Multiple sequence alignment - TraesCS1D01G024900

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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 TraesCS1D01G024900 chr1D 100.000 2198 0 0 1 2198 10389612 10391809 0.000000e+00 4060.0
1 TraesCS1D01G024900 chr1D 95.153 392 11 3 59 449 444908969 444909353 1.440000e-171 612.0
2 TraesCS1D01G024900 chr1D 84.615 195 27 3 1415 1607 298624001 298624194 8.010000e-45 191.0
3 TraesCS1D01G024900 chr1D 96.364 110 4 0 462 571 125853097 125853206 4.820000e-42 182.0
4 TraesCS1D01G024900 chr1D 96.364 110 4 0 462 571 240741144 240741035 4.820000e-42 182.0
5 TraesCS1D01G024900 chr1D 96.364 110 4 0 462 571 486133206 486133315 4.820000e-42 182.0
6 TraesCS1D01G024900 chr1D 96.386 83 3 0 628 710 10443689 10443607 1.060000e-28 137.0
7 TraesCS1D01G024900 chr1D 92.683 82 5 1 628 708 9875681 9875600 1.380000e-22 117.0
8 TraesCS1D01G024900 chr1D 92.500 80 5 1 630 708 9879846 9879767 1.780000e-21 113.0
9 TraesCS1D01G024900 chr1A 85.129 1587 162 27 628 2197 12138484 12140013 0.000000e+00 1555.0
10 TraesCS1D01G024900 chr1A 82.886 596 55 26 628 1206 12108998 12109563 1.960000e-135 492.0
11 TraesCS1D01G024900 chr1A 82.886 596 55 23 628 1206 12171235 12170670 1.960000e-135 492.0
12 TraesCS1D01G024900 chr1A 83.453 417 43 14 790 1198 12129421 12129819 4.460000e-97 364.0
13 TraesCS1D01G024900 chr1A 92.417 211 16 0 1988 2198 8345277 8345067 3.550000e-78 302.0
14 TraesCS1D01G024900 chr1A 92.683 82 5 1 628 708 11665651 11665570 1.380000e-22 117.0
15 TraesCS1D01G024900 chr1A 95.522 67 3 0 630 696 12108664 12108730 8.300000e-20 108.0
16 TraesCS1D01G024900 chr7D 97.661 513 10 2 59 571 573905021 573904511 0.000000e+00 880.0
17 TraesCS1D01G024900 chr7D 97.076 513 14 1 59 571 629331620 629332131 0.000000e+00 863.0
18 TraesCS1D01G024900 chr7D 94.413 358 20 0 1608 1965 615779981 615779624 3.190000e-153 551.0
19 TraesCS1D01G024900 chr7D 89.175 194 19 2 1415 1607 600765040 600764848 7.840000e-60 241.0
20 TraesCS1D01G024900 chr7D 97.273 110 3 0 462 571 515829887 515829996 1.040000e-43 187.0
21 TraesCS1D01G024900 chr3D 97.661 513 11 1 59 571 422011117 422011628 0.000000e+00 880.0
22 TraesCS1D01G024900 chr5D 97.466 513 12 1 59 571 225862478 225862989 0.000000e+00 874.0
23 TraesCS1D01G024900 chr5D 97.076 513 13 2 59 571 532807388 532807898 0.000000e+00 863.0
24 TraesCS1D01G024900 chr5D 95.408 392 10 3 59 449 502393967 502394351 3.100000e-173 617.0
25 TraesCS1D01G024900 chr5D 95.251 358 17 0 1608 1965 41778135 41777778 3.170000e-158 568.0
26 TraesCS1D01G024900 chr5D 86.344 227 15 7 1988 2198 41776993 41776767 1.310000e-57 233.0
27 TraesCS1D01G024900 chr5D 81.865 193 24 3 1416 1607 4980140 4980322 3.780000e-33 152.0
28 TraesCS1D01G024900 chr5D 76.263 198 38 7 1415 1607 223234563 223234370 1.800000e-16 97.1
29 TraesCS1D01G024900 chr6D 96.084 383 7 3 59 441 444637499 444637873 3.100000e-173 617.0
30 TraesCS1D01G024900 chr6D 94.972 358 18 0 1608 1965 429475323 429474966 1.470000e-156 562.0
31 TraesCS1D01G024900 chr6D 93.548 155 10 0 2044 2198 429474107 429473953 4.720000e-57 231.0
32 TraesCS1D01G024900 chr2D 95.153 392 11 5 59 449 50743111 50742727 1.440000e-171 612.0
33 TraesCS1D01G024900 chr2D 95.291 361 17 0 1605 1965 46692261 46692621 6.810000e-160 573.0
34 TraesCS1D01G024900 chr2D 93.548 155 10 0 2044 2198 46693480 46693634 4.720000e-57 231.0
35 TraesCS1D01G024900 chr2D 97.183 71 2 0 628 698 617637460 617637390 1.070000e-23 121.0
36 TraesCS1D01G024900 chr1B 95.251 358 17 0 1608 1965 6397868 6397511 3.170000e-158 568.0
