Multiple sequence alignment - TraesCS4B01G369000

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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 TraesCS4B01G369000 chr4B 100.000 1489 0 0 1 1489 654807983 654806495 0.000000e+00 2750.0
1 TraesCS4B01G369000 chr4B 91.359 1111 70 4 380 1489 654732458 654731373 0.000000e+00 1496.0
2 TraesCS4B01G369000 chr4B 89.296 682 44 8 811 1489 655111574 655110919 0.000000e+00 828.0
3 TraesCS4B01G369000 chr4B 100.000 416 0 0 1975 2390 654806009 654805594 0.000000e+00 769.0
4 TraesCS4B01G369000 chr4B 88.133 632 48 8 862 1489 655078009 655077401 0.000000e+00 726.0
5 TraesCS4B01G369000 chr4B 95.204 417 16 2 1975 2390 654731370 654730957 0.000000e+00 656.0
6 TraesCS4B01G369000 chr4B 94.724 417 16 3 1975 2390 655077398 655076987 0.000000e+00 643.0
7 TraesCS4B01G369000 chr4B 94.172 326 15 2 2064 2388 654605986 654605664 5.930000e-136 494.0
8 TraesCS4B01G369000 chr4B 92.086 278 19 1 2113 2390 655107455 655107181 2.880000e-104 388.0
9 TraesCS4B01G369000 chr4B 90.514 253 21 2 538 790 655083917 655083668 4.920000e-87 331.0
10 TraesCS4B01G369000 chr4B 90.119 253 22 2 538 790 655111896 655111647 2.290000e-85 326.0
11 TraesCS4B01G369000 chr4B 93.197 147 9 1 1975 2120 655110916 655110770 5.170000e-52 215.0
12 TraesCS4B01G369000 chr4B 85.128 195 21 2 2062 2256 654746081 654745895 2.420000e-45 193.0
13 TraesCS4B01G369000 chr4B 81.553 206 26 7 2062 2256 654706503 654706299 2.460000e-35 159.0
14 TraesCS4B01G369000 chr4B 86.777 121 8 2 2062 2182 654647116 654647004 6.930000e-26 128.0
15 TraesCS4B01G369000 chr4B 86.777 121 8 3 2062 2182 654766616 654766504 6.930000e-26 128.0
16 TraesCS4B01G369000 chr4B 89.333 75 5 2 141 215 655083983 655083912 9.100000e-15 91.6
17 TraesCS4B01G369000 chr4B 97.872 47 1 0 168 214 655111938 655111892 5.480000e-12 82.4
18 TraesCS4B01G369000 chrUn 87.296 614 65 5 878 1489 154542493 154543095 0.000000e+00 689.0
19 TraesCS4B01G369000 chrUn 87.542 602 62 5 890 1489 189575692 189575102 0.000000e+00 684.0
20 TraesCS4B01G369000 chrUn 87.070 611 66 5 881 1489 201369050 201369649 0.000000e+00 678.0
21 TraesCS4B01G369000 chrUn 87.209 602 63 6 890 1489 189562004 189561415 0.000000e+00 673.0
22 TraesCS4B01G369000 chrUn 86.907 611 66 6 881 1489 279543188 279543786 0.000000e+00 673.0
23 TraesCS4B01G369000 chrUn 86.907 611 67 5 881 1489 363336768 363337367 0.000000e+00 673.0
24 TraesCS4B01G369000 chrUn 87.402 381 31 9 1975 2353 154568369 154568734 2.840000e-114 422.0
25 TraesCS4B01G369000 chrUn 88.627 255 26 3 538 790 189576105 189575852 8.300000e-80 307.0
26 TraesCS4B01G369000 chrUn 88.627 255 26 3 538 790 201368646 201368899 8.300000e-80 307.0
27 TraesCS4B01G369000 chrUn 88.627 255 26 3 538 790 346445306 346445053 8.300000e-80 307.0
28 TraesCS4B01G369000 chrUn 88.627 255 26 3 538 790 363336364 363336617 8.300000e-80 307.0
29 TraesCS4B01G369000 chrUn 88.235 255 27 3 538 790 377346079 377345826 3.860000e-78 302.0
30 TraesCS4B01G369000 chrUn 87.597 258 25 6 538 789 154567389 154567645 2.320000e-75 292.0
31 TraesCS4B01G369000 chrUn 82.437 279 27 9 1979 2256 201369656 201369913 8.600000e-55 224.0
32 TraesCS4B01G369000 chrUn 82.143 280 28 9 1978 2256 189561409 189561151 1.110000e-53 220.0
33 TraesCS4B01G369000 chrUn 81.979 283 29 9 1975 2256 279543789 279544050 1.110000e-53 220.0
