Multiple sequence alignment - TraesCS6A01G242100

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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 TraesCS6A01G242100 chr6A 100.000 4700 0 0 1 4700 453872302 453867603 0.000000e+00 8680
1 TraesCS6A01G242100 chr6A 95.833 312 13 0 4120 4431 23376965 23377276 5.430000e-139 505
2 TraesCS6A01G242100 chr6A 95.489 266 12 0 4435 4700 23377311 23377576 4.350000e-115 425
3 TraesCS6A01G242100 chr6B 93.514 3500 149 37 599 4068 508818966 508822417 0.000000e+00 5134
4 TraesCS6A01G242100 chr6B 80.142 141 28 0 1997 2137 16554555 16554415 6.430000e-19 106
5 TraesCS6A01G242100 chr6D 93.857 2637 103 26 599 3199 315985864 315983251 0.000000e+00 3917
6 TraesCS6A01G242100 chr6D 95.726 889 24 3 3247 4123 315983255 315982369 0.000000e+00 1419
7 TraesCS6A01G242100 chr6D 93.585 530 29 4 1 526 107938159 107938687 0.000000e+00 785
8 TraesCS6A01G242100 chr3D 93.482 537 31 3 1 533 135754235 135753699 0.000000e+00 795
9 TraesCS6A01G242100 chr7B 93.284 536 33 2 1 533 150053482 150052947 0.000000e+00 787
10 TraesCS6A01G242100 chr7B 89.425 435 42 2 2082 2512 715318874 715319308 3.200000e-151 545
11 TraesCS6A01G242100 chr7B 93.151 73 4 1 2750 2822 715319312 715319383 6.430000e-19 106
12 TraesCS6A01G242100 chr4D 93.045 532 32 4 1 529 487284862 487284333 0.000000e+00 773
13 TraesCS6A01G242100 chr7A 92.830 530 34 3 1 526 629345350 629345879 0.000000e+00 765
14 TraesCS6A01G242100 chr7A 80.676 207 28 6 2215 2417 689329215 689329413 2.930000e-32 150
15 TraesCS6A01G242100 chr5D 92.537 536 35 3 1 533 272143299 272142766 0.000000e+00 763
16 TraesCS6A01G242100 chr1D 92.669 532 35 3 1 529 201527919 201527389 0.000000e+00 763
17 TraesCS6A01G242100 chr1D 92.817 529 31 6 1 526 299572757 299573281 0.000000e+00 760
18 TraesCS6A01G242100 chr1D 96.519 316 9 2 4120 4434 425579398 425579084 5.390000e-144 521
19 TraesCS6A01G242100 chr2D 92.830 530 30 6 3 529 193270654 193270130 0.000000e+00 761
20 TraesCS6A01G242100 chr5B 90.345 435 38 2 2082 2512 154054242 154054676 6.830000e-158 568
21 TraesCS6A01G242100 chr5B 89.885 435 40 2 2082 2512 154015550 154015116 1.480000e-154 556
22 TraesCS6A01G242100 chr5B 93.151 73 4 1 2750 2822 154054680 154054751 6.430000e-19 106
23 TraesCS6A01G242100 chr5B 92.857 70 4 1 2753 2822 154015109 154015041 2.990000e-17 100
24 TraesCS6A01G242100 chrUn 96.474 312 11 0 4120 4431 341542269 341541958 2.510000e-142 516
25 TraesCS6A01G242100 chrUn 96.474 312 11 0 4120 4431 341589955 341589644 2.510000e-142 516
26 TraesCS6A01G242100 chrUn 93.910 312 18 1 4120 4431 365012742 365013052 1.980000e-128 470
27 TraesCS6A01G242100 chrUn 94.737 266 14 0 4435 4700 341541923 341541658 9.410000e-112 414
28 TraesCS6A01G242100 chrUn 94.737 266 14 0 4435 4700 341589609 341589344 9.410000e-112 414
29 TraesCS6A01G242100 chrUn 92.776 263 19 0 4435 4697 365013087 365013349 9.540000e-102 381
30 TraesCS6A01G242100 chrUn 92.776 263 19 0 4435 4697 406529091 406529353 9.540000e-102 381
31 TraesCS6A01G242100 chrUn 92.481 266 20 0 4435 4700 468825464 468825199 9.540000e-102 381
32 TraesCS6A01G242100 chrUn 97.207 179 4 1 4253 4431 406528879 406529056 7.640000e-78 302
33 TraesCS6A01G242100 chr2A 96.474 312 11 0 4120 4431 9679866 9680177 2.510000e-142 516
34 TraesCS6A01G242100 chr2A 96.474 312 11 0 4120 4431 10415059 10414748 2.510000e-142 516
35 TraesCS6A01G242100 chr2A 94.737 266 14 0 4435 4700 9680212 9680477 9.410000e-112 414
36 TraesCS6A01G242100 chr2A 94.737 266 14 0 4435 4700 10414713 10414448 9.410000e-112 414
