Multiple sequence alignment - TraesCS7A01G270400

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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 TraesCS7A01G270400 chr7A 100.000 2111 0 0 1 2111 278412422 278414532 0.000000e+00 3899.0
1 TraesCS7A01G270400 chr7A 92.835 656 41 4 5 655 383950849 383950195 0.000000e+00 946.0
2 TraesCS7A01G270400 chr2D 92.416 923 56 11 1192 2109 372832918 372833831 0.000000e+00 1304.0
3 TraesCS7A01G270400 chr2D 90.244 41 4 0 647 687 175482419 175482459 1.000000e-03 54.7
4 TraesCS7A01G270400 chr7D 92.316 924 59 10 1192 2111 266718571 266719486 0.000000e+00 1303.0
5 TraesCS7A01G270400 chr7D 92.324 925 57 10 1192 2111 475133475 475134390 0.000000e+00 1303.0
6 TraesCS7A01G270400 chr7D 93.344 646 38 3 5 645 427848892 427848247 0.000000e+00 950.0
7 TraesCS7A01G270400 chr7D 92.835 656 40 4 5 655 147026175 147026828 0.000000e+00 944.0
8 TraesCS7A01G270400 chr4D 91.983 923 63 9 1192 2111 294305221 294306135 0.000000e+00 1284.0
9 TraesCS7A01G270400 chr4D 91.775 924 63 12 1192 2111 294328022 294328936 0.000000e+00 1273.0
10 TraesCS7A01G270400 chr4A 91.965 921 66 6 1192 2111 563894088 563893175 0.000000e+00 1284.0
11 TraesCS7A01G270400 chr4A 92.576 660 43 4 1 655 533848002 533848660 0.000000e+00 942.0
12 TraesCS7A01G270400 chr4A 92.157 510 34 5 687 1192 309506717 309506210 0.000000e+00 715.0
13 TraesCS7A01G270400 chr3A 92.048 918 62 8 1196 2111 490542181 490541273 0.000000e+00 1280.0
14 TraesCS7A01G270400 chr3A 92.553 658 43 4 3 655 703578547 703577891 0.000000e+00 939.0
15 TraesCS7A01G270400 chr2A 91.784 925 64 9 1192 2111 261812970 261812053 0.000000e+00 1277.0
16 TraesCS7A01G270400 chr5D 91.775 924 56 15 1192 2111 236341143 236342050 0.000000e+00 1267.0
17 TraesCS7A01G270400 chr5D 92.996 514 28 5 687 1192 6180516 6180003 0.000000e+00 743.0
18 TraesCS7A01G270400 chr5D 92.996 514 28 5 687 1192 512409118 512408605 0.000000e+00 743.0
19 TraesCS7A01G270400 chr5D 93.010 515 27 5 687 1192 512416055 512415541 0.000000e+00 743.0
20 TraesCS7A01G270400 chr5D 92.982 513 29 5 687 1192 120800299 120800811 0.000000e+00 741.0
21 TraesCS7A01G270400 chr5D 92.578 512 31 6 687 1192 167072366 167072876 0.000000e+00 728.0
22 TraesCS7A01G270400 chr5D 92.427 515 30 7 687 1192 503287730 503288244 0.000000e+00 726.0
23 TraesCS7A01G270400 chr1A 93.538 650 37 3 1 645 58897224 58897873 0.000000e+00 963.0
24 TraesCS7A01G270400 chr3D 93.385 650 37 4 5 648 34688147 34688796 0.000000e+00 957.0
25 TraesCS7A01G270400 chr6A 93.231 650 37 5 1 645 349602260 349601613 0.000000e+00 950.0
26 TraesCS7A01G270400 chr6A 95.122 41 2 0 647 687 167690887 167690927 4.860000e-07 65.8
27 TraesCS7A01G270400 chr6A 94.737 38 2 0 650 687 397831668 397831631 2.260000e-05 60.2
28 TraesCS7A01G270400 chr6D 93.077 650 39 4 5 649 23985842 23986490 0.000000e+00 946.0
29 TraesCS7A01G270400 chr6D 93.372 513 26 6 687 1192 45511139 45510628 0.000000e+00 752.0
30 TraesCS7A01G270400 chr1D 93.164 512 28 6 687 1192 51877642 51877132 0.000000e+00 745.0
31 TraesCS7A01G270400 chr4B 97.561 41 1 0 647 687 311144267 311144307 1.040000e-08 71.3


