Multiple sequence alignment - TraesCS2D01G072000

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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 TraesCS2D01G072000 chr2D 100.000 4929 0 0 1 4929 30392807 30387879 0.000000e+00 9103
1 TraesCS2D01G072000 chr2D 87.364 459 36 8 4212 4667 3301736 3301297 1.580000e-139 507
2 TraesCS2D01G072000 chr2D 97.378 267 6 1 4664 4929 565980785 565980519 2.090000e-123 453
3 TraesCS2D01G072000 chr7D 97.652 4685 45 10 1 4665 173723760 173719121 0.000000e+00 7982
4 TraesCS2D01G072000 chr7D 94.000 2400 77 17 2285 4664 365922612 365924964 0.000000e+00 3572
5 TraesCS2D01G072000 chr7D 95.989 1870 18 8 2813 4664 632316103 632317933 0.000000e+00 2985
6 TraesCS2D01G072000 chr7D 98.120 266 5 0 4664 4929 589472412 589472147 9.660000e-127 464
7 TraesCS2D01G072000 chr7D 96.992 266 8 0 4664 4929 458591010 458590745 9.730000e-122 448
8 TraesCS2D01G072000 chr1A 96.543 4686 110 10 1 4664 577257163 577261818 0.000000e+00 7709
9 TraesCS2D01G072000 chr1A 90.934 739 45 2 2312 3050 129243041 129243757 0.000000e+00 974
10 TraesCS2D01G072000 chr6A 95.408 4682 148 12 1 4662 578395936 578400570 0.000000e+00 7393
11 TraesCS2D01G072000 chr2A 96.862 3888 94 6 1 3868 70004614 70008493 0.000000e+00 6479
12 TraesCS2D01G072000 chr2A 91.908 655 20 4 4008 4660 70008497 70009120 0.000000e+00 885
13 TraesCS2D01G072000 chr5A 95.424 3387 89 18 1305 4668 436153665 436157008 0.000000e+00 5336
14 TraesCS2D01G072000 chr5A 92.660 2139 150 5 1 2137 544668983 544671116 0.000000e+00 3073
15 TraesCS2D01G072000 chr5A 88.453 459 42 5 4208 4664 544673060 544673509 1.210000e-150 544
16 TraesCS2D01G072000 chr3A 94.799 2557 71 10 2128 4664 135386005 135388519 0.000000e+00 3928
17 TraesCS2D01G072000 chr2B 91.768 2138 169 4 1 2137 269869636 269871767 0.000000e+00 2966
18 TraesCS2D01G072000 chr2B 92.047 679 51 3 2234 2911 269871928 269872604 0.000000e+00 952
19 TraesCS2D01G072000 chr2B 93.217 457 18 4 4212 4665 520419436 520419882 0.000000e+00 660
20 TraesCS2D01G072000 chr2B 92.625 461 22 6 4206 4665 520424742 520425191 0.000000e+00 652
21 TraesCS2D01G072000 chr7A 93.000 2043 85 12 2143 4167 656098678 656096676 0.000000e+00 2928
22 TraesCS2D01G072000 chr7A 96.617 266 8 1 4664 4929 57795730 57795466 1.630000e-119 440
23 TraesCS2D01G072000 chr7A 86.594 276 31 5 3903 4175 546010462 546010190 2.880000e-77 300
24 TraesCS2D01G072000 chr3D 95.385 1495 38 6 2514 3992 357733526 357732047 0.000000e+00 2350
25 TraesCS2D01G072000 chr3D 95.500 400 15 2 4268 4665 357725194 357724796 1.940000e-178 636
26 TraesCS2D01G072000 chr6B 86.251 2102 257 18 51 2133 713860168 713862256 0.000000e+00 2252
27 TraesCS2D01G072000 chr6B 86.108 2102 258 24 51 2133 713306607 713308693 0.000000e+00 2233
28 TraesCS2D01G072000 chr5B 97.128 1149 32 1 127 1274 26733627 26734775 0.000000e+00 1938
29 TraesCS2D01G072000 chr1B 88.095 462 34 6 4206 4664 420714988 420715431 3.380000e-146 529
30 TraesCS2D01G072000 chr4D 87.939 456 33 10 4212 4664 229898912 229898476 7.310000e-143 518
31 TraesCS2D01G072000 chr5D 97.744 266 6 0 4664 4929 361611906 361612171 4.500000e-125 459
32 TraesCS2D01G072000 chr5D 97.348 264 6 1 4664 4927 551967501 551967239 9.730000e-122 448
33 TraesCS2D01G072000 chr6D 97.368 266 7 0 4664 4929 4153531 4153796 2.090000e-123 453
34 TraesCS2D01G072000 chr4B 96.617 266 9 0 4664 4929 63844887 63844622 4.530000e-120 442
35 TraesCS2D01G072000 chr4B 87.387 222 26 1 2135 2354 167328416 167328637 2.280000e-63 254
36 TraesCS2D01G072000 chr3B 96.617 266 9 0 4664 4929 22698474 22698209 4.530000e-120 442


