Multiple sequence alignment - TraesCS2B01G005500

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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 TraesCS2B01G005500 chr2B 100.000 3557 0 0 1 3557 3662311 3658755 0.000000e+00 6569.0
1 TraesCS2B01G005500 chr2B 98.885 3229 28 3 336 3557 1311192 1307965 0.000000e+00 5757.0
2 TraesCS2B01G005500 chr2B 98.610 3238 28 4 336 3557 3684063 3687299 0.000000e+00 5716.0
3 TraesCS2B01G005500 chr2B 84.939 2065 292 9 1508 3556 1249522 1251583 0.000000e+00 2073.0
4 TraesCS2B01G005500 chr2B 84.981 2064 285 14 1511 3555 3409833 3407776 0.000000e+00 2071.0
5 TraesCS2B01G005500 chr2B 84.045 2062 308 11 1508 3552 4883046 4885103 0.000000e+00 1965.0
6 TraesCS2B01G005500 chr2B 100.000 262 0 0 1 262 1311447 1311186 5.340000e-133 484.0
7 TraesCS2B01G005500 chr2B 100.000 262 0 0 1 262 3683808 3684069 5.340000e-133 484.0
8 TraesCS2B01G005500 chr2B 82.081 519 85 6 1013 1524 4882329 4882846 1.520000e-118 436.0
9 TraesCS2B01G005500 chr2A 94.958 2856 99 20 737 3557 4943899 4946744 0.000000e+00 4434.0
10 TraesCS2B01G005500 chr2D 96.236 2683 80 9 893 3557 6599875 6602554 0.000000e+00 4375.0
11 TraesCS2B01G005500 chr2D 84.095 2496 356 31 1092 3557 6522474 6524958 0.000000e+00 2372.0
12 TraesCS2B01G005500 chr2D 84.466 2002 296 10 1567 3557 6594551 6596548 0.000000e+00 1960.0
13 TraesCS2B01G005500 chr2D 82.261 513 80 7 1013 1515 6593766 6594277 1.960000e-117 433.0
14 TraesCS2B01G005500 chr2D 87.273 55 6 1 836 889 6599800 6599854 1.070000e-05 62.1
15 TraesCS2B01G005500 chrUn 99.175 1575 13 0 336 1910 321155485 321153911 0.000000e+00 2837.0
16 TraesCS2B01G005500 chrUn 100.000 262 0 0 1 262 321155740 321155479 5.340000e-133 484.0
17 TraesCS2B01G005500 chrUn 84.262 413 53 9 930 1337 287165422 287165827 3.330000e-105 392.0
18 TraesCS2B01G005500 chr5A 94.444 36 2 0 129 164 631619187 631619152 4.960000e-04 56.5
19 TraesCS2B01G005500 chr5A 94.444 36 2 0 129 164 631641480 631641445 4.960000e-04 56.5


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 TraesCS2B01G005500 chr2B 3658755 3662311 3556 True 6569.000 6569 100.0000 1 3557 1 chr2B.!!$R2 3556
1 TraesCS2B01G005500 chr2B 1307965 1311447 3482 True 3120.500 5757 99.4425 1 3557 2 chr2B.!!$R3 3556
2 TraesCS2B01G005500 chr2B 3683808 3687299 3491 False 3100.000 5716 99.3050 1 3557 2 chr2B.!!$F2 3556
3 TraesCS2B01G005500 chr2B 1249522 1251583 2061 False 2073.000 2073 84.9390 1508 3556 1 chr2B.!!$F1 2048
4 TraesCS2B01G005500 chr2B 3407776 3409833 2057 True 2071.000 2071 84.9810 1511 3555 1 chr2B.!!$R1 2044
