Multiple sequence alignment - TraesCS1A01G345300

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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 TraesCS1A01G345300 chr1A 100.000 2967 0 0 1 2967 532735318 532732352 0.000000e+00 5480
1 TraesCS1A01G345300 chr1A 93.163 1960 94 13 1 1955 584970316 584972240 0.000000e+00 2841
2 TraesCS1A01G345300 chr1A 96.672 1262 33 3 1 1262 12307863 12309115 0.000000e+00 2089
3 TraesCS1A01G345300 chr1A 93.456 978 34 4 1299 2266 12309363 12310320 0.000000e+00 1424
4 TraesCS1A01G345300 chr1A 90.274 329 19 3 1949 2266 584972292 584972618 4.570000e-113 418
5 TraesCS1A01G345300 chr3A 96.842 2280 32 6 1 2270 698295944 698298193 0.000000e+00 3775
6 TraesCS1A01G345300 chr5A 96.484 2275 62 9 1 2266 673237896 673240161 0.000000e+00 3742
7 TraesCS1A01G345300 chr5A 90.909 319 23 4 1950 2266 566207713 566208027 9.830000e-115 424
8 TraesCS1A01G345300 chr5A 97.403 154 4 0 2814 2967 680118001 680118154 2.270000e-66 263
9 TraesCS1A01G345300 chr5A 96.711 152 5 0 2816 2967 100641994 100642145 1.360000e-63 254
10 TraesCS1A01G345300 chr2A 95.989 2269 75 10 1 2266 776173549 776175804 0.000000e+00 3672
11 TraesCS1A01G345300 chr2A 95.784 2277 70 10 1 2266 9951379 9953640 0.000000e+00 3650
12 TraesCS1A01G345300 chr7B 93.357 1957 89 13 1 1955 706976360 706974443 0.000000e+00 2856
13 TraesCS1A01G345300 chr7B 96.104 154 6 0 2814 2967 469741866 469741713 4.910000e-63 252
14 TraesCS1A01G345300 chr7B 80.368 326 46 11 1953 2266 670949046 670949365 6.400000e-57 231
15 TraesCS1A01G345300 chr7B 80.061 326 47 11 1953 2266 670907417 670907736 2.980000e-55 226
16 TraesCS1A01G345300 chr3B 92.755 1960 94 14 1 1955 772227381 772229297 0.000000e+00 2789
17 TraesCS1A01G345300 chr3B 95.597 159 6 1 2810 2967 750436322 750436480 1.360000e-63 254
18 TraesCS1A01G345300 chr5B 92.573 1939 102 16 23 1955 26737059 26735157 0.000000e+00 2745
19 TraesCS1A01G345300 chr5B 90.691 333 18 4 1949 2270 26735105 26734775 5.880000e-117 431
20 TraesCS1A01G345300 chrUn 94.080 946 45 5 1010 1955 117079696 117080630 0.000000e+00 1426
21 TraesCS1A01G345300 chrUn 92.125 927 59 7 1 925 117078754 117079668 0.000000e+00 1295
22 TraesCS1A01G345300 chrUn 90.625 160 15 0 2110 2269 45576525 45576366 2.320000e-51 213
23 TraesCS1A01G345300 chr1D 86.553 528 20 26 2274 2762 435145000 435144485 4.350000e-148 534
24 TraesCS1A01G345300 chr1B 85.493 517 33 21 2273 2762 588480844 588480343 4.410000e-138 501
25 TraesCS1A01G345300 chr1B 90.120 334 21 3 1949 2270 182060466 182060799 9.830000e-115 424
26 TraesCS1A01G345300 chr4D 97.368 152 4 0 2816 2967 213305490 213305339 2.930000e-65 259
27 TraesCS1A01G345300 chr5D 96.753 154 5 0 2814 2967 536591625 536591472 1.060000e-64 257
28 TraesCS1A01G345300 chr5D 96.753 154 5 0 2814 2967 536623538 536623385 1.060000e-64 257
29 TraesCS1A01G345300 chr2D 96.711 152 5 0 2816 2967 220344928 220344777 1.360000e-63 254
30 TraesCS1A01G345300 chr2D 80.122 327 51 10 1953 2266 6828259 6828584 6.400000e-57 231
31 TraesCS1A01G345300 chr7D 96.104 154 6 0 2814 2967 227049058 227048905 4.910000e-63 252
