Multiple sequence alignment - TraesCS3A01G201900

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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 TraesCS3A01G201900 chr3A 100.000 2411 0 0 1 2411 340258524 340260934 0.000000e+00 4453.0
1 TraesCS3A01G201900 chr3A 97.708 1440 28 2 895 2330 17494227 17492789 0.000000e+00 2471.0
2 TraesCS3A01G201900 chr3A 97.699 1434 31 1 899 2330 599892295 599890862 0.000000e+00 2464.0
3 TraesCS3A01G201900 chr3A 89.984 619 43 12 1 602 682033509 682032893 0.000000e+00 782.0
4 TraesCS3A01G201900 chr3A 94.545 110 4 2 676 784 599892838 599892730 4.120000e-38 169.0
5 TraesCS3A01G201900 chr1A 96.344 1176 42 1 676 1851 494701694 494700520 0.000000e+00 1932.0
6 TraesCS3A01G201900 chr1A 91.950 1118 83 5 676 1788 152714625 152713510 0.000000e+00 1559.0
7 TraesCS3A01G201900 chr1A 88.274 614 56 8 1 603 504741794 504741186 0.000000e+00 721.0
8 TraesCS3A01G201900 chr1A 93.850 439 17 1 1903 2331 152703604 152703166 0.000000e+00 652.0
9 TraesCS3A01G201900 chr1A 97.368 76 2 0 1848 1923 152703680 152703605 1.950000e-26 130.0
10 TraesCS3A01G201900 chr6A 97.921 1058 22 0 794 1851 60606806 60605749 0.000000e+00 1832.0
11 TraesCS3A01G201900 chr6A 86.935 620 62 15 1 606 577762479 577761865 0.000000e+00 678.0
12 TraesCS3A01G201900 chr6A 96.220 291 11 0 2040 2330 60591896 60591606 6.030000e-131 477.0
13 TraesCS3A01G201900 chr6A 83.984 512 43 16 1848 2331 195274993 195274493 2.830000e-124 455.0
14 TraesCS3A01G201900 chr6A 94.146 205 4 1 1848 2044 60603552 60603348 3.010000e-79 305.0
15 TraesCS3A01G201900 chr6A 96.774 124 2 2 675 798 60616431 60616310 3.140000e-49 206.0
16 TraesCS3A01G201900 chr3B 95.238 1113 48 2 676 1788 499928302 499927195 0.000000e+00 1757.0
17 TraesCS3A01G201900 chr3B 95.706 489 15 1 1848 2330 499924821 499924333 0.000000e+00 782.0
18 TraesCS3A01G201900 chr3B 84.669 711 108 1 676 1386 815401222 815401931 0.000000e+00 708.0
19 TraesCS3A01G201900 chr3B 87.907 430 39 9 1903 2330 815446608 815447026 5.990000e-136 494.0
20 TraesCS3A01G201900 chr3B 89.855 69 0 1 2343 2411 341204630 341204691 5.520000e-12 82.4
21 TraesCS3A01G201900 chr5A 97.858 747 16 0 675 1421 536904940 536905686 0.000000e+00 1291.0
22 TraesCS3A01G201900 chr5A 91.433 607 48 2 1 603 509986872 509986266 0.000000e+00 830.0
23 TraesCS3A01G201900 chr5A 91.225 604 47 4 2 601 679366480 679367081 0.000000e+00 817.0
24 TraesCS3A01G201900 chr5A 89.968 618 42 11 1 601 525153859 525154473 0.000000e+00 780.0
25 TraesCS3A01G201900 chr5A 87.923 621 58 6 1 605 438931522 438932141 0.000000e+00 715.0
26 TraesCS3A01G201900 chr2A 90.835 611 47 7 1 603 28153003 28152394 0.000000e+00 809.0
27 TraesCS3A01G201900 chr2A 88.834 609 58 8 3 603 214422968 214422362 0.000000e+00 739.0
28 TraesCS3A01G201900 chr2A 89.269 438 37 9 171 603 758540092 758539660 7.580000e-150 540.0
29 TraesCS3A01G201900 chr7A 90.099 606 55 4 1 601 63408790 63409395 0.000000e+00 782.0
30 TraesCS3A01G201900 chr4A 88.274 614 57 11 1 601 604016756 604017367 0.000000e+00 721.0
31 TraesCS3A01G201900 chr6D 83.171 820 94 28 675 1466 149885244 149886047 0.000000e+00 710.0
32 TraesCS3A01G201900 chr6D 83.280 311 21 12 1848 2138 149888444 149888743 8.550000e-65 257.0
33 TraesCS3A01G201900 chr6B 82.801 814 98 20 675 1460 274388528 274389327 0.000000e+00 689.0
34 TraesCS3A01G201900 chr6B 86.079 431 45 8 1903 2331 274391798 274392215 1.310000e-122 449.0
35 TraesCS3A01G201900 chr6B 88.679 53 6 0 1845 1897 274391719 274391771 5.560000e-07 65.8
