Multiple sequence alignment - TraesCS7A01G169600

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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 TraesCS7A01G169600 chr7A 100.000 2960 0 0 1 2960 126117519 126114560 0.000000e+00 5467.0
1 TraesCS7A01G169600 chr7D 93.449 1435 56 10 727 2131 123164068 123162642 0.000000e+00 2095.0
2 TraesCS7A01G169600 chr7D 81.899 674 47 22 9 666 123203792 123203178 1.580000e-137 499.0
3 TraesCS7A01G169600 chr7B 92.917 1440 59 9 727 2131 84380439 84379008 0.000000e+00 2054.0
4 TraesCS7A01G169600 chr7B 81.443 679 85 28 14 666 84382179 84381516 4.370000e-143 518.0
5 TraesCS7A01G169600 chr7B 81.538 390 30 16 171 523 84458138 84457754 1.740000e-72 283.0
6 TraesCS7A01G169600 chr7B 100.000 28 0 0 380 407 506032531 506032504 5.000000e-03 52.8
7 TraesCS7A01G169600 chr1A 84.456 772 103 12 2197 2960 349349701 349350463 0.000000e+00 745.0
8 TraesCS7A01G169600 chr4D 83.354 793 96 19 2200 2960 477542797 477542009 0.000000e+00 701.0
9 TraesCS7A01G169600 chr6D 84.485 709 82 12 2280 2960 411197213 411196505 0.000000e+00 675.0
10 TraesCS7A01G169600 chr6D 79.839 744 99 23 2179 2882 107769038 107769770 2.050000e-136 496.0
11 TraesCS7A01G169600 chr6A 83.541 723 100 11 2197 2906 599704564 599705280 0.000000e+00 658.0
12 TraesCS7A01G169600 chr2B 83.216 709 93 12 2276 2960 759544418 759545124 6.960000e-176 627.0
13 TraesCS7A01G169600 chr2B 76.512 711 130 23 2200 2900 719959018 719958335 1.310000e-93 353.0
14 TraesCS7A01G169600 chr6B 88.672 512 55 2 2452 2960 498671120 498671631 3.240000e-174 621.0
15 TraesCS7A01G169600 chr5D 88.566 516 54 3 2447 2960 456605749 456605237 3.240000e-174 621.0
16 TraesCS7A01G169600 chr3D 82.055 691 105 13 2198 2874 154597642 154598327 3.310000e-159 571.0
17 TraesCS7A01G169600 chr1B 86.301 511 65 4 2452 2960 16995320 16994813 4.310000e-153 551.0
18 TraesCS7A01G169600 chr5A 80.919 718 108 18 2200 2891 522097970 522098684 9.330000e-150 540.0
19 TraesCS7A01G169600 chr5A 79.944 718 115 15 2200 2888 522085277 522085994 4.400000e-138 501.0
20 TraesCS7A01G169600 chr5A 82.900 269 42 2 2200 2465 704580883 704580616 3.810000e-59 239.0
21 TraesCS7A01G169600 chr2D 85.853 516 63 8 2452 2960 7094555 7094043 9.330000e-150 540.0
22 TraesCS7A01G169600 chr4B 85.941 505 68 3 2457 2960 404909364 404908862 1.210000e-148 536.0
23 TraesCS7A01G169600 chr3B 78.837 808 100 35 2197 2958 672004425 672005207 2.060000e-131 479.0
24 TraesCS7A01G169600 chr3A 82.857 490 61 6 2202 2674 69061778 69062261 4.560000e-113 418.0
25 TraesCS7A01G169600 chr5B 79.720 572 71 25 2194 2735 528674889 528675445 3.600000e-99 372.0


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 TraesCS7A01G169600 chr7A 126114560 126117519 2959 True 5467 5467 100.000 1 2960 1 chr7A.!!$R1 2959
1 TraesCS7A01G169600 chr7D 123162642 123164068 1426 True 2095 2095 93.449 727 2131 1 chr7D.!!$R1 1404
2 TraesCS7A01G169600 chr7D 123203178 123203792 614 True 499 499 81.899 9 666 1 chr7D.!!$R2 657
3 TraesCS7A01G169600 chr7B 84379008 84382179 3171 True 1286 2054 87.180 14 2131 2 chr7B.!!$R3 2117
4 TraesCS7A01G169600 chr1A 349349701 349350463 762 False 745 745 84.456 2197 2960 1 chr1A.!!$F1 763
5 TraesCS7A01G169600 chr4D 477542009 477542797 788 True 701 701 83.354 2200 2960 1 chr4D.!!$R1 760
