Multiple sequence alignment - TraesCS5D01G473900

Loading Multiple Alignment...

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 TraesCS5D01G473900 chr5D 100.000 2810 0 0 1 2810 513903952 513906761 0.000000e+00 5190.0
1 TraesCS5D01G473900 chr5D 81.588 831 115 22 996 1801 514454913 514455730 0.000000e+00 652.0
2 TraesCS5D01G473900 chr5D 82.363 584 86 13 1228 1804 515862453 515861880 2.510000e-135 492.0
3 TraesCS5D01G473900 chr5D 81.029 622 81 21 1 618 49145603 49146191 7.090000e-126 460.0
4 TraesCS5D01G473900 chr5D 74.533 589 124 15 1217 1798 515690174 515690743 1.680000e-57 233.0
5 TraesCS5D01G473900 chr5D 76.864 389 68 14 231 614 49292457 49292828 1.710000e-47 200.0
6 TraesCS5D01G473900 chr5D 77.328 247 47 6 1560 1805 515774764 515775002 1.360000e-28 137.0
7 TraesCS5D01G473900 chr5D 86.842 76 5 4 943 1017 513896343 513896414 2.320000e-11 80.5
8 TraesCS5D01G473900 chr5B 90.792 1857 92 36 985 2810 644862475 644864283 0.000000e+00 2409.0
9 TraesCS5D01G473900 chr5B 87.167 1013 91 15 954 1932 644894951 644893944 0.000000e+00 1114.0
10 TraesCS5D01G473900 chr5B 82.924 814 113 14 1000 1800 646473407 646474207 0.000000e+00 710.0
11 TraesCS5D01G473900 chr5B 84.505 768 55 28 12 773 644861427 644862136 0.000000e+00 701.0
12 TraesCS5D01G473900 chr5B 80.707 622 86 22 1 618 51855227 51855818 1.190000e-123 453.0
13 TraesCS5D01G473900 chr5B 81.144 472 74 8 997 1464 645548100 645547640 5.720000e-97 364.0
14 TraesCS5D01G473900 chr5B 76.294 599 109 21 1221 1804 647875581 647876161 3.540000e-74 289.0
15 TraesCS5D01G473900 chr5B 79.736 227 36 10 1484 1705 644950577 644950356 3.750000e-34 156.0
16 TraesCS5D01G473900 chr5B 75.328 381 62 27 231 605 51853545 51853899 1.350000e-33 154.0
17 TraesCS5D01G473900 chr5B 88.525 122 5 2 43 164 51965494 51965606 3.770000e-29 139.0
18 TraesCS5D01G473900 chr5B 95.833 48 1 1 1 47 51965368 51965415 3.000000e-10 76.8
19 TraesCS5D01G473900 chr5A 88.095 504 51 6 941 1437 641739124 641738623 8.670000e-165 590.0
20 TraesCS5D01G473900 chr5A 80.065 612 86 22 1 607 38762743 38763323 3.350000e-114 422.0
21 TraesCS5D01G473900 chr5A 76.294 599 106 24 1221 1804 643300082 643299505 1.270000e-73 287.0
22 TraesCS5D01G473900 chr5A 74.388 531 117 12 1278 1798 643954234 643954755 2.840000e-50 209.0
23 TraesCS5D01G473900 chr5A 77.368 380 59 18 231 605 38743708 38744065 1.710000e-47 200.0
24 TraesCS5D01G473900 chr5A 100.000 63 0 0 1887 1949 641735485 641735423 1.770000e-22 117.0
25 TraesCS5D01G473900 chr5A 92.424 66 5 0 1800 1865 641735547 641735482 8.290000e-16 95.3
26 TraesCS5D01G473900 chr7D 84.026 626 56 18 2193 2810 10131611 10132200 1.890000e-156 562.0


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 TraesCS5D01G473900 chr5D 513903952 513906761 2809 False 5190.000000 5190 100.000000 1 2810 1 chr5D.!!$F4 2809
1 TraesCS5D01G473900 chr5D 514454913 514455730 817 False 652.000000 652 81.588000 996 1801 1 chr5D.!!$F5 805
2 TraesCS5D01G473900 chr5D 515861880 515862453 573 True 492.000000 492 82.363000 1228 1804 1 chr5D.!!$R1 576
