Multiple sequence alignment - TraesCS4A01G363600

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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 TraesCS4A01G363600 chr4A 100.000 2894 0 0 1 2894 636670020 636667127 0.000000e+00 5345.0
1 TraesCS4A01G363600 chr4A 81.081 222 31 7 25 242 88087638 88087424 1.780000e-37 167.0
2 TraesCS4A01G363600 chr4A 80.882 204 28 6 37 231 88092830 88092629 1.800000e-32 150.0
3 TraesCS4A01G363600 chr5D 92.692 1984 81 16 386 2326 534870245 534872207 0.000000e+00 2802.0
4 TraesCS4A01G363600 chr5D 88.820 483 34 7 2366 2843 534872426 534872893 2.500000e-160 575.0
5 TraesCS4A01G363600 chr5D 91.561 237 16 4 1 237 534870014 534870246 1.000000e-84 324.0
6 TraesCS4A01G363600 chr5D 94.545 55 3 0 2302 2356 173749845 173749791 5.140000e-13 86.1
7 TraesCS4A01G363600 chr5D 96.970 33 1 0 2145 2177 534872085 534872117 4.030000e-04 56.5
8 TraesCS4A01G363600 chr5B 92.114 1433 70 15 897 2302 675870267 675871683 0.000000e+00 1980.0
9 TraesCS4A01G363600 chr5B 94.925 532 25 2 372 901 675869707 675870238 0.000000e+00 832.0
10 TraesCS4A01G363600 chr5B 83.984 487 54 16 2363 2843 675871677 675872145 2.050000e-121 446.0
11 TraesCS4A01G363600 chr5B 82.775 209 23 7 25 232 343824807 343825003 1.070000e-39 174.0
12 TraesCS4A01G363600 chr5B 79.781 183 24 7 56 233 20150795 20150621 1.410000e-23 121.0
13 TraesCS4A01G363600 chr7B 85.253 217 21 6 25 231 509733849 509734064 2.260000e-51 213.0
14 TraesCS4A01G363600 chr7B 94.309 123 6 1 112 233 123654722 123654600 1.370000e-43 187.0
15 TraesCS4A01G363600 chr7B 92.982 57 3 1 2302 2358 202105438 202105493 6.650000e-12 82.4
16 TraesCS4A01G363600 chr7A 83.908 174 22 3 23 190 64778219 64778392 8.300000e-36 161.0
17 TraesCS4A01G363600 chr7A 87.857 140 10 4 95 233 64778523 64778656 1.070000e-34 158.0
18 TraesCS4A01G363600 chr3A 94.545 55 2 1 2307 2361 34827885 34827938 1.850000e-12 84.2
19 TraesCS4A01G363600 chr2A 94.444 54 3 0 2308 2361 510433114 510433061 1.850000e-12 84.2
20 TraesCS4A01G363600 chr7D 92.857 56 4 0 2301 2356 540570515 540570460 6.650000e-12 82.4
21 TraesCS4A01G363600 chr1D 96.000 50 2 0 2301 2350 469153910 469153959 6.650000e-12 82.4
22 TraesCS4A01G363600 chr1D 92.857 56 3 1 2301 2356 279945342 279945288 2.390000e-11 80.5
23 TraesCS4A01G363600 chr2D 88.060 67 7 1 2306 2371 326405523 326405457 8.600000e-11 78.7
24 TraesCS4A01G363600 chr2B 88.060 67 5 2 2292 2356 174925554 174925489 3.090000e-10 76.8


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 TraesCS4A01G363600 chr4A 636667127 636670020 2893 True 5345.000 5345 100.00000 1 2894 1 chr4A.!!$R3 2893
1 TraesCS4A01G363600 chr5D 534870014 534872893 2879 False 939.375 2802 92.51075 1 2843 4 chr5D.!!$F1 2842
2 TraesCS4A01G363600 chr5B 675869707 675872145 2438 False 1086.000 1980 90.34100 372 2843 3 chr5B.!!$F2 2471

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
260 261 0.034896 GCGAAGGAGGAGGTTGTTGA 59.965 55.0 0.0 0.0 0.0 3.18 F
286 287 0.179089 GCGATGGAGATGAGTGCAGT 60.179 55.0 0.0 0.0 0.0 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1666 1711 0.605589 CTCTTCTCGCAGAACCACCT 59.394 55.000 0.00 0.0 34.09 4.00 R
