Multiple sequence alignment - TraesCS5D01G376700

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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 TraesCS5D01G376700 chr5D 100.000 2273 0 0 1 2273 449148343 449150615 0.000000e+00 4198.0
1 TraesCS5D01G376700 chr5D 96.252 587 22 0 1 587 390190784 390190198 0.000000e+00 963.0
2 TraesCS5D01G376700 chr5D 96.404 584 21 0 1 584 539093546 539094129 0.000000e+00 963.0
3 TraesCS5D01G376700 chr5D 99.029 206 2 0 586 791 463831067 463830862 9.920000e-99 370.0
4 TraesCS5D01G376700 chr7B 98.957 1438 14 1 836 2273 662733729 662735165 0.000000e+00 2571.0
5 TraesCS5D01G376700 chr7B 97.708 1440 30 2 836 2273 90404149 90402711 0.000000e+00 2473.0
6 TraesCS5D01G376700 chrUn 98.750 1440 16 1 836 2273 351215174 351213735 0.000000e+00 2558.0
7 TraesCS5D01G376700 chr3B 98.748 1438 18 0 836 2273 201564566 201563129 0.000000e+00 2556.0
8 TraesCS5D01G376700 chr1D 98.748 1438 17 1 836 2273 254532413 254533849 0.000000e+00 2555.0
9 TraesCS5D01G376700 chr1D 96.082 587 23 0 1 587 236615219 236614633 0.000000e+00 957.0
10 TraesCS5D01G376700 chr1D 99.517 207 1 0 585 791 154824146 154823940 5.930000e-101 377.0
11 TraesCS5D01G376700 chr3A 98.541 1439 18 3 836 2273 672882213 672880777 0.000000e+00 2538.0
12 TraesCS5D01G376700 chr3A 98.790 1405 17 0 836 2240 695637215 695638619 0.000000e+00 2501.0
13 TraesCS5D01G376700 chr6B 98.406 1443 17 3 836 2273 615600790 615599349 0.000000e+00 2532.0
14 TraesCS5D01G376700 chr1B 98.124 1439 24 3 836 2273 633732655 633731219 0.000000e+00 2505.0
15 TraesCS5D01G376700 chr3D 96.934 587 18 0 1 587 546555781 546556367 0.000000e+00 985.0
16 TraesCS5D01G376700 chr3D 96.252 587 22 0 1 587 536685983 536685397 0.000000e+00 963.0
17 TraesCS5D01G376700 chr3D 99.029 206 2 0 586 791 483839372 483839167 9.920000e-99 370.0
18 TraesCS5D01G376700 chr2D 96.747 584 18 1 1 584 136314943 136315525 0.000000e+00 972.0
19 TraesCS5D01G376700 chr2D 96.233 584 21 1 1 584 96810617 96811199 0.000000e+00 955.0
20 TraesCS5D01G376700 chr7D 96.422 587 21 0 1 587 182660578 182659992 0.000000e+00 968.0
21 TraesCS5D01G376700 chr7D 99.515 206 1 0 586 791 51775165 51774960 2.130000e-100 375.0
22 TraesCS5D01G376700 chr7D 99.034 207 1 1 585 791 111559382 111559177 9.920000e-99 370.0
23 TraesCS5D01G376700 chr7D 87.778 90 7 4 569 656 69562019 69562106 3.990000e-18 102.0
24 TraesCS5D01G376700 chr6D 95.911 587 24 0 1 587 88229181 88228595 0.000000e+00 952.0
25 TraesCS5D01G376700 chr6D 86.420 81 7 3 562 639 463750039 463750118 4.020000e-13 86.1
26 TraesCS5D01G376700 chr4D 99.038 208 2 0 584 791 2149187 2148980 7.670000e-100 374.0
27 TraesCS5D01G376700 chr4D 99.034 207 2 0 585 791 254503647 254503853 2.760000e-99 372.0
28 TraesCS5D01G376700 chr4D 99.029 206 2 0 586 791 262069440 262069235 9.920000e-99 370.0
29 TraesCS5D01G376700 chr4D 98.551 207 3 0 585 791 178140104 178140310 1.280000e-97 366.0
