Multiple sequence alignment - TraesCS7A01G226800

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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 TraesCS7A01G226800 chr7A 100.000 2888 0 0 1 2888 196513996 196511109 0.000000e+00 5334
1 TraesCS7A01G226800 chr7A 97.233 253 7 0 2636 2888 507579413 507579665 2.060000e-116 429
2 TraesCS7A01G226800 chr7A 96.124 258 9 1 2631 2888 645404608 645404352 1.240000e-113 420
3 TraesCS7A01G226800 chr7D 93.634 2639 158 10 1 2634 187792715 187795348 0.000000e+00 3934
4 TraesCS7A01G226800 chr7B 91.963 2588 200 6 52 2635 331354525 331357108 0.000000e+00 3620
5 TraesCS7A01G226800 chr7B 97.244 254 7 0 2635 2888 405701831 405702084 5.720000e-117 431
6 TraesCS7A01G226800 chr7B 96.850 254 7 1 2635 2888 608065917 608065665 9.570000e-115 424
7 TraesCS7A01G226800 chr7B 96.838 253 7 1 2635 2887 608096162 608095911 3.440000e-114 422
8 TraesCS7A01G226800 chr1B 97.244 254 7 0 2635 2888 392841779 392841526 5.720000e-117 431
9 TraesCS7A01G226800 chr1A 97.244 254 6 1 2635 2888 408855687 408855939 2.060000e-116 429
10 TraesCS7A01G226800 chr1A 96.838 253 7 1 2636 2888 437344375 437344626 3.440000e-114 422
11 TraesCS7A01G226800 chr5B 96.850 254 7 1 2635 2888 374546372 374546120 9.570000e-115 424


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 TraesCS7A01G226800 chr7A 196511109 196513996 2887 True 5334 5334 100.000 1 2888 1 chr7A.!!$R1 2887
1 TraesCS7A01G226800 chr7D 187792715 187795348 2633 False 3934 3934 93.634 1 2634 1 chr7D.!!$F1 2633
2 TraesCS7A01G226800 chr7B 331354525 331357108 2583 False 3620 3620 91.963 52 2635 1 chr7B.!!$F1 2583

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
60 61 2.281761 CCTTCCGCACTTGCAGGT 60.282 61.111 0.00 0.00 42.21 4.00 F
76 77 2.421952 GCAGGTCATCATGGGTACACAT 60.422 50.000 4.28 4.28 0.00 3.21 F
1104 1109 2.583024 TGATGTGGAATGAAGGCACA 57.417 45.000 0.00 0.00 0.00 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1275 1280 0.704076 AAACCCTGGCAGGAGCATTA 59.296 50.000 34.84 0.0 44.61 1.90 R
1289 1294 1.901464 TTGCGAGGCAAGGAAACCC 60.901 57.895 0.00 0.0 43.99 4.11 R
2721 2730 0.040204 CCTTGGAGGGTCTTGGCATT 59.960 55.000 0.00 0.0 0.00 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
48 49 8.387190 TCTAAAAAGCTACAACTAAACCTTCC 57.613 34.615 0.00 0.00 0.00 3.46
49 50 5.684550 AAAAGCTACAACTAAACCTTCCG 57.315 39.130 0.00 0.00 0.00 4.30
60 61 2.281761 CCTTCCGCACTTGCAGGT 60.282 61.111 0.00 0.00 42.21 4.00
76 77 2.421952 GCAGGTCATCATGGGTACACAT 60.422 50.000 4.28 4.28 0.00 3.21
103 104 5.971202 ACATGTTCGTGTGTGAAGAAATTTC 59.029 36.000 10.33 10.33 0.00 2.17
112 113 5.927689 TGTGTGAAGAAATTTCCATTGCATC 59.072 36.000 14.61 3.47 0.00 3.91
116 117 7.716123 TGTGAAGAAATTTCCATTGCATCTTTT 59.284 29.630 14.61 0.00 0.00 2.27
119 120 7.012661 AGAAATTTCCATTGCATCTTTTCCT 57.987 32.000 14.61 0.00 0.00 3.36
130 131 5.007034 TGCATCTTTTCCTAAATTCCGACA 58.993 37.500 0.00 0.00 0.00 4.35
316 317 8.650143 AATGGTTCAAAATAAGTGATACTGGT 57.350 30.769 0.00 0.00 0.00 4.00
443 444 4.776308 ACGACCCTTACTCTACAAAATCCT 59.224 41.667 0.00 0.00 0.00 3.24
478 479 4.104579 TGGATGTACCATATCTGCACCAAT 59.895 41.667 0.00 0.00 44.64 3.16
596 597 4.820716 AGCAGAGCCATGAATCAATAGAAC 59.179 41.667 0.00 0.00 0.00 3.01
629 630 3.095912 ACTTACCAAACATTAGGGGGC 57.904 47.619 0.00 0.00 0.00 5.80
765 770 8.196771 TGATCCCAATGAACAATAAGCAATTAC 58.803 33.333 0.00 0.00 0.00 1.89
773 778 7.081349 TGAACAATAAGCAATTACTTTCGTGG 58.919 34.615 0.00 0.00 0.00 4.94
778 783 8.973378 CAATAAGCAATTACTTTCGTGGAAAAA 58.027 29.630 0.00 0.00 30.84 1.94
