Multiple sequence alignment - TraesCS1D01G372100

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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 TraesCS1D01G372100 chr1D 100.000 3530 0 0 1 3530 450144875 450141346 0.000000e+00 6519.0
1 TraesCS1D01G372100 chr1D 86.130 721 71 15 12 709 391958791 391958077 0.000000e+00 750.0
2 TraesCS1D01G372100 chr1A 94.444 2052 83 13 736 2775 545418959 545416927 0.000000e+00 3129.0
3 TraesCS1D01G372100 chr1A 87.500 752 81 10 2779 3527 545350077 545349336 0.000000e+00 856.0
4 TraesCS1D01G372100 chr1A 87.500 752 81 10 2779 3527 545415701 545414960 0.000000e+00 856.0
5 TraesCS1D01G372100 chr1A 93.182 44 2 1 707 750 545419018 545418976 2.940000e-06 63.9
6 TraesCS1D01G372100 chr1B 93.787 2028 89 18 707 2717 616771502 616769495 0.000000e+00 3013.0
7 TraesCS1D01G372100 chr1B 84.874 714 83 14 1 697 321115169 321115874 0.000000e+00 697.0
8 TraesCS1D01G372100 chr6D 83.611 1501 214 19 1041 2530 157452102 157450623 0.000000e+00 1380.0
9 TraesCS1D01G372100 chr6D 86.501 726 69 13 4 705 174296751 174296031 0.000000e+00 771.0
10 TraesCS1D01G372100 chr6D 85.216 717 75 18 4 697 352834802 352834094 0.000000e+00 708.0
11 TraesCS1D01G372100 chr2B 81.373 1428 243 15 1119 2539 105895518 105896929 0.000000e+00 1142.0
12 TraesCS1D01G372100 chr2B 83.465 127 20 1 1117 1242 780784529 780784403 2.230000e-22 117.0
13 TraesCS1D01G372100 chr2A 81.228 1433 223 21 1115 2539 69313560 69314954 0.000000e+00 1114.0
14 TraesCS1D01G372100 chr7D 77.952 1406 259 30 1120 2507 266207362 266208734 0.000000e+00 832.0
15 TraesCS1D01G372100 chr7B 77.969 1398 253 36 1123 2506 246387256 246385900 0.000000e+00 824.0
16 TraesCS1D01G372100 chr3D 86.648 719 72 12 1 697 283014991 283015707 0.000000e+00 774.0
17 TraesCS1D01G372100 chr4D 86.364 726 73 10 4 705 427612510 427611787 0.000000e+00 769.0
18 TraesCS1D01G372100 chr3B 85.455 715 84 12 4 705 695518394 695517687 0.000000e+00 726.0
19 TraesCS1D01G372100 chr5D 85.437 721 74 20 1 697 311378525 311379238 0.000000e+00 721.0
20 TraesCS1D01G372100 chr5D 84.993 713 79 17 4 697 76211493 76210790 0.000000e+00 699.0
21 TraesCS1D01G372100 chr5D 96.000 50 1 1 3105 3154 553332576 553332624 2.920000e-11 80.5
22 TraesCS1D01G372100 chr7A 78.280 1128 200 26 1395 2507 291659831 291660928 0.000000e+00 684.0
23 TraesCS1D01G372100 chr6B 84.571 525 76 3 2010 2530 280999281 280998758 1.880000e-142 516.0


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 TraesCS1D01G372100 chr1D 450141346 450144875 3529 True 6519.000000 6519 100.000000 1 3530 1 chr1D.!!$R2 3529
1 TraesCS1D01G372100 chr1D 391958077 391958791 714 True 750.000000 750 86.130000 12 709 1 chr1D.!!$R1 697
2 TraesCS1D01G372100 chr1A 545414960 545419018 4058 True 1349.633333 3129 91.708667 707 3527 3 chr1A.!!$R2 2820
3 TraesCS1D01G372100 chr1A 545349336 545350077 741 True 856.000000 856 87.500000 2779 3527 1 chr1A.!!$R1 748
4 TraesCS1D01G372100 chr1B 616769495 616771502 2007 True 3013.000000 3013 93.787000 707 2717 1 chr1B.!!$R1 2010
