Multiple sequence alignment - TraesCS7A01G028700

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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 TraesCS7A01G028700 chr7A 100.000 2547 0 0 1 2547 11678891 11676345 0.000000e+00 4704.0
1 TraesCS7A01G028700 chr7A 95.732 164 5 2 229 391 11678502 11678340 1.940000e-66 263.0
2 TraesCS7A01G028700 chr7A 95.732 164 5 2 390 552 11678663 11678501 1.940000e-66 263.0
3 TraesCS7A01G028700 chr2B 99.431 1582 9 0 966 2547 15783761 15782180 0.000000e+00 2872.0
4 TraesCS7A01G028700 chr2B 99.178 1582 13 0 966 2547 15856217 15854636 0.000000e+00 2850.0
5 TraesCS7A01G028700 chr2B 98.421 1583 8 2 966 2547 15719656 15718090 0.000000e+00 2769.0
6 TraesCS7A01G028700 chr2B 91.653 599 16 10 390 956 15720595 15719999 0.000000e+00 798.0
7 TraesCS7A01G028700 chr2B 91.653 599 16 10 390 956 15857156 15856560 0.000000e+00 798.0
8 TraesCS7A01G028700 chr2B 91.486 599 17 10 390 956 15784700 15784104 0.000000e+00 793.0
9 TraesCS7A01G028700 chr2B 91.319 599 18 10 390 956 15956124 15955528 0.000000e+00 787.0
10 TraesCS7A01G028700 chr2B 98.000 200 4 0 192 391 15720632 15720433 5.220000e-92 348.0
11 TraesCS7A01G028700 chr2B 97.500 200 5 0 192 391 15857193 15856994 2.430000e-90 342.0
12 TraesCS7A01G028700 chr2B 97.500 200 5 0 192 391 15956161 15955962 2.430000e-90 342.0
13 TraesCS7A01G028700 chr2B 97.000 200 6 0 192 391 15784737 15784538 1.130000e-88 337.0
14 TraesCS7A01G028700 chrUn 98.421 1583 8 2 966 2547 333312251 333313817 0.000000e+00 2769.0
15 TraesCS7A01G028700 chrUn 91.653 599 16 10 390 956 380901045 380900449 0.000000e+00 798.0
16 TraesCS7A01G028700 chrUn 90.487 431 33 3 1073 1495 124973510 124973940 1.710000e-156 562.0
17 TraesCS7A01G028700 chrUn 98.000 200 4 0 192 391 380901082 380900883 5.220000e-92 348.0
18 TraesCS7A01G028700 chrUn 98.958 192 2 0 966 1157 380900106 380899915 6.750000e-91 344.0
19 TraesCS7A01G028700 chrUn 95.833 168 4 3 14 178 10638633 10638800 4.180000e-68 268.0
20 TraesCS7A01G028700 chrUn 95.833 168 4 3 14 178 68262859 68263026 4.180000e-68 268.0
21 TraesCS7A01G028700 chrUn 93.011 186 4 3 1511 1687 124974237 124974422 1.940000e-66 263.0
22 TraesCS7A01G028700 chrUn 98.658 149 1 1 808 956 333311761 333311908 1.940000e-66 263.0
23 TraesCS7A01G028700 chrUn 92.473 186 5 3 1511 1687 259181287 259181472 9.040000e-65 257.0
24 TraesCS7A01G028700 chr6D 89.245 1060 72 23 968 1997 420749535 420748488 0.000000e+00 1288.0
25 TraesCS7A01G028700 chr6D 94.065 556 27 4 1997 2547 420748217 420747663 0.000000e+00 839.0
26 TraesCS7A01G028700 chr6D 83.036 112 19 0 176 287 390793746 390793857 4.480000e-18 102.0
27 TraesCS7A01G028700 chr6D 80.000 100 15 4 392 490 9138493 9138398 4.550000e-08 69.4
28 TraesCS7A01G028700 chr6B 88.900 1009 61 36 974 1953 633916628 633915642 0.000000e+00 1195.0
29 TraesCS7A01G028700 chr6B 95.315 555 22 2 1997 2547 633915333 633914779 0.000000e+00 878.0
30 TraesCS7A01G028700 chr6A 86.334 1061 79 26 964 1997 563711859 563710838 0.000000e+00 1096.0
31 TraesCS7A01G028700 chr6A 94.775 555 25 2 1997 2547 563710567 563710013 0.000000e+00 861.0
32 TraesCS7A01G028700 chr3B 94.193 706 19 2 966 1670 745704170 745704854 0.000000e+00 1057.0
33 TraesCS7A01G028700 chr3B 84.071 226 20 9 1677 1886 380277483 380277708 1.190000e-48 204.0
34 TraesCS7A01G028700 chr4D 96.825 504 15 1 2045 2547 508464387 508463884 0.000000e+00 841.0
35 TraesCS7A01G028700 chr4D 98.171 164 3 0 1834 1997 508472187 508472024 1.150000e-73 287.0
36 TraesCS7A01G028700 chr4D 96.407 167 4 2 14 178 262807492 262807658 8.980000e-70 274.0
37 TraesCS7A01G028700 chr4D 87.097 217 22 4 673 889 508472741 508472531 9.110000e-60 241.0
