Multiple sequence alignment - TraesCS7A01G306300

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 TraesCS7A01G306300 chr7A 100.000 3491 0 0 1 3491 432137659 432141149 0.000000e+00 6447
1 TraesCS7A01G306300 chr7A 95.431 197 9 0 3295 3491 149927815 149928011 7.270000e-82 315
2 TraesCS7A01G306300 chr7D 93.618 3353 139 27 5 3298 383269100 383272436 0.000000e+00 4937
3 TraesCS7A01G306300 chr7B 93.570 2566 115 20 3 2550 377812558 377815091 0.000000e+00 3779
4 TraesCS7A01G306300 chr7B 88.010 809 42 21 2540 3298 377815517 377816320 0.000000e+00 905
5 TraesCS7A01G306300 chr5A 97.436 195 5 0 3297 3491 1223391 1223197 2.010000e-87 333
6 TraesCS7A01G306300 chr5A 94.444 198 11 0 3294 3491 80113225 80113422 4.380000e-79 305
7 TraesCS7A01G306300 chr2A 96.939 196 6 0 3296 3491 777643749 777643944 2.600000e-86 329
8 TraesCS7A01G306300 chr2A 93.171 205 13 1 3287 3491 456570446 456570649 2.040000e-77 300
9 TraesCS7A01G306300 chr4A 95.918 196 8 0 3296 3491 71161988 71162183 5.620000e-83 318
10 TraesCS7A01G306300 chr3A 94.634 205 11 0 3287 3491 57431349 57431553 5.620000e-83 318
11 TraesCS7A01G306300 chr3A 95.361 194 9 0 3298 3491 705144882 705144689 3.380000e-80 309
12 TraesCS7A01G306300 chr1A 95.385 195 9 0 3297 3491 412137651 412137845 9.410000e-81 311


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 TraesCS7A01G306300 chr7A 432137659 432141149 3490 False 6447 6447 100.000 1 3491 1 chr7A.!!$F2 3490
1 TraesCS7A01G306300 chr7D 383269100 383272436 3336 False 4937 4937 93.618 5 3298 1 chr7D.!!$F1 3293
2 TraesCS7A01G306300 chr7B 377812558 377816320 3762 False 2342 3779 90.790 3 3298 2 chr7B.!!$F1 3295

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
685 691 0.313672 TTGACCGATTTGGCAGCAAC 59.686 50.000 0.00 0.00 43.94 4.17 F
689 695 1.153978 CGATTTGGCAGCAACGCAT 60.154 52.632 0.00 0.00 0.00 4.73 F
1707 1716 0.104120 TAATCATCGCACTCCGTGGG 59.896 55.000 4.86 4.86 45.77 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1551 1560 1.736645 CACGGACGAGGTTGCGAAT 60.737 57.895 0.0 0.0 33.96 3.34 R
2205 2214 2.123554 GGACGGAGGTACGGGGAT 60.124 66.667 0.0 0.0 38.39 3.85 R
2747 3204 0.108329 ATCGCCCTTTCACACGTAGG 60.108 55.000 0.0 0.0 0.00 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
31 32 3.448660 AGCCTAAACGTAAGGTAATCCGT 59.551 43.478 16.04 0.00 46.39 4.69
42 43 7.029563 CGTAAGGTAATCCGTAGTTTAACACT 58.970 38.462 0.00 0.00 37.96 3.55
88 89 1.379044 GCCATGTGGTAGCAGCCTT 60.379 57.895 0.00 0.00 37.57 4.35
108 109 2.985957 AAAACAACATGTGGCTGCTT 57.014 40.000 0.00 0.00 0.00 3.91
111 112 1.696063 ACAACATGTGGCTGCTTTCT 58.304 45.000 0.00 0.00 0.00 2.52
113 114 3.221771 ACAACATGTGGCTGCTTTCTTA 58.778 40.909 0.00 0.00 0.00 2.10
244 245 5.587388 ATTCCTCGTTTATTCACGGACTA 57.413 39.130 0.00 0.00 40.74 2.59
249 250 3.114065 CGTTTATTCACGGACTAGCCTC 58.886 50.000 0.00 0.00 36.47 4.70
269 270 0.880718 GACGATCCGAAATCCCCTGC 60.881 60.000 0.00 0.00 0.00 4.85
300 302 8.709308 CCCTAAATCAATGGAGATATAGGTAGG 58.291 40.741 0.00 0.00 0.00 3.18
302 304 6.567602 AATCAATGGAGATATAGGTAGGCC 57.432 41.667 0.00 0.00 0.00 5.19
313 316 4.814294 GTAGGCCAGCGTGTCCGG 62.814 72.222 5.01 0.00 33.68 5.14
405 411 7.211897 TCCTTCCCTCTCATATTTTCATTGA 57.788 36.000 0.00 0.00 0.00 2.57
415 421 9.258629 TCTCATATTTTCATTGAACAAAGGGAT 57.741 29.630 0.00 0.00 0.00 3.85
422 428 7.789202 TTCATTGAACAAAGGGATGGATAAA 57.211 32.000 0.00 0.00 0.00 1.40
