Multiple sequence alignment - TraesCS2B01G480800

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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 TraesCS2B01G480800 chr2B 100.000 3003 0 0 1 3003 679032331 679029329 0.000000e+00 5546.0
1 TraesCS2B01G480800 chr2B 84.116 1341 155 43 788 2100 679696308 679697618 0.000000e+00 1243.0
2 TraesCS2B01G480800 chr2B 81.635 1040 133 39 1045 2057 679071596 679070588 0.000000e+00 809.0
3 TraesCS2B01G480800 chr2B 88.908 586 59 6 1517 2100 679743830 679744411 0.000000e+00 717.0
4 TraesCS2B01G480800 chr2B 82.444 712 84 33 788 1477 679729837 679730529 4.310000e-163 584.0
5 TraesCS2B01G480800 chr2B 87.419 461 29 11 559 1010 679072032 679071592 1.240000e-138 503.0
6 TraesCS2B01G480800 chr2B 90.244 287 23 2 291 575 679072334 679072051 1.310000e-98 370.0
7 TraesCS2B01G480800 chr2D 90.547 2486 120 41 131 2519 566263758 566261291 0.000000e+00 3182.0
8 TraesCS2B01G480800 chr2D 83.616 1355 168 32 790 2120 566656870 566655546 0.000000e+00 1223.0
9 TraesCS2B01G480800 chr2D 87.199 539 64 3 1519 2057 566302380 566301847 2.560000e-170 608.0
10 TraesCS2B01G480800 chr2D 88.720 461 24 11 559 1010 566303373 566302932 3.410000e-149 538.0
11 TraesCS2B01G480800 chr2D 78.758 805 122 34 1270 2057 566480585 566479813 7.480000e-136 494.0
12 TraesCS2B01G480800 chr2D 82.385 545 83 11 1513 2056 558376249 558376781 2.110000e-126 462.0
13 TraesCS2B01G480800 chr2D 77.920 779 126 31 1294 2057 566454242 566453495 7.640000e-121 444.0
14 TraesCS2B01G480800 chr2D 80.702 513 66 15 1 485 566303961 566303454 4.730000e-98 368.0
15 TraesCS2B01G480800 chr2D 81.044 364 44 16 1049 1392 566302932 566302574 1.770000e-67 267.0
16 TraesCS2B01G480800 chr2D 84.158 303 14 12 2505 2794 566261261 566260980 2.300000e-66 263.0
17 TraesCS2B01G480800 chr2D 95.238 84 2 1 494 575 566303475 566303392 6.750000e-27 132.0
18 TraesCS2B01G480800 chr2A 89.961 2281 139 35 1 2217 706490403 706488149 0.000000e+00 2861.0
19 TraesCS2B01G480800 chr2A 82.097 1469 172 57 720 2144 706530805 706529384 0.000000e+00 1171.0
20 TraesCS2B01G480800 chr2A 80.426 986 125 43 1049 2004 706510968 706510021 0.000000e+00 689.0
21 TraesCS2B01G480800 chr2A 81.913 575 59 29 80 625 706511847 706511289 7.640000e-121 444.0
22 TraesCS2B01G480800 chr2A 93.625 251 13 1 660 910 706511289 706511042 3.660000e-99 372.0
23 TraesCS2B01G480800 chr2A 89.600 250 14 5 2271 2519 706487951 706487713 1.050000e-79 307.0
24 TraesCS2B01G480800 chr2A 83.224 304 24 12 2505 2794 706487683 706487393 1.380000e-63 254.0
25 TraesCS2B01G480800 chr1A 96.203 79 2 1 2828 2905 530756590 530756668 8.740000e-26 128.0
26 TraesCS2B01G480800 chr1A 94.203 69 4 0 2832 2900 544730190 544730258 4.090000e-19 106.0
27 TraesCS2B01G480800 chr1A 97.368 38 1 0 2790 2827 292747170 292747207 6.950000e-07 65.8
28 TraesCS2B01G480800 chr5B 97.222 72 2 0 2828 2899 134923397 134923468 4.070000e-24 122.0
29 TraesCS2B01G480800 chr1D 95.775 71 3 0 2828 2898 318382809 318382879 6.800000e-22 115.0
30 TraesCS2B01G480800 chr1D 91.111 45 1 3 2783 2824 203430656 203430700 1.160000e-04 58.4