36 TraesCS3A01G201900 chr4B 86.848 479 52 10 136 605 670273641 670273165 2.120000e-145 525.0
37 TraesCS3A01G201900 chr7B 87.007 431 42 10 1905 2331 619083181 619083601 7.800000e-130 473.0
38 TraesCS3A01G201900 chr2B 86.311 431 42 9 1903 2330 381501573 381501989 1.020000e-123 453.0
39 TraesCS3A01G201900 chr5D 75.359 487 69 29 1873 2331 491788182 491787719 1.140000e-43 187.0
40 TraesCS3A01G201900 chr3D 98.810 84 0 1 2329 2411 239569229 239569312 5.370000e-32 148.0


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 TraesCS3A01G201900 chr3A 340258524 340260934 2410 False 4453.000000 4453 100.0000 1 2411 1 chr3A.!!$F1 2410
1 TraesCS3A01G201900 chr3A 17492789 17494227 1438 True 2471.000000 2471 97.7080 895 2330 1 chr3A.!!$R1 1435
2 TraesCS3A01G201900 chr3A 599890862 599892838 1976 True 1316.500000 2464 96.1220 676 2330 2 chr3A.!!$R3 1654
3 TraesCS3A01G201900 chr3A 682032893 682033509 616 True 782.000000 782 89.9840 1 602 1 chr3A.!!$R2 601
4 TraesCS3A01G201900 chr1A 494700520 494701694 1174 True 1932.000000 1932 96.3440 676 1851 1 chr1A.!!$R2 1175
5 TraesCS3A01G201900 chr1A 152713510 152714625 1115 True 1559.000000 1559 91.9500 676 1788 1 chr1A.!!$R1 1112
6 TraesCS3A01G201900 chr1A 504741186 504741794 608 True 721.000000 721 88.2740 1 603 1 chr1A.!!$R3 602
7 TraesCS3A01G201900 chr1A 152703166 152703680 514 True 391.000000 652 95.6090 1848 2331 2 chr1A.!!$R4 483
8 TraesCS3A01G201900 chr6A 60603348 60606806 3458 True 1068.500000 1832 96.0335 794 2044 2 chr6A.!!$R5 1250
9 TraesCS3A01G201900 chr6A 577761865 577762479 614 True 678.000000 678 86.9350 1 606 1 chr6A.!!$R4 605
10 TraesCS3A01G201900 chr6A 195274493 195274993 500 True 455.000000 455 83.9840 1848 2331 1 chr6A.!!$R3 483
11 TraesCS3A01G201900 chr3B 499924333 499928302 3969 True 1269.500000 1757 95.4720 676 2330 2 chr3B.!!$R1 1654
12 TraesCS3A01G201900 chr3B 815401222 815401931 709 False 708.000000 708 84.6690 676 1386 1 chr3B.!!$F2 710
13 TraesCS3A01G201900 chr5A 536904940 536905686 746 False 1291.000000 1291 97.8580 675 1421 1 chr5A.!!$F3 746
14 TraesCS3A01G201900 chr5A 509986266 509986872 606 True 830.000000 830 91.4330 1 603 1 chr5A.!!$R1 602
15 TraesCS3A01G201900 chr5A 679366480 679367081 601 False 817.000000 817 91.2250 2 601 1 chr5A.!!$F4 599
16 TraesCS3A01G201900 chr5A 525153859 525154473 614 False 780.000000 780 89.9680 1 601 1 chr5A.!!$F2 600
17 TraesCS3A01G201900 chr5A 438931522 438932141 619 False 715.000000 715 87.9230 1 605 1 chr5A.!!$F1 604
18 TraesCS3A01G201900 chr2A 28152394 28153003 609 True 809.000000 809 90.8350 1 603 1 chr2A.!!$R1 602
19 TraesCS3A01G201900 chr2A 214422362 214422968 606 True 739.000000 739 88.8340 3 603 1 chr2A.!!$R2 600
20 TraesCS3A01G201900 chr7A 63408790 63409395 605 False 782.000000 782 90.0990 1 601 1 chr7A.!!$F1 600
21 TraesCS3A01G201900 chr4A 604016756 604017367 611 False 721.000000 721 88.2740 1 601 1 chr4A.!!$F1 600
22 TraesCS3A01G201900 chr6D 149885244 149888743 3499 False 483.500000 710 83.2255 675 2138 2 chr6D.!!$F1 1463
23 TraesCS3A01G201900 chr6B 274388528 274392215 3687 False 401.266667 689 85.8530 675 2331 3 chr6B.!!$F1 1656

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
653 698 0.03918 TCTGTCTCGAGGCCTACCAA 59.961 55.0 15.72 0.0 39.06 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2345 7531 0.320421 CGACGAGGGAAGCAAAGGAA 60.32 55.0 0.0 0.0 0.0 3.36 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
