Multiple sequence alignment - TraesCS4D01G228500

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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 TraesCS4D01G228500 chr4D 100.000 2729 0 0 1 2729 388116448 388119176 0.000000e+00 5040
1 TraesCS4D01G228500 chr4A 93.118 2194 87 26 1 2147 69313313 69315489 0.000000e+00 3157
2 TraesCS4D01G228500 chr4A 89.508 305 9 4 2300 2602 69315699 69315982 5.550000e-97 364
3 TraesCS4D01G228500 chr4A 89.691 97 8 2 2507 2602 6192390 6192485 3.690000e-24 122
4 TraesCS4D01G228500 chr4B 88.383 2307 129 71 3 2232 476264460 476266704 0.000000e+00 2647
5 TraesCS4D01G228500 chr4B 93.103 87 6 0 2516 2602 114602981 114602895 7.930000e-26 128
6 TraesCS4D01G228500 chr5A 92.913 127 9 0 2603 2729 509054630 509054756 4.640000e-43 185
7 TraesCS4D01G228500 chr7B 91.954 87 7 0 2516 2602 62453473 62453387 3.690000e-24 122
8 TraesCS4D01G228500 chr7B 91.860 86 7 0 2516 2601 28394328 28394243 1.330000e-23 121
9 TraesCS4D01G228500 chr5B 91.954 87 7 0 2516 2602 694193046 694192960 3.690000e-24 122
10 TraesCS4D01G228500 chr3A 91.954 87 7 0 2516 2602 242024833 242024919 3.690000e-24 122
11 TraesCS4D01G228500 chr2B 91.954 87 7 0 2516 2602 368375863 368375949 3.690000e-24 122
12 TraesCS4D01G228500 chr6B 91.954 87 6 1 2516 2602 604594656 604594741 1.330000e-23 121
13 TraesCS4D01G228500 chr3B 87.500 104 11 2 2500 2602 155821969 155822071 4.770000e-23 119


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 TraesCS4D01G228500 chr4D 388116448 388119176 2728 False 5040.0 5040 100.000 1 2729 1 chr4D.!!$F1 2728
1 TraesCS4D01G228500 chr4A 69313313 69315982 2669 False 1760.5 3157 91.313 1 2602 2 chr4A.!!$F2 2601
2 TraesCS4D01G228500 chr4B 476264460 476266704 2244 False 2647.0 2647 88.383 3 2232 1 chr4B.!!$F1 2229

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
576 607 0.395312 ACCCCCACAAGTACTCAACG 59.605 55.0 0.0 0.0 0.0 4.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2504 2687 0.107508 CGGAGGGAGACACATGCATT 60.108 55.0 0.0 0.0 0.0 3.56 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
24 25 5.122554 ACATAATTTGGCAACGTCGTAATCA 59.877 36.000 0.00 0.00 42.51 2.57
33 34 5.731263 GGCAACGTCGTAATCAAAATCTAAC 59.269 40.000 0.00 0.00 0.00 2.34
36 37 6.695292 ACGTCGTAATCAAAATCTAACGTT 57.305 33.333 5.88 5.88 37.54 3.99
191 195 5.334414 GCAATGTGCATGTACTATAAGGCTC 60.334 44.000 15.25 0.00 44.26 4.70
196 200 3.822996 CATGTACTATAAGGCTCGGTCG 58.177 50.000 0.00 0.00 0.00 4.79
225 229 8.129211 GGATTGCACTATGTTGTACTTATTTCC 58.871 37.037 0.00 0.00 0.00 3.13
226 230 6.995511 TGCACTATGTTGTACTTATTTCCC 57.004 37.500 0.00 0.00 0.00 3.97
476 490 4.136051 CAAAAGTTTCTAACCCCCGTACA 58.864 43.478 0.00 0.00 0.00 2.90
513 529 3.503827 GCAAACCTGCCATTAGTAACC 57.496 47.619 0.00 0.00 43.26 2.85
524 555 5.598830 TGCCATTAGTAACCCACAAGAAAAA 59.401 36.000 0.00 0.00 0.00 1.94
535 566 4.702131 CCCACAAGAAAAATCGAGGAAGAT 59.298 41.667 0.00 0.00 0.00 2.40
563 594 0.404040 GTGAGGTCAAATCACCCCCA 59.596 55.000 0.00 0.00 40.99 4.96
564 595 0.404040 TGAGGTCAAATCACCCCCAC 59.596 55.000 0.00 0.00 37.09 4.61
565 596 0.404040 GAGGTCAAATCACCCCCACA 59.596 55.000 0.00 0.00 37.09 4.17
576 607 0.395312 ACCCCCACAAGTACTCAACG 59.605 55.000 0.00 0.00 0.00 4.10
584 615 3.869246 CACAAGTACTCAACGAACCAACT 59.131 43.478 0.00 0.00 0.00 3.16
586 617 5.521010 CACAAGTACTCAACGAACCAACTAA 59.479 40.000 0.00 0.00 0.00 2.24
