Multiple sequence alignment - TraesCS5A01G300000

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 TraesCS5A01G300000 chr5A 100.000 3261 0 0 1 3261 509127975 509131235 0.000000e+00 6023
1 TraesCS5A01G300000 chr5A 88.050 477 39 10 172 632 484838663 484838189 1.710000e-152 549
2 TraesCS5A01G300000 chr5A 91.575 273 17 3 86 353 484833695 484833424 3.970000e-99 372
3 TraesCS5A01G300000 chr7A 97.337 2629 68 2 633 3261 704256925 704259551 0.000000e+00 4466
4 TraesCS5A01G300000 chr1A 96.805 2629 82 2 633 3261 376489597 376492223 0.000000e+00 4388
5 TraesCS5A01G300000 chr1A 95.166 2110 83 6 633 2741 549429753 549431844 0.000000e+00 3314
6 TraesCS5A01G300000 chr4A 96.919 2629 59 3 633 3261 37984867 37982261 0.000000e+00 4386
7 TraesCS5A01G300000 chr6A 96.731 2631 74 4 632 3261 558828813 558831432 0.000000e+00 4372
8 TraesCS5A01G300000 chr6A 96.464 2630 89 4 633 3260 532336336 532333709 0.000000e+00 4338
9 TraesCS5A01G300000 chr3A 95.551 2630 94 3 632 3261 741177983 741175377 0.000000e+00 4187
10 TraesCS5A01G300000 chr3A 96.774 1891 60 1 1371 3261 721546641 721548530 0.000000e+00 3153
11 TraesCS5A01G300000 chr2D 94.270 1972 102 6 633 2596 633747075 633749043 0.000000e+00 3005
12 TraesCS5A01G300000 chr2D 91.384 708 35 12 2555 3261 535664192 535664874 0.000000e+00 946
13 TraesCS5A01G300000 chr2D 91.159 690 45 9 2578 3261 633748921 633749600 0.000000e+00 922
14 TraesCS5A01G300000 chr7B 90.483 725 53 12 2546 3261 733270266 733269549 0.000000e+00 942
15 TraesCS5A01G300000 chr5D 96.047 506 15 3 130 632 404879251 404878748 0.000000e+00 819
16 TraesCS5A01G300000 chr5D 87.480 615 53 14 35 632 384152941 384152334 0.000000e+00 688
17 TraesCS5A01G300000 chr5D 86.321 636 53 15 1 632 384141656 384141051 0.000000e+00 662
18 TraesCS5A01G300000 chr5D 94.444 270 11 3 86 353 373215353 373215086 2.340000e-111 412
19 TraesCS5A01G300000 chr5D 95.489 133 6 0 1 133 404879505 404879373 2.550000e-51 213
20 TraesCS5A01G300000 chr5D 86.290 124 14 2 512 632 373215079 373214956 7.340000e-27 132
21 TraesCS5A01G300000 chr5B 90.278 504 35 8 35 531 460941741 460941245 0.000000e+00 647
22 TraesCS5A01G300000 chr5B 94.074 270 12 3 86 353 443289969 443289702 1.090000e-109 407
23 TraesCS5A01G300000 chr5B 87.097 124 13 2 512 632 443289695 443289572 1.580000e-28 137


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 TraesCS5A01G300000 chr5A 509127975 509131235 3260 False 6023.0 6023 100.0000 1 3261 1 chr5A.!!$F1 3260
1 TraesCS5A01G300000 chr7A 704256925 704259551 2626 False 4466.0 4466 97.3370 633 3261 1 chr7A.!!$F1 2628
2 TraesCS5A01G300000 chr1A 376489597 376492223 2626 False 4388.0 4388 96.8050 633 3261 1 chr1A.!!$F1 2628
3 TraesCS5A01G300000 chr1A 549429753 549431844 2091 False 3314.0 3314 95.1660 633 2741 1 chr1A.!!$F2 2108
4 TraesCS5A01G300000 chr4A 37982261 37984867 2606 True 4386.0 4386 96.9190 633 3261 1 chr4A.!!$R1 2628
5 TraesCS5A01G300000 chr6A 558828813 558831432 2619 False 4372.0 4372 96.7310 632 3261 1 chr6A.!!$F1 2629
6 TraesCS5A01G300000 chr6A 532333709 532336336 2627 True 4338.0 4338 96.4640 633 3260 1 chr6A.!!$R1 2627
7 TraesCS5A01G300000 chr3A 741175377 741177983 2606 True 4187.0 4187 95.5510 632 3261 1 chr3A.!!$R1 2629
8 TraesCS5A01G300000 chr3A 721546641 721548530 1889 False 3153.0 3153 96.7740 1371 3261 1 chr3A.!!$F1 1890
9 TraesCS5A01G300000 chr2D 633747075 633749600 2525 False 1963.5 3005 92.7145 633 3261 2 chr2D.!!$F2 2628
