Multiple sequence alignment - TraesCS5B01G366200

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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 TraesCS5B01G366200 chr5B 100.000 5301 0 0 1 5301 544910565 544905265 0.000000e+00 9790
1 TraesCS5B01G366200 chr5B 79.197 1245 166 42 3385 4564 544767407 544766191 0.000000e+00 778
2 TraesCS5B01G366200 chr5B 81.423 253 42 5 4311 4560 544813038 544812788 9.000000e-48 202
3 TraesCS5B01G366200 chr5D 87.085 2563 212 52 2618 5091 446758235 446755703 0.000000e+00 2789
4 TraesCS5B01G366200 chr5D 95.398 1282 47 9 1 1274 446760230 446758953 0.000000e+00 2030
5 TraesCS5B01G366200 chr5D 89.591 269 27 1 4175 4442 446684284 446684016 1.830000e-89 340
6 TraesCS5B01G366200 chr5D 78.556 471 73 19 1689 2140 446758421 446757960 8.690000e-73 285
7 TraesCS5B01G366200 chr5D 90.000 170 16 1 5133 5301 446755446 446755277 8.940000e-53 219
8 TraesCS5B01G366200 chr5D 81.781 247 40 5 4320 4563 446742680 446742436 9.000000e-48 202
9 TraesCS5B01G366200 chr5A 91.197 1579 95 10 3324 4878 564596452 564594894 0.000000e+00 2106
10 TraesCS5B01G366200 chr5A 95.469 1280 40 10 1 1274 564601325 564600058 0.000000e+00 2026
11 TraesCS5B01G366200 chr5A 93.868 1109 54 12 2219 3324 564599069 564597972 0.000000e+00 1659
12 TraesCS5B01G366200 chr5A 87.848 395 27 7 4910 5301 564594898 564594522 1.350000e-120 444
13 TraesCS5B01G366200 chr5A 88.462 234 24 3 4156 4389 564536138 564535908 4.040000e-71 279
14 TraesCS5B01G366200 chr5A 92.481 133 10 0 4175 4307 564582687 564582555 1.950000e-44 191
15 TraesCS5B01G366200 chr5A 80.972 247 42 5 4320 4563 564589693 564589449 1.950000e-44 191
16 TraesCS5B01G366200 chr5A 88.235 153 17 1 4291 4442 564580064 564579912 1.170000e-41 182
17 TraesCS5B01G366200 chr6B 94.167 1200 54 8 1222 2416 655218660 655217472 0.000000e+00 1814
18 TraesCS5B01G366200 chr6B 94.049 857 35 8 1562 2413 380971697 380972542 0.000000e+00 1286
19 TraesCS5B01G366200 chr2B 93.985 1197 56 8 1222 2413 472575384 472576569 0.000000e+00 1797
20 TraesCS5B01G366200 chr2B 94.166 857 33 8 1562 2413 103485718 103486562 0.000000e+00 1290
21 TraesCS5B01G366200 chr3B 93.488 860 39 9 1562 2416 778613877 778613030 0.000000e+00 1262
22 TraesCS5B01G366200 chr3B 84.562 434 61 6 4870 5299 726991822 726992253 4.910000e-115 425
23 TraesCS5B01G366200 chr3D 84.758 433 61 5 4870 5299 136750995 136751425 3.790000e-116 429
24 TraesCS5B01G366200 chr2D 84.065 433 64 5 4870 5299 106377422 106376992 3.820000e-111 412
25 TraesCS5B01G366200 chr4B 91.209 273 12 5 2146 2413 630238171 630238436 1.400000e-95 361
26 TraesCS5B01G366200 chr4B 94.737 190 6 3 1562 1751 630237991 630238176 5.190000e-75 292
27 TraesCS5B01G366200 chr4A 81.293 433 72 7 4870 5299 252715911 252716337 5.080000e-90 342
28 TraesCS5B01G366200 chr4D 80.876 434 71 9 4870 5299 268064550 268064125 1.100000e-86 331


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 TraesCS5B01G366200 chr5B 544905265 544910565 5300 True 9790.00 9790 100.00000 1 5301 1 chr5B.!!$R3 5300
1 TraesCS5B01G366200 chr5B 544766191 544767407 1216 True 778.00 778 79.19700 3385 4564 1 chr5B.!!$R1 1179
2 TraesCS5B01G366200 chr5D 446755277 446760230 4953 True 1330.75 2789 87.75975 1 5301 4 chr5D.!!$R3 5300
3 TraesCS5B01G366200 chr5A 564594522 564601325 6803 True 1558.75 2106 92.09550 1 5301 4 chr5A.!!$R4 5300
