Multiple sequence alignment - TraesCS1D01G230900

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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 TraesCS1D01G230900 chr1D 100.000 2738 0 0 1 2738 319428516 319431253 0.000000e+00 5057.0
1 TraesCS1D01G230900 chr1B 92.810 1377 51 21 669 2000 432116381 432117754 0.000000e+00 1951.0
2 TraesCS1D01G230900 chr1B 88.514 592 26 16 82 638 432115796 432116380 0.000000e+00 678.0
3 TraesCS1D01G230900 chr1A 88.754 907 58 15 1199 2068 403831074 403830175 0.000000e+00 1070.0
4 TraesCS1D01G230900 chr1A 92.327 391 17 7 714 1094 403831496 403831109 6.670000e-151 544.0
5 TraesCS1D01G230900 chr1A 93.567 342 13 3 299 638 403831865 403831531 4.070000e-138 501.0
6 TraesCS1D01G230900 chr1A 89.394 66 6 1 242 306 403835514 403835449 6.280000e-12 82.4
7 TraesCS1D01G230900 chr2D 94.808 520 13 3 2220 2738 413772462 413772968 0.000000e+00 798.0
8 TraesCS1D01G230900 chr2D 97.222 144 4 0 2077 2220 413772346 413772489 7.570000e-61 244.0
9 TraesCS1D01G230900 chr2D 82.781 151 25 1 2589 2738 109706739 109706889 1.710000e-27 134.0
10 TraesCS1D01G230900 chr2D 87.826 115 11 3 2221 2332 109707278 109707164 6.150000e-27 132.0
11 TraesCS1D01G230900 chr2D 86.275 102 7 5 2275 2369 220669397 220669296 1.340000e-18 104.0
12 TraesCS1D01G230900 chr5A 86.081 467 29 12 2078 2541 568325068 568324635 1.150000e-128 470.0
13 TraesCS1D01G230900 chr5A 92.021 188 15 0 2550 2737 568324539 568324352 5.810000e-67 265.0
14 TraesCS1D01G230900 chr4D 93.056 144 10 0 2077 2220 119418241 119418384 7.680000e-51 211.0
15 TraesCS1D01G230900 chr4D 90.780 141 13 0 2078 2218 193873000 193872860 3.600000e-44 189.0
16 TraesCS1D01G230900 chr4D 81.250 160 20 9 2221 2375 430880353 430880199 1.330000e-23 121.0
17 TraesCS1D01G230900 chr7D 92.308 143 11 0 2078 2220 450264512 450264370 1.290000e-48 204.0
18 TraesCS1D01G230900 chr7D 91.608 143 11 1 2078 2220 575812762 575812903 2.150000e-46 196.0
19 TraesCS1D01G230900 chr7D 87.500 88 8 3 2246 2332 548207064 548206979 6.240000e-17 99.0
20 TraesCS1D01G230900 chr3D 92.754 138 10 0 2083 2220 498427244 498427107 1.660000e-47 200.0
21 TraesCS1D01G230900 chr3D 90.476 147 14 0 2074 2220 268049605 268049459 7.740000e-46 195.0
22 TraesCS1D01G230900 chr3D 84.028 144 17 3 2596 2738 566074412 566074274 1.710000e-27 134.0
23 TraesCS1D01G230900 chr3D 82.353 170 15 13 2221 2375 582738440 582738271 1.710000e-27 134.0
24 TraesCS1D01G230900 chr5D 91.608 143 12 0 2077 2219 495074957 495075099 5.980000e-47 198.0
25 TraesCS1D01G230900 chr5D 74.310 580 83 42 2221 2738 362041290 362040715 4.660000e-43 185.0
26 TraesCS1D01G230900 chr6B 89.404 151 15 1 2069 2219 5068220 5068071 3.600000e-44 189.0
27 TraesCS1D01G230900 chr6B 83.212 137 18 5 2236 2369 519728707 519728573 1.330000e-23 121.0
28 TraesCS1D01G230900 chr6D 84.106 151 23 1 2589 2738 255525248 255525098 7.900000e-31 145.0
29 TraesCS1D01G230900 chr6D 81.646 158 19 9 2222 2374 446510635 446510483 3.700000e-24 122.0
30 TraesCS1D01G230900 chr3B 89.320 103 8 2 2222 2322 637609241 637609140 2.860000e-25 126.0
31 TraesCS1D01G230900 chr3B 80.337 178 20 9 2562 2738 754619236 754619073 1.330000e-23 121.0


