Multiple sequence alignment - TraesCS4B01G340500

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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 TraesCS4B01G340500 chr4B 100.000 2789 0 0 1 2789 633758938 633761726 0.000000e+00 5151.0
1 TraesCS4B01G340500 chr4D 89.306 2291 119 51 550 2789 494266644 494268859 0.000000e+00 2758.0
2 TraesCS4B01G340500 chr5A 90.895 1999 99 40 824 2789 673772773 673774721 0.000000e+00 2606.0
3 TraesCS4B01G340500 chr4A 95.176 539 14 4 1039 1565 494074157 494073619 0.000000e+00 841.0
4 TraesCS4B01G340500 chr4A 85.276 163 7 4 1158 1320 246254891 246255036 4.810000e-33 152.0
5 TraesCS4B01G340500 chr2B 92.878 337 12 5 1241 1565 109134267 109133931 1.940000e-131 479.0
6 TraesCS4B01G340500 chr2B 98.969 194 2 0 1039 1232 109134946 109134753 5.720000e-92 348.0
7 TraesCS4B01G340500 chr2B 88.772 285 20 8 1813 2095 130656618 130656892 3.440000e-89 339.0
8 TraesCS4B01G340500 chr2B 88.506 87 8 2 39 125 713924534 713924450 1.370000e-18 104.0
9 TraesCS4B01G340500 chr5D 90.106 283 17 6 1815 2095 189932374 189932647 9.500000e-95 357.0
10 TraesCS4B01G340500 chr7D 89.474 285 19 6 1813 2095 184648341 184648066 1.590000e-92 350.0
11 TraesCS4B01G340500 chr6B 88.421 285 22 6 1813 2095 148519708 148519433 1.600000e-87 333.0
12 TraesCS4B01G340500 chr6B 88.070 285 21 8 1813 2095 148438167 148437894 2.680000e-85 326.0
13 TraesCS4B01G340500 chr2D 88.421 285 21 7 1813 2095 477223519 477223793 1.600000e-87 333.0
14 TraesCS4B01G340500 chr5B 90.947 243 16 3 1320 1562 248767145 248767381 3.470000e-84 322.0
15 TraesCS4B01G340500 chr5B 99.270 137 1 0 1039 1175 248766996 248767132 5.970000e-62 248.0
16 TraesCS4B01G340500 chr6A 87.676 284 22 8 1815 2095 75254327 75254054 4.480000e-83 318.0
17 TraesCS4B01G340500 chr7A 89.565 115 9 3 324 438 548575574 548575685 2.900000e-30 143.0
18 TraesCS4B01G340500 chr3D 85.938 64 7 2 464 526 184636158 184636096 1.790000e-07 67.6
19 TraesCS4B01G340500 chr1B 97.297 37 1 0 1039 1075 375808059 375808095 2.320000e-06 63.9


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 TraesCS4B01G340500 chr4B 633758938 633761726 2788 False 5151.0 5151 100.0000 1 2789 1 chr4B.!!$F1 2788
1 TraesCS4B01G340500 chr4D 494266644 494268859 2215 False 2758.0 2758 89.3060 550 2789 1 chr4D.!!$F1 2239
2 TraesCS4B01G340500 chr5A 673772773 673774721 1948 False 2606.0 2606 90.8950 824 2789 1 chr5A.!!$F1 1965
3 TraesCS4B01G340500 chr4A 494073619 494074157 538 True 841.0 841 95.1760 1039 1565 1 chr4A.!!$R1 526
4 TraesCS4B01G340500 chr2B 109133931 109134946 1015 True 413.5 479 95.9235 1039 1565 2 chr2B.!!$R2 526

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
542 543 1.265236 TTTTTGGTATGCAGCCCCTG 58.735 50.0 7.52 0.0 34.12 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1949 2466 0.251297 TTGAGGGGTGATGCACAAGG 60.251 55.0 0.0 0.0 35.86 3.61 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
135 136 9.804758 TTTGAATACACGGTAAAAACATTTTCT 57.195 25.926 0.00 0.00 0.00 2.52
136 137 9.804758 TTGAATACACGGTAAAAACATTTTCTT 57.195 25.926 0.00 0.00 0.00 2.52
142 143 9.240159 ACACGGTAAAAACATTTTCTTAATGAC 57.760 29.630 4.64 0.00 0.00 3.06
143 144 9.239002 CACGGTAAAAACATTTTCTTAATGACA 57.761 29.630 4.64 0.00 0.00 3.58
144 145 9.804758 ACGGTAAAAACATTTTCTTAATGACAA 57.195 25.926 4.64 0.00 0.00 3.18
179 180 8.766000 TTTTGAAACTTCCTAAAACAACTTCC 57.234 30.769 0.00 0.00 0.00 3.46
180 181 7.712204 TTGAAACTTCCTAAAACAACTTCCT 57.288 32.000 0.00 0.00 0.00 3.36