726 762 0.464916 TCCACCGTAGATAGAGCGCA 60.465 55.000 11.47 0.00 0.00 6.09
768 811 9.319060 TCTTCACTGATATAGATAGCTTCCATT 57.681 33.333 0.00 0.00 0.00 3.16
830 873 5.591472 TCTTCTCGATCTAAAACCACCGATA 59.409 40.000 0.00 0.00 0.00 2.92
914 971 9.226345 GCAGATTTCATGCAAAACTAATACTAC 57.774 33.333 0.00 0.00 43.31 2.73
994 1079 5.249852 TCTTCTCCTCCTACTCCTATCTAGC 59.750 48.000 0.00 0.00 0.00 3.42
1146 1231 1.207593 CTTCCAGAAAAGTGGCGCG 59.792 57.895 0.00 0.00 37.53 6.86
1278 1363 1.525442 GCCCACCGCTACCAAGTAT 59.475 57.895 0.00 0.00 0.00 2.12
1632 1717 1.371267 CGTCGTCAAAGCGTCTCCA 60.371 57.895 0.00 0.00 0.00 3.86
1736 1821 0.875728 CTCCGCCTCTAGTATCGTGG 59.124 60.000 0.00 0.00 0.00 4.94
1793 1882 1.796459 GGTGTACCGTTGCTACTGTTG 59.204 52.381 0.33 0.00 0.00 3.33
1841 1930 2.093128 CCTGGCTGGGAAAATACGTACT 60.093 50.000 0.00 0.00 0.00 2.73
1842 1931 3.133362 CCTGGCTGGGAAAATACGTACTA 59.867 47.826 0.00 0.00 0.00 1.82
1843 1932 4.117685 CTGGCTGGGAAAATACGTACTAC 58.882 47.826 0.00 0.00 0.00 2.73
1882 1972 4.754114 AGAAAGAAGAGTTGTGTGATGCTC 59.246 41.667 0.00 0.00 0.00 4.26
2004 2117 7.651304 TGTTGATTAAGCTTTAATTGTGTGGTG 59.349 33.333 3.20 0.00 0.00 4.17
2160 2307 6.552859 TGTATGTGGTGATGTTTAAGTGTG 57.447 37.500 0.00 0.00 0.00 3.82
2217 2371 3.234284 GCGCGTGTACATATTGTTTTTCG 59.766 43.478 8.43 0.00 0.00 3.46
2246 2400 7.607607 TGATCTTTGTATGCATGTATGTATCCC 59.392 37.037 10.16 0.00 34.85 3.85
2257 2411 3.633525 TGTATGTATCCCGTGGACACTAC 59.366 47.826 0.56 4.48 32.98 2.73
2271 2425 5.357314 GTGGACACTACTAGCTAGACATCAA 59.643 44.000 27.45 7.80 0.00 2.57
2401 2584 6.936335 TGGAAACTATATAGATGCACACATGG 59.064 38.462 16.79 0.00 36.35 3.66
2454 2637 4.741928 AGAAATACCCCTTGTTCCACTT 57.258 40.909 0.00 0.00 0.00 3.16
2499 2682 6.992766 ACATTTTTCTTTTCTTGAACAAGCG 58.007 32.000 9.38 0.00 38.28 4.68
2500 2683 6.589907 ACATTTTTCTTTTCTTGAACAAGCGT 59.410 30.769 9.38 0.00 38.28 5.07
2501 2684 6.626199 TTTTTCTTTTCTTGAACAAGCGTC 57.374 33.333 9.38 0.00 38.28 5.19
2502 2685 4.955925 TTCTTTTCTTGAACAAGCGTCA 57.044 36.364 9.38 0.00 38.28 4.35
2503 2686 4.955925 TCTTTTCTTGAACAAGCGTCAA 57.044 36.364 9.38 0.00 38.28 3.18
2504 2687 5.303747 TCTTTTCTTGAACAAGCGTCAAA 57.696 34.783 9.38 3.17 38.28 2.69
2505 2688 5.704888 TCTTTTCTTGAACAAGCGTCAAAA 58.295 33.333 9.38 9.56 38.28 2.44
2506 2689 6.329496 TCTTTTCTTGAACAAGCGTCAAAAT 58.671 32.000 9.38 0.00 38.28 1.82
2507 2690 5.947503 TTTCTTGAACAAGCGTCAAAATG 57.052 34.783 9.38 0.00 38.28 2.32
2508 2691 3.371168 TCTTGAACAAGCGTCAAAATGC 58.629 40.909 9.38 0.00 38.28 3.56
2509 2692 2.859526 TGAACAAGCGTCAAAATGCA 57.140 40.000 0.00 0.00 40.06 3.96
2510 2693 3.367992 TGAACAAGCGTCAAAATGCAT 57.632 38.095 0.00 0.00 40.06 3.96
2511 2694 3.051327 TGAACAAGCGTCAAAATGCATG 58.949 40.909 0.00 0.00 40.94 4.06
2512 2695 2.798976 ACAAGCGTCAAAATGCATGT 57.201 40.000 0.00 0.00 42.76 3.21
2513 2696 2.396601 ACAAGCGTCAAAATGCATGTG 58.603 42.857 0.00 1.60 45.05 3.21
2514 2697 2.223782 ACAAGCGTCAAAATGCATGTGT 60.224 40.909 0.00 0.00 45.05 3.72
2515 2698 2.336554 AGCGTCAAAATGCATGTGTC 57.663 45.000 0.00 0.00 40.06 3.67
2516 2699 1.881973 AGCGTCAAAATGCATGTGTCT 59.118 42.857 0.00 0.00 40.06 3.41
2517 2700 2.095567 AGCGTCAAAATGCATGTGTCTC 60.096 45.455 0.00 0.00 40.06 3.36
2518 2701 2.855180 CGTCAAAATGCATGTGTCTCC 58.145 47.619 0.00 0.00 0.00 3.71
2519 2702 2.414559 CGTCAAAATGCATGTGTCTCCC 60.415 50.000 0.00 0.00 0.00 4.30
2541 2724 4.094442 CCTCCGTTTCTAAATGTAAGGTGC 59.906 45.833 5.67 0.00 0.00 5.01