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G270400 chr7A 278412422 278414532 2110 False 3899 3899 100.000 1 2111 1 chr7A.!!$F1 2110
1 TraesCS7A01G270400 chr7A 383950195 383950849 654 True 946 946 92.835 5 655 1 chr7A.!!$R1 650
2 TraesCS7A01G270400 chr2D 372832918 372833831 913 False 1304 1304 92.416 1192 2109 1 chr2D.!!$F2 917
3 TraesCS7A01G270400 chr7D 266718571 266719486 915 False 1303 1303 92.316 1192 2111 1 chr7D.!!$F2 919
4 TraesCS7A01G270400 chr7D 475133475 475134390 915 False 1303 1303 92.324 1192 2111 1 chr7D.!!$F3 919
5 TraesCS7A01G270400 chr7D 427848247 427848892 645 True 950 950 93.344 5 645 1 chr7D.!!$R1 640
6 TraesCS7A01G270400 chr7D 147026175 147026828 653 False 944 944 92.835 5 655 1 chr7D.!!$F1 650
7 TraesCS7A01G270400 chr4D 294305221 294306135 914 False 1284 1284 91.983 1192 2111 1 chr4D.!!$F1 919
8 TraesCS7A01G270400 chr4D 294328022 294328936 914 False 1273 1273 91.775 1192 2111 1 chr4D.!!$F2 919
9 TraesCS7A01G270400 chr4A 563893175 563894088 913 True 1284 1284 91.965 1192 2111 1 chr4A.!!$R2 919
10 TraesCS7A01G270400 chr4A 533848002 533848660 658 False 942 942 92.576 1 655 1 chr4A.!!$F1 654
11 TraesCS7A01G270400 chr4A 309506210 309506717 507 True 715 715 92.157 687 1192 1 chr4A.!!$R1 505
12 TraesCS7A01G270400 chr3A 490541273 490542181 908 True 1280 1280 92.048 1196 2111 1 chr3A.!!$R1 915
13 TraesCS7A01G270400 chr3A 703577891 703578547 656 True 939 939 92.553 3 655 1 chr3A.!!$R2 652
14 TraesCS7A01G270400 chr2A 261812053 261812970 917 True 1277 1277 91.784 1192 2111 1 chr2A.!!$R1 919
15 TraesCS7A01G270400 chr5D 236341143 236342050 907 False 1267 1267 91.775 1192 2111 1 chr5D.!!$F3 919
16 TraesCS7A01G270400 chr5D 6180003 6180516 513 True 743 743 92.996 687 1192 1 chr5D.!!$R1 505
17 TraesCS7A01G270400 chr5D 512408605 512409118 513 True 743 743 92.996 687 1192 1 chr5D.!!$R2 505
18 TraesCS7A01G270400 chr5D 512415541 512416055 514 True 743 743 93.010 687 1192 1 chr5D.!!$R3 505
19 TraesCS7A01G270400 chr5D 120800299 120800811 512 False 741 741 92.982 687 1192 1 chr5D.!!$F1 505
20 TraesCS7A01G270400 chr5D 167072366 167072876 510 False 728 728 92.578 687 1192 1 chr5D.!!$F2 505
21 TraesCS7A01G270400 chr5D 503287730 503288244 514 False 726 726 92.427 687 1192 1 chr5D.!!$F4 505
22 TraesCS7A01G270400 chr1A 58897224 58897873 649 False 963 963 93.538 1 645 1 chr1A.!!$F1 644
23 TraesCS7A01G270400 chr3D 34688147 34688796 649 False 957 957 93.385 5 648 1 chr3D.!!$F1 643
24 TraesCS7A01G270400 chr6A 349601613 349602260 647 True 950 950 93.231 1 645 1 chr6A.!!$R1 644
25 TraesCS7A01G270400 chr6D 23985842 23986490 648 False 946 946 93.077 5 649 1 chr6D.!!$F1 644
26 TraesCS7A01G270400 chr6D 45510628 45511139 511 True 752 752 93.372 687 1192 1 chr6D.!!$R1 505
27 TraesCS7A01G270400 chr1D 51877132 51877642 510 True 745 745 93.164 687 1192 1 chr1D.!!$R1 505

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
655 662 0.677288 TCTCCAACAGTACACCCACG 59.323 55.0 0.0 0.0 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1947 2073 1.590932 GTGAGCCATGGACATAGCAG 58.409 55.0 18.4 0.0 0.0 4.24 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
