Multiple sequence alignment - TraesCS1D01G172100

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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 TraesCS1D01G172100 chr1D 100.000 2325 0 0 1 2325 246005448 246003124 0.000000e+00 4294.0
1 TraesCS1D01G172100 chr1A 98.146 863 14 2 1465 2325 306684226 306683364 0.000000e+00 1504.0
2 TraesCS1D01G172100 chr1A 93.917 674 31 3 758 1428 306684891 306684225 0.000000e+00 1009.0
3 TraesCS1D01G172100 chr1A 89.531 277 24 4 2 275 307030011 307029737 1.710000e-91 346.0
4 TraesCS1D01G172100 chr1A 87.151 179 12 7 580 756 307029617 307029448 2.360000e-45 193.0
5 TraesCS1D01G172100 chr1B 97.564 862 20 1 1465 2325 332092028 332092889 0.000000e+00 1474.0
6 TraesCS1D01G172100 chr1B 94.699 698 29 6 739 1428 332091332 332092029 0.000000e+00 1077.0
7 TraesCS1D01G172100 chr1B 89.354 526 36 11 1813 2325 337942010 337941492 0.000000e+00 643.0
8 TraesCS1D01G172100 chr1B 85.167 209 19 11 2 206 332090457 332090657 1.090000e-48 204.0
9 TraesCS1D01G172100 chr1B 93.985 133 8 0 568 700 332091012 332091144 3.920000e-48 202.0
10 TraesCS1D01G172100 chr3A 82.450 302 36 13 1019 1315 46837877 46837588 4.960000e-62 248.0
11 TraesCS1D01G172100 chr3A 92.683 123 6 3 447 566 607110044 607110166 8.540000e-40 174.0
12 TraesCS1D01G172100 chr3A 93.421 76 4 1 1989 2064 466803610 466803536 6.790000e-21 111.0
13 TraesCS1D01G172100 chr3B 81.288 326 38 15 1003 1318 59040204 59039892 2.310000e-60 243.0
14 TraesCS1D01G172100 chr3B 93.421 76 4 1 1989 2064 447635579 447635505 6.790000e-21 111.0
15 TraesCS1D01G172100 chr3D 81.402 328 32 16 1003 1318 36171709 36171399 8.300000e-60 241.0
16 TraesCS1D01G172100 chr3D 80.952 294 29 17 1019 1302 36018275 36017999 8.420000e-50 207.0
17 TraesCS1D01G172100 chr3D 93.421 76 4 1 1989 2064 347598775 347598701 6.790000e-21 111.0
18 TraesCS1D01G172100 chr5A 88.177 203 14 5 624 823 625711516 625711321 1.390000e-57 233.0
19 TraesCS1D01G172100 chr5A 91.270 126 8 3 444 566 156158160 156158035 3.970000e-38 169.0
20 TraesCS1D01G172100 chr5A 97.436 39 1 0 180 218 510493234 510493196 1.490000e-07 67.6
21 TraesCS1D01G172100 chr4A 92.063 126 7 3 444 566 199406658 199406533 8.540000e-40 174.0
22 TraesCS1D01G172100 chr4A 87.209 86 9 2 1985 2070 541683919 541684002 1.900000e-16 97.1
23 TraesCS1D01G172100 chrUn 91.870 123 7 3 447 566 229900216 229900338 3.970000e-38 169.0
24 TraesCS1D01G172100 chrUn 90.984 122 9 2 447 566 319723480 319723601 1.850000e-36 163.0
25 TraesCS1D01G172100 chrUn 90.984 122 9 2 447 566 319750621 319750742 1.850000e-36 163.0
26 TraesCS1D01G172100 chrUn 90.984 122 9 2 447 566 329305206 329305327 1.850000e-36 163.0
27 TraesCS1D01G172100 chr7B 91.870 123 7 3 447 566 188548050 188547928 3.970000e-38 169.0
28 TraesCS1D01G172100 chr7B 90.196 102 10 0 717 818 708505530 708505429 1.450000e-27 134.0
29 TraesCS1D01G172100 chr7A 91.803 122 8 2 447 566 189327498 189327619 3.970000e-38 169.0


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 TraesCS1D01G172100 chr1D 246003124 246005448 2324 True 4294.00 4294 100.00000 1 2325 1 chr1D.!!$R1 2324
1 TraesCS1D01G172100 chr1A 306683364 306684891 1527 True 1256.50 1504 96.03150 758 2325 2 chr1A.!!$R1 1567
2 TraesCS1D01G172100 chr1A 307029448 307030011 563 True 269.50 346 88.34100 2 756 2 chr1A.!!$R2 754
3 TraesCS1D01G172100 chr1B 332090457 332092889 2432 False 739.25 1474 92.85375 2 2325 4 chr1B.!!$F1 2323