2556 2739 9.995003 AATGTAAGGTGCATTATTCTTTCAAAA 57.005 25.926 0.00 0.00 35.09 2.44
2557 2740 9.995003 ATGTAAGGTGCATTATTCTTTCAAAAA 57.005 25.926 0.00 0.00 0.00 1.94
2585 2768 8.262227 TCAAACTTCTCTAACTTTGACCAAGTA 58.738 33.333 0.00 0.00 45.77 2.24
2602 2785 9.515226 TGACCAAGTATATAGGCAAAAATATCC 57.485 33.333 0.00 0.00 0.00 2.59
2603 2786 8.879427 ACCAAGTATATAGGCAAAAATATCCC 57.121 34.615 0.00 0.00 0.00 3.85
2604 2787 7.893833 ACCAAGTATATAGGCAAAAATATCCCC 59.106 37.037 0.00 0.00 0.00 4.81
2605 2788 8.116026 CCAAGTATATAGGCAAAAATATCCCCT 58.884 37.037 0.00 0.00 0.00 4.79
2606 2789 9.178758 CAAGTATATAGGCAAAAATATCCCCTC 57.821 37.037 0.00 0.00 0.00 4.30
2607 2790 7.873195 AGTATATAGGCAAAAATATCCCCTCC 58.127 38.462 0.00 0.00 0.00 4.30
2608 2791 2.775490 AGGCAAAAATATCCCCTCCC 57.225 50.000 0.00 0.00 0.00 4.30
2609 2792 1.133482 AGGCAAAAATATCCCCTCCCG 60.133 52.381 0.00 0.00 0.00 5.14
2610 2793 1.411074 GGCAAAAATATCCCCTCCCGT 60.411 52.381 0.00 0.00 0.00 5.28
2611 2794 1.681264 GCAAAAATATCCCCTCCCGTG 59.319 52.381 0.00 0.00 0.00 4.94
2612 2795 2.306847 CAAAAATATCCCCTCCCGTGG 58.693 52.381 0.00 0.00 0.00 4.94
2613 2796 1.901648 AAAATATCCCCTCCCGTGGA 58.098 50.000 0.00 0.00 34.54 4.02
2614 2797 1.137697 AAATATCCCCTCCCGTGGAC 58.862 55.000 0.00 0.00 32.36 4.02
2615 2798 1.119574 AATATCCCCTCCCGTGGACG 61.120 60.000 0.00 0.00 39.44 4.79
2634 2817 2.126424 GTCGCGACGCTTTCTCCT 60.126 61.111 25.19 0.00 0.00 3.69
2635 2818 2.126463 TCGCGACGCTTTCTCCTG 60.126 61.111 19.02 0.00 0.00 3.86
2636 2819 2.126463 CGCGACGCTTTCTCCTGA 60.126 61.111 19.02 0.00 0.00 3.86
2637 2820 2.155194 CGCGACGCTTTCTCCTGAG 61.155 63.158 19.02 0.00 0.00 3.35
2638 2821 2.448705 GCGACGCTTTCTCCTGAGC 61.449 63.158 13.73 0.00 35.58 4.26
2639 2822 1.214062 CGACGCTTTCTCCTGAGCT 59.786 57.895 0.00 0.00 36.76 4.09
2640 2823 0.452184 CGACGCTTTCTCCTGAGCTA 59.548 55.000 0.00 0.00 36.76 3.32
2641 2824 1.066303 CGACGCTTTCTCCTGAGCTAT 59.934 52.381 0.00 0.00 36.76 2.97
2642 2825 2.468831 GACGCTTTCTCCTGAGCTATG 58.531 52.381 0.00 0.00 36.76 2.23
2643 2826 1.827969 ACGCTTTCTCCTGAGCTATGT 59.172 47.619 0.00 0.00 36.76 2.29
2644 2827 2.200067 CGCTTTCTCCTGAGCTATGTG 58.800 52.381 0.00 0.00 36.76 3.21
2645 2828 2.559440 GCTTTCTCCTGAGCTATGTGG 58.441 52.381 0.00 0.00 36.01 4.17
2646 2829 2.169352 GCTTTCTCCTGAGCTATGTGGA 59.831 50.000 0.00 0.00 36.01 4.02
2647 2830 3.181456 GCTTTCTCCTGAGCTATGTGGAT 60.181 47.826 0.00 0.00 36.01 3.41
2648 2831 4.685575 GCTTTCTCCTGAGCTATGTGGATT 60.686 45.833 0.00 0.00 36.01 3.01
2649 2832 4.679373 TTCTCCTGAGCTATGTGGATTC 57.321 45.455 0.00 0.00 0.00 2.52
2650 2833 2.625314 TCTCCTGAGCTATGTGGATTCG 59.375 50.000 0.00 0.00 0.00 3.34
2651 2834 1.069204 TCCTGAGCTATGTGGATTCGC 59.931 52.381 0.00 0.00 0.00 4.70
2652 2835 1.069823 CCTGAGCTATGTGGATTCGCT 59.930 52.381 0.00 0.00 0.00 4.93
2653 2836 2.133553 CTGAGCTATGTGGATTCGCTG 58.866 52.381 0.00 0.00 0.00 5.18
2654 2837 1.756538 TGAGCTATGTGGATTCGCTGA 59.243 47.619 0.00 0.00 0.00 4.26
2655 2838 2.366590 TGAGCTATGTGGATTCGCTGAT 59.633 45.455 0.00 0.00 0.00 2.90
2656 2839 2.992543 GAGCTATGTGGATTCGCTGATC 59.007 50.000 0.00 0.00 0.00 2.92
2657 2840 1.723542 GCTATGTGGATTCGCTGATCG 59.276 52.381 0.00 0.00 40.15 3.69
2658 2841 2.332104 CTATGTGGATTCGCTGATCGG 58.668 52.381 0.00 0.00 39.05 4.18
2659 2842 0.882042 ATGTGGATTCGCTGATCGGC 60.882 55.000 17.01 17.01 39.05 5.54
2667 2850 4.427394 GCTGATCGGCGTTCAGAT 57.573 55.556 38.12 14.30 42.63 2.90
