Multiple sequence alignment - TraesCS1D01G308400

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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 TraesCS1D01G308400 chr1D 100.000 3147 0 0 1 3147 404262047 404258901 0.000000e+00 5812.0
1 TraesCS1D01G308400 chr1D 83.717 1259 94 47 1018 2199 404240027 404238803 0.000000e+00 1086.0
2 TraesCS1D01G308400 chr1D 89.299 542 30 7 460 987 404240553 404240026 0.000000e+00 654.0
3 TraesCS1D01G308400 chr1D 92.708 192 11 3 1 191 404241101 404240912 1.110000e-69 274.0
4 TraesCS1D01G308400 chr1D 92.174 115 7 2 2389 2501 404238386 404238272 9.030000e-36 161.0
5 TraesCS1D01G308400 chr1D 98.077 52 1 0 2229 2280 404238734 404238683 1.200000e-14 91.6
6 TraesCS1D01G308400 chr1A 90.075 1340 76 31 466 1791 499928220 499926924 0.000000e+00 1685.0
7 TraesCS1D01G308400 chr1A 85.072 1380 103 47 460 1787 499809713 499808385 0.000000e+00 1312.0
8 TraesCS1D01G308400 chr1A 91.962 423 33 1 2724 3146 499923232 499922811 2.700000e-165 592.0
9 TraesCS1D01G308400 chr1A 87.857 420 25 8 1793 2199 499808268 499807862 1.320000e-128 470.0
10 TraesCS1D01G308400 chr1A 87.980 391 22 8 1834 2199 499926841 499926451 3.730000e-119 438.0
11 TraesCS1D01G308400 chr1A 88.034 351 25 6 1 350 499810072 499809738 1.760000e-107 399.0
12 TraesCS1D01G308400 chr1A 95.067 223 10 1 1 223 499928995 499928774 1.800000e-92 350.0
13 TraesCS1D01G308400 chr1A 86.920 237 23 5 2389 2622 499926118 499925887 3.110000e-65 259.0
14 TraesCS1D01G308400 chr1A 91.071 56 5 0 2277 2332 499807659 499807604 3.370000e-10 76.8
15 TraesCS1D01G308400 chr1B 83.955 1608 145 46 668 2199 543741406 543739836 0.000000e+00 1435.0
16 TraesCS1D01G308400 chr1B 83.794 1592 124 64 650 2153 543581593 543580048 0.000000e+00 1387.0
17 TraesCS1D01G308400 chr1B 91.168 351 26 4 1 350 543582120 543581774 3.670000e-129 472.0
18 TraesCS1D01G308400 chr1B 93.119 218 11 4 1 215 543742112 543741896 1.820000e-82 316.0
19 TraesCS1D01G308400 chr1B 86.928 153 12 5 2389 2539 543739545 543739399 6.980000e-37 165.0
20 TraesCS1D01G308400 chr1B 95.385 65 3 0 594 658 543741572 543741508 1.540000e-18 104.0
21 TraesCS1D01G308400 chr1B 100.000 33 0 0 2202 2234 543739812 543739780 9.420000e-06 62.1
22 TraesCS1D01G308400 chr1B 100.000 28 0 0 822 849 543741304 543741277 6.000000e-03 52.8
23 TraesCS1D01G308400 chr7D 86.111 180 21 4 2968 3143 457363495 457363674 1.150000e-44 191.0
24 TraesCS1D01G308400 chr5B 88.125 160 17 2 2986 3143 629907349 629907190 4.140000e-44 189.0
25 TraesCS1D01G308400 chr5D 86.628 172 20 3 2978 3147 436344224 436344394 1.490000e-43 187.0
26 TraesCS1D01G308400 chrUn 87.117 163 19 1 2977 3137 162964096 162964258 1.930000e-42 183.0
27 TraesCS1D01G308400 chrUn 87.117 163 19 1 2977 3137 163023437 163023599 1.930000e-42 183.0
28 TraesCS1D01G308400 chrUn 87.117 163 19 1 2977 3137 388609752 388609914 1.930000e-42 183.0
29 TraesCS1D01G308400 chrUn 85.714 168 22 2 2972 3137 23913011 23913178 3.230000e-40 176.0
30 TraesCS1D01G308400 chr4A 84.324 185 23 6 2968 3147 512368445 512368628 3.230000e-40 176.0


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 TraesCS1D01G308400 chr1D 404258901 404262047 3146 True 5812.000000 5812 100.000000 1 3147 1 chr1D.!!$R1 3146
