Multiple sequence alignment - TraesCS3B01G002400

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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 TraesCS3B01G002400 chr3B 100.000 4164 0 0 1 4164 2131539 2127376 0.000000e+00 7690.0
1 TraesCS3B01G002400 chr3B 98.753 3368 13 6 308 3647 2322219 2325585 0.000000e+00 5960.0
2 TraesCS3B01G002400 chr3B 99.438 534 3 0 3631 4164 2327315 2327848 0.000000e+00 970.0
3 TraesCS3B01G002400 chr3B 81.767 532 88 7 1898 2428 2344936 2345459 1.780000e-118 436.0
4 TraesCS3B01G002400 chr3B 81.967 488 80 6 1940 2425 2256529 2256048 1.390000e-109 407.0
5 TraesCS3B01G002400 chr3B 80.725 524 90 7 1907 2425 2109712 2109195 8.390000e-107 398.0
6 TraesCS3B01G002400 chr3B 80.435 276 42 9 1443 1710 2145421 2145150 2.540000e-47 200.0
7 TraesCS3B01G002400 chr3B 80.488 246 26 12 974 1218 2257396 2257172 7.160000e-38 169.0
8 TraesCS3B01G002400 chr3B 91.139 79 7 0 3094 3172 2169579 2169501 1.580000e-19 108.0
9 TraesCS3B01G002400 chr3B 93.617 47 3 0 841 887 2110709 2110663 2.080000e-08 71.3
10 TraesCS3B01G002400 chr3B 100.000 30 0 0 336 365 476291454 476291425 5.820000e-04 56.5
11 TraesCS3B01G002400 chr3D 89.389 1800 160 15 1893 3672 3098283 3096495 0.000000e+00 2237.0
12 TraesCS3B01G002400 chr3D 89.787 705 45 8 546 1240 3100011 3099324 0.000000e+00 878.0
13 TraesCS3B01G002400 chr3D 82.260 823 120 21 2159 2974 3151921 3151118 0.000000e+00 688.0
14 TraesCS3B01G002400 chr3D 89.157 498 51 2 3668 4163 3096125 3095629 5.910000e-173 617.0
15 TraesCS3B01G002400 chr3D 91.045 335 22 3 912 1245 3155080 3154753 2.950000e-121 446.0
16 TraesCS3B01G002400 chr3D 79.213 712 81 33 565 1245 3181797 3181122 2.300000e-117 433.0
17 TraesCS3B01G002400 chr3D 88.315 368 15 8 1351 1714 3152974 3152631 2.320000e-112 416.0
18 TraesCS3B01G002400 chr3D 81.967 488 79 7 1940 2425 3073689 3073209 5.010000e-109 405.0
19 TraesCS3B01G002400 chr3D 89.062 320 27 3 1298 1612 3099052 3098736 1.400000e-104 390.0
20 TraesCS3B01G002400 chr3D 74.398 914 167 38 2578 3447 3053500 3052610 3.100000e-86 329.0
21 TraesCS3B01G002400 chr3D 95.960 198 8 0 1687 1884 3098709 3098512 5.190000e-84 322.0
22 TraesCS3B01G002400 chr3D 88.199 161 15 3 1 160 583150988 583150831 5.500000e-44 189.0
23 TraesCS3B01G002400 chr3D 80.435 276 27 17 974 1242 3085831 3085576 7.110000e-43 185.0
24 TraesCS3B01G002400 chr3D 78.986 276 48 7 3008 3283 3072691 3072426 3.310000e-41 180.0
25 TraesCS3B01G002400 chr3D 85.165 182 9 8 366 529 3155619 3155438 1.990000e-38 171.0
26 TraesCS3B01G002400 chr3D 92.000 75 6 0 3094 3168 3196784 3196710 5.690000e-19 106.0
27 TraesCS3B01G002400 chr3D 100.000 30 0 0 336 365 365789823 365789794 5.820000e-04 56.5
28 TraesCS3B01G002400 chr3A 85.297 1061 120 23 1886 2922 206526 205478 0.000000e+00 1062.0
29 TraesCS3B01G002400 chr3A 84.091 616 91 7 3059 3671 205036 204425 4.640000e-164 588.0
30 TraesCS3B01G002400 chr3A 83.218 578 85 9 1301 1876 207397 206830 1.720000e-143 520.0
31 TraesCS3B01G002400 chr3A 82.377 488 79 6 1940 2425 131440 130958 6.440000e-113 418.0
32 TraesCS3B01G002400 chr3A 88.604 351 23 4 546 896 208204 207871 1.080000e-110 411.0
33 TraesCS3B01G002400 chr3A 85.979 378 48 2 921 1294 207887 207511 2.330000e-107 399.0
34 TraesCS3B01G002400 chr3A 79.849 531 95 10 1901 2428 141541 141020 1.090000e-100 377.0
35 TraesCS3B01G002400 chr3A 78.555 443 73 12 3007 3447 140340 139918 5.300000e-69 272.0
36 TraesCS3B01G002400 chr3A 84.746 177 14 8 366 529 208456 208280 9.260000e-37 165.0
