Multiple sequence alignment - TraesCS1A01G321800

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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 TraesCS1A01G321800 chr1A 100.000 3607 0 0 1 3607 512651240 512654846 0.000000e+00 6661
1 TraesCS1A01G321800 chr1A 85.265 1622 169 25 688 2262 513859193 513857595 0.000000e+00 1607
2 TraesCS1A01G321800 chr1A 81.918 1554 190 44 1616 3134 512622155 512623652 0.000000e+00 1229
3 TraesCS1A01G321800 chr1A 97.386 153 2 1 546 696 512659282 512659434 3.570000e-65 259
4 TraesCS1A01G321800 chr1A 80.556 252 34 7 2369 2607 513839718 513839469 2.860000e-41 180
5 TraesCS1A01G321800 chr3B 86.133 2048 215 30 688 2697 782449077 782447061 0.000000e+00 2145
6 TraesCS1A01G321800 chr3B 83.677 582 53 25 1 573 782449658 782449110 8.930000e-141 510
7 TraesCS1A01G321800 chr3B 96.739 92 2 1 545 635 560090444 560090353 6.240000e-33 152
8 TraesCS1A01G321800 chr1B 88.711 1683 173 10 688 2362 561500185 561501858 0.000000e+00 2039
9 TraesCS1A01G321800 chr1B 83.642 1620 189 28 688 2262 563228236 563226648 0.000000e+00 1454
10 TraesCS1A01G321800 chr1B 89.094 651 35 20 1 626 561499463 561500102 0.000000e+00 776
11 TraesCS1A01G321800 chr1B 91.667 288 13 3 3323 3607 561504396 561504675 4.370000e-104 388
12 TraesCS1A01G321800 chr1B 81.895 475 22 18 2616 3062 561503378 561503816 3.450000e-90 342
13 TraesCS1A01G321800 chr1B 96.040 101 3 1 546 646 561508661 561508760 2.880000e-36 163
14 TraesCS1A01G321800 chr1B 92.929 99 7 0 2435 2533 561501874 561501972 1.040000e-30 145
15 TraesCS1A01G321800 chr1D 92.887 1195 81 3 724 1918 415287889 415289079 0.000000e+00 1733
16 TraesCS1A01G321800 chr1D 86.513 1520 109 32 1582 3029 415289090 415290585 0.000000e+00 1583
17 TraesCS1A01G321800 chr1D 84.081 1627 172 44 688 2262 416592366 416590775 0.000000e+00 1489
18 TraesCS1A01G321800 chr1D 86.735 588 30 18 3040 3600 415290866 415291432 8.560000e-171 610
19 TraesCS1A01G321800 chr1D 98.283 233 4 0 1 233 415286552 415286784 3.350000e-110 409
20 TraesCS1A01G321800 chr1D 93.684 190 9 2 724 913 415287010 415287196 7.620000e-72 281
21 TraesCS1A01G321800 chr1D 93.158 190 10 2 724 913 415287657 415287843 3.550000e-70 276
22 TraesCS1A01G321800 chr1D 85.256 156 12 10 482 629 415286810 415286962 2.240000e-32 150
23 TraesCS1A01G321800 chr1D 82.716 162 15 5 2458 2607 416510470 416510310 8.130000e-27 132
24 TraesCS1A01G321800 chr7A 86.486 962 116 8 1298 2258 119510142 119511090 0.000000e+00 1044
25 TraesCS1A01G321800 chr7A 85.000 320 34 9 1039 1345 119509829 119510147 2.700000e-81 313
26 TraesCS1A01G321800 chr7A 96.809 94 2 1 536 628 15776893 15776986 4.820000e-34 156
27 TraesCS1A01G321800 chr7A 96.809 94 2 1 536 628 15805018 15805111 4.820000e-34 156
28 TraesCS1A01G321800 chr7A 93.204 103 5 2 545 647 16422105 16422005 2.240000e-32 150
29 TraesCS1A01G321800 chr7B 86.260 968 114 11 1298 2261 74091039 74091991 0.000000e+00 1033
30 TraesCS1A01G321800 chr7B 87.662 308 31 2 1045 1345 74090737 74091044 5.730000e-93 351
31 TraesCS1A01G321800 chr7D 89.577 307 25 3 1039 1345 114583951 114584250 2.030000e-102 383
32 TraesCS1A01G321800 chr3D 89.610 231 21 2 2 232 428762297 428762070 1.270000e-74 291
33 TraesCS1A01G321800 chr3A 90.323 217 21 0 2 218 557006620 557006836 5.890000e-73 285
34 TraesCS1A01G321800 chr4A 93.000 100 7 0 528 627 661302360 661302459 2.900000e-31 147
35 TraesCS1A01G321800 chr4A 90.741 108 7 1 528 635 661318492 661318596 1.350000e-29 141


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 TraesCS1A01G321800 chr1A 512651240 512654846 3606 False 6661.000000 6661 100.000000 1 3607 1 chr1A.!!$F2 3606
