Multiple sequence alignment - TraesCS6B01G044100

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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 TraesCS6B01G044100 chr6B 100.000 3524 0 0 1 3524 26598775 26595252 0.000000e+00 6508.0
1 TraesCS6B01G044100 chr6B 90.433 1526 146 0 1001 2526 26634792 26633267 0.000000e+00 2010.0
2 TraesCS6B01G044100 chr6B 90.170 1526 146 2 1001 2526 26645632 26644111 0.000000e+00 1984.0
3 TraesCS6B01G044100 chr6B 92.381 105 4 1 541 645 26618809 26618709 2.830000e-31 147.0
4 TraesCS6B01G044100 chr6B 76.068 234 32 14 11 239 26619383 26619169 2.240000e-17 100.0
5 TraesCS6B01G044100 chr6A 92.264 2301 131 19 496 2789 15765484 15767744 0.000000e+00 3219.0
6 TraesCS6B01G044100 chr6A 90.039 1526 152 0 1001 2526 15734520 15736045 0.000000e+00 1977.0
7 TraesCS6B01G044100 chr6A 89.695 1543 156 2 986 2526 15727828 15729369 0.000000e+00 1965.0
8 TraesCS6B01G044100 chr6A 93.000 500 17 5 1 491 15764933 15765423 0.000000e+00 713.0
9 TraesCS6B01G044100 chr6A 83.183 333 51 3 3194 3522 15768231 15768562 2.060000e-77 300.0
10 TraesCS6B01G044100 chr6A 86.397 272 33 4 2812 3081 15767724 15767993 9.570000e-76 294.0
11 TraesCS6B01G044100 chr6A 76.132 243 32 9 11 252 15755867 15756084 1.730000e-18 104.0
12 TraesCS6B01G044100 chr6A 100.000 28 0 0 2716 2743 414553827 414553854 6.000000e-03 52.8
13 TraesCS6B01G044100 chr6D 93.819 2071 120 6 495 2565 14626483 14624421 0.000000e+00 3109.0
14 TraesCS6B01G044100 chr6D 90.957 1526 138 0 1001 2526 14680775 14679250 0.000000e+00 2054.0
15 TraesCS6B01G044100 chr6D 86.954 1832 189 25 710 2527 14633254 14631459 0.000000e+00 2013.0
16 TraesCS6B01G044100 chr6D 90.098 1525 151 0 1001 2525 14656589 14655065 0.000000e+00 1980.0
17 TraesCS6B01G044100 chr6D 93.042 503 12 6 1 491 14627035 14626544 0.000000e+00 713.0
18 TraesCS6B01G044100 chr6D 84.887 311 34 4 2817 3126 14624289 14623991 5.720000e-78 302.0
19 TraesCS6B01G044100 chr6D 90.476 105 5 2 541 645 14633383 14633284 2.210000e-27 134.0
20 TraesCS6B01G044100 chr5A 90.909 55 4 1 3130 3183 449018303 449018249 4.880000e-09 73.1
21 TraesCS6B01G044100 chr3B 97.561 41 1 0 3139 3179 587989279 587989319 1.760000e-08 71.3
22 TraesCS6B01G044100 chr3D 97.500 40 1 0 3141 3180 448268587 448268626 6.310000e-08 69.4
23 TraesCS6B01G044100 chr2B 95.238 42 2 0 3141 3182 338755919 338755878 2.270000e-07 67.6
24 TraesCS6B01G044100 chr2B 91.837 49 3 1 3136 3184 541012228 541012275 2.270000e-07 67.6
25 TraesCS6B01G044100 chr1A 95.238 42 2 0 3141 3182 259202156 259202115 2.270000e-07 67.6
26 TraesCS6B01G044100 chr7B 87.931 58 4 3 3131 3186 496779880 496779824 8.170000e-07 65.8
27 TraesCS6B01G044100 chr2D 93.182 44 3 0 3141 3184 472445840 472445883 8.170000e-07 65.8


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 TraesCS6B01G044100 chr6B 26595252 26598775 3523 True 6508.000000 6508 100.000000 1 3524 1 chr6B.!!$R1 3523
1 TraesCS6B01G044100 chr6B 26633267 26634792 1525 True 2010.000000 2010 90.433000 1001 2526 1 chr6B.!!$R2 1525
2 TraesCS6B01G044100 chr6B 26644111 26645632 1521 True 1984.000000 1984 90.170000 1001 2526 1 chr6B.!!$R3 1525
3 TraesCS6B01G044100 chr6A 15734520 15736045 1525 False 1977.000000 1977 90.039000 1001 2526 1 chr6A.!!$F2 1525
4 TraesCS6B01G044100 chr6A 15727828 15729369 1541 False 1965.000000 1965 89.695000 986 2526 1 chr6A.!!$F1 1540
5 TraesCS6B01G044100 chr6A 15764933 15768562 3629 False 1131.500000 3219 88.711000 1 3522 4 chr6A.!!$F5 3521
6 TraesCS6B01G044100 chr6D 14679250 14680775 1525 True 2054.000000 2054 90.957000 1001 2526 1 chr6D.!!$R2 1525