838 843 2.875296 ACACACACATAGGGCATGTTT 58.125 42.857 0.00 0.00 46.01 2.83
946 951 4.164221 CCCAAGCCACTTCCTATAAGAAGA 59.836 45.833 16.40 0.00 45.08 2.87
947 952 5.363939 CCAAGCCACTTCCTATAAGAAGAG 58.636 45.833 16.40 9.29 45.08 2.85
1004 1009 4.572389 GTCTACCAAATCACTAGCCATGTG 59.428 45.833 0.00 0.00 36.82 3.21
1018 1023 3.264193 AGCCATGTGTTCAAGAGATGGTA 59.736 43.478 11.90 0.00 0.00 3.25
1103 1108 3.431922 CATGATGTGGAATGAAGGCAC 57.568 47.619 0.00 0.00 0.00 5.01
1104 1109 2.583024 TGATGTGGAATGAAGGCACA 57.417 45.000 0.00 0.00 0.00 4.57
1122 1127 3.496160 GCACAGTGGAAAAGAAGGAGGTA 60.496 47.826 1.84 0.00 0.00 3.08
1167 1172 3.287222 CACCTCCTTCAAGTGTTTCCAA 58.713 45.455 0.00 0.00 0.00 3.53
1251 1256 2.926242 TTCCGGAAGAGGGCGGTT 60.926 61.111 14.35 0.00 0.00 4.44
1254 1259 4.394712 CGGAAGAGGGCGGTTGCT 62.395 66.667 0.00 0.00 42.25 3.91
1275 1280 4.099266 GCTAGACACACCAATCAGATCTCT 59.901 45.833 0.00 0.00 0.00 3.10
1289 1294 2.633967 AGATCTCTAATGCTCCTGCCAG 59.366 50.000 0.00 0.00 38.71 4.85
1297 1302 2.911926 GCTCCTGCCAGGGTTTCCT 61.912 63.158 11.68 0.00 46.26 3.36
1311 1316 2.351924 TTTCCTTGCCTCGCAACCCT 62.352 55.000 0.00 0.00 43.99 4.34
1364 1369 1.608590 CATCCACTTTTGGTGTTCGCT 59.391 47.619 0.00 0.00 44.35 4.93
1368 1373 1.021968 ACTTTTGGTGTTCGCTGGAC 58.978 50.000 0.00 0.00 0.00 4.02
1473 1478 2.093128 GGTGACGGTTCCATACCTTGAT 60.093 50.000 0.00 0.00 45.40 2.57
1474 1479 3.606687 GTGACGGTTCCATACCTTGATT 58.393 45.455 0.00 0.00 45.40 2.57
1477 1482 5.644636 GTGACGGTTCCATACCTTGATTTAA 59.355 40.000 0.00 0.00 45.40 1.52
1480 1485 7.066525 TGACGGTTCCATACCTTGATTTAAATC 59.933 37.037 19.37 19.37 45.40 2.17
1520 1525 4.102210 ACCAGTGATGATGGATCCAACTAG 59.898 45.833 20.67 12.59 40.51 2.57
1609 1614 7.104974 AGAGCCTTTGTCCCTATCTATAGTA 57.895 40.000 0.00 0.00 0.00 1.82
1619 1624 7.130442 TGTCCCTATCTATAGTATGCCATCCTA 59.870 40.741 0.00 0.00 0.00 2.94
1673 1678 4.074627 TGTCCTTGACGAATACACCAAA 57.925 40.909 0.00 0.00 34.95 3.28
1707 1712 1.902508 GATCTGACACTCCAGTTGGGA 59.097 52.381 0.00 0.00 45.89 4.37
1906 1911 4.461781 GCTAGTTGTGTACTAAGGTGGAGA 59.538 45.833 0.00 0.00 38.84 3.71
1945 1950 3.997681 CCAGCAATCAAATTGTGATGCAA 59.002 39.130 17.22 0.00 46.80 4.08
1974 1979 8.591940 TGAGATCAATAAGCTATAGATTGCACT 58.408 33.333 13.46 10.69 31.86 4.40
2005 2011 6.633500 TTTGTGGAAACTTCTTAGATGTGG 57.367 37.500 1.47 0.00 0.00 4.17
2168 2175 6.901081 AAGAAAGTGTATCTTCCCAAAAGG 57.099 37.500 0.00 0.00 35.02 3.11
2269 2276 9.342308 TCTTGTCTGAACATAGAAGAAAACATT 57.658 29.630 0.00 0.00 34.73 2.71
2304 2311 6.515272 ACTTAGGCAAGTGATGGTAAAATG 57.485 37.500 2.25 0.00 43.50 2.32
2323 2330 3.029483 TGCATGCTTCCCCATAATTCA 57.971 42.857 20.33 0.00 0.00 2.57
2324 2331 3.578978 TGCATGCTTCCCCATAATTCAT 58.421 40.909 20.33 0.00 0.00 2.57
2392 2400 3.186613 GGCAATATAGACTTTGGCGCTAC 59.813 47.826 7.64 0.00 38.41 3.58
2460 2468 6.928520 AGATATGCTCAAACAAAGAAAAGGG 58.071 36.000 0.00 0.00 0.00 3.95
2499 2507 3.264193 TGTGCTTCTATCCTCAACATGGT 59.736 43.478 0.00 0.00 0.00 3.55
2625 2634 3.933861 ACATATCACCAGGACCCTTTC 57.066 47.619 0.00 0.00 0.00 2.62
2636 2645 2.711542 GGACCCTTTCCATACACACTG 58.288 52.381 0.00 0.00 45.10 3.66
2637 2646 2.039879 GGACCCTTTCCATACACACTGT 59.960 50.000 0.00 0.00 45.10 3.55
2638 2647 3.335579 GACCCTTTCCATACACACTGTC 58.664 50.000 0.00 0.00 0.00 3.51
2639 2648 2.289444 ACCCTTTCCATACACACTGTCG 60.289 50.000 0.00 0.00 0.00 4.35
2640 2649 2.346803 CCTTTCCATACACACTGTCGG 58.653 52.381 0.00 0.00 0.00 4.79
