Multiple sequence alignment - TraesCS3B01G446400

Loading Multiple Alignment...

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 TraesCS3B01G446400 chr3B 100.000 2627 0 0 1 2627 685876181 685873555 0.000000e+00 4852.0
1 TraesCS3B01G446400 chr3B 96.441 1714 59 2 807 2519 685763763 685762051 0.000000e+00 2826.0
2 TraesCS3B01G446400 chr3B 88.084 1519 115 27 636 2120 685910491 685909005 0.000000e+00 1742.0
3 TraesCS3B01G446400 chr3B 85.624 1579 164 28 636 2169 685941987 685940427 0.000000e+00 1600.0
4 TraesCS3B01G446400 chr3B 86.532 1485 153 22 636 2092 685980443 685978978 0.000000e+00 1591.0
5 TraesCS3B01G446400 chr3B 92.344 627 35 8 1 616 685764418 685763794 0.000000e+00 880.0
6 TraesCS3B01G446400 chr3B 87.481 671 78 5 1857 2527 685698662 685697998 0.000000e+00 769.0
7 TraesCS3B01G446400 chr3B 100.000 160 0 0 2813 2972 685873369 685873210 2.240000e-76 296.0
8 TraesCS3B01G446400 chr3B 84.689 209 27 5 323 527 686045881 686045674 1.400000e-48 204.0
9 TraesCS3B01G446400 chr3B 88.750 160 12 1 2813 2972 685699760 685699607 1.090000e-44 191.0
10 TraesCS3B01G446400 chr3A 93.345 2284 112 24 1 2262 655937621 655935356 0.000000e+00 3339.0
11 TraesCS3B01G446400 chr3A 93.211 2283 115 23 1 2262 658185859 658188122 0.000000e+00 3321.0
12 TraesCS3B01G446400 chr3A 87.508 1521 119 26 639 2120 655995303 655993815 0.000000e+00 1690.0
13 TraesCS3B01G446400 chr3A 94.332 247 14 0 2262 2508 658189163 658189409 2.160000e-101 379.0
14 TraesCS3B01G446400 chr3A 93.927 247 14 1 2262 2508 655934318 655934073 3.620000e-99 372.0
15 TraesCS3B01G446400 chr3D 94.859 1634 77 3 1000 2627 520641870 520640238 0.000000e+00 2545.0
16 TraesCS3B01G446400 chr3D 88.735 1518 108 21 636 2120 520678575 520677088 0.000000e+00 1797.0
17 TraesCS3B01G446400 chr3D 87.492 1519 154 19 1119 2627 520640133 520638641 0.000000e+00 1720.0
18 TraesCS3B01G446400 chr3D 87.173 1489 149 17 712 2169 520684429 520682952 0.000000e+00 1653.0
19 TraesCS3B01G446400 chr3D 86.336 1493 143 26 636 2092 520703896 520702429 0.000000e+00 1570.0
20 TraesCS3B01G446400 chr3D 93.496 984 43 11 1 965 520642853 520641872 0.000000e+00 1443.0
21 TraesCS3B01G446400 chr3D 83.591 323 41 9 269 582 520704240 520703921 2.900000e-75 292.0
22 TraesCS3B01G446400 chr3D 87.586 145 16 2 819 961 520656991 520656847 1.830000e-37 167.0
23 TraesCS3B01G446400 chr3D 84.677 124 15 3 447 569 520676674 520676554 1.450000e-23 121.0
24 TraesCS3B01G446400 chr1A 87.302 63 8 0 25 87 547278613 547278675 4.110000e-09 73.1
25 TraesCS3B01G446400 chr5D 85.484 62 8 1 24 84 108989717 108989778 2.470000e-06 63.9
26 TraesCS3B01G446400 chr7D 81.250 80 10 5 23 101 551552423 551552498 3.200000e-05 60.2
27 TraesCS3B01G446400 chr2B 85.455 55 8 0 24 78 185500239 185500293 1.150000e-04 58.4
28 TraesCS3B01G446400 chr6B 94.444 36 2 0 24 59 529698298 529698333 4.140000e-04 56.5


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 TraesCS3B01G446400 chr3B 685873210 685876181 2971 True 2574.000000 4852 100.0000 1 2972 2 chr3B.!!$R7 2971
1 TraesCS3B01G446400 chr3B 685762051 685764418 2367 True 1853.000000 2826 94.3925 1 2519 2 chr3B.!!$R6 2518
2 TraesCS3B01G446400 chr3B 685909005 685910491 1486 True 1742.000000 1742 88.0840 636 2120 1 chr3B.!!$R1 1484
3 TraesCS3B01G446400 chr3B 685940427 685941987 1560 True 1600.000000 1600 85.6240 636 2169 1 chr3B.!!$R2 1533
4 TraesCS3B01G446400 chr3B 685978978 685980443 1465 True 1591.000000 1591 86.5320 636 2092 1 chr3B.!!$R3 1456