7 TraesCS6B01G044100 chr6D 14655065 14656589 1524 True 1980.000000 1980 90.098000 1001 2525 1 chr6D.!!$R1 1524
8 TraesCS6B01G044100 chr6D 14623991 14627035 3044 True 1374.666667 3109 90.582667 1 3126 3 chr6D.!!$R3 3125
9 TraesCS6B01G044100 chr6D 14631459 14633383 1924 True 1073.500000 2013 88.715000 541 2527 2 chr6D.!!$R4 1986

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
175 176 0.096976 GTGTATGTGCGTGTGATGCC 59.903 55.0 0.0 0.0 0.00 4.40 F
2040 2152 0.172803 CTTTCTGCATCTGGCTTGGC 59.827 55.0 0.0 0.0 45.15 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2142 2254 0.036388 TGATGCCAAGGGAACGTCTC 60.036 55.0 0.0 0.0 0.00 3.36 R
2880 3000 0.037326 TTAACAGAGAGCCACTGCCG 60.037 55.0 0.0 0.0 38.74 5.69 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
76 77 2.365105 TCCCCTACTCCCCTTGCG 60.365 66.667 0.00 0.00 0.00 4.85
96 97 0.961753 TGCTGTCACTGTCGAGTCAT 59.038 50.000 0.00 0.00 0.00 3.06
175 176 0.096976 GTGTATGTGCGTGTGATGCC 59.903 55.000 0.00 0.00 0.00 4.40
176 177 1.348250 GTATGTGCGTGTGATGCCG 59.652 57.895 0.00 0.00 0.00 5.69
289 297 7.936584 TGTTCCCATTTCAGTAACAAACTAAG 58.063 34.615 0.00 0.00 35.76 2.18
410 438 4.536364 AATATTTGGACGCTTCATGACG 57.464 40.909 0.00 0.00 0.00 4.35
411 439 1.808411 ATTTGGACGCTTCATGACGT 58.192 45.000 10.77 10.77 46.91 4.34
412 440 2.442212 TTTGGACGCTTCATGACGTA 57.558 45.000 10.93 0.00 43.71 3.57
413 441 1.705256 TTGGACGCTTCATGACGTAC 58.295 50.000 12.85 12.85 43.71 3.67
471 499 4.156008 CCTTGTGCCGCTAAGTAATCTTTT 59.844 41.667 0.00 0.00 35.36 2.27
493 521 9.987901 CTTTTTACACATTTTATGTTGTTAGCG 57.012 29.630 0.00 0.00 42.70 4.26
533 620 5.416947 GGCAGTCCTAATAGTTTTCTTCGA 58.583 41.667 0.00 0.00 0.00 3.71
534 621 5.291371 GGCAGTCCTAATAGTTTTCTTCGAC 59.709 44.000 0.00 0.00 0.00 4.20
535 622 5.291371 GCAGTCCTAATAGTTTTCTTCGACC 59.709 44.000 0.00 0.00 0.00 4.79
536 623 5.515626 CAGTCCTAATAGTTTTCTTCGACCG 59.484 44.000 0.00 0.00 0.00 4.79
602 689 5.075493 GCATATTCTGATCCTTGGTCCATT 58.925 41.667 0.00 0.00 0.00 3.16
706 793 3.435671 GCTGTACGTGCCTTGTTTAATCT 59.564 43.478 0.00 0.00 0.00 2.40
936 1045 0.323178 ACATTCCAGGCCAAGCTCAG 60.323 55.000 5.01 0.00 0.00 3.35
1152 1264 2.493675 CTCGTGGATCTCCTTCTTCACA 59.506 50.000 0.00 0.00 36.82 3.58
1176 1288 2.343758 GTCTCCACCTTCGCTGCA 59.656 61.111 0.00 0.00 0.00 4.41
1383 1495 2.320587 GGCCGTCATCGATGATGCC 61.321 63.158 35.85 35.85 44.55 4.40
1404 1516 4.580551 GGGTACATCGCCGTCCGG 62.581 72.222 0.24 0.24 37.59 5.14
1446 1558 0.888736 CCACCTTCGTGTCATGCCAA 60.889 55.000 0.00 0.00 38.41 4.52
2004 2116 3.879321 GCCTTTGGAACATCTGGATCCTT 60.879 47.826 14.23 0.00 39.30 3.36
2019 2131 1.528309 CCTTCAAACCGCTGGTGGT 60.528 57.895 0.00 0.00 46.67 4.16
2040 2152 0.172803 CTTTCTGCATCTGGCTTGGC 59.827 55.000 0.00 0.00 45.15 4.52
2070 2182 2.664081 CCTCCCTGCCTCAGTGACC 61.664 68.421 0.00 0.00 0.00 4.02
2133 2245 2.665185 GTCTTTGGCGTCGCACCT 60.665 61.111 20.50 0.00 0.00 4.00
2139 2251 3.774702 GGCGTCGCACCTTTCGTC 61.775 66.667 20.50 0.00 0.00 4.20
2142 2254 2.426183 CGTCGCACCTTTCGTCTCG 61.426 63.158 0.00 0.00 0.00 4.04
2163 2275 1.004745 AGACGTTCCCTTGGCATCATT 59.995 47.619 0.00 0.00 0.00 2.57
2170 2282 1.620524 CCCTTGGCATCATTTCTGGGT 60.621 52.381 0.00 0.00 0.00 4.51
2184 2296 3.948719 GGGTTGACCGGTGCTGGA 61.949 66.667 14.63 0.00 36.71 3.86
2253 2365 1.926426 AATACTCCACTGGCAGGGGC 61.926 60.000 31.35 0.00 39.16 5.80
2489 2601 0.392998 GTCATCCTTGCCACATCCGT 60.393 55.000 0.00 0.00 0.00 4.69
2534 2646 1.732259 GCACGTGTAAGACTGGATTGG 59.268 52.381 18.38 0.00 0.00 3.16
