Multiple sequence alignment - TraesCS3D01G263900

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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 TraesCS3D01G263900 chr3D 100.000 2618 0 0 1 2618 365843090 365840473 0.000000e+00 4835.0
1 TraesCS3D01G263900 chr3D 98.529 1835 27 0 784 2618 134599598 134597764 0.000000e+00 3240.0
2 TraesCS3D01G263900 chr3D 97.557 1842 38 2 784 2618 593933534 593935375 0.000000e+00 3145.0
3 TraesCS3D01G263900 chr3D 98.129 1603 27 3 1018 2618 535654891 535656492 0.000000e+00 2791.0
4 TraesCS3D01G263900 chr3D 92.468 770 52 4 4 769 407864536 407863769 0.000000e+00 1096.0
5 TraesCS3D01G263900 chr3D 94.521 438 20 2 4 438 115017036 115016600 0.000000e+00 673.0
6 TraesCS3D01G263900 chr2D 96.750 1846 39 5 784 2618 472192671 472190836 0.000000e+00 3057.0
7 TraesCS3D01G263900 chr2D 93.793 435 23 3 4 435 503652543 503652976 0.000000e+00 651.0
8 TraesCS3D01G263900 chr2D 90.370 135 7 4 784 918 12974763 12974635 3.460000e-39 172.0
9 TraesCS3D01G263900 chr5D 96.676 1835 40 3 784 2618 498267538 498269351 0.000000e+00 3031.0
10 TraesCS3D01G263900 chr5D 98.607 1507 20 1 1112 2618 100988722 100990227 0.000000e+00 2665.0
11 TraesCS3D01G263900 chr5D 92.718 769 50 4 4 768 221267761 221266995 0.000000e+00 1105.0
12 TraesCS3D01G263900 chr5D 91.299 770 60 6 4 769 424935988 424935222 0.000000e+00 1044.0
13 TraesCS3D01G263900 chr5D 93.348 451 24 4 1 447 7917406 7917854 0.000000e+00 662.0
14 TraesCS3D01G263900 chr5D 94.226 433 21 2 6 435 373550364 373550795 0.000000e+00 658.0
15 TraesCS3D01G263900 chr5D 87.922 563 59 4 223 785 470737914 470737361 0.000000e+00 654.0
16 TraesCS3D01G263900 chr5D 96.073 331 9 3 784 1114 100987849 100988175 1.070000e-148 536.0
17 TraesCS3D01G263900 chr5D 91.667 96 5 2 783 877 402714441 402714534 2.110000e-26 130.0
18 TraesCS3D01G263900 chr5D 88.288 111 5 6 784 891 217012558 217012453 2.740000e-25 126.0
19 TraesCS3D01G263900 chr4B 94.941 1858 63 9 784 2618 592155477 592153628 0.000000e+00 2881.0
20 TraesCS3D01G263900 chr4B 96.794 1497 46 1 1122 2618 592031411 592029917 0.000000e+00 2497.0
21 TraesCS3D01G263900 chr4B 88.579 359 20 6 784 1126 592032074 592031721 1.450000e-112 416.0
22 TraesCS3D01G263900 chr4B 91.815 281 13 5 825 1105 24341999 24341729 1.470000e-102 383.0
23 TraesCS3D01G263900 chr4B 85.517 145 9 11 784 921 409002301 409002162 9.770000e-30 141.0
24 TraesCS3D01G263900 chr6D 98.529 1564 23 0 1055 2618 466182370 466183933 0.000000e+00 2761.0
25 TraesCS3D01G263900 chr6D 98.903 1458 16 0 1161 2618 47793110 47794567 0.000000e+00 2604.0
26 TraesCS3D01G263900 chr6D 97.581 248 6 0 870 1117 47792731 47792978 2.410000e-115 425.0
27 TraesCS3D01G263900 chr6D 90.157 254 5 4 782 1031 466181884 466182121 1.960000e-81 313.0
28 TraesCS3D01G263900 chr6D 93.684 95 4 2 784 877 436883880 436883787 9.770000e-30 141.0
29 TraesCS3D01G263900 chr6D 93.258 89 5 1 779 867 2396585 2396498 2.110000e-26 130.0
30 TraesCS3D01G263900 chr6D 91.489 94 8 0 784 877 458370605 458370698 2.110000e-26 130.0
31 TraesCS3D01G263900 chr6D 93.258 89 3 3 779 865 69905773 69905860 7.610000e-26 128.0
32 TraesCS3D01G263900 chr6D 94.937 79 4 0 783 861 270572669 270572591 9.840000e-25 124.0
33 TraesCS3D01G263900 chr6D 96.104 77 1 2 777 851 433247114 433247190 9.840000e-25 124.0
