Multiple sequence alignment - TraesCS3D01G189000

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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 TraesCS3D01G189000 chr3D 100.000 2834 0 0 1 2834 176528140 176525307 0.000000e+00 5234.0
1 TraesCS3D01G189000 chr3D 96.503 143 4 1 2692 2834 273984660 273984519 4.720000e-58 235.0
2 TraesCS3D01G189000 chr3A 92.610 1962 110 15 733 2691 216466964 216465035 0.000000e+00 2787.0
3 TraesCS3D01G189000 chr3A 94.040 151 5 4 2684 2834 400335281 400335427 2.840000e-55 226.0
4 TraesCS3D01G189000 chr3B 97.352 1095 26 2 951 2045 255706466 255705375 0.000000e+00 1858.0
5 TraesCS3D01G189000 chr3B 89.185 638 57 10 2044 2676 255699552 255698922 0.000000e+00 785.0
6 TraesCS3D01G189000 chr3B 90.000 130 7 2 764 892 255706949 255706825 2.260000e-36 163.0
7 TraesCS3D01G189000 chr1A 88.921 686 52 6 1 682 16305249 16304584 0.000000e+00 824.0
8 TraesCS3D01G189000 chr2A 94.206 535 30 1 1 535 612308929 612308396 0.000000e+00 815.0
9 TraesCS3D01G189000 chr2A 88.785 107 12 0 574 680 612308208 612308102 6.370000e-27 132.0
10 TraesCS3D01G189000 chr4D 86.152 751 82 14 1 733 72125644 72124898 0.000000e+00 791.0
11 TraesCS3D01G189000 chr4D 95.333 150 4 3 2685 2834 281108734 281108880 4.720000e-58 235.0
12 TraesCS3D01G189000 chr4D 95.270 148 6 1 2688 2834 268606387 268606240 1.700000e-57 233.0
13 TraesCS3D01G189000 chr5B 86.735 686 78 9 7 682 28673179 28673861 0.000000e+00 750.0
14 TraesCS3D01G189000 chr5B 86.337 505 54 11 42 537 29707855 29707357 1.160000e-148 536.0
15 TraesCS3D01G189000 chr5B 97.872 47 1 0 1 47 63550840 63550794 6.510000e-12 82.4
16 TraesCS3D01G189000 chr1B 78.151 595 86 20 120 679 590416003 590415418 3.500000e-89 339.0
17 TraesCS3D01G189000 chr6D 95.333 150 5 2 2685 2834 326599981 326600128 1.310000e-58 237.0
18 TraesCS3D01G189000 chr6D 90.385 52 5 0 682 733 4399077 4399128 5.070000e-08 69.4
19 TraesCS3D01G189000 chr2D 95.833 144 6 0 2691 2834 251021593 251021736 1.700000e-57 233.0
20 TraesCS3D01G189000 chr2D 94.667 150 6 2 2685 2834 109520720 109520867 6.110000e-57 231.0
21 TraesCS3D01G189000 chr1D 95.833 144 6 0 2691 2834 168535265 168535408 1.700000e-57 233.0
22 TraesCS3D01G189000 chr7B 95.139 144 6 1 2692 2834 337939511 337939368 2.840000e-55 226.0
23 TraesCS3D01G189000 chr7D 86.538 52 7 0 682 733 532376589 532376640 1.100000e-04 58.4


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 TraesCS3D01G189000 chr3D 176525307 176528140 2833 True 5234.0 5234 100.0000 1 2834 1 chr3D.!!$R1 2833
1 TraesCS3D01G189000 chr3A 216465035 216466964 1929 True 2787.0 2787 92.6100 733 2691 1 chr3A.!!$R1 1958
2 TraesCS3D01G189000 chr3B 255705375 255706949 1574 True 1010.5 1858 93.6760 764 2045 2 chr3B.!!$R2 1281
3 TraesCS3D01G189000 chr3B 255698922 255699552 630 True 785.0 785 89.1850 2044 2676 1 chr3B.!!$R1 632
4 TraesCS3D01G189000 chr1A 16304584 16305249 665 True 824.0 824 88.9210 1 682 1 chr1A.!!$R1 681
5 TraesCS3D01G189000 chr2A 612308102 612308929 827 True 473.5 815 91.4955 1 680 2 chr2A.!!$R1 679
6 TraesCS3D01G189000 chr4D 72124898 72125644 746 True 791.0 791 86.1520 1 733 1 chr4D.!!$R1 732
7 TraesCS3D01G189000 chr5B 28673179 28673861 682 False 750.0 750 86.7350 7 682 1 chr5B.!!$F1 675
8 TraesCS3D01G189000 chr1B 590415418 590416003 585 True 339.0 339 78.1510 120 679 1 chr1B.!!$R1 559

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
