Multiple sequence alignment - TraesCS7B01G234500

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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 TraesCS7B01G234500 chr7B 100.000 2972 0 0 1 2972 438881867 438878896 0.000000e+00 5489.0
1 TraesCS7B01G234500 chr7D 91.975 1919 84 17 364 2237 422209701 422211594 0.000000e+00 2627.0
2 TraesCS7B01G234500 chr7D 79.372 223 25 8 2 204 422726663 422726884 1.440000e-28 137.0
3 TraesCS7B01G234500 chr7D 89.583 96 9 1 902 996 621067871 621067966 1.450000e-23 121.0
4 TraesCS7B01G234500 chr7D 97.368 38 0 1 298 334 422209674 422209711 2.470000e-06 63.9
5 TraesCS7B01G234500 chr7A 89.892 1939 106 29 432 2300 510907800 510905882 0.000000e+00 2412.0
6 TraesCS7B01G234500 chr1B 95.165 393 17 2 1190 1581 650473593 650473202 1.170000e-173 619.0
7 TraesCS7B01G234500 chr1B 96.296 108 4 0 1031 1138 650473010 650473117 8.470000e-41 178.0
8 TraesCS7B01G234500 chr2B 83.571 700 68 24 2298 2972 557224165 557223488 1.960000e-171 612.0
9 TraesCS7B01G234500 chr2B 77.451 306 53 14 2 299 3905465 3905762 5.090000e-38 169.0
10 TraesCS7B01G234500 chr2D 81.745 745 101 15 902 1622 649879999 649880732 9.180000e-165 590.0
11 TraesCS7B01G234500 chr2A 80.052 762 99 19 914 1640 734293246 734292503 1.580000e-142 516.0
12 TraesCS7B01G234500 chr4D 81.305 567 100 4 2405 2971 337474134 337473574 3.490000e-124 455.0
13 TraesCS7B01G234500 chr3D 82.143 504 70 6 905 1396 575514726 575514231 5.930000e-112 414.0
14 TraesCS7B01G234500 chr3D 80.815 417 67 7 2298 2710 11421164 11421571 6.180000e-82 315.0
15 TraesCS7B01G234500 chr5B 79.327 416 71 8 2298 2710 596702214 596702617 8.110000e-71 278.0
16 TraesCS7B01G234500 chr5B 78.333 420 66 12 2298 2710 511659390 511659791 6.360000e-62 248.0
17 TraesCS7B01G234500 chr5B 79.819 332 33 9 2 299 591133611 591133280 8.350000e-51 211.0
18 TraesCS7B01G234500 chr1A 82.075 318 33 12 2 296 562071587 562071903 1.770000e-62 250.0
19 TraesCS7B01G234500 chr1A 82.488 217 38 0 1075 1291 4159727 4159511 1.090000e-44 191.0


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 TraesCS7B01G234500 chr7B 438878896 438881867 2971 True 5489.00 5489 100.0000 1 2972 1 chr7B.!!$R1 2971
1 TraesCS7B01G234500 chr7D 422209674 422211594 1920 False 1345.45 2627 94.6715 298 2237 2 chr7D.!!$F3 1939
2 TraesCS7B01G234500 chr7A 510905882 510907800 1918 True 2412.00 2412 89.8920 432 2300 1 chr7A.!!$R1 1868
3 TraesCS7B01G234500 chr2B 557223488 557224165 677 True 612.00 612 83.5710 2298 2972 1 chr2B.!!$R1 674
4 TraesCS7B01G234500 chr2D 649879999 649880732 733 False 590.00 590 81.7450 902 1622 1 chr2D.!!$F1 720
5 TraesCS7B01G234500 chr2A 734292503 734293246 743 True 516.00 516 80.0520 914 1640 1 chr2A.!!$R1 726
6 TraesCS7B01G234500 chr4D 337473574 337474134 560 True 455.00 455 81.3050 2405 2971 1 chr4D.!!$R1 566

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
74 75 0.034337 GTAGTTCAGGTTGTCGCCCA 59.966 55.0 0.0 0.0 0.0 5.36 F
75 76 0.034337 TAGTTCAGGTTGTCGCCCAC 59.966 55.0 0.0 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1024 1083 0.027586 GCAGCGTCGTCAAAAGTGTT 59.972 50.0 0.0 0.0 0.0 3.32 R
2023 2133 0.961019 TCAGTGCCATTGTTGCTTCC 59.039 50.0 0.0 0.0 0.0 3.46 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
18 19 3.372557 AGGCCAGATCCCGATCTAG 57.627 57.895 5.01 1.58 45.78 2.43
19 20 0.780637 AGGCCAGATCCCGATCTAGA 59.219 55.000 5.01 0.00 45.78 2.43