34 TraesCS4B01G369000 chrUn 82.143 280 28 9 1978 2256 396088343 396088085 1.110000e-53 220.0
35 TraesCS4B01G369000 chrUn 81.786 280 29 9 1978 2256 189575096 189574838 5.170000e-52 215.0
36 TraesCS4B01G369000 chrUn 81.457 151 23 4 315 462 346548250 346548102 4.170000e-23 119.0
37 TraesCS4B01G369000 chr7D 84.170 259 30 7 216 466 521687889 521688144 8.540000e-60 241.0
38 TraesCS4B01G369000 chr7B 78.731 268 37 10 287 536 555315894 555316159 6.840000e-36 161.0
39 TraesCS4B01G369000 chr7B 81.022 137 17 4 216 352 181607803 181607676 1.510000e-17 100.0
40 TraesCS4B01G369000 chr3D 76.875 320 41 17 236 535 247910337 247910031 1.480000e-32 150.0
41 TraesCS4B01G369000 chr3D 80.874 183 28 6 282 463 48526353 48526529 1.150000e-28 137.0
42 TraesCS4B01G369000 chr3D 78.995 219 23 9 289 495 82547999 82548206 6.930000e-26 128.0
43 TraesCS4B01G369000 chr3D 81.203 133 21 4 308 438 563612579 563612449 1.170000e-18 104.0
44 TraesCS4B01G369000 chr7A 81.006 179 26 3 216 393 696860575 696860746 4.140000e-28 135.0
45 TraesCS4B01G369000 chr7A 86.957 69 9 0 468 536 393039222 393039290 7.080000e-11 78.7
46 TraesCS4B01G369000 chr1A 74.926 339 58 17 219 535 424014703 424014370 1.930000e-26 130.0
47 TraesCS4B01G369000 chr1A 80.892 157 25 4 306 459 394480913 394481067 4.170000e-23 119.0
48 TraesCS4B01G369000 chr1A 76.959 217 35 10 315 520 474811252 474811464 2.510000e-20 110.0
49 TraesCS4B01G369000 chr5B 82.000 150 25 2 213 360 346957166 346957315 2.490000e-25 126.0
50 TraesCS4B01G369000 chr5B 81.818 143 25 1 216 357 562222500 562222642 4.170000e-23 119.0
51 TraesCS4B01G369000 chr1B 82.707 133 22 1 216 347 300339124 300338992 1.500000e-22 117.0
52 TraesCS4B01G369000 chr4A 80.851 141 25 2 216 355 709791810 709791671 2.510000e-20 110.0
53 TraesCS4B01G369000 chr1D 79.487 156 30 2 208 361 431964547 431964392 2.510000e-20 110.0
54 TraesCS4B01G369000 chr6A 76.585 205 28 13 307 501 8185310 8185504 7.030000e-16 95.3
55 TraesCS4B01G369000 chr6B 86.250 80 11 0 456 535 144966891 144966812 1.180000e-13 87.9


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 TraesCS4B01G369000 chr4B 654805594 654807983 2389 True 1759.50 2750 100.000000 1 2390 2 chr4B.!!$R7 2389
1 TraesCS4B01G369000 chr4B 654730957 654732458 1501 True 1076.00 1496 93.281500 380 2390 2 chr4B.!!$R6 2010
2 TraesCS4B01G369000 chr4B 655076987 655078009 1022 True 684.50 726 91.428500 862 2390 2 chr4B.!!$R8 1528
3 TraesCS4B01G369000 chr4B 655107181 655111938 4757 True 367.88 828 92.514000 168 2390 5 chr4B.!!$R10 2222
4 TraesCS4B01G369000 chrUn 154542493 154543095 602 False 689.00 689 87.296000 878 1489 1 chrUn.!!$F1 611
5 TraesCS4B01G369000 chrUn 363336364 363337367 1003 False 490.00 673 87.767000 538 1489 2 chrUn.!!$F5 951
6 TraesCS4B01G369000 chrUn 189561151 189562004 853 True 446.50 673 84.676000 890 2256 2 chrUn.!!$R5 1366
7 TraesCS4B01G369000 chrUn 279543188 279544050 862 False 446.50 673 84.443000 881 2256 2 chrUn.!!$F4 1375
8 TraesCS4B01G369000 chrUn 201368646 201369913 1267 False 403.00 678 86.044667 538 2256 3 chrUn.!!$F3 1718
9 TraesCS4B01G369000 chrUn 189574838 189576105 1267 True 402.00 684 85.985000 538 2256 3 chrUn.!!$R6 1718
10 TraesCS4B01G369000 chrUn 154567389 154568734 1345 False 357.00 422 87.499500 538 2353 2 chrUn.!!$F2 1815

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
