Multiple sequence alignment - TraesCS3D01G495600

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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 TraesCS3D01G495600 chr3D 100.000 5619 0 0 1 5619 587649500 587643882 0.000000e+00 10377.0
1 TraesCS3D01G495600 chr3D 80.964 1266 124 60 729 1937 587745418 587746623 0.000000e+00 894.0
2 TraesCS3D01G495600 chr3D 81.720 837 105 29 998 1831 587596520 587595729 0.000000e+00 654.0
3 TraesCS3D01G495600 chr3D 80.130 770 100 27 1014 1776 587586573 587585850 4.990000e-145 525.0
4 TraesCS3D01G495600 chr3D 80.417 240 40 6 8 244 381192638 381192873 5.790000e-40 176.0
5 TraesCS3D01G495600 chr3B 93.023 3325 175 29 537 3834 785043647 785040353 0.000000e+00 4802.0
6 TraesCS3D01G495600 chr3B 92.474 1807 85 21 3827 5593 785040176 785038381 0.000000e+00 2536.0
7 TraesCS3D01G495600 chr3B 82.512 1075 109 43 729 1778 785280472 785281492 0.000000e+00 870.0
8 TraesCS3D01G495600 chr3B 79.161 787 96 27 1014 1776 784870596 784869854 3.040000e-132 483.0
9 TraesCS3D01G495600 chr3B 86.207 406 49 5 1426 1831 784900510 784900112 3.110000e-117 433.0
10 TraesCS3D01G495600 chr3B 91.288 264 19 3 1 264 785044577 785044318 1.930000e-94 357.0
11 TraesCS3D01G495600 chr3B 92.308 208 16 0 320 527 49950053 49949846 4.260000e-76 296.0
12 TraesCS3D01G495600 chr3B 92.308 208 16 0 320 527 235884215 235884008 4.260000e-76 296.0
13 TraesCS3D01G495600 chr3B 92.233 206 16 0 323 528 798950914 798951119 5.510000e-75 292.0
14 TraesCS3D01G495600 chr3B 90.741 216 20 0 320 535 434646798 434647013 7.120000e-74 289.0
15 TraesCS3D01G495600 chr3B 72.935 569 117 28 3187 3733 773165456 773166009 4.500000e-36 163.0
16 TraesCS3D01G495600 chr3B 76.761 284 44 17 3467 3733 499814493 499814215 7.590000e-29 139.0
17 TraesCS3D01G495600 chr3B 84.397 141 14 7 3598 3733 335232808 335232945 1.270000e-26 132.0
18 TraesCS3D01G495600 chr3B 89.189 74 4 4 180 250 279666650 279666722 7.750000e-14 89.8
19 TraesCS3D01G495600 chr3A 92.490 2570 156 12 2194 4742 717009444 717006891 0.000000e+00 3642.0
20 TraesCS3D01G495600 chr3A 92.798 1680 77 16 537 2195 717011465 717009809 0.000000e+00 2392.0
21 TraesCS3D01G495600 chr3A 93.348 902 32 15 4742 5619 717003995 717003098 0.000000e+00 1308.0
22 TraesCS3D01G495600 chr3A 82.045 841 103 29 994 1831 716966961 716966166 0.000000e+00 673.0
23 TraesCS3D01G495600 chr3A 85.338 532 40 16 1425 1922 717297620 717298147 3.000000e-142 516.0
24 TraesCS3D01G495600 chr3A 81.126 604 64 23 732 1313 717296960 717297535 6.680000e-119 438.0
25 TraesCS3D01G495600 chr3A 92.444 225 16 1 6 230 717012778 717012555 2.530000e-83 320.0
26 TraesCS3D01G495600 chr2A 92.130 216 15 2 320 534 777253128 777252914 2.540000e-78 303.0
27 TraesCS3D01G495600 chr5B 92.683 205 15 0 320 524 146825623 146825827 4.260000e-76 296.0
28 TraesCS3D01G495600 chr5B 85.878 262 29 7 320 578 613652248 613652504 7.170000e-69 272.0
29 TraesCS3D01G495600 chr4B 92.195 205 16 0 320 524 68116572 68116776 1.980000e-74 291.0
30 TraesCS3D01G495600 chr4B 84.733 131 14 6 3604 3733 404845114 404845239 5.910000e-25 126.0
31 TraesCS3D01G495600 chr2B 91.707 205 17 0 318 522 52914269 52914473 9.210000e-73 285.0
32 TraesCS3D01G495600 chr2B 89.189 74 4 4 180 250 206686448 206686520 7.750000e-14 89.8
33 TraesCS3D01G495600 chr5D 73.473 573 115 34 3187 3740 7034842 7034288 1.240000e-41 182.0
34 TraesCS3D01G495600 chr6D 72.680 571 117 26 3187 3733 19204725 19205280 2.710000e-33 154.0
35 TraesCS3D01G495600 chr6D 72.251 573 118 30 3187 3733 19142896 19143453 7.590000e-29 139.0
36 TraesCS3D01G495600 chr7B 87.597 129 15 1 8 136 63139275 63139148 1.260000e-31 148.0