2668 2851 2.220761 GCTGATCGGCGTTCAGATC 58.779 57.895 38.12 23.88 42.63 2.75
2671 2854 1.640428 TGATCGGCGTTCAGATCAAC 58.360 50.000 16.07 0.00 46.93 3.18
2672 2855 0.931005 GATCGGCGTTCAGATCAACC 59.069 55.000 12.77 0.00 41.97 3.77
2673 2856 0.462047 ATCGGCGTTCAGATCAACCC 60.462 55.000 6.85 0.00 0.00 4.11
2674 2857 2.106683 CGGCGTTCAGATCAACCCC 61.107 63.158 0.00 0.00 0.00 4.95
2675 2858 1.002624 GGCGTTCAGATCAACCCCA 60.003 57.895 0.00 0.00 0.00 4.96
2676 2859 0.608035 GGCGTTCAGATCAACCCCAA 60.608 55.000 0.00 0.00 0.00 4.12
2677 2860 0.521735 GCGTTCAGATCAACCCCAAC 59.478 55.000 0.00 0.00 0.00 3.77
2678 2861 1.890876 CGTTCAGATCAACCCCAACA 58.109 50.000 0.00 0.00 0.00 3.33
2679 2862 1.535462 CGTTCAGATCAACCCCAACAC 59.465 52.381 0.00 0.00 0.00 3.32
2680 2863 1.886542 GTTCAGATCAACCCCAACACC 59.113 52.381 0.00 0.00 0.00 4.16
2681 2864 0.036164 TCAGATCAACCCCAACACCG 59.964 55.000 0.00 0.00 0.00 4.94
2682 2865 0.036164 CAGATCAACCCCAACACCGA 59.964 55.000 0.00 0.00 0.00 4.69
2683 2866 0.991920 AGATCAACCCCAACACCGAT 59.008 50.000 0.00 0.00 0.00 4.18
2684 2867 1.065418 AGATCAACCCCAACACCGATC 60.065 52.381 0.00 0.00 0.00 3.69
2685 2868 0.034477 ATCAACCCCAACACCGATCC 60.034 55.000 0.00 0.00 0.00 3.36
2686 2869 1.131303 TCAACCCCAACACCGATCCT 61.131 55.000 0.00 0.00 0.00 3.24
2687 2870 0.960364 CAACCCCAACACCGATCCTG 60.960 60.000 0.00 0.00 0.00 3.86
2688 2871 1.423794 AACCCCAACACCGATCCTGT 61.424 55.000 0.00 0.00 0.00 4.00
2689 2872 1.377202 CCCCAACACCGATCCTGTG 60.377 63.158 8.16 8.16 39.63 3.66
2690 2873 1.676968 CCCAACACCGATCCTGTGA 59.323 57.895 14.99 0.00 37.18 3.58
2691 2874 0.036164 CCCAACACCGATCCTGTGAA 59.964 55.000 14.99 0.00 37.18 3.18
2692 2875 1.442769 CCAACACCGATCCTGTGAAG 58.557 55.000 14.99 7.79 37.18 3.02
2693 2876 1.442769 CAACACCGATCCTGTGAAGG 58.557 55.000 14.99 0.00 37.18 3.46
2694 2877 0.324943 AACACCGATCCTGTGAAGGG 59.675 55.000 14.99 0.00 37.18 3.95
2695 2878 1.450312 CACCGATCCTGTGAAGGGC 60.450 63.158 4.41 0.00 35.74 5.19
2696 2879 1.918293 ACCGATCCTGTGAAGGGCA 60.918 57.895 0.00 0.00 0.00 5.36
2697 2880 1.299648 CCGATCCTGTGAAGGGCAA 59.700 57.895 0.00 0.00 0.00 4.52
2698 2881 0.745845 CCGATCCTGTGAAGGGCAAG 60.746 60.000 0.00 0.00 0.00 4.01
2699 2882 1.372087 CGATCCTGTGAAGGGCAAGC 61.372 60.000 0.00 0.00 0.00 4.01
2700 2883 0.322816 GATCCTGTGAAGGGCAAGCA 60.323 55.000 0.00 0.00 0.00 3.91
2701 2884 0.112995 ATCCTGTGAAGGGCAAGCAA 59.887 50.000 0.00 0.00 0.00 3.91
2702 2885 0.538057 TCCTGTGAAGGGCAAGCAAG 60.538 55.000 0.00 0.00 0.00 4.01
2703 2886 0.825010 CCTGTGAAGGGCAAGCAAGT 60.825 55.000 0.00 0.00 0.00 3.16
2704 2887 1.545428 CCTGTGAAGGGCAAGCAAGTA 60.545 52.381 0.00 0.00 0.00 2.24
2705 2888 2.229792 CTGTGAAGGGCAAGCAAGTAA 58.770 47.619 0.00 0.00 0.00 2.24
2706 2889 2.821969 CTGTGAAGGGCAAGCAAGTAAT 59.178 45.455 0.00 0.00 0.00 1.89
2707 2890 3.230134 TGTGAAGGGCAAGCAAGTAATT 58.770 40.909 0.00 0.00 0.00 1.40
2708 2891 4.402829 TGTGAAGGGCAAGCAAGTAATTA 58.597 39.130 0.00 0.00 0.00 1.40
2709 2892 4.830046 TGTGAAGGGCAAGCAAGTAATTAA 59.170 37.500 0.00 0.00 0.00 1.40
2710 2893 5.480073 TGTGAAGGGCAAGCAAGTAATTAAT 59.520 36.000 0.00 0.00 0.00 1.40
2711 2894 5.807011 GTGAAGGGCAAGCAAGTAATTAATG 59.193 40.000 0.00 0.00 0.00 1.90
2712 2895 4.391405 AGGGCAAGCAAGTAATTAATGC 57.609 40.909 13.88 13.88 40.34 3.56
2713 2896 3.768757 AGGGCAAGCAAGTAATTAATGCA 59.231 39.130 20.52 0.00 42.45 3.96
