Multiple sequence alignment - TraesCS5B01G124100

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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 TraesCS5B01G124100 chr5B 100.000 3380 0 0 1 3380 223986799 223983420 0.000000e+00 6242.0
1 TraesCS5B01G124100 chr5B 100.000 640 0 0 3728 4367 223983072 223982433 0.000000e+00 1182.0
2 TraesCS5B01G124100 chr5B 90.580 276 22 3 568 839 691604289 691604564 3.210000e-96 363.0
3 TraesCS5B01G124100 chr5D 95.977 2560 60 15 832 3380 210376813 210374286 0.000000e+00 4117.0
4 TraesCS5B01G124100 chr5D 91.888 641 40 9 3728 4362 210374161 210373527 0.000000e+00 885.0
5 TraesCS5B01G124100 chr5D 91.019 579 48 3 1 578 210377385 210376810 0.000000e+00 778.0
6 TraesCS5B01G124100 chr5D 82.850 379 65 0 1860 2238 389377 388999 1.500000e-89 340.0
7 TraesCS5B01G124100 chr5A 97.797 1997 37 4 1364 3357 272133537 272131545 0.000000e+00 3437.0
8 TraesCS5B01G124100 chr5A 91.718 652 40 8 3728 4367 272131125 272130476 0.000000e+00 893.0
9 TraesCS5B01G124100 chr5A 87.219 579 70 4 1 578 272135025 272134450 0.000000e+00 656.0
10 TraesCS5B01G124100 chr5A 91.892 444 22 4 832 1275 272134453 272134024 3.730000e-170 608.0
11 TraesCS5B01G124100 chr5A 83.824 476 72 4 1 472 495342219 495342693 8.620000e-122 448.0
12 TraesCS5B01G124100 chr1D 86.378 624 83 2 2331 2953 8713585 8714207 0.000000e+00 680.0
13 TraesCS5B01G124100 chr1D 84.304 618 97 0 2336 2953 252528696 252528079 4.830000e-169 604.0
14 TraesCS5B01G124100 chr1D 80.978 552 89 12 1717 2258 8712802 8713347 1.450000e-114 424.0
15 TraesCS5B01G124100 chr1B 86.196 623 86 0 2331 2953 11859020 11859642 0.000000e+00 675.0
16 TraesCS5B01G124100 chr1B 85.275 618 91 0 2336 2953 360808768 360809385 4.760000e-179 638.0
17 TraesCS5B01G124100 chr1B 81.341 552 87 12 1717 2258 11858235 11858780 6.710000e-118 435.0
18 TraesCS5B01G124100 chr1B 91.729 266 20 1 573 836 386772390 386772655 6.900000e-98 368.0
19 TraesCS5B01G124100 chr1B 93.750 64 4 0 1717 1780 360808078 360808141 3.590000e-16 97.1
20 TraesCS5B01G124100 chr1A 86.196 623 86 0 2331 2953 10068025 10068647 0.000000e+00 675.0
21 TraesCS5B01G124100 chr1A 83.819 618 100 0 2336 2953 323643083 323642466 4.870000e-164 588.0
22 TraesCS5B01G124100 chr1A 80.085 472 83 10 10 476 573222148 573221683 1.500000e-89 340.0
23 TraesCS5B01G124100 chr1A 95.312 64 3 0 1717 1780 10067167 10067230 7.730000e-18 102.0
24 TraesCS5B01G124100 chr1A 93.750 64 4 0 1717 1780 323643773 323643710 3.590000e-16 97.1
25 TraesCS5B01G124100 chr4B 83.840 625 99 2 2335 2958 39121251 39121874 1.050000e-165 593.0
26 TraesCS5B01G124100 chr4B 85.714 399 57 0 1859 2257 39120608 39121006 5.220000e-114 422.0
27 TraesCS5B01G124100 chr4B 90.123 81 8 0 391 471 572211505 572211425 5.970000e-19 106.0
28 TraesCS5B01G124100 chr4D 85.213 399 59 0 1859 2257 26668446 26668844 1.130000e-110 411.0
29 TraesCS5B01G124100 chr4A 85.213 399 59 0 1859 2257 576703436 576703038 1.130000e-110 411.0
30 TraesCS5B01G124100 chr4A 79.661 472 51 27 10 479 86928534 86928106 9.180000e-77 298.0
31 TraesCS5B01G124100 chr7B 83.184 446 70 5 2 444 245171480 245171923 1.890000e-108 403.0
32 TraesCS5B01G124100 chr3B 92.045 264 19 2 574 835 168523814 168523551 1.920000e-98 370.0
33 TraesCS5B01G124100 chr3B 81.840 413 70 5 1856 2266 647078352 647078761 4.180000e-90 342.0
34 TraesCS5B01G124100 chr2D 91.513 271 20 2 569 836 6206066 6206336 1.920000e-98 370.0