1 TraesCS1A01G321800 chr1A 513857595 513859193 1598 True 1607.000000 1607 85.265000 688 2262 1 chr1A.!!$R2 1574
2 TraesCS1A01G321800 chr1A 512622155 512623652 1497 False 1229.000000 1229 81.918000 1616 3134 1 chr1A.!!$F1 1518
3 TraesCS1A01G321800 chr3B 782447061 782449658 2597 True 1327.500000 2145 84.905000 1 2697 2 chr3B.!!$R2 2696
4 TraesCS1A01G321800 chr1B 563226648 563228236 1588 True 1454.000000 1454 83.642000 688 2262 1 chr1B.!!$R1 1574
5 TraesCS1A01G321800 chr1B 561499463 561508760 9297 False 642.166667 2039 90.056000 1 3607 6 chr1B.!!$F1 3606
6 TraesCS1A01G321800 chr1D 416590775 416592366 1591 True 1489.000000 1489 84.081000 688 2262 1 chr1D.!!$R2 1574
7 TraesCS1A01G321800 chr1D 415286552 415291432 4880 False 720.285714 1733 90.930857 1 3600 7 chr1D.!!$F1 3599
8 TraesCS1A01G321800 chr7A 119509829 119511090 1261 False 678.500000 1044 85.743000 1039 2258 2 chr7A.!!$F3 1219
9 TraesCS1A01G321800 chr7B 74090737 74091991 1254 False 692.000000 1033 86.961000 1045 2261 2 chr7B.!!$F1 1216

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
683 733 0.252197 AGGGTTTGTACATCGAGGCC 59.748 55.0 0.00 0.00 0.0 5.19 F
684 734 0.252197 GGGTTTGTACATCGAGGCCT 59.748 55.0 3.86 3.86 0.0 5.19 F
1873 3342 0.680280 AGGTGATAGCTGACGTCGGT 60.680 55.0 24.68 19.02 0.0 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1853 3322 0.029567 CCGACGTCAGCTATCACCTC 59.970 60.0 17.16 0.0 0.00 3.85 R
2235 3710 0.173481 TTCTTCATCCTGAGCCGACG 59.827 55.0 0.00 0.0 0.00 5.12 R
2730 5564 0.805322 CAGCGCAGATGGAGTGTCTC 60.805 60.0 11.47 0.0 42.04 3.36 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
237 249 3.013921 ACGACTTCTCCTTCTAGCTCTG 58.986 50.000 0.00 0.00 0.00 3.35
238 250 2.357637 CGACTTCTCCTTCTAGCTCTGG 59.642 54.545 0.00 0.00 0.00 3.86
239 251 2.100749 GACTTCTCCTTCTAGCTCTGGC 59.899 54.545 0.00 0.00 39.06 4.85
240 252 2.106566 CTTCTCCTTCTAGCTCTGGCA 58.893 52.381 0.00 0.00 41.70 4.92
241 253 2.468301 TCTCCTTCTAGCTCTGGCAT 57.532 50.000 0.00 0.00 41.70 4.40
242 254 2.756907 TCTCCTTCTAGCTCTGGCATT 58.243 47.619 0.00 0.00 41.70 3.56
248 260 4.387598 CTTCTAGCTCTGGCATTAGCATT 58.612 43.478 20.14 6.80 44.61 3.56
363 399 3.511146 CAGAGAAGAGGAGAAGTGAGCTT 59.489 47.826 0.00 0.00 37.71 3.74
377 413 4.816990 GCTTCAGCTACGAGTCCC 57.183 61.111 0.00 0.00 38.21 4.46
378 414 1.226717 GCTTCAGCTACGAGTCCCG 60.227 63.158 0.00 0.00 40.33 5.14
379 415 1.654954 GCTTCAGCTACGAGTCCCGA 61.655 60.000 0.00 0.00 38.81 5.14
380 416 0.809385 CTTCAGCTACGAGTCCCGAA 59.191 55.000 0.00 0.00 41.76 4.30
381 417 1.405821 CTTCAGCTACGAGTCCCGAAT 59.594 52.381 0.00 0.00 41.76 3.34
401 437 1.265635 TGGAATGAACGAAAAGCGGTG 59.734 47.619 0.00 0.00 42.25 4.94
404 440 1.821216 ATGAACGAAAAGCGGTGGAT 58.179 45.000 0.00 0.00 42.25 3.41
434 472 4.035091 TGTGTTTGCAGAATATGGCGATAC 59.965 41.667 0.00 0.00 0.00 2.24
445 483 6.650807 AGAATATGGCGATACGAATTGTGAAT 59.349 34.615 0.00 0.00 0.00 2.57
475 513 5.790003 CGTACATACGTCGAAAGTGTTCTTA 59.210 40.000 0.00 0.00 44.13 2.10
511 556 9.797642 TTATGAAGCAAATATCCTATCACATGT 57.202 29.630 0.00 0.00 0.00 3.21
530 575 9.104965 TCACATGTTAATACCTATGCAGTAAAC 57.895 33.333 0.00 0.00 0.00 2.01
532 579 9.627123 ACATGTTAATACCTATGCAGTAAACAT 57.373 29.630 0.00 8.02 34.08 2.71
535 582 9.456147 TGTTAATACCTATGCAGTAAACATTGT 57.544 29.630 0.00 0.00 0.00 2.71
542 589 4.598406 TGCAGTAAACATTGTAGCATCG 57.402 40.909 0.00 0.00 0.00 3.84
543 590 3.373748 TGCAGTAAACATTGTAGCATCGG 59.626 43.478 0.00 0.00 0.00 4.18