67 68 3.134623 TGCTTATCTTGGTCGGATCACAT 59.865 43.478 0.00 0.00 0.00 3.21
174 176 4.392047 CCCGAAACCTACCTTTGTAACTT 58.608 43.478 0.00 0.00 0.00 2.66
195 197 1.645034 CCAGTCACGGAGTAGCATTG 58.355 55.000 0.00 0.00 41.61 2.82
196 198 1.066858 CCAGTCACGGAGTAGCATTGT 60.067 52.381 0.00 0.00 41.61 2.71
269 276 9.128404 TCTTAGGACATAGAACGTATGTTGTAT 57.872 33.333 10.83 10.83 43.21 2.29
355 362 3.346315 TCAACTCGGATCCAACTACGTA 58.654 45.455 13.41 0.00 0.00 3.57
395 402 3.899360 TCCGAGTCCATATTATCCGGTTT 59.101 43.478 0.00 0.00 37.06 3.27
415 422 2.046938 CATCCAATGCTCCATGGGC 58.953 57.895 13.02 14.76 35.02 5.36
437 444 1.191489 TGAGACCAAGCCATCGACCA 61.191 55.000 0.00 0.00 0.00 4.02
458 465 6.310941 ACCATGTCATATGCTAGTCTAGTCT 58.689 40.000 8.68 0.00 0.00 3.24
459 466 7.462590 ACCATGTCATATGCTAGTCTAGTCTA 58.537 38.462 8.68 1.68 0.00 2.59
462 469 9.660180 CATGTCATATGCTAGTCTAGTCTACTA 57.340 37.037 8.68 0.00 0.00 1.82
464 471 8.648693 TGTCATATGCTAGTCTAGTCTACTACA 58.351 37.037 8.68 4.87 0.00 2.74
502 509 4.261411 TCGACTAGGGACCTTTTAGGAT 57.739 45.455 0.00 0.00 37.67 3.24
526 533 6.355747 TGTTCATCATACAATGCATAGTCCA 58.644 36.000 0.00 0.00 0.00 4.02
540 547 4.036262 GCATAGTCCAACAAACAAGTCACA 59.964 41.667 0.00 0.00 0.00 3.58
581 588 9.948964 CATCATTGATAATGTCCAAGGACTATA 57.051 33.333 19.20 12.42 44.80 1.31
612 619 9.476202 TTCATAAACACATAGGAAGTATCATCG 57.524 33.333 0.00 0.00 0.00 3.84
613 620 8.638873 TCATAAACACATAGGAAGTATCATCGT 58.361 33.333 0.00 0.00 0.00 3.73
614 621 9.908152 CATAAACACATAGGAAGTATCATCGTA 57.092 33.333 0.00 0.00 0.00 3.43
615 622 9.909644 ATAAACACATAGGAAGTATCATCGTAC 57.090 33.333 0.00 0.00 0.00 3.67
616 623 6.954487 ACACATAGGAAGTATCATCGTACA 57.046 37.500 0.00 0.00 0.00 2.90
617 624 7.526142 ACACATAGGAAGTATCATCGTACAT 57.474 36.000 0.00 0.00 0.00 2.29
618 625 7.371159 ACACATAGGAAGTATCATCGTACATG 58.629 38.462 0.00 0.00 0.00 3.21
619 626 7.230712 ACACATAGGAAGTATCATCGTACATGA 59.769 37.037 0.00 9.46 0.00 3.07
620 627 8.246871 CACATAGGAAGTATCATCGTACATGAT 58.753 37.037 18.50 18.50 41.25 2.45
621 628 8.807118 ACATAGGAAGTATCATCGTACATGATT 58.193 33.333 19.23 8.34 39.30 2.57
622 629 9.080915 CATAGGAAGTATCATCGTACATGATTG 57.919 37.037 19.23 9.93 39.30 2.67
623 630 5.928839 AGGAAGTATCATCGTACATGATTGC 59.071 40.000 19.23 14.49 39.30 3.56
624 631 5.120830 GGAAGTATCATCGTACATGATTGCC 59.879 44.000 19.23 11.08 39.30 4.52
625 632 5.474578 AGTATCATCGTACATGATTGCCT 57.525 39.130 19.23 12.94 39.30 4.75
626 633 5.473931 AGTATCATCGTACATGATTGCCTC 58.526 41.667 19.23 9.94 39.30 4.70
627 634 4.613925 ATCATCGTACATGATTGCCTCT 57.386 40.909 0.00 0.00 35.39 3.69
628 635 5.728637 ATCATCGTACATGATTGCCTCTA 57.271 39.130 0.00 0.00 35.39 2.43
629 636 5.126396 TCATCGTACATGATTGCCTCTAG 57.874 43.478 0.00 0.00 0.00 2.43
630 637 4.021981 TCATCGTACATGATTGCCTCTAGG 60.022 45.833 0.00 0.00 38.53 3.02
631 638 2.628178 TCGTACATGATTGCCTCTAGGG 59.372 50.000 0.00 0.00 35.18 3.53
643 650 3.971245 CCTCTAGGGCATATCTCCAAC 57.029 52.381 0.00 0.00 0.00 3.77
644 651 3.242867 CCTCTAGGGCATATCTCCAACA 58.757 50.000 0.00 0.00 0.00 3.33
