Multiple sequence alignment - TraesCS4D01G216700

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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 TraesCS4D01G216700 chr4D 100.000 2815 0 0 1 2815 370693506 370690692 0.000000e+00 5199
1 TraesCS4D01G216700 chr4D 100.000 68 0 0 3119 3186 370690388 370690321 3.340000e-25 126
2 TraesCS4D01G216700 chr4A 92.043 2300 113 43 562 2815 93687542 93685267 0.000000e+00 3169
3 TraesCS4D01G216700 chr4A 88.121 564 57 3 1 564 93688356 93687803 0.000000e+00 662
4 TraesCS4D01G216700 chr4A 91.892 74 0 3 3119 3186 93685158 93685085 7.270000e-17 99
5 TraesCS4D01G216700 chr4B 94.638 1753 46 23 1093 2815 455910354 455908620 0.000000e+00 2673
6 TraesCS4D01G216700 chr4B 89.043 1150 69 28 1 1102 455911740 455910600 0.000000e+00 1373


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 TraesCS4D01G216700 chr4D 370690321 370693506 3185 True 2662.5 5199 100.000000 1 3186 2 chr4D.!!$R1 3185
1 TraesCS4D01G216700 chr4A 93685085 93688356 3271 True 1310.0 3169 90.685333 1 3186 3 chr4A.!!$R1 3185
2 TraesCS4D01G216700 chr4B 455908620 455911740 3120 True 2023.0 2673 91.840500 1 2815 2 chr4B.!!$R1 2814

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
60 61 0.039035 AAAATGCTAGGGGGCGACAA 59.961 50.0 0.0 0.0 34.52 3.18 F
76 77 0.178987 ACAAACCGGCCATACCACAA 60.179 50.0 0.0 0.0 39.03 3.33 F
958 1261 0.327576 TCCCCTCTTCCTTCCATCCC 60.328 60.0 0.0 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1744 2322 1.187087 AAAAGTTTGTTCCGGGTGCA 58.813 45.0 0.00 0.0 0.0 4.57 R
1965 2560 5.046520 CCCCACTAGATTAATACCAGTAGCC 60.047 48.0 0.00 0.0 0.0 3.93 R
2289 2889 0.244450 AAACCATTCTACGGACGCGA 59.756 50.0 15.93 0.0 0.0 5.87 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
27 28 2.504367 CCACTAGTTTCCCAACACCAG 58.496 52.381 0.00 0.00 35.05 4.00
32 33 1.890041 TTTCCCAACACCAGCGTCG 60.890 57.895 0.00 0.00 0.00 5.12
60 61 0.039035 AAAATGCTAGGGGGCGACAA 59.961 50.000 0.00 0.00 34.52 3.18
73 74 1.376166 CGACAAACCGGCCATACCA 60.376 57.895 0.00 0.00 39.03 3.25
76 77 0.178987 ACAAACCGGCCATACCACAA 60.179 50.000 0.00 0.00 39.03 3.33
103 104 2.198827 TTCCAAGCATGTCAATCCGT 57.801 45.000 0.00 0.00 0.00 4.69
104 105 2.198827 TCCAAGCATGTCAATCCGTT 57.801 45.000 0.00 0.00 0.00 4.44
113 114 1.302112 TCAATCCGTTGAAGCGCCA 60.302 52.632 2.29 0.00 41.22 5.69
127 128 2.035421 CGCCACCCCATCATCAATG 58.965 57.895 0.00 0.00 34.93 2.82
151 152 1.715862 CGACGAGGAGAATGAGCCGA 61.716 60.000 0.00 0.00 0.00 5.54
196 197 3.127533 GTGCCGCCGAGCAAGAAT 61.128 61.111 1.90 0.00 46.19 2.40
228 251 0.950555 TCGCAACGCAGAGCAAGATT 60.951 50.000 0.00 0.00 33.01 2.40
234 257 2.636830 ACGCAGAGCAAGATTAGCAAT 58.363 42.857 0.00 0.00 0.00 3.56