6 TraesCS7A01G169600 chr6D 411196505 411197213 708 True 675 675 84.485 2280 2960 1 chr6D.!!$R1 680
7 TraesCS7A01G169600 chr6D 107769038 107769770 732 False 496 496 79.839 2179 2882 1 chr6D.!!$F1 703
8 TraesCS7A01G169600 chr6A 599704564 599705280 716 False 658 658 83.541 2197 2906 1 chr6A.!!$F1 709
9 TraesCS7A01G169600 chr2B 759544418 759545124 706 False 627 627 83.216 2276 2960 1 chr2B.!!$F1 684
10 TraesCS7A01G169600 chr2B 719958335 719959018 683 True 353 353 76.512 2200 2900 1 chr2B.!!$R1 700
11 TraesCS7A01G169600 chr6B 498671120 498671631 511 False 621 621 88.672 2452 2960 1 chr6B.!!$F1 508
12 TraesCS7A01G169600 chr5D 456605237 456605749 512 True 621 621 88.566 2447 2960 1 chr5D.!!$R1 513
13 TraesCS7A01G169600 chr3D 154597642 154598327 685 False 571 571 82.055 2198 2874 1 chr3D.!!$F1 676
14 TraesCS7A01G169600 chr1B 16994813 16995320 507 True 551 551 86.301 2452 2960 1 chr1B.!!$R1 508
15 TraesCS7A01G169600 chr5A 522097970 522098684 714 False 540 540 80.919 2200 2891 1 chr5A.!!$F2 691
16 TraesCS7A01G169600 chr5A 522085277 522085994 717 False 501 501 79.944 2200 2888 1 chr5A.!!$F1 688
17 TraesCS7A01G169600 chr2D 7094043 7094555 512 True 540 540 85.853 2452 2960 1 chr2D.!!$R1 508
18 TraesCS7A01G169600 chr4B 404908862 404909364 502 True 536 536 85.941 2457 2960 1 chr4B.!!$R1 503
19 TraesCS7A01G169600 chr3B 672004425 672005207 782 False 479 479 78.837 2197 2958 1 chr3B.!!$F1 761
20 TraesCS7A01G169600 chr5B 528674889 528675445 556 False 372 372 79.720 2194 2735 1 chr5B.!!$F1 541

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
701 774 0.099082 TGTTTTGTTTCGGCGGTGTC 59.901 50.0 7.21 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2189 3307 0.032678 TAGATGCTCTAAGCGCTGGC 59.967 55.0 12.58 14.14 46.26 4.85 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
20 21 0.735287 GTTTCTCTACGACACGGGGC 60.735 60.000 0.00 0.00 0.00 5.80
91 93 4.523083 TCTAAAAGAAAGCGGGCATGTAT 58.477 39.130 0.00 0.00 0.00 2.29
98 100 3.417069 AAGCGGGCATGTATATTGCTA 57.583 42.857 9.62 0.00 40.03 3.49
104 106 3.310774 GGGCATGTATATTGCTATGAGCG 59.689 47.826 9.62 0.00 46.26 5.03
148 150 6.369065 CACCGAAGATAAAATATACCCTGAGC 59.631 42.308 0.00 0.00 0.00 4.26
207 210 8.682128 TTGAAAATTCGCTCAAAATATGTACC 57.318 30.769 0.00 0.00 0.00 3.34
217 223 9.400638 CGCTCAAAATATGTACCTTTTTAACAA 57.599 29.630 0.00 0.00 0.00 2.83
336 360 9.677567 AAATAGATTTATTTCACACACACACAC 57.322 29.630 0.00 0.00 35.10 3.82
337 361 6.691754 AGATTTATTTCACACACACACACA 57.308 33.333 0.00 0.00 0.00 3.72
338 362 6.494842 AGATTTATTTCACACACACACACAC 58.505 36.000 0.00 0.00 0.00 3.82
347 371 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
363 387 8.503196 ACACACACACACACATTAATTATACAG 58.497 33.333 0.00 0.00 0.00 2.74
547 587 8.146053 TCACCCATTAAAGAGAGAACTATTCA 57.854 34.615 0.00 0.00 0.00 2.57
611 670 9.898152 TCACATACTTACAATAATGTTCATGGA 57.102 29.630 0.00 0.00 41.05 3.41
618 677 6.630444 ACAATAATGTTCATGGATGAGAGC 57.370 37.500 0.00 0.00 35.91 4.09
646 705 2.881513 TGCCACATGCGAAGACTAAAAA 59.118 40.909 0.00 0.00 45.60 1.94
647 706 3.505680 TGCCACATGCGAAGACTAAAAAT 59.494 39.130 0.00 0.00 45.60 1.82
666 725 3.740397 TGCGGCTGCTGCACAATC 61.740 61.111 30.82 3.26 41.16 2.67
667 726 3.740397 GCGGCTGCTGCACAATCA 61.740 61.111 27.51 0.00 41.91 2.57
