Multiple sequence alignment - TraesCS1B01G183400

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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 TraesCS1B01G183400 chr1B 100.000 2594 0 0 1 2594 330230576 330233169 0.000000e+00 4791.0
1 TraesCS1B01G183400 chr1D 94.625 2307 81 11 62 2358 247508591 247506318 0.000000e+00 3533.0
2 TraesCS1B01G183400 chr1D 92.373 118 9 0 2475 2592 247506319 247506202 4.440000e-38 169.0
3 TraesCS1B01G183400 chr1D 100.000 43 0 0 1 43 247508621 247508579 2.140000e-11 80.5
4 TraesCS1B01G183400 chr1A 94.180 2079 72 21 62 2120 299718260 299720309 0.000000e+00 3123.0
5 TraesCS1B01G183400 chr1A 92.562 121 9 0 2472 2592 299720379 299720499 9.540000e-40 174.0
6 TraesCS1B01G183400 chr1A 96.875 64 2 0 2295 2358 299720320 299720383 9.820000e-20 108.0
7 TraesCS1B01G183400 chr1A 100.000 43 0 0 1 43 299718230 299718272 2.140000e-11 80.5
8 TraesCS1B01G183400 chr5D 79.713 488 95 3 1112 1597 493714159 493714644 1.480000e-92 350.0
9 TraesCS1B01G183400 chr5D 79.713 488 95 3 1112 1597 493721608 493722093 1.480000e-92 350.0
10 TraesCS1B01G183400 chr5D 79.713 488 95 3 1112 1597 493724091 493724576 1.480000e-92 350.0
11 TraesCS1B01G183400 chr5D 79.508 488 96 3 1112 1597 493710587 493711072 6.870000e-91 344.0
12 TraesCS1B01G183400 chr5D 79.508 488 96 3 1112 1597 493716640 493717125 6.870000e-91 344.0
13 TraesCS1B01G183400 chr5D 79.508 488 96 3 1112 1597 493719124 493719609 6.870000e-91 344.0
14 TraesCS1B01G183400 chrUn 79.508 488 96 3 1112 1597 338978897 338979382 6.870000e-91 344.0
15 TraesCS1B01G183400 chrUn 87.273 55 7 0 2111 2165 44501411 44501357 2.160000e-06 63.9
16 TraesCS1B01G183400 chrUn 87.273 55 7 0 2111 2165 44530106 44530052 2.160000e-06 63.9
17 TraesCS1B01G183400 chr6D 98.347 121 2 0 2354 2474 348647457 348647337 2.020000e-51 213.0
18 TraesCS1B01G183400 chr6D 96.667 120 4 0 2362 2481 9063579 9063698 1.570000e-47 200.0
19 TraesCS1B01G183400 chr2D 97.500 120 3 0 2354 2473 377306006 377306125 3.380000e-49 206.0
20 TraesCS1B01G183400 chr2D 96.032 126 4 1 2356 2481 441576672 441576796 1.220000e-48 204.0
21 TraesCS1B01G183400 chr7D 96.694 121 4 0 2354 2474 578069835 578069955 4.380000e-48 202.0
22 TraesCS1B01G183400 chr3D 96.667 120 4 0 2356 2475 607000537 607000656 1.570000e-47 200.0
23 TraesCS1B01G183400 chr3D 87.500 56 7 0 2120 2175 130508492 130508547 5.990000e-07 65.8
24 TraesCS1B01G183400 chr4D 95.200 125 5 1 2353 2476 15768039 15768163 2.040000e-46 196.0
25 TraesCS1B01G183400 chr5A 94.488 127 5 2 2348 2474 505594266 505594142 7.320000e-46 195.0
26 TraesCS1B01G183400 chr3B 91.667 132 10 1 2354 2485 504148925 504148795 5.700000e-42 182.0
27 TraesCS1B01G183400 chr7A 87.719 57 7 0 2121 2177 69219975 69219919 1.670000e-07 67.6


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 TraesCS1B01G183400 chr1B 330230576 330233169 2593 False 4791.000000 4791 100.00000 1 2594 1 chr1B.!!$F1 2593
1 TraesCS1B01G183400 chr1D 247506202 247508621 2419 True 1260.833333 3533 95.66600 1 2592 3 chr1D.!!$R1 2591
2 TraesCS1B01G183400 chr1A 299718230 299720499 2269 False 871.375000 3123 95.90425 1 2592 4 chr1A.!!$F1 2591
3 TraesCS1B01G183400 chr5D 493710587 493724576 13989 False 347.000000 350 79.61050 1112 1597 6 chr5D.!!$F1 485

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
287 293 0.310543 GAAACACGCACTTGGATGCA 59.689 50.0 0.0 0.0 46.47 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2215 14007 0.833287 TGATTGGCTACTCTGGCTCC 59.167 55.0 0.0 0.0 0.0 4.7 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