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 TraesCS2D01G072000 chr2D 30387879 30392807 4928 True 9103.0 9103 100.0000 1 4929 1 chr2D.!!$R2 4928
1 TraesCS2D01G072000 chr7D 173719121 173723760 4639 True 7982.0 7982 97.6520 1 4665 1 chr7D.!!$R1 4664
2 TraesCS2D01G072000 chr7D 365922612 365924964 2352 False 3572.0 3572 94.0000 2285 4664 1 chr7D.!!$F1 2379
3 TraesCS2D01G072000 chr7D 632316103 632317933 1830 False 2985.0 2985 95.9890 2813 4664 1 chr7D.!!$F2 1851
4 TraesCS2D01G072000 chr1A 577257163 577261818 4655 False 7709.0 7709 96.5430 1 4664 1 chr1A.!!$F2 4663
5 TraesCS2D01G072000 chr1A 129243041 129243757 716 False 974.0 974 90.9340 2312 3050 1 chr1A.!!$F1 738
6 TraesCS2D01G072000 chr6A 578395936 578400570 4634 False 7393.0 7393 95.4080 1 4662 1 chr6A.!!$F1 4661
7 TraesCS2D01G072000 chr2A 70004614 70009120 4506 False 3682.0 6479 94.3850 1 4660 2 chr2A.!!$F1 4659
8 TraesCS2D01G072000 chr5A 436153665 436157008 3343 False 5336.0 5336 95.4240 1305 4668 1 chr5A.!!$F1 3363
9 TraesCS2D01G072000 chr5A 544668983 544673509 4526 False 1808.5 3073 90.5565 1 4664 2 chr5A.!!$F2 4663
10 TraesCS2D01G072000 chr3A 135386005 135388519 2514 False 3928.0 3928 94.7990 2128 4664 1 chr3A.!!$F1 2536
11 TraesCS2D01G072000 chr2B 269869636 269872604 2968 False 1959.0 2966 91.9075 1 2911 2 chr2B.!!$F3 2910
12 TraesCS2D01G072000 chr7A 656096676 656098678 2002 True 2928.0 2928 93.0000 2143 4167 1 chr7A.!!$R3 2024
13 TraesCS2D01G072000 chr3D 357732047 357733526 1479 True 2350.0 2350 95.3850 2514 3992 1 chr3D.!!$R2 1478
14 TraesCS2D01G072000 chr6B 713860168 713862256 2088 False 2252.0 2252 86.2510 51 2133 1 chr6B.!!$F2 2082
15 TraesCS2D01G072000 chr6B 713306607 713308693 2086 False 2233.0 2233 86.1080 51 2133 1 chr6B.!!$F1 2082
16 TraesCS2D01G072000 chr5B 26733627 26734775 1148 False 1938.0 1938 97.1280 127 1274 1 chr5B.!!$F1 1147

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
497 498 2.057137 TCCATATGCTTGCACTTCCC 57.943 50.000 0.0 0.0 0.00 3.97 F
1138 1153 3.949754 TCTTCCTGCTGCTATTCCAAATG 59.050 43.478 0.0 0.0 0.00 2.32 F
2208 2305 3.878778 ACACATCCTTATGAAGTCTGGC 58.121 45.455 0.0 0.0 36.54 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1847 1867 2.221169 ACTTTGAGCTGCAACGATTGA 58.779 42.857 1.02 0.0 35.91 2.57 R
3026 3133 6.585416 AGGATTTGTTTCTTTTTGAGCACAT 58.415 32.000 0.00 0.0 0.00 3.21 R
4188 4597 2.753055 AGTGTGTGTGTGTGTGTGTA 57.247 45.000 0.00 0.0 0.00 2.90 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
497 498 2.057137 TCCATATGCTTGCACTTCCC 57.943 50.000 0.00 0.00 0.00 3.97
1138 1153 3.949754 TCTTCCTGCTGCTATTCCAAATG 59.050 43.478 0.00 0.00 0.00 2.32
1461 1477 5.904941 TGTTGCAGACAAAATTGAAGATGT 58.095 33.333 0.00 0.00 37.58 3.06
1847 1867 5.837437 TGCAAAATCAAAGAAATACCGTGT 58.163 33.333 0.00 0.00 0.00 4.49
1910 1930 6.916932 GGTTCCAACTCGATGACTACTATAAC 59.083 42.308 0.00 0.00 0.00 1.89
2133 2155 7.867403 CAGAAGCAACTAAATGTTTGGTATGTT 59.133 33.333 0.00 0.00 36.63 2.71
2208 2305 3.878778 ACACATCCTTATGAAGTCTGGC 58.121 45.455 0.00 0.00 36.54 4.85
2755 2854 7.524717 AGCATTTGAAAGTAACCACTATGTT 57.475 32.000 0.00 0.00 33.48 2.71
3026 3133 2.436417 AGCAAAGAATCGCCAGCTTTA 58.564 42.857 0.00 0.00 31.21 1.85
3059 3166 9.965824 CAAAAAGAAACAAATCCTAGCTCTAAA 57.034 29.630 0.00 0.00 0.00 1.85
3423 3546 2.474526 GCAGCGTGTGTAGTTGCATTAG 60.475 50.000 0.00 0.00 43.72 1.73
4047 4439 7.145985 CCTACATCAGTATGTACGTGCTAATT 58.854 38.462 5.29 0.00 44.66 1.40
4080 4472 8.718102 TTAATCAGTTAGATGTAGCAAACTCC 57.282 34.615 0.00 0.00 36.96 3.85