181 182 7.712204 TGAAACTTCCTAAAACAACTTCCTT 57.288 32.000 0.00 0.00 0.00 3.36
182 183 8.810990 TGAAACTTCCTAAAACAACTTCCTTA 57.189 30.769 0.00 0.00 0.00 2.69
183 184 9.245481 TGAAACTTCCTAAAACAACTTCCTTAA 57.755 29.630 0.00 0.00 0.00 1.85
185 186 9.865321 AAACTTCCTAAAACAACTTCCTTAAAC 57.135 29.630 0.00 0.00 0.00 2.01
186 187 8.818622 ACTTCCTAAAACAACTTCCTTAAACT 57.181 30.769 0.00 0.00 0.00 2.66
187 188 9.910267 ACTTCCTAAAACAACTTCCTTAAACTA 57.090 29.630 0.00 0.00 0.00 2.24
189 190 9.683870 TTCCTAAAACAACTTCCTTAAACTACA 57.316 29.630 0.00 0.00 0.00 2.74
190 191 9.856162 TCCTAAAACAACTTCCTTAAACTACAT 57.144 29.630 0.00 0.00 0.00 2.29
226 227 7.819644 ACACGGTAACATATTTTAAACTTCCC 58.180 34.615 0.00 0.00 0.00 3.97
227 228 7.666804 ACACGGTAACATATTTTAAACTTCCCT 59.333 33.333 0.00 0.00 0.00 4.20
228 229 9.165035 CACGGTAACATATTTTAAACTTCCCTA 57.835 33.333 0.00 0.00 0.00 3.53
229 230 9.737844 ACGGTAACATATTTTAAACTTCCCTAA 57.262 29.630 0.00 0.00 0.00 2.69
315 316 7.835634 TTTGTAAACAATTGTCCAGTTTTCC 57.164 32.000 12.39 0.00 36.85 3.13
316 317 5.908341 TGTAAACAATTGTCCAGTTTTCCC 58.092 37.500 12.39 0.00 36.85 3.97
317 318 4.415881 AAACAATTGTCCAGTTTTCCCC 57.584 40.909 12.39 0.00 31.95 4.81
318 319 3.039252 ACAATTGTCCAGTTTTCCCCA 57.961 42.857 4.92 0.00 0.00 4.96
319 320 3.379452 ACAATTGTCCAGTTTTCCCCAA 58.621 40.909 4.92 0.00 0.00 4.12
320 321 3.387699 ACAATTGTCCAGTTTTCCCCAAG 59.612 43.478 4.92 0.00 0.00 3.61
321 322 3.611025 ATTGTCCAGTTTTCCCCAAGA 57.389 42.857 0.00 0.00 0.00 3.02
322 323 2.358322 TGTCCAGTTTTCCCCAAGAC 57.642 50.000 0.00 0.00 0.00 3.01
323 324 1.566703 TGTCCAGTTTTCCCCAAGACA 59.433 47.619 0.00 0.00 0.00 3.41
324 325 2.024846 TGTCCAGTTTTCCCCAAGACAA 60.025 45.455 0.00 0.00 30.35 3.18
325 326 3.028130 GTCCAGTTTTCCCCAAGACAAA 58.972 45.455 0.00 0.00 0.00 2.83
326 327 3.641436 GTCCAGTTTTCCCCAAGACAAAT 59.359 43.478 0.00 0.00 0.00 2.32
327 328 4.830600 GTCCAGTTTTCCCCAAGACAAATA 59.169 41.667 0.00 0.00 0.00 1.40
328 329 5.303333 GTCCAGTTTTCCCCAAGACAAATAA 59.697 40.000 0.00 0.00 0.00 1.40
329 330 6.014584 GTCCAGTTTTCCCCAAGACAAATAAT 60.015 38.462 0.00 0.00 0.00 1.28
330 331 6.556874 TCCAGTTTTCCCCAAGACAAATAATT 59.443 34.615 0.00 0.00 0.00 1.40
331 332 7.071824 TCCAGTTTTCCCCAAGACAAATAATTT 59.928 33.333 0.00 0.00 0.00 1.82
332 333 8.371699 CCAGTTTTCCCCAAGACAAATAATTTA 58.628 33.333 0.00 0.00 0.00 1.40
333 334 9.942850 CAGTTTTCCCCAAGACAAATAATTTAT 57.057 29.630 0.00 0.00 0.00 1.40
401 402 9.698309 TGAAAATCCGAAACAATTTTTATAGCA 57.302 25.926 0.00 0.00 35.72 3.49
404 405 9.651913 AAATCCGAAACAATTTTTATAGCATGT 57.348 25.926 0.00 0.00 0.00 3.21
405 406 8.633075 ATCCGAAACAATTTTTATAGCATGTG 57.367 30.769 0.00 0.00 0.00 3.21
406 407 7.821652 TCCGAAACAATTTTTATAGCATGTGA 58.178 30.769 0.00 0.00 0.00 3.58
407 408 8.300286 TCCGAAACAATTTTTATAGCATGTGAA 58.700 29.630 0.00 0.00 0.00 3.18
408 409 8.920665 CCGAAACAATTTTTATAGCATGTGAAA 58.079 29.630 0.00 0.00 0.00 2.69
433 434 9.594478 AAAAACTGTTCTAATTCCGAACATTTT 57.406 25.926 20.74 20.74 46.68 1.82
434 435 9.594478 AAAACTGTTCTAATTCCGAACATTTTT 57.406 25.926 25.58 25.58 46.96 1.94
459 460 9.973450 TTTGAAGCTTGAGAGTAGTATGATATC 57.027 33.333 2.10 0.00 0.00 1.63
460 461 8.116651 TGAAGCTTGAGAGTAGTATGATATCC 57.883 38.462 2.10 0.00 0.00 2.59
461 462 7.725844 TGAAGCTTGAGAGTAGTATGATATCCA 59.274 37.037 2.10 0.00 0.00 3.41
462 463 8.484214 AAGCTTGAGAGTAGTATGATATCCAA 57.516 34.615 0.00 0.00 0.00 3.53
463 464 8.484214 AGCTTGAGAGTAGTATGATATCCAAA 57.516 34.615 0.00 0.00 0.00 3.28