34 TraesCS3D01G263900 chr7D 86.875 640 66 12 150 785 443429509 443430134 0.000000e+00 701.0
35 TraesCS3D01G263900 chr7D 94.059 404 20 3 385 785 420188165 420187763 6.190000e-171 610.0
36 TraesCS3D01G263900 chr4D 86.342 637 71 11 150 785 344446160 344445539 0.000000e+00 680.0
37 TraesCS3D01G263900 chr4D 93.891 442 22 3 1 438 66979543 66979103 0.000000e+00 662.0
38 TraesCS3D01G263900 chr4D 94.030 402 22 2 385 785 318588559 318588159 2.230000e-170 608.0
39 TraesCS3D01G263900 chr4D 92.308 104 5 3 775 877 410646849 410646950 7.550000e-31 145.0
40 TraesCS3D01G263900 chr4D 93.684 95 4 2 784 877 31537723 31537816 9.770000e-30 141.0
41 TraesCS3D01G263900 chr4D 92.553 94 7 0 784 877 440274766 440274673 4.540000e-28 135.0
42 TraesCS3D01G263900 chr4D 91.489 94 7 1 784 877 484240341 484240433 7.610000e-26 128.0
43 TraesCS3D01G263900 chr2B 84.894 662 85 8 126 784 462081633 462080984 0.000000e+00 654.0
44 TraesCS3D01G263900 chr1D 93.379 438 25 2 4 438 137176098 137175662 0.000000e+00 645.0
45 TraesCS3D01G263900 chr1D 92.534 442 23 6 875 1316 59971 59540 2.210000e-175 625.0
46 TraesCS3D01G263900 chr1D 92.632 95 7 0 783 877 50904679 50904585 1.260000e-28 137.0
47 TraesCS3D01G263900 chr1D 90.566 106 6 2 781 886 333336564 333336463 1.260000e-28 137.0
48 TraesCS3D01G263900 chr1D 95.181 83 3 1 784 866 462983821 462983740 2.110000e-26 130.0
49 TraesCS3D01G263900 chr2A 88.983 472 26 10 787 1257 659088709 659088263 6.330000e-156 560.0
50 TraesCS3D01G263900 chr7B 88.255 298 18 10 820 1117 699546962 699546682 8.970000e-90 340.0
51 TraesCS3D01G263900 chr5B 88.525 122 6 7 784 900 25288299 25288417 9.770000e-30 141.0
52 TraesCS3D01G263900 chrUn 96.386 83 3 0 785 867 90486443 90486525 1.260000e-28 137.0
53 TraesCS3D01G263900 chrUn 94.118 85 4 1 783 867 414321322 414321405 7.610000e-26 128.0
54 TraesCS3D01G263900 chrUn 93.182 88 3 3 780 866 92586355 92586270 2.740000e-25 126.0
55 TraesCS3D01G263900 chrUn 92.500 80 5 1 783 862 252250958 252251036 2.130000e-21 113.0
56 TraesCS3D01G263900 chrUn 92.500 80 5 1 783 862 362469965 362469887 2.130000e-21 113.0
57 TraesCS3D01G263900 chrUn 98.305 59 1 0 784 842 70952618 70952560 1.280000e-18 104.0
58 TraesCS3D01G263900 chrUn 86.316 95 8 5 783 875 199235067 199235158 5.960000e-17 99.0
59 TraesCS3D01G263900 chrUn 94.915 59 3 0 784 842 26614127 26614185 2.770000e-15 93.5
60 TraesCS3D01G263900 chrUn 94.915 59 3 0 784 842 38416276 38416334 2.770000e-15 93.5
61 TraesCS3D01G263900 chrUn 83.158 95 10 5 784 877 34343751 34343840 6.010000e-12 82.4


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 TraesCS3D01G263900 chr3D 365840473 365843090 2617 True 4835.0 4835 100.0000 1 2618 1 chr3D.!!$R3 2617
1 TraesCS3D01G263900 chr3D 134597764 134599598 1834 True 3240.0 3240 98.5290 784 2618 1 chr3D.!!$R2 1834
2 TraesCS3D01G263900 chr3D 593933534 593935375 1841 False 3145.0 3145 97.5570 784 2618 1 chr3D.!!$F2 1834
3 TraesCS3D01G263900 chr3D 535654891 535656492 1601 False 2791.0 2791 98.1290 1018 2618 1 chr3D.!!$F1 1600
4 TraesCS3D01G263900 chr3D 407863769 407864536 767 True 1096.0 1096 92.4680 4 769 1 chr3D.!!$R4 765
5 TraesCS3D01G263900 chr2D 472190836 472192671 1835 True 3057.0 3057 96.7500 784 2618 1 chr2D.!!$R2 1834
6 TraesCS3D01G263900 chr5D 498267538 498269351 1813 False 3031.0 3031 96.6760 784 2618 1 chr5D.!!$F4 1834
