Multiple sequence alignment - TraesCS2A01G342400

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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 TraesCS2A01G342400 chr2A 100.000 5465 0 0 1 5465 579448057 579442593 0.000000e+00 10093.0
1 TraesCS2A01G342400 chr2D 96.036 3179 104 9 1034 4200 411959848 411956680 0.000000e+00 5153.0
2 TraesCS2A01G342400 chr2D 89.408 1048 69 7 1 1025 411960937 411959909 0.000000e+00 1282.0
3 TraesCS2A01G342400 chr2D 90.087 343 14 4 4303 4626 411956689 411956348 1.410000e-115 427.0
4 TraesCS2A01G342400 chr2D 94.667 75 3 1 2840 2914 411957971 411957898 1.240000e-21 115.0
5 TraesCS2A01G342400 chr2D 93.333 75 4 1 2913 2986 411958044 411957970 5.790000e-20 110.0
6 TraesCS2A01G342400 chr2B 95.791 2922 103 7 1031 3944 485316145 485313236 0.000000e+00 4697.0
7 TraesCS2A01G342400 chr2B 92.057 705 26 4 3952 4626 485307828 485307124 0.000000e+00 965.0
8 TraesCS2A01G342400 chr2B 84.026 770 85 19 4625 5373 21741026 21740274 0.000000e+00 706.0
9 TraesCS2A01G342400 chr2B 79.365 819 120 28 4690 5465 373064767 373065579 1.040000e-146 531.0
10 TraesCS2A01G342400 chr2B 82.869 502 66 8 1 485 485342978 485342480 3.020000e-117 433.0
11 TraesCS2A01G342400 chr2B 96.000 75 2 1 2840 2914 485314272 485314199 2.670000e-23 121.0
12 TraesCS2A01G342400 chr2B 96.154 52 2 0 4575 4626 485442205 485442154 9.750000e-13 86.1
13 TraesCS2A01G342400 chr3A 79.422 865 123 28 4625 5452 36081870 36082716 1.330000e-155 560.0
14 TraesCS2A01G342400 chr3A 83.417 597 88 8 4877 5465 328930695 328930102 1.340000e-150 544.0
15 TraesCS2A01G342400 chr6B 78.555 872 135 28 4626 5463 239738801 239739654 1.350000e-145 527.0
16 TraesCS2A01G342400 chr6B 81.003 379 51 13 200 576 145550251 145549892 1.160000e-71 281.0
17 TraesCS2A01G342400 chr6B 80.000 270 40 10 4616 4879 389903110 389903371 2.600000e-43 187.0
18 TraesCS2A01G342400 chr4B 78.434 881 132 33 4626 5465 450698220 450697357 6.270000e-144 521.0
19 TraesCS2A01G342400 chr4B 86.207 145 19 1 420 564 186610906 186610763 7.330000e-34 156.0
20 TraesCS2A01G342400 chr5D 78.196 876 134 30 4627 5465 527144906 527145761 1.760000e-139 507.0
21 TraesCS2A01G342400 chr5A 77.940 893 134 30 4625 5465 10843946 10844827 2.940000e-137 499.0
22 TraesCS2A01G342400 chr4A 81.773 598 91 13 4877 5465 613370903 613371491 8.230000e-133 484.0
23 TraesCS2A01G342400 chr4A 75.129 776 127 24 4618 5351 636377123 636377874 2.470000e-78 303.0
24 TraesCS2A01G342400 chrUn 81.481 594 98 9 4877 5462 306349786 306350375 1.380000e-130 477.0
25 TraesCS2A01G342400 chrUn 80.976 594 101 9 4877 5462 337029118 337029707 1.390000e-125 460.0
26 TraesCS2A01G342400 chr3D 81.469 599 96 9 4879 5465 120894843 120894248 1.380000e-130 477.0
27 TraesCS2A01G342400 chr3B 74.969 811 132 30 4626 5399 574377890 574378666 1.910000e-79 307.0
28 TraesCS2A01G342400 chr3B 86.076 237 29 4 357 591 782357110 782357344 9.090000e-63 252.0
29 TraesCS2A01G342400 chr3B 80.843 261 31 15 4626 4879 574339557 574339805 2.600000e-43 187.0
30 TraesCS2A01G342400 chr7A 82.197 264 35 9 4625 4879 56979891 56980151 3.310000e-52 217.0
31 TraesCS2A01G342400 chr1A 79.310 319 45 11 200 513 577989310 577989008 2.580000e-48 204.0
