Multiple sequence alignment - TraesCS2A01G085600

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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 TraesCS2A01G085600 chr2A 100.000 3104 0 0 1 3104 39411596 39408493 0.000000e+00 5733.0
1 TraesCS2A01G085600 chr2A 91.854 2271 118 26 873 3101 39452889 39450644 0.000000e+00 3107.0
2 TraesCS2A01G085600 chr2A 94.870 1969 80 11 1000 2959 39355228 39357184 0.000000e+00 3057.0
3 TraesCS2A01G085600 chr2A 90.244 410 38 2 1550 1959 39418930 39418523 4.560000e-148 534.0
4 TraesCS2A01G085600 chr2A 92.000 50 3 1 238 287 638876202 638876250 5.550000e-08 69.4
5 TraesCS2A01G085600 chr2A 90.196 51 5 0 237 287 107179762 107179712 2.000000e-07 67.6
6 TraesCS2A01G085600 chr2D 94.221 2111 92 18 873 2959 36052118 36054222 0.000000e+00 3195.0
7 TraesCS2A01G085600 chr2D 76.816 1363 259 40 869 2204 35927531 35928863 0.000000e+00 713.0
8 TraesCS2A01G085600 chr2D 91.562 320 24 2 2772 3088 36198016 36198335 3.670000e-119 438.0
9 TraesCS2A01G085600 chr2D 75.660 871 166 31 916 1764 35978633 35979479 2.900000e-105 392.0
10 TraesCS2A01G085600 chr2D 86.770 257 20 8 1 244 35925238 35925493 1.100000e-69 274.0
11 TraesCS2A01G085600 chr2D 90.698 172 3 5 661 831 35927372 35927531 1.870000e-52 217.0
12 TraesCS2A01G085600 chr2D 88.462 52 6 0 236 287 596208039 596208090 2.580000e-06 63.9
13 TraesCS2A01G085600 chr2B 91.741 2131 90 36 984 3077 61476428 61474347 0.000000e+00 2881.0
14 TraesCS2A01G085600 chr2B 93.225 738 48 2 1000 1736 61367431 61368167 0.000000e+00 1085.0
15 TraesCS2A01G085600 chr2B 92.105 684 52 2 1326 2008 61311780 61312462 0.000000e+00 963.0
16 TraesCS2A01G085600 chr2B 91.667 660 40 9 1723 2374 61369454 61370106 0.000000e+00 900.0
17 TraesCS2A01G085600 chr2B 76.443 1265 238 35 873 2104 61362015 61363252 5.650000e-177 630.0
18 TraesCS2A01G085600 chr2B 76.862 1007 176 33 610 1605 61491761 61490801 1.650000e-142 516.0
19 TraesCS2A01G085600 chr2B 95.556 45 2 0 239 283 676586530 676586486 4.290000e-09 73.1
20 TraesCS2A01G085600 chr3D 91.986 836 56 6 1160 1993 380122973 380123799 0.000000e+00 1162.0
21 TraesCS2A01G085600 chr3D 91.311 610 40 9 1980 2587 380132158 380132756 0.000000e+00 821.0
22 TraesCS2A01G085600 chr7A 86.111 108 7 3 2699 2798 710797023 710797130 3.270000e-20 110.0
23 TraesCS2A01G085600 chr1D 85.981 107 5 4 2702 2798 254459833 254459727 4.230000e-19 106.0
24 TraesCS2A01G085600 chr1D 84.404 109 8 3 2699 2798 51831534 51831642 7.080000e-17 99.0
25 TraesCS2A01G085600 chr1D 95.349 43 2 0 241 283 258980731 258980689 5.550000e-08 69.4
26 TraesCS2A01G085600 chrUn 85.321 109 7 3 2699 2798 261568265 261568373 1.520000e-18 104.0
27 TraesCS2A01G085600 chrUn 84.112 107 7 2 2702 2798 111203619 111203513 9.160000e-16 95.3
28 TraesCS2A01G085600 chr6B 93.443 61 4 0 2699 2759 450091714 450091774 1.190000e-14 91.6
29 TraesCS2A01G085600 chr4D 82.243 107 9 2 2702 2798 19901149 19901043 1.980000e-12 84.2
30 TraesCS2A01G085600 chr4D 91.304 46 4 0 242 287 102739823 102739868 2.580000e-06 63.9
31 TraesCS2A01G085600 chr7B 80.556 108 9 3 2707 2803 327633734 327633840 4.290000e-09 73.1
32 TraesCS2A01G085600 chr7D 95.238 42 2 0 242 283 105375304 105375263 2.000000e-07 67.6
33 TraesCS2A01G085600 chr3B 93.333 45 3 0 240 284 53192523 53192567 2.000000e-07 67.6