4 TraesCS1D01G172100 chr1B 337941492 337942010 518 True 643.00 643 89.35400 1813 2325 1 chr1B.!!$R1 512

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
462 645 0.410663 TCCTACTCCCTTGGTCCGAA 59.589 55.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1450 1790 0.249238 CGAGTATCTCAGCTGTGCCC 60.249 60.0 14.67 2.6 0.0 5.36 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 8.649973 TTTTTGTTGGCTATAAATCAAACGTT 57.350 26.923 0.00 0.00 0.00 3.99
49 50 7.630470 TTTGTTGGCTATAAATCAAACGTTG 57.370 32.000 0.00 0.00 0.00 4.10
80 84 6.243811 AGCATGGCAAATACAATGTTTTTG 57.756 33.333 19.96 19.96 37.46 2.44
85 89 3.496507 GCAAATACAATGTTTTTGCCGGT 59.503 39.130 30.41 0.00 46.58 5.28
92 96 8.696410 ATACAATGTTTTTGCCGGTAAATTAG 57.304 30.769 18.81 8.34 0.00 1.73
106 110 5.983720 CGGTAAATTAGATTGTCACGAGGAT 59.016 40.000 0.00 0.00 0.00 3.24
118 122 4.096231 TGTCACGAGGATTGGCAATTTATG 59.904 41.667 14.93 8.95 0.00 1.90
120 124 4.335315 TCACGAGGATTGGCAATTTATGTC 59.665 41.667 14.93 0.60 0.00 3.06
297 475 3.926821 TTTTTGAAGCGGGGACATAAC 57.073 42.857 0.00 0.00 0.00 1.89
298 476 1.444836 TTTGAAGCGGGGACATAACG 58.555 50.000 0.00 0.00 0.00 3.18
299 477 0.609151 TTGAAGCGGGGACATAACGA 59.391 50.000 0.00 0.00 0.00 3.85
300 478 0.609151 TGAAGCGGGGACATAACGAA 59.391 50.000 0.00 0.00 0.00 3.85
301 479 1.002201 TGAAGCGGGGACATAACGAAA 59.998 47.619 0.00 0.00 0.00 3.46
302 480 2.078392 GAAGCGGGGACATAACGAAAA 58.922 47.619 0.00 0.00 0.00 2.29
303 481 2.413310 AGCGGGGACATAACGAAAAT 57.587 45.000 0.00 0.00 0.00 1.82
304 482 3.547054 AGCGGGGACATAACGAAAATA 57.453 42.857 0.00 0.00 0.00 1.40
305 483 3.200483 AGCGGGGACATAACGAAAATAC 58.800 45.455 0.00 0.00 0.00 1.89
306 484 2.937799 GCGGGGACATAACGAAAATACA 59.062 45.455 0.00 0.00 0.00 2.29
307 485 3.374678 GCGGGGACATAACGAAAATACAA 59.625 43.478 0.00 0.00 0.00 2.41
308 486 4.728595 GCGGGGACATAACGAAAATACAAC 60.729 45.833 0.00 0.00 0.00 3.32
309 487 4.201841 CGGGGACATAACGAAAATACAACC 60.202 45.833 0.00 0.00 0.00 3.77
310 488 4.701171 GGGGACATAACGAAAATACAACCA 59.299 41.667 0.00 0.00 0.00 3.67
311 489 5.358725 GGGGACATAACGAAAATACAACCAT 59.641 40.000 0.00 0.00 0.00 3.55
312 490 6.262601 GGGACATAACGAAAATACAACCATG 58.737 40.000 0.00 0.00 0.00 3.66
313 491 6.127842 GGGACATAACGAAAATACAACCATGT 60.128 38.462 0.00 0.00 43.74 3.21
314 492 7.066043 GGGACATAACGAAAATACAACCATGTA 59.934 37.037 0.00 0.00 45.67 2.29
315 493 7.906527 GGACATAACGAAAATACAACCATGTAC 59.093 37.037 0.00 0.00 44.47 2.90
316 494 8.325421 ACATAACGAAAATACAACCATGTACA 57.675 30.769 0.00 0.00 44.47 2.90
317 495 8.447833 ACATAACGAAAATACAACCATGTACAG 58.552 33.333 0.33 0.00 44.47 2.74
318 496 8.661257 CATAACGAAAATACAACCATGTACAGA 58.339 33.333 0.33 0.00 44.47 3.41
319 497 6.721571 ACGAAAATACAACCATGTACAGAG 57.278 37.500 0.33 0.00 44.47 3.35
320 498 5.642063 ACGAAAATACAACCATGTACAGAGG 59.358 40.000 13.94 13.94 44.47 3.69
321 499 5.064707 CGAAAATACAACCATGTACAGAGGG 59.935 44.000 18.34 13.78 44.47 4.30
322 500 5.772393 AAATACAACCATGTACAGAGGGA 57.228 39.130 18.34 4.61 44.47 4.20
323 501 5.772393 AATACAACCATGTACAGAGGGAA 57.228 39.130 18.34 4.50 44.47 3.97
324 502 5.772393 ATACAACCATGTACAGAGGGAAA 57.228 39.130 18.34 4.78 44.47 3.13
363 541 6.287589 ACTCTGGATCTAATTTGAACGAGT 57.712 37.500 8.40 10.39 0.00 4.18
364 542 6.702329 ACTCTGGATCTAATTTGAACGAGTT 58.298 36.000 8.40 0.00 0.00 3.01