32 TraesCS2A01G342400 chr7B 71.550 826 187 42 1241 2043 688553471 688552671 4.350000e-41 180.0
33 TraesCS2A01G342400 chr6A 86.164 159 20 2 357 513 408021695 408021537 2.620000e-38 171.0
34 TraesCS2A01G342400 chr6D 84.158 101 16 0 413 513 406656968 406656868 1.250000e-16 99.0
35 TraesCS2A01G342400 chr1D 84.158 101 16 0 413 513 442409896 442409796 1.250000e-16 99.0


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 TraesCS2A01G342400 chr2A 579442593 579448057 5464 True 10093.0 10093 100.0000 1 5465 1 chr2A.!!$R1 5464
1 TraesCS2A01G342400 chr2D 411956348 411960937 4589 True 1417.4 5153 92.7062 1 4626 5 chr2D.!!$R1 4625
2 TraesCS2A01G342400 chr2B 485313236 485316145 2909 True 2409.0 4697 95.8955 1031 3944 2 chr2B.!!$R5 2913
3 TraesCS2A01G342400 chr2B 485307124 485307828 704 True 965.0 965 92.0570 3952 4626 1 chr2B.!!$R2 674
4 TraesCS2A01G342400 chr2B 21740274 21741026 752 True 706.0 706 84.0260 4625 5373 1 chr2B.!!$R1 748
5 TraesCS2A01G342400 chr2B 373064767 373065579 812 False 531.0 531 79.3650 4690 5465 1 chr2B.!!$F1 775
6 TraesCS2A01G342400 chr3A 36081870 36082716 846 False 560.0 560 79.4220 4625 5452 1 chr3A.!!$F1 827
7 TraesCS2A01G342400 chr3A 328930102 328930695 593 True 544.0 544 83.4170 4877 5465 1 chr3A.!!$R1 588
8 TraesCS2A01G342400 chr6B 239738801 239739654 853 False 527.0 527 78.5550 4626 5463 1 chr6B.!!$F1 837
9 TraesCS2A01G342400 chr4B 450697357 450698220 863 True 521.0 521 78.4340 4626 5465 1 chr4B.!!$R2 839
10 TraesCS2A01G342400 chr5D 527144906 527145761 855 False 507.0 507 78.1960 4627 5465 1 chr5D.!!$F1 838
11 TraesCS2A01G342400 chr5A 10843946 10844827 881 False 499.0 499 77.9400 4625 5465 1 chr5A.!!$F1 840
12 TraesCS2A01G342400 chr4A 613370903 613371491 588 False 484.0 484 81.7730 4877 5465 1 chr4A.!!$F1 588
13 TraesCS2A01G342400 chr4A 636377123 636377874 751 False 303.0 303 75.1290 4618 5351 1 chr4A.!!$F2 733
14 TraesCS2A01G342400 chrUn 306349786 306350375 589 False 477.0 477 81.4810 4877 5462 1 chrUn.!!$F1 585
15 TraesCS2A01G342400 chrUn 337029118 337029707 589 False 460.0 460 80.9760 4877 5462 1 chrUn.!!$F2 585
16 TraesCS2A01G342400 chr3D 120894248 120894843 595 True 477.0 477 81.4690 4879 5465 1 chr3D.!!$R1 586
17 TraesCS2A01G342400 chr3B 574377890 574378666 776 False 307.0 307 74.9690 4626 5399 1 chr3B.!!$F2 773

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
655 675 0.036164 AAGCTACAACCGTCATGCCA 59.964 50.000 0.00 0.00 0.00 4.92 F
1869 1947 0.106868 TATGGCTTGCAGCAGCTCAT 60.107 50.000 10.12 12.84 44.75 2.90 F
1974 2052 0.252881 ATCTCAGCCCCTCAACTGGA 60.253 55.000 0.00 0.00 34.57 3.86 F
1975 2053 0.473694 TCTCAGCCCCTCAACTGGAA 60.474 55.000 0.00 0.00 34.57 3.53 F
2105 2184 0.973632 TGACTACACACCCAATCGCT 59.026 50.000 0.00 0.00 0.00 4.93 F
4016 4101 1.278985 TGGCATGTAGAAGAGTGGTGG 59.721 52.381 0.00 0.00 0.00 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1945 2023 0.109597 GGGCTGAGATGTTTGCAACG 60.110 55.000 0.00 0.0 0.00 4.10 R
3848 3933 3.462021 CTGGAGAAGCCTAGTAACATGC 58.538 50.000 0.00 0.0 37.63 4.06 R
3947 4032 6.095021 AGCTTCTAAAAACTGAAAAGAACGGT 59.905 34.615 0.00 0.0 0.00 4.83 R
4028 4114 9.918630 GCCAATCATAAATGCATTAATCTAACT 57.081 29.630 13.39 0.0 0.00 2.24 R
4114 4200 2.043252 ACTAAGCTACACACTCCCTCCT 59.957 50.000 0.00 0.0 0.00 3.69 R