37 TraesCS1D01G024900 chr1B 89.709 447 27 8 764 1206 15421590 15422021 8.870000e-154 553.0
38 TraesCS1D01G024900 chr1B 81.655 447 47 17 765 1198 15531145 15530721 2.700000e-89 339.0
39 TraesCS1D01G024900 chr1B 80.046 436 55 19 765 1189 15582114 15581700 5.930000e-76 294.0
40 TraesCS1D01G024900 chr1B 84.722 288 33 4 968 1255 15339941 15340217 5.980000e-71 278.0
41 TraesCS1D01G024900 chr1B 92.683 82 5 1 628 708 14847841 14847760 1.380000e-22 117.0
42 TraesCS1D01G024900 chr1B 89.412 85 9 0 630 714 15299035 15299119 8.300000e-20 108.0
43 TraesCS1D01G024900 chr6B 94.972 358 18 0 1608 1965 712153405 712153048 1.470000e-156 562.0
44 TraesCS1D01G024900 chr6B 87.611 226 12 8 1988 2197 366595929 366596154 4.690000e-62 248.0
45 TraesCS1D01G024900 chr6B 87.611 226 12 8 1988 2197 712152255 712152030 4.690000e-62 248.0
46 TraesCS1D01G024900 chr7A 94.460 361 20 0 1605 1965 12767843 12768203 6.860000e-155 556.0
47 TraesCS1D01G024900 chr7A 87.168 226 13 7 1988 2197 11051087 11051312 2.180000e-60 243.0
48 TraesCS1D01G024900 chr7A 93.182 88 6 0 1988 2075 708601926 708601839 1.770000e-26 130.0
49 TraesCS1D01G024900 chr4A 94.134 358 21 0 1608 1965 58509168 58508811 1.480000e-151 545.0
50 TraesCS1D01G024900 chr4A 87.611 226 12 8 1988 2197 58508028 58507803 4.690000e-62 248.0
51 TraesCS1D01G024900 chr7B 91.000 200 18 0 1006 1205 4137807 4137608 1.000000e-68 270.0
52 TraesCS1D01G024900 chr7B 82.778 180 27 4 1415 1591 74649915 74650093 8.120000e-35 158.0
53 TraesCS1D01G024900 chr3B 84.236 203 28 4 1415 1614 795112338 795112137 6.190000e-46 195.0
54 TraesCS1D01G024900 chr5A 81.675 191 31 4 1416 1604 388647542 388647730 2.920000e-34 156.0
55 TraesCS1D01G024900 chr2B 98.592 71 1 0 628 698 753927857 753927927 2.290000e-25 126.0
56 TraesCS1D01G024900 chr4B 82.609 69 12 0 1415 1483 76742991 76742923 6.550000e-06 62.1


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 TraesCS1D01G024900 chr1D 10389612 10391809 2197 False 4060.0 4060 100.0000 1 2198 1 chr1D.!!$F1 2197
1 TraesCS1D01G024900 chr1A 12138484 12140013 1529 False 1555.0 1555 85.1290 628 2197 1 chr1A.!!$F2 1569
2 TraesCS1D01G024900 chr1A 12170670 12171235 565 True 492.0 492 82.8860 628 1206 1 chr1A.!!$R3 578
3 TraesCS1D01G024900 chr1A 12108664 12109563 899 False 300.0 492 89.2040 628 1206 2 chr1A.!!$F3 578
4 TraesCS1D01G024900 chr7D 573904511 573905021 510 True 880.0 880 97.6610 59 571 1 chr7D.!!$R1 512
5 TraesCS1D01G024900 chr7D 629331620 629332131 511 False 863.0 863 97.0760 59 571 1 chr7D.!!$F2 512
6 TraesCS1D01G024900 chr3D 422011117 422011628 511 False 880.0 880 97.6610 59 571 1 chr3D.!!$F1 512
7 TraesCS1D01G024900 chr5D 225862478 225862989 511 False 874.0 874 97.4660 59 571 1 chr5D.!!$F2 512
8 TraesCS1D01G024900 chr5D 532807388 532807898 510 False 863.0 863 97.0760 59 571 1 chr5D.!!$F4 512
9 TraesCS1D01G024900 chr5D 41776767 41778135 1368 True 400.5 568 90.7975 1608 2198 2 chr5D.!!$R2 590
10 TraesCS1D01G024900 chr6D 429473953 429475323 1370 True 396.5 562 94.2600 1608 2198 2 chr6D.!!$R1 590
11 TraesCS1D01G024900 chr2D 46692261 46693634 1373 False 402.0 573 94.4195 1605 2198 2 chr2D.!!$F1 593
12 TraesCS1D01G024900 chr6B 712152030 712153405 1375 True 405.0 562 91.2915 1608 2197 2 chr6B.!!$R1 589
13 TraesCS1D01G024900 chr4A 58507803 58509168 1365 True 396.5 545 90.8725 1608 2197 2 chr4A.!!$R1 589

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
746 747 0.381801 CAACGCCTGAGTTTGCAAGT 59.618 50.0 0.0 0.0 30.96 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1640 1676 0.034059 ACTCGTCTTGCTCAACCCAG 59.966 55.0 0.0 0.0 0.0 4.45 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