4 TraesCS5B01G366200 chr6B 655217472 655218660 1188 True 1814.00 1814 94.16700 1222 2416 1 chr6B.!!$R1 1194
5 TraesCS5B01G366200 chr6B 380971697 380972542 845 False 1286.00 1286 94.04900 1562 2413 1 chr6B.!!$F1 851
6 TraesCS5B01G366200 chr2B 472575384 472576569 1185 False 1797.00 1797 93.98500 1222 2413 1 chr2B.!!$F2 1191
7 TraesCS5B01G366200 chr2B 103485718 103486562 844 False 1290.00 1290 94.16600 1562 2413 1 chr2B.!!$F1 851
8 TraesCS5B01G366200 chr3B 778613030 778613877 847 True 1262.00 1262 93.48800 1562 2416 1 chr3B.!!$R1 854

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
938 943 0.469892 CCAGCCCAACCCAACTTCTT 60.470 55.000 0.00 0.00 0.00 2.52 F
2504 2755 0.107017 TATGAGCTGCTGCCCCTTTC 60.107 55.000 7.01 3.45 40.80 2.62 F
2568 2819 1.136891 GTCAAGCTTGGGTGCAAAACT 59.863 47.619 25.73 0.00 34.99 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2551 2802 2.235898 TGAAAGTTTTGCACCCAAGCTT 59.764 40.909 0.00 0.0 32.90 3.74 R
3504 5287 0.180642 CAGCTGGCATGGATGTCTCT 59.819 55.000 5.57 0.0 32.56 3.10 R
4363 6211 0.251297 TGGCACAGGGGAAATCAGTG 60.251 55.000 0.00 0.0 0.00 3.66 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
30 31 1.815212 CTGATTCTGTGATCGCCGCG 61.815 60.000 6.39 6.39 0.00 6.46
57 58 4.063529 CCACTCGTGGCAATGTGT 57.936 55.556 2.72 3.28 44.73 3.72
58 59 1.575922 CCACTCGTGGCAATGTGTG 59.424 57.895 8.30 8.30 44.73 3.82
208 209 1.067425 CAGCCACAACCATCAACCATG 60.067 52.381 0.00 0.00 0.00 3.66
229 230 2.733026 GACAACCAAAATGCAGCACATC 59.267 45.455 0.00 0.00 38.34 3.06
244 245 0.739561 ACATCCTACTTCTCGCGGTC 59.260 55.000 6.13 0.00 0.00 4.79
273 274 4.260538 GGCATCTGATCGTCAGTGAAATTC 60.261 45.833 12.62 0.00 44.58 2.17
398 400 4.653888 CCGGCGAGGTTGGGGTTT 62.654 66.667 9.30 0.00 34.51 3.27
503 505 3.296709 GAGGAGCGCGGAGTGGAAA 62.297 63.158 8.83 0.00 39.19 3.13
865 870 1.160137 CGGAAGGAAGGAAGCAACTG 58.840 55.000 0.00 0.00 0.00 3.16
873 878 3.261137 GGAAGGAAGCAACTGGTAGTAGT 59.739 47.826 0.00 0.00 0.00 2.73
896 901 1.450312 CAGAAGCTGGCCCGTTAGG 60.450 63.158 0.00 0.00 39.47 2.69
934 939 4.621087 GCCCAGCCCAACCCAACT 62.621 66.667 0.00 0.00 0.00 3.16
935 940 2.201210 CCCAGCCCAACCCAACTT 59.799 61.111 0.00 0.00 0.00 2.66
938 943 0.469892 CCAGCCCAACCCAACTTCTT 60.470 55.000 0.00 0.00 0.00 2.52
939 944 0.961753 CAGCCCAACCCAACTTCTTC 59.038 55.000 0.00 0.00 0.00 2.87
940 945 0.853530 AGCCCAACCCAACTTCTTCT 59.146 50.000 0.00 0.00 0.00 2.85
954 960 0.683504 TCTTCTCTCCTACCGGCACC 60.684 60.000 0.00 0.00 0.00 5.01
973 984 1.045911 CGAAGGAGGAGGAAGAGGGG 61.046 65.000 0.00 0.00 0.00 4.79
1290 1325 3.400054 CTTCGACTCCCCCACCCC 61.400 72.222 0.00 0.00 0.00 4.95
1325 1361 5.090139 ACTAATCGATCTTGGGAGGATGAT 58.910 41.667 0.00 0.00 0.00 2.45
1354 1402 2.760650 GTTGGAGTTGGATTTGGGGATC 59.239 50.000 0.00 0.00 0.00 3.36
1415 1481 6.534793 CCGATTTCTTGGGTAAATGAAATTGG 59.465 38.462 15.06 15.06 45.80 3.16
1416 1482 7.319646 CGATTTCTTGGGTAAATGAAATTGGA 58.680 34.615 0.00 0.00 38.67 3.53
1480 1547 1.876664 GAACAGCCGAGCCCTTTTC 59.123 57.895 0.00 0.00 0.00 2.29
1500 1567 4.855715 TCGCTCCGAAATCTATCAGAAT 57.144 40.909 0.00 0.00 31.06 2.40
1501 1568 5.201713 TCGCTCCGAAATCTATCAGAATT 57.798 39.130 0.00 0.00 31.06 2.17
1611 1689 7.602644 TGTTAGTTTACTATGTTCCAGCTTGAG 59.397 37.037 0.00 0.00 0.00 3.02