333 334 0.180406 GGCCTAGATTTTGAGCCCGA 59.82 55.0 0.0 0.0 37.66 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2136 5564 1.153628 CATATAGTAGGCGCCCGGC 60.154 63.158 26.15 13.94 42.51 6.13 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
32 33 9.541143 TTTTTGCAGGAAACTTTTTAGAATAGG 57.459 29.630 0.00 0.00 40.21 2.57
33 34 7.833285 TTGCAGGAAACTTTTTAGAATAGGT 57.167 32.000 0.00 0.00 40.21 3.08
34 35 8.927675 TTGCAGGAAACTTTTTAGAATAGGTA 57.072 30.769 0.00 0.00 40.21 3.08
35 36 8.927675 TGCAGGAAACTTTTTAGAATAGGTAA 57.072 30.769 0.00 0.00 40.21 2.85
36 37 9.528489 TGCAGGAAACTTTTTAGAATAGGTAAT 57.472 29.630 0.00 0.00 40.21 1.89
68 69 9.638239 TGGCTTTCTTTTTGAAATACATATCAC 57.362 29.630 0.00 0.00 42.96 3.06
69 70 9.860898 GGCTTTCTTTTTGAAATACATATCACT 57.139 29.630 0.00 0.00 42.96 3.41
111 112 2.891191 TTTTTGTAGGCCCGGATCTT 57.109 45.000 0.73 0.00 0.00 2.40
112 113 2.413310 TTTTGTAGGCCCGGATCTTC 57.587 50.000 0.73 0.00 0.00 2.87
113 114 1.580059 TTTGTAGGCCCGGATCTTCT 58.420 50.000 0.73 0.00 0.00 2.85
114 115 1.580059 TTGTAGGCCCGGATCTTCTT 58.420 50.000 0.73 0.00 0.00 2.52
115 116 1.580059 TGTAGGCCCGGATCTTCTTT 58.420 50.000 0.73 0.00 0.00 2.52
116 117 1.913419 TGTAGGCCCGGATCTTCTTTT 59.087 47.619 0.73 0.00 0.00 2.27
117 118 2.307686 TGTAGGCCCGGATCTTCTTTTT 59.692 45.455 0.73 0.00 0.00 1.94
118 119 3.520317 TGTAGGCCCGGATCTTCTTTTTA 59.480 43.478 0.73 0.00 0.00 1.52
119 120 3.283259 AGGCCCGGATCTTCTTTTTAG 57.717 47.619 0.73 0.00 0.00 1.85
120 121 2.844348 AGGCCCGGATCTTCTTTTTAGA 59.156 45.455 0.73 0.00 0.00 2.10
121 122 3.459969 AGGCCCGGATCTTCTTTTTAGAT 59.540 43.478 0.73 0.00 35.12 1.98
122 123 4.658901 AGGCCCGGATCTTCTTTTTAGATA 59.341 41.667 0.73 0.00 32.64 1.98
123 124 4.755629 GGCCCGGATCTTCTTTTTAGATAC 59.244 45.833 0.73 0.00 32.64 2.24
124 125 5.365619 GCCCGGATCTTCTTTTTAGATACA 58.634 41.667 0.73 0.00 33.35 2.29
125 126 5.236695 GCCCGGATCTTCTTTTTAGATACAC 59.763 44.000 0.73 0.00 33.35 2.90
126 127 5.462398 CCCGGATCTTCTTTTTAGATACACG 59.538 44.000 0.73 0.00 33.35 4.49
127 128 6.040878 CCGGATCTTCTTTTTAGATACACGT 58.959 40.000 0.00 0.00 33.35 4.49
128 129 6.534079 CCGGATCTTCTTTTTAGATACACGTT 59.466 38.462 0.00 0.00 33.35 3.99
129 130 7.391786 CGGATCTTCTTTTTAGATACACGTTG 58.608 38.462 0.00 0.00 33.35 4.10
130 131 7.274904 CGGATCTTCTTTTTAGATACACGTTGA 59.725 37.037 0.00 0.00 33.35 3.18
131 132 8.932791 GGATCTTCTTTTTAGATACACGTTGAA 58.067 33.333 0.00 0.00 33.85 2.69
199 200 1.270412 GGATACGTGTCCACACCAACA 60.270 52.381 24.84 0.00 43.66 3.33
207 208 0.396278 TCCACACCAACAACCATGCA 60.396 50.000 0.00 0.00 0.00 3.96
208 209 0.680618 CCACACCAACAACCATGCAT 59.319 50.000 0.00 0.00 0.00 3.96
209 210 1.605968 CCACACCAACAACCATGCATG 60.606 52.381 20.19 20.19 0.00 4.06
210 211 1.068895 CACACCAACAACCATGCATGT 59.931 47.619 24.58 10.59 0.00 3.21
211 212 2.295629 CACACCAACAACCATGCATGTA 59.704 45.455 24.58 0.00 0.00 2.29
212 213 3.056678 CACACCAACAACCATGCATGTAT 60.057 43.478 24.58 10.27 0.00 2.29
213 214 4.157472 CACACCAACAACCATGCATGTATA 59.843 41.667 24.58 0.00 0.00 1.47
214 215 4.769488 ACACCAACAACCATGCATGTATAA 59.231 37.500 24.58 0.00 0.00 0.98
215 216 5.421693 ACACCAACAACCATGCATGTATAAT 59.578 36.000 24.58 5.88 0.00 1.28
216 217 6.605194 ACACCAACAACCATGCATGTATAATA 59.395 34.615 24.58 0.00 0.00 0.98
217 218 7.287466 ACACCAACAACCATGCATGTATAATAT 59.713 33.333 24.58 2.72 0.00 1.28
218 219 8.791675 CACCAACAACCATGCATGTATAATATA 58.208 33.333 24.58 0.00 0.00 0.86