424 430 6.723515 TCATTGAACAAAGGGATGGATAAACA 59.276 34.615 0.00 0.00 0.00 2.83
448 454 0.473755 ATAGCATTGGATGACCGGCA 59.526 50.000 0.00 0.00 39.42 5.69
510 516 3.896888 TCCATGAGCATTTGAAGGTGTTT 59.103 39.130 0.00 0.00 0.00 2.83
518 524 4.441356 GCATTTGAAGGTGTTTGAGGTGAA 60.441 41.667 0.00 0.00 0.00 3.18
614 620 1.692411 AAGAATTTGATAGGCCGCCC 58.308 50.000 5.55 0.00 0.00 6.13
650 656 9.585099 ACGATTCATGTTAAATGCAATACAATT 57.415 25.926 0.00 0.00 0.00 2.32
685 691 0.313672 TTGACCGATTTGGCAGCAAC 59.686 50.000 0.00 0.00 43.94 4.17
689 695 1.153978 CGATTTGGCAGCAACGCAT 60.154 52.632 0.00 0.00 0.00 4.73
772 781 7.684670 TCATGTCAAAATCTAAGACGTATTGC 58.315 34.615 5.52 0.00 35.09 3.56
778 787 7.386573 TCAAAATCTAAGACGTATTGCTGTTCA 59.613 33.333 5.52 0.00 0.00 3.18
866 875 2.665185 GACGCCAACTTCGCTGGT 60.665 61.111 0.00 0.00 36.24 4.00
952 961 1.838112 ATCTTGGACGTACGTACCCA 58.162 50.000 27.15 23.96 0.00 4.51
966 975 2.855963 CGTACCCAACTTACTGTATGCG 59.144 50.000 1.03 0.00 0.00 4.73
1707 1716 0.104120 TAATCATCGCACTCCGTGGG 59.896 55.000 4.86 4.86 45.77 4.61
1731 1740 2.526873 ACGGTCCTTGAGTGGGCT 60.527 61.111 0.00 0.00 0.00 5.19
1875 1884 1.080501 TTCGCCGAGCTTGTCAGAG 60.081 57.895 0.00 0.00 0.00 3.35
1905 1914 1.073216 CCGAAGTGCGCAGACTACTG 61.073 60.000 12.22 0.00 45.91 2.74
1914 1923 3.739300 TGCGCAGACTACTGAAAAAGTAC 59.261 43.478 5.66 0.00 46.03 2.73
2040 2049 1.152989 TGACGGTGTTTTCGTTCGGG 61.153 55.000 0.00 0.00 41.22 5.14
2043 2052 1.227913 GGTGTTTTCGTTCGGGGGA 60.228 57.895 0.00 0.00 0.00 4.81
2220 2229 3.152400 GCATCCCCGTACCTCCGT 61.152 66.667 0.00 0.00 0.00 4.69
2747 3204 3.839293 TGTACAAAAACAGTGGTGTTGC 58.161 40.909 11.19 0.00 46.68 4.17
2802 3270 3.053455 GCTGTCAGCGAGTGGATAATAC 58.947 50.000 9.53 0.00 0.00 1.89
2809 3277 5.407691 TCAGCGAGTGGATAATACTACTACG 59.592 44.000 0.00 0.00 32.06 3.51
2822 3290 6.964741 ATACTACTACGTCCAGATACATCG 57.035 41.667 0.00 0.00 0.00 3.84
2829 3297 5.201713 ACGTCCAGATACATCGATTTCAT 57.798 39.130 0.00 0.00 0.00 2.57
2862 3330 5.916661 TTCTGGACAGAGGTAGTATGTTC 57.083 43.478 1.92 0.00 38.88 3.18
3013 3497 7.575720 GCAACTAGCATTGTAGTCCTTGAAAAT 60.576 37.037 0.00 0.00 44.79 1.82
3022 3506 1.664151 GTCCTTGAAAATACGAGGGCG 59.336 52.381 0.00 0.00 40.74 6.13
3023 3507 0.377203 CCTTGAAAATACGAGGGCGC 59.623 55.000 0.00 0.00 42.48 6.53
3135 3626 6.354130 TGCAAAACACTCCTATAGGTATTCC 58.646 40.000 18.51 1.18 36.34 3.01
3140 3631 6.142259 ACACTCCTATAGGTATTCCTCGAT 57.858 41.667 18.51 0.00 43.94 3.59
3142 3633 5.294799 CACTCCTATAGGTATTCCTCGATCG 59.705 48.000 18.51 9.36 43.94 3.69
3252 3759 4.917906 AGGTAAGAGGCATTTTCTCACT 57.082 40.909 0.00 0.00 33.92 3.41
3253 3760 6.213600 AGAAGGTAAGAGGCATTTTCTCACTA 59.786 38.462 0.00 0.00 33.92 2.74
3254 3761 5.983540 AGGTAAGAGGCATTTTCTCACTAG 58.016 41.667 0.00 0.00 33.92 2.57
3255 3762 5.485708 AGGTAAGAGGCATTTTCTCACTAGT 59.514 40.000 0.00 0.00 33.92 2.57
3256 3763 6.013293 AGGTAAGAGGCATTTTCTCACTAGTT 60.013 38.462 0.00 0.00 33.92 2.24
3257 3764 7.180408 AGGTAAGAGGCATTTTCTCACTAGTTA 59.820 37.037 0.00 0.00 33.92 2.24
3258 3765 7.988028 GGTAAGAGGCATTTTCTCACTAGTTAT 59.012 37.037 0.00 0.00 33.92 1.89
3298 3805 9.582431 TCACTACTTGTGTCTAATAATTAGCAC 57.418 33.333 0.00 0.00 46.27 4.40
3299 3806 9.587772 CACTACTTGTGTCTAATAATTAGCACT 57.412 33.333 3.70 0.00 41.53 4.40
3313 3820 6.910536 AATTAGCACTATTCAAGAACTCGG 57.089 37.500 0.00 0.00 0.00 4.63
3314 3821 2.622436 AGCACTATTCAAGAACTCGGC 58.378 47.619 0.00 0.00 0.00 5.54
