Multiple sequence alignment - TraesCS3A01G094500

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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 TraesCS3A01G094500 chr3A 100.000 3659 0 0 1 3659 60443995 60440337 0.000000e+00 6758.0
1 TraesCS3A01G094500 chr3A 90.958 2046 123 18 708 2725 60471207 60473218 0.000000e+00 2697.0
2 TraesCS3A01G094500 chr3B 89.180 2782 165 49 143 2886 75959128 75956445 0.000000e+00 3345.0
3 TraesCS3A01G094500 chr3B 91.974 1819 103 25 834 2644 76114913 76116696 0.000000e+00 2510.0
4 TraesCS3A01G094500 chr3B 82.382 613 64 26 26 635 75993645 75994216 9.130000e-136 494.0
5 TraesCS3A01G094500 chr3D 94.290 1944 64 13 740 2644 48252569 48250634 0.000000e+00 2931.0
6 TraesCS3A01G094500 chr3D 91.965 2066 102 22 736 2762 48348390 48350430 0.000000e+00 2837.0
7 TraesCS3A01G094500 chr3D 88.889 783 70 13 2883 3659 589432024 589431253 0.000000e+00 948.0
8 TraesCS3A01G094500 chr3D 89.773 704 50 14 2961 3659 549376646 549377332 0.000000e+00 881.0
9 TraesCS3A01G094500 chr3D 86.224 784 81 24 2888 3659 501791541 501792309 0.000000e+00 824.0
10 TraesCS3A01G094500 chr3D 90.401 573 45 8 3087 3659 143236022 143236584 0.000000e+00 745.0
11 TraesCS3A01G094500 chr3D 88.324 531 55 3 2067 2593 48295879 48295352 6.670000e-177 630.0
12 TraesCS3A01G094500 chr3D 83.673 637 63 23 2 635 48346594 48347192 2.470000e-156 562.0
13 TraesCS3A01G094500 chr3D 82.895 456 42 17 623 1071 48283532 48283958 9.590000e-101 377.0
14 TraesCS3A01G094500 chr3D 79.082 196 34 3 140 333 397207854 397207664 1.070000e-25 128.0
15 TraesCS3A01G094500 chr3D 76.961 204 41 5 1124 1327 592592434 592592631 1.070000e-20 111.0
16 TraesCS3A01G094500 chr5A 88.660 776 78 5 2883 3653 685998462 685999232 0.000000e+00 937.0
17 TraesCS3A01G094500 chr5A 87.282 747 80 9 2884 3625 73805185 73804449 0.000000e+00 839.0
18 TraesCS3A01G094500 chr5A 75.758 528 104 16 2034 2546 520208754 520208236 1.010000e-60 244.0
19 TraesCS3A01G094500 chr5A 74.641 627 116 30 1124 1733 520209665 520209065 1.700000e-58 237.0
20 TraesCS3A01G094500 chr5A 97.059 34 1 0 430 463 626220784 626220817 1.420000e-04 58.4
21 TraesCS3A01G094500 chr5A 82.609 69 3 6 3 63 705150764 705150831 7.000000e-03 52.8
22 TraesCS3A01G094500 chr6D 88.363 782 77 5 2882 3659 16177686 16178457 0.000000e+00 928.0
23 TraesCS3A01G094500 chr6D 74.876 808 157 34 1124 1914 143092290 143091512 3.520000e-85 326.0
24 TraesCS3A01G094500 chr6D 100.000 28 0 0 202 229 317011061 317011034 7.000000e-03 52.8
25 TraesCS3A01G094500 chr6B 87.933 779 75 12 2888 3659 27918239 27919005 0.000000e+00 900.0
26 TraesCS3A01G094500 chr6B 81.429 70 7 4 160 229 507588048 507588111 7.000000e-03 52.8
27 TraesCS3A01G094500 chr5D 88.114 774 70 11 2891 3659 539037296 539036540 0.000000e+00 900.0
28 TraesCS3A01G094500 chr5D 77.632 152 29 5 2322 2472 380076340 380076193 1.810000e-13 87.9
29 TraesCS3A01G094500 chr6A 77.498 1551 267 63 1132 2642 205114773 205116281 0.000000e+00 856.0
