Multiple sequence alignment - TraesCS4B01G292300

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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 TraesCS4B01G292300 chr4B 100.000 2936 0 0 1 2936 577699631 577696696 0.000000e+00 5422.0
1 TraesCS4B01G292300 chr4D 94.374 1973 63 19 997 2932 461813592 461811631 0.000000e+00 2985.0
2 TraesCS4B01G292300 chr4D 79.844 1027 86 67 7 965 461814569 461813596 3.190000e-179 638.0
3 TraesCS4B01G292300 chr4D 87.081 209 23 3 1266 1474 140889511 140889307 1.760000e-57 233.0
4 TraesCS4B01G292300 chr4A 89.644 1236 48 33 989 2151 6922226 6923454 0.000000e+00 1500.0
5 TraesCS4B01G292300 chr4A 81.906 619 53 25 2343 2932 6923606 6924194 4.430000e-128 468.0
6 TraesCS4B01G292300 chr4A 88.489 278 18 7 700 968 6921856 6922128 1.010000e-84 324.0
7 TraesCS4B01G292300 chr5D 84.195 329 38 8 1194 1513 313139365 313139688 1.020000e-79 307.0
8 TraesCS4B01G292300 chr7D 80.180 333 40 11 1184 1515 49820517 49820824 2.940000e-55 226.0
9 TraesCS4B01G292300 chr5A 85.841 113 13 3 1187 1299 18922940 18922831 1.850000e-22 117.0
10 TraesCS4B01G292300 chr5A 98.000 50 1 0 1701 1750 438847487 438847438 1.450000e-13 87.9
11 TraesCS4B01G292300 chr5A 94.737 38 2 0 1324 1361 18922824 18922787 3.160000e-05 60.2
12 TraesCS4B01G292300 chr2B 88.710 62 4 3 1218 1279 788064463 788064405 4.060000e-09 73.1
13 TraesCS4B01G292300 chr2B 82.500 80 5 5 1218 1291 788070562 788070486 8.790000e-06 62.1


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 TraesCS4B01G292300 chr4B 577696696 577699631 2935 True 5422.0 5422 100.000000 1 2936 1 chr4B.!!$R1 2935
1 TraesCS4B01G292300 chr4D 461811631 461814569 2938 True 1811.5 2985 87.109000 7 2932 2 chr4D.!!$R2 2925
2 TraesCS4B01G292300 chr4A 6921856 6924194 2338 False 764.0 1500 86.679667 700 2932 3 chr4A.!!$F1 2232

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
392 426 0.108396 ACAAATTTTGCACCAGCCCC 59.892 50.0 9.04 0.0 41.13 5.8 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2070 2291 0.535553 TACACTCCACGCCCCAAAAC 60.536 55.0 0.0 0.0 0.0 2.43 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
63 64 0.462047 CGCCACGCCCTCTTTATTCT 60.462 55.000 0.00 0.00 0.00 2.40
67 68 3.195661 CCACGCCCTCTTTATTCTGTAC 58.804 50.000 0.00 0.00 0.00 2.90
69 70 2.159142 ACGCCCTCTTTATTCTGTACGG 60.159 50.000 0.00 0.00 0.00 4.02
70 71 2.159142 CGCCCTCTTTATTCTGTACGGT 60.159 50.000 0.64 0.00 0.00 4.83
78 90 2.779951 ATTCTGTACGGTGCAGCGCA 62.780 55.000 35.78 25.05 35.60 6.09
88 100 2.097160 GCAGCGCACTGTTGATCG 59.903 61.111 11.47 0.00 46.30 3.69
97 109 5.034797 GCGCACTGTTGATCGCTATATATA 58.965 41.667 0.30 0.00 43.70 0.86
136 151 1.553308 GCGGTTCCACGTACAGATAC 58.447 55.000 0.00 0.00 35.98 2.24
189 204 2.439883 GGGAGAGACGCCGTACCT 60.440 66.667 0.00 0.00 0.00 3.08
192 207 2.675423 AGAGACGCCGTACCTGCA 60.675 61.111 0.00 0.00 0.00 4.41
223 238 4.699522 ACGGGGCCTGCGTTTCTC 62.700 66.667 13.63 0.00 0.00 2.87
246 268 7.023171 TCTATTTGCTTGGTTAAGGAAGGTA 57.977 36.000 0.00 0.00 43.68 3.08
247 269 7.110155 TCTATTTGCTTGGTTAAGGAAGGTAG 58.890 38.462 0.00 0.00 43.68 3.18
252 274 5.163131 TGCTTGGTTAAGGAAGGTAGTTTCT 60.163 40.000 0.00 0.00 34.40 2.52
278 304 2.659897 GAGCACGCATCGCTAGGG 60.660 66.667 0.00 0.00 40.63 3.53
291 317 0.880718 GCTAGGGCGTTAGATGTGGC 60.881 60.000 0.00 0.00 0.00 5.01
292 318 0.597637 CTAGGGCGTTAGATGTGGCG 60.598 60.000 0.00 0.00 0.00 5.69
295 321 4.575245 GCGTTAGATGTGGCGCGC 62.575 66.667 25.94 25.94 40.46 6.86