32 TraesCS1A01G345300 chr4A 80.066 301 49 8 1953 2247 636046766 636047061 2.320000e-51 213
33 TraesCS1A01G345300 chr2B 86.093 151 15 4 2110 2255 68604669 68604818 1.100000e-34 158


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 TraesCS1A01G345300 chr1A 532732352 532735318 2966 True 5480.0 5480 100.0000 1 2967 1 chr1A.!!$R1 2966
1 TraesCS1A01G345300 chr1A 12307863 12310320 2457 False 1756.5 2089 95.0640 1 2266 2 chr1A.!!$F1 2265
2 TraesCS1A01G345300 chr1A 584970316 584972618 2302 False 1629.5 2841 91.7185 1 2266 2 chr1A.!!$F2 2265
3 TraesCS1A01G345300 chr3A 698295944 698298193 2249 False 3775.0 3775 96.8420 1 2270 1 chr3A.!!$F1 2269
4 TraesCS1A01G345300 chr5A 673237896 673240161 2265 False 3742.0 3742 96.4840 1 2266 1 chr5A.!!$F3 2265
5 TraesCS1A01G345300 chr2A 776173549 776175804 2255 False 3672.0 3672 95.9890 1 2266 1 chr2A.!!$F2 2265
6 TraesCS1A01G345300 chr2A 9951379 9953640 2261 False 3650.0 3650 95.7840 1 2266 1 chr2A.!!$F1 2265
7 TraesCS1A01G345300 chr7B 706974443 706976360 1917 True 2856.0 2856 93.3570 1 1955 1 chr7B.!!$R2 1954
8 TraesCS1A01G345300 chr3B 772227381 772229297 1916 False 2789.0 2789 92.7550 1 1955 1 chr3B.!!$F2 1954
9 TraesCS1A01G345300 chr5B 26734775 26737059 2284 True 1588.0 2745 91.6320 23 2270 2 chr5B.!!$R1 2247
10 TraesCS1A01G345300 chrUn 117078754 117080630 1876 False 1360.5 1426 93.1025 1 1955 2 chrUn.!!$F1 1954
11 TraesCS1A01G345300 chr1D 435144485 435145000 515 True 534.0 534 86.5530 2274 2762 1 chr1D.!!$R1 488
12 TraesCS1A01G345300 chr1B 588480343 588480844 501 True 501.0 501 85.4930 2273 2762 1 chr1B.!!$R1 489

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
885 914 0.17899 GGAAGCGGGCCAAGGATTAT 60.179 55.0 4.39 0.0 0.0 1.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2768 3147 0.03601 AGCCATTGACGAACTCTGGG 60.036 55.0 0.0 0.0 0.0 4.45 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
218 221 1.352352 CTTCTCCCTTTCTCTGCCCAA 59.648 52.381 0.00 0.00 0.00 4.12
366 373 1.336517 CGAACGACAGGAGCAGGTAAA 60.337 52.381 0.00 0.00 0.00 2.01
507 530 6.168270 CTAGGCTAGCTAGGAAACAAGATT 57.832 41.667 22.10 0.00 0.00 2.40
651 674 7.118390 GTGCTTGATTGTGTAGACTGATTAGTT 59.882 37.037 0.00 0.00 37.25 2.24
746 773 3.253188 CGCAAGAATGGACAAGGAAAAGA 59.747 43.478 0.00 0.00 43.02 2.52
885 914 0.178990 GGAAGCGGGCCAAGGATTAT 60.179 55.000 4.39 0.00 0.00 1.28
1477 1726 3.719268 ATATGTGTGTCCAAGCTTCCA 57.281 42.857 0.00 0.00 0.00 3.53
2174 2486 2.125269 GAGCCGAGCCGCCTAAAA 60.125 61.111 0.00 0.00 0.00 1.52
2222 2549 0.671781 GCTTGAGAGCGAGCCAAAGA 60.672 55.000 0.00 0.00 44.34 2.52
2251 2578 1.888436 ATCAAACTCGGCTCGGCTCA 61.888 55.000 0.00 0.00 0.00 4.26
2270 2597 1.185618 AGCTCGTGTCCAGCCTTACA 61.186 55.000 0.00 0.00 37.63 2.41
2271 2598 0.737715 GCTCGTGTCCAGCCTTACAG 60.738 60.000 0.00 0.00 0.00 2.74
2314 2641 1.138883 GCCGTAGTCGATGCTGACA 59.861 57.895 7.00 0.00 41.41 3.58
2331 2658 0.597118 ACAAAACCTGCGCGTACGTA 60.597 50.000 17.90 3.04 42.83 3.57
2336 2663 3.011789 CTGCGCGTACGTAGCTCG 61.012 66.667 28.09 19.32 44.96 5.03
2338 2665 2.052414 GCGCGTACGTAGCTCGAT 60.052 61.111 23.63 0.95 42.83 3.59
