Multiple sequence alignment - TraesCS6B01G165600

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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 TraesCS6B01G165600 chr6B 100.000 3276 0 0 1 3276 172327422 172324147 0.000000e+00 6050.0
1 TraesCS6B01G165600 chr6B 95.149 639 28 1 701 1336 534034046 534034684 0.000000e+00 1005.0
2 TraesCS6B01G165600 chr6B 97.561 574 14 0 133 706 534012333 534012906 0.000000e+00 983.0
3 TraesCS6B01G165600 chr6B 83.990 406 51 8 108 509 673541631 673541236 8.580000e-101 377.0
4 TraesCS6B01G165600 chr6B 89.427 227 22 2 3050 3275 172265366 172265141 5.350000e-73 285.0
5 TraesCS6B01G165600 chr6D 97.465 1144 21 3 1366 2501 89824562 89823419 0.000000e+00 1945.0
6 TraesCS6B01G165600 chr6D 96.192 604 12 2 2669 3270 89823403 89822809 0.000000e+00 977.0
7 TraesCS6B01G165600 chr6D 89.868 227 21 2 3050 3275 89734338 89734113 1.150000e-74 291.0
8 TraesCS6B01G165600 chr6D 91.398 93 4 3 11 103 89825016 89824928 1.230000e-24 124.0
9 TraesCS6B01G165600 chr6D 100.000 31 0 0 1335 1365 89824932 89824902 1.270000e-04 58.4
10 TraesCS6B01G165600 chr7B 94.497 1272 43 9 102 1349 28812437 28811169 0.000000e+00 1936.0
11 TraesCS6B01G165600 chr7B 89.286 140 15 0 1915 2054 614220612 614220473 3.360000e-40 176.0
12 TraesCS6B01G165600 chr7B 92.000 50 1 2 2494 2541 513813934 513813886 2.110000e-07 67.6
13 TraesCS6B01G165600 chr2D 89.536 1099 66 18 248 1336 345856137 345855078 0.000000e+00 1347.0
14 TraesCS6B01G165600 chr2D 87.857 140 17 0 1915 2054 558943717 558943578 7.270000e-37 165.0
15 TraesCS6B01G165600 chr2D 90.741 54 1 3 2491 2541 421789898 421789950 5.870000e-08 69.4
16 TraesCS6B01G165600 chr2D 83.871 62 5 5 2479 2538 136468202 136468260 2.000000e-03 54.7
17 TraesCS6B01G165600 chr5A 97.619 714 15 2 97 809 238341539 238342251 0.000000e+00 1223.0
18 TraesCS6B01G165600 chr5A 94.154 479 25 1 865 1340 238342464 238342942 0.000000e+00 726.0
19 TraesCS6B01G165600 chr5A 83.168 101 12 3 2528 2627 570006224 570006128 1.620000e-13 87.9
20 TraesCS6B01G165600 chr5A 83.696 92 12 3 2536 2627 570006127 570006215 2.090000e-12 84.2
21 TraesCS6B01G165600 chr5A 92.157 51 1 2 2491 2538 474539858 474539908 5.870000e-08 69.4
22 TraesCS6B01G165600 chr6A 93.651 756 34 8 1364 2105 108203409 108202654 0.000000e+00 1118.0
23 TraesCS6B01G165600 chr6A 94.785 652 21 3 2629 3276 108202276 108201634 0.000000e+00 1003.0
24 TraesCS6B01G165600 chr6A 87.603 363 35 5 2134 2493 108202656 108202301 2.350000e-111 412.0
25 TraesCS6B01G165600 chr6A 89.091 220 23 1 3057 3275 108180132 108179913 4.170000e-69 272.0
26 TraesCS6B01G165600 chr6A 90.625 96 5 2 11 103 108203878 108203784 1.230000e-24 124.0
27 TraesCS6B01G165600 chr4A 84.096 415 52 8 99 509 209307498 209307902 3.960000e-104 388.0
28 TraesCS6B01G165600 chr4A 81.609 87 12 3 2545 2631 731354543 731354461 5.870000e-08 69.4
29 TraesCS6B01G165600 chr3A 83.508 382 47 10 133 509 701238035 701237665 3.130000e-90 342.0
30 TraesCS6B01G165600 chr3A 83.014 365 48 8 149 509 572651491 572651845 5.270000e-83 318.0
31 TraesCS6B01G165600 chr1D 83.146 356 46 8 158 509 89984335 89984680 2.450000e-81 313.0
32 TraesCS6B01G165600 chr1D 88.571 140 16 0 1915 2054 421493999 421494138 1.560000e-38 171.0
33 TraesCS6B01G165600 chr7A 76.577 444 75 21 1419 1853 649425856 649425433 1.980000e-52 217.0