31 TraesCS2B01G480800 chr4A 96.970 66 2 0 2832 2897 454816408 454816343 8.800000e-21 111.0
32 TraesCS2B01G480800 chr7B 92.208 77 4 2 2832 2907 505750341 505750266 1.140000e-19 108.0
33 TraesCS2B01G480800 chr7D 90.476 84 2 3 2828 2910 204868588 204868666 4.090000e-19 106.0
34 TraesCS2B01G480800 chr7D 92.683 41 3 0 2784 2824 586784252 586784212 3.230000e-05 60.2
35 TraesCS2B01G480800 chr6D 93.056 72 5 0 2828 2899 38155321 38155392 4.090000e-19 106.0
36 TraesCS2B01G480800 chr6D 93.056 72 5 0 2828 2899 105560533 105560462 4.090000e-19 106.0
37 TraesCS2B01G480800 chr6D 95.000 40 2 0 2785 2824 29232288 29232327 2.500000e-06 63.9
38 TraesCS2B01G480800 chr4B 79.365 126 11 13 2784 2899 481601205 481601325 1.150000e-09 75.0
39 TraesCS2B01G480800 chr3D 93.023 43 2 1 2783 2824 522776876 522776918 8.990000e-06 62.1
40 TraesCS2B01G480800 chrUn 92.683 41 3 0 2784 2824 84293686 84293646 3.230000e-05 60.2
41 TraesCS2B01G480800 chrUn 92.683 41 3 0 2784 2824 226947011 226946971 3.230000e-05 60.2
42 TraesCS2B01G480800 chr3B 92.683 41 3 0 2784 2824 252583690 252583650 3.230000e-05 60.2


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 TraesCS2B01G480800 chr2B 679029329 679032331 3002 True 5546.000000 5546 100.000000 1 3003 1 chr2B.!!$R1 3002
1 TraesCS2B01G480800 chr2B 679696308 679697618 1310 False 1243.000000 1243 84.116000 788 2100 1 chr2B.!!$F1 1312
2 TraesCS2B01G480800 chr2B 679743830 679744411 581 False 717.000000 717 88.908000 1517 2100 1 chr2B.!!$F3 583
3 TraesCS2B01G480800 chr2B 679729837 679730529 692 False 584.000000 584 82.444000 788 1477 1 chr2B.!!$F2 689
4 TraesCS2B01G480800 chr2B 679070588 679072334 1746 True 560.666667 809 86.432667 291 2057 3 chr2B.!!$R2 1766
5 TraesCS2B01G480800 chr2D 566260980 566263758 2778 True 1722.500000 3182 87.352500 131 2794 2 chr2D.!!$R4 2663
6 TraesCS2B01G480800 chr2D 566655546 566656870 1324 True 1223.000000 1223 83.616000 790 2120 1 chr2D.!!$R3 1330
7 TraesCS2B01G480800 chr2D 566479813 566480585 772 True 494.000000 494 78.758000 1270 2057 1 chr2D.!!$R2 787
8 TraesCS2B01G480800 chr2D 558376249 558376781 532 False 462.000000 462 82.385000 1513 2056 1 chr2D.!!$F1 543
9 TraesCS2B01G480800 chr2D 566453495 566454242 747 True 444.000000 444 77.920000 1294 2057 1 chr2D.!!$R1 763
10 TraesCS2B01G480800 chr2D 566301847 566303961 2114 True 382.600000 608 86.580600 1 2057 5 chr2D.!!$R5 2056
11 TraesCS2B01G480800 chr2A 706529384 706530805 1421 True 1171.000000 1171 82.097000 720 2144 1 chr2A.!!$R1 1424
12 TraesCS2B01G480800 chr2A 706487393 706490403 3010 True 1140.666667 2861 87.595000 1 2794 3 chr2A.!!$R2 2793
13 TraesCS2B01G480800 chr2A 706510021 706511847 1826 True 501.666667 689 85.321333 80 2004 3 chr2A.!!$R3 1924

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
976 1122 0.175531 GAGGAAGCAGAGCAGAGGTC 59.824 60.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2614 3143 0.31179 CATGGATTTGGATTCGGCGG 59.688 55.0 7.21 0.0 0.0 6.13 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