2177 2252 1.001487 CGATGCTGCAAAGTGGTTTCA 60.001 47.619 6.36 0.0 0.00 2.69 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
26 27 5.369404 TGGTATTCCTCTTTCTCCATATGCA 59.631 40.000 0.00 0.00 34.23 3.96
47 48 2.434336 AGCTGTTATGATCCCGTGCTTA 59.566 45.455 0.00 0.00 0.00 3.09
48 49 2.544267 GCTGTTATGATCCCGTGCTTAC 59.456 50.000 0.00 0.00 0.00 2.34
59 60 1.626654 CGTGCTTACGTGAGCTTGGG 61.627 60.000 29.42 14.07 43.11 4.12
66 67 0.107410 ACGTGAGCTTGGGTGAACAA 60.107 50.000 0.00 0.00 0.00 2.83
74 75 7.375053 GTGAGCTTGGGTGAACAATAAAATTA 58.625 34.615 0.00 0.00 0.00 1.40
79 80 9.877137 GCTTGGGTGAACAATAAAATTAAAAAG 57.123 29.630 0.00 0.00 0.00 2.27
145 146 6.279123 TGACAAATGTTTTGATAGCTTGCAA 58.721 32.000 0.00 0.00 0.00 4.08
157 158 2.340337 AGCTTGCAAAATTTCATCGCC 58.660 42.857 0.00 0.00 0.00 5.54
183 184 7.171167 CAGATGAAATTTGTGTAAAATGTGGCA 59.829 33.333 0.00 0.00 0.00 4.92
237 238 3.874400 TTCAAACGCATTTTGGCAATG 57.126 38.095 0.00 0.00 44.30 2.82
238 239 2.831333 TCAAACGCATTTTGGCAATGT 58.169 38.095 0.00 0.00 44.30 2.71
239 240 2.543012 TCAAACGCATTTTGGCAATGTG 59.457 40.909 11.69 11.69 44.30 3.21
240 241 2.522836 AACGCATTTTGGCAATGTGA 57.477 40.000 18.35 0.00 39.73 3.58
241 242 2.068837 ACGCATTTTGGCAATGTGAG 57.931 45.000 18.35 15.12 39.73 3.51
242 243 0.717224 CGCATTTTGGCAATGTGAGC 59.283 50.000 14.29 8.11 39.73 4.26
243 244 0.717224 GCATTTTGGCAATGTGAGCG 59.283 50.000 14.29 0.00 0.00 5.03
244 245 1.669502 GCATTTTGGCAATGTGAGCGA 60.670 47.619 14.29 0.00 0.00 4.93
245 246 2.674954 CATTTTGGCAATGTGAGCGAA 58.325 42.857 0.00 0.00 0.00 4.70
246 247 2.420628 TTTTGGCAATGTGAGCGAAG 57.579 45.000 0.00 0.00 31.47 3.79
247 248 0.597568 TTTGGCAATGTGAGCGAAGG 59.402 50.000 0.00 0.00 31.47 3.46
248 249 0.250684 TTGGCAATGTGAGCGAAGGA 60.251 50.000 0.00 0.00 0.00 3.36
249 250 0.674581 TGGCAATGTGAGCGAAGGAG 60.675 55.000 0.00 0.00 0.00 3.69
250 251 1.372087 GGCAATGTGAGCGAAGGAGG 61.372 60.000 0.00 0.00 0.00 4.30
251 252 0.391661 GCAATGTGAGCGAAGGAGGA 60.392 55.000 0.00 0.00 0.00 3.71
252 253 1.649664 CAATGTGAGCGAAGGAGGAG 58.350 55.000 0.00 0.00 0.00 3.69
253 254 0.539051 AATGTGAGCGAAGGAGGAGG 59.461 55.000 0.00 0.00 0.00 4.30
254 255 0.616111 ATGTGAGCGAAGGAGGAGGT 60.616 55.000 0.00 0.00 0.00 3.85
255 256 0.832135 TGTGAGCGAAGGAGGAGGTT 60.832 55.000 0.00 0.00 0.00 3.50
256 257 0.390472 GTGAGCGAAGGAGGAGGTTG 60.390 60.000 0.00 0.00 0.00 3.77
257 258 0.832135 TGAGCGAAGGAGGAGGTTGT 60.832 55.000 0.00 0.00 0.00 3.32
258 259 0.321996 GAGCGAAGGAGGAGGTTGTT 59.678 55.000 0.00 0.00 0.00 2.83
259 260 0.035458 AGCGAAGGAGGAGGTTGTTG 59.965 55.000 0.00 0.00 0.00 3.33
260 261 0.034896 GCGAAGGAGGAGGTTGTTGA 59.965 55.000 0.00 0.00 0.00 3.18
261 262 1.941668 GCGAAGGAGGAGGTTGTTGAG 60.942 57.143 0.00 0.00 0.00 3.02
262 263 1.618837 CGAAGGAGGAGGTTGTTGAGA 59.381 52.381 0.00 0.00 0.00 3.27
263 264 2.037251 CGAAGGAGGAGGTTGTTGAGAA 59.963 50.000 0.00 0.00 0.00 2.87
264 265 3.403968 GAAGGAGGAGGTTGTTGAGAAC 58.596 50.000 0.00 0.00 0.00 3.01
265 266 2.695585 AGGAGGAGGTTGTTGAGAACT 58.304 47.619 0.00 0.00 0.00 3.01
