Multiple sequence alignment - TraesCS3B01G458000

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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 TraesCS3B01G458000 chr3B 100.000 2742 0 0 1 2742 700361405 700364146 0.000000e+00 5064.0
1 TraesCS3B01G458000 chr3B 92.179 179 10 4 561 736 583031940 583031763 1.630000e-62 250.0
2 TraesCS3B01G458000 chr3D 90.671 954 42 20 742 1664 529773623 529774560 0.000000e+00 1225.0
3 TraesCS3B01G458000 chr3D 96.591 440 10 3 2304 2742 361172514 361172079 0.000000e+00 725.0
4 TraesCS3B01G458000 chr3D 96.591 440 10 3 2304 2742 361176316 361175881 0.000000e+00 725.0
5 TraesCS3B01G458000 chr3D 86.287 474 44 8 2 456 529773008 529773479 1.900000e-136 496.0
6 TraesCS3B01G458000 chr3D 85.287 401 48 7 2343 2742 592908276 592907886 1.180000e-108 403.0
7 TraesCS3B01G458000 chr3D 96.680 241 5 1 2066 2306 361172942 361172705 5.500000e-107 398.0
8 TraesCS3B01G458000 chr3D 96.680 241 5 2 2066 2306 361176744 361176507 5.500000e-107 398.0
9 TraesCS3B01G458000 chr3D 89.078 293 20 5 1784 2065 529775880 529776171 1.210000e-93 353.0
10 TraesCS3B01G458000 chr3D 92.135 178 11 3 561 736 533955696 533955520 5.860000e-62 248.0
11 TraesCS3B01G458000 chr3D 98.551 138 1 1 2066 2203 361169142 361169006 2.730000e-60 243.0
12 TraesCS3B01G458000 chr3D 88.235 85 10 0 458 542 529773516 529773600 4.830000e-18 102.0
13 TraesCS3B01G458000 chr3A 87.871 775 34 30 943 1663 663577334 663578102 0.000000e+00 856.0
14 TraesCS3B01G458000 chr3A 83.838 396 38 13 1664 2059 663578162 663578531 1.210000e-93 353.0
15 TraesCS3B01G458000 chr3A 80.000 140 24 4 2 138 131460921 131460783 1.740000e-17 100.0
16 TraesCS3B01G458000 chr7A 96.364 440 13 3 2304 2742 287233840 287234277 0.000000e+00 721.0
17 TraesCS3B01G458000 chr7A 92.835 321 19 4 2423 2742 74925893 74925576 1.920000e-126 462.0
18 TraesCS3B01G458000 chr7A 95.745 235 8 2 2074 2306 287233414 287233648 7.170000e-101 377.0
19 TraesCS3B01G458000 chr7A 87.259 259 14 12 2066 2306 74927072 74926815 7.480000e-71 278.0
20 TraesCS3B01G458000 chr7A 91.061 179 14 2 568 744 696046315 696046137 9.810000e-60 241.0
21 TraesCS3B01G458000 chr7A 88.945 199 17 4 555 749 701211924 701212121 9.810000e-60 241.0
22 TraesCS3B01G458000 chr7A 91.667 132 4 4 2304 2432 74926771 74926644 2.810000e-40 176.0
23 TraesCS3B01G458000 chr2A 96.136 440 9 4 2304 2742 114340457 114340025 0.000000e+00 712.0
24 TraesCS3B01G458000 chr2A 96.708 243 5 2 2066 2306 114340890 114340649 4.250000e-108 401.0
25 TraesCS3B01G458000 chr4A 95.000 440 16 3 2304 2742 590355049 590354615 0.000000e+00 686.0
26 TraesCS3B01G458000 chr4A 97.685 216 3 2 2091 2306 590355455 590355242 1.200000e-98 370.0
27 TraesCS3B01G458000 chr6A 94.773 440 14 3 2304 2742 431215947 431215516 0.000000e+00 676.0
28 TraesCS3B01G458000 chr6A 93.852 244 12 2 2063 2306 431216381 431216141 5.580000e-97 364.0
29 TraesCS3B01G458000 chr7B 97.954 391 3 3 2066 2455 656532915 656532529 0.000000e+00 673.0
30 TraesCS3B01G458000 chr7B 98.288 292 5 0 2451 2742 656532296 656532005 1.880000e-141 512.0
31 TraesCS3B01G458000 chr7B 96.111 180 4 2 2066 2245 666603524 666603700 9.610000e-75 291.0
32 TraesCS3B01G458000 chr7B 88.780 205 16 5 549 750 606591276 606591076 7.580000e-61 244.0
33 TraesCS3B01G458000 chr2D 90.909 187 13 4 568 750 481596952 481596766 5.860000e-62 248.0
34 TraesCS3B01G458000 chr1A 91.573 178 11 3 560 734 590760907 590760731 2.730000e-60 243.0
