Multiple sequence alignment - TraesCS5A01G241500

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 TraesCS5A01G241500 chr5A 100.000 3587 0 0 1 3587 457259915 457263501 0.000000e+00 6625
1 TraesCS5A01G241500 chr5D 97.766 1880 39 3 720 2597 355012928 355014806 0.000000e+00 3236
2 TraesCS5A01G241500 chr5D 86.078 747 74 15 2 720 404103939 404104683 0.000000e+00 776
3 TraesCS5A01G241500 chr5D 85.389 746 73 14 1 720 499408210 499407475 0.000000e+00 741
4 TraesCS5A01G241500 chr5D 84.513 749 83 16 1 722 15348556 15347814 0.000000e+00 710
5 TraesCS5A01G241500 chr2D 88.289 871 95 4 2714 3580 584225769 584226636 0.000000e+00 1037
6 TraesCS5A01G241500 chr4D 87.813 878 102 2 2714 3587 110903432 110902556 0.000000e+00 1024
7 TraesCS5A01G241500 chr4D 85.007 727 95 11 2 720 488180097 488180817 0.000000e+00 726
8 TraesCS5A01G241500 chr6D 87.472 878 104 3 2714 3587 52041291 52040416 0.000000e+00 1007
9 TraesCS5A01G241500 chr6D 85.306 735 93 10 1 724 58898782 58899512 0.000000e+00 745
10 TraesCS5A01G241500 chr6D 84.268 731 90 19 1 720 467016930 467017646 0.000000e+00 689
11 TraesCS5A01G241500 chr1D 87.215 876 104 5 2714 3585 487672892 487672021 0.000000e+00 990
12 TraesCS5A01G241500 chr7B 86.622 897 105 11 2698 3587 410895788 410894900 0.000000e+00 977
13 TraesCS5A01G241500 chr7B 88.273 631 56 14 1 615 1476726 1476098 0.000000e+00 739
14 TraesCS5A01G241500 chr7D 86.812 872 105 6 2714 3580 608403867 608404733 0.000000e+00 965
15 TraesCS5A01G241500 chr7D 87.362 633 59 15 16 631 433878110 433877482 0.000000e+00 706
16 TraesCS5A01G241500 chr3B 86.312 884 111 7 2711 3587 818893188 818894068 0.000000e+00 953
17 TraesCS5A01G241500 chr1B 86.301 876 113 4 2714 3585 647964739 647965611 0.000000e+00 946
18 TraesCS5A01G241500 chr6B 86.219 878 114 4 2714 3587 622192631 622193505 0.000000e+00 944
19 TraesCS5A01G241500 chr3A 87.865 651 57 12 1 635 81665503 81666147 0.000000e+00 745
20 TraesCS5A01G241500 chr3A 81.350 622 64 25 3 604 353189182 353188593 3.260000e-125 459


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 TraesCS5A01G241500 chr5A 457259915 457263501 3586 False 6625 6625 100.000 1 3587 1 chr5A.!!$F1 3586
1 TraesCS5A01G241500 chr5D 355012928 355014806 1878 False 3236 3236 97.766 720 2597 1 chr5D.!!$F1 1877
2 TraesCS5A01G241500 chr5D 404103939 404104683 744 False 776 776 86.078 2 720 1 chr5D.!!$F2 718
3 TraesCS5A01G241500 chr5D 499407475 499408210 735 True 741 741 85.389 1 720 1 chr5D.!!$R2 719
4 TraesCS5A01G241500 chr5D 15347814 15348556 742 True 710 710 84.513 1 722 1 chr5D.!!$R1 721
5 TraesCS5A01G241500 chr2D 584225769 584226636 867 False 1037 1037 88.289 2714 3580 1 chr2D.!!$F1 866
6 TraesCS5A01G241500 chr4D 110902556 110903432 876 True 1024 1024 87.813 2714 3587 1 chr4D.!!$R1 873
7 TraesCS5A01G241500 chr4D 488180097 488180817 720 False 726 726 85.007 2 720 1 chr4D.!!$F1 718
8 TraesCS5A01G241500 chr6D 52040416 52041291 875 True 1007 1007 87.472 2714 3587 1 chr6D.!!$R1 873
9 TraesCS5A01G241500 chr6D 58898782 58899512 730 False 745 745 85.306 1 724 1 chr6D.!!$F1 723
10 TraesCS5A01G241500 chr6D 467016930 467017646 716 False 689 689 84.268 1 720 1 chr6D.!!$F2 719
11 TraesCS5A01G241500 chr1D 487672021 487672892 871 True 990 990 87.215 2714 3585 1 chr1D.!!$R1 871
12 TraesCS5A01G241500 chr7B 410894900 410895788 888 True 977 977 86.622 2698 3587 1 chr7B.!!$R2 889
13 TraesCS5A01G241500 chr7B 1476098 1476726 628 True 739 739 88.273 1 615 1 chr7B.!!$R1 614
14 TraesCS5A01G241500 chr7D 608403867 608404733 866 False 965 965 86.812 2714 3580 1 chr7D.!!$F1 866
