Multiple sequence alignment - TraesCS7A01G314500

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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 TraesCS7A01G314500 chr7A 100.000 2762 0 0 1 2762 448267572 448264811 0.000000e+00 5101.0
1 TraesCS7A01G314500 chr7A 88.670 203 17 5 2356 2552 545933319 545933521 2.750000e-60 243.0
2 TraesCS7A01G314500 chr7B 93.629 1554 52 22 815 2352 394780975 394779453 0.000000e+00 2278.0
3 TraesCS7A01G314500 chr7B 99.259 135 1 0 2628 2762 394779293 394779159 7.640000e-61 244.0
4 TraesCS7A01G314500 chr7B 97.826 46 1 0 2549 2594 394779458 394779413 2.280000e-11 80.5
5 TraesCS7A01G314500 chr7D 95.043 1291 38 10 1076 2353 394992211 394990934 0.000000e+00 2006.0
6 TraesCS7A01G314500 chr7D 90.814 762 42 15 1 737 30239312 30240070 0.000000e+00 994.0
7 TraesCS7A01G314500 chr7D 91.321 265 8 6 815 1067 394992792 394992531 5.660000e-92 348.0
8 TraesCS7A01G314500 chr7D 94.964 139 3 2 2628 2762 394990786 394990648 5.990000e-52 215.0
9 TraesCS7A01G314500 chr7D 100.000 47 0 0 2548 2594 394990940 394990894 1.360000e-13 87.9
10 TraesCS7A01G314500 chr5D 90.625 768 41 17 1 738 379392781 379392015 0.000000e+00 990.0
11 TraesCS7A01G314500 chr5D 92.188 192 12 2 2355 2545 288133468 288133279 4.530000e-68 268.0
12 TraesCS7A01G314500 chr5D 90.816 196 12 3 2356 2545 377315163 377314968 9.810000e-65 257.0
13 TraesCS7A01G314500 chr5D 82.609 92 13 2 650 738 469309027 469308936 8.200000e-11 78.7
14 TraesCS7A01G314500 chr6D 90.314 764 47 12 1 738 457348826 457348064 0.000000e+00 976.0
15 TraesCS7A01G314500 chr6D 90.786 738 43 12 1 714 389708868 389708132 0.000000e+00 963.0
16 TraesCS7A01G314500 chr2A 89.348 751 56 17 1 732 218147185 218146440 0.000000e+00 922.0
17 TraesCS7A01G314500 chr2A 88.904 748 63 14 1 732 142401318 142400575 0.000000e+00 904.0
18 TraesCS7A01G314500 chr2A 91.327 196 11 3 2356 2549 68865394 68865585 2.110000e-66 263.0
19 TraesCS7A01G314500 chr1D 91.693 638 23 16 1 610 471749183 471749818 0.000000e+00 857.0
20 TraesCS7A01G314500 chr1D 91.311 610 33 15 37 626 438309891 438310500 0.000000e+00 815.0
21 TraesCS7A01G314500 chr1D 90.625 192 12 2 2356 2545 191375257 191375444 1.640000e-62 250.0
22 TraesCS7A01G314500 chr3D 91.879 628 24 13 1 606 89934252 89933630 0.000000e+00 852.0
23 TraesCS7A01G314500 chr3A 87.109 768 51 18 1 738 455234438 455235187 0.000000e+00 826.0
24 TraesCS7A01G314500 chr6A 91.837 196 13 3 2353 2545 592186976 592186781 1.260000e-68 270.0
25 TraesCS7A01G314500 chr2D 91.099 191 16 1 2356 2545 91365735 91365545 9.810000e-65 257.0
26 TraesCS7A01G314500 chr1A 91.099 191 13 2 2356 2545 580149012 580149199 3.530000e-64 255.0
27 TraesCS7A01G314500 chr6B 90.206 194 15 3 2356 2545 707003445 707003252 1.640000e-62 250.0


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 TraesCS7A01G314500 chr7A 448264811 448267572 2761 True 5101.000 5101 100.000000 1 2762 1 chr7A.!!$R1 2761
1 TraesCS7A01G314500 chr7B 394779159 394780975 1816 True 867.500 2278 96.904667 815 2762 3 chr7B.!!$R1 1947
2 TraesCS7A01G314500 chr7D 30239312 30240070 758 False 994.000 994 90.814000 1 737 1 chr7D.!!$F1 736
3 TraesCS7A01G314500 chr7D 394990648 394992792 2144 True 664.225 2006 95.332000 815 2762 4 chr7D.!!$R1 1947
4 TraesCS7A01G314500 chr5D 379392015 379392781 766 True 990.000 990 90.625000 1 738 1 chr5D.!!$R3 737
