Multiple sequence alignment - TraesCS6D01G058800

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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 TraesCS6D01G058800 chr6D 100.000 3808 0 0 1 3808 27684721 27680914 0.000000e+00 7033.0
1 TraesCS6D01G058800 chr6D 84.282 1107 142 21 996 2091 27711107 27712192 0.000000e+00 1051.0
2 TraesCS6D01G058800 chr6D 80.920 587 112 0 1005 1591 27845350 27845936 7.450000e-127 464.0
3 TraesCS6D01G058800 chr6D 79.196 423 69 16 1609 2014 28415382 28414962 3.750000e-70 276.0
4 TraesCS6D01G058800 chr6D 75.414 362 70 17 1741 2094 36324680 36325030 1.420000e-34 158.0
5 TraesCS6D01G058800 chr6D 73.056 360 84 12 1748 2104 35717212 35716863 8.640000e-22 115.0
6 TraesCS6D01G058800 chr6A 95.225 3016 118 14 814 3804 30422426 30425440 0.000000e+00 4748.0
7 TraesCS6D01G058800 chr6A 83.094 976 128 18 1001 1945 30283473 30282504 0.000000e+00 854.0
8 TraesCS6D01G058800 chr6A 84.759 643 71 12 1293 1926 30263664 30263040 1.500000e-173 619.0
9 TraesCS6D01G058800 chr6A 81.208 596 112 0 996 1591 30036460 30035865 7.400000e-132 481.0
10 TraesCS6D01G058800 chr6A 88.936 235 20 3 2042 2276 30263020 30262792 6.230000e-73 285.0
11 TraesCS6D01G058800 chr6A 74.380 363 72 19 1741 2094 40622737 40622387 6.640000e-28 135.0
12 TraesCS6D01G058800 chr6A 94.253 87 5 0 403 489 30421957 30422043 2.390000e-27 134.0
13 TraesCS6D01G058800 chr6A 87.209 86 11 0 2001 2086 30282506 30282421 8.710000e-17 99.0
14 TraesCS6D01G058800 chr6B 95.000 3000 132 11 814 3804 51435958 51432968 0.000000e+00 4693.0
15 TraesCS6D01G058800 chr6B 84.258 775 107 12 996 1763 51537981 51538747 0.000000e+00 741.0
16 TraesCS6D01G058800 chr6B 88.211 492 49 6 1 489 51439427 51438942 2.550000e-161 579.0
17 TraesCS6D01G058800 chr6B 76.383 1139 210 43 999 2095 51559011 51560132 3.320000e-155 558.0
18 TraesCS6D01G058800 chr6B 80.617 583 111 2 996 1577 51732102 51732683 2.090000e-122 449.0
19 TraesCS6D01G058800 chr6B 89.607 356 31 3 1916 2271 51553674 51554023 7.500000e-122 448.0
20 TraesCS6D01G058800 chr6B 76.772 508 81 24 1610 2092 51732743 51733238 2.270000e-62 250.0
21 TraesCS6D01G058800 chr6B 87.500 160 19 1 18 177 51502430 51502272 2.340000e-42 183.0
22 TraesCS6D01G058800 chr6B 87.786 131 16 0 2097 2227 51560173 51560303 1.830000e-33 154.0
23 TraesCS6D01G058800 chr6B 82.632 190 11 10 486 672 51438914 51438744 8.520000e-32 148.0
24 TraesCS6D01G058800 chr6B 82.394 142 21 4 1760 1899 49700652 49700513 1.860000e-23 121.0
25 TraesCS6D01G058800 chr6B 72.022 361 86 14 1748 2104 75422681 75422332 4.050000e-15 93.5
26 TraesCS6D01G058800 chrUn 81.022 137 12 6 349 482 137673054 137673179 3.130000e-16 97.1


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 TraesCS6D01G058800 chr6D 27680914 27684721 3807 True 7033.000000 7033 100.000000 1 3808 1 chr6D.!!$R1 3807
1 TraesCS6D01G058800 chr6D 27711107 27712192 1085 False 1051.000000 1051 84.282000 996 2091 1 chr6D.!!$F1 1095
2 TraesCS6D01G058800 chr6D 27845350 27845936 586 False 464.000000 464 80.920000 1005 1591 1 chr6D.!!$F2 586
