Multiple sequence alignment - TraesCS5A01G243500

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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 TraesCS5A01G243500 chr5A 100.000 5411 0 0 1 5411 458101660 458107070 0.000000e+00 9993.0
1 TraesCS5A01G243500 chr5A 81.338 284 25 11 1 258 458002975 458003256 7.100000e-49 206.0
2 TraesCS5A01G243500 chr5D 95.375 4519 135 26 361 4847 356619124 356623600 0.000000e+00 7119.0
3 TraesCS5A01G243500 chr5D 83.558 742 84 14 3283 4018 35483908 35483199 0.000000e+00 660.0
4 TraesCS5A01G243500 chr5D 83.558 742 84 14 3283 4018 539778930 539778221 0.000000e+00 660.0
5 TraesCS5A01G243500 chr5D 90.724 442 29 8 2283 2716 35484340 35483903 3.630000e-161 579.0
6 TraesCS5A01G243500 chr5D 90.724 442 29 8 2283 2716 539779362 539778925 3.630000e-161 579.0
7 TraesCS5A01G243500 chr5D 87.594 266 14 7 1 264 356618761 356619009 1.910000e-74 291.0
8 TraesCS5A01G243500 chr5B 93.866 4532 172 41 351 4847 421446587 421451047 0.000000e+00 6732.0
9 TraesCS5A01G243500 chr5B 91.698 265 12 4 2 264 421446217 421446473 5.150000e-95 359.0
10 TraesCS5A01G243500 chr5B 91.667 60 3 2 3036 3094 670997069 670997127 1.250000e-11 82.4
11 TraesCS5A01G243500 chr5B 90.909 55 4 1 3038 3092 656510521 656510468 7.520000e-09 73.1
12 TraesCS5A01G243500 chr6B 92.054 516 37 4 4897 5411 698069099 698068587 0.000000e+00 723.0
13 TraesCS5A01G243500 chr6B 83.936 249 27 5 2237 2473 304153962 304154209 5.450000e-55 226.0
14 TraesCS5A01G243500 chr1B 84.626 735 80 17 3288 4018 653970113 653970818 0.000000e+00 701.0
15 TraesCS5A01G243500 chr1B 84.076 741 84 13 3283 4018 252373683 252374394 0.000000e+00 684.0
16 TraesCS5A01G243500 chr1B 90.500 200 13 5 2523 2716 252373489 252373688 5.380000e-65 259.0
17 TraesCS5A01G243500 chr1B 85.171 263 24 4 2237 2487 252373237 252373496 6.960000e-64 255.0
18 TraesCS5A01G243500 chr7A 92.593 486 32 4 1664 2146 665439470 665439954 0.000000e+00 695.0
19 TraesCS5A01G243500 chr7A 78.253 561 92 17 4844 5397 203016329 203016866 3.120000e-87 333.0
20 TraesCS5A01G243500 chr1A 92.608 487 31 4 1664 2146 466349109 466349594 0.000000e+00 695.0
21 TraesCS5A01G243500 chr6D 83.378 740 88 12 3283 4018 231080972 231080264 0.000000e+00 652.0
22 TraesCS5A01G243500 chr6D 90.583 446 27 9 2283 2716 231081409 231080967 1.310000e-160 577.0
23 TraesCS5A01G243500 chr7D 90.724 442 30 7 2283 2716 598731683 598732121 3.630000e-161 579.0
24 TraesCS5A01G243500 chr7D 84.310 580 69 11 3283 3857 598732116 598732678 1.020000e-151 547.0
25 TraesCS5A01G243500 chr7B 86.391 507 39 11 2237 2716 82146999 82147502 1.330000e-145 527.0
26 TraesCS5A01G243500 chr7B 82.759 116 15 4 3037 3151 426840124 426840013 1.240000e-16 99.0
27 TraesCS5A01G243500 chr7B 82.178 101 12 5 3036 3134 553431252 553431348 1.250000e-11 82.4
28 TraesCS5A01G243500 chrUn 80.233 516 65 25 4843 5328 19797583 19797075 2.400000e-93 353.0
29 TraesCS5A01G243500 chr2D 92.135 89 7 0 1037 1125 405062396 405062484 5.690000e-25 126.0
30 TraesCS5A01G243500 chr2D 100.000 29 0 0 4844 4872 576460303 576460331 3.000000e-03 54.7