851 1039 0.326595 TTTCACGCAGGGCCAATAGA 59.673 50.0 6.18 0.0 0.0 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2512 3003 0.321996 GAGGGGAGGCGGATATTGAC 59.678 60.0 0.0 0.0 0.0 3.18 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
66 69 3.689347 TGGAACTAGTAAGTGTCGGCTA 58.311 45.455 0.00 0.00 35.62 3.93
128 131 2.813754 CGGAGAGAAAATGCTTCAACCA 59.186 45.455 0.00 0.00 0.00 3.67
195 200 4.379302 AGAGGAAAAGATTCAAGTGGCT 57.621 40.909 0.00 0.00 37.29 4.75
276 285 2.892852 TGATGGAAAAGCTTCAACCAGG 59.107 45.455 18.92 0.00 34.08 4.45
293 302 0.701147 AGGGGGAGGAAAAGCTTCAG 59.299 55.000 0.00 0.00 32.75 3.02
346 356 2.702270 AAAGCTTCAACCAGGGGAAT 57.298 45.000 0.00 0.00 0.00 3.01
457 467 2.289631 TGGTGAAACATGAGATGCGTCT 60.290 45.455 8.55 8.55 39.98 4.18
459 469 2.738846 GTGAAACATGAGATGCGTCTGT 59.261 45.455 14.59 3.04 36.32 3.41
586 755 2.324014 ACCTGTTGCGAGGTCTGCAA 62.324 55.000 0.00 0.00 43.33 4.08
620 790 0.892755 CGGTGGTGCAGGAACTACTA 59.107 55.000 0.00 0.00 36.02 1.82
665 837 1.215382 CTCGCGATGGTGGAAGACA 59.785 57.895 10.36 0.00 0.00 3.41
694 881 1.002624 GGGACAATCAGGCGGTTGA 60.003 57.895 8.85 0.00 0.00 3.18
739 926 2.281208 CGACCGGCCCACTTTCAA 60.281 61.111 0.00 0.00 0.00 2.69
744 931 0.527565 CCGGCCCACTTTCAAGATTG 59.472 55.000 0.00 0.00 0.00 2.67
750 937 2.029649 CCCACTTTCAAGATTGCACTGG 60.030 50.000 0.00 0.00 0.00 4.00
777 964 4.622220 GCCCCGATTAACTGTCTTCTGTTA 60.622 45.833 0.00 0.00 37.09 2.41
786 973 3.190874 CTGTCTTCTGTTATTCGGGCTC 58.809 50.000 0.00 0.00 0.00 4.70
789 976 3.619038 GTCTTCTGTTATTCGGGCTCAAG 59.381 47.826 0.00 0.00 0.00 3.02
826 1013 1.323412 AACAACATTTACAGGCGCCA 58.677 45.000 31.54 7.75 0.00 5.69
827 1014 0.881118 ACAACATTTACAGGCGCCAG 59.119 50.000 31.54 24.99 0.00 4.85
850 1038 1.173043 TTTTCACGCAGGGCCAATAG 58.827 50.000 6.18 0.00 0.00 1.73
851 1039 0.326595 TTTCACGCAGGGCCAATAGA 59.673 50.000 6.18 0.00 0.00 1.98
852 1040 0.392461 TTCACGCAGGGCCAATAGAC 60.392 55.000 6.18 0.00 0.00 2.59
853 1041 1.819632 CACGCAGGGCCAATAGACC 60.820 63.158 6.18 0.00 0.00 3.85
1362 1850 3.195002 CGGTCGCGCATCACCATT 61.195 61.111 17.67 0.00 32.33 3.16
1892 2380 8.425577 TCTCTTCGATTTGTTTTATCATCTCC 57.574 34.615 0.00 0.00 0.00 3.71
1893 2381 7.495934 TCTCTTCGATTTGTTTTATCATCTCCC 59.504 37.037 0.00 0.00 0.00 4.30
1913 2401 2.648059 CCCCAGCCTTCTCTGTTTATG 58.352 52.381 0.00 0.00 32.32 1.90
1938 2426 7.434013 TGTTACGTATGTGTGCATAGATTGTAG 59.566 37.037 0.00 0.00 38.17 2.74
2010 2498 8.071122 TGTAGCAAAATGTGAAATTTAACTGC 57.929 30.769 7.22 8.12 0.00 4.40
2035 2523 7.439655 GCAAATTGATAGAATAGGAGTTCTCGT 59.560 37.037 0.00 0.90 39.15 4.18
2133 2621 4.743558 CGACGTCATGCGCAAATT 57.256 50.000 17.11 0.00 46.11 1.82
2151 2639 0.465460 TTTCCACACACACCTCTGCC 60.465 55.000 0.00 0.00 0.00 4.85
2179 2667 3.143728 TCCATCATGGAGCAATCATTCG 58.856 45.455 0.66 0.00 42.67 3.34
2256 2744 6.373759 ACATTTCCCCTACCTATCCATTTTC 58.626 40.000 0.00 0.00 0.00 2.29
2306 2795 0.318614 TTTTAAGCACAAGCCGCAGC 60.319 50.000 0.00 0.00 43.56 5.25
2326 2816 1.315257 GCGCCCTGGAATGTCATGTT 61.315 55.000 0.00 0.00 0.00 2.71
2333 2823 3.559811 CCTGGAATGTCATGTTGTCCTCA 60.560 47.826 3.50 0.00 0.00 3.86
2350 2840 2.928396 ACCGACCACCTCCCCTTG 60.928 66.667 0.00 0.00 0.00 3.61
2379 2870 2.835431 CTCCAGATCCGGTCGCCT 60.835 66.667 0.00 0.00 0.00 5.52
2421 2912 1.610624 GCAAGACCCCGATCTTTGTCA 60.611 52.381 7.74 0.00 36.78 3.58
