Multiple sequence alignment - TraesCS3D01G323500

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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 TraesCS3D01G323500 chr3D 100.000 2510 0 0 1 2510 436181188 436178679 0.000000e+00 4636
1 TraesCS3D01G323500 chr3B 89.555 967 67 10 694 1646 571887167 571886221 0.000000e+00 1195
2 TraesCS3D01G323500 chr3B 94.737 95 4 1 1805 1899 571885932 571885839 2.010000e-31 147
3 TraesCS3D01G323500 chr2D 96.494 599 20 1 1912 2510 437959431 437958834 0.000000e+00 989
4 TraesCS3D01G323500 chr2D 77.401 531 86 28 164 684 514944546 514944040 4.090000e-73 285
5 TraesCS3D01G323500 chr5D 89.286 532 52 2 1981 2507 548372235 548372766 0.000000e+00 662
6 TraesCS3D01G323500 chr5D 80.798 401 57 15 164 555 243287156 243286767 1.890000e-76 296
7 TraesCS3D01G323500 chrUn 86.172 593 82 0 1912 2504 314891153 314891745 2.100000e-180 641
8 TraesCS3D01G323500 chr7A 86.172 593 82 0 1912 2504 88938340 88938932 2.100000e-180 641
9 TraesCS3D01G323500 chr5A 85.689 566 81 0 1945 2510 656477228 656476663 4.620000e-167 597
10 TraesCS3D01G323500 chr5A 82.078 385 54 6 161 543 308087150 308087521 5.210000e-82 315
11 TraesCS3D01G323500 chr5A 82.078 385 54 6 161 543 308173624 308173995 5.210000e-82 315
12 TraesCS3D01G323500 chr3A 87.028 424 31 8 1228 1646 574915554 574915150 8.180000e-125 457
13 TraesCS3D01G323500 chr3A 89.826 344 19 4 5 343 574917745 574917413 6.420000e-116 427
14 TraesCS3D01G323500 chr3A 94.253 87 4 1 1813 1899 574914990 574914905 5.630000e-27 132
15 TraesCS3D01G323500 chr5B 83.417 398 51 8 161 555 254951559 254951944 3.070000e-94 355
16 TraesCS3D01G323500 chr6D 83.607 366 43 9 111 459 373050034 373049669 6.690000e-86 327
17 TraesCS3D01G323500 chr6D 77.500 360 64 10 1292 1646 426893084 426892737 1.520000e-47 200
18 TraesCS3D01G323500 chr1D 78.817 524 84 20 164 679 370203142 370202638 6.690000e-86 327
19 TraesCS3D01G323500 chr6A 86.268 284 35 4 167 448 578688746 578688465 3.140000e-79 305
20 TraesCS3D01G323500 chr6A 84.083 289 42 3 164 451 29684799 29685084 2.460000e-70 276
21 TraesCS3D01G323500 chr6A 76.866 536 92 21 1119 1646 571650946 571650435 8.850000e-70 274
22 TraesCS3D01G323500 chr2B 77.547 530 90 26 164 684 606611172 606610663 2.440000e-75 292
23 TraesCS3D01G323500 chr2B 80.667 300 32 17 394 680 119172093 119171807 2.530000e-50 209
24 TraesCS3D01G323500 chr6B 76.786 504 89 17 1119 1611 642384710 642384224 8.910000e-65 257


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 TraesCS3D01G323500 chr3D 436178679 436181188 2509 True 4636.000000 4636 100.000 1 2510 1 chr3D.!!$R1 2509
1 TraesCS3D01G323500 chr3B 571885839 571887167 1328 True 671.000000 1195 92.146 694 1899 2 chr3B.!!$R1 1205
2 TraesCS3D01G323500 chr2D 437958834 437959431 597 True 989.000000 989 96.494 1912 2510 1 chr2D.!!$R1 598
3 TraesCS3D01G323500 chr2D 514944040 514944546 506 True 285.000000 285 77.401 164 684 1 chr2D.!!$R2 520
4 TraesCS3D01G323500 chr5D 548372235 548372766 531 False 662.000000 662 89.286 1981 2507 1 chr5D.!!$F1 526
5 TraesCS3D01G323500 chrUn 314891153 314891745 592 False 641.000000 641 86.172 1912 2504 1 chrUn.!!$F1 592
6 TraesCS3D01G323500 chr7A 88938340 88938932 592 False 641.000000 641 86.172 1912 2504 1 chr7A.!!$F1 592
7 TraesCS3D01G323500 chr5A 656476663 656477228 565 True 597.000000 597 85.689 1945 2510 1 chr5A.!!$R1 565
8 TraesCS3D01G323500 chr3A 574914905 574917745 2840 True 338.666667 457 90.369 5 1899 3 chr3A.!!$R1 1894
9 TraesCS3D01G323500 chr1D 370202638 370203142 504 True 327.000000 327 78.817 164 679 1 chr1D.!!$R1 515