34 TraesCS6B01G165600 chr7A 89.286 140 15 0 1915 2054 649425286 649425147 3.360000e-40 176.0
35 TraesCS6B01G165600 chr7A 89.796 98 9 1 92 189 454353373 454353277 1.230000e-24 124.0
36 TraesCS6B01G165600 chr7D 89.286 140 15 0 1915 2054 563825365 563825504 3.360000e-40 176.0
37 TraesCS6B01G165600 chr7D 83.516 91 11 2 2535 2625 562248050 562247964 7.530000e-12 82.4
38 TraesCS6B01G165600 chr3D 86.429 140 19 0 1915 2054 577441695 577441834 1.570000e-33 154.0
39 TraesCS6B01G165600 chr5B 85.106 94 11 3 2535 2627 591655338 591655429 3.480000e-15 93.5
40 TraesCS6B01G165600 chr5B 92.000 50 0 4 2495 2541 522929085 522929037 2.110000e-07 67.6
41 TraesCS6B01G165600 chr4B 84.337 83 12 1 2545 2627 657468728 657468647 2.710000e-11 80.5
42 TraesCS6B01G165600 chr4B 84.615 78 11 1 2535 2612 657468645 657468721 3.510000e-10 76.8
43 TraesCS6B01G165600 chr4B 93.750 48 0 2 2496 2541 322692940 322692986 5.870000e-08 69.4
44 TraesCS6B01G165600 chr2A 81.818 99 15 3 2536 2631 555925778 555925680 2.710000e-11 80.5
45 TraesCS6B01G165600 chr2A 90.566 53 2 2 2491 2541 16133148 16133199 2.110000e-07 67.6
46 TraesCS6B01G165600 chr3B 81.250 96 16 2 2536 2630 502804997 502805091 3.510000e-10 76.8
47 TraesCS6B01G165600 chr5D 89.286 56 1 3 2488 2541 352456275 352456327 7.590000e-07 65.8
48 TraesCS6B01G165600 chrUn 85.484 62 5 3 2475 2534 97740046 97740105 9.810000e-06 62.1


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 TraesCS6B01G165600 chr6B 172324147 172327422 3275 True 6050.00 6050 100.00000 1 3276 1 chr6B.!!$R2 3275
1 TraesCS6B01G165600 chr6B 534034046 534034684 638 False 1005.00 1005 95.14900 701 1336 1 chr6B.!!$F2 635
2 TraesCS6B01G165600 chr6B 534012333 534012906 573 False 983.00 983 97.56100 133 706 1 chr6B.!!$F1 573
3 TraesCS6B01G165600 chr6D 89822809 89825016 2207 True 776.10 1945 96.26375 11 3270 4 chr6D.!!$R2 3259
4 TraesCS6B01G165600 chr7B 28811169 28812437 1268 True 1936.00 1936 94.49700 102 1349 1 chr7B.!!$R1 1247
5 TraesCS6B01G165600 chr2D 345855078 345856137 1059 True 1347.00 1347 89.53600 248 1336 1 chr2D.!!$R1 1088
6 TraesCS6B01G165600 chr5A 238341539 238342942 1403 False 974.50 1223 95.88650 97 1340 2 chr5A.!!$F3 1243
7 TraesCS6B01G165600 chr6A 108201634 108203878 2244 True 664.25 1118 91.66600 11 3276 4 chr6A.!!$R2 3265

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
95 99 4.133013 GCATTGGCAGATTTTGGAAGAT 57.867 40.909 0.0 0.0 40.72 2.40 F
1331 1528 2.164624 TCCAAAAGTCCAACCAAACACG 59.835 45.455 0.0 0.0 0.00 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1622 2170 1.300156 TCAGTGACGTGCTGCAGAC 60.300 57.895 20.43 11.85 34.21 3.51 R
2766 3335 0.179004 TGCTCCTTTTCAAAGCCGGA 60.179 50.000 5.05 0.00 35.12 5.14 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
95 99 4.133013 GCATTGGCAGATTTTGGAAGAT 57.867 40.909 0.00 0.00 40.72 2.40
100 104 5.649782 TGGCAGATTTTGGAAGATTTCTC 57.350 39.130 0.00 0.00 0.00 2.87
1331 1528 2.164624 TCCAAAAGTCCAACCAAACACG 59.835 45.455 0.00 0.00 0.00 4.49
1390 1938 7.083230 TGTTGTGCAATTATGTCAAGTATGTG 58.917 34.615 0.00 0.00 0.00 3.21
1393 1941 6.597280 TGTGCAATTATGTCAAGTATGTGCTA 59.403 34.615 0.00 0.00 0.00 3.49
1622 2170 1.822990 TCTTACTGGTGTTAGCCTCCG 59.177 52.381 0.00 0.00 0.00 4.63