31 TraesCS5A01G243500 chr2A 92.135 89 7 0 1037 1125 543120696 543120784 5.690000e-25 126.0
32 TraesCS5A01G243500 chr4B 93.333 60 2 2 3036 3094 619360034 619360092 2.680000e-13 87.9
33 TraesCS5A01G243500 chr3B 90.000 60 4 2 3036 3094 228824178 228824236 5.810000e-10 76.8


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 TraesCS5A01G243500 chr5A 458101660 458107070 5410 False 9993.000000 9993 100.000000 1 5411 1 chr5A.!!$F2 5410
1 TraesCS5A01G243500 chr5D 356618761 356623600 4839 False 3705.000000 7119 91.484500 1 4847 2 chr5D.!!$F1 4846
2 TraesCS5A01G243500 chr5D 35483199 35484340 1141 True 619.500000 660 87.141000 2283 4018 2 chr5D.!!$R1 1735
3 TraesCS5A01G243500 chr5D 539778221 539779362 1141 True 619.500000 660 87.141000 2283 4018 2 chr5D.!!$R2 1735
4 TraesCS5A01G243500 chr5B 421446217 421451047 4830 False 3545.500000 6732 92.782000 2 4847 2 chr5B.!!$F2 4845
5 TraesCS5A01G243500 chr6B 698068587 698069099 512 True 723.000000 723 92.054000 4897 5411 1 chr6B.!!$R1 514
6 TraesCS5A01G243500 chr1B 653970113 653970818 705 False 701.000000 701 84.626000 3288 4018 1 chr1B.!!$F1 730
7 TraesCS5A01G243500 chr1B 252373237 252374394 1157 False 399.333333 684 86.582333 2237 4018 3 chr1B.!!$F2 1781
8 TraesCS5A01G243500 chr7A 203016329 203016866 537 False 333.000000 333 78.253000 4844 5397 1 chr7A.!!$F1 553
9 TraesCS5A01G243500 chr6D 231080264 231081409 1145 True 614.500000 652 86.980500 2283 4018 2 chr6D.!!$R1 1735
10 TraesCS5A01G243500 chr7D 598731683 598732678 995 False 563.000000 579 87.517000 2283 3857 2 chr7D.!!$F1 1574
11 TraesCS5A01G243500 chr7B 82146999 82147502 503 False 527.000000 527 86.391000 2237 2716 1 chr7B.!!$F1 479
12 TraesCS5A01G243500 chrUn 19797075 19797583 508 True 353.000000 353 80.233000 4843 5328 1 chrUn.!!$R1 485

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
722 772 0.318699 GAGAGGTTTGGTTTTGCGGC 60.319 55.000 0.00 0.0 0.00 6.53 F
1377 1437 0.105913 GAGGTCGGGGGAGAGAGAAT 60.106 60.000 0.00 0.0 0.00 2.40 F
1379 1439 0.397254 GGTCGGGGGAGAGAGAATGA 60.397 60.000 0.00 0.0 0.00 2.57 F
1745 1806 0.597377 CCCGTTTTCAGTTTGGCAGC 60.597 55.000 0.00 0.0 0.00 5.25 F
1776 1837 0.940126 GGATGTGCTGATTAGGTGCG 59.060 55.000 0.00 0.0 0.00 5.34 F
2195 2272 1.128507 TGCTCATCGTTTTTAGCAGCG 59.871 47.619 0.00 0.0 39.92 5.18 F
4007 4135 3.285484 GCTCTGTCACCATGATGGAATT 58.715 45.455 20.11 0.0 40.96 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2108 2184 0.828022 TGTTCTGGAGGTGACAACGT 59.172 50.000 0.00 0.0 0.00 3.99 R
3053 3170 4.726583 GAACAGTTAAGGGAGGGAACTTT 58.273 43.478 0.00 0.0 44.43 2.66 R
3415 3534 3.892588 TCCAAAAAGGTAGTGCGGAAAAT 59.107 39.130 0.00 0.0 39.02 1.82 R
3707 3834 7.872993 ACGATGTATATTGCATAAGTTACAGCT 59.127 33.333 9.72 0.0 28.94 4.24 R
3811 3938 6.373774 AGGTTTGCTTAAGATCATCTTCACTG 59.626 38.462 2.18 0.0 37.89 3.66 R
4148 4276 3.004106 GGAAGGCAACATGAGCATATGAC 59.996 47.826 6.97 0.0 41.41 3.06 R
4893 5028 3.059868 CACACGCGAACAGAGTTAAACAT 60.060 43.478 15.93 0.0 0.00 2.71 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
36 38 6.016276 AGAGCACAAAATGTAGGTTAAACTGG 60.016 38.462 2.38 0.00 0.00 4.00