10 TraesCS3D01G323500 chr6A 571650435 571650946 511 True 274.000000 274 76.866 1119 1646 1 chr6A.!!$R1 527
11 TraesCS3D01G323500 chr2B 606610663 606611172 509 True 292.000000 292 77.547 164 684 1 chr2B.!!$R2 520

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
905 923 0.03467 GCCCTCTGCCTCAAGTTGAT 60.035 55.0 5.91 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2421 4276 0.035458 AACCAGAAGGAGACCAAGCG 59.965 55.0 0.0 0.0 38.69 4.68 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
74 75 0.996727 GCATTGACGTTGTTGTCGGC 60.997 55.000 0.00 0.00 41.87 5.54
102 103 2.091499 TGGTAGCCGAAGATTAGAGGGA 60.091 50.000 0.00 0.00 0.00 4.20
107 108 2.028567 GCCGAAGATTAGAGGGATCTGG 60.029 54.545 0.00 0.00 34.24 3.86
108 109 3.501349 CCGAAGATTAGAGGGATCTGGA 58.499 50.000 0.00 0.00 34.24 3.86
109 110 4.093011 CCGAAGATTAGAGGGATCTGGAT 58.907 47.826 0.00 0.00 34.24 3.41
110 111 4.530161 CCGAAGATTAGAGGGATCTGGATT 59.470 45.833 0.00 0.00 34.24 3.01
111 112 5.477510 CGAAGATTAGAGGGATCTGGATTG 58.522 45.833 0.00 0.00 34.24 2.67
112 113 4.906747 AGATTAGAGGGATCTGGATTGC 57.093 45.455 0.00 0.00 32.79 3.56
113 114 4.501433 AGATTAGAGGGATCTGGATTGCT 58.499 43.478 0.00 0.00 32.79 3.91
114 115 4.912744 AGATTAGAGGGATCTGGATTGCTT 59.087 41.667 0.00 0.00 32.79 3.91
115 116 4.428294 TTAGAGGGATCTGGATTGCTTG 57.572 45.455 0.00 0.00 0.00 4.01
116 117 2.203584 AGAGGGATCTGGATTGCTTGT 58.796 47.619 0.00 0.00 0.00 3.16
117 118 2.092538 AGAGGGATCTGGATTGCTTGTG 60.093 50.000 0.00 0.00 0.00 3.33
121 122 4.079558 AGGGATCTGGATTGCTTGTGTAAT 60.080 41.667 0.00 0.00 0.00 1.89
132 133 7.850982 GGATTGCTTGTGTAATATTAGACAACG 59.149 37.037 26.06 22.22 40.57 4.10
159 160 4.009675 TGTCGAGGATGAAAGGAATTTGG 58.990 43.478 0.00 0.00 0.00 3.28
162 163 3.378427 CGAGGATGAAAGGAATTTGGACC 59.622 47.826 0.00 0.00 0.00 4.46
204 205 3.574074 AAGCCTGCCAGGAACGCAT 62.574 57.895 16.85 0.00 37.67 4.73
233 234 9.323985 GAGTTCACTGCATTTCTTAAGATCTAT 57.676 33.333 5.89 0.00 0.00 1.98
296 302 7.105588 AGCATGATATTATTAAGCATCGGTGA 58.894 34.615 0.00 0.00 0.00 4.02
366 375 5.347342 GTGTGTGATTTGACAATTTGGTGA 58.653 37.500 0.78 0.00 0.00 4.02
443 455 4.202202 TGTGATTTGCTTTTCGGACCATTT 60.202 37.500 0.00 0.00 0.00 2.32
444 456 5.010112 TGTGATTTGCTTTTCGGACCATTTA 59.990 36.000 0.00 0.00 0.00 1.40
445 457 6.099341 GTGATTTGCTTTTCGGACCATTTAT 58.901 36.000 0.00 0.00 0.00 1.40
446 458 7.094162 TGTGATTTGCTTTTCGGACCATTTATA 60.094 33.333 0.00 0.00 0.00 0.98
447 459 7.920682 GTGATTTGCTTTTCGGACCATTTATAT 59.079 33.333 0.00 0.00 0.00 0.86
448 460 7.920151 TGATTTGCTTTTCGGACCATTTATATG 59.080 33.333 0.00 0.00 0.00 1.78
449 461 6.767524 TTGCTTTTCGGACCATTTATATGT 57.232 33.333 0.00 0.00 0.00 2.29
450 462 6.767524 TGCTTTTCGGACCATTTATATGTT 57.232 33.333 0.00 0.00 0.00 2.71
451 463 6.791303 TGCTTTTCGGACCATTTATATGTTC 58.209 36.000 0.00 0.00 0.00 3.18
452 464 6.375736 TGCTTTTCGGACCATTTATATGTTCA 59.624 34.615 0.00 0.00 0.00 3.18
543 555 5.339177 TGATGCTATGCAAAATTTACGGTG 58.661 37.500 0.00 0.00 43.62 4.94
564 578 1.375523 GTGAGCGTTCCGGTGGAAT 60.376 57.895 0.00 0.00 44.04 3.01
582 596 4.813027 GGAATAGATCCCGTAAATGCGTA 58.187 43.478 0.00 0.00 43.00 4.42
585 599 1.758280 AGATCCCGTAAATGCGTACCA 59.242 47.619 0.00 0.00 0.00 3.25
586 600 2.168936 AGATCCCGTAAATGCGTACCAA 59.831 45.455 0.00 0.00 0.00 3.67
612 626 2.404265 TTTGCGAGACGAGTTTACGA 57.596 45.000 0.00 0.00 37.03 3.43
613 627 2.624316 TTGCGAGACGAGTTTACGAT 57.376 45.000 0.00 0.00 37.03 3.73
627 641 4.097437 AGTTTACGATATCTGTTCCGCTGA 59.903 41.667 0.34 0.00 0.00 4.26
630 644 1.789464 CGATATCTGTTCCGCTGAAGC 59.211 52.381 0.34 0.00 37.78 3.86