3 TraesCS5D01G473900 chr5D 49145603 49146191 588 False 460.000000 460 81.029000 1 618 1 chr5D.!!$F1 617
4 TraesCS5D01G473900 chr5D 515690174 515690743 569 False 233.000000 233 74.533000 1217 1798 1 chr5D.!!$F6 581
5 TraesCS5D01G473900 chr5B 644861427 644864283 2856 False 1555.000000 2409 87.648500 12 2810 2 chr5B.!!$F5 2798
6 TraesCS5D01G473900 chr5B 644893944 644894951 1007 True 1114.000000 1114 87.167000 954 1932 1 chr5B.!!$R1 978
7 TraesCS5D01G473900 chr5B 646473407 646474207 800 False 710.000000 710 82.924000 1000 1800 1 chr5B.!!$F1 800
8 TraesCS5D01G473900 chr5B 51853545 51855818 2273 False 303.500000 453 78.017500 1 618 2 chr5B.!!$F3 617
9 TraesCS5D01G473900 chr5B 647875581 647876161 580 False 289.000000 289 76.294000 1221 1804 1 chr5B.!!$F2 583
10 TraesCS5D01G473900 chr5A 38762743 38763323 580 False 422.000000 422 80.065000 1 607 1 chr5A.!!$F2 606
11 TraesCS5D01G473900 chr5A 643299505 643300082 577 True 287.000000 287 76.294000 1221 1804 1 chr5A.!!$R1 583
12 TraesCS5D01G473900 chr5A 641735423 641739124 3701 True 267.433333 590 93.506333 941 1949 3 chr5A.!!$R2 1008
13 TraesCS5D01G473900 chr5A 643954234 643954755 521 False 209.000000 209 74.388000 1278 1798 1 chr5A.!!$F3 520
14 TraesCS5D01G473900 chr7D 10131611 10132200 589 False 562.000000 562 84.026000 2193 2810 1 chr7D.!!$F1 617

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
993 1119 0.035881 TGCTGCTTCTCCACCAAGAG 59.964 55.0 0.0 0.0 35.04 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1984 6569 0.322546 CCCACCTGTTAAGCTCCCAC 60.323 60.0 0.0 0.0 0.0 4.61 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
59 61 6.331577 TGGGTTGTACTAGACATAGACCTA 57.668 41.667 0.00 0.00 36.87 3.08
78 80 5.989477 ACCTAACTAACATAGCTTGCATGA 58.011 37.500 3.33 0.00 0.00 3.07
134 136 2.515926 TTGTCATCTCGATAGCCTGC 57.484 50.000 0.00 0.00 0.00 4.85
186 188 9.667107 AAATAAAATCCTACTGATCGAAGTCAA 57.333 29.630 0.00 0.00 31.61 3.18
192 194 5.186992 TCCTACTGATCGAAGTCAATTCCAA 59.813 40.000 0.00 0.00 34.10 3.53
193 195 5.874810 CCTACTGATCGAAGTCAATTCCAAA 59.125 40.000 0.00 0.00 34.10 3.28
194 196 6.540189 CCTACTGATCGAAGTCAATTCCAAAT 59.460 38.462 0.00 0.00 34.10 2.32
195 197 6.824305 ACTGATCGAAGTCAATTCCAAATT 57.176 33.333 0.00 0.00 34.10 1.82
196 198 7.921786 ACTGATCGAAGTCAATTCCAAATTA 57.078 32.000 0.00 0.00 34.10 1.40
197 199 8.335532 ACTGATCGAAGTCAATTCCAAATTAA 57.664 30.769 0.00 0.00 34.10 1.40
198 200 8.960591 ACTGATCGAAGTCAATTCCAAATTAAT 58.039 29.630 0.00 0.00 34.10 1.40
199 201 9.229784 CTGATCGAAGTCAATTCCAAATTAATG 57.770 33.333 0.00 0.00 34.10 1.90
200 202 8.955388 TGATCGAAGTCAATTCCAAATTAATGA 58.045 29.630 0.00 0.00 34.10 2.57
201 203 9.956720 GATCGAAGTCAATTCCAAATTAATGAT 57.043 29.630 0.00 0.00 34.10 2.45
202 204 9.956720 ATCGAAGTCAATTCCAAATTAATGATC 57.043 29.630 0.00 0.00 34.10 2.92
283 285 7.906327 AGCTCTTGCCTTTTGGAATTAAAATA 58.094 30.769 0.00 0.00 44.07 1.40
333 335 3.840890 TCTTTCTCTCGCTCTTCACTC 57.159 47.619 0.00 0.00 0.00 3.51