1 TraesCS1D01G308400 chr1D 404238272 404241101 2829 True 453.320000 1086 91.195000 1 2501 5 chr1D.!!$R2 2500
2 TraesCS1D01G308400 chr1A 499922811 499928995 6184 True 664.800000 1685 90.400800 1 3146 5 chr1A.!!$R2 3145
3 TraesCS1D01G308400 chr1A 499807604 499810072 2468 True 564.450000 1312 88.008500 1 2332 4 chr1A.!!$R1 2331
4 TraesCS1D01G308400 chr1B 543580048 543582120 2072 True 929.500000 1387 87.481000 1 2153 2 chr1B.!!$R1 2152
5 TraesCS1D01G308400 chr1B 543739399 543742112 2713 True 355.816667 1435 93.231167 1 2539 6 chr1B.!!$R2 2538

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
936 1628 0.389426 GGAGTTCACACGCGTACCAT 60.389 55.0 13.44 0.0 0.0 3.55 F
1513 2270 0.398318 ACCAAACTGTGAGCCTCTCC 59.602 55.0 0.00 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1966 2909 0.108945 AGGACGGGAAAACGATCGAC 60.109 55.0 24.34 9.68 37.61 4.20 R
2750 6573 0.179100 CTGTCTATGCCACAGGACGG 60.179 60.0 0.00 0.00 38.10 4.79 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
22 23 2.752903 GTGGGCCAAGTACCAATAAGTG 59.247 50.000 8.40 0.00 38.73 3.16
130 135 1.376466 CTACAGGTGGCCAAGCACT 59.624 57.895 7.24 0.00 0.00 4.40
226 488 5.179368 ACACATGAAGAAACGATGTACCAAG 59.821 40.000 0.00 0.00 0.00 3.61
312 737 9.811995 ATGCATTGATCAAAATATATACATGGC 57.188 29.630 13.09 0.19 0.00 4.40
382 807 9.158233 TGTGGGCTAATTAAATATACTATTCGC 57.842 33.333 0.00 0.00 0.00 4.70
383 808 8.325997 GTGGGCTAATTAAATATACTATTCGCG 58.674 37.037 0.00 0.00 0.00 5.87
384 809 8.036575 TGGGCTAATTAAATATACTATTCGCGT 58.963 33.333 5.77 0.00 0.00 6.01
385 810 8.325997 GGGCTAATTAAATATACTATTCGCGTG 58.674 37.037 5.77 0.00 0.00 5.34
386 811 8.866956 GGCTAATTAAATATACTATTCGCGTGT 58.133 33.333 5.77 4.04 0.00 4.49
387 812 9.671521 GCTAATTAAATATACTATTCGCGTGTG 57.328 33.333 5.77 0.00 0.00 3.82
388 813 9.671521 CTAATTAAATATACTATTCGCGTGTGC 57.328 33.333 5.77 0.00 37.91 4.57
389 814 7.646446 ATTAAATATACTATTCGCGTGTGCA 57.354 32.000 5.77 0.00 42.97 4.57
390 815 5.977171 AAATATACTATTCGCGTGTGCAA 57.023 34.783 5.77 0.00 42.97 4.08
415 841 5.982890 AAAAATGTGTGTATGGAAGGGAG 57.017 39.130 0.00 0.00 0.00 4.30
416 842 4.657814 AAATGTGTGTATGGAAGGGAGT 57.342 40.909 0.00 0.00 0.00 3.85
417 843 3.634397 ATGTGTGTATGGAAGGGAGTG 57.366 47.619 0.00 0.00 0.00 3.51
418 844 1.628340 TGTGTGTATGGAAGGGAGTGG 59.372 52.381 0.00 0.00 0.00 4.00
419 845 1.065418 GTGTGTATGGAAGGGAGTGGG 60.065 57.143 0.00 0.00 0.00 4.61
420 846 0.546598 GTGTATGGAAGGGAGTGGGG 59.453 60.000 0.00 0.00 0.00 4.96
421 847 0.623324 TGTATGGAAGGGAGTGGGGG 60.623 60.000 0.00 0.00 0.00 5.40
436 862 2.757077 GGGGTGGGTGTGGAAGAG 59.243 66.667 0.00 0.00 0.00 2.85
438 864 2.829384 GGGTGGGTGTGGAAGAGCA 61.829 63.158 0.00 0.00 0.00 4.26
441 867 0.668535 GTGGGTGTGGAAGAGCAAAC 59.331 55.000 0.00 0.00 0.00 2.93
444 870 2.224523 TGGGTGTGGAAGAGCAAACTAG 60.225 50.000 0.00 0.00 0.00 2.57
446 872 2.038557 GGTGTGGAAGAGCAAACTAGGA 59.961 50.000 0.00 0.00 0.00 2.94
447 873 3.330267 GTGTGGAAGAGCAAACTAGGAG 58.670 50.000 0.00 0.00 0.00 3.69
448 874 3.006967 GTGTGGAAGAGCAAACTAGGAGA 59.993 47.826 0.00 0.00 0.00 3.71
453 879 6.879458 GTGGAAGAGCAAACTAGGAGAAATTA 59.121 38.462 0.00 0.00 0.00 1.40
454 880 7.554476 GTGGAAGAGCAAACTAGGAGAAATTAT 59.446 37.037 0.00 0.00 0.00 1.28