219 220 8.792633 ACCAACAACCATGCATGTATAATATAC 58.207 33.333 24.58 3.56 0.00 1.47
220 221 8.243426 CCAACAACCATGCATGTATAATATACC 58.757 37.037 24.58 0.00 0.00 2.73
221 222 9.013229 CAACAACCATGCATGTATAATATACCT 57.987 33.333 24.58 0.00 0.00 3.08
222 223 8.565896 ACAACCATGCATGTATAATATACCTG 57.434 34.615 24.58 9.12 0.00 4.00
223 224 8.163408 ACAACCATGCATGTATAATATACCTGT 58.837 33.333 24.58 8.10 0.00 4.00
224 225 8.668353 CAACCATGCATGTATAATATACCTGTC 58.332 37.037 24.58 9.05 0.00 3.51
225 226 7.338710 ACCATGCATGTATAATATACCTGTCC 58.661 38.462 24.58 3.34 0.00 4.02
226 227 7.037658 ACCATGCATGTATAATATACCTGTCCA 60.038 37.037 24.58 7.57 0.00 4.02
227 228 7.994911 CCATGCATGTATAATATACCTGTCCAT 59.005 37.037 24.58 9.02 0.00 3.41
228 229 8.833493 CATGCATGTATAATATACCTGTCCATG 58.167 37.037 18.91 14.56 0.00 3.66
229 230 7.337938 TGCATGTATAATATACCTGTCCATGG 58.662 38.462 4.97 4.97 0.00 3.66
230 231 6.767902 GCATGTATAATATACCTGTCCATGGG 59.232 42.308 13.02 0.00 0.00 4.00
231 232 6.308015 TGTATAATATACCTGTCCATGGGC 57.692 41.667 10.20 10.20 0.00 5.36
232 233 5.788014 TGTATAATATACCTGTCCATGGGCA 59.212 40.000 20.07 20.07 0.00 5.36
233 234 3.795688 AATATACCTGTCCATGGGCAG 57.204 47.619 35.13 35.13 0.00 4.85
234 235 2.190398 TATACCTGTCCATGGGCAGT 57.810 50.000 37.56 28.34 0.00 4.40
235 236 0.839946 ATACCTGTCCATGGGCAGTC 59.160 55.000 37.56 13.53 0.00 3.51
236 237 1.271840 TACCTGTCCATGGGCAGTCC 61.272 60.000 37.56 9.91 0.00 3.85
237 238 2.124983 CTGTCCATGGGCAGTCCG 60.125 66.667 33.99 13.40 38.76 4.79
238 239 4.408821 TGTCCATGGGCAGTCCGC 62.409 66.667 17.02 0.00 38.76 5.54
280 281 3.496131 CACGAAATGCCCGACCCG 61.496 66.667 0.00 0.00 0.00 5.28
297 298 4.740822 GGCCTGGCCCGACATTGT 62.741 66.667 27.77 0.00 44.06 2.71
298 299 3.443045 GCCTGGCCCGACATTGTG 61.443 66.667 7.66 0.00 0.00 3.33
299 300 3.443045 CCTGGCCCGACATTGTGC 61.443 66.667 0.00 0.00 0.00 4.57
300 301 2.672651 CTGGCCCGACATTGTGCA 60.673 61.111 0.00 0.00 0.00 4.57
301 302 2.035469 TGGCCCGACATTGTGCAT 59.965 55.556 0.00 0.00 0.00 3.96
302 303 0.747644 CTGGCCCGACATTGTGCATA 60.748 55.000 0.00 0.00 0.00 3.14
303 304 0.747644 TGGCCCGACATTGTGCATAG 60.748 55.000 0.00 0.00 0.00 2.23
304 305 0.463654 GGCCCGACATTGTGCATAGA 60.464 55.000 0.00 0.00 0.00 1.98
305 306 0.657840 GCCCGACATTGTGCATAGAC 59.342 55.000 0.00 0.00 0.00 2.59
306 307 1.299541 CCCGACATTGTGCATAGACC 58.700 55.000 0.00 0.00 0.00 3.85
307 308 0.930310 CCGACATTGTGCATAGACCG 59.070 55.000 0.00 0.00 0.00 4.79
308 309 0.930310 CGACATTGTGCATAGACCGG 59.070 55.000 0.00 0.00 0.00 5.28
309 310 1.299541 GACATTGTGCATAGACCGGG 58.700 55.000 6.32 0.00 0.00 5.73
310 311 0.748005 ACATTGTGCATAGACCGGGC 60.748 55.000 6.32 0.52 0.00 6.13
311 312 1.152963 ATTGTGCATAGACCGGGCC 60.153 57.895 1.76 0.00 0.00 5.80
312 313 1.635817 ATTGTGCATAGACCGGGCCT 61.636 55.000 1.76 3.24 0.00 5.19
313 314 2.203070 GTGCATAGACCGGGCCTG 60.203 66.667 1.76 3.88 0.00 4.85
314 315 3.479203 TGCATAGACCGGGCCTGG 61.479 66.667 30.26 30.26 0.00 4.45
315 316 4.256180 GCATAGACCGGGCCTGGG 62.256 72.222 34.33 22.42 0.00 4.45
316 317 4.256180 CATAGACCGGGCCTGGGC 62.256 72.222 34.33 33.00 37.26 5.36
327 328 3.903208 GCCTGGGCCTAGATTTTGA 57.097 52.632 19.36 0.00 34.56 2.69
328 329 1.685148 GCCTGGGCCTAGATTTTGAG 58.315 55.000 19.36 0.00 34.56 3.02
329 330 1.685148 CCTGGGCCTAGATTTTGAGC 58.315 55.000 19.36 0.00 0.00 4.26
330 331 1.685148 CTGGGCCTAGATTTTGAGCC 58.315 55.000 11.42 0.00 43.09 4.70
