Multiple sequence alignment - TraesCS3A01G332500

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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 TraesCS3A01G332500 chr3A 100.000 3028 0 0 1 3028 577065161 577068188 0.000000e+00 5592.0
1 TraesCS3A01G332500 chr3D 90.447 2104 141 29 381 2451 438470320 438472396 0.000000e+00 2717.0
2 TraesCS3A01G332500 chr3D 92.839 391 17 7 1 384 438469818 438470204 9.480000e-155 556.0
3 TraesCS3A01G332500 chr3D 86.344 227 28 1 2708 2931 438515306 438515532 8.390000e-61 244.0
4 TraesCS3A01G332500 chr3B 93.193 999 51 13 1387 2376 574266875 574267865 0.000000e+00 1452.0
5 TraesCS3A01G332500 chr3B 88.934 985 77 13 380 1357 574265919 574266878 0.000000e+00 1186.0
6 TraesCS3A01G332500 chr3B 94.103 390 17 2 1 384 574265427 574265816 3.360000e-164 588.0
7 TraesCS3A01G332500 chr3B 86.340 388 42 8 2551 2931 574326777 574327160 2.170000e-111 412.0
8 TraesCS3A01G332500 chr3B 93.333 60 3 1 2970 3028 574327249 574327308 1.500000e-13 87.9


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 TraesCS3A01G332500 chr3A 577065161 577068188 3027 False 5592.000000 5592 100.000000 1 3028 1 chr3A.!!$F1 3027
1 TraesCS3A01G332500 chr3D 438469818 438472396 2578 False 1636.500000 2717 91.643000 1 2451 2 chr3D.!!$F2 2450
2 TraesCS3A01G332500 chr3B 574265427 574267865 2438 False 1075.333333 1452 92.076667 1 2376 3 chr3B.!!$F1 2375
3 TraesCS3A01G332500 chr3B 574326777 574327308 531 False 249.950000 412 89.836500 2551 3028 2 chr3B.!!$F2 477

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
256 266 0.447406 CATCGTTGGCAAATCGAGCA 59.553 50.0 16.36 0.00 37.04 4.26 F
1525 1788 0.391130 TGCGAGTGGCCAACATACTC 60.391 55.0 7.24 8.84 42.61 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1781 2044 0.098200 TCAGTGAGTTATCGACGGCG 59.902 55.0 2.87 2.87 39.35 6.46 R
2881 3166 0.027455 TCGCACAAAAACGCACTCAG 59.973 50.0 0.00 0.00 0.00 3.35 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
200 201 1.524008 CGGTCAGGGAAAGGGTTTGC 61.524 60.000 0.00 0.00 0.00 3.68
219 226 3.950397 TGCGATCAGGTTCAGGTAAAAT 58.050 40.909 0.00 0.00 0.00 1.82
226 233 7.094975 CGATCAGGTTCAGGTAAAATACAAACA 60.095 37.037 0.00 0.00 0.00 2.83
227 234 8.650143 ATCAGGTTCAGGTAAAATACAAACAT 57.350 30.769 0.00 0.00 0.00 2.71
235 242 9.126151 TCAGGTAAAATACAAACATGTTCTTCA 57.874 29.630 12.39 0.00 0.00 3.02
242 252 5.947228 ACAAACATGTTCTTCATCATCGT 57.053 34.783 12.39 0.00 34.09 3.73
256 266 0.447406 CATCGTTGGCAAATCGAGCA 59.553 50.000 16.36 0.00 37.04 4.26
265 275 3.315142 AAATCGAGCAGCTGCCGGA 62.315 57.895 33.83 30.18 43.38 5.14
481 721 2.507102 ACCTTCGATCGCAGCACG 60.507 61.111 11.09 0.00 45.62 5.34
483 723 2.507102 CTTCGATCGCAGCACGGT 60.507 61.111 11.09 0.00 43.89 4.83
495 735 2.243957 GCACGGTTTGGCCTTTTGC 61.244 57.895 3.32 0.09 40.16 3.68
558 799 2.543012 CTGGATTCGTGCAGCTCATTAG 59.457 50.000 0.00 0.00 0.00 1.73
598 844 4.256920 GAGCAGAAGCAAGAATACCAGAA 58.743 43.478 0.00 0.00 45.49 3.02
679 928 4.021925 GCCCTTCCAGCCGACTGT 62.022 66.667 0.00 0.00 42.81 3.55
736 985 1.743623 CGCCATGGTTGCCGAGTAA 60.744 57.895 14.67 0.00 0.00 2.24
895 1148 3.648528 TCGCCACATCGAGATCAAG 57.351 52.632 0.00 0.00 34.09 3.02
957 1214 2.168728 GGATAAGAGTGGCCGTTCTTCT 59.831 50.000 20.98 13.75 35.42 2.85
1017 1277 2.117865 CTCATGGCTTCTTCCTCCTCT 58.882 52.381 0.00 0.00 0.00 3.69