30 TraesCS5D01G376700 chr2A 92.925 212 8 4 575 780 578110182 578109972 3.670000e-78 302.0
31 TraesCS5D01G376700 chr4A 81.166 223 30 12 567 779 31849392 31849612 3.880000e-38 169.0
32 TraesCS5D01G376700 chr5A 89.381 113 9 3 582 692 156376533 156376422 3.040000e-29 139.0


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 TraesCS5D01G376700 chr5D 449148343 449150615 2272 False 4198 4198 100.000 1 2273 1 chr5D.!!$F1 2272
1 TraesCS5D01G376700 chr5D 390190198 390190784 586 True 963 963 96.252 1 587 1 chr5D.!!$R1 586
2 TraesCS5D01G376700 chr5D 539093546 539094129 583 False 963 963 96.404 1 584 1 chr5D.!!$F2 583
3 TraesCS5D01G376700 chr7B 662733729 662735165 1436 False 2571 2571 98.957 836 2273 1 chr7B.!!$F1 1437
4 TraesCS5D01G376700 chr7B 90402711 90404149 1438 True 2473 2473 97.708 836 2273 1 chr7B.!!$R1 1437
5 TraesCS5D01G376700 chrUn 351213735 351215174 1439 True 2558 2558 98.750 836 2273 1 chrUn.!!$R1 1437
6 TraesCS5D01G376700 chr3B 201563129 201564566 1437 True 2556 2556 98.748 836 2273 1 chr3B.!!$R1 1437
7 TraesCS5D01G376700 chr1D 254532413 254533849 1436 False 2555 2555 98.748 836 2273 1 chr1D.!!$F1 1437
8 TraesCS5D01G376700 chr1D 236614633 236615219 586 True 957 957 96.082 1 587 1 chr1D.!!$R2 586
9 TraesCS5D01G376700 chr3A 672880777 672882213 1436 True 2538 2538 98.541 836 2273 1 chr3A.!!$R1 1437
10 TraesCS5D01G376700 chr3A 695637215 695638619 1404 False 2501 2501 98.790 836 2240 1 chr3A.!!$F1 1404
11 TraesCS5D01G376700 chr6B 615599349 615600790 1441 True 2532 2532 98.406 836 2273 1 chr6B.!!$R1 1437
12 TraesCS5D01G376700 chr1B 633731219 633732655 1436 True 2505 2505 98.124 836 2273 1 chr1B.!!$R1 1437
13 TraesCS5D01G376700 chr3D 546555781 546556367 586 False 985 985 96.934 1 587 1 chr3D.!!$F1 586
14 TraesCS5D01G376700 chr3D 536685397 536685983 586 True 963 963 96.252 1 587 1 chr3D.!!$R2 586
15 TraesCS5D01G376700 chr2D 136314943 136315525 582 False 972 972 96.747 1 584 1 chr2D.!!$F2 583
16 TraesCS5D01G376700 chr2D 96810617 96811199 582 False 955 955 96.233 1 584 1 chr2D.!!$F1 583
17 TraesCS5D01G376700 chr7D 182659992 182660578 586 True 968 968 96.422 1 587 1 chr7D.!!$R3 586
18 TraesCS5D01G376700 chr6D 88228595 88229181 586 True 952 952 95.911 1 587 1 chr6D.!!$R1 586

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
793 795 0.396811 GCGCACCAGGGGATAGTATT 59.603 55.0 0.3 0.0 0.0 1.89 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2202 2214 5.188163 TCCCTCATTTCACCAATTCGTACTA 59.812 40.0 0.0 0.0 0.0 1.82 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
53 54 7.901029 ACATATGTCTCGGTTATTGATCTCAT 58.099 34.615 1.41 0.00 0.00 2.90
180 182 0.762842 GGCCCCCTGACAAAGGTTTT 60.763 55.000 0.00 0.00 45.78 2.43
285 287 1.682451 CCCGGTTATCCTCCTTCGCA 61.682 60.000 0.00 0.00 0.00 5.10
302 304 0.548510 GCAGAGGCACTAATTCCCCT 59.451 55.000 0.00 0.00 41.55 4.79