5 TraesCS1D01G372100 chr1B 321115169 321115874 705 False 697.000000 697 84.874000 1 697 1 chr1B.!!$F1 696
6 TraesCS1D01G372100 chr6D 157450623 157452102 1479 True 1380.000000 1380 83.611000 1041 2530 1 chr6D.!!$R1 1489
7 TraesCS1D01G372100 chr6D 174296031 174296751 720 True 771.000000 771 86.501000 4 705 1 chr6D.!!$R2 701
8 TraesCS1D01G372100 chr6D 352834094 352834802 708 True 708.000000 708 85.216000 4 697 1 chr6D.!!$R3 693
9 TraesCS1D01G372100 chr2B 105895518 105896929 1411 False 1142.000000 1142 81.373000 1119 2539 1 chr2B.!!$F1 1420
10 TraesCS1D01G372100 chr2A 69313560 69314954 1394 False 1114.000000 1114 81.228000 1115 2539 1 chr2A.!!$F1 1424
11 TraesCS1D01G372100 chr7D 266207362 266208734 1372 False 832.000000 832 77.952000 1120 2507 1 chr7D.!!$F1 1387
12 TraesCS1D01G372100 chr7B 246385900 246387256 1356 True 824.000000 824 77.969000 1123 2506 1 chr7B.!!$R1 1383
13 TraesCS1D01G372100 chr3D 283014991 283015707 716 False 774.000000 774 86.648000 1 697 1 chr3D.!!$F1 696
14 TraesCS1D01G372100 chr4D 427611787 427612510 723 True 769.000000 769 86.364000 4 705 1 chr4D.!!$R1 701
15 TraesCS1D01G372100 chr3B 695517687 695518394 707 True 726.000000 726 85.455000 4 705 1 chr3B.!!$R1 701
16 TraesCS1D01G372100 chr5D 311378525 311379238 713 False 721.000000 721 85.437000 1 697 1 chr5D.!!$F1 696
17 TraesCS1D01G372100 chr5D 76210790 76211493 703 True 699.000000 699 84.993000 4 697 1 chr5D.!!$R1 693
18 TraesCS1D01G372100 chr7A 291659831 291660928 1097 False 684.000000 684 78.280000 1395 2507 1 chr7A.!!$F1 1112
19 TraesCS1D01G372100 chr6B 280998758 280999281 523 True 516.000000 516 84.571000 2010 2530 1 chr6B.!!$R1 520

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
968 1043 1.000506 GGAACAGTACAAGCTCGGTCA 59.999 52.381 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2907 4250 0.106149 CGGTTAGACATGGGTAGGCC 59.894 60.0 0.0 0.0 0.0 5.19 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
27 29 9.670180 GATTTTCGGCTTAAAAATGTTTTATCG 57.330 29.630 8.32 1.42 36.66 2.92
170 182 9.845740 ATGATATTTACACTGTAGTTGCCATAA 57.154 29.630 0.00 0.00 0.00 1.90
247 259 9.737844 ATTTTAGTATTTTGACCATGGCAATTT 57.262 25.926 13.04 9.77 0.00 1.82
252 264 4.686191 TTTGACCATGGCAATTTCAGTT 57.314 36.364 13.04 0.00 0.00 3.16
253 265 3.663995 TGACCATGGCAATTTCAGTTG 57.336 42.857 13.04 0.00 0.00 3.16
254 266 3.229293 TGACCATGGCAATTTCAGTTGA 58.771 40.909 13.04 0.00 0.00 3.18
255 267 3.005684 TGACCATGGCAATTTCAGTTGAC 59.994 43.478 13.04 0.00 37.63 3.18
256 268 2.299867 ACCATGGCAATTTCAGTTGACC 59.700 45.455 13.04 0.00 36.24 4.02
257 269 2.299582 CCATGGCAATTTCAGTTGACCA 59.700 45.455 0.00 0.00 36.24 4.02
258 270 3.055675 CCATGGCAATTTCAGTTGACCAT 60.056 43.478 0.00 8.66 41.90 3.55
259 271 3.663995 TGGCAATTTCAGTTGACCATG 57.336 42.857 0.00 0.00 36.24 3.66
422 450 5.186409 AGCTGAAACATATCATGGCAAAGTT 59.814 36.000 0.00 0.00 33.60 2.66
465 495 6.000891 TGTGCAATAGACATGACAACTTTC 57.999 37.500 0.00 0.00 0.00 2.62