38 TraesCS7A01G028700 chr4D 91.250 80 6 1 312 391 508472999 508472921 9.640000e-20 108.0
39 TraesCS7A01G028700 chr7B 96.407 167 4 2 14 178 635167356 635167522 8.980000e-70 274.0
40 TraesCS7A01G028700 chr5D 96.429 168 3 3 14 178 370545403 370545570 8.980000e-70 274.0
41 TraesCS7A01G028700 chr5D 93.333 180 9 3 2 178 401851487 401851308 1.940000e-66 263.0
42 TraesCS7A01G028700 chr1D 96.407 167 4 2 14 178 51796055 51796221 8.980000e-70 274.0
43 TraesCS7A01G028700 chr3D 92.896 183 8 4 1 178 525659324 525659142 6.990000e-66 261.0
44 TraesCS7A01G028700 chr2D 93.296 179 8 4 2 178 381184539 381184715 6.990000e-66 261.0
45 TraesCS7A01G028700 chr1B 83.929 224 22 7 1677 1886 514932181 514931958 4.300000e-48 202.0
46 TraesCS7A01G028700 chr3A 88.820 161 18 0 726 886 260204815 260204975 5.560000e-47 198.0
47 TraesCS7A01G028700 chr5A 80.000 155 25 5 176 327 347410293 347410444 2.680000e-20 110.0
48 TraesCS7A01G028700 chr5A 81.443 97 13 4 388 482 2879714 2879621 9.770000e-10 75.0
49 TraesCS7A01G028700 chr4B 93.548 62 2 2 702 762 211498150 211498210 9.700000e-15 91.6
50 TraesCS7A01G028700 chr1A 93.548 62 2 2 702 762 464086889 464086829 9.700000e-15 91.6
51 TraesCS7A01G028700 chr2A 85.915 71 8 2 392 461 363340336 363340405 9.770000e-10 75.0


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 TraesCS7A01G028700 chr7A 11676345 11678891 2546 True 1743.333333 4704 97.154667 1 2547 3 chr7A.!!$R1 2546
1 TraesCS7A01G028700 chr2B 15782180 15784737 2557 True 1334.000000 2872 95.972333 192 2547 3 chr2B.!!$R2 2355
2 TraesCS7A01G028700 chr2B 15854636 15857193 2557 True 1330.000000 2850 96.110333 192 2547 3 chr2B.!!$R3 2355
3 TraesCS7A01G028700 chr2B 15718090 15720632 2542 True 1305.000000 2769 96.024667 192 2547 3 chr2B.!!$R1 2355
4 TraesCS7A01G028700 chr2B 15955528 15956161 633 True 564.500000 787 94.409500 192 956 2 chr2B.!!$R4 764
5 TraesCS7A01G028700 chrUn 333311761 333313817 2056 False 1516.000000 2769 98.539500 808 2547 2 chrUn.!!$F5 1739
6 TraesCS7A01G028700 chrUn 380899915 380901082 1167 True 496.666667 798 96.203667 192 1157 3 chrUn.!!$R1 965
7 TraesCS7A01G028700 chrUn 124973510 124974422 912 False 412.500000 562 91.749000 1073 1687 2 chrUn.!!$F4 614
8 TraesCS7A01G028700 chr6D 420747663 420749535 1872 True 1063.500000 1288 91.655000 968 2547 2 chr6D.!!$R2 1579
9 TraesCS7A01G028700 chr6B 633914779 633916628 1849 True 1036.500000 1195 92.107500 974 2547 2 chr6B.!!$R1 1573
10 TraesCS7A01G028700 chr6A 563710013 563711859 1846 True 978.500000 1096 90.554500 964 2547 2 chr6A.!!$R1 1583
11 TraesCS7A01G028700 chr3B 745704170 745704854 684 False 1057.000000 1057 94.193000 966 1670 1 chr3B.!!$F2 704
12 TraesCS7A01G028700 chr4D 508463884 508464387 503 True 841.000000 841 96.825000 2045 2547 1 chr4D.!!$R1 502
13 TraesCS7A01G028700 chr4D 508472024 508472999 975 True 212.000000 287 92.172667 312 1997 3 chr4D.!!$R2 1685

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
156 157 0.036105 GGTCGGTTGGTATTTCCGGT 60.036 55.0 0.0 0.0 43.75 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2114 3244 4.019174 CCATGAGCTTTGGTTCCACTTAT 58.981 43.478 8.18 0.0 0.0 1.73 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
20 21 3.928727 CCGCATTGCATCCATCTTTAT 57.071 42.857 9.69 0.00 0.00 1.40
21 22 3.829948 CCGCATTGCATCCATCTTTATC 58.170 45.455 9.69 0.00 0.00 1.75
22 23 3.253921 CCGCATTGCATCCATCTTTATCA 59.746 43.478 9.69 0.00 0.00 2.15
23 24 4.082408 CCGCATTGCATCCATCTTTATCAT 60.082 41.667 9.69 0.00 0.00 2.45
24 25 5.093457 CGCATTGCATCCATCTTTATCATC 58.907 41.667 9.69 0.00 0.00 2.92
25 26 5.335348 CGCATTGCATCCATCTTTATCATCA 60.335 40.000 9.69 0.00 0.00 3.07
26 27 6.452242 GCATTGCATCCATCTTTATCATCAA 58.548 36.000 3.15 0.00 0.00 2.57