4086 4478 4.826274 AGATGTAGCAAACTCCAGCTAA 57.174 40.909 0.00 0.00 44.18 3.09
4252 4662 9.767228 TCATTTCATAATTATGGCTCCATTTTG 57.233 29.630 22.31 9.57 37.82 2.44
4253 4663 9.767228 CATTTCATAATTATGGCTCCATTTTGA 57.233 29.630 22.31 0.00 37.82 2.69
4254 4664 9.768662 ATTTCATAATTATGGCTCCATTTTGAC 57.231 29.630 22.31 0.00 37.82 3.18
4255 4665 8.537728 TTCATAATTATGGCTCCATTTTGACT 57.462 30.769 22.31 0.00 37.82 3.41
4256 4666 8.537728 TCATAATTATGGCTCCATTTTGACTT 57.462 30.769 22.31 0.00 37.82 3.01
4257 4667 9.639563 TCATAATTATGGCTCCATTTTGACTTA 57.360 29.630 22.31 0.00 37.82 2.24
4333 4745 7.697946 TGAATTATGTCTGCATATGGGGAATA 58.302 34.615 4.56 0.00 37.42 1.75
4411 4824 1.284785 CCACAATCTTTCCCTAGGGCA 59.715 52.381 24.42 10.18 34.68 5.36
4443 4856 5.389531 GGTAAACAACCTATCCACGTGGAC 61.390 50.000 38.46 20.97 45.71 4.02
4665 5080 8.665685 GGTAAAATGTGGATTTCTAGTAGTGTG 58.334 37.037 0.00 0.00 30.02 3.82
4666 5081 9.216117 GTAAAATGTGGATTTCTAGTAGTGTGT 57.784 33.333 0.00 0.00 30.02 3.72
4668 5083 9.959721 AAAATGTGGATTTCTAGTAGTGTGTAT 57.040 29.630 0.00 0.00 30.02 2.29
4669 5084 9.959721 AAATGTGGATTTCTAGTAGTGTGTATT 57.040 29.630 0.00 0.00 0.00 1.89
4674 5089 9.961265 TGGATTTCTAGTAGTGTGTATTATTCG 57.039 33.333 0.00 0.00 0.00 3.34
4675 5090 8.913656 GGATTTCTAGTAGTGTGTATTATTCGC 58.086 37.037 0.00 0.00 0.00 4.70
4676 5091 9.680315 GATTTCTAGTAGTGTGTATTATTCGCT 57.320 33.333 0.00 0.00 0.00 4.93
4677 5092 8.851960 TTTCTAGTAGTGTGTATTATTCGCTG 57.148 34.615 0.00 0.00 0.00 5.18
4678 5093 6.967135 TCTAGTAGTGTGTATTATTCGCTGG 58.033 40.000 0.00 0.00 0.00 4.85
4679 5094 4.369182 AGTAGTGTGTATTATTCGCTGGC 58.631 43.478 0.00 0.00 0.00 4.85
4680 5095 2.201732 AGTGTGTATTATTCGCTGGCG 58.798 47.619 8.80 8.80 41.35 5.69
4681 5096 1.260561 GTGTGTATTATTCGCTGGCGG 59.739 52.381 14.94 0.00 40.25 6.13
4682 5097 1.134640 TGTGTATTATTCGCTGGCGGT 60.135 47.619 14.94 7.02 40.25 5.68
4683 5098 1.937899 GTGTATTATTCGCTGGCGGTT 59.062 47.619 14.94 5.61 40.25 4.44
4684 5099 1.937223 TGTATTATTCGCTGGCGGTTG 59.063 47.619 14.94 0.00 40.25 3.77
4685 5100 0.941542 TATTATTCGCTGGCGGTTGC 59.058 50.000 14.94 0.00 40.25 4.17
4691 5106 4.700365 GCTGGCGGTTGCGTTTCC 62.700 66.667 0.00 0.00 44.10 3.13
4692 5107 4.038080 CTGGCGGTTGCGTTTCCC 62.038 66.667 0.00 0.00 44.10 3.97
4730 5145 0.719465 CGTGTGCGTGGATAGTTTCC 59.281 55.000 0.00 0.00 45.69 3.13
4755 5170 5.648330 AAAAAGGCCCCTAGTATAAGAGG 57.352 43.478 0.00 0.00 0.00 3.69
4756 5171 4.571366 AAAGGCCCCTAGTATAAGAGGA 57.429 45.455 0.00 0.00 34.46 3.71
4757 5172 3.837399 AGGCCCCTAGTATAAGAGGAG 57.163 52.381 0.00 0.00 34.46 3.69
4758 5173 2.384029 AGGCCCCTAGTATAAGAGGAGG 59.616 54.545 0.00 4.34 34.46 4.30
4759 5174 2.181125 GCCCCTAGTATAAGAGGAGGC 58.819 57.143 13.42 13.42 40.04 4.70
4760 5175 2.448453 CCCCTAGTATAAGAGGAGGCG 58.552 57.143 3.20 0.00 34.46 5.52
4761 5176 2.041350 CCCCTAGTATAAGAGGAGGCGA 59.959 54.545 3.20 0.00 34.46 5.54
4762 5177 3.499926 CCCCTAGTATAAGAGGAGGCGAA 60.500 52.174 3.20 0.00 34.46 4.70
4763 5178 3.506844 CCCTAGTATAAGAGGAGGCGAAC 59.493 52.174 3.20 0.00 34.46 3.95
4764 5179 4.142790 CCTAGTATAAGAGGAGGCGAACA 58.857 47.826 0.00 0.00 34.46 3.18
4765 5180 4.216687 CCTAGTATAAGAGGAGGCGAACAG 59.783 50.000 0.00 0.00 34.46 3.16
4766 5181 2.959707 AGTATAAGAGGAGGCGAACAGG 59.040 50.000 0.00 0.00 0.00 4.00
4792 5207 2.759560 GCATCGCCCACCCCATTT 60.760 61.111 0.00 0.00 0.00 2.32
4793 5208 2.785425 GCATCGCCCACCCCATTTC 61.785 63.158 0.00 0.00 0.00 2.17
4794 5209 2.127232 CATCGCCCACCCCATTTCC 61.127 63.158 0.00 0.00 0.00 3.13