2339 2666 2.068157 GCGCGTACGTAGCTCGATC 61.068 63.158 23.63 2.78 42.83 3.69
2374 2709 6.428159 AGATGTGAGGAAACAGTGTAATTCAC 59.572 38.462 16.80 16.80 46.46 3.18
2530 2874 2.860972 TAGCACATGCCGCCGCTAAA 62.861 55.000 0.00 0.00 43.38 1.85
2531 2875 2.874019 CACATGCCGCCGCTAAAA 59.126 55.556 0.00 0.00 35.36 1.52
2570 2918 9.760660 ACTCGTACGTTACACTAAATTAAGTAG 57.239 33.333 16.05 0.83 0.00 2.57
2571 2919 8.601243 TCGTACGTTACACTAAATTAAGTAGC 57.399 34.615 16.05 0.00 0.00 3.58
2572 2920 8.450964 TCGTACGTTACACTAAATTAAGTAGCT 58.549 33.333 16.05 0.00 0.00 3.32
2573 2921 9.702726 CGTACGTTACACTAAATTAAGTAGCTA 57.297 33.333 7.22 0.00 0.00 3.32
2581 2929 7.711339 ACACTAAATTAAGTAGCTAGGTCATGC 59.289 37.037 0.00 0.00 0.00 4.06
2582 2930 7.171678 CACTAAATTAAGTAGCTAGGTCATGCC 59.828 40.741 0.00 0.00 37.58 4.40
2595 2943 0.249868 TCATGCCTACGTAGCCATGC 60.250 55.000 31.57 22.63 0.00 4.06
2640 3010 6.422776 TGGAGACGAATCTTAATTCTTTGC 57.577 37.500 0.00 0.00 39.36 3.68
2651 3021 5.998981 TCTTAATTCTTTGCCTCGGTAAACA 59.001 36.000 0.00 0.00 0.00 2.83
2676 3055 4.923871 CGTATGATTAGCCAGTGGTACATC 59.076 45.833 11.74 9.92 44.52 3.06
2677 3056 5.508994 CGTATGATTAGCCAGTGGTACATCA 60.509 44.000 11.74 14.96 44.52 3.07
2727 3106 4.368808 CGCCGCGGTGTCAAACTG 62.369 66.667 30.21 0.00 38.30 3.16
2728 3107 3.276846 GCCGCGGTGTCAAACTGT 61.277 61.111 28.70 0.00 37.49 3.55
2729 3108 2.935955 CCGCGGTGTCAAACTGTC 59.064 61.111 19.50 0.00 37.49 3.51
2730 3109 1.885388 CCGCGGTGTCAAACTGTCA 60.885 57.895 19.50 0.00 37.49 3.58
2731 3110 1.433053 CCGCGGTGTCAAACTGTCAA 61.433 55.000 19.50 0.00 37.49 3.18
2767 3146 3.159353 CATGCATGCTGCTTGTATTGT 57.841 42.857 20.33 0.00 45.31 2.71
2768 3147 2.925578 TGCATGCTGCTTGTATTGTC 57.074 45.000 20.33 0.59 45.31 3.18
2769 3148 1.473677 TGCATGCTGCTTGTATTGTCC 59.526 47.619 20.33 0.00 45.31 4.02
2770 3149 1.202336 GCATGCTGCTTGTATTGTCCC 60.202 52.381 11.37 0.00 40.96 4.46
2771 3150 2.093890 CATGCTGCTTGTATTGTCCCA 58.906 47.619 7.32 0.00 0.00 4.37
2772 3151 1.825090 TGCTGCTTGTATTGTCCCAG 58.175 50.000 0.00 0.00 0.00 4.45
2773 3152 1.350684 TGCTGCTTGTATTGTCCCAGA 59.649 47.619 0.00 0.00 0.00 3.86
2774 3153 2.012673 GCTGCTTGTATTGTCCCAGAG 58.987 52.381 0.00 0.00 0.00 3.35
2775 3154 2.616510 GCTGCTTGTATTGTCCCAGAGT 60.617 50.000 0.00 0.00 0.00 3.24
2776 3155 3.679389 CTGCTTGTATTGTCCCAGAGTT 58.321 45.455 0.00 0.00 0.00 3.01
2777 3156 3.674997 TGCTTGTATTGTCCCAGAGTTC 58.325 45.455 0.00 0.00 0.00 3.01
2778 3157 2.673368 GCTTGTATTGTCCCAGAGTTCG 59.327 50.000 0.00 0.00 0.00 3.95
2779 3158 3.864921 GCTTGTATTGTCCCAGAGTTCGT 60.865 47.826 0.00 0.00 0.00 3.85
2780 3159 3.587797 TGTATTGTCCCAGAGTTCGTC 57.412 47.619 0.00 0.00 0.00 4.20
2781 3160 2.894765 TGTATTGTCCCAGAGTTCGTCA 59.105 45.455 0.00 0.00 0.00 4.35
2782 3161 3.322541 TGTATTGTCCCAGAGTTCGTCAA 59.677 43.478 0.00 0.00 0.00 3.18
2783 3162 3.703001 ATTGTCCCAGAGTTCGTCAAT 57.297 42.857 0.00 0.00 0.00 2.57
2784 3163 2.455674 TGTCCCAGAGTTCGTCAATG 57.544 50.000 0.00 0.00 0.00 2.82
2785 3164 1.001974 TGTCCCAGAGTTCGTCAATGG 59.998 52.381 0.00 0.00 0.00 3.16