266 267 3.049344 AGGAGGAGGTTGTTGAGAACTT 58.951 45.455 0.00 0.00 0.00 2.66
267 268 3.142174 GGAGGAGGTTGTTGAGAACTTG 58.858 50.000 0.00 0.00 0.00 3.16
268 269 2.550180 GAGGAGGTTGTTGAGAACTTGC 59.450 50.000 0.00 0.00 0.00 4.01
269 270 1.264288 GGAGGTTGTTGAGAACTTGCG 59.736 52.381 0.00 0.00 0.00 4.85
270 271 2.210116 GAGGTTGTTGAGAACTTGCGA 58.790 47.619 0.00 0.00 0.00 5.10
271 272 2.808543 GAGGTTGTTGAGAACTTGCGAT 59.191 45.455 0.00 0.00 0.00 4.58
272 273 2.549754 AGGTTGTTGAGAACTTGCGATG 59.450 45.455 0.00 0.00 0.00 3.84
273 274 2.350772 GGTTGTTGAGAACTTGCGATGG 60.351 50.000 0.00 0.00 0.00 3.51
274 275 2.542020 TGTTGAGAACTTGCGATGGA 57.458 45.000 0.00 0.00 0.00 3.41
275 276 2.416747 TGTTGAGAACTTGCGATGGAG 58.583 47.619 0.00 0.00 0.00 3.86
276 277 2.037121 TGTTGAGAACTTGCGATGGAGA 59.963 45.455 0.00 0.00 0.00 3.71
277 278 3.265791 GTTGAGAACTTGCGATGGAGAT 58.734 45.455 0.00 0.00 0.00 2.75
278 279 2.897436 TGAGAACTTGCGATGGAGATG 58.103 47.619 0.00 0.00 0.00 2.90
279 280 2.497273 TGAGAACTTGCGATGGAGATGA 59.503 45.455 0.00 0.00 0.00 2.92
280 281 3.122297 GAGAACTTGCGATGGAGATGAG 58.878 50.000 0.00 0.00 0.00 2.90
281 282 2.499289 AGAACTTGCGATGGAGATGAGT 59.501 45.455 0.00 0.00 0.00 3.41
282 283 2.306341 ACTTGCGATGGAGATGAGTG 57.694 50.000 0.00 0.00 0.00 3.51
283 284 0.935898 CTTGCGATGGAGATGAGTGC 59.064 55.000 0.00 0.00 0.00 4.40
284 285 0.249955 TTGCGATGGAGATGAGTGCA 59.750 50.000 0.00 0.00 0.00 4.57
285 286 0.179092 TGCGATGGAGATGAGTGCAG 60.179 55.000 0.00 0.00 0.00 4.41
286 287 0.179089 GCGATGGAGATGAGTGCAGT 60.179 55.000 0.00 0.00 0.00 4.40
287 288 1.568606 CGATGGAGATGAGTGCAGTG 58.431 55.000 0.00 0.00 0.00 3.66
288 289 1.135721 CGATGGAGATGAGTGCAGTGA 59.864 52.381 0.00 0.00 0.00 3.41
289 290 2.798853 CGATGGAGATGAGTGCAGTGAG 60.799 54.545 0.00 0.00 0.00 3.51
290 291 0.900421 TGGAGATGAGTGCAGTGAGG 59.100 55.000 0.00 0.00 0.00 3.86
291 292 0.461693 GGAGATGAGTGCAGTGAGGC 60.462 60.000 0.00 0.00 0.00 4.70
292 293 0.248565 GAGATGAGTGCAGTGAGGCA 59.751 55.000 0.00 0.00 42.53 4.75
293 294 0.910338 AGATGAGTGCAGTGAGGCAT 59.090 50.000 0.00 0.00 46.92 4.40
294 295 1.281287 AGATGAGTGCAGTGAGGCATT 59.719 47.619 0.00 0.00 46.92 3.56
295 296 2.089980 GATGAGTGCAGTGAGGCATTT 58.910 47.619 0.00 0.00 46.92 2.32
296 297 1.985473 TGAGTGCAGTGAGGCATTTT 58.015 45.000 0.00 0.00 46.92 1.82
297 298 2.309613 TGAGTGCAGTGAGGCATTTTT 58.690 42.857 0.00 0.00 46.92 1.94
326 327 2.360475 GGCCAGTGAGGACCAAGC 60.360 66.667 0.00 0.00 40.85 4.01
327 328 2.431683 GCCAGTGAGGACCAAGCA 59.568 61.111 0.00 0.00 41.22 3.91
328 329 1.673665 GCCAGTGAGGACCAAGCAG 60.674 63.158 0.00 0.00 41.22 4.24
329 330 1.673665 CCAGTGAGGACCAAGCAGC 60.674 63.158 0.00 0.00 41.22 5.25
330 331 1.673665 CAGTGAGGACCAAGCAGCC 60.674 63.158 0.00 0.00 0.00 4.85
331 332 2.149383 AGTGAGGACCAAGCAGCCA 61.149 57.895 0.00 0.00 0.00 4.75
332 333 1.968540 GTGAGGACCAAGCAGCCAC 60.969 63.158 0.00 0.00 0.00 5.01
333 334 2.149383 TGAGGACCAAGCAGCCACT 61.149 57.895 0.00 0.00 0.00 4.00
334 335 1.673665 GAGGACCAAGCAGCCACTG 60.674 63.158 0.00 0.00 34.12 3.66