569 602 6.596106 TGAAAACGGATCTTCAATCGGATTTA 59.404 34.615 0.00 0.00 0.00 1.40
575 608 7.118390 ACGGATCTTCAATCGGATTTATCATTC 59.882 37.037 0.00 0.00 0.00 2.67
580 613 8.830580 TCTTCAATCGGATTTATCATTCAAGAC 58.169 33.333 0.00 0.00 0.00 3.01
588 621 9.158364 CGGATTTATCATTCAAGACATAAAACG 57.842 33.333 0.00 0.00 0.00 3.60
638 672 3.345414 TCACATACATGCATGCAGTGAA 58.655 40.909 30.79 20.73 35.04 3.18
653 695 5.098893 TGCAGTGAAATTTGTGTGTTGTAC 58.901 37.500 0.00 0.00 0.00 2.90
684 726 1.202806 CGGGTATTGCTCCCATCACAT 60.203 52.381 1.91 0.00 44.81 3.21
711 753 3.251571 GGAGTTATCAGCGTCTTTTCGT 58.748 45.455 0.00 0.00 0.00 3.85
713 755 4.499758 GGAGTTATCAGCGTCTTTTCGTAG 59.500 45.833 0.00 0.00 0.00 3.51
912 987 3.204827 GCCCATACGCCAGCACTG 61.205 66.667 0.00 0.00 0.00 3.66
928 1003 2.356069 GCACTGGCAATAGGAAAGTAGC 59.644 50.000 0.00 0.00 40.72 3.58
968 1043 1.000506 GGAACAGTACAAGCTCGGTCA 59.999 52.381 0.00 0.00 0.00 4.02
970 1045 1.617322 ACAGTACAAGCTCGGTCAGA 58.383 50.000 0.00 0.00 0.00 3.27
1047 1123 2.005451 CTTTTGCTCATCACCCTCTCG 58.995 52.381 0.00 0.00 0.00 4.04
1110 1186 2.509561 GGCGTCGAGAAGAAGGCC 60.510 66.667 0.00 0.00 45.44 5.19
1178 1254 4.143333 GTTCCTAGCGCTCCGGCA 62.143 66.667 16.34 2.97 38.60 5.69
1440 1516 4.735132 CGCAACCTCGCCTCCGAA 62.735 66.667 0.00 0.00 43.87 4.30
2022 2116 1.295423 GCAGGCCAAGGTCTACGAA 59.705 57.895 5.01 0.00 0.00 3.85
2145 2247 2.439701 CTCCTCCCTCACGGCGTA 60.440 66.667 14.22 0.07 0.00 4.42
2160 2265 1.208358 CGTACAGAGCGACACGGAA 59.792 57.895 0.00 0.00 0.00 4.30
2493 2598 4.665451 TGGATTTCACCACACTCATGAAT 58.335 39.130 0.00 0.00 34.77 2.57
2547 2657 3.443099 TGAAGCTACGTCTCATCCATG 57.557 47.619 0.00 0.00 0.00 3.66
2652 2771 8.508800 AATTCGAAAATTGTAATTACGCAACA 57.491 26.923 10.92 0.00 33.78 3.33
2716 2837 5.816955 TTTCTTTTTAACATGGGAAGGGG 57.183 39.130 0.00 0.00 0.00 4.79
2717 2838 4.479156 TCTTTTTAACATGGGAAGGGGT 57.521 40.909 0.00 0.00 0.00 4.95
2730 2851 1.003696 GAAGGGGTCCAGAAAGTCCTG 59.996 57.143 0.00 0.00 0.00 3.86
2755 2876 6.074142 GGAAGCTGCTTCATAAAACAAAAGTG 60.074 38.462 35.27 0.00 41.77 3.16
2760 4102 5.809562 TGCTTCATAAAACAAAAGTGTGTGG 59.190 36.000 0.00 0.00 38.27 4.17
2761 4103 5.234116 GCTTCATAAAACAAAAGTGTGTGGG 59.766 40.000 0.00 0.00 38.27 4.61
2767 4109 1.152546 AAAAGTGTGTGGGGGAGCC 60.153 57.895 0.00 0.00 0.00 4.70
2768 4110 1.655114 AAAAGTGTGTGGGGGAGCCT 61.655 55.000 0.00 0.00 0.00 4.58
2769 4111 2.069165 AAAGTGTGTGGGGGAGCCTC 62.069 60.000 0.00 0.00 0.00 4.70
2771 4113 1.612442 GTGTGTGGGGGAGCCTCTA 60.612 63.158 0.00 0.00 0.00 2.43
2776 4118 2.711547 GTGTGGGGGAGCCTCTATTAAT 59.288 50.000 0.00 0.00 0.00 1.40
2777 4119 2.979678 TGTGGGGGAGCCTCTATTAATC 59.020 50.000 0.00 0.00 0.00 1.75
2783 4125 3.648545 GGGAGCCTCTATTAATCAGGTGT 59.351 47.826 12.79 3.76 0.00 4.16
2804 4147 4.037327 TGTCTGAAAAATGGATTGCGTCAA 59.963 37.500 0.00 0.00 0.00 3.18
2826 4169 2.093075 TCACTTTTTACCACGACCACCA 60.093 45.455 0.00 0.00 0.00 4.17
2827 4170 2.683867 CACTTTTTACCACGACCACCAA 59.316 45.455 0.00 0.00 0.00 3.67