35 TraesCS5B01G124100 chr2D 90.809 272 21 4 568 837 64978495 64978226 1.150000e-95 361.0
36 TraesCS5B01G124100 chr2D 77.223 461 84 17 14 471 99504817 99504375 2.610000e-62 250.0
37 TraesCS5B01G124100 chr2B 91.729 266 20 2 572 835 634968165 634968430 6.900000e-98 368.0
38 TraesCS5B01G124100 chr2B 91.571 261 20 1 577 835 475256407 475256667 4.150000e-95 359.0
39 TraesCS5B01G124100 chr2B 73.176 425 101 11 49 467 53941526 53941109 1.640000e-29 141.0
40 TraesCS5B01G124100 chr2B 100.000 30 0 0 121 150 116212501 116212472 6.100000e-04 56.5
41 TraesCS5B01G124100 chr2B 100.000 28 0 0 86 113 545401295 545401322 8.000000e-03 52.8
42 TraesCS5B01G124100 chr7A 91.418 268 20 2 570 835 558085169 558084903 8.930000e-97 364.0
43 TraesCS5B01G124100 chr7A 80.846 449 72 11 1 443 289037859 289038299 1.500000e-89 340.0
44 TraesCS5B01G124100 chr7A 75.336 223 40 11 10 226 40860902 40860689 4.650000e-15 93.5
45 TraesCS5B01G124100 chr6D 91.386 267 21 1 572 836 151317478 151317212 8.930000e-97 364.0
46 TraesCS5B01G124100 chr3D 81.707 410 70 5 1859 2266 484287523 484287929 1.950000e-88 337.0
47 TraesCS5B01G124100 chr3A 81.220 410 72 5 1859 2266 627252618 627253024 4.210000e-85 326.0
48 TraesCS5B01G124100 chr6A 74.561 228 45 8 185 404 45903236 45903014 2.160000e-13 87.9
49 TraesCS5B01G124100 chr6A 97.436 39 1 0 430 468 41559930 41559968 2.820000e-07 67.6


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 TraesCS5B01G124100 chr5B 223982433 223986799 4366 True 3712.000000 6242 100.000000 1 4367 2 chr5B.!!$R1 4366
1 TraesCS5B01G124100 chr5D 210373527 210377385 3858 True 1926.666667 4117 92.961333 1 4362 3 chr5D.!!$R2 4361
2 TraesCS5B01G124100 chr5A 272130476 272135025 4549 True 1398.500000 3437 92.156500 1 4367 4 chr5A.!!$R1 4366
3 TraesCS5B01G124100 chr1D 252528079 252528696 617 True 604.000000 604 84.304000 2336 2953 1 chr1D.!!$R1 617
4 TraesCS5B01G124100 chr1D 8712802 8714207 1405 False 552.000000 680 83.678000 1717 2953 2 chr1D.!!$F1 1236
5 TraesCS5B01G124100 chr1B 11858235 11859642 1407 False 555.000000 675 83.768500 1717 2953 2 chr1B.!!$F2 1236
6 TraesCS5B01G124100 chr1B 360808078 360809385 1307 False 367.550000 638 89.512500 1717 2953 2 chr1B.!!$F3 1236
7 TraesCS5B01G124100 chr1A 10067167 10068647 1480 False 388.500000 675 90.754000 1717 2953 2 chr1A.!!$F1 1236
8 TraesCS5B01G124100 chr1A 323642466 323643773 1307 True 342.550000 588 88.784500 1717 2953 2 chr1A.!!$R2 1236
9 TraesCS5B01G124100 chr4B 39120608 39121874 1266 False 507.500000 593 84.777000 1859 2958 2 chr4B.!!$F1 1099

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
415 418 0.108329 CACCTTGTATCGTTCGGCCT 60.108 55.000 0.0 0.0 0.00 5.19 F
1168 1171 0.954452 CCTCGCAGCAGTTTCCTTTT 59.046 50.000 0.0 0.0 0.00 2.27 F
1304 1307 1.047801 TCTTGCTTTGCCTTTTCCCC 58.952 50.000 0.0 0.0 0.00 4.81 F
2264 2764 2.546368 GACGCACAACAGGTAATTGTCA 59.454 45.455 0.0 0.0 38.22 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1817 2227 2.511600 CACGATGAAGGCCGGACC 60.512 66.667 1.76 4.96 39.61 4.46 R
2264 2764 6.435430 TTTTAGAATATGTGTGCTCGCAAT 57.565 33.333 6.06 0.00 37.62 3.56 R
3300 4168 3.555966 GGTCAAATATAGCAGCCCACTT 58.444 45.455 0.00 0.00 0.00 3.16 R
3799 4717 0.546122 AGTGAACTGGAGCACCAACA 59.454 50.000 3.90 2.52 46.32 3.33 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
115 116 2.492090 GCTCTGGCATCGACGACT 59.508 61.111 0.00 0.00 38.54 4.18
154 155 4.818642 CTGCTCTCTTCTTGAAGACATCA 58.181 43.478 8.80 1.47 35.85 3.07
