Multiple sequence alignment - TraesCS1A01G194100

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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 TraesCS1A01G194100 chr1A 100.000 3207 0 0 1 3207 351351709 351348503 0.000000e+00 5923.0
1 TraesCS1A01G194100 chr1A 78.571 238 39 11 4 237 286011230 286011001 2.580000e-31 147.0
2 TraesCS1A01G194100 chr1D 95.381 2728 89 14 495 3207 279105235 279102530 0.000000e+00 4305.0
3 TraesCS1A01G194100 chr1D 80.108 372 53 13 1 368 279106191 279105837 1.140000e-64 257.0
4 TraesCS1A01G194100 chr1D 95.556 45 2 0 386 430 279105854 279105810 4.440000e-09 73.1
5 TraesCS1A01G194100 chr1B 96.021 2513 69 10 700 3207 378839261 378836775 0.000000e+00 4058.0
6 TraesCS1A01G194100 chr1B 86.473 207 22 2 404 604 378855238 378855032 4.160000e-54 222.0
7 TraesCS1A01G194100 chr1B 93.617 47 3 0 637 683 40598865 40598819 1.600000e-08 71.3
8 TraesCS1A01G194100 chr1B 100.000 28 0 0 638 665 674075293 674075320 6.000000e-03 52.8
9 TraesCS1A01G194100 chr4B 84.277 159 18 7 480 634 649711223 649711378 7.170000e-32 148.0
10 TraesCS1A01G194100 chr5D 86.029 136 19 0 492 627 483707919 483708054 2.580000e-31 147.0
11 TraesCS1A01G194100 chrUn 85.496 131 16 3 489 618 40740614 40740742 2.010000e-27 134.0
12 TraesCS1A01G194100 chrUn 85.496 131 16 3 489 618 40747291 40747163 2.010000e-27 134.0
13 TraesCS1A01G194100 chrUn 85.496 131 16 3 489 618 303400168 303400296 2.010000e-27 134.0
14 TraesCS1A01G194100 chr2D 82.278 158 25 3 480 635 65534977 65535133 2.010000e-27 134.0
15 TraesCS1A01G194100 chr2D 74.043 235 50 10 4 233 17458616 17458844 5.700000e-13 86.1
16 TraesCS1A01G194100 chr2A 84.058 138 19 3 493 628 539305083 539305219 2.600000e-26 130.0
17 TraesCS1A01G194100 chr2A 83.088 136 22 1 493 628 15463309 15463175 4.340000e-24 122.0
18 TraesCS1A01G194100 chr6B 83.212 137 19 3 493 628 178665473 178665340 4.340000e-24 122.0
19 TraesCS1A01G194100 chr2B 83.544 79 12 1 137 215 682864869 682864792 4.440000e-09 73.1


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 TraesCS1A01G194100 chr1A 351348503 351351709 3206 True 5923.000000 5923 100.000000 1 3207 1 chr1A.!!$R2 3206
1 TraesCS1A01G194100 chr1D 279102530 279106191 3661 True 1545.033333 4305 90.348333 1 3207 3 chr1D.!!$R1 3206
2 TraesCS1A01G194100 chr1B 378836775 378839261 2486 True 4058.000000 4058 96.021000 700 3207 1 chr1B.!!$R2 2507

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
651 1176 0.107456 AGGCTGCGTTCATAGGGATG 59.893 55.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2531 3063 1.203063 ACCCCTTTCTTTCAAGGAGGC 60.203 52.381 0.77 0.0 45.79 4.7 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
30 31 1.471153 GGCGCTAGTCCTTAAGGTCAC 60.471 57.143 21.04 12.84 36.34 3.67
32 33 1.798079 CGCTAGTCCTTAAGGTCACGC 60.798 57.143 21.04 18.34 36.34 5.34
33 34 1.203994 GCTAGTCCTTAAGGTCACGCA 59.796 52.381 21.04 6.07 36.34 5.24
36 37 1.145803 GTCCTTAAGGTCACGCACAC 58.854 55.000 21.04 5.72 36.34 3.82
37 38 0.753867 TCCTTAAGGTCACGCACACA 59.246 50.000 21.04 0.00 36.34 3.72
49 51 0.670546 CGCACACAAGACTTCCCGAT 60.671 55.000 0.00 0.00 0.00 4.18
56 58 3.753272 CACAAGACTTCCCGATTGTCATT 59.247 43.478 0.00 0.00 33.76 2.57
57 59 3.753272 ACAAGACTTCCCGATTGTCATTG 59.247 43.478 0.00 0.00 30.25 2.82
