Multiple sequence alignment - TraesCS5B01G315600

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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 TraesCS5B01G315600 chr5B 100.000 4965 0 0 1 4965 497759068 497754104 0.000000e+00 9169.0
1 TraesCS5B01G315600 chr5B 83.178 214 31 4 1100 1309 416851146 416850934 1.820000e-44 191.0
2 TraesCS5B01G315600 chr5A 92.783 3090 150 40 99 3158 525080261 525077215 0.000000e+00 4403.0
3 TraesCS5B01G315600 chr5A 83.178 214 31 4 1100 1309 453877126 453876914 1.820000e-44 191.0
4 TraesCS5B01G315600 chr5D 93.039 2988 116 47 203 3167 413059867 413056949 0.000000e+00 4281.0
5 TraesCS5B01G315600 chr5D 82.805 221 33 4 1100 1316 352219234 352219453 5.070000e-45 193.0
6 TraesCS5B01G315600 chr5D 92.661 109 7 1 1 109 120890810 120890703 6.650000e-34 156.0
7 TraesCS5B01G315600 chr5D 94.059 101 6 0 1 101 519214274 519214174 2.390000e-33 154.0
8 TraesCS5B01G315600 chr5D 78.281 221 41 7 1100 1318 558247775 558247560 8.670000e-28 135.0
9 TraesCS5B01G315600 chr7B 99.424 1216 7 0 3750 4965 144285675 144286890 0.000000e+00 2207.0
10 TraesCS5B01G315600 chr7B 94.118 102 6 0 1 102 141814455 141814556 6.650000e-34 156.0
11 TraesCS5B01G315600 chr7B 93.333 105 7 0 1 105 537793021 537792917 6.650000e-34 156.0
12 TraesCS5B01G315600 chr7B 89.109 101 11 0 1432 1532 235449833 235449733 5.220000e-25 126.0
13 TraesCS5B01G315600 chr7B 82.500 80 4 3 96 165 203142500 203142579 1.490000e-05 62.1
14 TraesCS5B01G315600 chr2D 96.268 911 27 6 3169 4075 89094250 89093343 0.000000e+00 1487.0
15 TraesCS5B01G315600 chr2D 94.891 920 38 6 3161 4075 105005352 105006267 0.000000e+00 1430.0
16 TraesCS5B01G315600 chr4D 96.154 910 31 3 3169 4075 491710636 491709728 0.000000e+00 1483.0
17 TraesCS5B01G315600 chr1D 94.697 792 27 5 3296 4075 293918188 293917400 0.000000e+00 1216.0
18 TraesCS5B01G315600 chr1D 96.923 130 4 0 3169 3298 293930269 293930140 8.370000e-53 219.0
19 TraesCS5B01G315600 chr1D 92.035 113 8 1 1 113 69193999 69193888 1.850000e-34 158.0
20 TraesCS5B01G315600 chr1D 94.059 101 6 0 1 101 28313537 28313637 2.390000e-33 154.0
21 TraesCS5B01G315600 chr1D 80.628 191 33 4 1120 1308 439022280 439022468 1.440000e-30 145.0
22 TraesCS5B01G315600 chr1D 80.392 102 12 7 100 194 444148373 444148473 2.480000e-08 71.3
23 TraesCS5B01G315600 chr1A 90.220 409 38 2 4556 4964 564771015 564770609 2.630000e-147 532.0
24 TraesCS5B01G315600 chr1A 82.292 192 28 6 1120 1308 535312154 535312342 1.430000e-35 161.0
25 TraesCS5B01G315600 chr7A 88.780 410 45 1 4556 4965 669701054 669700646 7.420000e-138 501.0
26 TraesCS5B01G315600 chr7A 88.537 410 47 0 4556 4965 706431859 706431450 9.600000e-137 497.0
27 TraesCS5B01G315600 chr7A 89.109 101 11 0 1432 1532 276185855 276185755 5.220000e-25 126.0
28 TraesCS5B01G315600 chr1B 86.585 410 55 0 4556 4965 159865697 159865288 2.110000e-123 453.0
29 TraesCS5B01G315600 chr1B 82.292 192 28 6 1120 1308 595176892 595177080 1.430000e-35 161.0
30 TraesCS5B01G315600 chr3A 97.297 148 4 0 3168 3315 579515952 579516099 8.250000e-63 252.0