335 336 2.674380 GGACCAAGCAGCCACTGG 60.674 66.667 4.54 4.54 31.21 4.00
354 355 3.803082 CGCTGGGACGCCACAATG 61.803 66.667 0.00 0.00 0.00 2.82
355 356 3.443045 GCTGGGACGCCACAATGG 61.443 66.667 0.00 0.00 41.55 3.16
356 357 2.751436 CTGGGACGCCACAATGGG 60.751 66.667 0.00 0.00 38.19 4.00
365 366 3.286404 CCACAATGGGCCTTCATCA 57.714 52.632 4.53 0.00 32.67 3.07
366 367 1.784358 CCACAATGGGCCTTCATCAT 58.216 50.000 4.53 0.00 32.67 2.45
367 368 2.112998 CCACAATGGGCCTTCATCATT 58.887 47.619 4.53 0.00 32.67 2.57
369 370 2.112998 ACAATGGGCCTTCATCATTGG 58.887 47.619 25.82 13.93 46.94 3.16
370 371 1.125633 AATGGGCCTTCATCATTGGC 58.874 50.000 4.53 0.00 45.42 4.52
389 390 2.074948 AGGCAGGCCCATCGATTCT 61.075 57.895 6.70 0.00 36.58 2.40
395 396 1.025041 GGCCCATCGATTCTTTGTCC 58.975 55.000 0.00 0.00 0.00 4.02
461 464 1.599542 CGGAAAATCTGGCGATCTTCC 59.400 52.381 11.81 11.81 41.43 3.46
491 494 3.101437 TCTGGGCGATTACCTCTGTAAA 58.899 45.455 0.00 0.00 40.21 2.01
496 499 2.028883 GCGATTACCTCTGTAAACACGC 59.971 50.000 14.01 14.01 43.25 5.34
937 973 1.379977 AAGCCCGACCTCTCGATCA 60.380 57.895 0.00 0.00 43.06 2.92
1206 1251 4.111016 TCCTCGTACCGCGTGCTG 62.111 66.667 4.92 0.00 42.13 4.41
1257 1302 3.955101 CGGCGCTACTCCTCGGAG 61.955 72.222 7.64 11.35 46.91 4.63
1641 1686 2.049063 ACGCTGAACACGGAGCTC 60.049 61.111 4.71 4.71 32.70 4.09
1666 1711 3.535629 CTGCAGGCGGTGAGGTTGA 62.536 63.158 5.57 0.00 0.00 3.18
1724 1769 4.785453 GAGGAACAGGGGCGGCAG 62.785 72.222 12.47 2.10 0.00 4.85
1979 2050 9.840427 AATGACTGCAAATTGTAGTATTTGTAC 57.160 29.630 16.30 3.68 43.31 2.90
2002 2074 7.190920 ACAGGAGTATTATAATGCTTTTCGC 57.809 36.000 16.03 4.52 39.77 4.70
2038 2110 0.030638 CTGCAACCCAAACTGGTTCG 59.969 55.000 0.00 0.00 45.51 3.95
2046 2118 3.267483 CCCAAACTGGTTCGATTATCGT 58.733 45.455 14.47 0.00 37.17 3.73
2058 2130 3.796717 TCGATTATCGTCACTGTCATTGC 59.203 43.478 14.47 0.00 41.35 3.56
2072 2144 3.058293 TGTCATTGCTCTCGCGAAAATTT 60.058 39.130 11.33 0.00 39.65 1.82
2111 2183 1.760192 ACCAAGCATCTCATGAAGGC 58.240 50.000 0.00 1.70 0.00 4.35
2136 2209 7.225145 GCACATGGATTGTTTGCATATAAACAT 59.775 33.333 2.68 2.87 46.43 2.71
2146 2219 8.190122 TGTTTGCATATAAACATCAATGACCTC 58.810 33.333 0.00 0.00 43.46 3.85
2195 2270 2.034124 ACTGAAACCACTTTGCAGCAT 58.966 42.857 0.00 0.00 0.00 3.79
2197 2272 1.001487 TGAAACCACTTTGCAGCATCG 60.001 47.619 0.00 0.00 0.00 3.84
2199 2274 1.890876 AACCACTTTGCAGCATCGTA 58.109 45.000 0.00 0.00 0.00 3.43
2215 2290 7.505646 CAGCATCGTAGAAATATAAGTTCTGC 58.494 38.462 10.76 8.96 43.58 4.26
2217 2292 7.875041 AGCATCGTAGAAATATAAGTTCTGCAT 59.125 33.333 14.03 7.19 43.58 3.96
2225 2300 7.934120 AGAAATATAAGTTCTGCATGTACCCTC 59.066 37.037 0.00 0.00 34.03 4.30
2226 2301 2.386661 AAGTTCTGCATGTACCCTCG 57.613 50.000 0.00 0.00 0.00 4.63
2233 2308 1.070914 TGCATGTACCCTCGTGAACAA 59.929 47.619 0.00 0.00 0.00 2.83
2245 2320 6.921307 ACCCTCGTGAACAATTAAATTGAAAC 59.079 34.615 0.00 0.00 42.83 2.78
2249 2324 9.618410 CTCGTGAACAATTAAATTGAAACAAAC 57.382 29.630 0.00 0.00 42.83 2.93
2317 2395 4.827835 TCGGTGAATATTCTACTCCCTCTG 59.172 45.833 16.24 3.19 0.00 3.35