45 46 9.686683 ACAGAGTTAAAATAGGAATATGCAACT 57.313 29.630 0.00 0.00 0.00 3.16
51 52 7.751768 AAAATAGGAATATGCAACTAGGAGC 57.248 36.000 0.00 0.00 0.00 4.70
52 53 3.778954 AGGAATATGCAACTAGGAGCC 57.221 47.619 0.00 0.00 0.00 4.70
53 54 3.321950 AGGAATATGCAACTAGGAGCCT 58.678 45.455 0.00 0.00 0.00 4.58
54 55 3.326297 AGGAATATGCAACTAGGAGCCTC 59.674 47.826 0.00 0.00 0.00 4.70
55 56 3.558109 GGAATATGCAACTAGGAGCCTCC 60.558 52.174 1.26 1.26 36.58 4.30
56 57 1.040646 TATGCAACTAGGAGCCTCCG 58.959 55.000 4.80 0.00 42.75 4.63
57 58 0.978146 ATGCAACTAGGAGCCTCCGT 60.978 55.000 4.80 0.00 42.75 4.69
58 59 1.153549 GCAACTAGGAGCCTCCGTG 60.154 63.158 4.80 4.81 42.75 4.94
59 60 1.153549 CAACTAGGAGCCTCCGTGC 60.154 63.158 4.80 0.00 42.75 5.34
60 61 2.711922 AACTAGGAGCCTCCGTGCG 61.712 63.158 4.80 0.00 42.75 5.34
61 62 2.829003 CTAGGAGCCTCCGTGCGA 60.829 66.667 4.80 0.00 42.75 5.10
62 63 2.123854 TAGGAGCCTCCGTGCGAT 60.124 61.111 4.80 0.00 42.75 4.58
63 64 0.889638 CTAGGAGCCTCCGTGCGATA 60.890 60.000 4.80 0.00 42.75 2.92
64 65 0.889638 TAGGAGCCTCCGTGCGATAG 60.890 60.000 4.80 0.00 42.75 2.08
65 66 2.336809 GAGCCTCCGTGCGATAGG 59.663 66.667 8.07 8.07 36.02 2.57
66 67 2.123854 AGCCTCCGTGCGATAGGA 60.124 61.111 14.22 0.00 36.02 2.94
67 68 1.735376 GAGCCTCCGTGCGATAGGAA 61.735 60.000 14.22 0.00 39.13 3.36
68 69 1.115930 AGCCTCCGTGCGATAGGAAT 61.116 55.000 14.22 2.75 39.13 3.01
69 70 0.601558 GCCTCCGTGCGATAGGAATA 59.398 55.000 14.22 0.00 39.13 1.75
70 71 1.204941 GCCTCCGTGCGATAGGAATAT 59.795 52.381 14.22 0.00 39.13 1.28
71 72 2.426024 GCCTCCGTGCGATAGGAATATA 59.574 50.000 14.22 0.00 39.13 0.86
72 73 3.119245 GCCTCCGTGCGATAGGAATATAA 60.119 47.826 14.22 0.00 39.13 0.98
155 156 2.653726 TGGGAGTAATTTGCGATGCAT 58.346 42.857 0.00 0.00 38.76 3.96
156 157 2.358582 TGGGAGTAATTTGCGATGCATG 59.641 45.455 2.46 0.00 38.76 4.06
173 174 1.618343 CATGGACAACCCCCAAACTTC 59.382 52.381 0.00 0.00 37.22 3.01
193 197 7.301868 ACTTCCAATGCCTTTATCTGAAAAA 57.698 32.000 0.00 0.00 0.00 1.94
249 255 9.606631 GTAGAAAACCAGATATTGAGACAATCT 57.393 33.333 0.00 0.00 0.00 2.40
287 293 0.310543 GAAACACGCACTTGGATGCA 59.689 50.000 0.00 0.00 46.47 3.96
288 294 0.961019 AAACACGCACTTGGATGCAT 59.039 45.000 0.00 0.00 46.47 3.96
323 329 6.627087 TCTTTAGTGTCCAGGAAATCTGAT 57.373 37.500 0.00 0.00 46.18 2.90
328 334 3.873952 GTGTCCAGGAAATCTGATACAGC 59.126 47.826 0.00 0.00 46.18 4.40
773 798 4.367039 ACATGCCTACTTAAACCAGTGT 57.633 40.909 0.00 0.00 0.00 3.55
782 807 7.820872 GCCTACTTAAACCAGTGTTATAGTTCA 59.179 37.037 0.00 0.00 33.15 3.18
921 946 5.730010 GCAATTGCTGATTTCTGAGCTCTAC 60.730 44.000 23.21 0.89 36.11 2.59
941 966 4.783560 ACATAAAGTACCCACCCATACC 57.216 45.455 0.00 0.00 0.00 2.73
952 977 2.172505 CCACCCATACCACTTGAGCATA 59.827 50.000 0.00 0.00 0.00 3.14
980 1005 3.004024 AGTTCAATTGAAAGCTGCACG 57.996 42.857 22.07 0.00 35.58 5.34
1091 1117 0.393132 TCGTCCACAGCCAACAAACA 60.393 50.000 0.00 0.00 0.00 2.83
1257 9820 0.546122 AGACAGTGGCAACCTTGACA 59.454 50.000 0.00 0.00 45.70 3.58
1455 12502 0.877213 TCGTCGACGAGTGTGACTCA 60.877 55.000 34.97 10.59 45.30 3.41
1558 12605 1.856265 GCTGGGGCTCAACAAGAACG 61.856 60.000 0.00 0.00 35.22 3.95
1564 12611 1.214367 GCTCAACAAGAACGTCGGAA 58.786 50.000 0.00 0.00 0.00 4.30
1626 12673 0.659427 CCATGGCAATGTCGTGCTAG 59.341 55.000 0.00 0.00 44.31 3.42