464 465 9.099071 AGCTTGAGAGTAGTATGATATCCAAAT 57.901 33.333 0.00 0.00 0.00 2.32
465 466 9.717942 GCTTGAGAGTAGTATGATATCCAAATT 57.282 33.333 0.00 0.00 0.00 1.82
469 470 9.360093 GAGAGTAGTATGATATCCAAATTTCCG 57.640 37.037 0.00 0.00 0.00 4.30
470 471 8.314751 AGAGTAGTATGATATCCAAATTTCCGG 58.685 37.037 0.00 0.00 0.00 5.14
471 472 7.394816 AGTAGTATGATATCCAAATTTCCGGG 58.605 38.462 0.00 0.00 0.00 5.73
472 473 5.570320 AGTATGATATCCAAATTTCCGGGG 58.430 41.667 0.00 0.00 0.00 5.73
473 474 3.963476 TGATATCCAAATTTCCGGGGT 57.037 42.857 0.00 0.00 0.00 4.95
474 475 4.258457 TGATATCCAAATTTCCGGGGTT 57.742 40.909 0.00 0.00 0.00 4.11
475 476 4.615513 TGATATCCAAATTTCCGGGGTTT 58.384 39.130 0.00 0.00 0.00 3.27
476 477 5.767670 TGATATCCAAATTTCCGGGGTTTA 58.232 37.500 0.00 0.00 0.00 2.01
477 478 6.195700 TGATATCCAAATTTCCGGGGTTTAA 58.804 36.000 0.00 0.00 0.00 1.52
478 479 6.668283 TGATATCCAAATTTCCGGGGTTTAAA 59.332 34.615 0.00 0.00 0.00 1.52
479 480 4.875561 TCCAAATTTCCGGGGTTTAAAG 57.124 40.909 0.00 0.00 0.00 1.85
480 481 4.224762 TCCAAATTTCCGGGGTTTAAAGT 58.775 39.130 0.00 0.00 0.00 2.66
481 482 4.654724 TCCAAATTTCCGGGGTTTAAAGTT 59.345 37.500 0.00 0.00 0.00 2.66
482 483 4.992319 CCAAATTTCCGGGGTTTAAAGTTC 59.008 41.667 0.00 0.00 0.00 3.01
483 484 5.453480 CCAAATTTCCGGGGTTTAAAGTTCA 60.453 40.000 0.00 0.00 0.00 3.18
484 485 5.462530 AATTTCCGGGGTTTAAAGTTCAG 57.537 39.130 0.00 0.00 0.00 3.02
485 486 3.860968 TTCCGGGGTTTAAAGTTCAGA 57.139 42.857 0.00 0.00 0.00 3.27
486 487 3.412237 TCCGGGGTTTAAAGTTCAGAG 57.588 47.619 0.00 0.00 0.00 3.35
487 488 2.707257 TCCGGGGTTTAAAGTTCAGAGT 59.293 45.455 0.00 0.00 0.00 3.24
488 489 3.136992 TCCGGGGTTTAAAGTTCAGAGTT 59.863 43.478 0.00 0.00 0.00 3.01
489 490 3.887110 CCGGGGTTTAAAGTTCAGAGTTT 59.113 43.478 0.00 0.00 33.19 2.66
490 491 4.261447 CCGGGGTTTAAAGTTCAGAGTTTG 60.261 45.833 0.00 0.00 31.14 2.93
491 492 4.577283 CGGGGTTTAAAGTTCAGAGTTTGA 59.423 41.667 0.00 0.00 31.14 2.69
492 493 5.240844 CGGGGTTTAAAGTTCAGAGTTTGAT 59.759 40.000 0.00 0.00 35.27 2.57
493 494 6.238925 CGGGGTTTAAAGTTCAGAGTTTGATT 60.239 38.462 0.00 0.00 35.27 2.57
494 495 7.497595 GGGGTTTAAAGTTCAGAGTTTGATTT 58.502 34.615 0.00 0.00 35.27 2.17
495 496 8.635328 GGGGTTTAAAGTTCAGAGTTTGATTTA 58.365 33.333 0.00 0.00 35.27 1.40
496 497 9.678941 GGGTTTAAAGTTCAGAGTTTGATTTAG 57.321 33.333 0.00 0.00 35.27 1.85
502 503 9.503427 AAAGTTCAGAGTTTGATTTAGTTTTCG 57.497 29.630 0.00 0.00 35.27 3.46
503 504 8.209917 AGTTCAGAGTTTGATTTAGTTTTCGT 57.790 30.769 0.00 0.00 35.27 3.85
504 505 8.336080 AGTTCAGAGTTTGATTTAGTTTTCGTC 58.664 33.333 0.00 0.00 35.27 4.20
505 506 8.336080 GTTCAGAGTTTGATTTAGTTTTCGTCT 58.664 33.333 0.00 0.00 35.27 4.18
506 507 9.537192 TTCAGAGTTTGATTTAGTTTTCGTCTA 57.463 29.630 0.00 0.00 35.27 2.59
507 508 9.706691 TCAGAGTTTGATTTAGTTTTCGTCTAT 57.293 29.630 0.00 0.00 0.00 1.98
521 522 9.321562 AGTTTTCGTCTATAACTTCAAGTTTGA 57.678 29.630 8.41 2.40 39.51 2.69
541 542 3.784429 TTTTTGGTATGCAGCCCCT 57.216 47.368 7.52 0.00 0.00 4.79
542 543 1.265236 TTTTTGGTATGCAGCCCCTG 58.735 50.000 7.52 0.00 34.12 4.45
631 633 2.924105 GCCAGGGAGTGCAAGCAAC 61.924 63.158 0.00 0.00 0.00 4.17
632 634 2.270986 CCAGGGAGTGCAAGCAACC 61.271 63.158 0.00 3.70 0.00 3.77
633 635 2.281761 AGGGAGTGCAAGCAACCG 60.282 61.111 0.00 0.00 0.00 4.44
634 636 2.281484 GGGAGTGCAAGCAACCGA 60.281 61.111 0.00 0.00 0.00 4.69
635 637 2.328099 GGGAGTGCAAGCAACCGAG 61.328 63.158 0.00 0.00 0.00 4.63