35 TraesCS3B01G458000 chr5D 88.442 199 17 5 558 751 521487993 521487796 4.560000e-58 235.0
36 TraesCS3B01G458000 chr4D 90.110 182 14 4 558 736 35722298 35722478 1.640000e-57 233.0
37 TraesCS3B01G458000 chr1D 81.579 190 24 9 1 181 33601537 33601350 2.200000e-31 147.0
38 TraesCS3B01G458000 chr5B 83.688 141 18 4 1 138 666799324 666799186 7.970000e-26 128.0
39 TraesCS3B01G458000 chr5B 82.979 141 19 4 1 138 666824412 666824274 3.710000e-24 122.0
40 TraesCS3B01G458000 chr5B 97.826 46 1 0 1507 1552 678891567 678891612 2.260000e-11 80.5
41 TraesCS3B01G458000 chr6B 97.826 46 1 0 1507 1552 446283735 446283780 2.260000e-11 80.5
42 TraesCS3B01G458000 chr4B 89.130 46 5 0 1507 1552 20111417 20111372 1.060000e-04 58.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G458000 chr3B 700361405 700364146 2741 False 5064.000000 5064 100.00000 1 2742 1 chr3B.!!$F1 2741
1 TraesCS3B01G458000 chr3D 529773008 529776171 3163 False 544.000000 1225 88.56775 2 2065 4 chr3D.!!$F1 2063
2 TraesCS3B01G458000 chr3D 361169006 361176744 7738 True 497.800000 725 97.01860 2066 2742 5 chr3D.!!$R3 676
3 TraesCS3B01G458000 chr3A 663577334 663578531 1197 False 604.500000 856 85.85450 943 2059 2 chr3A.!!$F1 1116
4 TraesCS3B01G458000 chr7A 287233414 287234277 863 False 549.000000 721 96.05450 2074 2742 2 chr7A.!!$F2 668
5 TraesCS3B01G458000 chr7A 74925576 74927072 1496 True 305.333333 462 90.58700 2066 2742 3 chr7A.!!$R2 676
6 TraesCS3B01G458000 chr2A 114340025 114340890 865 True 556.500000 712 96.42200 2066 2742 2 chr2A.!!$R1 676
7 TraesCS3B01G458000 chr4A 590354615 590355455 840 True 528.000000 686 96.34250 2091 2742 2 chr4A.!!$R1 651
8 TraesCS3B01G458000 chr6A 431215516 431216381 865 True 520.000000 676 94.31250 2063 2742 2 chr6A.!!$R1 679
9 TraesCS3B01G458000 chr7B 656532005 656532915 910 True 592.500000 673 98.12100 2066 2742 2 chr7B.!!$R2 676

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
283 303 0.036306 GGATTCTGGGTGGACAACGT 59.964 55.0 0.0 0.0 0.00 3.99 F
489 544 0.098728 GGATGACAAATTGCGACCGG 59.901 55.0 0.0 0.0 0.00 5.28 F
951 1007 0.389948 ACCGACGTTCTGATGAAGCC 60.390 55.0 0.0 0.0 32.15 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1189 1264 0.179070 GGAGGAAGAGGAACCGATGC 60.179 60.0 0.00 0.0 0.00 3.91 R
1455 1572 0.249120 ATCGAACAGGCATCGTGGAA 59.751 50.0 0.00 0.0 40.99 3.53 R
1922 3325 1.398692 TTTTGGAAGGCGTCTTGCTT 58.601 45.0 22.09 0.0 45.43 3.91 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
52 53 2.046313 CTCGTGAAACAAAGCATGCAC 58.954 47.619 21.98 5.42 35.74 4.57
69 70 1.326245 GCACGTTTTGCCAAAAAGGTC 59.674 47.619 17.86 7.16 46.22 3.85
70 71 1.586123 CACGTTTTGCCAAAAAGGTCG 59.414 47.619 17.86 13.12 46.22 4.79
86 87 1.691801 GGTCGAGTCCCCTTCCCTTAT 60.692 57.143 0.00 0.00 0.00 1.73
151 152 0.603569 CATCCTTCCCGAGTATCCCG 59.396 60.000 0.00 0.00 0.00 5.14
166 167 1.729284 TCCCGGCGTCATTTTACTTC 58.271 50.000 6.01 0.00 0.00 3.01
177 178 6.470877 GCGTCATTTTACTTCTGAAACAACAA 59.529 34.615 0.00 0.00 0.00 2.83
199 212 6.040166 ACAAGAAAGCTCAATGACATTTGACT 59.960 34.615 0.00 0.00 32.39 3.41
200 213 6.010294 AGAAAGCTCAATGACATTTGACTG 57.990 37.500 0.00 0.00 32.39 3.51
204 217 4.083643 AGCTCAATGACATTTGACTGAACG 60.084 41.667 0.00 0.00 32.39 3.95
205 218 4.715896 CTCAATGACATTTGACTGAACGG 58.284 43.478 0.00 0.00 32.39 4.44
206 219 3.501828 TCAATGACATTTGACTGAACGGG 59.498 43.478 0.00 0.00 30.82 5.28
207 220 1.234821 TGACATTTGACTGAACGGGC 58.765 50.000 0.00 0.00 0.00 6.13
210 223 0.110238 CATTTGACTGAACGGGCGTG 60.110 55.000 0.00 0.00 0.00 5.34