43 44 7.935338 AGAGCACATGTAAAACATTTTTCTG 57.065 32.000 0.00 0.00 36.53 3.02
44 45 7.715657 AGAGCACATGTAAAACATTTTTCTGA 58.284 30.769 0.00 0.00 36.53 3.27
45 46 8.362639 AGAGCACATGTAAAACATTTTTCTGAT 58.637 29.630 0.00 0.00 36.53 2.90
46 47 9.624697 GAGCACATGTAAAACATTTTTCTGATA 57.375 29.630 0.00 0.00 36.53 2.15
47 48 9.410556 AGCACATGTAAAACATTTTTCTGATAC 57.589 29.630 0.00 0.00 36.53 2.24
48 49 9.190858 GCACATGTAAAACATTTTTCTGATACA 57.809 29.630 0.00 0.00 36.53 2.29
53 54 9.409312 TGTAAAACATTTTTCTGATACATGCTG 57.591 29.630 0.00 0.00 0.00 4.41
54 55 7.894376 AAAACATTTTTCTGATACATGCTGG 57.106 32.000 0.00 0.00 0.00 4.85
55 56 6.839124 AACATTTTTCTGATACATGCTGGA 57.161 33.333 0.00 0.00 0.00 3.86
57 58 7.035840 ACATTTTTCTGATACATGCTGGATC 57.964 36.000 0.00 2.41 38.21 3.36
538 539 6.542574 TTTTCCATTGTGATGAACATTTGC 57.457 33.333 0.00 0.00 38.99 3.68
552 553 9.195411 GATGAACATTTGCTTTGAAAGTTATCA 57.805 29.630 6.81 3.22 0.00 2.15
571 572 4.560136 TCAACATTTTCAAACTGCGCTA 57.440 36.364 9.73 0.00 0.00 4.26
572 573 4.926244 TCAACATTTTCAAACTGCGCTAA 58.074 34.783 9.73 0.00 0.00 3.09
573 574 5.527951 TCAACATTTTCAAACTGCGCTAAT 58.472 33.333 9.73 0.00 0.00 1.73
574 575 5.982516 TCAACATTTTCAAACTGCGCTAATT 59.017 32.000 9.73 0.00 0.00 1.40
575 576 6.478344 TCAACATTTTCAAACTGCGCTAATTT 59.522 30.769 9.73 3.44 0.00 1.82
576 577 6.843069 ACATTTTCAAACTGCGCTAATTTT 57.157 29.167 9.73 0.00 0.00 1.82
577 578 7.245419 ACATTTTCAAACTGCGCTAATTTTT 57.755 28.000 9.73 0.00 0.00 1.94
645 646 0.902531 GAGGTTTCGATCCTGGGACA 59.097 55.000 13.28 0.00 35.20 4.02
698 699 2.669364 GCCACTCTGATTTGCTTGTTG 58.331 47.619 0.00 0.00 0.00 3.33
706 707 5.358090 TCTGATTTGCTTGTTGAATTTGCA 58.642 33.333 0.00 0.00 0.00 4.08
717 718 5.448926 GTTGAATTTGCAACGTCAAAGTT 57.551 34.783 20.19 3.87 39.06 2.66
718 719 6.561945 GTTGAATTTGCAACGTCAAAGTTA 57.438 33.333 20.19 0.67 39.06 2.24
719 720 6.627274 GTTGAATTTGCAACGTCAAAGTTAG 58.373 36.000 20.19 0.00 39.06 2.34
720 721 6.125327 TGAATTTGCAACGTCAAAGTTAGA 57.875 33.333 0.00 0.00 39.06 2.10
721 722 6.734137 TGAATTTGCAACGTCAAAGTTAGAT 58.266 32.000 0.00 0.00 39.06 1.98
722 723 7.866729 TGAATTTGCAACGTCAAAGTTAGATA 58.133 30.769 0.00 0.00 39.06 1.98
723 724 8.346300 TGAATTTGCAACGTCAAAGTTAGATAA 58.654 29.630 0.00 0.00 39.06 1.75
724 725 8.502161 AATTTGCAACGTCAAAGTTAGATAAC 57.498 30.769 0.00 0.00 39.06 1.89
725 726 5.258685 TGCAACGTCAAAGTTAGATAACG 57.741 39.130 0.00 0.00 40.96 3.18
726 727 4.150980 TGCAACGTCAAAGTTAGATAACGG 59.849 41.667 0.00 0.00 40.96 4.44
727 728 4.634991 CAACGTCAAAGTTAGATAACGGC 58.365 43.478 0.00 0.00 40.96 5.68
728 729 3.916761 ACGTCAAAGTTAGATAACGGCA 58.083 40.909 0.00 0.00 40.96 5.69
730 731 4.151157 ACGTCAAAGTTAGATAACGGCAAC 59.849 41.667 0.00 0.00 40.96 4.17
742 743 2.050077 GGCAACGCCTGAGTTTGC 60.050 61.111 0.00 2.97 46.69 3.68
743 744 2.721231 GCAACGCCTGAGTTTGCA 59.279 55.556 5.98 0.00 32.48 4.08
744 745 1.065600 GCAACGCCTGAGTTTGCAA 59.934 52.632 0.00 0.00 32.48 4.08
746 747 0.381801 CAACGCCTGAGTTTGCAAGT 59.618 50.000 0.00 0.00 30.96 3.16
750 751 1.873591 CGCCTGAGTTTGCAAGTAAGT 59.126 47.619 0.00 0.00 0.00 2.24
756 757 4.065088 TGAGTTTGCAAGTAAGTAGGCAG 58.935 43.478 0.00 0.00 37.59 4.85
761 762 1.679032 GCAAGTAAGTAGGCAGGGGTG 60.679 57.143 0.00 0.00 0.00 4.61
787 788 4.202161 GGACGGTCACTCTTATGATGATGT 60.202 45.833 10.76 0.00 0.00 3.06
789 790 5.111989 ACGGTCACTCTTATGATGATGTTG 58.888 41.667 0.00 0.00 0.00 3.33
793 794 6.372659 GGTCACTCTTATGATGATGTTGTTGT 59.627 38.462 0.00 0.00 0.00 3.32
833 836 0.806884 GTCCACGGACGACAACAACA 60.807 55.000 0.00 0.00 35.30 3.33