5107 5331 0.389948 CGCACCCTCTCACCACTTAC 60.390 60.000 0.00 0.0 0.00 2.34 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
19 20 3.612681 CTCCCCCACACACGACGT 61.613 66.667 0.00 0.00 0.00 4.34
65 66 2.102252 CTCCTTTTCCTCCATCTCCGAG 59.898 54.545 0.00 0.00 0.00 4.63
69 70 3.610669 CCTCCATCTCCGAGGCCG 61.611 72.222 0.00 0.00 40.55 6.13
90 91 4.783621 ACCGCGCACCAGCATGAT 62.784 61.111 8.75 0.00 39.69 2.45
92 93 3.197092 CGCGCACCAGCATGATGA 61.197 61.111 13.69 0.00 39.69 2.92
105 106 0.813184 ATGATGAGCCCGTTTTGCTG 59.187 50.000 0.00 0.00 39.69 4.41
168 186 2.669569 AGCTGCAAATGACCGCGT 60.670 55.556 4.92 0.00 0.00 6.01
190 208 1.315257 AATGCTGGTGCCCGTCAATC 61.315 55.000 0.00 0.00 38.71 2.67
193 211 4.321966 TGGTGCCCGTCAATCGCA 62.322 61.111 0.00 0.00 38.35 5.10
198 216 1.447140 GCCCGTCAATCGCACACTA 60.447 57.895 0.00 0.00 38.35 2.74
215 233 5.350365 GCACACTAGAACCGTTCATATGAAA 59.650 40.000 19.55 1.86 35.58 2.69
221 239 5.491982 AGAACCGTTCATATGAAAGCTTCT 58.508 37.500 24.48 24.48 35.30 2.85
233 251 9.591404 CATATGAAAGCTTCTATCGTTTGATTC 57.409 33.333 0.00 0.00 35.99 2.52
269 287 6.579666 CGTAGGTATATAAAGCTGGTACCA 57.420 41.667 15.39 15.39 37.78 3.25
275 293 7.292591 AGGTATATAAAGCTGGTACCAAGACAT 59.707 37.037 17.11 8.26 37.78 3.06
298 316 7.330208 ACATTCTGCAATTGAAAAGCTACAATC 59.670 33.333 10.34 4.54 35.99 2.67
303 321 7.153315 TGCAATTGAAAAGCTACAATCATTCA 58.847 30.769 10.34 0.00 35.99 2.57
366 384 3.119280 ACAACCGTTCAACTGGAAAAAGG 60.119 43.478 5.55 0.00 37.23 3.11
373 391 5.458779 CGTTCAACTGGAAAAAGGATTCAAC 59.541 40.000 0.00 0.00 37.23 3.18
388 406 7.166691 AGGATTCAACCAGAAGATTGATTTG 57.833 36.000 0.00 0.00 40.15 2.32
396 414 4.568380 CCAGAAGATTGATTTGGGAGGTGA 60.568 45.833 0.00 0.00 0.00 4.02
405 423 0.472925 TTGGGAGGTGAGGCACTACA 60.473 55.000 0.00 0.00 41.55 2.74
437 455 1.352156 CTGCAACCGGCTACGAGAAC 61.352 60.000 0.00 0.00 45.15 3.01
449 467 0.108615 ACGAGAACTGCTTCATCCGG 60.109 55.000 0.00 0.00 0.00 5.14
479 497 3.880047 AAATTCCGACCATAGACGACA 57.120 42.857 0.00 0.00 32.72 4.35
517 535 0.238553 GAAAAGCTGCAACCGACTCC 59.761 55.000 1.02 0.00 0.00 3.85
598 618 0.598942 CACACCACCGACATGAACGA 60.599 55.000 15.70 0.00 0.00 3.85
604 624 2.503158 CGACATGAACGACGGCGA 60.503 61.111 22.49 0.00 41.64 5.54
641 661 1.734137 GCCGTCTCCATCGAAGCTA 59.266 57.895 0.00 0.00 0.00 3.32
650 670 1.403647 CCATCGAAGCTACAACCGTCA 60.404 52.381 0.00 0.00 0.00 4.35
655 675 0.036164 AAGCTACAACCGTCATGCCA 59.964 50.000 0.00 0.00 0.00 4.92
696 716 1.073763 AGTTGTTGCATGGTGGAGCTA 59.926 47.619 0.00 0.00 0.00 3.32
697 717 1.470098 GTTGTTGCATGGTGGAGCTAG 59.530 52.381 0.00 0.00 0.00 3.42
698 718 0.692476 TGTTGCATGGTGGAGCTAGT 59.308 50.000 0.00 0.00 0.00 2.57
768 788 3.458163 GCGGGACCGGTGATGAGA 61.458 66.667 14.63 0.00 40.19 3.27
777 797 2.264794 GTGATGAGAACGGCCGGT 59.735 61.111 31.76 27.03 0.00 5.28
802 822 4.554036 GGGCATCGGAGAGGGTGC 62.554 72.222 0.00 0.00 43.63 5.01
825 845 0.545646 AGGCAAGATGAAGGAGAGCC 59.454 55.000 0.00 0.00 40.85 4.70
837 857 1.292242 AGGAGAGCCAGATGTAAGGGA 59.708 52.381 0.00 0.00 36.29 4.20
841 861 4.385754 GGAGAGCCAGATGTAAGGGAAATT 60.386 45.833 0.00 0.00 0.00 1.82
848 868 5.648092 CCAGATGTAAGGGAAATTCTTTCGT 59.352 40.000 0.00 0.00 40.57 3.85