2641 2650 2.289444 CCTTTCCATACACACTGTCGGT 60.289 50.000 0.00 0.00 0.00 4.69
2654 2663 5.171147 CACTGTCGGTGTACTAGAATAGG 57.829 47.826 3.41 0.00 41.05 2.57
2655 2664 4.036498 CACTGTCGGTGTACTAGAATAGGG 59.964 50.000 3.41 0.00 41.05 3.53
2656 2665 3.559069 TGTCGGTGTACTAGAATAGGGG 58.441 50.000 0.00 0.00 44.97 4.79
2657 2666 3.053395 TGTCGGTGTACTAGAATAGGGGT 60.053 47.826 0.00 0.00 44.97 4.95
2658 2667 4.165950 TGTCGGTGTACTAGAATAGGGGTA 59.834 45.833 0.00 0.00 44.97 3.69
2659 2668 4.517075 GTCGGTGTACTAGAATAGGGGTAC 59.483 50.000 0.00 0.00 44.97 3.34
2675 2684 2.443958 GTACCCTAGTACCCCGAACT 57.556 55.000 0.00 0.00 42.66 3.01
2676 2685 2.739943 GTACCCTAGTACCCCGAACTT 58.260 52.381 0.00 0.00 42.66 2.66
2677 2686 1.565067 ACCCTAGTACCCCGAACTTG 58.435 55.000 0.00 0.00 0.00 3.16
2678 2687 1.203225 ACCCTAGTACCCCGAACTTGT 60.203 52.381 0.00 0.00 0.00 3.16
2679 2688 1.206371 CCCTAGTACCCCGAACTTGTG 59.794 57.143 0.00 0.00 0.00 3.33
2680 2689 1.405121 CCTAGTACCCCGAACTTGTGC 60.405 57.143 0.00 0.00 0.00 4.57
2681 2690 1.274167 CTAGTACCCCGAACTTGTGCA 59.726 52.381 0.00 0.00 0.00 4.57
2682 2691 0.250166 AGTACCCCGAACTTGTGCAC 60.250 55.000 10.75 10.75 0.00 4.57
2683 2692 1.301087 TACCCCGAACTTGTGCACG 60.301 57.895 13.13 0.65 0.00 5.34
2684 2693 1.746322 TACCCCGAACTTGTGCACGA 61.746 55.000 13.13 9.87 0.00 4.35
2685 2694 2.317609 CCCCGAACTTGTGCACGAG 61.318 63.158 29.07 29.07 0.00 4.18
2686 2695 2.551270 CCGAACTTGTGCACGAGC 59.449 61.111 30.31 16.15 42.57 5.03
2696 2705 3.653009 GCACGAGCAGTTGCAGCA 61.653 61.111 2.55 0.00 45.16 4.41
2697 2706 2.250485 CACGAGCAGTTGCAGCAC 59.750 61.111 2.55 0.00 45.16 4.40
2698 2707 2.974698 ACGAGCAGTTGCAGCACC 60.975 61.111 2.55 0.00 45.16 5.01
2699 2708 3.730761 CGAGCAGTTGCAGCACCC 61.731 66.667 2.55 0.00 45.16 4.61
2700 2709 3.368571 GAGCAGTTGCAGCACCCC 61.369 66.667 2.55 0.00 45.16 4.95
2722 2731 2.668212 CAAGGCTTGTCGGGCGAA 60.668 61.111 19.07 0.00 36.85 4.70
2723 2732 2.040544 CAAGGCTTGTCGGGCGAAT 61.041 57.895 19.07 0.00 36.85 3.34
2724 2733 2.040544 AAGGCTTGTCGGGCGAATG 61.041 57.895 0.00 0.00 36.85 2.67
2725 2734 4.179579 GGCTTGTCGGGCGAATGC 62.180 66.667 0.00 0.00 41.71 3.56
2735 2744 3.502572 GCGAATGCCAAGACCCTC 58.497 61.111 0.00 0.00 33.98 4.30
2736 2745 2.115291 GCGAATGCCAAGACCCTCC 61.115 63.158 0.00 0.00 33.98 4.30
2737 2746 1.299648 CGAATGCCAAGACCCTCCA 59.700 57.895 0.00 0.00 0.00 3.86
2738 2747 0.322456 CGAATGCCAAGACCCTCCAA 60.322 55.000 0.00 0.00 0.00 3.53
2739 2748 1.467920 GAATGCCAAGACCCTCCAAG 58.532 55.000 0.00 0.00 0.00 3.61
2740 2749 0.040204 AATGCCAAGACCCTCCAAGG 59.960 55.000 0.00 0.00 34.30 3.61
2741 2750 1.142688 ATGCCAAGACCCTCCAAGGT 61.143 55.000 0.00 0.00 45.12 3.50
2742 2751 1.360393 TGCCAAGACCCTCCAAGGTT 61.360 55.000 0.00 0.00 41.42 3.50
2743 2752 0.609406 GCCAAGACCCTCCAAGGTTC 60.609 60.000 0.00 0.00 41.42 3.62
2744 2753 0.038310 CCAAGACCCTCCAAGGTTCC 59.962 60.000 0.00 0.00 41.42 3.62
2745 2754 0.038310 CAAGACCCTCCAAGGTTCCC 59.962 60.000 0.00 0.00 41.42 3.97
2746 2755 0.103876 AAGACCCTCCAAGGTTCCCT 60.104 55.000 0.00 0.00 41.42 4.20
2747 2756 0.103876 AGACCCTCCAAGGTTCCCTT 60.104 55.000 0.00 0.00 45.88 3.95
2757 2766 4.666105 GTTCCCTTGGAGCCATCC 57.334 61.111 0.00 0.00 46.87 3.51
2767 2776 2.035530 GGAGCCATCCAAGAACAGAG 57.964 55.000 0.00 0.00 45.87 3.35
2768 2777 1.280421 GGAGCCATCCAAGAACAGAGT 59.720 52.381 0.00 0.00 45.87 3.24
2769 2778 2.501723 GGAGCCATCCAAGAACAGAGTA 59.498 50.000 0.00 0.00 45.87 2.59
2770 2779 3.135530 GGAGCCATCCAAGAACAGAGTAT 59.864 47.826 0.00 0.00 45.87 2.12
