Multiple sequence alignment - TraesCS6B01G199400

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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 TraesCS6B01G199400 chr6B 100.000 3461 0 0 1 3461 239282250 239285710 0.000000e+00 6392.0
1 TraesCS6B01G199400 chr6D 95.173 2921 75 25 519 3415 139307703 139310581 0.000000e+00 4553.0
2 TraesCS6B01G199400 chr6D 91.341 358 20 5 16 368 139290245 139290596 2.420000e-131 479.0
3 TraesCS6B01G199400 chr6D 94.000 50 2 1 3412 3460 139310608 139310657 1.330000e-09 75.0
4 TraesCS6B01G199400 chr6A 94.942 2946 72 33 532 3415 181893727 181896657 0.000000e+00 4543.0
5 TraesCS6B01G199400 chr6A 88.011 367 22 15 16 368 181893339 181893697 6.910000e-112 414.0
6 TraesCS6B01G199400 chr6A 92.000 50 3 1 3412 3460 181896684 181896733 6.200000e-08 69.4
7 TraesCS6B01G199400 chr3B 82.353 119 9 7 368 482 217136293 217136403 3.680000e-15 93.5
8 TraesCS6B01G199400 chr5A 81.197 117 17 5 368 482 178503579 178503692 4.760000e-14 89.8
9 TraesCS6B01G199400 chr5B 83.505 97 12 3 366 462 350408345 350408253 1.710000e-13 87.9
10 TraesCS6B01G199400 chr5B 80.508 118 8 8 366 482 51975776 51975673 3.700000e-10 76.8
11 TraesCS6B01G199400 chr7B 91.228 57 4 1 366 421 676406464 676406520 3.700000e-10 76.8


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 TraesCS6B01G199400 chr6B 239282250 239285710 3460 False 6392.000000 6392 100.0000 1 3461 1 chr6B.!!$F1 3460
1 TraesCS6B01G199400 chr6D 139307703 139310657 2954 False 2314.000000 4553 94.5865 519 3460 2 chr6D.!!$F2 2941
2 TraesCS6B01G199400 chr6A 181893339 181896733 3394 False 1675.466667 4543 91.6510 16 3460 3 chr6A.!!$F1 3444

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
688 710 0.256177 TCCTCTTCCGCTCTAGCAGA 59.744 55.000 2.44 0.0 42.21 4.26 F
830 864 1.486726 CACCTTCACAGGATCTACCCC 59.513 57.143 0.00 0.0 44.19 4.95 F
2100 2172 0.107508 CCATCGTGGCAGACTCCATT 60.108 55.000 0.00 0.0 38.57 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1908 1980 0.394899 GAATTCCCAGGTGCCTCAGG 60.395 60.0 0.00 0.0 0.0 3.86 R
2323 2395 0.831966 ATCAAGAGCTCAGGCAGGAG 59.168 55.0 17.77 2.2 41.7 3.69 R
3183 3292 1.200519 TAGTAAGGCGGCAATCAGGT 58.799 50.0 13.08 0.0 0.0 4.00 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
26 27 0.798776 CAGCGTCCTTTGCCTTAGTG 59.201 55.000 0.00 0.00 0.00 2.74
33 34 4.439563 CGTCCTTTGCCTTAGTGTTTGTTT 60.440 41.667 0.00 0.00 0.00 2.83
37 38 6.048509 CCTTTGCCTTAGTGTTTGTTTGATT 58.951 36.000 0.00 0.00 0.00 2.57
39 40 5.843673 TGCCTTAGTGTTTGTTTGATTGA 57.156 34.783 0.00 0.00 0.00 2.57
90 91 5.500234 TCAATAGGAGGTTTGAGTGAATGG 58.500 41.667 0.00 0.00 0.00 3.16
94 95 5.003096 AGGAGGTTTGAGTGAATGGAAAT 57.997 39.130 0.00 0.00 0.00 2.17
105 106 8.367943 TGAGTGAATGGAAATTTTCAAATGTG 57.632 30.769 2.57 0.00 0.00 3.21
160 161 2.233676 ACTCGGCAATACAGATCACACA 59.766 45.455 0.00 0.00 0.00 3.72
165 166 3.127548 GGCAATACAGATCACACAACTGG 59.872 47.826 0.00 0.00 36.17 4.00
211 214 6.385766 AGAGATTCCAATTCTCCAAAGTCT 57.614 37.500 0.00 0.00 0.00 3.24
213 216 7.563906 AGAGATTCCAATTCTCCAAAGTCTAG 58.436 38.462 0.00 0.00 0.00 2.43
214 217 7.401493 AGAGATTCCAATTCTCCAAAGTCTAGA 59.599 37.037 0.00 0.00 0.00 2.43
219 222 7.865820 TCCAATTCTCCAAAGTCTAGATGAAT 58.134 34.615 0.00 0.00 0.00 2.57
220 223 7.772292 TCCAATTCTCCAAAGTCTAGATGAATG 59.228 37.037 0.00 0.00 0.00 2.67