15 TraesCS5A01G241500 chr7D 433877482 433878110 628 True 706 706 87.362 16 631 1 chr7D.!!$R1 615
16 TraesCS5A01G241500 chr3B 818893188 818894068 880 False 953 953 86.312 2711 3587 1 chr3B.!!$F1 876
17 TraesCS5A01G241500 chr1B 647964739 647965611 872 False 946 946 86.301 2714 3585 1 chr1B.!!$F1 871
18 TraesCS5A01G241500 chr6B 622192631 622193505 874 False 944 944 86.219 2714 3587 1 chr6B.!!$F1 873
19 TraesCS5A01G241500 chr3A 81665503 81666147 644 False 745 745 87.865 1 635 1 chr3A.!!$F1 634
20 TraesCS5A01G241500 chr3A 353188593 353189182 589 True 459 459 81.350 3 604 1 chr3A.!!$R1 601

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
24 25 0.742635 TCGCACTGCAATATCGCCAA 60.743 50.0 1.11 0.0 0.0 4.52 F
1614 1675 0.331278 ATGAAGATTTGGGCGGTGGA 59.669 50.0 0.00 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1700 1761 0.390492 TTCATGGCGCTCGATGATCT 59.610 50.0 7.64 0.0 0.0 2.75 R
2636 2697 0.892755 CGCACTGGACAACTACCCTA 59.107 55.0 0.00 0.0 0.0 3.53 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
24 25 0.742635 TCGCACTGCAATATCGCCAA 60.743 50.000 1.11 0.00 0.00 4.52
57 58 3.382832 CCTCTCCAACCGCTCCGT 61.383 66.667 0.00 0.00 0.00 4.69
261 263 1.661509 CTGCTCGCACGTGAAGACA 60.662 57.895 22.23 15.21 0.00 3.41
438 441 4.849329 CCGCGGTAGCCAGACGAC 62.849 72.222 19.50 0.00 41.18 4.34
491 513 2.659610 GAGGAAGCGGCAGAGTGT 59.340 61.111 1.45 0.00 0.00 3.55
507 529 0.798776 GTGTGCAGCAAAGTAGCGAT 59.201 50.000 0.00 0.00 40.15 4.58
609 636 2.600173 CTGCCGCCTTTTTCCCCA 60.600 61.111 0.00 0.00 0.00 4.96
651 712 2.813100 CTGGAACACGGCAAAATGC 58.187 52.632 0.00 0.00 44.08 3.56
687 748 2.281002 AAAGTTTACCCCGCGCGT 60.281 55.556 29.95 13.36 0.00 6.01
723 784 2.039480 AGCTGTTGGAGATGCTCTGAAA 59.961 45.455 0.00 0.00 0.00 2.69
724 785 2.161211 GCTGTTGGAGATGCTCTGAAAC 59.839 50.000 0.00 0.00 0.00 2.78
725 786 3.405831 CTGTTGGAGATGCTCTGAAACA 58.594 45.455 0.00 0.00 32.33 2.83
726 787 3.141398 TGTTGGAGATGCTCTGAAACAC 58.859 45.455 0.00 0.00 30.21 3.32
727 788 2.479566 TGGAGATGCTCTGAAACACC 57.520 50.000 0.00 0.00 0.00 4.16
728 789 1.980765 TGGAGATGCTCTGAAACACCT 59.019 47.619 0.00 0.00 0.00 4.00
738 799 3.202906 TCTGAAACACCTTGTGTAGCAC 58.797 45.455 0.00 0.00 46.79 4.40
834 895 6.470160 CACACAGAATAAAATCGAGCTACAC 58.530 40.000 0.00 0.00 0.00 2.90
889 950 3.317149 CGGAGTACGTAATCCAGATCCAA 59.683 47.826 33.87 0.00 40.30 3.53
900 961 6.940430 AATCCAGATCCAAAATTCCAACTT 57.060 33.333 0.00 0.00 0.00 2.66
954 1015 2.223572 CGCCATCCAAGCTTACAATTCC 60.224 50.000 0.00 0.00 0.00 3.01
996 1057 7.703058 TTAATTCTGAAACCTTTCTCCCATC 57.297 36.000 0.00 0.00 38.02 3.51
1015 1076 2.823593 TCATGGGCGGATGCGTTG 60.824 61.111 8.84 1.75 44.10 4.10
1129 1190 2.033602 AACCCAGCGGCAAGTACC 59.966 61.111 1.45 0.00 0.00 3.34
1296 1357 2.047560 AAGTACTGGGCGGCGAAC 60.048 61.111 12.98 1.90 0.00 3.95
1308 1369 2.325082 GGCGAACCAACTGCACGAT 61.325 57.895 0.00 0.00 35.26 3.73
1314 1375 2.743752 CCAACTGCACGATGGCGAG 61.744 63.158 0.00 0.00 41.64 5.03
1402 1463 1.908066 GCTGTTTAAGACCACGCCCG 61.908 60.000 0.00 0.00 0.00 6.13
1437 1498 1.792949 GGCTATATCAGGTGCGTTTCG 59.207 52.381 0.00 0.00 0.00 3.46
1468 1529 5.473039 CCAAGGTTCATTTTCCTCATGTTC 58.527 41.667 0.00 0.00 33.09 3.18
1491 1552 7.311092 TCTGTAAGAAGGTCCAACTTAATCA 57.689 36.000 8.64 4.73 42.31 2.57
1614 1675 0.331278 ATGAAGATTTGGGCGGTGGA 59.669 50.000 0.00 0.00 0.00 4.02
1700 1761 2.584064 CATGTACCTCTGCCCGCA 59.416 61.111 0.00 0.00 0.00 5.69
1725 1786 0.464036 TCGAGCGCCATGAATACCTT 59.536 50.000 2.29 0.00 0.00 3.50
