Multiple sequence alignment - TraesCS4A01G461500

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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 TraesCS4A01G461500 chr4A 100.000 2723 0 0 1 2723 726101767 726099045 0.000000e+00 5029
1 TraesCS4A01G461500 chr4A 83.784 1073 145 17 835 1889 725801870 725802931 0.000000e+00 990
2 TraesCS4A01G461500 chr4A 83.691 1073 146 17 835 1889 725754749 725755810 0.000000e+00 985
3 TraesCS4A01G461500 chr7A 90.881 1941 115 23 835 2723 11249544 11251474 0.000000e+00 2547
4 TraesCS4A01G461500 chr7A 83.147 1074 146 22 838 1887 11991590 11990528 0.000000e+00 948
5 TraesCS4A01G461500 chr7A 88.304 171 8 7 680 840 11249350 11249518 7.690000e-46 195
6 TraesCS4A01G461500 chr7A 85.321 109 7 4 692 792 11991808 11991701 1.330000e-18 104
7 TraesCS4A01G461500 chr7D 83.271 1076 147 21 838 1889 12380934 12379868 0.000000e+00 959
8 TraesCS4A01G461500 chr7D 93.379 589 33 3 93 676 543914008 543914595 0.000000e+00 867
9 TraesCS4A01G461500 chr7D 92.699 589 39 2 93 678 40387655 40388242 0.000000e+00 846
10 TraesCS4A01G461500 chr7D 92.675 587 37 5 93 676 631093348 631092765 0.000000e+00 841
11 TraesCS4A01G461500 chr7D 92.373 590 41 2 93 679 62676370 62676958 0.000000e+00 837
12 TraesCS4A01G461500 chr7D 85.321 109 7 4 692 792 12381152 12381045 1.330000e-18 104
13 TraesCS4A01G461500 chr3D 94.595 592 27 3 93 681 22955464 22954875 0.000000e+00 911
14 TraesCS4A01G461500 chr3D 93.174 586 36 2 93 675 22263979 22264563 0.000000e+00 857
15 TraesCS4A01G461500 chr1D 93.686 586 33 2 93 675 1448913 1448329 0.000000e+00 874
16 TraesCS4A01G461500 chr1D 93.664 584 33 2 96 676 1073459 1074041 0.000000e+00 870
17 TraesCS4A01G461500 chr5D 92.833 586 38 2 93 675 47671379 47671963 0.000000e+00 846


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 TraesCS4A01G461500 chr4A 726099045 726101767 2722 True 5029.0 5029 100.0000 1 2723 1 chr4A.!!$R1 2722
1 TraesCS4A01G461500 chr4A 725801870 725802931 1061 False 990.0 990 83.7840 835 1889 1 chr4A.!!$F2 1054
2 TraesCS4A01G461500 chr4A 725754749 725755810 1061 False 985.0 985 83.6910 835 1889 1 chr4A.!!$F1 1054
3 TraesCS4A01G461500 chr7A 11249350 11251474 2124 False 1371.0 2547 89.5925 680 2723 2 chr7A.!!$F1 2043
4 TraesCS4A01G461500 chr7A 11990528 11991808 1280 True 526.0 948 84.2340 692 1887 2 chr7A.!!$R1 1195
5 TraesCS4A01G461500 chr7D 543914008 543914595 587 False 867.0 867 93.3790 93 676 1 chr7D.!!$F3 583
6 TraesCS4A01G461500 chr7D 40387655 40388242 587 False 846.0 846 92.6990 93 678 1 chr7D.!!$F1 585
7 TraesCS4A01G461500 chr7D 631092765 631093348 583 True 841.0 841 92.6750 93 676 1 chr7D.!!$R1 583
8 TraesCS4A01G461500 chr7D 62676370 62676958 588 False 837.0 837 92.3730 93 679 1 chr7D.!!$F2 586
9 TraesCS4A01G461500 chr7D 12379868 12381152 1284 True 531.5 959 84.2960 692 1889 2 chr7D.!!$R2 1197
10 TraesCS4A01G461500 chr3D 22954875 22955464 589 True 911.0 911 94.5950 93 681 1 chr3D.!!$R1 588
11 TraesCS4A01G461500 chr3D 22263979 22264563 584 False 857.0 857 93.1740 93 675 1 chr3D.!!$F1 582
12 TraesCS4A01G461500 chr1D 1448329 1448913 584 True 874.0 874 93.6860 93 675 1 chr1D.!!$R1 582
13 TraesCS4A01G461500 chr1D 1073459 1074041 582 False 870.0 870 93.6640 96 676 1 chr1D.!!$F1 580
14 TraesCS4A01G461500 chr5D 47671379 47671963 584 False 846.0 846 92.8330 93 675 1 chr5D.!!$F1 582

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
48 49 0.037160 TTTAGCTCCGGTGGGGTTTC 59.963 55.0 0.0 0.0 37.0 2.78 F