5 TraesCS3B01G446400 chr3B 685697998 685699760 1762 True 480.000000 769 88.1155 1857 2972 2 chr3B.!!$R5 1115
6 TraesCS3B01G446400 chr3A 655934073 655937621 3548 True 1855.500000 3339 93.6360 1 2508 2 chr3A.!!$R2 2507
7 TraesCS3B01G446400 chr3A 658185859 658189409 3550 False 1850.000000 3321 93.7715 1 2508 2 chr3A.!!$F1 2507
8 TraesCS3B01G446400 chr3A 655993815 655995303 1488 True 1690.000000 1690 87.5080 639 2120 1 chr3A.!!$R1 1481
9 TraesCS3B01G446400 chr3D 520638641 520642853 4212 True 1902.666667 2545 91.9490 1 2627 3 chr3D.!!$R3 2626
10 TraesCS3B01G446400 chr3D 520682952 520684429 1477 True 1653.000000 1653 87.1730 712 2169 1 chr3D.!!$R2 1457
11 TraesCS3B01G446400 chr3D 520676554 520678575 2021 True 959.000000 1797 86.7060 447 2120 2 chr3D.!!$R4 1673
12 TraesCS3B01G446400 chr3D 520702429 520704240 1811 True 931.000000 1570 84.9635 269 2092 2 chr3D.!!$R5 1823

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
383 391 0.304705 AGCGTTGCTTGTTGAAGACG 59.695 50.0 0.00 0.0 33.89 4.18 F
487 497 1.188871 TACACGGTGTGGCTGATCCA 61.189 55.0 23.36 0.0 44.18 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1919 1998 1.054978 GTTCCTAATCTCCCCGGCCT 61.055 60.000 0.0 0.0 0.00 5.19 R
2396 5167 1.063114 GTGGCTCCTCTAGGGTCCTAA 60.063 57.143 0.0 0.0 36.25 2.69 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
81 82 5.826208 ACCCCGATAGAATGTGGTAAAAATC 59.174 40.000 0.00 0.00 39.76 2.17
103 105 7.648039 ATCTGAGAGTATTACGAGAAAACCT 57.352 36.000 0.00 0.00 0.00 3.50
139 141 2.167693 ACAAACCGAACACTCTCTGACA 59.832 45.455 0.00 0.00 0.00 3.58
336 344 6.213677 ACAAAATCTTAAAAGACTTTCCGCC 58.786 36.000 0.00 0.00 32.73 6.13
383 391 0.304705 AGCGTTGCTTGTTGAAGACG 59.695 50.000 0.00 0.00 33.89 4.18
385 393 1.730176 CGTTGCTTGTTGAAGACGTG 58.270 50.000 0.00 0.00 29.26 4.49
421 429 4.278975 AGAAGCGAAAGGTCTCTCATTT 57.721 40.909 0.00 0.00 43.76 2.32
422 430 5.407407 AGAAGCGAAAGGTCTCTCATTTA 57.593 39.130 0.00 0.00 43.76 1.40
423 431 5.983540 AGAAGCGAAAGGTCTCTCATTTAT 58.016 37.500 0.00 0.00 43.76 1.40
426 436 8.041323 AGAAGCGAAAGGTCTCTCATTTATAAA 58.959 33.333 0.00 0.00 43.76 1.40
487 497 1.188871 TACACGGTGTGGCTGATCCA 61.189 55.000 23.36 0.00 44.18 3.41
534 553 4.212636 GTGGCAACTACATACAAAGTCGTT 59.787 41.667 0.00 0.00 37.61 3.85
790 832 1.922570 ACGGCAGCGTTAATACTCAG 58.077 50.000 0.00 0.00 0.00 3.35
974 1047 6.939622 AGCTTGCAAATTAATTCTAGCCTTT 58.060 32.000 15.01 1.25 0.00 3.11
1010 1089 1.278985 AGTAGTGCACATGGCTGCTTA 59.721 47.619 21.04 0.00 45.15 3.09
1563 1642 2.020720 GACTCTCTCGAGATGCTCCAA 58.979 52.381 17.03 0.00 39.74 3.53
1623 1702 2.679716 GCCCTCCAAGGAGCACAT 59.320 61.111 10.68 0.00 37.67 3.21
2003 2082 8.627208 AGATTGATGTTATGAGTTGTGAACTT 57.373 30.769 0.00 0.00 43.03 2.66
2111 2485 4.177165 TCAGCATGTGATTTTCGCAAAT 57.823 36.364 0.00 0.00 40.59 2.32
2241 2668 7.393216 AGTTTATGCCATTGCCTTATCAAAAA 58.607 30.769 0.00 0.00 36.33 1.94
2249 2676 7.094677 GCCATTGCCTTATCAAAAACTTTCATT 60.095 33.333 0.00 0.00 0.00 2.57
2299 5069 6.884472 TTAACATATTGACAGGAAGGAGGA 57.116 37.500 0.00 0.00 0.00 3.71
2340 5110 3.334583 TCAAGATTTTCCGGACTCTGG 57.665 47.619 1.83 4.69 0.00 3.86
2396 5167 3.450457 TGGAGACAACAAAACTGCCAAAT 59.550 39.130 0.00 0.00 37.44 2.32
2417 5188 1.001760 GGACCCTAGAGGAGCCACA 59.998 63.158 0.00 0.00 39.89 4.17
2529 5300 0.598065 ATGACCGCTTCCTTTTGCAC 59.402 50.000 0.00 0.00 0.00 4.57
2530 5301 1.285950 GACCGCTTCCTTTTGCACC 59.714 57.895 0.00 0.00 0.00 5.01