1742 1803 0.671781 CTTCAGTTCTCAGCACGGGG 60.672 60.000 0.00 0.00 0.00 5.73
1809 1870 1.126079 CGTGCCGTATATGGTCGAAC 58.874 55.000 18.88 0.00 33.01 3.95
2166 2227 1.803519 CTCTGCTCTCAACGACGCC 60.804 63.158 0.00 0.00 0.00 5.68
2192 2253 2.375766 GCGACACGGCTCAACTCAG 61.376 63.158 0.00 0.00 0.00 3.35
2257 2318 0.032403 TACGGTGAACCTTGGTGTCG 59.968 55.000 0.00 0.00 0.00 4.35
2381 2442 1.880027 AGAAACAACCAAGGATGTCGC 59.120 47.619 2.31 0.00 30.77 5.19
2401 2462 2.798148 CTACCAAGTCACCGTGCCCC 62.798 65.000 0.00 0.00 0.00 5.80
2418 2479 1.208776 CCCCCAAAGACTAGGGTAACG 59.791 57.143 11.02 0.00 43.89 3.18
2502 2563 3.189910 CACTGTTGGATGGACATCAAGTG 59.810 47.826 13.72 14.86 39.54 3.16
2531 2592 2.898729 ATGAACGATGGCCTCTACAG 57.101 50.000 3.32 0.00 0.00 2.74
2597 2658 9.967346 CGAGGAAAATATCTAATGTCAGTCTTA 57.033 33.333 0.00 0.00 0.00 2.10
2607 2668 8.429493 TCTAATGTCAGTCTTAATTGCTGATG 57.571 34.615 6.92 0.00 40.72 3.07
2608 2669 8.043113 TCTAATGTCAGTCTTAATTGCTGATGT 58.957 33.333 6.92 0.00 40.72 3.06
2609 2670 5.868043 TGTCAGTCTTAATTGCTGATGTG 57.132 39.130 6.92 0.00 40.72 3.21
2610 2671 5.308014 TGTCAGTCTTAATTGCTGATGTGT 58.692 37.500 6.92 0.00 40.72 3.72
2611 2672 5.179929 TGTCAGTCTTAATTGCTGATGTGTG 59.820 40.000 6.92 0.00 40.72 3.82
2612 2673 4.696877 TCAGTCTTAATTGCTGATGTGTGG 59.303 41.667 0.00 0.00 34.72 4.17
2613 2674 4.696877 CAGTCTTAATTGCTGATGTGTGGA 59.303 41.667 0.00 0.00 32.39 4.02
2614 2675 4.940046 AGTCTTAATTGCTGATGTGTGGAG 59.060 41.667 0.00 0.00 0.00 3.86
2615 2676 4.697352 GTCTTAATTGCTGATGTGTGGAGT 59.303 41.667 0.00 0.00 0.00 3.85
2616 2677 5.874810 GTCTTAATTGCTGATGTGTGGAGTA 59.125 40.000 0.00 0.00 0.00 2.59
2617 2678 6.540189 GTCTTAATTGCTGATGTGTGGAGTAT 59.460 38.462 0.00 0.00 0.00 2.12
2618 2679 6.539826 TCTTAATTGCTGATGTGTGGAGTATG 59.460 38.462 0.00 0.00 0.00 2.39
2619 2680 2.696989 TGCTGATGTGTGGAGTATGG 57.303 50.000 0.00 0.00 0.00 2.74
2620 2681 2.187100 TGCTGATGTGTGGAGTATGGA 58.813 47.619 0.00 0.00 0.00 3.41
2621 2682 2.773661 TGCTGATGTGTGGAGTATGGAT 59.226 45.455 0.00 0.00 0.00 3.41
2622 2683 3.136763 GCTGATGTGTGGAGTATGGATG 58.863 50.000 0.00 0.00 0.00 3.51
2623 2684 3.181462 GCTGATGTGTGGAGTATGGATGA 60.181 47.826 0.00 0.00 0.00 2.92
2624 2685 4.504514 GCTGATGTGTGGAGTATGGATGAT 60.505 45.833 0.00 0.00 0.00 2.45
2625 2686 4.964593 TGATGTGTGGAGTATGGATGATG 58.035 43.478 0.00 0.00 0.00 3.07
2626 2687 3.843893 TGTGTGGAGTATGGATGATGG 57.156 47.619 0.00 0.00 0.00 3.51
2627 2688 3.114606 TGTGTGGAGTATGGATGATGGT 58.885 45.455 0.00 0.00 0.00 3.55
2628 2689 3.523157 TGTGTGGAGTATGGATGATGGTT 59.477 43.478 0.00 0.00 0.00 3.67
2629 2690 4.018506 TGTGTGGAGTATGGATGATGGTTT 60.019 41.667 0.00 0.00 0.00 3.27
2630 2691 4.336433 GTGTGGAGTATGGATGATGGTTTG 59.664 45.833 0.00 0.00 0.00 2.93
2631 2692 4.227073 TGTGGAGTATGGATGATGGTTTGA 59.773 41.667 0.00 0.00 0.00 2.69
2632 2693 4.576463 GTGGAGTATGGATGATGGTTTGAC 59.424 45.833 0.00 0.00 0.00 3.18
2633 2694 4.227073 TGGAGTATGGATGATGGTTTGACA 59.773 41.667 0.00 0.00 0.00 3.58
2634 2695 4.576463 GGAGTATGGATGATGGTTTGACAC 59.424 45.833 0.00 0.00 0.00 3.67
2635 2696 5.178096 AGTATGGATGATGGTTTGACACA 57.822 39.130 0.00 0.00 0.00 3.72
2636 2697 5.759059 AGTATGGATGATGGTTTGACACAT 58.241 37.500 0.00 0.00 0.00 3.21
2637 2698 6.899089 AGTATGGATGATGGTTTGACACATA 58.101 36.000 0.00 0.00 0.00 2.29
2638 2699 6.994496 AGTATGGATGATGGTTTGACACATAG 59.006 38.462 0.00 0.00 0.00 2.23
2639 2700 4.525996 TGGATGATGGTTTGACACATAGG 58.474 43.478 0.00 0.00 0.00 2.57
2640 2701 3.885297 GGATGATGGTTTGACACATAGGG 59.115 47.826 0.00 0.00 0.00 3.53