30 TraesCS3A01G094500 chr6A 74.481 1493 290 69 1124 2584 188354889 188353456 2.470000e-156 562.0
31 TraesCS3A01G094500 chr6A 100.000 28 0 0 202 229 454653609 454653582 7.000000e-03 52.8
32 TraesCS3A01G094500 chr2D 88.486 469 41 5 2880 3346 426940912 426940455 4.130000e-154 555.0
33 TraesCS3A01G094500 chr7B 79.462 818 137 25 1132 1938 682283706 682282909 5.340000e-153 551.0
34 TraesCS3A01G094500 chr1D 87.814 279 23 4 2911 3179 468133890 468133613 2.120000e-82 316.0
35 TraesCS3A01G094500 chr1D 76.613 620 116 25 1124 1734 337217318 337217917 7.630000e-82 315.0
36 TraesCS3A01G094500 chr1D 84.932 73 8 3 395 464 62873025 62872953 1.820000e-08 71.3
37 TraesCS3A01G094500 chr1D 81.013 79 14 1 202 279 434081600 434081522 1.100000e-05 62.1
38 TraesCS3A01G094500 chr2A 77.612 335 52 15 140 463 179286257 179286579 8.070000e-42 182.0
39 TraesCS3A01G094500 chr2A 71.990 382 91 15 2168 2541 35655392 35655765 8.360000e-17 99.0
40 TraesCS3A01G094500 chr2A 83.824 68 10 1 395 462 715217521 715217455 3.050000e-06 63.9
41 TraesCS3A01G094500 chrUn 71.842 380 95 11 2168 2541 24901470 24901843 8.360000e-17 99.0
42 TraesCS3A01G094500 chr4B 78.344 157 24 7 183 334 55310631 55310782 3.890000e-15 93.5
43 TraesCS3A01G094500 chr5B 89.855 69 7 0 395 463 62019090 62019158 5.030000e-14 89.8


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 TraesCS3A01G094500 chr3A 60440337 60443995 3658 True 6758.0 6758 100.0000 1 3659 1 chr3A.!!$R1 3658
1 TraesCS3A01G094500 chr3A 60471207 60473218 2011 False 2697.0 2697 90.9580 708 2725 1 chr3A.!!$F1 2017
2 TraesCS3A01G094500 chr3B 75956445 75959128 2683 True 3345.0 3345 89.1800 143 2886 1 chr3B.!!$R1 2743
3 TraesCS3A01G094500 chr3B 76114913 76116696 1783 False 2510.0 2510 91.9740 834 2644 1 chr3B.!!$F2 1810
4 TraesCS3A01G094500 chr3B 75993645 75994216 571 False 494.0 494 82.3820 26 635 1 chr3B.!!$F1 609
5 TraesCS3A01G094500 chr3D 48250634 48252569 1935 True 2931.0 2931 94.2900 740 2644 1 chr3D.!!$R1 1904
6 TraesCS3A01G094500 chr3D 48346594 48350430 3836 False 1699.5 2837 87.8190 2 2762 2 chr3D.!!$F6 2760
7 TraesCS3A01G094500 chr3D 589431253 589432024 771 True 948.0 948 88.8890 2883 3659 1 chr3D.!!$R4 776
8 TraesCS3A01G094500 chr3D 549376646 549377332 686 False 881.0 881 89.7730 2961 3659 1 chr3D.!!$F4 698
9 TraesCS3A01G094500 chr3D 501791541 501792309 768 False 824.0 824 86.2240 2888 3659 1 chr3D.!!$F3 771
10 TraesCS3A01G094500 chr3D 143236022 143236584 562 False 745.0 745 90.4010 3087 3659 1 chr3D.!!$F2 572
11 TraesCS3A01G094500 chr3D 48295352 48295879 527 True 630.0 630 88.3240 2067 2593 1 chr3D.!!$R2 526
12 TraesCS3A01G094500 chr5A 685998462 685999232 770 False 937.0 937 88.6600 2883 3653 1 chr5A.!!$F2 770
13 TraesCS3A01G094500 chr5A 73804449 73805185 736 True 839.0 839 87.2820 2884 3625 1 chr5A.!!$R1 741
14 TraesCS3A01G094500 chr5A 520208236 520209665 1429 True 240.5 244 75.1995 1124 2546 2 chr5A.!!$R2 1422
