Multiple sequence alignment - TraesCS5A01G082300

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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 TraesCS5A01G082300 chr5A 100.000 4726 0 0 1 4726 106732362 106727637 0.000000e+00 8728.0
1 TraesCS5A01G082300 chr5A 89.295 738 38 12 3646 4350 106723227 106722498 0.000000e+00 887.0
2 TraesCS5A01G082300 chr5A 95.276 127 6 0 4485 4611 106722357 106722231 8.020000e-48 202.0
3 TraesCS5A01G082300 chr5A 87.640 89 6 2 4353 4437 106722444 106722357 1.080000e-16 99.0
4 TraesCS5A01G082300 chr5B 94.773 4056 128 35 1 4007 105774355 105778375 0.000000e+00 6239.0
5 TraesCS5A01G082300 chr5B 94.220 4066 129 39 1 4019 103575219 103579225 0.000000e+00 6109.0
6 TraesCS5A01G082300 chr5B 93.636 220 9 4 4015 4230 105778413 105778631 1.640000e-84 324.0
7 TraesCS5A01G082300 chr5B 83.459 133 11 4 4219 4347 103579419 103579544 3.870000e-21 113.0
8 TraesCS5A01G082300 chr5B 80.198 101 16 3 4611 4707 605838726 605838626 6.560000e-09 73.1
9 TraesCS5A01G082300 chr5D 92.726 4372 171 54 1 4284 97330128 97334440 0.000000e+00 6176.0
10 TraesCS5A01G082300 chr5D 94.000 150 8 1 4468 4617 97334690 97334838 4.760000e-55 226.0
11 TraesCS5A01G082300 chr5D 79.612 103 17 3 4610 4708 112941385 112941283 2.360000e-08 71.3
12 TraesCS5A01G082300 chr4A 90.511 137 10 3 4592 4726 21031223 21031088 1.350000e-40 178.0
13 TraesCS5A01G082300 chr6D 87.129 101 11 2 4609 4707 417501767 417501867 3.870000e-21 113.0
14 TraesCS5A01G082300 chr6D 78.992 119 16 7 4609 4720 143976498 143976614 6.560000e-09 73.1
15 TraesCS5A01G082300 chr6A 80.531 113 16 5 4601 4708 518389271 518389382 1.090000e-11 82.4
16 TraesCS5A01G082300 chr4D 80.734 109 17 3 4604 4708 210834561 210834453 1.090000e-11 82.4
17 TraesCS5A01G082300 chrUn 80.583 103 16 3 4610 4708 254084501 254084603 5.070000e-10 76.8
18 TraesCS5A01G082300 chr3D 79.612 103 17 3 4610 4708 608392941 608392839 2.360000e-08 71.3


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 TraesCS5A01G082300 chr5A 106727637 106732362 4725 True 8728.0 8728 100.0000 1 4726 1 chr5A.!!$R1 4725
1 TraesCS5A01G082300 chr5A 106722231 106723227 996 True 396.0 887 90.7370 3646 4611 3 chr5A.!!$R2 965
2 TraesCS5A01G082300 chr5B 105774355 105778631 4276 False 3281.5 6239 94.2045 1 4230 2 chr5B.!!$F2 4229
3 TraesCS5A01G082300 chr5B 103575219 103579544 4325 False 3111.0 6109 88.8395 1 4347 2 chr5B.!!$F1 4346
4 TraesCS5A01G082300 chr5D 97330128 97334838 4710 False 3201.0 6176 93.3630 1 4617 2 chr5D.!!$F1 4616

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
350 365 0.691413 GACCAACCCCAAACCCCAAA 60.691 55.0 0.00 0.0 0.00 3.28 F
1142 1169 0.391263 AGGAACTCCGTTCATTCGCC 60.391 55.0 8.76 0.0 43.54 5.54 F
1723 1750 0.461961 GATTGCTCCGCTACCTGAGT 59.538 55.0 0.00 0.0 0.00 3.41 F
3238 3295 0.179181 CAGGCGCAACTGCACATAAG 60.179 55.0 10.83 0.0 42.21 1.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1995 2022 0.695924 TTCCACACATGACGGGGAAT 59.304 50.0 16.48 0.0 32.95 3.01 R
2536 2593 1.251251 GCTTCAGTGTGCCCTTCAAT 58.749 50.0 0.00 0.0 0.00 2.57 R
3246 3303 0.241213 TGTTCGGAGAAGACTCGCTG 59.759 55.0 0.00 0.0 45.90 5.18 R
4699 4937 0.099259 CGAACACGCCAGGACGTATA 59.901 55.0 8.37 0.0 46.34 1.47 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
36 38 1.675641 GATGTGGCTGAGGGCGTTT 60.676 57.895 0.00 0.00 42.94 3.60