10 TraesCS5A01G300000 chr2D 535664192 535664874 682 False 946.0 946 91.3840 2555 3261 1 chr2D.!!$F1 706
11 TraesCS5A01G300000 chr7B 733269549 733270266 717 True 942.0 942 90.4830 2546 3261 1 chr7B.!!$R1 715
12 TraesCS5A01G300000 chr5D 384152334 384152941 607 True 688.0 688 87.4800 35 632 1 chr5D.!!$R2 597
13 TraesCS5A01G300000 chr5D 384141051 384141656 605 True 662.0 662 86.3210 1 632 1 chr5D.!!$R1 631
14 TraesCS5A01G300000 chr5D 404878748 404879505 757 True 516.0 819 95.7680 1 632 2 chr5D.!!$R4 631

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
847 973 0.040781 GCGCCGTTTGCTTAAGACAA 60.041 50.0 6.67 7.41 38.05 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2813 3075 1.380302 GGCCAAGAAGAAGAGGGCA 59.62 57.895 0.0 0.0 46.37 5.36 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
50 51 6.370994 ACTCATGAGTCATGACAGACATTTTC 59.629 38.462 28.18 13.54 44.60 2.29
196 321 4.018324 AGAGCATTCATAGCCCATCATCAT 60.018 41.667 0.00 0.00 0.00 2.45
229 354 1.225704 CCTCTGGAAGATGTGGCCC 59.774 63.158 0.00 0.00 45.62 5.80
233 358 2.276740 GGAAGATGTGGCCCAGGG 59.723 66.667 0.00 0.00 0.00 4.45
241 366 1.382629 GTGGCCCAGGGTATTGTGT 59.617 57.895 7.55 0.00 0.00 3.72
244 369 1.182667 GGCCCAGGGTATTGTGTTTC 58.817 55.000 7.55 0.00 0.00 2.78
249 374 2.556622 CCAGGGTATTGTGTTTCACCAC 59.443 50.000 0.00 0.00 32.73 4.16
258 383 1.407618 GTGTTTCACCACCTTGGGAAC 59.592 52.381 0.00 0.25 43.37 3.62
263 388 2.626785 TCACCACCTTGGGAACTATGA 58.373 47.619 0.00 0.00 43.37 2.15
268 393 4.202441 CCACCTTGGGAACTATGATCTTG 58.798 47.826 0.00 0.00 32.67 3.02
277 402 4.702131 GGAACTATGATCTTGTTTGCAGGT 59.298 41.667 0.00 0.00 0.00 4.00
297 422 3.809905 GTTGAGTCCTTTCTGTCAACCT 58.190 45.455 3.21 0.00 41.89 3.50
299 424 4.503714 TGAGTCCTTTCTGTCAACCTTT 57.496 40.909 0.00 0.00 0.00 3.11
322 447 0.622136 TCAGCTGGTCCATCTGCAAT 59.378 50.000 16.54 0.00 34.63 3.56
351 476 3.947910 CATGATTGCAGGTGGAAAGTT 57.052 42.857 0.00 0.00 0.00 2.66
353 478 4.737054 CATGATTGCAGGTGGAAAGTTAC 58.263 43.478 0.00 0.00 0.00 2.50
357 482 2.582052 TGCAGGTGGAAAGTTACAAGG 58.418 47.619 0.00 0.00 0.00 3.61
401 527 3.904571 TGCACATGCTGAAACAGAAATC 58.095 40.909 5.31 0.00 42.66 2.17
407 533 6.019640 CACATGCTGAAACAGAAATCGTTTTT 60.020 34.615 2.81 0.00 36.72 1.94
409 535 5.890334 TGCTGAAACAGAAATCGTTTTTCT 58.110 33.333 9.36 9.36 36.72 2.52
410 536 6.329496 TGCTGAAACAGAAATCGTTTTTCTT 58.671 32.000 11.63 1.43 36.72 2.52
412 538 6.567769 TGAAACAGAAATCGTTTTTCTTGC 57.432 33.333 11.63 1.75 36.72 4.01
459 585 3.399330 CTTTTCGAGCTAGACACCCAAA 58.601 45.455 0.00 0.00 0.00 3.28
466 592 4.378459 CGAGCTAGACACCCAAATTTCAAC 60.378 45.833 0.00 0.00 0.00 3.18
478 604 8.611757 CACCCAAATTTCAACTAAAGAAAAAGG 58.388 33.333 0.00 0.00 38.36 3.11
487 613 9.665719 TTCAACTAAAGAAAAAGGCTTTTGAAT 57.334 25.926 24.73 10.40 36.92 2.57
497 623 9.651913 GAAAAAGGCTTTTGAATGACCATATAA 57.348 29.630 24.73 0.00 34.83 0.98
522 648 5.791336 TGGTACAAAACATTGCAATACCA 57.209 34.783 19.38 19.38 38.56 3.25
523 649 5.533482 TGGTACAAAACATTGCAATACCAC 58.467 37.500 19.38 8.63 36.53 4.16
524 650 4.926832 GGTACAAAACATTGCAATACCACC 59.073 41.667 12.53 8.81 32.52 4.61
525 651 4.001618 ACAAAACATTGCAATACCACCC 57.998 40.909 12.53 0.00 0.00 4.61
526 652 3.389329 ACAAAACATTGCAATACCACCCA 59.611 39.130 12.53 0.00 0.00 4.51
527 653 4.141620 ACAAAACATTGCAATACCACCCAA 60.142 37.500 12.53 0.00 0.00 4.12