34 TraesCS2A01G085600 chr3B 95.238 42 2 0 242 283 155020642 155020683 2.000000e-07 67.6


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 TraesCS2A01G085600 chr2A 39408493 39411596 3103 True 5733.000000 5733 100.000000 1 3104 1 chr2A.!!$R1 3103
1 TraesCS2A01G085600 chr2A 39450644 39452889 2245 True 3107.000000 3107 91.854000 873 3101 1 chr2A.!!$R3 2228
2 TraesCS2A01G085600 chr2A 39355228 39357184 1956 False 3057.000000 3057 94.870000 1000 2959 1 chr2A.!!$F1 1959
3 TraesCS2A01G085600 chr2D 36052118 36054222 2104 False 3195.000000 3195 94.221000 873 2959 1 chr2D.!!$F2 2086
4 TraesCS2A01G085600 chr2D 35925238 35928863 3625 False 401.333333 713 84.761333 1 2204 3 chr2D.!!$F5 2203
5 TraesCS2A01G085600 chr2D 35978633 35979479 846 False 392.000000 392 75.660000 916 1764 1 chr2D.!!$F1 848
6 TraesCS2A01G085600 chr2B 61474347 61476428 2081 True 2881.000000 2881 91.741000 984 3077 1 chr2B.!!$R1 2093
7 TraesCS2A01G085600 chr2B 61367431 61370106 2675 False 992.500000 1085 92.446000 1000 2374 2 chr2B.!!$F3 1374
8 TraesCS2A01G085600 chr2B 61311780 61312462 682 False 963.000000 963 92.105000 1326 2008 1 chr2B.!!$F1 682
9 TraesCS2A01G085600 chr2B 61362015 61363252 1237 False 630.000000 630 76.443000 873 2104 1 chr2B.!!$F2 1231
10 TraesCS2A01G085600 chr2B 61490801 61491761 960 True 516.000000 516 76.862000 610 1605 1 chr2B.!!$R2 995
11 TraesCS2A01G085600 chr3D 380122973 380123799 826 False 1162.000000 1162 91.986000 1160 1993 1 chr3D.!!$F1 833
12 TraesCS2A01G085600 chr3D 380132158 380132756 598 False 821.000000 821 91.311000 1980 2587 1 chr3D.!!$F2 607

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
551 2019 0.040958 AAGCAGACGCGCAAAGAAAG 60.041 50.0 5.73 0.0 45.49 2.62 F
554 2022 0.164647 CAGACGCGCAAAGAAAGGAG 59.835 55.0 5.73 0.0 0.00 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1938 4917 0.618680 TGCATGTAGGCTCCACTCCT 60.619 55.000 0.0 0.0 37.72 3.69 R
2520 5560 3.645434 TCCATGCCATTAATCCTGCTTT 58.355 40.909 0.0 0.0 0.00 3.51 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
26 27 7.810759 CCATGTACTTTAAACAAATGGTGTACC 59.189 37.037 6.25 0.00 40.60 3.34
136 144 8.454570 TCATGAAAGCTATTTAGAATGCATGA 57.545 30.769 0.00 0.00 36.89 3.07
142 150 8.867112 AAGCTATTTAGAATGCATGAACATTG 57.133 30.769 0.00 0.00 40.31 2.82
230 243 2.817258 TGTATTTTCTTGGTGGCTTCGG 59.183 45.455 0.00 0.00 0.00 4.30
244 257 2.334838 GCTTCGGCCGGTAATATGTAG 58.665 52.381 27.83 9.61 34.32 2.74
246 259 3.572584 CTTCGGCCGGTAATATGTAGTC 58.427 50.000 27.83 0.00 0.00 2.59
247 260 1.888512 TCGGCCGGTAATATGTAGTCC 59.111 52.381 27.83 0.00 0.00 3.85
248 261 1.067354 CGGCCGGTAATATGTAGTCCC 60.067 57.143 20.10 0.00 0.00 4.46
249 262 2.254508 GGCCGGTAATATGTAGTCCCT 58.745 52.381 1.90 0.00 0.00 4.20
250 263 2.233186 GGCCGGTAATATGTAGTCCCTC 59.767 54.545 1.90 0.00 0.00 4.30
251 264 2.233186 GCCGGTAATATGTAGTCCCTCC 59.767 54.545 1.90 0.00 0.00 4.30
252 265 2.830321 CCGGTAATATGTAGTCCCTCCC 59.170 54.545 0.00 0.00 0.00 4.30
253 266 3.501751 CCGGTAATATGTAGTCCCTCCCT 60.502 52.174 0.00 0.00 0.00 4.20
254 267 4.264083 CCGGTAATATGTAGTCCCTCCCTA 60.264 50.000 0.00 0.00 0.00 3.53
255 268 5.327732 CGGTAATATGTAGTCCCTCCCTAA 58.672 45.833 0.00 0.00 0.00 2.69
256 269 5.776716 CGGTAATATGTAGTCCCTCCCTAAA 59.223 44.000 0.00 0.00 0.00 1.85
257 270 6.071503 CGGTAATATGTAGTCCCTCCCTAAAG 60.072 46.154 0.00 0.00 0.00 1.85
