Multiple sequence alignment - TraesCS3A01G011400

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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 TraesCS3A01G011400 chr3A 100.000 2760 0 0 1 2760 9209098 9211857 0.000000e+00 5097
1 TraesCS3A01G011400 chr3A 83.412 639 58 18 1783 2398 9230343 9230956 1.440000e-152 549
2 TraesCS3A01G011400 chr3A 78.418 607 51 31 570 1152 9229488 9230038 3.430000e-84 322
3 TraesCS3A01G011400 chr3A 89.732 224 23 0 1562 1785 9230040 9230263 1.250000e-73 287
4 TraesCS3A01G011400 chr3D 94.580 1974 75 12 1 1949 346851 344885 0.000000e+00 3024
5 TraesCS3A01G011400 chrUn 86.297 883 73 21 1543 2402 35909234 35910091 0.000000e+00 917
6 TraesCS3A01G011400 chrUn 81.818 385 36 13 563 920 35908666 35909043 2.690000e-75 292
7 TraesCS3A01G011400 chrUn 84.434 212 25 7 2516 2725 35910116 35910321 4.660000e-48 202
8 TraesCS3A01G011400 chrUn 80.137 146 26 3 1289 1433 293209731 293209874 3.760000e-19 106
9 TraesCS3A01G011400 chr3B 86.297 883 73 21 1543 2402 6170293 6171150 0.000000e+00 917
10 TraesCS3A01G011400 chr3B 81.818 385 36 13 563 920 6169725 6170102 2.690000e-75 292
11 TraesCS3A01G011400 chr3B 84.434 212 25 7 2516 2725 6171175 6171380 4.660000e-48 202
12 TraesCS3A01G011400 chr2D 80.456 307 46 12 1151 1451 508106696 508106398 3.580000e-54 222
13 TraesCS3A01G011400 chr2D 77.409 301 46 15 1151 1446 378895609 378895326 2.850000e-35 159
14 TraesCS3A01G011400 chr2D 82.390 159 18 8 1164 1321 470429603 470429752 2.230000e-26 130
15 TraesCS3A01G011400 chr2B 78.758 306 52 11 1151 1451 597274382 597274085 2.810000e-45 193
16 TraesCS3A01G011400 chr2B 76.868 281 49 13 1147 1418 719138272 719138545 7.970000e-31 145
17 TraesCS3A01G011400 chr7A 79.211 279 36 18 1156 1425 481570841 481570576 1.020000e-39 174
18 TraesCS3A01G011400 chr7A 80.137 146 26 3 1289 1433 33653158 33653301 3.760000e-19 106
19 TraesCS3A01G011400 chr5D 85.057 174 21 4 1151 1321 435928787 435928616 3.650000e-39 172
20 TraesCS3A01G011400 chr2A 82.412 199 24 6 1151 1345 513838952 513838761 2.200000e-36 163
21 TraesCS3A01G011400 chr2A 78.682 258 41 10 1153 1403 651617947 651617697 2.850000e-35 159
22 TraesCS3A01G011400 chr4B 77.155 232 37 12 1225 1450 95432746 95432525 1.340000e-23 121


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 TraesCS3A01G011400 chr3A 9209098 9211857 2759 False 5097.000000 5097 100.000 1 2760 1 chr3A.!!$F1 2759
1 TraesCS3A01G011400 chr3A 9229488 9230956 1468 False 386.000000 549 83.854 570 2398 3 chr3A.!!$F2 1828
2 TraesCS3A01G011400 chr3D 344885 346851 1966 True 3024.000000 3024 94.580 1 1949 1 chr3D.!!$R1 1948
3 TraesCS3A01G011400 chrUn 35908666 35910321 1655 False 470.333333 917 84.183 563 2725 3 chrUn.!!$F2 2162
4 TraesCS3A01G011400 chr3B 6169725 6171380 1655 False 470.333333 917 84.183 563 2725 3 chr3B.!!$F1 2162

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
449 470 0.096976 CCGTGCCACATTCTTAAGCG 59.903 55.0 0.0 0.0 0.0 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2434 2631 0.392461 TTGGCAGATGGTTACCGAGC 60.392 55.0 0.0 0.0 0.0 5.03 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
180 182 3.393089 ACTCAGAAAAGCTCATCGTGT 57.607 42.857 0.00 0.00 0.00 4.49
188 190 6.857964 CAGAAAAGCTCATCGTGTATGTTTTT 59.142 34.615 0.00 0.00 36.89 1.94
344 365 3.302365 AATTCCCAACACGCATTCTTG 57.698 42.857 0.00 0.00 0.00 3.02
362 383 8.301720 GCATTCTTGAATAGCCATTGATAATGA 58.698 33.333 3.24 0.00 41.46 2.57
405 426 8.472413 CCAGATTTCCAAATACAGATGAACATT 58.528 33.333 0.00 0.00 0.00 2.71
432 453 1.258982 GTATGCGCTGAACATTCTCCG 59.741 52.381 9.73 0.00 0.00 4.63
