Multiple sequence alignment - TraesCS5B01G089200

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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 TraesCS5B01G089200 chr5B 100.000 2931 0 0 1 2931 115073808 115076738 0.000000e+00 5413.0
1 TraesCS5B01G089200 chr5A 97.862 2619 40 8 326 2931 109278712 109281327 0.000000e+00 4512.0
2 TraesCS5B01G089200 chr5A 89.145 304 14 7 1 286 109278440 109278742 7.720000e-96 361.0
3 TraesCS5B01G089200 chr5A 92.537 67 5 0 7 73 668224067 668224001 2.400000e-16 97.1
4 TraesCS5B01G089200 chr5A 92.537 67 5 0 7 73 668269491 668269425 2.400000e-16 97.1
5 TraesCS5B01G089200 chr5D 99.345 1986 12 1 283 2268 105102965 105104949 0.000000e+00 3594.0
6 TraesCS5B01G089200 chr5D 98.080 677 6 4 2260 2930 105105079 105105754 0.000000e+00 1171.0
7 TraesCS5B01G089200 chr5D 96.644 298 6 2 1 294 105102653 105102950 2.620000e-135 492.0
8 TraesCS5B01G089200 chr4D 96.000 50 1 1 283 331 470854832 470854881 2.420000e-11 80.5
9 TraesCS5B01G089200 chr2B 92.857 56 2 2 272 326 360978280 360978226 2.420000e-11 80.5
10 TraesCS5B01G089200 chr2B 85.714 70 6 1 8 73 787815763 787815694 1.460000e-08 71.3
11 TraesCS5B01G089200 chr1D 96.000 50 1 1 283 331 54972635 54972586 2.420000e-11 80.5
12 TraesCS5B01G089200 chr1A 96.000 50 1 1 283 331 107775042 107775091 2.420000e-11 80.5
13 TraesCS5B01G089200 chr1A 94.231 52 2 1 283 334 219931022 219930972 8.710000e-11 78.7
14 TraesCS5B01G089200 chr1A 97.297 37 1 0 1494 1530 10227983 10227947 2.440000e-06 63.9
15 TraesCS5B01G089200 chr7B 92.727 55 3 1 283 336 509579816 509579870 8.710000e-11 78.7
16 TraesCS5B01G089200 chr2A 94.231 52 2 1 283 334 329701784 329701834 8.710000e-11 78.7
17 TraesCS5B01G089200 chr2A 95.652 46 2 0 283 328 59062339 59062384 1.130000e-09 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 TraesCS5B01G089200 chr5B 115073808 115076738 2930 False 5413.000000 5413 100.0000 1 2931 1 chr5B.!!$F1 2930
1 TraesCS5B01G089200 chr5A 109278440 109281327 2887 False 2436.500000 4512 93.5035 1 2931 2 chr5A.!!$F1 2930
2 TraesCS5B01G089200 chr5D 105102653 105105754 3101 False 1752.333333 3594 98.0230 1 2930 3 chr5D.!!$F1 2929

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
322 437 1.995376 CAAACAAGTTGGGGTAGGCT 58.005 50.0 7.96 0.0 33.18 4.58 F
325 440 2.337359 ACAAGTTGGGGTAGGCTAGA 57.663 50.0 7.96 0.0 0.00 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1571 1691 4.202440 GGATGAAGATGATGAGGGTGACAT 60.202 45.833 0.0 0.0 0.0 3.06 R
2053 2173 9.712305 ACATAGTAGATACATAAAACATGAGCC 57.288 33.333 0.0 0.0 0.0 4.70 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
147 148 8.607713 TGAGGTTTCCCACAGTATAATTCTTAA 58.392 33.333 0.00 0.00 0.00 1.85
269 384 6.144854 CACTCGCAATAATGAATAATGGTGG 58.855 40.000 0.00 0.00 0.00 4.61
270 385 5.241506 ACTCGCAATAATGAATAATGGTGGG 59.758 40.000 0.00 0.00 0.00 4.61
