Multiple sequence alignment - TraesCS1D01G067600

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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 TraesCS1D01G067600 chr1D 100.000 3098 0 0 1 3098 49425985 49422888 0.000000e+00 5722.0
1 TraesCS1D01G067600 chr1D 83.295 2167 328 30 1 2146 50059586 50061739 0.000000e+00 1965.0
2 TraesCS1D01G067600 chr1D 82.348 2283 362 32 1 2257 49617381 49619648 0.000000e+00 1945.0
3 TraesCS1D01G067600 chr1D 82.733 2166 346 22 2 2149 49956629 49958784 0.000000e+00 1903.0
4 TraesCS1D01G067600 chr1D 81.250 80 14 1 2494 2572 49589750 49589671 2.580000e-06 63.9
5 TraesCS1D01G067600 chr1B 96.246 2797 84 7 11 2794 69549357 69546569 0.000000e+00 4564.0
6 TraesCS1D01G067600 chr1B 82.108 2286 368 32 1 2258 70170142 70172414 0.000000e+00 1917.0
7 TraesCS1D01G067600 chr1B 82.022 2275 374 28 3 2257 70185828 70188087 0.000000e+00 1903.0
8 TraesCS1D01G067600 chr1B 92.079 101 7 1 2796 2895 69544090 69543990 1.160000e-29 141.0
9 TraesCS1D01G067600 chr1A 94.504 2256 83 12 553 2794 48994350 48992122 0.000000e+00 3441.0
10 TraesCS1D01G067600 chr1A 81.704 2301 366 46 1 2270 49347121 49349397 0.000000e+00 1866.0
11 TraesCS1D01G067600 chr1A 80.067 898 150 18 1388 2263 49304907 49305797 9.370000e-180 640.0
12 TraesCS1D01G067600 chr1A 95.000 100 5 0 2796 2895 48983367 48983268 1.150000e-34 158.0
13 TraesCS1D01G067600 chr1A 81.250 80 14 1 2494 2572 49100256 49100177 2.580000e-06 63.9
14 TraesCS1D01G067600 chr6B 83.995 2443 346 28 1 2410 601866197 601868627 0.000000e+00 2303.0
15 TraesCS1D01G067600 chr6B 79.644 393 50 17 2419 2794 601868733 601869112 3.960000e-64 255.0
16 TraesCS1D01G067600 chr6A 83.627 2443 355 28 1 2410 547815495 547817925 0.000000e+00 2254.0
17 TraesCS1D01G067600 chr6D 80.053 376 46 16 2435 2794 401296653 401297015 5.130000e-63 252.0
18 TraesCS1D01G067600 chr2D 80.672 238 39 5 2814 3045 203042381 203042145 8.830000e-41 178.0
19 TraesCS1D01G067600 chr2B 80.426 235 41 3 2814 3043 256952011 256951777 1.140000e-39 174.0
20 TraesCS1D01G067600 chr7B 83.333 180 22 4 2814 2985 275461321 275461500 3.200000e-35 159.0
21 TraesCS1D01G067600 chr7B 83.824 68 5 5 2930 2992 522084310 522084376 3.340000e-05 60.2
22 TraesCS1D01G067600 chr2A 79.487 234 41 5 2814 3045 231349933 231349705 3.200000e-35 159.0
23 TraesCS1D01G067600 chr7A 86.861 137 16 2 2814 2948 323433956 323433820 5.350000e-33 152.0
24 TraesCS1D01G067600 chr5A 81.667 180 28 4 2814 2989 467578008 467577830 8.950000e-31 145.0
25 TraesCS1D01G067600 chr7D 81.768 181 24 4 2814 2985 285229227 285229047 3.220000e-30 143.0


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 TraesCS1D01G067600 chr1D 49422888 49425985 3097 True 5722.0 5722 100.0000 1 3098 1 chr1D.!!$R1 3097
1 TraesCS1D01G067600 chr1D 50059586 50061739 2153 False 1965.0 1965 83.2950 1 2146 1 chr1D.!!$F3 2145
2 TraesCS1D01G067600 chr1D 49617381 49619648 2267 False 1945.0 1945 82.3480 1 2257 1 chr1D.!!$F1 2256
3 TraesCS1D01G067600 chr1D 49956629 49958784 2155 False 1903.0 1903 82.7330 2 2149 1 chr1D.!!$F2 2147