20 21 1.360852 AGGCCAGATCCCGATCTAGAT 59.639 52.381 5.01 4.47 45.78 1.98
21 22 1.754226 GGCCAGATCCCGATCTAGATC 59.246 57.143 20.93 20.93 45.78 2.75
29 30 2.179517 GATCTAGATCGGCCGCGG 59.820 66.667 24.05 24.05 0.00 6.46
30 31 2.597805 ATCTAGATCGGCCGCGGT 60.598 61.111 28.70 6.29 0.00 5.68
31 32 2.804368 GATCTAGATCGGCCGCGGTG 62.804 65.000 28.70 19.94 0.00 4.94
49 50 3.314331 CAGACACGCCCCTCCACT 61.314 66.667 0.00 0.00 0.00 4.00
50 51 3.314331 AGACACGCCCCTCCACTG 61.314 66.667 0.00 0.00 0.00 3.66
51 52 3.626924 GACACGCCCCTCCACTGT 61.627 66.667 0.00 0.00 0.00 3.55
52 53 3.883744 GACACGCCCCTCCACTGTG 62.884 68.421 0.00 0.00 36.64 3.66
53 54 3.625897 CACGCCCCTCCACTGTGA 61.626 66.667 9.86 0.00 32.39 3.58
54 55 3.314331 ACGCCCCTCCACTGTGAG 61.314 66.667 9.86 4.94 0.00 3.51
62 63 2.248248 CCTCCACTGTGAGGTAGTTCA 58.752 52.381 9.86 0.00 45.76 3.18
63 64 2.232452 CCTCCACTGTGAGGTAGTTCAG 59.768 54.545 9.86 0.00 45.76 3.02
64 65 2.232452 CTCCACTGTGAGGTAGTTCAGG 59.768 54.545 9.86 0.00 32.92 3.86
65 66 1.971357 CCACTGTGAGGTAGTTCAGGT 59.029 52.381 9.86 0.00 32.92 4.00
66 67 2.368875 CCACTGTGAGGTAGTTCAGGTT 59.631 50.000 9.86 0.00 32.92 3.50
67 68 3.393800 CACTGTGAGGTAGTTCAGGTTG 58.606 50.000 0.32 0.00 32.92 3.77
68 69 3.039011 ACTGTGAGGTAGTTCAGGTTGT 58.961 45.455 0.00 0.00 32.92 3.32
69 70 3.069729 ACTGTGAGGTAGTTCAGGTTGTC 59.930 47.826 0.00 0.00 32.92 3.18
70 71 2.035449 TGTGAGGTAGTTCAGGTTGTCG 59.965 50.000 0.00 0.00 0.00 4.35
71 72 1.000506 TGAGGTAGTTCAGGTTGTCGC 59.999 52.381 0.00 0.00 0.00 5.19
72 73 0.320697 AGGTAGTTCAGGTTGTCGCC 59.679 55.000 0.00 0.00 0.00 5.54
73 74 0.672711 GGTAGTTCAGGTTGTCGCCC 60.673 60.000 0.00 0.00 0.00 6.13
74 75 0.034337 GTAGTTCAGGTTGTCGCCCA 59.966 55.000 0.00 0.00 0.00 5.36
75 76 0.034337 TAGTTCAGGTTGTCGCCCAC 59.966 55.000 0.00 0.00 0.00 4.61
76 77 2.112297 TTCAGGTTGTCGCCCACC 59.888 61.111 0.00 0.00 0.00 4.61
77 78 3.485346 TTCAGGTTGTCGCCCACCC 62.485 63.158 0.00 0.00 0.00 4.61
174 175 4.377760 ACCCCGAGCGAGGAGGAA 62.378 66.667 0.00 0.00 0.00 3.36
175 176 3.075005 CCCCGAGCGAGGAGGAAA 61.075 66.667 1.91 0.00 0.00 3.13
176 177 2.656069 CCCCGAGCGAGGAGGAAAA 61.656 63.158 1.91 0.00 0.00 2.29
177 178 1.295423 CCCGAGCGAGGAGGAAAAA 59.705 57.895 1.91 0.00 0.00 1.94
178 179 0.741221 CCCGAGCGAGGAGGAAAAAG 60.741 60.000 1.91 0.00 0.00 2.27
179 180 0.741221 CCGAGCGAGGAGGAAAAAGG 60.741 60.000 0.00 0.00 0.00 3.11
180 181 1.362406 CGAGCGAGGAGGAAAAAGGC 61.362 60.000 0.00 0.00 0.00 4.35
181 182 1.002011 AGCGAGGAGGAAAAAGGCC 60.002 57.895 0.00 0.00 0.00 5.19
182 183 2.046864 GCGAGGAGGAAAAAGGCCC 61.047 63.158 0.00 0.00 0.00 5.80
183 184 1.378646 CGAGGAGGAAAAAGGCCCC 60.379 63.158 0.00 0.00 0.00 5.80
184 185 1.378646 GAGGAGGAAAAAGGCCCCG 60.379 63.158 0.00 0.00 0.00 5.73
185 186 3.068691 GGAGGAAAAAGGCCCCGC 61.069 66.667 0.00 0.00 0.00 6.13
224 225 4.572571 TTTGCCCGGCCACGTCTT 62.573 61.111 7.03 0.00 38.78 3.01
227 228 3.766691 GCCCGGCCACGTCTTCTA 61.767 66.667 2.24 0.00 38.78 2.10
228 229 2.494918 CCCGGCCACGTCTTCTAG 59.505 66.667 2.24 0.00 38.78 2.43
229 230 2.202756 CCGGCCACGTCTTCTAGC 60.203 66.667 2.24 0.00 38.78 3.42
230 231 2.579787 CGGCCACGTCTTCTAGCG 60.580 66.667 2.24 0.00 34.81 4.26
231 232 2.202756 GGCCACGTCTTCTAGCGG 60.203 66.667 0.00 0.00 0.00 5.52
232 233 2.886124 GCCACGTCTTCTAGCGGC 60.886 66.667 0.00 0.00 0.00 6.53
233 234 2.579787 CCACGTCTTCTAGCGGCG 60.580 66.667 0.51 0.51 0.00 6.46