7 TraesCS3D01G263900 chr5D 100987849 100990227 2378 False 1600.5 2665 97.3400 784 2618 2 chr5D.!!$F5 1834
8 TraesCS3D01G263900 chr5D 221266995 221267761 766 True 1105.0 1105 92.7180 4 768 1 chr5D.!!$R2 764
9 TraesCS3D01G263900 chr5D 424935222 424935988 766 True 1044.0 1044 91.2990 4 769 1 chr5D.!!$R3 765
10 TraesCS3D01G263900 chr5D 470737361 470737914 553 True 654.0 654 87.9220 223 785 1 chr5D.!!$R4 562
11 TraesCS3D01G263900 chr4B 592153628 592155477 1849 True 2881.0 2881 94.9410 784 2618 1 chr4B.!!$R3 1834
12 TraesCS3D01G263900 chr4B 592029917 592032074 2157 True 1456.5 2497 92.6865 784 2618 2 chr4B.!!$R4 1834
13 TraesCS3D01G263900 chr6D 466181884 466183933 2049 False 1537.0 2761 94.3430 782 2618 2 chr6D.!!$F5 1836
14 TraesCS3D01G263900 chr6D 47792731 47794567 1836 False 1514.5 2604 98.2420 870 2618 2 chr6D.!!$F4 1748
15 TraesCS3D01G263900 chr7D 443429509 443430134 625 False 701.0 701 86.8750 150 785 1 chr7D.!!$F1 635
16 TraesCS3D01G263900 chr4D 344445539 344446160 621 True 680.0 680 86.3420 150 785 1 chr4D.!!$R3 635
17 TraesCS3D01G263900 chr2B 462080984 462081633 649 True 654.0 654 84.8940 126 784 1 chr2B.!!$R1 658

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
134 135 0.179 AGCCATTCGAATCCGAGCTT 59.821 50.0 7.92 0.0 46.39 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2130 3556 1.063114 TGTTCCTAGCTACTCCCTCCC 60.063 57.143 0.0 0.0 0.0 4.3 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
22 23 3.746045 TTATATCCGAGCTCCAACACC 57.254 47.619 8.47 0.00 0.00 4.16
23 24 0.389391 ATATCCGAGCTCCAACACCG 59.611 55.000 8.47 0.00 0.00 4.94
24 25 0.681887 TATCCGAGCTCCAACACCGA 60.682 55.000 8.47 0.00 0.00 4.69
25 26 1.541310 ATCCGAGCTCCAACACCGAA 61.541 55.000 8.47 0.00 0.00 4.30
26 27 2.027625 CCGAGCTCCAACACCGAAC 61.028 63.158 8.47 0.00 0.00 3.95
27 28 1.006102 CGAGCTCCAACACCGAACT 60.006 57.895 8.47 0.00 0.00 3.01
28 29 0.242825 CGAGCTCCAACACCGAACTA 59.757 55.000 8.47 0.00 0.00 2.24
29 30 1.135083 CGAGCTCCAACACCGAACTAT 60.135 52.381 8.47 0.00 0.00 2.12
30 31 2.098607 CGAGCTCCAACACCGAACTATA 59.901 50.000 8.47 0.00 0.00 1.31
31 32 3.243434 CGAGCTCCAACACCGAACTATAT 60.243 47.826 8.47 0.00 0.00 0.86
32 33 4.299978 GAGCTCCAACACCGAACTATATC 58.700 47.826 0.87 0.00 0.00 1.63
33 34 3.961408 AGCTCCAACACCGAACTATATCT 59.039 43.478 0.00 0.00 0.00 1.98
34 35 4.051922 GCTCCAACACCGAACTATATCTG 58.948 47.826 0.00 0.00 0.00 2.90
35 36 4.202121 GCTCCAACACCGAACTATATCTGA 60.202 45.833 0.00 0.00 0.00 3.27
36 37 5.515797 TCCAACACCGAACTATATCTGAG 57.484 43.478 0.00 0.00 0.00 3.35
37 38 4.341235 TCCAACACCGAACTATATCTGAGG 59.659 45.833 0.00 0.00 0.00 3.86
38 39 4.099573 CCAACACCGAACTATATCTGAGGT 59.900 45.833 0.00 0.00 0.00 3.85
40 41 4.920640 CACCGAACTATATCTGAGGTGT 57.079 45.455 3.77 0.00 41.76 4.16
41 42 4.861210 CACCGAACTATATCTGAGGTGTC 58.139 47.826 3.77 0.00 41.76 3.67
42 43 4.338400 CACCGAACTATATCTGAGGTGTCA 59.662 45.833 3.77 0.00 41.76 3.58
43 44 5.010112 CACCGAACTATATCTGAGGTGTCAT 59.990 44.000 3.77 0.00 41.76 3.06
44 45 6.206829 CACCGAACTATATCTGAGGTGTCATA 59.793 42.308 3.77 0.00 41.76 2.15
45 46 6.431543 ACCGAACTATATCTGAGGTGTCATAG 59.568 42.308 0.00 0.00 30.18 2.23
46 47 6.655425 CCGAACTATATCTGAGGTGTCATAGA 59.345 42.308 0.00 0.00 30.18 1.98