2539 2651 4.885325 ACGTGTAAGACTGGATTGGTTTTT 59.115 37.500 0.00 0.00 0.00 1.94
2540 2652 5.008316 ACGTGTAAGACTGGATTGGTTTTTC 59.992 40.000 0.00 0.00 0.00 2.29
2541 2653 5.008217 CGTGTAAGACTGGATTGGTTTTTCA 59.992 40.000 0.00 0.00 0.00 2.69
2542 2654 6.293955 CGTGTAAGACTGGATTGGTTTTTCAT 60.294 38.462 0.00 0.00 0.00 2.57
2543 2655 7.094975 CGTGTAAGACTGGATTGGTTTTTCATA 60.095 37.037 0.00 0.00 0.00 2.15
2544 2656 8.739972 GTGTAAGACTGGATTGGTTTTTCATAT 58.260 33.333 0.00 0.00 0.00 1.78
2545 2657 9.967451 TGTAAGACTGGATTGGTTTTTCATATA 57.033 29.630 0.00 0.00 0.00 0.86
2572 2684 8.737175 CCTATGTACAAGTACTGAAACTACAGA 58.263 37.037 0.00 0.00 40.63 3.41
2574 2686 7.812690 TGTACAAGTACTGAAACTACAGAGA 57.187 36.000 11.27 0.00 40.63 3.10
2576 2688 8.133627 TGTACAAGTACTGAAACTACAGAGAAC 58.866 37.037 11.27 0.00 40.63 3.01
2580 2692 4.258702 ACTGAAACTACAGAGAACGCAT 57.741 40.909 0.00 0.00 40.63 4.73
2586 2698 9.847706 CTGAAACTACAGAGAACGCATATATAT 57.152 33.333 0.00 0.00 39.94 0.86
2591 2703 9.227777 ACTACAGAGAACGCATATATATACACA 57.772 33.333 0.00 0.00 0.00 3.72
2592 2704 9.491934 CTACAGAGAACGCATATATATACACAC 57.508 37.037 0.00 0.00 0.00 3.82
2593 2705 7.882179 ACAGAGAACGCATATATATACACACA 58.118 34.615 0.00 0.00 0.00 3.72
2594 2706 8.523658 ACAGAGAACGCATATATATACACACAT 58.476 33.333 0.00 0.00 0.00 3.21
2595 2707 9.014533 CAGAGAACGCATATATATACACACATC 57.985 37.037 0.00 0.00 0.00 3.06
2596 2708 7.910683 AGAGAACGCATATATATACACACATCG 59.089 37.037 0.00 0.00 0.00 3.84
2617 2729 5.761003 TCGTATACGAATATCGCCTTTTCA 58.239 37.500 24.97 0.00 46.30 2.69
2618 2730 6.384224 TCGTATACGAATATCGCCTTTTCAT 58.616 36.000 24.97 0.00 46.30 2.57
2619 2731 7.529158 TCGTATACGAATATCGCCTTTTCATA 58.471 34.615 24.97 0.00 46.30 2.15
2620 2732 8.186163 TCGTATACGAATATCGCCTTTTCATAT 58.814 33.333 24.97 0.00 46.30 1.78
2621 2733 9.442033 CGTATACGAATATCGCCTTTTCATATA 57.558 33.333 20.58 0.00 45.12 0.86
2625 2737 8.336498 ACGAATATCGCCTTTTCATATATACG 57.664 34.615 0.00 0.00 45.12 3.06
2626 2738 7.972277 ACGAATATCGCCTTTTCATATATACGT 59.028 33.333 0.00 0.00 45.12 3.57
2627 2739 9.442033 CGAATATCGCCTTTTCATATATACGTA 57.558 33.333 0.00 0.00 31.14 3.57
2680 2792 9.939802 AAGGTGTACGAATTTAGATTTCTAGTT 57.060 29.630 0.00 0.00 0.00 2.24
2786 2904 9.921637 TTTACAACAACTTTGAGATTTTGTTCT 57.078 25.926 0.00 0.00 39.56 3.01
2787 2905 9.921637 TTACAACAACTTTGAGATTTTGTTCTT 57.078 25.926 0.00 0.00 39.56 2.52
2788 2906 8.243289 ACAACAACTTTGAGATTTTGTTCTTG 57.757 30.769 0.00 0.00 39.56 3.02
2789 2907 6.892310 ACAACTTTGAGATTTTGTTCTTGC 57.108 33.333 0.00 0.00 0.00 4.01
2790 2908 6.397272 ACAACTTTGAGATTTTGTTCTTGCA 58.603 32.000 0.00 0.00 0.00 4.08
2791 2909 6.873076 ACAACTTTGAGATTTTGTTCTTGCAA 59.127 30.769 0.00 0.00 0.00 4.08
2792 2910 7.387397 ACAACTTTGAGATTTTGTTCTTGCAAA 59.613 29.630 0.00 0.00 36.67 3.68
2794 2912 7.742151 ACTTTGAGATTTTGTTCTTGCAAAAC 58.258 30.769 0.00 8.83 46.74 2.43
2795 2913 7.387397 ACTTTGAGATTTTGTTCTTGCAAAACA 59.613 29.630 17.55 17.55 46.74 2.83
2796 2914 7.664082 TTGAGATTTTGTTCTTGCAAAACAA 57.336 28.000 23.79 23.79 46.74 2.83
2805 2923 7.905031 TGTTCTTGCAAAACAAAAACAAAAG 57.095 28.000 18.56 0.00 44.27 2.27
2806 2924 7.475840 TGTTCTTGCAAAACAAAAACAAAAGT 58.524 26.923 18.56 0.00 44.27 2.66
2807 2925 7.430502 TGTTCTTGCAAAACAAAAACAAAAGTG 59.569 29.630 18.56 0.00 44.27 3.16
2808 2926 7.251704 TCTTGCAAAACAAAAACAAAAGTGA 57.748 28.000 0.00 0.00 37.96 3.41
2809 2927 7.869800 TCTTGCAAAACAAAAACAAAAGTGAT 58.130 26.923 0.00 0.00 37.96 3.06
2810 2928 8.348507 TCTTGCAAAACAAAAACAAAAGTGATT 58.651 25.926 0.00 0.00 37.96 2.57