636 638 1.598130 GGAGTGCAAGCAACCGAGT 60.598 57.895 0.00 0.00 0.00 4.18
637 639 1.569479 GGAGTGCAAGCAACCGAGTC 61.569 60.000 0.00 0.00 0.00 3.36
638 640 1.891060 GAGTGCAAGCAACCGAGTCG 61.891 60.000 5.29 5.29 0.00 4.18
639 641 3.345808 TGCAAGCAACCGAGTCGC 61.346 61.111 7.12 0.00 0.00 5.19
640 642 4.430423 GCAAGCAACCGAGTCGCG 62.430 66.667 7.12 0.00 40.47 5.87
649 651 2.956964 CGAGTCGCGGCAGATTCC 60.957 66.667 15.58 0.00 36.03 3.01
650 652 2.586357 GAGTCGCGGCAGATTCCC 60.586 66.667 15.58 0.00 0.00 3.97
671 673 1.831652 CTCCCACTCCGGCATATCCC 61.832 65.000 0.00 0.00 0.00 3.85
672 674 2.146724 CCCACTCCGGCATATCCCA 61.147 63.158 0.00 0.00 0.00 4.37
674 676 1.300931 CACTCCGGCATATCCCACG 60.301 63.158 0.00 0.00 0.00 4.94
675 677 2.357517 CTCCGGCATATCCCACGC 60.358 66.667 0.00 0.00 0.00 5.34
680 682 4.927782 GCATATCCCACGCGGCCA 62.928 66.667 12.47 0.00 0.00 5.36
763 765 4.933064 GGCATCTCGTCTCGGCCG 62.933 72.222 22.12 22.12 34.56 6.13
764 766 4.933064 GCATCTCGTCTCGGCCGG 62.933 72.222 27.83 16.54 0.00 6.13
792 802 3.207778 CACACCGGTCAACCTAGAAAAA 58.792 45.455 2.59 0.00 0.00 1.94
890 904 4.925861 GCTCCTCCCGGCAGCATC 62.926 72.222 0.00 0.00 35.12 3.91
891 905 4.247380 CTCCTCCCGGCAGCATCC 62.247 72.222 0.00 0.00 0.00 3.51
906 920 2.680370 ATCCCGGGCTCCACCTTTC 61.680 63.158 18.49 0.00 39.10 2.62
907 921 4.426313 CCCGGGCTCCACCTTTCC 62.426 72.222 8.08 0.00 39.10 3.13
937 951 3.467119 CGACAGGCGTTTCCGTCG 61.467 66.667 11.48 11.48 46.54 5.12
945 959 3.408851 GTTTCCGTCGCGTCCCAC 61.409 66.667 5.77 0.00 0.00 4.61
956 970 4.083862 GTCCCACCCACCGCTCTC 62.084 72.222 0.00 0.00 0.00 3.20
982 996 3.099170 CCCCCTATGGCCTGTGCT 61.099 66.667 3.32 0.00 37.74 4.40
983 997 2.194056 CCCCTATGGCCTGTGCTG 59.806 66.667 3.32 0.00 37.74 4.41
1356 1859 2.540910 ACCCTCCTCCTCCTCCCA 60.541 66.667 0.00 0.00 0.00 4.37
1357 1860 2.182858 GACCCTCCTCCTCCTCCCAA 62.183 65.000 0.00 0.00 0.00 4.12
1630 2145 3.254024 TTCCTCGGCTTCACCAGGC 62.254 63.158 0.00 0.00 45.01 4.85
1632 2147 4.785453 CTCGGCTTCACCAGGCCC 62.785 72.222 0.00 0.00 45.74 5.80
1689 2204 0.951040 CCCAGGTTGTGCTCTTCGAC 60.951 60.000 0.00 0.00 0.00 4.20
1791 2306 4.106925 CCCCTGCCTGCCTGAGAC 62.107 72.222 0.00 0.00 0.00 3.36
1906 2423 2.925578 TTGATCCAATGCTTGCTTCG 57.074 45.000 0.00 0.00 0.00 3.79
1909 2426 2.677836 TGATCCAATGCTTGCTTCGTAC 59.322 45.455 0.00 0.00 0.00 3.67
1910 2427 2.472695 TCCAATGCTTGCTTCGTACT 57.527 45.000 0.00 0.00 0.00 2.73
1911 2428 3.603158 TCCAATGCTTGCTTCGTACTA 57.397 42.857 0.00 0.00 0.00 1.82
1912 2429 3.521560 TCCAATGCTTGCTTCGTACTAG 58.478 45.455 0.00 0.00 0.00 2.57
1913 2430 2.030946 CCAATGCTTGCTTCGTACTAGC 59.969 50.000 9.25 9.25 39.10 3.42
1914 2431 2.932614 CAATGCTTGCTTCGTACTAGCT 59.067 45.455 15.20 0.00 39.38 3.32
1920 2437 3.972950 TGCTTCGTACTAGCTCTCATC 57.027 47.619 15.20 0.00 39.38 2.92
1931 2448 3.591196 AGCTCTCATCTGTGTCAGTTC 57.409 47.619 0.00 0.00 32.61 3.01
1942 2459 5.833082 TCTGTGTCAGTTCTTCAGTTAGTC 58.167 41.667 0.00 0.00 32.61 2.59
1945 2462 2.987821 GTCAGTTCTTCAGTTAGTCGCC 59.012 50.000 0.00 0.00 0.00 5.54
1949 2466 2.987821 GTTCTTCAGTTAGTCGCCACTC 59.012 50.000 0.00 0.00 33.62 3.51
1969 2490 0.883833 CTTGTGCATCACCCCTCAAC 59.116 55.000 0.00 0.00 32.73 3.18
1979 2500 2.510382 TCACCCCTCAACCAACAAGTAA 59.490 45.455 0.00 0.00 0.00 2.24
2020 2544 3.895232 TTATGCTCACTCCTTGTCTCC 57.105 47.619 0.00 0.00 0.00 3.71
2021 2545 1.649321 ATGCTCACTCCTTGTCTCCA 58.351 50.000 0.00 0.00 0.00 3.86
2022 2546 1.649321 TGCTCACTCCTTGTCTCCAT 58.351 50.000 0.00 0.00 0.00 3.41