15 TraesCS3A01G094500 chr6D 16177686 16178457 771 False 928.0 928 88.3630 2882 3659 1 chr6D.!!$F1 777
16 TraesCS3A01G094500 chr6D 143091512 143092290 778 True 326.0 326 74.8760 1124 1914 1 chr6D.!!$R1 790
17 TraesCS3A01G094500 chr6B 27918239 27919005 766 False 900.0 900 87.9330 2888 3659 1 chr6B.!!$F1 771
18 TraesCS3A01G094500 chr5D 539036540 539037296 756 True 900.0 900 88.1140 2891 3659 1 chr5D.!!$R2 768
19 TraesCS3A01G094500 chr6A 205114773 205116281 1508 False 856.0 856 77.4980 1132 2642 1 chr6A.!!$F1 1510
20 TraesCS3A01G094500 chr6A 188353456 188354889 1433 True 562.0 562 74.4810 1124 2584 1 chr6A.!!$R1 1460
21 TraesCS3A01G094500 chr7B 682282909 682283706 797 True 551.0 551 79.4620 1132 1938 1 chr7B.!!$R1 806
22 TraesCS3A01G094500 chr1D 337217318 337217917 599 False 315.0 315 76.6130 1124 1734 1 chr1D.!!$F1 610

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
956 2128 0.030638 AAACAACACATCAGCGCACC 59.969 50.0 11.47 0.00 0.0 5.01 F
994 2166 0.809385 TCGACCGAGCTCCAAGTTAG 59.191 55.0 8.47 2.79 0.0 2.34 F
2011 3209 0.872388 ATCGAAAGGCGTCAACCAAC 59.128 50.0 0.00 0.00 41.8 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1926 3107 1.001158 GGATTCGGGAGAGAGCTTACG 60.001 57.143 0.0 0.00 41.75 3.18 R
2647 3916 1.808945 CGAGTACGTCTACCCTGTTGT 59.191 52.381 0.0 0.00 34.56 3.32 R
3494 4842 0.034089 TCTCAGTCTGGCCGAGATGA 60.034 55.000 0.0 5.42 30.94 2.92 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
17 18 4.187056 GTTCTAGTGCGCTGGTCC 57.813 61.111 10.80 0.00 0.00 4.46
18 19 1.592223 GTTCTAGTGCGCTGGTCCT 59.408 57.895 10.80 0.00 0.00 3.85
19 20 0.037232 GTTCTAGTGCGCTGGTCCTT 60.037 55.000 10.80 0.00 0.00 3.36
20 21 0.037326 TTCTAGTGCGCTGGTCCTTG 60.037 55.000 10.80 0.00 0.00 3.61
30 31 2.356667 GGTCCTTGGGGCCTCAAG 59.643 66.667 34.85 34.85 42.63 3.02
31 32 2.231380 GGTCCTTGGGGCCTCAAGA 61.231 63.158 41.43 26.07 44.98 3.02
35 36 0.040204 CCTTGGGGCCTCAAGACAAT 59.960 55.000 41.43 0.00 44.98 2.71
46 47 4.083590 GCCTCAAGACAATGACTTTCTGAC 60.084 45.833 0.00 0.00 0.00 3.51
56 57 8.128322 ACAATGACTTTCTGACTGTCTACTAT 57.872 34.615 9.51 0.00 0.00 2.12
88 90 6.013379 AGTTTGATGTACTTCAATGAGGGAGA 60.013 38.462 21.00 4.99 35.64 3.71
93 95 0.826715 CTTCAATGAGGGAGAGGCGA 59.173 55.000 0.00 0.00 0.00 5.54
127 129 8.255394 ACCTTAAATATTGAAATGTTGCTTGC 57.745 30.769 0.00 0.00 0.00 4.01
137 139 7.551035 TGAAATGTTGCTTGCAACTTAATTT 57.449 28.000 30.21 26.28 36.15 1.82
147 149 8.668353 TGCTTGCAACTTAATTTCACTAGATAG 58.332 33.333 0.00 0.00 0.00 2.08
158 160 1.007271 CTAGATAGCACCCCGCACG 60.007 63.158 0.00 0.00 46.13 5.34
182 184 6.665474 TTGCTGCCAAAATTTATAGCAATG 57.335 33.333 18.97 8.51 43.67 2.82
183 185 5.975282 TGCTGCCAAAATTTATAGCAATGA 58.025 33.333 13.02 0.07 38.12 2.57
184 186 6.404708 TGCTGCCAAAATTTATAGCAATGAA 58.595 32.000 13.02 0.00 38.12 2.57
185 187 6.877855 TGCTGCCAAAATTTATAGCAATGAAA 59.122 30.769 13.02 0.00 38.12 2.69
186 188 7.553402 TGCTGCCAAAATTTATAGCAATGAAAT 59.447 29.630 13.02 0.00 38.12 2.17
