Multiple sequence alignment - TraesCS6B01G269500

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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 TraesCS6B01G269500 chr6B 100.000 5362 0 0 1 5362 485300620 485305981 0.000000e+00 9902.0
1 TraesCS6B01G269500 chr6B 100.000 161 0 0 5555 5715 485306174 485306334 1.200000e-76 298.0
2 TraesCS6B01G269500 chr6A 91.680 3894 171 61 1 3771 474988496 474984633 0.000000e+00 5254.0
3 TraesCS6B01G269500 chr6A 96.041 1061 36 4 4234 5291 474982909 474981852 0.000000e+00 1722.0
4 TraesCS6B01G269500 chr6A 91.951 410 16 8 3837 4243 474984625 474984230 5.000000e-155 558.0
5 TraesCS6B01G269500 chr6A 93.496 123 4 3 5563 5681 474981558 474981436 4.550000e-41 180.0
6 TraesCS6B01G269500 chr6A 95.000 80 3 1 5280 5358 474981707 474981628 2.160000e-24 124.0
7 TraesCS6B01G269500 chr6D 94.337 2490 86 16 367 2817 335340354 335337881 0.000000e+00 3766.0
8 TraesCS6B01G269500 chr6D 93.730 1531 55 14 3837 5358 335336847 335335349 0.000000e+00 2257.0
9 TraesCS6B01G269500 chr6D 93.672 964 50 6 2813 3770 335337814 335336856 0.000000e+00 1432.0
10 TraesCS6B01G269500 chr6D 88.191 398 24 8 1 380 335340762 335340370 2.430000e-123 453.0
11 TraesCS6B01G269500 chr2B 87.126 334 41 2 1346 1678 600000036 600000368 1.500000e-100 377.0
12 TraesCS6B01G269500 chr2A 87.126 334 41 2 1346 1678 654364940 654365272 1.500000e-100 377.0
13 TraesCS6B01G269500 chr2D 86.866 335 42 2 1346 1679 510615429 510615762 1.940000e-99 374.0
14 TraesCS6B01G269500 chr2D 95.833 48 2 0 3764 3811 691512 691559 1.710000e-10 78.7
15 TraesCS6B01G269500 chr2D 90.566 53 5 0 3759 3811 99134620 99134672 2.860000e-08 71.3
16 TraesCS6B01G269500 chr4A 95.918 49 2 0 3764 3812 2776842 2776890 4.750000e-11 80.5
17 TraesCS6B01G269500 chr4A 93.878 49 3 0 3763 3811 142348618 142348570 2.210000e-09 75.0
18 TraesCS6B01G269500 chr1B 92.727 55 4 0 3758 3812 39580046 39580100 4.750000e-11 80.5
19 TraesCS6B01G269500 chr3D 94.118 51 3 0 3762 3812 54783315 54783365 1.710000e-10 78.7
20 TraesCS6B01G269500 chr5A 95.745 47 2 0 3765 3811 307710897 307710851 6.140000e-10 76.8
21 TraesCS6B01G269500 chr7A 93.878 49 3 0 3764 3812 618684975 618684927 2.210000e-09 75.0
22 TraesCS6B01G269500 chr1D 93.878 49 3 0 3764 3812 367684837 367684885 2.210000e-09 75.0


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 TraesCS6B01G269500 chr6B 485300620 485306334 5714 False 5100.0 9902 100.0000 1 5715 2 chr6B.!!$F1 5714
1 TraesCS6B01G269500 chr6A 474981436 474988496 7060 True 1567.6 5254 93.6336 1 5681 5 chr6A.!!$R1 5680
2 TraesCS6B01G269500 chr6D 335335349 335340762 5413 True 1977.0 3766 92.4825 1 5358 4 chr6D.!!$R1 5357

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
687 767 0.107897 AACACCACAGCACACGAGAA 60.108 50.000 0.0 0.0 0.00 2.87 F
1680 1777 0.108756 GCCTCTCCACCGTAAGACAC 60.109 60.000 0.0 0.0 43.02 3.67 F
2045 2162 0.324943 CTCACGGAACCCACTCCATT 59.675 55.000 0.0 0.0 34.91 3.16 F
2231 2348 0.906756 TGAGGAGGGAGAAGCCTGTG 60.907 60.000 0.0 0.0 36.66 3.66 F
2341 2458 1.536284 GCTCATTACCGAGAACCCGAG 60.536 57.143 0.0 0.0 34.79 4.63 F
3736 3989 1.675310 TTGCCAGAGAACCGCATGG 60.675 57.895 0.0 0.0 42.84 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1793 1896 0.248498 CGATCAGCTTCTTCGCGGTA 60.248 55.000 6.13 0.00 34.40 4.02 R
3214 3434 0.391927 TAAACGCCAATGGGTCCTCG 60.392 55.000 0.00 0.00 36.50 4.63 R
3340 3560 1.277842 TGCCGGAAGTTAGATTCAGCA 59.722 47.619 5.05 0.00 37.54 4.41 R
4174 4433 1.218854 GCATGGCCGCATCCTTTTT 59.781 52.632 0.00 0.00 0.00 1.94 R
