Multiple sequence alignment - TraesCS6A01G383300

Loading Multiple Alignment...

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 TraesCS6A01G383300 chr6A 100.000 4232 0 0 1 4232 602324469 602320238 0.000000e+00 7816
1 TraesCS6A01G383300 chr6A 99.068 1824 14 3 1 1822 503826136 503827958 0.000000e+00 3271
2 TraesCS6A01G383300 chr6A 99.596 991 3 1 3243 4232 503827968 503828958 0.000000e+00 1807
3 TraesCS6A01G383300 chr1D 95.156 1858 73 13 694 2547 43298885 43300729 0.000000e+00 2916
4 TraesCS6A01G383300 chr1D 95.122 1435 63 6 2802 4231 43300725 43302157 0.000000e+00 2255
5 TraesCS6A01G383300 chr1D 95.987 623 22 2 3609 4231 482900969 482900350 0.000000e+00 1009
6 TraesCS6A01G383300 chr1D 96.371 496 15 3 1 494 482901462 482900968 0.000000e+00 813
7 TraesCS6A01G383300 chr1D 87.141 731 56 16 1 696 43298035 43298762 0.000000e+00 795
8 TraesCS6A01G383300 chr7D 92.390 1590 106 8 962 2547 578060838 578059260 0.000000e+00 2252
9 TraesCS6A01G383300 chr7D 92.463 1433 100 6 2802 4231 578059264 578057837 0.000000e+00 2041
10 TraesCS6A01G383300 chr7D 85.217 1610 206 18 945 2546 540516037 540517622 0.000000e+00 1626
11 TraesCS6A01G383300 chr7D 85.817 557 59 11 326 865 578061507 578060954 1.320000e-159 573
12 TraesCS6A01G383300 chr7D 95.652 46 2 0 247 292 578061563 578061518 1.630000e-09 75
13 TraesCS6A01G383300 chr7A 91.808 1587 111 10 962 2547 694709346 694710914 0.000000e+00 2193
14 TraesCS6A01G383300 chr7A 91.347 1017 83 5 2802 3816 694710910 694711923 0.000000e+00 1386
15 TraesCS6A01G383300 chr7A 82.243 321 34 12 470 778 695201734 695202043 5.430000e-64 255
16 TraesCS6A01G383300 chr4A 91.178 1587 121 10 962 2547 632303831 632305399 0.000000e+00 2137
17 TraesCS6A01G383300 chr4A 85.420 631 77 11 22 646 571319681 571319060 3.570000e-180 641
18 TraesCS6A01G383300 chr4A 97.358 265 7 0 2542 2806 608002166 608002430 6.450000e-123 451
19 TraesCS6A01G383300 chr7B 88.881 1457 127 11 2802 4230 120433206 120434655 0.000000e+00 1760
20 TraesCS6A01G383300 chr7B 90.948 1160 97 7 1388 2547 120432059 120433210 0.000000e+00 1554
21 TraesCS6A01G383300 chr5A 85.329 1595 202 17 960 2546 355170510 355168940 0.000000e+00 1620
22 TraesCS6A01G383300 chr5A 91.183 896 72 3 3041 3935 617996476 617995587 0.000000e+00 1210
23 TraesCS6A01G383300 chr5A 97.388 268 5 2 2539 2805 448842186 448842452 4.990000e-124 455
24 TraesCS6A01G383300 chr5A 97.701 261 5 1 2544 2804 300647757 300648016 8.350000e-122 448
25 TraesCS6A01G383300 chr5A 96.654 269 9 0 2542 2810 704864893 704864625 8.350000e-122 448
26 TraesCS6A01G383300 chr5A 96.629 267 9 0 2539 2805 262327361 262327095 1.080000e-120 444
27 TraesCS6A01G383300 chr5A 94.366 284 12 4 2524 2806 83333571 83333851 2.340000e-117 433
28 TraesCS6A01G383300 chr3A 85.084 1609 212 14 945 2546 60779480 60781067 0.000000e+00 1616
29 TraesCS6A01G383300 chr1A 84.711 1609 217 17 948 2547 16080169 16081757 0.000000e+00 1581
30 TraesCS6A01G383300 chr1A 96.283 269 8 2 2544 2812 49277963 49277697 1.400000e-119 440