296 322 2.885644 CGTTAGATGTGGCGCGCT 60.886 61.111 32.29 11.46 0.00 5.92
297 323 2.860628 CGTTAGATGTGGCGCGCTC 61.861 63.158 32.29 23.45 0.00 5.03
298 324 1.809619 GTTAGATGTGGCGCGCTCA 60.810 57.895 32.29 28.02 0.00 4.26
299 325 1.519234 TTAGATGTGGCGCGCTCAG 60.519 57.895 32.29 0.00 0.00 3.35
300 326 2.225791 TTAGATGTGGCGCGCTCAGT 62.226 55.000 32.29 21.04 0.00 3.41
301 327 2.225791 TAGATGTGGCGCGCTCAGTT 62.226 55.000 32.29 21.24 0.00 3.16
302 328 3.088500 GATGTGGCGCGCTCAGTTC 62.089 63.158 32.29 19.70 0.00 3.01
333 367 0.454285 ATGACGTTTCGCGCCATTTG 60.454 50.000 0.00 0.00 40.73 2.32
340 374 1.482278 TTCGCGCCATTTGTTTGTTC 58.518 45.000 0.00 0.00 0.00 3.18
353 387 0.941542 TTTGTTCGTTCAGAAGCCCG 59.058 50.000 0.00 0.00 39.95 6.13
391 425 1.228533 CACAAATTTTGCACCAGCCC 58.771 50.000 9.04 0.00 41.13 5.19
392 426 0.108396 ACAAATTTTGCACCAGCCCC 59.892 50.000 9.04 0.00 41.13 5.80
394 428 2.110757 AAATTTTGCACCAGCCCCGG 62.111 55.000 0.00 0.00 41.13 5.73
409 443 0.455815 CCCGGGCAGATTAAGCAAAC 59.544 55.000 8.08 0.00 0.00 2.93
410 444 0.455815 CCGGGCAGATTAAGCAAACC 59.544 55.000 0.00 0.00 0.00 3.27
411 445 1.463674 CGGGCAGATTAAGCAAACCT 58.536 50.000 0.00 0.00 0.00 3.50
412 446 1.818674 CGGGCAGATTAAGCAAACCTT 59.181 47.619 0.00 0.00 37.57 3.50
413 447 2.231235 CGGGCAGATTAAGCAAACCTTT 59.769 45.455 0.00 0.00 34.95 3.11
414 448 3.306019 CGGGCAGATTAAGCAAACCTTTT 60.306 43.478 0.00 0.00 34.95 2.27
415 449 4.245660 GGGCAGATTAAGCAAACCTTTTC 58.754 43.478 0.00 0.00 34.95 2.29
416 450 4.262420 GGGCAGATTAAGCAAACCTTTTCA 60.262 41.667 0.00 0.00 34.95 2.69
417 451 4.686091 GGCAGATTAAGCAAACCTTTTCAC 59.314 41.667 0.00 0.00 34.95 3.18
418 452 4.382754 GCAGATTAAGCAAACCTTTTCACG 59.617 41.667 0.00 0.00 34.95 4.35
421 455 6.797033 CAGATTAAGCAAACCTTTTCACGTAG 59.203 38.462 0.00 0.00 34.95 3.51
425 459 2.030274 GCAAACCTTTTCACGTAGGCAT 60.030 45.455 1.87 0.00 34.79 4.40
427 461 1.165270 ACCTTTTCACGTAGGCATGC 58.835 50.000 9.90 9.90 34.79 4.06
428 462 1.164411 CCTTTTCACGTAGGCATGCA 58.836 50.000 21.36 0.00 0.00 3.96
429 463 1.745087 CCTTTTCACGTAGGCATGCAT 59.255 47.619 21.36 16.31 0.00 3.96
430 464 2.478370 CCTTTTCACGTAGGCATGCATG 60.478 50.000 22.70 22.70 0.00 4.06
431 465 2.106477 TTTCACGTAGGCATGCATGA 57.894 45.000 30.64 6.68 0.00 3.07
432 466 2.330440 TTCACGTAGGCATGCATGAT 57.670 45.000 30.64 19.08 0.00 2.45
434 468 1.134431 TCACGTAGGCATGCATGATGT 60.134 47.619 30.64 17.26 34.14 3.06
435 469 1.003223 CACGTAGGCATGCATGATGTG 60.003 52.381 30.64 23.82 34.14 3.21
436 470 1.302366 CGTAGGCATGCATGATGTGT 58.698 50.000 30.64 10.87 34.14 3.72
437 471 1.003223 CGTAGGCATGCATGATGTGTG 60.003 52.381 30.64 10.50 34.14 3.82
438 472 2.019249 GTAGGCATGCATGATGTGTGT 58.981 47.619 30.64 7.81 34.14 3.72
440 474 0.528924 GGCATGCATGATGTGTGTGT 59.471 50.000 30.64 0.00 34.14 3.72
442 476 1.068125 GCATGCATGATGTGTGTGTGT 60.068 47.619 30.64 0.00 34.14 3.72
443 477 2.591133 CATGCATGATGTGTGTGTGTG 58.409 47.619 22.59 0.00 0.00 3.82
445 479 1.334243 TGCATGATGTGTGTGTGTGTG 59.666 47.619 0.00 0.00 0.00 3.82
446 480 1.334556 GCATGATGTGTGTGTGTGTGT 59.665 47.619 0.00 0.00 0.00 3.72
447 481 2.855570 GCATGATGTGTGTGTGTGTGTG 60.856 50.000 0.00 0.00 0.00 3.82
448 482 0.731994 TGATGTGTGTGTGTGTGTGC 59.268 50.000 0.00 0.00 0.00 4.57
449 483 0.731994 GATGTGTGTGTGTGTGTGCA 59.268 50.000 0.00 0.00 0.00 4.57
450 484 0.734309 ATGTGTGTGTGTGTGTGCAG 59.266 50.000 0.00 0.00 0.00 4.41
451 485 1.304509 TGTGTGTGTGTGTGTGCAGG 61.305 55.000 0.00 0.00 0.00 4.85
452 486 2.405805 TGTGTGTGTGTGTGCAGGC 61.406 57.895 0.00 0.00 0.00 4.85