47 48 7.338196 CCGAACTATATCTGAGGTGTCATAGAT 59.662 40.741 0.00 0.00 30.18 1.98
48 49 8.394877 CGAACTATATCTGAGGTGTCATAGATC 58.605 40.741 0.00 0.00 30.18 2.75
49 50 9.237187 GAACTATATCTGAGGTGTCATAGATCA 57.763 37.037 0.00 0.00 30.18 2.92
50 51 8.574251 ACTATATCTGAGGTGTCATAGATCAC 57.426 38.462 0.00 0.00 30.18 3.06
57 58 3.550437 GTGTCATAGATCACCTTGGCT 57.450 47.619 0.00 0.00 0.00 4.75
58 59 3.878778 GTGTCATAGATCACCTTGGCTT 58.121 45.455 0.00 0.00 0.00 4.35
59 60 3.624861 GTGTCATAGATCACCTTGGCTTG 59.375 47.826 0.00 0.00 0.00 4.01
60 61 3.519107 TGTCATAGATCACCTTGGCTTGA 59.481 43.478 0.00 0.00 0.00 3.02
61 62 4.019411 TGTCATAGATCACCTTGGCTTGAA 60.019 41.667 0.00 0.00 0.00 2.69
62 63 4.943705 GTCATAGATCACCTTGGCTTGAAA 59.056 41.667 0.00 0.00 0.00 2.69
63 64 5.415701 GTCATAGATCACCTTGGCTTGAAAA 59.584 40.000 0.00 0.00 0.00 2.29
64 65 6.009589 TCATAGATCACCTTGGCTTGAAAAA 58.990 36.000 0.00 0.00 0.00 1.94
65 66 4.861102 AGATCACCTTGGCTTGAAAAAG 57.139 40.909 0.00 0.00 0.00 2.27
66 67 4.218312 AGATCACCTTGGCTTGAAAAAGT 58.782 39.130 0.00 0.00 0.00 2.66
67 68 4.651045 AGATCACCTTGGCTTGAAAAAGTT 59.349 37.500 0.00 0.00 0.00 2.66
68 69 4.385358 TCACCTTGGCTTGAAAAAGTTC 57.615 40.909 0.00 0.00 0.00 3.01
69 70 3.115554 CACCTTGGCTTGAAAAAGTTCG 58.884 45.455 0.00 0.00 36.46 3.95
70 71 3.020984 ACCTTGGCTTGAAAAAGTTCGA 58.979 40.909 0.00 0.00 36.46 3.71
71 72 3.445805 ACCTTGGCTTGAAAAAGTTCGAA 59.554 39.130 0.00 0.00 36.46 3.71
72 73 4.044426 CCTTGGCTTGAAAAAGTTCGAAG 58.956 43.478 0.00 0.00 36.46 3.79
73 74 3.708563 TGGCTTGAAAAAGTTCGAAGG 57.291 42.857 0.00 0.00 36.46 3.46
74 75 3.283751 TGGCTTGAAAAAGTTCGAAGGA 58.716 40.909 0.00 0.00 36.46 3.36
75 76 3.315191 TGGCTTGAAAAAGTTCGAAGGAG 59.685 43.478 0.00 0.00 36.46 3.69
76 77 3.304726 GGCTTGAAAAAGTTCGAAGGAGG 60.305 47.826 0.00 0.00 36.46 4.30
77 78 3.315470 GCTTGAAAAAGTTCGAAGGAGGT 59.685 43.478 0.00 0.00 36.46 3.85
78 79 4.202020 GCTTGAAAAAGTTCGAAGGAGGTT 60.202 41.667 0.00 0.00 36.46 3.50
79 80 5.008316 GCTTGAAAAAGTTCGAAGGAGGTTA 59.992 40.000 0.00 0.00 36.46 2.85
80 81 6.294010 GCTTGAAAAAGTTCGAAGGAGGTTAT 60.294 38.462 0.00 0.00 36.46 1.89
81 82 6.796705 TGAAAAAGTTCGAAGGAGGTTATC 57.203 37.500 0.00 0.00 36.46 1.75
82 83 5.704053 TGAAAAAGTTCGAAGGAGGTTATCC 59.296 40.000 0.00 0.00 41.70 2.59
83 84 7.507425 TGAAAAAGTTCGAAGGAGGTTATCCG 61.507 42.308 0.00 0.00 44.15 4.18
84 85 9.566778 TGAAAAAGTTCGAAGGAGGTTATCCGA 62.567 40.741 0.00 0.00 44.15 4.55
93 94 2.862536 GGAGGTTATCCGAGTTTAACGC 59.137 50.000 0.00 0.00 38.67 4.84
94 95 3.429960 GGAGGTTATCCGAGTTTAACGCT 60.430 47.826 0.00 0.00 38.67 5.07
95 96 3.518590 AGGTTATCCGAGTTTAACGCTG 58.481 45.455 0.00 0.00 39.05 5.18
96 97 3.194116 AGGTTATCCGAGTTTAACGCTGA 59.806 43.478 0.00 0.00 39.05 4.26
97 98 3.928375 GGTTATCCGAGTTTAACGCTGAA 59.072 43.478 0.00 0.00 30.66 3.02
98 99 4.389687 GGTTATCCGAGTTTAACGCTGAAA 59.610 41.667 0.00 0.00 30.66 2.69
99 100 5.106987 GGTTATCCGAGTTTAACGCTGAAAA 60.107 40.000 0.00 0.00 30.66 2.29
100 101 4.663636 ATCCGAGTTTAACGCTGAAAAG 57.336 40.909 0.00 0.00 0.00 2.27
101 102 3.460103 TCCGAGTTTAACGCTGAAAAGT 58.540 40.909 0.00 0.00 0.00 2.66
102 103 3.872771 TCCGAGTTTAACGCTGAAAAGTT 59.127 39.130 0.00 0.00 0.00 2.66
103 104 4.025480 TCCGAGTTTAACGCTGAAAAGTTC 60.025 41.667 0.00 0.00 0.00 3.01
104 105 4.025145 CCGAGTTTAACGCTGAAAAGTTCT 60.025 41.667 0.00 0.00 0.00 3.01