31 TraesCS5B01G315600 chr2B 83.077 195 31 2 1119 1312 146442441 146442248 5.110000e-40 176.0
32 TraesCS5B01G315600 chr2A 83.077 195 31 2 1119 1312 92318255 92318062 5.110000e-40 176.0
33 TraesCS5B01G315600 chr4A 94.444 108 5 1 1 107 702148809 702148916 1.110000e-36 165.0
34 TraesCS5B01G315600 chr4B 93.269 104 7 0 1 104 165306609 165306506 2.390000e-33 154.0
35 TraesCS5B01G315600 chrUn 90.909 110 10 0 1 110 284430873 284430982 1.110000e-31 148.0
36 TraesCS5B01G315600 chr7D 89.109 101 11 0 1432 1532 256444267 256444167 5.220000e-25 126.0


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 TraesCS5B01G315600 chr5B 497754104 497759068 4964 True 9169 9169 100.000 1 4965 1 chr5B.!!$R2 4964
1 TraesCS5B01G315600 chr5A 525077215 525080261 3046 True 4403 4403 92.783 99 3158 1 chr5A.!!$R2 3059
2 TraesCS5B01G315600 chr5D 413056949 413059867 2918 True 4281 4281 93.039 203 3167 1 chr5D.!!$R2 2964
3 TraesCS5B01G315600 chr7B 144285675 144286890 1215 False 2207 2207 99.424 3750 4965 1 chr7B.!!$F2 1215
4 TraesCS5B01G315600 chr2D 89093343 89094250 907 True 1487 1487 96.268 3169 4075 1 chr2D.!!$R1 906
5 TraesCS5B01G315600 chr2D 105005352 105006267 915 False 1430 1430 94.891 3161 4075 1 chr2D.!!$F1 914
6 TraesCS5B01G315600 chr4D 491709728 491710636 908 True 1483 1483 96.154 3169 4075 1 chr4D.!!$R1 906
7 TraesCS5B01G315600 chr1D 293917400 293918188 788 True 1216 1216 94.697 3296 4075 1 chr1D.!!$R2 779

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
607 613 0.748005 ACCAAATCTCGCCCGAATGG 60.748 55.0 8.81 8.81 32.96 3.16 F
924 931 1.360393 TTTCCTTGGTGAGGTGGCCT 61.360 55.0 3.32 0.00 46.39 5.19 F
1687 1700 0.469331 AGGTCCTGTCGTCCAACTCA 60.469 55.0 0.00 0.00 0.00 3.41 F
2125 2138 0.109689 ACGAAGAAGAAGACGGCGAG 60.110 55.0 16.62 0.00 0.00 5.03 F
2957 3019 0.030235 CGTGTGAACGTCACCAGAGA 59.970 55.0 13.24 0.00 46.40 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1408 1421 0.318869 CGCCACAGCAAGCAAAATCA 60.319 50.000 0.0 0.0 39.83 2.57 R
1771 1784 0.673985 CGTTCTCCTCGCCCATATCA 59.326 55.000 0.0 0.0 0.00 2.15 R
2927 2964 0.101579 GTTCACACGGGGTTGGTTTG 59.898 55.000 0.0 0.0 0.00 2.93 R
3095 3158 0.462759 GGCACGGAAGAGGGAGAATG 60.463 60.000 0.0 0.0 0.00 2.67 R
4538 4614 4.884668 TTGGACCACTACCTAGTTGAAG 57.115 45.455 0.0 0.0 33.46 3.02 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
23 24 6.683974 AAATACTTGTCGGAGGAATGAATG 57.316 37.500 0.00 0.00 0.00 2.67
24 25 3.703001 ACTTGTCGGAGGAATGAATGT 57.297 42.857 0.00 0.00 0.00 2.71
25 26 4.819105 ACTTGTCGGAGGAATGAATGTA 57.181 40.909 0.00 0.00 0.00 2.29
26 27 5.359194 ACTTGTCGGAGGAATGAATGTAT 57.641 39.130 0.00 0.00 0.00 2.29
27 28 5.360591 ACTTGTCGGAGGAATGAATGTATC 58.639 41.667 0.00 0.00 0.00 2.24
28 29 5.129485 ACTTGTCGGAGGAATGAATGTATCT 59.871 40.000 0.00 0.00 0.00 1.98
29 30 6.323996 ACTTGTCGGAGGAATGAATGTATCTA 59.676 38.462 0.00 0.00 0.00 1.98
30 31 6.332735 TGTCGGAGGAATGAATGTATCTAG 57.667 41.667 0.00 0.00 0.00 2.43
31 32 6.068670 TGTCGGAGGAATGAATGTATCTAGA 58.931 40.000 0.00 0.00 0.00 2.43