60 62 3.007940 AGACTTCCCGATTGTCATTGACA 59.992 43.478 15.41 15.41 41.09 3.58
78 80 1.697982 ACAAAGGTTAGGTCGGCTTCT 59.302 47.619 0.00 0.00 0.00 2.85
96 98 1.729470 CTGTAGGAGAGCGGCGACAT 61.729 60.000 12.98 0.00 0.00 3.06
98 100 2.543802 TAGGAGAGCGGCGACATCG 61.544 63.158 12.98 0.00 43.27 3.84
121 123 1.215647 GTCGGTGGCTCGTTCTGAT 59.784 57.895 1.40 0.00 0.00 2.90
123 125 1.215382 CGGTGGCTCGTTCTGATGA 59.785 57.895 0.00 0.00 0.00 2.92
124 126 0.179100 CGGTGGCTCGTTCTGATGAT 60.179 55.000 0.00 0.00 0.00 2.45
126 128 1.134699 GGTGGCTCGTTCTGATGATGA 60.135 52.381 0.00 0.00 0.00 2.92
129 131 3.986572 GTGGCTCGTTCTGATGATGATAG 59.013 47.826 0.00 0.00 0.00 2.08
130 132 2.992543 GGCTCGTTCTGATGATGATAGC 59.007 50.000 0.00 0.00 0.00 2.97
134 136 2.983136 CGTTCTGATGATGATAGCGGTC 59.017 50.000 0.00 0.00 0.00 4.79
140 142 4.067192 TGATGATGATAGCGGTCATTTGG 58.933 43.478 8.05 0.00 38.88 3.28
145 147 2.290641 TGATAGCGGTCATTTGGTGGTT 60.291 45.455 0.00 0.00 0.00 3.67
146 148 1.816074 TAGCGGTCATTTGGTGGTTC 58.184 50.000 0.00 0.00 0.00 3.62
150 152 1.806542 CGGTCATTTGGTGGTTCAGAG 59.193 52.381 0.00 0.00 0.00 3.35
152 154 2.814336 GGTCATTTGGTGGTTCAGAGAC 59.186 50.000 0.00 0.00 0.00 3.36
153 155 2.814336 GTCATTTGGTGGTTCAGAGACC 59.186 50.000 0.00 0.00 40.23 3.85
155 157 3.138283 TCATTTGGTGGTTCAGAGACCTT 59.862 43.478 0.00 0.00 40.47 3.50
164 166 5.582665 GTGGTTCAGAGACCTTGATGTAATC 59.417 44.000 0.00 0.00 41.30 1.75
166 168 5.814705 GGTTCAGAGACCTTGATGTAATCTG 59.185 44.000 0.00 0.00 39.35 2.90
200 202 9.862371 TTTAAGATGCTTTGTACTTTTTGTGAA 57.138 25.926 0.00 0.00 0.00 3.18
201 203 7.755582 AAGATGCTTTGTACTTTTTGTGAAC 57.244 32.000 0.00 0.00 0.00 3.18
203 205 7.547227 AGATGCTTTGTACTTTTTGTGAACTT 58.453 30.769 0.00 0.00 0.00 2.66
204 206 8.034804 AGATGCTTTGTACTTTTTGTGAACTTT 58.965 29.630 0.00 0.00 0.00 2.66
205 207 9.296400 GATGCTTTGTACTTTTTGTGAACTTTA 57.704 29.630 0.00 0.00 0.00 1.85
206 208 9.816354 ATGCTTTGTACTTTTTGTGAACTTTAT 57.184 25.926 0.00 0.00 0.00 1.40
284 286 2.708216 TTCCGCTCATGCTATTTGGA 57.292 45.000 0.00 0.00 36.97 3.53
288 290 3.378112 TCCGCTCATGCTATTTGGAAAAG 59.622 43.478 0.00 0.00 36.97 2.27
289 291 3.129287 CCGCTCATGCTATTTGGAAAAGT 59.871 43.478 0.00 0.00 36.97 2.66
290 292 4.100529 CGCTCATGCTATTTGGAAAAGTG 58.899 43.478 0.00 0.00 36.97 3.16
291 293 3.861689 GCTCATGCTATTTGGAAAAGTGC 59.138 43.478 0.00 0.00 36.03 4.40
292 294 4.095410 TCATGCTATTTGGAAAAGTGCG 57.905 40.909 0.00 0.00 0.00 5.34
293 295 3.755905 TCATGCTATTTGGAAAAGTGCGA 59.244 39.130 0.00 0.00 0.00 5.10
294 296 3.552604 TGCTATTTGGAAAAGTGCGAC 57.447 42.857 0.00 0.00 0.00 5.19
298 302 4.742659 GCTATTTGGAAAAGTGCGACAAAA 59.257 37.500 0.00 0.00 35.06 2.44
315 319 7.094592 TGCGACAAAAGTCATGTATCCAAATTA 60.095 33.333 0.00 0.00 0.00 1.40
335 339 9.184523 CAAATTAAGGTATCATTTGGACACCTA 57.815 33.333 0.00 0.00 38.67 3.08
336 340 9.762381 AAATTAAGGTATCATTTGGACACCTAA 57.238 29.630 0.00 0.00 38.67 2.69
337 341 9.762381 AATTAAGGTATCATTTGGACACCTAAA 57.238 29.630 0.00 0.00 38.67 1.85
377 381 9.605275 TGACCTAGAAAGAATATCATGTTCAAG 57.395 33.333 0.00 0.00 0.00 3.02
378 382 9.606631 GACCTAGAAAGAATATCATGTTCAAGT 57.393 33.333 0.00 0.00 0.00 3.16
383 387 9.965902 AGAAAGAATATCATGTTCAAGTAAGGT 57.034 29.630 0.00 0.00 0.00 3.50