454 488 1.676967 TGTGTGTGTGTGCAGGCAA 60.677 52.632 0.00 0.00 0.00 4.52
455 489 1.036481 TGTGTGTGTGTGCAGGCAAT 61.036 50.000 0.00 0.00 0.00 3.56
456 490 0.595567 GTGTGTGTGTGCAGGCAATG 60.596 55.000 0.00 0.00 0.00 2.82
457 491 1.036481 TGTGTGTGTGCAGGCAATGT 61.036 50.000 0.00 0.00 0.00 2.71
459 493 0.950836 TGTGTGTGCAGGCAATGTAC 59.049 50.000 0.00 2.98 44.13 2.90
464 498 1.522668 GTGCAGGCAATGTACAGTCA 58.477 50.000 0.33 0.00 43.41 3.41
465 499 2.086869 GTGCAGGCAATGTACAGTCAT 58.913 47.619 0.33 0.00 43.41 3.06
466 500 2.489329 GTGCAGGCAATGTACAGTCATT 59.511 45.455 0.33 0.00 43.41 2.57
467 501 3.689161 GTGCAGGCAATGTACAGTCATTA 59.311 43.478 0.33 0.00 43.41 1.90
468 502 3.940852 TGCAGGCAATGTACAGTCATTAG 59.059 43.478 0.33 0.00 36.44 1.73
469 503 3.941483 GCAGGCAATGTACAGTCATTAGT 59.059 43.478 0.33 0.00 36.44 2.24
470 504 5.116180 GCAGGCAATGTACAGTCATTAGTA 58.884 41.667 0.33 0.00 36.44 1.82
471 505 5.235186 GCAGGCAATGTACAGTCATTAGTAG 59.765 44.000 0.33 0.00 36.44 2.57
472 506 6.341316 CAGGCAATGTACAGTCATTAGTAGT 58.659 40.000 0.33 0.00 36.44 2.73
473 507 6.256539 CAGGCAATGTACAGTCATTAGTAGTG 59.743 42.308 0.33 0.00 36.44 2.74
474 508 5.523916 GGCAATGTACAGTCATTAGTAGTGG 59.476 44.000 0.33 0.00 36.44 4.00
475 509 5.006746 GCAATGTACAGTCATTAGTAGTGGC 59.993 44.000 0.33 0.00 36.44 5.01
476 510 4.365899 TGTACAGTCATTAGTAGTGGCG 57.634 45.455 0.00 0.00 0.00 5.69
477 511 4.011698 TGTACAGTCATTAGTAGTGGCGA 58.988 43.478 0.00 0.00 0.00 5.54
478 512 4.460034 TGTACAGTCATTAGTAGTGGCGAA 59.540 41.667 0.00 0.00 0.00 4.70
479 513 4.530710 ACAGTCATTAGTAGTGGCGAAA 57.469 40.909 0.00 0.00 0.00 3.46
480 514 5.086104 ACAGTCATTAGTAGTGGCGAAAT 57.914 39.130 0.00 0.00 0.00 2.17
481 515 5.488341 ACAGTCATTAGTAGTGGCGAAATT 58.512 37.500 0.00 0.00 0.00 1.82
482 516 6.636705 ACAGTCATTAGTAGTGGCGAAATTA 58.363 36.000 0.00 0.00 0.00 1.40
483 517 6.757010 ACAGTCATTAGTAGTGGCGAAATTAG 59.243 38.462 0.00 0.00 0.00 1.73
484 518 6.757010 CAGTCATTAGTAGTGGCGAAATTAGT 59.243 38.462 0.00 0.00 0.00 2.24
485 519 7.919091 CAGTCATTAGTAGTGGCGAAATTAGTA 59.081 37.037 0.00 0.00 0.00 1.82
486 520 7.919621 AGTCATTAGTAGTGGCGAAATTAGTAC 59.080 37.037 0.00 0.00 0.00 2.73
510 544 2.989253 GGACGTGCCAAAAGGGGG 60.989 66.667 0.00 0.00 37.04 5.40
517 551 2.290287 GCCAAAAGGGGGCGGATTT 61.290 57.895 0.00 0.00 42.39 2.17
523 557 2.543037 AAGGGGGCGGATTTACATTT 57.457 45.000 0.00 0.00 0.00 2.32
527 561 3.717913 AGGGGGCGGATTTACATTTACTA 59.282 43.478 0.00 0.00 0.00 1.82
528 562 3.817084 GGGGGCGGATTTACATTTACTAC 59.183 47.826 0.00 0.00 0.00 2.73
529 563 4.445305 GGGGGCGGATTTACATTTACTACT 60.445 45.833 0.00 0.00 0.00 2.57
530 564 4.514066 GGGGCGGATTTACATTTACTACTG 59.486 45.833 0.00 0.00 0.00 2.74
531 565 4.514066 GGGCGGATTTACATTTACTACTGG 59.486 45.833 0.00 0.00 0.00 4.00
532 566 5.362263 GGCGGATTTACATTTACTACTGGA 58.638 41.667 0.00 0.00 0.00 3.86
533 567 5.465724 GGCGGATTTACATTTACTACTGGAG 59.534 44.000 0.00 0.00 0.00 3.86
534 568 6.047231 GCGGATTTACATTTACTACTGGAGT 58.953 40.000 0.00 0.00 42.69 3.85
535 569 6.018994 GCGGATTTACATTTACTACTGGAGTG 60.019 42.308 1.88 0.00 39.39 3.51
536 570 6.479001 CGGATTTACATTTACTACTGGAGTGG 59.521 42.308 1.88 0.00 39.39 4.00
551 598 2.550208 GGAGTGGTGTCTGGTAACCTTG 60.550 54.545 0.00 0.00 37.36 3.61
555 602 2.506231 TGGTGTCTGGTAACCTTGTTGA 59.494 45.455 0.00 0.00 37.36 3.18
563 610 7.069331 TGTCTGGTAACCTTGTTGAATGAAAAT 59.931 33.333 0.00 0.00 0.00 1.82
564 611 7.926018 GTCTGGTAACCTTGTTGAATGAAAATT 59.074 33.333 0.00 0.00 0.00 1.82