834 837 0.806884 TCCACGGACGACAACAACAC 60.807 55.000 0.00 0.00 0.00 3.32
835 838 1.639534 CACGGACGACAACAACACC 59.360 57.895 0.00 0.00 0.00 4.16
837 840 0.391395 ACGGACGACAACAACACCAA 60.391 50.000 0.00 0.00 0.00 3.67
838 841 0.727970 CGGACGACAACAACACCAAA 59.272 50.000 0.00 0.00 0.00 3.28
839 842 1.130749 CGGACGACAACAACACCAAAA 59.869 47.619 0.00 0.00 0.00 2.44
850 853 3.949113 ACAACACCAAAAACGGTACTGAT 59.051 39.130 9.17 0.00 37.07 2.90
866 869 2.550606 ACTGATAAAACGAGGCGCAAAA 59.449 40.909 10.83 0.00 0.00 2.44
870 873 1.496934 AAAACGAGGCGCAAAATTGG 58.503 45.000 10.83 0.00 0.00 3.16
880 883 3.181521 GGCGCAAAATTGGTTAGAAATGC 60.182 43.478 10.83 0.00 0.00 3.56
882 885 4.093261 GCGCAAAATTGGTTAGAAATGCAT 59.907 37.500 0.30 0.00 33.00 3.96
889 892 2.694628 TGGTTAGAAATGCATGATGGCC 59.305 45.455 0.00 0.00 0.00 5.36
892 895 1.991121 AGAAATGCATGATGGCCGAT 58.009 45.000 0.00 0.00 0.00 4.18
893 896 1.611977 AGAAATGCATGATGGCCGATG 59.388 47.619 0.00 1.10 0.00 3.84
897 900 1.825191 GCATGATGGCCGATGTGGT 60.825 57.895 0.00 0.00 41.21 4.16
920 927 5.499004 TCTCCCTATAAATACACCATGGC 57.501 43.478 13.04 0.00 0.00 4.40
927 934 6.653320 CCTATAAATACACCATGGCGTAACAT 59.347 38.462 16.30 11.61 0.00 2.71
942 949 3.181774 CGTAACATGCCACTTAGATACGC 59.818 47.826 0.00 0.00 0.00 4.42
944 951 2.550978 ACATGCCACTTAGATACGCAC 58.449 47.619 0.00 0.00 31.17 5.34
956 976 3.752665 AGATACGCACCTTAGCTAGCTA 58.247 45.455 20.67 20.67 0.00 3.32
957 977 4.337145 AGATACGCACCTTAGCTAGCTAT 58.663 43.478 24.69 10.79 0.00 2.97
958 978 4.396790 AGATACGCACCTTAGCTAGCTATC 59.603 45.833 24.69 16.14 0.00 2.08
961 981 3.502979 ACGCACCTTAGCTAGCTATCTAC 59.497 47.826 24.69 12.49 0.00 2.59
970 990 4.013728 AGCTAGCTATCTACCATCTTCCG 58.986 47.826 17.69 0.00 0.00 4.30
973 993 2.814919 AGCTATCTACCATCTTCCGTCG 59.185 50.000 0.00 0.00 0.00 5.12
1135 1163 3.675619 ATGCCCGACTACAACGCCC 62.676 63.158 0.00 0.00 0.00 6.13
1215 1248 4.473520 CCTCCCGCGAATGGCACT 62.474 66.667 8.23 0.00 43.84 4.40
1224 1257 1.997606 GCGAATGGCACTTAGTAACGT 59.002 47.619 0.00 0.00 42.87 3.99
1227 1260 4.491441 GCGAATGGCACTTAGTAACGTAAC 60.491 45.833 0.00 0.00 42.87 2.50
1262 1295 2.226712 TACCAGCGTGTACGTCGTCG 62.227 60.000 0.00 0.01 42.22 5.12
1272 1305 4.112341 CGTCGTCGTCCCTGTCCC 62.112 72.222 0.00 0.00 0.00 4.46
1273 1306 2.675772 GTCGTCGTCCCTGTCCCT 60.676 66.667 0.00 0.00 0.00 4.20
1274 1307 2.675423 TCGTCGTCCCTGTCCCTG 60.675 66.667 0.00 0.00 0.00 4.45
1275 1308 4.436998 CGTCGTCCCTGTCCCTGC 62.437 72.222 0.00 0.00 0.00 4.85
1276 1309 4.083862 GTCGTCCCTGTCCCTGCC 62.084 72.222 0.00 0.00 0.00 4.85
1279 1312 3.721706 GTCCCTGTCCCTGCCCTG 61.722 72.222 0.00 0.00 0.00 4.45
1308 1341 3.065510 CGCTGCTGTGACTACTGTACTAT 59.934 47.826 0.00 0.00 0.00 2.12
1309 1342 4.272748 CGCTGCTGTGACTACTGTACTATA 59.727 45.833 0.00 0.00 0.00 1.31
1310 1343 5.049336 CGCTGCTGTGACTACTGTACTATAT 60.049 44.000 0.00 0.00 0.00 0.86
1311 1344 6.147328 CGCTGCTGTGACTACTGTACTATATA 59.853 42.308 0.00 0.00 0.00 0.86
1312 1345 7.299586 GCTGCTGTGACTACTGTACTATATAC 58.700 42.308 0.00 0.00 0.00 1.47
1313 1346 7.417496 TGCTGTGACTACTGTACTATATACG 57.583 40.000 0.00 0.00 0.00 3.06
1314 1347 7.212274 TGCTGTGACTACTGTACTATATACGA 58.788 38.462 0.00 0.00 0.00 3.43
1315 1348 7.876582 TGCTGTGACTACTGTACTATATACGAT 59.123 37.037 0.00 0.00 0.00 3.73
1316 1349 9.363763 GCTGTGACTACTGTACTATATACGATA 57.636 37.037 0.00 0.00 0.00 2.92
1340 1373 5.995282 ACAATGGAAGAATGAAGTGACGTTA 59.005 36.000 0.00 0.00 0.00 3.18
1349 1382 4.203950 TGAAGTGACGTTATGTGTTTGC 57.796 40.909 0.00 0.00 0.00 3.68
1366 1399 2.640346 TGCGCTACGTGATTTCTACA 57.360 45.000 9.73 0.00 0.00 2.74