650 700 9.979578 TTTTGAATTTTACTTGTACATGATGCT 57.020 25.926 15.13 0.00 0.00 3.79
651 701 9.624697 TTTGAATTTTACTTGTACATGATGCTC 57.375 29.630 15.13 5.07 0.00 4.26
652 702 7.463544 TGAATTTTACTTGTACATGATGCTCG 58.536 34.615 15.13 0.00 0.00 5.03
653 703 7.333174 TGAATTTTACTTGTACATGATGCTCGA 59.667 33.333 15.13 0.00 0.00 4.04
654 704 7.792374 ATTTTACTTGTACATGATGCTCGAT 57.208 32.000 15.13 0.00 0.00 3.59
655 705 7.609760 TTTTACTTGTACATGATGCTCGATT 57.390 32.000 15.13 0.00 0.00 3.34
656 706 8.710835 TTTTACTTGTACATGATGCTCGATTA 57.289 30.769 15.13 0.00 0.00 1.75
657 707 7.694388 TTACTTGTACATGATGCTCGATTAC 57.306 36.000 15.13 0.00 0.00 1.89
658 708 5.907207 ACTTGTACATGATGCTCGATTACT 58.093 37.500 15.13 0.00 0.00 2.24
659 709 5.750547 ACTTGTACATGATGCTCGATTACTG 59.249 40.000 15.13 0.00 0.00 2.74
660 710 4.620982 TGTACATGATGCTCGATTACTGG 58.379 43.478 0.00 0.00 0.00 4.00
661 711 4.340950 TGTACATGATGCTCGATTACTGGA 59.659 41.667 0.00 0.00 0.00 3.86
662 712 3.722147 ACATGATGCTCGATTACTGGAC 58.278 45.455 0.00 0.00 0.00 4.02
663 713 3.386078 ACATGATGCTCGATTACTGGACT 59.614 43.478 0.00 0.00 0.00 3.85
664 714 4.584743 ACATGATGCTCGATTACTGGACTA 59.415 41.667 0.00 0.00 0.00 2.59
665 715 4.837896 TGATGCTCGATTACTGGACTAG 57.162 45.455 0.00 0.00 0.00 2.57
666 716 3.570125 TGATGCTCGATTACTGGACTAGG 59.430 47.826 0.00 0.00 0.00 3.02
667 717 2.307768 TGCTCGATTACTGGACTAGGG 58.692 52.381 0.00 0.00 0.00 3.53
668 718 2.308690 GCTCGATTACTGGACTAGGGT 58.691 52.381 0.00 0.00 0.00 4.34
669 719 2.694109 GCTCGATTACTGGACTAGGGTT 59.306 50.000 0.00 0.00 0.00 4.11
670 720 3.132467 GCTCGATTACTGGACTAGGGTTT 59.868 47.826 0.00 0.00 0.00 3.27
671 721 4.683832 CTCGATTACTGGACTAGGGTTTG 58.316 47.826 0.00 0.00 0.00 2.93
672 722 4.091549 TCGATTACTGGACTAGGGTTTGT 58.908 43.478 0.00 0.00 0.00 2.83
673 723 5.263599 TCGATTACTGGACTAGGGTTTGTA 58.736 41.667 0.00 0.00 0.00 2.41
674 724 5.126061 TCGATTACTGGACTAGGGTTTGTAC 59.874 44.000 0.00 0.00 0.00 2.90
675 725 5.105635 CGATTACTGGACTAGGGTTTGTACA 60.106 44.000 0.00 0.00 0.00 2.90
676 726 6.406624 CGATTACTGGACTAGGGTTTGTACAT 60.407 42.308 0.00 0.00 0.00 2.29
677 727 4.820894 ACTGGACTAGGGTTTGTACATC 57.179 45.455 0.00 0.00 0.00 3.06
678 728 3.194968 ACTGGACTAGGGTTTGTACATCG 59.805 47.826 0.00 0.00 0.00 3.84
679 729 3.433343 TGGACTAGGGTTTGTACATCGA 58.567 45.455 0.00 0.00 0.00 3.59
680 730 3.446161 TGGACTAGGGTTTGTACATCGAG 59.554 47.826 0.00 0.00 0.00 4.04
681 731 3.181478 GGACTAGGGTTTGTACATCGAGG 60.181 52.174 0.00 0.00 0.00 4.63
682 732 2.167900 ACTAGGGTTTGTACATCGAGGC 59.832 50.000 0.00 0.00 0.00 4.70
683 733 0.252197 AGGGTTTGTACATCGAGGCC 59.748 55.000 0.00 0.00 0.00 5.19
684 734 0.252197 GGGTTTGTACATCGAGGCCT 59.748 55.000 3.86 3.86 0.00 5.19
685 735 1.483415 GGGTTTGTACATCGAGGCCTA 59.517 52.381 4.42 0.00 0.00 3.93
686 736 2.547826 GGTTTGTACATCGAGGCCTAC 58.452 52.381 4.42 0.00 0.00 3.18
691 741 2.308690 GTACATCGAGGCCTACTTCCT 58.691 52.381 4.42 0.00 36.46 3.36
699 749 3.550436 CGAGGCCTACTTCCTATTTCGTC 60.550 52.174 4.42 0.00 33.24 4.20
702 752 3.071167 GGCCTACTTCCTATTTCGTCCAT 59.929 47.826 0.00 0.00 0.00 3.41
766 1554 5.852827 AGGCGATTTTTCATTCTTTCCAAA 58.147 33.333 0.00 0.00 0.00 3.28
835 1624 6.699642 TGAAAGGAAAAATAGGCGTTTCTTTG 59.300 34.615 0.00 0.00 37.33 2.77
913 1708 5.180492 TCCTATTTTGAAACGAATGCGAACT 59.820 36.000 0.00 0.00 41.64 3.01
1059 2091 1.265454 CCACCTCCACCTCCACCTAC 61.265 65.000 0.00 0.00 0.00 3.18
1167 2214 1.882912 TCGTTGACAATGAAGCAGCT 58.117 45.000 7.65 0.00 0.00 4.24
1345 2455 2.227626 CGATGACAGCTATGACGAGGAT 59.772 50.000 0.00 0.00 0.00 3.24