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 TraesCS1D01G230900 chr1D 319428516 319431253 2737 False 5057.00 5057 100.0000 1 2738 1 chr1D.!!$F1 2737
1 TraesCS1D01G230900 chr1B 432115796 432117754 1958 False 1314.50 1951 90.6620 82 2000 2 chr1B.!!$F1 1918
2 TraesCS1D01G230900 chr1A 403830175 403835514 5339 True 549.35 1070 91.0105 242 2068 4 chr1A.!!$R1 1826
3 TraesCS1D01G230900 chr2D 413772346 413772968 622 False 521.00 798 96.0150 2077 2738 2 chr2D.!!$F2 661
4 TraesCS1D01G230900 chr5A 568324352 568325068 716 True 367.50 470 89.0510 2078 2737 2 chr5A.!!$R1 659

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
649 4279 0.536006 GACACTTGAGCAAGCCCACT 60.536 55.0 9.99 0.0 41.99 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2242 5939 0.039035 GGCCCACCTGTCATAAACCA 59.961 55.0 0.0 0.0 0.0 3.67 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
22 23 5.470047 AGTATCCGGATTCCTTATGTGTC 57.530 43.478 24.71 0.00 0.00 3.67
23 24 4.899457 AGTATCCGGATTCCTTATGTGTCA 59.101 41.667 24.71 0.00 0.00 3.58
24 25 3.536956 TCCGGATTCCTTATGTGTCAC 57.463 47.619 0.00 0.00 0.00 3.67
25 26 2.169769 TCCGGATTCCTTATGTGTCACC 59.830 50.000 0.00 0.00 0.00 4.02
26 27 2.201732 CGGATTCCTTATGTGTCACCG 58.798 52.381 0.00 0.00 0.00 4.94
27 28 2.418197 CGGATTCCTTATGTGTCACCGT 60.418 50.000 0.00 0.00 34.39 4.83
28 29 3.606687 GGATTCCTTATGTGTCACCGTT 58.393 45.455 0.00 0.00 0.00 4.44
29 30 4.007659 GGATTCCTTATGTGTCACCGTTT 58.992 43.478 0.00 0.00 0.00 3.60
30 31 4.457949 GGATTCCTTATGTGTCACCGTTTT 59.542 41.667 0.00 0.00 0.00 2.43
31 32 5.048294 GGATTCCTTATGTGTCACCGTTTTT 60.048 40.000 0.00 0.00 0.00 1.94
32 33 4.822036 TCCTTATGTGTCACCGTTTTTG 57.178 40.909 0.00 0.00 0.00 2.44
33 34 4.452825 TCCTTATGTGTCACCGTTTTTGA 58.547 39.130 0.00 0.00 0.00 2.69
34 35 4.513692 TCCTTATGTGTCACCGTTTTTGAG 59.486 41.667 0.00 0.00 0.00 3.02
35 36 4.513692 CCTTATGTGTCACCGTTTTTGAGA 59.486 41.667 0.00 0.00 0.00 3.27
36 37 5.334105 CCTTATGTGTCACCGTTTTTGAGAG 60.334 44.000 0.00 0.00 0.00 3.20
37 38 1.668751 TGTGTCACCGTTTTTGAGAGC 59.331 47.619 0.00 0.00 0.00 4.09
38 39 1.940613 GTGTCACCGTTTTTGAGAGCT 59.059 47.619 0.00 0.00 0.00 4.09
39 40 3.128349 GTGTCACCGTTTTTGAGAGCTA 58.872 45.455 0.00 0.00 0.00 3.32
40 41 3.558418 GTGTCACCGTTTTTGAGAGCTAA 59.442 43.478 0.00 0.00 0.00 3.09
41 42 4.034742 GTGTCACCGTTTTTGAGAGCTAAA 59.965 41.667 0.00 0.00 0.00 1.85
42 43 4.819630 TGTCACCGTTTTTGAGAGCTAAAT 59.180 37.500 0.00 0.00 0.00 1.40
43 44 5.992829 TGTCACCGTTTTTGAGAGCTAAATA 59.007 36.000 0.00 0.00 0.00 1.40
44 45 6.653320 TGTCACCGTTTTTGAGAGCTAAATAT 59.347 34.615 0.00 0.00 0.00 1.28
45 46 7.174253 TGTCACCGTTTTTGAGAGCTAAATATT 59.826 33.333 0.00 0.00 0.00 1.28
46 47 8.021396 GTCACCGTTTTTGAGAGCTAAATATTT 58.979 33.333 5.89 5.89 0.00 1.40
47 48 8.573035 TCACCGTTTTTGAGAGCTAAATATTTT 58.427 29.630 5.91 0.00 0.00 1.82
48 49 8.850452 CACCGTTTTTGAGAGCTAAATATTTTC 58.150 33.333 5.91 0.00 0.00 2.29
49 50 8.027189 ACCGTTTTTGAGAGCTAAATATTTTCC 58.973 33.333 5.91 0.00 0.00 3.13
50 51 7.488150 CCGTTTTTGAGAGCTAAATATTTTCCC 59.512 37.037 5.91 0.00 0.00 3.97
51 52 8.026607 CGTTTTTGAGAGCTAAATATTTTCCCA 58.973 33.333 5.91 0.00 0.00 4.37