32 33 6.016192 TGTCGGAGGAATGAATGTATCTAGAC 60.016 42.308 0.00 0.00 0.00 2.59
33 34 5.181433 TCGGAGGAATGAATGTATCTAGACG 59.819 44.000 0.00 0.00 0.00 4.18
34 35 5.048643 CGGAGGAATGAATGTATCTAGACGT 60.049 44.000 0.00 0.00 0.00 4.34
35 36 6.148976 CGGAGGAATGAATGTATCTAGACGTA 59.851 42.308 0.00 0.00 0.00 3.57
36 37 7.148222 CGGAGGAATGAATGTATCTAGACGTAT 60.148 40.741 0.00 0.00 0.00 3.06
37 38 8.524487 GGAGGAATGAATGTATCTAGACGTATT 58.476 37.037 0.00 0.00 0.00 1.89
38 39 9.915629 GAGGAATGAATGTATCTAGACGTATTT 57.084 33.333 0.00 0.00 0.00 1.40
55 56 9.962783 AGACGTATTTTAGTTGTAGATACATCC 57.037 33.333 0.00 0.00 35.89 3.51
56 57 9.740239 GACGTATTTTAGTTGTAGATACATCCA 57.260 33.333 0.00 0.00 35.89 3.41
91 92 5.585500 TTTTCGACAAGTATTTCCAGACG 57.415 39.130 0.00 0.00 0.00 4.18
92 93 3.226346 TCGACAAGTATTTCCAGACGG 57.774 47.619 0.00 0.00 0.00 4.79
93 94 2.821378 TCGACAAGTATTTCCAGACGGA 59.179 45.455 0.00 0.00 40.60 4.69
140 142 7.619050 AGTATAGATTCACCCATCTTGCATAG 58.381 38.462 0.00 0.00 35.08 2.23
147 149 1.544093 CCCATCTTGCATAGTCCGCAT 60.544 52.381 0.00 0.00 39.58 4.73
150 152 1.667236 TCTTGCATAGTCCGCATTGG 58.333 50.000 0.00 0.00 39.58 3.16
165 167 6.620678 TCCGCATTGGAATCTTTAAAAAGAG 58.379 36.000 10.64 0.00 46.38 2.85
166 168 6.208599 TCCGCATTGGAATCTTTAAAAAGAGT 59.791 34.615 10.64 8.06 46.38 3.24
167 169 7.392113 TCCGCATTGGAATCTTTAAAAAGAGTA 59.608 33.333 10.64 0.00 46.38 2.59
194 197 3.390175 TCAGGAAGGAAGGGAGTAGAG 57.610 52.381 0.00 0.00 0.00 2.43
199 202 3.264706 GGAAGGAAGGGAGTAGAGCTTTT 59.735 47.826 0.00 0.00 0.00 2.27
281 285 1.666189 GTTCTTCGAATGGTAGGCTGC 59.334 52.381 0.00 0.00 0.00 5.25
330 335 4.810790 TCGAAGCTTAGAGAACCTTCTTG 58.189 43.478 5.03 0.00 37.73 3.02
336 341 6.645306 AGCTTAGAGAACCTTCTTGGAATAC 58.355 40.000 0.00 0.00 37.73 1.89
337 342 6.213600 AGCTTAGAGAACCTTCTTGGAATACA 59.786 38.462 0.00 0.00 37.73 2.29
338 343 6.536941 GCTTAGAGAACCTTCTTGGAATACAG 59.463 42.308 0.00 0.00 37.73 2.74
339 344 7.554959 TTAGAGAACCTTCTTGGAATACAGT 57.445 36.000 0.00 0.00 37.73 3.55
340 345 8.660295 TTAGAGAACCTTCTTGGAATACAGTA 57.340 34.615 0.00 0.00 37.73 2.74
454 459 1.805945 GATGGTCGACACGTGCTCC 60.806 63.158 17.22 13.08 0.00 4.70
500 505 2.486548 CGGACCTGAACCTTCCAGAAAA 60.487 50.000 0.00 0.00 33.65 2.29
502 507 2.548480 GACCTGAACCTTCCAGAAAACG 59.452 50.000 0.00 0.00 33.65 3.60
544 549 4.602340 AGTTTCTCGCTCTTTCCTAACA 57.398 40.909 0.00 0.00 0.00 2.41
547 552 1.549170 TCTCGCTCTTTCCTAACACCC 59.451 52.381 0.00 0.00 0.00 4.61
605 611 1.065418 AGAACCAAATCTCGCCCGAAT 60.065 47.619 0.00 0.00 0.00 3.34
607 613 0.748005 ACCAAATCTCGCCCGAATGG 60.748 55.000 8.81 8.81 32.96 3.16
646 652 3.009275 CCACCAGATGCCCATCCA 58.991 61.111 4.72 0.00 38.58 3.41
859 866 2.026641 TCCCGTTGGGTATAAGTCTCG 58.973 52.381 1.04 0.00 44.74 4.04
909 916 2.730550 TCTTCCGTACGTTCCTTTCC 57.269 50.000 15.21 0.00 0.00 3.13
924 931 1.360393 TTTCCTTGGTGAGGTGGCCT 61.360 55.000 3.32 0.00 46.39 5.19
1407 1420 1.838112 TGCCCATGTTGTTGATCCTC 58.162 50.000 0.00 0.00 0.00 3.71