3 TraesCS6D01G058800 chr6A 30421957 30425440 3483 False 2441.000000 4748 94.739000 403 3804 2 chr6A.!!$F1 3401
4 TraesCS6D01G058800 chr6A 30035865 30036460 595 True 481.000000 481 81.208000 996 1591 1 chr6A.!!$R1 595
5 TraesCS6D01G058800 chr6A 30282421 30283473 1052 True 476.500000 854 85.151500 1001 2086 2 chr6A.!!$R4 1085
6 TraesCS6D01G058800 chr6A 30262792 30263664 872 True 452.000000 619 86.847500 1293 2276 2 chr6A.!!$R3 983
7 TraesCS6D01G058800 chr6B 51432968 51439427 6459 True 1806.666667 4693 88.614333 1 3804 3 chr6B.!!$R4 3803
8 TraesCS6D01G058800 chr6B 51537981 51538747 766 False 741.000000 741 84.258000 996 1763 1 chr6B.!!$F1 767
9 TraesCS6D01G058800 chr6B 51559011 51560303 1292 False 356.000000 558 82.084500 999 2227 2 chr6B.!!$F3 1228
10 TraesCS6D01G058800 chr6B 51732102 51733238 1136 False 349.500000 449 78.694500 996 2092 2 chr6B.!!$F4 1096

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
903 3697 0.235926 GGCTTTTCAGTCACACTCGC 59.764 55.0 0.0 0.0 0.0 5.03 F
1672 4541 0.819259 TGCTGGGTGTTTCTGTGCTC 60.819 55.0 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2741 5676 0.663153 GTTCACCGCCAATGCCTATC 59.337 55.0 0.0 0.0 0.00 2.08 R
3095 6030 1.312815 AGCTGGTGAAGTGAAAGCAC 58.687 50.0 0.0 0.0 45.49 4.40 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
19 20 2.040544 CCTAGCCGTTGGTTGCCTG 61.041 63.158 0.00 0.00 0.00 4.85
20 21 1.302511 CTAGCCGTTGGTTGCCTGT 60.303 57.895 0.00 0.00 0.00 4.00
21 22 0.889186 CTAGCCGTTGGTTGCCTGTT 60.889 55.000 0.00 0.00 0.00 3.16
27 28 0.319813 GTTGGTTGCCTGTTCCATGC 60.320 55.000 0.00 0.00 0.00 4.06
29 30 1.607467 GGTTGCCTGTTCCATGCCT 60.607 57.895 0.00 0.00 0.00 4.75
31 32 1.675310 TTGCCTGTTCCATGCCTCG 60.675 57.895 0.00 0.00 0.00 4.63
33 34 2.825836 CCTGTTCCATGCCTCGCC 60.826 66.667 0.00 0.00 0.00 5.54
34 35 2.046023 CTGTTCCATGCCTCGCCA 60.046 61.111 0.00 0.00 0.00 5.69
35 36 1.452651 CTGTTCCATGCCTCGCCAT 60.453 57.895 0.00 0.00 0.00 4.40
59 60 2.420138 GAGCTGTGATAGGGCTCGA 58.580 57.895 0.00 0.00 42.03 4.04
71 72 1.556911 AGGGCTCGACATTTGAGTCAT 59.443 47.619 0.00 0.00 39.84 3.06
72 73 1.667724 GGGCTCGACATTTGAGTCATG 59.332 52.381 0.00 0.00 39.84 3.07
79 80 2.941720 GACATTTGAGTCATGGCTCTCC 59.058 50.000 26.71 3.08 38.40 3.71
116 117 3.376918 GGCTTTGCTGGAGTGGGC 61.377 66.667 0.00 0.00 0.00 5.36
126 127 2.359850 GAGTGGGCGTCATTGGCA 60.360 61.111 0.00 0.00 35.84 4.92
143 144 1.140589 CATGCTCGTCGCTTCCTCT 59.859 57.895 0.00 0.00 40.11 3.69
144 145 1.140589 ATGCTCGTCGCTTCCTCTG 59.859 57.895 0.00 0.00 40.11 3.35
172 173 1.416401 TCGCTTGAGGTTTGGTCTTCT 59.584 47.619 0.00 0.00 0.00 2.85
173 174 1.532868 CGCTTGAGGTTTGGTCTTCTG 59.467 52.381 0.00 0.00 0.00 3.02
174 175 2.576615 GCTTGAGGTTTGGTCTTCTGT 58.423 47.619 0.00 0.00 0.00 3.41
175 176 2.550180 GCTTGAGGTTTGGTCTTCTGTC 59.450 50.000 0.00 0.00 0.00 3.51
176 177 2.526304 TGAGGTTTGGTCTTCTGTCG 57.474 50.000 0.00 0.00 0.00 4.35
177 178 1.070134 TGAGGTTTGGTCTTCTGTCGG 59.930 52.381 0.00 0.00 0.00 4.79
184 185 2.531771 TGGTCTTCTGTCGGATGGTAA 58.468 47.619 0.00 0.00 0.00 2.85
190 191 0.742505 CTGTCGGATGGTAACGGCTA 59.257 55.000 0.00 0.00 42.51 3.93
