Multiple sequence alignment - TraesCS5B01G377400

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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 TraesCS5B01G377400 chr5B 100.000 4022 0 0 1 4022 554824682 554820661 0.000000e+00 7428.0
1 TraesCS5B01G377400 chr5B 94.479 163 7 2 3501 3662 607838401 607838562 2.400000e-62 250.0
2 TraesCS5B01G377400 chr5B 92.899 169 9 3 3486 3653 583291745 583291579 4.020000e-60 243.0
3 TraesCS5B01G377400 chr5B 97.436 39 1 0 448 486 554824180 554824142 2.590000e-07 67.6
4 TraesCS5B01G377400 chr5B 97.436 39 1 0 503 541 554824235 554824197 2.590000e-07 67.6
5 TraesCS5B01G377400 chr5D 94.670 3490 108 34 1 3483 454113409 454109991 0.000000e+00 5343.0
6 TraesCS5B01G377400 chr5D 89.037 301 12 3 3481 3777 454109905 454109622 1.780000e-93 353.0
7 TraesCS5B01G377400 chr5D 93.413 167 9 2 3490 3656 12270501 12270337 3.100000e-61 246.0
8 TraesCS5B01G377400 chr5D 83.234 167 25 3 740 905 408170066 408170230 2.500000e-32 150.0
9 TraesCS5B01G377400 chr5D 82.840 169 22 6 740 905 76637977 76638141 1.170000e-30 145.0
10 TraesCS5B01G377400 chr5D 91.837 98 6 1 3927 4022 454108930 454108833 7.010000e-28 135.0
11 TraesCS5B01G377400 chr5D 97.368 76 2 0 3854 3929 454109096 454109021 3.260000e-26 130.0
12 TraesCS5B01G377400 chr5D 100.000 39 0 0 503 541 454112963 454112925 5.580000e-09 73.1
13 TraesCS5B01G377400 chr5D 92.308 39 3 0 448 486 454112908 454112870 5.620000e-04 56.5
14 TraesCS5B01G377400 chr5A 94.233 1630 63 18 1859 3483 573101584 573099981 0.000000e+00 2460.0
15 TraesCS5B01G377400 chr5A 85.876 1324 107 28 510 1793 573102869 573101586 0.000000e+00 1336.0
16 TraesCS5B01G377400 chr5A 88.259 494 43 7 1 486 573103323 573102837 9.690000e-161 577.0
17 TraesCS5B01G377400 chr5A 97.115 104 3 0 3674 3777 573099882 573099779 4.130000e-40 176.0
18 TraesCS5B01G377400 chr5A 97.059 34 0 1 1476 1509 573101787 573101819 5.620000e-04 56.5
19 TraesCS5B01G377400 chr3B 95.808 167 6 1 3488 3654 201028671 201028506 6.630000e-68 268.0
20 TraesCS5B01G377400 chr3D 94.611 167 8 1 3488 3654 137982511 137982346 1.430000e-64 257.0
21 TraesCS5B01G377400 chr3A 94.012 167 7 2 3488 3654 155828569 155828406 2.400000e-62 250.0
22 TraesCS5B01G377400 chr3A 95.062 81 3 1 3763 3842 54981440 54981520 4.220000e-25 126.0
23 TraesCS5B01G377400 chr1B 93.413 167 8 2 3490 3656 586282131 586282294 1.120000e-60 244.0
24 TraesCS5B01G377400 chr4D 92.857 168 10 2 3488 3655 334164389 334164554 4.020000e-60 243.0
25 TraesCS5B01G377400 chr1D 91.429 175 13 2 3484 3657 396035324 396035497 5.200000e-59 239.0
26 TraesCS5B01G377400 chr1D 100.000 28 0 0 127 154 462462271 462462298 7.000000e-03 52.8
27 TraesCS5B01G377400 chr4B 87.943 141 15 2 742 882 134121279 134121141 8.940000e-37 165.0
28 TraesCS5B01G377400 chr2A 87.500 144 16 2 740 883 601333353 601333212 8.940000e-37 165.0
29 TraesCS5B01G377400 chr6B 83.432 169 21 7 740 905 114566506 114566342 2.500000e-32 150.0
30 TraesCS5B01G377400 chr6D 83.041 171 21 7 740 907 229422026 229421861 9.010000e-32 148.0
31 TraesCS5B01G377400 chr4A 100.000 72 0 0 3771 3842 729095007 729094936 2.520000e-27 134.0
32 TraesCS5B01G377400 chr4A 95.122 82 2 2 3761 3842 582530154 582530075 1.170000e-25 128.0
33 TraesCS5B01G377400 chr4A 92.308 91 3 3 3762 3848 661959580 661959670 4.220000e-25 126.0
34 TraesCS5B01G377400 chr2D 93.258 89 3 3 3755 3842 348190822 348190736 1.170000e-25 128.0