1408 1421 1.355381 TGCCCATGTTGTTGATCCTCT 59.645 47.619 0.00 0.00 0.00 3.69
1672 1685 2.043852 TCCTCCGAGGAGCAGGTC 60.044 66.667 13.54 0.00 40.06 3.85
1687 1700 0.469331 AGGTCCTGTCGTCCAACTCA 60.469 55.000 0.00 0.00 0.00 3.41
2086 2099 0.392461 GGCTGTTTGGCGTCTCCATA 60.392 55.000 0.00 0.00 46.04 2.74
2125 2138 0.109689 ACGAAGAAGAAGACGGCGAG 60.110 55.000 16.62 0.00 0.00 5.03
2376 2398 9.726438 GAGCACCTACTAATTATTAATCACCAT 57.274 33.333 0.00 0.00 0.00 3.55
2533 2560 1.722011 AATTTGTCGTGGTAGAGCGG 58.278 50.000 0.00 0.00 0.00 5.52
2538 2565 1.303074 TCGTGGTAGAGCGGACTGT 60.303 57.895 0.00 0.00 0.00 3.55
2617 2645 0.390340 TAGCTCCTTCTGCTTGTGCG 60.390 55.000 0.00 0.00 43.34 5.34
2618 2646 2.684843 GCTCCTTCTGCTTGTGCGG 61.685 63.158 0.00 0.00 46.48 5.69
2633 2661 2.026915 TGTGCGGGAGACAGTAGTAGTA 60.027 50.000 0.00 0.00 0.00 1.82
2635 2663 2.502947 TGCGGGAGACAGTAGTAGTAGA 59.497 50.000 0.00 0.00 0.00 2.59
2640 2668 5.370679 GGGAGACAGTAGTAGTAGAAGAGG 58.629 50.000 0.00 0.00 0.00 3.69
2661 2689 6.038997 AGGAAGAGTAACTACGATTTGCTT 57.961 37.500 0.00 0.00 0.00 3.91
2723 2760 2.111999 TTTAGTCAGCTGCGTGGGCT 62.112 55.000 9.47 0.00 40.82 5.19
2767 2804 1.064003 TGGCGGCCAGATATATGGTT 58.936 50.000 19.77 0.00 42.75 3.67
2768 2805 2.261729 TGGCGGCCAGATATATGGTTA 58.738 47.619 19.77 0.00 42.75 2.85
2769 2806 2.843730 TGGCGGCCAGATATATGGTTAT 59.156 45.455 19.77 0.00 42.75 1.89
2770 2807 4.034410 TGGCGGCCAGATATATGGTTATA 58.966 43.478 19.77 0.00 42.75 0.98
2773 2810 5.396436 GGCGGCCAGATATATGGTTATAAGT 60.396 44.000 17.48 0.00 42.75 2.24
2774 2811 5.523916 GCGGCCAGATATATGGTTATAAGTG 59.476 44.000 17.48 1.25 42.75 3.16
2775 2812 5.523916 CGGCCAGATATATGGTTATAAGTGC 59.476 44.000 17.48 0.08 42.75 4.40
2776 2813 6.630413 CGGCCAGATATATGGTTATAAGTGCT 60.630 42.308 17.48 0.00 42.75 4.40
2777 2814 7.417456 CGGCCAGATATATGGTTATAAGTGCTA 60.417 40.741 17.48 0.00 42.75 3.49
2778 2815 7.711339 GGCCAGATATATGGTTATAAGTGCTAC 59.289 40.741 17.48 0.00 42.75 3.58
2779 2816 7.435488 GCCAGATATATGGTTATAAGTGCTACG 59.565 40.741 17.48 0.00 42.75 3.51
2804 2841 2.859165 ATGTTCAGACGGGTCAATGT 57.141 45.000 1.17 0.00 0.00 2.71
2857 2894 3.372060 GCTTGGTTCCAACTCGAAAAAG 58.628 45.455 0.00 0.00 0.00 2.27
2925 2962 4.382320 GTCTGGCGGGGCACGTAA 62.382 66.667 12.27 0.00 46.52 3.18
2926 2963 4.382320 TCTGGCGGGGCACGTAAC 62.382 66.667 12.27 1.86 46.52 2.50
2930 2967 2.979120 GCGGGGCACGTAACCAAA 60.979 61.111 12.27 0.00 46.52 3.28
2931 2968 2.948323 CGGGGCACGTAACCAAAC 59.052 61.111 0.00 0.00 37.93 2.93
2932 2969 2.619165 CGGGGCACGTAACCAAACC 61.619 63.158 0.00 0.82 37.93 3.27
2933 2970 1.528776 GGGGCACGTAACCAAACCA 60.529 57.895 8.88 0.00 0.00 3.67
2934 2971 1.108132 GGGGCACGTAACCAAACCAA 61.108 55.000 8.88 0.00 0.00 3.67
2935 2972 0.031043 GGGCACGTAACCAAACCAAC 59.969 55.000 8.88 0.00 0.00 3.77
2936 2973 0.031043 GGCACGTAACCAAACCAACC 59.969 55.000 1.99 0.00 0.00 3.77
2937 2974 0.031043 GCACGTAACCAAACCAACCC 59.969 55.000 0.00 0.00 0.00 4.11
2938 2975 0.669619 CACGTAACCAAACCAACCCC 59.330 55.000 0.00 0.00 0.00 4.95