2554 5325 6.530534 CCTCATGAACTTTACTACACTTACGG 59.469 42.308 0.00 0.00 0.00 4.02
2566 5337 2.356695 ACACTTACGGGCAACTTTTCAC 59.643 45.455 0.00 0.00 0.00 3.18
2574 5345 1.339929 GGCAACTTTTCACGGAATGGT 59.660 47.619 0.00 0.00 0.00 3.55
2603 5380 2.219080 TGGCAAGGCATGATTGAGAA 57.781 45.000 13.52 0.00 0.00 2.87
2606 5383 2.231964 GGCAAGGCATGATTGAGAAACA 59.768 45.455 13.52 0.00 0.00 2.83
2615 5392 4.292186 TGATTGAGAAACAAGGGGAGAG 57.708 45.455 0.00 0.00 42.02 3.20
2618 5395 0.621082 GAGAAACAAGGGGAGAGGGG 59.379 60.000 0.00 0.00 0.00 4.79
2833 5610 3.389925 AACGTGGAGTTATTTCCGTGA 57.610 42.857 0.00 0.00 42.14 4.35
2834 5611 2.955614 ACGTGGAGTTATTTCCGTGAG 58.044 47.619 0.00 0.00 40.27 3.51
2835 5612 2.298163 ACGTGGAGTTATTTCCGTGAGT 59.702 45.455 0.00 0.00 40.27 3.41
2836 5613 3.243975 ACGTGGAGTTATTTCCGTGAGTT 60.244 43.478 0.00 0.00 40.27 3.01
2837 5614 3.122948 CGTGGAGTTATTTCCGTGAGTTG 59.877 47.826 0.00 0.00 40.27 3.16
2838 5615 3.071479 TGGAGTTATTTCCGTGAGTTGC 58.929 45.455 0.00 0.00 40.27 4.17
2839 5616 3.244422 TGGAGTTATTTCCGTGAGTTGCT 60.244 43.478 0.00 0.00 40.27 3.91
2840 5617 3.751698 GGAGTTATTTCCGTGAGTTGCTT 59.248 43.478 0.00 0.00 0.00 3.91
2841 5618 4.215613 GGAGTTATTTCCGTGAGTTGCTTT 59.784 41.667 0.00 0.00 0.00 3.51
2842 5619 5.278315 GGAGTTATTTCCGTGAGTTGCTTTT 60.278 40.000 0.00 0.00 0.00 2.27
2843 5620 5.758924 AGTTATTTCCGTGAGTTGCTTTTC 58.241 37.500 0.00 0.00 0.00 2.29
2844 5621 2.748461 TTTCCGTGAGTTGCTTTTCG 57.252 45.000 0.00 0.00 0.00 3.46
2845 5622 1.658994 TTCCGTGAGTTGCTTTTCGT 58.341 45.000 0.00 0.00 0.00 3.85
2846 5623 2.512485 TCCGTGAGTTGCTTTTCGTA 57.488 45.000 0.00 0.00 0.00 3.43
2847 5624 2.400399 TCCGTGAGTTGCTTTTCGTAG 58.600 47.619 0.00 0.00 0.00 3.51
2848 5625 2.034939 TCCGTGAGTTGCTTTTCGTAGA 59.965 45.455 0.00 0.00 0.00 2.59
2849 5626 2.993899 CCGTGAGTTGCTTTTCGTAGAT 59.006 45.455 0.00 0.00 35.04 1.98
2850 5627 3.181530 CCGTGAGTTGCTTTTCGTAGATG 60.182 47.826 0.00 0.00 35.04 2.90
2851 5628 3.673338 CGTGAGTTGCTTTTCGTAGATGA 59.327 43.478 0.00 0.00 35.04 2.92
2852 5629 4.327357 CGTGAGTTGCTTTTCGTAGATGAT 59.673 41.667 0.00 0.00 35.04 2.45
2853 5630 5.163953 CGTGAGTTGCTTTTCGTAGATGATT 60.164 40.000 0.00 0.00 35.04 2.57
2854 5631 6.603095 GTGAGTTGCTTTTCGTAGATGATTT 58.397 36.000 0.00 0.00 35.04 2.17
2855 5632 6.738649 GTGAGTTGCTTTTCGTAGATGATTTC 59.261 38.462 0.00 0.00 35.04 2.17
2856 5633 6.128282 TGAGTTGCTTTTCGTAGATGATTTCC 60.128 38.462 0.00 0.00 35.04 3.13
2857 5634 5.705441 AGTTGCTTTTCGTAGATGATTTCCA 59.295 36.000 0.00 0.00 35.04 3.53
2858 5635 6.375455 AGTTGCTTTTCGTAGATGATTTCCAT 59.625 34.615 0.00 0.00 38.43 3.41
2859 5636 7.552687 AGTTGCTTTTCGTAGATGATTTCCATA 59.447 33.333 0.00 0.00 35.17 2.74
2860 5637 7.857734 TGCTTTTCGTAGATGATTTCCATAA 57.142 32.000 0.00 0.00 35.17 1.90
2861 5638 7.919690 TGCTTTTCGTAGATGATTTCCATAAG 58.080 34.615 0.00 0.00 35.17 1.73
2862 5639 7.552687 TGCTTTTCGTAGATGATTTCCATAAGT 59.447 33.333 0.00 0.00 35.17 2.24
2863 5640 8.398665 GCTTTTCGTAGATGATTTCCATAAGTT 58.601 33.333 0.00 0.00 35.17 2.66
2867 5644 9.542462 TTCGTAGATGATTTCCATAAGTTTAGG 57.458 33.333 0.00 0.00 35.17 2.69
2868 5645 8.920174 TCGTAGATGATTTCCATAAGTTTAGGA 58.080 33.333 0.00 0.00 35.17 2.94
2869 5646 9.712305 CGTAGATGATTTCCATAAGTTTAGGAT 57.288 33.333 0.00 0.00 35.17 3.24
2880 5657 9.135189 TCCATAAGTTTAGGATTTTGATCATGG 57.865 33.333 0.00 0.00 0.00 3.66
2881 5658 8.917088 CCATAAGTTTAGGATTTTGATCATGGT 58.083 33.333 0.00 0.00 0.00 3.55
