Multiple sequence alignment - TraesCS6A01G281500

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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 TraesCS6A01G281500 chr6A 100.000 2591 0 0 1 2591 511426271 511423681 0.000000e+00 4785.0
1 TraesCS6A01G281500 chr6B 90.714 1820 68 27 706 2426 555557634 555555817 0.000000e+00 2331.0
2 TraesCS6A01G281500 chr6B 80.781 666 70 27 1 622 555558457 555557806 3.900000e-128 468.0
3 TraesCS6A01G281500 chr6B 97.826 46 1 0 617 662 555557758 555557713 2.140000e-11 80.5
4 TraesCS6A01G281500 chr6D 96.334 1173 21 8 706 1858 370368792 370367622 0.000000e+00 1908.0
5 TraesCS6A01G281500 chr6D 85.942 626 47 14 1 600 370369587 370368977 4.710000e-177 630.0
6 TraesCS6A01G281500 chr6D 85.393 356 28 6 2099 2430 370367352 370366997 5.310000e-92 348.0
7 TraesCS6A01G281500 chr6D 75.652 460 85 18 1 444 340201920 340201472 1.220000e-48 204.0
8 TraesCS6A01G281500 chr6D 98.246 114 2 0 1922 2035 370367620 370367507 1.570000e-47 200.0
9 TraesCS6A01G281500 chr1D 92.254 142 11 0 1383 1524 44620954 44620813 4.370000e-48 202.0
10 TraesCS6A01G281500 chr3A 78.400 250 45 7 23 270 371327257 371327499 1.240000e-33 154.0
11 TraesCS6A01G281500 chr4D 92.391 92 2 5 1382 1473 472678340 472678254 2.710000e-25 126.0
12 TraesCS6A01G281500 chr4D 98.485 66 1 0 1500 1565 472678178 472678243 1.630000e-22 117.0


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 TraesCS6A01G281500 chr6A 511423681 511426271 2590 True 4785.000000 4785 100.000000 1 2591 1 chr6A.!!$R1 2590
1 TraesCS6A01G281500 chr6B 555555817 555558457 2640 True 959.833333 2331 89.773667 1 2426 3 chr6B.!!$R1 2425
2 TraesCS6A01G281500 chr6D 370366997 370369587 2590 True 771.500000 1908 91.478750 1 2430 4 chr6D.!!$R2 2429

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
39 40 0.035725 TCTTGGCATGCCTGAGTCTG 60.036 55.0 35.53 17.33 36.94 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1605 1808 3.003173 CGACCAAGAGAGGGGGCA 61.003 66.667 0.0 0.0 30.28 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
32 33 1.604593 ACGCTTTCTTGGCATGCCT 60.605 52.632 35.53 11.01 36.94 4.75
39 40 0.035725 TCTTGGCATGCCTGAGTCTG 60.036 55.000 35.53 17.33 36.94 3.51
98 99 2.105821 TGTTAGGTTGACTGAAGGGTGG 59.894 50.000 0.00 0.00 0.00 4.61
102 103 0.178990 GTTGACTGAAGGGTGGGCTT 60.179 55.000 0.00 0.00 0.00 4.35
127 136 4.506654 CCGTGTAACTATACTGTCAATGGC 59.493 45.833 0.00 0.00 32.98 4.40
143 152 5.008980 TCAATGGCAATGACTACAACATGA 58.991 37.500 0.00 0.00 0.00 3.07
208 218 2.663602 CGTCAAGACCATCTTTGAGTCG 59.336 50.000 0.00 0.00 33.78 4.18
214 224 1.420138 ACCATCTTTGAGTCGGTTGGT 59.580 47.619 7.20 7.20 0.00 3.67
226 236 4.969484 AGTCGGTTGGTGAGAAAATAACT 58.031 39.130 0.00 0.00 0.00 2.24
258 268 4.343814 CCAAAGACAAAAGGGGCTAGAAAA 59.656 41.667 0.00 0.00 0.00 2.29
260 270 3.767711 AGACAAAAGGGGCTAGAAAAGG 58.232 45.455 0.00 0.00 0.00 3.11
261 271 3.397955 AGACAAAAGGGGCTAGAAAAGGA 59.602 43.478 0.00 0.00 0.00 3.36
262 272 4.044698 AGACAAAAGGGGCTAGAAAAGGAT 59.955 41.667 0.00 0.00 0.00 3.24
263 273 5.253096 AGACAAAAGGGGCTAGAAAAGGATA 59.747 40.000 0.00 0.00 0.00 2.59
264 274 6.068794 AGACAAAAGGGGCTAGAAAAGGATAT 60.069 38.462 0.00 0.00 0.00 1.63