27 28 6.365247 GCATTGCATCCATCTTTATCATCAAC 59.635 38.462 3.15 0.00 0.00 3.18
28 29 5.678132 TGCATCCATCTTTATCATCAACG 57.322 39.130 0.00 0.00 0.00 4.10
29 30 5.367302 TGCATCCATCTTTATCATCAACGA 58.633 37.500 0.00 0.00 0.00 3.85
30 31 5.237127 TGCATCCATCTTTATCATCAACGAC 59.763 40.000 0.00 0.00 0.00 4.34
31 32 5.237127 GCATCCATCTTTATCATCAACGACA 59.763 40.000 0.00 0.00 0.00 4.35
32 33 6.072838 GCATCCATCTTTATCATCAACGACAT 60.073 38.462 0.00 0.00 0.00 3.06
33 34 7.516481 CATCCATCTTTATCATCAACGACATC 58.484 38.462 0.00 0.00 0.00 3.06
34 35 5.991606 TCCATCTTTATCATCAACGACATCC 59.008 40.000 0.00 0.00 0.00 3.51
35 36 5.107337 CCATCTTTATCATCAACGACATCCG 60.107 44.000 0.00 0.00 45.44 4.18
36 37 3.802139 TCTTTATCATCAACGACATCCGC 59.198 43.478 0.00 0.00 43.32 5.54
37 38 2.880963 TATCATCAACGACATCCGCA 57.119 45.000 0.00 0.00 43.32 5.69
38 39 2.022764 ATCATCAACGACATCCGCAA 57.977 45.000 0.00 0.00 43.32 4.85
39 40 1.075542 TCATCAACGACATCCGCAAC 58.924 50.000 0.00 0.00 43.32 4.17
40 41 0.795698 CATCAACGACATCCGCAACA 59.204 50.000 0.00 0.00 43.32 3.33
41 42 1.398041 CATCAACGACATCCGCAACAT 59.602 47.619 0.00 0.00 43.32 2.71
42 43 0.795698 TCAACGACATCCGCAACATG 59.204 50.000 0.00 0.00 43.32 3.21
43 44 0.794229 CAACGACATCCGCAACATGC 60.794 55.000 0.00 0.00 43.32 4.06
44 45 1.233950 AACGACATCCGCAACATGCA 61.234 50.000 2.99 0.00 45.36 3.96
45 46 1.233950 ACGACATCCGCAACATGCAA 61.234 50.000 2.99 0.00 45.36 4.08
46 47 0.794229 CGACATCCGCAACATGCAAC 60.794 55.000 2.99 0.00 45.36 4.17
47 48 0.523072 GACATCCGCAACATGCAACT 59.477 50.000 2.99 0.00 45.36 3.16
48 49 0.523072 ACATCCGCAACATGCAACTC 59.477 50.000 2.99 0.00 45.36 3.01
49 50 0.179156 CATCCGCAACATGCAACTCC 60.179 55.000 2.99 0.00 45.36 3.85
50 51 0.608856 ATCCGCAACATGCAACTCCA 60.609 50.000 2.99 0.00 45.36 3.86
51 52 0.821301 TCCGCAACATGCAACTCCAA 60.821 50.000 2.99 0.00 45.36 3.53
52 53 0.244450 CCGCAACATGCAACTCCAAT 59.756 50.000 2.99 0.00 45.36 3.16
53 54 1.472082 CCGCAACATGCAACTCCAATA 59.528 47.619 2.99 0.00 45.36 1.90
54 55 2.099592 CCGCAACATGCAACTCCAATAT 59.900 45.455 2.99 0.00 45.36 1.28
55 56 3.365832 CGCAACATGCAACTCCAATATC 58.634 45.455 2.99 0.00 45.36 1.63
56 57 3.181498 CGCAACATGCAACTCCAATATCA 60.181 43.478 2.99 0.00 45.36 2.15
57 58 4.498513 CGCAACATGCAACTCCAATATCAT 60.499 41.667 2.99 0.00 45.36 2.45
58 59 5.277925 CGCAACATGCAACTCCAATATCATA 60.278 40.000 2.99 0.00 45.36 2.15
59 60 6.569035 CGCAACATGCAACTCCAATATCATAT 60.569 38.462 2.99 0.00 45.36 1.78
60 61 7.149973 GCAACATGCAACTCCAATATCATATT 58.850 34.615 0.00 0.00 44.26 1.28
61 62 7.327761 GCAACATGCAACTCCAATATCATATTC 59.672 37.037 0.00 0.00 44.26 1.75
62 63 8.573885 CAACATGCAACTCCAATATCATATTCT 58.426 33.333 0.00 0.00 0.00 2.40
63 64 8.332996 ACATGCAACTCCAATATCATATTCTC 57.667 34.615 0.00 0.00 0.00 2.87
64 65 7.392673 ACATGCAACTCCAATATCATATTCTCC 59.607 37.037 0.00 0.00 0.00 3.71
65 66 7.083062 TGCAACTCCAATATCATATTCTCCT 57.917 36.000 0.00 0.00 0.00 3.69
66 67 7.164122 TGCAACTCCAATATCATATTCTCCTC 58.836 38.462 0.00 0.00 0.00 3.71
67 68 6.597280 GCAACTCCAATATCATATTCTCCTCC 59.403 42.308 0.00 0.00 0.00 4.30
68 69 7.528543 GCAACTCCAATATCATATTCTCCTCCT 60.529 40.741 0.00 0.00 0.00 3.69
69 70 7.732222 ACTCCAATATCATATTCTCCTCCTC 57.268 40.000 0.00 0.00 0.00 3.71
70 71 7.251936 ACTCCAATATCATATTCTCCTCCTCA 58.748 38.462 0.00 0.00 0.00 3.86
71 72 7.736691 ACTCCAATATCATATTCTCCTCCTCAA 59.263 37.037 0.00 0.00 0.00 3.02
72 73 8.691194 TCCAATATCATATTCTCCTCCTCAAT 57.309 34.615 0.00 0.00 0.00 2.57
73 74 9.120658 TCCAATATCATATTCTCCTCCTCAATT 57.879 33.333 0.00 0.00 0.00 2.32
74 75 9.750783 CCAATATCATATTCTCCTCCTCAATTT 57.249 33.333 0.00 0.00 0.00 1.82