2771 2780 4.345257 GGAGCCATCCAAGAACAGAGTATA 59.655 45.833 0.00 0.00 45.87 1.47
2772 2781 5.012561 GGAGCCATCCAAGAACAGAGTATAT 59.987 44.000 0.00 0.00 45.87 0.86
2773 2782 6.211584 GGAGCCATCCAAGAACAGAGTATATA 59.788 42.308 0.00 0.00 45.87 0.86
2774 2783 7.256332 GGAGCCATCCAAGAACAGAGTATATAA 60.256 40.741 0.00 0.00 45.87 0.98
2775 2784 7.675062 AGCCATCCAAGAACAGAGTATATAAG 58.325 38.462 0.00 0.00 0.00 1.73
2776 2785 6.370166 GCCATCCAAGAACAGAGTATATAAGC 59.630 42.308 0.00 0.00 0.00 3.09
2777 2786 7.675062 CCATCCAAGAACAGAGTATATAAGCT 58.325 38.462 0.00 0.00 0.00 3.74
2778 2787 8.807118 CCATCCAAGAACAGAGTATATAAGCTA 58.193 37.037 0.00 0.00 0.00 3.32
2781 2790 8.861086 TCCAAGAACAGAGTATATAAGCTAAGG 58.139 37.037 0.00 0.00 0.00 2.69
2782 2791 8.861086 CCAAGAACAGAGTATATAAGCTAAGGA 58.139 37.037 0.00 0.00 0.00 3.36
2783 2792 9.906660 CAAGAACAGAGTATATAAGCTAAGGAG 57.093 37.037 0.00 0.00 0.00 3.69
2784 2793 9.869667 AAGAACAGAGTATATAAGCTAAGGAGA 57.130 33.333 0.00 0.00 0.00 3.71
2785 2794 9.292195 AGAACAGAGTATATAAGCTAAGGAGAC 57.708 37.037 0.00 0.00 0.00 3.36
2786 2795 8.998277 AACAGAGTATATAAGCTAAGGAGACA 57.002 34.615 0.00 0.00 0.00 3.41
2787 2796 8.998277 ACAGAGTATATAAGCTAAGGAGACAA 57.002 34.615 0.00 0.00 0.00 3.18
2788 2797 9.073475 ACAGAGTATATAAGCTAAGGAGACAAG 57.927 37.037 0.00 0.00 0.00 3.16
2789 2798 9.290988 CAGAGTATATAAGCTAAGGAGACAAGA 57.709 37.037 0.00 0.00 0.00 3.02
2790 2799 9.292195 AGAGTATATAAGCTAAGGAGACAAGAC 57.708 37.037 0.00 0.00 0.00 3.01
2791 2800 8.411991 AGTATATAAGCTAAGGAGACAAGACC 57.588 38.462 0.00 0.00 0.00 3.85
2792 2801 6.673839 ATATAAGCTAAGGAGACAAGACCC 57.326 41.667 0.00 0.00 0.00 4.46
2793 2802 1.574263 AGCTAAGGAGACAAGACCCC 58.426 55.000 0.00 0.00 0.00 4.95
2794 2803 0.175989 GCTAAGGAGACAAGACCCCG 59.824 60.000 0.00 0.00 0.00 5.73
2795 2804 0.824759 CTAAGGAGACAAGACCCCGG 59.175 60.000 0.00 0.00 0.00 5.73
2796 2805 1.262640 TAAGGAGACAAGACCCCGGC 61.263 60.000 0.00 0.00 0.00 6.13
2797 2806 3.319198 GGAGACAAGACCCCGGCA 61.319 66.667 0.00 0.00 0.00 5.69
2798 2807 2.747686 GAGACAAGACCCCGGCAA 59.252 61.111 0.00 0.00 0.00 4.52
2799 2808 1.376037 GAGACAAGACCCCGGCAAG 60.376 63.158 0.00 0.00 0.00 4.01
2800 2809 1.827399 GAGACAAGACCCCGGCAAGA 61.827 60.000 0.00 0.00 0.00 3.02
2801 2810 1.376037 GACAAGACCCCGGCAAGAG 60.376 63.158 0.00 0.00 0.00 2.85
2802 2811 2.045926 CAAGACCCCGGCAAGAGG 60.046 66.667 0.00 0.00 0.00 3.69
2803 2812 2.203938 AAGACCCCGGCAAGAGGA 60.204 61.111 0.00 0.00 0.00 3.71
2804 2813 2.294078 AAGACCCCGGCAAGAGGAG 61.294 63.158 0.00 0.00 0.00 3.69
2805 2814 4.475135 GACCCCGGCAAGAGGAGC 62.475 72.222 0.00 0.00 0.00 4.70
2807 2816 3.721706 CCCCGGCAAGAGGAGCTT 61.722 66.667 0.00 0.00 37.29 3.74
2813 2822 2.437359 CAAGAGGAGCTTGCCGGG 60.437 66.667 2.18 0.00 46.67 5.73
2814 2823 2.607750 AAGAGGAGCTTGCCGGGA 60.608 61.111 2.18 0.00 34.93 5.14
2815 2824 2.224159 AAGAGGAGCTTGCCGGGAA 61.224 57.895 8.57 8.57 34.93 3.97
2816 2825 2.124942 GAGGAGCTTGCCGGGAAG 60.125 66.667 29.63 29.63 0.00 3.46
2817 2826 3.689002 GAGGAGCTTGCCGGGAAGG 62.689 68.421 33.31 17.41 44.97 3.46
2826 2835 3.924507 CCGGGAAGGCCAATCAAG 58.075 61.111 5.01 0.57 35.15 3.02
2827 2836 1.754234 CCGGGAAGGCCAATCAAGG 60.754 63.158 5.01 6.35 35.15 3.61
2834 2843 3.372730 GCCAATCAAGGCGCACCA 61.373 61.111 10.83 0.00 46.12 4.17
2835 2844 2.929903 GCCAATCAAGGCGCACCAA 61.930 57.895 10.83 0.00 46.12 3.67
2836 2845 1.213537 CCAATCAAGGCGCACCAAG 59.786 57.895 10.83 0.00 39.06 3.61
2837 2846 1.213537 CAATCAAGGCGCACCAAGG 59.786 57.895 10.83 0.00 39.06 3.61