2334 2412 9.495382 ACTCCCTCTGTAAAGAAATATAAGAGT 57.505 33.333 0.00 0.00 0.00 3.24
2335 2413 9.757227 CTCCCTCTGTAAAGAAATATAAGAGTG 57.243 37.037 0.00 0.00 0.00 3.51
2336 2414 9.268282 TCCCTCTGTAAAGAAATATAAGAGTGT 57.732 33.333 0.00 0.00 0.00 3.55
2337 2415 9.892130 CCCTCTGTAAAGAAATATAAGAGTGTT 57.108 33.333 0.00 0.00 0.00 3.32
2400 2657 8.621532 AACATTGCTAATACTCTGTCAAAAGA 57.378 30.769 0.00 0.00 0.00 2.52
2436 2693 7.201384 GCTCCAGAAAGAATATTTTTGAAAGCG 60.201 37.037 0.00 0.00 0.00 4.68
2444 2701 8.871686 AGAATATTTTTGAAAGCGTTTTGAGT 57.128 26.923 0.59 0.00 0.00 3.41
2456 2713 3.602265 GCGTTTTGAGTTGCTGATTTTGC 60.602 43.478 0.00 0.00 0.00 3.68
2457 2714 3.360956 CGTTTTGAGTTGCTGATTTTGCG 60.361 43.478 0.00 0.00 0.00 4.85
2461 2718 4.039151 TGAGTTGCTGATTTTGCGAAAA 57.961 36.364 2.54 0.00 34.41 2.29
2462 2719 4.043750 TGAGTTGCTGATTTTGCGAAAAG 58.956 39.130 2.54 0.00 33.22 2.27
2466 2723 5.754890 AGTTGCTGATTTTGCGAAAAGAATT 59.245 32.000 2.54 0.00 33.22 2.17
2485 2742 6.942976 AGAATTCTAAACCTCCACGAATGTA 58.057 36.000 6.06 0.00 0.00 2.29
2526 2783 5.032863 GCATGCACATAGAAAACTAAGCAG 58.967 41.667 14.21 0.00 33.94 4.24
2531 2788 5.853282 GCACATAGAAAACTAAGCAGTGTTG 59.147 40.000 0.00 0.00 32.01 3.33
2534 2791 6.204882 ACATAGAAAACTAAGCAGTGTTGGTC 59.795 38.462 0.00 0.00 32.01 4.02
2596 2855 5.485353 TCTTGAGCTTGAGATTAGAAGGGAA 59.515 40.000 0.00 0.00 0.00 3.97
2597 2856 5.350504 TGAGCTTGAGATTAGAAGGGAAG 57.649 43.478 0.00 0.00 0.00 3.46
2598 2857 5.026121 TGAGCTTGAGATTAGAAGGGAAGA 58.974 41.667 0.00 0.00 0.00 2.87
2599 2858 5.105146 TGAGCTTGAGATTAGAAGGGAAGAC 60.105 44.000 0.00 0.00 0.00 3.01
2602 2861 6.012945 AGCTTGAGATTAGAAGGGAAGACTTT 60.013 38.462 0.00 0.00 0.00 2.66
2603 2862 6.315144 GCTTGAGATTAGAAGGGAAGACTTTC 59.685 42.308 0.00 0.00 0.00 2.62
2604 2863 5.967088 TGAGATTAGAAGGGAAGACTTTCG 58.033 41.667 0.00 0.00 33.98 3.46
2607 2866 0.325272 AGAAGGGAAGACTTTCGCCC 59.675 55.000 2.75 2.75 44.80 6.13
2608 2867 1.003718 AAGGGAAGACTTTCGCCCG 60.004 57.895 5.10 0.00 44.80 6.13
2625 2887 0.955178 CCGGCATTGTTTACACACCA 59.045 50.000 0.00 0.00 30.32 4.17
2676 2938 3.670500 CTGAACTGCAGCAACATCG 57.330 52.632 15.27 0.00 37.90 3.84
2746 3009 4.176271 GCACATTCAAATACTCCCTTTGC 58.824 43.478 0.00 0.00 34.36 3.68
2797 3060 3.499048 TGAGACGAAGCGAGTATGTTTC 58.501 45.455 0.00 0.00 0.00 2.78
2853 3116 8.846943 TCATTAGAAGATGTAAAAGCAAGTGA 57.153 30.769 0.00 0.00 0.00 3.41
2854 3117 9.453572 TCATTAGAAGATGTAAAAGCAAGTGAT 57.546 29.630 0.00 0.00 0.00 3.06
2855 3118 9.499585 CATTAGAAGATGTAAAAGCAAGTGATG 57.500 33.333 0.00 0.00 0.00 3.07
2856 3119 8.621532 TTAGAAGATGTAAAAGCAAGTGATGT 57.378 30.769 0.00 0.00 0.00 3.06
2857 3120 9.719355 TTAGAAGATGTAAAAGCAAGTGATGTA 57.281 29.630 0.00 0.00 0.00 2.29
2858 3121 8.798859 AGAAGATGTAAAAGCAAGTGATGTAT 57.201 30.769 0.00 0.00 0.00 2.29
2859 3122 9.890629 AGAAGATGTAAAAGCAAGTGATGTATA 57.109 29.630 0.00 0.00 0.00 1.47
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 5.869579 TGCATATGGAGAAAGAGGAATACC 58.130 41.667 4.56 0.00 0.00 2.73
13 14 5.683681 TCATAACAGCTGCATATGGAGAAA 58.316 37.500 26.59 13.57 35.31 2.52