111 112 9.184523 TCCTTCAAGTAATTGTTTTCTTCTTCA 57.815 29.630 2.43 0.00 0.00 3.02
112 113 9.801873 CCTTCAAGTAATTGTTTTCTTCTTCAA 57.198 29.630 2.43 0.00 0.00 2.69
129 130 9.204570 TCTTCTTCAACTAAATTTAACCTCTCG 57.795 33.333 0.00 0.00 0.00 4.04
130 131 9.204570 CTTCTTCAACTAAATTTAACCTCTCGA 57.795 33.333 0.00 0.00 0.00 4.04
131 132 8.530269 TCTTCAACTAAATTTAACCTCTCGAC 57.470 34.615 0.00 0.00 0.00 4.20
132 133 8.145767 TCTTCAACTAAATTTAACCTCTCGACA 58.854 33.333 0.00 0.00 0.00 4.35
133 134 8.665643 TTCAACTAAATTTAACCTCTCGACAA 57.334 30.769 0.00 0.00 0.00 3.18
134 135 8.842358 TCAACTAAATTTAACCTCTCGACAAT 57.158 30.769 0.00 0.00 0.00 2.71
135 136 9.932207 TCAACTAAATTTAACCTCTCGACAATA 57.068 29.630 0.00 0.00 0.00 1.90
137 138 8.943909 ACTAAATTTAACCTCTCGACAATAGG 57.056 34.615 0.00 0.00 36.42 2.57
138 139 7.985752 ACTAAATTTAACCTCTCGACAATAGGG 59.014 37.037 0.00 0.00 34.52 3.53
139 140 5.952347 ATTTAACCTCTCGACAATAGGGT 57.048 39.130 0.00 0.00 34.52 4.34
140 141 4.996788 TTAACCTCTCGACAATAGGGTC 57.003 45.455 0.00 0.00 34.52 4.46
149 150 3.832615 GACAATAGGGTCGGTTGGTAT 57.167 47.619 0.00 0.00 0.00 2.73
150 151 4.146745 GACAATAGGGTCGGTTGGTATT 57.853 45.455 0.00 0.00 0.00 1.89
151 152 4.520179 GACAATAGGGTCGGTTGGTATTT 58.480 43.478 0.00 0.00 0.00 1.40
152 153 4.520179 ACAATAGGGTCGGTTGGTATTTC 58.480 43.478 0.00 0.00 0.00 2.17
153 154 3.851458 ATAGGGTCGGTTGGTATTTCC 57.149 47.619 0.00 0.00 0.00 3.13
154 155 0.251073 AGGGTCGGTTGGTATTTCCG 59.749 55.000 0.00 0.00 44.76 4.30
155 156 0.745486 GGGTCGGTTGGTATTTCCGG 60.745 60.000 0.00 0.00 43.75 5.14
156 157 0.036105 GGTCGGTTGGTATTTCCGGT 60.036 55.000 0.00 0.00 43.75 5.28
157 158 1.611410 GGTCGGTTGGTATTTCCGGTT 60.611 52.381 0.00 0.00 43.75 4.44
158 159 1.733912 GTCGGTTGGTATTTCCGGTTC 59.266 52.381 0.00 0.00 43.75 3.62
159 160 1.347050 TCGGTTGGTATTTCCGGTTCA 59.653 47.619 0.00 0.00 43.75 3.18
160 161 2.152830 CGGTTGGTATTTCCGGTTCAA 58.847 47.619 0.00 0.00 40.49 2.69
161 162 2.095617 CGGTTGGTATTTCCGGTTCAAC 60.096 50.000 0.00 8.30 40.49 3.18
162 163 2.229543 GGTTGGTATTTCCGGTTCAACC 59.770 50.000 18.85 18.85 44.46 3.77
163 164 2.885894 GTTGGTATTTCCGGTTCAACCA 59.114 45.455 7.52 14.61 38.47 3.67
164 165 2.506444 TGGTATTTCCGGTTCAACCAC 58.494 47.619 7.52 0.00 38.47 4.16
165 166 1.814394 GGTATTTCCGGTTCAACCACC 59.186 52.381 7.52 1.19 38.47 4.61
166 167 2.553685 GGTATTTCCGGTTCAACCACCT 60.554 50.000 7.52 0.00 38.47 4.00
167 168 1.905637 ATTTCCGGTTCAACCACCTC 58.094 50.000 7.52 0.00 38.47 3.85
168 169 0.841289 TTTCCGGTTCAACCACCTCT 59.159 50.000 7.52 0.00 38.47 3.69
169 170 0.841289 TTCCGGTTCAACCACCTCTT 59.159 50.000 7.52 0.00 38.47 2.85
170 171 1.719529 TCCGGTTCAACCACCTCTTA 58.280 50.000 7.52 0.00 38.47 2.10
171 172 1.621814 TCCGGTTCAACCACCTCTTAG 59.378 52.381 7.52 0.00 38.47 2.18
172 173 1.621814 CCGGTTCAACCACCTCTTAGA 59.378 52.381 7.52 0.00 38.47 2.10
173 174 2.236395 CCGGTTCAACCACCTCTTAGAT 59.764 50.000 7.52 0.00 38.47 1.98
174 175 3.449737 CCGGTTCAACCACCTCTTAGATA 59.550 47.826 7.52 0.00 38.47 1.98
175 176 4.081309 CCGGTTCAACCACCTCTTAGATAA 60.081 45.833 7.52 0.00 38.47 1.75
176 177 5.484715 CGGTTCAACCACCTCTTAGATAAA 58.515 41.667 7.52 0.00 38.47 1.40
177 178 6.113411 CGGTTCAACCACCTCTTAGATAAAT 58.887 40.000 7.52 0.00 38.47 1.40
178 179 6.258068 CGGTTCAACCACCTCTTAGATAAATC 59.742 42.308 7.52 0.00 38.47 2.17
179 180 7.339482 GGTTCAACCACCTCTTAGATAAATCT 58.661 38.462 0.01 0.00 38.42 2.40
180 181 7.829706 GGTTCAACCACCTCTTAGATAAATCTT 59.170 37.037 0.01 0.00 38.42 2.40
181 182 9.232473 GTTCAACCACCTCTTAGATAAATCTTT 57.768 33.333 0.00 0.00 38.32 2.52
182 183 9.449719 TTCAACCACCTCTTAGATAAATCTTTC 57.550 33.333 0.00 0.00 38.32 2.62
183 184 8.047310 TCAACCACCTCTTAGATAAATCTTTCC 58.953 37.037 0.00 0.00 38.32 3.13