2426 2917 1.079127 CCCGATCTTTGTCACCGCT 60.079 57.895 0.00 0.00 0.00 5.52
2497 2988 1.522569 GGCTGAGACCACGCCTATT 59.477 57.895 0.00 0.00 40.62 1.73
2499 2990 0.175760 GCTGAGACCACGCCTATTCA 59.824 55.000 0.00 0.00 0.00 2.57
2504 2995 1.222115 GACCACGCCTATTCATCGCC 61.222 60.000 0.00 0.00 0.00 5.54
2512 3003 2.744202 GCCTATTCATCGCCACCAATAG 59.256 50.000 0.00 0.00 0.00 1.73
2513 3004 3.807209 GCCTATTCATCGCCACCAATAGT 60.807 47.826 0.00 0.00 30.01 2.12
2521 3012 4.002906 TCGCCACCAATAGTCAATATCC 57.997 45.455 0.00 0.00 0.00 2.59
2538 3029 2.107141 CGCCTCCCCTCGTCATTC 59.893 66.667 0.00 0.00 0.00 2.67
2569 3060 4.118995 ATGTGCAATGCGGTGGCG 62.119 61.111 0.00 0.00 44.10 5.69
2608 3099 2.093106 ACCGTAGAGAGTCACCATCAC 58.907 52.381 0.00 0.00 0.00 3.06
2612 3103 3.243234 CGTAGAGAGTCACCATCACCATC 60.243 52.174 0.00 0.00 0.00 3.51
2619 3110 2.236146 GTCACCATCACCATCCACTACA 59.764 50.000 0.00 0.00 0.00 2.74
2628 3119 2.290323 ACCATCCACTACAAGGTTGAGC 60.290 50.000 0.00 0.00 0.00 4.26
2647 3138 1.519455 CTCCGATGGTCGAAGTGGC 60.519 63.158 0.22 0.00 43.74 5.01
2677 3168 2.016704 GAGTACCGCCGCATCATCG 61.017 63.158 0.00 0.00 0.00 3.84
2691 3182 0.466372 TCATCGACCTCGCCATCTCT 60.466 55.000 0.00 0.00 39.60 3.10
2692 3183 0.318529 CATCGACCTCGCCATCTCTG 60.319 60.000 0.00 0.00 39.60 3.35
2693 3184 0.753479 ATCGACCTCGCCATCTCTGT 60.753 55.000 0.00 0.00 39.60 3.41
2694 3185 0.107361 TCGACCTCGCCATCTCTGTA 60.107 55.000 0.00 0.00 39.60 2.74
2695 3186 0.309302 CGACCTCGCCATCTCTGTAG 59.691 60.000 0.00 0.00 0.00 2.74
2696 3187 0.671251 GACCTCGCCATCTCTGTAGG 59.329 60.000 0.00 0.00 0.00 3.18
2697 3188 0.259065 ACCTCGCCATCTCTGTAGGA 59.741 55.000 0.00 0.00 0.00 2.94
2698 3189 1.133325 ACCTCGCCATCTCTGTAGGAT 60.133 52.381 0.00 0.00 0.00 3.24
2699 3190 1.543802 CCTCGCCATCTCTGTAGGATC 59.456 57.143 0.00 0.00 0.00 3.36
2700 3191 1.198867 CTCGCCATCTCTGTAGGATCG 59.801 57.143 0.00 0.00 0.00 3.69
2701 3192 1.202770 TCGCCATCTCTGTAGGATCGA 60.203 52.381 0.00 0.00 0.00 3.59
2702 3193 1.609072 CGCCATCTCTGTAGGATCGAA 59.391 52.381 0.00 0.00 0.00 3.71
2703 3194 2.034685 CGCCATCTCTGTAGGATCGAAA 59.965 50.000 0.00 0.00 0.00 3.46
2704 3195 3.648009 GCCATCTCTGTAGGATCGAAAG 58.352 50.000 0.00 0.00 0.00 2.62
2705 3196 3.068873 GCCATCTCTGTAGGATCGAAAGT 59.931 47.826 0.00 0.00 0.00 2.66
2706 3197 4.278669 GCCATCTCTGTAGGATCGAAAGTA 59.721 45.833 0.00 0.00 0.00 2.24
2707 3198 5.563867 GCCATCTCTGTAGGATCGAAAGTAG 60.564 48.000 0.00 0.00 0.00 2.57
2708 3199 5.048364 CCATCTCTGTAGGATCGAAAGTAGG 60.048 48.000 0.00 0.00 0.00 3.18
2709 3200 5.113446 TCTCTGTAGGATCGAAAGTAGGT 57.887 43.478 0.00 0.00 0.00 3.08
2710 3201 5.124645 TCTCTGTAGGATCGAAAGTAGGTC 58.875 45.833 0.00 0.00 0.00 3.85
2711 3202 5.104444 TCTCTGTAGGATCGAAAGTAGGTCT 60.104 44.000 0.00 0.00 0.00 3.85
2712 3203 6.099413 TCTCTGTAGGATCGAAAGTAGGTCTA 59.901 42.308 0.00 0.00 0.00 2.59
2713 3204 6.289834 TCTGTAGGATCGAAAGTAGGTCTAG 58.710 44.000 0.00 0.00 0.00 2.43
2714 3205 6.099413 TCTGTAGGATCGAAAGTAGGTCTAGA 59.901 42.308 0.00 0.00 0.00 2.43
2715 3206 6.289834 TGTAGGATCGAAAGTAGGTCTAGAG 58.710 44.000 0.00 0.00 0.00 2.43
2716 3207 4.721132 AGGATCGAAAGTAGGTCTAGAGG 58.279 47.826 0.00 0.00 0.00 3.69
2717 3208 3.822167 GGATCGAAAGTAGGTCTAGAGGG 59.178 52.174 0.00 0.00 0.00 4.30
2718 3209 3.294038 TCGAAAGTAGGTCTAGAGGGG 57.706 52.381 0.00 0.00 0.00 4.79
2719 3210 2.091994 TCGAAAGTAGGTCTAGAGGGGG 60.092 54.545 0.00 0.00 0.00 5.40
