Multiple sequence alignment - TraesCS4A01G430400

Loading Multiple Alignment...

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 TraesCS4A01G430400 chr4A 100.000 4994 0 0 1 4994 701756478 701761471 0.000000e+00 9223
1 TraesCS4A01G430400 chr7D 95.700 4279 155 15 367 4633 28034741 28039002 0.000000e+00 6855
2 TraesCS4A01G430400 chr7D 74.561 2052 448 59 1935 3954 18693892 18691883 0.000000e+00 830
3 TraesCS4A01G430400 chr7D 95.146 309 10 4 1 309 28034311 28034614 2.700000e-132 483
4 TraesCS4A01G430400 chr7D 89.967 299 22 4 4641 4937 28039074 28039366 3.650000e-101 379
5 TraesCS4A01G430400 chr7A 94.855 4334 173 24 319 4633 28453525 28457827 0.000000e+00 6722
6 TraesCS4A01G430400 chr7A 96.190 315 11 1 3 317 28453127 28453440 9.590000e-142 514
7 TraesCS4A01G430400 chr7A 90.033 301 22 4 4639 4937 28457897 28458191 2.820000e-102 383
8 TraesCS4A01G430400 chr3D 78.797 981 187 15 2963 3939 9634699 9635662 1.520000e-179 640
9 TraesCS4A01G430400 chr3D 78.485 990 188 20 2963 3947 4958018 4957049 4.240000e-175 625
10 TraesCS4A01G430400 chr3D 73.368 965 215 32 693 1636 4960287 4959344 2.240000e-83 320
11 TraesCS4A01G430400 chr3D 85.385 130 19 0 693 822 4999416 4999287 8.720000e-28 135
12 TraesCS4A01G430400 chr3B 78.593 981 188 16 2963 3939 13816455 13817417 3.280000e-176 628
13 TraesCS4A01G430400 chr1A 78.092 954 188 13 2582 3528 402229745 402230684 7.200000e-163 584
14 TraesCS4A01G430400 chrUn 78.862 861 160 16 2963 3819 284401434 284400592 3.380000e-156 562
15 TraesCS4A01G430400 chrUn 78.862 861 160 16 2963 3819 284407968 284407126 3.380000e-156 562
16 TraesCS4A01G430400 chrUn 78.862 861 160 16 2963 3819 302991593 302990751 3.380000e-156 562
17 TraesCS4A01G430400 chrUn 78.746 861 161 16 2963 3819 257885879 257885037 1.570000e-154 556
18 TraesCS4A01G430400 chrUn 72.698 923 228 23 726 1636 35294251 35295161 2.280000e-73 287
19 TraesCS4A01G430400 chrUn 72.698 923 228 23 726 1636 229344091 229345001 2.280000e-73 287
20 TraesCS4A01G430400 chr3A 74.070 968 215 29 693 1642 10885498 10884549 1.020000e-96 364
21 TraesCS4A01G430400 chr5B 78.451 297 57 6 663 957 695493791 695493500 2.370000e-43 187
22 TraesCS4A01G430400 chr2A 77.959 245 43 9 685 924 762741751 762741513 5.210000e-30 143


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 TraesCS4A01G430400 chr4A 701756478 701761471 4993 False 9223.000000 9223 100.000000 1 4994 1 chr4A.!!$F1 4993
1 TraesCS4A01G430400 chr7D 28034311 28039366 5055 False 2572.333333 6855 93.604333 1 4937 3 chr7D.!!$F1 4936
2 TraesCS4A01G430400 chr7D 18691883 18693892 2009 True 830.000000 830 74.561000 1935 3954 1 chr7D.!!$R1 2019
3 TraesCS4A01G430400 chr7A 28453127 28458191 5064 False 2539.666667 6722 93.692667 3 4937 3 chr7A.!!$F1 4934
4 TraesCS4A01G430400 chr3D 9634699 9635662 963 False 640.000000 640 78.797000 2963 3939 1 chr3D.!!$F1 976
5 TraesCS4A01G430400 chr3D 4957049 4960287 3238 True 472.500000 625 75.926500 693 3947 2 chr3D.!!$R2 3254
6 TraesCS4A01G430400 chr3B 13816455 13817417 962 False 628.000000 628 78.593000 2963 3939 1 chr3B.!!$F1 976