1091 1351 4.127040 CACGCGCTCCTCTGCTCT 62.127 66.667 5.73 0.00 0.00 4.09
1104 1364 2.152297 CTGCTCTCCACGCTGTGTCT 62.152 60.000 7.68 0.00 0.00 3.41
1106 1366 1.735920 CTCTCCACGCTGTGTCTGC 60.736 63.158 7.68 0.00 0.00 4.26
1155 1415 2.583593 CCTCTCGCGGTTGCTAGC 60.584 66.667 8.10 8.10 39.65 3.42
1314 1574 3.182996 ACCACCAAGGACACCCCC 61.183 66.667 0.00 0.00 41.22 5.40
1339 1599 2.187946 GGGCTGGTGATCACTCGG 59.812 66.667 24.50 19.15 0.00 4.63
1358 1620 3.510360 TCGGTTCTTGCTACTTTCTAGCT 59.490 43.478 0.00 0.00 40.95 3.32
1378 1640 3.887716 GCTATCTCCATGCATTGTTCCTT 59.112 43.478 0.00 0.00 0.00 3.36
1382 1644 4.661222 TCTCCATGCATTGTTCCTTGTTA 58.339 39.130 0.00 0.00 0.00 2.41
1429 1691 1.621317 TGCACCCTGTCGATTAGTCAA 59.379 47.619 0.00 0.00 0.00 3.18
1474 1737 3.668141 TCAGGCAATGTGGAACCATAT 57.332 42.857 0.00 0.00 34.36 1.78
1525 1788 0.391130 TGCGAGTGGCCAACATACTC 60.391 55.000 7.24 8.84 42.61 2.59
1534 1797 1.747206 GCCAACATACTCTCCGGCAAT 60.747 52.381 0.00 0.00 39.38 3.56
1801 2073 1.466866 CGCCGTCGATAACTCACTGAA 60.467 52.381 0.00 0.00 38.10 3.02
2085 2357 0.387239 GCGGGTTTGCTTGCTTACTG 60.387 55.000 0.00 0.00 0.00 2.74
2095 2367 2.143122 CTTGCTTACTGCTTCCACGAA 58.857 47.619 0.00 0.00 43.37 3.85
2101 2373 4.261031 GCTTACTGCTTCCACGAAAGAAAA 60.261 41.667 0.00 0.00 38.95 2.29
2129 2401 3.491447 CCTGTTTTTGAGGCTTGGAACAG 60.491 47.826 18.75 18.75 42.39 3.16
2239 2516 5.819901 CAGAATCAGTTGGTATCTTCTTCCC 59.180 44.000 0.00 0.00 0.00 3.97
2251 2529 5.813513 ATCTTCTTCCCAACAGCAAAAAT 57.186 34.783 0.00 0.00 0.00 1.82
2252 2530 4.947645 TCTTCTTCCCAACAGCAAAAATG 58.052 39.130 0.00 0.00 0.00 2.32
2253 2531 4.405358 TCTTCTTCCCAACAGCAAAAATGT 59.595 37.500 0.00 0.00 0.00 2.71
2260 2538 4.635324 CCCAACAGCAAAAATGTTTGAGTT 59.365 37.500 12.75 12.08 45.99 3.01
2266 2544 8.715191 ACAGCAAAAATGTTTGAGTTTGAATA 57.285 26.923 12.75 0.00 45.99 1.75
2292 2570 1.009078 CATGCACGTGAGGTACCATG 58.991 55.000 22.23 17.36 33.81 3.66
2293 2571 0.744414 ATGCACGTGAGGTACCATGC 60.744 55.000 22.23 15.09 38.03 4.06
2294 2572 1.375396 GCACGTGAGGTACCATGCA 60.375 57.895 22.23 6.35 37.67 3.96
2298 2578 1.079127 GTGAGGTACCATGCAGCGT 60.079 57.895 15.94 0.00 0.00 5.07
2316 2596 1.134699 CGTTTGGAGCATCTCTAGCCA 60.135 52.381 0.00 0.00 33.73 4.75
2328 2608 6.991531 AGCATCTCTAGCCAATCTCTTAAAAG 59.008 38.462 0.00 0.00 0.00 2.27
2393 2674 7.661536 ATCTAGCCGATCCTTATTAGCATTA 57.338 36.000 0.00 0.00 0.00 1.90
2415 2697 9.449719 CATTAGAGGAGTAAAACATTTACACCT 57.550 33.333 23.19 23.19 44.73 4.00
2416 2698 8.842358 TTAGAGGAGTAAAACATTTACACCTG 57.158 34.615 26.11 0.00 43.02 4.00
2417 2699 6.238648 AGAGGAGTAAAACATTTACACCTGG 58.761 40.000 26.11 0.00 43.02 4.45
2420 2702 4.139038 AGTAAAACATTTACACCTGGCGT 58.861 39.130 13.65 0.00 0.00 5.68
2439 2721 2.747135 CGTCGGTGGCCCCTTAATTTAT 60.747 50.000 0.00 0.00 0.00 1.40
2441 2723 3.317149 GTCGGTGGCCCCTTAATTTATTC 59.683 47.826 0.00 0.00 0.00 1.75
2451 2733 1.219646 TAATTTATTCGACCGGCGCC 58.780 50.000 19.07 19.07 40.61 6.53
2452 2734 0.745128 AATTTATTCGACCGGCGCCA 60.745 50.000 28.98 5.63 40.61 5.69
2453 2735 1.433837 ATTTATTCGACCGGCGCCAC 61.434 55.000 28.98 15.91 40.61 5.01
2454 2736 2.510064 TTTATTCGACCGGCGCCACT 62.510 55.000 28.98 10.44 40.61 4.00
2455 2737 2.894240 TTATTCGACCGGCGCCACTC 62.894 60.000 28.98 18.42 40.61 3.51
2468 2750 3.827898 CACTCTCCCCCGCTCGAC 61.828 72.222 0.00 0.00 0.00 4.20