365 543 7.837863 ACTCTGGATCTAATTTGAACGAGTTA 58.162 34.615 8.40 0.00 0.00 2.24
432 615 5.184287 TGTGTGAATGTGATTTGATCAGCAT 59.816 36.000 0.00 0.00 40.53 3.79
446 629 7.649533 TTGATCAGCATACAATTTGAATCCT 57.350 32.000 2.79 0.00 0.00 3.24
447 630 8.750515 TTGATCAGCATACAATTTGAATCCTA 57.249 30.769 2.79 0.00 0.00 2.94
448 631 8.158169 TGATCAGCATACAATTTGAATCCTAC 57.842 34.615 2.79 0.00 0.00 3.18
449 632 7.994911 TGATCAGCATACAATTTGAATCCTACT 59.005 33.333 2.79 0.00 0.00 2.57
450 633 7.792374 TCAGCATACAATTTGAATCCTACTC 57.208 36.000 2.79 0.00 0.00 2.59
451 634 6.767902 TCAGCATACAATTTGAATCCTACTCC 59.232 38.462 2.79 0.00 0.00 3.85
452 635 6.016777 CAGCATACAATTTGAATCCTACTCCC 60.017 42.308 2.79 0.00 0.00 4.30
453 636 6.064717 GCATACAATTTGAATCCTACTCCCT 58.935 40.000 2.79 0.00 0.00 4.20
454 637 6.547510 GCATACAATTTGAATCCTACTCCCTT 59.452 38.462 2.79 0.00 0.00 3.95
455 638 7.469181 GCATACAATTTGAATCCTACTCCCTTG 60.469 40.741 2.79 0.00 0.00 3.61
456 639 5.264395 ACAATTTGAATCCTACTCCCTTGG 58.736 41.667 2.79 0.00 0.00 3.61
457 640 5.222337 ACAATTTGAATCCTACTCCCTTGGT 60.222 40.000 2.79 0.00 0.00 3.67
458 641 4.569719 TTTGAATCCTACTCCCTTGGTC 57.430 45.455 0.00 0.00 0.00 4.02
459 642 2.478292 TGAATCCTACTCCCTTGGTCC 58.522 52.381 0.00 0.00 0.00 4.46
460 643 1.413077 GAATCCTACTCCCTTGGTCCG 59.587 57.143 0.00 0.00 0.00 4.79
461 644 0.635009 ATCCTACTCCCTTGGTCCGA 59.365 55.000 0.00 0.00 0.00 4.55
462 645 0.410663 TCCTACTCCCTTGGTCCGAA 59.589 55.000 0.00 0.00 0.00 4.30
463 646 1.203212 TCCTACTCCCTTGGTCCGAAA 60.203 52.381 0.00 0.00 0.00 3.46
464 647 1.626825 CCTACTCCCTTGGTCCGAAAA 59.373 52.381 0.00 0.00 0.00 2.29
465 648 2.238898 CCTACTCCCTTGGTCCGAAAAT 59.761 50.000 0.00 0.00 0.00 1.82
466 649 3.453353 CCTACTCCCTTGGTCCGAAAATA 59.547 47.826 0.00 0.00 0.00 1.40
467 650 3.345508 ACTCCCTTGGTCCGAAAATAC 57.654 47.619 0.00 0.00 0.00 1.89
468 651 2.910977 ACTCCCTTGGTCCGAAAATACT 59.089 45.455 0.00 0.00 0.00 2.12
469 652 3.329814 ACTCCCTTGGTCCGAAAATACTT 59.670 43.478 0.00 0.00 0.00 2.24
470 653 3.681593 TCCCTTGGTCCGAAAATACTTG 58.318 45.455 0.00 0.00 0.00 3.16
471 654 3.073356 TCCCTTGGTCCGAAAATACTTGT 59.927 43.478 0.00 0.00 0.00 3.16
472 655 3.439129 CCCTTGGTCCGAAAATACTTGTC 59.561 47.826 0.00 0.00 0.00 3.18
473 656 4.069304 CCTTGGTCCGAAAATACTTGTCA 58.931 43.478 0.00 0.00 0.00 3.58
474 657 4.083484 CCTTGGTCCGAAAATACTTGTCAC 60.083 45.833 0.00 0.00 0.00 3.67
475 658 3.404899 TGGTCCGAAAATACTTGTCACC 58.595 45.455 0.00 0.00 0.00 4.02
476 659 3.181453 TGGTCCGAAAATACTTGTCACCA 60.181 43.478 0.00 0.00 0.00 4.17
477 660 3.816523 GGTCCGAAAATACTTGTCACCAA 59.183 43.478 0.00 0.00 0.00 3.67
478 661 4.276431 GGTCCGAAAATACTTGTCACCAAA 59.724 41.667 0.00 0.00 0.00 3.28
479 662 5.221087 GGTCCGAAAATACTTGTCACCAAAA 60.221 40.000 0.00 0.00 0.00 2.44
480 663 6.443792 GTCCGAAAATACTTGTCACCAAAAT 58.556 36.000 0.00 0.00 0.00 1.82
481 664 6.362283 GTCCGAAAATACTTGTCACCAAAATG 59.638 38.462 0.00 0.00 0.00 2.32
482 665 6.263392 TCCGAAAATACTTGTCACCAAAATGA 59.737 34.615 0.00 0.00 0.00 2.57
483 666 7.040062 TCCGAAAATACTTGTCACCAAAATGAT 60.040 33.333 0.00 0.00 0.00 2.45
484 667 8.240682 CCGAAAATACTTGTCACCAAAATGATA 58.759 33.333 0.00 0.00 0.00 2.15
485 668 9.619316 CGAAAATACTTGTCACCAAAATGATAA 57.381 29.630 0.00 0.00 0.00 1.75
490 673 9.927668 ATACTTGTCACCAAAATGATAAAAAGG 57.072 29.630 0.00 0.00 0.00 3.11
491 674 8.017418 ACTTGTCACCAAAATGATAAAAAGGA 57.983 30.769 0.00 0.00 0.00 3.36
