Multiple sequence alignment - TraesCS3D01G012300

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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 TraesCS3D01G012300 chr3D 100.000 3452 0 0 1 3452 4316765 4320216 0.000000e+00 6375.0
1 TraesCS3D01G012300 chr3D 84.665 2765 310 70 81 2753 4344517 4347259 0.000000e+00 2652.0
2 TraesCS3D01G012300 chr3D 93.069 101 5 2 2751 2850 65607314 65607215 2.780000e-31 147.0
3 TraesCS3D01G012300 chr3A 93.669 2701 113 13 73 2754 9887412 9890073 0.000000e+00 3988.0
4 TraesCS3D01G012300 chr3A 85.764 2283 244 50 509 2753 9950404 9952643 0.000000e+00 2340.0
5 TraesCS3D01G012300 chr3A 86.948 498 50 9 2893 3381 9890131 9890622 2.340000e-151 545.0
6 TraesCS3D01G012300 chr3A 79.020 510 51 21 32 530 9948541 9949005 7.240000e-77 298.0
7 TraesCS3D01G012300 chr3A 94.845 97 5 0 2751 2847 659039418 659039514 5.970000e-33 152.0
8 TraesCS3D01G012300 chr3A 88.333 60 1 1 1 54 9887354 9887413 2.220000e-07 67.6
9 TraesCS3D01G012300 chrUn 94.370 2007 97 9 596 2595 308557574 308559571 0.000000e+00 3066.0
10 TraesCS3D01G012300 chrUn 86.721 2101 225 36 670 2731 35644408 35646493 0.000000e+00 2285.0
11 TraesCS3D01G012300 chrUn 86.250 720 95 3 1333 2049 35630966 35631684 0.000000e+00 778.0
12 TraesCS3D01G012300 chrUn 93.598 328 9 4 23 342 35849445 35849122 2.410000e-131 479.0
13 TraesCS3D01G012300 chrUn 93.598 328 9 4 23 342 339652139 339651816 2.410000e-131 479.0
14 TraesCS3D01G012300 chrUn 93.657 268 15 2 327 593 35849106 35848840 1.930000e-107 399.0
15 TraesCS3D01G012300 chrUn 93.657 268 15 2 327 593 339651800 339651534 1.930000e-107 399.0
16 TraesCS3D01G012300 chrUn 85.197 304 34 3 3042 3345 308560030 308560322 5.600000e-78 302.0
17 TraesCS3D01G012300 chr2D 72.770 1076 260 25 1386 2440 9371912 9372975 1.990000e-87 333.0
18 TraesCS3D01G012300 chr2D 94.949 99 4 1 2752 2850 148738030 148738127 1.660000e-33 154.0
19 TraesCS3D01G012300 chr7B 93.939 99 5 1 2752 2850 153939434 153939337 7.720000e-32 148.0
20 TraesCS3D01G012300 chr7B 90.265 113 10 1 2735 2846 506378255 506378367 2.780000e-31 147.0
21 TraesCS3D01G012300 chr5D 92.233 103 7 1 2747 2849 367519707 367519808 9.990000e-31 145.0
22 TraesCS3D01G012300 chr5A 93.750 96 6 0 2751 2846 27637137 27637042 9.990000e-31 145.0
23 TraesCS3D01G012300 chr6A 88.793 116 10 3 2735 2850 438961766 438961878 4.650000e-29 139.0
24 TraesCS3D01G012300 chr5B 88.696 115 11 2 2724 2838 680748126 680748238 4.650000e-29 139.0


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 TraesCS3D01G012300 chr3D 4316765 4320216 3451 False 6375.000000 6375 100.0000 1 3452 1 chr3D.!!$F1 3451
1 TraesCS3D01G012300 chr3D 4344517 4347259 2742 False 2652.000000 2652 84.6650 81 2753 1 chr3D.!!$F2 2672
2 TraesCS3D01G012300 chr3A 9887354 9890622 3268 False 1533.533333 3988 89.6500 1 3381 3 chr3A.!!$F2 3380
3 TraesCS3D01G012300 chr3A 9948541 9952643 4102 False 1319.000000 2340 82.3920 32 2753 2 chr3A.!!$F3 2721
4 TraesCS3D01G012300 chrUn 35644408 35646493 2085 False 2285.000000 2285 86.7210 670 2731 1 chrUn.!!$F2 2061