1689 2237 5.240183 TCGTATTACTGGTATGCTCTGTACC 59.760 44.000 0.00 0.00 41.59 3.34
1888 2442 4.223144 ACTATTTTCTGTTTGGGTGCCTT 58.777 39.130 0.00 0.00 0.00 4.35
2321 2883 5.003160 TCATGGTCGTCATCAAGAATTTGT 58.997 37.500 0.00 0.00 35.73 2.83
2426 2988 0.250038 AGCTGTGCTTCGCTTCAGAA 60.250 50.000 12.74 0.00 33.89 3.02
2450 3012 3.702330 TCTCTGGTCGTGTATTTATGCG 58.298 45.455 0.00 0.00 0.00 4.73
2466 3031 1.552226 TGCGAAAGTATTAGTCCGCG 58.448 50.000 0.00 0.00 44.76 6.46
2482 3047 1.330306 CGCGCATGCCTTTATTATGC 58.670 50.000 13.15 5.19 42.75 3.14
2503 3068 9.998106 TTATGCTTTCTGATAAGTAATACTCCC 57.002 33.333 0.00 0.00 0.00 4.30
2504 3069 7.676683 TGCTTTCTGATAAGTAATACTCCCT 57.323 36.000 0.00 0.00 0.00 4.20
2505 3070 7.500992 TGCTTTCTGATAAGTAATACTCCCTG 58.499 38.462 0.00 0.00 0.00 4.45
2507 3072 7.654116 GCTTTCTGATAAGTAATACTCCCTGTC 59.346 40.741 0.00 0.00 0.00 3.51
2508 3073 7.598759 TTCTGATAAGTAATACTCCCTGTCC 57.401 40.000 0.00 0.00 0.00 4.02
2509 3074 5.768662 TCTGATAAGTAATACTCCCTGTCCG 59.231 44.000 0.00 0.00 0.00 4.79
2510 3075 4.831155 TGATAAGTAATACTCCCTGTCCGG 59.169 45.833 0.00 0.00 0.00 5.14
2511 3076 3.393426 AAGTAATACTCCCTGTCCGGA 57.607 47.619 0.00 0.00 33.16 5.14
2512 3077 3.393426 AGTAATACTCCCTGTCCGGAA 57.607 47.619 5.23 0.00 33.16 4.30
2514 3079 4.296056 AGTAATACTCCCTGTCCGGAAAT 58.704 43.478 5.23 0.00 33.16 2.17
2515 3080 5.461327 AGTAATACTCCCTGTCCGGAAATA 58.539 41.667 5.23 0.00 33.16 1.40
2516 3081 4.684484 AATACTCCCTGTCCGGAAATAC 57.316 45.455 5.23 0.00 33.16 1.89
2517 3082 2.249309 ACTCCCTGTCCGGAAATACT 57.751 50.000 5.23 0.00 33.16 2.12
2518 3083 2.547990 ACTCCCTGTCCGGAAATACTT 58.452 47.619 5.23 0.00 33.16 2.24
2519 3084 2.236395 ACTCCCTGTCCGGAAATACTTG 59.764 50.000 5.23 0.00 33.16 3.16
2520 3085 2.236395 CTCCCTGTCCGGAAATACTTGT 59.764 50.000 5.23 0.00 33.16 3.16
2521 3086 2.235402 TCCCTGTCCGGAAATACTTGTC 59.765 50.000 5.23 0.00 33.16 3.18
2522 3087 2.268298 CCTGTCCGGAAATACTTGTCG 58.732 52.381 5.23 0.00 33.16 4.35
2523 3088 2.094390 CCTGTCCGGAAATACTTGTCGA 60.094 50.000 5.23 0.00 33.16 4.20
2524 3089 3.581755 CTGTCCGGAAATACTTGTCGAA 58.418 45.455 5.23 0.00 0.00 3.71
2525 3090 3.581755 TGTCCGGAAATACTTGTCGAAG 58.418 45.455 5.23 0.00 35.07 3.79
2526 3091 3.256383 TGTCCGGAAATACTTGTCGAAGA 59.744 43.478 5.23 0.00 32.98 2.87
2527 3092 4.240096 GTCCGGAAATACTTGTCGAAGAA 58.760 43.478 5.23 0.00 39.69 2.52
2528 3093 4.687483 GTCCGGAAATACTTGTCGAAGAAA 59.313 41.667 5.23 0.00 39.69 2.52
2529 3094 5.350640 GTCCGGAAATACTTGTCGAAGAAAT 59.649 40.000 5.23 0.00 39.69 2.17
2530 3095 5.350365 TCCGGAAATACTTGTCGAAGAAATG 59.650 40.000 0.00 0.00 39.69 2.32
2531 3096 5.447279 CCGGAAATACTTGTCGAAGAAATGG 60.447 44.000 0.00 0.00 39.69 3.16
2532 3097 5.350365 CGGAAATACTTGTCGAAGAAATGGA 59.650 40.000 0.00 0.00 39.69 3.41
2533 3098 6.037172 CGGAAATACTTGTCGAAGAAATGGAT 59.963 38.462 0.00 0.00 39.69 3.41
2534 3099 7.189512 GGAAATACTTGTCGAAGAAATGGATG 58.810 38.462 0.00 0.00 39.69 3.51
2535 3100 7.148239 GGAAATACTTGTCGAAGAAATGGATGT 60.148 37.037 0.00 0.00 39.69 3.06
2536 3101 8.786826 AAATACTTGTCGAAGAAATGGATGTA 57.213 30.769 0.00 0.00 39.69 2.29
2537 3102 7.772332 ATACTTGTCGAAGAAATGGATGTAC 57.228 36.000 0.00 0.00 39.69 2.90
2538 3103 5.794894 ACTTGTCGAAGAAATGGATGTACT 58.205 37.500 0.00 0.00 39.69 2.73