492 675 8.650490 ACTTGTCACCAAAATGATAAAAAGGAT 58.350 29.630 0.00 0.00 0.00 3.24
493 676 8.830201 TTGTCACCAAAATGATAAAAAGGATG 57.170 30.769 0.00 0.00 0.00 3.51
494 677 7.961351 TGTCACCAAAATGATAAAAAGGATGT 58.039 30.769 0.00 0.00 0.00 3.06
495 678 9.083422 TGTCACCAAAATGATAAAAAGGATGTA 57.917 29.630 0.00 0.00 0.00 2.29
561 744 5.621197 TGATGACAAGTATTTTTGGACGG 57.379 39.130 0.00 0.00 32.32 4.79
562 745 5.309638 TGATGACAAGTATTTTTGGACGGA 58.690 37.500 0.00 0.00 32.32 4.69
563 746 5.411361 TGATGACAAGTATTTTTGGACGGAG 59.589 40.000 0.00 0.00 32.32 4.63
564 747 4.069304 TGACAAGTATTTTTGGACGGAGG 58.931 43.478 0.00 0.00 32.32 4.30
565 748 3.418047 ACAAGTATTTTTGGACGGAGGG 58.582 45.455 0.00 0.00 32.32 4.30
566 749 3.181437 ACAAGTATTTTTGGACGGAGGGT 60.181 43.478 0.00 0.00 32.32 4.34
585 768 4.706962 AGGGTTATTCGTTTACGGTCTACT 59.293 41.667 2.09 0.00 40.29 2.57
589 772 6.325596 GTTATTCGTTTACGGTCTACTTCCT 58.674 40.000 2.09 0.00 40.29 3.36
597 780 1.064611 CGGTCTACTTCCTCTCTCCCA 60.065 57.143 0.00 0.00 0.00 4.37
609 792 1.205655 TCTCTCCCACAAGCAATCTCG 59.794 52.381 0.00 0.00 0.00 4.04
634 817 9.040543 CGTTTGCTTCTTTTTCTTTTCTTTTTC 57.959 29.630 0.00 0.00 0.00 2.29
702 885 1.003118 TGGCCACAAGGTCACATACTC 59.997 52.381 0.00 0.00 46.77 2.59
703 886 1.003118 GGCCACAAGGTCACATACTCA 59.997 52.381 0.00 0.00 40.10 3.41
704 887 2.076863 GCCACAAGGTCACATACTCAC 58.923 52.381 0.00 0.00 37.19 3.51
705 888 2.549992 GCCACAAGGTCACATACTCACA 60.550 50.000 0.00 0.00 37.19 3.58
706 889 3.869912 GCCACAAGGTCACATACTCACAT 60.870 47.826 0.00 0.00 37.19 3.21
708 891 5.674525 CCACAAGGTCACATACTCACATAT 58.325 41.667 0.00 0.00 0.00 1.78
713 896 8.874156 ACAAGGTCACATACTCACATATATCAT 58.126 33.333 0.00 0.00 0.00 2.45
714 897 9.716531 CAAGGTCACATACTCACATATATCATT 57.283 33.333 0.00 0.00 0.00 2.57
913 1252 4.459337 GCAACCAGCAATCTTAGTTTAGGT 59.541 41.667 0.00 0.00 44.79 3.08
936 1275 3.319122 CCGACATGTCATAGACTCATGGA 59.681 47.826 24.93 0.00 41.91 3.41
953 1292 1.229529 GACCTCCCCTCAACCCTCA 60.230 63.158 0.00 0.00 0.00 3.86
1083 1422 2.432628 GCCGTCACCTTCGTCCTG 60.433 66.667 0.00 0.00 0.00 3.86
1105 1444 3.632604 GTCATTCATCCTCCTGAGTACGA 59.367 47.826 0.00 0.00 0.00 3.43
1135 1474 2.359975 CACCTTGGCTCGTTCCCC 60.360 66.667 0.00 0.00 0.00 4.81
1152 1491 1.669265 CCCCTTTAATTTCGGCTCGTC 59.331 52.381 0.00 0.00 0.00 4.20
1276 1616 4.299796 GTCAAGCCCAAGCCCCCA 62.300 66.667 0.00 0.00 41.25 4.96
1325 1665 2.743928 CGCAAGCCCAGAGGTGAC 60.744 66.667 0.00 0.00 34.57 3.67
1385 1725 1.401761 TTTGGATGTGCTGCTGTTGT 58.598 45.000 0.00 0.00 0.00 3.32
1400 1740 1.950216 TGTTGTGTTCTGCGGCAATTA 59.050 42.857 3.44 0.00 0.00 1.40
1402 1742 3.005261 TGTTGTGTTCTGCGGCAATTAAT 59.995 39.130 3.44 0.00 0.00 1.40
1428 1768 4.761739 TCACCCACTTTTGCTCAATTCTAG 59.238 41.667 0.00 0.00 0.00 2.43
1429 1769 3.507622 ACCCACTTTTGCTCAATTCTAGC 59.492 43.478 2.88 2.88 40.50 3.42
1432 1772 4.022068 CCACTTTTGCTCAATTCTAGCCAA 60.022 41.667 6.81 0.50 39.30 4.52
1433 1773 5.159209 CACTTTTGCTCAATTCTAGCCAAG 58.841 41.667 6.81 10.18 39.30 3.61
1434 1774 5.048504 CACTTTTGCTCAATTCTAGCCAAGA 60.049 40.000 17.28 5.63 39.30 3.02
1435 1775 5.713861 ACTTTTGCTCAATTCTAGCCAAGAT 59.286 36.000 17.28 6.54 39.30 2.40
1436 1776 6.210185 ACTTTTGCTCAATTCTAGCCAAGATT 59.790 34.615 17.28 2.91 39.30 2.40
1437 1777 6.594788 TTTGCTCAATTCTAGCCAAGATTT 57.405 33.333 6.81 0.00 39.30 2.17
