Multiple sequence alignment - TraesCS3D01G142600

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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 TraesCS3D01G142600 chr3D 100.000 2711 0 0 1 2711 104402375 104405085 0.000000e+00 5007
1 TraesCS3D01G142600 chr3B 94.206 2330 68 24 174 2458 155656076 155658383 0.000000e+00 3493
2 TraesCS3D01G142600 chr3B 96.026 151 5 1 2562 2711 155658381 155658531 7.500000e-61 244
3 TraesCS3D01G142600 chr3B 92.126 127 6 1 56 182 155655781 155655903 2.770000e-40 176
4 TraesCS3D01G142600 chr3A 88.676 1722 121 36 502 2192 551693287 551691609 0.000000e+00 2032
5 TraesCS3D01G142600 chr3A 82.573 482 44 20 57 502 551693793 551693316 3.270000e-104 388
6 TraesCS3D01G142600 chrUn 95.536 112 5 0 2452 2563 94181982 94181871 2.140000e-41 180
7 TraesCS3D01G142600 chr6B 96.330 109 4 0 2456 2564 506128090 506127982 2.140000e-41 180
8 TraesCS3D01G142600 chr7D 94.643 112 5 1 2456 2567 60693479 60693369 3.590000e-39 172
9 TraesCS3D01G142600 chr2B 94.595 111 6 0 2453 2563 741215970 741216080 3.590000e-39 172
10 TraesCS3D01G142600 chr2B 94.595 111 6 0 2453 2563 741245542 741245652 3.590000e-39 172
11 TraesCS3D01G142600 chr1D 95.370 108 5 0 2456 2563 465596911 465596804 3.590000e-39 172
12 TraesCS3D01G142600 chr6D 94.495 109 6 0 2456 2564 318149817 318149925 4.640000e-38 169
13 TraesCS3D01G142600 chr5A 94.495 109 6 0 2455 2563 658993695 658993803 4.640000e-38 169
14 TraesCS3D01G142600 chr4D 94.495 109 6 0 2455 2563 494122895 494123003 4.640000e-38 169


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 TraesCS3D01G142600 chr3D 104402375 104405085 2710 False 5007.000000 5007 100.000000 1 2711 1 chr3D.!!$F1 2710
1 TraesCS3D01G142600 chr3B 155655781 155658531 2750 False 1304.333333 3493 94.119333 56 2711 3 chr3B.!!$F1 2655
2 TraesCS3D01G142600 chr3A 551691609 551693793 2184 True 1210.000000 2032 85.624500 57 2192 2 chr3A.!!$R1 2135

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
584 839 0.032952 GCTGGTCACCACGTACTCAA 59.967 55.0 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2410 2734 0.323816 CTTCCCTTTCTCTTGGGGGC 60.324 60.0 0.0 0.0 43.51 5.8 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
19 20 2.959507 GCAGTGGTGAAAAAGGTTGT 57.040 45.000 0.00 0.00 0.00 3.32
20 21 3.245518 GCAGTGGTGAAAAAGGTTGTT 57.754 42.857 0.00 0.00 0.00 2.83
21 22 3.186909 GCAGTGGTGAAAAAGGTTGTTC 58.813 45.455 0.00 0.00 0.00 3.18
22 23 3.119137 GCAGTGGTGAAAAAGGTTGTTCT 60.119 43.478 0.00 0.00 0.00 3.01
23 24 4.097286 GCAGTGGTGAAAAAGGTTGTTCTA 59.903 41.667 0.00 0.00 0.00 2.10
24 25 5.393678 GCAGTGGTGAAAAAGGTTGTTCTAA 60.394 40.000 0.00 0.00 0.00 2.10
25 26 6.626302 CAGTGGTGAAAAAGGTTGTTCTAAA 58.374 36.000 0.00 0.00 0.00 1.85
26 27 7.093992 CAGTGGTGAAAAAGGTTGTTCTAAAA 58.906 34.615 0.00 0.00 0.00 1.52
27 28 7.600752 CAGTGGTGAAAAAGGTTGTTCTAAAAA 59.399 33.333 0.00 0.00 0.00 1.94
28 29 8.318412 AGTGGTGAAAAAGGTTGTTCTAAAAAT 58.682 29.630 0.00 0.00 0.00 1.82
29 30 8.387354 GTGGTGAAAAAGGTTGTTCTAAAAATG 58.613 33.333 0.00 0.00 0.00 2.32
30 31 8.097662 TGGTGAAAAAGGTTGTTCTAAAAATGT 58.902 29.630 0.00 0.00 0.00 2.71
31 32 8.941977 GGTGAAAAAGGTTGTTCTAAAAATGTT 58.058 29.630 0.00 0.00 0.00 2.71