322 355 1.960040 AATGGCAGGCTGATCGACGA 61.960 55.000 20.86 0.00 0.00 4.20
338 377 1.062587 GACGACCTTGGCATTGATTCG 59.937 52.381 0.00 0.00 0.00 3.34
345 384 3.572539 GCATTGATTCGCCGCGGA 61.573 61.111 33.48 8.89 0.00 5.54
369 408 1.339247 ACTGAGACGATGAGGACGACT 60.339 52.381 0.00 0.00 38.25 4.18
411 450 1.664306 GGTCCCGTCACTCTTTCGT 59.336 57.895 0.00 0.00 0.00 3.85
428 467 3.578272 TGCCAAAACGTTCGCGCT 61.578 55.556 5.56 0.00 46.04 5.92
429 468 2.245346 TGCCAAAACGTTCGCGCTA 61.245 52.632 5.56 0.00 46.04 4.26
502 541 0.614415 AATTTCGGCCCAATCCAGCA 60.614 50.000 0.00 0.00 0.00 4.41
603 648 0.179073 GCGGCTGGAGATGCTCTTAA 60.179 55.000 0.00 0.00 0.00 1.85
604 649 1.576356 CGGCTGGAGATGCTCTTAAC 58.424 55.000 0.00 0.00 0.00 2.01
605 650 1.137872 CGGCTGGAGATGCTCTTAACT 59.862 52.381 0.00 0.00 0.00 2.24
606 651 2.362397 CGGCTGGAGATGCTCTTAACTA 59.638 50.000 0.00 0.00 0.00 2.24
607 652 3.006323 CGGCTGGAGATGCTCTTAACTAT 59.994 47.826 0.00 0.00 0.00 2.12
608 653 4.565022 GGCTGGAGATGCTCTTAACTATC 58.435 47.826 0.00 0.00 0.00 2.08
609 654 4.283212 GGCTGGAGATGCTCTTAACTATCT 59.717 45.833 0.00 0.00 32.87 1.98
610 655 5.221621 GGCTGGAGATGCTCTTAACTATCTT 60.222 44.000 0.00 0.00 30.49 2.40
611 656 5.925969 GCTGGAGATGCTCTTAACTATCTTC 59.074 44.000 0.00 0.00 30.49 2.87
612 657 6.239289 GCTGGAGATGCTCTTAACTATCTTCT 60.239 42.308 0.00 0.00 30.49 2.85
613 658 7.040062 GCTGGAGATGCTCTTAACTATCTTCTA 60.040 40.741 0.00 0.00 30.49 2.10
614 659 8.948401 TGGAGATGCTCTTAACTATCTTCTAT 57.052 34.615 0.00 0.00 30.49 1.98
615 660 9.019656 TGGAGATGCTCTTAACTATCTTCTATC 57.980 37.037 0.00 0.00 30.49 2.08
616 661 9.243105 GGAGATGCTCTTAACTATCTTCTATCT 57.757 37.037 0.00 0.00 30.49 1.98
618 663 8.946085 AGATGCTCTTAACTATCTTCTATCTCG 58.054 37.037 0.00 0.00 0.00 4.04
619 664 8.856153 ATGCTCTTAACTATCTTCTATCTCGA 57.144 34.615 0.00 0.00 0.00 4.04
620 665 8.317891 TGCTCTTAACTATCTTCTATCTCGAG 57.682 38.462 5.93 5.93 0.00 4.04
621 666 8.151596 TGCTCTTAACTATCTTCTATCTCGAGA 58.848 37.037 19.19 19.19 0.00 4.04
622 667 8.656849 GCTCTTAACTATCTTCTATCTCGAGAG 58.343 40.741 21.52 8.34 0.00 3.20
623 668 8.542497 TCTTAACTATCTTCTATCTCGAGAGC 57.458 38.462 21.52 0.00 0.00 4.09
624 669 8.372459 TCTTAACTATCTTCTATCTCGAGAGCT 58.628 37.037 21.52 7.56 0.00 4.09
625 670 6.801539 AACTATCTTCTATCTCGAGAGCTG 57.198 41.667 21.52 12.73 0.00 4.24
626 671 5.865085 ACTATCTTCTATCTCGAGAGCTGT 58.135 41.667 21.52 6.38 0.00 4.40
627 672 5.932303 ACTATCTTCTATCTCGAGAGCTGTC 59.068 44.000 21.52 0.00 0.00 3.51
628 673 4.143986 TCTTCTATCTCGAGAGCTGTCA 57.856 45.455 21.52 0.52 0.00 3.58
629 674 4.518249 TCTTCTATCTCGAGAGCTGTCAA 58.482 43.478 21.52 6.57 0.00 3.18
630 675 4.944317 TCTTCTATCTCGAGAGCTGTCAAA 59.056 41.667 21.52 7.05 0.00 2.69
631 676 5.416013 TCTTCTATCTCGAGAGCTGTCAAAA 59.584 40.000 21.52 5.62 0.00 2.44
632 677 4.987832 TCTATCTCGAGAGCTGTCAAAAC 58.012 43.478 21.52 0.00 0.00 2.43
633 678 3.667497 ATCTCGAGAGCTGTCAAAACA 57.333 42.857 21.52 0.00 0.00 2.83
634 679 3.667497 TCTCGAGAGCTGTCAAAACAT 57.333 42.857 12.08 0.00 34.13 2.71
635 680 3.579709 TCTCGAGAGCTGTCAAAACATC 58.420 45.455 12.08 0.00 34.13 3.06
636 681 3.256879 TCTCGAGAGCTGTCAAAACATCT 59.743 43.478 12.08 0.00 34.63 2.90
637 682 3.320626 TCGAGAGCTGTCAAAACATCTG 58.679 45.455 11.90 0.00 32.15 2.90
638 683 3.062763 CGAGAGCTGTCAAAACATCTGT 58.937 45.455 11.90 0.00 32.15 3.41
639 684 3.122613 CGAGAGCTGTCAAAACATCTGTC 59.877 47.826 11.90 0.00 38.11 3.51