4795 5210 3.373932 ATCGCCCACCCCATTTCCC 62.374 63.158 0.00 0.00 0.00 3.97
4797 5212 4.796775 GCCCACCCCATTTCCCCC 62.797 72.222 0.00 0.00 0.00 5.40
4798 5213 3.280151 CCCACCCCATTTCCCCCA 61.280 66.667 0.00 0.00 0.00 4.96
4799 5214 2.865600 CCACCCCATTTCCCCCAA 59.134 61.111 0.00 0.00 0.00 4.12
4800 5215 1.159664 CCACCCCATTTCCCCCAAA 59.840 57.895 0.00 0.00 0.00 3.28
4801 5216 0.253113 CCACCCCATTTCCCCCAAAT 60.253 55.000 0.00 0.00 34.79 2.32
4802 5217 1.203237 CACCCCATTTCCCCCAAATC 58.797 55.000 0.00 0.00 31.79 2.17
4803 5218 0.325203 ACCCCATTTCCCCCAAATCG 60.325 55.000 0.00 0.00 31.79 3.34
4804 5219 1.685355 CCCCATTTCCCCCAAATCGC 61.685 60.000 0.00 0.00 31.79 4.58
4805 5220 1.685355 CCCATTTCCCCCAAATCGCC 61.685 60.000 0.00 0.00 31.79 5.54
4806 5221 0.687427 CCATTTCCCCCAAATCGCCT 60.687 55.000 0.00 0.00 31.79 5.52
4807 5222 0.746659 CATTTCCCCCAAATCGCCTC 59.253 55.000 0.00 0.00 31.79 4.70
4808 5223 0.397114 ATTTCCCCCAAATCGCCTCC 60.397 55.000 0.00 0.00 27.18 4.30
4809 5224 2.508407 TTTCCCCCAAATCGCCTCCC 62.508 60.000 0.00 0.00 0.00 4.30
4810 5225 3.420482 CCCCCAAATCGCCTCCCT 61.420 66.667 0.00 0.00 0.00 4.20
4811 5226 2.193248 CCCCAAATCGCCTCCCTC 59.807 66.667 0.00 0.00 0.00 4.30
4812 5227 2.378634 CCCCAAATCGCCTCCCTCT 61.379 63.158 0.00 0.00 0.00 3.69
4813 5228 1.147153 CCCAAATCGCCTCCCTCTC 59.853 63.158 0.00 0.00 0.00 3.20
4814 5229 1.147153 CCAAATCGCCTCCCTCTCC 59.853 63.158 0.00 0.00 0.00 3.71
4815 5230 1.147153 CAAATCGCCTCCCTCTCCC 59.853 63.158 0.00 0.00 0.00 4.30
4816 5231 1.003573 AAATCGCCTCCCTCTCCCT 59.996 57.895 0.00 0.00 0.00 4.20
4817 5232 1.051556 AAATCGCCTCCCTCTCCCTC 61.052 60.000 0.00 0.00 0.00 4.30
4818 5233 2.956077 AATCGCCTCCCTCTCCCTCC 62.956 65.000 0.00 0.00 0.00 4.30
4819 5234 4.150454 CGCCTCCCTCTCCCTCCT 62.150 72.222 0.00 0.00 0.00 3.69
4820 5235 2.123033 GCCTCCCTCTCCCTCCTC 60.123 72.222 0.00 0.00 0.00 3.71
4821 5236 2.710826 GCCTCCCTCTCCCTCCTCT 61.711 68.421 0.00 0.00 0.00 3.69
4822 5237 1.541672 CCTCCCTCTCCCTCCTCTC 59.458 68.421 0.00 0.00 0.00 3.20
4823 5238 0.998945 CCTCCCTCTCCCTCCTCTCT 60.999 65.000 0.00 0.00 0.00 3.10
4824 5239 0.185901 CTCCCTCTCCCTCCTCTCTG 59.814 65.000 0.00 0.00 0.00 3.35
4825 5240 1.457455 CCCTCTCCCTCCTCTCTGC 60.457 68.421 0.00 0.00 0.00 4.26
4826 5241 1.620259 CCTCTCCCTCCTCTCTGCT 59.380 63.158 0.00 0.00 0.00 4.24
4827 5242 0.468029 CCTCTCCCTCCTCTCTGCTC 60.468 65.000 0.00 0.00 0.00 4.26
4828 5243 0.552848 CTCTCCCTCCTCTCTGCTCT 59.447 60.000 0.00 0.00 0.00 4.09
4829 5244 0.258484 TCTCCCTCCTCTCTGCTCTG 59.742 60.000 0.00 0.00 0.00 3.35
4830 5245 1.381056 TCCCTCCTCTCTGCTCTGC 60.381 63.158 0.00 0.00 0.00 4.26
4831 5246 2.433994 CCCTCCTCTCTGCTCTGCC 61.434 68.421 0.00 0.00 0.00 4.85
4832 5247 1.381599 CCTCCTCTCTGCTCTGCCT 60.382 63.158 0.00 0.00 0.00 4.75
4833 5248 1.394266 CCTCCTCTCTGCTCTGCCTC 61.394 65.000 0.00 0.00 0.00 4.70
4834 5249 0.683828 CTCCTCTCTGCTCTGCCTCA 60.684 60.000 0.00 0.00 0.00 3.86
4835 5250 0.032316 TCCTCTCTGCTCTGCCTCAT 60.032 55.000 0.00 0.00 0.00 2.90
4836 5251 0.390124 CCTCTCTGCTCTGCCTCATC 59.610 60.000 0.00 0.00 0.00 2.92
4837 5252 0.031043 CTCTCTGCTCTGCCTCATCG 59.969 60.000 0.00 0.00 0.00 3.84
4838 5253 0.682532 TCTCTGCTCTGCCTCATCGT 60.683 55.000 0.00 0.00 0.00 3.73
4839 5254 0.248990 CTCTGCTCTGCCTCATCGTC 60.249 60.000 0.00 0.00 0.00 4.20
4840 5255 0.682532 TCTGCTCTGCCTCATCGTCT 60.683 55.000 0.00 0.00 0.00 4.18
4841 5256 0.248990 CTGCTCTGCCTCATCGTCTC 60.249 60.000 0.00 0.00 0.00 3.36
4842 5257 1.067250 GCTCTGCCTCATCGTCTCC 59.933 63.158 0.00 0.00 0.00 3.71