105 106 5.499047 CGAGTTTAACGCTGAAAAGTTCTT 58.501 37.500 0.00 0.00 0.00 2.52
106 107 5.963586 CGAGTTTAACGCTGAAAAGTTCTTT 59.036 36.000 0.00 0.00 0.00 2.52
107 108 7.121272 CGAGTTTAACGCTGAAAAGTTCTTTA 58.879 34.615 0.00 0.00 0.00 1.85
108 109 7.797123 CGAGTTTAACGCTGAAAAGTTCTTTAT 59.203 33.333 0.00 0.00 0.00 1.40
109 110 8.782533 AGTTTAACGCTGAAAAGTTCTTTATG 57.217 30.769 0.00 0.00 0.00 1.90
110 111 7.860872 AGTTTAACGCTGAAAAGTTCTTTATGG 59.139 33.333 0.00 0.00 0.00 2.74
111 112 7.499321 TTAACGCTGAAAAGTTCTTTATGGA 57.501 32.000 0.00 0.00 0.00 3.41
112 113 6.385649 AACGCTGAAAAGTTCTTTATGGAA 57.614 33.333 0.00 0.00 0.00 3.53
113 114 5.758924 ACGCTGAAAAGTTCTTTATGGAAC 58.241 37.500 0.00 0.00 44.02 3.62
114 115 4.846137 CGCTGAAAAGTTCTTTATGGAACG 59.154 41.667 0.00 0.00 46.99 3.95
115 116 5.333798 CGCTGAAAAGTTCTTTATGGAACGA 60.334 40.000 0.00 0.00 46.99 3.85
116 117 6.080406 GCTGAAAAGTTCTTTATGGAACGAG 58.920 40.000 0.00 0.00 46.99 4.18
117 118 5.997385 TGAAAAGTTCTTTATGGAACGAGC 58.003 37.500 0.00 0.00 46.99 5.03
118 119 5.048991 TGAAAAGTTCTTTATGGAACGAGCC 60.049 40.000 0.00 0.00 46.99 4.70
119 120 3.695830 AGTTCTTTATGGAACGAGCCA 57.304 42.857 3.65 3.65 46.99 4.75
121 122 4.589908 AGTTCTTTATGGAACGAGCCATT 58.410 39.130 16.56 4.54 46.29 3.16
122 123 4.636206 AGTTCTTTATGGAACGAGCCATTC 59.364 41.667 16.56 0.00 46.29 2.67
134 135 0.179000 AGCCATTCGAATCCGAGCTT 59.821 50.000 7.92 0.00 46.39 3.74
135 136 1.017387 GCCATTCGAATCCGAGCTTT 58.983 50.000 7.92 0.00 46.39 3.51
137 138 2.808543 GCCATTCGAATCCGAGCTTTAT 59.191 45.455 7.92 0.00 46.39 1.40
138 139 3.364366 GCCATTCGAATCCGAGCTTTATG 60.364 47.826 7.92 0.00 46.39 1.90
139 140 3.364366 CCATTCGAATCCGAGCTTTATGC 60.364 47.826 7.92 0.00 46.39 3.14
141 142 0.508641 CGAATCCGAGCTTTATGCCG 59.491 55.000 0.00 0.00 44.23 5.69
146 147 1.153449 CGAGCTTTATGCCGGACCA 60.153 57.895 5.05 0.00 44.23 4.02
147 148 1.429148 CGAGCTTTATGCCGGACCAC 61.429 60.000 5.05 0.00 44.23 4.16
163 165 1.289066 CACTTCCGAGCTCCAACGA 59.711 57.895 8.47 0.00 0.00 3.85
175 177 3.465990 CCAACGATGGTCAGCATCT 57.534 52.632 14.79 0.00 42.18 2.90
183 185 1.059098 TGGTCAGCATCTGAGGTGTT 58.941 50.000 0.00 0.00 41.46 3.32
225 512 8.864069 TTTTAAAAGATTGAACGAATTCAGCA 57.136 26.923 6.22 0.00 45.54 4.41
243 530 1.202188 GCAGAGCTTAATGCCGGAAAC 60.202 52.381 5.05 0.00 44.23 2.78
435 728 2.169769 TCGGCCTAAAAATCCGAGATGT 59.830 45.455 0.00 0.00 46.12 3.06
456 749 9.875708 AGATGTACTTTAGAGGAGATAGTGATT 57.124 33.333 0.00 0.00 0.00 2.57
459 752 7.839705 TGTACTTTAGAGGAGATAGTGATTGGT 59.160 37.037 0.00 0.00 0.00 3.67
528 822 0.468226 TTGATGCCGGATAGGTCCAC 59.532 55.000 5.05 0.00 45.37 4.02
823 1119 0.883833 GTTGGTAGTCTCCGTTCCGA 59.116 55.000 0.00 0.00 0.00 4.55
843 1139 3.499157 CGAGTTTATTTTCGTCCCACCAA 59.501 43.478 0.00 0.00 32.44 3.67
851 1147 0.682852 TCGTCCCACCAATTTCGTCT 59.317 50.000 0.00 0.00 0.00 4.18
1819 3243 5.450818 AAGAATACTATCTTGGGTGGCAA 57.549 39.130 0.00 0.00 38.22 4.52
1932 3358 0.119155 TGTCTGGTTGGGGAGAGGAT 59.881 55.000 0.00 0.00 0.00 3.24
2045 3471 5.368256 ACGGACTACATTCGGATGTATAC 57.632 43.478 16.89 12.96 45.20 1.47
2263 3689 4.810033 GCAGATGGGCATCCTTAGATTCAT 60.810 45.833 0.00 0.00 38.58 2.57
2312 3738 0.119155 AACCCACCTCCCTGATGAGA 59.881 55.000 0.00 0.00 34.11 3.27