640 685 4.314121 GAGAGCTGTCAAAACATCTGTCT 58.686 43.478 5.89 0.00 38.32 3.41
641 686 4.314121 AGAGCTGTCAAAACATCTGTCTC 58.686 43.478 0.00 0.00 32.15 3.36
642 687 3.062763 AGCTGTCAAAACATCTGTCTCG 58.937 45.455 0.00 0.00 30.84 4.04
643 688 3.059884 GCTGTCAAAACATCTGTCTCGA 58.940 45.455 0.00 0.00 34.13 4.04
644 689 3.122613 GCTGTCAAAACATCTGTCTCGAG 59.877 47.826 5.93 5.93 34.13 4.04
645 690 3.653344 TGTCAAAACATCTGTCTCGAGG 58.347 45.455 13.56 0.00 0.00 4.63
646 691 2.413453 GTCAAAACATCTGTCTCGAGGC 59.587 50.000 10.89 10.89 0.00 4.70
647 692 1.734465 CAAAACATCTGTCTCGAGGCC 59.266 52.381 15.72 5.30 0.00 5.19
648 693 1.270907 AAACATCTGTCTCGAGGCCT 58.729 50.000 15.72 3.86 0.00 5.19
649 694 2.145397 AACATCTGTCTCGAGGCCTA 57.855 50.000 15.72 2.29 0.00 3.93
650 695 1.394618 ACATCTGTCTCGAGGCCTAC 58.605 55.000 15.72 0.00 0.00 3.18
651 696 0.671251 CATCTGTCTCGAGGCCTACC 59.329 60.000 15.72 0.00 0.00 3.18
652 697 0.259065 ATCTGTCTCGAGGCCTACCA 59.741 55.000 15.72 0.00 39.06 3.25
653 698 0.039180 TCTGTCTCGAGGCCTACCAA 59.961 55.000 15.72 0.00 39.06 3.67
654 699 0.895530 CTGTCTCGAGGCCTACCAAA 59.104 55.000 15.72 0.00 39.06 3.28
655 700 1.275291 CTGTCTCGAGGCCTACCAAAA 59.725 52.381 15.72 0.00 39.06 2.44
656 701 1.001633 TGTCTCGAGGCCTACCAAAAC 59.998 52.381 15.72 0.00 39.06 2.43
657 702 1.001633 GTCTCGAGGCCTACCAAAACA 59.998 52.381 13.56 0.00 39.06 2.83
658 703 1.001633 TCTCGAGGCCTACCAAAACAC 59.998 52.381 13.56 0.00 39.06 3.32
659 704 1.002087 CTCGAGGCCTACCAAAACACT 59.998 52.381 4.42 0.00 39.06 3.55
660 705 1.418637 TCGAGGCCTACCAAAACACTT 59.581 47.619 4.42 0.00 39.06 3.16
661 706 1.535462 CGAGGCCTACCAAAACACTTG 59.465 52.381 4.42 0.00 39.06 3.16
662 707 2.583143 GAGGCCTACCAAAACACTTGT 58.417 47.619 4.42 0.00 39.06 3.16
663 708 2.552743 GAGGCCTACCAAAACACTTGTC 59.447 50.000 4.42 0.00 39.06 3.18
664 709 2.174854 AGGCCTACCAAAACACTTGTCT 59.825 45.455 1.29 0.00 39.06 3.41
665 710 2.293399 GGCCTACCAAAACACTTGTCTG 59.707 50.000 0.00 0.00 35.26 3.51
666 711 2.949644 GCCTACCAAAACACTTGTCTGT 59.050 45.455 0.00 0.00 0.00 3.41
667 712 3.003378 GCCTACCAAAACACTTGTCTGTC 59.997 47.826 0.00 0.00 0.00 3.51
668 713 4.451900 CCTACCAAAACACTTGTCTGTCT 58.548 43.478 0.00 0.00 0.00 3.41
669 714 5.607477 CCTACCAAAACACTTGTCTGTCTA 58.393 41.667 0.00 0.00 0.00 2.59
670 715 6.053005 CCTACCAAAACACTTGTCTGTCTAA 58.947 40.000 0.00 0.00 0.00 2.10
671 716 6.202954 CCTACCAAAACACTTGTCTGTCTAAG 59.797 42.308 0.00 0.00 0.00 2.18
672 717 5.741011 ACCAAAACACTTGTCTGTCTAAGA 58.259 37.500 0.00 0.00 0.00 2.10
1028 1423 2.711922 GCGGAGGAGAAGAAGCCGA 61.712 63.158 0.00 0.00 44.43 5.54
1390 1785 1.444553 GACGCCGTGGAGAAGACAG 60.445 63.158 0.00 0.00 0.00 3.51
1424 1819 0.739561 CCGTGAGTACCAGTAGCTCC 59.260 60.000 0.00 0.00 0.00 4.70
1616 2012 3.273434 GCTGGATGCAATCTAAGTGTGA 58.727 45.455 0.00 0.00 44.71 3.58
1696 2095 4.640771 ATGGTTGGTAGATGACAGTGTT 57.359 40.909 0.00 0.00 0.00 3.32
1764 2163 4.762251 ACAATAAGTCCTGGTCTTTGAAGC 59.238 41.667 11.33 0.00 0.00 3.86
1827 2335 6.959311 CGTGCATACTAAATAAACAGTTGGAC 59.041 38.462 0.00 0.00 0.00 4.02
2111 7295 9.257651 CTTTGTTGTTTTACTAGTACTACAGCT 57.742 33.333 20.95 0.00 31.30 4.24
2134 7318 5.450453 TGTTGGAGGGAACAGTGAAAATTA 58.550 37.500 0.00 0.00 32.05 1.40
2267 7453 8.401955 AAATGAGGAGAGTAAGGGGTTTTATA 57.598 34.615 0.00 0.00 0.00 0.98
2331 7517 3.525545 GCGGACGGAGGGAGTACC 61.526 72.222 0.00 0.00 40.67 3.34
2342 7528 1.822506 GGGAGTACCTTTGCAGTTCC 58.177 55.000 0.00 0.00 35.85 3.62
2343 7529 1.073284 GGGAGTACCTTTGCAGTTCCA 59.927 52.381 0.00 0.00 35.85 3.53