1438 1778 5.824904 TGCTCAATTCTAGCCAAGATTTC 57.175 39.130 6.81 0.00 39.30 2.17
1439 1779 5.503927 TGCTCAATTCTAGCCAAGATTTCT 58.496 37.500 6.81 0.00 39.30 2.52
1440 1780 6.653020 TGCTCAATTCTAGCCAAGATTTCTA 58.347 36.000 6.81 0.00 39.30 2.10
1441 1781 7.285566 TGCTCAATTCTAGCCAAGATTTCTAT 58.714 34.615 6.81 0.00 39.30 1.98
1442 1782 7.776969 TGCTCAATTCTAGCCAAGATTTCTATT 59.223 33.333 6.81 0.00 39.30 1.73
1443 1783 8.288913 GCTCAATTCTAGCCAAGATTTCTATTC 58.711 37.037 0.00 0.00 33.05 1.75
1444 1784 8.682936 TCAATTCTAGCCAAGATTTCTATTCC 57.317 34.615 0.00 0.00 33.05 3.01
1445 1785 7.442364 TCAATTCTAGCCAAGATTTCTATTCCG 59.558 37.037 0.00 0.00 33.05 4.30
1446 1786 4.632153 TCTAGCCAAGATTTCTATTCCGC 58.368 43.478 0.00 0.00 0.00 5.54
1447 1787 3.567478 AGCCAAGATTTCTATTCCGCT 57.433 42.857 0.00 0.00 0.00 5.52
1448 1788 3.209410 AGCCAAGATTTCTATTCCGCTG 58.791 45.455 0.00 0.00 0.00 5.18
1449 1789 2.945668 GCCAAGATTTCTATTCCGCTGT 59.054 45.455 0.00 0.00 0.00 4.40
1450 1790 3.242870 GCCAAGATTTCTATTCCGCTGTG 60.243 47.826 0.00 0.00 0.00 3.66
1451 1791 3.313526 CCAAGATTTCTATTCCGCTGTGG 59.686 47.826 0.00 0.00 40.09 4.17
1452 1792 3.199880 AGATTTCTATTCCGCTGTGGG 57.800 47.619 7.51 0.00 38.76 4.61
1453 1793 1.604278 GATTTCTATTCCGCTGTGGGC 59.396 52.381 7.51 0.00 38.76 5.36
1454 1794 0.326595 TTTCTATTCCGCTGTGGGCA 59.673 50.000 7.51 0.00 41.91 5.36
1455 1795 0.392461 TTCTATTCCGCTGTGGGCAC 60.392 55.000 7.51 0.00 41.91 5.01
1456 1796 1.078497 CTATTCCGCTGTGGGCACA 60.078 57.895 7.51 0.00 41.91 4.57
1464 1804 3.487211 TGTGGGCACAGCTGAGAT 58.513 55.556 23.35 0.00 36.21 2.75
1465 1805 2.682631 TGTGGGCACAGCTGAGATA 58.317 52.632 23.35 0.00 36.21 1.98
1466 1806 0.250234 TGTGGGCACAGCTGAGATAC 59.750 55.000 23.35 12.57 36.21 2.24
1467 1807 0.539051 GTGGGCACAGCTGAGATACT 59.461 55.000 23.35 0.00 0.00 2.12
1468 1808 0.826715 TGGGCACAGCTGAGATACTC 59.173 55.000 23.35 4.94 0.00 2.59
1476 1816 1.133982 AGCTGAGATACTCGTGCTGTG 59.866 52.381 14.41 0.00 39.79 3.66
1501 1841 6.039382 GGAATGTAGATTGGGTTGGTGTATTC 59.961 42.308 0.00 0.00 0.00 1.75
1542 1882 1.394917 GTTCGCAATTGCTCACGAGAT 59.605 47.619 26.86 0.00 39.32 2.75
1591 1931 9.270576 CTTTTATCGAAACTGATCTGTGAAATG 57.729 33.333 5.96 0.00 0.00 2.32
1946 2286 9.472361 GTTTCAAAACTTTTTATCCCTTCTACC 57.528 33.333 0.00 0.00 36.03 3.18
2211 2565 6.935208 GGGCATTTTTATCCGTAGAGAGTAAT 59.065 38.462 0.00 0.00 0.00 1.89
2303 2658 5.311265 TGTTGTCTCCGTAGAGTCTTCTTA 58.689 41.667 0.00 0.00 41.26 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 4.143137 GCCATGCTAAAAATCCAACGTTTG 60.143 41.667 0.00 0.00 0.00 2.93
42 43 3.993736 GCCATGCTAAAAATCCAACGTTT 59.006 39.130 0.00 0.00 0.00 3.60
48 49 6.291648 TGTATTTGCCATGCTAAAAATCCA 57.708 33.333 0.00 0.00 0.00 3.41
49 50 7.280652 ACATTGTATTTGCCATGCTAAAAATCC 59.719 33.333 0.00 0.00 0.00 3.01
80 84 3.866910 TCGTGACAATCTAATTTACCGGC 59.133 43.478 0.00 0.00 0.00 6.13
81 85 4.506654 CCTCGTGACAATCTAATTTACCGG 59.493 45.833 0.00 0.00 0.00 5.28
85 89 6.260050 GCCAATCCTCGTGACAATCTAATTTA 59.740 38.462 0.00 0.00 0.00 1.40
92 96 1.737838 TGCCAATCCTCGTGACAATC 58.262 50.000 0.00 0.00 0.00 2.67
106 110 3.006644 TGCTTGCTGACATAAATTGCCAA 59.993 39.130 0.00 0.00 0.00 4.52
120 124 5.731694 ACAAGGATTTGGCATGCTTGCTG 62.732 47.826 22.27 13.08 46.84 4.41
166 170 7.966246 TTTTCTTTAGCATGCAAATGACAAT 57.034 28.000 21.98 0.00 0.00 2.71
168 172 7.571613 GCAATTTTCTTTAGCATGCAAATGACA 60.572 33.333 21.98 3.14 32.80 3.58