2811 2929 9.604626 CTTGCAAAACAAAAACAAAAGTGATTA 57.395 25.926 0.00 0.00 37.96 1.75
2812 2930 8.941127 TGCAAAACAAAAACAAAAGTGATTAC 57.059 26.923 0.00 0.00 0.00 1.89
2813 2931 8.778358 TGCAAAACAAAAACAAAAGTGATTACT 58.222 25.926 0.00 0.00 39.32 2.24
2817 2935 8.973835 AACAAAAACAAAAGTGATTACTTCGA 57.026 26.923 3.00 0.00 46.14 3.71
2818 2936 8.614994 ACAAAAACAAAAGTGATTACTTCGAG 57.385 30.769 3.00 0.00 46.14 4.04
2819 2937 8.455682 ACAAAAACAAAAGTGATTACTTCGAGA 58.544 29.630 3.00 0.00 46.14 4.04
2820 2938 9.450807 CAAAAACAAAAGTGATTACTTCGAGAT 57.549 29.630 3.00 0.00 46.14 2.75
2822 2940 9.665264 AAAACAAAAGTGATTACTTCGAGATTC 57.335 29.630 3.00 0.00 46.14 2.52
2828 2946 7.392494 AGTGATTACTTCGAGATTCTGTGTA 57.608 36.000 0.00 0.00 31.66 2.90
2833 2951 9.731819 GATTACTTCGAGATTCTGTGTATTGTA 57.268 33.333 0.00 0.00 0.00 2.41
2841 2959 7.255486 CGAGATTCTGTGTATTGTATACCTCCA 60.255 40.741 0.00 0.00 0.00 3.86
2894 3014 0.886490 CAAAACGGCAGTGGCTCTCT 60.886 55.000 15.48 0.00 40.87 3.10
2908 3028 4.093556 GTGGCTCTCTGTTAATTTTCTCCG 59.906 45.833 0.00 0.00 0.00 4.63
2912 3032 5.291371 GCTCTCTGTTAATTTTCTCCGTACC 59.709 44.000 0.00 0.00 0.00 3.34
2915 3035 6.014840 TCTCTGTTAATTTTCTCCGTACCTGT 60.015 38.462 0.00 0.00 0.00 4.00
2928 3048 7.043565 TCTCCGTACCTGTGTTATTAATTTCC 58.956 38.462 0.00 0.00 0.00 3.13
2973 3093 4.999311 ACCCAAATCGTGAACCTAAGTTAC 59.001 41.667 0.00 0.00 35.94 2.50
3020 3140 8.970691 ATACTTCATTCAAATTTGAGGTTTCG 57.029 30.769 19.64 11.08 38.61 3.46
3029 3149 6.536582 TCAAATTTGAGGTTTCGCATTTCAAA 59.463 30.769 16.91 1.09 40.68 2.69
3030 3150 6.917217 AATTTGAGGTTTCGCATTTCAAAA 57.083 29.167 2.57 0.00 40.07 2.44
3031 3151 6.917217 ATTTGAGGTTTCGCATTTCAAAAA 57.083 29.167 2.57 0.00 40.07 1.94
3032 3152 5.964887 TTGAGGTTTCGCATTTCAAAAAG 57.035 34.783 0.00 0.00 0.00 2.27
3033 3153 4.367450 TGAGGTTTCGCATTTCAAAAAGG 58.633 39.130 0.00 0.00 0.00 3.11
3034 3154 4.142049 TGAGGTTTCGCATTTCAAAAAGGT 60.142 37.500 0.00 0.00 0.00 3.50
3035 3155 5.067936 TGAGGTTTCGCATTTCAAAAAGGTA 59.932 36.000 0.00 0.00 0.00 3.08
3036 3156 5.908341 AGGTTTCGCATTTCAAAAAGGTAA 58.092 33.333 0.00 0.00 0.00 2.85
3037 3157 6.342111 AGGTTTCGCATTTCAAAAAGGTAAA 58.658 32.000 0.00 0.00 0.00 2.01
3039 3159 7.497579 AGGTTTCGCATTTCAAAAAGGTAAATT 59.502 29.630 0.00 0.00 0.00 1.82
3040 3160 7.796660 GGTTTCGCATTTCAAAAAGGTAAATTC 59.203 33.333 0.00 0.00 0.00 2.17
3043 3163 6.361214 TCGCATTTCAAAAAGGTAAATTCGAC 59.639 34.615 0.00 0.00 34.80 4.20
3051 3171 7.916450 TCAAAAAGGTAAATTCGACGTTTCAAT 59.084 29.630 10.02 0.00 34.68 2.57
3070 3190 5.588845 TCAATCCCACCAAATAATTCCACT 58.411 37.500 0.00 0.00 0.00 4.00
3081 3201 6.295236 CCAAATAATTCCACTTCTCCTGCAAA 60.295 38.462 0.00 0.00 0.00 3.68
3084 3204 3.297134 TTCCACTTCTCCTGCAAACTT 57.703 42.857 0.00 0.00 0.00 2.66
3085 3205 3.297134 TCCACTTCTCCTGCAAACTTT 57.703 42.857 0.00 0.00 0.00 2.66
3096 3311 5.656480 TCCTGCAAACTTTTAGTTGTTTCC 58.344 37.500 0.00 0.00 38.66 3.13
3127 3342 0.035458 CACTTCCACTCTCACCCACC 59.965 60.000 0.00 0.00 0.00 4.61
3133 3350 3.050089 TCCACTCTCACCCACCTTAAAA 58.950 45.455 0.00 0.00 0.00 1.52
3156 3373 4.837093 AACATTACTCCCTCCGATTCAA 57.163 40.909 0.00 0.00 0.00 2.69
3158 3375 5.373812 ACATTACTCCCTCCGATTCAAAT 57.626 39.130 0.00 0.00 0.00 2.32
3160 3377 6.895782 ACATTACTCCCTCCGATTCAAATTA 58.104 36.000 0.00 0.00 0.00 1.40
3161 3378 7.343357 ACATTACTCCCTCCGATTCAAATTAA 58.657 34.615 0.00 0.00 0.00 1.40
3162 3379 7.998964 ACATTACTCCCTCCGATTCAAATTAAT 59.001 33.333 0.00 0.00 0.00 1.40
3163 3380 8.850156 CATTACTCCCTCCGATTCAAATTAATT 58.150 33.333 0.00 0.00 0.00 1.40