35 TraesCS5B01G377400 chr2D 93.023 86 3 2 3757 3842 575354489 575354407 5.460000e-24 122.0
36 TraesCS5B01G377400 chr7D 100.000 68 0 0 3775 3842 517575400 517575333 4.220000e-25 126.0
37 TraesCS5B01G377400 chr2B 93.103 87 3 3 3757 3842 439444382 439444298 1.520000e-24 124.0
38 TraesCS5B01G377400 chr2B 94.048 84 2 3 3760 3842 503924350 503924269 1.520000e-24 124.0
39 TraesCS5B01G377400 chr1A 100.000 28 0 0 127 154 554287312 554287339 7.000000e-03 52.8


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 TraesCS5B01G377400 chr5B 554820661 554824682 4021 True 2521.066667 7428 98.290667 1 4022 3 chr5B.!!$R2 4021
1 TraesCS5B01G377400 chr5D 454108833 454113409 4576 True 1015.100000 5343 94.203333 1 4022 6 chr5D.!!$R2 4021
2 TraesCS5B01G377400 chr5A 573099779 573103323 3544 True 1137.250000 2460 91.370750 1 3777 4 chr5A.!!$R1 3776

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
274 282 0.643820 CGTCGCTCCATAAACGTTCC 59.356 55.0 0.00 0.00 0.00 3.62 F
887 913 0.669077 ATCGCCTAGAGCCTAACACG 59.331 55.0 0.00 0.00 38.78 4.49 F
2394 2457 1.183549 CTTCGGTAGGATATCCCCGG 58.816 60.0 28.62 19.28 40.03 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2273 2336 1.190643 CTTCTCCCTCAGGTCTGGAC 58.809 60.000 0.0 0.0 0.00 4.02 R
2449 2512 3.008704 GGAGTACCTTTTTCAGCCTGGTA 59.991 47.826 0.0 0.0 32.74 3.25 R
3925 4532 0.533308 AGACAGCCCGCAAAAACGTA 60.533 50.000 0.0 0.0 0.00 3.57 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
29 30 4.280494 CCGTCCCCGCTGTATCCG 62.280 72.222 0.00 0.00 0.00 4.18
174 175 2.584608 GCGGCCTAGACCACACAT 59.415 61.111 0.00 0.00 0.00 3.21
194 196 1.090728 GTTTCCTGCCTCTAGCTTGC 58.909 55.000 0.00 0.00 44.23 4.01
238 245 4.805719 GCCTGCCAAAGCTCATTTAATAAC 59.194 41.667 0.00 0.00 40.80 1.89
274 282 0.643820 CGTCGCTCCATAAACGTTCC 59.356 55.000 0.00 0.00 0.00 3.62
275 283 1.004595 GTCGCTCCATAAACGTTCCC 58.995 55.000 0.00 0.00 0.00 3.97
333 341 2.981784 TGTCCATATGCCTGGATTAGCT 59.018 45.455 0.00 0.00 46.67 3.32
424 432 5.127519 TGCAGGATCCAAATCTTGTTTATGG 59.872 40.000 15.82 0.00 40.26 2.74
481 489 4.404394 TGGGTGAATTATCTAGCGACTTCA 59.596 41.667 0.00 0.00 0.00 3.02
532 540 4.051922 CAGTGGGTGAATTATCTAGCGAC 58.948 47.826 0.00 0.00 0.00 5.19
535 543 4.745620 GTGGGTGAATTATCTAGCGACTTC 59.254 45.833 0.00 0.00 0.00 3.01
557 566 2.424601 GCAGTGCAGGATGAAGCATTTA 59.575 45.455 11.09 0.00 43.44 1.40
559 568 3.693085 CAGTGCAGGATGAAGCATTTAGT 59.307 43.478 0.00 0.00 43.44 2.24
584 593 1.336755 ACAGATTTTGGCACCACGAAC 59.663 47.619 0.00 0.00 0.00 3.95
628 637 9.634021 TCGAATATTCACCTCTATAGCATCTAT 57.366 33.333 15.57 0.00 0.00 1.98
629 638 9.891828 CGAATATTCACCTCTATAGCATCTATC 57.108 37.037 15.57 0.00 0.00 2.08
822 848 2.230992 GACCAAGGCACACATTTATGCA 59.769 45.455 0.00 0.00 43.93 3.96
823 849 2.029110 ACCAAGGCACACATTTATGCAC 60.029 45.455 0.00 0.00 43.93 4.57
824 850 2.029200 CCAAGGCACACATTTATGCACA 60.029 45.455 0.00 0.00 43.93 4.57
825 851 3.554544 CCAAGGCACACATTTATGCACAA 60.555 43.478 0.00 0.00 43.93 3.33
826 852 4.247258 CAAGGCACACATTTATGCACAAT 58.753 39.130 0.00 0.00 43.93 2.71
827 853 4.540359 AGGCACACATTTATGCACAATT 57.460 36.364 0.00 0.00 43.93 2.32
828 854 5.657826 AGGCACACATTTATGCACAATTA 57.342 34.783 0.00 0.00 43.93 1.40
829 855 6.224665 AGGCACACATTTATGCACAATTAT 57.775 33.333 0.00 0.00 43.93 1.28