335 337 0.169230 TTCTCTCGCTCTTCACTCGC 59.831 55.000 0.00 0.00 0.00 5.03
336 338 0.955919 TCTCTCGCTCTTCACTCGCA 60.956 55.000 0.00 0.00 0.00 5.10
368 370 9.475620 TCAGATAAGTTCATAGTCCTTACTTCA 57.524 33.333 0.00 0.00 37.15 3.02
372 374 7.617041 AAGTTCATAGTCCTTACTTCATTGC 57.383 36.000 0.00 0.00 37.15 3.56
373 375 6.951971 AGTTCATAGTCCTTACTTCATTGCT 58.048 36.000 0.00 0.00 37.15 3.91
374 376 6.820656 AGTTCATAGTCCTTACTTCATTGCTG 59.179 38.462 0.00 0.00 37.15 4.41
426 428 9.515226 TTAGCAGTAATTCTGTCCTTGTATTTT 57.485 29.630 6.72 0.00 45.23 1.82
459 463 3.295093 TGCTTTGGTGTCCATTCAAGAA 58.705 40.909 3.73 0.00 31.53 2.52
475 479 7.556275 CCATTCAAGAACCATTACTAGCCTAAA 59.444 37.037 0.00 0.00 0.00 1.85
486 490 9.819267 CCATTACTAGCCTAAATATTAGGTAGC 57.181 37.037 15.57 4.06 37.06 3.58
489 493 9.818270 TTACTAGCCTAAATATTAGGTAGCTCA 57.182 33.333 15.57 0.00 37.06 4.26
490 494 8.903059 ACTAGCCTAAATATTAGGTAGCTCAT 57.097 34.615 15.57 0.00 37.06 2.90
491 495 8.754080 ACTAGCCTAAATATTAGGTAGCTCATG 58.246 37.037 15.57 0.00 37.06 3.07
492 496 7.798710 AGCCTAAATATTAGGTAGCTCATGA 57.201 36.000 15.57 0.00 37.06 3.07
493 497 7.846066 AGCCTAAATATTAGGTAGCTCATGAG 58.154 38.462 18.84 18.84 37.06 2.90
494 498 7.676043 AGCCTAAATATTAGGTAGCTCATGAGA 59.324 37.037 27.04 3.12 37.06 3.27
495 499 8.314751 GCCTAAATATTAGGTAGCTCATGAGAA 58.685 37.037 27.04 10.66 37.06 2.87
499 503 9.553064 AAATATTAGGTAGCTCATGAGAAACTG 57.447 33.333 27.04 0.00 0.00 3.16
500 504 6.552445 ATTAGGTAGCTCATGAGAAACTGT 57.448 37.500 27.04 14.92 0.00 3.55
501 505 4.899352 AGGTAGCTCATGAGAAACTGTT 57.101 40.909 27.04 9.70 0.00 3.16
502 506 5.234466 AGGTAGCTCATGAGAAACTGTTT 57.766 39.130 27.04 5.29 0.00 2.83
503 507 5.625150 AGGTAGCTCATGAGAAACTGTTTT 58.375 37.500 27.04 5.56 0.00 2.43
504 508 6.064717 AGGTAGCTCATGAGAAACTGTTTTT 58.935 36.000 27.04 1.12 0.00 1.94
505 509 7.224297 AGGTAGCTCATGAGAAACTGTTTTTA 58.776 34.615 27.04 0.00 0.00 1.52
506 510 7.885399 AGGTAGCTCATGAGAAACTGTTTTTAT 59.115 33.333 27.04 0.36 0.00 1.40
507 511 8.515414 GGTAGCTCATGAGAAACTGTTTTTATT 58.485 33.333 27.04 0.00 0.00 1.40
508 512 9.899226 GTAGCTCATGAGAAACTGTTTTTATTT 57.101 29.630 27.04 0.00 0.00 1.40
540 544 1.301716 GGAACTTCTGGCGCACTGA 60.302 57.895 10.83 5.52 0.00 3.41
553 557 3.003378 GGCGCACTGACTAAAAGTTCTTT 59.997 43.478 10.83 0.00 0.00 2.52
629 633 9.416794 TGTTTGTTGCCTTGTATTTTGTATATG 57.583 29.630 0.00 0.00 0.00 1.78
785 817 7.615582 CAGGATCTGCTGTTCTTTTATGTAA 57.384 36.000 0.00 0.00 0.00 2.41
787 819 7.119699 CAGGATCTGCTGTTCTTTTATGTAACA 59.880 37.037 0.00 0.00 0.00 2.41
788 820 7.665559 AGGATCTGCTGTTCTTTTATGTAACAA 59.334 33.333 0.00 0.00 33.05 2.83
789 821 8.462016 GGATCTGCTGTTCTTTTATGTAACAAT 58.538 33.333 0.00 0.00 33.05 2.71
792 824 9.462174 TCTGCTGTTCTTTTATGTAACAATTTG 57.538 29.630 0.00 0.00 33.05 2.32
850 886 0.037232 GCGAACACTACTCTTGGGCT 60.037 55.000 0.00 0.00 0.00 5.19
882 927 1.522258 CAGCAACGCAACAACAATTCC 59.478 47.619 0.00 0.00 0.00 3.01
892 937 4.681483 GCAACAACAATTCCTAGCACTTTC 59.319 41.667 0.00 0.00 0.00 2.62
