Multiple sequence alignment - TraesCS2A01G261400

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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 TraesCS2A01G261400 chr2A 100.000 2620 0 0 1 2620 412370086 412372705 0.000000e+00 4839.0
1 TraesCS2A01G261400 chr2A 89.623 212 14 3 1 211 752725294 752725090 2.000000e-66 263.0
2 TraesCS2A01G261400 chr2A 86.826 167 19 3 521 685 587444077 587444242 1.600000e-42 183.0
3 TraesCS2A01G261400 chr2A 96.774 62 2 0 2531 2592 412372393 412372454 1.280000e-18 104.0
4 TraesCS2A01G261400 chr2D 96.387 1190 42 1 684 1873 318715941 318714753 0.000000e+00 1958.0
5 TraesCS2A01G261400 chr2D 85.549 173 21 3 521 691 494637238 494637068 7.450000e-41 178.0
6 TraesCS2A01G261400 chr2B 92.709 1207 65 7 688 1873 387153460 387152256 0.000000e+00 1720.0
7 TraesCS2A01G261400 chr2B 90.459 566 41 5 1972 2527 738649629 738650191 0.000000e+00 734.0
8 TraesCS2A01G261400 chr2B 86.932 176 19 3 1865 2038 495433830 495434003 7.400000e-46 195.0
9 TraesCS2A01G261400 chr2B 82.192 219 35 4 304 520 604324305 604324089 4.450000e-43 185.0
10 TraesCS2A01G261400 chr7D 92.208 616 38 3 1924 2530 42798441 42797827 0.000000e+00 863.0
11 TraesCS2A01G261400 chr7D 92.045 616 39 3 1924 2530 168497651 168497037 0.000000e+00 857.0
12 TraesCS2A01G261400 chr7D 91.639 598 40 6 1939 2527 556181017 556181613 0.000000e+00 819.0
13 TraesCS2A01G261400 chr7D 88.571 210 19 5 3 211 42204174 42204379 1.560000e-62 250.0
14 TraesCS2A01G261400 chr7D 84.080 201 31 1 320 520 25280060 25279861 2.660000e-45 193.0
15 TraesCS2A01G261400 chr7D 77.204 329 49 12 217 522 42204487 42204812 4.480000e-38 169.0
16 TraesCS2A01G261400 chr7D 80.000 215 38 5 315 527 25280098 25280309 1.260000e-33 154.0
17 TraesCS2A01G261400 chr7D 96.226 53 2 0 1868 1920 42798524 42798472 1.290000e-13 87.9
18 TraesCS2A01G261400 chr7D 95.745 47 2 0 1874 1920 168497728 168497682 2.800000e-10 76.8
19 TraesCS2A01G261400 chr3D 92.208 616 38 3 1921 2527 566066675 566067289 0.000000e+00 863.0
20 TraesCS2A01G261400 chr3D 92.045 616 39 3 1921 2527 546669132 546669746 0.000000e+00 857.0
21 TraesCS2A01G261400 chr3D 87.500 168 16 4 521 685 394053494 394053659 3.440000e-44 189.0
22 TraesCS2A01G261400 chr3D 86.826 167 18 3 521 685 481230277 481230113 1.600000e-42 183.0
23 TraesCS2A01G261400 chr3D 93.443 61 2 2 1860 1920 104031824 104031882 3.590000e-14 89.8
24 TraesCS2A01G261400 chr3D 95.745 47 2 0 1874 1920 546669058 546669104 2.800000e-10 76.8
25 TraesCS2A01G261400 chr1A 92.320 612 36 4 1921 2522 463816084 463815474 0.000000e+00 859.0
26 TraesCS2A01G261400 chr1A 84.571 175 23 3 521 693 358813034 358812862 1.250000e-38 171.0
27 TraesCS2A01G261400 chr1A 93.548 62 4 0 2531 2592 75802691 75802752 2.780000e-15 93.5
28 TraesCS2A01G261400 chr1B 91.883 616 40 3 1921 2527 513309946 513310560 0.000000e+00 852.0
29 TraesCS2A01G261400 chr6A 91.613 620 41 4 1921 2530 65536801 65536183 0.000000e+00 846.0
30 TraesCS2A01G261400 chr6A 91.571 261 13 2 1921 2172 143485819 143486079 4.150000e-93 351.0
31 TraesCS2A01G261400 chr6A 87.425 167 16 3 521 685 202900650 202900813 1.240000e-43 187.0
32 TraesCS2A01G261400 chr6A 86.667 165 21 1 357 520 596488366 596488202 5.760000e-42 182.0
33 TraesCS2A01G261400 chr4D 89.019 683 47 12 1874 2530 506852435 506851755 0.000000e+00 821.0
34 TraesCS2A01G261400 chr4D 86.826 167 16 5 521 685 494589629 494589791 5.760000e-42 182.0