2478 2760 4.498520 CGCTCGACCGCATCCACT 62.499 66.667 0.00 0.00 0.00 4.00
2479 2761 2.583593 GCTCGACCGCATCCACTC 60.584 66.667 0.00 0.00 0.00 3.51
2480 2762 2.105128 CTCGACCGCATCCACTCC 59.895 66.667 0.00 0.00 0.00 3.85
2481 2763 2.678580 TCGACCGCATCCACTCCA 60.679 61.111 0.00 0.00 0.00 3.86
2482 2764 2.202797 CGACCGCATCCACTCCAG 60.203 66.667 0.00 0.00 0.00 3.86
2483 2765 2.710902 CGACCGCATCCACTCCAGA 61.711 63.158 0.00 0.00 0.00 3.86
2484 2766 1.142748 GACCGCATCCACTCCAGAG 59.857 63.158 0.00 0.00 0.00 3.35
2485 2767 2.202987 CCGCATCCACTCCAGAGC 60.203 66.667 0.00 0.00 0.00 4.09
2486 2768 2.584418 CGCATCCACTCCAGAGCG 60.584 66.667 0.00 0.00 39.17 5.03
2487 2769 2.202987 GCATCCACTCCAGAGCGG 60.203 66.667 0.00 0.00 32.02 5.52
2488 2770 2.202987 CATCCACTCCAGAGCGGC 60.203 66.667 0.00 0.00 30.87 6.53
2489 2771 3.474570 ATCCACTCCAGAGCGGCC 61.475 66.667 0.00 0.00 30.87 6.13
2491 2773 3.790437 CCACTCCAGAGCGGCCAT 61.790 66.667 2.24 0.00 33.14 4.40
2492 2774 2.202987 CACTCCAGAGCGGCCATC 60.203 66.667 2.24 0.00 33.14 3.51
2493 2775 3.474570 ACTCCAGAGCGGCCATCC 61.475 66.667 2.24 0.00 33.14 3.51
2494 2776 4.247380 CTCCAGAGCGGCCATCCC 62.247 72.222 2.24 0.00 33.14 3.85
2495 2777 4.804420 TCCAGAGCGGCCATCCCT 62.804 66.667 2.24 0.00 33.14 4.20
2496 2778 3.801997 CCAGAGCGGCCATCCCTT 61.802 66.667 2.24 0.00 0.00 3.95
2497 2779 2.273449 CAGAGCGGCCATCCCTTT 59.727 61.111 2.24 0.00 0.00 3.11
2498 2780 1.821332 CAGAGCGGCCATCCCTTTC 60.821 63.158 2.24 0.00 0.00 2.62
2499 2781 2.517166 GAGCGGCCATCCCTTTCC 60.517 66.667 2.24 0.00 0.00 3.13
2500 2782 3.017581 AGCGGCCATCCCTTTCCT 61.018 61.111 2.24 0.00 0.00 3.36
2501 2783 2.517166 GCGGCCATCCCTTTCCTC 60.517 66.667 2.24 0.00 0.00 3.71
2502 2784 2.193248 CGGCCATCCCTTTCCTCC 59.807 66.667 2.24 0.00 0.00 4.30
2503 2785 2.679342 CGGCCATCCCTTTCCTCCA 61.679 63.158 2.24 0.00 0.00 3.86
2504 2786 1.076705 GGCCATCCCTTTCCTCCAC 60.077 63.158 0.00 0.00 0.00 4.02
2505 2787 1.076705 GCCATCCCTTTCCTCCACC 60.077 63.158 0.00 0.00 0.00 4.61
2506 2788 1.863155 GCCATCCCTTTCCTCCACCA 61.863 60.000 0.00 0.00 0.00 4.17
2507 2789 0.257039 CCATCCCTTTCCTCCACCAG 59.743 60.000 0.00 0.00 0.00 4.00
2508 2790 0.394899 CATCCCTTTCCTCCACCAGC 60.395 60.000 0.00 0.00 0.00 4.85
2509 2791 1.575447 ATCCCTTTCCTCCACCAGCC 61.575 60.000 0.00 0.00 0.00 4.85
2510 2792 2.538141 CCCTTTCCTCCACCAGCCA 61.538 63.158 0.00 0.00 0.00 4.75
2511 2793 1.303643 CCTTTCCTCCACCAGCCAC 60.304 63.158 0.00 0.00 0.00 5.01
2512 2794 1.303643 CTTTCCTCCACCAGCCACC 60.304 63.158 0.00 0.00 0.00 4.61
2513 2795 2.067932 CTTTCCTCCACCAGCCACCA 62.068 60.000 0.00 0.00 0.00 4.17
2514 2796 1.434513 TTTCCTCCACCAGCCACCAT 61.435 55.000 0.00 0.00 0.00 3.55
2515 2797 1.434513 TTCCTCCACCAGCCACCATT 61.435 55.000 0.00 0.00 0.00 3.16
2516 2798 1.379044 CCTCCACCAGCCACCATTC 60.379 63.158 0.00 0.00 0.00 2.67
2517 2799 1.379916 CTCCACCAGCCACCATTCA 59.620 57.895 0.00 0.00 0.00 2.57
2518 2800 0.962356 CTCCACCAGCCACCATTCAC 60.962 60.000 0.00 0.00 0.00 3.18
2519 2801 1.978617 CCACCAGCCACCATTCACC 60.979 63.158 0.00 0.00 0.00 4.02
2520 2802 1.228521 CACCAGCCACCATTCACCA 60.229 57.895 0.00 0.00 0.00 4.17
2521 2803 1.228552 ACCAGCCACCATTCACCAC 60.229 57.895 0.00 0.00 0.00 4.16
2522 2804 1.075482 CCAGCCACCATTCACCACT 59.925 57.895 0.00 0.00 0.00 4.00
2523 2805 1.246056 CCAGCCACCATTCACCACTG 61.246 60.000 0.00 0.00 0.00 3.66