4 TraesCS1D01G067600 chr1B 69543990 69549357 5367 True 2352.5 4564 94.1625 11 2895 2 chr1B.!!$R1 2884
5 TraesCS1D01G067600 chr1B 70170142 70172414 2272 False 1917.0 1917 82.1080 1 2258 1 chr1B.!!$F1 2257
6 TraesCS1D01G067600 chr1B 70185828 70188087 2259 False 1903.0 1903 82.0220 3 2257 1 chr1B.!!$F2 2254
7 TraesCS1D01G067600 chr1A 48992122 48994350 2228 True 3441.0 3441 94.5040 553 2794 1 chr1A.!!$R2 2241
8 TraesCS1D01G067600 chr1A 49347121 49349397 2276 False 1866.0 1866 81.7040 1 2270 1 chr1A.!!$F2 2269
9 TraesCS1D01G067600 chr1A 49304907 49305797 890 False 640.0 640 80.0670 1388 2263 1 chr1A.!!$F1 875
10 TraesCS1D01G067600 chr6B 601866197 601869112 2915 False 1279.0 2303 81.8195 1 2794 2 chr6B.!!$F1 2793
11 TraesCS1D01G067600 chr6A 547815495 547817925 2430 False 2254.0 2254 83.6270 1 2410 1 chr6A.!!$F1 2409

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
344 359 1.08437 CGGTCATCCACGGCTTCTTC 61.084 60.0 0.0 0.0 0.0 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2121 2159 0.251634 GAGAGGGAGCTCCAAACCAG 59.748 60.0 33.29 0.0 38.24 4.0 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
207 214 1.734465 GTGTGCCTAACTGCATCTCAC 59.266 52.381 0.00 0.00 44.30 3.51
211 218 1.645034 CCTAACTGCATCTCACACGG 58.355 55.000 0.00 0.00 0.00 4.94
344 359 1.084370 CGGTCATCCACGGCTTCTTC 61.084 60.000 0.00 0.00 0.00 2.87
354 369 1.270893 ACGGCTTCTTCAAGGAAGGAC 60.271 52.381 6.17 0.00 41.93 3.85
488 503 2.504367 GCAAGGCAGAGTTGTTCCTAA 58.496 47.619 0.00 0.00 0.00 2.69
541 556 7.360361 CAGATAACGTGACATATACTGCAGTA 58.640 38.462 27.91 27.91 34.67 2.74
609 624 7.530426 AAATGTTTAGAGAAATGACAAGCCT 57.470 32.000 0.00 0.00 0.00 4.58
645 660 6.128172 CCAAATACTGTCACTTGGAACTCATC 60.128 42.308 8.89 0.00 40.72 2.92
1210 1228 5.013704 TGCAAAGAAGGAAGGGTTACAGATA 59.986 40.000 0.00 0.00 0.00 1.98
1347 1365 5.602561 AGTACTTGATACCATGGCATCAGTA 59.397 40.000 23.71 22.35 33.85 2.74
1714 1738 4.270084 CCATGATCAATGCAATGTTCAAGC 59.730 41.667 17.17 0.00 33.91 4.01
1747 1771 7.497925 AGAGAAGAAGCTAACGATTTGTTTT 57.502 32.000 0.00 0.00 42.09 2.43
1950 1974 3.057946 GTGAGATTGTCAAGGCTGGAAAC 60.058 47.826 0.00 0.00 36.74 2.78
2121 2159 4.083271 GCACTAGACAGAAAACCATTGGTC 60.083 45.833 9.22 0.00 33.12 4.02
2462 2615 1.885887 TCTTGGTGCAGGTGTTTATGC 59.114 47.619 0.00 0.00 42.86 3.14
2725 2890 4.503741 AAATGTCACCCTTCATTTGACG 57.496 40.909 0.00 0.00 42.20 4.35
2776 2942 1.941294 GCATCATCCAAGCACTCTCAG 59.059 52.381 0.00 0.00 0.00 3.35
2794 2960 2.693074 TCAGTTTTTCTTCCTTGGGCAC 59.307 45.455 0.00 0.00 0.00 5.01
2826 5469 4.919653 GCTGTCAAGCGAGGATCA 57.080 55.556 0.00 0.00 40.27 2.92
2827 5470 2.378028 GCTGTCAAGCGAGGATCAC 58.622 57.895 0.00 0.00 40.27 3.06
2876 5520 3.041946 GGGCTCCTCCTAAAATCTCTCA 58.958 50.000 0.00 0.00 34.39 3.27
2883 5527 5.604650 TCCTCCTAAAATCTCTCATTCCCTC 59.395 44.000 0.00 0.00 0.00 4.30
2895 5539 6.041865 TCTCTCATTCCCTCTTCATCATCTTC 59.958 42.308 0.00 0.00 0.00 2.87
2896 5540 5.664457 TCTCATTCCCTCTTCATCATCTTCA 59.336 40.000 0.00 0.00 0.00 3.02