528 654 3.959535 AACATTGCAATACCACCCAAG 57.040 42.857 12.53 0.00 0.00 3.61
529 655 2.888212 ACATTGCAATACCACCCAAGT 58.112 42.857 12.53 0.00 0.00 3.16
530 656 4.040936 ACATTGCAATACCACCCAAGTA 57.959 40.909 12.53 0.00 0.00 2.24
531 657 4.609301 ACATTGCAATACCACCCAAGTAT 58.391 39.130 12.53 0.00 31.71 2.12
532 658 4.644685 ACATTGCAATACCACCCAAGTATC 59.355 41.667 12.53 0.00 30.10 2.24
533 659 4.584638 TTGCAATACCACCCAAGTATCT 57.415 40.909 0.00 0.00 30.10 1.98
534 660 4.150897 TGCAATACCACCCAAGTATCTC 57.849 45.455 0.00 0.00 30.10 2.75
535 661 3.118038 TGCAATACCACCCAAGTATCTCC 60.118 47.826 0.00 0.00 30.10 3.71
536 662 3.728845 CAATACCACCCAAGTATCTCCG 58.271 50.000 0.00 0.00 30.10 4.63
537 663 1.117150 TACCACCCAAGTATCTCCGC 58.883 55.000 0.00 0.00 0.00 5.54
538 664 1.227263 CCACCCAAGTATCTCCGCG 60.227 63.158 0.00 0.00 0.00 6.46
539 665 1.227263 CACCCAAGTATCTCCGCGG 60.227 63.158 22.12 22.12 0.00 6.46
540 666 1.684734 ACCCAAGTATCTCCGCGGT 60.685 57.895 27.15 8.80 0.00 5.68
541 667 1.227263 CCCAAGTATCTCCGCGGTG 60.227 63.158 27.15 23.87 0.00 4.94
542 668 1.883084 CCAAGTATCTCCGCGGTGC 60.883 63.158 27.15 9.91 0.00 5.01
543 669 1.141881 CAAGTATCTCCGCGGTGCT 59.858 57.895 27.15 17.32 0.00 4.40
544 670 0.872021 CAAGTATCTCCGCGGTGCTC 60.872 60.000 27.15 15.21 0.00 4.26
545 671 1.320344 AAGTATCTCCGCGGTGCTCA 61.320 55.000 27.15 7.35 0.00 4.26
546 672 1.141019 GTATCTCCGCGGTGCTCAA 59.859 57.895 27.15 6.94 0.00 3.02
547 673 0.459585 GTATCTCCGCGGTGCTCAAA 60.460 55.000 27.15 6.51 0.00 2.69
548 674 0.459585 TATCTCCGCGGTGCTCAAAC 60.460 55.000 27.15 0.00 0.00 2.93
549 675 2.449031 ATCTCCGCGGTGCTCAAACA 62.449 55.000 27.15 4.88 0.00 2.83
550 676 2.203084 TCCGCGGTGCTCAAACAA 60.203 55.556 27.15 0.00 0.00 2.83
551 677 1.781025 CTCCGCGGTGCTCAAACAAA 61.781 55.000 27.15 0.00 0.00 2.83
552 678 1.169661 TCCGCGGTGCTCAAACAAAT 61.170 50.000 27.15 0.00 0.00 2.32
553 679 0.519519 CCGCGGTGCTCAAACAAATA 59.480 50.000 19.50 0.00 0.00 1.40
554 680 1.068885 CCGCGGTGCTCAAACAAATAA 60.069 47.619 19.50 0.00 0.00 1.40
555 681 2.605823 CCGCGGTGCTCAAACAAATAAA 60.606 45.455 19.50 0.00 0.00 1.40
556 682 3.046390 CGCGGTGCTCAAACAAATAAAA 58.954 40.909 0.00 0.00 0.00 1.52
557 683 3.121496 CGCGGTGCTCAAACAAATAAAAC 60.121 43.478 0.00 0.00 0.00 2.43
558 684 3.799420 GCGGTGCTCAAACAAATAAAACA 59.201 39.130 0.00 0.00 0.00 2.83
559 685 4.268884 GCGGTGCTCAAACAAATAAAACAA 59.731 37.500 0.00 0.00 0.00 2.83
560 686 5.556194 GCGGTGCTCAAACAAATAAAACAAG 60.556 40.000 0.00 0.00 0.00 3.16
561 687 5.746245 CGGTGCTCAAACAAATAAAACAAGA 59.254 36.000 0.00 0.00 0.00 3.02
562 688 6.291585 CGGTGCTCAAACAAATAAAACAAGAC 60.292 38.462 0.00 0.00 0.00 3.01
563 689 6.533367 GGTGCTCAAACAAATAAAACAAGACA 59.467 34.615 0.00 0.00 0.00 3.41
564 690 7.254084 GGTGCTCAAACAAATAAAACAAGACAG 60.254 37.037 0.00 0.00 0.00 3.51
565 691 6.756074 TGCTCAAACAAATAAAACAAGACAGG 59.244 34.615 0.00 0.00 0.00 4.00
566 692 6.200854 GCTCAAACAAATAAAACAAGACAGGG 59.799 38.462 0.00 0.00 0.00 4.45
567 693 6.578023 TCAAACAAATAAAACAAGACAGGGG 58.422 36.000 0.00 0.00 0.00 4.79
568 694 6.381420 TCAAACAAATAAAACAAGACAGGGGA 59.619 34.615 0.00 0.00 0.00 4.81
569 695 6.800072 AACAAATAAAACAAGACAGGGGAA 57.200 33.333 0.00 0.00 0.00 3.97
570 696 6.156748 ACAAATAAAACAAGACAGGGGAAC 57.843 37.500 0.00 0.00 0.00 3.62
571 697 5.219633 CAAATAAAACAAGACAGGGGAACG 58.780 41.667 0.00 0.00 0.00 3.95
572 698 1.029681 AAAACAAGACAGGGGAACGC 58.970 50.000 0.00 0.00 43.76 4.84
