Multiple sequence alignment - TraesCS2A01G456000

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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 TraesCS2A01G456000 chr2A 100.000 4776 0 0 1 4776 704768659 704773434 0.000000e+00 8820
1 TraesCS2A01G456000 chr2B 95.785 4437 155 12 350 4776 675348366 675352780 0.000000e+00 7129
2 TraesCS2A01G456000 chr2B 91.667 336 24 2 1 336 675347985 675348316 3.370000e-126 462
3 TraesCS2A01G456000 chr2D 95.449 4461 148 22 337 4776 564087682 564092108 0.000000e+00 7062
4 TraesCS2A01G456000 chr2D 87.500 336 26 6 1 336 564087324 564087643 1.620000e-99 374


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 TraesCS2A01G456000 chr2A 704768659 704773434 4775 False 8820.0 8820 100.0000 1 4776 1 chr2A.!!$F1 4775
1 TraesCS2A01G456000 chr2B 675347985 675352780 4795 False 3795.5 7129 93.7260 1 4776 2 chr2B.!!$F1 4775
2 TraesCS2A01G456000 chr2D 564087324 564092108 4784 False 3718.0 7062 91.4745 1 4776 2 chr2D.!!$F1 4775

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
251 252 0.320247 CCTGACAGAGCACACCTGAC 60.320 60.0 3.32 0.0 35.69 3.51 F
1997 2052 0.325296 AGGTGATTCGGAGCCTACCA 60.325 55.0 0.00 0.0 0.00 3.25 F
2010 2065 1.821216 CCTACCACACATTGACCCAC 58.179 55.0 0.00 0.0 0.00 4.61 F
3529 3584 0.548031 GGGATCATGAACCTGCCTGA 59.452 55.0 20.25 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2090 2145 0.324614 ATGCCACAGTGTTCCGATCA 59.675 50.0 0.0 0.0 0.00 2.92 R
3195 3250 0.250513 GAATCAGGCGAGTCCAGGTT 59.749 55.0 0.0 0.0 37.29 3.50 R
3611 3666 1.076332 GAATCACAAACTCCCGACCG 58.924 55.0 0.0 0.0 0.00 4.79 R
4410 4472 0.819582 CCATGATGACCAAGGGCAAC 59.180 55.0 0.0 0.0 30.22 4.17 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
21 22 1.066303 CAGATGAGGTAGTGAGCCGAC 59.934 57.143 0.00 0.00 0.00 4.79
46 47 1.067295 ACCCTTCCTCAAGATGTGCA 58.933 50.000 0.00 0.00 0.00 4.57
79 80 6.127591 TGGAAAGATCAGCAGAGTAGTACTTC 60.128 42.308 0.00 0.00 0.00 3.01
177 178 5.238583 GTCCACTAATTCTGCAAGTACACT 58.761 41.667 0.00 0.00 33.76 3.55
178 179 5.348997 GTCCACTAATTCTGCAAGTACACTC 59.651 44.000 0.00 0.00 33.76 3.51
181 182 5.877012 CACTAATTCTGCAAGTACACTCCAT 59.123 40.000 0.00 0.00 33.76 3.41
197 198 4.628766 CACTCCATCACTCATACACAACAG 59.371 45.833 0.00 0.00 0.00 3.16
198 199 4.528206 ACTCCATCACTCATACACAACAGA 59.472 41.667 0.00 0.00 0.00 3.41
206 207 6.101650 ACTCATACACAACAGAGTGATTCA 57.898 37.500 0.57 0.00 42.05 2.57
207 208 6.524734 ACTCATACACAACAGAGTGATTCAA 58.475 36.000 0.57 0.00 42.05 2.69