893 938 5.222631 CAACAACAATTCCTAGCACTTTCC 58.777 41.667 0.00 0.00 0.00 3.13
894 939 4.469657 ACAACAATTCCTAGCACTTTCCA 58.530 39.130 0.00 0.00 0.00 3.53
895 940 4.278419 ACAACAATTCCTAGCACTTTCCAC 59.722 41.667 0.00 0.00 0.00 4.02
896 941 4.373156 ACAATTCCTAGCACTTTCCACT 57.627 40.909 0.00 0.00 0.00 4.00
990 1116 1.601759 GCTGCTGCTTCTCCACCAA 60.602 57.895 8.53 0.00 36.03 3.67
991 1117 1.584380 GCTGCTGCTTCTCCACCAAG 61.584 60.000 8.53 0.00 36.03 3.61
993 1119 0.035881 TGCTGCTTCTCCACCAAGAG 59.964 55.000 0.00 0.00 35.04 2.85
994 1120 0.676151 GCTGCTTCTCCACCAAGAGG 60.676 60.000 0.00 0.00 42.21 3.69
1665 4421 2.363147 GAGCTGGAGGACCCTCGT 60.363 66.667 9.73 0.00 43.59 4.18
1842 6422 7.175641 TCAAGCTTGCTTCTTTTAATTAGAGCT 59.824 33.333 21.99 0.00 0.00 4.09
1970 6555 5.508994 GCTTAACAGGGTTGCACTATTTTGT 60.509 40.000 0.00 0.00 0.00 2.83
1982 6567 6.980593 TGCACTATTTTGTTAGCAAATCTGT 58.019 32.000 5.52 2.76 43.26 3.41
1984 6569 6.308766 GCACTATTTTGTTAGCAAATCTGTGG 59.691 38.462 21.08 9.53 43.26 4.17
1985 6570 7.370383 CACTATTTTGTTAGCAAATCTGTGGT 58.630 34.615 5.52 0.00 43.26 4.16
1986 6571 7.326789 CACTATTTTGTTAGCAAATCTGTGGTG 59.673 37.037 5.52 7.25 43.26 4.17
1987 6572 4.582701 TTTGTTAGCAAATCTGTGGTGG 57.417 40.909 0.00 0.00 39.43 4.61
1988 6573 2.513753 TGTTAGCAAATCTGTGGTGGG 58.486 47.619 0.00 0.00 0.00 4.61
1989 6574 2.107378 TGTTAGCAAATCTGTGGTGGGA 59.893 45.455 0.00 0.00 0.00 4.37
1990 6575 2.749621 GTTAGCAAATCTGTGGTGGGAG 59.250 50.000 0.00 0.00 0.00 4.30
1991 6576 0.610232 AGCAAATCTGTGGTGGGAGC 60.610 55.000 0.00 0.00 0.00 4.70
1992 6577 0.610232 GCAAATCTGTGGTGGGAGCT 60.610 55.000 0.00 0.00 0.00 4.09
1993 6578 1.915141 CAAATCTGTGGTGGGAGCTT 58.085 50.000 0.00 0.00 0.00 3.74
1994 6579 2.879756 GCAAATCTGTGGTGGGAGCTTA 60.880 50.000 0.00 0.00 0.00 3.09
1995 6580 3.420893 CAAATCTGTGGTGGGAGCTTAA 58.579 45.455 0.00 0.00 0.00 1.85
1996 6581 2.789409 ATCTGTGGTGGGAGCTTAAC 57.211 50.000 0.00 0.00 0.00 2.01
1997 6582 1.429930 TCTGTGGTGGGAGCTTAACA 58.570 50.000 0.00 0.00 0.00 2.41
1998 6583 1.347707 TCTGTGGTGGGAGCTTAACAG 59.652 52.381 0.00 0.00 37.07 3.16
1999 6584 0.400213 TGTGGTGGGAGCTTAACAGG 59.600 55.000 0.00 0.00 0.00 4.00
2000 6585 0.400594 GTGGTGGGAGCTTAACAGGT 59.599 55.000 0.00 0.00 0.00 4.00
2001 6586 0.400213 TGGTGGGAGCTTAACAGGTG 59.600 55.000 0.00 0.00 0.00 4.00
2002 6587 0.322546 GGTGGGAGCTTAACAGGTGG 60.323 60.000 0.00 0.00 0.00 4.61
2003 6588 0.322546 GTGGGAGCTTAACAGGTGGG 60.323 60.000 0.00 0.00 0.00 4.61
2004 6589 1.378646 GGGAGCTTAACAGGTGGGC 60.379 63.158 0.00 0.00 0.00 5.36
2005 6590 1.378646 GGAGCTTAACAGGTGGGCC 60.379 63.158 0.00 0.00 0.00 5.80
2007 6592 0.909623 GAGCTTAACAGGTGGGCCTA 59.090 55.000 4.53 0.00 44.97 3.93
2008 6593 1.280998 GAGCTTAACAGGTGGGCCTAA 59.719 52.381 4.53 0.00 44.97 2.69
2009 6594 1.923148 AGCTTAACAGGTGGGCCTAAT 59.077 47.619 4.53 0.00 44.97 1.73
2010 6595 2.092375 AGCTTAACAGGTGGGCCTAATC 60.092 50.000 4.53 0.00 44.97 1.75
2011 6596 2.092375 GCTTAACAGGTGGGCCTAATCT 60.092 50.000 4.53 0.00 44.97 2.40