2539 3104 5.869888 ACTTGTCGAAGAAATGGATGTACTC 59.130 40.000 0.00 0.00 39.69 2.59
2540 3105 5.661056 TGTCGAAGAAATGGATGTACTCT 57.339 39.130 0.00 0.00 39.69 3.24
2541 3106 5.651530 TGTCGAAGAAATGGATGTACTCTC 58.348 41.667 0.00 0.00 39.69 3.20
2542 3107 5.419155 TGTCGAAGAAATGGATGTACTCTCT 59.581 40.000 0.00 0.00 39.69 3.10
2543 3108 6.071334 TGTCGAAGAAATGGATGTACTCTCTT 60.071 38.462 0.00 0.00 39.69 2.85
2544 3109 6.474102 GTCGAAGAAATGGATGTACTCTCTTC 59.526 42.308 0.00 0.00 39.69 2.87
2545 3110 6.820470 GAAGAAATGGATGTACTCTCTTCG 57.180 41.667 0.00 0.00 31.10 3.79
2546 3111 5.923733 AGAAATGGATGTACTCTCTTCGT 57.076 39.130 0.00 0.00 0.00 3.85
2547 3112 5.897050 AGAAATGGATGTACTCTCTTCGTC 58.103 41.667 0.00 0.00 0.00 4.20
2548 3113 4.657436 AATGGATGTACTCTCTTCGTCC 57.343 45.455 0.00 0.00 37.66 4.79
2549 3114 2.014857 TGGATGTACTCTCTTCGTCCG 58.985 52.381 0.00 0.00 39.36 4.79
2550 3115 1.334243 GGATGTACTCTCTTCGTCCGG 59.666 57.143 0.00 0.00 0.00 5.14
2551 3116 2.286872 GATGTACTCTCTTCGTCCGGA 58.713 52.381 0.00 0.00 0.00 5.14
2552 3117 2.189594 TGTACTCTCTTCGTCCGGAA 57.810 50.000 5.23 0.00 0.00 4.30
2553 3118 2.507484 TGTACTCTCTTCGTCCGGAAA 58.493 47.619 5.23 0.00 33.34 3.13
2554 3119 3.087031 TGTACTCTCTTCGTCCGGAAAT 58.913 45.455 5.23 0.00 33.34 2.17
2555 3120 4.264253 TGTACTCTCTTCGTCCGGAAATA 58.736 43.478 5.23 0.00 33.34 1.40
2556 3121 3.779271 ACTCTCTTCGTCCGGAAATAC 57.221 47.619 5.23 0.00 33.34 1.89
2557 3122 3.354467 ACTCTCTTCGTCCGGAAATACT 58.646 45.455 5.23 0.00 33.34 2.12
2558 3123 3.762823 ACTCTCTTCGTCCGGAAATACTT 59.237 43.478 5.23 0.00 33.34 2.24
2559 3124 4.106029 TCTCTTCGTCCGGAAATACTTG 57.894 45.455 5.23 0.00 33.34 3.16
2560 3125 3.508793 TCTCTTCGTCCGGAAATACTTGT 59.491 43.478 5.23 0.00 33.34 3.16
2561 3126 3.841643 TCTTCGTCCGGAAATACTTGTC 58.158 45.455 5.23 0.00 33.34 3.18
2562 3127 3.256383 TCTTCGTCCGGAAATACTTGTCA 59.744 43.478 5.23 0.00 33.34 3.58
2563 3128 3.880047 TCGTCCGGAAATACTTGTCAT 57.120 42.857 5.23 0.00 0.00 3.06
2564 3129 3.777478 TCGTCCGGAAATACTTGTCATC 58.223 45.455 5.23 0.00 0.00 2.92
2565 3130 3.193903 TCGTCCGGAAATACTTGTCATCA 59.806 43.478 5.23 0.00 0.00 3.07
2566 3131 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
2567 3132 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
2568 3133 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
2569 3134 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
2570 3135 6.747280 GTCCGGAAATACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
2571 3136 6.035843 CCGGAAATACTTGTCATCAAAATGG 58.964 40.000 0.00 0.00 33.42 3.16
2572 3137 6.127758 CCGGAAATACTTGTCATCAAAATGGA 60.128 38.462 0.00 0.00 33.42 3.41
2573 3138 7.416664 CCGGAAATACTTGTCATCAAAATGGAT 60.417 37.037 0.00 0.00 33.42 3.41
2574 3139 8.620416 CGGAAATACTTGTCATCAAAATGGATA 58.380 33.333 0.00 0.00 33.42 2.59
2581 3146 9.918630 ACTTGTCATCAAAATGGATAAAAGAAG 57.081 29.630 0.00 0.00 33.42 2.85
2587 3152 9.865321 CATCAAAATGGATAAAAGAAGATGTGT 57.135 29.630 0.00 0.00 0.00 3.72
2600 3165 9.710900 AAAAGAAGATGTGTTATCCATTTTTCC 57.289 29.630 0.00 0.00 0.00 3.13
2601 3166 7.088589 AGAAGATGTGTTATCCATTTTTCCG 57.911 36.000 0.00 0.00 0.00 4.30
2602 3167 6.884295 AGAAGATGTGTTATCCATTTTTCCGA 59.116 34.615 0.00 0.00 0.00 4.55
2603 3168 6.436843 AGATGTGTTATCCATTTTTCCGAC 57.563 37.500 0.00 0.00 0.00 4.79