184 185 6.901300 ACCACCTCTTAGATAAATCTTTCCC 58.099 40.000 0.00 0.00 38.32 3.97
185 186 6.678857 ACCACCTCTTAGATAAATCTTTCCCT 59.321 38.462 0.00 0.00 38.32 4.20
186 187 7.849904 ACCACCTCTTAGATAAATCTTTCCCTA 59.150 37.037 0.00 0.00 38.32 3.53
187 188 8.151596 CCACCTCTTAGATAAATCTTTCCCTAC 58.848 40.741 0.00 0.00 38.32 3.18
188 189 8.929487 CACCTCTTAGATAAATCTTTCCCTACT 58.071 37.037 0.00 0.00 38.32 2.57
392 393 2.816958 CATCTCGCCTGCGCAGTT 60.817 61.111 33.75 10.12 39.59 3.16
393 394 2.046892 ATCTCGCCTGCGCAGTTT 60.047 55.556 33.75 10.47 39.59 2.66
394 395 2.393768 ATCTCGCCTGCGCAGTTTG 61.394 57.895 33.75 22.70 39.59 2.93
395 396 4.748679 CTCGCCTGCGCAGTTTGC 62.749 66.667 33.75 27.65 40.69 3.68
397 398 4.627447 CGCCTGCGCAGTTTGCAA 62.627 61.111 33.75 0.00 45.36 4.08
398 399 2.279385 GCCTGCGCAGTTTGCAAA 60.279 55.556 33.75 8.05 45.36 3.68
399 400 1.882167 GCCTGCGCAGTTTGCAAAA 60.882 52.632 33.75 0.00 45.36 2.44
400 401 1.427592 GCCTGCGCAGTTTGCAAAAA 61.428 50.000 33.75 0.00 45.36 1.94
434 435 2.776659 GGTATTCAACCCGCAGTCC 58.223 57.895 0.00 0.00 43.16 3.85
435 436 0.252197 GGTATTCAACCCGCAGTCCT 59.748 55.000 0.00 0.00 43.16 3.85
436 437 1.483415 GGTATTCAACCCGCAGTCCTA 59.517 52.381 0.00 0.00 43.16 2.94
437 438 2.104281 GGTATTCAACCCGCAGTCCTAT 59.896 50.000 0.00 0.00 43.16 2.57
438 439 3.433173 GGTATTCAACCCGCAGTCCTATT 60.433 47.826 0.00 0.00 43.16 1.73
439 440 2.871096 TTCAACCCGCAGTCCTATTT 57.129 45.000 0.00 0.00 0.00 1.40
440 441 2.871096 TCAACCCGCAGTCCTATTTT 57.129 45.000 0.00 0.00 0.00 1.82
441 442 3.985019 TCAACCCGCAGTCCTATTTTA 57.015 42.857 0.00 0.00 0.00 1.52
442 443 4.289238 TCAACCCGCAGTCCTATTTTAA 57.711 40.909 0.00 0.00 0.00 1.52
443 444 4.258543 TCAACCCGCAGTCCTATTTTAAG 58.741 43.478 0.00 0.00 0.00 1.85
444 445 3.994931 ACCCGCAGTCCTATTTTAAGT 57.005 42.857 0.00 0.00 0.00 2.24
445 446 3.606687 ACCCGCAGTCCTATTTTAAGTG 58.393 45.455 0.00 0.00 0.00 3.16
446 447 2.943033 CCCGCAGTCCTATTTTAAGTGG 59.057 50.000 0.00 0.00 0.00 4.00
447 448 3.370103 CCCGCAGTCCTATTTTAAGTGGA 60.370 47.826 0.00 0.00 0.00 4.02
448 449 4.451900 CCGCAGTCCTATTTTAAGTGGAT 58.548 43.478 0.00 0.00 0.00 3.41
449 450 5.454187 CCCGCAGTCCTATTTTAAGTGGATA 60.454 44.000 0.00 0.00 0.00 2.59
450 451 6.231211 CCGCAGTCCTATTTTAAGTGGATAT 58.769 40.000 0.00 0.00 0.00 1.63
451 452 6.710744 CCGCAGTCCTATTTTAAGTGGATATT 59.289 38.462 0.00 0.00 0.00 1.28
452 453 7.095187 CCGCAGTCCTATTTTAAGTGGATATTC 60.095 40.741 0.00 0.00 0.00 1.75
453 454 7.657761 CGCAGTCCTATTTTAAGTGGATATTCT 59.342 37.037 0.00 0.00 0.00 2.40
454 455 9.998106 GCAGTCCTATTTTAAGTGGATATTCTA 57.002 33.333 0.00 0.00 0.00 2.10
500 501 3.790089 AAAAGTCCCTAGGGAGTGTTG 57.210 47.619 32.68 6.45 46.46 3.33
501 502 0.984995 AAGTCCCTAGGGAGTGTTGC 59.015 55.000 34.62 20.42 46.46 4.17
502 503 1.218316 GTCCCTAGGGAGTGTTGCG 59.782 63.158 31.88 0.00 46.16 4.85
503 504 2.125106 CCCTAGGGAGTGTTGCGC 60.125 66.667 24.99 0.00 37.50 6.09
504 505 2.125106 CCTAGGGAGTGTTGCGCC 60.125 66.667 4.18 0.00 36.22 6.53
519 520 3.423154 GCCCCTCGCGTCACAAAG 61.423 66.667 5.77 0.00 0.00 2.77
520 521 3.423154 CCCCTCGCGTCACAAAGC 61.423 66.667 5.77 0.00 0.00 3.51
521 522 2.357517 CCCTCGCGTCACAAAGCT 60.358 61.111 5.77 0.00 0.00 3.74
522 523 2.383527 CCCTCGCGTCACAAAGCTC 61.384 63.158 5.77 0.00 0.00 4.09
523 524 1.373497 CCTCGCGTCACAAAGCTCT 60.373 57.895 5.77 0.00 0.00 4.09
524 525 1.621301 CCTCGCGTCACAAAGCTCTG 61.621 60.000 5.77 0.00 0.00 3.35
525 526 2.171940 CGCGTCACAAAGCTCTGC 59.828 61.111 0.00 0.00 0.00 4.26
526 527 2.558313 GCGTCACAAAGCTCTGCC 59.442 61.111 0.00 0.00 0.00 4.85
527 528 2.253758 GCGTCACAAAGCTCTGCCA 61.254 57.895 0.00 0.00 0.00 4.92