1480 2590 0.690762 GGTCCCTTGAGCCAACACTA 59.309 55.000 0.00 0.00 32.76 2.74
1751 3220 2.651361 CTTGGTCGTCTCTGGCGT 59.349 61.111 0.00 0.00 0.00 5.68
1861 3330 1.712018 CCACGCGTCTCGAGGTGATA 61.712 60.000 9.86 0.00 42.79 2.15
1873 3342 0.680280 AGGTGATAGCTGACGTCGGT 60.680 55.000 24.68 19.02 0.00 4.69
1896 3365 1.440938 CTCCGGCTCGAGGACTACAG 61.441 65.000 15.58 0.00 33.58 2.74
1910 3379 1.209504 ACTACAGGTATTGGCGCATGT 59.790 47.619 10.83 4.46 0.00 3.21
2031 3506 1.153823 CGGACGAAGATGAAGCCGT 60.154 57.895 0.00 0.00 38.01 5.68
2034 3509 1.743855 GACGAAGATGAAGCCGTCGC 61.744 60.000 0.00 0.00 41.22 5.19
2037 3512 1.696832 GAAGATGAAGCCGTCGCCAC 61.697 60.000 0.00 0.00 34.57 5.01
2113 3588 2.281761 AAGTGCCCCGTCTGCTTG 60.282 61.111 0.00 0.00 0.00 4.01
2177 3652 2.350895 CCCACGTCTTCCATGGCA 59.649 61.111 6.96 0.00 31.66 4.92
2297 3772 0.249955 TCTTCTGCGGTGATGATGCA 59.750 50.000 0.00 0.00 37.07 3.96
2302 3777 0.107557 TGCGGTGATGATGCATGAGT 60.108 50.000 2.46 0.00 32.86 3.41
2327 3802 5.746245 GCATTGCAGTACACACAAGTAAAAA 59.254 36.000 3.15 0.00 0.00 1.94
2340 3815 8.879759 CACACAAGTAAAAAGAAGTAGTTCTCA 58.120 33.333 13.22 0.00 42.59 3.27
2358 3833 6.603997 AGTTCTCAACGAATACATCCTACTCT 59.396 38.462 0.00 0.00 36.23 3.24
2362 3837 5.236695 TCAACGAATACATCCTACTCTCTCG 59.763 44.000 0.00 0.00 0.00 4.04
2403 3879 5.613964 CGTTTTGACATTACGCTTGTTTT 57.386 34.783 0.00 0.00 0.00 2.43
2404 3880 6.015268 CGTTTTGACATTACGCTTGTTTTT 57.985 33.333 0.00 0.00 0.00 1.94
2422 3898 4.678509 TTTTGTAATGGAGCATCGTGTC 57.321 40.909 0.00 0.00 34.37 3.67
2427 3903 2.425143 ATGGAGCATCGTGTCCAAAT 57.575 45.000 0.00 0.00 46.01 2.32
2433 3909 3.407698 AGCATCGTGTCCAAATGTTGTA 58.592 40.909 0.00 0.00 0.00 2.41
2479 3955 6.961554 CGCACTACCTCAGTTTCAAAATAATC 59.038 38.462 0.00 0.00 34.26 1.75
2498 3974 3.936902 TCGAAGTTTTGAGTTTGTCCG 57.063 42.857 0.00 0.00 0.00 4.79
2564 4052 8.152898 CACCCAATTAGTCTCATGAGATTATCA 58.847 37.037 27.51 14.18 43.70 2.15
2571 4059 9.978044 TTAGTCTCATGAGATTATCAGTGAATG 57.022 33.333 27.51 0.00 42.53 2.67
2572 4060 8.020777 AGTCTCATGAGATTATCAGTGAATGT 57.979 34.615 27.51 0.00 42.53 2.71
2573 4061 8.484575 AGTCTCATGAGATTATCAGTGAATGTT 58.515 33.333 27.51 0.00 42.53 2.71
2574 4062 9.107177 GTCTCATGAGATTATCAGTGAATGTTT 57.893 33.333 27.51 0.00 42.53 2.83
2604 4102 4.790937 TCATGGCCAGCTATGTTGAAATA 58.209 39.130 13.05 0.00 36.49 1.40
2616 5425 7.549488 AGCTATGTTGAAATAAACGAGCTTACT 59.451 33.333 9.32 0.00 43.77 2.24
2617 5426 8.175716 GCTATGTTGAAATAAACGAGCTTACTT 58.824 33.333 0.00 0.00 38.04 2.24
2620 5429 8.597662 TGTTGAAATAAACGAGCTTACTTACT 57.402 30.769 0.00 0.00 32.47 2.24
2621 5430 9.048446 TGTTGAAATAAACGAGCTTACTTACTT 57.952 29.630 0.00 0.00 32.47 2.24
2638 5447 7.681939 ACTTACTTTTCACAACAAAGACAGA 57.318 32.000 0.00 0.00 35.54 3.41
2653 5462 0.329596 ACAGAAGGCTCATCCAACCC 59.670 55.000 0.00 0.00 37.29 4.11
2657 5466 0.779997 AAGGCTCATCCAACCCACTT 59.220 50.000 0.00 0.00 37.29 3.16
2661 5493 2.492088 GGCTCATCCAACCCACTTAAAC 59.508 50.000 0.00 0.00 34.01 2.01
2662 5494 3.421844 GCTCATCCAACCCACTTAAACT 58.578 45.455 0.00 0.00 0.00 2.66
2663 5495 4.566907 GGCTCATCCAACCCACTTAAACTA 60.567 45.833 0.00 0.00 34.01 2.24
2664 5496 5.007682 GCTCATCCAACCCACTTAAACTAA 58.992 41.667 0.00 0.00 0.00 2.24
2665 5497 5.475564 GCTCATCCAACCCACTTAAACTAAA 59.524 40.000 0.00 0.00 0.00 1.85
2675 5507 9.650714 AACCCACTTAAACTAAAAAGGACTTAT 57.349 29.630 0.00 0.00 0.00 1.73
2676 5508 9.650714 ACCCACTTAAACTAAAAAGGACTTATT 57.349 29.630 0.00 0.00 0.00 1.40
2708 5542 5.163248 ACCCCACCTGAATTTTTGTAAAAGG 60.163 40.000 0.00 0.00 0.00 3.11
