Multiple sequence alignment - TraesCS4D01G081700

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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 TraesCS4D01G081700 chr4D 100.000 3849 0 0 1 3849 55287811 55283963 0.000000e+00 7108
1 TraesCS4D01G081700 chr4D 100.000 253 0 0 4378 4630 55283434 55283182 7.010000e-128 468
2 TraesCS4D01G081700 chr4A 92.030 3212 200 21 680 3849 541783820 541787017 0.000000e+00 4462
3 TraesCS4D01G081700 chr4A 91.518 1733 129 9 2005 3732 541800962 541802681 0.000000e+00 2370
4 TraesCS4D01G081700 chr4A 93.854 1383 73 5 2472 3849 541876660 541878035 0.000000e+00 2073
5 TraesCS4D01G081700 chr4A 86.508 378 30 13 1 374 541782989 541783349 3.360000e-106 396
6 TraesCS4D01G081700 chr4A 92.342 222 16 1 4410 4630 541787134 541787355 9.670000e-82 315
7 TraesCS4D01G081700 chr4A 93.529 170 9 1 4461 4628 541878071 541878240 7.690000e-63 252
8 TraesCS4D01G081700 chr4A 94.444 108 6 0 3742 3849 541865831 541865938 2.870000e-37 167
9 TraesCS4D01G081700 chr4A 90.909 110 9 1 581 690 541783525 541783633 3.730000e-31 147
10 TraesCS4D01G081700 chr4B 94.565 2723 142 4 1133 3849 82311876 82309154 0.000000e+00 4204
11 TraesCS4D01G081700 chr4B 92.625 461 29 4 680 1138 82312358 82311901 0.000000e+00 658
12 TraesCS4D01G081700 chr4B 91.111 225 10 6 4415 4630 82309028 82308805 3.500000e-76 296
13 TraesCS4D01G081700 chr4B 81.934 393 25 18 1 374 82313202 82312837 1.630000e-74 291
14 TraesCS4D01G081700 chr3D 72.146 2251 517 89 1612 3803 1636276 1634077 2.400000e-162 582
15 TraesCS4D01G081700 chr3A 71.931 2191 523 72 1668 3808 7472138 7469990 5.230000e-154 555
16 TraesCS4D01G081700 chr3A 74.745 1077 229 32 2762 3807 36480557 36479493 4.250000e-120 442
17 TraesCS4D01G081700 chr3B 74.513 1130 243 29 2707 3808 5173791 5174903 2.540000e-122 449


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 TraesCS4D01G081700 chr4D 55283182 55287811 4629 True 3788.00 7108 100.00000 1 4630 2 chr4D.!!$R1 4629
1 TraesCS4D01G081700 chr4A 541800962 541802681 1719 False 2370.00 2370 91.51800 2005 3732 1 chr4A.!!$F1 1727
2 TraesCS4D01G081700 chr4A 541782989 541787355 4366 False 1330.00 4462 90.44725 1 4630 4 chr4A.!!$F3 4629
3 TraesCS4D01G081700 chr4A 541876660 541878240 1580 False 1162.50 2073 93.69150 2472 4628 2 chr4A.!!$F4 2156
4 TraesCS4D01G081700 chr4B 82308805 82313202 4397 True 1362.25 4204 90.05875 1 4630 4 chr4B.!!$R1 4629
5 TraesCS4D01G081700 chr3D 1634077 1636276 2199 True 582.00 582 72.14600 1612 3803 1 chr3D.!!$R1 2191
6 TraesCS4D01G081700 chr3A 7469990 7472138 2148 True 555.00 555 71.93100 1668 3808 1 chr3A.!!$R1 2140
7 TraesCS4D01G081700 chr3A 36479493 36480557 1064 True 442.00 442 74.74500 2762 3807 1 chr3A.!!$R2 1045
8 TraesCS4D01G081700 chr3B 5173791 5174903 1112 False 449.00 449 74.51300 2707 3808 1 chr3B.!!$F1 1101

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
502 526 0.036010 CGGGCATTCTGAGTTCACCT 60.036 55.0 0.00 0.00 0.00 4.00 F
512 536 0.108019 GAGTTCACCTCCACCGGTTT 59.892 55.0 2.97 0.00 34.29 3.27 F
2076 2343 0.035439 ACATACCGACAAGCTTGGGG 60.035 55.0 29.18 28.31 33.66 4.96 F
2684 2951 0.166814 CTTTCACCGCTTGCTGTAGC 59.833 55.0 0.00 0.00 42.50 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1849 2116 0.179137 GGAAAGTTTGCTATGCCGGC 60.179 55.000 22.73 22.73 0.00 6.13 R
2338 2605 1.106285 GAAGTGGGGATGTTGCCATC 58.894 55.000 0.00 0.00 45.65 3.51 R
3475 3781 2.069273 CAGCGGTAGAAACTTGACCAG 58.931 52.381 0.00 0.00 32.39 4.00 R