7 TraesCS4A01G430400 chr1A 402229745 402230684 939 False 584.000000 584 78.092000 2582 3528 1 chr1A.!!$F1 946
8 TraesCS4A01G430400 chrUn 284400592 284401434 842 True 562.000000 562 78.862000 2963 3819 1 chrUn.!!$R2 856
9 TraesCS4A01G430400 chrUn 284407126 284407968 842 True 562.000000 562 78.862000 2963 3819 1 chrUn.!!$R3 856
10 TraesCS4A01G430400 chrUn 302990751 302991593 842 True 562.000000 562 78.862000 2963 3819 1 chrUn.!!$R4 856
11 TraesCS4A01G430400 chrUn 257885037 257885879 842 True 556.000000 556 78.746000 2963 3819 1 chrUn.!!$R1 856
12 TraesCS4A01G430400 chrUn 35294251 35295161 910 False 287.000000 287 72.698000 726 1636 1 chrUn.!!$F1 910
13 TraesCS4A01G430400 chrUn 229344091 229345001 910 False 287.000000 287 72.698000 726 1636 1 chrUn.!!$F2 910
14 TraesCS4A01G430400 chr3A 10884549 10885498 949 True 364.000000 364 74.070000 693 1642 1 chr3A.!!$R1 949

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
195 198 1.000866 TGCTGCTCTGCTCCTCCTA 59.999 57.895 0.00 0.00 0.00 2.94 F
281 284 1.003646 AGGTGAGAGAGTGAGGGCTA 58.996 55.000 0.00 0.00 0.00 3.93 F
1599 1693 0.620556 TCTTGGGTGGGAATGAGCTC 59.379 55.000 6.82 6.82 0.00 4.09 F
1675 1769 1.337703 TGTCATTCTGCAAGTTGGCAC 59.662 47.619 4.75 0.00 39.25 5.01 F
2815 2916 2.998097 CCCAATCCCCGCTCAAGA 59.002 61.111 0.00 0.00 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1003 1097 0.179073 CTACCCGACAGGCCATTCAG 60.179 60.000 5.01 0.0 40.58 3.02 R
1982 2076 0.250338 AGAGAGGTTTCCAACGTGGC 60.250 55.000 0.00 0.0 37.47 5.01 R
2774 2873 1.003464 GGCATGGCAAAAATCCCAAGT 59.997 47.619 15.47 0.0 34.25 3.16 R
3624 3768 1.822990 CCAAGGAACCGTACTCTGCTA 59.177 52.381 0.00 0.0 0.00 3.49 R
4723 4954 0.390492 CGCTCCTATGAGATGGCACA 59.610 55.000 0.00 0.0 41.42 4.57 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
116 117 2.806244 CTCGAACCAAACACACCCTAAG 59.194 50.000 0.00 0.00 0.00 2.18
178 181 5.288232 CCTGTAAAACAAACATGTGTGTGTG 59.712 40.000 22.32 5.02 45.20 3.82
195 198 1.000866 TGCTGCTCTGCTCCTCCTA 59.999 57.895 0.00 0.00 0.00 2.94
276 279 2.028567 GGGAACAAGGTGAGAGAGTGAG 60.029 54.545 0.00 0.00 0.00 3.51
281 284 1.003646 AGGTGAGAGAGTGAGGGCTA 58.996 55.000 0.00 0.00 0.00 3.93
303 306 6.347725 GCTATTGCCAACATATAACCTCTTCG 60.348 42.308 0.00 0.00 0.00 3.79
317 320 4.991472 ACCTCTTCGGAAGACGTATTAAC 58.009 43.478 16.19 0.00 44.69 2.01
353 446 7.201461 GCATGTTGTTAATATGCCACTTTCAAG 60.201 37.037 10.88 0.00 46.45 3.02
360 453 1.896660 GCCACTTTCAAGCACGGGA 60.897 57.895 0.00 0.00 0.00 5.14
378 472 1.137086 GGAGAGCTTTCTATCGTGCCA 59.863 52.381 4.01 0.00 31.50 4.92
400 494 6.865205 GCCATGCTTAGTGGAATTAATCATTC 59.135 38.462 0.00 0.00 40.79 2.67
494 588 4.215109 ACTTTTGAGTGTTTGGGTAGCAT 58.785 39.130 0.00 0.00 0.00 3.79
533 627 1.717194 GCGGAAACCTCATACGAACA 58.283 50.000 0.00 0.00 0.00 3.18
534 628 2.277084 GCGGAAACCTCATACGAACAT 58.723 47.619 0.00 0.00 0.00 2.71
535 629 2.284417 GCGGAAACCTCATACGAACATC 59.716 50.000 0.00 0.00 0.00 3.06
536 630 3.517602 CGGAAACCTCATACGAACATCA 58.482 45.455 0.00 0.00 0.00 3.07
573 667 4.397103 CCAGCAAAGCTAGATGAATGAACA 59.603 41.667 5.97 0.00 36.40 3.18