37 TraesCS3D01G495600 chr7B 90.826 109 9 1 137 245 63138799 63138692 1.630000e-30 145.0
38 TraesCS3D01G495600 chr7B 89.610 77 4 4 180 253 328496354 328496279 1.670000e-15 95.3
39 TraesCS3D01G495600 chr7B 80.000 80 15 1 3471 3549 749544157 749544236 2.190000e-04 58.4
40 TraesCS3D01G495600 chr1A 73.427 429 81 26 3310 3725 22485426 22485834 4.570000e-26 130.0
41 TraesCS3D01G495600 chr1A 89.744 78 3 5 181 255 313745602 313745527 1.670000e-15 95.3
42 TraesCS3D01G495600 chr5A 90.667 75 3 4 180 251 402121694 402121621 4.630000e-16 97.1


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 TraesCS3D01G495600 chr3D 587643882 587649500 5618 True 10377.0 10377 100.000000 1 5619 1 chr3D.!!$R3 5618
1 TraesCS3D01G495600 chr3D 587745418 587746623 1205 False 894.0 894 80.964000 729 1937 1 chr3D.!!$F2 1208
2 TraesCS3D01G495600 chr3D 587595729 587596520 791 True 654.0 654 81.720000 998 1831 1 chr3D.!!$R2 833
3 TraesCS3D01G495600 chr3D 587585850 587586573 723 True 525.0 525 80.130000 1014 1776 1 chr3D.!!$R1 762
4 TraesCS3D01G495600 chr3B 785038381 785044577 6196 True 2565.0 4802 92.261667 1 5593 3 chr3B.!!$R6 5592
5 TraesCS3D01G495600 chr3B 785280472 785281492 1020 False 870.0 870 82.512000 729 1778 1 chr3B.!!$F5 1049
6 TraesCS3D01G495600 chr3B 784869854 784870596 742 True 483.0 483 79.161000 1014 1776 1 chr3B.!!$R4 762
7 TraesCS3D01G495600 chr3A 717003098 717012778 9680 True 1915.5 3642 92.770000 6 5619 4 chr3A.!!$R2 5613
8 TraesCS3D01G495600 chr3A 716966166 716966961 795 True 673.0 673 82.045000 994 1831 1 chr3A.!!$R1 837
9 TraesCS3D01G495600 chr3A 717296960 717298147 1187 False 477.0 516 83.232000 732 1922 2 chr3A.!!$F1 1190

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
327 641 0.033208 ATTTCATGGCATCCCGGTGT 60.033 50.0 0.00 0.0 0.0 4.16 F
895 2082 0.035820 ATTGCTCGGCGGTTAGGAAA 60.036 50.0 7.21 0.0 0.0 3.13 F
1720 2965 0.174389 GTCTTCGCCTCATCAGCTCA 59.826 55.0 0.00 0.0 0.0 4.26 F
2599 4259 0.392461 TGGGTCAATGAAGGTAGCGC 60.392 55.0 0.00 0.0 0.0 5.92 F
3515 5176 0.179094 TGGTGCGGATATGGTCGTTC 60.179 55.0 0.00 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2000 3284 0.471617 GGCAGTGCCTGACCAGATAT 59.528 55.0 27.48 0.00 46.69 1.63 R
2837 4497 0.323302 TGAACCACCTAGCATCGCAA 59.677 50.0 0.00 0.00 0.00 4.85 R
2915 4575 0.964700 TGTGGCGCAAAATTGATCCA 59.035 45.0 10.83 0.49 0.00 3.41 R
3851 5695 0.900182 TGCTCGTGTCTCCCATGTCT 60.900 55.0 0.00 0.00 0.00 3.41 R
4990 9761 0.033109 GGGAAGGGATGGGTGGAAAG 60.033 60.0 0.00 0.00 0.00 2.62 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
91 92 6.403636 GGCGATCTAGAAAATTTCTTTGCAGA 60.404 38.462 13.89 10.50 41.14 4.26
107 108 2.103941 TGCAGAGTTGTGTATGTGGACA 59.896 45.455 0.00 0.00 0.00 4.02
128 129 3.690139 CACAGCGAGAGTAGTTCCTTAGA 59.310 47.826 0.00 0.00 0.00 2.10
242 243 2.159531 GCATGCTTGTGCGTATTTGAGA 60.160 45.455 11.37 0.00 43.34 3.27
244 245 4.475028 CATGCTTGTGCGTATTTGAGAAA 58.525 39.130 0.00 0.00 43.34 2.52
268 269 1.986698 AAACGAAAGCAGCATCATGC 58.013 45.000 0.00 0.00 46.88 4.06
289 290 4.017958 TGCAATGGAGAAATACTACCCCAA 60.018 41.667 0.00 0.00 0.00 4.12
290 291 4.580580 GCAATGGAGAAATACTACCCCAAG 59.419 45.833 0.00 0.00 0.00 3.61
304 618 2.378547 ACCCCAAGAAAGCTCCACATTA 59.621 45.455 0.00 0.00 0.00 1.90
316 630 9.252962 GAAAGCTCCACATTAATTATTTCATGG 57.747 33.333 0.00 0.00 0.00 3.66
317 631 6.752168 AGCTCCACATTAATTATTTCATGGC 58.248 36.000 0.00 0.00 0.00 4.40
318 632 6.324512 AGCTCCACATTAATTATTTCATGGCA 59.675 34.615 0.00 0.00 0.00 4.92
319 633 7.015877 AGCTCCACATTAATTATTTCATGGCAT 59.984 33.333 0.00 0.00 0.00 4.40
322 636 6.875195 CCACATTAATTATTTCATGGCATCCC 59.125 38.462 0.00 0.00 0.00 3.85