4331 5920 5.514169 TCAGACAGATAGGTGAGTCAAGAT 58.486 41.667 0.00 0.00 33.56 2.40 R
5693 7446 0.034960 CTCTGTCTCACCTCGAGGGA 60.035 60.000 34.04 25.15 42.55 4.20 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
181 196 2.340337 GGCATTTGACAATTCTGGTGC 58.660 47.619 0.00 0.00 0.00 5.01
201 216 1.053424 GCCGGTGGATATTCTACCCA 58.947 55.000 1.90 0.00 44.19 4.51
272 290 3.981071 TCCACAGAGTTTACATGGGAG 57.019 47.619 0.00 0.00 0.00 4.30
273 291 2.571653 TCCACAGAGTTTACATGGGAGG 59.428 50.000 0.00 0.00 0.00 4.30
275 293 1.282157 ACAGAGTTTACATGGGAGGGC 59.718 52.381 0.00 0.00 0.00 5.19
311 340 9.561069 ACAGTTCACAAGTACTATGATTTCTTT 57.439 29.630 9.86 2.39 0.00 2.52
337 366 1.072331 ACAACAGACCTTCGCATTCCT 59.928 47.619 0.00 0.00 0.00 3.36
343 377 1.068741 GACCTTCGCATTCCTACCGAT 59.931 52.381 0.00 0.00 0.00 4.18
475 551 0.521242 GCATGGCTTAGTGTTTCGCG 60.521 55.000 0.00 0.00 0.00 5.87
482 558 3.308866 GGCTTAGTGTTTCGCGTAATCAT 59.691 43.478 5.77 0.00 0.00 2.45
589 669 1.903877 CTCACGGACAAGGGCCAGAT 61.904 60.000 6.18 0.00 0.00 2.90
680 760 1.196808 CGGAACATAACACCACAGCAC 59.803 52.381 0.00 0.00 0.00 4.40
687 767 0.107897 AACACCACAGCACACGAGAA 60.108 50.000 0.00 0.00 0.00 2.87
718 799 2.989166 CGCAAGCTTGGAAGGATTTTTC 59.011 45.455 27.10 5.49 0.00 2.29
732 813 6.319141 AGGATTTTTCTCCGTCAAAAAGAG 57.681 37.500 0.00 0.00 40.46 2.85
733 814 6.062095 AGGATTTTTCTCCGTCAAAAAGAGA 58.938 36.000 0.00 0.00 40.46 3.10
1285 1382 4.939439 TCAGTTCATGATCACATTGGACTG 59.061 41.667 22.54 22.54 39.54 3.51
1332 1429 2.751259 GCTTGCTCTGACATTGATTGGA 59.249 45.455 0.00 0.00 0.00 3.53
1340 1437 5.072055 TCTGACATTGATTGGATGTGTGTT 58.928 37.500 0.00 0.00 37.83 3.32
1464 1561 0.541063 TGTTCGAGAGCTGGTACCCA 60.541 55.000 10.07 0.00 0.00 4.51
1679 1776 1.255667 GGCCTCTCCACCGTAAGACA 61.256 60.000 0.00 0.00 34.79 3.41
1680 1777 0.108756 GCCTCTCCACCGTAAGACAC 60.109 60.000 0.00 0.00 43.02 3.67
1689 1788 2.165641 CACCGTAAGACACCATGCTCTA 59.834 50.000 0.00 0.00 43.02 2.43
1691 1790 4.037565 CACCGTAAGACACCATGCTCTATA 59.962 45.833 0.00 0.00 43.02 1.31
1696 1795 5.876651 AAGACACCATGCTCTATACATGA 57.123 39.130 0.00 0.00 46.33 3.07
1698 1797 5.605534 AGACACCATGCTCTATACATGAAC 58.394 41.667 0.00 0.00 46.33 3.18
1702 1801 5.631096 CACCATGCTCTATACATGAACTACG 59.369 44.000 0.00 0.00 46.33 3.51
1732 1835 7.646314 ACTGCATTTAACATCATCAGATTAGC 58.354 34.615 0.00 0.00 30.20 3.09
1733 1836 7.501559 ACTGCATTTAACATCATCAGATTAGCT 59.498 33.333 0.00 0.00 30.20 3.32
1734 1837 8.907222 TGCATTTAACATCATCAGATTAGCTA 57.093 30.769 0.00 0.00 30.20 3.32
1735 1838 8.996271 TGCATTTAACATCATCAGATTAGCTAG 58.004 33.333 0.00 0.00 30.20 3.42
1776 1879 4.081322 TCTCCTGTTTGTTACTTGTCCC 57.919 45.455 0.00 0.00 0.00 4.46
1787 1890 6.126863 TGTTACTTGTCCCAGATGATCTTT 57.873 37.500 0.00 0.00 0.00 2.52
1793 1896 5.183530 TGTCCCAGATGATCTTTGACATT 57.816 39.130 15.86 0.00 32.63 2.71
1907 2010 2.750237 GTGAACATCCCCGGCACC 60.750 66.667 0.00 0.00 0.00 5.01
1922 2025 0.806102 GCACCGCGTATCATGAGTGT 60.806 55.000 4.92 0.00 0.00 3.55
1948 2065 1.202313 GGTACGCACAAAGCCACAAAA 60.202 47.619 0.00 0.00 41.38 2.44
1963 2080 0.665369 CAAAAGCTTCTTGGCCAGCG 60.665 55.000 5.11 0.87 41.24 5.18
2043 2160 1.152419 TCTCACGGAACCCACTCCA 60.152 57.895 0.00 0.00 34.91 3.86
2044 2161 0.544357 TCTCACGGAACCCACTCCAT 60.544 55.000 0.00 0.00 34.91 3.41
2045 2162 0.324943 CTCACGGAACCCACTCCATT 59.675 55.000 0.00 0.00 34.91 3.16
2046 2163 1.553248 CTCACGGAACCCACTCCATTA 59.447 52.381 0.00 0.00 34.91 1.90
2047 2164 1.979308 TCACGGAACCCACTCCATTAA 59.021 47.619 0.00 0.00 34.91 1.40