265 275 5.893824 ACAAAAGGGGCTAGAAAAGGATATG 59.106 40.000 0.00 0.00 0.00 1.78
266 276 4.731313 AAGGGGCTAGAAAAGGATATGG 57.269 45.455 0.00 0.00 0.00 2.74
267 277 3.954662 AGGGGCTAGAAAAGGATATGGA 58.045 45.455 0.00 0.00 0.00 3.41
268 278 3.913163 AGGGGCTAGAAAAGGATATGGAG 59.087 47.826 0.00 0.00 0.00 3.86
269 279 3.910627 GGGGCTAGAAAAGGATATGGAGA 59.089 47.826 0.00 0.00 0.00 3.71
273 291 5.471797 GGCTAGAAAAGGATATGGAGAAAGC 59.528 44.000 0.00 0.00 0.00 3.51
274 292 6.058183 GCTAGAAAAGGATATGGAGAAAGCA 58.942 40.000 0.00 0.00 0.00 3.91
289 307 1.029681 AAGCACTCCAACCCGTTTTC 58.970 50.000 0.00 0.00 0.00 2.29
293 311 0.822121 ACTCCAACCCGTTTTCCAGC 60.822 55.000 0.00 0.00 0.00 4.85
295 313 0.536460 TCCAACCCGTTTTCCAGCTC 60.536 55.000 0.00 0.00 0.00 4.09
371 390 1.946081 TGTGTCATCACGCACAACATT 59.054 42.857 0.00 0.00 46.49 2.71
376 395 2.159430 TCATCACGCACAACATTACTGC 59.841 45.455 0.00 0.00 0.00 4.40
388 407 2.236146 ACATTACTGCGGAGGATGACAA 59.764 45.455 22.74 0.00 0.00 3.18
398 417 2.570135 GAGGATGACAATGAAGGAGCC 58.430 52.381 0.00 0.00 0.00 4.70
413 432 1.178276 GAGCCGACGGAGATATGGAT 58.822 55.000 20.50 0.00 0.00 3.41
462 500 3.259625 ACTTCTAGCTCAGAGTTTGTCCC 59.740 47.826 0.00 0.00 33.83 4.46
464 502 3.445008 TCTAGCTCAGAGTTTGTCCCAT 58.555 45.455 0.00 0.00 0.00 4.00
485 523 5.290885 CCATTGCATCAACAGATTTGACATG 59.709 40.000 0.00 0.00 0.00 3.21
490 528 3.753815 TCAACAGATTTGACATGGAGCA 58.246 40.909 0.00 0.00 0.00 4.26
587 630 4.715534 TGTTTGAATTGTACTCCCTCCA 57.284 40.909 0.00 0.00 0.00 3.86
590 633 6.969043 TGTTTGAATTGTACTCCCTCCATAT 58.031 36.000 0.00 0.00 0.00 1.78
663 773 8.568732 TTTTGAAGTATTGCGGACTTAAAAAG 57.431 30.769 12.88 0.00 40.20 2.27
666 776 7.932335 TGAAGTATTGCGGACTTAAAAAGAAA 58.068 30.769 0.00 0.00 37.27 2.52
667 777 8.407064 TGAAGTATTGCGGACTTAAAAAGAAAA 58.593 29.630 0.00 0.00 37.27 2.29
668 778 9.240159 GAAGTATTGCGGACTTAAAAAGAAAAA 57.760 29.630 0.00 0.00 37.27 1.94
669 779 8.797266 AGTATTGCGGACTTAAAAAGAAAAAG 57.203 30.769 0.00 0.00 0.00 2.27
670 780 8.626526 AGTATTGCGGACTTAAAAAGAAAAAGA 58.373 29.630 0.00 0.00 0.00 2.52
672 782 7.514573 TTGCGGACTTAAAAAGAAAAAGAAC 57.485 32.000 0.00 0.00 0.00 3.01
673 783 6.622549 TGCGGACTTAAAAAGAAAAAGAACA 58.377 32.000 0.00 0.00 0.00 3.18
674 784 7.262048 TGCGGACTTAAAAAGAAAAAGAACAT 58.738 30.769 0.00 0.00 0.00 2.71
675 785 8.407064 TGCGGACTTAAAAAGAAAAAGAACATA 58.593 29.630 0.00 0.00 0.00 2.29
676 786 9.406828 GCGGACTTAAAAAGAAAAAGAACATAT 57.593 29.630 0.00 0.00 0.00 1.78
686 796 9.939802 AAAGAAAAAGAACATATAGTACCGAGT 57.060 29.630 0.00 0.00 0.00 4.18
687 797 9.583765 AAGAAAAAGAACATATAGTACCGAGTC 57.416 33.333 0.00 0.00 0.00 3.36
688 798 8.196103 AGAAAAAGAACATATAGTACCGAGTCC 58.804 37.037 0.00 0.00 0.00 3.85
689 799 5.686159 AAGAACATATAGTACCGAGTCCG 57.314 43.478 0.00 0.00 0.00 4.79
967 1154 1.214325 CGAAATCCAAAACCCCGCC 59.786 57.895 0.00 0.00 0.00 6.13
1605 1808 1.002134 CTGATCCGGCCTGGTTTGT 60.002 57.895 12.46 0.07 39.52 2.83
1834 2038 3.378112 CCCTCTTTTGCGCATATTCTTGA 59.622 43.478 12.75 2.30 0.00 3.02
1884 2088 1.645455 CGCTGCATCTTATTGCGCT 59.355 52.632 9.73 0.00 45.77 5.92
1905 2109 6.146347 GCGCTAATTTGACAAATTGGGTTAAA 59.854 34.615 28.48 11.58 41.01 1.52
1932 2136 0.035152 CCTGCTGTTGTCATGGGCTA 60.035 55.000 0.00 0.00 0.00 3.93