2604 3169 5.943416 AGATGTGTTATCCATTTTTCCGACA 59.057 36.000 0.00 0.00 0.00 4.35
2605 3170 6.432783 AGATGTGTTATCCATTTTTCCGACAA 59.567 34.615 0.00 0.00 0.00 3.18
2606 3171 6.007936 TGTGTTATCCATTTTTCCGACAAG 57.992 37.500 0.00 0.00 0.00 3.16
2607 3172 5.533154 TGTGTTATCCATTTTTCCGACAAGT 59.467 36.000 0.00 0.00 0.00 3.16
2608 3173 6.711194 TGTGTTATCCATTTTTCCGACAAGTA 59.289 34.615 0.00 0.00 0.00 2.24
2609 3174 7.392113 TGTGTTATCCATTTTTCCGACAAGTAT 59.608 33.333 0.00 0.00 0.00 2.12
2610 3175 8.241367 GTGTTATCCATTTTTCCGACAAGTATT 58.759 33.333 0.00 0.00 0.00 1.89
2611 3176 8.798402 TGTTATCCATTTTTCCGACAAGTATTT 58.202 29.630 0.00 0.00 0.00 1.40
2612 3177 9.285770 GTTATCCATTTTTCCGACAAGTATTTC 57.714 33.333 0.00 0.00 0.00 2.17
2613 3178 6.262193 TCCATTTTTCCGACAAGTATTTCC 57.738 37.500 0.00 0.00 0.00 3.13
2614 3179 6.007703 TCCATTTTTCCGACAAGTATTTCCT 58.992 36.000 0.00 0.00 0.00 3.36
2615 3180 6.492087 TCCATTTTTCCGACAAGTATTTCCTT 59.508 34.615 0.00 0.00 0.00 3.36
2616 3181 7.666388 TCCATTTTTCCGACAAGTATTTCCTTA 59.334 33.333 0.00 0.00 0.00 2.69
2617 3182 8.466798 CCATTTTTCCGACAAGTATTTCCTTAT 58.533 33.333 0.00 0.00 0.00 1.73
2618 3183 9.289303 CATTTTTCCGACAAGTATTTCCTTATG 57.711 33.333 0.00 0.00 0.00 1.90
2619 3184 6.995511 TTTCCGACAAGTATTTCCTTATGG 57.004 37.500 0.00 0.00 0.00 2.74
2620 3185 5.943349 TCCGACAAGTATTTCCTTATGGA 57.057 39.130 0.00 0.00 41.36 3.41
2621 3186 5.914033 TCCGACAAGTATTTCCTTATGGAG 58.086 41.667 0.00 0.00 44.24 3.86
2623 3188 5.057149 CGACAAGTATTTCCTTATGGAGGG 58.943 45.833 0.00 0.00 46.31 4.30
2624 3189 5.163343 CGACAAGTATTTCCTTATGGAGGGA 60.163 44.000 0.00 0.00 46.31 4.20
2625 3190 6.253946 ACAAGTATTTCCTTATGGAGGGAG 57.746 41.667 0.00 0.00 46.31 4.30
2626 3191 5.731678 ACAAGTATTTCCTTATGGAGGGAGT 59.268 40.000 0.00 0.00 46.31 3.85
2627 3192 6.126739 ACAAGTATTTCCTTATGGAGGGAGTC 60.127 42.308 0.00 0.00 46.31 3.36
2661 3228 1.395635 CTGCTGGAATGCCAATGCTA 58.604 50.000 5.59 0.00 45.41 3.49
2662 3229 1.337071 CTGCTGGAATGCCAATGCTAG 59.663 52.381 5.59 0.00 45.41 3.42
2734 3301 3.616379 CGGAAAAGAATCTGAGCAGAGAC 59.384 47.826 6.34 3.07 41.33 3.36
2766 3335 5.942826 CCTCTGAAAAGGAGCAAATAGTCTT 59.057 40.000 0.00 0.00 38.87 3.01
2788 3357 2.151202 CGGCTTTGAAAAGGAGCAGTA 58.849 47.619 5.02 0.00 38.14 2.74
2931 3500 2.047560 GGCCGGCGTTGAGTTACT 60.048 61.111 22.54 0.00 0.00 2.24
2936 3505 4.573162 GCGTTGAGTTACTCGCCT 57.427 55.556 7.92 0.00 42.33 5.52
2937 3506 2.360794 GCGTTGAGTTACTCGCCTC 58.639 57.895 7.92 0.00 42.33 4.70
2938 3507 0.388134 GCGTTGAGTTACTCGCCTCA 60.388 55.000 7.92 0.00 42.33 3.86
2939 3508 1.337821 CGTTGAGTTACTCGCCTCAC 58.662 55.000 7.92 0.00 37.43 3.51
2940 3509 1.711206 GTTGAGTTACTCGCCTCACC 58.289 55.000 7.92 0.00 37.43 4.02
2941 3510 0.606604 TTGAGTTACTCGCCTCACCC 59.393 55.000 7.92 0.00 37.43 4.61
2942 3511 1.139095 GAGTTACTCGCCTCACCCG 59.861 63.158 0.00 0.00 0.00 5.28
2943 3512 2.508663 GTTACTCGCCTCACCCGC 60.509 66.667 0.00 0.00 0.00 6.13
2944 3513 3.766691 TTACTCGCCTCACCCGCC 61.767 66.667 0.00 0.00 0.00 6.13
3271 3840 1.292061 GGTACACGAACACTGCACAA 58.708 50.000 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.221703 TCTTAGCCTCCTTCTGTTTCTCTG 59.778 45.833 0.00 0.00 0.00 3.35
2 3 4.810191 TCTTAGCCTCCTTCTGTTTCTC 57.190 45.455 0.00 0.00 0.00 2.87