2337 3763 1.696884 TGTTGGTCTCAGGCATACACA 59.303 47.619 0.00 0.00 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.246458 GGTGTTGGAGCTCGGATATAATC 58.754 47.826 7.83 0.00 0.00 1.75
3 4 1.611977 CGGTGTTGGAGCTCGGATATA 59.388 52.381 7.83 0.00 0.00 0.86
4 5 0.389391 CGGTGTTGGAGCTCGGATAT 59.611 55.000 7.83 0.00 0.00 1.63
5 6 0.681887 TCGGTGTTGGAGCTCGGATA 60.682 55.000 7.83 0.00 0.00 2.59
6 7 1.541310 TTCGGTGTTGGAGCTCGGAT 61.541 55.000 7.83 0.00 0.00 4.18
7 8 2.204461 TTCGGTGTTGGAGCTCGGA 61.204 57.895 7.83 0.00 0.00 4.55
8 9 2.027625 GTTCGGTGTTGGAGCTCGG 61.028 63.158 7.83 0.00 0.00 4.63
9 10 0.242825 TAGTTCGGTGTTGGAGCTCG 59.757 55.000 7.83 0.00 0.00 5.03
10 11 2.674796 ATAGTTCGGTGTTGGAGCTC 57.325 50.000 4.71 4.71 0.00 4.09
11 12 3.961408 AGATATAGTTCGGTGTTGGAGCT 59.039 43.478 0.00 0.00 0.00 4.09
12 13 4.051922 CAGATATAGTTCGGTGTTGGAGC 58.948 47.826 0.00 0.00 0.00 4.70
13 14 5.508153 CCTCAGATATAGTTCGGTGTTGGAG 60.508 48.000 0.00 0.00 0.00 3.86
14 15 4.341235 CCTCAGATATAGTTCGGTGTTGGA 59.659 45.833 0.00 0.00 0.00 3.53
15 16 4.099573 ACCTCAGATATAGTTCGGTGTTGG 59.900 45.833 0.00 0.00 0.00 3.77
16 17 5.043903 CACCTCAGATATAGTTCGGTGTTG 58.956 45.833 0.00 0.00 36.56 3.33
17 18 5.263968 CACCTCAGATATAGTTCGGTGTT 57.736 43.478 0.00 0.00 36.56 3.32
18 19 4.279145 ACACCTCAGATATAGTTCGGTGT 58.721 43.478 5.43 5.43 46.20 4.16
19 20 4.338400 TGACACCTCAGATATAGTTCGGTG 59.662 45.833 0.00 0.00 44.41 4.94
20 21 4.533815 TGACACCTCAGATATAGTTCGGT 58.466 43.478 0.00 0.00 0.00 4.69
21 22 5.713792 ATGACACCTCAGATATAGTTCGG 57.286 43.478 0.00 0.00 0.00 4.30
22 23 7.674471 TCTATGACACCTCAGATATAGTTCG 57.326 40.000 0.00 0.00 0.00 3.95
23 24 9.237187 TGATCTATGACACCTCAGATATAGTTC 57.763 37.037 0.00 0.00 0.00 3.01
24 25 9.019656 GTGATCTATGACACCTCAGATATAGTT 57.980 37.037 0.00 0.00 0.00 2.24
25 26 8.574251 GTGATCTATGACACCTCAGATATAGT 57.426 38.462 0.00 0.00 0.00 2.12
37 38 3.550437 AGCCAAGGTGATCTATGACAC 57.450 47.619 0.00 0.00 36.44 3.67
38 39 3.519107 TCAAGCCAAGGTGATCTATGACA 59.481 43.478 0.00 0.00 0.00 3.58
39 40 4.142609 TCAAGCCAAGGTGATCTATGAC 57.857 45.455 0.00 0.00 0.00 3.06
40 41 4.842531 TTCAAGCCAAGGTGATCTATGA 57.157 40.909 0.00 0.00 0.00 2.15
41 42 5.902613 TTTTCAAGCCAAGGTGATCTATG 57.097 39.130 0.00 0.00 0.00 2.23
42 43 6.012745 ACTTTTTCAAGCCAAGGTGATCTAT 58.987 36.000 0.00 0.00 32.57 1.98
43 44 5.385198 ACTTTTTCAAGCCAAGGTGATCTA 58.615 37.500 0.00 0.00 32.57 1.98
44 45 4.218312 ACTTTTTCAAGCCAAGGTGATCT 58.782 39.130 0.00 0.00 32.57 2.75
45 46 4.590850 ACTTTTTCAAGCCAAGGTGATC 57.409 40.909 0.00 0.00 32.57 2.92
46 47 4.499696 CGAACTTTTTCAAGCCAAGGTGAT 60.500 41.667 0.00 0.00 32.57 3.06
47 48 3.181491 CGAACTTTTTCAAGCCAAGGTGA 60.181 43.478 0.00 0.00 32.57 4.02
48 49 3.115554 CGAACTTTTTCAAGCCAAGGTG 58.884 45.455 0.00 0.00 32.57 4.00
49 50 3.020984 TCGAACTTTTTCAAGCCAAGGT 58.979 40.909 0.00 0.00 32.57 3.50
50 51 3.708563 TCGAACTTTTTCAAGCCAAGG 57.291 42.857 0.00 0.00 32.57 3.61
51 52 4.044426 CCTTCGAACTTTTTCAAGCCAAG 58.956 43.478 0.00 0.00 32.57 3.61
52 53 3.697045 TCCTTCGAACTTTTTCAAGCCAA 59.303 39.130 0.00 0.00 32.57 4.52
53 54 3.283751 TCCTTCGAACTTTTTCAAGCCA 58.716 40.909 0.00 0.00 32.57 4.75
54 55 3.304726 CCTCCTTCGAACTTTTTCAAGCC 60.305 47.826 0.00 0.00 32.57 4.35
55 56 3.315470 ACCTCCTTCGAACTTTTTCAAGC 59.685 43.478 0.00 0.00 32.57 4.01