385 389 9.739276 AAAGAATATCATGTTCAAGTAAGGTCA 57.261 29.630 0.00 0.00 0.00 4.02
386 390 9.911788 AAGAATATCATGTTCAAGTAAGGTCAT 57.088 29.630 0.00 0.00 0.00 3.06
387 391 9.334947 AGAATATCATGTTCAAGTAAGGTCATG 57.665 33.333 0.00 0.00 35.47 3.07
388 392 9.330063 GAATATCATGTTCAAGTAAGGTCATGA 57.670 33.333 7.84 7.84 43.21 3.07
389 393 6.992063 ATCATGTTCAAGTAAGGTCATGAC 57.008 37.500 17.91 17.91 42.35 3.06
390 394 5.863965 TCATGTTCAAGTAAGGTCATGACA 58.136 37.500 26.47 4.11 37.38 3.58
391 395 6.475504 TCATGTTCAAGTAAGGTCATGACAT 58.524 36.000 26.47 18.11 37.38 3.06
392 396 7.619965 TCATGTTCAAGTAAGGTCATGACATA 58.380 34.615 26.47 15.88 37.38 2.29
393 397 7.765819 TCATGTTCAAGTAAGGTCATGACATAG 59.234 37.037 26.47 8.90 37.38 2.23
394 398 7.239763 TGTTCAAGTAAGGTCATGACATAGA 57.760 36.000 26.47 9.39 0.00 1.98
395 399 7.676004 TGTTCAAGTAAGGTCATGACATAGAA 58.324 34.615 26.47 15.45 0.00 2.10
396 400 8.154203 TGTTCAAGTAAGGTCATGACATAGAAA 58.846 33.333 26.47 7.25 0.00 2.52
440 444 9.798994 CTAGATAAAATGAGTAACTTACCACGT 57.201 33.333 0.00 0.00 0.00 4.49
445 449 8.436046 AAAATGAGTAACTTACCACGTTAACA 57.564 30.769 6.39 0.00 0.00 2.41
446 450 8.436046 AAATGAGTAACTTACCACGTTAACAA 57.564 30.769 6.39 0.00 0.00 2.83
450 454 7.927629 TGAGTAACTTACCACGTTAACAATTCT 59.072 33.333 6.39 0.00 0.00 2.40
451 455 8.302965 AGTAACTTACCACGTTAACAATTCTC 57.697 34.615 6.39 0.00 0.00 2.87
452 456 6.549912 AACTTACCACGTTAACAATTCTCC 57.450 37.500 6.39 0.00 0.00 3.71
455 459 4.094830 ACCACGTTAACAATTCTCCCTT 57.905 40.909 6.39 0.00 0.00 3.95
456 460 3.818773 ACCACGTTAACAATTCTCCCTTG 59.181 43.478 6.39 0.00 0.00 3.61
458 462 4.320202 CCACGTTAACAATTCTCCCTTGTG 60.320 45.833 6.39 1.15 36.95 3.33
459 463 4.274950 CACGTTAACAATTCTCCCTTGTGT 59.725 41.667 6.39 0.00 36.95 3.72
460 464 5.467399 CACGTTAACAATTCTCCCTTGTGTA 59.533 40.000 6.39 0.00 36.95 2.90
461 465 5.699458 ACGTTAACAATTCTCCCTTGTGTAG 59.301 40.000 6.39 0.00 36.95 2.74
462 466 5.390567 CGTTAACAATTCTCCCTTGTGTAGC 60.391 44.000 6.39 0.00 36.95 3.58
464 468 5.499004 AACAATTCTCCCTTGTGTAGCTA 57.501 39.130 0.00 0.00 36.95 3.32
465 469 5.700402 ACAATTCTCCCTTGTGTAGCTAT 57.300 39.130 0.00 0.00 35.57 2.97
466 470 5.675538 ACAATTCTCCCTTGTGTAGCTATC 58.324 41.667 0.00 0.00 35.57 2.08
467 471 5.189736 ACAATTCTCCCTTGTGTAGCTATCA 59.810 40.000 0.00 0.00 35.57 2.15
468 472 5.957771 ATTCTCCCTTGTGTAGCTATCAA 57.042 39.130 0.00 5.51 0.00 2.57
469 473 4.737855 TCTCCCTTGTGTAGCTATCAAC 57.262 45.455 0.00 0.00 0.00 3.18
470 474 4.093743 TCTCCCTTGTGTAGCTATCAACA 58.906 43.478 0.00 0.00 0.00 3.33
472 476 4.575885 TCCCTTGTGTAGCTATCAACAAC 58.424 43.478 12.83 0.00 0.00 3.32
473 477 4.286032 TCCCTTGTGTAGCTATCAACAACT 59.714 41.667 12.83 0.00 0.00 3.16
474 478 5.003804 CCCTTGTGTAGCTATCAACAACTT 58.996 41.667 12.83 0.00 0.00 2.66
476 480 5.106555 CCTTGTGTAGCTATCAACAACTTGG 60.107 44.000 12.83 10.31 0.00 3.61
477 481 4.968259 TGTGTAGCTATCAACAACTTGGT 58.032 39.130 0.00 0.00 0.00 3.67
478 482 4.754618 TGTGTAGCTATCAACAACTTGGTG 59.245 41.667 0.00 0.00 36.12 4.17
479 483 4.755123 GTGTAGCTATCAACAACTTGGTGT 59.245 41.667 6.70 0.00 36.24 4.16
480 484 4.754618 TGTAGCTATCAACAACTTGGTGTG 59.245 41.667 6.70 0.86 36.24 3.82
482 486 4.460263 AGCTATCAACAACTTGGTGTGAA 58.540 39.130 6.70 0.00 36.24 3.18