853 873 5.634859 TGTAAGGGAAATTCTTTCGTACGAC 59.365 40.000 19.36 3.41 40.57 4.34
854 874 4.532314 AGGGAAATTCTTTCGTACGACT 57.468 40.909 19.36 4.61 40.57 4.18
928 948 4.702274 AGCTGGCCGGCCCAAATT 62.702 61.111 41.75 20.25 44.81 1.82
929 949 3.705289 GCTGGCCGGCCCAAATTT 61.705 61.111 41.75 0.00 44.81 1.82
930 950 2.265424 CTGGCCGGCCCAAATTTG 59.735 61.111 41.75 18.53 44.81 2.32
931 951 3.313713 CTGGCCGGCCCAAATTTGG 62.314 63.158 41.75 27.46 44.81 3.28
969 989 0.318120 AGCACCCGCCAATTGAAAAG 59.682 50.000 7.12 0.00 39.83 2.27
1025 1049 8.012957 AGAAAGAGACTTGTTTTCACTCTCTA 57.987 34.615 0.00 0.00 40.49 2.43
1026 1050 8.141268 AGAAAGAGACTTGTTTTCACTCTCTAG 58.859 37.037 0.00 0.00 40.49 2.43
1027 1051 6.339587 AGAGACTTGTTTTCACTCTCTAGG 57.660 41.667 0.00 0.00 40.02 3.02
1028 1052 5.245075 AGAGACTTGTTTTCACTCTCTAGGG 59.755 44.000 0.00 0.00 40.02 3.53
1029 1053 5.148502 AGACTTGTTTTCACTCTCTAGGGA 58.851 41.667 0.00 0.00 31.53 4.20
1052 1128 3.197895 ACCCCAAACCCTTCCCCC 61.198 66.667 0.00 0.00 0.00 5.40
1083 1159 1.664649 GCGCATTCGATCCGATCCA 60.665 57.895 0.30 0.00 35.23 3.41
1299 1376 1.684386 CGGCATCCTCCTCAAGCTCT 61.684 60.000 0.00 0.00 0.00 4.09
1377 1454 2.598985 CCCTCCTCCCGGATCTCG 60.599 72.222 0.73 0.00 39.01 4.04
1412 1489 1.809619 CGACCACCACCGCATACTG 60.810 63.158 0.00 0.00 0.00 2.74
1455 1532 3.854669 CGGTGCTCCAGGGCCTAG 61.855 72.222 5.28 1.30 0.00 3.02
1466 1543 4.893601 GGCCTAGGCGCCTTCGTC 62.894 72.222 37.74 22.80 46.10 4.20
1484 1561 1.583967 CGACGACATCTCTGCCGAC 60.584 63.158 0.00 0.00 32.08 4.79
1578 1655 0.332972 GAACCAGGCCAGGGAAAGAT 59.667 55.000 19.81 0.00 0.00 2.40
1606 1683 3.184683 GCTGCCACGCTTCGAGAG 61.185 66.667 0.00 0.00 0.00 3.20
1639 1716 2.165030 TCGTGTTCGACCTAGGATTTCC 59.835 50.000 17.98 0.51 41.35 3.13
1698 1775 1.542030 TCGTCTCTCTCTGGCTGTTTC 59.458 52.381 0.00 0.00 0.00 2.78
1777 1855 5.302059 CCCATCCTTACGAGAACTCAAGATA 59.698 44.000 0.00 0.00 0.00 1.98
1780 1858 4.940046 TCCTTACGAGAACTCAAGATACGT 59.060 41.667 0.00 0.00 36.52 3.57
1795 1873 1.613317 TACGTGATGCCTGGGGTCTG 61.613 60.000 0.00 0.00 0.00 3.51
1869 1947 0.106868 TATGGCTTGCAGCAGCTCAT 60.107 50.000 10.12 12.84 44.75 2.90
1879 1957 2.353323 CAGCAGCTCATTGTAGAAGCA 58.647 47.619 0.00 0.00 0.00 3.91
1906 1984 8.191534 AGGTACTTAAAGAGTTACATGTGAGT 57.808 34.615 9.11 2.40 39.86 3.41
1916 1994 6.203723 AGAGTTACATGTGAGTTCTTGCTTTC 59.796 38.462 9.11 0.00 0.00 2.62
1923 2001 7.229306 ACATGTGAGTTCTTGCTTTCAGAATTA 59.771 33.333 0.00 0.00 0.00 1.40
1925 2003 7.587629 TGTGAGTTCTTGCTTTCAGAATTATG 58.412 34.615 0.00 0.00 0.00 1.90
1932 2010 6.712095 TCTTGCTTTCAGAATTATGTCACTGT 59.288 34.615 0.00 0.00 0.00 3.55
1945 2023 0.468226 TCACTGTGGTGAGTCAACCC 59.532 55.000 5.53 0.00 46.19 4.11
1974 2052 0.252881 ATCTCAGCCCCTCAACTGGA 60.253 55.000 0.00 0.00 34.57 3.86
1975 2053 0.473694 TCTCAGCCCCTCAACTGGAA 60.474 55.000 0.00 0.00 34.57 3.53
2063 2142 3.323979 ACGTCTGGATACTGGTCACTTTT 59.676 43.478 0.00 0.00 35.97 2.27
2105 2184 0.973632 TGACTACACACCCAATCGCT 59.026 50.000 0.00 0.00 0.00 4.93
2116 2195 2.092968 ACCCAATCGCTATTGCTTGAGA 60.093 45.455 5.45 0.00 41.06 3.27
2238 2317 3.945434 CGATGCAGGCATGGCGTC 61.945 66.667 12.12 8.93 42.47 5.19