587 589 1.537202 GATTGCAGTTCAGACCCACAC 59.463 52.381 0.00 0.00 0.00 3.82
588 590 0.546122 TTGCAGTTCAGACCCACACT 59.454 50.000 0.00 0.00 0.00 3.55
589 591 1.419381 TGCAGTTCAGACCCACACTA 58.581 50.000 0.00 0.00 0.00 2.74
590 592 1.070134 TGCAGTTCAGACCCACACTAC 59.930 52.381 0.00 0.00 0.00 2.73
591 593 1.344763 GCAGTTCAGACCCACACTACT 59.655 52.381 0.00 0.00 0.00 2.57
592 594 2.561419 GCAGTTCAGACCCACACTACTA 59.439 50.000 0.00 0.00 0.00 1.82
593 595 3.367498 GCAGTTCAGACCCACACTACTAG 60.367 52.174 0.00 0.00 0.00 2.57
594 596 3.193691 CAGTTCAGACCCACACTACTAGG 59.806 52.174 0.00 0.00 0.00 3.02
595 597 3.075582 AGTTCAGACCCACACTACTAGGA 59.924 47.826 0.00 0.00 0.00 2.94
596 598 3.820195 TCAGACCCACACTACTAGGAA 57.180 47.619 0.00 0.00 0.00 3.36
597 599 4.122337 TCAGACCCACACTACTAGGAAA 57.878 45.455 0.00 0.00 0.00 3.13
598 600 4.485875 TCAGACCCACACTACTAGGAAAA 58.514 43.478 0.00 0.00 0.00 2.29
599 601 4.527038 TCAGACCCACACTACTAGGAAAAG 59.473 45.833 0.00 0.00 0.00 2.27
600 602 3.838903 AGACCCACACTACTAGGAAAAGG 59.161 47.826 0.00 0.00 0.00 3.11
601 603 2.910977 ACCCACACTACTAGGAAAAGGG 59.089 50.000 0.00 0.00 39.66 3.95
602 604 2.355818 CCCACACTACTAGGAAAAGGGC 60.356 54.545 0.00 0.00 0.00 5.19
603 605 2.572104 CCACACTACTAGGAAAAGGGCT 59.428 50.000 0.00 0.00 0.00 5.19
604 606 3.773119 CCACACTACTAGGAAAAGGGCTA 59.227 47.826 0.00 0.00 0.00 3.93
605 607 4.409247 CCACACTACTAGGAAAAGGGCTAT 59.591 45.833 0.00 0.00 0.00 2.97
606 608 5.601313 CCACACTACTAGGAAAAGGGCTATA 59.399 44.000 0.00 0.00 0.00 1.31
607 609 6.239345 CCACACTACTAGGAAAAGGGCTATAG 60.239 46.154 0.00 0.00 0.00 1.31
608 610 6.550108 CACACTACTAGGAAAAGGGCTATAGA 59.450 42.308 3.21 0.00 0.00 1.98
609 611 7.233757 CACACTACTAGGAAAAGGGCTATAGAT 59.766 40.741 3.21 0.00 0.00 1.98
610 612 8.454494 ACACTACTAGGAAAAGGGCTATAGATA 58.546 37.037 3.21 0.00 0.00 1.98
611 613 9.310449 CACTACTAGGAAAAGGGCTATAGATAA 57.690 37.037 3.21 0.00 0.00 1.75
616 618 9.454859 CTAGGAAAAGGGCTATAGATAATTTGG 57.545 37.037 3.21 0.00 0.00 3.28
617 619 8.057246 AGGAAAAGGGCTATAGATAATTTGGA 57.943 34.615 3.21 0.00 0.00 3.53
618 620 7.945109 AGGAAAAGGGCTATAGATAATTTGGAC 59.055 37.037 3.21 0.00 0.00 4.02
619 621 7.724061 GGAAAAGGGCTATAGATAATTTGGACA 59.276 37.037 3.21 0.00 0.00 4.02
620 622 8.465273 AAAAGGGCTATAGATAATTTGGACAC 57.535 34.615 3.21 0.00 0.00 3.67
621 623 7.394144 AAGGGCTATAGATAATTTGGACACT 57.606 36.000 3.21 0.00 0.00 3.55
622 624 8.506196 AAGGGCTATAGATAATTTGGACACTA 57.494 34.615 3.21 0.00 0.00 2.74
623 625 8.506196 AGGGCTATAGATAATTTGGACACTAA 57.494 34.615 3.21 0.00 0.00 2.24
624 626 9.117223 AGGGCTATAGATAATTTGGACACTAAT 57.883 33.333 3.21 0.00 0.00 1.73
625 627 9.167311 GGGCTATAGATAATTTGGACACTAATG 57.833 37.037 3.21 0.00 0.00 1.90
626 628 9.167311 GGCTATAGATAATTTGGACACTAATGG 57.833 37.037 3.21 0.00 0.00 3.16
627 629 8.669243 GCTATAGATAATTTGGACACTAATGGC 58.331 37.037 3.21 0.00 0.00 4.40