449 470 0.096976 CCGTGCCACATTCTTAAGCG 59.903 55.000 0.00 0.00 0.00 4.68
486 507 2.363276 ACATCTACCGTGCGGGGA 60.363 61.111 15.44 12.31 41.60 4.81
503 524 4.935205 GCGGGGATTTTGAGCTTTTTATTT 59.065 37.500 0.00 0.00 0.00 1.40
506 527 7.279981 GCGGGGATTTTGAGCTTTTTATTTATT 59.720 33.333 0.00 0.00 0.00 1.40
703 742 6.122850 TGAAGAAACAGTCAACATCACAAG 57.877 37.500 0.00 0.00 0.00 3.16
886 935 1.011019 CTCTACGTACGCGAGCAGG 60.011 63.158 15.93 5.67 42.00 4.85
968 1021 3.264574 TGGTGCTACCATTCCTTGC 57.735 52.632 4.16 0.00 44.79 4.01
1006 1073 0.105593 CTGGGACGTGATCATGGAGG 59.894 60.000 18.97 1.38 0.00 4.30
1017 1084 0.547471 TCATGGAGGGCTCTTCCACA 60.547 55.000 6.89 0.00 36.24 4.17
1044 1114 1.942677 CTCTCTTGCTGGCTCTCATG 58.057 55.000 0.00 0.00 0.00 3.07
1107 1192 5.939457 GGTAACTACTCAATTGCTGTTTCC 58.061 41.667 0.00 6.59 0.00 3.13
1108 1193 5.106277 GGTAACTACTCAATTGCTGTTTCCC 60.106 44.000 0.00 3.83 0.00 3.97
1114 1205 2.061028 CAATTGCTGTTTCCCTTTCGC 58.939 47.619 0.00 0.00 0.00 4.70
1127 1218 2.099098 CCCTTTCGCACACACTCTTTTT 59.901 45.455 0.00 0.00 0.00 1.94
1205 1296 9.294030 CTATCAATTTTTCCTAGACATGCAAAC 57.706 33.333 0.00 0.00 0.00 2.93
1278 1369 9.472361 TTTCGTATTACTCTATGTAGAATTGCC 57.528 33.333 0.00 0.00 32.08 4.52
1280 1371 6.033619 CGTATTACTCTATGTAGAATTGCCGC 59.966 42.308 0.00 0.00 32.08 6.53
1360 1452 3.165875 ACAGTATATGTGCTAGGGCGAT 58.834 45.455 0.00 0.00 41.91 4.58
1367 1459 0.461961 GTGCTAGGGCGATCAGAACT 59.538 55.000 0.00 0.00 42.25 3.01
1368 1460 0.747255 TGCTAGGGCGATCAGAACTC 59.253 55.000 0.00 0.00 42.25 3.01
1516 1608 5.980715 TGCATTTCGTTTAAAAAGGTTCCTC 59.019 36.000 0.00 0.00 0.00 3.71
1524 1616 0.106419 AAAAGGTTCCTCCGGCAACA 60.106 50.000 0.00 0.00 41.99 3.33
1570 1662 9.297037 AGTATGTTTAATTATTATGTCTGGCCC 57.703 33.333 0.00 0.00 0.00 5.80
1753 1845 1.794437 GCTGCGAACGTCGACTTCTAT 60.794 52.381 14.70 0.00 43.74 1.98
1764 1856 4.504097 CGTCGACTTCTATGCATGAATCAA 59.496 41.667 14.70 0.00 0.00 2.57
1811 1985 4.155063 ACAAGTATCATGCACAGCCATA 57.845 40.909 0.00 0.00 0.00 2.74
1849 2023 6.594788 ATTGTTGTCCTCTTTTGTATGCAT 57.405 33.333 3.79 3.79 0.00 3.96
1981 2156 4.096833 TGCCTTCATGATCATTACTTGCAC 59.903 41.667 5.16 0.00 0.00 4.57
1985 2160 7.469043 GCCTTCATGATCATTACTTGCACATTA 60.469 37.037 5.16 0.00 0.00 1.90
1998 2173 0.659427 CACATTATGGCCAGCGTCAG 59.341 55.000 13.05 1.00 0.00 3.51
2012 2187 1.511850 CGTCAGCAACTGGATTGTCA 58.488 50.000 0.00 0.00 40.77 3.58
2035 2210 3.622612 CCATCATCGCTGTTATTGTCACA 59.377 43.478 0.00 0.00 0.00 3.58
2037 2212 4.661993 TCATCGCTGTTATTGTCACAAC 57.338 40.909 0.00 0.00 0.00 3.32
2038 2213 3.435327 TCATCGCTGTTATTGTCACAACC 59.565 43.478 0.00 0.00 0.00 3.77
2068 2243 1.132721 CCCCACCTCTCCATCCTCATA 60.133 57.143 0.00 0.00 0.00 2.15
2108 2283 2.158449 GTCGTCACCATCAGCTTCTTTG 59.842 50.000 0.00 0.00 0.00 2.77
2109 2284 2.037121 TCGTCACCATCAGCTTCTTTGA 59.963 45.455 0.00 0.00 0.00 2.69
2110 2285 2.414481 CGTCACCATCAGCTTCTTTGAG 59.586 50.000 0.00 0.00 0.00 3.02
2173 2349 2.822561 TGTTCCAAAGCAACTGACACAA 59.177 40.909 0.00 0.00 0.00 3.33
2208 2405 5.597806 CTGTGCCATTTCATCATTGCTAAT 58.402 37.500 0.00 0.00 0.00 1.73
2209 2406 6.712179 TGTGCCATTTCATCATTGCTAATA 57.288 33.333 0.00 0.00 0.00 0.98
2230 2427 3.370840 AAATAGGTCATGCTGCAAGGA 57.629 42.857 6.36 4.71 40.11 3.36
2241 2438 2.024080 TGCTGCAAGGAAAATCCCCTAT 60.024 45.455 0.00 0.00 37.19 2.57
2280 2477 2.712057 CACAGTTGTGGGAAAGATGC 57.288 50.000 4.34 0.00 42.10 3.91
2296 2493 6.542005 GGAAAGATGCAAAAAGGAAAGGAAAA 59.458 34.615 0.00 0.00 0.00 2.29