3 4 5.770685 AATCTTAGCCTCCTTCTGTTTCT 57.229 39.130 0.00 0.00 0.00 2.52
4 5 7.608376 AGTTAAATCTTAGCCTCCTTCTGTTTC 59.392 37.037 0.00 0.00 0.00 2.78
5 6 7.462590 AGTTAAATCTTAGCCTCCTTCTGTTT 58.537 34.615 0.00 0.00 0.00 2.83
6 7 7.021998 AGTTAAATCTTAGCCTCCTTCTGTT 57.978 36.000 0.00 0.00 0.00 3.16
7 8 6.628644 AGTTAAATCTTAGCCTCCTTCTGT 57.371 37.500 0.00 0.00 0.00 3.41
8 9 9.449719 TTTAAGTTAAATCTTAGCCTCCTTCTG 57.550 33.333 3.88 0.00 32.55 3.02
9 10 9.451002 GTTTAAGTTAAATCTTAGCCTCCTTCT 57.549 33.333 11.12 0.00 32.55 2.85
10 11 9.451002 AGTTTAAGTTAAATCTTAGCCTCCTTC 57.549 33.333 11.12 0.00 32.55 3.46
11 12 9.451002 GAGTTTAAGTTAAATCTTAGCCTCCTT 57.549 33.333 11.12 0.00 32.55 3.36
12 13 8.603304 TGAGTTTAAGTTAAATCTTAGCCTCCT 58.397 33.333 11.12 0.31 33.09 3.69
13 14 8.788325 TGAGTTTAAGTTAAATCTTAGCCTCC 57.212 34.615 11.12 0.00 33.09 4.30
49 50 8.977505 GCAGTATTCTCAGCAATTAAACAAAAA 58.022 29.630 0.00 0.00 0.00 1.94
59 60 3.067742 GCCAATGCAGTATTCTCAGCAAT 59.932 43.478 0.00 0.00 40.76 3.56
95 99 2.951642 CAACCAAACAGAGCCTGAGAAA 59.048 45.455 8.91 0.00 35.18 2.52
100 104 0.595095 GCTCAACCAAACAGAGCCTG 59.405 55.000 0.00 1.16 46.82 4.85
1390 1938 5.764487 AGGCAAATCAGATTTAGCTTAGC 57.236 39.130 20.40 13.89 31.53 3.09
1393 1941 4.465305 AGCAAGGCAAATCAGATTTAGCTT 59.535 37.500 20.40 14.74 31.53 3.74
1622 2170 1.300156 TCAGTGACGTGCTGCAGAC 60.300 57.895 20.43 11.85 34.21 3.51
2131 2693 4.400884 ACCACAATGAAACAGCAAAGTACA 59.599 37.500 0.00 0.00 0.00 2.90
2426 2988 5.050490 GCATAAATACACGACCAGAGATGT 58.950 41.667 0.00 0.00 0.00 3.06
2450 3012 2.348591 GCATGCGCGGACTAATACTTTC 60.349 50.000 8.83 0.00 0.00 2.62
2466 3031 5.835257 TCAGAAAGCATAATAAAGGCATGC 58.165 37.500 9.90 9.90 44.29 4.06
2482 3047 8.145122 GGACAGGGAGTATTACTTATCAGAAAG 58.855 40.741 0.00 0.00 0.00 2.62
2499 3064 2.236395 ACAAGTATTTCCGGACAGGGAG 59.764 50.000 1.83 0.00 41.52 4.30
2500 3065 2.235402 GACAAGTATTTCCGGACAGGGA 59.765 50.000 1.83 0.00 41.52 4.20
2501 3066 2.629051 GACAAGTATTTCCGGACAGGG 58.371 52.381 1.83 0.00 41.52 4.45
2503 3068 3.226346 TCGACAAGTATTTCCGGACAG 57.774 47.619 1.83 0.00 0.00 3.51
2504 3069 3.256383 TCTTCGACAAGTATTTCCGGACA 59.744 43.478 1.83 0.00 0.00 4.02
2505 3070 3.841643 TCTTCGACAAGTATTTCCGGAC 58.158 45.455 1.83 0.00 0.00 4.79
2507 3072 5.447279 CCATTTCTTCGACAAGTATTTCCGG 60.447 44.000 0.00 0.00 0.00 5.14
2508 3073 5.350365 TCCATTTCTTCGACAAGTATTTCCG 59.650 40.000 0.00 0.00 0.00 4.30
2509 3074 6.737254 TCCATTTCTTCGACAAGTATTTCC 57.263 37.500 0.00 0.00 0.00 3.13
2510 3075 7.752695 ACATCCATTTCTTCGACAAGTATTTC 58.247 34.615 0.00 0.00 0.00 2.17
2511 3076 7.687941 ACATCCATTTCTTCGACAAGTATTT 57.312 32.000 0.00 0.00 0.00 1.40
2512 3077 8.041323 AGTACATCCATTTCTTCGACAAGTATT 58.959 33.333 0.00 0.00 0.00 1.89
2514 3079 6.931838 AGTACATCCATTTCTTCGACAAGTA 58.068 36.000 0.00 0.00 0.00 2.24
2515 3080 5.794894 AGTACATCCATTTCTTCGACAAGT 58.205 37.500 0.00 0.00 0.00 3.16
2516 3081 6.102663 AGAGTACATCCATTTCTTCGACAAG 58.897 40.000 0.00 0.00 0.00 3.16
2517 3082 6.037786 AGAGTACATCCATTTCTTCGACAA 57.962 37.500 0.00 0.00 0.00 3.18
2518 3083 5.419155 AGAGAGTACATCCATTTCTTCGACA 59.581 40.000 0.00 0.00 0.00 4.35
2519 3084 5.897050 AGAGAGTACATCCATTTCTTCGAC 58.103 41.667 0.00 0.00 0.00 4.20
2520 3085 6.531503 AAGAGAGTACATCCATTTCTTCGA 57.468 37.500 0.00 0.00 0.00 3.71