2939 2976 0.818852 ACGTAACCAAACCAACCCCG 60.819 55.000 0.00 0.00 0.00 5.73
2940 2977 0.818852 CGTAACCAAACCAACCCCGT 60.819 55.000 0.00 0.00 0.00 5.28
2941 2978 0.669619 GTAACCAAACCAACCCCGTG 59.330 55.000 0.00 0.00 0.00 4.94
2942 2979 0.258194 TAACCAAACCAACCCCGTGT 59.742 50.000 0.00 0.00 0.00 4.49
2943 2980 1.324005 AACCAAACCAACCCCGTGTG 61.324 55.000 0.00 0.00 0.00 3.82
2944 2981 1.454111 CCAAACCAACCCCGTGTGA 60.454 57.895 0.00 0.00 0.00 3.58
2945 2982 1.038130 CCAAACCAACCCCGTGTGAA 61.038 55.000 0.00 0.00 0.00 3.18
2946 2983 0.101579 CAAACCAACCCCGTGTGAAC 59.898 55.000 0.00 0.00 0.00 3.18
2947 2984 1.378124 AAACCAACCCCGTGTGAACG 61.378 55.000 0.00 0.00 0.00 3.95
2948 2985 2.203098 CCAACCCCGTGTGAACGT 60.203 61.111 0.00 0.00 0.00 3.99
2957 3019 0.030235 CGTGTGAACGTCACCAGAGA 59.970 55.000 13.24 0.00 46.40 3.10
2961 3023 2.167693 TGTGAACGTCACCAGAGAACTT 59.832 45.455 13.24 0.00 46.40 2.66
3026 3089 2.768344 AACGGATGGGGCGGAGAT 60.768 61.111 0.00 0.00 0.00 2.75
3043 3106 3.939837 ATGGCGACGTGCTGTCCAG 62.940 63.158 0.00 0.00 45.23 3.86
3060 3123 3.755628 GTCGCTGCGGGTCAGGTA 61.756 66.667 23.03 0.00 43.06 3.08
3095 3158 0.249699 CCTTTTTGCCCGGTTGTTCC 60.250 55.000 0.00 0.00 0.00 3.62
3096 3159 0.461961 CTTTTTGCCCGGTTGTTCCA 59.538 50.000 0.00 0.00 35.57 3.53
3102 3165 1.313091 GCCCGGTTGTTCCATTCTCC 61.313 60.000 0.00 0.00 35.57 3.71
3152 3216 4.963318 TCTTTCTGATGAGAAGGTGTGT 57.037 40.909 4.06 0.00 39.44 3.72
3153 3217 4.635223 TCTTTCTGATGAGAAGGTGTGTG 58.365 43.478 4.06 0.00 39.44 3.82
3158 3223 2.301870 TGATGAGAAGGTGTGTGGTACC 59.698 50.000 4.43 4.43 38.52 3.34
3272 3337 1.066430 GGTACTTGCGAAGATGGTCCA 60.066 52.381 0.00 0.00 0.00 4.02
3382 3447 1.583054 GGCCGCATCGTTTTCTCTAT 58.417 50.000 0.00 0.00 0.00 1.98
3386 3451 3.802685 GCCGCATCGTTTTCTCTATAGTT 59.197 43.478 0.00 0.00 0.00 2.24
3391 3456 5.751028 GCATCGTTTTCTCTATAGTTGAGCT 59.249 40.000 0.00 0.00 0.00 4.09
3409 3474 1.197949 GCTTGAGAAGCGGAAACTTCC 59.802 52.381 0.00 0.00 45.95 3.46
3434 3499 4.261801 TGTTCGATCCCCAATTCTTTCTC 58.738 43.478 0.00 0.00 0.00 2.87
3648 3713 1.517913 GTACAAGGCGGCGGACTAC 60.518 63.158 9.78 0.00 0.00 2.73
3649 3714 1.978080 TACAAGGCGGCGGACTACA 60.978 57.895 9.78 0.00 0.00 2.74
3651 3716 1.449601 CAAGGCGGCGGACTACAAT 60.450 57.895 9.78 0.00 0.00 2.71
3669 3734 1.488705 ATGTGGAGGCGGAGTGGAAA 61.489 55.000 0.00 0.00 0.00 3.13
3876 3943 4.052229 CAGACGCCGTCCGGAAGT 62.052 66.667 14.60 9.53 42.52 3.01
4356 4432 6.577103 TCAGAAAGTAGGCAATAGATCACAG 58.423 40.000 0.00 0.00 0.00 3.66
4396 4472 6.319911 TCAGGAAACACAAACAACATATCACA 59.680 34.615 0.00 0.00 0.00 3.58
4450 4526 5.983720 ACAACATATACTAATCTGACGGCAC 59.016 40.000 0.00 0.00 0.00 5.01
4538 4614 6.808212 AGCACATGTGACAAAATAAACATAGC 59.192 34.615 29.80 7.37 35.32 2.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.180472 ACATTCATTCCTCCGACAAGTATTT 58.820 36.000 0.00 0.00 0.00 1.40
3 4 4.819105 ACATTCATTCCTCCGACAAGTA 57.181 40.909 0.00 0.00 0.00 2.24
4 5 3.703001 ACATTCATTCCTCCGACAAGT 57.297 42.857 0.00 0.00 0.00 3.16
