Multiple sequence alignment - TraesCS2A01G298000

Loading Multiple Alignment...

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 TraesCS2A01G298000 chr2A 100.000 3296 0 0 1 3296 513095644 513092349 0.000000e+00 6087.0
1 TraesCS2A01G298000 chr2B 94.656 2657 80 18 159 2780 449516869 449514240 0.000000e+00 4063.0
2 TraesCS2A01G298000 chr2B 89.421 397 38 3 2793 3188 449514156 449513763 6.350000e-137 497.0
3 TraesCS2A01G298000 chr2B 96.875 32 1 0 1 32 449516899 449516868 2.000000e-03 54.7
4 TraesCS2A01G298000 chr2D 95.788 2493 67 12 159 2619 378364570 378362084 0.000000e+00 3988.0
5 TraesCS2A01G298000 chr2D 90.141 497 45 4 2801 3296 378360574 378360081 0.000000e+00 643.0
6 TraesCS2A01G298000 chr2D 89.005 191 9 7 167 346 378365424 378365235 3.310000e-55 226.0
7 TraesCS2A01G298000 chr2D 92.366 131 10 0 31 161 632057861 632057991 1.560000e-43 187.0
8 TraesCS2A01G298000 chr2D 92.373 118 5 1 2663 2780 378360747 378360634 7.320000e-37 165.0
9 TraesCS2A01G298000 chr2D 98.182 55 1 0 2619 2673 378362056 378362002 2.710000e-16 97.1
10 TraesCS2A01G298000 chr2D 91.379 58 4 1 2717 2774 378360838 378360782 9.810000e-11 78.7
11 TraesCS2A01G298000 chr2D 83.133 83 12 2 3098 3179 58750686 58750605 1.270000e-09 75.0
12 TraesCS2A01G298000 chr2D 90.909 44 3 1 3097 3140 83955860 83955902 1.280000e-04 58.4
13 TraesCS2A01G298000 chr2D 96.875 32 1 0 1 32 378364600 378364569 2.000000e-03 54.7
14 TraesCS2A01G298000 chrUn 93.130 131 9 0 28 158 128516407 128516277 3.360000e-45 193.0
15 TraesCS2A01G298000 chr7B 93.130 131 7 2 31 160 540065247 540065376 1.210000e-44 191.0
16 TraesCS2A01G298000 chr7B 92.366 131 10 0 30 160 678632357 678632487 1.560000e-43 187.0
17 TraesCS2A01G298000 chr1B 92.366 131 10 0 31 161 71638883 71639013 1.560000e-43 187.0
18 TraesCS2A01G298000 chr1D 92.308 130 10 0 31 160 290446592 290446463 5.620000e-43 185.0
19 TraesCS2A01G298000 chr1D 90.647 139 12 1 31 169 43298886 43298749 2.020000e-42 183.0
20 TraesCS2A01G298000 chr7D 91.176 136 11 1 30 165 447766701 447766835 2.020000e-42 183.0
21 TraesCS2A01G298000 chr7D 80.800 125 18 5 2811 2934 557415511 557415630 3.500000e-15 93.5
22 TraesCS2A01G298000 chr3B 89.041 146 14 2 21 165 378689302 378689158 2.610000e-41 180.0
23 TraesCS2A01G298000 chr3B 85.366 82 11 1 3105 3185 400325338 400325257 2.110000e-12 84.2
24 TraesCS2A01G298000 chr4D 85.217 115 16 1 3075 3189 500497560 500497447 2.080000e-22 117.0
25 TraesCS2A01G298000 chr6B 88.298 94 8 3 2817 2908 446845389 446845481 3.480000e-20 110.0
26 TraesCS2A01G298000 chr3D 85.882 85 11 1 3096 3179 319839370 319839454 4.530000e-14 89.8
27 TraesCS2A01G298000 chr3A 85.366 82 11 1 3105 3185 405990775 405990694 2.110000e-12 84.2


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 TraesCS2A01G298000 chr2A 513092349 513095644 3295 True 6087.000000 6087 100.000000 1 3296 1 chr2A.!!$R1 3295
1 TraesCS2A01G298000 chr2B 449513763 449516899 3136 True 1538.233333 4063 93.650667 1 3188 3 chr2B.!!$R1 3187
2 TraesCS2A01G298000 chr2D 378360081 378365424 5343 True 750.357143 3988 93.391857 1 3296 7 chr2D.!!$R2 3295

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
157 982 0.978907 TTTTGGGACGGAGGGAGTAC 59.021 55.000 0.0 0.0 0.00 2.73 F