125 126 0.038166 CAAAGTTGCCCCTCAGCCTA 59.962 55.0 0.0 0.0 0.0 3.93 F
1646 1748 0.034059 CTTGTTGGTGAGTCGGAGCT 59.966 55.0 0.0 0.0 0.0 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1326 1428 0.767375 GGCCATGGAGATCCTTAGCA 59.233 55.000 18.40 0.0 36.82 3.49 R
1674 1776 1.076412 TTTGACCAGCTTGCCCACA 60.076 52.632 0.00 0.0 0.00 4.17 R
2581 2713 0.309612 ATGCACCCACGAACGAAAAC 59.690 50.000 0.14 0.0 0.00 2.43 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
26 27 7.920160 ACAAACAAAATGACCAAATGAAGTT 57.080 28.000 0.00 0.00 0.00 2.66
27 28 8.334263 ACAAACAAAATGACCAAATGAAGTTT 57.666 26.923 0.00 0.00 0.00 2.66
28 29 8.235905 ACAAACAAAATGACCAAATGAAGTTTG 58.764 29.630 0.00 0.00 45.44 2.93
29 30 7.920160 AACAAAATGACCAAATGAAGTTTGT 57.080 28.000 0.00 0.00 44.58 2.83
30 31 7.920160 ACAAAATGACCAAATGAAGTTTGTT 57.080 28.000 0.00 0.00 44.58 2.83
31 32 8.334263 ACAAAATGACCAAATGAAGTTTGTTT 57.666 26.923 0.00 0.00 44.58 2.83
32 33 9.442047 ACAAAATGACCAAATGAAGTTTGTTTA 57.558 25.926 0.00 0.00 44.58 2.01
33 34 9.919348 CAAAATGACCAAATGAAGTTTGTTTAG 57.081 29.630 0.55 0.00 44.58 1.85
34 35 7.713764 AATGACCAAATGAAGTTTGTTTAGC 57.286 32.000 0.55 0.00 44.58 3.09
35 36 6.463995 TGACCAAATGAAGTTTGTTTAGCT 57.536 33.333 0.00 0.00 44.58 3.32
36 37 6.503524 TGACCAAATGAAGTTTGTTTAGCTC 58.496 36.000 0.00 0.00 44.58 4.09
37 38 5.842907 ACCAAATGAAGTTTGTTTAGCTCC 58.157 37.500 0.00 0.00 44.58 4.70
38 39 4.917415 CCAAATGAAGTTTGTTTAGCTCCG 59.083 41.667 0.00 0.00 44.58 4.63
39 40 4.766404 AATGAAGTTTGTTTAGCTCCGG 57.234 40.909 0.00 0.00 0.00 5.14
40 41 3.202829 TGAAGTTTGTTTAGCTCCGGT 57.797 42.857 0.00 0.00 0.00 5.28
41 42 2.875933 TGAAGTTTGTTTAGCTCCGGTG 59.124 45.455 0.00 0.00 0.00 4.94
42 43 1.892209 AGTTTGTTTAGCTCCGGTGG 58.108 50.000 0.00 0.00 0.00 4.61
43 44 0.879090 GTTTGTTTAGCTCCGGTGGG 59.121 55.000 0.00 0.00 0.00 4.61
44 45 0.250989 TTTGTTTAGCTCCGGTGGGG 60.251 55.000 0.00 0.00 37.02 4.96
45 46 1.420532 TTGTTTAGCTCCGGTGGGGT 61.421 55.000 0.00 1.38 37.00 4.95
46 47 1.377612 GTTTAGCTCCGGTGGGGTT 59.622 57.895 0.00 0.00 37.00 4.11
47 48 0.251033 GTTTAGCTCCGGTGGGGTTT 60.251 55.000 0.00 0.00 37.00 3.27
48 49 0.037160 TTTAGCTCCGGTGGGGTTTC 59.963 55.000 0.00 0.00 37.00 2.78
49 50 0.838987 TTAGCTCCGGTGGGGTTTCT 60.839 55.000 0.00 0.00 37.00 2.52
50 51 0.838987 TAGCTCCGGTGGGGTTTCTT 60.839 55.000 0.00 0.00 37.00 2.52
51 52 1.971695 GCTCCGGTGGGGTTTCTTG 60.972 63.158 0.00 0.00 37.00 3.02
52 53 1.303317 CTCCGGTGGGGTTTCTTGG 60.303 63.158 0.00 0.00 37.00 3.61
53 54 2.282887 CCGGTGGGGTTTCTTGGG 60.283 66.667 0.00 0.00 0.00 4.12
54 55 2.836187 CCGGTGGGGTTTCTTGGGA 61.836 63.158 0.00 0.00 0.00 4.37
55 56 1.151908 CGGTGGGGTTTCTTGGGAA 59.848 57.895 0.00 0.00 0.00 3.97
56 57 0.893727 CGGTGGGGTTTCTTGGGAAG 60.894 60.000 0.00 0.00 32.61 3.46
57 58 1.185618 GGTGGGGTTTCTTGGGAAGC 61.186 60.000 0.00 0.00 32.61 3.86
58 59 0.178961 GTGGGGTTTCTTGGGAAGCT 60.179 55.000 0.00 0.00 33.96 3.74
59 60 1.074889 GTGGGGTTTCTTGGGAAGCTA 59.925 52.381 0.00 0.00 33.96 3.32
60 61 2.000048 TGGGGTTTCTTGGGAAGCTAT 59.000 47.619 0.00 0.00 33.96 2.97
61 62 2.381961 TGGGGTTTCTTGGGAAGCTATT 59.618 45.455 0.00 0.00 33.96 1.73
62 63 3.181412 TGGGGTTTCTTGGGAAGCTATTT 60.181 43.478 0.00 0.00 33.96 1.40
63 64 3.447586 GGGGTTTCTTGGGAAGCTATTTC 59.552 47.826 0.00 0.00 33.96 2.17
64 65 4.344978 GGGTTTCTTGGGAAGCTATTTCT 58.655 43.478 0.00 0.00 36.03 2.52
65 66 5.506708 GGGTTTCTTGGGAAGCTATTTCTA 58.493 41.667 0.00 0.00 36.03 2.10
66 67 5.590663 GGGTTTCTTGGGAAGCTATTTCTAG 59.409 44.000 0.00 0.00 36.03 2.43
