTTGAAGGTGAAATTCC 58.981 41.667 0.00 0.00 0.00 3.01
256 264 6.887002 AGTAGGGAGATTTGAAGGTGAAATTC 59.113 38.462 0.00 0.00 0.00 2.17
262 270 4.826274 TGAGTAGGGAGATTTGAAGGTG 57.174 45.455 0.00 0.00 0.00 4.00
274 282 3.387699 TCGAATTGATGCATGAGTAGGGA 59.612 43.478 2.46 0.00 0.00 4.20
275 283 3.732212 TCGAATTGATGCATGAGTAGGG 58.268 45.455 2.46 0.00 0.00 3.53
276 284 5.936686 AATCGAATTGATGCATGAGTAGG 57.063 39.130 2.46 0.00 37.39 3.18
277 285 9.888878 ATTAAAATCGAATTGATGCATGAGTAG 57.111 29.630 2.46 0.00 37.39 2.57
285 293 9.624697 TGGCTATAATTAAAATCGAATTGATGC 57.375 29.630 0.00 0.00 37.39 3.91
306 314 7.612244 TGCTAATTAACAGGTTAAATGTGGCTA 59.388 33.333 8.53 1.69 38.38 3.93
309 317 7.598278 TGTGCTAATTAACAGGTTAAATGTGG 58.402 34.615 8.53 2.04 38.38 4.17
368 376 8.980143 TTGGGTTTCTAATTTTGATCGAATTC 57.020 30.769 9.39 0.00 0.00 2.17
400 408 6.183360 CCTCTCATTTAATTGATGGCATTGGT 60.183 38.462 0.00 0.00 0.00 3.67
407 415 6.064060 TGGTAGCCTCTCATTTAATTGATGG 58.936 40.000 11.85 11.85 0.00 3.51
416 424 5.163152 CCTTAGGATTGGTAGCCTCTCATTT 60.163 44.000 0.00 0.00 40.03 2.32
438 446 7.101054 CGAGTCTACTATATCAGTAAGCTCCT 58.899 42.308 0.00 0.00 39.28 3.69
447 455 6.730175 ACTGCAAACGAGTCTACTATATCAG 58.270 40.000 0.00 0.00 0.00 2.90
524 536 4.799949 CCACAACAAATGCTAATGAATCCG 59.200 41.667 0.00 0.00 0.00 4.18
525 537 5.111293 CCCACAACAAATGCTAATGAATCC 58.889 41.667 0.00 0.00 0.00 3.01
544 556 8.073467 TCAATCCTAATTAATTTGTTCCCCAC 57.927 34.615 5.91 0.00 0.00 4.61
566 578 7.405292 AGATTTGTCCTTCCATCTGTAATCAA 58.595 34.615 0.00 0.00 0.00 2.57
568 580 7.442666 GGTAGATTTGTCCTTCCATCTGTAATC 59.557 40.741 0.00 0.00 0.00 1.75
583 595 4.385825 TGACTGGTTGTGGTAGATTTGTC 58.614 43.478 0.00 0.00 0.00 3.18
610 626 8.866970 AGGGTTTGGTAATTTCGTATTTTCTA 57.133 30.769 0.00 0.00 0.00 2.10
619 635 4.076394 TCAAGGAGGGTTTGGTAATTTCG 58.924 43.478 0.00 0.00 0.00 3.46
633 649 2.887152 CCCAAAGTTTGTCTCAAGGAGG 59.113 50.000 14.36 1.61 0.00 4.30
643 659 6.493189 AATTATGTTGGACCCAAAGTTTGT 57.507 33.333 14.36 0.00 37.70 2.83
670 686 9.312904 CCAATAGTAATTATGGTTGGATCCAAT 57.687 33.333 29.37 16.59 41.09 3.16
671 687 8.506921 TCCAATAGTAATTATGGTTGGATCCAA 58.493 33.333 23.63 23.63 39.92 3.53
672 688 8.051468 TCCAATAGTAATTATGGTTGGATCCA 57.949 34.615 11.44 11.44 39.92 3.41
676 692 8.723365 ACTGATCCAATAGTAATTATGGTTGGA 58.277 33.333 20.90 20.90 46.25 3.53