2786 3165 0.036388 TCCCAGAGTTCGTCAATGGC 60.036 55.000 0.00 0.00 0.00 4.40
2787 3166 0.036010 CCCAGAGTTCGTCAATGGCT 60.036 55.000 0.00 0.00 0.00 4.75
2788 3167 1.363744 CCAGAGTTCGTCAATGGCTC 58.636 55.000 0.00 0.00 0.00 4.70
2789 3168 1.363744 CAGAGTTCGTCAATGGCTCC 58.636 55.000 0.00 0.00 0.00 4.70
2790 3169 0.108615 AGAGTTCGTCAATGGCTCCG 60.109 55.000 0.00 0.00 0.00 4.63
2791 3170 1.696832 GAGTTCGTCAATGGCTCCGC 61.697 60.000 0.00 0.00 0.00 5.54
2792 3171 1.741770 GTTCGTCAATGGCTCCGCT 60.742 57.895 0.00 0.00 0.00 5.52
2793 3172 1.741401 TTCGTCAATGGCTCCGCTG 60.741 57.895 0.00 0.00 0.00 5.18
2794 3173 3.197790 CGTCAATGGCTCCGCTGG 61.198 66.667 0.00 0.00 0.00 4.85
2795 3174 3.512516 GTCAATGGCTCCGCTGGC 61.513 66.667 0.00 0.00 0.00 4.85
2803 3182 3.136123 CTCCGCTGGCCACCATTG 61.136 66.667 0.00 0.00 30.82 2.82
2806 3185 4.124351 CGCTGGCCACCATTGCAG 62.124 66.667 13.69 3.64 30.82 4.41
2807 3186 2.677524 GCTGGCCACCATTGCAGA 60.678 61.111 0.00 0.00 30.82 4.26
2808 3187 2.056223 GCTGGCCACCATTGCAGAT 61.056 57.895 0.00 0.00 30.82 2.90
2809 3188 1.610554 GCTGGCCACCATTGCAGATT 61.611 55.000 0.00 0.00 30.82 2.40
2810 3189 0.899720 CTGGCCACCATTGCAGATTT 59.100 50.000 0.00 0.00 30.82 2.17
2811 3190 0.609151 TGGCCACCATTGCAGATTTG 59.391 50.000 0.00 0.00 0.00 2.32
2826 3205 4.495422 CAGATTTGCAGTACTACCTTCGT 58.505 43.478 0.00 0.00 0.00 3.85
2827 3206 4.929808 CAGATTTGCAGTACTACCTTCGTT 59.070 41.667 0.00 0.00 0.00 3.85
2828 3207 5.408604 CAGATTTGCAGTACTACCTTCGTTT 59.591 40.000 0.00 0.00 0.00 3.60
2829 3208 5.638234 AGATTTGCAGTACTACCTTCGTTTC 59.362 40.000 0.00 0.00 0.00 2.78
2830 3209 4.325028 TTGCAGTACTACCTTCGTTTCA 57.675 40.909 0.00 0.00 0.00 2.69
2831 3210 3.909430 TGCAGTACTACCTTCGTTTCAG 58.091 45.455 0.00 0.00 0.00 3.02
2832 3211 3.319972 TGCAGTACTACCTTCGTTTCAGT 59.680 43.478 0.00 0.00 0.00 3.41
2833 3212 4.202182 TGCAGTACTACCTTCGTTTCAGTT 60.202 41.667 0.00 0.00 0.00 3.16
2834 3213 4.748600 GCAGTACTACCTTCGTTTCAGTTT 59.251 41.667 0.00 0.00 0.00 2.66
2835 3214 5.922544 GCAGTACTACCTTCGTTTCAGTTTA 59.077 40.000 0.00 0.00 0.00 2.01
2836 3215 6.128982 GCAGTACTACCTTCGTTTCAGTTTAC 60.129 42.308 0.00 0.00 0.00 2.01
2837 3216 6.919662 CAGTACTACCTTCGTTTCAGTTTACA 59.080 38.462 0.00 0.00 0.00 2.41
2838 3217 7.436080 CAGTACTACCTTCGTTTCAGTTTACAA 59.564 37.037 0.00 0.00 0.00 2.41
2839 3218 6.839820 ACTACCTTCGTTTCAGTTTACAAG 57.160 37.500 0.00 0.00 0.00 3.16
2840 3219 6.343703 ACTACCTTCGTTTCAGTTTACAAGT 58.656 36.000 0.00 0.00 0.00 3.16
2841 3220 5.729974 ACCTTCGTTTCAGTTTACAAGTC 57.270 39.130 0.00 0.00 0.00 3.01
2842 3221 4.573607 ACCTTCGTTTCAGTTTACAAGTCC 59.426 41.667 0.00 0.00 0.00 3.85
2843 3222 4.814771 CCTTCGTTTCAGTTTACAAGTCCT 59.185 41.667 0.00 0.00 0.00 3.85
2844 3223 5.987347 CCTTCGTTTCAGTTTACAAGTCCTA 59.013 40.000 0.00 0.00 0.00 2.94
2845 3224 6.073927 CCTTCGTTTCAGTTTACAAGTCCTAC 60.074 42.308 0.00 0.00 0.00 3.18
2846 3225 4.977963 TCGTTTCAGTTTACAAGTCCTACG 59.022 41.667 0.00 0.00 0.00 3.51
2847 3226 4.375706 CGTTTCAGTTTACAAGTCCTACGC 60.376 45.833 0.00 0.00 0.00 4.42
2848 3227 2.937591 TCAGTTTACAAGTCCTACGCG 58.062 47.619 3.53 3.53 0.00 6.01
