Multiple sequence alignment - TraesCS1A01G014400

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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 TraesCS1A01G014400 chr1A 100.000 2669 0 0 1 2669 7829271 7831939 0.000000e+00 4929.0
1 TraesCS1A01G014400 chr1A 94.482 1033 41 3 682 1698 8158349 8157317 0.000000e+00 1578.0
2 TraesCS1A01G014400 chr1A 87.917 960 97 4 713 1656 8328679 8329635 0.000000e+00 1112.0
3 TraesCS1A01G014400 chr1A 85.967 1019 125 5 687 1687 8333478 8334496 0.000000e+00 1074.0
4 TraesCS1A01G014400 chr1A 85.185 729 82 9 991 1693 9370820 9370092 0.000000e+00 725.0
5 TraesCS1A01G014400 chr1A 88.743 533 50 4 2116 2648 8156244 8155722 0.000000e+00 643.0
6 TraesCS1A01G014400 chr1A 96.285 323 9 1 221 543 8158662 8158343 6.540000e-146 527.0
7 TraesCS1A01G014400 chr1A 94.505 182 10 0 41 222 8159377 8159196 5.630000e-72 281.0
8 TraesCS1A01G014400 chr1A 90.854 164 14 1 41 204 8338468 8338630 4.470000e-53 219.0
9 TraesCS1A01G014400 chr1A 86.875 160 21 0 41 200 8144012 8143853 2.110000e-41 180.0
10 TraesCS1A01G014400 chr1B 94.951 1030 36 3 682 1698 8865717 8864691 0.000000e+00 1600.0
11 TraesCS1A01G014400 chr1B 93.030 1033 53 5 682 1698 9163311 9164340 0.000000e+00 1491.0
12 TraesCS1A01G014400 chr1B 85.977 1034 118 10 687 1693 10005972 10004939 0.000000e+00 1081.0
13 TraesCS1A01G014400 chr1B 86.508 1008 107 11 713 1698 548198349 548197349 0.000000e+00 1081.0
14 TraesCS1A01G014400 chr1B 89.767 557 51 4 2116 2668 8862209 8861655 0.000000e+00 708.0
15 TraesCS1A01G014400 chr1B 95.046 323 16 0 221 543 9162995 9163317 2.370000e-140 508.0
16 TraesCS1A01G014400 chr1B 94.118 323 19 0 221 543 8866033 8865711 2.390000e-135 492.0
17 TraesCS1A01G014400 chr1B 95.604 182 8 0 41 222 9162280 9162461 2.600000e-75 292.0
18 TraesCS1A01G014400 chr1B 94.505 182 10 0 41 222 8866748 8866567 5.630000e-72 281.0
19 TraesCS1A01G014400 chr1B 89.394 132 12 2 544 674 416081610 416081480 5.910000e-37 165.0
20 TraesCS1A01G014400 chr1D 93.417 1033 52 3 682 1698 6720081 6719049 0.000000e+00 1517.0
21 TraesCS1A01G014400 chr1D 87.311 993 96 14 725 1696 6900012 6900995 0.000000e+00 1109.0
22 TraesCS1A01G014400 chr1D 94.737 323 17 0 221 543 6720397 6720075 1.100000e-138 503.0
23 TraesCS1A01G014400 chr1D 96.591 176 6 0 47 222 6721106 6720931 2.600000e-75 292.0
24 TraesCS1A01G014400 chr1D 86.875 160 21 0 41 200 6714120 6713961 2.110000e-41 180.0
25 TraesCS1A01G014400 chr5B 87.287 999 97 10 713 1690 549549516 549550505 0.000000e+00 1114.0
26 TraesCS1A01G014400 chr5B 89.313 131 12 2 543 672 622890881 622890752 2.130000e-36 163.0
27 TraesCS1A01G014400 chr5B 100.000 40 0 0 1 40 522490208 522490169 1.020000e-09 75.0
28 TraesCS1A01G014400 chr5B 97.500 40 1 0 1 40 576865402 576865363 4.770000e-08 69.4
29 TraesCS1A01G014400 chr2A 85.045 1003 120 13 713 1694 611297904 611298897 0.000000e+00 994.0
30 TraesCS1A01G014400 chr2A 84.348 1035 137 10 687 1697 611304359 611305392 0.000000e+00 990.0
31 TraesCS1A01G014400 chr2A 85.404 322 44 1 221 539 611304035 611304356 5.510000e-87 331.0
32 TraesCS1A01G014400 chr2A 97.500 40 1 0 1 40 761542379 761542418 4.770000e-08 69.4
33 TraesCS1A01G014400 chr2A 100.000 32 0 0 2278 2309 611305359 611305390 2.870000e-05 60.2
34 TraesCS1A01G014400 chr2D 85.085 999 119 15 712 1689 599927966 599928955 0.000000e+00 992.0
35 TraesCS1A01G014400 chr2D 83.851 322 49 1 221 539 469985237 469985558 1.200000e-78 303.0
36 TraesCS1A01G014400 chr2D 100.000 32 0 0 2278 2309 469993119 469993150 2.870000e-05 60.2
37 TraesCS1A01G014400 chr2B 84.783 322 46 1 221 539 548625197 548625518 1.190000e-83 320.0