2714 2897 4.222588 AGGGCAAGCAAGTAATTAATGCAA 59.777 37.500 20.52 0.00 42.45 4.08
2715 2898 4.934602 GGGCAAGCAAGTAATTAATGCAAA 59.065 37.500 20.52 0.00 42.45 3.68
2716 2899 5.163864 GGGCAAGCAAGTAATTAATGCAAAC 60.164 40.000 20.52 11.80 42.45 2.93
2717 2900 5.163864 GGCAAGCAAGTAATTAATGCAAACC 60.164 40.000 20.52 15.36 42.45 3.27
2718 2901 5.639082 GCAAGCAAGTAATTAATGCAAACCT 59.361 36.000 20.52 3.47 42.45 3.50
2719 2902 6.183360 GCAAGCAAGTAATTAATGCAAACCTC 60.183 38.462 20.52 5.81 42.45 3.85
2720 2903 6.588719 AGCAAGTAATTAATGCAAACCTCA 57.411 33.333 20.52 0.00 42.45 3.86
2721 2904 6.389906 AGCAAGTAATTAATGCAAACCTCAC 58.610 36.000 20.52 0.00 42.45 3.51
2722 2905 5.576774 GCAAGTAATTAATGCAAACCTCACC 59.423 40.000 15.90 0.00 39.81 4.02
2723 2906 6.686630 CAAGTAATTAATGCAAACCTCACCA 58.313 36.000 0.00 0.00 0.00 4.17
2724 2907 7.322664 CAAGTAATTAATGCAAACCTCACCAT 58.677 34.615 0.00 0.00 0.00 3.55
2725 2908 6.866480 AGTAATTAATGCAAACCTCACCATG 58.134 36.000 0.00 0.00 0.00 3.66
2726 2909 3.591196 TTAATGCAAACCTCACCATGC 57.409 42.857 0.00 0.00 39.22 4.06
2727 2910 4.595031 TGCAAACCTCACCATGCA 57.405 50.000 0.00 0.00 45.75 3.96
2728 2911 2.343506 TGCAAACCTCACCATGCAG 58.656 52.632 0.00 0.00 43.32 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 7.503991 TCACAACGTTAGATTTTGATTACGAC 58.496 34.615 0.00 0.00 33.60 4.34
88 91 2.298729 GCCAACTGAGGGTAAAAATGCA 59.701 45.455 0.00 0.00 0.00 3.96
191 195 2.040009 ATAGTGCAATCCCCCGACCG 62.040 60.000 0.00 0.00 0.00 4.79
196 200 2.143876 ACAACATAGTGCAATCCCCC 57.856 50.000 0.00 0.00 0.00 5.40
278 288 0.110373 GCTTTAGGTTGCGTTCGGTG 60.110 55.000 0.00 0.00 0.00 4.94
316 326 1.486211 TTTTGCGGGGAAAAGAACCA 58.514 45.000 0.00 0.00 0.00 3.67
385 399 4.082190 CGGGAGCATTATTCGGAGAATAGA 60.082 45.833 3.20 0.00 45.90 1.98
476 490 7.302524 CAGGTTTGCACGTGTTAATTACTATT 58.697 34.615 18.38 0.00 34.61 1.73
513 529 5.886960 ATCTTCCTCGATTTTTCTTGTGG 57.113 39.130 0.00 0.00 0.00 4.17
524 555 7.070074 ACCTCACATAAACTAATCTTCCTCGAT 59.930 37.037 0.00 0.00 0.00 3.59
535 566 6.657541 GGGTGATTTGACCTCACATAAACTAA 59.342 38.462 5.87 0.00 43.85 2.24
563 594 4.133013 AGTTGGTTCGTTGAGTACTTGT 57.867 40.909 0.00 0.00 0.00 3.16
564 595 5.050567 GGTTAGTTGGTTCGTTGAGTACTTG 60.051 44.000 0.00 0.00 0.00 3.16
565 596 5.052481 GGTTAGTTGGTTCGTTGAGTACTT 58.948 41.667 0.00 0.00 0.00 2.24
576 607 4.843728 TGATGAGATGGGTTAGTTGGTTC 58.156 43.478 0.00 0.00 0.00 3.62
584 615 4.111577 AGGAAGGTTGATGAGATGGGTTA 58.888 43.478 0.00 0.00 0.00 2.85
586 617 2.507471 GAGGAAGGTTGATGAGATGGGT 59.493 50.000 0.00 0.00 0.00 4.51
726 762 2.158667 TGAAGAACCGAAGAAAAGGCCT 60.159 45.455 0.00 0.00 0.00 5.19
787 830 5.875910 AGAAGAGATCAAGAACATGCAAGAG 59.124 40.000 0.00 0.00 0.00 2.85
912 969 6.710744 GGAATGAAGAACTGGAAGAACTTGTA 59.289 38.462 0.00 0.00 37.43 2.41
913 970 5.532779 GGAATGAAGAACTGGAAGAACTTGT 59.467 40.000 0.00 0.00 37.43 3.16
914 971 5.048434 GGGAATGAAGAACTGGAAGAACTTG 60.048 44.000 0.00 0.00 37.43 3.16
926 983 7.888250 ATAAAGAAGGATGGGAATGAAGAAC 57.112 36.000 0.00 0.00 0.00 3.01
927 984 8.899887 AAATAAAGAAGGATGGGAATGAAGAA 57.100 30.769 0.00 0.00 0.00 2.52
928 985 8.339247 AGAAATAAAGAAGGATGGGAATGAAGA 58.661 33.333 0.00 0.00 0.00 2.87
994 1079 2.341257 CAGAACGTTCTCCATGTCTGG 58.659 52.381 27.54 9.75 44.64 3.86
1278 1363 1.464395 TGGGTAGGGGAAAGTGGCA 60.464 57.895 0.00 0.00 0.00 4.92
1371 1456 2.049156 CTCAGCTGGCGTGACGAA 60.049 61.111 15.13 0.00 0.00 3.85