4474 4887 0.458889 TCGTAAAACCAGATCCGGCG 60.459 55.000 0.00 0.00 0.00 6.46 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
70 73 4.983671 AACTTGGTGTTTCTTTGACTCC 57.016 40.909 0.00 0.00 34.84 3.85
71 74 2.943033 ACTTGGTGTTTCTTTGACTCCG 59.057 45.455 0.00 0.00 34.28 4.63
72 75 2.992124 TGGTGTTTCTTTGACTCCGA 57.008 45.000 0.00 0.00 34.28 4.55
73 76 2.833794 TGGTGTTTCTTTGACTCCGAG 58.166 47.619 0.00 0.00 34.28 4.63
74 77 2.432874 TGGTGTTTCTTTGACTCCGAGA 59.567 45.455 1.33 0.00 34.28 4.04
75 78 3.118555 TGGTGTTTCTTTGACTCCGAGAA 60.119 43.478 1.33 0.00 34.28 2.87
76 79 3.495001 GGTGTTTCTTTGACTCCGAGAAG 59.505 47.826 1.33 0.00 31.67 2.85
77 80 3.059529 GTGTTTCTTTGACTCCGAGAAGC 60.060 47.826 1.33 0.00 33.10 3.86
78 81 3.181465 TGTTTCTTTGACTCCGAGAAGCT 60.181 43.478 1.33 0.00 33.49 3.74
79 82 3.305398 TTCTTTGACTCCGAGAAGCTC 57.695 47.619 1.33 0.00 0.00 4.09
80 83 1.546476 TCTTTGACTCCGAGAAGCTCC 59.454 52.381 1.33 0.00 0.00 4.70
84 87 0.103937 GACTCCGAGAAGCTCCATGG 59.896 60.000 4.97 4.97 0.00 3.66
159 163 1.629043 GCGTCCCTATCCAGGTGATA 58.371 55.000 0.00 0.00 40.79 2.15
192 198 5.431765 CTCCAGTGTAATATTCTTGCAGGT 58.568 41.667 0.00 0.00 0.00 4.00
246 270 3.105659 GCCAAGGCATCTTCGAGC 58.894 61.111 6.14 0.00 41.49 5.03
247 271 1.451028 GCCAAGGCATCTTCGAGCT 60.451 57.895 6.14 0.00 41.49 4.09
248 272 1.028868 GCCAAGGCATCTTCGAGCTT 61.029 55.000 6.14 0.00 41.49 3.74
249 273 1.457346 CCAAGGCATCTTCGAGCTTT 58.543 50.000 0.00 0.00 0.00 3.51
250 274 1.815003 CCAAGGCATCTTCGAGCTTTT 59.185 47.619 0.00 0.00 0.00 2.27
251 275 2.415090 CCAAGGCATCTTCGAGCTTTTG 60.415 50.000 0.00 1.18 0.00 2.44
252 276 2.479566 AGGCATCTTCGAGCTTTTGA 57.520 45.000 0.00 0.00 0.00 2.69
374 398 1.065273 GCATGGAAAGCAGCGGATG 59.935 57.895 0.00 0.00 0.00 3.51
375 399 1.378882 GCATGGAAAGCAGCGGATGA 61.379 55.000 0.00 0.00 0.00 2.92
376 400 1.315690 CATGGAAAGCAGCGGATGAT 58.684 50.000 0.00 0.00 0.00 2.45
377 401 2.497138 CATGGAAAGCAGCGGATGATA 58.503 47.619 0.00 0.00 0.00 2.15
378 402 2.936919 TGGAAAGCAGCGGATGATAT 57.063 45.000 0.00 0.00 0.00 1.63
379 403 2.497138 TGGAAAGCAGCGGATGATATG 58.503 47.619 0.00 0.00 0.00 1.78
380 404 1.808945 GGAAAGCAGCGGATGATATGG 59.191 52.381 0.00 0.00 0.00 2.74
381 405 2.498167 GAAAGCAGCGGATGATATGGT 58.502 47.619 0.00 0.00 0.00 3.55
382 406 2.645838 AAGCAGCGGATGATATGGTT 57.354 45.000 0.00 0.00 0.00 3.67
383 407 1.888215 AGCAGCGGATGATATGGTTG 58.112 50.000 0.00 0.00 0.00 3.77
384 408 1.141657 AGCAGCGGATGATATGGTTGT 59.858 47.619 0.00 0.00 0.00 3.32
385 409 1.265095 GCAGCGGATGATATGGTTGTG 59.735 52.381 0.00 0.00 0.00 3.33
386 410 2.837498 CAGCGGATGATATGGTTGTGA 58.163 47.619 0.00 0.00 0.00 3.58
387 411 2.545526 CAGCGGATGATATGGTTGTGAC 59.454 50.000 0.00 0.00 0.00 3.67
388 412 2.170397 AGCGGATGATATGGTTGTGACA 59.830 45.455 0.00 0.00 0.00 3.58
405 429 8.134895 GGTTGTGACAGAATGAGTTTTGAATAA 58.865 33.333 0.00 0.00 39.69 1.40
413 437 7.116805 CAGAATGAGTTTTGAATAAAGTTGCCC 59.883 37.037 0.00 0.00 39.69 5.36
424 448 6.877322 TGAATAAAGTTGCCCTGACTTACTAC 59.123 38.462 0.00 0.00 36.38 2.73
425 449 4.976540 AAAGTTGCCCTGACTTACTACT 57.023 40.909 0.00 0.00 36.38 2.57
426 450 7.729124 ATAAAGTTGCCCTGACTTACTACTA 57.271 36.000 0.00 0.00 36.38 1.82
427 451 5.402997 AAGTTGCCCTGACTTACTACTAC 57.597 43.478 0.00 0.00 35.68 2.73
428 452 4.675038 AGTTGCCCTGACTTACTACTACT 58.325 43.478 0.00 0.00 0.00 2.57
429 453 5.824421 AGTTGCCCTGACTTACTACTACTA 58.176 41.667 0.00 0.00 0.00 1.82
433 457 5.651139 TGCCCTGACTTACTACTACTAGTTG 59.349 44.000 0.00 0.59 34.79 3.16
442 466 7.714813 ACTTACTACTACTAGTTGGTAGCTAGC 59.285 40.741 23.72 16.08 41.88 3.42