2641 2702 4.526970 GATGATGGTTTGACACATAGGGT 58.473 43.478 0.00 0.00 0.00 4.34
2642 2703 5.397447 GGATGATGGTTTGACACATAGGGTA 60.397 44.000 0.00 0.00 0.00 3.69
2643 2704 5.097742 TGATGGTTTGACACATAGGGTAG 57.902 43.478 0.00 0.00 0.00 3.18
2644 2705 4.534500 TGATGGTTTGACACATAGGGTAGT 59.466 41.667 0.00 0.00 0.00 2.73
2645 2706 4.986054 TGGTTTGACACATAGGGTAGTT 57.014 40.909 0.00 0.00 0.00 2.24
2646 2707 4.647611 TGGTTTGACACATAGGGTAGTTG 58.352 43.478 0.00 0.00 0.00 3.16
2647 2708 4.103469 TGGTTTGACACATAGGGTAGTTGT 59.897 41.667 0.00 0.00 0.00 3.32
2648 2709 4.694037 GGTTTGACACATAGGGTAGTTGTC 59.306 45.833 0.00 0.00 0.00 3.18
2649 2710 4.546829 TTGACACATAGGGTAGTTGTCC 57.453 45.455 0.00 0.00 0.00 4.02
2650 2711 3.512496 TGACACATAGGGTAGTTGTCCA 58.488 45.455 0.00 0.00 0.00 4.02
2651 2712 3.513912 TGACACATAGGGTAGTTGTCCAG 59.486 47.826 0.00 0.00 0.00 3.86
2652 2713 3.514309 GACACATAGGGTAGTTGTCCAGT 59.486 47.826 0.00 0.00 0.00 4.00
2653 2714 3.260884 ACACATAGGGTAGTTGTCCAGTG 59.739 47.826 0.00 0.00 0.00 3.66
2654 2715 2.236395 ACATAGGGTAGTTGTCCAGTGC 59.764 50.000 0.00 0.00 0.00 4.40
2655 2716 0.892755 TAGGGTAGTTGTCCAGTGCG 59.107 55.000 0.00 0.00 0.00 5.34
2656 2717 1.375523 GGGTAGTTGTCCAGTGCGG 60.376 63.158 0.00 0.00 0.00 5.69
2657 2718 2.033194 GGTAGTTGTCCAGTGCGGC 61.033 63.158 0.00 0.00 33.14 6.53
2658 2719 2.048597 TAGTTGTCCAGTGCGGCG 60.049 61.111 0.51 0.51 33.14 6.46
2659 2720 2.566570 TAGTTGTCCAGTGCGGCGA 61.567 57.895 12.98 0.00 33.14 5.54
2660 2721 1.884075 TAGTTGTCCAGTGCGGCGAT 61.884 55.000 12.98 0.00 33.14 4.58
2661 2722 2.741985 TTGTCCAGTGCGGCGATG 60.742 61.111 12.98 5.55 33.14 3.84
2662 2723 4.758251 TGTCCAGTGCGGCGATGG 62.758 66.667 12.98 15.57 35.30 3.51
2663 2724 4.760047 GTCCAGTGCGGCGATGGT 62.760 66.667 12.98 0.00 35.51 3.55
2664 2725 4.451150 TCCAGTGCGGCGATGGTC 62.451 66.667 12.98 0.00 35.51 4.02
2674 2735 3.410516 CGATGGTCGCACGTTGCA 61.411 61.111 9.95 0.00 45.36 4.08
2675 2736 2.739704 CGATGGTCGCACGTTGCAT 61.740 57.895 9.95 0.00 45.36 3.96
2676 2737 1.226101 GATGGTCGCACGTTGCATG 60.226 57.895 9.95 0.00 45.36 4.06
2677 2738 1.911293 GATGGTCGCACGTTGCATGT 61.911 55.000 9.95 0.00 45.36 3.21
2678 2739 0.672091 ATGGTCGCACGTTGCATGTA 60.672 50.000 9.95 0.00 45.36 2.29
2679 2740 1.131826 GGTCGCACGTTGCATGTAC 59.868 57.895 9.95 0.00 45.36 2.90
2680 2741 1.131826 GTCGCACGTTGCATGTACC 59.868 57.895 9.95 0.00 45.36 3.34
2681 2742 1.005512 TCGCACGTTGCATGTACCT 60.006 52.632 9.95 0.00 45.36 3.08
2682 2743 0.244178 TCGCACGTTGCATGTACCTA 59.756 50.000 9.95 0.00 45.36 3.08
2683 2744 0.368907 CGCACGTTGCATGTACCTAC 59.631 55.000 9.95 0.00 45.36 3.18
2684 2745 1.434555 GCACGTTGCATGTACCTACA 58.565 50.000 5.30 0.00 44.26 2.74
2685 2746 1.393539 GCACGTTGCATGTACCTACAG 59.606 52.381 5.30 0.00 44.26 2.74
2686 2747 1.999735 CACGTTGCATGTACCTACAGG 59.000 52.381 0.00 0.00 39.92 4.00
2687 2748 1.066430 ACGTTGCATGTACCTACAGGG 60.066 52.381 0.00 0.00 39.92 4.45
2688 2749 1.742411 CGTTGCATGTACCTACAGGGG 60.742 57.143 0.00 0.00 39.92 4.79
2689 2750 1.280998 GTTGCATGTACCTACAGGGGT 59.719 52.381 0.00 0.00 39.92 4.95
2690 2751 1.200519 TGCATGTACCTACAGGGGTC 58.799 55.000 0.00 0.00 39.92 4.46
2691 2752 1.200519 GCATGTACCTACAGGGGTCA 58.799 55.000 0.00 0.00 39.92 4.02
2692 2753 1.768870 GCATGTACCTACAGGGGTCAT 59.231 52.381 0.00 0.00 39.92 3.06
2693 2754 2.485479 GCATGTACCTACAGGGGTCATG 60.485 54.545 17.37 17.37 41.78 3.07
2694 2755 1.874129 TGTACCTACAGGGGTCATGG 58.126 55.000 0.00 0.00 40.48 3.66
2695 2756 1.363280 TGTACCTACAGGGGTCATGGA 59.637 52.381 0.00 0.00 40.48 3.41