1372 1457 4.724602 GCTCAGCTGGCGTGACGA 62.725 66.667 15.13 0.00 0.00 4.20
1374 1459 4.687215 TGGCTCAGCTGGCGTGAC 62.687 66.667 15.13 4.89 35.06 3.67
1736 1821 4.552745 GCGCGGCAGGGTAATTGC 62.553 66.667 8.83 0.00 40.80 3.56
1759 1846 4.037858 GGTACACCGAGATCACGTAAAT 57.962 45.455 11.61 0.00 0.00 1.40
1760 1847 3.492421 GGTACACCGAGATCACGTAAA 57.508 47.619 11.61 0.00 0.00 2.01
1842 1931 9.796180 TCTTCTTTCTTGTCTTCTAGTAGTAGT 57.204 33.333 4.51 0.00 0.00 2.73
1882 1972 3.499737 GCCACCGACCATTGCTCG 61.500 66.667 0.00 0.00 0.00 5.03
1887 1977 2.358247 GTCACGCCACCGACCATT 60.358 61.111 0.00 0.00 38.29 3.16
2028 2144 2.733227 GCAGGCACGTAACGTACAGTAT 60.733 50.000 0.00 0.00 38.32 2.12
2160 2307 7.201350 CGCCAAGCACAAGATTTAATTTAAGTC 60.201 37.037 4.05 4.05 0.00 3.01
2176 2326 1.135141 GCCAATATTTCGCCAAGCACA 60.135 47.619 0.00 0.00 0.00 4.57
2217 2371 7.019774 ACATACATGCATACAAAGATCACAC 57.980 36.000 0.00 0.00 0.00 3.82
2246 2400 3.268330 TGTCTAGCTAGTAGTGTCCACG 58.732 50.000 20.10 0.00 36.20 4.94
2257 2411 9.149225 GTCCATTCATAATTGATGTCTAGCTAG 57.851 37.037 15.01 15.01 36.84 3.42
2288 2442 5.397334 GGACTTGGAAGAAAGCTGGATAGAT 60.397 44.000 0.00 0.00 0.00 1.98
2290 2444 4.195416 GGACTTGGAAGAAAGCTGGATAG 58.805 47.826 0.00 0.00 0.00 2.08
2292 2446 2.291217 GGGACTTGGAAGAAAGCTGGAT 60.291 50.000 0.00 0.00 0.00 3.41
2295 2449 2.575805 AGGGACTTGGAAGAAAGCTG 57.424 50.000 0.00 0.00 27.25 4.24
2354 2537 7.162761 TCCACTACCGAATTTCAGTTCAAATA 58.837 34.615 0.00 0.00 0.00 1.40
2370 2553 6.807230 GTGCATCTATATAGTTTCCACTACCG 59.193 42.308 9.58 0.00 38.38 4.02
2439 2622 3.223674 CTTGTAAGTGGAACAAGGGGT 57.776 47.619 7.86 0.00 46.52 4.95
2454 2637 5.344743 GTCCTGGAGACATTGATCTTGTA 57.655 43.478 0.00 0.00 45.55 2.41
2499 2682 2.821969 AGGGAGACACATGCATTTTGAC 59.178 45.455 11.31 5.89 0.00 3.18
2500 2683 3.084039 GAGGGAGACACATGCATTTTGA 58.916 45.455 11.31 0.00 0.00 2.69
2501 2684 2.165030 GGAGGGAGACACATGCATTTTG 59.835 50.000 0.00 0.00 0.00 2.44
2502 2685 2.450476 GGAGGGAGACACATGCATTTT 58.550 47.619 0.00 0.00 0.00 1.82
2503 2686 1.679944 CGGAGGGAGACACATGCATTT 60.680 52.381 0.00 0.00 0.00 2.32
2504 2687 0.107508 CGGAGGGAGACACATGCATT 60.108 55.000 0.00 0.00 0.00 3.56
2505 2688 1.267574 ACGGAGGGAGACACATGCAT 61.268 55.000 0.00 0.00 0.00 3.96
2506 2689 1.480212 AACGGAGGGAGACACATGCA 61.480 55.000 0.00 0.00 0.00 3.96
2507 2690 0.321653 AAACGGAGGGAGACACATGC 60.322 55.000 0.00 0.00 0.00 4.06
2508 2691 1.276421 AGAAACGGAGGGAGACACATG 59.724 52.381 0.00 0.00 0.00 3.21
2509 2692 1.645710 AGAAACGGAGGGAGACACAT 58.354 50.000 0.00 0.00 0.00 3.21
2510 2693 2.297698 TAGAAACGGAGGGAGACACA 57.702 50.000 0.00 0.00 0.00 3.72
2511 2694 3.672767 TTTAGAAACGGAGGGAGACAC 57.327 47.619 0.00 0.00 0.00 3.67
2512 2695 3.581332 ACATTTAGAAACGGAGGGAGACA 59.419 43.478 0.00 0.00 0.00 3.41
2513 2696 4.203654 ACATTTAGAAACGGAGGGAGAC 57.796 45.455 0.00 0.00 0.00 3.36
2514 2697 5.105064 CCTTACATTTAGAAACGGAGGGAGA 60.105 44.000 0.00 0.00 0.00 3.71
2515 2698 5.116882 CCTTACATTTAGAAACGGAGGGAG 58.883 45.833 0.00 0.00 0.00 4.30
2516 2699 4.533311 ACCTTACATTTAGAAACGGAGGGA 59.467 41.667 0.00 0.00 0.00 4.20
2517 2700 4.634443 CACCTTACATTTAGAAACGGAGGG 59.366 45.833 0.00 0.00 0.00 4.30
2518 2701 4.094442 GCACCTTACATTTAGAAACGGAGG 59.906 45.833 0.00 0.00 0.00 4.30
2519 2702 4.693566 TGCACCTTACATTTAGAAACGGAG 59.306 41.667 0.00 0.00 0.00 4.63
2585 2768 5.340027 CGGGAGGGGATATTTTTGCCTATAT 60.340 44.000 0.00 0.00 0.00 0.86