37 TraesCS3B01G002400 chr3A 84.828 145 19 3 19 162 738603638 738603496 4.340000e-30 143.0
38 TraesCS3B01G002400 chr3A 84.828 145 19 3 19 162 738682575 738682433 4.340000e-30 143.0
39 TraesCS3B01G002400 chr3A 76.494 251 41 14 3094 3336 398129 397889 2.030000e-23 121.0
40 TraesCS3B01G002400 chr3A 82.278 79 10 3 288 366 35436901 35436827 9.660000e-07 65.8
41 TraesCS3B01G002400 chr3A 97.059 34 0 1 339 372 97047705 97047673 5.820000e-04 56.5
42 TraesCS3B01G002400 chr3A 100.000 30 0 0 336 365 487459520 487459491 5.820000e-04 56.5
43 TraesCS3B01G002400 chr2B 92.500 160 10 2 3 162 768107637 768107794 1.160000e-55 228.0
44 TraesCS3B01G002400 chr4A 90.000 160 15 1 3 162 709618196 709618354 5.460000e-49 206.0
45 TraesCS3B01G002400 chr6D 86.875 160 20 1 3 162 80175764 80175922 1.190000e-40 178.0
46 TraesCS3B01G002400 chr6D 81.690 71 5 6 295 365 54266601 54266663 8.000000e-03 52.8
47 TraesCS3B01G002400 chr7B 85.161 155 16 5 12 162 629014354 629014203 7.210000e-33 152.0
48 TraesCS3B01G002400 chr4B 79.279 222 24 12 981 1195 653431838 653431632 7.260000e-28 135.0
49 TraesCS3B01G002400 chr4B 78.924 223 25 12 980 1195 653009321 653009528 9.390000e-27 132.0
50 TraesCS3B01G002400 chrUn 78.829 222 25 12 981 1195 126953973 126953767 3.380000e-26 130.0
51 TraesCS3B01G002400 chr5A 78.607 201 25 11 998 1195 690561077 690561262 2.630000e-22 117.0
52 TraesCS3B01G002400 chr5A 96.875 32 1 0 296 327 525124397 525124366 2.000000e-03 54.7
53 TraesCS3B01G002400 chr2A 100.000 30 0 0 336 365 738435354 738435383 5.820000e-04 56.5
54 TraesCS3B01G002400 chr2D 94.286 35 1 1 338 372 169042518 169042551 8.000000e-03 52.8
55 TraesCS3B01G002400 chr1A 92.105 38 2 1 328 365 14074798 14074762 8.000000e-03 52.8


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 TraesCS3B01G002400 chr3B 2127376 2131539 4163 True 7690.000000 7690 100.00000 1 4164 1 chr3B.!!$R1 4163
1 TraesCS3B01G002400 chr3B 2322219 2327848 5629 False 3465.000000 5960 99.09550 308 4164 2 chr3B.!!$F2 3856
2 TraesCS3B01G002400 chr3B 2344936 2345459 523 False 436.000000 436 81.76700 1898 2428 1 chr3B.!!$F1 530
3 TraesCS3B01G002400 chr3B 2256048 2257396 1348 True 288.000000 407 81.22750 974 2425 2 chr3B.!!$R6 1451
4 TraesCS3B01G002400 chr3B 2109195 2110709 1514 True 234.650000 398 87.17100 841 2425 2 chr3B.!!$R5 1584
5 TraesCS3B01G002400 chr3D 3095629 3100011 4382 True 888.800000 2237 90.67100 546 4163 5 chr3D.!!$R8 3617
6 TraesCS3B01G002400 chr3D 3181122 3181797 675 True 433.000000 433 79.21300 565 1245 1 chr3D.!!$R3 680
7 TraesCS3B01G002400 chr3D 3151118 3155619 4501 True 430.250000 688 86.69625 366 2974 4 chr3D.!!$R9 2608
8 TraesCS3B01G002400 chr3D 3052610 3053500 890 True 329.000000 329 74.39800 2578 3447 1 chr3D.!!$R1 869
9 TraesCS3B01G002400 chr3D 3072426 3073689 1263 True 292.500000 405 80.47650 1940 3283 2 chr3D.!!$R7 1343
10 TraesCS3B01G002400 chr3A 204425 208456 4031 True 524.166667 1062 85.32250 366 3671 6 chr3A.!!$R9 3305
11 TraesCS3B01G002400 chr3A 139918 141541 1623 True 324.500000 377 79.20200 1901 3447 2 chr3A.!!$R8 1546

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
176 177 0.03601 CGAGGTTGCTCCAAGGACAT 60.036 55.0 1.79 0.0 39.02 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3530 6981 6.767524 TGTATTTTGTTGGGGCTATAACTG 57.232 37.5 0.0 0.0 0.0 3.16 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 2.770164 ACCAAGACGAGAAAGATGGG 57.230 50.000 0.00 0.00 32.21 4.00