197 198 3.740141 CGGATGGTAACGGCTAGTGAAAT 60.740 47.826 0.00 0.00 42.51 2.17
201 202 2.199236 GTAACGGCTAGTGAAATCGGG 58.801 52.381 0.00 0.00 0.00 5.14
212 213 2.542211 GAAATCGGGGCAACGGCTTG 62.542 60.000 1.08 0.00 40.87 4.01
220 221 1.007387 GCAACGGCTTGGGAAGTTG 60.007 57.895 3.15 3.15 44.66 3.16
241 242 2.351726 GCCTTCATGTTTAGCGTGGTAG 59.648 50.000 0.00 0.00 34.91 3.18
245 246 3.259064 TCATGTTTAGCGTGGTAGCTTC 58.741 45.455 0.00 0.00 46.80 3.86
277 278 6.313744 ACCTTGTTTATGTGTTGACTTAGC 57.686 37.500 0.00 0.00 0.00 3.09
280 281 3.187637 TGTTTATGTGTTGACTTAGCCGC 59.812 43.478 0.00 0.00 0.00 6.53
345 347 6.883217 ACTTTCGGTAGAGTGAAGTGACTATA 59.117 38.462 0.00 0.00 0.00 1.31
349 351 7.960262 TCGGTAGAGTGAAGTGACTATATCTA 58.040 38.462 0.00 0.00 0.00 1.98
350 352 8.427276 TCGGTAGAGTGAAGTGACTATATCTAA 58.573 37.037 0.00 0.00 0.00 2.10
375 379 3.738982 TGTCTGATTTCGAAGGCAAGAA 58.261 40.909 0.00 0.00 0.00 2.52
381 385 1.448985 TTCGAAGGCAAGAAATCGGG 58.551 50.000 0.00 0.00 36.05 5.14
389 393 2.533266 GCAAGAAATCGGGCTCAAATG 58.467 47.619 0.00 0.00 0.00 2.32
393 397 3.554934 AGAAATCGGGCTCAAATGCATA 58.445 40.909 0.00 0.00 34.04 3.14
497 532 3.498018 GCAAAACCTTTGCCCAGTTAATG 59.502 43.478 12.10 0.00 39.38 1.90
535 570 7.710044 TGTGTAGCACATTTCAATTGTTTTGAT 59.290 29.630 5.13 0.00 39.62 2.57
536 571 8.550376 GTGTAGCACATTTCAATTGTTTTGATT 58.450 29.630 5.13 0.00 34.08 2.57
569 604 7.821134 AAGGGTGATGGCTTCTATATAGAAT 57.179 36.000 22.46 10.22 41.12 2.40
570 605 8.917414 AAGGGTGATGGCTTCTATATAGAATA 57.083 34.615 22.46 13.75 41.12 1.75
571 606 8.917414 AGGGTGATGGCTTCTATATAGAATAA 57.083 34.615 22.46 12.97 41.12 1.40
572 607 9.338968 AGGGTGATGGCTTCTATATAGAATAAA 57.661 33.333 22.46 12.67 41.12 1.40
573 608 9.959721 GGGTGATGGCTTCTATATAGAATAAAA 57.040 33.333 22.46 11.20 41.12 1.52
602 643 8.779354 AAAGATCGCTAGTTCTTTTCTACAAT 57.221 30.769 10.03 0.00 41.21 2.71
603 644 7.763172 AGATCGCTAGTTCTTTTCTACAATG 57.237 36.000 0.00 0.00 0.00 2.82
613 655 9.971922 AGTTCTTTTCTACAATGAAATTCCAAG 57.028 29.630 0.00 0.00 36.07 3.61
620 662 9.739276 TTCTACAATGAAATTCCAAGTGTATCT 57.261 29.630 0.00 0.00 31.22 1.98
675 805 6.952773 TTCCAAAGAAATTTCCTTTCGAGA 57.047 33.333 14.61 8.11 46.53 4.04
737 3495 4.055178 GCAGGATGGCCCCATTTT 57.945 55.556 0.00 0.00 36.70 1.82
738 3496 3.222287 GCAGGATGGCCCCATTTTA 57.778 52.632 0.00 0.00 36.70 1.52
739 3497 1.043022 GCAGGATGGCCCCATTTTAG 58.957 55.000 0.00 0.00 36.70 1.85
740 3498 1.708341 CAGGATGGCCCCATTTTAGG 58.292 55.000 0.00 0.00 36.70 2.69
762 3520 3.367395 GGGTTGCAGCAAAAGGATTAGTC 60.367 47.826 10.11 0.00 0.00 2.59
764 3522 4.700213 GGTTGCAGCAAAAGGATTAGTCTA 59.300 41.667 10.11 0.00 0.00 2.59
769 3533 8.574251 TGCAGCAAAAGGATTAGTCTATTTTA 57.426 30.769 0.00 0.00 0.00 1.52
770 3534 8.677300 TGCAGCAAAAGGATTAGTCTATTTTAG 58.323 33.333 0.00 0.00 0.00 1.85
771 3535 8.893727 GCAGCAAAAGGATTAGTCTATTTTAGA 58.106 33.333 0.00 0.00 0.00 2.10
796 3560 7.827819 AACTTTTGTTTCTGTTTTCTTAGGC 57.172 32.000 0.00 0.00 40.17 3.93
797 3561 6.930731 ACTTTTGTTTCTGTTTTCTTAGGCA 58.069 32.000 0.00 0.00 0.00 4.75
798 3562 7.382898 ACTTTTGTTTCTGTTTTCTTAGGCAA 58.617 30.769 0.00 0.00 0.00 4.52