176 177 2.430367 GGTGCTCCCCTTCGTGTT 59.570 61.111 0.00 0.00 0.00 3.32
177 178 1.228154 GGTGCTCCCCTTCGTGTTT 60.228 57.895 0.00 0.00 0.00 2.83
266 267 2.108075 TCATGAGGGTGTTGTTGTGGAT 59.892 45.455 0.00 0.00 0.00 3.41
267 268 2.270352 TGAGGGTGTTGTTGTGGATC 57.730 50.000 0.00 0.00 0.00 3.36
291 292 0.810031 GTGTACTAGGGCGTGGCATG 60.810 60.000 1.31 1.31 0.00 4.06
293 294 3.101796 TACTAGGGCGTGGCATGGC 62.102 63.158 23.81 23.81 0.00 4.40
316 318 4.116238 GCTGTACTCAGTTCCTCTTATGC 58.884 47.826 0.00 0.00 43.05 3.14
355 358 2.241880 GCTTGCGGTGTACGTGTGT 61.242 57.895 0.00 0.00 46.52 3.72
368 371 5.747197 GTGTACGTGTGTGATTATTCTAGGG 59.253 44.000 0.00 0.00 0.00 3.53
373 376 4.028131 TGTGTGATTATTCTAGGGTCGGT 58.972 43.478 0.00 0.00 0.00 4.69
394 397 5.987347 CGGTTTTTGTAAGAGAACTACCTCA 59.013 40.000 0.00 0.00 35.68 3.86
415 418 0.108329 CACCTTGTATCGTTCGGCCT 60.108 55.000 0.00 0.00 0.00 5.19
420 423 3.454375 CTTGTATCGTTCGGCCTTGTAT 58.546 45.455 0.00 0.00 0.00 2.29
493 496 2.749621 GGAAAAGATGAGATGTTGGCGT 59.250 45.455 0.00 0.00 0.00 5.68
494 497 3.426695 GGAAAAGATGAGATGTTGGCGTG 60.427 47.826 0.00 0.00 0.00 5.34
499 502 4.012374 AGATGAGATGTTGGCGTGAATTT 58.988 39.130 0.00 0.00 0.00 1.82
514 517 5.227184 GCGTGAATTTGCTCTTTTTATACCG 59.773 40.000 0.00 0.00 0.00 4.02
516 519 6.090129 GTGAATTTGCTCTTTTTATACCGCA 58.910 36.000 0.00 0.00 0.00 5.69
517 520 6.251376 GTGAATTTGCTCTTTTTATACCGCAG 59.749 38.462 0.00 0.00 0.00 5.18
580 583 9.754382 TTTTTATATCGGGACATTGTAGTACTC 57.246 33.333 0.00 0.00 0.00 2.59
581 584 8.701908 TTTATATCGGGACATTGTAGTACTCT 57.298 34.615 0.00 0.00 0.00 3.24
582 585 6.821031 ATATCGGGACATTGTAGTACTCTC 57.179 41.667 0.00 0.00 0.00 3.20
583 586 4.232188 TCGGGACATTGTAGTACTCTCT 57.768 45.455 0.00 0.00 0.00 3.10
584 587 4.597004 TCGGGACATTGTAGTACTCTCTT 58.403 43.478 0.00 0.00 0.00 2.85
585 588 4.639310 TCGGGACATTGTAGTACTCTCTTC 59.361 45.833 0.00 0.00 0.00 2.87
586 589 4.398358 CGGGACATTGTAGTACTCTCTTCA 59.602 45.833 0.00 0.00 0.00 3.02
587 590 5.067936 CGGGACATTGTAGTACTCTCTTCAT 59.932 44.000 0.00 0.00 0.00 2.57
588 591 6.405953 CGGGACATTGTAGTACTCTCTTCATT 60.406 42.308 0.00 0.00 0.00 2.57
589 592 6.981559 GGGACATTGTAGTACTCTCTTCATTC 59.018 42.308 0.00 0.00 0.00 2.67
590 593 6.981559 GGACATTGTAGTACTCTCTTCATTCC 59.018 42.308 0.00 0.00 0.00 3.01
591 594 7.363880 GGACATTGTAGTACTCTCTTCATTCCA 60.364 40.741 0.00 0.00 0.00 3.53
592 595 7.324178 ACATTGTAGTACTCTCTTCATTCCAC 58.676 38.462 0.00 0.00 0.00 4.02
593 596 6.911250 TTGTAGTACTCTCTTCATTCCACA 57.089 37.500 0.00 0.00 0.00 4.17
594 597 6.911250 TGTAGTACTCTCTTCATTCCACAA 57.089 37.500 0.00 0.00 0.00 3.33
595 598 7.482169 TGTAGTACTCTCTTCATTCCACAAT 57.518 36.000 0.00 0.00 0.00 2.71
596 599 7.323420 TGTAGTACTCTCTTCATTCCACAATG 58.677 38.462 0.00 0.00 40.91 2.82
597 600 6.365970 AGTACTCTCTTCATTCCACAATGT 57.634 37.500 0.00 0.00 40.47 2.71
598 601 7.482169 AGTACTCTCTTCATTCCACAATGTA 57.518 36.000 0.00 0.00 40.47 2.29
599 602 7.324178 AGTACTCTCTTCATTCCACAATGTAC 58.676 38.462 0.00 0.00 40.47 2.90
600 603 6.365970 ACTCTCTTCATTCCACAATGTACT 57.634 37.500 0.00 0.00 40.47 2.73
601 604 6.169094 ACTCTCTTCATTCCACAATGTACTG 58.831 40.000 0.00 0.00 40.47 2.74
602 605 4.937620 TCTCTTCATTCCACAATGTACTGC 59.062 41.667 0.00 0.00 40.47 4.40
603 606 4.009675 TCTTCATTCCACAATGTACTGCC 58.990 43.478 0.00 0.00 40.47 4.85
604 607 3.719268 TCATTCCACAATGTACTGCCT 57.281 42.857 0.00 0.00 40.47 4.75
605 608 4.835284 TCATTCCACAATGTACTGCCTA 57.165 40.909 0.00 0.00 40.47 3.93