628 630 7.672983 ATAGATAATTTGGACACTAATGGCG 57.327 36.000 0.00 0.00 32.81 5.69
629 631 2.939460 AATTTGGACACTAATGGCGC 57.061 45.000 0.00 0.00 32.81 6.53
630 632 1.832883 ATTTGGACACTAATGGCGCA 58.167 45.000 10.83 0.00 32.81 6.09
631 633 0.878416 TTTGGACACTAATGGCGCAC 59.122 50.000 10.83 0.00 32.81 5.34
632 634 0.958382 TTGGACACTAATGGCGCACC 60.958 55.000 10.83 0.00 32.81 5.01
641 643 3.285982 TGGCGCACCACACATGTG 61.286 61.111 24.25 24.25 42.67 3.21
660 662 3.928727 TGGTGCGCCACTACTATATAC 57.071 47.619 16.89 0.00 40.46 1.47
661 663 3.493334 TGGTGCGCCACTACTATATACT 58.507 45.455 16.89 0.00 40.46 2.12
662 664 4.654915 TGGTGCGCCACTACTATATACTA 58.345 43.478 16.89 0.00 40.46 1.82
663 665 5.072055 TGGTGCGCCACTACTATATACTAA 58.928 41.667 16.89 0.00 40.46 2.24
664 666 5.713389 TGGTGCGCCACTACTATATACTAAT 59.287 40.000 16.89 0.00 40.46 1.73
665 667 6.034591 GGTGCGCCACTACTATATACTAATG 58.965 44.000 12.58 0.00 34.40 1.90
666 668 6.034591 GTGCGCCACTACTATATACTAATGG 58.965 44.000 4.18 0.00 0.00 3.16
667 669 5.041940 GCGCCACTACTATATACTAATGGC 58.958 45.833 10.25 10.25 46.34 4.40
669 671 5.041940 GCCACTACTATATACTAATGGCGC 58.958 45.833 0.00 0.00 41.74 6.53
670 672 5.393787 GCCACTACTATATACTAATGGCGCA 60.394 44.000 10.83 0.00 41.74 6.09
671 673 6.034591 CCACTACTATATACTAATGGCGCAC 58.965 44.000 10.83 0.00 0.00 5.34
672 674 6.034591 CACTACTATATACTAATGGCGCACC 58.965 44.000 10.83 0.00 0.00 5.01
688 690 4.388229 CCATGTGTTGGTACGCCA 57.612 55.556 0.00 0.00 44.38 5.69
689 691 2.866872 CCATGTGTTGGTACGCCAT 58.133 52.632 0.00 0.00 45.56 4.40
690 692 1.173043 CCATGTGTTGGTACGCCATT 58.827 50.000 0.00 0.00 45.56 3.16
691 693 2.360844 CCATGTGTTGGTACGCCATTA 58.639 47.619 0.00 0.00 45.56 1.90
692 694 2.354510 CCATGTGTTGGTACGCCATTAG 59.645 50.000 0.00 0.00 45.56 1.73
693 695 2.843401 TGTGTTGGTACGCCATTAGT 57.157 45.000 0.00 0.00 45.56 2.24
694 696 2.418692 TGTGTTGGTACGCCATTAGTG 58.581 47.619 0.00 0.00 45.56 2.74
695 697 2.224329 TGTGTTGGTACGCCATTAGTGT 60.224 45.455 0.00 0.00 45.56 3.55
696 698 2.414138 GTGTTGGTACGCCATTAGTGTC 59.586 50.000 0.00 0.00 45.56 3.67
697 699 2.004733 GTTGGTACGCCATTAGTGTCC 58.995 52.381 0.00 0.00 45.56 4.02
698 700 1.268066 TGGTACGCCATTAGTGTCCA 58.732 50.000 0.00 0.00 40.46 4.02
699 701 1.624312 TGGTACGCCATTAGTGTCCAA 59.376 47.619 0.00 0.00 40.46 3.53
700 702 2.038689 TGGTACGCCATTAGTGTCCAAA 59.961 45.455 0.00 0.00 40.46 3.28
701 703 3.275999 GGTACGCCATTAGTGTCCAAAT 58.724 45.455 0.00 0.00 40.51 2.32
702 704 4.081031 TGGTACGCCATTAGTGTCCAAATA 60.081 41.667 0.00 0.00 40.46 1.40
703 705 4.271776 GGTACGCCATTAGTGTCCAAATAC 59.728 45.833 0.00 0.00 40.51 1.89
704 706 4.216411 ACGCCATTAGTGTCCAAATACT 57.784 40.909 0.00 0.00 32.22 2.12
705 707 5.347620 ACGCCATTAGTGTCCAAATACTA 57.652 39.130 0.00 0.00 32.22 1.82
706 708 5.736813 ACGCCATTAGTGTCCAAATACTAA 58.263 37.500 0.00 0.00 41.50 2.24
707 709 6.354130 ACGCCATTAGTGTCCAAATACTAAT 58.646 36.000 0.00 0.00 45.40 1.73