5 TraesCS3D01G012300 chrUn 308557574 308560322 2748 False 1684.000000 3066 89.7835 596 3345 2 chrUn.!!$F3 2749
6 TraesCS3D01G012300 chrUn 35630966 35631684 718 False 778.000000 778 86.2500 1333 2049 1 chrUn.!!$F1 716
7 TraesCS3D01G012300 chrUn 35848840 35849445 605 True 439.000000 479 93.6275 23 593 2 chrUn.!!$R1 570
8 TraesCS3D01G012300 chrUn 339651534 339652139 605 True 439.000000 479 93.6275 23 593 2 chrUn.!!$R2 570
9 TraesCS3D01G012300 chr2D 9371912 9372975 1063 False 333.000000 333 72.7700 1386 2440 1 chr2D.!!$F1 1054

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
897 2422 1.131638 TGTCCTTTCAGCTCACCACT 58.868 50.0 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2553 4117 0.674895 AAAGCATGCCCGAGTGACTC 60.675 55.0 15.66 1.65 0.0 3.36 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
79 86 4.260375 CGGTGCAGTGTATTATTCTTCAGC 60.260 45.833 0.00 0.00 0.00 4.26
298 333 2.378038 TGCACCTGAATATTGAAGGCC 58.622 47.619 11.98 0.00 34.18 5.19
661 2173 8.038492 AGCTTGCTCTTTAAAAGATACAAGAG 57.962 34.615 18.70 15.27 45.28 2.85
737 2255 4.216902 TCCTTCTCATGCATTGTTGTCAAG 59.783 41.667 0.00 0.00 36.97 3.02
776 2298 4.814234 AGTCAAACACTAGACGCATTGAAA 59.186 37.500 0.00 0.00 39.67 2.69
896 2421 1.876156 CTTGTCCTTTCAGCTCACCAC 59.124 52.381 0.00 0.00 0.00 4.16
897 2422 1.131638 TGTCCTTTCAGCTCACCACT 58.868 50.000 0.00 0.00 0.00 4.00
898 2423 2.325484 TGTCCTTTCAGCTCACCACTA 58.675 47.619 0.00 0.00 0.00 2.74
899 2424 2.300152 TGTCCTTTCAGCTCACCACTAG 59.700 50.000 0.00 0.00 0.00 2.57
1238 2788 1.949525 CATGTACCAAGGCTACCATGC 59.050 52.381 0.00 0.00 0.00 4.06
1416 2966 3.382865 TGGAAAGCATGCAAAGTGTTGTA 59.617 39.130 21.98 0.00 37.06 2.41
1486 3036 3.802685 GGTGCGTAGACCTTATGATTCAC 59.197 47.826 0.00 0.00 32.69 3.18
1569 3126 0.820871 TGTTGCAACAGAACCAACCC 59.179 50.000 27.96 0.00 38.38 4.11
1601 3158 4.018960 ACCAGCTGTTCTTCCAATCATAGT 60.019 41.667 13.81 0.00 0.00 2.12
1617 3174 1.624336 TAGTTGGTCGCACAGTAGGT 58.376 50.000 0.00 0.00 0.00 3.08
1873 3430 5.703130 AGTAAACTTCAAAGATCAGCCAGAC 59.297 40.000 0.00 0.00 0.00 3.51
2220 3780 1.538047 ATGCTTTGAATCCACTGCGT 58.462 45.000 0.00 0.00 0.00 5.24
2284 3844 0.471211 AAAGGTGACACTCGGGGAGA 60.471 55.000 5.39 0.00 33.32 3.71
2298 3858 2.827755 GGGGAGATCCTAGAAGATCCC 58.172 57.143 12.28 12.28 43.14 3.85
2415 3975 0.031414 ATACGCCTGAAGGTACCCCT 60.031 55.000 8.74 0.00 45.63 4.79
2643 4267 9.278978 GACTCATTCTCTTTCTCCTTTTACTTT 57.721 33.333 0.00 0.00 0.00 2.66
2715 4376 9.294030 GAACTCTTAAAATGGACAATATTGCAG 57.706 33.333 15.48 1.33 0.00 4.41
2754 4415 5.129485 CAGGACTTGGACACAATATCCTACT 59.871 44.000 11.04 0.00 44.30 2.57
2755 4416 5.364157 AGGACTTGGACACAATATCCTACTC 59.636 44.000 10.14 0.00 44.29 2.59
2756 4417 5.453480 GGACTTGGACACAATATCCTACTCC 60.453 48.000 0.00 0.00 38.13 3.85
2757 4418 4.409247 ACTTGGACACAATATCCTACTCCC 59.591 45.833 0.00 0.00 37.13 4.30
2759 4420 4.223953 TGGACACAATATCCTACTCCCTC 58.776 47.826 0.00 0.00 37.13 4.30