4843 5258 1.739049 CTCTGCCTCATCGTCTCCC 59.261 63.158 0.00 0.00 0.00 4.30
4844 5259 0.754957 CTCTGCCTCATCGTCTCCCT 60.755 60.000 0.00 0.00 0.00 4.20
4845 5260 0.753479 TCTGCCTCATCGTCTCCCTC 60.753 60.000 0.00 0.00 0.00 4.30
4846 5261 1.000359 TGCCTCATCGTCTCCCTCA 60.000 57.895 0.00 0.00 0.00 3.86
4847 5262 1.323271 TGCCTCATCGTCTCCCTCAC 61.323 60.000 0.00 0.00 0.00 3.51
4848 5263 2.022240 GCCTCATCGTCTCCCTCACC 62.022 65.000 0.00 0.00 0.00 4.02
4849 5264 1.729470 CCTCATCGTCTCCCTCACCG 61.729 65.000 0.00 0.00 0.00 4.94
4850 5265 1.729470 CTCATCGTCTCCCTCACCGG 61.729 65.000 0.00 0.00 0.00 5.28
4851 5266 3.148279 ATCGTCTCCCTCACCGGC 61.148 66.667 0.00 0.00 0.00 6.13
4854 5269 4.083862 GTCTCCCTCACCGGCCAC 62.084 72.222 0.00 0.00 0.00 5.01
4869 5284 4.767255 CACCCCACCTGCTCGCTC 62.767 72.222 0.00 0.00 0.00 5.03
4871 5286 4.767255 CCCCACCTGCTCGCTCAC 62.767 72.222 0.00 0.00 0.00 3.51
4872 5287 4.767255 CCCACCTGCTCGCTCACC 62.767 72.222 0.00 0.00 0.00 4.02
4873 5288 4.007644 CCACCTGCTCGCTCACCA 62.008 66.667 0.00 0.00 0.00 4.17
4874 5289 2.740055 CACCTGCTCGCTCACCAC 60.740 66.667 0.00 0.00 0.00 4.16
4875 5290 4.008933 ACCTGCTCGCTCACCACC 62.009 66.667 0.00 0.00 0.00 4.61
4892 5307 4.214327 CGCCGCCTCCCTCTCTTC 62.214 72.222 0.00 0.00 0.00 2.87
4893 5308 2.762043 GCCGCCTCCCTCTCTTCT 60.762 66.667 0.00 0.00 0.00 2.85
4894 5309 2.791868 GCCGCCTCCCTCTCTTCTC 61.792 68.421 0.00 0.00 0.00 2.87
4895 5310 2.131067 CCGCCTCCCTCTCTTCTCC 61.131 68.421 0.00 0.00 0.00 3.71
4896 5311 1.076339 CGCCTCCCTCTCTTCTCCT 60.076 63.158 0.00 0.00 0.00 3.69
4897 5312 1.391157 CGCCTCCCTCTCTTCTCCTG 61.391 65.000 0.00 0.00 0.00 3.86
4898 5313 1.685355 GCCTCCCTCTCTTCTCCTGC 61.685 65.000 0.00 0.00 0.00 4.85
4899 5314 0.032217 CCTCCCTCTCTTCTCCTGCT 60.032 60.000 0.00 0.00 0.00 4.24
4900 5315 1.622173 CCTCCCTCTCTTCTCCTGCTT 60.622 57.143 0.00 0.00 0.00 3.91
4901 5316 1.481772 CTCCCTCTCTTCTCCTGCTTG 59.518 57.143 0.00 0.00 0.00 4.01
4902 5317 0.107752 CCCTCTCTTCTCCTGCTTGC 60.108 60.000 0.00 0.00 0.00 4.01
4903 5318 0.903942 CCTCTCTTCTCCTGCTTGCT 59.096 55.000 0.00 0.00 0.00 3.91
4904 5319 1.278699 CCTCTCTTCTCCTGCTTGCTT 59.721 52.381 0.00 0.00 0.00 3.91
4905 5320 2.620242 CTCTCTTCTCCTGCTTGCTTC 58.380 52.381 0.00 0.00 0.00 3.86
4906 5321 2.234414 CTCTCTTCTCCTGCTTGCTTCT 59.766 50.000 0.00 0.00 0.00 2.85
4907 5322 2.028294 TCTCTTCTCCTGCTTGCTTCTG 60.028 50.000 0.00 0.00 0.00 3.02
4908 5323 1.002888 TCTTCTCCTGCTTGCTTCTGG 59.997 52.381 0.00 0.00 0.00 3.86
4909 5324 0.607489 TTCTCCTGCTTGCTTCTGGC 60.607 55.000 0.00 0.00 42.22 4.85
4910 5325 1.002379 CTCCTGCTTGCTTCTGGCT 60.002 57.895 0.00 0.00 42.39 4.75
4911 5326 1.002868 TCCTGCTTGCTTCTGGCTC 60.003 57.895 0.00 0.00 42.39 4.70
4912 5327 2.396955 CCTGCTTGCTTCTGGCTCG 61.397 63.158 0.00 0.00 42.39 5.03
4913 5328 2.359107 TGCTTGCTTCTGGCTCGG 60.359 61.111 0.00 0.00 42.39 4.63
4914 5329 2.046892 GCTTGCTTCTGGCTCGGA 60.047 61.111 0.00 0.00 42.39 4.55
4915 5330 1.451028 GCTTGCTTCTGGCTCGGAT 60.451 57.895 0.00 0.00 42.39 4.18
4916 5331 1.712977 GCTTGCTTCTGGCTCGGATG 61.713 60.000 0.00 0.00 42.39 3.51
4917 5332 1.078214 TTGCTTCTGGCTCGGATGG 60.078 57.895 0.00 0.00 42.39 3.51
4918 5333 1.552799 TTGCTTCTGGCTCGGATGGA 61.553 55.000 0.00 0.00 42.39 3.41
4919 5334 1.227497 GCTTCTGGCTCGGATGGAG 60.227 63.158 0.00 0.00 46.06 3.86
4926 5341 2.203126 CTCGGATGGAGCAAGGCC 60.203 66.667 0.00 0.00 35.63 5.19
4927 5342 4.161295 TCGGATGGAGCAAGGCCG 62.161 66.667 0.00 0.00 43.11 6.13
4928 5343 4.473520 CGGATGGAGCAAGGCCGT 62.474 66.667 0.00 0.00 37.35 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1138 1153 5.904080 GTCGAATGATTGGACGATTTTCATC 59.096 40.000 4.60 0.00 37.14 2.92