2897 5541 5.678583 TCATTCCCTCTTCATCATCTTCAC 58.321 41.667 0.00 0.00 0.00 3.18
2898 5542 5.190330 TCATTCCCTCTTCATCATCTTCACA 59.810 40.000 0.00 0.00 0.00 3.58
2899 5543 5.705397 TTCCCTCTTCATCATCTTCACAT 57.295 39.130 0.00 0.00 0.00 3.21
2900 5544 5.705397 TCCCTCTTCATCATCTTCACATT 57.295 39.130 0.00 0.00 0.00 2.71
2901 5545 5.678583 TCCCTCTTCATCATCTTCACATTC 58.321 41.667 0.00 0.00 0.00 2.67
2902 5546 5.427806 TCCCTCTTCATCATCTTCACATTCT 59.572 40.000 0.00 0.00 0.00 2.40
2903 5547 6.612863 TCCCTCTTCATCATCTTCACATTCTA 59.387 38.462 0.00 0.00 0.00 2.10
2904 5548 6.705381 CCCTCTTCATCATCTTCACATTCTAC 59.295 42.308 0.00 0.00 0.00 2.59
2905 5549 7.270779 CCTCTTCATCATCTTCACATTCTACA 58.729 38.462 0.00 0.00 0.00 2.74
2906 5550 7.767659 CCTCTTCATCATCTTCACATTCTACAA 59.232 37.037 0.00 0.00 0.00 2.41
2907 5551 8.484641 TCTTCATCATCTTCACATTCTACAAC 57.515 34.615 0.00 0.00 0.00 3.32
2908 5552 8.096414 TCTTCATCATCTTCACATTCTACAACA 58.904 33.333 0.00 0.00 0.00 3.33
2909 5553 7.601073 TCATCATCTTCACATTCTACAACAC 57.399 36.000 0.00 0.00 0.00 3.32
2910 5554 6.311200 TCATCATCTTCACATTCTACAACACG 59.689 38.462 0.00 0.00 0.00 4.49
2911 5555 5.778862 TCATCTTCACATTCTACAACACGA 58.221 37.500 0.00 0.00 0.00 4.35
2912 5556 6.398095 TCATCTTCACATTCTACAACACGAT 58.602 36.000 0.00 0.00 0.00 3.73
2913 5557 6.531594 TCATCTTCACATTCTACAACACGATC 59.468 38.462 0.00 0.00 0.00 3.69
2914 5558 6.025749 TCTTCACATTCTACAACACGATCT 57.974 37.500 0.00 0.00 0.00 2.75
2915 5559 6.455647 TCTTCACATTCTACAACACGATCTT 58.544 36.000 0.00 0.00 0.00 2.40
2916 5560 7.599171 TCTTCACATTCTACAACACGATCTTA 58.401 34.615 0.00 0.00 0.00 2.10
2917 5561 7.755373 TCTTCACATTCTACAACACGATCTTAG 59.245 37.037 0.00 0.00 0.00 2.18
2918 5562 5.805486 TCACATTCTACAACACGATCTTAGC 59.195 40.000 0.00 0.00 0.00 3.09
2919 5563 5.005779 CACATTCTACAACACGATCTTAGCC 59.994 44.000 0.00 0.00 0.00 3.93
2920 5564 3.416119 TCTACAACACGATCTTAGCCG 57.584 47.619 0.00 0.00 0.00 5.52
2921 5565 3.011818 TCTACAACACGATCTTAGCCGA 58.988 45.455 0.00 0.00 0.00 5.54
2922 5566 2.961526 ACAACACGATCTTAGCCGAT 57.038 45.000 0.00 0.00 0.00 4.18
2923 5567 2.540515 ACAACACGATCTTAGCCGATG 58.459 47.619 0.00 0.00 0.00 3.84
2924 5568 2.165641 ACAACACGATCTTAGCCGATGA 59.834 45.455 0.00 0.00 0.00 2.92
2925 5569 2.493713 ACACGATCTTAGCCGATGAC 57.506 50.000 0.00 0.00 0.00 3.06
2926 5570 2.025155 ACACGATCTTAGCCGATGACT 58.975 47.619 0.00 0.00 0.00 3.41
2927 5571 2.427453 ACACGATCTTAGCCGATGACTT 59.573 45.455 0.00 0.00 0.00 3.01
2928 5572 3.046390 CACGATCTTAGCCGATGACTTC 58.954 50.000 0.00 0.00 0.00 3.01
2940 5584 2.555199 GATGACTTCGATGTGGGAAGG 58.445 52.381 8.91 0.00 44.02 3.46
2941 5585 1.639722 TGACTTCGATGTGGGAAGGA 58.360 50.000 8.91 0.00 44.02 3.36
2942 5586 1.275291 TGACTTCGATGTGGGAAGGAC 59.725 52.381 8.91 0.00 44.02 3.85
2943 5587 0.613777 ACTTCGATGTGGGAAGGACC 59.386 55.000 2.72 0.00 44.02 4.46
2944 5588 0.613260 CTTCGATGTGGGAAGGACCA 59.387 55.000 0.00 0.00 41.20 4.02
2945 5589 1.210478 CTTCGATGTGGGAAGGACCAT 59.790 52.381 0.00 0.00 43.59 3.55
2946 5590 2.168458 TCGATGTGGGAAGGACCATA 57.832 50.000 0.00 0.00 43.59 2.74