211 224 0.250124 ATTTGACTGAACGGGCGTGA 60.250 50.000 0.00 0.00 0.00 4.35
212 225 0.250124 TTTGACTGAACGGGCGTGAT 60.250 50.000 0.00 0.00 0.00 3.06
215 228 1.352156 GACTGAACGGGCGTGATGTC 61.352 60.000 0.00 0.00 0.00 3.06
217 230 0.670546 CTGAACGGGCGTGATGTCTT 60.671 55.000 0.00 0.00 0.00 3.01
228 248 3.062639 GCGTGATGTCTTTCATGAACGAT 59.937 43.478 16.68 3.09 41.61 3.73
242 262 3.632333 TGAACGATGTCAGTAGAGGGAT 58.368 45.455 0.00 0.00 0.00 3.85
250 270 2.432510 GTCAGTAGAGGGATGAAGGGTG 59.567 54.545 0.00 0.00 0.00 4.61
254 274 1.225704 GAGGGATGAAGGGTGCCTG 59.774 63.158 0.00 0.00 37.56 4.85
257 277 1.566298 GGGATGAAGGGTGCCTGTCT 61.566 60.000 0.00 0.00 32.13 3.41
280 300 0.323629 GACGGATTCTGGGTGGACAA 59.676 55.000 0.00 0.00 0.00 3.18
283 303 0.036306 GGATTCTGGGTGGACAACGT 59.964 55.000 0.00 0.00 0.00 3.99
301 321 1.339097 GTCATAGTCCAGGCGGGTAT 58.661 55.000 2.94 0.00 38.11 2.73
328 348 3.884774 TGGGGGCTGCAAACGTCT 61.885 61.111 0.50 0.00 0.00 4.18
332 352 2.328099 GGGCTGCAAACGTCTGAGG 61.328 63.158 0.50 0.00 0.00 3.86
333 353 2.558313 GCTGCAAACGTCTGAGGC 59.442 61.111 0.00 0.00 0.00 4.70
342 362 2.753029 GTCTGAGGCTGCCTGGTT 59.247 61.111 28.82 0.57 31.76 3.67
346 366 0.835941 CTGAGGCTGCCTGGTTAGAT 59.164 55.000 28.82 0.00 31.76 1.98
350 370 2.182842 GCTGCCTGGTTAGATGCCG 61.183 63.158 0.00 0.00 0.00 5.69
362 382 1.122019 AGATGCCGGGGAGGTACATC 61.122 60.000 2.18 5.68 43.70 3.06
367 387 2.822399 GGGGAGGTACATCTGCGG 59.178 66.667 7.56 0.00 0.00 5.69
420 440 2.632996 AGGAAACTCATGAACGGAGTGA 59.367 45.455 0.00 0.00 44.50 3.41
422 442 4.003648 GGAAACTCATGAACGGAGTGAAT 58.996 43.478 0.00 0.00 45.00 2.57
432 452 3.417069 ACGGAGTGAATGAACAATGGA 57.583 42.857 0.00 0.00 42.51 3.41
441 461 2.366640 TGAACAATGGAACGGGGAAA 57.633 45.000 0.00 0.00 0.00 3.13
456 476 2.562738 GGGGAAAAGATTTGAGTGGGTG 59.437 50.000 0.00 0.00 0.00 4.61
459 514 3.888930 GGAAAAGATTTGAGTGGGTGTGA 59.111 43.478 0.00 0.00 0.00 3.58
466 521 1.080025 GAGTGGGTGTGAGTACCGC 60.080 63.158 0.00 0.00 41.79 5.68
475 530 0.108992 GTGAGTACCGCGTTGGATGA 60.109 55.000 4.92 0.00 42.00 2.92
484 539 0.984109 GCGTTGGATGACAAATTGCG 59.016 50.000 0.00 0.00 41.58 4.85
489 544 0.098728 GGATGACAAATTGCGACCGG 59.901 55.000 0.00 0.00 0.00 5.28
491 546 1.670811 GATGACAAATTGCGACCGGAT 59.329 47.619 9.46 0.00 0.00 4.18
526 581 4.532834 ACAGTTGTATGTGTTTTGAGGGT 58.467 39.130 0.00 0.00 30.46 4.34
527 582 4.953579 ACAGTTGTATGTGTTTTGAGGGTT 59.046 37.500 0.00 0.00 30.46 4.11
528 583 5.420739 ACAGTTGTATGTGTTTTGAGGGTTT 59.579 36.000 0.00 0.00 30.46 3.27
531 586 2.908688 ATGTGTTTTGAGGGTTTGCC 57.091 45.000 0.00 0.00 0.00 4.52
542 597 2.166459 GAGGGTTTGCCTTAAAGATGCC 59.834 50.000 0.00 0.00 34.45 4.40
543 598 1.207089 GGGTTTGCCTTAAAGATGCCC 59.793 52.381 0.00 0.00 34.45 5.36
548 603 5.279758 GGTTTGCCTTAAAGATGCCCTAAAA 60.280 40.000 0.00 0.00 0.00 1.52
549 604 6.406370 GTTTGCCTTAAAGATGCCCTAAAAT 58.594 36.000 0.00 0.00 0.00 1.82
550 605 5.596836 TGCCTTAAAGATGCCCTAAAATG 57.403 39.130 0.00 0.00 0.00 2.32
552 607 5.483583 TGCCTTAAAGATGCCCTAAAATGTT 59.516 36.000 0.00 0.00 0.00 2.71
555 610 8.204160 GCCTTAAAGATGCCCTAAAATGTTATT 58.796 33.333 0.00 0.00 0.00 1.40
633 688 9.299963 TCTAAACTGATGTTCATTTTGTTTGTG 57.700 29.630 14.89 10.74 32.60 3.33
634 689 6.907206 AACTGATGTTCATTTTGTTTGTGG 57.093 33.333 0.00 0.00 0.00 4.17
635 690 5.976458 ACTGATGTTCATTTTGTTTGTGGT 58.024 33.333 0.00 0.00 0.00 4.16
636 691 6.042143 ACTGATGTTCATTTTGTTTGTGGTC 58.958 36.000 0.00 0.00 0.00 4.02