668 727 2.177531 CGGCTGCTGCACAATCAC 59.822 61.111 17.89 0.00 41.91 3.06
693 766 5.178809 CCTTCTACCCTAGTGTTTTGTTTCG 59.821 44.000 0.00 0.00 0.00 3.46
694 767 4.634199 TCTACCCTAGTGTTTTGTTTCGG 58.366 43.478 0.00 0.00 0.00 4.30
696 769 1.069500 CCCTAGTGTTTTGTTTCGGCG 60.069 52.381 0.00 0.00 0.00 6.46
697 770 1.069500 CCTAGTGTTTTGTTTCGGCGG 60.069 52.381 7.21 0.00 0.00 6.13
698 771 1.600485 CTAGTGTTTTGTTTCGGCGGT 59.400 47.619 7.21 0.00 0.00 5.68
699 772 0.099791 AGTGTTTTGTTTCGGCGGTG 59.900 50.000 7.21 0.00 0.00 4.94
700 773 0.179158 GTGTTTTGTTTCGGCGGTGT 60.179 50.000 7.21 0.00 0.00 4.16
701 774 0.099082 TGTTTTGTTTCGGCGGTGTC 59.901 50.000 7.21 0.00 0.00 3.67
702 775 0.099082 GTTTTGTTTCGGCGGTGTCA 59.901 50.000 7.21 0.00 0.00 3.58
713 786 0.944386 GCGGTGTCAAGTGTCAACAT 59.056 50.000 0.00 0.00 0.00 2.71
720 793 6.338146 GGTGTCAAGTGTCAACATATAGCTA 58.662 40.000 0.00 0.00 0.00 3.32
723 796 6.816640 TGTCAAGTGTCAACATATAGCTAACC 59.183 38.462 0.00 0.00 0.00 2.85
724 797 6.019801 GTCAAGTGTCAACATATAGCTAACCG 60.020 42.308 0.00 0.00 0.00 4.44
725 798 4.945246 AGTGTCAACATATAGCTAACCGG 58.055 43.478 0.00 0.00 0.00 5.28
820 1902 0.713883 GTGCGTCACTTGACATACCG 59.286 55.000 9.94 0.00 44.99 4.02
847 1929 3.935203 ACAAGCCAGAATCGTATTCTGTG 59.065 43.478 23.75 19.85 43.19 3.66
857 1939 4.386867 TCGTATTCTGTGTCCATCTTCC 57.613 45.455 0.00 0.00 0.00 3.46
858 1940 4.023980 TCGTATTCTGTGTCCATCTTCCT 58.976 43.478 0.00 0.00 0.00 3.36
859 1941 4.115516 CGTATTCTGTGTCCATCTTCCTG 58.884 47.826 0.00 0.00 0.00 3.86
864 1946 1.028868 GTGTCCATCTTCCTGCAGCC 61.029 60.000 8.66 0.00 0.00 4.85
882 1964 0.814010 CCAACGCTATTCCTTCCCGG 60.814 60.000 0.00 0.00 0.00 5.73
919 2001 2.556766 TCCACCATCACCCTACATGAA 58.443 47.619 0.00 0.00 0.00 2.57
980 2084 4.639171 GCCTAGCGAGCGAGCTCC 62.639 72.222 18.19 11.44 45.67 4.70
1575 2682 1.005340 GCAAGGATGAGTTCGAGCTG 58.995 55.000 6.48 0.00 0.00 4.24
1643 2750 4.758251 CATCGTGCCGTGGCTCCA 62.758 66.667 12.84 0.00 42.51 3.86
1746 2859 3.519930 GGAGGCGAGGAGACGGTC 61.520 72.222 0.00 0.00 0.00 4.79
1939 3052 1.323136 CGTCGCTGCTTGCTTTTTCG 61.323 55.000 0.00 0.00 40.11 3.46
1993 3106 0.786581 GAGACTGTCACGTGTGCATG 59.213 55.000 16.51 11.55 0.00 4.06
2014 3128 7.869937 TGCATGTCATTATTCCGAAAAGAAAAA 59.130 29.630 0.00 0.00 0.00 1.94
2033 3147 1.696063 ACCAAGTTTCATGTGCAGCT 58.304 45.000 0.00 0.00 0.00 4.24
2131 3249 8.344831 TGCATATCATTATTCGGAACAGAAAAG 58.655 33.333 0.00 0.00 33.43 2.27
2132 3250 7.324616 GCATATCATTATTCGGAACAGAAAAGC 59.675 37.037 0.00 0.00 33.43 3.51
2133 3251 5.216566 TCATTATTCGGAACAGAAAAGCG 57.783 39.130 0.00 0.00 33.43 4.68
2134 3252 4.693566 TCATTATTCGGAACAGAAAAGCGT 59.306 37.500 0.00 0.00 33.43 5.07
2135 3253 5.870433 TCATTATTCGGAACAGAAAAGCGTA 59.130 36.000 0.00 0.00 33.43 4.42
2136 3254 6.369340 TCATTATTCGGAACAGAAAAGCGTAA 59.631 34.615 0.00 0.00 33.43 3.18
2137 3255 6.730960 TTATTCGGAACAGAAAAGCGTAAT 57.269 33.333 0.00 0.00 33.43 1.89
2138 3256 5.622770 ATTCGGAACAGAAAAGCGTAATT 57.377 34.783 0.00 0.00 33.43 1.40
2139 3257 4.657075 TCGGAACAGAAAAGCGTAATTC 57.343 40.909 0.00 0.00 0.00 2.17
2140 3258 4.312443 TCGGAACAGAAAAGCGTAATTCT 58.688 39.130 0.00 0.00 36.35 2.40
2141 3259 4.753107 TCGGAACAGAAAAGCGTAATTCTT 59.247 37.500 0.00 0.00 33.73 2.52