1392 1425 6.920569 AACTAGCTAAAATATTCGTGGGTG 57.079 37.500 0.00 0.00 0.00 4.61
1393 1426 5.985911 ACTAGCTAAAATATTCGTGGGTGT 58.014 37.500 0.00 0.00 0.00 4.16
1395 1428 7.558604 ACTAGCTAAAATATTCGTGGGTGTTA 58.441 34.615 0.00 0.00 0.00 2.41
1396 1429 8.208903 ACTAGCTAAAATATTCGTGGGTGTTAT 58.791 33.333 0.00 0.00 0.00 1.89
1400 1434 7.201750 GCTAAAATATTCGTGGGTGTTATGGAA 60.202 37.037 0.00 0.00 0.00 3.53
1421 1455 6.720288 TGGAATAACAAATTTTTCGGAGGGTA 59.280 34.615 0.00 0.00 29.27 3.69
1435 1469 5.380043 TCGGAGGGTATAACTCGTTTATCT 58.620 41.667 0.00 0.00 35.82 1.98
1436 1470 5.829924 TCGGAGGGTATAACTCGTTTATCTT 59.170 40.000 0.00 0.00 35.82 2.40
1452 1486 8.181573 TCGTTTATCTTGCTCATGTTTATTTCC 58.818 33.333 0.00 0.00 0.00 3.13
1468 1502 0.244450 TTCCGTGTTAGCCGTACTGG 59.756 55.000 0.00 0.00 42.50 4.00
1486 1520 1.872952 TGGCATTATGCGTAGATGTGC 59.127 47.619 11.28 7.58 46.21 4.57
1487 1521 1.197721 GGCATTATGCGTAGATGTGCC 59.802 52.381 11.28 14.08 46.21 5.01
1497 1531 3.585862 CGTAGATGTGCCTACTGTTTGT 58.414 45.455 0.00 0.00 37.47 2.83
1498 1532 4.740268 CGTAGATGTGCCTACTGTTTGTA 58.260 43.478 0.00 0.00 37.47 2.41
1505 1539 6.593268 TGTGCCTACTGTTTGTATAGTACA 57.407 37.500 0.00 0.00 36.79 2.90
1557 1591 7.546667 GTCATTAATTCTGTCAATGCCATGTTT 59.453 33.333 0.00 0.00 31.21 2.83
1563 1597 6.778834 TCTGTCAATGCCATGTTTATGATT 57.221 33.333 0.00 0.00 36.36 2.57
1640 1676 7.467557 TTTGATTTTTCTTGAACATGCTCAC 57.532 32.000 0.00 0.00 0.00 3.51
1665 1701 1.621992 TGAGCAAGACGAGTCTCCTT 58.378 50.000 6.19 0.00 39.39 3.36
1704 1740 3.930336 TGATATCATCAAGGCTTAGCCG 58.070 45.455 18.36 4.58 43.72 5.52
1790 1826 1.873486 GCTTGCCCACAAATGGTTCAC 60.873 52.381 0.00 0.00 45.66 3.18
1825 1861 0.439985 CAGCCACGTCATTCTTGTCG 59.560 55.000 0.00 0.00 39.74 4.35
1903 1939 4.331992 CCTGCATACTCAGTCACTGATTTG 59.668 45.833 8.28 7.60 39.92 2.32
1904 1940 4.898320 TGCATACTCAGTCACTGATTTGT 58.102 39.130 8.28 5.67 39.92 2.83
1921 1957 5.068987 TGATTTGTAGCCTTGCTTCAAGTTT 59.931 36.000 7.92 0.00 44.15 2.66
1998 2809 8.782339 TGTAATTAGTTAGTCCTTAGGTTTGC 57.218 34.615 0.00 0.00 0.00 3.68
2036 2847 0.529337 AGCTTGGAGATGATGTCGCG 60.529 55.000 0.00 0.00 0.00 5.87
2042 2869 0.872021 GAGATGATGTCGCGGGTCAC 60.872 60.000 6.13 0.00 0.00 3.67
2086 2913 1.795872 CAGTAAATCACGGCGACACAA 59.204 47.619 16.62 0.00 0.00 3.33
2089 2916 1.234821 AAATCACGGCGACACAACAT 58.765 45.000 16.62 0.00 0.00 2.71
2112 2939 2.159382 CAATTAGCCGTCACCAAGGTT 58.841 47.619 0.00 0.00 0.00 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 8.196771 TCAGAAAAATGTTTTACATGTGCTCTT 58.803 29.630 9.11 0.00 37.97 2.85
19 20 7.715657 TCAGAAAAATGTTTTACATGTGCTCT 58.284 30.769 9.11 0.00 37.97 4.09
21 22 9.410556 GTATCAGAAAAATGTTTTACATGTGCT 57.589 29.630 9.11 0.00 37.97 4.40
27 28 9.409312 CAGCATGTATCAGAAAAATGTTTTACA 57.591 29.630 0.00 0.00 0.00 2.41
29 30 8.801299 TCCAGCATGTATCAGAAAAATGTTTTA 58.199 29.630 0.00 0.00 0.00 1.52
30 31 7.669427 TCCAGCATGTATCAGAAAAATGTTTT 58.331 30.769 0.00 0.00 0.00 2.43
31 32 7.230849 TCCAGCATGTATCAGAAAAATGTTT 57.769 32.000 0.00 0.00 0.00 2.83
32 33 6.839124 TCCAGCATGTATCAGAAAAATGTT 57.161 33.333 0.00 0.00 0.00 2.71
35 36 7.893124 AAGATCCAGCATGTATCAGAAAAAT 57.107 32.000 0.00 0.00 0.00 1.82
36 37 7.707624 AAAGATCCAGCATGTATCAGAAAAA 57.292 32.000 0.00 0.00 0.00 1.94
37 38 7.707624 AAAAGATCCAGCATGTATCAGAAAA 57.292 32.000 0.00 0.00 0.00 2.29
38 39 8.806429 TTAAAAGATCCAGCATGTATCAGAAA 57.194 30.769 0.00 0.00 0.00 2.52
39 40 8.985315 ATTAAAAGATCCAGCATGTATCAGAA 57.015 30.769 0.00 0.00 0.00 3.02
552 553 6.843069 AAATTAGCGCAGTTTGAAAATGTT 57.157 29.167 11.47 0.00 0.00 2.71