21 22 1.279271 ACCAAGACGAGAAAGATGGGG 59.721 52.381 0.00 0.00 32.21 4.96
22 23 1.555075 CCAAGACGAGAAAGATGGGGA 59.445 52.381 0.00 0.00 0.00 4.81
23 24 2.419297 CCAAGACGAGAAAGATGGGGAG 60.419 54.545 0.00 0.00 0.00 4.30
24 25 2.497675 CAAGACGAGAAAGATGGGGAGA 59.502 50.000 0.00 0.00 0.00 3.71
25 26 2.821437 AGACGAGAAAGATGGGGAGAA 58.179 47.619 0.00 0.00 0.00 2.87
26 27 2.763448 AGACGAGAAAGATGGGGAGAAG 59.237 50.000 0.00 0.00 0.00 2.85
27 28 1.208293 ACGAGAAAGATGGGGAGAAGC 59.792 52.381 0.00 0.00 0.00 3.86
28 29 1.474143 CGAGAAAGATGGGGAGAAGCC 60.474 57.143 0.00 0.00 0.00 4.35
87 88 4.504916 CAGACAGCGGCGAGGAGG 62.505 72.222 12.98 0.00 0.00 4.30
94 95 2.904866 CGGCGAGGAGGGAGAGAG 60.905 72.222 0.00 0.00 0.00 3.20
95 96 2.520741 GGCGAGGAGGGAGAGAGG 60.521 72.222 0.00 0.00 0.00 3.69
96 97 3.223589 GCGAGGAGGGAGAGAGGC 61.224 72.222 0.00 0.00 0.00 4.70
97 98 2.904866 CGAGGAGGGAGAGAGGCG 60.905 72.222 0.00 0.00 0.00 5.52
98 99 2.520741 GAGGAGGGAGAGAGGCGG 60.521 72.222 0.00 0.00 0.00 6.13
99 100 3.024356 AGGAGGGAGAGAGGCGGA 61.024 66.667 0.00 0.00 0.00 5.54
100 101 2.520741 GGAGGGAGAGAGGCGGAG 60.521 72.222 0.00 0.00 0.00 4.63
101 102 2.520741 GAGGGAGAGAGGCGGAGG 60.521 72.222 0.00 0.00 0.00 4.30
102 103 3.024356 AGGGAGAGAGGCGGAGGA 61.024 66.667 0.00 0.00 0.00 3.71
103 104 2.520741 GGGAGAGAGGCGGAGGAG 60.521 72.222 0.00 0.00 0.00 3.69
104 105 2.520741 GGAGAGAGGCGGAGGAGG 60.521 72.222 0.00 0.00 0.00 4.30
105 106 2.277404 GAGAGAGGCGGAGGAGGT 59.723 66.667 0.00 0.00 0.00 3.85
106 107 2.043450 AGAGAGGCGGAGGAGGTG 60.043 66.667 0.00 0.00 0.00 4.00
107 108 3.844090 GAGAGGCGGAGGAGGTGC 61.844 72.222 0.00 0.00 0.00 5.01
112 113 4.373116 GCGGAGGAGGTGCGTGAA 62.373 66.667 0.00 0.00 43.07 3.18
113 114 2.125912 CGGAGGAGGTGCGTGAAG 60.126 66.667 0.00 0.00 34.79 3.02
130 131 2.189784 GCGGAGGCTAGGGTTTCC 59.810 66.667 0.00 0.00 35.83 3.13
131 132 2.908796 CGGAGGCTAGGGTTTCCC 59.091 66.667 0.00 0.00 45.90 3.97
169 170 4.717629 CGACGCGAGGTTGCTCCA 62.718 66.667 15.93 0.00 39.02 3.86
170 171 2.357034 GACGCGAGGTTGCTCCAA 60.357 61.111 15.93 0.00 39.02 3.53
171 172 2.357517 ACGCGAGGTTGCTCCAAG 60.358 61.111 15.93 0.00 39.02 3.61
172 173 3.121030 CGCGAGGTTGCTCCAAGG 61.121 66.667 0.00 0.00 39.02 3.61
173 174 2.347490 GCGAGGTTGCTCCAAGGA 59.653 61.111 0.00 0.00 39.02 3.36
174 175 2.035442 GCGAGGTTGCTCCAAGGAC 61.035 63.158 0.00 0.00 39.02 3.85
175 176 1.371183 CGAGGTTGCTCCAAGGACA 59.629 57.895 1.79 0.00 39.02 4.02
176 177 0.036010 CGAGGTTGCTCCAAGGACAT 60.036 55.000 1.79 0.00 39.02 3.06
177 178 1.457346 GAGGTTGCTCCAAGGACATG 58.543 55.000 0.00 0.00 39.02 3.21
178 179 0.610232 AGGTTGCTCCAAGGACATGC 60.610 55.000 0.00 0.00 39.02 4.06
179 180 0.895100 GGTTGCTCCAAGGACATGCA 60.895 55.000 0.00 0.00 35.97 3.96
180 181 0.242017 GTTGCTCCAAGGACATGCAC 59.758 55.000 1.46 0.00 33.13 4.57
181 182 0.178995 TTGCTCCAAGGACATGCACA 60.179 50.000 1.46 0.00 33.13 4.57
182 183 0.178995 TGCTCCAAGGACATGCACAA 60.179 50.000 0.00 0.00 0.00 3.33
183 184 0.242017 GCTCCAAGGACATGCACAAC 59.758 55.000 0.00 0.00 0.00 3.32
184 185 1.901591 CTCCAAGGACATGCACAACT 58.098 50.000 0.00 0.00 0.00 3.16
185 186 2.233271 CTCCAAGGACATGCACAACTT 58.767 47.619 0.00 0.00 0.00 2.66
186 187 2.624838 CTCCAAGGACATGCACAACTTT 59.375 45.455 0.00 0.00 0.00 2.66
187 188 3.030291 TCCAAGGACATGCACAACTTTT 58.970 40.909 0.00 0.00 0.00 2.27
188 189 4.211125 TCCAAGGACATGCACAACTTTTA 58.789 39.130 0.00 0.00 0.00 1.52
189 190 4.832266 TCCAAGGACATGCACAACTTTTAT 59.168 37.500 0.00 0.00 0.00 1.40