2737 3228 4.403585 GGGGGTGATTAGACTACTTGAC 57.596 50.000 0.00 0.00 0.00 3.18
2738 3229 3.134262 GGGGGTGATTAGACTACTTGACC 59.866 52.174 0.00 0.00 0.00 4.02
2739 3230 3.773119 GGGGTGATTAGACTACTTGACCA 59.227 47.826 0.00 0.00 0.00 4.02
2740 3231 4.224370 GGGGTGATTAGACTACTTGACCAA 59.776 45.833 0.00 0.00 0.00 3.67
2741 3232 5.280317 GGGGTGATTAGACTACTTGACCAAA 60.280 44.000 0.00 0.00 0.00 3.28
2742 3233 6.415573 GGGTGATTAGACTACTTGACCAAAT 58.584 40.000 0.00 0.00 0.00 2.32
2743 3234 7.365295 GGGGTGATTAGACTACTTGACCAAATA 60.365 40.741 0.00 0.00 0.00 1.40
2744 3235 8.044908 GGGTGATTAGACTACTTGACCAAATAA 58.955 37.037 0.00 0.00 0.00 1.40
2745 3236 9.444600 GGTGATTAGACTACTTGACCAAATAAA 57.555 33.333 0.00 0.00 0.00 1.40
2751 3242 8.934023 AGACTACTTGACCAAATAAAAATCCA 57.066 30.769 0.00 0.00 0.00 3.41
2752 3243 9.362151 AGACTACTTGACCAAATAAAAATCCAA 57.638 29.630 0.00 0.00 0.00 3.53
2753 3244 9.406828 GACTACTTGACCAAATAAAAATCCAAC 57.593 33.333 0.00 0.00 0.00 3.77
2754 3245 9.143155 ACTACTTGACCAAATAAAAATCCAACT 57.857 29.630 0.00 0.00 0.00 3.16
2755 3246 9.981114 CTACTTGACCAAATAAAAATCCAACTT 57.019 29.630 0.00 0.00 0.00 2.66
2757 3248 9.679661 ACTTGACCAAATAAAAATCCAACTTTT 57.320 25.926 0.00 0.00 0.00 2.27
2760 3251 9.114952 TGACCAAATAAAAATCCAACTTTTTCC 57.885 29.630 0.00 0.00 38.76 3.13
2761 3252 8.458573 ACCAAATAAAAATCCAACTTTTTCCC 57.541 30.769 0.00 0.00 38.76 3.97
2762 3253 8.055790 ACCAAATAAAAATCCAACTTTTTCCCA 58.944 29.630 0.00 0.00 38.76 4.37
2763 3254 8.907885 CCAAATAAAAATCCAACTTTTTCCCAA 58.092 29.630 0.00 0.00 38.76 4.12
2770 3261 9.693739 AAAATCCAACTTTTTCCCAATTTTAGT 57.306 25.926 0.00 0.00 0.00 2.24
2771 3262 9.693739 AAATCCAACTTTTTCCCAATTTTAGTT 57.306 25.926 0.00 0.00 0.00 2.24
2772 3263 8.675705 ATCCAACTTTTTCCCAATTTTAGTTG 57.324 30.769 0.00 0.00 40.19 3.16
2773 3264 7.625469 TCCAACTTTTTCCCAATTTTAGTTGT 58.375 30.769 0.00 0.00 39.34 3.32
2774 3265 7.550906 TCCAACTTTTTCCCAATTTTAGTTGTG 59.449 33.333 0.00 0.00 39.34 3.33
2775 3266 7.201688 CCAACTTTTTCCCAATTTTAGTTGTGG 60.202 37.037 0.00 0.00 39.34 4.17
2779 3270 3.317603 CCCAATTTTAGTTGTGGGCAG 57.682 47.619 0.00 0.00 44.17 4.85
2780 3271 2.896685 CCCAATTTTAGTTGTGGGCAGA 59.103 45.455 0.00 0.00 44.17 4.26
2781 3272 3.515104 CCCAATTTTAGTTGTGGGCAGAT 59.485 43.478 0.00 0.00 44.17 2.90
2782 3273 4.020307 CCCAATTTTAGTTGTGGGCAGATT 60.020 41.667 0.00 0.00 44.17 2.40
2783 3274 5.512921 CCCAATTTTAGTTGTGGGCAGATTT 60.513 40.000 0.00 0.00 44.17 2.17
2784 3275 5.997129 CCAATTTTAGTTGTGGGCAGATTTT 59.003 36.000 0.00 0.00 0.00 1.82
2785 3276 7.158021 CCAATTTTAGTTGTGGGCAGATTTTA 58.842 34.615 0.00 0.00 0.00 1.52
2786 3277 7.331687 CCAATTTTAGTTGTGGGCAGATTTTAG 59.668 37.037 0.00 0.00 0.00 1.85
2787 3278 5.385509 TTTAGTTGTGGGCAGATTTTAGC 57.614 39.130 0.00 0.00 0.00 3.09
2788 3279 2.875296 AGTTGTGGGCAGATTTTAGCA 58.125 42.857 0.00 0.00 0.00 3.49
2789 3280 3.230134 AGTTGTGGGCAGATTTTAGCAA 58.770 40.909 0.00 0.00 0.00 3.91
2790 3281 3.834231 AGTTGTGGGCAGATTTTAGCAAT 59.166 39.130 0.00 0.00 0.00 3.56
2791 3282 4.284234 AGTTGTGGGCAGATTTTAGCAATT 59.716 37.500 0.00 0.00 0.00 2.32
2792 3283 4.888326 TGTGGGCAGATTTTAGCAATTT 57.112 36.364 0.00 0.00 0.00 1.82
2793 3284 5.991933 TGTGGGCAGATTTTAGCAATTTA 57.008 34.783 0.00 0.00 0.00 1.40
2794 3285 5.964758 TGTGGGCAGATTTTAGCAATTTAG 58.035 37.500 0.00 0.00 0.00 1.85
2795 3286 4.805719 GTGGGCAGATTTTAGCAATTTAGC 59.194 41.667 0.00 0.00 0.00 3.09