447 471 2.422832 ACTAGTTGGTAGCTAGCGACAC 59.577 50.000 33.97 22.48 39.85 3.67
449 473 1.473278 AGTTGGTAGCTAGCGACACTC 59.527 52.381 33.97 15.61 39.85 3.51
450 474 0.450583 TTGGTAGCTAGCGACACTCG 59.549 55.000 26.27 0.00 43.89 4.18
453 477 1.008329 GTAGCTAGCGACACTCGAGT 58.992 55.000 21.42 13.58 43.74 4.18
462 486 3.312973 AGCGACACTCGAGTCCTATAAAG 59.687 47.826 16.96 4.28 43.74 1.85
464 488 4.553156 GCGACACTCGAGTCCTATAAAGAG 60.553 50.000 16.96 2.68 43.74 2.85
465 489 4.553156 CGACACTCGAGTCCTATAAAGAGC 60.553 50.000 16.96 0.00 43.74 4.09
470 494 4.783055 TCGAGTCCTATAAAGAGCAGAGT 58.217 43.478 0.00 0.00 0.00 3.24
471 495 4.576873 TCGAGTCCTATAAAGAGCAGAGTG 59.423 45.833 0.00 0.00 0.00 3.51
472 496 4.336993 CGAGTCCTATAAAGAGCAGAGTGT 59.663 45.833 0.00 0.00 0.00 3.55
473 497 5.527951 CGAGTCCTATAAAGAGCAGAGTGTA 59.472 44.000 0.00 0.00 0.00 2.90
474 498 6.293190 CGAGTCCTATAAAGAGCAGAGTGTAG 60.293 46.154 0.00 0.00 0.00 2.74
476 500 6.770785 AGTCCTATAAAGAGCAGAGTGTAGAG 59.229 42.308 0.00 0.00 0.00 2.43
477 501 6.768861 GTCCTATAAAGAGCAGAGTGTAGAGA 59.231 42.308 0.00 0.00 0.00 3.10
478 502 7.283580 GTCCTATAAAGAGCAGAGTGTAGAGAA 59.716 40.741 0.00 0.00 0.00 2.87
479 503 7.834681 TCCTATAAAGAGCAGAGTGTAGAGAAA 59.165 37.037 0.00 0.00 0.00 2.52
480 504 8.470805 CCTATAAAGAGCAGAGTGTAGAGAAAA 58.529 37.037 0.00 0.00 0.00 2.29
481 505 9.515020 CTATAAAGAGCAGAGTGTAGAGAAAAG 57.485 37.037 0.00 0.00 0.00 2.27
483 507 5.385509 AGAGCAGAGTGTAGAGAAAAGTC 57.614 43.478 0.00 0.00 0.00 3.01
486 510 3.839293 CAGAGTGTAGAGAAAAGTCGGG 58.161 50.000 0.00 0.00 0.00 5.14
487 511 2.231721 AGAGTGTAGAGAAAAGTCGGGC 59.768 50.000 0.00 0.00 0.00 6.13
488 512 1.968493 AGTGTAGAGAAAAGTCGGGCA 59.032 47.619 0.00 0.00 0.00 5.36
490 514 3.008049 AGTGTAGAGAAAAGTCGGGCATT 59.992 43.478 0.00 0.00 0.00 3.56
491 515 3.371285 GTGTAGAGAAAAGTCGGGCATTC 59.629 47.826 0.00 0.00 0.00 2.67
492 516 3.260884 TGTAGAGAAAAGTCGGGCATTCT 59.739 43.478 1.02 1.02 34.96 2.40
493 517 2.704572 AGAGAAAAGTCGGGCATTCTG 58.295 47.619 5.55 0.00 32.54 3.02
494 518 2.303022 AGAGAAAAGTCGGGCATTCTGA 59.697 45.455 5.55 0.00 32.54 3.27
495 519 2.675348 GAGAAAAGTCGGGCATTCTGAG 59.325 50.000 5.55 0.00 32.54 3.35
496 520 2.039084 AGAAAAGTCGGGCATTCTGAGT 59.961 45.455 0.66 0.00 36.01 3.41
498 522 2.100605 AAGTCGGGCATTCTGAGTTC 57.899 50.000 0.00 0.00 39.55 3.01
499 523 0.976641 AGTCGGGCATTCTGAGTTCA 59.023 50.000 0.00 0.00 30.44 3.18
500 524 1.079503 GTCGGGCATTCTGAGTTCAC 58.920 55.000 0.00 0.00 0.00 3.18
502 526 0.036010 CGGGCATTCTGAGTTCACCT 60.036 55.000 0.00 0.00 0.00 4.00
505 529 1.003580 GGCATTCTGAGTTCACCTCCA 59.996 52.381 0.00 0.00 39.65 3.86
507 531 2.704572 CATTCTGAGTTCACCTCCACC 58.295 52.381 0.00 0.00 39.65 4.61
508 532 0.679505 TTCTGAGTTCACCTCCACCG 59.320 55.000 0.00 0.00 39.65 4.94
509 533 1.185618 TCTGAGTTCACCTCCACCGG 61.186 60.000 0.00 0.00 39.65 5.28
510 534 1.458777 TGAGTTCACCTCCACCGGT 60.459 57.895 0.00 0.00 39.65 5.28
512 536 0.108019 GAGTTCACCTCCACCGGTTT 59.892 55.000 2.97 0.00 34.29 3.27
513 537 1.345415 GAGTTCACCTCCACCGGTTTA 59.655 52.381 2.97 0.00 34.29 2.01
514 538 1.071228 AGTTCACCTCCACCGGTTTAC 59.929 52.381 2.97 0.00 34.29 2.01
515 539 1.071228 GTTCACCTCCACCGGTTTACT 59.929 52.381 2.97 0.00 34.29 2.24
516 540 0.682852 TCACCTCCACCGGTTTACTG 59.317 55.000 2.97 0.00 34.29 2.74
517 541 0.682852 CACCTCCACCGGTTTACTGA 59.317 55.000 2.97 0.00 34.29 3.41
518 542 0.683412 ACCTCCACCGGTTTACTGAC 59.317 55.000 2.97 0.00 31.94 3.51
523 554 0.953960 CACCGGTTTACTGACCCAGC 60.954 60.000 2.97 0.00 36.28 4.85