35 TraesCS2A01G261400 chr7A 90.732 615 48 2 1921 2526 672874681 672875295 0.000000e+00 811.0
36 TraesCS2A01G261400 chr7A 85.099 302 36 4 226 520 35169963 35170262 1.520000e-77 300.0
37 TraesCS2A01G261400 chr7A 91.509 212 14 3 1 211 35169686 35169894 3.300000e-74 289.0
38 TraesCS2A01G261400 chr7A 82.724 301 45 5 225 520 515737235 515736937 7.190000e-66 261.0
39 TraesCS2A01G261400 chr7A 88.496 113 9 3 94 206 247317715 247317607 1.640000e-27 134.0
40 TraesCS2A01G261400 chr7A 96.364 55 2 0 2535 2589 672875081 672875135 9.990000e-15 91.6
41 TraesCS2A01G261400 chr7A 95.556 45 2 0 1 45 515737385 515737341 3.620000e-09 73.1
42 TraesCS2A01G261400 chr3B 90.615 618 45 6 1924 2530 803764471 803763856 0.000000e+00 808.0
43 TraesCS2A01G261400 chr3B 86.747 166 18 3 522 685 17848167 17848004 5.760000e-42 182.0
44 TraesCS2A01G261400 chr5A 87.730 163 14 4 521 680 509107307 509107466 4.450000e-43 185.0
45 TraesCS2A01G261400 chr5A 84.314 102 13 2 400 501 463615918 463615820 2.150000e-16 97.1
46 TraesCS2A01G261400 chr6B 81.065 169 27 4 354 520 64860165 64860330 2.120000e-26 130.0
47 TraesCS2A01G261400 chr4B 97.959 49 1 0 1872 1920 180054974 180054926 4.650000e-13 86.1
48 TraesCS2A01G261400 chr5D 97.872 47 1 0 1874 1920 557801830 557801876 6.010000e-12 82.4


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 TraesCS2A01G261400 chr2A 412370086 412372705 2619 False 2471.50 4839 98.3870 1 2620 2 chr2A.!!$F2 2619
1 TraesCS2A01G261400 chr2D 318714753 318715941 1188 True 1958.00 1958 96.3870 684 1873 1 chr2D.!!$R1 1189
2 TraesCS2A01G261400 chr2B 387152256 387153460 1204 True 1720.00 1720 92.7090 688 1873 1 chr2B.!!$R1 1185
3 TraesCS2A01G261400 chr2B 738649629 738650191 562 False 734.00 734 90.4590 1972 2527 1 chr2B.!!$F2 555
4 TraesCS2A01G261400 chr7D 556181017 556181613 596 False 819.00 819 91.6390 1939 2527 1 chr7D.!!$F2 588
5 TraesCS2A01G261400 chr7D 42797827 42798524 697 True 475.45 863 94.2170 1868 2530 2 chr7D.!!$R2 662
6 TraesCS2A01G261400 chr7D 168497037 168497728 691 True 466.90 857 93.8950 1874 2530 2 chr7D.!!$R3 656
7 TraesCS2A01G261400 chr7D 42204174 42204812 638 False 209.50 250 82.8875 3 522 2 chr7D.!!$F3 519
8 TraesCS2A01G261400 chr3D 566066675 566067289 614 False 863.00 863 92.2080 1921 2527 1 chr3D.!!$F3 606
9 TraesCS2A01G261400 chr3D 546669058 546669746 688 False 466.90 857 93.8950 1874 2527 2 chr3D.!!$F4 653
10 TraesCS2A01G261400 chr1A 463815474 463816084 610 True 859.00 859 92.3200 1921 2522 1 chr1A.!!$R2 601
11 TraesCS2A01G261400 chr1B 513309946 513310560 614 False 852.00 852 91.8830 1921 2527 1 chr1B.!!$F1 606
12 TraesCS2A01G261400 chr6A 65536183 65536801 618 True 846.00 846 91.6130 1921 2530 1 chr6A.!!$R1 609
13 TraesCS2A01G261400 chr4D 506851755 506852435 680 True 821.00 821 89.0190 1874 2530 1 chr4D.!!$R1 656
14 TraesCS2A01G261400 chr7A 672874681 672875295 614 False 451.30 811 93.5480 1921 2589 2 chr7A.!!$F2 668
15 TraesCS2A01G261400 chr7A 35169686 35170262 576 False 294.50 300 88.3040 1 520 2 chr7A.!!$F1 519
16 TraesCS2A01G261400 chr3B 803763856 803764471 615 True 808.00 808 90.6150 1924 2530 1 chr3B.!!$R2 606

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
680 810 0.317479 ACTCTTCACCGAACGAAGGG 59.683 55.0 6.73 6.73 44.96 3.95 F
681 811 0.601558 CTCTTCACCGAACGAAGGGA 59.398 55.0 3.09 0.00 42.57 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1545 1675 0.320247 ACGTTCCTGAGCTTGAGCAG 60.320 55.000 5.7 0.0 45.16 4.24 R