31 TraesCS6A01G383300 chr2A 88.202 1068 109 10 3166 4232 298644631 298643580 0.000000e+00 1258
32 TraesCS6A01G383300 chr2A 82.549 871 98 22 23 863 298666946 298666100 0.000000e+00 717
33 TraesCS6A01G383300 chr2A 91.243 354 31 0 2814 3167 298664424 298664071 2.290000e-132 483
34 TraesCS6A01G383300 chr2A 97.358 265 7 0 2543 2807 653300229 653300493 6.450000e-123 451
35 TraesCS6A01G383300 chr2D 90.543 920 79 8 2802 3718 130067398 130068312 0.000000e+00 1210
36 TraesCS6A01G383300 chr2B 89.674 920 87 8 2802 3718 183465431 183466345 0.000000e+00 1166
37 TraesCS6A01G383300 chr2B 97.727 264 4 2 2543 2805 780671196 780671458 1.790000e-123 453
38 TraesCS6A01G383300 chr5B 84.122 888 87 16 1 865 548045717 548046573 0.000000e+00 809
39 TraesCS6A01G383300 chr5B 90.476 168 14 1 4064 4231 548047330 548047495 1.980000e-53 220
40 TraesCS6A01G383300 chr1B 89.744 624 57 6 1 619 207171327 207170706 0.000000e+00 791


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 TraesCS6A01G383300 chr6A 602320238 602324469 4231 True 7816.000000 7816 100.0000 1 4232 1 chr6A.!!$R1 4231
1 TraesCS6A01G383300 chr6A 503826136 503828958 2822 False 2539.000000 3271 99.3320 1 4232 2 chr6A.!!$F1 4231
2 TraesCS6A01G383300 chr1D 43298035 43302157 4122 False 1988.666667 2916 92.4730 1 4231 3 chr1D.!!$F1 4230
3 TraesCS6A01G383300 chr1D 482900350 482901462 1112 True 911.000000 1009 96.1790 1 4231 2 chr1D.!!$R1 4230
4 TraesCS6A01G383300 chr7D 540516037 540517622 1585 False 1626.000000 1626 85.2170 945 2546 1 chr7D.!!$F1 1601
5 TraesCS6A01G383300 chr7D 578057837 578061563 3726 True 1235.250000 2252 91.5805 247 4231 4 chr7D.!!$R1 3984
6 TraesCS6A01G383300 chr7A 694709346 694711923 2577 False 1789.500000 2193 91.5775 962 3816 2 chr7A.!!$F2 2854
7 TraesCS6A01G383300 chr4A 632303831 632305399 1568 False 2137.000000 2137 91.1780 962 2547 1 chr4A.!!$F2 1585
8 TraesCS6A01G383300 chr4A 571319060 571319681 621 True 641.000000 641 85.4200 22 646 1 chr4A.!!$R1 624
9 TraesCS6A01G383300 chr7B 120432059 120434655 2596 False 1657.000000 1760 89.9145 1388 4230 2 chr7B.!!$F1 2842
10 TraesCS6A01G383300 chr5A 355168940 355170510 1570 True 1620.000000 1620 85.3290 960 2546 1 chr5A.!!$R2 1586
11 TraesCS6A01G383300 chr5A 617995587 617996476 889 True 1210.000000 1210 91.1830 3041 3935 1 chr5A.!!$R3 894
12 TraesCS6A01G383300 chr3A 60779480 60781067 1587 False 1616.000000 1616 85.0840 945 2546 1 chr3A.!!$F1 1601
13 TraesCS6A01G383300 chr1A 16080169 16081757 1588 False 1581.000000 1581 84.7110 948 2547 1 chr1A.!!$F1 1599
14 TraesCS6A01G383300 chr2A 298643580 298644631 1051 True 1258.000000 1258 88.2020 3166 4232 1 chr2A.!!$R1 1066
15 TraesCS6A01G383300 chr2A 298664071 298666946 2875 True 600.000000 717 86.8960 23 3167 2 chr2A.!!$R2 3144
16 TraesCS6A01G383300 chr2D 130067398 130068312 914 False 1210.000000 1210 90.5430 2802 3718 1 chr2D.!!$F1 916
17 TraesCS6A01G383300 chr2B 183465431 183466345 914 False 1166.000000 1166 89.6740 2802 3718 1 chr2B.!!$F1 916