2524 2806 1.604593 AGCCACCATTCACCACTGC 60.605 57.895 0.00 0.00 0.00 4.40
2525 2807 1.902918 GCCACCATTCACCACTGCA 60.903 57.895 0.00 0.00 0.00 4.41
2526 2808 1.870055 GCCACCATTCACCACTGCAG 61.870 60.000 13.48 13.48 0.00 4.41
2527 2809 0.538057 CCACCATTCACCACTGCAGT 60.538 55.000 15.25 15.25 0.00 4.40
2528 2810 0.877071 CACCATTCACCACTGCAGTC 59.123 55.000 18.64 0.00 0.00 3.51
2529 2811 0.603707 ACCATTCACCACTGCAGTCG 60.604 55.000 18.64 14.11 0.00 4.18
2530 2812 1.499056 CATTCACCACTGCAGTCGC 59.501 57.895 18.64 0.00 39.24 5.19
2531 2813 1.672356 ATTCACCACTGCAGTCGCC 60.672 57.895 18.64 0.00 37.32 5.54
2532 2814 2.116983 ATTCACCACTGCAGTCGCCT 62.117 55.000 18.64 0.00 37.32 5.52
2533 2815 2.994387 TTCACCACTGCAGTCGCCTG 62.994 60.000 18.64 6.04 41.91 4.85
2534 2816 4.320456 ACCACTGCAGTCGCCTGG 62.320 66.667 18.64 17.40 39.72 4.45
2536 2818 4.994471 CACTGCAGTCGCCTGGCA 62.994 66.667 18.64 2.90 39.22 4.92
2537 2819 4.996434 ACTGCAGTCGCCTGGCAC 62.996 66.667 15.25 15.32 39.22 5.01
2565 2847 1.668294 CTCCTCGTCCTTGCACTGT 59.332 57.895 0.00 0.00 0.00 3.55
2573 2855 1.197721 GTCCTTGCACTGTTGGATTCG 59.802 52.381 0.00 0.00 0.00 3.34
2575 2857 1.197721 CCTTGCACTGTTGGATTCGAC 59.802 52.381 0.00 0.00 0.00 4.20
2578 2860 1.416049 CACTGTTGGATTCGACGCG 59.584 57.895 3.53 3.53 0.00 6.01
2579 2861 2.380410 ACTGTTGGATTCGACGCGC 61.380 57.895 5.73 0.00 0.00 6.86
2580 2862 2.356433 TGTTGGATTCGACGCGCA 60.356 55.556 5.73 0.00 0.00 6.09
2582 2864 3.115892 TTGGATTCGACGCGCACC 61.116 61.111 5.73 1.17 0.00 5.01
2597 2879 2.366435 ACCCCCACCGGATTCGAT 60.366 61.111 9.46 0.00 39.00 3.59
2605 2887 1.227943 CCGGATTCGATGCACCCAT 60.228 57.895 0.00 0.00 39.00 4.00
2661 2943 4.753662 TAGCCACCCGGAGCTCGT 62.754 66.667 15.62 0.00 40.56 4.18
2683 2965 1.366366 GCCGCCTCGTGGTATGTAT 59.634 57.895 5.26 0.00 35.34 2.29
2685 2967 1.779569 CCGCCTCGTGGTATGTATTC 58.220 55.000 5.26 0.00 35.27 1.75
2700 2982 3.371965 TGTATTCCTCCTCTTACCGCTT 58.628 45.455 0.00 0.00 0.00 4.68
2705 2987 1.407437 CCTCCTCTTACCGCTTGCATT 60.407 52.381 0.00 0.00 0.00 3.56
2706 2988 1.667724 CTCCTCTTACCGCTTGCATTG 59.332 52.381 0.00 0.00 0.00 2.82
2720 3002 1.112315 GCATTGTCACCCAACCACCA 61.112 55.000 0.00 0.00 35.44 4.17
2721 3003 0.961019 CATTGTCACCCAACCACCAG 59.039 55.000 0.00 0.00 35.44 4.00
2723 3005 2.194597 GTCACCCAACCACCAGCA 59.805 61.111 0.00 0.00 0.00 4.41
2724 3006 1.898574 GTCACCCAACCACCAGCAG 60.899 63.158 0.00 0.00 0.00 4.24
2730 3012 0.393537 CCAACCACCAGCAGATCCTC 60.394 60.000 0.00 0.00 0.00 3.71
2735 3017 2.415010 CCAGCAGATCCTCGTCGG 59.585 66.667 0.00 0.00 0.00 4.79
2739 3021 3.133014 CAGATCCTCGTCGGCCAT 58.867 61.111 2.24 0.00 0.00 4.40
2743 3025 2.071844 GATCCTCGTCGGCCATTCGA 62.072 60.000 2.24 8.66 36.76 3.71
2752 3034 4.838152 GCCATTCGAGCGGGCTCA 62.838 66.667 19.65 2.47 44.32 4.26
2753 3035 2.587194 CCATTCGAGCGGGCTCAG 60.587 66.667 19.65 12.44 42.86 3.35
2816 3101 1.322538 TGATGACTGCTAGCGGCTGA 61.323 55.000 23.72 7.81 41.52 4.26
2821 3106 0.179089 ACTGCTAGCGGCTGATTCTG 60.179 55.000 23.72 5.53 41.52 3.02
2824 3109 1.770085 GCTAGCGGCTGATTCTGTGC 61.770 60.000 13.86 0.61 38.06 4.57
2838 3123 0.389166 CTGTGCCAGGTCTCGAAGAC 60.389 60.000 6.50 6.50 44.32 3.01
2839 3124 1.444553 GTGCCAGGTCTCGAAGACG 60.445 63.158 8.33 0.00 45.96 4.18
2843 3128 1.002251 GCCAGGTCTCGAAGACGATAG 60.002 57.143 0.00 0.00 45.96 2.08
2844 3129 2.562635 CCAGGTCTCGAAGACGATAGA 58.437 52.381 0.00 0.00 45.96 1.98