37 TraesCS6A01G242100 chr1B 90.415 313 30 0 4119 4431 539526393 539526705 3.380000e-111 412
38 TraesCS6A01G242100 chr1B 90.875 263 23 1 4435 4697 539526740 539527001 7.480000e-93 351
39 TraesCS6A01G242100 chr3B 81.560 141 26 0 1997 2137 16704528 16704388 2.970000e-22 117


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 TraesCS6A01G242100 chr6A 453867603 453872302 4699 True 8680.0 8680 100.0000 1 4700 1 chr6A.!!$R1 4699
1 TraesCS6A01G242100 chr6A 23376965 23377576 611 False 465.0 505 95.6610 4120 4700 2 chr6A.!!$F1 580
2 TraesCS6A01G242100 chr6B 508818966 508822417 3451 False 5134.0 5134 93.5140 599 4068 1 chr6B.!!$F1 3469
3 TraesCS6A01G242100 chr6D 315982369 315985864 3495 True 2668.0 3917 94.7915 599 4123 2 chr6D.!!$R1 3524
4 TraesCS6A01G242100 chr6D 107938159 107938687 528 False 785.0 785 93.5850 1 526 1 chr6D.!!$F1 525
5 TraesCS6A01G242100 chr3D 135753699 135754235 536 True 795.0 795 93.4820 1 533 1 chr3D.!!$R1 532
6 TraesCS6A01G242100 chr7B 150052947 150053482 535 True 787.0 787 93.2840 1 533 1 chr7B.!!$R1 532
7 TraesCS6A01G242100 chr7B 715318874 715319383 509 False 325.5 545 91.2880 2082 2822 2 chr7B.!!$F1 740
8 TraesCS6A01G242100 chr4D 487284333 487284862 529 True 773.0 773 93.0450 1 529 1 chr4D.!!$R1 528
9 TraesCS6A01G242100 chr7A 629345350 629345879 529 False 765.0 765 92.8300 1 526 1 chr7A.!!$F1 525
10 TraesCS6A01G242100 chr5D 272142766 272143299 533 True 763.0 763 92.5370 1 533 1 chr5D.!!$R1 532
11 TraesCS6A01G242100 chr1D 201527389 201527919 530 True 763.0 763 92.6690 1 529 1 chr1D.!!$R1 528
12 TraesCS6A01G242100 chr1D 299572757 299573281 524 False 760.0 760 92.8170 1 526 1 chr1D.!!$F1 525
13 TraesCS6A01G242100 chr2D 193270130 193270654 524 True 761.0 761 92.8300 3 529 1 chr2D.!!$R1 526
14 TraesCS6A01G242100 chr5B 154054242 154054751 509 False 337.0 568 91.7480 2082 2822 2 chr5B.!!$F1 740
15 TraesCS6A01G242100 chr5B 154015041 154015550 509 True 328.0 556 91.3710 2082 2822 2 chr5B.!!$R1 740
16 TraesCS6A01G242100 chrUn 341541658 341542269 611 True 465.0 516 95.6055 4120 4700 2 chrUn.!!$R2 580
17 TraesCS6A01G242100 chrUn 341589344 341589955 611 True 465.0 516 95.6055 4120 4700 2 chrUn.!!$R3 580
18 TraesCS6A01G242100 chrUn 365012742 365013349 607 False 425.5 470 93.3430 4120 4697 2 chrUn.!!$F1 577
19 TraesCS6A01G242100 chr2A 9679866 9680477 611 False 465.0 516 95.6055 4120 4700 2 chr2A.!!$F1 580
20 TraesCS6A01G242100 chr2A 10414448 10415059 611 True 465.0 516 95.6055 4120 4700 2 chr2A.!!$R1 580
21 TraesCS6A01G242100 chr1B 539526393 539527001 608 False 381.5 412 90.6450 4119 4697 2 chr1B.!!$F1 578

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
862 883 0.042131 TCCTTTTCCTCTCCCGCCTA 59.958 55.0 0.00 0.0 0.00 3.93 F
1617 1664 0.179051 TTTGCCTTTTGCCTTGCCTG 60.179 50.0 0.00 0.0 40.16 4.85 F
1911 1958 0.679640 CTTTATGAAGTGGGGGCGCA 60.680 55.0 10.83 0.0 0.00 6.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1903 1950 0.955919 GCAAGATATAGTGCGCCCCC 60.956 60.0 4.18 0.00 0.00 5.40 R
3453 3518 1.118838 TTTGTTCCAAACAGGCCCTG 58.881 50.0 9.83 9.83 43.27 4.45 R
3836 3902 0.758734 CATGAGAGCCCGGGTTATCA 59.241 55.0 32.84 32.84 0.00 2.15 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
114 115 3.994392 GTCTGTACGATCAAGGCTTTCAA 59.006 43.478 0.00 0.00 0.00 2.69
125 127 3.243359 AGGCTTTCAATTCAGGGTGAA 57.757 42.857 0.00 0.00 41.09 3.18
140 142 4.097741 CAGGGTGAAAATGTTGTGTCTGAA 59.902 41.667 0.00 0.00 0.00 3.02