234 235 2.579787 CACGTCTTCTAGCGGCGG 60.580 66.667 9.78 0.00 0.00 6.13
235 236 4.493747 ACGTCTTCTAGCGGCGGC 62.494 66.667 9.78 8.43 40.37 6.53
237 238 4.189188 GTCTTCTAGCGGCGGCGA 62.189 66.667 36.87 14.73 46.35 5.54
238 239 3.889044 TCTTCTAGCGGCGGCGAG 61.889 66.667 36.87 24.09 46.35 5.03
239 240 4.933064 CTTCTAGCGGCGGCGAGG 62.933 72.222 36.87 22.16 46.35 4.63
250 251 4.154347 GGCGAGGGAGGAGTGCAG 62.154 72.222 0.00 0.00 0.00 4.41
251 252 4.154347 GCGAGGGAGGAGTGCAGG 62.154 72.222 0.00 0.00 0.00 4.85
252 253 3.465403 CGAGGGAGGAGTGCAGGG 61.465 72.222 0.00 0.00 0.00 4.45
253 254 3.086600 GAGGGAGGAGTGCAGGGG 61.087 72.222 0.00 0.00 0.00 4.79
254 255 4.748798 AGGGAGGAGTGCAGGGGG 62.749 72.222 0.00 0.00 0.00 5.40
255 256 4.741239 GGGAGGAGTGCAGGGGGA 62.741 72.222 0.00 0.00 0.00 4.81
256 257 3.086600 GGAGGAGTGCAGGGGGAG 61.087 72.222 0.00 0.00 0.00 4.30
257 258 2.039624 GAGGAGTGCAGGGGGAGA 59.960 66.667 0.00 0.00 0.00 3.71
258 259 2.040278 AGGAGTGCAGGGGGAGAG 59.960 66.667 0.00 0.00 0.00 3.20
259 260 2.039624 GGAGTGCAGGGGGAGAGA 59.960 66.667 0.00 0.00 0.00 3.10
260 261 2.063378 GGAGTGCAGGGGGAGAGAG 61.063 68.421 0.00 0.00 0.00 3.20
261 262 1.000993 GAGTGCAGGGGGAGAGAGA 59.999 63.158 0.00 0.00 0.00 3.10
262 263 1.305718 AGTGCAGGGGGAGAGAGAC 60.306 63.158 0.00 0.00 0.00 3.36
263 264 2.039624 TGCAGGGGGAGAGAGACC 59.960 66.667 0.00 0.00 0.00 3.85
264 265 3.151022 GCAGGGGGAGAGAGACCG 61.151 72.222 0.00 0.00 0.00 4.79
265 266 2.443016 CAGGGGGAGAGAGACCGG 60.443 72.222 0.00 0.00 0.00 5.28
266 267 4.467107 AGGGGGAGAGAGACCGGC 62.467 72.222 0.00 0.00 0.00 6.13
298 299 4.075793 AGCCCTCCCTGTCGCCTA 62.076 66.667 0.00 0.00 0.00 3.93
299 300 3.081409 GCCCTCCCTGTCGCCTAA 61.081 66.667 0.00 0.00 0.00 2.69
300 301 2.901042 CCCTCCCTGTCGCCTAAC 59.099 66.667 0.00 0.00 0.00 2.34
301 302 1.987855 CCCTCCCTGTCGCCTAACA 60.988 63.158 0.00 0.00 0.00 2.41
334 335 4.569943 TCATGTACCAAAGAGAGAGTTGC 58.430 43.478 0.00 0.00 0.00 4.17
336 337 2.972713 TGTACCAAAGAGAGAGTTGCCT 59.027 45.455 0.00 0.00 0.00 4.75
337 338 3.391296 TGTACCAAAGAGAGAGTTGCCTT 59.609 43.478 0.00 0.00 0.00 4.35
338 339 3.133141 ACCAAAGAGAGAGTTGCCTTC 57.867 47.619 0.00 0.00 0.00 3.46
339 340 2.708325 ACCAAAGAGAGAGTTGCCTTCT 59.292 45.455 0.00 0.00 0.00 2.85
340 341 3.244387 ACCAAAGAGAGAGTTGCCTTCTC 60.244 47.826 2.04 2.04 41.08 2.87
348 349 4.696479 AGAGTTGCCTTCTCTCTCAAAA 57.304 40.909 0.00 0.00 37.70 2.44
349 350 5.041191 AGAGTTGCCTTCTCTCTCAAAAA 57.959 39.130 0.00 0.00 37.70 1.94
350 351 5.062528 AGAGTTGCCTTCTCTCTCAAAAAG 58.937 41.667 0.00 0.00 37.70 2.27
351 352 5.041191 AGTTGCCTTCTCTCTCAAAAAGA 57.959 39.130 0.00 0.00 0.00 2.52
367 368 6.778821 TCAAAAAGAGAGAGAGAGAGAGAGA 58.221 40.000 0.00 0.00 0.00 3.10
368 369 6.881065 TCAAAAAGAGAGAGAGAGAGAGAGAG 59.119 42.308 0.00 0.00 0.00 3.20
369 370 6.627087 AAAAGAGAGAGAGAGAGAGAGAGA 57.373 41.667 0.00 0.00 0.00 3.10
370 371 5.867903 AAGAGAGAGAGAGAGAGAGAGAG 57.132 47.826 0.00 0.00 0.00 3.20
371 372 4.877773 AGAGAGAGAGAGAGAGAGAGAGT 58.122 47.826 0.00 0.00 0.00 3.24
372 373 5.276440 AGAGAGAGAGAGAGAGAGAGAGTT 58.724 45.833 0.00 0.00 0.00 3.01
373 374 5.128499 AGAGAGAGAGAGAGAGAGAGAGTTG 59.872 48.000 0.00 0.00 0.00 3.16
374 375 3.873952 GAGAGAGAGAGAGAGAGAGTTGC 59.126 52.174 0.00 0.00 0.00 4.17
375 376 2.945668 GAGAGAGAGAGAGAGAGTTGCC 59.054 54.545 0.00 0.00 0.00 4.52
376 377 2.578021 AGAGAGAGAGAGAGAGTTGCCT 59.422 50.000 0.00 0.00 0.00 4.75