644 658 4.367023 AAGCGCTTCGGCACCGTA 62.367 61.111 18.98 0.00 41.88 4.02
648 662 1.131826 CGCTTCGGCACCGTAAAAG 59.868 57.895 9.23 6.80 41.88 2.27
651 665 1.467342 GCTTCGGCACCGTAAAAGAAT 59.533 47.619 9.23 0.00 41.33 2.40
673 687 0.249953 TTGCGAGTGCCCTTAAACGA 60.250 50.000 0.00 0.00 41.78 3.85
674 688 0.669318 TGCGAGTGCCCTTAAACGAG 60.669 55.000 0.00 0.00 41.78 4.18
678 692 2.546789 CGAGTGCCCTTAAACGAGTTTT 59.453 45.455 6.53 0.00 34.23 2.43
684 698 1.605232 CCTTAAACGAGTTTTGCGGGT 59.395 47.619 6.53 0.00 34.23 5.28
685 699 2.350102 CCTTAAACGAGTTTTGCGGGTC 60.350 50.000 6.53 0.00 34.23 4.46
686 700 0.860533 TAAACGAGTTTTGCGGGTCG 59.139 50.000 6.53 0.00 38.40 4.79
687 701 1.778027 AAACGAGTTTTGCGGGTCGG 61.778 55.000 0.00 0.00 36.74 4.79
688 702 4.084888 CGAGTTTTGCGGGTCGGC 62.085 66.667 0.00 0.00 0.00 5.54
689 703 3.733960 GAGTTTTGCGGGTCGGCC 61.734 66.667 0.00 0.00 0.00 6.13
700 714 3.637184 GGTCGGCCCTAAAGTTCAA 57.363 52.632 0.00 0.00 0.00 2.69
706 720 2.163613 CGGCCCTAAAGTTCAATCAACC 59.836 50.000 0.00 0.00 35.28 3.77
707 721 3.161866 GGCCCTAAAGTTCAATCAACCA 58.838 45.455 0.00 0.00 35.28 3.67
742 756 8.617290 TGAATTCTAGCATACGTATCTGACTA 57.383 34.615 4.74 4.80 0.00 2.59
743 757 8.722394 TGAATTCTAGCATACGTATCTGACTAG 58.278 37.037 4.74 13.36 0.00 2.57
753 767 9.607988 CATACGTATCTGACTAGGAGATCTTAT 57.392 37.037 4.74 0.00 32.32 1.73
763 777 9.661954 TGACTAGGAGATCTTATAAGGAATGTT 57.338 33.333 12.54 0.00 0.00 2.71
831 849 9.326413 TGTTTAGAAGGCAAGCTATTAATCTAC 57.674 33.333 0.00 0.00 0.00 2.59
862 880 4.209538 TGCACCATCATTTTAGGGATCTG 58.790 43.478 0.00 0.00 0.00 2.90
873 891 6.662865 TTTTAGGGATCTGTTTTGATTGCA 57.337 33.333 0.00 0.00 0.00 4.08
881 899 3.313803 TCTGTTTTGATTGCACGCTACAA 59.686 39.130 0.00 0.00 0.00 2.41
893 911 0.798776 CGCTACAACTTTGCCCTCTG 59.201 55.000 0.00 0.00 0.00 3.35
905 923 0.034670 GCCCTCTGCCTCAAGTTGAT 60.035 55.000 5.91 0.00 0.00 2.57
924 942 5.499004 TGATTGCTGGGTATATTAGGACC 57.501 43.478 0.00 0.00 34.75 4.46
950 968 3.892162 CCCCACCACCCCAACGAA 61.892 66.667 0.00 0.00 0.00 3.85
967 985 7.144000 CCCAACGAAGGTACTGTATTATAGAC 58.856 42.308 0.00 0.00 40.86 2.59
974 992 7.321717 AGGTACTGTATTATAGACCCGTAGA 57.678 40.000 0.00 0.00 37.18 2.59
1017 1036 4.577096 TCCCCATGGACAAGTATAGGAAT 58.423 43.478 15.22 0.00 35.03 3.01
1026 1045 5.353123 GGACAAGTATAGGAATCGTTTGCAA 59.647 40.000 0.00 0.00 0.00 4.08
1060 1079 4.865776 ACTAGCGATGCTTCTTCTCATAC 58.134 43.478 0.00 0.00 40.44 2.39
1061 1080 4.582656 ACTAGCGATGCTTCTTCTCATACT 59.417 41.667 0.00 0.00 40.44 2.12
1073 1092 3.520290 TCTCATACTGTTTGCTACCCG 57.480 47.619 0.00 0.00 0.00 5.28
1092 1111 2.233355 CGTGCGCAATGTAAGTTTCAG 58.767 47.619 14.00 0.00 0.00 3.02
1411 3062 7.475771 TGTTTTGCAAACCATCTTTGTTATC 57.524 32.000 12.39 0.00 0.00 1.75
1436 3087 1.391577 TTGGATGATTGCATGGTCGG 58.608 50.000 0.00 0.00 34.11 4.79
1440 3091 1.731433 ATGATTGCATGGTCGGCTGC 61.731 55.000 0.00 0.00 38.87 5.25
1531 3182 6.966534 AGTCATATGGCTTTTTAAGGATGG 57.033 37.500 3.33 0.00 0.00 3.51
1537 3188 2.501316 GGCTTTTTAAGGATGGTGCCAT 59.499 45.455 2.95 2.95 38.99 4.40
1695 3346 6.915300 TGTCTTATTGGTTTGTTGATTTGACG 59.085 34.615 0.00 0.00 0.00 4.35
1696 3347 6.915843 GTCTTATTGGTTTGTTGATTTGACGT 59.084 34.615 0.00 0.00 0.00 4.34
1697 3348 7.112984 GTCTTATTGGTTTGTTGATTTGACGTC 59.887 37.037 9.11 9.11 0.00 4.34
1700 3351 3.697045 TGGTTTGTTGATTTGACGTCCTT 59.303 39.130 14.12 0.00 0.00 3.36
1701 3352 4.158764 TGGTTTGTTGATTTGACGTCCTTT 59.841 37.500 14.12 0.00 0.00 3.11
1702 3353 5.106442 GGTTTGTTGATTTGACGTCCTTTT 58.894 37.500 14.12 0.00 0.00 2.27
1717 3393 4.367039 TCCTTTTGGGAAACTCTACCTG 57.633 45.455 0.00 0.00 41.91 4.00