69 71 5.008712 GCAGGCTAAATTATGTGGAGTAACC 59.991 44.000 0.00 0.00 39.54 2.85
70 72 5.236478 CAGGCTAAATTATGTGGAGTAACCG 59.764 44.000 0.00 0.00 42.61 4.44
71 73 5.129815 AGGCTAAATTATGTGGAGTAACCGA 59.870 40.000 0.00 0.00 42.61 4.69
72 74 5.465724 GGCTAAATTATGTGGAGTAACCGAG 59.534 44.000 0.00 0.00 42.61 4.63
73 75 6.047231 GCTAAATTATGTGGAGTAACCGAGT 58.953 40.000 0.00 0.00 42.61 4.18
74 76 7.205297 GCTAAATTATGTGGAGTAACCGAGTA 58.795 38.462 0.00 0.00 42.61 2.59
75 77 7.707893 GCTAAATTATGTGGAGTAACCGAGTAA 59.292 37.037 0.00 0.00 42.61 2.24
76 78 9.245962 CTAAATTATGTGGAGTAACCGAGTAAG 57.754 37.037 0.00 0.00 42.61 2.34
77 79 3.521947 ATGTGGAGTAACCGAGTAAGC 57.478 47.619 0.00 0.00 42.61 3.09
195 197 0.661483 GCAGCTCAGCCGTGAAAAAC 60.661 55.000 0.00 0.00 30.14 2.43
209 211 5.052238 CCGTGAAAAACAACCGTGAAATTAC 60.052 40.000 0.00 0.00 0.00 1.89
260 264 1.106351 ATGCAACGTTGACCAGCCAA 61.106 50.000 31.62 6.56 0.00 4.52
264 268 1.069022 CAACGTTGACCAGCCAAGATG 60.069 52.381 23.90 0.00 0.00 2.90
265 269 0.396435 ACGTTGACCAGCCAAGATGA 59.604 50.000 0.00 0.00 0.00 2.92
266 270 1.202758 ACGTTGACCAGCCAAGATGAA 60.203 47.619 0.00 0.00 0.00 2.57
327 367 9.706691 ACTTACTTATCATATGATTGTAACCGG 57.293 33.333 22.84 18.67 36.05 5.28
328 368 9.706691 CTTACTTATCATATGATTGTAACCGGT 57.293 33.333 22.84 0.00 36.05 5.28
342 382 9.940166 GATTGTAACCGGTAATTAATTAACCAG 57.060 33.333 8.00 10.87 0.00 4.00
343 383 7.862512 TGTAACCGGTAATTAATTAACCAGG 57.137 36.000 8.00 14.31 0.00 4.45
344 384 6.827762 TGTAACCGGTAATTAATTAACCAGGG 59.172 38.462 8.00 13.72 0.00 4.45
345 385 5.455392 ACCGGTAATTAATTAACCAGGGT 57.545 39.130 15.95 14.26 0.00 4.34
346 386 6.573712 ACCGGTAATTAATTAACCAGGGTA 57.426 37.500 15.95 0.00 0.00 3.69
347 387 6.594744 ACCGGTAATTAATTAACCAGGGTAG 58.405 40.000 15.95 2.28 0.00 3.18
348 388 6.158520 ACCGGTAATTAATTAACCAGGGTAGT 59.841 38.462 15.95 2.23 0.00 2.73
349 389 6.484308 CCGGTAATTAATTAACCAGGGTAGTG 59.516 42.308 15.95 1.04 0.00 2.74
367 407 6.263617 GGGTAGTGGTGTTTTTCAGTTCATTA 59.736 38.462 0.00 0.00 0.00 1.90
368 408 7.201839 GGGTAGTGGTGTTTTTCAGTTCATTAA 60.202 37.037 0.00 0.00 0.00 1.40
369 409 8.357402 GGTAGTGGTGTTTTTCAGTTCATTAAT 58.643 33.333 0.00 0.00 0.00 1.40
388 428 8.798402 TCATTAATAATTTATTTACGGGCAGGG 58.202 33.333 6.95 0.00 0.00 4.45
414 454 2.124901 CATCCGCGCCCTAAACCA 60.125 61.111 0.00 0.00 0.00 3.67
489 529 2.511600 CGTGGATCCGGTCAAGGC 60.512 66.667 7.39 0.00 0.00 4.35
626 666 1.221909 TACTGCTCCTCCCTCCTCCA 61.222 60.000 0.00 0.00 0.00 3.86
627 667 2.039624 TGCTCCTCCCTCCTCCAC 59.960 66.667 0.00 0.00 0.00 4.02
636 676 2.443016 CTCCTCCACCCTCCTCCG 60.443 72.222 0.00 0.00 0.00 4.63
640 680 4.779733 TCCACCCTCCTCCGCCTC 62.780 72.222 0.00 0.00 0.00 4.70
641 681 4.787280 CCACCCTCCTCCGCCTCT 62.787 72.222 0.00 0.00 0.00 3.69
642 682 2.685380 CACCCTCCTCCGCCTCTT 60.685 66.667 0.00 0.00 0.00 2.85
655 702 0.916845 GCCTCTTCTTCCCTCCCCTT 60.917 60.000 0.00 0.00 0.00 3.95
667 714 1.188863 CTCCCCTTGCCTCCAAATTG 58.811 55.000 0.00 0.00 0.00 2.32
722 772 0.318699 GAGAGGTTTGGTTTTGCGGC 60.319 55.000 0.00 0.00 0.00 6.53