258 271 7.015064 GGTAATATGTAGTCCCTCCCTAAAGA 58.985 42.308 0.00 0.00 0.00 2.52
259 272 7.511714 GGTAATATGTAGTCCCTCCCTAAAGAA 59.488 40.741 0.00 0.00 0.00 2.52
260 273 8.931568 GTAATATGTAGTCCCTCCCTAAAGAAA 58.068 37.037 0.00 0.00 0.00 2.52
261 274 8.582891 AATATGTAGTCCCTCCCTAAAGAAAT 57.417 34.615 0.00 0.00 0.00 2.17
262 275 9.684702 AATATGTAGTCCCTCCCTAAAGAAATA 57.315 33.333 0.00 0.00 0.00 1.40
263 276 9.860393 ATATGTAGTCCCTCCCTAAAGAAATAT 57.140 33.333 0.00 0.00 0.00 1.28
265 278 9.684702 ATGTAGTCCCTCCCTAAAGAAATATAA 57.315 33.333 0.00 0.00 0.00 0.98
266 279 9.684702 TGTAGTCCCTCCCTAAAGAAATATAAT 57.315 33.333 0.00 0.00 0.00 1.28
269 282 8.827758 AGTCCCTCCCTAAAGAAATATAATAGC 58.172 37.037 0.00 0.00 0.00 2.97
270 283 7.764901 GTCCCTCCCTAAAGAAATATAATAGCG 59.235 40.741 0.00 0.00 0.00 4.26
271 284 7.456902 TCCCTCCCTAAAGAAATATAATAGCGT 59.543 37.037 0.00 0.00 0.00 5.07
272 285 8.101419 CCCTCCCTAAAGAAATATAATAGCGTT 58.899 37.037 0.00 0.00 0.00 4.84
273 286 9.503399 CCTCCCTAAAGAAATATAATAGCGTTT 57.497 33.333 0.00 0.00 0.00 3.60
295 308 9.582431 CGTTTAGATCACTATTTTTACAGAGGA 57.418 33.333 0.00 0.00 0.00 3.71
316 329 9.444600 AGAGGAATTATTTGTTTTAGCGAAGTA 57.555 29.630 0.00 0.00 0.00 2.24
482 1950 3.627395 TGAGATTTACAATGGAGGCGT 57.373 42.857 0.00 0.00 0.00 5.68
489 1957 0.976641 ACAATGGAGGCGTCTGAAGA 59.023 50.000 0.00 0.00 0.00 2.87
510 1978 1.002366 AGAATAGCAGACGCGCAAAG 58.998 50.000 5.73 0.00 45.49 2.77
511 1979 0.721718 GAATAGCAGACGCGCAAAGT 59.278 50.000 5.73 0.00 45.49 2.66
512 1980 1.924524 GAATAGCAGACGCGCAAAGTA 59.075 47.619 5.73 0.00 45.49 2.24
513 1981 1.560923 ATAGCAGACGCGCAAAGTAG 58.439 50.000 5.73 0.00 45.49 2.57
514 1982 1.076533 TAGCAGACGCGCAAAGTAGC 61.077 55.000 5.73 5.50 45.49 3.58
515 1983 2.778679 CAGACGCGCAAAGTAGCC 59.221 61.111 5.73 0.00 0.00 3.93
516 1984 2.434359 AGACGCGCAAAGTAGCCC 60.434 61.111 5.73 0.00 0.00 5.19
517 1985 2.434359 GACGCGCAAAGTAGCCCT 60.434 61.111 5.73 0.00 0.00 5.19
518 1986 2.434359 ACGCGCAAAGTAGCCCTC 60.434 61.111 5.73 0.00 0.00 4.30
519 1987 2.434185 CGCGCAAAGTAGCCCTCA 60.434 61.111 8.75 0.00 0.00 3.86
520 1988 2.032634 CGCGCAAAGTAGCCCTCAA 61.033 57.895 8.75 0.00 0.00 3.02
521 1989 1.573829 CGCGCAAAGTAGCCCTCAAA 61.574 55.000 8.75 0.00 0.00 2.69
522 1990 0.596082 GCGCAAAGTAGCCCTCAAAA 59.404 50.000 0.30 0.00 0.00 2.44
523 1991 1.401539 GCGCAAAGTAGCCCTCAAAAG 60.402 52.381 0.30 0.00 0.00 2.27
524 1992 2.151202 CGCAAAGTAGCCCTCAAAAGA 58.849 47.619 0.00 0.00 0.00 2.52
525 1993 2.552315 CGCAAAGTAGCCCTCAAAAGAA 59.448 45.455 0.00 0.00 0.00 2.52
526 1994 3.004315 CGCAAAGTAGCCCTCAAAAGAAA 59.996 43.478 0.00 0.00 0.00 2.52
527 1995 4.499019 CGCAAAGTAGCCCTCAAAAGAAAA 60.499 41.667 0.00 0.00 0.00 2.29
528 1996 4.984785 GCAAAGTAGCCCTCAAAAGAAAAG 59.015 41.667 0.00 0.00 0.00 2.27
529 1997 5.221244 GCAAAGTAGCCCTCAAAAGAAAAGA 60.221 40.000 0.00 0.00 0.00 2.52
530 1998 6.682861 GCAAAGTAGCCCTCAAAAGAAAAGAA 60.683 38.462 0.00 0.00 0.00 2.52
531 1999 7.264947 CAAAGTAGCCCTCAAAAGAAAAGAAA 58.735 34.615 0.00 0.00 0.00 2.52
532 2000 7.418337 AAGTAGCCCTCAAAAGAAAAGAAAA 57.582 32.000 0.00 0.00 0.00 2.29
533 2001 7.418337 AGTAGCCCTCAAAAGAAAAGAAAAA 57.582 32.000 0.00 0.00 0.00 1.94
534 2002 7.492524 AGTAGCCCTCAAAAGAAAAGAAAAAG 58.507 34.615 0.00 0.00 0.00 2.27
535 2003 5.118990 AGCCCTCAAAAGAAAAGAAAAAGC 58.881 37.500 0.00 0.00 0.00 3.51