2282 2361 6.708885 TTGGGATATCTGAGAATAGCCATT 57.291 37.500 2.05 0.00 39.05 3.16
2481 2561 4.783227 AGGAGACCATTACCTGTGTGTTAT 59.217 41.667 0.00 0.00 32.39 1.89
2488 2568 6.775629 ACCATTACCTGTGTGTTATTCACTTT 59.224 34.615 0.00 0.00 46.27 2.66
2750 2830 8.375506 CCTAGCAATCTGGAGGTAACATTATTA 58.624 37.037 0.00 0.00 41.41 0.98
3060 3140 3.267551 GGGGGACTTATAAACCCAGACAA 59.732 47.826 21.50 0.00 45.19 3.18
3061 3141 4.267536 GGGGACTTATAAACCCAGACAAC 58.732 47.826 21.50 6.55 44.87 3.32
3223 3303 5.880901 AGTACATTTGATGGGAAGTTGACT 58.119 37.500 0.00 0.00 33.60 3.41
3374 3454 5.584649 TCTGAAATTTGGGTTATCACTAGCG 59.415 40.000 0.00 0.00 0.00 4.26
3391 3471 3.838244 AGCGCAATACCTGAGGATTTA 57.162 42.857 11.47 0.00 0.00 1.40
3848 3933 4.785453 GGCTGAGGAGTTGGGCCG 62.785 72.222 0.00 0.00 33.30 6.13
3944 4029 2.814097 GCTCCACAAGGCTCCAACTTTA 60.814 50.000 0.00 0.00 33.74 1.85
3945 4030 2.814336 CTCCACAAGGCTCCAACTTTAC 59.186 50.000 0.00 0.00 33.74 2.01
3946 4031 2.441750 TCCACAAGGCTCCAACTTTACT 59.558 45.455 0.00 0.00 33.74 2.24
3947 4032 3.649023 TCCACAAGGCTCCAACTTTACTA 59.351 43.478 0.00 0.00 33.74 1.82
4016 4101 1.278985 TGGCATGTAGAAGAGTGGTGG 59.721 52.381 0.00 0.00 0.00 4.61
4023 4108 5.304686 TGTAGAAGAGTGGTGGTGAATTT 57.695 39.130 0.00 0.00 0.00 1.82
4028 4114 6.126409 AGAAGAGTGGTGGTGAATTTGTAAA 58.874 36.000 0.00 0.00 0.00 2.01
4059 4145 3.889520 TGCATTTATGATTGGCTTGCA 57.110 38.095 0.00 0.00 36.37 4.08
4114 4200 5.665916 TCTCTGTTAGATGAGATGCACAA 57.334 39.130 0.00 0.00 34.77 3.33
4121 4207 1.487976 GATGAGATGCACAAGGAGGGA 59.512 52.381 0.00 0.00 0.00 4.20
4209 4306 7.738437 ATGAAATATTGGTGGATCCTTTGTT 57.262 32.000 14.23 0.00 37.07 2.83
4244 4341 8.736751 TTTTTCTGAACTTTGTGTGAAACTAC 57.263 30.769 0.00 0.00 38.04 2.73
4249 4346 5.408909 TGAACTTTGTGTGAAACTACGAACA 59.591 36.000 0.00 0.00 38.04 3.18
4442 4557 5.197451 TGGTCCAAAGTTTGTGTTAGTCAT 58.803 37.500 14.36 0.00 0.00 3.06
4545 4660 4.927978 TTGTTGGGTTAAAGTGTCATGG 57.072 40.909 0.00 0.00 0.00 3.66
4578 4694 4.866508 AACGACAAGTATGAAGGAGTCA 57.133 40.909 0.00 0.00 41.67 3.41
4600 4717 8.055181 AGTCATCATTGGGTACTTGTGATTTAT 58.945 33.333 0.00 0.00 0.00 1.40
4646 4763 2.835701 TAGAAGGGTTGAGCGCGCTG 62.836 60.000 41.82 0.00 34.93 5.18
4672 4791 2.307049 CGCGGTTCATGTTCTTGTTTC 58.693 47.619 0.00 0.00 0.00 2.78
4853 4994 8.628630 TTCTGTGTAATATTGTGGATGTCAAA 57.371 30.769 0.00 0.00 0.00 2.69
4992 5209 2.159382 TGATTTGGAAGGCCTTTCGTC 58.841 47.619 21.54 16.82 36.62 4.20
5011 5228 5.038683 TCGTCGTGTGATTATGTGTTATCC 58.961 41.667 0.00 0.00 0.00 2.59
5012 5229 4.085772 CGTCGTGTGATTATGTGTTATCCG 60.086 45.833 0.00 0.00 0.00 4.18
5013 5230 4.802039 GTCGTGTGATTATGTGTTATCCGT 59.198 41.667 0.00 0.00 0.00 4.69
5020 5237 7.279090 TGTGATTATGTGTTATCCGTTAACCAG 59.721 37.037 0.00 0.00 39.63 4.00
5027 5244 5.693555 GTGTTATCCGTTAACCAGCCTATAC 59.306 44.000 0.00 0.00 39.63 1.47
5030 5247 4.395959 TCCGTTAACCAGCCTATACTTG 57.604 45.455 0.00 0.00 0.00 3.16
5043 5260 5.192923 AGCCTATACTTGTGTGGGGAAATTA 59.807 40.000 2.58 0.00 0.00 1.40
5107 5331 3.486841 CACATTGTGACGCTTCCTTTTTG 59.513 43.478 11.45 0.00 35.23 2.44
5157 5382 7.293402 TGATACGTTTTTATAAGTCGGTTGG 57.707 36.000 0.00 0.00 0.00 3.77
5203 5428 6.625740 CGTTGGCCTGATCAAAATCATAAACT 60.626 38.462 3.32 0.00 41.05 2.66