41 43 3.435186 GCTGAGGGCGTTTGCTCC 61.435 66.667 0.00 0.00 45.33 4.70
48 50 1.582610 GGGCGTTTGCTCCGATTTCA 61.583 55.000 0.00 0.00 42.25 2.69
105 107 4.141505 TGGCGAAATCATCTCCATAGGAAA 60.142 41.667 0.00 0.00 38.01 3.13
109 111 7.174946 GGCGAAATCATCTCCATAGGAAATTAA 59.825 37.037 0.00 0.00 32.86 1.40
110 112 8.734386 GCGAAATCATCTCCATAGGAAATTAAT 58.266 33.333 0.00 0.00 0.00 1.40
193 196 5.009010 TGAGCTGAGCTGGAAAAGTAAAAAG 59.991 40.000 13.71 0.00 39.88 2.27
347 350 2.203728 GGACCAACCCCAAACCCC 60.204 66.667 0.00 0.00 0.00 4.95
350 365 0.691413 GACCAACCCCAAACCCCAAA 60.691 55.000 0.00 0.00 0.00 3.28
357 372 1.987306 CCAAACCCCAAATCCCCCG 60.987 63.158 0.00 0.00 0.00 5.73
369 384 4.499633 CCCCCGTCCCAAATCCCG 62.500 72.222 0.00 0.00 0.00 5.14
391 406 2.348998 CCTCCTGTCCAGTGGTGC 59.651 66.667 9.54 4.31 0.00 5.01
392 407 2.219875 CCTCCTGTCCAGTGGTGCT 61.220 63.158 9.54 0.00 0.00 4.40
595 613 6.062095 TGTTTCTGGGTTTTCTTTAGAGGAG 58.938 40.000 0.00 0.00 0.00 3.69
598 616 2.647802 TGGGTTTTCTTTAGAGGAGGGG 59.352 50.000 0.00 0.00 0.00 4.79
599 617 2.917600 GGGTTTTCTTTAGAGGAGGGGA 59.082 50.000 0.00 0.00 0.00 4.81
709 735 2.512745 TTGGTCTTGTGCGCGTGT 60.513 55.556 8.43 0.00 0.00 4.49
710 736 2.700334 CTTGGTCTTGTGCGCGTGTG 62.700 60.000 8.43 0.00 0.00 3.82
751 777 1.201414 GGTGGGCGTTTGTTTATGGAG 59.799 52.381 0.00 0.00 0.00 3.86
754 780 1.614850 GGGCGTTTGTTTATGGAGGGA 60.615 52.381 0.00 0.00 0.00 4.20
755 781 2.375146 GGCGTTTGTTTATGGAGGGAT 58.625 47.619 0.00 0.00 0.00 3.85
765 791 5.046663 TGTTTATGGAGGGATTTTTGCCTTC 60.047 40.000 0.00 0.00 0.00 3.46
770 796 3.508402 GGAGGGATTTTTGCCTTCGTTTA 59.492 43.478 0.00 0.00 32.70 2.01
839 866 7.540400 TCGTTTGTTTCGAATGAATATTGCATT 59.460 29.630 0.00 10.84 38.58 3.56
840 867 8.161610 CGTTTGTTTCGAATGAATATTGCATTT 58.838 29.630 0.00 0.00 36.19 2.32
843 870 6.589139 TGTTTCGAATGAATATTGCATTTGCA 59.411 30.769 0.00 0.05 40.87 4.08
844 871 7.278203 TGTTTCGAATGAATATTGCATTTGCAT 59.722 29.630 6.00 0.00 41.63 3.96
845 872 7.790673 GTTTCGAATGAATATTGCATTTGCATC 59.209 33.333 6.00 1.67 41.63 3.91
846 873 7.306109 TTTCGAATGAATATTGCATTTGCATCG 60.306 33.333 6.00 9.84 41.63 3.84
889 916 3.066621 TGCTAATTTCGTTGCCCATCATC 59.933 43.478 0.00 0.00 0.00 2.92
1142 1169 0.391263 AGGAACTCCGTTCATTCGCC 60.391 55.000 8.76 0.00 43.54 5.54
1143 1170 0.672401 GGAACTCCGTTCATTCGCCA 60.672 55.000 8.76 0.00 43.54 5.69
1206 1233 4.681978 GCCGGTGCTGAGTCGGTT 62.682 66.667 1.90 0.00 44.97 4.44
1215 1242 1.229082 TGAGTCGGTTAGCCCAGGT 60.229 57.895 0.00 0.00 0.00 4.00
1233 1260 3.004210 CAGGTGAGTATGTCAGAGATCCG 59.996 52.174 0.00 0.00 35.13 4.18
1248 1275 3.772025 GAGATCCGGGATCCATATTGAGT 59.228 47.826 28.99 10.82 39.66 3.41
1281 1308 3.254166 GGATTTTCAAGAGAAGCAGCACA 59.746 43.478 0.00 0.00 34.71 4.57
1407 1434 0.609406 GAAGCCCTGGTCTTGGTTCC 60.609 60.000 0.00 0.00 31.98 3.62
1536 1563 4.962155 AGAACTTCGAGTTTGAGGAATGT 58.038 39.130 2.51 0.00 38.80 2.71
1623 1650 9.416794 AGAATCATTAGTAAATCACGCTATGAG 57.583 33.333 0.00 0.00 41.91 2.90
1687 1714 3.738982 TCTCGAAATGGCTCAAAAGTGA 58.261 40.909 0.00 0.00 0.00 3.41
1723 1750 0.461961 GATTGCTCCGCTACCTGAGT 59.538 55.000 0.00 0.00 0.00 3.41
1816 1843 2.557924 TCACACCACAATTCCTGCAATC 59.442 45.455 0.00 0.00 0.00 2.67
2160 2214 3.370840 TGCTTGCTTGGGTCATTAGAT 57.629 42.857 0.00 0.00 0.00 1.98
2762 2819 4.951715 ACAGATGGCAATATCAAAGCTCAA 59.048 37.500 0.00 0.00 0.00 3.02