190 191 6.007076 TCCAAGGACATGCACAACTTTTATA 58.993 36.000 0.00 0.00 0.00 0.98
191 192 6.150976 TCCAAGGACATGCACAACTTTTATAG 59.849 38.462 0.00 0.00 0.00 1.31
192 193 6.324819 CAAGGACATGCACAACTTTTATAGG 58.675 40.000 0.00 0.00 0.00 2.57
193 194 5.570320 AGGACATGCACAACTTTTATAGGT 58.430 37.500 0.00 0.00 0.00 3.08
194 195 6.010219 AGGACATGCACAACTTTTATAGGTT 58.990 36.000 0.00 0.00 0.00 3.50
195 196 7.172342 AGGACATGCACAACTTTTATAGGTTA 58.828 34.615 0.00 0.00 0.00 2.85
196 197 7.834181 AGGACATGCACAACTTTTATAGGTTAT 59.166 33.333 0.00 0.00 0.00 1.89
197 198 8.466798 GGACATGCACAACTTTTATAGGTTATT 58.533 33.333 0.00 0.00 0.00 1.40
198 199 9.289303 GACATGCACAACTTTTATAGGTTATTG 57.711 33.333 0.00 0.00 0.00 1.90
199 200 7.759433 ACATGCACAACTTTTATAGGTTATTGC 59.241 33.333 0.00 6.86 35.75 3.56
200 201 7.220741 TGCACAACTTTTATAGGTTATTGCA 57.779 32.000 10.43 10.43 39.30 4.08
201 202 7.661968 TGCACAACTTTTATAGGTTATTGCAA 58.338 30.769 0.00 0.00 38.99 4.08
202 203 7.596995 TGCACAACTTTTATAGGTTATTGCAAC 59.403 33.333 0.00 0.00 38.99 4.17
203 204 7.596995 GCACAACTTTTATAGGTTATTGCAACA 59.403 33.333 0.00 0.00 35.50 3.33
204 205 8.911662 CACAACTTTTATAGGTTATTGCAACAC 58.088 33.333 0.00 0.98 0.00 3.32
205 206 8.634444 ACAACTTTTATAGGTTATTGCAACACA 58.366 29.630 0.00 0.00 0.00 3.72
206 207 9.638239 CAACTTTTATAGGTTATTGCAACACAT 57.362 29.630 0.00 1.70 0.00 3.21
211 212 9.899661 TTTATAGGTTATTGCAACACATACTCT 57.100 29.630 0.00 0.00 0.00 3.24
216 217 8.150945 AGGTTATTGCAACACATACTCTATAGG 58.849 37.037 0.00 0.00 0.00 2.57
217 218 7.931948 GGTTATTGCAACACATACTCTATAGGT 59.068 37.037 0.00 0.00 0.00 3.08
218 219 8.765219 GTTATTGCAACACATACTCTATAGGTG 58.235 37.037 0.00 2.42 35.66 4.00
219 220 5.932619 TGCAACACATACTCTATAGGTGT 57.067 39.130 0.00 3.06 43.93 4.16
220 221 7.412853 TTGCAACACATACTCTATAGGTGTA 57.587 36.000 10.82 9.52 41.45 2.90
221 222 7.597288 TGCAACACATACTCTATAGGTGTAT 57.403 36.000 10.82 11.00 41.45 2.29
222 223 8.018537 TGCAACACATACTCTATAGGTGTATT 57.981 34.615 10.82 0.99 41.45 1.89
223 224 8.482943 TGCAACACATACTCTATAGGTGTATTT 58.517 33.333 10.82 6.11 41.45 1.40
224 225 9.326413 GCAACACATACTCTATAGGTGTATTTT 57.674 33.333 10.82 6.04 41.45 1.82
246 247 7.517614 TTTTTGTAGACATTGTCCATTAGCA 57.482 32.000 13.14 1.71 32.18 3.49
247 248 6.494893 TTTGTAGACATTGTCCATTAGCAC 57.505 37.500 13.14 1.93 32.18 4.40
248 249 5.420725 TGTAGACATTGTCCATTAGCACT 57.579 39.130 13.14 0.00 32.18 4.40
249 250 6.538945 TGTAGACATTGTCCATTAGCACTA 57.461 37.500 13.14 0.00 32.18 2.74
250 251 6.941857 TGTAGACATTGTCCATTAGCACTAA 58.058 36.000 13.14 0.00 32.18 2.24
251 252 6.816640 TGTAGACATTGTCCATTAGCACTAAC 59.183 38.462 13.14 0.00 32.18 2.34
252 253 5.186198 AGACATTGTCCATTAGCACTAACC 58.814 41.667 13.14 0.00 32.18 2.85
253 254 4.917385 ACATTGTCCATTAGCACTAACCA 58.083 39.130 0.00 0.00 0.00 3.67
254 255 4.700213 ACATTGTCCATTAGCACTAACCAC 59.300 41.667 0.00 0.00 0.00 4.16
255 256 4.359434 TTGTCCATTAGCACTAACCACA 57.641 40.909 0.00 0.00 0.00 4.17
256 257 4.568072 TGTCCATTAGCACTAACCACAT 57.432 40.909 0.00 0.00 0.00 3.21
257 258 4.513442 TGTCCATTAGCACTAACCACATC 58.487 43.478 0.00 0.00 0.00 3.06
258 259 3.877508 GTCCATTAGCACTAACCACATCC 59.122 47.826 0.00 0.00 0.00 3.51
259 260 3.521531 TCCATTAGCACTAACCACATCCA 59.478 43.478 0.00 0.00 0.00 3.41
260 261 3.879295 CCATTAGCACTAACCACATCCAG 59.121 47.826 0.00 0.00 0.00 3.86
261 262 4.517285 CATTAGCACTAACCACATCCAGT 58.483 43.478 0.00 0.00 0.00 4.00