1634 1765 1.400846 GTCAGTCATTGAGCTGCCATG 59.599 52.381 0.0 0.0 36.21 3.66 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
66 68 6.818233 TGGCATGCATATTCAACATGTAAAT 58.182 32.000 21.36 5.21 42.50 1.40
68 70 7.769507 TGGCATGCATATTCAACATGTAAATTT 59.230 29.630 21.36 0.00 42.50 1.82
77 79 6.893958 TCAACATGTAAATTTTGCACGTTT 57.106 29.167 8.59 0.00 29.58 3.60
118 120 0.888619 TTCTAGGCTCTGGTCGTGTG 59.111 55.000 0.00 0.00 0.00 3.82
119 121 0.965866 TCTAGGCTCTGGTCGTGTGG 60.966 60.000 0.00 0.00 0.00 4.17
142 144 2.180276 ACGAGACCTGGCTTCTACAAT 58.820 47.619 0.00 0.00 0.00 2.71
201 203 4.518590 TGGGCCATCGTTCAATACATATTG 59.481 41.667 0.00 5.42 43.32 1.90
215 217 8.024865 TCAATACATATTGATTTGCTATGCTGC 58.975 33.333 9.75 0.00 45.03 5.25
217 219 6.010294 ACATATTGATTTGCTATGCTGCTC 57.990 37.500 0.00 0.00 0.00 4.26
223 225 3.616956 TTTGCTATGCTGCTCAGTACT 57.383 42.857 0.00 0.00 0.00 2.73
232 288 2.613977 GCTGCTCAGTACTGTGGTTCAT 60.614 50.000 21.99 0.00 0.00 2.57
240 343 6.119536 TCAGTACTGTGGTTCATTTTTCTGT 58.880 36.000 21.99 0.00 0.00 3.41
245 348 6.877236 ACTGTGGTTCATTTTTCTGTGAATT 58.123 32.000 0.00 0.00 36.79 2.17
246 349 8.006298 ACTGTGGTTCATTTTTCTGTGAATTA 57.994 30.769 0.00 0.00 36.79 1.40
247 350 7.920682 ACTGTGGTTCATTTTTCTGTGAATTAC 59.079 33.333 0.00 0.00 36.79 1.89
301 404 5.600696 TCATTGCAGTTCTTTCCTTTTTCC 58.399 37.500 0.00 0.00 0.00 3.13
302 405 4.400529 TTGCAGTTCTTTCCTTTTTCCC 57.599 40.909 0.00 0.00 0.00 3.97
347 456 2.295629 TGCAAAAATGCGTCATCCAAGA 59.704 40.909 0.00 0.00 37.69 3.02
349 458 3.612479 GCAAAAATGCGTCATCCAAGAGT 60.612 43.478 0.00 0.00 0.00 3.24
431 561 1.308047 ATGTGCACGCTTGAGTCAAA 58.692 45.000 13.13 0.00 0.00 2.69
459 589 6.913170 AGTGACTGCAATTTCGTATTTTCAT 58.087 32.000 0.00 0.00 0.00 2.57
461 591 8.511321 AGTGACTGCAATTTCGTATTTTCATAA 58.489 29.630 0.00 0.00 0.00 1.90
495 625 5.931441 AACTGAACATAGAGTGCAAGTTC 57.069 39.130 0.00 0.00 34.61 3.01
523 653 8.879427 TGATTTCCGGTGATATTATCTCTAGA 57.121 34.615 0.00 0.00 0.00 2.43
524 654 9.309224 TGATTTCCGGTGATATTATCTCTAGAA 57.691 33.333 0.00 6.21 0.00 2.10
554 684 9.950680 AAGAAGACTATGTGTACAATGTTTTTG 57.049 29.630 0.00 0.00 0.00 2.44
555 685 8.567948 AGAAGACTATGTGTACAATGTTTTTGG 58.432 33.333 0.00 0.00 0.00 3.28
556 686 7.817418 AGACTATGTGTACAATGTTTTTGGT 57.183 32.000 0.00 0.00 0.00 3.67
557 687 7.871853 AGACTATGTGTACAATGTTTTTGGTC 58.128 34.615 0.00 0.00 0.00 4.02
558 688 7.719633 AGACTATGTGTACAATGTTTTTGGTCT 59.280 33.333 0.00 0.02 0.00 3.85
559 689 8.232913 ACTATGTGTACAATGTTTTTGGTCTT 57.767 30.769 0.00 0.00 0.00 3.01
560 690 8.134895 ACTATGTGTACAATGTTTTTGGTCTTG 58.865 33.333 0.00 0.00 0.00 3.02
561 691 6.516739 TGTGTACAATGTTTTTGGTCTTGA 57.483 33.333 0.00 0.00 0.00 3.02
562 692 7.106439 TGTGTACAATGTTTTTGGTCTTGAT 57.894 32.000 0.00 0.00 0.00 2.57
563 693 7.551585 TGTGTACAATGTTTTTGGTCTTGATT 58.448 30.769 0.00 0.00 0.00 2.57
564 694 8.687242 TGTGTACAATGTTTTTGGTCTTGATTA 58.313 29.630 0.00 0.00 0.00 1.75
565 695 8.964150 GTGTACAATGTTTTTGGTCTTGATTAC 58.036 33.333 0.00 0.00 0.00 1.89
566 696 8.138712 TGTACAATGTTTTTGGTCTTGATTACC 58.861 33.333 0.00 0.00 37.53 2.85
567 697 6.212955 ACAATGTTTTTGGTCTTGATTACCG 58.787 36.000 0.00 0.00 40.08 4.02
568 698 6.183360 ACAATGTTTTTGGTCTTGATTACCGT 60.183 34.615 0.00 0.00 40.08 4.83
569 699 5.176407 TGTTTTTGGTCTTGATTACCGTG 57.824 39.130 0.00 0.00 40.08 4.94
570 700 4.641094 TGTTTTTGGTCTTGATTACCGTGT 59.359 37.500 0.00 0.00 40.08 4.49
571 701 4.822036 TTTTGGTCTTGATTACCGTGTG 57.178 40.909 0.00 0.00 40.08 3.82