456 882 9.785982 GGAAGAGCAAACTAGGAGAAATTATAT 57.214 33.333 0.00 0.00 0.00 0.86
464 1031 9.799106 AAACTAGGAGAAATTATATGGACATGG 57.201 33.333 0.00 0.00 0.00 3.66
508 1083 3.313526 GCGTTGTAAGATGCCATCTTCAT 59.686 43.478 22.62 2.88 46.17 2.57
526 1101 7.107639 TCTTCATATATGACTCGGACAACAA 57.892 36.000 15.10 0.00 36.36 2.83
536 1111 8.742554 ATGACTCGGACAACAAAAATATTTTC 57.257 30.769 13.68 0.73 0.00 2.29
537 1112 7.936584 TGACTCGGACAACAAAAATATTTTCT 58.063 30.769 13.68 2.48 0.00 2.52
708 1380 9.328845 CCAACAAAATGGCAAAAGCTATATATT 57.671 29.630 0.00 0.00 32.78 1.28
858 1533 4.668636 CCATTGTCCAAAACCCTACCTTA 58.331 43.478 0.00 0.00 0.00 2.69
936 1628 0.389426 GGAGTTCACACGCGTACCAT 60.389 55.000 13.44 0.00 0.00 3.55
1077 1771 0.621571 CCCTCAGATCACCTCCCCAA 60.622 60.000 0.00 0.00 0.00 4.12
1342 2064 1.226802 CGAGATGTGAGTGAGGCCG 60.227 63.158 0.00 0.00 0.00 6.13
1343 2065 1.520342 GAGATGTGAGTGAGGCCGC 60.520 63.158 0.00 0.00 0.00 6.53
1344 2066 2.512515 GATGTGAGTGAGGCCGCC 60.513 66.667 3.22 0.00 0.00 6.13
1378 2103 1.965414 TCCCTTCCATACTGCTTCCA 58.035 50.000 0.00 0.00 0.00 3.53
1512 2269 2.262423 AACCAAACTGTGAGCCTCTC 57.738 50.000 0.00 0.00 0.00 3.20
1513 2270 0.398318 ACCAAACTGTGAGCCTCTCC 59.602 55.000 0.00 0.00 0.00 3.71
1744 2542 1.869767 CTGAAACAGCTGTGAGTCCAC 59.130 52.381 22.49 7.54 43.46 4.02
1758 2556 3.118992 TGAGTCCACGATCTCCAGATTTG 60.119 47.826 0.00 0.00 34.37 2.32
1806 2717 6.183360 TGTTTTCAAGTAAGTTTGGCTCTGAG 60.183 38.462 0.00 0.00 0.00 3.35
1828 2739 4.768448 AGGTCTGAACATTTGCATGATGAA 59.232 37.500 15.21 0.00 34.11 2.57
1888 2810 2.586245 CAAGCGAGCTGGATGGGA 59.414 61.111 0.00 0.00 0.00 4.37
1896 2818 0.982852 AGCTGGATGGGATGTCCGAA 60.983 55.000 0.00 0.00 38.64 4.30
1915 2837 4.530388 CGAACAGACGAGTGTGTAAGTTA 58.470 43.478 6.45 0.00 35.94 2.24
1935 2878 6.616947 AGTTAGACGATTGTTCTCTTCTCTG 58.383 40.000 0.00 0.00 0.00 3.35
1966 2909 8.228464 CGATCAATTAATCCAGTGATCTTCATG 58.772 37.037 18.83 6.08 42.70 3.07
2005 2948 5.181245 GTCCTGTTTTGCTTGCAGTAATCTA 59.819 40.000 0.00 0.00 0.00 1.98
2114 3057 1.945387 CAACTGCTAGACCGATGCAT 58.055 50.000 0.00 0.00 36.07 3.96
2274 3295 1.468520 GTATGTTGTGCACAAGCCGAT 59.531 47.619 31.81 21.36 39.50 4.18
2296 3485 8.451748 CCGATATCGAATCTATTCACAGAGTTA 58.548 37.037 26.32 0.00 43.02 2.24
2298 3487 9.268255 GATATCGAATCTATTCACAGAGTTACG 57.732 37.037 3.76 0.00 36.61 3.18
2338 3527 3.684103 TGACTGCATTCGTTCGTTTTT 57.316 38.095 0.00 0.00 0.00 1.94
2339 3528 3.613563 TGACTGCATTCGTTCGTTTTTC 58.386 40.909 0.00 0.00 0.00 2.29
2369 3575 3.372822 TCGCGACGCTGACATATATGATA 59.627 43.478 19.63 6.61 0.00 2.15
2375 3581 5.724328 ACGCTGACATATATGATAACAGGG 58.276 41.667 26.59 26.59 40.69 4.45
2386 3592 5.999205 ATGATAACAGGGCAAATTTGACA 57.001 34.783 25.05 4.87 38.18 3.58
2395 3602 6.152492 ACAGGGCAAATTTGACAAATGTTTTT 59.848 30.769 25.05 3.09 38.18 1.94
2503 3748 1.207329 CTTGGCAGTACCCACTACCTC 59.793 57.143 0.00 0.00 38.82 3.85
2509 3754 2.001558 AGTACCCACTACCTCTGGAGT 58.998 52.381 0.00 0.00 31.45 3.85
2510 3755 2.382649 AGTACCCACTACCTCTGGAGTT 59.617 50.000 0.00 0.00 31.45 3.01
2548 3793 4.315803 GCACTACCTTTTGAGTTAGCAGA 58.684 43.478 0.00 0.00 0.00 4.26
2557 3802 2.068519 TGAGTTAGCAGACATTGTGCG 58.931 47.619 0.00 0.00 46.06 5.34