5241 5468 8.329203 AGTAGGTCAATTGAATGAAAGAGTTC 57.671 34.615 10.35 0.00 0.00 3.01
5298 5531 4.589908 GGAGAGCTCCTAAAATTTGGTGA 58.410 43.478 10.93 0.00 46.16 4.02
5303 5551 4.524328 AGCTCCTAAAATTTGGTGACCAAG 59.476 41.667 17.50 4.41 44.84 3.61
5305 5553 5.564848 GCTCCTAAAATTTGGTGACCAAGTC 60.565 44.000 17.50 0.00 44.84 3.01
5454 5704 8.629158 TCAAAATCGGGTTATCCAATTCTAATG 58.371 33.333 0.00 0.00 34.36 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 2.760092 AGTGATTGCAACAACACTTGGT 59.240 40.909 21.79 7.85 40.03 3.67
41 42 2.840651 GGAGATGGAGGAAAAGGAGTGA 59.159 50.000 0.00 0.00 0.00 3.41
90 91 0.322456 ATAGCAGCAAAACGGGCTCA 60.322 50.000 0.00 0.00 40.23 4.26
92 93 1.315257 CCATAGCAGCAAAACGGGCT 61.315 55.000 0.00 0.00 43.77 5.19
121 122 3.296709 TTGTCTTCTCCGCTCCCGC 62.297 63.158 0.00 0.00 0.00 6.13
138 139 3.322466 CAGCTCCCCCACCTCGTT 61.322 66.667 0.00 0.00 0.00 3.85
190 208 1.710013 ATGAACGGTTCTAGTGTGCG 58.290 50.000 20.53 0.00 0.00 5.34
193 211 5.581085 GCTTTCATATGAACGGTTCTAGTGT 59.419 40.000 17.76 4.17 33.13 3.55
195 213 5.978814 AGCTTTCATATGAACGGTTCTAGT 58.021 37.500 17.76 10.01 31.35 2.57
215 233 5.220491 GCTTTCGAATCAAACGATAGAAGCT 60.220 40.000 0.00 0.00 42.50 3.74
221 239 6.304126 GTTGAAGCTTTCGAATCAAACGATA 58.696 36.000 12.23 0.00 39.45 2.92
233 251 1.792006 ACCTACGGTTGAAGCTTTCG 58.208 50.000 0.00 5.70 27.29 3.46
263 281 4.458989 TCAATTGCAGAATGTCTTGGTACC 59.541 41.667 4.43 4.43 39.31 3.34
264 282 5.627499 TCAATTGCAGAATGTCTTGGTAC 57.373 39.130 0.00 0.00 39.31 3.34
268 286 5.694910 AGCTTTTCAATTGCAGAATGTCTTG 59.305 36.000 0.00 0.00 39.31 3.02
269 287 5.850614 AGCTTTTCAATTGCAGAATGTCTT 58.149 33.333 0.00 0.00 39.31 3.01
275 293 6.747125 TGATTGTAGCTTTTCAATTGCAGAA 58.253 32.000 0.00 0.00 34.92 3.02
298 316 9.241317 GCTATGGTTGAAGTTTTCATATGAATG 57.759 33.333 18.61 0.00 39.84 2.67
366 384 6.153340 TCCCAAATCAATCTTCTGGTTGAATC 59.847 38.462 0.00 0.00 37.82 2.52
373 391 3.698040 CACCTCCCAAATCAATCTTCTGG 59.302 47.826 0.00 0.00 0.00 3.86
388 406 1.192146 TGTGTAGTGCCTCACCTCCC 61.192 60.000 0.00 0.00 34.49 4.30
396 414 0.470766 TTCGGGTTTGTGTAGTGCCT 59.529 50.000 0.00 0.00 0.00 4.75
405 423 0.102300 GTTGCAGCTTTCGGGTTTGT 59.898 50.000 0.00 0.00 0.00 2.83
461 479 2.651455 TCTGTCGTCTATGGTCGGAAT 58.349 47.619 0.00 0.00 0.00 3.01
473 491 1.078759 CGTCCATGGCTTCTGTCGTC 61.079 60.000 6.96 0.00 0.00 4.20
479 497 1.215647 GTCGTCGTCCATGGCTTCT 59.784 57.895 6.96 0.00 0.00 2.85
578 598 0.878523 CGTTCATGTCGGTGGTGTGT 60.879 55.000 0.00 0.00 0.00 3.72
615 635 2.409241 GATGGAGACGGCCGTAGCTC 62.409 65.000 34.36 31.43 39.73 4.09
616 636 2.442272 ATGGAGACGGCCGTAGCT 60.442 61.111 34.36 25.70 39.73 3.32
641 661 1.237285 GCTCTTGGCATGACGGTTGT 61.237 55.000 0.00 0.00 41.35 3.32
650 670 2.338015 CGGTTGCAGCTCTTGGCAT 61.338 57.895 0.00 0.00 44.79 4.40
727 747 2.176055 CGACTGTCCTCGTCACCG 59.824 66.667 1.55 0.00 0.00 4.94
730 750 2.322830 CCGTCGACTGTCCTCGTCA 61.323 63.158 14.70 0.00 35.10 4.35
777 797 4.770362 TCCGATGCCCGTCCCTCA 62.770 66.667 0.00 0.00 36.31 3.86
802 822 1.078214 TCCTTCATCTTGCCTGCCG 60.078 57.895 0.00 0.00 0.00 5.69
806 826 0.545646 GGCTCTCCTTCATCTTGCCT 59.454 55.000 0.00 0.00 36.32 4.75