1633 1711 4.857037 AGAGTTTCGTTTGTTCAAAGTTGC 59.143 37.500 0.00 0.00 0.00 4.17
1687 1847 6.538021 AGCATCCAGATAATTATCATTCGAGC 59.462 38.462 24.00 18.96 35.17 5.03
1700 1860 1.145759 TTCGAGCGATAAAGGCTGCG 61.146 55.000 0.00 0.00 41.72 5.18
1788 1952 3.006110 CAGATCTTTTGTGCCATGTTGGT 59.994 43.478 0.00 0.00 40.46 3.67
1856 2037 2.226200 TGTGTTGTGAATCAGCGAATGG 59.774 45.455 0.00 0.00 0.00 3.16
1995 2188 7.039011 AGTGTGTGTATTGTCTAGATTCTTGGA 60.039 37.037 0.00 0.00 0.00 3.53
2038 2231 8.271458 TCCCATTTATATTAGCAACTCAGTTCA 58.729 33.333 0.00 0.00 0.00 3.18
2083 2276 5.032220 CCTTTGGTCGTTGTTTGACTAAAC 58.968 41.667 1.28 0.00 40.44 2.01
2103 2296 4.173036 ACAATAACAAGGAATTGGCGTG 57.827 40.909 0.00 0.00 37.40 5.34
2171 2407 5.714806 GGTCTGAATTCCCATTTCCAAACTA 59.285 40.000 2.27 0.00 0.00 2.24
2183 2419 6.985059 CCATTTCCAAACTACTAGCCTAGTAC 59.015 42.308 7.53 0.00 40.14 2.73
2251 2494 4.920640 ATATGTACCTGAGAAGTGGTCG 57.079 45.455 0.00 0.00 37.74 4.79
2271 2514 5.911838 GGTCGGACAGTTATATCGAACTTAC 59.088 44.000 10.76 0.00 37.57 2.34
2362 2613 0.768622 ACCGTTTTCCTGGACCATGA 59.231 50.000 0.00 0.00 0.00 3.07
2405 2656 4.770010 GGTTTCCACTTTCCATGGTGATTA 59.230 41.667 12.58 0.00 38.47 1.75
2449 2700 5.796350 TTTCTAGAAAATAGCTTCCGCAC 57.204 39.130 15.57 0.00 39.10 5.34
2463 2714 4.678309 GCTTCCGCACTTACAGAGTATTCT 60.678 45.833 0.00 0.00 36.65 2.40
2504 2755 0.107017 TATGAGCTGCTGCCCCTTTC 60.107 55.000 7.01 3.45 40.80 2.62
2533 2784 5.616270 TGCCTGACAAACTTAATGTAGTCA 58.384 37.500 0.00 0.00 39.70 3.41
2551 2802 8.669946 TGTAGTCAAACACTTGATAAATGTCA 57.330 30.769 0.00 0.00 43.39 3.58
2568 2819 1.136891 GTCAAGCTTGGGTGCAAAACT 59.863 47.619 25.73 0.00 34.99 2.66
2578 2829 3.764434 TGGGTGCAAAACTTTCAGTTACA 59.236 39.130 0.00 0.00 37.47 2.41
2625 2876 8.400186 TCAAATACTGAAATGACATGTGCTATG 58.600 33.333 1.15 0.79 0.00 2.23
2657 2909 1.149101 AGCCAAAAGTTCCTCCTGGA 58.851 50.000 0.00 0.00 41.36 3.86
2675 2927 4.887071 CCTGGAATCGGAAAATGACCATTA 59.113 41.667 0.00 0.00 0.00 1.90
2693 2945 9.982651 TGACCATTATATAGCTAGAAACACTTC 57.017 33.333 0.00 0.00 0.00 3.01
2705 2957 4.461198 AGAAACACTTCATCCGTTCCTTT 58.539 39.130 0.00 0.00 33.64 3.11
2828 3080 5.184096 TCAGCCTTTTGTTGTTGTTTGACTA 59.816 36.000 0.00 0.00 0.00 2.59
2854 3106 5.003096 ACAAGGAATTGGTCTTCCATCTT 57.997 39.130 5.70 0.00 46.02 2.40
2862 3114 3.242867 TGGTCTTCCATCTTGAGACAGT 58.757 45.455 5.26 0.00 41.15 3.55
2877 3129 5.912892 TGAGACAGTGTACATGAAAGAACA 58.087 37.500 0.00 0.00 0.00 3.18
2975 3227 4.899502 AGTAGTTCTGTCCTCACAATTGG 58.100 43.478 10.83 0.00 29.82 3.16
3013 3265 2.878406 ACATTTCTTGGTCAGACGGTTG 59.122 45.455 0.00 0.00 0.00 3.77
3020 3272 3.313012 TGGTCAGACGGTTGTATTGAG 57.687 47.619 0.00 0.00 0.00 3.02
3029 3281 3.933332 ACGGTTGTATTGAGCTTAGCTTC 59.067 43.478 8.58 2.43 39.88 3.86
3030 3282 4.184629 CGGTTGTATTGAGCTTAGCTTCT 58.815 43.478 8.58 0.00 39.88 2.85
3031 3283 4.268884 CGGTTGTATTGAGCTTAGCTTCTC 59.731 45.833 8.58 0.00 39.88 2.87
3032 3284 5.423886 GGTTGTATTGAGCTTAGCTTCTCT 58.576 41.667 8.58 0.00 39.88 3.10
3035 3287 6.286240 TGTATTGAGCTTAGCTTCTCTTGA 57.714 37.500 8.58 0.00 39.88 3.02
3041 3293 4.967036 AGCTTAGCTTCTCTTGAACTTGT 58.033 39.130 0.00 0.00 33.89 3.16
3055 3307 7.568349 TCTTGAACTTGTAGATGCTGGATAAT 58.432 34.615 0.00 0.00 0.00 1.28