273 274 3.827008 ACATCCAGTGAGCATCGTATT 57.173 42.857 0.00 0.00 38.61 1.89
274 275 4.937201 ACATCCAGTGAGCATCGTATTA 57.063 40.909 0.00 0.00 38.61 0.98
275 276 5.474578 ACATCCAGTGAGCATCGTATTAT 57.525 39.130 0.00 0.00 38.61 1.28
276 277 5.858381 ACATCCAGTGAGCATCGTATTATT 58.142 37.500 0.00 0.00 38.61 1.40
277 278 5.698089 ACATCCAGTGAGCATCGTATTATTG 59.302 40.000 0.00 0.00 38.61 1.90
278 279 5.276461 TCCAGTGAGCATCGTATTATTGT 57.724 39.130 0.00 0.00 38.61 2.71
279 280 5.289595 TCCAGTGAGCATCGTATTATTGTC 58.710 41.667 0.00 0.00 38.61 3.18
280 281 5.069119 TCCAGTGAGCATCGTATTATTGTCT 59.931 40.000 0.00 0.00 38.61 3.41
281 282 6.264518 TCCAGTGAGCATCGTATTATTGTCTA 59.735 38.462 0.00 0.00 38.61 2.59
282 283 6.923508 CCAGTGAGCATCGTATTATTGTCTAA 59.076 38.462 0.00 0.00 38.61 2.10
283 284 7.600375 CCAGTGAGCATCGTATTATTGTCTAAT 59.400 37.037 0.00 0.00 38.61 1.73
284 285 8.982685 CAGTGAGCATCGTATTATTGTCTAATT 58.017 33.333 0.00 0.00 38.61 1.40
285 286 9.197694 AGTGAGCATCGTATTATTGTCTAATTC 57.802 33.333 0.00 0.00 38.61 2.17
286 287 9.197694 GTGAGCATCGTATTATTGTCTAATTCT 57.802 33.333 0.00 0.00 38.61 2.40
306 307 6.939132 TTCTATTGTTCTACTACTCCCTCG 57.061 41.667 0.00 0.00 0.00 4.63
321 322 4.528596 ACTCCCTCGGATCCATATTAGTTG 59.471 45.833 13.41 0.00 0.00 3.16
323 324 4.905456 TCCCTCGGATCCATATTAGTTGTT 59.095 41.667 13.41 0.00 0.00 2.83
331 332 7.415095 CGGATCCATATTAGTTGTTGCTCAAAA 60.415 37.037 13.41 0.00 37.81 2.44
334 335 5.799936 CCATATTAGTTGTTGCTCAAAACCG 59.200 40.000 0.00 0.00 37.81 4.44
338 339 1.786579 GTTGTTGCTCAAAACCGATGC 59.213 47.619 0.00 0.00 37.81 3.91
339 340 1.028130 TGTTGCTCAAAACCGATGCA 58.972 45.000 0.00 0.00 0.00 3.96
347 348 0.881118 AAAACCGATGCAGCGACAAT 59.119 45.000 28.29 6.39 0.00 2.71
360 361 4.436050 GCAGCGACAATTAATATGGATCGG 60.436 45.833 0.00 0.00 0.00 4.18
369 380 6.945636 ATTAATATGGATCGGAGGGTTGTA 57.054 37.500 0.00 0.00 0.00 2.41
3530 6981 9.261180 TGAATATCGAGGTTGAATAGAATTGTC 57.739 33.333 0.00 0.00 0.00 3.18
3852 9427 3.517901 CAGTTCTGACTACCCCCATGTTA 59.482 47.826 0.00 0.00 33.90 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.290323 CCCCATCTTTCTCGTCTTGGTT 60.290 50.000 0.00 0.00 0.00 3.67
2 3 1.555075 TCCCCATCTTTCTCGTCTTGG 59.445 52.381 0.00 0.00 0.00 3.61
5 6 2.534042 TCTCCCCATCTTTCTCGTCT 57.466 50.000 0.00 0.00 0.00 4.18
6 7 2.740256 GCTTCTCCCCATCTTTCTCGTC 60.740 54.545 0.00 0.00 0.00 4.20
7 8 1.208293 GCTTCTCCCCATCTTTCTCGT 59.792 52.381 0.00 0.00 0.00 4.18
8 9 1.474143 GGCTTCTCCCCATCTTTCTCG 60.474 57.143 0.00 0.00 0.00 4.04
9 10 2.340210 GGCTTCTCCCCATCTTTCTC 57.660 55.000 0.00 0.00 0.00 2.87
70 71 4.504916 CCTCCTCGCCGCTGTCTG 62.505 72.222 0.00 0.00 0.00 3.51
77 78 2.904866 CTCTCTCCCTCCTCGCCG 60.905 72.222 0.00 0.00 0.00 6.46
78 79 2.520741 CCTCTCTCCCTCCTCGCC 60.521 72.222 0.00 0.00 0.00 5.54
79 80 3.223589 GCCTCTCTCCCTCCTCGC 61.224 72.222 0.00 0.00 0.00 5.03
80 81 2.904866 CGCCTCTCTCCCTCCTCG 60.905 72.222 0.00 0.00 0.00 4.63
81 82 2.520741 CCGCCTCTCTCCCTCCTC 60.521 72.222 0.00 0.00 0.00 3.71
82 83 3.024356 TCCGCCTCTCTCCCTCCT 61.024 66.667 0.00 0.00 0.00 3.69
83 84 2.520741 CTCCGCCTCTCTCCCTCC 60.521 72.222 0.00 0.00 0.00 4.30
84 85 2.520741 CCTCCGCCTCTCTCCCTC 60.521 72.222 0.00 0.00 0.00 4.30
85 86 3.024356 TCCTCCGCCTCTCTCCCT 61.024 66.667 0.00 0.00 0.00 4.20
86 87 2.520741 CTCCTCCGCCTCTCTCCC 60.521 72.222 0.00 0.00 0.00 4.30
87 88 2.520741 CCTCCTCCGCCTCTCTCC 60.521 72.222 0.00 0.00 0.00 3.71
88 89 2.124693 CACCTCCTCCGCCTCTCTC 61.125 68.421 0.00 0.00 0.00 3.20