830 856 6.044046 AGGCACACATTTATGCACAATTATG 58.956 36.000 0.00 0.00 43.93 1.90
831 857 5.276963 GGCACACATTTATGCACAATTATGC 60.277 40.000 0.56 0.56 43.93 3.14
885 911 3.293337 TGTTATCGCCTAGAGCCTAACA 58.707 45.455 14.83 14.83 40.81 2.41
887 913 0.669077 ATCGCCTAGAGCCTAACACG 59.331 55.000 0.00 0.00 38.78 4.49
905 931 4.372656 ACACGCCTTCTTTAGCTATGATC 58.627 43.478 0.00 0.00 0.00 2.92
910 936 5.237048 GCCTTCTTTAGCTATGATCTGGAG 58.763 45.833 0.00 0.00 0.00 3.86
1323 1349 5.871524 TCTGTACATCTCTTCTGCAAATGTC 59.128 40.000 0.00 0.00 33.01 3.06
1355 1381 3.375299 GCACTCTTGATAAATGCGAAGGT 59.625 43.478 0.00 0.00 0.00 3.50
1397 1423 3.214696 AGCTTTGGTCTGCTGTAACTT 57.785 42.857 0.00 0.00 38.21 2.66
1535 1561 7.213216 TCATGTTTTGTAGCTTTGCTTGATA 57.787 32.000 0.00 0.00 40.44 2.15
1653 1713 6.209589 ACGTATATGTTGATCTGTCATAGGCT 59.790 38.462 0.00 0.00 33.56 4.58
1736 1796 7.720957 AGTTCATGAGTGCCATATGCTTATAAA 59.279 33.333 0.00 0.00 42.00 1.40
1799 1859 7.096106 CGCTTTTTGAATTCTTATGCAAGTTGA 60.096 33.333 7.16 0.00 30.89 3.18
1848 1908 9.778741 TCATTATAACAGGGTCAAATACTCATC 57.221 33.333 0.00 0.00 0.00 2.92
1849 1909 9.559732 CATTATAACAGGGTCAAATACTCATCA 57.440 33.333 0.00 0.00 0.00 3.07
1856 1916 9.561069 ACAGGGTCAAATACTCATCATTATAAC 57.439 33.333 0.00 0.00 0.00 1.89
1857 1917 9.559732 CAGGGTCAAATACTCATCATTATAACA 57.440 33.333 0.00 0.00 0.00 2.41
1858 1918 9.784531 AGGGTCAAATACTCATCATTATAACAG 57.215 33.333 0.00 0.00 0.00 3.16
1859 1919 9.003658 GGGTCAAATACTCATCATTATAACAGG 57.996 37.037 0.00 0.00 0.00 4.00
1860 1920 9.003658 GGTCAAATACTCATCATTATAACAGGG 57.996 37.037 0.00 0.00 0.00 4.45
1861 1921 9.561069 GTCAAATACTCATCATTATAACAGGGT 57.439 33.333 0.00 0.00 0.00 4.34
1862 1922 9.778741 TCAAATACTCATCATTATAACAGGGTC 57.221 33.333 0.00 0.00 0.00 4.46
1863 1923 9.559732 CAAATACTCATCATTATAACAGGGTCA 57.440 33.333 0.00 0.00 0.00 4.02
2394 2457 1.183549 CTTCGGTAGGATATCCCCGG 58.816 60.000 28.62 19.28 40.03 5.73
2449 2512 5.360714 TCCTTGTTTCAACTCTCTTGCATTT 59.639 36.000 0.00 0.00 0.00 2.32
2589 2652 3.130633 CAAACATCGCCATAAGGATCGA 58.869 45.455 0.00 0.00 36.89 3.59
2625 2688 7.784633 AGACAAAGACAAAGAGAAAGAGAAG 57.215 36.000 0.00 0.00 0.00 2.85
2626 2689 6.765512 AGACAAAGACAAAGAGAAAGAGAAGG 59.234 38.462 0.00 0.00 0.00 3.46
2627 2690 6.653989 ACAAAGACAAAGAGAAAGAGAAGGA 58.346 36.000 0.00 0.00 0.00 3.36
2628 2691 6.765512 ACAAAGACAAAGAGAAAGAGAAGGAG 59.234 38.462 0.00 0.00 0.00 3.69
2629 2692 6.739331 AAGACAAAGAGAAAGAGAAGGAGA 57.261 37.500 0.00 0.00 0.00 3.71
2630 2693 6.739331 AGACAAAGAGAAAGAGAAGGAGAA 57.261 37.500 0.00 0.00 0.00 2.87
2640 2703 7.670364 AGAAAGAGAAGGAGAAAGAGAAAGAG 58.330 38.462 0.00 0.00 0.00 2.85
2652 2715 9.196552 GAGAAAGAGAAAGAGAAAGAGAAAGAG 57.803 37.037 0.00 0.00 0.00 2.85
2661 2724 9.898152 AAAGAGAAAGAGAAAGAGAAAGAGAAA 57.102 29.630 0.00 0.00 0.00 2.52
2670 2733 9.196552 GAGAAAGAGAAAGAGAAAGAGAAAGAG 57.803 37.037 0.00 0.00 0.00 2.85
2671 2734 8.923270 AGAAAGAGAAAGAGAAAGAGAAAGAGA 58.077 33.333 0.00 0.00 0.00 3.10
2672 2735 9.541143 GAAAGAGAAAGAGAAAGAGAAAGAGAA 57.459 33.333 0.00 0.00 0.00 2.87
2673 2736 9.546428 AAAGAGAAAGAGAAAGAGAAAGAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
2674 2737 7.670364 AGAGAAAGAGAAAGAGAAAGAGAAGG 58.330 38.462 0.00 0.00 0.00 3.46
2675 2738 7.508977 AGAGAAAGAGAAAGAGAAAGAGAAGGA 59.491 37.037 0.00 0.00 0.00 3.36
2676 2739 7.670364 AGAAAGAGAAAGAGAAAGAGAAGGAG 58.330 38.462 0.00 0.00 0.00 3.69
