Multiple sequence alignment - TraesCS5D01G292300

Loading Multiple Alignment...

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 TraesCS5D01G292300 chr5D 100.000 2912 0 0 1 2912 389696423 389699334 0.000000e+00 5378
1 TraesCS5D01G292300 chr5D 92.455 1723 94 16 4 1717 388814120 388812425 0.000000e+00 2429
2 TraesCS5D01G292300 chr5D 87.945 365 25 5 2121 2482 388810414 388810066 2.090000e-111 412
3 TraesCS5D01G292300 chr5D 90.583 223 15 4 1739 1958 388812431 388812212 1.020000e-74 291
4 TraesCS5D01G292300 chr5B 92.755 2940 153 25 1 2912 469972702 469975609 0.000000e+00 4194
5 TraesCS5D01G292300 chr5B 90.738 1965 115 31 1 1954 467166681 467164773 0.000000e+00 2558
6 TraesCS5D01G292300 chr5B 89.216 204 19 2 2280 2482 467161634 467161433 4.820000e-63 252
7 TraesCS5D01G292300 chr5B 82.353 255 14 7 2035 2285 467164445 467164218 2.960000e-45 193
8 TraesCS5D01G292300 chr5A 92.871 2637 129 23 284 2912 493018141 493020726 0.000000e+00 3773
9 TraesCS5D01G292300 chr5A 94.292 1962 88 12 2 1954 491710025 491711971 0.000000e+00 2981
10 TraesCS5D01G292300 chr5A 85.480 427 26 10 1997 2418 491712252 491712647 2.090000e-111 412
11 TraesCS5D01G292300 chr5A 92.742 124 6 2 179 299 493017269 493017392 2.980000e-40 176


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 TraesCS5D01G292300 chr5D 389696423 389699334 2911 False 5378.0 5378 100.000000 1 2912 1 chr5D.!!$F1 2911
1 TraesCS5D01G292300 chr5D 388810066 388814120 4054 True 1044.0 2429 90.327667 4 2482 3 chr5D.!!$R1 2478
2 TraesCS5D01G292300 chr5B 469972702 469975609 2907 False 4194.0 4194 92.755000 1 2912 1 chr5B.!!$F1 2911
3 TraesCS5D01G292300 chr5B 467161433 467166681 5248 True 1001.0 2558 87.435667 1 2482 3 chr5B.!!$R1 2481
4 TraesCS5D01G292300 chr5A 493017269 493020726 3457 False 1974.5 3773 92.806500 179 2912 2 chr5A.!!$F2 2733
5 TraesCS5D01G292300 chr5A 491710025 491712647 2622 False 1696.5 2981 89.886000 2 2418 2 chr5A.!!$F1 2416

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
543 1314 0.517132 CGATGCACTCTTTTGACGCG 60.517 55.000 3.53 3.53 0.0 6.01 F
550 1321 1.195448 ACTCTTTTGACGCGATGCAAG 59.805 47.619 15.93 9.78 0.0 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1812 2603 1.003355 CACCTCCACAAGTGCGGAT 60.003 57.895 11.93 0.0 0.00 4.18 R
2305 7453 1.067516 AGCAGATGCACGCTTTGTTTT 59.932 42.857 7.68 0.0 45.16 2.43 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