660 754 3.704061 CCTTCTCTTTAGCTGCTCTAGGT 59.296 47.826 4.91 0.00 40.87 3.08
963 1057 1.064685 ACCGGTTCAATCCCTGATTCC 60.065 52.381 0.00 0.00 32.78 3.01
975 1069 5.418692 TCCCTGATTCCATAGGAAGACTA 57.581 43.478 4.65 0.00 45.48 2.59
1005 1099 9.599322 CGCCTAAAATATCTAAACTTTATGCTG 57.401 33.333 0.00 0.00 0.00 4.41
1014 1108 4.460948 AAACTTTATGCTGAATGGCCTG 57.539 40.909 3.32 0.00 0.00 4.85
1122 1216 2.688958 GGTCGAGCTACAGAACCTACAT 59.311 50.000 7.51 0.00 0.00 2.29
1123 1217 3.489398 GGTCGAGCTACAGAACCTACATG 60.489 52.174 7.51 0.00 0.00 3.21
1140 1234 4.559862 ACATGGTCTCAACCTCCTAAAG 57.440 45.455 0.00 0.00 46.60 1.85
1156 1250 5.509498 TCCTAAAGCTGCAACATAATTCCT 58.491 37.500 1.02 0.00 0.00 3.36
1579 1673 3.522553 CTGGTCAATCTCCGTTACCTTC 58.477 50.000 0.00 0.00 0.00 3.46
1599 1693 0.620556 TCTTGGGTGGGAATGAGCTC 59.379 55.000 6.82 6.82 0.00 4.09
1675 1769 1.337703 TGTCATTCTGCAAGTTGGCAC 59.662 47.619 4.75 0.00 39.25 5.01
1744 1838 3.369471 GCACCTTGCCACTAGTCATCTAA 60.369 47.826 0.00 0.00 37.42 2.10
1989 2083 3.043999 GCCCATCCCTAGCCACGTT 62.044 63.158 0.00 0.00 0.00 3.99
2012 2106 4.202223 TGGAAACCTCTCTACACAGTTGAC 60.202 45.833 0.00 0.00 0.00 3.18
2463 2557 5.469373 TCGATCAAATGGACATTTCTTCG 57.531 39.130 21.16 21.16 38.84 3.79
2475 2569 5.330271 ACATTTCTTCGAACTTCTTGACG 57.670 39.130 0.00 0.00 0.00 4.35
2508 2602 6.823689 TCCCACAATCATTTTCTCTACTTAGC 59.176 38.462 0.00 0.00 0.00 3.09
2815 2916 2.998097 CCCAATCCCCGCTCAAGA 59.002 61.111 0.00 0.00 0.00 3.02
2914 3018 9.383519 CTATTGATAGGAAGAAAGCTTACACAA 57.616 33.333 0.00 0.00 37.43 3.33
3637 3781 4.222145 TGAATTCCTTTAGCAGAGTACGGT 59.778 41.667 2.27 0.00 0.00 4.83
3944 4098 5.048083 TGGTTGTGATGCTGGAGAAAATAAC 60.048 40.000 0.00 0.00 0.00 1.89
4019 4173 2.943690 TCACTCTCGCCTATCTGTGTAC 59.056 50.000 0.00 0.00 0.00 2.90
4022 4176 0.311165 CTCGCCTATCTGTGTACGGG 59.689 60.000 0.00 0.00 0.00 5.28
4023 4177 1.299926 CGCCTATCTGTGTACGGGC 60.300 63.158 0.00 0.00 36.60 6.13
4032 4186 3.770040 TGTACGGGCGCATCTGCT 61.770 61.111 10.83 0.00 39.32 4.24
4036 4190 4.827087 CGGGCGCATCTGCTCTGT 62.827 66.667 10.83 0.00 39.32 3.41
4037 4191 2.501128 GGGCGCATCTGCTCTGTA 59.499 61.111 10.83 0.00 39.32 2.74
4038 4192 1.070445 GGGCGCATCTGCTCTGTAT 59.930 57.895 10.83 0.00 39.32 2.29
4039 4193 0.318441 GGGCGCATCTGCTCTGTATA 59.682 55.000 10.83 0.00 39.32 1.47
4040 4194 1.066573 GGGCGCATCTGCTCTGTATAT 60.067 52.381 10.83 0.00 39.32 0.86
4080 4234 4.324402 GCATCCATTGTGAAACGAATGTTC 59.676 41.667 0.00 0.00 42.39 3.18
4123 4277 5.732633 ACTGATCAGAGAAAATGAGAGGTG 58.267 41.667 29.27 0.00 0.00 4.00
4149 4303 5.533903 CCTGAATATAATGTGCAGCTTCCTT 59.466 40.000 0.00 0.00 0.00 3.36
4154 4308 1.726853 ATGTGCAGCTTCCTTACGTC 58.273 50.000 0.00 0.00 0.00 4.34
4209 4363 1.272313 ACATGAATGCAACCTGGAGCT 60.272 47.619 14.77 0.00 0.00 4.09
4230 4384 6.195700 AGCTTACTCCAATAACTGAGAGGTA 58.804 40.000 0.00 0.00 32.84 3.08
4250 4404 2.724977 TTGTAGCAGTGAGAAGGTCG 57.275 50.000 0.00 0.00 0.00 4.79
4281 4435 9.710900 AAATGAAGTCCTGGAAAATCAAAATAC 57.289 29.630 0.00 0.00 0.00 1.89