572 702 2.465860 TGGTCTTGATTACCGTGTGG 57.534 50.000 0.00 0.00 40.08 4.17
583 713 3.802613 CCGTGTGGTGAGAGAGAAG 57.197 57.895 0.00 0.00 0.00 2.85
584 714 1.248486 CCGTGTGGTGAGAGAGAAGA 58.752 55.000 0.00 0.00 0.00 2.87
585 715 1.613925 CCGTGTGGTGAGAGAGAAGAA 59.386 52.381 0.00 0.00 0.00 2.52
586 716 2.232452 CCGTGTGGTGAGAGAGAAGAAT 59.768 50.000 0.00 0.00 0.00 2.40
587 717 3.306364 CCGTGTGGTGAGAGAGAAGAATT 60.306 47.826 0.00 0.00 0.00 2.17
588 718 4.310769 CGTGTGGTGAGAGAGAAGAATTT 58.689 43.478 0.00 0.00 0.00 1.82
589 719 4.752101 CGTGTGGTGAGAGAGAAGAATTTT 59.248 41.667 0.00 0.00 0.00 1.82
590 720 5.237344 CGTGTGGTGAGAGAGAAGAATTTTT 59.763 40.000 0.00 0.00 0.00 1.94
629 759 9.959721 AGTGTATTGGAAAAATAGATGTACACT 57.040 29.630 0.00 8.14 42.64 3.55
651 781 9.034544 ACACTCTTTTATGAACAAATTTGAAGC 57.965 29.630 24.64 12.72 0.00 3.86
652 782 8.490355 CACTCTTTTATGAACAAATTTGAAGCC 58.510 33.333 24.64 10.24 0.00 4.35
653 783 8.203485 ACTCTTTTATGAACAAATTTGAAGCCA 58.797 29.630 24.64 14.89 0.00 4.75
654 784 8.954950 TCTTTTATGAACAAATTTGAAGCCAA 57.045 26.923 24.64 9.59 0.00 4.52
655 785 9.388506 TCTTTTATGAACAAATTTGAAGCCAAA 57.611 25.926 24.64 14.28 45.28 3.28
667 797 5.689383 TTGAAGCCAAATGTACACTCTTC 57.311 39.130 0.00 7.46 0.00 2.87
668 798 4.713553 TGAAGCCAAATGTACACTCTTCA 58.286 39.130 16.38 16.38 36.93 3.02
669 799 4.515191 TGAAGCCAAATGTACACTCTTCAC 59.485 41.667 16.38 2.08 35.12 3.18
670 800 3.412386 AGCCAAATGTACACTCTTCACC 58.588 45.455 0.00 0.00 0.00 4.02
671 801 2.159627 GCCAAATGTACACTCTTCACCG 59.840 50.000 0.00 0.00 0.00 4.94
672 802 3.659786 CCAAATGTACACTCTTCACCGA 58.340 45.455 0.00 0.00 0.00 4.69
673 803 4.062293 CCAAATGTACACTCTTCACCGAA 58.938 43.478 0.00 0.00 0.00 4.30
674 804 4.084013 CCAAATGTACACTCTTCACCGAAC 60.084 45.833 0.00 0.00 0.00 3.95
675 805 2.410785 TGTACACTCTTCACCGAACG 57.589 50.000 0.00 0.00 0.00 3.95
676 806 1.948834 TGTACACTCTTCACCGAACGA 59.051 47.619 0.00 0.00 0.00 3.85
677 807 2.358582 TGTACACTCTTCACCGAACGAA 59.641 45.455 0.00 0.00 0.00 3.85
678 808 2.135664 ACACTCTTCACCGAACGAAG 57.864 50.000 0.00 0.00 41.05 3.79
679 809 1.269621 ACACTCTTCACCGAACGAAGG 60.270 52.381 0.00 0.00 40.27 3.46
680 810 0.317479 ACTCTTCACCGAACGAAGGG 59.683 55.000 6.73 6.73 44.96 3.95
681 811 0.601558 CTCTTCACCGAACGAAGGGA 59.398 55.000 3.09 0.00 42.57 4.20
682 812 0.601558 TCTTCACCGAACGAAGGGAG 59.398 55.000 0.00 0.00 40.27 4.30
723 853 2.807967 CGACACACCAGAATGTTGATGT 59.192 45.455 0.00 0.00 32.72 3.06
828 958 7.996385 AGCAGAGTACAAATAACACAAAGTTT 58.004 30.769 0.00 0.00 41.64 2.66
892 1022 2.934887 CCATGCATGTCTACATTCCCA 58.065 47.619 24.58 0.00 33.61 4.37
900 1030 5.068198 GCATGTCTACATTCCCACATCATTT 59.932 40.000 0.00 0.00 33.61 2.32
913 1043 6.013553 TCCCACATCATTTTGGTGATCATTTT 60.014 34.615 0.00 0.00 36.72 1.82
914 1044 6.092944 CCCACATCATTTTGGTGATCATTTTG 59.907 38.462 0.00 0.00 36.72 2.44
921 1051 3.159213 TGGTGATCATTTTGTGCCTCT 57.841 42.857 0.00 0.00 0.00 3.69
975 1105 5.122869 ACATTCCAAGATCAGATCAACAACG 59.877 40.000 13.14 0.00 0.00 4.10
1168 1298 1.448497 GTGAACCCGGTCTGGAACA 59.552 57.895 0.00 0.00 42.00 3.18
1204 1334 1.804151 CCGTCACGAATCCAACAACAT 59.196 47.619 0.00 0.00 0.00 2.71
1222 1352 8.535592 CAACAACATCGATCAAGATAGTAAGTC 58.464 37.037 0.00 0.00 0.00 3.01
1285 1415 5.463499 TGCATGCATACAACTTAGTTACG 57.537 39.130 18.46 0.00 0.00 3.18
1358 1488 2.417719 GACAAGTTCAGCAAGGACGAT 58.582 47.619 0.00 0.00 0.00 3.73