18 TraesCS6A01G383300 chr5B 548045717 548047495 1778 False 514.500000 809 87.2990 1 4231 2 chr5B.!!$F1 4230
19 TraesCS6A01G383300 chr1B 207170706 207171327 621 True 791.000000 791 89.7440 1 619 1 chr1B.!!$R1 618

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
221 248 5.763088 TGAGATACACGACTGCAGATATTC 58.237 41.667 23.35 6.33 0.00 1.75 F
1504 1784 4.134563 GGAAGAGGTTTGTTTGTGCTAGA 58.865 43.478 0.00 0.00 0.00 2.43 F
2546 2832 0.036765 TTGGCGGAATCTTGCGTACT 60.037 50.000 5.75 0.00 44.21 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1913 2194 0.259647 AATGCTGGATTGGCAGCCTA 59.740 50.0 14.15 5.25 43.15 3.93 R
2789 3075 0.257039 TGTAGTACTCCCTCCGGTCC 59.743 60.0 0.00 0.00 0.00 4.46 R
3416 3727 1.808411 TCTCCTCACAATGTTTCGCC 58.192 50.0 0.00 0.00 0.00 5.54 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
221 248 5.763088 TGAGATACACGACTGCAGATATTC 58.237 41.667 23.35 6.33 0.00 1.75
428 463 7.101054 GGTTGTTCTGTTATCCATGTACAGTA 58.899 38.462 0.33 0.00 40.08 2.74
781 970 9.988815 ATGTACTATATGAACTTCTTCCACATC 57.011 33.333 0.00 0.00 0.00 3.06
1504 1784 4.134563 GGAAGAGGTTTGTTTGTGCTAGA 58.865 43.478 0.00 0.00 0.00 2.43
1954 2235 7.640240 GCATTCTATTTTGATTACCAAGTCGAC 59.360 37.037 7.70 7.70 35.94 4.20
2225 2506 1.202568 CGCCTAAGCTCATCATGACCA 60.203 52.381 0.00 0.00 36.60 4.02
2251 2535 5.045651 TGAAGACCAAAGCATGAGAATAGGA 60.046 40.000 0.00 0.00 0.00 2.94
2252 2536 5.033589 AGACCAAAGCATGAGAATAGGAG 57.966 43.478 0.00 0.00 0.00 3.69
2329 2613 3.317993 TGAAGCTTACTGAAAAGGTTGGC 59.682 43.478 0.00 4.85 44.79 4.52
2369 2655 5.119931 TCCAGATTTTCATGAACGGTTTG 57.880 39.130 7.89 3.70 0.00 2.93
2370 2656 4.824537 TCCAGATTTTCATGAACGGTTTGA 59.175 37.500 7.89 0.00 0.00 2.69
2375 2661 4.545823 TTTCATGAACGGTTTGAGTCAC 57.454 40.909 7.89 0.00 0.00 3.67
2376 2662 3.186702 TCATGAACGGTTTGAGTCACA 57.813 42.857 0.00 0.00 0.00 3.58
2377 2663 3.536570 TCATGAACGGTTTGAGTCACAA 58.463 40.909 0.00 0.00 36.65 3.33
2378 2664 4.133820 TCATGAACGGTTTGAGTCACAAT 58.866 39.130 0.00 0.00 38.36 2.71
2379 2665 3.961477 TGAACGGTTTGAGTCACAATG 57.039 42.857 0.00 0.00 38.36 2.82
2438 2724 6.375455 AGTCACAATGGTGTTCAATAATCTCC 59.625 38.462 0.00 0.00 45.45 3.71
2545 2831 0.373716 CTTGGCGGAATCTTGCGTAC 59.626 55.000 5.75 0.67 44.21 3.67
2546 2832 0.036765 TTGGCGGAATCTTGCGTACT 60.037 50.000 5.75 0.00 44.21 2.73
2547 2833 0.459585 TGGCGGAATCTTGCGTACTC 60.460 55.000 5.75 0.00 44.21 2.59
2548 2834 1.152383 GGCGGAATCTTGCGTACTCC 61.152 60.000 5.75 0.00 44.21 3.85
2549 2835 1.152383 GCGGAATCTTGCGTACTCCC 61.152 60.000 5.75 0.00 44.21 4.30
2550 2836 0.460311 CGGAATCTTGCGTACTCCCT 59.540 55.000 0.00 0.00 37.24 4.20
2551 2837 1.536284 CGGAATCTTGCGTACTCCCTC 60.536 57.143 0.00 0.00 37.24 4.30
2552 2838 1.202545 GGAATCTTGCGTACTCCCTCC 60.203 57.143 0.00 0.00 0.00 4.30
2553 2839 0.460311 AATCTTGCGTACTCCCTCCG 59.540 55.000 0.00 0.00 0.00 4.63
2554 2840 1.392710 ATCTTGCGTACTCCCTCCGG 61.393 60.000 0.00 0.00 0.00 5.14
2555 2841 2.283388 TTGCGTACTCCCTCCGGT 60.283 61.111 0.00 0.00 0.00 5.28
2556 2842 2.280823 CTTGCGTACTCCCTCCGGTC 62.281 65.000 0.00 0.00 0.00 4.79