2054 2578 6.128795 CCTTTTCAGTTAGCTGTTACTTCTCG 60.129 42.308 6.47 0.00 43.05 4.04
2133 2667 3.713858 TTCAATATGGCAATGCTTCCG 57.286 42.857 4.82 0.00 0.00 4.30
2227 2761 4.583073 GGAACTTTTGCTGGAACCTTAGAA 59.417 41.667 0.00 0.00 0.00 2.10
2228 2762 5.243954 GGAACTTTTGCTGGAACCTTAGAAT 59.756 40.000 0.00 0.00 0.00 2.40
2371 2921 8.647143 ATGTTTATGTTTTGTTGTCAAGAAGG 57.353 30.769 0.00 0.00 34.88 3.46
2386 2936 2.050144 AGAAGGCAAGAACCTCTCACA 58.950 47.619 0.00 0.00 39.93 3.58
2436 2987 4.739195 TGTAAAAATAGCGCCCATTGTTC 58.261 39.130 2.29 1.55 0.00 3.18
2469 3021 4.995487 CACCTTTGAGTTCTACTACAACCC 59.005 45.833 0.00 0.00 0.00 4.11
2614 3168 3.559069 TCTTGTAACCGACCCGATCTAT 58.441 45.455 0.00 0.00 0.00 1.98
2641 3195 4.500035 GGTTCGGCCTAGAATAGTTCAGAG 60.500 50.000 0.00 0.00 36.82 3.35
2647 3201 5.137551 GCCTAGAATAGTTCAGAGTCCTCT 58.862 45.833 0.00 0.00 37.43 3.69
2648 3202 6.300703 GCCTAGAATAGTTCAGAGTCCTCTA 58.699 44.000 0.00 0.00 35.68 2.43
2773 3327 8.329502 ACTAACTAAAATATGGAGTTCTTGGCT 58.670 33.333 1.54 0.00 35.17 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
109 110 9.804758 AGAAAATGTTTTTACCGTGTATTCAAA 57.195 25.926 0.00 0.00 0.00 2.69
110 111 9.804758 AAGAAAATGTTTTTACCGTGTATTCAA 57.195 25.926 0.00 0.00 0.00 2.69
116 117 9.240159 GTCATTAAGAAAATGTTTTTACCGTGT 57.760 29.630 0.00 0.00 0.00 4.49
117 118 9.239002 TGTCATTAAGAAAATGTTTTTACCGTG 57.761 29.630 0.00 0.00 0.00 4.94
118 119 9.804758 TTGTCATTAAGAAAATGTTTTTACCGT 57.195 25.926 0.00 0.00 0.00 4.83
153 154 9.378551 GGAAGTTGTTTTAGGAAGTTTCAAAAT 57.621 29.630 0.00 0.00 0.00 1.82
154 155 8.590204 AGGAAGTTGTTTTAGGAAGTTTCAAAA 58.410 29.630 0.00 0.00 0.00 2.44
155 156 8.129496 AGGAAGTTGTTTTAGGAAGTTTCAAA 57.871 30.769 0.00 0.00 0.00 2.69
156 157 7.712204 AGGAAGTTGTTTTAGGAAGTTTCAA 57.288 32.000 0.00 0.00 0.00 2.69
157 158 7.712204 AAGGAAGTTGTTTTAGGAAGTTTCA 57.288 32.000 0.00 0.00 0.00 2.69
159 160 9.865321 GTTTAAGGAAGTTGTTTTAGGAAGTTT 57.135 29.630 0.00 0.00 0.00 2.66
160 161 9.251440 AGTTTAAGGAAGTTGTTTTAGGAAGTT 57.749 29.630 0.00 0.00 0.00 2.66
161 162 8.818622 AGTTTAAGGAAGTTGTTTTAGGAAGT 57.181 30.769 0.00 0.00 0.00 3.01
163 164 9.683870 TGTAGTTTAAGGAAGTTGTTTTAGGAA 57.316 29.630 0.00 0.00 0.00 3.36
164 165 9.856162 ATGTAGTTTAAGGAAGTTGTTTTAGGA 57.144 29.630 0.00 0.00 0.00 2.94
200 201 8.945057 GGGAAGTTTAAAATATGTTACCGTGTA 58.055 33.333 0.00 0.00 0.00 2.90
201 202 7.666804 AGGGAAGTTTAAAATATGTTACCGTGT 59.333 33.333 0.00 0.00 0.00 4.49
202 203 8.047413 AGGGAAGTTTAAAATATGTTACCGTG 57.953 34.615 0.00 0.00 0.00 4.94
203 204 9.737844 TTAGGGAAGTTTAAAATATGTTACCGT 57.262 29.630 0.00 0.00 0.00 4.83
289 290 8.888716 GGAAAACTGGACAATTGTTTACAAATT 58.111 29.630 13.36 7.21 39.55 1.82
290 291 7.497579 GGGAAAACTGGACAATTGTTTACAAAT 59.502 33.333 13.36 0.00 39.55 2.32
291 292 6.819146 GGGAAAACTGGACAATTGTTTACAAA 59.181 34.615 13.36 0.00 39.55 2.83
292 293 6.342111 GGGAAAACTGGACAATTGTTTACAA 58.658 36.000 13.36 0.00 40.51 2.41
293 294 5.163395 GGGGAAAACTGGACAATTGTTTACA 60.163 40.000 13.36 11.30 34.09 2.41
294 295 5.163395 TGGGGAAAACTGGACAATTGTTTAC 60.163 40.000 13.36 7.19 34.09 2.01
295 296 4.962995 TGGGGAAAACTGGACAATTGTTTA 59.037 37.500 13.36 4.12 34.09 2.01
296 297 3.777522 TGGGGAAAACTGGACAATTGTTT 59.222 39.130 13.36 1.23 35.71 2.83
297 298 3.379452 TGGGGAAAACTGGACAATTGTT 58.621 40.909 13.36 0.00 0.00 2.83
298 299 3.039252 TGGGGAAAACTGGACAATTGT 57.961 42.857 11.78 11.78 0.00 2.71