52 53 9.705290 GTTTTTGAGAGCTAAATATTTTCCCAA 57.295 29.630 5.91 0.00 0.00 4.12
54 55 9.874205 TTTTGAGAGCTAAATATTTTCCCAATG 57.126 29.630 5.91 0.00 0.00 2.82
55 56 7.587037 TGAGAGCTAAATATTTTCCCAATGG 57.413 36.000 5.91 0.00 0.00 3.16
56 57 6.040842 TGAGAGCTAAATATTTTCCCAATGGC 59.959 38.462 5.91 0.00 0.00 4.40
57 58 5.898972 AGAGCTAAATATTTTCCCAATGGCA 59.101 36.000 5.91 0.00 0.00 4.92
58 59 6.383726 AGAGCTAAATATTTTCCCAATGGCAA 59.616 34.615 5.91 0.00 0.00 4.52
59 60 6.956497 AGCTAAATATTTTCCCAATGGCAAA 58.044 32.000 5.91 0.00 31.18 3.68
60 61 7.401246 AGCTAAATATTTTCCCAATGGCAAAA 58.599 30.769 3.30 3.30 30.39 2.44
61 62 7.336679 AGCTAAATATTTTCCCAATGGCAAAAC 59.663 33.333 2.82 0.00 30.39 2.43
62 63 7.120432 GCTAAATATTTTCCCAATGGCAAAACA 59.880 33.333 2.82 0.00 30.39 2.83
63 64 6.816134 AATATTTTCCCAATGGCAAAACAC 57.184 33.333 2.82 0.00 30.39 3.32
64 65 3.922171 TTTTCCCAATGGCAAAACACT 57.078 38.095 0.00 0.00 0.00 3.55
65 66 3.467374 TTTCCCAATGGCAAAACACTC 57.533 42.857 0.00 0.00 0.00 3.51
66 67 2.079170 TCCCAATGGCAAAACACTCA 57.921 45.000 0.00 0.00 0.00 3.41
67 68 1.962807 TCCCAATGGCAAAACACTCAG 59.037 47.619 0.00 0.00 0.00 3.35
68 69 1.606224 CCCAATGGCAAAACACTCAGC 60.606 52.381 0.00 0.00 0.00 4.26
69 70 1.068895 CCAATGGCAAAACACTCAGCA 59.931 47.619 0.00 0.00 0.00 4.41
70 71 2.483363 CCAATGGCAAAACACTCAGCAA 60.483 45.455 0.00 0.00 0.00 3.91
71 72 2.798283 CAATGGCAAAACACTCAGCAAG 59.202 45.455 0.00 0.00 0.00 4.01
72 73 1.761449 TGGCAAAACACTCAGCAAGA 58.239 45.000 0.00 0.00 0.00 3.02
73 74 2.098614 TGGCAAAACACTCAGCAAGAA 58.901 42.857 0.00 0.00 0.00 2.52
74 75 2.099592 TGGCAAAACACTCAGCAAGAAG 59.900 45.455 0.00 0.00 0.00 2.85
75 76 2.544486 GGCAAAACACTCAGCAAGAAGG 60.544 50.000 0.00 0.00 0.00 3.46
76 77 2.735823 CAAAACACTCAGCAAGAAGGC 58.264 47.619 0.00 0.00 0.00 4.35
77 78 0.947244 AAACACTCAGCAAGAAGGCG 59.053 50.000 0.00 0.00 39.27 5.52
78 79 0.886490 AACACTCAGCAAGAAGGCGG 60.886 55.000 0.00 0.00 39.27 6.13
79 80 2.359230 ACTCAGCAAGAAGGCGGC 60.359 61.111 0.00 0.00 39.27 6.53
80 81 3.494336 CTCAGCAAGAAGGCGGCG 61.494 66.667 0.51 0.51 39.27 6.46
178 188 7.273381 GCAAATAATGTCGTTTATGAACTTGCT 59.727 33.333 10.48 0.00 33.20 3.91
186 196 5.579511 TCGTTTATGAACTTGCTAGGTTAGC 59.420 40.000 0.00 1.21 41.61 3.09
216 227 6.928979 TTTTGTCGACTTCTGATTGGTTTA 57.071 33.333 17.92 0.00 0.00 2.01
222 233 5.408604 TCGACTTCTGATTGGTTTAAGAAGC 59.591 40.000 10.39 4.24 46.22 3.86
225 236 5.474876 ACTTCTGATTGGTTTAAGAAGCCTG 59.525 40.000 10.39 0.00 46.22 4.85
235 246 4.672587 TTAAGAAGCCTGTGAGCGATAT 57.327 40.909 0.00 0.00 38.01 1.63
269 305 5.623264 TGATGAATAAAGCGTTTCGTGTTTG 59.377 36.000 0.00 0.00 0.00 2.93
287 323 5.854338 GTGTTTGAAAAAGACAGAACGTGAA 59.146 36.000 0.00 0.00 0.00 3.18
372 4000 2.282462 AGCTTCAGCAAACCGGGG 60.282 61.111 6.32 0.00 45.16 5.73
373 4001 4.056125 GCTTCAGCAAACCGGGGC 62.056 66.667 6.32 6.66 41.59 5.80
374 4002 3.737172 CTTCAGCAAACCGGGGCG 61.737 66.667 6.32 3.65 34.54 6.13
402 4030 2.030958 GCGTACCCACCGTTTCCTG 61.031 63.158 0.00 0.00 0.00 3.86
458 4086 1.952133 CGACGCGACTTTTCACCCA 60.952 57.895 15.93 0.00 0.00 4.51
638 4268 3.923864 ACCCGCTGCGACACTTGA 61.924 61.111 25.45 0.00 0.00 3.02