2872 3157 2.351738 CGGATGGGTTTTCTTCAAGTGC 60.352 50.000 0.00 0.00 0.00 4.40
2876 3161 2.755655 TGGGTTTTCTTCAAGTGCGAAA 59.244 40.909 0.00 0.00 0.00 3.46
2881 3166 3.896648 TTCTTCAAGTGCGAAATGGAC 57.103 42.857 0.00 0.00 39.61 4.02
2899 3184 0.248054 ACTGAGTGCGTTTTTGTGCG 60.248 50.000 0.00 0.00 0.00 5.34
2908 3193 3.002862 TGCGTTTTTGTGCGATAGTTCTT 59.997 39.130 0.00 0.00 39.35 2.52
2909 3194 3.972502 GCGTTTTTGTGCGATAGTTCTTT 59.027 39.130 0.00 0.00 39.35 2.52
2910 3195 4.143824 GCGTTTTTGTGCGATAGTTCTTTG 60.144 41.667 0.00 0.00 39.35 2.77
2931 3216 7.821846 TCTTTGGTTCAACTAAAATTTGTGCTT 59.178 29.630 0.31 0.00 28.18 3.91
2961 3282 3.389329 ACCAAGTCTCAGTCAAGTCACAT 59.611 43.478 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
200 201 6.978343 TTGTATTTTACCTGAACCTGATCG 57.022 37.500 0.00 0.00 0.00 3.69
219 226 7.297391 CAACGATGATGAAGAACATGTTTGTA 58.703 34.615 13.36 0.53 39.56 2.41
226 233 3.346315 TGCCAACGATGATGAAGAACAT 58.654 40.909 0.00 0.00 42.47 2.71
227 234 2.777094 TGCCAACGATGATGAAGAACA 58.223 42.857 0.00 0.00 0.00 3.18
235 242 1.331756 GCTCGATTTGCCAACGATGAT 59.668 47.619 0.00 0.00 35.58 2.45
242 252 1.878070 CAGCTGCTCGATTTGCCAA 59.122 52.632 0.00 0.00 0.00 4.52
256 266 0.253044 TCTAGCAAAATCCGGCAGCT 59.747 50.000 0.00 3.76 39.22 4.24
265 275 6.827762 CCTCCTCTTCATTTCTCTAGCAAAAT 59.172 38.462 0.00 0.00 0.00 1.82
464 704 2.507102 CGTGCTGCGATCGAAGGT 60.507 61.111 24.43 0.00 44.77 3.50
481 721 1.134551 TGTTCTGCAAAAGGCCAAACC 60.135 47.619 5.01 0.00 43.89 3.27
483 723 4.141846 TGTTATGTTCTGCAAAAGGCCAAA 60.142 37.500 5.01 0.00 43.89 3.28
558 799 2.670509 GCTCCATGCTCTTTTCTTGTGC 60.671 50.000 0.00 0.00 38.95 4.57
562 803 3.430042 TCTGCTCCATGCTCTTTTCTT 57.570 42.857 0.00 0.00 43.37 2.52
563 804 3.345414 CTTCTGCTCCATGCTCTTTTCT 58.655 45.455 0.00 0.00 43.37 2.52
564 805 2.159407 GCTTCTGCTCCATGCTCTTTTC 60.159 50.000 0.00 0.00 43.37 2.29
565 806 1.817447 GCTTCTGCTCCATGCTCTTTT 59.183 47.619 0.00 0.00 43.37 2.27
566 807 1.271762 TGCTTCTGCTCCATGCTCTTT 60.272 47.619 0.00 0.00 43.37 2.52
588 834 1.141053 ACTCCGGCCATTCTGGTATTC 59.859 52.381 2.24 0.00 40.46 1.75
667 913 1.979155 CTCTCCACAGTCGGCTGGA 60.979 63.158 22.98 10.08 46.62 3.86
670 919 2.336478 CGTCTCTCCACAGTCGGCT 61.336 63.158 0.00 0.00 0.00 5.52
676 925 1.153939 CCTTCGCGTCTCTCCACAG 60.154 63.158 5.77 0.00 0.00 3.66
677 926 1.602605 TCCTTCGCGTCTCTCCACA 60.603 57.895 5.77 0.00 0.00 4.17
679 928 2.687805 CGTCCTTCGCGTCTCTCCA 61.688 63.158 5.77 0.00 0.00 3.86
736 985 2.034879 CGAGCAGCAACGGTGGAAT 61.035 57.895 0.90 0.00 0.00 3.01
780 1033 4.202182 CGTCGAGGATAAGGTGGGATAAAA 60.202 45.833 0.00 0.00 0.00 1.52
890 1143 1.756375 GACGCGCTCGCATTCTTGAT 61.756 55.000 5.73 0.00 42.06 2.57
891 1144 2.432456 ACGCGCTCGCATTCTTGA 60.432 55.556 5.73 0.00 42.06 3.02
895 1148 4.253273 GTCGACGCGCTCGCATTC 62.253 66.667 20.94 8.65 42.62 2.67
996 1256 0.545646 AGGAGGAAGAAGCCATGAGC 59.454 55.000 0.00 0.00 44.25 4.26
997 1257 2.117865 AGAGGAGGAAGAAGCCATGAG 58.882 52.381 0.00 0.00 0.00 2.90
998 1258 2.260639 AGAGGAGGAAGAAGCCATGA 57.739 50.000 0.00 0.00 0.00 3.07
999 1259 2.421248 GGAAGAGGAGGAAGAAGCCATG 60.421 54.545 0.00 0.00 0.00 3.66
1017 1277 2.283676 AGCGGGGAGAAGACGGAA 60.284 61.111 0.00 0.00 0.00 4.30
1088 1348 1.735920 GCAGACACAGCGTGGAGAG 60.736 63.158 12.18 2.49 37.94 3.20