4287 4442 4.866486 CCTGGAAAATCAAAATACTGCAGC 59.134 41.667 15.27 0.00 0.00 5.25
4324 4479 6.523201 CACGAAAGAACAGAAAAATAATCGGG 59.477 38.462 0.00 0.00 0.00 5.14
4334 4489 6.007703 AGAAAAATAATCGGGTGGACAAAGA 58.992 36.000 0.00 0.00 0.00 2.52
4340 4497 1.491332 TCGGGTGGACAAAGAAAAGGA 59.509 47.619 0.00 0.00 0.00 3.36
4400 4558 2.159296 AGTTTGTCAACCAAAAGCGACC 60.159 45.455 0.00 0.00 44.36 4.79
4427 4585 1.421646 CACTCTTGGGGGTGTTCTTCT 59.578 52.381 0.00 0.00 0.00 2.85
4443 4602 5.116882 GTTCTTCTGCCCGTCAATAGTAAT 58.883 41.667 0.00 0.00 0.00 1.89
4505 4664 0.037326 TCTTAACCGCTGGTGCTGAG 60.037 55.000 0.94 0.00 35.34 3.35
4522 4681 0.458025 GAGGAACACCACCGACGATC 60.458 60.000 0.00 0.00 0.00 3.69
4533 4692 1.433879 CGACGATCCCAGTGACCTC 59.566 63.158 0.00 0.00 0.00 3.85
4538 4697 0.463620 GATCCCAGTGACCTCTCAGC 59.536 60.000 0.00 0.00 0.00 4.26
4565 4724 7.201410 GCATGTTCAATTTAGTTCATTCAGCTG 60.201 37.037 7.63 7.63 0.00 4.24
4690 4921 0.251916 CTAAGTCCGGAATGCCACCA 59.748 55.000 5.23 0.00 0.00 4.17
4695 4926 2.264480 CGGAATGCCACCAGACGA 59.736 61.111 0.00 0.00 0.00 4.20
4699 4930 1.453155 GAATGCCACCAGACGAATGT 58.547 50.000 0.00 0.00 0.00 2.71
4701 4932 3.206150 GAATGCCACCAGACGAATGTAT 58.794 45.455 0.00 0.00 0.00 2.29
4734 4965 1.210967 TCATGAGCATGTGCCATCTCA 59.789 47.619 10.01 13.82 43.38 3.27
4746 4977 2.163509 GCCATCTCATAGGAGCGAGTA 58.836 52.381 0.00 0.00 41.13 2.59
4748 4979 3.149981 CCATCTCATAGGAGCGAGTACA 58.850 50.000 0.00 0.00 41.13 2.90
4751 4982 4.152284 TCTCATAGGAGCGAGTACAAGA 57.848 45.455 0.00 0.00 41.13 3.02
4752 4983 4.524053 TCTCATAGGAGCGAGTACAAGAA 58.476 43.478 0.00 0.00 41.13 2.52
4753 4984 4.948004 TCTCATAGGAGCGAGTACAAGAAA 59.052 41.667 0.00 0.00 41.13 2.52
4754 4985 5.417894 TCTCATAGGAGCGAGTACAAGAAAA 59.582 40.000 0.00 0.00 41.13 2.29
4821 5053 2.358582 TGTTGTCGACCGTCTAGTTCAA 59.641 45.455 14.12 0.00 0.00 2.69
4828 5060 4.099120 CGACCGTCTAGTTCAATTCAGAG 58.901 47.826 0.00 0.00 0.00 3.35
4831 5063 3.614616 CCGTCTAGTTCAATTCAGAGCAC 59.385 47.826 0.00 0.00 0.00 4.40
4848 5080 1.066929 GCACCCACCAACCAATCATTC 60.067 52.381 0.00 0.00 0.00 2.67
4916 5148 6.734502 AATCATGACATATTCAATTGGCCA 57.265 33.333 0.00 0.00 37.92 5.36
4937 5169 2.804986 TGCCATCTCCATTGTGCTAA 57.195 45.000 0.00 0.00 0.00 3.09
4938 5170 3.301794 TGCCATCTCCATTGTGCTAAT 57.698 42.857 0.00 0.00 0.00 1.73
4939 5171 3.634504 TGCCATCTCCATTGTGCTAATT 58.365 40.909 0.00 0.00 0.00 1.40
4940 5172 3.382227 TGCCATCTCCATTGTGCTAATTG 59.618 43.478 0.00 0.00 0.00 2.32
4941 5173 3.382546 GCCATCTCCATTGTGCTAATTGT 59.617 43.478 0.00 0.00 0.00 2.71
4942 5174 4.142093 GCCATCTCCATTGTGCTAATTGTT 60.142 41.667 0.00 0.00 0.00 2.83
4943 5175 5.625197 GCCATCTCCATTGTGCTAATTGTTT 60.625 40.000 0.00 0.00 0.00 2.83
4944 5176 5.808540 CCATCTCCATTGTGCTAATTGTTTG 59.191 40.000 0.00 0.00 0.00 2.93
4945 5177 6.350361 CCATCTCCATTGTGCTAATTGTTTGA 60.350 38.462 0.00 0.00 0.00 2.69
4946 5178 6.839124 TCTCCATTGTGCTAATTGTTTGAT 57.161 33.333 0.00 0.00 0.00 2.57
4947 5179 6.623486 TCTCCATTGTGCTAATTGTTTGATG 58.377 36.000 0.00 0.00 0.00 3.07