2142 3260 5.237779 TCGGAACAGAAAAGCGTAATTCTTT 59.762 36.000 0.00 0.00 33.73 2.52
2143 3261 5.912955 CGGAACAGAAAAGCGTAATTCTTTT 59.087 36.000 3.68 3.68 43.91 2.27
2144 3262 7.041916 TCGGAACAGAAAAGCGTAATTCTTTTA 60.042 33.333 3.97 0.00 42.02 1.52
2145 3263 7.749126 CGGAACAGAAAAGCGTAATTCTTTTAT 59.251 33.333 3.97 0.00 42.02 1.40
2146 3264 9.406828 GGAACAGAAAAGCGTAATTCTTTTATT 57.593 29.630 3.97 1.08 42.02 1.40
2148 3266 8.655378 ACAGAAAAGCGTAATTCTTTTATTCG 57.345 30.769 3.97 0.00 42.02 3.34
2149 3267 7.749126 ACAGAAAAGCGTAATTCTTTTATTCGG 59.251 33.333 3.97 0.00 42.02 4.30
2150 3268 7.960738 CAGAAAAGCGTAATTCTTTTATTCGGA 59.039 33.333 3.97 0.00 42.02 4.55
2151 3269 8.508875 AGAAAAGCGTAATTCTTTTATTCGGAA 58.491 29.630 3.97 0.00 42.02 4.30
2152 3270 8.443898 AAAAGCGTAATTCTTTTATTCGGAAC 57.556 30.769 0.00 0.00 40.69 3.62
2153 3271 6.730960 AGCGTAATTCTTTTATTCGGAACA 57.269 33.333 0.00 0.00 0.00 3.18
2154 3272 6.772078 AGCGTAATTCTTTTATTCGGAACAG 58.228 36.000 0.00 0.00 0.00 3.16
2155 3273 6.592607 AGCGTAATTCTTTTATTCGGAACAGA 59.407 34.615 0.00 0.00 0.00 3.41
2156 3274 7.118680 AGCGTAATTCTTTTATTCGGAACAGAA 59.881 33.333 0.00 0.00 34.31 3.02
2157 3275 7.747357 GCGTAATTCTTTTATTCGGAACAGAAA 59.253 33.333 0.00 0.00 33.43 2.52
2158 3276 9.601971 CGTAATTCTTTTATTCGGAACAGAAAA 57.398 29.630 0.00 0.33 33.43 2.29
2160 3278 8.812147 AATTCTTTTATTCGGAACAGAAAACC 57.188 30.769 0.00 0.00 33.43 3.27
2161 3279 6.321848 TCTTTTATTCGGAACAGAAAACCC 57.678 37.500 0.00 0.00 33.43 4.11
2162 3280 4.752661 TTTATTCGGAACAGAAAACCCG 57.247 40.909 0.00 0.00 43.02 5.28
2164 3282 3.599412 TCGGAACAGAAAACCCGAG 57.401 52.632 0.00 0.00 45.04 4.63
2165 3283 0.601841 TCGGAACAGAAAACCCGAGC 60.602 55.000 0.00 0.00 45.04 5.03
2166 3284 1.866925 GGAACAGAAAACCCGAGCG 59.133 57.895 0.00 0.00 0.00 5.03
2167 3285 1.574702 GGAACAGAAAACCCGAGCGG 61.575 60.000 1.06 1.06 37.81 5.52
2168 3286 0.601841 GAACAGAAAACCCGAGCGGA 60.602 55.000 11.05 0.00 37.50 5.54
2169 3287 0.602905 AACAGAAAACCCGAGCGGAG 60.603 55.000 11.05 3.23 37.50 4.63
2170 3288 1.292223 CAGAAAACCCGAGCGGAGA 59.708 57.895 11.05 0.00 37.50 3.71
2171 3289 0.320421 CAGAAAACCCGAGCGGAGAA 60.320 55.000 11.05 0.00 37.50 2.87
2172 3290 0.395312 AGAAAACCCGAGCGGAGAAA 59.605 50.000 11.05 0.00 37.50 2.52
2173 3291 0.796927 GAAAACCCGAGCGGAGAAAG 59.203 55.000 11.05 0.00 37.50 2.62
2174 3292 0.108019 AAAACCCGAGCGGAGAAAGT 59.892 50.000 11.05 0.00 37.50 2.66
2175 3293 0.971386 AAACCCGAGCGGAGAAAGTA 59.029 50.000 11.05 0.00 37.50 2.24
2176 3294 0.971386 AACCCGAGCGGAGAAAGTAA 59.029 50.000 11.05 0.00 37.50 2.24
2177 3295 0.245813 ACCCGAGCGGAGAAAGTAAC 59.754 55.000 11.05 0.00 37.50 2.50
2178 3296 0.245539 CCCGAGCGGAGAAAGTAACA 59.754 55.000 11.05 0.00 37.50 2.41
2179 3297 1.347320 CCGAGCGGAGAAAGTAACAC 58.653 55.000 2.00 0.00 37.50 3.32
2180 3298 1.336517 CCGAGCGGAGAAAGTAACACA 60.337 52.381 2.00 0.00 37.50 3.72
2181 3299 2.607187 CGAGCGGAGAAAGTAACACAT 58.393 47.619 0.00 0.00 0.00 3.21
2182 3300 2.599082 CGAGCGGAGAAAGTAACACATC 59.401 50.000 0.00 0.00 0.00 3.06
2183 3301 3.673594 CGAGCGGAGAAAGTAACACATCT 60.674 47.826 0.00 0.00 0.00 2.90
2184 3302 4.246458 GAGCGGAGAAAGTAACACATCTT 58.754 43.478 0.00 0.00 0.00 2.40
2185 3303 4.246458 AGCGGAGAAAGTAACACATCTTC 58.754 43.478 0.00 0.00 0.00 2.87