2836 2901 9.970395 TTGGCTATGCTCTAAATTTTAATGATG 57.030 29.630 0.00 0.00 0.00 3.07
3013 3079 0.848305 GACAGCACAAAAGCGCAAAG 59.152 50.000 11.47 0.00 40.15 2.77
3024 3090 4.777140 AAAGCGCAAAGTTCAATGAAAC 57.223 36.364 11.47 0.00 0.00 2.78
3046 3112 1.202627 GGCAATGGACTTTGTTTGGCA 60.203 47.619 3.55 0.00 42.34 4.92
3049 3115 3.928375 GCAATGGACTTTGTTTGGCATAG 59.072 43.478 0.00 0.00 33.26 2.23
3341 3407 8.770438 TTTTATATGGTTCCTTTTGCATTGTC 57.230 30.769 0.00 0.00 0.00 3.18
3347 3413 4.279420 GGTTCCTTTTGCATTGTCTCTCTT 59.721 41.667 0.00 0.00 0.00 2.85
3492 3646 7.775561 ACTGGAAATAGGAAGTTGATGATTACC 59.224 37.037 0.00 0.00 0.00 2.85
3497 3651 3.858638 AGGAAGTTGATGATTACCCCCTT 59.141 43.478 0.00 0.00 0.00 3.95
3498 3652 4.294970 AGGAAGTTGATGATTACCCCCTTT 59.705 41.667 0.00 0.00 0.00 3.11
3503 3657 4.946160 TGATGATTACCCCCTTTGTTCT 57.054 40.909 0.00 0.00 0.00 3.01
3505 3659 5.016173 TGATGATTACCCCCTTTGTTCTTG 58.984 41.667 0.00 0.00 0.00 3.02
3515 3669 6.890268 ACCCCCTTTGTTCTTGAATATAAGTC 59.110 38.462 0.00 0.00 0.00 3.01
3542 3696 9.901172 TTTTTAGAGATTCCAATAAGGGACTAC 57.099 33.333 0.00 0.00 38.49 2.73
3543 3697 8.618240 TTTAGAGATTCCAATAAGGGACTACA 57.382 34.615 0.00 0.00 38.49 2.74
3544 3698 8.798975 TTAGAGATTCCAATAAGGGACTACAT 57.201 34.615 0.00 0.00 38.49 2.29
3545 3699 9.892444 TTAGAGATTCCAATAAGGGACTACATA 57.108 33.333 0.00 0.00 38.49 2.29
3546 3700 8.196378 AGAGATTCCAATAAGGGACTACATAC 57.804 38.462 0.00 0.00 38.49 2.39
3547 3701 6.994221 AGATTCCAATAAGGGACTACATACG 58.006 40.000 0.00 0.00 38.49 3.06
3548 3702 5.540400 TTCCAATAAGGGACTACATACGG 57.460 43.478 0.00 0.00 38.49 4.02
3549 3703 4.806892 TCCAATAAGGGACTACATACGGA 58.193 43.478 0.00 0.00 38.49 4.69
3550 3704 4.831155 TCCAATAAGGGACTACATACGGAG 59.169 45.833 0.00 0.00 38.49 4.63
3551 3705 4.557205 CAATAAGGGACTACATACGGAGC 58.443 47.826 0.00 0.00 38.49 4.70
3552 3706 2.154567 AAGGGACTACATACGGAGCA 57.845 50.000 0.00 0.00 38.49 4.26
3553 3707 2.154567 AGGGACTACATACGGAGCAA 57.845 50.000 0.00 0.00 36.02 3.91
3554 3708 2.463752 AGGGACTACATACGGAGCAAA 58.536 47.619 0.00 0.00 36.02 3.68
3555 3709 2.835764 AGGGACTACATACGGAGCAAAA 59.164 45.455 0.00 0.00 36.02 2.44
3556 3710 3.454812 AGGGACTACATACGGAGCAAAAT 59.545 43.478 0.00 0.00 36.02 1.82
3568 3722 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
3780 3938 6.466885 TTAAGCATCTACCAGTTCTACTCC 57.533 41.667 0.00 0.00 0.00 3.85
3781 3939 3.301274 AGCATCTACCAGTTCTACTCCC 58.699 50.000 0.00 0.00 0.00 4.30
3783 3941 3.319689 GCATCTACCAGTTCTACTCCCTC 59.680 52.174 0.00 0.00 0.00 4.30
3784 3942 3.666345 TCTACCAGTTCTACTCCCTCC 57.334 52.381 0.00 0.00 0.00 4.30
3785 3943 2.092538 TCTACCAGTTCTACTCCCTCCG 60.093 54.545 0.00 0.00 0.00 4.63
3786 3944 0.408700 ACCAGTTCTACTCCCTCCGT 59.591 55.000 0.00 0.00 0.00 4.69
3787 3945 1.203149 ACCAGTTCTACTCCCTCCGTT 60.203 52.381 0.00 0.00 0.00 4.44
3788 3946 1.477295 CCAGTTCTACTCCCTCCGTTC 59.523 57.143 0.00 0.00 0.00 3.95
3789 3947 1.477295 CAGTTCTACTCCCTCCGTTCC 59.523 57.143 0.00 0.00 0.00 3.62
3791 3949 2.579860 AGTTCTACTCCCTCCGTTCCTA 59.420 50.000 0.00 0.00 0.00 2.94
3792 3950 3.011032 AGTTCTACTCCCTCCGTTCCTAA 59.989 47.826 0.00 0.00 0.00 2.69
3793 3951 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
3794 3952 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
3795 3953 5.393068 TCTACTCCCTCCGTTCCTAAATA 57.607 43.478 0.00 0.00 0.00 1.40