2012 6597 3.545703 CTTAACAGGTGGGCCTAATCTG 58.454 50.000 15.27 15.27 44.97 2.90
2013 6598 0.625849 AACAGGTGGGCCTAATCTGG 59.374 55.000 19.39 5.93 44.97 3.86
2014 6599 1.281925 ACAGGTGGGCCTAATCTGGG 61.282 60.000 19.39 0.98 44.97 4.45
2065 6650 0.863956 AAATCTGGGTTGGTTGGGGA 59.136 50.000 0.00 0.00 0.00 4.81
2068 6653 1.074951 CTGGGTTGGTTGGGGAGAC 59.925 63.158 0.00 0.00 0.00 3.36
2083 6668 1.737793 GGAGACGCAATTAACAGGGTG 59.262 52.381 3.81 0.00 0.00 4.61
2093 6678 4.675063 ATTAACAGGGTGGGAACTTGAT 57.325 40.909 0.00 0.00 0.00 2.57
2098 6683 3.282021 CAGGGTGGGAACTTGATACATG 58.718 50.000 0.00 0.00 0.00 3.21
2181 6766 5.460419 GCTTAGTTAGCTGCTAGTATGTGTG 59.540 44.000 9.62 0.00 46.77 3.82
2182 6767 6.525578 TTAGTTAGCTGCTAGTATGTGTGT 57.474 37.500 9.62 0.00 0.00 3.72
2183 6768 4.748892 AGTTAGCTGCTAGTATGTGTGTG 58.251 43.478 9.62 0.00 0.00 3.82
2221 6806 3.176708 GCAATGTGATGCAAGCTTAGTG 58.823 45.455 0.00 0.00 45.70 2.74
2253 6838 3.885976 TTGGGGTTTAATCAGTGGTCA 57.114 42.857 0.00 0.00 0.00 4.02
2273 6858 5.408909 GGTCAAAGCTACTGTTCCTTAACTC 59.591 44.000 0.00 0.00 36.51 3.01
2298 6883 3.737266 GTCATGCATGGTTTTGTTGTGAG 59.263 43.478 25.97 0.00 0.00 3.51
2326 6912 2.689983 ACTTGAAACAGTTTGCAGGAGG 59.310 45.455 2.34 0.00 0.00 4.30
2328 6914 3.228188 TGAAACAGTTTGCAGGAGGAT 57.772 42.857 2.34 0.00 0.00 3.24
2384 6970 6.972901 TGTTCTCTGAACATACGTGCTATAAG 59.027 38.462 8.81 0.00 0.00 1.73
2385 6971 5.520632 TCTCTGAACATACGTGCTATAAGC 58.479 41.667 0.00 0.00 42.82 3.09
2386 6972 4.617959 TCTGAACATACGTGCTATAAGCC 58.382 43.478 0.00 0.00 41.51 4.35
2387 6973 4.341235 TCTGAACATACGTGCTATAAGCCT 59.659 41.667 0.00 0.00 41.51 4.58
2388 6974 5.533528 TCTGAACATACGTGCTATAAGCCTA 59.466 40.000 0.00 0.00 41.51 3.93
2390 6976 7.392393 TCTGAACATACGTGCTATAAGCCTATA 59.608 37.037 0.00 0.00 41.51 1.31
2392 6978 7.811236 TGAACATACGTGCTATAAGCCTATAAC 59.189 37.037 0.00 0.00 41.51 1.89
2462 7053 4.455533 CAGCACTAGCAAACCAAATGAGTA 59.544 41.667 0.00 0.00 45.49 2.59
2478 7069 9.526713 CCAAATGAGTATATATAGCTGCTACAG 57.473 37.037 12.26 0.00 34.12 2.74
2501 7093 8.918116 ACAGACTCTGAAATAGTATCAGCATTA 58.082 33.333 13.25 0.00 43.19 1.90
2502 7094 9.926158 CAGACTCTGAAATAGTATCAGCATTAT 57.074 33.333 0.00 0.00 43.19 1.28
2564 7156 4.326504 AGTGGATGTTTTTCTTTGCAGG 57.673 40.909 0.00 0.00 0.00 4.85
2588 7180 6.103997 GCTTGCTATGTAGTTACAGTTACCA 58.896 40.000 0.00 0.00 39.92 3.25
2590 7182 7.118680 GCTTGCTATGTAGTTACAGTTACCAAA 59.881 37.037 0.00 0.00 39.92 3.28
2603 7195 7.034685 ACAGTTACCAAAAATTACCACAGAC 57.965 36.000 0.00 0.00 0.00 3.51
2654 7246 3.891366 AGCTACCAAAAGTTTGACAGCAT 59.109 39.130 21.37 10.85 42.30 3.79
2664 7256 1.155889 TTGACAGCATAGCAACCACG 58.844 50.000 0.00 0.00 0.00 4.94
2720 7314 5.875910 GCAGATCATCATCTATTTCTGAGGG 59.124 44.000 0.00 0.00 37.25 4.30
2766 7379 1.973281 ACATTGGAGCACCGCCTTG 60.973 57.895 0.00 0.00 39.42 3.61
2798 7411 8.564574 GTGACACTAGTTCAAACCAAATTGATA 58.435 33.333 0.00 0.00 38.98 2.15