483 487 5.072741 AGCTATCAACAACTTGGTGTGAAT 58.927 37.500 6.70 0.00 36.24 2.57
484 488 5.536161 AGCTATCAACAACTTGGTGTGAATT 59.464 36.000 6.70 0.00 36.24 2.17
485 489 5.630680 GCTATCAACAACTTGGTGTGAATTG 59.369 40.000 6.70 0.00 36.24 2.32
492 1006 6.099341 ACAACTTGGTGTGAATTGAAGTTTC 58.901 36.000 0.00 0.00 35.24 2.78
493 1007 5.913137 ACTTGGTGTGAATTGAAGTTTCA 57.087 34.783 0.00 0.00 34.92 2.69
547 1061 4.634184 TGCTCGTTAAGTGAGAGGATAC 57.366 45.455 8.48 0.00 35.43 2.24
551 1065 5.633830 TCGTTAAGTGAGAGGATACGTTT 57.366 39.130 0.00 0.00 46.39 3.60
553 1067 5.413833 TCGTTAAGTGAGAGGATACGTTTCT 59.586 40.000 5.97 0.00 46.39 2.52
576 1090 3.332034 TCGACTACGAAGATGTCTGTGA 58.668 45.455 0.00 0.00 45.74 3.58
584 1098 3.545475 CGAAGATGTCTGTGATGACTTCG 59.455 47.826 0.00 0.00 42.37 3.79
585 1099 2.886081 AGATGTCTGTGATGACTTCGC 58.114 47.619 0.00 0.00 42.37 4.70
587 1101 0.678950 TGTCTGTGATGACTTCGCCA 59.321 50.000 0.00 0.00 37.79 5.69
598 1112 4.424061 TGACTTCGCCAATCTCAAAATG 57.576 40.909 0.00 0.00 0.00 2.32
605 1119 4.022935 TCGCCAATCTCAAAATGATATGCC 60.023 41.667 0.00 0.00 0.00 4.40
606 1120 4.232221 GCCAATCTCAAAATGATATGCCG 58.768 43.478 0.00 0.00 0.00 5.69
609 1123 3.213206 TCTCAAAATGATATGCCGGCT 57.787 42.857 29.70 15.76 0.00 5.52
619 1133 0.395724 TATGCCGGCTCAGTCTCTCA 60.396 55.000 29.70 2.45 0.00 3.27
620 1134 1.260538 ATGCCGGCTCAGTCTCTCAA 61.261 55.000 29.70 1.81 0.00 3.02
622 1136 0.107945 GCCGGCTCAGTCTCTCAAAT 60.108 55.000 22.15 0.00 0.00 2.32
623 1137 1.649664 CCGGCTCAGTCTCTCAAATG 58.350 55.000 0.00 0.00 0.00 2.32
635 1149 3.753272 TCTCTCAAATGTGCTTACAAGGC 59.247 43.478 0.00 0.00 0.00 4.35
646 1171 2.030946 GCTTACAAGGCTGCGTTCATAG 59.969 50.000 4.36 3.99 0.00 2.23
647 1172 2.309528 TACAAGGCTGCGTTCATAGG 57.690 50.000 4.36 0.00 0.00 2.57
648 1173 0.392998 ACAAGGCTGCGTTCATAGGG 60.393 55.000 4.36 0.00 0.00 3.53
651 1176 0.107456 AGGCTGCGTTCATAGGGATG 59.893 55.000 0.00 0.00 0.00 3.51
653 1178 1.506493 GCTGCGTTCATAGGGATGAG 58.494 55.000 0.00 0.00 43.03 2.90
659 1184 4.830600 TGCGTTCATAGGGATGAGTGTATA 59.169 41.667 0.00 0.00 43.03 1.47
661 1186 6.661805 TGCGTTCATAGGGATGAGTGTATATA 59.338 38.462 0.00 0.00 43.03 0.86
668 1193 6.452494 AGGGATGAGTGTATATACGTATGC 57.548 41.667 18.37 8.67 0.00 3.14
683 1208 2.002586 GTATGCATGAGTGTCTGCGTT 58.997 47.619 10.16 0.00 41.32 4.84
696 1221 2.627945 TCTGCGTTCAGACTGTGTTTT 58.372 42.857 1.59 0.00 43.95 2.43
697 1222 2.351418 TCTGCGTTCAGACTGTGTTTTG 59.649 45.455 1.59 0.00 43.95 2.44
894 1425 1.758906 GGAGAGGAGACGAAGGGGG 60.759 68.421 0.00 0.00 0.00 5.40
958 1489 6.374333 TGTTTATAAAAGAGAGGGCATCACAC 59.626 38.462 0.58 0.00 0.00 3.82
1644 2176 4.071875 AACCACGGCGGCGTCATA 62.072 61.111 35.40 0.00 39.03 2.15
1933 2465 4.090588 GGGATGTTCGTGCCGGGA 62.091 66.667 2.18 0.00 0.00 5.14
2382 2914 2.838637 AGAACAAAAGTGGGGGAACA 57.161 45.000 0.00 0.00 0.00 3.18
2403 2935 4.696479 AGAAGCCAAGTTCTGAAGAAGA 57.304 40.909 0.00 0.00 35.37 2.87
2427 2959 8.408601 AGATATATTTGTTCTGGATGTGCAAAC 58.591 33.333 0.00 0.00 32.85 2.93
2467 2999 1.901159 CTGGATGAATGGCAACCCAAA 59.099 47.619 0.00 0.00 46.14 3.28
2468 3000 2.302445 CTGGATGAATGGCAACCCAAAA 59.698 45.455 0.00 0.00 46.14 2.44
2469 3001 2.911636 TGGATGAATGGCAACCCAAAAT 59.088 40.909 0.00 0.00 46.14 1.82
2482 3014 5.335661 GCAACCCAAAATCTTAGTGGTACTG 60.336 44.000 0.00 0.00 0.00 2.74