2563 3808 0.376152 GCAGACATTGTGCGATCAGG 59.624 55.000 0.00 0.00 0.00 3.86
2565 3810 0.251354 AGACATTGTGCGATCAGGCT 59.749 50.000 0.00 0.00 0.00 4.58
2581 3826 2.555325 CAGGCTGTGATGAACATGTGTT 59.445 45.455 6.28 0.00 38.39 3.32
2584 3829 3.983344 GGCTGTGATGAACATGTGTTTTC 59.017 43.478 0.00 0.00 38.39 2.29
2592 3837 8.905702 GTGATGAACATGTGTTTTCTAATGAAC 58.094 33.333 0.00 0.00 38.56 3.18
2594 3839 7.022055 TGAACATGTGTTTTCTAATGAACGT 57.978 32.000 0.00 0.00 38.56 3.99
2598 3843 7.021196 ACATGTGTTTTCTAATGAACGTATGC 58.979 34.615 0.00 0.00 30.99 3.14
2607 3852 7.724305 TCTAATGAACGTATGCTATTTTCCC 57.276 36.000 0.00 0.00 0.00 3.97
2608 3853 5.767816 AATGAACGTATGCTATTTTCCCC 57.232 39.130 0.00 0.00 0.00 4.81
2622 3867 8.966868 TGCTATTTTCCCCTAATAAGACAAAAG 58.033 33.333 0.00 0.00 0.00 2.27
2623 3868 8.414003 GCTATTTTCCCCTAATAAGACAAAAGG 58.586 37.037 0.00 0.00 0.00 3.11
2629 3897 5.253330 CCCTAATAAGACAAAAGGCTCACA 58.747 41.667 0.00 0.00 0.00 3.58
2641 3909 2.658707 GCTCACACGCCTCGACAAC 61.659 63.158 0.00 0.00 0.00 3.32
2645 3913 2.338620 CACGCCTCGACAACAGGA 59.661 61.111 0.00 0.00 31.91 3.86
2647 3915 1.006102 ACGCCTCGACAACAGGAAG 60.006 57.895 0.00 0.00 31.91 3.46
2648 3916 1.289066 CGCCTCGACAACAGGAAGA 59.711 57.895 0.00 0.00 31.91 2.87
2649 3917 0.319555 CGCCTCGACAACAGGAAGAA 60.320 55.000 0.00 0.00 31.91 2.52
2650 3918 1.433534 GCCTCGACAACAGGAAGAAG 58.566 55.000 0.00 0.00 31.91 2.85
2651 3919 1.000955 GCCTCGACAACAGGAAGAAGA 59.999 52.381 0.00 0.00 31.91 2.87
2652 3920 2.548067 GCCTCGACAACAGGAAGAAGAA 60.548 50.000 0.00 0.00 31.91 2.52
2653 3921 3.321497 CCTCGACAACAGGAAGAAGAAG 58.679 50.000 0.00 0.00 31.91 2.85
2654 3922 3.005897 CCTCGACAACAGGAAGAAGAAGA 59.994 47.826 0.00 0.00 31.91 2.87
2656 3924 2.734079 CGACAACAGGAAGAAGAAGAGC 59.266 50.000 0.00 0.00 0.00 4.09
2657 3925 3.733337 GACAACAGGAAGAAGAAGAGCA 58.267 45.455 0.00 0.00 0.00 4.26
2658 3926 4.130118 GACAACAGGAAGAAGAAGAGCAA 58.870 43.478 0.00 0.00 0.00 3.91
2659 3927 4.133078 ACAACAGGAAGAAGAAGAGCAAG 58.867 43.478 0.00 0.00 0.00 4.01
2660 3928 3.415457 ACAGGAAGAAGAAGAGCAAGG 57.585 47.619 0.00 0.00 0.00 3.61
2661 3929 2.975489 ACAGGAAGAAGAAGAGCAAGGA 59.025 45.455 0.00 0.00 0.00 3.36
2662 3930 3.392616 ACAGGAAGAAGAAGAGCAAGGAA 59.607 43.478 0.00 0.00 0.00 3.36
2663 3931 4.002316 CAGGAAGAAGAAGAGCAAGGAAG 58.998 47.826 0.00 0.00 0.00 3.46
2664 3932 3.906846 AGGAAGAAGAAGAGCAAGGAAGA 59.093 43.478 0.00 0.00 0.00 2.87
2665 3933 4.349342 AGGAAGAAGAAGAGCAAGGAAGAA 59.651 41.667 0.00 0.00 0.00 2.52
2666 3934 4.694982 GGAAGAAGAAGAGCAAGGAAGAAG 59.305 45.833 0.00 0.00 0.00 2.85
2667 3935 5.512232 GGAAGAAGAAGAGCAAGGAAGAAGA 60.512 44.000 0.00 0.00 0.00 2.87
2668 3936 5.559148 AGAAGAAGAGCAAGGAAGAAGAA 57.441 39.130 0.00 0.00 0.00 2.52
2669 3937 5.550290 AGAAGAAGAGCAAGGAAGAAGAAG 58.450 41.667 0.00 0.00 0.00 2.85
2670 3938 5.306678 AGAAGAAGAGCAAGGAAGAAGAAGA 59.693 40.000 0.00 0.00 0.00 2.87
2671 3939 5.559148 AGAAGAGCAAGGAAGAAGAAGAA 57.441 39.130 0.00 0.00 0.00 2.52
2672 3940 5.550290 AGAAGAGCAAGGAAGAAGAAGAAG 58.450 41.667 0.00 0.00 0.00 2.85
2673 3941 5.306678 AGAAGAGCAAGGAAGAAGAAGAAGA 59.693 40.000 0.00 0.00 0.00 2.87
2674 3942 5.151297 AGAGCAAGGAAGAAGAAGAAGAG 57.849 43.478 0.00 0.00 0.00 2.85