2760 4421 3.579151 GGACACAATATCCTACTCCCTCC 59.421 52.174 0.00 0.00 33.03 4.30
2761 4422 3.231818 ACACAATATCCTACTCCCTCCG 58.768 50.000 0.00 0.00 0.00 4.63
2763 4424 3.641906 CACAATATCCTACTCCCTCCGTT 59.358 47.826 0.00 0.00 0.00 4.44
2764 4425 3.896272 ACAATATCCTACTCCCTCCGTTC 59.104 47.826 0.00 0.00 0.00 3.95
2765 4426 2.671896 TATCCTACTCCCTCCGTTCC 57.328 55.000 0.00 0.00 0.00 3.62
2766 4427 0.635009 ATCCTACTCCCTCCGTTCCA 59.365 55.000 0.00 0.00 0.00 3.53
2767 4428 0.410663 TCCTACTCCCTCCGTTCCAA 59.589 55.000 0.00 0.00 0.00 3.53
2768 4429 1.203212 TCCTACTCCCTCCGTTCCAAA 60.203 52.381 0.00 0.00 0.00 3.28
2769 4430 1.838077 CCTACTCCCTCCGTTCCAAAT 59.162 52.381 0.00 0.00 0.00 2.32
2770 4431 2.238898 CCTACTCCCTCCGTTCCAAATT 59.761 50.000 0.00 0.00 0.00 1.82
2771 4432 3.453353 CCTACTCCCTCCGTTCCAAATTA 59.547 47.826 0.00 0.00 0.00 1.40
2772 4433 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
2773 4434 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
2774 4435 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
2775 4436 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
2776 4437 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
2777 4438 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
2778 4439 3.581755 CTCCGTTCCAAATTACTCGTCA 58.418 45.455 0.00 0.00 0.00 4.35
2779 4440 4.181578 CTCCGTTCCAAATTACTCGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
2780 4441 3.930229 TCCGTTCCAAATTACTCGTCATG 59.070 43.478 0.00 0.00 0.00 3.07
2781 4442 3.063452 CCGTTCCAAATTACTCGTCATGG 59.937 47.826 0.00 0.00 0.00 3.66
2782 4443 3.682858 CGTTCCAAATTACTCGTCATGGT 59.317 43.478 0.00 0.00 0.00 3.55
2783 4444 4.153475 CGTTCCAAATTACTCGTCATGGTT 59.847 41.667 0.00 0.00 0.00 3.67
2784 4445 5.334569 CGTTCCAAATTACTCGTCATGGTTT 60.335 40.000 0.00 0.00 0.00 3.27
2785 4446 6.443792 GTTCCAAATTACTCGTCATGGTTTT 58.556 36.000 0.00 0.00 0.00 2.43
2786 4447 7.571613 CGTTCCAAATTACTCGTCATGGTTTTA 60.572 37.037 0.00 0.00 0.00 1.52
2787 4448 7.372451 TCCAAATTACTCGTCATGGTTTTAG 57.628 36.000 0.00 0.00 0.00 1.85
2788 4449 6.938030 TCCAAATTACTCGTCATGGTTTTAGT 59.062 34.615 0.00 0.00 0.00 2.24
2789 4450 7.446013 TCCAAATTACTCGTCATGGTTTTAGTT 59.554 33.333 0.00 0.00 0.00 2.24
2790 4451 7.749126 CCAAATTACTCGTCATGGTTTTAGTTC 59.251 37.037 0.00 0.00 0.00 3.01
2791 4452 7.972832 AATTACTCGTCATGGTTTTAGTTCA 57.027 32.000 0.00 0.00 0.00 3.18
2792 4453 7.972832 ATTACTCGTCATGGTTTTAGTTCAA 57.027 32.000 0.00 0.00 0.00 2.69
2793 4454 7.789273 TTACTCGTCATGGTTTTAGTTCAAA 57.211 32.000 0.00 0.00 0.00 2.69
2794 4455 6.877611 ACTCGTCATGGTTTTAGTTCAAAT 57.122 33.333 0.00 0.00 0.00 2.32
2795 4456 7.272037 ACTCGTCATGGTTTTAGTTCAAATT 57.728 32.000 0.00 0.00 0.00 1.82
2796 4457 7.712797 ACTCGTCATGGTTTTAGTTCAAATTT 58.287 30.769 0.00 0.00 0.00 1.82
2797 4458 7.647715 ACTCGTCATGGTTTTAGTTCAAATTTG 59.352 33.333 12.15 12.15 0.00 2.32
2798 4459 7.708051 TCGTCATGGTTTTAGTTCAAATTTGA 58.292 30.769 16.91 16.91 34.92 2.69
2799 4460 8.191446 TCGTCATGGTTTTAGTTCAAATTTGAA 58.809 29.630 26.01 26.01 44.31 2.69