2483 3015 4.332828 ACCCAAAATCTTAGTGGTACTGC 58.667 43.478 0.00 0.00 0.00 4.40
2484 3016 3.374058 CCCAAAATCTTAGTGGTACTGCG 59.626 47.826 0.00 0.00 0.00 5.18
2515 3047 2.639065 TGTTTCCAATGATACCGGAGC 58.361 47.619 9.46 0.00 0.00 4.70
2518 3050 1.048601 TCCAATGATACCGGAGCTCC 58.951 55.000 23.79 23.79 0.00 4.70
2531 3063 3.927552 GGAGCTCCGAAAGTTTTATCG 57.072 47.619 19.06 0.00 38.74 2.92
2538 3070 3.007635 CCGAAAGTTTTATCGCCTCCTT 58.992 45.455 0.00 0.00 37.73 3.36
2552 3084 2.519013 CCTCCTTGAAAGAAAGGGGTG 58.481 52.381 2.34 0.00 45.15 4.61
2557 3089 2.978156 TGAAAGAAAGGGGTGATGCT 57.022 45.000 0.00 0.00 0.00 3.79
2616 3148 1.069765 AGTTCTGTCTGTGGCACCG 59.930 57.895 16.26 9.23 0.00 4.94
2628 3160 0.104120 TGGCACCGGTTCTATCATCG 59.896 55.000 2.97 0.00 0.00 3.84
2652 3184 8.067784 TCGAAAACTGAATTTTACATCTGTGAC 58.932 33.333 0.00 0.00 40.73 3.67
2716 3248 6.808321 ACCCTATGCTTGACTATCTGTTTA 57.192 37.500 0.00 0.00 0.00 2.01
2726 3258 8.391106 GCTTGACTATCTGTTTATGAAATTCGT 58.609 33.333 0.00 0.00 0.00 3.85
2747 3279 7.223260 TCGTTTTACTGGAGAAACTCTCATA 57.777 36.000 6.05 0.00 45.12 2.15
2748 3280 7.663827 TCGTTTTACTGGAGAAACTCTCATAA 58.336 34.615 6.05 0.00 45.12 1.90
2791 3323 2.821378 TGTGAACATGGATTCCTGCTTG 59.179 45.455 3.95 0.00 0.00 4.01
2792 3324 1.820519 TGAACATGGATTCCTGCTTGC 59.179 47.619 3.95 0.00 0.00 4.01
2930 3462 3.386768 TTACTGGACTCTGTGCAACTC 57.613 47.619 0.00 0.00 38.04 3.01
3038 3570 4.952335 AGGGAAGAATTTGGCTGTTATCTG 59.048 41.667 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.228567 GGACTAGCGCCCTGGAGC 62.229 72.222 2.29 3.47 41.21 4.70
6 7 0.105039 CTTAAGGACTAGCGCCCTGG 59.895 60.000 2.29 0.00 32.12 4.45
24 25 0.178068 AAGTCTTGTGTGCGTGACCT 59.822 50.000 0.00 0.00 0.00 3.85
30 31 0.670546 ATCGGGAAGTCTTGTGTGCG 60.671 55.000 0.00 0.00 0.00 5.34
32 33 2.480419 GACAATCGGGAAGTCTTGTGTG 59.520 50.000 0.00 0.00 32.28 3.82
33 34 2.104111 TGACAATCGGGAAGTCTTGTGT 59.896 45.455 0.00 0.00 32.28 3.72
36 37 4.002982 TCAATGACAATCGGGAAGTCTTG 58.997 43.478 0.00 0.00 33.56 3.02
37 38 4.003648 GTCAATGACAATCGGGAAGTCTT 58.996 43.478 8.74 0.00 33.56 3.01
56 58 1.053424 AGCCGACCTAACCTTTGTCA 58.947 50.000 0.00 0.00 0.00 3.58
57 59 2.074576 GAAGCCGACCTAACCTTTGTC 58.925 52.381 0.00 0.00 0.00 3.18
60 62 1.697982 ACAGAAGCCGACCTAACCTTT 59.302 47.619 0.00 0.00 0.00 3.11
66 68 1.562942 TCTCCTACAGAAGCCGACCTA 59.437 52.381 0.00 0.00 0.00 3.08
70 72 1.377366 CGCTCTCCTACAGAAGCCGA 61.377 60.000 0.00 0.00 0.00 5.54
78 80 1.725557 GATGTCGCCGCTCTCCTACA 61.726 60.000 0.00 0.00 0.00 2.74
101 103 4.719369 AGAACGAGCCACCGACGC 62.719 66.667 0.00 0.00 0.00 5.19
102 104 2.543687 ATCAGAACGAGCCACCGACG 62.544 60.000 0.00 0.00 0.00 5.12
105 107 0.179100 ATCATCAGAACGAGCCACCG 60.179 55.000 0.00 0.00 0.00 4.94
106 108 1.134699 TCATCATCAGAACGAGCCACC 60.135 52.381 0.00 0.00 0.00 4.61
121 123 3.205338 CACCAAATGACCGCTATCATCA 58.795 45.455 0.52 0.00 38.40 3.07
123 125 2.092429 ACCACCAAATGACCGCTATCAT 60.092 45.455 0.00 0.00 41.20 2.45
124 126 1.280710 ACCACCAAATGACCGCTATCA 59.719 47.619 0.00 0.00 0.00 2.15
126 128 2.290641 TGAACCACCAAATGACCGCTAT 60.291 45.455 0.00 0.00 0.00 2.97
129 131 0.240945 CTGAACCACCAAATGACCGC 59.759 55.000 0.00 0.00 0.00 5.68