89 90 2.043450 CACCTCCTCCGCCTCTCT 60.043 66.667 0.00 0.00 0.00 3.10
90 91 3.844090 GCACCTCCTCCGCCTCTC 61.844 72.222 0.00 0.00 0.00 3.20
95 96 4.373116 TTCACGCACCTCCTCCGC 62.373 66.667 0.00 0.00 0.00 5.54
96 97 2.125912 CTTCACGCACCTCCTCCG 60.126 66.667 0.00 0.00 0.00 4.63
97 98 2.435059 GCTTCACGCACCTCCTCC 60.435 66.667 0.00 0.00 38.92 4.30
98 99 2.811317 CGCTTCACGCACCTCCTC 60.811 66.667 0.00 0.00 39.08 3.71
99 100 4.379243 CCGCTTCACGCACCTCCT 62.379 66.667 0.00 0.00 41.76 3.69
100 101 4.373116 TCCGCTTCACGCACCTCC 62.373 66.667 0.00 0.00 41.76 4.30
101 102 2.811317 CTCCGCTTCACGCACCTC 60.811 66.667 0.00 0.00 41.76 3.85
102 103 4.379243 CCTCCGCTTCACGCACCT 62.379 66.667 0.00 0.00 41.76 4.00
104 105 3.642778 TAGCCTCCGCTTCACGCAC 62.643 63.158 0.00 0.00 45.55 5.34
105 106 3.356639 CTAGCCTCCGCTTCACGCA 62.357 63.158 0.00 0.00 45.55 5.24
106 107 2.583593 CTAGCCTCCGCTTCACGC 60.584 66.667 0.00 0.00 45.55 5.34
107 108 2.105128 CCTAGCCTCCGCTTCACG 59.895 66.667 0.00 0.00 45.55 4.35
108 109 1.900545 AACCCTAGCCTCCGCTTCAC 61.901 60.000 0.00 0.00 45.55 3.18
109 110 1.198759 AAACCCTAGCCTCCGCTTCA 61.199 55.000 0.00 0.00 45.55 3.02
110 111 0.462225 GAAACCCTAGCCTCCGCTTC 60.462 60.000 0.00 0.00 45.55 3.86
111 112 1.602771 GAAACCCTAGCCTCCGCTT 59.397 57.895 0.00 0.00 45.55 4.68
113 114 2.189784 GGAAACCCTAGCCTCCGC 59.810 66.667 0.00 0.00 0.00 5.54
152 153 4.717629 TGGAGCAACCTCGCGTCG 62.718 66.667 5.77 0.00 39.06 5.12
153 154 2.357034 TTGGAGCAACCTCGCGTC 60.357 61.111 5.77 0.00 39.06 5.19
154 155 2.357517 CTTGGAGCAACCTCGCGT 60.358 61.111 5.77 0.00 39.06 6.01
155 156 3.121030 CCTTGGAGCAACCTCGCG 61.121 66.667 0.00 0.00 39.06 5.87
156 157 2.035442 GTCCTTGGAGCAACCTCGC 61.035 63.158 1.91 0.00 39.06 5.03
157 158 0.036010 ATGTCCTTGGAGCAACCTCG 60.036 55.000 1.91 0.00 39.06 4.63
158 159 1.457346 CATGTCCTTGGAGCAACCTC 58.543 55.000 1.91 0.00 39.86 3.85
159 160 0.610232 GCATGTCCTTGGAGCAACCT 60.610 55.000 0.00 0.00 39.86 3.50
160 161 0.895100 TGCATGTCCTTGGAGCAACC 60.895 55.000 0.00 0.00 39.54 3.77
161 162 0.242017 GTGCATGTCCTTGGAGCAAC 59.758 55.000 4.06 0.00 36.91 4.17
162 163 0.178995 TGTGCATGTCCTTGGAGCAA 60.179 50.000 4.06 0.00 36.91 3.91
163 164 0.178995 TTGTGCATGTCCTTGGAGCA 60.179 50.000 0.00 0.00 0.00 4.26
164 165 0.242017 GTTGTGCATGTCCTTGGAGC 59.758 55.000 0.00 0.00 0.00 4.70
165 166 1.901591 AGTTGTGCATGTCCTTGGAG 58.098 50.000 0.00 0.00 0.00 3.86
166 167 2.363306 AAGTTGTGCATGTCCTTGGA 57.637 45.000 0.00 0.00 0.00 3.53
167 168 3.457610 AAAAGTTGTGCATGTCCTTGG 57.542 42.857 0.00 0.00 0.00 3.61
168 169 6.071952 ACCTATAAAAGTTGTGCATGTCCTTG 60.072 38.462 0.00 0.00 0.00 3.61
169 170 6.010219 ACCTATAAAAGTTGTGCATGTCCTT 58.990 36.000 0.00 0.00 0.00 3.36
170 171 5.570320 ACCTATAAAAGTTGTGCATGTCCT 58.430 37.500 0.00 0.00 0.00 3.85
171 172 5.897377 ACCTATAAAAGTTGTGCATGTCC 57.103 39.130 0.00 0.00 0.00 4.02
172 173 9.289303 CAATAACCTATAAAAGTTGTGCATGTC 57.711 33.333 0.00 0.00 0.00 3.06
173 174 7.759433 GCAATAACCTATAAAAGTTGTGCATGT 59.241 33.333 0.00 0.00 37.83 3.21
174 175 7.758980 TGCAATAACCTATAAAAGTTGTGCATG 59.241 33.333 10.25 0.00 40.44 4.06
175 176 7.835822 TGCAATAACCTATAAAAGTTGTGCAT 58.164 30.769 10.25 0.00 40.44 3.96
176 177 7.220741 TGCAATAACCTATAAAAGTTGTGCA 57.779 32.000 10.25 10.25 41.77 4.57
177 178 7.596995 TGTTGCAATAACCTATAAAAGTTGTGC 59.403 33.333 0.59 0.00 38.13 4.57
178 179 8.911662 GTGTTGCAATAACCTATAAAAGTTGTG 58.088 33.333 0.59 0.00 0.00 3.33