2812 4473 7.743520 TTCAAATTTGAACTAAAACCACGAC 57.256 32.000 26.01 0.00 41.88 4.34
2813 4474 6.267070 TCAAATTTGAACTAAAACCACGACC 58.733 36.000 18.45 0.00 33.55 4.79
2814 4475 5.838531 AATTTGAACTAAAACCACGACCA 57.161 34.783 0.00 0.00 0.00 4.02
2815 4476 4.886247 TTTGAACTAAAACCACGACCAG 57.114 40.909 0.00 0.00 0.00 4.00
2816 4477 3.547054 TGAACTAAAACCACGACCAGT 57.453 42.857 0.00 0.00 0.00 4.00
2817 4478 4.669206 TGAACTAAAACCACGACCAGTA 57.331 40.909 0.00 0.00 0.00 2.74
2818 4479 5.021033 TGAACTAAAACCACGACCAGTAA 57.979 39.130 0.00 0.00 0.00 2.24
2819 4480 5.613329 TGAACTAAAACCACGACCAGTAAT 58.387 37.500 0.00 0.00 0.00 1.89
2820 4481 6.056884 TGAACTAAAACCACGACCAGTAATT 58.943 36.000 0.00 0.00 0.00 1.40
2821 4482 6.543100 TGAACTAAAACCACGACCAGTAATTT 59.457 34.615 0.00 0.00 0.00 1.82
2822 4483 6.308371 ACTAAAACCACGACCAGTAATTTG 57.692 37.500 0.00 0.00 0.00 2.32
2823 4484 4.577834 AAAACCACGACCAGTAATTTGG 57.422 40.909 0.00 0.00 44.09 3.28
2824 4485 3.495434 AACCACGACCAGTAATTTGGA 57.505 42.857 3.10 0.00 40.87 3.53
2825 4486 3.495434 ACCACGACCAGTAATTTGGAA 57.505 42.857 3.10 0.00 40.87 3.53
2826 4487 3.143728 ACCACGACCAGTAATTTGGAAC 58.856 45.455 3.10 0.00 40.87 3.62
2827 4488 2.158841 CCACGACCAGTAATTTGGAACG 59.841 50.000 3.10 9.99 40.87 3.95
2828 4489 2.158841 CACGACCAGTAATTTGGAACGG 59.841 50.000 17.33 5.85 40.87 4.44
2829 4490 2.037511 ACGACCAGTAATTTGGAACGGA 59.962 45.455 17.33 0.00 40.87 4.69
2830 4491 3.068560 CGACCAGTAATTTGGAACGGAA 58.931 45.455 3.10 0.00 40.87 4.30
2831 4492 3.124636 CGACCAGTAATTTGGAACGGAAG 59.875 47.826 3.10 0.00 40.87 3.46
2832 4493 3.418047 ACCAGTAATTTGGAACGGAAGG 58.582 45.455 3.10 0.00 40.87 3.46
2833 4494 3.073356 ACCAGTAATTTGGAACGGAAGGA 59.927 43.478 3.10 0.00 40.87 3.36
2834 4495 3.689649 CCAGTAATTTGGAACGGAAGGAG 59.310 47.826 0.00 0.00 40.87 3.69
2835 4496 4.324267 CAGTAATTTGGAACGGAAGGAGT 58.676 43.478 0.00 0.00 0.00 3.85
2864 4525 7.836842 AGTTAAATGTTTATAGCTTTGGTGGG 58.163 34.615 0.00 0.00 0.00 4.61
2873 4534 3.628646 CTTTGGTGGGGCGGAGGAG 62.629 68.421 0.00 0.00 0.00 3.69
2877 4538 3.541713 GTGGGGCGGAGGAGCTAG 61.542 72.222 0.00 0.00 37.29 3.42
2885 4546 0.894141 CGGAGGAGCTAGGATCCATG 59.106 60.000 15.82 7.09 39.47 3.66
2898 4570 5.053978 AGGATCCATGTATTGAGGGTTTC 57.946 43.478 15.82 0.00 0.00 2.78
2992 4691 5.022122 TCCCATCTATGGCAAAATGAACAA 58.978 37.500 3.27 0.00 46.70 2.83
2994 4693 4.807304 CCATCTATGGCAAAATGAACAAGC 59.193 41.667 0.00 0.00 41.75 4.01
3000 4699 3.005684 TGGCAAAATGAACAAGCTACCTG 59.994 43.478 0.00 0.00 0.00 4.00
3003 4702 4.616835 GCAAAATGAACAAGCTACCTGGAG 60.617 45.833 0.00 0.00 0.00 3.86
3024 4723 3.005791 AGGTTTGCCAAGTCAAGTAATGC 59.994 43.478 0.00 0.00 37.19 3.56
3107 4810 5.585844 CCCAAAAGGTTATTGCCATGATTTC 59.414 40.000 0.00 0.00 0.00 2.17
3123 4826 6.744537 CCATGATTTCAAATTGTTCGAGACTC 59.255 38.462 0.00 0.00 0.00 3.36
3183 4888 7.813148 TGTTACGAAATTTGACTTCCAACAAAA 59.187 29.630 0.00 0.00 39.01 2.44
3187 4892 9.541143 ACGAAATTTGACTTCCAACAAAATTAT 57.459 25.926 0.00 0.00 39.01 1.28