677 693 8.924511 ACTGATCCAATAGTAATTATGGTTGG 57.075 34.615 14.64 14.64 37.91 3.77
771 787 9.700831 AAATTAAGCAACCCTCTTACTTCATAT 57.299 29.630 0.00 0.00 0.00 1.78
778 794 6.349363 CCTCACAAATTAAGCAACCCTCTTAC 60.349 42.308 0.00 0.00 0.00 2.34
799 815 9.621629 TGAAAAGTGAAATTAAGTAGAACCTCA 57.378 29.630 0.00 0.00 0.00 3.86
833 849 1.324134 CACGTGCCAAAAACTTTGCAG 59.676 47.619 0.82 0.00 33.80 4.41
838 854 1.639280 CAAGCACGTGCCAAAAACTT 58.361 45.000 35.51 19.18 43.38 2.66
899 918 5.180117 GTGACCATCTGCATAATAAAGCGAT 59.820 40.000 0.00 0.00 0.00 4.58
906 925 6.209589 GTCTCTAGGTGACCATCTGCATAATA 59.790 42.308 3.63 0.00 0.00 0.98
957 978 0.478072 ATGCCTCACTGTTGGTTGGA 59.522 50.000 0.00 0.00 0.00 3.53
1014 1035 8.378565 ACCATCTTTTCAATGACTAGAAGAAGA 58.621 33.333 0.00 0.00 31.79 2.87
1040 1062 2.479837 CTCCATTTGCTACGGCGATTA 58.520 47.619 16.62 0.00 42.25 1.75
1048 1070 3.119388 TGATTTGCTGCTCCATTTGCTAC 60.119 43.478 0.00 0.00 0.00 3.58
1287 1309 0.837272 ACCCAGTATCATGTTCCCGG 59.163 55.000 0.00 0.00 0.00 5.73
1314 1336 5.422214 TTCTAAGCCCTTTCTTCAGGTAG 57.578 43.478 0.00 0.00 30.96 3.18
1569 1591 1.351017 ACATCGTCACTTCCCAACCAT 59.649 47.619 0.00 0.00 0.00 3.55
1629 1651 2.029110 TGATGCTAAAGCTGTTTTGCCC 60.029 45.455 3.26 0.00 41.90 5.36
1647 1669 9.653516 TCTCTCTCTTTCCTATAGACATTTGAT 57.346 33.333 0.00 0.00 0.00 2.57
1753 1775 7.286546 TGGACCACTGACTTCATTTTTGAATAA 59.713 33.333 0.00 0.00 0.00 1.40
1762 1784 4.371624 TTGATGGACCACTGACTTCATT 57.628 40.909 0.00 0.00 0.00 2.57
1765 1787 3.476552 TGTTTGATGGACCACTGACTTC 58.523 45.455 0.00 0.00 0.00 3.01
1800 1822 4.890158 TGTCTCTTCAAGGCTTGTGATA 57.110 40.909 25.39 14.67 0.00 2.15
1927 1949 6.402442 CGTGTTGTGATTATCAATCTGCTTCA 60.402 38.462 0.00 0.00 38.72 3.02
2323 2345 8.331742 GCGAAAAAGATAGTCTTCTGGAAATAG 58.668 37.037 0.00 0.00 35.27 1.73
2346 2368 2.798283 CCGTACAAGAGTTTTTCTGCGA 59.202 45.455 0.00 0.00 35.91 5.10
2348 2370 4.547406 AACCGTACAAGAGTTTTTCTGC 57.453 40.909 0.00 0.00 35.91 4.26
2357 2379 2.805845 CCGTCCATAACCGTACAAGAG 58.194 52.381 0.00 0.00 0.00 2.85
2358 2380 1.135024 GCCGTCCATAACCGTACAAGA 60.135 52.381 0.00 0.00 0.00 3.02
2405 2427 4.905429 TGCCACTTCTTCTAATGTGCTTA 58.095 39.130 0.00 0.00 0.00 3.09
2433 2455 6.271391 TCCTGTTAACCAACTCCTTCAGATAA 59.729 38.462 2.48 0.00 35.56 1.75
2457 2479 3.226347 GCGAACAAGTTGTAGCATGTTC 58.774 45.455 23.37 10.36 45.04 3.18
2478 2500 4.209538 TCATCCTACCAAATGCATTCCTG 58.790 43.478 13.38 8.28 0.00 3.86