39 40 5.880901 AGAGGAACTTATGTCACCACAAAT 58.119 37.500 0.00 0.00 41.55 2.32
111 115 2.429767 GCTACACCCTCCCCGGTAC 61.430 68.421 0.00 0.00 33.67 3.34
148 152 4.837860 TGTAAGATTTTGGTCCAAGGCATT 59.162 37.500 4.09 2.46 0.00 3.56
149 153 4.980339 AAGATTTTGGTCCAAGGCATTT 57.020 36.364 4.09 0.00 0.00 2.32
167 171 3.692406 GTCGGTTCCTGGCTCCGT 61.692 66.667 21.72 0.00 43.94 4.69
172 176 1.079750 GTTCCTGGCTCCGTCACTC 60.080 63.158 0.00 0.00 0.00 3.51
173 177 1.228894 TTCCTGGCTCCGTCACTCT 60.229 57.895 0.00 0.00 0.00 3.24
188 192 8.100508 TCCGTCACTCTTGTTATCTATGATAG 57.899 38.462 0.00 0.00 0.00 2.08
228 232 4.272991 GCAACAAATGGTTTTGCTCATTCA 59.727 37.500 0.00 0.00 45.01 2.57
266 272 2.103941 GAGGTCAATCAGCTCCTTAGGG 59.896 54.545 0.00 0.00 42.98 3.53
414 1185 2.900122 ATCTCCGCGTGAAATTTGTG 57.100 45.000 4.92 0.00 0.00 3.33
446 1217 3.648067 ACATCAAGAGTGTCTTTCCTCCA 59.352 43.478 0.00 0.00 33.78 3.86
543 1314 0.517132 CGATGCACTCTTTTGACGCG 60.517 55.000 3.53 3.53 0.00 6.01
550 1321 1.195448 ACTCTTTTGACGCGATGCAAG 59.805 47.619 15.93 9.78 0.00 4.01
564 1335 4.809426 GCGATGCAAGTTTACCACTATAGT 59.191 41.667 0.00 0.00 32.94 2.12
565 1336 5.293569 GCGATGCAAGTTTACCACTATAGTT 59.706 40.000 1.56 0.00 32.94 2.24
714 1493 2.976490 GCCATGCAGTGAGACCCCT 61.976 63.158 0.00 0.00 0.00 4.79
738 1517 7.809806 CCTTGTTTAATTCAAGAGCTCGAATTT 59.190 33.333 25.12 13.29 43.17 1.82
774 1553 1.929836 CAGGCTCTTGACATAGTTCGC 59.070 52.381 0.00 0.00 0.00 4.70
931 1712 1.750193 AGGTACCCATTTGATGTGCG 58.250 50.000 8.74 0.00 0.00 5.34
965 1746 2.874014 TGATTTGTGATTGTGGCCTCA 58.126 42.857 3.32 2.96 0.00 3.86
968 1749 4.283978 TGATTTGTGATTGTGGCCTCAATT 59.716 37.500 28.68 15.26 38.03 2.32
985 1769 5.632347 CCTCAATTCACAGCTGATTTTTGTC 59.368 40.000 23.35 0.00 0.00 3.18
1095 1879 3.868757 GAAGTTGGCTTCCCCATAAAC 57.131 47.619 0.00 0.00 44.89 2.01
1136 1920 3.380637 GCAAGAGACCAGGTCGACTATAA 59.619 47.826 16.46 0.00 37.67 0.98
1199 1983 1.272490 CATCACCTCGGCGGTATGTAT 59.728 52.381 7.21 0.00 46.94 2.29
1200 1984 1.405872 TCACCTCGGCGGTATGTATT 58.594 50.000 7.21 0.00 46.94 1.89
1201 1985 1.758280 TCACCTCGGCGGTATGTATTT 59.242 47.619 7.21 0.00 46.94 1.40
1202 1986 1.864711 CACCTCGGCGGTATGTATTTG 59.135 52.381 7.21 0.00 46.94 2.32
1236 2024 9.512588 CTCCAATCTTTTCCTATGCTTATGTAT 57.487 33.333 0.00 0.00 0.00 2.29
1320 2108 6.350445 GCAAGTTAACTTTGATGGATCCATGT 60.350 38.462 32.05 19.62 33.46 3.21