2799 7412 9.295825 TGACACTAGTTCAAACCAAATTGATAT 57.704 29.630 0.00 0.00 38.98 1.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 61 9.123902 TGATTATTCATGCAAGCTATGTTAGTT 57.876 29.630 0.00 0.00 0.00 2.24
108 110 7.371159 CAGGCTATCGAGATGACAATAGTTAA 58.629 38.462 0.00 0.00 0.00 2.01
129 131 4.455877 ACAAAGAATGTTACACTAGCAGGC 59.544 41.667 0.00 0.00 40.06 4.85
174 176 8.955388 TCATTAATTTGGAATTGACTTCGATCA 58.045 29.630 0.00 0.00 34.45 2.92
201 203 7.336176 CAGGAAAAGACTCAGATCATTCATTGA 59.664 37.037 0.00 0.00 39.12 2.57
202 204 7.120873 ACAGGAAAAGACTCAGATCATTCATTG 59.879 37.037 0.00 0.00 0.00 2.82
220 222 8.634335 TTCATTGAACATAGATCACAGGAAAA 57.366 30.769 0.00 0.00 0.00 2.29
299 301 7.824779 AGCGAGAGAAAGAAATAAAGGTACAAT 59.175 33.333 0.00 0.00 0.00 2.71
317 319 0.955919 TGCGAGTGAAGAGCGAGAGA 60.956 55.000 0.00 0.00 0.00 3.10
333 335 3.334691 TGAACTTATCTGAACCCTTGCG 58.665 45.455 0.00 0.00 0.00 4.85
335 337 6.763610 GGACTATGAACTTATCTGAACCCTTG 59.236 42.308 0.00 0.00 0.00 3.61
336 338 6.674419 AGGACTATGAACTTATCTGAACCCTT 59.326 38.462 0.00 0.00 0.00 3.95
347 349 8.540388 AGCAATGAAGTAAGGACTATGAACTTA 58.460 33.333 0.00 0.00 33.58 2.24
350 352 6.818644 TCAGCAATGAAGTAAGGACTATGAAC 59.181 38.462 0.00 0.00 33.58 3.18
366 368 1.552792 TCCACGGTACATCAGCAATGA 59.447 47.619 6.14 0.00 38.83 2.57
367 369 2.022764 TCCACGGTACATCAGCAATG 57.977 50.000 0.00 0.00 41.48 2.82
368 370 3.281727 AATCCACGGTACATCAGCAAT 57.718 42.857 0.00 0.00 0.00 3.56
369 371 2.746904 CAAATCCACGGTACATCAGCAA 59.253 45.455 0.00 0.00 0.00 3.91
370 372 2.290008 ACAAATCCACGGTACATCAGCA 60.290 45.455 0.00 0.00 0.00 4.41
371 373 2.351726 GACAAATCCACGGTACATCAGC 59.648 50.000 0.00 0.00 0.00 4.26
372 374 3.595173 TGACAAATCCACGGTACATCAG 58.405 45.455 0.00 0.00 0.00 2.90
373 375 3.686916 TGACAAATCCACGGTACATCA 57.313 42.857 0.00 0.00 0.00 3.07
374 376 3.242739 GCATGACAAATCCACGGTACATC 60.243 47.826 0.00 0.00 0.00 3.06
426 428 5.140747 ACACCAAAGCAAAAACAGTGTAA 57.859 34.783 0.00 0.00 35.36 2.41
430 432 2.564947 TGGACACCAAAGCAAAAACAGT 59.435 40.909 0.00 0.00 0.00 3.55
433 435 4.187694 TGAATGGACACCAAAGCAAAAAC 58.812 39.130 0.00 0.00 36.95 2.43
475 479 8.256356 ACAGTTTCTCATGAGCTACCTAATAT 57.744 34.615 18.36 0.00 0.00 1.28
477 481 6.552445 ACAGTTTCTCATGAGCTACCTAAT 57.448 37.500 18.36 0.13 0.00 1.73
480 484 4.899352 AACAGTTTCTCATGAGCTACCT 57.101 40.909 18.36 7.87 0.00 3.08
481 485 5.948992 AAAACAGTTTCTCATGAGCTACC 57.051 39.130 18.36 5.71 0.00 3.18
482 486 9.899226 AAATAAAAACAGTTTCTCATGAGCTAC 57.101 29.630 18.36 16.54 0.00 3.58
484 488 9.468532 GAAAATAAAAACAGTTTCTCATGAGCT 57.531 29.630 18.36 6.68 31.53 4.09
506 510 8.850156 CCAGAAGTTCCTTTGATAAGAAGAAAA 58.150 33.333 0.00 0.00 32.92 2.29
507 511 7.040409 GCCAGAAGTTCCTTTGATAAGAAGAAA 60.040 37.037 0.00 0.00 32.92 2.52
508 512 6.431234 GCCAGAAGTTCCTTTGATAAGAAGAA 59.569 38.462 0.00 0.00 32.92 2.52
509 513 5.940470 GCCAGAAGTTCCTTTGATAAGAAGA 59.060 40.000 0.00 0.00 32.92 2.87
523 527 0.601311 AGTCAGTGCGCCAGAAGTTC 60.601 55.000 4.18 0.00 0.00 3.01