36 37 8.951787 AAAGGTTGTTCTAAAAATGTTTACCC 57.048 30.769 0.00 0.00 0.00 3.69
37 38 7.058023 AGGTTGTTCTAAAAATGTTTACCCC 57.942 36.000 0.00 0.00 0.00 4.95
38 39 6.842280 AGGTTGTTCTAAAAATGTTTACCCCT 59.158 34.615 0.00 0.00 0.00 4.79
39 40 7.014905 AGGTTGTTCTAAAAATGTTTACCCCTC 59.985 37.037 0.00 0.00 0.00 4.30
40 41 7.201929 GGTTGTTCTAAAAATGTTTACCCCTCA 60.202 37.037 0.00 0.00 0.00 3.86
41 42 7.899648 TGTTCTAAAAATGTTTACCCCTCAA 57.100 32.000 0.00 0.00 0.00 3.02
42 43 8.307582 TGTTCTAAAAATGTTTACCCCTCAAA 57.692 30.769 0.00 0.00 0.00 2.69
43 44 8.759782 TGTTCTAAAAATGTTTACCCCTCAAAA 58.240 29.630 0.00 0.00 0.00 2.44
44 45 9.602568 GTTCTAAAAATGTTTACCCCTCAAAAA 57.397 29.630 0.00 0.00 0.00 1.94
99 100 2.202797 CTCCTCCGTCCATGCACG 60.203 66.667 1.05 1.05 39.61 5.34
101 102 2.021068 CTCCTCCGTCCATGCACGAT 62.021 60.000 11.61 0.00 42.69 3.73
151 162 1.922135 GAACGAACCCATGCACGCAT 61.922 55.000 0.00 0.00 37.08 4.73
197 401 0.035598 TTGCAAAGCACCGCCTACTA 59.964 50.000 0.00 0.00 38.71 1.82
247 454 2.561373 GGAAGGCGCCTCAAAACG 59.439 61.111 32.93 0.00 0.00 3.60
279 497 5.594725 TCAGTAACATAATCTCTCCTCGCTT 59.405 40.000 0.00 0.00 0.00 4.68
297 517 3.649073 GCTTGGCTTTTCCACGTAAATT 58.351 40.909 0.00 0.00 46.55 1.82
364 585 9.508642 TCCCACATAATTGCGACATATAAAATA 57.491 29.630 0.00 0.00 0.00 1.40
550 805 2.589159 GCTGGCTAGCTAACCGCC 60.589 66.667 15.78 14.13 46.57 6.13
551 806 3.095347 GCTGGCTAGCTAACCGCCT 62.095 63.158 15.78 0.00 46.57 5.52
552 807 1.745320 GCTGGCTAGCTAACCGCCTA 61.745 60.000 15.78 8.54 46.57 3.93
553 808 0.750850 CTGGCTAGCTAACCGCCTAA 59.249 55.000 19.86 3.84 44.09 2.69
554 809 0.462789 TGGCTAGCTAACCGCCTAAC 59.537 55.000 19.86 0.00 44.09 2.34
555 810 0.249784 GGCTAGCTAACCGCCTAACC 60.250 60.000 15.72 0.00 40.62 2.85
584 839 0.032952 GCTGGTCACCACGTACTCAA 59.967 55.000 0.00 0.00 0.00 3.02
586 841 1.067974 CTGGTCACCACGTACTCAACA 59.932 52.381 0.00 0.00 0.00 3.33
593 848 4.081697 TCACCACGTACTCAACATCATCAT 60.082 41.667 0.00 0.00 0.00 2.45
594 849 4.268644 CACCACGTACTCAACATCATCATC 59.731 45.833 0.00 0.00 0.00 2.92
595 850 4.081697 ACCACGTACTCAACATCATCATCA 60.082 41.667 0.00 0.00 0.00 3.07
596 851 5.052481 CCACGTACTCAACATCATCATCAT 58.948 41.667 0.00 0.00 0.00 2.45
597 852 5.176406 CCACGTACTCAACATCATCATCATC 59.824 44.000 0.00 0.00 0.00 2.92
707 969 0.982673 CGTTACGCTCCTCTTCGTTG 59.017 55.000 0.00 0.00 39.79 4.10
729 991 6.073447 TGCTTAATTCTTAAGTCCCATCCA 57.927 37.500 1.63 0.00 43.52 3.41
797 1064 2.710440 CCGGGCCTTTAAATACGGG 58.290 57.895 0.84 0.77 37.80 5.28
876 1143 2.687935 GCAAAAGTTGTTCCACTCTCCA 59.312 45.455 0.00 0.00 0.00 3.86
878 1145 2.640316 AAGTTGTTCCACTCTCCACC 57.360 50.000 0.00 0.00 0.00 4.61
965 1235 1.948104 CTCGACGGTGATCTCTCTCT 58.052 55.000 0.00 0.00 0.00 3.10
967 1237 2.281517 TCGACGGTGATCTCTCTCTTC 58.718 52.381 0.00 0.00 0.00 2.87
968 1238 2.093394 TCGACGGTGATCTCTCTCTTCT 60.093 50.000 0.00 0.00 0.00 2.85
970 1240 3.541632 GACGGTGATCTCTCTCTTCTCT 58.458 50.000 0.00 0.00 0.00 3.10
983 1253 0.957395 CTTCTCTGCATTGCCACGGT 60.957 55.000 6.12 0.00 0.00 4.83
1338 1614 1.286260 GGACGTCGAGTTCAGCTGT 59.714 57.895 14.67 0.00 0.00 4.40