162 164 1.904287 TGGAGTAGCGGCAACATTTT 58.096 45.000 1.45 0.00 0.00 1.82
167 169 2.161609 AGTAGCGGCAACATTTTAGCAC 59.838 45.455 1.45 0.00 0.00 4.40
242 244 7.554211 TGCAAAATGATTTGGTTGAGCATATA 58.446 30.769 0.00 0.00 44.93 0.86
247 249 5.704354 TGATTTGGTTGAGCATATATGGGT 58.296 37.500 14.51 1.14 0.00 4.51
256 258 5.939447 TGAGCATATATGGGTTCATGTTGA 58.061 37.500 14.51 0.00 34.96 3.18
354 357 8.756486 AAAACTATACTATTTATTTGGGCGGT 57.244 30.769 0.00 0.00 0.00 5.68
413 420 7.690228 ACAATATGTTGAATGCAAATCAATGC 58.310 30.769 17.93 9.36 41.35 3.56
463 474 1.669049 ATATGGGTCGACGCGTTGGA 61.669 55.000 29.22 17.35 0.00 3.53
533 544 2.415776 GACCCAAACGGACGAATAACA 58.584 47.619 0.00 0.00 34.64 2.41
534 545 3.004862 GACCCAAACGGACGAATAACAT 58.995 45.455 0.00 0.00 34.64 2.71
535 546 4.183101 GACCCAAACGGACGAATAACATA 58.817 43.478 0.00 0.00 34.64 2.29
536 547 4.577875 ACCCAAACGGACGAATAACATAA 58.422 39.130 0.00 0.00 34.64 1.90
537 548 5.002516 ACCCAAACGGACGAATAACATAAA 58.997 37.500 0.00 0.00 34.64 1.40
538 549 5.122711 ACCCAAACGGACGAATAACATAAAG 59.877 40.000 0.00 0.00 34.64 1.85
539 550 5.352016 CCCAAACGGACGAATAACATAAAGA 59.648 40.000 0.00 0.00 0.00 2.52
540 551 6.037830 CCCAAACGGACGAATAACATAAAGAT 59.962 38.462 0.00 0.00 0.00 2.40
541 552 7.414762 CCCAAACGGACGAATAACATAAAGATT 60.415 37.037 0.00 0.00 0.00 2.40
542 553 7.966204 CCAAACGGACGAATAACATAAAGATTT 59.034 33.333 0.00 0.00 0.00 2.17
543 554 8.785101 CAAACGGACGAATAACATAAAGATTTG 58.215 33.333 0.00 0.00 0.00 2.32
544 555 6.483687 ACGGACGAATAACATAAAGATTTGC 58.516 36.000 0.00 0.00 0.00 3.68
545 556 6.092944 ACGGACGAATAACATAAAGATTTGCA 59.907 34.615 0.00 0.00 0.00 4.08
546 557 7.132213 CGGACGAATAACATAAAGATTTGCAT 58.868 34.615 0.00 0.00 0.00 3.96
547 558 7.321271 CGGACGAATAACATAAAGATTTGCATC 59.679 37.037 0.00 0.00 0.00 3.91
548 559 8.345565 GGACGAATAACATAAAGATTTGCATCT 58.654 33.333 0.00 0.00 42.05 2.90
556 567 8.693542 ACATAAAGATTTGCATCTACAAAAGC 57.306 30.769 0.00 0.00 42.45 3.51
557 568 8.306038 ACATAAAGATTTGCATCTACAAAAGCA 58.694 29.630 0.00 0.00 42.45 3.91
558 569 9.309516 CATAAAGATTTGCATCTACAAAAGCAT 57.690 29.630 0.00 0.00 42.45 3.79
559 570 7.823149 AAAGATTTGCATCTACAAAAGCATC 57.177 32.000 0.00 0.00 42.45 3.91
560 571 5.899299 AGATTTGCATCTACAAAAGCATCC 58.101 37.500 0.00 0.00 42.45 3.51
561 572 5.655532 AGATTTGCATCTACAAAAGCATCCT 59.344 36.000 0.00 0.00 42.45 3.24
562 573 4.707030 TTGCATCTACAAAAGCATCCTG 57.293 40.909 0.00 0.00 36.80 3.86
563 574 3.689347 TGCATCTACAAAAGCATCCTGT 58.311 40.909 0.00 0.00 31.05 4.00
564 575 4.081406 TGCATCTACAAAAGCATCCTGTT 58.919 39.130 0.00 0.00 31.05 3.16
565 576 4.523943 TGCATCTACAAAAGCATCCTGTTT 59.476 37.500 0.00 0.00 31.05 2.83
566 577 5.709631 TGCATCTACAAAAGCATCCTGTTTA 59.290 36.000 0.00 0.00 31.05 2.01
567 578 6.377996 TGCATCTACAAAAGCATCCTGTTTAT 59.622 34.615 0.00 0.00 31.05 1.40
568 579 7.555914 TGCATCTACAAAAGCATCCTGTTTATA 59.444 33.333 0.00 0.00 31.05 0.98
569 580 7.857885 GCATCTACAAAAGCATCCTGTTTATAC 59.142 37.037 0.00 0.00 0.00 1.47
570 581 7.534085 TCTACAAAAGCATCCTGTTTATACG 57.466 36.000 0.00 0.00 0.00 3.06
571 582 4.981794 ACAAAAGCATCCTGTTTATACGC 58.018 39.130 0.00 0.00 0.00 4.42
572 583 4.142469 ACAAAAGCATCCTGTTTATACGCC 60.142 41.667 0.00 0.00 0.00 5.68
573 584 2.256117 AGCATCCTGTTTATACGCCC 57.744 50.000 0.00 0.00 0.00 6.13
574 585 1.768870 AGCATCCTGTTTATACGCCCT 59.231 47.619 0.00 0.00 0.00 5.19
575 586 2.172717 AGCATCCTGTTTATACGCCCTT 59.827 45.455 0.00 0.00 0.00 3.95
576 587 3.389983 AGCATCCTGTTTATACGCCCTTA 59.610 43.478 0.00 0.00 0.00 2.69