645 652 3.260380 CCTCTAGGGCATATCTCCAACAG 59.740 52.174 0.00 0.00 0.00 3.16
646 653 3.900601 CTCTAGGGCATATCTCCAACAGT 59.099 47.826 0.00 0.00 0.00 3.55
647 654 5.074746 TCTAGGGCATATCTCCAACAGTA 57.925 43.478 0.00 0.00 0.00 2.74
648 655 4.833380 TCTAGGGCATATCTCCAACAGTAC 59.167 45.833 0.00 0.00 0.00 2.73
649 656 3.384168 AGGGCATATCTCCAACAGTACA 58.616 45.455 0.00 0.00 0.00 2.90
650 657 3.134804 AGGGCATATCTCCAACAGTACAC 59.865 47.826 0.00 0.00 0.00 2.90
651 658 3.467803 GGCATATCTCCAACAGTACACC 58.532 50.000 0.00 0.00 0.00 4.16
652 659 3.467803 GCATATCTCCAACAGTACACCC 58.532 50.000 0.00 0.00 0.00 4.61
653 660 3.118408 GCATATCTCCAACAGTACACCCA 60.118 47.826 0.00 0.00 0.00 4.51
654 661 4.442706 CATATCTCCAACAGTACACCCAC 58.557 47.826 0.00 0.00 0.00 4.61
655 662 0.677288 TCTCCAACAGTACACCCACG 59.323 55.000 0.00 0.00 0.00 4.94
656 663 0.677288 CTCCAACAGTACACCCACGA 59.323 55.000 0.00 0.00 0.00 4.35
657 664 1.275291 CTCCAACAGTACACCCACGAT 59.725 52.381 0.00 0.00 0.00 3.73
658 665 2.494471 CTCCAACAGTACACCCACGATA 59.506 50.000 0.00 0.00 0.00 2.92
659 666 3.101437 TCCAACAGTACACCCACGATAT 58.899 45.455 0.00 0.00 0.00 1.63
660 667 4.279982 TCCAACAGTACACCCACGATATA 58.720 43.478 0.00 0.00 0.00 0.86
661 668 4.098349 TCCAACAGTACACCCACGATATAC 59.902 45.833 0.00 0.00 0.00 1.47
662 669 4.142116 CCAACAGTACACCCACGATATACA 60.142 45.833 0.00 0.00 0.00 2.29
663 670 5.452776 CCAACAGTACACCCACGATATACAT 60.453 44.000 0.00 0.00 0.00 2.29
664 671 5.864418 ACAGTACACCCACGATATACATT 57.136 39.130 0.00 0.00 0.00 2.71
665 672 5.839621 ACAGTACACCCACGATATACATTC 58.160 41.667 0.00 0.00 0.00 2.67
666 673 5.221382 ACAGTACACCCACGATATACATTCC 60.221 44.000 0.00 0.00 0.00 3.01
667 674 5.010719 CAGTACACCCACGATATACATTCCT 59.989 44.000 0.00 0.00 0.00 3.36
668 675 5.601313 AGTACACCCACGATATACATTCCTT 59.399 40.000 0.00 0.00 0.00 3.36
669 676 6.779049 AGTACACCCACGATATACATTCCTTA 59.221 38.462 0.00 0.00 0.00 2.69
670 677 6.488769 ACACCCACGATATACATTCCTTAA 57.511 37.500 0.00 0.00 0.00 1.85
671 678 6.891388 ACACCCACGATATACATTCCTTAAA 58.109 36.000 0.00 0.00 0.00 1.52
672 679 7.340256 ACACCCACGATATACATTCCTTAAAA 58.660 34.615 0.00 0.00 0.00 1.52
673 680 7.281549 ACACCCACGATATACATTCCTTAAAAC 59.718 37.037 0.00 0.00 0.00 2.43
674 681 7.281324 CACCCACGATATACATTCCTTAAAACA 59.719 37.037 0.00 0.00 0.00 2.83
675 682 7.497909 ACCCACGATATACATTCCTTAAAACAG 59.502 37.037 0.00 0.00 0.00 3.16
676 683 7.352739 CCACGATATACATTCCTTAAAACAGC 58.647 38.462 0.00 0.00 0.00 4.40
677 684 7.352739 CACGATATACATTCCTTAAAACAGCC 58.647 38.462 0.00 0.00 0.00 4.85
678 685 7.011950 CACGATATACATTCCTTAAAACAGCCA 59.988 37.037 0.00 0.00 0.00 4.75
679 686 7.012044 ACGATATACATTCCTTAAAACAGCCAC 59.988 37.037 0.00 0.00 0.00 5.01
680 687 5.914898 ATACATTCCTTAAAACAGCCACC 57.085 39.130 0.00 0.00 0.00 4.61
681 688 3.571590 ACATTCCTTAAAACAGCCACCA 58.428 40.909 0.00 0.00 0.00 4.17
682 689 4.159557 ACATTCCTTAAAACAGCCACCAT 58.840 39.130 0.00 0.00 0.00 3.55
683 690 5.329399 ACATTCCTTAAAACAGCCACCATA 58.671 37.500 0.00 0.00 0.00 2.74
684 691 5.185056 ACATTCCTTAAAACAGCCACCATAC 59.815 40.000 0.00 0.00 0.00 2.39