1651 1782 3.354948 TTACATGGCAGCTCAATGACT 57.645 42.857 0.00 0.00 0.00 3.41
1861 2012 7.966339 TGTTAATACTAAGGCCTCTCTAACA 57.034 36.000 5.23 11.59 0.00 2.41
1915 2066 3.552068 GCTTTAACTTGCCATGGACGTTT 60.552 43.478 18.40 5.11 0.00 3.60
1966 2144 2.607635 CGTGCAAATACGGTGCTAATCT 59.392 45.455 0.00 0.00 42.69 2.40
2113 2300 1.670967 GCCTGCCTGTCAGCAAAATTC 60.671 52.381 0.00 0.00 43.52 2.17
2154 2342 1.073284 GGGACTTGAACCAGCAACCTA 59.927 52.381 0.00 0.00 0.00 3.08
2179 2368 1.153745 GTGAGCTGGTCGCACTAGG 60.154 63.158 14.90 0.00 41.48 3.02
2225 2415 3.899726 ACTAAGACGGCCTCTCATTCTA 58.100 45.455 0.00 0.00 0.00 2.10
2375 2565 7.439955 TGTGTTACTAATAATTACCTCATGCCG 59.560 37.037 0.00 0.00 0.00 5.69
2527 2718 5.358090 GTGATGATGATGTGTCTGTCATCT 58.642 41.667 14.27 3.16 46.83 2.90
2530 2721 5.156608 TGATGATGTGTCTGTCATCTGTT 57.843 39.130 14.27 0.00 46.83 3.16
2531 2722 6.284891 TGATGATGTGTCTGTCATCTGTTA 57.715 37.500 14.27 0.00 46.83 2.41
2532 2723 6.700352 TGATGATGTGTCTGTCATCTGTTAA 58.300 36.000 14.27 0.00 46.83 2.01
2533 2724 6.591448 TGATGATGTGTCTGTCATCTGTTAAC 59.409 38.462 14.27 0.00 46.83 2.01
2534 2725 6.101650 TGATGTGTCTGTCATCTGTTAACT 57.898 37.500 7.22 0.00 41.30 2.24
2535 2726 7.227049 TGATGTGTCTGTCATCTGTTAACTA 57.773 36.000 7.22 0.00 41.30 2.24
2536 2727 7.666623 TGATGTGTCTGTCATCTGTTAACTAA 58.333 34.615 7.22 0.00 41.30 2.24
2537 2728 8.314021 TGATGTGTCTGTCATCTGTTAACTAAT 58.686 33.333 7.22 0.00 41.30 1.73
2538 2729 9.803315 GATGTGTCTGTCATCTGTTAACTAATA 57.197 33.333 7.22 0.00 38.72 0.98
2614 2805 9.582648 ACCTATAAAAATTGTGAGGTAAGTTGT 57.417 29.630 0.00 0.00 35.53 3.32
2615 2806 9.840427 CCTATAAAAATTGTGAGGTAAGTTGTG 57.160 33.333 0.00 0.00 0.00 3.33
2618 2809 5.767816 AAATTGTGAGGTAAGTTGTGACC 57.232 39.130 0.00 0.00 35.83 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.426024 ACTAGAATAAAGGCGCTCGTGA 59.574 45.455 7.64 0.00 0.00 4.35
66 68 3.549221 GCTAGCCACTAAAACGTGCAAAA 60.549 43.478 2.29 0.00 33.60 2.44
68 70 1.533731 GCTAGCCACTAAAACGTGCAA 59.466 47.619 2.29 0.00 33.60 4.08
77 79 1.669049 TAAGCCGCGCTAGCCACTAA 61.669 55.000 9.66 0.00 38.25 2.24
118 120 1.404843 AGAAGCCAGGTCTCGTATCC 58.595 55.000 0.00 0.00 0.00 2.59
119 121 2.950309 TGTAGAAGCCAGGTCTCGTATC 59.050 50.000 0.00 0.00 0.00 2.24
201 203 4.025061 CAGTACTGAGCAGCATAGCAAATC 60.025 45.833 18.45 0.00 36.85 2.17
207 209 2.167281 ACCACAGTACTGAGCAGCATAG 59.833 50.000 29.30 9.09 0.00 2.23
211 213 1.270305 TGAACCACAGTACTGAGCAGC 60.270 52.381 29.30 14.69 0.00 5.25
213 215 3.769739 AATGAACCACAGTACTGAGCA 57.230 42.857 29.30 17.34 0.00 4.26
214 216 5.239525 AGAAAAATGAACCACAGTACTGAGC 59.760 40.000 29.30 12.74 0.00 4.26
215 217 6.260936 ACAGAAAAATGAACCACAGTACTGAG 59.739 38.462 29.30 20.86 32.13 3.35
217 219 6.038161 TCACAGAAAAATGAACCACAGTACTG 59.962 38.462 21.44 21.44 33.04 2.74
223 225 7.776107 TGTAATTCACAGAAAAATGAACCACA 58.224 30.769 0.00 0.00 37.64 4.17
313 422 6.016718 CGCATTTTTGCATAAAACATCCTTG 58.983 36.000 6.41 0.45 35.62 3.61
318 427 6.183360 GGATGACGCATTTTTGCATAAAACAT 60.183 34.615 6.41 7.54 35.62 2.71
347 456 3.535561 CACCTGTCAGTGAGTGAAAACT 58.464 45.455 5.30 0.00 40.34 2.66
349 458 2.421388 CCCACCTGTCAGTGAGTGAAAA 60.421 50.000 11.51 0.00 40.34 2.29
431 561 9.341899 GAAAATACGAAATTGCAGTCACTTAAT 57.658 29.630 0.00 0.00 0.00 1.40
461 591 9.950496 ACTCTATGTTCAGTTTGATGTTAGAAT 57.050 29.630 0.00 0.00 0.00 2.40
467 597 5.308014 TGCACTCTATGTTCAGTTTGATGT 58.692 37.500 0.00 0.00 0.00 3.06