231 1057 1.756430 TGCAGTGTACCAAGCACAAA 58.244 45.000 0.0 0.0 39.17 2.83 F
767 1621 2.038557 TCTGCCCAACTAAGACTTCCAC 59.961 50.000 0.0 0.0 0.00 4.02 F
1171 2033 2.268920 GCCCGATGACCAAGCAGA 59.731 61.111 0.0 0.0 0.00 4.26 F
1701 2563 0.679002 GCATCCAGCTTCTCAAGGCA 60.679 55.000 0.0 0.0 41.15 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1035 1897 1.067821 GAGATCGGGCACAGGAAGTAG 59.932 57.143 0.00 0.0 0.00 2.57 R
1470 2332 1.341976 TGGGATTCTAAAGGCTTGGGC 60.342 52.381 0.00 0.0 37.82 5.36 R
1701 2563 2.125106 GGCATCTCCGAAACCGCT 60.125 61.111 0.00 0.0 0.00 5.52 R
2153 3015 2.149383 ACCAGGAACAGCAGCCTCA 61.149 57.895 0.00 0.0 30.41 3.86 R
3221 5453 0.802494 ATTTTAGTTGGCGAGCACGG 59.198 50.000 5.52 0.0 40.15 4.94 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
30 855 5.488919 TCCTTCAGGATCTACCAAAACAGAT 59.511 40.000 0.00 0.00 39.78 2.90
31 856 6.672218 TCCTTCAGGATCTACCAAAACAGATA 59.328 38.462 0.00 0.00 39.78 1.98
32 857 6.763610 CCTTCAGGATCTACCAAAACAGATAC 59.236 42.308 0.00 0.00 42.04 2.24
33 858 7.365117 CCTTCAGGATCTACCAAAACAGATACT 60.365 40.741 0.00 0.00 42.17 2.12
34 859 7.113658 TCAGGATCTACCAAAACAGATACTC 57.886 40.000 0.00 0.00 39.92 2.59
35 860 6.098409 TCAGGATCTACCAAAACAGATACTCC 59.902 42.308 0.00 0.00 39.92 3.85
36 861 5.964477 AGGATCTACCAAAACAGATACTCCA 59.036 40.000 0.00 0.00 37.87 3.86
37 862 6.617371 AGGATCTACCAAAACAGATACTCCAT 59.383 38.462 0.00 0.00 37.87 3.41
38 863 6.931840 GGATCTACCAAAACAGATACTCCATC 59.068 42.308 0.00 0.00 38.79 3.51
39 864 6.235231 TCTACCAAAACAGATACTCCATCC 57.765 41.667 0.00 0.00 33.75 3.51
40 865 3.873910 ACCAAAACAGATACTCCATCCG 58.126 45.455 0.00 0.00 33.75 4.18
41 866 3.263425 ACCAAAACAGATACTCCATCCGT 59.737 43.478 0.00 0.00 33.75 4.69
42 867 3.871594 CCAAAACAGATACTCCATCCGTC 59.128 47.826 0.00 0.00 33.75 4.79
43 868 4.383118 CCAAAACAGATACTCCATCCGTCT 60.383 45.833 0.00 0.00 33.75 4.18
44 869 4.657436 AAACAGATACTCCATCCGTCTC 57.343 45.455 0.00 0.00 33.75 3.36
45 870 3.298686 ACAGATACTCCATCCGTCTCA 57.701 47.619 0.00 0.00 33.75 3.27
46 871 3.632333 ACAGATACTCCATCCGTCTCAA 58.368 45.455 0.00 0.00 33.75 3.02
47 872 4.023980 ACAGATACTCCATCCGTCTCAAA 58.976 43.478 0.00 0.00 33.75 2.69
48 873 4.466370 ACAGATACTCCATCCGTCTCAAAA 59.534 41.667 0.00 0.00 33.75 2.44
49 874 5.129485 ACAGATACTCCATCCGTCTCAAAAT 59.871 40.000 0.00 0.00 33.75 1.82
50 875 6.051717 CAGATACTCCATCCGTCTCAAAATT 58.948 40.000 0.00 0.00 33.75 1.82
51 876 6.201806 CAGATACTCCATCCGTCTCAAAATTC 59.798 42.308 0.00 0.00 33.75 2.17
52 877 4.559862 ACTCCATCCGTCTCAAAATTCT 57.440 40.909 0.00 0.00 0.00 2.40
53 878 4.911390 ACTCCATCCGTCTCAAAATTCTT 58.089 39.130 0.00 0.00 0.00 2.52
54 879 4.697352 ACTCCATCCGTCTCAAAATTCTTG 59.303 41.667 0.00 0.00 0.00 3.02
55 880 4.651778 TCCATCCGTCTCAAAATTCTTGT 58.348 39.130 0.00 0.00 0.00 3.16
56 881 4.695455 TCCATCCGTCTCAAAATTCTTGTC 59.305 41.667 0.00 0.00 0.00 3.18
57 882 4.697352 CCATCCGTCTCAAAATTCTTGTCT 59.303 41.667 0.00 0.00 0.00 3.41
58 883 5.182001 CCATCCGTCTCAAAATTCTTGTCTT 59.818 40.000 0.00 0.00 0.00 3.01
59 884 6.371548 CCATCCGTCTCAAAATTCTTGTCTTA 59.628 38.462 0.00 0.00 0.00 2.10
60 885 7.094805 CCATCCGTCTCAAAATTCTTGTCTTAA 60.095 37.037 0.00 0.00 0.00 1.85
61 886 7.795482 TCCGTCTCAAAATTCTTGTCTTAAA 57.205 32.000 0.00 0.00 0.00 1.52