2521 3086 6.820470 GAAGAGAGTACATCCATTTCTTCG 57.180 41.667 0.00 0.00 32.58 3.79
2522 3087 6.334202 ACGAAGAGAGTACATCCATTTCTTC 58.666 40.000 0.00 0.00 37.04 2.87
2523 3088 6.287589 ACGAAGAGAGTACATCCATTTCTT 57.712 37.500 0.00 0.00 0.00 2.52
2524 3089 5.163499 GGACGAAGAGAGTACATCCATTTCT 60.163 44.000 0.00 0.00 0.00 2.52
2525 3090 5.044558 GGACGAAGAGAGTACATCCATTTC 58.955 45.833 0.00 0.00 0.00 2.17
2526 3091 4.440250 CGGACGAAGAGAGTACATCCATTT 60.440 45.833 0.00 0.00 0.00 2.32
2527 3092 3.066900 CGGACGAAGAGAGTACATCCATT 59.933 47.826 0.00 0.00 0.00 3.16
2528 3093 2.619177 CGGACGAAGAGAGTACATCCAT 59.381 50.000 0.00 0.00 0.00 3.41
2529 3094 2.014857 CGGACGAAGAGAGTACATCCA 58.985 52.381 0.00 0.00 0.00 3.41
2530 3095 1.334243 CCGGACGAAGAGAGTACATCC 59.666 57.143 0.00 0.00 0.00 3.51
2531 3096 2.286872 TCCGGACGAAGAGAGTACATC 58.713 52.381 0.00 0.00 0.00 3.06
2532 3097 2.414994 TCCGGACGAAGAGAGTACAT 57.585 50.000 0.00 0.00 0.00 2.29
2533 3098 2.189594 TTCCGGACGAAGAGAGTACA 57.810 50.000 1.83 0.00 0.00 2.90
2534 3099 3.779271 ATTTCCGGACGAAGAGAGTAC 57.221 47.619 1.83 0.00 0.00 2.73
2535 3100 4.521146 AGTATTTCCGGACGAAGAGAGTA 58.479 43.478 1.83 0.00 0.00 2.59
2536 3101 3.354467 AGTATTTCCGGACGAAGAGAGT 58.646 45.455 1.83 0.00 0.00 3.24
2537 3102 4.106197 CAAGTATTTCCGGACGAAGAGAG 58.894 47.826 1.83 0.00 0.00 3.20
2538 3103 3.508793 ACAAGTATTTCCGGACGAAGAGA 59.491 43.478 1.83 0.00 0.00 3.10
2539 3104 3.846360 ACAAGTATTTCCGGACGAAGAG 58.154 45.455 1.83 0.00 0.00 2.85
2540 3105 3.256383 TGACAAGTATTTCCGGACGAAGA 59.744 43.478 1.83 0.00 0.00 2.87
2541 3106 3.581755 TGACAAGTATTTCCGGACGAAG 58.418 45.455 1.83 0.00 0.00 3.79
2542 3107 3.663995 TGACAAGTATTTCCGGACGAA 57.336 42.857 1.83 0.00 0.00 3.85
2543 3108 3.193903 TGATGACAAGTATTTCCGGACGA 59.806 43.478 1.83 0.00 0.00 4.20
2544 3109 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
2545 3110 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
2546 3111 6.127758 CCATTTTGATGACAAGTATTTCCGGA 60.128 38.462 0.00 0.00 37.32 5.14
2547 3112 6.035843 CCATTTTGATGACAAGTATTTCCGG 58.964 40.000 0.00 0.00 37.32 5.14
2548 3113 6.851609 TCCATTTTGATGACAAGTATTTCCG 58.148 36.000 0.00 0.00 37.32 4.30
2555 3120 9.918630 CTTCTTTTATCCATTTTGATGACAAGT 57.081 29.630 0.00 0.00 37.32 3.16
2561 3126 9.865321 ACACATCTTCTTTTATCCATTTTGATG 57.135 29.630 0.00 0.00 35.23 3.07
2567 3132 9.699410 TGGATAACACATCTTCTTTTATCCATT 57.301 29.630 14.55 0.00 46.91 3.16
2574 3139 9.710900 GGAAAAATGGATAACACATCTTCTTTT 57.289 29.630 0.00 0.00 0.00 2.27
2575 3140 8.028938 CGGAAAAATGGATAACACATCTTCTTT 58.971 33.333 0.00 0.00 0.00 2.52
2576 3141 7.393234 TCGGAAAAATGGATAACACATCTTCTT 59.607 33.333 0.00 0.00 0.00 2.52
2577 3142 6.884295 TCGGAAAAATGGATAACACATCTTCT 59.116 34.615 0.00 0.00 0.00 2.85
2578 3143 6.967199 GTCGGAAAAATGGATAACACATCTTC 59.033 38.462 0.00 0.00 0.00 2.87
2579 3144 6.432783 TGTCGGAAAAATGGATAACACATCTT 59.567 34.615 0.00 0.00 0.00 2.40
2580 3145 5.943416 TGTCGGAAAAATGGATAACACATCT 59.057 36.000 0.00 0.00 0.00 2.90
2581 3146 6.189677 TGTCGGAAAAATGGATAACACATC 57.810 37.500 0.00 0.00 0.00 3.06
2582 3147 6.208599 ACTTGTCGGAAAAATGGATAACACAT 59.791 34.615 0.00 0.00 0.00 3.21
2583 3148 5.533154 ACTTGTCGGAAAAATGGATAACACA 59.467 36.000 0.00 0.00 0.00 3.72