2085 2400 3.433709 TGTTTCATTTCACAAGTGTGCG 58.566 40.909 6.56 0.00 45.25 5.34
2100 2415 3.253188 AGTGTGCGTATGCTTGTGAAAAT 59.747 39.130 8.69 0.00 43.34 1.82
2101 2416 4.454161 AGTGTGCGTATGCTTGTGAAAATA 59.546 37.500 8.69 0.00 43.34 1.40
2251 2569 9.507329 AGATTCATTCCGTACATAATAAGCAAT 57.493 29.630 0.00 0.00 0.00 3.56
2252 2570 9.546909 GATTCATTCCGTACATAATAAGCAATG 57.453 33.333 0.00 0.00 0.00 2.82
2281 2599 5.428496 TTGTATACCTACCGAGATCGTTG 57.572 43.478 0.00 0.00 37.74 4.10
2286 2604 3.288964 ACCTACCGAGATCGTTGAGATT 58.711 45.455 1.09 0.00 40.26 2.40
2289 2607 1.212616 CCGAGATCGTTGAGATTGCC 58.787 55.000 1.09 0.00 40.26 4.52
2387 2706 1.213537 GCAGCTCACCCGTACGTAA 59.786 57.895 15.21 0.00 0.00 3.18
2410 2734 7.653767 AACGTCTACTCTTTTAACTTCATGG 57.346 36.000 0.00 0.00 0.00 3.66
2424 2748 0.332632 TCATGGCCCCCAAGAGAAAG 59.667 55.000 0.00 0.00 36.95 2.62
2465 2789 6.658188 AAAGAGAGAATATTACTCCCTCCG 57.342 41.667 14.55 0.00 35.27 4.63
2466 2790 4.083565 AGAGAGAATATTACTCCCTCCGC 58.916 47.826 14.55 2.72 35.27 5.54
2467 2791 4.083565 GAGAGAATATTACTCCCTCCGCT 58.916 47.826 9.62 0.00 35.27 5.52
2468 2792 4.083565 AGAGAATATTACTCCCTCCGCTC 58.916 47.826 9.79 0.00 35.27 5.03
2469 2793 3.827302 GAGAATATTACTCCCTCCGCTCA 59.173 47.826 0.00 0.00 0.00 4.26
2470 2794 4.421131 AGAATATTACTCCCTCCGCTCAT 58.579 43.478 0.00 0.00 0.00 2.90
2471 2795 4.841246 AGAATATTACTCCCTCCGCTCATT 59.159 41.667 0.00 0.00 0.00 2.57
2472 2796 5.308237 AGAATATTACTCCCTCCGCTCATTT 59.692 40.000 0.00 0.00 0.00 2.32
2473 2797 3.933861 ATTACTCCCTCCGCTCATTTT 57.066 42.857 0.00 0.00 0.00 1.82
2474 2798 3.713826 TTACTCCCTCCGCTCATTTTT 57.286 42.857 0.00 0.00 0.00 1.94
2475 2799 4.829872 TTACTCCCTCCGCTCATTTTTA 57.170 40.909 0.00 0.00 0.00 1.52
2476 2800 3.933861 ACTCCCTCCGCTCATTTTTAT 57.066 42.857 0.00 0.00 0.00 1.40
2477 2801 6.488769 TTACTCCCTCCGCTCATTTTTATA 57.511 37.500 0.00 0.00 0.00 0.98
2478 2802 5.367945 ACTCCCTCCGCTCATTTTTATAA 57.632 39.130 0.00 0.00 0.00 0.98
2479 2803 5.368989 ACTCCCTCCGCTCATTTTTATAAG 58.631 41.667 0.00 0.00 0.00 1.73
2480 2804 5.104485 ACTCCCTCCGCTCATTTTTATAAGT 60.104 40.000 0.00 0.00 0.00 2.24
2481 2805 5.365619 TCCCTCCGCTCATTTTTATAAGTC 58.634 41.667 0.00 0.00 0.00 3.01
2482 2806 4.211374 CCCTCCGCTCATTTTTATAAGTCG 59.789 45.833 0.00 0.00 0.00 4.18
2483 2807 4.809426 CCTCCGCTCATTTTTATAAGTCGT 59.191 41.667 0.00 0.00 0.00 4.34
2484 2808 5.293569 CCTCCGCTCATTTTTATAAGTCGTT 59.706 40.000 0.00 0.00 0.00 3.85
2485 2809 6.183360 CCTCCGCTCATTTTTATAAGTCGTTT 60.183 38.462 0.00 0.00 0.00 3.60
2486 2810 6.768078 TCCGCTCATTTTTATAAGTCGTTTC 58.232 36.000 0.00 0.00 0.00 2.78
2487 2811 6.369340 TCCGCTCATTTTTATAAGTCGTTTCA 59.631 34.615 0.00 0.00 0.00 2.69
2488 2812 6.682863 CCGCTCATTTTTATAAGTCGTTTCAG 59.317 38.462 0.00 0.00 0.00 3.02
2489 2813 7.412563 CCGCTCATTTTTATAAGTCGTTTCAGA 60.413 37.037 0.00 0.00 0.00 3.27
2490 2814 7.422746 CGCTCATTTTTATAAGTCGTTTCAGAC 59.577 37.037 0.00 0.00 41.23 3.51
2491 2815 8.227791 GCTCATTTTTATAAGTCGTTTCAGACA 58.772 33.333 0.00 0.00 43.24 3.41
2493 2817 9.872757 TCATTTTTATAAGTCGTTTCAGACAAC 57.127 29.630 0.00 0.00 43.24 3.32
2494 2818 9.878599 CATTTTTATAAGTCGTTTCAGACAACT 57.121 29.630 0.00 0.00 43.24 3.16