2713 5547 8.951243 CCACCTGAATTTTTGTAAAAGGAAAAA 58.049 29.630 0.00 0.00 35.95 1.94
2858 5713 0.173481 TCCTTCCAGATTCGCACTCG 59.827 55.000 0.00 0.00 0.00 4.18
2928 5786 2.004120 ACCCATACCCAATCCGCCA 61.004 57.895 0.00 0.00 0.00 5.69
2934 5792 1.415672 TACCCAATCCGCCATCCCTC 61.416 60.000 0.00 0.00 0.00 4.30
3164 6642 3.956377 GGATCTCCTCCGCTTCCA 58.044 61.111 0.00 0.00 33.29 3.53
3219 6697 0.877649 CGCTTGCGCTGATGGATAGT 60.878 55.000 9.73 0.00 0.00 2.12
3389 6904 1.617947 TTTTTGGTGGGTGTGGGTGC 61.618 55.000 0.00 0.00 0.00 5.01
3390 6905 4.885270 TTGGTGGGTGTGGGTGCG 62.885 66.667 0.00 0.00 0.00 5.34
3421 6936 5.450550 GCTTTGTTGCCACTATAGGGAATTC 60.451 44.000 2.68 0.00 41.22 2.17
3430 6945 4.772624 CACTATAGGGAATTCGGGATCTGA 59.227 45.833 4.43 0.00 0.00 3.27
3434 6949 1.421646 GGGAATTCGGGATCTGACCAT 59.578 52.381 0.00 0.00 0.00 3.55
3479 6994 1.282875 GTGGAGTTCGGTTTGCTGC 59.717 57.895 0.00 0.00 0.00 5.25
3480 6995 1.896660 TGGAGTTCGGTTTGCTGCC 60.897 57.895 0.00 0.00 0.00 4.85
3551 7066 0.107654 CGACAGGTGGGGAAATCTCC 60.108 60.000 0.00 0.00 41.59 3.71
3552 7067 0.991920 GACAGGTGGGGAAATCTCCA 59.008 55.000 0.00 0.00 44.51 3.86
3557 7072 2.517166 GGGGAAATCTCCAGCGGC 60.517 66.667 0.00 0.00 44.51 6.53
3603 7118 1.087771 ATGCCCGGTCGATTTTCGTC 61.088 55.000 0.00 0.00 41.35 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
237 249 2.908073 CGGCGGGAATGCTAATGCC 61.908 63.158 0.00 0.00 38.71 4.40
238 250 2.117941 GACGGCGGGAATGCTAATGC 62.118 60.000 13.24 0.00 40.20 3.56
239 251 1.831389 CGACGGCGGGAATGCTAATG 61.831 60.000 13.24 0.00 34.52 1.90
240 252 1.594293 CGACGGCGGGAATGCTAAT 60.594 57.895 13.24 0.00 34.52 1.73
241 253 2.202824 CGACGGCGGGAATGCTAA 60.203 61.111 13.24 0.00 34.52 3.09
242 254 3.454573 ACGACGGCGGGAATGCTA 61.455 61.111 18.49 0.00 43.17 3.49
321 352 2.356382 TGTACAAACAAAGCCAGTTCCG 59.644 45.455 0.00 0.00 30.91 4.30
363 399 0.738975 CATTCGGGACTCGTAGCTGA 59.261 55.000 0.00 0.00 40.32 4.26
376 412 3.171277 GCTTTTCGTTCATTCCATTCGG 58.829 45.455 0.00 0.00 0.00 4.30
377 413 2.840176 CGCTTTTCGTTCATTCCATTCG 59.160 45.455 0.00 0.00 0.00 3.34
378 414 3.171277 CCGCTTTTCGTTCATTCCATTC 58.829 45.455 0.00 0.00 36.19 2.67
379 415 2.556622 ACCGCTTTTCGTTCATTCCATT 59.443 40.909 0.00 0.00 36.19 3.16
380 416 2.095263 CACCGCTTTTCGTTCATTCCAT 60.095 45.455 0.00 0.00 36.19 3.41
381 417 1.265635 CACCGCTTTTCGTTCATTCCA 59.734 47.619 0.00 0.00 36.19 3.53
401 437 4.764679 TCTGCAAACACACACAATATCC 57.235 40.909 0.00 0.00 0.00 2.59
404 440 6.619744 CCATATTCTGCAAACACACACAATA 58.380 36.000 0.00 0.00 0.00 1.90
434 472 6.583912 ATGTACGGTAAGATTCACAATTCG 57.416 37.500 0.00 0.00 0.00 3.34
499 543 8.201242 TGCATAGGTATTAACATGTGATAGGA 57.799 34.615 0.00 0.00 30.99 2.94
503 547 9.845740 TTTACTGCATAGGTATTAACATGTGAT 57.154 29.630 0.00 0.00 30.99 3.06
506 550 9.627123 ATGTTTACTGCATAGGTATTAACATGT 57.373 29.630 11.14 0.00 33.30 3.21
517 562 6.564686 CGATGCTACAATGTTTACTGCATAGG 60.565 42.308 0.00 0.00 39.36 2.57
518 563 6.357980 CGATGCTACAATGTTTACTGCATAG 58.642 40.000 0.00 0.00 39.36 2.23
527 572 2.930040 CGACTCCGATGCTACAATGTTT 59.070 45.455 0.00 0.00 38.22 2.83
530 575 2.209838 ACGACTCCGATGCTACAATG 57.790 50.000 0.00 0.00 39.50 2.82
532 579 1.271379 ACAACGACTCCGATGCTACAA 59.729 47.619 0.00 0.00 41.46 2.41
535 582 2.362736 ACTACAACGACTCCGATGCTA 58.637 47.619 0.00 0.00 41.46 3.49
537 584 2.838386 TACTACAACGACTCCGATGC 57.162 50.000 0.00 0.00 41.46 3.91
542 589 6.317391 ACTTACCACTATACTACAACGACTCC 59.683 42.308 0.00 0.00 0.00 3.85
543 590 7.313951 ACTTACCACTATACTACAACGACTC 57.686 40.000 0.00 0.00 0.00 3.36