2846 4189 3.243501 CCAAATATTCATCCAACGGCCAG 60.244 47.826 2.24 0.00 0.00 4.85
2852 4195 0.606401 CATCCAACGGCCAGAACTGT 60.606 55.000 2.24 0.00 0.00 3.55
2856 4199 0.999406 CAACGGCCAGAACTGTATCG 59.001 55.000 2.24 4.63 0.00 2.92
2858 4201 2.230940 CGGCCAGAACTGTATCGCG 61.231 63.158 2.24 0.00 0.00 5.87
2864 4207 2.852413 CCAGAACTGTATCGCGTTACTG 59.148 50.000 24.13 24.13 0.00 2.74
2865 4208 2.279136 CAGAACTGTATCGCGTTACTGC 59.721 50.000 25.10 14.82 0.00 4.40
2869 4212 2.099263 ACTGTATCGCGTTACTGCTCAT 59.901 45.455 25.10 10.23 0.00 2.90
2879 4222 4.109050 CGTTACTGCTCATCTTCTTCCTC 58.891 47.826 0.00 0.00 0.00 3.71
2892 4235 3.005529 TCTTCCTCCCCTTCCTTCTTT 57.994 47.619 0.00 0.00 0.00 2.52
2895 4238 2.552367 TCCTCCCCTTCCTTCTTTCTC 58.448 52.381 0.00 0.00 0.00 2.87
2899 4242 1.348036 CCCCTTCCTTCTTTCTCGTGT 59.652 52.381 0.00 0.00 0.00 4.49
2900 4243 2.565834 CCCCTTCCTTCTTTCTCGTGTA 59.434 50.000 0.00 0.00 0.00 2.90
2903 4246 3.056465 CCTTCCTTCTTTCTCGTGTAGCT 60.056 47.826 0.00 0.00 0.00 3.32
2905 4248 2.891580 TCCTTCTTTCTCGTGTAGCTGT 59.108 45.455 0.00 0.00 0.00 4.40
2907 4250 3.430218 CCTTCTTTCTCGTGTAGCTGTTG 59.570 47.826 0.00 0.00 0.00 3.33
2917 4260 0.546598 GTAGCTGTTGGCCTACCCAT 59.453 55.000 15.00 2.95 44.89 4.00
2919 4262 1.000896 GCTGTTGGCCTACCCATGT 60.001 57.895 15.00 0.00 44.89 3.21
2920 4263 1.032114 GCTGTTGGCCTACCCATGTC 61.032 60.000 15.00 0.00 44.89 3.06
2926 4269 0.106149 GGCCTACCCATGTCTAACCG 59.894 60.000 0.00 0.00 0.00 4.44
2930 4273 2.313317 CTACCCATGTCTAACCGCCTA 58.687 52.381 0.00 0.00 0.00 3.93
2934 4277 1.068741 CCATGTCTAACCGCCTACCTC 59.931 57.143 0.00 0.00 0.00 3.85
2986 4329 2.764547 CCTCCCCTCGAACTCCCC 60.765 72.222 0.00 0.00 0.00 4.81
3001 4344 4.704833 CCCCCACTGTCGTGCTGG 62.705 72.222 0.00 0.00 39.86 4.85
3005 4348 4.969196 CACTGTCGTGCTGGCCGT 62.969 66.667 0.00 0.00 33.82 5.68
3026 4369 4.883354 CCGGCCATCCCTCCAAGC 62.883 72.222 2.24 0.00 0.00 4.01
3045 4388 4.796231 CCGCCGAACAGACTCCGG 62.796 72.222 0.00 0.00 45.51 5.14
3056 4399 4.779733 ACTCCGGCGATCCCCTGT 62.780 66.667 9.30 0.00 0.00 4.00
3063 4406 2.808206 GCGATCCCCTGTACCCCTG 61.808 68.421 0.00 0.00 0.00 4.45
3071 4414 1.770518 CTGTACCCCTGGATCCCCC 60.771 68.421 9.90 0.00 0.00 5.40
3072 4415 2.375173 GTACCCCTGGATCCCCCA 59.625 66.667 9.90 0.00 44.25 4.96
3078 4421 4.455137 CTGGATCCCCCACCCCCT 62.455 72.222 9.90 0.00 40.82 4.79
3079 4422 2.967612 TGGATCCCCCACCCCCTA 60.968 66.667 9.90 0.00 40.82 3.53
3080 4423 2.379365 GGATCCCCCACCCCCTAA 59.621 66.667 0.00 0.00 34.14 2.69
3081 4424 1.774631 GGATCCCCCACCCCCTAAG 60.775 68.421 0.00 0.00 34.14 2.18
3107 4450 4.846940 AGATAATAGGTCCATGTCTTCCCC 59.153 45.833 0.00 0.00 0.00 4.81
3108 4451 2.897823 ATAGGTCCATGTCTTCCCCT 57.102 50.000 0.00 0.00 0.00 4.79
3110 4453 2.661176 AGGTCCATGTCTTCCCCTTA 57.339 50.000 0.00 0.00 0.00 2.69
3116 4461 5.221742 GGTCCATGTCTTCCCCTTAAGATAG 60.222 48.000 3.36 0.00 37.78 2.08
3143 4488 1.309688 GCCATGGCTTCCCCCTAAA 59.690 57.895 29.98 0.00 38.26 1.85