221 224 7.772292 CCAATTCTCCAAAGTCTAGATGAATGA 59.228 37.037 0.00 0.00 0.00 2.57
222 225 9.170734 CAATTCTCCAAAGTCTAGATGAATGAA 57.829 33.333 0.00 0.00 0.00 2.57
223 226 9.745018 AATTCTCCAAAGTCTAGATGAATGAAA 57.255 29.630 0.00 0.00 0.00 2.69
224 227 9.745018 ATTCTCCAAAGTCTAGATGAATGAAAA 57.255 29.630 0.00 0.00 0.00 2.29
229 232 8.619546 CCAAAGTCTAGATGAATGAAAATCCTC 58.380 37.037 0.00 0.00 0.00 3.71
249 252 5.053145 CCTCTAAATGAAAGAGACCCGATG 58.947 45.833 1.72 0.00 42.63 3.84
250 253 5.395768 CCTCTAAATGAAAGAGACCCGATGT 60.396 44.000 1.72 0.00 42.63 3.06
251 254 5.661458 TCTAAATGAAAGAGACCCGATGTC 58.339 41.667 0.00 0.00 44.82 3.06
264 271 1.599419 CCGATGTCACGTATCGCATGA 60.599 52.381 12.60 0.00 44.41 3.07
312 323 9.912634 TCTTGAAATTGTCAAATCAAAGGTATC 57.087 29.630 14.50 0.00 45.67 2.24
363 374 6.638873 CCACATTAGTGTCATCTCGTCTATTC 59.361 42.308 0.00 0.00 44.39 1.75
368 379 8.693120 TTAGTGTCATCTCGTCTATTCCTAAT 57.307 34.615 0.00 0.00 0.00 1.73
370 381 8.693120 AGTGTCATCTCGTCTATTCCTAATTA 57.307 34.615 0.00 0.00 0.00 1.40
373 384 9.078990 TGTCATCTCGTCTATTCCTAATTATGT 57.921 33.333 0.00 0.00 0.00 2.29
374 385 9.562583 GTCATCTCGTCTATTCCTAATTATGTC 57.437 37.037 0.00 0.00 0.00 3.06
375 386 9.297037 TCATCTCGTCTATTCCTAATTATGTCA 57.703 33.333 0.00 0.00 0.00 3.58
376 387 9.347934 CATCTCGTCTATTCCTAATTATGTCAC 57.652 37.037 0.00 0.00 0.00 3.67
379 390 9.347934 CTCGTCTATTCCTAATTATGTCACATC 57.652 37.037 0.00 0.00 0.00 3.06
380 391 9.078990 TCGTCTATTCCTAATTATGTCACATCT 57.921 33.333 0.00 0.00 0.00 2.90
386 397 9.784531 ATTCCTAATTATGTCACATCTAACCTG 57.215 33.333 0.00 0.00 0.00 4.00
387 398 8.547481 TCCTAATTATGTCACATCTAACCTGA 57.453 34.615 0.00 0.00 0.00 3.86
388 399 9.159254 TCCTAATTATGTCACATCTAACCTGAT 57.841 33.333 0.00 0.00 0.00 2.90
389 400 9.212641 CCTAATTATGTCACATCTAACCTGATG 57.787 37.037 0.00 0.00 46.61 3.07
437 448 9.591792 TTTTATTTTTGCCCCAATTTTTCTTTG 57.408 25.926 0.00 0.00 0.00 2.77
438 449 6.788598 ATTTTTGCCCCAATTTTTCTTTGT 57.211 29.167 0.00 0.00 0.00 2.83
439 450 6.596309 TTTTTGCCCCAATTTTTCTTTGTT 57.404 29.167 0.00 0.00 0.00 2.83
440 451 6.596309 TTTTGCCCCAATTTTTCTTTGTTT 57.404 29.167 0.00 0.00 0.00 2.83
441 452 5.826601 TTGCCCCAATTTTTCTTTGTTTC 57.173 34.783 0.00 0.00 0.00 2.78
442 453 5.109500 TGCCCCAATTTTTCTTTGTTTCT 57.891 34.783 0.00 0.00 0.00 2.52
443 454 5.504853 TGCCCCAATTTTTCTTTGTTTCTT 58.495 33.333 0.00 0.00 0.00 2.52
444 455 5.356470 TGCCCCAATTTTTCTTTGTTTCTTG 59.644 36.000 0.00 0.00 0.00 3.02
445 456 5.356751 GCCCCAATTTTTCTTTGTTTCTTGT 59.643 36.000 0.00 0.00 0.00 3.16
446 457 6.127758 GCCCCAATTTTTCTTTGTTTCTTGTT 60.128 34.615 0.00 0.00 0.00 2.83
447 458 7.249858 CCCCAATTTTTCTTTGTTTCTTGTTG 58.750 34.615 0.00 0.00 0.00 3.33
448 459 6.746822 CCCAATTTTTCTTTGTTTCTTGTTGC 59.253 34.615 0.00 0.00 0.00 4.17
449 460 7.361971 CCCAATTTTTCTTTGTTTCTTGTTGCT 60.362 33.333 0.00 0.00 0.00 3.91
450 461 7.482428 CCAATTTTTCTTTGTTTCTTGTTGCTG 59.518 33.333 0.00 0.00 0.00 4.41
451 462 5.529014 TTTTCTTTGTTTCTTGTTGCTGC 57.471 34.783 0.00 0.00 0.00 5.25
452 463 3.865011 TCTTTGTTTCTTGTTGCTGCA 57.135 38.095 0.00 0.00 0.00 4.41
453 464 4.389890 TCTTTGTTTCTTGTTGCTGCAT 57.610 36.364 1.84 0.00 0.00 3.96
454 465 4.757594 TCTTTGTTTCTTGTTGCTGCATT 58.242 34.783 1.84 0.00 0.00 3.56
455 466 5.900425 TCTTTGTTTCTTGTTGCTGCATTA 58.100 33.333 1.84 0.00 0.00 1.90
456 467 6.514947 TCTTTGTTTCTTGTTGCTGCATTAT 58.485 32.000 1.84 0.00 0.00 1.28