323 637 6.587226 CACATTAATTATTTCATGGCATCCCG 59.413 38.462 0.00 0.00 0.00 5.14
325 639 2.746279 TTATTTCATGGCATCCCGGT 57.254 45.000 0.00 0.00 0.00 5.28
326 640 1.979855 TATTTCATGGCATCCCGGTG 58.020 50.000 0.00 0.00 0.00 4.94
327 641 0.033208 ATTTCATGGCATCCCGGTGT 60.033 50.000 0.00 0.00 0.00 4.16
328 642 0.621082 TTTCATGGCATCCCGGTGTA 59.379 50.000 0.00 0.00 0.00 2.90
329 643 0.107410 TTCATGGCATCCCGGTGTAC 60.107 55.000 0.00 0.00 0.00 2.90
330 644 1.223211 CATGGCATCCCGGTGTACA 59.777 57.895 0.00 0.00 0.00 2.90
331 645 0.393673 CATGGCATCCCGGTGTACAA 60.394 55.000 0.00 0.00 0.00 2.41
332 646 0.107214 ATGGCATCCCGGTGTACAAG 60.107 55.000 0.00 0.00 0.00 3.16
338 652 3.343617 CATCCCGGTGTACAAGTCATTT 58.656 45.455 0.00 0.00 0.00 2.32
339 653 2.773487 TCCCGGTGTACAAGTCATTTG 58.227 47.619 0.00 0.00 42.68 2.32
341 655 1.136085 CCGGTGTACAAGTCATTTGCG 60.136 52.381 0.00 0.00 40.59 4.85
342 656 1.529438 CGGTGTACAAGTCATTTGCGT 59.471 47.619 0.00 0.00 40.59 5.24
344 658 3.181534 CGGTGTACAAGTCATTTGCGTAG 60.182 47.826 0.00 0.00 40.59 3.51
346 690 4.212636 GGTGTACAAGTCATTTGCGTAGTT 59.787 41.667 0.00 0.00 40.59 2.24
349 693 6.364165 GTGTACAAGTCATTTGCGTAGTTCTA 59.636 38.462 0.00 0.00 40.59 2.10
351 695 4.929808 ACAAGTCATTTGCGTAGTTCTAGG 59.070 41.667 0.00 0.00 40.59 3.02
435 779 6.716934 ACATCCGTGTAGAAATCTAGTGAT 57.283 37.500 0.00 0.00 36.63 3.06
436 780 7.818997 ACATCCGTGTAGAAATCTAGTGATA 57.181 36.000 0.00 0.00 36.63 2.15
437 781 8.410673 ACATCCGTGTAGAAATCTAGTGATAT 57.589 34.615 0.00 0.00 36.63 1.63
438 782 9.516546 ACATCCGTGTAGAAATCTAGTGATATA 57.483 33.333 0.00 0.00 36.63 0.86
439 783 9.776158 CATCCGTGTAGAAATCTAGTGATATAC 57.224 37.037 0.00 0.00 31.70 1.47
440 784 9.742144 ATCCGTGTAGAAATCTAGTGATATACT 57.258 33.333 0.00 0.00 43.56 2.12
441 785 9.570468 TCCGTGTAGAAATCTAGTGATATACTT 57.430 33.333 0.00 0.00 40.89 2.24
491 835 9.838339 AATTTCTCAAATCGATGACCTATAACT 57.162 29.630 0.00 0.00 0.00 2.24
493 837 9.745880 TTTCTCAAATCGATGACCTATAACTAC 57.254 33.333 0.00 0.00 0.00 2.73
494 838 7.582352 TCTCAAATCGATGACCTATAACTACG 58.418 38.462 0.00 0.00 0.00 3.51
495 839 6.147581 TCAAATCGATGACCTATAACTACGC 58.852 40.000 0.00 0.00 0.00 4.42
496 840 3.800929 TCGATGACCTATAACTACGCG 57.199 47.619 3.53 3.53 0.00 6.01
498 842 3.809279 TCGATGACCTATAACTACGCGAA 59.191 43.478 15.93 0.00 0.00 4.70
501 845 5.616204 CGATGACCTATAACTACGCGAATGA 60.616 44.000 15.93 0.00 0.00 2.57
502 846 4.852138 TGACCTATAACTACGCGAATGAC 58.148 43.478 15.93 0.00 0.00 3.06
506 850 7.040892 TGACCTATAACTACGCGAATGACTTAT 60.041 37.037 15.93 7.21 0.00 1.73
507 851 7.655490 ACCTATAACTACGCGAATGACTTATT 58.345 34.615 15.93 0.00 0.00 1.40
508 852 7.806960 ACCTATAACTACGCGAATGACTTATTC 59.193 37.037 15.93 0.00 41.46 1.75
510 854 5.697848 AACTACGCGAATGACTTATTCAC 57.302 39.130 15.93 0.00 44.42 3.18
512 856 1.924524 ACGCGAATGACTTATTCACCG 59.075 47.619 15.93 0.00 44.42 4.94
513 857 2.190161 CGCGAATGACTTATTCACCGA 58.810 47.619 0.00 0.00 44.42 4.69
514 858 2.216488 CGCGAATGACTTATTCACCGAG 59.784 50.000 0.00 0.00 44.42 4.63
515 859 3.444916 GCGAATGACTTATTCACCGAGA 58.555 45.455 0.00 0.00 44.42 4.04
516 860 3.243177 GCGAATGACTTATTCACCGAGAC 59.757 47.826 0.00 0.00 44.42 3.36
517 861 3.482472 CGAATGACTTATTCACCGAGACG 59.518 47.826 0.00 0.00 44.42 4.18
518 862 3.797256 GAATGACTTATTCACCGAGACGG 59.203 47.826 8.67 8.67 43.79 4.79
520 864 6.238416 GAATGACTTATTCACCGAGACGGAG 61.238 48.000 16.99 9.14 45.73 4.63
535 1682 5.850128 CGAGACGGAGGTAATAACTATTTCG 59.150 44.000 0.00 0.00 0.00 3.46
553 1700 8.712363 ACTATTTCGTGATATCATTGATTTCCG 58.288 33.333 9.02 11.53 0.00 4.30
554 1701 4.990543 TCGTGATATCATTGATTTCCGC 57.009 40.909 9.02 2.45 0.00 5.54
