Multiple sequence alignment - TraesCS4A01G207800

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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 TraesCS4A01G207800 chr4A 100.000 3988 0 0 1 3988 501126005 501122018 0.000000e+00 7365.0
1 TraesCS4A01G207800 chr4A 82.301 113 20 0 1610 1722 681918134 681918022 9.120000e-17 99.0
2 TraesCS4A01G207800 chr4D 94.192 1894 67 14 2114 3988 88141883 88140014 0.000000e+00 2848.0
3 TraesCS4A01G207800 chr4D 94.785 1304 38 11 788 2077 88143170 88141883 0.000000e+00 2004.0
4 TraesCS4A01G207800 chr4D 89.281 737 47 12 6 714 88143928 88143196 0.000000e+00 894.0
5 TraesCS4A01G207800 chr4D 81.739 115 20 1 1610 1723 475176603 475176489 1.180000e-15 95.3
6 TraesCS4A01G207800 chr4B 95.550 1191 36 2 788 1977 124918461 124917287 0.000000e+00 1890.0
7 TraesCS4A01G207800 chr4B 95.991 848 28 5 2492 3339 124916466 124915625 0.000000e+00 1373.0
8 TraesCS4A01G207800 chr4B 93.958 662 28 3 3338 3988 124759404 124758744 0.000000e+00 990.0
9 TraesCS4A01G207800 chr4B 86.449 797 38 30 6 771 124919203 124918446 0.000000e+00 809.0
10 TraesCS4A01G207800 chr4B 90.494 263 23 2 2235 2496 124916812 124916551 2.950000e-91 346.0
11 TraesCS4A01G207800 chr4B 87.654 81 10 0 1610 1690 599884662 599884582 1.180000e-15 95.3
12 TraesCS4A01G207800 chr1D 90.909 66 6 0 1396 1461 366689561 366689626 5.490000e-14 89.8
13 TraesCS4A01G207800 chr7D 87.013 77 8 2 1385 1461 225199175 225199101 7.100000e-13 86.1


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 TraesCS4A01G207800 chr4A 501122018 501126005 3987 True 7365.000000 7365 100.000000 1 3988 1 chr4A.!!$R1 3987
1 TraesCS4A01G207800 chr4D 88140014 88143928 3914 True 1915.333333 2848 92.752667 6 3988 3 chr4D.!!$R2 3982
2 TraesCS4A01G207800 chr4B 124915625 124919203 3578 True 1104.500000 1890 92.121000 6 3339 4 chr4B.!!$R3 3333
3 TraesCS4A01G207800 chr4B 124758744 124759404 660 True 990.000000 990 93.958000 3338 3988 1 chr4B.!!$R1 650

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
777 826 0.314302 ATATACCTGTGCGGACGCTC 59.686 55.0 18.04 14.56 42.51 5.03 F
935 984 0.458260 GCGACTCTTCCTCTTCCTCC 59.542 60.0 0.00 0.00 0.00 4.30 F
2071 2552 1.016415 AGGACTAGCCCTTGGAGGTA 58.984 55.0 0.00 0.00 37.37 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1985 2458 0.323178 GGACGAGGTGGGTCTACTGA 60.323 60.0 0.00 0.0 34.82 3.41 R
2091 2572 0.517316 GGGCGACTTGTTGTGCTTAG 59.483 55.0 0.00 0.0 0.00 2.18 R
3243 3814 0.104304 GTGTATACAGCGGGGGTGAG 59.896 60.0 5.62 0.0 34.87 3.51 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
47 48 1.925888 CATGGGAAGAAGGGGAGGG 59.074 63.158 0.00 0.00 0.00 4.30
138 139 1.678123 CCATGAAGCTAGCACTGCTGT 60.678 52.381 18.83 0.00 40.10 4.40
167 171 5.715434 TTACCTGATGGTTTTTGCTTACC 57.285 39.130 0.00 0.00 46.05 2.85
168 172 2.897326 ACCTGATGGTTTTTGCTTACCC 59.103 45.455 0.00 0.00 46.05 3.69
208 222 4.026145 GCTCTCTGACGTGAATCTTTATGC 60.026 45.833 0.00 0.00 0.00 3.14
209 223 4.105486 TCTCTGACGTGAATCTTTATGCG 58.895 43.478 0.00 0.00 0.00 4.73
210 224 3.186909 TCTGACGTGAATCTTTATGCGG 58.813 45.455 0.00 0.00 0.00 5.69
327 347 7.045725 AGTAGAACGTGTGAAATATGTTTCG 57.954 36.000 9.97 2.02 45.34 3.46