130 132 1.806542 CTCTGAACCACCAAATGACCG 59.193 52.381 0.00 0.00 0.00 4.79
134 136 3.146104 AGGTCTCTGAACCACCAAATG 57.854 47.619 10.30 0.00 42.12 2.32
140 142 3.409026 ACATCAAGGTCTCTGAACCAC 57.591 47.619 10.30 0.00 42.12 4.16
145 147 7.904558 ATACAGATTACATCAAGGTCTCTGA 57.095 36.000 11.78 0.00 35.69 3.27
173 175 9.296400 TCACAAAAAGTACAAAGCATCTTAAAC 57.704 29.630 0.00 0.00 0.00 2.01
234 236 4.985538 TCAGTATGGCTTTTCTGGACTTT 58.014 39.130 0.00 0.00 36.16 2.66
238 240 5.441718 AATCTCAGTATGGCTTTTCTGGA 57.558 39.130 0.00 0.00 36.16 3.86
239 241 7.814264 AATAATCTCAGTATGGCTTTTCTGG 57.186 36.000 0.00 0.00 36.16 3.86
244 246 7.682021 GCGGAAAAATAATCTCAGTATGGCTTT 60.682 37.037 0.00 0.00 36.16 3.51
249 251 7.482654 TGAGCGGAAAAATAATCTCAGTATG 57.517 36.000 0.00 0.00 37.54 2.39
251 253 6.017934 GCATGAGCGGAAAAATAATCTCAGTA 60.018 38.462 0.00 0.00 34.57 2.74
252 254 5.220931 GCATGAGCGGAAAAATAATCTCAGT 60.221 40.000 0.00 0.00 34.57 3.41
361 365 9.334947 CATGACCTTACTTGAACATGATATTCT 57.665 33.333 0.00 0.00 37.77 2.40
362 366 9.330063 TCATGACCTTACTTGAACATGATATTC 57.670 33.333 0.00 0.00 38.99 1.75
363 367 9.113838 GTCATGACCTTACTTGAACATGATATT 57.886 33.333 15.31 0.00 43.28 1.28
364 368 8.267183 TGTCATGACCTTACTTGAACATGATAT 58.733 33.333 22.85 0.00 43.28 1.63
365 369 7.619965 TGTCATGACCTTACTTGAACATGATA 58.380 34.615 22.85 0.00 43.28 2.15
366 370 6.475504 TGTCATGACCTTACTTGAACATGAT 58.524 36.000 22.85 0.00 43.28 2.45
367 371 5.863965 TGTCATGACCTTACTTGAACATGA 58.136 37.500 22.85 0.00 40.69 3.07
368 372 6.748333 ATGTCATGACCTTACTTGAACATG 57.252 37.500 22.85 0.00 37.18 3.21
369 373 7.851228 TCTATGTCATGACCTTACTTGAACAT 58.149 34.615 22.85 8.23 0.00 2.71
370 374 7.239763 TCTATGTCATGACCTTACTTGAACA 57.760 36.000 22.85 0.55 0.00 3.18
371 375 8.547967 TTTCTATGTCATGACCTTACTTGAAC 57.452 34.615 22.85 0.00 0.00 3.18
372 376 8.593679 TCTTTCTATGTCATGACCTTACTTGAA 58.406 33.333 22.85 13.38 0.00 2.69
373 377 8.134202 TCTTTCTATGTCATGACCTTACTTGA 57.866 34.615 22.85 10.88 0.00 3.02
374 378 8.777865 TTCTTTCTATGTCATGACCTTACTTG 57.222 34.615 22.85 8.85 0.00 3.16
430 434 4.999311 GGGAGAATTGTTAACGTGGTAAGT 59.001 41.667 0.26 0.00 0.00 2.24
431 435 5.243207 AGGGAGAATTGTTAACGTGGTAAG 58.757 41.667 0.26 0.00 0.00 2.34
434 438 3.782656 AGGGAGAATTGTTAACGTGGT 57.217 42.857 0.26 0.00 0.00 4.16
435 439 3.818773 ACAAGGGAGAATTGTTAACGTGG 59.181 43.478 0.26 0.00 37.61 4.94
436 440 4.274950 ACACAAGGGAGAATTGTTAACGTG 59.725 41.667 0.26 1.22 38.80 4.49
437 441 4.457466 ACACAAGGGAGAATTGTTAACGT 58.543 39.130 0.26 0.00 38.80 3.99
438 442 5.390567 GCTACACAAGGGAGAATTGTTAACG 60.391 44.000 0.26 0.00 38.80 3.18
440 444 5.876357 AGCTACACAAGGGAGAATTGTTAA 58.124 37.500 0.00 0.00 38.80 2.01
441 445 5.499004 AGCTACACAAGGGAGAATTGTTA 57.501 39.130 0.00 0.00 38.80 2.41
444 448 5.674525 TGATAGCTACACAAGGGAGAATTG 58.325 41.667 0.00 0.00 0.00 2.32
445 449 5.957771 TGATAGCTACACAAGGGAGAATT 57.042 39.130 0.00 0.00 0.00 2.17
446 450 5.189736 TGTTGATAGCTACACAAGGGAGAAT 59.810 40.000 13.26 0.00 0.00 2.40
450 454 4.286032 AGTTGTTGATAGCTACACAAGGGA 59.714 41.667 12.93 3.26 29.63 4.20
451 455 4.579869 AGTTGTTGATAGCTACACAAGGG 58.420 43.478 12.93 0.00 29.63 3.95
452 456 5.106555 CCAAGTTGTTGATAGCTACACAAGG 60.107 44.000 12.93 8.85 35.46 3.61