2696 2757 2.225675 TGTACCTACAGGGGTCATGGAA 60.226 50.000 0.00 0.00 40.48 3.53
2702 2763 3.541242 ACAGGGGTCATGGAAAAATGA 57.459 42.857 0.00 0.00 34.16 2.57
2709 2770 5.221382 GGGGTCATGGAAAAATGATGATGAG 60.221 44.000 0.00 0.00 38.76 2.90
2712 2773 6.095860 GGTCATGGAAAAATGATGATGAGACA 59.904 38.462 0.00 0.00 38.76 3.41
2744 2805 3.614092 TGAGACTACGTCGGTATTTCCT 58.386 45.455 0.00 0.00 37.67 3.36
2745 2806 4.769688 TGAGACTACGTCGGTATTTCCTA 58.230 43.478 0.00 0.00 37.67 2.94
2749 2810 6.924111 AGACTACGTCGGTATTTCCTAAAAA 58.076 36.000 0.00 0.00 37.67 1.94
2778 2839 0.599060 TGATACAACACAGCGACGGA 59.401 50.000 0.00 0.00 0.00 4.69
2779 2840 1.203758 TGATACAACACAGCGACGGAT 59.796 47.619 0.00 0.00 0.00 4.18
2782 2843 1.710013 ACAACACAGCGACGGATAAG 58.290 50.000 0.00 0.00 0.00 1.73
2784 2845 2.229543 ACAACACAGCGACGGATAAGTA 59.770 45.455 0.00 0.00 0.00 2.24
2787 2848 4.119442 ACACAGCGACGGATAAGTATTT 57.881 40.909 0.00 0.00 0.00 1.40
2790 2851 4.441415 CACAGCGACGGATAAGTATTTCTC 59.559 45.833 0.00 0.00 0.00 2.87
2874 2935 8.879759 CGATACCTACACACAAAGAACAAATAT 58.120 33.333 0.00 0.00 0.00 1.28
2901 2962 2.086869 CTCGACACGTAAGAGGGGTTA 58.913 52.381 0.00 0.00 43.62 2.85
2915 2976 2.418669 GGGGTTATCAATCCCTCCTGA 58.581 52.381 0.00 0.00 43.00 3.86
3138 3199 6.974932 TCTCTCAAGAAATAGCACATTGTC 57.025 37.500 0.00 0.00 0.00 3.18
3208 3270 7.845066 ATGATGATATCCAAGACAATGATCG 57.155 36.000 0.00 0.00 0.00 3.69
3222 3284 7.615403 AGACAATGATCGTGTATATAGGCATT 58.385 34.615 2.06 0.00 0.00 3.56
3264 3326 3.549827 CGACTCCTGCTTGCATCTACTAG 60.550 52.174 0.00 0.00 0.00 2.57
3328 3390 7.159372 AGTGTATTAAGTTCATGGAGAAACGT 58.841 34.615 0.00 0.00 38.13 3.99
3347 3409 5.961395 ACGTAGTAATGCAATAAGAACGG 57.039 39.130 13.25 1.17 41.94 4.44
3360 3422 3.401033 AAGAACGGTGACATGATGTGA 57.599 42.857 1.23 0.00 0.00 3.58
3397 3464 8.787818 TGTAGGAATAGACCCCATCTTTTTATT 58.212 33.333 0.00 0.00 39.04 1.40
3437 3504 4.684134 TGCCTTGCTGCCCCTTCC 62.684 66.667 0.00 0.00 0.00 3.46
3485 3552 2.790433 GAACCCATCACAAAGCACCTA 58.210 47.619 0.00 0.00 0.00 3.08
3529 3596 5.422012 AGATCAAGTTGACCAAACAAAACCT 59.578 36.000 7.96 0.00 41.61 3.50
3538 3606 7.747155 TGACCAAACAAAACCTAAATATCGA 57.253 32.000 0.00 0.00 0.00 3.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 0.535102 CGGAAGGCCTTGGCGATATT 60.535 55.000 26.25 0.00 0.00 1.28
68 69 4.016706 CTGGGCGGAAAGGACGGT 62.017 66.667 0.00 0.00 0.00 4.83
175 177 2.163390 CAGAGCACCATCGACAGCG 61.163 63.158 0.00 0.00 39.35 5.18
178 180 3.059099 TGCAGAGCACCATCGACA 58.941 55.556 0.00 0.00 31.71 4.35
198 200 3.371034 TCATCTTATCACGGACCAGGAA 58.629 45.455 0.00 0.00 0.00 3.36
251 253 1.340248 ACTTCCACGATGTCTTCACGT 59.660 47.619 0.00 0.00 40.87 4.49
261 263 2.481449 GGCGTAGATGAACTTCCACGAT 60.481 50.000 11.17 0.00 32.04 3.73
477 499 2.666190 TGCACACTCTGCCGCTTC 60.666 61.111 0.00 0.00 46.51 3.86
491 513 1.066929 TCTCATCGCTACTTTGCTGCA 60.067 47.619 0.00 0.00 0.00 4.41
494 516 1.800655 CGCTCTCATCGCTACTTTGCT 60.801 52.381 0.00 0.00 0.00 3.91
495 517 0.574454 CGCTCTCATCGCTACTTTGC 59.426 55.000 0.00 0.00 0.00 3.68
507 529 3.733960 ACACTACGCGCGCTCTCA 61.734 61.111 32.58 9.15 0.00 3.27
546 571 1.136690 CGAGCGCGCCTATAAATTGA 58.863 50.000 30.33 0.00 0.00 2.57
651 712 3.045492 ACTTTAACGCGCACGGGG 61.045 61.111 5.73 0.00 46.04 5.73
656 717 3.408288 AAACTTTCACTTTAACGCGCA 57.592 38.095 5.73 0.00 0.00 6.09
662 723 3.250521 CGCGGGGTAAACTTTCACTTTAA 59.749 43.478 0.00 0.00 0.00 1.52
687 748 0.657312 CAGCTGTGTCAAAAGACGCA 59.343 50.000 5.25 10.91 42.45 5.24