2557 2843 3.525545 GCGTACTCCCTCCGGTCC 61.526 72.222 0.00 0.00 0.00 4.46
2558 2844 2.274760 CGTACTCCCTCCGGTCCT 59.725 66.667 0.00 0.00 0.00 3.85
2559 2845 1.379576 CGTACTCCCTCCGGTCCTT 60.380 63.158 0.00 0.00 0.00 3.36
2560 2846 0.969409 CGTACTCCCTCCGGTCCTTT 60.969 60.000 0.00 0.00 0.00 3.11
2561 2847 1.273759 GTACTCCCTCCGGTCCTTTT 58.726 55.000 0.00 0.00 0.00 2.27
2562 2848 1.627329 GTACTCCCTCCGGTCCTTTTT 59.373 52.381 0.00 0.00 0.00 1.94
2563 2849 2.034436 ACTCCCTCCGGTCCTTTTTA 57.966 50.000 0.00 0.00 0.00 1.52
2564 2850 1.907255 ACTCCCTCCGGTCCTTTTTAG 59.093 52.381 0.00 0.00 0.00 1.85
2565 2851 1.907255 CTCCCTCCGGTCCTTTTTAGT 59.093 52.381 0.00 0.00 0.00 2.24
2566 2852 2.305052 CTCCCTCCGGTCCTTTTTAGTT 59.695 50.000 0.00 0.00 0.00 2.24
2567 2853 2.303890 TCCCTCCGGTCCTTTTTAGTTC 59.696 50.000 0.00 0.00 0.00 3.01
2568 2854 2.344025 CCTCCGGTCCTTTTTAGTTCG 58.656 52.381 0.00 0.00 0.00 3.95
2569 2855 1.730612 CTCCGGTCCTTTTTAGTTCGC 59.269 52.381 0.00 0.00 0.00 4.70
2570 2856 1.070445 TCCGGTCCTTTTTAGTTCGCA 59.930 47.619 0.00 0.00 0.00 5.10
2571 2857 2.081462 CCGGTCCTTTTTAGTTCGCAT 58.919 47.619 0.00 0.00 0.00 4.73
2572 2858 3.055963 TCCGGTCCTTTTTAGTTCGCATA 60.056 43.478 0.00 0.00 0.00 3.14
2573 2859 3.875134 CCGGTCCTTTTTAGTTCGCATAT 59.125 43.478 0.00 0.00 0.00 1.78
2574 2860 5.051816 CCGGTCCTTTTTAGTTCGCATATA 58.948 41.667 0.00 0.00 0.00 0.86
2575 2861 5.524646 CCGGTCCTTTTTAGTTCGCATATAA 59.475 40.000 0.00 0.00 0.00 0.98
2576 2862 6.292703 CCGGTCCTTTTTAGTTCGCATATAAG 60.293 42.308 0.00 0.00 0.00 1.73
2577 2863 6.477688 CGGTCCTTTTTAGTTCGCATATAAGA 59.522 38.462 0.00 0.00 0.00 2.10
2578 2864 7.170998 CGGTCCTTTTTAGTTCGCATATAAGAT 59.829 37.037 0.00 0.00 0.00 2.40
2579 2865 8.837389 GGTCCTTTTTAGTTCGCATATAAGATT 58.163 33.333 0.00 0.00 0.00 2.40
2589 2875 9.601217 AGTTCGCATATAAGATTTGACTAAAGT 57.399 29.630 0.00 0.00 0.00 2.66
2590 2876 9.851043 GTTCGCATATAAGATTTGACTAAAGTC 57.149 33.333 3.08 3.08 44.97 3.01
2604 2890 5.536260 GACTAAAGTCAAGTCCCGTAAAGT 58.464 41.667 5.24 0.00 44.18 2.66
2605 2891 5.922053 ACTAAAGTCAAGTCCCGTAAAGTT 58.078 37.500 0.00 0.00 0.00 2.66
2606 2892 6.351711 ACTAAAGTCAAGTCCCGTAAAGTTT 58.648 36.000 0.00 0.00 0.00 2.66
2607 2893 5.494632 AAAGTCAAGTCCCGTAAAGTTTG 57.505 39.130 0.00 0.00 0.00 2.93
2608 2894 4.411256 AGTCAAGTCCCGTAAAGTTTGA 57.589 40.909 0.00 0.00 0.00 2.69
2609 2895 4.124970 AGTCAAGTCCCGTAAAGTTTGAC 58.875 43.478 0.00 6.98 42.72 3.18
2610 2896 3.249320 GTCAAGTCCCGTAAAGTTTGACC 59.751 47.826 0.00 0.00 38.79 4.02
2611 2897 3.118334 TCAAGTCCCGTAAAGTTTGACCA 60.118 43.478 0.00 0.00 0.00 4.02
2612 2898 3.564053 AGTCCCGTAAAGTTTGACCAA 57.436 42.857 0.00 0.00 0.00 3.67
2613 2899 3.208594 AGTCCCGTAAAGTTTGACCAAC 58.791 45.455 0.00 0.00 35.32 3.77
2647 2933 7.581213 AAAAGTACCAACATTCACAATCTGA 57.419 32.000 0.00 0.00 0.00 3.27
2648 2934 7.581213 AAAGTACCAACATTCACAATCTGAA 57.419 32.000 0.00 0.00 43.28 3.02
2649 2935 7.581213 AAGTACCAACATTCACAATCTGAAA 57.419 32.000 0.00 0.00 42.37 2.69