38 TraesCS1A01G014400 chr2B 83.591 323 49 2 221 539 548610710 548611032 1.550000e-77 300.0
39 TraesCS1A01G014400 chr2B 82.663 323 51 4 221 539 729767793 729768114 5.630000e-72 281.0
40 TraesCS1A01G014400 chr2B 100.000 132 0 0 543 674 41070504 41070373 7.380000e-61 244.0
41 TraesCS1A01G014400 chr2B 89.630 135 14 0 540 674 671771778 671771912 3.530000e-39 172.0
42 TraesCS1A01G014400 chr2B 100.000 40 0 0 1 40 46236060 46236099 1.020000e-09 75.0
43 TraesCS1A01G014400 chr2B 100.000 32 0 0 2278 2309 548626513 548626544 2.870000e-05 60.2
44 TraesCS1A01G014400 chr4A 91.729 133 9 2 543 674 666934037 666933906 1.630000e-42 183.0
45 TraesCS1A01G014400 chr4A 97.500 40 1 0 1 40 718820074 718820035 4.770000e-08 69.4
46 TraesCS1A01G014400 chr6A 90.840 131 10 2 543 672 327762682 327762553 9.820000e-40 174.0
47 TraesCS1A01G014400 chr6A 88.636 132 15 0 543 674 1740964 1740833 7.650000e-36 161.0
48 TraesCS1A01G014400 chr4B 84.795 171 26 0 41 211 36635370 36635200 3.530000e-39 172.0
49 TraesCS1A01G014400 chr7B 90.076 131 13 0 544 674 198966016 198966146 1.270000e-38 171.0
50 TraesCS1A01G014400 chr7B 100.000 40 0 0 1 40 657319225 657319186 1.020000e-09 75.0
51 TraesCS1A01G014400 chr7B 97.500 40 1 0 1 40 657425037 657424998 4.770000e-08 69.4
52 TraesCS1A01G014400 chrUn 88.636 132 15 0 543 674 271417917 271417786 7.650000e-36 161.0
53 TraesCS1A01G014400 chr5A 84.722 144 20 2 67 209 12193712 12193570 2.770000e-30 143.0
54 TraesCS1A01G014400 chr3B 100.000 40 0 0 1 40 36015570 36015531 1.020000e-09 75.0
55 TraesCS1A01G014400 chr3D 97.500 40 1 0 1 40 18127025 18126986 4.770000e-08 69.4


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 TraesCS1A01G014400 chr1A 7829271 7831939 2668 False 4929.000000 4929 100.000000 1 2669 1 chr1A.!!$F1 2668
1 TraesCS1A01G014400 chr1A 8328679 8338630 9951 False 801.666667 1112 88.246000 41 1687 3 chr1A.!!$F2 1646
2 TraesCS1A01G014400 chr1A 8155722 8159377 3655 True 757.250000 1578 93.503750 41 2648 4 chr1A.!!$R3 2607
3 TraesCS1A01G014400 chr1A 9370092 9370820 728 True 725.000000 725 85.185000 991 1693 1 chr1A.!!$R2 702
4 TraesCS1A01G014400 chr1B 10004939 10005972 1033 True 1081.000000 1081 85.977000 687 1693 1 chr1B.!!$R1 1006
5 TraesCS1A01G014400 chr1B 548197349 548198349 1000 True 1081.000000 1081 86.508000 713 1698 1 chr1B.!!$R3 985
6 TraesCS1A01G014400 chr1B 8861655 8866748 5093 True 770.250000 1600 93.335250 41 2668 4 chr1B.!!$R4 2627
7 TraesCS1A01G014400 chr1B 9162280 9164340 2060 False 763.666667 1491 94.560000 41 1698 3 chr1B.!!$F1 1657
8 TraesCS1A01G014400 chr1D 6900012 6900995 983 False 1109.000000 1109 87.311000 725 1696 1 chr1D.!!$F1 971
9 TraesCS1A01G014400 chr1D 6719049 6721106 2057 True 770.666667 1517 94.915000 47 1698 3 chr1D.!!$R2 1651
10 TraesCS1A01G014400 chr5B 549549516 549550505 989 False 1114.000000 1114 87.287000 713 1690 1 chr5B.!!$F1 977
11 TraesCS1A01G014400 chr2A 611297904 611298897 993 False 994.000000 994 85.045000 713 1694 1 chr2A.!!$F1 981
12 TraesCS1A01G014400 chr2A 611304035 611305392 1357 False 460.400000 990 89.917333 221 2309 3 chr2A.!!$F3 2088
13 TraesCS1A01G014400 chr2D 599927966 599928955 989 False 992.000000 992 85.085000 712 1689 1 chr2D.!!$F3 977

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
65 3789 0.034059 CCCATCATCTGACCTACCGC 59.966 60.0 0.0 0.0 0.0 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1965 7017 0.383949 TTGACGTGCTCCCTTTTTGC 59.616 50.0 0.0 0.0 0.0 3.68 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
17 18 2.664851 CAAACGCTGGCTCGGTCA 60.665 61.111 4.93 0.00 0.00 4.02