525 556 0.391263 CCGGTTTACTGACCCAGCTC 60.391 60.000 0.00 0.00 36.28 4.09
526 557 0.736325 CGGTTTACTGACCCAGCTCG 60.736 60.000 0.00 0.00 36.28 5.03
527 558 0.320697 GGTTTACTGACCCAGCTCGT 59.679 55.000 0.00 0.00 34.37 4.18
529 560 0.242825 TTTACTGACCCAGCTCGTCG 59.757 55.000 6.09 0.00 34.37 5.12
530 561 2.209064 TTACTGACCCAGCTCGTCGC 62.209 60.000 6.09 0.00 34.37 5.19
569 600 2.027751 GCTCTCGCCACGGATACC 59.972 66.667 0.00 0.00 0.00 2.73
570 601 2.782222 GCTCTCGCCACGGATACCA 61.782 63.158 0.00 0.00 0.00 3.25
571 602 1.065928 CTCTCGCCACGGATACCAC 59.934 63.158 0.00 0.00 0.00 4.16
572 603 2.106332 CTCGCCACGGATACCACC 59.894 66.667 0.00 0.00 0.00 4.61
573 604 3.441011 CTCGCCACGGATACCACCC 62.441 68.421 0.00 0.00 0.00 4.61
574 605 3.776781 CGCCACGGATACCACCCA 61.777 66.667 0.00 0.00 0.00 4.51
575 606 2.124860 GCCACGGATACCACCCAC 60.125 66.667 0.00 0.00 0.00 4.61
576 607 2.587889 CCACGGATACCACCCACC 59.412 66.667 0.00 0.00 0.00 4.61
579 610 4.540735 CGGATACCACCCACCGGC 62.541 72.222 0.00 0.00 41.41 6.13
616 647 5.701290 AGCAAGTAAGCTTCACTCGTTTAAT 59.299 36.000 0.00 0.00 43.70 1.40
622 653 6.654793 AAGCTTCACTCGTTTAATCATCTC 57.345 37.500 0.00 0.00 0.00 2.75
680 713 9.093970 CAAATTGCATACATCATTCATGTTCTT 57.906 29.630 0.00 0.00 43.89 2.52
730 966 7.564793 AGTATAACACAATGAAGGATGCTGTA 58.435 34.615 0.00 0.00 0.00 2.74
738 974 1.334869 GAAGGATGCTGTAATTGGGCG 59.665 52.381 0.00 0.00 0.00 6.13
787 1023 1.960763 TGCTGTTGCACTAGCCGTG 60.961 57.895 16.34 0.00 45.31 4.94
803 1039 4.660521 TGGCCACCTCCACTTACT 57.339 55.556 0.00 0.00 0.00 2.24
804 1040 3.798948 TGGCCACCTCCACTTACTA 57.201 52.632 0.00 0.00 0.00 1.82
805 1041 1.272807 TGGCCACCTCCACTTACTAC 58.727 55.000 0.00 0.00 0.00 2.73
806 1042 0.175073 GGCCACCTCCACTTACTACG 59.825 60.000 0.00 0.00 0.00 3.51
807 1043 0.175073 GCCACCTCCACTTACTACGG 59.825 60.000 0.00 0.00 0.00 4.02
808 1044 0.175073 CCACCTCCACTTACTACGGC 59.825 60.000 0.00 0.00 0.00 5.68
867 1103 2.885644 CATCGTCCTTGACCCGCG 60.886 66.667 0.00 0.00 0.00 6.46
987 1223 1.762471 CCAACCGGGGTTTAGTGGA 59.238 57.895 6.32 0.00 36.00 4.02
1044 1280 2.432146 TCAGAAATCTAGCACTGCCGAT 59.568 45.455 0.00 0.00 0.00 4.18
1152 1419 0.254178 AGCATAAGGTCCTGTGGCTG 59.746 55.000 9.87 0.00 0.00 4.85
1155 1422 2.684927 GCATAAGGTCCTGTGGCTGAAT 60.685 50.000 0.00 0.00 0.00 2.57
1289 1556 1.015868 GCAATGAGGAAGCTCAGCTC 58.984 55.000 0.00 0.00 38.25 4.09
1301 1568 2.093764 AGCTCAGCTCTGCGTTTAATCT 60.094 45.455 0.00 0.00 30.62 2.40
1334 1601 2.866085 ATCCCTGACGAGCTTGCAGC 62.866 60.000 15.90 0.47 42.84 5.25
1758 2025 6.470877 GTCTCTCGTTAGCAAGTAATCTTCTG 59.529 42.308 0.00 0.00 0.00 3.02
1769 2036 2.797177 AATCTTCTGGAAGGTCAGGC 57.203 50.000 10.01 0.00 38.88 4.85
1884 2151 5.473066 ACTTTCCCAACCTGATCATTTTG 57.527 39.130 0.00 2.62 0.00 2.44
1899 2166 5.975693 TCATTTTGGGATTGGACTACAAC 57.024 39.130 0.00 0.00 42.94 3.32
2076 2343 0.035439 ACATACCGACAAGCTTGGGG 60.035 55.000 29.18 28.31 33.66 4.96
2301 2568 1.361271 CACTGTGGGTGCTTGCAAG 59.639 57.895 22.44 22.44 39.22 4.01
2310 2577 1.000938 GGTGCTTGCAAGAGTTTGGAG 60.001 52.381 30.39 0.65 35.96 3.86
2338 2605 9.787532 ACATTGAGTTGGACAATAATATTTTCG 57.212 29.630 0.00 0.00 36.40 3.46
2422 2689 9.760077 CTTACAATAACTTAACCGGATCAGTAT 57.240 33.333 9.46 0.00 0.00 2.12
2549 2816 5.296531 CCACACATATTGACGGAAATCATGA 59.703 40.000 0.00 0.00 0.00 3.07
2550 2817 6.183360 CCACACATATTGACGGAAATCATGAA 60.183 38.462 0.00 0.00 0.00 2.57
2566 2833 0.754957 TGAACTTTGTGGTGGGGCAG 60.755 55.000 0.00 0.00 0.00 4.85
2588 2855 1.614317 GGACTTACACCTGCCTGCATT 60.614 52.381 0.00 0.00 0.00 3.56