2947 5591 2.473070 TCGATGTGGGAAGGACCATAA 58.527 47.619 0.00 0.00 43.59 1.90
2948 5592 2.841266 TCGATGTGGGAAGGACCATAAA 59.159 45.455 0.00 0.00 43.59 1.40
2949 5593 3.264706 TCGATGTGGGAAGGACCATAAAA 59.735 43.478 0.00 0.00 43.59 1.52
2950 5594 4.013728 CGATGTGGGAAGGACCATAAAAA 58.986 43.478 0.00 0.00 43.59 1.94
2972 5616 6.757897 AAAAACTCACAATGTCTCTGTTGA 57.242 33.333 0.00 0.00 0.00 3.18
2973 5617 5.998454 AAACTCACAATGTCTCTGTTGAG 57.002 39.130 0.00 0.00 41.51 3.02
2974 5618 4.000331 ACTCACAATGTCTCTGTTGAGG 58.000 45.455 0.00 0.00 40.58 3.86
2975 5619 2.740981 CTCACAATGTCTCTGTTGAGGC 59.259 50.000 0.00 0.00 44.68 4.70
2980 5624 2.245159 TGTCTCTGTTGAGGCACTTG 57.755 50.000 0.00 0.00 46.67 3.16
2981 5625 1.486310 TGTCTCTGTTGAGGCACTTGT 59.514 47.619 0.00 0.00 46.67 3.16
2982 5626 2.698274 TGTCTCTGTTGAGGCACTTGTA 59.302 45.455 0.00 0.00 46.67 2.41
2983 5627 3.133901 TGTCTCTGTTGAGGCACTTGTAA 59.866 43.478 0.00 0.00 46.67 2.41
2984 5628 4.202357 TGTCTCTGTTGAGGCACTTGTAAT 60.202 41.667 0.00 0.00 46.67 1.89
2985 5629 4.757149 GTCTCTGTTGAGGCACTTGTAATT 59.243 41.667 0.00 0.00 43.92 1.40
2986 5630 4.756642 TCTCTGTTGAGGCACTTGTAATTG 59.243 41.667 0.00 0.00 41.55 2.32
2987 5631 4.713553 TCTGTTGAGGCACTTGTAATTGA 58.286 39.130 0.00 0.00 41.55 2.57
2988 5632 5.316167 TCTGTTGAGGCACTTGTAATTGAT 58.684 37.500 0.00 0.00 41.55 2.57
2989 5633 6.472016 TCTGTTGAGGCACTTGTAATTGATA 58.528 36.000 0.00 0.00 41.55 2.15
2990 5634 7.112122 TCTGTTGAGGCACTTGTAATTGATAT 58.888 34.615 0.00 0.00 41.55 1.63
2991 5635 7.611467 TCTGTTGAGGCACTTGTAATTGATATT 59.389 33.333 0.00 0.00 41.55 1.28
2992 5636 7.537715 TGTTGAGGCACTTGTAATTGATATTG 58.462 34.615 0.00 0.00 41.55 1.90
2993 5637 7.392953 TGTTGAGGCACTTGTAATTGATATTGA 59.607 33.333 0.00 0.00 41.55 2.57
2994 5638 7.936496 TGAGGCACTTGTAATTGATATTGAA 57.064 32.000 0.00 0.00 41.55 2.69
2995 5639 8.523915 TGAGGCACTTGTAATTGATATTGAAT 57.476 30.769 0.00 0.00 41.55 2.57
2996 5640 8.623903 TGAGGCACTTGTAATTGATATTGAATC 58.376 33.333 0.00 0.00 41.55 2.52
2997 5641 8.523915 AGGCACTTGTAATTGATATTGAATCA 57.476 30.769 0.00 0.00 27.25 2.57
2998 5642 8.408601 AGGCACTTGTAATTGATATTGAATCAC 58.591 33.333 0.00 0.00 27.25 3.06
2999 5643 8.408601 GGCACTTGTAATTGATATTGAATCACT 58.591 33.333 0.00 0.00 0.00 3.41
3000 5644 9.229784 GCACTTGTAATTGATATTGAATCACTG 57.770 33.333 0.00 0.00 0.00 3.66
3016 5660 9.513906 TTGAATCACTGAAATATGTTTACCTCA 57.486 29.630 0.00 0.00 0.00 3.86
3017 5661 9.166173 TGAATCACTGAAATATGTTTACCTCAG 57.834 33.333 1.37 1.37 0.00 3.35
3018 5662 9.167311 GAATCACTGAAATATGTTTACCTCAGT 57.833 33.333 2.44 2.44 37.64 3.41
3019 5663 9.520515 AATCACTGAAATATGTTTACCTCAGTT 57.479 29.630 4.94 0.00 35.35 3.16
3020 5664 8.322906 TCACTGAAATATGTTTACCTCAGTTG 57.677 34.615 4.94 2.93 35.35 3.16
3021 5665 7.023575 CACTGAAATATGTTTACCTCAGTTGC 58.976 38.462 4.94 0.00 35.35 4.17
3022 5666 6.714810 ACTGAAATATGTTTACCTCAGTTGCA 59.285 34.615 2.44 0.00 34.04 4.08
3023 5667 7.230510 ACTGAAATATGTTTACCTCAGTTGCAA 59.769 33.333 0.00 0.00 34.04 4.08