187 189 8.400186 GCTGCCAAAATTTATAGCAATGAAATT 58.600 29.630 9.97 0.00 36.63 1.82
343 363 7.998753 ATTTGTTGCTCAAAAGAAGAAGAAG 57.001 32.000 10.52 0.00 46.97 2.85
344 364 6.757897 TTGTTGCTCAAAAGAAGAAGAAGA 57.242 33.333 0.00 0.00 32.64 2.87
345 365 6.757897 TGTTGCTCAAAAGAAGAAGAAGAA 57.242 33.333 0.00 0.00 0.00 2.52
346 366 6.789262 TGTTGCTCAAAAGAAGAAGAAGAAG 58.211 36.000 0.00 0.00 0.00 2.85
347 367 6.599244 TGTTGCTCAAAAGAAGAAGAAGAAGA 59.401 34.615 0.00 0.00 0.00 2.87
348 368 7.121168 TGTTGCTCAAAAGAAGAAGAAGAAGAA 59.879 33.333 0.00 0.00 0.00 2.52
349 369 7.256756 TGCTCAAAAGAAGAAGAAGAAGAAG 57.743 36.000 0.00 0.00 0.00 2.85
366 386 8.644318 AAGAAGAAGATGCAAAATAATGATGC 57.356 30.769 0.00 0.00 40.45 3.91
391 411 1.542915 GACTTGCATGTGCTTGATGGT 59.457 47.619 10.37 0.00 42.66 3.55
392 412 1.542915 ACTTGCATGTGCTTGATGGTC 59.457 47.619 4.14 0.00 42.66 4.02
393 413 1.542472 CTTGCATGTGCTTGATGGTCA 59.458 47.619 6.55 0.00 42.66 4.02
394 414 1.170442 TGCATGTGCTTGATGGTCAG 58.830 50.000 6.55 0.00 42.66 3.51
395 415 1.271488 TGCATGTGCTTGATGGTCAGA 60.271 47.619 6.55 0.00 42.66 3.27
396 416 2.022195 GCATGTGCTTGATGGTCAGAT 58.978 47.619 0.00 0.00 38.21 2.90
397 417 2.223502 GCATGTGCTTGATGGTCAGATG 60.224 50.000 0.00 0.00 38.21 2.90
398 418 2.118313 TGTGCTTGATGGTCAGATGG 57.882 50.000 0.00 0.00 0.00 3.51
412 433 1.808945 CAGATGGTGTGGAGAACTTGC 59.191 52.381 0.00 0.00 0.00 4.01
561 583 5.568747 AATGCAACGTGTTTTAAAATCCG 57.431 34.783 16.09 16.09 0.00 4.18
568 590 5.923665 ACGTGTTTTAAAATCCGCTTAGAG 58.076 37.500 17.07 0.00 0.00 2.43
570 592 6.646240 ACGTGTTTTAAAATCCGCTTAGAGTA 59.354 34.615 17.07 0.00 0.00 2.59
572 594 6.952083 GTGTTTTAAAATCCGCTTAGAGTACG 59.048 38.462 3.52 0.00 0.00 3.67
582 604 4.852104 CCGCTTAGAGTACGCTAATGTATG 59.148 45.833 17.84 8.44 30.56 2.39
627 649 2.678324 GTAGATTGGACGGATGCTAGC 58.322 52.381 8.10 8.10 0.00 3.42
638 660 2.033407 CGGATGCTAGCGAATCAAGTTG 60.033 50.000 10.77 0.00 0.00 3.16
645 667 5.064707 TGCTAGCGAATCAAGTTGGTAAATC 59.935 40.000 10.77 0.00 0.00 2.17
687 709 4.349663 TGATGTAAAACCAAGCGTATGC 57.650 40.909 0.00 0.00 43.24 3.14
689 711 3.822594 TGTAAAACCAAGCGTATGCAG 57.177 42.857 10.11 0.85 46.23 4.41
693 715 5.644206 TGTAAAACCAAGCGTATGCAGATAA 59.356 36.000 10.11 0.00 46.23 1.75
694 716 4.882671 AAACCAAGCGTATGCAGATAAG 57.117 40.909 10.11 0.00 46.23 1.73
696 718 4.342862 ACCAAGCGTATGCAGATAAGAT 57.657 40.909 10.11 0.00 46.23 2.40
699 721 6.467677 ACCAAGCGTATGCAGATAAGATAAT 58.532 36.000 10.11 0.00 46.23 1.28
701 723 6.183360 CCAAGCGTATGCAGATAAGATAATGG 60.183 42.308 10.11 0.00 46.23 3.16
703 725 5.187772 AGCGTATGCAGATAAGATAATGGGA 59.812 40.000 10.11 0.00 46.23 4.37
704 726 6.051717 GCGTATGCAGATAAGATAATGGGAT 58.948 40.000 0.89 0.00 42.15 3.85
705 727 7.069950 AGCGTATGCAGATAAGATAATGGGATA 59.930 37.037 10.11 0.00 46.23 2.59
720 1854 3.314693 TGGGATAATTAGAAGGAGCGGT 58.685 45.455 0.00 0.00 0.00 5.68
721 1855 4.485875 TGGGATAATTAGAAGGAGCGGTA 58.514 43.478 0.00 0.00 0.00 4.02