528 529 1.571460 CGTCACAAAGCTCTGCCAC 59.429 57.895 0.00 0.00 0.00 5.01
529 530 0.882042 CGTCACAAAGCTCTGCCACT 60.882 55.000 0.00 0.00 0.00 4.00
530 531 0.871057 GTCACAAAGCTCTGCCACTC 59.129 55.000 0.00 0.00 0.00 3.51
531 532 0.761187 TCACAAAGCTCTGCCACTCT 59.239 50.000 0.00 0.00 0.00 3.24
532 533 0.873054 CACAAAGCTCTGCCACTCTG 59.127 55.000 0.00 0.00 0.00 3.35
533 534 0.250640 ACAAAGCTCTGCCACTCTGG 60.251 55.000 0.00 0.00 41.55 3.86
2114 3244 8.918202 ACATTTACTGGAAAACTATTGAGTGA 57.082 30.769 0.00 0.00 35.52 3.41
2209 3339 5.220796 GGCGATAACTCCTTTCCAAACATAC 60.221 44.000 0.00 0.00 0.00 2.39
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.253921 TGATAAAGATGGATGCAATGCGG 59.746 43.478 0.00 0.00 37.56 5.69
1 2 4.492791 TGATAAAGATGGATGCAATGCG 57.507 40.909 0.00 0.00 37.56 4.73
2 3 6.020971 TGATGATAAAGATGGATGCAATGC 57.979 37.500 0.00 0.00 33.97 3.56
3 4 6.581166 CGTTGATGATAAAGATGGATGCAATG 59.419 38.462 0.00 0.00 0.00 2.82
4 5 6.487668 TCGTTGATGATAAAGATGGATGCAAT 59.512 34.615 0.00 0.00 0.00 3.56
7 8 5.237127 TGTCGTTGATGATAAAGATGGATGC 59.763 40.000 0.00 0.00 0.00 3.91
8 9 6.849588 TGTCGTTGATGATAAAGATGGATG 57.150 37.500 0.00 0.00 0.00 3.51
9 10 6.652481 GGATGTCGTTGATGATAAAGATGGAT 59.348 38.462 0.00 0.00 0.00 3.41
10 11 5.991606 GGATGTCGTTGATGATAAAGATGGA 59.008 40.000 0.00 0.00 0.00 3.41
11 12 5.107337 CGGATGTCGTTGATGATAAAGATGG 60.107 44.000 0.00 0.00 0.00 3.51
12 13 5.613360 GCGGATGTCGTTGATGATAAAGATG 60.613 44.000 0.00 0.00 41.72 2.90
13 14 4.449068 GCGGATGTCGTTGATGATAAAGAT 59.551 41.667 0.00 0.00 41.72 2.40
14 15 3.802139 GCGGATGTCGTTGATGATAAAGA 59.198 43.478 0.00 0.00 41.72 2.52
15 16 3.555547 TGCGGATGTCGTTGATGATAAAG 59.444 43.478 0.00 0.00 41.72 1.85
16 17 3.526534 TGCGGATGTCGTTGATGATAAA 58.473 40.909 0.00 0.00 41.72 1.40
17 18 3.172229 TGCGGATGTCGTTGATGATAA 57.828 42.857 0.00 0.00 41.72 1.75
18 19 2.863740 GTTGCGGATGTCGTTGATGATA 59.136 45.455 0.00 0.00 41.72 2.15
19 20 1.665679 GTTGCGGATGTCGTTGATGAT 59.334 47.619 0.00 0.00 41.72 2.45
20 21 1.075542 GTTGCGGATGTCGTTGATGA 58.924 50.000 0.00 0.00 41.72 2.92
21 22 0.795698 TGTTGCGGATGTCGTTGATG 59.204 50.000 0.00 0.00 41.72 3.07
22 23 1.398041 CATGTTGCGGATGTCGTTGAT 59.602 47.619 0.00 0.00 41.72 2.57
23 24 0.795698 CATGTTGCGGATGTCGTTGA 59.204 50.000 0.00 0.00 41.72 3.18
24 25 0.794229 GCATGTTGCGGATGTCGTTG 60.794 55.000 0.00 0.00 41.72 4.10
25 26 1.501741 GCATGTTGCGGATGTCGTT 59.498 52.632 0.00 0.00 41.72 3.85
26 27 3.177600 GCATGTTGCGGATGTCGT 58.822 55.556 0.00 0.00 41.72 4.34
35 36 4.374843 TGATATTGGAGTTGCATGTTGC 57.625 40.909 0.00 0.00 45.29 4.17
36 37 8.573885 AGAATATGATATTGGAGTTGCATGTTG 58.426 33.333 1.80 0.00 0.00 3.33
37 38 8.701908 AGAATATGATATTGGAGTTGCATGTT 57.298 30.769 1.80 0.00 0.00 2.71
38 39 7.392673 GGAGAATATGATATTGGAGTTGCATGT 59.607 37.037 1.80 0.00 0.00 3.21
39 40 7.610692 AGGAGAATATGATATTGGAGTTGCATG 59.389 37.037 1.80 0.00 0.00 4.06
40 41 7.696981 AGGAGAATATGATATTGGAGTTGCAT 58.303 34.615 1.80 0.00 0.00 3.96
41 42 7.083062 AGGAGAATATGATATTGGAGTTGCA 57.917 36.000 1.80 0.00 0.00 4.08
42 43 6.597280 GGAGGAGAATATGATATTGGAGTTGC 59.403 42.308 1.80 0.00 0.00 4.17
43 44 7.915930 AGGAGGAGAATATGATATTGGAGTTG 58.084 38.462 1.80 0.00 0.00 3.16
44 45 7.736691 TGAGGAGGAGAATATGATATTGGAGTT 59.263 37.037 1.80 0.00 0.00 3.01
45 46 7.251936 TGAGGAGGAGAATATGATATTGGAGT 58.748 38.462 1.80 0.00 0.00 3.85
46 47 7.730672 TGAGGAGGAGAATATGATATTGGAG 57.269 40.000 1.80 0.00 0.00 3.86
47 48 8.691194 ATTGAGGAGGAGAATATGATATTGGA 57.309 34.615 1.80 0.00 0.00 3.53
48 49 9.750783 AAATTGAGGAGGAGAATATGATATTGG 57.249 33.333 1.80 0.00 0.00 3.16
85 86 9.184523 TGAAGAAGAAAACAATTACTTGAAGGA 57.815 29.630 0.00 0.00 36.20 3.36