723 773 1.300620 GAGGTTTGGTTTTGCGGCC 60.301 57.895 0.00 0.00 0.00 6.13
1202 1262 1.875157 GCCAAAGCTGCCAAAAAGAGG 60.875 52.381 0.00 0.00 35.50 3.69
1278 1338 1.141881 AAGCCCGCGAGATACACTG 59.858 57.895 8.23 0.00 0.00 3.66
1304 1364 1.404035 GTGGTTAAATCACGCCCCATC 59.596 52.381 0.00 0.00 0.00 3.51
1376 1436 1.306970 GAGGTCGGGGGAGAGAGAA 59.693 63.158 0.00 0.00 0.00 2.87
1377 1437 0.105913 GAGGTCGGGGGAGAGAGAAT 60.106 60.000 0.00 0.00 0.00 2.40
1378 1438 0.397816 AGGTCGGGGGAGAGAGAATG 60.398 60.000 0.00 0.00 0.00 2.67
1379 1439 0.397254 GGTCGGGGGAGAGAGAATGA 60.397 60.000 0.00 0.00 0.00 2.57
1380 1440 1.036707 GTCGGGGGAGAGAGAATGAG 58.963 60.000 0.00 0.00 0.00 2.90
1381 1441 0.927029 TCGGGGGAGAGAGAATGAGA 59.073 55.000 0.00 0.00 0.00 3.27
1382 1442 1.133637 TCGGGGGAGAGAGAATGAGAG 60.134 57.143 0.00 0.00 0.00 3.20
1383 1443 1.133637 CGGGGGAGAGAGAATGAGAGA 60.134 57.143 0.00 0.00 0.00 3.10
1384 1444 2.597455 GGGGGAGAGAGAATGAGAGAG 58.403 57.143 0.00 0.00 0.00 3.20
1385 1445 2.176798 GGGGGAGAGAGAATGAGAGAGA 59.823 54.545 0.00 0.00 0.00 3.10
1386 1446 3.373658 GGGGGAGAGAGAATGAGAGAGAA 60.374 52.174 0.00 0.00 0.00 2.87
1427 1487 3.163616 AGACTGGGTAGAGCCTATAGC 57.836 52.381 0.00 0.00 44.25 2.97
1566 1626 2.557372 GCGGCCGGAAACTGGAAAA 61.557 57.895 29.38 0.00 0.00 2.29
1567 1627 1.284715 CGGCCGGAAACTGGAAAAC 59.715 57.895 20.10 0.00 0.00 2.43
1611 1672 1.202770 GCAACGCAAGATACCCCCTAT 60.203 52.381 0.00 0.00 43.62 2.57
1614 1675 1.132817 ACGCAAGATACCCCCTATCCT 60.133 52.381 0.00 0.00 43.62 3.24
1619 1680 4.243643 CAAGATACCCCCTATCCTTTCCT 58.756 47.826 0.00 0.00 32.74 3.36
1621 1682 1.815757 TACCCCCTATCCTTTCCTGC 58.184 55.000 0.00 0.00 0.00 4.85
1734 1795 1.604147 CCCCTCATTGGCCCGTTTTC 61.604 60.000 0.00 0.00 0.00 2.29
1745 1806 0.597377 CCCGTTTTCAGTTTGGCAGC 60.597 55.000 0.00 0.00 0.00 5.25
1776 1837 0.940126 GGATGTGCTGATTAGGTGCG 59.060 55.000 0.00 0.00 0.00 5.34
1777 1838 1.656652 GATGTGCTGATTAGGTGCGT 58.343 50.000 0.00 0.00 0.00 5.24
1778 1839 1.328680 GATGTGCTGATTAGGTGCGTG 59.671 52.381 0.00 0.00 0.00 5.34
1779 1840 1.298157 TGTGCTGATTAGGTGCGTGC 61.298 55.000 0.00 0.00 0.00 5.34
1827 1891 2.868899 ACTTCTTGGCAGAAAAGGAGG 58.131 47.619 9.45 0.00 38.63 4.30
1851 1919 9.349713 AGGACATTTACATTTTCTCAAACTACA 57.650 29.630 0.00 0.00 0.00 2.74
1852 1920 9.394477 GGACATTTACATTTTCTCAAACTACAC 57.606 33.333 0.00 0.00 0.00 2.90
1858 1926 9.997482 TTACATTTTCTCAAACTACACTCAAAC 57.003 29.630 0.00 0.00 0.00 2.93
1860 1928 7.122055 ACATTTTCTCAAACTACACTCAAACCA 59.878 33.333 0.00 0.00 0.00 3.67
1861 1929 6.677781 TTTCTCAAACTACACTCAAACCAG 57.322 37.500 0.00 0.00 0.00 4.00
1862 1930 5.353394 TCTCAAACTACACTCAAACCAGT 57.647 39.130 0.00 0.00 0.00 4.00
1863 1931 5.741011 TCTCAAACTACACTCAAACCAGTT 58.259 37.500 0.00 0.00 0.00 3.16
1864 1932 6.880484 TCTCAAACTACACTCAAACCAGTTA 58.120 36.000 0.00 0.00 0.00 2.24
1865 1933 6.984474 TCTCAAACTACACTCAAACCAGTTAG 59.016 38.462 0.00 0.00 0.00 2.34
1866 1934 6.880484 TCAAACTACACTCAAACCAGTTAGA 58.120 36.000 0.00 0.00 0.00 2.10
2104 2180 2.536761 TGTAGCAGCTAAAACGTGGT 57.463 45.000 2.87 0.00 0.00 4.16
2108 2184 1.837538 GCAGCTAAAACGTGGTGCGA 61.838 55.000 11.30 0.00 45.42 5.10