577 588 4.131596 GCATCCTGTTTATACGCCCTTAA 58.868 43.478 0.00 0.00 0.00 1.85
578 589 4.577283 GCATCCTGTTTATACGCCCTTAAA 59.423 41.667 0.00 0.00 0.00 1.52
579 590 5.066764 GCATCCTGTTTATACGCCCTTAAAA 59.933 40.000 0.00 0.00 0.00 1.52
580 591 6.404954 GCATCCTGTTTATACGCCCTTAAAAA 60.405 38.462 0.00 0.00 0.00 1.94
624 635 5.065914 CACAAATACCCCGAATCAGATCAT 58.934 41.667 0.00 0.00 0.00 2.45
855 876 1.562008 CCCTTCCCTCCTTTTCCTCTC 59.438 57.143 0.00 0.00 0.00 3.20
857 878 1.562008 CTTCCCTCCTTTTCCTCTCCC 59.438 57.143 0.00 0.00 0.00 4.30
862 883 0.042131 TCCTTTTCCTCTCCCGCCTA 59.958 55.000 0.00 0.00 0.00 3.93
864 885 1.196012 CTTTTCCTCTCCCGCCTACT 58.804 55.000 0.00 0.00 0.00 2.57
866 887 0.902531 TTTCCTCTCCCGCCTACTTG 59.097 55.000 0.00 0.00 0.00 3.16
873 894 2.421739 CCGCCTACTTGGGATCCG 59.578 66.667 5.45 0.00 36.00 4.18
874 895 2.280186 CGCCTACTTGGGATCCGC 60.280 66.667 5.45 0.14 36.00 5.54
875 896 2.797278 CGCCTACTTGGGATCCGCT 61.797 63.158 5.45 0.00 36.00 5.52
876 897 1.069935 GCCTACTTGGGATCCGCTC 59.930 63.158 5.45 0.00 36.00 5.03
877 898 1.364171 CCTACTTGGGATCCGCTCG 59.636 63.158 5.45 0.00 0.00 5.03
878 899 1.300233 CTACTTGGGATCCGCTCGC 60.300 63.158 5.45 0.00 37.34 5.03
879 900 3.133767 TACTTGGGATCCGCTCGCG 62.134 63.158 5.45 0.00 39.62 5.87
1112 1133 1.375326 GTTGGCCCTTCTCCGACTT 59.625 57.895 0.00 0.00 35.55 3.01
1144 1188 1.334869 CTTCGCCAATGGATGCTTACC 59.665 52.381 2.05 0.00 0.00 2.85
1155 1199 2.480759 GGATGCTTACCTTACGCTTCGA 60.481 50.000 0.00 0.00 0.00 3.71
1314 1358 1.794714 TAGCTTAGCTCCCCCTTCAG 58.205 55.000 11.09 0.00 40.44 3.02
1331 1375 2.278245 TCAGTCATTTGATCCCCAGGT 58.722 47.619 0.00 0.00 0.00 4.00
1336 1380 1.207811 CATTTGATCCCCAGGTTTGCC 59.792 52.381 0.00 0.00 0.00 4.52
1355 1399 1.808945 CCTCTCTGGTGTCAATGTTGC 59.191 52.381 0.00 0.00 0.00 4.17
1358 1402 1.081242 CTGGTGTCAATGTTGCGCC 60.081 57.895 4.18 10.68 36.26 6.53
1382 1426 1.076533 TTTGGAGAACGATCGCGAGC 61.077 55.000 15.67 15.67 41.64 5.03
1416 1463 1.945354 CTTAGCGTCCCCGAAGCTCA 61.945 60.000 5.35 0.00 43.16 4.26
1427 1474 1.391485 CCGAAGCTCATCTCGTGTTTG 59.609 52.381 4.94 0.00 0.00 2.93
1477 1524 7.992180 GCTTTATGCACTTTTATGCTTACAT 57.008 32.000 0.00 0.00 46.28 2.29
1479 1526 8.958043 GCTTTATGCACTTTTATGCTTACATAC 58.042 33.333 0.00 0.00 46.28 2.39
1494 1541 9.215771 ATGCTTACATACTGCAGTGCAACTAAC 62.216 40.741 29.57 12.52 39.45 2.34
1517 1564 3.888323 TGGCTTTCATGCTACTTTGAACA 59.112 39.130 0.00 0.00 31.87 3.18
1518 1565 4.229876 GGCTTTCATGCTACTTTGAACAC 58.770 43.478 0.00 0.00 31.87 3.32
1617 1664 0.179051 TTTGCCTTTTGCCTTGCCTG 60.179 50.000 0.00 0.00 40.16 4.85
1700 1747 2.366916 ACATAGAGCATCAGGTACCTGC 59.633 50.000 33.39 24.12 43.31 4.85
1787 1834 0.756294 TTCTGTTCAGAAGTGGGCGA 59.244 50.000 10.67 0.00 0.00 5.54
1824 1871 7.031975 GCCAAATTTCCTCAACTAATCTCTTG 58.968 38.462 0.00 0.00 0.00 3.02
1886 1933 7.593653 AGTTAGGTAGTTCTGGTAGTCCATAT 58.406 38.462 0.00 0.00 43.43 1.78
1911 1958 0.679640 CTTTATGAAGTGGGGGCGCA 60.680 55.000 10.83 0.00 0.00 6.09
1965 2012 9.983024 TGACCCTTCATAAATTGGAACTATTTA 57.017 29.630 0.00 0.00 33.40 1.40
2330 2377 9.987272 TGTATCCTATGATTCATTTAGTCACTG 57.013 33.333 4.14 0.00 32.18 3.66
2382 2429 8.418662 TCTTCACTCTTTAGCAGTTAACACTTA 58.581 33.333 8.61 0.00 0.00 2.24
2452 2503 5.894807 GTGCTAAATATGAAATGTGGCACT 58.105 37.500 19.83 0.00 42.51 4.40
2567 2618 8.543774 CAGTAGACTAAATAAAGCGAATCCAAG 58.456 37.037 0.00 0.00 0.00 3.61
2612 2663 6.303839 TGCAGAAATAGTCCAGTTTTACCTT 58.696 36.000 0.00 0.00 0.00 3.50