3315 3822 1.666189 GCACTATTCAAGAACTCGGCC 59.334 52.381 0.00 0.00 0.00 6.13
3316 3823 1.927174 CACTATTCAAGAACTCGGCCG 59.073 52.381 22.12 22.12 0.00 6.13
3317 3824 1.822990 ACTATTCAAGAACTCGGCCGA 59.177 47.619 29.03 29.03 0.00 5.54
3318 3825 2.159226 ACTATTCAAGAACTCGGCCGAG 60.159 50.000 45.26 45.26 46.91 4.63
3327 3834 3.453559 CTCGGCCGAGTTACCATTT 57.546 52.632 40.77 0.00 37.47 2.32
3328 3835 2.589798 CTCGGCCGAGTTACCATTTA 57.410 50.000 40.77 10.80 37.47 1.40
3329 3836 2.896168 CTCGGCCGAGTTACCATTTAA 58.104 47.619 40.77 10.58 37.47 1.52
3330 3837 3.264104 CTCGGCCGAGTTACCATTTAAA 58.736 45.455 40.77 10.11 37.47 1.52
3331 3838 3.875134 CTCGGCCGAGTTACCATTTAAAT 59.125 43.478 40.77 0.00 37.47 1.40
3332 3839 3.623960 TCGGCCGAGTTACCATTTAAATG 59.376 43.478 27.28 19.40 36.17 2.32
3333 3840 3.702330 GGCCGAGTTACCATTTAAATGC 58.298 45.455 20.67 8.68 35.08 3.56
3334 3841 3.490249 GGCCGAGTTACCATTTAAATGCC 60.490 47.826 20.67 12.42 35.08 4.40
3335 3842 3.490249 GCCGAGTTACCATTTAAATGCCC 60.490 47.826 20.67 8.94 35.08 5.36
3336 3843 3.697045 CCGAGTTACCATTTAAATGCCCA 59.303 43.478 20.67 6.59 35.08 5.36
3337 3844 4.340950 CCGAGTTACCATTTAAATGCCCAT 59.659 41.667 20.67 9.42 35.08 4.00
3338 3845 5.163457 CCGAGTTACCATTTAAATGCCCATT 60.163 40.000 20.67 7.38 35.08 3.16
3339 3846 6.337356 CGAGTTACCATTTAAATGCCCATTT 58.663 36.000 20.67 10.69 42.95 2.32
3340 3847 7.416890 CCGAGTTACCATTTAAATGCCCATTTA 60.417 37.037 20.67 8.88 40.99 1.40
3341 3848 7.976734 CGAGTTACCATTTAAATGCCCATTTAA 59.023 33.333 20.67 17.64 45.93 1.52
3342 3849 9.830975 GAGTTACCATTTAAATGCCCATTTAAT 57.169 29.630 20.67 12.05 46.46 1.40
3343 3850 9.830975 AGTTACCATTTAAATGCCCATTTAATC 57.169 29.630 20.67 9.88 46.46 1.75
3344 3851 8.760569 GTTACCATTTAAATGCCCATTTAATCG 58.239 33.333 20.67 15.72 46.46 3.34
3345 3852 5.757808 ACCATTTAAATGCCCATTTAATCGC 59.242 36.000 20.67 0.00 46.46 4.58
3346 3853 5.990996 CCATTTAAATGCCCATTTAATCGCT 59.009 36.000 20.67 8.66 46.46 4.93
3347 3854 7.151308 CCATTTAAATGCCCATTTAATCGCTA 58.849 34.615 20.67 10.42 46.46 4.26
3348 3855 7.116233 CCATTTAAATGCCCATTTAATCGCTAC 59.884 37.037 20.67 0.00 46.46 3.58
3349 3856 6.952773 TTAAATGCCCATTTAATCGCTACT 57.047 33.333 17.64 0.00 44.01 2.57
3350 3857 5.438761 AAATGCCCATTTAATCGCTACTC 57.561 39.130 4.52 0.00 39.08 2.59
3351 3858 3.552132 TGCCCATTTAATCGCTACTCA 57.448 42.857 0.00 0.00 0.00 3.41
3352 3859 3.879998 TGCCCATTTAATCGCTACTCAA 58.120 40.909 0.00 0.00 0.00 3.02
3353 3860 4.460263 TGCCCATTTAATCGCTACTCAAT 58.540 39.130 0.00 0.00 0.00 2.57
3354 3861 4.275689 TGCCCATTTAATCGCTACTCAATG 59.724 41.667 0.00 0.00 0.00 2.82
3355 3862 4.787598 CCCATTTAATCGCTACTCAATGC 58.212 43.478 0.00 0.00 0.00 3.56
3356 3863 4.320494 CCCATTTAATCGCTACTCAATGCC 60.320 45.833 0.00 0.00 0.00 4.40
3357 3864 4.516698 CCATTTAATCGCTACTCAATGCCT 59.483 41.667 0.00 0.00 0.00 4.75
3358 3865 5.700832 CCATTTAATCGCTACTCAATGCCTA 59.299 40.000 0.00 0.00 0.00 3.93
3359 3866 6.204688 CCATTTAATCGCTACTCAATGCCTAA 59.795 38.462 0.00 0.00 0.00 2.69
3360 3867 6.598753 TTTAATCGCTACTCAATGCCTAAC 57.401 37.500 0.00 0.00 0.00 2.34
3361 3868 4.408182 AATCGCTACTCAATGCCTAACT 57.592 40.909 0.00 0.00 0.00 2.24
3362 3869 3.165058 TCGCTACTCAATGCCTAACTG 57.835 47.619 0.00 0.00 0.00 3.16
3363 3870 2.758423 TCGCTACTCAATGCCTAACTGA 59.242 45.455 0.00 0.00 0.00 3.41
3364 3871 3.119291 CGCTACTCAATGCCTAACTGAG 58.881 50.000 0.00 0.00 41.93 3.35
3391 3898 7.751047 GAGTAGCATGTACTCGTTTCATTAA 57.249 36.000 15.18 0.00 35.23 1.40