1710 12775 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1711 12776 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1712 12777 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1713 12778 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1714 12779 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1715 12780 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1716 12781 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1717 12782 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1718 12783 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1719 12784 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1720 12785 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1721 12786 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1722 12787 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1723 12788 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1724 12789 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1725 12790 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1726 12791 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1727 12792 1.152510 GTGTGTGTGTGTGTGTGTGA 58.847 50.000 0.00 0.00 0.00 3.58
1728 12793 1.737236 GTGTGTGTGTGTGTGTGTGAT 59.263 47.619 0.00 0.00 0.00 3.06
1729 12794 1.736681 TGTGTGTGTGTGTGTGTGATG 59.263 47.619 0.00 0.00 0.00 3.07
1730 12795 2.006169 GTGTGTGTGTGTGTGTGATGA 58.994 47.619 0.00 0.00 0.00 2.92
1731 12796 2.613595 GTGTGTGTGTGTGTGTGATGAT 59.386 45.455 0.00 0.00 0.00 2.45
1762 12827 2.418368 TGGCGATGGAGCAAATAAGT 57.582 45.000 0.00 0.00 39.27 2.24
2023 13812 2.783135 GAAGAGAACCAGACAATGCCA 58.217 47.619 0.00 0.00 0.00 4.92
2103 13895 4.388118 CCTTAAGAGATACTCCCCCTGTCT 60.388 50.000 3.36 0.00 0.00 3.41
2105 13897 1.144093 AGAGATACTCCCCCTGTCTCG 59.856 57.143 0.00 0.00 40.08 4.04
2109 13901 1.255667 TACTCCCCCTGTCTCGCAAC 61.256 60.000 0.00 0.00 0.00 4.17
2118 13910 3.126831 CCTGTCTCGCAACATAAGATCC 58.873 50.000 0.00 0.00 0.00 3.36
2152 13944 7.763172 CTAACATAGCTTGAGAAACGATCTT 57.237 36.000 0.00 0.00 38.96 2.40
2153 13945 8.858003 CTAACATAGCTTGAGAAACGATCTTA 57.142 34.615 0.00 0.00 38.96 2.10
2154 13946 9.469807 CTAACATAGCTTGAGAAACGATCTTAT 57.530 33.333 0.00 0.00 38.96 1.73
2156 13948 9.988815 AACATAGCTTGAGAAACGATCTTATAT 57.011 29.630 0.00 0.00 38.96 0.86
2168 13960 6.946229 ACGATCTTATATTATGGAACGCAC 57.054 37.500 0.00 0.00 0.00 5.34
2182 13974 3.504863 GAACGCACGGAGTACATCTTTA 58.495 45.455 0.00 0.00 41.61 1.85
2215 14007 6.851330 GTCCAAATTTGTTCTTCGTCTAACAG 59.149 38.462 16.73 0.00 36.96 3.16
2234 14026 0.833287 GGAGCCAGAGTAGCCAATCA 59.167 55.000 0.00 0.00 0.00 2.57
2240 14032 3.432186 GCCAGAGTAGCCAATCACATGTA 60.432 47.826 0.00 0.00 0.00 2.29
2299 14091 6.822667 ACTGAAGACAACATATGCATTTGA 57.177 33.333 21.91 0.00 0.00 2.69
2301 14093 6.432162 ACTGAAGACAACATATGCATTTGAGT 59.568 34.615 21.91 18.18 0.00 3.41
2357 14149 8.327271 ACCAGTTAGTCTACTCACAGTCTAATA 58.673 37.037 0.00 0.00 31.77 0.98
2358 14150 8.614346 CCAGTTAGTCTACTCACAGTCTAATAC 58.386 40.741 0.00 0.00 31.77 1.89
2359 14151 9.386010 CAGTTAGTCTACTCACAGTCTAATACT 57.614 37.037 0.00 0.00 39.81 2.12
2369 14161 2.308690 AGTCTAATACTGCCTCCGTCC 58.691 52.381 0.00 0.00 36.93 4.79
2370 14162 1.001597 GTCTAATACTGCCTCCGTCCG 60.002 57.143 0.00 0.00 0.00 4.79
2371 14163 0.314302 CTAATACTGCCTCCGTCCGG 59.686 60.000 0.00 0.00 0.00 5.14
2372 14164 0.106569 TAATACTGCCTCCGTCCGGA 60.107 55.000 0.00 0.00 42.90 5.14
2373 14165 0.974010 AATACTGCCTCCGTCCGGAA 60.974 55.000 5.23 0.00 44.66 4.30
2374 14166 0.974010 ATACTGCCTCCGTCCGGAAA 60.974 55.000 5.23 0.00 44.66 3.13