5 TraesCS7A01G314500 chr6D 457348064 457348826 762 True 976.000 976 90.314000 1 738 1 chr6D.!!$R2 737
6 TraesCS7A01G314500 chr6D 389708132 389708868 736 True 963.000 963 90.786000 1 714 1 chr6D.!!$R1 713
7 TraesCS7A01G314500 chr2A 218146440 218147185 745 True 922.000 922 89.348000 1 732 1 chr2A.!!$R2 731
8 TraesCS7A01G314500 chr2A 142400575 142401318 743 True 904.000 904 88.904000 1 732 1 chr2A.!!$R1 731
9 TraesCS7A01G314500 chr1D 471749183 471749818 635 False 857.000 857 91.693000 1 610 1 chr1D.!!$F3 609
10 TraesCS7A01G314500 chr1D 438309891 438310500 609 False 815.000 815 91.311000 37 626 1 chr1D.!!$F2 589
11 TraesCS7A01G314500 chr3D 89933630 89934252 622 True 852.000 852 91.879000 1 606 1 chr3D.!!$R1 605
12 TraesCS7A01G314500 chr3A 455234438 455235187 749 False 826.000 826 87.109000 1 738 1 chr3A.!!$F1 737

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
716 772 0.25589 ATGCTGGCGGTAAGGTTGAT 59.744 50.0 0.0 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2433 2833 0.111253 CTGATATTCAGGGGGTGGGC 59.889 60.0 0.0 0.0 40.71 5.36 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
56 63 7.725844 GGGTTCATCTTAAACATATTCCTCCAT 59.274 37.037 0.00 0.00 0.00 3.41
137 144 4.987963 TCCTCCAACATGCATCATATCT 57.012 40.909 0.00 0.00 0.00 1.98
214 228 7.225341 TCTCCAAACAACATCTTCATATCATCG 59.775 37.037 0.00 0.00 0.00 3.84
400 423 9.066892 AGAACTACAATCAAGCTAAAACAATCA 57.933 29.630 0.00 0.00 0.00 2.57
449 480 7.820872 ACAAAAATATGAGGGATTTCAAGCAAG 59.179 33.333 0.00 0.00 0.00 4.01
525 557 3.769844 AGCTTATGTTTCTCTCTTCGGGA 59.230 43.478 0.00 0.00 0.00 5.14
598 647 4.467107 GGGAGAGAGGGGCGAGGT 62.467 72.222 0.00 0.00 0.00 3.85
647 700 4.880426 GAGGGGCGGGGAGATGGA 62.880 72.222 0.00 0.00 0.00 3.41
676 731 1.405105 CGGGGTCGGACGAAATAACTA 59.595 52.381 1.43 0.00 0.00 2.24
690 745 2.512692 TAACTACTCGCACCCTACCA 57.487 50.000 0.00 0.00 0.00 3.25
709 764 2.589540 CAGGGATGCTGGCGGTAA 59.410 61.111 0.00 0.00 0.00 2.85
716 772 0.255890 ATGCTGGCGGTAAGGTTGAT 59.744 50.000 0.00 0.00 0.00 2.57
719 775 1.134491 GCTGGCGGTAAGGTTGATAGT 60.134 52.381 0.00 0.00 0.00 2.12
722 778 2.167693 TGGCGGTAAGGTTGATAGTCTG 59.832 50.000 0.00 0.00 0.00 3.51
723 779 2.167900 GGCGGTAAGGTTGATAGTCTGT 59.832 50.000 0.00 0.00 0.00 3.41
726 782 3.128242 CGGTAAGGTTGATAGTCTGTCGT 59.872 47.826 0.00 0.00 0.00 4.34
749 805 4.402616 AGGGACCCTGAATTGATTTCAA 57.597 40.909 13.95 0.00 43.64 2.69
750 806 4.089361 AGGGACCCTGAATTGATTTCAAC 58.911 43.478 13.95 0.00 43.64 3.18
751 807 3.195610 GGGACCCTGAATTGATTTCAACC 59.804 47.826 2.09 0.00 43.64 3.77
752 808 3.119495 GGACCCTGAATTGATTTCAACCG 60.119 47.826 0.00 0.00 43.64 4.44
753 809 3.756434 GACCCTGAATTGATTTCAACCGA 59.244 43.478 0.00 0.00 43.64 4.69
754 810 4.148838 ACCCTGAATTGATTTCAACCGAA 58.851 39.130 0.00 0.00 43.64 4.30
755 811 4.586841 ACCCTGAATTGATTTCAACCGAAA 59.413 37.500 0.00 0.00 43.64 3.46
769 825 8.885494 TTTCAACCGAAATCAAATTCTGAATT 57.115 26.923 9.76 9.76 37.67 2.17
770 826 7.872163 TCAACCGAAATCAAATTCTGAATTG 57.128 32.000 15.80 10.31 37.67 2.32
771 827 7.656412 TCAACCGAAATCAAATTCTGAATTGA 58.344 30.769 15.80 14.51 37.67 2.57
772 828 8.306038 TCAACCGAAATCAAATTCTGAATTGAT 58.694 29.630 15.80 15.82 37.67 2.57
773 829 9.571810 CAACCGAAATCAAATTCTGAATTGATA 57.428 29.630 15.80 5.74 37.67 2.15
802 858 8.686397 AAAAAGGTCAAAACATGAAATTTTGC 57.314 26.923 12.74 9.14 43.62 3.68