277 455 2.226912 CGTTATGTCCCCGCTTCAAAAA 59.773 45.455 0.00 0.00 0.00 1.94
278 456 1.807742 CGTTATGTCCCCGCTTCAAAA 59.192 47.619 0.00 0.00 0.00 2.44
279 457 1.002201 TCGTTATGTCCCCGCTTCAAA 59.998 47.619 0.00 0.00 0.00 2.69
280 458 0.609151 TCGTTATGTCCCCGCTTCAA 59.391 50.000 0.00 0.00 0.00 2.69
281 459 0.609151 TTCGTTATGTCCCCGCTTCA 59.391 50.000 0.00 0.00 0.00 3.02
282 460 1.729284 TTTCGTTATGTCCCCGCTTC 58.271 50.000 0.00 0.00 0.00 3.86
283 461 2.188062 TTTTCGTTATGTCCCCGCTT 57.812 45.000 0.00 0.00 0.00 4.68
284 462 2.413310 ATTTTCGTTATGTCCCCGCT 57.587 45.000 0.00 0.00 0.00 5.52
285 463 2.937799 TGTATTTTCGTTATGTCCCCGC 59.062 45.455 0.00 0.00 0.00 6.13
286 464 4.201841 GGTTGTATTTTCGTTATGTCCCCG 60.202 45.833 0.00 0.00 0.00 5.73
287 465 4.701171 TGGTTGTATTTTCGTTATGTCCCC 59.299 41.667 0.00 0.00 0.00 4.81
288 466 5.883503 TGGTTGTATTTTCGTTATGTCCC 57.116 39.130 0.00 0.00 0.00 4.46
289 467 6.848451 ACATGGTTGTATTTTCGTTATGTCC 58.152 36.000 0.00 0.00 33.16 4.02
290 468 8.444715 TGTACATGGTTGTATTTTCGTTATGTC 58.555 33.333 0.00 0.00 40.35 3.06
291 469 8.325421 TGTACATGGTTGTATTTTCGTTATGT 57.675 30.769 0.00 0.00 40.35 2.29
292 470 8.661257 TCTGTACATGGTTGTATTTTCGTTATG 58.339 33.333 0.00 0.00 40.35 1.90
293 471 8.780846 TCTGTACATGGTTGTATTTTCGTTAT 57.219 30.769 0.00 0.00 40.35 1.89
294 472 7.332430 CCTCTGTACATGGTTGTATTTTCGTTA 59.668 37.037 0.00 0.00 40.35 3.18
295 473 6.148811 CCTCTGTACATGGTTGTATTTTCGTT 59.851 38.462 0.00 0.00 40.35 3.85
296 474 5.642063 CCTCTGTACATGGTTGTATTTTCGT 59.358 40.000 0.00 0.00 40.35 3.85
297 475 5.064707 CCCTCTGTACATGGTTGTATTTTCG 59.935 44.000 12.29 0.00 40.35 3.46
298 476 6.177610 TCCCTCTGTACATGGTTGTATTTTC 58.822 40.000 12.29 0.00 40.35 2.29
299 477 6.134535 TCCCTCTGTACATGGTTGTATTTT 57.865 37.500 12.29 0.00 40.35 1.82
300 478 5.772393 TCCCTCTGTACATGGTTGTATTT 57.228 39.130 12.29 0.00 40.35 1.40
301 479 5.772393 TTCCCTCTGTACATGGTTGTATT 57.228 39.130 12.29 0.00 40.35 1.89
302 480 5.772393 TTTCCCTCTGTACATGGTTGTAT 57.228 39.130 12.29 0.00 40.35 2.29
303 481 5.570205 TTTTCCCTCTGTACATGGTTGTA 57.430 39.130 12.29 0.00 37.28 2.41
304 482 4.447138 TTTTCCCTCTGTACATGGTTGT 57.553 40.909 12.29 0.00 39.98 3.32
324 502 6.049955 TCCAGAGTTATCTCATCCGTTTTT 57.950 37.500 3.70 0.00 42.66 1.94
374 554 7.141758 ACCTATCAATACATTCACAGATGGT 57.858 36.000 0.00 0.00 0.00 3.55
408 591 4.519730 TGCTGATCAAATCACATTCACACA 59.480 37.500 0.00 0.00 35.06 3.72
432 615 6.011981 ACCAAGGGAGTAGGATTCAAATTGTA 60.012 38.462 0.00 0.00 0.00 2.41
446 629 4.098894 AGTATTTTCGGACCAAGGGAGTA 58.901 43.478 0.00 0.00 0.00 2.59
447 630 2.910977 AGTATTTTCGGACCAAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
448 631 3.629142 AGTATTTTCGGACCAAGGGAG 57.371 47.619 0.00 0.00 0.00 4.30
449 632 3.073356 ACAAGTATTTTCGGACCAAGGGA 59.927 43.478 0.00 0.00 0.00 4.20
450 633 3.418047 ACAAGTATTTTCGGACCAAGGG 58.582 45.455 0.00 0.00 0.00 3.95
451 634 4.069304 TGACAAGTATTTTCGGACCAAGG 58.931 43.478 0.00 0.00 0.00 3.61
452 635 4.083484 GGTGACAAGTATTTTCGGACCAAG 60.083 45.833 0.00 0.00 0.00 3.61
453 636 3.816523 GGTGACAAGTATTTTCGGACCAA 59.183 43.478 0.00 0.00 0.00 3.67
454 637 3.181453 TGGTGACAAGTATTTTCGGACCA 60.181 43.478 0.00 0.00 37.44 4.02
455 638 3.404899 TGGTGACAAGTATTTTCGGACC 58.595 45.455 0.00 0.00 37.44 4.46
469 652 7.961351 ACATCCTTTTTATCATTTTGGTGACA 58.039 30.769 0.00 0.00 39.83 3.58