217 218 2.299013 AGAGTGATTCAACGTGTAGGCA 59.701 45.455 0.00 0.00 0.00 4.75
223 224 4.517075 TGATTCAACGTGTAGGCATTCAAA 59.483 37.500 0.00 0.00 0.00 2.69
251 252 0.320247 CCTGACAGAGCACACCTGAC 60.320 60.000 3.32 0.00 35.69 3.51
257 258 0.464036 AGAGCACACCTGACGACAAA 59.536 50.000 0.00 0.00 0.00 2.83
469 516 1.003718 CCTTCCCCGTCAACTCCAC 60.004 63.158 0.00 0.00 0.00 4.02
484 531 7.462856 CGTCAACTCCACATTAACTATTTCTCG 60.463 40.741 0.00 0.00 0.00 4.04
495 542 5.456192 AACTATTTCTCGCACTGAAATCG 57.544 39.130 10.49 8.21 41.49 3.34
536 585 3.551082 CGAAATCTTCTCACTAGCAGCAG 59.449 47.826 0.00 0.00 0.00 4.24
571 620 0.460635 CGGCGGATTCGAACCCTAAA 60.461 55.000 7.06 0.00 39.00 1.85
573 622 0.648958 GCGGATTCGAACCCTAAACG 59.351 55.000 7.06 2.65 39.00 3.60
603 652 4.573607 CCAATCAGGACATGTACAGATGTG 59.426 45.833 16.05 14.64 41.22 3.21
607 656 4.958581 TCAGGACATGTACAGATGTGAGAT 59.041 41.667 11.55 0.00 36.67 2.75
610 659 4.375272 GACATGTACAGATGTGAGATGGG 58.625 47.826 6.83 0.00 36.67 4.00
611 660 3.135348 ACATGTACAGATGTGAGATGGGG 59.865 47.826 0.00 0.00 35.17 4.96
762 811 1.614241 AACCCTGTACCCTAGCGCTG 61.614 60.000 22.90 10.13 0.00 5.18
766 815 2.356818 CTGTACCCTAGCGCTGCTCC 62.357 65.000 22.90 3.35 40.44 4.70
859 908 0.527385 GAGCAGAGCTACAGAAGGCG 60.527 60.000 0.00 0.00 39.88 5.52
864 913 1.889530 GAGCTACAGAAGGCGGGTGT 61.890 60.000 0.00 0.00 0.00 4.16
946 998 2.422803 CCTTTTTGGTCCACACTCAGGA 60.423 50.000 0.00 0.00 0.00 3.86
952 1004 1.270893 GGTCCACACTCAGGAAAGGTC 60.271 57.143 0.00 0.00 36.80 3.85
1067 1122 2.684104 CCGTCTCCTCCTCCTCCA 59.316 66.667 0.00 0.00 0.00 3.86
1486 1541 0.747644 TTCATGTCCATGCGCCGAAT 60.748 50.000 4.18 0.00 38.65 3.34
1520 1575 1.866925 GAACGCCTTCACTTTCGGG 59.133 57.895 0.00 0.00 0.00 5.14
1652 1707 2.480037 TGTTGACATGTTCGTGAGATGC 59.520 45.455 0.00 0.00 41.60 3.91
1692 1747 3.320626 TCGAAGCAGTTCAGTCAGATTG 58.679 45.455 0.00 0.00 32.36 2.67
1733 1788 0.464452 GGAACAGTATGCTAGCGGGT 59.536 55.000 10.77 1.07 42.53 5.28
1760 1815 3.370978 CCAAGTCATACGGTGTTGATCAC 59.629 47.826 0.00 0.00 45.47 3.06
1997 2052 0.325296 AGGTGATTCGGAGCCTACCA 60.325 55.000 0.00 0.00 0.00 3.25
2010 2065 1.821216 CCTACCACACATTGACCCAC 58.179 55.000 0.00 0.00 0.00 4.61
2012 2067 2.290896 CCTACCACACATTGACCCACAT 60.291 50.000 0.00 0.00 0.00 3.21
2058 2113 5.866335 ATATGCAAAATGTGGCTGTTTTG 57.134 34.783 14.04 14.04 44.22 2.44
2068 2123 2.106566 TGGCTGTTTTGAGGAAGCAAA 58.893 42.857 0.00 0.00 37.40 3.68
2090 2145 3.890147 AGAGAGTGTTCAGTTCCTTACGT 59.110 43.478 0.00 0.00 0.00 3.57