639 4269 3.114616 CCCGCTGCGACACTTGAG 61.115 66.667 25.45 3.47 0.00 3.02
640 4270 3.782244 CCGCTGCGACACTTGAGC 61.782 66.667 25.45 0.00 0.00 4.26
641 4271 3.037833 CGCTGCGACACTTGAGCA 61.038 61.111 18.66 4.62 39.25 4.26
642 4272 2.597713 CGCTGCGACACTTGAGCAA 61.598 57.895 18.66 0.00 40.63 3.91
643 4273 1.206072 GCTGCGACACTTGAGCAAG 59.794 57.895 8.60 8.60 40.63 4.01
644 4274 1.206072 CTGCGACACTTGAGCAAGC 59.794 57.895 9.99 0.00 41.99 4.01
645 4275 2.180131 CTGCGACACTTGAGCAAGCC 62.180 60.000 9.99 0.08 41.99 4.35
646 4276 2.970974 GCGACACTTGAGCAAGCCC 61.971 63.158 9.99 0.00 41.99 5.19
647 4277 1.597854 CGACACTTGAGCAAGCCCA 60.598 57.895 9.99 0.00 41.99 5.36
648 4278 1.845809 CGACACTTGAGCAAGCCCAC 61.846 60.000 9.99 0.10 41.99 4.61
649 4279 0.536006 GACACTTGAGCAAGCCCACT 60.536 55.000 9.99 0.00 41.99 4.00
650 4280 0.820891 ACACTTGAGCAAGCCCACTG 60.821 55.000 9.99 3.66 41.99 3.66
651 4281 1.228367 ACTTGAGCAAGCCCACTGG 60.228 57.895 9.99 0.00 41.99 4.00
662 4292 1.078426 CCCACTGGCCTAAACCTCG 60.078 63.158 3.32 0.00 0.00 4.63
663 4293 1.550130 CCCACTGGCCTAAACCTCGA 61.550 60.000 3.32 0.00 0.00 4.04
664 4294 0.541863 CCACTGGCCTAAACCTCGAT 59.458 55.000 3.32 0.00 0.00 3.59
665 4295 1.473434 CCACTGGCCTAAACCTCGATC 60.473 57.143 3.32 0.00 0.00 3.69
666 4296 0.831307 ACTGGCCTAAACCTCGATCC 59.169 55.000 3.32 0.00 0.00 3.36
667 4297 0.830648 CTGGCCTAAACCTCGATCCA 59.169 55.000 3.32 0.00 0.00 3.41
805 4435 2.577112 CGTCGGCTAGTCACGCTG 60.577 66.667 6.42 0.00 35.10 5.18
807 4437 3.062466 TCGGCTAGTCACGCTGCT 61.062 61.111 0.00 0.00 33.82 4.24
859 4489 6.924913 TCTTGGACTCTGCTTGCTATATAT 57.075 37.500 0.00 0.00 0.00 0.86
860 4490 8.422577 TTCTTGGACTCTGCTTGCTATATATA 57.577 34.615 0.00 0.00 0.00 0.86
872 4502 5.860941 TGCTATATATAGAGCAAGGGAGC 57.139 43.478 25.77 6.86 46.27 4.70
965 4596 2.046314 GCCGAGGTAGCTGCCAAA 60.046 61.111 23.78 0.00 0.00 3.28
966 4597 2.109126 GCCGAGGTAGCTGCCAAAG 61.109 63.158 23.78 12.79 0.00 2.77
967 4598 1.596934 CCGAGGTAGCTGCCAAAGA 59.403 57.895 23.78 0.00 0.00 2.52
1011 4650 2.124901 TAGGAAATGTGCGGCGGG 60.125 61.111 9.78 0.00 0.00 6.13
1221 4866 6.872020 TCTTTTGTAATGTAGCTAGCGTCTTT 59.128 34.615 9.55 12.48 0.00 2.52
1235 4880 7.973388 AGCTAGCGTCTTTCATATCTATGATTC 59.027 37.037 9.55 0.00 41.86 2.52
1277 4933 7.274686 GCTAATCTGTTCTGTACTGTTCTCTTC 59.725 40.741 0.00 0.00 0.00 2.87
1832 5506 8.904834 TCTTTTGATTAGCTAGAGTATCGTTCT 58.095 33.333 0.00 0.00 42.67 3.01
1929 5608 4.518211 AGAAGAAATGTGGAGAACTTGCAG 59.482 41.667 0.00 0.00 0.00 4.41
1951 5631 7.090173 GCAGCAACTTTCCTGACATAAAATAA 58.910 34.615 0.00 0.00 0.00 1.40
2000 5686 3.603857 CGAAACAGTTCATGTCCGTGTTC 60.604 47.826 0.00 0.00 43.00 3.18
2001 5687 2.613026 ACAGTTCATGTCCGTGTTCA 57.387 45.000 0.00 0.00 37.75 3.18
2003 5689 2.158957 ACAGTTCATGTCCGTGTTCACT 60.159 45.455 0.00 0.00 37.75 3.41
2004 5690 2.872245 CAGTTCATGTCCGTGTTCACTT 59.128 45.455 0.00 0.00 0.00 3.16
2005 5691 3.312421 CAGTTCATGTCCGTGTTCACTTT 59.688 43.478 0.00 0.00 0.00 2.66
2006 5692 3.312421 AGTTCATGTCCGTGTTCACTTTG 59.688 43.478 0.00 0.00 0.00 2.77
2011 5697 5.354513 TCATGTCCGTGTTCACTTTGTTTTA 59.645 36.000 0.00 0.00 0.00 1.52