2838 2847 1.074775 AATCAAGGCGCACCAAGGA 59.925 52.632 10.83 0.00 39.06 3.36
2839 2848 0.539438 AATCAAGGCGCACCAAGGAA 60.539 50.000 10.83 0.00 39.06 3.36
2840 2849 1.244019 ATCAAGGCGCACCAAGGAAC 61.244 55.000 10.83 0.00 39.06 3.62
2870 2879 4.704833 GCCACTCCGCTCCAGCAA 62.705 66.667 0.00 0.00 42.21 3.91
2871 2880 2.435586 CCACTCCGCTCCAGCAAG 60.436 66.667 0.00 0.00 42.21 4.01
2872 2881 2.435586 CACTCCGCTCCAGCAAGG 60.436 66.667 0.00 0.00 42.21 3.61
2873 2882 4.400961 ACTCCGCTCCAGCAAGGC 62.401 66.667 0.00 0.00 42.21 4.35
2879 2888 3.437795 CTCCAGCAAGGCGGCAAG 61.438 66.667 13.08 3.69 37.29 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 5.506815 GCGGAAGGTTTAGTTGTAGCTTTTT 60.507 40.000 0.00 0.00 32.68 1.94
48 49 0.098200 CATGATGACCTGCAAGTGCG 59.902 55.000 0.00 0.00 45.83 5.34
49 50 0.454600 CCATGATGACCTGCAAGTGC 59.545 55.000 0.00 0.00 42.50 4.40
60 61 4.566426 TGTCAATGTGTACCCATGATGA 57.434 40.909 0.00 0.00 0.00 2.92
76 77 3.526534 TCTTCACACACGAACATGTCAA 58.473 40.909 0.00 0.00 0.00 3.18
103 104 5.750067 CGGAATTTAGGAAAAGATGCAATGG 59.250 40.000 0.00 0.00 0.00 3.16
112 113 5.897377 ACCATGTCGGAATTTAGGAAAAG 57.103 39.130 0.00 0.00 38.63 2.27
116 117 5.687166 AGTTACCATGTCGGAATTTAGGA 57.313 39.130 0.00 0.00 38.63 2.94
119 120 6.478129 AGGAAAGTTACCATGTCGGAATTTA 58.522 36.000 0.00 0.00 38.63 1.40
130 131 8.437575 CCATTATACTGGTAGGAAAGTTACCAT 58.562 37.037 4.73 0.00 46.91 3.55
171 172 4.705023 GGCACATTAAAAGTGACCACCTAT 59.295 41.667 13.70 0.00 39.12 2.57
224 225 1.239347 GTCTCCACTGTTGGCTTTCC 58.761 55.000 0.00 0.00 43.56 3.13
332 333 6.402981 ACCCCTTTACTATTCCATTCTTGT 57.597 37.500 0.00 0.00 0.00 3.16
337 338 6.045577 CCCTCATACCCCTTTACTATTCCATT 59.954 42.308 0.00 0.00 0.00 3.16
345 346 3.113043 GTGACCCTCATACCCCTTTACT 58.887 50.000 0.00 0.00 0.00 2.24
565 566 1.117994 CATGGCTCTGCTCCTGACTA 58.882 55.000 0.00 0.00 0.00 2.59
679 682 3.448660 CCCACCCCAGATTGAGAAAATTC 59.551 47.826 0.00 0.00 0.00 2.17
698 701 2.006415 GATCCATGACCCCACCCCA 61.006 63.158 0.00 0.00 0.00 4.96
797 802 2.480845 ACACGTGTAAAGGTTGAGCTC 58.519 47.619 21.98 6.82 0.00 4.09
838 843 1.341482 TGTGAAAAGTGGGTTGAGGCA 60.341 47.619 0.00 0.00 0.00 4.75
846 851 0.385390 GTGGTGCTGTGAAAAGTGGG 59.615 55.000 0.00 0.00 0.00 4.61
929 934 6.183360 GGAAGGTCTCTTCTTATAGGAAGTGG 60.183 46.154 20.44 15.28 46.42 4.00
959 964 7.275183 AGACGATGTTGGATTCTTATCAATGA 58.725 34.615 0.00 0.00 32.09 2.57
963 968 6.097696 TGGTAGACGATGTTGGATTCTTATCA 59.902 38.462 0.00 0.00 32.09 2.15
970 975 5.354234 GTGATTTGGTAGACGATGTTGGATT 59.646 40.000 0.00 0.00 0.00 3.01
1004 1009 6.672266 TCTGGGATATACCATCTCTTGAAC 57.328 41.667 7.26 0.00 40.36 3.18
1087 1092 2.165167 CACTGTGCCTTCATTCCACAT 58.835 47.619 0.00 0.00 38.63 3.21
1101 1106 3.214696 ACCTCCTTCTTTTCCACTGTG 57.785 47.619 0.00 0.00 0.00 3.66
1103 1108 3.008485 AGCTACCTCCTTCTTTTCCACTG 59.992 47.826 0.00 0.00 0.00 3.66
1104 1109 3.252351 AGCTACCTCCTTCTTTTCCACT 58.748 45.455 0.00 0.00 0.00 4.00
1167 1172 2.299867 GGTTGGGAATGTCTTGTTGCAT 59.700 45.455 0.00 0.00 0.00 3.96
1251 1256 3.771479 AGATCTGATTGGTGTGTCTAGCA 59.229 43.478 0.00 0.00 0.00 3.49
1254 1259 7.685398 GCATTAGAGATCTGATTGGTGTGTCTA 60.685 40.741 0.00 0.00 0.00 2.59
1275 1280 0.704076 AAACCCTGGCAGGAGCATTA 59.296 50.000 34.84 0.00 44.61 1.90
1289 1294 1.901464 TTGCGAGGCAAGGAAACCC 60.901 57.895 0.00 0.00 43.99 4.11
1297 1302 3.565214 TGGAGGGTTGCGAGGCAA 61.565 61.111 0.00 0.00 46.80 4.52
1364 1369 3.041211 CTCCTGGTTGAGATATGGTCCA 58.959 50.000 0.00 0.00 34.11 4.02