299 300 3.640967 TCTTGGGGAAAACTGGACAATTG 59.359 43.478 3.24 3.24 0.00 2.32
300 301 3.641436 GTCTTGGGGAAAACTGGACAATT 59.359 43.478 0.00 0.00 0.00 2.32
301 302 3.230976 GTCTTGGGGAAAACTGGACAAT 58.769 45.455 0.00 0.00 0.00 2.71
302 303 2.024846 TGTCTTGGGGAAAACTGGACAA 60.025 45.455 0.00 0.00 30.81 3.18
303 304 1.566703 TGTCTTGGGGAAAACTGGACA 59.433 47.619 0.00 0.00 0.00 4.02
304 305 2.358322 TGTCTTGGGGAAAACTGGAC 57.642 50.000 0.00 0.00 0.00 4.02
305 306 3.390175 TTTGTCTTGGGGAAAACTGGA 57.610 42.857 0.00 0.00 0.00 3.86
306 307 5.799827 TTATTTGTCTTGGGGAAAACTGG 57.200 39.130 0.00 0.00 0.00 4.00
307 308 9.942850 ATAAATTATTTGTCTTGGGGAAAACTG 57.057 29.630 0.00 0.00 0.00 3.16
375 376 9.698309 TGCTATAAAAATTGTTTCGGATTTTCA 57.302 25.926 0.00 0.00 35.14 2.69
378 379 9.651913 ACATGCTATAAAAATTGTTTCGGATTT 57.348 25.926 0.00 0.00 0.00 2.17
379 380 9.086336 CACATGCTATAAAAATTGTTTCGGATT 57.914 29.630 0.00 0.00 0.00 3.01
380 381 8.465999 TCACATGCTATAAAAATTGTTTCGGAT 58.534 29.630 0.00 0.00 0.00 4.18
381 382 7.821652 TCACATGCTATAAAAATTGTTTCGGA 58.178 30.769 0.00 0.00 0.00 4.55
382 383 8.459521 TTCACATGCTATAAAAATTGTTTCGG 57.540 30.769 0.00 0.00 0.00 4.30
433 434 9.973450 GATATCATACTACTCTCAAGCTTCAAA 57.027 33.333 0.00 0.00 0.00 2.69
434 435 8.580720 GGATATCATACTACTCTCAAGCTTCAA 58.419 37.037 4.83 0.00 0.00 2.69
435 436 7.725844 TGGATATCATACTACTCTCAAGCTTCA 59.274 37.037 4.83 0.00 0.00 3.02
436 437 8.116651 TGGATATCATACTACTCTCAAGCTTC 57.883 38.462 4.83 0.00 0.00 3.86
437 438 8.484214 TTGGATATCATACTACTCTCAAGCTT 57.516 34.615 4.83 0.00 0.00 3.74
438 439 8.484214 TTTGGATATCATACTACTCTCAAGCT 57.516 34.615 4.83 0.00 0.00 3.74
439 440 9.717942 AATTTGGATATCATACTACTCTCAAGC 57.282 33.333 4.83 0.00 0.00 4.01
443 444 9.360093 CGGAAATTTGGATATCATACTACTCTC 57.640 37.037 4.83 0.00 0.00 3.20
444 445 8.314751 CCGGAAATTTGGATATCATACTACTCT 58.685 37.037 0.00 0.00 0.00 3.24
445 446 7.549488 CCCGGAAATTTGGATATCATACTACTC 59.451 40.741 0.73 0.00 0.00 2.59
446 447 7.394816 CCCGGAAATTTGGATATCATACTACT 58.605 38.462 0.73 0.00 0.00 2.57
447 448 6.598064 CCCCGGAAATTTGGATATCATACTAC 59.402 42.308 0.73 0.00 0.00 2.73
448 449 6.273730 ACCCCGGAAATTTGGATATCATACTA 59.726 38.462 0.73 0.00 0.00 1.82
449 450 5.074515 ACCCCGGAAATTTGGATATCATACT 59.925 40.000 0.73 0.00 0.00 2.12
450 451 5.321927 ACCCCGGAAATTTGGATATCATAC 58.678 41.667 0.73 0.00 0.00 2.39
451 452 5.592587 ACCCCGGAAATTTGGATATCATA 57.407 39.130 0.73 0.00 0.00 2.15
452 453 4.469469 ACCCCGGAAATTTGGATATCAT 57.531 40.909 0.73 0.00 0.00 2.45
453 454 3.963476 ACCCCGGAAATTTGGATATCA 57.037 42.857 0.73 0.00 0.00 2.15
454 455 6.718522 TTAAACCCCGGAAATTTGGATATC 57.281 37.500 0.73 0.00 0.00 1.63
455 456 6.670464 ACTTTAAACCCCGGAAATTTGGATAT 59.330 34.615 0.73 0.00 0.00 1.63
456 457 6.017830 ACTTTAAACCCCGGAAATTTGGATA 58.982 36.000 0.73 0.00 0.00 2.59
457 458 4.841813 ACTTTAAACCCCGGAAATTTGGAT 59.158 37.500 0.73 0.00 0.00 3.41
458 459 4.224762 ACTTTAAACCCCGGAAATTTGGA 58.775 39.130 0.73 0.00 0.00 3.53
459 460 4.610605 ACTTTAAACCCCGGAAATTTGG 57.389 40.909 0.73 0.00 0.00 3.28
460 461 5.602628 TGAACTTTAAACCCCGGAAATTTG 58.397 37.500 0.73 0.00 0.00 2.32
461 462 5.599242 TCTGAACTTTAAACCCCGGAAATTT 59.401 36.000 0.73 2.60 0.00 1.82
462 463 5.141910 TCTGAACTTTAAACCCCGGAAATT 58.858 37.500 0.73 0.00 0.00 1.82
463 464 4.732065 TCTGAACTTTAAACCCCGGAAAT 58.268 39.130 0.73 0.00 0.00 2.17
464 465 4.139038 CTCTGAACTTTAAACCCCGGAAA 58.861 43.478 0.73 0.00 0.00 3.13