2012 5698 4.972201 TGTCCGTGTTCACTTTGTTTTAC 58.028 39.130 1.53 0.00 0.00 2.01
2013 5699 4.023783 GTCCGTGTTCACTTTGTTTTACG 58.976 43.478 1.53 0.00 0.00 3.18
2014 5700 2.779471 CCGTGTTCACTTTGTTTTACGC 59.221 45.455 1.53 0.00 0.00 4.42
2015 5701 2.457537 CGTGTTCACTTTGTTTTACGCG 59.542 45.455 3.53 3.53 34.00 6.01
2016 5702 2.212466 GTGTTCACTTTGTTTTACGCGC 59.788 45.455 5.73 0.00 0.00 6.86
2017 5703 2.159558 TGTTCACTTTGTTTTACGCGCA 60.160 40.909 5.73 0.00 0.00 6.09
2020 5711 4.671880 TCACTTTGTTTTACGCGCATAT 57.328 36.364 5.73 0.00 0.00 1.78
2028 5719 0.871722 TTACGCGCATATGGCAATCC 59.128 50.000 5.73 0.00 45.17 3.01
2047 5743 7.082602 GCAATCCATAGAATGCATTAGAACAG 58.917 38.462 12.97 0.28 46.36 3.16
2070 5766 9.971922 ACAGATTGTCTAAATTTTCCTTCTTTG 57.028 29.630 0.00 0.00 0.00 2.77
2199 5896 2.719531 AAAAACCCAAAATGCCCGTT 57.280 40.000 0.00 0.00 0.00 4.44
2200 5897 1.960417 AAAACCCAAAATGCCCGTTG 58.040 45.000 0.00 0.00 0.00 4.10
2201 5898 0.533978 AAACCCAAAATGCCCGTTGC 60.534 50.000 0.00 0.00 41.77 4.17
2202 5899 1.406860 AACCCAAAATGCCCGTTGCT 61.407 50.000 0.00 0.00 42.00 3.91
2203 5900 0.540830 ACCCAAAATGCCCGTTGCTA 60.541 50.000 0.00 0.00 42.00 3.49
2204 5901 0.605589 CCCAAAATGCCCGTTGCTAA 59.394 50.000 0.00 0.00 42.00 3.09
2205 5902 1.404047 CCCAAAATGCCCGTTGCTAAG 60.404 52.381 0.00 0.00 42.00 2.18
2206 5903 1.543802 CCAAAATGCCCGTTGCTAAGA 59.456 47.619 0.00 0.00 42.00 2.10
2207 5904 2.029470 CCAAAATGCCCGTTGCTAAGAA 60.029 45.455 0.00 0.00 42.00 2.52
2208 5905 3.553922 CCAAAATGCCCGTTGCTAAGAAA 60.554 43.478 0.00 0.00 42.00 2.52
2209 5906 4.244862 CAAAATGCCCGTTGCTAAGAAAT 58.755 39.130 0.00 0.00 42.00 2.17
2210 5907 4.535526 AAATGCCCGTTGCTAAGAAATT 57.464 36.364 0.00 0.00 42.00 1.82
2211 5908 5.652994 AAATGCCCGTTGCTAAGAAATTA 57.347 34.783 0.00 0.00 42.00 1.40
2212 5909 5.652994 AATGCCCGTTGCTAAGAAATTAA 57.347 34.783 0.00 0.00 42.00 1.40
2213 5910 5.852282 ATGCCCGTTGCTAAGAAATTAAT 57.148 34.783 0.00 0.00 42.00 1.40
2214 5911 5.243426 TGCCCGTTGCTAAGAAATTAATC 57.757 39.130 0.00 0.00 42.00 1.75
2215 5912 4.097286 TGCCCGTTGCTAAGAAATTAATCC 59.903 41.667 0.00 0.00 42.00 3.01
2216 5913 4.788521 GCCCGTTGCTAAGAAATTAATCCG 60.789 45.833 0.00 0.00 36.87 4.18
2217 5914 4.261031 CCCGTTGCTAAGAAATTAATCCGG 60.261 45.833 0.00 0.00 0.00 5.14
2218 5915 4.334481 CCGTTGCTAAGAAATTAATCCGGT 59.666 41.667 0.00 0.00 0.00 5.28
2219 5916 5.163693 CCGTTGCTAAGAAATTAATCCGGTT 60.164 40.000 0.00 0.00 0.00 4.44
2242 5939 4.947388 TGCCCGTTGCTAAGAAATTAATCT 59.053 37.500 0.00 0.00 42.00 2.40
2260 5957 1.004277 TCTGGTTTATGACAGGTGGGC 59.996 52.381 0.00 0.00 35.47 5.36
2262 5959 0.039035 GGTTTATGACAGGTGGGCCA 59.961 55.000 0.00 0.00 37.19 5.36
2402 6102 0.178970 AGTACACCGGAGACAGTGGT 60.179 55.000 9.46 0.00 38.34 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.899457 TGACACATAAGGAATCCGGATACT 59.101 41.667 19.48 16.30 0.00 2.12
1 2 4.989168 GTGACACATAAGGAATCCGGATAC 59.011 45.833 19.48 14.11 0.00 2.24
2 3 4.039973 GGTGACACATAAGGAATCCGGATA 59.960 45.833 19.48 0.88 0.00 2.59
3 4 3.181454 GGTGACACATAAGGAATCCGGAT 60.181 47.826 12.38 12.38 0.00 4.18
4 5 2.169769 GGTGACACATAAGGAATCCGGA 59.830 50.000 6.61 6.61 0.00 5.14