799 3563 7.875554 ACTTTTGTTTCTGTTTTCTTAGGCAAA 59.124 29.630 0.00 0.00 0.00 3.68
800 3564 7.826260 TTTGTTTCTGTTTTCTTAGGCAAAG 57.174 32.000 0.00 0.00 36.45 2.77
801 3565 5.348164 TGTTTCTGTTTTCTTAGGCAAAGC 58.652 37.500 0.00 0.00 34.97 3.51
855 3619 2.159240 GCACACACCGAGAGATGATGTA 60.159 50.000 0.00 0.00 0.00 2.29
876 3670 0.976641 TCGTGGGCTTTCACTCTCAT 59.023 50.000 0.00 0.00 35.63 2.90
877 3671 1.081892 CGTGGGCTTTCACTCTCATG 58.918 55.000 0.00 0.00 35.63 3.07
878 3672 1.457346 GTGGGCTTTCACTCTCATGG 58.543 55.000 0.00 0.00 34.98 3.66
879 3673 1.067295 TGGGCTTTCACTCTCATGGT 58.933 50.000 0.00 0.00 0.00 3.55
880 3674 2.027192 GTGGGCTTTCACTCTCATGGTA 60.027 50.000 0.00 0.00 34.98 3.25
881 3675 2.237143 TGGGCTTTCACTCTCATGGTAG 59.763 50.000 0.00 0.00 0.00 3.18
882 3676 2.237392 GGGCTTTCACTCTCATGGTAGT 59.763 50.000 0.00 0.00 0.00 2.73
884 3678 3.265791 GCTTTCACTCTCATGGTAGTGG 58.734 50.000 21.01 11.19 42.72 4.00
885 3679 3.866651 CTTTCACTCTCATGGTAGTGGG 58.133 50.000 21.01 12.06 42.72 4.61
887 3681 1.198713 CACTCTCATGGTAGTGGGCT 58.801 55.000 16.31 0.00 39.55 5.19
888 3682 1.556911 CACTCTCATGGTAGTGGGCTT 59.443 52.381 16.31 0.00 39.55 4.35
890 3684 2.644798 ACTCTCATGGTAGTGGGCTTTT 59.355 45.455 0.00 0.00 0.00 2.27
891 3685 3.274288 CTCTCATGGTAGTGGGCTTTTC 58.726 50.000 0.00 0.00 0.00 2.29
892 3686 2.642311 TCTCATGGTAGTGGGCTTTTCA 59.358 45.455 0.00 0.00 0.00 2.69
893 3687 3.012518 CTCATGGTAGTGGGCTTTTCAG 58.987 50.000 0.00 0.00 0.00 3.02
894 3688 2.375174 TCATGGTAGTGGGCTTTTCAGT 59.625 45.455 0.00 0.00 0.00 3.41
895 3689 2.561478 TGGTAGTGGGCTTTTCAGTC 57.439 50.000 0.00 0.00 0.00 3.51
896 3690 1.771854 TGGTAGTGGGCTTTTCAGTCA 59.228 47.619 0.00 0.00 0.00 3.41
897 3691 2.152016 GGTAGTGGGCTTTTCAGTCAC 58.848 52.381 0.00 0.00 0.00 3.67
898 3692 2.486548 GGTAGTGGGCTTTTCAGTCACA 60.487 50.000 0.00 0.00 32.28 3.58
899 3693 1.680338 AGTGGGCTTTTCAGTCACAC 58.320 50.000 0.00 0.00 33.20 3.82
900 3694 1.212935 AGTGGGCTTTTCAGTCACACT 59.787 47.619 0.00 0.00 36.52 3.55
901 3695 1.604278 GTGGGCTTTTCAGTCACACTC 59.396 52.381 0.00 0.00 31.43 3.51
902 3696 0.868406 GGGCTTTTCAGTCACACTCG 59.132 55.000 0.00 0.00 0.00 4.18
903 3697 0.235926 GGCTTTTCAGTCACACTCGC 59.764 55.000 0.00 0.00 0.00 5.03
904 3698 0.937304 GCTTTTCAGTCACACTCGCA 59.063 50.000 0.00 0.00 0.00 5.10
905 3699 1.070309 GCTTTTCAGTCACACTCGCAG 60.070 52.381 0.00 0.00 0.00 5.18
906 3700 1.528586 CTTTTCAGTCACACTCGCAGG 59.471 52.381 0.00 0.00 0.00 4.85
907 3701 0.880278 TTTCAGTCACACTCGCAGGC 60.880 55.000 0.00 0.00 0.00 4.85
908 3702 1.748329 TTCAGTCACACTCGCAGGCT 61.748 55.000 0.00 0.00 0.00 4.58
909 3703 0.893727 TCAGTCACACTCGCAGGCTA 60.894 55.000 0.00 0.00 0.00 3.93
931 3725 1.624865 CTGCTGCACTTCTCACGCTC 61.625 60.000 0.00 0.00 0.00 5.03
968 3762 1.439353 CCAGCATTTCGCCGCATAGT 61.439 55.000 0.00 0.00 44.04 2.12
971 3765 1.068588 AGCATTTCGCCGCATAGTAGA 59.931 47.619 0.00 0.00 44.04 2.59
1047 3849 2.229784 GGACGAAAACCTACTCTCCGAA 59.770 50.000 0.00 0.00 0.00 4.30
1062 3864 1.522569 CGAAATCCTCCTCCGCCTT 59.477 57.895 0.00 0.00 0.00 4.35