837 857 5.045215 TCACACAGTCGTACGAAAGAATTT 58.955 37.500 21.39 0.00 43.98 1.82
841 861 2.031420 CCTCACACAGTCGTACGAAAGA 60.031 50.000 21.39 10.37 0.00 2.52
848 868 1.534163 CGTCTTCCTCACACAGTCGTA 59.466 52.381 0.00 0.00 0.00 3.43
853 873 1.937108 GCCTTCGTCTTCCTCACACAG 60.937 57.143 0.00 0.00 0.00 3.66
854 874 0.033504 GCCTTCGTCTTCCTCACACA 59.966 55.000 0.00 0.00 0.00 3.72
957 977 2.001872 CGGGATTGCTTTTCAATTGGC 58.998 47.619 5.42 1.34 44.95 4.52
969 989 1.103398 CCATCAGAACCCGGGATTGC 61.103 60.000 32.02 13.09 0.00 3.56
1027 1051 2.274432 GGTTTGGGGTCGGGATCC 59.726 66.667 1.92 1.92 0.00 3.36
1028 1052 1.859841 AAGGGTTTGGGGTCGGGATC 61.860 60.000 0.00 0.00 0.00 3.36
1029 1053 1.855451 AAGGGTTTGGGGTCGGGAT 60.855 57.895 0.00 0.00 0.00 3.85
1083 1159 0.251787 GGCTGGGAAAGTGTGGGAAT 60.252 55.000 0.00 0.00 0.00 3.01
1351 1428 4.423209 GGAGGAGGGCCCAGAGGT 62.423 72.222 27.56 0.88 37.41 3.85
1371 1448 1.586564 CGCCGGTGAAGTCGAGATC 60.587 63.158 10.20 0.00 0.00 2.75
1466 1543 1.583967 GTCGGCAGAGATGTCGTCG 60.584 63.158 1.93 3.11 38.18 5.12
1530 1607 4.562082 ACAGCGTTGTAAAGCAGTATACA 58.438 39.130 1.89 0.00 35.25 2.29
1578 1655 2.110835 TGGCAGCTCAAAGACGCA 59.889 55.556 0.00 0.00 0.00 5.24
1606 1683 1.641577 GAACACGATAGAGGTGGTGC 58.358 55.000 0.00 0.00 39.69 5.01
1671 1748 2.438795 GAGAGAGACGAGGCGGGT 60.439 66.667 0.00 0.00 0.00 5.28
1733 1810 3.137459 CCGCGTGAGGAGAGAGCT 61.137 66.667 4.92 0.00 0.00 4.09
1777 1855 2.607750 AGACCCCAGGCATCACGT 60.608 61.111 0.00 0.00 0.00 4.49
1780 1858 2.484868 TACCCAGACCCCAGGCATCA 62.485 60.000 0.00 0.00 0.00 3.07
1795 1873 2.355818 GGAGTGGATGGTGAAGTTACCC 60.356 54.545 0.00 0.00 40.09 3.69
1869 1947 8.208903 ACTCTTTAAGTACCTTTGCTTCTACAA 58.791 33.333 0.00 0.00 36.07 2.41
1879 1957 9.490379 CTCACATGTAACTCTTTAAGTACCTTT 57.510 33.333 0.00 0.00 37.17 3.11
1898 1976 5.428496 TTCTGAAAGCAAGAACTCACATG 57.572 39.130 0.00 0.00 0.00 3.21
1906 1984 7.229306 ACAGTGACATAATTCTGAAAGCAAGAA 59.771 33.333 0.00 0.00 0.00 2.52
1932 2010 1.525077 GCAACGGGTTGACTCACCA 60.525 57.895 15.31 0.00 42.93 4.17
1945 2023 0.109597 GGGCTGAGATGTTTGCAACG 60.110 55.000 0.00 0.00 0.00 4.10
1974 2052 1.208052 CATCCGTCCAGTGGAGTGATT 59.792 52.381 13.61 0.26 39.30 2.57
1975 2053 0.826715 CATCCGTCCAGTGGAGTGAT 59.173 55.000 13.61 14.37 39.30 3.06
2063 2142 7.655328 GTCATCCAAATAATGTCCAAACACAAA 59.345 33.333 0.00 0.00 38.48 2.83
2105 2184 3.005554 GCTGCAAGAGTCTCAAGCAATA 58.994 45.455 16.77 0.00 34.07 1.90
2116 2195 2.555757 GACCTCAAATTGCTGCAAGAGT 59.444 45.455 20.72 10.58 34.07 3.24
2161 2240 4.397481 TGAACTCACCAGCAGATAGATG 57.603 45.455 0.00 0.00 0.00 2.90
2238 2317 4.989875 AATGAGATACCCCTCCATTCAG 57.010 45.455 0.00 0.00 32.32 3.02
2282 2361 5.004922 AGCAAAACAAGTGAAAATTCGGA 57.995 34.783 0.00 0.00 0.00 4.55
2404 2484 8.503196 TGAATAACTAAATGTACAAGTGCAGTG 58.497 33.333 0.00 0.00 0.00 3.66
2481 2561 7.962373 CACGCATATCATTTTCTACAAAGTGAA 59.038 33.333 0.00 0.00 40.48 3.18
2488 2568 5.670485 AGGACACGCATATCATTTTCTACA 58.330 37.500 0.00 0.00 0.00 2.74
2799 2879 6.924111 TCTGGTCAAATTTAGGCTCAAAATC 58.076 36.000 0.00 0.00 0.00 2.17
2999 3079 7.497909 TCCTAACTTTGACCTGAAGTTTTACTG 59.502 37.037 7.45 0.00 42.90 2.74
3060 3140 5.302360 TGGCAATTCAAGTACTACTTTCGT 58.698 37.500 0.00 0.00 36.03 3.85