2650 2936 7.765695 AGTACCAACATTCACAATCTGAAAT 57.234 32.000 0.00 0.00 42.37 2.17
2651 2937 7.820648 AGTACCAACATTCACAATCTGAAATC 58.179 34.615 0.00 0.00 42.37 2.17
2652 2938 6.653526 ACCAACATTCACAATCTGAAATCA 57.346 33.333 0.00 0.00 42.37 2.57
2653 2939 7.053316 ACCAACATTCACAATCTGAAATCAA 57.947 32.000 0.00 0.00 42.37 2.57
2654 2940 7.673180 ACCAACATTCACAATCTGAAATCAAT 58.327 30.769 0.00 0.00 42.37 2.57
2655 2941 8.805175 ACCAACATTCACAATCTGAAATCAATA 58.195 29.630 0.00 0.00 42.37 1.90
2656 2942 9.811995 CCAACATTCACAATCTGAAATCAATAT 57.188 29.630 0.00 0.00 42.37 1.28
2681 2967 9.896645 ATCAATAGATGTGTCATGACTTAAAGT 57.103 29.630 25.55 9.39 31.91 2.66
2682 2968 9.725019 TCAATAGATGTGTCATGACTTAAAGTT 57.275 29.630 25.55 10.34 0.00 2.66
2685 2971 9.725019 ATAGATGTGTCATGACTTAAAGTTTCA 57.275 29.630 25.55 11.05 0.00 2.69
2686 2972 8.627208 AGATGTGTCATGACTTAAAGTTTCAT 57.373 30.769 25.55 14.42 0.00 2.57
2687 2973 9.725019 AGATGTGTCATGACTTAAAGTTTCATA 57.275 29.630 25.55 1.27 0.00 2.15
2713 2999 7.864108 TGTATAACTTTAGCATTGCAGATGT 57.136 32.000 11.91 4.45 0.00 3.06
2714 3000 8.279970 TGTATAACTTTAGCATTGCAGATGTT 57.720 30.769 11.91 13.91 0.00 2.71
2715 3001 8.183536 TGTATAACTTTAGCATTGCAGATGTTG 58.816 33.333 11.91 0.00 0.00 3.33
2716 3002 5.710513 AACTTTAGCATTGCAGATGTTGA 57.289 34.783 11.91 0.45 0.00 3.18
2717 3003 5.909621 ACTTTAGCATTGCAGATGTTGAT 57.090 34.783 11.91 0.00 0.00 2.57
2718 3004 7.395190 AACTTTAGCATTGCAGATGTTGATA 57.605 32.000 11.91 0.00 0.00 2.15
2719 3005 7.578310 ACTTTAGCATTGCAGATGTTGATAT 57.422 32.000 11.91 0.00 0.00 1.63
2720 3006 8.004087 ACTTTAGCATTGCAGATGTTGATATT 57.996 30.769 11.91 0.00 0.00 1.28
2721 3007 8.472413 ACTTTAGCATTGCAGATGTTGATATTT 58.528 29.630 11.91 0.00 0.00 1.40
2722 3008 9.309516 CTTTAGCATTGCAGATGTTGATATTTT 57.690 29.630 11.91 0.00 0.00 1.82
2723 3009 9.656040 TTTAGCATTGCAGATGTTGATATTTTT 57.344 25.926 11.91 0.00 0.00 1.94
2750 3036 9.438228 TCATATAAATACGGTCAAACTTTGTGA 57.562 29.630 1.44 0.00 0.00 3.58
2781 3067 9.671279 TGACTTCAAAGAATTCTAATATGCAGA 57.329 29.630 8.75 0.00 0.00 4.26
2783 3069 9.678260 ACTTCAAAGAATTCTAATATGCAGAGT 57.322 29.630 8.75 7.81 0.00 3.24
2793 3079 8.732746 TTCTAATATGCAGAGTAAAAAGGACC 57.267 34.615 0.00 0.00 0.00 4.46
2794 3080 6.984474 TCTAATATGCAGAGTAAAAAGGACCG 59.016 38.462 0.00 0.00 0.00 4.79
2795 3081 2.178912 TGCAGAGTAAAAAGGACCGG 57.821 50.000 0.00 0.00 0.00 5.28
2796 3082 1.695242 TGCAGAGTAAAAAGGACCGGA 59.305 47.619 9.46 0.00 0.00 5.14
2797 3083 2.289444 TGCAGAGTAAAAAGGACCGGAG 60.289 50.000 9.46 0.00 0.00 4.63
2910 3198 6.202226 GTTTGAAACAGCTTTAGAGGAACAG 58.798 40.000 2.68 0.00 0.00 3.16
2917 3205 1.734465 CTTTAGAGGAACAGCGGCAAG 59.266 52.381 1.45 0.00 0.00 4.01
2955 3243 3.054434 ACAATGCCAGCCTTCATACACTA 60.054 43.478 0.00 0.00 0.00 2.74
3003 3291 4.527944 TCGAGAGTCATGGTAGAGATGTT 58.472 43.478 0.00 0.00 0.00 2.71
3138 3426 5.406780 CAGCAAGAGTGGTAAAGTTAGAGTG 59.593 44.000 0.00 0.00 33.05 3.51
3183 3471 2.213499 GCAGCACACTGTTCTTGTAGT 58.787 47.619 0.00 0.00 46.30 2.73