3198 4903 7.372451 TCCAACAAAATTATTAGTCTGACGG 57.628 36.000 1.52 0.00 0.00 4.79
3242 4949 3.375610 ACACACCGCGATATTTTGCAATA 59.624 39.130 8.23 0.00 32.00 1.90
3288 4996 9.793259 TGAAGTCACTCATCCTTAATTAGTTTT 57.207 29.630 0.00 0.00 0.00 2.43
3335 5043 4.459852 AATTGCTACCTGCCCATAGAAT 57.540 40.909 0.00 0.00 42.00 2.40
3348 5056 1.056700 ATAGAATGGTCGCCCCTGCT 61.057 55.000 0.00 0.00 34.43 4.24
3351 5059 2.819984 GAATGGTCGCCCCTGCTTGA 62.820 60.000 0.00 0.00 34.43 3.02
3363 5071 3.073446 GCTTGACTAGCGCGTGTC 58.927 61.111 22.60 22.60 40.71 3.67
3364 5072 2.445438 GCTTGACTAGCGCGTGTCC 61.445 63.158 25.00 11.91 40.71 4.02
3366 5074 1.344942 CTTGACTAGCGCGTGTCCAC 61.345 60.000 25.00 8.92 32.67 4.02
3381 5089 1.593006 GTCCACGCGTGATTGGATTAG 59.407 52.381 39.10 19.30 43.85 1.73
3382 5090 0.937304 CCACGCGTGATTGGATTAGG 59.063 55.000 39.10 15.64 34.46 2.69
3383 5091 1.651987 CACGCGTGATTGGATTAGGT 58.348 50.000 34.93 0.00 0.00 3.08
3384 5092 2.482316 CCACGCGTGATTGGATTAGGTA 60.482 50.000 39.10 0.00 34.46 3.08
3385 5093 2.538449 CACGCGTGATTGGATTAGGTAC 59.462 50.000 34.93 0.00 0.00 3.34
3386 5094 2.429610 ACGCGTGATTGGATTAGGTACT 59.570 45.455 12.93 0.00 46.37 2.73
3387 5095 2.794910 CGCGTGATTGGATTAGGTACTG 59.205 50.000 0.00 0.00 41.52 2.74
3388 5096 2.544267 GCGTGATTGGATTAGGTACTGC 59.456 50.000 0.00 0.00 41.52 4.40
3389 5097 3.131396 CGTGATTGGATTAGGTACTGCC 58.869 50.000 0.00 0.00 41.52 4.85
3390 5098 3.131396 GTGATTGGATTAGGTACTGCCG 58.869 50.000 0.00 0.00 41.52 5.69
3391 5099 2.769663 TGATTGGATTAGGTACTGCCGT 59.230 45.455 0.00 0.00 41.52 5.68
3392 5100 3.962063 TGATTGGATTAGGTACTGCCGTA 59.038 43.478 0.00 0.00 41.52 4.02
3393 5101 4.591498 TGATTGGATTAGGTACTGCCGTAT 59.409 41.667 0.00 0.00 41.52 3.06
3394 5102 4.330944 TTGGATTAGGTACTGCCGTATG 57.669 45.455 0.00 0.00 41.52 2.39
3395 5103 2.036733 TGGATTAGGTACTGCCGTATGC 59.963 50.000 0.00 0.00 41.52 3.14
3416 5124 6.045072 TGCATATCAGCATATGACATCAGA 57.955 37.500 6.97 0.00 43.37 3.27
3417 5125 6.650120 TGCATATCAGCATATGACATCAGAT 58.350 36.000 6.97 0.00 43.37 2.90
3418 5126 7.788026 TGCATATCAGCATATGACATCAGATA 58.212 34.615 6.97 1.70 43.37 1.98
3419 5127 8.429641 TGCATATCAGCATATGACATCAGATAT 58.570 33.333 6.97 3.92 43.37 1.63
3420 5128 9.274206 GCATATCAGCATATGACATCAGATATT 57.726 33.333 6.97 0.00 43.37 1.28
3449 5157 9.482627 AATTTCACAACAGTTTGAAGTTTAACA 57.517 25.926 0.00 0.00 36.48 2.41
3450 5158 8.873215 TTTCACAACAGTTTGAAGTTTAACAA 57.127 26.923 0.00 0.00 36.48 2.83
3451 5159 8.514136 TTCACAACAGTTTGAAGTTTAACAAG 57.486 30.769 0.00 1.05 36.48 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
249 261 9.613428 AACTGCTCTTGTAAAACATGCTATATA 57.387 29.630 0.00 0.00 0.00 0.86
250 262 8.511604 AACTGCTCTTGTAAAACATGCTATAT 57.488 30.769 0.00 0.00 0.00 0.86
251 263 7.921786 AACTGCTCTTGTAAAACATGCTATA 57.078 32.000 0.00 0.00 0.00 1.31
252 264 6.824305 AACTGCTCTTGTAAAACATGCTAT 57.176 33.333 0.00 0.00 0.00 2.97
283 318 3.444742 TGTGCTTGGCCTTCAATATTCAG 59.555 43.478 3.32 0.00 34.45 3.02
298 333 0.956633 ATCTGGTGCACTTGTGCTTG 59.043 50.000 23.53 12.34 35.49 4.01