803 859 6.375945 AAGGTCAAAACATGAAATTTTGCC 57.624 33.333 12.74 15.01 43.62 4.52
804 860 4.821260 AGGTCAAAACATGAAATTTTGCCC 59.179 37.500 18.72 15.28 42.64 5.36
805 861 4.023279 GGTCAAAACATGAAATTTTGCCCC 60.023 41.667 12.74 11.32 43.62 5.80
806 862 4.578105 GTCAAAACATGAAATTTTGCCCCA 59.422 37.500 12.74 0.00 43.62 4.96
807 863 5.241285 GTCAAAACATGAAATTTTGCCCCAT 59.759 36.000 12.74 0.00 43.62 4.00
808 864 6.429385 GTCAAAACATGAAATTTTGCCCCATA 59.571 34.615 12.74 0.00 43.62 2.74
809 865 6.654161 TCAAAACATGAAATTTTGCCCCATAG 59.346 34.615 12.74 0.00 43.62 2.23
810 866 6.371595 AAACATGAAATTTTGCCCCATAGA 57.628 33.333 0.00 0.00 0.00 1.98
811 867 5.603170 ACATGAAATTTTGCCCCATAGAG 57.397 39.130 0.00 0.00 0.00 2.43
812 868 4.406649 ACATGAAATTTTGCCCCATAGAGG 59.593 41.667 0.00 0.00 37.03 3.69
850 906 0.804933 GGCGTACAGGTCGTCATTCC 60.805 60.000 0.00 0.00 32.96 3.01
908 971 1.674817 CCCCAACTCGCACGTAATTCT 60.675 52.381 0.00 0.00 0.00 2.40
909 972 2.073816 CCCAACTCGCACGTAATTCTT 58.926 47.619 0.00 0.00 0.00 2.52
910 973 2.159707 CCCAACTCGCACGTAATTCTTG 60.160 50.000 0.00 0.00 0.00 3.02
972 1035 1.449601 CCGCCTCGCCACATTAACT 60.450 57.895 0.00 0.00 0.00 2.24
977 1040 2.021380 CGCCACATTAACTCGCGC 59.979 61.111 0.00 0.00 36.02 6.86
1632 2012 2.183555 CGCGGGGACAAGTACTCC 59.816 66.667 0.00 0.00 0.00 3.85
1654 2034 3.264866 AACGACCTGCTCGACGTCC 62.265 63.158 10.58 0.00 46.14 4.79
1812 2192 4.589216 ATTCTCAAACCACCACACAATG 57.411 40.909 0.00 0.00 0.00 2.82
1853 2233 0.034337 TCTTTCTGTGTACACCGGGC 59.966 55.000 22.91 0.00 0.00 6.13
1924 2304 4.486574 CACGCATTGCATACATCCATTA 57.513 40.909 9.69 0.00 0.00 1.90
1932 2312 7.115805 GCATTGCATACATCCATTATTCTTGTG 59.884 37.037 3.15 0.00 0.00 3.33
1984 2365 9.869757 TTACAGACAAGATATGAGAATTTTCGA 57.130 29.630 0.00 0.00 0.00 3.71
1987 2368 8.877779 CAGACAAGATATGAGAATTTTCGAAGT 58.122 33.333 0.00 0.00 0.00 3.01
2006 2399 7.221450 TCGAAGTAAAAGAAGATGAAAGGGAA 58.779 34.615 0.00 0.00 0.00 3.97
2032 2425 3.058639 GCAGTGAGTAGGTTTTCAGCTTG 60.059 47.826 0.00 0.00 31.45 4.01
2067 2460 5.007626 TGGATCACTTTTGTTCTTCTTGTCG 59.992 40.000 0.00 0.00 0.00 4.35
2169 2562 1.341285 TGGAGCAGCATAATTGTGCCT 60.341 47.619 21.90 13.58 46.19 4.75
2195 2588 4.462483 GCAGGGTTAGAAAATGATGGTCAA 59.538 41.667 0.00 0.00 0.00 3.18
2196 2589 5.047377 GCAGGGTTAGAAAATGATGGTCAAA 60.047 40.000 0.00 0.00 0.00 2.69
2287 2687 4.278419 ACACATAAGTTTGGAACCTTGCTC 59.722 41.667 0.00 0.00 0.00 4.26
2289 2689 5.010012 CACATAAGTTTGGAACCTTGCTCTT 59.990 40.000 0.00 0.00 0.00 2.85
2290 2690 5.010012 ACATAAGTTTGGAACCTTGCTCTTG 59.990 40.000 0.00 0.00 0.00 3.02
2291 2691 1.683385 AGTTTGGAACCTTGCTCTTGC 59.317 47.619 0.00 0.00 40.20 4.01
2292 2692 1.683385 GTTTGGAACCTTGCTCTTGCT 59.317 47.619 0.00 0.00 40.48 3.91
2293 2693 1.321474 TTGGAACCTTGCTCTTGCTG 58.679 50.000 0.00 0.00 40.48 4.41
2294 2694 0.538057 TGGAACCTTGCTCTTGCTGG 60.538 55.000 0.00 0.00 40.48 4.85
2295 2695 0.538287 GGAACCTTGCTCTTGCTGGT 60.538 55.000 0.00 0.00 43.98 4.00
2296 2696 3.520623 AACCTTGCTCTTGCTGGTT 57.479 47.368 11.02 11.02 44.73 3.67
2297 2697 2.656947 AACCTTGCTCTTGCTGGTTA 57.343 45.000 13.69 0.00 46.20 2.85
2298 2698 2.191128 ACCTTGCTCTTGCTGGTTAG 57.809 50.000 0.00 0.00 41.25 2.34
2306 2706 5.479306 TGCTCTTGCTGGTTAGTAACTTAG 58.521 41.667 12.65 11.82 40.48 2.18
2310 2710 6.472887 TCTTGCTGGTTAGTAACTTAGCATT 58.527 36.000 29.00 0.00 44.48 3.56