271 386 4.022416 TCGCAATAATGAATAATGGTGGGC 60.022 41.667 0.00 0.00 0.00 5.36
272 387 4.261952 CGCAATAATGAATAATGGTGGGCA 60.262 41.667 0.00 0.00 0.00 5.36
273 388 5.567224 CGCAATAATGAATAATGGTGGGCAT 60.567 40.000 0.00 0.00 0.00 4.40
274 389 6.350027 CGCAATAATGAATAATGGTGGGCATA 60.350 38.462 0.00 0.00 0.00 3.14
275 390 7.558604 GCAATAATGAATAATGGTGGGCATAT 58.441 34.615 0.00 0.00 0.00 1.78
276 391 8.694540 GCAATAATGAATAATGGTGGGCATATA 58.305 33.333 0.00 0.00 0.00 0.86
281 396 7.885009 TGAATAATGGTGGGCATATATGATG 57.115 36.000 17.10 0.00 0.00 3.07
282 397 6.321945 TGAATAATGGTGGGCATATATGATGC 59.678 38.462 17.10 3.49 43.85 3.91
283 398 3.743092 ATGGTGGGCATATATGATGCA 57.257 42.857 17.10 0.00 46.21 3.96
284 399 3.522392 TGGTGGGCATATATGATGCAA 57.478 42.857 17.10 0.00 46.21 4.08
285 400 3.156293 TGGTGGGCATATATGATGCAAC 58.844 45.455 17.10 6.24 46.21 4.17
286 401 3.156293 GGTGGGCATATATGATGCAACA 58.844 45.455 17.10 0.00 46.21 3.33
287 402 3.573538 GGTGGGCATATATGATGCAACAA 59.426 43.478 17.10 0.00 46.21 2.83
288 403 4.549458 GTGGGCATATATGATGCAACAAC 58.451 43.478 17.10 0.00 46.21 3.32
289 404 4.037803 GTGGGCATATATGATGCAACAACA 59.962 41.667 17.10 0.00 46.21 3.33
290 405 4.648307 TGGGCATATATGATGCAACAACAA 59.352 37.500 17.10 0.00 46.21 2.83
291 406 5.128335 TGGGCATATATGATGCAACAACAAA 59.872 36.000 17.10 0.00 46.21 2.83
292 407 6.047870 GGGCATATATGATGCAACAACAAAA 58.952 36.000 17.10 0.00 46.21 2.44
293 408 6.018832 GGGCATATATGATGCAACAACAAAAC 60.019 38.462 17.10 0.00 46.21 2.43
294 409 6.018832 GGCATATATGATGCAACAACAAAACC 60.019 38.462 17.10 0.00 46.21 3.27
295 410 6.757947 GCATATATGATGCAACAACAAAACCT 59.242 34.615 17.10 0.00 44.00 3.50
296 411 7.278424 GCATATATGATGCAACAACAAAACCTT 59.722 33.333 17.10 0.00 44.00 3.50
297 412 9.153721 CATATATGATGCAACAACAAAACCTTT 57.846 29.630 6.92 0.00 0.00 3.11
299 414 8.761575 ATATGATGCAACAACAAAACCTTTAG 57.238 30.769 0.00 0.00 0.00 1.85
300 415 5.971763 TGATGCAACAACAAAACCTTTAGT 58.028 33.333 0.00 0.00 0.00 2.24
301 416 6.039616 TGATGCAACAACAAAACCTTTAGTC 58.960 36.000 0.00 0.00 0.00 2.59
302 417 4.749976 TGCAACAACAAAACCTTTAGTCC 58.250 39.130 0.00 0.00 0.00 3.85
303 418 4.116961 GCAACAACAAAACCTTTAGTCCC 58.883 43.478 0.00 0.00 0.00 4.46
304 419 4.382147 GCAACAACAAAACCTTTAGTCCCA 60.382 41.667 0.00 0.00 0.00 4.37
305 420 5.725362 CAACAACAAAACCTTTAGTCCCAA 58.275 37.500 0.00 0.00 0.00 4.12
306 421 6.166982 CAACAACAAAACCTTTAGTCCCAAA 58.833 36.000 0.00 0.00 0.00 3.28
307 422 5.726397 ACAACAAAACCTTTAGTCCCAAAC 58.274 37.500 0.00 0.00 0.00 2.93
308 423 5.246429 ACAACAAAACCTTTAGTCCCAAACA 59.754 36.000 0.00 0.00 0.00 2.83
309 424 6.166982 CAACAAAACCTTTAGTCCCAAACAA 58.833 36.000 0.00 0.00 0.00 2.83
310 425 5.972935 ACAAAACCTTTAGTCCCAAACAAG 58.027 37.500 0.00 0.00 0.00 3.16
311 426 5.482526 ACAAAACCTTTAGTCCCAAACAAGT 59.517 36.000 0.00 0.00 0.00 3.16