462 556 9.342308 TGTCACAGAGATAAATCTTGTCTTTTT 57.658 29.630 0.00 0.00 37.25 1.94
534 2046 9.764363 ATTTCTTTTCCTTATCACTTTTGGTTC 57.236 29.630 0.00 0.00 0.00 3.62
661 2173 1.929836 CGTTTCATGGAGTAGCTCTGC 59.070 52.381 0.00 0.00 35.00 4.26
767 2289 3.311106 ACATGCTTGAACTTTCAATGCG 58.689 40.909 6.60 3.42 45.26 4.73
776 2298 4.397417 GGATAGCTTCAACATGCTTGAACT 59.603 41.667 15.17 16.85 40.35 3.01
897 2422 9.865152 AGCTGATCTCTCATGATATATTAGCTA 57.135 33.333 17.92 0.00 0.00 3.32
898 2423 8.771521 AGCTGATCTCTCATGATATATTAGCT 57.228 34.615 15.33 15.33 0.00 3.32
899 2424 9.467258 GAAGCTGATCTCTCATGATATATTAGC 57.533 37.037 12.34 12.34 0.00 3.09
1350 2900 3.807622 TCGCTACTTTGTCCTTTCTTGTG 59.192 43.478 0.00 0.00 0.00 3.33
1416 2966 6.349611 GCACAACAAACTCCATCATGTTATCT 60.350 38.462 0.00 0.00 34.45 1.98
1601 3158 2.241160 TCTTACCTACTGTGCGACCAA 58.759 47.619 0.00 0.00 0.00 3.67
1617 3174 4.336993 ACGTGAGCAACCAATGTTTTCTTA 59.663 37.500 0.00 0.00 30.42 2.10
1873 3430 4.796038 AAATTGGCTTCACTGATCCAAG 57.204 40.909 14.81 0.00 41.32 3.61
2105 3665 7.551974 TCCTTTCAATCATTCTTCTGCTCTTAG 59.448 37.037 0.00 0.00 0.00 2.18
2106 3666 7.397221 TCCTTTCAATCATTCTTCTGCTCTTA 58.603 34.615 0.00 0.00 0.00 2.10
2220 3780 3.284617 TGTAGCTGAGTAAGGTATCGCA 58.715 45.455 0.00 0.00 40.84 5.10
2284 3844 5.151454 CCTAACACTGGGATCTTCTAGGAT 58.849 45.833 0.00 0.00 0.00 3.24
2298 3858 1.203001 TCCCCTTTTGGCCTAACACTG 60.203 52.381 3.32 0.00 38.58 3.66
2415 3975 1.533033 TCGCTTCCTCCCTGACACA 60.533 57.895 0.00 0.00 0.00 3.72
2553 4117 0.674895 AAAGCATGCCCGAGTGACTC 60.675 55.000 15.66 1.65 0.00 3.36
2616 4211 7.967908 AGTAAAAGGAGAAAGAGAATGAGTCA 58.032 34.615 0.00 0.00 0.00 3.41
2617 4212 8.840833 AAGTAAAAGGAGAAAGAGAATGAGTC 57.159 34.615 0.00 0.00 0.00 3.36
2754 4415 2.093869 CGAGTAATTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
2755 4416 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
2756 4417 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
2757 4418 3.581755 TGACGAGTAATTTGGAACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
2759 4420 3.063452 CCATGACGAGTAATTTGGAACGG 59.937 47.826 0.00 0.00 0.00 4.44
2760 4421 3.682858 ACCATGACGAGTAATTTGGAACG 59.317 43.478 0.00 0.00 0.00 3.95
2761 4422 5.622770 AACCATGACGAGTAATTTGGAAC 57.377 39.130 0.00 0.00 0.00 3.62
2763 4424 6.938030 ACTAAAACCATGACGAGTAATTTGGA 59.062 34.615 0.00 0.00 0.00 3.53
2764 4425 7.141100 ACTAAAACCATGACGAGTAATTTGG 57.859 36.000 0.00 0.00 0.00 3.28
2765 4426 8.286800 TGAACTAAAACCATGACGAGTAATTTG 58.713 33.333 0.00 0.00 0.00 2.32
2766 4427 8.385898 TGAACTAAAACCATGACGAGTAATTT 57.614 30.769 0.00 0.00 0.00 1.82
2767 4428 7.972832 TGAACTAAAACCATGACGAGTAATT 57.027 32.000 0.00 0.00 0.00 1.40
2768 4429 7.972832 TTGAACTAAAACCATGACGAGTAAT 57.027 32.000 0.00 0.00 0.00 1.89
2769 4430 7.789273 TTTGAACTAAAACCATGACGAGTAA 57.211 32.000 0.00 0.00 0.00 2.24
2770 4431 7.972832 ATTTGAACTAAAACCATGACGAGTA 57.027 32.000 0.00 0.00 0.00 2.59