457 468 6.985645 TCTTTGTTTCTTGTTGCTGCATTATT 59.014 30.769 1.84 0.00 0.00 1.40
458 469 7.495279 TCTTTGTTTCTTGTTGCTGCATTATTT 59.505 29.630 1.84 0.00 0.00 1.40
459 470 6.528014 TGTTTCTTGTTGCTGCATTATTTG 57.472 33.333 1.84 0.00 0.00 2.32
460 471 6.047870 TGTTTCTTGTTGCTGCATTATTTGT 58.952 32.000 1.84 0.00 0.00 2.83
461 472 6.018913 TGTTTCTTGTTGCTGCATTATTTGTG 60.019 34.615 1.84 0.00 0.00 3.33
462 473 5.450592 TCTTGTTGCTGCATTATTTGTGA 57.549 34.783 1.84 0.00 0.00 3.58
463 474 5.840715 TCTTGTTGCTGCATTATTTGTGAA 58.159 33.333 1.84 0.00 0.00 3.18
464 475 6.279123 TCTTGTTGCTGCATTATTTGTGAAA 58.721 32.000 1.84 0.00 0.00 2.69
465 476 6.421501 TCTTGTTGCTGCATTATTTGTGAAAG 59.578 34.615 1.84 0.00 0.00 2.62
466 477 4.989797 TGTTGCTGCATTATTTGTGAAAGG 59.010 37.500 1.84 0.00 0.00 3.11
467 478 4.870123 TGCTGCATTATTTGTGAAAGGT 57.130 36.364 0.00 0.00 0.00 3.50
468 479 5.212532 TGCTGCATTATTTGTGAAAGGTT 57.787 34.783 0.00 0.00 0.00 3.50
469 480 5.229423 TGCTGCATTATTTGTGAAAGGTTC 58.771 37.500 0.00 0.00 0.00 3.62
470 481 5.010922 TGCTGCATTATTTGTGAAAGGTTCT 59.989 36.000 0.00 0.00 0.00 3.01
471 482 6.208402 TGCTGCATTATTTGTGAAAGGTTCTA 59.792 34.615 0.00 0.00 0.00 2.10
472 483 6.749118 GCTGCATTATTTGTGAAAGGTTCTAG 59.251 38.462 0.00 0.00 0.00 2.43
473 484 7.362056 GCTGCATTATTTGTGAAAGGTTCTAGA 60.362 37.037 0.00 0.00 0.00 2.43
474 485 8.579850 TGCATTATTTGTGAAAGGTTCTAGAT 57.420 30.769 0.00 0.00 0.00 1.98
475 486 8.461222 TGCATTATTTGTGAAAGGTTCTAGATG 58.539 33.333 0.00 0.00 0.00 2.90
476 487 8.462016 GCATTATTTGTGAAAGGTTCTAGATGT 58.538 33.333 0.00 0.00 0.00 3.06
477 488 9.778993 CATTATTTGTGAAAGGTTCTAGATGTG 57.221 33.333 0.00 0.00 0.00 3.21
478 489 9.739276 ATTATTTGTGAAAGGTTCTAGATGTGA 57.261 29.630 0.00 0.00 0.00 3.58
479 490 9.567776 TTATTTGTGAAAGGTTCTAGATGTGAA 57.432 29.630 0.00 0.00 0.00 3.18
480 491 8.641498 ATTTGTGAAAGGTTCTAGATGTGAAT 57.359 30.769 0.00 0.00 0.00 2.57
481 492 7.672983 TTGTGAAAGGTTCTAGATGTGAATC 57.327 36.000 0.00 0.00 0.00 2.52
482 493 6.768483 TGTGAAAGGTTCTAGATGTGAATCA 58.232 36.000 0.00 0.00 0.00 2.57
483 494 6.875726 TGTGAAAGGTTCTAGATGTGAATCAG 59.124 38.462 0.00 0.00 0.00 2.90
484 495 7.099764 GTGAAAGGTTCTAGATGTGAATCAGA 58.900 38.462 0.00 0.00 0.00 3.27
485 496 7.277539 GTGAAAGGTTCTAGATGTGAATCAGAG 59.722 40.741 0.00 0.00 0.00 3.35
486 497 7.179160 TGAAAGGTTCTAGATGTGAATCAGAGA 59.821 37.037 0.00 0.00 0.00 3.10
487 498 7.487822 AAGGTTCTAGATGTGAATCAGAGAA 57.512 36.000 0.00 0.00 0.00 2.87
488 499 7.487822 AGGTTCTAGATGTGAATCAGAGAAA 57.512 36.000 0.00 0.00 30.50 2.52
489 500 7.327214 AGGTTCTAGATGTGAATCAGAGAAAC 58.673 38.462 0.00 9.00 34.19 2.78
490 501 7.180051 AGGTTCTAGATGTGAATCAGAGAAACT 59.820 37.037 11.95 11.95 36.89 2.66
491 502 7.277539 GGTTCTAGATGTGAATCAGAGAAACTG 59.722 40.741 0.00 0.00 46.97 3.16
492 503 7.473735 TCTAGATGTGAATCAGAGAAACTGT 57.526 36.000 0.00 0.00 45.86 3.55
493 504 7.901029 TCTAGATGTGAATCAGAGAAACTGTT 58.099 34.615 0.00 0.00 45.86 3.16
494 505 8.370940 TCTAGATGTGAATCAGAGAAACTGTTT 58.629 33.333 5.29 5.29 45.86 2.83
495 506 7.199541 AGATGTGAATCAGAGAAACTGTTTG 57.800 36.000 11.03 0.00 45.86 2.93
496 507 6.769822 AGATGTGAATCAGAGAAACTGTTTGT 59.230 34.615 11.03 6.56 45.86 2.83
497 508 6.122850 TGTGAATCAGAGAAACTGTTTGTG 57.877 37.500 11.03 5.63 45.86 3.33
498 509 5.879777 TGTGAATCAGAGAAACTGTTTGTGA 59.120 36.000 11.03 10.59 45.86 3.58