1108 3935 1.228894 ACCTCCCTCGTCTGCAAGA 60.229 57.895 0.00 0.00 43.69 3.02
1119 3946 4.648626 TGCAAGAGCTGGCGCCTT 62.649 61.111 29.70 13.53 42.74 4.35
1145 3972 3.781307 CGACCCCGGCTTCATCCA 61.781 66.667 0.00 0.00 0.00 3.41
1200 4027 2.700897 CCTCCTCGGTTACTTCATCCAT 59.299 50.000 0.00 0.00 0.00 3.41
1641 4510 3.389221 CGTTTTGGTTGGGAATTCCTTG 58.611 45.455 23.63 0.00 36.20 3.61
1672 4541 0.819259 TGCTGGGTGTTTCTGTGCTC 60.819 55.000 0.00 0.00 0.00 4.26
1751 4632 5.808030 GTGAGGAGAATAGCTTCACTGTTAC 59.192 44.000 0.00 0.00 33.50 2.50
2095 5028 4.275936 CAGGTAATAGCATGCCTTTACACC 59.724 45.833 27.91 21.26 0.00 4.16
2098 5031 2.772077 TAGCATGCCTTTACACCGAA 57.228 45.000 15.66 0.00 0.00 4.30
2137 5072 3.379372 CCTCTCATGCCAACCTAACAATG 59.621 47.826 0.00 0.00 0.00 2.82
2147 5082 8.865420 TGCCAACCTAACAATGTTAAATAGTA 57.135 30.769 7.30 0.00 0.00 1.82
2200 5135 9.494271 TTTGATGACCTCTTCAATATATAGTGC 57.506 33.333 5.30 0.00 38.99 4.40
2234 5169 2.300152 GTGTTCTGTCCTGATCCTGACA 59.700 50.000 12.31 12.31 39.08 3.58
2287 5222 8.812329 GTTATGAACTAGCAAGTCAATCTAGTG 58.188 37.037 2.39 0.00 41.33 2.74
2741 5676 7.624360 TGTTTGACTTATTATGCTTGTAGGG 57.376 36.000 0.00 0.00 0.00 3.53
2985 5920 3.552132 TGACACTTGGCTCAGTTGTTA 57.448 42.857 0.00 0.00 0.00 2.41
3082 6017 4.008916 TCCCTATCCTTACCAGCTTTCT 57.991 45.455 0.00 0.00 0.00 2.52
3095 6030 3.812053 CCAGCTTTCTATTCCCTTCATCG 59.188 47.826 0.00 0.00 0.00 3.84
3140 6075 0.460987 GGCTGACTGATGTTCTCCCG 60.461 60.000 0.00 0.00 0.00 5.14
3141 6076 1.086634 GCTGACTGATGTTCTCCCGC 61.087 60.000 0.00 0.00 0.00 6.13
3157 6092 2.409870 CGCCTGGATGTGCCCTTTC 61.410 63.158 0.00 0.00 34.97 2.62
3258 6193 1.543208 CCAGTTGCTTCTGGTAGTGCA 60.543 52.381 16.03 0.00 46.92 4.57
3459 6396 2.825861 TGACACCCTCCGTTTAGTTC 57.174 50.000 0.00 0.00 0.00 3.01
3464 6401 1.270678 ACCCTCCGTTTAGTTCTGTGC 60.271 52.381 0.00 0.00 0.00 4.57
3704 6641 5.696270 CCATTGGTCAAAGGCTTTTTCTAAC 59.304 40.000 10.36 4.02 0.00 2.34
3779 6718 2.928757 GTTTTTGTGATGTTGTGCTGCA 59.071 40.909 0.00 0.00 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 3.113745 CATGGCGAGGCATGGAAC 58.886 61.111 25.89 0.00 0.00 3.62
33 34 1.542767 CCTATCACAGCTCCAGCCATG 60.543 57.143 0.00 0.00 43.38 3.66
34 35 0.763652 CCTATCACAGCTCCAGCCAT 59.236 55.000 0.00 0.00 43.38 4.40
35 36 1.340399 CCCTATCACAGCTCCAGCCA 61.340 60.000 0.00 0.00 43.38 4.75
37 38 1.227793 GCCCTATCACAGCTCCAGC 60.228 63.158 0.00 0.00 42.49 4.85
39 40 2.521103 GAGCCCTATCACAGCTCCA 58.479 57.895 0.00 0.00 45.83 3.86
59 60 2.306805 TGGAGAGCCATGACTCAAATGT 59.693 45.455 11.88 0.00 39.92 2.71
71 72 0.110486 GGTTTTCACCTGGAGAGCCA 59.890 55.000 0.00 0.00 40.44 4.75
72 73 0.110486 TGGTTTTCACCTGGAGAGCC 59.890 55.000 0.00 2.79 44.61 4.70
79 80 3.247411 GCCGAAATTTTGGTTTTCACCTG 59.753 43.478 22.94 0.00 44.61 4.00
116 117 1.349627 GACGAGCATGCCAATGACG 59.650 57.895 15.66 12.84 39.36 4.35
143 144 2.145397 ACCTCAAGCGATACCTCTCA 57.855 50.000 0.00 0.00 0.00 3.27
144 145 3.190874 CAAACCTCAAGCGATACCTCTC 58.809 50.000 0.00 0.00 0.00 3.20
151 152 2.039084 AGAAGACCAAACCTCAAGCGAT 59.961 45.455 0.00 0.00 0.00 4.58