2771 4432 6.877611 ATTTGAACTAAAACCATGACGAGT 57.122 33.333 0.00 0.00 0.00 4.18
2772 4433 7.860373 TCAAATTTGAACTAAAACCATGACGAG 59.140 33.333 18.45 0.00 33.55 4.18
2773 4434 7.708051 TCAAATTTGAACTAAAACCATGACGA 58.292 30.769 18.45 0.00 33.55 4.20
2774 4435 7.922505 TCAAATTTGAACTAAAACCATGACG 57.077 32.000 18.45 0.00 33.55 4.35
2788 4449 6.752815 GGTCGTGGTTTTAGTTCAAATTTGAA 59.247 34.615 26.01 26.01 44.31 2.69
2789 4450 6.127703 TGGTCGTGGTTTTAGTTCAAATTTGA 60.128 34.615 16.91 16.91 34.92 2.69
2790 4451 6.037098 TGGTCGTGGTTTTAGTTCAAATTTG 58.963 36.000 12.15 12.15 0.00 2.32
2791 4452 6.127563 ACTGGTCGTGGTTTTAGTTCAAATTT 60.128 34.615 0.00 0.00 0.00 1.82
2792 4453 5.358725 ACTGGTCGTGGTTTTAGTTCAAATT 59.641 36.000 0.00 0.00 0.00 1.82
2793 4454 4.885325 ACTGGTCGTGGTTTTAGTTCAAAT 59.115 37.500 0.00 0.00 0.00 2.32
2794 4455 4.263435 ACTGGTCGTGGTTTTAGTTCAAA 58.737 39.130 0.00 0.00 0.00 2.69
2795 4456 3.876341 ACTGGTCGTGGTTTTAGTTCAA 58.124 40.909 0.00 0.00 0.00 2.69
2796 4457 3.547054 ACTGGTCGTGGTTTTAGTTCA 57.453 42.857 0.00 0.00 0.00 3.18
2797 4458 6.549912 AATTACTGGTCGTGGTTTTAGTTC 57.450 37.500 0.00 0.00 0.00 3.01
2798 4459 6.238814 CCAAATTACTGGTCGTGGTTTTAGTT 60.239 38.462 0.00 0.00 0.00 2.24
2799 4460 5.239963 CCAAATTACTGGTCGTGGTTTTAGT 59.760 40.000 0.00 0.00 0.00 2.24
2800 4461 5.470777 TCCAAATTACTGGTCGTGGTTTTAG 59.529 40.000 0.00 0.00 37.74 1.85
2801 4462 5.374921 TCCAAATTACTGGTCGTGGTTTTA 58.625 37.500 0.00 0.00 37.74 1.52
2802 4463 4.208746 TCCAAATTACTGGTCGTGGTTTT 58.791 39.130 0.00 0.00 37.74 2.43
2803 4464 3.822940 TCCAAATTACTGGTCGTGGTTT 58.177 40.909 0.00 0.00 37.74 3.27
2804 4465 3.495434 TCCAAATTACTGGTCGTGGTT 57.505 42.857 0.00 0.00 37.74 3.67
2805 4466 3.143728 GTTCCAAATTACTGGTCGTGGT 58.856 45.455 0.00 0.00 37.74 4.16
2806 4467 2.158841 CGTTCCAAATTACTGGTCGTGG 59.841 50.000 0.00 0.00 37.74 4.94
2807 4468 2.158841 CCGTTCCAAATTACTGGTCGTG 59.841 50.000 11.95 4.65 37.74 4.35
2808 4469 2.037511 TCCGTTCCAAATTACTGGTCGT 59.962 45.455 11.95 0.00 37.74 4.34
2809 4470 2.690786 TCCGTTCCAAATTACTGGTCG 58.309 47.619 0.00 3.69 37.74 4.79
2810 4471 3.439129 CCTTCCGTTCCAAATTACTGGTC 59.561 47.826 0.00 0.00 37.74 4.02
2811 4472 3.073356 TCCTTCCGTTCCAAATTACTGGT 59.927 43.478 0.00 0.00 37.74 4.00
2812 4473 3.681593 TCCTTCCGTTCCAAATTACTGG 58.318 45.455 0.00 0.00 37.87 4.00
2813 4474 4.324267 ACTCCTTCCGTTCCAAATTACTG 58.676 43.478 0.00 0.00 0.00 2.74
2814 4475 4.635699 ACTCCTTCCGTTCCAAATTACT 57.364 40.909 0.00 0.00 0.00 2.24
2815 4476 6.110707 TCATACTCCTTCCGTTCCAAATTAC 58.889 40.000 0.00 0.00 0.00 1.89
2816 4477 6.070424 ACTCATACTCCTTCCGTTCCAAATTA 60.070 38.462 0.00 0.00 0.00 1.40
2817 4478 5.174037 TCATACTCCTTCCGTTCCAAATT 57.826 39.130 0.00 0.00 0.00 1.82
2818 4479 4.225267 ACTCATACTCCTTCCGTTCCAAAT 59.775 41.667 0.00 0.00 0.00 2.32
2819 4480 3.581332 ACTCATACTCCTTCCGTTCCAAA 59.419 43.478 0.00 0.00 0.00 3.28
2820 4481 3.170717 ACTCATACTCCTTCCGTTCCAA 58.829 45.455 0.00 0.00 0.00 3.53
2821 4482 2.816411 ACTCATACTCCTTCCGTTCCA 58.184 47.619 0.00 0.00 0.00 3.53