62 887 8.391075 TCCGTCTCAAAATTCTTGTCTTAAAT 57.609 30.769 0.00 0.00 0.00 1.40
63 888 8.846211 TCCGTCTCAAAATTCTTGTCTTAAATT 58.154 29.630 0.00 0.00 0.00 1.82
64 889 9.118236 CCGTCTCAAAATTCTTGTCTTAAATTC 57.882 33.333 0.00 0.00 0.00 2.17
65 890 8.831372 CGTCTCAAAATTCTTGTCTTAAATTCG 58.169 33.333 0.00 0.00 0.00 3.34
66 891 9.665264 GTCTCAAAATTCTTGTCTTAAATTCGT 57.335 29.630 0.00 0.00 0.00 3.85
67 892 9.878599 TCTCAAAATTCTTGTCTTAAATTCGTC 57.121 29.630 0.00 0.00 0.00 4.20
68 893 9.884465 CTCAAAATTCTTGTCTTAAATTCGTCT 57.116 29.630 0.00 0.00 0.00 4.18
75 900 7.780313 TCTTGTCTTAAATTCGTCTACAAACG 58.220 34.615 0.00 0.00 43.92 3.60
76 901 6.456447 TGTCTTAAATTCGTCTACAAACGG 57.544 37.500 0.00 0.00 42.80 4.44
77 902 6.215121 TGTCTTAAATTCGTCTACAAACGGA 58.785 36.000 0.00 0.00 42.80 4.69
78 903 6.869913 TGTCTTAAATTCGTCTACAAACGGAT 59.130 34.615 0.00 0.00 42.62 4.18
79 904 7.148705 TGTCTTAAATTCGTCTACAAACGGATG 60.149 37.037 0.00 0.00 39.94 3.51
80 905 4.336532 AAATTCGTCTACAAACGGATGC 57.663 40.909 0.00 0.00 39.94 3.91
81 906 2.442212 TTCGTCTACAAACGGATGCA 57.558 45.000 0.00 0.00 42.80 3.96
82 907 2.665649 TCGTCTACAAACGGATGCAT 57.334 45.000 0.00 0.00 42.80 3.96
83 908 2.967362 TCGTCTACAAACGGATGCATT 58.033 42.857 0.00 0.00 42.80 3.56
84 909 3.331150 TCGTCTACAAACGGATGCATTT 58.669 40.909 0.00 0.00 42.80 2.32
85 910 4.496360 TCGTCTACAAACGGATGCATTTA 58.504 39.130 0.00 0.00 42.80 1.40
86 911 4.565166 TCGTCTACAAACGGATGCATTTAG 59.435 41.667 0.00 0.00 42.80 1.85
87 912 4.328983 CGTCTACAAACGGATGCATTTAGT 59.671 41.667 0.00 0.00 38.96 2.24
88 913 5.517411 CGTCTACAAACGGATGCATTTAGTA 59.483 40.000 0.00 0.00 38.96 1.82
89 914 6.507456 CGTCTACAAACGGATGCATTTAGTAC 60.507 42.308 0.00 0.00 38.96 2.73
90 915 6.534079 GTCTACAAACGGATGCATTTAGTACT 59.466 38.462 0.00 0.00 0.00 2.73
91 916 7.703621 GTCTACAAACGGATGCATTTAGTACTA 59.296 37.037 0.00 0.00 0.00 1.82
92 917 8.252417 TCTACAAACGGATGCATTTAGTACTAA 58.748 33.333 11.38 11.38 0.00 2.24
93 918 7.675962 ACAAACGGATGCATTTAGTACTAAA 57.324 32.000 26.07 26.07 39.12 1.85
94 919 8.101654 ACAAACGGATGCATTTAGTACTAAAA 57.898 30.769 27.24 14.66 38.38 1.52
95 920 8.019094 ACAAACGGATGCATTTAGTACTAAAAC 58.981 33.333 27.24 22.20 38.38 2.43
96 921 7.675962 AACGGATGCATTTAGTACTAAAACA 57.324 32.000 27.24 25.92 38.38 2.83
97 922 7.859325 ACGGATGCATTTAGTACTAAAACAT 57.141 32.000 29.25 29.25 38.38 2.71
98 923 7.693952 ACGGATGCATTTAGTACTAAAACATG 58.306 34.615 31.64 25.21 38.38 3.21
99 924 7.551262 ACGGATGCATTTAGTACTAAAACATGA 59.449 33.333 31.64 18.22 38.38 3.07
100 925 7.850982 CGGATGCATTTAGTACTAAAACATGAC 59.149 37.037 31.64 25.48 38.38 3.06
101 926 8.893727 GGATGCATTTAGTACTAAAACATGACT 58.106 33.333 31.64 19.60 38.38 3.41
104 929 9.278978 TGCATTTAGTACTAAAACATGACTTGA 57.721 29.630 27.24 5.14 38.38 3.02
111 936 9.601217 AGTACTAAAACATGACTTGATACATCC 57.399 33.333 0.00 0.00 0.00 3.51
112 937 7.539712 ACTAAAACATGACTTGATACATCCG 57.460 36.000 0.00 0.00 0.00 4.18
113 938 7.103641 ACTAAAACATGACTTGATACATCCGT 58.896 34.615 0.00 0.00 0.00 4.69
114 939 8.255206 ACTAAAACATGACTTGATACATCCGTA 58.745 33.333 0.00 0.00 0.00 4.02
115 940 9.261180 CTAAAACATGACTTGATACATCCGTAT 57.739 33.333 0.00 0.00 41.16 3.06