2377 2777 6.887376 AGAGTAATGCTACATGTACAAACG 57.113 37.500 0.08 0.00 0.00 3.60
2378 2778 6.627243 AGAGTAATGCTACATGTACAAACGA 58.373 36.000 0.08 0.00 0.00 3.85
2379 2779 6.752351 AGAGTAATGCTACATGTACAAACGAG 59.248 38.462 0.08 0.00 0.00 4.18
2380 2780 6.395629 AGTAATGCTACATGTACAAACGAGT 58.604 36.000 0.08 0.00 0.00 4.18
2381 2781 6.872020 AGTAATGCTACATGTACAAACGAGTT 59.128 34.615 0.08 0.00 0.00 3.01
2382 2782 8.030692 AGTAATGCTACATGTACAAACGAGTTA 58.969 33.333 0.08 0.00 0.00 2.24
2383 2783 6.642683 ATGCTACATGTACAAACGAGTTAC 57.357 37.500 0.08 0.00 0.00 2.50
2384 2784 5.530712 TGCTACATGTACAAACGAGTTACA 58.469 37.500 0.08 0.00 0.00 2.41
2385 2785 5.984323 TGCTACATGTACAAACGAGTTACAA 59.016 36.000 0.08 0.00 0.00 2.41
2386 2786 6.144886 TGCTACATGTACAAACGAGTTACAAG 59.855 38.462 0.08 0.00 0.00 3.16
2387 2787 5.338614 ACATGTACAAACGAGTTACAAGC 57.661 39.130 0.00 0.00 0.00 4.01
2388 2788 5.054477 ACATGTACAAACGAGTTACAAGCT 58.946 37.500 0.00 0.00 0.00 3.74
2389 2789 5.526111 ACATGTACAAACGAGTTACAAGCTT 59.474 36.000 0.00 0.00 0.00 3.74
2390 2790 6.037830 ACATGTACAAACGAGTTACAAGCTTT 59.962 34.615 0.00 0.00 0.00 3.51
2391 2791 6.425577 TGTACAAACGAGTTACAAGCTTTT 57.574 33.333 0.00 0.00 0.00 2.27
2392 2792 7.536895 TGTACAAACGAGTTACAAGCTTTTA 57.463 32.000 0.00 0.00 0.00 1.52
2393 2793 7.401080 TGTACAAACGAGTTACAAGCTTTTAC 58.599 34.615 0.00 0.00 0.00 2.01
2394 2794 6.425577 ACAAACGAGTTACAAGCTTTTACA 57.574 33.333 0.00 0.00 0.00 2.41
2395 2795 6.844254 ACAAACGAGTTACAAGCTTTTACAA 58.156 32.000 0.00 0.00 0.00 2.41
2396 2796 7.306953 ACAAACGAGTTACAAGCTTTTACAAA 58.693 30.769 0.00 0.00 0.00 2.83
2397 2797 7.808856 ACAAACGAGTTACAAGCTTTTACAAAA 59.191 29.630 0.00 0.00 0.00 2.44
2398 2798 8.640291 CAAACGAGTTACAAGCTTTTACAAAAA 58.360 29.630 0.00 0.00 0.00 1.94
2399 2799 8.920509 AACGAGTTACAAGCTTTTACAAAAAT 57.079 26.923 0.00 0.00 0.00 1.82
2400 2800 8.335256 ACGAGTTACAAGCTTTTACAAAAATG 57.665 30.769 0.00 0.00 0.00 2.32
2401 2801 7.434013 ACGAGTTACAAGCTTTTACAAAAATGG 59.566 33.333 0.00 0.00 0.00 3.16
2402 2802 7.434013 CGAGTTACAAGCTTTTACAAAAATGGT 59.566 33.333 0.00 0.00 33.38 3.55
2403 2803 9.093970 GAGTTACAAGCTTTTACAAAAATGGTT 57.906 29.630 0.00 0.00 39.59 3.67
2417 2817 8.970859 ACAAAAATGGTTAATTTGATTGGTCA 57.029 26.923 5.68 0.00 38.52 4.02
2418 2818 9.401058 ACAAAAATGGTTAATTTGATTGGTCAA 57.599 25.926 5.68 0.00 42.41 3.18
2422 2822 9.889128 AAATGGTTAATTTGATTGGTCAATAGG 57.111 29.630 0.00 0.00 43.49 2.57
2423 2823 8.608185 ATGGTTAATTTGATTGGTCAATAGGT 57.392 30.769 0.00 0.00 43.49 3.08
2424 2824 7.835822 TGGTTAATTTGATTGGTCAATAGGTG 58.164 34.615 0.00 0.00 43.49 4.00
2425 2825 7.093552 TGGTTAATTTGATTGGTCAATAGGTGG 60.094 37.037 0.00 0.00 43.49 4.61
2426 2826 5.937975 AATTTGATTGGTCAATAGGTGGG 57.062 39.130 0.00 0.00 43.49 4.61
2427 2827 3.380471 TTGATTGGTCAATAGGTGGGG 57.620 47.619 0.00 0.00 39.36 4.96
2428 2828 2.567862 TGATTGGTCAATAGGTGGGGA 58.432 47.619 0.00 0.00 0.00 4.81
2429 2829 2.509548 TGATTGGTCAATAGGTGGGGAG 59.490 50.000 0.00 0.00 0.00 4.30
2430 2830 1.295020 TTGGTCAATAGGTGGGGAGG 58.705 55.000 0.00 0.00 0.00 4.30
2431 2831 1.279025 TGGTCAATAGGTGGGGAGGC 61.279 60.000 0.00 0.00 0.00 4.70
2432 2832 1.146263 GTCAATAGGTGGGGAGGCG 59.854 63.158 0.00 0.00 0.00 5.52
2433 2833 2.070039 TCAATAGGTGGGGAGGCGG 61.070 63.158 0.00 0.00 0.00 6.13
2434 2834 3.489513 AATAGGTGGGGAGGCGGC 61.490 66.667 0.00 0.00 0.00 6.53