2344 7530 2.488347 GGGAGTACCTTTGCAGTTCCAA 60.488 50.000 0.00 0.00 35.85 3.53
2345 7531 3.421844 GGAGTACCTTTGCAGTTCCAAT 58.578 45.455 0.00 0.00 0.00 3.16
2346 7532 3.826729 GGAGTACCTTTGCAGTTCCAATT 59.173 43.478 0.00 0.00 0.00 2.32
2347 7533 4.082733 GGAGTACCTTTGCAGTTCCAATTC 60.083 45.833 0.00 0.00 0.00 2.17
2348 7534 3.826729 AGTACCTTTGCAGTTCCAATTCC 59.173 43.478 0.00 0.00 0.00 3.01
2349 7535 2.962859 ACCTTTGCAGTTCCAATTCCT 58.037 42.857 0.00 0.00 0.00 3.36
2350 7536 3.308401 ACCTTTGCAGTTCCAATTCCTT 58.692 40.909 0.00 0.00 0.00 3.36
2351 7537 3.711190 ACCTTTGCAGTTCCAATTCCTTT 59.289 39.130 0.00 0.00 0.00 3.11
2352 7538 4.060205 CCTTTGCAGTTCCAATTCCTTTG 58.940 43.478 0.00 0.00 34.93 2.77
2353 7539 2.818130 TGCAGTTCCAATTCCTTTGC 57.182 45.000 0.00 0.00 33.73 3.68
2354 7540 2.318908 TGCAGTTCCAATTCCTTTGCT 58.681 42.857 0.00 0.00 33.73 3.91
2355 7541 2.699846 TGCAGTTCCAATTCCTTTGCTT 59.300 40.909 0.00 0.00 33.73 3.91
2356 7542 3.243839 TGCAGTTCCAATTCCTTTGCTTC 60.244 43.478 0.00 0.00 33.73 3.86
2357 7543 3.862264 GCAGTTCCAATTCCTTTGCTTCC 60.862 47.826 0.00 0.00 33.73 3.46
2358 7544 2.899900 AGTTCCAATTCCTTTGCTTCCC 59.100 45.455 0.00 0.00 33.73 3.97
2359 7545 2.899900 GTTCCAATTCCTTTGCTTCCCT 59.100 45.455 0.00 0.00 33.73 4.20
2360 7546 2.807676 TCCAATTCCTTTGCTTCCCTC 58.192 47.619 0.00 0.00 33.73 4.30
2361 7547 1.474077 CCAATTCCTTTGCTTCCCTCG 59.526 52.381 0.00 0.00 33.73 4.63
2362 7548 2.162681 CAATTCCTTTGCTTCCCTCGT 58.837 47.619 0.00 0.00 0.00 4.18
2363 7549 2.115343 ATTCCTTTGCTTCCCTCGTC 57.885 50.000 0.00 0.00 0.00 4.20
2364 7550 0.320421 TTCCTTTGCTTCCCTCGTCG 60.320 55.000 0.00 0.00 0.00 5.12
2365 7551 1.741770 CCTTTGCTTCCCTCGTCGG 60.742 63.158 0.00 0.00 0.00 4.79
2366 7552 2.358247 TTTGCTTCCCTCGTCGGC 60.358 61.111 0.00 0.00 0.00 5.54
2367 7553 3.894547 TTTGCTTCCCTCGTCGGCC 62.895 63.158 0.00 0.00 0.00 6.13
2369 7555 4.162690 GCTTCCCTCGTCGGCCAT 62.163 66.667 2.24 0.00 0.00 4.40
2370 7556 2.107141 CTTCCCTCGTCGGCCATC 59.893 66.667 2.24 0.00 0.00 3.51
2371 7557 3.447025 CTTCCCTCGTCGGCCATCC 62.447 68.421 2.24 0.00 0.00 3.51
2374 7560 3.781307 CCTCGTCGGCCATCCCAA 61.781 66.667 2.24 0.00 0.00 4.12
2375 7561 2.505982 CTCGTCGGCCATCCCAAT 59.494 61.111 2.24 0.00 0.00 3.16
2376 7562 1.153168 CTCGTCGGCCATCCCAATT 60.153 57.895 2.24 0.00 0.00 2.32
2377 7563 1.153249 TCGTCGGCCATCCCAATTC 60.153 57.895 2.24 0.00 0.00 2.17
2378 7564 2.186826 CGTCGGCCATCCCAATTCC 61.187 63.158 2.24 0.00 0.00 3.01
2379 7565 1.828224 GTCGGCCATCCCAATTCCC 60.828 63.158 2.24 0.00 0.00 3.97
2380 7566 2.521708 CGGCCATCCCAATTCCCC 60.522 66.667 2.24 0.00 0.00 4.81
2381 7567 2.695597 GGCCATCCCAATTCCCCA 59.304 61.111 0.00 0.00 0.00 4.96
2382 7568 1.002792 GGCCATCCCAATTCCCCAA 59.997 57.895 0.00 0.00 0.00 4.12
2383 7569 1.337384 GGCCATCCCAATTCCCCAAC 61.337 60.000 0.00 0.00 0.00 3.77
2384 7570 0.617249 GCCATCCCAATTCCCCAACA 60.617 55.000 0.00 0.00 0.00 3.33
2385 7571 1.971215 GCCATCCCAATTCCCCAACAT 60.971 52.381 0.00 0.00 0.00 2.71
2386 7572 2.041701 CCATCCCAATTCCCCAACATC 58.958 52.381 0.00 0.00 0.00 3.06
2387 7573 2.359568 CCATCCCAATTCCCCAACATCT 60.360 50.000 0.00 0.00 0.00 2.90
2388 7574 2.826674 TCCCAATTCCCCAACATCTC 57.173 50.000 0.00 0.00 0.00 2.75
2389 7575 1.287739 TCCCAATTCCCCAACATCTCC 59.712 52.381 0.00 0.00 0.00 3.71
2390 7576 1.006998 CCCAATTCCCCAACATCTCCA 59.993 52.381 0.00 0.00 0.00 3.86
2391 7577 2.102578 CCAATTCCCCAACATCTCCAC 58.897 52.381 0.00 0.00 0.00 4.02