131 956 8.693120 ACATCCGTATCTAGACAAATCTAAGA 57.307 34.615 0.00 0.00 36.98 2.10
132 957 8.569641 ACATCCGTATCTAGACAAATCTAAGAC 58.430 37.037 0.00 0.00 36.98 3.01
133 958 8.568794 CATCCGTATCTAGACAAATCTAAGACA 58.431 37.037 0.00 0.00 36.98 3.41
134 959 8.515695 TCCGTATCTAGACAAATCTAAGACAA 57.484 34.615 0.00 0.00 36.98 3.18
135 960 8.622157 TCCGTATCTAGACAAATCTAAGACAAG 58.378 37.037 0.00 0.00 36.98 3.16
136 961 8.622157 CCGTATCTAGACAAATCTAAGACAAGA 58.378 37.037 0.00 0.00 36.98 3.02
144 969 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
145 970 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
146 971 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
147 972 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
148 973 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
149 974 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
150 975 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
151 976 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
152 977 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
153 978 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
154 979 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
155 980 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.00 0.00 3.85
156 981 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
157 982 0.978907 TTTTGGGACGGAGGGAGTAC 59.021 55.000 0.00 0.00 0.00 2.73
198 1023 3.778629 AGGTATTAACTCCATGGTCGGTT 59.221 43.478 12.58 16.51 0.00 4.44
231 1057 1.756430 TGCAGTGTACCAAGCACAAA 58.244 45.000 0.00 0.00 39.17 2.83
312 1138 6.208797 TGAAGCTAGAAAACTCTACTGCACTA 59.791 38.462 0.00 0.00 0.00 2.74
324 1150 2.162681 ACTGCACTAATCAACCTTGGC 58.837 47.619 0.00 0.00 0.00 4.52
338 1164 4.961438 ACCTTGGCATTTCAAAGTCAAT 57.039 36.364 0.00 0.00 0.00 2.57
350 1176 2.747460 GTCAATGCGAGCCAGGCA 60.747 61.111 15.80 0.00 45.71 4.75
659 1508 2.779755 ATTGTTCATCGCCACACCTA 57.220 45.000 0.00 0.00 0.00 3.08
670 1519 5.029807 TCGCCACACCTATCATTTCATTA 57.970 39.130 0.00 0.00 0.00 1.90
671 1520 5.620206 TCGCCACACCTATCATTTCATTAT 58.380 37.500 0.00 0.00 0.00 1.28
749 1603 3.553511 GCATGGTCGTGTAGAAGAATCTG 59.446 47.826 0.00 0.00 37.10 2.90
767 1621 2.038557 TCTGCCCAACTAAGACTTCCAC 59.961 50.000 0.00 0.00 0.00 4.02
839 1695 4.464597 GCCCTATAAATCCATCTCTCGTCT 59.535 45.833 0.00 0.00 0.00 4.18
943 1805 8.071177 TCATGCATGTGTACATAGCTAGATAT 57.929 34.615 25.43 0.00 34.26 1.63
944 1806 9.189156 TCATGCATGTGTACATAGCTAGATATA 57.811 33.333 25.43 0.00 34.26 0.86
1035 1897 2.663196 CAGGTGGAGGTTCCGTCC 59.337 66.667 0.00 0.00 40.17 4.79
1171 2033 2.268920 GCCCGATGACCAAGCAGA 59.731 61.111 0.00 0.00 0.00 4.26
1593 2455 2.946791 GCTTAGACTCTCCGAGGGAAGT 60.947 54.545 1.07 0.00 33.35 3.01
1646 2508 2.665185 GGATACCATGGCGTCCGC 60.665 66.667 13.04 2.45 41.06 5.54
1701 2563 0.679002 GCATCCAGCTTCTCAAGGCA 60.679 55.000 0.00 0.00 41.15 4.75
1719 2581 2.435938 GCGGTTTCGGAGATGCCA 60.436 61.111 0.00 0.00 35.04 4.92
1833 2695 3.774528 CAGGTGCTCTGCCGGCTA 61.775 66.667 29.70 15.12 36.60 3.93
1916 2778 1.135139 GTTGCTCCTCGATGAGTGCTA 59.865 52.381 17.48 1.55 34.74 3.49
2372 3237 7.575155 GCAGTTGTCCTTTTAGGTTTCCTAATC 60.575 40.741 8.75 0.98 44.38 1.75
2383 3248 5.837829 AGGTTTCCTAATCTGGCCATTTTA 58.162 37.500 5.51 6.62 28.47 1.52