711 713 6.861065 ATTAGTGTCCAAATACTAATGGCG 57.139 37.500 8.38 0.00 43.86 5.69
712 714 2.943033 AGTGTCCAAATACTAATGGCGC 59.057 45.455 0.00 0.00 36.62 6.53
713 715 2.680841 GTGTCCAAATACTAATGGCGCA 59.319 45.455 10.83 0.00 36.62 6.09
714 716 2.680841 TGTCCAAATACTAATGGCGCAC 59.319 45.455 10.83 0.00 36.62 5.34
715 717 2.032924 GTCCAAATACTAATGGCGCACC 59.967 50.000 10.83 0.00 36.62 5.01
729 731 3.422303 CACCACATCCACGGTGCG 61.422 66.667 1.68 0.00 45.77 5.34
735 737 3.387091 ATCCACGGTGCGCCACTA 61.387 61.111 18.18 0.00 34.40 2.74
736 738 3.659089 ATCCACGGTGCGCCACTAC 62.659 63.158 18.18 0.00 34.40 2.73
737 739 4.373116 CCACGGTGCGCCACTACT 62.373 66.667 18.18 0.00 34.40 2.57
738 740 2.569657 CACGGTGCGCCACTACTA 59.430 61.111 18.18 0.00 34.40 1.82
739 741 1.080366 CACGGTGCGCCACTACTAA 60.080 57.895 18.18 0.00 34.40 2.24
740 742 1.080298 ACGGTGCGCCACTACTAAC 60.080 57.895 18.18 0.00 34.40 2.34
741 743 1.080366 CGGTGCGCCACTACTAACA 60.080 57.895 18.18 0.00 34.40 2.41
742 744 0.668096 CGGTGCGCCACTACTAACAA 60.668 55.000 18.18 0.00 34.40 2.83
743 745 1.734163 GGTGCGCCACTACTAACAAT 58.266 50.000 12.58 0.00 34.40 2.71
744 746 2.081462 GGTGCGCCACTACTAACAATT 58.919 47.619 12.58 0.00 34.40 2.32
745 747 2.486592 GGTGCGCCACTACTAACAATTT 59.513 45.455 12.58 0.00 34.40 1.82
746 748 3.057806 GGTGCGCCACTACTAACAATTTT 60.058 43.478 12.58 0.00 34.40 1.82
747 749 4.542735 GTGCGCCACTACTAACAATTTTT 58.457 39.130 4.18 0.00 0.00 1.94
778 780 5.440234 TTTTCAAAACTAGTAATGGCGCA 57.560 34.783 10.83 0.00 0.00 6.09
779 781 4.413495 TTCAAAACTAGTAATGGCGCAC 57.587 40.909 10.83 0.00 0.00 5.34
780 782 2.745281 TCAAAACTAGTAATGGCGCACC 59.255 45.455 10.83 0.00 0.00 5.01
789 791 3.479203 TGGCGCACCAGGGGATAG 61.479 66.667 10.83 0.00 42.67 2.08
790 792 3.480133 GGCGCACCAGGGGATAGT 61.480 66.667 10.83 0.00 35.26 2.12
791 793 2.138179 GGCGCACCAGGGGATAGTA 61.138 63.158 10.83 0.00 35.26 1.82
792 794 1.481056 GGCGCACCAGGGGATAGTAT 61.481 60.000 10.83 0.00 35.26 2.12
793 795 0.396811 GCGCACCAGGGGATAGTATT 59.603 55.000 0.30 0.00 0.00 1.89
794 796 1.202770 GCGCACCAGGGGATAGTATTT 60.203 52.381 0.30 0.00 0.00 1.40
795 797 2.748465 GCGCACCAGGGGATAGTATTTT 60.748 50.000 0.30 0.00 0.00 1.82
796 798 3.139077 CGCACCAGGGGATAGTATTTTC 58.861 50.000 0.00 0.00 0.00 2.29
797 799 3.487372 GCACCAGGGGATAGTATTTTCC 58.513 50.000 0.00 0.00 0.00 3.13
798 800 3.117663 GCACCAGGGGATAGTATTTTCCA 60.118 47.826 0.00 0.00 33.43 3.53
799 801 4.630184 GCACCAGGGGATAGTATTTTCCAA 60.630 45.833 0.00 0.00 33.43 3.53
800 802 5.515106 CACCAGGGGATAGTATTTTCCAAA 58.485 41.667 0.00 0.00 33.43 3.28
801 803 5.359860 CACCAGGGGATAGTATTTTCCAAAC 59.640 44.000 0.00 0.00 33.43 2.93
802 804 5.255443 ACCAGGGGATAGTATTTTCCAAACT 59.745 40.000 0.00 0.00 33.43 2.66
803 805 6.449041 ACCAGGGGATAGTATTTTCCAAACTA 59.551 38.462 0.00 0.00 33.43 2.24