2849 3228 2.294233 TCAGTTTACAAGTCCTACGCGT 59.706 45.455 19.17 19.17 0.00 6.01
2850 3229 3.501828 TCAGTTTACAAGTCCTACGCGTA 59.498 43.478 19.40 19.40 0.00 4.42
2851 3230 4.156556 TCAGTTTACAAGTCCTACGCGTAT 59.843 41.667 20.91 5.41 0.00 3.06
2852 3231 5.353956 TCAGTTTACAAGTCCTACGCGTATA 59.646 40.000 20.91 8.44 0.00 1.47
2853 3232 6.038603 TCAGTTTACAAGTCCTACGCGTATAT 59.961 38.462 20.91 3.11 0.00 0.86
2854 3233 6.359087 CAGTTTACAAGTCCTACGCGTATATC 59.641 42.308 20.91 12.33 0.00 1.63
2855 3234 6.261826 AGTTTACAAGTCCTACGCGTATATCT 59.738 38.462 20.91 14.33 0.00 1.98
2856 3235 7.442364 AGTTTACAAGTCCTACGCGTATATCTA 59.558 37.037 20.91 0.00 0.00 1.98
2857 3236 5.859521 ACAAGTCCTACGCGTATATCTAG 57.140 43.478 20.91 8.56 0.00 2.43
2858 3237 4.694509 ACAAGTCCTACGCGTATATCTAGG 59.305 45.833 20.91 18.03 0.00 3.02
2859 3238 4.550076 AGTCCTACGCGTATATCTAGGT 57.450 45.455 20.91 0.00 0.00 3.08
2860 3239 4.904241 AGTCCTACGCGTATATCTAGGTT 58.096 43.478 20.91 8.23 0.00 3.50
2861 3240 4.694509 AGTCCTACGCGTATATCTAGGTTG 59.305 45.833 20.91 3.59 0.00 3.77
2862 3241 3.438087 TCCTACGCGTATATCTAGGTTGC 59.562 47.826 20.91 0.00 0.00 4.17
2863 3242 2.719426 ACGCGTATATCTAGGTTGCC 57.281 50.000 11.67 0.00 0.00 4.52
2864 3243 1.958579 ACGCGTATATCTAGGTTGCCA 59.041 47.619 11.67 0.00 0.00 4.92
2865 3244 2.363038 ACGCGTATATCTAGGTTGCCAA 59.637 45.455 11.67 0.00 0.00 4.52
2866 3245 3.006537 ACGCGTATATCTAGGTTGCCAAT 59.993 43.478 11.67 0.00 0.00 3.16
2867 3246 3.994392 CGCGTATATCTAGGTTGCCAATT 59.006 43.478 0.00 0.00 0.00 2.32
2868 3247 4.451096 CGCGTATATCTAGGTTGCCAATTT 59.549 41.667 0.00 0.00 0.00 1.82
2869 3248 5.049680 CGCGTATATCTAGGTTGCCAATTTT 60.050 40.000 0.00 0.00 0.00 1.82
2870 3249 6.146510 CGCGTATATCTAGGTTGCCAATTTTA 59.853 38.462 0.00 0.00 0.00 1.52
2871 3250 7.148474 CGCGTATATCTAGGTTGCCAATTTTAT 60.148 37.037 0.00 0.00 0.00 1.40
2872 3251 8.512138 GCGTATATCTAGGTTGCCAATTTTATT 58.488 33.333 0.00 0.00 0.00 1.40
2928 3307 7.668525 ATACCTTTTGAAAGTAGAAACTCCG 57.331 36.000 3.09 0.00 33.75 4.63
2929 3308 5.677567 ACCTTTTGAAAGTAGAAACTCCGA 58.322 37.500 3.09 0.00 33.75 4.55
2930 3309 6.117488 ACCTTTTGAAAGTAGAAACTCCGAA 58.883 36.000 3.09 0.00 33.75 4.30
2931 3310 6.260271 ACCTTTTGAAAGTAGAAACTCCGAAG 59.740 38.462 3.09 0.00 33.75 3.79
2932 3311 6.260271 CCTTTTGAAAGTAGAAACTCCGAAGT 59.740 38.462 3.09 0.00 33.75 3.01
2933 3312 7.201705 CCTTTTGAAAGTAGAAACTCCGAAGTT 60.202 37.037 3.09 0.00 39.62 2.66
2948 3327 9.457436 AACTCCGAAGTTTATGTTGGTATATTT 57.543 29.630 0.00 0.00 43.28 1.40
2949 3328 9.457436 ACTCCGAAGTTTATGTTGGTATATTTT 57.543 29.630 0.00 0.00 28.74 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
366 373 2.024846 TGGGAAGGAGAGAAGAGATCGT 60.025 50.000 0.00 0.00 0.00 3.73
487 510 4.770795 TCAATCTTGTTTCCTAGCTAGCC 58.229 43.478 15.74 3.43 0.00 3.93
488 511 5.238214 CCATCAATCTTGTTTCCTAGCTAGC 59.762 44.000 15.74 6.62 0.00 3.42
489 512 6.586344 TCCATCAATCTTGTTTCCTAGCTAG 58.414 40.000 14.20 14.20 0.00 3.42
490 513 6.560003 TCCATCAATCTTGTTTCCTAGCTA 57.440 37.500 0.00 0.00 0.00 3.32
491 514 5.441718 TCCATCAATCTTGTTTCCTAGCT 57.558 39.130 0.00 0.00 0.00 3.32