565 612 8.482128 TCTGGTAACCTTGTTGAATGAAAATTT 58.518 29.630 0.00 0.00 0.00 1.82
566 613 8.430801 TGGTAACCTTGTTGAATGAAAATTTG 57.569 30.769 0.00 0.00 0.00 2.32
567 614 8.043710 TGGTAACCTTGTTGAATGAAAATTTGT 58.956 29.630 0.00 0.00 0.00 2.83
568 615 8.334632 GGTAACCTTGTTGAATGAAAATTTGTG 58.665 33.333 0.00 0.00 0.00 3.33
569 616 7.920160 AACCTTGTTGAATGAAAATTTGTGT 57.080 28.000 0.00 0.00 0.00 3.72
570 617 7.920160 ACCTTGTTGAATGAAAATTTGTGTT 57.080 28.000 0.00 0.00 0.00 3.32
597 644 1.301401 GCGTGGTTGGCTACAGTGA 60.301 57.895 0.00 0.00 0.00 3.41
599 646 1.808411 CGTGGTTGGCTACAGTGATT 58.192 50.000 0.00 0.00 0.00 2.57
645 692 2.371841 GGGTGGTGACATGGATAGCATA 59.628 50.000 0.00 0.00 46.14 3.14
672 719 1.711375 AGACAGGTAGACAGAGGGTGA 59.289 52.381 0.00 0.00 0.00 4.02
680 727 1.662438 GACAGAGGGTGAGCGAGGAG 61.662 65.000 0.00 0.00 0.00 3.69
721 768 1.153127 ACGCCCAAAACCGACTGAA 60.153 52.632 0.00 0.00 0.00 3.02
722 769 1.164041 ACGCCCAAAACCGACTGAAG 61.164 55.000 0.00 0.00 0.00 3.02
723 770 1.285950 GCCCAAAACCGACTGAAGC 59.714 57.895 0.00 0.00 0.00 3.86
724 771 1.574428 CCCAAAACCGACTGAAGCG 59.426 57.895 0.00 0.00 0.00 4.68
725 772 0.882927 CCCAAAACCGACTGAAGCGA 60.883 55.000 0.00 0.00 0.00 4.93
766 814 4.003788 CTCCCCGTTGCCACGTCT 62.004 66.667 9.67 0.00 45.62 4.18
845 915 4.411013 CTTCTTTCCTCCAACCTTTCCAT 58.589 43.478 0.00 0.00 0.00 3.41
856 926 4.325344 CCAACCTTTCCATACCATCTCCTT 60.325 45.833 0.00 0.00 0.00 3.36
944 1020 4.314440 TGCCTCGCGCCACTTTCT 62.314 61.111 0.00 0.00 36.24 2.52
947 1023 3.043713 CTCGCGCCACTTTCTGCA 61.044 61.111 0.00 0.00 0.00 4.41
970 1107 3.840437 ACAGCGCATTGTTGGTGT 58.160 50.000 11.47 0.00 41.59 4.16
971 1108 0.248990 AACAGCGCATTGTTGGTGTG 60.249 50.000 13.58 0.00 45.24 3.82
974 1111 1.067250 GCGCATTGTTGGTGTGGTT 59.933 52.632 0.30 0.00 0.00 3.67
995 1148 2.327940 GTGTCCGTGTGTTGCTGC 59.672 61.111 0.00 0.00 0.00 5.25
1162 1336 0.109689 CAAGAAGAAGCAGCAGCAGC 60.110 55.000 3.17 0.46 45.49 5.25
1163 1337 0.536687 AAGAAGAAGCAGCAGCAGCA 60.537 50.000 12.92 0.00 45.49 4.41
1587 1770 2.738139 TCGTCGTACTCGCGGTCA 60.738 61.111 6.13 0.00 37.27 4.02
1809 1995 3.181967 CTGGAGAACTTCGCCGCG 61.182 66.667 6.39 6.39 39.36 6.46
1955 2141 3.570638 TCGCTCGGACGATCGGAC 61.571 66.667 20.98 12.70 37.09 4.79
2070 2291 6.072783 GGTGTTCTCTCTGAGATTTTCTTTGG 60.073 42.308 8.00 0.00 38.56 3.28
2079 2300 4.065088 GAGATTTTCTTTGGTTTTGGGGC 58.935 43.478 0.00 0.00 0.00 5.80
2097 2318 1.469940 GGCGTGGAGTGTACTCAGATG 60.470 57.143 13.51 6.32 44.60 2.90
2151 2379 6.554334 TCAGTAAAATGTTGTTCCTAGTGC 57.446 37.500 0.00 0.00 0.00 4.40
2183 2411 3.895232 TGCCCTCTGCTTTTCTACTAG 57.105 47.619 0.00 0.00 42.00 2.57
2209 2438 6.760291 ACTAAGAAAGTCTTGAATTCCTCGT 58.240 36.000 2.27 0.00 37.29 4.18
2264 2493 4.098654 TGGAAGCAAATTTCTTGGACGAAA 59.901 37.500 7.37 0.00 37.31 3.46
2273 2502 2.147958 TCTTGGACGAAACAAATCGGG 58.852 47.619 1.59 0.00 46.82 5.14
2275 2504 0.108963 TGGACGAAACAAATCGGGGT 59.891 50.000 1.59 0.00 46.82 4.95
2277 2506 1.733912 GGACGAAACAAATCGGGGTAC 59.266 52.381 1.59 0.00 46.82 3.34
2278 2507 2.613725 GGACGAAACAAATCGGGGTACT 60.614 50.000 1.59 0.00 46.82 2.73
2281 2510 3.996363 ACGAAACAAATCGGGGTACTTAC 59.004 43.478 1.59 0.00 46.82 2.34
2388 2618 3.561310 CCACCGTGCGTATTCTACTACTA 59.439 47.826 0.00 0.00 0.00 1.82
2423 2653 2.811101 CTAGGAGGCCAGCGTGAG 59.189 66.667 5.01 0.00 0.00 3.51
2467 2698 4.458295 TGTAAAGACGAGGGAGTACAAGAG 59.542 45.833 0.00 0.00 0.00 2.85
2489 2723 3.053320 GGAATGAGGAGGGGATTGAAAGT 60.053 47.826 0.00 0.00 0.00 2.66