483 613 4.872691 CGGAAATCATAGAACTTGCACTCT 59.127 41.667 0.00 0.00 0.00 3.24
528 658 9.950680 CAAAAACATTGTACACATAGTCTTCTT 57.049 29.630 0.00 0.00 0.00 2.52
529 659 8.567948 CCAAAAACATTGTACACATAGTCTTCT 58.432 33.333 0.00 0.00 0.00 2.85
530 660 8.349983 ACCAAAAACATTGTACACATAGTCTTC 58.650 33.333 0.00 0.00 0.00 2.87
531 661 8.232913 ACCAAAAACATTGTACACATAGTCTT 57.767 30.769 0.00 0.00 0.00 3.01
532 662 7.719633 AGACCAAAAACATTGTACACATAGTCT 59.280 33.333 0.00 0.00 0.00 3.24
533 663 7.871853 AGACCAAAAACATTGTACACATAGTC 58.128 34.615 0.00 0.00 0.00 2.59
534 664 7.817418 AGACCAAAAACATTGTACACATAGT 57.183 32.000 0.00 0.00 0.00 2.12
535 665 8.349245 TCAAGACCAAAAACATTGTACACATAG 58.651 33.333 0.00 0.00 0.00 2.23
536 666 8.226819 TCAAGACCAAAAACATTGTACACATA 57.773 30.769 0.00 0.00 0.00 2.29
537 667 7.106439 TCAAGACCAAAAACATTGTACACAT 57.894 32.000 0.00 0.00 0.00 3.21
538 668 6.516739 TCAAGACCAAAAACATTGTACACA 57.483 33.333 0.00 0.00 0.00 3.72
539 669 8.964150 GTAATCAAGACCAAAAACATTGTACAC 58.036 33.333 0.00 0.00 0.00 2.90
540 670 8.138712 GGTAATCAAGACCAAAAACATTGTACA 58.861 33.333 0.00 0.00 36.91 2.90
541 671 7.325097 CGGTAATCAAGACCAAAAACATTGTAC 59.675 37.037 0.00 0.00 36.72 2.90
542 672 7.013464 ACGGTAATCAAGACCAAAAACATTGTA 59.987 33.333 0.00 0.00 36.72 2.41
543 673 6.183360 ACGGTAATCAAGACCAAAAACATTGT 60.183 34.615 0.00 0.00 36.72 2.71
544 674 6.143758 CACGGTAATCAAGACCAAAAACATTG 59.856 38.462 0.00 0.00 36.72 2.82
545 675 6.183360 ACACGGTAATCAAGACCAAAAACATT 60.183 34.615 0.00 0.00 36.72 2.71
546 676 5.300792 ACACGGTAATCAAGACCAAAAACAT 59.699 36.000 0.00 0.00 36.72 2.71
547 677 4.641094 ACACGGTAATCAAGACCAAAAACA 59.359 37.500 0.00 0.00 36.72 2.83
548 678 4.973663 CACACGGTAATCAAGACCAAAAAC 59.026 41.667 0.00 0.00 36.72 2.43
549 679 4.036971 CCACACGGTAATCAAGACCAAAAA 59.963 41.667 0.00 0.00 36.72 1.94
550 680 3.566322 CCACACGGTAATCAAGACCAAAA 59.434 43.478 0.00 0.00 36.72 2.44
551 681 3.142951 CCACACGGTAATCAAGACCAAA 58.857 45.455 0.00 0.00 36.72 3.28
552 682 2.105134 ACCACACGGTAATCAAGACCAA 59.895 45.455 0.00 0.00 46.71 3.67
553 683 1.695242 ACCACACGGTAATCAAGACCA 59.305 47.619 0.00 0.00 46.71 4.02
554 684 2.073816 CACCACACGGTAATCAAGACC 58.926 52.381 0.00 0.00 46.94 3.85
555 685 2.993899 CTCACCACACGGTAATCAAGAC 59.006 50.000 0.00 0.00 46.94 3.01
556 686 2.894765 TCTCACCACACGGTAATCAAGA 59.105 45.455 0.00 0.00 46.94 3.02
557 687 3.056821 TCTCTCACCACACGGTAATCAAG 60.057 47.826 0.00 0.00 46.94 3.02
558 688 2.894765 TCTCTCACCACACGGTAATCAA 59.105 45.455 0.00 0.00 46.94 2.57
559 689 2.492088 CTCTCTCACCACACGGTAATCA 59.508 50.000 0.00 0.00 46.94 2.57
560 690 2.753452 TCTCTCTCACCACACGGTAATC 59.247 50.000 0.00 0.00 46.94 1.75
561 691 2.803956 TCTCTCTCACCACACGGTAAT 58.196 47.619 0.00 0.00 46.94 1.89
562 692 2.281539 TCTCTCTCACCACACGGTAA 57.718 50.000 0.00 0.00 46.94 2.85
563 693 2.160205 CTTCTCTCTCACCACACGGTA 58.840 52.381 0.00 0.00 46.94 4.02
565 695 1.248486 TCTTCTCTCTCACCACACGG 58.752 55.000 0.00 0.00 38.77 4.94
566 696 3.584406 ATTCTTCTCTCTCACCACACG 57.416 47.619 0.00 0.00 0.00 4.49
567 697 6.625873 AAAAATTCTTCTCTCTCACCACAC 57.374 37.500 0.00 0.00 0.00 3.82
603 733 9.959721 AGTGTACATCTATTTTTCCAATACACT 57.040 29.630 0.00 7.27 43.18 3.55
625 755 9.034544 GCTTCAAATTTGTTCATAAAAGAGTGT 57.965 29.630 17.47 0.00 0.00 3.55
626 756 8.490355 GGCTTCAAATTTGTTCATAAAAGAGTG 58.510 33.333 17.47 0.00 0.00 3.51
627 757 8.203485 TGGCTTCAAATTTGTTCATAAAAGAGT 58.797 29.630 17.47 0.00 0.00 3.24