733 1867 3.158676 AGGAGCGGTATCCAAGTATCTC 58.841 50.000 0.00 0.00 42.26 2.75
793 1936 0.179108 GGATGTCGTAGCAGGTGACC 60.179 60.000 0.00 0.00 0.00 4.02
943 2115 3.888930 TCCAAACCTCCTCATGAAACAAC 59.111 43.478 0.00 0.00 0.00 3.32
956 2128 0.030638 AAACAACACATCAGCGCACC 59.969 50.000 11.47 0.00 0.00 5.01
979 2151 3.607987 CGCTTGACGCCGATCGAC 61.608 66.667 18.66 3.27 41.67 4.20
980 2152 3.255379 GCTTGACGCCGATCGACC 61.255 66.667 18.66 6.16 41.67 4.79
981 2153 2.949678 CTTGACGCCGATCGACCG 60.950 66.667 18.66 20.14 41.67 4.79
982 2154 3.391160 CTTGACGCCGATCGACCGA 62.391 63.158 26.72 9.41 41.67 4.69
987 2159 4.632458 GCCGATCGACCGAGCTCC 62.632 72.222 18.66 0.00 0.00 4.70
994 2166 0.809385 TCGACCGAGCTCCAAGTTAG 59.191 55.000 8.47 2.79 0.00 2.34
1023 2195 2.109517 CTGCCGAGAGCCCAGCATAT 62.110 60.000 0.00 0.00 42.71 1.78
1165 2337 1.293498 GTGATCGGACACCTGCACT 59.707 57.895 0.00 0.00 35.07 4.40
1885 3066 2.276869 CAGGACGACATGGACTCCA 58.723 57.895 0.00 0.00 38.19 3.86
1926 3107 6.038356 GGACAACATCAAATTGGTCATCATC 58.962 40.000 0.00 0.00 0.00 2.92
2010 3208 1.153353 GATCGAAAGGCGTCAACCAA 58.847 50.000 0.00 0.00 41.80 3.67
2011 3209 0.872388 ATCGAAAGGCGTCAACCAAC 59.128 50.000 0.00 0.00 41.80 3.77
2012 3210 1.161563 TCGAAAGGCGTCAACCAACC 61.162 55.000 0.00 0.00 41.80 3.77
2013 3211 1.440938 CGAAAGGCGTCAACCAACCA 61.441 55.000 0.00 0.00 34.64 3.67
2532 3801 1.293924 CGCTGCTCTTCCATTTCGAT 58.706 50.000 0.00 0.00 0.00 3.59
2585 3854 1.857965 CTGGACATGACTGAGGAGGA 58.142 55.000 0.00 0.00 0.00 3.71
2647 3916 2.187958 CTGTCCCTCATGTCCCTGTTA 58.812 52.381 0.00 0.00 0.00 2.41
2649 3918 1.906574 GTCCCTCATGTCCCTGTTACA 59.093 52.381 0.00 0.00 0.00 2.41
2652 3921 2.039746 CCCTCATGTCCCTGTTACAACA 59.960 50.000 0.00 0.00 37.37 3.33
2731 4017 0.535335 TTGGGGTGACTATCGTGAGC 59.465 55.000 0.00 0.00 0.00 4.26
2732 4018 1.065928 GGGGTGACTATCGTGAGCG 59.934 63.158 0.00 0.00 39.92 5.03
2733 4019 1.664321 GGGGTGACTATCGTGAGCGT 61.664 60.000 0.00 0.00 39.49 5.07
2740 4027 1.001633 ACTATCGTGAGCGTTGGGTTT 59.998 47.619 0.00 0.00 39.49 3.27
2750 4037 5.118510 GTGAGCGTTGGGTTTTGAATTTATG 59.881 40.000 0.00 0.00 0.00 1.90
2784 4071 2.366266 TGTCTTGGCTACCGTTGTAAGT 59.634 45.455 0.00 0.00 0.00 2.24
2786 4073 4.221262 TGTCTTGGCTACCGTTGTAAGTAT 59.779 41.667 0.00 0.00 0.00 2.12
2793 4080 3.955650 ACCGTTGTAAGTATCTGCAGT 57.044 42.857 14.67 3.75 0.00 4.40
2810 4097 7.608308 TCTGCAGTTTTTATTTTGCTGTTTT 57.392 28.000 14.67 0.00 37.45 2.43
2831 4118 0.925558 TAGGGAAAGGCATCATGGCA 59.074 50.000 14.65 0.00 46.46 4.92
2835 4122 1.551883 GGAAAGGCATCATGGCAACTT 59.448 47.619 14.65 3.44 46.46 2.66
2886 4174 7.773099 AAGATAAAAGAGGAGGTTCCCTAAT 57.227 36.000 0.00 0.00 37.19 1.73
2889 4177 5.977821 AAAAGAGGAGGTTCCCTAATAGG 57.022 43.478 0.00 0.00 37.19 2.57
2900 4188 6.447084 AGGTTCCCTAATAGGATCTTCAACAA 59.553 38.462 8.12 0.00 37.67 2.83
2908 4196 2.076863 GGATCTTCAACAACCGTCCAG 58.923 52.381 0.00 0.00 0.00 3.86