499 510 6.374053 TGTGAATCAGAGAAACTGTTTGTGAA 59.626 34.615 11.03 0.00 45.86 3.18
500 511 6.688813 GTGAATCAGAGAAACTGTTTGTGAAC 59.311 38.462 11.03 9.38 45.86 3.18
501 512 5.757850 ATCAGAGAAACTGTTTGTGAACC 57.242 39.130 11.03 0.00 45.86 3.62
502 513 4.843728 TCAGAGAAACTGTTTGTGAACCT 58.156 39.130 11.03 0.00 45.86 3.50
503 514 4.876107 TCAGAGAAACTGTTTGTGAACCTC 59.124 41.667 11.03 9.49 45.86 3.85
504 515 4.635765 CAGAGAAACTGTTTGTGAACCTCA 59.364 41.667 11.03 0.00 41.30 3.86
505 516 5.123820 CAGAGAAACTGTTTGTGAACCTCAA 59.876 40.000 11.03 0.00 41.30 3.02
506 517 5.710099 AGAGAAACTGTTTGTGAACCTCAAA 59.290 36.000 11.03 0.00 34.80 2.69
507 518 6.208599 AGAGAAACTGTTTGTGAACCTCAAAA 59.791 34.615 11.03 0.00 36.71 2.44
508 519 6.754193 AGAAACTGTTTGTGAACCTCAAAAA 58.246 32.000 11.03 0.00 36.71 1.94
672 694 2.165112 TCCTATTCCCCAGATCCTCCT 58.835 52.381 0.00 0.00 0.00 3.69
688 710 0.256177 TCCTCTTCCGCTCTAGCAGA 59.744 55.000 2.44 0.00 42.21 4.26
730 754 3.652869 TGGAGGGTTTGAAGAGAGACAAT 59.347 43.478 0.00 0.00 0.00 2.71
741 775 6.766429 TGAAGAGAGACAATCATATCCATGG 58.234 40.000 4.97 4.97 32.61 3.66
805 839 2.125912 CCTCTTGTCCCGACGCTG 60.126 66.667 0.00 0.00 0.00 5.18
830 864 1.486726 CACCTTCACAGGATCTACCCC 59.513 57.143 0.00 0.00 44.19 4.95
872 906 4.250305 GGACGGCAGTGGTGGTGT 62.250 66.667 0.00 0.00 0.00 4.16
896 935 4.394712 CACACCACTCCGCCCTCC 62.395 72.222 0.00 0.00 0.00 4.30
901 940 3.465403 CACTCCGCCCTCCCTCAG 61.465 72.222 0.00 0.00 0.00 3.35
906 945 4.154347 CGCCCTCCCTCAGCTCAC 62.154 72.222 0.00 0.00 0.00 3.51
907 946 3.791586 GCCCTCCCTCAGCTCACC 61.792 72.222 0.00 0.00 0.00 4.02
908 947 2.040278 CCCTCCCTCAGCTCACCT 59.960 66.667 0.00 0.00 0.00 4.00
909 948 2.063378 CCCTCCCTCAGCTCACCTC 61.063 68.421 0.00 0.00 0.00 3.85
910 949 2.063378 CCTCCCTCAGCTCACCTCC 61.063 68.421 0.00 0.00 0.00 4.30
911 950 2.039624 TCCCTCAGCTCACCTCCC 59.960 66.667 0.00 0.00 0.00 4.30
912 951 3.086600 CCCTCAGCTCACCTCCCC 61.087 72.222 0.00 0.00 0.00 4.81
913 952 2.040278 CCTCAGCTCACCTCCCCT 59.960 66.667 0.00 0.00 0.00 4.79
914 953 2.063378 CCTCAGCTCACCTCCCCTC 61.063 68.421 0.00 0.00 0.00 4.30
915 954 2.039624 TCAGCTCACCTCCCCTCC 59.960 66.667 0.00 0.00 0.00 4.30
916 955 3.086600 CAGCTCACCTCCCCTCCC 61.087 72.222 0.00 0.00 0.00 4.30
917 956 3.288381 AGCTCACCTCCCCTCCCT 61.288 66.667 0.00 0.00 0.00 4.20
918 957 2.766229 GCTCACCTCCCCTCCCTC 60.766 72.222 0.00 0.00 0.00 4.30
919 958 2.443016 CTCACCTCCCCTCCCTCG 60.443 72.222 0.00 0.00 0.00 4.63
920 959 4.779733 TCACCTCCCCTCCCTCGC 62.780 72.222 0.00 0.00 0.00 5.03
1548 1620 2.110213 GTGGTCCACAACGAGGCA 59.890 61.111 17.59 0.00 34.08 4.75
2100 2172 0.107508 CCATCGTGGCAGACTCCATT 60.108 55.000 0.00 0.00 38.57 3.16
2118 2190 2.902705 TTGTGCGGTTTCTAGACACT 57.097 45.000 8.85 0.00 32.49 3.55
2121 2193 1.000506 GTGCGGTTTCTAGACACTGGA 59.999 52.381 17.51 13.04 0.00 3.86
2124 2196 3.244422 TGCGGTTTCTAGACACTGGAAAT 60.244 43.478 17.51 0.00 41.51 2.17
2127 2199 4.652822 GGTTTCTAGACACTGGAAATGGT 58.347 43.478 8.85 0.00 41.51 3.55
2531 2611 6.427853 GGTCTTTGATTTTGGCATAGCTTTTT 59.572 34.615 0.00 0.00 0.00 1.94
2532 2612 7.360353 GGTCTTTGATTTTGGCATAGCTTTTTC 60.360 37.037 0.00 0.00 0.00 2.29
2533 2613 7.386025 GTCTTTGATTTTGGCATAGCTTTTTCT 59.614 33.333 0.00 0.00 0.00 2.52
2534 2614 7.599998 TCTTTGATTTTGGCATAGCTTTTTCTC 59.400 33.333 0.00 0.00 0.00 2.87
2537 2617 7.215789 TGATTTTGGCATAGCTTTTTCTCAAA 58.784 30.769 0.00 0.00 0.00 2.69