3392 3899 8.181487 GAGTAGCATGTACTCGTTTCATTAAA 57.819 34.615 15.18 0.00 35.23 1.52
3393 3900 8.718102 AGTAGCATGTACTCGTTTCATTAAAT 57.282 30.769 0.00 0.00 0.00 1.40
3394 3901 8.604035 AGTAGCATGTACTCGTTTCATTAAATG 58.396 33.333 0.00 0.00 33.61 2.32
3395 3902 6.785191 AGCATGTACTCGTTTCATTAAATGG 58.215 36.000 0.00 0.00 33.23 3.16
3396 3903 6.374333 AGCATGTACTCGTTTCATTAAATGGT 59.626 34.615 0.00 0.00 33.23 3.55
3397 3904 6.687105 GCATGTACTCGTTTCATTAAATGGTC 59.313 38.462 0.00 0.00 33.23 4.02
3398 3905 7.625395 GCATGTACTCGTTTCATTAAATGGTCA 60.625 37.037 0.00 0.00 33.23 4.02
3399 3906 7.731882 TGTACTCGTTTCATTAAATGGTCAA 57.268 32.000 0.00 0.00 33.23 3.18
3400 3907 7.802738 TGTACTCGTTTCATTAAATGGTCAAG 58.197 34.615 0.00 0.00 33.23 3.02
3401 3908 5.699839 ACTCGTTTCATTAAATGGTCAAGC 58.300 37.500 0.00 0.00 33.23 4.01
3402 3909 5.473504 ACTCGTTTCATTAAATGGTCAAGCT 59.526 36.000 0.00 0.00 33.23 3.74
3403 3910 5.698832 TCGTTTCATTAAATGGTCAAGCTG 58.301 37.500 0.00 0.00 33.23 4.24
3404 3911 5.471797 TCGTTTCATTAAATGGTCAAGCTGA 59.528 36.000 0.00 0.00 33.23 4.26
3405 3912 6.150976 TCGTTTCATTAAATGGTCAAGCTGAT 59.849 34.615 0.00 0.00 33.23 2.90
3406 3913 6.808212 CGTTTCATTAAATGGTCAAGCTGATT 59.192 34.615 0.00 0.00 0.00 2.57
3407 3914 7.967854 CGTTTCATTAAATGGTCAAGCTGATTA 59.032 33.333 0.00 0.00 0.00 1.75
3408 3915 9.638239 GTTTCATTAAATGGTCAAGCTGATTAA 57.362 29.630 0.00 0.00 0.00 1.40
3409 3916 9.638239 TTTCATTAAATGGTCAAGCTGATTAAC 57.362 29.630 0.00 0.00 0.00 2.01
3410 3917 8.579850 TCATTAAATGGTCAAGCTGATTAACT 57.420 30.769 0.00 0.00 0.00 2.24
3411 3918 8.461222 TCATTAAATGGTCAAGCTGATTAACTG 58.539 33.333 0.00 0.00 0.00 3.16
3412 3919 5.649782 AAATGGTCAAGCTGATTAACTGG 57.350 39.130 0.00 0.00 0.00 4.00
3413 3920 2.436417 TGGTCAAGCTGATTAACTGGC 58.564 47.619 0.00 0.00 0.00 4.85
3414 3921 2.224744 TGGTCAAGCTGATTAACTGGCA 60.225 45.455 0.00 0.00 0.00 4.92
3415 3922 3.019564 GGTCAAGCTGATTAACTGGCAT 58.980 45.455 0.00 0.00 0.00 4.40
3416 3923 3.445096 GGTCAAGCTGATTAACTGGCATT 59.555 43.478 0.00 0.00 0.00 3.56
3417 3924 4.082026 GGTCAAGCTGATTAACTGGCATTT 60.082 41.667 0.00 0.00 0.00 2.32
3418 3925 5.125417 GGTCAAGCTGATTAACTGGCATTTA 59.875 40.000 0.00 0.00 0.00 1.40
3419 3926 6.350110 GGTCAAGCTGATTAACTGGCATTTAA 60.350 38.462 11.74 11.74 0.00 1.52
3420 3927 7.260603 GTCAAGCTGATTAACTGGCATTTAAT 58.739 34.615 19.10 19.10 32.86 1.40
3421 3928 7.433425 GTCAAGCTGATTAACTGGCATTTAATC 59.567 37.037 29.15 29.15 42.56 1.75
3422 3929 6.064846 AGCTGATTAACTGGCATTTAATCG 57.935 37.500 29.43 25.66 44.07 3.34
3423 3930 5.009010 AGCTGATTAACTGGCATTTAATCGG 59.991 40.000 33.29 33.29 46.34 4.18
3424 3931 5.221048 GCTGATTAACTGGCATTTAATCGGT 60.221 40.000 35.00 16.20 45.83 4.69
3425 3932 6.680378 GCTGATTAACTGGCATTTAATCGGTT 60.680 38.462 35.00 19.19 45.83 4.44
3426 3933 6.559810 TGATTAACTGGCATTTAATCGGTTG 58.440 36.000 29.43 3.76 44.07 3.77
3427 3934 5.968528 TTAACTGGCATTTAATCGGTTGT 57.031 34.783 5.99 0.00 32.87 3.32
3428 3935 4.434713 AACTGGCATTTAATCGGTTGTC 57.565 40.909 0.00 0.00 0.00 3.18
3429 3936 3.417101 ACTGGCATTTAATCGGTTGTCA 58.583 40.909 0.00 0.00 0.00 3.58
3430 3937 3.440173 ACTGGCATTTAATCGGTTGTCAG 59.560 43.478 0.00 0.00 45.08 3.51
3431 3938 3.680490 TGGCATTTAATCGGTTGTCAGA 58.320 40.909 0.00 0.00 0.00 3.27
3432 3939 3.438781 TGGCATTTAATCGGTTGTCAGAC 59.561 43.478 0.00 0.00 0.00 3.51
3433 3940 3.485216 GGCATTTAATCGGTTGTCAGACG 60.485 47.826 0.00 0.00 0.00 4.18