628 758 8.592105 TGGCTTCAAATTTGTTCATAAAAGAG 57.408 30.769 17.47 3.77 0.00 2.85
629 759 8.954950 TTGGCTTCAAATTTGTTCATAAAAGA 57.045 26.923 17.47 0.00 0.00 2.52
631 761 9.947669 CATTTGGCTTCAAATTTGTTCATAAAA 57.052 25.926 17.47 12.21 45.71 1.52
632 762 9.118300 ACATTTGGCTTCAAATTTGTTCATAAA 57.882 25.926 17.47 13.99 45.71 1.40
633 763 8.674263 ACATTTGGCTTCAAATTTGTTCATAA 57.326 26.923 17.47 3.84 45.71 1.90
634 764 9.202273 GTACATTTGGCTTCAAATTTGTTCATA 57.798 29.630 17.47 7.83 45.71 2.15
635 765 7.714377 TGTACATTTGGCTTCAAATTTGTTCAT 59.286 29.630 17.47 0.24 45.71 2.57
636 766 7.010923 GTGTACATTTGGCTTCAAATTTGTTCA 59.989 33.333 17.47 9.11 45.71 3.18
637 767 7.224557 AGTGTACATTTGGCTTCAAATTTGTTC 59.775 33.333 17.47 8.01 45.71 3.18
638 768 7.047271 AGTGTACATTTGGCTTCAAATTTGTT 58.953 30.769 17.47 0.00 45.71 2.83
639 769 6.581712 AGTGTACATTTGGCTTCAAATTTGT 58.418 32.000 17.47 0.00 45.71 2.83
640 770 6.925165 AGAGTGTACATTTGGCTTCAAATTTG 59.075 34.615 12.15 12.15 45.71 2.32
641 771 7.054491 AGAGTGTACATTTGGCTTCAAATTT 57.946 32.000 0.00 0.00 45.71 1.82
642 772 6.655078 AGAGTGTACATTTGGCTTCAAATT 57.345 33.333 0.00 0.00 45.71 1.82
644 774 5.592282 TGAAGAGTGTACATTTGGCTTCAAA 59.408 36.000 14.64 0.00 43.53 2.69
645 775 5.008613 GTGAAGAGTGTACATTTGGCTTCAA 59.991 40.000 17.16 5.21 41.02 2.69
646 776 4.515191 GTGAAGAGTGTACATTTGGCTTCA 59.485 41.667 13.58 13.58 38.23 3.02
647 777 4.083271 GGTGAAGAGTGTACATTTGGCTTC 60.083 45.833 0.00 5.19 0.00 3.86
648 778 3.821033 GGTGAAGAGTGTACATTTGGCTT 59.179 43.478 0.00 0.00 0.00 4.35
649 779 3.412386 GGTGAAGAGTGTACATTTGGCT 58.588 45.455 0.00 0.00 0.00 4.75
650 780 2.159627 CGGTGAAGAGTGTACATTTGGC 59.840 50.000 0.00 0.00 0.00 4.52
651 781 3.659786 TCGGTGAAGAGTGTACATTTGG 58.340 45.455 0.00 0.00 0.00 3.28
652 782 4.376008 CGTTCGGTGAAGAGTGTACATTTG 60.376 45.833 0.00 0.00 0.00 2.32
653 783 3.739300 CGTTCGGTGAAGAGTGTACATTT 59.261 43.478 0.00 0.00 0.00 2.32
654 784 3.005050 TCGTTCGGTGAAGAGTGTACATT 59.995 43.478 0.00 0.00 0.00 2.71
655 785 2.555325 TCGTTCGGTGAAGAGTGTACAT 59.445 45.455 0.00 0.00 0.00 2.29
656 786 1.948834 TCGTTCGGTGAAGAGTGTACA 59.051 47.619 0.00 0.00 0.00 2.90
657 787 2.693797 TCGTTCGGTGAAGAGTGTAC 57.306 50.000 0.00 0.00 0.00 2.90
658 788 2.030540 CCTTCGTTCGGTGAAGAGTGTA 60.031 50.000 11.96 0.00 44.42 2.90
659 789 1.269621 CCTTCGTTCGGTGAAGAGTGT 60.270 52.381 11.96 0.00 44.42 3.55
660 790 1.419374 CCTTCGTTCGGTGAAGAGTG 58.581 55.000 11.96 0.00 44.42 3.51
661 791 0.317479 CCCTTCGTTCGGTGAAGAGT 59.683 55.000 11.96 0.00 44.42 3.24
662 792 0.601558 TCCCTTCGTTCGGTGAAGAG 59.398 55.000 11.96 1.84 44.42 2.85
663 793 0.601558 CTCCCTTCGTTCGGTGAAGA 59.398 55.000 11.96 0.00 44.42 2.87
664 794 0.317479 ACTCCCTTCGTTCGGTGAAG 59.683 55.000 5.56 5.56 41.95 3.02
665 795 1.542915 CTACTCCCTTCGTTCGGTGAA 59.457 52.381 0.00 0.00 0.00 3.18
666 796 1.171308 CTACTCCCTTCGTTCGGTGA 58.829 55.000 0.00 0.00 0.00 4.02
667 797 0.172803 CCTACTCCCTTCGTTCGGTG 59.827 60.000 0.00 0.00 0.00 4.94
668 798 0.251519 ACCTACTCCCTTCGTTCGGT 60.252 55.000 0.00 0.00 0.00 4.69
669 799 0.455005 GACCTACTCCCTTCGTTCGG 59.545 60.000 0.00 0.00 0.00 4.30
670 800 1.135460 GTGACCTACTCCCTTCGTTCG 60.135 57.143 0.00 0.00 0.00 3.95
671 801 1.891150 TGTGACCTACTCCCTTCGTTC 59.109 52.381 0.00 0.00 0.00 3.95
672 802 2.005370 TGTGACCTACTCCCTTCGTT 57.995 50.000 0.00 0.00 0.00 3.85
673 803 1.617357 GTTGTGACCTACTCCCTTCGT 59.383 52.381 0.00 0.00 0.00 3.85