154 155 2.550180 GACAGAAGACCAAACCTCAAGC 59.450 50.000 0.00 0.00 0.00 4.01
172 173 0.742505 CTAGCCGTTACCATCCGACA 59.257 55.000 0.00 0.00 0.00 4.35
173 174 0.743097 ACTAGCCGTTACCATCCGAC 59.257 55.000 0.00 0.00 0.00 4.79
174 175 0.742505 CACTAGCCGTTACCATCCGA 59.257 55.000 0.00 0.00 0.00 4.55
175 176 0.742505 TCACTAGCCGTTACCATCCG 59.257 55.000 0.00 0.00 0.00 4.18
176 177 2.973694 TTCACTAGCCGTTACCATCC 57.026 50.000 0.00 0.00 0.00 3.51
177 178 3.489785 CGATTTCACTAGCCGTTACCATC 59.510 47.826 0.00 0.00 0.00 3.51
184 185 1.520666 CCCCGATTTCACTAGCCGT 59.479 57.895 0.00 0.00 0.00 5.68
190 191 1.674322 CCGTTGCCCCGATTTCACT 60.674 57.895 0.00 0.00 0.00 3.41
201 202 2.200337 AACTTCCCAAGCCGTTGCC 61.200 57.895 0.00 0.00 38.69 4.52
220 221 1.165270 ACCACGCTAAACATGAAGGC 58.835 50.000 0.00 0.00 0.00 4.35
234 235 3.949313 GCTTTTCGAAGCTACCACG 57.051 52.632 1.75 0.00 42.32 4.94
241 242 3.898517 AACAAGGTAGCTTTTCGAAGC 57.101 42.857 3.96 0.62 45.81 3.86
245 246 5.997385 ACACATAAACAAGGTAGCTTTTCG 58.003 37.500 3.96 0.00 0.00 3.46
253 254 6.428771 GGCTAAGTCAACACATAAACAAGGTA 59.571 38.462 0.00 0.00 0.00 3.08
345 347 6.481644 GCCTTCGAAATCAGACATTCTTAGAT 59.518 38.462 0.00 0.00 0.00 1.98
349 351 4.326826 TGCCTTCGAAATCAGACATTCTT 58.673 39.130 0.00 0.00 0.00 2.52
350 352 3.942829 TGCCTTCGAAATCAGACATTCT 58.057 40.909 0.00 0.00 0.00 2.40
375 379 2.559668 CCATATGCATTTGAGCCCGATT 59.440 45.455 17.53 0.00 0.00 3.34
379 383 0.038892 CGCCATATGCATTTGAGCCC 60.039 55.000 17.53 3.63 41.33 5.19
381 385 2.658285 CTTCGCCATATGCATTTGAGC 58.342 47.619 17.53 16.35 41.33 4.26
389 393 0.040603 GCAGAAGCTTCGCCATATGC 60.041 55.000 23.84 20.68 37.91 3.14
475 479 2.900716 TAACTGGGCAAAGGTTTTGC 57.099 45.000 16.05 16.05 44.22 3.68
535 570 3.153919 GCCATCACCCTTAACTTGTCAA 58.846 45.455 0.00 0.00 0.00 3.18
536 571 2.375174 AGCCATCACCCTTAACTTGTCA 59.625 45.455 0.00 0.00 0.00 3.58
634 676 8.567948 TCTTTGGAAATAGTAGCAAGAAACTTG 58.432 33.333 7.07 7.07 0.00 3.16
671 801 4.361451 AAGCCTTTTGTAATGCATCTCG 57.639 40.909 0.00 0.00 0.00 4.04
675 805 6.015940 GCTATCCTAAGCCTTTTGTAATGCAT 60.016 38.462 0.00 0.00 36.45 3.96
721 3479 1.708341 CCTAAAATGGGGCCATCCTG 58.292 55.000 4.39 0.00 35.31 3.86
722 3480 0.562674 CCCTAAAATGGGGCCATCCT 59.437 55.000 4.39 0.00 43.45 3.24
723 3481 3.147826 CCCTAAAATGGGGCCATCC 57.852 57.895 4.39 0.00 43.45 3.51
731 3489 1.265236 TGCTGCAACCCCTAAAATGG 58.735 50.000 0.00 0.00 0.00 3.16
732 3490 3.399440 TTTGCTGCAACCCCTAAAATG 57.601 42.857 15.72 0.00 0.00 2.32
733 3491 3.244526 CCTTTTGCTGCAACCCCTAAAAT 60.245 43.478 15.72 0.00 0.00 1.82
734 3492 2.103941 CCTTTTGCTGCAACCCCTAAAA 59.896 45.455 15.72 3.94 0.00 1.52
735 3493 1.691434 CCTTTTGCTGCAACCCCTAAA 59.309 47.619 15.72 4.68 0.00 1.85
736 3494 1.133325 TCCTTTTGCTGCAACCCCTAA 60.133 47.619 15.72 5.43 0.00 2.69
737 3495 0.480690 TCCTTTTGCTGCAACCCCTA 59.519 50.000 15.72 0.00 0.00 3.53
738 3496 0.178924 ATCCTTTTGCTGCAACCCCT 60.179 50.000 15.72 0.00 0.00 4.79
739 3497 0.686789 AATCCTTTTGCTGCAACCCC 59.313 50.000 15.72 0.00 0.00 4.95
740 3498 2.562738 ACTAATCCTTTTGCTGCAACCC 59.437 45.455 15.72 0.00 0.00 4.11