18 19 2.357517 AAACGCTGGCTCGGTCAG 60.358 61.111 1.64 1.64 38.44 3.51
22 23 4.459089 GCTGGCTCGGTCAGGGAC 62.459 72.222 7.47 0.00 35.59 4.46
65 3789 0.034059 CCCATCATCTGACCTACCGC 59.966 60.000 0.00 0.00 0.00 5.68
139 3863 1.583495 GCTGGAACAAGGTTACCGGC 61.583 60.000 0.00 0.00 45.37 6.13
270 4532 3.550842 GCCAATGCGAAGAAACTTGTCTT 60.551 43.478 0.00 0.00 40.62 3.01
325 4587 3.810812 GCAGATGCTCTGTCTGGC 58.189 61.111 12.71 0.00 45.94 4.85
363 4625 0.461548 TGAGTCTGGATGATGGCGTC 59.538 55.000 0.00 0.00 0.00 5.19
430 4692 5.702349 AGATTTCTTGCCAAGTTTGAGAG 57.298 39.130 4.04 0.00 0.00 3.20
471 4733 0.519519 TTGGAATTGTTACTGCCGCG 59.480 50.000 0.00 0.00 0.00 6.46
543 4811 4.951715 TGGAGGATCAAATTCAAGTCATGG 59.048 41.667 0.00 0.00 36.25 3.66
544 4812 5.195940 GGAGGATCAAATTCAAGTCATGGA 58.804 41.667 0.00 0.00 36.25 3.41
545 4813 5.067023 GGAGGATCAAATTCAAGTCATGGAC 59.933 44.000 0.00 0.00 36.25 4.02
546 4814 4.637534 AGGATCAAATTCAAGTCATGGACG 59.362 41.667 0.00 0.00 37.67 4.79
547 4815 4.635765 GGATCAAATTCAAGTCATGGACGA 59.364 41.667 0.00 0.00 37.67 4.20
548 4816 5.123820 GGATCAAATTCAAGTCATGGACGAA 59.876 40.000 0.00 0.00 37.67 3.85
549 4817 5.611796 TCAAATTCAAGTCATGGACGAAG 57.388 39.130 0.00 0.00 37.67 3.79
550 4818 4.083324 TCAAATTCAAGTCATGGACGAAGC 60.083 41.667 0.00 0.00 37.67 3.86
551 4819 2.839486 TTCAAGTCATGGACGAAGCT 57.161 45.000 0.00 0.00 37.67 3.74
552 4820 3.953712 TTCAAGTCATGGACGAAGCTA 57.046 42.857 0.00 0.00 37.67 3.32
553 4821 3.510388 TCAAGTCATGGACGAAGCTAG 57.490 47.619 0.00 0.00 37.67 3.42
554 4822 3.089284 TCAAGTCATGGACGAAGCTAGA 58.911 45.455 0.00 0.00 37.67 2.43
555 4823 3.509967 TCAAGTCATGGACGAAGCTAGAA 59.490 43.478 0.00 0.00 37.67 2.10
556 4824 4.021456 TCAAGTCATGGACGAAGCTAGAAA 60.021 41.667 0.00 0.00 37.67 2.52
557 4825 4.537135 AGTCATGGACGAAGCTAGAAAA 57.463 40.909 0.00 0.00 37.67 2.29
558 4826 4.894784 AGTCATGGACGAAGCTAGAAAAA 58.105 39.130 0.00 0.00 37.67 1.94
578 4846 4.871933 AAAAGTTTGATGGGGTCATGTC 57.128 40.909 0.00 0.00 36.54 3.06
579 4847 3.814504 AAGTTTGATGGGGTCATGTCT 57.185 42.857 0.00 0.00 36.54 3.41
580 4848 4.927267 AAGTTTGATGGGGTCATGTCTA 57.073 40.909 0.00 0.00 36.54 2.59
581 4849 5.456921 AAGTTTGATGGGGTCATGTCTAT 57.543 39.130 0.00 0.00 36.54 1.98
582 4850 4.785301 AGTTTGATGGGGTCATGTCTATG 58.215 43.478 0.00 0.00 36.54 2.23
583 4851 4.474651 AGTTTGATGGGGTCATGTCTATGA 59.525 41.667 0.00 0.00 40.92 2.15
592 4860 2.832838 TCATGTCTATGACAGTGGGGT 58.167 47.619 6.55 0.00 46.04 4.95
593 4861 2.766263 TCATGTCTATGACAGTGGGGTC 59.234 50.000 6.55 0.00 46.04 4.46
600 4868 2.030027 TGACAGTGGGGTCATCTTCT 57.970 50.000 0.00 0.00 42.56 2.85
601 4869 2.338809 TGACAGTGGGGTCATCTTCTT 58.661 47.619 0.00 0.00 42.56 2.52
602 4870 2.711009 TGACAGTGGGGTCATCTTCTTT 59.289 45.455 0.00 0.00 42.56 2.52
603 4871 3.907474 TGACAGTGGGGTCATCTTCTTTA 59.093 43.478 0.00 0.00 42.56 1.85
604 4872 4.349636 TGACAGTGGGGTCATCTTCTTTAA 59.650 41.667 0.00 0.00 42.56 1.52
605 4873 5.163141 TGACAGTGGGGTCATCTTCTTTAAA 60.163 40.000 0.00 0.00 42.56 1.52
606 4874 5.892348 ACAGTGGGGTCATCTTCTTTAAAT 58.108 37.500 0.00 0.00 0.00 1.40
607 4875 7.027874 ACAGTGGGGTCATCTTCTTTAAATA 57.972 36.000 0.00 0.00 0.00 1.40
608 4876 7.466804 ACAGTGGGGTCATCTTCTTTAAATAA 58.533 34.615 0.00 0.00 0.00 1.40
609 4877 7.947890 ACAGTGGGGTCATCTTCTTTAAATAAA 59.052 33.333 0.00 0.00 0.00 1.40
610 4878 8.971073 CAGTGGGGTCATCTTCTTTAAATAAAT 58.029 33.333 0.00 0.00 0.00 1.40
654 4922 7.830739 AGTGAAGGCTTTACTAATTTCATTGG 58.169 34.615 21.63 0.00 0.00 3.16
655 4923 7.451566 AGTGAAGGCTTTACTAATTTCATTGGT 59.548 33.333 21.63 0.00 37.70 3.67