1719 3395 4.167307 TCCTTTTGGGAAACTCTACCTGTT 59.833 41.667 0.00 0.00 41.91 3.16
1738 3587 1.118838 TTCAAGTGGCAAAACAGGGG 58.881 50.000 0.00 0.00 0.00 4.79
1760 3609 1.381076 GGGGGTTGGATTTGTCGGA 59.619 57.895 0.00 0.00 0.00 4.55
1762 3611 1.389555 GGGGTTGGATTTGTCGGATC 58.610 55.000 0.00 0.00 0.00 3.36
1763 3612 1.014352 GGGTTGGATTTGTCGGATCG 58.986 55.000 0.00 0.00 0.00 3.69
1764 3613 1.406341 GGGTTGGATTTGTCGGATCGA 60.406 52.381 0.00 0.00 0.00 3.59
1765 3614 2.561569 GGTTGGATTTGTCGGATCGAT 58.438 47.619 0.00 0.00 38.42 3.59
1766 3615 2.943033 GGTTGGATTTGTCGGATCGATT 59.057 45.455 0.00 0.00 38.42 3.34
1767 3616 3.242739 GGTTGGATTTGTCGGATCGATTG 60.243 47.826 0.00 0.00 38.42 2.67
1768 3617 3.260475 TGGATTTGTCGGATCGATTGT 57.740 42.857 0.00 0.00 38.42 2.71
1769 3618 3.605634 TGGATTTGTCGGATCGATTGTT 58.394 40.909 0.00 0.00 38.42 2.83
1770 3619 4.006989 TGGATTTGTCGGATCGATTGTTT 58.993 39.130 0.00 0.00 38.42 2.83
1771 3620 4.142708 TGGATTTGTCGGATCGATTGTTTG 60.143 41.667 0.00 0.00 38.42 2.93
1772 3621 2.892373 TTGTCGGATCGATTGTTTGC 57.108 45.000 0.00 0.00 38.42 3.68
1773 3622 2.093306 TGTCGGATCGATTGTTTGCT 57.907 45.000 0.00 0.00 38.42 3.91
1774 3623 1.999735 TGTCGGATCGATTGTTTGCTC 59.000 47.619 0.00 0.00 38.42 4.26
1775 3624 1.005975 GTCGGATCGATTGTTTGCTCG 60.006 52.381 0.00 0.00 38.42 5.03
1776 3625 1.135228 TCGGATCGATTGTTTGCTCGA 60.135 47.619 0.00 0.00 46.71 4.04
1777 3626 1.005975 CGGATCGATTGTTTGCTCGAC 60.006 52.381 0.00 0.00 45.63 4.20
1778 3627 1.327764 GGATCGATTGTTTGCTCGACC 59.672 52.381 0.00 0.00 45.63 4.79
1779 3628 1.327764 GATCGATTGTTTGCTCGACCC 59.672 52.381 0.00 0.00 45.63 4.46
1780 3629 0.320374 TCGATTGTTTGCTCGACCCT 59.680 50.000 0.00 0.00 38.86 4.34
1781 3630 0.721718 CGATTGTTTGCTCGACCCTC 59.278 55.000 0.00 0.00 37.05 4.30
1782 3631 1.087501 GATTGTTTGCTCGACCCTCC 58.912 55.000 0.00 0.00 0.00 4.30
1783 3632 0.322546 ATTGTTTGCTCGACCCTCCC 60.323 55.000 0.00 0.00 0.00 4.30
1784 3633 1.415672 TTGTTTGCTCGACCCTCCCT 61.416 55.000 0.00 0.00 0.00 4.20
1785 3634 1.079057 GTTTGCTCGACCCTCCCTC 60.079 63.158 0.00 0.00 0.00 4.30
1786 3635 2.291043 TTTGCTCGACCCTCCCTCC 61.291 63.158 0.00 0.00 0.00 4.30
1787 3636 2.748641 TTTGCTCGACCCTCCCTCCT 62.749 60.000 0.00 0.00 0.00 3.69
1788 3637 2.364448 GCTCGACCCTCCCTCCTT 60.364 66.667 0.00 0.00 0.00 3.36
1789 3638 1.076192 GCTCGACCCTCCCTCCTTA 60.076 63.158 0.00 0.00 0.00 2.69
1790 3639 1.110518 GCTCGACCCTCCCTCCTTAG 61.111 65.000 0.00 0.00 0.00 2.18
1791 3640 1.076192 TCGACCCTCCCTCCTTAGC 60.076 63.158 0.00 0.00 0.00 3.09
1792 3641 2.491022 CGACCCTCCCTCCTTAGCG 61.491 68.421 0.00 0.00 0.00 4.26
1793 3642 1.381463 GACCCTCCCTCCTTAGCGT 60.381 63.158 0.00 0.00 0.00 5.07
1794 3643 1.381463 ACCCTCCCTCCTTAGCGTC 60.381 63.158 0.00 0.00 0.00 5.19
1795 3644 2.134933 CCCTCCCTCCTTAGCGTCC 61.135 68.421 0.00 0.00 0.00 4.79
1796 3645 1.381327 CCTCCCTCCTTAGCGTCCA 60.381 63.158 0.00 0.00 0.00 4.02
1797 3646 0.976073 CCTCCCTCCTTAGCGTCCAA 60.976 60.000 0.00 0.00 0.00 3.53
1798 3647 0.902531 CTCCCTCCTTAGCGTCCAAA 59.097 55.000 0.00 0.00 0.00 3.28
1799 3648 1.278127 CTCCCTCCTTAGCGTCCAAAA 59.722 52.381 0.00 0.00 0.00 2.44
1800 3649 1.700739 TCCCTCCTTAGCGTCCAAAAA 59.299 47.619 0.00 0.00 0.00 1.94
1824 3673 4.039730 AGAATGTGATTGATCCTACCCTCG 59.960 45.833 0.00 0.00 0.00 4.63
1891 3740 3.057596 CCAACGATTGCAGGTTACAACAT 60.058 43.478 0.00 0.00 0.00 2.71
1892 3741 3.829886 ACGATTGCAGGTTACAACATG 57.170 42.857 2.51 2.51 43.07 3.21
1893 3742 3.407698 ACGATTGCAGGTTACAACATGA 58.592 40.909 10.68 0.00 42.86 3.07
1894 3743 3.818210 ACGATTGCAGGTTACAACATGAA 59.182 39.130 10.68 0.00 42.86 2.57