685 692 3.692690 TCCTTAAAACAGCCACCATACC 58.307 45.455 0.00 0.00 0.00 2.73
749 756 8.988060 TCTTCTACATTGAATGGGTATCTACAA 58.012 33.333 10.27 0.00 33.60 2.41
843 850 6.758806 ATACCTAACCACCTAACCCTATTG 57.241 41.667 0.00 0.00 0.00 1.90
866 873 7.539712 TGTTGCTATTGATAAGAGTGCTTAC 57.460 36.000 0.00 0.00 39.29 2.34
950 963 3.338249 CATCCTAGTGGAGTTGTTGGTG 58.662 50.000 0.00 0.00 46.91 4.17
1016 1030 9.890629 AGATTATGTAATGCTTACTCTCAAACA 57.109 29.630 7.33 0.00 37.06 2.83
1088 1102 6.043243 GGATTCTTATCTAATGACCCAGGACA 59.957 42.308 0.00 0.00 0.00 4.02
1194 1214 7.171508 GTCAGAATTCTTTCCAATTCAAAACCC 59.828 37.037 4.86 0.00 42.86 4.11
1233 1253 2.945668 GCCATTCCGAGATATATTGCCC 59.054 50.000 0.00 0.00 0.00 5.36
1234 1254 3.622206 GCCATTCCGAGATATATTGCCCA 60.622 47.826 0.00 0.00 0.00 5.36
1279 1299 9.567848 GTTTTATTATGACACGTTCCATCATTT 57.432 29.630 6.67 0.54 34.86 2.32
1292 1312 7.818930 ACGTTCCATCATTTTCATATTGCTTTT 59.181 29.630 0.00 0.00 0.00 2.27
1345 1365 4.183865 GCAAAGCCACCTTTCATAATTCC 58.816 43.478 0.00 0.00 39.20 3.01
1505 1526 2.093075 AGAGCATTGTCCCATGTGAGAG 60.093 50.000 0.00 0.00 0.00 3.20
1506 1527 1.911357 AGCATTGTCCCATGTGAGAGA 59.089 47.619 0.00 0.00 0.00 3.10
1507 1528 2.306805 AGCATTGTCCCATGTGAGAGAA 59.693 45.455 0.00 0.00 0.00 2.87
1531 1556 9.461312 GAAAAATAAATAAAAGGGAGGCCAAAT 57.539 29.630 5.01 0.00 0.00 2.32
1567 1595 4.757692 AGGAGAGAAAAAGAGAGAAGGGA 58.242 43.478 0.00 0.00 0.00 4.20
1653 1683 5.542779 AGTCTCCTATGTTGTCACTTTCAC 58.457 41.667 0.00 0.00 0.00 3.18
1759 1789 2.629656 GCAAGTTGGATGCACGCCT 61.630 57.895 4.75 0.00 43.29 5.52
1761 1791 1.164411 CAAGTTGGATGCACGCCTAA 58.836 50.000 8.72 0.08 0.00 2.69
1768 1798 3.616219 TGGATGCACGCCTAATTAGTTT 58.384 40.909 11.50 0.00 0.00 2.66
1809 1934 9.764363 CATAAACTTATAGTTCTAGTGCATCCA 57.236 33.333 0.00 0.00 37.47 3.41
1855 1980 8.098912 CACTCACATTGATATCTATTGATGGGA 58.901 37.037 3.98 6.39 34.32 4.37
1882 2007 3.118261 CCATAGCCCGTTGATATGCCTAT 60.118 47.826 2.82 0.00 0.00 2.57
1892 2017 6.017192 CCGTTGATATGCCTATTTGATGTGAA 60.017 38.462 0.00 0.00 0.00 3.18
1895 2020 7.275888 TGATATGCCTATTTGATGTGAAACC 57.724 36.000 0.00 0.00 34.36 3.27
1939 2065 6.157820 TCTCCACAACCACCATATTCTATTCA 59.842 38.462 0.00 0.00 0.00 2.57
2009 2135 4.981806 TGAAAAGGTTTGAGAACACCAG 57.018 40.909 0.00 0.00 37.51 4.00
2020 2146 7.040409 GGTTTGAGAACACCAGAAGTATGAAAT 60.040 37.037 0.00 0.00 37.51 2.17
2022 2148 6.768483 TGAGAACACCAGAAGTATGAAATGA 58.232 36.000 0.00 0.00 0.00 2.57
2023 2149 7.397221 TGAGAACACCAGAAGTATGAAATGAT 58.603 34.615 0.00 0.00 0.00 2.45
2024 2150 7.884877 TGAGAACACCAGAAGTATGAAATGATT 59.115 33.333 0.00 0.00 0.00 2.57
2091 2217 4.162888 TGTGTGATGAAGATGGAGCATAGT 59.837 41.667 0.00 0.00 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 0.105142 GGTATACTCTGGGCCCCTCA 60.105 60.000 22.27 0.00 0.00 3.86
90 91 1.202818 GGATTTTCCCCTCCGATCAGG 60.203 57.143 0.00 0.00 42.97 3.86
174 176 0.324368 ATGCTACTCCGTGACTGGGA 60.324 55.000 0.00 0.00 0.00 4.37
195 197 1.604278 GTGACAGACTTGCTTTGGGAC 59.396 52.381 0.00 0.00 0.00 4.46
196 198 1.476833 GGTGACAGACTTGCTTTGGGA 60.477 52.381 0.00 0.00 0.00 4.37