656 4924 7.542130 GTGAAGGCTTTACTAATTTCATTGGTG 59.458 37.037 14.30 0.00 35.49 4.17
657 4925 7.232534 TGAAGGCTTTACTAATTTCATTGGTGT 59.767 33.333 0.00 0.00 35.49 4.16
658 4926 7.158099 AGGCTTTACTAATTTCATTGGTGTC 57.842 36.000 0.00 0.00 35.49 3.67
659 4927 6.719370 AGGCTTTACTAATTTCATTGGTGTCA 59.281 34.615 0.00 0.00 35.49 3.58
660 4928 7.232534 AGGCTTTACTAATTTCATTGGTGTCAA 59.767 33.333 0.00 0.00 35.49 3.18
661 4929 8.034804 GGCTTTACTAATTTCATTGGTGTCAAT 58.965 33.333 0.00 0.00 43.79 2.57
662 4930 9.423061 GCTTTACTAATTTCATTGGTGTCAATT 57.577 29.630 0.00 0.00 41.29 2.32
665 4933 9.906660 TTACTAATTTCATTGGTGTCAATTGAC 57.093 29.630 28.10 28.10 41.29 3.18
666 4934 7.378181 ACTAATTTCATTGGTGTCAATTGACC 58.622 34.615 30.66 22.24 44.15 4.02
667 4935 4.599047 TTTCATTGGTGTCAATTGACCC 57.401 40.909 30.66 28.39 44.15 4.46
668 4936 2.524306 TCATTGGTGTCAATTGACCCC 58.476 47.619 30.66 29.07 44.15 4.95
671 4939 2.692709 TGGTGTCAATTGACCCCAAT 57.307 45.000 32.54 0.00 46.90 3.16
672 4940 2.246469 TGGTGTCAATTGACCCCAATG 58.754 47.619 32.54 0.00 46.90 2.82
673 4941 1.066929 GGTGTCAATTGACCCCAATGC 60.067 52.381 28.77 13.70 41.42 3.56
674 4942 0.887247 TGTCAATTGACCCCAATGCG 59.113 50.000 30.66 0.00 41.84 4.73
675 4943 0.887933 GTCAATTGACCCCAATGCGT 59.112 50.000 25.26 0.00 41.84 5.24
676 4944 1.135402 GTCAATTGACCCCAATGCGTC 60.135 52.381 25.26 0.00 41.84 5.19
677 4945 0.173255 CAATTGACCCCAATGCGTCC 59.827 55.000 0.00 0.00 41.84 4.79
678 4946 0.970427 AATTGACCCCAATGCGTCCC 60.970 55.000 0.00 0.00 41.84 4.46
679 4947 1.863155 ATTGACCCCAATGCGTCCCT 61.863 55.000 0.00 0.00 41.18 4.20
680 4948 2.438434 GACCCCAATGCGTCCCTG 60.438 66.667 0.00 0.00 0.00 4.45
681 4949 2.933287 ACCCCAATGCGTCCCTGA 60.933 61.111 0.00 0.00 0.00 3.86
682 4950 2.124570 CCCCAATGCGTCCCTGAG 60.125 66.667 0.00 0.00 0.00 3.35
683 4951 2.671070 CCCAATGCGTCCCTGAGT 59.329 61.111 0.00 0.00 0.00 3.41
684 4952 1.450312 CCCAATGCGTCCCTGAGTC 60.450 63.158 0.00 0.00 0.00 3.36
685 4953 1.296392 CCAATGCGTCCCTGAGTCA 59.704 57.895 0.00 0.00 0.00 3.41
722 4990 6.018425 GCCGATATACTATGGCAATCAAGATG 60.018 42.308 0.00 0.00 46.76 2.90
855 5124 4.650131 AGTGACCCAAAGACTACTATAGCC 59.350 45.833 0.00 0.00 0.00 3.93
1362 5649 5.104193 ACTGCTGGAAATCATATCAGGAAGT 60.104 40.000 0.00 0.00 0.00 3.01
1530 5826 3.117888 TGGAAGAGGCTGAAAGAGTTTGT 60.118 43.478 0.00 0.00 34.07 2.83
1539 5835 5.450550 GGCTGAAAGAGTTTGTAAAGTTGCT 60.451 40.000 0.00 0.00 34.07 3.91
1545 5841 5.102313 AGAGTTTGTAAAGTTGCTTGTTGC 58.898 37.500 0.00 0.00 43.25 4.17
1677 5975 1.878088 ACAGAACACTGATGCTGCAAG 59.122 47.619 6.36 2.63 35.80 4.01
1776 6121 7.911362 AATAATTCGTAGAGTAGTTCGCTTC 57.089 36.000 0.00 0.00 38.43 3.86
1783 6128 3.973657 AGAGTAGTTCGCTTCGTTTCAA 58.026 40.909 0.00 0.00 0.00 2.69
1812 6165 7.672351 TTTTGTAAAGTTGTAATGTGAAGCG 57.328 32.000 0.00 0.00 0.00 4.68
1836 6189 4.675063 AGGAATAAAGGAAGGAGGCAAA 57.325 40.909 0.00 0.00 0.00 3.68
1841 6194 2.755952 AAGGAAGGAGGCAAACTTGT 57.244 45.000 0.00 0.00 0.00 3.16
1842 6195 1.986882 AGGAAGGAGGCAAACTTGTG 58.013 50.000 0.00 0.00 0.00 3.33
1847 6200 0.249447 GGAGGCAAACTTGTGGTTGC 60.249 55.000 9.97 9.97 38.29 4.17
1856 6209 3.665745 ACTTGTGGTTGCCAAATCATC 57.334 42.857 0.00 0.00 34.18 2.92
1857 6210 3.233507 ACTTGTGGTTGCCAAATCATCT 58.766 40.909 0.00 0.00 34.18 2.90
1867 6220 5.422666 TGCCAAATCATCTGCTATTTACG 57.577 39.130 0.00 0.00 0.00 3.18
1903 6257 6.432783 TGGTAAGCAAGTGTAGCAAAATATGT 59.567 34.615 0.00 0.00 0.00 2.29
1905 6259 6.824305 AAGCAAGTGTAGCAAAATATGTCT 57.176 33.333 0.00 0.00 0.00 3.41
1948 6352 2.613595 TGTGTCACTTGTAAGCTGCTTG 59.386 45.455 24.35 10.29 0.00 4.01