2456 3321 2.026822 TCTGAAACTGGGGAGAGCATTC 60.027 50.000 0.00 0.00 0.00 2.67
2567 3433 9.410556 GTGATCATGCTTGTTACTAAAACAATT 57.589 29.630 0.00 0.00 39.16 2.32
2681 4839 4.004314 GAGGGAGGTTGAGCTTTCTTAAC 58.996 47.826 0.00 0.00 37.89 2.01
2699 4857 6.806751 TCTTAACTCTTTTCGATCGGATGAT 58.193 36.000 16.41 0.00 37.60 2.45
2700 4858 7.937649 TCTTAACTCTTTTCGATCGGATGATA 58.062 34.615 16.41 0.00 34.09 2.15
2701 4859 8.410912 TCTTAACTCTTTTCGATCGGATGATAA 58.589 33.333 16.41 0.00 34.09 1.75
2702 4860 9.197694 CTTAACTCTTTTCGATCGGATGATAAT 57.802 33.333 16.41 0.00 34.09 1.28
2755 4913 7.847078 CACACTTTAAAATCTGCAACAATGTTG 59.153 33.333 20.77 20.77 0.00 3.33
2760 4918 1.412079 TCTGCAACAATGTTGCCCTT 58.588 45.000 37.91 0.00 44.32 3.95
2808 5038 5.065235 TGGATTGACCACTACATATGCATG 58.935 41.667 10.16 0.00 44.64 4.06
2945 5175 6.968263 TTTACATGAAGGATGACCAAAACA 57.032 33.333 0.00 0.00 38.94 2.83
3051 5283 2.276732 ACCCTTTGGATCATATGCCG 57.723 50.000 0.00 0.00 34.81 5.69
3057 5289 4.218200 CCTTTGGATCATATGCCGCATTTA 59.782 41.667 11.97 0.00 0.00 1.40
3103 5335 4.421058 TGAATATCCAACGAACGTCAGAG 58.579 43.478 0.00 0.00 0.00 3.35
3125 5357 4.160252 AGTTTTAGGCATGGCAAATCGAAT 59.840 37.500 22.64 0.00 0.00 3.34
3134 5366 5.610975 CATGGCAAATCGAATGTTTTTCAC 58.389 37.500 0.00 0.00 0.00 3.18
3159 5391 5.389859 CAAATTATGTTTGCTGAGGGTGA 57.610 39.130 0.00 0.00 0.00 4.02
3171 5403 4.101898 TGCTGAGGGTGACAAGTTTAGTTA 59.898 41.667 0.00 0.00 0.00 2.24
3193 5425 0.579156 GAGCATCGCAAATCCGTCTC 59.421 55.000 0.00 0.00 0.00 3.36
3196 5428 1.070309 GCATCGCAAATCCGTCTCATC 60.070 52.381 0.00 0.00 0.00 2.92
3199 5431 1.751351 TCGCAAATCCGTCTCATCTCT 59.249 47.619 0.00 0.00 0.00 3.10
3201 5433 2.932614 CGCAAATCCGTCTCATCTCTTT 59.067 45.455 0.00 0.00 0.00 2.52
3203 5435 4.493220 CGCAAATCCGTCTCATCTCTTTTC 60.493 45.833 0.00 0.00 0.00 2.29
3204 5436 4.201861 GCAAATCCGTCTCATCTCTTTTCC 60.202 45.833 0.00 0.00 0.00 3.13
3209 5441 5.621193 TCCGTCTCATCTCTTTTCCTTTTT 58.379 37.500 0.00 0.00 0.00 1.94
3239 5471 1.847890 GCCGTGCTCGCCAACTAAAA 61.848 55.000 1.89 0.00 35.54 1.52
3248 5480 4.662145 CTCGCCAACTAAAATTGTCATCC 58.338 43.478 0.00 0.00 0.00 3.51
3253 5485 5.358160 GCCAACTAAAATTGTCATCCTAGCT 59.642 40.000 0.00 0.00 0.00 3.32
3257 5489 6.352516 ACTAAAATTGTCATCCTAGCTCCAG 58.647 40.000 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 855 5.677319 AGAATTTTGAGACGGATGGAGTA 57.323 39.130 0.00 0.00 0.00 2.59
31 856 4.559862 AGAATTTTGAGACGGATGGAGT 57.440 40.909 0.00 0.00 0.00 3.85
32 857 4.697352 ACAAGAATTTTGAGACGGATGGAG 59.303 41.667 7.18 0.00 0.00 3.86
33 858 4.651778 ACAAGAATTTTGAGACGGATGGA 58.348 39.130 7.18 0.00 0.00 3.41
34 859 4.697352 AGACAAGAATTTTGAGACGGATGG 59.303 41.667 7.18 0.00 0.00 3.51
35 860 5.869753 AGACAAGAATTTTGAGACGGATG 57.130 39.130 7.18 0.00 0.00 3.51
36 861 7.979444 TTAAGACAAGAATTTTGAGACGGAT 57.021 32.000 7.18 0.00 0.00 4.18
37 862 7.795482 TTTAAGACAAGAATTTTGAGACGGA 57.205 32.000 7.18 0.00 0.00 4.69
38 863 9.118236 GAATTTAAGACAAGAATTTTGAGACGG 57.882 33.333 7.18 0.00 0.00 4.79
39 864 8.831372 CGAATTTAAGACAAGAATTTTGAGACG 58.169 33.333 7.18 0.00 0.00 4.18
40 865 9.665264 ACGAATTTAAGACAAGAATTTTGAGAC 57.335 29.630 0.00 0.00 0.00 3.36