2882 5659 9.740239 CATAAGTTTAGGATTTTGATCATGGTG 57.260 33.333 0.00 0.00 0.00 4.17
2883 5660 9.699410 ATAAGTTTAGGATTTTGATCATGGTGA 57.301 29.630 0.00 0.00 0.00 4.02
2884 5661 8.599624 AAGTTTAGGATTTTGATCATGGTGAT 57.400 30.769 0.00 0.00 40.34 3.06
2885 5662 8.004087 AGTTTAGGATTTTGATCATGGTGATG 57.996 34.615 0.00 0.00 37.20 3.07
2886 5663 7.616935 AGTTTAGGATTTTGATCATGGTGATGT 59.383 33.333 0.00 0.00 37.20 3.06
2887 5664 7.572523 TTAGGATTTTGATCATGGTGATGTC 57.427 36.000 0.00 0.00 37.20 3.06
2888 5665 4.891756 AGGATTTTGATCATGGTGATGTCC 59.108 41.667 0.00 0.00 37.20 4.02
2889 5666 4.261322 GGATTTTGATCATGGTGATGTCCG 60.261 45.833 0.00 0.00 37.20 4.79
2890 5667 3.348647 TTTGATCATGGTGATGTCCGT 57.651 42.857 0.00 0.00 37.20 4.69
2891 5668 2.314323 TGATCATGGTGATGTCCGTG 57.686 50.000 0.00 0.00 43.59 4.94
2892 5669 0.940126 GATCATGGTGATGTCCGTGC 59.060 55.000 0.00 0.00 42.39 5.34
2893 5670 0.464373 ATCATGGTGATGTCCGTGCC 60.464 55.000 0.00 0.00 42.39 5.01
2894 5671 1.377072 CATGGTGATGTCCGTGCCA 60.377 57.895 0.00 0.00 37.62 4.92
2895 5672 1.078214 ATGGTGATGTCCGTGCCAG 60.078 57.895 0.00 0.00 32.28 4.85
2896 5673 2.436646 GGTGATGTCCGTGCCAGG 60.437 66.667 0.00 0.00 0.00 4.45
2897 5674 2.347490 GTGATGTCCGTGCCAGGT 59.653 61.111 0.00 0.00 0.00 4.00
2898 5675 1.302511 GTGATGTCCGTGCCAGGTT 60.303 57.895 0.00 0.00 0.00 3.50
2899 5676 1.302431 TGATGTCCGTGCCAGGTTG 60.302 57.895 0.00 0.00 0.00 3.77
2900 5677 1.003839 GATGTCCGTGCCAGGTTGA 60.004 57.895 0.00 0.00 0.00 3.18
2901 5678 1.003355 ATGTCCGTGCCAGGTTGAG 60.003 57.895 0.00 0.00 0.00 3.02
2902 5679 3.050275 GTCCGTGCCAGGTTGAGC 61.050 66.667 0.00 0.00 0.00 4.26
2903 5680 3.241530 TCCGTGCCAGGTTGAGCT 61.242 61.111 0.00 0.00 0.00 4.09
2904 5681 2.743928 CCGTGCCAGGTTGAGCTC 60.744 66.667 6.82 6.82 0.00 4.09
2905 5682 2.031012 CGTGCCAGGTTGAGCTCA 59.969 61.111 13.74 13.74 0.00 4.26
2906 5683 1.376424 CGTGCCAGGTTGAGCTCAT 60.376 57.895 19.04 0.00 0.00 2.90
2907 5684 1.364626 CGTGCCAGGTTGAGCTCATC 61.365 60.000 19.04 16.87 0.00 2.92
2908 5685 1.028868 GTGCCAGGTTGAGCTCATCC 61.029 60.000 29.24 29.24 36.27 3.51
2909 5686 1.203441 TGCCAGGTTGAGCTCATCCT 61.203 55.000 32.17 32.17 44.57 3.24
2910 5687 0.034670 GCCAGGTTGAGCTCATCCTT 60.035 55.000 34.28 21.16 41.89 3.36
2911 5688 2.016096 GCCAGGTTGAGCTCATCCTTC 61.016 57.143 34.28 26.11 41.89 3.46
2912 5689 1.558756 CCAGGTTGAGCTCATCCTTCT 59.441 52.381 34.28 18.00 41.89 2.85
2913 5690 2.768527 CCAGGTTGAGCTCATCCTTCTA 59.231 50.000 34.28 10.51 41.89 2.10
2914 5691 3.390639 CCAGGTTGAGCTCATCCTTCTAT 59.609 47.826 34.28 17.37 41.89 1.98
2915 5692 4.378774 CAGGTTGAGCTCATCCTTCTATG 58.621 47.826 34.28 23.19 41.89 2.23
2916 5693 4.100653 CAGGTTGAGCTCATCCTTCTATGA 59.899 45.833 34.28 8.33 41.89 2.15
2917 5694 4.906664 AGGTTGAGCTCATCCTTCTATGAT 59.093 41.667 32.17 14.31 41.89 2.45
2918 5695 4.996122 GGTTGAGCTCATCCTTCTATGATG 59.004 45.833 29.16 0.00 40.77 3.07
2919 5696 5.221601 GGTTGAGCTCATCCTTCTATGATGA 60.222 44.000 29.16 3.92 44.70 2.92
2920 5697 5.465532 TGAGCTCATCCTTCTATGATGAC 57.534 43.478 13.74 0.00 42.68 3.06
2921 5698 4.022503 TGAGCTCATCCTTCTATGATGACG 60.023 45.833 13.74 0.00 42.68 4.35
2922 5699 3.257873 AGCTCATCCTTCTATGATGACGG 59.742 47.826 0.00 0.00 42.68 4.79
2923 5700 3.616076 GCTCATCCTTCTATGATGACGGG 60.616 52.174 0.00 0.00 42.68 5.28
2924 5701 3.576118 CTCATCCTTCTATGATGACGGGT 59.424 47.826 0.00 0.00 42.68 5.28
2925 5702 4.736473 TCATCCTTCTATGATGACGGGTA 58.264 43.478 0.00 0.00 42.68 3.69