108 109 4.504858 GATGCTAGTATCCCCGTATTTGG 58.495 47.826 9.51 0.00 0.00 3.28
318 349 6.183360 CCGCCTAATATAGTACTCCAGAATCC 60.183 46.154 0.00 0.00 0.00 3.01
333 368 8.717717 ACTCCAGAATCCATTAGACATTAATCA 58.282 33.333 0.00 0.00 0.00 2.57
429 471 4.214383 CGACGCGGCAATGCTCAG 62.214 66.667 14.85 0.00 0.00 3.35
430 472 3.121030 GACGCGGCAATGCTCAGT 61.121 61.111 7.34 2.32 0.00 3.41
431 473 2.669569 ACGCGGCAATGCTCAGTT 60.670 55.556 12.47 0.00 0.00 3.16
432 474 2.187599 GACGCGGCAATGCTCAGTTT 62.188 55.000 7.34 0.00 0.00 2.66
829 942 4.827087 CTCCACGCTCGCTGGCAT 62.827 66.667 0.00 0.00 0.00 4.40
879 994 1.969208 GCCTCCCGGTATATATAGGGC 59.031 57.143 16.52 7.93 43.46 5.19
904 1022 1.827789 ACCACGCACTGCCAAACAT 60.828 52.632 0.00 0.00 0.00 2.71
969 1115 2.483491 CACAGAAAAGAGGAAGCAGAGC 59.517 50.000 0.00 0.00 0.00 4.09
971 1117 2.743126 CAGAAAAGAGGAAGCAGAGCAG 59.257 50.000 0.00 0.00 0.00 4.24
972 1118 2.636893 AGAAAAGAGGAAGCAGAGCAGA 59.363 45.455 0.00 0.00 0.00 4.26
973 1119 2.766345 AAAGAGGAAGCAGAGCAGAG 57.234 50.000 0.00 0.00 0.00 3.35
974 1120 0.903942 AAGAGGAAGCAGAGCAGAGG 59.096 55.000 0.00 0.00 0.00 3.69
975 1121 0.252193 AGAGGAAGCAGAGCAGAGGT 60.252 55.000 0.00 0.00 0.00 3.85
976 1122 0.175531 GAGGAAGCAGAGCAGAGGTC 59.824 60.000 0.00 0.00 0.00 3.85
1302 1479 1.298041 GTGCGTTCGTGTTTGGTGG 60.298 57.895 0.00 0.00 0.00 4.61
1333 1510 2.203294 GCCCGTGTGGTTCCTGTT 60.203 61.111 0.00 0.00 36.04 3.16
1347 1524 4.938226 GGTTCCTGTTCGAGATGAAATTCT 59.062 41.667 0.00 0.00 38.60 2.40
1388 1576 4.280174 TCCTAGGTTAGATTATGTCCGCAC 59.720 45.833 9.08 0.00 0.00 5.34
1392 1580 4.345257 AGGTTAGATTATGTCCGCACATCT 59.655 41.667 0.00 0.00 42.66 2.90
1393 1581 5.057149 GGTTAGATTATGTCCGCACATCTT 58.943 41.667 0.00 0.00 42.66 2.40
1394 1582 5.177696 GGTTAGATTATGTCCGCACATCTTC 59.822 44.000 0.00 0.00 42.66 2.87
1476 1749 9.390795 CAGAGTTTTTGTTCTTCATGTTCATAG 57.609 33.333 0.00 0.00 0.00 2.23
1753 2040 3.371063 TCGTCTGCGTCCACCTCC 61.371 66.667 0.00 0.00 39.49 4.30
2026 2319 8.906867 TGAATGGGAAAAGATGATAGACAATTC 58.093 33.333 0.00 0.00 0.00 2.17
2071 2373 5.453567 AGTTTTTCCAGTCATTAGTTGGC 57.546 39.130 0.00 0.00 31.94 4.52
2075 2378 4.901197 TTCCAGTCATTAGTTGGCACTA 57.099 40.909 0.00 0.00 34.06 2.74
2166 2469 9.918630 CAAATCAGATATTCAAGTTGGACTTTT 57.081 29.630 2.34 0.00 36.03 2.27
2213 2537 7.413438 CCCTTCAATTCTTATCTGTTCTGTTCG 60.413 40.741 0.00 0.00 0.00 3.95
2217 2541 6.969828 ATTCTTATCTGTTCTGTTCGTTCC 57.030 37.500 0.00 0.00 0.00 3.62
2221 2545 1.000607 TCTGTTCTGTTCGTTCCCTCG 60.001 52.381 0.00 0.00 0.00 4.63
2223 2547 1.005394 TTCTGTTCGTTCCCTCGCC 60.005 57.895 0.00 0.00 0.00 5.54
2238 2562 2.033801 CCTCGCCAATTAGCAATGGAAG 59.966 50.000 0.00 0.00 39.12 3.46
2436 2924 2.684881 ACGTACGAGTACCCTGGTATTG 59.315 50.000 24.41 0.00 34.87 1.90
2519 3007 6.073494 TGTGTGGTACAAAATCACGATACAAG 60.073 38.462 0.00 0.00 44.16 3.16
2555 3084 3.902150 TCATCGATCGAGCCTTATCAAC 58.098 45.455 23.84 0.00 0.00 3.18
2571 3100 6.375736 CCTTATCAACTGGAGAGCGATATAGA 59.624 42.308 0.00 0.00 0.00 1.98
2572 3101 5.637006 ATCAACTGGAGAGCGATATAGAC 57.363 43.478 0.00 0.00 0.00 2.59