2448 2848 3.093835 CGGCCCACCCCCTGAATA 61.094 66.667 0.00 0.00 0.00 1.75
2449 2849 2.460853 CGGCCCACCCCCTGAATAT 61.461 63.158 0.00 0.00 0.00 1.28
2450 2850 1.460699 GGCCCACCCCCTGAATATC 59.539 63.158 0.00 0.00 0.00 1.63
2451 2851 1.360393 GGCCCACCCCCTGAATATCA 61.360 60.000 0.00 0.00 0.00 2.15
2452 2852 0.111253 GCCCACCCCCTGAATATCAG 59.889 60.000 0.32 0.32 43.91 2.90
2477 2877 1.618343 GGGGGACAAGTTTGTGATTGG 59.382 52.381 1.62 0.00 42.43 3.16
2478 2878 2.316108 GGGGACAAGTTTGTGATTGGT 58.684 47.619 1.62 0.00 42.43 3.67
2479 2879 2.698274 GGGGACAAGTTTGTGATTGGTT 59.302 45.455 1.62 0.00 42.43 3.67
2480 2880 3.892588 GGGGACAAGTTTGTGATTGGTTA 59.107 43.478 1.62 0.00 42.43 2.85
2481 2881 4.022329 GGGGACAAGTTTGTGATTGGTTAG 60.022 45.833 1.62 0.00 42.43 2.34
2482 2882 4.583073 GGGACAAGTTTGTGATTGGTTAGT 59.417 41.667 1.62 0.00 42.43 2.24
2483 2883 5.766174 GGGACAAGTTTGTGATTGGTTAGTA 59.234 40.000 1.62 0.00 42.43 1.82
2484 2884 6.072673 GGGACAAGTTTGTGATTGGTTAGTAG 60.073 42.308 1.62 0.00 42.43 2.57
2485 2885 6.708949 GGACAAGTTTGTGATTGGTTAGTAGA 59.291 38.462 1.62 0.00 42.43 2.59
2486 2886 7.390718 GGACAAGTTTGTGATTGGTTAGTAGAT 59.609 37.037 1.62 0.00 42.43 1.98
2487 2887 8.099364 ACAAGTTTGTGATTGGTTAGTAGATG 57.901 34.615 0.00 0.00 40.49 2.90
2488 2888 7.936847 ACAAGTTTGTGATTGGTTAGTAGATGA 59.063 33.333 0.00 0.00 40.49 2.92
2489 2889 8.783093 CAAGTTTGTGATTGGTTAGTAGATGAA 58.217 33.333 0.00 0.00 0.00 2.57
2490 2890 8.918202 AGTTTGTGATTGGTTAGTAGATGAAA 57.082 30.769 0.00 0.00 0.00 2.69
2491 2891 9.349713 AGTTTGTGATTGGTTAGTAGATGAAAA 57.650 29.630 0.00 0.00 0.00 2.29
2492 2892 9.959749 GTTTGTGATTGGTTAGTAGATGAAAAA 57.040 29.630 0.00 0.00 0.00 1.94
2512 2912 5.897377 AAAAATTCTAGCCAGCGTGTAAT 57.103 34.783 0.00 0.00 0.00 1.89
2513 2913 5.897377 AAAATTCTAGCCAGCGTGTAATT 57.103 34.783 0.00 0.00 0.00 1.40
2514 2914 4.882671 AATTCTAGCCAGCGTGTAATTG 57.117 40.909 0.00 0.00 0.00 2.32
2515 2915 1.651987 TCTAGCCAGCGTGTAATTGC 58.348 50.000 0.00 0.00 0.00 3.56
2516 2916 1.066502 TCTAGCCAGCGTGTAATTGCA 60.067 47.619 0.00 0.00 0.00 4.08
2517 2917 1.942657 CTAGCCAGCGTGTAATTGCAT 59.057 47.619 0.00 0.00 0.00 3.96
2518 2918 0.452987 AGCCAGCGTGTAATTGCATG 59.547 50.000 11.04 11.04 0.00 4.06
2525 2925 3.476295 CGTGTAATTGCATGCAACTCT 57.524 42.857 34.10 22.71 38.88 3.24
2526 2926 3.825308 CGTGTAATTGCATGCAACTCTT 58.175 40.909 34.10 25.46 38.88 2.85
2527 2927 4.229096 CGTGTAATTGCATGCAACTCTTT 58.771 39.130 34.10 25.12 38.88 2.52
2528 2928 4.088923 CGTGTAATTGCATGCAACTCTTTG 59.911 41.667 34.10 18.93 38.88 2.77
2529 2929 4.984161 GTGTAATTGCATGCAACTCTTTGT 59.016 37.500 34.10 14.77 38.88 2.83
2530 2930 6.148948 GTGTAATTGCATGCAACTCTTTGTA 58.851 36.000 34.10 14.78 38.88 2.41
2531 2931 6.808212 GTGTAATTGCATGCAACTCTTTGTAT 59.192 34.615 34.10 13.24 38.47 2.29
2595 2995 0.250513 CACTGTTAGGTCAGGGGAGC 59.749 60.000 0.00 0.00 41.86 4.70
2622 3096 8.557864 ACAAATTTTCAAATGCGATTGAATCAA 58.442 25.926 14.99 0.00 45.77 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 63 6.790232 TCCATCATGTGTAGTAGATGTTGA 57.210 37.500 0.00 0.00 36.91 3.18
214 228 9.956797 GTTTTGTTTTATGATGCATGTTGATAC 57.043 29.630 2.46 0.00 0.00 2.24
449 480 1.071436 GCTTCCGATTCGACGCATTAC 60.071 52.381 7.83 0.00 0.00 1.89
525 557 1.737793 GTTTTTGCGGATCGAGATGGT 59.262 47.619 0.00 0.00 0.00 3.55
562 608 2.359143 CCCTCTCTCATCTCCTCCACTT 60.359 54.545 0.00 0.00 0.00 3.16