2110 2186 1.154727 GCTAAAACGTGGTGCGACG 60.155 57.895 5.26 5.26 44.77 5.12
2146 2222 7.082602 CAGAACAATGGAGAAAAGACTTGATG 58.917 38.462 0.00 0.00 0.00 3.07
2148 2224 6.566197 ACAATGGAGAAAAGACTTGATGAC 57.434 37.500 0.00 0.00 0.00 3.06
2175 2252 7.623278 ACATGGGGTTTATATGAGGACAAAAAT 59.377 33.333 0.00 0.00 0.00 1.82
2195 2272 1.128507 TGCTCATCGTTTTTAGCAGCG 59.871 47.619 0.00 0.00 39.92 5.18
2319 2414 6.611381 TGTGTCTTCTTATGCAATTTACAGC 58.389 36.000 0.00 0.00 0.00 4.40
2348 2454 5.934625 ACTATCCAAGCTCAAACTTGTACTG 59.065 40.000 3.82 0.00 44.55 2.74
2351 2457 4.756642 TCCAAGCTCAAACTTGTACTGATG 59.243 41.667 3.82 0.00 44.55 3.07
2408 2518 5.504392 GTTATTCGTAATAAGCAAACCGGG 58.496 41.667 6.32 0.00 34.23 5.73
2827 2943 4.401925 ACTCCCAGAAAATCTTCAGGTTG 58.598 43.478 0.00 0.00 36.68 3.77
3053 3170 6.323225 TGATTTTAAAACGTGGTTAAAGGGGA 59.677 34.615 1.97 4.43 33.28 4.81
3453 3572 6.826231 CCTTTTTGGAAAGTGGGTTTGTATTT 59.174 34.615 0.00 0.00 40.53 1.40
3932 4059 4.019174 GAGGTATGGATTATTGGCCATGG 58.981 47.826 6.09 7.63 44.30 3.66
3968 4096 4.367166 TCAGTTCCTCCCCACATACAATA 58.633 43.478 0.00 0.00 0.00 1.90
4007 4135 3.285484 GCTCTGTCACCATGATGGAATT 58.715 45.455 20.11 0.00 40.96 2.17
4021 4149 6.169419 TGATGGAATTCGATCGATTAATGC 57.831 37.500 20.18 8.20 34.37 3.56
4042 4170 3.428316 GCTGTCAACGTTTTTCCCTTTCA 60.428 43.478 0.00 0.00 0.00 2.69
4147 4275 1.142870 TCCAGCAAACAAGCAGGTACT 59.857 47.619 0.00 0.00 41.46 2.73
4239 4367 1.135139 TGACGCTACTGCATCTCTTCC 59.865 52.381 0.00 0.00 39.64 3.46
4278 4406 0.467290 ACGGCAACCAGTGGAACAAT 60.467 50.000 18.40 0.00 44.16 2.71
4359 4487 4.157120 GACCCGGGCATGTACGCT 62.157 66.667 24.08 0.00 0.00 5.07
4368 4496 1.766143 GCATGTACGCTGCTGCCTAC 61.766 60.000 10.24 12.93 36.68 3.18
4553 4688 9.027202 TGACTGGTCATGTAAAGTACATTACTA 57.973 33.333 18.76 8.44 46.69 1.82
4608 4743 0.465705 AATGACTCGATCGCCATGGT 59.534 50.000 14.67 3.85 0.00 3.55
4836 4971 5.938322 AGCAATTTCGTCACATAAATCGTT 58.062 33.333 0.00 0.00 0.00 3.85
4893 5028 6.587273 TGACGTCATATGTAAATTGATCCCA 58.413 36.000 15.76 0.00 0.00 4.37
4943 5087 1.738432 GGTTTTCGTGTTCGTTCTGC 58.262 50.000 0.00 0.00 38.33 4.26
5001 5154 2.205074 GGCTGTATTGTCATCGTCCAG 58.795 52.381 0.00 0.00 0.00 3.86
5011 5164 0.943673 CATCGTCCAGTTGTTGTGCA 59.056 50.000 0.00 0.00 0.00 4.57
5059 5218 4.859245 GTGCTTGCTTTTTACTAGATTGCC 59.141 41.667 0.00 0.00 0.00 4.52
5088 5247 2.292016 TGTTCCGTTTGGTGTATTGCTG 59.708 45.455 0.00 0.00 36.30 4.41
5123 5282 6.627243 TGTAGCTCTTAATTTTGTCGCTAGA 58.373 36.000 0.00 0.00 0.00 2.43
5292 5463 8.964476 AGACAATTTAATTATCTGTGACCGAT 57.036 30.769 0.00 0.00 0.00 4.18
5325 5496 2.979814 TATGCAGCCGACTAATGTGT 57.020 45.000 0.00 0.00 0.00 3.72
5332 5503 4.188462 CAGCCGACTAATGTGTAATTGGA 58.812 43.478 0.00 0.00 0.00 3.53
5372 5544 4.853924 AGGTGAAAAGTAAGTTGCATGG 57.146 40.909 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 5.957842 TTAACCTACATTTTGTGCTCTGG 57.042 39.130 0.00 0.00 0.00 3.86
36 38 0.107654 ATTTAGCCTGCTCCGGTGAC 60.108 55.000 7.92 0.00 0.00 3.67
69 71 2.490115 AGTCTCTGGAACTGCTTACTCG 59.510 50.000 0.00 0.00 0.00 4.18