23 24 0.541392 ACGGGATCATAACAGCTGCA 59.459 50.000 15.27 1.58 0.00 4.41
26 27 0.833287 AGCACGGGATCATAACAGCT 59.167 50.000 0.00 0.00 0.00 4.24
47 48 0.107410 TTGTTCACCCAAGCTCACGT 60.107 50.000 0.00 0.00 0.00 4.49
48 49 1.238439 ATTGTTCACCCAAGCTCACG 58.762 50.000 0.00 0.00 0.00 4.35
129 130 7.685304 CGATGAAATTTTGCAAGCTATCAAAAC 59.315 33.333 21.07 13.08 42.62 2.43
157 158 7.171167 TGCCACATTTTACACAAATTTCATCTG 59.829 33.333 0.00 0.00 0.00 2.90
237 238 0.390472 CAACCTCCTCCTTCGCTCAC 60.390 60.000 0.00 0.00 0.00 3.51
238 239 0.832135 ACAACCTCCTCCTTCGCTCA 60.832 55.000 0.00 0.00 0.00 4.26
239 240 0.321996 AACAACCTCCTCCTTCGCTC 59.678 55.000 0.00 0.00 0.00 5.03
240 241 0.035458 CAACAACCTCCTCCTTCGCT 59.965 55.000 0.00 0.00 0.00 4.93
241 242 0.034896 TCAACAACCTCCTCCTTCGC 59.965 55.000 0.00 0.00 0.00 4.70
242 243 1.618837 TCTCAACAACCTCCTCCTTCG 59.381 52.381 0.00 0.00 0.00 3.79
243 244 3.071747 AGTTCTCAACAACCTCCTCCTTC 59.928 47.826 0.00 0.00 0.00 3.46
244 245 3.049344 AGTTCTCAACAACCTCCTCCTT 58.951 45.455 0.00 0.00 0.00 3.36
245 246 2.695585 AGTTCTCAACAACCTCCTCCT 58.304 47.619 0.00 0.00 0.00 3.69
246 247 3.142174 CAAGTTCTCAACAACCTCCTCC 58.858 50.000 0.00 0.00 0.00 4.30
247 248 2.550180 GCAAGTTCTCAACAACCTCCTC 59.450 50.000 0.00 0.00 0.00 3.71
248 249 2.576615 GCAAGTTCTCAACAACCTCCT 58.423 47.619 0.00 0.00 0.00 3.69
249 250 1.264288 CGCAAGTTCTCAACAACCTCC 59.736 52.381 0.00 0.00 0.00 4.30
250 251 2.210116 TCGCAAGTTCTCAACAACCTC 58.790 47.619 0.00 0.00 39.48 3.85
251 252 2.325583 TCGCAAGTTCTCAACAACCT 57.674 45.000 0.00 0.00 39.48 3.50
252 253 2.350772 CCATCGCAAGTTCTCAACAACC 60.351 50.000 0.00 0.00 39.48 3.77
253 254 2.548057 TCCATCGCAAGTTCTCAACAAC 59.452 45.455 0.00 0.00 39.48 3.32
254 255 2.807967 CTCCATCGCAAGTTCTCAACAA 59.192 45.455 0.00 0.00 39.48 2.83
255 256 2.037121 TCTCCATCGCAAGTTCTCAACA 59.963 45.455 0.00 0.00 39.48 3.33
256 257 2.688507 TCTCCATCGCAAGTTCTCAAC 58.311 47.619 0.00 0.00 39.48 3.18
257 258 3.055891 TCATCTCCATCGCAAGTTCTCAA 60.056 43.478 0.00 0.00 39.48 3.02
258 259 2.497273 TCATCTCCATCGCAAGTTCTCA 59.503 45.455 0.00 0.00 39.48 3.27
259 260 3.122297 CTCATCTCCATCGCAAGTTCTC 58.878 50.000 0.00 0.00 39.48 2.87
260 261 2.499289 ACTCATCTCCATCGCAAGTTCT 59.501 45.455 0.00 0.00 39.48 3.01
261 262 2.606725 CACTCATCTCCATCGCAAGTTC 59.393 50.000 0.00 0.00 39.48 3.01
262 263 2.625737 CACTCATCTCCATCGCAAGTT 58.374 47.619 0.00 0.00 39.48 2.66
263 264 1.741732 GCACTCATCTCCATCGCAAGT 60.742 52.381 0.00 0.00 39.48 3.16
264 265 0.935898 GCACTCATCTCCATCGCAAG 59.064 55.000 0.00 0.00 0.00 4.01
265 266 0.249955 TGCACTCATCTCCATCGCAA 59.750 50.000 0.00 0.00 0.00 4.85
266 267 0.179092 CTGCACTCATCTCCATCGCA 60.179 55.000 0.00 0.00 0.00 5.10
267 268 0.179089 ACTGCACTCATCTCCATCGC 60.179 55.000 0.00 0.00 0.00 4.58
268 269 1.135721 TCACTGCACTCATCTCCATCG 59.864 52.381 0.00 0.00 0.00 3.84
269 270 2.483363 CCTCACTGCACTCATCTCCATC 60.483 54.545 0.00 0.00 0.00 3.51
270 271 1.485480 CCTCACTGCACTCATCTCCAT 59.515 52.381 0.00 0.00 0.00 3.41
271 272 0.900421 CCTCACTGCACTCATCTCCA 59.100 55.000 0.00 0.00 0.00 3.86