2495 2819 9.878599 ATTTTTATAAGTCGTTTCAGACAACTG 57.121 29.630 0.00 0.00 43.24 3.16
2509 2833 6.551385 CAGACAACTGAAAATGAGCTACTT 57.449 37.500 0.00 0.00 46.03 2.24
2510 2834 6.963796 CAGACAACTGAAAATGAGCTACTTT 58.036 36.000 0.00 0.00 46.03 2.66
2511 2835 6.854892 CAGACAACTGAAAATGAGCTACTTTG 59.145 38.462 0.00 0.00 46.03 2.77
2512 2836 5.523369 ACAACTGAAAATGAGCTACTTTGC 58.477 37.500 0.00 0.00 0.00 3.68
2513 2837 5.067674 ACAACTGAAAATGAGCTACTTTGCA 59.932 36.000 0.00 0.00 34.99 4.08
2514 2838 5.113502 ACTGAAAATGAGCTACTTTGCAC 57.886 39.130 0.00 0.00 34.99 4.57
2515 2839 4.022849 ACTGAAAATGAGCTACTTTGCACC 60.023 41.667 0.00 0.00 34.99 5.01
2516 2840 3.255642 TGAAAATGAGCTACTTTGCACCC 59.744 43.478 0.00 0.00 34.99 4.61
2517 2841 2.887151 AATGAGCTACTTTGCACCCT 57.113 45.000 0.00 0.00 34.99 4.34
2518 2842 2.119801 ATGAGCTACTTTGCACCCTG 57.880 50.000 0.00 0.00 34.99 4.45
2519 2843 0.764890 TGAGCTACTTTGCACCCTGT 59.235 50.000 0.00 0.00 34.99 4.00
2520 2844 1.270839 TGAGCTACTTTGCACCCTGTC 60.271 52.381 0.00 0.00 34.99 3.51
2521 2845 1.002544 GAGCTACTTTGCACCCTGTCT 59.997 52.381 0.00 0.00 34.99 3.41
2522 2846 1.160137 GCTACTTTGCACCCTGTCTG 58.840 55.000 0.00 0.00 0.00 3.51
2523 2847 1.270839 GCTACTTTGCACCCTGTCTGA 60.271 52.381 0.00 0.00 0.00 3.27
2524 2848 2.810400 GCTACTTTGCACCCTGTCTGAA 60.810 50.000 0.00 0.00 0.00 3.02
2525 2849 2.435372 ACTTTGCACCCTGTCTGAAA 57.565 45.000 0.00 0.00 0.00 2.69
2526 2850 2.949447 ACTTTGCACCCTGTCTGAAAT 58.051 42.857 0.00 0.00 0.00 2.17
2527 2851 2.624838 ACTTTGCACCCTGTCTGAAATG 59.375 45.455 0.00 0.00 0.00 2.32
2528 2852 2.363306 TTGCACCCTGTCTGAAATGT 57.637 45.000 0.00 0.00 0.00 2.71
2529 2853 1.896220 TGCACCCTGTCTGAAATGTC 58.104 50.000 0.00 0.00 0.00 3.06
2530 2854 1.421268 TGCACCCTGTCTGAAATGTCT 59.579 47.619 0.00 0.00 0.00 3.41
2531 2855 2.158623 TGCACCCTGTCTGAAATGTCTT 60.159 45.455 0.00 0.00 0.00 3.01
2532 2856 2.485814 GCACCCTGTCTGAAATGTCTTC 59.514 50.000 0.00 0.00 0.00 2.87
2533 2857 3.743521 CACCCTGTCTGAAATGTCTTCA 58.256 45.455 0.00 0.00 0.00 3.02
2534 2858 4.136796 CACCCTGTCTGAAATGTCTTCAA 58.863 43.478 0.00 0.00 0.00 2.69
2535 2859 4.214971 CACCCTGTCTGAAATGTCTTCAAG 59.785 45.833 0.00 0.00 0.00 3.02
2536 2860 3.755378 CCCTGTCTGAAATGTCTTCAAGG 59.245 47.826 0.00 0.00 0.00 3.61
2537 2861 3.190118 CCTGTCTGAAATGTCTTCAAGGC 59.810 47.826 0.00 0.00 0.00 4.35
2538 2862 4.070716 CTGTCTGAAATGTCTTCAAGGCT 58.929 43.478 0.00 0.00 0.00 4.58
2539 2863 4.464008 TGTCTGAAATGTCTTCAAGGCTT 58.536 39.130 0.00 0.00 0.00 4.35
2540 2864 4.889409 TGTCTGAAATGTCTTCAAGGCTTT 59.111 37.500 0.00 0.00 0.00 3.51
2541 2865 6.061441 TGTCTGAAATGTCTTCAAGGCTTTA 58.939 36.000 0.00 0.00 0.00 1.85
2542 2866 6.716628 TGTCTGAAATGTCTTCAAGGCTTTAT 59.283 34.615 0.00 0.00 0.00 1.40
2543 2867 7.882791 TGTCTGAAATGTCTTCAAGGCTTTATA 59.117 33.333 0.00 0.00 0.00 0.98
2544 2868 8.730680 GTCTGAAATGTCTTCAAGGCTTTATAA 58.269 33.333 0.00 0.00 0.00 0.98
2545 2869 9.295825 TCTGAAATGTCTTCAAGGCTTTATAAA 57.704 29.630 0.00 0.00 0.00 1.40
2546 2870 9.912634 CTGAAATGTCTTCAAGGCTTTATAAAA 57.087 29.630 0.00 0.00 0.00 1.52
2547 2871 9.912634 TGAAATGTCTTCAAGGCTTTATAAAAG 57.087 29.630 0.00 0.00 0.00 2.27