4948 5180 6.209192 TCTCCATTGTGCTAATTGTTTGATGT 59.791 34.615 0.00 0.00 0.00 3.06
4949 5181 6.757237 TCCATTGTGCTAATTGTTTGATGTT 58.243 32.000 0.00 0.00 0.00 2.71
4950 5182 7.215789 TCCATTGTGCTAATTGTTTGATGTTT 58.784 30.769 0.00 0.00 0.00 2.83
4951 5183 7.714377 TCCATTGTGCTAATTGTTTGATGTTTT 59.286 29.630 0.00 0.00 0.00 2.43
4952 5184 8.344098 CCATTGTGCTAATTGTTTGATGTTTTT 58.656 29.630 0.00 0.00 0.00 1.94
4953 5185 9.160576 CATTGTGCTAATTGTTTGATGTTTTTG 57.839 29.630 0.00 0.00 0.00 2.44
4954 5186 8.484641 TTGTGCTAATTGTTTGATGTTTTTGA 57.515 26.923 0.00 0.00 0.00 2.69
4955 5187 8.659925 TGTGCTAATTGTTTGATGTTTTTGAT 57.340 26.923 0.00 0.00 0.00 2.57
4956 5188 8.549548 TGTGCTAATTGTTTGATGTTTTTGATG 58.450 29.630 0.00 0.00 0.00 3.07
4957 5189 8.763356 GTGCTAATTGTTTGATGTTTTTGATGA 58.237 29.630 0.00 0.00 0.00 2.92
4958 5190 8.763356 TGCTAATTGTTTGATGTTTTTGATGAC 58.237 29.630 0.00 0.00 0.00 3.06
4959 5191 8.763356 GCTAATTGTTTGATGTTTTTGATGACA 58.237 29.630 0.00 0.00 0.00 3.58
4961 5193 7.718272 ATTGTTTGATGTTTTTGATGACAGG 57.282 32.000 0.00 0.00 0.00 4.00
4962 5194 6.462552 TGTTTGATGTTTTTGATGACAGGA 57.537 33.333 0.00 0.00 0.00 3.86
4963 5195 6.871844 TGTTTGATGTTTTTGATGACAGGAA 58.128 32.000 0.00 0.00 0.00 3.36
4964 5196 7.326454 TGTTTGATGTTTTTGATGACAGGAAA 58.674 30.769 0.00 0.00 0.00 3.13
4965 5197 7.821359 TGTTTGATGTTTTTGATGACAGGAAAA 59.179 29.630 0.00 0.00 0.00 2.29
4966 5198 7.769272 TTGATGTTTTTGATGACAGGAAAAC 57.231 32.000 12.99 12.99 37.30 2.43
4967 5199 6.871844 TGATGTTTTTGATGACAGGAAAACA 58.128 32.000 19.79 19.79 43.91 2.83
4968 5200 7.326454 TGATGTTTTTGATGACAGGAAAACAA 58.674 30.769 20.67 10.09 43.47 2.83
4969 5201 7.821359 TGATGTTTTTGATGACAGGAAAACAAA 59.179 29.630 20.67 13.89 43.47 2.83
4970 5202 8.735692 ATGTTTTTGATGACAGGAAAACAAAT 57.264 26.923 20.67 10.09 43.47 2.32
4971 5203 7.972527 TGTTTTTGATGACAGGAAAACAAATG 58.027 30.769 17.23 0.00 40.52 2.32
4972 5204 7.821359 TGTTTTTGATGACAGGAAAACAAATGA 59.179 29.630 17.23 2.62 40.52 2.57
4973 5205 8.829612 GTTTTTGATGACAGGAAAACAAATGAT 58.170 29.630 14.17 0.00 37.02 2.45
4975 5207 9.474920 TTTTGATGACAGGAAAACAAATGATAC 57.525 29.630 0.00 0.00 0.00 2.24
4976 5208 8.408043 TTGATGACAGGAAAACAAATGATACT 57.592 30.769 0.00 0.00 0.00 2.12
4977 5209 8.044060 TGATGACAGGAAAACAAATGATACTC 57.956 34.615 0.00 0.00 0.00 2.59
4978 5210 7.665145 TGATGACAGGAAAACAAATGATACTCA 59.335 33.333 0.00 0.00 0.00 3.41
4979 5211 7.815840 TGACAGGAAAACAAATGATACTCAA 57.184 32.000 0.00 0.00 0.00 3.02
4980 5212 7.648142 TGACAGGAAAACAAATGATACTCAAC 58.352 34.615 0.00 0.00 0.00 3.18
4981 5213 7.502226 TGACAGGAAAACAAATGATACTCAACT 59.498 33.333 0.00 0.00 0.00 3.16
4982 5214 8.918202 ACAGGAAAACAAATGATACTCAACTA 57.082 30.769 0.00 0.00 0.00 2.24
4983 5215 8.784043 ACAGGAAAACAAATGATACTCAACTAC 58.216 33.333 0.00 0.00 0.00 2.73
4984 5216 9.003658 CAGGAAAACAAATGATACTCAACTACT 57.996 33.333 0.00 0.00 0.00 2.57
4985 5217 9.003658 AGGAAAACAAATGATACTCAACTACTG 57.996 33.333 0.00 0.00 0.00 2.74
4986 5218 7.750903 GGAAAACAAATGATACTCAACTACTGC 59.249 37.037 0.00 0.00 0.00 4.40
4987 5219 7.986085 AAACAAATGATACTCAACTACTGCT 57.014 32.000 0.00 0.00 0.00 4.24