2186 3304 3.994392 GCGGAGAAAGTAACACATCTTCA 59.006 43.478 0.00 0.00 0.00 3.02
2187 3305 4.451096 GCGGAGAAAGTAACACATCTTCAA 59.549 41.667 0.00 0.00 0.00 2.69
2188 3306 5.122396 GCGGAGAAAGTAACACATCTTCAAT 59.878 40.000 0.00 0.00 0.00 2.57
2189 3307 6.537566 CGGAGAAAGTAACACATCTTCAATG 58.462 40.000 0.00 0.00 0.00 2.82
2190 3308 6.317857 GGAGAAAGTAACACATCTTCAATGC 58.682 40.000 0.00 0.00 0.00 3.56
2191 3309 6.259550 AGAAAGTAACACATCTTCAATGCC 57.740 37.500 0.00 0.00 0.00 4.40
2192 3310 5.769662 AGAAAGTAACACATCTTCAATGCCA 59.230 36.000 0.00 0.00 0.00 4.92
2193 3311 5.633830 AAGTAACACATCTTCAATGCCAG 57.366 39.130 0.00 0.00 0.00 4.85
2194 3312 3.441572 AGTAACACATCTTCAATGCCAGC 59.558 43.478 0.00 0.00 0.00 4.85
2195 3313 0.806868 ACACATCTTCAATGCCAGCG 59.193 50.000 0.00 0.00 0.00 5.18
2232 3350 6.359804 ACAGCCATGTATGACAAATATGACT 58.640 36.000 1.70 0.00 38.09 3.41
2249 3367 1.002134 CTCCTCAAATGCCCGTGGT 60.002 57.895 0.00 0.00 0.00 4.16
2297 3422 1.905894 ACCGGGCATGCCTTAAATTTT 59.094 42.857 34.70 9.20 36.10 1.82
2305 3430 7.278868 CGGGCATGCCTTAAATTTTATTTGTTA 59.721 33.333 34.70 0.00 36.10 2.41
2394 3528 6.771749 ACATACTACGTTGATCCTAGCTACTT 59.228 38.462 3.44 0.00 0.00 2.24
2632 3843 2.032681 GGCAAACTCCGCCTCTGT 59.967 61.111 0.00 0.00 46.56 3.41
2703 3959 3.884318 GAGCCATCTCCTCCTCCC 58.116 66.667 0.00 0.00 33.19 4.30
2706 3962 2.525381 CCATCTCCTCCTCCCCCG 60.525 72.222 0.00 0.00 0.00 5.73
2707 3963 2.525381 CATCTCCTCCTCCCCCGG 60.525 72.222 0.00 0.00 0.00 5.73
2743 4022 3.535962 CTCCTCCTCCGGCTCTGC 61.536 72.222 0.00 0.00 0.00 4.26
2913 4195 4.530857 GAGCGTCCGACCATGGGG 62.531 72.222 18.09 8.84 41.29 4.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.735287 GCCCCGTGTCGTAGAGAAAC 60.735 60.000 0.00 0.00 36.95 2.78
2 3 0.896940 AGCCCCGTGTCGTAGAGAAA 60.897 55.000 0.00 0.00 36.95 2.52
4 5 0.463295 CTAGCCCCGTGTCGTAGAGA 60.463 60.000 0.00 0.00 36.95 3.10
5 6 1.445716 CCTAGCCCCGTGTCGTAGAG 61.446 65.000 0.00 0.00 36.95 2.43
20 21 1.939974 ACGCATGCACACATACCTAG 58.060 50.000 19.57 0.00 33.67 3.02
91 93 1.347378 TGCATCCCGCTCATAGCAATA 59.653 47.619 0.00 0.00 42.58 1.90
98 100 2.827423 CTCCTGCATCCCGCTCAT 59.173 61.111 0.00 0.00 43.06 2.90
104 106 2.134287 TAGACGGCTCCTGCATCCC 61.134 63.158 0.00 0.00 41.91 3.85
148 150 1.525619 GCACCTTAGTTAATAGCCGCG 59.474 52.381 0.00 0.00 0.00 6.46
262 268 9.926158 TTTACAACATGCATACAAATCAGATTT 57.074 25.926 0.00 2.20 0.00 2.17
315 339 6.196353 GTGTGTGTGTGTGTGTGAAATAAATC 59.804 38.462 0.00 0.00 0.00 2.17
327 351 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
328 352 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
329 353 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
330 354 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
331 355 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
332 356 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
333 357 1.819928 ATGTGTGTGTGTGTGTGTGT 58.180 45.000 0.00 0.00 0.00 3.72
334 358 2.917701 AATGTGTGTGTGTGTGTGTG 57.082 45.000 0.00 0.00 0.00 3.82
335 359 5.574891 AATTAATGTGTGTGTGTGTGTGT 57.425 34.783 0.00 0.00 0.00 3.72
336 360 8.286097 TGTATAATTAATGTGTGTGTGTGTGTG 58.714 33.333 0.00 0.00 0.00 3.82
337 361 8.384607 TGTATAATTAATGTGTGTGTGTGTGT 57.615 30.769 0.00 0.00 0.00 3.72