381 401 0.889994 TGTGGATGTGAATGCCAAGC 59.110 50.000 0.00 0.00 32.68 4.01
440 463 3.675775 GCTTGTTGGAGCTAGACAGAGAG 60.676 52.174 0.00 0.00 39.57 3.20
534 569 3.946558 TGTTTTACTGTTTGGTTAGCCGT 59.053 39.130 0.00 0.00 37.67 5.68
547 582 0.675083 TAGCCGTTCTCCGTGTGAAA 59.325 50.000 0.00 0.00 33.66 2.69
559 594 4.693283 TCCGTGTGAAATATGTCCTGATC 58.307 43.478 0.00 0.00 0.00 2.92
585 620 8.324163 TCTTACAAAGTTTAGGATCAAGAAGC 57.676 34.615 0.00 0.00 0.00 3.86
587 622 6.566197 ACAAAGTTTAGGATCAAGAAGCAG 57.434 37.500 0.00 0.00 0.00 4.24
588 623 6.064717 ACAAAGTTTAGGATCAAGAAGCAGT 58.935 36.000 0.00 0.00 0.00 4.40
589 624 7.224297 ACAAAGTTTAGGATCAAGAAGCAGTA 58.776 34.615 0.00 0.00 0.00 2.74
590 625 7.719633 ACAAAGTTTAGGATCAAGAAGCAGTAA 59.280 33.333 0.00 0.00 0.00 2.24
593 628 7.454225 AGTTTAGGATCAAGAAGCAGTAAGTT 58.546 34.615 0.00 0.00 0.00 2.66
595 630 5.489792 AGGATCAAGAAGCAGTAAGTTCA 57.510 39.130 0.00 0.00 0.00 3.18
603 650 6.551385 AGAAGCAGTAAGTTCAACAGATTG 57.449 37.500 0.00 0.00 37.14 2.67
609 656 0.877071 AGTTCAACAGATTGCAGCCG 59.123 50.000 0.00 0.00 35.63 5.52
629 676 3.296628 CGTCGCAAACTAAGCACAAAAT 58.703 40.909 0.00 0.00 0.00 1.82
641 688 4.083581 AGCACAAAATAGACGCATGTTC 57.916 40.909 0.00 0.00 0.00 3.18
642 689 2.840176 GCACAAAATAGACGCATGTTCG 59.160 45.455 0.00 0.00 0.00 3.95
643 690 2.840176 CACAAAATAGACGCATGTTCGC 59.160 45.455 0.00 0.00 0.00 4.70
644 691 2.159572 ACAAAATAGACGCATGTTCGCC 60.160 45.455 0.00 0.00 0.00 5.54
650 697 0.447801 GACGCATGTTCGCCTTGAAT 59.552 50.000 0.00 0.00 39.21 2.57
655 702 2.223203 GCATGTTCGCCTTGAATCTGAG 60.223 50.000 0.00 0.00 39.21 3.35
683 731 2.995258 GCCCGTCGAACACAAAGTATAA 59.005 45.455 0.00 0.00 0.00 0.98
714 762 6.716934 TCATATCAGGTTCTCCTTCAGTAC 57.283 41.667 0.00 0.00 43.07 2.73
715 763 6.436027 TCATATCAGGTTCTCCTTCAGTACT 58.564 40.000 0.00 0.00 43.07 2.73
716 764 6.322456 TCATATCAGGTTCTCCTTCAGTACTG 59.678 42.308 17.17 17.17 43.07 2.74
717 765 4.114015 TCAGGTTCTCCTTCAGTACTGA 57.886 45.455 21.74 21.74 43.07 3.41
718 766 4.082845 TCAGGTTCTCCTTCAGTACTGAG 58.917 47.826 23.97 17.56 43.07 3.35
719 767 3.829601 CAGGTTCTCCTTCAGTACTGAGT 59.170 47.826 23.97 0.00 43.07 3.41
720 768 3.829601 AGGTTCTCCTTCAGTACTGAGTG 59.170 47.826 23.97 19.65 42.12 3.51
721 769 3.574826 GGTTCTCCTTCAGTACTGAGTGT 59.425 47.826 23.97 0.00 41.13 3.55
722 770 4.765856 GGTTCTCCTTCAGTACTGAGTGTA 59.234 45.833 23.97 9.96 41.13 2.90
723 771 5.419471 GGTTCTCCTTCAGTACTGAGTGTAT 59.581 44.000 23.97 0.00 41.13 2.29
724 772 6.071278 GGTTCTCCTTCAGTACTGAGTGTATT 60.071 42.308 23.97 0.00 41.13 1.89
725 773 7.379750 GTTCTCCTTCAGTACTGAGTGTATTT 58.620 38.462 23.97 0.00 41.13 1.40
759 808 5.824904 GTGCATCAAATGTACTCCAGAAT 57.175 39.130 0.00 0.00 41.79 2.40
760 809 6.925610 GTGCATCAAATGTACTCCAGAATA 57.074 37.500 0.00 0.00 41.79 1.75
761 810 7.502120 GTGCATCAAATGTACTCCAGAATAT 57.498 36.000 0.00 0.00 41.79 1.28
762 811 8.607441 GTGCATCAAATGTACTCCAGAATATA 57.393 34.615 0.00 0.00 41.79 0.86
763 812 8.499162 GTGCATCAAATGTACTCCAGAATATAC 58.501 37.037 0.00 0.00 41.79 1.47
764 813 7.661437 TGCATCAAATGTACTCCAGAATATACC 59.339 37.037 0.00 0.00 0.00 2.73
765 814 7.880195 GCATCAAATGTACTCCAGAATATACCT 59.120 37.037 0.00 0.00 0.00 3.08