2926 5703 4.523173 TCATCCTTCTATGATGACGGGTAC 59.477 45.833 0.00 0.00 42.68 3.34
2927 5704 4.322049 CATCCTTCTATGATGACGGGTACC 60.322 50.000 2.17 2.17 43.37 3.34
2928 5705 7.302725 CATCCTTCTATGATGACGGGTACCC 62.303 52.000 22.19 22.19 43.69 3.69
2939 5716 4.904466 GGTACCCTAGTGTGCGTG 57.096 61.111 0.00 0.00 0.00 5.34
2940 5717 2.269978 GGTACCCTAGTGTGCGTGA 58.730 57.895 0.00 0.00 0.00 4.35
2941 5718 0.108945 GGTACCCTAGTGTGCGTGAC 60.109 60.000 0.00 0.00 0.00 3.67
2942 5719 0.599558 GTACCCTAGTGTGCGTGACA 59.400 55.000 0.00 0.00 0.00 3.58
2943 5720 1.203994 GTACCCTAGTGTGCGTGACAT 59.796 52.381 0.00 0.00 36.78 3.06
2944 5721 0.685097 ACCCTAGTGTGCGTGACATT 59.315 50.000 0.00 0.00 36.78 2.71
2945 5722 1.897133 ACCCTAGTGTGCGTGACATTA 59.103 47.619 0.00 0.00 36.78 1.90
2946 5723 2.500098 ACCCTAGTGTGCGTGACATTAT 59.500 45.455 0.00 0.00 36.78 1.28
2947 5724 3.123804 CCCTAGTGTGCGTGACATTATC 58.876 50.000 0.00 0.00 36.78 1.75
2948 5725 2.789339 CCTAGTGTGCGTGACATTATCG 59.211 50.000 0.00 0.00 36.78 2.92
2949 5726 2.647529 AGTGTGCGTGACATTATCGA 57.352 45.000 0.00 0.00 36.78 3.59
2950 5727 3.165058 AGTGTGCGTGACATTATCGAT 57.835 42.857 2.16 2.16 36.78 3.59
2951 5728 2.860136 AGTGTGCGTGACATTATCGATG 59.140 45.455 8.54 0.00 41.71 3.84
2952 5729 1.592543 TGTGCGTGACATTATCGATGC 59.407 47.619 8.54 0.21 39.47 3.91
2953 5730 1.592543 GTGCGTGACATTATCGATGCA 59.407 47.619 8.54 3.23 39.47 3.96
2954 5731 2.221749 GTGCGTGACATTATCGATGCAT 59.778 45.455 8.54 0.00 39.47 3.96
2955 5732 2.871633 TGCGTGACATTATCGATGCATT 59.128 40.909 8.54 0.00 39.47 3.56
2956 5733 4.054671 TGCGTGACATTATCGATGCATTA 58.945 39.130 8.54 0.00 39.47 1.90
2957 5734 4.690280 TGCGTGACATTATCGATGCATTAT 59.310 37.500 8.54 0.28 39.47 1.28
2958 5735 5.163963 TGCGTGACATTATCGATGCATTATC 60.164 40.000 8.54 1.60 39.47 1.75
2959 5736 5.725042 GCGTGACATTATCGATGCATTATCC 60.725 44.000 8.54 0.00 39.47 2.59
2960 5737 5.348451 CGTGACATTATCGATGCATTATCCA 59.652 40.000 8.54 0.00 39.47 3.41
2961 5738 6.454715 CGTGACATTATCGATGCATTATCCAG 60.455 42.308 8.54 0.00 39.47 3.86
2962 5739 6.591448 GTGACATTATCGATGCATTATCCAGA 59.409 38.462 8.54 0.00 39.47 3.86
2963 5740 7.118245 GTGACATTATCGATGCATTATCCAGAA 59.882 37.037 8.54 0.00 39.47 3.02
2964 5741 7.118245 TGACATTATCGATGCATTATCCAGAAC 59.882 37.037 8.54 0.00 39.47 3.01
2965 5742 6.936335 ACATTATCGATGCATTATCCAGAACA 59.064 34.615 8.54 0.00 39.47 3.18
2966 5743 7.609146 ACATTATCGATGCATTATCCAGAACAT 59.391 33.333 8.54 0.00 39.47 2.71
2967 5744 7.984422 TTATCGATGCATTATCCAGAACATT 57.016 32.000 8.54 0.00 31.82 2.71
2968 5745 5.678132 TCGATGCATTATCCAGAACATTG 57.322 39.130 0.00 0.00 31.82 2.82
2969 5746 4.023792 TCGATGCATTATCCAGAACATTGC 60.024 41.667 0.00 0.00 31.82 3.56
2970 5747 4.553323 GATGCATTATCCAGAACATTGCC 58.447 43.478 0.00 0.00 0.00 4.52
2971 5748 3.634504 TGCATTATCCAGAACATTGCCT 58.365 40.909 0.00 0.00 0.00 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 3.233507 ACACCATGCCAAGTTTCATCTT 58.766 40.909 0.00 0.00 0.00 2.40
27 28 2.821969 GACACCATGCCAAGTTTCATCT 59.178 45.455 0.00 0.00 0.00 2.90
81 82 9.239002 CATTAGGTTTTCTCGTAATACTCTCAG 57.761 37.037 0.00 0.00 30.58 3.35
139 141 4.602340 ACTGTTCGAAACCTGATACTGT 57.398 40.909 0.00 0.00 0.00 3.55
220 225 9.691362 GATTTTGAGTGGTGTGTGTTAAATATT 57.309 29.630 0.00 0.00 0.00 1.28
278 283 2.049372 AGGAAGCAAGTGGGCATTTTT 58.951 42.857 0.00 0.00 35.83 1.94
286 291 1.341209 GTGGGAAAAGGAAGCAAGTGG 59.659 52.381 0.00 0.00 0.00 4.00