3024 5668 7.367285 TGAAATATGTTTACCTCAGTTGCAAC 58.633 34.615 22.17 22.17 0.00 4.17
3025 5669 3.896648 ATGTTTACCTCAGTTGCAACG 57.103 42.857 23.21 17.58 0.00 4.10
3026 5670 2.634600 TGTTTACCTCAGTTGCAACGT 58.365 42.857 23.21 16.89 0.00 3.99
3027 5671 2.610374 TGTTTACCTCAGTTGCAACGTC 59.390 45.455 23.21 0.15 0.00 4.34
3028 5672 1.873698 TTACCTCAGTTGCAACGTCC 58.126 50.000 23.21 0.00 0.00 4.79
3029 5673 0.753867 TACCTCAGTTGCAACGTCCA 59.246 50.000 23.21 8.10 0.00 4.02
3030 5674 0.532862 ACCTCAGTTGCAACGTCCAG 60.533 55.000 23.21 16.19 0.00 3.86
3031 5675 1.230635 CCTCAGTTGCAACGTCCAGG 61.231 60.000 23.21 20.49 0.00 4.45
3032 5676 1.845809 CTCAGTTGCAACGTCCAGGC 61.846 60.000 23.21 0.00 0.00 4.85
3033 5677 2.186160 CAGTTGCAACGTCCAGGCA 61.186 57.895 23.21 0.00 35.41 4.75
3034 5678 1.453015 AGTTGCAACGTCCAGGCAA 60.453 52.632 23.21 11.31 44.50 4.52
3035 5679 4.172625 TTGCAACGTCCAGGCAAT 57.827 50.000 11.31 0.00 42.12 3.56
3036 5680 1.659233 TTGCAACGTCCAGGCAATG 59.341 52.632 11.31 0.00 42.12 2.82
3037 5681 0.821301 TTGCAACGTCCAGGCAATGA 60.821 50.000 11.31 0.00 42.12 2.57
3038 5682 1.236616 TGCAACGTCCAGGCAATGAG 61.237 55.000 0.00 0.00 34.05 2.90
3039 5683 1.503542 CAACGTCCAGGCAATGAGC 59.496 57.895 0.00 0.00 44.65 4.26
3040 5684 0.957395 CAACGTCCAGGCAATGAGCT 60.957 55.000 0.00 0.00 44.79 4.09
3041 5685 0.613260 AACGTCCAGGCAATGAGCTA 59.387 50.000 0.00 0.00 44.79 3.32
3042 5686 0.176680 ACGTCCAGGCAATGAGCTAG 59.823 55.000 0.00 0.00 44.79 3.42
3043 5687 0.176680 CGTCCAGGCAATGAGCTAGT 59.823 55.000 0.00 0.00 44.79 2.57
3044 5688 1.409064 CGTCCAGGCAATGAGCTAGTA 59.591 52.381 0.00 0.00 44.79 1.82
3045 5689 2.799917 CGTCCAGGCAATGAGCTAGTAC 60.800 54.545 0.00 0.00 44.79 2.73
3046 5690 2.168521 GTCCAGGCAATGAGCTAGTACA 59.831 50.000 0.00 0.00 44.79 2.90
3047 5691 3.041211 TCCAGGCAATGAGCTAGTACAT 58.959 45.455 0.00 0.00 44.79 2.29
3048 5692 4.039245 GTCCAGGCAATGAGCTAGTACATA 59.961 45.833 0.00 0.00 44.79 2.29
3049 5693 4.840680 TCCAGGCAATGAGCTAGTACATAT 59.159 41.667 0.00 0.00 44.79 1.78
3050 5694 6.016555 TCCAGGCAATGAGCTAGTACATATA 58.983 40.000 0.00 0.00 44.79 0.86
3051 5695 6.496911 TCCAGGCAATGAGCTAGTACATATAA 59.503 38.462 0.00 0.00 44.79 0.98
3052 5696 7.180946 TCCAGGCAATGAGCTAGTACATATAAT 59.819 37.037 0.00 0.00 44.79 1.28
3053 5697 7.826252 CCAGGCAATGAGCTAGTACATATAATT 59.174 37.037 0.00 0.00 44.79 1.40
3054 5698 8.663025 CAGGCAATGAGCTAGTACATATAATTG 58.337 37.037 0.00 0.00 44.79 2.32
3055 5699 8.378565 AGGCAATGAGCTAGTACATATAATTGT 58.621 33.333 0.00 0.00 44.79 2.71
3056 5700 9.653287 GGCAATGAGCTAGTACATATAATTGTA 57.347 33.333 0.00 0.00 44.79 2.41
3084 5728 9.851686 AGTATATGTCTATGAATTTCCAGCAAA 57.148 29.630 0.00 0.00 0.00 3.68
3089 5733 9.729281 ATGTCTATGAATTTCCAGCAAATTTTT 57.271 25.926 0.00 0.00 43.56 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 2.751837 CCGAAGAAGGCAAGCCCC 60.752 66.667 7.62 0.00 36.58 5.80
207 214 3.786635 AGCTCTTTAGAACTATGCCGTG 58.213 45.455 0.00 0.00 0.00 4.94
211 218 4.493220 CGCACAAGCTCTTTAGAACTATGC 60.493 45.833 0.00 8.30 39.10 3.14
344 359 3.503748 CCTTGCTTACTTGTCCTTCCTTG 59.496 47.826 0.00 0.00 0.00 3.61