67 68 6.415573 GGTTTCTTGGGAAGCTATTTCTAGA 58.584 40.000 0.00 0.00 36.03 2.43
68 69 6.540551 GGTTTCTTGGGAAGCTATTTCTAGAG 59.459 42.308 0.00 0.00 36.03 2.43
69 70 6.875972 TTCTTGGGAAGCTATTTCTAGAGT 57.124 37.500 0.00 0.00 36.03 3.24
70 71 6.227298 TCTTGGGAAGCTATTTCTAGAGTG 57.773 41.667 0.00 0.00 36.03 3.51
71 72 4.408182 TGGGAAGCTATTTCTAGAGTGC 57.592 45.455 0.00 0.00 36.03 4.40
72 73 3.774766 TGGGAAGCTATTTCTAGAGTGCA 59.225 43.478 0.00 0.00 36.03 4.57
73 74 4.410228 TGGGAAGCTATTTCTAGAGTGCAT 59.590 41.667 0.00 0.00 36.03 3.96
74 75 5.602561 TGGGAAGCTATTTCTAGAGTGCATA 59.397 40.000 0.00 0.00 36.03 3.14
75 76 5.929415 GGGAAGCTATTTCTAGAGTGCATAC 59.071 44.000 0.00 0.00 36.03 2.39
76 77 6.463049 GGGAAGCTATTTCTAGAGTGCATACA 60.463 42.308 0.00 0.00 36.03 2.29
77 78 6.422400 GGAAGCTATTTCTAGAGTGCATACAC 59.578 42.308 0.00 0.00 40.25 2.90
78 79 6.980978 GAAGCTATTTCTAGAGTGCATACACA 59.019 38.462 0.00 0.00 39.81 3.72
79 80 7.655328 GAAGCTATTTCTAGAGTGCATACACAT 59.345 37.037 0.00 0.00 39.81 3.21
103 104 6.567602 ATGTATCCTTTTAGAGTGGCTCTT 57.432 37.500 3.87 0.00 41.50 2.85
125 126 0.038166 CAAAGTTGCCCCTCAGCCTA 59.962 55.000 0.00 0.00 0.00 3.93
140 141 2.056906 GCCTATTCGCCTGGTCCCAT 62.057 60.000 0.00 0.00 0.00 4.00
186 187 3.288099 CCTATTGGGTGGCTTTGCT 57.712 52.632 0.00 0.00 0.00 3.91
192 193 2.338785 GGGTGGCTTTGCTGAGAGC 61.339 63.158 0.00 0.00 42.82 4.09
258 262 2.433838 CAGGAGCTGACACGCAGG 60.434 66.667 0.00 0.00 45.03 4.85
457 461 0.390860 GCCATCACCGTCTGCTATCT 59.609 55.000 0.00 0.00 0.00 1.98
498 504 2.230508 CGAGTGGTACTGTTTGGCTCTA 59.769 50.000 0.00 0.00 0.00 2.43
657 663 4.710695 CGTGGCACTCGGCGTACA 62.711 66.667 16.72 0.00 46.16 2.90
658 664 2.125673 GTGGCACTCGGCGTACAT 60.126 61.111 11.13 0.00 46.16 2.29
680 686 7.397221 ACATCAGAATTCCAGTAGTGAATGAA 58.603 34.615 0.65 0.00 32.91 2.57
681 687 7.884877 ACATCAGAATTCCAGTAGTGAATGAAA 59.115 33.333 0.65 0.00 32.91 2.69
682 688 8.733458 CATCAGAATTCCAGTAGTGAATGAAAA 58.267 33.333 0.65 0.00 32.91 2.29
683 689 8.868522 TCAGAATTCCAGTAGTGAATGAAAAT 57.131 30.769 0.65 0.00 32.91 1.82
684 690 9.958180 TCAGAATTCCAGTAGTGAATGAAAATA 57.042 29.630 0.65 0.00 32.91 1.40
685 691 9.994432 CAGAATTCCAGTAGTGAATGAAAATAC 57.006 33.333 0.65 0.00 32.91 1.89
686 692 9.965902 AGAATTCCAGTAGTGAATGAAAATACT 57.034 29.630 0.65 0.00 32.91 2.12
721 727 7.771927 AATGTGAGAAGATCCAAATTGAACT 57.228 32.000 0.00 0.00 0.00 3.01
725 731 5.222109 TGAGAAGATCCAAATTGAACTCCCA 60.222 40.000 0.00 0.00 0.00 4.37
774 788 8.738645 AAGTATTAATGTGAGGAGATCCAAAC 57.261 34.615 0.92 0.00 38.89 2.93
792 806 4.878397 CCAAACTGAAGACCCACATATCTC 59.122 45.833 0.00 0.00 0.00 2.75
793 807 4.762289 AACTGAAGACCCACATATCTCC 57.238 45.455 0.00 0.00 0.00 3.71
794 808 3.724478 ACTGAAGACCCACATATCTCCA 58.276 45.455 0.00 0.00 0.00 3.86
798 821 4.103153 TGAAGACCCACATATCTCCATTCC 59.897 45.833 0.00 0.00 0.00 3.01
808 831 6.015918 ACATATCTCCATTCCTGGACTCTAG 58.984 44.000 0.00 0.00 46.95 2.43
953 1038 0.816825 ATCTATGGCCAAGCAGCACG 60.817 55.000 10.96 0.00 0.00 5.34
955 1040 3.916414 TATGGCCAAGCAGCACGCA 62.916 57.895 10.96 0.00 46.13 5.24
968 1053 3.825308 CAGCACGCAACATTTATGAACT 58.175 40.909 0.00 0.00 0.00 3.01
1111 1211 5.822519 CCAACTAGCCTTATAGCAATGTCAA 59.177 40.000 0.00 0.00 34.23 3.18
1170 1270 3.054139 TCCTTTCCACTATCATTGCTGCT 60.054 43.478 0.00 0.00 0.00 4.24
1314 1416 3.020984 GTCAACCCTCAAGTTGGACAAA 58.979 45.455 2.34 0.00 45.81 2.83
1486 1588 2.165301 GTGGACTACGACCGCATGC 61.165 63.158 7.91 7.91 37.78 4.06