70 72 3.257127 ACAGTCTCTGGAACTGCTTACTC 59.743 47.826 3.30 0.00 35.51 2.59
71 73 3.235200 ACAGTCTCTGGAACTGCTTACT 58.765 45.455 3.30 0.00 35.51 2.24
72 74 3.257127 AGACAGTCTCTGGAACTGCTTAC 59.743 47.826 0.00 0.00 35.51 2.34
73 75 3.501349 AGACAGTCTCTGGAACTGCTTA 58.499 45.455 0.00 0.00 35.51 3.09
74 76 2.324541 AGACAGTCTCTGGAACTGCTT 58.675 47.619 0.00 0.00 35.51 3.91
75 77 2.008242 AGACAGTCTCTGGAACTGCT 57.992 50.000 0.00 0.01 35.51 4.24
76 78 4.464069 AATAGACAGTCTCTGGAACTGC 57.536 45.455 6.27 0.00 35.51 4.40
77 79 7.607250 ACTAAAATAGACAGTCTCTGGAACTG 58.393 38.462 6.27 1.89 35.51 3.16
195 197 2.486592 GGGAGGTGTAATTTCACGGTTG 59.513 50.000 8.84 0.00 39.00 3.77
209 211 2.859165 TAGCTTTTGACTGGGAGGTG 57.141 50.000 0.00 0.00 0.00 4.00
236 238 1.285641 GGTCAACGTTGCATGGGTG 59.714 57.895 23.47 0.00 0.00 4.61
238 240 1.580942 CTGGTCAACGTTGCATGGG 59.419 57.895 23.47 8.31 0.00 4.00
247 250 1.522668 TTCATCTTGGCTGGTCAACG 58.477 50.000 0.00 0.00 0.00 4.10
301 341 9.706691 CCGGTTACAATCATATGATAAGTAAGT 57.293 33.333 27.34 18.16 36.61 2.24
321 361 6.967897 ACCCTGGTTAATTAATTACCGGTTA 58.032 36.000 15.04 2.98 0.00 2.85
322 362 5.829986 ACCCTGGTTAATTAATTACCGGTT 58.170 37.500 15.04 0.00 0.00 4.44
324 364 6.484308 CACTACCCTGGTTAATTAATTACCGG 59.516 42.308 19.00 19.00 0.00 5.28
325 365 6.484308 CCACTACCCTGGTTAATTAATTACCG 59.516 42.308 7.43 8.62 0.00 4.02
326 366 7.283807 CACCACTACCCTGGTTAATTAATTACC 59.716 40.741 7.43 12.03 42.29 2.85
327 367 7.830697 ACACCACTACCCTGGTTAATTAATTAC 59.169 37.037 7.43 3.87 42.29 1.89
328 368 7.931046 ACACCACTACCCTGGTTAATTAATTA 58.069 34.615 3.71 3.71 42.29 1.40
330 370 6.397217 ACACCACTACCCTGGTTAATTAAT 57.603 37.500 0.31 0.00 42.29 1.40
332 372 5.846528 AACACCACTACCCTGGTTAATTA 57.153 39.130 0.00 0.00 42.29 1.40
334 374 4.734843 AAACACCACTACCCTGGTTAAT 57.265 40.909 0.00 0.00 42.29 1.40
336 376 4.079901 TGAAAAACACCACTACCCTGGTTA 60.080 41.667 0.00 0.00 42.29 2.85
337 377 3.293337 GAAAAACACCACTACCCTGGTT 58.707 45.455 0.00 0.00 42.29 3.67
338 378 2.242708 TGAAAAACACCACTACCCTGGT 59.757 45.455 0.00 0.00 46.18 4.00
342 382 3.949113 TGAACTGAAAAACACCACTACCC 59.051 43.478 0.00 0.00 0.00 3.69
343 383 5.767816 ATGAACTGAAAAACACCACTACC 57.232 39.130 0.00 0.00 0.00 3.18
367 407 5.221362 GCACCCTGCCCGTAAATAAATTATT 60.221 40.000 0.00 0.00 37.42 1.40
368 408 4.279922 GCACCCTGCCCGTAAATAAATTAT 59.720 41.667 0.00 0.00 37.42 1.28
369 409 3.633065 GCACCCTGCCCGTAAATAAATTA 59.367 43.478 0.00 0.00 37.42 1.40
370 410 2.429250 GCACCCTGCCCGTAAATAAATT 59.571 45.455 0.00 0.00 37.42 1.82
626 666 2.364448 GAAGAGGCGGAGGAGGGT 60.364 66.667 0.00 0.00 0.00 4.34
627 667 1.681486 GAAGAAGAGGCGGAGGAGGG 61.681 65.000 0.00 0.00 0.00 4.30
636 676 0.916845 AAGGGGAGGGAAGAAGAGGC 60.917 60.000 0.00 0.00 0.00 4.70
640 680 1.210885 AGGCAAGGGGAGGGAAGAAG 61.211 60.000 0.00 0.00 0.00 2.85
641 681 1.151587 AGGCAAGGGGAGGGAAGAA 60.152 57.895 0.00 0.00 0.00 2.52
642 682 1.616628 GAGGCAAGGGGAGGGAAGA 60.617 63.158 0.00 0.00 0.00 2.87
655 702 0.400213 ACGGAGACAATTTGGAGGCA 59.600 50.000 0.78 0.00 0.00 4.75