2822 4483 3.889520 AACTCATACTCCTTCCGTTCC 57.110 47.619 0.00 0.00 0.00 3.62
2823 4484 6.817140 ACATTTAACTCATACTCCTTCCGTTC 59.183 38.462 0.00 0.00 0.00 3.95
2824 4485 6.708285 ACATTTAACTCATACTCCTTCCGTT 58.292 36.000 0.00 0.00 0.00 4.44
2825 4486 6.295719 ACATTTAACTCATACTCCTTCCGT 57.704 37.500 0.00 0.00 0.00 4.69
2826 4487 7.611213 AAACATTTAACTCATACTCCTTCCG 57.389 36.000 0.00 0.00 0.00 4.30
2862 4523 3.837213 ATCCTAGCTCCTCCGCCCC 62.837 68.421 0.00 0.00 0.00 5.80
2864 4525 2.279810 GGATCCTAGCTCCTCCGCC 61.280 68.421 3.84 0.00 0.00 6.13
2873 4534 3.584848 ACCCTCAATACATGGATCCTAGC 59.415 47.826 14.23 0.00 0.00 3.42
2877 4538 4.580580 GTGAAACCCTCAATACATGGATCC 59.419 45.833 4.20 4.20 35.22 3.36
2885 4546 5.163854 CGAGTCATTGTGAAACCCTCAATAC 60.164 44.000 0.00 0.00 36.99 1.89
2898 4570 1.462283 CTCACCTTGCGAGTCATTGTG 59.538 52.381 0.00 0.68 0.00 3.33
2919 4591 4.381505 GCCCAGATTTTTCGCCATTTCTTA 60.382 41.667 0.00 0.00 0.00 2.10
2976 4648 5.016173 AGGTAGCTTGTTCATTTTGCCATA 58.984 37.500 0.00 0.00 0.00 2.74
3000 4699 1.692411 ACTTGACTTGGCAAACCTCC 58.308 50.000 0.00 0.00 36.63 4.30
3003 4702 3.243704 TGCATTACTTGACTTGGCAAACC 60.244 43.478 0.00 0.00 0.00 3.27
3077 4776 6.882768 TGGCAATAACCTTTTGGGATTTAT 57.117 33.333 0.00 0.00 46.08 1.40
3092 4791 7.816513 TCGAACAATTTGAAATCATGGCAATAA 59.183 29.630 2.79 0.00 0.00 1.40
3097 4800 5.287035 GTCTCGAACAATTTGAAATCATGGC 59.713 40.000 2.79 0.00 0.00 4.40
3107 4810 1.798223 TGCCGAGTCTCGAACAATTTG 59.202 47.619 23.74 5.24 43.74 2.32
3123 4826 3.782046 AGTTTACTACTGTAGCATGCCG 58.218 45.455 15.66 3.08 35.19 5.69
3183 4888 3.067742 CCGGTCACCGTCAGACTAATAAT 59.932 47.826 16.87 0.00 46.80 1.28
3187 4892 0.250858 TCCGGTCACCGTCAGACTAA 60.251 55.000 16.87 0.00 46.80 2.24
3188 4893 0.957395 GTCCGGTCACCGTCAGACTA 60.957 60.000 16.87 0.00 46.80 2.59
3198 4903 1.153429 GCCATACAGGTCCGGTCAC 60.153 63.158 0.00 0.00 40.61 3.67
3204 4909 1.165270 GTGTGTTGCCATACAGGTCC 58.835 55.000 0.00 0.00 40.61 4.46
3304 5012 4.898370 GCAGGTAGCAATTTCTAAACGAG 58.102 43.478 0.00 0.00 44.79 4.18
3348 5056 1.372499 GTGGACACGCGCTAGTCAA 60.372 57.895 24.16 14.73 36.50 3.18
3363 5071 0.937304 CCTAATCCAATCACGCGTGG 59.063 55.000 36.41 22.33 36.13 4.94
3364 5072 1.651987 ACCTAATCCAATCACGCGTG 58.348 50.000 32.76 32.76 0.00 5.34
3366 5074 2.794910 CAGTACCTAATCCAATCACGCG 59.205 50.000 3.53 3.53 0.00 6.01
3369 5077 3.131396 CGGCAGTACCTAATCCAATCAC 58.869 50.000 0.00 0.00 35.61 3.06
3372 5080 4.802918 GCATACGGCAGTACCTAATCCAAT 60.803 45.833 0.00 0.00 43.97 3.16
3394 5102 8.834749 ATATCTGATGTCATATGCTGATATGC 57.165 34.615 14.18 0.00 40.92 3.14
3423 5131 9.482627 TGTTAAACTTCAAACTGTTGTGAAATT 57.517 25.926 14.47 10.55 36.07 1.82
3424 5132 9.482627 TTGTTAAACTTCAAACTGTTGTGAAAT 57.517 25.926 14.47 6.60 36.07 2.17
3425 5133 8.873215 TTGTTAAACTTCAAACTGTTGTGAAA 57.127 26.923 14.47 3.40 36.07 2.69
3426 5134 8.514136 CTTGTTAAACTTCAAACTGTTGTGAA 57.486 30.769 13.53 13.53 36.07 3.18


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

AutoCloner maintained by Alex Coulton.