804 806 7.036425 ACCAGGGGATAGTATTTTCCAAACTAA 60.036 37.037 0.00 0.00 33.43 2.24
805 807 8.004801 CCAGGGGATAGTATTTTCCAAACTAAT 58.995 37.037 0.00 0.00 33.43 1.73
833 835 9.683069 AATCATGACTTCAAACAAATTAGTGTC 57.317 29.630 0.00 0.00 0.00 3.67
834 836 7.648142 TCATGACTTCAAACAAATTAGTGTCC 58.352 34.615 0.00 0.00 0.00 4.02
1804 1809 2.583593 GATCTCGGCGCACAGACC 60.584 66.667 10.83 0.00 0.00 3.85
2102 2112 2.223829 CCGATGTTACGAGCTTCTGGAT 60.224 50.000 0.00 0.00 35.09 3.41
2202 2214 3.391049 GGGATTCGTTAGCTCGCTATTT 58.609 45.455 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 6.755461 GACATATGTCTTGTAGTTCGGATG 57.245 41.667 25.52 0.00 41.65 3.51
180 182 6.245890 ACAATGGTTTTCAAATGAGGGAAA 57.754 33.333 0.00 0.00 0.00 3.13
285 287 3.423058 ACTAGGGGAATTAGTGCCTCT 57.577 47.619 0.00 0.00 37.99 3.69
302 304 6.767902 GCCTCACTCATTATTCATCCAAACTA 59.232 38.462 0.00 0.00 0.00 2.24
590 592 9.454859 CCAAATTATCTATAGCCCTTTTCCTAG 57.545 37.037 0.00 0.00 0.00 3.02
591 593 9.177927 TCCAAATTATCTATAGCCCTTTTCCTA 57.822 33.333 0.00 0.00 0.00 2.94
592 594 7.945109 GTCCAAATTATCTATAGCCCTTTTCCT 59.055 37.037 0.00 0.00 0.00 3.36
593 595 7.724061 TGTCCAAATTATCTATAGCCCTTTTCC 59.276 37.037 0.00 0.00 0.00 3.13
594 596 8.568794 GTGTCCAAATTATCTATAGCCCTTTTC 58.431 37.037 0.00 0.00 0.00 2.29
595 597 8.282256 AGTGTCCAAATTATCTATAGCCCTTTT 58.718 33.333 0.00 0.00 0.00 2.27
596 598 7.816411 AGTGTCCAAATTATCTATAGCCCTTT 58.184 34.615 0.00 0.00 0.00 3.11
597 599 7.394144 AGTGTCCAAATTATCTATAGCCCTT 57.606 36.000 0.00 0.00 0.00 3.95
598 600 8.506196 TTAGTGTCCAAATTATCTATAGCCCT 57.494 34.615 0.00 0.00 0.00 5.19
599 601 9.167311 CATTAGTGTCCAAATTATCTATAGCCC 57.833 37.037 0.00 0.00 0.00 5.19
600 602 9.167311 CCATTAGTGTCCAAATTATCTATAGCC 57.833 37.037 0.00 0.00 0.00 3.93
601 603 8.669243 GCCATTAGTGTCCAAATTATCTATAGC 58.331 37.037 0.00 0.00 0.00 2.97
602 604 8.873830 CGCCATTAGTGTCCAAATTATCTATAG 58.126 37.037 0.00 0.00 0.00 1.31
603 605 7.333423 GCGCCATTAGTGTCCAAATTATCTATA 59.667 37.037 0.00 0.00 0.00 1.31
604 606 6.149474 GCGCCATTAGTGTCCAAATTATCTAT 59.851 38.462 0.00 0.00 0.00 1.98
605 607 5.468746 GCGCCATTAGTGTCCAAATTATCTA 59.531 40.000 0.00 0.00 0.00 1.98
606 608 4.275936 GCGCCATTAGTGTCCAAATTATCT 59.724 41.667 0.00 0.00 0.00 1.98
607 609 4.036262 TGCGCCATTAGTGTCCAAATTATC 59.964 41.667 4.18 0.00 0.00 1.75
608 610 3.951037 TGCGCCATTAGTGTCCAAATTAT 59.049 39.130 4.18 0.00 0.00 1.28
609 611 3.127895 GTGCGCCATTAGTGTCCAAATTA 59.872 43.478 4.18 0.00 0.00 1.40
610 612 2.094752 GTGCGCCATTAGTGTCCAAATT 60.095 45.455 4.18 0.00 0.00 1.82
611 613 1.472480 GTGCGCCATTAGTGTCCAAAT 59.528 47.619 4.18 0.00 0.00 2.32
612 614 0.878416 GTGCGCCATTAGTGTCCAAA 59.122 50.000 4.18 0.00 0.00 3.28
613 615 0.958382 GGTGCGCCATTAGTGTCCAA 60.958 55.000 12.58 0.00 34.09 3.53
614 616 1.376683 GGTGCGCCATTAGTGTCCA 60.377 57.895 12.58 0.00 34.09 4.02
615 617 1.376683 TGGTGCGCCATTAGTGTCC 60.377 57.895 16.89 0.00 40.46 4.02