261 284 0.871592 CGCGCAAGAGCACTATAGCA 60.872 55.000 8.75 0.00 42.27 3.49
360 383 2.414559 CCGATGAAGTGCCAATGTTGAC 60.415 50.000 0.00 0.00 0.00 3.18
415 438 2.747686 GAACCTGCCTTCCGTGGA 59.252 61.111 0.00 0.00 0.00 4.02
438 461 2.595009 GATGAGCCGAAGACACCCCC 62.595 65.000 0.00 0.00 0.00 5.40
512 535 2.668850 AGGGGAGAAAGGATGGAGAA 57.331 50.000 0.00 0.00 0.00 2.87
533 556 4.165486 GGCGGCGGCTAGGGTTTA 62.165 66.667 27.22 0.00 39.81 2.01
534 557 2.110420 GCGGCGGCTAGGGTTTAT 59.890 61.111 9.78 0.00 35.83 1.40
543 566 1.138266 GCTAGGGTTTATCCACTCGCA 59.862 52.381 0.00 0.00 38.11 5.10
574 860 6.501781 GCTCAAGTTTGATATGAGAATTGGG 58.498 40.000 6.21 0.00 42.48 4.12
579 865 6.371278 AGTTTGATATGAGAATTGGGCAGAT 58.629 36.000 0.00 0.00 0.00 2.90
592 878 9.131791 AGAATTGGGCAGATATTTAAAACGTAT 57.868 29.630 0.00 0.00 0.00 3.06
620 906 3.403038 AGATTCAGAAAACACGGGACAG 58.597 45.455 0.00 0.00 0.00 3.51
628 914 0.390735 AACACGGGACAGCCGATTAC 60.391 55.000 0.00 0.00 33.83 1.89
791 1082 1.153429 GACGCAAGCCCGGTATTCT 60.153 57.895 0.00 0.00 45.62 2.40
804 1095 4.864247 CCCGGTATTCTTTTTCTGCAAATG 59.136 41.667 0.00 0.00 0.00 2.32
895 1196 5.313712 CACCACTTATTTACACCCACTTCT 58.686 41.667 0.00 0.00 0.00 2.85
955 1258 2.578480 GACTTTCCCCTCTTCCTTCCAT 59.422 50.000 0.00 0.00 0.00 3.41
956 1259 2.578480 ACTTTCCCCTCTTCCTTCCATC 59.422 50.000 0.00 0.00 0.00 3.51
958 1261 0.327576 TCCCCTCTTCCTTCCATCCC 60.328 60.000 0.00 0.00 0.00 3.85
959 1262 0.624500 CCCCTCTTCCTTCCATCCCA 60.625 60.000 0.00 0.00 0.00 4.37
961 1264 1.589414 CCTCTTCCTTCCATCCCACT 58.411 55.000 0.00 0.00 0.00 4.00
962 1265 1.488393 CCTCTTCCTTCCATCCCACTC 59.512 57.143 0.00 0.00 0.00 3.51
963 1266 1.137872 CTCTTCCTTCCATCCCACTCG 59.862 57.143 0.00 0.00 0.00 4.18
1255 1827 1.045350 TCATCTTCCTCGCCCTCCTG 61.045 60.000 0.00 0.00 0.00 3.86
1597 2175 2.704193 CGTCGACCGCTTCAACGTC 61.704 63.158 10.58 0.00 0.00 4.34
1744 2322 4.882842 AAAATTTTACCACCGCAATCCT 57.117 36.364 0.37 0.00 0.00 3.24
2095 2691 5.249420 GGTAAATTTTGAGCTCTCACCTCT 58.751 41.667 16.19 0.00 39.66 3.69
2107 2703 0.331954 TCACCTCTCCTCGCCTTAGT 59.668 55.000 0.00 0.00 0.00 2.24
2277 2877 4.394712 ACCCCTTTCCGCTCGCTG 62.395 66.667 0.00 0.00 0.00 5.18
2283 2883 3.240134 TTTCCGCTCGCTGCTCCTT 62.240 57.895 0.00 0.00 40.11 3.36
2284 2884 3.939837 TTCCGCTCGCTGCTCCTTG 62.940 63.158 0.00 0.00 40.11 3.61
2289 2889 1.670406 CTCGCTGCTCCTTGCTGTT 60.670 57.895 0.00 0.00 43.37 3.16
2299 2908 1.731613 CTTGCTGTTCGCGTCCGTA 60.732 57.895 5.77 0.00 43.27 4.02
2324 2933 0.379316 GTTTCCCTTCGCGTGTTTGT 59.621 50.000 5.77 0.00 0.00 2.83
2325 2934 1.096416 TTTCCCTTCGCGTGTTTGTT 58.904 45.000 5.77 0.00 0.00 2.83
2326 2935 0.658897 TTCCCTTCGCGTGTTTGTTC 59.341 50.000 5.77 0.00 0.00 3.18
