Multiple sequence alignment - TraesCS1A01G120400

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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 TraesCS1A01G120400 chr1A 100.000 2948 0 0 1 2948 132800173 132797226 0.000000e+00 5445.0
1 TraesCS1A01G120400 chr1A 88.889 54 6 0 2505 2558 25574260 25574207 1.900000e-07 67.6
2 TraesCS1A01G120400 chr1A 86.207 58 4 3 2503 2558 29197073 29197018 3.170000e-05 60.2
3 TraesCS1A01G120400 chr1B 95.817 1243 40 6 1157 2389 184219054 184217814 0.000000e+00 1997.0
4 TraesCS1A01G120400 chr1B 95.709 1142 29 9 1 1141 184220161 184219039 0.000000e+00 1820.0
5 TraesCS1A01G120400 chr1B 96.911 259 8 0 2690 2948 184195938 184195680 4.510000e-118 435.0
6 TraesCS1A01G120400 chr1B 98.571 70 1 0 2623 2692 184196033 184195964 1.110000e-24 124.0
7 TraesCS1A01G120400 chr1D 94.708 1285 40 13 1157 2428 121241016 121239747 0.000000e+00 1971.0
8 TraesCS1A01G120400 chr1D 96.310 813 21 5 332 1141 121241807 121241001 0.000000e+00 1327.0
9 TraesCS1A01G120400 chr1D 90.399 552 20 4 2430 2948 121239137 121238586 0.000000e+00 695.0
10 TraesCS1A01G120400 chr1D 91.740 339 15 5 1 338 121242259 121241933 2.680000e-125 459.0
11 TraesCS1A01G120400 chr6D 90.972 144 11 1 2467 2610 209917398 209917257 3.000000e-45 193.0
12 TraesCS1A01G120400 chr6B 87.742 155 16 2 2468 2622 399738009 399737858 8.400000e-41 178.0
13 TraesCS1A01G120400 chr7A 79.503 161 16 7 2430 2590 63590957 63591100 6.720000e-17 99.0


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 TraesCS1A01G120400 chr1A 132797226 132800173 2947 True 5445.0 5445 100.00000 1 2948 1 chr1A.!!$R3 2947
1 TraesCS1A01G120400 chr1B 184217814 184220161 2347 True 1908.5 1997 95.76300 1 2389 2 chr1B.!!$R2 2388
2 TraesCS1A01G120400 chr1D 121238586 121242259 3673 True 1113.0 1971 93.28925 1 2948 4 chr1D.!!$R1 2947

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
304 306 1.068055 CAAAGCTGTTGTCCATGAGGC 60.068 52.381 0.0 0.0 33.74 4.70 F
620 754 1.344438 CAGTGAGCTGTGTACTTCCCA 59.656 52.381 0.0 0.0 37.92 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1840 1981 0.104671 ATTGCCTGCACACACCAAAC 59.895 50.000 0.0 0.0 0.00 2.93 R
2059 2200 2.213499 CAATCCTTCGATTTCTCCCGG 58.787 52.381 0.0 0.0 36.54 5.73 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
22 23 3.077359 CAGGGACAAGTCAAAGTGGATC 58.923 50.000 2.29 0.00 0.00 3.36
128 130 4.276926 GTGAGCTTGTTTCCATCAAGTTCT 59.723 41.667 17.88 5.30 46.01 3.01
168 170 4.218417 GGCCTTGACAATTTATGAGTGTGT 59.782 41.667 0.00 0.00 36.56 3.72
169 171 5.156355 GCCTTGACAATTTATGAGTGTGTG 58.844 41.667 0.00 0.00 36.56 3.82
170 172 5.278463 GCCTTGACAATTTATGAGTGTGTGT 60.278 40.000 0.00 0.00 36.56 3.72
171 173 6.144854 CCTTGACAATTTATGAGTGTGTGTG 58.855 40.000 0.00 0.00 36.56 3.82