269 276 9.306777 AGCAATATGTCATCTATGAGTCTCTAA 57.693 33.333 0.65 0.00 37.51 2.10
355 362 2.043227 GGAAGGATCTGGTCGGATTCT 58.957 52.381 0.00 0.00 33.29 2.40
414 421 1.364626 CGATGGCTTGGTCTCACTGC 61.365 60.000 0.00 0.00 0.00 4.40
415 422 0.247460 TCGATGGCTTGGTCTCACTG 59.753 55.000 0.00 0.00 0.00 3.66
437 444 9.661563 GTAGTAGACTAGACTAGCATATGACAT 57.338 37.037 6.97 0.00 30.08 3.06
458 465 0.599558 GGCTGTGTGGACGTGTAGTA 59.400 55.000 0.00 0.00 0.00 1.82
459 466 1.366366 GGCTGTGTGGACGTGTAGT 59.634 57.895 0.00 0.00 0.00 2.73
462 469 2.265467 AAAGGGCTGTGTGGACGTGT 62.265 55.000 0.00 0.00 0.00 4.49
464 471 1.227853 GAAAGGGCTGTGTGGACGT 60.228 57.895 0.00 0.00 0.00 4.34
502 509 6.355747 TGGACTATGCATTGTATGATGAACA 58.644 36.000 13.85 1.69 0.00 3.18
540 547 9.783081 TTATCAATGATGTGTATCAGCAAGTAT 57.217 29.630 5.91 0.00 45.65 2.12
586 593 9.476202 CGATGATACTTCCTATGTGTTTATGAA 57.524 33.333 0.00 0.00 0.00 2.57
587 594 8.638873 ACGATGATACTTCCTATGTGTTTATGA 58.361 33.333 0.00 0.00 0.00 2.15
588 595 8.818141 ACGATGATACTTCCTATGTGTTTATG 57.182 34.615 0.00 0.00 0.00 1.90
589 596 9.909644 GTACGATGATACTTCCTATGTGTTTAT 57.090 33.333 0.00 0.00 0.00 1.40
590 597 8.905850 TGTACGATGATACTTCCTATGTGTTTA 58.094 33.333 0.00 0.00 0.00 2.01
591 598 7.778083 TGTACGATGATACTTCCTATGTGTTT 58.222 34.615 0.00 0.00 0.00 2.83
592 599 7.342769 TGTACGATGATACTTCCTATGTGTT 57.657 36.000 0.00 0.00 0.00 3.32
593 600 6.954487 TGTACGATGATACTTCCTATGTGT 57.046 37.500 0.00 0.00 0.00 3.72
594 601 7.593825 TCATGTACGATGATACTTCCTATGTG 58.406 38.462 0.00 0.00 0.00 3.21
595 602 7.761038 TCATGTACGATGATACTTCCTATGT 57.239 36.000 0.00 0.00 0.00 2.29
596 603 9.080915 CAATCATGTACGATGATACTTCCTATG 57.919 37.037 16.24 8.45 37.75 2.23
597 604 7.761704 GCAATCATGTACGATGATACTTCCTAT 59.238 37.037 16.24 2.25 37.75 2.57
598 605 7.090808 GCAATCATGTACGATGATACTTCCTA 58.909 38.462 16.24 0.00 37.75 2.94
599 606 5.928839 GCAATCATGTACGATGATACTTCCT 59.071 40.000 16.24 3.26 37.75 3.36
600 607 5.120830 GGCAATCATGTACGATGATACTTCC 59.879 44.000 16.24 12.36 37.75 3.46
601 608 5.928839 AGGCAATCATGTACGATGATACTTC 59.071 40.000 16.24 9.72 37.75 3.01
602 609 5.858381 AGGCAATCATGTACGATGATACTT 58.142 37.500 16.24 9.07 37.75 2.24
603 610 5.244851 AGAGGCAATCATGTACGATGATACT 59.755 40.000 16.24 14.66 37.75 2.12
604 611 5.473931 AGAGGCAATCATGTACGATGATAC 58.526 41.667 16.24 12.79 37.75 2.24
605 612 5.728637 AGAGGCAATCATGTACGATGATA 57.271 39.130 16.24 0.00 37.75 2.15
606 613 4.613925 AGAGGCAATCATGTACGATGAT 57.386 40.909 12.32 12.32 40.20 2.45
607 614 4.021981 CCTAGAGGCAATCATGTACGATGA 60.022 45.833 9.46 9.46 0.00 2.92
608 615 4.240888 CCTAGAGGCAATCATGTACGATG 58.759 47.826 0.00 0.00 0.00 3.84
609 616 3.259374 CCCTAGAGGCAATCATGTACGAT 59.741 47.826 0.00 0.00 0.00 3.73
610 617 2.628178 CCCTAGAGGCAATCATGTACGA 59.372 50.000 0.00 0.00 0.00 3.43
611 618 3.032017 CCCTAGAGGCAATCATGTACG 57.968 52.381 0.00 0.00 0.00 3.67
623 630 3.242867 TGTTGGAGATATGCCCTAGAGG 58.757 50.000 0.00 0.00 39.47 3.69
624 631 3.900601 ACTGTTGGAGATATGCCCTAGAG 59.099 47.826 0.00 0.00 0.00 2.43
625 632 3.928754 ACTGTTGGAGATATGCCCTAGA 58.071 45.455 0.00 0.00 0.00 2.43