2073 2190 2.168313 GCTTCTCTCTTCTCTTCCTGGG 59.832 54.545 0.00 0.00 0.00 4.45
2157 2274 0.975887 GAGGATGATGAGGGAGAGGC 59.024 60.000 0.00 0.00 0.00 4.70
2228 2345 1.688884 GCTGAGGAGGGAGAAGCCT 60.689 63.158 0.00 0.00 36.66 4.58
2231 2348 0.906756 TGAGGAGGGAGAAGCCTGTG 60.907 60.000 0.00 0.00 36.66 3.66
2341 2458 1.536284 GCTCATTACCGAGAACCCGAG 60.536 57.143 0.00 0.00 34.79 4.63
2368 2485 4.656041 CTCGAGGTGTTAACGGTTAGTAG 58.344 47.826 3.91 0.00 0.00 2.57
2389 2508 7.262772 AGTAGTTAGTATAAACTGCATGCGAA 58.737 34.615 14.09 0.00 42.49 4.70
2676 2799 6.556212 ACTCGATGTAACAGTGACTAATGAG 58.444 40.000 0.00 0.00 0.00 2.90
2684 2807 3.257393 CAGTGACTAATGAGTGGCTGTC 58.743 50.000 0.00 0.00 35.45 3.51
2906 3123 2.462723 ACTTAGAGCCTCTGAAGGACC 58.537 52.381 3.98 0.00 46.67 4.46
3059 3276 2.237143 GAGTGAGTGGTGGATTCCATGA 59.763 50.000 9.01 0.00 39.81 3.07
3134 3354 3.500558 GCTTTTTGCATTCTCCTCCTC 57.499 47.619 0.00 0.00 42.31 3.71
3214 3434 5.992217 AGTGCATCTAAATCCCGAAATCTAC 59.008 40.000 0.00 0.00 0.00 2.59
3449 3680 2.242043 CAAGGTTCAATTCCCAGTGCT 58.758 47.619 0.00 0.00 0.00 4.40
3481 3712 6.071503 ACGACTACAGCTATAAATCATACCCC 60.072 42.308 0.00 0.00 0.00 4.95
3516 3754 9.778741 CCACTCTAATCAAAATATAAGCTACCA 57.221 33.333 0.00 0.00 0.00 3.25
3559 3812 6.609237 GCAATATTCATGCTACTCAGTCAA 57.391 37.500 0.00 0.00 40.64 3.18
3580 3833 1.814394 TGACTCCATGCAATGCTTGAC 59.186 47.619 20.65 10.32 44.97 3.18
3592 3845 5.706833 TGCAATGCTTGACTCTCTGAATTTA 59.293 36.000 6.82 0.00 0.00 1.40
3637 3890 7.858583 ACCAACTTGAAACGTTAAATAGAGTC 58.141 34.615 0.00 0.00 0.00 3.36
3706 3959 9.043548 ACTTGGTGTAGTGGTTATCTAATTAGT 57.956 33.333 12.19 3.08 0.00 2.24
3710 3963 8.693625 GGTGTAGTGGTTATCTAATTAGTCAGT 58.306 37.037 12.19 9.19 0.00 3.41
3734 3987 1.675641 GGTTGCCAGAGAACCGCAT 60.676 57.895 0.00 0.00 33.85 4.73
3736 3989 1.675310 TTGCCAGAGAACCGCATGG 60.675 57.895 0.00 0.00 42.84 3.66
3779 4032 9.845214 ACCAAAATCATATATAGTACTCCCTCT 57.155 33.333 0.00 0.00 0.00 3.69
3794 4047 9.810870 AGTACTCCCTCTGTAAACTAATATAGG 57.189 37.037 0.00 0.00 0.00 2.57
3795 4048 9.804977 GTACTCCCTCTGTAAACTAATATAGGA 57.195 37.037 0.00 0.00 0.00 2.94
3797 4050 9.900112 ACTCCCTCTGTAAACTAATATAGGATT 57.100 33.333 0.00 0.00 0.00 3.01
3799 4052 9.670442 TCCCTCTGTAAACTAATATAGGATTGT 57.330 33.333 0.00 0.00 0.00 2.71
3815 4068 5.593010 AGGATTGTTTAGATCACTACGAGC 58.407 41.667 0.00 0.00 0.00 5.03
3816 4069 5.361285 AGGATTGTTTAGATCACTACGAGCT 59.639 40.000 0.00 0.00 44.39 4.09
3817 4070 6.043411 GGATTGTTTAGATCACTACGAGCTT 58.957 40.000 0.00 0.00 36.88 3.74
3818 4071 7.068348 AGGATTGTTTAGATCACTACGAGCTTA 59.932 37.037 0.00 0.00 36.88 3.09
3819 4072 7.167801 GGATTGTTTAGATCACTACGAGCTTAC 59.832 40.741 0.00 0.00 36.88 2.34
3820 4073 6.505044 TGTTTAGATCACTACGAGCTTACA 57.495 37.500 0.00 0.00 36.88 2.41
3821 4074 7.096884 TGTTTAGATCACTACGAGCTTACAT 57.903 36.000 0.00 0.00 36.88 2.29
3822 4075 7.544622 TGTTTAGATCACTACGAGCTTACATT 58.455 34.615 0.00 0.00 36.88 2.71
3823 4076 8.680001 TGTTTAGATCACTACGAGCTTACATTA 58.320 33.333 0.00 0.00 36.88 1.90
3824 4077 9.171701 GTTTAGATCACTACGAGCTTACATTAG 57.828 37.037 0.00 0.00 36.88 1.73
3825 4078 6.945938 AGATCACTACGAGCTTACATTAGT 57.054 37.500 0.00 0.00 36.88 2.24
3826 4079 7.336161 AGATCACTACGAGCTTACATTAGTT 57.664 36.000 0.00 0.00 36.88 2.24
3827 4080 7.773149 AGATCACTACGAGCTTACATTAGTTT 58.227 34.615 0.00 0.00 36.88 2.66
3828 4081 8.900781 AGATCACTACGAGCTTACATTAGTTTA 58.099 33.333 0.00 0.00 36.88 2.01
3829 4082 8.853469 ATCACTACGAGCTTACATTAGTTTAC 57.147 34.615 0.00 0.00 0.00 2.01
3830 4083 7.819644 TCACTACGAGCTTACATTAGTTTACA 58.180 34.615 0.00 0.00 0.00 2.41