390 391 1.653094 TTGCCTTATTTCGCAGCCGG 61.653 55.000 0.00 0.00 36.14 6.13
397 398 0.958822 ATTTCGCAGCCGGAAAACTT 59.041 45.000 5.05 0.00 35.20 2.66
409 410 1.666888 GGAAAACTTGGTGCATCGCTG 60.667 52.381 0.00 0.00 0.00 5.18
411 412 0.311790 AAACTTGGTGCATCGCTGTG 59.688 50.000 0.00 0.00 0.00 3.66
430 431 1.798735 CATCTTGTGCCTGCGAAGG 59.201 57.895 4.49 4.49 0.00 3.46
469 480 3.493503 CGTTTTAGACCGAAGAGTTGCTT 59.506 43.478 0.00 0.00 40.25 3.91
508 519 5.617252 ACTTATCGTTTTGAACCTTCTCCA 58.383 37.500 0.00 0.00 0.00 3.86
518 529 4.836825 TGAACCTTCTCCAGATCATGTTC 58.163 43.478 0.00 0.00 33.32 3.18
523 534 3.808466 TCTCCAGATCATGTTCTTCGG 57.192 47.619 3.44 4.03 0.00 4.30
542 553 2.017049 GGAAAGGATTGTGTCATCGGG 58.983 52.381 0.00 0.00 0.00 5.14
546 557 2.408565 AGGATTGTGTCATCGGGGTAT 58.591 47.619 0.00 0.00 0.00 2.73
567 578 2.803956 TGTACTATGGATAGGCCCTCG 58.196 52.381 0.00 0.00 34.69 4.63
573 584 1.067582 GGATAGGCCCTCGTCAACG 59.932 63.158 0.00 0.00 41.45 4.10
774 823 1.521450 CCACCAGCAGCAAAGTCCAG 61.521 60.000 0.00 0.00 0.00 3.86
911 970 2.333938 CGTCGACGACCACACCTT 59.666 61.111 33.35 0.00 43.02 3.50
996 1055 2.255252 CAGAGGTTTTTGGCCGCG 59.745 61.111 0.00 0.00 0.00 6.46
1210 1286 2.046023 CGCCTCCAGCATTCCACA 60.046 61.111 0.00 0.00 44.04 4.17
1671 1767 3.832276 CGAATCGAAGGAGAGGATCATC 58.168 50.000 0.00 0.00 37.82 2.92
1728 1824 5.189539 TGATTACACCATGTCAAGATCTCCA 59.810 40.000 0.00 0.00 0.00 3.86
1773 1875 2.305127 GGTGGACGAACGGTGTTCG 61.305 63.158 25.30 25.30 46.36 3.95
1788 1890 3.145422 TTCGCTGTCACAGTCGCCA 62.145 57.895 14.47 3.87 33.56 5.69
1902 2004 1.212616 GCACAGATGCGAGTATGTCC 58.787 55.000 0.00 0.00 43.33 4.02
1997 2107 3.304928 GGTGCAGGAACAAAGTCAATCAG 60.305 47.826 0.00 0.00 0.00 2.90
2011 2121 2.291465 TCAATCAGTTCAGTTGCACAGC 59.709 45.455 0.00 0.00 0.00 4.40
2013 2123 0.461870 TCAGTTCAGTTGCACAGCGT 60.462 50.000 0.00 0.00 0.00 5.07
2038 2148 3.577848 AGTAAATGGAAGCAACAATGGCA 59.422 39.130 0.00 0.00 0.00 4.92
2114 2231 1.403323 GCTGCCATCCAACTCTTTAGC 59.597 52.381 0.00 0.00 0.00 3.09
2165 2282 8.662781 ATGTAAATATTCAGCGTTGAGTATGT 57.337 30.769 16.04 13.60 36.64 2.29
2203 2320 4.942761 AGAAAATGACCAAAGTGCATGT 57.057 36.364 0.00 0.00 0.00 3.21
2216 2333 4.789012 AGTGCATGTCCATAAACCTTTG 57.211 40.909 0.00 0.00 0.00 2.77
2238 2355 5.511363 TGTTTGTCCCCAGTTTCTTCTTAA 58.489 37.500 0.00 0.00 0.00 1.85
2269 2387 9.614792 TTTTTGAGTTAGAGTTTCTTCTTAGCT 57.385 29.630 0.00 0.00 0.00 3.32
2300 2423 1.574702 GCCGTACACAACAAGAGGGC 61.575 60.000 0.00 0.00 0.00 5.19
2301 2424 1.289109 CCGTACACAACAAGAGGGCG 61.289 60.000 0.00 0.00 0.00 6.13
2302 2425 0.319211 CGTACACAACAAGAGGGCGA 60.319 55.000 0.00 0.00 0.00 5.54
2303 2426 1.145803 GTACACAACAAGAGGGCGAC 58.854 55.000 0.00 0.00 0.00 5.19
2345 2468 4.062032 GGGTTTCCCTCCCCAGCC 62.062 72.222 0.00 0.00 41.34 4.85
2428 2552 1.973812 GGGGCTGTTTGTCTCCTGC 60.974 63.158 0.00 0.00 0.00 4.85
2464 2588 3.679755 GGGCTCCATCCCCTTGAT 58.320 61.111 0.00 0.00 40.51 2.57
2522 2646 1.601419 TTTCTCCCGACGCCCTACTG 61.601 60.000 0.00 0.00 0.00 2.74
2549 2673 1.026182 GGCACGACATCCATCTTGCA 61.026 55.000 6.58 0.00 43.69 4.08
2566 2714 0.890542 GCAGTGGATCTGTGTTGGCA 60.891 55.000 0.00 0.00 45.23 4.92
2642 2790 1.749033 GGGATGGAGGCTAAGGACG 59.251 63.158 0.00 0.00 0.00 4.79
2653 2801 1.077212 TAAGGACGTAGGAGCGGCT 60.077 57.895 0.00 0.00 40.27 5.52
2702 2850 2.311070 ATCTGGTGGCCATGCTCCA 61.311 57.895 9.72 11.15 30.82 3.86