766 815 9.212641 CATCAAATGTACTCCAGAATATACCTG 57.787 37.037 0.00 0.00 0.00 4.00
767 816 8.319057 TCAAATGTACTCCAGAATATACCTGT 57.681 34.615 0.00 0.00 0.00 4.00
768 817 8.204160 TCAAATGTACTCCAGAATATACCTGTG 58.796 37.037 0.00 1.33 0.00 3.66
769 818 5.531122 TGTACTCCAGAATATACCTGTGC 57.469 43.478 0.00 0.00 0.00 4.57
770 819 3.735237 ACTCCAGAATATACCTGTGCG 57.265 47.619 4.85 0.00 0.00 5.34
771 820 2.365617 ACTCCAGAATATACCTGTGCGG 59.634 50.000 4.85 0.00 39.35 5.69
772 821 2.628178 CTCCAGAATATACCTGTGCGGA 59.372 50.000 4.85 0.00 36.31 5.54
773 822 2.364324 TCCAGAATATACCTGTGCGGAC 59.636 50.000 0.00 0.00 36.31 4.79
774 823 2.394708 CAGAATATACCTGTGCGGACG 58.605 52.381 1.60 0.00 36.31 4.79
775 824 1.137513 GAATATACCTGTGCGGACGC 58.862 55.000 10.13 10.13 42.35 5.19
776 825 0.750850 AATATACCTGTGCGGACGCT 59.249 50.000 18.04 0.00 42.51 5.07
777 826 0.314302 ATATACCTGTGCGGACGCTC 59.686 55.000 18.04 14.56 42.51 5.03
778 827 1.033202 TATACCTGTGCGGACGCTCA 61.033 55.000 18.04 18.29 41.45 4.26
779 828 1.884075 ATACCTGTGCGGACGCTCAA 61.884 55.000 19.71 8.18 42.76 3.02
780 829 2.089887 TACCTGTGCGGACGCTCAAA 62.090 55.000 19.71 8.05 42.76 2.69
781 830 2.250939 CCTGTGCGGACGCTCAAAA 61.251 57.895 19.71 0.00 42.76 2.44
782 831 1.646540 CTGTGCGGACGCTCAAAAA 59.353 52.632 19.71 0.58 42.76 1.94
829 878 1.447489 CACGGCCTGCAGAAGAGAG 60.447 63.158 17.39 0.00 0.00 3.20
867 916 2.064762 CAGCAGTCAAAGTCTTCCTCG 58.935 52.381 0.00 0.00 0.00 4.63
909 958 2.664436 CCGCCGAACGTTCTTGACC 61.664 63.158 24.80 8.25 41.42 4.02
935 984 0.458260 GCGACTCTTCCTCTTCCTCC 59.542 60.000 0.00 0.00 0.00 4.30
955 1004 3.384789 TCCCACTCTCACGAATCAATAGG 59.615 47.826 0.00 0.00 0.00 2.57
980 1035 1.192146 TCTTCCTCCCCACTTCCGTG 61.192 60.000 0.00 0.00 40.89 4.94
1150 1205 3.812019 CGTCGTCGTCCCTCCCAG 61.812 72.222 0.00 0.00 0.00 4.45
1860 1916 1.403323 TGCGCATGTTTTCAGTGTTGA 59.597 42.857 5.66 0.00 0.00 3.18
1861 1917 2.159324 TGCGCATGTTTTCAGTGTTGAA 60.159 40.909 5.66 0.00 41.44 2.69
1944 2000 5.171476 AGACGACATGAAATTCGACTGAAT 58.829 37.500 10.08 0.00 46.75 2.57
1945 2001 6.330278 AGACGACATGAAATTCGACTGAATA 58.670 36.000 10.08 0.00 44.02 1.75
1981 2454 5.880332 TGGATGAGGCATAGTTTAAACTGAC 59.120 40.000 27.40 16.58 40.07 3.51
1985 2458 7.817418 TGAGGCATAGTTTAAACTGACTTTT 57.183 32.000 27.40 10.91 40.07 2.27
2012 2485 4.436998 CACCTCGTCCTGCCGTCC 62.437 72.222 0.00 0.00 0.00 4.79
2061 2542 4.276058 ACGAGACTATCTAGGACTAGCC 57.724 50.000 1.45 0.00 33.32 3.93
2066 2547 4.083565 GACTATCTAGGACTAGCCCTTGG 58.916 52.174 1.70 0.00 37.74 3.61
2071 2552 1.016415 AGGACTAGCCCTTGGAGGTA 58.984 55.000 0.00 0.00 37.37 3.08
2074 2555 3.406498 AGGACTAGCCCTTGGAGGTATAT 59.594 47.826 0.00 0.00 37.37 0.86
2076 2557 4.597940 GGACTAGCCCTTGGAGGTATATTT 59.402 45.833 0.00 0.00 31.93 1.40
2077 2558 5.280062 GGACTAGCCCTTGGAGGTATATTTC 60.280 48.000 0.00 0.00 31.93 2.17
2078 2559 5.477913 ACTAGCCCTTGGAGGTATATTTCT 58.522 41.667 0.00 0.00 31.93 2.52
2079 2560 6.631107 ACTAGCCCTTGGAGGTATATTTCTA 58.369 40.000 0.00 0.00 31.93 2.10
2080 2561 7.257146 ACTAGCCCTTGGAGGTATATTTCTAT 58.743 38.462 0.00 0.00 31.93 1.98