332 333 2.707902 GGCCTAGATTTTGAGCCCG 58.292 57.895 0.00 0.00 37.66 6.13
333 334 0.180406 GGCCTAGATTTTGAGCCCGA 59.820 55.000 0.00 0.00 37.66 5.14
334 335 1.408266 GGCCTAGATTTTGAGCCCGAA 60.408 52.381 0.00 0.00 37.66 4.30
335 336 1.943340 GCCTAGATTTTGAGCCCGAAG 59.057 52.381 0.00 0.00 0.00 3.79
369 370 4.314440 GCCGGCCCGCTCATATCA 62.314 66.667 18.11 0.00 0.00 2.15
370 371 2.047844 CCGGCCCGCTCATATCAG 60.048 66.667 0.00 0.00 0.00 2.90
371 372 2.047844 CGGCCCGCTCATATCAGG 60.048 66.667 0.00 0.00 0.00 3.86
372 373 2.348998 GGCCCGCTCATATCAGGG 59.651 66.667 0.00 0.00 46.44 4.45
373 374 2.217038 GGCCCGCTCATATCAGGGA 61.217 63.158 3.19 0.00 46.64 4.20
374 375 1.557269 GGCCCGCTCATATCAGGGAT 61.557 60.000 3.19 0.00 46.64 3.85
375 376 0.326264 GCCCGCTCATATCAGGGATT 59.674 55.000 3.19 0.00 46.64 3.01
376 377 1.271597 GCCCGCTCATATCAGGGATTT 60.272 52.381 3.19 0.00 46.64 2.17
377 378 2.027192 GCCCGCTCATATCAGGGATTTA 60.027 50.000 3.19 0.00 46.64 1.40
378 379 3.559171 GCCCGCTCATATCAGGGATTTAA 60.559 47.826 3.19 0.00 46.64 1.52
391 392 3.117360 AGGGATTTAATGAAGAGGCCCAG 60.117 47.826 0.00 0.00 36.79 4.45
417 418 1.602323 CCTGGCGGGCTTTTACACA 60.602 57.895 0.00 0.00 0.00 3.72
418 419 1.175983 CCTGGCGGGCTTTTACACAA 61.176 55.000 0.00 0.00 0.00 3.33
421 422 0.885196 GGCGGGCTTTTACACAATCA 59.115 50.000 0.00 0.00 0.00 2.57
433 434 2.361610 CAATCAGGCCGGGCTTGT 60.362 61.111 30.73 17.26 36.96 3.16
448 449 3.236632 GCTTGTGGCCTGATTTTTAGG 57.763 47.619 3.32 0.00 38.39 2.69
479 480 1.135575 GGGCTTGAGTTTTCTGCATCG 60.136 52.381 0.00 0.00 0.00 3.84
486 487 0.598065 GTTTTCTGCATCGGGCTTGT 59.402 50.000 0.00 0.00 45.15 3.16
498 499 2.044555 GGCTTGTTTAGGCCCGTCC 61.045 63.158 0.00 0.00 43.40 4.79
504 505 3.319441 TTTAGGCCCGTCCCGAAGC 62.319 63.158 0.00 0.00 34.51 3.86
536 537 1.535437 CGAGTGACGGCCAGGTATAAC 60.535 57.143 2.24 0.00 38.46 1.89
565 566 5.254339 GCCAAAGCTAGCTATGAAACATT 57.746 39.130 19.70 2.59 35.50 2.71
591 592 3.006752 AGTTGACTTCTCTTGCTCTCCAG 59.993 47.826 0.00 0.00 0.00 3.86
598 599 7.124901 TGACTTCTCTTGCTCTCCAGTTAATAT 59.875 37.037 0.00 0.00 0.00 1.28
603 604 5.586243 TCTTGCTCTCCAGTTAATATTGCAC 59.414 40.000 0.00 0.00 0.00 4.57
720 726 0.260816 TCCAGCCACTAGTATCCCGT 59.739 55.000 0.00 0.00 0.00 5.28
888 988 2.131972 TGGATCAACATATACGTGCGC 58.868 47.619 0.00 0.00 0.00 6.09
1069 1173 1.068417 GTCACCACTGTGCACGGTA 59.932 57.895 30.14 12.95 42.46 4.02
1076 1180 1.006220 CTGTGCACGGTAGCTGTGA 60.006 57.895 17.96 0.00 42.79 3.58
1080 1184 1.004918 GCACGGTAGCTGTGAACCT 60.005 57.895 17.09 0.00 42.79 3.50
1152 1256 1.271108 TGCCCTATTGACACGCTGAAA 60.271 47.619 0.00 0.00 0.00 2.69
1283 1388 2.046023 CCTCTGCACCGCCATCAA 60.046 61.111 0.00 0.00 0.00 2.57
1286 1391 2.360350 CTGCACCGCCATCAAGGT 60.360 61.111 0.00 0.00 42.34 3.50
1391 1496 1.549243 TTCACCTGCCCGCACTGATA 61.549 55.000 0.00 0.00 0.00 2.15
1430 1535 2.027325 CATGGCATGCTGCGTACAT 58.973 52.632 18.92 8.35 46.21 2.29
1449 1554 2.889617 TGCCATGCATGCAGCTTC 59.110 55.556 26.69 14.64 45.94 3.86
2000 2105 2.898705 CATGCCTAGGTTCTCTGTCAC 58.101 52.381 11.31 0.00 0.00 3.67
2126 5554 2.878406 CGGGGGTTTGTATCATCATGTC 59.122 50.000 0.00 0.00 0.00 3.06
2129 5557 4.339247 GGGGGTTTGTATCATCATGTCAAG 59.661 45.833 0.00 0.00 0.00 3.02
2136 5564 7.832503 TTGTATCATCATGTCAAGTACTGTG 57.167 36.000 0.00 0.00 0.00 3.66
2287 5720 5.602561 AGATCAAAGCCAACCCTAAGTTTTT 59.397 36.000 0.00 0.00 36.18 1.94