4988 5220 9.502091 AAAACAAATGATACTCAACTACTGCTA 57.498 29.630 0.00 0.00 0.00 3.49
4989 5221 9.672673 AAACAAATGATACTCAACTACTGCTAT 57.327 29.630 0.00 0.00 0.00 2.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
116 117 2.677337 GCTCTGCTCTTTTGATGTCCTC 59.323 50.000 0.00 0.00 0.00 3.71
177 180 0.398239 ATAGGAGGAGCAGAGCAGCA 60.398 55.000 0.00 0.00 36.85 4.41
178 181 0.033781 CATAGGAGGAGCAGAGCAGC 59.966 60.000 0.00 0.00 0.00 5.25
195 198 4.512571 GCAAATGGACAGAAGCAAAAACAT 59.487 37.500 0.00 0.00 0.00 2.71
281 284 4.821805 CCGAAGAGGTTATATGTTGGCAAT 59.178 41.667 1.92 0.00 34.51 3.56
303 306 4.933505 AGGCTAGGTTAATACGTCTTCC 57.066 45.455 0.00 0.00 0.00 3.46
343 436 0.250295 TCTCCCGTGCTTGAAAGTGG 60.250 55.000 0.00 0.00 0.00 4.00
353 446 1.859383 GATAGAAAGCTCTCCCGTGC 58.141 55.000 0.00 0.00 32.70 5.34
360 453 2.831333 CATGGCACGATAGAAAGCTCT 58.169 47.619 0.00 0.00 41.38 4.09
364 457 4.025396 CACTAAGCATGGCACGATAGAAAG 60.025 45.833 0.00 0.00 41.38 2.62
370 463 0.541392 TCCACTAAGCATGGCACGAT 59.459 50.000 0.00 0.00 37.13 3.73
378 472 6.488006 AGCGAATGATTAATTCCACTAAGCAT 59.512 34.615 0.00 0.00 41.55 3.79
400 494 2.349886 GCAATCACAAAGGACTCTAGCG 59.650 50.000 0.00 0.00 0.00 4.26
488 582 2.787601 TCGGACGTATTGGATGCTAC 57.212 50.000 0.00 0.00 0.00 3.58
494 588 1.135315 CGGACTTTCGGACGTATTGGA 60.135 52.381 0.00 0.00 0.00 3.53
533 627 6.364568 TTGCTGGTGATATATAGTGCTGAT 57.635 37.500 0.00 0.00 0.00 2.90
534 628 5.806654 TTGCTGGTGATATATAGTGCTGA 57.193 39.130 0.00 0.00 0.00 4.26
535 629 5.106791 GCTTTGCTGGTGATATATAGTGCTG 60.107 44.000 0.00 0.00 0.00 4.41
536 630 4.999950 GCTTTGCTGGTGATATATAGTGCT 59.000 41.667 0.00 0.00 0.00 4.40
573 667 0.327259 TTGAGCTGCTTCTGCCTGAT 59.673 50.000 2.53 0.00 38.71 2.90
687 781 3.943034 TCGTTGCCGTTGCCGTTG 61.943 61.111 0.00 0.00 36.33 4.10
688 782 3.944233 GTCGTTGCCGTTGCCGTT 61.944 61.111 0.00 0.00 36.33 4.44
690 784 4.659874 GTGTCGTTGCCGTTGCCG 62.660 66.667 0.00 0.00 36.33 5.69
691 785 4.659874 CGTGTCGTTGCCGTTGCC 62.660 66.667 0.00 0.00 36.33 4.52
692 786 4.659874 CCGTGTCGTTGCCGTTGC 62.660 66.667 0.00 0.00 38.26 4.17
701 795 4.657824 CGGCAAGGTCCGTGTCGT 62.658 66.667 21.69 0.00 44.18 4.34
963 1057 5.707242 TTAGGCGATGTAGTCTTCCTATG 57.293 43.478 0.00 0.00 32.99 2.23
999 1093 0.179048 CCGACAGGCCATTCAGCATA 60.179 55.000 5.01 0.00 0.00 3.14
1001 1095 2.046023 CCGACAGGCCATTCAGCA 60.046 61.111 5.01 0.00 0.00 4.41
1003 1097 0.179073 CTACCCGACAGGCCATTCAG 60.179 60.000 5.01 0.00 40.58 3.02
1005 1099 1.523938 GCTACCCGACAGGCCATTC 60.524 63.158 5.01 0.00 40.58 2.67
1092 1186 2.131709 TAGCTCGACCGGGATTGGG 61.132 63.158 6.32 0.00 0.00 4.12
1123 1217 2.937433 GCAGCTTTAGGAGGTTGAGACC 60.937 54.545 0.00 0.00 46.92 3.85
1133 1227 5.509498 AGGAATTATGTTGCAGCTTTAGGA 58.491 37.500 1.17 0.00 0.00 2.94
1140 1234 3.731867 CGGTGAAGGAATTATGTTGCAGC 60.732 47.826 0.00 0.00 0.00 5.25
1156 1250 2.266372 CGGTATGGTGCCGGTGAA 59.734 61.111 1.90 0.00 44.98 3.18
1177 1271 6.384224 ACATTGCTGTGTTGTTGAATAGATG 58.616 36.000 0.00 0.00 33.22 2.90