2954 4242 1.376466 AGCGTCAGGTGAGCCAATT 59.624 52.632 0.00 0.00 37.19 2.32
2958 4246 2.664916 CGTCAGGTGAGCCAATTTTTG 58.335 47.619 0.00 0.00 37.19 2.44
3067 4361 3.777465 TGACGCCTACTATGTGAACTC 57.223 47.619 0.00 0.00 0.00 3.01
3089 4383 5.662456 TCCGATTCGATACACATTTGGTTA 58.338 37.500 7.83 0.00 0.00 2.85
3115 4458 8.873215 CGATAGTACAAATGTGGAGATAGTTT 57.127 34.615 0.00 0.00 0.00 2.66
3179 4522 8.212312 AGATAGTTCATAGTCTTCTCCTACGAA 58.788 37.037 0.00 0.00 0.00 3.85
3180 4523 8.927675 ATAGTTCATAGTCTTCTCCTACGAAT 57.072 34.615 0.00 0.00 0.00 3.34
3181 4524 7.266922 AGTTCATAGTCTTCTCCTACGAATC 57.733 40.000 0.00 0.00 0.00 2.52
3182 4525 5.926214 TCATAGTCTTCTCCTACGAATCG 57.074 43.478 0.00 0.00 0.00 3.34
3183 4526 5.608449 TCATAGTCTTCTCCTACGAATCGA 58.392 41.667 10.55 0.00 0.00 3.59
3184 4527 6.231951 TCATAGTCTTCTCCTACGAATCGAT 58.768 40.000 10.55 0.00 0.00 3.59
3185 4528 4.822036 AGTCTTCTCCTACGAATCGATG 57.178 45.455 10.55 0.92 0.00 3.84
3186 4529 4.452825 AGTCTTCTCCTACGAATCGATGA 58.547 43.478 10.55 1.49 0.00 2.92
3221 4568 5.924825 AGACGAAAAATTGCTACTACTCGTT 59.075 36.000 0.00 0.00 38.31 3.85
3247 4594 1.585006 GACTCGGACTTTGCCTCGA 59.415 57.895 0.00 0.00 0.00 4.04
3381 4729 1.591863 GTTGTCCTCGCGATAGGCC 60.592 63.158 10.36 0.00 38.94 5.19
3402 4750 1.994885 CTCGCTCCTCCCTCCTCTCT 61.995 65.000 0.00 0.00 0.00 3.10
3404 4752 1.391157 CGCTCCTCCCTCCTCTCTTG 61.391 65.000 0.00 0.00 0.00 3.02
3494 4842 2.436646 CGCCATGGCTTCCTCGTT 60.437 61.111 33.07 0.00 39.32 3.85
3507 4855 1.667154 CCTCGTTCATCTCGGCCAGA 61.667 60.000 2.24 5.36 34.78 3.86
3545 4897 2.202570 CCGGTTCTCGCGACGATT 60.203 61.111 17.12 0.00 34.61 3.34
3563 4915 3.732774 CGATTCTCGTCGGTGATAAACCA 60.733 47.826 0.00 0.00 41.28 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.037232 AAGGACCAGCGCACTAGAAC 60.037 55.000 11.47 0.00 0.00 3.01
15 16 1.065410 TTGTCTTGAGGCCCCAAGGA 61.065 55.000 25.11 10.86 42.72 3.36
17 18 1.180029 CATTGTCTTGAGGCCCCAAG 58.820 55.000 20.45 20.45 43.58 3.61
18 19 0.776810 TCATTGTCTTGAGGCCCCAA 59.223 50.000 0.00 0.00 0.00 4.12
19 20 0.038166 GTCATTGTCTTGAGGCCCCA 59.962 55.000 0.00 0.00 0.00 4.96
20 21 0.329596 AGTCATTGTCTTGAGGCCCC 59.670 55.000 0.00 0.00 0.00 5.80
30 31 6.451393 AGTAGACAGTCAGAAAGTCATTGTC 58.549 40.000 2.66 0.00 34.80 3.18
31 32 6.412362 AGTAGACAGTCAGAAAGTCATTGT 57.588 37.500 2.66 0.00 34.80 2.71
35 36 9.074576 TGTTTATAGTAGACAGTCAGAAAGTCA 57.925 33.333 2.66 0.00 34.80 3.41
70 72 2.501723 GCCTCTCCCTCATTGAAGTACA 59.498 50.000 0.00 0.00 0.00 2.90
72 74 1.757118 CGCCTCTCCCTCATTGAAGTA 59.243 52.381 0.00 0.00 0.00 2.24
73 75 0.539051 CGCCTCTCCCTCATTGAAGT 59.461 55.000 0.00 0.00 0.00 3.01
78 80 1.727062 ATCATCGCCTCTCCCTCATT 58.273 50.000 0.00 0.00 0.00 2.57
127 129 7.012421 GGGGTGCTATCTAGTGAAATTAAGTTG 59.988 40.741 0.00 0.00 0.00 3.16
137 139 0.396556 TGCGGGGTGCTATCTAGTGA 60.397 55.000 0.00 0.00 46.63 3.41
340 360 8.753175 GCATCATTATTTTGCATCTTCTTCTTC 58.247 33.333 0.00 0.00 36.40 2.87