3920 4241 4.979943 TTTGCAAATGTGTCACTGAAGA 57.020 36.364 8.05 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
221 248 5.756195 TTGCATAGGCTATTTTGCAGTAG 57.244 39.130 17.79 0.90 44.99 2.57
428 463 2.024080 TGGCCTGGAGGAAGCAAATATT 60.024 45.455 3.32 0.00 37.39 1.28
781 970 2.224079 CCGTTCCCATTTCATATCAGCG 59.776 50.000 0.00 0.00 0.00 5.18
1504 1784 1.662686 CCTCCTTTCTCCAACCCTCT 58.337 55.000 0.00 0.00 0.00 3.69
1913 2194 0.259647 AATGCTGGATTGGCAGCCTA 59.740 50.000 14.15 5.25 43.15 3.93
1936 2217 4.873817 TCTCGTCGACTTGGTAATCAAAA 58.126 39.130 14.70 0.00 34.56 2.44
2182 2463 2.676748 ACCCCAGACATTGCTTTCAAA 58.323 42.857 0.00 0.00 35.56 2.69
2225 2506 6.320672 CCTATTCTCATGCTTTGGTCTTCATT 59.679 38.462 0.00 0.00 0.00 2.57
2251 2535 7.462571 AGTGTTTGGAAAAACTTGTTCTACT 57.537 32.000 3.29 0.00 32.61 2.57
2252 2536 9.285770 CTTAGTGTTTGGAAAAACTTGTTCTAC 57.714 33.333 0.29 0.00 37.61 2.59
2329 2613 6.528537 TCTGGATTATTTTTCATGGTGGTG 57.471 37.500 0.00 0.00 0.00 4.17
2369 2655 1.613437 CCCCAAACACCATTGTGACTC 59.387 52.381 3.55 0.00 45.76 3.36
2370 2656 1.216678 TCCCCAAACACCATTGTGACT 59.783 47.619 3.55 0.00 45.76 3.41
2375 2661 2.756760 CTCTGATCCCCAAACACCATTG 59.243 50.000 0.00 0.00 0.00 2.82
2376 2662 2.649312 TCTCTGATCCCCAAACACCATT 59.351 45.455 0.00 0.00 0.00 3.16
2377 2663 2.025887 GTCTCTGATCCCCAAACACCAT 60.026 50.000 0.00 0.00 0.00 3.55
2378 2664 1.351017 GTCTCTGATCCCCAAACACCA 59.649 52.381 0.00 0.00 0.00 4.17
2379 2665 1.351017 TGTCTCTGATCCCCAAACACC 59.649 52.381 0.00 0.00 0.00 4.16
2438 2724 2.890808 TATCTGCTAGCCCAAAGTCG 57.109 50.000 13.29 0.00 0.00 4.18
2549 2835 1.730612 GCGAACTAAAAAGGACCGGAG 59.269 52.381 9.46 0.00 0.00 4.63
2550 2836 1.070445 TGCGAACTAAAAAGGACCGGA 59.930 47.619 9.46 0.00 0.00 5.14
2551 2837 1.515081 TGCGAACTAAAAAGGACCGG 58.485 50.000 0.00 0.00 0.00 5.28
2552 2838 6.477688 TCTTATATGCGAACTAAAAAGGACCG 59.522 38.462 0.00 0.00 0.00 4.79
2553 2839 7.781548 TCTTATATGCGAACTAAAAAGGACC 57.218 36.000 0.00 0.00 0.00 4.46
2563 2849 9.601217 ACTTTAGTCAAATCTTATATGCGAACT 57.399 29.630 0.00 0.00 0.00 3.01
2564 2850 9.851043 GACTTTAGTCAAATCTTATATGCGAAC 57.149 33.333 5.04 0.00 44.18 3.95
2581 2867 5.536260 ACTTTACGGGACTTGACTTTAGTC 58.464 41.667 2.92 2.92 44.97 2.59
2582 2868 5.541953 ACTTTACGGGACTTGACTTTAGT 57.458 39.130 0.00 0.00 0.00 2.24
2583 2869 6.480981 TCAAACTTTACGGGACTTGACTTTAG 59.519 38.462 0.00 0.00 0.00 1.85
2584 2870 6.258507 GTCAAACTTTACGGGACTTGACTTTA 59.741 38.462 5.69 0.00 39.54 1.85
2585 2871 5.065602 GTCAAACTTTACGGGACTTGACTTT 59.934 40.000 5.69 0.00 39.54 2.66
2586 2872 4.573607 GTCAAACTTTACGGGACTTGACTT 59.426 41.667 5.69 0.00 39.54 3.01
2587 2873 4.124970 GTCAAACTTTACGGGACTTGACT 58.875 43.478 5.69 0.00 39.54 3.41
2588 2874 3.249320 GGTCAAACTTTACGGGACTTGAC 59.751 47.826 4.55 4.55 41.09 3.18
2589 2875 3.118334 TGGTCAAACTTTACGGGACTTGA 60.118 43.478 0.00 0.00 0.00 3.02
2590 2876 3.207778 TGGTCAAACTTTACGGGACTTG 58.792 45.455 0.00 0.00 0.00 3.16
2591 2877 3.564053 TGGTCAAACTTTACGGGACTT 57.436 42.857 0.00 0.00 0.00 3.01