1488 1590 1.033202 TGGACTACGACCGCATGCTA 61.033 55.000 17.13 0.00 0.00 3.49
1511 1613 6.839124 AAGCATCCTCAAAATATGTGACAA 57.161 33.333 0.00 0.00 0.00 3.18
1520 1622 9.726232 CCTCAAAATATGTGACAACATGATAAG 57.274 33.333 0.00 0.00 46.66 1.73
1521 1623 9.229784 CTCAAAATATGTGACAACATGATAAGC 57.770 33.333 0.00 0.00 46.66 3.09
1531 1633 4.180817 CAACATGATAAGCGAGTACCACA 58.819 43.478 0.00 0.00 0.00 4.17
1534 1636 4.643334 ACATGATAAGCGAGTACCACAGTA 59.357 41.667 0.00 0.00 0.00 2.74
1571 1673 0.103208 GATGGATCGCGGTCTTCTGT 59.897 55.000 20.42 0.69 0.00 3.41
1581 1683 3.630013 TCTTCTGTGCTGCCCGCT 61.630 61.111 0.00 0.00 40.11 5.52
1589 1691 2.050077 GCTGCCCGCTTGTTTGAC 60.050 61.111 0.00 0.00 35.14 3.18
1630 1732 3.181530 CGTCGACATTTGGCTAAGACTTG 60.182 47.826 17.16 0.00 0.00 3.16
1634 1736 4.613622 CGACATTTGGCTAAGACTTGTTGG 60.614 45.833 0.00 0.00 0.00 3.77
1636 1738 4.037923 ACATTTGGCTAAGACTTGTTGGTG 59.962 41.667 0.00 0.00 0.00 4.17
1638 1740 3.126001 TGGCTAAGACTTGTTGGTGAG 57.874 47.619 0.00 0.00 0.00 3.51
1645 1747 0.249911 ACTTGTTGGTGAGTCGGAGC 60.250 55.000 0.00 0.00 0.00 4.70
1646 1748 0.034059 CTTGTTGGTGAGTCGGAGCT 59.966 55.000 0.00 0.00 0.00 4.09
1674 1776 3.123804 GTTGTCCGATGATTACGATGCT 58.876 45.455 0.00 0.00 0.00 3.79
1862 1964 5.520288 CACTTGTGATATATGCGTATAGGCC 59.480 44.000 14.48 0.00 0.00 5.19
1918 2020 4.008933 GTGGCTCTCGGGTGCTGT 62.009 66.667 9.52 0.00 33.10 4.40
1939 2041 6.357579 TGTTGGACCTGAATTGCAATAATT 57.642 33.333 13.39 0.00 0.00 1.40
1940 2042 6.767456 TGTTGGACCTGAATTGCAATAATTT 58.233 32.000 13.39 0.00 0.00 1.82
2052 2156 2.890808 TGCCTTCTAGCGTAATCTGG 57.109 50.000 0.00 0.00 34.65 3.86
2061 2165 0.461339 GCGTAATCTGGGCGGAAAGA 60.461 55.000 0.00 0.00 0.00 2.52
2072 2176 4.123506 TGGGCGGAAAGAAAAACAAAATC 58.876 39.130 0.00 0.00 0.00 2.17
2109 2213 9.877178 ACGAGTTACTATTCATGATTTTTCTCT 57.123 29.630 0.00 0.00 0.00 3.10
2116 2220 9.745018 ACTATTCATGATTTTTCTCTCAGGAAA 57.255 29.630 0.00 0.00 43.03 3.13
2121 2225 9.745018 TCATGATTTTTCTCTCAGGAAATTAGT 57.255 29.630 0.00 0.00 35.51 2.24
2128 2232 9.801873 TTTTCTCTCAGGAAATTAGTTGTTTTG 57.198 29.630 0.00 0.00 35.51 2.44
2130 2234 8.924511 TCTCTCAGGAAATTAGTTGTTTTGAT 57.075 30.769 0.00 0.00 0.00 2.57
2131 2235 9.354673 TCTCTCAGGAAATTAGTTGTTTTGATT 57.645 29.630 0.00 0.00 0.00 2.57
2133 2237 8.576442 TCTCAGGAAATTAGTTGTTTTGATTCC 58.424 33.333 0.00 0.00 36.25 3.01
2137 2241 6.304683 GGAAATTAGTTGTTTTGATTCCGACG 59.695 38.462 0.00 0.00 0.00 5.12
2202 2306 7.222000 ACAAAAGTAGGTCAACTTTGTTTCA 57.778 32.000 2.97 0.00 46.40 2.69
2204 2308 8.145122 ACAAAAGTAGGTCAACTTTGTTTCAAA 58.855 29.630 2.97 0.00 46.40 2.69
2206 2310 9.549078 AAAAGTAGGTCAACTTTGTTTCAAAAA 57.451 25.926 2.97 0.00 46.40 1.94
2289 2394 7.939588 GGTATTTCCCATCTAGAAAACAGCTAT 59.060 37.037 0.00 0.00 36.83 2.97
2292 2397 4.721776 TCCCATCTAGAAAACAGCTATGGT 59.278 41.667 0.00 0.00 0.00 3.55
2302 2407 0.532417 CAGCTATGGTGCAGCTCCTC 60.532 60.000 18.08 4.22 46.37 3.71
2321 2426 1.064134 CATGAGCACGGATCGACGA 59.936 57.895 0.00 0.00 37.61 4.20
2322 2427 0.525455 CATGAGCACGGATCGACGAA 60.525 55.000 0.00 0.00 37.61 3.85
2324 2429 0.038983 TGAGCACGGATCGACGAAAA 60.039 50.000 0.00 0.00 37.61 2.29
2334 2439 0.320946 TCGACGAAAATGTGGGACCC 60.321 55.000 2.45 2.45 0.00 4.46
2350 2455 3.787001 CCGGCCTCCACTCCCTTC 61.787 72.222 0.00 0.00 0.00 3.46
2356 2461 0.036875 CCTCCACTCCCTTCACCAAC 59.963 60.000 0.00 0.00 0.00 3.77
2384 2489 2.607187 CAGTGGGAGTACAAAGTAGCG 58.393 52.381 0.00 0.00 0.00 4.26