5 TraesCS2B01G005500 chr2B 4882329 4885103 2774 False 1200.500 1965 83.0630 1013 3552 2 chr2B.!!$F3 2539
6 TraesCS2B01G005500 chr2A 4943899 4946744 2845 False 4434.000 4434 94.9580 737 3557 1 chr2A.!!$F1 2820
7 TraesCS2B01G005500 chr2D 6522474 6524958 2484 False 2372.000 2372 84.0950 1092 3557 1 chr2D.!!$F1 2465
8 TraesCS2B01G005500 chr2D 6593766 6602554 8788 False 1707.525 4375 87.5590 836 3557 4 chr2D.!!$F2 2721
9 TraesCS2B01G005500 chrUn 321153911 321155740 1829 True 1660.500 2837 99.5875 1 1910 2 chrUn.!!$R1 1909

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
265 266 0.178938 TTCCAAATGCCAGCCCTTGA 60.179 50.0 3.16 0.0 0.0 3.02 F
268 269 0.529378 CAAATGCCAGCCCTTGAGAC 59.471 55.0 0.00 0.0 0.0 3.36 F
1150 6383 0.543883 TCTGCTCTGCCTCAAGTCCT 60.544 55.0 0.00 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1379 6615 2.156051 GAGCCGACCAAGTTCCGACT 62.156 60.000 0.00 0.0 37.87 4.18 R
1446 6682 3.099905 CACACCAAGACTGAGAGGGATA 58.900 50.000 0.00 0.0 0.00 2.59 R
2977 8454 1.202806 AGGCAAGTGCAACAAGAGCTA 60.203 47.619 5.52 0.0 44.36 3.32 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
263 264 1.072173 GTTTTCCAAATGCCAGCCCTT 59.928 47.619 0.00 0.00 0.00 3.95
265 266 0.178938 TTCCAAATGCCAGCCCTTGA 60.179 50.000 3.16 0.00 0.00 3.02
266 267 0.612732 TCCAAATGCCAGCCCTTGAG 60.613 55.000 3.16 0.00 0.00 3.02
267 268 0.612732 CCAAATGCCAGCCCTTGAGA 60.613 55.000 3.16 0.00 0.00 3.27
268 269 0.529378 CAAATGCCAGCCCTTGAGAC 59.471 55.000 0.00 0.00 0.00 3.36
270 271 3.984193 ATGCCAGCCCTTGAGACGC 62.984 63.158 0.00 0.00 0.00 5.19
273 274 4.379243 CAGCCCTTGAGACGCCGT 62.379 66.667 0.00 0.00 0.00 5.68
274 275 4.379243 AGCCCTTGAGACGCCGTG 62.379 66.667 0.00 0.00 0.00 4.94
278 279 2.664851 CTTGAGACGCCGTGGCAA 60.665 61.111 12.06 0.00 42.06 4.52
279 280 2.031919 TTGAGACGCCGTGGCAAT 59.968 55.556 12.06 0.00 42.06 3.56
280 281 2.244436 CTTGAGACGCCGTGGCAATG 62.244 60.000 12.06 0.00 42.06 2.82
281 282 2.434185 GAGACGCCGTGGCAATGA 60.434 61.111 12.06 0.00 42.06 2.57
283 284 4.166011 GACGCCGTGGCAATGAGC 62.166 66.667 12.06 0.00 42.06 4.26
304 305 6.737720 AGCAGAATGATCTCCACTATAACA 57.262 37.500 0.00 0.00 39.69 2.41
305 306 7.129457 AGCAGAATGATCTCCACTATAACAA 57.871 36.000 0.00 0.00 39.69 2.83
306 307 7.215789 AGCAGAATGATCTCCACTATAACAAG 58.784 38.462 0.00 0.00 39.69 3.16
308 309 6.988580 CAGAATGATCTCCACTATAACAAGCA 59.011 38.462 0.00 0.00 39.69 3.91
309 310 7.171167 CAGAATGATCTCCACTATAACAAGCAG 59.829 40.741 0.00 0.00 39.69 4.24