536 2004 4.875536 GCCCTCAAAAGAAAAGAAAAAGCA 59.124 37.500 0.00 0.00 0.00 3.91
537 2005 5.007039 GCCCTCAAAAGAAAAGAAAAAGCAG 59.993 40.000 0.00 0.00 0.00 4.24
538 2006 6.340522 CCCTCAAAAGAAAAGAAAAAGCAGA 58.659 36.000 0.00 0.00 0.00 4.26
539 2007 6.256539 CCCTCAAAAGAAAAGAAAAAGCAGAC 59.743 38.462 0.00 0.00 0.00 3.51
540 2008 6.020360 CCTCAAAAGAAAAGAAAAAGCAGACG 60.020 38.462 0.00 0.00 0.00 4.18
541 2009 5.288472 TCAAAAGAAAAGAAAAAGCAGACGC 59.712 36.000 0.00 0.00 38.99 5.19
542 2010 2.987046 AGAAAAGAAAAAGCAGACGCG 58.013 42.857 3.53 3.53 45.49 6.01
543 2011 1.448308 GAAAAGAAAAAGCAGACGCGC 59.552 47.619 5.73 0.00 45.49 6.86
544 2012 0.380378 AAAGAAAAAGCAGACGCGCA 59.620 45.000 5.73 0.00 45.49 6.09
545 2013 0.380378 AAGAAAAAGCAGACGCGCAA 59.620 45.000 5.73 0.00 45.49 4.85
546 2014 0.380378 AGAAAAAGCAGACGCGCAAA 59.620 45.000 5.73 0.00 45.49 3.68
547 2015 0.772341 GAAAAAGCAGACGCGCAAAG 59.228 50.000 5.73 0.00 45.49 2.77
548 2016 0.380378 AAAAAGCAGACGCGCAAAGA 59.620 45.000 5.73 0.00 45.49 2.52
549 2017 0.380378 AAAAGCAGACGCGCAAAGAA 59.620 45.000 5.73 0.00 45.49 2.52
550 2018 0.380378 AAAGCAGACGCGCAAAGAAA 59.620 45.000 5.73 0.00 45.49 2.52
551 2019 0.040958 AAGCAGACGCGCAAAGAAAG 60.041 50.000 5.73 0.00 45.49 2.62
552 2020 1.441016 GCAGACGCGCAAAGAAAGG 60.441 57.895 5.73 0.00 0.00 3.11
553 2021 1.841663 GCAGACGCGCAAAGAAAGGA 61.842 55.000 5.73 0.00 0.00 3.36
554 2022 0.164647 CAGACGCGCAAAGAAAGGAG 59.835 55.000 5.73 0.00 0.00 3.69
555 2023 0.951040 AGACGCGCAAAGAAAGGAGG 60.951 55.000 5.73 0.00 0.00 4.30
556 2024 1.912371 GACGCGCAAAGAAAGGAGGG 61.912 60.000 5.73 0.00 0.00 4.30
557 2025 2.690778 CGCGCAAAGAAAGGAGGGG 61.691 63.158 8.75 0.00 0.00 4.79
558 2026 1.303317 GCGCAAAGAAAGGAGGGGA 60.303 57.895 0.30 0.00 0.00 4.81
559 2027 0.893727 GCGCAAAGAAAGGAGGGGAA 60.894 55.000 0.30 0.00 0.00 3.97
560 2028 1.168714 CGCAAAGAAAGGAGGGGAAG 58.831 55.000 0.00 0.00 0.00 3.46
561 2029 0.891373 GCAAAGAAAGGAGGGGAAGC 59.109 55.000 0.00 0.00 0.00 3.86
562 2030 1.823250 GCAAAGAAAGGAGGGGAAGCA 60.823 52.381 0.00 0.00 0.00 3.91
563 2031 2.165998 CAAAGAAAGGAGGGGAAGCAG 58.834 52.381 0.00 0.00 0.00 4.24
571 2039 3.803162 GGGGAAGCAGAGGAGGGC 61.803 72.222 0.00 0.00 0.00 5.19
599 2067 1.139520 GCCGGCCACATCAACATTC 59.860 57.895 18.11 0.00 0.00 2.67
600 2068 1.809207 CCGGCCACATCAACATTCC 59.191 57.895 2.24 0.00 0.00 3.01
608 2076 1.451387 ATCAACATTCCGGCGACCC 60.451 57.895 9.30 0.00 0.00 4.46
679 2321 0.909610 TCTTGGCTGTCCTGTAGGGG 60.910 60.000 0.00 0.00 35.41 4.79
741 2383 2.274760 CCGACTCGGGGTCTAGGT 59.725 66.667 9.85 0.00 44.15 3.08
742 2384 1.823041 CCGACTCGGGGTCTAGGTC 60.823 68.421 9.85 0.00 44.15 3.85
743 2385 2.178890 CGACTCGGGGTCTAGGTCG 61.179 68.421 6.43 0.00 42.44 4.79
744 2386 1.823041 GACTCGGGGTCTAGGTCGG 60.823 68.421 0.00 0.00 41.46 4.79
745 2387 2.518825 CTCGGGGTCTAGGTCGGG 60.519 72.222 0.00 0.00 0.00 5.14
746 2388 3.016971 TCGGGGTCTAGGTCGGGA 61.017 66.667 0.00 0.00 0.00 5.14
841 2486 1.894699 GGAGGGGTTCCAAGACCTAT 58.105 55.000 0.00 0.00 46.01 2.57
842 2487 3.056201 GGAGGGGTTCCAAGACCTATA 57.944 52.381 0.00 0.00 46.01 1.31
844 2489 3.391626 GGAGGGGTTCCAAGACCTATAAG 59.608 52.174 0.00 0.00 46.01 1.73
845 2490 4.038633 GAGGGGTTCCAAGACCTATAAGT 58.961 47.826 0.00 0.00 39.71 2.24
846 2491 5.214293 GAGGGGTTCCAAGACCTATAAGTA 58.786 45.833 0.00 0.00 39.71 2.24