1949 6353 2.031682 GTGTCACTTGTAAGCTGCTTGG 60.032 50.000 24.35 13.41 0.00 3.61
1952 6356 3.076621 TCACTTGTAAGCTGCTTGGATG 58.923 45.455 24.35 14.39 0.00 3.51
1953 6357 3.076621 CACTTGTAAGCTGCTTGGATGA 58.923 45.455 24.35 1.07 0.00 2.92
1955 6359 4.157289 CACTTGTAAGCTGCTTGGATGATT 59.843 41.667 24.35 0.00 0.00 2.57
1956 6360 4.768968 ACTTGTAAGCTGCTTGGATGATTT 59.231 37.500 24.35 0.00 0.00 2.17
1959 7011 0.822164 AGCTGCTTGGATGATTTGGC 59.178 50.000 0.00 0.00 0.00 4.52
1962 7014 2.419574 GCTGCTTGGATGATTTGGCAAT 60.420 45.455 0.00 0.00 0.00 3.56
1965 7017 5.013568 TGCTTGGATGATTTGGCAATAAG 57.986 39.130 0.00 0.00 0.00 1.73
1966 7018 3.805971 GCTTGGATGATTTGGCAATAAGC 59.194 43.478 0.00 5.67 44.65 3.09
1979 7031 2.995939 GCAATAAGCAAAAAGGGAGCAC 59.004 45.455 0.00 0.00 44.79 4.40
2009 8431 4.703379 TTTCTGGGAAATGCCAAAATGT 57.297 36.364 0.00 0.00 38.95 2.71
2020 8442 7.855409 GGAAATGCCAAAATGTTCAAACTTAAC 59.145 33.333 0.00 0.00 36.34 2.01
2021 8443 8.504812 AAATGCCAAAATGTTCAAACTTAACT 57.495 26.923 0.00 0.00 0.00 2.24
2023 8445 9.606631 AATGCCAAAATGTTCAAACTTAACTTA 57.393 25.926 0.00 0.00 0.00 2.24
2024 8446 9.606631 ATGCCAAAATGTTCAAACTTAACTTAA 57.393 25.926 0.00 0.00 0.00 1.85
2025 8447 9.436957 TGCCAAAATGTTCAAACTTAACTTAAA 57.563 25.926 0.00 0.00 0.00 1.52
2026 8448 9.914923 GCCAAAATGTTCAAACTTAACTTAAAG 57.085 29.630 0.00 0.00 0.00 1.85
2077 8499 5.009631 TCTGCCTTGTTGCAACTATAATGT 58.990 37.500 28.61 0.00 41.51 2.71
2090 8512 8.397906 TGCAACTATAATGTTTTCTGTGATAGC 58.602 33.333 0.00 0.00 0.00 2.97
2091 8513 8.397906 GCAACTATAATGTTTTCTGTGATAGCA 58.602 33.333 0.00 0.00 0.00 3.49
2095 8517 4.644103 ATGTTTTCTGTGATAGCATGGC 57.356 40.909 0.00 0.00 0.00 4.40
2104 8526 2.038952 GTGATAGCATGGCCATGGACTA 59.961 50.000 39.72 32.23 39.16 2.59
2125 8547 3.731652 TGGCTGAAGTGGAAAACAATG 57.268 42.857 0.00 0.00 0.00 2.82
2158 10232 2.480419 CCAACGATGAGTGAAGTGGTTC 59.520 50.000 0.00 0.00 0.00 3.62
2159 10233 3.130633 CAACGATGAGTGAAGTGGTTCA 58.869 45.455 0.00 0.00 40.55 3.18
2160 10234 3.685139 ACGATGAGTGAAGTGGTTCAT 57.315 42.857 0.00 0.00 44.58 2.57
2163 10237 3.369147 CGATGAGTGAAGTGGTTCATGTC 59.631 47.826 0.00 0.00 44.58 3.06
2238 10312 0.460284 CCGGGTTCTCGATGGTTCTG 60.460 60.000 0.00 0.00 0.00 3.02
2240 10314 1.475280 CGGGTTCTCGATGGTTCTGTA 59.525 52.381 0.00 0.00 0.00 2.74
2254 10328 3.939592 GGTTCTGTAATGCCAAGACTACC 59.060 47.826 0.00 0.00 0.00 3.18
2322 10396 8.975410 TGTAATAATAATTCATAGTCCGTCCG 57.025 34.615 0.00 0.00 0.00 4.79
2340 10414 4.143389 CGTCCGTGTTACTGATTCTTGTTC 60.143 45.833 0.00 0.00 0.00 3.18
2343 10417 4.513692 CCGTGTTACTGATTCTTGTTCCAA 59.486 41.667 0.00 0.00 0.00 3.53
2390 10468 7.112122 GGATGATTATGTATGGTATGCAAGGA 58.888 38.462 0.00 0.00 0.00 3.36
2392 10470 7.078249 TGATTATGTATGGTATGCAAGGACT 57.922 36.000 0.00 0.00 0.00 3.85
2397 10475 0.249120 TGGTATGCAAGGACTGACCG 59.751 55.000 0.00 0.00 44.74 4.79
2416 10494 2.481104 CCGCTGAAAAGTTTCCTTGCAA 60.481 45.455 0.00 0.00 36.36 4.08
2430 10509 3.069300 TCCTTGCAAAGCATTGTAGCAAA 59.931 39.130 0.00 0.00 44.44 3.68
2537 10660 1.832167 GGAAAGCCAACCTGCACCA 60.832 57.895 0.00 0.00 0.00 4.17
2539 10662 0.032540 GAAAGCCAACCTGCACCAAG 59.967 55.000 0.00 0.00 0.00 3.61
2553 10676 6.014669 ACCTGCACCAAGCTTTTATTGAATTA 60.015 34.615 0.00 0.00 45.94 1.40
2584 10869 3.179433 GGCGCAACCAAGAGAAAAC 57.821 52.632 10.83 0.00 38.86 2.43
2636 10921 6.710597 AGGGTAAGTTCAACTTCTTTTTCC 57.289 37.500 5.92 1.29 39.51 3.13
2644 10929 5.722021 TCAACTTCTTTTTCCATTAGGCC 57.278 39.130 0.00 0.00 33.74 5.19
2649 10934 5.414765 ACTTCTTTTTCCATTAGGCCGTTAG 59.585 40.000 0.00 0.00 33.74 2.34