573 699 0.106918 AAACAAGACAGGGGAACGCA 60.107 50.000 0.00 0.00 46.88 5.24
574 700 0.110486 AACAAGACAGGGGAACGCAT 59.890 50.000 0.00 0.00 46.88 4.73
575 701 0.981183 ACAAGACAGGGGAACGCATA 59.019 50.000 0.00 0.00 46.88 3.14
576 702 1.349688 ACAAGACAGGGGAACGCATAA 59.650 47.619 0.00 0.00 46.88 1.90
577 703 2.026262 ACAAGACAGGGGAACGCATAAT 60.026 45.455 0.00 0.00 46.88 1.28
578 704 2.614057 CAAGACAGGGGAACGCATAATC 59.386 50.000 0.00 0.00 46.88 1.75
579 705 1.202533 AGACAGGGGAACGCATAATCG 60.203 52.381 0.00 0.00 46.88 3.34
580 706 0.828022 ACAGGGGAACGCATAATCGA 59.172 50.000 0.00 0.00 46.88 3.59
581 707 1.217882 CAGGGGAACGCATAATCGAC 58.782 55.000 0.00 0.00 46.88 4.20
582 708 0.828022 AGGGGAACGCATAATCGACA 59.172 50.000 0.00 0.00 46.88 4.35
583 709 1.202533 AGGGGAACGCATAATCGACAG 60.203 52.381 0.00 0.00 46.88 3.51
584 710 1.217882 GGGAACGCATAATCGACAGG 58.782 55.000 0.00 0.00 0.00 4.00
585 711 1.217882 GGAACGCATAATCGACAGGG 58.782 55.000 0.00 0.00 0.00 4.45
586 712 1.472728 GGAACGCATAATCGACAGGGT 60.473 52.381 0.00 0.00 0.00 4.34
587 713 1.593006 GAACGCATAATCGACAGGGTG 59.407 52.381 0.00 0.00 0.00 4.61
588 714 0.810031 ACGCATAATCGACAGGGTGC 60.810 55.000 0.00 0.00 0.00 5.01
589 715 0.809636 CGCATAATCGACAGGGTGCA 60.810 55.000 9.67 0.00 33.09 4.57
590 716 1.597742 GCATAATCGACAGGGTGCAT 58.402 50.000 0.00 0.00 33.09 3.96
591 717 2.766313 GCATAATCGACAGGGTGCATA 58.234 47.619 0.00 0.00 33.09 3.14
592 718 2.738846 GCATAATCGACAGGGTGCATAG 59.261 50.000 0.00 0.00 33.09 2.23
593 719 3.554960 GCATAATCGACAGGGTGCATAGA 60.555 47.826 0.00 0.00 33.09 1.98
594 720 4.825422 CATAATCGACAGGGTGCATAGAT 58.175 43.478 0.00 0.00 0.00 1.98
595 721 5.624509 GCATAATCGACAGGGTGCATAGATA 60.625 44.000 0.00 0.00 33.09 1.98
596 722 4.527509 AATCGACAGGGTGCATAGATAG 57.472 45.455 0.00 0.00 0.00 2.08
597 723 2.945456 TCGACAGGGTGCATAGATAGT 58.055 47.619 0.00 0.00 0.00 2.12
598 724 2.885266 TCGACAGGGTGCATAGATAGTC 59.115 50.000 0.00 0.00 0.00 2.59
599 725 2.623416 CGACAGGGTGCATAGATAGTCA 59.377 50.000 0.00 0.00 0.00 3.41
600 726 3.068165 CGACAGGGTGCATAGATAGTCAA 59.932 47.826 0.00 0.00 0.00 3.18
601 727 4.372656 GACAGGGTGCATAGATAGTCAAC 58.627 47.826 0.00 0.00 0.00 3.18
602 728 4.033709 ACAGGGTGCATAGATAGTCAACT 58.966 43.478 0.00 0.00 0.00 3.16
603 729 4.471386 ACAGGGTGCATAGATAGTCAACTT 59.529 41.667 0.00 0.00 0.00 2.66
604 730 4.813161 CAGGGTGCATAGATAGTCAACTTG 59.187 45.833 0.00 0.00 0.00 3.16
605 731 4.130118 GGGTGCATAGATAGTCAACTTGG 58.870 47.826 0.00 0.00 0.00 3.61
606 732 4.130118 GGTGCATAGATAGTCAACTTGGG 58.870 47.826 0.00 0.00 0.00 4.12
607 733 3.561725 GTGCATAGATAGTCAACTTGGGC 59.438 47.826 0.00 0.00 0.00 5.36
608 734 3.455910 TGCATAGATAGTCAACTTGGGCT 59.544 43.478 0.00 0.00 0.00 5.19
609 735 4.061596 GCATAGATAGTCAACTTGGGCTC 58.938 47.826 0.00 0.00 0.00 4.70
610 736 4.636249 CATAGATAGTCAACTTGGGCTCC 58.364 47.826 0.00 0.00 0.00 4.70
611 737 1.840635 AGATAGTCAACTTGGGCTCCC 59.159 52.381 0.00 0.00 0.00 4.30
612 738 0.919710 ATAGTCAACTTGGGCTCCCC 59.080 55.000 1.89 0.00 45.71 4.81
613 739 0.178873 TAGTCAACTTGGGCTCCCCT 60.179 55.000 1.89 0.00 45.70 4.79
614 740 0.178873 AGTCAACTTGGGCTCCCCTA 60.179 55.000 1.89 0.00 45.70 3.53
615 741 0.919710 GTCAACTTGGGCTCCCCTAT 59.080 55.000 1.89 0.00 45.70 2.57
616 742 0.918983 TCAACTTGGGCTCCCCTATG 59.081 55.000 1.89 0.00 45.70 2.23
617 743 0.625849 CAACTTGGGCTCCCCTATGT 59.374 55.000 1.89 0.00 45.70 2.29
618 744 1.005924 CAACTTGGGCTCCCCTATGTT 59.994 52.381 1.89 1.89 45.70 2.71