290 295 2.091333 AGAAGGTGGGAAAAGGAAGCAA 60.091 45.455 0.00 0.00 0.00 3.91
336 344 7.431249 TGGTTTAGAATACTACTAGCCATTCG 58.569 38.462 0.00 0.00 33.57 3.34
383 391 5.740569 TCGCTTCTATTTGTATACACGACAC 59.259 40.000 4.68 0.00 0.00 3.67
385 393 6.801367 TTCGCTTCTATTTGTATACACGAC 57.199 37.500 4.68 0.00 0.00 4.34
487 497 1.051812 CAGGAATGGGCCGATAGACT 58.948 55.000 0.00 0.00 39.76 3.24
534 553 9.460019 TTTCCTTATTCAACATGTGATATGTCA 57.540 29.630 0.00 0.00 35.70 3.58
790 832 1.169661 TCCACATGCCGTTGTCAACC 61.170 55.000 10.12 0.00 0.00 3.77
974 1047 2.364324 ACTACTGCACGTTCAGAAGGAA 59.636 45.455 22.14 1.26 37.51 3.36
1010 1089 0.977395 AGCTAACGGGAAGCAAGAGT 59.023 50.000 8.35 0.00 42.62 3.24
1563 1642 3.321968 GCCCCATGTTTTTGAACTTCTCT 59.678 43.478 0.00 0.00 0.00 3.10
1812 1891 3.524648 AACGATCCGTGCGGTGGTT 62.525 57.895 10.60 9.92 39.99 3.67
1919 1998 1.054978 GTTCCTAATCTCCCCGGCCT 61.055 60.000 0.00 0.00 0.00 5.19
2003 2082 9.868277 AAAAGAATGATTTACACAAAGACAACA 57.132 25.926 0.00 0.00 0.00 3.33
2224 2651 7.910441 ATGAAAGTTTTTGATAAGGCAATGG 57.090 32.000 0.00 0.00 0.00 3.16
2282 5052 5.843019 AACTTTCCTCCTTCCTGTCAATA 57.157 39.130 0.00 0.00 0.00 1.90
2299 5069 8.093927 TCTTGAAATTGGAGACACAAAAACTTT 58.906 29.630 0.00 0.00 42.67 2.66
2385 5156 3.542969 AGGGTCCTAATTTGGCAGTTT 57.457 42.857 0.45 0.00 0.00 2.66
2396 5167 1.063114 GTGGCTCCTCTAGGGTCCTAA 60.063 57.143 0.00 0.00 36.25 2.69
2513 5284 1.152756 AGGTGCAAAAGGAAGCGGT 60.153 52.632 0.00 0.00 0.00 5.68
2529 5300 6.530534 CCGTAAGTGTAGTAAAGTTCATGAGG 59.469 42.308 0.00 0.00 0.00 3.86
2530 5301 6.530534 CCCGTAAGTGTAGTAAAGTTCATGAG 59.469 42.308 0.00 0.00 0.00 2.90
2554 5325 1.339929 ACCATTCCGTGAAAAGTTGCC 59.660 47.619 0.00 0.00 0.00 4.52
2566 5337 1.382522 CAACTCATCCCACCATTCCG 58.617 55.000 0.00 0.00 0.00 4.30
2574 5345 1.304381 GCCTTGCCAACTCATCCCA 60.304 57.895 0.00 0.00 0.00 4.37
2603 5380 2.941583 GGCCCCTCTCCCCTTGTT 60.942 66.667 0.00 0.00 0.00 2.83
2812 5589 4.022068 ACTCACGGAAATAACTCCACGTTA 60.022 41.667 0.00 0.00 41.97 3.18
2813 5590 3.243975 ACTCACGGAAATAACTCCACGTT 60.244 43.478 0.00 0.00 39.64 3.99
2814 5591 2.298163 ACTCACGGAAATAACTCCACGT 59.702 45.455 0.00 0.00 34.91 4.49
2815 5592 2.955614 ACTCACGGAAATAACTCCACG 58.044 47.619 0.00 0.00 34.91 4.94
2816 5593 3.120304 GCAACTCACGGAAATAACTCCAC 60.120 47.826 0.00 0.00 34.91 4.02
2817 5594 3.071479 GCAACTCACGGAAATAACTCCA 58.929 45.455 0.00 0.00 34.91 3.86
2818 5595 3.335579 AGCAACTCACGGAAATAACTCC 58.664 45.455 0.00 0.00 0.00 3.85
2819 5596 5.358298 AAAGCAACTCACGGAAATAACTC 57.642 39.130 0.00 0.00 0.00 3.01
2820 5597 5.560183 CGAAAAGCAACTCACGGAAATAACT 60.560 40.000 0.00 0.00 0.00 2.24
2821 5598 4.611366 CGAAAAGCAACTCACGGAAATAAC 59.389 41.667 0.00 0.00 0.00 1.89
2822 5599 4.273969 ACGAAAAGCAACTCACGGAAATAA 59.726 37.500 0.00 0.00 0.00 1.40
2823 5600 3.810941 ACGAAAAGCAACTCACGGAAATA 59.189 39.130 0.00 0.00 0.00 1.40
2824 5601 2.616842 ACGAAAAGCAACTCACGGAAAT 59.383 40.909 0.00 0.00 0.00 2.17
2825 5602 2.011222 ACGAAAAGCAACTCACGGAAA 58.989 42.857 0.00 0.00 0.00 3.13
2826 5603 1.658994 ACGAAAAGCAACTCACGGAA 58.341 45.000 0.00 0.00 0.00 4.30
2827 5604 2.034939 TCTACGAAAAGCAACTCACGGA 59.965 45.455 0.00 0.00 0.00 4.69
2828 5605 2.400399 TCTACGAAAAGCAACTCACGG 58.600 47.619 0.00 0.00 0.00 4.94
2829 5606 3.673338 TCATCTACGAAAAGCAACTCACG 59.327 43.478 0.00 0.00 0.00 4.35
2830 5607 5.786401 ATCATCTACGAAAAGCAACTCAC 57.214 39.130 0.00 0.00 0.00 3.51