2548 2872 9.914131 GAAATGTCTTCAAGGCTTTATAAAAGT 57.086 29.630 0.00 0.00 0.00 2.66
2549 2873 9.696917 AAATGTCTTCAAGGCTTTATAAAAGTG 57.303 29.630 0.00 0.00 0.00 3.16
2550 2874 8.635765 ATGTCTTCAAGGCTTTATAAAAGTGA 57.364 30.769 0.00 0.00 0.00 3.41
2551 2875 8.458573 TGTCTTCAAGGCTTTATAAAAGTGAA 57.541 30.769 0.00 6.03 0.00 3.18
2552 2876 8.908903 TGTCTTCAAGGCTTTATAAAAGTGAAA 58.091 29.630 0.00 0.00 0.00 2.69
2553 2877 9.744468 GTCTTCAAGGCTTTATAAAAGTGAAAA 57.256 29.630 0.00 0.00 0.00 2.29
2554 2878 9.965824 TCTTCAAGGCTTTATAAAAGTGAAAAG 57.034 29.630 0.00 1.23 33.15 2.27
2555 2879 9.965824 CTTCAAGGCTTTATAAAAGTGAAAAGA 57.034 29.630 0.00 0.00 31.96 2.52
2556 2880 9.965824 TTCAAGGCTTTATAAAAGTGAAAAGAG 57.034 29.630 0.00 0.00 31.96 2.85
2557 2881 8.576442 TCAAGGCTTTATAAAAGTGAAAAGAGG 58.424 33.333 0.00 0.00 31.96 3.69
2558 2882 7.468141 AGGCTTTATAAAAGTGAAAAGAGGG 57.532 36.000 0.00 0.00 31.96 4.30
2559 2883 7.238710 AGGCTTTATAAAAGTGAAAAGAGGGA 58.761 34.615 0.00 0.00 31.96 4.20
2560 2884 7.394641 AGGCTTTATAAAAGTGAAAAGAGGGAG 59.605 37.037 0.00 0.00 31.96 4.30
2600 2924 3.305110 GGTGAATGTTACCTTTGTTGCG 58.695 45.455 0.00 0.00 35.30 4.85
2654 2978 5.357032 CCTATTGATTTAAGCCCGTTCACTT 59.643 40.000 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.959507 ACAACCTTTTTCACCACTGC 57.040 45.000 0.00 0.00 0.00 4.40
1 2 4.718940 AGAACAACCTTTTTCACCACTG 57.281 40.909 0.00 0.00 0.00 3.66
3 4 7.892778 TTTTTAGAACAACCTTTTTCACCAC 57.107 32.000 0.00 0.00 0.00 4.16
5 6 8.487313 ACATTTTTAGAACAACCTTTTTCACC 57.513 30.769 0.00 0.00 0.00 4.02
10 11 9.386010 GGGTAAACATTTTTAGAACAACCTTTT 57.614 29.630 0.00 0.00 0.00 2.27
11 12 7.988599 GGGGTAAACATTTTTAGAACAACCTTT 59.011 33.333 0.00 0.00 0.00 3.11
12 13 7.346175 AGGGGTAAACATTTTTAGAACAACCTT 59.654 33.333 0.00 0.00 0.00 3.50
13 14 6.842280 AGGGGTAAACATTTTTAGAACAACCT 59.158 34.615 0.00 0.00 0.00 3.50
14 15 7.058023 AGGGGTAAACATTTTTAGAACAACC 57.942 36.000 0.00 0.00 0.00 3.77
15 16 7.718525 TGAGGGGTAAACATTTTTAGAACAAC 58.281 34.615 0.00 0.00 0.00 3.32
16 17 7.899648 TGAGGGGTAAACATTTTTAGAACAA 57.100 32.000 0.00 0.00 0.00 2.83
17 18 7.899648 TTGAGGGGTAAACATTTTTAGAACA 57.100 32.000 0.00 0.00 0.00 3.18
18 19 9.602568 TTTTTGAGGGGTAAACATTTTTAGAAC 57.397 29.630 0.00 0.00 0.00 3.01
54 55 3.181455 GCCATTTCAGGGTTCCAGTTTTT 60.181 43.478 0.00 0.00 0.00 1.94
55 56 2.368548 GCCATTTCAGGGTTCCAGTTTT 59.631 45.455 0.00 0.00 0.00 2.43
56 57 1.970640 GCCATTTCAGGGTTCCAGTTT 59.029 47.619 0.00 0.00 0.00 2.66
57 58 1.133199 TGCCATTTCAGGGTTCCAGTT 60.133 47.619 0.00 0.00 0.00 3.16
58 59 0.482446 TGCCATTTCAGGGTTCCAGT 59.518 50.000 0.00 0.00 0.00 4.00
59 60 1.180029 CTGCCATTTCAGGGTTCCAG 58.820 55.000 0.00 0.00 0.00 3.86
60 61 3.362040 CTGCCATTTCAGGGTTCCA 57.638 52.632 0.00 0.00 0.00 3.53
151 162 1.003839 CTAGCTTTGGTCCCGTGCA 60.004 57.895 0.00 0.00 0.00 4.57
279 497 5.715070 CCAATAATTTACGTGGAAAAGCCA 58.285 37.500 0.00 0.00 46.96 4.75
297 517 2.240160 ACCGTATGGAAAGGTGCCAATA 59.760 45.455 8.33 0.00 38.68 1.90
364 585 5.182169 TGGAAAGTTACCGGTTATTCCAT 57.818 39.130 26.23 6.79 40.87 3.41
384 609 2.784957 CTTGCGTGCACCGTTCATGG 62.785 60.000 12.15 0.00 39.32 3.66
