Multiple sequence alignment - TraesCS7D01G121500

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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 TraesCS7D01G121500 chr7D 100.000 3176 0 0 1 3176 75359216 75356041 0.000000e+00 5866.0
1 TraesCS7D01G121500 chr7D 89.679 2335 176 25 787 3068 75807044 75804722 0.000000e+00 2916.0
2 TraesCS7D01G121500 chr7D 98.802 1252 8 5 1 1252 75401342 75400098 0.000000e+00 2222.0
3 TraesCS7D01G121500 chr7D 80.379 1794 281 42 859 2625 75890014 75888265 0.000000e+00 1297.0
4 TraesCS7D01G121500 chr7D 96.078 51 1 1 647 697 75807168 75807119 7.300000e-12 82.4
5 TraesCS7D01G121500 chr7B 92.034 1908 127 16 347 2245 21822395 21820504 0.000000e+00 2658.0
6 TraesCS7D01G121500 chr7B 93.186 1541 67 12 1660 3176 21819665 21818139 0.000000e+00 2230.0
7 TraesCS7D01G121500 chr7B 82.531 1786 251 43 790 2542 21722066 21720309 0.000000e+00 1513.0
8 TraesCS7D01G121500 chr7B 82.754 1467 220 20 872 2322 21936314 21934865 0.000000e+00 1277.0
9 TraesCS7D01G121500 chr7B 95.574 723 32 0 790 1512 21671797 21671075 0.000000e+00 1158.0
10 TraesCS7D01G121500 chr7B 84.238 571 47 29 91 641 21823161 21822614 1.690000e-142 516.0
11 TraesCS7D01G121500 chr7B 82.993 147 18 4 2797 2936 21820023 21819877 3.330000e-25 126.0
12 TraesCS7D01G121500 chr7B 95.082 61 3 0 2715 2775 21820141 21820081 2.610000e-16 97.1
13 TraesCS7D01G121500 chr7B 94.000 50 2 1 309 357 205388387 205388436 1.220000e-09 75.0
14 TraesCS7D01G121500 chr7A 91.236 1472 110 4 784 2236 79654015 79652544 0.000000e+00 1986.0
15 TraesCS7D01G121500 chr7A 90.897 1461 116 6 790 2236 79650125 79648668 0.000000e+00 1945.0
16 TraesCS7D01G121500 chr7A 80.484 1860 278 47 870 2698 79811383 79809578 0.000000e+00 1345.0
17 TraesCS7D01G121500 chr7A 81.925 1444 210 26 859 2293 79816747 79815346 0.000000e+00 1173.0
18 TraesCS7D01G121500 chr7A 87.582 765 74 13 790 1541 79646247 79645491 0.000000e+00 867.0
19 TraesCS7D01G121500 chr7A 84.821 224 21 8 2858 3071 79644241 79644021 2.480000e-51 213.0
20 TraesCS7D01G121500 chr7A 89.610 77 8 0 675 751 79654090 79654014 7.250000e-17 99.0
21 TraesCS7D01G121500 chr1B 81.319 91 10 5 279 365 604300138 604300225 2.040000e-07 67.6


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 TraesCS7D01G121500 chr7D 75356041 75359216 3175 True 5866.00 5866 100.0000 1 3176 1 chr7D.!!$R1 3175
1 TraesCS7D01G121500 chr7D 75400098 75401342 1244 True 2222.00 2222 98.8020 1 1252 1 chr7D.!!$R2 1251
2 TraesCS7D01G121500 chr7D 75804722 75807168 2446 True 1499.20 2916 92.8785 647 3068 2 chr7D.!!$R4 2421
3 TraesCS7D01G121500 chr7D 75888265 75890014 1749 True 1297.00 1297 80.3790 859 2625 1 chr7D.!!$R3 1766
4 TraesCS7D01G121500 chr7B 21720309 21722066 1757 True 1513.00 1513 82.5310 790 2542 1 chr7B.!!$R2 1752
5 TraesCS7D01G121500 chr7B 21934865 21936314 1449 True 1277.00 1277 82.7540 872 2322 1 chr7B.!!$R3 1450
6 TraesCS7D01G121500 chr7B 21671075 21671797 722 True 1158.00 1158 95.5740 790 1512 1 chr7B.!!$R1 722
7 TraesCS7D01G121500 chr7B 21818139 21823161 5022 True 1125.42 2658 89.5066 91 3176 5 chr7B.!!$R4 3085
8 TraesCS7D01G121500 chr7A 79809578 79816747 7169 True 1259.00 1345 81.2045 859 2698 2 chr7A.!!$R2 1839
9 TraesCS7D01G121500 chr7A 79644021 79654090 10069 True 1022.00 1986 88.8292 675 3071 5 chr7A.!!$R1 2396