452 467 1.574526 TTGCCCATAGCTCTGGCCTT 61.575 55.000 12.62 0.00 44.72 4.35
453 468 1.992519 CTTGCCCATAGCTCTGGCCT 61.993 60.000 12.62 0.00 44.72 5.19
488 503 1.559682 ACCGTTATCAACCATCTGCCT 59.440 47.619 0.00 0.00 0.00 4.75
645 660 2.905935 CTTGCAGAGGGAGGCCATGG 62.906 65.000 7.63 7.63 0.00 3.66
1109 1125 7.780064 TCTGTTCATCATTTCAGAAACCAAAA 58.220 30.769 0.00 0.00 34.61 2.44
1110 1126 7.345422 TCTGTTCATCATTTCAGAAACCAAA 57.655 32.000 0.00 0.00 34.61 3.28
1178 1196 5.104735 ACCCTTCCTTCTTTGCATAGACTAG 60.105 44.000 6.34 2.91 0.00 2.57
1210 1228 3.321111 ACGAAGTCAAGGATACTGTGTGT 59.679 43.478 0.00 0.00 45.31 3.72
1262 1280 6.472163 CCCGTCAATCAGCAAATTAAATGTAC 59.528 38.462 0.00 0.00 0.00 2.90
1714 1738 5.799936 CGTTAGCTTCTTCTCTTCTCTGAAG 59.200 44.000 0.00 1.23 40.53 3.02
1747 1771 0.538584 CCACTGGCTGATACTGCAGA 59.461 55.000 23.35 4.31 38.14 4.26
1921 1945 3.823304 GCCTTGACAATCTCACCTTTCTT 59.177 43.478 0.00 0.00 0.00 2.52
1950 1974 7.445121 TCCTGCCATCAACTTTAGACATATAG 58.555 38.462 0.00 0.00 0.00 1.31
2121 2159 0.251634 GAGAGGGAGCTCCAAACCAG 59.748 60.000 33.29 0.00 38.24 4.00
2350 2407 9.944376 AGATCTTAAAACAGCAACAGTAGAATA 57.056 29.630 0.00 0.00 0.00 1.75
2725 2890 7.223777 GCAGAACTTGAGAGTCAACTATTATCC 59.776 40.741 0.00 0.00 34.21 2.59
2776 2942 3.751479 ATGTGCCCAAGGAAGAAAAAC 57.249 42.857 0.00 0.00 0.00 2.43
2794 2960 2.203394 AGCGCCTGGGCCATTATG 60.203 61.111 6.72 0.00 37.98 1.90
2835 5478 7.454694 GGAGCCCACATAAATAATATTTTCCCT 59.545 37.037 3.36 0.00 0.00 4.20
2836 5479 7.454694 AGGAGCCCACATAAATAATATTTTCCC 59.545 37.037 3.36 0.00 0.00 3.97
2839 5482 8.234525 AGGAGGAGCCCACATAAATAATATTTT 58.765 33.333 3.36 0.00 37.37 1.82
2876 5520 5.705397 TGTGAAGATGATGAAGAGGGAAT 57.295 39.130 0.00 0.00 0.00 3.01
2883 5527 8.173775 GTGTTGTAGAATGTGAAGATGATGAAG 58.826 37.037 0.00 0.00 0.00 3.02
2895 5539 5.005779 GGCTAAGATCGTGTTGTAGAATGTG 59.994 44.000 0.00 0.00 0.00 3.21
2896 5540 5.109903 GGCTAAGATCGTGTTGTAGAATGT 58.890 41.667 0.00 0.00 0.00 2.71
2897 5541 4.207224 CGGCTAAGATCGTGTTGTAGAATG 59.793 45.833 0.00 0.00 0.00 2.67
2898 5542 4.097437 TCGGCTAAGATCGTGTTGTAGAAT 59.903 41.667 0.00 0.00 0.00 2.40
2899 5543 3.441222 TCGGCTAAGATCGTGTTGTAGAA 59.559 43.478 0.00 0.00 0.00 2.10
2900 5544 3.011818 TCGGCTAAGATCGTGTTGTAGA 58.988 45.455 0.00 0.00 0.00 2.59
2901 5545 3.416119 TCGGCTAAGATCGTGTTGTAG 57.584 47.619 0.00 0.00 0.00 2.74
2902 5546 3.379057 TCATCGGCTAAGATCGTGTTGTA 59.621 43.478 0.00 0.00 0.00 2.41
2903 5547 2.165641 TCATCGGCTAAGATCGTGTTGT 59.834 45.455 0.00 0.00 0.00 3.32
2904 5548 2.535984 GTCATCGGCTAAGATCGTGTTG 59.464 50.000 0.00 0.00 0.00 3.33
2905 5549 2.427453 AGTCATCGGCTAAGATCGTGTT 59.573 45.455 0.00 0.00 0.00 3.32
2906 5550 2.025155 AGTCATCGGCTAAGATCGTGT 58.975 47.619 0.00 0.00 0.00 4.49
2907 5551 2.783828 AGTCATCGGCTAAGATCGTG 57.216 50.000 0.00 0.00 0.00 4.35
2908 5552 3.357166 GAAGTCATCGGCTAAGATCGT 57.643 47.619 0.00 0.00 0.00 3.73
2920 5564 2.168521 TCCTTCCCACATCGAAGTCATC 59.831 50.000 0.00 0.00 35.90 2.92