2664 10949 2.353704 CCGTTAGCTCATGAACTGGTCA 60.354 50.000 8.93 0.00 41.67 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.459089 GTCCCTGACCGAGCCAGC 62.459 72.222 0.00 0.00 0.00 4.85
6 7 3.775654 GGTCCCTGACCGAGCCAG 61.776 72.222 0.00 0.00 43.14 4.85
37 38 4.709840 GATGATGGGCCATCTCGG 57.290 61.111 38.44 0.00 41.06 4.63
44 45 0.398318 GGTAGGTCAGATGATGGGCC 59.602 60.000 0.00 0.00 0.00 5.80
65 3789 0.528017 TAGTCGAAGCTCTGCCACAG 59.472 55.000 0.00 0.00 0.00 3.66
139 3863 6.426025 TCTTTGAGATGATATGGCGATTCAAG 59.574 38.462 0.00 0.00 0.00 3.02
325 4587 3.355378 TCACACTAAGCAATTCCCCATG 58.645 45.455 0.00 0.00 0.00 3.66
430 4692 7.026562 CCAACATTTGGTTTTCTTTTGGTTTC 58.973 34.615 0.00 0.00 45.93 2.78
471 4733 1.767759 ACCCAATACCAGCAATGCTC 58.232 50.000 4.03 0.00 36.40 4.26
556 4824 4.901250 AGACATGACCCCATCAAACTTTTT 59.099 37.500 0.00 0.00 41.93 1.94
557 4825 4.482990 AGACATGACCCCATCAAACTTTT 58.517 39.130 0.00 0.00 41.93 2.27
558 4826 4.118168 AGACATGACCCCATCAAACTTT 57.882 40.909 0.00 0.00 41.93 2.66
559 4827 3.814504 AGACATGACCCCATCAAACTT 57.185 42.857 0.00 0.00 41.93 2.66
560 4828 4.474651 TCATAGACATGACCCCATCAAACT 59.525 41.667 0.00 0.00 41.93 2.66
561 4829 4.780815 TCATAGACATGACCCCATCAAAC 58.219 43.478 0.00 0.00 41.93 2.93
572 4840 2.766263 GACCCCACTGTCATAGACATGA 59.234 50.000 0.00 0.00 41.94 3.07
573 4841 2.501316 TGACCCCACTGTCATAGACATG 59.499 50.000 0.00 0.00 41.94 3.21
574 4842 2.832838 TGACCCCACTGTCATAGACAT 58.167 47.619 0.00 0.00 41.94 3.06
575 4843 2.319025 TGACCCCACTGTCATAGACA 57.681 50.000 0.00 0.00 40.22 3.41
582 4850 3.425162 AAAGAAGATGACCCCACTGTC 57.575 47.619 0.00 0.00 35.77 3.51
583 4851 4.993705 TTAAAGAAGATGACCCCACTGT 57.006 40.909 0.00 0.00 0.00 3.55
584 4852 7.938140 TTATTTAAAGAAGATGACCCCACTG 57.062 36.000 0.00 0.00 0.00 3.66
628 4896 8.956426 CCAATGAAATTAGTAAAGCCTTCACTA 58.044 33.333 0.00 0.00 32.46 2.74
629 4897 7.451566 ACCAATGAAATTAGTAAAGCCTTCACT 59.548 33.333 0.00 0.00 32.46 3.41
630 4898 7.542130 CACCAATGAAATTAGTAAAGCCTTCAC 59.458 37.037 0.00 0.00 32.46 3.18
631 4899 7.232534 ACACCAATGAAATTAGTAAAGCCTTCA 59.767 33.333 0.00 0.00 32.46 3.02
632 4900 7.602753 ACACCAATGAAATTAGTAAAGCCTTC 58.397 34.615 0.00 0.00 32.46 3.46
633 4901 7.232534 TGACACCAATGAAATTAGTAAAGCCTT 59.767 33.333 0.00 0.00 32.46 4.35
634 4902 6.719370 TGACACCAATGAAATTAGTAAAGCCT 59.281 34.615 0.00 0.00 32.46 4.58
635 4903 6.919721 TGACACCAATGAAATTAGTAAAGCC 58.080 36.000 0.00 0.00 32.46 4.35
636 4904 8.986477 ATTGACACCAATGAAATTAGTAAAGC 57.014 30.769 0.00 0.00 41.18 3.51
639 4907 9.906660 GTCAATTGACACCAATGAAATTAGTAA 57.093 29.630 29.43 0.00 41.84 2.24
640 4908 8.519526 GGTCAATTGACACCAATGAAATTAGTA 58.480 33.333 33.42 0.00 46.47 1.82
641 4909 7.378181 GGTCAATTGACACCAATGAAATTAGT 58.622 34.615 33.42 0.00 46.47 2.24
642 4910 6.813152 GGGTCAATTGACACCAATGAAATTAG 59.187 38.462 33.42 0.00 46.47 1.73
643 4911 6.696411 GGGTCAATTGACACCAATGAAATTA 58.304 36.000 33.42 0.00 46.47 1.40
644 4912 5.550290 GGGTCAATTGACACCAATGAAATT 58.450 37.500 33.42 0.00 46.47 1.82
645 4913 5.151297 GGGTCAATTGACACCAATGAAAT 57.849 39.130 33.42 0.00 46.47 2.17
646 4914 4.599047 GGGTCAATTGACACCAATGAAA 57.401 40.909 33.42 0.00 46.47 2.69
655 4923 0.887247 CGCATTGGGGTCAATTGACA 59.113 50.000 33.42 17.80 46.47 3.58
656 4924 0.887933 ACGCATTGGGGTCAATTGAC 59.112 50.000 27.16 27.16 41.29 3.18
657 4925 3.355077 ACGCATTGGGGTCAATTGA 57.645 47.368 3.38 3.38 41.29 2.57
664 4932 2.933287 TCAGGGACGCATTGGGGT 60.933 61.111 5.65 0.00 43.72 4.95
665 4933 2.124570 CTCAGGGACGCATTGGGG 60.125 66.667 5.65 0.00 0.00 4.96
666 4934 1.450312 GACTCAGGGACGCATTGGG 60.450 63.158 0.00 0.00 0.00 4.12