2592 2878 3.208594 GTTGGTCAAACTTTACGGGACT 58.791 45.455 0.00 0.00 35.75 3.85
2593 2879 3.614159 GTTGGTCAAACTTTACGGGAC 57.386 47.619 0.00 0.00 35.75 4.46
2622 2908 8.006298 TCAGATTGTGAATGTTGGTACTTTTT 57.994 30.769 0.00 0.00 29.64 1.94
2623 2909 7.581213 TCAGATTGTGAATGTTGGTACTTTT 57.419 32.000 0.00 0.00 29.64 2.27
2624 2910 7.581213 TTCAGATTGTGAATGTTGGTACTTT 57.419 32.000 0.00 0.00 40.45 2.66
2625 2911 7.581213 TTTCAGATTGTGAATGTTGGTACTT 57.419 32.000 0.00 0.00 44.89 2.24
2626 2912 7.448161 TGATTTCAGATTGTGAATGTTGGTACT 59.552 33.333 0.00 0.00 44.89 2.73
2627 2913 7.592938 TGATTTCAGATTGTGAATGTTGGTAC 58.407 34.615 0.00 0.00 44.89 3.34
2628 2914 7.757941 TGATTTCAGATTGTGAATGTTGGTA 57.242 32.000 0.00 0.00 44.89 3.25
2629 2915 6.653526 TGATTTCAGATTGTGAATGTTGGT 57.346 33.333 0.00 0.00 44.89 3.67
2630 2916 9.811995 ATATTGATTTCAGATTGTGAATGTTGG 57.188 29.630 0.00 0.00 44.89 3.77
2655 2941 9.896645 ACTTTAAGTCATGACACATCTATTGAT 57.103 29.630 27.02 0.00 0.00 2.57
2656 2942 9.725019 AACTTTAAGTCATGACACATCTATTGA 57.275 29.630 27.02 5.47 0.00 2.57
2659 2945 9.725019 TGAAACTTTAAGTCATGACACATCTAT 57.275 29.630 27.02 7.36 0.00 1.98
2660 2946 9.725019 ATGAAACTTTAAGTCATGACACATCTA 57.275 29.630 27.02 7.86 30.84 1.98
2661 2947 8.627208 ATGAAACTTTAAGTCATGACACATCT 57.373 30.769 27.02 3.53 30.84 2.90
2687 2973 8.906867 ACATCTGCAATGCTAAAGTTATACAAT 58.093 29.630 6.82 0.00 0.00 2.71
2688 2974 8.279970 ACATCTGCAATGCTAAAGTTATACAA 57.720 30.769 6.82 0.00 0.00 2.41
2689 2975 7.864108 ACATCTGCAATGCTAAAGTTATACA 57.136 32.000 6.82 0.00 0.00 2.29
2690 2976 8.397906 TCAACATCTGCAATGCTAAAGTTATAC 58.602 33.333 6.82 0.00 0.00 1.47
2691 2977 8.504812 TCAACATCTGCAATGCTAAAGTTATA 57.495 30.769 6.82 0.00 0.00 0.98
2692 2978 7.395190 TCAACATCTGCAATGCTAAAGTTAT 57.605 32.000 6.82 0.00 0.00 1.89
2693 2979 6.816134 TCAACATCTGCAATGCTAAAGTTA 57.184 33.333 6.82 0.00 0.00 2.24
2694 2980 5.710513 TCAACATCTGCAATGCTAAAGTT 57.289 34.783 6.82 3.96 0.00 2.66
2695 2981 5.909621 ATCAACATCTGCAATGCTAAAGT 57.090 34.783 6.82 0.00 0.00 2.66
2696 2982 8.867112 AAATATCAACATCTGCAATGCTAAAG 57.133 30.769 6.82 0.00 0.00 1.85
2697 2983 9.656040 AAAAATATCAACATCTGCAATGCTAAA 57.344 25.926 6.82 0.00 0.00 1.85
2724 3010 9.438228 TCACAAAGTTTGACCGTATTTATATGA 57.562 29.630 22.23 7.49 0.00 2.15
2727 3013 9.275398 ACTTCACAAAGTTTGACCGTATTTATA 57.725 29.630 22.23 0.00 43.28 0.98
2728 3014 8.161699 ACTTCACAAAGTTTGACCGTATTTAT 57.838 30.769 22.23 0.00 43.28 1.40
2729 3015 7.556733 ACTTCACAAAGTTTGACCGTATTTA 57.443 32.000 22.23 0.00 43.28 1.40
2730 3016 6.445357 ACTTCACAAAGTTTGACCGTATTT 57.555 33.333 22.23 0.00 43.28 1.40
2755 3041 9.671279 TCTGCATATTAGAATTCTTTGAAGTCA 57.329 29.630 14.36 3.90 0.00 3.41
2757 3043 9.678260 ACTCTGCATATTAGAATTCTTTGAAGT 57.322 29.630 14.36 8.33 0.00 3.01
2767 3053 9.343539 GGTCCTTTTTACTCTGCATATTAGAAT 57.656 33.333 0.00 0.00 0.00 2.40
2768 3054 7.494625 CGGTCCTTTTTACTCTGCATATTAGAA 59.505 37.037 0.00 0.00 0.00 2.10
2769 3055 6.984474 CGGTCCTTTTTACTCTGCATATTAGA 59.016 38.462 0.00 0.00 0.00 2.10