3065 3317 9.851686 TGTAGATGCTGGATAATTATTCAGTTT 57.148 29.630 27.35 18.21 40.67 2.66
3103 3355 5.739752 TGATAATCACATAACACTGCTGC 57.260 39.130 0.00 0.00 0.00 5.25
3235 3491 4.225042 ACAGCCATGTTGACTTATGACCTA 59.775 41.667 1.85 0.00 35.63 3.08
3246 3502 3.200165 ACTTATGACCTACTGCCCCTTTC 59.800 47.826 0.00 0.00 0.00 2.62
3324 3580 5.566623 CAAGCACTGCACTATCAAATACTG 58.433 41.667 3.30 0.00 0.00 2.74
3325 3581 5.089970 AGCACTGCACTATCAAATACTGA 57.910 39.130 3.30 0.00 38.81 3.41
3326 3582 5.491070 AGCACTGCACTATCAAATACTGAA 58.509 37.500 3.30 0.00 37.67 3.02
3327 3583 5.939883 AGCACTGCACTATCAAATACTGAAA 59.060 36.000 3.30 0.00 37.67 2.69
3329 3585 6.690098 GCACTGCACTATCAAATACTGAAATG 59.310 38.462 0.00 0.00 37.67 2.32
3330 3586 7.191551 CACTGCACTATCAAATACTGAAATGG 58.808 38.462 0.00 0.00 37.67 3.16
3331 3587 6.135290 TGCACTATCAAATACTGAAATGGC 57.865 37.500 0.00 0.00 37.67 4.40
3445 5226 4.320641 GCTACCGTTTGCCTTTGAAATGTA 60.321 41.667 0.00 0.00 0.00 2.29
3450 5231 5.799936 CCGTTTGCCTTTGAAATGTATACAG 59.200 40.000 11.91 0.00 0.00 2.74
3504 5287 5.324409 ACAAAGGATAGAAAGATGTTGGCA 58.676 37.500 0.00 0.00 0.00 4.92
3515 5298 2.928334 GATGTTGGCAGAGACATCCAT 58.072 47.619 16.44 0.00 43.92 3.41
3569 5352 2.084546 GAGTTGTGTACCATTGGAGGC 58.915 52.381 10.37 0.00 0.00 4.70
3832 5661 5.602978 TCTCTTCAGAACTGGGGTATTATCC 59.397 44.000 1.93 0.00 0.00 2.59
3853 5682 2.263077 CAGATGTACGCAAGAGTGGAC 58.737 52.381 0.00 0.00 39.62 4.02
3854 5683 2.094494 CAGATGTACGCAAGAGTGGACT 60.094 50.000 0.00 0.00 39.89 3.85
3939 5780 5.415701 TGAAGTATGGTGCCTTTTGAAGATC 59.584 40.000 0.00 0.00 0.00 2.75
4041 5887 6.481976 TCGAACAACTTACATGATTGTCACTT 59.518 34.615 0.00 0.00 35.54 3.16
4046 5892 7.064609 ACAACTTACATGATTGTCACTTATCGG 59.935 37.037 0.00 0.00 37.28 4.18
4059 5905 2.355132 ACTTATCGGCTAGTCACAGTCG 59.645 50.000 0.00 0.00 44.89 4.18
4070 5916 3.141398 AGTCACAGTCGCATCACATTTT 58.859 40.909 0.00 0.00 0.00 1.82
4071 5917 3.058708 AGTCACAGTCGCATCACATTTTG 60.059 43.478 0.00 0.00 0.00 2.44
4106 5952 6.536582 TGATTTCTTCGGAGTTCTCATTGATC 59.463 38.462 2.24 0.00 0.00 2.92
4119 5966 1.583856 CATTGATCGACGTCTTGACGG 59.416 52.381 23.99 9.92 36.39 4.79
4127 5974 2.479049 CGACGTCTTGACGGTTATCCAT 60.479 50.000 23.99 3.60 37.45 3.41
4130 5977 2.418197 CGTCTTGACGGTTATCCATGGT 60.418 50.000 12.58 1.59 0.00 3.55
4253 6101 0.318955 CCGGAAAAGGCAAGCAAGTG 60.319 55.000 0.00 0.00 0.00 3.16
4310 6158 2.344025 CTAGGTTTTAGCACGGACCAC 58.656 52.381 0.00 0.00 34.60 4.16
4323 6171 2.640826 ACGGACCACTTAAAGGGATTCA 59.359 45.455 0.00 0.00 0.00 2.57
4363 6211 3.296322 TCGTCATGCCATTTTGGTTTC 57.704 42.857 0.00 0.00 40.46 2.78
4364 6212 2.625314 TCGTCATGCCATTTTGGTTTCA 59.375 40.909 0.00 0.00 40.46 2.69
4390 6238 2.917713 TCCCCTGTGCCATTGTAATT 57.082 45.000 0.00 0.00 0.00 1.40
4404 6253 7.095816 TGCCATTGTAATTTATCTATCGACACG 60.096 37.037 0.00 0.00 0.00 4.49
4446 6295 1.270625 TGGCAGGACTAGAAAACCACG 60.271 52.381 0.00 0.00 0.00 4.94
4549 6402 4.919754 GTGCCTTTTTCTTTATCACAGCAG 59.080 41.667 0.00 0.00 0.00 4.24
4714 6567 5.636903 ATCTATTGGCACTAACATCCTGT 57.363 39.130 0.00 0.00 0.00 4.00
4717 6570 2.768253 TGGCACTAACATCCTGTGAG 57.232 50.000 0.00 0.00 34.91 3.51
4794 6647 5.193099 ACCAATGGCCTACTAAATGAACT 57.807 39.130 3.32 0.00 0.00 3.01