3152 4497 5.232347 TGGCTTCCCCCTAAAATAGATAGT 58.768 41.667 0.00 0.00 0.00 2.12
3154 4499 5.004448 GCTTCCCCCTAAAATAGATAGTGC 58.996 45.833 0.00 0.00 0.00 4.40
3157 4502 3.326880 CCCCCTAAAATAGATAGTGCGGT 59.673 47.826 0.00 0.00 0.00 5.68
3163 4508 7.170998 CCCTAAAATAGATAGTGCGGTTACTTG 59.829 40.741 0.00 0.00 32.19 3.16
3170 4515 1.414919 AGTGCGGTTACTTGTTCTCCA 59.585 47.619 0.00 0.00 0.00 3.86
3190 4535 3.505680 CCATCTATGTCTCTCCTTCTCCG 59.494 52.174 0.00 0.00 0.00 4.63
3221 4566 6.472887 TCGGGATGAACTAAGAAAAAGTGAT 58.527 36.000 0.00 0.00 0.00 3.06
3225 4570 7.281100 GGGATGAACTAAGAAAAAGTGATCGAT 59.719 37.037 0.00 0.00 0.00 3.59
3261 4606 5.435686 TCAGGTGCCTGATAAATAACAGT 57.564 39.130 16.28 0.00 46.80 3.55
3263 4608 6.346096 TCAGGTGCCTGATAAATAACAGTAC 58.654 40.000 16.28 0.00 46.80 2.73
3265 4610 5.190925 AGGTGCCTGATAAATAACAGTACCA 59.809 40.000 16.42 3.36 39.57 3.25
3268 4613 7.094118 GGTGCCTGATAAATAACAGTACCAAAA 60.094 37.037 0.00 0.00 38.32 2.44
3280 4625 5.108517 ACAGTACCAAAATTTGTGCAGTTG 58.891 37.500 4.92 0.00 0.00 3.16
3284 4629 2.545106 CCAAAATTTGTGCAGTTGAGGC 59.455 45.455 4.92 0.00 0.00 4.70
3301 4646 1.079888 GCAATTTCACCGGGCCTTG 60.080 57.895 6.32 3.26 0.00 3.61
3322 4667 3.754766 GGAGACGGGGTAATGTGTC 57.245 57.895 0.00 0.00 0.00 3.67
3323 4668 0.179119 GGAGACGGGGTAATGTGTCG 60.179 60.000 0.00 0.00 36.49 4.35
3327 4672 3.199891 GGGGTAATGTGTCGCCGC 61.200 66.667 0.00 0.00 0.00 6.53
3331 4676 1.296056 GGTAATGTGTCGCCGCTGTT 61.296 55.000 0.00 0.00 0.00 3.16
3342 4687 0.179189 GCCGCTGTTGAAGGAATTCG 60.179 55.000 0.00 0.00 0.00 3.34
3359 4704 1.970092 TCGTGTTTGTAGGTTTGGGG 58.030 50.000 0.00 0.00 0.00 4.96
3361 4706 1.335496 CGTGTTTGTAGGTTTGGGGTG 59.665 52.381 0.00 0.00 0.00 4.61
3362 4707 1.067974 GTGTTTGTAGGTTTGGGGTGC 59.932 52.381 0.00 0.00 0.00 5.01
3363 4708 1.342076 TGTTTGTAGGTTTGGGGTGCA 60.342 47.619 0.00 0.00 0.00 4.57
3374 4719 3.443045 GGGTGCAGGTTGCCGATG 61.443 66.667 0.00 0.00 44.23 3.84
3388 4733 1.506493 CCGATGCTAGAGTTCATGGC 58.494 55.000 0.00 0.00 0.00 4.40
3405 4750 2.726821 TGGCTGCAATTTAGAGGGAAG 58.273 47.619 0.50 0.00 0.00 3.46
3421 4766 2.701163 GAAGGCTAGGGCGATGACGG 62.701 65.000 0.00 0.00 39.81 4.79
3429 4774 3.485110 GCGATGACGGCATGACAA 58.515 55.556 9.52 0.00 40.15 3.18
3469 4814 2.978010 CAGGTGGTGGTGTTCCGC 60.978 66.667 0.00 0.00 42.95 5.54
3492 4837 4.393990 CCGGCGTAGGTTAAAAGAGAAAAT 59.606 41.667 6.01 0.00 0.00 1.82
3493 4838 5.106436 CCGGCGTAGGTTAAAAGAGAAAATT 60.106 40.000 6.01 0.00 0.00 1.82
3528 4873 7.615582 TCTTAAATGCATACTTCAAGACTGG 57.384 36.000 0.00 0.00 0.00 4.00
3529 4874 7.168219 TCTTAAATGCATACTTCAAGACTGGT 58.832 34.615 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 84 4.747605 GGGATCTACTTTTGAAGATCTCGC 59.252 45.833 11.05 0.00 37.77 5.03
130 142 9.311916 GTGTAAATATCATAGCAATTTTTGGCA 57.688 29.630 0.00 0.00 0.00 4.92
149 161 7.938140 ACATTATGGCAACTACAGTGTAAAT 57.062 32.000 4.21 0.00 37.61 1.40
170 182 6.873076 CCACATGGCAATTTTAGTGTAAACAT 59.127 34.615 0.00 0.00 0.00 2.71