2921 5565 2.093447 GTCCTTCCCACATCGAAGTCAT 60.093 50.000 0.00 0.00 35.90 3.06
2922 5566 1.275291 GTCCTTCCCACATCGAAGTCA 59.725 52.381 0.00 0.00 35.90 3.41
2923 5567 1.405661 GGTCCTTCCCACATCGAAGTC 60.406 57.143 0.00 0.00 35.90 3.01
2924 5568 0.613777 GGTCCTTCCCACATCGAAGT 59.386 55.000 0.00 0.00 35.90 3.01
2925 5569 0.613260 TGGTCCTTCCCACATCGAAG 59.387 55.000 0.00 0.00 37.14 3.79
2926 5570 1.285280 ATGGTCCTTCCCACATCGAA 58.715 50.000 0.00 0.00 37.31 3.71
2927 5571 2.168458 TATGGTCCTTCCCACATCGA 57.832 50.000 0.00 0.00 37.31 3.59
2928 5572 3.275617 TTTATGGTCCTTCCCACATCG 57.724 47.619 0.00 0.00 37.31 3.84
2949 5593 6.183360 CCTCAACAGAGACATTGTGAGTTTTT 60.183 38.462 0.00 0.00 0.00 1.94
2950 5594 5.297776 CCTCAACAGAGACATTGTGAGTTTT 59.702 40.000 0.00 0.00 0.00 2.43
2951 5595 4.818546 CCTCAACAGAGACATTGTGAGTTT 59.181 41.667 0.00 0.00 0.00 2.66
2952 5596 4.384056 CCTCAACAGAGACATTGTGAGTT 58.616 43.478 0.00 0.00 0.00 3.01
2953 5597 3.805108 GCCTCAACAGAGACATTGTGAGT 60.805 47.826 0.00 0.00 0.00 3.41
2954 5598 2.740981 GCCTCAACAGAGACATTGTGAG 59.259 50.000 0.00 0.00 0.00 3.51
2955 5599 2.104622 TGCCTCAACAGAGACATTGTGA 59.895 45.455 0.00 0.00 0.00 3.58
2956 5600 2.225019 GTGCCTCAACAGAGACATTGTG 59.775 50.000 0.00 0.00 0.00 3.33
2957 5601 2.105477 AGTGCCTCAACAGAGACATTGT 59.895 45.455 0.00 0.00 0.00 2.71
2958 5602 2.775890 AGTGCCTCAACAGAGACATTG 58.224 47.619 0.00 0.00 0.00 2.82
2959 5603 3.144506 CAAGTGCCTCAACAGAGACATT 58.855 45.455 0.00 0.00 0.00 2.71
2960 5604 2.105477 ACAAGTGCCTCAACAGAGACAT 59.895 45.455 0.00 0.00 0.00 3.06
2961 5605 1.486310 ACAAGTGCCTCAACAGAGACA 59.514 47.619 0.00 0.00 0.00 3.41
2962 5606 2.246719 ACAAGTGCCTCAACAGAGAC 57.753 50.000 0.00 0.00 0.00 3.36
2963 5607 4.623932 ATTACAAGTGCCTCAACAGAGA 57.376 40.909 0.00 0.00 0.00 3.10
2964 5608 4.756642 TCAATTACAAGTGCCTCAACAGAG 59.243 41.667 0.00 0.00 0.00 3.35
2965 5609 4.713553 TCAATTACAAGTGCCTCAACAGA 58.286 39.130 0.00 0.00 0.00 3.41
2966 5610 5.633830 ATCAATTACAAGTGCCTCAACAG 57.366 39.130 0.00 0.00 0.00 3.16
2967 5611 7.392953 TCAATATCAATTACAAGTGCCTCAACA 59.607 33.333 0.00 0.00 0.00 3.33
2968 5612 7.761409 TCAATATCAATTACAAGTGCCTCAAC 58.239 34.615 0.00 0.00 0.00 3.18
2969 5613 7.936496 TCAATATCAATTACAAGTGCCTCAA 57.064 32.000 0.00 0.00 0.00 3.02
2970 5614 7.936496 TTCAATATCAATTACAAGTGCCTCA 57.064 32.000 0.00 0.00 0.00 3.86
2971 5615 8.623903 TGATTCAATATCAATTACAAGTGCCTC 58.376 33.333 0.00 0.00 0.00 4.70
2972 5616 8.408601 GTGATTCAATATCAATTACAAGTGCCT 58.591 33.333 0.00 0.00 0.00 4.75
2973 5617 8.408601 AGTGATTCAATATCAATTACAAGTGCC 58.591 33.333 0.00 0.00 0.00 5.01
2974 5618 9.229784 CAGTGATTCAATATCAATTACAAGTGC 57.770 33.333 0.00 0.00 0.00 4.40
2990 5634 9.513906 TGAGGTAAACATATTTCAGTGATTCAA 57.486 29.630 0.00 0.00 0.00 2.69
2991 5635 9.166173 CTGAGGTAAACATATTTCAGTGATTCA 57.834 33.333 0.00 0.00 0.00 2.57
2992 5636 9.167311 ACTGAGGTAAACATATTTCAGTGATTC 57.833 33.333 4.33 0.00 36.09 2.52
2993 5637 9.520515 AACTGAGGTAAACATATTTCAGTGATT 57.479 29.630 5.79 0.00 37.29 2.57
2994 5638 8.950210 CAACTGAGGTAAACATATTTCAGTGAT 58.050 33.333 5.79 0.00 37.29 3.06