2385 2490 1.067071 AGTGGGAGTACAAAGTAGCGC 60.067 52.381 0.00 0.00 0.00 5.92
2386 2491 0.248289 TGGGAGTACAAAGTAGCGCC 59.752 55.000 2.29 0.00 0.00 6.53
2410 2515 0.813610 TTGCGGTGTGTTGTCCTGAG 60.814 55.000 0.00 0.00 0.00 3.35
2412 2517 1.498865 GCGGTGTGTTGTCCTGAGTG 61.499 60.000 0.00 0.00 0.00 3.51
2425 2530 4.394920 TGTCCTGAGTGAAAACTTGTTGAC 59.605 41.667 0.00 0.00 0.00 3.18
2431 2536 2.851824 GTGAAAACTTGTTGACTTGCCG 59.148 45.455 0.00 0.00 0.00 5.69
2434 2539 0.100503 AACTTGTTGACTTGCCGTGC 59.899 50.000 0.00 0.00 0.00 5.34
2463 2595 5.820947 GTCCGATGGATGTAAGGTGTATTTT 59.179 40.000 0.00 0.00 32.73 1.82
2475 2607 4.389374 AGGTGTATTTTGTCAGTGACAGG 58.611 43.478 24.25 0.00 43.69 4.00
2476 2608 3.058224 GGTGTATTTTGTCAGTGACAGGC 60.058 47.826 24.25 14.40 43.69 4.85
2562 2694 8.146412 GTCTGTACTAGTTTCTTTACTTCCCAA 58.854 37.037 0.00 0.00 0.00 4.12
2591 2726 2.093783 GGATGCACTAGGTTTTCGTTCG 59.906 50.000 0.00 0.00 0.00 3.95
2594 2729 1.193874 GCACTAGGTTTTCGTTCGTGG 59.806 52.381 0.00 0.00 0.00 4.94
2608 2743 2.665649 TCGTGGGTGCATACTAGTTG 57.334 50.000 0.00 0.52 0.00 3.16
2619 2754 7.367285 GGTGCATACTAGTTGAGATTCTAGAG 58.633 42.308 0.00 0.00 37.60 2.43
2706 2842 1.938585 TCTGTGTCCTCACTAAGGGG 58.061 55.000 0.00 0.00 46.23 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.442047 AAACTTCATTTGGTCATTTTGTTTGTA 57.558 25.926 0.00 0.00 0.00 2.41
3 4 8.603983 CAAACTTCATTTGGTCATTTTGTTTG 57.396 30.769 0.00 0.00 43.52 2.93
4 5 8.791675 AACAAACTTCATTTGGTCATTTTGTTT 58.208 25.926 0.00 0.00 45.54 2.83
5 6 8.334263 AACAAACTTCATTTGGTCATTTTGTT 57.666 26.923 0.00 0.00 45.54 2.83
6 7 7.920160 AACAAACTTCATTTGGTCATTTTGT 57.080 28.000 4.55 0.00 45.54 2.83
17 18 4.583073 ACCGGAGCTAAACAAACTTCATTT 59.417 37.500 9.46 0.00 0.00 2.32
18 19 4.023193 CACCGGAGCTAAACAAACTTCATT 60.023 41.667 9.46 0.00 0.00 2.57
19 20 3.502211 CACCGGAGCTAAACAAACTTCAT 59.498 43.478 9.46 0.00 0.00 2.57
20 21 2.875933 CACCGGAGCTAAACAAACTTCA 59.124 45.455 9.46 0.00 0.00 3.02
21 22 2.225727 CCACCGGAGCTAAACAAACTTC 59.774 50.000 9.46 0.00 0.00 3.01
22 23 2.227194 CCACCGGAGCTAAACAAACTT 58.773 47.619 9.46 0.00 0.00 2.66
23 24 1.544759 CCCACCGGAGCTAAACAAACT 60.545 52.381 9.46 0.00 0.00 2.66
24 25 0.879090 CCCACCGGAGCTAAACAAAC 59.121 55.000 9.46 0.00 0.00 2.93
25 26 0.250989 CCCCACCGGAGCTAAACAAA 60.251 55.000 9.46 0.00 0.00 2.83
26 27 1.377229 CCCCACCGGAGCTAAACAA 59.623 57.895 9.46 0.00 0.00 2.83
27 28 1.420532 AACCCCACCGGAGCTAAACA 61.421 55.000 9.46 0.00 34.64 2.83
28 29 0.251033 AAACCCCACCGGAGCTAAAC 60.251 55.000 9.46 0.00 34.64 2.01
29 30 0.037160 GAAACCCCACCGGAGCTAAA 59.963 55.000 9.46 0.00 34.64 1.85
30 31 0.838987 AGAAACCCCACCGGAGCTAA 60.839 55.000 9.46 0.00 34.64 3.09
31 32 0.838987 AAGAAACCCCACCGGAGCTA 60.839 55.000 9.46 0.00 34.64 3.32
32 33 2.154074 AAGAAACCCCACCGGAGCT 61.154 57.895 9.46 0.00 34.64 4.09
33 34 1.971695 CAAGAAACCCCACCGGAGC 60.972 63.158 9.46 0.00 34.64 4.70
34 35 1.303317 CCAAGAAACCCCACCGGAG 60.303 63.158 9.46 0.00 34.64 4.63
35 36 2.836187 CCCAAGAAACCCCACCGGA 61.836 63.158 9.46 0.00 34.64 5.14
36 37 2.282887 CCCAAGAAACCCCACCGG 60.283 66.667 0.00 0.00 37.81 5.28
37 38 0.893727 CTTCCCAAGAAACCCCACCG 60.894 60.000 0.00 0.00 0.00 4.94
38 39 1.185618 GCTTCCCAAGAAACCCCACC 61.186 60.000 0.00 0.00 0.00 4.61
39 40 0.178961 AGCTTCCCAAGAAACCCCAC 60.179 55.000 0.00 0.00 0.00 4.61
40 41 1.451449 TAGCTTCCCAAGAAACCCCA 58.549 50.000 0.00 0.00 0.00 4.96
41 42 2.828661 ATAGCTTCCCAAGAAACCCC 57.171 50.000 0.00 0.00 0.00 4.95
42 43 4.344978 AGAAATAGCTTCCCAAGAAACCC 58.655 43.478 0.00 0.00 34.21 4.11