848 2493 5.427806 AGGGGTTCCAAGACCTATAAGTAAC 59.572 44.000 0.00 0.00 39.71 2.50
849 2494 5.190330 GGGGTTCCAAGACCTATAAGTAACA 59.810 44.000 0.00 0.00 39.71 2.41
850 2495 6.111382 GGGTTCCAAGACCTATAAGTAACAC 58.889 44.000 0.00 0.00 39.71 3.32
851 2496 6.296030 GGGTTCCAAGACCTATAAGTAACACA 60.296 42.308 0.00 0.00 39.71 3.72
852 2497 6.592994 GGTTCCAAGACCTATAAGTAACACAC 59.407 42.308 0.00 0.00 36.73 3.82
868 2515 2.041620 ACACACCATTGCCAGGTTAGAT 59.958 45.455 0.00 0.00 37.23 1.98
869 2516 3.265737 ACACACCATTGCCAGGTTAGATA 59.734 43.478 0.00 0.00 37.23 1.98
870 2517 3.879295 CACACCATTGCCAGGTTAGATAG 59.121 47.826 0.00 0.00 37.23 2.08
871 2518 3.780294 ACACCATTGCCAGGTTAGATAGA 59.220 43.478 0.00 0.00 37.23 1.98
910 2560 2.269241 GTCTCCTTGCCCTTCCGG 59.731 66.667 0.00 0.00 0.00 5.14
934 2591 2.338500 GTTTCTTCTCCTGTACTGGCG 58.662 52.381 13.72 8.14 0.00 5.69
950 2611 1.445582 GCGACCTCGTAACCACCAG 60.446 63.158 0.00 0.00 42.22 4.00
951 2612 1.870055 GCGACCTCGTAACCACCAGA 61.870 60.000 0.00 0.00 42.22 3.86
954 2615 1.342174 GACCTCGTAACCACCAGAACA 59.658 52.381 0.00 0.00 0.00 3.18
957 2618 3.207778 CCTCGTAACCACCAGAACAAAA 58.792 45.455 0.00 0.00 0.00 2.44
958 2619 3.628487 CCTCGTAACCACCAGAACAAAAA 59.372 43.478 0.00 0.00 0.00 1.94
982 2643 3.662759 AAATCAATCTTTAGGGCCGGA 57.337 42.857 5.05 0.00 0.00 5.14
984 2645 2.710096 TCAATCTTTAGGGCCGGAAG 57.290 50.000 5.05 13.65 0.00 3.46
985 2646 2.193127 TCAATCTTTAGGGCCGGAAGA 58.807 47.619 21.41 21.41 34.27 2.87
987 2648 3.142174 CAATCTTTAGGGCCGGAAGATC 58.858 50.000 26.70 0.00 38.74 2.75
989 2650 0.837272 CTTTAGGGCCGGAAGATCCA 59.163 55.000 5.05 0.00 35.91 3.41
990 2651 1.421646 CTTTAGGGCCGGAAGATCCAT 59.578 52.381 5.05 0.00 35.91 3.41
991 2652 1.518367 TTAGGGCCGGAAGATCCATT 58.482 50.000 5.05 0.00 35.91 3.16
992 2653 0.764890 TAGGGCCGGAAGATCCATTG 59.235 55.000 5.05 0.00 35.91 2.82
993 2654 2.196245 GGGCCGGAAGATCCATTGC 61.196 63.158 5.05 0.00 35.91 3.56
994 2655 1.453745 GGCCGGAAGATCCATTGCA 60.454 57.895 5.05 0.00 35.91 4.08
997 2669 2.018644 GCCGGAAGATCCATTGCAGAA 61.019 52.381 5.05 0.00 35.91 3.02
998 2670 1.945394 CCGGAAGATCCATTGCAGAAG 59.055 52.381 0.00 0.00 35.91 2.85
1003 2675 6.806209 GGAAGATCCATTGCAGAAGCATGC 62.806 50.000 10.51 10.51 43.17 4.06
1181 2856 0.322546 GTGCAGTTAGGGTTCCCTGG 60.323 60.000 19.58 8.14 37.64 4.45
1298 2973 1.680522 CCACAGACTCCCATCCTCGG 61.681 65.000 0.00 0.00 0.00 4.63
1689 3366 3.681302 TGGCATGGGGAATGGGCA 61.681 61.111 0.00 0.00 36.71 5.36
1938 4917 2.555782 GATTGTGTGCAGCGCGAA 59.444 55.556 12.10 0.00 0.00 4.70
2061 5051 3.428316 GCTCTAGCTCTTGTGTAGTGTCC 60.428 52.174 0.00 0.00 38.21 4.02
2266 5268 6.998074 AGATGGTCACATGTTTCAAGAACTAA 59.002 34.615 0.00 0.00 37.47 2.24
2298 5301 3.501828 ACTTTTGTGCTTGCGATATCACA 59.498 39.130 3.12 0.00 37.63 3.58
2433 5449 6.678568 AGAGTTATAAGATCCCCATGTCTG 57.321 41.667 0.00 0.00 0.00 3.51
2441 5481 1.568504 TCCCCATGTCTGGTCACTAC 58.431 55.000 0.00 0.00 41.37 2.73
2443 5483 1.066143 CCCCATGTCTGGTCACTACAC 60.066 57.143 0.00 0.00 41.37 2.90
2520 5560 4.022068 GTCATCAGAAAAACAATGGCAGGA 60.022 41.667 0.00 0.00 0.00 3.86
2690 5743 2.431782 AGCTTTCCAATGTTGTTGCAGT 59.568 40.909 0.00 0.00 0.00 4.40
2745 5798 2.424956 GGATGGCCAGTGAGCTAAAAAG 59.575 50.000 13.05 0.00 0.00 2.27
2798 5854 9.239002 CTTATAGATAGGACGAACAAAGAACAG 57.761 37.037 0.00 0.00 0.00 3.16