1368 1373 3.209410 GTTGCTCCTGGTTGAGATATGG 58.791 50.000 0.00 0.00 34.11 2.74
1502 1507 6.331042 AGGATTTCTAGTTGGATCCATCATCA 59.669 38.462 22.09 2.23 40.39 3.07
1520 1525 4.084011 AGAGGCTCTAATGCAGGATTTC 57.916 45.455 17.09 0.00 34.04 2.17
1673 1678 2.802816 GTCAGATCAGTTTCTGTGCGTT 59.197 45.455 0.00 0.00 43.02 4.84
1707 1712 7.007723 TCTTTTGGGTGTGTTTATTACCAGAT 58.992 34.615 0.00 0.00 36.19 2.90
1720 1725 2.348411 AGTGTCCTCTTTTGGGTGTG 57.652 50.000 0.00 0.00 0.00 3.82
1854 1859 4.592485 ATGTAACTCCAGATCTAAGCCG 57.408 45.455 0.00 0.00 0.00 5.52
1906 1911 3.117169 TGCTGGGGTGCATCCTTATTAAT 60.117 43.478 17.44 0.00 38.12 1.40
1984 1990 5.560722 TCCACATCTAAGAAGTTTCCACA 57.439 39.130 0.00 0.00 0.00 4.17
2160 2167 0.900182 GGGCCTTCTGTCCTTTTGGG 60.900 60.000 0.84 0.00 40.87 4.12
2168 2175 3.389329 TCATAAGATGAGGGCCTTCTGTC 59.611 47.826 16.82 13.59 33.59 3.51
2232 2239 9.605275 CTATGTTCAGACAAGATAATTCTCCAA 57.395 33.333 0.00 0.00 39.66 3.53
2304 2311 4.612264 AATGAATTATGGGGAAGCATGC 57.388 40.909 10.51 10.51 0.00 4.06
2323 2330 3.507162 TGTGTCACACCCTCATGAAAT 57.493 42.857 5.21 0.00 32.73 2.17
2324 2331 3.507162 ATGTGTCACACCCTCATGAAA 57.493 42.857 8.08 0.00 32.73 2.69
2372 2380 6.422223 CAAAGTAGCGCCAAAGTCTATATTG 58.578 40.000 2.29 0.00 0.00 1.90
2377 2385 2.073816 GCAAAGTAGCGCCAAAGTCTA 58.926 47.619 2.29 0.00 0.00 2.59
2392 2400 3.803778 GGAGGTCAAACATTGTTGCAAAG 59.196 43.478 0.00 0.00 0.00 2.77
2519 2527 9.996554 GCTAAAAATATATAAAACTTGGGCCAT 57.003 29.630 7.26 0.00 0.00 4.40
2542 2551 9.539825 TTGTTGAAAAGAATATTTTTGCTGCTA 57.460 25.926 0.00 0.00 30.78 3.49
2592 2601 8.988060 TCCTGGTGATATGTAAGATTAAAGTGA 58.012 33.333 0.00 0.00 0.00 3.41
2601 2610 4.280789 AGGGTCCTGGTGATATGTAAGA 57.719 45.455 0.00 0.00 0.00 2.10
2635 2644 3.053395 ACCCCTATTCTAGTACACCGACA 60.053 47.826 0.00 0.00 0.00 4.35
2636 2645 3.560105 ACCCCTATTCTAGTACACCGAC 58.440 50.000 0.00 0.00 0.00 4.79
2637 2646 3.959495 ACCCCTATTCTAGTACACCGA 57.041 47.619 0.00 0.00 0.00 4.69
2638 2647 3.823304 GGTACCCCTATTCTAGTACACCG 59.177 52.174 0.00 0.00 37.42 4.94
2656 2665 2.428530 CAAGTTCGGGGTACTAGGGTAC 59.571 54.545 0.00 0.00 45.38 3.34
2657 2666 2.042979 ACAAGTTCGGGGTACTAGGGTA 59.957 50.000 0.00 0.00 0.00 3.69
2658 2667 1.203225 ACAAGTTCGGGGTACTAGGGT 60.203 52.381 0.00 0.00 0.00 4.34
2659 2668 1.206371 CACAAGTTCGGGGTACTAGGG 59.794 57.143 0.00 0.00 0.00 3.53
2660 2669 1.405121 GCACAAGTTCGGGGTACTAGG 60.405 57.143 0.00 0.00 0.00 3.02
2661 2670 1.274167 TGCACAAGTTCGGGGTACTAG 59.726 52.381 0.00 0.00 0.00 2.57
2662 2671 1.001181 GTGCACAAGTTCGGGGTACTA 59.999 52.381 13.17 0.00 0.00 1.82
2663 2672 0.250166 GTGCACAAGTTCGGGGTACT 60.250 55.000 13.17 0.00 0.00 2.73
2664 2673 1.562575 CGTGCACAAGTTCGGGGTAC 61.563 60.000 18.64 0.00 0.00 3.34
2665 2674 1.301087 CGTGCACAAGTTCGGGGTA 60.301 57.895 18.64 0.00 0.00 3.69
2666 2675 2.590575 CGTGCACAAGTTCGGGGT 60.591 61.111 18.64 0.00 0.00 4.95
2667 2676 2.280524 TCGTGCACAAGTTCGGGG 60.281 61.111 18.64 0.00 0.00 5.73
2668 2677 2.954753 GCTCGTGCACAAGTTCGGG 61.955 63.158 18.64 2.17 39.41 5.14
2669 2678 2.162921 CTGCTCGTGCACAAGTTCGG 62.163 60.000 18.64 0.00 45.31 4.30
2670 2679 1.202568 CTGCTCGTGCACAAGTTCG 59.797 57.895 18.64 1.10 45.31 3.95
2671 2680 0.657840 AACTGCTCGTGCACAAGTTC 59.342 50.000 18.64 0.00 45.31 3.01
2672 2681 0.378257 CAACTGCTCGTGCACAAGTT 59.622 50.000 18.64 16.33 45.31 2.66
2673 2682 2.016961 CAACTGCTCGTGCACAAGT 58.983 52.632 18.64 11.29 45.31 3.16
2674 2683 1.369689 GCAACTGCTCGTGCACAAG 60.370 57.895 18.64 9.47 45.31 3.16