2831 5608 6.128282 GGAAATCATCTACGAAAAGCAACTCA 60.128 38.462 0.00 0.00 0.00 3.41
2832 5609 6.128282 TGGAAATCATCTACGAAAAGCAACTC 60.128 38.462 0.00 0.00 0.00 3.01
2833 5610 5.705441 TGGAAATCATCTACGAAAAGCAACT 59.295 36.000 0.00 0.00 0.00 3.16
2834 5611 5.938322 TGGAAATCATCTACGAAAAGCAAC 58.062 37.500 0.00 0.00 0.00 4.17
2835 5612 6.757897 ATGGAAATCATCTACGAAAAGCAA 57.242 33.333 0.00 0.00 0.00 3.91
2836 5613 7.552687 ACTTATGGAAATCATCTACGAAAAGCA 59.447 33.333 0.00 0.00 37.30 3.91
2837 5614 7.920738 ACTTATGGAAATCATCTACGAAAAGC 58.079 34.615 0.00 0.00 37.30 3.51
2841 5618 9.542462 CCTAAACTTATGGAAATCATCTACGAA 57.458 33.333 0.00 0.00 37.30 3.85
2842 5619 8.920174 TCCTAAACTTATGGAAATCATCTACGA 58.080 33.333 0.00 0.00 37.30 3.43
2843 5620 9.712305 ATCCTAAACTTATGGAAATCATCTACG 57.288 33.333 0.00 0.00 37.30 3.51
2854 5631 9.135189 CCATGATCAAAATCCTAAACTTATGGA 57.865 33.333 0.00 0.00 30.25 3.41
2855 5632 8.917088 ACCATGATCAAAATCCTAAACTTATGG 58.083 33.333 0.00 0.00 32.89 2.74
2856 5633 9.740239 CACCATGATCAAAATCCTAAACTTATG 57.260 33.333 0.00 0.00 0.00 1.90
2857 5634 9.699410 TCACCATGATCAAAATCCTAAACTTAT 57.301 29.630 0.00 0.00 0.00 1.73
2858 5635 9.699410 ATCACCATGATCAAAATCCTAAACTTA 57.301 29.630 0.00 0.00 29.59 2.24
2859 5636 8.472413 CATCACCATGATCAAAATCCTAAACTT 58.528 33.333 0.00 0.00 34.28 2.66
2860 5637 7.616935 ACATCACCATGATCAAAATCCTAAACT 59.383 33.333 0.00 0.00 34.28 2.66
2861 5638 7.775120 ACATCACCATGATCAAAATCCTAAAC 58.225 34.615 0.00 0.00 34.28 2.01
2862 5639 7.068593 GGACATCACCATGATCAAAATCCTAAA 59.931 37.037 0.00 0.00 34.28 1.85
2863 5640 6.547141 GGACATCACCATGATCAAAATCCTAA 59.453 38.462 0.00 0.00 34.28 2.69
2864 5641 6.064060 GGACATCACCATGATCAAAATCCTA 58.936 40.000 0.00 0.00 34.28 2.94
2865 5642 4.891756 GGACATCACCATGATCAAAATCCT 59.108 41.667 0.00 0.00 34.28 3.24
2866 5643 4.261322 CGGACATCACCATGATCAAAATCC 60.261 45.833 0.00 0.00 34.28 3.01
2867 5644 4.336433 ACGGACATCACCATGATCAAAATC 59.664 41.667 0.00 0.00 34.28 2.17
2868 5645 4.096833 CACGGACATCACCATGATCAAAAT 59.903 41.667 0.00 0.00 34.28 1.82
2869 5646 3.439825 CACGGACATCACCATGATCAAAA 59.560 43.478 0.00 0.00 34.28 2.44
2870 5647 3.009026 CACGGACATCACCATGATCAAA 58.991 45.455 0.00 0.00 34.28 2.69
2871 5648 2.631267 CACGGACATCACCATGATCAA 58.369 47.619 0.00 0.00 34.28 2.57
2872 5649 1.743431 GCACGGACATCACCATGATCA 60.743 52.381 0.00 0.00 34.28 2.92
2873 5650 0.940126 GCACGGACATCACCATGATC 59.060 55.000 0.00 0.00 34.28 2.92
2874 5651 0.464373 GGCACGGACATCACCATGAT 60.464 55.000 0.00 0.00 37.65 2.45
2875 5652 1.078497 GGCACGGACATCACCATGA 60.078 57.895 0.00 0.00 33.72 3.07
2876 5653 1.371337 CTGGCACGGACATCACCATG 61.371 60.000 0.00 0.00 36.31 3.66
2877 5654 1.078214 CTGGCACGGACATCACCAT 60.078 57.895 0.00 0.00 36.31 3.55
2878 5655 2.347114 CTGGCACGGACATCACCA 59.653 61.111 0.00 0.00 36.31 4.17
2879 5656 2.436646 CCTGGCACGGACATCACC 60.437 66.667 0.00 0.00 36.31 4.02
2880 5657 1.302511 AACCTGGCACGGACATCAC 60.303 57.895 9.53 0.00 36.31 3.06
2881 5658 1.302431 CAACCTGGCACGGACATCA 60.302 57.895 9.53 0.00 36.31 3.07
2882 5659 1.003839 TCAACCTGGCACGGACATC 60.004 57.895 9.53 0.00 36.31 3.06
2883 5660 1.003355 CTCAACCTGGCACGGACAT 60.003 57.895 9.53 0.00 36.31 3.06
2884 5661 2.425592 CTCAACCTGGCACGGACA 59.574 61.111 9.53 0.00 36.31 4.02
2885 5662 3.050275 GCTCAACCTGGCACGGAC 61.050 66.667 9.53 0.00 36.31 4.79
2886 5663 3.240134 GAGCTCAACCTGGCACGGA 62.240 63.158 9.40 0.00 36.31 4.69
2887 5664 2.743928 GAGCTCAACCTGGCACGG 60.744 66.667 9.40 2.01 0.00 4.94