606 609 5.372343 TCATTCCACAATGTACTGCCTAT 57.628 39.130 0.00 0.00 40.47 2.57
607 610 6.493189 TCATTCCACAATGTACTGCCTATA 57.507 37.500 0.00 0.00 40.47 1.31
608 611 6.524734 TCATTCCACAATGTACTGCCTATAG 58.475 40.000 0.00 0.00 40.47 1.31
609 612 6.326323 TCATTCCACAATGTACTGCCTATAGA 59.674 38.462 0.00 0.00 40.47 1.98
610 613 6.747414 TTCCACAATGTACTGCCTATAGAT 57.253 37.500 0.00 0.00 0.00 1.98
611 614 6.747414 TCCACAATGTACTGCCTATAGATT 57.253 37.500 0.00 0.00 0.00 2.40
612 615 7.136822 TCCACAATGTACTGCCTATAGATTT 57.863 36.000 0.00 0.00 0.00 2.17
613 616 7.573710 TCCACAATGTACTGCCTATAGATTTT 58.426 34.615 0.00 0.00 0.00 1.82
614 617 8.052748 TCCACAATGTACTGCCTATAGATTTTT 58.947 33.333 0.00 0.00 0.00 1.94
615 618 9.337396 CCACAATGTACTGCCTATAGATTTTTA 57.663 33.333 0.00 0.00 0.00 1.52
646 649 7.769272 TCAAACTTTGCTAAATTTGACCAAG 57.231 32.000 12.31 3.20 36.42 3.61
647 650 7.327214 TCAAACTTTGCTAAATTTGACCAAGT 58.673 30.769 12.31 3.79 36.42 3.16
648 651 8.470805 TCAAACTTTGCTAAATTTGACCAAGTA 58.529 29.630 12.31 0.00 36.42 2.24
649 652 9.260002 CAAACTTTGCTAAATTTGACCAAGTAT 57.740 29.630 8.77 0.00 34.62 2.12
664 667 9.871238 TTGACCAAGTATATAGAGAAAACAGTC 57.129 33.333 0.00 0.00 0.00 3.51
665 668 9.256228 TGACCAAGTATATAGAGAAAACAGTCT 57.744 33.333 0.00 0.00 0.00 3.24
679 682 9.303537 GAGAAAACAGTCTACATCTACAATACC 57.696 37.037 0.00 0.00 0.00 2.73
680 683 8.812972 AGAAAACAGTCTACATCTACAATACCA 58.187 33.333 0.00 0.00 0.00 3.25
681 684 9.431887 GAAAACAGTCTACATCTACAATACCAA 57.568 33.333 0.00 0.00 0.00 3.67
682 685 9.787435 AAAACAGTCTACATCTACAATACCAAA 57.213 29.630 0.00 0.00 0.00 3.28
683 686 8.773404 AACAGTCTACATCTACAATACCAAAC 57.227 34.615 0.00 0.00 0.00 2.93
684 687 7.903145 ACAGTCTACATCTACAATACCAAACA 58.097 34.615 0.00 0.00 0.00 2.83
685 688 8.540388 ACAGTCTACATCTACAATACCAAACAT 58.460 33.333 0.00 0.00 0.00 2.71
686 689 8.820933 CAGTCTACATCTACAATACCAAACATG 58.179 37.037 0.00 0.00 0.00 3.21
687 690 8.540388 AGTCTACATCTACAATACCAAACATGT 58.460 33.333 0.00 0.00 0.00 3.21
688 691 9.811995 GTCTACATCTACAATACCAAACATGTA 57.188 33.333 0.00 0.00 0.00 2.29
689 692 9.811995 TCTACATCTACAATACCAAACATGTAC 57.188 33.333 0.00 0.00 0.00 2.90
690 693 9.594478 CTACATCTACAATACCAAACATGTACA 57.406 33.333 0.00 0.00 0.00 2.90
692 695 9.461312 ACATCTACAATACCAAACATGTACATT 57.539 29.630 5.37 0.00 0.00 2.71
693 696 9.935682 CATCTACAATACCAAACATGTACATTC 57.064 33.333 5.37 0.00 0.00 2.67
694 697 9.905713 ATCTACAATACCAAACATGTACATTCT 57.094 29.630 5.37 0.00 0.00 2.40
695 698 9.161629 TCTACAATACCAAACATGTACATTCTG 57.838 33.333 5.37 0.00 0.00 3.02
696 699 7.994425 ACAATACCAAACATGTACATTCTGA 57.006 32.000 5.37 0.00 0.00 3.27
697 700 8.402798 ACAATACCAAACATGTACATTCTGAA 57.597 30.769 5.37 0.00 0.00 3.02
698 701 8.855110 ACAATACCAAACATGTACATTCTGAAA 58.145 29.630 5.37 0.00 0.00 2.69
699 702 9.689976 CAATACCAAACATGTACATTCTGAAAA 57.310 29.630 5.37 0.00 0.00 2.29
728 731 7.444629 ACTCATGATGTATCCAATGTTATGC 57.555 36.000 0.00 0.00 0.00 3.14
729 732 6.999871 ACTCATGATGTATCCAATGTTATGCA 59.000 34.615 0.00 0.00 0.00 3.96
730 733 7.668469 ACTCATGATGTATCCAATGTTATGCAT 59.332 33.333 3.79 3.79 40.03 3.96
732 735 8.862085 TCATGATGTATCCAATGTTATGCATTT 58.138 29.630 3.54 0.00 44.82 2.32
733 736 8.921670 CATGATGTATCCAATGTTATGCATTTG 58.078 33.333 3.54 2.84 44.82 2.32
734 737 8.235359 TGATGTATCCAATGTTATGCATTTGA 57.765 30.769 3.54 0.00 44.82 2.69
735 738 8.862085 TGATGTATCCAATGTTATGCATTTGAT 58.138 29.630 3.54 12.56 44.82 2.57