2081 2562 7.739904 ACTAGCCCTTGGAGGTATATTTCTATT 59.260 37.037 0.00 0.00 31.93 1.73
2082 2563 6.784031 AGCCCTTGGAGGTATATTTCTATTG 58.216 40.000 0.00 0.00 31.93 1.90
2083 2564 6.562608 AGCCCTTGGAGGTATATTTCTATTGA 59.437 38.462 0.00 0.00 31.93 2.57
2084 2565 7.073725 AGCCCTTGGAGGTATATTTCTATTGAA 59.926 37.037 0.00 0.00 31.93 2.69
2085 2566 7.391833 GCCCTTGGAGGTATATTTCTATTGAAG 59.608 40.741 0.00 0.00 31.93 3.02
2086 2567 8.660435 CCCTTGGAGGTATATTTCTATTGAAGA 58.340 37.037 0.00 0.00 31.93 2.87
2099 2580 8.902540 TTTCTATTGAAGAAACTCTAAGCACA 57.097 30.769 0.00 0.00 46.88 4.57
2100 2581 8.902540 TTCTATTGAAGAAACTCTAAGCACAA 57.097 30.769 0.00 0.00 41.35 3.33
2101 2582 8.311650 TCTATTGAAGAAACTCTAAGCACAAC 57.688 34.615 0.00 0.00 0.00 3.32
2102 2583 6.942532 ATTGAAGAAACTCTAAGCACAACA 57.057 33.333 0.00 0.00 0.00 3.33
2103 2584 6.751514 TTGAAGAAACTCTAAGCACAACAA 57.248 33.333 0.00 0.00 0.00 2.83
2104 2585 6.363577 TGAAGAAACTCTAAGCACAACAAG 57.636 37.500 0.00 0.00 0.00 3.16
2105 2586 5.880332 TGAAGAAACTCTAAGCACAACAAGT 59.120 36.000 0.00 0.00 0.00 3.16
2106 2587 5.993106 AGAAACTCTAAGCACAACAAGTC 57.007 39.130 0.00 0.00 0.00 3.01
2107 2588 4.508124 AGAAACTCTAAGCACAACAAGTCG 59.492 41.667 0.00 0.00 0.00 4.18
2108 2589 2.135933 ACTCTAAGCACAACAAGTCGC 58.864 47.619 0.00 0.00 0.00 5.19
2109 2590 1.461127 CTCTAAGCACAACAAGTCGCC 59.539 52.381 0.00 0.00 0.00 5.54
2110 2591 0.517316 CTAAGCACAACAAGTCGCCC 59.483 55.000 0.00 0.00 0.00 6.13
2111 2592 0.887387 TAAGCACAACAAGTCGCCCC 60.887 55.000 0.00 0.00 0.00 5.80
2112 2593 4.025401 GCACAACAAGTCGCCCCG 62.025 66.667 0.00 0.00 0.00 5.73
2144 2625 0.643820 GCGTATACGGTGACTGTTGC 59.356 55.000 25.55 2.04 40.23 4.17
2145 2626 1.734707 GCGTATACGGTGACTGTTGCT 60.735 52.381 25.55 0.00 40.23 3.91
2146 2627 1.917955 CGTATACGGTGACTGTTGCTG 59.082 52.381 17.61 0.00 35.37 4.41
2153 2634 4.374702 GACTGTTGCTGCGCACCG 62.375 66.667 5.66 0.00 38.71 4.94
2165 2646 1.485838 GCGCACCGATGTGATCTCAG 61.486 60.000 0.30 0.00 45.76 3.35
2170 2651 3.243535 GCACCGATGTGATCTCAGTATCA 60.244 47.826 3.58 0.00 45.76 2.15
2175 2656 5.122396 CCGATGTGATCTCAGTATCATACGA 59.878 44.000 3.58 0.00 38.13 3.43
2183 2664 8.398665 TGATCTCAGTATCATACGATAAATCGG 58.601 37.037 16.07 0.00 41.32 4.18
2220 2701 8.871686 ATGACCAACAAGTGAATTTTTAGAAC 57.128 30.769 0.00 0.00 0.00 3.01
2242 2723 6.808008 ACAAGTTCAATGACCACTAATGAG 57.192 37.500 0.00 0.00 0.00 2.90
2283 2764 2.614057 GCCCAACATCGTTTCTATGGAG 59.386 50.000 0.00 0.00 0.00 3.86
2296 2777 1.689273 CTATGGAGGCAGGAGTGGTAC 59.311 57.143 0.00 0.00 0.00 3.34
2311 2792 0.546598 GGTACCACCTGCCAAGCTAT 59.453 55.000 7.15 0.00 34.73 2.97
2324 2805 4.943705 TGCCAAGCTATGTTTTTCTAGGAG 59.056 41.667 0.00 0.00 0.00 3.69
2326 2807 5.745227 CCAAGCTATGTTTTTCTAGGAGGA 58.255 41.667 0.00 0.00 0.00 3.71
2384 2866 9.108449 CATGTTTTGCATTTTTGTTCACATATG 57.892 29.630 0.00 0.00 35.19 1.78
2434 2916 0.516439 GAAGACAAGCTCAGTGCAGC 59.484 55.000 6.49 6.49 45.94 5.25
2470 2953 5.009210 TGTTGTAGTTACGGTAGTACGGTTT 59.991 40.000 17.45 7.83 38.39 3.27
2549 3120 6.189677 TCGGTATTACAATGCCTTTCTTTG 57.810 37.500 7.37 0.00 38.81 2.77
2552 3123 6.162777 GGTATTACAATGCCTTTCTTTGCAA 58.837 36.000 0.00 0.00 41.50 4.08