465 466 3.136992 ACTCTGAACTTTAAACCCCGGAA 59.863 43.478 0.73 0.00 0.00 4.30
466 467 2.707257 ACTCTGAACTTTAAACCCCGGA 59.293 45.455 0.73 0.00 0.00 5.14
467 468 3.136009 ACTCTGAACTTTAAACCCCGG 57.864 47.619 0.00 0.00 0.00 5.73
468 469 4.577283 TCAAACTCTGAACTTTAAACCCCG 59.423 41.667 0.00 0.00 0.00 5.73
469 470 6.650427 ATCAAACTCTGAACTTTAAACCCC 57.350 37.500 0.00 0.00 37.67 4.95
470 471 9.678941 CTAAATCAAACTCTGAACTTTAAACCC 57.321 33.333 0.00 0.00 37.67 4.11
476 477 9.503427 CGAAAACTAAATCAAACTCTGAACTTT 57.497 29.630 0.00 0.00 37.67 2.66
477 478 8.674607 ACGAAAACTAAATCAAACTCTGAACTT 58.325 29.630 0.00 0.00 37.67 2.66
478 479 8.209917 ACGAAAACTAAATCAAACTCTGAACT 57.790 30.769 0.00 0.00 37.67 3.01
479 480 8.336080 AGACGAAAACTAAATCAAACTCTGAAC 58.664 33.333 0.00 0.00 37.67 3.18
480 481 8.433421 AGACGAAAACTAAATCAAACTCTGAA 57.567 30.769 0.00 0.00 37.67 3.02
481 482 9.706691 ATAGACGAAAACTAAATCAAACTCTGA 57.293 29.630 0.00 0.00 38.81 3.27
495 496 9.321562 TCAAACTTGAAGTTATAGACGAAAACT 57.678 29.630 11.43 0.00 37.47 2.66
523 524 1.265236 CAGGGGCTGCATACCAAAAA 58.735 50.000 0.50 0.00 0.00 1.94
524 525 2.974623 CAGGGGCTGCATACCAAAA 58.025 52.632 0.50 0.00 0.00 2.44
525 526 4.762016 CAGGGGCTGCATACCAAA 57.238 55.556 0.50 0.00 0.00 3.28
543 544 4.129737 ATCGGTCGGTGGTCGCAG 62.130 66.667 0.00 0.00 39.05 5.18
544 545 4.124351 GATCGGTCGGTGGTCGCA 62.124 66.667 0.00 0.00 39.05 5.10
617 619 2.281484 TCGGTTGCTTGCACTCCC 60.281 61.111 0.00 0.00 0.00 4.30
632 634 2.956964 GGAATCTGCCGCGACTCG 60.957 66.667 8.23 0.00 38.08 4.18
633 635 2.586357 GGGAATCTGCCGCGACTC 60.586 66.667 8.23 0.00 0.00 3.36
634 636 3.390521 TGGGAATCTGCCGCGACT 61.391 61.111 8.23 0.00 0.00 4.18
635 637 3.195698 GTGGGAATCTGCCGCGAC 61.196 66.667 8.23 0.00 0.00 5.19
636 638 3.371097 GAGTGGGAATCTGCCGCGA 62.371 63.158 8.23 0.00 43.61 5.87
637 639 2.892425 GAGTGGGAATCTGCCGCG 60.892 66.667 0.00 0.00 43.61 6.46
638 640 2.514824 GGAGTGGGAATCTGCCGC 60.515 66.667 0.00 0.00 38.78 6.53
639 641 2.190578 GGGAGTGGGAATCTGCCG 59.809 66.667 0.00 0.00 34.07 5.69
640 642 1.077429 GTGGGAGTGGGAATCTGCC 60.077 63.158 0.00 0.00 42.47 4.85
641 643 0.107459 GAGTGGGAGTGGGAATCTGC 60.107 60.000 0.00 0.00 0.00 4.26
642 644 0.543749 GGAGTGGGAGTGGGAATCTG 59.456 60.000 0.00 0.00 0.00 2.90
643 645 0.978146 CGGAGTGGGAGTGGGAATCT 60.978 60.000 0.00 0.00 0.00 2.40
644 646 1.522569 CGGAGTGGGAGTGGGAATC 59.477 63.158 0.00 0.00 0.00 2.52
645 647 1.995626 CCGGAGTGGGAGTGGGAAT 60.996 63.158 0.00 0.00 0.00 3.01
646 648 2.606519 CCGGAGTGGGAGTGGGAA 60.607 66.667 0.00 0.00 0.00 3.97
649 651 1.410850 ATATGCCGGAGTGGGAGTGG 61.411 60.000 5.05 0.00 43.72 4.00
650 652 0.034059 GATATGCCGGAGTGGGAGTG 59.966 60.000 5.05 0.00 43.72 3.51
677 679 2.892425 CTGATTCCGGCGAGTGGC 60.892 66.667 9.30 0.00 42.51 5.01
726 728 1.149148 GATTCCGAAGAATAGCCGCC 58.851 55.000 0.00 0.00 42.93 6.13
768 770 0.037605 CTAGGTTGACCGGTGTGTCC 60.038 60.000 14.63 9.32 42.08 4.02
776 786 3.127030 GCCAGATTTTTCTAGGTTGACCG 59.873 47.826 0.00 0.00 42.08 4.79
887 901 2.893682 GAAAGGTGGAGCCCGGGATG 62.894 65.000 29.31 0.00 38.26 3.51
888 902 2.614013 AAAGGTGGAGCCCGGGAT 60.614 61.111 29.31 22.30 38.26 3.85
889 903 3.327404 GAAAGGTGGAGCCCGGGA 61.327 66.667 29.31 0.00 38.26 5.14
890 904 4.426313 GGAAAGGTGGAGCCCGGG 62.426 72.222 19.09 19.09 38.26 5.73
891 905 4.426313 GGGAAAGGTGGAGCCCGG 62.426 72.222 0.00 0.00 38.26 5.73
892 906 4.426313 GGGGAAAGGTGGAGCCCG 62.426 72.222 0.00 0.00 41.63 6.13
893 907 4.062032 GGGGGAAAGGTGGAGCCC 62.062 72.222 0.00 0.00 39.93 5.19