700 761 3.547567 GAGCATCTCCAACAGCTGT 57.452 52.632 15.25 15.25 37.48 4.40
724 785 1.069906 GCGAAAGTGCTACACAAGGTG 60.070 52.381 0.00 0.00 36.74 4.00
725 786 1.226746 GCGAAAGTGCTACACAAGGT 58.773 50.000 0.00 0.00 36.74 3.50
726 787 0.517316 GGCGAAAGTGCTACACAAGG 59.483 55.000 0.00 0.00 36.74 3.61
727 788 1.225855 TGGCGAAAGTGCTACACAAG 58.774 50.000 0.00 0.00 36.74 3.16
728 789 1.332375 GTTGGCGAAAGTGCTACACAA 59.668 47.619 0.00 0.00 36.74 3.33
738 799 1.604604 TTTCTCCCAGTTGGCGAAAG 58.395 50.000 8.74 0.00 32.84 2.62
834 895 1.079503 CGGAGGAAAAAGAAGAGGCG 58.920 55.000 0.00 0.00 0.00 5.52
889 950 7.001073 AGAAGAAGTAGCAGAAGTTGGAATTT 58.999 34.615 0.00 0.00 0.00 1.82
900 961 3.306364 GGCTGTGAAGAAGAAGTAGCAGA 60.306 47.826 0.00 0.00 0.00 4.26
954 1015 8.080417 CAGAATTAATATGCAGGGTTTGATGAG 58.920 37.037 0.00 0.00 0.00 2.90
1296 1357 2.741985 TCGCCATCGTGCAGTTGG 60.742 61.111 5.35 5.35 41.56 3.77
1437 1498 4.503910 GAAAATGAACCTTGGGCCAATAC 58.496 43.478 21.25 11.65 0.00 1.89
1468 1529 7.824289 TCATGATTAAGTTGGACCTTCTTACAG 59.176 37.037 0.00 0.00 0.00 2.74
1585 1646 4.337836 GCCCAAATCTTCATCTCCTTTCTC 59.662 45.833 0.00 0.00 0.00 2.87
1700 1761 0.390492 TTCATGGCGCTCGATGATCT 59.610 50.000 7.64 0.00 0.00 2.75
1725 1786 3.059982 CCCCGTGCTGAGAACTGA 58.940 61.111 0.00 0.00 0.00 3.41
1742 1803 1.648467 GACCAAGGCTTGATCCACGC 61.648 60.000 28.18 5.63 0.00 5.34
1753 1814 3.723348 GACGCGGTTGACCAAGGC 61.723 66.667 12.47 0.00 35.14 4.35
1809 1870 1.372087 GCCAGAATCTGCCGAAGTGG 61.372 60.000 4.40 0.00 42.50 4.00
2192 2253 0.179150 CGTGTCTCTGCACTCTAGCC 60.179 60.000 0.00 0.00 37.24 3.93
2202 2263 2.610727 GGTCCTTTTCTCCGTGTCTCTG 60.611 54.545 0.00 0.00 0.00 3.35
2257 2318 1.895707 CAGCATGGATCTTCGCCCC 60.896 63.158 0.00 0.00 0.00 5.80
2381 2442 1.375523 GGCACGGTGACTTGGTAGG 60.376 63.158 13.29 0.00 0.00 3.18
2401 2462 2.301009 ACACCGTTACCCTAGTCTTTGG 59.699 50.000 0.00 0.00 0.00 3.28
2418 2479 1.112315 TTGTTGCCACCATGGACACC 61.112 55.000 21.47 6.76 40.96 4.16
2502 2563 3.681897 GGCCATCGTTCATATCATGAGTC 59.318 47.826 0.09 0.00 40.94 3.36
2531 2592 5.905480 AAAATCGAAGCAATTTTGACCAC 57.095 34.783 0.00 0.00 35.54 4.16
2597 2658 3.949754 CCATACTCCACACATCAGCAATT 59.050 43.478 0.00 0.00 0.00 2.32
2598 2659 3.200605 TCCATACTCCACACATCAGCAAT 59.799 43.478 0.00 0.00 0.00 3.56
2599 2660 2.571202 TCCATACTCCACACATCAGCAA 59.429 45.455 0.00 0.00 0.00 3.91
2600 2661 2.187100 TCCATACTCCACACATCAGCA 58.813 47.619 0.00 0.00 0.00 4.41
2601 2662 2.988010 TCCATACTCCACACATCAGC 57.012 50.000 0.00 0.00 0.00 4.26
2602 2663 4.677673 TCATCCATACTCCACACATCAG 57.322 45.455 0.00 0.00 0.00 2.90
2603 2664 4.202388 CCATCATCCATACTCCACACATCA 60.202 45.833 0.00 0.00 0.00 3.07
2604 2665 4.202398 ACCATCATCCATACTCCACACATC 60.202 45.833 0.00 0.00 0.00 3.06
2605 2666 3.718434 ACCATCATCCATACTCCACACAT 59.282 43.478 0.00 0.00 0.00 3.21
2606 2667 3.114606 ACCATCATCCATACTCCACACA 58.885 45.455 0.00 0.00 0.00 3.72
2607 2668 3.845781 ACCATCATCCATACTCCACAC 57.154 47.619 0.00 0.00 0.00 3.82
2608 2669 4.227073 TCAAACCATCATCCATACTCCACA 59.773 41.667 0.00 0.00 0.00 4.17
2609 2670 4.576463 GTCAAACCATCATCCATACTCCAC 59.424 45.833 0.00 0.00 0.00 4.02
2610 2671 4.227073 TGTCAAACCATCATCCATACTCCA 59.773 41.667 0.00 0.00 0.00 3.86
2611 2672 4.576463 GTGTCAAACCATCATCCATACTCC 59.424 45.833 0.00 0.00 0.00 3.85
2612 2673 5.185454 TGTGTCAAACCATCATCCATACTC 58.815 41.667 0.00 0.00 0.00 2.59
2613 2674 5.178096 TGTGTCAAACCATCATCCATACT 57.822 39.130 0.00 0.00 0.00 2.12
2614 2675 6.205464 CCTATGTGTCAAACCATCATCCATAC 59.795 42.308 0.00 0.00 0.00 2.39