593 1750 2.854963 TCTGCATGGATATTGGAGCAC 58.145 47.619 0.00 0.00 33.07 4.40
594 1751 2.440627 TCTGCATGGATATTGGAGCACT 59.559 45.455 0.00 0.00 33.07 4.40
595 1752 2.812591 CTGCATGGATATTGGAGCACTC 59.187 50.000 0.00 0.00 0.00 3.51
596 1753 2.440627 TGCATGGATATTGGAGCACTCT 59.559 45.455 0.00 0.00 0.00 3.24
597 1754 3.072944 GCATGGATATTGGAGCACTCTC 58.927 50.000 0.00 0.00 38.62 3.20
599 1756 4.711399 CATGGATATTGGAGCACTCTCAA 58.289 43.478 0.00 1.43 41.13 3.02
600 1757 5.314529 CATGGATATTGGAGCACTCTCAAT 58.685 41.667 14.57 14.57 41.13 2.57
601 1758 6.470278 CATGGATATTGGAGCACTCTCAATA 58.530 40.000 16.79 16.79 41.13 1.90
602 1759 6.692849 TGGATATTGGAGCACTCTCAATAT 57.307 37.500 21.54 21.54 41.10 1.28
604 1761 8.384693 TGGATATTGGAGCACTCTCAATATAT 57.615 34.615 21.48 11.76 40.00 0.86
698 1879 2.114616 GACACTGACATCCCCTCATCT 58.885 52.381 0.00 0.00 0.00 2.90
723 1904 3.432326 CGGCCTATATAAATGGGAGCTCC 60.432 52.174 25.59 25.59 35.79 4.70
844 2031 4.268687 CGCTTCCTCTTGCGTCTT 57.731 55.556 0.00 0.00 46.09 3.01
855 2042 5.007332 TCCTCTTGCGTCTTACAAAGAAAAC 59.993 40.000 0.00 0.00 39.67 2.43
885 2072 3.328189 GCAGCTAGATTGCTCGGC 58.672 61.111 11.21 0.00 41.98 5.54
895 2082 0.035820 ATTGCTCGGCGGTTAGGAAA 60.036 50.000 7.21 0.00 0.00 3.13
954 2143 3.444388 GTCTCTAACCTCTCCACACGAAT 59.556 47.826 0.00 0.00 0.00 3.34
970 2159 1.429463 GAATTCGTCGACCAAGCAGT 58.571 50.000 10.58 0.00 0.00 4.40
1720 2965 0.174389 GTCTTCGCCTCATCAGCTCA 59.826 55.000 0.00 0.00 0.00 4.26
1821 3078 2.232208 TCTCTGTCATCGATGCTTGTGT 59.768 45.455 20.81 0.00 0.00 3.72
1850 3107 8.527810 TGATATTTTGTGGATTCCTTTTGGTAC 58.472 33.333 3.95 0.00 41.38 3.34
2106 3391 7.598278 TGTAATATTGGAATGACGTTTGCTTT 58.402 30.769 0.00 0.00 0.00 3.51
2203 3856 7.064728 GGACTGTAGCCTACACTTTGAATTTAG 59.935 40.741 0.00 0.00 34.46 1.85
2531 4191 0.863956 CTCCTACCTCCCCATCCTCT 59.136 60.000 0.00 0.00 0.00 3.69
2568 4228 2.746947 TAGAGACCAGTGGCCAGGCA 62.747 60.000 15.19 0.95 0.00 4.75
2599 4259 0.392461 TGGGTCAATGAAGGTAGCGC 60.392 55.000 0.00 0.00 0.00 5.92
2639 4299 1.000607 GTAGCCTTCGACAGTGACACA 60.001 52.381 8.59 0.00 0.00 3.72
2736 4396 2.614481 GGTTTCTAATGGTGAGGCGTCA 60.614 50.000 4.68 4.68 0.00 4.35
2774 4434 3.371097 CTGGTACGCAGGCGATGGT 62.371 63.158 21.62 0.00 42.83 3.55
2795 4455 4.082125 GTGACATCCTTCTTTGTCCCAAT 58.918 43.478 0.00 0.00 41.22 3.16
2837 4497 4.552365 CGGATGGCGCCATGGTCT 62.552 66.667 44.96 24.17 36.70 3.85
2867 4527 0.975887 GGTGGTTCATGCAATGGGTT 59.024 50.000 0.00 0.00 46.73 4.11
2916 4576 5.235305 GGCAACAAGGAGTATGTATTGTG 57.765 43.478 0.00 0.00 36.09 3.33
2960 4620 1.888436 GACGGTGGAGCATGAGGACA 61.888 60.000 0.00 0.00 0.00 4.02
2965 4625 0.817654 TGGAGCATGAGGACAGTACG 59.182 55.000 0.00 0.00 0.00 3.67
2971 4631 2.943690 GCATGAGGACAGTACGAGACTA 59.056 50.000 0.00 0.00 35.64 2.59
2979 4639 4.382470 GGACAGTACGAGACTACCAGACTA 60.382 50.000 0.00 0.00 35.64 2.59
3043 4703 5.246981 TCTCCAATCTTCACCTCATGTTT 57.753 39.130 0.00 0.00 0.00 2.83
3057 4717 4.935205 CCTCATGTTTTACGATGACCTTCA 59.065 41.667 0.00 0.00 0.00 3.02
3081 4741 3.530535 GTTTTGAGTGTTTGGTGGCAAT 58.469 40.909 0.00 0.00 0.00 3.56
3130 4790 0.405198 TGTGTGGGCATGGACTTCAT 59.595 50.000 0.00 0.00 36.31 2.57
3162 4822 4.081476 TGTCTCATGTCAAGACCATGGTAG 60.081 45.833 19.80 11.26 42.03 3.18
3167 4827 2.292267 GTCAAGACCATGGTAGGCATG 58.708 52.381 19.80 9.16 0.00 4.06
3176 4836 4.104738 ACCATGGTAGGCATGTAGCTATTT 59.895 41.667 18.10 0.00 44.79 1.40
3177 4837 5.309543 ACCATGGTAGGCATGTAGCTATTTA 59.690 40.000 18.10 0.00 44.79 1.40
3201 4861 1.864711 CACGTAAAGTGGTGGTGACAG 59.135 52.381 0.00 0.00 46.77 3.51