2587 3158 9.125026 ACCACATTTCTCATATTTTAGACCATC 57.875 33.333 0.00 0.00 0.00 3.51
2718 3289 2.293122 GCAGATGTGTACAGTTTTGGCA 59.707 45.455 0.00 0.00 0.00 4.92
2786 3357 7.829211 CCAATGAAGAACATTAGAGGTAAGGAA 59.171 37.037 0.00 0.00 46.01 3.36
2827 3398 1.977009 GGGAAAAGGTTGAGGCCGG 60.977 63.158 0.00 0.00 0.00 6.13
2992 3563 3.084786 GGCTCAATAGGCTGTGAAAGTT 58.915 45.455 0.00 0.00 44.73 2.66
3046 3617 3.698029 TGACAACAAGAAAAGCTCAGC 57.302 42.857 0.00 0.00 0.00 4.26
3090 3661 5.836024 ATTTGAGTTCCCCTACTGTAACA 57.164 39.130 0.00 0.00 0.00 2.41
3101 3672 8.060727 TCCCCTACTGTAACATATAGGTCTTA 57.939 38.462 0.00 0.00 33.60 2.10
3258 3829 2.768344 CCCTCACCCCCGCTGTAT 60.768 66.667 0.00 0.00 0.00 2.29
3273 3844 3.692576 GCTGTATACACACCACTACTCG 58.307 50.000 0.08 0.00 0.00 4.18
3310 3881 6.156949 TCCAGTAGGCATCTTTCTTCATTACT 59.843 38.462 0.00 0.00 33.74 2.24
3313 3884 8.821894 CAGTAGGCATCTTTCTTCATTACTAAC 58.178 37.037 0.00 0.00 0.00 2.34
3438 4009 6.183360 ACAAGCTAGGTAAAACTGTTGAAACC 60.183 38.462 0.00 9.85 0.00 3.27
3443 4014 6.144078 AGGTAAAACTGTTGAAACCATGTC 57.856 37.500 16.70 0.00 0.00 3.06
3491 4073 2.035832 AGCAAGGTGGGAATGTTTTTCG 59.964 45.455 0.00 0.00 0.00 3.46
3573 4155 7.775053 AAGACTCTCAAACTGAACTATCTCT 57.225 36.000 0.00 0.00 0.00 3.10
3574 4156 7.156876 AGACTCTCAAACTGAACTATCTCTG 57.843 40.000 0.00 0.00 0.00 3.35
3615 4197 4.696455 AGGGCATTTTCTTCAAACACTTG 58.304 39.130 0.00 0.00 0.00 3.16
3629 4211 4.340894 AACACTTGCGCATACAATACAG 57.659 40.909 12.75 5.24 0.00 2.74
3642 4224 7.076362 GCATACAATACAGAATGCATTCTCAG 58.924 38.462 33.95 26.33 44.84 3.35
3688 4270 7.093322 TGAACGATTACCTAGTTACTCTTCC 57.907 40.000 0.00 0.00 0.00 3.46
3690 4272 8.049117 TGAACGATTACCTAGTTACTCTTCCTA 58.951 37.037 0.00 0.00 0.00 2.94
3697 4279 9.571816 TTACCTAGTTACTCTTCCTATAAGAGC 57.428 37.037 13.33 0.12 45.78 4.09
3833 4415 2.519013 GGTTTGGGCTGATCTTGACTT 58.481 47.619 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.139917 TGCAAAGCGACGAATGTTAGT 58.860 42.857 0.00 0.00 0.00 2.24
1 2 2.474526 CCTGCAAAGCGACGAATGTTAG 60.475 50.000 0.00 0.00 0.00 2.34
2 3 1.463056 CCTGCAAAGCGACGAATGTTA 59.537 47.619 0.00 0.00 0.00 2.41
3 4 0.238289 CCTGCAAAGCGACGAATGTT 59.762 50.000 0.00 0.00 0.00 2.71
4 5 0.884704 ACCTGCAAAGCGACGAATGT 60.885 50.000 0.00 0.00 0.00 2.71
13 14 2.629656 ATGCCACGACCTGCAAAGC 61.630 57.895 0.00 0.00 41.50 3.51
15 16 2.267351 CCATGCCACGACCTGCAAA 61.267 57.895 0.00 0.00 41.50 3.68
17 18 4.720902 CCCATGCCACGACCTGCA 62.721 66.667 0.00 0.00 42.52 4.41
18 19 3.918253 TTCCCATGCCACGACCTGC 62.918 63.158 0.00 0.00 0.00 4.85
77 78 2.487934 CCAGTTCAATCTAGCATCGGG 58.512 52.381 0.00 0.00 0.00 5.14
117 118 0.617413 AGCAGTGCTAGCTTCATGGT 59.383 50.000 18.11 11.44 39.87 3.55
167 171 1.679977 CCCCACATGGAGCAACAGG 60.680 63.158 0.00 0.00 37.39 4.00
168 172 2.345760 GCCCCACATGGAGCAACAG 61.346 63.158 0.00 0.00 37.39 3.16
208 222 0.452184 AGTCGTACAGCATCAGACCG 59.548 55.000 0.00 0.00 32.70 4.79
209 223 2.263077 CAAGTCGTACAGCATCAGACC 58.737 52.381 0.00 0.00 32.70 3.85
210 224 1.656095 GCAAGTCGTACAGCATCAGAC 59.344 52.381 0.00 0.00 0.00 3.51
327 347 2.545322 CGAGATAACTAAACGGGAGGCC 60.545 54.545 0.00 0.00 0.00 5.19