619 745 0.625849 ACTTGGGCTCCCCTATGTTG 59.374 55.000 1.89 0.00 45.70 3.33
620 746 0.625849 CTTGGGCTCCCCTATGTTGT 59.374 55.000 1.89 0.00 45.70 3.32
621 747 0.331278 TTGGGCTCCCCTATGTTGTG 59.669 55.000 1.89 0.00 45.70 3.33
622 748 0.844661 TGGGCTCCCCTATGTTGTGT 60.845 55.000 1.89 0.00 45.70 3.72
623 749 0.331616 GGGCTCCCCTATGTTGTGTT 59.668 55.000 0.00 0.00 41.34 3.32
624 750 1.463674 GGCTCCCCTATGTTGTGTTG 58.536 55.000 0.00 0.00 0.00 3.33
625 751 0.811281 GCTCCCCTATGTTGTGTTGC 59.189 55.000 0.00 0.00 0.00 4.17
626 752 1.463674 CTCCCCTATGTTGTGTTGCC 58.536 55.000 0.00 0.00 0.00 4.52
627 753 0.774276 TCCCCTATGTTGTGTTGCCA 59.226 50.000 0.00 0.00 0.00 4.92
628 754 1.145945 TCCCCTATGTTGTGTTGCCAA 59.854 47.619 0.00 0.00 0.00 4.52
629 755 1.545582 CCCCTATGTTGTGTTGCCAAG 59.454 52.381 0.00 0.00 0.00 3.61
630 756 1.545582 CCCTATGTTGTGTTGCCAAGG 59.454 52.381 0.00 0.00 0.00 3.61
645 771 2.297033 GCCAAGGAGAGTGAATTGCAAA 59.703 45.455 1.71 0.00 0.00 3.68
668 794 1.133009 ACCACCACATTTGGGGCTTAA 60.133 47.619 2.32 0.00 46.42 1.85
847 973 0.040781 GCGCCGTTTGCTTAAGACAA 60.041 50.000 6.67 7.41 38.05 3.18
875 1001 3.366629 GTCGCCAGAGACAGACCA 58.633 61.111 0.00 0.00 40.65 4.02
946 1072 2.917227 TGCTCCCACACTCGCTCA 60.917 61.111 0.00 0.00 0.00 4.26
961 1087 0.332972 GCTCACTCCCCTCCCATTTT 59.667 55.000 0.00 0.00 0.00 1.82
972 1098 2.849318 CCTCCCATTTTCTCCTCTCCTT 59.151 50.000 0.00 0.00 0.00 3.36
1060 1186 1.729470 CGCGCAGTACATCTCCTCCT 61.729 60.000 8.75 0.00 0.00 3.69
1061 1187 0.031449 GCGCAGTACATCTCCTCCTC 59.969 60.000 0.30 0.00 0.00 3.71
1079 1205 2.266055 CGACTCCCCTGTCAAGGC 59.734 66.667 0.00 0.00 42.96 4.35
1211 1337 0.108615 CGTTCGAGGGTCTTGCTGAT 60.109 55.000 0.00 0.00 0.00 2.90
1652 1850 2.092753 CAGTGGGTAGATGAGCATTGGT 60.093 50.000 0.00 0.00 0.00 3.67
1802 2000 4.651045 TGCAGGAGACATATGAGAAGCTTA 59.349 41.667 10.38 0.00 0.00 3.09
1847 2045 5.599751 TGGATTATAAGGATAGCCAGCCTA 58.400 41.667 0.00 0.00 40.64 3.93
1870 2069 4.273318 AGGTAAACCAGAAGAATGATGCC 58.727 43.478 1.26 0.00 38.89 4.40
1871 2070 4.016444 GGTAAACCAGAAGAATGATGCCA 58.984 43.478 0.00 0.00 35.64 4.92
1881 2080 6.425721 CAGAAGAATGATGCCAACAACATTTT 59.574 34.615 3.53 0.00 45.94 1.82
1993 2193 5.415701 TCAAGCCACTGTCATTAGGAATTTC 59.584 40.000 0.00 0.00 0.00 2.17
2539 2752 5.645929 AGATAGTCTGACATAGATAGTGGCG 59.354 44.000 10.88 0.00 37.83 5.69
2813 3075 0.586319 CGTCATTGTTGTTCACCGCT 59.414 50.000 0.00 0.00 0.00 5.52
2945 3207 5.271598 TCCACATCAATTGGGCTATTCTTT 58.728 37.500 5.42 0.00 34.56 2.52
3170 3432 0.690762 AGTAGGCGTTGTTGATGGGT 59.309 50.000 0.00 0.00 0.00 4.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 4.468153 AGTGTTAGATCCCCTCTTGTCTTC 59.532 45.833 0.00 0.00 35.28 2.87
179 304 4.356405 AACGATGATGATGGGCTATGAA 57.644 40.909 0.00 0.00 0.00 2.57
196 321 0.892755 AGAGGTACGCCATGAAACGA 59.107 50.000 9.28 0.00 37.19 3.85
229 354 2.556622 GGTGGTGAAACACAATACCCTG 59.443 50.000 0.19 0.00 43.08 4.45
233 358 3.005367 CCCAAGGTGGTGAAACACAATAC 59.995 47.826 0.19 0.00 43.08 1.89
241 366 3.396276 TCATAGTTCCCAAGGTGGTGAAA 59.604 43.478 0.00 0.00 35.17 2.69
244 369 3.200825 AGATCATAGTTCCCAAGGTGGTG 59.799 47.826 0.00 0.00 35.17 4.17
249 374 5.393461 GCAAACAAGATCATAGTTCCCAAGG 60.393 44.000 0.00 0.00 0.00 3.61
258 383 5.413833 ACTCAACCTGCAAACAAGATCATAG 59.586 40.000 0.00 0.00 0.00 2.23
263 388 2.887152 GGACTCAACCTGCAAACAAGAT 59.113 45.455 0.00 0.00 0.00 2.40