3235 4895 1.278985 ACGATTTGGTGATGCTCCTCA 59.721 47.619 0.00 0.00 0.00 3.86
3293 4953 5.519183 TGCATGACCCTAATTGCCTATAT 57.481 39.130 0.00 0.00 34.20 0.86
3295 4955 4.884164 GCATGACCCTAATTGCCTATATCC 59.116 45.833 0.00 0.00 0.00 2.59
3350 5010 9.921637 TTATTGAAGGCATTTCTTTACGATTTT 57.078 25.926 0.00 0.00 36.71 1.82
3354 5014 6.817765 AGGCATTTCTTTACGATTTTCTCA 57.182 33.333 0.00 0.00 0.00 3.27
3355 5015 7.214467 AGGCATTTCTTTACGATTTTCTCAA 57.786 32.000 0.00 0.00 0.00 3.02
3461 5122 6.954684 TCCTTGAGACTTTACTACTGGAGAAT 59.045 38.462 0.00 0.00 0.00 2.40
3498 5159 7.226441 TCCTTATGATGTGAAGATATGGTTGG 58.774 38.462 0.00 0.00 0.00 3.77
3515 5176 0.179094 TGGTGCGGATATGGTCGTTC 60.179 55.000 0.00 0.00 0.00 3.95
3525 5186 5.469421 CGGATATGGTCGTTCTAGTAGTTCT 59.531 44.000 0.00 0.00 0.00 3.01
3623 5284 2.373224 TGTGCATTTGTGTGGTTCTGA 58.627 42.857 0.00 0.00 0.00 3.27
3631 5292 6.690530 CATTTGTGTGGTTCTGATTATGGTT 58.309 36.000 0.00 0.00 0.00 3.67
3683 5344 3.181397 GTGCGCTCATTGCATTTGTATT 58.819 40.909 9.73 0.00 45.34 1.89
3743 5404 6.348704 CCCTTTTGTCGAAAACGTATTATGGT 60.349 38.462 0.00 0.00 0.00 3.55
3750 5411 5.577945 TCGAAAACGTATTATGGTCTCCAAC 59.422 40.000 0.00 0.00 36.95 3.77
3777 5438 6.816640 TCCAAGGATTCAAACTACGAACATAG 59.183 38.462 0.00 0.00 0.00 2.23
3826 5487 4.129380 CACACTTGTCAAAGAGGACATGA 58.871 43.478 13.83 0.00 46.37 3.07
3882 5726 1.238439 CACGAGCACTTGGTTGGATT 58.762 50.000 0.00 0.00 0.00 3.01
3889 5733 3.010420 GCACTTGGTTGGATTAGGACTC 58.990 50.000 0.00 0.00 0.00 3.36
3901 5745 4.406003 GGATTAGGACTCTGCTTCTTACCA 59.594 45.833 0.00 0.00 0.00 3.25
3933 5777 1.535437 GCTGGGTCGGTTCATACTACG 60.535 57.143 0.00 0.00 0.00 3.51
3949 5793 7.993101 TCATACTACGCTAAATCTAAGTGTGT 58.007 34.615 0.00 0.00 38.15 3.72
4000 5844 2.236146 ACATGCACCTCGATTGGTCTTA 59.764 45.455 0.00 0.00 38.45 2.10
4060 5909 1.990327 AGGGGCATCATGATCATGCTA 59.010 47.619 27.68 14.35 45.18 3.49
4227 6077 8.120465 AGTGTAACAAGTAAACAAAGAACATCG 58.880 33.333 0.00 0.00 41.43 3.84
4261 6111 6.595326 CGTTAGGCAATGACATATATGGATGT 59.405 38.462 16.96 0.00 42.82 3.06
4275 6125 9.338622 CATATATGGATGTGATAGAATGCATGT 57.661 33.333 0.00 0.00 35.84 3.21
4316 6183 3.130693 AGAGTCGATTAGTTGTACCAGCC 59.869 47.826 0.00 0.00 0.00 4.85
4419 6286 5.985781 AGCAGTAACACTAAAAATGTGTCG 58.014 37.500 0.00 0.00 46.46 4.35
4425 6292 9.101655 AGTAACACTAAAAATGTGTCGTAAACT 57.898 29.630 0.00 0.00 46.46 2.66
4573 6445 5.008613 GTGTCCAGCATTTTGTGAAGAACTA 59.991 40.000 0.00 0.00 0.00 2.24
4615 6487 1.863454 GCAGGATTGCGTCTACATCAG 59.137 52.381 0.00 0.00 41.13 2.90
4687 6559 8.556213 ACTATGAACCAAAACGTATGTTGTAT 57.444 30.769 0.00 0.00 38.62 2.29
4688 6560 9.656040 ACTATGAACCAAAACGTATGTTGTATA 57.344 29.630 0.00 0.00 38.62 1.47
4907 9678 5.028549 TCCTGAAAGACATCCATCTAAGC 57.971 43.478 0.00 0.00 34.07 3.09
4920 9691 1.988293 TCTAAGCGCATCTCTAGCCT 58.012 50.000 11.47 0.00 0.00 4.58
4928 9699 2.547211 CGCATCTCTAGCCTTTTCCATG 59.453 50.000 0.00 0.00 0.00 3.66
4935 9706 4.589908 TCTAGCCTTTTCCATGTCCTTTC 58.410 43.478 0.00 0.00 0.00 2.62
5065 9836 0.892063 AAGAGTCTGTCTCCGCCTTC 59.108 55.000 0.00 0.00 43.71 3.46
5072 9843 1.273606 CTGTCTCCGCCTTCTTCTTCA 59.726 52.381 0.00 0.00 0.00 3.02
5110 9881 3.031736 ACGACTTATGGCCTGTAGATGT 58.968 45.455 3.32 0.10 0.00 3.06
5206 9978 0.034337 GTACACGTGCAAGGGAGGAA 59.966 55.000 17.22 0.00 0.00 3.36
5283 10055 7.113658 TGTCTCAATGGGTTCTTCTACTATC 57.886 40.000 0.00 0.00 0.00 2.08
5360 10135 1.000274 CGATGACGGCTGACATCCATA 60.000 52.381 25.56 0.00 42.05 2.74
5489 10277 9.787435 AAATTTTACACACTCCTAATACACTCA 57.213 29.630 0.00 0.00 0.00 3.41
5614 10406 2.162408 GGAATGTTGTTGTCCTAGCTGC 59.838 50.000 0.00 0.00 0.00 5.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