795 798 9.644993 GGTTAATTTGTAATGTTTGACTTTTGC 57.355 29.630 0.00 0.00 0.00 3.68
802 805 9.766277 TTGTAATGTTTGACTTTTGCAAAAATC 57.234 25.926 22.90 22.90 37.03 2.17
803 806 9.160496 TGTAATGTTTGACTTTTGCAAAAATCT 57.840 25.926 27.69 13.35 37.03 2.40
808 811 9.474920 TGTTTGACTTTTGCAAAAATCTATAGG 57.525 29.630 27.69 15.71 37.03 2.57
809 812 8.435430 GTTTGACTTTTGCAAAAATCTATAGGC 58.565 33.333 27.69 16.81 37.03 3.93
810 813 7.225784 TGACTTTTGCAAAAATCTATAGGCA 57.774 32.000 27.69 18.92 0.00 4.75
811 814 7.090173 TGACTTTTGCAAAAATCTATAGGCAC 58.910 34.615 27.69 12.10 0.00 5.01
812 815 7.039784 TGACTTTTGCAAAAATCTATAGGCACT 60.040 33.333 27.69 1.15 46.37 4.40
907 910 5.299279 ACCTGGCGGATGAAATTAAATACTG 59.701 40.000 0.00 0.00 0.00 2.74
910 913 7.254227 TGGCGGATGAAATTAAATACTGTAC 57.746 36.000 0.00 0.00 0.00 2.90
912 915 7.554835 TGGCGGATGAAATTAAATACTGTACTT 59.445 33.333 0.00 0.00 0.00 2.24
913 916 8.403236 GGCGGATGAAATTAAATACTGTACTTT 58.597 33.333 0.00 0.00 0.00 2.66
941 944 1.705186 CCCCAGGGAAAACAAGAGAGA 59.295 52.381 7.25 0.00 37.50 3.10
952 955 3.415457 ACAAGAGAGAGCTGGGAAAAG 57.585 47.619 0.00 0.00 0.00 2.27
953 956 2.039613 ACAAGAGAGAGCTGGGAAAAGG 59.960 50.000 0.00 0.00 0.00 3.11
956 959 2.982488 AGAGAGAGCTGGGAAAAGGAAA 59.018 45.455 0.00 0.00 0.00 3.13
981 984 2.772077 TGCGTATAAAAGAGGGCACA 57.228 45.000 0.00 0.00 0.00 4.57
1168 1171 0.954452 CCTCGCAGCAGTTTCCTTTT 59.046 50.000 0.00 0.00 0.00 2.27
1191 1194 2.158667 TCTTTTCCGGATTATCCCTGCC 60.159 50.000 4.15 0.00 31.13 4.85
1255 1258 1.336702 GGGCGTGCTAGATCTGATGAG 60.337 57.143 5.18 0.00 0.00 2.90
1268 1271 5.600484 AGATCTGATGAGTTACCCGAGAAAT 59.400 40.000 0.00 0.00 0.00 2.17
1304 1307 1.047801 TCTTGCTTTGCCTTTTCCCC 58.952 50.000 0.00 0.00 0.00 4.81
1420 1821 2.957680 TGCATGTGGATGTTCTTGTGTT 59.042 40.909 0.00 0.00 31.50 3.32
1426 1827 4.335315 TGTGGATGTTCTTGTGTTGTTCTC 59.665 41.667 0.00 0.00 0.00 2.87
1455 1856 3.706594 AGTGTAGATGATTGGACCATCGT 59.293 43.478 0.00 0.00 43.73 3.73
1543 1945 4.623932 AAATGGGAGAAAAGAAAAGGCC 57.376 40.909 0.00 0.00 0.00 5.19
1647 2056 5.818336 TGGTGAATTTTCTTCTGTTCGTGTA 59.182 36.000 0.00 0.00 0.00 2.90
1648 2057 6.018262 TGGTGAATTTTCTTCTGTTCGTGTAG 60.018 38.462 0.00 0.00 0.00 2.74
1789 2199 3.848726 CATGGTCAAGGTTTGTATTGCC 58.151 45.455 0.00 0.00 0.00 4.52
1817 2227 6.573664 TCTGTCAATTGGTGTAAATCCTTG 57.426 37.500 5.42 0.00 0.00 3.61
2264 2764 2.546368 GACGCACAACAGGTAATTGTCA 59.454 45.455 0.00 0.00 38.22 3.58
3217 4085 6.765989 CCTTGCCATGTAAGCTACTATGTTTA 59.234 38.462 0.00 0.00 0.00 2.01
3299 4167 8.830580 GTGTACCTTGTAGACTCGTAATATGTA 58.169 37.037 0.00 0.00 0.00 2.29
3300 4168 9.394767 TGTACCTTGTAGACTCGTAATATGTAA 57.605 33.333 0.00 0.00 0.00 2.41
3327 4195 1.873591 CTGCTATATTTGACCGGTGCC 59.126 52.381 14.63 0.00 0.00 5.01
3799 4717 0.887247 TACTTGCGCAAACATGGCAT 59.113 45.000 25.01 0.00 36.44 4.40
3838 4756 1.089920 GAATGCACGATCAAGGCAGT 58.910 50.000 8.60 6.09 41.40 4.40
3876 4794 2.359850 GAACATGCGGTGGCCTGA 60.360 61.111 3.32 0.00 38.08 3.86
4133 5052 3.368571 GGTGCACTTGGCTGGCTC 61.369 66.667 17.98 0.00 45.15 4.70
4162 5081 1.401761 TTGTGATTTGTGGTGCTGCT 58.598 45.000 0.00 0.00 0.00 4.24
4293 5272 0.252696 TCCTTCCTTGGCTAGGCAGA 60.253 55.000 19.32 11.45 44.37 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
154 155 2.990479 GAAGGGGAGCACCACGAT 59.010 61.111 1.58 0.00 45.76 3.73
176 177 1.112950 GGTTTTCACCCGAAACCCAA 58.887 50.000 7.37 0.00 46.58 4.12