3434 3941 3.369756 GCATTTAATCGGTTGTCAGACGA 59.630 43.478 0.00 3.84 41.20 4.20
3441 3948 5.718649 ATCGGTTGTCAGACGATTAATTG 57.281 39.130 7.64 0.78 44.03 2.32
3442 3949 3.930229 TCGGTTGTCAGACGATTAATTGG 59.070 43.478 7.61 0.00 0.00 3.16
3443 3950 3.682858 CGGTTGTCAGACGATTAATTGGT 59.317 43.478 7.61 0.50 0.00 3.67
3444 3951 4.153475 CGGTTGTCAGACGATTAATTGGTT 59.847 41.667 7.61 0.00 0.00 3.67
3445 3952 5.390613 GGTTGTCAGACGATTAATTGGTTG 58.609 41.667 7.61 5.27 0.00 3.77
3446 3953 5.048991 GGTTGTCAGACGATTAATTGGTTGT 60.049 40.000 7.61 0.00 0.00 3.32
3447 3954 5.856126 TGTCAGACGATTAATTGGTTGTC 57.144 39.130 7.61 4.04 0.00 3.18
3448 3955 5.301555 TGTCAGACGATTAATTGGTTGTCA 58.698 37.500 7.61 6.21 32.31 3.58
3449 3956 5.760743 TGTCAGACGATTAATTGGTTGTCAA 59.239 36.000 7.61 0.00 40.01 3.18
3450 3957 6.261158 TGTCAGACGATTAATTGGTTGTCAAA 59.739 34.615 7.61 1.33 39.05 2.69
3451 3958 6.577427 GTCAGACGATTAATTGGTTGTCAAAC 59.423 38.462 7.61 0.00 39.05 2.93
3472 3979 3.106242 CGATTATTCGGTGATGGGTCA 57.894 47.619 0.00 0.00 41.74 4.02
3473 3980 3.059884 CGATTATTCGGTGATGGGTCAG 58.940 50.000 0.00 0.00 41.74 3.51
3474 3981 3.403038 GATTATTCGGTGATGGGTCAGG 58.597 50.000 0.00 0.00 34.36 3.86
3475 3982 1.874129 TATTCGGTGATGGGTCAGGT 58.126 50.000 0.00 0.00 34.36 4.00
3476 3983 1.874129 ATTCGGTGATGGGTCAGGTA 58.126 50.000 0.00 0.00 34.36 3.08
3477 3984 1.646912 TTCGGTGATGGGTCAGGTAA 58.353 50.000 0.00 0.00 34.36 2.85
3478 3985 0.899720 TCGGTGATGGGTCAGGTAAC 59.100 55.000 0.00 0.00 34.36 2.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.423290 ACCTTACGTTTAGGCTTATGGTAGT 59.577 40.000 14.40 0.00 36.17 2.73
1 2 5.910614 ACCTTACGTTTAGGCTTATGGTAG 58.089 41.667 14.40 0.00 36.17 3.18
42 43 6.070481 GGGTTTCAGCCCCTTTAATAAAATGA 60.070 38.462 0.00 0.00 42.89 2.57
71 72 2.418368 TTAAGGCTGCTACCACATGG 57.582 50.000 0.00 0.00 42.17 3.66
88 89 4.099266 AGAAAGCAGCCACATGTTGTTTTA 59.901 37.500 9.84 0.00 0.00 1.52
224 225 3.181493 GCTAGTCCGTGAATAAACGAGGA 60.181 47.826 0.00 0.00 46.49 3.71
244 245 0.030908 GATTTCGGATCGTCGAGGCT 59.969 55.000 0.00 0.00 40.42 4.58
249 250 0.597637 CAGGGGATTTCGGATCGTCG 60.598 60.000 0.00 0.00 0.00 5.12
269 270 2.438021 TCTCCATTGATTTAGGGACGGG 59.562 50.000 0.00 0.00 0.00 5.28
302 304 4.012895 GTGTTGCCGGACACGCTG 62.013 66.667 5.05 0.00 40.34 5.18
386 392 7.977853 CCTTTGTTCAATGAAAATATGAGAGGG 59.022 37.037 0.00 0.00 0.00 4.30
397 403 7.789202 TTATCCATCCCTTTGTTCAATGAAA 57.211 32.000 0.00 0.00 0.00 2.69
405 411 5.650283 TCCTTGTTTATCCATCCCTTTGTT 58.350 37.500 0.00 0.00 0.00 2.83
415 421 6.430864 TCCAATGCTATTCCTTGTTTATCCA 58.569 36.000 0.00 0.00 0.00 3.41
422 428 4.210331 GGTCATCCAATGCTATTCCTTGT 58.790 43.478 0.00 0.00 0.00 3.16
424 430 3.480470 CGGTCATCCAATGCTATTCCTT 58.520 45.455 0.00 0.00 0.00 3.36
462 468 1.132640 GAATGTGTTCGCGGACAGC 59.867 57.895 23.22 16.19 43.95 4.40
482 488 2.076100 TCAAATGCTCATGGACACGTC 58.924 47.619 0.00 0.00 0.00 4.34
518 524 1.681793 CGGTCGATCTAATGTGGAGGT 59.318 52.381 0.00 0.00 0.00 3.85
521 527 2.617308 GAGTCGGTCGATCTAATGTGGA 59.383 50.000 0.00 0.00 0.00 4.02
614 620 4.864916 AACATGAATCGTCCGAGAAATG 57.135 40.909 0.00 1.87 0.00 2.32
666 672 0.313672 GTTGCTGCCAAATCGGTCAA 59.686 50.000 0.00 0.00 36.97 3.18
673 679 1.135024 CCTTATGCGTTGCTGCCAAAT 60.135 47.619 0.00 0.00 31.68 2.32
732 741 4.869215 TGACATGATTTCAAACACGCAAT 58.131 34.783 0.00 0.00 0.00 3.56
748 757 7.637519 CAGCAATACGTCTTAGATTTTGACATG 59.362 37.037 0.00 0.00 0.00 3.21