928 942 3.408851 GTGGGACGCGACGGAAAC 61.409 66.667 15.93 0.00 0.00 2.78
929 943 4.668118 GGTGGGACGCGACGGAAA 62.668 66.667 15.93 0.00 41.51 3.13
939 953 4.083862 GAGAGCGGTGGGTGGGAC 62.084 72.222 0.00 0.00 0.00 4.46
965 979 3.099170 AGCACAGGCCATAGGGGG 61.099 66.667 5.01 0.00 42.56 5.40
967 981 2.517875 GCAGCACAGGCCATAGGG 60.518 66.667 5.01 0.00 42.56 3.53
987 1001 4.489771 GGCATGGGGAGTGGACGG 62.490 72.222 0.00 0.00 0.00 4.79
1419 1934 3.591023 GGAGTTCTTGGAGAGCTTGTAC 58.409 50.000 0.00 0.00 35.86 2.90
1518 2033 1.080093 GATGACGGCGACCTTGACA 60.080 57.895 16.62 2.21 0.00 3.58
1630 2145 3.391665 CTAGGACAAGGCTGCCGGG 62.392 68.421 13.96 11.96 0.00 5.73
1632 2147 2.512515 GCTAGGACAAGGCTGCCG 60.513 66.667 13.96 2.09 0.00 5.69
1633 2148 2.124529 GGCTAGGACAAGGCTGCC 60.125 66.667 11.65 11.65 38.92 4.85
1634 2149 2.512515 CGGCTAGGACAAGGCTGC 60.513 66.667 0.00 0.00 39.79 5.25
1635 2150 2.187946 CCGGCTAGGACAAGGCTG 59.812 66.667 0.00 0.00 45.00 4.85
1637 2152 3.387225 GACCCGGCTAGGACAAGGC 62.387 68.421 0.00 0.00 45.00 4.35
1639 2154 1.517832 CAGACCCGGCTAGGACAAG 59.482 63.158 0.00 0.00 45.00 3.16
1641 2156 3.075005 GCAGACCCGGCTAGGACA 61.075 66.667 0.00 0.00 45.00 4.02
1689 2204 3.649277 CTCGACGGCAGTTCCAGGG 62.649 68.421 0.00 0.00 34.01 4.45
1791 2306 4.671766 GCAACTAACTCACTAATTTGGCCG 60.672 45.833 0.00 0.00 0.00 6.13
1827 2342 7.992608 TGATGATATAAGCAAATGTACACCAGT 59.007 33.333 0.00 0.00 0.00 4.00
1871 2388 6.078202 TGGATCAAAATTGAAAAGCGTACA 57.922 33.333 0.00 0.00 41.13 2.90
1906 2423 4.638421 ACTGACACAGATGAGAGCTAGTAC 59.362 45.833 5.76 0.00 35.18 2.73
1909 2426 4.398988 AGAACTGACACAGATGAGAGCTAG 59.601 45.833 5.76 0.00 35.18 3.42
1910 2427 4.339748 AGAACTGACACAGATGAGAGCTA 58.660 43.478 5.76 0.00 35.18 3.32
1911 2428 3.164268 AGAACTGACACAGATGAGAGCT 58.836 45.455 5.76 0.00 35.18 4.09
1912 2429 3.591196 AGAACTGACACAGATGAGAGC 57.409 47.619 5.76 0.00 35.18 4.09
1913 2430 5.131594 TGAAGAACTGACACAGATGAGAG 57.868 43.478 5.76 0.00 35.18 3.20
1914 2431 4.586421 ACTGAAGAACTGACACAGATGAGA 59.414 41.667 5.76 0.00 35.18 3.27
1920 2437 4.677378 CGACTAACTGAAGAACTGACACAG 59.323 45.833 0.00 0.00 37.52 3.66
1931 2448 1.546476 AGGAGTGGCGACTAACTGAAG 59.454 52.381 0.00 0.00 30.16 3.02
1949 2466 0.251297 TTGAGGGGTGATGCACAAGG 60.251 55.000 0.00 0.00 35.86 3.61
1979 2500 9.361315 GCATAAACCACCGATTTTATTTACTTT 57.639 29.630 0.00 0.00 0.00 2.66
2054 2578 9.161629 CAAATTCCCAAACTCAATATAAAACCC 57.838 33.333 0.00 0.00 0.00 4.11
2133 2667 1.003696 CTCCCCTCCAGAAGTGAAACC 59.996 57.143 0.00 0.00 37.80 3.27
2192 2726 3.572255 GCAAAAGTTCCAACCTGACCATA 59.428 43.478 0.00 0.00 0.00 2.74
2193 2727 2.365293 GCAAAAGTTCCAACCTGACCAT 59.635 45.455 0.00 0.00 0.00 3.55
2194 2728 1.754226 GCAAAAGTTCCAACCTGACCA 59.246 47.619 0.00 0.00 0.00 4.02
2371 2921 2.545946 GAGTGTTGTGAGAGGTTCTTGC 59.454 50.000 0.00 0.00 0.00 4.01
2386 2936 7.228314 TGTACTCAGTAATGCTAAGAGTGTT 57.772 36.000 0.00 0.00 39.65 3.32
2425 2976 1.808411 AGTACACAGAACAATGGGCG 58.192 50.000 0.00 0.00 0.00 6.13
2528 3080 7.545615 CAGGCCCAAGATAAAGAAATAACAAAC 59.454 37.037 0.00 0.00 0.00 2.93
2614 3168 3.919834 ACTATTCTAGGCCGAACCCTTA 58.080 45.455 0.00 0.00 40.58 2.69
2647 3201 4.263550 CGGGACAGAAGAGATCCTCCTATA 60.264 50.000 0.00 0.00 32.70 1.31
2648 3202 3.499563 CGGGACAGAAGAGATCCTCCTAT 60.500 52.174 0.00 0.00 32.70 2.57
2661 3215 4.011023 TGAGAAAAACAAACGGGACAGAA 58.989 39.130 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.