2675 3943 3.673902 AGCAAGGAAGAAGAAGAAGAGC 58.326 45.455 0.00 0.00 0.00 4.09
2676 3944 3.072184 AGCAAGGAAGAAGAAGAAGAGCA 59.928 43.478 0.00 0.00 0.00 4.26
2677 3945 3.817647 GCAAGGAAGAAGAAGAAGAGCAA 59.182 43.478 0.00 0.00 0.00 3.91
2678 3946 4.083377 GCAAGGAAGAAGAAGAAGAGCAAG 60.083 45.833 0.00 0.00 0.00 4.01
2679 3947 4.284829 AGGAAGAAGAAGAAGAGCAAGG 57.715 45.455 0.00 0.00 0.00 3.61
2680 3948 2.746904 GGAAGAAGAAGAAGAGCAAGGC 59.253 50.000 0.00 0.00 0.00 4.35
2681 3949 2.488204 AGAAGAAGAAGAGCAAGGCC 57.512 50.000 0.00 0.00 0.00 5.19
2711 3979 2.747446 TCAGCCGAGTCCTAAATTTTGC 59.253 45.455 0.00 0.00 0.00 3.68
2712 3980 2.749621 CAGCCGAGTCCTAAATTTTGCT 59.250 45.455 0.00 0.00 0.00 3.91
2721 3989 5.985530 AGTCCTAAATTTTGCTGTGAAAAGC 59.014 36.000 0.00 0.00 43.82 3.51
2731 6554 2.806244 GCTGTGAAAAGCGTAAGGAAGA 59.194 45.455 0.00 0.00 32.56 2.87
2746 6569 1.082690 GAAGAAGAAGAGCAAGGCCG 58.917 55.000 0.00 0.00 0.00 6.13
2750 6573 3.808656 GAAGAGCAAGGCCGCTGC 61.809 66.667 21.49 21.49 44.01 5.25
2767 6590 4.835927 CCGTCCTGTGGCATAGAC 57.164 61.111 13.32 8.46 0.00 2.59
2782 6605 4.384978 GGCATAGACAGGATGGATGCATAT 60.385 45.833 0.00 0.00 46.23 1.78
2874 6697 8.319143 TCAGTCTACTAAAAATACCAAGTTGC 57.681 34.615 0.00 0.00 0.00 4.17
2876 6699 6.370718 AGTCTACTAAAAATACCAAGTTGCCG 59.629 38.462 0.00 0.00 0.00 5.69
2895 6718 1.587034 CGTCGAATTAAACTCCGAGCC 59.413 52.381 0.00 0.00 0.00 4.70
2902 6725 3.322211 TTAAACTCCGAGCCGATTTCA 57.678 42.857 0.00 0.00 0.00 2.69
2936 6759 1.589716 ATTGGGTTTGCAGCTCGCTC 61.590 55.000 9.12 1.70 43.06 5.03
2980 6803 5.009854 CAAATTTGGAGGTTGTGTCTGTT 57.990 39.130 10.49 0.00 0.00 3.16
2981 6804 5.418676 CAAATTTGGAGGTTGTGTCTGTTT 58.581 37.500 10.49 0.00 0.00 2.83
3118 6941 6.874134 TGAAATCTAAGGCACAGACTAGAAAC 59.126 38.462 0.00 0.00 0.00 2.78
3119 6942 4.436242 TCTAAGGCACAGACTAGAAACG 57.564 45.455 0.00 0.00 0.00 3.60
3120 6943 3.825014 TCTAAGGCACAGACTAGAAACGT 59.175 43.478 0.00 0.00 0.00 3.99
3127 6950 5.686397 GGCACAGACTAGAAACGTGATATAC 59.314 44.000 0.00 0.00 0.00 1.47
3130 6953 7.426410 CACAGACTAGAAACGTGATATACCAT 58.574 38.462 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 5.472137 TCTGTTTCACTTATTGGTACTTGGC 59.528 40.000 0.00 0.00 0.00 4.52
93 98 6.970613 CCTGTAGTTTGTGGTAAAACTTTGTC 59.029 38.462 7.55 0.00 45.84 3.18
130 135 6.825213 CCACACATCATCCTCTTAAAATCTCA 59.175 38.462 0.00 0.00 0.00 3.27
356 781 9.158233 GCGAATAGTATATTTAATTAGCCCACA 57.842 33.333 0.00 0.00 0.00 4.17
357 782 8.325997 CGCGAATAGTATATTTAATTAGCCCAC 58.674 37.037 0.00 0.00 29.45 4.61
358 783 8.036575 ACGCGAATAGTATATTTAATTAGCCCA 58.963 33.333 15.93 0.00 29.45 5.36
359 784 8.325997 CACGCGAATAGTATATTTAATTAGCCC 58.674 37.037 15.93 0.00 29.45 5.19
360 785 8.866956 ACACGCGAATAGTATATTTAATTAGCC 58.133 33.333 15.93 0.00 29.45 3.93
361 786 9.671521 CACACGCGAATAGTATATTTAATTAGC 57.328 33.333 15.93 0.00 0.00 3.09
362 787 9.671521 GCACACGCGAATAGTATATTTAATTAG 57.328 33.333 15.93 0.00 0.00 1.73
363 788 9.194271 TGCACACGCGAATAGTATATTTAATTA 57.806 29.630 15.93 0.00 42.97 1.40
364 789 8.078959 TGCACACGCGAATAGTATATTTAATT 57.921 30.769 15.93 0.00 42.97 1.40
365 790 7.646446 TGCACACGCGAATAGTATATTTAAT 57.354 32.000 15.93 0.00 42.97 1.40