2621 2672 6.745116 AGTCCAGTTTTACCTTTAATGTTGC 58.255 36.000 0.00 0.00 0.00 4.17
2658 2709 7.123847 ACTGAAACAGTAATCTCGTACCCTTAT 59.876 37.037 2.43 0.00 43.46 1.73
2659 2710 7.844009 TGAAACAGTAATCTCGTACCCTTATT 58.156 34.615 0.00 0.00 0.00 1.40
2660 2711 8.316214 TGAAACAGTAATCTCGTACCCTTATTT 58.684 33.333 0.00 0.00 0.00 1.40
2661 2712 9.159364 GAAACAGTAATCTCGTACCCTTATTTT 57.841 33.333 0.00 0.00 0.00 1.82
2693 2749 6.682423 TTATGGTCATCACACTAAGCAATG 57.318 37.500 0.00 0.00 0.00 2.82
2697 2753 4.348656 GTCATCACACTAAGCAATGCATG 58.651 43.478 8.35 2.59 0.00 4.06
2927 2983 4.676471 CCATTTTCATGTTGAACTGACACG 59.324 41.667 0.00 0.00 35.89 4.49
3030 3086 8.409358 TTTCTTTCCTCTTTCCTTTTATGGAG 57.591 34.615 0.00 0.00 37.43 3.86
3061 3117 4.677584 AGAATCTACAAGAGCTGCTTACG 58.322 43.478 2.53 0.00 34.31 3.18
3223 3288 8.408601 CAAAGCCAGCATATCATACTTTTTAGT 58.591 33.333 0.00 0.00 0.00 2.24
3224 3289 8.525290 AAGCCAGCATATCATACTTTTTAGTT 57.475 30.769 0.00 0.00 0.00 2.24
3225 3290 9.627123 AAGCCAGCATATCATACTTTTTAGTTA 57.373 29.630 0.00 0.00 0.00 2.24
3226 3291 9.799106 AGCCAGCATATCATACTTTTTAGTTAT 57.201 29.630 0.00 0.00 0.00 1.89
3272 3337 8.300286 CACCACATACTACTAATACTCCTGATG 58.700 40.741 0.00 0.00 0.00 3.07
3410 3475 4.581824 ACATGGACTTCAATGTATGATGCC 59.418 41.667 0.00 0.00 38.03 4.40
3411 3476 3.205338 TGGACTTCAATGTATGATGCCG 58.795 45.455 0.00 0.00 38.03 5.69
3418 3483 4.377021 TCAATGTATGATGCCGTTCTACC 58.623 43.478 0.00 0.00 31.50 3.18
3440 3505 4.222588 CCCAAATTCTTGCAACCAGGAATA 59.777 41.667 10.91 0.00 44.19 1.75
3441 3506 5.104817 CCCAAATTCTTGCAACCAGGAATAT 60.105 40.000 10.91 1.90 44.19 1.28
3449 3514 2.959030 GCAACCAGGAATATTTCTCCCC 59.041 50.000 0.00 0.00 32.95 4.81
3453 3518 6.241645 CAACCAGGAATATTTCTCCCCTATC 58.758 44.000 0.00 0.00 32.95 2.08
3495 3560 2.878406 ACCGACACTTCACCAAGAAATG 59.122 45.455 0.00 0.00 39.29 2.32
3546 3611 7.043192 CCTTAACACTTTTTGAACAGCTTCATG 60.043 37.037 0.00 0.00 36.26 3.07
3590 3655 7.093465 CCTTCCTGACCTGATTACACTACTAAA 60.093 40.741 0.00 0.00 0.00 1.85
3621 3687 1.393539 GTCATGAAATCCACACGACGG 59.606 52.381 0.00 0.00 0.00 4.79
3782 3848 2.555199 CAGCCAGTGTCCTTATACAGC 58.445 52.381 0.00 0.00 0.00 4.40
3820 3886 3.780294 TGTAGATGCCCCTGTATCTTGTT 59.220 43.478 0.00 0.00 40.56 2.83
3836 3902 4.952460 TCTTGTTGCGTTTTAGGTACTCT 58.048 39.130 0.00 0.00 41.75 3.24
3889 3955 0.681175 GGTTTTCTTGGCCAGCATGT 59.319 50.000 5.11 0.00 0.00 3.21
4129 4207 5.865552 CGATGTTTTCTTCATTGCTTTCCAT 59.134 36.000 0.00 0.00 0.00 3.41
4141 4219 3.509442 TGCTTTCCATGACAGGGATTTT 58.491 40.909 10.13 0.00 33.63 1.82
4276 4354 5.578727 TGATAAAATGGCCGGAAAAATTTCG 59.421 36.000 5.05 0.00 38.06 3.46
4504 4613 4.098349 TCAAAAACATTGACTGCTTCAGCT 59.902 37.500 0.00 0.00 42.66 4.24
4615 4724 0.451135 GCAGTTGTTTACGAGCTGCG 60.451 55.000 0.00 0.00 42.16 5.18
4624 4733 2.860690 TACGAGCTGCGCGTCGATTT 62.861 55.000 32.89 11.84 46.04 2.17
4684 4793 3.408853 GGCTAAACGGGGAGGCCT 61.409 66.667 3.86 3.86 39.68 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
114 115 4.895297 AGACACAACATTTTCACCCTGAAT 59.105 37.500 0.00 0.00 36.11 2.57
125 127 4.889409 ACTCCATGTTCAGACACAACATTT 59.111 37.500 0.00 0.00 41.58 2.32
140 142 0.253044 ATGTTGCCGCTACTCCATGT 59.747 50.000 6.52 0.00 0.00 3.21
162 164 6.936335 TCTTCATGAAATTGAGTGAAGTGCTA 59.064 34.615 9.88 5.22 44.78 3.49
242 244 2.956132 TGGTTGTCAACATGAACCCAT 58.044 42.857 17.29 0.00 38.75 4.00
247 249 8.806429 ATACATCTATTGGTTGTCAACATGAA 57.194 30.769 17.29 7.18 38.31 2.57
413 420 1.446618 GGCTGGCCGCTCAATTTTG 60.447 57.895 17.07 0.00 39.13 2.44