2392 2589 2.360165 GGGCTTCATGTTGACATCCATC 59.640 50.000 0.00 0.00 33.61 3.51
2398 2595 6.255020 GCTTCATGTTGACATCCATCAAAATC 59.745 38.462 0.00 0.00 40.22 2.17
2400 2597 7.470935 TCATGTTGACATCCATCAAAATCTT 57.529 32.000 0.00 0.00 40.22 2.40
2403 2600 6.916440 TGTTGACATCCATCAAAATCTTCTG 58.084 36.000 0.00 0.00 40.22 3.02
2404 2601 6.491062 TGTTGACATCCATCAAAATCTTCTGT 59.509 34.615 0.00 0.00 40.22 3.41
2406 2603 8.680903 GTTGACATCCATCAAAATCTTCTGTAT 58.319 33.333 0.00 0.00 40.22 2.29
2408 2605 8.680001 TGACATCCATCAAAATCTTCTGTATTG 58.320 33.333 0.00 0.00 0.00 1.90
2409 2606 7.486647 ACATCCATCAAAATCTTCTGTATTGC 58.513 34.615 0.00 0.00 0.00 3.56
2410 2607 6.455360 TCCATCAAAATCTTCTGTATTGCC 57.545 37.500 0.00 0.00 0.00 4.52
2411 2608 5.951148 TCCATCAAAATCTTCTGTATTGCCA 59.049 36.000 0.00 0.00 0.00 4.92
2412 2609 6.436847 TCCATCAAAATCTTCTGTATTGCCAA 59.563 34.615 0.00 0.00 0.00 4.52
2414 2611 7.277098 CCATCAAAATCTTCTGTATTGCCAAAG 59.723 37.037 0.00 0.00 0.00 2.77
2417 2614 8.084073 TCAAAATCTTCTGTATTGCCAAAGAAG 58.916 33.333 9.97 9.97 44.54 2.85
2418 2615 5.573337 ATCTTCTGTATTGCCAAAGAAGC 57.427 39.130 11.00 0.00 43.43 3.86
2419 2616 4.655963 TCTTCTGTATTGCCAAAGAAGCT 58.344 39.130 11.00 0.00 43.43 3.74
2421 2618 6.418101 TCTTCTGTATTGCCAAAGAAGCTAT 58.582 36.000 11.00 0.00 43.43 2.97
2422 2619 7.564793 TCTTCTGTATTGCCAAAGAAGCTATA 58.435 34.615 11.00 0.00 43.43 1.31
2424 2621 8.752005 TTCTGTATTGCCAAAGAAGCTATAAT 57.248 30.769 0.00 0.00 31.40 1.28
2425 2622 8.752005 TCTGTATTGCCAAAGAAGCTATAATT 57.248 30.769 0.00 0.00 31.40 1.40
2426 2623 8.840321 TCTGTATTGCCAAAGAAGCTATAATTC 58.160 33.333 0.00 0.00 31.40 2.17
2427 2624 8.518430 TGTATTGCCAAAGAAGCTATAATTCA 57.482 30.769 0.00 0.00 31.40 2.57
2428 2625 8.623903 TGTATTGCCAAAGAAGCTATAATTCAG 58.376 33.333 0.00 0.00 31.40 3.02
2429 2626 6.455360 TTGCCAAAGAAGCTATAATTCAGG 57.545 37.500 0.00 0.00 0.00 3.86
2430 2627 4.889409 TGCCAAAGAAGCTATAATTCAGGG 59.111 41.667 0.00 0.00 0.00 4.45
2431 2628 4.261783 GCCAAAGAAGCTATAATTCAGGGC 60.262 45.833 0.00 0.00 34.52 5.19
2432 2629 4.023707 CCAAAGAAGCTATAATTCAGGGCG 60.024 45.833 0.00 0.00 0.00 6.13
2433 2630 4.689612 AAGAAGCTATAATTCAGGGCGA 57.310 40.909 0.00 0.00 0.00 5.54
2434 2631 4.264460 AGAAGCTATAATTCAGGGCGAG 57.736 45.455 0.00 0.00 0.00 5.03
2435 2632 2.464157 AGCTATAATTCAGGGCGAGC 57.536 50.000 0.00 0.00 0.00 5.03
2436 2633 1.974236 AGCTATAATTCAGGGCGAGCT 59.026 47.619 0.00 0.00 34.05 4.09
2437 2634 2.028567 AGCTATAATTCAGGGCGAGCTC 60.029 50.000 2.73 2.73 33.65 4.09
2438 2635 2.600731 CTATAATTCAGGGCGAGCTCG 58.399 52.381 31.37 31.37 43.27 5.03
2439 2636 0.034059 ATAATTCAGGGCGAGCTCGG 59.966 55.000 35.10 19.74 40.23 4.63
2440 2637 1.327690 TAATTCAGGGCGAGCTCGGT 61.328 55.000 35.10 7.49 40.23 4.69
2441 2638 1.327690 AATTCAGGGCGAGCTCGGTA 61.328 55.000 35.10 14.31 40.23 4.02
2442 2639 1.327690 ATTCAGGGCGAGCTCGGTAA 61.328 55.000 35.10 15.24 40.23 2.85
2443 2640 2.202756 CAGGGCGAGCTCGGTAAC 60.203 66.667 35.10 19.36 40.23 2.50
2444 2641 3.459063 AGGGCGAGCTCGGTAACC 61.459 66.667 35.10 26.46 40.23 2.85
2445 2642 3.766691 GGGCGAGCTCGGTAACCA 61.767 66.667 35.10 0.00 40.23 3.67
2446 2643 2.499685 GGCGAGCTCGGTAACCAT 59.500 61.111 35.10 0.00 40.23 3.55
2447 2644 1.591863 GGCGAGCTCGGTAACCATC 60.592 63.158 35.10 16.82 40.23 3.51
2448 2645 1.437986 GCGAGCTCGGTAACCATCT 59.562 57.895 35.10 0.00 40.23 2.90
2449 2646 0.872021 GCGAGCTCGGTAACCATCTG 60.872 60.000 35.10 5.37 40.23 2.90
2450 2647 0.872021 CGAGCTCGGTAACCATCTGC 60.872 60.000 28.40 0.00 35.37 4.26
2451 2648 0.530870 GAGCTCGGTAACCATCTGCC 60.531 60.000 0.00 0.00 0.00 4.85