3179 3396 9.787532 TCAAATTAATTGATGCAGCTTTAGTAC 57.212 29.630 2.53 0.00 43.08 2.73
3182 3399 9.573133 AATTAATTGATGCAGCTTTAGTACAAC 57.427 29.630 2.53 0.00 0.00 3.32
3183 3400 6.824305 AATTGATGCAGCTTTAGTACAACT 57.176 33.333 2.53 0.00 0.00 3.16
3184 3401 7.921786 AATTGATGCAGCTTTAGTACAACTA 57.078 32.000 2.53 0.00 0.00 2.24
3186 3403 7.921786 TTGATGCAGCTTTAGTACAACTAAT 57.078 32.000 2.53 0.00 40.08 1.73
3188 3405 7.974675 TGATGCAGCTTTAGTACAACTAATTC 58.025 34.615 2.53 0.00 40.08 2.17
3190 3407 7.364522 TGCAGCTTTAGTACAACTAATTCTG 57.635 36.000 16.39 16.39 40.08 3.02
3191 3408 6.934645 TGCAGCTTTAGTACAACTAATTCTGT 59.065 34.615 19.05 1.35 40.08 3.41
3212 3457 8.299262 TCTGTAAGTATTATACCGACGACTAC 57.701 38.462 0.00 0.00 30.46 2.73
3225 3470 6.731164 ACCGACGACTACAAATTTCAAATTT 58.269 32.000 1.98 1.98 0.00 1.82
3226 3471 6.854381 ACCGACGACTACAAATTTCAAATTTC 59.146 34.615 5.04 0.00 0.00 2.17
3234 3479 9.476202 ACTACAAATTTCAAATTTCCAACTAGC 57.524 29.630 5.04 0.00 0.00 3.42
3290 3538 4.712476 AGAAGTCATGATGGAAGTATGGC 58.288 43.478 0.00 0.00 0.00 4.40
3291 3539 3.117491 AGTCATGATGGAAGTATGGCG 57.883 47.619 0.00 0.00 32.00 5.69
3299 3547 1.094785 GGAAGTATGGCGCATGTTGT 58.905 50.000 10.83 0.00 0.00 3.32
3300 3548 1.472480 GGAAGTATGGCGCATGTTGTT 59.528 47.619 10.83 0.00 0.00 2.83
3305 3553 0.895100 ATGGCGCATGTTGTTGAGGT 60.895 50.000 10.83 0.00 0.00 3.85
3313 3561 4.084952 CGCATGTTGTTGAGGTTTGAAATG 60.085 41.667 0.00 0.00 0.00 2.32
3354 3602 9.471702 AGATTCAAAACTTCAACTATGATCCAT 57.528 29.630 0.00 0.00 34.96 3.41
3360 3608 6.566079 ACTTCAACTATGATCCATCCTTCA 57.434 37.500 0.00 0.00 34.96 3.02
3369 3617 3.588842 TGATCCATCCTTCAGTGGACTTT 59.411 43.478 0.00 0.00 46.55 2.66
3386 3634 9.533253 AGTGGACTTTTAATTGAATTTCAACTG 57.467 29.630 13.80 4.30 39.45 3.16
3390 3638 8.141835 ACTTTTAATTGAATTTCAACTGCCAC 57.858 30.769 13.80 0.00 39.45 5.01
3392 3640 8.729805 TTTTAATTGAATTTCAACTGCCACTT 57.270 26.923 13.80 5.72 39.45 3.16
3396 3644 8.907222 AATTGAATTTCAACTGCCACTTTTAT 57.093 26.923 13.80 0.00 39.45 1.40
3401 3649 9.638239 GAATTTCAACTGCCACTTTTATAATGA 57.362 29.630 0.00 0.00 0.00 2.57
3450 3699 3.618351 TCAACGGTTTGGACAGGTTTTA 58.382 40.909 0.00 0.00 33.06 1.52
3452 3701 5.374921 TCAACGGTTTGGACAGGTTTTATA 58.625 37.500 0.00 0.00 33.06 0.98
3456 3705 5.934043 ACGGTTTGGACAGGTTTTATAGTAC 59.066 40.000 0.00 0.00 0.00 2.73
3458 3707 6.479006 GGTTTGGACAGGTTTTATAGTACCT 58.521 40.000 2.80 2.80 45.54 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 77 0.030773 TGACTCGACAGTGACAGCAC 59.969 55.000 0.00 0.00 45.49 4.40
96 97 3.193267 GCCTGGAAAGCATATGTCAAACA 59.807 43.478 4.29 0.00 0.00 2.83
289 297 1.966451 CCAGGCCGACAGGTTGTTC 60.966 63.158 0.00 0.00 40.50 3.18
405 433 4.647853 TGGTGCCTTCTAATAGTACGTCAT 59.352 41.667 0.00 0.00 0.00 3.06
406 434 4.018490 TGGTGCCTTCTAATAGTACGTCA 58.982 43.478 0.00 0.00 0.00 4.35
407 435 4.644103 TGGTGCCTTCTAATAGTACGTC 57.356 45.455 0.00 0.00 0.00 4.34
408 436 5.609533 ATTGGTGCCTTCTAATAGTACGT 57.390 39.130 0.00 0.00 0.00 3.57
409 437 6.046593 TGAATTGGTGCCTTCTAATAGTACG 58.953 40.000 0.00 0.00 0.00 3.67
410 438 9.726438 ATATGAATTGGTGCCTTCTAATAGTAC 57.274 33.333 0.00 0.00 0.00 2.73
411 439 9.725019 CATATGAATTGGTGCCTTCTAATAGTA 57.275 33.333 0.00 0.00 0.00 1.82
412 440 7.175641 GCATATGAATTGGTGCCTTCTAATAGT 59.824 37.037 6.97 0.00 0.00 2.12
413 441 7.175467 TGCATATGAATTGGTGCCTTCTAATAG 59.825 37.037 6.97 0.00 36.79 1.73
471 499 6.087522 GCCGCTAACAACATAAAATGTGTAA 58.912 36.000 0.00 0.00 44.07 2.41
491 519 4.520846 CGCATTTCACTCCGCCGC 62.521 66.667 0.00 0.00 0.00 6.53
492 520 4.520846 GCGCATTTCACTCCGCCG 62.521 66.667 0.30 0.00 40.51 6.46