2919 5977 7.166167 ACATAAGTTATTTCCGAGGAACAGTT 58.834 34.615 3.71 4.15 33.41 3.16
3025 6084 5.602978 AGGAGACCGATGGTTATAGTTTCAT 59.397 40.000 0.00 0.00 35.25 2.57
3055 6116 5.666969 TGTTCGAGTTGTACAATCCAAAG 57.333 39.130 12.26 1.38 0.00 2.77
3079 6140 6.604795 AGAATGGTGGAGTCAAGATTAAATGG 59.395 38.462 0.00 0.00 0.00 3.16
3101 6162 5.853936 GGTATGCAACCCTCTTTTCTTTTT 58.146 37.500 0.00 0.00 43.16 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
126 134 8.095792 TGGATTAAAACAATGTTCATGCATTCT 58.904 29.630 0.00 0.00 37.00 2.40
204 212 7.012894 CCGAAGCCACCAAGAAAATACATATTA 59.987 37.037 0.00 0.00 0.00 0.98
230 243 2.233186 GGAGGGACTACATATTACCGGC 59.767 54.545 0.00 0.00 40.63 6.13
244 257 7.764901 CGCTATTATATTTCTTTAGGGAGGGAC 59.235 40.741 0.00 0.00 0.00 4.46
246 259 7.621796 ACGCTATTATATTTCTTTAGGGAGGG 58.378 38.462 0.00 0.00 0.00 4.30
247 260 9.503399 AAACGCTATTATATTTCTTTAGGGAGG 57.497 33.333 0.00 0.00 0.00 4.30
267 280 8.997621 TCTGTAAAAATAGTGATCTAAACGCT 57.002 30.769 0.00 0.00 0.00 5.07
268 281 8.328864 CCTCTGTAAAAATAGTGATCTAAACGC 58.671 37.037 0.00 0.00 0.00 4.84
269 282 9.582431 TCCTCTGTAAAAATAGTGATCTAAACG 57.418 33.333 0.00 0.00 0.00 3.60
285 298 9.834628 CGCTAAAACAAATAATTCCTCTGTAAA 57.165 29.630 0.00 0.00 0.00 2.01
286 299 9.221933 TCGCTAAAACAAATAATTCCTCTGTAA 57.778 29.630 0.00 0.00 0.00 2.41
287 300 8.780846 TCGCTAAAACAAATAATTCCTCTGTA 57.219 30.769 0.00 0.00 0.00 2.74
288 301 7.681939 TCGCTAAAACAAATAATTCCTCTGT 57.318 32.000 0.00 0.00 0.00 3.41
458 518 5.242838 ACGCCTCCATTGTAAATCTCAAAAA 59.757 36.000 0.00 0.00 0.00 1.94
462 522 3.197766 AGACGCCTCCATTGTAAATCTCA 59.802 43.478 0.00 0.00 0.00 3.27
463 523 3.557595 CAGACGCCTCCATTGTAAATCTC 59.442 47.826 0.00 0.00 0.00 2.75
464 524 3.197766 TCAGACGCCTCCATTGTAAATCT 59.802 43.478 0.00 0.00 0.00 2.40
465 525 3.531538 TCAGACGCCTCCATTGTAAATC 58.468 45.455 0.00 0.00 0.00 2.17
466 526 3.627395 TCAGACGCCTCCATTGTAAAT 57.373 42.857 0.00 0.00 0.00 1.40
467 527 3.007506 TCTTCAGACGCCTCCATTGTAAA 59.992 43.478 0.00 0.00 0.00 2.01
468 528 2.565391 TCTTCAGACGCCTCCATTGTAA 59.435 45.455 0.00 0.00 0.00 2.41
469 529 2.176045 TCTTCAGACGCCTCCATTGTA 58.824 47.619 0.00 0.00 0.00 2.41
470 530 0.976641 TCTTCAGACGCCTCCATTGT 59.023 50.000 0.00 0.00 0.00 2.71
471 531 2.099141 TTCTTCAGACGCCTCCATTG 57.901 50.000 0.00 0.00 0.00 2.82
472 532 2.303022 TCTTTCTTCAGACGCCTCCATT 59.697 45.455 0.00 0.00 0.00 3.16
473 533 1.902508 TCTTTCTTCAGACGCCTCCAT 59.097 47.619 0.00 0.00 0.00 3.41
474 534 1.338107 TCTTTCTTCAGACGCCTCCA 58.662 50.000 0.00 0.00 0.00 3.86
476 536 3.553917 GCTATTCTTTCTTCAGACGCCTC 59.446 47.826 0.00 0.00 0.00 4.70
482 1950 4.177026 GCGTCTGCTATTCTTTCTTCAGA 58.823 43.478 0.00 0.00 38.39 3.27
489 1957 1.438651 TTGCGCGTCTGCTATTCTTT 58.561 45.000 8.43 0.00 39.65 2.52
510 1978 6.201044 GCTTTTTCTTTTCTTTTGAGGGCTAC 59.799 38.462 0.00 0.00 0.00 3.58
511 1979 6.127196 TGCTTTTTCTTTTCTTTTGAGGGCTA 60.127 34.615 0.00 0.00 0.00 3.93
512 1980 5.118990 GCTTTTTCTTTTCTTTTGAGGGCT 58.881 37.500 0.00 0.00 0.00 5.19
513 1981 4.875536 TGCTTTTTCTTTTCTTTTGAGGGC 59.124 37.500 0.00 0.00 0.00 5.19
514 1982 6.256539 GTCTGCTTTTTCTTTTCTTTTGAGGG 59.743 38.462 0.00 0.00 0.00 4.30
515 1983 6.020360 CGTCTGCTTTTTCTTTTCTTTTGAGG 60.020 38.462 0.00 0.00 0.00 3.86
516 1984 6.506984 GCGTCTGCTTTTTCTTTTCTTTTGAG 60.507 38.462 0.00 0.00 38.39 3.02