952 961 1.470979 CGGAGCCGCATACAGTAAGTT 60.471 52.381 0.00 0.00 0.00 2.66
1215 1224 2.391389 CCGCTTGAAGAAGGACGGC 61.391 63.158 0.00 0.00 30.97 5.68
1551 1560 1.736645 CACGGACGAGGTTGCGAAT 60.737 57.895 0.00 0.00 33.96 3.34
1557 1566 3.236003 GAAGCCCACGGACGAGGTT 62.236 63.158 7.38 3.45 0.00 3.50
1647 1656 4.988716 ACCTCGTCGGGGCTGTCA 62.989 66.667 12.23 0.00 36.97 3.58
1905 1914 3.119065 CCTCCTCTCCCTCGTACTTTTTC 60.119 52.174 0.00 0.00 0.00 2.29
1914 1923 2.124693 GCTCACCTCCTCTCCCTCG 61.125 68.421 0.00 0.00 0.00 4.63
2205 2214 2.123554 GGACGGAGGTACGGGGAT 60.124 66.667 0.00 0.00 38.39 3.85
2626 3083 4.491676 GCTGATCAAAGCAACACATCATT 58.508 39.130 0.00 0.00 43.01 2.57
2747 3204 0.108329 ATCGCCCTTTCACACGTAGG 60.108 55.000 0.00 0.00 0.00 3.18
2822 3290 5.977725 TCCAGAATTACTCGACGATGAAATC 59.022 40.000 0.00 0.00 40.89 2.17
2829 3297 3.340928 TCTGTCCAGAATTACTCGACGA 58.659 45.455 0.00 0.00 39.09 4.20
2862 3330 7.615582 ACATCTGTATTGACAGGTTTACATG 57.384 36.000 5.31 0.00 45.17 3.21
2885 3353 7.145323 ACAAGTACCAATGCTTTATCACAAAC 58.855 34.615 0.00 0.00 0.00 2.93
2897 3365 9.672673 ATTATCATATAGGACAAGTACCAATGC 57.327 33.333 0.00 0.00 0.00 3.56
3013 3497 0.317160 CATAAGATGGCGCCCTCGTA 59.683 55.000 26.77 25.38 38.14 3.43
3022 3506 8.117988 CACATTAAAATGTTTGCATAAGATGGC 58.882 33.333 5.60 0.00 46.95 4.40
3023 3507 9.153721 ACACATTAAAATGTTTGCATAAGATGG 57.846 29.630 5.60 0.00 46.95 3.51
3135 3626 4.323070 GCACTAACATGATCATCGATCGAG 59.677 45.833 23.84 14.92 41.51 4.04
3203 3710 9.396022 CTTTTGCTCTTAGGGAATGAGTAATAA 57.604 33.333 0.00 0.00 33.76 1.40
3292 3799 4.181578 GCCGAGTTCTTGAATAGTGCTAA 58.818 43.478 0.00 0.00 0.00 3.09
3298 3805 2.464865 CTCGGCCGAGTTCTTGAATAG 58.535 52.381 40.77 16.90 37.47 1.73
3299 3806 2.579207 CTCGGCCGAGTTCTTGAATA 57.421 50.000 40.77 10.80 37.47 1.75
3300 3807 3.442996 CTCGGCCGAGTTCTTGAAT 57.557 52.632 40.77 0.00 37.47 2.57
3301 3808 4.988065 CTCGGCCGAGTTCTTGAA 57.012 55.556 40.77 12.14 37.47 2.69
3308 3815 6.650958 CATTTAAATGGTAACTCGGCCGAGT 61.651 44.000 46.64 46.64 43.28 4.18
3309 3816 2.589798 TAAATGGTAACTCGGCCGAG 57.410 50.000 45.26 45.26 46.91 4.63
3310 3817 3.331478 TTTAAATGGTAACTCGGCCGA 57.669 42.857 29.03 29.03 37.61 5.54
3311 3818 3.790789 GCATTTAAATGGTAACTCGGCCG 60.791 47.826 25.61 22.12 36.90 6.13
3312 3819 3.490249 GGCATTTAAATGGTAACTCGGCC 60.490 47.826 25.61 15.20 36.90 6.13
3313 3820 3.490249 GGGCATTTAAATGGTAACTCGGC 60.490 47.826 25.61 11.80 36.90 5.54
3314 3821 3.697045 TGGGCATTTAAATGGTAACTCGG 59.303 43.478 25.61 1.79 36.90 4.63
3315 3822 4.974368 TGGGCATTTAAATGGTAACTCG 57.026 40.909 25.61 2.46 36.90 4.18
3327 3834 6.058833 TGAGTAGCGATTAAATGGGCATTTA 58.941 36.000 0.00 0.00 40.99 1.40
3328 3835 4.887071 TGAGTAGCGATTAAATGGGCATTT 59.113 37.500 0.00 0.00 42.95 2.32
3329 3836 4.460263 TGAGTAGCGATTAAATGGGCATT 58.540 39.130 0.00 0.00 0.00 3.56
3330 3837 4.085357 TGAGTAGCGATTAAATGGGCAT 57.915 40.909 0.00 0.00 0.00 4.40
3331 3838 3.552132 TGAGTAGCGATTAAATGGGCA 57.448 42.857 0.00 0.00 0.00 5.36
3332 3839 4.787598 CATTGAGTAGCGATTAAATGGGC 58.212 43.478 0.00 0.00 0.00 5.36
3333 3840 4.320494 GGCATTGAGTAGCGATTAAATGGG 60.320 45.833 2.33 0.00 0.00 4.00
3334 3841 4.516698 AGGCATTGAGTAGCGATTAAATGG 59.483 41.667 2.33 0.00 0.00 3.16
3335 3842 5.679734 AGGCATTGAGTAGCGATTAAATG 57.320 39.130 0.00 0.00 0.00 2.32
3336 3843 6.992715 AGTTAGGCATTGAGTAGCGATTAAAT 59.007 34.615 0.00 0.00 0.00 1.40