2761 2909 3.991051 CGTGGAGGTGCGAGGTGT 61.991 66.667 0.00 0.00 0.00 4.16
2763 2911 1.961277 GTGGAGGTGCGAGGTGTTG 60.961 63.158 0.00 0.00 0.00 3.33
2792 2940 4.457496 GGAGCACCAGCGCTGCTA 62.457 66.667 31.96 0.00 45.23 3.49
2801 2949 2.743928 GCGCTGCTAAGGTGCTGT 60.744 61.111 0.00 0.00 37.25 4.40
2859 3007 1.134401 GGTTCATTGAGCAGATCCGGA 60.134 52.381 6.61 6.61 0.00 5.14
2865 3013 3.348647 TTGAGCAGATCCGGATGAAAA 57.651 42.857 24.82 4.62 0.00 2.29
2870 3018 3.706594 AGCAGATCCGGATGAAAACTCTA 59.293 43.478 24.82 0.00 0.00 2.43
2872 3020 4.045104 CAGATCCGGATGAAAACTCTACG 58.955 47.826 24.82 0.00 0.00 3.51
2884 3032 2.835580 ACTCTACGCTCGGCTAGATA 57.164 50.000 0.00 0.00 0.00 1.98
2899 3047 1.961277 GATACCAAGGCCGGCGATG 60.961 63.158 22.54 21.01 0.00 3.84
2929 3077 2.125633 GGCGTCGTCCCCTTCTTC 60.126 66.667 0.00 0.00 0.00 2.87
2930 3078 2.125633 GCGTCGTCCCCTTCTTCC 60.126 66.667 0.00 0.00 0.00 3.46
2949 3097 0.389817 CAGGCATCGTCGTGGAGAAA 60.390 55.000 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.780637 TCTAGATCGGGATCTGGCCT 59.219 55.000 18.96 0.00 46.80 5.19
12 13 2.179517 CCGCGGCCGATCTAGATC 59.820 66.667 33.48 20.93 36.29 2.75
13 14 2.597805 ACCGCGGCCGATCTAGAT 60.598 61.111 33.48 4.47 36.29 1.98
14 15 3.592814 CACCGCGGCCGATCTAGA 61.593 66.667 33.48 0.00 36.29 2.43
32 33 3.314331 AGTGGAGGGGCGTGTCTG 61.314 66.667 0.00 0.00 0.00 3.51
33 34 3.314331 CAGTGGAGGGGCGTGTCT 61.314 66.667 0.00 0.00 0.00 3.41
34 35 3.626924 ACAGTGGAGGGGCGTGTC 61.627 66.667 0.00 0.00 0.00 3.67
35 36 3.941188 CACAGTGGAGGGGCGTGT 61.941 66.667 0.00 0.00 0.00 4.49
36 37 3.596066 CTCACAGTGGAGGGGCGTG 62.596 68.421 0.00 0.00 0.00 5.34
37 38 3.314331 CTCACAGTGGAGGGGCGT 61.314 66.667 0.00 0.00 0.00 5.68
43 44 2.232452 CCTGAACTACCTCACAGTGGAG 59.768 54.545 0.00 0.00 34.62 3.86
44 45 2.248248 CCTGAACTACCTCACAGTGGA 58.752 52.381 0.00 0.00 0.00 4.02
45 46 1.971357 ACCTGAACTACCTCACAGTGG 59.029 52.381 0.00 0.00 0.00 4.00
46 47 3.181465 ACAACCTGAACTACCTCACAGTG 60.181 47.826 0.00 0.00 0.00 3.66
47 48 3.039011 ACAACCTGAACTACCTCACAGT 58.961 45.455 0.00 0.00 0.00 3.55
48 49 3.654414 GACAACCTGAACTACCTCACAG 58.346 50.000 0.00 0.00 0.00 3.66
49 50 2.035449 CGACAACCTGAACTACCTCACA 59.965 50.000 0.00 0.00 0.00 3.58
50 51 2.673833 CGACAACCTGAACTACCTCAC 58.326 52.381 0.00 0.00 0.00 3.51
51 52 1.000506 GCGACAACCTGAACTACCTCA 59.999 52.381 0.00 0.00 0.00 3.86
52 53 1.672145 GGCGACAACCTGAACTACCTC 60.672 57.143 0.00 0.00 0.00 3.85
53 54 0.320697 GGCGACAACCTGAACTACCT 59.679 55.000 0.00 0.00 0.00 3.08
54 55 0.672711 GGGCGACAACCTGAACTACC 60.673 60.000 0.00 0.00 0.00 3.18
55 56 0.034337 TGGGCGACAACCTGAACTAC 59.966 55.000 0.00 0.00 0.00 2.73
56 57 0.034337 GTGGGCGACAACCTGAACTA 59.966 55.000 0.00 0.00 0.00 2.24
57 58 1.227853 GTGGGCGACAACCTGAACT 60.228 57.895 0.00 0.00 0.00 3.01
58 59 2.258726 GGTGGGCGACAACCTGAAC 61.259 63.158 7.91 0.00 0.00 3.18
59 60 2.112297 GGTGGGCGACAACCTGAA 59.888 61.111 7.91 0.00 0.00 3.02
157 158 3.899545 TTTCCTCCTCGCTCGGGGT 62.900 63.158 8.17 0.00 37.00 4.95
158 159 2.180159 TTTTTCCTCCTCGCTCGGGG 62.180 60.000 0.89 0.89 37.02 5.73
159 160 0.741221 CTTTTTCCTCCTCGCTCGGG 60.741 60.000 0.00 0.00 0.00 5.14
160 161 0.741221 CCTTTTTCCTCCTCGCTCGG 60.741 60.000 0.00 0.00 0.00 4.63
161 162 1.362406 GCCTTTTTCCTCCTCGCTCG 61.362 60.000 0.00 0.00 0.00 5.03
162 163 1.027255 GGCCTTTTTCCTCCTCGCTC 61.027 60.000 0.00 0.00 0.00 5.03