455 459 4.754618 CACCAAGTTGTTGATAGCTACACA 59.245 41.667 0.00 0.00 35.46 3.72
456 460 4.755123 ACACCAAGTTGTTGATAGCTACAC 59.245 41.667 7.48 0.00 35.46 2.90
458 462 4.994852 TCACACCAAGTTGTTGATAGCTAC 59.005 41.667 7.48 0.00 35.46 3.58
459 463 5.222079 TCACACCAAGTTGTTGATAGCTA 57.778 39.130 7.48 0.00 35.46 3.32
460 464 4.085357 TCACACCAAGTTGTTGATAGCT 57.915 40.909 7.48 0.00 35.46 3.32
461 465 4.829064 TTCACACCAAGTTGTTGATAGC 57.171 40.909 7.48 0.00 35.46 2.97
462 466 6.969366 TCAATTCACACCAAGTTGTTGATAG 58.031 36.000 7.48 0.00 35.46 2.08
464 468 5.850557 TCAATTCACACCAAGTTGTTGAT 57.149 34.783 7.48 0.00 35.46 2.57
465 469 5.184864 ACTTCAATTCACACCAAGTTGTTGA 59.815 36.000 7.48 3.31 35.46 3.18
466 470 5.410067 ACTTCAATTCACACCAAGTTGTTG 58.590 37.500 1.45 0.00 0.00 3.33
467 471 5.659440 ACTTCAATTCACACCAAGTTGTT 57.341 34.783 1.45 0.00 0.00 2.83
468 472 5.659440 AACTTCAATTCACACCAAGTTGT 57.341 34.783 1.45 0.00 36.24 3.32
469 473 6.098679 TGAAACTTCAATTCACACCAAGTTG 58.901 36.000 0.00 0.00 37.37 3.16
470 474 6.279513 TGAAACTTCAATTCACACCAAGTT 57.720 33.333 0.00 0.00 38.62 2.66
472 476 7.775397 AAATGAAACTTCAATTCACACCAAG 57.225 32.000 0.00 0.00 41.13 3.61
473 477 8.558973 AAAAATGAAACTTCAATTCACACCAA 57.441 26.923 0.00 0.00 41.13 3.67
474 478 8.040132 AGAAAAATGAAACTTCAATTCACACCA 58.960 29.630 13.71 0.00 41.13 4.17
476 480 8.330302 CCAGAAAAATGAAACTTCAATTCACAC 58.670 33.333 13.71 0.00 41.13 3.82
477 481 8.256605 TCCAGAAAAATGAAACTTCAATTCACA 58.743 29.630 13.71 0.00 41.13 3.58
478 482 8.647143 TCCAGAAAAATGAAACTTCAATTCAC 57.353 30.769 13.71 4.74 41.13 3.18
479 483 9.835389 AATCCAGAAAAATGAAACTTCAATTCA 57.165 25.926 13.71 0.00 41.13 2.57
547 1061 3.179010 TCTTCGTAGTCGACAGAAACG 57.821 47.619 19.50 19.74 46.03 3.60
551 1065 3.371285 CAGACATCTTCGTAGTCGACAGA 59.629 47.826 19.50 11.63 46.03 3.41
553 1067 3.072211 ACAGACATCTTCGTAGTCGACA 58.928 45.455 19.50 0.48 46.03 4.35
568 1082 0.678950 TGGCGAAGTCATCACAGACA 59.321 50.000 0.00 0.00 36.97 3.41
584 1098 4.232221 CGGCATATCATTTTGAGATTGGC 58.768 43.478 0.00 0.00 0.00 4.52
585 1099 4.801891 CCGGCATATCATTTTGAGATTGG 58.198 43.478 0.00 0.00 0.00 3.16
587 1101 4.147321 AGCCGGCATATCATTTTGAGATT 58.853 39.130 31.54 0.00 0.00 2.40
598 1112 0.965439 AGAGACTGAGCCGGCATATC 59.035 55.000 31.54 18.63 0.00 1.63
605 1119 1.998315 CACATTTGAGAGACTGAGCCG 59.002 52.381 0.00 0.00 0.00 5.52
606 1120 1.736681 GCACATTTGAGAGACTGAGCC 59.263 52.381 0.00 0.00 0.00 4.70
609 1123 5.213891 TGTAAGCACATTTGAGAGACTGA 57.786 39.130 0.00 0.00 0.00 3.41
619 1133 1.068333 CGCAGCCTTGTAAGCACATTT 60.068 47.619 0.00 0.00 33.76 2.32
620 1134 0.523072 CGCAGCCTTGTAAGCACATT 59.477 50.000 0.00 0.00 33.76 2.71
622 1136 0.817634 AACGCAGCCTTGTAAGCACA 60.818 50.000 0.00 0.00 0.00 4.57
623 1137 0.110192 GAACGCAGCCTTGTAAGCAC 60.110 55.000 0.00 0.00 0.00 4.40
635 1149 2.159043 ACACTCATCCCTATGAACGCAG 60.159 50.000 0.00 0.00 41.57 5.18
646 1171 6.203808 TGCATACGTATATACACTCATCCC 57.796 41.667 7.96 0.00 0.00 3.85
647 1172 7.480810 TCATGCATACGTATATACACTCATCC 58.519 38.462 7.96 0.00 0.00 3.51
648 1173 8.184848 ACTCATGCATACGTATATACACTCATC 58.815 37.037 7.96 0.00 0.00 2.92
651 1176 7.306213 ACACTCATGCATACGTATATACACTC 58.694 38.462 7.96 0.00 0.00 3.51
653 1178 7.271438 CAGACACTCATGCATACGTATATACAC 59.729 40.741 7.96 0.00 0.00 2.90