2017 2221 8.662781 ACTATGCGATTTAACATAGATGTGTT 57.337 30.769 15.00 0.60 45.65 3.32
2141 2436 0.534652 GCAGCTCCTTGGATGCCTAG 60.535 60.000 4.38 0.00 41.99 3.02
2150 2445 5.930135 TCCTTGGATGCCTAGAAAGATTAC 58.070 41.667 0.00 0.00 0.00 1.89
2166 2461 2.552599 TTACGGCAGTGGTTGATTCA 57.447 45.000 0.00 0.00 0.00 2.57
2196 2509 5.417580 TGTTCTTGGCCCAATATAACTTGAC 59.582 40.000 0.00 0.00 0.00 3.18
2203 2516 6.126332 TGGCCCAATATAACTTGACTTGGATA 60.126 38.462 0.00 0.00 38.92 2.59
2207 2520 7.661847 CCCAATATAACTTGACTTGGATAGACC 59.338 40.741 1.31 0.00 38.92 3.85
2238 2551 7.149973 CAGATTTCATGTCTGTTTTCATGGTT 58.850 34.615 4.11 0.00 40.94 3.67
2240 2553 4.852134 TCATGTCTGTTTTCATGGTTGG 57.148 40.909 0.00 0.00 40.94 3.77
2285 2599 7.382898 AGTTTAGTTGATCTCCTTGAGTTCTC 58.617 38.462 0.00 0.00 31.76 2.87
2290 2604 3.196469 TGATCTCCTTGAGTTCTCGCAAT 59.804 43.478 0.00 0.00 33.38 3.56
2303 2617 9.383519 TGAGTTCTCGCAATTAAGAATTAAGAT 57.616 29.630 1.75 0.00 44.82 2.40
2329 2643 4.519540 TGGAGTTCTTTTAAATGCAGCC 57.480 40.909 0.00 0.00 0.00 4.85
2393 2714 2.417586 TGAGAATGATCTTTGTGCTGCG 59.582 45.455 0.00 0.00 35.54 5.18
2405 2726 5.182190 TCTTTGTGCTGCGGTTTTATTATGA 59.818 36.000 0.00 0.00 0.00 2.15
2406 2727 4.349663 TGTGCTGCGGTTTTATTATGAC 57.650 40.909 0.00 0.00 0.00 3.06
2417 2738 7.745594 GCGGTTTTATTATGACGTGTTTCTTTA 59.254 33.333 0.00 0.00 0.00 1.85
2426 2747 5.421277 TGACGTGTTTCTTTACTCCTGAAA 58.579 37.500 0.00 0.00 0.00 2.69
2447 2768 4.434713 AAAACCAATGTATTCTGTCCGC 57.565 40.909 0.00 0.00 0.00 5.54
2448 2769 3.350219 AACCAATGTATTCTGTCCGCT 57.650 42.857 0.00 0.00 0.00 5.52
2449 2770 2.632377 ACCAATGTATTCTGTCCGCTG 58.368 47.619 0.00 0.00 0.00 5.18
2450 2771 2.236146 ACCAATGTATTCTGTCCGCTGA 59.764 45.455 0.00 0.00 0.00 4.26
2451 2772 3.270027 CCAATGTATTCTGTCCGCTGAA 58.730 45.455 0.00 0.00 37.06 3.02
2452 2773 3.879295 CCAATGTATTCTGTCCGCTGAAT 59.121 43.478 0.00 0.00 42.96 2.57
2453 2774 4.260907 CCAATGTATTCTGTCCGCTGAATG 60.261 45.833 9.08 0.00 41.36 2.67
2454 2775 2.279741 TGTATTCTGTCCGCTGAATGC 58.720 47.619 9.08 8.42 41.36 3.56
2455 2776 2.093500 TGTATTCTGTCCGCTGAATGCT 60.093 45.455 13.06 0.00 42.02 3.79
2456 2777 2.119801 ATTCTGTCCGCTGAATGCTT 57.880 45.000 0.00 0.00 40.31 3.91
2457 2778 2.760634 TTCTGTCCGCTGAATGCTTA 57.239 45.000 0.00 0.00 40.11 3.09
2458 2779 2.988010 TCTGTCCGCTGAATGCTTAT 57.012 45.000 0.00 0.00 40.11 1.73
2459 2780 4.400529 TTCTGTCCGCTGAATGCTTATA 57.599 40.909 0.00 0.00 40.11 0.98
2460 2781 4.400529 TCTGTCCGCTGAATGCTTATAA 57.599 40.909 0.00 0.00 40.11 0.98
2461 2782 4.960938 TCTGTCCGCTGAATGCTTATAAT 58.039 39.130 0.00 0.00 40.11 1.28
2462 2783 5.368145 TCTGTCCGCTGAATGCTTATAATT 58.632 37.500 0.00 0.00 40.11 1.40
2463 2784 5.237127 TCTGTCCGCTGAATGCTTATAATTG 59.763 40.000 0.00 0.00 40.11 2.32
2464 2785 4.275689 TGTCCGCTGAATGCTTATAATTGG 59.724 41.667 0.00 0.00 40.11 3.16
2465 2786 3.820467 TCCGCTGAATGCTTATAATTGGG 59.180 43.478 0.00 0.00 40.11 4.12
2466 2787 3.568538 CGCTGAATGCTTATAATTGGGC 58.431 45.455 0.00 0.00 40.11 5.36
2467 2788 3.004629 CGCTGAATGCTTATAATTGGGCA 59.995 43.478 0.20 0.20 40.11 5.36
2468 2789 4.321452 CGCTGAATGCTTATAATTGGGCAT 60.321 41.667 4.53 4.53 45.65 4.40