5 6 5.605534 AGATACATTCATTCCTCCGACAAG 58.394 41.667 0.00 0.00 0.00 3.16
6 7 5.614324 AGATACATTCATTCCTCCGACAA 57.386 39.130 0.00 0.00 0.00 3.18
7 8 6.016192 GTCTAGATACATTCATTCCTCCGACA 60.016 42.308 0.00 0.00 0.00 4.35
8 9 6.383415 GTCTAGATACATTCATTCCTCCGAC 58.617 44.000 0.00 0.00 0.00 4.79
9 10 5.181433 CGTCTAGATACATTCATTCCTCCGA 59.819 44.000 0.00 0.00 0.00 4.55
10 11 5.048643 ACGTCTAGATACATTCATTCCTCCG 60.049 44.000 0.00 0.00 0.00 4.63
11 12 6.334102 ACGTCTAGATACATTCATTCCTCC 57.666 41.667 0.00 0.00 0.00 4.30
12 13 9.915629 AAATACGTCTAGATACATTCATTCCTC 57.084 33.333 0.00 0.00 0.00 3.71
29 30 9.962783 GGATGTATCTACAACTAAAATACGTCT 57.037 33.333 0.00 0.00 39.99 4.18
30 31 9.740239 TGGATGTATCTACAACTAAAATACGTC 57.260 33.333 0.00 0.00 39.99 4.34
68 69 5.049954 CCGTCTGGAAATACTTGTCGAAAAA 60.050 40.000 0.00 0.00 37.49 1.94
69 70 4.449743 CCGTCTGGAAATACTTGTCGAAAA 59.550 41.667 0.00 0.00 37.49 2.29
70 71 3.991773 CCGTCTGGAAATACTTGTCGAAA 59.008 43.478 0.00 0.00 37.49 3.46
71 72 3.256383 TCCGTCTGGAAATACTTGTCGAA 59.744 43.478 0.00 0.00 42.85 3.71
72 73 2.821378 TCCGTCTGGAAATACTTGTCGA 59.179 45.455 0.00 0.00 42.85 4.20
73 74 3.226346 TCCGTCTGGAAATACTTGTCG 57.774 47.619 0.00 0.00 42.85 4.35
84 85 5.837770 TCTATATACTCCTTCCGTCTGGA 57.162 43.478 0.00 0.00 44.61 3.86
85 86 8.754991 AATATCTATATACTCCTTCCGTCTGG 57.245 38.462 0.00 0.00 0.00 3.86
114 115 5.858381 TGCAAGATGGGTGAATCTATACTC 58.142 41.667 0.00 0.00 35.83 2.59
116 117 7.390027 ACTATGCAAGATGGGTGAATCTATAC 58.610 38.462 0.00 0.00 35.83 1.47
121 123 3.817647 GGACTATGCAAGATGGGTGAATC 59.182 47.826 0.00 0.00 0.00 2.52
127 129 0.179048 TGCGGACTATGCAAGATGGG 60.179 55.000 0.00 0.00 39.87 4.00
128 130 1.888215 ATGCGGACTATGCAAGATGG 58.112 50.000 0.00 0.00 46.87 3.51
129 131 2.031420 CCAATGCGGACTATGCAAGATG 60.031 50.000 0.00 0.00 46.87 2.90
132 134 1.667236 TCCAATGCGGACTATGCAAG 58.333 50.000 0.00 0.00 46.87 4.01
135 137 2.498167 AGATTCCAATGCGGACTATGC 58.502 47.619 0.00 0.00 46.36 3.14
140 142 6.386654 TCTTTTTAAAGATTCCAATGCGGAC 58.613 36.000 0.89 0.00 40.96 4.79
162 164 6.100424 CCCTTCCTTCCTGAATACAATACTCT 59.900 42.308 0.00 0.00 0.00 3.24
165 167 6.126739 ACTCCCTTCCTTCCTGAATACAATAC 60.127 42.308 0.00 0.00 0.00 1.89
166 168 5.970640 ACTCCCTTCCTTCCTGAATACAATA 59.029 40.000 0.00 0.00 0.00 1.90
167 169 4.790790 ACTCCCTTCCTTCCTGAATACAAT 59.209 41.667 0.00 0.00 0.00 2.71
181 183 3.983044 TCAAAAGCTCTACTCCCTTCC 57.017 47.619 0.00 0.00 0.00 3.46
194 197 5.689383 TTGTCAGTCCACTATTCAAAAGC 57.311 39.130 0.00 0.00 0.00 3.51
199 202 6.939730 TGCTATTTTTGTCAGTCCACTATTCA 59.060 34.615 0.00 0.00 0.00 2.57
330 335 4.284178 TGGTCACCCTACTACTGTATTCC 58.716 47.826 0.00 0.00 0.00 3.01
364 369 1.400494 GCGTCGGATGCTTGGTATTTT 59.600 47.619 14.80 0.00 0.00 1.82
827 834 1.982938 AACGGGAGGAGGAGAACGG 60.983 63.158 0.00 0.00 0.00 4.44
924 931 0.901827 TAGCTTCCAGATGCGGTTGA 59.098 50.000 0.00 0.00 36.69 3.18
925 932 1.009829 GTAGCTTCCAGATGCGGTTG 58.990 55.000 0.00 0.00 36.69 3.77