188 190 3.262420 GTGTGCCAGTACACCATCTAAG 58.738 50.000 7.69 0.00 43.94 2.18
189 191 2.280628 GTGCCAGTACACCATCTAAGC 58.719 52.381 0.00 0.00 34.35 3.09
192 194 1.141053 CCAGTACACCATCTAAGCCCC 59.859 57.143 0.00 0.00 0.00 5.80
230 232 4.792068 TCTTTCAGTTGAACCCACTTCAT 58.208 39.130 0.00 0.00 38.74 2.57
269 271 9.764363 CCAATAGTAGCACTAAAACTATCATCA 57.236 33.333 0.00 0.00 35.82 3.07
290 292 5.869579 TCATCTACAGGAAAAGTCAAAGCT 58.130 37.500 0.00 0.00 0.00 3.74
292 294 5.036117 TCTACAGGAAAAGTCAAAGCTGT 57.964 39.130 0.00 0.00 0.00 4.40
304 306 1.068055 CAAAGCTGTTGTCCATGAGGC 60.068 52.381 0.00 0.00 33.74 4.70
362 496 9.034544 GCAAGTTTGATCAAGTCAGTAAAATTT 57.965 29.630 8.41 0.00 38.29 1.82
382 516 5.543507 TTTGGTTCATTGCCACAGTTTAT 57.456 34.783 0.00 0.00 35.46 1.40
385 519 2.916716 GTTCATTGCCACAGTTTATGCG 59.083 45.455 0.00 0.00 0.00 4.73
601 735 4.497340 GGTCTGAAAAGAATTGTTGCGTCA 60.497 41.667 0.00 0.00 0.00 4.35
620 754 1.344438 CAGTGAGCTGTGTACTTCCCA 59.656 52.381 0.00 0.00 37.92 4.37
750 885 7.122204 TCTGTAGTGCACTATCTAAAACTGCTA 59.878 37.037 28.37 0.63 0.00 3.49
756 891 8.879759 GTGCACTATCTAAAACTGCTATTTGTA 58.120 33.333 10.32 0.00 0.00 2.41
832 967 4.682860 CCATTTTCTCATGTTTCTGTGCAC 59.317 41.667 10.75 10.75 0.00 4.57
846 981 3.004629 TCTGTGCACCTGCTTAATGTTTG 59.995 43.478 15.69 0.00 42.66 2.93
1095 1234 9.453572 AACACTCTCATCTTATTAAAAGCATGA 57.546 29.630 0.00 0.00 0.00 3.07
1116 1255 7.466455 GCATGATCGTTGATCTGTAAAAGACAT 60.466 37.037 0.00 0.00 39.56 3.06
1237 1376 5.530915 TCACTGTTTTGTGTTCCATAGGAAG 59.469 40.000 0.00 0.00 42.88 3.46
1244 1383 4.072131 TGTGTTCCATAGGAAGCTCAAAC 58.928 43.478 0.00 0.00 42.88 2.93
1262 1401 3.932545 AACGAATATTGCAGTTGCCAA 57.067 38.095 1.06 0.00 41.18 4.52
1310 1449 2.754552 TGGCGATGAAGAAAATCCAAGG 59.245 45.455 0.00 0.00 0.00 3.61
1399 1538 7.821359 CAGTCTACTCCTTCATTCTTTCATTCA 59.179 37.037 0.00 0.00 0.00 2.57
1557 1696 4.517075 GCTTCTGCTCTTCTGGTTAGTTTT 59.483 41.667 0.00 0.00 36.03 2.43
1725 1865 4.178956 TGGCCTTCTTTACTTCCTTGTT 57.821 40.909 3.32 0.00 0.00 2.83
1739 1879 3.275143 TCCTTGTTATGTACGGGCATTG 58.725 45.455 0.00 0.00 0.00 2.82
1812 1953 7.328277 TGTTTTCTTGTACACTGTTAGCAAT 57.672 32.000 0.00 0.00 0.00 3.56
1822 1963 6.699575 ACACTGTTAGCAATTGAGTTTTCT 57.300 33.333 10.34 0.00 0.00 2.52
1840 1981 8.171164 AGTTTTCTTTCTTATGTTTCCTCTGG 57.829 34.615 0.00 0.00 0.00 3.86
1886 2027 6.280643 TGTTTACAGCAGCGACTATCATTAT 58.719 36.000 0.00 0.00 0.00 1.28
1983 2124 5.069648 ACAGTAGCTAGCTGCAAGATATTCA 59.930 40.000 30.79 3.46 45.94 2.57
2059 2200 8.882736 CCTTTGTTAATCAATTGCTTAAATCCC 58.117 33.333 14.33 5.08 35.84 3.85
2120 2269 1.654105 CCGTCATTTGCTCGAGTGTAC 59.346 52.381 15.13 0.00 0.00 2.90
2222 2372 4.077300 TCAGGCGCAATCAGAAGATTAT 57.923 40.909 10.83 0.00 42.46 1.28
2223 2373 4.454678 TCAGGCGCAATCAGAAGATTATT 58.545 39.130 10.83 0.00 42.46 1.40