616 618 4.294523 TGGTGCGCCATTAGTGTC 57.705 55.556 16.89 0.00 40.46 3.67
624 626 3.285982 CACATGTGTGGTGCGCCA 61.286 61.111 16.89 16.89 42.10 5.69
640 642 3.493334 AGTATATAGTAGTGGCGCACCA 58.507 45.455 10.83 0.00 46.51 4.17
641 643 5.633830 TTAGTATATAGTAGTGGCGCACC 57.366 43.478 10.83 0.00 34.49 5.01
642 644 6.034591 CCATTAGTATATAGTAGTGGCGCAC 58.965 44.000 20.32 5.73 33.88 5.34
643 645 6.203808 CCATTAGTATATAGTAGTGGCGCA 57.796 41.667 20.32 0.00 33.88 6.09
647 649 6.034591 GTGCGCCATTAGTATATAGTAGTGG 58.965 44.000 24.81 24.81 40.19 4.00
648 650 6.034591 GGTGCGCCATTAGTATATAGTAGTG 58.965 44.000 12.58 11.39 34.09 2.74
649 651 5.713389 TGGTGCGCCATTAGTATATAGTAGT 59.287 40.000 16.89 0.00 40.46 2.73
650 652 6.203808 TGGTGCGCCATTAGTATATAGTAG 57.796 41.667 16.89 0.00 40.46 2.57
680 682 2.389962 TTGGACACTAATGGCGTACC 57.610 50.000 0.00 0.00 32.81 3.34
681 683 5.114081 AGTATTTGGACACTAATGGCGTAC 58.886 41.667 0.00 0.00 32.81 3.67
682 684 5.347620 AGTATTTGGACACTAATGGCGTA 57.652 39.130 0.00 0.00 32.81 4.42
683 685 4.216411 AGTATTTGGACACTAATGGCGT 57.784 40.909 0.00 0.00 32.81 5.68
684 686 6.861065 ATTAGTATTTGGACACTAATGGCG 57.139 37.500 6.26 0.00 43.17 5.69
688 690 5.238650 GCGCCATTAGTATTTGGACACTAAT 59.761 40.000 0.00 2.01 44.78 1.73
689 691 4.573201 GCGCCATTAGTATTTGGACACTAA 59.427 41.667 0.00 0.00 40.50 2.24
690 692 4.124238 GCGCCATTAGTATTTGGACACTA 58.876 43.478 0.00 0.00 34.81 2.74
691 693 2.943033 GCGCCATTAGTATTTGGACACT 59.057 45.455 0.00 0.00 34.81 3.55
692 694 2.680841 TGCGCCATTAGTATTTGGACAC 59.319 45.455 4.18 0.00 34.81 3.67
693 695 2.680841 GTGCGCCATTAGTATTTGGACA 59.319 45.455 4.18 0.00 34.81 4.02
694 696 2.032924 GGTGCGCCATTAGTATTTGGAC 59.967 50.000 12.58 0.00 34.81 4.02
695 697 2.294074 GGTGCGCCATTAGTATTTGGA 58.706 47.619 12.58 0.00 34.81 3.53
696 698 2.020720 TGGTGCGCCATTAGTATTTGG 58.979 47.619 16.89 0.00 40.46 3.28
717 719 3.657448 TAGTGGCGCACCGTGGATG 62.657 63.158 10.83 0.00 39.70 3.51
718 720 3.387091 TAGTGGCGCACCGTGGAT 61.387 61.111 10.83 0.00 39.70 3.41
719 721 4.367023 GTAGTGGCGCACCGTGGA 62.367 66.667 10.83 0.00 39.70 4.02
720 722 2.495366 TTAGTAGTGGCGCACCGTGG 62.495 60.000 10.83 0.00 39.70 4.94
721 723 1.080366 TTAGTAGTGGCGCACCGTG 60.080 57.895 10.83 0.00 39.70 4.94
722 724 1.080298 GTTAGTAGTGGCGCACCGT 60.080 57.895 10.83 0.00 39.70 4.83
723 725 0.668096 TTGTTAGTAGTGGCGCACCG 60.668 55.000 10.83 0.00 39.70 4.94
724 726 1.734163 ATTGTTAGTAGTGGCGCACC 58.266 50.000 10.83 0.00 34.49 5.01
725 727 3.824414 AAATTGTTAGTAGTGGCGCAC 57.176 42.857 10.83 5.73 34.10 5.34
726 728 4.839668 AAAAATTGTTAGTAGTGGCGCA 57.160 36.364 10.83 0.00 0.00 6.09
755 757 5.688176 GTGCGCCATTACTAGTTTTGAAAAA 59.312 36.000 4.18 0.00 0.00 1.94
756 758 5.216648 GTGCGCCATTACTAGTTTTGAAAA 58.783 37.500 4.18 0.00 0.00 2.29
757 759 4.320641 GGTGCGCCATTACTAGTTTTGAAA 60.321 41.667 12.58 0.00 34.09 2.69