2614 2881 8.689251 TTCTGTTACGTCTTCAAATCTATCTG 57.311 34.615 0.00 0.00 0.00 2.90
2672 2939 0.455633 CTCGCTTGCATGCTTTCACC 60.456 55.000 20.33 0.55 0.00 4.02
2680 2947 0.731514 CATGCTTTCACCGCTTGCTG 60.732 55.000 0.00 0.00 0.00 4.41
2682 2949 0.533978 TGCTTTCACCGCTTGCTGTA 60.534 50.000 0.00 0.00 0.00 2.74
2684 2951 0.166814 CTTTCACCGCTTGCTGTAGC 59.833 55.000 0.00 0.00 42.50 3.58
2808 3075 3.176552 AGAGCAACTGATGGATTCTCG 57.823 47.619 0.00 0.00 0.00 4.04
2810 3077 0.659957 GCAACTGATGGATTCTCGGC 59.340 55.000 0.00 0.00 0.00 5.54
2892 3159 2.034558 AGAAAATGTGGTTGCCGTGAAG 59.965 45.455 0.00 0.00 0.00 3.02
2928 3195 1.159664 AAGGGGAGCACAGAGGAGT 59.840 57.895 0.00 0.00 0.00 3.85
3475 3781 3.601443 ATCTACAGAATATGGAGCGGC 57.399 47.619 0.00 0.00 40.06 6.53
3542 3848 7.222224 GTCGTTCTCCTTGAAATATTCATACGT 59.778 37.037 0.00 0.00 39.84 3.57
3635 3946 2.768253 TTGCAGATCGTTGATCCACT 57.232 45.000 3.28 0.00 39.66 4.00
3639 3950 3.951680 TGCAGATCGTTGATCCACTACTA 59.048 43.478 3.28 0.00 39.66 1.82
3732 4050 1.342174 CTGAATGTTGGCCTTTGCTGT 59.658 47.619 3.32 0.00 37.74 4.40
4432 4845 6.844696 AACGATGCCATACTTAATGTACAG 57.155 37.500 0.33 0.00 33.45 2.74
4433 4846 5.297547 ACGATGCCATACTTAATGTACAGG 58.702 41.667 0.33 0.00 33.45 4.00
4443 4856 4.650131 ACTTAATGTACAGGTAGAGCTCCC 59.350 45.833 10.93 5.39 0.00 4.30
4474 4887 2.414594 GCCATTCAATCCGCTGGC 59.585 61.111 0.00 0.00 46.54 4.85
4492 4905 2.003672 CGCCGGATCTGGTTTTACG 58.996 57.895 21.88 12.29 0.00 3.18
4508 4927 5.005490 GGTTTTACGACAGCTAAGAGCATAC 59.995 44.000 0.64 0.00 45.56 2.39
4561 4983 2.502142 AAAGGATGAGCAGCATGTGA 57.498 45.000 0.00 0.00 37.34 3.58
4577 4999 0.039618 GTGAGGGGAGGGCAATGAAA 59.960 55.000 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 10 4.734266 AGCAAGGACTCCTGAAAATTCTT 58.266 39.130 0.00 0.00 32.13 2.52
26 28 8.637986 AGTTTTTCACAACATTAATCCTAGCAA 58.362 29.630 0.00 0.00 0.00 3.91
27 29 8.177119 AGTTTTTCACAACATTAATCCTAGCA 57.823 30.769 0.00 0.00 0.00 3.49
28 30 8.915654 CAAGTTTTTCACAACATTAATCCTAGC 58.084 33.333 0.00 0.00 0.00 3.42
70 73 0.467384 ATGGACCATGGAGCTTCTCG 59.533 55.000 21.47 0.00 0.00 4.04
71 74 1.964552 CATGGACCATGGAGCTTCTC 58.035 55.000 24.65 3.68 38.11 2.87
72 75 0.106819 GCATGGACCATGGAGCTTCT 60.107 55.000 31.08 0.00 41.64 2.85
73 76 0.394762 TGCATGGACCATGGAGCTTC 60.395 55.000 31.08 16.36 41.64 3.86
74 77 1.693034 TGCATGGACCATGGAGCTT 59.307 52.632 31.08 0.00 41.64 3.74
75 78 3.418687 TGCATGGACCATGGAGCT 58.581 55.556 31.08 0.00 41.64 4.09
78 81 2.276409 GGCTGCATGGACCATGGA 59.724 61.111 31.08 28.24 41.64 3.41
79 82 2.043752 TGGCTGCATGGACCATGG 60.044 61.111 31.08 18.79 41.64 3.66
80 83 2.420568 GGTGGCTGCATGGACCATG 61.421 63.158 27.39 27.39 43.91 3.66
84 87 0.895100 TTCAAGGTGGCTGCATGGAC 60.895 55.000 0.50 0.00 0.00 4.02
121 124 0.179000 CCAGGATCTCCTTTCCCACG 59.821 60.000 0.00 0.00 46.09 4.94
163 167 5.543507 AGAATATTACACTGGAGCTCCTG 57.456 43.478 31.73 31.73 40.37 3.86
242 266 2.680913 CCGGCTGGTCAAAAGCTCG 61.681 63.158 2.29 0.00 40.64 5.03
243 267 2.982744 GCCGGCTGGTCAAAAGCTC 61.983 63.158 22.15 0.00 40.64 4.09
244 268 2.985847 GCCGGCTGGTCAAAAGCT 60.986 61.111 22.15 0.00 40.64 3.74
245 269 4.056125 GGCCGGCTGGTCAAAAGC 62.056 66.667 28.56 0.41 40.65 3.51
246 270 3.737172 CGGCCGGCTGGTCAAAAG 61.737 66.667 28.47 0.00 41.18 2.27
274 298 2.925578 TGCTGATCATTTTCTTGGCG 57.074 45.000 0.00 0.00 0.00 5.69
277 301 4.142315 ACCGGAATGCTGATCATTTTCTTG 60.142 41.667 9.46 0.00 44.95 3.02
374 398 6.992063 AACTCATTCTGTCACAACCATATC 57.008 37.500 0.00 0.00 0.00 1.63