41 866 9.878599 GACGAATTTAAGACAAGAATTTTGAGA 57.121 29.630 0.00 0.00 0.00 3.27
42 867 9.884465 AGACGAATTTAAGACAAGAATTTTGAG 57.116 29.630 0.00 0.00 0.00 3.02
49 874 8.270799 CGTTTGTAGACGAATTTAAGACAAGAA 58.729 33.333 0.00 0.00 45.47 2.52
50 875 7.095940 CCGTTTGTAGACGAATTTAAGACAAGA 60.096 37.037 0.00 0.00 45.47 3.02
51 876 7.007697 CCGTTTGTAGACGAATTTAAGACAAG 58.992 38.462 0.00 0.00 45.47 3.16
52 877 6.700960 TCCGTTTGTAGACGAATTTAAGACAA 59.299 34.615 0.00 0.00 45.47 3.18
53 878 6.215121 TCCGTTTGTAGACGAATTTAAGACA 58.785 36.000 0.00 0.00 45.47 3.41
54 879 6.695292 TCCGTTTGTAGACGAATTTAAGAC 57.305 37.500 0.00 0.00 45.47 3.01
55 880 6.183360 GCATCCGTTTGTAGACGAATTTAAGA 60.183 38.462 0.00 0.00 45.47 2.10
56 881 5.957796 GCATCCGTTTGTAGACGAATTTAAG 59.042 40.000 0.00 0.00 45.47 1.85
57 882 5.408909 TGCATCCGTTTGTAGACGAATTTAA 59.591 36.000 0.00 0.00 45.47 1.52
58 883 4.930405 TGCATCCGTTTGTAGACGAATTTA 59.070 37.500 0.00 0.00 45.47 1.40
59 884 3.749088 TGCATCCGTTTGTAGACGAATTT 59.251 39.130 0.00 0.00 45.47 1.82
60 885 3.331150 TGCATCCGTTTGTAGACGAATT 58.669 40.909 0.00 0.00 45.47 2.17
61 886 2.967362 TGCATCCGTTTGTAGACGAAT 58.033 42.857 0.00 0.00 45.47 3.34
62 887 2.442212 TGCATCCGTTTGTAGACGAA 57.558 45.000 0.00 0.00 45.47 3.85
63 888 2.665649 ATGCATCCGTTTGTAGACGA 57.334 45.000 0.00 0.00 45.47 4.20
64 889 3.740044 AAATGCATCCGTTTGTAGACG 57.260 42.857 0.00 0.00 42.43 4.18
65 890 5.796350 ACTAAATGCATCCGTTTGTAGAC 57.204 39.130 0.00 0.00 32.64 2.59
66 891 6.636705 AGTACTAAATGCATCCGTTTGTAGA 58.363 36.000 0.00 0.00 32.64 2.59
67 892 6.903883 AGTACTAAATGCATCCGTTTGTAG 57.096 37.500 0.00 0.00 32.64 2.74
68 893 8.774890 TTTAGTACTAAATGCATCCGTTTGTA 57.225 30.769 21.52 0.00 32.64 2.41
69 894 7.675962 TTTAGTACTAAATGCATCCGTTTGT 57.324 32.000 21.52 0.63 32.64 2.83
70 895 8.018520 TGTTTTAGTACTAAATGCATCCGTTTG 58.981 33.333 24.89 0.00 35.27 2.93
71 896 8.101654 TGTTTTAGTACTAAATGCATCCGTTT 57.898 30.769 24.89 0.00 35.27 3.60
72 897 7.675962 TGTTTTAGTACTAAATGCATCCGTT 57.324 32.000 24.89 0.00 35.27 4.44
73 898 7.551262 TCATGTTTTAGTACTAAATGCATCCGT 59.449 33.333 26.32 14.73 35.27 4.69
74 899 7.850982 GTCATGTTTTAGTACTAAATGCATCCG 59.149 37.037 26.32 20.66 35.27 4.18
75 900 8.893727 AGTCATGTTTTAGTACTAAATGCATCC 58.106 33.333 26.32 21.93 35.27 3.51
78 903 9.278978 TCAAGTCATGTTTTAGTACTAAATGCA 57.721 29.630 24.89 24.06 35.27 3.96
85 910 9.601217 GGATGTATCAAGTCATGTTTTAGTACT 57.399 33.333 0.00 0.00 0.00 2.73
86 911 8.540492 CGGATGTATCAAGTCATGTTTTAGTAC 58.460 37.037 0.00 0.00 0.00 2.73
87 912 8.255206 ACGGATGTATCAAGTCATGTTTTAGTA 58.745 33.333 0.00 0.00 0.00 1.82
88 913 7.103641 ACGGATGTATCAAGTCATGTTTTAGT 58.896 34.615 0.00 0.00 0.00 2.24
89 914 7.539712 ACGGATGTATCAAGTCATGTTTTAG 57.460 36.000 0.00 0.00 0.00 1.85
105 930 9.788889 TCTTAGATTTGTCTAGATACGGATGTA 57.211 33.333 0.00 0.00 34.45 2.29
106 931 8.569641 GTCTTAGATTTGTCTAGATACGGATGT 58.430 37.037 0.00 0.00 0.00 3.06
107 932 8.568794 TGTCTTAGATTTGTCTAGATACGGATG 58.431 37.037 0.00 0.00 0.00 3.51
108 933 8.693120 TGTCTTAGATTTGTCTAGATACGGAT 57.307 34.615 0.00 0.00 0.00 4.18
109 934 8.515695 TTGTCTTAGATTTGTCTAGATACGGA 57.484 34.615 0.00 0.00 0.00 4.69
110 935 8.622157 TCTTGTCTTAGATTTGTCTAGATACGG 58.378 37.037 0.00 0.00 0.00 4.02