5 6 2.561569 GGTGACACATAAGGAATCCGG 58.438 52.381 8.08 0.00 0.00 5.14
6 7 2.201732 CGGTGACACATAAGGAATCCG 58.798 52.381 8.08 0.00 0.00 4.18
7 8 3.261981 ACGGTGACACATAAGGAATCC 57.738 47.619 8.08 0.00 0.00 3.01
8 9 5.622770 AAAACGGTGACACATAAGGAATC 57.377 39.130 8.08 0.00 0.00 2.52
9 10 5.533154 TCAAAAACGGTGACACATAAGGAAT 59.467 36.000 8.08 0.00 0.00 3.01
10 11 4.882427 TCAAAAACGGTGACACATAAGGAA 59.118 37.500 8.08 0.00 0.00 3.36
11 12 4.452825 TCAAAAACGGTGACACATAAGGA 58.547 39.130 8.08 0.00 0.00 3.36
12 13 4.513692 TCTCAAAAACGGTGACACATAAGG 59.486 41.667 8.08 0.00 0.00 2.69
13 14 5.666969 TCTCAAAAACGGTGACACATAAG 57.333 39.130 8.08 0.00 0.00 1.73
14 15 4.024387 GCTCTCAAAAACGGTGACACATAA 60.024 41.667 8.08 0.00 0.00 1.90
15 16 3.496884 GCTCTCAAAAACGGTGACACATA 59.503 43.478 8.08 0.00 0.00 2.29
16 17 2.290641 GCTCTCAAAAACGGTGACACAT 59.709 45.455 8.08 0.00 0.00 3.21
17 18 1.668751 GCTCTCAAAAACGGTGACACA 59.331 47.619 8.08 0.00 0.00 3.72
18 19 1.940613 AGCTCTCAAAAACGGTGACAC 59.059 47.619 0.00 0.00 0.00 3.67
19 20 2.325583 AGCTCTCAAAAACGGTGACA 57.674 45.000 0.00 0.00 0.00 3.58
20 21 4.806342 TTTAGCTCTCAAAAACGGTGAC 57.194 40.909 0.00 0.00 0.00 3.67
21 22 7.681939 AATATTTAGCTCTCAAAAACGGTGA 57.318 32.000 0.00 0.00 0.00 4.02
22 23 8.742554 AAAATATTTAGCTCTCAAAAACGGTG 57.257 30.769 0.01 0.00 0.00 4.94
23 24 8.027189 GGAAAATATTTAGCTCTCAAAAACGGT 58.973 33.333 0.01 0.00 0.00 4.83
24 25 7.488150 GGGAAAATATTTAGCTCTCAAAAACGG 59.512 37.037 0.01 0.00 0.00 4.44
25 26 8.026607 TGGGAAAATATTTAGCTCTCAAAAACG 58.973 33.333 0.01 0.00 0.00 3.60
26 27 9.705290 TTGGGAAAATATTTAGCTCTCAAAAAC 57.295 29.630 10.06 0.00 0.00 2.43
28 29 9.874205 CATTGGGAAAATATTTAGCTCTCAAAA 57.126 29.630 14.60 3.23 0.00 2.44
29 30 8.477256 CCATTGGGAAAATATTTAGCTCTCAAA 58.523 33.333 14.60 3.50 35.59 2.69
30 31 7.417797 GCCATTGGGAAAATATTTAGCTCTCAA 60.418 37.037 13.47 13.47 35.59 3.02
31 32 6.040842 GCCATTGGGAAAATATTTAGCTCTCA 59.959 38.462 4.53 0.00 35.59 3.27
32 33 6.040842 TGCCATTGGGAAAATATTTAGCTCTC 59.959 38.462 4.53 0.00 35.59 3.20
33 34 5.898972 TGCCATTGGGAAAATATTTAGCTCT 59.101 36.000 4.53 0.00 35.59 4.09
34 35 6.160576 TGCCATTGGGAAAATATTTAGCTC 57.839 37.500 4.53 0.00 35.59 4.09
35 36 6.558488 TTGCCATTGGGAAAATATTTAGCT 57.442 33.333 7.23 0.00 35.59 3.32
36 37 7.622893 TTTTGCCATTGGGAAAATATTTAGC 57.377 32.000 25.74 0.00 45.43 3.09
45 46 2.768527 TGAGTGTTTTGCCATTGGGAAA 59.231 40.909 17.39 17.39 41.09 3.13
46 47 2.364970 CTGAGTGTTTTGCCATTGGGAA 59.635 45.455 5.41 5.41 35.59 3.97
47 48 1.962807 CTGAGTGTTTTGCCATTGGGA 59.037 47.619 4.53 0.00 35.59 4.37
48 49 1.606224 GCTGAGTGTTTTGCCATTGGG 60.606 52.381 4.53 0.00 37.18 4.12
49 50 1.068895 TGCTGAGTGTTTTGCCATTGG 59.931 47.619 0.00 0.00 0.00 3.16
50 51 2.512485 TGCTGAGTGTTTTGCCATTG 57.488 45.000 0.00 0.00 0.00 2.82
51 52 2.694628 TCTTGCTGAGTGTTTTGCCATT 59.305 40.909 0.00 0.00 0.00 3.16
52 53 2.309613 TCTTGCTGAGTGTTTTGCCAT 58.690 42.857 0.00 0.00 0.00 4.40
53 54 1.761449 TCTTGCTGAGTGTTTTGCCA 58.239 45.000 0.00 0.00 0.00 4.92
54 55 2.544486 CCTTCTTGCTGAGTGTTTTGCC 60.544 50.000 0.00 0.00 0.00 4.52
55 56 2.735823 CCTTCTTGCTGAGTGTTTTGC 58.264 47.619 0.00 0.00 0.00 3.68