43 44 6.415573 TCTAGAAATAGCTTCCCAAGAAACC 58.584 40.000 0.00 0.00 34.21 3.27
44 45 7.065204 CACTCTAGAAATAGCTTCCCAAGAAAC 59.935 40.741 0.00 0.00 34.21 2.78
45 46 7.106239 CACTCTAGAAATAGCTTCCCAAGAAA 58.894 38.462 0.00 0.00 34.21 2.52
46 47 6.644347 CACTCTAGAAATAGCTTCCCAAGAA 58.356 40.000 0.00 0.00 34.21 2.52
47 48 5.395768 GCACTCTAGAAATAGCTTCCCAAGA 60.396 44.000 0.00 0.00 34.21 3.02
48 49 4.813697 GCACTCTAGAAATAGCTTCCCAAG 59.186 45.833 0.00 0.00 34.21 3.61
49 50 4.225042 TGCACTCTAGAAATAGCTTCCCAA 59.775 41.667 0.00 0.00 34.21 4.12
50 51 3.774766 TGCACTCTAGAAATAGCTTCCCA 59.225 43.478 0.00 0.00 34.21 4.37
51 52 4.408182 TGCACTCTAGAAATAGCTTCCC 57.592 45.455 0.00 0.00 34.21 3.97
52 53 6.422400 GTGTATGCACTCTAGAAATAGCTTCC 59.578 42.308 6.69 0.00 42.13 3.46
53 54 6.980978 TGTGTATGCACTCTAGAAATAGCTTC 59.019 38.462 15.25 0.00 45.44 3.86
54 55 6.878317 TGTGTATGCACTCTAGAAATAGCTT 58.122 36.000 15.25 0.00 45.44 3.74
55 56 6.471233 TGTGTATGCACTCTAGAAATAGCT 57.529 37.500 15.25 0.00 45.44 3.32
56 57 8.867935 CATATGTGTATGCACTCTAGAAATAGC 58.132 37.037 15.25 0.00 45.44 2.97
57 58 9.920133 ACATATGTGTATGCACTCTAGAAATAG 57.080 33.333 15.25 1.12 45.44 1.73
73 74 8.148351 GCCACTCTAAAAGGATACATATGTGTA 58.852 37.037 18.81 4.66 44.43 2.90
74 75 6.992715 GCCACTCTAAAAGGATACATATGTGT 59.007 38.462 18.81 12.06 42.39 3.72
75 76 7.220030 AGCCACTCTAAAAGGATACATATGTG 58.780 38.462 18.81 0.00 41.41 3.21
76 77 7.291182 AGAGCCACTCTAAAAGGATACATATGT 59.709 37.037 13.93 13.93 39.28 2.29
77 78 7.675062 AGAGCCACTCTAAAAGGATACATATG 58.325 38.462 0.00 0.00 39.28 1.78
78 79 7.863901 AGAGCCACTCTAAAAGGATACATAT 57.136 36.000 0.00 0.00 39.28 1.78
79 80 7.419057 CCAAGAGCCACTCTAAAAGGATACATA 60.419 40.741 0.00 0.00 40.28 2.29
80 81 6.352516 CAAGAGCCACTCTAAAAGGATACAT 58.647 40.000 0.00 0.00 40.28 2.29
81 82 5.338381 CCAAGAGCCACTCTAAAAGGATACA 60.338 44.000 0.00 0.00 40.28 2.29
82 83 5.119694 CCAAGAGCCACTCTAAAAGGATAC 58.880 45.833 0.00 0.00 40.28 2.24
83 84 4.384208 GCCAAGAGCCACTCTAAAAGGATA 60.384 45.833 0.00 0.00 40.28 2.59
84 85 3.623453 GCCAAGAGCCACTCTAAAAGGAT 60.623 47.826 0.00 0.00 40.28 3.24
85 86 2.290323 GCCAAGAGCCACTCTAAAAGGA 60.290 50.000 0.00 0.00 40.28 3.36
86 87 2.087646 GCCAAGAGCCACTCTAAAAGG 58.912 52.381 0.00 0.19 40.28 3.11
87 88 2.783135 TGCCAAGAGCCACTCTAAAAG 58.217 47.619 0.00 0.00 40.28 2.27
88 89 2.949177 TGCCAAGAGCCACTCTAAAA 57.051 45.000 0.00 0.00 40.28 1.52
89 90 2.949177 TTGCCAAGAGCCACTCTAAA 57.051 45.000 0.00 0.00 40.28 1.85
90 91 2.106511 ACTTTGCCAAGAGCCACTCTAA 59.893 45.455 4.25 0.00 40.28 2.10
91 92 1.699634 ACTTTGCCAAGAGCCACTCTA 59.300 47.619 4.25 0.00 40.28 2.43
114 115 2.427753 GGCGAATAGGCTGAGGGG 59.572 66.667 0.00 0.00 42.90 4.79
125 126 1.072331 GACATATGGGACCAGGCGAAT 59.928 52.381 7.80 0.00 0.00 3.34
186 187 1.955495 TTTGCCGATAGCCGCTCTCA 61.955 55.000 0.00 0.00 42.71 3.27
192 193 1.721487 CCAACTTTGCCGATAGCCG 59.279 57.895 0.00 0.00 42.71 5.52
457 461 5.935789 ACTCGGCAAAATAAAGTAGCTAACA 59.064 36.000 0.00 0.00 0.00 2.41
626 632 1.890041 CCACGGACACTCGGCAAAA 60.890 57.895 0.00 0.00 0.00 2.44
656 662 7.854557 TTCATTCACTACTGGAATTCTGATG 57.145 36.000 5.23 2.04 32.86 3.07
657 663 8.868522 TTTTCATTCACTACTGGAATTCTGAT 57.131 30.769 5.23 0.00 32.86 2.90
658 664 8.868522 ATTTTCATTCACTACTGGAATTCTGA 57.131 30.769 5.23 0.00 32.86 3.27
705 711 6.745794 TTTTGGGAGTTCAATTTGGATCTT 57.254 33.333 0.00 0.00 0.00 2.40
715 721 5.048083 GCACACAGATATTTTGGGAGTTCAA 60.048 40.000 0.00 0.00 0.00 2.69