118 943 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
119 944 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
120 945 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
121 946 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
122 947 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
123 948 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
124 949 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
125 950 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
126 951 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
127 952 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
128 953 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
129 954 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
130 955 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
131 956 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
132 957 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
133 958 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
134 959 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
135 960 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
136 961 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
137 962 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
138 963 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
139 964 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
140 965 1.002069 TAGTACTCCCTCCGTCCCAA 58.998 55.000 0.00 0.00 0.00 4.12
141 966 0.549950 CTAGTACTCCCTCCGTCCCA 59.450 60.000 0.00 0.00 0.00 4.37
142 967 0.178995 CCTAGTACTCCCTCCGTCCC 60.179 65.000 0.00 0.00 0.00 4.46
143 968 0.842635 TCCTAGTACTCCCTCCGTCC 59.157 60.000 0.00 0.00 0.00 4.79
144 969 2.955342 ATCCTAGTACTCCCTCCGTC 57.045 55.000 0.00 0.00 0.00 4.79
145 970 2.486907 CGAATCCTAGTACTCCCTCCGT 60.487 54.545 0.00 0.00 0.00 4.69
146 971 2.152830 CGAATCCTAGTACTCCCTCCG 58.847 57.143 0.00 0.00 0.00 4.63
147 972 3.226682 ACGAATCCTAGTACTCCCTCC 57.773 52.381 0.00 0.00 0.00 4.30
148 973 5.558818 TGATACGAATCCTAGTACTCCCTC 58.441 45.833 0.00 0.00 0.00 4.30
149 974 5.579753 TGATACGAATCCTAGTACTCCCT 57.420 43.478 0.00 0.00 0.00 4.20
150 975 6.433404 TGATTGATACGAATCCTAGTACTCCC 59.567 42.308 0.00 0.00 32.20 4.30
151 976 7.450124 TGATTGATACGAATCCTAGTACTCC 57.550 40.000 0.00 0.00 32.20 3.85
152 977 8.024285 CCTTGATTGATACGAATCCTAGTACTC 58.976 40.741 0.00 0.00 32.20 2.59
153 978 7.506261 ACCTTGATTGATACGAATCCTAGTACT 59.494 37.037 0.00 0.00 32.20 2.73
154 979 7.659186 ACCTTGATTGATACGAATCCTAGTAC 58.341 38.462 0.00 0.00 32.20 2.73
155 980 7.834881 ACCTTGATTGATACGAATCCTAGTA 57.165 36.000 0.00 0.00 32.20 1.82
156 981 6.732896 ACCTTGATTGATACGAATCCTAGT 57.267 37.500 0.00 0.00 32.20 2.57
231 1057 3.132289 TCTTCTCCGTCCAATAATTCGCT 59.868 43.478 0.00 0.00 0.00 4.93
245 1071 1.998315 CATGTGCAGTTCTCTTCTCCG 59.002 52.381 0.00 0.00 0.00 4.63
312 1138 5.163322 TGACTTTGAAATGCCAAGGTTGATT 60.163 36.000 0.00 0.00 36.64 2.57
324 1150 2.919229 GGCTCGCATTGACTTTGAAATG 59.081 45.455 0.00 0.00 36.95 2.32
338 1164 4.081185 TCGATTGCCTGGCTCGCA 62.081 61.111 21.43 10.58 32.62 5.10
350 1176 1.381327 TTCTCCCGGCCTCTCGATT 60.381 57.895 0.00 0.00 0.00 3.34
424 1250 5.854338 CGGCTTCGCTAATTTCTTTGTTTTA 59.146 36.000 0.00 0.00 0.00 1.52