163 164 1.002011 GGCCTTTTTCCTCCTCGCT 60.002 57.895 0.00 0.00 0.00 4.93
164 165 2.046864 GGGCCTTTTTCCTCCTCGC 61.047 63.158 0.84 0.00 0.00 5.03
165 166 1.378646 GGGGCCTTTTTCCTCCTCG 60.379 63.158 0.84 0.00 0.00 4.63
166 167 1.378646 CGGGGCCTTTTTCCTCCTC 60.379 63.158 0.84 0.00 0.00 3.71
167 168 2.763902 CGGGGCCTTTTTCCTCCT 59.236 61.111 0.84 0.00 0.00 3.69
168 169 3.068691 GCGGGGCCTTTTTCCTCC 61.069 66.667 0.84 0.00 0.00 4.30
169 170 3.068691 GGCGGGGCCTTTTTCCTC 61.069 66.667 0.84 0.00 46.69 3.71
207 208 4.572571 AAGACGTGGCCGGGCAAA 62.573 61.111 34.51 8.45 38.78 3.68
210 211 3.718210 CTAGAAGACGTGGCCGGGC 62.718 68.421 23.42 23.42 38.78 6.13
211 212 2.494918 CTAGAAGACGTGGCCGGG 59.505 66.667 2.18 0.00 38.78 5.73
212 213 2.202756 GCTAGAAGACGTGGCCGG 60.203 66.667 0.00 0.00 38.78 6.13
213 214 2.579787 CGCTAGAAGACGTGGCCG 60.580 66.667 0.00 0.00 40.83 6.13
214 215 2.202756 CCGCTAGAAGACGTGGCC 60.203 66.667 0.00 0.00 0.00 5.36
216 217 2.579787 CGCCGCTAGAAGACGTGG 60.580 66.667 0.00 0.00 0.00 4.94
217 218 2.579787 CCGCCGCTAGAAGACGTG 60.580 66.667 0.00 0.00 0.00 4.49
218 219 4.493747 GCCGCCGCTAGAAGACGT 62.494 66.667 0.00 0.00 0.00 4.34
220 221 4.189188 TCGCCGCCGCTAGAAGAC 62.189 66.667 0.00 0.00 0.00 3.01
221 222 3.889044 CTCGCCGCCGCTAGAAGA 61.889 66.667 0.00 0.00 29.27 2.87
222 223 4.933064 CCTCGCCGCCGCTAGAAG 62.933 72.222 0.00 0.00 29.27 2.85
233 234 4.154347 CTGCACTCCTCCCTCGCC 62.154 72.222 0.00 0.00 0.00 5.54
234 235 4.154347 CCTGCACTCCTCCCTCGC 62.154 72.222 0.00 0.00 0.00 5.03
235 236 3.465403 CCCTGCACTCCTCCCTCG 61.465 72.222 0.00 0.00 0.00 4.63
236 237 3.086600 CCCCTGCACTCCTCCCTC 61.087 72.222 0.00 0.00 0.00 4.30
237 238 4.748798 CCCCCTGCACTCCTCCCT 62.749 72.222 0.00 0.00 0.00 4.20
238 239 4.741239 TCCCCCTGCACTCCTCCC 62.741 72.222 0.00 0.00 0.00 4.30
239 240 3.086600 CTCCCCCTGCACTCCTCC 61.087 72.222 0.00 0.00 0.00 4.30
240 241 2.039624 TCTCCCCCTGCACTCCTC 59.960 66.667 0.00 0.00 0.00 3.71
241 242 2.040278 CTCTCCCCCTGCACTCCT 59.960 66.667 0.00 0.00 0.00 3.69
242 243 2.039624 TCTCTCCCCCTGCACTCC 59.960 66.667 0.00 0.00 0.00 3.85
243 244 1.000993 TCTCTCTCCCCCTGCACTC 59.999 63.158 0.00 0.00 0.00 3.51
244 245 1.305718 GTCTCTCTCCCCCTGCACT 60.306 63.158 0.00 0.00 0.00 4.40
245 246 2.363172 GGTCTCTCTCCCCCTGCAC 61.363 68.421 0.00 0.00 0.00 4.57
246 247 2.039624 GGTCTCTCTCCCCCTGCA 59.960 66.667 0.00 0.00 0.00 4.41
247 248 3.151022 CGGTCTCTCTCCCCCTGC 61.151 72.222 0.00 0.00 0.00 4.85
248 249 2.443016 CCGGTCTCTCTCCCCCTG 60.443 72.222 0.00 0.00 0.00 4.45
249 250 4.467107 GCCGGTCTCTCTCCCCCT 62.467 72.222 1.90 0.00 0.00 4.79
281 282 3.618855 TTAGGCGACAGGGAGGGCT 62.619 63.158 0.00 0.00 40.02 5.19
282 283 3.081409 TTAGGCGACAGGGAGGGC 61.081 66.667 0.00 0.00 0.00 5.19
283 284 1.550130 TTGTTAGGCGACAGGGAGGG 61.550 60.000 0.00 0.00 0.00 4.30
284 285 0.391263 GTTGTTAGGCGACAGGGAGG 60.391 60.000 0.00 0.00 0.00 4.30
285 286 0.391263 GGTTGTTAGGCGACAGGGAG 60.391 60.000 0.00 0.00 33.06 4.30
286 287 1.122632 TGGTTGTTAGGCGACAGGGA 61.123 55.000 0.00 0.00 33.06 4.20
287 288 0.673644 CTGGTTGTTAGGCGACAGGG 60.674 60.000 0.00 0.00 33.06 4.45
288 289 0.320374 TCTGGTTGTTAGGCGACAGG 59.680 55.000 0.00 0.00 33.06 4.00
289 290 2.069273 CTTCTGGTTGTTAGGCGACAG 58.931 52.381 0.00 0.00 33.06 3.51
290 291 1.689813 TCTTCTGGTTGTTAGGCGACA 59.310 47.619 0.00 0.00 33.06 4.35
291 292 2.067013 GTCTTCTGGTTGTTAGGCGAC 58.933 52.381 0.00 0.00 0.00 5.19