3831 4084 7.966753 TCACTACGAGCTTACATTAGTTTACAG 59.033 37.037 0.00 0.00 0.00 2.74
3832 4085 7.966753 CACTACGAGCTTACATTAGTTTACAGA 59.033 37.037 0.00 0.00 0.00 3.41
3833 4086 8.182881 ACTACGAGCTTACATTAGTTTACAGAG 58.817 37.037 0.00 0.00 0.00 3.35
3834 4087 6.921914 ACGAGCTTACATTAGTTTACAGAGT 58.078 36.000 0.00 0.00 0.00 3.24
3835 4088 8.048534 ACGAGCTTACATTAGTTTACAGAGTA 57.951 34.615 0.00 0.00 0.00 2.59
3889 4143 5.067936 AGCTCGTAATGTACTCTAGCATGTT 59.932 40.000 0.00 0.00 32.49 2.71
3895 4150 4.634012 TGTACTCTAGCATGTTTGGGTT 57.366 40.909 1.43 0.00 0.00 4.11
3896 4151 4.575885 TGTACTCTAGCATGTTTGGGTTC 58.424 43.478 1.43 0.00 0.00 3.62
3897 4152 4.286032 TGTACTCTAGCATGTTTGGGTTCT 59.714 41.667 1.43 0.00 0.00 3.01
3898 4153 5.482526 TGTACTCTAGCATGTTTGGGTTCTA 59.517 40.000 1.43 0.00 0.00 2.10
3899 4154 5.091261 ACTCTAGCATGTTTGGGTTCTAG 57.909 43.478 0.00 0.00 0.00 2.43
4080 4339 2.413837 GTGATTAGTCCACTTGTGCGT 58.586 47.619 0.00 0.00 0.00 5.24
4137 4396 8.598916 TCAAATGATACTTAACCCTCACTGTTA 58.401 33.333 0.00 0.00 0.00 2.41
4154 4413 6.371548 TCACTGTTATGTTGATAAGGAACAGC 59.628 38.462 11.42 0.00 44.81 4.40
4155 4414 5.648092 ACTGTTATGTTGATAAGGAACAGCC 59.352 40.000 11.42 0.00 44.81 4.85
4156 4415 4.634004 TGTTATGTTGATAAGGAACAGCCG 59.366 41.667 0.00 0.00 43.43 5.52
4157 4416 3.627395 ATGTTGATAAGGAACAGCCGA 57.373 42.857 0.00 0.00 43.43 5.54
4158 4417 3.410631 TGTTGATAAGGAACAGCCGAA 57.589 42.857 0.00 0.00 43.43 4.30
4159 4418 3.071479 TGTTGATAAGGAACAGCCGAAC 58.929 45.455 0.00 0.00 43.43 3.95
4160 4419 3.071479 GTTGATAAGGAACAGCCGAACA 58.929 45.455 0.00 0.00 43.43 3.18
4161 4420 2.972625 TGATAAGGAACAGCCGAACAG 58.027 47.619 0.00 0.00 43.43 3.16
4174 4433 3.773119 AGCCGAACAGGTAGGAATAAAGA 59.227 43.478 0.00 0.00 43.70 2.52
4331 5920 6.885376 TGTTGTGTTTACTTTTGGGTCTAGAA 59.115 34.615 0.00 0.00 0.00 2.10
4383 5972 4.420522 ACACTTACGGGTTTTACTTGGA 57.579 40.909 0.00 0.00 0.00 3.53
4397 5986 3.618690 ACTTGGACTGCAGGATAAGAC 57.381 47.619 23.91 7.15 0.00 3.01
4437 6026 0.960364 AGCATTTCATGGCGTTCGGT 60.960 50.000 0.00 0.00 34.54 4.69
4447 6036 3.307906 CGTTCGGTGGGGGTCTCA 61.308 66.667 0.00 0.00 0.00 3.27
4558 6149 5.675684 TGTACACAGTCACATATGGACAT 57.324 39.130 19.88 9.64 37.74 3.06
4573 6164 8.840321 ACATATGGACATTGTTTCACTATAAGC 58.160 33.333 7.80 0.00 0.00 3.09
4577 6168 7.390823 TGGACATTGTTTCACTATAAGCACTA 58.609 34.615 0.00 0.00 0.00 2.74
4593 6184 3.197766 AGCACTATGAAGGTGAAATCGGA 59.802 43.478 0.00 0.00 36.89 4.55
4666 6257 0.472471 ACATAATGCGTACCCCAGGG 59.528 55.000 0.00 0.00 42.03 4.45
4736 6327 1.960417 TCACATGTTTGTCGGCTCAA 58.040 45.000 0.00 0.00 32.34 3.02
4741 6332 1.522668 TGTTTGTCGGCTCAATCTGG 58.477 50.000 0.00 0.00 0.00 3.86
4747 6338 0.036732 TCGGCTCAATCTGGCTGTTT 59.963 50.000 0.00 0.00 36.35 2.83
4880 6471 6.588204 AGTATTGTAGTCACACCACAGAAAA 58.412 36.000 0.00 0.00 33.30 2.29
5075 6666 6.463995 TTGTTTCCCATGATGGTAATTAGC 57.536 37.500 11.09 7.74 35.17 3.09
5076 6667 4.578516 TGTTTCCCATGATGGTAATTAGCG 59.421 41.667 11.09 0.00 35.17 4.26
5077 6668 2.778299 TCCCATGATGGTAATTAGCGC 58.222 47.619 11.09 0.00 35.17 5.92
5112 6704 5.641709 ACGTGTCTACTCATATGTTGTCTG 58.358 41.667 1.90 1.66 0.00 3.51
5243 6835 7.410728 GCTGAATACGACATTTCATTTTGTTGG 60.411 37.037 0.00 0.00 32.51 3.77
5278 6871 6.481313 TCATTCCGAGCTCTTCTATTTCATTG 59.519 38.462 12.85 0.00 0.00 2.82
5288 7037 9.448294 GCTCTTCTATTTCATTGTCATTGAATC 57.552 33.333 10.20 0.00 33.37 2.52
5681 7434 6.169557 ACCACAACTGAGTTAACAGATACA 57.830 37.500 8.61 0.00 40.63 2.29