598 647 3.131396 GTCGGCAGTTTCTTCTTTCTCA 58.869 45.455 0.00 0.00 0.00 3.27
628 681 4.888325 CATCTCCCCGCCCCTCCT 62.888 72.222 0.00 0.00 0.00 3.69
636 689 2.294078 GCCCCTATCCATCTCCCCG 61.294 68.421 0.00 0.00 0.00 5.73
676 731 2.203728 TGGTGGTAGGGTGCGAGT 60.204 61.111 0.00 0.00 0.00 4.18
709 764 2.755655 CCTGACGACAGACTATCAACCT 59.244 50.000 16.58 0.00 46.03 3.50
716 772 0.323178 GGGTCCCTGACGACAGACTA 60.323 60.000 16.58 0.00 46.03 2.59
719 775 2.851801 AGGGTCCCTGACGACAGA 59.148 61.111 10.61 0.00 46.03 3.41
745 801 8.140628 TCAATTCAGAATTTGATTTCGGTTGAA 58.859 29.630 5.58 0.00 35.27 2.69
746 802 7.656412 TCAATTCAGAATTTGATTTCGGTTGA 58.344 30.769 5.58 0.00 35.27 3.18
747 803 7.872163 TCAATTCAGAATTTGATTTCGGTTG 57.128 32.000 5.58 0.00 35.27 3.77
777 833 7.758980 GGCAAAATTTCATGTTTTGACCTTTTT 59.241 29.630 18.93 2.23 44.81 1.94
778 834 7.257003 GGCAAAATTTCATGTTTTGACCTTTT 58.743 30.769 18.93 3.30 44.81 2.27
779 835 6.794374 GGCAAAATTTCATGTTTTGACCTTT 58.206 32.000 18.93 0.00 44.81 3.11
780 836 6.375945 GGCAAAATTTCATGTTTTGACCTT 57.624 33.333 18.93 0.00 44.81 3.50
784 840 4.785301 TGGGGCAAAATTTCATGTTTTGA 58.215 34.783 18.93 1.38 45.02 2.69
785 841 5.708877 ATGGGGCAAAATTTCATGTTTTG 57.291 34.783 13.09 13.09 45.01 2.44
786 842 6.777782 TCTATGGGGCAAAATTTCATGTTTT 58.222 32.000 0.00 0.00 0.00 2.43
787 843 6.371595 TCTATGGGGCAAAATTTCATGTTT 57.628 33.333 0.00 0.00 0.00 2.83
788 844 5.104817 CCTCTATGGGGCAAAATTTCATGTT 60.105 40.000 0.00 0.00 0.00 2.71
789 845 4.406649 CCTCTATGGGGCAAAATTTCATGT 59.593 41.667 0.00 0.00 0.00 3.21
790 846 4.952460 CCTCTATGGGGCAAAATTTCATG 58.048 43.478 0.00 0.00 0.00 3.07
804 860 2.210711 GGAGACCGCCCCTCTATGG 61.211 68.421 0.00 0.00 0.00 2.74
805 861 2.565645 CGGAGACCGCCCCTCTATG 61.566 68.421 0.00 0.00 41.17 2.23
806 862 2.203509 CGGAGACCGCCCCTCTAT 60.204 66.667 0.00 0.00 41.17 1.98
836 892 0.175760 CGGATGGAATGACGACCTGT 59.824 55.000 0.00 0.00 0.00 4.00
837 893 0.459899 TCGGATGGAATGACGACCTG 59.540 55.000 0.00 0.00 28.99 4.00
850 906 3.917760 GGGCCTCTCGGTCGGATG 61.918 72.222 0.84 0.00 35.04 3.51
897 960 6.128391 TGTTGGATAGAACAAGAATTACGTGC 60.128 38.462 0.00 0.00 32.84 5.34
1812 2192 5.521372 AGATTTCAGTTTCTTTGCAAGTTGC 59.479 36.000 21.17 21.17 45.29 4.17
1853 2233 4.755123 ACAGTAACAAATCGACCCAGAAAG 59.245 41.667 0.00 0.00 0.00 2.62
1924 2304 6.869206 TTCCTACTAGGTAAGCACAAGAAT 57.131 37.500 1.83 0.00 36.53 2.40
1959 2339 9.869757 TTCGAAAATTCTCATATCTTGTCTGTA 57.130 29.630 0.00 0.00 0.00 2.74
1960 2340 8.777865 TTCGAAAATTCTCATATCTTGTCTGT 57.222 30.769 0.00 0.00 0.00 3.41
1961 2341 8.877779 ACTTCGAAAATTCTCATATCTTGTCTG 58.122 33.333 0.00 0.00 0.00 3.51
1987 2368 8.017418 TGCTTTTTCCCTTTCATCTTCTTTTA 57.983 30.769 0.00 0.00 0.00 1.52
2006 2399 4.036852 GCTGAAAACCTACTCACTGCTTTT 59.963 41.667 0.00 0.00 0.00 2.27
2032 2425 5.166398 CAAAAGTGATCCAGAAAAGATGGC 58.834 41.667 0.00 0.00 37.76 4.40
2067 2460 8.890124 AGTTAGGAAGAGAAGAACTAAAACAC 57.110 34.615 0.00 0.00 0.00 3.32
2169 2562 3.763360 CCATCATTTTCTAACCCTGCACA 59.237 43.478 0.00 0.00 0.00 4.57
2195 2588 7.520614 GCTTCTAGTACTGTCTTGTGCAAATTT 60.521 37.037 5.39 0.00 0.00 1.82
2196 2589 6.073003 GCTTCTAGTACTGTCTTGTGCAAATT 60.073 38.462 5.39 0.00 0.00 1.82
2271 2671 1.683385 GCAAGAGCAAGGTTCCAAACT 59.317 47.619 0.00 0.00 41.58 2.66
2287 2687 6.595716 AGAATGCTAAGTTACTAACCAGCAAG 59.404 38.462 21.14 5.24 46.47 4.01