603 604 9.810545 CCTCTTACCAACTTTAAAAACATGAAA 57.189 29.630 0.00 0.00 0.00 2.69
604 605 8.973182 ACCTCTTACCAACTTTAAAAACATGAA 58.027 29.630 0.00 0.00 0.00 2.57
605 606 8.528044 ACCTCTTACCAACTTTAAAAACATGA 57.472 30.769 0.00 0.00 0.00 3.07
606 607 9.594478 AAACCTCTTACCAACTTTAAAAACATG 57.406 29.630 0.00 0.00 0.00 3.21
607 608 9.811995 GAAACCTCTTACCAACTTTAAAAACAT 57.188 29.630 0.00 0.00 0.00 2.71
608 609 7.969508 CGAAACCTCTTACCAACTTTAAAAACA 59.030 33.333 0.00 0.00 0.00 2.83
609 610 8.183536 TCGAAACCTCTTACCAACTTTAAAAAC 58.816 33.333 0.00 0.00 0.00 2.43
610 611 8.278729 TCGAAACCTCTTACCAACTTTAAAAA 57.721 30.769 0.00 0.00 0.00 1.94
611 612 7.862512 TCGAAACCTCTTACCAACTTTAAAA 57.137 32.000 0.00 0.00 0.00 1.52
612 613 7.173735 GGATCGAAACCTCTTACCAACTTTAAA 59.826 37.037 0.00 0.00 0.00 1.52
613 614 6.652062 GGATCGAAACCTCTTACCAACTTTAA 59.348 38.462 0.00 0.00 0.00 1.52
614 615 6.013984 AGGATCGAAACCTCTTACCAACTTTA 60.014 38.462 8.44 0.00 31.43 1.85
615 616 5.001874 GGATCGAAACCTCTTACCAACTTT 58.998 41.667 0.00 0.00 0.00 2.66
616 617 4.286291 AGGATCGAAACCTCTTACCAACTT 59.714 41.667 8.44 0.00 31.43 2.66
617 618 3.838903 AGGATCGAAACCTCTTACCAACT 59.161 43.478 8.44 0.00 31.43 3.16
618 619 3.933332 CAGGATCGAAACCTCTTACCAAC 59.067 47.826 10.88 0.00 35.35 3.77
619 620 3.055385 CCAGGATCGAAACCTCTTACCAA 60.055 47.826 10.88 0.00 35.35 3.67
620 621 2.500098 CCAGGATCGAAACCTCTTACCA 59.500 50.000 10.88 0.00 35.35 3.25
621 622 2.158943 CCCAGGATCGAAACCTCTTACC 60.159 54.545 10.88 0.00 35.35 2.85
622 623 2.764572 TCCCAGGATCGAAACCTCTTAC 59.235 50.000 10.88 0.00 35.35 2.34
623 624 2.764572 GTCCCAGGATCGAAACCTCTTA 59.235 50.000 10.88 0.00 35.35 2.10
624 625 1.555533 GTCCCAGGATCGAAACCTCTT 59.444 52.381 10.88 0.00 35.35 2.85
625 626 1.196012 GTCCCAGGATCGAAACCTCT 58.804 55.000 10.88 0.00 35.35 3.69
626 627 0.902531 TGTCCCAGGATCGAAACCTC 59.097 55.000 10.88 2.56 35.35 3.85
698 699 8.627428 GTTATCTAACTTTGACGTTGCAAATTC 58.373 33.333 0.00 0.54 37.16 2.17
706 707 4.309099 TGCCGTTATCTAACTTTGACGTT 58.691 39.130 0.00 0.00 34.12 3.99
713 714 2.004733 GGCGTTGCCGTTATCTAACTT 58.995 47.619 0.00 0.00 39.62 2.66
714 715 1.648504 GGCGTTGCCGTTATCTAACT 58.351 50.000 0.00 0.00 39.62 2.24
726 727 0.936297 CTTGCAAACTCAGGCGTTGC 60.936 55.000 0.00 3.63 0.00 4.17
727 728 0.381801 ACTTGCAAACTCAGGCGTTG 59.618 50.000 0.00 0.00 0.00 4.10
728 729 1.961793 TACTTGCAAACTCAGGCGTT 58.038 45.000 0.00 0.00 0.00 4.84
730 731 1.873591 ACTTACTTGCAAACTCAGGCG 59.126 47.619 0.00 0.00 0.00 5.52
731 732 3.437049 CCTACTTACTTGCAAACTCAGGC 59.563 47.826 0.00 0.00 0.00 4.85
732 733 3.437049 GCCTACTTACTTGCAAACTCAGG 59.563 47.826 0.00 4.02 0.00 3.86
734 735 4.065088 CTGCCTACTTACTTGCAAACTCA 58.935 43.478 0.00 0.00 32.58 3.41
736 737 3.412386 CCTGCCTACTTACTTGCAAACT 58.588 45.455 0.00 0.00 32.58 2.66
737 738 2.488153 CCCTGCCTACTTACTTGCAAAC 59.512 50.000 0.00 0.00 32.58 2.93
739 740 1.004277 CCCCTGCCTACTTACTTGCAA 59.996 52.381 0.00 0.00 32.58 4.08
740 741 0.618458 CCCCTGCCTACTTACTTGCA 59.382 55.000 0.00 0.00 0.00 4.08
741 742 0.618981 ACCCCTGCCTACTTACTTGC 59.381 55.000 0.00 0.00 0.00 4.01
742 743 1.679032 GCACCCCTGCCTACTTACTTG 60.679 57.143 0.00 0.00 37.45 3.16
743 744 0.618981 GCACCCCTGCCTACTTACTT 59.381 55.000 0.00 0.00 37.45 2.24
744 745 0.252742 AGCACCCCTGCCTACTTACT 60.253 55.000 0.00 0.00 45.53 2.24
746 747 1.271840 CCAGCACCCCTGCCTACTTA 61.272 60.000 0.00 0.00 45.53 2.24
750 751 3.009115 GTCCAGCACCCCTGCCTA 61.009 66.667 0.00 0.00 45.53 3.93
756 757 4.699522 GTGACCGTCCAGCACCCC 62.700 72.222 0.00 0.00 0.00 4.95
761 762 1.476891 TCATAAGAGTGACCGTCCAGC 59.523 52.381 0.00 0.00 0.00 4.85