628 678 7.684670 TCGAGCATCATGTACAAGTAAAATTC 58.315 34.615 0.00 0.00 33.17 2.17
629 679 7.609760 TCGAGCATCATGTACAAGTAAAATT 57.390 32.000 0.00 0.00 33.17 1.82
630 680 7.792374 ATCGAGCATCATGTACAAGTAAAAT 57.208 32.000 0.00 0.00 33.17 1.82
631 681 7.609760 AATCGAGCATCATGTACAAGTAAAA 57.390 32.000 0.00 0.00 33.17 1.52
632 682 7.979537 AGTAATCGAGCATCATGTACAAGTAAA 59.020 33.333 0.00 0.00 33.17 2.01
633 683 7.435192 CAGTAATCGAGCATCATGTACAAGTAA 59.565 37.037 0.00 0.00 33.17 2.24
634 684 6.918022 CAGTAATCGAGCATCATGTACAAGTA 59.082 38.462 0.00 0.00 33.17 2.24
635 685 5.750547 CAGTAATCGAGCATCATGTACAAGT 59.249 40.000 0.00 0.00 33.17 3.16
636 686 5.176406 CCAGTAATCGAGCATCATGTACAAG 59.824 44.000 0.00 0.00 33.17 3.16
637 687 5.049828 CCAGTAATCGAGCATCATGTACAA 58.950 41.667 0.00 0.00 33.17 2.41
638 688 4.340950 TCCAGTAATCGAGCATCATGTACA 59.659 41.667 0.00 0.00 33.17 2.90
639 689 4.681942 GTCCAGTAATCGAGCATCATGTAC 59.318 45.833 0.00 0.00 33.17 2.90
640 690 4.584743 AGTCCAGTAATCGAGCATCATGTA 59.415 41.667 0.00 0.00 33.17 2.29
641 691 3.386078 AGTCCAGTAATCGAGCATCATGT 59.614 43.478 0.00 0.00 33.17 3.21
642 692 3.987547 AGTCCAGTAATCGAGCATCATG 58.012 45.455 0.00 0.00 33.17 3.07
643 693 4.219507 CCTAGTCCAGTAATCGAGCATCAT 59.780 45.833 0.00 0.00 33.17 2.45
644 694 3.570125 CCTAGTCCAGTAATCGAGCATCA 59.430 47.826 0.00 0.00 33.17 3.07
645 695 3.057174 CCCTAGTCCAGTAATCGAGCATC 60.057 52.174 0.00 0.00 0.00 3.91
646 696 2.894126 CCCTAGTCCAGTAATCGAGCAT 59.106 50.000 0.00 0.00 0.00 3.79
647 697 2.307768 CCCTAGTCCAGTAATCGAGCA 58.692 52.381 0.00 0.00 0.00 4.26
648 698 2.308690 ACCCTAGTCCAGTAATCGAGC 58.691 52.381 0.00 0.00 0.00 5.03
649 699 4.159879 ACAAACCCTAGTCCAGTAATCGAG 59.840 45.833 0.00 0.00 0.00 4.04
650 700 4.091549 ACAAACCCTAGTCCAGTAATCGA 58.908 43.478 0.00 0.00 0.00 3.59
651 701 4.467198 ACAAACCCTAGTCCAGTAATCG 57.533 45.455 0.00 0.00 0.00 3.34
652 702 6.290294 TGTACAAACCCTAGTCCAGTAATC 57.710 41.667 0.00 0.00 0.00 1.75
653 703 6.406624 CGATGTACAAACCCTAGTCCAGTAAT 60.407 42.308 0.00 0.00 0.00 1.89
654 704 5.105635 CGATGTACAAACCCTAGTCCAGTAA 60.106 44.000 0.00 0.00 0.00 2.24
655 705 4.400251 CGATGTACAAACCCTAGTCCAGTA 59.600 45.833 0.00 0.00 0.00 2.74
656 706 3.194968 CGATGTACAAACCCTAGTCCAGT 59.805 47.826 0.00 0.00 0.00 4.00
657 707 3.446161 TCGATGTACAAACCCTAGTCCAG 59.554 47.826 0.00 0.00 0.00 3.86
658 708 3.433343 TCGATGTACAAACCCTAGTCCA 58.567 45.455 0.00 0.00 0.00 4.02
659 709 3.181478 CCTCGATGTACAAACCCTAGTCC 60.181 52.174 0.00 0.00 0.00 3.85
660 710 3.737355 GCCTCGATGTACAAACCCTAGTC 60.737 52.174 0.00 0.00 0.00 2.59
661 711 2.167900 GCCTCGATGTACAAACCCTAGT 59.832 50.000 0.00 0.00 0.00 2.57
662 712 2.483188 GGCCTCGATGTACAAACCCTAG 60.483 54.545 0.00 0.00 0.00 3.02
663 713 1.483415 GGCCTCGATGTACAAACCCTA 59.517 52.381 0.00 0.00 0.00 3.53
664 714 0.252197 GGCCTCGATGTACAAACCCT 59.748 55.000 0.00 0.00 0.00 4.34
665 715 0.252197 AGGCCTCGATGTACAAACCC 59.748 55.000 0.00 0.00 0.00 4.11
666 716 2.167900 AGTAGGCCTCGATGTACAAACC 59.832 50.000 9.68 0.00 0.00 3.27
667 717 3.521947 AGTAGGCCTCGATGTACAAAC 57.478 47.619 9.68 0.00 0.00 2.93
668 718 3.118884 GGAAGTAGGCCTCGATGTACAAA 60.119 47.826 9.68 0.00 0.00 2.83
669 719 2.429610 GGAAGTAGGCCTCGATGTACAA 59.570 50.000 9.68 0.00 0.00 2.41
670 720 2.029623 GGAAGTAGGCCTCGATGTACA 58.970 52.381 9.68 0.00 0.00 2.90
671 721 2.308690 AGGAAGTAGGCCTCGATGTAC 58.691 52.381 9.68 0.00 0.00 2.90
672 722 2.750141 AGGAAGTAGGCCTCGATGTA 57.250 50.000 9.68 0.00 0.00 2.29
673 723 2.750141 TAGGAAGTAGGCCTCGATGT 57.250 50.000 9.68 0.00 36.96 3.06