403 628 5.163963 CCATTATTTTTCAACAGAAAGGCGC 60.164 40.000 0.00 0.00 33.20 6.53
548 803 3.186345 GCCTTGGTTAGGGTTAGGC 57.814 57.895 0.00 0.00 44.91 3.93
584 839 4.863131 CGATGACGATGATGATGATGATGT 59.137 41.667 0.00 0.00 42.66 3.06
586 841 4.081807 ACCGATGACGATGATGATGATGAT 60.082 41.667 0.00 0.00 42.66 2.45
593 848 1.067060 GACCACCGATGACGATGATGA 59.933 52.381 0.00 0.00 42.66 2.92
594 849 1.202405 TGACCACCGATGACGATGATG 60.202 52.381 0.00 0.00 42.66 3.07
595 850 1.111277 TGACCACCGATGACGATGAT 58.889 50.000 0.00 0.00 42.66 2.45
596 851 0.172578 GTGACCACCGATGACGATGA 59.827 55.000 0.00 0.00 42.66 2.92
597 852 0.173481 AGTGACCACCGATGACGATG 59.827 55.000 0.00 0.00 42.66 3.84
678 933 0.598158 GAGCGTAACGTTGGGTGTGA 60.598 55.000 11.99 0.00 0.00 3.58
683 945 0.037605 AAGAGGAGCGTAACGTTGGG 60.038 55.000 11.99 3.40 0.00 4.12
876 1143 2.041153 CTTCGCTTTGCTTTGGGGT 58.959 52.632 0.00 0.00 0.00 4.95
878 1145 1.373371 GGCTTCGCTTTGCTTTGGG 60.373 57.895 0.00 0.00 0.00 4.12
965 1235 0.537143 AACCGTGGCAATGCAGAGAA 60.537 50.000 7.79 0.00 0.00 2.87
967 1237 1.236616 TGAACCGTGGCAATGCAGAG 61.237 55.000 7.79 0.00 0.00 3.35
968 1238 1.228094 TGAACCGTGGCAATGCAGA 60.228 52.632 7.79 0.00 0.00 4.26
970 1240 2.902419 CGTGAACCGTGGCAATGCA 61.902 57.895 7.79 0.00 0.00 3.96
1365 1641 1.834263 CCGATCTTGAAGGGGAAGACT 59.166 52.381 0.00 0.00 32.30 3.24
1407 1683 3.315949 TCCAGCCCGCCGTAGTTT 61.316 61.111 0.00 0.00 0.00 2.66
2214 2532 4.452455 ACGGAATGAATCTGTTGTGTTCTC 59.548 41.667 0.00 0.00 45.67 2.87
2251 2569 4.525996 TCGGTAGGTATACAAGCTGTACA 58.474 43.478 5.01 0.00 35.42 2.90
2252 2570 4.818546 TCTCGGTAGGTATACAAGCTGTAC 59.181 45.833 5.01 0.00 35.42 2.90
2261 2579 4.993584 TCTCAACGATCTCGGTAGGTATAC 59.006 45.833 4.44 0.00 44.95 1.47
2281 2599 5.907207 TGTCAGACTTATGTAGGCAATCTC 58.093 41.667 1.31 0.00 32.58 2.75
2286 2604 5.541845 GCATATGTCAGACTTATGTAGGCA 58.458 41.667 26.08 0.00 38.06 4.75
2289 2607 5.773575 ACCGCATATGTCAGACTTATGTAG 58.226 41.667 26.08 21.46 38.06 2.74
2347 2665 3.758755 TGATTCCATCTCCAAGATCCG 57.241 47.619 0.00 0.00 31.32 4.18
2387 2706 5.638234 GCCATGAAGTTAAAAGAGTAGACGT 59.362 40.000 0.00 0.00 0.00 4.34
2394 2718 2.760650 GGGGGCCATGAAGTTAAAAGAG 59.239 50.000 4.39 0.00 0.00 2.85
2410 2734 0.323816 CTTCCCTTTCTCTTGGGGGC 60.324 60.000 0.00 0.00 43.51 5.80
2424 2748 6.574350 TCTCTTTAATCATCTCGTTCTTCCC 58.426 40.000 0.00 0.00 0.00 3.97
2455 2779 6.099269 ACTTATAAAAATGAGCGGAGGGAGTA 59.901 38.462 0.00 0.00 0.00 2.59
2456 2780 3.933861 ATAAAAATGAGCGGAGGGAGT 57.066 42.857 0.00 0.00 0.00 3.85
2457 2781 5.368989 ACTTATAAAAATGAGCGGAGGGAG 58.631 41.667 0.00 0.00 0.00 4.30
2458 2782 5.365619 GACTTATAAAAATGAGCGGAGGGA 58.634 41.667 0.00 0.00 0.00 4.20
2459 2783 4.211374 CGACTTATAAAAATGAGCGGAGGG 59.789 45.833 0.00 0.00 0.00 4.30
2460 2784 4.809426 ACGACTTATAAAAATGAGCGGAGG 59.191 41.667 0.00 0.00 0.00 4.30
2461 2785 5.968387 ACGACTTATAAAAATGAGCGGAG 57.032 39.130 0.00 0.00 0.00 4.63
2462 2786 6.369340 TGAAACGACTTATAAAAATGAGCGGA 59.631 34.615 0.00 0.00 0.00 5.54
2463 2787 6.539324 TGAAACGACTTATAAAAATGAGCGG 58.461 36.000 0.00 0.00 0.00 5.52
2464 2788 7.422746 GTCTGAAACGACTTATAAAAATGAGCG 59.577 37.037 0.00 0.00 0.00 5.03