2428 2580 7.909485 AAAATCTAGCCTCCATCATCAATTT 57.091 32.000 0.00 0.00 0.00 1.82
2441 3201 8.464404 TCCATCATCAATTTTAGCTTCAAGAAG 58.536 33.333 5.46 5.46 41.24 2.85
2464 3224 4.036262 GGTGCATGTCTTCAACAGTTAACA 59.964 41.667 8.61 0.00 42.37 2.41
2465 3225 5.449862 GGTGCATGTCTTCAACAGTTAACAA 60.450 40.000 8.61 0.00 42.37 2.83
2499 3262 6.768029 ATTTCTACGTTAAGTTACGCACAA 57.232 33.333 0.00 0.00 45.06 3.33
2536 3299 8.190888 CAGGTCTTCTGTATTGTTGATACTTC 57.809 38.462 0.00 0.00 41.05 3.01
2728 3521 4.458989 AGAATATGCAACGAAAAGCCTGAA 59.541 37.500 0.00 0.00 0.00 3.02
2750 3543 4.888038 TTCATTCATCTTCATCAAGCCG 57.112 40.909 0.00 0.00 0.00 5.52
2752 3545 1.382522 TTCATCTTCATCAAGCCGCC 58.617 50.000 0.00 0.00 0.00 6.13
2766 3559 1.219393 CCGCCTCCCTTCTCTTGAC 59.781 63.158 0.00 0.00 0.00 3.18
2866 3659 4.783227 ACCCGGAAGTTATATATGATGGCT 59.217 41.667 0.73 0.00 0.00 4.75
2888 3681 2.464459 GCGGCGATCTTGAGGTTGG 61.464 63.158 12.98 0.00 0.00 3.77
2912 3705 4.052518 CCAGGTCCTTGCCCAGGG 62.053 72.222 0.00 0.00 44.12 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 5.792741 TGGCAAATTTTAAACCTCATGGAG 58.207 37.500 0.00 0.00 37.04 3.86
128 130 5.598830 TCAAGGCCAATGTGGTTTTACTAAA 59.401 36.000 5.01 0.00 40.46 1.85
168 170 2.354704 GCTTAGATGGTGTACTGGCACA 60.355 50.000 0.00 0.00 40.89 4.57
169 171 2.280628 GCTTAGATGGTGTACTGGCAC 58.719 52.381 0.00 0.00 38.56 5.01
170 172 1.209504 GGCTTAGATGGTGTACTGGCA 59.790 52.381 0.00 0.00 0.00 4.92
171 173 1.475213 GGGCTTAGATGGTGTACTGGC 60.475 57.143 0.00 0.00 0.00 4.85
197 199 0.695347 ACTGAAAGAAGCAGAGGGGG 59.305 55.000 0.00 0.00 37.43 5.40
198 200 2.157738 CAACTGAAAGAAGCAGAGGGG 58.842 52.381 0.00 0.00 37.43 4.79
199 201 3.131709 TCAACTGAAAGAAGCAGAGGG 57.868 47.619 0.00 0.00 37.43 4.30
200 202 3.251972 GGTTCAACTGAAAGAAGCAGAGG 59.748 47.826 0.00 0.00 40.80 3.69
201 203 3.251972 GGGTTCAACTGAAAGAAGCAGAG 59.748 47.826 0.00 0.00 42.37 3.35
202 204 3.214328 GGGTTCAACTGAAAGAAGCAGA 58.786 45.455 0.00 0.00 42.37 4.26
230 232 6.649155 TGCTACTATTGGAAGCACTTTCATA 58.351 36.000 3.09 0.00 41.15 2.15
269 271 5.625150 ACAGCTTTGACTTTTCCTGTAGAT 58.375 37.500 0.00 0.00 32.32 1.98
290 292 0.821301 TTTGCGCCTCATGGACAACA 60.821 50.000 4.18 0.00 32.89 3.33
292 294 0.537143 AGTTTGCGCCTCATGGACAA 60.537 50.000 4.18 0.00 34.57 3.18
362 496 3.305950 GCATAAACTGTGGCAATGAACCA 60.306 43.478 0.00 0.00 33.84 3.67
382 516 1.608717 AACAAACCTTTGGGCACGCA 61.609 50.000 2.94 0.00 42.34 5.24
385 519 1.480545 ACTCAACAAACCTTTGGGCAC 59.519 47.619 2.94 0.00 42.34 5.01
601 735 1.717032 TGGGAAGTACACAGCTCACT 58.283 50.000 0.00 0.00 0.00 3.41
620 754 2.513753 TGAGCAATTCCCACAACGAAT 58.486 42.857 0.00 0.00 0.00 3.34
832 967 7.538575 AGTAATTAGCACAAACATTAAGCAGG 58.461 34.615 0.00 0.00 0.00 4.85