637 692 6.127366 ACTGATGTTCATTTTGTTTGTGGTCT 60.127 34.615 0.00 0.00 0.00 3.85
638 693 7.068103 ACTGATGTTCATTTTGTTTGTGGTCTA 59.932 33.333 0.00 0.00 0.00 2.59
639 694 7.950512 TGATGTTCATTTTGTTTGTGGTCTAT 58.049 30.769 0.00 0.00 0.00 1.98
640 695 8.420222 TGATGTTCATTTTGTTTGTGGTCTATT 58.580 29.630 0.00 0.00 0.00 1.73
641 696 9.260002 GATGTTCATTTTGTTTGTGGTCTATTT 57.740 29.630 0.00 0.00 0.00 1.40
642 697 9.612066 ATGTTCATTTTGTTTGTGGTCTATTTT 57.388 25.926 0.00 0.00 0.00 1.82
643 698 9.442047 TGTTCATTTTGTTTGTGGTCTATTTTT 57.558 25.926 0.00 0.00 0.00 1.94
674 729 2.370281 TTTTGTTTCTTGTTGCGGCA 57.630 40.000 0.00 0.00 0.00 5.69
675 730 2.593346 TTTGTTTCTTGTTGCGGCAT 57.407 40.000 2.28 0.00 0.00 4.40
676 731 2.593346 TTGTTTCTTGTTGCGGCATT 57.407 40.000 2.28 0.00 0.00 3.56
677 732 3.717400 TTGTTTCTTGTTGCGGCATTA 57.283 38.095 2.28 0.00 0.00 1.90
678 733 3.932545 TGTTTCTTGTTGCGGCATTAT 57.067 38.095 2.28 0.00 0.00 1.28
679 734 5.378292 TTGTTTCTTGTTGCGGCATTATA 57.622 34.783 2.28 0.00 0.00 0.98
680 735 5.574891 TGTTTCTTGTTGCGGCATTATAT 57.425 34.783 2.28 0.00 0.00 0.86
681 736 6.685527 TGTTTCTTGTTGCGGCATTATATA 57.314 33.333 2.28 0.00 0.00 0.86
682 737 7.270757 TGTTTCTTGTTGCGGCATTATATAT 57.729 32.000 2.28 0.00 0.00 0.86
683 738 7.711846 TGTTTCTTGTTGCGGCATTATATATT 58.288 30.769 2.28 0.00 0.00 1.28
684 739 8.194104 TGTTTCTTGTTGCGGCATTATATATTT 58.806 29.630 2.28 0.00 0.00 1.40
685 740 8.479280 GTTTCTTGTTGCGGCATTATATATTTG 58.521 33.333 2.28 0.00 0.00 2.32
686 741 7.270757 TCTTGTTGCGGCATTATATATTTGT 57.729 32.000 2.28 0.00 0.00 2.83
687 742 7.138081 TCTTGTTGCGGCATTATATATTTGTG 58.862 34.615 2.28 0.00 0.00 3.33
688 743 6.625873 TGTTGCGGCATTATATATTTGTGA 57.374 33.333 2.28 0.00 0.00 3.58
689 744 7.032377 TGTTGCGGCATTATATATTTGTGAA 57.968 32.000 2.28 0.00 0.00 3.18
690 745 7.484140 TGTTGCGGCATTATATATTTGTGAAA 58.516 30.769 2.28 0.00 0.00 2.69
691 746 7.647318 TGTTGCGGCATTATATATTTGTGAAAG 59.353 33.333 2.28 0.00 0.00 2.62
692 747 7.270757 TGCGGCATTATATATTTGTGAAAGT 57.729 32.000 0.00 0.00 0.00 2.66
693 748 7.711846 TGCGGCATTATATATTTGTGAAAGTT 58.288 30.769 0.00 0.00 0.00 2.66
694 749 8.194104 TGCGGCATTATATATTTGTGAAAGTTT 58.806 29.630 0.00 0.00 0.00 2.66
695 750 9.672086 GCGGCATTATATATTTGTGAAAGTTTA 57.328 29.630 0.00 0.00 0.00 2.01
707 762 9.683069 ATTTGTGAAAGTTTAGATGTGACATTC 57.317 29.630 0.00 0.00 0.00 2.67
708 763 8.450578 TTGTGAAAGTTTAGATGTGACATTCT 57.549 30.769 0.00 1.32 0.00 2.40
709 764 8.450578 TGTGAAAGTTTAGATGTGACATTCTT 57.549 30.769 0.00 0.00 0.00 2.52
710 765 9.554395 TGTGAAAGTTTAGATGTGACATTCTTA 57.446 29.630 0.00 0.00 0.00 2.10
780 835 4.458989 TGGACATTATGAAGTTGAAGCCAC 59.541 41.667 0.00 0.00 0.00 5.01
808 864 4.536765 AGACTGACAAAACCAGAACCAAT 58.463 39.130 0.00 0.00 35.69 3.16
832 888 2.267006 AGGCCATCTGCGTCACTG 59.733 61.111 5.01 0.00 42.61 3.66
895 951 0.880718 GATTTTAGAGCGAGGCCCCG 60.881 60.000 0.47 0.47 0.00 5.73
925 981 1.515088 CAGACAGAGTAGCGCACGG 60.515 63.158 11.47 1.18 0.00 4.94
945 1001 1.733041 CGTGCACCGACGTTCTGAT 60.733 57.895 12.15 0.00 39.56 2.90
951 1007 0.389948 ACCGACGTTCTGATGAAGCC 60.390 55.000 0.00 0.00 32.15 4.35
980 1036 4.332428 AAACCCTACATATACTCGGCAC 57.668 45.455 0.00 0.00 0.00 5.01
981 1037 2.953453 ACCCTACATATACTCGGCACA 58.047 47.619 0.00 0.00 0.00 4.57
982 1038 2.891580 ACCCTACATATACTCGGCACAG 59.108 50.000 0.00 0.00 0.00 3.66
983 1039 2.891580 CCCTACATATACTCGGCACAGT 59.108 50.000 0.00 0.00 0.00 3.55