2796 3287 4.465660 TGGGCAGATTTTAGCAATTTAGCA 59.534 37.500 0.00 0.00 36.85 3.49
2797 3288 5.129155 TGGGCAGATTTTAGCAATTTAGCAT 59.871 36.000 0.00 0.00 36.85 3.79
2798 3289 6.323482 TGGGCAGATTTTAGCAATTTAGCATA 59.677 34.615 0.00 0.00 36.85 3.14
2799 3290 7.147759 TGGGCAGATTTTAGCAATTTAGCATAA 60.148 33.333 0.00 0.00 36.85 1.90
2800 3291 7.383300 GGGCAGATTTTAGCAATTTAGCATAAG 59.617 37.037 0.00 0.00 36.85 1.73
2801 3292 7.922811 GGCAGATTTTAGCAATTTAGCATAAGT 59.077 33.333 0.00 0.00 36.85 2.24
2802 3293 8.962111 GCAGATTTTAGCAATTTAGCATAAGTC 58.038 33.333 0.00 0.00 36.85 3.01
2806 3297 8.687824 TTTTAGCAATTTAGCATAAGTCAAGC 57.312 30.769 0.00 0.00 36.85 4.01
2807 3298 5.902613 AGCAATTTAGCATAAGTCAAGCA 57.097 34.783 0.00 0.00 36.85 3.91
2808 3299 6.271488 AGCAATTTAGCATAAGTCAAGCAA 57.729 33.333 0.00 0.00 36.85 3.91
2809 3300 6.870769 AGCAATTTAGCATAAGTCAAGCAAT 58.129 32.000 0.00 0.00 36.85 3.56
2810 3301 6.976925 AGCAATTTAGCATAAGTCAAGCAATC 59.023 34.615 0.00 0.00 36.85 2.67
2811 3302 6.753279 GCAATTTAGCATAAGTCAAGCAATCA 59.247 34.615 0.00 0.00 0.00 2.57
2812 3303 7.276218 GCAATTTAGCATAAGTCAAGCAATCAA 59.724 33.333 0.00 0.00 0.00 2.57
2813 3304 8.589629 CAATTTAGCATAAGTCAAGCAATCAAC 58.410 33.333 0.00 0.00 0.00 3.18
2814 3305 4.708726 AGCATAAGTCAAGCAATCAACC 57.291 40.909 0.00 0.00 0.00 3.77
2815 3306 4.338879 AGCATAAGTCAAGCAATCAACCT 58.661 39.130 0.00 0.00 0.00 3.50
2816 3307 4.397417 AGCATAAGTCAAGCAATCAACCTC 59.603 41.667 0.00 0.00 0.00 3.85
2817 3308 4.439289 GCATAAGTCAAGCAATCAACCTCC 60.439 45.833 0.00 0.00 0.00 4.30
2818 3309 2.957402 AGTCAAGCAATCAACCTCCA 57.043 45.000 0.00 0.00 0.00 3.86
2819 3310 2.508526 AGTCAAGCAATCAACCTCCAC 58.491 47.619 0.00 0.00 0.00 4.02
2820 3311 2.158623 AGTCAAGCAATCAACCTCCACA 60.159 45.455 0.00 0.00 0.00 4.17
2821 3312 2.821969 GTCAAGCAATCAACCTCCACAT 59.178 45.455 0.00 0.00 0.00 3.21
2822 3313 2.821378 TCAAGCAATCAACCTCCACATG 59.179 45.455 0.00 0.00 0.00 3.21
2823 3314 1.180029 AGCAATCAACCTCCACATGC 58.820 50.000 0.00 0.00 0.00 4.06
2824 3315 0.889994 GCAATCAACCTCCACATGCA 59.110 50.000 0.00 0.00 32.80 3.96
2825 3316 1.273048 GCAATCAACCTCCACATGCAA 59.727 47.619 0.00 0.00 32.80 4.08
2826 3317 2.093869 GCAATCAACCTCCACATGCAAT 60.094 45.455 0.00 0.00 32.80 3.56
2827 3318 3.618019 GCAATCAACCTCCACATGCAATT 60.618 43.478 0.00 0.00 32.80 2.32
2828 3319 4.178540 CAATCAACCTCCACATGCAATTC 58.821 43.478 0.00 0.00 0.00 2.17
2829 3320 3.159213 TCAACCTCCACATGCAATTCT 57.841 42.857 0.00 0.00 0.00 2.40
2830 3321 4.299586 TCAACCTCCACATGCAATTCTA 57.700 40.909 0.00 0.00 0.00 2.10
2831 3322 4.661222 TCAACCTCCACATGCAATTCTAA 58.339 39.130 0.00 0.00 0.00 2.10
2832 3323 4.701651 TCAACCTCCACATGCAATTCTAAG 59.298 41.667 0.00 0.00 0.00 2.18
2833 3324 4.574674 ACCTCCACATGCAATTCTAAGA 57.425 40.909 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 69 1.273327 CCGCCTTGAAGCTTTTTCCAT 59.727 47.619 0.00 0.00 0.00 3.41
128 131 4.126437 CCGGTTGAAGCTTTTTCCAAAAT 58.874 39.130 0.00 0.00 0.00 1.82
195 200 2.556622 GCGGTGGAAGATTTTTCCTCAA 59.443 45.455 7.43 0.00 39.31 3.02
276 285 0.967887 GCCTGAAGCTTTTCCTCCCC 60.968 60.000 0.00 0.00 38.99 4.81
293 302 1.344226 GCTTTTTCGTCATTGCCGCC 61.344 55.000 0.00 0.00 0.00 6.13
346 356 1.743431 CGTCTGCTCATACCATTGGCA 60.743 52.381 1.54 0.00 0.00 4.92
407 417 4.271816 CGTCTCCATAGCGCGCCT 62.272 66.667 30.33 17.79 0.00 5.52
417 427 2.829003 CTAGCCTCGCCGTCTCCA 60.829 66.667 0.00 0.00 0.00 3.86