525 529 0.679505 TTAGTCAGTGCGCCAGAAGT 59.320 50.000 4.18 0.00 0.00 3.01
529 533 1.512926 ACTTTTAGTCAGTGCGCCAG 58.487 50.000 4.18 0.00 0.00 4.85
532 536 3.879932 AAGAACTTTTAGTCAGTGCGC 57.120 42.857 0.00 0.00 0.00 6.09
589 593 5.757808 GGCAACAAACAAATACTTGTCCATT 59.242 36.000 0.00 0.00 45.25 3.16
595 599 7.945033 ATACAAGGCAACAAACAAATACTTG 57.055 32.000 0.00 0.00 39.76 3.16
596 600 8.956533 AAATACAAGGCAACAAACAAATACTT 57.043 26.923 0.00 0.00 41.41 2.24
601 605 8.723942 ATACAAAATACAAGGCAACAAACAAA 57.276 26.923 0.00 0.00 41.41 2.83
603 607 9.416794 CATATACAAAATACAAGGCAACAAACA 57.583 29.630 0.00 0.00 41.41 2.83
604 608 9.418045 ACATATACAAAATACAAGGCAACAAAC 57.582 29.630 0.00 0.00 41.41 2.93
761 768 7.119699 TGTTACATAAAAGAACAGCAGATCCTG 59.880 37.037 0.00 0.00 38.78 3.86
785 817 3.773860 TTGCGTCTGAACACAAATTGT 57.226 38.095 0.00 0.00 41.74 2.71
822 854 4.901868 AGAGTAGTGTTCGCCCATAAAAA 58.098 39.130 0.00 0.00 0.00 1.94
823 855 4.546829 AGAGTAGTGTTCGCCCATAAAA 57.453 40.909 0.00 0.00 0.00 1.52
824 856 4.250464 CAAGAGTAGTGTTCGCCCATAAA 58.750 43.478 0.00 0.00 0.00 1.40
825 857 3.369052 CCAAGAGTAGTGTTCGCCCATAA 60.369 47.826 0.00 0.00 0.00 1.90
826 858 2.167693 CCAAGAGTAGTGTTCGCCCATA 59.832 50.000 0.00 0.00 0.00 2.74
827 859 1.066143 CCAAGAGTAGTGTTCGCCCAT 60.066 52.381 0.00 0.00 0.00 4.00
828 860 0.320374 CCAAGAGTAGTGTTCGCCCA 59.680 55.000 0.00 0.00 0.00 5.36
832 868 2.069273 CAAGCCCAAGAGTAGTGTTCG 58.931 52.381 0.00 0.00 0.00 3.95
862 898 1.522258 GGAATTGTTGTTGCGTTGCTG 59.478 47.619 0.00 0.00 0.00 4.41
866 902 2.621055 TGCTAGGAATTGTTGTTGCGTT 59.379 40.909 0.00 0.00 0.00 4.84
867 903 2.031157 GTGCTAGGAATTGTTGTTGCGT 60.031 45.455 0.00 0.00 0.00 5.24
951 1021 2.509336 CGGGTGGAAGTGCTAGCG 60.509 66.667 10.77 0.00 0.00 4.26
952 1022 2.125106 CCGGGTGGAAGTGCTAGC 60.125 66.667 8.10 8.10 37.49 3.42
1641 4397 4.136978 TCCTCCAGCTCAAGGACC 57.863 61.111 9.17 0.00 36.75 4.46
1665 4421 1.381327 GACCTCGTGGGGGATCTCA 60.381 63.158 8.63 0.00 40.03 3.27
1878 6458 7.672660 TCACATTCCCTGAAGAACTAACTAGTA 59.327 37.037 0.00 0.00 34.99 1.82
1880 6460 6.936279 TCACATTCCCTGAAGAACTAACTAG 58.064 40.000 0.00 0.00 0.00 2.57
1970 6555 2.879756 GCTCCCACCACAGATTTGCTAA 60.880 50.000 0.00 0.00 0.00 3.09
1982 6567 0.400213 CACCTGTTAAGCTCCCACCA 59.600 55.000 0.00 0.00 0.00 4.17
1984 6569 0.322546 CCCACCTGTTAAGCTCCCAC 60.323 60.000 0.00 0.00 0.00 4.61
1985 6570 2.074967 CCCACCTGTTAAGCTCCCA 58.925 57.895 0.00 0.00 0.00 4.37
1986 6571 1.378646 GCCCACCTGTTAAGCTCCC 60.379 63.158 0.00 0.00 0.00 4.30
1987 6572 1.378646 GGCCCACCTGTTAAGCTCC 60.379 63.158 0.00 0.00 0.00 4.70
1988 6573 4.320910 GGCCCACCTGTTAAGCTC 57.679 61.111 0.00 0.00 0.00 4.09
1998 6583 2.195956 GCCCAGATTAGGCCCACC 59.804 66.667 0.00 0.00 45.16 4.61
2004 6589 1.141657 TGCAGCTAAGCCCAGATTAGG 59.858 52.381 0.00 0.00 32.88 2.69
2005 6590 2.627515 TGCAGCTAAGCCCAGATTAG 57.372 50.000 0.00 0.00 35.02 1.73
2006 6591 3.582998 ATTGCAGCTAAGCCCAGATTA 57.417 42.857 0.00 0.00 0.00 1.75
2007 6592 2.449137 ATTGCAGCTAAGCCCAGATT 57.551 45.000 0.00 0.00 0.00 2.40