769 770 7.369803 ACAACAACATCATCATAAGAGTGAC 57.630 36.000 0.00 0.00 0.00 3.67
787 788 5.049267 GCGGAATTAAGTAGGACAACAACAA 60.049 40.000 0.00 0.00 0.00 2.83
789 790 4.142752 GGCGGAATTAAGTAGGACAACAAC 60.143 45.833 0.00 0.00 0.00 3.32
793 794 2.419021 CGGGCGGAATTAAGTAGGACAA 60.419 50.000 0.00 0.00 0.00 3.18
824 827 2.949142 ACCGTTTTTGGTGTTGTTGTC 58.051 42.857 0.00 0.00 41.85 3.18
827 830 3.757493 TCAGTACCGTTTTTGGTGTTGTT 59.243 39.130 0.00 0.00 43.68 2.83
830 833 6.696441 TTTATCAGTACCGTTTTTGGTGTT 57.304 33.333 0.00 0.00 43.68 3.32
833 836 5.526846 TCGTTTTATCAGTACCGTTTTTGGT 59.473 36.000 0.00 0.00 46.26 3.67
834 837 5.988092 TCGTTTTATCAGTACCGTTTTTGG 58.012 37.500 0.00 0.00 0.00 3.28
835 838 6.075280 CCTCGTTTTATCAGTACCGTTTTTG 58.925 40.000 0.00 0.00 0.00 2.44
837 840 4.152938 GCCTCGTTTTATCAGTACCGTTTT 59.847 41.667 0.00 0.00 0.00 2.43
838 841 3.681417 GCCTCGTTTTATCAGTACCGTTT 59.319 43.478 0.00 0.00 0.00 3.60
839 842 3.256558 GCCTCGTTTTATCAGTACCGTT 58.743 45.455 0.00 0.00 0.00 4.44
850 853 2.034812 ACCAATTTTGCGCCTCGTTTTA 59.965 40.909 4.18 0.00 0.00 1.52
866 869 4.202284 GGCCATCATGCATTTCTAACCAAT 60.202 41.667 0.00 0.00 0.00 3.16
870 873 2.618241 TCGGCCATCATGCATTTCTAAC 59.382 45.455 2.24 0.00 0.00 2.34
880 883 0.664761 GAACCACATCGGCCATCATG 59.335 55.000 2.24 3.98 39.03 3.07
882 885 0.107703 GAGAACCACATCGGCCATCA 60.108 55.000 2.24 0.00 39.03 3.07
889 892 6.645415 GTGTATTTATAGGGAGAACCACATCG 59.355 42.308 0.00 0.00 43.89 3.84
892 895 5.727279 TGGTGTATTTATAGGGAGAACCACA 59.273 40.000 0.00 0.00 43.89 4.17
893 896 6.243216 TGGTGTATTTATAGGGAGAACCAC 57.757 41.667 0.00 0.00 43.89 4.16
897 900 5.512404 CGCCATGGTGTATTTATAGGGAGAA 60.512 44.000 17.59 0.00 0.00 2.87
920 927 3.181774 GCGTATCTAAGTGGCATGTTACG 59.818 47.826 0.00 5.00 35.54 3.18
927 934 1.191535 AGGTGCGTATCTAAGTGGCA 58.808 50.000 0.00 0.00 0.00 4.92
942 949 5.949354 AGATGGTAGATAGCTAGCTAAGGTG 59.051 44.000 27.47 0.00 43.72 4.00
944 951 6.096282 GGAAGATGGTAGATAGCTAGCTAAGG 59.904 46.154 27.47 0.00 43.72 2.69
956 976 1.681793 CACCGACGGAAGATGGTAGAT 59.318 52.381 23.38 0.00 39.42 1.98
957 977 1.100510 CACCGACGGAAGATGGTAGA 58.899 55.000 23.38 0.00 39.42 2.59
958 978 0.527817 GCACCGACGGAAGATGGTAG 60.528 60.000 23.38 0.00 39.42 3.18
961 981 1.519455 GAGCACCGACGGAAGATGG 60.519 63.158 23.38 3.61 35.56 3.51
988 1008 4.202161 CGACTTGCTCATCTTGGTACCTAT 60.202 45.833 14.36 1.20 0.00 2.57
989 1009 3.130516 CGACTTGCTCATCTTGGTACCTA 59.869 47.826 14.36 4.36 0.00 3.08
991 1011 2.271800 CGACTTGCTCATCTTGGTACC 58.728 52.381 4.43 4.43 0.00 3.34
993 1013 2.415491 CGACGACTTGCTCATCTTGGTA 60.415 50.000 0.00 0.00 0.00 3.25
1262 1295 3.721706 CAGGGCAGGGACAGGGAC 61.722 72.222 0.00 0.00 0.00 4.46
1284 1317 1.080230 CAGTAGTCACAGCAGCGCT 60.080 57.895 2.64 2.64 40.77 5.92
1285 1318 0.109272 TACAGTAGTCACAGCAGCGC 60.109 55.000 0.00 0.00 0.00 5.92
1286 1319 1.200252 AGTACAGTAGTCACAGCAGCG 59.800 52.381 0.00 0.00 0.00 5.18
1287 1320 4.640789 ATAGTACAGTAGTCACAGCAGC 57.359 45.455 0.00 0.00 0.00 5.25
1288 1321 7.384387 TCGTATATAGTACAGTAGTCACAGCAG 59.616 40.741 0.00 0.00 0.00 4.24
1289 1322 7.212274 TCGTATATAGTACAGTAGTCACAGCA 58.788 38.462 0.00 0.00 0.00 4.41
1290 1323 7.649370 TCGTATATAGTACAGTAGTCACAGC 57.351 40.000 0.00 0.00 0.00 4.40
1308 1341 9.476202 CACTTCATTCTTCCATTGTATCGTATA 57.524 33.333 0.00 0.00 0.00 1.47
1309 1342 8.204160 TCACTTCATTCTTCCATTGTATCGTAT 58.796 33.333 0.00 0.00 0.00 3.06
1310 1343 7.491372 GTCACTTCATTCTTCCATTGTATCGTA 59.509 37.037 0.00 0.00 0.00 3.43
1311 1344 6.313905 GTCACTTCATTCTTCCATTGTATCGT 59.686 38.462 0.00 0.00 0.00 3.73