5682 7435 6.588204 ACCACAACTGAGTTAACAGATACAA 58.412 36.000 8.61 0.00 40.63 2.41
5683 7436 6.482308 ACCACAACTGAGTTAACAGATACAAC 59.518 38.462 8.61 0.00 40.63 3.32
5684 7437 6.481976 CCACAACTGAGTTAACAGATACAACA 59.518 38.462 8.61 0.00 40.63 3.33
5685 7438 7.173218 CCACAACTGAGTTAACAGATACAACAT 59.827 37.037 8.61 0.00 40.63 2.71
5686 7439 8.559536 CACAACTGAGTTAACAGATACAACATT 58.440 33.333 8.61 0.00 40.63 2.71
5687 7440 9.120538 ACAACTGAGTTAACAGATACAACATTT 57.879 29.630 8.61 0.00 40.63 2.32
5698 7451 8.682936 ACAGATACAACATTTAATGATCCCTC 57.317 34.615 12.28 3.31 0.00 4.30
5699 7452 7.442364 ACAGATACAACATTTAATGATCCCTCG 59.558 37.037 12.28 0.00 0.00 4.63
5700 7453 7.657354 CAGATACAACATTTAATGATCCCTCGA 59.343 37.037 12.28 0.00 0.00 4.04
5701 7454 7.875041 AGATACAACATTTAATGATCCCTCGAG 59.125 37.037 12.28 5.13 0.00 4.04
5702 7455 5.126067 ACAACATTTAATGATCCCTCGAGG 58.874 41.667 25.36 25.36 0.00 4.63
5703 7456 5.126067 CAACATTTAATGATCCCTCGAGGT 58.874 41.667 29.25 12.84 36.75 3.85
5704 7457 4.708177 ACATTTAATGATCCCTCGAGGTG 58.292 43.478 29.25 20.21 36.75 4.00
5705 7458 4.408921 ACATTTAATGATCCCTCGAGGTGA 59.591 41.667 29.25 24.40 36.75 4.02
5706 7459 4.672587 TTTAATGATCCCTCGAGGTGAG 57.327 45.455 29.25 14.90 44.83 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 33 2.001269 GTAGACCCACAGCCCCCAT 61.001 63.158 0.00 0.00 0.00 4.00
124 138 6.964934 AGTCAACACTTGTTTTTGTTATCGAC 59.035 34.615 0.00 0.00 35.83 4.20
181 196 0.037605 GGGTAGAATATCCACCGGCG 60.038 60.000 0.00 0.00 43.10 6.46
201 216 8.305317 GGTACACAGTAGAACAGTAGAAGAAAT 58.695 37.037 0.00 0.00 0.00 2.17
272 290 1.623811 TGAACTGTCAAGACTAGGCCC 59.376 52.381 0.00 0.00 0.00 5.80
273 291 2.037251 TGTGAACTGTCAAGACTAGGCC 59.963 50.000 0.00 0.00 34.87 5.19
275 293 4.950050 ACTTGTGAACTGTCAAGACTAGG 58.050 43.478 12.88 0.00 42.22 3.02
311 340 4.794278 TGCGAAGGTCTGTTGTATTAGA 57.206 40.909 0.00 0.00 0.00 2.10
343 377 5.462530 TTAGTTCGACAGGATCAAACAGA 57.537 39.130 0.00 0.00 0.00 3.41
442 506 5.391312 AAGCCATGCACTTAGGTTTAAAG 57.609 39.130 0.00 0.00 0.00 1.85
482 558 4.890158 TGTTCTCTTGGCATCTGTTAGA 57.110 40.909 0.00 0.00 0.00 2.10
529 605 4.556104 GCATGTCCAGCTAGCAATGTATTG 60.556 45.833 18.83 4.08 40.66 1.90
609 689 4.737054 AGCTGTTGTGTTCTGAACTTTTG 58.263 39.130 20.18 7.90 0.00 2.44
680 760 0.368227 GCGCAAGATCTGTTCTCGTG 59.632 55.000 0.30 0.00 43.02 4.35
687 767 0.520404 CAAGCTTGCGCAAGATCTGT 59.480 50.000 45.25 27.07 40.79 3.41
707 787 6.735130 TCTTTTTGACGGAGAAAAATCCTTC 58.265 36.000 0.00 0.00 37.96 3.46
708 788 6.546034 TCTCTTTTTGACGGAGAAAAATCCTT 59.454 34.615 0.00 0.00 37.20 3.36
709 789 6.062095 TCTCTTTTTGACGGAGAAAAATCCT 58.938 36.000 0.00 0.00 37.20 3.24
710 790 6.313744 TCTCTTTTTGACGGAGAAAAATCC 57.686 37.500 0.00 0.00 33.10 3.01
711 791 7.165977 GTGTTCTCTTTTTGACGGAGAAAAATC 59.834 37.037 6.26 0.00 44.30 2.17
713 793 6.072397 TGTGTTCTCTTTTTGACGGAGAAAAA 60.072 34.615 6.26 0.00 44.30 1.94
714 794 5.413213 TGTGTTCTCTTTTTGACGGAGAAAA 59.587 36.000 6.26 0.00 44.30 2.29
718 799 3.871594 AGTGTGTTCTCTTTTTGACGGAG 59.128 43.478 0.00 0.00 0.00 4.63
732 813 3.057946 GCAGAATCCTTCCAAGTGTGTTC 60.058 47.826 0.00 0.00 0.00 3.18
733 814 2.887152 GCAGAATCCTTCCAAGTGTGTT 59.113 45.455 0.00 0.00 0.00 3.32
842 923 1.001406 GGAGCTATGTTGGGAGATCGG 59.999 57.143 0.00 0.00 0.00 4.18
1285 1382 5.521735 CAGTCTCATGCATACTTACTCCAAC 59.478 44.000 0.00 0.00 0.00 3.77
1332 1429 2.027561 ACCGTACCTATGCAACACACAT 60.028 45.455 0.00 0.00 0.00 3.21
1401 1498 1.079612 GTGGTTAAGGTCCGGGTCG 60.080 63.158 0.00 0.00 0.00 4.79
1464 1561 0.693049 AAATCTCGGTGAAGGTGGCT 59.307 50.000 0.00 0.00 0.00 4.75