2452 2649 1.220749 GCTCGGTAACCATCTGCCA 59.779 57.895 0.00 0.00 0.00 4.92
2453 2650 0.392461 GCTCGGTAACCATCTGCCAA 60.392 55.000 0.00 0.00 0.00 4.52
2454 2651 1.948611 GCTCGGTAACCATCTGCCAAA 60.949 52.381 0.00 0.00 0.00 3.28
2455 2652 2.432444 CTCGGTAACCATCTGCCAAAA 58.568 47.619 0.00 0.00 0.00 2.44
2456 2653 2.817258 CTCGGTAACCATCTGCCAAAAA 59.183 45.455 0.00 0.00 0.00 1.94
2512 2709 3.634397 CCAGTCCATGGTAATGTGACT 57.366 47.619 12.58 2.61 44.91 3.41
2513 2710 3.955471 CCAGTCCATGGTAATGTGACTT 58.045 45.455 12.58 0.00 44.91 3.01
2514 2711 3.691118 CCAGTCCATGGTAATGTGACTTG 59.309 47.826 12.58 0.00 44.91 3.16
2527 2724 7.013274 GGTAATGTGACTTGCCATGTATATGTT 59.987 37.037 0.00 0.00 31.80 2.71
2529 2726 7.734924 ATGTGACTTGCCATGTATATGTTAG 57.265 36.000 0.00 0.00 32.21 2.34
2532 2730 7.826744 TGTGACTTGCCATGTATATGTTAGAAA 59.173 33.333 0.00 0.00 32.21 2.52
2558 2756 7.894376 AAAGTTTCAATAAACATCATGCCAG 57.106 32.000 4.04 0.00 46.18 4.85
2561 2759 6.869913 AGTTTCAATAAACATCATGCCAGTTG 59.130 34.615 4.04 0.00 46.18 3.16
2604 2802 1.373748 TCTGCCGCGACAACCTTAC 60.374 57.895 8.23 0.00 0.00 2.34
2605 2803 1.374252 CTGCCGCGACAACCTTACT 60.374 57.895 8.23 0.00 0.00 2.24
2607 2805 2.388232 GCCGCGACAACCTTACTGG 61.388 63.158 8.23 0.00 42.93 4.00
2609 2807 1.666553 CGCGACAACCTTACTGGCA 60.667 57.895 0.00 0.00 40.22 4.92
2610 2808 1.225376 CGCGACAACCTTACTGGCAA 61.225 55.000 0.00 0.00 40.22 4.52
2617 2815 0.320771 ACCTTACTGGCAAGCTCGTG 60.321 55.000 0.00 0.00 40.22 4.35
2622 2820 2.280797 TGGCAAGCTCGTGTGTCC 60.281 61.111 0.00 0.00 0.00 4.02
2624 2822 1.891919 GGCAAGCTCGTGTGTCCAA 60.892 57.895 0.00 0.00 0.00 3.53
2625 2823 1.571460 GCAAGCTCGTGTGTCCAAG 59.429 57.895 0.00 0.00 0.00 3.61
2626 2824 1.160329 GCAAGCTCGTGTGTCCAAGT 61.160 55.000 0.00 0.00 0.00 3.16
2627 2825 0.583438 CAAGCTCGTGTGTCCAAGTG 59.417 55.000 0.00 0.00 0.00 3.16
2628 2826 0.464036 AAGCTCGTGTGTCCAAGTGA 59.536 50.000 0.00 0.00 0.00 3.41
2629 2827 0.249489 AGCTCGTGTGTCCAAGTGAC 60.249 55.000 0.00 0.00 44.72 3.67
2630 2828 0.249489 GCTCGTGTGTCCAAGTGACT 60.249 55.000 0.00 0.00 44.75 3.41
2631 2829 1.000607 GCTCGTGTGTCCAAGTGACTA 60.001 52.381 0.00 0.00 44.75 2.59
2632 2830 2.662700 CTCGTGTGTCCAAGTGACTAC 58.337 52.381 0.00 0.00 44.75 2.73
2633 2831 2.025898 TCGTGTGTCCAAGTGACTACA 58.974 47.619 0.00 0.00 44.75 2.74
2634 2832 2.626266 TCGTGTGTCCAAGTGACTACAT 59.374 45.455 0.00 0.00 44.75 2.29
2635 2833 2.987149 CGTGTGTCCAAGTGACTACATC 59.013 50.000 0.00 0.00 44.75 3.06
2636 2834 3.305403 CGTGTGTCCAAGTGACTACATCT 60.305 47.826 0.00 0.00 44.75 2.90
2647 2845 7.119699 CCAAGTGACTACATCTAAGCATTCAAA 59.880 37.037 0.00 0.00 0.00 2.69
2655 2853 5.184479 ACATCTAAGCATTCAAAGTGCACAT 59.816 36.000 21.04 3.48 44.87 3.21
2656 2854 5.710513 TCTAAGCATTCAAAGTGCACATT 57.289 34.783 21.04 11.14 44.87 2.71
2667 2865 1.542915 AGTGCACATTGATGTCAAGCC 59.457 47.619 21.04 0.00 39.39 4.35
2669 2867 2.094390 GTGCACATTGATGTCAAGCCAT 60.094 45.455 13.17 0.00 39.39 4.40
2686 2884 3.446161 AGCCATTTGACATCCAAGATGTG 59.554 43.478 14.62 1.23 35.94 3.21
2710 2908 7.223582 GTGGACATACATGTTCTACTTCATGAG 59.776 40.741 2.30 0.00 42.52 2.90
2717 2915 6.432162 ACATGTTCTACTTCATGAGTGCAAAT 59.568 34.615 11.27 0.00 42.52 2.32
2718 2916 7.607607 ACATGTTCTACTTCATGAGTGCAAATA 59.392 33.333 11.27 0.00 42.52 1.40
2719 2917 7.364522 TGTTCTACTTCATGAGTGCAAATAC 57.635 36.000 0.00 0.00 39.48 1.89
2720 2918 7.161404 TGTTCTACTTCATGAGTGCAAATACT 58.839 34.615 0.00 0.00 39.48 2.12
2722 2920 7.601073 TCTACTTCATGAGTGCAAATACTTG 57.399 36.000 0.00 0.00 39.48 3.16