984 1040 4.077108 CCCTACATATACTCGGCACAGTA 58.923 47.826 0.00 0.00 33.32 2.74
985 1041 4.156190 CCCTACATATACTCGGCACAGTAG 59.844 50.000 0.00 0.00 32.28 2.57
986 1042 3.644884 ACATATACTCGGCACAGTAGC 57.355 47.619 1.05 0.00 32.28 3.58
1013 1069 4.087489 TCGCAGACAGAGAGCAGT 57.913 55.556 0.00 0.00 0.00 4.40
1067 1139 3.174987 CCCTCCACACCACCACCA 61.175 66.667 0.00 0.00 0.00 4.17
1068 1140 2.113139 CCTCCACACCACCACCAC 59.887 66.667 0.00 0.00 0.00 4.16
1069 1141 2.113139 CTCCACACCACCACCACC 59.887 66.667 0.00 0.00 0.00 4.61
1070 1142 2.692741 TCCACACCACCACCACCA 60.693 61.111 0.00 0.00 0.00 4.17
1071 1143 2.518349 CCACACCACCACCACCAC 60.518 66.667 0.00 0.00 0.00 4.16
1072 1144 2.518349 CACACCACCACCACCACC 60.518 66.667 0.00 0.00 0.00 4.61
1073 1145 3.018193 ACACCACCACCACCACCA 61.018 61.111 0.00 0.00 0.00 4.17
1074 1146 2.518349 CACCACCACCACCACCAC 60.518 66.667 0.00 0.00 0.00 4.16
1075 1147 3.018193 ACCACCACCACCACCACA 61.018 61.111 0.00 0.00 0.00 4.17
1189 1264 4.947147 CCCACCACCACCACCACG 62.947 72.222 0.00 0.00 0.00 4.94
1326 1413 1.002773 GAGGAAGTTTACCTCGGGCAA 59.997 52.381 0.00 0.00 43.25 4.52
1447 1564 2.544069 CCTCGTTCTCCCTCGCTAATTC 60.544 54.545 0.00 0.00 0.00 2.17
1455 1572 1.059913 CCTCGCTAATTCCTCCCCAT 58.940 55.000 0.00 0.00 0.00 4.00
1459 1576 1.142870 CGCTAATTCCTCCCCATTCCA 59.857 52.381 0.00 0.00 0.00 3.53
1460 1577 2.587522 GCTAATTCCTCCCCATTCCAC 58.412 52.381 0.00 0.00 0.00 4.02
1466 1583 1.526917 CTCCCCATTCCACGATGCC 60.527 63.158 0.00 0.00 0.00 4.40
1524 1651 2.203379 TGCAGCCAAGCAGCAGAA 60.203 55.556 2.26 0.00 45.45 3.02
1599 1732 3.489513 GACAGGGGCCCGGCTTAT 61.490 66.667 23.55 2.38 0.00 1.73
1600 1733 2.040254 ACAGGGGCCCGGCTTATA 60.040 61.111 23.55 0.00 0.00 0.98
1604 1737 2.112507 GGGCCCGGCTTATACCAC 59.887 66.667 5.69 0.00 0.00 4.16
1606 1739 1.227853 GGCCCGGCTTATACCACAG 60.228 63.158 9.86 0.00 0.00 3.66
1610 1743 1.414919 CCCGGCTTATACCACAGCTTA 59.585 52.381 0.00 0.00 36.20 3.09
1618 1751 5.121454 GCTTATACCACAGCTTATGATGCTC 59.879 44.000 0.00 0.00 38.92 4.26
1693 1959 0.608640 TTCGAGAGGGAGCTTGGTTC 59.391 55.000 0.00 0.00 0.00 3.62
1773 2040 8.871686 ATAATCACAAGGAAAACAGTGTTTTC 57.128 30.769 37.06 37.06 37.60 2.29
1808 3208 5.585820 TCAGTTTGTTTTCTGGTTTACCC 57.414 39.130 0.00 0.00 34.29 3.69
1859 3262 6.483687 TGTTAGAAAACAAGTTCTTTCTCGC 58.516 36.000 11.16 7.66 42.60 5.03
1920 3323 0.939419 ACGAACTAAACGGTTGTGGC 59.061 50.000 0.00 0.00 34.93 5.01
1921 3324 1.223187 CGAACTAAACGGTTGTGGCT 58.777 50.000 0.00 0.00 0.00 4.75
1922 3325 2.224018 ACGAACTAAACGGTTGTGGCTA 60.224 45.455 0.00 0.00 34.93 3.93
1960 3370 0.311790 ATTTGGCAGCACACTTGTCG 59.688 50.000 0.00 0.00 0.00 4.35
1978 3388 7.326063 CACTTGTCGGATTACCAAAATCTTTTC 59.674 37.037 0.00 0.00 35.59 2.29
1988 3399 4.033932 ACCAAAATCTTTTCTTTTGCGTGC 59.966 37.500 3.58 0.00 40.57 5.34
1992 3403 1.606668 TCTTTTCTTTTGCGTGCCGAT 59.393 42.857 0.00 0.00 0.00 4.18
2019 3430 4.261405 CCCAAATCTTGTAACGCAAACTGA 60.261 41.667 0.00 0.00 36.53 3.41
2393 8122 6.842437 AGATCAAGTACTAGAGAAGCAACA 57.158 37.500 0.00 0.00 0.00 3.33
2394 8123 7.233389 AGATCAAGTACTAGAGAAGCAACAA 57.767 36.000 0.00 0.00 0.00 2.83
2731 9462 8.947055 AACCATTAAATCATTAAGCCAATCAC 57.053 30.769 0.00 0.00 34.62 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.447801 CGCCCTACAACTTGCATGTC 59.552 55.000 5.61 0.00 32.27 3.06
3 4 0.036164 TCACGCCCTACAACTTGCAT 59.964 50.000 0.00 0.00 0.00 3.96
30 31 2.357323 TGCATGCTTTGTTTCACGAGAA 59.643 40.909 20.33 0.00 0.00 2.87