2375 14167 0.974010 TACTGCCTCCGTCCGGAAAT 60.974 55.000 5.23 0.00 44.66 2.17
2376 14168 0.974010 ACTGCCTCCGTCCGGAAATA 60.974 55.000 5.23 0.00 44.66 1.40
2377 14169 0.529992 CTGCCTCCGTCCGGAAATAC 60.530 60.000 5.23 0.00 44.66 1.89
2378 14170 0.974010 TGCCTCCGTCCGGAAATACT 60.974 55.000 5.23 0.00 44.66 2.12
2379 14171 0.177373 GCCTCCGTCCGGAAATACTT 59.823 55.000 5.23 0.00 44.66 2.24
2380 14172 1.935933 CCTCCGTCCGGAAATACTTG 58.064 55.000 5.23 0.00 44.66 3.16
2381 14173 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
2382 14174 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
2383 14175 1.135315 TCCGTCCGGAAATACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
2384 14176 1.403249 CCGTCCGGAAATACTTGTCGT 60.403 52.381 5.23 0.00 37.50 4.34
2385 14177 2.159393 CCGTCCGGAAATACTTGTCGTA 60.159 50.000 5.23 0.00 37.50 3.43
2386 14178 3.103738 CGTCCGGAAATACTTGTCGTAG 58.896 50.000 5.23 0.00 0.00 3.51
2387 14179 3.181507 CGTCCGGAAATACTTGTCGTAGA 60.182 47.826 5.23 0.00 0.00 2.59
2388 14180 4.672542 CGTCCGGAAATACTTGTCGTAGAA 60.673 45.833 5.23 0.00 39.69 2.10
2389 14181 5.163513 GTCCGGAAATACTTGTCGTAGAAA 58.836 41.667 5.23 0.00 39.69 2.52
2390 14182 5.809051 GTCCGGAAATACTTGTCGTAGAAAT 59.191 40.000 5.23 0.00 39.69 2.17
2391 14183 5.808540 TCCGGAAATACTTGTCGTAGAAATG 59.191 40.000 0.00 0.00 39.69 2.32
2392 14184 5.006358 CCGGAAATACTTGTCGTAGAAATGG 59.994 44.000 0.00 0.00 39.69 3.16
2393 14185 5.808540 CGGAAATACTTGTCGTAGAAATGGA 59.191 40.000 0.00 0.00 39.69 3.41
2394 14186 6.479001 CGGAAATACTTGTCGTAGAAATGGAT 59.521 38.462 0.00 0.00 39.69 3.41
2395 14187 7.650504 CGGAAATACTTGTCGTAGAAATGGATA 59.349 37.037 0.00 0.00 39.69 2.59
2396 14188 8.762426 GGAAATACTTGTCGTAGAAATGGATAC 58.238 37.037 0.00 0.00 39.69 2.24
2445 14237 6.522625 ACATCTAGATACATCCATTCCTCG 57.477 41.667 4.54 0.00 0.00 4.63
2446 14238 5.420421 ACATCTAGATACATCCATTCCTCGG 59.580 44.000 4.54 0.00 0.00 4.63
2447 14239 5.256806 TCTAGATACATCCATTCCTCGGA 57.743 43.478 0.00 0.00 36.84 4.55
2448 14240 5.010933 TCTAGATACATCCATTCCTCGGAC 58.989 45.833 0.00 0.00 34.69 4.79
2449 14241 3.576861 AGATACATCCATTCCTCGGACA 58.423 45.455 0.00 0.00 34.69 4.02
2450 14242 3.967326 AGATACATCCATTCCTCGGACAA 59.033 43.478 0.00 0.00 34.69 3.18
2451 14243 2.698855 ACATCCATTCCTCGGACAAG 57.301 50.000 0.00 0.00 34.69 3.16
2452 14244 1.909302 ACATCCATTCCTCGGACAAGT 59.091 47.619 0.00 0.00 34.69 3.16
2453 14245 3.104512 ACATCCATTCCTCGGACAAGTA 58.895 45.455 0.00 0.00 34.69 2.24
2454 14246 3.711704 ACATCCATTCCTCGGACAAGTAT 59.288 43.478 0.00 0.00 34.69 2.12
2455 14247 4.164221 ACATCCATTCCTCGGACAAGTATT 59.836 41.667 0.00 0.00 34.69 1.89
2456 14248 4.837093 TCCATTCCTCGGACAAGTATTT 57.163 40.909 0.00 0.00 0.00 1.40
2457 14249 5.174037 TCCATTCCTCGGACAAGTATTTT 57.826 39.130 0.00 0.00 0.00 1.82
2458 14250 5.566469 TCCATTCCTCGGACAAGTATTTTT 58.434 37.500 0.00 0.00 0.00 1.94
2459 14251 5.414454 TCCATTCCTCGGACAAGTATTTTTG 59.586 40.000 0.00 0.00 0.00 2.44
2460 14252 5.393027 CCATTCCTCGGACAAGTATTTTTGG 60.393 44.000 0.00 0.00 32.32 3.28
2461 14253 4.627284 TCCTCGGACAAGTATTTTTGGA 57.373 40.909 0.00 0.00 32.32 3.53
2462 14254 4.320870 TCCTCGGACAAGTATTTTTGGAC 58.679 43.478 0.00 0.00 32.32 4.02
2463 14255 3.124636 CCTCGGACAAGTATTTTTGGACG 59.875 47.826 0.00 0.00 34.68 4.79
2464 14256 3.068560 TCGGACAAGTATTTTTGGACGG 58.931 45.455 0.00 0.00 34.38 4.79
2465 14257 3.068560 CGGACAAGTATTTTTGGACGGA 58.931 45.455 0.00 0.00 31.88 4.69