3337 3844 6.257849 CAGTTAGGCATTGAGTAGCGATTAAA 59.742 38.462 0.00 0.00 0.00 1.52
3338 3845 5.753438 CAGTTAGGCATTGAGTAGCGATTAA 59.247 40.000 0.00 0.00 0.00 1.40
3339 3846 5.068591 TCAGTTAGGCATTGAGTAGCGATTA 59.931 40.000 0.00 0.00 0.00 1.75
3340 3847 4.122776 CAGTTAGGCATTGAGTAGCGATT 58.877 43.478 0.00 0.00 0.00 3.34
3341 3848 3.384789 TCAGTTAGGCATTGAGTAGCGAT 59.615 43.478 0.00 0.00 0.00 4.58
3342 3849 2.758423 TCAGTTAGGCATTGAGTAGCGA 59.242 45.455 0.00 0.00 0.00 4.93
3343 3850 3.119291 CTCAGTTAGGCATTGAGTAGCG 58.881 50.000 0.00 0.00 34.92 4.26
3344 3851 3.462021 CCTCAGTTAGGCATTGAGTAGC 58.538 50.000 0.00 0.00 38.97 3.58
3356 3863 2.099921 ACATGCTACTCGCCTCAGTTAG 59.900 50.000 0.00 0.00 38.05 2.34
3357 3864 2.100197 ACATGCTACTCGCCTCAGTTA 58.900 47.619 0.00 0.00 38.05 2.24
3358 3865 0.898320 ACATGCTACTCGCCTCAGTT 59.102 50.000 0.00 0.00 38.05 3.16
3359 3866 1.405821 GTACATGCTACTCGCCTCAGT 59.594 52.381 0.00 0.00 38.05 3.41
3360 3867 1.678627 AGTACATGCTACTCGCCTCAG 59.321 52.381 0.00 0.00 38.05 3.35
3361 3868 1.676529 GAGTACATGCTACTCGCCTCA 59.323 52.381 15.18 0.00 38.05 3.86
3362 3869 2.409152 GAGTACATGCTACTCGCCTC 57.591 55.000 15.18 0.00 38.05 4.70
3367 3874 7.751047 TTAATGAAACGAGTACATGCTACTC 57.249 36.000 18.14 18.14 40.26 2.59
3368 3875 8.604035 CATTTAATGAAACGAGTACATGCTACT 58.396 33.333 0.00 7.43 0.00 2.57
3369 3876 7.850982 CCATTTAATGAAACGAGTACATGCTAC 59.149 37.037 6.50 0.00 0.00 3.58
3370 3877 7.551262 ACCATTTAATGAAACGAGTACATGCTA 59.449 33.333 6.50 0.00 0.00 3.49
3371 3878 6.374333 ACCATTTAATGAAACGAGTACATGCT 59.626 34.615 6.50 0.00 0.00 3.79
3372 3879 6.551736 ACCATTTAATGAAACGAGTACATGC 58.448 36.000 6.50 0.00 0.00 4.06
3373 3880 7.747888 TGACCATTTAATGAAACGAGTACATG 58.252 34.615 6.50 0.00 0.00 3.21
3374 3881 7.915293 TGACCATTTAATGAAACGAGTACAT 57.085 32.000 6.50 0.00 0.00 2.29
3375 3882 7.572353 GCTTGACCATTTAATGAAACGAGTACA 60.572 37.037 6.50 0.00 0.00 2.90
3376 3883 6.741358 GCTTGACCATTTAATGAAACGAGTAC 59.259 38.462 6.50 0.00 0.00 2.73
3377 3884 6.653320 AGCTTGACCATTTAATGAAACGAGTA 59.347 34.615 6.50 0.00 0.00 2.59
3378 3885 5.473504 AGCTTGACCATTTAATGAAACGAGT 59.526 36.000 6.50 0.00 0.00 4.18
3379 3886 5.796935 CAGCTTGACCATTTAATGAAACGAG 59.203 40.000 6.50 7.46 0.00 4.18
3380 3887 5.471797 TCAGCTTGACCATTTAATGAAACGA 59.528 36.000 6.50 0.00 0.00 3.85
3381 3888 5.698832 TCAGCTTGACCATTTAATGAAACG 58.301 37.500 6.50 0.00 0.00 3.60
3382 3889 9.638239 TTAATCAGCTTGACCATTTAATGAAAC 57.362 29.630 6.50 0.00 0.00 2.78
3383 3890 9.638239 GTTAATCAGCTTGACCATTTAATGAAA 57.362 29.630 6.50 0.00 0.00 2.69
3384 3891 9.023962 AGTTAATCAGCTTGACCATTTAATGAA 57.976 29.630 6.50 0.00 0.00 2.57
3385 3892 8.461222 CAGTTAATCAGCTTGACCATTTAATGA 58.539 33.333 6.50 0.00 0.00 2.57
3386 3893 7.703621 CCAGTTAATCAGCTTGACCATTTAATG 59.296 37.037 0.00 0.00 0.00 1.90
3387 3894 7.631377 GCCAGTTAATCAGCTTGACCATTTAAT 60.631 37.037 0.00 0.00 0.00 1.40
3388 3895 6.350110 GCCAGTTAATCAGCTTGACCATTTAA 60.350 38.462 0.00 0.00 0.00 1.52
3389 3896 5.125417 GCCAGTTAATCAGCTTGACCATTTA 59.875 40.000 0.00 0.00 0.00 1.40
3390 3897 4.082026 GCCAGTTAATCAGCTTGACCATTT 60.082 41.667 0.00 0.00 0.00 2.32
3391 3898 3.445096 GCCAGTTAATCAGCTTGACCATT 59.555 43.478 0.00 0.00 0.00 3.16
3392 3899 3.019564 GCCAGTTAATCAGCTTGACCAT 58.980 45.455 0.00 0.00 0.00 3.55
3393 3900 2.224744 TGCCAGTTAATCAGCTTGACCA 60.225 45.455 0.00 0.00 0.00 4.02
3394 3901 2.436417 TGCCAGTTAATCAGCTTGACC 58.564 47.619 0.00 0.00 0.00 4.02