667 4935 0.107508 ATGACTCAGGGACGCATTGG 60.108 55.000 0.00 0.00 0.00 3.16
668 4936 1.012086 CATGACTCAGGGACGCATTG 58.988 55.000 0.00 0.00 0.00 2.82
669 4937 0.615331 ACATGACTCAGGGACGCATT 59.385 50.000 0.00 0.00 0.00 3.56
670 4938 0.107993 CACATGACTCAGGGACGCAT 60.108 55.000 0.00 0.00 0.00 4.73
671 4939 1.293179 CACATGACTCAGGGACGCA 59.707 57.895 0.00 0.00 0.00 5.24
672 4940 1.448540 CCACATGACTCAGGGACGC 60.449 63.158 0.00 0.00 0.00 5.19
673 4941 0.321671 AACCACATGACTCAGGGACG 59.678 55.000 0.00 0.00 0.00 4.79
674 4942 2.427506 GAAACCACATGACTCAGGGAC 58.572 52.381 0.00 0.00 0.00 4.46
675 4943 1.351017 GGAAACCACATGACTCAGGGA 59.649 52.381 0.00 0.00 0.00 4.20
676 4944 1.352352 AGGAAACCACATGACTCAGGG 59.648 52.381 0.00 0.00 0.00 4.45
677 4945 2.430465 CAGGAAACCACATGACTCAGG 58.570 52.381 0.00 0.00 0.00 3.86
678 4946 1.808945 GCAGGAAACCACATGACTCAG 59.191 52.381 0.00 0.00 0.00 3.35
679 4947 1.545428 GGCAGGAAACCACATGACTCA 60.545 52.381 0.00 0.00 0.00 3.41
680 4948 1.168714 GGCAGGAAACCACATGACTC 58.831 55.000 0.00 0.00 0.00 3.36
681 4949 0.606401 CGGCAGGAAACCACATGACT 60.606 55.000 0.00 0.00 0.00 3.41
682 4950 0.605319 TCGGCAGGAAACCACATGAC 60.605 55.000 0.00 0.00 0.00 3.06
683 4951 0.327924 ATCGGCAGGAAACCACATGA 59.672 50.000 0.00 0.00 0.00 3.07
684 4952 2.036958 TATCGGCAGGAAACCACATG 57.963 50.000 0.00 0.00 0.00 3.21
685 4953 3.391296 AGTATATCGGCAGGAAACCACAT 59.609 43.478 0.00 0.00 0.00 3.21
722 4990 1.882623 GGCTATAATTCCAGCAGCACC 59.117 52.381 11.95 0.00 39.63 5.01
855 5124 1.666888 GCACCATCAAGCCTTTTGACG 60.667 52.381 0.00 0.00 0.00 4.35
1362 5649 7.405292 ATGATGTTTCAAGTGAGGAATTCCTA 58.595 34.615 27.12 12.55 40.20 2.94
1539 5835 4.705991 TCATTATCTTGGATGCAGCAACAA 59.294 37.500 3.51 13.44 0.00 2.83
1545 5841 6.688637 TCAAACTCATTATCTTGGATGCAG 57.311 37.500 0.00 0.00 0.00 4.41
1750 6048 9.609950 GAAGCGAACTACTCTACGAATTATTAT 57.390 33.333 0.00 0.00 0.00 1.28
1751 6049 7.795734 CGAAGCGAACTACTCTACGAATTATTA 59.204 37.037 0.00 0.00 0.00 0.98
1752 6050 6.632035 CGAAGCGAACTACTCTACGAATTATT 59.368 38.462 0.00 0.00 0.00 1.40
1755 6053 4.142730 ACGAAGCGAACTACTCTACGAATT 60.143 41.667 0.00 0.00 0.00 2.17
1756 6054 3.373439 ACGAAGCGAACTACTCTACGAAT 59.627 43.478 0.00 0.00 0.00 3.34
1808 6161 3.265995 TCCTTCCTTTATTCCTTCCGCTT 59.734 43.478 0.00 0.00 0.00 4.68
1812 6165 3.053619 TGCCTCCTTCCTTTATTCCTTCC 60.054 47.826 0.00 0.00 0.00 3.46
1836 6189 3.006110 CAGATGATTTGGCAACCACAAGT 59.994 43.478 0.00 0.00 30.78 3.16
1841 6194 1.927487 AGCAGATGATTTGGCAACCA 58.073 45.000 0.00 1.16 0.00 3.67
1842 6195 4.660789 AATAGCAGATGATTTGGCAACC 57.339 40.909 0.00 0.00 0.00 3.77
1847 6200 8.687824 AAAAACGTAAATAGCAGATGATTTGG 57.312 30.769 0.00 0.00 0.00 3.28
1877 6230 5.982890 ATTTTGCTACACTTGCTTACCAT 57.017 34.783 0.00 0.00 0.00 3.55
1879 6232 6.852664 ACATATTTTGCTACACTTGCTTACC 58.147 36.000 0.00 0.00 0.00 2.85
1880 6233 7.693951 CAGACATATTTTGCTACACTTGCTTAC 59.306 37.037 0.00 0.00 0.00 2.34
1881 6234 7.390440 ACAGACATATTTTGCTACACTTGCTTA 59.610 33.333 0.00 0.00 0.00 3.09
1887 6241 5.248640 AGCACAGACATATTTTGCTACACT 58.751 37.500 0.00 0.00 41.72 3.55
1888 6242 5.551760 AGCACAGACATATTTTGCTACAC 57.448 39.130 0.00 0.00 41.72 2.90
1948 6352 6.183360 CCTTTTTGCTTATTGCCAAATCATCC 60.183 38.462 0.00 0.00 42.00 3.51
1949 6353 6.183360 CCCTTTTTGCTTATTGCCAAATCATC 60.183 38.462 0.00 0.00 42.00 2.92
1952 6356 5.244755 TCCCTTTTTGCTTATTGCCAAATC 58.755 37.500 0.00 0.00 42.00 2.17
1953 6357 5.240013 TCCCTTTTTGCTTATTGCCAAAT 57.760 34.783 0.00 0.00 42.00 2.32
1955 6359 3.556843 GCTCCCTTTTTGCTTATTGCCAA 60.557 43.478 0.00 0.00 42.00 4.52