2466 14258 3.124636 CGGACAAGTATTTTTGGACGGAG 59.875 47.826 0.00 0.00 31.88 4.63
2467 14259 3.439129 GGACAAGTATTTTTGGACGGAGG 59.561 47.826 0.00 0.00 32.32 4.30
2468 14260 3.418047 ACAAGTATTTTTGGACGGAGGG 58.582 45.455 0.00 0.00 32.32 4.30
2469 14261 3.073356 ACAAGTATTTTTGGACGGAGGGA 59.927 43.478 0.00 0.00 32.32 4.20
2470 14262 3.629142 AGTATTTTTGGACGGAGGGAG 57.371 47.619 0.00 0.00 0.00 4.30
2471 14263 2.910977 AGTATTTTTGGACGGAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
2472 14264 4.098894 AGTATTTTTGGACGGAGGGAGTA 58.901 43.478 0.00 0.00 0.00 2.59
2473 14265 2.845363 TTTTTGGACGGAGGGAGTAC 57.155 50.000 0.00 0.00 0.00 2.73
2482 14274 4.273318 GACGGAGGGAGTACTAGGTTAAA 58.727 47.826 0.00 0.00 0.00 1.52
2503 14295 9.443323 GTTAAAATTACTTGTTATTGGCCCATT 57.557 29.630 0.00 0.00 0.00 3.16
2559 14351 2.481952 GGCATCAGAAGTCACAACTCAC 59.518 50.000 0.00 0.00 33.48 3.51
2560 14352 2.481952 GCATCAGAAGTCACAACTCACC 59.518 50.000 0.00 0.00 33.48 4.02
2592 14384 4.299586 TGAACACATCAAGGCCATCTAA 57.700 40.909 5.01 0.00 34.30 2.10
2593 14385 4.858850 TGAACACATCAAGGCCATCTAAT 58.141 39.130 5.01 0.00 34.30 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 2.711922 CGCACGGAGGCTCCTAGTT 61.712 63.158 29.81 9.77 33.30 2.24
43 44 2.912987 ATCGCACGGAGGCTCCTAGT 62.913 60.000 29.81 19.00 33.30 2.57
44 45 0.889638 TATCGCACGGAGGCTCCTAG 60.890 60.000 29.81 22.06 33.30 3.02
45 46 0.889638 CTATCGCACGGAGGCTCCTA 60.890 60.000 29.81 13.99 33.30 2.94
46 47 2.123854 TATCGCACGGAGGCTCCT 60.124 61.111 29.81 15.02 33.30 3.69
47 48 2.336809 CTATCGCACGGAGGCTCC 59.663 66.667 24.06 24.06 0.00 4.70
48 49 1.735376 TTCCTATCGCACGGAGGCTC 61.735 60.000 5.78 5.78 0.00 4.70
49 50 1.115930 ATTCCTATCGCACGGAGGCT 61.116 55.000 6.95 0.00 0.00 4.58
50 51 0.601558 TATTCCTATCGCACGGAGGC 59.398 55.000 6.95 0.00 0.00 4.70
51 52 4.713824 TTATATTCCTATCGCACGGAGG 57.286 45.455 5.79 5.79 0.00 4.30
52 53 6.590292 ACAATTTATATTCCTATCGCACGGAG 59.410 38.462 0.00 0.00 0.00 4.63
53 54 6.460781 ACAATTTATATTCCTATCGCACGGA 58.539 36.000 0.00 0.00 0.00 4.69
54 55 6.183360 GGACAATTTATATTCCTATCGCACGG 60.183 42.308 0.00 0.00 0.00 4.94
55 56 6.183360 GGGACAATTTATATTCCTATCGCACG 60.183 42.308 0.00 0.00 0.00 5.34
56 57 6.879458 AGGGACAATTTATATTCCTATCGCAC 59.121 38.462 0.00 0.00 0.00 5.34
57 58 6.878923 CAGGGACAATTTATATTCCTATCGCA 59.121 38.462 0.00 0.00 0.00 5.10
58 59 6.879458 ACAGGGACAATTTATATTCCTATCGC 59.121 38.462 0.00 0.00 0.00 4.58
59 60 9.938280 TTACAGGGACAATTTATATTCCTATCG 57.062 33.333 0.00 0.00 0.00 2.92
131 132 4.065088 GCATCGCAAATTACTCCCATAGA 58.935 43.478 0.00 0.00 0.00 1.98
155 156 0.105913 GGAAGTTTGGGGGTTGTCCA 60.106 55.000 0.00 0.00 37.22 4.02
156 157 0.105913 TGGAAGTTTGGGGGTTGTCC 60.106 55.000 0.00 0.00 0.00 4.02
194 198 8.621286 CCTGTGTAGTCACTTAATTCTGTTTTT 58.379 33.333 0.00 0.00 44.14 1.94
199 203 6.706270 ACAACCTGTGTAGTCACTTAATTCTG 59.294 38.462 0.00 0.00 44.14 3.02
221 225 9.739276 ATTGTCTCAATATCTGGTTTTCTACAA 57.261 29.630 0.00 0.00 0.00 2.41
230 234 4.039730 CCCGAGATTGTCTCAATATCTGGT 59.960 45.833 14.68 0.00 43.55 4.00
232 236 5.459536 TCCCGAGATTGTCTCAATATCTG 57.540 43.478 12.85 7.97 43.55 2.90
249 255 0.181114 CTGGATGATTTGGCTCCCGA 59.819 55.000 0.00 0.00 0.00 5.14
304 310 5.163405 GCTGTATCAGATTTCCTGGACACTA 60.163 44.000 0.00 0.00 43.12 2.74
323 329 8.995027 AAATATGGTCTGATTATTTGGCTGTA 57.005 30.769 0.00 0.00 0.00 2.74
328 334 8.469309 ACTGGAAATATGGTCTGATTATTTGG 57.531 34.615 7.49 3.17 0.00 3.28