2008 6593 2.449137 AATTGCAGCTAAGCCCAGAT 57.551 45.000 0.00 0.00 0.00 2.90
2009 6594 3.216800 CATAATTGCAGCTAAGCCCAGA 58.783 45.455 0.00 0.00 0.00 3.86
2010 6595 3.637998 CATAATTGCAGCTAAGCCCAG 57.362 47.619 0.00 0.00 0.00 4.45
2040 6625 4.081697 CCCAACCAACCCAGATTTCATAAC 60.082 45.833 0.00 0.00 0.00 1.89
2043 6628 2.539302 CCCAACCAACCCAGATTTCAT 58.461 47.619 0.00 0.00 0.00 2.57
2053 6638 2.671963 GCGTCTCCCCAACCAACC 60.672 66.667 0.00 0.00 0.00 3.77
2065 6650 1.613255 CCCACCCTGTTAATTGCGTCT 60.613 52.381 0.00 0.00 0.00 4.18
2068 6653 1.201414 GTTCCCACCCTGTTAATTGCG 59.799 52.381 0.00 0.00 0.00 4.85
2078 6663 2.919602 ACATGTATCAAGTTCCCACCCT 59.080 45.455 0.00 0.00 0.00 4.34
2083 6668 3.129287 CCTGCAACATGTATCAAGTTCCC 59.871 47.826 0.00 0.00 0.00 3.97
2181 6766 2.488937 TGCATCAACATCATCCACACAC 59.511 45.455 0.00 0.00 0.00 3.82
2182 6767 2.792878 TGCATCAACATCATCCACACA 58.207 42.857 0.00 0.00 0.00 3.72
2183 6768 3.853831 TTGCATCAACATCATCCACAC 57.146 42.857 0.00 0.00 0.00 3.82
2221 6806 1.839424 AACCCCAATCAAGCTACAGC 58.161 50.000 0.00 0.00 42.49 4.40
2253 6838 7.232941 TGACTAGAGTTAAGGAACAGTAGCTTT 59.767 37.037 0.00 0.00 38.10 3.51
2273 6858 4.919168 CACAACAAAACCATGCATGACTAG 59.081 41.667 28.31 13.38 0.00 2.57
2298 6883 6.221858 TGCAAACTGTTTCAAGTTCAAAAC 57.778 33.333 2.13 4.22 39.48 2.43
2326 6912 4.887748 ACAGGATCGTATGGATTGACATC 58.112 43.478 0.00 0.00 34.82 3.06
2328 6914 3.960755 AGACAGGATCGTATGGATTGACA 59.039 43.478 0.00 0.00 34.82 3.58
2384 6970 6.255887 GCATCACCAAGTATATCGTTATAGGC 59.744 42.308 0.00 0.00 0.00 3.93
2385 6971 7.548097 AGCATCACCAAGTATATCGTTATAGG 58.452 38.462 0.00 0.00 0.00 2.57
2386 6972 9.504710 GTAGCATCACCAAGTATATCGTTATAG 57.495 37.037 0.00 0.00 0.00 1.31
2387 6973 9.016438 TGTAGCATCACCAAGTATATCGTTATA 57.984 33.333 0.00 0.00 0.00 0.98
2388 6974 7.813148 GTGTAGCATCACCAAGTATATCGTTAT 59.187 37.037 0.70 0.00 32.81 1.89
2390 6976 5.983720 GTGTAGCATCACCAAGTATATCGTT 59.016 40.000 0.70 0.00 32.81 3.85
2440 7031 3.490348 ACTCATTTGGTTTGCTAGTGCT 58.510 40.909 0.00 0.00 40.48 4.40
2462 7053 8.642935 TTTCAGAGTCTGTAGCAGCTATATAT 57.357 34.615 19.53 0.00 32.61 0.86
2523 7115 6.379703 TCCACTTTGTGAAATGGAAAGAAAGA 59.620 34.615 0.00 0.00 38.30 2.52
2534 7126 8.667463 CAAAGAAAAACATCCACTTTGTGAAAT 58.333 29.630 0.00 0.00 41.00 2.17
2540 7132 5.006941 CCTGCAAAGAAAAACATCCACTTTG 59.993 40.000 0.00 0.00 45.41 2.77
2564 7156 6.103997 TGGTAACTGTAACTACATAGCAAGC 58.896 40.000 0.00 0.00 35.36 4.01
2633 7225 3.708563 TGCTGTCAAACTTTTGGTAGC 57.291 42.857 17.12 17.12 42.40 3.58
2634 7226 5.048782 TGCTATGCTGTCAAACTTTTGGTAG 60.049 40.000 1.94 2.73 38.66 3.18
2664 7256 6.169529 CGACTATCGTTCAGCATAGCATGC 62.170 50.000 10.51 10.51 44.98 4.06
2694 7288 7.162761 CCTCAGAAATAGATGATGATCTGCTT 58.837 38.462 4.77 0.00 39.44 3.91
2720 7314 1.078709 TCAAGCGAACATGTAGCAGC 58.921 50.000 22.80 15.02 0.00 5.25
2766 7379 5.221382 TGGTTTGAACTAGTGTCACCTCTAC 60.221 44.000 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.