2475 2796 6.882610 TGCTTATAATTGGGCATTAGAGTG 57.117 37.500 0.00 0.00 30.48 3.51
2476 2797 6.600388 TGCTTATAATTGGGCATTAGAGTGA 58.400 36.000 0.00 0.00 30.48 3.41
2477 2798 6.486657 TGCTTATAATTGGGCATTAGAGTGAC 59.513 38.462 0.00 0.00 30.48 3.67
2483 2804 3.567478 GGGCATTAGAGTGACCTGAAT 57.433 47.619 0.00 0.00 44.34 2.57
2484 2805 3.891049 GGGCATTAGAGTGACCTGAATT 58.109 45.455 0.00 0.00 44.34 2.17
2485 2806 4.273318 GGGCATTAGAGTGACCTGAATTT 58.727 43.478 0.00 0.00 44.34 1.82
2486 2807 5.437060 GGGCATTAGAGTGACCTGAATTTA 58.563 41.667 0.00 0.00 44.34 1.40
2487 2808 5.529060 GGGCATTAGAGTGACCTGAATTTAG 59.471 44.000 0.00 0.00 44.34 1.85
2488 2809 6.116126 GGCATTAGAGTGACCTGAATTTAGT 58.884 40.000 0.00 0.00 0.00 2.24
2489 2810 6.599638 GGCATTAGAGTGACCTGAATTTAGTT 59.400 38.462 0.00 0.00 0.00 2.24
2490 2811 7.414540 GGCATTAGAGTGACCTGAATTTAGTTG 60.415 40.741 0.00 0.00 0.00 3.16
2491 2812 7.467623 CATTAGAGTGACCTGAATTTAGTTGC 58.532 38.462 0.00 0.00 0.00 4.17
2492 2813 4.973168 AGAGTGACCTGAATTTAGTTGCA 58.027 39.130 0.00 0.00 0.00 4.08
2493 2814 5.564550 AGAGTGACCTGAATTTAGTTGCAT 58.435 37.500 0.00 0.00 0.00 3.96
2494 2815 6.711277 AGAGTGACCTGAATTTAGTTGCATA 58.289 36.000 0.00 0.00 0.00 3.14
2495 2816 6.820656 AGAGTGACCTGAATTTAGTTGCATAG 59.179 38.462 0.00 0.00 0.00 2.23
2496 2817 6.476378 AGTGACCTGAATTTAGTTGCATAGT 58.524 36.000 0.00 0.00 0.00 2.12
2497 2818 6.942576 AGTGACCTGAATTTAGTTGCATAGTT 59.057 34.615 0.00 0.00 0.00 2.24
2498 2819 7.448469 AGTGACCTGAATTTAGTTGCATAGTTT 59.552 33.333 0.00 0.00 0.00 2.66
2499 2820 7.750903 GTGACCTGAATTTAGTTGCATAGTTTC 59.249 37.037 0.00 0.00 0.00 2.78
2500 2821 7.094377 TGACCTGAATTTAGTTGCATAGTTTCC 60.094 37.037 0.00 0.00 0.00 3.13
2501 2822 6.948309 ACCTGAATTTAGTTGCATAGTTTCCT 59.052 34.615 0.00 0.00 0.00 3.36
2502 2823 7.094205 ACCTGAATTTAGTTGCATAGTTTCCTG 60.094 37.037 0.00 0.00 0.00 3.86
2503 2824 7.156876 TGAATTTAGTTGCATAGTTTCCTGG 57.843 36.000 0.00 0.00 0.00 4.45
2504 2825 6.945435 TGAATTTAGTTGCATAGTTTCCTGGA 59.055 34.615 0.00 0.00 0.00 3.86
2505 2826 7.121168 TGAATTTAGTTGCATAGTTTCCTGGAG 59.879 37.037 0.00 0.00 0.00 3.86
2506 2827 3.356529 AGTTGCATAGTTTCCTGGAGG 57.643 47.619 0.00 0.00 0.00 4.30
2507 2828 2.025887 AGTTGCATAGTTTCCTGGAGGG 60.026 50.000 0.00 0.00 35.41 4.30
2508 2829 1.965414 TGCATAGTTTCCTGGAGGGA 58.035 50.000 0.00 0.00 43.41 4.20
2509 2830 2.492025 TGCATAGTTTCCTGGAGGGAT 58.508 47.619 0.00 0.00 44.66 3.85
2510 2831 2.173356 TGCATAGTTTCCTGGAGGGATG 59.827 50.000 0.00 1.48 44.66 3.51
2511 2832 2.439507 GCATAGTTTCCTGGAGGGATGA 59.560 50.000 11.75 0.00 44.66 2.92
2512 2833 3.117888 GCATAGTTTCCTGGAGGGATGAA 60.118 47.826 11.75 0.00 44.66 2.57
2513 2834 4.628715 GCATAGTTTCCTGGAGGGATGAAA 60.629 45.833 11.75 0.00 44.66 2.69
2514 2835 5.509498 CATAGTTTCCTGGAGGGATGAAAA 58.491 41.667 0.00 0.00 44.66 2.29
2515 2836 4.682021 AGTTTCCTGGAGGGATGAAAAT 57.318 40.909 0.00 0.00 44.66 1.82
2516 2837 5.796502 AGTTTCCTGGAGGGATGAAAATA 57.203 39.130 0.00 0.00 44.66 1.40
2517 2838 6.347061 AGTTTCCTGGAGGGATGAAAATAT 57.653 37.500 0.00 0.00 44.66 1.28
2518 2839 7.465900 AGTTTCCTGGAGGGATGAAAATATA 57.534 36.000 0.00 0.00 44.66 0.86
2519 2840 7.882755 AGTTTCCTGGAGGGATGAAAATATAA 58.117 34.615 0.00 0.00 44.66 0.98