268 393 2.952310 AGAAAGGACTCAACCTGCAAAC 59.048 45.455 0.00 0.00 40.49 2.93
277 402 4.503714 AAGGTTGACAGAAAGGACTCAA 57.496 40.909 0.00 0.00 0.00 3.02
297 422 3.726557 AGATGGACCAGCTGATTCAAA 57.273 42.857 17.39 4.01 0.00 2.69
338 463 2.858745 TCCTTGTAACTTTCCACCTGC 58.141 47.619 0.00 0.00 0.00 4.85
389 515 5.518487 GGCAAGAAAAACGATTTCTGTTTCA 59.482 36.000 17.34 0.00 38.52 2.69
401 527 4.678622 ACTAAAGTTGGGCAAGAAAAACG 58.321 39.130 0.00 0.00 0.00 3.60
407 533 3.882888 CTGTTGACTAAAGTTGGGCAAGA 59.117 43.478 0.00 0.00 37.34 3.02
409 535 3.892284 TCTGTTGACTAAAGTTGGGCAA 58.108 40.909 0.00 0.00 34.00 4.52
410 536 3.569194 TCTGTTGACTAAAGTTGGGCA 57.431 42.857 0.00 0.00 0.00 5.36
412 538 7.542130 GCATTATTTCTGTTGACTAAAGTTGGG 59.458 37.037 0.00 0.00 0.00 4.12
459 585 9.665719 TCAAAAGCCTTTTTCTTTAGTTGAAAT 57.334 25.926 0.00 0.00 34.34 2.17
466 592 7.710475 TGGTCATTCAAAAGCCTTTTTCTTTAG 59.290 33.333 0.00 0.00 34.34 1.85
497 623 7.172361 GTGGTATTGCAATGTTTTGTACCAATT 59.828 33.333 23.11 0.00 40.67 2.32
505 631 4.000331 TGGGTGGTATTGCAATGTTTTG 58.000 40.909 22.27 0.00 35.85 2.44
506 632 4.102367 ACTTGGGTGGTATTGCAATGTTTT 59.898 37.500 22.27 0.00 0.00 2.43
507 633 3.645687 ACTTGGGTGGTATTGCAATGTTT 59.354 39.130 22.27 0.00 0.00 2.83
508 634 3.238597 ACTTGGGTGGTATTGCAATGTT 58.761 40.909 22.27 0.00 0.00 2.71
509 635 2.888212 ACTTGGGTGGTATTGCAATGT 58.112 42.857 22.27 4.85 0.00 2.71
510 636 4.889409 AGATACTTGGGTGGTATTGCAATG 59.111 41.667 22.27 4.20 31.03 2.82
511 637 5.129368 AGATACTTGGGTGGTATTGCAAT 57.871 39.130 17.56 17.56 31.03 3.56
512 638 4.523083 GAGATACTTGGGTGGTATTGCAA 58.477 43.478 0.00 0.00 31.03 4.08
513 639 3.118038 GGAGATACTTGGGTGGTATTGCA 60.118 47.826 0.00 0.00 31.03 4.08
514 640 3.477530 GGAGATACTTGGGTGGTATTGC 58.522 50.000 0.00 0.00 31.03 3.56
515 641 3.728845 CGGAGATACTTGGGTGGTATTG 58.271 50.000 0.00 0.00 31.03 1.90
516 642 2.104281 GCGGAGATACTTGGGTGGTATT 59.896 50.000 0.00 0.00 31.03 1.89
517 643 1.692519 GCGGAGATACTTGGGTGGTAT 59.307 52.381 0.00 0.00 33.22 2.73
518 644 1.117150 GCGGAGATACTTGGGTGGTA 58.883 55.000 0.00 0.00 0.00 3.25
519 645 1.905512 GCGGAGATACTTGGGTGGT 59.094 57.895 0.00 0.00 0.00 4.16
520 646 1.227263 CGCGGAGATACTTGGGTGG 60.227 63.158 0.00 0.00 0.00 4.61
521 647 1.227263 CCGCGGAGATACTTGGGTG 60.227 63.158 24.07 0.00 0.00 4.61
522 648 1.684734 ACCGCGGAGATACTTGGGT 60.685 57.895 35.90 0.00 0.00 4.51
523 649 1.227263 CACCGCGGAGATACTTGGG 60.227 63.158 35.90 0.00 0.00 4.12
524 650 1.883084 GCACCGCGGAGATACTTGG 60.883 63.158 35.90 9.89 0.00 3.61
525 651 0.872021 GAGCACCGCGGAGATACTTG 60.872 60.000 35.90 19.16 0.00 3.16
526 652 1.320344 TGAGCACCGCGGAGATACTT 61.320 55.000 35.90 3.57 0.00 2.24
527 653 1.320344 TTGAGCACCGCGGAGATACT 61.320 55.000 35.90 20.24 0.00 2.12
528 654 0.459585 TTTGAGCACCGCGGAGATAC 60.460 55.000 35.90 16.99 0.00 2.24
529 655 0.459585 GTTTGAGCACCGCGGAGATA 60.460 55.000 35.90 5.47 0.00 1.98
530 656 1.741770 GTTTGAGCACCGCGGAGAT 60.742 57.895 35.90 25.66 0.00 2.75
531 657 2.357034 GTTTGAGCACCGCGGAGA 60.357 61.111 35.90 4.98 0.00 3.71
532 658 1.781025 TTTGTTTGAGCACCGCGGAG 61.781 55.000 35.90 27.15 0.00 4.63
533 659 1.169661 ATTTGTTTGAGCACCGCGGA 61.170 50.000 35.90 5.52 0.00 5.54
534 660 0.519519 TATTTGTTTGAGCACCGCGG 59.480 50.000 26.86 26.86 0.00 6.46
535 661 2.323939 TTATTTGTTTGAGCACCGCG 57.676 45.000 0.00 0.00 0.00 6.46
536 662 3.799420 TGTTTTATTTGTTTGAGCACCGC 59.201 39.130 0.00 0.00 0.00 5.68