2591 2774 1.681264 CACGGGAGGGGATATTTTTGC 59.319 52.381 0.00 0.00 0.00 3.68
2617 2800 2.126424 AGGAGAAAGCGTCGCGAC 60.126 61.111 28.96 28.96 0.00 5.19
2618 2801 2.126463 CAGGAGAAAGCGTCGCGA 60.126 61.111 12.30 3.71 0.00 5.87
2619 2802 2.126463 TCAGGAGAAAGCGTCGCG 60.126 61.111 12.30 0.00 0.00 5.87
2620 2803 2.448705 GCTCAGGAGAAAGCGTCGC 61.449 63.158 9.80 9.80 0.00 5.19
2621 2804 0.452184 TAGCTCAGGAGAAAGCGTCG 59.548 55.000 0.00 0.00 43.37 5.12
2622 2805 2.159170 ACATAGCTCAGGAGAAAGCGTC 60.159 50.000 0.00 0.00 43.37 5.19
2623 2806 1.827969 ACATAGCTCAGGAGAAAGCGT 59.172 47.619 0.00 0.00 43.37 5.07
2624 2807 2.200067 CACATAGCTCAGGAGAAAGCG 58.800 52.381 0.00 0.00 43.37 4.68
2625 2808 2.169352 TCCACATAGCTCAGGAGAAAGC 59.831 50.000 0.00 0.00 38.84 3.51
2626 2809 4.686191 ATCCACATAGCTCAGGAGAAAG 57.314 45.455 0.00 0.00 32.91 2.62
2627 2810 4.442052 CGAATCCACATAGCTCAGGAGAAA 60.442 45.833 0.00 0.00 32.91 2.52
2628 2811 3.068732 CGAATCCACATAGCTCAGGAGAA 59.931 47.826 0.00 0.00 32.91 2.87
2629 2812 2.625314 CGAATCCACATAGCTCAGGAGA 59.375 50.000 0.00 0.00 32.91 3.71
2630 2813 2.865670 GCGAATCCACATAGCTCAGGAG 60.866 54.545 0.00 0.00 32.91 3.69
2631 2814 1.069204 GCGAATCCACATAGCTCAGGA 59.931 52.381 0.00 0.00 34.12 3.86
2632 2815 1.069823 AGCGAATCCACATAGCTCAGG 59.930 52.381 0.00 0.00 31.94 3.86
2633 2816 2.133553 CAGCGAATCCACATAGCTCAG 58.866 52.381 0.00 0.00 35.82 3.35
2634 2817 1.756538 TCAGCGAATCCACATAGCTCA 59.243 47.619 0.00 0.00 35.82 4.26
2635 2818 2.515926 TCAGCGAATCCACATAGCTC 57.484 50.000 0.00 0.00 35.82 4.09
2636 2819 2.608998 CGATCAGCGAATCCACATAGCT 60.609 50.000 0.00 0.00 44.57 3.32
2637 2820 1.723542 CGATCAGCGAATCCACATAGC 59.276 52.381 0.00 0.00 44.57 2.97
2638 2821 2.332104 CCGATCAGCGAATCCACATAG 58.668 52.381 0.00 0.00 44.57 2.23
2639 2822 1.605457 GCCGATCAGCGAATCCACATA 60.605 52.381 0.00 0.00 44.57 2.29
2640 2823 0.882042 GCCGATCAGCGAATCCACAT 60.882 55.000 0.00 0.00 44.57 3.21
2641 2824 1.521457 GCCGATCAGCGAATCCACA 60.521 57.895 0.00 0.00 44.57 4.17
2642 2825 3.324035 GCCGATCAGCGAATCCAC 58.676 61.111 0.00 0.00 44.57 4.02
2650 2833 0.528466 TGATCTGAACGCCGATCAGC 60.528 55.000 18.28 7.19 43.19 4.26
2651 2834 1.590238 GTTGATCTGAACGCCGATCAG 59.410 52.381 17.17 17.17 44.66 2.90
2652 2835 1.640428 GTTGATCTGAACGCCGATCA 58.360 50.000 0.00 0.00 42.96 2.92
2653 2836 0.931005 GGTTGATCTGAACGCCGATC 59.069 55.000 0.00 0.00 37.22 3.69
2654 2837 0.462047 GGGTTGATCTGAACGCCGAT 60.462 55.000 0.00 0.00 33.74 4.18
2655 2838 1.079405 GGGTTGATCTGAACGCCGA 60.079 57.895 0.00 0.00 33.74 5.54
2656 2839 2.106683 GGGGTTGATCTGAACGCCG 61.107 63.158 13.93 0.00 45.68 6.46
2658 2841 0.521735 GTTGGGGTTGATCTGAACGC 59.478 55.000 4.85 4.85 37.90 4.84
2659 2842 1.535462 GTGTTGGGGTTGATCTGAACG 59.465 52.381 0.00 0.00 0.00 3.95
2660 2843 1.886542 GGTGTTGGGGTTGATCTGAAC 59.113 52.381 0.00 0.00 0.00 3.18
2661 2844 1.544537 CGGTGTTGGGGTTGATCTGAA 60.545 52.381 0.00 0.00 0.00 3.02
2662 2845 0.036164 CGGTGTTGGGGTTGATCTGA 59.964 55.000 0.00 0.00 0.00 3.27
2663 2846 0.036164 TCGGTGTTGGGGTTGATCTG 59.964 55.000 0.00 0.00 0.00 2.90
2664 2847 0.991920 ATCGGTGTTGGGGTTGATCT 59.008 50.000 0.00 0.00 0.00 2.75
2665 2848 1.379527 GATCGGTGTTGGGGTTGATC 58.620 55.000 0.00 0.00 0.00 2.92
2666 2849 0.034477 GGATCGGTGTTGGGGTTGAT 60.034 55.000 0.00 0.00 0.00 2.57
2667 2850 1.131303 AGGATCGGTGTTGGGGTTGA 61.131 55.000 0.00 0.00 0.00 3.18
2668 2851 0.960364 CAGGATCGGTGTTGGGGTTG 60.960 60.000 0.00 0.00 0.00 3.77