1589 1686 4.664677 AGGCAGTGTCCGTGTCGC 62.665 66.667 0.00 0.00 0.00 5.19
1679 1776 5.302059 ACGTAGTTCATGTATAGAGCATGGT 59.698 40.000 0.00 0.00 37.78 3.55
1680 1777 5.631096 CACGTAGTTCATGTATAGAGCATGG 59.369 44.000 0.00 0.00 41.61 3.66
1689 1788 4.158949 TGCAGTACCACGTAGTTCATGTAT 59.841 41.667 0.00 0.00 41.61 2.29
1691 1790 2.297880 TGCAGTACCACGTAGTTCATGT 59.702 45.455 0.00 0.00 41.61 3.21
1696 1795 5.299148 TGTTAAATGCAGTACCACGTAGTT 58.701 37.500 0.00 0.00 41.61 2.24
1698 1797 5.579119 TGATGTTAAATGCAGTACCACGTAG 59.421 40.000 0.00 0.00 0.00 3.51
1702 1801 6.316140 TCTGATGATGTTAAATGCAGTACCAC 59.684 38.462 0.00 0.00 0.00 4.16
1732 1835 4.377897 TGCACATCAGCAATGATCTCTAG 58.622 43.478 6.14 0.00 42.46 2.43
1733 1836 4.411256 TGCACATCAGCAATGATCTCTA 57.589 40.909 6.14 0.00 42.46 2.43
1734 1837 3.277142 TGCACATCAGCAATGATCTCT 57.723 42.857 6.14 0.00 42.46 3.10
1776 1879 4.318333 CGCGGTAATGTCAAAGATCATCTG 60.318 45.833 0.00 0.00 0.00 2.90
1787 1890 1.067142 AGCTTCTTCGCGGTAATGTCA 60.067 47.619 6.13 0.00 34.40 3.58
1793 1896 0.248498 CGATCAGCTTCTTCGCGGTA 60.248 55.000 6.13 0.00 34.40 4.02
1907 2010 3.670523 CCTTCATACACTCATGATACGCG 59.329 47.826 3.53 3.53 34.95 6.01
1922 2025 2.289756 TGGCTTTGTGCGTACCTTCATA 60.290 45.455 0.00 0.00 44.05 2.15
1948 2065 1.376037 GTACGCTGGCCAAGAAGCT 60.376 57.895 7.01 0.00 37.27 3.74
1957 2074 2.126228 TGCACTACGTACGCTGGC 60.126 61.111 16.72 14.39 0.00 4.85
1963 2080 2.899977 GCAGTTTTGTGCACTACGTAC 58.100 47.619 19.41 8.60 43.41 3.67
2043 2160 9.830975 GGAAGAGAAGAGAGAAGCTTAATTAAT 57.169 33.333 0.00 0.00 0.00 1.40
2044 2161 9.041354 AGGAAGAGAAGAGAGAAGCTTAATTAA 57.959 33.333 0.00 0.00 0.00 1.40
2045 2162 8.474025 CAGGAAGAGAAGAGAGAAGCTTAATTA 58.526 37.037 0.00 0.00 0.00 1.40
2046 2163 7.330262 CAGGAAGAGAAGAGAGAAGCTTAATT 58.670 38.462 0.00 0.00 0.00 1.40
2047 2164 6.127083 CCAGGAAGAGAAGAGAGAAGCTTAAT 60.127 42.308 0.00 0.00 0.00 1.40
2228 2345 2.910479 ACGGTCTCGGTGAGCACA 60.910 61.111 9.55 0.00 42.88 4.57
2258 2375 1.714794 CGAAGAGGAGCACGAACATT 58.285 50.000 0.00 0.00 0.00 2.71
2291 2408 2.360475 GTGAGGGCCAAGGCAGTC 60.360 66.667 13.87 9.01 44.11 3.51
2341 2458 1.012486 CGTTAACACCTCGAGCACCC 61.012 60.000 6.99 0.00 0.00 4.61
2368 2485 9.155053 GTAAATTCGCATGCAGTTTATACTAAC 57.845 33.333 19.57 5.49 31.96 2.34
2676 2799 4.648626 TGCAGCCCTGACAGCCAC 62.649 66.667 0.00 0.00 0.00 5.01
2684 2807 0.747255 ACTATCGTAGTGCAGCCCTG 59.253 55.000 0.00 0.00 37.69 4.45
2838 3054 7.440255 TCCTCGATCTCGTTTCTTTTACTTTTT 59.560 33.333 0.00 0.00 40.80 1.94
2839 3055 6.927381 TCCTCGATCTCGTTTCTTTTACTTTT 59.073 34.615 0.00 0.00 40.80 2.27
2906 3123 0.948623 TGGGCGTGTCAGTTTCATCG 60.949 55.000 0.00 0.00 0.00 3.84
3076 3296 3.215151 TCACGCCATGAACCAAAAAGTA 58.785 40.909 0.00 0.00 33.02 2.24
3134 3354 0.833287 ATAGTGTAGCCTGCACCCAG 59.167 55.000 9.45 0.00 37.56 4.45
3214 3434 0.391927 TAAACGCCAATGGGTCCTCG 60.392 55.000 0.00 0.00 36.50 4.63
3337 3557 1.324736 CGGAAGTTAGATTCAGCACGC 59.675 52.381 0.00 0.00 0.00 5.34
3340 3560 1.277842 TGCCGGAAGTTAGATTCAGCA 59.722 47.619 5.05 0.00 37.54 4.41
3396 3624 3.595190 AACAAAACCCTGAAGCTACCT 57.405 42.857 0.00 0.00 0.00 3.08
3449 3680 7.923878 TGATTTATAGCTGTAGTCGTTTGCATA 59.076 33.333 0.00 0.00 0.00 3.14
3540 3785 7.117285 AGTCATTGACTGAGTAGCATGAATA 57.883 36.000 18.35 0.00 41.76 1.75
3542 3787 5.411831 AGTCATTGACTGAGTAGCATGAA 57.588 39.130 18.35 0.00 41.76 2.57
3546 3799 3.165071 TGGAGTCATTGACTGAGTAGCA 58.835 45.455 23.57 0.00 43.53 3.49
3549 3802 3.515104 TGCATGGAGTCATTGACTGAGTA 59.485 43.478 23.57 7.54 43.53 2.59