2490 2724 4.570719 GGAATGAGGAGGGGATTGAAAGTT 60.571 45.833 0.00 0.00 0.00 2.66
2491 2725 3.439857 TGAGGAGGGGATTGAAAGTTG 57.560 47.619 0.00 0.00 0.00 3.16
2708 2955 2.740055 CGTCAGCTCCAGCACACC 60.740 66.667 0.48 0.00 45.16 4.16
2711 2958 2.142761 TCAGCTCCAGCACACCAGT 61.143 57.895 0.48 0.00 45.16 4.00
2713 2960 2.670934 GCTCCAGCACACCAGTGG 60.671 66.667 7.91 7.91 45.98 4.00
2714 2961 2.670934 CTCCAGCACACCAGTGGC 60.671 66.667 9.78 3.23 45.98 5.01
2715 2962 4.624364 TCCAGCACACCAGTGGCG 62.624 66.667 9.78 1.17 45.98 5.69
2716 2963 4.624364 CCAGCACACCAGTGGCGA 62.624 66.667 9.78 0.00 45.98 5.54
2717 2964 3.046087 CAGCACACCAGTGGCGAG 61.046 66.667 9.78 0.00 45.98 5.03
2718 2965 3.550431 AGCACACCAGTGGCGAGT 61.550 61.111 9.78 2.51 45.98 4.18
2759 3019 4.906060 TGATCCCAGATGATGAGTCAGATT 59.094 41.667 0.00 0.00 37.87 2.40
2768 3028 3.956848 TGATGAGTCAGATTGATCGGTCT 59.043 43.478 0.00 0.00 0.00 3.85
2839 3109 2.211468 GAATCCGGGAAACAGGGCCT 62.211 60.000 0.00 0.00 46.86 5.19
2907 3183 2.019249 CATCGTCCATGGATTGTTGCT 58.981 47.619 19.62 0.00 0.00 3.91
2932 3208 3.632145 AGCAAGAAACTTAGGTGTGTTGG 59.368 43.478 7.10 0.00 35.32 3.77
2933 3209 3.630312 GCAAGAAACTTAGGTGTGTTGGA 59.370 43.478 7.10 0.00 35.32 3.53
2934 3210 4.261197 GCAAGAAACTTAGGTGTGTTGGAG 60.261 45.833 7.10 0.00 35.32 3.86
2935 3211 4.772886 AGAAACTTAGGTGTGTTGGAGT 57.227 40.909 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.728490 CCTTGATTAAGCCGCTGCCC 61.728 60.000 0.00 0.00 38.69 5.36
1 2 0.748005 TCCTTGATTAAGCCGCTGCC 60.748 55.000 0.00 0.00 38.69 4.85
2 3 0.378610 GTCCTTGATTAAGCCGCTGC 59.621 55.000 0.00 0.00 37.95 5.25
3 4 0.652592 CGTCCTTGATTAAGCCGCTG 59.347 55.000 0.00 0.00 32.40 5.18
4 5 0.462047 CCGTCCTTGATTAAGCCGCT 60.462 55.000 0.00 0.00 32.40 5.52
5 6 1.436983 CCCGTCCTTGATTAAGCCGC 61.437 60.000 0.00 0.00 32.40 6.53
9 10 4.051922 CGAGATTCCCGTCCTTGATTAAG 58.948 47.826 0.00 0.00 0.00 1.85
70 71 2.670210 CGATCAACAGTGCGCTGCA 61.670 57.895 26.78 11.67 46.30 4.41
97 109 3.546815 CGCGCTTTGCAGCTTAATAATCT 60.547 43.478 5.56 0.00 46.97 2.40
171 186 2.753043 GGTACGGCGTCTCTCCCA 60.753 66.667 19.21 0.00 0.00 4.37
173 188 2.799371 CAGGTACGGCGTCTCTCC 59.201 66.667 19.21 15.13 0.00 3.71
215 230 3.831715 ACCAAGCAAATAGAGAAACGC 57.168 42.857 0.00 0.00 0.00 4.84
223 238 6.884836 ACTACCTTCCTTAACCAAGCAAATAG 59.115 38.462 0.00 0.00 0.00 1.73
246 268 1.664965 GCTCCGTGTCGCAGAAACT 60.665 57.895 0.00 0.00 44.00 2.66
247 269 1.954146 TGCTCCGTGTCGCAGAAAC 60.954 57.895 0.00 0.00 42.42 2.78
281 307 1.519234 CTGAGCGCGCCACATCTAA 60.519 57.895 30.33 0.00 0.00 2.10
305 331 4.717927 AAACGTCATGCGCGCGTG 62.718 61.111 40.31 40.31 46.11 5.34
306 332 4.424430 GAAACGTCATGCGCGCGT 62.424 61.111 32.35 25.30 46.11 6.01
317 343 0.248702 AAACAAATGGCGCGAAACGT 60.249 45.000 12.10 0.00 46.11 3.99
333 367 1.333791 CGGGCTTCTGAACGAACAAAC 60.334 52.381 0.00 0.00 0.00 2.93
340 374 2.358737 AAGCCGGGCTTCTGAACG 60.359 61.111 28.12 0.00 46.77 3.95
353 387 1.308783 GCAGTGCTCCTACCAAAGCC 61.309 60.000 8.18 0.00 37.73 4.35
360 394 3.923017 AAATTTGTGCAGTGCTCCTAC 57.077 42.857 17.60 6.51 0.00 3.18
391 425 0.455815 GGTTTGCTTAATCTGCCCGG 59.544 55.000 0.00 0.00 0.00 5.73
392 426 1.463674 AGGTTTGCTTAATCTGCCCG 58.536 50.000 0.00 0.00 0.00 6.13
394 428 4.686091 GTGAAAAGGTTTGCTTAATCTGCC 59.314 41.667 0.00 0.00 0.00 4.85
396 430 5.519722 ACGTGAAAAGGTTTGCTTAATCTG 58.480 37.500 0.00 0.00 0.00 2.90
397 431 5.767816 ACGTGAAAAGGTTTGCTTAATCT 57.232 34.783 0.00 0.00 0.00 2.40