107 108 3.952931 TCTAAGGAACTACTCTCGCTGT 58.047 45.455 0.00 0.00 38.49 4.40
128 129 8.884323 ACTCTGTCCATCATACATTATACCAAT 58.116 33.333 0.00 0.00 0.00 3.16
146 147 4.056050 ACGACAATGTAACAACTCTGTCC 58.944 43.478 0.00 0.00 33.45 4.02
247 248 2.733026 GCATGATGCTGCTTTCGTTTTT 59.267 40.909 10.72 0.00 40.96 1.94
250 251 0.883153 TGCATGATGCTGCTTTCGTT 59.117 45.000 19.19 0.00 45.31 3.85
252 253 1.852280 CATTGCATGATGCTGCTTTCG 59.148 47.619 19.19 0.00 45.31 3.46
258 259 3.793797 TTTCTCCATTGCATGATGCTG 57.206 42.857 19.19 9.26 45.31 4.41
260 261 5.449107 AGTATTTCTCCATTGCATGATGC 57.551 39.130 11.12 11.12 45.29 3.91
264 265 4.520492 GGGGTAGTATTTCTCCATTGCATG 59.480 45.833 0.00 0.00 0.00 4.06
267 268 4.164843 TGGGGTAGTATTTCTCCATTGC 57.835 45.455 0.00 0.00 0.00 3.56
268 269 6.001449 TCTTGGGGTAGTATTTCTCCATTG 57.999 41.667 0.00 0.00 0.00 2.82
274 275 5.339282 GGAGCTTTCTTGGGGTAGTATTTCT 60.339 44.000 0.00 0.00 0.00 2.52
290 291 9.252962 CCATGAAATAATTAATGTGGAGCTTTC 57.747 33.333 0.00 0.00 0.00 2.62
304 618 3.321682 CACCGGGATGCCATGAAATAATT 59.678 43.478 6.32 0.00 0.00 1.40
314 628 1.298340 CTTGTACACCGGGATGCCA 59.702 57.895 6.32 0.00 0.00 4.92
316 630 0.036765 TGACTTGTACACCGGGATGC 60.037 55.000 6.32 0.00 0.00 3.91
317 631 2.691409 ATGACTTGTACACCGGGATG 57.309 50.000 6.32 0.00 0.00 3.51
318 632 3.343617 CAAATGACTTGTACACCGGGAT 58.656 45.455 6.32 0.00 0.00 3.85
319 633 2.773487 CAAATGACTTGTACACCGGGA 58.227 47.619 6.32 0.00 0.00 5.14
322 636 1.529438 ACGCAAATGACTTGTACACCG 59.471 47.619 0.00 0.00 37.36 4.94
323 637 3.744426 ACTACGCAAATGACTTGTACACC 59.256 43.478 0.00 0.00 37.36 4.16
325 639 5.294356 AGAACTACGCAAATGACTTGTACA 58.706 37.500 0.00 0.00 37.36 2.90
326 640 5.840940 AGAACTACGCAAATGACTTGTAC 57.159 39.130 0.00 0.00 37.36 2.90
327 641 6.097356 CCTAGAACTACGCAAATGACTTGTA 58.903 40.000 0.00 0.00 37.36 2.41
328 642 4.929808 CCTAGAACTACGCAAATGACTTGT 59.070 41.667 0.00 0.00 37.36 3.16
329 643 4.929808 ACCTAGAACTACGCAAATGACTTG 59.070 41.667 0.00 0.00 38.15 3.16
330 644 5.148651 ACCTAGAACTACGCAAATGACTT 57.851 39.130 0.00 0.00 0.00 3.01
331 645 4.803098 ACCTAGAACTACGCAAATGACT 57.197 40.909 0.00 0.00 0.00 3.41
332 646 6.956299 TTAACCTAGAACTACGCAAATGAC 57.044 37.500 0.00 0.00 0.00 3.06
410 754 9.000486 TATCACTAGATTTCTACACGGATGTAG 58.000 37.037 7.95 7.95 45.22 2.74
411 755 7.818997 ATCACTAGATTTCTACACGGATGTA 57.181 36.000 0.00 0.00 40.48 2.29
412 756 6.716934 ATCACTAGATTTCTACACGGATGT 57.283 37.500 0.00 0.00 43.30 3.06
413 757 9.776158 GTATATCACTAGATTTCTACACGGATG 57.224 37.037 0.00 0.00 35.67 3.51
414 758 9.742144 AGTATATCACTAGATTTCTACACGGAT 57.258 33.333 0.00 0.00 34.98 4.18
415 759 9.570468 AAGTATATCACTAGATTTCTACACGGA 57.430 33.333 0.00 0.00 36.04 4.69
469 813 7.582352 CGTAGTTATAGGTCATCGATTTGAGA 58.418 38.462 0.00 0.00 0.00 3.27
473 817 5.049198 TCGCGTAGTTATAGGTCATCGATTT 60.049 40.000 5.77 0.00 0.00 2.17
475 819 3.999001 TCGCGTAGTTATAGGTCATCGAT 59.001 43.478 5.77 0.00 0.00 3.59
478 822 5.568296 GTCATTCGCGTAGTTATAGGTCATC 59.432 44.000 5.77 0.00 0.00 2.92
481 825 5.105834 AGTCATTCGCGTAGTTATAGGTC 57.894 43.478 5.77 0.00 0.00 3.85
482 826 5.511234 AAGTCATTCGCGTAGTTATAGGT 57.489 39.130 5.77 0.00 0.00 3.08
483 827 7.806487 TGAATAAGTCATTCGCGTAGTTATAGG 59.194 37.037 5.77 0.00 45.25 2.57
486 830 7.390918 GTGAATAAGTCATTCGCGTAGTTAT 57.609 36.000 5.77 6.86 45.25 1.89
487 831 6.801367 GTGAATAAGTCATTCGCGTAGTTA 57.199 37.500 5.77 4.79 45.25 2.24
488 832 5.697848 GTGAATAAGTCATTCGCGTAGTT 57.302 39.130 5.77 2.59 45.25 2.24
495 839 3.482472 CGTCTCGGTGAATAAGTCATTCG 59.518 47.826 0.00 0.00 45.25 3.34