3796 3954 5.961897 TCTACTCCCTCCGTTCCTAAATAT 58.038 41.667 0.00 0.00 0.00 1.28
3799 3957 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
3800 3958 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
3801 3959 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
3802 3960 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
3804 3962 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
3805 3963 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
3806 3964 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
3808 3966 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
3809 3967 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
3823 3981 8.370493 TGTCTTTCTAGAGATTTCAACAAGTG 57.630 34.615 0.00 0.00 0.00 3.16
3825 3983 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
3826 3984 8.424918 TCTTTCTAGAGATTTCAACAAGTGACT 58.575 33.333 0.00 0.00 35.39 3.41
3827 3985 9.698309 CTTTCTAGAGATTTCAACAAGTGACTA 57.302 33.333 0.00 0.00 35.39 2.59
3828 3986 9.477484 TTTCTAGAGATTTCAACAAGTGACTAC 57.523 33.333 0.00 0.00 35.39 2.73
3829 3987 8.178313 TCTAGAGATTTCAACAAGTGACTACA 57.822 34.615 0.00 0.00 35.39 2.74
3832 3990 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
3834 3992 6.590292 AGATTTCAACAAGTGACTACATACGG 59.410 38.462 0.00 0.00 35.39 4.02
3835 3993 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
3837 3995 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
3838 3996 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
3839 3997 3.257375 ACAAGTGACTACATACGGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
3841 3999 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
3842 4000 4.243270 AGTGACTACATACGGAGCAAAAC 58.757 43.478 0.00 0.00 0.00 2.43
3843 4001 3.991773 GTGACTACATACGGAGCAAAACA 59.008 43.478 0.00 0.00 0.00 2.83
3844 4002 4.449743 GTGACTACATACGGAGCAAAACAA 59.550 41.667 0.00 0.00 0.00 2.83
3845 4003 5.121768 GTGACTACATACGGAGCAAAACAAT 59.878 40.000 0.00 0.00 0.00 2.71
3847 4005 3.848272 ACATACGGAGCAAAACAATGG 57.152 42.857 0.00 0.00 0.00 3.16
3848 4006 3.153919 ACATACGGAGCAAAACAATGGT 58.846 40.909 0.00 0.00 0.00 3.55
3850 4008 4.762765 ACATACGGAGCAAAACAATGGTTA 59.237 37.500 0.00 0.00 35.82 2.85
3851 4009 3.915437 ACGGAGCAAAACAATGGTTAG 57.085 42.857 0.00 0.00 35.82 2.34
3852 4010 3.482436 ACGGAGCAAAACAATGGTTAGA 58.518 40.909 0.00 0.00 35.82 2.10
3863 4470 9.689976 CAAAACAATGGTTAGAATCACATAACA 57.310 29.630 0.00 0.00 35.82 2.41
3925 4532 7.164230 TGGTGTTTACAAACTCTCAAACATT 57.836 32.000 6.41 0.00 41.43 2.71
3936 4636 4.967575 ACTCTCAAACATTACGTTTTTGCG 59.032 37.500 0.00 0.00 45.79 4.85
3966 4666 2.587060 TATTGTGGGATGGAGGGAGT 57.413 50.000 0.00 0.00 0.00 3.85
3967 4667 0.921896 ATTGTGGGATGGAGGGAGTG 59.078 55.000 0.00 0.00 0.00 3.51
3983 4683 3.372025 GGGAGTGAGTTCTAATGGCCATT 60.372 47.826 32.59 32.59 34.93 3.16
4004 4704 7.357303 CCATTTTTCAGCCTCTTCAAAAATTG 58.643 34.615 0.00 0.00 36.66 2.32
4007 4707 8.735692 TTTTTCAGCCTCTTCAAAAATTGATT 57.264 26.923 0.00 0.00 39.84 2.57
4014 4714 6.089954 GCCTCTTCAAAAATTGATTGTACTGC 59.910 38.462 0.00 0.00 39.84 4.40
4015 4715 6.587608 CCTCTTCAAAAATTGATTGTACTGCC 59.412 38.462 0.00 0.00 39.84 4.85
4016 4716 7.048629 TCTTCAAAAATTGATTGTACTGCCA 57.951 32.000 0.00 0.00 39.84 4.92
4017 4717 7.669427 TCTTCAAAAATTGATTGTACTGCCAT 58.331 30.769 0.00 0.00 39.84 4.40