56 57 5.500645 AACCTCCTTCGAACTTTTTCAAG 57.499 39.130 0.00 0.00 35.92 3.02
57 58 6.206048 GGATAACCTCCTTCGAACTTTTTCAA 59.794 38.462 0.00 0.00 41.29 2.69
58 59 5.704053 GGATAACCTCCTTCGAACTTTTTCA 59.296 40.000 0.00 0.00 41.29 2.69
59 60 5.163884 CGGATAACCTCCTTCGAACTTTTTC 60.164 44.000 0.00 0.00 42.47 2.29
60 61 4.694037 CGGATAACCTCCTTCGAACTTTTT 59.306 41.667 0.00 0.00 42.47 1.94
61 62 4.020839 TCGGATAACCTCCTTCGAACTTTT 60.021 41.667 0.00 0.00 42.47 2.27
62 63 3.512724 TCGGATAACCTCCTTCGAACTTT 59.487 43.478 0.00 0.00 42.47 2.66
63 64 3.094572 TCGGATAACCTCCTTCGAACTT 58.905 45.455 0.00 0.00 42.47 2.66
64 65 2.688958 CTCGGATAACCTCCTTCGAACT 59.311 50.000 0.00 0.00 42.47 3.01
65 66 2.426381 ACTCGGATAACCTCCTTCGAAC 59.574 50.000 0.00 0.00 42.47 3.95
66 67 2.731572 ACTCGGATAACCTCCTTCGAA 58.268 47.619 0.00 0.00 42.47 3.71
67 68 2.431954 ACTCGGATAACCTCCTTCGA 57.568 50.000 0.00 0.00 42.47 3.71
68 69 3.521947 AAACTCGGATAACCTCCTTCG 57.478 47.619 0.00 0.00 42.47 3.79
69 70 4.802563 CGTTAAACTCGGATAACCTCCTTC 59.197 45.833 0.00 0.00 42.47 3.46
70 71 4.752146 CGTTAAACTCGGATAACCTCCTT 58.248 43.478 0.00 0.00 42.47 3.36
71 72 3.429960 GCGTTAAACTCGGATAACCTCCT 60.430 47.826 0.00 0.00 42.47 3.69
72 73 2.862536 GCGTTAAACTCGGATAACCTCC 59.137 50.000 0.00 0.00 41.07 4.30
73 74 3.550678 CAGCGTTAAACTCGGATAACCTC 59.449 47.826 0.00 0.00 0.00 3.85
74 75 3.194116 TCAGCGTTAAACTCGGATAACCT 59.806 43.478 0.00 0.00 0.00 3.50
75 76 3.514645 TCAGCGTTAAACTCGGATAACC 58.485 45.455 0.00 0.00 0.00 2.85
76 77 5.520022 TTTCAGCGTTAAACTCGGATAAC 57.480 39.130 0.00 0.00 0.00 1.89
77 78 5.697633 ACTTTTCAGCGTTAAACTCGGATAA 59.302 36.000 0.00 0.00 0.00 1.75
78 79 5.232463 ACTTTTCAGCGTTAAACTCGGATA 58.768 37.500 0.00 0.00 0.00 2.59
79 80 4.062991 ACTTTTCAGCGTTAAACTCGGAT 58.937 39.130 0.00 0.00 0.00 4.18
80 81 3.460103 ACTTTTCAGCGTTAAACTCGGA 58.540 40.909 0.00 0.00 0.00 4.55
81 82 3.872560 ACTTTTCAGCGTTAAACTCGG 57.127 42.857 0.00 0.00 0.00 4.63
82 83 5.079397 AGAACTTTTCAGCGTTAAACTCG 57.921 39.130 0.00 0.00 0.00 4.18
83 84 8.892905 CATAAAGAACTTTTCAGCGTTAAACTC 58.107 33.333 5.14 0.00 34.23 3.01
84 85 7.860872 CCATAAAGAACTTTTCAGCGTTAAACT 59.139 33.333 5.14 0.00 34.23 2.66
85 86 7.858879 TCCATAAAGAACTTTTCAGCGTTAAAC 59.141 33.333 5.14 0.00 34.23 2.01
86 87 7.932335 TCCATAAAGAACTTTTCAGCGTTAAA 58.068 30.769 5.14 0.00 34.23 1.52
87 88 7.499321 TCCATAAAGAACTTTTCAGCGTTAA 57.501 32.000 5.14 0.00 34.23 2.01
88 89 7.357303 GTTCCATAAAGAACTTTTCAGCGTTA 58.643 34.615 5.14 0.00 42.37 3.18
89 90 6.206498 GTTCCATAAAGAACTTTTCAGCGTT 58.794 36.000 5.14 0.00 42.37 4.84
90 91 5.560183 CGTTCCATAAAGAACTTTTCAGCGT 60.560 40.000 5.14 0.00 43.27 5.07
91 92 4.846137 CGTTCCATAAAGAACTTTTCAGCG 59.154 41.667 5.14 1.31 43.27 5.18
92 93 5.997385 TCGTTCCATAAAGAACTTTTCAGC 58.003 37.500 5.14 0.00 43.27 4.26
93 94 6.080406 GCTCGTTCCATAAAGAACTTTTCAG 58.920 40.000 5.14 0.00 43.27 3.02
94 95 5.048991 GGCTCGTTCCATAAAGAACTTTTCA 60.049 40.000 5.14 0.00 43.27 2.69
95 96 5.048991 TGGCTCGTTCCATAAAGAACTTTTC 60.049 40.000 5.14 0.00 43.27 2.29
96 97 4.825085 TGGCTCGTTCCATAAAGAACTTTT 59.175 37.500 5.14 0.00 43.27 2.27
97 98 4.394729 TGGCTCGTTCCATAAAGAACTTT 58.605 39.130 5.18 5.18 43.27 2.66
98 99 4.015872 TGGCTCGTTCCATAAAGAACTT 57.984 40.909 3.23 0.00 43.27 2.66
99 100 3.695830 TGGCTCGTTCCATAAAGAACT 57.304 42.857 3.23 0.00 43.27 3.01