1847 1867 2.221169 ACTTTGAGCTGCAACGATTGA 58.779 42.857 1.02 0.00 35.91 2.57
2208 2305 6.700960 TGACATGCAAAAACACTAAATTCAGG 59.299 34.615 0.00 0.00 0.00 3.86
3026 3133 6.585416 AGGATTTGTTTCTTTTTGAGCACAT 58.415 32.000 0.00 0.00 0.00 3.21
3423 3546 8.942338 TCTCAACTTATCCATACACACATAAC 57.058 34.615 0.00 0.00 0.00 1.89
4047 4439 7.869937 GCTACATCTAACTGATTAAGCATCTCA 59.130 37.037 0.00 0.00 38.89 3.27
4181 4590 8.474831 AGTGTGTGTGTGTGTGTGTATATATAT 58.525 33.333 0.00 0.00 0.00 0.86
4182 4591 7.832769 AGTGTGTGTGTGTGTGTGTATATATA 58.167 34.615 0.00 0.00 0.00 0.86
4183 4592 6.697395 AGTGTGTGTGTGTGTGTGTATATAT 58.303 36.000 0.00 0.00 0.00 0.86
4184 4593 6.091718 AGTGTGTGTGTGTGTGTGTATATA 57.908 37.500 0.00 0.00 0.00 0.86
4185 4594 4.956085 AGTGTGTGTGTGTGTGTGTATAT 58.044 39.130 0.00 0.00 0.00 0.86
4186 4595 4.394439 AGTGTGTGTGTGTGTGTGTATA 57.606 40.909 0.00 0.00 0.00 1.47
4187 4596 3.260475 AGTGTGTGTGTGTGTGTGTAT 57.740 42.857 0.00 0.00 0.00 2.29
4188 4597 2.753055 AGTGTGTGTGTGTGTGTGTA 57.247 45.000 0.00 0.00 0.00 2.90
4189 4598 2.753055 TAGTGTGTGTGTGTGTGTGT 57.247 45.000 0.00 0.00 0.00 3.72
4190 4599 4.614555 AATTAGTGTGTGTGTGTGTGTG 57.385 40.909 0.00 0.00 0.00 3.82
4191 4600 6.935741 AATAATTAGTGTGTGTGTGTGTGT 57.064 33.333 0.00 0.00 0.00 3.72
4192 4601 7.413644 TCAAATAATTAGTGTGTGTGTGTGTG 58.586 34.615 0.00 0.00 0.00 3.82
4193 4602 7.561021 TCAAATAATTAGTGTGTGTGTGTGT 57.439 32.000 0.00 0.00 0.00 3.72
4194 4603 8.075574 ACATCAAATAATTAGTGTGTGTGTGTG 58.924 33.333 0.00 0.00 0.00 3.82
4195 4604 8.165239 ACATCAAATAATTAGTGTGTGTGTGT 57.835 30.769 0.00 0.00 0.00 3.72
4333 4745 7.735326 AGAGTTACATACTGTAGGGAAACAT 57.265 36.000 16.66 7.05 37.17 2.71
4443 4856 8.792831 GAAAGATTTCCATATGTATGTTGCAG 57.207 34.615 1.24 0.00 31.82 4.41
4665 5080 1.333791 GCAACCGCCAGCGAATAATAC 60.334 52.381 14.67 0.00 42.83 1.89
4666 5081 0.941542 GCAACCGCCAGCGAATAATA 59.058 50.000 14.67 0.00 42.83 0.98
4667 5082 1.727467 GCAACCGCCAGCGAATAAT 59.273 52.632 14.67 0.00 42.83 1.28
4668 5083 3.183259 GCAACCGCCAGCGAATAA 58.817 55.556 14.67 0.00 42.83 1.40
4674 5089 4.700365 GGAAACGCAACCGCCAGC 62.700 66.667 0.00 0.00 38.22 4.85
4675 5090 4.038080 GGGAAACGCAACCGCCAG 62.038 66.667 0.00 0.00 38.22 4.85
4733 5148 5.294473 TCCTCTTATACTAGGGGCCTTTTT 58.706 41.667 0.84 0.00 35.61 1.94
4734 5149 4.904373 TCCTCTTATACTAGGGGCCTTTT 58.096 43.478 0.84 0.00 35.61 2.27
4735 5150 4.494591 CTCCTCTTATACTAGGGGCCTTT 58.505 47.826 0.84 0.00 35.61 3.11
4736 5151 3.181405 CCTCCTCTTATACTAGGGGCCTT 60.181 52.174 0.84 0.00 35.61 4.35
4737 5152 2.384029 CCTCCTCTTATACTAGGGGCCT 59.616 54.545 0.84 0.00 35.61 5.19
4738 5153 2.822697 CCTCCTCTTATACTAGGGGCC 58.177 57.143 0.00 0.00 35.61 5.80
4739 5154 2.181125 GCCTCCTCTTATACTAGGGGC 58.819 57.143 12.47 12.47 40.03 5.80
4740 5155 2.041350 TCGCCTCCTCTTATACTAGGGG 59.959 54.545 0.00 0.00 40.59 4.79
4741 5156 3.436577 TCGCCTCCTCTTATACTAGGG 57.563 52.381 0.00 0.00 33.40 3.53
4742 5157 4.142790 TGTTCGCCTCCTCTTATACTAGG 58.857 47.826 0.00 0.00 0.00 3.02
4743 5158 4.216687 CCTGTTCGCCTCCTCTTATACTAG 59.783 50.000 0.00 0.00 0.00 2.57
4744 5159 4.142790 CCTGTTCGCCTCCTCTTATACTA 58.857 47.826 0.00 0.00 0.00 1.82
4745 5160 2.959707 CCTGTTCGCCTCCTCTTATACT 59.040 50.000 0.00 0.00 0.00 2.12
4746 5161 2.546162 GCCTGTTCGCCTCCTCTTATAC 60.546 54.545 0.00 0.00 0.00 1.47
4747 5162 1.687123 GCCTGTTCGCCTCCTCTTATA 59.313 52.381 0.00 0.00 0.00 0.98
4748 5163 0.466124 GCCTGTTCGCCTCCTCTTAT 59.534 55.000 0.00 0.00 0.00 1.73