4801 6654 9.646522 AATGGCCTACTAAATGAACTGATAATT 57.353 29.630 3.32 0.00 0.00 1.40
4810 6663 4.200838 TGAACTGATAATTCGGCACTCA 57.799 40.909 0.00 0.00 0.00 3.41
4825 6678 0.597637 ACTCACAAGAGACAACGGCG 60.598 55.000 4.80 4.80 44.98 6.46
4855 6708 4.442706 AGTAATCTGGCACTCGTAAATGG 58.557 43.478 0.00 0.00 0.00 3.16
4865 6718 3.927142 CACTCGTAAATGGTGAGAAGTCC 59.073 47.826 0.00 0.00 33.93 3.85
4888 6741 1.605712 GGAGCGACCTTATTGATCCCG 60.606 57.143 0.00 0.00 40.99 5.14
4891 6744 1.068741 GCGACCTTATTGATCCCGACT 59.931 52.381 0.00 0.00 0.00 4.18
4977 6830 6.516718 TCTTGCTATCCCTTTATCTTCTTCG 58.483 40.000 0.00 0.00 0.00 3.79
5015 6868 1.899814 TGCTTGGAACCTGACTCGTAT 59.100 47.619 0.00 0.00 0.00 3.06
5016 6869 2.271800 GCTTGGAACCTGACTCGTATG 58.728 52.381 0.00 0.00 0.00 2.39
5032 6885 3.572682 TCGTATGACCACTTTCTCTGTGT 59.427 43.478 0.00 0.00 33.92 3.72
5045 6898 3.528532 TCTCTGTGTGCTCAGCATATTG 58.471 45.455 0.54 0.00 41.91 1.90
5064 6917 2.229792 TGTGCTGAATGGGAAGAACAC 58.770 47.619 0.00 0.00 26.36 3.32
5065 6918 1.541588 GTGCTGAATGGGAAGAACACC 59.458 52.381 0.00 0.00 0.00 4.16
5081 6934 1.967779 ACACCATGGCCAAAGGTTAAC 59.032 47.619 25.95 0.00 32.15 2.01
5112 7192 7.178274 AGGTCACCAAGCAATTGATATTAAACA 59.822 33.333 10.34 0.00 0.00 2.83
5128 7208 6.889595 ATTAAACATCATCCAATTTGGGGT 57.110 33.333 15.37 2.27 38.32 4.95
5129 7209 7.986553 ATTAAACATCATCCAATTTGGGGTA 57.013 32.000 15.37 1.73 38.32 3.69
5130 7210 7.798710 TTAAACATCATCCAATTTGGGGTAA 57.201 32.000 15.37 0.00 38.32 2.85
5131 7211 5.937975 AACATCATCCAATTTGGGGTAAG 57.062 39.130 15.37 6.16 38.32 2.34
5132 7212 5.205517 ACATCATCCAATTTGGGGTAAGA 57.794 39.130 15.37 7.03 38.32 2.10
5133 7213 5.780731 ACATCATCCAATTTGGGGTAAGAT 58.219 37.500 15.37 8.78 38.32 2.40
5134 7214 6.204555 ACATCATCCAATTTGGGGTAAGATT 58.795 36.000 15.37 2.32 38.32 2.40
5135 7215 6.673537 ACATCATCCAATTTGGGGTAAGATTT 59.326 34.615 15.37 3.36 38.32 2.17
5136 7216 6.543430 TCATCCAATTTGGGGTAAGATTTG 57.457 37.500 15.37 1.23 38.32 2.32
5137 7217 5.424895 TCATCCAATTTGGGGTAAGATTTGG 59.575 40.000 15.37 0.00 38.32 3.28
5138 7218 4.100373 TCCAATTTGGGGTAAGATTTGGG 58.900 43.478 15.37 0.00 38.32 4.12
5139 7219 3.199727 CCAATTTGGGGTAAGATTTGGGG 59.800 47.826 7.60 0.00 32.67 4.96
5154 7234 2.438434 GGGACTCAATGTGCCGGG 60.438 66.667 2.18 0.00 46.95 5.73
5192 7273 5.638596 TCTTTCGCGAGCTATCCATAATA 57.361 39.130 9.59 0.00 0.00 0.98
5193 7274 5.641709 TCTTTCGCGAGCTATCCATAATAG 58.358 41.667 9.59 0.00 40.42 1.73
5213 7295 1.551883 GCTTCCTTGTCGGTTACCCTA 59.448 52.381 0.00 0.00 0.00 3.53
5220 7302 2.959967 TCGGTTACCCTAGCGAACA 58.040 52.632 0.00 0.00 44.05 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 1.878522 CACGAGTGGAGCGCATACC 60.879 63.158 11.47 10.90 0.00 2.73
57 58 1.272648 CCTTGGGAAGGGAAGATTGCA 60.273 52.381 0.00 0.00 45.27 4.08
58 59 1.478631 CCTTGGGAAGGGAAGATTGC 58.521 55.000 0.00 0.00 45.27 3.56
208 209 2.222007 TGTGCTGCATTTTGGTTGTC 57.778 45.000 5.27 0.00 0.00 3.18
229 230 0.030908 GATGGACCGCGAGAAGTAGG 59.969 60.000 8.23 0.00 0.00 3.18
244 245 0.668706 GACGATCAGATGCCGGATGG 60.669 60.000 5.05 0.00 38.77 3.51
273 274 1.063616 CACATTGCTCGCTCATTCTGG 59.936 52.381 0.00 0.00 0.00 3.86
503 505 3.483869 GGGATCTCCTGCGGGCTT 61.484 66.667 6.73 0.00 35.95 4.35
838 840 1.117142 TCCTTCCTTCCGTCGGTTGT 61.117 55.000 11.88 0.00 0.00 3.32