1895 3744 4.158384 CGATTGCAGGTTACAACATGAAC 58.842 43.478 10.68 0.00 42.86 3.18
1896 3745 4.320129 CGATTGCAGGTTACAACATGAACA 60.320 41.667 10.68 0.00 42.86 3.18
1897 3746 3.980646 TGCAGGTTACAACATGAACAC 57.019 42.857 10.68 0.00 42.86 3.32
1898 3747 2.289274 TGCAGGTTACAACATGAACACG 59.711 45.455 10.68 0.00 42.86 4.49
1899 3748 2.546368 GCAGGTTACAACATGAACACGA 59.454 45.455 10.68 0.00 42.86 4.35
1900 3749 3.002862 GCAGGTTACAACATGAACACGAA 59.997 43.478 10.68 0.00 42.86 3.85
1901 3750 4.496673 GCAGGTTACAACATGAACACGAAA 60.497 41.667 10.68 0.00 42.86 3.46
1902 3751 5.204833 CAGGTTACAACATGAACACGAAAG 58.795 41.667 0.00 0.00 42.86 2.62
1903 3752 5.220777 CAGGTTACAACATGAACACGAAAGT 60.221 40.000 0.00 0.00 44.29 2.66
1996 3845 3.386237 GCGCCTCCTCTCACCTGT 61.386 66.667 0.00 0.00 0.00 4.00
2001 3850 0.617413 CCTCCTCTCACCTGTTGCAT 59.383 55.000 0.00 0.00 0.00 3.96
2058 3907 1.077501 ACTTATGCCATGGCTGCGT 60.078 52.632 35.53 23.21 42.51 5.24
2398 4252 1.134965 GCCACTGTATCGTGCTCTCTT 60.135 52.381 0.00 0.00 33.60 2.85
2408 4262 2.268802 TGCTCTCTTCACGGTCGCT 61.269 57.895 0.00 0.00 0.00 4.93
2449 4304 3.255149 GTCTCCTTCTGGTTCGACAACTA 59.745 47.826 0.00 0.00 32.50 2.24
2507 4362 2.411748 TCTCTTTTCGCATGCTGTTACG 59.588 45.455 17.13 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 92 4.501433 AGCAATCCAGATCCCTCTAATCT 58.499 43.478 0.00 0.00 33.74 2.40
102 103 9.277783 GTCTAATATTACACAAGCAATCCAGAT 57.722 33.333 0.00 0.00 0.00 2.90
107 108 8.388103 ACGTTGTCTAATATTACACAAGCAATC 58.612 33.333 14.38 4.58 29.48 2.67
108 109 8.175069 CACGTTGTCTAATATTACACAAGCAAT 58.825 33.333 14.38 1.62 29.48 3.56
109 110 7.385478 TCACGTTGTCTAATATTACACAAGCAA 59.615 33.333 14.38 3.42 29.48 3.91
110 111 6.869388 TCACGTTGTCTAATATTACACAAGCA 59.131 34.615 14.38 0.00 29.48 3.91
111 112 7.285783 TCACGTTGTCTAATATTACACAAGC 57.714 36.000 14.38 9.76 29.48 4.01
112 113 9.689075 CAATCACGTTGTCTAATATTACACAAG 57.311 33.333 14.38 11.50 33.01 3.16
132 133 3.861840 TCCTTTCATCCTCGACAATCAC 58.138 45.455 0.00 0.00 0.00 3.06
143 144 4.711355 TCATGGTCCAAATTCCTTTCATCC 59.289 41.667 0.00 0.00 0.00 3.51
159 160 2.423538 GGCTACCAACATTGTCATGGTC 59.576 50.000 14.90 4.22 43.90 4.02
162 163 2.083774 ACGGCTACCAACATTGTCATG 58.916 47.619 0.00 0.00 36.34 3.07
204 205 9.102757 GATCTTAAGAAATGCAGTGAACTCATA 57.897 33.333 9.71 0.00 0.00 2.15
233 234 2.160205 ACACAGTTCTCGATTCTCCGA 58.840 47.619 0.00 0.00 37.03 4.55
296 302 3.210074 ACCTATCTCCCCCATAGAGTTGT 59.790 47.826 0.00 0.00 32.93 3.32
409 421 8.910666 CGAAAAGCAAATCACAATACAACAATA 58.089 29.630 0.00 0.00 0.00 1.90
425 437 7.164230 ACATATAAATGGTCCGAAAAGCAAA 57.836 32.000 0.00 0.00 37.43 3.68
499 511 9.962759 GCATCAAACAAATTACAGATTTCAATC 57.037 29.630 0.00 0.00 35.64 2.67
500 512 9.715121 AGCATCAAACAAATTACAGATTTCAAT 57.285 25.926 0.00 0.00 0.00 2.57
517 529 6.310224 ACCGTAAATTTTGCATAGCATCAAAC 59.690 34.615 0.00 0.00 38.76 2.93
518 530 6.309980 CACCGTAAATTTTGCATAGCATCAAA 59.690 34.615 0.00 0.00 38.76 2.69
519 531 5.804473 CACCGTAAATTTTGCATAGCATCAA 59.196 36.000 0.00 0.00 38.76 2.57
520 532 5.339177 CACCGTAAATTTTGCATAGCATCA 58.661 37.500 0.00 0.00 38.76 3.07
523 535 3.506810 GCACCGTAAATTTTGCATAGCA 58.493 40.909 7.53 0.00 36.47 3.49
552 564 1.270147 CGGGATCTATTCCACCGGAAC 60.270 57.143 9.46 0.00 45.07 3.62
564 578 2.957680 TGGTACGCATTTACGGGATCTA 59.042 45.455 0.00 0.00 37.37 1.98
586 600 3.963383 ACTCGTCTCGCAAATGTTTTT 57.037 38.095 0.00 0.00 0.00 1.94
591 605 2.659757 TCGTAAACTCGTCTCGCAAATG 59.340 45.455 0.00 0.00 0.00 2.32
599 613 5.503683 CGGAACAGATATCGTAAACTCGTCT 60.504 44.000 0.00 0.00 0.00 4.18