2573 3102 4.720046 TCAACTGGAGAGCGATATAGACT 58.280 43.478 0.00 0.00 0.00 3.24
2575 3104 2.817258 ACTGGAGAGCGATATAGACTGC 59.183 50.000 0.00 0.00 0.00 4.40
2576 3105 2.163412 CTGGAGAGCGATATAGACTGCC 59.837 54.545 0.00 0.00 0.00 4.85
2577 3106 1.131504 GGAGAGCGATATAGACTGCCG 59.868 57.143 0.00 0.00 0.00 5.69
2579 3108 3.755404 GCGATATAGACTGCCGCG 58.245 61.111 0.00 0.00 36.53 6.46
2581 3110 1.066114 GCGATATAGACTGCCGCGTC 61.066 60.000 4.92 0.00 36.53 5.19
2582 3111 0.454620 CGATATAGACTGCCGCGTCC 60.455 60.000 4.92 0.00 34.46 4.79
2584 3113 0.882474 ATATAGACTGCCGCGTCCTC 59.118 55.000 4.92 0.00 34.46 3.71
2656 3185 1.252215 TGCGACTGACCGTATTGGGA 61.252 55.000 0.00 0.00 44.64 4.37
2706 3235 9.551734 AGAAATTTACTCTACCGTGTAAAACTT 57.448 29.630 0.00 0.00 40.42 2.66
2794 3337 4.694037 ACTTTGCGTCCCAAAATACTACTC 59.306 41.667 0.00 0.00 42.51 2.59
2795 3338 3.255969 TGCGTCCCAAAATACTACTCC 57.744 47.619 0.00 0.00 0.00 3.85
2796 3339 2.093341 TGCGTCCCAAAATACTACTCCC 60.093 50.000 0.00 0.00 0.00 4.30
2797 3340 2.169978 GCGTCCCAAAATACTACTCCCT 59.830 50.000 0.00 0.00 0.00 4.20
2798 3341 3.740452 GCGTCCCAAAATACTACTCCCTC 60.740 52.174 0.00 0.00 0.00 4.30
2799 3342 3.705072 CGTCCCAAAATACTACTCCCTCT 59.295 47.826 0.00 0.00 0.00 3.69
2800 3343 4.441634 CGTCCCAAAATACTACTCCCTCTG 60.442 50.000 0.00 0.00 0.00 3.35
2801 3344 4.470304 GTCCCAAAATACTACTCCCTCTGT 59.530 45.833 0.00 0.00 0.00 3.41
2802 3345 5.659971 GTCCCAAAATACTACTCCCTCTGTA 59.340 44.000 0.00 0.00 0.00 2.74
2803 3346 6.155737 GTCCCAAAATACTACTCCCTCTGTAA 59.844 42.308 0.00 0.00 0.00 2.41
2804 3347 6.731919 TCCCAAAATACTACTCCCTCTGTAAA 59.268 38.462 0.00 0.00 0.00 2.01
2805 3348 7.048512 CCCAAAATACTACTCCCTCTGTAAAG 58.951 42.308 0.00 0.00 0.00 1.85
2806 3349 7.093024 CCCAAAATACTACTCCCTCTGTAAAGA 60.093 40.741 0.00 0.00 0.00 2.52
2807 3350 8.319146 CCAAAATACTACTCCCTCTGTAAAGAA 58.681 37.037 0.00 0.00 0.00 2.52
2808 3351 9.720769 CAAAATACTACTCCCTCTGTAAAGAAA 57.279 33.333 0.00 0.00 0.00 2.52
2817 3360 9.397280 ACTCCCTCTGTAAAGAAATATAAAAGC 57.603 33.333 0.00 0.00 0.00 3.51
2818 3361 8.433421 TCCCTCTGTAAAGAAATATAAAAGCG 57.567 34.615 0.00 0.00 0.00 4.68
2819 3362 8.044908 TCCCTCTGTAAAGAAATATAAAAGCGT 58.955 33.333 0.00 0.00 0.00 5.07
2820 3363 9.321562 CCCTCTGTAAAGAAATATAAAAGCGTA 57.678 33.333 0.00 0.00 0.00 4.42
2838 3381 9.517609 AAAAGCGTATAGTGTGAAGTATAAGAG 57.482 33.333 0.00 0.00 0.00 2.85
2839 3382 6.670233 AGCGTATAGTGTGAAGTATAAGAGC 58.330 40.000 0.00 0.00 0.00 4.09
2840 3383 5.564504 GCGTATAGTGTGAAGTATAAGAGCG 59.435 44.000 0.00 0.00 0.00 5.03
2841 3384 6.656945 CGTATAGTGTGAAGTATAAGAGCGT 58.343 40.000 0.00 0.00 0.00 5.07
2842 3385 7.130917 CGTATAGTGTGAAGTATAAGAGCGTT 58.869 38.462 0.00 0.00 0.00 4.84
2843 3386 7.642978 CGTATAGTGTGAAGTATAAGAGCGTTT 59.357 37.037 0.00 0.00 0.00 3.60
2844 3387 9.941664 GTATAGTGTGAAGTATAAGAGCGTTTA 57.058 33.333 0.00 0.00 0.00 2.01
2846 3389 7.154435 AGTGTGAAGTATAAGAGCGTTTAGA 57.846 36.000 0.00 0.00 0.00 2.10
2847 3390 7.773149 AGTGTGAAGTATAAGAGCGTTTAGAT 58.227 34.615 0.00 0.00 0.00 1.98