2538 2618 7.879160 TGATTTTGGCATAGCTTTTTCTCAAAT 59.121 29.630 0.00 0.00 0.00 2.32
2758 2856 8.397906 CAAAAGGTCTCGCATAATCATAGAAAA 58.602 33.333 0.00 0.00 0.00 2.29
2899 2997 2.341464 CGACTAACATGCTGTACACACG 59.659 50.000 0.00 0.00 0.00 4.49
2900 2998 2.666508 GACTAACATGCTGTACACACGG 59.333 50.000 0.00 0.00 0.00 4.94
2920 3018 4.035208 ACGGTTGATTTGAGAACACAGTTC 59.965 41.667 1.77 1.77 0.00 3.01
3041 3147 4.571984 TCAACTGTCTGAACAACTCATGTG 59.428 41.667 0.00 0.00 42.99 3.21
3084 3190 4.096382 CCCAATTCTTGTATTTGACCCTCG 59.904 45.833 0.00 0.00 0.00 4.63
3135 3244 4.630644 TGCTCAGAAGGAAATGTCTCTT 57.369 40.909 0.00 0.00 0.00 2.85
3138 3247 4.759183 GCTCAGAAGGAAATGTCTCTTGTT 59.241 41.667 0.00 0.00 0.00 2.83
3159 3268 0.390472 CTCCTTCACGTTCTGGAGCC 60.390 60.000 12.62 0.00 39.46 4.70
3183 3292 5.012768 CCTGTAAGAAAACCCTAGTTCCTCA 59.987 44.000 0.00 0.00 31.73 3.86
3444 3613 9.988815 AGTACTTGCAATATTAATCAGACTAGG 57.011 33.333 0.00 0.00 0.00 3.02
3457 3626 4.014406 TCAGACTAGGCACGTTAGATTGA 58.986 43.478 0.00 1.27 0.00 2.57
3459 3628 4.800993 CAGACTAGGCACGTTAGATTGAAG 59.199 45.833 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.247695 GCAAAGGACGCTGATAACGC 60.248 55.000 0.00 0.00 0.00 4.84
1 2 0.373716 GGCAAAGGACGCTGATAACG 59.626 55.000 0.00 0.00 0.00 3.18
2 3 1.739067 AGGCAAAGGACGCTGATAAC 58.261 50.000 0.00 0.00 0.00 1.89
3 4 2.489938 AAGGCAAAGGACGCTGATAA 57.510 45.000 0.00 0.00 0.00 1.75
4 5 2.500098 ACTAAGGCAAAGGACGCTGATA 59.500 45.455 0.00 0.00 0.00 2.15
5 6 1.279271 ACTAAGGCAAAGGACGCTGAT 59.721 47.619 0.00 0.00 0.00 2.90
6 7 0.685097 ACTAAGGCAAAGGACGCTGA 59.315 50.000 0.00 0.00 0.00 4.26
7 8 0.798776 CACTAAGGCAAAGGACGCTG 59.201 55.000 0.00 0.00 0.00 5.18
8 9 0.396811 ACACTAAGGCAAAGGACGCT 59.603 50.000 0.00 0.00 0.00 5.07
9 10 1.235724 AACACTAAGGCAAAGGACGC 58.764 50.000 0.00 0.00 0.00 5.19
10 11 2.616842 ACAAACACTAAGGCAAAGGACG 59.383 45.455 0.00 0.00 0.00 4.79
11 12 4.649088 AACAAACACTAAGGCAAAGGAC 57.351 40.909 0.00 0.00 0.00 3.85
12 13 4.707448 TCAAACAAACACTAAGGCAAAGGA 59.293 37.500 0.00 0.00 0.00 3.36
13 14 5.004922 TCAAACAAACACTAAGGCAAAGG 57.995 39.130 0.00 0.00 0.00 3.11
14 15 6.756074 TCAATCAAACAAACACTAAGGCAAAG 59.244 34.615 0.00 0.00 0.00 2.77
52 53 7.164803 CCTCCTATTGAAAACTCTCTCTTGTT 58.835 38.462 0.00 0.00 0.00 2.83
57 58 7.162082 TCAAACCTCCTATTGAAAACTCTCTC 58.838 38.462 0.00 0.00 32.89 3.20
63 64 6.877611 TCACTCAAACCTCCTATTGAAAAC 57.122 37.500 0.00 0.00 35.31 2.43
67 68 5.250543 TCCATTCACTCAAACCTCCTATTGA 59.749 40.000 0.00 0.00 34.57 2.57
71 72 5.576563 TTTCCATTCACTCAAACCTCCTA 57.423 39.130 0.00 0.00 0.00 2.94
72 73 4.453480 TTTCCATTCACTCAAACCTCCT 57.547 40.909 0.00 0.00 0.00 3.69
73 74 5.728637 AATTTCCATTCACTCAAACCTCC 57.271 39.130 0.00 0.00 0.00 4.30
119 120 7.362142 GCCGAGTCCTAAAGATTTTCTTCAAAT 60.362 37.037 0.00 0.00 35.27 2.32
189 192 7.560368 TCTAGACTTTGGAGAATTGGAATCTC 58.440 38.462 0.00 0.00 42.09 2.75
194 197 6.874278 TCATCTAGACTTTGGAGAATTGGA 57.126 37.500 0.00 0.00 0.00 3.53
219 222 7.611855 GGGTCTCTTTCATTTAGAGGATTTTCA 59.388 37.037 0.00 0.00 39.66 2.69
220 223 7.201652 CGGGTCTCTTTCATTTAGAGGATTTTC 60.202 40.741 0.00 0.00 39.66 2.29
221 224 6.599638 CGGGTCTCTTTCATTTAGAGGATTTT 59.400 38.462 0.00 0.00 39.66 1.82
222 225 6.070194 TCGGGTCTCTTTCATTTAGAGGATTT 60.070 38.462 0.00 0.00 39.66 2.17