272 273 0.461693 GCCTCACTGCACTCATCTCC 60.462 60.000 0.00 0.00 0.00 3.71
273 274 0.248565 TGCCTCACTGCACTCATCTC 59.751 55.000 0.00 0.00 36.04 2.75
274 275 0.910338 ATGCCTCACTGCACTCATCT 59.090 50.000 0.00 0.00 45.48 2.90
275 276 1.747709 AATGCCTCACTGCACTCATC 58.252 50.000 0.00 0.00 45.48 2.92
276 277 2.211250 AAATGCCTCACTGCACTCAT 57.789 45.000 0.00 0.00 45.48 2.90
277 278 1.985473 AAAATGCCTCACTGCACTCA 58.015 45.000 0.00 0.00 45.48 3.41
303 304 1.777878 TGGTCCTCACTGGCCTAAAAA 59.222 47.619 3.32 0.00 34.48 1.94
304 305 1.440618 TGGTCCTCACTGGCCTAAAA 58.559 50.000 3.32 0.00 34.48 1.52
305 306 1.351017 CTTGGTCCTCACTGGCCTAAA 59.649 52.381 3.32 0.00 34.48 1.85
306 307 0.984230 CTTGGTCCTCACTGGCCTAA 59.016 55.000 3.32 0.00 34.48 2.69
307 308 1.553690 GCTTGGTCCTCACTGGCCTA 61.554 60.000 3.32 0.00 34.48 3.93
308 309 2.900106 GCTTGGTCCTCACTGGCCT 61.900 63.158 3.32 0.00 34.48 5.19
309 310 2.360475 GCTTGGTCCTCACTGGCC 60.360 66.667 0.00 0.00 35.26 5.36
310 311 1.673665 CTGCTTGGTCCTCACTGGC 60.674 63.158 0.00 0.00 35.26 4.85
311 312 1.673665 GCTGCTTGGTCCTCACTGG 60.674 63.158 0.00 0.00 37.10 4.00
312 313 1.673665 GGCTGCTTGGTCCTCACTG 60.674 63.158 0.00 0.00 0.00 3.66
313 314 2.149383 TGGCTGCTTGGTCCTCACT 61.149 57.895 0.00 0.00 0.00 3.41
314 315 1.968540 GTGGCTGCTTGGTCCTCAC 60.969 63.158 0.00 0.00 0.00 3.51
315 316 2.149383 AGTGGCTGCTTGGTCCTCA 61.149 57.895 0.00 0.00 0.00 3.86
316 317 1.673665 CAGTGGCTGCTTGGTCCTC 60.674 63.158 0.00 0.00 0.00 3.71
317 318 2.433446 CAGTGGCTGCTTGGTCCT 59.567 61.111 0.00 0.00 0.00 3.85
318 319 2.674380 CCAGTGGCTGCTTGGTCC 60.674 66.667 0.00 0.00 0.00 4.46
319 320 3.368571 GCCAGTGGCTGCTTGGTC 61.369 66.667 27.48 0.00 46.69 4.02
337 338 3.803082 CATTGTGGCGTCCCAGCG 61.803 66.667 0.00 0.00 43.18 5.18
338 339 3.443045 CCATTGTGGCGTCCCAGC 61.443 66.667 0.00 0.00 43.18 4.85
339 340 2.751436 CCCATTGTGGCGTCCCAG 60.751 66.667 0.00 0.00 43.18 4.45
347 348 1.784358 ATGATGAAGGCCCATTGTGG 58.216 50.000 0.00 0.00 37.25 4.17
348 349 2.159014 CCAATGATGAAGGCCCATTGTG 60.159 50.000 22.40 14.06 43.19 3.33
349 350 2.112998 CCAATGATGAAGGCCCATTGT 58.887 47.619 22.40 3.59 43.19 2.71
350 351 1.202604 GCCAATGATGAAGGCCCATTG 60.203 52.381 19.26 19.26 43.89 2.82
351 352 1.125633 GCCAATGATGAAGGCCCATT 58.874 50.000 0.00 0.00 42.58 3.16
352 353 2.830475 GCCAATGATGAAGGCCCAT 58.170 52.632 0.00 0.00 42.58 4.00
353 354 4.360643 GCCAATGATGAAGGCCCA 57.639 55.556 0.00 0.00 42.58 5.36
357 358 0.744874 CTGCCTGCCAATGATGAAGG 59.255 55.000 0.00 0.00 34.83 3.46
358 359 0.744874 CCTGCCTGCCAATGATGAAG 59.255 55.000 0.00 0.00 0.00 3.02
359 360 1.324740 GCCTGCCTGCCAATGATGAA 61.325 55.000 0.00 0.00 0.00 2.57
360 361 1.755395 GCCTGCCTGCCAATGATGA 60.755 57.895 0.00 0.00 0.00 2.92
361 362 2.812499 GCCTGCCTGCCAATGATG 59.188 61.111 0.00 0.00 0.00 3.07
369 370 4.575973 ATCGATGGGCCTGCCTGC 62.576 66.667 4.53 0.00 36.10 4.85
370 371 1.895707 GAATCGATGGGCCTGCCTG 60.896 63.158 4.53 0.00 36.10 4.85
461 464 2.240493 AATCGCCCAGATCCGTAAAG 57.760 50.000 0.00 0.00 38.98 1.85
918 954 1.360911 GATCGAGAGGTCGGGCTTC 59.639 63.158 0.00 0.00 46.80 3.86