179 180 8.634444 TGTGTTGCAATAACCTATAAAAGTTGT 58.366 29.630 0.59 0.00 0.00 3.32
180 181 9.638239 ATGTGTTGCAATAACCTATAAAAGTTG 57.362 29.630 0.59 0.00 0.00 3.16
185 186 9.899661 AGAGTATGTGTTGCAATAACCTATAAA 57.100 29.630 0.59 0.00 0.00 1.40
190 191 8.150945 CCTATAGAGTATGTGTTGCAATAACCT 58.849 37.037 0.59 0.35 0.00 3.50
191 192 7.931948 ACCTATAGAGTATGTGTTGCAATAACC 59.068 37.037 0.59 0.00 0.00 2.85
192 193 8.765219 CACCTATAGAGTATGTGTTGCAATAAC 58.235 37.037 0.59 5.29 0.00 1.89
193 194 8.482943 ACACCTATAGAGTATGTGTTGCAATAA 58.517 33.333 0.59 0.00 36.84 1.40
194 195 8.018537 ACACCTATAGAGTATGTGTTGCAATA 57.981 34.615 0.59 0.00 36.84 1.90
195 196 6.889198 ACACCTATAGAGTATGTGTTGCAAT 58.111 36.000 0.59 0.00 36.84 3.56
196 197 6.294361 ACACCTATAGAGTATGTGTTGCAA 57.706 37.500 0.00 0.00 36.84 4.08
197 198 5.932619 ACACCTATAGAGTATGTGTTGCA 57.067 39.130 0.00 0.00 36.84 4.08
198 199 8.888579 AAATACACCTATAGAGTATGTGTTGC 57.111 34.615 14.37 0.00 40.39 4.17
222 223 7.230510 AGTGCTAATGGACAATGTCTACAAAAA 59.769 33.333 13.53 0.00 36.96 1.94
223 224 6.714810 AGTGCTAATGGACAATGTCTACAAAA 59.285 34.615 13.53 0.00 36.96 2.44
224 225 6.237901 AGTGCTAATGGACAATGTCTACAAA 58.762 36.000 13.53 0.00 36.96 2.83
225 226 5.804639 AGTGCTAATGGACAATGTCTACAA 58.195 37.500 13.53 0.00 36.96 2.41
226 227 5.420725 AGTGCTAATGGACAATGTCTACA 57.579 39.130 13.53 4.09 36.96 2.74
227 228 6.258068 GGTTAGTGCTAATGGACAATGTCTAC 59.742 42.308 13.53 0.00 36.96 2.59
228 229 6.070481 TGGTTAGTGCTAATGGACAATGTCTA 60.070 38.462 13.53 7.72 36.96 2.59
229 230 5.186198 GGTTAGTGCTAATGGACAATGTCT 58.814 41.667 13.53 0.00 36.96 3.41
230 231 4.941263 TGGTTAGTGCTAATGGACAATGTC 59.059 41.667 4.51 4.51 36.96 3.06
231 232 4.700213 GTGGTTAGTGCTAATGGACAATGT 59.300 41.667 0.00 0.00 36.96 2.71
232 233 4.699735 TGTGGTTAGTGCTAATGGACAATG 59.300 41.667 0.00 0.00 36.96 2.82
233 234 4.917385 TGTGGTTAGTGCTAATGGACAAT 58.083 39.130 0.00 0.00 36.96 2.71
234 235 4.359434 TGTGGTTAGTGCTAATGGACAA 57.641 40.909 0.00 0.00 36.96 3.18
235 236 4.513442 GATGTGGTTAGTGCTAATGGACA 58.487 43.478 0.00 0.55 36.96 4.02
236 237 3.877508 GGATGTGGTTAGTGCTAATGGAC 59.122 47.826 0.00 0.00 34.56 4.02
237 238 3.521531 TGGATGTGGTTAGTGCTAATGGA 59.478 43.478 0.00 0.00 0.00 3.41
238 239 3.879295 CTGGATGTGGTTAGTGCTAATGG 59.121 47.826 0.00 0.00 0.00 3.16
239 240 4.333649 CACTGGATGTGGTTAGTGCTAATG 59.666 45.833 0.00 0.00 42.68 1.90
240 241 4.225042 TCACTGGATGTGGTTAGTGCTAAT 59.775 41.667 0.00 0.00 46.20 1.73
241 242 3.580895 TCACTGGATGTGGTTAGTGCTAA 59.419 43.478 0.00 0.00 46.20 3.09
242 243 3.169908 TCACTGGATGTGGTTAGTGCTA 58.830 45.455 0.00 0.00 46.20 3.49
243 244 1.977854 TCACTGGATGTGGTTAGTGCT 59.022 47.619 0.00 0.00 46.20 4.40
244 245 2.350522 CTCACTGGATGTGGTTAGTGC 58.649 52.381 0.00 0.00 46.20 4.40
245 246 2.289631 TGCTCACTGGATGTGGTTAGTG 60.290 50.000 0.00 0.00 46.20 2.74
246 247 1.977854 TGCTCACTGGATGTGGTTAGT 59.022 47.619 0.00 0.00 46.20 2.24
247 248 2.768253 TGCTCACTGGATGTGGTTAG 57.232 50.000 0.00 0.00 46.20 2.34
248 249 2.418609 CGATGCTCACTGGATGTGGTTA 60.419 50.000 0.00 0.00 46.20 2.85
249 250 1.676916 CGATGCTCACTGGATGTGGTT 60.677 52.381 0.00 0.00 46.20 3.67
250 251 0.107993 CGATGCTCACTGGATGTGGT 60.108 55.000 0.00 0.00 46.20 4.16
251 252 0.107993 ACGATGCTCACTGGATGTGG 60.108 55.000 0.00 0.00 46.20 4.17
253 254 3.827008 AATACGATGCTCACTGGATGT 57.173 42.857 0.00 0.00 0.00 3.06
254 255 5.698089 ACAATAATACGATGCTCACTGGATG 59.302 40.000 0.00 0.00 0.00 3.51