568 576 8.830580 CGAATAGAATGGTAGTTGATCAATTGT 58.169 33.333 12.12 1.92 0.00 2.71
761 786 8.827177 TCACTGAACTATAACACTGGTTTAAG 57.173 34.615 0.00 0.00 38.45 1.85
773 798 5.204409 ACCGTGTGTTCACTGAACTATAA 57.796 39.130 20.18 0.21 42.39 0.98
782 807 2.561419 ACTATGCTACCGTGTGTTCACT 59.439 45.455 4.59 0.00 41.89 3.41
921 946 4.165372 AGTGGTATGGGTGGGTACTTTATG 59.835 45.833 0.00 0.00 0.00 1.90
941 966 6.845302 TGAACTATTGCTTTATGCTCAAGTG 58.155 36.000 0.00 0.00 43.37 3.16
952 977 6.146673 GCAGCTTTCAATTGAACTATTGCTTT 59.853 34.615 20.35 3.62 35.86 3.51
980 1005 2.099405 TGCTATTTGCCACCTTAAGCC 58.901 47.619 0.00 0.00 42.00 4.35
1091 1117 2.906897 CACTGGGCTTTGGCACGT 60.907 61.111 0.00 0.00 46.54 4.49
1257 9820 2.555547 GCGGGCAAAGCTGTTCAGT 61.556 57.895 0.00 0.00 0.00 3.41
1423 12470 2.743928 GACGACCTTGGCCAGCAG 60.744 66.667 5.11 0.33 0.00 4.24
1455 12502 0.892358 CCTTGTCACAGCCATGCACT 60.892 55.000 0.00 0.00 0.00 4.40
1626 12673 7.371936 CCTTGTGTATGCCTCTAAGTATAGAC 58.628 42.308 0.00 0.00 34.45 2.59
1710 12775 2.006169 TCATCACACACACACACACAC 58.994 47.619 0.00 0.00 0.00 3.82
1711 12776 2.393271 TCATCACACACACACACACA 57.607 45.000 0.00 0.00 0.00 3.72
1712 12777 2.871633 TCATCATCACACACACACACAC 59.128 45.455 0.00 0.00 0.00 3.82
1713 12778 3.191078 TCATCATCACACACACACACA 57.809 42.857 0.00 0.00 0.00 3.72
1714 12779 3.747529 TCATCATCATCACACACACACAC 59.252 43.478 0.00 0.00 0.00 3.82
1715 12780 4.005487 TCATCATCATCACACACACACA 57.995 40.909 0.00 0.00 0.00 3.72
1716 12781 6.667007 TTATCATCATCATCACACACACAC 57.333 37.500 0.00 0.00 0.00 3.82
1717 12782 7.277396 AGATTATCATCATCATCACACACACA 58.723 34.615 0.00 0.00 0.00 3.72
1718 12783 7.725818 AGATTATCATCATCATCACACACAC 57.274 36.000 0.00 0.00 0.00 3.82
1719 12784 7.227910 CCAAGATTATCATCATCATCACACACA 59.772 37.037 0.00 0.00 0.00 3.72
1720 12785 7.582352 CCAAGATTATCATCATCATCACACAC 58.418 38.462 0.00 0.00 0.00 3.82
1721 12786 6.206048 GCCAAGATTATCATCATCATCACACA 59.794 38.462 0.00 0.00 0.00 3.72
1722 12787 6.609533 GCCAAGATTATCATCATCATCACAC 58.390 40.000 0.00 0.00 0.00 3.82
1723 12788 5.410439 CGCCAAGATTATCATCATCATCACA 59.590 40.000 0.00 0.00 0.00 3.58
1724 12789 5.640783 TCGCCAAGATTATCATCATCATCAC 59.359 40.000 0.00 0.00 0.00 3.06
1725 12790 5.797051 TCGCCAAGATTATCATCATCATCA 58.203 37.500 0.00 0.00 0.00 3.07
1726 12791 6.238402 CCATCGCCAAGATTATCATCATCATC 60.238 42.308 0.00 0.00 37.52 2.92
1727 12792 5.589050 CCATCGCCAAGATTATCATCATCAT 59.411 40.000 0.00 0.00 37.52 2.45
1728 12793 4.939439 CCATCGCCAAGATTATCATCATCA 59.061 41.667 0.00 0.00 37.52 3.07
1729 12794 5.181009 TCCATCGCCAAGATTATCATCATC 58.819 41.667 0.00 0.00 37.52 2.92
1730 12795 5.169992 TCCATCGCCAAGATTATCATCAT 57.830 39.130 0.00 0.00 37.52 2.45
1731 12796 4.572909 CTCCATCGCCAAGATTATCATCA 58.427 43.478 0.00 0.00 37.52 3.07
1762 12827 6.093495 CACTTTTCTTGGGATAGCAAATACGA 59.907 38.462 0.00 0.00 0.00 3.43
2128 13920 7.763172 AAGATCGTTTCTCAAGCTATGTTAG 57.237 36.000 0.00 0.00 31.78 2.34
2152 13944 4.859304 ACTCCGTGCGTTCCATAATATA 57.141 40.909 0.00 0.00 0.00 0.86
2153 13945 3.746045 ACTCCGTGCGTTCCATAATAT 57.254 42.857 0.00 0.00 0.00 1.28
2154 13946 3.380954 TGTACTCCGTGCGTTCCATAATA 59.619 43.478 0.00 0.00 0.00 0.98
2155 13947 2.166870 TGTACTCCGTGCGTTCCATAAT 59.833 45.455 0.00 0.00 0.00 1.28
2156 13948 1.545136 TGTACTCCGTGCGTTCCATAA 59.455 47.619 0.00 0.00 0.00 1.90
2168 13960 4.158025 ACAGGTGTCTAAAGATGTACTCCG 59.842 45.833 0.00 0.00 32.20 4.63
2182 13974 4.536765 AGAACAAATTTGGACAGGTGTCT 58.463 39.130 21.74 8.15 44.20 3.41