2392 7578 2.102578 CAATTCCCCAACATCTCCACC 58.897 52.381 0.00 0.00 0.00 4.61
2393 7579 1.381867 ATTCCCCAACATCTCCACCA 58.618 50.000 0.00 0.00 0.00 4.17
2394 7580 0.698238 TTCCCCAACATCTCCACCAG 59.302 55.000 0.00 0.00 0.00 4.00
2395 7581 1.379044 CCCCAACATCTCCACCAGC 60.379 63.158 0.00 0.00 0.00 4.85
2396 7582 1.379044 CCCAACATCTCCACCAGCC 60.379 63.158 0.00 0.00 0.00 4.85
2397 7583 1.379044 CCAACATCTCCACCAGCCC 60.379 63.158 0.00 0.00 0.00 5.19
2398 7584 1.379044 CAACATCTCCACCAGCCCC 60.379 63.158 0.00 0.00 0.00 5.80
2399 7585 2.971598 AACATCTCCACCAGCCCCG 61.972 63.158 0.00 0.00 0.00 5.73
2400 7586 4.864334 CATCTCCACCAGCCCCGC 62.864 72.222 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 96 3.121030 GCAACCATGAGCGCGAGT 61.121 61.111 12.10 0.00 0.00 4.18
130 143 3.068691 CCCTCTCTCCGCCGTTCA 61.069 66.667 0.00 0.00 0.00 3.18
169 188 2.765807 CATCGGCAGTCCTCCCCT 60.766 66.667 0.00 0.00 0.00 4.79
338 377 1.206831 GTCTCAGTTTTTCCGCGGC 59.793 57.895 23.51 5.81 0.00 6.53
345 384 3.005472 TCGTCCTCATCGTCTCAGTTTTT 59.995 43.478 0.00 0.00 0.00 1.94
369 408 1.801332 GTCAGCGAGACGAAGGCTA 59.199 57.895 0.00 0.00 37.53 3.93
411 450 2.165362 CTAGCGCGAACGTTTTGGCA 62.165 55.000 12.10 0.00 42.83 4.92
455 494 3.943691 CACCCAACCCGAACCCGA 61.944 66.667 0.00 0.00 38.22 5.14
566 606 2.286523 CGTCCTCAACAGGCCTCCT 61.287 63.158 0.00 0.00 40.12 3.69
603 648 5.865085 ACAGCTCTCGAGATAGAAGATAGT 58.135 41.667 17.03 1.49 0.00 2.12
604 649 5.931724 TGACAGCTCTCGAGATAGAAGATAG 59.068 44.000 17.03 1.64 0.00 2.08
605 650 5.859495 TGACAGCTCTCGAGATAGAAGATA 58.141 41.667 17.03 0.00 0.00 1.98
606 651 4.713553 TGACAGCTCTCGAGATAGAAGAT 58.286 43.478 17.03 0.00 0.00 2.40
607 652 4.143986 TGACAGCTCTCGAGATAGAAGA 57.856 45.455 17.03 0.00 0.00 2.87
608 653 4.891627 TTGACAGCTCTCGAGATAGAAG 57.108 45.455 17.03 4.82 0.00 2.85
609 654 5.048013 TGTTTTGACAGCTCTCGAGATAGAA 60.048 40.000 17.03 0.77 0.00 2.10
610 655 4.459337 TGTTTTGACAGCTCTCGAGATAGA 59.541 41.667 17.03 0.00 0.00 1.98
611 656 4.738124 TGTTTTGACAGCTCTCGAGATAG 58.262 43.478 17.03 11.16 0.00 2.08
612 657 4.783764 TGTTTTGACAGCTCTCGAGATA 57.216 40.909 17.03 0.00 0.00 1.98
613 658 3.667497 TGTTTTGACAGCTCTCGAGAT 57.333 42.857 17.03 0.00 0.00 2.75
614 659 3.256879 AGATGTTTTGACAGCTCTCGAGA 59.743 43.478 15.70 15.70 29.41 4.04
615 660 3.367327 CAGATGTTTTGACAGCTCTCGAG 59.633 47.826 5.93 5.93 33.69 4.04
616 661 3.243873 ACAGATGTTTTGACAGCTCTCGA 60.244 43.478 0.00 0.00 33.69 4.04
617 662 3.062763 ACAGATGTTTTGACAGCTCTCG 58.937 45.455 0.00 0.00 33.69 4.04
618 663 4.314121 AGACAGATGTTTTGACAGCTCTC 58.686 43.478 0.00 0.00 33.69 3.20
619 664 4.314121 GAGACAGATGTTTTGACAGCTCT 58.686 43.478 0.00 0.00 33.69 4.09
620 665 3.122613 CGAGACAGATGTTTTGACAGCTC 59.877 47.826 0.00 0.00 33.69 4.09
621 666 3.062763 CGAGACAGATGTTTTGACAGCT 58.937 45.455 0.00 0.00 36.74 4.24
622 667 3.059884 TCGAGACAGATGTTTTGACAGC 58.940 45.455 0.00 0.00 0.00 4.40
623 668 3.677121 CCTCGAGACAGATGTTTTGACAG 59.323 47.826 15.71 0.00 0.00 3.51
624 669 3.653344 CCTCGAGACAGATGTTTTGACA 58.347 45.455 15.71 0.00 0.00 3.58
625 670 2.413453 GCCTCGAGACAGATGTTTTGAC 59.587 50.000 15.71 0.00 0.00 3.18
626 671 2.612972 GGCCTCGAGACAGATGTTTTGA 60.613 50.000 15.71 0.00 0.00 2.69
627 672 1.734465 GGCCTCGAGACAGATGTTTTG 59.266 52.381 15.71 0.00 0.00 2.44
628 673 1.625818 AGGCCTCGAGACAGATGTTTT 59.374 47.619 15.71 0.00 0.00 2.43
629 674 1.270907 AGGCCTCGAGACAGATGTTT 58.729 50.000 15.71 0.00 0.00 2.83