2465 2789 8.227791 TGTCTGAAACGACTTATAAAAATGAGC 58.772 33.333 0.00 0.00 35.00 4.26
2467 2791 9.872757 GTTGTCTGAAACGACTTATAAAAATGA 57.127 29.630 0.00 0.00 38.97 2.57
2486 2810 6.551385 AAGTAGCTCATTTTCAGTTGTCTG 57.449 37.500 0.00 0.00 42.54 3.51
2487 2811 6.514048 GCAAAGTAGCTCATTTTCAGTTGTCT 60.514 38.462 0.00 0.00 0.00 3.41
2488 2812 5.626955 GCAAAGTAGCTCATTTTCAGTTGTC 59.373 40.000 0.00 0.00 0.00 3.18
2489 2813 5.067674 TGCAAAGTAGCTCATTTTCAGTTGT 59.932 36.000 0.00 0.00 34.99 3.32
2490 2814 5.400485 GTGCAAAGTAGCTCATTTTCAGTTG 59.600 40.000 0.00 0.00 34.99 3.16
2491 2815 5.507985 GGTGCAAAGTAGCTCATTTTCAGTT 60.508 40.000 0.00 0.00 34.99 3.16
2492 2816 4.022849 GGTGCAAAGTAGCTCATTTTCAGT 60.023 41.667 0.00 0.00 34.99 3.41
2493 2817 4.479619 GGTGCAAAGTAGCTCATTTTCAG 58.520 43.478 0.00 0.00 34.99 3.02
2494 2818 3.255642 GGGTGCAAAGTAGCTCATTTTCA 59.744 43.478 0.00 0.00 34.99 2.69
2495 2819 3.507622 AGGGTGCAAAGTAGCTCATTTTC 59.492 43.478 0.00 0.00 34.99 2.29
2496 2820 3.256631 CAGGGTGCAAAGTAGCTCATTTT 59.743 43.478 0.00 0.00 34.99 1.82
2497 2821 2.821969 CAGGGTGCAAAGTAGCTCATTT 59.178 45.455 0.00 0.00 34.99 2.32
2498 2822 2.224867 ACAGGGTGCAAAGTAGCTCATT 60.225 45.455 0.00 0.00 34.99 2.57
2499 2823 1.352352 ACAGGGTGCAAAGTAGCTCAT 59.648 47.619 0.00 0.00 34.99 2.90
2500 2824 0.764890 ACAGGGTGCAAAGTAGCTCA 59.235 50.000 0.00 0.00 34.99 4.26
2501 2825 1.002544 AGACAGGGTGCAAAGTAGCTC 59.997 52.381 0.00 0.00 34.99 4.09
2502 2826 1.059913 AGACAGGGTGCAAAGTAGCT 58.940 50.000 0.00 0.00 34.99 3.32
2503 2827 1.160137 CAGACAGGGTGCAAAGTAGC 58.840 55.000 0.00 0.00 0.00 3.58
2504 2828 2.839486 TCAGACAGGGTGCAAAGTAG 57.161 50.000 0.00 0.00 0.00 2.57
2505 2829 3.569194 TTTCAGACAGGGTGCAAAGTA 57.431 42.857 0.00 0.00 0.00 2.24
2506 2830 2.435372 TTTCAGACAGGGTGCAAAGT 57.565 45.000 0.00 0.00 0.00 2.66
2507 2831 2.624838 ACATTTCAGACAGGGTGCAAAG 59.375 45.455 0.00 0.00 0.00 2.77
2508 2832 2.622942 GACATTTCAGACAGGGTGCAAA 59.377 45.455 0.00 0.00 0.00 3.68
2509 2833 2.158623 AGACATTTCAGACAGGGTGCAA 60.159 45.455 0.00 0.00 0.00 4.08
2510 2834 1.421268 AGACATTTCAGACAGGGTGCA 59.579 47.619 0.00 0.00 0.00 4.57
2511 2835 2.191128 AGACATTTCAGACAGGGTGC 57.809 50.000 0.00 0.00 0.00 5.01
2512 2836 3.743521 TGAAGACATTTCAGACAGGGTG 58.256 45.455 0.00 0.00 0.00 4.61
2513 2837 4.392940 CTTGAAGACATTTCAGACAGGGT 58.607 43.478 0.00 0.00 0.00 4.34
2514 2838 3.755378 CCTTGAAGACATTTCAGACAGGG 59.245 47.826 0.00 0.00 0.00 4.45
2515 2839 3.190118 GCCTTGAAGACATTTCAGACAGG 59.810 47.826 0.00 3.03 30.77 4.00
2516 2840 4.070716 AGCCTTGAAGACATTTCAGACAG 58.929 43.478 0.00 0.00 0.00 3.51
2517 2841 4.090761 AGCCTTGAAGACATTTCAGACA 57.909 40.909 0.00 0.00 0.00 3.41
2518 2842 5.444663 AAAGCCTTGAAGACATTTCAGAC 57.555 39.130 0.00 0.00 0.00 3.51
2519 2843 8.862325 TTATAAAGCCTTGAAGACATTTCAGA 57.138 30.769 0.00 0.00 0.00 3.27
2520 2844 9.912634 TTTTATAAAGCCTTGAAGACATTTCAG 57.087 29.630 0.00 0.00 0.00 3.02
2521 2845 9.912634 CTTTTATAAAGCCTTGAAGACATTTCA 57.087 29.630 0.00 0.00 0.00 2.69
2522 2846 9.914131 ACTTTTATAAAGCCTTGAAGACATTTC 57.086 29.630 0.00 0.00 0.00 2.17