2444 3056 2.815647 GGAAACGCGAGCAGGAGG 60.816 66.667 15.93 0.00 0.00 4.30
2478 3090 1.632589 GGTTGGTTTCCTGCTTCCAT 58.367 50.000 0.00 0.00 0.00 3.41
2642 3258 3.692791 TCGACAGACGACAGGAATATG 57.307 47.619 0.00 0.00 46.45 1.78
2643 3259 2.120232 CGACAGACGACAGGAATATGC 58.880 52.381 0.00 0.00 45.77 3.14
2644 3260 2.223595 CGACAGACGACAGGAATATGCT 60.224 50.000 0.00 0.00 45.77 3.79
2645 3261 3.003378 CGACAGACGACAGGAATATGCTA 59.997 47.826 0.00 0.00 45.77 3.49
2646 3262 4.541779 GACAGACGACAGGAATATGCTAG 58.458 47.826 0.00 0.00 0.00 3.42
2647 3263 3.954904 ACAGACGACAGGAATATGCTAGT 59.045 43.478 0.00 0.00 0.00 2.57
2648 3264 5.131067 ACAGACGACAGGAATATGCTAGTA 58.869 41.667 0.00 0.00 0.00 1.82
2649 3265 5.008811 ACAGACGACAGGAATATGCTAGTAC 59.991 44.000 0.00 0.00 0.00 2.73
2651 3267 6.427242 CAGACGACAGGAATATGCTAGTACTA 59.573 42.308 1.89 1.89 0.00 1.82
2652 3268 6.427547 AGACGACAGGAATATGCTAGTACTAC 59.572 42.308 0.00 0.00 0.00 2.73
2653 3269 5.178996 ACGACAGGAATATGCTAGTACTACG 59.821 44.000 0.00 0.00 0.00 3.51
2654 3270 5.178996 CGACAGGAATATGCTAGTACTACGT 59.821 44.000 0.00 0.00 0.00 3.57
2657 3273 6.320672 ACAGGAATATGCTAGTACTACGTGTT 59.679 38.462 0.00 3.04 0.00 3.32
2662 3278 9.245962 GAATATGCTAGTACTACGTGTTTTGAT 57.754 33.333 0.00 0.00 0.00 2.57
2663 3279 9.595823 AATATGCTAGTACTACGTGTTTTGATT 57.404 29.630 0.00 0.00 0.00 2.57
2785 3407 3.324268 TGGCATGACATGGTTTTTGTGAT 59.676 39.130 17.03 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.156736 CGCTGGTGTTGGGAAACTAG 58.843 55.000 0.00 0.00 0.00 2.57
11 12 0.470766 ACGCTGGTGTTGGGAAACTA 59.529 50.000 0.00 0.00 0.00 2.24
12 13 0.818040 GACGCTGGTGTTGGGAAACT 60.818 55.000 0.00 0.00 0.00 2.66
27 28 0.248458 CATTTTATGCCCACCGACGC 60.248 55.000 0.00 0.00 0.00 5.19
60 61 2.488347 GGATATTGTGGTATGGCCGGTT 60.488 50.000 1.90 0.00 41.21 4.44
73 74 4.549668 ACATGCTTGGAATGGGATATTGT 58.450 39.130 4.44 0.00 0.00 2.71
76 77 4.458256 TGACATGCTTGGAATGGGATAT 57.542 40.909 4.44 0.00 0.00 1.63
103 104 2.361104 GATGGGGTGGCGCTTCAA 60.361 61.111 7.64 0.00 0.00 2.69
104 105 2.891941 GATGATGGGGTGGCGCTTCA 62.892 60.000 7.64 0.00 0.00 3.02
113 114 1.141657 CGAGGACATTGATGATGGGGT 59.858 52.381 0.00 0.00 40.21 4.95
151 152 1.002379 CTTGCTCTCTGGCCTGCTT 60.002 57.895 3.32 0.00 0.00 3.91
195 196 2.263077 GTTGCGACGAAGATGTCTCAT 58.737 47.619 0.00 0.00 33.95 2.90
196 197 1.698165 GTTGCGACGAAGATGTCTCA 58.302 50.000 0.00 0.00 36.71 3.27
360 383 4.609018 CATCGGCTACGCAGGGGG 62.609 72.222 0.00 0.00 40.69 5.40
373 396 0.234625 CAACGTTGTGGTGGTCATCG 59.765 55.000 20.21 0.00 35.18 3.84
376 399 1.377333 TGCAACGTTGTGGTGGTCA 60.377 52.632 27.78 13.46 0.00 4.02
403 426 3.030168 ATCGCATCCACGGAAGGCA 62.030 57.895 12.02 2.42 0.00 4.75