2520 2841 8.514504 AGTTTCCTGGAGGGATGAAAATATAAT 58.485 33.333 0.00 0.00 44.66 1.28
2521 2842 8.579863 GTTTCCTGGAGGGATGAAAATATAATG 58.420 37.037 0.00 0.00 44.66 1.90
2522 2843 7.406620 TCCTGGAGGGATGAAAATATAATGT 57.593 36.000 0.00 0.00 39.58 2.71
2523 2844 7.233632 TCCTGGAGGGATGAAAATATAATGTG 58.766 38.462 0.00 0.00 39.58 3.21
2524 2845 7.006509 CCTGGAGGGATGAAAATATAATGTGT 58.993 38.462 0.00 0.00 37.23 3.72
2525 2846 7.506938 CCTGGAGGGATGAAAATATAATGTGTT 59.493 37.037 0.00 0.00 37.23 3.32
2526 2847 8.236585 TGGAGGGATGAAAATATAATGTGTTG 57.763 34.615 0.00 0.00 0.00 3.33
2527 2848 7.838696 TGGAGGGATGAAAATATAATGTGTTGT 59.161 33.333 0.00 0.00 0.00 3.32
2528 2849 8.137437 GGAGGGATGAAAATATAATGTGTTGTG 58.863 37.037 0.00 0.00 0.00 3.33
2529 2850 8.821686 AGGGATGAAAATATAATGTGTTGTGA 57.178 30.769 0.00 0.00 0.00 3.58
2530 2851 8.906867 AGGGATGAAAATATAATGTGTTGTGAG 58.093 33.333 0.00 0.00 0.00 3.51
2531 2852 8.902806 GGGATGAAAATATAATGTGTTGTGAGA 58.097 33.333 0.00 0.00 0.00 3.27
2538 2859 9.859427 AAATATAATGTGTTGTGAGATGTTTGG 57.141 29.630 0.00 0.00 0.00 3.28
2539 2860 8.806429 ATATAATGTGTTGTGAGATGTTTGGA 57.194 30.769 0.00 0.00 0.00 3.53
2540 2861 7.707624 ATAATGTGTTGTGAGATGTTTGGAT 57.292 32.000 0.00 0.00 0.00 3.41
2541 2862 5.633830 ATGTGTTGTGAGATGTTTGGATC 57.366 39.130 0.00 0.00 0.00 3.36
2542 2863 4.717877 TGTGTTGTGAGATGTTTGGATCT 58.282 39.130 0.00 0.00 35.27 2.75
2543 2864 4.756642 TGTGTTGTGAGATGTTTGGATCTC 59.243 41.667 0.00 0.00 46.00 2.75
2556 2877 9.956720 GATGTTTGGATCTCAACAATAATAAGG 57.043 33.333 12.40 0.00 34.67 2.69
2557 2878 9.699410 ATGTTTGGATCTCAACAATAATAAGGA 57.301 29.630 12.40 0.00 34.67 3.36
2558 2879 9.699410 TGTTTGGATCTCAACAATAATAAGGAT 57.301 29.630 7.53 0.00 34.67 3.24
2584 2905 7.730364 ACATTTAGCCATCCTTTTATACTCG 57.270 36.000 0.00 0.00 0.00 4.18
2585 2906 7.280356 ACATTTAGCCATCCTTTTATACTCGT 58.720 34.615 0.00 0.00 0.00 4.18
2586 2907 8.426489 ACATTTAGCCATCCTTTTATACTCGTA 58.574 33.333 0.00 0.00 0.00 3.43
2587 2908 8.709646 CATTTAGCCATCCTTTTATACTCGTAC 58.290 37.037 0.00 0.00 0.00 3.67
2588 2909 5.864418 AGCCATCCTTTTATACTCGTACA 57.136 39.130 0.00 0.00 0.00 2.90
2589 2910 6.420913 AGCCATCCTTTTATACTCGTACAT 57.579 37.500 0.00 0.00 0.00 2.29
2590 2911 6.223852 AGCCATCCTTTTATACTCGTACATG 58.776 40.000 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 1.582968 CATGCCAAGAAAGCGTGCT 59.417 52.632 0.00 0.00 40.14 4.40
32 33 4.959723 TGTTGATGTCATTGTCAGACTCA 58.040 39.130 1.31 0.00 36.94 3.41
98 99 4.752146 ACAGTATAGTTACACGGAAAGCC 58.248 43.478 0.00 0.00 0.00 4.35
102 103 6.334989 CCATTGACAGTATAGTTACACGGAA 58.665 40.000 0.00 0.00 0.00 4.30
127 136 9.809096 AGATAGTAACTCATGTTGTAGTCATTG 57.191 33.333 0.00 0.00 37.59 2.82
179 189 6.301720 AAAGATGGTCTTGACGAAGGTCGT 62.302 45.833 2.40 2.40 45.78 4.34
214 224 5.136828 TGGGCAAAGTGAGTTATTTTCTCA 58.863 37.500 0.00 0.00 39.25 3.27
226 236 3.118811 CCTTTTGTCTTTGGGCAAAGTGA 60.119 43.478 0.00 0.00 45.88 3.41
266 276 0.250338 ACGGGTTGGAGTGCTTTCTC 60.250 55.000 0.00 0.00 0.00 2.87
267 277 0.182775 AACGGGTTGGAGTGCTTTCT 59.817 50.000 0.00 0.00 0.00 2.52
268 278 1.029681 AAACGGGTTGGAGTGCTTTC 58.970 50.000 0.00 0.00 0.00 2.62
269 279 1.407618 GAAAACGGGTTGGAGTGCTTT 59.592 47.619 0.00 0.00 0.00 3.51