3580 3833 8.669243 GTTACAACTTGGGATAAATTCAGAGAG 58.331 37.037 0.00 0.00 0.00 3.20
3661 3914 1.683385 GTGCACTTTGGCTTCCTCTTT 59.317 47.619 10.32 0.00 34.04 2.52
3706 3959 3.719871 TCTCTGGCAACCCTAATACTGA 58.280 45.455 0.00 0.00 0.00 3.41
3710 3963 2.169769 CGGTTCTCTGGCAACCCTAATA 59.830 50.000 0.63 0.00 40.37 0.98
3734 3987 4.483950 TGGTACATTTTTCCAATGTCCCA 58.516 39.130 7.67 7.67 42.10 4.37
3736 3989 7.659390 TGATTTTGGTACATTTTTCCAATGTCC 59.341 33.333 3.50 6.42 40.87 4.02
3771 4024 9.900112 AATCCTATATTAGTTTACAGAGGGAGT 57.100 33.333 0.00 0.00 0.00 3.85
3773 4026 9.670442 ACAATCCTATATTAGTTTACAGAGGGA 57.330 33.333 0.00 0.00 0.00 4.20
3789 4042 8.512956 GCTCGTAGTGATCTAAACAATCCTATA 58.487 37.037 0.00 0.00 0.00 1.31
3790 4043 7.231722 AGCTCGTAGTGATCTAAACAATCCTAT 59.768 37.037 0.00 0.00 0.00 2.57
3791 4044 6.546403 AGCTCGTAGTGATCTAAACAATCCTA 59.454 38.462 0.00 0.00 0.00 2.94
3792 4045 5.361285 AGCTCGTAGTGATCTAAACAATCCT 59.639 40.000 0.00 0.00 0.00 3.24
3793 4046 5.593010 AGCTCGTAGTGATCTAAACAATCC 58.407 41.667 0.00 0.00 0.00 3.01
3794 4047 7.701078 TGTAAGCTCGTAGTGATCTAAACAATC 59.299 37.037 0.00 0.00 0.00 2.67
3795 4048 7.544622 TGTAAGCTCGTAGTGATCTAAACAAT 58.455 34.615 0.00 0.00 0.00 2.71
3796 4049 6.916440 TGTAAGCTCGTAGTGATCTAAACAA 58.084 36.000 0.00 0.00 0.00 2.83
3797 4050 6.505044 TGTAAGCTCGTAGTGATCTAAACA 57.495 37.500 0.00 0.00 0.00 2.83
3798 4051 7.988904 AATGTAAGCTCGTAGTGATCTAAAC 57.011 36.000 0.00 0.00 0.00 2.01
3799 4052 8.900781 ACTAATGTAAGCTCGTAGTGATCTAAA 58.099 33.333 0.00 0.00 0.00 1.85
3800 4053 8.447924 ACTAATGTAAGCTCGTAGTGATCTAA 57.552 34.615 0.00 0.00 0.00 2.10
3801 4054 8.447924 AACTAATGTAAGCTCGTAGTGATCTA 57.552 34.615 0.00 0.00 0.00 1.98
3802 4055 6.945938 ACTAATGTAAGCTCGTAGTGATCT 57.054 37.500 0.00 0.00 0.00 2.75
3803 4056 7.988904 AAACTAATGTAAGCTCGTAGTGATC 57.011 36.000 0.00 0.00 0.00 2.92
3804 4057 8.464404 TGTAAACTAATGTAAGCTCGTAGTGAT 58.536 33.333 0.00 0.00 0.00 3.06
3805 4058 7.819644 TGTAAACTAATGTAAGCTCGTAGTGA 58.180 34.615 0.00 0.00 0.00 3.41
3806 4059 7.966753 TCTGTAAACTAATGTAAGCTCGTAGTG 59.033 37.037 0.00 0.00 0.00 2.74
3807 4060 8.048534 TCTGTAAACTAATGTAAGCTCGTAGT 57.951 34.615 0.00 0.00 0.00 2.73
3808 4061 8.182881 ACTCTGTAAACTAATGTAAGCTCGTAG 58.817 37.037 0.00 0.00 0.00 3.51
3809 4062 8.048534 ACTCTGTAAACTAATGTAAGCTCGTA 57.951 34.615 0.00 0.00 0.00 3.43
3810 4063 6.921914 ACTCTGTAAACTAATGTAAGCTCGT 58.078 36.000 0.00 0.00 0.00 4.18
3811 4064 9.517609 AATACTCTGTAAACTAATGTAAGCTCG 57.482 33.333 0.00 0.00 0.00 5.03
3889 4143 2.043939 TGGAGTCCTAGCTAGAACCCAA 59.956 50.000 22.70 0.00 0.00 4.12
3895 4150 3.884091 GTCGAATTGGAGTCCTAGCTAGA 59.116 47.826 22.70 5.59 0.00 2.43
3896 4151 3.632604 TGTCGAATTGGAGTCCTAGCTAG 59.367 47.826 14.20 14.20 0.00 3.42
3897 4152 3.628008 TGTCGAATTGGAGTCCTAGCTA 58.372 45.455 11.33 0.00 0.00 3.32
3898 4153 2.457598 TGTCGAATTGGAGTCCTAGCT 58.542 47.619 11.33 0.00 0.00 3.32
3899 4154 2.961526 TGTCGAATTGGAGTCCTAGC 57.038 50.000 11.33 0.00 0.00 3.42
4025 4282 5.482175 ACAGAGGACTGAGCTTATTGTTACT 59.518 40.000 0.00 0.00 46.03 2.24
4137 4396 3.627395 TCGGCTGTTCCTTATCAACAT 57.373 42.857 0.00 0.00 33.30 2.71
4154 4413 7.361799 CCTTTTTCTTTATTCCTACCTGTTCGG 60.362 40.741 0.00 0.00 39.35 4.30
4155 4414 7.389607 TCCTTTTTCTTTATTCCTACCTGTTCG 59.610 37.037 0.00 0.00 0.00 3.95
4156 4415 8.631480 TCCTTTTTCTTTATTCCTACCTGTTC 57.369 34.615 0.00 0.00 0.00 3.18
4157 4416 9.025041 CATCCTTTTTCTTTATTCCTACCTGTT 57.975 33.333 0.00 0.00 0.00 3.16
4158 4417 7.122799 GCATCCTTTTTCTTTATTCCTACCTGT 59.877 37.037 0.00 0.00 0.00 4.00