457 467 7.539712 TTCAAAAACAACACAAAAGACAACA 57.460 28.000 0.00 0.00 0.00 3.33
459 469 7.010183 TCGTTTCAAAAACAACACAAAAGACAA 59.990 29.630 3.72 0.00 0.00 3.18
665 837 3.403038 CTGATTGTCCCTCGTTGACTTT 58.597 45.455 0.00 0.00 33.83 2.66
728 915 1.615392 AGTGCAATCTTGAAAGTGGGC 59.385 47.619 0.00 0.00 0.00 5.36
750 937 1.207329 AGACAGTTAATCGGGGCACTC 59.793 52.381 0.00 0.00 0.00 3.51
754 941 2.280628 CAGAAGACAGTTAATCGGGGC 58.719 52.381 0.00 0.00 0.00 5.80
756 943 6.019801 CGAATAACAGAAGACAGTTAATCGGG 60.020 42.308 12.42 0.00 42.26 5.14
777 964 2.039084 ACTTTCTCACTTGAGCCCGAAT 59.961 45.455 0.99 0.00 41.80 3.34
786 973 6.785191 TGTTTTGCTTAGACTTTCTCACTTG 58.215 36.000 0.00 0.00 0.00 3.16
789 976 6.551736 TGTTGTTTTGCTTAGACTTTCTCAC 58.448 36.000 0.00 0.00 0.00 3.51
826 1013 1.032114 GGCCCTGCGTGAAAATAGCT 61.032 55.000 0.00 0.00 0.00 3.32
827 1014 1.312371 TGGCCCTGCGTGAAAATAGC 61.312 55.000 0.00 0.00 0.00 2.97
1362 1850 4.329545 GGGCTGTCGTGGAAGGCA 62.330 66.667 0.00 0.00 40.58 4.75
1639 2127 3.153270 TGGACGTGGCGTACAGCAA 62.153 57.895 2.13 0.00 46.30 3.91
1892 2380 0.991920 TAAACAGAGAAGGCTGGGGG 59.008 55.000 0.00 0.00 40.20 5.40
1893 2381 2.025887 ACATAAACAGAGAAGGCTGGGG 60.026 50.000 0.00 0.00 40.20 4.96
1913 2401 6.583912 ACAATCTATGCACACATACGTAAC 57.416 37.500 0.00 0.00 37.74 2.50
2010 2498 8.879342 ACGAGAACTCCTATTCTATCAATTTG 57.121 34.615 0.00 0.00 39.08 2.32
2092 2580 2.309898 ACTATTTTTGTGTCGCGTGC 57.690 45.000 5.77 0.57 0.00 5.34
2094 2582 4.399978 GCATAACTATTTTTGTGTCGCGT 58.600 39.130 5.77 0.00 0.00 6.01
2097 2585 4.717299 CGTCGCATAACTATTTTTGTGTCG 59.283 41.667 3.41 3.41 32.84 4.35
2133 2621 1.148273 GGCAGAGGTGTGTGTGGAA 59.852 57.895 0.00 0.00 0.00 3.53
2173 2661 3.489229 CGATGAAGTACTGGAGCGAATGA 60.489 47.826 6.25 0.00 0.00 2.57
2175 2663 2.799917 GCGATGAAGTACTGGAGCGAAT 60.800 50.000 14.33 0.00 0.00 3.34
2179 2667 1.846541 GAGCGATGAAGTACTGGAGC 58.153 55.000 0.00 0.00 0.00 4.70
2185 2673 2.169663 TCGTTCGAGCGATGAAGTAC 57.830 50.000 20.80 0.00 35.83 2.73
2256 2744 1.224075 CATGGCTAGCAGATTGTCGG 58.776 55.000 18.24 0.00 0.00 4.79
2306 2795 2.514592 ATGACATTCCAGGGCGCG 60.515 61.111 0.00 0.00 0.00 6.86
2309 2798 1.474077 GACAACATGACATTCCAGGGC 59.526 52.381 0.00 0.00 0.00 5.19
2313 2802 3.411446 GTGAGGACAACATGACATTCCA 58.589 45.455 0.00 0.00 0.00 3.53
2326 2816 1.906824 GAGGTGGTCGGTGAGGACA 60.907 63.158 0.00 0.00 38.70 4.02
2333 2823 2.928396 CAAGGGGAGGTGGTCGGT 60.928 66.667 0.00 0.00 0.00 4.69
2426 2917 4.802051 GGCGAGGGCTTGATGGCA 62.802 66.667 0.00 0.00 43.83 4.92
2488 2979 1.498865 GGTGGCGATGAATAGGCGTG 61.499 60.000 0.00 0.00 35.52 5.34
2497 2988 3.558931 ATTGACTATTGGTGGCGATGA 57.441 42.857 0.00 0.00 0.00 2.92
2499 2990 4.579869 GGATATTGACTATTGGTGGCGAT 58.420 43.478 0.00 0.00 0.00 4.58
2504 2995 3.997021 GAGGCGGATATTGACTATTGGTG 59.003 47.826 0.00 0.00 0.00 4.17
2512 3003 0.321996 GAGGGGAGGCGGATATTGAC 59.678 60.000 0.00 0.00 0.00 3.18
2513 3004 1.185618 CGAGGGGAGGCGGATATTGA 61.186 60.000 0.00 0.00 0.00 2.57
2521 3012 1.961180 AAGAATGACGAGGGGAGGCG 61.961 60.000 0.00 0.00 0.00 5.52
2569 3060 0.465460 TCAAACAGTGAGGGTGGCAC 60.465 55.000 9.70 9.70 36.53 5.01
2570 3061 0.465460 GTCAAACAGTGAGGGTGGCA 60.465 55.000 0.00 0.00 36.74 4.92
2580 3071 3.004524 GTGACTCTCTACGGTCAAACAGT 59.995 47.826 0.00 0.00 42.88 3.55
2608 3099 2.359900 GCTCAACCTTGTAGTGGATGG 58.640 52.381 0.00 0.00 0.00 3.51