758 760 3.189702 GGTGCGCCATTACTAGTTTTGAA 59.810 43.478 12.58 0.00 34.09 2.69
759 761 2.745281 GGTGCGCCATTACTAGTTTTGA 59.255 45.455 12.58 0.00 34.09 2.69
760 762 2.486203 TGGTGCGCCATTACTAGTTTTG 59.514 45.455 16.89 0.00 40.46 2.44
761 763 2.747446 CTGGTGCGCCATTACTAGTTTT 59.253 45.455 21.54 0.00 45.05 2.43
762 764 2.356135 CTGGTGCGCCATTACTAGTTT 58.644 47.619 21.54 0.00 45.05 2.66
763 765 1.406887 CCTGGTGCGCCATTACTAGTT 60.407 52.381 21.54 0.00 45.05 2.24
764 766 0.178068 CCTGGTGCGCCATTACTAGT 59.822 55.000 21.54 0.00 45.05 2.57
765 767 0.532862 CCCTGGTGCGCCATTACTAG 60.533 60.000 21.54 6.73 45.05 2.57
766 768 1.524961 CCCTGGTGCGCCATTACTA 59.475 57.895 21.54 0.00 45.05 1.82
767 769 2.272146 CCCTGGTGCGCCATTACT 59.728 61.111 21.54 0.00 45.05 2.24
768 770 2.624674 ATCCCCTGGTGCGCCATTAC 62.625 60.000 21.54 0.00 45.05 1.89
769 771 1.057275 TATCCCCTGGTGCGCCATTA 61.057 55.000 21.54 5.96 45.05 1.90
770 772 2.343475 CTATCCCCTGGTGCGCCATT 62.343 60.000 21.54 5.33 45.05 3.16
771 773 2.772191 TATCCCCTGGTGCGCCAT 60.772 61.111 21.54 7.06 45.05 4.40
772 774 2.882403 TACTATCCCCTGGTGCGCCA 62.882 60.000 19.93 19.93 43.73 5.69
773 775 1.481056 ATACTATCCCCTGGTGCGCC 61.481 60.000 10.11 10.11 0.00 6.53
774 776 0.396811 AATACTATCCCCTGGTGCGC 59.603 55.000 0.00 0.00 0.00 6.09
775 777 2.930826 AAATACTATCCCCTGGTGCG 57.069 50.000 0.00 0.00 0.00 5.34
776 778 3.117663 TGGAAAATACTATCCCCTGGTGC 60.118 47.826 0.00 0.00 34.68 5.01
777 779 4.788925 TGGAAAATACTATCCCCTGGTG 57.211 45.455 0.00 0.00 34.68 4.17
778 780 5.255443 AGTTTGGAAAATACTATCCCCTGGT 59.745 40.000 0.00 0.00 34.68 4.00
779 781 5.766590 AGTTTGGAAAATACTATCCCCTGG 58.233 41.667 0.00 0.00 34.68 4.45
780 782 8.996651 ATTAGTTTGGAAAATACTATCCCCTG 57.003 34.615 0.00 0.00 34.68 4.45
807 809 9.683069 GACACTAATTTGTTTGAAGTCATGATT 57.317 29.630 0.00 0.00 0.00 2.57
808 810 8.299570 GGACACTAATTTGTTTGAAGTCATGAT 58.700 33.333 0.00 0.00 0.00 2.45
809 811 7.284261 TGGACACTAATTTGTTTGAAGTCATGA 59.716 33.333 0.00 0.00 0.00 3.07
810 812 7.424803 TGGACACTAATTTGTTTGAAGTCATG 58.575 34.615 8.77 0.00 0.00 3.07
811 813 7.581213 TGGACACTAATTTGTTTGAAGTCAT 57.419 32.000 8.77 0.00 0.00 3.06
812 814 7.397892 TTGGACACTAATTTGTTTGAAGTCA 57.602 32.000 8.77 0.00 0.00 3.41
813 815 8.871686 ATTTGGACACTAATTTGTTTGAAGTC 57.128 30.769 0.00 0.00 0.00 3.01
830 832 9.403583 GGGTACATTCTTTCTAATATTTGGACA 57.596 33.333 0.00 0.00 0.00 4.02
831 833 9.628500 AGGGTACATTCTTTCTAATATTTGGAC 57.372 33.333 0.00 0.00 0.00 4.02
1249 1254 6.861065 TTACTGCTCCCGAATATTCAAATC 57.139 37.500 15.57 1.41 0.00 2.17
1251 1256 7.639113 AAATTACTGCTCCCGAATATTCAAA 57.361 32.000 15.57 0.00 0.00 2.69
1407 1412 5.364157 AGCGGTAGACTCATATCCTTTCTTT 59.636 40.000 0.00 0.00 0.00 2.52
2102 2112 8.070034 TCTACTTTACGAAGATCCCATTGTAA 57.930 34.615 0.00 0.00 36.69 2.41
2202 2214 5.188163 TCCCTCATTTCACCAATTCGTACTA 59.812 40.000 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.