721 727 3.760738 TGTGCACACAGATATTTTGGGA 58.239 40.909 17.42 0.00 36.21 4.37
725 731 9.630098 CTTCTTATTTGTGCACACAGATATTTT 57.370 29.630 21.56 0.00 42.94 1.82
774 788 4.970860 ATGGAGATATGTGGGTCTTCAG 57.029 45.455 0.00 0.00 33.65 3.02
792 806 5.163258 ACAAATAGCTAGAGTCCAGGAATGG 60.163 44.000 0.00 0.00 0.00 3.16
793 807 5.923204 ACAAATAGCTAGAGTCCAGGAATG 58.077 41.667 0.00 0.00 0.00 2.67
794 808 7.863901 ATACAAATAGCTAGAGTCCAGGAAT 57.136 36.000 0.00 0.00 0.00 3.01
808 831 9.515226 TCCCATAGGTTCATTAATACAAATAGC 57.485 33.333 0.00 0.00 0.00 2.97
953 1038 6.851609 TGTCATGGTAGTTCATAAATGTTGC 58.148 36.000 0.00 0.00 0.00 4.17
955 1040 9.466497 AGAATGTCATGGTAGTTCATAAATGTT 57.534 29.630 0.00 0.00 0.00 2.71
1059 1144 6.372659 GTCTTGAAATGTATTGAAGCTGAGGA 59.627 38.462 0.00 0.00 0.00 3.71
1061 1146 7.375106 AGTCTTGAAATGTATTGAAGCTGAG 57.625 36.000 0.00 0.00 0.00 3.35
1062 1147 7.094634 GGAAGTCTTGAAATGTATTGAAGCTGA 60.095 37.037 0.00 0.00 0.00 4.26
1111 1211 2.371510 CAAAAACATGGTTGGGGGATGT 59.628 45.455 0.00 0.00 31.54 3.06
1326 1428 0.767375 GGCCATGGAGATCCTTAGCA 59.233 55.000 18.40 0.00 36.82 3.49
1486 1588 7.558161 TGTCACATATTTTGAGGATGCTTAG 57.442 36.000 0.00 0.00 0.00 2.18
1488 1590 6.209192 TGTTGTCACATATTTTGAGGATGCTT 59.791 34.615 0.00 0.00 0.00 3.91
1500 1602 6.763135 ACTCGCTTATCATGTTGTCACATATT 59.237 34.615 0.00 0.00 42.14 1.28
1511 1613 3.447586 ACTGTGGTACTCGCTTATCATGT 59.552 43.478 0.00 0.00 0.00 3.21
1520 1622 1.630148 CTTGCTACTGTGGTACTCGC 58.370 55.000 0.00 0.00 0.00 5.03
1521 1623 1.135083 CCCTTGCTACTGTGGTACTCG 60.135 57.143 0.00 0.00 0.00 4.18
1531 1633 4.410400 GGCACCGCCCTTGCTACT 62.410 66.667 0.00 0.00 44.06 2.57
1581 1683 4.396519 GTTCGTCAAGTTTCGTCAAACAA 58.603 39.130 2.97 0.00 43.98 2.83
1589 1691 1.714460 CGAGAGGTTCGTCAAGTTTCG 59.286 52.381 0.00 0.00 44.27 3.46
1609 1711 3.746492 ACAAGTCTTAGCCAAATGTCGAC 59.254 43.478 9.11 9.11 0.00 4.20
1630 1732 1.374758 CCAGCTCCGACTCACCAAC 60.375 63.158 0.00 0.00 0.00 3.77
1634 1736 1.270358 ACTTTTCCAGCTCCGACTCAC 60.270 52.381 0.00 0.00 0.00 3.51
1636 1738 1.801178 CAACTTTTCCAGCTCCGACTC 59.199 52.381 0.00 0.00 0.00 3.36
1638 1740 1.531578 GACAACTTTTCCAGCTCCGAC 59.468 52.381 0.00 0.00 0.00 4.79
1645 1747 5.445939 CGTAATCATCGGACAACTTTTCCAG 60.446 44.000 0.00 0.00 31.94 3.86
1646 1748 4.390603 CGTAATCATCGGACAACTTTTCCA 59.609 41.667 0.00 0.00 31.94 3.53
1674 1776 1.076412 TTTGACCAGCTTGCCCACA 60.076 52.632 0.00 0.00 0.00 4.17
1862 1964 5.291971 AGGCAGCTTTGTTATCAACTTTTG 58.708 37.500 0.00 0.00 32.93 2.44
2048 2152 2.060050 TGTTTTTCTTTCCGCCCAGA 57.940 45.000 0.00 0.00 0.00 3.86
2052 2156 5.522097 TCTTGATTTTGTTTTTCTTTCCGCC 59.478 36.000 0.00 0.00 0.00 6.13
2098 2202 9.354673 ACAACTAATTTCCTGAGAGAAAAATCA 57.645 29.630 1.33 0.00 39.11 2.57
2102 2206 9.801873 CAAAACAACTAATTTCCTGAGAGAAAA 57.198 29.630 1.33 0.00 39.11 2.29
2109 2213 7.229707 TCGGAATCAAAACAACTAATTTCCTGA 59.770 33.333 0.00 0.00 0.00 3.86
2110 2214 7.326063 GTCGGAATCAAAACAACTAATTTCCTG 59.674 37.037 0.00 0.00 0.00 3.86
2116 2220 5.934935 ACGTCGGAATCAAAACAACTAAT 57.065 34.783 0.00 0.00 0.00 1.73
2118 2222 4.211794 GGAACGTCGGAATCAAAACAACTA 59.788 41.667 0.00 0.00 0.00 2.24
2119 2223 3.002965 GGAACGTCGGAATCAAAACAACT 59.997 43.478 0.00 0.00 0.00 3.16
2120 2224 3.294102 GGAACGTCGGAATCAAAACAAC 58.706 45.455 0.00 0.00 0.00 3.32
2121 2225 2.291190 GGGAACGTCGGAATCAAAACAA 59.709 45.455 0.00 0.00 0.00 2.83
2122 2226 1.874872 GGGAACGTCGGAATCAAAACA 59.125 47.619 0.00 0.00 0.00 2.83