2630 3121 0.681887 TAGCCACTTCGACCATCGGA 60.682 55.000 0.00 0.00 40.88 4.55
2631 3122 0.389391 ATAGCCACTTCGACCATCGG 59.611 55.000 0.00 0.00 40.88 4.18
2647 3138 3.326747 GGCGGTACTCAAATGGCTATAG 58.673 50.000 0.00 0.00 0.00 1.31
2657 3148 0.529773 GATGATGCGGCGGTACTCAA 60.530 55.000 9.78 0.00 0.00 3.02
2677 3168 0.671251 CCTACAGAGATGGCGAGGTC 59.329 60.000 0.00 0.00 0.00 3.85
2691 3182 6.244552 TCTAGACCTACTTTCGATCCTACA 57.755 41.667 0.00 0.00 0.00 2.74
2692 3183 5.702209 CCTCTAGACCTACTTTCGATCCTAC 59.298 48.000 0.00 0.00 0.00 3.18
2693 3184 5.221884 CCCTCTAGACCTACTTTCGATCCTA 60.222 48.000 0.00 0.00 0.00 2.94
2694 3185 4.446600 CCCTCTAGACCTACTTTCGATCCT 60.447 50.000 0.00 0.00 0.00 3.24
2695 3186 3.822167 CCCTCTAGACCTACTTTCGATCC 59.178 52.174 0.00 0.00 0.00 3.36
2696 3187 3.822167 CCCCTCTAGACCTACTTTCGATC 59.178 52.174 0.00 0.00 0.00 3.69
2697 3188 3.436761 CCCCCTCTAGACCTACTTTCGAT 60.437 52.174 0.00 0.00 0.00 3.59
2698 3189 2.091994 CCCCCTCTAGACCTACTTTCGA 60.092 54.545 0.00 0.00 0.00 3.71
2699 3190 2.308690 CCCCCTCTAGACCTACTTTCG 58.691 57.143 0.00 0.00 0.00 3.46
2716 3207 3.134262 GGTCAAGTAGTCTAATCACCCCC 59.866 52.174 0.00 0.00 0.00 5.40
2717 3208 3.773119 TGGTCAAGTAGTCTAATCACCCC 59.227 47.826 6.13 0.00 0.00 4.95
2718 3209 5.416271 TTGGTCAAGTAGTCTAATCACCC 57.584 43.478 6.13 0.00 0.00 4.61
2719 3210 9.444600 TTTATTTGGTCAAGTAGTCTAATCACC 57.555 33.333 2.72 2.72 0.00 4.02
2726 3217 8.934023 TGGATTTTTATTTGGTCAAGTAGTCT 57.066 30.769 0.00 0.00 0.00 3.24
2727 3218 9.406828 GTTGGATTTTTATTTGGTCAAGTAGTC 57.593 33.333 0.00 0.00 0.00 2.59
2728 3219 9.143155 AGTTGGATTTTTATTTGGTCAAGTAGT 57.857 29.630 0.00 0.00 0.00 2.73
2729 3220 9.981114 AAGTTGGATTTTTATTTGGTCAAGTAG 57.019 29.630 0.00 0.00 0.00 2.57
2731 3222 9.679661 AAAAGTTGGATTTTTATTTGGTCAAGT 57.320 25.926 0.00 0.00 0.00 3.16
2734 3225 9.114952 GGAAAAAGTTGGATTTTTATTTGGTCA 57.885 29.630 0.00 0.00 41.28 4.02
2735 3226 8.564574 GGGAAAAAGTTGGATTTTTATTTGGTC 58.435 33.333 0.00 0.00 41.28 4.02
2736 3227 8.055790 TGGGAAAAAGTTGGATTTTTATTTGGT 58.944 29.630 0.00 0.00 41.28 3.67
2737 3228 8.457238 TGGGAAAAAGTTGGATTTTTATTTGG 57.543 30.769 0.00 0.00 41.28 3.28
2744 3235 9.693739 ACTAAAATTGGGAAAAAGTTGGATTTT 57.306 25.926 0.00 0.00 33.86 1.82
2745 3236 9.693739 AACTAAAATTGGGAAAAAGTTGGATTT 57.306 25.926 0.00 0.00 0.00 2.17
2746 3237 9.119418 CAACTAAAATTGGGAAAAAGTTGGATT 57.881 29.630 0.00 0.00 38.94 3.01
2747 3238 8.271458 ACAACTAAAATTGGGAAAAAGTTGGAT 58.729 29.630 14.61 0.00 44.04 3.41
2748 3239 7.550906 CACAACTAAAATTGGGAAAAAGTTGGA 59.449 33.333 14.61 0.00 44.04 3.53
2749 3240 7.201688 CCACAACTAAAATTGGGAAAAAGTTGG 60.202 37.037 14.61 5.84 44.04 3.77
2750 3241 7.693020 CCACAACTAAAATTGGGAAAAAGTTG 58.307 34.615 9.97 9.97 44.83 3.16
2751 3242 7.857734 CCACAACTAAAATTGGGAAAAAGTT 57.142 32.000 0.00 0.00 34.72 2.66
2760 3251 4.806640 ATCTGCCCACAACTAAAATTGG 57.193 40.909 0.00 0.00 33.63 3.16
2761 3252 7.148590 GCTAAAATCTGCCCACAACTAAAATTG 60.149 37.037 0.00 0.00 35.59 2.32
2762 3253 6.873605 GCTAAAATCTGCCCACAACTAAAATT 59.126 34.615 0.00 0.00 0.00 1.82
2763 3254 6.014669 TGCTAAAATCTGCCCACAACTAAAAT 60.015 34.615 0.00 0.00 0.00 1.82
2764 3255 5.303078 TGCTAAAATCTGCCCACAACTAAAA 59.697 36.000 0.00 0.00 0.00 1.52
2765 3256 4.830046 TGCTAAAATCTGCCCACAACTAAA 59.170 37.500 0.00 0.00 0.00 1.85
2766 3257 4.402829 TGCTAAAATCTGCCCACAACTAA 58.597 39.130 0.00 0.00 0.00 2.24