366 791 7.466193 TTGCACACGCGAATAGTATATTTAA 57.534 32.000 15.93 0.00 42.97 1.52
367 792 7.466193 TTTGCACACGCGAATAGTATATTTA 57.534 32.000 15.93 0.00 42.97 1.40
368 793 5.977171 TTGCACACGCGAATAGTATATTT 57.023 34.783 15.93 0.00 42.97 1.40
369 794 5.977171 TTTGCACACGCGAATAGTATATT 57.023 34.783 15.93 0.00 42.97 1.28
370 795 5.977171 TTTTGCACACGCGAATAGTATAT 57.023 34.783 15.93 0.00 41.26 0.86
371 796 5.781452 TTTTTGCACACGCGAATAGTATA 57.219 34.783 15.93 0.00 41.26 1.47
372 797 4.671880 TTTTTGCACACGCGAATAGTAT 57.328 36.364 15.93 0.00 41.26 2.12
401 827 0.546598 CCCCACTCCCTTCCATACAC 59.453 60.000 0.00 0.00 0.00 2.90
404 830 4.851784 CCCCCACTCCCTTCCATA 57.148 61.111 0.00 0.00 0.00 2.74
418 844 2.856988 TCTTCCACACCCACCCCC 60.857 66.667 0.00 0.00 0.00 5.40
419 845 2.757077 CTCTTCCACACCCACCCC 59.243 66.667 0.00 0.00 0.00 4.95
420 846 2.034221 GCTCTTCCACACCCACCC 59.966 66.667 0.00 0.00 0.00 4.61
421 847 0.467290 TTTGCTCTTCCACACCCACC 60.467 55.000 0.00 0.00 0.00 4.61
422 848 0.668535 GTTTGCTCTTCCACACCCAC 59.331 55.000 0.00 0.00 0.00 4.61
423 849 0.550914 AGTTTGCTCTTCCACACCCA 59.449 50.000 0.00 0.00 0.00 4.51
424 850 2.427506 CTAGTTTGCTCTTCCACACCC 58.572 52.381 0.00 0.00 0.00 4.61
425 851 2.038557 TCCTAGTTTGCTCTTCCACACC 59.961 50.000 0.00 0.00 0.00 4.16
426 852 3.006967 TCTCCTAGTTTGCTCTTCCACAC 59.993 47.826 0.00 0.00 0.00 3.82
427 853 3.239449 TCTCCTAGTTTGCTCTTCCACA 58.761 45.455 0.00 0.00 0.00 4.17
428 854 3.963428 TCTCCTAGTTTGCTCTTCCAC 57.037 47.619 0.00 0.00 0.00 4.02
430 856 9.785982 ATATAATTTCTCCTAGTTTGCTCTTCC 57.214 33.333 0.00 0.00 0.00 3.46
433 859 8.938883 TCCATATAATTTCTCCTAGTTTGCTCT 58.061 33.333 0.00 0.00 0.00 4.09
436 862 8.677148 TGTCCATATAATTTCTCCTAGTTTGC 57.323 34.615 0.00 0.00 0.00 3.68
438 864 9.799106 CCATGTCCATATAATTTCTCCTAGTTT 57.201 33.333 0.00 0.00 0.00 2.66
441 867 7.397221 TGCCATGTCCATATAATTTCTCCTAG 58.603 38.462 0.00 0.00 0.00 3.02
444 870 7.318141 CAATGCCATGTCCATATAATTTCTCC 58.682 38.462 0.00 0.00 0.00 3.71
446 872 6.495872 AGCAATGCCATGTCCATATAATTTCT 59.504 34.615 0.00 0.00 0.00 2.52
447 873 6.694447 AGCAATGCCATGTCCATATAATTTC 58.306 36.000 0.00 0.00 0.00 2.17
448 874 6.675413 AGCAATGCCATGTCCATATAATTT 57.325 33.333 0.00 0.00 0.00 1.82
453 879 3.319972 GTGAAGCAATGCCATGTCCATAT 59.680 43.478 0.00 0.00 0.00 1.78
454 880 2.689471 GTGAAGCAATGCCATGTCCATA 59.311 45.455 0.00 0.00 0.00 2.74
456 882 0.889994 GTGAAGCAATGCCATGTCCA 59.110 50.000 0.00 0.00 0.00 4.02
457 883 0.889994 TGTGAAGCAATGCCATGTCC 59.110 50.000 0.00 0.00 0.00 4.02
464 1031 2.427232 TTGAAGCTGTGAAGCAATGC 57.573 45.000 0.00 0.00 37.25 3.56
483 1050 1.396996 GATGGCATCTTACAACGCGTT 59.603 47.619 20.79 20.79 0.00 4.84
858 1533 3.000041 CAAATGCAATGTGCTGCTCAAT 59.000 40.909 8.59 0.00 45.31 2.57
1342 2064 1.671379 GAAGAAGGACCGGTGTGGC 60.671 63.158 14.63 0.00 43.94 5.01
1343 2065 1.003718 GGAAGAAGGACCGGTGTGG 60.004 63.158 14.63 0.00 46.41 4.17
1344 2066 1.003718 GGGAAGAAGGACCGGTGTG 60.004 63.158 14.63 0.00 0.00 3.82
1351 2076 3.682999 GCAGTATGGAAGGGAAGAAGGAC 60.683 52.174 0.00 0.00 35.86 3.85
1378 2103 8.656849 GCGTCCAGAAATATTGAAATATACGAT 58.343 33.333 13.78 0.00 32.09 3.73
1512 2269 3.777522 AGAAACAGATGGGTTAGAGAGGG 59.222 47.826 0.00 0.00 0.00 4.30