3395 3902 4.708726 AATGCCAGTTAATCAGCTTGAC 57.291 40.909 0.00 0.00 0.00 3.18
3396 3903 6.832520 TTAAATGCCAGTTAATCAGCTTGA 57.167 33.333 0.00 0.00 0.00 3.02
3397 3904 6.415867 CGATTAAATGCCAGTTAATCAGCTTG 59.584 38.462 27.36 13.56 43.53 4.01
3398 3905 6.460123 CCGATTAAATGCCAGTTAATCAGCTT 60.460 38.462 27.36 2.90 43.53 3.74
3399 3906 5.009010 CCGATTAAATGCCAGTTAATCAGCT 59.991 40.000 27.36 3.52 43.53 4.24
3400 3907 5.215160 CCGATTAAATGCCAGTTAATCAGC 58.785 41.667 27.36 10.21 43.53 4.26
3401 3908 6.377327 ACCGATTAAATGCCAGTTAATCAG 57.623 37.500 27.36 21.70 43.53 2.90
3402 3909 6.151985 ACAACCGATTAAATGCCAGTTAATCA 59.848 34.615 27.36 0.00 43.53 2.57
3403 3910 6.560711 ACAACCGATTAAATGCCAGTTAATC 58.439 36.000 21.64 21.64 41.47 1.75
3404 3911 6.151985 TGACAACCGATTAAATGCCAGTTAAT 59.848 34.615 9.68 9.68 34.58 1.40
3405 3912 5.473846 TGACAACCGATTAAATGCCAGTTAA 59.526 36.000 0.00 0.00 0.00 2.01
3406 3913 5.004448 TGACAACCGATTAAATGCCAGTTA 58.996 37.500 0.00 0.00 0.00 2.24
3407 3914 3.823873 TGACAACCGATTAAATGCCAGTT 59.176 39.130 0.00 0.00 0.00 3.16
3408 3915 3.417101 TGACAACCGATTAAATGCCAGT 58.583 40.909 0.00 0.00 0.00 4.00
3409 3916 3.689161 TCTGACAACCGATTAAATGCCAG 59.311 43.478 0.00 0.00 0.00 4.85
3410 3917 3.438781 GTCTGACAACCGATTAAATGCCA 59.561 43.478 2.24 0.00 0.00 4.92
3411 3918 3.485216 CGTCTGACAACCGATTAAATGCC 60.485 47.826 8.73 0.00 0.00 4.40
3412 3919 3.369756 TCGTCTGACAACCGATTAAATGC 59.630 43.478 8.73 0.00 0.00 3.56
3413 3920 5.718649 ATCGTCTGACAACCGATTAAATG 57.281 39.130 8.73 0.00 38.06 2.32
3417 3924 6.256975 CCAATTAATCGTCTGACAACCGATTA 59.743 38.462 17.99 17.99 46.16 1.75
3419 3926 4.570772 CCAATTAATCGTCTGACAACCGAT 59.429 41.667 8.73 1.93 42.65 4.18
3420 3927 3.930229 CCAATTAATCGTCTGACAACCGA 59.070 43.478 8.73 0.00 34.79 4.69
3421 3928 3.682858 ACCAATTAATCGTCTGACAACCG 59.317 43.478 8.73 0.00 0.00 4.44
3422 3929 5.048991 ACAACCAATTAATCGTCTGACAACC 60.049 40.000 8.73 0.00 0.00 3.77
3423 3930 5.997385 ACAACCAATTAATCGTCTGACAAC 58.003 37.500 8.73 0.00 0.00 3.32
3424 3931 5.760743 TGACAACCAATTAATCGTCTGACAA 59.239 36.000 8.73 0.00 0.00 3.18
3425 3932 5.301555 TGACAACCAATTAATCGTCTGACA 58.698 37.500 8.73 0.00 0.00 3.58
3426 3933 5.856126 TGACAACCAATTAATCGTCTGAC 57.144 39.130 0.00 0.00 0.00 3.51
3427 3934 6.664515 GTTTGACAACCAATTAATCGTCTGA 58.335 36.000 0.00 0.00 34.23 3.27
3428 3935 6.911484 GTTTGACAACCAATTAATCGTCTG 57.089 37.500 0.00 0.00 34.23 3.51
3453 3960 3.181454 ACCTGACCCATCACCGAATAATC 60.181 47.826 0.00 0.00 0.00 1.75
3454 3961 2.777692 ACCTGACCCATCACCGAATAAT 59.222 45.455 0.00 0.00 0.00 1.28
3455 3962 2.193127 ACCTGACCCATCACCGAATAA 58.807 47.619 0.00 0.00 0.00 1.40
3456 3963 1.874129 ACCTGACCCATCACCGAATA 58.126 50.000 0.00 0.00 0.00 1.75
3457 3964 1.874129 TACCTGACCCATCACCGAAT 58.126 50.000 0.00 0.00 0.00 3.34
3458 3965 1.276989 GTTACCTGACCCATCACCGAA 59.723 52.381 0.00 0.00 0.00 4.30
3459 3966 0.899720 GTTACCTGACCCATCACCGA 59.100 55.000 0.00 0.00 0.00 4.69
3460 3967 0.902531 AGTTACCTGACCCATCACCG 59.097 55.000 0.00 0.00 0.00 4.94
3461 3968 1.906574 TCAGTTACCTGACCCATCACC 59.093 52.381 0.00 0.00 42.80 4.02
3470 3977 0.613260 ATGCCGCTTCAGTTACCTGA 59.387 50.000 0.00 0.00 45.95 3.86
3471 3978 1.009829 GATGCCGCTTCAGTTACCTG 58.990 55.000 1.48 0.00 40.25 4.00
3472 3979 3.460648 GATGCCGCTTCAGTTACCT 57.539 52.632 1.48 0.00 0.00 3.08


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

AutoCloner maintained by Alex Coulton.