343 363 6.143438 CCGCATCATTATTTTGCATCTTCTTC 59.857 38.462 0.00 0.00 36.15 2.87
344 364 5.981315 CCGCATCATTATTTTGCATCTTCTT 59.019 36.000 0.00 0.00 36.15 2.52
345 365 5.300034 TCCGCATCATTATTTTGCATCTTCT 59.700 36.000 0.00 0.00 36.15 2.85
346 366 5.522456 TCCGCATCATTATTTTGCATCTTC 58.478 37.500 0.00 0.00 36.15 2.87
347 367 5.518848 TCCGCATCATTATTTTGCATCTT 57.481 34.783 0.00 0.00 36.15 2.40
348 368 5.242171 TCATCCGCATCATTATTTTGCATCT 59.758 36.000 0.00 0.00 36.15 2.90
349 369 5.344128 GTCATCCGCATCATTATTTTGCATC 59.656 40.000 0.00 0.00 36.15 3.91
366 386 0.806868 AAGCACATGCAAGTCATCCG 59.193 50.000 6.64 0.00 45.16 4.18
391 411 2.550855 GCAAGTTCTCCACACCATCTGA 60.551 50.000 0.00 0.00 0.00 3.27
392 412 1.808945 GCAAGTTCTCCACACCATCTG 59.191 52.381 0.00 0.00 0.00 2.90
393 413 1.421268 TGCAAGTTCTCCACACCATCT 59.579 47.619 0.00 0.00 0.00 2.90
394 414 1.896220 TGCAAGTTCTCCACACCATC 58.104 50.000 0.00 0.00 0.00 3.51
395 415 2.165167 CATGCAAGTTCTCCACACCAT 58.835 47.619 0.00 0.00 0.00 3.55
396 416 1.133823 ACATGCAAGTTCTCCACACCA 60.134 47.619 0.00 0.00 0.00 4.17
397 417 1.267806 CACATGCAAGTTCTCCACACC 59.732 52.381 0.00 0.00 0.00 4.16
398 418 1.267806 CCACATGCAAGTTCTCCACAC 59.732 52.381 0.00 0.00 0.00 3.82
412 433 3.321682 ACCAATCCACTTTTCACCACATG 59.678 43.478 0.00 0.00 0.00 3.21
561 583 6.345882 GCAACATACATTAGCGTACTCTAAGC 60.346 42.308 10.80 3.25 32.66 3.09
568 590 4.272504 ACCATGCAACATACATTAGCGTAC 59.727 41.667 0.00 0.00 0.00 3.67
570 592 3.278574 ACCATGCAACATACATTAGCGT 58.721 40.909 0.00 0.00 0.00 5.07
572 594 6.427853 TCATCTACCATGCAACATACATTAGC 59.572 38.462 0.00 0.00 0.00 3.09
627 649 7.985476 ACCATTAGATTTACCAACTTGATTCG 58.015 34.615 0.00 0.00 0.00 3.34
659 681 6.454795 ACGCTTGGTTTTACATCATCAAAAT 58.545 32.000 0.00 0.00 0.00 1.82
679 701 5.187772 TCCCATTATCTTATCTGCATACGCT 59.812 40.000 0.00 0.00 39.64 5.07
693 715 7.365117 CCGCTCCTTCTAATTATCCCATTATCT 60.365 40.741 0.00 0.00 0.00 1.98
694 716 6.763610 CCGCTCCTTCTAATTATCCCATTATC 59.236 42.308 0.00 0.00 0.00 1.75
696 718 5.546499 ACCGCTCCTTCTAATTATCCCATTA 59.454 40.000 0.00 0.00 0.00 1.90
699 721 3.314693 ACCGCTCCTTCTAATTATCCCA 58.685 45.455 0.00 0.00 0.00 4.37
701 723 5.187186 TGGATACCGCTCCTTCTAATTATCC 59.813 44.000 0.00 0.00 36.20 2.59
703 725 6.270231 ACTTGGATACCGCTCCTTCTAATTAT 59.730 38.462 0.00 0.00 36.20 1.28
704 726 5.601313 ACTTGGATACCGCTCCTTCTAATTA 59.399 40.000 0.00 0.00 36.20 1.40
705 727 4.409247 ACTTGGATACCGCTCCTTCTAATT 59.591 41.667 0.00 0.00 36.20 1.40
720 1854 4.645136 AGCTCACAACGAGATACTTGGATA 59.355 41.667 0.00 0.00 45.45 2.59
721 1855 3.449018 AGCTCACAACGAGATACTTGGAT 59.551 43.478 0.00 0.00 45.45 3.41
774 1916 0.179108 GGTCACCTGCTACGACATCC 60.179 60.000 0.00 0.00 0.00 3.51
793 1936 0.238289 ACAAGTCAAAATCGCCTGCG 59.762 50.000 4.92 4.92 41.35 5.18
943 2115 1.736282 TACGTGGTGCGCTGATGTG 60.736 57.895 9.73 0.00 46.11 3.21
979 2151 0.741221 GCCACTAACTTGGAGCTCGG 60.741 60.000 7.83 0.63 39.24 4.63