86 87 9.801873 TTGAAGAAGAAAACAATTACTTGAAGG 57.198 29.630 0.00 0.00 36.20 3.46
103 104 9.204570 CGAGAGGTTAAATTTAGTTGAAGAAGA 57.795 33.333 0.00 0.00 0.00 2.87
104 105 9.204570 TCGAGAGGTTAAATTTAGTTGAAGAAG 57.795 33.333 0.00 0.00 0.00 2.85
105 106 8.985805 GTCGAGAGGTTAAATTTAGTTGAAGAA 58.014 33.333 0.00 0.00 0.00 2.52
106 107 8.145767 TGTCGAGAGGTTAAATTTAGTTGAAGA 58.854 33.333 0.00 0.00 0.00 2.87
107 108 8.306680 TGTCGAGAGGTTAAATTTAGTTGAAG 57.693 34.615 0.00 0.00 0.00 3.02
108 109 8.665643 TTGTCGAGAGGTTAAATTTAGTTGAA 57.334 30.769 0.00 0.00 0.00 2.69
109 110 8.842358 ATTGTCGAGAGGTTAAATTTAGTTGA 57.158 30.769 0.00 0.00 0.00 3.18
111 112 9.379791 CCTATTGTCGAGAGGTTAAATTTAGTT 57.620 33.333 0.00 0.00 31.83 2.24
112 113 7.985752 CCCTATTGTCGAGAGGTTAAATTTAGT 59.014 37.037 0.00 0.00 34.81 2.24
113 114 7.985752 ACCCTATTGTCGAGAGGTTAAATTTAG 59.014 37.037 0.00 0.00 34.81 1.85
114 115 7.854337 ACCCTATTGTCGAGAGGTTAAATTTA 58.146 34.615 0.00 0.00 34.81 1.40
115 116 6.718294 ACCCTATTGTCGAGAGGTTAAATTT 58.282 36.000 0.00 0.00 34.81 1.82
116 117 6.309389 ACCCTATTGTCGAGAGGTTAAATT 57.691 37.500 0.00 0.00 34.81 1.82
117 118 5.915175 GACCCTATTGTCGAGAGGTTAAAT 58.085 41.667 0.00 0.00 34.81 1.40
118 119 5.334724 GACCCTATTGTCGAGAGGTTAAA 57.665 43.478 0.00 0.00 34.81 1.52
119 120 4.996788 GACCCTATTGTCGAGAGGTTAA 57.003 45.455 0.00 0.00 34.81 2.01
129 130 3.832615 ATACCAACCGACCCTATTGTC 57.167 47.619 0.00 0.00 0.00 3.18
130 131 4.520179 GAAATACCAACCGACCCTATTGT 58.480 43.478 0.00 0.00 0.00 2.71
131 132 3.881089 GGAAATACCAACCGACCCTATTG 59.119 47.826 0.00 0.00 38.79 1.90
132 133 4.160642 GGAAATACCAACCGACCCTATT 57.839 45.455 0.00 0.00 38.79 1.73
133 134 3.851458 GGAAATACCAACCGACCCTAT 57.149 47.619 0.00 0.00 38.79 2.57
140 141 1.810959 TGAACCGGAAATACCAACCG 58.189 50.000 9.46 0.00 45.24 4.44
141 142 2.229543 GGTTGAACCGGAAATACCAACC 59.770 50.000 9.46 16.75 44.19 3.77
142 143 2.885894 TGGTTGAACCGGAAATACCAAC 59.114 45.455 9.46 11.91 42.58 3.77
143 144 2.885894 GTGGTTGAACCGGAAATACCAA 59.114 45.455 9.46 0.00 42.58 3.67
144 145 2.506444 GTGGTTGAACCGGAAATACCA 58.494 47.619 9.46 13.71 42.58 3.25
145 146 1.814394 GGTGGTTGAACCGGAAATACC 59.186 52.381 9.46 11.02 42.58 2.73
146 147 2.745821 GAGGTGGTTGAACCGGAAATAC 59.254 50.000 9.46 0.68 45.53 1.89
147 148 2.640826 AGAGGTGGTTGAACCGGAAATA 59.359 45.455 9.46 0.00 45.53 1.40
148 149 1.423921 AGAGGTGGTTGAACCGGAAAT 59.576 47.619 9.46 0.00 45.53 2.17
149 150 0.841289 AGAGGTGGTTGAACCGGAAA 59.159 50.000 9.46 0.00 45.53 3.13
150 151 0.841289 AAGAGGTGGTTGAACCGGAA 59.159 50.000 9.46 0.00 45.53 4.30
151 152 1.621814 CTAAGAGGTGGTTGAACCGGA 59.378 52.381 9.46 0.00 45.53 5.14
152 153 1.621814 TCTAAGAGGTGGTTGAACCGG 59.378 52.381 10.16 0.00 45.53 5.28
153 154 3.611766 ATCTAAGAGGTGGTTGAACCG 57.388 47.619 10.16 0.00 45.53 4.44
154 155 7.339482 AGATTTATCTAAGAGGTGGTTGAACC 58.661 38.462 7.57 7.57 36.51 3.62
155 156 8.794335 AAGATTTATCTAAGAGGTGGTTGAAC 57.206 34.615 0.00 0.00 35.76 3.18
156 157 9.449719 GAAAGATTTATCTAAGAGGTGGTTGAA 57.550 33.333 0.00 0.00 35.76 2.69
157 158 8.047310 GGAAAGATTTATCTAAGAGGTGGTTGA 58.953 37.037 0.00 0.00 35.76 3.18
158 159 7.283354 GGGAAAGATTTATCTAAGAGGTGGTTG 59.717 40.741 0.00 0.00 35.76 3.77
159 160 7.184753 AGGGAAAGATTTATCTAAGAGGTGGTT 59.815 37.037 0.00 0.00 35.76 3.67
160 161 6.678857 AGGGAAAGATTTATCTAAGAGGTGGT 59.321 38.462 0.00 0.00 35.76 4.16
161 162 7.142995 AGGGAAAGATTTATCTAAGAGGTGG 57.857 40.000 0.00 0.00 35.76 4.61
162 163 8.929487 AGTAGGGAAAGATTTATCTAAGAGGTG 58.071 37.037 0.00 0.00 35.76 4.00
174 175 9.755122 AAGTGCTTTATTAGTAGGGAAAGATTT 57.245 29.630 0.00 0.00 31.83 2.17
259 260 6.948309 ACTTAAAATAGGACTGCAGGTTGAAT 59.052 34.615 19.93 1.81 0.00 2.57