1151 1411 1.382420 AGCTCCCTCCTGTGGCTAG 60.382 63.158 0.00 0.00 0.00 3.42
1152 1412 1.687146 CAGCTCCCTCCTGTGGCTA 60.687 63.158 0.00 0.00 0.00 3.93
1155 1415 2.608988 ACCAGCTCCCTCCTGTGG 60.609 66.667 0.00 0.00 0.00 4.17
1339 1599 6.921307 GGAGATAGCTAGAAAGTAGCAAGAAC 59.079 42.308 0.00 0.00 42.68 3.01
1358 1620 4.858850 ACAAGGAACAATGCATGGAGATA 58.141 39.130 8.45 0.00 0.00 1.98
1429 1691 6.757897 TTTCATGACAAAACTCAACTCAGT 57.242 33.333 0.00 0.00 0.00 3.41
1474 1737 2.268920 GGCGGCAGGATGAACTCA 59.731 61.111 3.07 0.00 39.69 3.41
1534 1797 1.603455 GCACTTGGGCTGGCAGTAA 60.603 57.895 17.16 8.40 0.00 2.24
1624 1887 2.511600 CGGTTGGTGAGGCGGATC 60.512 66.667 0.00 0.00 0.00 3.36
1781 2044 0.098200 TCAGTGAGTTATCGACGGCG 59.902 55.000 2.87 2.87 39.35 6.46
1782 2045 2.186076 CTTCAGTGAGTTATCGACGGC 58.814 52.381 0.00 0.00 0.00 5.68
1783 2046 2.163815 ACCTTCAGTGAGTTATCGACGG 59.836 50.000 0.00 0.00 0.00 4.79
1784 2047 3.489180 ACCTTCAGTGAGTTATCGACG 57.511 47.619 0.00 0.00 0.00 5.12
1801 2073 2.435372 TTCAGGTTTCAGCAACACCT 57.565 45.000 0.00 0.00 41.97 4.00
1880 2152 4.704833 CCCGTCAGTGCCAGTGGG 62.705 72.222 12.15 0.00 37.18 4.61
2085 2357 3.643159 ACCATTTTCTTTCGTGGAAGC 57.357 42.857 0.00 0.00 35.69 3.86
2095 2367 6.685368 GCCTCAAAAACAGGTACCATTTTCTT 60.685 38.462 20.96 9.08 32.98 2.52
2101 2373 3.525800 AGCCTCAAAAACAGGTACCAT 57.474 42.857 15.94 0.00 32.98 3.55
2129 2401 6.037098 AGTCGATCAAGTAGCTCATTACAAC 58.963 40.000 0.00 0.00 0.00 3.32
2229 2506 5.070847 ACATTTTTGCTGTTGGGAAGAAGAT 59.929 36.000 0.00 0.00 0.00 2.40
2239 2516 6.829703 TCAAACTCAAACATTTTTGCTGTTG 58.170 32.000 12.72 9.88 41.78 3.33
2251 2529 8.243426 GCATGGTAGAATATTCAAACTCAAACA 58.757 33.333 17.56 8.25 0.00 2.83
2252 2530 8.243426 TGCATGGTAGAATATTCAAACTCAAAC 58.757 33.333 17.56 10.75 0.00 2.93
2253 2531 8.243426 GTGCATGGTAGAATATTCAAACTCAAA 58.757 33.333 17.56 4.25 0.00 2.69
2260 2538 5.423886 TCACGTGCATGGTAGAATATTCAA 58.576 37.500 17.56 0.94 0.00 2.69
2266 2544 1.555075 ACCTCACGTGCATGGTAGAAT 59.445 47.619 20.56 2.39 0.00 2.40
2292 2570 1.023513 AGAGATGCTCCAAACGCTGC 61.024 55.000 0.00 0.00 0.00 5.25
2293 2571 2.200067 CTAGAGATGCTCCAAACGCTG 58.800 52.381 0.00 0.00 0.00 5.18
2294 2572 1.472376 GCTAGAGATGCTCCAAACGCT 60.472 52.381 0.00 0.00 0.00 5.07
2298 2578 3.457380 AGATTGGCTAGAGATGCTCCAAA 59.543 43.478 0.00 0.00 39.85 3.28
2353 2634 3.745797 GCTAGATCCAGTTTAGGCCCTTG 60.746 52.174 0.00 0.00 0.00 3.61
2393 2674 6.238648 CCAGGTGTAAATGTTTTACTCCTCT 58.761 40.000 21.86 8.19 43.21 3.69
2405 2686 0.672401 ACCGACGCCAGGTGTAAATG 60.672 55.000 5.35 0.00 41.10 2.32
2417 2699 3.692370 ATTAAGGGGCCACCGACGC 62.692 63.158 0.00 0.00 46.96 5.19
2420 2702 3.558033 GAATAAATTAAGGGGCCACCGA 58.442 45.455 0.00 0.00 46.96 4.69
2425 2707 2.551032 CGGTCGAATAAATTAAGGGGCC 59.449 50.000 0.00 0.00 0.00 5.80
2451 2733 3.827898 GTCGAGCGGGGGAGAGTG 61.828 72.222 0.00 0.00 0.00 3.51
2461 2743 4.498520 AGTGGATGCGGTCGAGCG 62.499 66.667 31.08 31.08 40.67 5.03
2462 2744 2.583593 GAGTGGATGCGGTCGAGC 60.584 66.667 4.06 4.06 37.71 5.03
2463 2745 2.105128 GGAGTGGATGCGGTCGAG 59.895 66.667 0.00 0.00 0.00 4.04
2464 2746 2.678580 TGGAGTGGATGCGGTCGA 60.679 61.111 0.00 0.00 0.00 4.20
2465 2747 2.202797 CTGGAGTGGATGCGGTCG 60.203 66.667 0.00 0.00 0.00 4.79
2466 2748 1.142748 CTCTGGAGTGGATGCGGTC 59.857 63.158 0.00 0.00 0.00 4.79
2467 2749 3.023949 GCTCTGGAGTGGATGCGGT 62.024 63.158 0.00 0.00 0.00 5.68