4018 4718 8.149647 TCTTCAAAAATTGATTGTACTGCCATT 58.850 29.630 0.00 0.00 39.84 3.16
4021 4721 8.772705 TCAAAAATTGATTGTACTGCCATTTTC 58.227 29.630 0.00 0.00 34.08 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 3.896133 GCGGACGGAGCGGATACA 61.896 66.667 0.00 0.00 0.00 2.29
48 49 2.841442 AAAGCTCGTACCTCAAAGCT 57.159 45.000 0.00 0.00 46.66 3.74
50 51 3.371285 GGCTAAAAGCTCGTACCTCAAAG 59.629 47.826 0.00 0.00 41.99 2.77
174 175 1.611673 GCAAGCTAGAGGCAGGAAACA 60.612 52.381 0.00 0.00 44.79 2.83
238 245 1.859080 GACGGCGCAAAGTCCTTATAG 59.141 52.381 10.83 0.00 0.00 1.31
252 260 2.856346 CGTTTATGGAGCGACGGCG 61.856 63.158 6.12 6.12 46.35 6.46
274 282 1.613437 AGCACCAACAATTTCTTCCGG 59.387 47.619 0.00 0.00 0.00 5.14
275 283 4.226761 GTTAGCACCAACAATTTCTTCCG 58.773 43.478 0.00 0.00 0.00 4.30
333 341 0.468226 CCAGCAAGGGCCGATTAGTA 59.532 55.000 0.00 0.00 42.56 1.82
382 390 3.481453 TGCATACACAAGTACAAAGGCA 58.519 40.909 0.00 0.00 31.96 4.75
394 402 4.508551 AGATTTGGATCCTGCATACACA 57.491 40.909 14.23 0.00 32.44 3.72
532 540 0.725686 CTTCATCCTGCACTGCGAAG 59.274 55.000 0.00 0.00 0.00 3.79
535 543 1.374343 ATGCTTCATCCTGCACTGCG 61.374 55.000 0.00 0.00 42.26 5.18
557 566 5.356426 GTGGTGCCAAAATCTGTTAAAACT 58.644 37.500 0.00 0.00 0.00 2.66
559 568 4.098044 TCGTGGTGCCAAAATCTGTTAAAA 59.902 37.500 0.00 0.00 0.00 1.52
584 593 6.589830 ATTCGAGAAAACGATAGGTGAATG 57.410 37.500 0.00 0.00 41.82 2.67
659 668 8.370493 TGCATCTGCTAGTGTTAGAATATTTC 57.630 34.615 3.53 0.00 42.66 2.17
822 848 3.877064 CGCTTAATCTGCGCATAATTGT 58.123 40.909 21.82 5.67 46.72 2.71
849 875 3.241995 CGATAACAAAACGCCTAGCACTC 60.242 47.826 0.00 0.00 0.00 3.51
885 911 4.502259 CCAGATCATAGCTAAAGAAGGCGT 60.502 45.833 0.00 0.00 0.00 5.68
887 913 5.220710 TCCAGATCATAGCTAAAGAAGGC 57.779 43.478 0.00 0.00 0.00 4.35
910 936 4.757149 AGAAGCAAAGTCAACTGGATACAC 59.243 41.667 0.00 0.00 46.17 2.90
919 945 4.864247 TCAAGCAAAAGAAGCAAAGTCAAC 59.136 37.500 0.00 0.00 0.00 3.18
922 948 5.557703 GCAATCAAGCAAAAGAAGCAAAGTC 60.558 40.000 0.00 0.00 0.00 3.01
1074 1100 7.714813 ACCCATTTTTGTAAACAATGAAGAAGG 59.285 33.333 0.00 1.75 35.55 3.46
1091 1117 8.700973 GGTATGAATATGGTGTTACCCATTTTT 58.299 33.333 9.88 5.87 42.70 1.94
1355 1381 6.430925 AGCTAAAGCAACATAACATGACTTCA 59.569 34.615 0.00 0.00 45.16 3.02
1397 1423 9.784376 ATATATATACTAGACAAAGGCCCTGAA 57.216 33.333 9.39 0.00 0.00 3.02
1453 1479 8.669946 AGCTCACCTAGATTAATTTTTCTAGC 57.330 34.615 14.51 8.74 39.97 3.42
1535 1561 6.209026 ACTACTAGTCTAGTACTACCAGGGT 58.791 44.000 14.62 6.97 39.80 4.34
1653 1713 4.955811 AATGCCGACCTTCATACTATGA 57.044 40.909 0.00 0.00 37.55 2.15
1799 1859 8.757164 TGATGAATATTTCGCGTAGATAACAT 57.243 30.769 5.77 12.08 0.00 2.71
1809 1869 7.904977 CCCTGTTATAATGATGAATATTTCGCG 59.095 37.037 0.00 0.00 0.00 5.87
1854 1914 9.479549 AGTTAATGATGAATATTTGACCCTGTT 57.520 29.630 0.00 0.00 0.00 3.16
1858 1918 9.899226 GCTTAGTTAATGATGAATATTTGACCC 57.101 33.333 0.00 0.00 0.00 4.46
1866 1926 9.461312 ACCAACTTGCTTAGTTAATGATGAATA 57.539 29.630 4.78 0.00 45.29 1.75
1867 1927 8.246180 CACCAACTTGCTTAGTTAATGATGAAT 58.754 33.333 4.78 0.00 45.29 2.57
1868 1928 7.230510 ACACCAACTTGCTTAGTTAATGATGAA 59.769 33.333 15.44 0.00 45.29 2.57
1869 1929 6.714810 ACACCAACTTGCTTAGTTAATGATGA 59.285 34.615 15.44 0.00 45.29 2.92
1870 1930 6.913170 ACACCAACTTGCTTAGTTAATGATG 58.087 36.000 15.44 3.70 45.29 3.07