604 618 4.097437 TCAGCGGAACAGATATCGTAAACT 59.903 41.667 0.00 0.00 0.00 2.66
632 646 3.824414 AATTCTTTTACGGTGCCGAAG 57.176 42.857 18.16 10.47 42.83 3.79
634 648 4.291783 CAAAAATTCTTTTACGGTGCCGA 58.708 39.130 18.16 0.00 36.41 5.54
635 649 3.121160 GCAAAAATTCTTTTACGGTGCCG 60.121 43.478 9.29 9.29 37.79 5.69
636 650 3.121160 CGCAAAAATTCTTTTACGGTGCC 60.121 43.478 0.00 0.00 37.55 5.01
639 653 4.973663 CACTCGCAAAAATTCTTTTACGGT 59.026 37.500 3.83 0.00 40.29 4.83
640 654 4.143618 GCACTCGCAAAAATTCTTTTACGG 60.144 41.667 3.83 0.00 40.29 4.02
642 656 4.149922 GGGCACTCGCAAAAATTCTTTTAC 59.850 41.667 0.00 0.00 41.24 2.01
643 657 4.038642 AGGGCACTCGCAAAAATTCTTTTA 59.961 37.500 0.00 0.00 41.24 1.52
644 658 3.130633 GGGCACTCGCAAAAATTCTTTT 58.869 40.909 0.00 0.00 41.24 2.27
648 662 2.438868 AAGGGCACTCGCAAAAATTC 57.561 45.000 0.00 0.00 41.24 2.17
651 665 2.541999 CGTTTAAGGGCACTCGCAAAAA 60.542 45.455 0.00 0.00 41.24 1.94
659 673 2.034179 GCAAAACTCGTTTAAGGGCACT 59.966 45.455 0.00 0.00 31.63 4.40
661 675 1.002251 CGCAAAACTCGTTTAAGGGCA 60.002 47.619 0.00 0.00 31.63 5.36
684 698 3.078837 GTTGATTGAACTTTAGGGCCGA 58.921 45.455 0.00 0.00 0.00 5.54
685 699 2.163613 GGTTGATTGAACTTTAGGGCCG 59.836 50.000 0.00 0.00 34.66 6.13
686 700 3.161866 TGGTTGATTGAACTTTAGGGCC 58.838 45.455 0.00 0.00 34.66 5.80
687 701 4.864704 TTGGTTGATTGAACTTTAGGGC 57.135 40.909 0.00 0.00 34.66 5.19
688 702 6.155475 TGTTTGGTTGATTGAACTTTAGGG 57.845 37.500 0.00 0.00 34.66 3.53
689 703 7.710475 ACATTGTTTGGTTGATTGAACTTTAGG 59.290 33.333 0.00 0.00 34.66 2.69
690 704 8.647143 ACATTGTTTGGTTGATTGAACTTTAG 57.353 30.769 0.00 0.00 34.66 1.85
691 705 9.442047 AAACATTGTTTGGTTGATTGAACTTTA 57.558 25.926 13.80 0.00 32.68 1.85
692 706 7.920160 AACATTGTTTGGTTGATTGAACTTT 57.080 28.000 0.00 0.00 34.66 2.66
706 720 8.577939 CGTATGCTAGAATTCAAACATTGTTTG 58.422 33.333 28.44 28.44 0.00 2.93
707 721 8.296713 ACGTATGCTAGAATTCAAACATTGTTT 58.703 29.630 8.97 8.97 0.00 2.83
743 757 9.784531 TGATTCAACATTCCTTATAAGATCTCC 57.215 33.333 14.28 0.00 0.00 3.71
831 849 8.464404 CCCTAAAATGATGGTGCATTCTATATG 58.536 37.037 0.00 0.00 37.50 1.78
835 853 6.012337 TCCCTAAAATGATGGTGCATTCTA 57.988 37.500 0.00 0.00 37.50 2.10
837 855 5.537674 AGATCCCTAAAATGATGGTGCATTC 59.462 40.000 0.00 0.00 37.50 2.67
846 864 7.983484 GCAATCAAAACAGATCCCTAAAATGAT 59.017 33.333 0.00 0.00 0.00 2.45
862 880 3.628017 AGTTGTAGCGTGCAATCAAAAC 58.372 40.909 0.00 0.00 0.00 2.43
873 891 0.396811 AGAGGGCAAAGTTGTAGCGT 59.603 50.000 0.00 0.00 0.00 5.07
893 911 0.529378 CCCAGCAATCAACTTGAGGC 59.471 55.000 9.23 9.23 36.97 4.70
933 951 3.860930 CTTCGTTGGGGTGGTGGGG 62.861 68.421 0.00 0.00 0.00 4.96
934 952 2.282180 CTTCGTTGGGGTGGTGGG 60.282 66.667 0.00 0.00 0.00 4.61
935 953 1.770749 TACCTTCGTTGGGGTGGTGG 61.771 60.000 0.00 0.00 37.07 4.61
936 954 0.604511 GTACCTTCGTTGGGGTGGTG 60.605 60.000 0.00 0.00 37.07 4.17
937 955 0.765519 AGTACCTTCGTTGGGGTGGT 60.766 55.000 0.00 0.00 37.07 4.16
938 956 0.321298 CAGTACCTTCGTTGGGGTGG 60.321 60.000 0.00 0.00 37.07 4.61
939 957 0.395312 ACAGTACCTTCGTTGGGGTG 59.605 55.000 0.00 0.00 37.07 4.61
940 958 2.014010 TACAGTACCTTCGTTGGGGT 57.986 50.000 0.00 0.00 39.40 4.95
950 968 7.321717 TCTACGGGTCTATAATACAGTACCT 57.678 40.000 0.00 0.00 0.00 3.08
967 985 0.250553 TGTGGCCTTGTTTCTACGGG 60.251 55.000 3.32 0.00 0.00 5.28
974 992 5.304778 GGAAATTATTGTGTGGCCTTGTTT 58.695 37.500 3.32 0.00 0.00 2.83
1017 1036 5.165676 AGTACGATTGAGTATTGCAAACGA 58.834 37.500 1.71 0.00 41.92 3.85
1060 1079 2.860293 CGCACGGGTAGCAAACAG 59.140 61.111 0.00 0.00 0.00 3.16
1061 1080 3.350612 GCGCACGGGTAGCAAACA 61.351 61.111 0.30 0.00 0.00 2.83