273 291 0.951558 CTGGAAAACGGGTTGGAGTG 59.048 55.000 0.00 0.00 0.00 3.51
274 292 0.822121 GCTGGAAAACGGGTTGGAGT 60.822 55.000 0.00 0.00 0.00 3.85
323 342 4.099113 GTCATCACCTCACATGAGATCTCA 59.901 45.833 27.03 27.03 44.74 3.27
371 390 2.107366 TCATTGTCATCCTCCGCAGTA 58.893 47.619 0.00 0.00 0.00 2.74
376 395 2.831333 CTCCTTCATTGTCATCCTCCG 58.169 52.381 0.00 0.00 0.00 4.63
388 407 0.757188 ATCTCCGTCGGCTCCTTCAT 60.757 55.000 6.34 0.00 0.00 2.57
398 417 4.871513 TCTCAAAATCCATATCTCCGTCG 58.128 43.478 0.00 0.00 0.00 5.12
413 432 2.557317 GGGTCACTCACGTTCTCAAAA 58.443 47.619 0.00 0.00 0.00 2.44
462 500 5.290885 CCATGTCAAATCTGTTGATGCAATG 59.709 40.000 0.00 0.00 32.44 2.82
464 502 4.523558 TCCATGTCAAATCTGTTGATGCAA 59.476 37.500 0.00 0.00 32.44 4.08
485 523 9.113838 TCAATCAGATTATTCTTAAGTTGCTCC 57.886 33.333 1.63 0.00 0.00 4.70
662 772 8.196103 GGACTCGGTACTATATGTTCTTTTTCT 58.804 37.037 0.00 0.00 0.00 2.52
663 773 7.167136 CGGACTCGGTACTATATGTTCTTTTTC 59.833 40.741 0.00 0.00 0.00 2.29
666 776 6.069684 CGGACTCGGTACTATATGTTCTTT 57.930 41.667 0.00 0.00 0.00 2.52
667 777 5.686159 CGGACTCGGTACTATATGTTCTT 57.314 43.478 0.00 0.00 0.00 2.52
688 798 2.591311 CGTCAACAACACCGTCCCG 61.591 63.158 0.00 0.00 0.00 5.14
689 799 1.493134 GACGTCAACAACACCGTCCC 61.493 60.000 11.55 0.00 42.76 4.46
690 800 1.929376 GACGTCAACAACACCGTCC 59.071 57.895 11.55 0.00 42.76 4.79
692 802 1.003851 CAAGACGTCAACAACACCGT 58.996 50.000 19.50 0.00 36.04 4.83
693 803 1.003851 ACAAGACGTCAACAACACCG 58.996 50.000 19.50 0.00 0.00 4.94
694 804 1.735571 ACACAAGACGTCAACAACACC 59.264 47.619 19.50 0.00 0.00 4.16
695 805 3.120477 TGAACACAAGACGTCAACAACAC 60.120 43.478 19.50 4.93 0.00 3.32
698 808 3.997681 TCTTGAACACAAGACGTCAACAA 59.002 39.130 19.50 11.00 43.06 2.83
699 809 3.591023 TCTTGAACACAAGACGTCAACA 58.409 40.909 19.50 4.02 43.06 3.33
702 812 3.063452 GCTTTCTTGAACACAAGACGTCA 59.937 43.478 19.50 0.00 46.10 4.35
703 813 3.608456 GCTTTCTTGAACACAAGACGTC 58.392 45.455 7.70 7.70 46.10 4.34
704 814 2.030457 CGCTTTCTTGAACACAAGACGT 59.970 45.455 11.39 0.00 46.10 4.34
906 1093 4.794439 GGGTTTGATTGGCGCGGC 62.794 66.667 27.61 27.61 0.00 6.53
913 1100 1.861542 TTGCGGCGAGGGTTTGATTG 61.862 55.000 12.98 0.00 0.00 2.67
1605 1808 3.003173 CGACCAAGAGAGGGGGCA 61.003 66.667 0.00 0.00 30.28 5.36
1654 1858 3.200593 CAGCCGCAGCACAGATCC 61.201 66.667 0.00 0.00 43.56 3.36
1731 1935 6.938596 CCATTCAGGATTCAGCTCATATACAA 59.061 38.462 0.00 0.00 41.22 2.41
1834 2038 4.684484 TGCAGATCAGAATGTAGCTCAT 57.316 40.909 0.00 0.00 38.57 2.90
1905 2109 3.222173 TGACAACAGCAGGGTTAACAT 57.778 42.857 8.10 0.00 0.00 2.71
1932 2136 5.848921 AGAATAGAATAGCCCCTTCACAGAT 59.151 40.000 0.00 0.00 0.00 2.90
2077 2345 8.630917 GGACATTAGCATACTACAAGTTCTAGA 58.369 37.037 0.00 0.00 0.00 2.43
2090 2358 4.703897 TGCTGTTAGGGACATTAGCATAC 58.296 43.478 0.00 0.00 37.69 2.39
2141 2436 3.071479 TCAACCACTGCCGTAATCTTTC 58.929 45.455 0.00 0.00 0.00 2.62
2150 2445 1.742761 AGATGAATCAACCACTGCCG 58.257 50.000 0.00 0.00 0.00 5.69
2166 2461 2.978156 TTGGGCCAAGAACAGAAGAT 57.022 45.000 16.66 0.00 0.00 2.40
2203 2516 4.226846 AGACATGAAATCTGTCCATGGTCT 59.773 41.667 12.58 0.00 43.24 3.85
2268 2581 2.171003 TGCGAGAACTCAAGGAGATCA 58.829 47.619 0.00 0.00 34.57 2.92