398 432 6.084277 CCTACGTGAAAAGGTTTGCTTAATC 58.916 40.000 0.00 0.00 0.00 1.75
399 433 5.564063 GCCTACGTGAAAAGGTTTGCTTAAT 60.564 40.000 0.00 0.00 35.16 1.40
400 434 4.261280 GCCTACGTGAAAAGGTTTGCTTAA 60.261 41.667 0.00 0.00 35.16 1.85
401 435 3.251487 GCCTACGTGAAAAGGTTTGCTTA 59.749 43.478 0.00 0.00 35.16 3.09
404 438 1.335496 TGCCTACGTGAAAAGGTTTGC 59.665 47.619 0.00 0.00 35.16 3.68
405 439 3.564511 CATGCCTACGTGAAAAGGTTTG 58.435 45.455 0.00 0.00 34.49 2.93
409 443 1.164411 TGCATGCCTACGTGAAAAGG 58.836 50.000 16.68 0.00 34.49 3.11
410 444 2.419673 TCATGCATGCCTACGTGAAAAG 59.580 45.455 22.25 0.00 34.49 2.27
411 445 2.431454 TCATGCATGCCTACGTGAAAA 58.569 42.857 22.25 0.00 34.49 2.29
412 446 2.106477 TCATGCATGCCTACGTGAAA 57.894 45.000 22.25 0.00 34.49 2.69
413 447 1.941975 CATCATGCATGCCTACGTGAA 59.058 47.619 22.25 1.33 35.56 3.18
414 448 1.134431 ACATCATGCATGCCTACGTGA 60.134 47.619 22.25 11.66 35.65 4.35
415 449 1.003223 CACATCATGCATGCCTACGTG 60.003 52.381 22.25 17.61 35.65 4.49
416 450 1.302366 CACATCATGCATGCCTACGT 58.698 50.000 22.25 10.57 35.65 3.57
417 451 1.003223 CACACATCATGCATGCCTACG 60.003 52.381 22.25 10.98 35.65 3.51
418 452 2.019249 ACACACATCATGCATGCCTAC 58.981 47.619 22.25 0.00 35.65 3.18
421 455 0.528924 ACACACACATCATGCATGCC 59.471 50.000 22.25 0.00 35.65 4.40
425 459 1.334243 CACACACACACACATCATGCA 59.666 47.619 0.00 0.00 0.00 3.96
427 461 2.855570 GCACACACACACACACATCATG 60.856 50.000 0.00 0.00 0.00 3.07
428 462 1.334556 GCACACACACACACACATCAT 59.665 47.619 0.00 0.00 0.00 2.45
429 463 0.731994 GCACACACACACACACATCA 59.268 50.000 0.00 0.00 0.00 3.07
430 464 0.731994 TGCACACACACACACACATC 59.268 50.000 0.00 0.00 0.00 3.06
431 465 0.734309 CTGCACACACACACACACAT 59.266 50.000 0.00 0.00 0.00 3.21
432 466 1.304509 CCTGCACACACACACACACA 61.305 55.000 0.00 0.00 0.00 3.72
434 468 2.405805 GCCTGCACACACACACACA 61.406 57.895 0.00 0.00 0.00 3.72
435 469 1.932011 TTGCCTGCACACACACACAC 61.932 55.000 0.00 0.00 0.00 3.82
436 470 1.036481 ATTGCCTGCACACACACACA 61.036 50.000 0.00 0.00 0.00 3.72
437 471 0.595567 CATTGCCTGCACACACACAC 60.596 55.000 0.00 0.00 0.00 3.82
438 472 1.036481 ACATTGCCTGCACACACACA 61.036 50.000 0.00 0.00 0.00 3.72
440 474 0.950836 GTACATTGCCTGCACACACA 59.049 50.000 0.00 0.00 0.00 3.72
442 476 1.237533 CTGTACATTGCCTGCACACA 58.762 50.000 0.00 0.00 28.07 3.72
443 477 1.197721 GACTGTACATTGCCTGCACAC 59.802 52.381 0.00 0.00 28.07 3.82
445 479 1.522668 TGACTGTACATTGCCTGCAC 58.477 50.000 0.00 0.00 0.00 4.57
446 480 2.495155 ATGACTGTACATTGCCTGCA 57.505 45.000 0.00 0.00 0.00 4.41
447 481 3.941483 ACTAATGACTGTACATTGCCTGC 59.059 43.478 0.00 0.00 40.15 4.85
448 482 6.256539 CACTACTAATGACTGTACATTGCCTG 59.743 42.308 0.00 0.00 40.15 4.85
449 483 6.341316 CACTACTAATGACTGTACATTGCCT 58.659 40.000 0.00 0.00 40.15 4.75
450 484 5.523916 CCACTACTAATGACTGTACATTGCC 59.476 44.000 0.00 0.00 40.15 4.52
451 485 5.006746 GCCACTACTAATGACTGTACATTGC 59.993 44.000 0.00 0.00 40.15 3.56
452 486 5.232202 CGCCACTACTAATGACTGTACATTG 59.768 44.000 0.00 0.00 40.15 2.82
454 488 4.643334 TCGCCACTACTAATGACTGTACAT 59.357 41.667 0.00 0.00 0.00 2.29
455 489 4.011698 TCGCCACTACTAATGACTGTACA 58.988 43.478 0.00 0.00 0.00 2.90
456 490 4.627611 TCGCCACTACTAATGACTGTAC 57.372 45.455 0.00 0.00 0.00 2.90
457 491 5.648178 TTTCGCCACTACTAATGACTGTA 57.352 39.130 0.00 0.00 0.00 2.74
459 493 6.757010 ACTAATTTCGCCACTACTAATGACTG 59.243 38.462 0.00 0.00 0.00 3.51
460 494 6.875076 ACTAATTTCGCCACTACTAATGACT 58.125 36.000 0.00 0.00 0.00 3.41