674 724 4.561105 GAAATAGGAAGTAGGCCTCGATG 58.439 47.826 9.68 0.00 36.96 3.84
675 725 3.256136 CGAAATAGGAAGTAGGCCTCGAT 59.744 47.826 9.68 0.00 36.96 3.59
676 726 2.621998 CGAAATAGGAAGTAGGCCTCGA 59.378 50.000 9.68 0.00 36.96 4.04
677 727 2.361438 ACGAAATAGGAAGTAGGCCTCG 59.639 50.000 9.68 4.52 36.96 4.63
678 728 3.243805 GGACGAAATAGGAAGTAGGCCTC 60.244 52.174 9.68 0.21 36.96 4.70
679 729 2.699321 GGACGAAATAGGAAGTAGGCCT 59.301 50.000 11.78 11.78 39.56 5.19
680 730 2.433239 TGGACGAAATAGGAAGTAGGCC 59.567 50.000 0.00 0.00 0.00 5.19
681 731 3.814005 TGGACGAAATAGGAAGTAGGC 57.186 47.619 0.00 0.00 0.00 3.93
682 732 7.625828 AAAAATGGACGAAATAGGAAGTAGG 57.374 36.000 0.00 0.00 0.00 3.18
683 733 9.595823 TCTAAAAATGGACGAAATAGGAAGTAG 57.404 33.333 0.00 0.00 0.00 2.57
685 735 9.462606 AATCTAAAAATGGACGAAATAGGAAGT 57.537 29.630 0.00 0.00 0.00 3.01
691 741 8.471609 GGGGAAAATCTAAAAATGGACGAAATA 58.528 33.333 0.00 0.00 0.00 1.40
699 749 8.690203 AAACAAAGGGGAAAATCTAAAAATGG 57.310 30.769 0.00 0.00 0.00 3.16
748 889 7.226325 TGCACGAATTTGGAAAGAATGAAAAAT 59.774 29.630 0.00 0.00 0.00 1.82
754 895 4.549458 ACTGCACGAATTTGGAAAGAATG 58.451 39.130 0.00 0.00 0.00 2.67
766 1554 4.157840 GGGGAGATTTAAAACTGCACGAAT 59.842 41.667 16.72 0.00 0.00 3.34
937 1963 1.078426 CCAATCCGAAACCGGCTCT 60.078 57.895 0.00 0.00 46.35 4.09
1029 2057 2.422945 GGTGGAGGTGGAGTTTGTTCTT 60.423 50.000 0.00 0.00 0.00 2.52
1146 2193 2.618241 AGCTGCTTCATTGTCAACGAAA 59.382 40.909 0.00 0.00 0.00 3.46
1156 2203 2.103042 GTCGCCGAGCTGCTTCATT 61.103 57.895 2.53 0.00 0.00 2.57
1291 2338 4.710167 TCGTCCTCCTCGCCGTCA 62.710 66.667 0.00 0.00 0.00 4.35
1345 2455 2.541288 GACCTCGTCGTCACTCTCA 58.459 57.895 0.00 0.00 32.74 3.27
1464 2574 1.072331 ACTGTAGTGTTGGCTCAAGGG 59.928 52.381 0.00 0.00 0.00 3.95
1470 2580 1.133792 AGGCAAACTGTAGTGTTGGCT 60.134 47.619 19.78 19.78 44.10 4.75
1480 2590 2.750350 CCCGAGGAGGCAAACTGT 59.250 61.111 0.00 0.00 39.21 3.55
1640 3109 4.778415 CACCTCCACGCCGTCGAG 62.778 72.222 4.80 4.80 39.41 4.04
1643 3112 4.736896 GGACACCTCCACGCCGTC 62.737 72.222 0.00 0.00 36.42 4.79
1736 3205 3.733960 CGACGCCAGAGACGACCA 61.734 66.667 0.00 0.00 0.00 4.02
1751 3220 2.280552 GGGCGGGGTATATCAGCGA 61.281 63.158 0.00 0.00 0.00 4.93
1853 3322 0.029567 CCGACGTCAGCTATCACCTC 59.970 60.000 17.16 0.00 0.00 3.85
1861 3330 1.102222 GGAGGATACCGACGTCAGCT 61.102 60.000 17.16 0.00 37.17 4.24
1896 3365 3.773117 GCATACATGCGCCAATACC 57.227 52.632 4.18 0.00 44.67 2.73
2177 3652 4.003788 CGTCCCCTCAAGGCACGT 62.004 66.667 9.48 0.00 36.08 4.49
2235 3710 0.173481 TTCTTCATCCTGAGCCGACG 59.827 55.000 0.00 0.00 0.00 5.12
2297 3772 2.485426 GTGTGTACTGCAATGCACTCAT 59.515 45.455 17.04 0.00 36.29 2.90
2302 3777 2.296792 ACTTGTGTGTACTGCAATGCA 58.703 42.857 7.99 7.99 36.92 3.96
2327 3802 7.122948 AGGATGTATTCGTTGAGAACTACTTCT 59.877 37.037 0.00 0.00 42.39 2.85
2340 3815 4.515944 CCGAGAGAGTAGGATGTATTCGTT 59.484 45.833 0.00 0.00 0.00 3.85
2358 3833 5.616204 CGCGTCTTATATTATGTGACCGAGA 60.616 44.000 0.00 0.00 0.00 4.04
2362 3837 6.520792 AAACGCGTCTTATATTATGTGACC 57.479 37.500 14.44 0.00 0.00 4.02
2403 3879 2.027653 TGGACACGATGCTCCATTACAA 60.028 45.455 0.00 0.00 31.20 2.41
2404 3880 1.552792 TGGACACGATGCTCCATTACA 59.447 47.619 0.00 0.00 31.20 2.41
2422 3898 1.538075 GGTGACGGGTACAACATTTGG 59.462 52.381 0.00 0.00 34.12 3.28
2427 3903 1.831726 TCGGGTGACGGGTACAACA 60.832 57.895 0.00 0.00 44.45 3.33
2479 3955 3.936902 TCGGACAAACTCAAAACTTCG 57.063 42.857 0.00 0.00 0.00 3.79
2498 3974 6.695713 GGTCAACCATAAACAAGTTTGACTTC 59.304 38.462 8.37 0.00 34.21 3.01