2290 2690 6.986904 AAGAATGCTAAGTTACTAACCAGC 57.013 37.500 12.97 12.97 39.27 4.85
2291 2691 8.997621 TGTAAGAATGCTAAGTTACTAACCAG 57.002 34.615 0.00 0.00 0.00 4.00
2306 2706 9.559958 GCACATTATATGGTTATGTAAGAATGC 57.440 33.333 0.00 0.00 31.64 3.56
2351 2751 8.865978 CGTTTGTACATGTAGCATTACTCTAAA 58.134 33.333 5.62 0.00 0.00 1.85
2352 2752 8.245491 TCGTTTGTACATGTAGCATTACTCTAA 58.755 33.333 5.62 0.00 0.00 2.10
2353 2753 7.764331 TCGTTTGTACATGTAGCATTACTCTA 58.236 34.615 5.62 0.00 0.00 2.43
2354 2754 6.627243 TCGTTTGTACATGTAGCATTACTCT 58.373 36.000 5.62 0.00 0.00 3.24
2355 2755 6.530534 ACTCGTTTGTACATGTAGCATTACTC 59.469 38.462 5.62 0.00 0.00 2.59
2356 2756 6.395629 ACTCGTTTGTACATGTAGCATTACT 58.604 36.000 5.62 0.00 0.00 2.24
2357 2757 6.642683 ACTCGTTTGTACATGTAGCATTAC 57.357 37.500 5.62 8.00 0.00 1.89
2358 2758 7.813627 TGTAACTCGTTTGTACATGTAGCATTA 59.186 33.333 5.62 0.69 0.00 1.90
2359 2759 6.647481 TGTAACTCGTTTGTACATGTAGCATT 59.353 34.615 5.62 1.51 0.00 3.56
2360 2760 6.160684 TGTAACTCGTTTGTACATGTAGCAT 58.839 36.000 5.62 0.00 0.00 3.79
2361 2761 5.530712 TGTAACTCGTTTGTACATGTAGCA 58.469 37.500 5.62 5.01 0.00 3.49
2362 2762 6.456447 TTGTAACTCGTTTGTACATGTAGC 57.544 37.500 5.62 2.31 0.00 3.58
2363 2763 6.365247 AGCTTGTAACTCGTTTGTACATGTAG 59.635 38.462 5.62 0.00 0.00 2.74
2364 2764 6.218019 AGCTTGTAACTCGTTTGTACATGTA 58.782 36.000 0.08 0.08 0.00 2.29
2365 2765 5.054477 AGCTTGTAACTCGTTTGTACATGT 58.946 37.500 2.69 2.69 0.00 3.21
2366 2766 5.591643 AGCTTGTAACTCGTTTGTACATG 57.408 39.130 0.00 0.00 0.00 3.21
2367 2767 6.613755 AAAGCTTGTAACTCGTTTGTACAT 57.386 33.333 0.00 0.00 0.00 2.29
2368 2768 6.425577 AAAAGCTTGTAACTCGTTTGTACA 57.574 33.333 0.00 0.00 0.00 2.90
2369 2769 7.401080 TGTAAAAGCTTGTAACTCGTTTGTAC 58.599 34.615 0.00 0.00 0.00 2.90
2370 2770 7.536895 TGTAAAAGCTTGTAACTCGTTTGTA 57.463 32.000 0.00 0.00 0.00 2.41
2371 2771 6.425577 TGTAAAAGCTTGTAACTCGTTTGT 57.574 33.333 0.00 0.00 0.00 2.83
2372 2772 7.728580 TTTGTAAAAGCTTGTAACTCGTTTG 57.271 32.000 0.00 0.00 0.00 2.93
2373 2773 8.745464 TTTTTGTAAAAGCTTGTAACTCGTTT 57.255 26.923 0.00 0.00 0.00 3.60
2374 2774 8.803799 CATTTTTGTAAAAGCTTGTAACTCGTT 58.196 29.630 0.00 0.00 0.00 3.85
2375 2775 7.434013 CCATTTTTGTAAAAGCTTGTAACTCGT 59.566 33.333 0.00 0.00 0.00 4.18
2376 2776 7.434013 ACCATTTTTGTAAAAGCTTGTAACTCG 59.566 33.333 0.00 0.00 0.00 4.18
2377 2777 8.642908 ACCATTTTTGTAAAAGCTTGTAACTC 57.357 30.769 0.00 0.00 0.00 3.01
2392 2792 8.970859 TGACCAATCAAATTAACCATTTTTGT 57.029 26.923 0.00 0.00 32.24 2.83
2408 2808 2.509548 CTCCCCACCTATTGACCAATCA 59.490 50.000 0.00 0.00 32.50 2.57
2409 2809 2.158608 CCTCCCCACCTATTGACCAATC 60.159 54.545 0.00 0.00 32.50 2.67
2410 2810 1.852965 CCTCCCCACCTATTGACCAAT 59.147 52.381 0.64 0.64 34.93 3.16
2411 2811 1.295020 CCTCCCCACCTATTGACCAA 58.705 55.000 0.00 0.00 0.00 3.67
2412 2812 1.279025 GCCTCCCCACCTATTGACCA 61.279 60.000 0.00 0.00 0.00 4.02
2413 2813 1.532238 GCCTCCCCACCTATTGACC 59.468 63.158 0.00 0.00 0.00 4.02
2414 2814 1.146263 CGCCTCCCCACCTATTGAC 59.854 63.158 0.00 0.00 0.00 3.18
2415 2815 2.070039 CCGCCTCCCCACCTATTGA 61.070 63.158 0.00 0.00 0.00 2.57
2416 2816 2.510906 CCGCCTCCCCACCTATTG 59.489 66.667 0.00 0.00 0.00 1.90
2417 2817 3.489513 GCCGCCTCCCCACCTATT 61.490 66.667 0.00 0.00 0.00 1.73
2431 2831 2.411765 GATATTCAGGGGGTGGGCCG 62.412 65.000 0.00 0.00 34.97 6.13