56 57 2.735823 GCCTTCTTGCTGAGTGTTTTG 58.264 47.619 0.00 0.00 0.00 2.44
57 58 1.334869 CGCCTTCTTGCTGAGTGTTTT 59.665 47.619 0.00 0.00 0.00 2.43
58 59 0.947244 CGCCTTCTTGCTGAGTGTTT 59.053 50.000 0.00 0.00 0.00 2.83
59 60 0.886490 CCGCCTTCTTGCTGAGTGTT 60.886 55.000 0.00 0.00 0.00 3.32
60 61 1.302033 CCGCCTTCTTGCTGAGTGT 60.302 57.895 0.00 0.00 0.00 3.55
61 62 2.684843 GCCGCCTTCTTGCTGAGTG 61.685 63.158 0.00 0.00 0.00 3.51
62 63 2.359230 GCCGCCTTCTTGCTGAGT 60.359 61.111 0.00 0.00 0.00 3.41
63 64 3.494336 CGCCGCCTTCTTGCTGAG 61.494 66.667 0.00 0.00 0.00 3.35
75 76 3.925238 CATAGAACACGCCGCCGC 61.925 66.667 0.00 0.00 38.22 6.53
76 77 1.151777 AATCATAGAACACGCCGCCG 61.152 55.000 0.00 0.00 41.14 6.46
77 78 0.304705 CAATCATAGAACACGCCGCC 59.695 55.000 0.00 0.00 0.00 6.13
78 79 1.006832 ACAATCATAGAACACGCCGC 58.993 50.000 0.00 0.00 0.00 6.53
79 80 4.506288 TGATAACAATCATAGAACACGCCG 59.494 41.667 0.00 0.00 0.00 6.46
80 81 5.984233 TGATAACAATCATAGAACACGCC 57.016 39.130 0.00 0.00 0.00 5.68
108 109 9.743057 CAAACCAAAGAATAGTAAAATCACACA 57.257 29.630 0.00 0.00 0.00 3.72
125 127 8.925161 TCTCTAAAACAATGTTCAAACCAAAG 57.075 30.769 0.00 0.00 0.00 2.77
126 128 9.364989 CTTCTCTAAAACAATGTTCAAACCAAA 57.635 29.630 0.00 0.00 0.00 3.28
128 130 6.978080 GCTTCTCTAAAACAATGTTCAAACCA 59.022 34.615 0.00 0.00 0.00 3.67
178 188 4.957954 TCGACAAAATCCCTAGCTAACCTA 59.042 41.667 0.00 0.00 0.00 3.08
186 196 5.073311 TCAGAAGTCGACAAAATCCCTAG 57.927 43.478 19.50 2.05 0.00 3.02
189 199 4.142600 CCAATCAGAAGTCGACAAAATCCC 60.143 45.833 19.50 0.00 0.00 3.85
216 227 3.201290 CAATATCGCTCACAGGCTTCTT 58.799 45.455 0.00 0.00 0.00 2.52
222 233 3.431233 CACATAGCAATATCGCTCACAGG 59.569 47.826 0.00 0.00 42.62 4.00
225 236 4.051237 TCACACATAGCAATATCGCTCAC 58.949 43.478 0.00 0.00 42.62 3.51
235 246 5.353956 ACGCTTTATTCATCACACATAGCAA 59.646 36.000 0.00 0.00 0.00 3.91
269 305 6.532365 AGAGATTCACGTTCTGTCTTTTTC 57.468 37.500 0.00 0.00 0.00 2.29
287 323 9.267084 GAGTCTTGTGTCTTTTAAAGAAGAGAT 57.733 33.333 9.14 1.23 39.67 2.75
458 4086 0.169009 GCGCGATTCTGAAAAAGGCT 59.831 50.000 12.10 0.00 0.00 4.58
644 4274 1.078426 CGAGGTTTAGGCCAGTGGG 60.078 63.158 12.15 0.00 37.18 4.61
645 4275 0.541863 ATCGAGGTTTAGGCCAGTGG 59.458 55.000 5.01 4.20 0.00 4.00
646 4276 1.473434 GGATCGAGGTTTAGGCCAGTG 60.473 57.143 5.01 0.00 0.00 3.66
647 4277 0.831307 GGATCGAGGTTTAGGCCAGT 59.169 55.000 5.01 0.00 0.00 4.00
648 4278 0.830648 TGGATCGAGGTTTAGGCCAG 59.169 55.000 5.01 0.00 0.00 4.85
649 4279 1.416401 GATGGATCGAGGTTTAGGCCA 59.584 52.381 5.01 0.00 0.00 5.36
650 4280 2.171341 GATGGATCGAGGTTTAGGCC 57.829 55.000 0.00 0.00 0.00 5.19
805 4435 0.671781 CACAGTGGCAGAGGTACAGC 60.672 60.000 0.00 0.00 0.00 4.40
807 4437 1.121407 AGCACAGTGGCAGAGGTACA 61.121 55.000 1.84 0.00 35.83 2.90
859 4489 2.764128 CCCCGCTCCCTTGCTCTA 60.764 66.667 0.00 0.00 0.00 2.43
872 4502 3.365265 GCCTCAACTGCAACCCCG 61.365 66.667 0.00 0.00 0.00 5.73
965 4596 3.754323 CACGTTCTCCTCTTACTCAGTCT 59.246 47.826 0.00 0.00 0.00 3.24
966 4597 3.119779 CCACGTTCTCCTCTTACTCAGTC 60.120 52.174 0.00 0.00 0.00 3.51
967 4598 2.820787 CCACGTTCTCCTCTTACTCAGT 59.179 50.000 0.00 0.00 0.00 3.41