375 399 7.448161 TCAAAACTCATTCTGTCACAACCATAT 59.552 33.333 0.00 0.00 0.00 1.78
376 400 6.770303 TCAAAACTCATTCTGTCACAACCATA 59.230 34.615 0.00 0.00 0.00 2.74
377 401 5.593909 TCAAAACTCATTCTGTCACAACCAT 59.406 36.000 0.00 0.00 0.00 3.55
378 402 4.946772 TCAAAACTCATTCTGTCACAACCA 59.053 37.500 0.00 0.00 0.00 3.67
379 403 5.499139 TCAAAACTCATTCTGTCACAACC 57.501 39.130 0.00 0.00 0.00 3.77
380 404 9.515020 TTTATTCAAAACTCATTCTGTCACAAC 57.485 29.630 0.00 0.00 0.00 3.32
381 405 9.734620 CTTTATTCAAAACTCATTCTGTCACAA 57.265 29.630 0.00 0.00 0.00 3.33
382 406 8.902806 ACTTTATTCAAAACTCATTCTGTCACA 58.097 29.630 0.00 0.00 0.00 3.58
383 407 9.736023 AACTTTATTCAAAACTCATTCTGTCAC 57.264 29.630 0.00 0.00 0.00 3.67
384 408 9.734620 CAACTTTATTCAAAACTCATTCTGTCA 57.265 29.630 0.00 0.00 0.00 3.58
385 409 8.694394 GCAACTTTATTCAAAACTCATTCTGTC 58.306 33.333 0.00 0.00 0.00 3.51
386 410 7.653311 GGCAACTTTATTCAAAACTCATTCTGT 59.347 33.333 0.00 0.00 0.00 3.41
387 411 7.116805 GGGCAACTTTATTCAAAACTCATTCTG 59.883 37.037 0.00 0.00 0.00 3.02
388 412 7.015584 AGGGCAACTTTATTCAAAACTCATTCT 59.984 33.333 0.00 0.00 0.00 2.40
405 429 5.085219 AGTAGTAGTAAGTCAGGGCAACTT 58.915 41.667 4.85 4.85 40.06 2.66
413 437 7.769970 AGCTACCAACTAGTAGTAGTAAGTCAG 59.230 40.741 23.74 9.82 41.54 3.51
424 448 3.875727 TGTCGCTAGCTACCAACTAGTAG 59.124 47.826 16.05 0.00 42.25 2.57
425 449 3.624861 GTGTCGCTAGCTACCAACTAGTA 59.375 47.826 16.05 0.00 39.48 1.82
426 450 2.422832 GTGTCGCTAGCTACCAACTAGT 59.577 50.000 16.05 0.00 39.48 2.57
427 451 2.683867 AGTGTCGCTAGCTACCAACTAG 59.316 50.000 16.05 0.00 40.13 2.57
428 452 2.681848 GAGTGTCGCTAGCTACCAACTA 59.318 50.000 16.05 0.00 0.00 2.24
429 453 1.473278 GAGTGTCGCTAGCTACCAACT 59.527 52.381 16.05 13.28 0.00 3.16
433 457 0.305313 CTCGAGTGTCGCTAGCTACC 59.695 60.000 16.05 8.07 40.21 3.18
442 466 4.553156 GCTCTTTATAGGACTCGAGTGTCG 60.553 50.000 25.58 2.55 42.10 4.35
447 471 4.819630 ACTCTGCTCTTTATAGGACTCGAG 59.180 45.833 11.84 11.84 0.00 4.04
449 473 4.336993 ACACTCTGCTCTTTATAGGACTCG 59.663 45.833 0.00 0.00 0.00 4.18
450 474 5.845391 ACACTCTGCTCTTTATAGGACTC 57.155 43.478 0.00 0.00 0.00 3.36
453 477 6.901300 TCTCTACACTCTGCTCTTTATAGGA 58.099 40.000 0.00 0.00 0.00 2.94
462 486 4.162812 CGACTTTTCTCTACACTCTGCTC 58.837 47.826 0.00 0.00 0.00 4.26
464 488 3.246619 CCGACTTTTCTCTACACTCTGC 58.753 50.000 0.00 0.00 0.00 4.26
465 489 3.839293 CCCGACTTTTCTCTACACTCTG 58.161 50.000 0.00 0.00 0.00 3.35
470 494 3.260884 AGAATGCCCGACTTTTCTCTACA 59.739 43.478 0.00 0.00 0.00 2.74
471 495 3.619038 CAGAATGCCCGACTTTTCTCTAC 59.381 47.826 0.00 0.00 0.00 2.59
472 496 3.513912 TCAGAATGCCCGACTTTTCTCTA 59.486 43.478 0.00 0.00 34.76 2.43
473 497 2.303022 TCAGAATGCCCGACTTTTCTCT 59.697 45.455 0.00 0.00 34.76 3.10
474 498 2.675348 CTCAGAATGCCCGACTTTTCTC 59.325 50.000 0.00 0.00 34.76 2.87
476 500 2.427506 ACTCAGAATGCCCGACTTTTC 58.572 47.619 0.00 0.00 34.76 2.29
477 501 2.568623 ACTCAGAATGCCCGACTTTT 57.431 45.000 0.00 0.00 34.76 2.27
478 502 2.224523 TGAACTCAGAATGCCCGACTTT 60.225 45.455 0.00 0.00 34.76 2.66
479 503 1.347707 TGAACTCAGAATGCCCGACTT 59.652 47.619 0.00 0.00 34.76 3.01
480 504 0.976641 TGAACTCAGAATGCCCGACT 59.023 50.000 0.00 0.00 34.76 4.18
481 505 1.079503 GTGAACTCAGAATGCCCGAC 58.920 55.000 0.00 0.00 34.76 4.79
483 507 0.036010 AGGTGAACTCAGAATGCCCG 60.036 55.000 0.00 0.00 34.76 6.13
493 517 0.108019 AAACCGGTGGAGGTGAACTC 59.892 55.000 8.52 0.00 45.21 3.01
494 518 1.071228 GTAAACCGGTGGAGGTGAACT 59.929 52.381 8.52 0.00 45.21 3.01