381 401 1.334869 ACTTCGAAGCAAACAAGCCTG 59.665 47.619 24.86 0.00 34.23 4.85
440 463 7.507616 TCTCACCTTAATCTCCCTTCTCTAATC 59.492 40.741 0.00 0.00 0.00 1.75
534 569 4.221924 TCAGGACATATTTCACACGGAGAA 59.778 41.667 0.00 0.00 0.00 2.87
559 594 8.447053 GCTTCTTGATCCTAAACTTTGTAAGAG 58.553 37.037 0.00 0.00 0.00 2.85
585 620 4.470462 GCTGCAATCTGTTGAACTTACTG 58.530 43.478 0.00 0.00 37.53 2.74
587 622 3.667960 CGGCTGCAATCTGTTGAACTTAC 60.668 47.826 0.50 0.00 37.53 2.34
588 623 2.483877 CGGCTGCAATCTGTTGAACTTA 59.516 45.455 0.50 0.00 37.53 2.24
589 624 1.267806 CGGCTGCAATCTGTTGAACTT 59.732 47.619 0.50 0.00 37.53 2.66
590 625 0.877071 CGGCTGCAATCTGTTGAACT 59.123 50.000 0.50 0.00 37.53 3.01
593 628 1.291184 CGACGGCTGCAATCTGTTGA 61.291 55.000 0.50 0.00 37.53 3.18
595 630 2.680913 GCGACGGCTGCAATCTGTT 61.681 57.895 0.50 0.00 35.83 3.16
603 650 1.132640 CTTAGTTTGCGACGGCTGC 59.867 57.895 0.00 0.00 40.82 5.25
609 656 5.564127 GTCTATTTTGTGCTTAGTTTGCGAC 59.436 40.000 0.00 0.00 0.00 5.19
629 676 0.245266 TCAAGGCGAACATGCGTCTA 59.755 50.000 0.18 0.00 46.79 2.59
643 690 1.661341 CTTCCGCCTCAGATTCAAGG 58.339 55.000 1.70 1.70 35.65 3.61
644 691 1.012841 GCTTCCGCCTCAGATTCAAG 58.987 55.000 0.00 0.00 0.00 3.02
659 707 0.234884 CTTTGTGTTCGACGGGCTTC 59.765 55.000 0.00 0.00 0.00 3.86
683 731 5.605908 AGGAGAACCTGATATGATGTCACAT 59.394 40.000 0.00 0.00 45.92 3.21
700 748 4.857509 ACACTCAGTACTGAAGGAGAAC 57.142 45.455 25.14 0.00 39.39 3.01
729 777 6.540189 GGAGTACATTTGATGCACTTGATAGT 59.460 38.462 0.00 0.00 37.02 2.12
730 778 6.539826 TGGAGTACATTTGATGCACTTGATAG 59.460 38.462 0.00 0.00 37.02 2.08
733 781 4.650734 TGGAGTACATTTGATGCACTTGA 58.349 39.130 0.00 0.00 37.02 3.02
750 799 2.365617 CCGCACAGGTATATTCTGGAGT 59.634 50.000 9.77 0.00 36.62 3.85
751 800 2.628178 TCCGCACAGGTATATTCTGGAG 59.372 50.000 9.77 4.64 41.99 3.86
752 801 2.364324 GTCCGCACAGGTATATTCTGGA 59.636 50.000 9.77 0.00 41.99 3.86
753 802 2.755650 GTCCGCACAGGTATATTCTGG 58.244 52.381 9.77 2.51 41.99 3.86
754 803 2.394708 CGTCCGCACAGGTATATTCTG 58.605 52.381 4.98 4.98 41.99 3.02
755 804 1.269621 GCGTCCGCACAGGTATATTCT 60.270 52.381 6.82 0.00 41.99 2.40
756 805 1.137513 GCGTCCGCACAGGTATATTC 58.862 55.000 6.82 0.00 41.99 1.75
757 806 0.750850 AGCGTCCGCACAGGTATATT 59.249 50.000 14.70 0.00 44.88 1.28
758 807 0.314302 GAGCGTCCGCACAGGTATAT 59.686 55.000 14.70 0.00 44.88 0.86
759 808 1.033202 TGAGCGTCCGCACAGGTATA 61.033 55.000 14.70 0.00 44.88 1.47
760 809 1.884075 TTGAGCGTCCGCACAGGTAT 61.884 55.000 14.70 0.00 42.11 2.73
761 810 2.089887 TTTGAGCGTCCGCACAGGTA 62.090 55.000 14.70 0.00 42.11 3.08
762 811 2.933878 TTTTGAGCGTCCGCACAGGT 62.934 55.000 14.70 0.00 42.11 4.00
763 812 1.781025 TTTTTGAGCGTCCGCACAGG 61.781 55.000 14.70 0.00 42.11 4.00
764 813 1.646540 TTTTTGAGCGTCCGCACAG 59.353 52.632 14.70 0.00 42.11 3.66
765 814 3.814991 TTTTTGAGCGTCCGCACA 58.185 50.000 14.70 11.13 44.88 4.57
781 830 8.556213 TTTACGCACAGGTATATTCTCTTTTT 57.444 30.769 0.00 0.00 0.00 1.94
782 831 8.732746 ATTTACGCACAGGTATATTCTCTTTT 57.267 30.769 0.00 0.00 0.00 2.27
783 832 9.998106 ATATTTACGCACAGGTATATTCTCTTT 57.002 29.630 0.00 0.00 0.00 2.52
786 835 9.850628 TGTATATTTACGCACAGGTATATTCTC 57.149 33.333 0.00 0.00 0.00 2.87