310 311 6.737720 ATGATCTCCACTATAACAAGCAGA 57.262 37.500 0.00 0.00 0.00 4.26
311 312 6.544928 TGATCTCCACTATAACAAGCAGAA 57.455 37.500 0.00 0.00 0.00 3.02
312 313 6.577103 TGATCTCCACTATAACAAGCAGAAG 58.423 40.000 0.00 0.00 0.00 2.85
313 314 6.381133 TGATCTCCACTATAACAAGCAGAAGA 59.619 38.462 0.00 0.00 0.00 2.87
314 315 6.605471 TCTCCACTATAACAAGCAGAAGAA 57.395 37.500 0.00 0.00 0.00 2.52
315 316 6.398918 TCTCCACTATAACAAGCAGAAGAAC 58.601 40.000 0.00 0.00 0.00 3.01
317 318 5.012664 TCCACTATAACAAGCAGAAGAACCA 59.987 40.000 0.00 0.00 0.00 3.67
318 319 5.882557 CCACTATAACAAGCAGAAGAACCAT 59.117 40.000 0.00 0.00 0.00 3.55
319 320 6.183360 CCACTATAACAAGCAGAAGAACCATG 60.183 42.308 0.00 0.00 0.00 3.66
320 321 6.372659 CACTATAACAAGCAGAAGAACCATGT 59.627 38.462 0.00 0.00 0.00 3.21
322 323 2.508526 ACAAGCAGAAGAACCATGTCC 58.491 47.619 0.00 0.00 0.00 4.02
323 324 2.158623 ACAAGCAGAAGAACCATGTCCA 60.159 45.455 0.00 0.00 0.00 4.02
324 325 3.087031 CAAGCAGAAGAACCATGTCCAT 58.913 45.455 0.00 0.00 0.00 3.41
327 328 2.681848 GCAGAAGAACCATGTCCATCTG 59.318 50.000 10.21 10.21 36.10 2.90
328 329 3.276857 CAGAAGAACCATGTCCATCTGG 58.723 50.000 8.02 0.00 38.55 3.86
329 330 3.054875 CAGAAGAACCATGTCCATCTGGA 60.055 47.826 0.00 0.00 43.08 3.86
394 395 1.356624 GCTGTTGCACTCACACCAC 59.643 57.895 0.00 0.00 39.41 4.16
704 705 5.050499 GCATGGTCTGAATCTGTTAAGATCG 60.050 44.000 0.00 0.00 42.60 3.69
730 731 4.084223 GCGTGGTTATTGAAGACTTTCGAA 60.084 41.667 0.00 0.00 36.04 3.71
734 735 7.457060 GTGGTTATTGAAGACTTTCGAAGATC 58.543 38.462 0.00 0.00 36.04 2.75
779 780 6.953101 TGCATAAGAAGTAACTTGGGACATA 58.047 36.000 0.00 0.00 39.30 2.29
1150 6383 0.543883 TCTGCTCTGCCTCAAGTCCT 60.544 55.000 0.00 0.00 0.00 3.85
1153 6386 1.675801 CTCTGCCTCAAGTCCTGCA 59.324 57.895 0.00 0.00 0.00 4.41
1379 6615 1.152247 AGCTCTCCGGCCATATCCA 60.152 57.895 2.24 0.00 0.00 3.41
1466 6702 2.334006 ATCCCTCTCAGTCTTGGTGT 57.666 50.000 0.00 0.00 0.00 4.16
2977 8454 6.737720 TGTTCCTATGATGATAGCTCTGTT 57.262 37.500 0.00 0.00 31.52 3.16
3374 8851 7.055667 TCTAGTCTTTGAGTATATGGCCAAG 57.944 40.000 10.96 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
263 264 2.741985 CATTGCCACGGCGTCTCA 60.742 61.111 10.85 8.26 45.51 3.27
265 266 2.434884 CTCATTGCCACGGCGTCT 60.435 61.111 10.85 0.00 45.51 4.18
266 267 4.166011 GCTCATTGCCACGGCGTC 62.166 66.667 10.85 0.00 45.51 5.19
268 269 4.170062 CTGCTCATTGCCACGGCG 62.170 66.667 4.80 4.80 45.51 6.46
270 271 0.099968 CATTCTGCTCATTGCCACGG 59.900 55.000 0.00 0.00 42.00 4.94
271 272 1.089112 TCATTCTGCTCATTGCCACG 58.911 50.000 0.00 0.00 42.00 4.94