537 663 5.746245 TCTTGTTTTATTTGTTTGAGCACCG 59.254 36.000 0.00 0.00 0.00 4.94
538 664 6.533367 TGTCTTGTTTTATTTGTTTGAGCACC 59.467 34.615 0.00 0.00 0.00 5.01
539 665 7.254084 CCTGTCTTGTTTTATTTGTTTGAGCAC 60.254 37.037 0.00 0.00 0.00 4.40
540 666 6.756074 CCTGTCTTGTTTTATTTGTTTGAGCA 59.244 34.615 0.00 0.00 0.00 4.26
541 667 6.200854 CCCTGTCTTGTTTTATTTGTTTGAGC 59.799 38.462 0.00 0.00 0.00 4.26
542 668 6.701400 CCCCTGTCTTGTTTTATTTGTTTGAG 59.299 38.462 0.00 0.00 0.00 3.02
543 669 6.381420 TCCCCTGTCTTGTTTTATTTGTTTGA 59.619 34.615 0.00 0.00 0.00 2.69
544 670 6.578023 TCCCCTGTCTTGTTTTATTTGTTTG 58.422 36.000 0.00 0.00 0.00 2.93
545 671 6.800072 TCCCCTGTCTTGTTTTATTTGTTT 57.200 33.333 0.00 0.00 0.00 2.83
546 672 6.578944 GTTCCCCTGTCTTGTTTTATTTGTT 58.421 36.000 0.00 0.00 0.00 2.83
547 673 5.221165 CGTTCCCCTGTCTTGTTTTATTTGT 60.221 40.000 0.00 0.00 0.00 2.83
548 674 5.219633 CGTTCCCCTGTCTTGTTTTATTTG 58.780 41.667 0.00 0.00 0.00 2.32
549 675 4.261867 GCGTTCCCCTGTCTTGTTTTATTT 60.262 41.667 0.00 0.00 0.00 1.40
550 676 3.254903 GCGTTCCCCTGTCTTGTTTTATT 59.745 43.478 0.00 0.00 0.00 1.40
551 677 2.817844 GCGTTCCCCTGTCTTGTTTTAT 59.182 45.455 0.00 0.00 0.00 1.40
552 678 2.223745 GCGTTCCCCTGTCTTGTTTTA 58.776 47.619 0.00 0.00 0.00 1.52
553 679 1.029681 GCGTTCCCCTGTCTTGTTTT 58.970 50.000 0.00 0.00 0.00 2.43
554 680 0.106918 TGCGTTCCCCTGTCTTGTTT 60.107 50.000 0.00 0.00 0.00 2.83
555 681 0.110486 ATGCGTTCCCCTGTCTTGTT 59.890 50.000 0.00 0.00 0.00 2.83
556 682 0.981183 TATGCGTTCCCCTGTCTTGT 59.019 50.000 0.00 0.00 0.00 3.16
557 683 2.107950 TTATGCGTTCCCCTGTCTTG 57.892 50.000 0.00 0.00 0.00 3.02
558 684 2.741878 CGATTATGCGTTCCCCTGTCTT 60.742 50.000 0.00 0.00 0.00 3.01
559 685 1.202533 CGATTATGCGTTCCCCTGTCT 60.203 52.381 0.00 0.00 0.00 3.41
560 686 1.202486 TCGATTATGCGTTCCCCTGTC 60.202 52.381 0.00 0.00 0.00 3.51
561 687 0.828022 TCGATTATGCGTTCCCCTGT 59.172 50.000 0.00 0.00 0.00 4.00
562 688 1.217882 GTCGATTATGCGTTCCCCTG 58.782 55.000 0.00 0.00 0.00 4.45
563 689 0.828022 TGTCGATTATGCGTTCCCCT 59.172 50.000 0.00 0.00 0.00 4.79
564 690 1.217882 CTGTCGATTATGCGTTCCCC 58.782 55.000 0.00 0.00 0.00 4.81
565 691 1.217882 CCTGTCGATTATGCGTTCCC 58.782 55.000 0.00 0.00 0.00 3.97
566 692 1.217882 CCCTGTCGATTATGCGTTCC 58.782 55.000 0.00 0.00 0.00 3.62
567 693 1.593006 CACCCTGTCGATTATGCGTTC 59.407 52.381 0.00 0.00 0.00 3.95
568 694 1.651987 CACCCTGTCGATTATGCGTT 58.348 50.000 0.00 0.00 0.00 4.84
569 695 0.810031 GCACCCTGTCGATTATGCGT 60.810 55.000 0.00 0.00 0.00 5.24
570 696 0.809636 TGCACCCTGTCGATTATGCG 60.810 55.000 0.00 0.00 35.83 4.73
571 697 1.597742 ATGCACCCTGTCGATTATGC 58.402 50.000 0.00 0.00 0.00 3.14
572 698 4.257267 TCTATGCACCCTGTCGATTATG 57.743 45.455 0.00 0.00 0.00 1.90
573 699 5.717178 ACTATCTATGCACCCTGTCGATTAT 59.283 40.000 0.00 0.00 0.00 1.28
574 700 5.077564 ACTATCTATGCACCCTGTCGATTA 58.922 41.667 0.00 0.00 0.00 1.75
575 701 3.898123 ACTATCTATGCACCCTGTCGATT 59.102 43.478 0.00 0.00 0.00 3.34
576 702 3.501349 ACTATCTATGCACCCTGTCGAT 58.499 45.455 0.00 0.00 0.00 3.59
577 703 2.885266 GACTATCTATGCACCCTGTCGA 59.115 50.000 0.00 0.00 0.00 4.20
578 704 2.623416 TGACTATCTATGCACCCTGTCG 59.377 50.000 0.00 0.00 0.00 4.35
579 705 4.100189 AGTTGACTATCTATGCACCCTGTC 59.900 45.833 0.00 0.00 0.00 3.51
580 706 4.033709 AGTTGACTATCTATGCACCCTGT 58.966 43.478 0.00 0.00 0.00 4.00
581 707 4.679373 AGTTGACTATCTATGCACCCTG 57.321 45.455 0.00 0.00 0.00 4.45