2468 2750 2.202987 GCTCTGGAGTGGATGCGG 60.203 66.667 0.00 0.00 0.00 5.69
2469 2751 2.584418 CGCTCTGGAGTGGATGCG 60.584 66.667 3.48 0.00 35.41 4.73
2475 2757 2.202987 GATGGCCGCTCTGGAGTG 60.203 66.667 0.00 4.36 42.00 3.51
2476 2758 3.474570 GGATGGCCGCTCTGGAGT 61.475 66.667 0.00 0.00 42.00 3.85
2477 2759 4.247380 GGGATGGCCGCTCTGGAG 62.247 72.222 0.00 0.00 42.00 3.86
2478 2760 4.804420 AGGGATGGCCGCTCTGGA 62.804 66.667 0.00 0.00 42.00 3.86
2479 2761 3.350031 AAAGGGATGGCCGCTCTGG 62.350 63.158 0.00 0.00 37.02 3.86
2480 2762 1.821332 GAAAGGGATGGCCGCTCTG 60.821 63.158 0.00 0.00 37.02 3.35
2481 2763 2.592308 GAAAGGGATGGCCGCTCT 59.408 61.111 0.00 0.00 37.02 4.09
2482 2764 2.517166 GGAAAGGGATGGCCGCTC 60.517 66.667 0.00 0.00 37.02 5.03
2483 2765 3.017581 AGGAAAGGGATGGCCGCT 61.018 61.111 0.00 0.00 40.06 5.52
2484 2766 2.517166 GAGGAAAGGGATGGCCGC 60.517 66.667 0.00 0.00 33.83 6.53
2485 2767 2.193248 GGAGGAAAGGGATGGCCG 59.807 66.667 0.00 0.00 33.83 6.13
2486 2768 1.076705 GTGGAGGAAAGGGATGGCC 60.077 63.158 0.00 0.00 0.00 5.36
2487 2769 1.076705 GGTGGAGGAAAGGGATGGC 60.077 63.158 0.00 0.00 0.00 4.40
2488 2770 0.257039 CTGGTGGAGGAAAGGGATGG 59.743 60.000 0.00 0.00 0.00 3.51
2489 2771 0.394899 GCTGGTGGAGGAAAGGGATG 60.395 60.000 0.00 0.00 0.00 3.51
2490 2772 1.575447 GGCTGGTGGAGGAAAGGGAT 61.575 60.000 0.00 0.00 0.00 3.85
2491 2773 2.231380 GGCTGGTGGAGGAAAGGGA 61.231 63.158 0.00 0.00 0.00 4.20
2492 2774 2.356667 GGCTGGTGGAGGAAAGGG 59.643 66.667 0.00 0.00 0.00 3.95
2493 2775 1.303643 GTGGCTGGTGGAGGAAAGG 60.304 63.158 0.00 0.00 0.00 3.11
2494 2776 1.303643 GGTGGCTGGTGGAGGAAAG 60.304 63.158 0.00 0.00 0.00 2.62
2495 2777 1.434513 ATGGTGGCTGGTGGAGGAAA 61.435 55.000 0.00 0.00 0.00 3.13
2496 2778 1.434513 AATGGTGGCTGGTGGAGGAA 61.435 55.000 0.00 0.00 0.00 3.36
2497 2779 1.852157 AATGGTGGCTGGTGGAGGA 60.852 57.895 0.00 0.00 0.00 3.71
2498 2780 1.379044 GAATGGTGGCTGGTGGAGG 60.379 63.158 0.00 0.00 0.00 4.30
2499 2781 0.962356 GTGAATGGTGGCTGGTGGAG 60.962 60.000 0.00 0.00 0.00 3.86
2500 2782 1.074775 GTGAATGGTGGCTGGTGGA 59.925 57.895 0.00 0.00 0.00 4.02
2501 2783 1.978617 GGTGAATGGTGGCTGGTGG 60.979 63.158 0.00 0.00 0.00 4.61
2502 2784 1.228521 TGGTGAATGGTGGCTGGTG 60.229 57.895 0.00 0.00 0.00 4.17
2503 2785 1.228552 GTGGTGAATGGTGGCTGGT 60.229 57.895 0.00 0.00 0.00 4.00
2504 2786 1.075482 AGTGGTGAATGGTGGCTGG 59.925 57.895 0.00 0.00 0.00 4.85
2505 2787 1.870055 GCAGTGGTGAATGGTGGCTG 61.870 60.000 0.00 0.00 0.00 4.85
2506 2788 1.604593 GCAGTGGTGAATGGTGGCT 60.605 57.895 0.00 0.00 0.00 4.75
2507 2789 1.870055 CTGCAGTGGTGAATGGTGGC 61.870 60.000 5.25 0.00 0.00 5.01
2508 2790 0.538057 ACTGCAGTGGTGAATGGTGG 60.538 55.000 20.97 0.00 0.00 4.61
2509 2791 0.877071 GACTGCAGTGGTGAATGGTG 59.123 55.000 27.27 0.00 0.00 4.17
2510 2792 0.603707 CGACTGCAGTGGTGAATGGT 60.604 55.000 27.27 0.00 0.00 3.55
2511 2793 1.915614 GCGACTGCAGTGGTGAATGG 61.916 60.000 27.27 0.00 42.15 3.16
2512 2794 1.499056 GCGACTGCAGTGGTGAATG 59.501 57.895 27.27 5.90 42.15 2.67
2513 2795 1.672356 GGCGACTGCAGTGGTGAAT 60.672 57.895 27.27 0.00 45.35 2.57
2514 2796 2.280797 GGCGACTGCAGTGGTGAA 60.281 61.111 27.27 0.00 45.35 3.18
2515 2797 3.233980 AGGCGACTGCAGTGGTGA 61.234 61.111 27.27 0.00 45.35 4.02
2544 2826 4.069232 TGCAAGGACGAGGAGCGG 62.069 66.667 0.00 0.00 46.49 5.52
2546 2828 1.739562 CAGTGCAAGGACGAGGAGC 60.740 63.158 0.00 0.00 0.00 4.70