829 878 1.731093 GACTAGCCAGTCTCCTCGC 59.269 63.158 4.92 0.00 46.56 5.03
842 891 4.021544 AGGAAGACTTTGACTGCTGACTAG 60.022 45.833 0.00 0.00 0.00 2.57
867 916 1.666189 GCGGTTGACTATTTCTCCTGC 59.334 52.381 0.00 0.00 0.00 4.85
909 958 4.452733 GGAAGAGTCGCCCGTGGG 62.453 72.222 0.00 0.00 38.57 4.61
935 984 3.126831 GCCTATTGATTCGTGAGAGTGG 58.873 50.000 0.00 0.00 43.69 4.00
955 1004 1.077429 GTGGGGAGGAAGATGTGGC 60.077 63.158 0.00 0.00 0.00 5.01
1129 1184 4.157958 GAGGGACGACGACGACGG 62.158 72.222 22.36 6.21 44.46 4.79
1162 1217 0.322636 AGCTCCGACGATATCCCGAT 60.323 55.000 12.18 0.00 0.00 4.18
1242 1297 3.902086 GCCCTAGCGAGGTCGTCC 61.902 72.222 12.29 0.00 41.95 4.79
1865 1921 9.313118 GTCTGTTTGAAACTTGATTTGGTATTT 57.687 29.630 9.69 0.00 0.00 1.40
1866 1922 7.926018 GGTCTGTTTGAAACTTGATTTGGTATT 59.074 33.333 9.69 0.00 0.00 1.89
1944 2000 6.061022 TGCCTCATCCAACTTTTCACTATA 57.939 37.500 0.00 0.00 0.00 1.31
1945 2001 4.922206 TGCCTCATCCAACTTTTCACTAT 58.078 39.130 0.00 0.00 0.00 2.12
1981 2454 2.299297 ACGAGGTGGGTCTACTGAAAAG 59.701 50.000 0.00 0.00 0.00 2.27
1985 2458 0.323178 GGACGAGGTGGGTCTACTGA 60.323 60.000 0.00 0.00 34.82 3.41
2039 2520 4.222588 GGGCTAGTCCTAGATAGTCTCGTA 59.777 50.000 5.99 0.00 35.21 3.43
2040 2521 3.008266 GGGCTAGTCCTAGATAGTCTCGT 59.992 52.174 5.99 0.00 35.21 4.18
2076 2557 7.931407 TGTTGTGCTTAGAGTTTCTTCAATAGA 59.069 33.333 0.00 0.00 0.00 1.98
2077 2558 8.087982 TGTTGTGCTTAGAGTTTCTTCAATAG 57.912 34.615 0.00 0.00 0.00 1.73
2078 2559 8.445275 TTGTTGTGCTTAGAGTTTCTTCAATA 57.555 30.769 0.00 0.00 0.00 1.90
2079 2560 6.942532 TGTTGTGCTTAGAGTTTCTTCAAT 57.057 33.333 0.00 0.00 0.00 2.57
2080 2561 6.374333 ACTTGTTGTGCTTAGAGTTTCTTCAA 59.626 34.615 0.00 0.00 0.00 2.69
2081 2562 5.880332 ACTTGTTGTGCTTAGAGTTTCTTCA 59.120 36.000 0.00 0.00 0.00 3.02
2082 2563 6.364945 ACTTGTTGTGCTTAGAGTTTCTTC 57.635 37.500 0.00 0.00 0.00 2.87
2083 2564 5.006746 CGACTTGTTGTGCTTAGAGTTTCTT 59.993 40.000 0.00 0.00 0.00 2.52
2084 2565 4.508124 CGACTTGTTGTGCTTAGAGTTTCT 59.492 41.667 0.00 0.00 0.00 2.52
2085 2566 4.762809 CGACTTGTTGTGCTTAGAGTTTC 58.237 43.478 0.00 0.00 0.00 2.78
2086 2567 3.002348 GCGACTTGTTGTGCTTAGAGTTT 59.998 43.478 0.00 0.00 0.00 2.66
2087 2568 2.544267 GCGACTTGTTGTGCTTAGAGTT 59.456 45.455 0.00 0.00 0.00 3.01
2088 2569 2.135933 GCGACTTGTTGTGCTTAGAGT 58.864 47.619 0.00 0.00 0.00 3.24
2089 2570 1.461127 GGCGACTTGTTGTGCTTAGAG 59.539 52.381 0.00 0.00 0.00 2.43
2090 2571 1.508632 GGCGACTTGTTGTGCTTAGA 58.491 50.000 0.00 0.00 0.00 2.10
2091 2572 0.517316 GGGCGACTTGTTGTGCTTAG 59.483 55.000 0.00 0.00 0.00 2.18
2092 2573 0.887387 GGGGCGACTTGTTGTGCTTA 60.887 55.000 0.00 0.00 0.00 3.09
2093 2574 2.193536 GGGGCGACTTGTTGTGCTT 61.194 57.895 0.00 0.00 0.00 3.91
2094 2575 2.594592 GGGGCGACTTGTTGTGCT 60.595 61.111 0.00 0.00 0.00 4.40
2095 2576 4.025401 CGGGGCGACTTGTTGTGC 62.025 66.667 0.00 0.00 0.00 4.57
2096 2577 2.590575 ACGGGGCGACTTGTTGTG 60.591 61.111 0.00 0.00 0.00 3.33
2097 2578 2.590575 CACGGGGCGACTTGTTGT 60.591 61.111 0.00 0.00 0.00 3.32
2098 2579 2.280524 TCACGGGGCGACTTGTTG 60.281 61.111 0.00 0.00 0.00 3.33
2099 2580 2.280592 GTCACGGGGCGACTTGTT 60.281 61.111 0.00 0.00 0.00 2.83