1073 1092 3.536158 TCTGAAACTTACATTGCGCAC 57.464 42.857 11.12 0.00 0.00 5.34
1106 1159 9.173939 GCATTTGCATATAACAATTAGTCAGAC 57.826 33.333 0.00 0.00 41.59 3.51
1178 1585 7.109006 TCACGAATAAAAACCGTAAGAACTC 57.891 36.000 0.00 0.00 43.02 3.01
1280 2927 7.002250 TCCAAGATTCTGCCTATAGAAGATG 57.998 40.000 0.00 0.13 39.81 2.90
1411 3062 3.449737 ACCATGCAATCATCCAAAGAAGG 59.550 43.478 0.00 0.00 0.00 3.46
1436 3087 1.431036 GGAGAAGCATTTCGGCAGC 59.569 57.895 0.00 0.00 38.38 5.25
1440 3091 2.603560 GTCTAACGGAGAAGCATTTCGG 59.396 50.000 0.00 0.00 38.38 4.30
1531 3182 5.694231 TTATTCATGAGCACATATGGCAC 57.306 39.130 15.63 11.11 35.09 5.01
1662 3313 9.616156 TCAACAAACCAATAAGACAGTAAGTAA 57.384 29.630 0.00 0.00 0.00 2.24
1663 3314 9.787435 ATCAACAAACCAATAAGACAGTAAGTA 57.213 29.630 0.00 0.00 0.00 2.24
1664 3315 8.691661 ATCAACAAACCAATAAGACAGTAAGT 57.308 30.769 0.00 0.00 0.00 2.24
1665 3316 9.965824 AAATCAACAAACCAATAAGACAGTAAG 57.034 29.630 0.00 0.00 0.00 2.34
1666 3317 9.743057 CAAATCAACAAACCAATAAGACAGTAA 57.257 29.630 0.00 0.00 0.00 2.24
1667 3318 9.126151 TCAAATCAACAAACCAATAAGACAGTA 57.874 29.630 0.00 0.00 0.00 2.74
1668 3319 7.920682 GTCAAATCAACAAACCAATAAGACAGT 59.079 33.333 0.00 0.00 0.00 3.55
1669 3320 7.113404 CGTCAAATCAACAAACCAATAAGACAG 59.887 37.037 0.00 0.00 0.00 3.51
1670 3321 6.915300 CGTCAAATCAACAAACCAATAAGACA 59.085 34.615 0.00 0.00 0.00 3.41
1671 3322 6.915843 ACGTCAAATCAACAAACCAATAAGAC 59.084 34.615 0.00 0.00 0.00 3.01
1672 3323 7.033530 ACGTCAAATCAACAAACCAATAAGA 57.966 32.000 0.00 0.00 0.00 2.10
1673 3324 6.362283 GGACGTCAAATCAACAAACCAATAAG 59.638 38.462 18.91 0.00 0.00 1.73
1674 3325 6.039941 AGGACGTCAAATCAACAAACCAATAA 59.960 34.615 18.91 0.00 0.00 1.40
1675 3326 5.533154 AGGACGTCAAATCAACAAACCAATA 59.467 36.000 18.91 0.00 0.00 1.90
1676 3327 4.340950 AGGACGTCAAATCAACAAACCAAT 59.659 37.500 18.91 0.00 0.00 3.16
1696 3347 3.720002 ACAGGTAGAGTTTCCCAAAAGGA 59.280 43.478 0.00 0.00 45.68 3.36
1697 3348 4.100279 ACAGGTAGAGTTTCCCAAAAGG 57.900 45.455 0.00 0.00 0.00 3.11
1717 3393 2.549926 CCCTGTTTTGCCACTTGAAAC 58.450 47.619 0.00 0.00 34.67 2.78
1719 3395 1.118838 CCCCTGTTTTGCCACTTGAA 58.881 50.000 0.00 0.00 0.00 2.69
1721 3397 1.747774 CCCCCTGTTTTGCCACTTG 59.252 57.895 0.00 0.00 0.00 3.16
1722 3398 4.293610 CCCCCTGTTTTGCCACTT 57.706 55.556 0.00 0.00 0.00 3.16
1738 3587 0.902984 GACAAATCCAACCCCCACCC 60.903 60.000 0.00 0.00 0.00 4.61
1740 3589 1.248101 CCGACAAATCCAACCCCCAC 61.248 60.000 0.00 0.00 0.00 4.61
1762 3611 0.721718 GAGGGTCGAGCAAACAATCG 59.278 55.000 17.59 0.00 40.26 3.34
1763 3612 1.087501 GGAGGGTCGAGCAAACAATC 58.912 55.000 17.59 4.09 0.00 2.67
1764 3613 0.322546 GGGAGGGTCGAGCAAACAAT 60.323 55.000 17.59 0.00 0.00 2.71
1765 3614 1.072505 GGGAGGGTCGAGCAAACAA 59.927 57.895 17.59 0.00 0.00 2.83
1766 3615 1.827399 GAGGGAGGGTCGAGCAAACA 61.827 60.000 17.59 0.00 0.00 2.83
1767 3616 1.079057 GAGGGAGGGTCGAGCAAAC 60.079 63.158 17.59 6.66 0.00 2.93
1768 3617 2.291043 GGAGGGAGGGTCGAGCAAA 61.291 63.158 17.59 0.00 0.00 3.68
1769 3618 2.683933 GGAGGGAGGGTCGAGCAA 60.684 66.667 17.59 0.00 0.00 3.91
1770 3619 1.870941 TAAGGAGGGAGGGTCGAGCA 61.871 60.000 17.59 0.00 0.00 4.26
1771 3620 1.076192 TAAGGAGGGAGGGTCGAGC 60.076 63.158 5.93 5.93 0.00 5.03
1772 3621 1.110518 GCTAAGGAGGGAGGGTCGAG 61.111 65.000 0.00 0.00 0.00 4.04
1773 3622 1.076192 GCTAAGGAGGGAGGGTCGA 60.076 63.158 0.00 0.00 0.00 4.20
1774 3623 2.491022 CGCTAAGGAGGGAGGGTCG 61.491 68.421 0.00 0.00 37.85 4.79
1775 3624 1.381463 ACGCTAAGGAGGGAGGGTC 60.381 63.158 0.00 0.00 38.95 4.46
1776 3625 1.381463 GACGCTAAGGAGGGAGGGT 60.381 63.158 0.00 0.00 41.13 4.34