1871 1931 7.524717 AACACCAACTTGCTTAGTTAATGAT 57.475 32.000 15.44 6.80 45.29 2.45
2032 2095 8.225603 AGTCAAGACTTCTTTTATTTGCAAGA 57.774 30.769 0.00 0.00 38.83 3.02
2273 2336 1.190643 CTTCTCCCTCAGGTCTGGAC 58.809 60.000 0.00 0.00 0.00 4.02
2394 2457 9.899226 ATGTAGCAAAAGAAGAAAATGTTCTAC 57.101 29.630 0.00 0.00 43.59 2.59
2421 2484 5.118990 CAAGAGAGTTGAAACAAGGAGTGA 58.881 41.667 0.00 0.00 0.00 3.41
2449 2512 3.008704 GGAGTACCTTTTTCAGCCTGGTA 59.991 47.826 0.00 0.00 32.74 3.25
2589 2652 9.010029 TCTTTGTCTTTGTCTTTGTCTTTACTT 57.990 29.630 0.00 0.00 0.00 2.24
2625 2688 8.147704 TCTTTCTCTTTCTCTTTCTCTTTCTCC 58.852 37.037 0.00 0.00 0.00 3.71
2626 2689 9.196552 CTCTTTCTCTTTCTCTTTCTCTTTCTC 57.803 37.037 0.00 0.00 0.00 2.87
2627 2690 8.923270 TCTCTTTCTCTTTCTCTTTCTCTTTCT 58.077 33.333 0.00 0.00 0.00 2.52
2628 2691 9.541143 TTCTCTTTCTCTTTCTCTTTCTCTTTC 57.459 33.333 0.00 0.00 0.00 2.62
2629 2692 9.898152 TTTCTCTTTCTCTTTCTCTTTCTCTTT 57.102 29.630 0.00 0.00 0.00 2.52
2630 2693 9.546428 CTTTCTCTTTCTCTTTCTCTTTCTCTT 57.454 33.333 0.00 0.00 0.00 2.85
2640 2703 9.541143 TTCTCTTTCTCTTTCTCTTTCTCTTTC 57.459 33.333 0.00 0.00 0.00 2.62
2652 2715 7.666623 TCTCCTTCTCTTTCTCTTTCTCTTTC 58.333 38.462 0.00 0.00 0.00 2.62
2661 2724 6.739331 TTGTCTTTCTCCTTCTCTTTCTCT 57.261 37.500 0.00 0.00 0.00 3.10
2670 2733 6.927294 TCTTTGTCTTTGTCTTTCTCCTTC 57.073 37.500 0.00 0.00 0.00 3.46
2671 2734 7.703058 TTTCTTTGTCTTTGTCTTTCTCCTT 57.297 32.000 0.00 0.00 0.00 3.36
2672 2735 7.611855 TCTTTTCTTTGTCTTTGTCTTTCTCCT 59.388 33.333 0.00 0.00 0.00 3.69
2673 2736 7.762382 TCTTTTCTTTGTCTTTGTCTTTCTCC 58.238 34.615 0.00 0.00 0.00 3.71
2674 2737 9.626045 TTTCTTTTCTTTGTCTTTGTCTTTCTC 57.374 29.630 0.00 0.00 0.00 2.87
2675 2738 9.981114 TTTTCTTTTCTTTGTCTTTGTCTTTCT 57.019 25.926 0.00 0.00 0.00 2.52
3013 3079 2.029470 TCCATTGCCCGTTTCATTGAAC 60.029 45.455 0.00 0.00 0.00 3.18
3024 3090 1.605202 CCAAACAAAGTCCATTGCCCG 60.605 52.381 0.00 0.00 33.52 6.13
3046 3112 6.436843 GGAAACGAATTTGTCACATCCTAT 57.563 37.500 0.00 0.00 0.00 2.57
3341 3407 2.276732 TGGTTCCAAAGCCAAGAGAG 57.723 50.000 0.00 0.00 0.00 3.20
3347 3413 1.836604 GGCCTTGGTTCCAAAGCCA 60.837 57.895 28.82 0.00 46.89 4.75
3492 3646 8.581253 AAGACTTATATTCAAGAACAAAGGGG 57.419 34.615 0.00 0.00 0.00 4.79
3541 3695 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
3542 3696 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
3543 3697 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
3544 3698 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
3545 3699 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
3546 3700 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
3547 3701 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
3548 3702 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
3623 3777 7.346436 TCCCTCCGTTCCTTAAATATAAGTCTT 59.654 37.037 0.00 0.00 37.42 3.01
3637 3791 1.688627 GGATGTACTCCCTCCGTTCCT 60.689 57.143 0.00 0.00 38.19 3.36
3777 3935 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
3779 3937 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
3780 3938 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
3781 3939 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
3783 3941 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
3796 3954 9.396022 ACTTGTTGAAATCTCTAGAAAGACAAA 57.604 29.630 0.00 0.00 0.00 2.83