630 675 1.751924 GTAGGCCTCGAGACAGATGTT 59.248 52.381 9.68 0.00 0.00 2.71
631 676 1.394618 GTAGGCCTCGAGACAGATGT 58.605 55.000 9.68 0.00 0.00 3.06
632 677 0.671251 GGTAGGCCTCGAGACAGATG 59.329 60.000 9.68 0.00 0.00 2.90
633 678 0.259065 TGGTAGGCCTCGAGACAGAT 59.741 55.000 9.68 0.00 35.27 2.90
634 679 0.039180 TTGGTAGGCCTCGAGACAGA 59.961 55.000 9.68 0.00 35.27 3.41
635 680 0.895530 TTTGGTAGGCCTCGAGACAG 59.104 55.000 9.68 0.00 35.27 3.51
636 681 1.001633 GTTTTGGTAGGCCTCGAGACA 59.998 52.381 9.68 0.00 35.27 3.41
637 682 1.001633 TGTTTTGGTAGGCCTCGAGAC 59.998 52.381 9.68 0.57 35.27 3.36
638 683 1.001633 GTGTTTTGGTAGGCCTCGAGA 59.998 52.381 9.68 0.00 35.27 4.04
639 684 1.002087 AGTGTTTTGGTAGGCCTCGAG 59.998 52.381 9.68 5.13 35.27 4.04
640 685 1.053424 AGTGTTTTGGTAGGCCTCGA 58.947 50.000 9.68 0.00 35.27 4.04
641 686 1.535462 CAAGTGTTTTGGTAGGCCTCG 59.465 52.381 9.68 0.00 35.27 4.63
642 687 2.552743 GACAAGTGTTTTGGTAGGCCTC 59.447 50.000 9.68 0.00 35.27 4.70
643 688 2.174854 AGACAAGTGTTTTGGTAGGCCT 59.825 45.455 11.78 11.78 35.27 5.19
644 689 2.293399 CAGACAAGTGTTTTGGTAGGCC 59.707 50.000 0.00 0.00 0.00 5.19
645 690 2.949644 ACAGACAAGTGTTTTGGTAGGC 59.050 45.455 0.00 0.00 0.00 3.93
646 691 4.451900 AGACAGACAAGTGTTTTGGTAGG 58.548 43.478 0.00 0.00 0.00 3.18
647 692 6.984474 TCTTAGACAGACAAGTGTTTTGGTAG 59.016 38.462 0.00 0.00 0.00 3.18
648 693 6.880484 TCTTAGACAGACAAGTGTTTTGGTA 58.120 36.000 0.00 0.00 0.00 3.25
649 694 5.741011 TCTTAGACAGACAAGTGTTTTGGT 58.259 37.500 0.00 0.00 0.00 3.67
662 707 3.202595 GGAGGGAGTAGGTCTTAGACAGA 59.797 52.174 14.72 0.00 33.68 3.41
663 708 3.558033 GGAGGGAGTAGGTCTTAGACAG 58.442 54.545 14.72 0.00 33.68 3.51
664 709 2.092538 CGGAGGGAGTAGGTCTTAGACA 60.093 54.545 14.72 0.00 33.68 3.41
665 710 2.092484 ACGGAGGGAGTAGGTCTTAGAC 60.092 54.545 3.36 3.36 0.00 2.59
666 711 2.172293 GACGGAGGGAGTAGGTCTTAGA 59.828 54.545 0.00 0.00 0.00 2.10
667 712 2.574450 GACGGAGGGAGTAGGTCTTAG 58.426 57.143 0.00 0.00 0.00 2.18
668 713 1.213926 GGACGGAGGGAGTAGGTCTTA 59.786 57.143 0.00 0.00 0.00 2.10
669 714 0.033306 GGACGGAGGGAGTAGGTCTT 60.033 60.000 0.00 0.00 0.00 3.01
670 715 1.614160 GGACGGAGGGAGTAGGTCT 59.386 63.158 0.00 0.00 0.00 3.85
671 716 1.823041 CGGACGGAGGGAGTAGGTC 60.823 68.421 0.00 0.00 0.00 3.85
672 717 2.274760 CGGACGGAGGGAGTAGGT 59.725 66.667 0.00 0.00 0.00 3.08
673 718 3.217743 GCGGACGGAGGGAGTAGG 61.218 72.222 0.00 0.00 0.00 3.18
1028 1423 0.957395 CTTGACTTGCTGGCCATCGT 60.957 55.000 5.51 0.15 0.00 3.73
1390 1785 3.130693 ACTCACGGAGTAGTAGAATTGCC 59.869 47.826 4.93 0.00 41.61 4.52
1424 1819 1.882198 CTTGCATCGCCAAACTTACG 58.118 50.000 0.00 0.00 0.00 3.18
1696 2095 8.491152 CAAATTATGCAACCGAAAATTGTAACA 58.509 29.630 0.00 0.00 0.00 2.41
1764 2163 7.834803 TCATATCCAACATCTAGCATCTGTAG 58.165 38.462 0.00 0.00 0.00 2.74
1802 2310 6.959311 GTCCAACTGTTTATTTAGTATGCACG 59.041 38.462 0.00 0.00 0.00 5.34
1827 2335 9.942850 AGATGGACTTTGGGTTAAAATTATTTG 57.057 29.630 0.00 0.00 0.00 2.32
2111 7295 3.374042 TTTTCACTGTTCCCTCCAACA 57.626 42.857 0.00 0.00 34.99 3.33
2134 7318 1.293498 CCGCCAGCAAGTGTACTCT 59.707 57.895 0.00 0.00 0.00 3.24
2331 7517 3.495753 GCAAAGGAATTGGAACTGCAAAG 59.504 43.478 0.00 0.00 39.54 2.77
2332 7518 3.134442 AGCAAAGGAATTGGAACTGCAAA 59.866 39.130 0.00 0.00 39.54 3.68
2333 7519 2.699846 AGCAAAGGAATTGGAACTGCAA 59.300 40.909 0.00 0.00 39.54 4.08
2334 7520 2.318908 AGCAAAGGAATTGGAACTGCA 58.681 42.857 0.00 0.00 39.54 4.41
2335 7521 3.320626 GAAGCAAAGGAATTGGAACTGC 58.679 45.455 0.00 0.00 39.54 4.40