2675 2684 2.050639 CTGCAACTGCTCGTGCACAA 62.051 55.000 18.64 0.00 45.31 3.33
2676 2685 2.513435 TGCAACTGCTCGTGCACA 60.513 55.556 18.64 2.11 45.31 4.57
2677 2686 2.250485 CTGCAACTGCTCGTGCAC 59.750 61.111 8.30 6.82 45.31 4.57
2679 2688 3.653009 TGCTGCAACTGCTCGTGC 61.653 61.111 0.00 1.71 42.66 5.34
2680 2689 2.250485 GTGCTGCAACTGCTCGTG 59.750 61.111 2.77 0.00 42.66 4.35
2681 2690 2.974698 GGTGCTGCAACTGCTCGT 60.975 61.111 11.11 0.00 42.66 4.18
2682 2691 3.730761 GGGTGCTGCAACTGCTCG 61.731 66.667 18.32 0.00 42.66 5.03
2683 2692 3.368571 GGGGTGCTGCAACTGCTC 61.369 66.667 18.32 0.00 42.66 4.26
2705 2714 2.040544 ATTCGCCCGACAAGCCTTG 61.041 57.895 2.11 2.11 0.00 3.61
2706 2715 2.040544 CATTCGCCCGACAAGCCTT 61.041 57.895 0.00 0.00 0.00 4.35
2707 2716 2.436646 CATTCGCCCGACAAGCCT 60.437 61.111 0.00 0.00 0.00 4.58
2708 2717 4.179579 GCATTCGCCCGACAAGCC 62.180 66.667 0.00 0.00 0.00 4.35
2718 2727 2.115291 GGAGGGTCTTGGCATTCGC 61.115 63.158 0.00 0.00 37.44 4.70
2719 2728 0.322456 TTGGAGGGTCTTGGCATTCG 60.322 55.000 0.00 0.00 0.00 3.34
2720 2729 1.467920 CTTGGAGGGTCTTGGCATTC 58.532 55.000 0.00 0.00 0.00 2.67
2721 2730 0.040204 CCTTGGAGGGTCTTGGCATT 59.960 55.000 0.00 0.00 0.00 3.56
2722 2731 1.142688 ACCTTGGAGGGTCTTGGCAT 61.143 55.000 0.00 0.00 40.58 4.40
2723 2732 1.360393 AACCTTGGAGGGTCTTGGCA 61.360 55.000 0.00 0.00 40.58 4.92
2724 2733 1.460699 AACCTTGGAGGGTCTTGGC 59.539 57.895 0.00 0.00 40.58 4.52
2739 2748 1.076705 GGATGGCTCCAAGGGAACC 60.077 63.158 0.00 0.00 46.06 3.62
2740 2749 4.666105 GGATGGCTCCAAGGGAAC 57.334 61.111 0.00 0.00 41.64 3.62
2748 2757 1.280421 ACTCTGTTCTTGGATGGCTCC 59.720 52.381 0.00 0.00 42.45 4.70
2749 2758 2.777832 ACTCTGTTCTTGGATGGCTC 57.222 50.000 0.00 0.00 0.00 4.70
2750 2759 7.618019 TTATATACTCTGTTCTTGGATGGCT 57.382 36.000 0.00 0.00 0.00 4.75
2751 2760 6.370166 GCTTATATACTCTGTTCTTGGATGGC 59.630 42.308 0.00 0.00 0.00 4.40
2752 2761 7.675062 AGCTTATATACTCTGTTCTTGGATGG 58.325 38.462 0.00 0.00 0.00 3.51
2755 2764 8.861086 CCTTAGCTTATATACTCTGTTCTTGGA 58.139 37.037 0.00 0.00 0.00 3.53
2756 2765 8.861086 TCCTTAGCTTATATACTCTGTTCTTGG 58.139 37.037 0.00 0.00 0.00 3.61
2757 2766 9.906660 CTCCTTAGCTTATATACTCTGTTCTTG 57.093 37.037 0.00 0.00 0.00 3.02
2758 2767 9.869667 TCTCCTTAGCTTATATACTCTGTTCTT 57.130 33.333 0.00 0.00 0.00 2.52
2759 2768 9.292195 GTCTCCTTAGCTTATATACTCTGTTCT 57.708 37.037 0.00 0.00 0.00 3.01
2760 2769 9.069082 TGTCTCCTTAGCTTATATACTCTGTTC 57.931 37.037 0.00 0.00 0.00 3.18
2761 2770 8.998277 TGTCTCCTTAGCTTATATACTCTGTT 57.002 34.615 0.00 0.00 0.00 3.16
2762 2771 8.998277 TTGTCTCCTTAGCTTATATACTCTGT 57.002 34.615 0.00 0.00 0.00 3.41
2763 2772 9.290988 TCTTGTCTCCTTAGCTTATATACTCTG 57.709 37.037 0.00 0.00 0.00 3.35
2764 2773 9.292195 GTCTTGTCTCCTTAGCTTATATACTCT 57.708 37.037 0.00 0.00 0.00 3.24
2765 2774 8.517056 GGTCTTGTCTCCTTAGCTTATATACTC 58.483 40.741 0.00 0.00 0.00 2.59
2766 2775 7.452189 GGGTCTTGTCTCCTTAGCTTATATACT 59.548 40.741 0.00 0.00 0.00 2.12
2767 2776 7.309928 GGGGTCTTGTCTCCTTAGCTTATATAC 60.310 44.444 0.00 0.00 0.00 1.47
2768 2777 6.724905 GGGGTCTTGTCTCCTTAGCTTATATA 59.275 42.308 0.00 0.00 0.00 0.86
2769 2778 5.544562 GGGGTCTTGTCTCCTTAGCTTATAT 59.455 44.000 0.00 0.00 0.00 0.86
2770 2779 4.900054 GGGGTCTTGTCTCCTTAGCTTATA 59.100 45.833 0.00 0.00 0.00 0.98
2771 2780 3.712218 GGGGTCTTGTCTCCTTAGCTTAT 59.288 47.826 0.00 0.00 0.00 1.73
2772 2781 3.105283 GGGGTCTTGTCTCCTTAGCTTA 58.895 50.000 0.00 0.00 0.00 3.09
2773 2782 1.909986 GGGGTCTTGTCTCCTTAGCTT 59.090 52.381 0.00 0.00 0.00 3.74