338 362 8.503196 ACTGTATAATTAATGTGTGTGTGTGTG 58.497 33.333 0.00 0.00 0.00 3.82
592 651 8.288208 GCTCTCATCCATGAACATTATTGTAAG 58.712 37.037 0.00 0.00 36.18 2.34
593 652 7.994911 AGCTCTCATCCATGAACATTATTGTAA 59.005 33.333 0.00 0.00 36.18 2.41
594 653 7.443272 CAGCTCTCATCCATGAACATTATTGTA 59.557 37.037 0.00 0.00 36.18 2.41
595 654 6.262496 CAGCTCTCATCCATGAACATTATTGT 59.738 38.462 0.00 0.00 36.18 2.71
596 655 6.485648 TCAGCTCTCATCCATGAACATTATTG 59.514 38.462 0.00 0.00 36.18 1.90
597 656 6.598503 TCAGCTCTCATCCATGAACATTATT 58.401 36.000 0.00 0.00 36.18 1.40
598 657 6.183810 TCAGCTCTCATCCATGAACATTAT 57.816 37.500 0.00 0.00 36.18 1.28
599 658 5.454329 CCTCAGCTCTCATCCATGAACATTA 60.454 44.000 0.00 0.00 36.18 1.90
600 659 4.452825 CTCAGCTCTCATCCATGAACATT 58.547 43.478 0.00 0.00 36.18 2.71
601 660 3.181453 CCTCAGCTCTCATCCATGAACAT 60.181 47.826 0.00 0.00 36.18 2.71
602 661 2.169978 CCTCAGCTCTCATCCATGAACA 59.830 50.000 0.00 0.00 36.18 3.18
603 662 2.170187 ACCTCAGCTCTCATCCATGAAC 59.830 50.000 0.00 0.00 36.18 3.18
604 663 2.475155 ACCTCAGCTCTCATCCATGAA 58.525 47.619 0.00 0.00 36.18 2.57
605 664 2.169978 CAACCTCAGCTCTCATCCATGA 59.830 50.000 0.00 0.00 35.16 3.07
606 665 2.562635 CAACCTCAGCTCTCATCCATG 58.437 52.381 0.00 0.00 0.00 3.66
607 666 1.134159 GCAACCTCAGCTCTCATCCAT 60.134 52.381 0.00 0.00 0.00 3.41
608 667 0.251354 GCAACCTCAGCTCTCATCCA 59.749 55.000 0.00 0.00 0.00 3.41
609 668 0.463474 GGCAACCTCAGCTCTCATCC 60.463 60.000 0.00 0.00 0.00 3.51
610 669 0.251354 TGGCAACCTCAGCTCTCATC 59.749 55.000 0.00 0.00 0.00 2.92
611 670 0.035630 GTGGCAACCTCAGCTCTCAT 60.036 55.000 0.00 0.00 0.00 2.90
612 671 1.372683 GTGGCAACCTCAGCTCTCA 59.627 57.895 0.00 0.00 0.00 3.27
618 677 1.236616 TTCGCATGTGGCAACCTCAG 61.237 55.000 6.39 0.00 45.17 3.35
666 725 4.202430 ACAAAACACTAGGGTAGAAGGGTG 60.202 45.833 0.00 0.00 0.00 4.61
667 726 3.978672 ACAAAACACTAGGGTAGAAGGGT 59.021 43.478 0.00 0.00 0.00 4.34
668 727 4.635699 ACAAAACACTAGGGTAGAAGGG 57.364 45.455 0.00 0.00 0.00 3.95
693 766 1.092921 TGTTGACACTTGACACCGCC 61.093 55.000 0.00 0.00 0.00 6.13
694 767 0.944386 ATGTTGACACTTGACACCGC 59.056 50.000 0.00 0.00 0.00 5.68
696 769 5.178797 AGCTATATGTTGACACTTGACACC 58.821 41.667 0.00 0.00 0.00 4.16
697 770 7.201530 GGTTAGCTATATGTTGACACTTGACAC 60.202 40.741 0.00 0.00 0.00 3.67
698 771 6.816640 GGTTAGCTATATGTTGACACTTGACA 59.183 38.462 0.00 0.00 0.00 3.58
699 772 6.019801 CGGTTAGCTATATGTTGACACTTGAC 60.020 42.308 0.00 0.00 0.00 3.18
700 773 6.040247 CGGTTAGCTATATGTTGACACTTGA 58.960 40.000 0.00 0.00 0.00 3.02
701 774 5.234329 CCGGTTAGCTATATGTTGACACTTG 59.766 44.000 0.00 0.00 0.00 3.16
702 775 5.128171 TCCGGTTAGCTATATGTTGACACTT 59.872 40.000 0.00 0.00 0.00 3.16
713 786 1.683943 ACTGCGTCCGGTTAGCTATA 58.316 50.000 16.54 0.28 0.00 1.31
847 1929 0.322816 TTGGCTGCAGGAAGATGGAC 60.323 55.000 17.12 0.00 0.00 4.02
864 1946 1.436983 GCCGGGAAGGAATAGCGTTG 61.437 60.000 2.18 0.00 45.00 4.10
870 1952 0.177141 CGACTTGCCGGGAAGGAATA 59.823 55.000 35.08 1.11 45.00 1.75
963 2067 4.639171 GGAGCTCGCTCGCTAGGC 62.639 72.222 7.83 0.00 43.59 3.93
992 2096 1.812922 GGCTCTGACATGGCAGTCG 60.813 63.158 27.68 19.96 41.41 4.18
993 2097 1.451028 GGGCTCTGACATGGCAGTC 60.451 63.158 27.68 19.45 37.20 3.51
994 2098 2.673523 GGGCTCTGACATGGCAGT 59.326 61.111 27.68 0.00 37.20 4.40