538 721 5.765677 TCCGTCCAAAAATACTTGTCATCAA 59.234 36.000 0.00 0.00 0.00 2.57
539 722 5.309638 TCCGTCCAAAAATACTTGTCATCA 58.690 37.500 0.00 0.00 0.00 3.07
540 723 5.163754 CCTCCGTCCAAAAATACTTGTCATC 60.164 44.000 0.00 0.00 0.00 2.92
541 724 4.700213 CCTCCGTCCAAAAATACTTGTCAT 59.300 41.667 0.00 0.00 0.00 3.06
542 725 4.069304 CCTCCGTCCAAAAATACTTGTCA 58.931 43.478 0.00 0.00 0.00 3.58
543 726 3.439129 CCCTCCGTCCAAAAATACTTGTC 59.561 47.826 0.00 0.00 0.00 3.18
544 727 3.181437 ACCCTCCGTCCAAAAATACTTGT 60.181 43.478 0.00 0.00 0.00 3.16
545 728 3.418047 ACCCTCCGTCCAAAAATACTTG 58.582 45.455 0.00 0.00 0.00 3.16
546 729 3.801307 ACCCTCCGTCCAAAAATACTT 57.199 42.857 0.00 0.00 0.00 2.24
547 730 3.801307 AACCCTCCGTCCAAAAATACT 57.199 42.857 0.00 0.00 0.00 2.12
548 731 5.220719 CGAATAACCCTCCGTCCAAAAATAC 60.221 44.000 0.00 0.00 0.00 1.89
549 732 4.877251 CGAATAACCCTCCGTCCAAAAATA 59.123 41.667 0.00 0.00 0.00 1.40
550 733 3.692593 CGAATAACCCTCCGTCCAAAAAT 59.307 43.478 0.00 0.00 0.00 1.82
551 734 3.075884 CGAATAACCCTCCGTCCAAAAA 58.924 45.455 0.00 0.00 0.00 1.94
552 735 2.038820 ACGAATAACCCTCCGTCCAAAA 59.961 45.455 0.00 0.00 0.00 2.44
553 736 1.624813 ACGAATAACCCTCCGTCCAAA 59.375 47.619 0.00 0.00 0.00 3.28
554 737 1.269012 ACGAATAACCCTCCGTCCAA 58.731 50.000 0.00 0.00 0.00 3.53
555 738 1.269012 AACGAATAACCCTCCGTCCA 58.731 50.000 0.00 0.00 33.84 4.02
556 739 2.391616 AAACGAATAACCCTCCGTCC 57.608 50.000 0.00 0.00 33.84 4.79
557 740 2.854185 CGTAAACGAATAACCCTCCGTC 59.146 50.000 0.00 0.00 43.02 4.79
558 741 2.417243 CCGTAAACGAATAACCCTCCGT 60.417 50.000 3.65 0.00 43.02 4.69
559 742 2.195922 CCGTAAACGAATAACCCTCCG 58.804 52.381 3.65 0.00 43.02 4.63
560 743 3.118992 AGACCGTAAACGAATAACCCTCC 60.119 47.826 3.65 0.00 43.02 4.30
561 744 4.115401 AGACCGTAAACGAATAACCCTC 57.885 45.455 3.65 0.00 43.02 4.30
562 745 4.706962 AGTAGACCGTAAACGAATAACCCT 59.293 41.667 3.65 0.00 43.02 4.34
563 746 4.998788 AGTAGACCGTAAACGAATAACCC 58.001 43.478 3.65 0.00 43.02 4.11
564 747 5.516696 GGAAGTAGACCGTAAACGAATAACC 59.483 44.000 3.65 0.00 43.02 2.85
565 748 6.325596 AGGAAGTAGACCGTAAACGAATAAC 58.674 40.000 3.65 0.00 43.02 1.89
566 749 6.375455 AGAGGAAGTAGACCGTAAACGAATAA 59.625 38.462 3.65 0.00 43.02 1.40
585 768 1.434188 TTGCTTGTGGGAGAGAGGAA 58.566 50.000 0.00 0.00 0.00 3.36
589 772 1.205655 CGAGATTGCTTGTGGGAGAGA 59.794 52.381 0.00 0.00 0.00 3.10
702 885 3.367932 GGACGTGCCGAATGATATATGTG 59.632 47.826 0.00 0.00 0.00 3.21
703 886 3.258372 AGGACGTGCCGAATGATATATGT 59.742 43.478 2.38 0.00 43.43 2.29
704 887 3.849911 AGGACGTGCCGAATGATATATG 58.150 45.455 2.38 0.00 43.43 1.78
705 888 3.119101 GGAGGACGTGCCGAATGATATAT 60.119 47.826 2.38 0.00 43.43 0.86
706 889 2.230508 GGAGGACGTGCCGAATGATATA 59.769 50.000 2.38 0.00 43.43 0.86
708 891 0.387929 GGAGGACGTGCCGAATGATA 59.612 55.000 2.38 0.00 43.43 2.15
713 896 2.029964 GTTGGAGGACGTGCCGAA 59.970 61.111 2.38 0.00 43.43 4.30
714 897 3.998672 GGTTGGAGGACGTGCCGA 61.999 66.667 2.38 0.00 43.43 5.54
721 904 2.358737 CGCCTGTGGTTGGAGGAC 60.359 66.667 0.00 0.00 0.00 3.85
793 1125 1.874466 GTTCGCTCCTCGTAGCTGC 60.874 63.158 0.00 0.00 40.49 5.25
904 1241 6.039047 GTCTATGACATGTCGGACCTAAACTA 59.961 42.308 23.80 6.03 32.09 2.24
905 1242 4.954202 TCTATGACATGTCGGACCTAAACT 59.046 41.667 20.54 0.00 0.00 2.66
913 1252 3.319122 CCATGAGTCTATGACATGTCGGA 59.681 47.826 20.54 14.94 39.47 4.55
936 1275 0.621862 GATGAGGGTTGAGGGGAGGT 60.622 60.000 0.00 0.00 0.00 3.85