507 530 3.447229 TCAAACTCGTCTAGCATCCATCA 59.553 43.478 0.00 0.00 0.00 3.07
746 773 2.866515 TCTCCTCCTACTCTCCTTCCT 58.133 52.381 0.00 0.00 0.00 3.36
1477 1726 5.212532 TGGATAGCAAAAACAGCAAACAT 57.787 34.783 0.00 0.00 0.00 2.71
2046 2358 6.426646 AGACCAGTTTTGATCTTCTACAGT 57.573 37.500 0.00 0.00 0.00 3.55
2174 2486 2.345244 CTCAGCCAACGAGCCTGT 59.655 61.111 0.00 0.00 0.00 4.00
2222 2549 1.066573 CCGAGTTTGATCTGAGCCTGT 60.067 52.381 0.00 0.00 0.00 4.00
2230 2557 1.153549 GCCGAGCCGAGTTTGATCT 60.154 57.895 0.00 0.00 0.00 2.75
2251 2578 1.185618 TGTAAGGCTGGACACGAGCT 61.186 55.000 5.83 0.00 36.63 4.09
2300 2627 3.325870 CAGGTTTTGTCAGCATCGACTA 58.674 45.455 0.00 0.00 36.82 2.59
2314 2641 1.620413 GCTACGTACGCGCAGGTTTT 61.620 55.000 16.72 0.00 42.83 2.43
2331 2658 1.479730 TCTCAGTGCATTGATCGAGCT 59.520 47.619 12.75 0.00 0.00 4.09
2332 2659 1.931906 TCTCAGTGCATTGATCGAGC 58.068 50.000 12.75 0.00 0.00 5.03
2333 2660 3.245519 CACATCTCAGTGCATTGATCGAG 59.754 47.826 12.75 6.04 32.04 4.04
2335 2662 3.192466 TCACATCTCAGTGCATTGATCG 58.808 45.455 12.75 6.72 39.35 3.69
2336 2663 3.560481 CCTCACATCTCAGTGCATTGATC 59.440 47.826 12.75 0.00 39.35 2.92
2338 2665 2.568509 TCCTCACATCTCAGTGCATTGA 59.431 45.455 11.77 11.77 39.35 2.57
2339 2666 2.981898 TCCTCACATCTCAGTGCATTG 58.018 47.619 2.16 2.16 39.35 2.82
2379 2714 1.446272 GACAGCACCGGTGAGCTAC 60.446 63.158 38.30 19.53 39.50 3.58
2380 2715 2.970639 GACAGCACCGGTGAGCTA 59.029 61.111 38.30 0.00 39.50 3.32
2446 2790 4.803426 CGGTCGTGGCTGCTCCTC 62.803 72.222 0.00 0.00 35.26 3.71
2574 2922 4.752514 GGCTACGTAGGCATGACC 57.247 61.111 36.18 19.05 46.94 4.02
2581 2929 0.106708 ACATGGCATGGCTACGTAGG 59.893 55.000 29.49 8.34 33.60 3.18
2582 2930 2.404215 GTACATGGCATGGCTACGTAG 58.596 52.381 29.49 18.47 33.60 3.51
2583 2931 1.069513 GGTACATGGCATGGCTACGTA 59.930 52.381 29.49 14.88 33.60 3.57
2584 2932 0.179056 GGTACATGGCATGGCTACGT 60.179 55.000 29.49 15.84 33.60 3.57
2585 2933 0.884704 GGGTACATGGCATGGCTACG 60.885 60.000 29.49 10.83 33.60 3.51
2586 2934 0.182537 TGGGTACATGGCATGGCTAC 59.817 55.000 29.49 22.07 33.60 3.58
2587 2935 0.182537 GTGGGTACATGGCATGGCTA 59.817 55.000 29.49 12.56 33.60 3.93
2588 2936 1.076777 GTGGGTACATGGCATGGCT 60.077 57.895 29.49 13.59 33.60 4.75
2589 2937 1.076777 AGTGGGTACATGGCATGGC 60.077 57.895 29.49 20.92 33.60 4.40
2590 2938 0.255604 TCAGTGGGTACATGGCATGG 59.744 55.000 29.49 13.03 33.60 3.66
2595 2943 1.153369 CGCCTCAGTGGGTACATGG 60.153 63.158 0.00 0.00 36.00 3.66
2640 3010 5.051240 GCTAATCATACGTTGTTTACCGAGG 60.051 44.000 0.00 0.00 0.00 4.63
2651 3021 3.906720 ACCACTGGCTAATCATACGTT 57.093 42.857 0.00 0.00 0.00 3.99
2688 3067 3.344215 CGATCGGGAGCATGCAGC 61.344 66.667 21.98 11.35 46.19 5.25
2689 3068 1.953138 GTCGATCGGGAGCATGCAG 60.953 63.158 21.98 8.28 0.00 4.41
2690 3069 2.106938 GTCGATCGGGAGCATGCA 59.893 61.111 21.98 0.00 0.00 3.96
2691 3070 3.032609 CGTCGATCGGGAGCATGC 61.033 66.667 16.41 10.51 35.71 4.06
2726 3105 4.858680 TTGCACCGGCCGTTGACA 62.859 61.111 28.32 20.10 40.13 3.58
2727 3106 2.914908 ATTTGCACCGGCCGTTGAC 61.915 57.895 28.32 17.67 40.13 3.18