1053 2157 0.038526 ACACGTAGCACCAGTACAGC 60.039 55.000 0.00 0.00 0.00 4.40
1191 2295 3.997064 CTGGAAGAGCCGCTCGGTG 62.997 68.421 14.71 1.76 40.66 4.94
1401 2508 1.971695 GTTGGGGCCGGTGAAGAAG 60.972 63.158 1.90 0.00 0.00 2.85
1611 2718 0.525668 CGATGCAGTCGGAGTGGTAC 60.526 60.000 14.33 0.00 46.47 3.34
1643 2750 2.753029 GGCAGGAGTTGTGGAGCT 59.247 61.111 0.00 0.00 0.00 4.09
1683 2790 4.545706 TCATCACCGGCCGGCATC 62.546 66.667 43.58 11.20 39.32 3.91
1939 3052 4.369182 TCTCAAACGAGAAAGGAGACAAC 58.631 43.478 0.00 0.00 36.59 3.32
1993 3106 8.582433 TTGGTTTTTCTTTTCGGAATAATGAC 57.418 30.769 0.00 0.00 0.00 3.06
2014 3128 1.696063 AGCTGCACATGAAACTTGGT 58.304 45.000 0.00 0.00 0.00 3.67
2049 3167 8.988934 CACTGAAGTTTTAGCTCTGTACATAAA 58.011 33.333 0.00 0.00 0.00 1.40
2131 3249 6.768078 TCTGTTCCGAATAAAAGAATTACGC 58.232 36.000 0.00 0.00 0.00 4.42
2132 3250 9.601971 TTTTCTGTTCCGAATAAAAGAATTACG 57.398 29.630 0.00 0.00 0.00 3.18
2134 3252 9.902196 GGTTTTCTGTTCCGAATAAAAGAATTA 57.098 29.630 0.00 0.00 0.00 1.40
2135 3253 7.870954 GGGTTTTCTGTTCCGAATAAAAGAATT 59.129 33.333 0.00 0.00 0.00 2.17
2136 3254 7.375834 GGGTTTTCTGTTCCGAATAAAAGAAT 58.624 34.615 0.00 0.00 0.00 2.40
2137 3255 6.513720 CGGGTTTTCTGTTCCGAATAAAAGAA 60.514 38.462 0.00 0.00 44.69 2.52
2138 3256 5.049267 CGGGTTTTCTGTTCCGAATAAAAGA 60.049 40.000 0.00 0.00 44.69 2.52
2139 3257 5.049267 TCGGGTTTTCTGTTCCGAATAAAAG 60.049 40.000 0.00 0.00 46.93 2.27
2140 3258 4.820716 TCGGGTTTTCTGTTCCGAATAAAA 59.179 37.500 0.00 0.00 46.93 1.52
2141 3259 4.387598 TCGGGTTTTCTGTTCCGAATAAA 58.612 39.130 0.00 0.00 46.93 1.40
2142 3260 4.005487 TCGGGTTTTCTGTTCCGAATAA 57.995 40.909 0.00 0.00 46.93 1.40
2143 3261 3.681593 TCGGGTTTTCTGTTCCGAATA 57.318 42.857 0.00 0.00 46.93 1.75
2144 3262 2.554370 TCGGGTTTTCTGTTCCGAAT 57.446 45.000 0.00 0.00 46.93 3.34
2147 3265 1.866925 GCTCGGGTTTTCTGTTCCG 59.133 57.895 0.00 0.00 43.42 4.30
2148 3266 1.574702 CCGCTCGGGTTTTCTGTTCC 61.575 60.000 0.00 0.00 0.00 3.62
2149 3267 0.601841 TCCGCTCGGGTTTTCTGTTC 60.602 55.000 8.59 0.00 37.00 3.18
2150 3268 0.602905 CTCCGCTCGGGTTTTCTGTT 60.603 55.000 8.59 0.00 37.00 3.16
2151 3269 1.004918 CTCCGCTCGGGTTTTCTGT 60.005 57.895 8.59 0.00 37.00 3.41
2152 3270 0.320421 TTCTCCGCTCGGGTTTTCTG 60.320 55.000 8.59 0.00 37.00 3.02
2153 3271 0.395312 TTTCTCCGCTCGGGTTTTCT 59.605 50.000 8.59 0.00 37.00 2.52
2154 3272 0.796927 CTTTCTCCGCTCGGGTTTTC 59.203 55.000 8.59 0.00 37.00 2.29
2155 3273 0.108019 ACTTTCTCCGCTCGGGTTTT 59.892 50.000 8.59 0.00 37.00 2.43
2156 3274 0.971386 TACTTTCTCCGCTCGGGTTT 59.029 50.000 8.59 0.00 37.00 3.27
2157 3275 0.971386 TTACTTTCTCCGCTCGGGTT 59.029 50.000 8.59 0.00 37.00 4.11
2158 3276 0.245813 GTTACTTTCTCCGCTCGGGT 59.754 55.000 8.59 0.72 37.00 5.28
2159 3277 0.245539 TGTTACTTTCTCCGCTCGGG 59.754 55.000 8.59 0.00 35.59 5.14
2160 3278 1.336517 TGTGTTACTTTCTCCGCTCGG 60.337 52.381 1.14 1.14 0.00 4.63
2161 3279 2.060326 TGTGTTACTTTCTCCGCTCG 57.940 50.000 0.00 0.00 0.00 5.03
2162 3280 3.851098 AGATGTGTTACTTTCTCCGCTC 58.149 45.455 0.00 0.00 0.00 5.03
2163 3281 3.963428 AGATGTGTTACTTTCTCCGCT 57.037 42.857 0.00 0.00 0.00 5.52
2164 3282 3.994392 TGAAGATGTGTTACTTTCTCCGC 59.006 43.478 0.00 0.00 0.00 5.54
2165 3283 6.537566 CATTGAAGATGTGTTACTTTCTCCG 58.462 40.000 0.00 0.00 0.00 4.63