2100 2581 3.222354 GAGTCACGGGGCGACTTGT 62.222 63.158 0.00 0.00 43.72 3.16
2101 2582 2.432628 GAGTCACGGGGCGACTTG 60.433 66.667 0.00 0.00 43.72 3.16
2102 2583 3.692406 GGAGTCACGGGGCGACTT 61.692 66.667 0.00 0.00 43.72 3.01
2107 2588 3.934391 CTTCACGGAGTCACGGGGC 62.934 68.421 3.86 0.00 41.61 5.80
2108 2589 2.261671 CTTCACGGAGTCACGGGG 59.738 66.667 3.86 0.00 41.61 5.73
2109 2590 2.432628 GCTTCACGGAGTCACGGG 60.433 66.667 6.08 2.08 41.61 5.28
2110 2591 2.805353 CGCTTCACGGAGTCACGG 60.805 66.667 6.08 0.00 41.61 4.94
2121 2602 1.814394 ACAGTCACCGTATACGCTTCA 59.186 47.619 19.86 0.23 38.18 3.02
2144 2625 1.485838 GAGATCACATCGGTGCGCAG 61.486 60.000 12.22 0.00 44.87 5.18
2145 2626 1.519234 GAGATCACATCGGTGCGCA 60.519 57.895 5.66 5.66 44.87 6.09
2146 2627 1.485838 CTGAGATCACATCGGTGCGC 61.486 60.000 0.00 0.00 44.87 6.09
2183 2664 8.946085 TCACTTGTTGGTCATAATCAAGAATAC 58.054 33.333 9.63 0.00 38.82 1.89
2220 2701 6.808008 ACTCATTAGTGGTCATTGAACTTG 57.192 37.500 2.91 0.00 33.57 3.16
2242 2723 7.916914 TGGGCTACTTAAATCTGAGTAAAAC 57.083 36.000 0.00 0.00 0.00 2.43
2283 2764 1.918800 AGGTGGTACCACTCCTGCC 60.919 63.158 37.24 23.59 45.52 4.85
2296 2777 1.549203 AAACATAGCTTGGCAGGTGG 58.451 50.000 0.00 0.00 31.45 4.61
2311 2792 8.950007 ATAATTTTGGTCCTCCTAGAAAAACA 57.050 30.769 0.00 0.00 34.23 2.83
2377 2859 7.630242 AAACCACTCCTTGTATTCATATGTG 57.370 36.000 1.90 0.00 0.00 3.21
2434 2916 6.033196 CCGTAACTACAACATACTCAACTTCG 59.967 42.308 0.00 0.00 0.00 3.79
2549 3120 4.559153 AGAAATGTGGTGTTTGCTATTGC 58.441 39.130 0.00 0.00 40.20 3.56
2552 3123 7.886629 ATATGAGAAATGTGGTGTTTGCTAT 57.113 32.000 0.00 0.00 0.00 2.97
2587 3158 6.662414 TTTTGAAGCACAGTAATCCTATCG 57.338 37.500 0.00 0.00 0.00 2.92
2718 3289 4.444022 GGTCACTGTCTCCATCATTAGCAT 60.444 45.833 0.00 0.00 0.00 3.79
2786 3357 5.888161 CCTTGCCCATTTCAATAGTTCTACT 59.112 40.000 0.00 0.00 0.00 2.57
2827 3398 1.354040 CGCAATCTCCGAGGATATGC 58.646 55.000 11.50 11.50 32.22 3.14
3016 3587 8.632679 AGCTTTTCTTGTTGTCATTCAATCTTA 58.367 29.630 0.00 0.00 38.38 2.10
3028 3599 1.334869 CCGCTGAGCTTTTCTTGTTGT 59.665 47.619 1.78 0.00 0.00 3.32
3046 3617 3.667360 TGATCATGGCATAGTCAATCCG 58.333 45.455 0.00 0.00 0.00 4.18
3243 3814 0.104304 GTGTATACAGCGGGGGTGAG 59.896 60.000 5.62 0.00 34.87 3.51
3258 3829 4.334759 GCTAGAATCGAGTAGTGGTGTGTA 59.665 45.833 0.00 0.00 0.00 2.90
3438 4009 7.816945 TCATATTATGTGTATGAGCGACATG 57.183 36.000 9.13 0.00 39.77 3.21
3573 4155 4.318332 CCTCTCAACACTAGAATTGCACA 58.682 43.478 0.00 0.00 0.00 4.57
3574 4156 3.686726 CCCTCTCAACACTAGAATTGCAC 59.313 47.826 0.00 0.00 0.00 4.57
3615 4197 3.607422 TGCATTCTGTATTGTATGCGC 57.393 42.857 0.00 0.00 44.77 6.09
3642 4224 4.953940 AGTAATGCTCTCCCTCATCTTC 57.046 45.455 0.00 0.00 0.00 2.87
3736 4318 0.764752 GGCTACCTAGGGCCTGATGT 60.765 60.000 18.53 12.76 44.48 3.06
3822 4404 5.509501 GGAAACAATGGCAAAGTCAAGATCA 60.510 40.000 0.00 0.00 0.00 2.92
3833 4415 1.799933 AAGGGTGGAAACAATGGCAA 58.200 45.000 0.00 0.00 46.06 4.52
3915 4497 3.005684 TGCACAGCTTTCCAAACCAATAG 59.994 43.478 0.00 0.00 0.00 1.73


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

AutoCloner maintained by Alex Coulton.