292 293 1.968493 AGTCTTCTGGTTGTTAGGCGA 59.032 47.619 0.00 0.00 0.00 5.54
293 294 2.288825 TGAGTCTTCTGGTTGTTAGGCG 60.289 50.000 0.00 0.00 0.00 5.52
294 295 3.402628 TGAGTCTTCTGGTTGTTAGGC 57.597 47.619 0.00 0.00 0.00 3.93
295 296 4.899502 ACATGAGTCTTCTGGTTGTTAGG 58.100 43.478 0.00 0.00 0.00 2.69
296 297 5.869888 GGTACATGAGTCTTCTGGTTGTTAG 59.130 44.000 0.00 0.00 0.00 2.34
297 298 5.305902 TGGTACATGAGTCTTCTGGTTGTTA 59.694 40.000 0.00 0.00 0.00 2.41
298 299 4.102524 TGGTACATGAGTCTTCTGGTTGTT 59.897 41.667 0.00 0.00 0.00 2.83
299 300 3.646162 TGGTACATGAGTCTTCTGGTTGT 59.354 43.478 0.00 0.00 0.00 3.32
300 301 4.271696 TGGTACATGAGTCTTCTGGTTG 57.728 45.455 0.00 0.00 0.00 3.77
301 302 4.974645 TTGGTACATGAGTCTTCTGGTT 57.025 40.909 0.00 0.00 39.30 3.67
342 343 6.881065 TCTCTCTCTCTCTCTCTCTTTTTGAG 59.119 42.308 0.00 0.00 43.96 3.02
343 344 6.778821 TCTCTCTCTCTCTCTCTCTTTTTGA 58.221 40.000 0.00 0.00 0.00 2.69
344 345 6.881065 TCTCTCTCTCTCTCTCTCTCTTTTTG 59.119 42.308 0.00 0.00 0.00 2.44
345 346 7.020827 TCTCTCTCTCTCTCTCTCTCTTTTT 57.979 40.000 0.00 0.00 0.00 1.94
346 347 6.214412 ACTCTCTCTCTCTCTCTCTCTCTTTT 59.786 42.308 0.00 0.00 0.00 2.27
347 348 5.723887 ACTCTCTCTCTCTCTCTCTCTCTTT 59.276 44.000 0.00 0.00 0.00 2.52
348 349 5.276440 ACTCTCTCTCTCTCTCTCTCTCTT 58.724 45.833 0.00 0.00 0.00 2.85
349 350 4.877773 ACTCTCTCTCTCTCTCTCTCTCT 58.122 47.826 0.00 0.00 0.00 3.10
350 351 5.355596 CAACTCTCTCTCTCTCTCTCTCTC 58.644 50.000 0.00 0.00 0.00 3.20
351 352 4.383552 GCAACTCTCTCTCTCTCTCTCTCT 60.384 50.000 0.00 0.00 0.00 3.10
352 353 3.873952 GCAACTCTCTCTCTCTCTCTCTC 59.126 52.174 0.00 0.00 0.00 3.20
353 354 3.370953 GGCAACTCTCTCTCTCTCTCTCT 60.371 52.174 0.00 0.00 0.00 3.10
354 355 2.945668 GGCAACTCTCTCTCTCTCTCTC 59.054 54.545 0.00 0.00 0.00 3.20
355 356 3.004752 GGCAACTCTCTCTCTCTCTCT 57.995 52.381 0.00 0.00 0.00 3.10
370 371 0.523335 CGGCTGCGAAATAAGGCAAC 60.523 55.000 0.00 0.00 38.94 4.17
371 372 1.653094 CCGGCTGCGAAATAAGGCAA 61.653 55.000 0.00 0.00 38.94 4.52
372 373 2.112198 CCGGCTGCGAAATAAGGCA 61.112 57.895 0.00 0.00 38.83 4.75
373 374 1.373590 TTCCGGCTGCGAAATAAGGC 61.374 55.000 0.00 0.00 35.72 4.35
374 375 1.091537 TTTCCGGCTGCGAAATAAGG 58.908 50.000 0.00 0.00 0.00 2.69
375 376 2.161609 AGTTTTCCGGCTGCGAAATAAG 59.838 45.455 0.00 0.00 0.00 1.73
376 377 2.156098 AGTTTTCCGGCTGCGAAATAA 58.844 42.857 0.00 0.00 0.00 1.40
390 391 1.001378 ACAGCGATGCACCAAGTTTTC 60.001 47.619 0.00 0.00 0.00 2.29
429 430 6.555812 AAAACGGAACTTCAATAAGAGTCC 57.444 37.500 0.00 0.00 37.22 3.85
430 431 8.433893 GTCTAAAACGGAACTTCAATAAGAGTC 58.566 37.037 0.00 0.00 36.50 3.36
469 480 6.636705 ACGATAAGTTGTGCTCCTACATTTA 58.363 36.000 0.00 0.00 0.00 1.40
508 519 4.826274 TCCTTTCCGAAGAACATGATCT 57.174 40.909 0.00 0.00 34.71 2.75
518 529 3.062639 CGATGACACAATCCTTTCCGAAG 59.937 47.826 0.00 0.00 0.00 3.79
523 534 2.017049 CCCCGATGACACAATCCTTTC 58.983 52.381 0.00 0.00 0.00 2.62
542 553 5.030820 AGGGCCTATCCATAGTACAATACC 58.969 45.833 2.82 0.00 36.21 2.73
546 557 3.162666 CGAGGGCCTATCCATAGTACAA 58.837 50.000 5.73 0.00 36.21 2.41
567 578 4.631377 TCCATTGTGAATCATCTCGTTGAC 59.369 41.667 0.00 0.00 0.00 3.18
573 584 5.182760 GGGCTTATCCATTGTGAATCATCTC 59.817 44.000 0.00 0.00 36.21 2.75
577 588 4.079844 TGAGGGCTTATCCATTGTGAATCA 60.080 41.667 0.00 0.00 36.21 2.57
617 639 0.469917 ATGTGGTGAGGGCTTATCCG 59.530 55.000 0.00 0.00 34.94 4.18