2584 3149 6.009115 ACTTGTCGGAAAAATGGATAACAC 57.991 37.500 0.00 0.00 0.00 3.32
2585 3150 7.931578 ATACTTGTCGGAAAAATGGATAACA 57.068 32.000 0.00 0.00 0.00 2.41
2586 3151 9.285770 GAAATACTTGTCGGAAAAATGGATAAC 57.714 33.333 0.00 0.00 0.00 1.89
2587 3152 8.463607 GGAAATACTTGTCGGAAAAATGGATAA 58.536 33.333 0.00 0.00 0.00 1.75
2588 3153 7.832187 AGGAAATACTTGTCGGAAAAATGGATA 59.168 33.333 0.00 0.00 0.00 2.59
2589 3154 6.663523 AGGAAATACTTGTCGGAAAAATGGAT 59.336 34.615 0.00 0.00 0.00 3.41
2590 3155 6.007703 AGGAAATACTTGTCGGAAAAATGGA 58.992 36.000 0.00 0.00 0.00 3.41
2591 3156 6.267496 AGGAAATACTTGTCGGAAAAATGG 57.733 37.500 0.00 0.00 0.00 3.16
2592 3157 9.289303 CATAAGGAAATACTTGTCGGAAAAATG 57.711 33.333 0.00 0.00 32.02 2.32
2593 3158 8.466798 CCATAAGGAAATACTTGTCGGAAAAAT 58.533 33.333 0.00 0.00 36.89 1.82
2594 3159 7.666388 TCCATAAGGAAATACTTGTCGGAAAAA 59.334 33.333 0.00 0.00 42.23 1.94
2595 3160 7.169591 TCCATAAGGAAATACTTGTCGGAAAA 58.830 34.615 0.00 0.00 42.23 2.29
2596 3161 6.713276 TCCATAAGGAAATACTTGTCGGAAA 58.287 36.000 0.00 0.00 42.23 3.13
2597 3162 6.302535 TCCATAAGGAAATACTTGTCGGAA 57.697 37.500 0.00 0.00 42.23 4.30
2598 3163 5.914033 CTCCATAAGGAAATACTTGTCGGA 58.086 41.667 0.00 0.00 45.19 4.55
2612 3177 5.004361 TCAGATAGACTCCCTCCATAAGG 57.996 47.826 0.00 0.00 45.77 2.69
2613 3178 8.837099 ATTATCAGATAGACTCCCTCCATAAG 57.163 38.462 0.00 0.00 0.00 1.73
2615 3180 9.874195 CATATTATCAGATAGACTCCCTCCATA 57.126 37.037 0.00 0.00 0.00 2.74
2616 3181 7.289782 GCATATTATCAGATAGACTCCCTCCAT 59.710 40.741 0.00 0.00 0.00 3.41
2617 3182 6.609212 GCATATTATCAGATAGACTCCCTCCA 59.391 42.308 0.00 0.00 0.00 3.86
2618 3183 6.838612 AGCATATTATCAGATAGACTCCCTCC 59.161 42.308 0.00 0.00 0.00 4.30
2619 3184 7.684187 GCAGCATATTATCAGATAGACTCCCTC 60.684 44.444 0.00 0.00 0.00 4.30
2620 3185 6.098124 GCAGCATATTATCAGATAGACTCCCT 59.902 42.308 0.00 0.00 0.00 4.20
2621 3186 6.098124 AGCAGCATATTATCAGATAGACTCCC 59.902 42.308 0.00 0.00 0.00 4.30
2622 3187 6.979817 CAGCAGCATATTATCAGATAGACTCC 59.020 42.308 0.00 0.00 0.00 3.85
2623 3188 6.979817 CCAGCAGCATATTATCAGATAGACTC 59.020 42.308 0.00 0.00 0.00 3.36
2624 3189 6.666980 TCCAGCAGCATATTATCAGATAGACT 59.333 38.462 0.00 0.00 0.00 3.24
2625 3190 6.871844 TCCAGCAGCATATTATCAGATAGAC 58.128 40.000 0.00 0.00 0.00 2.59
2626 3191 7.486407 TTCCAGCAGCATATTATCAGATAGA 57.514 36.000 0.00 0.00 0.00 1.98
2627 3192 7.254829 GCATTCCAGCAGCATATTATCAGATAG 60.255 40.741 0.00 0.00 0.00 2.08
2661 3228 3.135530 GGTTCCTGAATGAGATAGCACCT 59.864 47.826 0.00 0.00 0.00 4.00
2662 3229 3.118261 TGGTTCCTGAATGAGATAGCACC 60.118 47.826 0.00 0.00 0.00 5.01
2734 3301 0.593128 CCTTTTCAGAGGGCAACGTG 59.407 55.000 0.00 0.00 32.94 4.49
2766 3335 0.179004 TGCTCCTTTTCAAAGCCGGA 60.179 50.000 5.05 0.00 35.12 5.14
2936 3505 4.028490 AAATGCTCCGGCGGGTGA 62.028 61.111 27.98 10.26 42.25 4.02
2937 3506 3.814268 CAAATGCTCCGGCGGGTG 61.814 66.667 27.98 19.90 42.25 4.61
2942 3511 2.679996 AACCCCAAATGCTCCGGC 60.680 61.111 0.00 0.00 39.26 6.13
2943 3512 3.005540 GCAACCCCAAATGCTCCGG 62.006 63.158 0.00 0.00 39.46 5.14
2944 3513 2.573340 GCAACCCCAAATGCTCCG 59.427 61.111 0.00 0.00 39.46 4.63
2958 3527 2.597217 CGCCAAACTCCCCAGCAA 60.597 61.111 0.00 0.00 0.00 3.91
3170 3739 2.061773 CACCTACGACAAGCAGTTCAG 58.938 52.381 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.