517 1985 5.288472 GCGTCTGCTTTTTCTTTTCTTTTGA 59.712 36.000 0.00 0.00 38.39 2.69
518 1986 5.484085 GCGTCTGCTTTTTCTTTTCTTTTG 58.516 37.500 0.00 0.00 38.39 2.44
519 1987 4.265320 CGCGTCTGCTTTTTCTTTTCTTTT 59.735 37.500 0.00 0.00 39.65 2.27
520 1988 3.791353 CGCGTCTGCTTTTTCTTTTCTTT 59.209 39.130 0.00 0.00 39.65 2.52
521 1989 3.363178 CGCGTCTGCTTTTTCTTTTCTT 58.637 40.909 0.00 0.00 39.65 2.52
522 1990 2.854805 GCGCGTCTGCTTTTTCTTTTCT 60.855 45.455 8.43 0.00 39.65 2.52
523 1991 1.448308 GCGCGTCTGCTTTTTCTTTTC 59.552 47.619 8.43 0.00 39.65 2.29
524 1992 1.202245 TGCGCGTCTGCTTTTTCTTTT 60.202 42.857 8.43 0.00 39.65 2.27
525 1993 0.380378 TGCGCGTCTGCTTTTTCTTT 59.620 45.000 8.43 0.00 39.65 2.52
526 1994 0.380378 TTGCGCGTCTGCTTTTTCTT 59.620 45.000 8.43 0.00 39.65 2.52
527 1995 0.380378 TTTGCGCGTCTGCTTTTTCT 59.620 45.000 8.43 0.00 39.65 2.52
528 1996 0.772341 CTTTGCGCGTCTGCTTTTTC 59.228 50.000 8.43 0.00 39.65 2.29
529 1997 0.380378 TCTTTGCGCGTCTGCTTTTT 59.620 45.000 8.43 0.00 39.65 1.94
530 1998 0.380378 TTCTTTGCGCGTCTGCTTTT 59.620 45.000 8.43 0.00 39.65 2.27
531 1999 0.380378 TTTCTTTGCGCGTCTGCTTT 59.620 45.000 8.43 0.00 39.65 3.51
532 2000 0.040958 CTTTCTTTGCGCGTCTGCTT 60.041 50.000 8.43 0.00 39.65 3.91
533 2001 1.571460 CTTTCTTTGCGCGTCTGCT 59.429 52.632 8.43 0.00 39.65 4.24
534 2002 1.441016 CCTTTCTTTGCGCGTCTGC 60.441 57.895 8.43 0.00 37.91 4.26
535 2003 0.164647 CTCCTTTCTTTGCGCGTCTG 59.835 55.000 8.43 0.00 0.00 3.51
536 2004 0.951040 CCTCCTTTCTTTGCGCGTCT 60.951 55.000 8.43 0.00 0.00 4.18
537 2005 1.497722 CCTCCTTTCTTTGCGCGTC 59.502 57.895 8.43 0.00 0.00 5.19
538 2006 1.966451 CCCTCCTTTCTTTGCGCGT 60.966 57.895 8.43 0.00 0.00 6.01
539 2007 2.690778 CCCCTCCTTTCTTTGCGCG 61.691 63.158 0.00 0.00 0.00 6.86
540 2008 0.893727 TTCCCCTCCTTTCTTTGCGC 60.894 55.000 0.00 0.00 0.00 6.09
541 2009 1.168714 CTTCCCCTCCTTTCTTTGCG 58.831 55.000 0.00 0.00 0.00 4.85
542 2010 0.891373 GCTTCCCCTCCTTTCTTTGC 59.109 55.000 0.00 0.00 0.00 3.68
543 2011 2.165998 CTGCTTCCCCTCCTTTCTTTG 58.834 52.381 0.00 0.00 0.00 2.77
544 2012 2.040947 CTCTGCTTCCCCTCCTTTCTTT 59.959 50.000 0.00 0.00 0.00 2.52
545 2013 1.632920 CTCTGCTTCCCCTCCTTTCTT 59.367 52.381 0.00 0.00 0.00 2.52
546 2014 1.284313 CTCTGCTTCCCCTCCTTTCT 58.716 55.000 0.00 0.00 0.00 2.52
547 2015 0.254462 CCTCTGCTTCCCCTCCTTTC 59.746 60.000 0.00 0.00 0.00 2.62
548 2016 0.178861 TCCTCTGCTTCCCCTCCTTT 60.179 55.000 0.00 0.00 0.00 3.11
549 2017 0.620121 CTCCTCTGCTTCCCCTCCTT 60.620 60.000 0.00 0.00 0.00 3.36
550 2018 1.002792 CTCCTCTGCTTCCCCTCCT 59.997 63.158 0.00 0.00 0.00 3.69
551 2019 2.069430 CCTCCTCTGCTTCCCCTCC 61.069 68.421 0.00 0.00 0.00 4.30
552 2020 2.069430 CCCTCCTCTGCTTCCCCTC 61.069 68.421 0.00 0.00 0.00 4.30
553 2021 2.041928 CCCTCCTCTGCTTCCCCT 59.958 66.667 0.00 0.00 0.00 4.79
554 2022 3.803162 GCCCTCCTCTGCTTCCCC 61.803 72.222 0.00 0.00 0.00 4.81
555 2023 3.803162 GGCCCTCCTCTGCTTCCC 61.803 72.222 0.00 0.00 0.00 3.97
556 2024 4.168291 CGGCCCTCCTCTGCTTCC 62.168 72.222 0.00 0.00 0.00 3.46
557 2025 4.168291 CCGGCCCTCCTCTGCTTC 62.168 72.222 0.00 0.00 0.00 3.86
558 2026 4.722535 TCCGGCCCTCCTCTGCTT 62.723 66.667 0.00 0.00 0.00 3.91
657 2229 1.625818 CCTACAGGACAGCCAAGAGTT 59.374 52.381 0.00 0.00 37.39 3.01
662 2304 1.923395 CCCCCTACAGGACAGCCAA 60.923 63.158 0.00 0.00 38.24 4.52