2533 4009 3.788227 TGAGACTAATTGGGTGTTGCT 57.212 42.857 0.00 0.00 0.00 3.91
2564 4052 4.563993 CCATGATGGCCAAAAACATTCACT 60.564 41.667 10.96 0.00 0.00 3.41
2589 4082 6.111768 AGCTCGTTTATTTCAACATAGCTG 57.888 37.500 0.00 0.00 41.06 4.24
2604 4102 6.913873 TGTGAAAAGTAAGTAAGCTCGTTT 57.086 33.333 0.00 0.00 0.00 3.60
2616 5425 7.535139 CCTTCTGTCTTTGTTGTGAAAAGTAA 58.465 34.615 0.00 0.00 36.29 2.24
2617 5426 6.404293 GCCTTCTGTCTTTGTTGTGAAAAGTA 60.404 38.462 0.00 0.00 36.29 2.24
2618 5427 5.622233 GCCTTCTGTCTTTGTTGTGAAAAGT 60.622 40.000 0.00 0.00 36.29 2.66
2619 5428 4.800471 GCCTTCTGTCTTTGTTGTGAAAAG 59.200 41.667 0.00 0.00 36.22 2.27
2620 5429 4.462483 AGCCTTCTGTCTTTGTTGTGAAAA 59.538 37.500 0.00 0.00 0.00 2.29
2621 5430 4.016444 AGCCTTCTGTCTTTGTTGTGAAA 58.984 39.130 0.00 0.00 0.00 2.69
2638 5447 0.779997 AAGTGGGTTGGATGAGCCTT 59.220 50.000 0.00 0.00 38.04 4.35
2661 5493 9.687210 GGGTGTTGTAAAATAAGTCCTTTTTAG 57.313 33.333 0.00 0.00 30.27 1.85
2662 5494 8.640651 GGGGTGTTGTAAAATAAGTCCTTTTTA 58.359 33.333 0.00 0.00 0.00 1.52
2663 5495 7.125963 TGGGGTGTTGTAAAATAAGTCCTTTTT 59.874 33.333 0.00 0.00 0.00 1.94
2664 5496 6.612049 TGGGGTGTTGTAAAATAAGTCCTTTT 59.388 34.615 0.00 0.00 0.00 2.27
2665 5497 6.041182 GTGGGGTGTTGTAAAATAAGTCCTTT 59.959 38.462 0.00 0.00 0.00 3.11
2675 5507 3.383698 TTCAGGTGGGGTGTTGTAAAA 57.616 42.857 0.00 0.00 0.00 1.52
2676 5508 3.603965 ATTCAGGTGGGGTGTTGTAAA 57.396 42.857 0.00 0.00 0.00 2.01
2713 5547 2.820197 GTCTCCCGCAGAATTTCCTTTT 59.180 45.455 0.00 0.00 30.72 2.27
2714 5548 2.224769 TGTCTCCCGCAGAATTTCCTTT 60.225 45.455 0.00 0.00 30.72 3.11
2715 5549 1.351017 TGTCTCCCGCAGAATTTCCTT 59.649 47.619 0.00 0.00 30.72 3.36
2716 5550 0.984230 TGTCTCCCGCAGAATTTCCT 59.016 50.000 0.00 0.00 30.72 3.36
2730 5564 0.805322 CAGCGCAGATGGAGTGTCTC 60.805 60.000 11.47 0.00 42.04 3.36
2880 5735 2.273449 CAGAGGTGGTGGATGGGC 59.727 66.667 0.00 0.00 0.00 5.36
2881 5736 0.911525 AGTCAGAGGTGGTGGATGGG 60.912 60.000 0.00 0.00 0.00 4.00
2885 5740 1.147191 ACTGTAGTCAGAGGTGGTGGA 59.853 52.381 2.17 0.00 43.76 4.02
3115 6592 4.475135 GGGTGGAAGAGGAGCGGC 62.475 72.222 0.00 0.00 0.00 6.53
3120 6597 4.649705 TGCGGGGGTGGAAGAGGA 62.650 66.667 0.00 0.00 0.00 3.71
3125 6602 3.407967 GGATCTGCGGGGGTGGAA 61.408 66.667 0.00 0.00 0.00 3.53
3204 6682 1.202568 CCTCAACTATCCATCAGCGCA 60.203 52.381 11.47 0.00 0.00 6.09
3206 6684 2.898729 ACCTCAACTATCCATCAGCG 57.101 50.000 0.00 0.00 0.00 5.18
3207 6685 3.126831 CGAACCTCAACTATCCATCAGC 58.873 50.000 0.00 0.00 0.00 4.26
3208 6686 3.722147 CCGAACCTCAACTATCCATCAG 58.278 50.000 0.00 0.00 0.00 2.90
3209 6687 2.158957 GCCGAACCTCAACTATCCATCA 60.159 50.000 0.00 0.00 0.00 3.07
3210 6688 2.158957 TGCCGAACCTCAACTATCCATC 60.159 50.000 0.00 0.00 0.00 3.51
3211 6689 1.837439 TGCCGAACCTCAACTATCCAT 59.163 47.619 0.00 0.00 0.00 3.41
3212 6690 1.207089 CTGCCGAACCTCAACTATCCA 59.793 52.381 0.00 0.00 0.00 3.41
3213 6691 1.941325 CTGCCGAACCTCAACTATCC 58.059 55.000 0.00 0.00 0.00 2.59
3219 6697 2.669569 GCTGCTGCCGAACCTCAA 60.670 61.111 3.85 0.00 0.00 3.02
3389 6904 4.999939 GCAACAAAGCCGCACCCG 63.000 66.667 0.00 0.00 0.00 5.28
3390 6905 4.662961 GGCAACAAAGCCGCACCC 62.663 66.667 0.00 0.00 46.12 4.61
3413 6928 1.132500 GGTCAGATCCCGAATTCCCT 58.868 55.000 0.00 0.00 0.00 4.20
3421 6936 1.766059 TCCCCATGGTCAGATCCCG 60.766 63.158 11.73 0.00 0.00 5.14
3446 6961 1.258982 CTCCACGAGCGATAAATGTGC 59.741 52.381 0.00 0.00 0.00 4.57
3557 7072 1.638133 CATCAGAGACAGCCTGAACG 58.362 55.000 0.00 0.00 43.07 3.95


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

AutoCloner maintained by Alex Coulton.