3129 3186 7.016268 AGACAAACTATCCTGTTTCACCTAGAA 59.984 37.037 0.00 0.00 37.98 2.10
3238 3295 0.179181 CAGGCGCAACTGCACATAAG 60.179 55.000 10.83 0.00 42.21 1.73
3495 3552 3.052082 CAGTGGACCGCAGCTTGG 61.052 66.667 7.99 0.04 0.00 3.61
3524 3581 1.474330 TGGAAGATGAGAGCGCTACA 58.526 50.000 11.50 14.99 0.00 2.74
3698 3769 4.115516 CACCTGTACTCATACATGCTCAC 58.884 47.826 0.00 0.00 40.57 3.51
3912 3992 4.380945 TGGTCAGGCATTGGGGGC 62.381 66.667 0.00 0.00 0.00 5.80
3992 4073 4.102524 CACACTGGGCTGGGAACTATTATA 59.897 45.833 0.00 0.00 0.00 0.98
4132 4273 4.142609 TCTGGACAGCAGATATTTCACC 57.857 45.455 0.00 0.00 0.00 4.02
4136 4277 2.609459 GACAGCAGATATTTCACCGTGG 59.391 50.000 0.00 0.00 0.00 4.94
4319 4467 4.142966 GCCCAGTTACACGATGTTTCTTAC 60.143 45.833 0.00 0.00 0.00 2.34
4332 4480 7.384387 ACGATGTTTCTTACTTACTCCTTGAAC 59.616 37.037 0.00 0.00 0.00 3.18
4336 4484 7.494625 TGTTTCTTACTTACTCCTTGAACTGTG 59.505 37.037 0.00 0.00 0.00 3.66
4337 4485 6.971726 TCTTACTTACTCCTTGAACTGTGA 57.028 37.500 0.00 0.00 0.00 3.58
4339 4487 7.603651 TCTTACTTACTCCTTGAACTGTGATC 58.396 38.462 0.00 0.00 0.00 2.92
4342 4490 6.169094 ACTTACTCCTTGAACTGTGATCATG 58.831 40.000 0.00 0.00 0.00 3.07
4343 4491 3.947868 ACTCCTTGAACTGTGATCATGG 58.052 45.455 0.00 7.68 41.25 3.66
4345 4493 4.202503 ACTCCTTGAACTGTGATCATGGTT 60.203 41.667 13.57 13.57 40.90 3.67
4346 4494 4.326826 TCCTTGAACTGTGATCATGGTTC 58.673 43.478 24.37 24.37 40.90 3.62
4347 4495 3.441572 CCTTGAACTGTGATCATGGTTCC 59.558 47.826 26.29 16.22 37.35 3.62
4348 4496 2.698803 TGAACTGTGATCATGGTTCCG 58.301 47.619 26.29 5.95 37.74 4.30
4351 4499 3.185246 ACTGTGATCATGGTTCCGATC 57.815 47.619 0.00 0.00 38.81 3.69
4356 4558 4.038042 TGTGATCATGGTTCCGATCTACTC 59.962 45.833 0.00 0.00 39.06 2.59
4392 4594 4.020839 CCAAAAGGAAGCCAATGAGACATT 60.021 41.667 0.00 0.00 0.00 2.71
4413 4615 0.574454 GTCGCTGCGTTCATCTCATC 59.426 55.000 22.48 0.00 0.00 2.92
4437 4647 1.142667 TGAAGGTTCAGCCATGTGTCA 59.857 47.619 0.00 0.00 40.61 3.58
4441 4651 4.032960 AGGTTCAGCCATGTGTCAAATA 57.967 40.909 0.00 0.00 40.61 1.40
4464 4674 2.811431 TGTTTGTCCTTGATTAGCACGG 59.189 45.455 0.00 0.00 37.26 4.94
4477 4687 5.351465 TGATTAGCACGGACAAGAAGAAATC 59.649 40.000 0.00 0.00 0.00 2.17
4483 4693 3.071023 ACGGACAAGAAGAAATCTCACCA 59.929 43.478 0.00 0.00 37.42 4.17
4484 4694 3.433615 CGGACAAGAAGAAATCTCACCAC 59.566 47.826 0.00 0.00 37.42 4.16
4485 4695 4.646572 GGACAAGAAGAAATCTCACCACT 58.353 43.478 0.00 0.00 37.42 4.00
4486 4696 5.066593 GGACAAGAAGAAATCTCACCACTT 58.933 41.667 0.00 0.00 37.42 3.16
4487 4697 5.532779 GGACAAGAAGAAATCTCACCACTTT 59.467 40.000 0.00 0.00 37.42 2.66
4488 4698 6.382869 ACAAGAAGAAATCTCACCACTTTG 57.617 37.500 0.00 0.00 37.42 2.77
4489 4699 5.888161 ACAAGAAGAAATCTCACCACTTTGT 59.112 36.000 0.00 0.00 37.42 2.83
4490 4700 6.378280 ACAAGAAGAAATCTCACCACTTTGTT 59.622 34.615 0.00 0.00 37.42 2.83
4491 4701 6.382869 AGAAGAAATCTCACCACTTTGTTG 57.617 37.500 0.00 0.00 30.46 3.33
4492 4702 5.888161 AGAAGAAATCTCACCACTTTGTTGT 59.112 36.000 0.00 0.00 30.46 3.32
4510 4748 3.662759 TGTGTTTCCCTCCAATATCCC 57.337 47.619 0.00 0.00 0.00 3.85
4539 4777 4.582240 GCTCAAAAAGATCCAATAGAGGGG 59.418 45.833 0.00 0.00 0.00 4.79
4611 4849 9.460906 GCGTAACTAGCATTCCCTAATATATAC 57.539 37.037 0.00 0.00 34.19 1.47
4623 4861 8.970859 TCCCTAATATATACTAGTAGAACGCC 57.029 38.462 8.85 0.00 0.00 5.68