462 496 7.774134 TGTACTAATTTCGCCACTACTAATGA 58.226 34.615 0.00 0.00 0.00 2.57
463 497 7.997107 TGTACTAATTTCGCCACTACTAATG 57.003 36.000 0.00 0.00 0.00 1.90
464 498 7.493645 GGTTGTACTAATTTCGCCACTACTAAT 59.506 37.037 0.00 0.00 0.00 1.73
465 499 6.813152 GGTTGTACTAATTTCGCCACTACTAA 59.187 38.462 0.00 0.00 0.00 2.24
466 500 6.153340 AGGTTGTACTAATTTCGCCACTACTA 59.847 38.462 0.00 0.00 0.00 1.82
467 501 5.046807 AGGTTGTACTAATTTCGCCACTACT 60.047 40.000 0.00 0.00 0.00 2.57
468 502 5.063060 CAGGTTGTACTAATTTCGCCACTAC 59.937 44.000 0.00 0.00 0.00 2.73
469 503 5.172934 CAGGTTGTACTAATTTCGCCACTA 58.827 41.667 0.00 0.00 0.00 2.74
470 504 4.000988 CAGGTTGTACTAATTTCGCCACT 58.999 43.478 0.00 0.00 0.00 4.00
471 505 3.126343 CCAGGTTGTACTAATTTCGCCAC 59.874 47.826 0.00 0.00 0.00 5.01
472 506 3.340034 CCAGGTTGTACTAATTTCGCCA 58.660 45.455 0.00 0.00 0.00 5.69
473 507 2.681344 CCCAGGTTGTACTAATTTCGCC 59.319 50.000 0.00 0.00 0.00 5.54
474 508 3.373130 GTCCCAGGTTGTACTAATTTCGC 59.627 47.826 0.00 0.00 0.00 4.70
475 509 3.615496 CGTCCCAGGTTGTACTAATTTCG 59.385 47.826 0.00 0.00 0.00 3.46
476 510 4.390909 CACGTCCCAGGTTGTACTAATTTC 59.609 45.833 0.00 0.00 0.00 2.17
477 511 4.320870 CACGTCCCAGGTTGTACTAATTT 58.679 43.478 0.00 0.00 0.00 1.82
478 512 3.867216 GCACGTCCCAGGTTGTACTAATT 60.867 47.826 0.00 0.00 0.00 1.40
479 513 2.354403 GCACGTCCCAGGTTGTACTAAT 60.354 50.000 0.00 0.00 0.00 1.73
480 514 1.001181 GCACGTCCCAGGTTGTACTAA 59.999 52.381 0.00 0.00 0.00 2.24
481 515 0.604578 GCACGTCCCAGGTTGTACTA 59.395 55.000 0.00 0.00 0.00 1.82
482 516 1.370064 GCACGTCCCAGGTTGTACT 59.630 57.895 0.00 0.00 0.00 2.73
483 517 1.670083 GGCACGTCCCAGGTTGTAC 60.670 63.158 0.00 0.00 0.00 2.90
484 518 1.697082 TTGGCACGTCCCAGGTTGTA 61.697 55.000 0.00 0.00 36.00 2.41
485 519 2.559922 TTTGGCACGTCCCAGGTTGT 62.560 55.000 0.00 0.00 36.00 3.32
486 520 1.388065 TTTTGGCACGTCCCAGGTTG 61.388 55.000 0.00 0.00 36.00 3.77
510 544 6.018994 CACTCCAGTAGTAAATGTAAATCCGC 60.019 42.308 0.00 0.00 35.76 5.54
517 551 6.014647 AGACACCACTCCAGTAGTAAATGTA 58.985 40.000 0.00 0.00 35.76 2.29
523 557 2.109480 ACCAGACACCACTCCAGTAGTA 59.891 50.000 0.00 0.00 35.76 1.82
527 561 1.692519 GTTACCAGACACCACTCCAGT 59.307 52.381 0.00 0.00 0.00 4.00
528 562 1.002087 GGTTACCAGACACCACTCCAG 59.998 57.143 0.00 0.00 32.74 3.86
529 563 1.053424 GGTTACCAGACACCACTCCA 58.947 55.000 0.00 0.00 32.74 3.86
530 564 1.349067 AGGTTACCAGACACCACTCC 58.651 55.000 3.51 0.00 35.25 3.85
531 565 2.104281 ACAAGGTTACCAGACACCACTC 59.896 50.000 3.51 0.00 35.25 3.51
532 566 2.124411 ACAAGGTTACCAGACACCACT 58.876 47.619 3.51 0.00 35.25 4.00
533 567 2.616842 CAACAAGGTTACCAGACACCAC 59.383 50.000 3.51 0.00 35.25 4.16
534 568 2.506231 TCAACAAGGTTACCAGACACCA 59.494 45.455 3.51 0.00 35.25 4.17
535 569 3.202829 TCAACAAGGTTACCAGACACC 57.797 47.619 3.51 0.00 0.00 4.16
536 570 4.819630 TCATTCAACAAGGTTACCAGACAC 59.180 41.667 3.51 0.00 0.00 3.67
555 602 8.655092 CGCACCATAATAACACAAATTTTCATT 58.345 29.630 0.00 0.00 0.00 2.57
563 610 3.821600 ACCACGCACCATAATAACACAAA 59.178 39.130 0.00 0.00 0.00 2.83
564 611 3.413327 ACCACGCACCATAATAACACAA 58.587 40.909 0.00 0.00 0.00 3.33
565 612 3.060736 ACCACGCACCATAATAACACA 57.939 42.857 0.00 0.00 0.00 3.72
566 613 3.426963 CCAACCACGCACCATAATAACAC 60.427 47.826 0.00 0.00 0.00 3.32
567 614 2.750166 CCAACCACGCACCATAATAACA 59.250 45.455 0.00 0.00 0.00 2.41
568 615 2.478879 GCCAACCACGCACCATAATAAC 60.479 50.000 0.00 0.00 0.00 1.89
569 616 1.746220 GCCAACCACGCACCATAATAA 59.254 47.619 0.00 0.00 0.00 1.40