659 1184 3.384668 GCAGACACTCATGCATACGTAT 58.615 45.455 1.14 1.14 42.11 3.06
661 1186 1.645034 GCAGACACTCATGCATACGT 58.355 50.000 0.00 0.00 42.11 3.57
668 1193 2.070262 TCTGAACGCAGACACTCATG 57.930 50.000 0.00 0.00 45.88 3.07
711 1237 3.725490 GACCTGTTAGTCCTTTTCACGT 58.275 45.455 0.00 0.00 0.00 4.49
894 1425 5.577554 GGAGTAATTCTCAGGTCGAAAGAAC 59.422 44.000 0.00 0.00 43.03 3.01
958 1489 1.149986 GGATAAAGGAAGGGGAGGGG 58.850 60.000 0.00 0.00 0.00 4.79
1635 2167 3.302221 CGTAAACCTTGAATATGACGCCG 60.302 47.826 0.00 0.00 0.00 6.46
1644 2176 2.331194 CCGACGACGTAAACCTTGAAT 58.669 47.619 0.00 0.00 37.88 2.57
1933 2465 2.494471 TGTCAATGACGAGATACCGGTT 59.506 45.455 15.04 0.00 34.95 4.44
2382 2914 4.696479 TCTTCTTCAGAACTTGGCTTCT 57.304 40.909 0.00 0.00 0.00 2.85
2403 2935 7.342799 AGGTTTGCACATCCAGAACAAATATAT 59.657 33.333 0.00 0.00 33.28 0.86
2427 2959 5.997746 TCCAGTACTCATCAAGAACAAAAGG 59.002 40.000 0.00 0.00 0.00 3.11
2467 2999 5.069119 TCATCATCGCAGTACCACTAAGATT 59.931 40.000 0.00 0.00 0.00 2.40
2468 3000 4.584743 TCATCATCGCAGTACCACTAAGAT 59.415 41.667 0.00 0.00 0.00 2.40
2469 3001 3.951680 TCATCATCGCAGTACCACTAAGA 59.048 43.478 0.00 0.00 0.00 2.10
2482 3014 6.671190 TCATTGGAAACATATTCATCATCGC 58.329 36.000 0.00 0.00 42.32 4.58
2483 3015 9.764870 GTATCATTGGAAACATATTCATCATCG 57.235 33.333 0.00 0.00 42.32 3.84
2515 3047 2.608090 GGAGGCGATAAAACTTTCGGAG 59.392 50.000 0.00 0.00 35.93 4.63
2518 3050 3.682858 TCAAGGAGGCGATAAAACTTTCG 59.317 43.478 0.00 0.00 38.37 3.46
2520 3052 5.768164 TCTTTCAAGGAGGCGATAAAACTTT 59.232 36.000 0.00 0.00 0.00 2.66
2521 3053 5.313712 TCTTTCAAGGAGGCGATAAAACTT 58.686 37.500 0.00 0.00 0.00 2.66
2531 3063 1.203063 ACCCCTTTCTTTCAAGGAGGC 60.203 52.381 0.77 0.00 45.79 4.70
2538 3070 2.978156 AGCATCACCCCTTTCTTTCA 57.022 45.000 0.00 0.00 0.00 2.69
2552 3084 7.545362 TGCTAAAAGTTCAGAGAATAGCATC 57.455 36.000 8.08 0.00 39.29 3.91
2585 3117 5.111989 CAGACAGAACTGACTCAAGTTTGA 58.888 41.667 8.87 0.00 40.48 2.69
2600 3132 1.978455 AACCGGTGCCACAGACAGAA 61.978 55.000 8.52 0.00 0.00 3.02
2628 3160 8.134895 TGGTCACAGATGTAAAATTCAGTTTTC 58.865 33.333 0.00 0.00 40.40 2.29
2716 3248 8.166422 AGTTTCTCCAGTAAAACGAATTTCAT 57.834 30.769 0.00 0.00 39.72 2.57
2724 3256 7.412020 GCTTATGAGAGTTTCTCCAGTAAAACG 60.412 40.741 3.81 0.00 42.73 3.60
2726 3258 7.387948 GTGCTTATGAGAGTTTCTCCAGTAAAA 59.612 37.037 3.81 0.00 42.73 1.52
2767 3299 4.858850 AGCAGGAATCCATGTTCACATTA 58.141 39.130 0.61 0.00 33.61 1.90
2768 3300 3.705051 AGCAGGAATCCATGTTCACATT 58.295 40.909 0.61 0.00 33.61 2.71
2769 3301 3.377253 AGCAGGAATCCATGTTCACAT 57.623 42.857 0.61 0.00 36.96 3.21
2883 3415 3.372060 GCAAGTGCACTCAAGGTTAAAC 58.628 45.455 21.95 0.00 41.59 2.01
2930 3462 3.056821 CCATGATGCAGCCAATAATCTGG 60.057 47.826 0.00 0.00 39.71 3.86
3038 3570 7.259290 TCACCTTTTCAACTGAAACTGATAC 57.741 36.000 4.38 0.00 43.01 2.24
3058 3590 4.199310 TGCTTATGGCTATCTTGTTCACC 58.801 43.478 0.00 0.00 42.39 4.02
3113 3645 3.850122 AGAGCGGCCAGAAAATAAAAC 57.150 42.857 2.24 0.00 0.00 2.43
3124 3656 0.613260 ACATGAAGTTAGAGCGGCCA 59.387 50.000 2.24 0.00 0.00 5.36
3188 3720 3.028916 CATCAACCACGGTCCCAAA 57.971 52.632 0.00 0.00 0.00 3.28


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

AutoCloner maintained by Alex Coulton.