1777 3626 2.134933 GGACGCTAAGGAGGGAGGG 61.135 68.421 0.00 0.00 38.95 4.30
1778 3627 0.976073 TTGGACGCTAAGGAGGGAGG 60.976 60.000 0.00 0.00 38.95 4.30
1779 3628 0.902531 TTTGGACGCTAAGGAGGGAG 59.097 55.000 0.00 0.00 38.95 4.30
1780 3629 1.354101 TTTTGGACGCTAAGGAGGGA 58.646 50.000 0.00 0.00 38.95 4.20
1781 3630 2.194201 TTTTTGGACGCTAAGGAGGG 57.806 50.000 0.00 0.00 41.37 4.30
1797 3646 7.184862 AGGGTAGGATCAATCACATTCTTTTT 58.815 34.615 0.00 0.00 0.00 1.94
1798 3647 6.735556 AGGGTAGGATCAATCACATTCTTTT 58.264 36.000 0.00 0.00 0.00 2.27
1799 3648 6.332976 AGGGTAGGATCAATCACATTCTTT 57.667 37.500 0.00 0.00 0.00 2.52
1800 3649 5.453903 CGAGGGTAGGATCAATCACATTCTT 60.454 44.000 0.00 0.00 0.00 2.52
1801 3650 4.039730 CGAGGGTAGGATCAATCACATTCT 59.960 45.833 0.00 0.00 0.00 2.40
1802 3651 4.310769 CGAGGGTAGGATCAATCACATTC 58.689 47.826 0.00 0.00 0.00 2.67
1803 3652 3.495100 GCGAGGGTAGGATCAATCACATT 60.495 47.826 0.00 0.00 0.00 2.71
1824 3673 3.370366 GCTCAGTCCATGATCGATTATGC 59.630 47.826 21.43 11.06 37.28 3.14
1850 3699 1.337728 GGAAACGCAATTCTTTGGGGG 60.338 52.381 7.54 0.00 46.88 5.40
1891 3740 4.902443 TTTTATGCCACTTTCGTGTTCA 57.098 36.364 0.00 0.00 39.55 3.18
1892 3741 5.173131 CAGTTTTTATGCCACTTTCGTGTTC 59.827 40.000 0.00 0.00 39.55 3.18
1893 3742 5.040635 CAGTTTTTATGCCACTTTCGTGTT 58.959 37.500 0.00 0.00 39.55 3.32
1894 3743 4.336993 TCAGTTTTTATGCCACTTTCGTGT 59.663 37.500 0.00 0.00 39.55 4.49
1895 3744 4.854399 TCAGTTTTTATGCCACTTTCGTG 58.146 39.130 0.00 0.00 40.89 4.35
1896 3745 4.023193 CCTCAGTTTTTATGCCACTTTCGT 60.023 41.667 0.00 0.00 0.00 3.85
1897 3746 4.023193 ACCTCAGTTTTTATGCCACTTTCG 60.023 41.667 0.00 0.00 0.00 3.46
1898 3747 5.453567 ACCTCAGTTTTTATGCCACTTTC 57.546 39.130 0.00 0.00 0.00 2.62
1899 3748 5.507315 CGAACCTCAGTTTTTATGCCACTTT 60.507 40.000 0.00 0.00 35.94 2.66
1900 3749 4.023193 CGAACCTCAGTTTTTATGCCACTT 60.023 41.667 0.00 0.00 35.94 3.16
1901 3750 3.502211 CGAACCTCAGTTTTTATGCCACT 59.498 43.478 0.00 0.00 35.94 4.00
1902 3751 3.500680 TCGAACCTCAGTTTTTATGCCAC 59.499 43.478 0.00 0.00 35.94 5.01
1903 3752 3.745799 TCGAACCTCAGTTTTTATGCCA 58.254 40.909 0.00 0.00 35.94 4.92
1904 3753 4.454504 TCTTCGAACCTCAGTTTTTATGCC 59.545 41.667 0.00 0.00 35.94 4.40
1905 3754 5.179555 AGTCTTCGAACCTCAGTTTTTATGC 59.820 40.000 0.00 0.00 35.94 3.14
1906 3755 6.787085 AGTCTTCGAACCTCAGTTTTTATG 57.213 37.500 0.00 0.00 35.94 1.90
1907 3756 6.427242 GGAAGTCTTCGAACCTCAGTTTTTAT 59.573 38.462 6.50 0.00 35.94 1.40
1908 3757 5.756833 GGAAGTCTTCGAACCTCAGTTTTTA 59.243 40.000 6.50 0.00 35.94 1.52
1909 3758 4.575236 GGAAGTCTTCGAACCTCAGTTTTT 59.425 41.667 6.50 0.00 35.94 1.94
1910 3759 4.127907 GGAAGTCTTCGAACCTCAGTTTT 58.872 43.478 6.50 0.00 35.94 2.43
1996 3845 1.340088 AATCAACACCAGGCATGCAA 58.660 45.000 21.36 0.00 0.00 4.08
2001 3850 2.492881 CAGCATTAATCAACACCAGGCA 59.507 45.455 0.00 0.00 0.00 4.75
2328 4182 1.376086 CCAGAGCATGGTCACCACA 59.624 57.895 25.71 0.00 44.91 4.17
2381 4235 3.495670 GTGAAGAGAGCACGATACAGT 57.504 47.619 0.00 0.00 0.00 3.55
2420 4275 1.743252 CCAGAAGGAGACCAAGCGC 60.743 63.158 0.00 0.00 36.89 5.92
2421 4276 0.035458 AACCAGAAGGAGACCAAGCG 59.965 55.000 0.00 0.00 38.69 4.68
2422 4277 1.814793 GAACCAGAAGGAGACCAAGC 58.185 55.000 0.00 0.00 38.69 4.01
2423 4278 1.618837 TCGAACCAGAAGGAGACCAAG 59.381 52.381 0.00 0.00 38.69 3.61
2424 4279 1.343465 GTCGAACCAGAAGGAGACCAA 59.657 52.381 0.00 0.00 38.69 3.67
2425 4280 0.966920 GTCGAACCAGAAGGAGACCA 59.033 55.000 0.00 0.00 38.69 4.02


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

AutoCloner maintained by Alex Coulton.