846 981 7.075741 ACAAACGAAATGTGAGTAATTAGCAC 58.924 34.615 10.14 10.14 0.00 4.40
1075 1214 9.378597 CAACGATCATGCTTTTAATAAGATGAG 57.621 33.333 0.00 0.00 0.00 2.90
1076 1215 9.108284 TCAACGATCATGCTTTTAATAAGATGA 57.892 29.630 0.00 0.00 0.00 2.92
1148 1287 9.316730 TGTACTTATAAACACTCTTGACGTTTT 57.683 29.630 0.00 0.00 34.78 2.43
1149 1288 8.876275 TGTACTTATAAACACTCTTGACGTTT 57.124 30.769 0.00 0.00 36.79 3.60
1237 1376 3.301642 GCAACTGCAATATTCGTTTGAGC 59.698 43.478 0.00 0.00 41.59 4.26
1244 1383 3.173599 CACTTGGCAACTGCAATATTCG 58.826 45.455 3.76 0.00 44.36 3.34
1310 1449 2.307049 CGTCTTTCGAACATTGCCAAC 58.693 47.619 0.00 0.00 42.86 3.77
1575 1714 4.901250 TCTAACAGGACATGATATGCTCCA 59.099 41.667 0.00 0.00 34.78 3.86
1617 1756 7.806409 AACAGGCAAAAAGAATTATTGCTTT 57.194 28.000 9.28 2.08 46.54 3.51
1789 1930 7.913297 TCAATTGCTAACAGTGTACAAGAAAAC 59.087 33.333 0.00 0.00 0.00 2.43
1812 1953 9.408648 AGAGGAAACATAAGAAAGAAAACTCAA 57.591 29.630 0.00 0.00 0.00 3.02
1822 1963 6.040391 CACCAAACCAGAGGAAACATAAGAAA 59.960 38.462 0.00 0.00 0.00 2.52
1840 1981 0.104671 ATTGCCTGCACACACCAAAC 59.895 50.000 0.00 0.00 0.00 2.93
1886 2027 7.012894 CACACATTACCAGTAAAACAGAAAGGA 59.987 37.037 0.00 0.00 0.00 3.36
1983 2124 6.371278 ACTTCATTCCTCAAGGATATGCATT 58.629 36.000 3.54 0.00 44.98 3.56
2059 2200 2.213499 CAATCCTTCGATTTCTCCCGG 58.787 52.381 0.00 0.00 36.54 5.73
2120 2269 5.345741 GCCAGCACAAAATTGTACAGTAATG 59.654 40.000 0.00 0.00 39.91 1.90
2222 2372 2.509052 ATTACTCAGCTCGCGCATAA 57.491 45.000 8.75 0.00 39.10 1.90
2223 2373 3.850122 ATATTACTCAGCTCGCGCATA 57.150 42.857 8.75 0.00 39.10 3.14
2416 2568 7.705325 CCTTCTTGAAGCTAAAATTGATGATGG 59.295 37.037 4.94 0.00 0.00 3.51
2428 2580 3.753272 GACATGCACCTTCTTGAAGCTAA 59.247 43.478 4.94 0.00 0.00 3.09
2441 3201 4.036262 TGTTAACTGTTGAAGACATGCACC 59.964 41.667 7.22 0.00 37.69 5.01
2443 3203 5.356751 AGTTGTTAACTGTTGAAGACATGCA 59.643 36.000 7.22 0.00 41.01 3.96
2464 3224 3.939066 ACGTAGAAATTGCTGGCTAGTT 58.061 40.909 0.00 0.00 0.00 2.24
2465 3225 3.611766 ACGTAGAAATTGCTGGCTAGT 57.388 42.857 0.00 0.00 0.00 2.57
2499 3262 2.307098 AGAAGACCTGTTTGGCTAGCAT 59.693 45.455 18.24 0.00 40.22 3.79
2631 3396 8.956533 TGTTTGTCGATCTGGATTTATCATAA 57.043 30.769 0.00 0.00 0.00 1.90
2728 3521 4.261489 GCGGCTTGATGAAGATGAATGAAT 60.261 41.667 0.00 0.00 0.00 2.57
2750 3543 0.988063 AAGGTCAAGAGAAGGGAGGC 59.012 55.000 0.00 0.00 0.00 4.70
2752 3545 3.583086 TGGTTAAGGTCAAGAGAAGGGAG 59.417 47.826 0.00 0.00 0.00 4.30
2766 3559 1.065418 AGAACGGCCTCATGGTTAAGG 60.065 52.381 0.00 0.00 35.27 2.69
2888 3681 2.352805 CAAGGACCTGGGGCTCAC 59.647 66.667 0.00 0.00 0.00 3.51
2912 3705 4.785453 CTGCGGGCCCAGGAGTTC 62.785 72.222 24.92 1.42 0.00 3.01


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

AutoCloner maintained by Alex Coulton.