2728 3107 2.596046 ATTTGCACCGGCCGTTGA 60.596 55.556 28.32 5.85 40.13 3.18
2729 3108 2.430582 CATTTGCACCGGCCGTTG 60.431 61.111 26.12 22.89 40.13 4.10
2730 3109 4.356442 GCATTTGCACCGGCCGTT 62.356 61.111 26.12 6.99 41.59 4.44
2757 3136 2.673368 CGAACTCTGGGACAATACAAGC 59.327 50.000 0.00 0.00 38.70 4.01
2758 3137 3.926616 ACGAACTCTGGGACAATACAAG 58.073 45.455 0.00 0.00 38.70 3.16
2759 3138 3.322541 TGACGAACTCTGGGACAATACAA 59.677 43.478 0.00 0.00 38.70 2.41
2761 3140 3.587797 TGACGAACTCTGGGACAATAC 57.412 47.619 0.00 0.00 38.70 1.89
2762 3141 4.503910 CATTGACGAACTCTGGGACAATA 58.496 43.478 0.00 0.00 38.70 1.90
2763 3142 3.338249 CATTGACGAACTCTGGGACAAT 58.662 45.455 0.00 0.00 38.70 2.71
2764 3143 2.549992 CCATTGACGAACTCTGGGACAA 60.550 50.000 0.00 0.00 38.70 3.18
2765 3144 1.001974 CCATTGACGAACTCTGGGACA 59.998 52.381 0.00 0.00 0.00 4.02
2766 3145 1.726853 CCATTGACGAACTCTGGGAC 58.273 55.000 0.00 0.00 0.00 4.46
2767 3146 0.036388 GCCATTGACGAACTCTGGGA 60.036 55.000 0.00 0.00 0.00 4.37
2768 3147 0.036010 AGCCATTGACGAACTCTGGG 60.036 55.000 0.00 0.00 0.00 4.45
2769 3148 1.363744 GAGCCATTGACGAACTCTGG 58.636 55.000 0.00 0.00 0.00 3.86
2770 3149 1.363744 GGAGCCATTGACGAACTCTG 58.636 55.000 0.00 0.00 0.00 3.35
2771 3150 0.108615 CGGAGCCATTGACGAACTCT 60.109 55.000 0.00 0.00 0.00 3.24
2772 3151 2.373938 CGGAGCCATTGACGAACTC 58.626 57.895 0.00 0.00 0.00 3.01
2773 3152 4.598257 CGGAGCCATTGACGAACT 57.402 55.556 0.00 0.00 0.00 3.01
2786 3165 3.136123 CAATGGTGGCCAGCGGAG 61.136 66.667 28.67 16.90 36.75 4.63
2789 3168 4.124351 CTGCAATGGTGGCCAGCG 62.124 66.667 28.67 16.39 36.75 5.18
2790 3169 1.610554 AATCTGCAATGGTGGCCAGC 61.611 55.000 28.15 28.15 36.75 4.85
2791 3170 0.899720 AAATCTGCAATGGTGGCCAG 59.100 50.000 5.11 0.00 36.75 4.85
2792 3171 0.609151 CAAATCTGCAATGGTGGCCA 59.391 50.000 0.00 0.00 38.19 5.36
2793 3172 3.446507 CAAATCTGCAATGGTGGCC 57.553 52.632 0.00 0.00 0.00 5.36
2804 3183 4.495422 ACGAAGGTAGTACTGCAAATCTG 58.505 43.478 13.26 6.71 0.00 2.90
2805 3184 4.803098 ACGAAGGTAGTACTGCAAATCT 57.197 40.909 13.26 0.00 0.00 2.40
2806 3185 5.407387 TGAAACGAAGGTAGTACTGCAAATC 59.593 40.000 13.26 6.56 0.00 2.17
2807 3186 5.302360 TGAAACGAAGGTAGTACTGCAAAT 58.698 37.500 13.26 0.00 0.00 2.32
2808 3187 4.695396 TGAAACGAAGGTAGTACTGCAAA 58.305 39.130 13.26 0.00 0.00 3.68
2809 3188 4.202182 ACTGAAACGAAGGTAGTACTGCAA 60.202 41.667 13.26 0.00 0.00 4.08
2810 3189 3.319972 ACTGAAACGAAGGTAGTACTGCA 59.680 43.478 13.26 0.00 0.00 4.41
2811 3190 3.910648 ACTGAAACGAAGGTAGTACTGC 58.089 45.455 5.39 3.50 0.00 4.40
2812 3191 6.919662 TGTAAACTGAAACGAAGGTAGTACTG 59.080 38.462 5.39 0.00 0.00 2.74
2813 3192 7.042797 TGTAAACTGAAACGAAGGTAGTACT 57.957 36.000 0.00 0.00 0.00 2.73
2814 3193 7.436376 ACTTGTAAACTGAAACGAAGGTAGTAC 59.564 37.037 0.00 0.00 0.00 2.73
2815 3194 7.491682 ACTTGTAAACTGAAACGAAGGTAGTA 58.508 34.615 0.00 0.00 0.00 1.82
2816 3195 6.343703 ACTTGTAAACTGAAACGAAGGTAGT 58.656 36.000 0.00 0.00 0.00 2.73
2817 3196 6.073927 GGACTTGTAAACTGAAACGAAGGTAG 60.074 42.308 0.00 0.00 0.00 3.18
2818 3197 5.754890 GGACTTGTAAACTGAAACGAAGGTA 59.245 40.000 0.00 0.00 0.00 3.08