4624 4862 7.995488 TCCCTAATATATACTAGTAGAACGCCC 59.005 40.741 8.85 0.00 0.00 6.13
4625 4863 7.041508 CCCTAATATATACTAGTAGAACGCCCG 60.042 44.444 8.85 0.00 0.00 6.13
4626 4864 7.497249 CCTAATATATACTAGTAGAACGCCCGT 59.503 40.741 8.85 0.00 0.00 5.28
4627 4865 6.674694 ATATATACTAGTAGAACGCCCGTG 57.325 41.667 8.85 0.00 0.00 4.94
4628 4866 0.734889 TACTAGTAGAACGCCCGTGC 59.265 55.000 3.59 0.00 0.00 5.34
4646 4884 3.661745 CGTTGCTACGGGCTAGAAT 57.338 52.632 13.04 0.00 43.94 2.40
4647 4885 1.488527 CGTTGCTACGGGCTAGAATC 58.511 55.000 13.04 0.00 43.94 2.52
4648 4886 1.202371 CGTTGCTACGGGCTAGAATCA 60.202 52.381 13.04 0.00 43.94 2.57
4649 4887 2.737359 CGTTGCTACGGGCTAGAATCAA 60.737 50.000 13.04 0.00 43.94 2.57
4650 4888 3.267483 GTTGCTACGGGCTAGAATCAAA 58.733 45.455 0.00 0.00 42.39 2.69
4651 4889 3.838244 TGCTACGGGCTAGAATCAAAT 57.162 42.857 0.00 0.00 42.39 2.32
4652 4890 3.728845 TGCTACGGGCTAGAATCAAATC 58.271 45.455 0.00 0.00 42.39 2.17
4653 4891 3.133901 TGCTACGGGCTAGAATCAAATCA 59.866 43.478 0.00 0.00 42.39 2.57
4654 4892 4.127171 GCTACGGGCTAGAATCAAATCAA 58.873 43.478 0.00 0.00 38.06 2.57
4655 4893 4.757149 GCTACGGGCTAGAATCAAATCAAT 59.243 41.667 0.00 0.00 38.06 2.57
4656 4894 5.932303 GCTACGGGCTAGAATCAAATCAATA 59.068 40.000 0.00 0.00 38.06 1.90
4657 4895 6.426937 GCTACGGGCTAGAATCAAATCAATAA 59.573 38.462 0.00 0.00 38.06 1.40
4658 4896 7.041372 GCTACGGGCTAGAATCAAATCAATAAA 60.041 37.037 0.00 0.00 38.06 1.40
4659 4897 7.823745 ACGGGCTAGAATCAAATCAATAAAT 57.176 32.000 0.00 0.00 0.00 1.40
4660 4898 7.651808 ACGGGCTAGAATCAAATCAATAAATG 58.348 34.615 0.00 0.00 0.00 2.32
4661 4899 7.502226 ACGGGCTAGAATCAAATCAATAAATGA 59.498 33.333 0.00 0.00 43.67 2.57
4680 4918 9.927081 ATAAATGATTAAGGTCATCTTCAAGGT 57.073 29.630 0.00 0.00 37.85 3.50
4681 4919 7.872113 AATGATTAAGGTCATCTTCAAGGTC 57.128 36.000 0.00 0.00 37.85 3.85
4682 4920 5.419542 TGATTAAGGTCATCTTCAAGGTCG 58.580 41.667 0.00 0.00 36.93 4.79
4683 4921 5.186992 TGATTAAGGTCATCTTCAAGGTCGA 59.813 40.000 0.00 0.00 36.93 4.20
4684 4922 5.477607 TTAAGGTCATCTTCAAGGTCGAA 57.522 39.130 0.00 0.00 36.93 3.71
4685 4923 3.601443 AGGTCATCTTCAAGGTCGAAG 57.399 47.619 0.00 0.00 43.17 3.79
4686 4924 2.003301 GGTCATCTTCAAGGTCGAAGC 58.997 52.381 0.00 0.00 41.84 3.86
4687 4925 2.612972 GGTCATCTTCAAGGTCGAAGCA 60.613 50.000 0.00 0.00 41.84 3.91
4688 4926 3.067106 GTCATCTTCAAGGTCGAAGCAA 58.933 45.455 0.00 0.00 41.84 3.91
4689 4927 3.498397 GTCATCTTCAAGGTCGAAGCAAA 59.502 43.478 0.00 0.00 41.84 3.68
4690 4928 4.154918 GTCATCTTCAAGGTCGAAGCAAAT 59.845 41.667 0.00 0.00 41.84 2.32
4691 4929 4.761739 TCATCTTCAAGGTCGAAGCAAATT 59.238 37.500 0.00 0.00 41.84 1.82
4692 4930 5.241506 TCATCTTCAAGGTCGAAGCAAATTT 59.758 36.000 0.00 0.00 41.84 1.82
4693 4931 5.108385 TCTTCAAGGTCGAAGCAAATTTC 57.892 39.130 0.00 0.00 41.84 2.17
4694 4932 4.821805 TCTTCAAGGTCGAAGCAAATTTCT 59.178 37.500 0.00 0.00 41.84 2.52
4695 4933 4.749245 TCAAGGTCGAAGCAAATTTCTC 57.251 40.909 0.00 0.00 0.00 2.87
4696 4934 3.502211 TCAAGGTCGAAGCAAATTTCTCC 59.498 43.478 0.00 0.00 0.00 3.71
4697 4935 2.437413 AGGTCGAAGCAAATTTCTCCC 58.563 47.619 0.00 0.00 0.00 4.30
4698 4936 2.040412 AGGTCGAAGCAAATTTCTCCCT 59.960 45.455 0.00 0.00 0.00 4.20
4699 4937 2.820197 GGTCGAAGCAAATTTCTCCCTT 59.180 45.455 0.00 0.00 0.00 3.95
4700 4938 4.007659 GGTCGAAGCAAATTTCTCCCTTA 58.992 43.478 0.00 0.00 0.00 2.69