2215 14007 0.833287 TGATTGGCTACTCTGGCTCC 59.167 55.000 0.00 0.00 0.00 4.70
2234 14026 9.642343 TTGTATTCTAGTACAGAGGATACATGT 57.358 33.333 21.10 2.69 37.07 3.21
2240 14032 9.823647 CAATTGTTGTATTCTAGTACAGAGGAT 57.176 33.333 0.00 0.00 36.08 3.24
2301 14093 9.017509 GTGGTACTGGTATATATAAGTGTAGCA 57.982 37.037 18.12 18.12 35.66 3.49
2357 14149 0.974010 TATTTCCGGACGGAGGCAGT 60.974 55.000 13.64 0.00 46.06 4.40
2358 14150 0.529992 GTATTTCCGGACGGAGGCAG 60.530 60.000 13.64 0.00 46.06 4.85
2359 14151 0.974010 AGTATTTCCGGACGGAGGCA 60.974 55.000 13.64 2.92 46.06 4.75
2360 14152 0.177373 AAGTATTTCCGGACGGAGGC 59.823 55.000 13.64 5.83 46.06 4.70
2361 14153 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
2362 14154 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
2363 14155 1.135315 CGACAAGTATTTCCGGACGGA 60.135 52.381 1.83 9.76 43.52 4.69
2364 14156 1.274596 CGACAAGTATTTCCGGACGG 58.725 55.000 1.83 3.96 0.00 4.79
2365 14157 1.986698 ACGACAAGTATTTCCGGACG 58.013 50.000 1.83 3.25 0.00 4.79
2366 14158 4.361451 TCTACGACAAGTATTTCCGGAC 57.639 45.455 1.83 0.00 34.34 4.79
2367 14159 5.389859 TTTCTACGACAAGTATTTCCGGA 57.610 39.130 0.00 0.00 34.34 5.14
2368 14160 5.006358 CCATTTCTACGACAAGTATTTCCGG 59.994 44.000 0.00 0.00 34.34 5.14
2369 14161 5.808540 TCCATTTCTACGACAAGTATTTCCG 59.191 40.000 0.00 0.00 34.34 4.30
2370 14162 7.787725 ATCCATTTCTACGACAAGTATTTCC 57.212 36.000 0.00 0.00 34.34 3.13
2371 14163 9.309516 TGTATCCATTTCTACGACAAGTATTTC 57.690 33.333 0.00 0.00 34.34 2.17
2372 14164 9.661563 TTGTATCCATTTCTACGACAAGTATTT 57.338 29.630 0.00 0.00 34.34 1.40
2373 14165 9.661563 TTTGTATCCATTTCTACGACAAGTATT 57.338 29.630 0.00 0.00 34.34 1.89
2374 14166 9.832445 ATTTGTATCCATTTCTACGACAAGTAT 57.168 29.630 0.00 0.00 34.34 2.12
2375 14167 9.093970 CATTTGTATCCATTTCTACGACAAGTA 57.906 33.333 0.00 0.00 0.00 2.24
2376 14168 7.065803 CCATTTGTATCCATTTCTACGACAAGT 59.934 37.037 0.00 0.00 0.00 3.16
2377 14169 7.279981 TCCATTTGTATCCATTTCTACGACAAG 59.720 37.037 0.00 0.00 0.00 3.16
2378 14170 7.106890 TCCATTTGTATCCATTTCTACGACAA 58.893 34.615 0.00 0.00 0.00 3.18
2379 14171 6.645306 TCCATTTGTATCCATTTCTACGACA 58.355 36.000 0.00 0.00 0.00 4.35
2380 14172 7.226720 ACATCCATTTGTATCCATTTCTACGAC 59.773 37.037 0.00 0.00 0.00 4.34
2381 14173 7.279615 ACATCCATTTGTATCCATTTCTACGA 58.720 34.615 0.00 0.00 0.00 3.43
2382 14174 7.496529 ACATCCATTTGTATCCATTTCTACG 57.503 36.000 0.00 0.00 0.00 3.51
2419 14211 8.690884 CGAGGAATGGATGTATCTAGATGTATT 58.309 37.037 15.79 6.57 0.00 1.89
2420 14212 7.286546 CCGAGGAATGGATGTATCTAGATGTAT 59.713 40.741 15.79 9.11 0.00 2.29
2421 14213 6.603599 CCGAGGAATGGATGTATCTAGATGTA 59.396 42.308 15.79 4.44 0.00 2.29
2422 14214 5.420421 CCGAGGAATGGATGTATCTAGATGT 59.580 44.000 15.79 1.25 0.00 3.06
2423 14215 5.654209 TCCGAGGAATGGATGTATCTAGATG 59.346 44.000 15.79 0.00 0.00 2.90
2424 14216 5.654650 GTCCGAGGAATGGATGTATCTAGAT 59.345 44.000 10.73 10.73 37.93 1.98
2425 14217 5.010933 GTCCGAGGAATGGATGTATCTAGA 58.989 45.833 0.00 0.00 37.93 2.43
2426 14218 4.767409 TGTCCGAGGAATGGATGTATCTAG 59.233 45.833 0.00 0.00 37.93 2.43
2427 14219 4.736473 TGTCCGAGGAATGGATGTATCTA 58.264 43.478 0.00 0.00 37.93 1.98
2428 14220 3.576861 TGTCCGAGGAATGGATGTATCT 58.423 45.455 0.00 0.00 37.93 1.98
2429 14221 4.202264 ACTTGTCCGAGGAATGGATGTATC 60.202 45.833 0.00 0.00 37.93 2.24
2430 14222 3.711704 ACTTGTCCGAGGAATGGATGTAT 59.288 43.478 0.00 0.00 37.93 2.29
2431 14223 3.104512 ACTTGTCCGAGGAATGGATGTA 58.895 45.455 0.00 0.00 37.93 2.29