223 226 5.425539 TCGGGTCTCTTTCATTTAGAGGATT 59.574 40.000 0.00 0.00 39.66 3.01
224 227 4.962995 TCGGGTCTCTTTCATTTAGAGGAT 59.037 41.667 0.00 0.00 39.66 3.24
229 232 5.975410 GACATCGGGTCTCTTTCATTTAG 57.025 43.478 1.55 0.00 43.46 1.85
249 252 1.452025 CCGATTCATGCGATACGTGAC 59.548 52.381 0.00 0.00 44.08 3.67
250 253 1.766069 CCGATTCATGCGATACGTGA 58.234 50.000 0.00 0.00 42.69 4.35
251 254 0.161658 GCCGATTCATGCGATACGTG 59.838 55.000 0.00 0.00 36.55 4.49
252 255 0.944311 GGCCGATTCATGCGATACGT 60.944 55.000 0.00 0.00 0.00 3.57
253 256 1.781555 GGCCGATTCATGCGATACG 59.218 57.895 0.00 0.00 0.00 3.06
254 257 1.626654 CCGGCCGATTCATGCGATAC 61.627 60.000 30.73 0.00 0.00 2.24
264 271 0.885596 TTCGAACAAACCGGCCGATT 60.886 50.000 30.73 15.33 0.00 3.34
363 374 9.212641 CATCAGGTTAGATGTGACATAATTAGG 57.787 37.037 0.00 0.00 40.35 2.69
411 422 9.591792 CAAAGAAAAATTGGGGCAAAAATAAAA 57.408 25.926 0.00 0.00 0.00 1.52
412 423 8.753133 ACAAAGAAAAATTGGGGCAAAAATAAA 58.247 25.926 0.00 0.00 32.02 1.40
413 424 8.298729 ACAAAGAAAAATTGGGGCAAAAATAA 57.701 26.923 0.00 0.00 32.02 1.40
414 425 7.888250 ACAAAGAAAAATTGGGGCAAAAATA 57.112 28.000 0.00 0.00 32.02 1.40
415 426 6.788598 ACAAAGAAAAATTGGGGCAAAAAT 57.211 29.167 0.00 0.00 32.02 1.82
416 427 6.596309 AACAAAGAAAAATTGGGGCAAAAA 57.404 29.167 0.00 0.00 32.02 1.94
417 428 6.435591 AGAAACAAAGAAAAATTGGGGCAAAA 59.564 30.769 0.00 0.00 32.02 2.44
418 429 5.948758 AGAAACAAAGAAAAATTGGGGCAAA 59.051 32.000 0.00 0.00 32.02 3.68
419 430 5.504853 AGAAACAAAGAAAAATTGGGGCAA 58.495 33.333 0.00 0.00 32.02 4.52
420 431 5.109500 AGAAACAAAGAAAAATTGGGGCA 57.891 34.783 0.00 0.00 32.02 5.36
421 432 5.356751 ACAAGAAACAAAGAAAAATTGGGGC 59.643 36.000 0.00 0.00 32.02 5.80
422 433 7.249858 CAACAAGAAACAAAGAAAAATTGGGG 58.750 34.615 0.00 0.00 32.02 4.96
423 434 6.746822 GCAACAAGAAACAAAGAAAAATTGGG 59.253 34.615 0.00 0.00 32.02 4.12
424 435 7.482428 CAGCAACAAGAAACAAAGAAAAATTGG 59.518 33.333 0.00 0.00 32.02 3.16
425 436 7.007636 GCAGCAACAAGAAACAAAGAAAAATTG 59.992 33.333 0.00 0.00 0.00 2.32
426 437 7.022979 GCAGCAACAAGAAACAAAGAAAAATT 58.977 30.769 0.00 0.00 0.00 1.82
427 438 6.149142 TGCAGCAACAAGAAACAAAGAAAAAT 59.851 30.769 0.00 0.00 0.00 1.82
428 439 5.468072 TGCAGCAACAAGAAACAAAGAAAAA 59.532 32.000 0.00 0.00 0.00 1.94
429 440 4.993584 TGCAGCAACAAGAAACAAAGAAAA 59.006 33.333 0.00 0.00 0.00 2.29
430 441 4.564041 TGCAGCAACAAGAAACAAAGAAA 58.436 34.783 0.00 0.00 0.00 2.52
431 442 4.185467 TGCAGCAACAAGAAACAAAGAA 57.815 36.364 0.00 0.00 0.00 2.52
432 443 3.865011 TGCAGCAACAAGAAACAAAGA 57.135 38.095 0.00 0.00 0.00 2.52
433 444 6.774354 ATAATGCAGCAACAAGAAACAAAG 57.226 33.333 0.00 0.00 0.00 2.77
434 445 7.065563 ACAAATAATGCAGCAACAAGAAACAAA 59.934 29.630 0.00 0.00 0.00 2.83
435 446 6.538021 ACAAATAATGCAGCAACAAGAAACAA 59.462 30.769 0.00 0.00 0.00 2.83
436 447 6.018913 CACAAATAATGCAGCAACAAGAAACA 60.019 34.615 0.00 0.00 0.00 2.83
437 448 6.200665 TCACAAATAATGCAGCAACAAGAAAC 59.799 34.615 0.00 0.00 0.00 2.78
438 449 6.279123 TCACAAATAATGCAGCAACAAGAAA 58.721 32.000 0.00 0.00 0.00 2.52
439 450 5.840715 TCACAAATAATGCAGCAACAAGAA 58.159 33.333 0.00 0.00 0.00 2.52
440 451 5.450592 TCACAAATAATGCAGCAACAAGA 57.549 34.783 0.00 0.00 0.00 3.02
441 452 6.347079 CCTTTCACAAATAATGCAGCAACAAG 60.347 38.462 0.00 0.00 0.00 3.16
442 453 5.466058 CCTTTCACAAATAATGCAGCAACAA 59.534 36.000 0.00 0.00 0.00 2.83