953 1292 1.478510 AGGAATCTCGTTCTGTGCGAT 59.521 47.619 0.00 0.00 37.74 4.58
1083 1422 3.632604 TCGTACTCAGGAGGATGAATGAC 59.367 47.826 0.85 0.00 34.48 3.06
1105 1444 2.231380 AAGGTGAAGGGATGGCCGT 61.231 57.895 0.00 0.00 33.83 5.68
1285 1625 1.141019 GTAGAACCTGGCGATGCGA 59.859 57.895 0.00 0.00 0.00 5.10
1325 1665 1.265454 ACTTGGGGAGGTTAGAGCCG 61.265 60.000 0.00 0.00 0.00 5.52
1385 1725 3.755905 TGAAGATTAATTGCCGCAGAACA 59.244 39.130 0.00 0.00 0.00 3.18
1400 1740 3.565307 TGAGCAAAAGTGGGTGAAGATT 58.435 40.909 0.00 0.00 0.00 2.40
1402 1742 2.727123 TGAGCAAAAGTGGGTGAAGA 57.273 45.000 0.00 0.00 0.00 2.87
1428 1768 2.945668 ACAGCGGAATAGAAATCTTGGC 59.054 45.455 0.00 0.00 0.00 4.52
1429 1769 3.313526 CCACAGCGGAATAGAAATCTTGG 59.686 47.826 0.00 0.00 36.56 3.61
1432 1772 2.746472 GCCCACAGCGGAATAGAAATCT 60.746 50.000 0.00 0.00 36.56 2.40
1433 1773 1.604278 GCCCACAGCGGAATAGAAATC 59.396 52.381 0.00 0.00 36.56 2.17
1434 1774 1.680338 GCCCACAGCGGAATAGAAAT 58.320 50.000 0.00 0.00 36.56 2.17
1435 1775 3.168773 GCCCACAGCGGAATAGAAA 57.831 52.632 0.00 0.00 36.56 2.52
1436 1776 4.954933 GCCCACAGCGGAATAGAA 57.045 55.556 0.00 0.00 36.56 2.10
1447 1787 0.250234 GTATCTCAGCTGTGCCCACA 59.750 55.000 14.67 0.71 39.32 4.17
1448 1788 0.539051 AGTATCTCAGCTGTGCCCAC 59.461 55.000 14.67 9.43 0.00 4.61
1449 1789 0.826715 GAGTATCTCAGCTGTGCCCA 59.173 55.000 14.67 0.00 0.00 5.36
1450 1790 0.249238 CGAGTATCTCAGCTGTGCCC 60.249 60.000 14.67 2.60 0.00 5.36
1451 1791 0.457851 ACGAGTATCTCAGCTGTGCC 59.542 55.000 14.67 2.95 0.00 5.01
1452 1792 1.554392 CACGAGTATCTCAGCTGTGC 58.446 55.000 14.67 0.00 0.00 4.57
1453 1793 1.133982 AGCACGAGTATCTCAGCTGTG 59.866 52.381 14.67 11.96 39.09 3.66
1454 1794 1.133982 CAGCACGAGTATCTCAGCTGT 59.866 52.381 14.67 0.00 45.56 4.40
1455 1795 1.837648 CAGCACGAGTATCTCAGCTG 58.162 55.000 7.63 7.63 45.48 4.24
1456 1796 1.133982 CACAGCACGAGTATCTCAGCT 59.866 52.381 0.00 7.54 40.44 4.24
1457 1797 1.554392 CACAGCACGAGTATCTCAGC 58.446 55.000 0.00 0.00 33.37 4.26
1458 1798 1.745653 TCCACAGCACGAGTATCTCAG 59.254 52.381 0.00 0.00 0.00 3.35
1459 1799 1.834188 TCCACAGCACGAGTATCTCA 58.166 50.000 0.00 0.00 0.00 3.27
1460 1800 2.941453 TTCCACAGCACGAGTATCTC 57.059 50.000 0.00 0.00 0.00 2.75
1461 1801 2.497675 ACATTCCACAGCACGAGTATCT 59.502 45.455 0.00 0.00 0.00 1.98
1462 1802 2.893637 ACATTCCACAGCACGAGTATC 58.106 47.619 0.00 0.00 0.00 2.24
1463 1803 3.699538 TCTACATTCCACAGCACGAGTAT 59.300 43.478 0.00 0.00 0.00 2.12
1464 1804 3.086282 TCTACATTCCACAGCACGAGTA 58.914 45.455 0.00 0.00 0.00 2.59
1465 1805 1.893137 TCTACATTCCACAGCACGAGT 59.107 47.619 0.00 0.00 0.00 4.18
1466 1806 2.654749 TCTACATTCCACAGCACGAG 57.345 50.000 0.00 0.00 0.00 4.18
1467 1807 3.261580 CAATCTACATTCCACAGCACGA 58.738 45.455 0.00 0.00 0.00 4.35
1468 1808 2.352651 CCAATCTACATTCCACAGCACG 59.647 50.000 0.00 0.00 0.00 5.34
1476 1816 3.697166 ACACCAACCCAATCTACATTCC 58.303 45.455 0.00 0.00 0.00 3.01
1501 1841 7.113965 GCGAACATCAAAATAAAGCTATCCATG 59.886 37.037 0.00 0.00 0.00 3.66
1542 1882 9.558396 AAAGGAAAACTGCAATGATAATCAAAA 57.442 25.926 0.00 0.00 0.00 2.44
1591 1931 9.205719 GGTAGGCAATAGATAGCTTAAACTAAC 57.794 37.037 0.00 0.00 0.00 2.34
1946 2286 6.471146 TCCAACCATATTTCCCACAAATTTG 58.529 36.000 16.67 16.67 0.00 2.32
2303 2658 4.916099 GGTCTACGCGTGAAAGTAAAAT 57.084 40.909 24.59 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.