3061 3141 5.637810 TCTGGCAATTCAAGTACTACTTTCG 59.362 40.000 0.00 0.00 36.03 3.46
3223 3303 6.599244 GGTTGATCCTGTCATGAAATTACTCA 59.401 38.462 0.00 0.00 36.54 3.41
3374 3454 8.854614 AATCTACATAAATCCTCAGGTATTGC 57.145 34.615 0.00 0.00 0.00 3.56
3510 3595 8.361889 AGACTGAATTCTCTGAGATATGACATG 58.638 37.037 8.42 0.00 0.00 3.21
3848 3933 3.462021 CTGGAGAAGCCTAGTAACATGC 58.538 50.000 0.00 0.00 37.63 4.06
3944 4029 8.496707 TTCTAAAAACTGAAAAGAACGGTAGT 57.503 30.769 0.00 0.00 0.00 2.73
3945 4030 7.586664 GCTTCTAAAAACTGAAAAGAACGGTAG 59.413 37.037 0.00 0.00 0.00 3.18
3946 4031 7.281549 AGCTTCTAAAAACTGAAAAGAACGGTA 59.718 33.333 0.00 0.00 0.00 4.02
3947 4032 6.095021 AGCTTCTAAAAACTGAAAAGAACGGT 59.905 34.615 0.00 0.00 0.00 4.83
4028 4114 9.918630 GCCAATCATAAATGCATTAATCTAACT 57.081 29.630 13.39 0.00 0.00 2.24
4059 4145 3.369042 AAGGCATCCTGCATTGTGT 57.631 47.368 0.00 0.00 46.26 3.72
4114 4200 2.043252 ACTAAGCTACACACTCCCTCCT 59.957 50.000 0.00 0.00 0.00 3.69
4121 4207 4.202264 ACAGCAGAAACTAAGCTACACACT 60.202 41.667 0.00 0.00 36.73 3.55
4198 4295 7.624360 AAAAGGAAAAACAAACAAAGGATCC 57.376 32.000 2.48 2.48 0.00 3.36
4209 4306 8.555361 CACAAAGTTCAGAAAAAGGAAAAACAA 58.445 29.630 0.00 0.00 0.00 2.83
4271 4368 6.249893 CACAAATGTATGTTGCTCGAATTCAG 59.750 38.462 6.22 3.63 0.00 3.02
4361 4459 1.089481 CGCCTCGCAGATAAAAGCCA 61.089 55.000 0.00 0.00 33.89 4.75
4545 4660 6.697455 TCATACTTGTCGTTAATCAGAGATGC 59.303 38.462 0.00 0.00 0.00 3.91
4578 4694 6.040842 GCCATAAATCACAAGTACCCAATGAT 59.959 38.462 0.00 0.00 0.00 2.45
4853 4994 3.490439 CCAAGTTTGGGGCAGAAAATT 57.510 42.857 2.87 0.00 44.70 1.82
4918 5114 1.285962 CATCTCCCTCACCCACCAAAT 59.714 52.381 0.00 0.00 0.00 2.32
4992 5209 5.712217 AACGGATAACACATAATCACACG 57.288 39.130 0.00 0.00 0.00 4.49
5011 5228 4.328983 CACACAAGTATAGGCTGGTTAACG 59.671 45.833 0.00 0.00 0.00 3.18
5012 5229 4.634443 CCACACAAGTATAGGCTGGTTAAC 59.366 45.833 0.00 0.00 0.00 2.01
5013 5230 4.323945 CCCACACAAGTATAGGCTGGTTAA 60.324 45.833 0.00 0.00 0.00 2.01
5020 5237 3.359695 TTTCCCCACACAAGTATAGGC 57.640 47.619 0.00 0.00 0.00 3.93
5027 5244 5.446741 CGACGTAATAATTTCCCCACACAAG 60.447 44.000 0.00 0.00 0.00 3.16
5030 5247 3.310501 CCGACGTAATAATTTCCCCACAC 59.689 47.826 0.00 0.00 0.00 3.82
5043 5260 1.089481 CATGCAGCCACCGACGTAAT 61.089 55.000 0.00 0.00 0.00 1.89
5107 5331 0.389948 CGCACCCTCTCACCACTTAC 60.390 60.000 0.00 0.00 0.00 2.34
5131 5355 7.901377 CCAACCGACTTATAAAAACGTATCAAG 59.099 37.037 0.00 0.00 0.00 3.02
5157 5382 7.111870 CCAACGATTTTTCAAATCAATTTGCAC 59.888 33.333 10.02 0.00 45.06 4.57
5217 5443 8.099364 TGAACTCTTTCATTCAATTGACCTAC 57.901 34.615 7.89 0.00 36.79 3.18
5220 5446 8.647143 TTTTGAACTCTTTCATTCAATTGACC 57.353 30.769 7.89 0.00 42.72 4.02
5291 5524 4.026744 TCCAATTTGACTTGGTCACCAAA 58.973 39.130 11.37 0.00 43.44 3.28
5292 5525 3.636679 TCCAATTTGACTTGGTCACCAA 58.363 40.909 9.51 9.51 42.60 3.67
5298 5531 4.676109 TGGATCATCCAATTTGACTTGGT 58.324 39.130 2.95 0.00 45.00 3.67
5403 5652 7.224297 ACTAGGTCAACAATTTCTCAAAGCTA 58.776 34.615 0.00 0.00 0.00 3.32
5440 5690 6.150332 TGAGGTCTCCCATTAGAATTGGATA 58.850 40.000 0.00 0.00 30.69 2.59


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

AutoCloner maintained by Alex Coulton.