570 617 1.065053 AGCCAACCACGCACCATAATA 60.065 47.619 0.00 0.00 0.00 0.98
637 684 3.826157 ACCTGTCTCTCAGCTATGCTATC 59.174 47.826 0.00 0.00 42.38 2.08
645 692 2.307392 TCTGTCTACCTGTCTCTCAGCT 59.693 50.000 0.00 0.00 42.38 4.24
715 762 0.037790 ACTCCAGCTTCGCTTCAGTC 60.038 55.000 0.00 0.00 36.40 3.51
721 768 1.893786 CCACTACTCCAGCTTCGCT 59.106 57.895 0.00 0.00 40.77 4.93
722 769 1.811679 GCCACTACTCCAGCTTCGC 60.812 63.158 0.00 0.00 0.00 4.70
723 770 1.153549 GGCCACTACTCCAGCTTCG 60.154 63.158 0.00 0.00 0.00 3.79
724 771 0.176910 GAGGCCACTACTCCAGCTTC 59.823 60.000 5.01 0.00 0.00 3.86
725 772 2.291856 GAGGCCACTACTCCAGCTT 58.708 57.895 5.01 0.00 0.00 3.74
845 915 3.263425 GTGGTGGAAAGAAGGAGATGGTA 59.737 47.826 0.00 0.00 0.00 3.25
856 926 1.072505 GCGAAGGGTGGTGGAAAGA 59.927 57.895 0.00 0.00 0.00 2.52
947 1023 1.806542 CCAACAATGCGCTGTTCTAGT 59.193 47.619 11.68 0.00 37.43 2.57
970 1107 1.817520 CACACGGACACAGCAACCA 60.818 57.895 0.00 0.00 0.00 3.67
971 1108 1.373590 AACACACGGACACAGCAACC 61.374 55.000 0.00 0.00 0.00 3.77
974 1111 2.468670 GCAACACACGGACACAGCA 61.469 57.895 0.00 0.00 0.00 4.41
995 1148 2.587194 CGCGCCTCTCCATTCCAG 60.587 66.667 0.00 0.00 0.00 3.86
1162 1336 4.486503 GGCCTCCTCCTGCTGCTG 62.487 72.222 0.00 0.00 0.00 4.41
1575 1758 1.878522 CAGGCATGACCGCGAGTAC 60.879 63.158 8.23 0.00 46.52 2.73
2070 2291 0.535553 TACACTCCACGCCCCAAAAC 60.536 55.000 0.00 0.00 0.00 2.43
2079 2300 1.819288 ACCATCTGAGTACACTCCACG 59.181 52.381 6.91 0.00 42.20 4.94
2097 2318 3.788937 TGCGGCTAGAAATTACAGTACC 58.211 45.455 0.00 0.00 0.00 3.34
2151 2379 2.097825 CAGAGGGCAAAGGAGAAATGG 58.902 52.381 0.00 0.00 0.00 3.16
2183 2411 7.813627 ACGAGGAATTCAAGACTTTCTTAGTAC 59.186 37.037 7.93 0.00 37.17 2.73
2209 2438 3.561310 GTGTCAGTGCATTCAAGACTTCA 59.439 43.478 0.00 0.00 33.33 3.02
2252 2481 2.550606 CCCGATTTGTTTCGTCCAAGAA 59.449 45.455 0.00 0.00 37.42 2.52
2254 2483 1.199097 CCCCGATTTGTTTCGTCCAAG 59.801 52.381 0.00 0.00 37.42 3.61
2264 2493 7.480760 TTAAGTAGTAAGTACCCCGATTTGT 57.519 36.000 0.00 0.00 31.06 2.83
2340 2570 2.118404 GCCGCCGATGAAATGGGAA 61.118 57.895 0.00 0.00 46.39 3.97
2388 2618 1.153628 GCAGATCGTACCCGCACTT 60.154 57.895 0.00 0.00 0.00 3.16
2423 2653 1.639298 GCTGTTGCGTCCTGTCCATC 61.639 60.000 0.00 0.00 0.00 3.51
2427 2657 1.230635 ACATGCTGTTGCGTCCTGTC 61.231 55.000 0.00 0.00 43.34 3.51
2467 2698 3.053320 ACTTTCAATCCCCTCCTCATTCC 60.053 47.826 0.00 0.00 0.00 3.01
2504 2738 3.636231 CTTCGCCCACCACCCTCA 61.636 66.667 0.00 0.00 0.00 3.86
2708 2955 3.439476 AGTGTACTAGTAACTCGCCACTG 59.561 47.826 16.54 0.00 31.22 3.66
2711 2958 3.624861 GCTAGTGTACTAGTAACTCGCCA 59.375 47.826 17.65 7.23 45.85 5.69
2713 2960 4.332268 ACTGCTAGTGTACTAGTAACTCGC 59.668 45.833 21.45 21.45 45.85 5.03
2714 2961 5.579904 TCACTGCTAGTGTACTAGTAACTCG 59.420 44.000 17.65 12.94 46.03 4.18
2715 2962 6.981762 TCACTGCTAGTGTACTAGTAACTC 57.018 41.667 17.65 8.05 46.03 3.01
2716 2963 6.543100 GGATCACTGCTAGTGTACTAGTAACT 59.457 42.308 17.65 12.31 46.03 2.24
2717 2964 6.238703 GGGATCACTGCTAGTGTACTAGTAAC 60.239 46.154 17.65 5.74 46.03 2.50
2718 2965 5.826737 GGGATCACTGCTAGTGTACTAGTAA 59.173 44.000 17.65 8.13 46.03 2.24
2737 2994 5.011840 TCAATCTGACTCATCATCTGGGATC 59.988 44.000 0.00 0.00 33.22 3.36
2759 3019 2.479560 CGTGTCATGCTTAGACCGATCA 60.480 50.000 0.00 0.00 35.15 2.92
2839 3109 2.055633 TACGGCGAGCCAGGATTGA 61.056 57.895 16.62 0.00 35.37 2.57
2907 3183 4.523083 ACACACCTAAGTTTCTTGCTTCA 58.477 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.