1442 1536 3.270027 TGACCTGTGAAACTGTTGTCTG 58.730 45.455 0.00 0.00 38.04 3.51
1444 1538 3.531538 TCTGACCTGTGAAACTGTTGTC 58.468 45.455 0.00 0.00 38.04 3.18
1561 1655 4.722361 AGAGAAGGTAACGGAGATTGAC 57.278 45.455 0.00 0.00 46.39 3.18
1562 1656 4.081642 CCAAGAGAAGGTAACGGAGATTGA 60.082 45.833 0.00 0.00 46.39 2.57
1579 1673 0.622665 AGCTCATTCCCACCCAAGAG 59.377 55.000 0.00 0.00 0.00 2.85
1599 1693 1.273327 GCAACTGGGATTGGACCAAAG 59.727 52.381 11.82 6.55 37.59 2.77
1631 1725 2.766263 TCTAGGGCATACAGTGAAGTGG 59.234 50.000 0.00 0.00 0.00 4.00
1852 1946 7.530010 TCTGTTAGAATAAGCATGTTCAAAGC 58.470 34.615 1.27 0.00 0.00 3.51
1982 2076 0.250338 AGAGAGGTTTCCAACGTGGC 60.250 55.000 0.00 0.00 37.47 5.01
1989 2083 3.964688 TCAACTGTGTAGAGAGGTTTCCA 59.035 43.478 0.00 0.00 0.00 3.53
2100 2194 1.672145 GCCTCGGTGAGTAGGTTGTTC 60.672 57.143 0.00 0.00 35.16 3.18
2463 2557 2.249844 TGGTTCCCGTCAAGAAGTTC 57.750 50.000 0.00 0.00 0.00 3.01
2508 2602 7.931407 TGTGACATATTTAGGTAGGTTAGCATG 59.069 37.037 0.00 0.00 0.00 4.06
2774 2873 1.003464 GGCATGGCAAAAATCCCAAGT 59.997 47.619 15.47 0.00 34.25 3.16
2815 2916 4.774200 AGAAATTCCAGCAAATGCCTACTT 59.226 37.500 0.94 0.00 43.38 2.24
2910 3011 4.460382 AGGCATTAACAACATCTCCTTGTG 59.540 41.667 0.00 0.00 32.07 3.33
2914 3018 3.535561 CGAGGCATTAACAACATCTCCT 58.464 45.455 0.00 0.00 0.00 3.69
3624 3768 1.822990 CCAAGGAACCGTACTCTGCTA 59.177 52.381 0.00 0.00 0.00 3.49
3637 3781 1.885887 CCGTGATGCTTTTCCAAGGAA 59.114 47.619 0.00 0.00 33.45 3.36
3787 3932 5.901413 AGATGGACATCTACAACATGGAT 57.099 39.130 12.86 0.00 45.69 3.41
4039 4193 9.499369 AATGGATGCTATTCTCAGTACCTATAT 57.501 33.333 0.00 0.00 0.00 0.86
4040 4194 8.753133 CAATGGATGCTATTCTCAGTACCTATA 58.247 37.037 0.00 0.00 0.00 1.31
4123 4277 3.152341 AGCTGCACATTATATTCAGGGC 58.848 45.455 1.02 0.00 0.00 5.19
4149 4303 7.972277 GGTAACTCAGATAATTGACAAGACGTA 59.028 37.037 0.00 0.00 0.00 3.57
4154 4308 6.037610 GCAGGGTAACTCAGATAATTGACAAG 59.962 42.308 0.00 0.00 0.00 3.16
4209 4363 8.375493 ACAATACCTCTCAGTTATTGGAGTAA 57.625 34.615 5.97 0.00 33.73 2.24
4224 4378 4.404073 CCTTCTCACTGCTACAATACCTCT 59.596 45.833 0.00 0.00 0.00 3.69
4230 4384 2.093973 CCGACCTTCTCACTGCTACAAT 60.094 50.000 0.00 0.00 0.00 2.71
4250 4404 7.666623 TGATTTTCCAGGACTTCATTTTTACC 58.333 34.615 0.00 0.00 0.00 2.85
4281 4435 2.282290 CGTGGTTTTCTTTTTGCTGCAG 59.718 45.455 10.11 10.11 0.00 4.41
4287 4442 6.584563 TCTGTTCTTTCGTGGTTTTCTTTTTG 59.415 34.615 0.00 0.00 0.00 2.44
4400 4558 1.376466 CCCCCAAGAGTGTGGAGTG 59.624 63.158 0.00 0.00 41.65 3.51
4427 4585 3.897141 TGTCATTACTATTGACGGGCA 57.103 42.857 6.61 0.00 45.14 5.36
4505 4664 1.447314 GGATCGTCGGTGGTGTTCC 60.447 63.158 0.00 0.00 0.00 3.62
4522 4681 2.575993 CGCTGAGAGGTCACTGGG 59.424 66.667 0.00 0.00 0.00 4.45
4533 4692 4.346734 ACTAAATTGAACATGCGCTGAG 57.653 40.909 9.73 0.08 0.00 3.35
4538 4697 6.237384 GCTGAATGAACTAAATTGAACATGCG 60.237 38.462 0.00 0.00 0.00 4.73
4667 4898 0.533085 GGCATTCCGGACTTAGAGCC 60.533 60.000 1.83 4.09 0.00 4.70
4674 4905 1.918293 TCTGGTGGCATTCCGGACT 60.918 57.895 1.83 0.00 35.68 3.85