865 870 3.181485 CCAGCTTCTGTGCTACTACTACC 60.181 52.174 0.00 0.00 41.98 3.18
873 878 2.671070 GGGCCAGCTTCTGTGCTA 59.329 61.111 4.39 0.00 41.98 3.49
897 902 1.153628 CTTAACGGGCAGGAGACGG 60.154 63.158 0.00 0.00 0.00 4.79
898 903 1.810030 GCTTAACGGGCAGGAGACG 60.810 63.158 0.00 0.00 0.00 4.18
899 904 1.810030 CGCTTAACGGGCAGGAGAC 60.810 63.158 0.00 0.00 38.44 3.36
934 939 1.183549 GTGCCGGTAGGAGAGAAGAA 58.816 55.000 1.90 0.00 41.02 2.52
935 940 0.683504 GGTGCCGGTAGGAGAGAAGA 60.684 60.000 1.90 0.00 41.02 2.87
938 943 2.439701 CGGTGCCGGTAGGAGAGA 60.440 66.667 1.90 0.00 41.02 3.10
939 944 2.005960 CTTCGGTGCCGGTAGGAGAG 62.006 65.000 10.94 0.00 41.02 3.20
940 945 2.036098 TTCGGTGCCGGTAGGAGA 59.964 61.111 10.94 0.00 41.02 3.71
954 960 1.045911 CCCCTCTTCCTCCTCCTTCG 61.046 65.000 0.00 0.00 0.00 3.79
967 973 0.990818 GATGCCTCCTTTCCCCCTCT 60.991 60.000 0.00 0.00 0.00 3.69
973 984 0.396278 CCCCAAGATGCCTCCTTTCC 60.396 60.000 0.00 0.00 0.00 3.13
1290 1325 2.793933 TCGATTAGTTTTCTCTCCGCG 58.206 47.619 0.00 0.00 0.00 6.46
1325 1361 5.010922 CCAAATCCAACTCCAACTCAATCAA 59.989 40.000 0.00 0.00 0.00 2.57
1480 1547 4.747108 ACAATTCTGATAGATTTCGGAGCG 59.253 41.667 0.00 0.00 32.74 5.03
1500 1567 8.834004 ATGTATACTCCTCCTACAACTAACAA 57.166 34.615 4.17 0.00 0.00 2.83
1501 1568 8.834004 AATGTATACTCCTCCTACAACTAACA 57.166 34.615 4.17 0.00 0.00 2.41
1564 1641 4.218417 ACAAAATTGATGTAGGCACTCACC 59.782 41.667 0.00 0.00 41.75 4.02
1611 1689 4.258860 CGCAACTTTGAACAAACGAAACTC 60.259 41.667 0.00 0.00 0.00 3.01
1633 1711 6.647212 TCACAATTTACTCTAACAGCATCG 57.353 37.500 0.00 0.00 0.00 3.84
1856 2037 4.006319 AGAAAGATAGCACACTTCAAGGC 58.994 43.478 0.00 0.00 0.00 4.35
2038 2231 5.131475 AGGCAGATGATTTTGGGCAATTATT 59.869 36.000 0.00 0.00 0.00 1.40
2083 2276 4.165779 GTCACGCCAATTCCTTGTTATTG 58.834 43.478 0.00 0.00 0.00 1.90
2103 2296 4.926238 CCATGTACTCTGTCTCAAGTTGTC 59.074 45.833 2.11 0.00 0.00 3.18
2171 2407 4.018233 AGTGGACAGAAGTACTAGGCTAGT 60.018 45.833 28.60 28.60 42.68 2.57
2183 2419 4.892433 AGTCTCAATTGAGTGGACAGAAG 58.108 43.478 29.80 6.52 42.60 2.85
2251 2494 7.714703 AGAAGGTAAGTTCGATATAACTGTCC 58.285 38.462 0.00 0.00 39.62 4.02
2271 2514 3.376546 GCAGCTACAAATCCAAGAGAAGG 59.623 47.826 0.00 0.00 0.00 3.46
2362 2613 5.048846 ACCTCACCTTATGCCGAATAAAT 57.951 39.130 0.00 0.00 30.24 1.40
2405 2656 3.641434 ATCTCCAAGTAAGCAGCACAT 57.359 42.857 0.00 0.00 0.00 3.21
2449 2700 7.013750 TCTGCTGGTGATAGAATACTCTGTAAG 59.986 40.741 0.00 0.00 32.70 2.34
2463 2714 3.324846 AGTCAACAAGTCTGCTGGTGATA 59.675 43.478 0.00 0.00 0.00 2.15
2551 2802 2.235898 TGAAAGTTTTGCACCCAAGCTT 59.764 40.909 0.00 0.00 32.90 3.74
2568 2819 3.278574 ACTTGCACAGCTGTAACTGAAA 58.721 40.909 21.20 7.18 40.25 2.69
2578 2829 4.462834 TGATAGTGTAGTACTTGCACAGCT 59.537 41.667 23.33 14.25 40.89 4.24
2625 2876 7.950963 AGGAACTTTTGGCTTTTATAGCACAAC 60.951 37.037 0.00 0.00 45.78 3.32
2652 2904 2.722094 TGGTCATTTTCCGATTCCAGG 58.278 47.619 0.00 0.00 0.00 4.45
2660 2912 9.653287 TTCTAGCTATATAATGGTCATTTTCCG 57.347 33.333 0.00 0.00 32.50 4.30
2675 2927 7.291411 ACGGATGAAGTGTTTCTAGCTATAT 57.709 36.000 0.00 0.00 34.31 0.86
2688 2940 6.540189 AGATTATGAAAGGAACGGATGAAGTG 59.460 38.462 0.00 0.00 0.00 3.16
2692 2944 9.929180 CTATAAGATTATGAAAGGAACGGATGA 57.071 33.333 0.00 0.00 0.00 2.92