2374 5807 1.171308 GACTTGCAGACACATGGCAT 58.829 50.000 0.00 0.00 37.39 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 9.541143 CCTATTCTAAAAAGTTTCCTGCAAAAA 57.459 29.630 0.00 0.00 0.00 1.94
7 8 8.700973 ACCTATTCTAAAAAGTTTCCTGCAAAA 58.299 29.630 0.00 0.00 0.00 2.44
8 9 8.245195 ACCTATTCTAAAAAGTTTCCTGCAAA 57.755 30.769 0.00 0.00 0.00 3.68
9 10 7.833285 ACCTATTCTAAAAAGTTTCCTGCAA 57.167 32.000 0.00 0.00 0.00 4.08
10 11 8.927675 TTACCTATTCTAAAAAGTTTCCTGCA 57.072 30.769 0.00 0.00 0.00 4.41
92 93 2.307686 AGAAGATCCGGGCCTACAAAAA 59.692 45.455 0.84 0.00 0.00 1.94
93 94 1.913419 AGAAGATCCGGGCCTACAAAA 59.087 47.619 0.84 0.00 0.00 2.44
94 95 1.580059 AGAAGATCCGGGCCTACAAA 58.420 50.000 0.84 0.00 0.00 2.83
95 96 1.580059 AAGAAGATCCGGGCCTACAA 58.420 50.000 0.84 0.00 0.00 2.41
96 97 1.580059 AAAGAAGATCCGGGCCTACA 58.420 50.000 0.84 0.00 0.00 2.74
97 98 2.711978 AAAAGAAGATCCGGGCCTAC 57.288 50.000 0.84 0.00 0.00 3.18
98 99 4.035112 TCTAAAAAGAAGATCCGGGCCTA 58.965 43.478 0.84 0.00 0.00 3.93
99 100 2.844348 TCTAAAAAGAAGATCCGGGCCT 59.156 45.455 0.84 0.00 0.00 5.19
100 101 3.277142 TCTAAAAAGAAGATCCGGGCC 57.723 47.619 0.00 0.00 0.00 5.80
101 102 5.236695 GTGTATCTAAAAAGAAGATCCGGGC 59.763 44.000 0.00 0.00 35.36 6.13
102 103 5.462398 CGTGTATCTAAAAAGAAGATCCGGG 59.538 44.000 0.00 0.00 35.36 5.73
103 104 6.040878 ACGTGTATCTAAAAAGAAGATCCGG 58.959 40.000 0.00 0.00 35.36 5.14
104 105 7.274904 TCAACGTGTATCTAAAAAGAAGATCCG 59.725 37.037 0.00 0.00 35.36 4.18
105 106 8.475331 TCAACGTGTATCTAAAAAGAAGATCC 57.525 34.615 0.00 0.00 35.36 3.36
149 150 9.965824 CACTGGTTTTTATAGAAAAGTGTTCAT 57.034 29.630 10.38 0.00 35.96 2.57
150 151 7.918562 GCACTGGTTTTTATAGAAAAGTGTTCA 59.081 33.333 16.16 1.94 35.96 3.18
151 152 7.112984 CGCACTGGTTTTTATAGAAAAGTGTTC 59.887 37.037 16.16 5.80 35.96 3.18
152 153 6.915843 CGCACTGGTTTTTATAGAAAAGTGTT 59.084 34.615 16.16 0.00 35.96 3.32
153 154 6.038936 ACGCACTGGTTTTTATAGAAAAGTGT 59.961 34.615 16.16 3.54 35.96 3.55
154 155 6.359617 CACGCACTGGTTTTTATAGAAAAGTG 59.640 38.462 12.82 12.82 35.96 3.16
155 156 6.435428 CACGCACTGGTTTTTATAGAAAAGT 58.565 36.000 0.00 0.00 35.96 2.66
156 157 5.856455 CCACGCACTGGTTTTTATAGAAAAG 59.144 40.000 0.00 0.00 35.96 2.27
157 158 5.531659 TCCACGCACTGGTTTTTATAGAAAA 59.468 36.000 0.00 0.00 41.52 2.29
158 159 5.064558 TCCACGCACTGGTTTTTATAGAAA 58.935 37.500 0.00 0.00 41.52 2.52
159 160 4.643463 TCCACGCACTGGTTTTTATAGAA 58.357 39.130 0.00 0.00 41.52 2.10
160 161 4.274602 TCCACGCACTGGTTTTTATAGA 57.725 40.909 0.00 0.00 41.52 1.98
161 162 5.276678 CGTATCCACGCACTGGTTTTTATAG 60.277 44.000 0.00 0.00 42.05 1.31
162 163 4.567558 CGTATCCACGCACTGGTTTTTATA 59.432 41.667 0.00 0.00 42.05 0.98
163 164 3.372822 CGTATCCACGCACTGGTTTTTAT 59.627 43.478 0.00 0.00 42.05 1.40
164 165 2.737783 CGTATCCACGCACTGGTTTTTA 59.262 45.455 0.00 0.00 42.05 1.52
165 166 1.533731 CGTATCCACGCACTGGTTTTT 59.466 47.619 0.00 0.00 42.05 1.94
166 167 1.153353 CGTATCCACGCACTGGTTTT 58.847 50.000 0.00 0.00 42.05 2.43
199 200 7.829211 GGACAGGTATATTATACATGCATGGTT 59.171 37.037 29.41 18.36 33.08 3.67
207 208 6.446759 TGCCCATGGACAGGTATATTATACAT 59.553 38.462 15.22 5.78 0.00 2.29
208 209 5.788014 TGCCCATGGACAGGTATATTATACA 59.212 40.000 15.22 0.00 0.00 2.29
209 210 6.070194 ACTGCCCATGGACAGGTATATTATAC 60.070 42.308 29.03 5.42 38.25 1.47
210 211 6.029431 ACTGCCCATGGACAGGTATATTATA 58.971 40.000 29.03 0.00 38.25 0.98