2432 14224 1.909302 ACTTGTCCGAGGAATGGATGT 59.091 47.619 0.00 0.00 37.93 3.06
2433 14225 2.698855 ACTTGTCCGAGGAATGGATG 57.301 50.000 0.00 0.00 37.93 3.51
2434 14226 5.373812 AAATACTTGTCCGAGGAATGGAT 57.626 39.130 0.00 0.00 37.93 3.41
2435 14227 4.837093 AAATACTTGTCCGAGGAATGGA 57.163 40.909 0.00 0.00 0.00 3.41
2436 14228 5.393027 CCAAAAATACTTGTCCGAGGAATGG 60.393 44.000 0.00 0.00 0.00 3.16
2437 14229 5.414454 TCCAAAAATACTTGTCCGAGGAATG 59.586 40.000 0.00 0.00 0.00 2.67
2438 14230 5.414765 GTCCAAAAATACTTGTCCGAGGAAT 59.585 40.000 0.00 0.00 0.00 3.01
2439 14231 4.758165 GTCCAAAAATACTTGTCCGAGGAA 59.242 41.667 0.00 0.00 0.00 3.36
2440 14232 4.320870 GTCCAAAAATACTTGTCCGAGGA 58.679 43.478 0.00 0.00 0.00 3.71
2441 14233 3.124636 CGTCCAAAAATACTTGTCCGAGG 59.875 47.826 0.00 0.00 0.00 4.63
2442 14234 3.124636 CCGTCCAAAAATACTTGTCCGAG 59.875 47.826 0.00 0.00 0.00 4.63
2443 14235 3.068560 CCGTCCAAAAATACTTGTCCGA 58.931 45.455 0.00 0.00 0.00 4.55
2444 14236 3.068560 TCCGTCCAAAAATACTTGTCCG 58.931 45.455 0.00 0.00 0.00 4.79
2445 14237 3.439129 CCTCCGTCCAAAAATACTTGTCC 59.561 47.826 0.00 0.00 0.00 4.02
2446 14238 3.439129 CCCTCCGTCCAAAAATACTTGTC 59.561 47.826 0.00 0.00 0.00 3.18
2447 14239 3.073356 TCCCTCCGTCCAAAAATACTTGT 59.927 43.478 0.00 0.00 0.00 3.16
2448 14240 3.681593 TCCCTCCGTCCAAAAATACTTG 58.318 45.455 0.00 0.00 0.00 3.16
2449 14241 3.329814 ACTCCCTCCGTCCAAAAATACTT 59.670 43.478 0.00 0.00 0.00 2.24
2450 14242 2.910977 ACTCCCTCCGTCCAAAAATACT 59.089 45.455 0.00 0.00 0.00 2.12
2451 14243 3.345508 ACTCCCTCCGTCCAAAAATAC 57.654 47.619 0.00 0.00 0.00 1.89
2452 14244 4.098894 AGTACTCCCTCCGTCCAAAAATA 58.901 43.478 0.00 0.00 0.00 1.40
2453 14245 2.910977 AGTACTCCCTCCGTCCAAAAAT 59.089 45.455 0.00 0.00 0.00 1.82
2454 14246 2.332117 AGTACTCCCTCCGTCCAAAAA 58.668 47.619 0.00 0.00 0.00 1.94
2455 14247 2.019807 AGTACTCCCTCCGTCCAAAA 57.980 50.000 0.00 0.00 0.00 2.44
2456 14248 2.622452 CCTAGTACTCCCTCCGTCCAAA 60.622 54.545 0.00 0.00 0.00 3.28
2457 14249 1.064166 CCTAGTACTCCCTCCGTCCAA 60.064 57.143 0.00 0.00 0.00 3.53
2458 14250 0.549950 CCTAGTACTCCCTCCGTCCA 59.450 60.000 0.00 0.00 0.00 4.02
2459 14251 0.550432 ACCTAGTACTCCCTCCGTCC 59.450 60.000 0.00 0.00 0.00 4.79
2460 14252 2.433662 AACCTAGTACTCCCTCCGTC 57.566 55.000 0.00 0.00 0.00 4.79
2461 14253 4.322057 TTTAACCTAGTACTCCCTCCGT 57.678 45.455 0.00 0.00 0.00 4.69
2462 14254 5.866159 ATTTTAACCTAGTACTCCCTCCG 57.134 43.478 0.00 0.00 0.00 4.63
2463 14255 8.316497 AGTAATTTTAACCTAGTACTCCCTCC 57.684 38.462 0.00 0.00 0.00 4.30
2464 14256 9.597170 CAAGTAATTTTAACCTAGTACTCCCTC 57.403 37.037 0.00 0.00 0.00 4.30
2465 14257 9.109246 ACAAGTAATTTTAACCTAGTACTCCCT 57.891 33.333 0.00 0.00 0.00 4.20
2466 14258 9.730705 AACAAGTAATTTTAACCTAGTACTCCC 57.269 33.333 0.00 0.00 0.00 4.30
2473 14265 9.797556 GGCCAATAACAAGTAATTTTAACCTAG 57.202 33.333 0.00 0.00 0.00 3.02
2482 14274 6.630188 GCTCAATGGGCCAATAACAAGTAATT 60.630 38.462 11.89 0.00 0.00 1.40
2503 14295 5.172687 TGTATGGTTATTTGACCTGCTCA 57.827 39.130 0.00 0.00 40.47 4.26
2515 14307 5.833131 CCAGGCCAAATAGTTGTATGGTTAT 59.167 40.000 5.01 0.00 35.34 1.89
2516 14308 5.197451 CCAGGCCAAATAGTTGTATGGTTA 58.803 41.667 5.01 0.00 35.34 2.85
2559 14351 4.588899 TGATGTGTTCATAGGGTTTCAGG 58.411 43.478 0.00 0.00 34.06 3.86
2560 14352 5.124457 CCTTGATGTGTTCATAGGGTTTCAG 59.876 44.000 0.00 0.00 33.34 3.02


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

AutoCloner maintained by Alex Coulton.