2162 2217 4.090761 TGGTTGCTTCAGTGAATCTCTT 57.909 40.909 5.91 0.00 0.00 2.85
2633 2688 9.431887 GTTACTTATGTTACATTGTTCAGAGGA 57.568 33.333 2.23 0.00 0.00 3.71
2672 2727 7.276438 GGTGCAAATAAACTTGGAGATCAAATC 59.724 37.037 0.00 0.00 34.56 2.17
2760 2815 3.644966 ACTCCAAATGCGGAAGGATAA 57.355 42.857 0.00 0.00 43.29 1.75
3086 3141 4.774124 TGATCGAAGCCAAGAATCTCATT 58.226 39.130 0.00 0.00 0.00 2.57
3161 3216 2.288579 CTGCAAGACACATGGCAACAAT 60.289 45.455 0.00 0.00 46.61 2.71
3195 3250 1.238439 GGCAGCTAAGCACTTGTTCA 58.762 50.000 0.00 0.00 35.83 3.18
3479 3534 0.616111 AGTCCCTGCGGTCTGAGATT 60.616 55.000 0.00 0.00 0.00 2.40
3522 3577 2.094026 GTGGCTTTTGGGATCATGAACC 60.094 50.000 13.47 13.47 0.00 3.62
3529 3584 0.548031 GGGATCATGAACCTGCCTGA 59.452 55.000 20.25 0.00 0.00 3.86
3560 3615 4.141413 CCCATCCACATCATGAAGAACCTA 60.141 45.833 4.68 0.00 0.00 3.08
3611 3666 2.858344 CAAGTTGATATCGACGGTGACC 59.142 50.000 18.28 0.00 35.42 4.02
3748 3803 2.677902 GCCCGTCAGATTCATTGAGACA 60.678 50.000 5.08 0.00 0.00 3.41
3882 3938 7.387673 CGATGAAAAACCCATGTGATAGCTATA 59.612 37.037 6.13 0.00 0.00 1.31
3949 4005 2.664402 AAACAGAGGCTTGGTCATGT 57.336 45.000 0.00 0.00 0.00 3.21
4017 4073 8.191446 CGAGTGATATGTAGAGAGAAAAGGAAA 58.809 37.037 0.00 0.00 0.00 3.13
4144 4200 3.508744 ACATTTTGCAGGGATTAAGCG 57.491 42.857 0.00 0.00 0.00 4.68
4266 4322 7.872483 ACAGGCATTTTACAAGATTCGAAAATT 59.128 29.630 0.00 0.00 30.91 1.82
4279 4335 5.514274 TTCGAAAATTGCAGGAAGTCTTT 57.486 34.783 0.00 0.00 0.00 2.52
4288 4344 3.008375 TGCAGGAAGTCTTTGTAGAGCAT 59.992 43.478 0.00 0.00 0.00 3.79
4410 4472 4.820744 CTTCGCCCCACCCCCATG 62.821 72.222 0.00 0.00 0.00 3.66
4600 4673 6.128145 GCCTCTCTGAACCAAACTATCTTTTC 60.128 42.308 0.00 0.00 0.00 2.29
4644 4717 7.253422 CACAAATCTATGTCCACTGGAATTTC 58.747 38.462 0.00 0.00 31.38 2.17
4652 4725 9.492973 CTATGTCCACTGGAATTTCAAAAATTT 57.507 29.630 0.00 0.00 31.38 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.001633 GGGTTTTCTGTCGGCTCACTA 59.998 52.381 0.00 0.00 0.00 2.74
13 14 0.472471 AAGGGTTTTCTGTCGGCTCA 59.528 50.000 0.00 0.00 0.00 4.26
21 22 4.217118 CACATCTTGAGGAAGGGTTTTCTG 59.783 45.833 0.00 0.00 0.00 3.02
46 47 4.015084 CTGCTGATCTTTCCATTTGGACT 58.985 43.478 0.00 0.00 45.39 3.85
60 61 4.095185 ACACGAAGTACTACTCTGCTGATC 59.905 45.833 0.00 0.00 41.61 2.92
79 80 2.226330 TCCAGGTGGAAAATTGACACG 58.774 47.619 0.00 0.00 42.18 4.49
134 135 4.695928 GGACCTAGTTTTCAGTTAAGCTGG 59.304 45.833 0.00 0.00 45.08 4.85