2693 2945 9.712305 ACTATAAGATTATGAAAGGAACGGATG 57.288 33.333 0.00 0.00 0.00 3.51
2793 3045 2.549064 AAAGGCTGACAATTTTGGGC 57.451 45.000 0.00 0.00 0.00 5.36
2854 3106 5.912892 TGTTCTTTCATGTACACTGTCTCA 58.087 37.500 0.00 0.00 0.00 3.27
2862 3114 5.238432 AGCGAACATTGTTCTTTCATGTACA 59.762 36.000 23.29 0.00 0.00 2.90
2877 3129 5.478233 TGCGTAATTTATGAGCGAACATT 57.522 34.783 0.00 0.00 0.00 2.71
2975 3227 7.365840 AGAAATGTTCAAATAAGGAGTCGAC 57.634 36.000 7.70 7.70 0.00 4.20
3013 3265 6.816140 AGTTCAAGAGAAGCTAAGCTCAATAC 59.184 38.462 12.09 6.06 38.25 1.89
3020 3272 6.159988 TCTACAAGTTCAAGAGAAGCTAAGC 58.840 40.000 0.00 0.00 33.63 3.09
3029 3281 4.825422 TCCAGCATCTACAAGTTCAAGAG 58.175 43.478 0.00 0.00 0.00 2.85
3030 3282 4.890158 TCCAGCATCTACAAGTTCAAGA 57.110 40.909 0.00 0.00 0.00 3.02
3031 3283 7.798596 ATTATCCAGCATCTACAAGTTCAAG 57.201 36.000 0.00 0.00 0.00 3.02
3032 3284 9.851686 ATAATTATCCAGCATCTACAAGTTCAA 57.148 29.630 0.00 0.00 0.00 2.69
3035 3287 9.851686 TGAATAATTATCCAGCATCTACAAGTT 57.148 29.630 0.00 0.00 0.00 2.66
3085 3337 2.489329 GGTGCAGCAGTGTTATGTGATT 59.511 45.455 11.86 0.00 0.00 2.57
3103 3355 3.598019 CCATGGTCCAGAAAAATGGTG 57.402 47.619 2.57 0.00 41.43 4.17
3226 3482 3.186283 TGAAAGGGGCAGTAGGTCATAA 58.814 45.455 0.00 0.00 0.00 1.90
3235 3491 3.105959 AGCAAATATGAAAGGGGCAGT 57.894 42.857 0.00 0.00 0.00 4.40
3396 5177 0.710567 CGCTGCAACAGTACTTCTCG 59.289 55.000 0.00 0.00 33.43 4.04
3445 5226 8.927675 TCTTTTGTACCATTTTGTACCTGTAT 57.072 30.769 0.00 0.00 40.29 2.29
3450 5231 8.161699 TCTCTTCTTTTGTACCATTTTGTACC 57.838 34.615 0.00 0.00 40.29 3.34
3504 5287 0.180642 CAGCTGGCATGGATGTCTCT 59.819 55.000 5.57 0.00 32.56 3.10
3569 5352 9.883142 AACCAAGAATAGATAGTTTCTCTTCAG 57.117 33.333 10.06 4.09 39.08 3.02
3623 5406 9.110502 GCAGCTTTATACTAGTAAGAACCAAAT 57.889 33.333 6.70 0.00 0.00 2.32
3779 5602 4.821805 ACAAAAGATTCTCGCTTCCTCAAA 59.178 37.500 0.00 0.00 0.00 2.69
3832 5661 1.204704 TCCACTCTTGCGTACATCTGG 59.795 52.381 0.00 0.00 0.00 3.86
3841 5670 6.258727 ACAAAATATATGAGTCCACTCTTGCG 59.741 38.462 8.19 0.00 43.25 4.85
3854 5683 9.202273 GCCACAAACTGAAAACAAAATATATGA 57.798 29.630 0.00 0.00 0.00 2.15
4041 5887 0.661552 GCGACTGTGACTAGCCGATA 59.338 55.000 0.00 0.00 0.00 2.92
4046 5892 1.272781 GTGATGCGACTGTGACTAGC 58.727 55.000 0.00 0.00 0.00 3.42
4059 5905 6.389091 TCAGGTTATCAACAAAATGTGATGC 58.611 36.000 0.00 0.00 30.29 3.91
4070 5916 5.800296 TCCGAAGAAATCAGGTTATCAACA 58.200 37.500 0.00 0.00 0.00 3.33
4071 5917 5.875359 ACTCCGAAGAAATCAGGTTATCAAC 59.125 40.000 0.00 0.00 0.00 3.18
4119 5966 3.190535 ACGCAAAACTCACCATGGATAAC 59.809 43.478 21.47 0.00 0.00 1.89
4127 5974 3.791973 AAAATGACGCAAAACTCACCA 57.208 38.095 0.00 0.00 0.00 4.17
4149 5997 4.645535 CTTTGGGATTCAGAGTCACAGAA 58.354 43.478 0.00 0.00 29.38 3.02
4253 6101 4.864704 TTCTTGAAACCCCTTGCATTAC 57.135 40.909 0.00 0.00 0.00 1.89
4310 6158 4.878397 AGCGATCTGTTGAATCCCTTTAAG 59.122 41.667 0.00 0.00 0.00 1.85
4323 6171 3.739810 CGAATCATCATGAGCGATCTGTT 59.260 43.478 0.90 0.00 32.28 3.16
4363 6211 0.251297 TGGCACAGGGGAAATCAGTG 60.251 55.000 0.00 0.00 0.00 3.66
4364 6212 2.163454 TGGCACAGGGGAAATCAGT 58.837 52.632 0.00 0.00 0.00 3.41
4390 6238 6.201615 CTGTAGGTACACGTGTCGATAGATAA 59.798 42.308 27.16 0.22 38.72 1.75
4404 6253 3.764972 AGAAGCTTCCTCTGTAGGTACAC 59.235 47.826 22.81 0.00 44.09 2.90