2723 2921 7.161404 TCTACTTCATGAGTGCAAATACTTGT 58.839 34.615 0.00 0.00 39.48 3.16
2724 2922 8.311109 TCTACTTCATGAGTGCAAATACTTGTA 58.689 33.333 0.00 0.00 39.48 2.41
2725 2923 7.133891 ACTTCATGAGTGCAAATACTTGTAC 57.866 36.000 0.00 0.00 45.52 2.90
2731 2929 3.014623 GTGCAAATACTTGTACTCCCCC 58.985 50.000 0.00 0.00 42.84 5.40
2732 2930 2.285977 GCAAATACTTGTACTCCCCCG 58.714 52.381 0.00 0.00 34.79 5.73
2733 2931 2.914059 CAAATACTTGTACTCCCCCGG 58.086 52.381 0.00 0.00 0.00 5.73
2734 2932 2.237893 CAAATACTTGTACTCCCCCGGT 59.762 50.000 0.00 0.00 0.00 5.28
2735 2933 1.492764 ATACTTGTACTCCCCCGGTG 58.507 55.000 0.00 0.00 0.00 4.94
2736 2934 0.114954 TACTTGTACTCCCCCGGTGT 59.885 55.000 0.00 0.00 33.75 4.16
2737 2935 0.765519 ACTTGTACTCCCCCGGTGTT 60.766 55.000 0.00 0.00 31.55 3.32
2738 2936 0.399075 CTTGTACTCCCCCGGTGTTT 59.601 55.000 0.00 0.00 31.55 2.83
2739 2937 0.108963 TTGTACTCCCCCGGTGTTTG 59.891 55.000 0.00 0.00 31.55 2.93
2740 2938 1.673337 GTACTCCCCCGGTGTTTGC 60.673 63.158 0.00 0.00 31.55 3.68
2741 2939 2.148052 TACTCCCCCGGTGTTTGCA 61.148 57.895 0.00 0.00 31.55 4.08
2742 2940 1.493854 TACTCCCCCGGTGTTTGCAT 61.494 55.000 0.00 0.00 31.55 3.96
2743 2941 2.034999 TCCCCCGGTGTTTGCATC 59.965 61.111 0.00 0.00 0.00 3.91
2744 2942 2.282816 CCCCCGGTGTTTGCATCA 60.283 61.111 0.00 0.00 0.00 3.07
2745 2943 2.342650 CCCCCGGTGTTTGCATCAG 61.343 63.158 0.00 0.00 0.00 2.90
2746 2944 2.342650 CCCCGGTGTTTGCATCAGG 61.343 63.158 0.00 0.00 0.00 3.86
2747 2945 2.342650 CCCGGTGTTTGCATCAGGG 61.343 63.158 0.00 0.00 34.82 4.45
2748 2946 2.342650 CCGGTGTTTGCATCAGGGG 61.343 63.158 0.00 0.00 0.00 4.79
2749 2947 1.303236 CGGTGTTTGCATCAGGGGA 60.303 57.895 0.00 0.00 0.00 4.81
2750 2948 0.680921 CGGTGTTTGCATCAGGGGAT 60.681 55.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
325 346 2.513753 TCAAGAATGCGTGTTGGGAAT 58.486 42.857 2.32 0.00 0.00 3.01
326 347 1.974265 TCAAGAATGCGTGTTGGGAA 58.026 45.000 2.32 0.00 0.00 3.97
330 351 3.119884 TGGCTATTCAAGAATGCGTGTTG 60.120 43.478 5.59 0.00 32.50 3.33
332 353 2.710377 TGGCTATTCAAGAATGCGTGT 58.290 42.857 5.59 0.00 32.50 4.49
362 383 8.689972 GGAAATCTGGTCATCATGTCTTTAAAT 58.310 33.333 0.00 0.00 0.00 1.40
405 426 6.851609 AGAATGTTCAGCGCATACATAAAAA 58.148 32.000 18.25 0.00 32.51 1.94
432 453 0.521291 TGCGCTTAAGAATGTGGCAC 59.479 50.000 11.55 11.55 0.00 5.01
695 733 8.327941 TCTTAGATGAAAAAGTCCTTGTGATG 57.672 34.615 0.00 0.00 0.00 3.07
733 772 6.847956 TCGACCTTTAATTTCTCACGAAAA 57.152 33.333 0.00 0.00 42.03 2.29
738 777 6.148811 TCCACATTCGACCTTTAATTTCTCAC 59.851 38.462 0.00 0.00 0.00 3.51
754 793 3.613737 GCAATTGGATTTGTCCACATTCG 59.386 43.478 7.72 0.00 39.90 3.34
771 810 3.469739 CAAGTTTCCTTTGGCTGCAATT 58.530 40.909 0.50 0.00 0.00 2.32
868 917 1.011019 CCTGCTCGCGTACGTAGAG 60.011 63.158 26.98 26.98 41.18 2.43
886 935 6.096282 GGATACCTATGATCTCTTCCTGCTAC 59.904 46.154 0.00 0.00 0.00 3.58
935 984 3.118531 AGCACCAGGAGAATTGGACTAT 58.881 45.455 0.00 0.00 39.08 2.12
968 1021 0.436531 GCGCTTCTCAGTGTTTCTCG 59.563 55.000 0.00 0.00 32.54 4.04
1006 1073 0.242017 GCAACATGTGTGGAAGAGCC 59.758 55.000 0.00 0.00 37.10 4.70
1017 1084 1.531423 CCAGCAAGAGAGCAACATGT 58.469 50.000 0.00 0.00 36.85 3.21
1044 1114 1.696063 ATGCCATGGAACAGCATACC 58.304 50.000 18.40 0.00 46.15 2.73
1094 1179 2.061028 GCGAAAGGGAAACAGCAATTG 58.939 47.619 0.00 0.00 0.00 2.32
1100 1185 1.021202 TGTGTGCGAAAGGGAAACAG 58.979 50.000 0.00 0.00 27.87 3.16
1103 1188 1.134220 AGAGTGTGTGCGAAAGGGAAA 60.134 47.619 0.00 0.00 0.00 3.13
1104 1189 0.468226 AGAGTGTGTGCGAAAGGGAA 59.532 50.000 0.00 0.00 0.00 3.97