2767 3258 4.027674 TGCTAAAATCTGCCCACAACTA 57.972 40.909 0.00 0.00 0.00 2.24
2768 3259 2.875296 TGCTAAAATCTGCCCACAACT 58.125 42.857 0.00 0.00 0.00 3.16
2769 3260 3.658757 TTGCTAAAATCTGCCCACAAC 57.341 42.857 0.00 0.00 0.00 3.32
2770 3261 4.888326 AATTGCTAAAATCTGCCCACAA 57.112 36.364 0.00 0.00 0.00 3.33
2771 3262 4.888326 AAATTGCTAAAATCTGCCCACA 57.112 36.364 0.00 0.00 0.00 4.17
2772 3263 4.805719 GCTAAATTGCTAAAATCTGCCCAC 59.194 41.667 0.00 0.00 0.00 4.61
2773 3264 4.465660 TGCTAAATTGCTAAAATCTGCCCA 59.534 37.500 0.00 0.00 0.00 5.36
2774 3265 5.009854 TGCTAAATTGCTAAAATCTGCCC 57.990 39.130 0.00 0.00 0.00 5.36
2775 3266 7.922811 ACTTATGCTAAATTGCTAAAATCTGCC 59.077 33.333 0.00 0.00 0.00 4.85
2776 3267 8.862550 ACTTATGCTAAATTGCTAAAATCTGC 57.137 30.769 0.00 0.00 0.00 4.26
2780 3271 9.305925 GCTTGACTTATGCTAAATTGCTAAAAT 57.694 29.630 0.00 0.00 0.00 1.82
2781 3272 8.303156 TGCTTGACTTATGCTAAATTGCTAAAA 58.697 29.630 0.00 0.00 0.00 1.52
2782 3273 7.825681 TGCTTGACTTATGCTAAATTGCTAAA 58.174 30.769 0.00 0.00 0.00 1.85
2783 3274 7.389803 TGCTTGACTTATGCTAAATTGCTAA 57.610 32.000 0.00 0.00 0.00 3.09
2784 3275 7.389803 TTGCTTGACTTATGCTAAATTGCTA 57.610 32.000 0.00 0.00 0.00 3.49
2785 3276 5.902613 TGCTTGACTTATGCTAAATTGCT 57.097 34.783 0.00 0.00 0.00 3.91
2786 3277 6.753279 TGATTGCTTGACTTATGCTAAATTGC 59.247 34.615 0.00 0.00 0.00 3.56
2787 3278 8.589629 GTTGATTGCTTGACTTATGCTAAATTG 58.410 33.333 0.00 0.00 0.00 2.32
2788 3279 7.761249 GGTTGATTGCTTGACTTATGCTAAATT 59.239 33.333 0.00 0.00 0.00 1.82
2789 3280 7.123247 AGGTTGATTGCTTGACTTATGCTAAAT 59.877 33.333 0.00 0.00 0.00 1.40
2790 3281 6.434028 AGGTTGATTGCTTGACTTATGCTAAA 59.566 34.615 0.00 0.00 0.00 1.85
2791 3282 5.945784 AGGTTGATTGCTTGACTTATGCTAA 59.054 36.000 0.00 0.00 0.00 3.09
2792 3283 5.500234 AGGTTGATTGCTTGACTTATGCTA 58.500 37.500 0.00 0.00 0.00 3.49
2793 3284 4.338879 AGGTTGATTGCTTGACTTATGCT 58.661 39.130 0.00 0.00 0.00 3.79
2794 3285 4.439289 GGAGGTTGATTGCTTGACTTATGC 60.439 45.833 0.00 0.00 0.00 3.14
2795 3286 4.701651 TGGAGGTTGATTGCTTGACTTATG 59.298 41.667 0.00 0.00 0.00 1.90
2796 3287 4.702131 GTGGAGGTTGATTGCTTGACTTAT 59.298 41.667 0.00 0.00 0.00 1.73
2797 3288 4.072131 GTGGAGGTTGATTGCTTGACTTA 58.928 43.478 0.00 0.00 0.00 2.24
2798 3289 2.887152 GTGGAGGTTGATTGCTTGACTT 59.113 45.455 0.00 0.00 0.00 3.01
2799 3290 2.158623 TGTGGAGGTTGATTGCTTGACT 60.159 45.455 0.00 0.00 0.00 3.41
2800 3291 2.229792 TGTGGAGGTTGATTGCTTGAC 58.770 47.619 0.00 0.00 0.00 3.18
2801 3292 2.655090 TGTGGAGGTTGATTGCTTGA 57.345 45.000 0.00 0.00 0.00 3.02
2802 3293 2.673043 GCATGTGGAGGTTGATTGCTTG 60.673 50.000 0.00 0.00 0.00 4.01
2803 3294 1.547372 GCATGTGGAGGTTGATTGCTT 59.453 47.619 0.00 0.00 0.00 3.91
2804 3295 1.180029 GCATGTGGAGGTTGATTGCT 58.820 50.000 0.00 0.00 0.00 3.91
2805 3296 0.889994 TGCATGTGGAGGTTGATTGC 59.110 50.000 0.00 0.00 0.00 3.56
2806 3297 3.880047 ATTGCATGTGGAGGTTGATTG 57.120 42.857 0.00 0.00 0.00 2.67
2807 3298 4.091549 AGAATTGCATGTGGAGGTTGATT 58.908 39.130 0.00 0.00 0.00 2.57
2808 3299 3.705051 AGAATTGCATGTGGAGGTTGAT 58.295 40.909 0.00 0.00 0.00 2.57
2809 3300 3.159213 AGAATTGCATGTGGAGGTTGA 57.841 42.857 0.00 0.00 0.00 3.18
2810 3301 4.701651 TCTTAGAATTGCATGTGGAGGTTG 59.298 41.667 0.00 0.00 0.00 3.77
2811 3302 4.922206 TCTTAGAATTGCATGTGGAGGTT 58.078 39.130 0.00 0.00 0.00 3.50
2812 3303 4.574674 TCTTAGAATTGCATGTGGAGGT 57.425 40.909 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.