2774 2783 1.574263 GGGGTCTTGTCTCCTTAGCT 58.426 55.000 0.00 0.00 0.00 3.32
2775 2784 0.175989 CGGGGTCTTGTCTCCTTAGC 59.824 60.000 0.00 0.00 0.00 3.09
2776 2785 0.824759 CCGGGGTCTTGTCTCCTTAG 59.175 60.000 0.00 0.00 0.00 2.18
2777 2786 1.262640 GCCGGGGTCTTGTCTCCTTA 61.263 60.000 2.18 0.00 0.00 2.69
2778 2787 2.593956 GCCGGGGTCTTGTCTCCTT 61.594 63.158 2.18 0.00 0.00 3.36
2779 2788 3.003763 GCCGGGGTCTTGTCTCCT 61.004 66.667 2.18 0.00 0.00 3.69
2780 2789 2.804828 CTTGCCGGGGTCTTGTCTCC 62.805 65.000 2.18 0.00 0.00 3.71
2781 2790 1.376037 CTTGCCGGGGTCTTGTCTC 60.376 63.158 2.18 0.00 0.00 3.36
2782 2791 1.831652 CTCTTGCCGGGGTCTTGTCT 61.832 60.000 2.18 0.00 0.00 3.41
2783 2792 1.376037 CTCTTGCCGGGGTCTTGTC 60.376 63.158 2.18 0.00 0.00 3.18
2784 2793 2.750350 CTCTTGCCGGGGTCTTGT 59.250 61.111 2.18 0.00 0.00 3.16
2785 2794 2.045926 CCTCTTGCCGGGGTCTTG 60.046 66.667 2.18 0.00 0.00 3.02
2786 2795 2.203938 TCCTCTTGCCGGGGTCTT 60.204 61.111 2.18 0.00 0.00 3.01
2787 2796 2.685380 CTCCTCTTGCCGGGGTCT 60.685 66.667 2.18 0.00 0.00 3.85
2788 2797 4.475135 GCTCCTCTTGCCGGGGTC 62.475 72.222 2.18 0.00 0.00 4.46
2790 2799 3.721706 AAGCTCCTCTTGCCGGGG 61.722 66.667 2.18 0.00 32.79 5.73
2791 2800 2.437359 CAAGCTCCTCTTGCCGGG 60.437 66.667 2.18 0.00 44.85 5.73
2797 2806 2.190488 CTTCCCGGCAAGCTCCTCTT 62.190 60.000 0.00 0.00 34.78 2.85
2798 2807 2.607750 TTCCCGGCAAGCTCCTCT 60.608 61.111 0.00 0.00 0.00 3.69
2799 2808 2.124942 CTTCCCGGCAAGCTCCTC 60.125 66.667 0.00 0.00 0.00 3.71
2800 2809 3.721706 CCTTCCCGGCAAGCTCCT 61.722 66.667 0.00 0.00 0.00 3.69
2809 2818 1.754234 CCTTGATTGGCCTTCCCGG 60.754 63.158 3.32 0.00 35.87 5.73
2810 2819 2.418083 GCCTTGATTGGCCTTCCCG 61.418 63.158 3.32 0.00 46.82 5.14
2811 2820 3.621225 GCCTTGATTGGCCTTCCC 58.379 61.111 3.32 0.00 46.82 3.97
2818 2827 1.213537 CTTGGTGCGCCTTGATTGG 59.786 57.895 18.96 0.00 35.27 3.16
2819 2828 1.213537 CCTTGGTGCGCCTTGATTG 59.786 57.895 18.96 1.20 35.27 2.67
2820 2829 0.539438 TTCCTTGGTGCGCCTTGATT 60.539 50.000 18.96 0.00 35.27 2.57
2821 2830 1.074775 TTCCTTGGTGCGCCTTGAT 59.925 52.632 18.96 0.00 35.27 2.57
2822 2831 1.896660 GTTCCTTGGTGCGCCTTGA 60.897 57.895 18.96 8.33 35.27 3.02
2823 2832 1.455383 AAGTTCCTTGGTGCGCCTTG 61.455 55.000 18.96 9.87 35.27 3.61
2824 2833 1.152756 AAGTTCCTTGGTGCGCCTT 60.153 52.632 18.96 0.00 35.27 4.35
2825 2834 1.898574 CAAGTTCCTTGGTGCGCCT 60.899 57.895 18.96 0.00 37.77 5.52
2826 2835 2.644992 CAAGTTCCTTGGTGCGCC 59.355 61.111 10.11 10.11 37.77 6.53
2827 2836 2.050077 GCAAGTTCCTTGGTGCGC 60.050 61.111 0.00 0.00 41.31 6.09
2828 2837 2.644992 GGCAAGTTCCTTGGTGCG 59.355 61.111 6.15 0.00 41.31 5.34
2829 2838 2.644992 CGGCAAGTTCCTTGGTGC 59.355 61.111 6.15 0.00 41.31 5.01
2830 2839 2.644992 GCGGCAAGTTCCTTGGTG 59.355 61.111 6.15 0.00 41.31 4.17
2831 2840 2.978010 CGCGGCAAGTTCCTTGGT 60.978 61.111 0.00 0.00 41.31 3.67
2832 2841 2.668212 TCGCGGCAAGTTCCTTGG 60.668 61.111 6.13 0.00 41.31 3.61
2833 2842 2.556287 GTCGCGGCAAGTTCCTTG 59.444 61.111 5.47 0.00 43.57 3.61
2834 2843 3.041940 CGTCGCGGCAAGTTCCTT 61.042 61.111 12.89 0.00 0.00 3.36
2853 2862 4.704833 TTGCTGGAGCGGAGTGGC 62.705 66.667 0.00 0.00 45.83 5.01
2854 2863 2.435586 CTTGCTGGAGCGGAGTGG 60.436 66.667 0.00 0.00 45.83 4.00
2855 2864 2.435586 CCTTGCTGGAGCGGAGTG 60.436 66.667 0.00 0.00 45.83 3.51
2856 2865 4.400961 GCCTTGCTGGAGCGGAGT 62.401 66.667 0.49 0.00 45.83 3.85
2862 2871 3.437795 CTTGCCGCCTTGCTGGAG 61.438 66.667 0.49 0.00 38.35 3.86


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

AutoCloner maintained by Alex Coulton.