926 933 0.905357 AGTAGCTTCCAGATGCGGTT 59.095 50.000 0.00 0.00 36.69 4.44
1352 1364 1.276138 CCAGAAAGGCCAAATCCCAAC 59.724 52.381 5.01 0.00 0.00 3.77
1407 1420 1.425412 GCCACAGCAAGCAAAATCAG 58.575 50.000 0.00 0.00 39.53 2.90
1408 1421 0.318869 CGCCACAGCAAGCAAAATCA 60.319 50.000 0.00 0.00 39.83 2.57
1672 1685 0.898320 ATCCTGAGTTGGACGACAGG 59.102 55.000 15.67 15.67 43.39 4.00
1687 1700 4.531426 AGCTCCTCCGCGGATCCT 62.531 66.667 31.19 18.65 42.12 3.24
1771 1784 0.673985 CGTTCTCCTCGCCCATATCA 59.326 55.000 0.00 0.00 0.00 2.15
2110 2123 3.007973 GCCCTCGCCGTCTTCTTCT 62.008 63.158 0.00 0.00 0.00 2.85
2125 2138 1.144276 GTTAGGAAGCTCCTCGCCC 59.856 63.158 7.85 0.00 45.66 6.13
2465 2492 7.523293 TGAAACAGGAACATCACAATTACAT 57.477 32.000 0.00 0.00 0.00 2.29
2533 2560 5.689383 TGCACCTTTTCATTTCTACAGTC 57.311 39.130 0.00 0.00 0.00 3.51
2538 2565 4.157656 CGGGAATGCACCTTTTCATTTCTA 59.842 41.667 0.00 0.00 33.49 2.10
2617 2645 5.130809 TCCTCTTCTACTACTACTGTCTCCC 59.869 48.000 0.00 0.00 0.00 4.30
2618 2646 6.237887 TCCTCTTCTACTACTACTGTCTCC 57.762 45.833 0.00 0.00 0.00 3.71
2633 2661 7.540299 CAAATCGTAGTTACTCTTCCTCTTCT 58.460 38.462 0.00 0.00 0.00 2.85
2635 2663 6.071278 AGCAAATCGTAGTTACTCTTCCTCTT 60.071 38.462 0.00 0.00 0.00 2.85
2640 2668 6.401153 CCACAAGCAAATCGTAGTTACTCTTC 60.401 42.308 0.00 0.00 0.00 2.87
2723 2760 2.420642 CCGCTACCGTCTACAGCTATA 58.579 52.381 0.00 0.00 33.03 1.31
2767 2804 9.112725 TCTGAACATAACTACGTAGCACTTATA 57.887 33.333 22.40 6.84 0.00 0.98
2768 2805 7.914346 GTCTGAACATAACTACGTAGCACTTAT 59.086 37.037 22.40 15.11 0.00 1.73
2769 2806 7.246311 GTCTGAACATAACTACGTAGCACTTA 58.754 38.462 22.40 13.56 0.00 2.24
2770 2807 6.091437 GTCTGAACATAACTACGTAGCACTT 58.909 40.000 22.40 11.80 0.00 3.16
2773 2810 4.437794 CCGTCTGAACATAACTACGTAGCA 60.438 45.833 22.40 11.04 0.00 3.49
2774 2811 4.033684 CCGTCTGAACATAACTACGTAGC 58.966 47.826 22.40 4.91 0.00 3.58
2775 2812 4.095483 ACCCGTCTGAACATAACTACGTAG 59.905 45.833 20.97 20.97 0.00 3.51
2776 2813 4.009675 ACCCGTCTGAACATAACTACGTA 58.990 43.478 0.00 0.00 0.00 3.57
2777 2814 2.821969 ACCCGTCTGAACATAACTACGT 59.178 45.455 0.00 0.00 0.00 3.57
2778 2815 3.119743 TGACCCGTCTGAACATAACTACG 60.120 47.826 0.00 0.00 0.00 3.51
2779 2816 4.445452 TGACCCGTCTGAACATAACTAC 57.555 45.455 0.00 0.00 0.00 2.73
2784 2821 3.259625 TCACATTGACCCGTCTGAACATA 59.740 43.478 0.00 0.00 0.00 2.29
2804 2841 0.946700 CACCGCACGTGTACCATTCA 60.947 55.000 18.38 0.00 37.73 2.57
2837 2874 4.893424 TCTTTTTCGAGTTGGAACCAAG 57.107 40.909 6.52 0.00 36.52 3.61
2872 2909 2.545731 CAAACCAAAACCAAACCCGAG 58.454 47.619 0.00 0.00 0.00 4.63
2873 2910 1.207329 CCAAACCAAAACCAAACCCGA 59.793 47.619 0.00 0.00 0.00 5.14
2874 2911 1.657822 CCAAACCAAAACCAAACCCG 58.342 50.000 0.00 0.00 0.00 5.28
2878 2915 1.207329 CCGACCCAAACCAAAACCAAA 59.793 47.619 0.00 0.00 0.00 3.28
2879 2916 0.824759 CCGACCCAAACCAAAACCAA 59.175 50.000 0.00 0.00 0.00 3.67
2881 2918 0.825410 AACCGACCCAAACCAAAACC 59.175 50.000 0.00 0.00 0.00 3.27
2883 2920 1.207329 CCAAACCGACCCAAACCAAAA 59.793 47.619 0.00 0.00 0.00 2.44