2285 2599 8.559536 TCCAAGCTATCTTAATTCTTAATTGCG 58.440 33.333 0.00 0.00 32.38 4.85
2303 2617 6.570378 GCTGCATTTAAAAGAACTCCAAGCTA 60.570 38.462 0.00 0.00 0.00 3.32
2378 2699 1.317613 AAACCGCAGCACAAAGATCA 58.682 45.000 0.00 0.00 0.00 2.92
2405 2726 6.746745 TTTTTCAGGAGTAAAGAAACACGT 57.253 33.333 0.00 0.00 31.60 4.49
2426 2747 4.079253 AGCGGACAGAATACATTGGTTTT 58.921 39.130 0.00 0.00 0.00 2.43
2430 2751 2.905075 TCAGCGGACAGAATACATTGG 58.095 47.619 0.00 0.00 0.00 3.16
2431 2752 4.787563 GCATTCAGCGGACAGAATACATTG 60.788 45.833 0.00 0.00 31.43 2.82
2432 2753 3.313526 GCATTCAGCGGACAGAATACATT 59.686 43.478 0.00 0.00 31.43 2.71
2433 2754 2.874701 GCATTCAGCGGACAGAATACAT 59.125 45.455 0.00 0.00 31.43 2.29
2434 2755 2.279741 GCATTCAGCGGACAGAATACA 58.720 47.619 0.00 0.00 31.43 2.29
2446 2767 4.589216 TGCCCAATTATAAGCATTCAGC 57.411 40.909 0.00 0.00 46.19 4.26
2452 2773 6.486657 GTCACTCTAATGCCCAATTATAAGCA 59.513 38.462 0.20 0.20 40.00 3.91
2453 2774 6.072452 GGTCACTCTAATGCCCAATTATAAGC 60.072 42.308 0.00 0.00 30.26 3.09
2454 2775 7.173907 CAGGTCACTCTAATGCCCAATTATAAG 59.826 40.741 0.00 0.00 30.26 1.73
2455 2776 6.998074 CAGGTCACTCTAATGCCCAATTATAA 59.002 38.462 0.00 0.00 30.26 0.98
2456 2777 6.328934 TCAGGTCACTCTAATGCCCAATTATA 59.671 38.462 0.00 0.00 30.26 0.98
2457 2778 5.132648 TCAGGTCACTCTAATGCCCAATTAT 59.867 40.000 0.00 0.00 30.26 1.28
2458 2779 4.473196 TCAGGTCACTCTAATGCCCAATTA 59.527 41.667 0.00 0.00 0.00 1.40
2459 2780 3.266772 TCAGGTCACTCTAATGCCCAATT 59.733 43.478 0.00 0.00 0.00 2.32
2460 2781 2.846206 TCAGGTCACTCTAATGCCCAAT 59.154 45.455 0.00 0.00 0.00 3.16
2461 2782 2.265367 TCAGGTCACTCTAATGCCCAA 58.735 47.619 0.00 0.00 0.00 4.12
2462 2783 1.951209 TCAGGTCACTCTAATGCCCA 58.049 50.000 0.00 0.00 0.00 5.36
2463 2784 3.567478 ATTCAGGTCACTCTAATGCCC 57.433 47.619 0.00 0.00 0.00 5.36
2464 2785 6.116126 ACTAAATTCAGGTCACTCTAATGCC 58.884 40.000 0.00 0.00 0.00 4.40
2465 2786 7.467623 CAACTAAATTCAGGTCACTCTAATGC 58.532 38.462 0.00 0.00 0.00 3.56
2466 2787 7.119699 TGCAACTAAATTCAGGTCACTCTAATG 59.880 37.037 0.00 0.00 0.00 1.90
2467 2788 7.168219 TGCAACTAAATTCAGGTCACTCTAAT 58.832 34.615 0.00 0.00 0.00 1.73
2468 2789 6.530120 TGCAACTAAATTCAGGTCACTCTAA 58.470 36.000 0.00 0.00 0.00 2.10
2469 2790 6.109156 TGCAACTAAATTCAGGTCACTCTA 57.891 37.500 0.00 0.00 0.00 2.43
2470 2791 4.973168 TGCAACTAAATTCAGGTCACTCT 58.027 39.130 0.00 0.00 0.00 3.24
2471 2792 5.886960 ATGCAACTAAATTCAGGTCACTC 57.113 39.130 0.00 0.00 0.00 3.51
2472 2793 6.476378 ACTATGCAACTAAATTCAGGTCACT 58.524 36.000 0.00 0.00 0.00 3.41
2473 2794 6.743575 ACTATGCAACTAAATTCAGGTCAC 57.256 37.500 0.00 0.00 0.00 3.67
2474 2795 7.094377 GGAAACTATGCAACTAAATTCAGGTCA 60.094 37.037 0.00 0.00 0.00 4.02
2475 2796 7.121315 AGGAAACTATGCAACTAAATTCAGGTC 59.879 37.037 0.00 0.00 40.61 3.85
2476 2797 6.948309 AGGAAACTATGCAACTAAATTCAGGT 59.052 34.615 0.00 0.00 40.61 4.00
2477 2798 7.253422 CAGGAAACTATGCAACTAAATTCAGG 58.747 38.462 0.00 0.00 40.21 3.86
2478 2799 7.121168 TCCAGGAAACTATGCAACTAAATTCAG 59.879 37.037 0.00 0.00 40.21 3.02
2479 2800 6.945435 TCCAGGAAACTATGCAACTAAATTCA 59.055 34.615 0.00 0.00 40.21 2.57
2480 2801 7.391148 TCCAGGAAACTATGCAACTAAATTC 57.609 36.000 0.00 0.00 40.21 2.17