493 521 4.520846 CGCGCATTTCACTCCGCC 62.521 66.667 8.75 0.00 43.16 6.13
533 620 4.081862 TCCAGAATCGAATTTCTACACGGT 60.082 41.667 1.07 0.00 34.21 4.83
534 621 4.267928 GTCCAGAATCGAATTTCTACACGG 59.732 45.833 1.07 0.00 34.21 4.94
535 622 4.862574 TGTCCAGAATCGAATTTCTACACG 59.137 41.667 1.07 0.00 34.21 4.49
536 623 5.220228 CGTGTCCAGAATCGAATTTCTACAC 60.220 44.000 17.37 17.37 39.55 2.90
945 1054 2.746277 GCAGCTAACGGTGGTGGG 60.746 66.667 4.67 0.00 39.02 4.61
1152 1264 0.108615 CGAAGGTGGAGACGAAGCAT 60.109 55.000 0.00 0.00 0.00 3.79
1383 1495 1.065928 GACGGCGATGTACCCTGAG 59.934 63.158 16.62 0.00 0.00 3.35
1404 1516 1.283321 AGGGAGAAGCCAATGAGGAAC 59.717 52.381 0.00 0.00 41.22 3.62
1446 1558 3.200605 TGAACATGGTGCTCATCCAGTAT 59.799 43.478 0.00 0.00 38.42 2.12
1824 1936 0.460284 ACTCGGCGATGACATTGTCC 60.460 55.000 11.27 4.30 0.00 4.02
2004 2116 2.902423 AAGCACCACCAGCGGTTTGA 62.902 55.000 9.10 0.00 37.07 2.69
2070 2182 1.144936 GGAGAAGAGGACCATGGCG 59.855 63.158 13.04 0.00 0.00 5.69
2139 2251 1.446272 GCCAAGGGAACGTCTCGAG 60.446 63.158 5.93 5.93 0.00 4.04
2142 2254 0.036388 TGATGCCAAGGGAACGTCTC 60.036 55.000 0.00 0.00 0.00 3.36
2163 2275 2.112297 GCACCGGTCAACCCAGAA 59.888 61.111 2.59 0.00 0.00 3.02
2170 2282 4.329545 GCCTCCAGCACCGGTCAA 62.330 66.667 2.59 0.00 42.97 3.18
2253 2365 0.752658 TGATGCCCATGTACTCGAGG 59.247 55.000 18.41 0.00 0.00 4.63
2489 2601 1.885560 CGTATTGTTGGGTGGTGTGA 58.114 50.000 0.00 0.00 0.00 3.58
2544 2656 9.519191 TGTAGTTTCAGTACTTGTACATAGGTA 57.481 33.333 12.64 0.00 0.00 3.08
2545 2657 8.413309 TGTAGTTTCAGTACTTGTACATAGGT 57.587 34.615 12.64 0.00 0.00 3.08
2546 2658 8.737175 TCTGTAGTTTCAGTACTTGTACATAGG 58.263 37.037 12.64 0.00 36.85 2.57
2572 2684 7.535997 ACGATGTGTGTATATATATGCGTTCT 58.464 34.615 5.44 0.00 0.00 3.01
2576 2688 9.037417 CGTATACGATGTGTGTATATATATGCG 57.963 37.037 20.58 0.00 43.02 4.73
2595 2707 6.627690 ATGAAAAGGCGATATTCGTATACG 57.372 37.500 19.23 19.23 42.81 3.06
2621 2733 7.921214 GCTGATATTGCAGGTGTATATACGTAT 59.079 37.037 13.54 13.54 36.41 3.06
2622 2734 7.122204 AGCTGATATTGCAGGTGTATATACGTA 59.878 37.037 8.33 0.00 44.23 3.57
2623 2735 6.071334 AGCTGATATTGCAGGTGTATATACGT 60.071 38.462 8.33 0.00 44.23 3.57
2624 2736 6.333416 AGCTGATATTGCAGGTGTATATACG 58.667 40.000 8.33 0.00 44.23 3.06
2633 2745 6.000219 CCTTATTACAGCTGATATTGCAGGT 59.000 40.000 23.35 0.00 46.63 4.00
2641 2753 6.947644 TCGTACACCTTATTACAGCTGATA 57.052 37.500 23.35 5.81 0.00 2.15
2645 2757 8.472413 TCTAAATTCGTACACCTTATTACAGCT 58.528 33.333 0.00 0.00 0.00 4.24
2680 2792 4.006989 AGAAACGCATTACACATGCCTAA 58.993 39.130 0.00 0.00 41.71 2.69
2733 2846 2.290287 ACAGGTACCCTCGCATGCA 61.290 57.895 19.57 4.02 0.00 3.96
2782 2900 7.641802 TCACTTTTGTTTTTGTTTTGCAAGAAC 59.358 29.630 13.98 13.98 46.32 3.01
2783 2901 7.697691 TCACTTTTGTTTTTGTTTTGCAAGAA 58.302 26.923 0.00 0.00 38.47 2.52
2784 2902 7.251704 TCACTTTTGTTTTTGTTTTGCAAGA 57.748 28.000 0.00 0.00 38.47 3.02
2785 2903 8.504812 AATCACTTTTGTTTTTGTTTTGCAAG 57.495 26.923 0.00 0.00 38.47 4.01
2786 2904 9.387123 GTAATCACTTTTGTTTTTGTTTTGCAA 57.613 25.926 0.00 0.00 34.87 4.08
2787 2905 8.778358 AGTAATCACTTTTGTTTTTGTTTTGCA 58.222 25.926 0.00 0.00 0.00 4.08
2788 2906 9.605955 AAGTAATCACTTTTGTTTTTGTTTTGC 57.394 25.926 0.00 0.00 42.51 3.68
2791 2909 9.413048 TCGAAGTAATCACTTTTGTTTTTGTTT 57.587 25.926 0.00 0.00 45.18 2.83
2792 2910 8.973835 TCGAAGTAATCACTTTTGTTTTTGTT 57.026 26.923 0.00 0.00 45.18 2.83
2793 2911 8.455682 TCTCGAAGTAATCACTTTTGTTTTTGT 58.544 29.630 0.00 0.00 45.18 2.83