463 474 2.473664 GATATAGGTCGGCAGCGCGT 62.474 60.000 8.43 0.00 0.00 6.01
477 488 3.199677 CGTCCGCCCTGTTTTTGATATA 58.800 45.455 0.00 0.00 0.00 0.86
530 541 9.143631 GCTTTTGTAGATGCAAATCTTTATGTT 57.856 29.630 0.00 0.00 38.05 2.71
531 542 8.306038 TGCTTTTGTAGATGCAAATCTTTATGT 58.694 29.630 0.00 0.00 38.05 2.29
532 543 8.692110 TGCTTTTGTAGATGCAAATCTTTATG 57.308 30.769 0.00 0.00 38.05 1.90
533 544 9.525409 GATGCTTTTGTAGATGCAAATCTTTAT 57.475 29.630 0.00 0.00 38.05 1.40
534 545 7.975616 GGATGCTTTTGTAGATGCAAATCTTTA 59.024 33.333 0.00 0.00 38.05 1.85
535 546 6.815142 GGATGCTTTTGTAGATGCAAATCTTT 59.185 34.615 0.00 0.00 38.05 2.52
536 547 6.154021 AGGATGCTTTTGTAGATGCAAATCTT 59.846 34.615 0.00 0.00 38.05 2.40
537 548 5.655532 AGGATGCTTTTGTAGATGCAAATCT 59.344 36.000 0.00 0.00 38.05 2.40
538 549 5.747197 CAGGATGCTTTTGTAGATGCAAATC 59.253 40.000 0.00 0.00 38.05 2.17
539 550 5.186409 ACAGGATGCTTTTGTAGATGCAAAT 59.814 36.000 0.00 0.00 42.53 2.32
540 551 4.523943 ACAGGATGCTTTTGTAGATGCAAA 59.476 37.500 0.00 0.00 42.53 3.68
541 552 4.081406 ACAGGATGCTTTTGTAGATGCAA 58.919 39.130 0.00 0.00 42.53 4.08
542 553 3.689347 ACAGGATGCTTTTGTAGATGCA 58.311 40.909 0.00 0.00 42.53 3.96
543 554 4.708726 AACAGGATGCTTTTGTAGATGC 57.291 40.909 0.00 0.00 42.53 3.91
544 555 8.064222 CGTATAAACAGGATGCTTTTGTAGATG 58.936 37.037 0.00 0.00 42.53 2.90
545 556 7.254795 GCGTATAAACAGGATGCTTTTGTAGAT 60.255 37.037 0.00 0.00 42.53 1.98
546 557 6.036735 GCGTATAAACAGGATGCTTTTGTAGA 59.963 38.462 0.00 0.00 42.53 2.59
547 558 6.192360 GCGTATAAACAGGATGCTTTTGTAG 58.808 40.000 0.00 0.00 42.53 2.74
548 559 5.065474 GGCGTATAAACAGGATGCTTTTGTA 59.935 40.000 0.00 0.00 42.53 2.41
549 560 4.142469 GGCGTATAAACAGGATGCTTTTGT 60.142 41.667 0.00 0.00 42.53 2.83
550 561 4.351192 GGCGTATAAACAGGATGCTTTTG 58.649 43.478 0.00 0.00 42.53 2.44
551 562 3.380320 GGGCGTATAAACAGGATGCTTTT 59.620 43.478 0.00 0.00 42.53 2.27
552 563 2.949644 GGGCGTATAAACAGGATGCTTT 59.050 45.455 0.00 0.00 42.53 3.51
553 564 2.172717 AGGGCGTATAAACAGGATGCTT 59.827 45.455 0.00 0.00 42.53 3.91
554 565 1.768870 AGGGCGTATAAACAGGATGCT 59.231 47.619 0.00 0.00 42.53 3.79
555 566 2.256117 AGGGCGTATAAACAGGATGC 57.744 50.000 0.00 0.00 42.53 3.91
556 567 6.687081 TTTTAAGGGCGTATAAACAGGATG 57.313 37.500 0.00 0.00 46.00 3.51
584 595 9.216117 GGTATTTGTGTTTGAATAGTACTGAGT 57.784 33.333 5.39 0.00 0.00 3.41
585 596 8.665685 GGGTATTTGTGTTTGAATAGTACTGAG 58.334 37.037 5.39 0.00 0.00 3.35
586 597 7.608761 GGGGTATTTGTGTTTGAATAGTACTGA 59.391 37.037 5.39 0.00 0.00 3.41
587 598 7.413657 CGGGGTATTTGTGTTTGAATAGTACTG 60.414 40.741 5.39 0.00 0.00 2.74
588 599 6.596497 CGGGGTATTTGTGTTTGAATAGTACT 59.404 38.462 0.00 0.00 0.00 2.73
589 600 6.594937 TCGGGGTATTTGTGTTTGAATAGTAC 59.405 38.462 0.00 0.00 0.00 2.73
590 601 6.709281 TCGGGGTATTTGTGTTTGAATAGTA 58.291 36.000 0.00 0.00 0.00 1.82
591 602 5.562635 TCGGGGTATTTGTGTTTGAATAGT 58.437 37.500 0.00 0.00 0.00 2.12
592 603 6.503589 TTCGGGGTATTTGTGTTTGAATAG 57.496 37.500 0.00 0.00 0.00 1.73
593 604 6.659668 TGATTCGGGGTATTTGTGTTTGAATA 59.340 34.615 0.00 0.00 0.00 1.75
594 605 5.478679 TGATTCGGGGTATTTGTGTTTGAAT 59.521 36.000 0.00 0.00 0.00 2.57
595 606 4.827835 TGATTCGGGGTATTTGTGTTTGAA 59.172 37.500 0.00 0.00 0.00 2.69
596 607 4.399219 TGATTCGGGGTATTTGTGTTTGA 58.601 39.130 0.00 0.00 0.00 2.69
597 608 4.457603 TCTGATTCGGGGTATTTGTGTTTG 59.542 41.667 0.00 0.00 0.00 2.93
605 616 6.935240 TTCTATGATCTGATTCGGGGTATT 57.065 37.500 0.00 0.00 0.00 1.89