1105 1190 0.468226 AAGAGTGTGTGCGAAAGGGA 59.532 50.000 0.00 0.00 0.00 4.20
1106 1191 1.308998 AAAGAGTGTGTGCGAAAGGG 58.691 50.000 0.00 0.00 0.00 3.95
1107 1192 3.181501 TGAAAAAGAGTGTGTGCGAAAGG 60.182 43.478 0.00 0.00 0.00 3.11
1108 1193 3.786048 GTGAAAAAGAGTGTGTGCGAAAG 59.214 43.478 0.00 0.00 0.00 2.62
1114 1205 4.857871 TTCTCGTGAAAAAGAGTGTGTG 57.142 40.909 0.00 0.00 36.03 3.82
1127 1218 6.988622 TTAGTTCCTTTTTGTTTCTCGTGA 57.011 33.333 0.00 0.00 0.00 4.35
1170 1261 6.345096 AGGAAAAATTGATAGTGGGTTGTG 57.655 37.500 0.00 0.00 0.00 3.33
1205 1296 3.804786 TGATTTGCTTATGTGGCATGG 57.195 42.857 0.00 0.00 39.54 3.66
1278 1369 1.857204 GCATGAATTGATGACGTGGCG 60.857 52.381 9.25 0.00 0.00 5.69
1280 1371 3.181494 ACATGCATGAATTGATGACGTGG 60.181 43.478 32.75 0.59 0.00 4.94
1360 1452 4.082190 GTGCACTACATAGGTGAGTTCTGA 60.082 45.833 10.32 0.00 36.89 3.27
1367 1459 2.247699 AGGGTGCACTACATAGGTGA 57.752 50.000 17.98 0.00 36.89 4.02
1368 1460 2.236146 TGAAGGGTGCACTACATAGGTG 59.764 50.000 17.98 0.00 37.70 4.00
1425 1517 8.736097 AAAGGGTATAAAAGGAGGAAAATTGT 57.264 30.769 0.00 0.00 0.00 2.71
1437 1529 6.059484 TGGGAAGCGATAAAGGGTATAAAAG 58.941 40.000 0.00 0.00 0.00 2.27
1570 1662 2.768833 AAGCTGCATGCACATAATCG 57.231 45.000 18.46 6.37 45.94 3.34
1696 1788 4.254709 TGTGGCGCAAGTCTGGCT 62.255 61.111 10.83 0.00 46.88 4.75
1753 1845 5.471556 AACTTCCACATTTGATTCATGCA 57.528 34.783 0.00 0.00 0.00 3.96
1764 1856 5.219633 GCATACAACGAAAACTTCCACATT 58.780 37.500 0.00 0.00 0.00 2.71
1875 2050 8.416329 AGAACCATAGAACAATTATTCAATGGC 58.584 33.333 0.00 0.00 0.00 4.40
1954 2129 2.425143 AATGATCATGAAGGCACCGT 57.575 45.000 9.46 0.00 0.00 4.83
1981 2156 1.096967 TGCTGACGCTGGCCATAATG 61.097 55.000 5.51 0.00 36.97 1.90
1985 2160 3.058160 GTTGCTGACGCTGGCCAT 61.058 61.111 5.51 0.00 36.97 4.40
2009 2184 3.623060 ACAATAACAGCGATGATGGTGAC 59.377 43.478 8.12 0.00 39.68 3.67
2012 2187 3.623060 GTGACAATAACAGCGATGATGGT 59.377 43.478 8.12 0.00 0.00 3.55
2035 2210 2.581246 GAGGTGGGGAAATAAGGAGGTT 59.419 50.000 0.00 0.00 0.00 3.50
2037 2212 2.439880 GAGAGGTGGGGAAATAAGGAGG 59.560 54.545 0.00 0.00 0.00 4.30
2038 2213 2.439880 GGAGAGGTGGGGAAATAAGGAG 59.560 54.545 0.00 0.00 0.00 3.69
2068 2243 3.430929 CGACGAGGAAATGAAGGAGGATT 60.431 47.826 0.00 0.00 0.00 3.01
2146 2322 2.624838 CAGTTGCTTTGGAACATCCTGT 59.375 45.455 4.90 0.00 39.30 4.00
2156 2332 2.746269 CCATTGTGTCAGTTGCTTTGG 58.254 47.619 0.00 0.00 0.00 3.28
2160 2336 2.566833 TAGCCATTGTGTCAGTTGCT 57.433 45.000 0.00 0.00 0.00 3.91
2162 2338 4.386652 GCAATTTAGCCATTGTGTCAGTTG 59.613 41.667 3.55 0.00 36.63 3.16
2164 2340 3.828451 AGCAATTTAGCCATTGTGTCAGT 59.172 39.130 3.55 0.00 36.63 3.41
2208 2405 4.854173 TCCTTGCAGCATGACCTATTTTA 58.146 39.130 9.87 0.00 39.69 1.52
2209 2406 3.700538 TCCTTGCAGCATGACCTATTTT 58.299 40.909 9.87 0.00 39.69 1.82
2241 2438 5.514274 GTGGAACAAGGTTGAAAATCTCA 57.486 39.130 0.00 0.00 35.13 3.27
2341 2538 9.457436 AACTACGTCAAGGTATAATCCATTTTT 57.543 29.630 0.00 0.00 0.00 1.94
2366 2563 4.402155 GGATGTCAACATGAAGCCCAATAA 59.598 41.667 0.00 0.00 36.57 1.40
2367 2564 3.953612 GGATGTCAACATGAAGCCCAATA 59.046 43.478 0.00 0.00 36.57 1.90
2392 2589 7.148689 GCTTCTTTGGCAATACAGAAGATTTTG 60.149 37.037 30.41 13.81 43.39 2.44
2398 2595 6.690194 ATAGCTTCTTTGGCAATACAGAAG 57.310 37.500 25.41 25.41 43.50 2.85
2400 2597 8.752005 AATTATAGCTTCTTTGGCAATACAGA 57.248 30.769 0.00 0.00 0.00 3.41
2403 2600 8.078596 CCTGAATTATAGCTTCTTTGGCAATAC 58.921 37.037 0.00 0.00 0.00 1.89
2404 2601 7.231317 CCCTGAATTATAGCTTCTTTGGCAATA 59.769 37.037 0.00 0.00 0.00 1.90
2406 2603 5.360714 CCCTGAATTATAGCTTCTTTGGCAA 59.639 40.000 0.00 0.00 0.00 4.52