1426 2214 3.982576 AAGGTGTGATCGTTTTCAACC 57.017 42.857 0.00 0.00 32.02 3.77
1489 2277 8.661345 TGAGTCTAAATAGCTATCTGAGTAGGA 58.339 37.037 6.72 0.00 0.00 2.94
1756 2547 3.900941 AGCGTTGGTGATGTTTTTGATC 58.099 40.909 0.00 0.00 0.00 2.92
1812 2603 9.851686 ACTGAGTTGATGCATTATAAATTAGGA 57.148 29.630 0.00 0.00 0.00 2.94
1918 2747 0.527113 CCTTTTGATGTGATGCGGCA 59.473 50.000 4.58 4.58 0.00 5.69
1930 2759 3.482783 GCGGCAGAGCGTCTGTTC 61.483 66.667 13.91 7.95 45.94 3.18
1958 2790 5.125578 GGATGGAAGACACCTGGAAAATTAC 59.874 44.000 0.00 0.00 0.00 1.89
2041 4596 7.490840 TCCAAAACAATTGCATAGGATGTATG 58.509 34.615 5.05 0.00 0.00 2.39
2208 4764 6.807230 AGCGTAAATCACTAGTACAAACAGAG 59.193 38.462 0.00 0.00 0.00 3.35
2271 4830 7.948363 CGTAGAATAAACAGTAAAGTTGTTCCG 59.052 37.037 0.00 0.00 37.77 4.30
2276 4835 3.284617 ACAGTAAAGTTGTTCCGGCTTT 58.715 40.909 0.00 2.57 36.54 3.51
2297 7445 6.258507 GCTTTTATAAAATGCACCATGGAAGG 59.741 38.462 21.47 8.64 0.00 3.46
2305 7453 2.170166 GCACCATGGAAGGATGAACAA 58.830 47.619 21.47 0.00 0.00 2.83
2309 7457 4.990426 CACCATGGAAGGATGAACAAAAAC 59.010 41.667 21.47 0.00 0.00 2.43
2380 7528 5.240623 TGGAAACCAACATTAGCAAGTACAG 59.759 40.000 0.00 0.00 0.00 2.74
2467 7616 2.114616 CAGACCTACTGCCTCCTTCAT 58.885 52.381 0.00 0.00 39.86 2.57
2518 7667 0.818445 ATAGACGGGCAGACGACGAT 60.818 55.000 0.00 0.00 37.61 3.73
2587 7736 1.843368 TCACTCCGGGACTCGTTATT 58.157 50.000 0.00 0.00 37.11 1.40
2604 7753 9.075519 ACTCGTTATTGCATGATAAATTTGTTG 57.924 29.630 0.00 0.00 0.00 3.33
2606 7755 8.031864 TCGTTATTGCATGATAAATTTGTTGGT 58.968 29.630 0.00 0.00 0.00 3.67
2620 7769 1.202604 TGTTGGTTTCTCGGTCACTCC 60.203 52.381 0.00 0.00 0.00 3.85
2650 7799 2.643232 GGACCTCACGGCGTAAGGT 61.643 63.158 34.01 34.01 46.03 3.50
2708 7857 5.975693 TCAACTCTTTTGTCAACAGGTTT 57.024 34.783 0.00 0.00 0.00 3.27
2716 7865 6.922957 TCTTTTGTCAACAGGTTTATTGATGC 59.077 34.615 0.00 0.00 37.19 3.91
2742 7891 4.020485 TGGAACTAGTAAAGGTGGAGAAGC 60.020 45.833 0.00 0.00 0.00 3.86
2743 7892 4.505808 GAACTAGTAAAGGTGGAGAAGCC 58.494 47.826 0.00 0.00 37.10 4.35
2807 7957 2.436115 GCTCCACCAACGGGCTAC 60.436 66.667 0.00 0.00 37.90 3.58
2834 7984 1.300311 CCACGTTGACGCTGGTGTA 60.300 57.895 3.05 0.00 44.43 2.90
2835 7985 1.554042 CCACGTTGACGCTGGTGTAC 61.554 60.000 3.05 0.00 44.43 2.90
2854 8004 2.481289 CTGAAAGTCAGGGGAGGTTC 57.519 55.000 0.00 0.00 40.71 3.62