495 519 1.071228 AGTAAACCGGTGGAGGTGAAC 59.929 52.381 8.52 0.00 45.21 3.18
496 520 1.071071 CAGTAAACCGGTGGAGGTGAA 59.929 52.381 8.52 0.00 45.21 3.18
498 522 0.682852 TCAGTAAACCGGTGGAGGTG 59.317 55.000 8.52 2.51 45.21 4.00
500 524 0.036671 GGTCAGTAAACCGGTGGAGG 60.037 60.000 8.52 0.00 37.30 4.30
502 526 0.763604 TGGGTCAGTAAACCGGTGGA 60.764 55.000 8.52 0.00 40.46 4.02
505 529 1.125711 AGCTGGGTCAGTAAACCGGT 61.126 55.000 0.00 0.00 40.46 5.28
507 531 0.736325 CGAGCTGGGTCAGTAAACCG 60.736 60.000 0.00 0.00 40.46 4.44
508 532 0.320697 ACGAGCTGGGTCAGTAAACC 59.679 55.000 0.00 0.00 38.69 3.27
509 533 1.711206 GACGAGCTGGGTCAGTAAAC 58.289 55.000 9.13 0.00 34.56 2.01
510 534 0.242825 CGACGAGCTGGGTCAGTAAA 59.757 55.000 13.30 0.00 34.04 2.01
512 536 2.697761 GCGACGAGCTGGGTCAGTA 61.698 63.158 13.30 0.00 44.04 2.74
513 537 4.057428 GCGACGAGCTGGGTCAGT 62.057 66.667 13.30 0.00 44.04 3.41
554 585 2.420568 GGTGGTATCCGTGGCGAGA 61.421 63.158 0.00 0.00 0.00 4.04
555 586 2.106332 GGTGGTATCCGTGGCGAG 59.894 66.667 0.00 0.00 0.00 5.03
556 587 3.463585 GGGTGGTATCCGTGGCGA 61.464 66.667 0.00 0.00 0.00 5.54
558 589 2.124860 GTGGGTGGTATCCGTGGC 60.125 66.667 0.00 0.00 0.00 5.01
559 590 2.587889 GGTGGGTGGTATCCGTGG 59.412 66.667 0.00 0.00 0.00 4.94
560 591 2.185867 CGGTGGGTGGTATCCGTG 59.814 66.667 0.00 0.00 38.45 4.94
561 592 3.078836 CCGGTGGGTGGTATCCGT 61.079 66.667 0.00 0.00 41.17 4.69
562 593 4.540735 GCCGGTGGGTGGTATCCG 62.541 72.222 1.90 0.00 42.22 4.18
563 594 4.185286 GGCCGGTGGGTGGTATCC 62.185 72.222 1.90 0.00 34.97 2.59
564 595 3.400599 CTGGCCGGTGGGTGGTATC 62.401 68.421 2.29 0.00 34.97 2.24
565 596 3.407967 CTGGCCGGTGGGTGGTAT 61.408 66.667 2.29 0.00 34.97 2.73
577 608 3.815396 GCTTGCTTACGGCTGGCC 61.815 66.667 0.00 0.00 42.39 5.36
578 609 2.533391 CTTGCTTGCTTACGGCTGGC 62.533 60.000 0.00 0.00 42.39 4.85
579 610 1.237285 ACTTGCTTGCTTACGGCTGG 61.237 55.000 0.00 0.00 42.39 4.85
603 634 6.308041 CACGAAGAGATGATTAAACGAGTGAA 59.692 38.462 0.00 0.00 0.00 3.18
609 640 6.575083 ATGACACGAAGAGATGATTAAACG 57.425 37.500 0.00 0.00 0.00 3.60
616 647 5.588958 AGATGAATGACACGAAGAGATGA 57.411 39.130 0.00 0.00 0.00 2.92
622 653 6.246449 CAAAAGCTAGATGAATGACACGAAG 58.754 40.000 0.00 0.00 0.00 3.79
658 691 7.555195 AGAGAAGAACATGAATGATGTATGCAA 59.445 33.333 0.00 0.00 45.12 4.08
680 713 4.164030 TGGCCAAATCTACATAGCAAGAGA 59.836 41.667 0.61 0.00 0.00 3.10
730 966 0.611896 CCAGGAGAAACCGCCCAATT 60.612 55.000 0.00 0.00 44.74 2.32
738 974 2.911484 CTATGAGCACCAGGAGAAACC 58.089 52.381 0.00 0.00 39.35 3.27
787 1023 0.175073 CGTAGTAAGTGGAGGTGGCC 59.825 60.000 0.00 0.00 0.00 5.36
800 1036 2.609350 GTCCGTTTCATTGCCGTAGTA 58.391 47.619 0.00 0.00 0.00 1.82
803 1039 1.015085 CGGTCCGTTTCATTGCCGTA 61.015 55.000 2.08 0.00 35.11 4.02
804 1040 2.322081 CGGTCCGTTTCATTGCCGT 61.322 57.895 2.08 0.00 35.11 5.68
805 1041 2.478746 CGGTCCGTTTCATTGCCG 59.521 61.111 2.08 0.00 0.00 5.69
806 1042 2.874751 CCGGTCCGTTTCATTGCC 59.125 61.111 11.06 0.00 0.00 4.52
807 1043 2.178273 GCCGGTCCGTTTCATTGC 59.822 61.111 11.06 0.15 0.00 3.56
808 1044 0.673644 AGAGCCGGTCCGTTTCATTG 60.674 55.000 11.06 0.00 0.00 2.82
987 1223 0.469070 GAGCCATGGAGAGATGTGCT 59.531 55.000 18.40 0.65 34.50 4.40
1044 1280 2.123589 TCTCCCCTGTGAAAGTGTTCA 58.876 47.619 0.00 0.00 41.57 3.18
1152 1419 3.319122 GGCCATCCAGACCATTGTTATTC 59.681 47.826 0.00 0.00 0.00 1.75
1155 1422 1.638070 TGGCCATCCAGACCATTGTTA 59.362 47.619 0.00 0.00 37.47 2.41
1289 1556 3.251004 GCCCTGGATAAGATTAAACGCAG 59.749 47.826 0.00 0.00 0.00 5.18