2848 3391 7.916450 AGTGTGAAGTATAAGAGCGTTTAGATC 59.084 37.037 0.00 0.00 35.01 2.75
2849 3392 7.701078 GTGTGAAGTATAAGAGCGTTTAGATCA 59.299 37.037 0.00 0.00 37.82 2.92
2850 3393 7.701078 TGTGAAGTATAAGAGCGTTTAGATCAC 59.299 37.037 0.00 0.00 37.82 3.06
2851 3394 7.916450 GTGAAGTATAAGAGCGTTTAGATCACT 59.084 37.037 0.00 0.00 37.82 3.41
2852 3395 9.117183 TGAAGTATAAGAGCGTTTAGATCACTA 57.883 33.333 0.00 0.00 37.82 2.74
2853 3396 9.947669 GAAGTATAAGAGCGTTTAGATCACTAA 57.052 33.333 0.00 0.00 37.82 2.24
2873 3416 7.393841 ACTAAACTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 37.69 4.09
2874 3417 7.828712 ACTAAACTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 37.69 2.85
2875 3418 8.305317 ACTAAACTAGTGATCTAAACGCTCTTT 58.695 33.333 0.00 0.00 37.69 2.52
2876 3419 7.964604 AAACTAGTGATCTAAACGCTCTTTT 57.035 32.000 0.00 0.00 0.00 2.27
2878 3421 9.654663 AAACTAGTGATCTAAACGCTCTTTTAT 57.345 29.630 0.00 0.00 0.00 1.40
2879 3422 9.654663 AACTAGTGATCTAAACGCTCTTTTATT 57.345 29.630 0.00 0.00 0.00 1.40
2880 3423 9.654663 ACTAGTGATCTAAACGCTCTTTTATTT 57.345 29.630 0.00 0.00 0.00 1.40
2882 3425 8.779354 AGTGATCTAAACGCTCTTTTATTTCT 57.221 30.769 0.00 0.00 0.00 2.52
2883 3426 9.220767 AGTGATCTAAACGCTCTTTTATTTCTT 57.779 29.630 0.00 0.00 0.00 2.52
2884 3427 9.827411 GTGATCTAAACGCTCTTTTATTTCTTT 57.173 29.630 0.00 0.00 0.00 2.52
2891 3434 7.365840 ACGCTCTTTTATTTCTTTACAGAGG 57.634 36.000 0.00 0.00 0.00 3.69
2892 3435 6.371825 ACGCTCTTTTATTTCTTTACAGAGGG 59.628 38.462 8.36 8.36 42.53 4.30
2893 3436 6.594159 CGCTCTTTTATTTCTTTACAGAGGGA 59.406 38.462 4.76 0.00 40.49 4.20
2894 3437 7.201565 CGCTCTTTTATTTCTTTACAGAGGGAG 60.202 40.741 4.76 0.00 40.49 4.30
2895 3438 7.608376 GCTCTTTTATTTCTTTACAGAGGGAGT 59.392 37.037 0.00 0.00 0.00 3.85
2897 3440 9.939802 TCTTTTATTTCTTTACAGAGGGAGTAC 57.060 33.333 0.00 0.00 0.00 2.73
2898 3441 9.945904 CTTTTATTTCTTTACAGAGGGAGTACT 57.054 33.333 0.00 0.00 0.00 2.73
2904 3447 9.765295 TTTCTTTACAGAGGGAGTACTAATAGT 57.235 33.333 0.00 0.00 0.00 2.12
2907 3450 9.287373 CTTTACAGAGGGAGTACTAATAGTAGG 57.713 40.741 0.00 0.00 30.12 3.18
2908 3451 8.572884 TTACAGAGGGAGTACTAATAGTAGGA 57.427 38.462 0.00 0.00 30.12 2.94
2909 3452 7.651229 ACAGAGGGAGTACTAATAGTAGGAT 57.349 40.000 0.00 0.00 30.12 3.24
2910 3453 8.059565 ACAGAGGGAGTACTAATAGTAGGATT 57.940 38.462 0.00 0.00 30.12 3.01
2911 3454 8.512813 ACAGAGGGAGTACTAATAGTAGGATTT 58.487 37.037 0.00 0.00 30.12 2.17
2912 3455 9.369672 CAGAGGGAGTACTAATAGTAGGATTTT 57.630 37.037 0.00 0.00 30.12 1.82
2913 3456 9.954992 AGAGGGAGTACTAATAGTAGGATTTTT 57.045 33.333 0.00 0.00 30.12 1.94
2935 3478 7.578458 TTTTTGGGTAGGGAATAGAAGTACT 57.422 36.000 0.00 0.00 0.00 2.73
2936 3479 7.578458 TTTTGGGTAGGGAATAGAAGTACTT 57.422 36.000 8.13 8.13 0.00 2.24
2937 3480 7.578458 TTTGGGTAGGGAATAGAAGTACTTT 57.422 36.000 10.02 2.79 0.00 2.66
2938 3481 6.555463 TGGGTAGGGAATAGAAGTACTTTG 57.445 41.667 10.02 0.00 0.00 2.77
2939 3482 6.027482 TGGGTAGGGAATAGAAGTACTTTGT 58.973 40.000 10.02 3.16 0.00 2.83
2940 3483 7.191210 TGGGTAGGGAATAGAAGTACTTTGTA 58.809 38.462 10.02 5.40 0.00 2.41