177 178 2.809952 GGTTTTCACCCGAAACCCA 58.190 52.632 7.37 0.00 46.58 4.51
226 227 3.641986 GGAAACCGACGCAACGCA 61.642 61.111 0.00 0.00 0.00 5.24
254 255 4.431416 ACACCTAAGATCCACAACAACA 57.569 40.909 0.00 0.00 0.00 3.33
266 267 2.372264 CACGCCCTAGTACACCTAAGA 58.628 52.381 0.00 0.00 0.00 2.10
267 268 1.407979 CCACGCCCTAGTACACCTAAG 59.592 57.143 0.00 0.00 0.00 2.18
291 292 0.458716 GAGGAACTGAGTACAGCGCC 60.459 60.000 2.29 0.00 46.95 6.53
293 294 4.355437 CATAAGAGGAACTGAGTACAGCG 58.645 47.826 0.00 0.00 46.95 5.18
294 295 4.116238 GCATAAGAGGAACTGAGTACAGC 58.884 47.826 0.00 0.00 46.95 4.40
355 358 6.478129 ACAAAAACCGACCCTAGAATAATCA 58.522 36.000 0.00 0.00 0.00 2.57
368 371 5.987953 AGGTAGTTCTCTTACAAAAACCGAC 59.012 40.000 0.00 0.00 0.00 4.79
373 376 7.660208 GGTGATGAGGTAGTTCTCTTACAAAAA 59.340 37.037 0.00 0.00 34.98 1.94
394 397 1.472728 GGCCGAACGATACAAGGTGAT 60.473 52.381 0.00 0.00 0.00 3.06
415 418 3.505680 AGCATCAACCGAGCAAAATACAA 59.494 39.130 0.00 0.00 0.00 2.41
420 423 4.782019 ATAAAGCATCAACCGAGCAAAA 57.218 36.364 0.00 0.00 0.00 2.44
471 474 3.012518 CGCCAACATCTCATCTTTTCCT 58.987 45.455 0.00 0.00 0.00 3.36
472 475 2.749621 ACGCCAACATCTCATCTTTTCC 59.250 45.455 0.00 0.00 0.00 3.13
493 496 6.260870 TGCGGTATAAAAAGAGCAAATTCA 57.739 33.333 0.00 0.00 0.00 2.57
494 497 5.743872 CCTGCGGTATAAAAAGAGCAAATTC 59.256 40.000 0.00 0.00 34.04 2.17
499 502 3.267483 GTCCTGCGGTATAAAAAGAGCA 58.733 45.455 0.00 0.00 0.00 4.26
514 517 9.120538 TCTTTAAATAGTATGAATTGGTCCTGC 57.879 33.333 0.00 0.00 0.00 4.85
566 569 7.489757 GTGGAATGAAGAGAGTACTACAATGTC 59.510 40.741 0.00 0.00 0.00 3.06
572 575 7.324178 ACATTGTGGAATGAAGAGAGTACTAC 58.676 38.462 0.00 0.00 41.49 2.73
574 577 6.365970 ACATTGTGGAATGAAGAGAGTACT 57.634 37.500 0.00 0.00 41.49 2.73
575 578 7.276658 CAGTACATTGTGGAATGAAGAGAGTAC 59.723 40.741 0.00 0.00 41.49 2.73
576 579 7.323420 CAGTACATTGTGGAATGAAGAGAGTA 58.677 38.462 0.00 0.00 41.49 2.59
577 580 6.169094 CAGTACATTGTGGAATGAAGAGAGT 58.831 40.000 0.00 0.00 41.49 3.24
578 581 5.064452 GCAGTACATTGTGGAATGAAGAGAG 59.936 44.000 0.00 0.00 41.49 3.20
579 582 4.937620 GCAGTACATTGTGGAATGAAGAGA 59.062 41.667 0.00 0.00 41.49 3.10
580 583 4.095483 GGCAGTACATTGTGGAATGAAGAG 59.905 45.833 0.00 0.00 41.49 2.85
581 584 4.009675 GGCAGTACATTGTGGAATGAAGA 58.990 43.478 0.00 0.00 41.49 2.87
582 585 4.012374 AGGCAGTACATTGTGGAATGAAG 58.988 43.478 0.00 0.00 41.49 3.02
583 586 4.032960 AGGCAGTACATTGTGGAATGAA 57.967 40.909 0.00 0.00 41.49 2.57
584 587 3.719268 AGGCAGTACATTGTGGAATGA 57.281 42.857 0.00 0.00 41.49 2.57
585 588 6.524734 TCTATAGGCAGTACATTGTGGAATG 58.475 40.000 0.00 0.00 44.11 2.67
586 589 6.747414 TCTATAGGCAGTACATTGTGGAAT 57.253 37.500 0.00 0.00 0.00 3.01
587 590 6.747414 ATCTATAGGCAGTACATTGTGGAA 57.253 37.500 0.00 0.00 0.00 3.53
588 591 6.747414 AATCTATAGGCAGTACATTGTGGA 57.253 37.500 0.00 0.00 0.00 4.02
589 592 7.807977 AAAATCTATAGGCAGTACATTGTGG 57.192 36.000 0.00 0.00 0.00 4.17
622 625 7.327214 ACTTGGTCAAATTTAGCAAAGTTTGA 58.673 30.769 19.82 5.12 38.01 2.69
623 626 7.538303 ACTTGGTCAAATTTAGCAAAGTTTG 57.462 32.000 11.41 11.41 34.24 2.93
638 641 9.871238 GACTGTTTTCTCTATATACTTGGTCAA 57.129 33.333 0.00 0.00 0.00 3.18
639 642 9.256228 AGACTGTTTTCTCTATATACTTGGTCA 57.744 33.333 0.00 0.00 0.00 4.02
653 656 9.303537 GGTATTGTAGATGTAGACTGTTTTCTC 57.696 37.037 0.00 0.00 0.00 2.87
654 657 8.812972 TGGTATTGTAGATGTAGACTGTTTTCT 58.187 33.333 0.00 0.00 0.00 2.52