2794 2912 8.835467 TCTCGAAGTAATCACTTTTGTTTTTG 57.165 30.769 0.00 0.00 45.18 2.44
2796 2914 9.665264 GAATCTCGAAGTAATCACTTTTGTTTT 57.335 29.630 0.00 0.00 45.18 2.43
2797 2915 9.057089 AGAATCTCGAAGTAATCACTTTTGTTT 57.943 29.630 0.00 0.00 45.18 2.83
2798 2916 8.499162 CAGAATCTCGAAGTAATCACTTTTGTT 58.501 33.333 0.00 0.00 45.18 2.83
2799 2917 7.657761 ACAGAATCTCGAAGTAATCACTTTTGT 59.342 33.333 0.00 0.00 45.18 2.83
2800 2918 7.954248 CACAGAATCTCGAAGTAATCACTTTTG 59.046 37.037 0.00 0.00 45.18 2.44
2801 2919 7.657761 ACACAGAATCTCGAAGTAATCACTTTT 59.342 33.333 0.00 0.00 45.18 2.27
2802 2920 7.155328 ACACAGAATCTCGAAGTAATCACTTT 58.845 34.615 0.00 0.00 45.18 2.66
2804 2922 6.274157 ACACAGAATCTCGAAGTAATCACT 57.726 37.500 0.00 0.00 36.19 3.41
2805 2923 8.535592 CAATACACAGAATCTCGAAGTAATCAC 58.464 37.037 0.00 0.00 0.00 3.06
2806 2924 8.251026 ACAATACACAGAATCTCGAAGTAATCA 58.749 33.333 0.00 0.00 0.00 2.57
2807 2925 8.635877 ACAATACACAGAATCTCGAAGTAATC 57.364 34.615 0.00 0.00 0.00 1.75
2811 2929 8.136165 GGTATACAATACACAGAATCTCGAAGT 58.864 37.037 5.01 0.00 0.00 3.01
2812 2930 8.353684 AGGTATACAATACACAGAATCTCGAAG 58.646 37.037 5.01 0.00 0.00 3.79
2813 2931 8.234136 AGGTATACAATACACAGAATCTCGAA 57.766 34.615 5.01 0.00 0.00 3.71
2814 2932 7.040617 GGAGGTATACAATACACAGAATCTCGA 60.041 40.741 5.01 0.00 0.00 4.04
2815 2933 7.085116 GGAGGTATACAATACACAGAATCTCG 58.915 42.308 5.01 0.00 0.00 4.04
2816 2934 7.952671 TGGAGGTATACAATACACAGAATCTC 58.047 38.462 5.01 0.00 0.00 2.75
2817 2935 7.914427 TGGAGGTATACAATACACAGAATCT 57.086 36.000 5.01 0.00 0.00 2.40
2818 2936 9.561069 AATTGGAGGTATACAATACACAGAATC 57.439 33.333 5.01 0.00 39.17 2.52
2828 2946 7.529560 GCCAGGAGATAATTGGAGGTATACAAT 60.530 40.741 5.01 0.00 42.08 2.71
2833 2951 4.242811 TGCCAGGAGATAATTGGAGGTAT 58.757 43.478 0.00 0.00 33.76 2.73
2841 2959 8.052748 TGTATGTAAACTTGCCAGGAGATAATT 58.947 33.333 0.00 0.00 0.00 1.40
2845 2963 5.435686 TGTATGTAAACTTGCCAGGAGAT 57.564 39.130 0.00 0.00 0.00 2.75
2880 3000 0.037326 TTAACAGAGAGCCACTGCCG 60.037 55.000 0.00 0.00 38.74 5.69
2894 3014 5.613329 ACACAGGTACGGAGAAAATTAACA 58.387 37.500 0.00 0.00 0.00 2.41
2934 3054 8.208903 ACGATTTGGGTATACTATTAGCACTTT 58.791 33.333 2.25 0.00 0.00 2.66
2936 3056 7.014905 TCACGATTTGGGTATACTATTAGCACT 59.985 37.037 2.25 0.00 0.00 4.40
2953 3073 5.106830 GGTGGTAACTTAGGTTCACGATTTG 60.107 44.000 0.00 0.00 36.92 2.32
2973 3093 4.664150 TTTGTTTTTCTAAGGCAGGTGG 57.336 40.909 0.00 0.00 0.00 4.61
3020 3140 6.143278 ACGTCGAATTTACCTTTTTGAAATGC 59.857 34.615 0.00 0.00 0.00 3.56
3029 3149 6.376177 GGATTGAAACGTCGAATTTACCTTT 58.624 36.000 0.00 0.00 0.00 3.11
3030 3150 5.106436 GGGATTGAAACGTCGAATTTACCTT 60.106 40.000 0.00 0.00 0.00 3.50
3031 3151 4.393990 GGGATTGAAACGTCGAATTTACCT 59.606 41.667 0.00 0.00 0.00 3.08
3032 3152 4.154556 TGGGATTGAAACGTCGAATTTACC 59.845 41.667 0.00 0.00 0.00 2.85
3033 3153 5.084055 GTGGGATTGAAACGTCGAATTTAC 58.916 41.667 0.00 0.00 0.00 2.01
3034 3154 4.154556 GGTGGGATTGAAACGTCGAATTTA 59.845 41.667 0.00 0.00 0.00 1.40
3035 3155 3.057806 GGTGGGATTGAAACGTCGAATTT 60.058 43.478 0.00 0.00 0.00 1.82
3036 3156 2.486592 GGTGGGATTGAAACGTCGAATT 59.513 45.455 0.00 0.00 0.00 2.17
3037 3157 2.081462 GGTGGGATTGAAACGTCGAAT 58.919 47.619 0.00 0.00 0.00 3.34
3039 3159 0.393448 TGGTGGGATTGAAACGTCGA 59.607 50.000 0.00 0.00 0.00 4.20
3040 3160 1.231221 TTGGTGGGATTGAAACGTCG 58.769 50.000 0.00 0.00 0.00 5.12
3043 3163 5.810074 GGAATTATTTGGTGGGATTGAAACG 59.190 40.000 0.00 0.00 0.00 3.60
3051 3171 5.261216 GAGAAGTGGAATTATTTGGTGGGA 58.739 41.667 0.00 0.00 0.00 4.37