2924 2961 1.000612 ACACGGGGTTGGTTTGGTT 59.999 52.632 0.00 0.00 0.00 3.67
2925 2962 1.755008 CACACGGGGTTGGTTTGGT 60.755 57.895 0.00 0.00 0.00 3.67
2926 2963 1.038130 TTCACACGGGGTTGGTTTGG 61.038 55.000 0.00 0.00 0.00 3.28
2927 2964 0.101579 GTTCACACGGGGTTGGTTTG 59.898 55.000 0.00 0.00 0.00 2.93
2928 2965 1.378124 CGTTCACACGGGGTTGGTTT 61.378 55.000 0.00 0.00 43.16 3.27
2929 2966 1.820481 CGTTCACACGGGGTTGGTT 60.820 57.895 0.00 0.00 43.16 3.67
2930 2967 2.203098 CGTTCACACGGGGTTGGT 60.203 61.111 0.00 0.00 43.16 3.67
2941 2978 2.510768 AGTTCTCTGGTGACGTTCAC 57.489 50.000 8.94 8.94 46.23 3.18
2942 2979 2.821546 CAAGTTCTCTGGTGACGTTCA 58.178 47.619 0.00 0.00 0.00 3.18
2943 2980 1.527311 GCAAGTTCTCTGGTGACGTTC 59.473 52.381 0.00 0.00 0.00 3.95
2944 2981 1.139058 AGCAAGTTCTCTGGTGACGTT 59.861 47.619 0.00 0.00 0.00 3.99
2945 2982 0.753262 AGCAAGTTCTCTGGTGACGT 59.247 50.000 0.00 0.00 0.00 4.34
2946 2983 2.229062 TCTAGCAAGTTCTCTGGTGACG 59.771 50.000 0.00 0.00 0.00 4.35
2947 2984 3.944055 TCTAGCAAGTTCTCTGGTGAC 57.056 47.619 0.00 0.00 0.00 3.67
2948 2985 3.259374 CCTTCTAGCAAGTTCTCTGGTGA 59.741 47.826 0.00 0.00 0.00 4.02
2957 3019 2.391389 GCGCGCCTTCTAGCAAGTT 61.391 57.895 23.24 0.00 0.00 2.66
3026 3089 4.662961 CTGGACAGCACGTCGCCA 62.663 66.667 6.39 0.00 46.42 5.69
3043 3106 3.291101 TTACCTGACCCGCAGCGAC 62.291 63.158 18.75 8.01 43.50 5.19
3095 3158 0.462759 GGCACGGAAGAGGGAGAATG 60.463 60.000 0.00 0.00 0.00 2.67
3096 3159 1.908483 GGCACGGAAGAGGGAGAAT 59.092 57.895 0.00 0.00 0.00 2.40
3167 3232 3.318017 GACTGTACGTGCAATTCACTCT 58.682 45.455 7.96 0.00 43.46 3.24
3232 3297 1.591863 GGATCGTAGCGAGGCAACC 60.592 63.158 0.00 0.00 39.91 3.77
3368 3433 7.489435 TCAAGCTCAACTATAGAGAAAACGATG 59.511 37.037 6.78 0.00 35.09 3.84
3404 3469 1.196012 GGGGATCGAACAGAGGAAGT 58.804 55.000 0.00 0.00 0.00 3.01
3409 3474 3.550437 AGAATTGGGGATCGAACAGAG 57.450 47.619 0.00 0.00 0.00 3.35
3434 3499 4.469945 TGGTTCTCTACAGTTAGGGATTGG 59.530 45.833 0.00 0.00 34.57 3.16
3475 3540 2.112297 GAACGCCTGTGGTTCCCA 59.888 61.111 0.00 0.00 38.23 4.37
3476 3541 3.047877 CGAACGCCTGTGGTTCCC 61.048 66.667 0.00 0.00 40.46 3.97
3478 3543 2.665185 AGCGAACGCCTGTGGTTC 60.665 61.111 15.44 0.00 43.17 3.62
3479 3544 2.972505 CAGCGAACGCCTGTGGTT 60.973 61.111 15.44 0.00 43.17 3.67
3538 3603 2.887568 GACATCCTGCACTCGCCG 60.888 66.667 0.00 0.00 37.32 6.46
3648 3713 1.746615 CCACTCCGCCTCCACATTG 60.747 63.158 0.00 0.00 0.00 2.82
3649 3714 1.488705 TTCCACTCCGCCTCCACATT 61.489 55.000 0.00 0.00 0.00 2.71
3651 3716 2.144078 TTTCCACTCCGCCTCCACA 61.144 57.895 0.00 0.00 0.00 4.17
3726 3791 2.847234 ACAGTGTCCTTCGGCCCA 60.847 61.111 0.00 0.00 0.00 5.36
4356 4432 6.753744 GTGTTTCCTGAGATTTGCAAATATCC 59.246 38.462 32.81 21.22 36.15 2.59
4396 4472 8.954834 TTCCTGTCATATATTGCCCAAATTAT 57.045 30.769 0.00 0.00 0.00 1.28
4538 4614 4.884668 TTGGACCACTACCTAGTTGAAG 57.115 45.455 0.00 0.00 33.46 3.02


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

AutoCloner maintained by Alex Coulton.