2615 2676 6.298361 CCTATGTGTCAAACCATCATCCATA 58.702 40.000 0.00 0.00 0.00 2.74
2616 2677 5.135383 CCTATGTGTCAAACCATCATCCAT 58.865 41.667 0.00 0.00 0.00 3.41
2617 2678 4.525996 CCTATGTGTCAAACCATCATCCA 58.474 43.478 0.00 0.00 0.00 3.41
2618 2679 3.885297 CCCTATGTGTCAAACCATCATCC 59.115 47.826 0.00 0.00 0.00 3.51
2619 2680 4.526970 ACCCTATGTGTCAAACCATCATC 58.473 43.478 0.00 0.00 0.00 2.92
2620 2681 4.591321 ACCCTATGTGTCAAACCATCAT 57.409 40.909 0.00 0.00 0.00 2.45
2621 2682 4.534500 ACTACCCTATGTGTCAAACCATCA 59.466 41.667 0.00 0.00 0.00 3.07
2622 2683 5.099042 ACTACCCTATGTGTCAAACCATC 57.901 43.478 0.00 0.00 0.00 3.51
2623 2684 5.222048 ACAACTACCCTATGTGTCAAACCAT 60.222 40.000 0.00 0.00 0.00 3.55
2624 2685 4.103469 ACAACTACCCTATGTGTCAAACCA 59.897 41.667 0.00 0.00 0.00 3.67
2625 2686 4.648651 ACAACTACCCTATGTGTCAAACC 58.351 43.478 0.00 0.00 0.00 3.27
2626 2687 4.694037 GGACAACTACCCTATGTGTCAAAC 59.306 45.833 4.67 0.00 0.00 2.93
2627 2688 4.348461 TGGACAACTACCCTATGTGTCAAA 59.652 41.667 4.67 0.00 0.00 2.69
2628 2689 3.904965 TGGACAACTACCCTATGTGTCAA 59.095 43.478 4.67 0.00 0.00 3.18
2629 2690 3.512496 TGGACAACTACCCTATGTGTCA 58.488 45.455 4.67 0.00 0.00 3.58
2630 2691 3.514309 ACTGGACAACTACCCTATGTGTC 59.486 47.826 0.00 0.00 0.00 3.67
2631 2692 3.260884 CACTGGACAACTACCCTATGTGT 59.739 47.826 0.00 0.00 0.00 3.72
2632 2693 3.861840 CACTGGACAACTACCCTATGTG 58.138 50.000 0.00 0.00 0.00 3.21
2633 2694 2.236395 GCACTGGACAACTACCCTATGT 59.764 50.000 0.00 0.00 0.00 2.29
2634 2695 2.738643 CGCACTGGACAACTACCCTATG 60.739 54.545 0.00 0.00 0.00 2.23
2635 2696 1.480954 CGCACTGGACAACTACCCTAT 59.519 52.381 0.00 0.00 0.00 2.57
2636 2697 0.892755 CGCACTGGACAACTACCCTA 59.107 55.000 0.00 0.00 0.00 3.53
2637 2698 1.671742 CGCACTGGACAACTACCCT 59.328 57.895 0.00 0.00 0.00 4.34
2638 2699 1.375523 CCGCACTGGACAACTACCC 60.376 63.158 0.00 0.00 42.00 3.69
2639 2700 2.033194 GCCGCACTGGACAACTACC 61.033 63.158 0.00 0.00 42.00 3.18
2640 2701 2.380410 CGCCGCACTGGACAACTAC 61.380 63.158 0.00 0.00 42.00 2.73
2641 2702 1.884075 ATCGCCGCACTGGACAACTA 61.884 55.000 0.00 0.00 42.00 2.24
2642 2703 3.240134 ATCGCCGCACTGGACAACT 62.240 57.895 0.00 0.00 42.00 3.16
2643 2704 2.742372 ATCGCCGCACTGGACAAC 60.742 61.111 0.00 0.00 42.00 3.32
2644 2705 2.741985 CATCGCCGCACTGGACAA 60.742 61.111 0.00 0.00 42.00 3.18
2645 2706 4.758251 CCATCGCCGCACTGGACA 62.758 66.667 2.63 0.00 42.00 4.02
2646 2707 4.760047 ACCATCGCCGCACTGGAC 62.760 66.667 13.71 0.00 42.00 4.02
2647 2708 4.451150 GACCATCGCCGCACTGGA 62.451 66.667 13.71 0.00 42.00 3.86
2664 2725 4.103976 CTGTAGGTACATGCAACGTGCG 62.104 54.545 0.00 0.00 37.91 5.34
2665 2726 1.393539 CTGTAGGTACATGCAACGTGC 59.606 52.381 0.00 0.00 36.62 5.34
2666 2727 1.999735 CCTGTAGGTACATGCAACGTG 59.000 52.381 0.00 0.00 35.36 4.49
2667 2728 1.066430 CCCTGTAGGTACATGCAACGT 60.066 52.381 0.00 0.00 35.36 3.99
2668 2729 1.651987 CCCTGTAGGTACATGCAACG 58.348 55.000 0.00 0.00 35.36 4.10
2669 2730 1.280998 ACCCCTGTAGGTACATGCAAC 59.719 52.381 0.00 0.00 38.79 4.17
2670 2731 1.557832 GACCCCTGTAGGTACATGCAA 59.442 52.381 0.00 0.00 41.42 4.08
2671 2732 1.200519 GACCCCTGTAGGTACATGCA 58.799 55.000 0.00 0.00 41.42 3.96
2672 2733 1.200519 TGACCCCTGTAGGTACATGC 58.799 55.000 0.00 0.00 41.42 4.06
2673 2734 2.104792 CCATGACCCCTGTAGGTACATG 59.895 54.545 15.61 15.61 41.42 3.21
2674 2735 2.022428 TCCATGACCCCTGTAGGTACAT 60.022 50.000 0.00 0.00 41.42 2.29
2675 2736 1.363280 TCCATGACCCCTGTAGGTACA 59.637 52.381 0.00 0.00 41.42 2.90
2676 2737 2.170012 TCCATGACCCCTGTAGGTAC 57.830 55.000 0.00 0.00 41.42 3.34