2523 2847 9.696917 CACTTTTATAAAGCCTTGAAGACATTT 57.303 29.630 0.00 0.00 0.00 2.32
2524 2848 9.077885 TCACTTTTATAAAGCCTTGAAGACATT 57.922 29.630 0.00 0.00 0.00 2.71
2525 2849 8.635765 TCACTTTTATAAAGCCTTGAAGACAT 57.364 30.769 0.00 0.00 0.00 3.06
2526 2850 8.458573 TTCACTTTTATAAAGCCTTGAAGACA 57.541 30.769 0.00 0.00 0.00 3.41
2527 2851 9.744468 TTTTCACTTTTATAAAGCCTTGAAGAC 57.256 29.630 0.00 0.00 0.00 3.01
2528 2852 9.965824 CTTTTCACTTTTATAAAGCCTTGAAGA 57.034 29.630 0.00 2.08 0.00 2.87
2529 2853 9.965824 TCTTTTCACTTTTATAAAGCCTTGAAG 57.034 29.630 0.00 2.17 0.00 3.02
2530 2854 9.965824 CTCTTTTCACTTTTATAAAGCCTTGAA 57.034 29.630 0.00 4.02 0.00 2.69
2531 2855 8.576442 CCTCTTTTCACTTTTATAAAGCCTTGA 58.424 33.333 0.00 0.00 0.00 3.02
2532 2856 7.814587 CCCTCTTTTCACTTTTATAAAGCCTTG 59.185 37.037 0.00 0.00 0.00 3.61
2533 2857 7.728532 TCCCTCTTTTCACTTTTATAAAGCCTT 59.271 33.333 0.00 0.00 0.00 4.35
2534 2858 7.238710 TCCCTCTTTTCACTTTTATAAAGCCT 58.761 34.615 0.00 0.00 0.00 4.58
2535 2859 7.176865 ACTCCCTCTTTTCACTTTTATAAAGCC 59.823 37.037 0.00 0.00 0.00 4.35
2536 2860 8.112016 ACTCCCTCTTTTCACTTTTATAAAGC 57.888 34.615 0.00 0.00 0.00 3.51
2538 2862 9.511272 GGTACTCCCTCTTTTCACTTTTATAAA 57.489 33.333 0.00 0.00 0.00 1.40
2539 2863 8.887393 AGGTACTCCCTCTTTTCACTTTTATAA 58.113 33.333 0.00 0.00 40.71 0.98
2540 2864 8.445361 AGGTACTCCCTCTTTTCACTTTTATA 57.555 34.615 0.00 0.00 40.71 0.98
2541 2865 7.331089 AGGTACTCCCTCTTTTCACTTTTAT 57.669 36.000 0.00 0.00 40.71 1.40
2542 2866 6.758806 AGGTACTCCCTCTTTTCACTTTTA 57.241 37.500 0.00 0.00 40.71 1.52
2543 2867 5.648330 AGGTACTCCCTCTTTTCACTTTT 57.352 39.130 0.00 0.00 40.71 2.27
2544 2868 5.648330 AAGGTACTCCCTCTTTTCACTTT 57.352 39.130 0.00 0.00 45.47 2.66
2545 2869 5.104067 ACAAAGGTACTCCCTCTTTTCACTT 60.104 40.000 0.00 0.00 45.47 3.16
2546 2870 4.412528 ACAAAGGTACTCCCTCTTTTCACT 59.587 41.667 0.00 0.00 45.47 3.41
2547 2871 4.715713 ACAAAGGTACTCCCTCTTTTCAC 58.284 43.478 0.00 0.00 45.47 3.18
2548 2872 5.382664 AACAAAGGTACTCCCTCTTTTCA 57.617 39.130 0.00 0.00 45.47 2.69
2549 2873 6.710597 AAAACAAAGGTACTCCCTCTTTTC 57.289 37.500 0.00 0.00 45.47 2.29
2550 2874 6.895756 AGAAAAACAAAGGTACTCCCTCTTTT 59.104 34.615 0.00 0.00 45.47 2.27
2551 2875 6.432581 AGAAAAACAAAGGTACTCCCTCTTT 58.567 36.000 0.00 0.00 45.47 2.52
2552 2876 6.014771 AGAAAAACAAAGGTACTCCCTCTT 57.985 37.500 0.00 0.00 45.47 2.85
2553 2877 5.648330 AGAAAAACAAAGGTACTCCCTCT 57.352 39.130 0.00 0.00 45.47 3.69
2554 2878 6.430308 CCTAAGAAAAACAAAGGTACTCCCTC 59.570 42.308 0.00 0.00 45.47 4.30
2556 2880 5.475909 CCCTAAGAAAAACAAAGGTACTCCC 59.524 44.000 0.00 0.00 38.49 4.30
2557 2881 6.016527 CACCCTAAGAAAAACAAAGGTACTCC 60.017 42.308 0.00 0.00 38.49 3.85
2558 2882 6.769341 TCACCCTAAGAAAAACAAAGGTACTC 59.231 38.462 0.00 0.00 38.49 2.59
2560 2884 6.947644 TCACCCTAAGAAAAACAAAGGTAC 57.052 37.500 0.00 0.00 0.00 3.34
2600 2924 7.435068 ACAAGTTATGATTGATTATACGGCC 57.565 36.000 0.00 0.00 0.00 6.13
2641 2965 2.488153 GCAAGATTAAGTGAACGGGCTT 59.512 45.455 0.00 0.00 0.00 4.35
2654 2978 6.883756 TGGTGTTGTAATCATGAGCAAGATTA 59.116 34.615 0.09 4.56 36.07 1.75


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

AutoCloner maintained by Alex Coulton.