31 32 1.946081 TGCATGCTTTGTTTCACGAGA 59.054 42.857 20.33 0.00 0.00 4.04
35 36 1.838913 ACGTGCATGCTTTGTTTCAC 58.161 45.000 20.33 4.81 0.00 3.18
52 53 2.116366 CTCGACCTTTTTGGCAAAACG 58.884 47.619 24.04 22.09 40.22 3.60
65 66 2.039137 GGGAAGGGGACTCGACCT 59.961 66.667 0.00 0.00 42.68 3.85
67 68 1.413077 CATAAGGGAAGGGGACTCGAC 59.587 57.143 0.00 0.00 42.68 4.20
68 69 1.789523 CATAAGGGAAGGGGACTCGA 58.210 55.000 0.00 0.00 42.68 4.04
69 70 0.106894 GCATAAGGGAAGGGGACTCG 59.893 60.000 0.00 0.00 42.68 4.18
70 71 0.474614 GGCATAAGGGAAGGGGACTC 59.525 60.000 0.00 0.00 42.68 3.36
110 111 2.051345 GTTTGCGTGCGTGGAAGG 60.051 61.111 0.00 0.00 0.00 3.46
111 112 1.063327 TTGTTTGCGTGCGTGGAAG 59.937 52.632 0.00 0.00 0.00 3.46
151 152 5.103290 TGTTTCAGAAGTAAAATGACGCC 57.897 39.130 0.00 0.00 0.00 5.68
166 167 6.197842 GTCATTGAGCTTTCTTGTTGTTTCAG 59.802 38.462 0.00 0.00 0.00 3.02
177 178 5.766670 TCAGTCAAATGTCATTGAGCTTTCT 59.233 36.000 0.00 0.00 39.84 2.52
199 212 0.250124 AAAGACATCACGCCCGTTCA 60.250 50.000 0.00 0.00 0.00 3.18
200 213 0.442699 GAAAGACATCACGCCCGTTC 59.557 55.000 0.00 0.00 0.00 3.95
204 217 1.737838 TCATGAAAGACATCACGCCC 58.262 50.000 0.00 0.00 37.07 6.13
205 218 2.474526 CGTTCATGAAAGACATCACGCC 60.475 50.000 15.34 0.00 36.54 5.68
206 219 2.411748 TCGTTCATGAAAGACATCACGC 59.588 45.455 18.50 0.00 40.06 5.34
207 220 4.091945 ACATCGTTCATGAAAGACATCACG 59.908 41.667 23.57 14.74 40.86 4.35
210 223 5.349817 ACTGACATCGTTCATGAAAGACATC 59.650 40.000 23.57 21.78 37.07 3.06
211 224 5.240891 ACTGACATCGTTCATGAAAGACAT 58.759 37.500 23.57 15.51 40.17 3.06
212 225 4.631131 ACTGACATCGTTCATGAAAGACA 58.369 39.130 23.57 16.53 36.21 3.41
215 228 5.518128 CCTCTACTGACATCGTTCATGAAAG 59.482 44.000 10.35 12.64 36.21 2.62
217 230 4.142160 CCCTCTACTGACATCGTTCATGAA 60.142 45.833 3.38 3.38 36.21 2.57
228 248 2.044492 ACCCTTCATCCCTCTACTGACA 59.956 50.000 0.00 0.00 0.00 3.58
242 262 2.431683 GCAGACAGGCACCCTTCA 59.568 61.111 0.00 0.00 0.00 3.02
250 270 3.665675 AATCCGTCCGCAGACAGGC 62.666 63.158 0.20 0.00 43.73 4.85
254 274 1.519455 CCAGAATCCGTCCGCAGAC 60.519 63.158 0.00 0.00 39.83 3.51
257 277 3.000819 ACCCAGAATCCGTCCGCA 61.001 61.111 0.00 0.00 0.00 5.69
264 284 0.036306 ACGTTGTCCACCCAGAATCC 59.964 55.000 0.00 0.00 0.00 3.01
269 289 1.275291 ACTATGACGTTGTCCACCCAG 59.725 52.381 0.00 0.00 0.00 4.45
280 300 2.423898 CCCGCCTGGACTATGACGT 61.424 63.158 0.00 0.00 37.49 4.34
283 303 1.338107 CATACCCGCCTGGACTATGA 58.662 55.000 0.00 0.00 37.49 2.15
307 327 2.524148 GTTTGCAGCCCCCACCTT 60.524 61.111 0.00 0.00 0.00 3.50
328 348 0.543277 CATCTAACCAGGCAGCCTCA 59.457 55.000 12.53 0.00 0.00 3.86
332 352 2.182842 CGGCATCTAACCAGGCAGC 61.183 63.158 0.00 0.00 0.00 5.25
333 353 1.524621 CCGGCATCTAACCAGGCAG 60.525 63.158 0.00 0.00 0.00 4.85
342 362 0.190069 ATGTACCTCCCCGGCATCTA 59.810 55.000 0.00 0.00 35.61 1.98
346 366 2.063979 CAGATGTACCTCCCCGGCA 61.064 63.158 0.00 0.00 35.61 5.69
350 370 2.822399 CCGCAGATGTACCTCCCC 59.178 66.667 0.00 0.00 0.00 4.81
380 400 1.383456 TTGCTTCGCATATGCACCCC 61.383 55.000 26.52 12.45 38.76 4.95
397 417 3.187227 CACTCCGTTCATGAGTTTCCTTG 59.813 47.826 0.00 0.00 41.02 3.61
402 422 4.641396 TCATTCACTCCGTTCATGAGTTT 58.359 39.130 0.00 0.00 41.02 2.66
420 440 2.595750 TCCCCGTTCCATTGTTCATT 57.404 45.000 0.00 0.00 0.00 2.57
422 442 2.366640 TTTCCCCGTTCCATTGTTCA 57.633 45.000 0.00 0.00 0.00 3.18
432 452 2.890945 CCACTCAAATCTTTTCCCCGTT 59.109 45.455 0.00 0.00 0.00 4.44
441 461 3.864789 ACTCACACCCACTCAAATCTT 57.135 42.857 0.00 0.00 0.00 2.40