4701 4939 4.640647 GGTCGAAGCAAATTTCTCCCTTAT 59.359 41.667 0.00 0.00 0.00 1.73
4702 4940 5.820947 GGTCGAAGCAAATTTCTCCCTTATA 59.179 40.000 0.00 0.00 0.00 0.98
4703 4941 6.238402 GGTCGAAGCAAATTTCTCCCTTATAC 60.238 42.308 0.00 0.00 0.00 1.47
4704 4942 5.522460 TCGAAGCAAATTTCTCCCTTATACG 59.478 40.000 0.00 0.00 0.00 3.06
4705 4943 5.293569 CGAAGCAAATTTCTCCCTTATACGT 59.706 40.000 0.00 0.00 0.00 3.57
4706 4944 6.509677 CGAAGCAAATTTCTCCCTTATACGTC 60.510 42.308 0.00 0.00 0.00 4.34
4707 4945 5.123936 AGCAAATTTCTCCCTTATACGTCC 58.876 41.667 0.00 0.00 0.00 4.79
4708 4946 5.104485 AGCAAATTTCTCCCTTATACGTCCT 60.104 40.000 0.00 0.00 0.00 3.85
4709 4947 5.007724 GCAAATTTCTCCCTTATACGTCCTG 59.992 44.000 0.00 0.00 0.00 3.86
4710 4948 4.957684 ATTTCTCCCTTATACGTCCTGG 57.042 45.455 0.00 0.00 0.00 4.45
4711 4949 1.700955 TCTCCCTTATACGTCCTGGC 58.299 55.000 0.00 0.00 0.00 4.85
4712 4950 0.314302 CTCCCTTATACGTCCTGGCG 59.686 60.000 0.00 8.60 37.94 5.69
4714 4952 0.249322 CCCTTATACGTCCTGGCGTG 60.249 60.000 20.94 8.40 45.33 5.34
4715 4953 0.458669 CCTTATACGTCCTGGCGTGT 59.541 55.000 20.94 17.71 45.33 4.49
4716 4954 1.134907 CCTTATACGTCCTGGCGTGTT 60.135 52.381 20.94 13.11 45.33 3.32
4717 4955 2.190981 CTTATACGTCCTGGCGTGTTC 58.809 52.381 20.94 0.00 45.33 3.18
4718 4956 0.099259 TATACGTCCTGGCGTGTTCG 59.901 55.000 20.94 7.67 45.33 3.95
4719 4957 2.552585 ATACGTCCTGGCGTGTTCGG 62.553 60.000 20.94 0.00 45.33 4.30
4720 4958 4.351938 CGTCCTGGCGTGTTCGGA 62.352 66.667 2.94 0.00 37.56 4.55
4721 4959 2.029964 GTCCTGGCGTGTTCGGAA 59.970 61.111 0.00 0.00 37.56 4.30
4722 4960 1.595929 GTCCTGGCGTGTTCGGAAA 60.596 57.895 0.00 0.00 37.56 3.13
4723 4961 0.953960 GTCCTGGCGTGTTCGGAAAT 60.954 55.000 0.00 0.00 37.56 2.17
4724 4962 0.672401 TCCTGGCGTGTTCGGAAATC 60.672 55.000 0.00 0.00 37.56 2.17
4725 4963 0.953471 CCTGGCGTGTTCGGAAATCA 60.953 55.000 0.00 0.00 37.56 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 22 2.594303 CAAACGCCCTCAGCCACA 60.594 61.111 0.00 0.00 38.78 4.17
36 38 3.127895 CCCGTAAAAATGAAATCGGAGCA 59.872 43.478 0.00 0.00 40.29 4.26
41 43 9.738832 ATTAATAACCCCGTAAAAATGAAATCG 57.261 29.630 0.00 0.00 0.00 3.34
125 127 5.768662 AGGATTGAATTGCCATGATGAGTAG 59.231 40.000 0.00 0.00 0.00 2.57
128 130 5.531122 AAGGATTGAATTGCCATGATGAG 57.469 39.130 0.00 0.00 0.00 2.90
193 196 1.821216 TTTCCTCGAATTCCACTGGC 58.179 50.000 0.00 0.00 0.00 4.85
343 346 3.344176 GGACGGGGGATTTGGGGT 61.344 66.667 0.00 0.00 0.00 4.95
347 350 1.111277 GATTTGGGACGGGGGATTTG 58.889 55.000 0.00 0.00 0.00 2.32
350 365 2.391972 GGGATTTGGGACGGGGGAT 61.392 63.158 0.00 0.00 0.00 3.85
357 372 0.395724 AGGCATTCGGGATTTGGGAC 60.396 55.000 0.00 0.00 0.00 4.46
369 384 0.393537 CCACTGGACAGGAGGCATTC 60.394 60.000 4.14 0.00 0.00 2.67
391 406 0.478507 GGGAGGGAGGAGAGAGAGAG 59.521 65.000 0.00 0.00 0.00 3.20
392 407 1.349542 CGGGAGGGAGGAGAGAGAGA 61.350 65.000 0.00 0.00 0.00 3.10
709 735 1.633432 ACCGAATCAAATCCCAGGTCA 59.367 47.619 0.00 0.00 0.00 4.02
710 736 2.017049 CACCGAATCAAATCCCAGGTC 58.983 52.381 0.00 0.00 0.00 3.85
751 777 6.606234 TTTTTAAACGAAGGCAAAAATCCC 57.394 33.333 0.00 0.00 0.00 3.85
754 780 6.630840 CGCAATTTTTAAACGAAGGCAAAAAT 59.369 30.769 0.00 0.00 40.48 1.82
755 781 5.960105 CGCAATTTTTAAACGAAGGCAAAAA 59.040 32.000 0.00 0.00 35.15 1.94
765 791 1.384076 GTCCGCCGCAATTTTTAAACG 59.616 47.619 0.00 0.00 0.00 3.60