690 2332 3.560636 AATGACTAATCCAACTCCCGG 57.439 47.619 0.00 0.00 0.00 5.73
740 2382 2.961526 TTGCAGATAGAACTCCCGAC 57.038 50.000 0.00 0.00 0.00 4.79
741 2383 2.365617 GGATTGCAGATAGAACTCCCGA 59.634 50.000 0.00 0.00 0.00 5.14
742 2384 2.760374 GGATTGCAGATAGAACTCCCG 58.240 52.381 0.00 0.00 0.00 5.14
743 2385 2.365617 TCGGATTGCAGATAGAACTCCC 59.634 50.000 0.00 0.00 0.00 4.30
744 2386 3.648009 CTCGGATTGCAGATAGAACTCC 58.352 50.000 0.00 0.00 0.00 3.85
745 2387 3.056304 GCTCGGATTGCAGATAGAACTC 58.944 50.000 0.00 0.00 0.00 3.01
746 2388 2.544694 CGCTCGGATTGCAGATAGAACT 60.545 50.000 0.00 0.00 0.00 3.01
841 2486 3.181438 ACCTGGCAATGGTGTGTTACTTA 60.181 43.478 0.00 0.00 36.30 2.24
842 2487 2.238521 CCTGGCAATGGTGTGTTACTT 58.761 47.619 0.00 0.00 0.00 2.24
844 2489 1.616159 ACCTGGCAATGGTGTGTTAC 58.384 50.000 0.00 0.00 36.30 2.50
845 2490 2.373335 AACCTGGCAATGGTGTGTTA 57.627 45.000 0.00 0.00 37.93 2.41
846 2491 2.158534 TCTAACCTGGCAATGGTGTGTT 60.159 45.455 0.00 0.00 37.93 3.32
848 2493 2.198827 TCTAACCTGGCAATGGTGTG 57.801 50.000 0.00 0.00 37.93 3.82
849 2494 3.780294 TCTATCTAACCTGGCAATGGTGT 59.220 43.478 0.00 0.00 37.93 4.16
850 2495 4.422073 TCTATCTAACCTGGCAATGGTG 57.578 45.455 0.00 0.00 37.93 4.17
851 2496 6.084738 TCTATCTATCTAACCTGGCAATGGT 58.915 40.000 0.00 0.00 39.91 3.55
852 2497 6.611613 TCTATCTATCTAACCTGGCAATGG 57.388 41.667 0.00 0.00 0.00 3.16
910 2560 3.246619 CAGTACAGGAGAAGAAACGAGC 58.753 50.000 0.00 0.00 0.00 5.03
934 2591 1.342174 TGTTCTGGTGGTTACGAGGTC 59.658 52.381 0.00 0.00 33.89 3.85
976 2637 1.450531 CTGCAATGGATCTTCCGGCC 61.451 60.000 0.00 0.00 40.17 6.13
977 2638 0.464373 TCTGCAATGGATCTTCCGGC 60.464 55.000 0.00 0.00 40.17 6.13
992 2653 1.354506 CGCTTAGGCATGCTTCTGC 59.645 57.895 18.92 16.07 41.53 4.26
993 2654 0.654683 GACGCTTAGGCATGCTTCTG 59.345 55.000 18.92 7.60 38.60 3.02
994 2655 0.250234 TGACGCTTAGGCATGCTTCT 59.750 50.000 18.92 9.75 38.60 2.85
997 2669 1.817099 GCTGACGCTTAGGCATGCT 60.817 57.895 18.92 6.26 37.16 3.79
998 2670 2.108514 TGCTGACGCTTAGGCATGC 61.109 57.895 9.90 9.90 37.16 4.06
1003 2675 4.079090 CGAGTGCTGACGCTTAGG 57.921 61.111 0.00 0.00 36.56 2.69
1449 3124 4.659172 CTTCCCGTGGCTGCCCAA 62.659 66.667 17.53 0.00 44.33 4.12
1938 4917 0.618680 TGCATGTAGGCTCCACTCCT 60.619 55.000 0.00 0.00 37.72 3.69
2061 5051 4.578105 GGAGAAAAGGACAGGATATGCTTG 59.422 45.833 0.00 0.00 0.00 4.01
2266 5268 3.775661 AGCACAAAAGTACAACGCTTT 57.224 38.095 0.00 0.00 37.73 3.51
2298 5301 5.716703 CCACCTTTTCTAATCCCTGTCAATT 59.283 40.000 0.00 0.00 0.00 2.32
2370 5373 5.474578 TCATGGCAGTTAGATACAGGATC 57.525 43.478 0.00 0.00 34.40 3.36
2433 5449 5.416271 TCCTGAAATAAGGTGTAGTGACC 57.584 43.478 0.00 0.00 38.58 4.02
2441 5481 5.192927 TGCCACTAATCCTGAAATAAGGTG 58.807 41.667 0.00 0.00 38.58 4.00
2443 5483 4.823989 CCTGCCACTAATCCTGAAATAAGG 59.176 45.833 0.00 0.00 38.84 2.69
2520 5560 3.645434 TCCATGCCATTAATCCTGCTTT 58.355 40.909 0.00 0.00 0.00 3.51
2690 5743 6.045072 TCGGGCTTTATACTGAAAAGAGAA 57.955 37.500 0.00 0.00 36.27 2.87
2745 5798 1.003866 GCGTATGACCCATTCTTTCGC 60.004 52.381 0.00 0.00 39.69 4.70
3025 6084 6.912203 TTGTACAACTCGAACAATTTCAGA 57.088 33.333 3.59 0.00 0.00 3.27
3055 6116 6.378280 ACCATTTAATCTTGACTCCACCATTC 59.622 38.462 0.00 0.00 0.00 2.67


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

AutoCloner maintained by Alex Coulton.