318 336 3.134574 AGACTTGCCACGACCATAAAA 57.865 42.857 0.00 0.00 0.00 1.52
328 347 7.306213 GGAAATTAAGAAACTAGACTTGCCAC 58.694 38.462 0.00 0.00 0.00 5.01
422 450 6.047870 GCACATGAATTGCCATGGTATTTAA 58.952 36.000 14.67 5.26 46.06 1.52
508 541 5.093457 TCGTGACGAGATCATTGAAACTAC 58.907 41.667 2.39 0.00 40.28 2.73
518 551 3.801114 AAATCCATCGTGACGAGATCA 57.199 42.857 14.71 0.00 39.91 2.92
623 657 3.743911 CACAAATTTCACTGCATGCATGT 59.256 39.130 26.79 16.78 0.00 3.21
638 672 3.371591 ACACGTCGTACAACACACAAATT 59.628 39.130 0.00 0.00 0.00 1.82
653 695 3.652539 AATACCCGCCCACACGTCG 62.653 63.158 0.00 0.00 0.00 5.12
669 711 2.519771 ACACATGTGATGGGAGCAAT 57.480 45.000 31.94 2.44 37.07 3.56
684 726 0.973632 ACGCTGATAACTCCCACACA 59.026 50.000 0.00 0.00 0.00 3.72
692 734 5.056894 ACTACGAAAAGACGCTGATAACT 57.943 39.130 0.00 0.00 36.70 2.24
711 753 6.117975 ACGGGAAAGAATTGACCTTAACTA 57.882 37.500 0.00 0.00 0.00 2.24
713 755 6.168389 TCTACGGGAAAGAATTGACCTTAAC 58.832 40.000 0.00 0.00 0.00 2.01
912 987 4.745620 CGAGTTAGCTACTTTCCTATTGCC 59.254 45.833 0.00 0.00 37.17 4.52
914 989 6.196724 CGTTCGAGTTAGCTACTTTCCTATTG 59.803 42.308 0.00 0.00 37.17 1.90
915 990 6.094603 TCGTTCGAGTTAGCTACTTTCCTATT 59.905 38.462 0.00 0.00 37.17 1.73
916 991 5.587844 TCGTTCGAGTTAGCTACTTTCCTAT 59.412 40.000 0.00 0.00 37.17 2.57
928 1003 2.345641 CCAGTGCAATCGTTCGAGTTAG 59.654 50.000 0.00 0.00 0.00 2.34
959 1034 1.964223 TGAGTTTCTTCTGACCGAGCT 59.036 47.619 0.00 0.00 0.00 4.09
968 1043 5.874261 GCTCAAGCTATTCTGAGTTTCTTCT 59.126 40.000 13.34 0.00 38.21 2.85
1029 1105 0.391661 GCGAGAGGGTGATGAGCAAA 60.392 55.000 0.00 0.00 0.00 3.68
1110 1186 2.732619 GGGGAGCTCCTTACCGGTG 61.733 68.421 31.36 0.00 35.95 4.94
1178 1254 2.357569 GGCTCAAGGTGGAAGATGGATT 60.358 50.000 0.00 0.00 0.00 3.01
2022 2116 2.654079 CGGCTTGCTCCTGACCTCT 61.654 63.158 0.00 0.00 0.00 3.69
2145 2247 0.732880 CGATTTCCGTGTCGCTCTGT 60.733 55.000 0.00 0.00 0.00 3.41
2160 2265 3.081409 ACCCTGTAGCCGCCGATT 61.081 61.111 0.00 0.00 0.00 3.34
2250 2355 4.831307 CGCTCCGGTCGGAACTCG 62.831 72.222 13.36 12.33 44.66 4.18
2484 2589 3.071602 CACGGAGGGGATTATTCATGAGT 59.928 47.826 0.00 0.00 0.00 3.41
2493 2598 1.518774 GCGAACACGGAGGGGATTA 59.481 57.895 0.00 0.00 0.00 1.75
2597 2707 2.228822 GACACCGCATCATGGACTTTTT 59.771 45.455 0.00 0.00 0.00 1.94
2598 2708 1.812571 GACACCGCATCATGGACTTTT 59.187 47.619 0.00 0.00 0.00 2.27
2599 2709 1.003580 AGACACCGCATCATGGACTTT 59.996 47.619 0.00 0.00 0.00 2.66
2661 2780 7.015682 TGGTTGTTTAAGGAATAGCAAATCCAA 59.984 33.333 4.75 0.00 38.23 3.53
2696 2817 4.412843 GACCCCTTCCCATGTTAAAAAGA 58.587 43.478 0.00 0.00 0.00 2.52
2697 2818 3.513912 GGACCCCTTCCCATGTTAAAAAG 59.486 47.826 0.00 0.00 38.70 2.27
2707 2828 0.402861 ACTTTCTGGACCCCTTCCCA 60.403 55.000 0.00 0.00 45.17 4.37
2730 2851 5.985530 ACTTTTGTTTTATGAAGCAGCTTCC 59.014 36.000 28.73 14.69 39.51 3.46
2734 2855 5.519927 ACACACTTTTGTTTTATGAAGCAGC 59.480 36.000 0.00 0.00 31.66 5.25