3799 3957 8.491950 GTCACTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 35.39 3.01
3800 3958 8.424918 AGTCACTTGTTGAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 35.39 2.52
3801 3959 8.600449 AGTCACTTGTTGAAATCTCTAGAAAG 57.400 34.615 0.00 0.00 35.39 2.62
3802 3960 9.477484 GTAGTCACTTGTTGAAATCTCTAGAAA 57.523 33.333 0.00 0.00 35.39 2.52
3804 3962 8.178313 TGTAGTCACTTGTTGAAATCTCTAGA 57.822 34.615 0.00 0.00 35.39 2.43
3805 3963 8.994429 ATGTAGTCACTTGTTGAAATCTCTAG 57.006 34.615 0.00 0.00 35.39 2.43
3806 3964 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
3808 3966 7.201444 CCGTATGTAGTCACTTGTTGAAATCTC 60.201 40.741 0.00 0.00 35.39 2.75
3809 3967 6.590292 CCGTATGTAGTCACTTGTTGAAATCT 59.410 38.462 0.00 0.00 35.39 2.40
3810 3968 6.588756 TCCGTATGTAGTCACTTGTTGAAATC 59.411 38.462 0.00 0.00 35.39 2.17
3811 3969 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
3812 3970 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
3813 3971 5.456548 TCCGTATGTAGTCACTTGTTGAA 57.543 39.130 0.00 0.00 35.39 2.69
3814 3972 4.617530 GCTCCGTATGTAGTCACTTGTTGA 60.618 45.833 0.00 0.00 0.00 3.18
3815 3973 3.612860 GCTCCGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
3816 3974 3.257375 TGCTCCGTATGTAGTCACTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
3818 3976 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
3819 3977 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
3820 3978 4.243270 GTTTTGCTCCGTATGTAGTCACT 58.757 43.478 0.00 0.00 0.00 3.41
3821 3979 3.991773 TGTTTTGCTCCGTATGTAGTCAC 59.008 43.478 0.00 0.00 0.00 3.67
3823 3981 5.447279 CCATTGTTTTGCTCCGTATGTAGTC 60.447 44.000 0.00 0.00 0.00 2.59
3825 3983 4.394920 ACCATTGTTTTGCTCCGTATGTAG 59.605 41.667 0.00 0.00 0.00 2.74
3826 3984 4.328536 ACCATTGTTTTGCTCCGTATGTA 58.671 39.130 0.00 0.00 0.00 2.29
3827 3985 3.153919 ACCATTGTTTTGCTCCGTATGT 58.846 40.909 0.00 0.00 0.00 2.29
3828 3986 3.848272 ACCATTGTTTTGCTCCGTATG 57.152 42.857 0.00 0.00 0.00 2.39
3829 3987 5.250200 TCTAACCATTGTTTTGCTCCGTAT 58.750 37.500 0.00 0.00 35.87 3.06
3831 3989 3.482436 TCTAACCATTGTTTTGCTCCGT 58.518 40.909 0.00 0.00 35.87 4.69
3832 3990 4.497473 TTCTAACCATTGTTTTGCTCCG 57.503 40.909 0.00 0.00 35.87 4.63
3834 3992 6.446318 TGTGATTCTAACCATTGTTTTGCTC 58.554 36.000 0.00 0.00 35.87 4.26
3835 3993 6.403866 TGTGATTCTAACCATTGTTTTGCT 57.596 33.333 0.00 0.00 35.87 3.91
3837 3995 9.689976 TGTTATGTGATTCTAACCATTGTTTTG 57.310 29.630 0.00 0.00 35.87 2.44
3841 3999 9.905713 ACTATGTTATGTGATTCTAACCATTGT 57.094 29.630 0.00 0.00 0.00 2.71
3850 4008 9.698309 CGGAATCTAACTATGTTATGTGATTCT 57.302 33.333 18.93 0.39 38.77 2.40
3851 4009 8.436200 GCGGAATCTAACTATGTTATGTGATTC 58.564 37.037 15.17 15.17 38.33 2.52
3852 4010 7.116376 CGCGGAATCTAACTATGTTATGTGATT 59.884 37.037 0.00 0.00 0.00 2.57
3863 4470 4.380841 TCAACACGCGGAATCTAACTAT 57.619 40.909 12.47 0.00 0.00 2.12
3925 4532 0.533308 AGACAGCCCGCAAAAACGTA 60.533 50.000 0.00 0.00 0.00 3.57
3936 4636 3.857157 TCCCACAATATAAGACAGCCC 57.143 47.619 0.00 0.00 0.00 5.19
3966 4666 5.336690 GCTGAAAAATGGCCATTAGAACTCA 60.337 40.000 30.84 23.37 0.00 3.41
3967 4667 5.105063 GCTGAAAAATGGCCATTAGAACTC 58.895 41.667 30.84 20.59 0.00 3.01
3983 4683 7.769970 ACAATCAATTTTTGAAGAGGCTGAAAA 59.230 29.630 0.00 0.00 43.95 2.29


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

AutoCloner maintained by Alex Coulton.