4749 5164 0.902984 TGCCTGTTCGCCTCCTCTTA 60.903 55.000 0.00 0.00 0.00 2.10
4750 5165 2.217038 TGCCTGTTCGCCTCCTCTT 61.217 57.895 0.00 0.00 0.00 2.85
4751 5166 2.604686 TGCCTGTTCGCCTCCTCT 60.605 61.111 0.00 0.00 0.00 3.69
4752 5167 2.435059 GTGCCTGTTCGCCTCCTC 60.435 66.667 0.00 0.00 0.00 3.71
4753 5168 4.021925 GGTGCCTGTTCGCCTCCT 62.022 66.667 0.00 0.00 33.93 3.69
4775 5190 2.759560 AAATGGGGTGGGCGATGC 60.760 61.111 0.00 0.00 0.00 3.91
4776 5191 2.127232 GGAAATGGGGTGGGCGATG 61.127 63.158 0.00 0.00 0.00 3.84
4777 5192 2.278738 GGAAATGGGGTGGGCGAT 59.721 61.111 0.00 0.00 0.00 4.58
4778 5193 4.055227 GGGAAATGGGGTGGGCGA 62.055 66.667 0.00 0.00 0.00 5.54
4780 5195 4.796775 GGGGGAAATGGGGTGGGC 62.797 72.222 0.00 0.00 0.00 5.36
4781 5196 2.408495 TTTGGGGGAAATGGGGTGGG 62.408 60.000 0.00 0.00 0.00 4.61
4782 5197 0.253113 ATTTGGGGGAAATGGGGTGG 60.253 55.000 0.00 0.00 32.69 4.61
4783 5198 1.203237 GATTTGGGGGAAATGGGGTG 58.797 55.000 0.00 0.00 34.18 4.61
4784 5199 0.325203 CGATTTGGGGGAAATGGGGT 60.325 55.000 0.00 0.00 34.18 4.95
4785 5200 1.685355 GCGATTTGGGGGAAATGGGG 61.685 60.000 0.00 0.00 34.18 4.96
4786 5201 1.685355 GGCGATTTGGGGGAAATGGG 61.685 60.000 0.00 0.00 34.18 4.00
4787 5202 0.687427 AGGCGATTTGGGGGAAATGG 60.687 55.000 0.00 0.00 34.18 3.16
4788 5203 0.746659 GAGGCGATTTGGGGGAAATG 59.253 55.000 0.00 0.00 34.18 2.32
4789 5204 0.397114 GGAGGCGATTTGGGGGAAAT 60.397 55.000 0.00 0.00 36.94 2.17
4790 5205 1.000145 GGAGGCGATTTGGGGGAAA 60.000 57.895 0.00 0.00 0.00 3.13
4791 5206 2.680965 GGAGGCGATTTGGGGGAA 59.319 61.111 0.00 0.00 0.00 3.97
4792 5207 3.416880 GGGAGGCGATTTGGGGGA 61.417 66.667 0.00 0.00 0.00 4.81
4793 5208 3.420482 AGGGAGGCGATTTGGGGG 61.420 66.667 0.00 0.00 0.00 5.40
4794 5209 2.193248 GAGGGAGGCGATTTGGGG 59.807 66.667 0.00 0.00 0.00 4.96
4795 5210 1.147153 GAGAGGGAGGCGATTTGGG 59.853 63.158 0.00 0.00 0.00 4.12
4796 5211 1.147153 GGAGAGGGAGGCGATTTGG 59.853 63.158 0.00 0.00 0.00 3.28
4797 5212 1.147153 GGGAGAGGGAGGCGATTTG 59.853 63.158 0.00 0.00 0.00 2.32
4798 5213 1.003573 AGGGAGAGGGAGGCGATTT 59.996 57.895 0.00 0.00 0.00 2.17
4799 5214 1.458588 GAGGGAGAGGGAGGCGATT 60.459 63.158 0.00 0.00 0.00 3.34
4800 5215 2.200092 GAGGGAGAGGGAGGCGAT 59.800 66.667 0.00 0.00 0.00 4.58
4801 5216 4.144727 GGAGGGAGAGGGAGGCGA 62.145 72.222 0.00 0.00 0.00 5.54
4802 5217 4.150454 AGGAGGGAGAGGGAGGCG 62.150 72.222 0.00 0.00 0.00 5.52
4803 5218 2.123033 GAGGAGGGAGAGGGAGGC 60.123 72.222 0.00 0.00 0.00 4.70
4804 5219 0.998945 AGAGAGGAGGGAGAGGGAGG 60.999 65.000 0.00 0.00 0.00 4.30
4805 5220 0.185901 CAGAGAGGAGGGAGAGGGAG 59.814 65.000 0.00 0.00 0.00 4.30
4806 5221 1.943730 GCAGAGAGGAGGGAGAGGGA 61.944 65.000 0.00 0.00 0.00 4.20
4807 5222 1.457455 GCAGAGAGGAGGGAGAGGG 60.457 68.421 0.00 0.00 0.00 4.30
4808 5223 0.468029 GAGCAGAGAGGAGGGAGAGG 60.468 65.000 0.00 0.00 0.00 3.69
4809 5224 0.552848 AGAGCAGAGAGGAGGGAGAG 59.447 60.000 0.00 0.00 0.00 3.20
4810 5225 0.258484 CAGAGCAGAGAGGAGGGAGA 59.742 60.000 0.00 0.00 0.00 3.71
4811 5226 1.394266 GCAGAGCAGAGAGGAGGGAG 61.394 65.000 0.00 0.00 0.00 4.30
4812 5227 1.381056 GCAGAGCAGAGAGGAGGGA 60.381 63.158 0.00 0.00 0.00 4.20
4813 5228 2.433994 GGCAGAGCAGAGAGGAGGG 61.434 68.421 0.00 0.00 0.00 4.30
4814 5229 1.381599 AGGCAGAGCAGAGAGGAGG 60.382 63.158 0.00 0.00 0.00 4.30
4815 5230 0.683828 TGAGGCAGAGCAGAGAGGAG 60.684 60.000 0.00 0.00 0.00 3.69
4816 5231 0.032316 ATGAGGCAGAGCAGAGAGGA 60.032 55.000 0.00 0.00 0.00 3.71
4817 5232 0.390124 GATGAGGCAGAGCAGAGAGG 59.610 60.000 0.00 0.00 0.00 3.69