741 3499 3.507622 AGACTAATCCTTTTGCTGCAACC 59.492 43.478 15.72 0.00 0.00 3.77
742 3500 4.773323 AGACTAATCCTTTTGCTGCAAC 57.227 40.909 15.72 0.00 0.00 4.17
743 3501 7.466746 AAATAGACTAATCCTTTTGCTGCAA 57.533 32.000 11.69 11.69 0.00 4.08
744 3502 7.466746 AAAATAGACTAATCCTTTTGCTGCA 57.533 32.000 0.00 0.00 0.00 4.41
745 3503 8.893727 TCTAAAATAGACTAATCCTTTTGCTGC 58.106 33.333 0.00 0.00 0.00 5.25
770 3534 8.380644 GCCTAAGAAAACAGAAACAAAAGTTTC 58.619 33.333 11.93 11.93 42.04 2.78
771 3535 7.875554 TGCCTAAGAAAACAGAAACAAAAGTTT 59.124 29.630 0.00 0.00 35.87 2.66
772 3536 7.382898 TGCCTAAGAAAACAGAAACAAAAGTT 58.617 30.769 0.00 0.00 0.00 2.66
773 3537 6.930731 TGCCTAAGAAAACAGAAACAAAAGT 58.069 32.000 0.00 0.00 0.00 2.66
774 3538 7.826260 TTGCCTAAGAAAACAGAAACAAAAG 57.174 32.000 0.00 0.00 0.00 2.27
775 3539 7.148490 GCTTTGCCTAAGAAAACAGAAACAAAA 60.148 33.333 0.22 0.00 35.80 2.44
776 3540 6.312672 GCTTTGCCTAAGAAAACAGAAACAAA 59.687 34.615 0.22 0.00 35.80 2.83
777 3541 5.810074 GCTTTGCCTAAGAAAACAGAAACAA 59.190 36.000 0.22 0.00 35.80 2.83
778 3542 5.348164 GCTTTGCCTAAGAAAACAGAAACA 58.652 37.500 0.22 0.00 35.80 2.83
779 3543 4.745125 GGCTTTGCCTAAGAAAACAGAAAC 59.255 41.667 0.73 0.00 46.69 2.78
780 3544 4.944048 GGCTTTGCCTAAGAAAACAGAAA 58.056 39.130 0.73 0.00 46.69 2.52
781 3545 4.584327 GGCTTTGCCTAAGAAAACAGAA 57.416 40.909 0.73 0.00 46.69 3.02
794 3558 1.202302 GCTAATCCTTTCGGCTTTGCC 60.202 52.381 0.00 0.00 46.75 4.52
795 3559 1.745653 AGCTAATCCTTTCGGCTTTGC 59.254 47.619 0.00 0.00 37.40 3.68
796 3560 3.009723 TCAGCTAATCCTTTCGGCTTTG 58.990 45.455 0.00 0.00 0.00 2.77
797 3561 3.350219 TCAGCTAATCCTTTCGGCTTT 57.650 42.857 0.00 0.00 0.00 3.51
798 3562 3.350219 TTCAGCTAATCCTTTCGGCTT 57.650 42.857 0.00 0.00 0.00 4.35
799 3563 3.010420 GTTTCAGCTAATCCTTTCGGCT 58.990 45.455 0.00 0.00 0.00 5.52
800 3564 3.010420 AGTTTCAGCTAATCCTTTCGGC 58.990 45.455 0.00 0.00 0.00 5.54
801 3565 4.095036 GGAAGTTTCAGCTAATCCTTTCGG 59.905 45.833 0.00 0.00 0.00 4.30
802 3566 4.938226 AGGAAGTTTCAGCTAATCCTTTCG 59.062 41.667 0.00 0.00 33.61 3.46
803 3567 5.392487 GCAGGAAGTTTCAGCTAATCCTTTC 60.392 44.000 0.00 0.00 35.16 2.62
804 3568 4.460731 GCAGGAAGTTTCAGCTAATCCTTT 59.539 41.667 0.00 0.00 35.16 3.11
805 3569 4.013050 GCAGGAAGTTTCAGCTAATCCTT 58.987 43.478 0.00 0.00 35.16 3.36
806 3570 3.615155 GCAGGAAGTTTCAGCTAATCCT 58.385 45.455 0.00 0.00 37.79 3.24
807 3571 2.685388 GGCAGGAAGTTTCAGCTAATCC 59.315 50.000 0.00 0.00 32.54 3.01
808 3572 2.352960 CGGCAGGAAGTTTCAGCTAATC 59.647 50.000 0.00 0.00 32.54 1.75
809 3573 2.359900 CGGCAGGAAGTTTCAGCTAAT 58.640 47.619 0.00 0.00 32.54 1.73
810 3574 1.610624 CCGGCAGGAAGTTTCAGCTAA 60.611 52.381 0.00 0.00 41.02 3.09
811 3575 0.036388 CCGGCAGGAAGTTTCAGCTA 60.036 55.000 0.00 0.00 41.02 3.32
812 3576 1.302832 CCGGCAGGAAGTTTCAGCT 60.303 57.895 0.00 0.00 41.02 4.24
839 3603 2.614520 ACGACTACATCATCTCTCGGTG 59.385 50.000 0.00 0.00 0.00 4.94
855 3619 0.318762 GAGAGTGAAAGCCCACGACT 59.681 55.000 0.00 0.00 41.67 4.18
876 3670 1.771854 TGACTGAAAAGCCCACTACCA 59.228 47.619 0.00 0.00 0.00 3.25
877 3671 2.152016 GTGACTGAAAAGCCCACTACC 58.848 52.381 0.00 0.00 0.00 3.18