4428 6277 1.270678 ACCGTGGTTTTCTAGTCCTGC 60.271 52.381 0.00 0.00 0.00 4.85
4446 6295 2.945668 CAATGTAAGAAGGCTAGCCACC 59.054 50.000 34.70 24.25 38.92 4.61
4524 6377 4.681483 GCTGTGATAAAGAAAAAGGCACAC 59.319 41.667 0.00 0.00 32.17 3.82
4549 6402 0.463833 ACCGATCAGGGAAATTCCGC 60.464 55.000 5.87 0.00 46.96 5.54
4717 6570 3.056821 GGTGCCCATTGGTAAGAGTTTTC 60.057 47.826 1.20 0.00 0.00 2.29
4794 6647 4.081697 TCTCTTGTGAGTGCCGAATTATCA 60.082 41.667 0.00 0.00 40.98 2.15
4801 6654 0.750249 TTGTCTCTTGTGAGTGCCGA 59.250 50.000 0.00 0.00 40.98 5.54
4810 6663 0.666577 GTAGCGCCGTTGTCTCTTGT 60.667 55.000 2.29 0.00 0.00 3.16
4825 6678 4.681942 CGAGTGCCAGATTACTTATGTAGC 59.318 45.833 0.00 0.00 0.00 3.58
4855 6708 1.444553 CGCTCCGTGGACTTCTCAC 60.445 63.158 0.00 0.00 0.00 3.51
4865 6718 2.128035 GATCAATAAGGTCGCTCCGTG 58.872 52.381 0.00 0.00 41.99 4.94
4888 6741 3.198635 TCCACATCCCAGAGATTTGAGTC 59.801 47.826 0.00 0.00 35.06 3.36
4891 6744 2.239654 GGTCCACATCCCAGAGATTTGA 59.760 50.000 0.00 0.00 35.06 2.69
4977 6830 1.787012 CAACAAAGTCTTGCATGCCC 58.213 50.000 16.68 0.09 35.84 5.36
5015 6868 1.486310 AGCACACAGAGAAAGTGGTCA 59.514 47.619 0.00 0.00 39.53 4.02
5016 6869 2.246719 AGCACACAGAGAAAGTGGTC 57.753 50.000 0.00 0.00 39.53 4.02
5045 6898 1.541588 GGTGTTCTTCCCATTCAGCAC 59.458 52.381 0.00 0.00 0.00 4.40
5060 6913 2.367241 GTTAACCTTTGGCCATGGTGTT 59.633 45.455 25.69 19.11 33.89 3.32
5064 6917 1.967066 TGTGTTAACCTTTGGCCATGG 59.033 47.619 20.06 20.06 0.00 3.66
5065 6918 3.959535 ATGTGTTAACCTTTGGCCATG 57.040 42.857 6.09 2.14 0.00 3.66
5081 6934 3.758023 TCAATTGCTTGGTGACCTATGTG 59.242 43.478 2.11 0.00 32.95 3.21
5112 7192 6.100134 CCAAATCTTACCCCAAATTGGATGAT 59.900 38.462 14.62 4.37 40.96 2.45
5128 7208 4.016444 GCACATTGAGTCCCCAAATCTTA 58.984 43.478 0.00 0.00 0.00 2.10
5129 7209 2.827921 GCACATTGAGTCCCCAAATCTT 59.172 45.455 0.00 0.00 0.00 2.40
5130 7210 2.450476 GCACATTGAGTCCCCAAATCT 58.550 47.619 0.00 0.00 0.00 2.40
5131 7211 1.478105 GGCACATTGAGTCCCCAAATC 59.522 52.381 0.00 0.00 0.00 2.17
5132 7212 1.560505 GGCACATTGAGTCCCCAAAT 58.439 50.000 0.00 0.00 0.00 2.32
5133 7213 0.893270 CGGCACATTGAGTCCCCAAA 60.893 55.000 0.00 0.00 0.00 3.28
5134 7214 1.303236 CGGCACATTGAGTCCCCAA 60.303 57.895 0.00 0.00 0.00 4.12
5135 7215 2.350895 CGGCACATTGAGTCCCCA 59.649 61.111 0.00 0.00 0.00 4.96
5136 7216 2.438434 CCGGCACATTGAGTCCCC 60.438 66.667 0.00 0.00 0.00 4.81
5137 7217 2.438434 CCCGGCACATTGAGTCCC 60.438 66.667 0.00 0.00 0.00 4.46
5138 7218 0.608035 TTTCCCGGCACATTGAGTCC 60.608 55.000 0.00 0.00 0.00 3.85
5139 7219 0.804989 CTTTCCCGGCACATTGAGTC 59.195 55.000 0.00 0.00 0.00 3.36
5167 7247 3.179443 TGGATAGCTCGCGAAAGAATT 57.821 42.857 11.33 0.00 0.00 2.17
5168 7248 2.890808 TGGATAGCTCGCGAAAGAAT 57.109 45.000 11.33 1.01 0.00 2.40
5185 7265 4.073293 ACCGACAAGGAAGCTATTATGG 57.927 45.455 0.00 0.00 45.00 2.74
5192 7273 3.929660 GGTAACCGACAAGGAAGCT 57.070 52.632 0.00 0.00 45.00 3.74
5213 7295 2.679837 CACTTTGATATGGCTGTTCGCT 59.320 45.455 0.00 0.00 39.13 4.93
5220 7302 3.264193 TGTCCACTCACTTTGATATGGCT 59.736 43.478 2.92 0.00 34.34 4.75
5250 7332 0.692476 TCCACTCCAATCCCACACAG 59.308 55.000 0.00 0.00 0.00 3.66
5266 7348 2.912956 AGGAGGTGCTTAATGTCTTCCA 59.087 45.455 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.