496 840 3.797256 CCGTCTCGGTGAATAAGTCATTC 59.203 47.826 0.00 0.00 42.73 2.67
498 842 3.438297 CCGTCTCGGTGAATAAGTCAT 57.562 47.619 0.00 0.00 42.73 3.06
512 856 6.636044 CACGAAATAGTTATTACCTCCGTCTC 59.364 42.308 0.00 0.00 0.00 3.36
513 857 6.319658 TCACGAAATAGTTATTACCTCCGTCT 59.680 38.462 0.00 0.00 0.00 4.18
514 858 6.498304 TCACGAAATAGTTATTACCTCCGTC 58.502 40.000 0.00 0.00 0.00 4.79
515 859 6.455360 TCACGAAATAGTTATTACCTCCGT 57.545 37.500 0.00 0.00 0.00 4.69
516 860 9.286946 GATATCACGAAATAGTTATTACCTCCG 57.713 37.037 0.00 0.00 0.00 4.63
535 1682 7.992180 AAAAAGCGGAAATCAATGATATCAC 57.008 32.000 7.78 0.00 0.00 3.06
698 1879 3.451178 GCTCCCATTTATATAGGCCGAGA 59.549 47.826 0.00 0.00 0.00 4.04
723 1904 5.380900 TGGTCTGATCTATGGAGTCTACTG 58.619 45.833 0.00 0.00 0.00 2.74
726 1907 4.402829 GCTGGTCTGATCTATGGAGTCTA 58.597 47.826 0.00 0.00 0.00 2.59
783 1966 3.908103 GGGGGAGGCTCACTAATGTAATA 59.092 47.826 17.73 0.00 0.00 0.98
844 2031 7.090173 GCTAATTGATGGCAGTTTTCTTTGTA 58.910 34.615 0.00 0.00 0.00 2.41
895 2082 7.422089 AGAGGGAATCTAGCTAGCTTAACTAGT 60.422 40.741 24.88 3.36 42.79 2.57
954 2143 4.647654 GACTGCTTGGTCGACGAA 57.352 55.556 12.62 12.62 0.00 3.85
962 2151 2.559840 CAGCTTGCGACTGCTTGG 59.440 61.111 0.00 0.00 43.34 3.61
1020 2209 2.506438 GCGAACGGGTCCTCGAAG 60.506 66.667 3.32 0.00 37.23 3.79
1720 2965 0.911769 TCTGGAATGCGGAAGTGGAT 59.088 50.000 0.00 0.00 0.00 3.41
1821 3078 9.282569 CCAAAAGGAATCCACAAAATATCAAAA 57.717 29.630 0.61 0.00 0.00 2.44
1850 3107 7.683437 AATCATAAGCATCCACATGACATAG 57.317 36.000 0.00 0.00 30.64 2.23
2000 3284 0.471617 GGCAGTGCCTGACCAGATAT 59.528 55.000 27.48 0.00 46.69 1.63
2106 3391 1.150135 GGGGGAGATCTATGGAGGTCA 59.850 57.143 0.00 0.00 34.97 4.02
2203 3856 3.343941 TGTTGTACTATGCCACCCTTC 57.656 47.619 0.00 0.00 0.00 3.46
2394 4049 3.557595 CCTAGAATGACGAGGTTTCATGC 59.442 47.826 0.00 0.00 36.78 4.06
2531 4191 2.364970 TCTAACGACGACAAGGGGAAAA 59.635 45.455 0.00 0.00 0.00 2.29
2568 4228 2.614134 TTGACCCATCCCGGAATTTT 57.386 45.000 0.73 0.00 36.56 1.82
2599 4259 3.041946 ACTAGAGCAAATACCTCCCCAG 58.958 50.000 0.00 0.00 0.00 4.45
2639 4299 1.204146 AGTGGTTGCCGGTAGATCAT 58.796 50.000 1.90 0.00 0.00 2.45
2686 4346 1.347378 GCCCAAAAACACCACCATCAT 59.653 47.619 0.00 0.00 0.00 2.45
2736 4396 1.758514 AGATGGGATCGCGACCACT 60.759 57.895 19.49 15.14 40.05 4.00
2837 4497 0.323302 TGAACCACCTAGCATCGCAA 59.677 50.000 0.00 0.00 0.00 4.85
2900 4560 9.479549 AAAATTGATCCACAATACATACTCCTT 57.520 29.630 0.00 0.00 46.90 3.36
2915 4575 0.964700 TGTGGCGCAAAATTGATCCA 59.035 45.000 10.83 0.49 0.00 3.41
2916 4576 1.928503 CATGTGGCGCAAAATTGATCC 59.071 47.619 10.83 0.00 0.00 3.36
2960 4620 4.202346 GGGATAGTCTGGTAGTCTCGTACT 60.202 50.000 0.00 0.00 42.62 2.73
2965 4625 3.211718 ACGGGATAGTCTGGTAGTCTC 57.788 52.381 0.00 0.00 0.00 3.36
3007 4667 1.075896 GGAGAGGGAGGACGGTCAT 60.076 63.158 10.76 1.86 0.00 3.06
3057 4717 2.223711 GCCACCAAACACTCAAAACGAT 60.224 45.455 0.00 0.00 0.00 3.73
3130 4790 3.274095 TGACATGAGACACCACACAAA 57.726 42.857 0.00 0.00 0.00 2.83
3162 4822 5.230942 ACGTGATCTAAATAGCTACATGCC 58.769 41.667 0.00 0.00 44.23 4.40
3167 4827 7.919621 ACCACTTTACGTGATCTAAATAGCTAC 59.080 37.037 0.00 0.00 46.81 3.58
3176 4836 3.827876 TCACCACCACTTTACGTGATCTA 59.172 43.478 0.00 0.00 46.81 1.98
3177 4837 2.631062 TCACCACCACTTTACGTGATCT 59.369 45.455 0.00 0.00 46.81 2.75
3201 4861 6.533723 TCACCAAATCGTAGTCATCAACATAC 59.466 38.462 0.00 0.00 0.00 2.39
3235 4895 2.912956 TGGAGCTTGAGACTGGGTATTT 59.087 45.455 0.00 0.00 0.00 1.40
3293 4953 1.698506 AAAACACCTTCATTGCCGGA 58.301 45.000 5.05 0.00 0.00 5.14
3295 4955 3.090952 TGAAAAACACCTTCATTGCCG 57.909 42.857 0.00 0.00 0.00 5.69