2819 3198 4.573607 GGACTTGTAAACTGAAACGAAGGT 59.426 41.667 0.00 0.00 0.00 3.50
2820 3199 4.814771 AGGACTTGTAAACTGAAACGAAGG 59.185 41.667 0.00 0.00 0.00 3.46
2821 3200 5.986004 AGGACTTGTAAACTGAAACGAAG 57.014 39.130 0.00 0.00 0.00 3.79
2822 3201 5.459762 CGTAGGACTTGTAAACTGAAACGAA 59.540 40.000 0.00 0.00 0.00 3.85
2823 3202 4.977963 CGTAGGACTTGTAAACTGAAACGA 59.022 41.667 0.00 0.00 0.00 3.85
2824 3203 4.375706 GCGTAGGACTTGTAAACTGAAACG 60.376 45.833 0.00 0.00 0.00 3.60
2825 3204 4.375706 CGCGTAGGACTTGTAAACTGAAAC 60.376 45.833 0.00 0.00 0.00 2.78
2826 3205 3.737266 CGCGTAGGACTTGTAAACTGAAA 59.263 43.478 0.00 0.00 0.00 2.69
2827 3206 3.243501 ACGCGTAGGACTTGTAAACTGAA 60.244 43.478 11.67 0.00 0.00 3.02
2828 3207 2.294233 ACGCGTAGGACTTGTAAACTGA 59.706 45.455 11.67 0.00 0.00 3.41
2829 3208 2.669364 ACGCGTAGGACTTGTAAACTG 58.331 47.619 11.67 0.00 0.00 3.16
2830 3209 4.708726 ATACGCGTAGGACTTGTAAACT 57.291 40.909 24.78 0.00 0.00 2.66
2831 3210 6.433766 AGATATACGCGTAGGACTTGTAAAC 58.566 40.000 24.78 8.64 0.00 2.01
2832 3211 6.624352 AGATATACGCGTAGGACTTGTAAA 57.376 37.500 24.78 0.00 0.00 2.01
2833 3212 6.369890 CCTAGATATACGCGTAGGACTTGTAA 59.630 42.308 24.78 0.00 34.99 2.41
2834 3213 5.871524 CCTAGATATACGCGTAGGACTTGTA 59.128 44.000 24.78 10.35 34.99 2.41
2835 3214 4.694509 CCTAGATATACGCGTAGGACTTGT 59.305 45.833 24.78 8.30 34.99 3.16
2836 3215 4.694509 ACCTAGATATACGCGTAGGACTTG 59.305 45.833 25.95 20.57 36.34 3.16
2837 3216 4.904241 ACCTAGATATACGCGTAGGACTT 58.096 43.478 25.95 11.92 36.34 3.01
2838 3217 4.550076 ACCTAGATATACGCGTAGGACT 57.450 45.455 25.95 22.48 36.34 3.85
2839 3218 4.671250 GCAACCTAGATATACGCGTAGGAC 60.671 50.000 25.95 17.64 36.34 3.85
2840 3219 3.438087 GCAACCTAGATATACGCGTAGGA 59.562 47.826 25.95 16.64 36.34 2.94
2841 3220 3.427233 GGCAACCTAGATATACGCGTAGG 60.427 52.174 24.78 21.85 38.45 3.18
2842 3221 3.189910 TGGCAACCTAGATATACGCGTAG 59.810 47.826 24.78 11.28 0.00 3.51
2843 3222 3.148412 TGGCAACCTAGATATACGCGTA 58.852 45.455 22.94 22.94 0.00 4.42
2844 3223 1.958579 TGGCAACCTAGATATACGCGT 59.041 47.619 19.17 19.17 0.00 6.01
2845 3224 2.717580 TGGCAACCTAGATATACGCG 57.282 50.000 3.53 3.53 0.00 6.01
2846 3225 5.941948 AAATTGGCAACCTAGATATACGC 57.058 39.130 0.00 0.00 0.00 4.42
2902 3281 9.211485 CGGAGTTTCTACTTTCAAAAGGTATAA 57.789 33.333 7.37 0.00 40.31 0.98
2903 3282 8.587608 TCGGAGTTTCTACTTTCAAAAGGTATA 58.412 33.333 7.37 0.00 40.31 1.47
2904 3283 7.447594 TCGGAGTTTCTACTTTCAAAAGGTAT 58.552 34.615 7.37 0.00 40.31 2.73
2905 3284 6.819284 TCGGAGTTTCTACTTTCAAAAGGTA 58.181 36.000 7.37 0.00 40.31 3.08
2906 3285 5.677567 TCGGAGTTTCTACTTTCAAAAGGT 58.322 37.500 7.37 0.00 40.31 3.50
2907 3286 6.260271 ACTTCGGAGTTTCTACTTTCAAAAGG 59.740 38.462 7.37 0.00 34.81 3.11
2908 3287 7.247929 ACTTCGGAGTTTCTACTTTCAAAAG 57.752 36.000 0.00 0.97 35.92 2.27
2909 3288 7.619964 AACTTCGGAGTTTCTACTTTCAAAA 57.380 32.000 2.29 0.00 43.48 2.44
2923 3302 9.457436 AAAATATACCAACATAAACTTCGGAGT 57.543 29.630 0.00 0.00 37.87 3.85


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

AutoCloner maintained by Alex Coulton.