2941 3484 7.847848 TGGGTAGGGAATAGAAGTACTTTGTAT 59.152 37.037 10.02 7.50 0.00 2.29
2942 3485 9.372189 GGGTAGGGAATAGAAGTACTTTGTATA 57.628 37.037 10.02 1.83 0.00 1.47
2970 3513 8.764524 AAAAATTGCGGCAATACTTTGTATAA 57.235 26.923 26.87 0.00 32.43 0.98
2971 3514 8.764524 AAAATTGCGGCAATACTTTGTATAAA 57.235 26.923 26.87 0.00 32.43 1.40
2972 3515 8.764524 AAATTGCGGCAATACTTTGTATAAAA 57.235 26.923 26.87 0.00 32.43 1.52
2973 3516 8.940768 AATTGCGGCAATACTTTGTATAAAAT 57.059 26.923 26.87 4.90 32.43 1.82
2974 3517 8.940768 ATTGCGGCAATACTTTGTATAAAATT 57.059 26.923 25.65 0.00 31.77 1.82
2976 3519 9.856488 TTGCGGCAATACTTTGTATAAAATTAA 57.144 25.926 12.11 0.00 35.17 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
179 182 7.796054 ACTGCATCCAGAGTACTGTATATTTT 58.204 34.615 0.00 0.00 41.77 1.82
228 233 5.342806 ACGATTAAATATCATGTGGTGCG 57.657 39.130 0.00 0.00 0.00 5.34
273 303 4.024302 GCGGTGCCAAAAGGAGTATTATAC 60.024 45.833 0.00 0.00 0.00 1.47
278 309 2.868253 GCGGTGCCAAAAGGAGTAT 58.132 52.632 0.00 0.00 0.00 2.12
429 471 7.763985 CCCATCCATATTTTAGGTCACAAAAAC 59.236 37.037 0.00 0.00 0.00 2.43
430 472 7.580495 GCCCATCCATATTTTAGGTCACAAAAA 60.580 37.037 0.00 0.00 0.00 1.94
431 473 6.127196 GCCCATCCATATTTTAGGTCACAAAA 60.127 38.462 0.00 0.00 0.00 2.44
432 474 5.362430 GCCCATCCATATTTTAGGTCACAAA 59.638 40.000 0.00 0.00 0.00 2.83
904 1022 0.248289 GAAAACGGAGATCGGTGGGA 59.752 55.000 0.00 0.00 44.45 4.37
969 1115 2.564553 CTTTCTCGGCGGGACCTCTG 62.565 65.000 10.05 0.00 35.61 3.35
971 1117 2.184579 CTTTCTCGGCGGGACCTC 59.815 66.667 10.05 0.00 35.61 3.85
972 1118 3.391382 CCTTTCTCGGCGGGACCT 61.391 66.667 10.05 0.00 35.61 3.85
973 1119 4.468689 CCCTTTCTCGGCGGGACC 62.469 72.222 10.05 0.00 40.55 4.46
974 1120 2.854187 CTTCCCTTTCTCGGCGGGAC 62.854 65.000 10.05 0.00 46.29 4.46
975 1121 2.605295 TTCCCTTTCTCGGCGGGA 60.605 61.111 4.77 4.77 45.02 5.14
976 1122 2.125106 CTTCCCTTTCTCGGCGGG 60.125 66.667 7.21 2.41 39.41 6.13
1290 1467 6.372185 CGAATTTATTAACCACCAAACACGA 58.628 36.000 0.00 0.00 0.00 4.35
1292 1469 5.059955 CGCGAATTTATTAACCACCAAACAC 59.940 40.000 0.00 0.00 0.00 3.32
1302 1479 2.223089 ACACGGGCGCGAATTTATTAAC 60.223 45.455 30.98 0.00 0.00 2.01
1360 1537 7.444487 GCGGACATAATCTAACCTAGGAAATTT 59.556 37.037 17.98 1.06 0.00 1.82
1388 1576 4.442733 GCTCTTAAACCGATCGAGAAGATG 59.557 45.833 18.66 12.59 40.26 2.90
1392 1580 3.861276 TGCTCTTAAACCGATCGAGAA 57.139 42.857 18.66 3.84 0.00 2.87
1393 1581 3.380320 TCATGCTCTTAAACCGATCGAGA 59.620 43.478 18.66 9.99 0.00 4.04
1394 1582 3.706698 TCATGCTCTTAAACCGATCGAG 58.293 45.455 18.66 9.42 0.00 4.04
1476 1749 3.896648 TGAAACAAGATCAAAGACGGC 57.103 42.857 0.00 0.00 0.00 5.68
1735 2022 2.126424 GAGGTGGACGCAGACGAC 60.126 66.667 0.00 0.00 43.93 4.34
1792 2079 2.357034 GACGCCGTGCTTGAAGGA 60.357 61.111 0.00 0.00 0.00 3.36
1948 2236 0.968901 TCTTCGGCTTCTTCCCGCTA 60.969 55.000 0.00 0.00 45.19 4.26
2120 2423 8.453681 TGATTTGACCCTATGATAGTAGGAGTA 58.546 37.037 0.00 0.00 43.27 2.59
2121 2424 7.306013 TGATTTGACCCTATGATAGTAGGAGT 58.694 38.462 0.00 0.00 43.27 3.85