1206 1251 1.448013 GCGGTGGTTGTAGAGGAGC 60.448 63.158 0.00 0.00 0.00 4.70
1359 1404 3.701604 GAGCCCGTACCAGCAGACG 62.702 68.421 4.73 0.00 38.79 4.18
1633 1678 3.790437 CAGGCCCATGAGCTCCGT 61.790 66.667 12.15 0.00 0.00 4.69
1663 1708 0.756294 TTCTCGCAGAACCACCTCAA 59.244 50.000 0.00 0.00 34.09 3.02
1666 1711 0.605589 CTCTTCTCGCAGAACCACCT 59.394 55.000 0.00 0.00 34.09 4.00
2013 2085 3.824443 ACCAGTTTGGGTTGCAGTATTAC 59.176 43.478 0.00 0.00 43.37 1.89
2038 2110 5.046529 AGAGCAATGACAGTGACGATAATC 58.953 41.667 7.16 0.00 0.00 1.75
2058 2130 3.618594 TCCAGATGAAATTTTCGCGAGAG 59.381 43.478 9.59 0.00 43.69 3.20
2136 2209 7.723616 TGAAAATTTTAGTCAGGAGGTCATTGA 59.276 33.333 2.75 0.00 0.00 2.57
2177 2252 1.001487 CGATGCTGCAAAGTGGTTTCA 60.001 47.619 6.36 0.00 0.00 2.69
2195 2270 9.459640 GTACATGCAGAACTTATATTTCTACGA 57.540 33.333 0.00 0.00 31.86 3.43
2197 2272 8.989980 GGGTACATGCAGAACTTATATTTCTAC 58.010 37.037 0.00 0.00 31.86 2.59
2199 2274 7.806180 AGGGTACATGCAGAACTTATATTTCT 58.194 34.615 0.00 0.00 33.38 2.52
2215 2290 6.489127 TTTAATTGTTCACGAGGGTACATG 57.511 37.500 0.00 0.00 0.00 3.21
2217 2292 6.711194 TCAATTTAATTGTTCACGAGGGTACA 59.289 34.615 16.06 0.00 41.02 2.90
2225 2300 9.407514 CTGTTTGTTTCAATTTAATTGTTCACG 57.592 29.630 16.06 0.00 41.02 4.35
2284 2362 4.336433 AGAATATTCACCGATGTTTGCTGG 59.664 41.667 17.56 0.00 0.00 4.85
2344 2422 7.801716 TTCACAAAATCAGCACTTTAGTAGT 57.198 32.000 0.00 0.00 37.68 2.73
2436 2693 3.796178 TCGCAAAATCAGCAACTCAAAAC 59.204 39.130 0.00 0.00 0.00 2.43
2444 2701 5.984926 AGAATTCTTTTCGCAAAATCAGCAA 59.015 32.000 0.88 0.00 0.00 3.91
2456 2713 5.407387 TCGTGGAGGTTTAGAATTCTTTTCG 59.593 40.000 14.36 6.49 0.00 3.46
2457 2714 6.796705 TCGTGGAGGTTTAGAATTCTTTTC 57.203 37.500 14.36 4.29 0.00 2.29
2461 2718 5.805728 ACATTCGTGGAGGTTTAGAATTCT 58.194 37.500 13.56 13.56 30.10 2.40
2462 2719 7.605410 TTACATTCGTGGAGGTTTAGAATTC 57.395 36.000 0.00 0.00 30.10 2.17
2466 2723 7.162761 TGAAATTACATTCGTGGAGGTTTAGA 58.837 34.615 0.00 0.00 31.80 2.10
2581 2840 5.624738 GCGAAAGTCTTCCCTTCTAATCTCA 60.625 44.000 0.00 0.00 0.00 3.27
2596 2855 2.040544 CAATGCCGGGCGAAAGTCT 61.041 57.895 15.40 0.00 34.89 3.24
2597 2856 1.862602 AACAATGCCGGGCGAAAGTC 61.863 55.000 15.40 0.00 0.00 3.01
2598 2857 1.460273 AAACAATGCCGGGCGAAAGT 61.460 50.000 15.40 7.44 0.00 2.66
2599 2858 0.523966 TAAACAATGCCGGGCGAAAG 59.476 50.000 15.40 6.77 0.00 2.62
2602 2861 1.302591 TGTAAACAATGCCGGGCGA 60.303 52.632 15.40 3.96 0.00 5.54
2603 2862 1.154112 GTGTAAACAATGCCGGGCG 60.154 57.895 15.40 2.33 0.00 6.13
2604 2863 0.388006 GTGTGTAAACAATGCCGGGC 60.388 55.000 13.32 13.32 0.00 6.13
2607 2866 2.783828 TTGGTGTGTAAACAATGCCG 57.216 45.000 0.00 0.00 0.00 5.69
2608 2867 3.553917 GTGTTTGGTGTGTAAACAATGCC 59.446 43.478 5.03 0.00 46.10 4.40
2625 2887 5.124297 TCGCTGATGAATGATGATTGTGTTT 59.876 36.000 0.00 0.00 0.00 2.83
2676 2938 1.009389 CCTCGAGAACACAAGGCGAC 61.009 60.000 15.71 0.00 0.00 5.19
2783 3046 2.618053 CCTTCCGAAACATACTCGCTT 58.382 47.619 0.00 0.00 34.95 4.68
2797 3060 2.418083 GCTCCAAATGCCCCTTCCG 61.418 63.158 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.