2408 2605 4.261783 GCCCTGAATTATAGCTTCTTTGGC 60.262 45.833 0.00 0.00 0.00 4.52
2409 2606 4.023707 CGCCCTGAATTATAGCTTCTTTGG 60.024 45.833 0.00 0.00 0.00 3.28
2410 2607 4.816385 TCGCCCTGAATTATAGCTTCTTTG 59.184 41.667 0.00 0.00 0.00 2.77
2411 2608 5.036117 TCGCCCTGAATTATAGCTTCTTT 57.964 39.130 0.00 0.00 0.00 2.52
2412 2609 4.636249 CTCGCCCTGAATTATAGCTTCTT 58.364 43.478 0.00 0.00 0.00 2.52
2414 2611 2.739379 GCTCGCCCTGAATTATAGCTTC 59.261 50.000 0.00 0.00 0.00 3.86
2417 2614 2.342179 GAGCTCGCCCTGAATTATAGC 58.658 52.381 0.00 0.00 0.00 2.97
2418 2615 2.600731 CGAGCTCGCCCTGAATTATAG 58.399 52.381 25.07 0.00 0.00 1.31
2419 2616 1.272490 CCGAGCTCGCCCTGAATTATA 59.728 52.381 30.49 0.00 38.18 0.98
2421 2618 1.327690 ACCGAGCTCGCCCTGAATTA 61.328 55.000 30.49 0.00 38.18 1.40
2422 2619 1.327690 TACCGAGCTCGCCCTGAATT 61.328 55.000 30.49 8.49 38.18 2.17
2424 2621 1.980232 TTACCGAGCTCGCCCTGAA 60.980 57.895 30.49 15.08 38.18 3.02
2425 2622 2.361992 TTACCGAGCTCGCCCTGA 60.362 61.111 30.49 10.84 38.18 3.86
2426 2623 2.202756 GTTACCGAGCTCGCCCTG 60.203 66.667 30.49 18.73 38.18 4.45
2427 2624 3.459063 GGTTACCGAGCTCGCCCT 61.459 66.667 30.49 16.40 38.18 5.19
2428 2625 2.973180 GATGGTTACCGAGCTCGCCC 62.973 65.000 30.49 23.81 38.18 6.13
2429 2626 1.591863 GATGGTTACCGAGCTCGCC 60.592 63.158 30.49 24.52 38.18 5.54
2430 2627 0.872021 CAGATGGTTACCGAGCTCGC 60.872 60.000 30.49 16.34 38.18 5.03
2431 2628 0.872021 GCAGATGGTTACCGAGCTCG 60.872 60.000 29.06 29.06 39.44 5.03
2432 2629 0.530870 GGCAGATGGTTACCGAGCTC 60.531 60.000 2.73 2.73 0.00 4.09
2433 2630 1.264749 TGGCAGATGGTTACCGAGCT 61.265 55.000 0.00 0.00 0.00 4.09
2434 2631 0.392461 TTGGCAGATGGTTACCGAGC 60.392 55.000 0.00 0.00 0.00 5.03
2435 2632 2.107950 TTTGGCAGATGGTTACCGAG 57.892 50.000 0.00 0.00 0.00 4.63
2436 2633 2.570415 TTTTGGCAGATGGTTACCGA 57.430 45.000 0.00 0.00 0.00 4.69
2476 2673 8.527810 CCATGGACTGGCTTTTTAAAACTATAA 58.472 33.333 5.56 0.00 38.47 0.98
2477 2674 8.062065 CCATGGACTGGCTTTTTAAAACTATA 57.938 34.615 5.56 0.00 38.47 1.31
2478 2675 6.935167 CCATGGACTGGCTTTTTAAAACTAT 58.065 36.000 5.56 0.00 38.47 2.12
2479 2676 6.339587 CCATGGACTGGCTTTTTAAAACTA 57.660 37.500 5.56 0.00 38.47 2.24
2480 2677 5.213891 CCATGGACTGGCTTTTTAAAACT 57.786 39.130 5.56 0.00 38.47 2.66
2493 2690 3.127548 GCAAGTCACATTACCATGGACTG 59.872 47.826 21.47 14.43 39.22 3.51
2494 2691 3.347216 GCAAGTCACATTACCATGGACT 58.653 45.455 21.47 6.45 40.16 3.85
2495 2692 2.423538 GGCAAGTCACATTACCATGGAC 59.576 50.000 21.47 3.75 34.27 4.02
2496 2693 2.040947 TGGCAAGTCACATTACCATGGA 59.959 45.455 21.47 0.00 34.27 3.41
2497 2694 2.445427 TGGCAAGTCACATTACCATGG 58.555 47.619 11.19 11.19 34.27 3.66
2498 2695 4.036567 CATGGCAAGTCACATTACCATG 57.963 45.455 5.51 5.51 43.97 3.66
2499 2696 3.700538 ACATGGCAAGTCACATTACCAT 58.299 40.909 0.00 0.00 36.87 3.55
2500 2697 3.153369 ACATGGCAAGTCACATTACCA 57.847 42.857 0.00 0.00 30.19 3.25
2501 2698 6.486657 ACATATACATGGCAAGTCACATTACC 59.513 38.462 0.00 0.00 36.39 2.85
2502 2699 7.496529 ACATATACATGGCAAGTCACATTAC 57.503 36.000 0.00 0.00 36.39 1.89
2503 2700 9.271828 CTAACATATACATGGCAAGTCACATTA 57.728 33.333 0.00 0.00 36.39 1.90
2504 2701 7.992608 TCTAACATATACATGGCAAGTCACATT 59.007 33.333 0.00 0.00 36.39 2.71
2505 2702 7.508687 TCTAACATATACATGGCAAGTCACAT 58.491 34.615 0.00 0.00 36.39 3.21
2506 2703 6.883744 TCTAACATATACATGGCAAGTCACA 58.116 36.000 0.00 0.00 36.39 3.58
2507 2704 7.786178 TTCTAACATATACATGGCAAGTCAC 57.214 36.000 0.00 0.00 36.39 3.67
2508 2705 8.800370 TTTTCTAACATATACATGGCAAGTCA 57.200 30.769 0.00 0.00 36.39 3.41