2669 2852 1.378762 CAGGATCGGTGTTGGGGTT 59.621 57.895 0.00 0.00 0.00 4.11
2670 2853 1.846124 ACAGGATCGGTGTTGGGGT 60.846 57.895 0.00 0.00 0.00 4.95
2671 2854 1.377202 CACAGGATCGGTGTTGGGG 60.377 63.158 7.73 0.00 0.00 4.96
2672 2855 0.036164 TTCACAGGATCGGTGTTGGG 59.964 55.000 13.75 0.00 37.52 4.12
2673 2856 1.442769 CTTCACAGGATCGGTGTTGG 58.557 55.000 13.75 4.60 37.52 3.77
2674 2857 1.442769 CCTTCACAGGATCGGTGTTG 58.557 55.000 13.75 8.96 44.19 3.33
2675 2858 0.324943 CCCTTCACAGGATCGGTGTT 59.675 55.000 13.75 0.00 44.19 3.32
2676 2859 1.983224 CCCTTCACAGGATCGGTGT 59.017 57.895 13.75 5.03 44.19 4.16
2677 2860 1.450312 GCCCTTCACAGGATCGGTG 60.450 63.158 9.25 9.25 44.19 4.94
2678 2861 1.488705 TTGCCCTTCACAGGATCGGT 61.489 55.000 0.00 0.00 44.19 4.69
2679 2862 0.745845 CTTGCCCTTCACAGGATCGG 60.746 60.000 0.00 0.00 44.19 4.18
2680 2863 1.372087 GCTTGCCCTTCACAGGATCG 61.372 60.000 0.00 0.00 44.19 3.69
2681 2864 0.322816 TGCTTGCCCTTCACAGGATC 60.323 55.000 0.00 0.00 44.19 3.36
2682 2865 0.112995 TTGCTTGCCCTTCACAGGAT 59.887 50.000 0.00 0.00 44.19 3.24
2683 2866 0.538057 CTTGCTTGCCCTTCACAGGA 60.538 55.000 0.00 0.00 44.19 3.86
2684 2867 0.825010 ACTTGCTTGCCCTTCACAGG 60.825 55.000 0.00 0.00 40.45 4.00
2685 2868 1.896220 TACTTGCTTGCCCTTCACAG 58.104 50.000 0.00 0.00 0.00 3.66
2686 2869 2.356665 TTACTTGCTTGCCCTTCACA 57.643 45.000 0.00 0.00 0.00 3.58
2687 2870 3.942130 AATTACTTGCTTGCCCTTCAC 57.058 42.857 0.00 0.00 0.00 3.18
2688 2871 5.624281 GCATTAATTACTTGCTTGCCCTTCA 60.624 40.000 10.83 0.00 33.61 3.02
2689 2872 4.805719 GCATTAATTACTTGCTTGCCCTTC 59.194 41.667 10.83 0.00 33.61 3.46
2690 2873 4.222588 TGCATTAATTACTTGCTTGCCCTT 59.777 37.500 16.48 0.00 37.28 3.95
2691 2874 3.768757 TGCATTAATTACTTGCTTGCCCT 59.231 39.130 16.48 0.00 37.28 5.19
2692 2875 4.122143 TGCATTAATTACTTGCTTGCCC 57.878 40.909 16.48 0.00 37.28 5.36
2693 2876 5.163864 GGTTTGCATTAATTACTTGCTTGCC 60.164 40.000 16.48 12.42 37.28 4.52
2694 2877 5.639082 AGGTTTGCATTAATTACTTGCTTGC 59.361 36.000 16.48 6.84 37.28 4.01
2695 2878 6.867816 TGAGGTTTGCATTAATTACTTGCTTG 59.132 34.615 16.48 0.00 37.28 4.01
2696 2879 6.868339 GTGAGGTTTGCATTAATTACTTGCTT 59.132 34.615 16.48 2.89 37.28 3.91
2697 2880 6.389906 GTGAGGTTTGCATTAATTACTTGCT 58.610 36.000 16.48 1.37 37.28 3.91
2698 2881 5.576774 GGTGAGGTTTGCATTAATTACTTGC 59.423 40.000 11.09 11.09 36.91 4.01
2699 2882 6.686630 TGGTGAGGTTTGCATTAATTACTTG 58.313 36.000 0.00 0.00 0.00 3.16
2700 2883 6.909550 TGGTGAGGTTTGCATTAATTACTT 57.090 33.333 0.00 0.00 0.00 2.24
2701 2884 6.627953 GCATGGTGAGGTTTGCATTAATTACT 60.628 38.462 0.00 0.00 35.22 2.24
2702 2885 5.519927 GCATGGTGAGGTTTGCATTAATTAC 59.480 40.000 0.00 0.00 35.22 1.89
2703 2886 5.186603 TGCATGGTGAGGTTTGCATTAATTA 59.813 36.000 0.00 0.00 39.98 1.40
2704 2887 4.020396 TGCATGGTGAGGTTTGCATTAATT 60.020 37.500 0.00 0.00 39.98 1.40
2705 2888 3.514706 TGCATGGTGAGGTTTGCATTAAT 59.485 39.130 0.00 0.00 39.98 1.40
2706 2889 2.896044 TGCATGGTGAGGTTTGCATTAA 59.104 40.909 0.00 0.00 39.98 1.40
2707 2890 2.492881 CTGCATGGTGAGGTTTGCATTA 59.507 45.455 0.00 0.00 43.51 1.90
2708 2891 1.274167 CTGCATGGTGAGGTTTGCATT 59.726 47.619 0.00 0.00 43.51 3.56
2709 2892 0.892755 CTGCATGGTGAGGTTTGCAT 59.107 50.000 0.00 0.00 43.51 3.96
2710 2893 2.343506 CTGCATGGTGAGGTTTGCA 58.656 52.632 0.00 0.00 42.41 4.08


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

AutoCloner maintained by Alex Coulton.