211 212 4.852118 ACTGCCCATGGACAGGTATATTAT 59.148 41.667 29.03 5.43 38.25 1.28
212 213 4.239495 ACTGCCCATGGACAGGTATATTA 58.761 43.478 29.03 0.00 38.25 0.98
213 214 3.056080 ACTGCCCATGGACAGGTATATT 58.944 45.455 29.03 6.88 38.25 1.28
214 215 2.639839 GACTGCCCATGGACAGGTATAT 59.360 50.000 29.03 10.22 38.25 0.86
215 216 2.047061 GACTGCCCATGGACAGGTATA 58.953 52.381 29.03 0.00 38.25 1.47
216 217 0.839946 GACTGCCCATGGACAGGTAT 59.160 55.000 29.03 10.96 38.25 2.73
217 218 1.271840 GGACTGCCCATGGACAGGTA 61.272 60.000 29.03 4.75 38.25 3.08
218 219 2.606587 GGACTGCCCATGGACAGGT 61.607 63.158 29.03 16.14 38.25 4.00
219 220 2.273449 GGACTGCCCATGGACAGG 59.727 66.667 29.03 13.25 38.25 4.00
220 221 2.124983 CGGACTGCCCATGGACAG 60.125 66.667 24.99 24.99 39.86 3.51
221 222 4.408821 GCGGACTGCCCATGGACA 62.409 66.667 15.22 7.03 37.76 4.02
263 264 3.496131 CGGGTCGGGCATTTCGTG 61.496 66.667 0.00 0.00 0.00 4.35
264 265 4.770874 CCGGGTCGGGCATTTCGT 62.771 66.667 0.00 0.00 44.15 3.85
281 282 3.443045 CACAATGTCGGGCCAGGC 61.443 66.667 4.39 1.26 0.00 4.85
282 283 3.443045 GCACAATGTCGGGCCAGG 61.443 66.667 4.39 0.00 0.00 4.45
283 284 0.747644 TATGCACAATGTCGGGCCAG 60.748 55.000 4.39 0.00 0.00 4.85
284 285 0.747644 CTATGCACAATGTCGGGCCA 60.748 55.000 4.39 0.00 0.00 5.36
285 286 0.463654 TCTATGCACAATGTCGGGCC 60.464 55.000 0.00 0.00 0.00 5.80
286 287 0.657840 GTCTATGCACAATGTCGGGC 59.342 55.000 0.00 0.00 0.00 6.13
287 288 1.299541 GGTCTATGCACAATGTCGGG 58.700 55.000 0.00 0.00 0.00 5.14
288 289 0.930310 CGGTCTATGCACAATGTCGG 59.070 55.000 0.00 0.00 0.00 4.79
289 290 0.930310 CCGGTCTATGCACAATGTCG 59.070 55.000 0.00 0.00 0.00 4.35
290 291 1.299541 CCCGGTCTATGCACAATGTC 58.700 55.000 0.00 0.00 0.00 3.06
291 292 0.748005 GCCCGGTCTATGCACAATGT 60.748 55.000 0.00 0.00 0.00 2.71
292 293 1.447317 GGCCCGGTCTATGCACAATG 61.447 60.000 0.00 0.00 0.00 2.82
293 294 1.152963 GGCCCGGTCTATGCACAAT 60.153 57.895 0.00 0.00 0.00 2.71
294 295 2.270850 GGCCCGGTCTATGCACAA 59.729 61.111 0.00 0.00 0.00 3.33
295 296 2.687200 AGGCCCGGTCTATGCACA 60.687 61.111 0.00 0.00 0.00 4.57
296 297 2.203070 CAGGCCCGGTCTATGCAC 60.203 66.667 0.00 0.00 0.00 4.57
297 298 3.479203 CCAGGCCCGGTCTATGCA 61.479 66.667 0.00 0.00 0.00 3.96
298 299 4.256180 CCCAGGCCCGGTCTATGC 62.256 72.222 3.77 0.00 0.00 3.14
299 300 4.256180 GCCCAGGCCCGGTCTATG 62.256 72.222 3.77 0.00 34.56 2.23
309 310 1.685148 CTCAAAATCTAGGCCCAGGC 58.315 55.000 0.00 0.00 41.06 4.85
310 311 1.685148 GCTCAAAATCTAGGCCCAGG 58.315 55.000 0.00 0.00 0.00 4.45
311 312 1.685148 GGCTCAAAATCTAGGCCCAG 58.315 55.000 0.00 0.00 37.12 4.45
312 313 3.903208 GGCTCAAAATCTAGGCCCA 57.097 52.632 0.00 0.00 37.12 5.36
315 316 1.943340 CTTCGGGCTCAAAATCTAGGC 59.057 52.381 0.00 0.00 37.55 3.93
316 317 2.565841 CCTTCGGGCTCAAAATCTAGG 58.434 52.381 0.00 0.00 0.00 3.02
352 353 4.314440 TGATATGAGCGGGCCGGC 62.314 66.667 29.48 26.78 0.00 6.13
353 354 2.047844 CTGATATGAGCGGGCCGG 60.048 66.667 29.48 9.71 0.00 6.13
354 355 2.047844 CCTGATATGAGCGGGCCG 60.048 66.667 24.35 24.35 0.00 6.13
355 356 1.557269 ATCCCTGATATGAGCGGGCC 61.557 60.000 0.00 0.00 36.61 5.80
356 357 0.326264 AATCCCTGATATGAGCGGGC 59.674 55.000 0.00 0.00 36.61 6.13
357 358 2.867109 AAATCCCTGATATGAGCGGG 57.133 50.000 0.00 0.00 38.07 6.13
358 359 5.491070 TCATTAAATCCCTGATATGAGCGG 58.509 41.667 0.00 0.00 0.00 5.52
359 360 6.875726 TCTTCATTAAATCCCTGATATGAGCG 59.124 38.462 0.00 0.00 0.00 5.03