4818 5233 0.031043 CGATGAGGCAGAGCAGAGAG 59.969 60.000 0.00 0.00 0.00 3.20
4819 5234 0.682532 ACGATGAGGCAGAGCAGAGA 60.683 55.000 0.00 0.00 0.00 3.10
4820 5235 0.248990 GACGATGAGGCAGAGCAGAG 60.249 60.000 0.00 0.00 0.00 3.35
4821 5236 0.682532 AGACGATGAGGCAGAGCAGA 60.683 55.000 0.00 0.00 0.00 4.26
4822 5237 0.248990 GAGACGATGAGGCAGAGCAG 60.249 60.000 0.00 0.00 0.00 4.24
4823 5238 1.670949 GGAGACGATGAGGCAGAGCA 61.671 60.000 0.00 0.00 0.00 4.26
4824 5239 1.067250 GGAGACGATGAGGCAGAGC 59.933 63.158 0.00 0.00 0.00 4.09
4825 5240 0.754957 AGGGAGACGATGAGGCAGAG 60.755 60.000 0.00 0.00 0.00 3.35
4826 5241 0.753479 GAGGGAGACGATGAGGCAGA 60.753 60.000 0.00 0.00 0.00 4.26
4827 5242 1.039785 TGAGGGAGACGATGAGGCAG 61.040 60.000 0.00 0.00 0.00 4.85
4828 5243 1.000359 TGAGGGAGACGATGAGGCA 60.000 57.895 0.00 0.00 0.00 4.75
4829 5244 1.439644 GTGAGGGAGACGATGAGGC 59.560 63.158 0.00 0.00 0.00 4.70
4830 5245 1.729470 CGGTGAGGGAGACGATGAGG 61.729 65.000 0.00 0.00 0.00 3.86
4831 5246 1.729470 CCGGTGAGGGAGACGATGAG 61.729 65.000 0.00 0.00 35.97 2.90
4832 5247 1.753078 CCGGTGAGGGAGACGATGA 60.753 63.158 0.00 0.00 35.97 2.92
4833 5248 2.808315 CCGGTGAGGGAGACGATG 59.192 66.667 0.00 0.00 35.97 3.84
4834 5249 3.148279 GCCGGTGAGGGAGACGAT 61.148 66.667 1.90 0.00 41.48 3.73
4837 5252 4.083862 GTGGCCGGTGAGGGAGAC 62.084 72.222 1.90 0.00 41.48 3.36
4852 5267 4.767255 GAGCGAGCAGGTGGGGTG 62.767 72.222 0.00 0.00 0.00 4.61
4854 5269 4.767255 GTGAGCGAGCAGGTGGGG 62.767 72.222 0.00 0.00 0.00 4.96
4855 5270 4.767255 GGTGAGCGAGCAGGTGGG 62.767 72.222 0.00 0.00 0.00 4.61
4856 5271 4.007644 TGGTGAGCGAGCAGGTGG 62.008 66.667 0.00 0.00 0.00 4.61
4857 5272 2.740055 GTGGTGAGCGAGCAGGTG 60.740 66.667 0.00 0.00 30.97 4.00
4858 5273 4.008933 GGTGGTGAGCGAGCAGGT 62.009 66.667 0.00 0.00 30.97 4.00
4875 5290 4.214327 GAAGAGAGGGAGGCGGCG 62.214 72.222 0.51 0.51 0.00 6.46
4876 5291 2.762043 AGAAGAGAGGGAGGCGGC 60.762 66.667 0.00 0.00 0.00 6.53
4877 5292 2.131067 GGAGAAGAGAGGGAGGCGG 61.131 68.421 0.00 0.00 0.00 6.13
4878 5293 1.076339 AGGAGAAGAGAGGGAGGCG 60.076 63.158 0.00 0.00 0.00 5.52
4879 5294 1.685355 GCAGGAGAAGAGAGGGAGGC 61.685 65.000 0.00 0.00 0.00 4.70
4880 5295 0.032217 AGCAGGAGAAGAGAGGGAGG 60.032 60.000 0.00 0.00 0.00 4.30
4881 5296 1.481772 CAAGCAGGAGAAGAGAGGGAG 59.518 57.143 0.00 0.00 0.00 4.30
4882 5297 1.566211 CAAGCAGGAGAAGAGAGGGA 58.434 55.000 0.00 0.00 0.00 4.20
4883 5298 0.107752 GCAAGCAGGAGAAGAGAGGG 60.108 60.000 0.00 0.00 0.00 4.30
4884 5299 0.903942 AGCAAGCAGGAGAAGAGAGG 59.096 55.000 0.00 0.00 0.00 3.69
4885 5300 2.234414 AGAAGCAAGCAGGAGAAGAGAG 59.766 50.000 0.00 0.00 0.00 3.20
4886 5301 2.028294 CAGAAGCAAGCAGGAGAAGAGA 60.028 50.000 0.00 0.00 0.00 3.10
4887 5302 2.348660 CAGAAGCAAGCAGGAGAAGAG 58.651 52.381 0.00 0.00 0.00 2.85
4888 5303 1.002888 CCAGAAGCAAGCAGGAGAAGA 59.997 52.381 0.00 0.00 0.00 2.87
4889 5304 1.451067 CCAGAAGCAAGCAGGAGAAG 58.549 55.000 0.00 0.00 0.00 2.85
4890 5305 0.607489 GCCAGAAGCAAGCAGGAGAA 60.607 55.000 0.00 0.00 42.97 2.87
4891 5306 1.002868 GCCAGAAGCAAGCAGGAGA 60.003 57.895 0.00 0.00 42.97 3.71
4892 5307 3.588336 GCCAGAAGCAAGCAGGAG 58.412 61.111 0.00 0.00 42.97 3.69
4901 5316 1.227497 CTCCATCCGAGCCAGAAGC 60.227 63.158 0.00 0.00 44.25 3.86
4909 5324 2.203126 GGCCTTGCTCCATCCGAG 60.203 66.667 0.00 0.00 42.04 4.63
4910 5325 4.161295 CGGCCTTGCTCCATCCGA 62.161 66.667 0.00 0.00 42.43 4.55
4911 5326 4.473520 ACGGCCTTGCTCCATCCG 62.474 66.667 0.00 0.00 45.04 4.18


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

AutoCloner maintained by Alex Coulton.