3350 5010 8.690203 TTTCACCATGAAGATAAAGTTTGAGA 57.310 30.769 0.00 0.00 37.70 3.27
3354 5014 8.912988 TGAGTTTTCACCATGAAGATAAAGTTT 58.087 29.630 0.00 0.00 37.70 2.66
3355 5015 8.463930 TGAGTTTTCACCATGAAGATAAAGTT 57.536 30.769 0.00 0.00 37.70 2.66
3490 5151 1.771854 ACCATATCCGCACCAACCATA 59.228 47.619 0.00 0.00 0.00 2.74
3498 5159 2.034305 ACTAGAACGACCATATCCGCAC 59.966 50.000 0.00 0.00 0.00 5.34
3525 5186 5.627367 CCAAAGCGATTAAAACATTGACGAA 59.373 36.000 0.00 0.00 0.00 3.85
3584 5245 5.297278 TGCACAAAAACTAATACAAGACCGT 59.703 36.000 0.00 0.00 0.00 4.83
3623 5284 8.579006 CATAATTAGGATGCACACAACCATAAT 58.421 33.333 0.00 0.00 41.12 1.28
3683 5344 6.039605 TGAACTCAAAATGAAGCATCAAGTGA 59.960 34.615 0.00 0.00 39.49 3.41
3743 5404 2.631384 TGAATCCTTGGAGGTTGGAGA 58.369 47.619 0.00 0.00 36.53 3.71
3750 5411 4.202245 TCGTAGTTTGAATCCTTGGAGG 57.798 45.455 0.00 0.00 36.46 4.30
3777 5438 6.441093 TGATTGATCACTAAGGAATGTTGC 57.559 37.500 0.00 0.00 0.00 4.17
3826 5487 4.492646 AGAAAGGACCAAAACATTGGGAT 58.507 39.130 11.92 0.00 46.23 3.85
3838 5499 3.913799 TCCCATGTCTAAAGAAAGGACCA 59.086 43.478 0.00 0.00 0.00 4.02
3840 5501 5.179533 GTCTCCCATGTCTAAAGAAAGGAC 58.820 45.833 0.00 0.00 0.00 3.85
3841 5502 4.844085 TGTCTCCCATGTCTAAAGAAAGGA 59.156 41.667 0.00 0.00 0.00 3.36
3842 5503 4.938226 GTGTCTCCCATGTCTAAAGAAAGG 59.062 45.833 0.00 0.00 0.00 3.11
3851 5695 0.900182 TGCTCGTGTCTCCCATGTCT 60.900 55.000 0.00 0.00 0.00 3.41
3882 5726 4.585162 GCTATGGTAAGAAGCAGAGTCCTA 59.415 45.833 1.80 0.00 42.91 2.94
3889 5733 1.863454 CGCAGCTATGGTAAGAAGCAG 59.137 52.381 0.00 0.00 38.75 4.24
3901 5745 1.749334 GACCCAGCCTACGCAGCTAT 61.749 60.000 0.00 0.00 38.95 2.97
3933 5777 4.833390 ACCCTGACACACTTAGATTTAGC 58.167 43.478 0.00 0.00 0.00 3.09
3949 5793 4.721776 AGCTACATTGGATTAAGACCCTGA 59.278 41.667 0.00 0.00 0.00 3.86
4008 5852 9.681062 CCTTTAGTTAAAGATGGAAAGGATGTA 57.319 33.333 12.11 0.00 43.67 2.29
4023 5871 2.650827 CCCCTCCCACCCTTTAGTTAAA 59.349 50.000 0.00 0.00 0.00 1.52
4025 5873 1.975471 CCCCTCCCACCCTTTAGTTA 58.025 55.000 0.00 0.00 0.00 2.24
4060 5909 8.718656 AGCTTGATCTATTCCCTTAGTTGTATT 58.281 33.333 0.00 0.00 0.00 1.89
4071 5920 7.573968 AATACAACAAGCTTGATCTATTCCC 57.426 36.000 32.50 0.00 0.00 3.97
4227 6077 4.095782 TGTCATTGCCTAACGAATTAAGGC 59.904 41.667 5.64 5.64 45.19 4.35
4261 6111 7.779326 TGGGAAAAAGATACATGCATTCTATCA 59.221 33.333 17.71 3.46 0.00 2.15
4275 6125 4.530946 ACTCTCGAAGGTGGGAAAAAGATA 59.469 41.667 0.00 0.00 0.00 1.98
4573 6445 3.499918 CCTTTTGCTTCATGACGTTCTCT 59.500 43.478 0.00 0.00 0.00 3.10
4601 6473 6.095021 ACAATCTACTACTGATGTAGACGCAA 59.905 38.462 9.79 0.00 46.76 4.85
4615 6487 7.359264 CGCCATTATTGTGCTACAATCTACTAC 60.359 40.741 14.94 5.09 44.91 2.73
4848 9619 2.658373 TCGCGGCAAACTCTACATTA 57.342 45.000 6.13 0.00 0.00 1.90
4879 9650 2.568956 TGGATGTCTTTCAGGAGAGTGG 59.431 50.000 0.00 0.00 0.00 4.00
4907 9678 2.315925 TGGAAAAGGCTAGAGATGCG 57.684 50.000 0.00 0.00 0.00 4.73
4920 9691 5.261040 AGGAGATGAAAGGACATGGAAAA 57.739 39.130 0.00 0.00 0.00 2.29
4928 9699 7.797062 AGGAATAGTTTAGGAGATGAAAGGAC 58.203 38.462 0.00 0.00 0.00 3.85
4935 9706 7.130681 AGGTTGAGGAATAGTTTAGGAGATG 57.869 40.000 0.00 0.00 0.00 2.90
4990 9761 0.033109 GGGAAGGGATGGGTGGAAAG 60.033 60.000 0.00 0.00 0.00 2.62
5065 9836 0.449388 GGCCGCACAGAATGAAGAAG 59.551 55.000 0.00 0.00 39.69 2.85
5072 9843 2.031919 TCGTTGGCCGCACAGAAT 59.968 55.556 0.00 0.00 36.19 2.40
5206 9978 5.240891 TCAGATTTCGCTGACTTTCTTGAT 58.759 37.500 0.00 0.00 39.84 2.57
5433 10221 7.417797 GGGCAAATGATTTAATGGAGCTTTAGA 60.418 37.037 0.00 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.