360 361 7.336427 CCTCTTCATTAAATCCCTGATATGAGC 59.664 40.741 0.00 0.00 0.00 4.26
361 362 7.336427 GCCTCTTCATTAAATCCCTGATATGAG 59.664 40.741 0.00 0.00 0.00 2.90
362 363 7.170965 GCCTCTTCATTAAATCCCTGATATGA 58.829 38.462 0.00 0.00 0.00 2.15
363 364 6.376581 GGCCTCTTCATTAAATCCCTGATATG 59.623 42.308 0.00 0.00 0.00 1.78
364 365 6.488715 GGCCTCTTCATTAAATCCCTGATAT 58.511 40.000 0.00 0.00 0.00 1.63
365 366 5.222130 GGGCCTCTTCATTAAATCCCTGATA 60.222 44.000 0.84 0.00 0.00 2.15
366 367 4.448347 GGGCCTCTTCATTAAATCCCTGAT 60.448 45.833 0.84 0.00 0.00 2.90
367 368 3.117512 GGGCCTCTTCATTAAATCCCTGA 60.118 47.826 0.84 0.00 0.00 3.86
368 369 3.225940 GGGCCTCTTCATTAAATCCCTG 58.774 50.000 0.84 0.00 0.00 4.45
369 370 2.858768 TGGGCCTCTTCATTAAATCCCT 59.141 45.455 4.53 0.00 33.77 4.20
370 371 3.225940 CTGGGCCTCTTCATTAAATCCC 58.774 50.000 4.53 0.00 0.00 3.85
371 372 2.625314 GCTGGGCCTCTTCATTAAATCC 59.375 50.000 4.53 0.00 0.00 3.01
372 373 2.625314 GGCTGGGCCTCTTCATTAAATC 59.375 50.000 4.53 0.00 46.69 2.17
373 374 2.670939 GGCTGGGCCTCTTCATTAAAT 58.329 47.619 4.53 0.00 46.69 1.40
374 375 2.143876 GGCTGGGCCTCTTCATTAAA 57.856 50.000 4.53 0.00 46.69 1.52
375 376 3.903208 GGCTGGGCCTCTTCATTAA 57.097 52.632 4.53 0.00 46.69 1.40
417 418 2.361610 CACAAGCCCGGCCTGATT 60.362 61.111 15.23 0.00 0.00 2.57
418 419 4.431131 CCACAAGCCCGGCCTGAT 62.431 66.667 15.23 0.00 0.00 2.90
458 459 0.883833 ATGCAGAAAACTCAAGCCCG 59.116 50.000 0.00 0.00 0.00 6.13
463 464 0.881118 GCCCGATGCAGAAAACTCAA 59.119 50.000 0.00 0.00 40.77 3.02
520 521 1.761449 TACGTTATACCTGGCCGTCA 58.239 50.000 0.00 0.00 33.32 4.35
523 524 3.248266 GCTTATACGTTATACCTGGCCG 58.752 50.000 0.00 0.00 0.00 6.13
565 566 6.437477 TGGAGAGCAAGAGAAGTCAACTATAA 59.563 38.462 0.00 0.00 0.00 0.98
581 582 5.500234 AGTGCAATATTAACTGGAGAGCAA 58.500 37.500 0.00 0.00 0.00 3.91
591 592 7.627340 ACACGTATAGCAAGTGCAATATTAAC 58.373 34.615 6.00 0.00 45.16 2.01
598 599 2.289133 TGGACACGTATAGCAAGTGCAA 60.289 45.455 6.00 0.00 45.16 4.08
603 604 2.549926 TGCATGGACACGTATAGCAAG 58.450 47.619 0.00 0.00 0.00 4.01
776 783 7.031975 GCTTAAACTATAATATACGTCCGGCT 58.968 38.462 0.00 0.00 0.00 5.52
888 988 1.003928 GGGTGGTATTTATAGCCCGGG 59.996 57.143 19.09 19.09 0.00 5.73
1076 1180 1.923909 GGGGTAGGGCAGTGAGGTT 60.924 63.158 0.00 0.00 0.00 3.50
1080 1184 2.682494 GTCGGGGTAGGGCAGTGA 60.682 66.667 0.00 0.00 0.00 3.41
1105 1209 1.320344 CCGTTGGTCGATGGAGGAGA 61.320 60.000 0.00 0.00 42.86 3.71
1107 1211 3.014085 GCCGTTGGTCGATGGAGGA 62.014 63.158 0.73 0.00 42.86 3.71
1283 1388 3.382832 CGCCGAGGACCTTGACCT 61.383 66.667 10.67 0.00 40.80 3.85
1286 1391 1.945354 GATGACGCCGAGGACCTTGA 61.945 60.000 10.67 0.00 0.00 3.02
1449 1554 6.282199 ACACAAACTGGAGTAGTGTATAGG 57.718 41.667 13.36 0.00 42.01 2.57
2126 5554 3.118454 CGCCCGGCACAGTACTTG 61.118 66.667 10.77 0.00 0.00 3.16
2136 5564 1.153628 CATATAGTAGGCGCCCGGC 60.154 63.158 26.15 13.94 42.51 6.13
2145 5577 6.607600 TGATACAAGCTAGGGGCATATAGTAG 59.392 42.308 0.00 0.00 44.79 2.57
2146 5578 6.499436 TGATACAAGCTAGGGGCATATAGTA 58.501 40.000 0.00 0.00 44.79 1.82
2147 5579 5.342017 TGATACAAGCTAGGGGCATATAGT 58.658 41.667 0.00 0.00 44.79 2.12
2287 5720 6.785337 TGTTTCTCTTCCTACGATCCATAA 57.215 37.500 0.00 0.00 0.00 1.90
2332 5765 6.418226 GTCGCTCGTCAATACTAAATTCATCT 59.582 38.462 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.