2432 2832 1.360393 TGATATTCAGGGGGTGGGCC 61.360 60.000 0.00 0.00 0.00 5.80
2433 2833 0.111253 CTGATATTCAGGGGGTGGGC 59.889 60.000 0.00 0.00 40.71 5.36
2457 2857 1.618343 CCAATCACAAACTTGTCCCCC 59.382 52.381 0.00 0.00 39.91 5.40
2458 2858 2.316108 ACCAATCACAAACTTGTCCCC 58.684 47.619 0.00 0.00 39.91 4.81
2459 2859 4.583073 ACTAACCAATCACAAACTTGTCCC 59.417 41.667 0.00 0.00 39.91 4.46
2460 2860 5.767816 ACTAACCAATCACAAACTTGTCC 57.232 39.130 0.00 0.00 39.91 4.02
2461 2861 7.724305 TCTACTAACCAATCACAAACTTGTC 57.276 36.000 0.00 0.00 39.91 3.18
2462 2862 7.936847 TCATCTACTAACCAATCACAAACTTGT 59.063 33.333 0.00 0.00 43.36 3.16
2463 2863 8.322906 TCATCTACTAACCAATCACAAACTTG 57.677 34.615 0.00 0.00 0.00 3.16
2464 2864 8.918202 TTCATCTACTAACCAATCACAAACTT 57.082 30.769 0.00 0.00 0.00 2.66
2465 2865 8.918202 TTTCATCTACTAACCAATCACAAACT 57.082 30.769 0.00 0.00 0.00 2.66
2466 2866 9.959749 TTTTTCATCTACTAACCAATCACAAAC 57.040 29.630 0.00 0.00 0.00 2.93
2490 2890 5.897377 ATTACACGCTGGCTAGAATTTTT 57.103 34.783 0.00 0.00 0.00 1.94
2491 2891 5.640732 CAATTACACGCTGGCTAGAATTTT 58.359 37.500 0.00 0.00 0.00 1.82
2492 2892 4.438744 GCAATTACACGCTGGCTAGAATTT 60.439 41.667 0.00 0.00 0.00 1.82
2493 2893 3.065371 GCAATTACACGCTGGCTAGAATT 59.935 43.478 0.00 0.00 0.00 2.17
2494 2894 2.614057 GCAATTACACGCTGGCTAGAAT 59.386 45.455 0.00 0.00 0.00 2.40
2495 2895 2.006888 GCAATTACACGCTGGCTAGAA 58.993 47.619 0.00 0.00 0.00 2.10
2496 2896 1.066502 TGCAATTACACGCTGGCTAGA 60.067 47.619 0.00 0.00 0.00 2.43
2497 2897 1.368641 TGCAATTACACGCTGGCTAG 58.631 50.000 0.00 0.00 0.00 3.42
2498 2898 1.670295 CATGCAATTACACGCTGGCTA 59.330 47.619 0.00 0.00 0.00 3.93
2499 2899 0.452987 CATGCAATTACACGCTGGCT 59.547 50.000 0.00 0.00 0.00 4.75
2500 2900 1.141591 GCATGCAATTACACGCTGGC 61.142 55.000 14.21 0.00 0.00 4.85
2501 2901 0.170784 TGCATGCAATTACACGCTGG 59.829 50.000 20.30 0.00 28.24 4.85
2502 2902 1.650153 GTTGCATGCAATTACACGCTG 59.350 47.619 33.94 0.00 38.28 5.18
2503 2903 1.541147 AGTTGCATGCAATTACACGCT 59.459 42.857 33.94 21.54 38.28 5.07
2504 2904 1.913403 GAGTTGCATGCAATTACACGC 59.087 47.619 33.94 20.13 38.28 5.34
2505 2905 3.476295 AGAGTTGCATGCAATTACACG 57.524 42.857 33.94 0.00 38.28 4.49
2506 2906 4.984161 ACAAAGAGTTGCATGCAATTACAC 59.016 37.500 33.94 22.13 38.39 2.90
2507 2907 5.199024 ACAAAGAGTTGCATGCAATTACA 57.801 34.783 33.94 10.90 38.39 2.41
2508 2908 6.808212 ACATACAAAGAGTTGCATGCAATTAC 59.192 34.615 33.94 25.39 40.75 1.89
2509 2909 6.923012 ACATACAAAGAGTTGCATGCAATTA 58.077 32.000 33.94 15.39 40.75 1.40
2510 2910 5.786311 ACATACAAAGAGTTGCATGCAATT 58.214 33.333 33.94 30.13 40.75 2.32
2511 2911 5.395682 ACATACAAAGAGTTGCATGCAAT 57.604 34.783 33.94 22.54 40.75 3.56
2512 2912 4.852134 ACATACAAAGAGTTGCATGCAA 57.148 36.364 28.80 28.80 40.75 4.08
2513 2913 4.852134 AACATACAAAGAGTTGCATGCA 57.148 36.364 18.46 18.46 40.75 3.96
2514 2914 6.381801 ACTAAACATACAAAGAGTTGCATGC 58.618 36.000 11.82 11.82 40.75 4.06
2551 2951 9.674068 TGGTAATTAAGCACTGTACATCATAAA 57.326 29.630 0.00 0.00 0.00 1.40
2594 2994 5.677936 TCAATCGCATTTGAAAATTTGTGC 58.322 33.333 0.00 0.00 32.82 4.57
2595 2995 8.010540 TGATTCAATCGCATTTGAAAATTTGTG 58.989 29.630 13.24 0.00 45.77 3.33
2622 3096 6.625532 AAAAGATTCCCCTTATTGCACAAT 57.374 33.333 0.94 0.94 34.93 2.71


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

AutoCloner maintained by Alex Coulton.