1513 2270 4.764172 CAGAAACAGATGGGTTAGAGAGG 58.236 47.826 0.00 0.00 0.00 3.69
1565 2353 9.671279 CCTGTGTTCATTAGATGCCATATATAA 57.329 33.333 0.00 0.00 0.00 0.98
1567 2355 7.609146 CACCTGTGTTCATTAGATGCCATATAT 59.391 37.037 0.00 0.00 0.00 0.86
1744 2542 6.317857 GGAAAGAAAACAAATCTGGAGATCG 58.682 40.000 0.00 0.00 32.75 3.69
1781 2582 5.650266 TCAGAGCCAAACTTACTTGAAAACA 59.350 36.000 0.00 0.00 0.00 2.83
1782 2583 6.131544 TCAGAGCCAAACTTACTTGAAAAC 57.868 37.500 0.00 0.00 0.00 2.43
1806 2717 4.707030 TCATCATGCAAATGTTCAGACC 57.293 40.909 11.05 0.00 0.00 3.85
1828 2739 4.574674 TCTGTTGAAGGTGCCTATCAAT 57.425 40.909 14.27 0.00 35.70 2.57
1888 2810 0.959553 ACACTCGTCTGTTCGGACAT 59.040 50.000 0.00 0.00 36.12 3.06
1896 2818 4.319333 CGTCTAACTTACACACTCGTCTGT 60.319 45.833 0.00 0.00 0.00 3.41
1915 2837 4.378978 CGACAGAGAAGAGAACAATCGTCT 60.379 45.833 0.00 0.00 40.17 4.18
1935 2878 5.041287 TCACTGGATTAATTGATCGTCGAC 58.959 41.667 5.18 5.18 0.00 4.20
1966 2909 0.108945 AGGACGGGAAAACGATCGAC 60.109 55.000 24.34 9.68 37.61 4.20
2005 2948 0.723414 CGCACAGATCGTTGCTTGAT 59.277 50.000 16.56 0.00 0.00 2.57
2200 3207 8.869897 CAGCTAAATTAAACTCACTCACGAATA 58.130 33.333 0.00 0.00 0.00 1.75
2274 3295 8.151141 ACGTAACTCTGTGAATAGATTCGATA 57.849 34.615 0.00 0.00 39.62 2.92
2296 3485 1.034838 TCAAGCACCCAAAGCAACGT 61.035 50.000 0.00 0.00 0.00 3.99
2298 3487 0.746659 ACTCAAGCACCCAAAGCAAC 59.253 50.000 0.00 0.00 0.00 4.17
2369 3575 4.779696 ACATTTGTCAAATTTGCCCTGTT 58.220 34.783 13.54 0.00 0.00 3.16
2395 3602 8.859236 TTGTCTAACTCTAGAGCAAAGTACTA 57.141 34.615 19.97 5.36 34.73 1.82
2445 3690 9.840427 CCGTTGAGTCATGTAATTAAAATTTCT 57.160 29.630 0.00 0.00 0.00 2.52
2446 3691 9.620660 ACCGTTGAGTCATGTAATTAAAATTTC 57.379 29.630 0.00 0.00 0.00 2.17
2520 3765 0.605319 TCAAAAGGTAGTGCCCGCTG 60.605 55.000 0.00 0.00 38.26 5.18
2548 3793 0.321919 ACAGCCTGATCGCACAATGT 60.322 50.000 0.00 0.00 0.00 2.71
2557 3802 3.064958 CACATGTTCATCACAGCCTGATC 59.935 47.826 0.00 0.00 37.53 2.92
2563 3808 4.863491 AGAAAACACATGTTCATCACAGC 58.137 39.130 0.00 0.00 39.40 4.40
2565 3810 8.164058 TCATTAGAAAACACATGTTCATCACA 57.836 30.769 0.00 0.00 40.71 3.58
2581 3826 8.617809 GGGAAAATAGCATACGTTCATTAGAAA 58.382 33.333 0.00 0.00 35.08 2.52
2584 3829 6.710744 AGGGGAAAATAGCATACGTTCATTAG 59.289 38.462 0.00 0.00 0.00 1.73
2592 3837 7.876068 TGTCTTATTAGGGGAAAATAGCATACG 59.124 37.037 0.00 0.00 0.00 3.06
2598 3843 8.414003 GCCTTTTGTCTTATTAGGGGAAAATAG 58.586 37.037 0.00 0.00 0.00 1.73
2604 3849 4.538490 TGAGCCTTTTGTCTTATTAGGGGA 59.462 41.667 0.00 0.00 0.00 4.81
2607 3852 5.163854 CGTGTGAGCCTTTTGTCTTATTAGG 60.164 44.000 0.00 0.00 0.00 2.69
2608 3853 5.671329 GCGTGTGAGCCTTTTGTCTTATTAG 60.671 44.000 0.00 0.00 0.00 1.73
2623 3868 2.355837 TTGTCGAGGCGTGTGAGC 60.356 61.111 0.00 0.00 0.00 4.26
2629 3897 1.006102 CTTCCTGTTGTCGAGGCGT 60.006 57.895 0.00 0.00 0.00 5.68
2641 3909 3.692257 TCCTTGCTCTTCTTCTTCCTG 57.308 47.619 0.00 0.00 0.00 3.86
2645 3913 5.559148 TCTTCTTCCTTGCTCTTCTTCTT 57.441 39.130 0.00 0.00 0.00 2.52
2647 3915 5.546526 TCTTCTTCTTCCTTGCTCTTCTTC 58.453 41.667 0.00 0.00 0.00 2.87
2648 3916 5.559148 TCTTCTTCTTCCTTGCTCTTCTT 57.441 39.130 0.00 0.00 0.00 2.52
2649 3917 5.306678 TCTTCTTCTTCTTCCTTGCTCTTCT 59.693 40.000 0.00 0.00 0.00 2.85