2336 7522 3.306294 GGGAAGCAAAGGAATTGGAACTG 60.306 47.826 0.00 0.00 39.54 3.16
2337 7523 2.899900 GGGAAGCAAAGGAATTGGAACT 59.100 45.455 0.00 0.00 39.54 3.01
2338 7524 2.899900 AGGGAAGCAAAGGAATTGGAAC 59.100 45.455 0.00 0.00 39.54 3.62
2339 7525 3.165071 GAGGGAAGCAAAGGAATTGGAA 58.835 45.455 0.00 0.00 39.54 3.53
2340 7526 2.807676 GAGGGAAGCAAAGGAATTGGA 58.192 47.619 0.00 0.00 39.54 3.53
2341 7527 1.474077 CGAGGGAAGCAAAGGAATTGG 59.526 52.381 0.00 0.00 39.54 3.16
2342 7528 2.162408 GACGAGGGAAGCAAAGGAATTG 59.838 50.000 0.00 0.00 42.21 2.32
2343 7529 2.437413 GACGAGGGAAGCAAAGGAATT 58.563 47.619 0.00 0.00 0.00 2.17
2344 7530 1.676014 CGACGAGGGAAGCAAAGGAAT 60.676 52.381 0.00 0.00 0.00 3.01
2345 7531 0.320421 CGACGAGGGAAGCAAAGGAA 60.320 55.000 0.00 0.00 0.00 3.36
2346 7532 1.292223 CGACGAGGGAAGCAAAGGA 59.708 57.895 0.00 0.00 0.00 3.36
2347 7533 1.741770 CCGACGAGGGAAGCAAAGG 60.742 63.158 0.00 0.00 35.97 3.11
2348 7534 2.391389 GCCGACGAGGGAAGCAAAG 61.391 63.158 0.00 0.00 41.48 2.77
2349 7535 2.358247 GCCGACGAGGGAAGCAAA 60.358 61.111 0.00 0.00 41.48 3.68
2350 7536 4.388499 GGCCGACGAGGGAAGCAA 62.388 66.667 0.00 0.00 41.48 3.91
2352 7538 4.162690 ATGGCCGACGAGGGAAGC 62.163 66.667 0.00 0.00 41.48 3.86
2353 7539 2.107141 GATGGCCGACGAGGGAAG 59.893 66.667 0.00 0.00 41.48 3.46
2354 7540 3.467226 GGATGGCCGACGAGGGAA 61.467 66.667 0.00 0.00 41.48 3.97
2357 7543 2.608970 AATTGGGATGGCCGACGAGG 62.609 60.000 0.00 0.00 44.97 4.63
2358 7544 1.153168 AATTGGGATGGCCGACGAG 60.153 57.895 0.00 0.00 33.83 4.18
2359 7545 1.153249 GAATTGGGATGGCCGACGA 60.153 57.895 0.00 0.00 33.83 4.20
2360 7546 2.186826 GGAATTGGGATGGCCGACG 61.187 63.158 0.00 0.00 33.83 5.12
2361 7547 1.828224 GGGAATTGGGATGGCCGAC 60.828 63.158 0.00 0.00 33.83 4.79
2362 7548 2.600731 GGGAATTGGGATGGCCGA 59.399 61.111 0.00 0.00 33.83 5.54
2363 7549 2.521708 GGGGAATTGGGATGGCCG 60.522 66.667 0.00 0.00 33.83 6.13
2364 7550 1.002792 TTGGGGAATTGGGATGGCC 59.997 57.895 0.00 0.00 0.00 5.36
2365 7551 0.617249 TGTTGGGGAATTGGGATGGC 60.617 55.000 0.00 0.00 0.00 4.40
2366 7552 2.041701 GATGTTGGGGAATTGGGATGG 58.958 52.381 0.00 0.00 0.00 3.51
2367 7553 2.961062 GAGATGTTGGGGAATTGGGATG 59.039 50.000 0.00 0.00 0.00 3.51
2368 7554 2.091111 GGAGATGTTGGGGAATTGGGAT 60.091 50.000 0.00 0.00 0.00 3.85
2369 7555 1.287739 GGAGATGTTGGGGAATTGGGA 59.712 52.381 0.00 0.00 0.00 4.37
2370 7556 1.006998 TGGAGATGTTGGGGAATTGGG 59.993 52.381 0.00 0.00 0.00 4.12
2371 7557 2.102578 GTGGAGATGTTGGGGAATTGG 58.897 52.381 0.00 0.00 0.00 3.16
2372 7558 2.102578 GGTGGAGATGTTGGGGAATTG 58.897 52.381 0.00 0.00 0.00 2.32
2373 7559 1.715931 TGGTGGAGATGTTGGGGAATT 59.284 47.619 0.00 0.00 0.00 2.17
2374 7560 1.285962 CTGGTGGAGATGTTGGGGAAT 59.714 52.381 0.00 0.00 0.00 3.01
2375 7561 0.698238 CTGGTGGAGATGTTGGGGAA 59.302 55.000 0.00 0.00 0.00 3.97
2376 7562 1.852157 GCTGGTGGAGATGTTGGGGA 61.852 60.000 0.00 0.00 0.00 4.81
2377 7563 1.379044 GCTGGTGGAGATGTTGGGG 60.379 63.158 0.00 0.00 0.00 4.96
2378 7564 1.379044 GGCTGGTGGAGATGTTGGG 60.379 63.158 0.00 0.00 0.00 4.12
2379 7565 1.379044 GGGCTGGTGGAGATGTTGG 60.379 63.158 0.00 0.00 0.00 3.77
2380 7566 1.379044 GGGGCTGGTGGAGATGTTG 60.379 63.158 0.00 0.00 0.00 3.33
2381 7567 2.971598 CGGGGCTGGTGGAGATGTT 61.972 63.158 0.00 0.00 0.00 2.71
2382 7568 3.402681 CGGGGCTGGTGGAGATGT 61.403 66.667 0.00 0.00 0.00 3.06
2383 7569 4.864334 GCGGGGCTGGTGGAGATG 62.864 72.222 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.