2677 2738 2.953093 TTCCATGACCCCTGTAGGTA 57.047 50.000 0.00 0.00 41.42 3.08
2678 2739 2.053747 TTTCCATGACCCCTGTAGGT 57.946 50.000 0.00 0.00 45.12 3.08
2679 2740 3.449746 TTTTTCCATGACCCCTGTAGG 57.550 47.619 0.00 0.00 0.00 3.18
2680 2741 4.599041 TCATTTTTCCATGACCCCTGTAG 58.401 43.478 0.00 0.00 0.00 2.74
2681 2742 4.666412 TCATTTTTCCATGACCCCTGTA 57.334 40.909 0.00 0.00 0.00 2.74
2682 2743 3.541242 TCATTTTTCCATGACCCCTGT 57.459 42.857 0.00 0.00 0.00 4.00
2683 2744 4.025360 TCATCATTTTTCCATGACCCCTG 58.975 43.478 0.00 0.00 35.97 4.45
2684 2745 4.335735 TCATCATTTTTCCATGACCCCT 57.664 40.909 0.00 0.00 35.97 4.79
2685 2746 4.650588 TCATCATCATTTTTCCATGACCCC 59.349 41.667 0.00 0.00 35.97 4.95
2686 2747 5.595542 TCTCATCATCATTTTTCCATGACCC 59.404 40.000 0.00 0.00 35.97 4.46
2687 2748 6.095860 TGTCTCATCATCATTTTTCCATGACC 59.904 38.462 0.00 0.00 35.97 4.02
2688 2749 7.092137 TGTCTCATCATCATTTTTCCATGAC 57.908 36.000 0.00 0.00 35.97 3.06
2689 2750 7.558444 TCATGTCTCATCATCATTTTTCCATGA 59.442 33.333 0.00 0.00 37.58 3.07
2690 2751 7.648112 GTCATGTCTCATCATCATTTTTCCATG 59.352 37.037 0.00 0.00 0.00 3.66
2691 2752 7.468220 CGTCATGTCTCATCATCATTTTTCCAT 60.468 37.037 0.00 0.00 0.00 3.41
2692 2753 6.183360 CGTCATGTCTCATCATCATTTTTCCA 60.183 38.462 0.00 0.00 0.00 3.53
2693 2754 6.183360 ACGTCATGTCTCATCATCATTTTTCC 60.183 38.462 0.00 0.00 0.00 3.13
2694 2755 6.685828 CACGTCATGTCTCATCATCATTTTTC 59.314 38.462 0.00 0.00 0.00 2.29
2695 2756 6.403964 CCACGTCATGTCTCATCATCATTTTT 60.404 38.462 0.00 0.00 0.00 1.94
2696 2757 5.065602 CCACGTCATGTCTCATCATCATTTT 59.934 40.000 0.00 0.00 0.00 1.82
2702 2763 1.483827 AGCCACGTCATGTCTCATCAT 59.516 47.619 0.00 0.00 0.00 2.45
2709 2770 1.071605 GTCTCAAGCCACGTCATGTC 58.928 55.000 0.00 0.00 0.00 3.06
2712 2773 1.135373 CGTAGTCTCAAGCCACGTCAT 60.135 52.381 0.00 0.00 0.00 3.06
2749 2810 4.702131 GCTGTGTTGTATCATCCCTTTCTT 59.298 41.667 0.00 0.00 0.00 2.52
2752 2813 3.009723 CGCTGTGTTGTATCATCCCTTT 58.990 45.455 0.00 0.00 0.00 3.11
2763 2824 1.000506 ACTTATCCGTCGCTGTGTTGT 59.999 47.619 0.00 0.00 0.00 3.32
2829 2890 8.689061 AGGTATCGTTTACATAGTGTTACATGA 58.311 33.333 0.00 0.00 0.00 3.07
2834 2895 8.955388 TGTGTAGGTATCGTTTACATAGTGTTA 58.045 33.333 0.00 0.00 30.79 2.41
2874 2935 3.551454 CCTCTTACGTGTCGAGTTGGAAA 60.551 47.826 0.00 0.00 0.00 3.13
2877 2938 1.402456 CCCTCTTACGTGTCGAGTTGG 60.402 57.143 0.00 0.00 0.00 3.77
2901 2962 6.838401 ATCTTTTACTCAGGAGGGATTGAT 57.162 37.500 0.83 0.00 0.00 2.57
3105 3166 3.601443 TTCTTGAGAGAAGCCACTAGC 57.399 47.619 0.00 0.00 36.99 3.42
3208 3270 9.672673 AATCTTGGATGTAATGCCTATATACAC 57.327 33.333 0.00 0.00 31.31 2.90
3222 3284 6.363065 AGTCGGTCTACTAATCTTGGATGTA 58.637 40.000 0.00 0.00 0.00 2.29
3264 3326 3.369385 CGGTCGATGTGTGGAGTAATAC 58.631 50.000 0.00 0.00 0.00 1.89
3328 3390 6.399743 TGTCACCGTTCTTATTGCATTACTA 58.600 36.000 0.00 0.00 0.00 1.82
3347 3409 4.696877 TGGATCTTGTTCACATCATGTCAC 59.303 41.667 0.00 0.00 0.00 3.67
3360 3422 6.183361 GGGTCTATTCCTACATGGATCTTGTT 60.183 42.308 0.00 0.00 45.68 2.83
3397 3464 8.783093 GGCACACATGTATTATTGCTATTAAGA 58.217 33.333 0.00 0.00 0.00 2.10
3410 3477 1.203052 GCAGCAAGGCACACATGTATT 59.797 47.619 0.00 0.00 0.00 1.89
3437 3504 1.402456 CGGTGTCCTTTCCTAGTGACG 60.402 57.143 0.00 0.00 30.88 4.35
3485 3552 8.945195 TGATCTATTTATCTTGCAATGGGAAT 57.055 30.769 0.00 1.79 0.00 3.01
3516 3583 8.398878 TCTTCGATATTTAGGTTTTGTTTGGT 57.601 30.769 0.00 0.00 0.00 3.67
3529 3596 8.358148 AGCCTCGTATTTCTTCTTCGATATTTA 58.642 33.333 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.