624 635 6.934645 TCTTTGATTCGCTCCTTTTCTTTCTA 59.065 34.615 0.00 0.00 0.00 2.10
771 790 0.605319 TTAGTTGGTTGGCTCGGCTG 60.605 55.000 0.00 0.00 0.00 4.85
778 797 0.312729 CCGTTGGTTAGTTGGTTGGC 59.687 55.000 0.00 0.00 0.00 4.52
815 834 2.897350 CCGGATTGGCGAGGCTTC 60.897 66.667 0.00 0.00 0.00 3.86
826 845 4.779486 AGGGAAGGGGGCCGGATT 62.779 66.667 5.05 0.00 0.00 3.01
855 876 2.829592 GGATCCCAAGTAGGCGGG 59.170 66.667 0.00 0.00 44.60 6.13
857 878 2.280186 GCGGATCCCAAGTAGGCG 60.280 66.667 6.06 0.00 35.39 5.52
862 883 4.514577 CGCGAGCGGATCCCAAGT 62.515 66.667 9.90 0.00 35.56 3.16
1112 1133 0.038310 TGGCGAAGAGGAGACAGAGA 59.962 55.000 0.00 0.00 0.00 3.10
1194 1238 1.179174 TCCCTATCCATGCCGTCGAG 61.179 60.000 0.00 0.00 0.00 4.04
1203 1247 1.162085 GAGCCCCCTCCCTATCCAT 59.838 63.158 0.00 0.00 31.68 3.41
1266 1310 2.668457 CTGAACGGGAGTCAAATCGAAG 59.332 50.000 0.00 0.00 46.69 3.79
1314 1358 2.094026 GCAAACCTGGGGATCAAATGAC 60.094 50.000 0.00 0.00 0.00 3.06
1331 1375 2.158623 ACATTGACACCAGAGAGGCAAA 60.159 45.455 0.00 0.00 43.14 3.68
1336 1380 1.462283 CGCAACATTGACACCAGAGAG 59.538 52.381 0.00 0.00 0.00 3.20
1355 1399 1.438651 TCGTTCTCCAAATTCTGGCG 58.561 50.000 2.75 0.00 45.98 5.69
1358 1402 2.285256 CGCGATCGTTCTCCAAATTCTG 60.285 50.000 17.81 0.00 0.00 3.02
1369 1413 1.265568 TTACAAGCTCGCGATCGTTC 58.734 50.000 17.81 0.00 36.96 3.95
1406 1453 0.108615 AACACGAGATGAGCTTCGGG 60.109 55.000 6.24 6.24 34.87 5.14
1416 1463 2.224426 TGTGGGTTAGCAAACACGAGAT 60.224 45.455 0.00 0.00 42.30 2.75
1427 1474 1.153229 GATCCGGGTGTGGGTTAGC 60.153 63.158 0.00 0.00 0.00 3.09
1468 1515 2.989909 TGCACTGCAGTATGTAAGCAT 58.010 42.857 21.20 0.00 37.02 3.79
1469 1516 2.470983 TGCACTGCAGTATGTAAGCA 57.529 45.000 21.20 20.38 38.90 3.91
1470 1517 2.744202 AGTTGCACTGCAGTATGTAAGC 59.256 45.455 21.20 17.87 40.61 3.09
1471 1518 5.639506 AGTTAGTTGCACTGCAGTATGTAAG 59.360 40.000 21.20 7.18 40.61 2.34
1473 1520 4.929211 CAGTTAGTTGCACTGCAGTATGTA 59.071 41.667 21.20 4.86 40.61 2.29
1474 1521 3.748048 CAGTTAGTTGCACTGCAGTATGT 59.252 43.478 21.20 5.35 40.61 2.29
1475 1522 3.125829 CCAGTTAGTTGCACTGCAGTATG 59.874 47.826 21.20 9.72 40.61 2.39
1476 1523 3.338249 CCAGTTAGTTGCACTGCAGTAT 58.662 45.455 21.20 6.01 40.61 2.12
1477 1524 2.766313 CCAGTTAGTTGCACTGCAGTA 58.234 47.619 21.20 1.09 40.61 2.74
1478 1525 1.597742 CCAGTTAGTTGCACTGCAGT 58.402 50.000 15.25 15.25 40.61 4.40
1479 1526 0.239347 GCCAGTTAGTTGCACTGCAG 59.761 55.000 13.48 13.48 40.61 4.41
1494 1541 4.022935 TGTTCAAAGTAGCATGAAAGCCAG 60.023 41.667 0.00 0.00 37.31 4.85
1517 1564 7.787725 AATTAGTCGAGAAAAACTGAAGTGT 57.212 32.000 0.00 0.00 0.00 3.55
1518 1565 8.947940 CAAAATTAGTCGAGAAAAACTGAAGTG 58.052 33.333 0.00 0.00 0.00 3.16
1617 1664 1.903183 AGTAGGCACTCTTCCTGGAAC 59.097 52.381 4.68 0.00 41.75 3.62
1700 1747 3.126171 TCGGTGGCAATATCAAGAAAACG 59.874 43.478 0.00 0.00 0.00 3.60
1837 1884 8.921205 ACTTAGTAACTAACTCCACTTTCAAGA 58.079 33.333 0.00 0.00 39.80 3.02
1886 1933 3.576550 GCCCCCACTTCATAAAGAAACAA 59.423 43.478 0.00 0.00 35.40 2.83
1903 1950 0.955919 GCAAGATATAGTGCGCCCCC 60.956 60.000 4.18 0.00 0.00 5.40
1911 1958 8.737168 TTGTATTGAAGCTTGCAAGATATAGT 57.263 30.769 30.39 14.68 0.00 2.12
1965 2012 4.142687 CGAAAAATGAGGTCACGGCTTAAT 60.143 41.667 0.00 0.00 0.00 1.40
1972 2019 2.069273 AGAGCGAAAAATGAGGTCACG 58.931 47.619 0.00 0.00 35.12 4.35
2128 2175 4.020928 TGGAGCGTAGTAACTGGAATGAAA 60.021 41.667 0.00 0.00 0.00 2.69
2145 2192 4.162072 CGACAGAATACTGATATGGAGCG 58.838 47.826 0.00 0.00 46.03 5.03
2330 2377 6.861065 TTGTCAGAACTTCATCCTGTAAAC 57.139 37.500 0.00 0.00 0.00 2.01