312 427 6.014070 ACAAAACCTTTAGTCCCAAACAAGTT 60.014 34.615 0.00 0.00 0.00 2.66
313 428 5.592104 AACCTTTAGTCCCAAACAAGTTG 57.408 39.130 0.00 0.00 36.94 3.16
322 437 1.995376 CAAACAAGTTGGGGTAGGCT 58.005 50.000 7.96 0.00 33.18 4.58
323 438 3.149005 CAAACAAGTTGGGGTAGGCTA 57.851 47.619 7.96 0.00 33.18 3.93
324 439 3.081804 CAAACAAGTTGGGGTAGGCTAG 58.918 50.000 7.96 0.00 33.18 3.42
325 440 2.337359 ACAAGTTGGGGTAGGCTAGA 57.663 50.000 7.96 0.00 0.00 2.43
326 441 2.627933 ACAAGTTGGGGTAGGCTAGAA 58.372 47.619 7.96 0.00 0.00 2.10
327 442 3.190439 ACAAGTTGGGGTAGGCTAGAAT 58.810 45.455 7.96 0.00 0.00 2.40
328 443 3.054361 ACAAGTTGGGGTAGGCTAGAATG 60.054 47.826 7.96 0.00 0.00 2.67
329 444 3.130734 AGTTGGGGTAGGCTAGAATGA 57.869 47.619 0.00 0.00 0.00 2.57
330 445 3.460825 AGTTGGGGTAGGCTAGAATGAA 58.539 45.455 0.00 0.00 0.00 2.57
331 446 4.047883 AGTTGGGGTAGGCTAGAATGAAT 58.952 43.478 0.00 0.00 0.00 2.57
332 447 5.224441 AGTTGGGGTAGGCTAGAATGAATA 58.776 41.667 0.00 0.00 0.00 1.75
333 448 5.670361 AGTTGGGGTAGGCTAGAATGAATAA 59.330 40.000 0.00 0.00 0.00 1.40
334 449 6.332901 AGTTGGGGTAGGCTAGAATGAATAAT 59.667 38.462 0.00 0.00 0.00 1.28
335 450 6.126863 TGGGGTAGGCTAGAATGAATAATG 57.873 41.667 0.00 0.00 0.00 1.90
336 451 5.014123 TGGGGTAGGCTAGAATGAATAATGG 59.986 44.000 0.00 0.00 0.00 3.16
337 452 5.014228 GGGGTAGGCTAGAATGAATAATGGT 59.986 44.000 0.00 0.00 0.00 3.55
338 453 6.214819 GGGGTAGGCTAGAATGAATAATGGTA 59.785 42.308 0.00 0.00 0.00 3.25
1571 1691 2.251818 CACAGGAGAGGAAGAGGAACA 58.748 52.381 0.00 0.00 0.00 3.18
2221 2341 2.113860 TGCTTGCAGATTGGGTCTAC 57.886 50.000 0.00 0.00 34.69 2.59
2392 2650 2.835764 ACTTGCAAGTTACGGGATAGGA 59.164 45.455 26.36 0.00 35.21 2.94
2708 2969 6.118170 GGAGGACAAGATTTCAGAATCATGA 58.882 40.000 0.00 0.00 41.28 3.07
2909 3173 4.286032 TGTTGTGCTGGGAGATAGTACTTT 59.714 41.667 0.00 0.00 32.82 2.66
2910 3174 5.482526 TGTTGTGCTGGGAGATAGTACTTTA 59.517 40.000 0.00 0.00 32.82 1.85
2911 3175 5.593679 TGTGCTGGGAGATAGTACTTTAC 57.406 43.478 0.00 0.00 32.82 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.089112 CCCAATAAACCCGAACGGAC 58.911 55.000 15.07 0.00 37.50 4.79
147 148 8.625786 AACTACATCCGTTTAACAAATTACCT 57.374 30.769 0.00 0.00 0.00 3.08
269 384 6.018832 GGTTTTGTTGTTGCATCATATATGCC 60.019 38.462 7.92 0.08 43.94 4.40
270 385 6.757947 AGGTTTTGTTGTTGCATCATATATGC 59.242 34.615 7.92 3.05 44.76 3.14
271 386 8.706492 AAGGTTTTGTTGTTGCATCATATATG 57.294 30.769 6.36 6.36 0.00 1.78
273 388 9.853555 CTAAAGGTTTTGTTGTTGCATCATATA 57.146 29.630 0.00 0.00 0.00 0.86
274 389 8.367156 ACTAAAGGTTTTGTTGTTGCATCATAT 58.633 29.630 0.00 0.00 0.00 1.78
275 390 7.721402 ACTAAAGGTTTTGTTGTTGCATCATA 58.279 30.769 0.00 0.00 0.00 2.15
276 391 6.581712 ACTAAAGGTTTTGTTGTTGCATCAT 58.418 32.000 0.00 0.00 0.00 2.45
277 392 5.971763 ACTAAAGGTTTTGTTGTTGCATCA 58.028 33.333 0.00 0.00 0.00 3.07
278 393 5.462068 GGACTAAAGGTTTTGTTGTTGCATC 59.538 40.000 0.00 0.00 0.00 3.91