4690 4921 0.747255 AGCGAGCCATACATTCGTCT 59.253 50.000 0.00 0.00 36.74 4.18
4723 4954 0.390492 CGCTCCTATGAGATGGCACA 59.610 55.000 0.00 0.00 41.42 4.57
4725 4956 0.964700 CTCGCTCCTATGAGATGGCA 59.035 55.000 0.00 0.00 41.42 4.92
4781 5012 8.495949 CGACAACAATTGTTTATACTTCTCAGT 58.504 33.333 21.10 11.06 45.52 3.41
4782 5013 8.708742 TCGACAACAATTGTTTATACTTCTCAG 58.291 33.333 21.10 8.02 45.52 3.35
4783 5014 8.492748 GTCGACAACAATTGTTTATACTTCTCA 58.507 33.333 21.10 0.00 45.52 3.27
4784 5015 7.955864 GGTCGACAACAATTGTTTATACTTCTC 59.044 37.037 21.10 6.16 45.52 2.87
4785 5016 7.359765 CGGTCGACAACAATTGTTTATACTTCT 60.360 37.037 21.10 0.00 45.52 2.85
4786 5017 6.735063 CGGTCGACAACAATTGTTTATACTTC 59.265 38.462 21.10 9.61 45.52 3.01
4788 5019 5.697633 ACGGTCGACAACAATTGTTTATACT 59.302 36.000 21.10 0.00 45.52 2.12
4789 5020 5.919196 ACGGTCGACAACAATTGTTTATAC 58.081 37.500 21.10 15.35 45.52 1.47
4796 5028 3.314553 ACTAGACGGTCGACAACAATTG 58.685 45.455 18.91 3.24 0.00 2.32
4805 5037 3.754850 TCTGAATTGAACTAGACGGTCGA 59.245 43.478 1.89 0.00 0.00 4.20
4806 5038 4.092771 TCTGAATTGAACTAGACGGTCG 57.907 45.455 1.89 0.00 0.00 4.79
4821 5053 0.251341 GGTTGGTGGGTGCTCTGAAT 60.251 55.000 0.00 0.00 0.00 2.57
4828 5060 0.975887 AATGATTGGTTGGTGGGTGC 59.024 50.000 0.00 0.00 0.00 5.01
4831 5063 2.528564 ACAGAATGATTGGTTGGTGGG 58.471 47.619 0.00 0.00 39.69 4.61
4848 5080 7.542477 CAGTACAACACTCATCTAGGTAAACAG 59.458 40.741 0.00 0.00 34.26 3.16
4916 5148 2.154567 AGCACAATGGAGATGGCATT 57.845 45.000 0.00 0.00 0.00 3.56
4928 5160 9.107177 TCAAAAACATCAAACAATTAGCACAAT 57.893 25.926 0.00 0.00 0.00 2.71
4937 5169 7.499292 TCCTGTCATCAAAAACATCAAACAAT 58.501 30.769 0.00 0.00 0.00 2.71
4938 5170 6.871844 TCCTGTCATCAAAAACATCAAACAA 58.128 32.000 0.00 0.00 0.00 2.83
4939 5171 6.462552 TCCTGTCATCAAAAACATCAAACA 57.537 33.333 0.00 0.00 0.00 2.83
4940 5172 7.769272 TTTCCTGTCATCAAAAACATCAAAC 57.231 32.000 0.00 0.00 0.00 2.93
4941 5173 7.821359 TGTTTTCCTGTCATCAAAAACATCAAA 59.179 29.630 12.59 0.00 43.11 2.69
4942 5174 7.326454 TGTTTTCCTGTCATCAAAAACATCAA 58.674 30.769 12.59 0.00 43.11 2.57
4943 5175 6.871844 TGTTTTCCTGTCATCAAAAACATCA 58.128 32.000 12.59 0.00 43.11 3.07
4944 5176 7.769272 TTGTTTTCCTGTCATCAAAAACATC 57.231 32.000 15.37 0.00 45.63 3.06
4945 5177 8.614346 CATTTGTTTTCCTGTCATCAAAAACAT 58.386 29.630 15.37 5.30 45.63 2.71
4946 5178 7.821359 TCATTTGTTTTCCTGTCATCAAAAACA 59.179 29.630 12.59 12.59 45.05 2.83
4947 5179 8.195617 TCATTTGTTTTCCTGTCATCAAAAAC 57.804 30.769 0.00 0.00 40.37 2.43
4948 5180 8.961294 ATCATTTGTTTTCCTGTCATCAAAAA 57.039 26.923 0.00 0.00 0.00 1.94
4949 5181 9.474920 GTATCATTTGTTTTCCTGTCATCAAAA 57.525 29.630 0.00 0.00 0.00 2.44
4950 5182 8.859090 AGTATCATTTGTTTTCCTGTCATCAAA 58.141 29.630 0.00 0.00 0.00 2.69
4951 5183 8.408043 AGTATCATTTGTTTTCCTGTCATCAA 57.592 30.769 0.00 0.00 0.00 2.57
4952 5184 7.665145 TGAGTATCATTTGTTTTCCTGTCATCA 59.335 33.333 0.00 0.00 42.56 3.07
4953 5185 8.044060 TGAGTATCATTTGTTTTCCTGTCATC 57.956 34.615 0.00 0.00 42.56 2.92


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

AutoCloner maintained by Alex Coulton.