4159 4418 7.484140 GCATCCTTTTTCTTTATTCCTACCTG 58.516 38.462 0.00 0.00 0.00 4.00
4160 4419 6.318900 CGCATCCTTTTTCTTTATTCCTACCT 59.681 38.462 0.00 0.00 0.00 3.08
4161 4420 6.459710 CCGCATCCTTTTTCTTTATTCCTACC 60.460 42.308 0.00 0.00 0.00 3.18
4174 4433 1.218854 GCATGGCCGCATCCTTTTT 59.781 52.632 0.00 0.00 0.00 1.94
4331 5920 5.514169 TCAGACAGATAGGTGAGTCAAGAT 58.486 41.667 0.00 0.00 33.56 2.40
4368 5957 1.134037 TGCAGTCCAAGTAAAACCCGT 60.134 47.619 0.00 0.00 0.00 5.28
4383 5972 3.197766 TGATTTCCGTCTTATCCTGCAGT 59.802 43.478 13.81 0.00 0.00 4.40
4437 6026 2.224159 GCAGAACCTGAGACCCCCA 61.224 63.158 0.00 0.00 32.44 4.96
4558 6149 8.100791 ACCTTCATAGTGCTTATAGTGAAACAA 58.899 33.333 0.00 0.00 41.43 2.83
4573 6164 4.759782 AGTCCGATTTCACCTTCATAGTG 58.240 43.478 0.00 0.00 36.54 2.74
4577 6168 5.316987 AGAAAAGTCCGATTTCACCTTCAT 58.683 37.500 2.32 0.00 38.86 2.57
4593 6184 7.562454 TGACGAAATTCAAGGTTAGAAAAGT 57.438 32.000 0.00 0.00 0.00 2.66
4666 6257 1.823041 GCCATCTGGGAAGCTCAGC 60.823 63.158 0.00 0.00 40.01 4.26
4747 6338 6.572519 AGTTATTTCTTGACTTTTTGCTGCA 58.427 32.000 0.00 0.00 0.00 4.41
4880 6471 5.721960 TCTTGCTTGGACTAGAGGACTAATT 59.278 40.000 0.00 0.00 0.00 1.40
5076 6667 0.739813 GACACGTAGACCATGTGGGC 60.740 60.000 3.77 0.00 46.73 5.36
5077 6668 0.895530 AGACACGTAGACCATGTGGG 59.104 55.000 3.77 0.00 46.73 4.61
5112 6704 8.733857 GCAATAATGGTGCAAATATAAGAGAC 57.266 34.615 0.00 0.00 41.80 3.36
5158 6750 5.652891 TGTACAAGTACAAACCCAAACACAT 59.347 36.000 10.42 0.00 42.49 3.21
5159 6751 5.008331 TGTACAAGTACAAACCCAAACACA 58.992 37.500 10.42 0.00 42.49 3.72
5243 6835 5.703876 AGAGCTCGGAATGAAAATTGTTTC 58.296 37.500 8.37 0.00 43.04 2.78
5554 7303 8.948145 AGTACTTCACTATCCATAATAGCGTAG 58.052 37.037 0.00 0.00 41.04 3.51
5555 7304 8.727910 CAGTACTTCACTATCCATAATAGCGTA 58.272 37.037 0.00 0.00 41.04 4.42
5556 7305 7.447545 TCAGTACTTCACTATCCATAATAGCGT 59.552 37.037 0.00 0.00 41.04 5.07
5557 7306 7.817641 TCAGTACTTCACTATCCATAATAGCG 58.182 38.462 0.00 0.00 41.04 4.26
5558 7307 9.982651 TTTCAGTACTTCACTATCCATAATAGC 57.017 33.333 0.00 0.00 41.04 2.97
5648 7401 4.269183 ACTCAGTTGTGGTTTCATCAACA 58.731 39.130 9.35 0.00 42.33 3.33
5681 7434 5.104527 TCACCTCGAGGGATCATTAAATGTT 60.105 40.000 34.04 6.01 40.27 2.71
5682 7435 4.408921 TCACCTCGAGGGATCATTAAATGT 59.591 41.667 34.04 6.48 40.27 2.71
5683 7436 4.960938 TCACCTCGAGGGATCATTAAATG 58.039 43.478 34.04 18.95 40.27 2.32
5684 7437 4.901849 TCTCACCTCGAGGGATCATTAAAT 59.098 41.667 34.04 7.26 42.55 1.40
5685 7438 4.099573 GTCTCACCTCGAGGGATCATTAAA 59.900 45.833 34.04 7.75 42.55 1.52
5686 7439 3.637229 GTCTCACCTCGAGGGATCATTAA 59.363 47.826 34.04 9.21 42.55 1.40
5687 7440 3.223435 GTCTCACCTCGAGGGATCATTA 58.777 50.000 34.04 10.80 42.55 1.90
5688 7441 2.035632 GTCTCACCTCGAGGGATCATT 58.964 52.381 34.04 10.46 42.55 2.57
5689 7442 1.063642 TGTCTCACCTCGAGGGATCAT 60.064 52.381 34.04 11.26 42.55 2.45
5690 7443 0.331616 TGTCTCACCTCGAGGGATCA 59.668 55.000 34.04 22.93 42.55 2.92
5691 7444 1.028905 CTGTCTCACCTCGAGGGATC 58.971 60.000 34.04 21.12 42.55 3.36
5692 7445 0.626382 TCTGTCTCACCTCGAGGGAT 59.374 55.000 34.04 12.90 42.55 3.85
5693 7446 0.034960 CTCTGTCTCACCTCGAGGGA 60.035 60.000 34.04 25.15 42.55 4.20
5694 7447 1.034838 CCTCTGTCTCACCTCGAGGG 61.035 65.000 34.04 22.55 42.55 4.30
5695 7448 0.322997 ACCTCTGTCTCACCTCGAGG 60.323 60.000 30.11 30.11 45.22 4.63
5696 7449 3.257935 ACCTCTGTCTCACCTCGAG 57.742 57.895 5.13 5.13 43.80 4.04


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

AutoCloner maintained by Alex Coulton.