655 658 8.997621 TGGTATTGTAGATGTAGACTGTTTTC 57.002 34.615 0.00 0.00 0.00 2.29
656 659 9.787435 TTTGGTATTGTAGATGTAGACTGTTTT 57.213 29.630 0.00 0.00 0.00 2.43
657 660 9.216117 GTTTGGTATTGTAGATGTAGACTGTTT 57.784 33.333 0.00 0.00 0.00 2.83
658 661 8.372459 TGTTTGGTATTGTAGATGTAGACTGTT 58.628 33.333 0.00 0.00 0.00 3.16
659 662 7.903145 TGTTTGGTATTGTAGATGTAGACTGT 58.097 34.615 0.00 0.00 0.00 3.55
660 663 8.820933 CATGTTTGGTATTGTAGATGTAGACTG 58.179 37.037 0.00 0.00 0.00 3.51
661 664 8.540388 ACATGTTTGGTATTGTAGATGTAGACT 58.460 33.333 0.00 0.00 0.00 3.24
662 665 8.718102 ACATGTTTGGTATTGTAGATGTAGAC 57.282 34.615 0.00 0.00 0.00 2.59
663 666 9.811995 GTACATGTTTGGTATTGTAGATGTAGA 57.188 33.333 2.30 0.00 0.00 2.59
664 667 9.594478 TGTACATGTTTGGTATTGTAGATGTAG 57.406 33.333 2.30 0.00 0.00 2.74
666 669 9.461312 AATGTACATGTTTGGTATTGTAGATGT 57.539 29.630 9.63 0.00 31.34 3.06
667 670 9.935682 GAATGTACATGTTTGGTATTGTAGATG 57.064 33.333 9.63 0.00 31.34 2.90
668 671 9.905713 AGAATGTACATGTTTGGTATTGTAGAT 57.094 29.630 9.63 0.00 31.99 1.98
669 672 9.161629 CAGAATGTACATGTTTGGTATTGTAGA 57.838 33.333 9.63 0.00 0.00 2.59
670 673 9.161629 TCAGAATGTACATGTTTGGTATTGTAG 57.838 33.333 9.63 0.00 37.40 2.74
671 674 9.508642 TTCAGAATGTACATGTTTGGTATTGTA 57.491 29.630 9.63 0.00 37.40 2.41
672 675 7.994425 TCAGAATGTACATGTTTGGTATTGT 57.006 32.000 9.63 0.00 37.40 2.71
673 676 9.689976 TTTTCAGAATGTACATGTTTGGTATTG 57.310 29.630 9.63 0.00 37.40 1.90
769 772 9.644993 GCAAAAGTCAAACATTACAAATTAACC 57.355 29.630 0.00 0.00 0.00 2.85
776 779 9.766277 GATTTTTGCAAAAGTCAAACATTACAA 57.234 25.926 31.15 12.48 35.47 2.41
777 780 9.160496 AGATTTTTGCAAAAGTCAAACATTACA 57.840 25.926 34.74 15.56 37.17 2.41
782 785 9.474920 CCTATAGATTTTTGCAAAAGTCAAACA 57.525 29.630 34.74 22.58 37.17 2.83
783 786 8.435430 GCCTATAGATTTTTGCAAAAGTCAAAC 58.565 33.333 34.74 20.44 37.17 2.93
784 787 8.147058 TGCCTATAGATTTTTGCAAAAGTCAAA 58.853 29.630 34.74 26.42 37.17 2.69
785 788 7.598493 GTGCCTATAGATTTTTGCAAAAGTCAA 59.402 33.333 34.74 23.52 37.17 3.18
786 789 7.039784 AGTGCCTATAGATTTTTGCAAAAGTCA 60.040 33.333 34.74 25.12 37.17 3.41
787 790 7.315890 AGTGCCTATAGATTTTTGCAAAAGTC 58.684 34.615 29.81 29.81 35.58 3.01
788 791 7.232118 AGTGCCTATAGATTTTTGCAAAAGT 57.768 32.000 22.78 20.72 0.00 2.66
789 792 7.429340 CGTAGTGCCTATAGATTTTTGCAAAAG 59.571 37.037 22.78 10.71 0.00 2.27
790 793 7.094549 ACGTAGTGCCTATAGATTTTTGCAAAA 60.095 33.333 20.46 20.46 42.51 2.44
791 794 6.373216 ACGTAGTGCCTATAGATTTTTGCAAA 59.627 34.615 8.05 8.05 42.51 3.68
792 795 5.878116 ACGTAGTGCCTATAGATTTTTGCAA 59.122 36.000 0.00 0.00 42.51 4.08
793 796 5.424757 ACGTAGTGCCTATAGATTTTTGCA 58.575 37.500 0.00 0.00 42.51 4.08
794 797 5.986004 ACGTAGTGCCTATAGATTTTTGC 57.014 39.130 0.00 0.00 42.51 3.68
795 798 8.495949 CCATAACGTAGTGCCTATAGATTTTTG 58.504 37.037 0.00 0.00 45.00 2.44
796 799 8.426489 TCCATAACGTAGTGCCTATAGATTTTT 58.574 33.333 0.00 0.00 45.00 1.94
797 800 7.959175 TCCATAACGTAGTGCCTATAGATTTT 58.041 34.615 0.00 0.00 45.00 1.82
798 801 7.534723 TCCATAACGTAGTGCCTATAGATTT 57.465 36.000 0.00 0.00 45.00 2.17
799 802 7.376615 GTTCCATAACGTAGTGCCTATAGATT 58.623 38.462 0.00 0.00 45.00 2.40
800 803 6.921914 GTTCCATAACGTAGTGCCTATAGAT 58.078 40.000 0.00 0.00 45.00 1.98
801 804 6.323203 GTTCCATAACGTAGTGCCTATAGA 57.677 41.667 0.00 0.00 45.00 1.98
815 818 2.857592 TACTCGCTCCGTTCCATAAC 57.142 50.000 0.00 0.00 0.00 1.89
816 819 4.392047 TCTATACTCGCTCCGTTCCATAA 58.608 43.478 0.00 0.00 0.00 1.90