279 394 5.356426 GGACTAAAGGTTTTGTTGTTGCAT 58.644 37.500 0.00 0.00 0.00 3.96
280 395 4.382147 GGGACTAAAGGTTTTGTTGTTGCA 60.382 41.667 0.00 0.00 0.00 4.08
281 396 4.116961 GGGACTAAAGGTTTTGTTGTTGC 58.883 43.478 0.00 0.00 0.00 4.17
282 397 5.331876 TGGGACTAAAGGTTTTGTTGTTG 57.668 39.130 0.00 0.00 0.00 3.33
283 398 6.167685 GTTTGGGACTAAAGGTTTTGTTGTT 58.832 36.000 0.00 0.00 0.00 2.83
284 399 5.246429 TGTTTGGGACTAAAGGTTTTGTTGT 59.754 36.000 0.00 0.00 0.00 3.32
285 400 5.725362 TGTTTGGGACTAAAGGTTTTGTTG 58.275 37.500 0.00 0.00 0.00 3.33
286 401 6.014070 ACTTGTTTGGGACTAAAGGTTTTGTT 60.014 34.615 0.00 0.00 0.00 2.83
287 402 5.482526 ACTTGTTTGGGACTAAAGGTTTTGT 59.517 36.000 0.00 0.00 0.00 2.83
288 403 5.972935 ACTTGTTTGGGACTAAAGGTTTTG 58.027 37.500 0.00 0.00 0.00 2.44
289 404 6.403049 CAACTTGTTTGGGACTAAAGGTTTT 58.597 36.000 0.00 0.00 0.00 2.43
290 405 5.972935 CAACTTGTTTGGGACTAAAGGTTT 58.027 37.500 0.00 0.00 0.00 3.27
291 406 5.592104 CAACTTGTTTGGGACTAAAGGTT 57.408 39.130 0.00 0.00 0.00 3.50
303 418 1.995376 AGCCTACCCCAACTTGTTTG 58.005 50.000 0.00 0.00 34.63 2.93
304 419 2.983898 TCTAGCCTACCCCAACTTGTTT 59.016 45.455 0.00 0.00 0.00 2.83
305 420 2.627933 TCTAGCCTACCCCAACTTGTT 58.372 47.619 0.00 0.00 0.00 2.83
306 421 2.337359 TCTAGCCTACCCCAACTTGT 57.663 50.000 0.00 0.00 0.00 3.16
307 422 3.199946 TCATTCTAGCCTACCCCAACTTG 59.800 47.826 0.00 0.00 0.00 3.16
308 423 3.460825 TCATTCTAGCCTACCCCAACTT 58.539 45.455 0.00 0.00 0.00 2.66
309 424 3.130734 TCATTCTAGCCTACCCCAACT 57.869 47.619 0.00 0.00 0.00 3.16
310 425 3.926058 TTCATTCTAGCCTACCCCAAC 57.074 47.619 0.00 0.00 0.00 3.77
311 426 6.467194 CCATTATTCATTCTAGCCTACCCCAA 60.467 42.308 0.00 0.00 0.00 4.12
312 427 5.014123 CCATTATTCATTCTAGCCTACCCCA 59.986 44.000 0.00 0.00 0.00 4.96
313 428 5.014228 ACCATTATTCATTCTAGCCTACCCC 59.986 44.000 0.00 0.00 0.00 4.95
314 429 6.128138 ACCATTATTCATTCTAGCCTACCC 57.872 41.667 0.00 0.00 0.00 3.69
315 430 7.331791 CCTACCATTATTCATTCTAGCCTACC 58.668 42.308 0.00 0.00 0.00 3.18
316 431 6.819146 GCCTACCATTATTCATTCTAGCCTAC 59.181 42.308 0.00 0.00 0.00 3.18
317 432 6.500400 TGCCTACCATTATTCATTCTAGCCTA 59.500 38.462 0.00 0.00 0.00 3.93
318 433 5.310594 TGCCTACCATTATTCATTCTAGCCT 59.689 40.000 0.00 0.00 0.00 4.58
319 434 5.560724 TGCCTACCATTATTCATTCTAGCC 58.439 41.667 0.00 0.00 0.00 3.93
320 435 8.834465 CATATGCCTACCATTATTCATTCTAGC 58.166 37.037 0.00 0.00 35.34 3.42
1186 1306 7.593825 AGTTATTAGCAAAGGTGACATTTGTC 58.406 34.615 21.52 14.49 44.97 3.18
1571 1691 4.202440 GGATGAAGATGATGAGGGTGACAT 60.202 45.833 0.00 0.00 0.00 3.06
2053 2173 9.712305 ACATAGTAGATACATAAAACATGAGCC 57.288 33.333 0.00 0.00 0.00 4.70
2634 2893 9.967559 ATGAAGGGTTAGGGGATAAAATTTTAT 57.032 29.630 20.77 20.77 36.14 1.40


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

AutoCloner maintained by Alex Coulton.