878 3672 2.548480 GTGTGACTGAAAAGCCCACTAC 59.452 50.000 0.00 0.00 0.00 2.73
879 3673 2.438021 AGTGTGACTGAAAAGCCCACTA 59.562 45.455 0.00 0.00 30.45 2.74
880 3674 1.212935 AGTGTGACTGAAAAGCCCACT 59.787 47.619 0.00 0.00 0.00 4.00
881 3675 1.604278 GAGTGTGACTGAAAAGCCCAC 59.396 52.381 0.00 0.00 0.00 4.61
882 3676 1.810031 CGAGTGTGACTGAAAAGCCCA 60.810 52.381 0.00 0.00 0.00 5.36
884 3678 0.235926 GCGAGTGTGACTGAAAAGCC 59.764 55.000 0.00 0.00 0.00 4.35
885 3679 0.937304 TGCGAGTGTGACTGAAAAGC 59.063 50.000 0.00 0.00 0.00 3.51
887 3681 1.581934 CCTGCGAGTGTGACTGAAAA 58.418 50.000 0.00 0.00 0.00 2.29
888 3682 0.880278 GCCTGCGAGTGTGACTGAAA 60.880 55.000 0.00 0.00 0.00 2.69
890 3684 0.893727 TAGCCTGCGAGTGTGACTGA 60.894 55.000 0.00 0.00 0.00 3.41
891 3685 0.038251 TTAGCCTGCGAGTGTGACTG 60.038 55.000 0.00 0.00 0.00 3.51
892 3686 0.038159 GTTAGCCTGCGAGTGTGACT 60.038 55.000 0.00 0.00 0.00 3.41
893 3687 1.014564 GGTTAGCCTGCGAGTGTGAC 61.015 60.000 0.00 0.00 0.00 3.67
894 3688 1.185618 AGGTTAGCCTGCGAGTGTGA 61.186 55.000 0.00 0.00 45.05 3.58
895 3689 1.293498 AGGTTAGCCTGCGAGTGTG 59.707 57.895 0.00 0.00 45.05 3.82
896 3690 3.793060 AGGTTAGCCTGCGAGTGT 58.207 55.556 0.00 0.00 45.05 3.55
905 3699 0.322008 AGAAGTGCAGCAGGTTAGCC 60.322 55.000 0.00 0.00 34.23 3.93
906 3700 1.082690 GAGAAGTGCAGCAGGTTAGC 58.917 55.000 0.00 0.00 0.00 3.09
907 3701 2.072298 GTGAGAAGTGCAGCAGGTTAG 58.928 52.381 0.00 0.00 0.00 2.34
908 3702 1.605457 CGTGAGAAGTGCAGCAGGTTA 60.605 52.381 0.00 0.00 0.00 2.85
909 3703 0.882042 CGTGAGAAGTGCAGCAGGTT 60.882 55.000 0.00 0.00 0.00 3.50
1047 3849 2.073101 GGGAAGGCGGAGGAGGATT 61.073 63.158 0.00 0.00 0.00 3.01
1090 3917 1.228894 TCTTGCAGACGAGGGAGGT 60.229 57.895 0.00 0.00 0.00 3.85
1108 3935 4.443266 GACGAGAAGGCGCCAGCT 62.443 66.667 31.54 24.85 44.37 4.24
1200 4027 2.725312 GGAGATGCCTCGGCTGTCA 61.725 63.158 9.65 0.00 40.33 3.58
1274 4101 2.202623 CGTAGCTGTGGTCGAGCC 60.203 66.667 12.85 4.60 37.12 4.70
1641 4510 1.741770 CCCAGCAAGACGCCAGTAC 60.742 63.158 0.00 0.00 44.04 2.73
1672 4541 4.629200 CCTCTCCAAATCAAACTCGAGAAG 59.371 45.833 21.68 8.29 0.00 2.85
2200 5135 4.034048 GGACAGAACACTACAACACAACAG 59.966 45.833 0.00 0.00 0.00 3.16
2234 5169 1.752683 TAAAACGGCACCACACAAGT 58.247 45.000 0.00 0.00 0.00 3.16
2741 5676 0.663153 GTTCACCGCCAATGCCTATC 59.337 55.000 0.00 0.00 0.00 2.08
3082 6017 3.938963 GTGAAAGCACGATGAAGGGAATA 59.061 43.478 0.00 0.00 34.94 1.75
3095 6030 1.312815 AGCTGGTGAAGTGAAAGCAC 58.687 50.000 0.00 0.00 45.49 4.40
3140 6075 2.409870 CGAAAGGGCACATCCAGGC 61.410 63.158 0.00 0.00 36.21 4.85
3141 6076 2.409870 GCGAAAGGGCACATCCAGG 61.410 63.158 0.00 0.00 36.21 4.45
3157 6092 1.821332 GATGGAAGGAGGGCAAGCG 60.821 63.158 0.00 0.00 0.00 4.68
3258 6193 3.012388 AGAAGCTAGAGGGAGAAGAACCT 59.988 47.826 0.00 0.00 40.54 3.50
3459 6396 3.197265 TGTGATTCATGATACCGCACAG 58.803 45.455 0.00 0.00 31.88 3.66
3464 6401 9.787532 AAGTAAAAATTGTGATTCATGATACCG 57.212 29.630 0.00 0.00 0.00 4.02
3704 6641 9.729023 TCAAAATACATTGCATATTAGGTTTCG 57.271 29.630 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.