1312 1345 6.508563 CGTCACTTCATTCTTCCATTGTATCG 60.509 42.308 0.00 0.00 0.00 2.92
1313 1346 6.313905 ACGTCACTTCATTCTTCCATTGTATC 59.686 38.462 0.00 0.00 0.00 2.24
1314 1347 6.173339 ACGTCACTTCATTCTTCCATTGTAT 58.827 36.000 0.00 0.00 0.00 2.29
1315 1348 5.547465 ACGTCACTTCATTCTTCCATTGTA 58.453 37.500 0.00 0.00 0.00 2.41
1316 1349 4.389374 ACGTCACTTCATTCTTCCATTGT 58.611 39.130 0.00 0.00 0.00 2.71
1317 1350 5.362556 AACGTCACTTCATTCTTCCATTG 57.637 39.130 0.00 0.00 0.00 2.82
1318 1351 6.655003 ACATAACGTCACTTCATTCTTCCATT 59.345 34.615 0.00 0.00 0.00 3.16
1319 1352 6.092670 CACATAACGTCACTTCATTCTTCCAT 59.907 38.462 0.00 0.00 0.00 3.41
1329 1362 3.215244 CGCAAACACATAACGTCACTTC 58.785 45.455 0.00 0.00 0.00 3.01
1340 1373 1.438651 ATCACGTAGCGCAAACACAT 58.561 45.000 11.47 0.00 0.00 3.21
1349 1382 5.912528 AGTTTTTGTAGAAATCACGTAGCG 58.087 37.500 0.00 0.00 0.00 4.26
1366 1399 8.241367 CACCCACGAATATTTTAGCTAGTTTTT 58.759 33.333 0.00 0.00 0.00 1.94
1392 1425 9.083080 CCTCCGAAAAATTTGTTATTCCATAAC 57.917 33.333 0.00 0.44 44.13 1.89
1393 1426 8.254508 CCCTCCGAAAAATTTGTTATTCCATAA 58.745 33.333 0.00 0.00 0.00 1.90
1395 1428 6.212589 ACCCTCCGAAAAATTTGTTATTCCAT 59.787 34.615 0.00 0.00 0.00 3.41
1396 1429 5.540719 ACCCTCCGAAAAATTTGTTATTCCA 59.459 36.000 0.00 0.00 0.00 3.53
1400 1434 9.470399 AGTTATACCCTCCGAAAAATTTGTTAT 57.530 29.630 0.00 0.00 0.00 1.89
1410 1444 4.806640 AAACGAGTTATACCCTCCGAAA 57.193 40.909 0.00 0.00 0.00 3.46
1421 1455 7.849804 AACATGAGCAAGATAAACGAGTTAT 57.150 32.000 0.00 0.00 34.97 1.89
1435 1469 5.446143 AACACGGAAATAAACATGAGCAA 57.554 34.783 0.00 0.00 0.00 3.91
1436 1470 5.391523 GCTAACACGGAAATAAACATGAGCA 60.392 40.000 0.00 0.00 0.00 4.26
1468 1502 2.146342 AGGCACATCTACGCATAATGC 58.854 47.619 0.00 0.00 40.69 3.56
1476 1510 3.585862 ACAAACAGTAGGCACATCTACG 58.414 45.455 0.00 0.00 43.10 3.51
1486 1520 9.982651 ATAAGCATGTACTATACAAACAGTAGG 57.017 33.333 0.00 0.00 42.76 3.18
1524 1558 8.615211 GCATTGACAGAATTAATGACATACTGA 58.385 33.333 0.00 0.00 34.55 3.41
1541 1575 7.837202 AAAATCATAAACATGGCATTGACAG 57.163 32.000 0.00 0.00 0.00 3.51
1584 1619 6.101997 GCTGCTGAGTAAATAGGCAATTTTT 58.898 36.000 0.00 0.00 38.71 1.94
1589 1624 3.009723 GTGCTGCTGAGTAAATAGGCAA 58.990 45.455 0.00 0.00 32.43 4.52
1591 1626 1.594862 CGTGCTGCTGAGTAAATAGGC 59.405 52.381 0.00 0.00 0.00 3.93
1592 1627 2.604914 CACGTGCTGCTGAGTAAATAGG 59.395 50.000 0.82 0.00 0.00 2.57
1594 1629 1.999735 GCACGTGCTGCTGAGTAAATA 59.000 47.619 32.55 0.00 43.33 1.40
1617 1653 6.698329 CAGTGAGCATGTTCAAGAAAAATCAA 59.302 34.615 14.30 0.00 0.00 2.57
1640 1676 0.034059 ACTCGTCTTGCTCAACCCAG 59.966 55.000 0.00 0.00 0.00 4.45
1665 1701 7.567458 TGATATCATTTCCAGTGTGATTGAGA 58.433 34.615 0.00 0.00 34.62 3.27
1704 1740 7.475840 CCAGCTAATATTCTCCAAAACTGAAC 58.524 38.462 0.00 0.00 0.00 3.18
1749 1785 3.317430 GCTCTTCCTTGATGGCCTAAATG 59.683 47.826 3.32 0.00 35.26 2.32
1825 1861 1.905637 ACCATCCTTTTCAACCCGTC 58.094 50.000 0.00 0.00 0.00 4.79
1864 1900 2.495270 TGCAGGTGAGATGAAGAGACTC 59.505 50.000 0.00 0.00 0.00 3.36
1866 1902 3.540314 ATGCAGGTGAGATGAAGAGAC 57.460 47.619 0.00 0.00 0.00 3.36
1903 1939 3.315191 TGACAAACTTGAAGCAAGGCTAC 59.685 43.478 11.40 0.00 44.81 3.58
1904 1940 3.550820 TGACAAACTTGAAGCAAGGCTA 58.449 40.909 11.40 0.00 44.81 3.93
1921 1957 1.456296 GCATCATGCAGGAGTTGACA 58.544 50.000 7.33 0.00 44.26 3.58
1982 2235 1.348366 TGCGGCAAACCTAAGGACTAA 59.652 47.619 0.00 0.00 0.00 2.24
2086 2913 2.290008 TGGTGACGGCTAATTGTGATGT 60.290 45.455 0.00 0.00 0.00 3.06
2089 2916 2.422597 CTTGGTGACGGCTAATTGTGA 58.577 47.619 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.