272 273 2.950309 AGATCATTCTGCTCATTGCCAC 59.050 45.455 0.00 0.00 42.00 5.01
273 274 3.211865 GAGATCATTCTGCTCATTGCCA 58.788 45.455 0.00 0.00 42.00 4.92
274 275 2.553172 GGAGATCATTCTGCTCATTGCC 59.447 50.000 0.00 0.00 42.00 4.52
276 277 4.452825 AGTGGAGATCATTCTGCTCATTG 58.547 43.478 0.00 0.00 40.72 2.82
278 279 7.015974 TGTTATAGTGGAGATCATTCTGCTCAT 59.984 37.037 0.00 0.00 40.72 2.90
279 280 6.324770 TGTTATAGTGGAGATCATTCTGCTCA 59.675 38.462 0.00 0.00 40.72 4.26
280 281 6.753180 TGTTATAGTGGAGATCATTCTGCTC 58.247 40.000 0.00 0.00 40.72 4.26
281 282 6.737720 TGTTATAGTGGAGATCATTCTGCT 57.262 37.500 0.00 0.00 40.72 4.24
283 284 6.988580 TGCTTGTTATAGTGGAGATCATTCTG 59.011 38.462 0.00 0.00 30.30 3.02
284 285 7.070447 TCTGCTTGTTATAGTGGAGATCATTCT 59.930 37.037 0.00 0.00 33.88 2.40
286 287 7.129457 TCTGCTTGTTATAGTGGAGATCATT 57.871 36.000 0.00 0.00 0.00 2.57
287 288 6.737720 TCTGCTTGTTATAGTGGAGATCAT 57.262 37.500 0.00 0.00 0.00 2.45
288 289 6.381133 TCTTCTGCTTGTTATAGTGGAGATCA 59.619 38.462 0.00 0.00 0.00 2.92
289 290 6.810911 TCTTCTGCTTGTTATAGTGGAGATC 58.189 40.000 0.00 0.00 0.00 2.75
290 291 6.798427 TCTTCTGCTTGTTATAGTGGAGAT 57.202 37.500 0.00 0.00 0.00 2.75
291 292 6.398918 GTTCTTCTGCTTGTTATAGTGGAGA 58.601 40.000 0.00 0.00 0.00 3.71
293 294 5.012664 TGGTTCTTCTGCTTGTTATAGTGGA 59.987 40.000 0.00 0.00 0.00 4.02
294 295 5.245531 TGGTTCTTCTGCTTGTTATAGTGG 58.754 41.667 0.00 0.00 0.00 4.00
295 296 6.372659 ACATGGTTCTTCTGCTTGTTATAGTG 59.627 38.462 0.00 0.00 0.00 2.74
296 297 6.476378 ACATGGTTCTTCTGCTTGTTATAGT 58.524 36.000 0.00 0.00 0.00 2.12
297 298 6.037610 GGACATGGTTCTTCTGCTTGTTATAG 59.962 42.308 0.00 0.00 0.00 1.31
298 299 5.880332 GGACATGGTTCTTCTGCTTGTTATA 59.120 40.000 0.00 0.00 0.00 0.98
299 300 4.702131 GGACATGGTTCTTCTGCTTGTTAT 59.298 41.667 0.00 0.00 0.00 1.89
300 301 4.072131 GGACATGGTTCTTCTGCTTGTTA 58.928 43.478 0.00 0.00 0.00 2.41
301 302 2.887152 GGACATGGTTCTTCTGCTTGTT 59.113 45.455 0.00 0.00 0.00 2.83
302 303 2.158623 TGGACATGGTTCTTCTGCTTGT 60.159 45.455 0.00 0.00 0.00 3.16
304 305 2.957402 TGGACATGGTTCTTCTGCTT 57.043 45.000 0.00 0.00 0.00 3.91
305 306 2.575279 AGATGGACATGGTTCTTCTGCT 59.425 45.455 0.00 0.00 26.62 4.24
306 307 2.681848 CAGATGGACATGGTTCTTCTGC 59.318 50.000 7.39 0.00 36.82 4.26
308 309 3.184628 TCCAGATGGACATGGTTCTTCT 58.815 45.455 0.00 0.00 39.78 2.85
309 310 3.634397 TCCAGATGGACATGGTTCTTC 57.366 47.619 0.00 0.00 39.78 2.87
310 311 3.562176 GGTTCCAGATGGACATGGTTCTT 60.562 47.826 0.00 0.00 45.39 2.52
311 312 2.025887 GGTTCCAGATGGACATGGTTCT 60.026 50.000 0.00 0.00 45.39 3.01