255 256 5.858381 ACAATAATACGATGCTCACTGGAT 58.142 37.500 0.00 0.00 0.00 3.41
256 257 5.069119 AGACAATAATACGATGCTCACTGGA 59.931 40.000 0.00 0.00 0.00 3.86
257 258 5.292765 AGACAATAATACGATGCTCACTGG 58.707 41.667 0.00 0.00 0.00 4.00
258 259 7.930513 TTAGACAATAATACGATGCTCACTG 57.069 36.000 0.00 0.00 0.00 3.66
259 260 9.197694 GAATTAGACAATAATACGATGCTCACT 57.802 33.333 0.00 0.00 0.00 3.41
260 261 9.197694 AGAATTAGACAATAATACGATGCTCAC 57.802 33.333 0.00 0.00 0.00 3.51
280 281 9.064706 CGAGGGAGTAGTAGAACAATAGAATTA 57.935 37.037 0.00 0.00 0.00 1.40
281 282 7.014422 CCGAGGGAGTAGTAGAACAATAGAATT 59.986 40.741 0.00 0.00 0.00 2.17
282 283 6.490721 CCGAGGGAGTAGTAGAACAATAGAAT 59.509 42.308 0.00 0.00 0.00 2.40
283 284 5.826737 CCGAGGGAGTAGTAGAACAATAGAA 59.173 44.000 0.00 0.00 0.00 2.10
284 285 5.131642 TCCGAGGGAGTAGTAGAACAATAGA 59.868 44.000 0.00 0.00 0.00 1.98
285 286 5.374921 TCCGAGGGAGTAGTAGAACAATAG 58.625 45.833 0.00 0.00 0.00 1.73
286 287 5.378230 TCCGAGGGAGTAGTAGAACAATA 57.622 43.478 0.00 0.00 0.00 1.90
287 288 4.246712 TCCGAGGGAGTAGTAGAACAAT 57.753 45.455 0.00 0.00 0.00 2.71
288 289 3.726557 TCCGAGGGAGTAGTAGAACAA 57.273 47.619 0.00 0.00 0.00 2.83
289 290 3.434739 GGATCCGAGGGAGTAGTAGAACA 60.435 52.174 0.00 0.00 34.05 3.18
290 291 3.148412 GGATCCGAGGGAGTAGTAGAAC 58.852 54.545 0.00 0.00 34.05 3.01
291 292 2.781757 TGGATCCGAGGGAGTAGTAGAA 59.218 50.000 7.39 0.00 34.05 2.10
292 293 2.415624 TGGATCCGAGGGAGTAGTAGA 58.584 52.381 7.39 0.00 34.05 2.59
293 294 2.953284 TGGATCCGAGGGAGTAGTAG 57.047 55.000 7.39 0.00 34.05 2.57
294 295 5.531753 AATATGGATCCGAGGGAGTAGTA 57.468 43.478 7.39 0.00 34.05 1.82
295 296 4.405756 AATATGGATCCGAGGGAGTAGT 57.594 45.455 7.39 0.00 34.05 2.73
296 297 5.511363 ACTAATATGGATCCGAGGGAGTAG 58.489 45.833 7.39 5.81 34.05 2.57
297 298 5.531753 ACTAATATGGATCCGAGGGAGTA 57.468 43.478 7.39 0.00 34.05 2.59
298 299 4.405756 ACTAATATGGATCCGAGGGAGT 57.594 45.455 7.39 4.98 34.05 3.85
299 300 4.528596 ACAACTAATATGGATCCGAGGGAG 59.471 45.833 7.39 4.32 34.05 4.30
300 301 4.489737 ACAACTAATATGGATCCGAGGGA 58.510 43.478 7.39 0.00 35.55 4.20
301 302 4.891992 ACAACTAATATGGATCCGAGGG 57.108 45.455 7.39 0.00 0.00 4.30
302 303 4.452455 GCAACAACTAATATGGATCCGAGG 59.548 45.833 7.39 0.00 0.00 4.63
303 304 5.300752 AGCAACAACTAATATGGATCCGAG 58.699 41.667 7.39 1.76 0.00 4.63
304 305 5.163353 TGAGCAACAACTAATATGGATCCGA 60.163 40.000 7.39 0.00 0.00 4.55
305 306 5.056480 TGAGCAACAACTAATATGGATCCG 58.944 41.667 7.39 0.00 0.00 4.18
306 307 6.942532 TTGAGCAACAACTAATATGGATCC 57.057 37.500 4.20 4.20 33.18 3.36
321 322 1.689959 CTGCATCGGTTTTGAGCAAC 58.310 50.000 0.00 0.00 34.45 4.17
323 324 1.580942 GCTGCATCGGTTTTGAGCA 59.419 52.632 0.00 0.00 0.00 4.26
331 332 1.732941 TTAATTGTCGCTGCATCGGT 58.267 45.000 10.42 0.00 0.00 4.69
334 335 5.611796 TCCATATTAATTGTCGCTGCATC 57.388 39.130 0.00 0.00 0.00 3.91
338 339 4.929211 TCCGATCCATATTAATTGTCGCTG 59.071 41.667 0.00 0.00 0.00 5.18
339 340 5.147330 TCCGATCCATATTAATTGTCGCT 57.853 39.130 0.00 0.00 0.00 4.93
347 348 5.842328 ACTACAACCCTCCGATCCATATTAA 59.158 40.000 0.00 0.00 0.00 1.40
360 361 3.067833 GTTGCTCTTCACTACAACCCTC 58.932 50.000 0.00 0.00 37.11 4.30
369 380 0.877071 CGCCATTGTTGCTCTTCACT 59.123 50.000 0.00 0.00 0.00 3.41
3530 6981 6.767524 TGTATTTTGTTGGGGCTATAACTG 57.232 37.500 0.00 0.00 0.00 3.16
3852 9427 6.127366 ACACCAACTTGTTTTGAGTCAATGAT 60.127 34.615 6.36 0.00 0.00 2.45


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

AutoCloner maintained by Alex Coulton.