177 178 4.528206 ACTCTGTTGTGTATGAGTGATGGA 59.472 41.667 0.00 0.00 38.22 3.41
178 179 4.825422 ACTCTGTTGTGTATGAGTGATGG 58.175 43.478 0.00 0.00 38.22 3.51
197 198 2.683968 TGCCTACACGTTGAATCACTC 58.316 47.619 0.00 0.00 0.00 3.51
198 199 2.831685 TGCCTACACGTTGAATCACT 57.168 45.000 0.00 0.00 0.00 3.41
206 207 2.946329 TGTGTTTGAATGCCTACACGTT 59.054 40.909 0.00 0.00 42.81 3.99
207 208 2.566913 TGTGTTTGAATGCCTACACGT 58.433 42.857 0.00 0.00 42.81 4.49
217 218 4.042809 TCTGTCAGGGGTATGTGTTTGAAT 59.957 41.667 0.00 0.00 0.00 2.57
223 224 0.905357 GCTCTGTCAGGGGTATGTGT 59.095 55.000 0.89 0.00 0.00 3.72
324 325 0.740737 GGCACATCCACCACTTATGC 59.259 55.000 0.00 0.00 34.01 3.14
331 332 1.152589 TGCTTTGGCACATCCACCA 60.153 52.632 0.00 0.00 46.55 4.17
469 516 7.580523 CGATTTCAGTGCGAGAAATAGTTAATG 59.419 37.037 9.80 0.00 43.60 1.90
484 531 3.675467 GGTGATTACCGATTTCAGTGC 57.325 47.619 0.00 0.00 37.19 4.40
536 585 1.597663 CGCCGTTTCCTGATTACATCC 59.402 52.381 0.00 0.00 0.00 3.51
546 595 1.017701 GTTCGAATCCGCCGTTTCCT 61.018 55.000 0.00 0.00 35.37 3.36
571 620 0.104304 GTCCTGATTGGGATACGCGT 59.896 55.000 19.17 19.17 37.73 6.01
573 622 2.146342 CATGTCCTGATTGGGATACGC 58.854 52.381 0.00 0.00 37.73 4.42
873 922 0.032952 AGCGTAAAGTGTTCCTCGCA 59.967 50.000 9.76 0.00 44.83 5.10
941 993 2.303022 GAGATGTGTGGACCTTTCCTGA 59.697 50.000 0.00 0.00 43.31 3.86
946 998 1.002087 GACCGAGATGTGTGGACCTTT 59.998 52.381 0.00 0.00 0.00 3.11
952 1004 1.079127 GTGGGACCGAGATGTGTGG 60.079 63.158 0.00 0.00 0.00 4.17
1297 1352 2.750237 GGGTGATGACGTTGGGCC 60.750 66.667 0.00 0.00 0.00 5.80
1406 1461 1.611673 CCAGACATGAGGGTGTTCCAC 60.612 57.143 0.00 0.00 38.24 4.02
1424 1479 1.787796 TCCTCCCTGGAAGTAGCCA 59.212 57.895 0.00 0.00 42.94 4.75
1437 1492 1.280421 AGCATCCAAGAACTGTCCTCC 59.720 52.381 0.00 0.00 0.00 4.30
1439 1494 2.027377 CAGAGCATCCAAGAACTGTCCT 60.027 50.000 0.00 0.00 33.66 3.85
1442 1497 1.980765 TCCAGAGCATCCAAGAACTGT 59.019 47.619 0.00 0.00 33.66 3.55
1449 1504 1.556911 GAAGGTCTCCAGAGCATCCAA 59.443 52.381 8.44 0.00 44.42 3.53
1489 1544 2.809601 CGTTCGGCAAGGAGTCCG 60.810 66.667 2.76 0.00 46.52 4.79
1520 1575 1.878775 GCAGGACTTCATGGTGCAC 59.121 57.895 8.80 8.80 34.18 4.57
1607 1662 2.028484 GTCGCAACGTCAGGGTCA 59.972 61.111 0.00 0.00 0.00 4.02
1652 1707 1.535204 AAGCAAAATCCACAGCCCCG 61.535 55.000 0.00 0.00 0.00 5.73
1733 1788 3.620427 ACACCGTATGACTTGGCATAA 57.380 42.857 0.00 0.00 32.92 1.90
1997 2052 1.340889 GCAACATGTGGGTCAATGTGT 59.659 47.619 0.00 0.00 0.00 3.72
2058 2113 3.733337 TGAACACTCTCTTTGCTTCCTC 58.267 45.455 0.00 0.00 0.00 3.71