674 804 1.067071 GGTTGTGACCTACTCCCTTCG 60.067 57.143 0.00 0.00 42.99 3.79
675 805 1.067071 CGGTTGTGACCTACTCCCTTC 60.067 57.143 0.00 0.00 44.20 3.46
676 806 0.974383 CGGTTGTGACCTACTCCCTT 59.026 55.000 0.00 0.00 44.20 3.95
677 807 1.542187 GCGGTTGTGACCTACTCCCT 61.542 60.000 0.00 0.00 44.20 4.20
678 808 1.079336 GCGGTTGTGACCTACTCCC 60.079 63.158 0.00 0.00 44.20 4.30
679 809 0.034337 TTGCGGTTGTGACCTACTCC 59.966 55.000 0.00 0.00 44.20 3.85
680 810 1.145803 GTTGCGGTTGTGACCTACTC 58.854 55.000 0.00 0.00 44.20 2.59
681 811 0.250166 GGTTGCGGTTGTGACCTACT 60.250 55.000 0.00 0.00 44.20 2.57
682 812 0.533308 TGGTTGCGGTTGTGACCTAC 60.533 55.000 0.00 0.00 44.20 3.18
723 853 0.461548 TTGTTGTGCCGAAAATGCCA 59.538 45.000 0.00 0.00 0.00 4.92
790 920 4.401519 TGTACTCTGCTATTTTAGGACGCT 59.598 41.667 0.00 0.00 0.00 5.07
823 953 1.021968 GGCCGTGTCTTGTGAAACTT 58.978 50.000 0.00 0.00 38.04 2.66
828 958 1.885388 CGTTGGCCGTGTCTTGTGA 60.885 57.895 0.00 0.00 0.00 3.58
892 1022 6.148150 GCACAAAATGATCACCAAAATGATGT 59.852 34.615 0.00 0.00 39.48 3.06
900 1030 3.499338 AGAGGCACAAAATGATCACCAA 58.501 40.909 0.00 0.00 0.00 3.67
913 1043 3.311322 CGTTTGTTCTTGTTAGAGGCACA 59.689 43.478 0.00 0.00 0.00 4.57
914 1044 3.558418 TCGTTTGTTCTTGTTAGAGGCAC 59.442 43.478 0.00 0.00 0.00 5.01
921 1051 5.516090 GCCAATTCTCGTTTGTTCTTGTTA 58.484 37.500 0.00 0.00 0.00 2.41
975 1105 6.422100 TCTCGATTGCTCTATTGCTAATTGTC 59.578 38.462 0.00 0.00 0.00 3.18
1050 1180 1.276421 CAGTTCACGAGGTTGATCCCT 59.724 52.381 0.00 0.00 37.62 4.20
1168 1298 2.427245 CGGCGAGGGTGAGATCCTT 61.427 63.158 0.00 0.00 34.21 3.36
1204 1334 7.280428 ACTTCTTCGACTTACTATCTTGATCGA 59.720 37.037 0.00 0.00 35.49 3.59
1222 1352 8.706936 CATCTATATGACCATTCAACTTCTTCG 58.293 37.037 0.00 0.00 34.61 3.79
1285 1415 2.028883 GCGCAAGTACGTTAGGATTCAC 59.971 50.000 0.30 0.00 41.68 3.18
1358 1488 2.042741 TCCGCGTCCCCCATCTTA 60.043 61.111 4.92 0.00 0.00 2.10
1545 1675 0.320247 ACGTTCCTGAGCTTGAGCAG 60.320 55.000 5.70 0.00 45.16 4.24
1634 1765 1.400846 GTCAGTCATTGAGCTGCCATG 59.599 52.381 0.00 0.00 36.21 3.66
1651 1782 6.471233 TCAACACAAAATAAACATGGGTCA 57.529 33.333 0.00 0.00 0.00 4.02
1764 1907 4.836125 AGAACACATGAAAATTGACGCT 57.164 36.364 0.00 0.00 0.00 5.07
1861 2012 7.996644 TGGTGTATTTACCTCTTCTTTCTTTGT 59.003 33.333 0.00 0.00 41.43 2.83
1915 2066 8.354426 GTGCCAAGTTTTAGAACCAATTAAGTA 58.646 33.333 0.00 0.00 36.39 2.24
1966 2144 3.691118 ACGCACTTTACGTCTATAGACCA 59.309 43.478 24.01 11.64 40.28 4.02
2113 2300 4.362279 CCTTCCGGCACATTTTTCATATG 58.638 43.478 0.00 0.00 0.00 1.78
2356 2546 4.754618 TGTGCGGCATGAGGTAATTATTAG 59.245 41.667 5.72 0.00 0.00 1.73
2588 2779 9.582648 ACAACTTACCTCACAATTTTTATAGGT 57.417 29.630 0.00 0.00 40.38 3.08
2589 2780 9.840427 CACAACTTACCTCACAATTTTTATAGG 57.160 33.333 0.00 0.00 0.00 2.57
2592 2783 8.357402 GGTCACAACTTACCTCACAATTTTTAT 58.643 33.333 0.00 0.00 32.72 1.40
2593 2784 7.558444 AGGTCACAACTTACCTCACAATTTTTA 59.442 33.333 0.00 0.00 42.60 1.52
2594 2785 6.379988 AGGTCACAACTTACCTCACAATTTTT 59.620 34.615 0.00 0.00 42.60 1.94
2595 2786 5.891551 AGGTCACAACTTACCTCACAATTTT 59.108 36.000 0.00 0.00 42.60 1.82
2596 2787 5.445964 AGGTCACAACTTACCTCACAATTT 58.554 37.500 0.00 0.00 42.60 1.82
2597 2788 5.048846 AGGTCACAACTTACCTCACAATT 57.951 39.130 0.00 0.00 42.60 2.32
2598 2789 4.706842 AGGTCACAACTTACCTCACAAT 57.293 40.909 0.00 0.00 42.60 2.71


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

AutoCloner maintained by Alex Coulton.