1149 1209 2.680352 ACGTGGGCGAGATCTGGT 60.680 61.111 0.00 0.00 42.00 4.00
1202 1262 2.027625 CGAAAGGGAGACGGTGTGC 61.028 63.158 0.00 0.00 0.00 4.57
1278 1338 3.498082 GGCGTGATTTAACCACACATTC 58.502 45.455 0.00 0.00 34.36 2.67
1304 1364 0.109781 CTGTCGCCATTTTTCGTGGG 60.110 55.000 0.00 0.00 37.22 4.61
1327 1387 2.956964 GACGAATCGCGCCTCTGG 60.957 66.667 0.00 0.00 46.04 3.86
1376 1436 2.031120 CCGCCTCTCTTTCTCTCTCAT 58.969 52.381 0.00 0.00 0.00 2.90
1377 1437 1.004862 TCCGCCTCTCTTTCTCTCTCA 59.995 52.381 0.00 0.00 0.00 3.27
1378 1438 1.757682 TCCGCCTCTCTTTCTCTCTC 58.242 55.000 0.00 0.00 0.00 3.20
1379 1439 2.091885 AGATCCGCCTCTCTTTCTCTCT 60.092 50.000 0.00 0.00 0.00 3.10
1380 1440 2.306847 AGATCCGCCTCTCTTTCTCTC 58.693 52.381 0.00 0.00 0.00 3.20
1381 1441 2.452600 AGATCCGCCTCTCTTTCTCT 57.547 50.000 0.00 0.00 0.00 3.10
1382 1442 4.142138 TGTTAAGATCCGCCTCTCTTTCTC 60.142 45.833 0.00 0.00 33.83 2.87
1383 1443 3.769844 TGTTAAGATCCGCCTCTCTTTCT 59.230 43.478 0.00 0.00 33.83 2.52
1384 1444 4.124851 TGTTAAGATCCGCCTCTCTTTC 57.875 45.455 0.00 0.00 33.83 2.62
1385 1445 4.553330 TTGTTAAGATCCGCCTCTCTTT 57.447 40.909 0.00 0.00 33.83 2.52
1386 1446 4.223032 TCTTTGTTAAGATCCGCCTCTCTT 59.777 41.667 0.00 0.00 35.49 2.85
1554 1614 1.001706 GACTGCGGTTTTCCAGTTTCC 60.002 52.381 0.00 0.00 42.01 3.13
1566 1626 1.338136 CCAATCTAGGGGACTGCGGT 61.338 60.000 0.00 0.00 43.88 5.68
1567 1627 1.447643 CCAATCTAGGGGACTGCGG 59.552 63.158 0.00 0.00 43.88 5.69
1611 1672 1.841302 ATGACCAGCGCAGGAAAGGA 61.841 55.000 27.14 4.24 0.00 3.36
1614 1675 1.675310 CCATGACCAGCGCAGGAAA 60.675 57.895 27.14 13.11 0.00 3.13
1619 1680 1.418097 ATATCCCCATGACCAGCGCA 61.418 55.000 11.47 0.00 0.00 6.09
1621 1682 0.957395 GCATATCCCCATGACCAGCG 60.957 60.000 0.00 0.00 0.00 5.18
1734 1795 2.336088 CCCAACGCTGCCAAACTG 59.664 61.111 0.00 0.00 0.00 3.16
1745 1806 1.666209 GCACATCCCAATCCCCAACG 61.666 60.000 0.00 0.00 0.00 4.10
1776 1837 6.477360 GGCTAGTTTCTACATAGAAGAAGCAC 59.523 42.308 21.20 10.83 42.66 4.40
1777 1838 6.574350 GGCTAGTTTCTACATAGAAGAAGCA 58.426 40.000 21.20 2.01 42.66 3.91
1778 1839 5.688176 CGGCTAGTTTCTACATAGAAGAAGC 59.312 44.000 16.17 16.17 42.66 3.86
1779 1840 7.028926 TCGGCTAGTTTCTACATAGAAGAAG 57.971 40.000 1.81 3.15 42.66 2.85
1852 1920 4.020128 AGCCCTAACTCTAACTGGTTTGAG 60.020 45.833 18.17 18.17 44.24 3.02
1858 1926 5.046520 AGTGTAAAGCCCTAACTCTAACTGG 60.047 44.000 0.00 0.00 0.00 4.00
1860 1928 6.683312 AAGTGTAAAGCCCTAACTCTAACT 57.317 37.500 0.00 0.00 0.00 2.24
1861 1929 8.309656 TCTAAAGTGTAAAGCCCTAACTCTAAC 58.690 37.037 0.00 0.00 0.00 2.34
1862 1930 8.426569 TCTAAAGTGTAAAGCCCTAACTCTAA 57.573 34.615 0.00 0.00 0.00 2.10
1863 1931 8.426569 TTCTAAAGTGTAAAGCCCTAACTCTA 57.573 34.615 0.00 0.00 0.00 2.43
1864 1932 6.930068 TCTAAAGTGTAAAGCCCTAACTCT 57.070 37.500 0.00 0.00 0.00 3.24
1865 1933 7.384477 TCTTCTAAAGTGTAAAGCCCTAACTC 58.616 38.462 0.00 0.00 0.00 3.01
1866 1934 7.312415 TCTTCTAAAGTGTAAAGCCCTAACT 57.688 36.000 0.00 0.00 0.00 2.24
2104 2180 2.028484 GGAGGTGACAACGTCGCA 59.972 61.111 9.65 0.00 43.87 5.10
2108 2184 0.828022 TGTTCTGGAGGTGACAACGT 59.172 50.000 0.00 0.00 0.00 3.99