456 476 0.108992 TCATCCAACGCGGTACTCAC 60.109 55.000 12.47 0.00 35.57 3.51
459 514 0.319083 TTGTCATCCAACGCGGTACT 59.681 50.000 12.47 0.00 35.57 2.73
466 521 2.241722 GTCGCAATTTGTCATCCAACG 58.758 47.619 0.00 0.00 31.20 4.10
475 530 1.014352 GCTATCCGGTCGCAATTTGT 58.986 50.000 0.00 0.00 0.00 2.83
484 539 1.524848 TCAGATCGAGCTATCCGGTC 58.475 55.000 1.25 0.00 37.42 4.79
489 544 4.677584 ACAACTGTTCAGATCGAGCTATC 58.322 43.478 1.25 0.00 0.00 2.08
491 546 5.125578 ACATACAACTGTTCAGATCGAGCTA 59.874 40.000 1.25 0.00 0.00 3.32
526 581 6.013812 ACATTTTAGGGCATCTTTAAGGCAAA 60.014 34.615 0.00 0.00 0.00 3.68
527 582 5.483583 ACATTTTAGGGCATCTTTAAGGCAA 59.516 36.000 0.00 0.00 0.00 4.52
528 583 5.022787 ACATTTTAGGGCATCTTTAAGGCA 58.977 37.500 0.00 0.00 0.00 4.75
558 613 2.303311 GTGTCCTAGACAGGCTCCTTTT 59.697 50.000 0.00 0.00 43.57 2.27
559 614 1.903183 GTGTCCTAGACAGGCTCCTTT 59.097 52.381 0.00 0.00 43.57 3.11
560 615 1.203187 TGTGTCCTAGACAGGCTCCTT 60.203 52.381 0.00 0.00 43.57 3.36
561 616 0.409876 TGTGTCCTAGACAGGCTCCT 59.590 55.000 0.00 0.00 43.57 3.69
562 617 1.410882 GATGTGTCCTAGACAGGCTCC 59.589 57.143 0.00 0.00 43.57 4.70
563 618 2.383855 AGATGTGTCCTAGACAGGCTC 58.616 52.381 0.00 0.00 43.57 4.70
564 619 2.541233 AGATGTGTCCTAGACAGGCT 57.459 50.000 0.00 0.00 43.57 4.58
565 620 3.556999 TCTAGATGTGTCCTAGACAGGC 58.443 50.000 0.00 0.00 43.57 4.85
566 621 5.703978 CATCTAGATGTGTCCTAGACAGG 57.296 47.826 22.42 0.00 43.57 4.00
607 662 9.299963 CACAAACAAAATGAACATCAGTTTAGA 57.700 29.630 5.59 0.00 41.92 2.10
608 663 8.542132 CCACAAACAAAATGAACATCAGTTTAG 58.458 33.333 5.59 4.18 41.92 1.85
609 664 8.037758 ACCACAAACAAAATGAACATCAGTTTA 58.962 29.630 5.59 0.00 41.92 2.01
610 665 6.878389 ACCACAAACAAAATGAACATCAGTTT 59.122 30.769 0.41 0.41 44.23 2.66
611 666 6.405538 ACCACAAACAAAATGAACATCAGTT 58.594 32.000 0.00 0.00 36.10 3.16
612 667 5.976458 ACCACAAACAAAATGAACATCAGT 58.024 33.333 0.00 0.00 0.00 3.41
613 668 6.275335 AGACCACAAACAAAATGAACATCAG 58.725 36.000 0.00 0.00 0.00 2.90
614 669 6.219417 AGACCACAAACAAAATGAACATCA 57.781 33.333 0.00 0.00 0.00 3.07
615 670 8.816640 AATAGACCACAAACAAAATGAACATC 57.183 30.769 0.00 0.00 0.00 3.06
616 671 9.612066 AAAATAGACCACAAACAAAATGAACAT 57.388 25.926 0.00 0.00 0.00 2.71
617 672 9.442047 AAAAATAGACCACAAACAAAATGAACA 57.558 25.926 0.00 0.00 0.00 3.18
654 709 2.688507 TGCCGCAACAAGAAACAAAAA 58.311 38.095 0.00 0.00 0.00 1.94
655 710 2.370281 TGCCGCAACAAGAAACAAAA 57.630 40.000 0.00 0.00 0.00 2.44
656 711 2.593346 ATGCCGCAACAAGAAACAAA 57.407 40.000 0.00 0.00 0.00 2.83
657 712 2.593346 AATGCCGCAACAAGAAACAA 57.407 40.000 0.00 0.00 0.00 2.83
658 713 3.932545 ATAATGCCGCAACAAGAAACA 57.067 38.095 0.00 0.00 0.00 2.83
659 714 8.479280 CAAATATATAATGCCGCAACAAGAAAC 58.521 33.333 0.00 0.00 0.00 2.78
660 715 8.194104 ACAAATATATAATGCCGCAACAAGAAA 58.806 29.630 0.00 0.00 0.00 2.52
661 716 7.647318 CACAAATATATAATGCCGCAACAAGAA 59.353 33.333 0.00 0.00 0.00 2.52
662 717 7.012799 TCACAAATATATAATGCCGCAACAAGA 59.987 33.333 0.00 0.00 0.00 3.02
663 718 7.138081 TCACAAATATATAATGCCGCAACAAG 58.862 34.615 0.00 0.00 0.00 3.16
664 719 7.032377 TCACAAATATATAATGCCGCAACAA 57.968 32.000 0.00 0.00 0.00 2.83
665 720 6.625873 TCACAAATATATAATGCCGCAACA 57.374 33.333 0.00 0.00 0.00 3.33
666 721 7.647715 ACTTTCACAAATATATAATGCCGCAAC 59.352 33.333 0.00 0.00 0.00 4.17
667 722 7.711846 ACTTTCACAAATATATAATGCCGCAA 58.288 30.769 0.00 0.00 0.00 4.85
668 723 7.270757 ACTTTCACAAATATATAATGCCGCA 57.729 32.000 0.00 0.00 0.00 5.69