2899 8051 3.850173 AGAGAAGGCCATTACTTGGGTAA 59.150 43.478 5.01 0.00 46.55 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
111 115 7.915397 CCAAAATCTTACATATCCTTGGTTTCG 59.085 37.037 0.00 0.00 0.00 3.46
148 152 2.747686 GGAGCCAGGAACCGACAA 59.252 61.111 0.00 0.00 0.00 3.18
167 171 9.290988 GACTCCTATCATAGATAACAAGAGTGA 57.709 37.037 3.12 0.00 31.38 3.41
172 176 6.804295 GCGTGACTCCTATCATAGATAACAAG 59.196 42.308 0.00 0.00 0.00 3.16
173 177 6.294564 GGCGTGACTCCTATCATAGATAACAA 60.295 42.308 0.00 0.00 0.00 2.83
188 192 0.679505 TGCTATATGGGCGTGACTCC 59.320 55.000 0.00 0.00 0.00 3.85
414 1185 8.715191 AAGACACTCTTGATGTTGAAGATATC 57.285 34.615 0.00 0.00 34.98 1.63
446 1217 7.055667 TGCTATCGTTTCTCCATCTAATTCT 57.944 36.000 0.00 0.00 0.00 2.40
738 1517 1.331214 CCTGCAAAGCCTTTTCCTCA 58.669 50.000 0.00 0.00 0.00 3.86
774 1553 4.103357 CGTATCCCGTAAACTCTTGACAG 58.897 47.826 0.00 0.00 0.00 3.51
807 1586 1.662122 CGGGTATTGGTGTAAGCGTTC 59.338 52.381 0.00 0.00 36.92 3.95
820 1599 5.699458 GGTTGAATATGTCGAATCGGGTATT 59.301 40.000 1.76 5.44 0.00 1.89
931 1712 7.945033 ATCACAAATCAAAACCAACATGTAC 57.055 32.000 0.00 0.00 0.00 2.90
965 1746 5.186996 ACGACAAAAATCAGCTGTGAATT 57.813 34.783 14.67 3.25 35.88 2.17
968 1749 2.548057 GGACGACAAAAATCAGCTGTGA 59.452 45.455 14.67 0.00 37.02 3.58
985 1769 1.151777 ATCATGTTAAGCCGCGGACG 61.152 55.000 33.48 6.29 39.67 4.79
1089 1873 5.272397 ACAACGGTACCAAAAACGTTTATG 58.728 37.500 15.03 8.27 45.97 1.90
1095 1879 2.287373 TGCTACAACGGTACCAAAAACG 59.713 45.455 13.54 0.00 0.00 3.60
1136 1920 6.170506 TCACGCCTAAAGAGATAAACACATT 58.829 36.000 0.00 0.00 0.00 2.71
1152 1936 1.416401 GGATCATCCCTTTCACGCCTA 59.584 52.381 0.00 0.00 0.00 3.93
1199 1983 4.751767 AAAGATTGGAGGCACAAACAAA 57.248 36.364 0.00 0.00 33.48 2.83
1200 1984 4.442753 GGAAAAGATTGGAGGCACAAACAA 60.443 41.667 0.00 0.00 33.48 2.83
1201 1985 3.069443 GGAAAAGATTGGAGGCACAAACA 59.931 43.478 0.00 0.00 33.48 2.83
1202 1986 3.321968 AGGAAAAGATTGGAGGCACAAAC 59.678 43.478 0.00 0.00 33.48 2.93
1236 2024 3.010027 TCCATGTGTTTTGGATCCAGCTA 59.990 43.478 15.53 0.00 38.35 3.32
1237 2025 2.173519 CCATGTGTTTTGGATCCAGCT 58.826 47.619 15.53 0.00 36.26 4.24
1238 2026 2.170166 TCCATGTGTTTTGGATCCAGC 58.830 47.619 15.53 10.03 38.35 4.85
1239 2027 4.523943 TCTTTCCATGTGTTTTGGATCCAG 59.476 41.667 15.53 0.08 42.69 3.86
1320 2108 4.388499 GCCGGAACAAGCCCTCGA 62.388 66.667 5.05 0.00 0.00 4.04