2166 3284 6.317857 GCATTGAAGATGTGTTACTTTCTCC 58.682 40.000 0.00 0.00 0.00 3.71
2167 3285 6.072508 TGGCATTGAAGATGTGTTACTTTCTC 60.073 38.462 0.00 0.00 0.00 2.87
2168 3286 5.769662 TGGCATTGAAGATGTGTTACTTTCT 59.230 36.000 0.00 0.00 0.00 2.52
2169 3287 6.012658 TGGCATTGAAGATGTGTTACTTTC 57.987 37.500 0.00 0.00 0.00 2.62
2170 3288 5.565439 GCTGGCATTGAAGATGTGTTACTTT 60.565 40.000 0.00 0.00 0.00 2.66
2171 3289 4.082571 GCTGGCATTGAAGATGTGTTACTT 60.083 41.667 0.00 0.00 0.00 2.24
2172 3290 3.441572 GCTGGCATTGAAGATGTGTTACT 59.558 43.478 0.00 0.00 0.00 2.24
2173 3291 3.728864 CGCTGGCATTGAAGATGTGTTAC 60.729 47.826 0.00 0.00 0.00 2.50
2174 3292 2.419673 CGCTGGCATTGAAGATGTGTTA 59.580 45.455 0.00 0.00 0.00 2.41
2175 3293 1.200716 CGCTGGCATTGAAGATGTGTT 59.799 47.619 0.00 0.00 0.00 3.32
2176 3294 0.806868 CGCTGGCATTGAAGATGTGT 59.193 50.000 0.00 0.00 0.00 3.72
2177 3295 0.524816 GCGCTGGCATTGAAGATGTG 60.525 55.000 0.00 0.00 39.62 3.21
2178 3296 0.679002 AGCGCTGGCATTGAAGATGT 60.679 50.000 10.39 0.00 43.41 3.06
2179 3297 0.454600 AAGCGCTGGCATTGAAGATG 59.545 50.000 12.58 0.00 43.41 2.90
2180 3298 1.945394 CTAAGCGCTGGCATTGAAGAT 59.055 47.619 12.58 0.00 43.41 2.40
2181 3299 1.066215 TCTAAGCGCTGGCATTGAAGA 60.066 47.619 12.58 1.26 43.41 2.87
2182 3300 1.329906 CTCTAAGCGCTGGCATTGAAG 59.670 52.381 12.58 0.00 43.41 3.02
2183 3301 1.372582 CTCTAAGCGCTGGCATTGAA 58.627 50.000 12.58 0.00 43.41 2.69
2184 3302 1.091771 GCTCTAAGCGCTGGCATTGA 61.092 55.000 12.58 0.00 43.41 2.57
2185 3303 1.354506 GCTCTAAGCGCTGGCATTG 59.645 57.895 12.58 0.00 43.41 2.82
2186 3304 0.465097 ATGCTCTAAGCGCTGGCATT 60.465 50.000 24.45 8.80 46.26 3.56
2187 3305 0.883814 GATGCTCTAAGCGCTGGCAT 60.884 55.000 27.79 27.79 46.26 4.40
2188 3306 1.522355 GATGCTCTAAGCGCTGGCA 60.522 57.895 22.74 22.74 46.26 4.92
2189 3307 0.032678 TAGATGCTCTAAGCGCTGGC 59.967 55.000 12.58 14.14 46.26 4.85
2190 3308 1.067669 TGTAGATGCTCTAAGCGCTGG 59.932 52.381 12.58 7.61 46.26 4.85
2191 3309 2.392821 CTGTAGATGCTCTAAGCGCTG 58.607 52.381 12.58 0.00 46.26 5.18
2192 3310 1.269517 GCTGTAGATGCTCTAAGCGCT 60.270 52.381 2.64 2.64 46.26 5.92
2193 3311 1.135867 GCTGTAGATGCTCTAAGCGC 58.864 55.000 0.00 0.00 46.26 5.92
2194 3312 1.067669 TGGCTGTAGATGCTCTAAGCG 59.932 52.381 13.88 0.00 46.26 4.68
2195 3313 2.898729 TGGCTGTAGATGCTCTAAGC 57.101 50.000 12.94 12.94 42.82 3.09
2215 3333 9.112725 CATTTGAGGAGTCATATTTGTCATACA 57.887 33.333 0.00 0.00 30.85 2.29
2216 3334 8.072567 GCATTTGAGGAGTCATATTTGTCATAC 58.927 37.037 0.00 0.00 30.85 2.39
2232 3350 1.002624 GACCACGGGCATTTGAGGA 60.003 57.895 0.00 0.00 0.00 3.71
2257 3375 3.760035 CTACCTGTGGACGCGCCT 61.760 66.667 18.14 0.00 37.63 5.52
2269 3387 3.031417 GCATGCCCGGTCACTACCT 62.031 63.158 6.36 0.00 44.35 3.08
2305 3430 8.766476 AGAATCAAATATGAGATATCCGGATGT 58.234 33.333 27.55 21.25 39.39 3.06
2380 3510 3.132160 CGACGAGAAGTAGCTAGGATCA 58.868 50.000 0.00 0.00 0.00 2.92
2561 3772 2.264455 GCCATCCTAGAGTCCATCCAT 58.736 52.381 0.00 0.00 0.00 3.41
2632 3843 0.033504 GACCTTCAACGTGGAGCAGA 59.966 55.000 0.00 0.00 0.00 4.26
2706 3962 2.123033 GGAGGAGGAGGAGGAGCC 60.123 72.222 0.00 0.00 0.00 4.70
2707 3963 1.152546 GAGGAGGAGGAGGAGGAGC 60.153 68.421 0.00 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.