2485 2507 6.866480 TGAATCTTTTCATCCTACCAAATGC 58.134 36.000 0.00 0.00 36.94 3.56
2556 2578 7.333423 TCCTCAGATTTAACACCAAAACGATAG 59.667 37.037 0.00 0.00 46.19 2.08
2557 2579 7.162761 TCCTCAGATTTAACACCAAAACGATA 58.837 34.615 0.00 0.00 0.00 2.92
2573 2595 5.072329 CCCCCGCATATATAATCCTCAGATT 59.928 44.000 0.00 0.00 44.95 2.40
2576 2598 3.711704 ACCCCCGCATATATAATCCTCAG 59.288 47.826 0.00 0.00 0.00 3.35
2584 2606 4.938028 TGAAGAGTACCCCCGCATATATA 58.062 43.478 0.00 0.00 0.00 0.86
2588 2610 2.097110 ATGAAGAGTACCCCCGCATA 57.903 50.000 0.00 0.00 0.00 3.14
2592 2614 1.133262 TCCCTATGAAGAGTACCCCCG 60.133 57.143 0.00 0.00 0.00 5.73
2599 2621 2.091278 TCCGTCCATCCCTATGAAGAGT 60.091 50.000 0.00 0.00 34.84 3.24
2607 2629 1.062428 ACCAATCTCCGTCCATCCCTA 60.062 52.381 0.00 0.00 0.00 3.53
2619 2641 6.426937 TCTTTAGTTTGTGCACTACCAATCTC 59.573 38.462 19.41 0.00 0.00 2.75
2620 2642 6.296026 TCTTTAGTTTGTGCACTACCAATCT 58.704 36.000 19.41 10.44 0.00 2.40
2655 2677 7.994911 AGTCCATGTATGCTAGAAAATGAATGA 59.005 33.333 0.00 0.00 0.00 2.57
2658 2680 7.011389 CGAAGTCCATGTATGCTAGAAAATGAA 59.989 37.037 0.00 0.00 0.00 2.57
2715 2737 1.490910 AGAGGTAGCAGGGTTAATGGC 59.509 52.381 0.00 0.00 0.00 4.40
2716 2738 5.568620 ATTAGAGGTAGCAGGGTTAATGG 57.431 43.478 0.00 0.00 0.00 3.16
2721 2743 5.716979 TCAGATATTAGAGGTAGCAGGGTT 58.283 41.667 0.00 0.00 0.00 4.11
2724 2746 7.716799 ATTCTCAGATATTAGAGGTAGCAGG 57.283 40.000 0.00 0.00 32.76 4.85
2727 2749 9.638239 CTTGAATTCTCAGATATTAGAGGTAGC 57.362 37.037 7.05 0.00 31.69 3.58
2777 2799 2.865079 TCTTCTCGATAGGTAGGCCAG 58.135 52.381 5.01 0.00 37.19 4.85
2802 2824 8.562892 AGATTAAAAAGATCACCAATAGCATCG 58.437 33.333 0.00 0.00 0.00 3.84
2861 2883 4.040461 TCTCGATGGATTTTGGGAGATACC 59.960 45.833 0.00 0.00 38.08 2.73
2863 2885 5.743130 GCTTCTCGATGGATTTTGGGAGATA 60.743 44.000 0.00 0.00 31.33 1.98
2864 2886 4.712476 CTTCTCGATGGATTTTGGGAGAT 58.288 43.478 0.00 0.00 31.33 2.75
2871 2893 5.964958 TCAAAAGCTTCTCGATGGATTTT 57.035 34.783 0.00 0.00 0.00 1.82
2877 2899 5.542616 ACAGATTCAAAAGCTTCTCGATG 57.457 39.130 0.00 0.00 0.00 3.84
2880 2902 5.142962 GTCAACAGATTCAAAAGCTTCTCG 58.857 41.667 0.00 0.00 0.00 4.04
2891 2913 2.705658 AGGTCCAGTGTCAACAGATTCA 59.294 45.455 0.00 0.00 0.00 2.57
2896 2918 1.414181 ACAGAGGTCCAGTGTCAACAG 59.586 52.381 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.