2888 5665 1.364626 GATGAGCTCAACCTGGCACG 61.365 60.000 22.50 0.00 0.00 5.34
2889 5666 1.028868 GGATGAGCTCAACCTGGCAC 61.029 60.000 30.23 7.69 36.07 5.01
2890 5667 1.203441 AGGATGAGCTCAACCTGGCA 61.203 55.000 36.80 7.34 45.82 4.92
2891 5668 0.034670 AAGGATGAGCTCAACCTGGC 60.035 55.000 37.58 16.20 46.70 4.85
2892 5669 1.558756 AGAAGGATGAGCTCAACCTGG 59.441 52.381 37.58 0.00 46.70 4.45
2893 5670 4.100653 TCATAGAAGGATGAGCTCAACCTG 59.899 45.833 37.58 27.20 46.70 4.00
2895 5672 4.679373 TCATAGAAGGATGAGCTCAACC 57.321 45.455 30.35 30.35 38.89 3.77
2896 5673 5.851720 TCATCATAGAAGGATGAGCTCAAC 58.148 41.667 22.50 18.57 44.51 3.18
2903 5680 3.576861 ACCCGTCATCATAGAAGGATGA 58.423 45.455 0.43 0.43 46.51 2.92
2904 5681 4.322049 GGTACCCGTCATCATAGAAGGATG 60.322 50.000 0.00 0.00 42.73 3.51
2905 5682 3.833070 GGTACCCGTCATCATAGAAGGAT 59.167 47.826 0.00 0.00 39.18 3.24
2906 5683 3.228453 GGTACCCGTCATCATAGAAGGA 58.772 50.000 0.00 0.00 39.18 3.36
2907 5684 3.662247 GGTACCCGTCATCATAGAAGG 57.338 52.381 0.00 0.00 36.98 3.46
2922 5699 4.045103 ATGTCACGCACACTAGGGTACC 62.045 54.545 2.17 2.17 45.02 3.34
2923 5700 0.599558 TGTCACGCACACTAGGGTAC 59.400 55.000 0.00 0.00 32.97 3.34
2924 5701 1.552578 ATGTCACGCACACTAGGGTA 58.447 50.000 0.00 0.00 38.04 3.69
2925 5702 0.685097 AATGTCACGCACACTAGGGT 59.315 50.000 0.00 0.00 38.04 4.34
2926 5703 2.665649 TAATGTCACGCACACTAGGG 57.334 50.000 0.00 0.00 38.04 3.53
2927 5704 2.789339 CGATAATGTCACGCACACTAGG 59.211 50.000 0.00 0.00 38.04 3.02
2928 5705 3.691498 TCGATAATGTCACGCACACTAG 58.309 45.455 0.00 0.00 38.04 2.57
2929 5706 3.768468 TCGATAATGTCACGCACACTA 57.232 42.857 0.00 0.00 38.04 2.74
2930 5707 2.647529 TCGATAATGTCACGCACACT 57.352 45.000 0.00 0.00 38.04 3.55
2931 5708 2.597505 GCATCGATAATGTCACGCACAC 60.598 50.000 0.00 0.00 38.04 3.82
2932 5709 1.592543 GCATCGATAATGTCACGCACA 59.407 47.619 0.00 0.00 40.18 4.57
2933 5710 1.592543 TGCATCGATAATGTCACGCAC 59.407 47.619 0.00 0.00 37.71 5.34
2934 5711 1.933247 TGCATCGATAATGTCACGCA 58.067 45.000 0.00 0.00 37.71 5.24
2935 5712 3.526385 AATGCATCGATAATGTCACGC 57.474 42.857 0.00 0.00 37.71 5.34
2936 5713 5.348451 TGGATAATGCATCGATAATGTCACG 59.652 40.000 0.00 0.00 37.71 4.35
2937 5714 6.591448 TCTGGATAATGCATCGATAATGTCAC 59.409 38.462 0.00 0.00 37.71 3.67
2938 5715 6.700352 TCTGGATAATGCATCGATAATGTCA 58.300 36.000 0.00 0.00 37.71 3.58
2939 5716 7.118245 TGTTCTGGATAATGCATCGATAATGTC 59.882 37.037 0.00 0.00 37.71 3.06
2940 5717 6.936335 TGTTCTGGATAATGCATCGATAATGT 59.064 34.615 0.00 0.00 37.71 2.71
2941 5718 7.368480 TGTTCTGGATAATGCATCGATAATG 57.632 36.000 0.00 0.00 38.50 1.90
2942 5719 8.456471 CAATGTTCTGGATAATGCATCGATAAT 58.544 33.333 0.00 0.00 34.12 1.28
2943 5720 7.573656 GCAATGTTCTGGATAATGCATCGATAA 60.574 37.037 0.00 0.00 34.12 1.75
2944 5721 6.128200 GCAATGTTCTGGATAATGCATCGATA 60.128 38.462 0.00 0.00 34.12 2.92
2945 5722 5.335426 GCAATGTTCTGGATAATGCATCGAT 60.335 40.000 0.00 0.00 34.12 3.59
2946 5723 4.023792 GCAATGTTCTGGATAATGCATCGA 60.024 41.667 0.00 0.00 34.12 3.59
2947 5724 4.224433 GCAATGTTCTGGATAATGCATCG 58.776 43.478 0.00 0.00 34.12 3.84
2948 5725 4.280174 AGGCAATGTTCTGGATAATGCATC 59.720 41.667 0.00 0.00 34.14 3.91
2949 5726 4.220724 AGGCAATGTTCTGGATAATGCAT 58.779 39.130 0.00 0.00 34.14 3.96
2950 5727 3.634504 AGGCAATGTTCTGGATAATGCA 58.365 40.909 0.00 0.00 34.14 3.96


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

AutoCloner maintained by Alex Coulton.