2122 2425 7.671819 TCTGATTTGACCCTATGATAGTAGGAG 59.328 40.741 0.00 0.00 43.27 3.69
2123 2426 7.535738 TCTGATTTGACCCTATGATAGTAGGA 58.464 38.462 0.00 0.00 43.27 2.94
2124 2427 7.782897 TCTGATTTGACCCTATGATAGTAGG 57.217 40.000 0.00 0.00 40.81 3.18
2187 2511 7.413438 CGAACAGAACAGATAAGAATTGAAGGG 60.413 40.741 0.00 0.00 0.00 3.95
2188 2512 7.118390 ACGAACAGAACAGATAAGAATTGAAGG 59.882 37.037 0.00 0.00 0.00 3.46
2201 2525 1.000607 CGAGGGAACGAACAGAACAGA 60.001 52.381 0.00 0.00 35.09 3.41
2213 2537 1.459450 TTGCTAATTGGCGAGGGAAC 58.541 50.000 9.40 0.00 34.52 3.62
2217 2541 1.679139 TCCATTGCTAATTGGCGAGG 58.321 50.000 9.79 9.18 34.52 4.63
2221 2545 4.884164 AGACTACTTCCATTGCTAATTGGC 59.116 41.667 6.88 6.88 0.00 4.52
2436 2924 2.203401 TGCGTATTTGCCACGGTATAC 58.797 47.619 0.00 0.00 39.75 1.47
2491 2979 4.130857 TCGTGATTTTGTACCACACATGT 58.869 39.130 0.00 0.00 36.90 3.21
2508 2996 3.000041 ACGTACGTACCTTGTATCGTGA 59.000 45.455 21.41 0.00 37.66 4.35
2519 3007 1.267732 CGATGAGACCACGTACGTACC 60.268 57.143 22.34 12.68 0.00 3.34
2555 3084 2.163412 GGCAGTCTATATCGCTCTCCAG 59.837 54.545 0.00 0.00 0.00 3.86
2597 3126 1.602377 GCGGCGGCAGTCTATATTTTT 59.398 47.619 9.78 0.00 39.62 1.94
2599 3128 0.602905 GGCGGCGGCAGTCTATATTT 60.603 55.000 29.41 0.00 42.47 1.40
2601 3130 2.657237 GGCGGCGGCAGTCTATAT 59.343 61.111 29.41 0.00 42.47 0.86
2611 3140 3.181169 GATTTGGATTCGGCGGCGG 62.181 63.158 31.73 13.01 0.00 6.13
2612 3141 2.327940 GATTTGGATTCGGCGGCG 59.672 61.111 27.15 27.15 0.00 6.46
2613 3142 1.455383 ATGGATTTGGATTCGGCGGC 61.455 55.000 7.21 0.00 0.00 6.53
2614 3143 0.311790 CATGGATTTGGATTCGGCGG 59.688 55.000 7.21 0.00 0.00 6.13
2656 3185 6.380079 ACCATCCACAGAAAAGACTAATCT 57.620 37.500 0.00 0.00 36.42 2.40
2706 3235 3.258123 TGCAATCTGCCTATACGATGCTA 59.742 43.478 0.00 0.00 44.23 3.49
2707 3236 2.037641 TGCAATCTGCCTATACGATGCT 59.962 45.455 0.00 0.00 44.23 3.79
2794 3337 8.209917 ACGCTTTTATATTTCTTTACAGAGGG 57.790 34.615 0.00 0.00 0.00 4.30
2812 3355 9.517609 CTCTTATACTTCACACTATACGCTTTT 57.482 33.333 0.00 0.00 0.00 2.27
2813 3356 7.648510 GCTCTTATACTTCACACTATACGCTTT 59.351 37.037 0.00 0.00 0.00 3.51
2814 3357 7.140048 GCTCTTATACTTCACACTATACGCTT 58.860 38.462 0.00 0.00 0.00 4.68
2815 3358 6.566187 CGCTCTTATACTTCACACTATACGCT 60.566 42.308 0.00 0.00 0.00 5.07
2816 3359 5.564504 CGCTCTTATACTTCACACTATACGC 59.435 44.000 0.00 0.00 0.00 4.42
2817 3360 6.656945 ACGCTCTTATACTTCACACTATACG 58.343 40.000 0.00 0.00 0.00 3.06
2818 3361 8.853469 AAACGCTCTTATACTTCACACTATAC 57.147 34.615 0.00 0.00 0.00 1.47
2820 3363 8.900781 TCTAAACGCTCTTATACTTCACACTAT 58.099 33.333 0.00 0.00 0.00 2.12
2821 3364 8.272545 TCTAAACGCTCTTATACTTCACACTA 57.727 34.615 0.00 0.00 0.00 2.74
2822 3365 7.154435 TCTAAACGCTCTTATACTTCACACT 57.846 36.000 0.00 0.00 0.00 3.55
2823 3366 7.701078 TGATCTAAACGCTCTTATACTTCACAC 59.299 37.037 0.00 0.00 0.00 3.82
2824 3367 7.701078 GTGATCTAAACGCTCTTATACTTCACA 59.299 37.037 0.00 0.00 0.00 3.58
2825 3368 7.916450 AGTGATCTAAACGCTCTTATACTTCAC 59.084 37.037 0.00 0.00 0.00 3.18
2826 3369 7.997482 AGTGATCTAAACGCTCTTATACTTCA 58.003 34.615 0.00 0.00 0.00 3.02