669 724 8.574196 AAACTTTCACAAATATATAATGCCGC 57.426 30.769 0.00 0.00 0.00 6.53
681 736 9.683069 GAATGTCACATCTAAACTTTCACAAAT 57.317 29.630 0.00 0.00 31.19 2.32
682 737 8.902806 AGAATGTCACATCTAAACTTTCACAAA 58.097 29.630 0.00 0.00 32.47 2.83
683 738 8.450578 AGAATGTCACATCTAAACTTTCACAA 57.549 30.769 0.00 0.00 32.47 3.33
684 739 8.450578 AAGAATGTCACATCTAAACTTTCACA 57.549 30.769 0.00 0.00 32.47 3.58
747 802 7.781324 ACTTCATAATGTCCACCTGAATTTT 57.219 32.000 0.00 0.00 0.00 1.82
804 860 2.505405 CAGATGGCCTCAGATGATTGG 58.495 52.381 3.32 0.00 0.00 3.16
808 864 1.332889 ACGCAGATGGCCTCAGATGA 61.333 55.000 3.32 0.00 40.31 2.92
832 888 0.451783 ATTTTCGCCATCAGTTCGCC 59.548 50.000 0.00 0.00 0.00 5.54
868 924 4.333926 GCCTCGCTCTAAAATCACAGAAAT 59.666 41.667 0.00 0.00 0.00 2.17
895 951 2.287909 ACTCTGTCTGTCGCACTCTTTC 60.288 50.000 0.00 0.00 0.00 2.62
932 988 0.389948 GGCTTCATCAGAACGTCGGT 60.390 55.000 0.00 0.00 0.00 4.69
934 990 0.732880 ACGGCTTCATCAGAACGTCG 60.733 55.000 0.00 0.00 32.98 5.12
945 1001 1.972795 AGGGTTTACACTACGGCTTCA 59.027 47.619 0.00 0.00 0.00 3.02
1013 1069 1.197949 CGTCTGCTCTGTTTCTCGAGA 59.802 52.381 12.08 12.08 0.00 4.04
1067 1139 3.570212 GGTGGAGCCTGTGGTGGT 61.570 66.667 0.00 0.00 0.00 4.16
1189 1264 0.179070 GGAGGAAGAGGAACCGATGC 60.179 60.000 0.00 0.00 0.00 3.91
1326 1413 0.252927 CCTCCTCTTCCCACCCTTCT 60.253 60.000 0.00 0.00 0.00 2.85
1429 1528 1.409427 AGGAATTAGCGAGGGAGAACG 59.591 52.381 0.00 0.00 0.00 3.95
1447 1564 1.526917 GCATCGTGGAATGGGGAGG 60.527 63.158 0.00 0.00 0.00 4.30
1455 1572 0.249120 ATCGAACAGGCATCGTGGAA 59.751 50.000 0.00 0.00 40.99 3.53
1459 1576 2.961526 AGTTATCGAACAGGCATCGT 57.038 45.000 0.00 0.00 40.99 3.73
1460 1577 4.142902 ACAAAAGTTATCGAACAGGCATCG 60.143 41.667 0.00 1.59 41.53 3.84
1466 1583 7.065894 CAGAAGACACAAAAGTTATCGAACAG 58.934 38.462 0.00 0.00 38.10 3.16
1524 1651 4.383226 GCTCCTATTTCTTCCGGTTCTTCT 60.383 45.833 0.00 0.00 0.00 2.85
1599 1732 2.224042 CGGAGCATCATAAGCTGTGGTA 60.224 50.000 0.00 0.00 43.58 3.25
1600 1733 1.473965 CGGAGCATCATAAGCTGTGGT 60.474 52.381 0.00 0.00 43.58 4.16
1604 1737 2.469274 ATCCGGAGCATCATAAGCTG 57.531 50.000 11.34 0.00 43.58 4.24
1606 1739 4.574599 AAAAATCCGGAGCATCATAAGC 57.425 40.909 11.34 0.00 36.25 3.09
1641 1775 3.265791 GTCATCTCCTCTCGCAAAATGT 58.734 45.455 0.00 0.00 0.00 2.71
1693 1959 5.514274 TTGGTGTCTTCTTAAAAGGCAAG 57.486 39.130 6.35 0.00 33.21 4.01
1755 2021 2.529894 CGCGAAAACACTGTTTTCCTTG 59.470 45.455 29.33 20.92 35.57 3.61
1773 2040 2.666508 ACAAACTGAGCTATTACACGCG 59.333 45.455 3.53 3.53 0.00 6.01
1808 3208 3.303132 GCCTGCTTGAATAATCGTAACGG 60.303 47.826 0.00 0.00 0.00 4.44
1859 3262 2.753043 GCAGTGCCTGTCCATGGG 60.753 66.667 13.02 0.00 33.43 4.00
1920 3323 1.808411 TTGGAAGGCGTCTTGCTTAG 58.192 50.000 22.09 0.00 45.43 2.18
1921 3324 2.264005 TTTGGAAGGCGTCTTGCTTA 57.736 45.000 22.09 7.64 45.43 3.09
1922 3325 1.398692 TTTTGGAAGGCGTCTTGCTT 58.601 45.000 22.09 0.00 45.43 3.91
1960 3370 7.170828 ACGCAAAAGAAAAGATTTTGGTAATCC 59.829 33.333 11.76 0.00 44.23 3.01
1992 3403 5.769484 TTGCGTTACAAGATTTGGGTAAA 57.231 34.783 0.00 0.00 33.24 2.01
2019 3430 5.171339 ACTTGAGCAATTCAGATAGGTGT 57.829 39.130 0.00 0.00 37.07 4.16
2055 3466 4.207281 CGCCGCTGCTAGTGCCTA 62.207 66.667 0.00 0.00 38.71 3.93
2449 8941 3.644265 TGGAGGTGTTCTGCAACTACTAA 59.356 43.478 0.00 0.00 46.91 2.24


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

AutoCloner maintained by Alex Coulton.