770 796 0.242555 ATTCGTCCGCCGCAATTTTT 59.757 45.000 0.00 0.00 36.19 1.94
847 874 3.562505 CACAAGAAGATGAGCACAAAGC 58.437 45.455 0.00 0.00 46.19 3.51
848 875 3.252701 AGCACAAGAAGATGAGCACAAAG 59.747 43.478 0.00 0.00 39.06 2.77
849 876 3.216800 AGCACAAGAAGATGAGCACAAA 58.783 40.909 0.00 0.00 39.06 2.83
889 916 1.311859 ACCTGCGCAATCATACATGG 58.688 50.000 13.05 8.40 0.00 3.66
1142 1169 1.503542 GCAGACGAGCCACCAAATG 59.496 57.895 0.00 0.00 0.00 2.32
1143 1170 3.987404 GCAGACGAGCCACCAAAT 58.013 55.556 0.00 0.00 0.00 2.32
1189 1216 3.291101 TAACCGACTCAGCACCGGC 62.291 63.158 0.00 0.00 46.54 6.13
1206 1233 2.024369 TCTGACATACTCACCTGGGCTA 60.024 50.000 0.00 0.00 0.00 3.93
1215 1242 2.174854 TCCCGGATCTCTGACATACTCA 59.825 50.000 0.73 0.00 0.00 3.41
1233 1260 3.005155 GCTGCAAACTCAATATGGATCCC 59.995 47.826 9.90 0.00 0.00 3.85
1248 1275 3.387374 TCTTGAAAATCCAAGGCTGCAAA 59.613 39.130 0.50 0.00 42.72 3.68
1281 1308 4.901250 ACCACCATTTCCTCATTGTTCTTT 59.099 37.500 0.00 0.00 0.00 2.52
1530 1557 4.142381 GGAACTGGAGCAAATGTACATTCC 60.142 45.833 21.02 17.59 0.00 3.01
1536 1563 3.620488 GGATGGAACTGGAGCAAATGTA 58.380 45.455 0.00 0.00 0.00 2.29
1687 1714 3.181476 GCAATCCCAACAACACTTTCTGT 60.181 43.478 0.00 0.00 32.89 3.41
1723 1750 5.665360 GGGATCCCCTTTTGGATTTATTCAA 59.335 40.000 21.42 0.00 45.25 2.69
1780 1807 4.096382 GTGGTGTGATGCTAAATTACCTGG 59.904 45.833 0.00 0.00 0.00 4.45
1791 1818 2.165167 CAGGAATTGTGGTGTGATGCT 58.835 47.619 0.00 0.00 0.00 3.79
1794 1821 2.291209 TGCAGGAATTGTGGTGTGAT 57.709 45.000 0.00 0.00 0.00 3.06
1995 2022 0.695924 TTCCACACATGACGGGGAAT 59.304 50.000 16.48 0.00 32.95 3.01
2210 2265 4.576053 TGAAATGATAAATCAGTCTGGCCG 59.424 41.667 0.00 0.00 40.64 6.13
2536 2593 1.251251 GCTTCAGTGTGCCCTTCAAT 58.749 50.000 0.00 0.00 0.00 2.57
2542 2599 1.503542 CATTCGCTTCAGTGTGCCC 59.496 57.895 5.57 0.00 0.00 5.36
2705 2762 8.482128 AGTGGAAAATAAAAAGGATCACAAACA 58.518 29.630 0.00 0.00 0.00 2.83
2762 2819 5.537674 GCTCATTGATATTGAATCAGGGGTT 59.462 40.000 0.00 0.00 0.00 4.11
3129 3186 2.096248 GTGGAGACGGAGACTGAGATT 58.904 52.381 0.00 0.00 29.49 2.40
3238 3295 2.844072 GAAGACTCGCTGTCCTGCCC 62.844 65.000 5.07 0.00 46.46 5.36
3243 3300 1.137825 CGGAGAAGACTCGCTGTCC 59.862 63.158 5.07 0.00 46.46 4.02
3246 3303 0.241213 TGTTCGGAGAAGACTCGCTG 59.759 55.000 0.00 0.00 45.90 5.18
3477 3534 3.052082 CAAGCTGCGGTCCACTGG 61.052 66.667 0.00 0.00 0.00 4.00
3495 3552 0.620556 TCATCTTCCAAGCCCCAGAC 59.379 55.000 0.00 0.00 0.00 3.51
3635 3701 5.363101 TCTACAATCTGTTGGATGAGCATC 58.637 41.667 1.86 1.86 39.70 3.91
3960 4040 1.078143 GCCCAGTGTGATCCCTGTC 60.078 63.158 0.00 0.00 0.00 3.51
3978 4058 6.479972 TGGAGTGTGTATAATAGTTCCCAG 57.520 41.667 0.00 0.00 0.00 4.45
3992 4073 5.489792 AGAGACATACATTTGGAGTGTGT 57.510 39.130 0.00 0.00 42.79 3.72
4008 4089 0.465460 AAAGGTGGCGCAAAGAGACA 60.465 50.000 10.83 0.00 0.00 3.41
4009 4090 0.040067 CAAAGGTGGCGCAAAGAGAC 60.040 55.000 10.83 0.00 0.00 3.36
4156 4300 6.642950 CACTATTCATTCTGTACGAATCCCTC 59.357 42.308 9.14 0.00 40.33 4.30
4157 4301 6.323996 TCACTATTCATTCTGTACGAATCCCT 59.676 38.462 9.14 2.34 40.33 4.20
4158 4302 6.513180 TCACTATTCATTCTGTACGAATCCC 58.487 40.000 9.14 0.00 40.33 3.85
4234 4382 3.173151 TCTGCTCTCCAGTATTCCACAA 58.827 45.455 0.00 0.00 42.38 3.33
4290 4438 2.953466 TCGTGTAACTGGGCACTATC 57.047 50.000 0.00 0.00 33.78 2.08