1153 4792 8.638873 TCTACTGTGACCGTATAATTTGATGAT 58.361 33.333 0.00 0.00 0.00 2.45
1221 4866 7.536159 AGCTCAGTGTGAATCATAGATATGA 57.464 36.000 5.06 5.06 45.78 2.15
1235 4880 1.445871 TAGCATGCAAGCTCAGTGTG 58.554 50.000 21.34 0.00 45.26 3.82
1277 4933 0.170561 CGTCACCTCCTCACCTTACG 59.829 60.000 0.00 0.00 0.00 3.18
1553 5209 0.389948 GACCATCCGACGCTTCTTGT 60.390 55.000 0.00 0.00 0.00 3.16
1832 5506 4.079446 CGAAAGCCCAGGAAAGCA 57.921 55.556 0.00 0.00 0.00 3.91
1929 5608 9.476202 AGTTTTATTTTATGTCAGGAAAGTTGC 57.524 29.630 0.00 0.00 0.00 4.17
1951 5631 7.556275 TCCTACAAATGAGAGTGTGAAAAGTTT 59.444 33.333 0.00 0.00 0.00 2.66
1962 5642 5.209818 TGTTTCGTCCTACAAATGAGAGT 57.790 39.130 0.00 0.00 0.00 3.24
2000 5686 3.541916 CCATATGCGCGTAAAACAAAGTG 59.458 43.478 14.31 4.58 0.00 3.16
2001 5687 3.753842 CCATATGCGCGTAAAACAAAGT 58.246 40.909 14.31 0.00 0.00 2.66
2003 5689 2.095212 TGCCATATGCGCGTAAAACAAA 60.095 40.909 14.31 0.00 45.60 2.83
2004 5690 1.468914 TGCCATATGCGCGTAAAACAA 59.531 42.857 14.31 0.00 45.60 2.83
2005 5691 1.087501 TGCCATATGCGCGTAAAACA 58.912 45.000 14.31 8.92 45.60 2.83
2006 5692 2.181426 TTGCCATATGCGCGTAAAAC 57.819 45.000 14.31 6.33 45.60 2.43
2011 5697 1.525765 TGGATTGCCATATGCGCGT 60.526 52.632 8.43 7.55 45.60 6.01
2012 5698 3.342909 TGGATTGCCATATGCGCG 58.657 55.556 0.00 0.00 45.60 6.86
2028 5719 9.053840 AGACAATCTGTTCTAATGCATTCTATG 57.946 33.333 16.86 5.34 0.00 2.23
2056 5752 8.531146 TCACTCAGTTTTCAAAGAAGGAAAATT 58.469 29.630 3.94 0.00 43.67 1.82
2068 5764 5.588246 TGTGTGCTATTCACTCAGTTTTCAA 59.412 36.000 0.00 0.00 45.81 2.69
2069 5765 5.122519 TGTGTGCTATTCACTCAGTTTTCA 58.877 37.500 0.00 0.00 45.81 2.69
2070 5766 5.673337 TGTGTGCTATTCACTCAGTTTTC 57.327 39.130 0.00 0.00 45.81 2.29
2071 5767 5.590259 AGTTGTGTGCTATTCACTCAGTTTT 59.410 36.000 0.00 0.00 46.08 2.43
2072 5768 5.126067 AGTTGTGTGCTATTCACTCAGTTT 58.874 37.500 0.00 0.00 46.08 2.66
2073 5769 4.708177 AGTTGTGTGCTATTCACTCAGTT 58.292 39.130 0.00 0.00 46.08 3.16
2074 5770 4.342862 AGTTGTGTGCTATTCACTCAGT 57.657 40.909 0.00 0.00 46.08 3.41
2075 5771 4.627467 GGTAGTTGTGTGCTATTCACTCAG 59.373 45.833 0.00 0.00 46.08 3.35
2128 5824 9.912634 AGTTATCAGTCACAAACAAATTTATGG 57.087 29.630 0.00 0.00 0.00 2.74
2193 5890 4.607955 GGATTAATTTCTTAGCAACGGGC 58.392 43.478 0.00 0.00 45.30 6.13
2194 5891 4.261031 CCGGATTAATTTCTTAGCAACGGG 60.261 45.833 0.00 0.00 33.37 5.28
2195 5892 4.334481 ACCGGATTAATTTCTTAGCAACGG 59.666 41.667 9.46 0.00 41.87 4.44
2196 5893 5.479716 ACCGGATTAATTTCTTAGCAACG 57.520 39.130 9.46 0.00 0.00 4.10
2197 5894 5.515270 GCAACCGGATTAATTTCTTAGCAAC 59.485 40.000 9.46 0.00 0.00 4.17
2198 5895 5.393678 GGCAACCGGATTAATTTCTTAGCAA 60.394 40.000 9.46 0.00 0.00 3.91
2199 5896 4.097286 GGCAACCGGATTAATTTCTTAGCA 59.903 41.667 9.46 0.00 0.00 3.49
2200 5897 4.607955 GGCAACCGGATTAATTTCTTAGC 58.392 43.478 9.46 0.00 0.00 3.09
2242 5939 0.039035 GGCCCACCTGTCATAAACCA 59.961 55.000 0.00 0.00 0.00 3.67
2260 5957 1.721487 CGGTTCATTTAGCCGCTGG 59.279 57.895 2.16 0.00 45.41 4.85
2280 5978 5.007234 CAGATGTCAGTTAACGGTCAAACAA 59.993 40.000 9.34 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.