980 2152 0.741221 GGCCACTAACTTGGAGCTCG 60.741 60.000 7.83 0.00 39.24 5.03
981 2153 0.324943 TGGCCACTAACTTGGAGCTC 59.675 55.000 0.00 4.71 39.24 4.09
982 2154 0.995024 ATGGCCACTAACTTGGAGCT 59.005 50.000 8.16 0.00 39.24 4.09
987 2159 0.813184 CAGCCATGGCCACTAACTTG 59.187 55.000 33.14 17.95 43.17 3.16
1023 2195 1.000486 AGGCAGGAGGAGCGAGTAA 60.000 57.895 0.00 0.00 0.00 2.24
1155 2327 2.657237 GCGAGGTAGTGCAGGTGT 59.343 61.111 0.00 0.00 0.00 4.16
1486 2658 4.479993 GAGCAGGCGTCCCAGCAT 62.480 66.667 11.42 0.00 45.38 3.79
1885 3066 1.553704 GTCCGTGGTGAAGGGATACTT 59.446 52.381 0.00 0.00 44.48 2.24
1926 3107 1.001158 GGATTCGGGAGAGAGCTTACG 60.001 57.143 0.00 0.00 41.75 3.18
2281 3534 3.175240 CACGTCGAAGCCGAGCAG 61.175 66.667 0.00 0.00 46.52 4.24
2532 3801 4.697756 CCGTCCGGCAGCTTCCAA 62.698 66.667 2.54 0.00 0.00 3.53
2647 3916 1.808945 CGAGTACGTCTACCCTGTTGT 59.191 52.381 0.00 0.00 34.56 3.32
2750 4037 9.233232 CGGTAGCCAAGACATTTATTTAAAATC 57.767 33.333 0.00 0.00 0.00 2.17
2784 4071 8.885494 AAACAGCAAAATAAAAACTGCAGATA 57.115 26.923 23.35 8.16 37.26 1.98
2786 4073 7.608308 AAAACAGCAAAATAAAAACTGCAGA 57.392 28.000 23.35 0.00 37.26 4.26
2810 4097 2.292126 TGCCATGATGCCTTTCCCTAAA 60.292 45.455 0.00 0.00 0.00 1.85
2821 4108 7.428020 TCTTCATAATAAAGTTGCCATGATGC 58.572 34.615 0.00 0.00 0.00 3.91
2855 4142 6.374417 ACCTCCTCTTTTATCTTAGCACAA 57.626 37.500 0.00 0.00 0.00 3.33
2886 4174 2.901192 TGGACGGTTGTTGAAGATCCTA 59.099 45.455 0.00 0.00 0.00 2.94
2889 4177 2.076863 CCTGGACGGTTGTTGAAGATC 58.923 52.381 0.00 0.00 0.00 2.75
2919 4207 5.237815 TGACGCTGTATTCTGATTTTGAGT 58.762 37.500 0.00 0.00 0.00 3.41
2922 4210 4.393062 ACCTGACGCTGTATTCTGATTTTG 59.607 41.667 0.00 0.00 0.00 2.44
3018 4306 2.620251 AAATATAGCGTGCCTGCTCA 57.380 45.000 2.72 0.00 45.87 4.26
3019 4307 3.971032 AAAAATATAGCGTGCCTGCTC 57.029 42.857 2.72 0.00 45.87 4.26
3067 4361 4.875544 AACCAAATGTGTATCGAATCGG 57.124 40.909 1.76 0.00 0.00 4.18
3089 4383 7.584122 ACTATCTCCACATTTGTACTATCGT 57.416 36.000 0.00 0.00 0.00 3.73
3115 4458 2.159240 CGTAGAAGCAGGCTATGTGACA 60.159 50.000 0.00 0.00 0.00 3.58
3198 4545 5.758570 ACGAGTAGTAGCAATTTTTCGTC 57.241 39.130 0.00 0.00 35.39 4.20
3207 4554 4.877823 TCGGAGAATAACGAGTAGTAGCAA 59.122 41.667 0.00 0.00 34.67 3.91
3209 4556 4.511082 AGTCGGAGAATAACGAGTAGTAGC 59.489 45.833 0.00 0.00 40.62 3.58
3239 4586 0.465705 GGAGGACATCATCGAGGCAA 59.534 55.000 0.00 0.00 0.00 4.52
3247 4594 0.395862 ACGTCGGAGGAGGACATCAT 60.396 55.000 4.48 0.00 34.04 2.45
3363 4711 1.591863 GGCCTATCGCGAGGACAAC 60.592 63.158 16.66 1.26 45.09 3.32
3404 4752 4.851214 AGAGGAGGGCGGAGAGGC 62.851 72.222 0.00 0.00 45.91 4.70
3438 4786 1.061131 CCGCAAGACATCATCAACGAC 59.939 52.381 0.00 0.00 43.02 4.34
3494 4842 0.034089 TCTCAGTCTGGCCGAGATGA 60.034 55.000 0.00 5.42 30.94 2.92
3567 4919 2.270205 CATGAGTTGGCGCCTCCT 59.730 61.111 29.70 22.59 35.26 3.69


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

AutoCloner maintained by Alex Coulton.