626 633 4.588951 TGTACTGTTGGAGATATGCCCTAG 59.411 45.833 0.00 0.00 0.00 3.02
627 634 4.344102 GTGTACTGTTGGAGATATGCCCTA 59.656 45.833 0.00 0.00 0.00 3.53
628 635 3.134804 GTGTACTGTTGGAGATATGCCCT 59.865 47.826 0.00 0.00 0.00 5.19
629 636 3.467803 GTGTACTGTTGGAGATATGCCC 58.532 50.000 0.00 0.00 0.00 5.36
630 637 3.467803 GGTGTACTGTTGGAGATATGCC 58.532 50.000 0.00 0.00 0.00 4.40
631 638 3.118408 TGGGTGTACTGTTGGAGATATGC 60.118 47.826 0.00 0.00 0.00 3.14
632 639 4.442706 GTGGGTGTACTGTTGGAGATATG 58.557 47.826 0.00 0.00 0.00 1.78
633 640 3.132289 CGTGGGTGTACTGTTGGAGATAT 59.868 47.826 0.00 0.00 0.00 1.63
634 641 2.494471 CGTGGGTGTACTGTTGGAGATA 59.506 50.000 0.00 0.00 0.00 1.98
635 642 1.275291 CGTGGGTGTACTGTTGGAGAT 59.725 52.381 0.00 0.00 0.00 2.75
636 643 0.677288 CGTGGGTGTACTGTTGGAGA 59.323 55.000 0.00 0.00 0.00 3.71
637 644 0.677288 TCGTGGGTGTACTGTTGGAG 59.323 55.000 0.00 0.00 0.00 3.86
638 645 1.344065 ATCGTGGGTGTACTGTTGGA 58.656 50.000 0.00 0.00 0.00 3.53
639 646 3.536956 ATATCGTGGGTGTACTGTTGG 57.463 47.619 0.00 0.00 0.00 3.77
640 647 5.001237 TGTATATCGTGGGTGTACTGTTG 57.999 43.478 0.00 0.00 0.00 3.33
641 648 5.864418 ATGTATATCGTGGGTGTACTGTT 57.136 39.130 0.00 0.00 0.00 3.16
642 649 5.221382 GGAATGTATATCGTGGGTGTACTGT 60.221 44.000 0.00 0.00 0.00 3.55
643 650 5.010719 AGGAATGTATATCGTGGGTGTACTG 59.989 44.000 0.00 0.00 0.00 2.74
644 651 5.145564 AGGAATGTATATCGTGGGTGTACT 58.854 41.667 0.00 0.00 0.00 2.73
645 652 5.464030 AGGAATGTATATCGTGGGTGTAC 57.536 43.478 0.00 0.00 0.00 2.90
646 653 7.600231 TTAAGGAATGTATATCGTGGGTGTA 57.400 36.000 0.00 0.00 0.00 2.90
647 654 6.488769 TTAAGGAATGTATATCGTGGGTGT 57.511 37.500 0.00 0.00 0.00 4.16
648 655 7.281324 TGTTTTAAGGAATGTATATCGTGGGTG 59.719 37.037 0.00 0.00 0.00 4.61
649 656 7.340256 TGTTTTAAGGAATGTATATCGTGGGT 58.660 34.615 0.00 0.00 0.00 4.51
650 657 7.519970 GCTGTTTTAAGGAATGTATATCGTGGG 60.520 40.741 0.00 0.00 0.00 4.61
651 658 7.352739 GCTGTTTTAAGGAATGTATATCGTGG 58.647 38.462 0.00 0.00 0.00 4.94
652 659 7.011950 TGGCTGTTTTAAGGAATGTATATCGTG 59.988 37.037 0.00 0.00 0.00 4.35
653 660 7.012044 GTGGCTGTTTTAAGGAATGTATATCGT 59.988 37.037 0.00 0.00 0.00 3.73
654 661 7.352739 GTGGCTGTTTTAAGGAATGTATATCG 58.647 38.462 0.00 0.00 0.00 2.92
655 662 7.284489 TGGTGGCTGTTTTAAGGAATGTATATC 59.716 37.037 0.00 0.00 0.00 1.63
656 663 7.122715 TGGTGGCTGTTTTAAGGAATGTATAT 58.877 34.615 0.00 0.00 0.00 0.86
657 664 6.486056 TGGTGGCTGTTTTAAGGAATGTATA 58.514 36.000 0.00 0.00 0.00 1.47
658 665 5.329399 TGGTGGCTGTTTTAAGGAATGTAT 58.671 37.500 0.00 0.00 0.00 2.29
659 666 4.730966 TGGTGGCTGTTTTAAGGAATGTA 58.269 39.130 0.00 0.00 0.00 2.29
660 667 3.571590 TGGTGGCTGTTTTAAGGAATGT 58.428 40.909 0.00 0.00 0.00 2.71
661 668 4.806640 ATGGTGGCTGTTTTAAGGAATG 57.193 40.909 0.00 0.00 0.00 2.67
662 669 4.709886 GGTATGGTGGCTGTTTTAAGGAAT 59.290 41.667 0.00 0.00 0.00 3.01
663 670 4.083565 GGTATGGTGGCTGTTTTAAGGAA 58.916 43.478 0.00 0.00 0.00 3.36
664 671 3.332485 AGGTATGGTGGCTGTTTTAAGGA 59.668 43.478 0.00 0.00 0.00 3.36
665 672 3.697166 AGGTATGGTGGCTGTTTTAAGG 58.303 45.455 0.00 0.00 0.00 2.69