2547 2829 0.034059 AACAGTGCAAGGACGAGGAG 59.966 55.000 0.00 0.00 0.00 3.69
2548 2830 0.249868 CAACAGTGCAAGGACGAGGA 60.250 55.000 0.00 0.00 0.00 3.71
2549 2831 1.230635 CCAACAGTGCAAGGACGAGG 61.231 60.000 0.00 0.00 0.00 4.63
2557 2839 0.865111 CGTCGAATCCAACAGTGCAA 59.135 50.000 0.00 0.00 0.00 4.08
2558 2840 1.565156 GCGTCGAATCCAACAGTGCA 61.565 55.000 0.00 0.00 0.00 4.57
2565 2847 3.115892 GGTGCGCGTCGAATCCAA 61.116 61.111 8.43 0.00 0.00 3.53
2579 2861 2.742116 ATCGAATCCGGTGGGGGTG 61.742 63.158 0.00 0.00 36.01 4.61
2580 2862 2.366435 ATCGAATCCGGTGGGGGT 60.366 61.111 0.00 0.00 36.01 4.95
2582 2864 2.591715 GCATCGAATCCGGTGGGG 60.592 66.667 0.00 0.00 46.39 4.96
2583 2865 2.180204 GTGCATCGAATCCGGTGGG 61.180 63.158 0.00 0.00 46.39 4.61
2584 2866 2.180204 GGTGCATCGAATCCGGTGG 61.180 63.158 0.00 0.00 46.39 4.61
2587 2869 1.227943 ATGGGTGCATCGAATCCGG 60.228 57.895 0.00 0.00 36.24 5.14
2609 2891 2.020832 CAAAATACGACGGCGCCG 59.979 61.111 44.88 44.88 42.48 6.46
2666 2948 1.604693 GGAATACATACCACGAGGCGG 60.605 57.143 0.00 0.00 39.06 6.13
2673 2955 5.278858 CGGTAAGAGGAGGAATACATACCAC 60.279 48.000 0.00 0.00 32.90 4.16
2683 2965 0.249398 GCAAGCGGTAAGAGGAGGAA 59.751 55.000 0.00 0.00 0.00 3.36
2685 2967 0.179000 ATGCAAGCGGTAAGAGGAGG 59.821 55.000 0.00 0.00 0.00 4.30
2700 2982 1.112315 GGTGGTTGGGTGACAATGCA 61.112 55.000 0.00 0.00 41.95 3.96
2705 2987 2.194597 GCTGGTGGTTGGGTGACA 59.805 61.111 0.00 0.00 0.00 3.58
2706 2988 1.898574 CTGCTGGTGGTTGGGTGAC 60.899 63.158 0.00 0.00 0.00 3.67
2720 3002 3.532155 GGCCGACGAGGATCTGCT 61.532 66.667 0.00 0.00 45.00 4.24
2721 3003 2.650813 AATGGCCGACGAGGATCTGC 62.651 60.000 0.00 0.00 45.00 4.26
2723 3005 1.742768 GAATGGCCGACGAGGATCT 59.257 57.895 0.00 0.00 45.00 2.75
2724 3006 1.661821 CGAATGGCCGACGAGGATC 60.662 63.158 9.82 0.00 45.00 3.36
2735 3017 4.838152 TGAGCCCGCTCGAATGGC 62.838 66.667 11.86 10.66 45.48 4.40
2752 3034 2.284699 AGTTGTCGGGCTAGGGCT 60.285 61.111 0.00 0.00 38.73 5.19
2753 3035 2.187163 GAGTTGTCGGGCTAGGGC 59.813 66.667 0.00 0.00 37.82 5.19
2808 3093 2.437359 GGCACAGAATCAGCCGCT 60.437 61.111 0.00 0.00 38.86 5.52
2821 3106 1.444553 CGTCTTCGAGACCTGGCAC 60.445 63.158 0.00 0.00 42.12 5.01
2838 3123 4.737855 ACCCATCCGGAATAATCTATCG 57.262 45.455 9.01 0.00 34.64 2.92
2839 3124 7.168905 AGAAAACCCATCCGGAATAATCTATC 58.831 38.462 9.01 1.35 34.64 2.08
2843 3128 5.592688 TGAAGAAAACCCATCCGGAATAATC 59.407 40.000 9.01 0.80 34.64 1.75
2844 3129 5.515106 TGAAGAAAACCCATCCGGAATAAT 58.485 37.500 9.01 0.00 34.64 1.28
2872 3157 1.148310 AACGCACTCAGTCCATTTCG 58.852 50.000 0.00 0.00 0.00 3.46
2876 3161 2.033299 CACAAAAACGCACTCAGTCCAT 59.967 45.455 0.00 0.00 0.00 3.41
2881 3166 0.027455 TCGCACAAAAACGCACTCAG 59.973 50.000 0.00 0.00 0.00 3.35
2908 3193 8.470805 TCTAAGCACAAATTTTAGTTGAACCAA 58.529 29.630 0.00 0.00 0.00 3.67
2909 3194 7.918562 GTCTAAGCACAAATTTTAGTTGAACCA 59.081 33.333 0.00 0.00 0.00 3.67
2910 3195 8.135529 AGTCTAAGCACAAATTTTAGTTGAACC 58.864 33.333 0.00 0.00 0.00 3.62
2986 3322 7.824289 AGATCTCACATGAAGATCCGTTTAAAA 59.176 33.333 25.66 0.00 39.24 1.52
2990 3326 5.105187 TGAGATCTCACATGAAGATCCGTTT 60.105 40.000 21.67 15.20 39.24 3.60
2991 3327 4.403752 TGAGATCTCACATGAAGATCCGTT 59.596 41.667 21.67 15.44 39.24 4.44


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

AutoCloner maintained by Alex Coulton.