1956 6360 2.028203 GCTCCCTTTTTGCTTATTGCCA 60.028 45.455 0.00 0.00 42.00 4.92
1959 7011 3.244976 CGTGCTCCCTTTTTGCTTATTG 58.755 45.455 0.00 0.00 0.00 1.90
1962 7014 1.877443 GACGTGCTCCCTTTTTGCTTA 59.123 47.619 0.00 0.00 0.00 3.09
1965 7017 0.383949 TTGACGTGCTCCCTTTTTGC 59.616 50.000 0.00 0.00 0.00 3.68
1966 7018 2.159310 TGTTTGACGTGCTCCCTTTTTG 60.159 45.455 0.00 0.00 0.00 2.44
1979 7031 3.674753 GCATTTCCCAGAAATGTTTGACG 59.325 43.478 23.73 4.99 39.25 4.35
2020 8442 7.250569 TGCACAGTTTCAAAGACTTCTTTAAG 58.749 34.615 3.91 0.00 43.72 1.85
2021 8443 7.151999 TGCACAGTTTCAAAGACTTCTTTAA 57.848 32.000 3.91 0.00 43.72 1.52
2023 8445 5.643379 TGCACAGTTTCAAAGACTTCTTT 57.357 34.783 0.00 0.00 46.23 2.52
2024 8446 5.643379 TTGCACAGTTTCAAAGACTTCTT 57.357 34.783 0.00 0.00 37.91 2.52
2025 8447 5.643379 TTTGCACAGTTTCAAAGACTTCT 57.357 34.783 0.00 0.00 0.00 2.85
2026 8448 5.863935 ACTTTTGCACAGTTTCAAAGACTTC 59.136 36.000 10.85 0.00 34.21 3.01
2027 8449 5.783111 ACTTTTGCACAGTTTCAAAGACTT 58.217 33.333 10.85 0.00 34.21 3.01
2028 8450 5.391312 ACTTTTGCACAGTTTCAAAGACT 57.609 34.783 10.85 0.00 34.21 3.24
2029 8451 6.751888 ACATACTTTTGCACAGTTTCAAAGAC 59.248 34.615 10.85 0.00 34.21 3.01
2030 8452 6.862209 ACATACTTTTGCACAGTTTCAAAGA 58.138 32.000 10.85 0.00 34.21 2.52
2031 8453 6.974622 AGACATACTTTTGCACAGTTTCAAAG 59.025 34.615 3.08 3.45 34.21 2.77
2032 8454 6.751425 CAGACATACTTTTGCACAGTTTCAAA 59.249 34.615 3.08 0.00 0.00 2.69
2038 8460 2.554032 GGCAGACATACTTTTGCACAGT 59.446 45.455 3.29 3.29 38.27 3.55
2077 8499 3.084536 TGGCCATGCTATCACAGAAAA 57.915 42.857 0.00 0.00 0.00 2.29
2104 8526 3.896888 TCATTGTTTTCCACTTCAGCCAT 59.103 39.130 0.00 0.00 0.00 4.40
2125 8547 3.002791 TCATCGTTGGCAGATCAAACTC 58.997 45.455 0.00 0.00 0.00 3.01
2158 10232 1.638133 CGCTTCACTCAGAGGACATG 58.362 55.000 1.53 0.00 0.00 3.21
2159 10233 0.534412 CCGCTTCACTCAGAGGACAT 59.466 55.000 1.53 0.00 35.83 3.06
2160 10234 0.539669 TCCGCTTCACTCAGAGGACA 60.540 55.000 1.53 0.00 37.80 4.02
2163 10237 1.801178 GTTTTCCGCTTCACTCAGAGG 59.199 52.381 1.53 0.00 35.12 3.69
2186 10260 1.541379 TCGTCGGGAGATCAAACTCA 58.459 50.000 0.00 0.00 43.27 3.41
2238 10312 1.296727 GCGGGTAGTCTTGGCATTAC 58.703 55.000 0.00 0.00 0.00 1.89
2240 10314 0.392998 CTGCGGGTAGTCTTGGCATT 60.393 55.000 0.00 0.00 32.55 3.56
2254 10328 0.465705 TGATTCTCTTAGGGCTGCGG 59.534 55.000 0.00 0.00 0.00 5.69
2311 10385 2.715046 TCAGTAACACGGACGGACTAT 58.285 47.619 0.00 0.00 0.00 2.12
2343 10417 6.648192 TCCAAATCACAACTCCAAAATTTGT 58.352 32.000 4.92 0.00 34.08 2.83
2348 10422 6.669125 ATCATCCAAATCACAACTCCAAAA 57.331 33.333 0.00 0.00 0.00 2.44
2363 10437 7.394077 CCTTGCATACCATACATAATCATCCAA 59.606 37.037 0.00 0.00 0.00 3.53
2383 10461 2.031012 CAGCGGTCAGTCCTTGCA 59.969 61.111 0.00 0.00 0.00 4.08
2390 10468 1.947456 GGAAACTTTTCAGCGGTCAGT 59.053 47.619 4.18 0.00 38.92 3.41
2392 10470 2.341846 AGGAAACTTTTCAGCGGTCA 57.658 45.000 4.18 0.00 37.44 4.02
2416 10494 4.220382 TGCCATACTTTTGCTACAATGCTT 59.780 37.500 0.00 0.00 0.00 3.91
2450 10529 6.148645 TGCAAAGTTTTCTTGCTCGATGTATA 59.851 34.615 8.80 0.00 40.37 1.47
2553 10676 3.066380 GGTTGCGCCAAATTCTTCAATT 58.934 40.909 4.18 0.00 37.17 2.32
2616 10901 9.678941 CCTAATGGAAAAAGAAGTTGAACTTAC 57.321 33.333 11.01 5.13 35.21 2.34
2635 10920 2.146342 CATGAGCTAACGGCCTAATGG 58.854 52.381 0.00 0.00 43.05 3.16
2636 10921 3.111853 TCATGAGCTAACGGCCTAATG 57.888 47.619 0.00 0.00 43.05 1.90
2644 10929 2.959516 TGACCAGTTCATGAGCTAACG 58.040 47.619 12.11 5.48 0.00 3.18


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

AutoCloner maintained by Alex Coulton.