2068 2123 3.890147 ACGTAAGGAACTGAACACTCTCT 59.110 43.478 0.00 0.00 40.86 3.10
2090 2145 0.324614 ATGCCACAGTGTTCCGATCA 59.675 50.000 0.00 0.00 0.00 2.92
2162 2217 4.934001 GCTCTCATCTGATTGAACAGTTCA 59.066 41.667 12.24 12.24 38.79 3.18
2402 2457 4.074259 GCATGCCAGTCCATGATACAATA 58.926 43.478 6.36 0.00 44.12 1.90
2633 2688 0.106769 TTGCACCCATATCCGCACAT 60.107 50.000 0.00 0.00 33.29 3.21
2672 2727 5.710099 ACCAACCTTTACAGTATGACCAATG 59.290 40.000 0.00 0.00 39.69 2.82
2735 2790 2.614057 CCTTCCGCATTTGGAGTACATC 59.386 50.000 0.00 0.00 39.72 3.06
2760 2815 7.440523 ACTCAAATATTTTTCGAGCTTCTGT 57.559 32.000 11.87 0.00 0.00 3.41
3086 3141 1.678728 GGTTTCATGGGCATCTCGTCA 60.679 52.381 0.00 0.00 0.00 4.35
3161 3216 0.674581 CTGCCAATTCTGCGAGGTCA 60.675 55.000 0.00 0.00 0.00 4.02
3195 3250 0.250513 GAATCAGGCGAGTCCAGGTT 59.749 55.000 0.00 0.00 37.29 3.50
3522 3577 1.076559 TGGGCATCCAATCAGGCAG 60.077 57.895 0.00 0.00 40.73 4.85
3611 3666 1.076332 GAATCACAAACTCCCGACCG 58.924 55.000 0.00 0.00 0.00 4.79
3748 3803 7.784470 AGAGTAGACATTTTACTCCTCTGTT 57.216 36.000 8.38 0.00 45.18 3.16
3798 3853 5.186198 CCTAAACCTCAGACAAATAGTGGG 58.814 45.833 0.00 0.00 0.00 4.61
3949 4005 9.836864 AACTAGACATGCTTATTGTCAATATGA 57.163 29.630 18.15 7.46 44.73 2.15
3968 4024 3.179830 CATGCTACCGTGTGAACTAGAC 58.820 50.000 0.00 0.00 0.00 2.59
4017 4073 5.045651 TGAACAGTCCTGGATGTGATGTTAT 60.046 40.000 14.10 0.00 34.19 1.89
4144 4200 0.950555 TGATCTCACACGTTGCTGCC 60.951 55.000 0.00 0.00 0.00 4.85
4266 4322 2.368548 TGCTCTACAAAGACTTCCTGCA 59.631 45.455 0.00 0.00 0.00 4.41
4279 4335 4.089361 TCTTCCTGTCTTCATGCTCTACA 58.911 43.478 0.00 0.00 0.00 2.74
4288 4344 4.319177 GCTTTAGCTTCTTCCTGTCTTCA 58.681 43.478 0.00 0.00 38.21 3.02
4410 4472 0.819582 CCATGATGACCAAGGGCAAC 59.180 55.000 0.00 0.00 30.22 4.17
4532 4605 9.472361 CATAGCTCATTTGCTGCTTTATTAATT 57.528 29.630 0.00 0.00 43.87 1.40
4533 4606 8.636213 ACATAGCTCATTTGCTGCTTTATTAAT 58.364 29.630 0.00 0.00 43.87 1.40
4600 4673 1.546029 TGCCCTATATAGTGCTGCTCG 59.454 52.381 16.70 0.00 0.00 5.03
4644 4717 6.589907 AGCAAGGCTTACGGATTAAATTTTTG 59.410 34.615 0.00 0.00 33.89 2.44
4675 4748 5.355071 CCACTTGAAGCTATGCACTATTCAA 59.645 40.000 14.06 14.06 37.49 2.69
4677 4750 5.118990 TCCACTTGAAGCTATGCACTATTC 58.881 41.667 0.00 0.00 0.00 1.75
4678 4751 5.102953 TCCACTTGAAGCTATGCACTATT 57.897 39.130 0.00 0.00 0.00 1.73


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

AutoCloner maintained by Alex Coulton.