2110 2186 2.554032 CCATTGTTCTGGAGGTGACAAC 59.446 50.000 0.00 0.00 38.69 3.32
2135 2211 3.181429 ACCCCATGTGTCATCAAGTCTTT 60.181 43.478 0.00 0.00 0.00 2.52
2146 2222 5.063880 GTCCTCATATAAACCCCATGTGTC 58.936 45.833 0.00 0.00 0.00 3.67
2148 2224 5.047566 TGTCCTCATATAAACCCCATGTG 57.952 43.478 0.00 0.00 0.00 3.21
2175 2252 1.128507 CGCTGCTAAAAACGATGAGCA 59.871 47.619 0.00 0.00 42.47 4.26
2319 2414 7.301068 CAAGTTTGAGCTTGGATAGTAAGAG 57.699 40.000 0.00 0.00 41.41 2.85
2348 2454 9.494271 ACAACCTACATCATATTCATACACATC 57.506 33.333 0.00 0.00 0.00 3.06
2351 2457 7.359264 GCGACAACCTACATCATATTCATACAC 60.359 40.741 0.00 0.00 0.00 2.90
2408 2518 6.645790 ACAAATCCATATCCTTCTGATTGC 57.354 37.500 0.00 0.00 34.76 3.56
2827 2943 7.444487 ACATAGGAACTGAGAAACTTGTTAACC 59.556 37.037 2.48 0.00 41.52 2.85
3053 3170 4.726583 GAACAGTTAAGGGAGGGAACTTT 58.273 43.478 0.00 0.00 44.43 2.66
3415 3534 3.892588 TCCAAAAAGGTAGTGCGGAAAAT 59.107 39.130 0.00 0.00 39.02 1.82
3707 3834 7.872993 ACGATGTATATTGCATAAGTTACAGCT 59.127 33.333 9.72 0.00 28.94 4.24
3751 3878 9.620660 GGACAATTAATGAGTTAAACAACGATT 57.379 29.630 0.00 0.00 33.76 3.34
3763 3890 9.975218 ACAAATACCTAAGGACAATTAATGAGT 57.025 29.630 0.00 0.00 0.00 3.41
3765 3892 9.104965 CGACAAATACCTAAGGACAATTAATGA 57.895 33.333 0.00 0.00 0.00 2.57
3766 3893 8.342634 CCGACAAATACCTAAGGACAATTAATG 58.657 37.037 0.00 0.00 0.00 1.90
3767 3894 8.050930 ACCGACAAATACCTAAGGACAATTAAT 58.949 33.333 0.00 0.00 0.00 1.40
3811 3938 6.373774 AGGTTTGCTTAAGATCATCTTCACTG 59.626 38.462 2.18 0.00 37.89 3.66
3932 4059 7.120873 GGGGAGGAACTGAAAAGTATAAAAGTC 59.879 40.741 0.00 0.00 41.55 3.01
3968 4096 6.591001 ACAGAGCCAATTTAACCAAACAAAT 58.409 32.000 0.00 0.00 0.00 2.32
4007 4135 3.485743 CGTTGACAGCATTAATCGATCGA 59.514 43.478 21.86 21.86 0.00 3.59
4021 4149 4.102649 GTGAAAGGGAAAAACGTTGACAG 58.897 43.478 0.00 0.00 0.00 3.51
4147 4275 3.286329 AGGCAACATGAGCATATGACA 57.714 42.857 6.97 6.20 41.41 3.58
4148 4276 3.004106 GGAAGGCAACATGAGCATATGAC 59.996 47.826 6.97 0.00 41.41 3.06
4239 4367 2.245159 TGTCACTCCTCAACTGCAAG 57.755 50.000 0.00 0.00 42.29 4.01
4278 4406 2.788640 GGGCGCGTAGTACATCCCA 61.789 63.158 8.43 0.00 34.01 4.37
4481 4616 2.727298 CGTCGTCGTCTACCTTCTTTCC 60.727 54.545 0.00 0.00 0.00 3.13
4553 4688 5.418209 AGTGGTGCTAGTTCTTCGTAATAGT 59.582 40.000 0.00 0.00 0.00 2.12
4608 4743 3.632604 CCTAGAACAATCCAGCTAGACGA 59.367 47.826 0.00 0.00 33.81 4.20
4729 4864 5.340667 GCTCAACATCAGTTCGAAATCAAAC 59.659 40.000 0.00 0.00 35.28 2.93
4880 5015 8.739972 ACAGAGTTAAACATGGGATCAATTTAC 58.260 33.333 0.00 0.00 0.00 2.01
4893 5028 3.059868 CACACGCGAACAGAGTTAAACAT 60.060 43.478 15.93 0.00 0.00 2.71
5028 5184 9.677567 TCTAGTAAAAAGCAAGCACAAATAAAG 57.322 29.630 0.00 0.00 0.00 1.85
5059 5218 3.315191 ACACCAAACGGAACAATCTTCTG 59.685 43.478 0.00 0.00 0.00 3.02
5088 5247 6.910536 ATTAAGAGCTACAATGTACTGTGC 57.089 37.500 0.00 0.00 0.00 4.57
5292 5463 5.185056 TCGGCTGCATATAGTTGCTTATCTA 59.815 40.000 0.50 0.00 43.18 1.98
5354 5525 4.038642 GGTTCCCATGCAACTTACTTTTCA 59.961 41.667 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.