427 1253 3.500680 TCGGCTTCGCTAATTTCTTTGTT 59.499 39.130 0.00 0.00 0.00 2.83
428 1254 3.071479 TCGGCTTCGCTAATTTCTTTGT 58.929 40.909 0.00 0.00 0.00 2.83
749 1603 1.439679 CGTGGAAGTCTTAGTTGGGC 58.560 55.000 0.00 0.00 0.00 5.36
944 1806 9.411801 CAACGCACTCTGTATATATGTTTATCT 57.588 33.333 0.00 0.00 0.00 1.98
1032 1894 1.218316 CGGGCACAGGAAGTAGGAC 59.782 63.158 0.00 0.00 0.00 3.85
1035 1897 1.067821 GAGATCGGGCACAGGAAGTAG 59.932 57.143 0.00 0.00 0.00 2.57
1149 2011 1.811266 CTTGGTCATCGGGCACTCG 60.811 63.158 0.00 0.00 0.00 4.18
1470 2332 1.341976 TGGGATTCTAAAGGCTTGGGC 60.342 52.381 0.00 0.00 37.82 5.36
1593 2455 2.548067 GCGTTCCAAGACTCTCTTCCAA 60.548 50.000 0.00 0.00 33.78 3.53
1701 2563 2.125106 GGCATCTCCGAAACCGCT 60.125 61.111 0.00 0.00 0.00 5.52
1916 2778 2.273449 CCCGCTTGCTTCCTCCAT 59.727 61.111 0.00 0.00 0.00 3.41
2153 3015 2.149383 ACCAGGAACAGCAGCCTCA 61.149 57.895 0.00 0.00 30.41 3.86
2275 3137 3.845781 TCAAGAAGGGTAGGATGCATC 57.154 47.619 18.81 18.81 0.00 3.91
2372 3237 4.340617 TCTTTACACCCTAAAATGGCCAG 58.659 43.478 13.05 0.00 0.00 4.85
2383 3248 8.650143 AACAATCAATACAATCTTTACACCCT 57.350 30.769 0.00 0.00 0.00 4.34
2451 3316 5.094812 TGAACATACTCATTTTGCGAATGC 58.905 37.500 7.53 0.00 43.20 3.56
2456 3321 6.417635 ACAGTTTTGAACATACTCATTTTGCG 59.582 34.615 0.00 0.00 0.00 4.85
2611 3482 4.494199 GGCGTCAACTATGCATTACAAGAC 60.494 45.833 3.54 6.71 42.33 3.01
2681 4839 8.651588 CCTTAATTATCATCCGATCGAAAAGAG 58.348 37.037 18.66 0.00 32.73 2.85
2699 4857 7.337480 TCACATGCGTCTAGTACCTTAATTA 57.663 36.000 0.00 0.00 0.00 1.40
2700 4858 6.216801 TCACATGCGTCTAGTACCTTAATT 57.783 37.500 0.00 0.00 0.00 1.40
2701 4859 5.736492 GCTCACATGCGTCTAGTACCTTAAT 60.736 44.000 0.00 0.00 0.00 1.40
2702 4860 4.439700 GCTCACATGCGTCTAGTACCTTAA 60.440 45.833 0.00 0.00 0.00 1.85
2755 4913 7.922811 CCAAATTCTACAGATTTTGATAAGGGC 59.077 37.037 20.34 0.00 42.98 5.19
2919 5149 7.708752 TGTTTTGGTCATCCTTCATGTAAAAAC 59.291 33.333 0.00 0.00 38.65 2.43
2920 5150 7.786030 TGTTTTGGTCATCCTTCATGTAAAAA 58.214 30.769 0.00 0.00 33.66 1.94
2927 5157 3.256631 GTGCTGTTTTGGTCATCCTTCAT 59.743 43.478 0.00 0.00 34.23 2.57
2933 5163 6.624423 AGAAATATGTGCTGTTTTGGTCATC 58.376 36.000 0.00 0.00 0.00 2.92
2945 5175 5.877012 CGCCTCCATATTAGAAATATGTGCT 59.123 40.000 15.11 0.00 31.77 4.40
3051 5283 5.275067 TGCTAAAATCCCCATGTAAATGC 57.725 39.130 0.00 0.00 0.00 3.56
3057 5289 4.447762 GGTCCTATGCTAAAATCCCCATGT 60.448 45.833 0.00 0.00 0.00 3.21
3069 5301 5.047306 CGTTGGATATTCAGGTCCTATGCTA 60.047 44.000 0.00 0.00 35.49 3.49
3071 5303 3.997021 CGTTGGATATTCAGGTCCTATGC 59.003 47.826 0.00 0.00 35.49 3.14
3103 5335 3.502191 TCGATTTGCCATGCCTAAAAC 57.498 42.857 0.00 0.00 0.00 2.43
3125 5357 6.709643 CAAACATAATTTGCCGTGAAAAACA 58.290 32.000 0.00 0.00 0.00 2.83
3159 5391 3.612860 CGATGCTCGCTAACTAAACTTGT 59.387 43.478 0.00 0.00 31.14 3.16
3209 5441 2.667171 GCGAGCACGGCAATTTTCTAAA 60.667 45.455 5.52 0.00 40.15 1.85
3221 5453 0.802494 ATTTTAGTTGGCGAGCACGG 59.198 50.000 5.52 0.00 40.15 4.94
3222 5454 2.241722 CAATTTTAGTTGGCGAGCACG 58.758 47.619 0.00 0.00 42.93 5.34
3239 5471 2.121948 TGCTGGAGCTAGGATGACAAT 58.878 47.619 0.00 0.00 42.66 2.71


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

AutoCloner maintained by Alex Coulton.