2390 2437 7.865820 AGCCATCTATATTATGCCTATTGTGT 58.134 34.615 0.00 0.00 0.00 3.72
2452 2503 4.323485 CCCTACATCCAGTAAGAGCAAACA 60.323 45.833 0.00 0.00 30.92 2.83
2536 2587 9.694137 ATTCGCTTTATTTAGTCTACTGGATAC 57.306 33.333 0.00 0.00 0.00 2.24
2567 2618 7.335924 TCTGCATTTTATTCTGTAAGGTGTACC 59.664 37.037 0.00 0.00 0.00 3.34
2612 2663 7.920160 TCAGTGTCATATTGAGCAACATTAA 57.080 32.000 0.00 0.00 0.00 1.40
2621 2672 9.376075 AGATTACTGTTTCAGTGTCATATTGAG 57.624 33.333 11.92 0.00 45.01 3.02
2693 2749 2.648059 AGATTTCTGTACAGGGCATGC 58.352 47.619 22.48 9.90 0.00 4.06
2697 2753 4.156739 CCTGAAAAGATTTCTGTACAGGGC 59.843 45.833 22.48 9.56 36.93 5.19
2698 2754 5.560724 TCCTGAAAAGATTTCTGTACAGGG 58.439 41.667 22.48 10.94 38.90 4.45
2704 2760 7.254932 CGAAGAAGTTCCTGAAAAGATTTCTGT 60.255 37.037 0.00 0.00 0.00 3.41
2927 2983 3.817647 ACTGCAGAGGAAACAAAGATCAC 59.182 43.478 23.35 0.00 0.00 3.06
3030 3086 4.566360 GCTCTTGTAGATTCTCAACTGCTC 59.434 45.833 0.00 0.00 0.00 4.26
3076 3133 2.549754 GCATATATTGTTCAGCTGCCGT 59.450 45.455 9.47 0.00 0.00 5.68
3078 3135 4.037208 ACAAGCATATATTGTTCAGCTGCC 59.963 41.667 9.47 2.21 37.61 4.85
3171 3236 5.882557 GCCATAAAGGAGAATTCAGAGAACA 59.117 40.000 8.44 0.00 41.22 3.18
3226 3291 9.135189 TGTGGTGTCTACTTTTAAGAAGTACTA 57.865 33.333 0.00 0.00 0.00 1.82
3227 3292 8.015185 TGTGGTGTCTACTTTTAAGAAGTACT 57.985 34.615 0.00 0.00 0.00 2.73
3228 3293 8.828688 ATGTGGTGTCTACTTTTAAGAAGTAC 57.171 34.615 0.00 0.00 0.00 2.73
3229 3294 9.918630 GTATGTGGTGTCTACTTTTAAGAAGTA 57.081 33.333 0.00 8.81 0.00 2.24
3230 3295 8.648693 AGTATGTGGTGTCTACTTTTAAGAAGT 58.351 33.333 0.00 7.76 0.00 3.01
3232 3297 9.918630 GTAGTATGTGGTGTCTACTTTTAAGAA 57.081 33.333 0.00 0.00 32.64 2.52
3233 3298 9.305555 AGTAGTATGTGGTGTCTACTTTTAAGA 57.694 33.333 0.00 0.00 39.66 2.10
3245 3310 7.351952 TCAGGAGTATTAGTAGTATGTGGTGT 58.648 38.462 0.00 0.00 0.00 4.16
3410 3475 4.226761 GTTGCAAGAATTTGGGTAGAACG 58.773 43.478 0.00 0.00 34.79 3.95
3411 3476 4.038642 TGGTTGCAAGAATTTGGGTAGAAC 59.961 41.667 0.00 0.00 34.79 3.01
3418 3483 3.749665 TTCCTGGTTGCAAGAATTTGG 57.250 42.857 0.00 0.00 34.79 3.28
3449 3514 2.290896 TGTTCCAAACAGGCCCTGATAG 60.291 50.000 19.90 5.93 36.25 2.08
3453 3518 1.118838 TTTGTTCCAAACAGGCCCTG 58.881 50.000 9.83 9.83 43.27 4.45
3546 3611 6.752815 CAGGAAGGACTCTTAAGTTCGAATAC 59.247 42.308 0.00 0.00 35.99 1.89
3590 3655 4.768448 TGGATTTCATGACTGTCTGCAATT 59.232 37.500 9.51 0.00 0.00 2.32
3764 3830 1.136305 TCGCTGTATAAGGACACTGGC 59.864 52.381 0.00 0.00 0.00 4.85
3782 3848 5.404968 GCATCTACATCTTGGAATTCTCTCG 59.595 44.000 5.23 0.00 0.00 4.04
3820 3886 5.413499 GGTTATCAGAGTACCTAAAACGCA 58.587 41.667 0.00 0.00 0.00 5.24
3836 3902 0.758734 CATGAGAGCCCGGGTTATCA 59.241 55.000 32.84 32.84 0.00 2.15
3900 3966 2.100989 AGTTGGTCGGATACTGGAGTC 58.899 52.381 0.00 0.00 0.00 3.36
4068 4146 3.868077 GGAGACTAGCAACAACAGCTATG 59.132 47.826 0.00 0.00 43.08 2.23
4078 4156 2.977772 ATCAGCTGGAGACTAGCAAC 57.022 50.000 15.13 0.00 43.53 4.17
4129 4207 4.277476 ACAACTGTTGAAAATCCCTGTCA 58.723 39.130 26.00 0.00 0.00 3.58
4276 4354 2.165998 AGCATTCTGCCTTTCCTCAAC 58.834 47.619 0.00 0.00 46.52 3.18
4431 4509 1.065401 CAAACTTGCTTCCAGTTGCGA 59.935 47.619 0.00 0.00 0.00 5.10
4504 4613 0.888619 CACCTTAGACGGAGAGCACA 59.111 55.000 0.00 0.00 0.00 4.57
4615 4724 0.102481 TCTCCCAGCTAAATCGACGC 59.898 55.000 0.00 0.00 0.00 5.19
4624 4733 1.264749 ATGTTGCCGTCTCCCAGCTA 61.265 55.000 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.