2995 5639 7.094805 GCAACTGAGGTAAACATATTTCAGTGA 60.095 37.037 5.79 0.00 37.29 3.41
2996 5640 7.023575 GCAACTGAGGTAAACATATTTCAGTG 58.976 38.462 5.79 2.82 37.29 3.66
2997 5641 6.714810 TGCAACTGAGGTAAACATATTTCAGT 59.285 34.615 0.00 0.00 38.62 3.41
2998 5642 7.144722 TGCAACTGAGGTAAACATATTTCAG 57.855 36.000 0.00 0.00 0.00 3.02
2999 5643 7.367285 GTTGCAACTGAGGTAAACATATTTCA 58.633 34.615 22.36 0.00 0.00 2.69
3000 5644 6.523201 CGTTGCAACTGAGGTAAACATATTTC 59.477 38.462 26.09 0.00 0.00 2.17
3001 5645 6.016610 ACGTTGCAACTGAGGTAAACATATTT 60.017 34.615 26.09 0.00 0.00 1.40
3002 5646 5.472137 ACGTTGCAACTGAGGTAAACATATT 59.528 36.000 26.09 0.00 0.00 1.28
3003 5647 5.001232 ACGTTGCAACTGAGGTAAACATAT 58.999 37.500 26.09 0.00 0.00 1.78
3004 5648 4.382291 ACGTTGCAACTGAGGTAAACATA 58.618 39.130 26.09 0.00 0.00 2.29
3005 5649 3.211045 ACGTTGCAACTGAGGTAAACAT 58.789 40.909 26.09 0.00 0.00 2.71
3006 5650 2.610374 GACGTTGCAACTGAGGTAAACA 59.390 45.455 26.09 0.00 0.00 2.83
3007 5651 2.032290 GGACGTTGCAACTGAGGTAAAC 60.032 50.000 26.09 7.88 0.00 2.01
3008 5652 2.215196 GGACGTTGCAACTGAGGTAAA 58.785 47.619 26.09 0.00 0.00 2.01
3009 5653 1.139256 TGGACGTTGCAACTGAGGTAA 59.861 47.619 26.09 6.99 0.00 2.85
3010 5654 0.753867 TGGACGTTGCAACTGAGGTA 59.246 50.000 26.09 6.08 0.00 3.08
3011 5655 0.532862 CTGGACGTTGCAACTGAGGT 60.533 55.000 26.09 16.71 0.00 3.85
3012 5656 1.230635 CCTGGACGTTGCAACTGAGG 61.231 60.000 26.09 19.57 0.00 3.86
3013 5657 1.845809 GCCTGGACGTTGCAACTGAG 61.846 60.000 26.09 13.96 0.00 3.35
3014 5658 1.891919 GCCTGGACGTTGCAACTGA 60.892 57.895 26.09 7.19 0.00 3.41
3015 5659 1.723608 TTGCCTGGACGTTGCAACTG 61.724 55.000 26.09 20.71 39.86 3.16
3016 5660 0.823356 ATTGCCTGGACGTTGCAACT 60.823 50.000 26.09 13.84 46.60 3.16
3017 5661 0.664166 CATTGCCTGGACGTTGCAAC 60.664 55.000 19.89 19.89 46.60 4.17
3019 5663 1.228094 TCATTGCCTGGACGTTGCA 60.228 52.632 0.00 0.00 0.00 4.08
3020 5664 1.503542 CTCATTGCCTGGACGTTGC 59.496 57.895 0.00 0.00 0.00 4.17
3021 5665 0.957395 AGCTCATTGCCTGGACGTTG 60.957 55.000 0.00 0.00 44.23 4.10
3022 5666 0.613260 TAGCTCATTGCCTGGACGTT 59.387 50.000 0.00 0.00 44.23 3.99
3023 5667 0.176680 CTAGCTCATTGCCTGGACGT 59.823 55.000 0.00 0.00 44.23 4.34
3024 5668 0.176680 ACTAGCTCATTGCCTGGACG 59.823 55.000 0.00 0.00 44.23 4.79
3025 5669 2.168521 TGTACTAGCTCATTGCCTGGAC 59.831 50.000 0.00 0.00 44.23 4.02
3026 5670 2.466846 TGTACTAGCTCATTGCCTGGA 58.533 47.619 0.00 0.00 44.23 3.86
3027 5671 2.988010 TGTACTAGCTCATTGCCTGG 57.012 50.000 0.00 0.00 44.23 4.45
3028 5672 8.663025 CAATTATATGTACTAGCTCATTGCCTG 58.337 37.037 0.00 0.00 44.23 4.85
3029 5673 8.378565 ACAATTATATGTACTAGCTCATTGCCT 58.621 33.333 0.00 0.00 44.23 4.75
3030 5674 8.553459 ACAATTATATGTACTAGCTCATTGCC 57.447 34.615 0.00 0.00 44.23 4.52
3058 5702 9.851686 TTTGCTGGAAATTCATAGACATATACT 57.148 29.630 0.00 0.00 0.00 2.12
3063 5707 9.729281 AAAAATTTGCTGGAAATTCATAGACAT 57.271 25.926 18.20 0.19 42.41 3.06


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

AutoCloner maintained by Alex Coulton.