4292 4440 1.897133 ACATCGTGTAACTGGGCACTA 59.103 47.619 0.00 0.00 33.78 2.74
4319 4467 5.583854 CCATGATCACAGTTCAAGGAGTAAG 59.416 44.000 0.00 0.00 34.62 2.34
4332 4480 3.465742 AGATCGGAACCATGATCACAG 57.534 47.619 0.00 0.00 42.72 3.66
4348 4496 1.874872 CCGGGAAGAGACGAGTAGATC 59.125 57.143 0.00 0.00 0.00 2.75
4351 4499 1.726533 GGCCGGGAAGAGACGAGTAG 61.727 65.000 2.18 0.00 0.00 2.57
4356 4558 1.298859 CTTTTGGCCGGGAAGAGACG 61.299 60.000 2.18 0.00 0.00 4.18
4392 4594 0.808755 TGAGATGAACGCAGCGACTA 59.191 50.000 24.65 6.96 35.08 2.59
4397 4599 1.930100 CGGATGAGATGAACGCAGC 59.070 57.895 0.00 0.00 34.20 5.25
4401 4603 1.857217 CTTCAGCGGATGAGATGAACG 59.143 52.381 0.00 0.00 40.96 3.95
4437 4647 7.754924 CGTGCTAATCAAGGACAAACAATATTT 59.245 33.333 0.00 0.00 46.35 1.40
4441 4651 4.082787 CCGTGCTAATCAAGGACAAACAAT 60.083 41.667 0.00 0.00 46.35 2.71
4464 4674 6.038714 ACAAAGTGGTGAGATTTCTTCTTGTC 59.961 38.462 0.00 0.00 33.74 3.18
4477 4687 3.428862 GGGAAACACAACAAAGTGGTGAG 60.429 47.826 11.38 0.00 39.65 3.51
4483 4693 3.094484 TGGAGGGAAACACAACAAAGT 57.906 42.857 0.00 0.00 0.00 2.66
4484 4694 4.670896 ATTGGAGGGAAACACAACAAAG 57.329 40.909 0.00 0.00 0.00 2.77
4485 4695 5.245075 GGATATTGGAGGGAAACACAACAAA 59.755 40.000 0.00 0.00 0.00 2.83
4486 4696 4.770010 GGATATTGGAGGGAAACACAACAA 59.230 41.667 0.00 0.00 0.00 2.83
4487 4697 4.340617 GGATATTGGAGGGAAACACAACA 58.659 43.478 0.00 0.00 0.00 3.33
4488 4698 3.699538 GGGATATTGGAGGGAAACACAAC 59.300 47.826 0.00 0.00 0.00 3.32
4489 4699 3.335183 TGGGATATTGGAGGGAAACACAA 59.665 43.478 0.00 0.00 0.00 3.33
4490 4700 2.922955 TGGGATATTGGAGGGAAACACA 59.077 45.455 0.00 0.00 0.00 3.72
4491 4701 3.202151 TCTGGGATATTGGAGGGAAACAC 59.798 47.826 0.00 0.00 0.00 3.32
4492 4702 3.459598 CTCTGGGATATTGGAGGGAAACA 59.540 47.826 0.00 0.00 0.00 2.83
4510 4748 2.079158 TGGATCTTTTTGAGCGCTCTG 58.921 47.619 35.27 20.07 30.59 3.35
4611 4849 4.396854 GCACGGGCGTTCTACTAG 57.603 61.111 0.00 0.00 0.00 2.57
4632 4870 3.728845 TGATTTGATTCTAGCCCGTAGC 58.271 45.455 0.00 0.00 44.25 3.58
4633 4871 7.962964 TTATTGATTTGATTCTAGCCCGTAG 57.037 36.000 0.00 0.00 0.00 3.51
4634 4872 8.783093 CATTTATTGATTTGATTCTAGCCCGTA 58.217 33.333 0.00 0.00 0.00 4.02
4635 4873 7.502226 TCATTTATTGATTTGATTCTAGCCCGT 59.498 33.333 0.00 0.00 0.00 5.28
4636 4874 7.874940 TCATTTATTGATTTGATTCTAGCCCG 58.125 34.615 0.00 0.00 0.00 6.13
4654 4892 9.927081 ACCTTGAAGATGACCTTAATCATTTAT 57.073 29.630 0.00 0.00 39.48 1.40
4655 4893 9.396022 GACCTTGAAGATGACCTTAATCATTTA 57.604 33.333 0.00 0.00 39.48 1.40
4656 4894 7.066284 CGACCTTGAAGATGACCTTAATCATTT 59.934 37.037 0.00 0.00 39.48 2.32
4657 4895 6.540189 CGACCTTGAAGATGACCTTAATCATT 59.460 38.462 0.00 0.00 39.48 2.57
4658 4896 6.051717 CGACCTTGAAGATGACCTTAATCAT 58.948 40.000 0.00 0.00 42.15 2.45
4659 4897 5.186992 TCGACCTTGAAGATGACCTTAATCA 59.813 40.000 0.00 0.00 34.68 2.57
4660 4898 5.661458 TCGACCTTGAAGATGACCTTAATC 58.339 41.667 0.00 0.00 34.68 1.75
4661 4899 5.677319 TCGACCTTGAAGATGACCTTAAT 57.323 39.130 0.00 0.00 34.68 1.40
4662 4900 5.477607 TTCGACCTTGAAGATGACCTTAA 57.522 39.130 0.00 0.00 34.68 1.85
4663 4901 4.620803 GCTTCGACCTTGAAGATGACCTTA 60.621 45.833 7.63 0.00 46.64 2.69
4664 4902 3.866449 GCTTCGACCTTGAAGATGACCTT 60.866 47.826 7.63 0.00 46.64 3.50
4665 4903 2.354203 GCTTCGACCTTGAAGATGACCT 60.354 50.000 7.63 0.00 46.64 3.85