2755 2876 1.802553 TAATAGAGGCTCCCCCACAC 58.197 55.000 11.71 0.00 35.39 3.82
2760 4102 3.008485 CACCTGATTAATAGAGGCTCCCC 59.992 52.174 11.71 0.00 0.00 4.81
2761 4103 3.648545 ACACCTGATTAATAGAGGCTCCC 59.351 47.826 11.71 0.00 0.00 4.30
2776 4118 4.022068 GCAATCCATTTTTCAGACACCTGA 60.022 41.667 0.00 0.00 46.95 3.86
2777 4119 4.240096 GCAATCCATTTTTCAGACACCTG 58.760 43.478 0.00 0.00 41.74 4.00
2783 4125 4.844998 TTGACGCAATCCATTTTTCAGA 57.155 36.364 0.00 0.00 0.00 3.27
2795 4138 5.219633 GTGGTAAAAAGTGATTGACGCAAT 58.780 37.500 5.01 5.01 36.72 3.56
2804 4147 3.143728 GGTGGTCGTGGTAAAAAGTGAT 58.856 45.455 0.00 0.00 0.00 3.06
2826 4169 3.897239 TCTGGCCGTTGGATGAATATTT 58.103 40.909 0.00 0.00 0.00 1.40
2827 4170 3.576078 TCTGGCCGTTGGATGAATATT 57.424 42.857 0.00 0.00 0.00 1.28
2846 4189 2.527100 AGCAGTAACGCGATACAGTTC 58.473 47.619 25.52 12.49 36.85 3.01
2852 4195 3.315470 AGAAGATGAGCAGTAACGCGATA 59.685 43.478 15.93 0.90 36.85 2.92
2856 4199 2.605366 GGAAGAAGATGAGCAGTAACGC 59.395 50.000 0.00 0.00 0.00 4.84
2858 4201 4.438148 GGAGGAAGAAGATGAGCAGTAAC 58.562 47.826 0.00 0.00 0.00 2.50
2864 4207 1.506025 AGGGGAGGAAGAAGATGAGC 58.494 55.000 0.00 0.00 0.00 4.26
2865 4208 2.437651 GGAAGGGGAGGAAGAAGATGAG 59.562 54.545 0.00 0.00 0.00 2.90
2869 4212 2.114506 AGAAGGAAGGGGAGGAAGAAGA 59.885 50.000 0.00 0.00 0.00 2.87
2879 4222 1.348036 ACACGAGAAAGAAGGAAGGGG 59.652 52.381 0.00 0.00 0.00 4.79
2892 4235 1.185618 AGGCCAACAGCTACACGAGA 61.186 55.000 5.01 0.00 43.05 4.04
2895 4238 0.739813 GGTAGGCCAACAGCTACACG 60.740 60.000 5.01 0.00 43.05 4.49
2899 4242 0.546122 CATGGGTAGGCCAACAGCTA 59.454 55.000 5.01 0.00 43.05 3.32
2900 4243 1.304282 CATGGGTAGGCCAACAGCT 59.696 57.895 5.01 0.00 43.05 4.24
2903 4246 1.959710 TAGACATGGGTAGGCCAACA 58.040 50.000 5.01 0.00 36.17 3.33
2905 4248 1.562475 GGTTAGACATGGGTAGGCCAA 59.438 52.381 5.01 0.00 36.17 4.52
2907 4250 0.106149 CGGTTAGACATGGGTAGGCC 59.894 60.000 0.00 0.00 0.00 5.19
2917 4260 1.471119 CAGAGGTAGGCGGTTAGACA 58.529 55.000 0.00 0.00 0.00 3.41
2919 4262 1.041447 GGCAGAGGTAGGCGGTTAGA 61.041 60.000 0.00 0.00 0.00 2.10
2920 4263 1.442148 GGCAGAGGTAGGCGGTTAG 59.558 63.158 0.00 0.00 0.00 2.34
2967 4310 3.471806 GGAGTTCGAGGGGAGGGC 61.472 72.222 0.00 0.00 0.00 5.19
3012 4355 4.529731 GGGGCTTGGAGGGATGGC 62.530 72.222 0.00 0.00 0.00 4.40
3022 4365 4.697756 TCTGTTCGGCGGGGCTTG 62.698 66.667 7.21 0.00 0.00 4.01
3026 4369 4.452733 GGAGTCTGTTCGGCGGGG 62.453 72.222 7.21 0.00 0.00 5.73
3034 4377 2.722201 GGGATCGCCGGAGTCTGTT 61.722 63.158 5.05 0.00 33.83 3.16
3045 4388 2.446036 AGGGGTACAGGGGATCGC 60.446 66.667 0.06 0.06 0.00 4.58
3063 4406 1.774631 CTTAGGGGGTGGGGGATCC 60.775 68.421 1.92 1.92 0.00 3.36
3071 4414 6.612049 GGACCTATTATCTATCTTAGGGGGTG 59.388 46.154 0.00 0.00 36.36 4.61
3072 4415 6.282107 TGGACCTATTATCTATCTTAGGGGGT 59.718 42.308 0.00 0.00 36.36 4.95
3076 4419 9.707957 AGACATGGACCTATTATCTATCTTAGG 57.292 37.037 0.00 0.00 37.75 2.69
3079 4422 9.041354 GGAAGACATGGACCTATTATCTATCTT 57.959 37.037 0.00 0.00 0.00 2.40