443 454 4.989797 CCTTTCACAAATAATGCAGCAACA 59.010 37.500 0.00 0.00 0.00 3.33
444 455 4.990426 ACCTTTCACAAATAATGCAGCAAC 59.010 37.500 0.00 0.00 0.00 4.17
445 456 5.212532 ACCTTTCACAAATAATGCAGCAA 57.787 34.783 0.00 0.00 0.00 3.91
446 457 4.870123 ACCTTTCACAAATAATGCAGCA 57.130 36.364 0.00 0.00 0.00 4.41
447 458 5.473039 AGAACCTTTCACAAATAATGCAGC 58.527 37.500 0.00 0.00 0.00 5.25
448 459 8.044060 TCTAGAACCTTTCACAAATAATGCAG 57.956 34.615 0.00 0.00 0.00 4.41
449 460 7.994425 TCTAGAACCTTTCACAAATAATGCA 57.006 32.000 0.00 0.00 0.00 3.96
450 461 8.462016 ACATCTAGAACCTTTCACAAATAATGC 58.538 33.333 0.00 0.00 0.00 3.56
451 462 9.778993 CACATCTAGAACCTTTCACAAATAATG 57.221 33.333 0.00 0.00 0.00 1.90
452 463 9.739276 TCACATCTAGAACCTTTCACAAATAAT 57.261 29.630 0.00 0.00 0.00 1.28
453 464 9.567776 TTCACATCTAGAACCTTTCACAAATAA 57.432 29.630 0.00 0.00 0.00 1.40
454 465 9.739276 ATTCACATCTAGAACCTTTCACAAATA 57.261 29.630 0.00 0.00 0.00 1.40
455 466 8.641498 ATTCACATCTAGAACCTTTCACAAAT 57.359 30.769 0.00 0.00 0.00 2.32
456 467 7.719193 TGATTCACATCTAGAACCTTTCACAAA 59.281 33.333 0.00 0.00 0.00 2.83
457 468 7.223584 TGATTCACATCTAGAACCTTTCACAA 58.776 34.615 0.00 0.00 0.00 3.33
458 469 6.768483 TGATTCACATCTAGAACCTTTCACA 58.232 36.000 0.00 0.00 0.00 3.58
459 470 7.099764 TCTGATTCACATCTAGAACCTTTCAC 58.900 38.462 0.00 0.00 0.00 3.18
460 471 7.179160 TCTCTGATTCACATCTAGAACCTTTCA 59.821 37.037 0.00 0.00 0.00 2.69
461 472 7.551585 TCTCTGATTCACATCTAGAACCTTTC 58.448 38.462 0.00 0.00 0.00 2.62
462 473 7.487822 TCTCTGATTCACATCTAGAACCTTT 57.512 36.000 0.00 0.00 0.00 3.11
463 474 7.487822 TTCTCTGATTCACATCTAGAACCTT 57.512 36.000 0.00 0.00 32.01 3.50
464 475 7.180051 AGTTTCTCTGATTCACATCTAGAACCT 59.820 37.037 0.00 0.00 34.49 3.50
465 476 7.277539 CAGTTTCTCTGATTCACATCTAGAACC 59.722 40.741 0.00 0.00 46.27 3.62
466 477 7.816995 ACAGTTTCTCTGATTCACATCTAGAAC 59.183 37.037 0.00 0.00 46.27 3.01
467 478 7.901029 ACAGTTTCTCTGATTCACATCTAGAA 58.099 34.615 0.00 0.00 46.27 2.10
468 479 7.473735 ACAGTTTCTCTGATTCACATCTAGA 57.526 36.000 0.00 0.00 46.27 2.43
469 480 8.441608 CAAACAGTTTCTCTGATTCACATCTAG 58.558 37.037 0.00 0.00 46.27 2.43
470 481 7.933577 ACAAACAGTTTCTCTGATTCACATCTA 59.066 33.333 0.00 0.00 46.27 1.98
471 482 6.769822 ACAAACAGTTTCTCTGATTCACATCT 59.230 34.615 0.00 0.00 46.27 2.90
472 483 6.854892 CACAAACAGTTTCTCTGATTCACATC 59.145 38.462 0.00 0.00 46.27 3.06
473 484 6.543465 TCACAAACAGTTTCTCTGATTCACAT 59.457 34.615 0.00 0.00 46.27 3.21
474 485 5.879777 TCACAAACAGTTTCTCTGATTCACA 59.120 36.000 0.00 0.00 46.27 3.58
475 486 6.363577 TCACAAACAGTTTCTCTGATTCAC 57.636 37.500 0.00 0.00 46.27 3.18
476 487 6.183360 GGTTCACAAACAGTTTCTCTGATTCA 60.183 38.462 0.00 0.00 46.27 2.57
477 488 6.038714 AGGTTCACAAACAGTTTCTCTGATTC 59.961 38.462 0.00 0.00 46.27 2.52
478 489 5.888161 AGGTTCACAAACAGTTTCTCTGATT 59.112 36.000 0.00 0.00 46.27 2.57
479 490 5.440610 AGGTTCACAAACAGTTTCTCTGAT 58.559 37.500 0.00 0.00 46.27 2.90
480 491 4.843728 AGGTTCACAAACAGTTTCTCTGA 58.156 39.130 0.00 0.00 46.27 3.27
482 493 4.843728 TGAGGTTCACAAACAGTTTCTCT 58.156 39.130 0.00 0.00 37.10 3.10
483 494 5.560966 TTGAGGTTCACAAACAGTTTCTC 57.439 39.130 0.00 0.00 37.10 2.87
484 495 5.975693 TTTGAGGTTCACAAACAGTTTCT 57.024 34.783 0.00 0.00 37.10 2.52
548 559 0.179054 GCCGTAGTGAATTCTCCCCC 60.179 60.000 7.05 0.00 0.00 5.40
550 561 0.831307 AGGCCGTAGTGAATTCTCCC 59.169 55.000 7.05 0.00 0.00 4.30