2650 3918 5.546526 TCTTCTTCTTCTTCCTTGCTCTTC 58.453 41.667 0.00 0.00 0.00 2.87
2651 3919 5.550290 CTCTTCTTCTTCTTCCTTGCTCTT 58.450 41.667 0.00 0.00 0.00 2.85
2652 3920 4.563374 GCTCTTCTTCTTCTTCCTTGCTCT 60.563 45.833 0.00 0.00 0.00 4.09
2653 3921 3.684305 GCTCTTCTTCTTCTTCCTTGCTC 59.316 47.826 0.00 0.00 0.00 4.26
2654 3922 3.072184 TGCTCTTCTTCTTCTTCCTTGCT 59.928 43.478 0.00 0.00 0.00 3.91
2656 3924 4.455190 CCTTGCTCTTCTTCTTCTTCCTTG 59.545 45.833 0.00 0.00 0.00 3.61
2657 3925 4.650734 CCTTGCTCTTCTTCTTCTTCCTT 58.349 43.478 0.00 0.00 0.00 3.36
2658 3926 3.558958 GCCTTGCTCTTCTTCTTCTTCCT 60.559 47.826 0.00 0.00 0.00 3.36
2659 3927 2.746904 GCCTTGCTCTTCTTCTTCTTCC 59.253 50.000 0.00 0.00 0.00 3.46
2660 3928 2.746904 GGCCTTGCTCTTCTTCTTCTTC 59.253 50.000 0.00 0.00 0.00 2.87
2661 3929 2.789213 GGCCTTGCTCTTCTTCTTCTT 58.211 47.619 0.00 0.00 0.00 2.52
2662 3930 1.338579 CGGCCTTGCTCTTCTTCTTCT 60.339 52.381 0.00 0.00 0.00 2.85
2663 3931 1.082690 CGGCCTTGCTCTTCTTCTTC 58.917 55.000 0.00 0.00 0.00 2.87
2664 3932 0.957888 GCGGCCTTGCTCTTCTTCTT 60.958 55.000 0.00 0.00 0.00 2.52
2665 3933 1.376553 GCGGCCTTGCTCTTCTTCT 60.377 57.895 0.00 0.00 0.00 2.85
2666 3934 1.376553 AGCGGCCTTGCTCTTCTTC 60.377 57.895 0.00 0.00 42.95 2.87
2667 3935 1.673665 CAGCGGCCTTGCTCTTCTT 60.674 57.895 0.00 0.00 45.23 2.52
2668 3936 2.046507 CAGCGGCCTTGCTCTTCT 60.047 61.111 0.00 0.00 45.23 2.85
2669 3937 2.359230 ACAGCGGCCTTGCTCTTC 60.359 61.111 0.00 0.00 45.23 2.87
2670 3938 2.670934 CACAGCGGCCTTGCTCTT 60.671 61.111 0.00 0.00 45.23 2.85
2689 3957 7.373531 CAGCAAAATTTAGGACTCGGCTGAG 62.374 48.000 21.32 21.32 46.68 3.35
2694 3962 3.751175 TCACAGCAAAATTTAGGACTCGG 59.249 43.478 0.00 0.00 0.00 4.63
2711 3979 4.750098 TCTTCTTCCTTACGCTTTTCACAG 59.250 41.667 0.00 0.00 0.00 3.66
2712 3980 4.699637 TCTTCTTCCTTACGCTTTTCACA 58.300 39.130 0.00 0.00 0.00 3.58
2721 3989 3.929610 CCTTGCTCTTCTTCTTCCTTACG 59.070 47.826 0.00 0.00 0.00 3.18
2731 6554 1.673665 CAGCGGCCTTGCTCTTCTT 60.674 57.895 0.00 0.00 45.23 2.52
2750 6573 0.179100 CTGTCTATGCCACAGGACGG 60.179 60.000 0.00 0.00 38.10 4.79
2767 6590 2.353323 CGGACATATGCATCCATCCTG 58.647 52.381 0.19 2.01 34.35 3.86
2782 6605 0.730265 GAATAATTGCACCGCGGACA 59.270 50.000 35.90 26.27 0.00 4.02
2857 6680 4.152759 TCGACGGCAACTTGGTATTTTTAG 59.847 41.667 0.00 0.00 0.00 1.85
2874 6697 1.587034 GCTCGGAGTTTAATTCGACGG 59.413 52.381 6.90 0.00 0.00 4.79
2876 6699 1.587034 CGGCTCGGAGTTTAATTCGAC 59.413 52.381 6.90 0.00 0.00 4.20
2895 6718 2.018670 CGCGCTCGTGTGAAATCG 59.981 61.111 5.56 0.00 0.00 3.34
2936 6759 1.002888 AGAATGGAGCCGCTCATATGG 59.997 52.381 21.76 0.00 31.08 2.74
3049 6872 5.361285 AGTCCGCATGAGTAGTTTAATCTCT 59.639 40.000 0.00 0.00 0.00 3.10
3055 6878 3.697542 TGCTAGTCCGCATGAGTAGTTTA 59.302 43.478 13.69 2.75 45.29 2.01
3056 6879 2.496070 TGCTAGTCCGCATGAGTAGTTT 59.504 45.455 13.69 0.00 45.29 2.66
3068 6891 9.676195 CATCTATTCATCTATTATGCTAGTCCG 57.324 37.037 0.00 0.00 0.00 4.79
3107 6930 7.649057 TCATGGTATATCACGTTTCTAGTCTG 58.351 38.462 0.00 0.00 0.00 3.51
3118 6941 9.513727 CTCTATTTGAGATCATGGTATATCACG 57.486 37.037 0.00 0.00 45.39 4.35


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

AutoCloner maintained by Alex Coulton.