2532 2730 8.674263 TGGCATGATGTTTATTGAAACTTTTT 57.326 26.923 0.00 0.00 44.52 1.94
2558 2756 1.026718 CCGATGGGTCCTTCAGCAAC 61.027 60.000 4.20 0.00 0.00 4.17
2561 2759 2.514824 GCCGATGGGTCCTTCAGC 60.515 66.667 0.00 0.60 34.97 4.26
2604 2802 2.320587 GGACACACGAGCTTGCCAG 61.321 63.158 0.00 0.00 0.00 4.85
2605 2803 2.280797 GGACACACGAGCTTGCCA 60.281 61.111 0.00 0.00 0.00 4.92
2607 2805 1.160329 ACTTGGACACACGAGCTTGC 61.160 55.000 0.00 0.00 0.00 4.01
2609 2807 0.464036 TCACTTGGACACACGAGCTT 59.536 50.000 0.00 0.00 0.00 3.74
2610 2808 0.249489 GTCACTTGGACACACGAGCT 60.249 55.000 0.00 0.00 46.19 4.09
2622 2820 7.601073 TTGAATGCTTAGATGTAGTCACTTG 57.399 36.000 0.00 0.00 0.00 3.16
2624 2822 7.332926 CACTTTGAATGCTTAGATGTAGTCACT 59.667 37.037 0.00 0.00 0.00 3.41
2625 2823 7.459486 CACTTTGAATGCTTAGATGTAGTCAC 58.541 38.462 0.00 0.00 0.00 3.67
2626 2824 6.092670 GCACTTTGAATGCTTAGATGTAGTCA 59.907 38.462 0.00 0.00 40.08 3.41
2627 2825 6.092670 TGCACTTTGAATGCTTAGATGTAGTC 59.907 38.462 0.00 0.00 43.77 2.59
2628 2826 5.939883 TGCACTTTGAATGCTTAGATGTAGT 59.060 36.000 0.00 0.00 43.77 2.73
2629 2827 6.128200 TGTGCACTTTGAATGCTTAGATGTAG 60.128 38.462 19.41 0.00 43.77 2.74
2630 2828 5.704978 TGTGCACTTTGAATGCTTAGATGTA 59.295 36.000 19.41 0.00 43.77 2.29
2631 2829 4.520111 TGTGCACTTTGAATGCTTAGATGT 59.480 37.500 19.41 0.00 43.77 3.06
2632 2830 5.050644 TGTGCACTTTGAATGCTTAGATG 57.949 39.130 19.41 0.00 43.77 2.90
2633 2831 5.909621 ATGTGCACTTTGAATGCTTAGAT 57.090 34.783 19.41 0.00 43.77 1.98
2634 2832 5.241285 TCAATGTGCACTTTGAATGCTTAGA 59.759 36.000 33.67 16.11 43.77 2.10
2635 2833 5.463286 TCAATGTGCACTTTGAATGCTTAG 58.537 37.500 33.67 13.95 43.77 2.18
2636 2834 5.450592 TCAATGTGCACTTTGAATGCTTA 57.549 34.783 33.67 17.27 43.77 3.09
2647 2845 1.542915 GGCTTGACATCAATGTGCACT 59.457 47.619 19.41 0.15 41.95 4.40
2678 2876 7.044181 AGTAGAACATGTATGTCCACATCTTG 58.956 38.462 0.00 0.87 40.80 3.02
2686 2884 7.223582 CACTCATGAAGTAGAACATGTATGTCC 59.776 40.741 0.00 0.00 42.75 4.02
2690 2888 6.643388 TGCACTCATGAAGTAGAACATGTAT 58.357 36.000 0.00 0.00 42.75 2.29
2696 2894 7.602517 AGTATTTGCACTCATGAAGTAGAAC 57.397 36.000 0.00 0.00 36.07 3.01
2698 2896 7.161404 ACAAGTATTTGCACTCATGAAGTAGA 58.839 34.615 0.00 0.00 37.85 2.59
2710 2908 3.014623 GGGGGAGTACAAGTATTTGCAC 58.985 50.000 0.00 0.00 37.85 4.57
2717 2915 0.114954 ACACCGGGGGAGTACAAGTA 59.885 55.000 9.50 0.00 0.00 2.24
2718 2916 0.765519 AACACCGGGGGAGTACAAGT 60.766 55.000 9.50 0.00 0.00 3.16
2719 2917 0.399075 AAACACCGGGGGAGTACAAG 59.601 55.000 9.50 0.00 0.00 3.16
2720 2918 0.108963 CAAACACCGGGGGAGTACAA 59.891 55.000 9.50 0.00 0.00 2.41
2722 2920 1.673337 GCAAACACCGGGGGAGTAC 60.673 63.158 9.50 0.00 0.00 2.73
2723 2921 1.493854 ATGCAAACACCGGGGGAGTA 61.494 55.000 9.50 0.00 0.00 2.59
2724 2922 2.764637 GATGCAAACACCGGGGGAGT 62.765 60.000 9.50 0.00 0.00 3.85
2725 2923 2.035626 ATGCAAACACCGGGGGAG 59.964 61.111 9.50 0.00 0.00 4.30
2726 2924 2.034999 GATGCAAACACCGGGGGA 59.965 61.111 9.50 0.00 0.00 4.81
2727 2925 2.282816 TGATGCAAACACCGGGGG 60.283 61.111 9.50 0.00 0.00 5.40
2728 2926 2.342650 CCTGATGCAAACACCGGGG 61.343 63.158 0.00 0.00 0.00 5.73
2729 2927 2.342650 CCCTGATGCAAACACCGGG 61.343 63.158 6.32 0.00 0.00 5.73
2730 2928 2.342650 CCCCTGATGCAAACACCGG 61.343 63.158 0.00 0.00 0.00 5.28
2731 2929 0.680921 ATCCCCTGATGCAAACACCG 60.681 55.000 0.00 0.00 0.00 4.94
2732 2930 0.819582 CATCCCCTGATGCAAACACC 59.180 55.000 0.00 0.00 41.81 4.16


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

AutoCloner maintained by Alex Coulton.