3080 4423 7.621683 GGGAAGACATGGACCTATTATCTATCT 59.378 40.741 0.00 0.00 0.00 1.98
3081 4424 7.147637 GGGGAAGACATGGACCTATTATCTATC 60.148 44.444 0.00 0.00 0.00 2.08
3107 4450 6.125029 CCATGGCCCCATTATCTATCTTAAG 58.875 44.000 0.00 0.00 33.90 1.85
3108 4451 5.575571 GCCATGGCCCCATTATCTATCTTAA 60.576 44.000 27.24 0.00 33.90 1.85
3110 4453 3.309410 GCCATGGCCCCATTATCTATCTT 60.309 47.826 27.24 0.00 33.90 2.40
3116 4461 1.260544 GAAGCCATGGCCCCATTATC 58.739 55.000 33.14 15.37 43.17 1.75
3143 4488 6.875076 AGAACAAGTAACCGCACTATCTATT 58.125 36.000 0.00 0.00 0.00 1.73
3152 4497 2.301870 AGATGGAGAACAAGTAACCGCA 59.698 45.455 0.00 0.00 0.00 5.69
3154 4499 5.661458 ACATAGATGGAGAACAAGTAACCG 58.339 41.667 0.00 0.00 0.00 4.44
3157 4502 7.068839 GGAGAGACATAGATGGAGAACAAGTAA 59.931 40.741 0.00 0.00 0.00 2.24
3163 4508 5.833131 AGAAGGAGAGACATAGATGGAGAAC 59.167 44.000 0.00 0.00 0.00 3.01
3170 4515 3.761897 CCGGAGAAGGAGAGACATAGAT 58.238 50.000 0.00 0.00 0.00 1.98
3190 4535 1.735376 TAGTTCATCCCGAGCTCGCC 61.735 60.000 30.49 10.73 36.46 5.54
3261 4606 4.739137 GCCTCAACTGCACAAATTTTGGTA 60.739 41.667 13.42 2.09 34.12 3.25
3263 4608 2.545106 GCCTCAACTGCACAAATTTTGG 59.455 45.455 13.42 4.11 34.12 3.28
3265 4610 3.540314 TGCCTCAACTGCACAAATTTT 57.460 38.095 0.00 0.00 32.85 1.82
3268 4613 3.756933 AATTGCCTCAACTGCACAAAT 57.243 38.095 0.00 0.00 38.72 2.32
3275 4620 1.068333 CCGGTGAAATTGCCTCAACTG 60.068 52.381 0.00 0.00 0.00 3.16
3280 4625 2.710902 GGCCCGGTGAAATTGCCTC 61.711 63.158 8.24 0.00 39.05 4.70
3284 4629 1.079888 GCAAGGCCCGGTGAAATTG 60.080 57.895 0.00 0.00 0.00 2.32
3317 4662 2.202946 TTCAACAGCGGCGACACA 60.203 55.556 12.98 0.00 0.00 3.72
3320 4665 1.298859 ATTCCTTCAACAGCGGCGAC 61.299 55.000 12.98 1.23 0.00 5.19
3322 4667 0.179189 GAATTCCTTCAACAGCGGCG 60.179 55.000 0.51 0.51 0.00 6.46
3323 4668 0.179189 CGAATTCCTTCAACAGCGGC 60.179 55.000 0.00 0.00 0.00 6.53
3327 4672 4.920376 ACAAACACGAATTCCTTCAACAG 58.080 39.130 0.00 0.00 0.00 3.16
3331 4676 4.710324 ACCTACAAACACGAATTCCTTCA 58.290 39.130 0.00 0.00 0.00 3.02
3342 4687 1.067974 GCACCCCAAACCTACAAACAC 59.932 52.381 0.00 0.00 0.00 3.32
3361 4706 1.153369 TCTAGCATCGGCAACCTGC 60.153 57.895 0.00 0.00 44.61 4.85
3362 4707 0.176680 ACTCTAGCATCGGCAACCTG 59.823 55.000 0.00 0.00 44.61 4.00
3363 4708 0.905357 AACTCTAGCATCGGCAACCT 59.095 50.000 0.00 0.00 44.61 3.50
3374 4719 1.742761 TTGCAGCCATGAACTCTAGC 58.257 50.000 0.00 0.00 0.00 3.42
3388 4733 3.010200 AGCCTTCCCTCTAAATTGCAG 57.990 47.619 0.00 0.00 0.00 4.41
3405 4750 4.971125 GCCGTCATCGCCCTAGCC 62.971 72.222 0.00 0.00 34.57 3.93
3421 4766 1.925946 GCGTTGTCACCTTTGTCATGC 60.926 52.381 0.00 0.00 0.00 4.06
3426 4771 0.107410 TCTGGCGTTGTCACCTTTGT 60.107 50.000 0.00 0.00 0.00 2.83
3429 4774 0.606401 CCATCTGGCGTTGTCACCTT 60.606 55.000 0.00 0.00 0.00 3.50
3451 4796 2.978010 CGGAACACCACCACCTGC 60.978 66.667 0.00 0.00 0.00 4.85
3469 4814 2.660189 TCTCTTTTAACCTACGCCGG 57.340 50.000 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.