688 710 2.172483 AAATCCGTCGGAGCAGTGCT 62.172 55.000 19.86 19.86 43.88 4.40
730 754 5.535783 CAGCACAAAATACCCATGGATATGA 59.464 40.000 15.22 0.00 36.36 2.15
741 775 1.153842 GCCGCCAGCACAAAATACC 60.154 57.895 0.00 0.00 42.97 2.73
805 839 0.678048 GATCCTGTGAAGGTGGTGCC 60.678 60.000 0.00 0.00 37.58 5.01
872 906 3.884774 GGAGTGGTGTGGTGGCCA 61.885 66.667 0.00 0.00 0.00 5.36
896 935 2.040278 AGGGGAGGTGAGCTGAGG 59.960 66.667 0.00 0.00 0.00 3.86
897 936 2.063378 GGAGGGGAGGTGAGCTGAG 61.063 68.421 0.00 0.00 0.00 3.35
898 937 2.039624 GGAGGGGAGGTGAGCTGA 59.960 66.667 0.00 0.00 0.00 4.26
899 938 3.086600 GGGAGGGGAGGTGAGCTG 61.087 72.222 0.00 0.00 0.00 4.24
900 939 3.288381 AGGGAGGGGAGGTGAGCT 61.288 66.667 0.00 0.00 0.00 4.09
901 940 2.766229 GAGGGAGGGGAGGTGAGC 60.766 72.222 0.00 0.00 0.00 4.26
902 941 2.443016 CGAGGGAGGGGAGGTGAG 60.443 72.222 0.00 0.00 0.00 3.51
903 942 4.779733 GCGAGGGAGGGGAGGTGA 62.780 72.222 0.00 0.00 0.00 4.02
922 961 1.052124 TATTGTAGAGTGGGGGCGGG 61.052 60.000 0.00 0.00 0.00 6.13
923 962 0.834612 TTATTGTAGAGTGGGGGCGG 59.165 55.000 0.00 0.00 0.00 6.13
924 963 1.485066 ACTTATTGTAGAGTGGGGGCG 59.515 52.381 0.00 0.00 0.00 6.13
1548 1620 0.831288 CGCAGATGAGGAGGGAGGAT 60.831 60.000 0.00 0.00 0.00 3.24
1659 1731 3.117372 CCGTAGGCGACCTGGTAG 58.883 66.667 0.00 0.00 46.14 3.18
1908 1980 0.394899 GAATTCCCAGGTGCCTCAGG 60.395 60.000 0.00 0.00 0.00 3.86
2100 2172 1.270094 CCAGTGTCTAGAAACCGCACA 60.270 52.381 9.58 0.00 32.99 4.57
2118 2190 3.602103 GCGATGCCACCATTTCCA 58.398 55.556 0.00 0.00 0.00 3.53
2323 2395 0.831966 ATCAAGAGCTCAGGCAGGAG 59.168 55.000 17.77 2.20 41.70 3.69
2531 2611 8.750515 TTTGCCAATCATAGATACATTTGAGA 57.249 30.769 0.00 0.00 0.00 3.27
2532 2612 8.843262 TCTTTGCCAATCATAGATACATTTGAG 58.157 33.333 0.00 0.00 29.59 3.02
2533 2613 8.750515 TCTTTGCCAATCATAGATACATTTGA 57.249 30.769 0.00 0.00 29.59 2.69
2534 2614 8.080417 CCTCTTTGCCAATCATAGATACATTTG 58.920 37.037 0.00 0.00 33.36 2.32
2537 2617 7.083062 TCCTCTTTGCCAATCATAGATACAT 57.917 36.000 0.00 0.00 33.36 2.29
2538 2618 6.499106 TCCTCTTTGCCAATCATAGATACA 57.501 37.500 0.00 0.00 33.36 2.29
2687 2785 2.727123 TCTGTGTTTGTCCACCATGT 57.273 45.000 0.00 0.00 34.35 3.21
2688 2786 3.148412 TGATCTGTGTTTGTCCACCATG 58.852 45.455 0.00 0.00 34.35 3.66
2689 2787 3.507162 TGATCTGTGTTTGTCCACCAT 57.493 42.857 0.00 0.00 34.35 3.55
2740 2838 9.334693 GGCTAAAATTTTCTATGATTATGCGAG 57.665 33.333 6.72 0.00 0.00 5.03
2899 2997 5.499139 TGAACTGTGTTCTCAAATCAACC 57.501 39.130 11.06 0.00 0.00 3.77
2900 2998 6.470235 CAGTTGAACTGTGTTCTCAAATCAAC 59.530 38.462 16.84 16.00 41.19 3.18
2920 3018 4.460382 TCGGGGTAGTCTACTTAACAGTTG 59.540 45.833 9.85 0.00 34.06 3.16
2927 3025 6.211184 TCATTTTGTTCGGGGTAGTCTACTTA 59.789 38.462 9.85 0.00 0.00 2.24
3023 3121 3.118445 TGGACACATGAGTTGTTCAGACA 60.118 43.478 0.00 0.00 39.68 3.41
3041 3147 2.939103 GGTGACTGCATATGAACTGGAC 59.061 50.000 6.97 0.00 0.00 4.02
3084 3190 3.751479 ATGGCAAAAGTGAAAAGGTCC 57.249 42.857 0.00 0.00 0.00 4.46
3135 3244 2.432874 TCCAGAACGTGAAGGAGAAACA 59.567 45.455 0.00 0.00 0.00 2.83
3159 3268 5.012768 TGAGGAACTAGGGTTTTCTTACAGG 59.987 44.000 0.00 0.00 41.55 4.00
3183 3292 1.200519 TAGTAAGGCGGCAATCAGGT 58.799 50.000 13.08 0.00 0.00 4.00
3364 3473 7.385894 AGTTATCCTGGCTCATCTCTTAAAT 57.614 36.000 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.