267 268 8.494433 AGAATATCCACTTAAAATAGGACTGCA 58.506 33.333 0.00 0.00 32.04 4.41
416 417 0.252197 AGGACTGCGGGTTGAATACC 59.748 55.000 0.00 0.00 46.99 2.73
417 418 2.973694 TAGGACTGCGGGTTGAATAC 57.026 50.000 0.00 0.00 0.00 1.89
418 419 4.497291 AAATAGGACTGCGGGTTGAATA 57.503 40.909 0.00 0.00 0.00 1.75
419 420 3.366052 AAATAGGACTGCGGGTTGAAT 57.634 42.857 0.00 0.00 0.00 2.57
420 421 2.871096 AAATAGGACTGCGGGTTGAA 57.129 45.000 0.00 0.00 0.00 2.69
421 422 2.871096 AAAATAGGACTGCGGGTTGA 57.129 45.000 0.00 0.00 0.00 3.18
422 423 4.007659 ACTTAAAATAGGACTGCGGGTTG 58.992 43.478 0.00 0.00 0.00 3.77
423 424 4.007659 CACTTAAAATAGGACTGCGGGTT 58.992 43.478 0.00 0.00 0.00 4.11
424 425 3.606687 CACTTAAAATAGGACTGCGGGT 58.393 45.455 0.00 0.00 0.00 5.28
425 426 2.943033 CCACTTAAAATAGGACTGCGGG 59.057 50.000 0.00 0.00 0.00 6.13
426 427 3.869065 TCCACTTAAAATAGGACTGCGG 58.131 45.455 0.00 0.00 0.00 5.69
427 428 7.657761 AGAATATCCACTTAAAATAGGACTGCG 59.342 37.037 0.00 0.00 32.04 5.18
428 429 8.910351 AGAATATCCACTTAAAATAGGACTGC 57.090 34.615 0.00 0.00 32.04 4.40
479 480 3.750922 GCAACACTCCCTAGGGACTTTTT 60.751 47.826 27.73 14.05 41.75 1.94
480 481 2.224793 GCAACACTCCCTAGGGACTTTT 60.225 50.000 27.73 15.83 41.75 2.27
481 482 1.351350 GCAACACTCCCTAGGGACTTT 59.649 52.381 27.73 16.19 41.75 2.66
482 483 0.984995 GCAACACTCCCTAGGGACTT 59.015 55.000 27.73 13.90 41.75 3.01
483 484 1.258445 CGCAACACTCCCTAGGGACT 61.258 60.000 27.73 15.47 46.37 3.85
484 485 1.218316 CGCAACACTCCCTAGGGAC 59.782 63.158 27.73 14.78 39.76 4.46
485 486 2.656069 GCGCAACACTCCCTAGGGA 61.656 63.158 29.25 29.25 42.90 4.20
486 487 2.125106 GCGCAACACTCCCTAGGG 60.125 66.667 23.22 23.22 0.00 3.53
487 488 2.125106 GGCGCAACACTCCCTAGG 60.125 66.667 10.83 0.06 0.00 3.02
488 489 2.125106 GGGCGCAACACTCCCTAG 60.125 66.667 10.83 0.00 37.08 3.02
489 490 3.712907 GGGGCGCAACACTCCCTA 61.713 66.667 10.83 0.00 39.95 3.53
502 503 3.423154 CTTTGTGACGCGAGGGGC 61.423 66.667 15.93 0.00 38.69 5.80
503 504 3.423154 GCTTTGTGACGCGAGGGG 61.423 66.667 15.93 0.00 0.00 4.79
504 505 2.357517 AGCTTTGTGACGCGAGGG 60.358 61.111 15.93 0.00 0.00 4.30
505 506 1.373497 AGAGCTTTGTGACGCGAGG 60.373 57.895 15.93 0.00 0.00 4.63
506 507 1.777819 CAGAGCTTTGTGACGCGAG 59.222 57.895 15.93 0.00 0.00 5.03
507 508 2.310233 GCAGAGCTTTGTGACGCGA 61.310 57.895 15.93 0.00 0.00 5.87
508 509 2.171940 GCAGAGCTTTGTGACGCG 59.828 61.111 3.53 3.53 0.00 6.01
509 510 2.253758 TGGCAGAGCTTTGTGACGC 61.254 57.895 6.08 0.00 0.00 5.19
510 511 0.882042 AGTGGCAGAGCTTTGTGACG 60.882 55.000 6.08 0.00 0.00 4.35
511 512 0.871057 GAGTGGCAGAGCTTTGTGAC 59.129 55.000 6.08 3.22 0.00 3.67
512 513 0.761187 AGAGTGGCAGAGCTTTGTGA 59.239 50.000 6.08 0.00 0.00 3.58
513 514 0.873054 CAGAGTGGCAGAGCTTTGTG 59.127 55.000 6.08 0.00 0.00 3.33
514 515 0.250640 CCAGAGTGGCAGAGCTTTGT 60.251 55.000 6.08 0.00 0.00 2.83
515 516 2.552802 CCAGAGTGGCAGAGCTTTG 58.447 57.895 0.00 0.00 0.00 2.77
525 526 2.584418 CGAGATGCGCCAGAGTGG 60.584 66.667 4.18 0.00 41.55 4.00
565 569 1.027792 GCGAGGAGAGGACGAGAAGT 61.028 60.000 0.00 0.00 0.00 3.01
682 742 4.681978 GCTCGTCCTTGTGGCGGT 62.682 66.667 0.00 0.00 34.97 5.68
957 1116 1.474077 CTATCAAACAACAGCTGGGGC 59.526 52.381 19.93 0.00 39.06 5.80
958 1117 3.071874 TCTATCAAACAACAGCTGGGG 57.928 47.619 19.93 12.01 0.00 4.96
961 1120 4.690184 TGCATCTATCAAACAACAGCTG 57.310 40.909 13.48 13.48 0.00 4.24
962 1121 5.710513 TTTGCATCTATCAAACAACAGCT 57.289 34.783 0.00 0.00 0.00 4.24
2114 3244 4.019174 CCATGAGCTTTGGTTCCACTTAT 58.981 43.478 8.18 0.00 0.00 1.73
2209 3339 6.640907 GCCGAATAATAACCCATTAGCAAAAG 59.359 38.462 0.00 0.00 32.61 2.27


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

AutoCloner maintained by Alex Coulton.