2827 3370 9.947669 TTAGTGATCTAAACGCTCTTATACTTC 57.052 33.333 0.00 0.00 33.79 3.01
2849 3392 7.393841 AGAGCGTTTAGATCACTAGTTTAGT 57.606 36.000 0.00 0.00 37.82 2.24
2850 3393 8.690680 AAAGAGCGTTTAGATCACTAGTTTAG 57.309 34.615 0.00 0.00 37.82 1.85
2852 3395 7.964604 AAAAGAGCGTTTAGATCACTAGTTT 57.035 32.000 0.00 0.00 37.82 2.66
2853 3396 9.654663 AATAAAAGAGCGTTTAGATCACTAGTT 57.345 29.630 0.00 0.00 37.82 2.24
2854 3397 9.654663 AAATAAAAGAGCGTTTAGATCACTAGT 57.345 29.630 0.00 0.00 37.82 2.57
2856 3399 9.871238 AGAAATAAAAGAGCGTTTAGATCACTA 57.129 29.630 0.00 0.00 37.82 2.74
2857 3400 8.779354 AGAAATAAAAGAGCGTTTAGATCACT 57.221 30.769 0.00 0.00 37.82 3.41
2858 3401 9.827411 AAAGAAATAAAAGAGCGTTTAGATCAC 57.173 29.630 0.00 0.00 37.82 3.06
2865 3408 8.290325 CCTCTGTAAAGAAATAAAAGAGCGTTT 58.710 33.333 0.00 0.00 0.00 3.60
2866 3409 7.094762 CCCTCTGTAAAGAAATAAAAGAGCGTT 60.095 37.037 0.00 0.00 0.00 4.84
2867 3410 6.371825 CCCTCTGTAAAGAAATAAAAGAGCGT 59.628 38.462 0.00 0.00 0.00 5.07
2868 3411 6.594159 TCCCTCTGTAAAGAAATAAAAGAGCG 59.406 38.462 0.00 0.00 0.00 5.03
2869 3412 7.608376 ACTCCCTCTGTAAAGAAATAAAAGAGC 59.392 37.037 0.00 0.00 0.00 4.09
2871 3414 9.939802 GTACTCCCTCTGTAAAGAAATAAAAGA 57.060 33.333 0.00 0.00 0.00 2.52
2872 3415 9.945904 AGTACTCCCTCTGTAAAGAAATAAAAG 57.054 33.333 0.00 0.00 0.00 2.27
2878 3421 9.765295 ACTATTAGTACTCCCTCTGTAAAGAAA 57.235 33.333 0.00 0.00 0.00 2.52
2881 3424 9.287373 CCTACTATTAGTACTCCCTCTGTAAAG 57.713 40.741 0.00 0.00 0.00 1.85
2882 3425 9.007494 TCCTACTATTAGTACTCCCTCTGTAAA 57.993 37.037 0.00 0.00 0.00 2.01
2883 3426 8.572884 TCCTACTATTAGTACTCCCTCTGTAA 57.427 38.462 0.00 0.00 0.00 2.41
2884 3427 8.754258 ATCCTACTATTAGTACTCCCTCTGTA 57.246 38.462 0.00 0.00 0.00 2.74
2885 3428 7.651229 ATCCTACTATTAGTACTCCCTCTGT 57.349 40.000 0.00 0.00 0.00 3.41
2886 3429 8.943594 AAATCCTACTATTAGTACTCCCTCTG 57.056 38.462 0.00 0.00 0.00 3.35
2887 3430 9.954992 AAAAATCCTACTATTAGTACTCCCTCT 57.045 33.333 0.00 0.00 0.00 3.69
2911 3454 7.578458 AGTACTTCTATTCCCTACCCAAAAA 57.422 36.000 0.00 0.00 0.00 1.94
2912 3455 7.578458 AAGTACTTCTATTCCCTACCCAAAA 57.422 36.000 1.12 0.00 0.00 2.44
2913 3456 7.017850 ACAAAGTACTTCTATTCCCTACCCAAA 59.982 37.037 8.95 0.00 0.00 3.28
2914 3457 6.502863 ACAAAGTACTTCTATTCCCTACCCAA 59.497 38.462 8.95 0.00 0.00 4.12
2915 3458 6.027482 ACAAAGTACTTCTATTCCCTACCCA 58.973 40.000 8.95 0.00 0.00 4.51
2916 3459 6.556974 ACAAAGTACTTCTATTCCCTACCC 57.443 41.667 8.95 0.00 0.00 3.69
2945 3488 8.764524 TTATACAAAGTATTGCCGCAATTTTT 57.235 26.923 23.14 19.12 40.34 1.94
2946 3489 8.764524 TTTATACAAAGTATTGCCGCAATTTT 57.235 26.923 23.14 15.33 40.34 1.82
2947 3490 8.764524 TTTTATACAAAGTATTGCCGCAATTT 57.235 26.923 23.14 10.24 40.34 1.82
2948 3491 8.940768 ATTTTATACAAAGTATTGCCGCAATT 57.059 26.923 23.14 7.37 40.34 2.32
2949 3492 8.940768 AATTTTATACAAAGTATTGCCGCAAT 57.059 26.923 21.79 21.79 40.34 3.56
2950 3493 9.856488 TTAATTTTATACAAAGTATTGCCGCAA 57.144 25.926 8.55 8.55 40.34 4.85


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

AutoCloner maintained by Alex Coulton.