2770 3056 6.202954 CCGGTCCTTTTTACTCTGCATATTAG 59.797 42.308 0.00 0.00 0.00 1.73
2771 3057 6.053005 CCGGTCCTTTTTACTCTGCATATTA 58.947 40.000 0.00 0.00 0.00 0.98
2772 3058 4.881850 CCGGTCCTTTTTACTCTGCATATT 59.118 41.667 0.00 0.00 0.00 1.28
2773 3059 4.163458 TCCGGTCCTTTTTACTCTGCATAT 59.837 41.667 0.00 0.00 0.00 1.78
2774 3060 3.516300 TCCGGTCCTTTTTACTCTGCATA 59.484 43.478 0.00 0.00 0.00 3.14
2775 3061 2.304761 TCCGGTCCTTTTTACTCTGCAT 59.695 45.455 0.00 0.00 0.00 3.96
2776 3062 1.695242 TCCGGTCCTTTTTACTCTGCA 59.305 47.619 0.00 0.00 0.00 4.41
2777 3063 2.347731 CTCCGGTCCTTTTTACTCTGC 58.652 52.381 0.00 0.00 0.00 4.26
2778 3064 2.354805 CCCTCCGGTCCTTTTTACTCTG 60.355 54.545 0.00 0.00 0.00 3.35
2779 3065 1.907255 CCCTCCGGTCCTTTTTACTCT 59.093 52.381 0.00 0.00 0.00 3.24
2780 3066 1.904537 TCCCTCCGGTCCTTTTTACTC 59.095 52.381 0.00 0.00 0.00 2.59
2781 3067 1.907255 CTCCCTCCGGTCCTTTTTACT 59.093 52.381 0.00 0.00 0.00 2.24
2782 3068 1.627329 ACTCCCTCCGGTCCTTTTTAC 59.373 52.381 0.00 0.00 0.00 2.01
2783 3069 2.034436 ACTCCCTCCGGTCCTTTTTA 57.966 50.000 0.00 0.00 0.00 1.52
2784 3070 1.627329 GTACTCCCTCCGGTCCTTTTT 59.373 52.381 0.00 0.00 0.00 1.94
2785 3071 1.203275 AGTACTCCCTCCGGTCCTTTT 60.203 52.381 0.00 0.00 0.00 2.27
2786 3072 0.412640 AGTACTCCCTCCGGTCCTTT 59.587 55.000 0.00 0.00 0.00 3.11
2787 3073 1.064091 GTAGTACTCCCTCCGGTCCTT 60.064 57.143 0.00 0.00 0.00 3.36
2788 3074 0.550432 GTAGTACTCCCTCCGGTCCT 59.450 60.000 0.00 0.00 0.00 3.85
2789 3075 0.257039 TGTAGTACTCCCTCCGGTCC 59.743 60.000 0.00 0.00 0.00 4.46
2790 3076 2.228925 GATGTAGTACTCCCTCCGGTC 58.771 57.143 0.00 0.00 0.00 4.79
2791 3077 1.567649 TGATGTAGTACTCCCTCCGGT 59.432 52.381 0.00 0.00 0.00 5.28
2792 3078 2.359981 TGATGTAGTACTCCCTCCGG 57.640 55.000 0.00 0.00 0.00 5.14
2793 3079 3.552875 TCTTGATGTAGTACTCCCTCCG 58.447 50.000 0.00 0.00 0.00 4.63
2794 3080 5.242838 CAGATCTTGATGTAGTACTCCCTCC 59.757 48.000 0.00 0.00 0.00 4.30
2795 3081 6.065374 TCAGATCTTGATGTAGTACTCCCTC 58.935 44.000 0.00 0.00 0.00 4.30
2796 3082 6.019656 TCAGATCTTGATGTAGTACTCCCT 57.980 41.667 0.00 0.00 0.00 4.20
2797 3083 6.065374 TCTCAGATCTTGATGTAGTACTCCC 58.935 44.000 0.00 0.00 34.68 4.30
2798 3084 6.770785 ACTCTCAGATCTTGATGTAGTACTCC 59.229 42.308 0.00 0.00 34.68 3.85
2799 3085 7.497579 TCACTCTCAGATCTTGATGTAGTACTC 59.502 40.741 0.00 0.00 34.68 2.59
2800 3086 7.342581 TCACTCTCAGATCTTGATGTAGTACT 58.657 38.462 0.00 0.00 34.68 2.73
2917 3205 4.624452 GGCATTGTCTTCTTGCAATTCTTC 59.376 41.667 0.00 0.00 38.12 2.87
2955 3243 2.093973 CCAACAAGTCTCGAGCATAGGT 60.094 50.000 7.81 0.00 0.00 3.08
3003 3291 7.994425 TTCAGCAAAAACCTCATGAGTATAA 57.006 32.000 21.11 0.00 0.00 0.98
3138 3426 7.330454 GCCTTAGTACTAGTGTTGAAACTAACC 59.670 40.741 5.39 0.00 32.35 2.85
3183 3471 5.862678 TGATACCCAGTGATTCGAACATA 57.137 39.130 0.00 0.00 0.00 2.29
3416 3727 1.808411 TCTCCTCACAATGTTTCGCC 58.192 50.000 0.00 0.00 0.00 5.54
3920 4241 9.265901 GAGTTACAGACATAGAACATATGCATT 57.734 33.333 3.54 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.