3070 3190 6.524101 AACAACTAAAAGTTTGCAGGAGAA 57.476 33.333 0.00 0.00 36.03 2.87
3081 3201 4.874199 TCCCCAAGGAAACAACTAAAAGT 58.126 39.130 0.00 0.00 40.08 2.66
3133 3350 5.174037 TGAATCGGAGGGAGTAATGTTTT 57.826 39.130 0.00 0.00 0.00 2.43
3137 3354 7.801716 TTAATTTGAATCGGAGGGAGTAATG 57.198 36.000 0.00 0.00 0.00 1.90
3139 3356 8.050325 TCAATTAATTTGAATCGGAGGGAGTAA 58.950 33.333 0.00 0.00 41.38 2.24
3156 3373 9.573133 GTTGTACTAAAGCTGCATCAATTAATT 57.427 29.630 1.02 0.00 0.00 1.40
3158 3375 8.335532 AGTTGTACTAAAGCTGCATCAATTAA 57.664 30.769 1.02 0.00 0.00 1.40
3160 3377 6.824305 AGTTGTACTAAAGCTGCATCAATT 57.176 33.333 1.02 0.00 0.00 2.32
3161 3378 7.921786 TTAGTTGTACTAAAGCTGCATCAAT 57.078 32.000 1.02 0.00 37.71 2.57
3162 3379 7.921786 ATTAGTTGTACTAAAGCTGCATCAA 57.078 32.000 1.02 0.00 43.16 2.57
3163 3380 7.824289 AGAATTAGTTGTACTAAAGCTGCATCA 59.176 33.333 1.02 0.00 43.16 3.07
3166 3383 6.934645 ACAGAATTAGTTGTACTAAAGCTGCA 59.065 34.615 20.20 0.00 43.16 4.41
3184 3401 8.844244 AGTCGTCGGTATAATACTTACAGAATT 58.156 33.333 0.00 0.00 0.00 2.17
3186 3403 7.792374 AGTCGTCGGTATAATACTTACAGAA 57.208 36.000 0.00 0.00 0.00 3.02
3188 3405 8.076714 TGTAGTCGTCGGTATAATACTTACAG 57.923 38.462 0.00 0.00 0.00 2.74
3190 3407 9.884465 ATTTGTAGTCGTCGGTATAATACTTAC 57.116 33.333 0.00 0.00 0.00 2.34
3197 3442 8.531622 TTTGAAATTTGTAGTCGTCGGTATAA 57.468 30.769 0.00 0.00 0.00 0.98
3203 3448 6.853872 TGGAAATTTGAAATTTGTAGTCGTCG 59.146 34.615 19.47 0.00 0.00 5.12
3204 3449 8.476925 GTTGGAAATTTGAAATTTGTAGTCGTC 58.523 33.333 19.47 3.78 0.00 4.20
3206 3451 8.574196 AGTTGGAAATTTGAAATTTGTAGTCG 57.426 30.769 19.47 0.00 0.00 4.18
3244 3492 9.656323 TCTTAATAAGAATACCTGAGCTCCTAA 57.344 33.333 12.15 0.00 33.83 2.69
3245 3493 9.656323 TTCTTAATAAGAATACCTGAGCTCCTA 57.344 33.333 12.15 0.00 42.31 2.94
3247 3495 8.425703 ACTTCTTAATAAGAATACCTGAGCTCC 58.574 37.037 14.98 0.00 45.75 4.70
3267 3515 5.128919 GCCATACTTCCATCATGACTTCTT 58.871 41.667 0.00 0.00 0.00 2.52
3271 3519 2.808202 GCGCCATACTTCCATCATGACT 60.808 50.000 0.00 0.00 0.00 3.41
3273 3521 1.140652 TGCGCCATACTTCCATCATGA 59.859 47.619 4.18 0.00 0.00 3.07
3278 3526 1.677576 CAACATGCGCCATACTTCCAT 59.322 47.619 4.18 0.00 0.00 3.41
3279 3527 1.093972 CAACATGCGCCATACTTCCA 58.906 50.000 4.18 0.00 0.00 3.53
3287 3535 1.106351 AACCTCAACAACATGCGCCA 61.106 50.000 4.18 0.00 0.00 5.69
3290 3538 2.772568 TCAAACCTCAACAACATGCG 57.227 45.000 0.00 0.00 0.00 4.73
3291 3539 5.049167 TCATTTCAAACCTCAACAACATGC 58.951 37.500 0.00 0.00 0.00 4.06
3347 3595 2.837947 AGTCCACTGAAGGATGGATCA 58.162 47.619 0.00 0.00 46.55 2.92
3349 3597 4.664688 AAAAGTCCACTGAAGGATGGAT 57.335 40.909 0.00 0.00 46.55 3.41
3354 3602 8.477419 AATTCAATTAAAAGTCCACTGAAGGA 57.523 30.769 0.00 0.00 34.64 3.36
3360 3608 9.533253 CAGTTGAAATTCAATTAAAAGTCCACT 57.467 29.630 11.87 0.00 38.79 4.00
3369 3617 8.729805 AAAAGTGGCAGTTGAAATTCAATTAA 57.270 26.923 11.87 0.00 38.79 1.40
3414 3662 8.342634 CCAAACCGTTGAACATTATATAAGGAG 58.657 37.037 13.77 2.99 36.83 3.69
3415 3663 8.047911 TCCAAACCGTTGAACATTATATAAGGA 58.952 33.333 13.77 0.93 36.83 3.36
3425 3673 1.953686 CCTGTCCAAACCGTTGAACAT 59.046 47.619 0.00 0.00 30.87 2.71
3427 3675 1.385528 ACCTGTCCAAACCGTTGAAC 58.614 50.000 0.00 0.00 36.83 3.18
3433 3681 5.352293 GGTACTATAAAACCTGTCCAAACCG 59.648 44.000 0.00 0.00 32.72 4.44
3444 3692 8.736244 TGCAGAAATTTCAGGTACTATAAAACC 58.264 33.333 19.99 0.00 36.02 3.27
3466 3715 9.926751 CAAAGTGAAGTTTGTATATAGATGCAG 57.073 33.333 0.00 0.00 33.48 4.41
3485 3734 4.898265 TGGGAAAATGGATGAACAAAGTGA 59.102 37.500 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.