1489 2277 3.118629 ACATACGCACATCTCACTTCCAT 60.119 43.478 0.00 0.00 0.00 3.41
1756 2547 4.155826 TCCTAAAGGTGCGATGATGTTTTG 59.844 41.667 0.00 0.00 36.34 2.44
1812 2603 1.003355 CACCTCCACAAGTGCGGAT 60.003 57.895 11.93 0.00 0.00 4.18
1918 2747 1.107114 ATCCATCGAACAGACGCTCT 58.893 50.000 0.00 0.00 0.00 4.09
1930 2759 1.473965 CCAGGTGTCTTCCATCCATCG 60.474 57.143 0.00 0.00 0.00 3.84
1958 2790 2.610833 TGCCTGTATACACTACGACTCG 59.389 50.000 0.08 0.00 0.00 4.18
2041 4596 2.061028 GCAGTTGTACATTTTGCCTGC 58.939 47.619 13.00 11.60 37.31 4.85
2208 4764 2.158561 AATGGCTGGCTCCAAAACGC 62.159 55.000 2.00 0.00 39.96 4.84
2271 4830 5.669477 TCCATGGTGCATTTTATAAAAGCC 58.331 37.500 12.58 13.84 0.00 4.35
2276 4835 6.838090 TCATCCTTCCATGGTGCATTTTATAA 59.162 34.615 12.58 0.00 0.00 0.98
2297 7445 3.305629 TGCACGCTTTGTTTTTGTTCATC 59.694 39.130 0.00 0.00 0.00 2.92
2305 7453 1.067516 AGCAGATGCACGCTTTGTTTT 59.932 42.857 7.68 0.00 45.16 2.43
2380 7528 9.926158 TCTATGCTCTCAAATTTCTGATCTATC 57.074 33.333 0.00 0.00 0.00 2.08
2448 7597 2.292521 TGATGAAGGAGGCAGTAGGTCT 60.293 50.000 0.00 0.00 0.00 3.85
2467 7616 8.783093 CATGTAATTTTCAGTACTTCCTGTTGA 58.217 33.333 0.00 0.00 34.02 3.18
2518 7667 2.447443 TGTTAGCCACAACCACACAAA 58.553 42.857 0.00 0.00 29.87 2.83
2569 7718 1.922570 CAATAACGAGTCCCGGAGTG 58.077 55.000 0.73 0.00 43.93 3.51
2587 7736 6.585702 CGAGAAACCAACAAATTTATCATGCA 59.414 34.615 0.00 0.00 0.00 3.96
2620 7769 2.046314 AGGTCCAAATCGCCCACG 60.046 61.111 0.00 0.00 42.01 4.94
2650 7799 6.392354 GTTTGAAAGATGCCTTCATGAATCA 58.608 36.000 8.96 10.47 31.96 2.57
2708 7857 7.047891 CCTTTACTAGTTCCAGTGCATCAATA 58.952 38.462 0.00 0.00 0.00 1.90
2716 7865 4.527038 TCTCCACCTTTACTAGTTCCAGTG 59.473 45.833 0.00 4.83 0.00 3.66
2743 7892 4.143333 CTCCCGGCCGTGTACTGG 62.143 72.222 26.12 17.10 0.00 4.00
2784 7934 2.429930 CGTTGGTGGAGCCTTGGA 59.570 61.111 0.00 0.00 38.35 3.53
2807 7957 1.785518 GCGTCAACGTGGATTTTAGCG 60.786 52.381 0.00 0.00 42.22 4.26
2834 7984 1.700186 GAACCTCCCCTGACTTTCAGT 59.300 52.381 2.63 0.00 42.80 3.41
2835 7985 1.338200 CGAACCTCCCCTGACTTTCAG 60.338 57.143 0.00 0.00 43.91 3.02
2871 8023 4.213564 AGTAATGGCCTTCTCTGTCTTG 57.786 45.455 3.32 0.00 0.00 3.02
2872 8024 4.566488 CCAAGTAATGGCCTTCTCTGTCTT 60.566 45.833 3.32 0.00 43.80 3.01


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

AutoCloner maintained by Alex Coulton.