415 438 0.807667 GTGTCTTCGGCTCATCGCAT 60.808 55.000 0.00 0.00 41.67 4.73
533 556 2.512286 CGGCACATGCGAGTGGAT 60.512 61.111 9.94 0.00 43.26 3.41
543 566 1.538047 ATCAAACTTGAGCGGCACAT 58.462 45.000 1.45 0.00 41.08 3.21
592 878 5.414454 CCCGTGTTTTCTGAATCTTGGATAA 59.586 40.000 0.00 0.00 0.00 1.75
604 890 1.949257 GGCTGTCCCGTGTTTTCTG 59.051 57.895 0.00 0.00 0.00 3.02
620 906 7.040494 AGAAAGGTCTTTTAGTAGTAATCGGC 58.960 38.462 0.00 0.00 32.11 5.54
791 1082 1.605202 GGCTCGGCATTTGCAGAAAAA 60.605 47.619 6.82 0.00 44.09 1.94
804 1095 3.564027 CGGTTCATTCGGCTCGGC 61.564 66.667 0.00 0.00 0.00 5.54
955 1258 3.936203 GTGGTGGTGCGAGTGGGA 61.936 66.667 0.00 0.00 0.00 4.37
958 1261 1.961277 GAAGGTGGTGGTGCGAGTG 60.961 63.158 0.00 0.00 0.00 3.51
959 1262 2.426023 GAAGGTGGTGGTGCGAGT 59.574 61.111 0.00 0.00 0.00 4.18
961 1264 3.948719 GGGAAGGTGGTGGTGCGA 61.949 66.667 0.00 0.00 0.00 5.10
963 1266 4.678743 GGGGGAAGGTGGTGGTGC 62.679 72.222 0.00 0.00 0.00 5.01
1744 2322 1.187087 AAAAGTTTGTTCCGGGTGCA 58.813 45.000 0.00 0.00 0.00 4.57
1965 2560 5.046520 CCCCACTAGATTAATACCAGTAGCC 60.047 48.000 0.00 0.00 0.00 3.93
2107 2703 5.091552 AGAATCAGTGGTAACCTCAACCTA 58.908 41.667 0.00 0.00 37.91 3.08
2284 2884 0.801067 ATTCTACGGACGCGAACAGC 60.801 55.000 15.93 0.00 43.95 4.40
2285 2885 0.914551 CATTCTACGGACGCGAACAG 59.085 55.000 15.93 9.92 0.00 3.16
2289 2889 0.244450 AAACCATTCTACGGACGCGA 59.756 50.000 15.93 0.00 0.00 5.87
2324 2933 2.852075 ACTCCCACCCCAAGCGAA 60.852 61.111 0.00 0.00 0.00 4.70
2325 2934 3.319198 GACTCCCACCCCAAGCGA 61.319 66.667 0.00 0.00 0.00 4.93
2326 2935 4.760047 CGACTCCCACCCCAAGCG 62.760 72.222 0.00 0.00 0.00 4.68
2328 2937 2.928396 ACCGACTCCCACCCCAAG 60.928 66.667 0.00 0.00 0.00 3.61
2329 2938 3.246112 CACCGACTCCCACCCCAA 61.246 66.667 0.00 0.00 0.00 4.12
2382 2994 1.826340 TACCGGCTGAAGCAGAGCAA 61.826 55.000 0.00 0.00 44.36 3.91
2478 3090 1.963855 CCACGACGAAATGGCACCA 60.964 57.895 0.00 0.00 0.00 4.17
2651 3267 9.974980 ACCATTTTCTAAATAATCAAAACACGT 57.025 25.926 0.00 0.00 0.00 4.49
2654 3270 9.717942 CCCACCATTTTCTAAATAATCAAAACA 57.282 29.630 0.00 0.00 0.00 2.83
2662 3278 9.627123 CTGTAGATCCCACCATTTTCTAAATAA 57.373 33.333 0.00 0.00 0.00 1.40
2663 3279 7.719633 GCTGTAGATCCCACCATTTTCTAAATA 59.280 37.037 0.00 0.00 0.00 1.40
2665 3281 5.885912 GCTGTAGATCCCACCATTTTCTAAA 59.114 40.000 0.00 0.00 0.00 1.85
2699 3316 5.304778 TCCCCTAGTTTAACACGGTTTAAC 58.695 41.667 0.00 9.28 0.00 2.01
2707 3324 5.823045 CCATCTTCATCCCCTAGTTTAACAC 59.177 44.000 0.00 0.00 0.00 3.32
2785 3407 3.894257 CTGGAAGTCTCGCACAGAA 57.106 52.632 0.00 0.00 30.72 3.02


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

AutoCloner maintained by Alex Coulton.