100 101 4.494199 CGAATGGCTCGTTCCATAAAGAAC 60.494 45.833 10.66 0.00 45.64 3.01
101 102 3.621268 CGAATGGCTCGTTCCATAAAGAA 59.379 43.478 10.66 0.00 45.64 2.52
102 103 3.118920 TCGAATGGCTCGTTCCATAAAGA 60.119 43.478 10.66 8.31 45.64 2.52
103 104 3.194861 TCGAATGGCTCGTTCCATAAAG 58.805 45.455 10.66 6.62 45.64 1.85
104 105 3.254470 TCGAATGGCTCGTTCCATAAA 57.746 42.857 10.66 0.00 45.64 1.40
105 106 2.971660 TCGAATGGCTCGTTCCATAA 57.028 45.000 10.66 0.08 45.64 1.90
106 107 2.971660 TTCGAATGGCTCGTTCCATA 57.028 45.000 10.66 0.00 45.64 2.74
114 115 0.249657 AGCTCGGATTCGAATGGCTC 60.250 55.000 16.96 1.09 45.47 4.70
115 116 0.179000 AAGCTCGGATTCGAATGGCT 59.821 50.000 16.96 15.42 45.47 4.75
116 117 1.017387 AAAGCTCGGATTCGAATGGC 58.983 50.000 16.96 13.51 45.47 4.40
117 118 3.364366 GCATAAAGCTCGGATTCGAATGG 60.364 47.826 16.96 7.42 45.47 3.16
118 119 3.364366 GGCATAAAGCTCGGATTCGAATG 60.364 47.826 16.96 1.85 45.47 2.67
119 120 2.808543 GGCATAAAGCTCGGATTCGAAT 59.191 45.455 11.20 11.20 45.47 3.34
120 121 2.210116 GGCATAAAGCTCGGATTCGAA 58.790 47.619 0.00 0.00 45.47 3.71
121 122 1.865865 GGCATAAAGCTCGGATTCGA 58.134 50.000 0.00 0.00 44.79 3.71
122 123 0.508641 CGGCATAAAGCTCGGATTCG 59.491 55.000 0.00 0.00 44.79 3.34
143 144 1.371558 GTTGGAGCTCGGAAGTGGT 59.628 57.895 7.83 0.00 38.10 4.16
144 145 1.738099 CGTTGGAGCTCGGAAGTGG 60.738 63.158 7.83 0.00 0.00 4.00
146 147 0.108615 CATCGTTGGAGCTCGGAAGT 60.109 55.000 7.83 0.00 0.00 3.01
147 148 0.807667 CCATCGTTGGAGCTCGGAAG 60.808 60.000 7.83 1.09 46.92 3.46
163 165 1.283347 ACACCTCAGATGCTGACCAT 58.717 50.000 0.00 0.00 35.39 3.55
167 169 4.065088 GTTTACAACACCTCAGATGCTGA 58.935 43.478 0.00 0.00 38.25 4.26
169 171 4.357918 AGTTTACAACACCTCAGATGCT 57.642 40.909 0.00 0.00 0.00 3.79
170 172 4.392138 GGTAGTTTACAACACCTCAGATGC 59.608 45.833 0.00 0.00 32.99 3.91
171 173 5.794894 AGGTAGTTTACAACACCTCAGATG 58.205 41.667 5.45 0.00 37.98 2.90
183 185 8.203485 TCTTTTAAAAGACCGAGGTAGTTTACA 58.797 33.333 23.65 0.00 39.95 2.41
225 512 1.369625 CGTTTCCGGCATTAAGCTCT 58.630 50.000 0.00 0.00 44.79 4.09
243 530 2.739784 CTGGCTCCATAGAGGGCG 59.260 66.667 0.00 0.00 40.79 6.13
342 629 9.153721 CTTGGCAGAGAATAAATTGCAATAAAA 57.846 29.630 13.39 1.39 38.27 1.52
346 633 6.534475 TCTTGGCAGAGAATAAATTGCAAT 57.466 33.333 5.99 5.99 38.27 3.56
435 728 7.287927 CCACCAATCACTATCTCCTCTAAAGTA 59.712 40.741 0.00 0.00 0.00 2.24
459 752 3.003173 CTCTCAAGGGCCCGTCCA 61.003 66.667 18.44 0.11 36.21 4.02
528 822 7.042051 CGTCTTTGGACAATAATAGGTACCATG 60.042 40.741 15.94 5.57 42.21 3.66
823 1119 6.413783 AAATTGGTGGGACGAAAATAAACT 57.586 33.333 0.00 0.00 0.00 2.66
1426 2850 3.622514 CTCTAGCACGAGCCCCTT 58.377 61.111 0.00 0.00 43.56 3.95
1642 3066 5.656416 ACGGTTTAATCATCATTTGGGACAT 59.344 36.000 0.00 0.00 39.30 3.06
1819 3243 2.035832 GCAAACCCTTGTGTTGCTATGT 59.964 45.455 0.53 0.00 34.79 2.29
1932 3358 5.429681 TGGACCCGAGAGATGAAATTTAA 57.570 39.130 0.00 0.00 0.00 1.52
2045 3471 8.636843 GTGAAACTACACTCTAAAATACGTCTG 58.363 37.037 0.00 0.00 37.73 3.51
2130 3556 1.063114 TGTTCCTAGCTACTCCCTCCC 60.063 57.143 0.00 0.00 0.00 4.30
2312 3738 0.111061 TGCCTGAGACCAACAAGCAT 59.889 50.000 0.00 0.00 31.15 3.79
2337 3763 5.109903 GCAACTTAGATACCAACGATGACT 58.890 41.667 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.