2481 2802 6.378280 CCTCCAGGAAACTATGCAACTAAATT 59.622 38.462 0.00 0.00 40.21 1.82
2482 2803 5.888161 CCTCCAGGAAACTATGCAACTAAAT 59.112 40.000 0.00 0.00 40.21 1.40
2483 2804 5.253330 CCTCCAGGAAACTATGCAACTAAA 58.747 41.667 0.00 0.00 40.21 1.85
2484 2805 4.324254 CCCTCCAGGAAACTATGCAACTAA 60.324 45.833 0.00 0.00 40.21 2.24
2485 2806 3.199946 CCCTCCAGGAAACTATGCAACTA 59.800 47.826 0.00 0.00 40.21 2.24
2486 2807 2.025887 CCCTCCAGGAAACTATGCAACT 60.026 50.000 0.00 0.00 40.21 3.16
2487 2808 2.026262 TCCCTCCAGGAAACTATGCAAC 60.026 50.000 0.00 0.00 43.78 4.17
2488 2809 2.274542 TCCCTCCAGGAAACTATGCAA 58.725 47.619 0.00 0.00 43.78 4.08
2489 2810 1.965414 TCCCTCCAGGAAACTATGCA 58.035 50.000 0.00 0.00 43.78 3.96
2499 2820 7.006509 ACACATTATATTTTCATCCCTCCAGG 58.993 38.462 0.00 0.00 0.00 4.45
2500 2821 8.355169 CAACACATTATATTTTCATCCCTCCAG 58.645 37.037 0.00 0.00 0.00 3.86
2501 2822 7.838696 ACAACACATTATATTTTCATCCCTCCA 59.161 33.333 0.00 0.00 0.00 3.86
2502 2823 8.137437 CACAACACATTATATTTTCATCCCTCC 58.863 37.037 0.00 0.00 0.00 4.30
2503 2824 8.902806 TCACAACACATTATATTTTCATCCCTC 58.097 33.333 0.00 0.00 0.00 4.30
2504 2825 8.821686 TCACAACACATTATATTTTCATCCCT 57.178 30.769 0.00 0.00 0.00 4.20
2505 2826 8.902806 TCTCACAACACATTATATTTTCATCCC 58.097 33.333 0.00 0.00 0.00 3.85
2512 2833 9.859427 CCAAACATCTCACAACACATTATATTT 57.141 29.630 0.00 0.00 0.00 1.40
2513 2834 9.241919 TCCAAACATCTCACAACACATTATATT 57.758 29.630 0.00 0.00 0.00 1.28
2514 2835 8.806429 TCCAAACATCTCACAACACATTATAT 57.194 30.769 0.00 0.00 0.00 0.86
2515 2836 8.806429 ATCCAAACATCTCACAACACATTATA 57.194 30.769 0.00 0.00 0.00 0.98
2516 2837 7.613022 AGATCCAAACATCTCACAACACATTAT 59.387 33.333 0.00 0.00 0.00 1.28
2517 2838 6.942005 AGATCCAAACATCTCACAACACATTA 59.058 34.615 0.00 0.00 0.00 1.90
2518 2839 5.771666 AGATCCAAACATCTCACAACACATT 59.228 36.000 0.00 0.00 0.00 2.71
2519 2840 5.319453 AGATCCAAACATCTCACAACACAT 58.681 37.500 0.00 0.00 0.00 3.21
2520 2841 4.717877 AGATCCAAACATCTCACAACACA 58.282 39.130 0.00 0.00 0.00 3.72
2521 2842 5.288543 GAGATCCAAACATCTCACAACAC 57.711 43.478 5.72 0.00 45.77 3.32
2530 2851 9.956720 CCTTATTATTGTTGAGATCCAAACATC 57.043 33.333 10.64 0.00 36.36 3.06
2531 2852 9.699410 TCCTTATTATTGTTGAGATCCAAACAT 57.301 29.630 10.64 5.47 36.36 2.71
2532 2853 9.699410 ATCCTTATTATTGTTGAGATCCAAACA 57.301 29.630 6.70 6.70 36.36 2.83
2558 2879 9.268268 CGAGTATAAAAGGATGGCTAAATGTAA 57.732 33.333 0.00 0.00 0.00 2.41
2559 2880 8.426489 ACGAGTATAAAAGGATGGCTAAATGTA 58.574 33.333 0.00 0.00 0.00 2.29
2560 2881 7.280356 ACGAGTATAAAAGGATGGCTAAATGT 58.720 34.615 0.00 0.00 0.00 2.71
2561 2882 7.730364 ACGAGTATAAAAGGATGGCTAAATG 57.270 36.000 0.00 0.00 0.00 2.32
2562 2883 8.426489 TGTACGAGTATAAAAGGATGGCTAAAT 58.574 33.333 0.00 0.00 0.00 1.40
2563 2884 7.784037 TGTACGAGTATAAAAGGATGGCTAAA 58.216 34.615 0.00 0.00 0.00 1.85
2564 2885 7.350744 TGTACGAGTATAAAAGGATGGCTAA 57.649 36.000 0.00 0.00 0.00 3.09
2565 2886 6.964807 TGTACGAGTATAAAAGGATGGCTA 57.035 37.500 0.00 0.00 0.00 3.93
2566 2887 5.864418 TGTACGAGTATAAAAGGATGGCT 57.136 39.130 0.00 0.00 0.00 4.75
2567 2888 6.467723 CATGTACGAGTATAAAAGGATGGC 57.532 41.667 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.