666 673 5.722021 AAAGGTATGGTGGCTGTTTTAAG 57.278 39.130 0.00 0.00 0.00 1.85
667 674 6.487299 AAAAAGGTATGGTGGCTGTTTTAA 57.513 33.333 0.00 0.00 0.00 1.52
668 675 7.784470 ATAAAAAGGTATGGTGGCTGTTTTA 57.216 32.000 0.00 0.00 0.00 1.52
669 676 6.680148 ATAAAAAGGTATGGTGGCTGTTTT 57.320 33.333 0.00 0.00 0.00 2.43
670 677 7.971368 ATATAAAAAGGTATGGTGGCTGTTT 57.029 32.000 0.00 0.00 0.00 2.83
671 678 7.971368 AATATAAAAAGGTATGGTGGCTGTT 57.029 32.000 0.00 0.00 0.00 3.16
672 679 9.077885 CATAATATAAAAAGGTATGGTGGCTGT 57.922 33.333 0.00 0.00 0.00 4.40
673 680 9.295825 TCATAATATAAAAAGGTATGGTGGCTG 57.704 33.333 0.00 0.00 0.00 4.85
674 681 9.875708 TTCATAATATAAAAAGGTATGGTGGCT 57.124 29.630 0.00 0.00 0.00 4.75
675 682 9.908152 GTTCATAATATAAAAAGGTATGGTGGC 57.092 33.333 0.00 0.00 0.00 5.01
743 750 7.611467 AGCATGATCCAAACTTATTGTTGTAGA 59.389 33.333 0.00 0.00 39.13 2.59
749 756 7.472334 AGAAAGCATGATCCAAACTTATTGT 57.528 32.000 0.00 0.00 0.00 2.71
756 763 4.336713 GGGAGTAGAAAGCATGATCCAAAC 59.663 45.833 0.00 0.00 0.00 2.93
766 773 0.324943 GTGCAGGGGAGTAGAAAGCA 59.675 55.000 0.00 0.00 0.00 3.91
767 774 0.393132 GGTGCAGGGGAGTAGAAAGC 60.393 60.000 0.00 0.00 0.00 3.51
843 850 7.778470 AGTAAGCACTCTTATCAATAGCAAC 57.222 36.000 0.00 0.00 37.16 4.17
1088 1102 1.561542 ACTCCTCGCATCCAGGATTTT 59.438 47.619 0.00 0.00 39.44 1.82
1163 1182 4.402616 TTGGAAAGAATTCTGACCCCAT 57.597 40.909 21.01 0.00 35.79 4.00
1164 1183 3.893753 TTGGAAAGAATTCTGACCCCA 57.106 42.857 21.01 16.55 35.79 4.96
1233 1253 1.068333 CGGAATGGTGGAAAGTTGCTG 60.068 52.381 0.00 0.00 0.00 4.41
1234 1254 1.247567 CGGAATGGTGGAAAGTTGCT 58.752 50.000 0.00 0.00 0.00 3.91
1345 1365 6.393171 TGACTCAAGAGTGACATGTATGAAG 58.607 40.000 7.57 0.00 42.66 3.02
1428 1448 9.530129 CTTACAACTCAAGAATTACAAATCGAC 57.470 33.333 0.00 0.00 0.00 4.20
1474 1495 6.252599 TGGGACAATGCTCTAGTAATGAAT 57.747 37.500 0.00 0.00 31.92 2.57
1505 1526 8.856153 TTTGGCCTCCCTTTTATTTATTTTTC 57.144 30.769 3.32 0.00 0.00 2.29
1531 1556 8.528044 TTTTTCTCTCCTTTTTGTTAGGCTTA 57.472 30.769 0.00 0.00 32.59 3.09
1546 1574 4.284746 TGTCCCTTCTCTCTTTTTCTCTCC 59.715 45.833 0.00 0.00 0.00 3.71
1567 1595 7.231467 AGTGTGGAAAAGGATAGTAACATTGT 58.769 34.615 0.00 0.00 0.00 2.71
1628 1658 4.442375 AAGTGACAACATAGGAGACTCG 57.558 45.455 0.00 0.00 43.67 4.18
1855 1980 5.126067 GCATATCAACGGGCTATGGATATT 58.874 41.667 0.00 0.00 30.83 1.28
1858 1983 2.356125 GGCATATCAACGGGCTATGGAT 60.356 50.000 0.00 0.00 0.00 3.41
1892 2017 6.794534 AGAAGACAAAAATAGGGAGATGGTT 58.205 36.000 0.00 0.00 0.00 3.67
1895 2020 6.317391 GTGGAGAAGACAAAAATAGGGAGATG 59.683 42.308 0.00 0.00 0.00 2.90
1939 2065 4.263068 GCCATGGACATAGCAGTATAGGTT 60.263 45.833 18.40 0.00 0.00 3.50
1947 2073 1.590932 GTGAGCCATGGACATAGCAG 58.409 55.000 18.40 0.00 0.00 4.24
2020 2146 5.066375 CCGATGACAAGCCAAGAAATAATCA 59.934 40.000 0.00 0.00 0.00 2.57
2022 2148 4.339247 CCCGATGACAAGCCAAGAAATAAT 59.661 41.667 0.00 0.00 0.00 1.28
2023 2149 3.694072 CCCGATGACAAGCCAAGAAATAA 59.306 43.478 0.00 0.00 0.00 1.40
2024 2150 3.278574 CCCGATGACAAGCCAAGAAATA 58.721 45.455 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.