4666 4904 2.003301 GCTTCGACCTTGAAGATGACC 58.997 52.381 7.63 0.00 46.64 4.02
4667 4905 2.688507 TGCTTCGACCTTGAAGATGAC 58.311 47.619 7.63 0.00 46.64 3.06
4668 4906 3.401033 TTGCTTCGACCTTGAAGATGA 57.599 42.857 7.63 0.00 46.64 2.92
4669 4907 4.691860 ATTTGCTTCGACCTTGAAGATG 57.308 40.909 7.63 0.00 46.64 2.90
4670 4908 5.474876 AGAAATTTGCTTCGACCTTGAAGAT 59.525 36.000 7.63 0.00 46.64 2.40
4671 4909 4.821805 AGAAATTTGCTTCGACCTTGAAGA 59.178 37.500 7.63 0.00 46.64 2.87
4672 4910 5.113502 AGAAATTTGCTTCGACCTTGAAG 57.886 39.130 0.00 0.00 46.47 3.02
4673 4911 4.023193 GGAGAAATTTGCTTCGACCTTGAA 60.023 41.667 0.00 0.00 0.00 2.69
4674 4912 3.502211 GGAGAAATTTGCTTCGACCTTGA 59.498 43.478 0.00 0.00 0.00 3.02
4675 4913 3.366374 GGGAGAAATTTGCTTCGACCTTG 60.366 47.826 0.00 0.00 31.80 3.61
4676 4914 2.820197 GGGAGAAATTTGCTTCGACCTT 59.180 45.455 0.00 0.00 31.80 3.50
4677 4915 2.040412 AGGGAGAAATTTGCTTCGACCT 59.960 45.455 0.00 0.00 33.92 3.85
4678 4916 2.437413 AGGGAGAAATTTGCTTCGACC 58.563 47.619 0.00 0.00 0.00 4.79
4679 4917 5.819825 ATAAGGGAGAAATTTGCTTCGAC 57.180 39.130 0.00 0.00 0.00 4.20
4680 4918 5.522460 CGTATAAGGGAGAAATTTGCTTCGA 59.478 40.000 0.00 0.00 0.00 3.71
4681 4919 5.293569 ACGTATAAGGGAGAAATTTGCTTCG 59.706 40.000 0.00 0.00 0.00 3.79
4682 4920 6.238402 GGACGTATAAGGGAGAAATTTGCTTC 60.238 42.308 0.00 0.00 0.00 3.86
4683 4921 5.589050 GGACGTATAAGGGAGAAATTTGCTT 59.411 40.000 0.00 0.00 0.00 3.91
4684 4922 5.104485 AGGACGTATAAGGGAGAAATTTGCT 60.104 40.000 0.00 0.00 0.00 3.91
4685 4923 5.007724 CAGGACGTATAAGGGAGAAATTTGC 59.992 44.000 0.00 0.00 0.00 3.68
4686 4924 5.527582 CCAGGACGTATAAGGGAGAAATTTG 59.472 44.000 0.00 0.00 0.00 2.32
4687 4925 5.681639 CCAGGACGTATAAGGGAGAAATTT 58.318 41.667 0.00 0.00 0.00 1.82
4688 4926 4.444449 GCCAGGACGTATAAGGGAGAAATT 60.444 45.833 0.00 0.00 0.00 1.82
4689 4927 3.071167 GCCAGGACGTATAAGGGAGAAAT 59.929 47.826 0.00 0.00 0.00 2.17
4690 4928 2.433239 GCCAGGACGTATAAGGGAGAAA 59.567 50.000 0.00 0.00 0.00 2.52
4691 4929 2.037144 GCCAGGACGTATAAGGGAGAA 58.963 52.381 0.00 0.00 0.00 2.87
4692 4930 1.700955 GCCAGGACGTATAAGGGAGA 58.299 55.000 0.00 0.00 0.00 3.71
4693 4931 0.314302 CGCCAGGACGTATAAGGGAG 59.686 60.000 0.00 0.00 0.00 4.30
4694 4932 0.396139 ACGCCAGGACGTATAAGGGA 60.396 55.000 7.09 0.00 46.19 4.20
4695 4933 0.249322 CACGCCAGGACGTATAAGGG 60.249 60.000 8.37 0.00 46.34 3.95
4696 4934 0.458669 ACACGCCAGGACGTATAAGG 59.541 55.000 8.37 0.00 46.34 2.69
4697 4935 2.190981 GAACACGCCAGGACGTATAAG 58.809 52.381 8.37 0.63 46.34 1.73
4698 4936 1.467883 CGAACACGCCAGGACGTATAA 60.468 52.381 8.37 0.00 46.34 0.98
4699 4937 0.099259 CGAACACGCCAGGACGTATA 59.901 55.000 8.37 0.00 46.34 1.47
4700 4938 1.153901 CGAACACGCCAGGACGTAT 60.154 57.895 8.37 0.00 46.34 3.06
4701 4939 2.256158 CGAACACGCCAGGACGTA 59.744 61.111 8.37 0.00 46.34 3.57
4703 4941 3.851845 TTCCGAACACGCCAGGACG 62.852 63.158 0.00 0.00 39.50 4.79
4704 4942 0.953960 ATTTCCGAACACGCCAGGAC 60.954 55.000 0.00 0.00 31.69 3.85
4705 4943 0.672401 GATTTCCGAACACGCCAGGA 60.672 55.000 0.00 0.00 0.00 3.86
4706 4944 0.953471 TGATTTCCGAACACGCCAGG 60.953 55.000 0.00 0.00 0.00 4.45
4707 4945 2.539003 TGATTTCCGAACACGCCAG 58.461 52.632 0.00 0.00 0.00 4.85
4708 4946 4.781570 TGATTTCCGAACACGCCA 57.218 50.000 0.00 0.00 0.00 5.69


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

AutoCloner maintained by Alex Coulton.