2123 2227 1.874872 TGGGAACGTCGGAATCAAAAC 59.125 47.619 0.00 0.00 0.00 2.43
2128 2232 0.464452 ATCCTGGGAACGTCGGAATC 59.536 55.000 0.00 0.00 0.00 2.52
2130 2234 0.688487 AAATCCTGGGAACGTCGGAA 59.312 50.000 0.00 0.00 0.00 4.30
2131 2235 0.688487 AAAATCCTGGGAACGTCGGA 59.312 50.000 0.00 0.00 0.00 4.55
2133 2237 2.870411 GGATAAAATCCTGGGAACGTCG 59.130 50.000 0.00 0.00 46.19 5.12
2156 2260 8.851541 TTGTACCCGTAAAAGAAGTTTATCAT 57.148 30.769 0.00 0.00 34.23 2.45
2157 2261 8.674263 TTTGTACCCGTAAAAGAAGTTTATCA 57.326 30.769 0.00 0.00 34.23 2.15
2159 2263 9.123902 ACTTTTGTACCCGTAAAAGAAGTTTAT 57.876 29.630 18.07 0.00 43.25 1.40
2163 2267 6.707608 CCTACTTTTGTACCCGTAAAAGAAGT 59.292 38.462 18.07 5.94 43.25 3.01
2164 2268 6.707608 ACCTACTTTTGTACCCGTAAAAGAAG 59.292 38.462 18.07 10.71 43.25 2.85
2167 2271 5.990996 TGACCTACTTTTGTACCCGTAAAAG 59.009 40.000 12.28 12.28 45.03 2.27
2256 2361 1.211949 AGATGGGAAATACCACGGTGG 59.788 52.381 25.21 25.21 44.72 4.61
2289 2394 1.907222 CTCATGGAGGAGCTGCACCA 61.907 60.000 25.38 25.38 34.07 4.17
2302 2407 1.946156 CGTCGATCCGTGCTCATGG 60.946 63.158 1.71 1.71 38.85 3.66
2311 2416 0.650512 CCCACATTTTCGTCGATCCG 59.349 55.000 0.00 0.00 0.00 4.18
2313 2418 1.664151 GGTCCCACATTTTCGTCGATC 59.336 52.381 0.00 0.00 0.00 3.69
2321 2426 2.283604 GGCCGGGTCCCACATTTT 60.284 61.111 9.12 0.00 0.00 1.82
2322 2427 3.264845 AGGCCGGGTCCCACATTT 61.265 61.111 9.12 0.00 0.00 2.32
2334 2439 3.003173 TGAAGGGAGTGGAGGCCG 61.003 66.667 0.00 0.00 0.00 6.13
2341 2446 4.379174 CCGTTGGTGAAGGGAGTG 57.621 61.111 0.00 0.00 39.14 3.51
2350 2455 3.953775 ACTGCCTCCCCGTTGGTG 61.954 66.667 0.00 0.00 34.77 4.17
2356 2461 3.976490 TACTCCCACTGCCTCCCCG 62.976 68.421 0.00 0.00 0.00 5.73
2384 2489 3.137637 AACACACCGCAAAGCAGGC 62.138 57.895 0.00 0.00 0.00 4.85
2385 2490 1.299316 CAACACACCGCAAAGCAGG 60.299 57.895 0.00 0.00 0.00 4.85
2386 2491 0.592247 GACAACACACCGCAAAGCAG 60.592 55.000 0.00 0.00 0.00 4.24
2395 2500 2.325583 TTCACTCAGGACAACACACC 57.674 50.000 0.00 0.00 0.00 4.16
2399 2504 4.331968 ACAAGTTTTCACTCAGGACAACA 58.668 39.130 0.00 0.00 31.51 3.33
2400 2505 4.965119 ACAAGTTTTCACTCAGGACAAC 57.035 40.909 0.00 0.00 30.45 3.32
2410 2515 2.851824 CGGCAAGTCAACAAGTTTTCAC 59.148 45.455 0.00 0.00 0.00 3.18
2412 2517 2.851824 CACGGCAAGTCAACAAGTTTTC 59.148 45.455 0.00 0.00 0.00 2.29
2425 2530 4.025401 GGACCAACGCACGGCAAG 62.025 66.667 0.00 0.00 0.00 4.01
2431 2536 1.449601 ATCCATCGGACCAACGCAC 60.450 57.895 0.00 0.00 32.98 5.34
2434 2539 2.201732 CTTACATCCATCGGACCAACG 58.798 52.381 0.00 0.00 32.98 4.10
2463 2595 2.229792 GATTTTGGCCTGTCACTGACA 58.770 47.619 11.44 11.44 40.50 3.58
2475 2607 3.248266 GCACTCATGAACTGATTTTGGC 58.752 45.455 0.00 0.00 32.10 4.52
2476 2608 4.508461 TGCACTCATGAACTGATTTTGG 57.492 40.909 0.00 0.00 32.10 3.28
2538 2670 8.897872 TTTGGGAAGTAAAGAAACTAGTACAG 57.102 34.615 0.00 0.00 0.00 2.74
2562 2694 7.093945 ACGAAAACCTAGTGCATCCAAATTATT 60.094 33.333 0.00 0.00 0.00 1.40
2577 2709 1.796459 CACCCACGAACGAAAACCTAG 59.204 52.381 0.14 0.00 0.00 3.02
2581 2713 0.309612 ATGCACCCACGAACGAAAAC 59.690 50.000 0.14 0.00 0.00 2.43
2591 2726 3.887621 TCTCAACTAGTATGCACCCAC 57.112 47.619 0.00 0.00 0.00 4.61
2594 2729 7.278461 TCTAGAATCTCAACTAGTATGCACC 57.722 40.000 0.00 0.00 37.78 5.01
2608 2743 6.756542 GGAAGTGAAGAAAGCTCTAGAATCTC 59.243 42.308 0.00 0.00 0.00 2.75
2619 2754 3.748568 CACACCTAGGAAGTGAAGAAAGC 59.251 47.826 25.16 0.00 38.63 3.51


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

AutoCloner maintained by Alex Coulton.