774 823 7.031226 TGTGATTGAGGCTGCTAAATAATTC 57.969 36.000 0.00 0.00 0.00 2.17
911 970 7.143514 TGTGAATCAATCAACGAATCATTGA 57.856 32.000 0.00 0.00 40.50 2.57
1024 1083 0.027586 GCAGCGTCGTCAAAAGTGTT 59.972 50.000 0.00 0.00 0.00 3.32
1210 1286 3.710722 CTCCAAGCTCAGCCCGGT 61.711 66.667 0.00 0.00 0.00 5.28
1728 1824 4.796231 GTCAGTGGCGTCCGCGAT 62.796 66.667 8.23 0.00 43.06 4.58
1773 1875 2.280119 TGTGGCGACTGTGACAGC 60.280 61.111 13.37 4.75 34.37 4.40
1788 1890 1.069765 CACAACCTCCAGCGTCTGT 59.930 57.895 6.19 0.00 0.00 3.41
1896 1998 2.027024 GACGGCGATGCGGACATA 59.973 61.111 16.62 0.00 36.35 2.29
1997 2107 4.595629 CACGCTGTGCAACTGAAC 57.404 55.556 0.00 0.00 38.12 3.18
2011 2121 2.031245 TGTTGCTTCCATTTACTGCACG 60.031 45.455 0.00 0.00 33.13 5.34
2013 2123 4.558178 CATTGTTGCTTCCATTTACTGCA 58.442 39.130 0.00 0.00 0.00 4.41
2023 2133 0.961019 TCAGTGCCATTGTTGCTTCC 59.039 50.000 0.00 0.00 0.00 3.46
2038 2148 4.021719 CCAAAATGAAGCAATGGTCTCAGT 60.022 41.667 0.00 0.00 0.00 3.41
2114 2231 3.887741 TGAAGTGACACAAAATGCATCG 58.112 40.909 8.59 0.00 0.00 3.84
2154 2271 6.482835 TGTCAAACTCAAAACATACTCAACG 58.517 36.000 0.00 0.00 0.00 4.10
2165 2282 8.707839 GTCATTTTCTTGTTGTCAAACTCAAAA 58.292 29.630 0.00 0.00 37.19 2.44
2203 2320 3.898741 GGGGACAAACAAAGGTTTATGGA 59.101 43.478 0.00 0.00 45.18 3.41
2216 2333 5.593095 AGTTAAGAAGAAACTGGGGACAAAC 59.407 40.000 0.00 0.00 42.06 2.93
2269 2387 5.358725 TGTTGTGTACGGCTCAATATCTAGA 59.641 40.000 0.00 0.00 33.82 2.43
2282 2400 1.289109 CGCCCTCTTGTTGTGTACGG 61.289 60.000 0.00 0.00 0.00 4.02
2383 2507 2.030562 AACGTCACGAGGGCCTTG 59.969 61.111 19.68 19.68 0.00 3.61
2384 2508 2.030562 CAACGTCACGAGGGCCTT 59.969 61.111 7.89 0.00 0.00 4.35
2385 2509 4.003788 CCAACGTCACGAGGGCCT 62.004 66.667 5.25 5.25 0.00 5.19
2428 2552 4.347453 GCACGCCACCCTGCAAAG 62.347 66.667 0.00 0.00 33.31 2.77
2457 2581 1.006102 CCTACGGCGCTATCAAGGG 60.006 63.158 6.90 0.00 38.66 3.95
2522 2646 2.202932 ATGTCGTGCCATCGAGCC 60.203 61.111 0.00 0.00 40.52 4.70
2529 2653 1.026182 GCAAGATGGATGTCGTGCCA 61.026 55.000 3.91 0.00 44.38 4.92
2549 2673 2.440409 GAATGCCAACACAGATCCACT 58.560 47.619 0.00 0.00 0.00 4.00
2554 2678 1.843368 CCAGGAATGCCAACACAGAT 58.157 50.000 0.00 0.00 36.29 2.90
2673 2821 1.575922 CACCAGATGCAACACCACG 59.424 57.895 0.00 0.00 0.00 4.94
2752 2900 2.203139 CCACCACAACACCTCGCA 60.203 61.111 0.00 0.00 0.00 5.10
2761 2909 2.515398 CTCCAGCCACCACCACAA 59.485 61.111 0.00 0.00 0.00 3.33
2763 2911 4.269523 TGCTCCAGCCACCACCAC 62.270 66.667 0.00 0.00 41.18 4.16
2784 2932 2.743928 ACAGCACCTTAGCAGCGC 60.744 61.111 0.00 0.00 36.85 5.92
2792 2940 1.003355 CGACCATCCACAGCACCTT 60.003 57.895 0.00 0.00 0.00 3.50
2801 2949 3.570125 GTGTATCAGATCTCGACCATCCA 59.430 47.826 0.00 0.00 0.00 3.41
2859 3007 1.204941 AGCCGAGCGTAGAGTTTTCAT 59.795 47.619 0.00 0.00 0.00 2.57
2865 3013 2.415776 GTATCTAGCCGAGCGTAGAGT 58.584 52.381 0.00 0.00 0.00 3.24
2870 3018 0.669077 CTTGGTATCTAGCCGAGCGT 59.331 55.000 0.00 0.00 31.41 5.07
2872 3020 0.319986 GCCTTGGTATCTAGCCGAGC 60.320 60.000 0.00 0.00 36.43 5.03
2914 3062 1.215647 CTGGAAGAAGGGGACGACG 59.784 63.158 0.00 0.00 34.07 5.12
2926 3074 1.811266 CCACGACGATGCCTGGAAG 60.811 63.158 0.00 0.00 0.00 3.46
2929 3077 2.202797 CTCCACGACGATGCCTGG 60.203 66.667 0.00 0.00 0.00 4.45
2930 3078 0.389817 TTTCTCCACGACGATGCCTG 60.390 55.000 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.