582 708 4.141620 CCAAGTTGACTATCTATGCACCCT 60.142 45.833 3.87 0.00 0.00 4.34
583 709 4.130118 CCAAGTTGACTATCTATGCACCC 58.870 47.826 3.87 0.00 0.00 4.61
584 710 4.130118 CCCAAGTTGACTATCTATGCACC 58.870 47.826 3.87 0.00 0.00 5.01
585 711 3.561725 GCCCAAGTTGACTATCTATGCAC 59.438 47.826 3.87 0.00 0.00 4.57
586 712 3.455910 AGCCCAAGTTGACTATCTATGCA 59.544 43.478 3.87 0.00 0.00 3.96
587 713 4.061596 GAGCCCAAGTTGACTATCTATGC 58.938 47.826 3.87 0.00 0.00 3.14
588 714 4.503991 GGGAGCCCAAGTTGACTATCTATG 60.504 50.000 3.87 0.00 35.81 2.23
589 715 3.648545 GGGAGCCCAAGTTGACTATCTAT 59.351 47.826 3.87 0.00 35.81 1.98
590 716 3.039011 GGGAGCCCAAGTTGACTATCTA 58.961 50.000 3.87 0.00 35.81 1.98
591 717 1.840635 GGGAGCCCAAGTTGACTATCT 59.159 52.381 3.87 0.00 35.81 1.98
592 718 1.134068 GGGGAGCCCAAGTTGACTATC 60.134 57.143 8.02 0.00 44.65 2.08
593 719 0.919710 GGGGAGCCCAAGTTGACTAT 59.080 55.000 8.02 0.00 44.65 2.12
594 720 2.383608 GGGGAGCCCAAGTTGACTA 58.616 57.895 8.02 0.00 44.65 2.59
595 721 3.171348 GGGGAGCCCAAGTTGACT 58.829 61.111 8.02 0.86 44.65 3.41
604 730 0.331616 AACACAACATAGGGGAGCCC 59.668 55.000 0.00 0.00 45.90 5.19
605 731 1.463674 CAACACAACATAGGGGAGCC 58.536 55.000 0.00 0.00 0.00 4.70
606 732 0.811281 GCAACACAACATAGGGGAGC 59.189 55.000 0.00 0.00 0.00 4.70
607 733 1.271871 TGGCAACACAACATAGGGGAG 60.272 52.381 0.00 0.00 46.17 4.30
608 734 0.774276 TGGCAACACAACATAGGGGA 59.226 50.000 0.00 0.00 46.17 4.81
609 735 3.355077 TGGCAACACAACATAGGGG 57.645 52.632 0.00 0.00 46.17 4.79
621 747 2.352127 GCAATTCACTCTCCTTGGCAAC 60.352 50.000 0.00 0.00 0.00 4.17
622 748 1.888512 GCAATTCACTCTCCTTGGCAA 59.111 47.619 0.00 0.00 0.00 4.52
623 749 1.202915 TGCAATTCACTCTCCTTGGCA 60.203 47.619 0.00 0.00 0.00 4.92
624 750 1.538047 TGCAATTCACTCTCCTTGGC 58.462 50.000 0.00 0.00 0.00 4.52
625 751 4.589216 TTTTGCAATTCACTCTCCTTGG 57.411 40.909 0.00 0.00 0.00 3.61
645 771 0.472044 GCCCCAAATGTGGTGGTTTT 59.528 50.000 0.00 0.00 44.30 2.43
668 794 1.816224 ACCACGTTGTTTTCTGCAAGT 59.184 42.857 0.00 0.00 33.76 3.16
946 1072 1.203622 AGGAGAAAATGGGAGGGGAGT 60.204 52.381 0.00 0.00 0.00 3.85
961 1087 0.408309 TGACCGGAAAGGAGAGGAGA 59.592 55.000 9.46 0.00 45.00 3.71
1060 1186 1.609501 CCTTGACAGGGGAGTCGGA 60.610 63.158 0.00 0.00 41.41 4.55
1061 1187 2.982130 CCTTGACAGGGGAGTCGG 59.018 66.667 0.00 0.00 41.41 4.79
1079 1205 7.555554 ACAGAAATGAGGAATAGAATGTTCTGG 59.444 37.037 12.63 0.00 42.26 3.86
1211 1337 4.579753 TGCTCACAAATCACATTCAAGTCA 59.420 37.500 0.00 0.00 0.00 3.41
1507 1704 9.722056 GTACCAGAATCACATTCATTTAATGAC 57.278 33.333 7.19 0.00 46.81 3.06
1847 2045 4.706962 GGCATCATTCTTCTGGTTTACCTT 59.293 41.667 0.00 0.00 36.82 3.50
1870 2069 8.918961 TTTCCACACTAACTAAAATGTTGTTG 57.081 30.769 0.00 0.00 0.00 3.33
1871 2070 7.704899 GCTTTCCACACTAACTAAAATGTTGTT 59.295 33.333 0.00 0.00 0.00 2.83
1881 2080 3.762407 TGCTGCTTTCCACACTAACTA 57.238 42.857 0.00 0.00 0.00 2.24
1993 2193 6.150140 CCTTCTCCTTAAGATGGTTGAACTTG 59.850 42.308 3.36 0.00 42.03 3.16
2229 2441 6.064060 TCATCACAAATAGCCTTAATCTGGG 58.936 40.000 0.00 0.00 0.00 4.45
2474 2687 9.355916 TGCTATCTATGTTCACTATCTACTTGT 57.644 33.333 0.00 0.00 0.00 3.16
2602 2841 6.576662 TGTAAGACTATCTATGCAGCTACC 57.423 41.667 0.00 0.00 0.00 3.18
2813 3075 1.380302 GGCCAAGAAGAAGAGGGCA 59.620 57.895 0.00 0.00 46.37 5.36


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

AutoCloner maintained by Alex Coulton.