312 313 2.025887 AGGTTCCAGATGGACATGGTTC 60.026 50.000 0.00 0.00 45.39 3.62
313 314 1.995542 AGGTTCCAGATGGACATGGTT 59.004 47.619 0.00 0.00 45.39 3.67
314 315 1.561542 GAGGTTCCAGATGGACATGGT 59.438 52.381 0.00 0.00 45.39 3.55
315 316 1.133976 GGAGGTTCCAGATGGACATGG 60.134 57.143 0.00 0.00 45.39 3.66
317 318 1.216990 GGGAGGTTCCAGATGGACAT 58.783 55.000 0.00 0.00 45.39 3.06
318 319 0.178876 TGGGAGGTTCCAGATGGACA 60.179 55.000 0.00 0.00 45.39 4.02
319 320 2.696864 TGGGAGGTTCCAGATGGAC 58.303 57.895 0.00 0.00 45.39 4.02
327 328 1.606601 GTTTGGGCTGGGAGGTTCC 60.607 63.158 0.00 0.00 35.23 3.62
328 329 1.606601 GGTTTGGGCTGGGAGGTTC 60.607 63.158 0.00 0.00 0.00 3.62
329 330 1.739608 ATGGTTTGGGCTGGGAGGTT 61.740 55.000 0.00 0.00 0.00 3.50
330 331 2.169810 ATGGTTTGGGCTGGGAGGT 61.170 57.895 0.00 0.00 0.00 3.85
331 332 1.683365 CATGGTTTGGGCTGGGAGG 60.683 63.158 0.00 0.00 0.00 4.30
332 333 0.542702 AACATGGTTTGGGCTGGGAG 60.543 55.000 0.00 0.00 0.00 4.30
333 334 0.831288 CAACATGGTTTGGGCTGGGA 60.831 55.000 0.00 0.00 0.00 4.37
334 335 0.831288 TCAACATGGTTTGGGCTGGG 60.831 55.000 0.00 0.00 0.00 4.45
335 336 1.269012 ATCAACATGGTTTGGGCTGG 58.731 50.000 0.00 0.00 0.00 4.85
336 337 3.181473 CCATATCAACATGGTTTGGGCTG 60.181 47.826 0.00 0.00 40.62 4.85
337 338 3.033184 CCATATCAACATGGTTTGGGCT 58.967 45.455 0.00 0.00 40.62 5.19
339 340 2.765135 TGCCATATCAACATGGTTTGGG 59.235 45.455 0.00 0.00 46.21 4.12
340 341 4.468765 TTGCCATATCAACATGGTTTGG 57.531 40.909 0.00 0.00 46.21 3.28
394 395 4.030913 TGACAATAGTACAAGAGAGGGGG 58.969 47.826 0.00 0.00 0.00 5.40
704 705 0.096454 GTCTTCAATAACCACGCGGC 59.904 55.000 12.47 0.00 34.57 6.53
730 731 7.414222 AGAAATTTACATGCCATTGTGATCT 57.586 32.000 0.00 0.00 0.00 2.75
734 735 5.408909 TGCAAGAAATTTACATGCCATTGTG 59.591 36.000 15.61 0.00 36.20 3.33
779 780 6.211184 CACTTCTCTATCTAGCCTTGGATCAT 59.789 42.308 0.00 0.00 0.00 2.45
1379 6615 2.156051 GAGCCGACCAAGTTCCGACT 62.156 60.000 0.00 0.00 37.87 4.18
1446 6682 3.099905 CACACCAAGACTGAGAGGGATA 58.900 50.000 0.00 0.00 0.00 2.59
1466 6702 4.156455 AGAGAAGAAAGGTTGTGAAGCA 57.844 40.909 0.00 0.00 0.00 3.91
1601 7059 7.570607 AGAGGTATGTAAGGGATGAGAGATTTT 59.429 37.037 0.00 0.00 0.00 1.82
2977 8454 1.202806 AGGCAAGTGCAACAAGAGCTA 60.203 47.619 5.52 0.00 44.36 3.32
3294 8771 1.949525 GCATGCGGTTATCACCTTCAT 59.050 47.619 0.00 0.00 41.64 2.57
3374 8851 2.269241 CGGTCTTCAAGGCTCCCC 59.731 66.667 0.00 0.00 0.00 4.81


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

AutoCloner maintained by Alex Coulton.