817 820 4.011966 TCTATACTCGCTCCGTTCCATA 57.988 45.455 0.00 0.00 0.00 2.74
818 821 2.860009 TCTATACTCGCTCCGTTCCAT 58.140 47.619 0.00 0.00 0.00 3.41
819 822 2.336945 TCTATACTCGCTCCGTTCCA 57.663 50.000 0.00 0.00 0.00 3.53
820 823 3.919223 AATCTATACTCGCTCCGTTCC 57.081 47.619 0.00 0.00 0.00 3.62
821 824 5.286558 GCAATAATCTATACTCGCTCCGTTC 59.713 44.000 0.00 0.00 0.00 3.95
822 825 5.162075 GCAATAATCTATACTCGCTCCGTT 58.838 41.667 0.00 0.00 0.00 4.44
823 826 4.217767 TGCAATAATCTATACTCGCTCCGT 59.782 41.667 0.00 0.00 0.00 4.69
824 827 4.733850 TGCAATAATCTATACTCGCTCCG 58.266 43.478 0.00 0.00 0.00 4.63
825 828 5.062809 GCTTGCAATAATCTATACTCGCTCC 59.937 44.000 0.00 0.00 0.00 4.70
826 829 5.062809 GGCTTGCAATAATCTATACTCGCTC 59.937 44.000 0.00 0.00 0.00 5.03
827 830 4.932200 GGCTTGCAATAATCTATACTCGCT 59.068 41.667 0.00 0.00 0.00 4.93
828 831 4.690748 TGGCTTGCAATAATCTATACTCGC 59.309 41.667 0.00 0.00 0.00 5.03
829 832 6.347725 GGTTGGCTTGCAATAATCTATACTCG 60.348 42.308 0.00 0.00 0.00 4.18
830 833 6.712547 AGGTTGGCTTGCAATAATCTATACTC 59.287 38.462 0.00 0.00 0.00 2.59
884 887 5.299279 ACAGTATTTAATTTCATCCGCCAGG 59.701 40.000 0.00 0.00 39.46 4.45
907 910 5.056553 TCCCTGGGGCAAATATAAAGTAC 57.943 43.478 14.00 0.00 34.68 2.73
910 913 5.188751 TGTTTTCCCTGGGGCAAATATAAAG 59.811 40.000 14.00 0.00 33.42 1.85
912 915 4.689062 TGTTTTCCCTGGGGCAAATATAA 58.311 39.130 14.00 0.00 33.42 0.98
913 916 4.338795 TGTTTTCCCTGGGGCAAATATA 57.661 40.909 14.00 1.75 33.42 0.86
914 917 3.197927 TGTTTTCCCTGGGGCAAATAT 57.802 42.857 14.00 0.00 33.42 1.28
923 926 2.039613 AGCTCTCTCTTGTTTTCCCTGG 59.960 50.000 0.00 0.00 0.00 4.45
941 944 3.070015 CACACATTTTCCTTTTCCCAGCT 59.930 43.478 0.00 0.00 0.00 4.24
952 955 6.027749 CCTCTTTTATACGCACACATTTTCC 58.972 40.000 0.00 0.00 0.00 3.13
953 956 6.027749 CCCTCTTTTATACGCACACATTTTC 58.972 40.000 0.00 0.00 0.00 2.29
956 959 3.377172 GCCCTCTTTTATACGCACACATT 59.623 43.478 0.00 0.00 0.00 2.71
1168 1171 3.951680 GCAGGGATAATCCGGAAAAGAAA 59.048 43.478 9.01 0.00 37.43 2.52
1201 1204 1.066605 GCAGAAATCGCATGCTTCCAT 59.933 47.619 17.13 0.00 37.00 3.41
1255 1258 7.373778 ACAAATTAGTCATTTCTCGGGTAAC 57.626 36.000 0.00 0.00 32.24 2.50
1268 1271 5.302360 AGCAAGAACCGTACAAATTAGTCA 58.698 37.500 0.00 0.00 0.00 3.41
1316 1319 3.578978 TCCAGGTCCTAACTGTTACACA 58.421 45.455 0.00 0.00 34.16 3.72
1420 1821 5.186198 TCATCTACACTCTGATCGAGAACA 58.814 41.667 17.60 0.00 42.62 3.18
1426 1827 5.218885 GTCCAATCATCTACACTCTGATCG 58.781 45.833 0.00 0.00 0.00 3.69
1543 1945 3.106672 GAGTTCTACATGCCGTAACTCG 58.893 50.000 12.31 0.00 31.51 4.18
1789 2199 5.782893 TTTACACCAATTGACAGAAAGGG 57.217 39.130 7.12 0.00 0.00 3.95
1817 2227 2.511600 CACGATGAAGGCCGGACC 60.512 66.667 1.76 4.96 39.61 4.46
2264 2764 6.435430 TTTTAGAATATGTGTGCTCGCAAT 57.565 33.333 6.06 0.00 37.62 3.56
3217 4085 3.760684 GTCAACAGAATCCCAGCAATCTT 59.239 43.478 0.00 0.00 0.00 2.40
3299 4167 3.954258 GGTCAAATATAGCAGCCCACTTT 59.046 43.478 0.00 0.00 0.00 2.66
3300 4168 3.555966 GGTCAAATATAGCAGCCCACTT 58.444 45.455 0.00 0.00 0.00 3.16
3327 4195 2.413239 GGAACATGCGGCATATGATTCG 60.413 50.000 16.21 7.94 0.00 3.34
3799 4717 0.546122 AGTGAACTGGAGCACCAACA 59.454 50.000 3.90 2.52 46.32 3.33
4064 4983 0.875059 AAGAAGAAAAAGGCGGCGAG 59.125 50.000 12.98 0.00 0.00 5.03
4133 5052 2.216940 CACAAATCACAAAAGCAGCACG 59.783 45.455 0.00 0.00 0.00 5.34
4293 5272 0.250901 GAGGAGCCACACCACACAAT 60.251 55.000 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.