1301 1568 1.846261 GGGATGCTGCCCTGGATAA 59.154 57.895 7.15 0.00 45.12 1.75
1334 1601 2.521958 AATCTCCAGCCCGTCCAACG 62.522 60.000 0.00 0.00 42.11 4.10
1340 1607 3.041946 AGATAAAGAATCTCCAGCCCGT 58.958 45.455 0.00 0.00 41.32 5.28
1758 2025 1.250840 AATTTGGCGCCTGACCTTCC 61.251 55.000 29.70 0.00 0.00 3.46
1848 2115 0.811281 GAAAGTTTGCTATGCCGGCT 59.189 50.000 29.70 15.76 0.00 5.52
1849 2116 0.179137 GGAAAGTTTGCTATGCCGGC 60.179 55.000 22.73 22.73 0.00 6.13
1884 2151 3.277142 AATCGGTTGTAGTCCAATCCC 57.723 47.619 0.00 0.00 35.02 3.85
1899 2166 2.624636 GGTACCACACCTGTAAATCGG 58.375 52.381 7.15 0.00 44.79 4.18
1989 2256 2.238084 AATTGGAAAGGGAGGAAGGC 57.762 50.000 0.00 0.00 0.00 4.35
2076 2343 3.668656 GTGTTGCAAGCGATTTAAGGTTC 59.331 43.478 0.00 0.00 0.00 3.62
2093 2360 4.481930 TTATTGGAAACGCTCAGTGTTG 57.518 40.909 3.86 0.00 36.34 3.33
2130 2397 2.957312 GCTGAAGATCCCCTCTGGTACT 60.957 54.545 0.00 0.00 33.29 2.73
2233 2500 4.936396 CTGAAAGCAACAAAATCACGAC 57.064 40.909 0.00 0.00 0.00 4.34
2301 2568 3.503748 CCAACTCAATGTCCTCCAAACTC 59.496 47.826 0.00 0.00 0.00 3.01
2338 2605 1.106285 GAAGTGGGGATGTTGCCATC 58.894 55.000 0.00 0.00 45.65 3.51
2422 2689 1.420430 AGGTTCCCAAGAGACGTTGA 58.580 50.000 0.00 0.00 0.00 3.18
2549 2816 2.133641 GCTGCCCCACCACAAAGTT 61.134 57.895 0.00 0.00 0.00 2.66
2550 2817 2.521708 GCTGCCCCACCACAAAGT 60.522 61.111 0.00 0.00 0.00 2.66
2566 2833 1.741770 CAGGCAGGTGTAAGTCCGC 60.742 63.158 0.00 0.00 0.00 5.54
2588 2855 9.140286 CAGATAGATTTGAAGACGTAACAGAAA 57.860 33.333 0.00 0.00 0.00 2.52
2680 2947 6.036735 TGCCAAAGTAATACAAAGATCGCTAC 59.963 38.462 0.00 0.00 0.00 3.58
2682 2949 4.941263 TGCCAAAGTAATACAAAGATCGCT 59.059 37.500 0.00 0.00 0.00 4.93
2684 2951 6.238211 CCTCTGCCAAAGTAATACAAAGATCG 60.238 42.308 0.00 0.00 0.00 3.69
2892 3159 4.640647 CCCCTTGTCTCTAAGCAAAATACC 59.359 45.833 0.00 0.00 0.00 2.73
3294 3567 5.624159 TCAAAGGATGATGACATGGGATAC 58.376 41.667 0.00 0.00 36.82 2.24
3475 3781 2.069273 CAGCGGTAGAAACTTGACCAG 58.931 52.381 0.00 0.00 32.39 4.00
3542 3848 3.882131 GCCATCTGTTGGGCTCTTA 57.118 52.632 6.87 0.00 46.55 2.10
3635 3946 6.517864 GCAAAGGTCCAACTCTTGTACTAGTA 60.518 42.308 0.00 0.00 0.00 1.82
3639 3950 3.477530 GCAAAGGTCCAACTCTTGTACT 58.522 45.455 0.00 0.00 0.00 2.73
3732 4050 3.254093 TCACTTGGAGAGGACTTGGTA 57.746 47.619 0.00 0.00 0.00 3.25
4406 4724 5.907391 GTACATTAAGTATGGCATCGTTTGC 59.093 40.000 1.65 4.80 41.97 3.68
4407 4725 7.010697 TGTACATTAAGTATGGCATCGTTTG 57.989 36.000 1.65 0.00 38.64 2.93
4408 4726 6.260050 CCTGTACATTAAGTATGGCATCGTTT 59.740 38.462 1.65 0.00 38.64 3.60
4409 4727 5.758296 CCTGTACATTAAGTATGGCATCGTT 59.242 40.000 1.65 0.93 38.64 3.85
4410 4728 5.163343 ACCTGTACATTAAGTATGGCATCGT 60.163 40.000 1.65 0.00 38.64 3.73
4411 4729 5.297547 ACCTGTACATTAAGTATGGCATCG 58.702 41.667 1.65 0.00 38.64 3.84
4432 4845 3.301274 AGAGTACATTGGGAGCTCTACC 58.699 50.000 14.64 7.93 35.09 3.18
4433 4846 4.211920 AGAGAGTACATTGGGAGCTCTAC 58.788 47.826 14.64 7.05 36.75 2.59
4443 4856 5.885230 TTGAATGGCAAGAGAGTACATTG 57.115 39.130 0.00 0.00 32.42 2.82
4474 4887 0.458889 TCGTAAAACCAGATCCGGCG 60.459 55.000 0.00 0.00 0.00 6.46
4492 4905 2.209838 TGCGTATGCTCTTAGCTGTC 57.790 50.000 8.69 0.00 42.97 3.51
4508 4927 5.572211 AGCATTATGACTTACACATTTGCG 58.428 37.500 0.00 0.00 38.94 4.85
4561 4983 0.712380 ATGTTTCATTGCCCTCCCCT 59.288 50.000 0.00 0.00 0.00 4.79
4577 4999 3.688414 GCAAGGCCCTACAAATCCTATGT 60.688 47.826 0.00 0.00 34.81 2.29


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

AutoCloner maintained by Alex Coulton.