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
692 1225 0.249447 GACAAAAGCCCAACACAGCC 60.249 55.000 0.0 0.0 0.0 4.85 F
782 1338 3.536956 AAAAATATCACCTCGCCTCGA 57.463 42.857 0.0 0.0 0.0 4.04 F
1596 2180 0.603569 AGTTCGTCAGAGCGGTTGAT 59.396 50.000 0.0 0.0 32.5 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1577 2161 0.603569 ATCAACCGCTCTGACGAACT 59.396 50.000 0.0 0.0 34.06 3.01 R
1929 7879 1.545841 TCAGATACCTGACGCTGTGT 58.454 50.000 0.0 0.0 44.01 3.72 R
3086 16975 2.359230 GACCTGAGGCACCAGCAC 60.359 66.667 0.0 0.0 44.61 4.40 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
177 178 1.295792 GTGTTGGACGCTTTCTGTGA 58.704 50.000 0.00 0.00 0.00 3.58
266 267 4.081087 TCCTAGGTTTTGGACACTCTATGC 60.081 45.833 9.08 0.00 0.00 3.14
692 1225 0.249447 GACAAAAGCCCAACACAGCC 60.249 55.000 0.00 0.00 0.00 4.85
782 1338 3.536956 AAAAATATCACCTCGCCTCGA 57.463 42.857 0.00 0.00 0.00 4.04
1577 2161 2.356695 ACGATGATGACGATGGTTACGA 59.643 45.455 0.00 0.00 34.70 3.43
1596 2180 0.603569 AGTTCGTCAGAGCGGTTGAT 59.396 50.000 0.00 0.00 32.50 2.57
1605 2189 3.821600 TCAGAGCGGTTGATATCTACTCC 59.178 47.826 15.41 8.00 0.00 3.85
1929 7879 1.843851 AGTGAAGTGTGGGTCTTGGAA 59.156 47.619 0.00 0.00 0.00 3.53
1977 7927 1.480954 GGAGTGAAGAATGTCCGGCTA 59.519 52.381 0.00 0.00 0.00 3.93
2088 8038 3.959495 ATGGATACTGGGAAAGTGCAT 57.041 42.857 0.00 0.00 40.26 3.96
2115 15922 2.025981 CCATGATCTTGGACAGGGTTCA 60.026 50.000 20.45 0.00 39.25 3.18
2225 16032 6.980397 CCATTGTTGACCTTTTAGATAATGGC 59.020 38.462 0.00 0.00 36.66 4.40
2236 16052 7.066284 CCTTTTAGATAATGGCGAATCATAGGG 59.934 40.741 0.00 0.00 0.00 3.53
2346 16164 3.643199 TGCACTTTATGTGGCCATCTA 57.357 42.857 9.72 0.00 46.27 1.98
2401 16247 2.890371 GCCAGCAGCAAATCCTGG 59.110 61.111 0.00 1.66 46.95 4.45
2703 16553 4.787551 TGTTCCTTTGCTCCTGTCTTTTA 58.212 39.130 0.00 0.00 0.00 1.52
2704 16554 5.197451 TGTTCCTTTGCTCCTGTCTTTTAA 58.803 37.500 0.00 0.00 0.00 1.52
2705 16555 5.654650 TGTTCCTTTGCTCCTGTCTTTTAAA 59.345 36.000 0.00 0.00 0.00 1.52
2706 16556 6.153680 TGTTCCTTTGCTCCTGTCTTTTAAAA 59.846 34.615 0.00 0.00 0.00 1.52
2707 16557 6.783708 TCCTTTGCTCCTGTCTTTTAAAAA 57.216 33.333 1.66 0.00 0.00 1.94
2708 16558 6.569780 TCCTTTGCTCCTGTCTTTTAAAAAC 58.430 36.000 1.66 4.59 0.00 2.43
2718 16568 9.377312 TCCTGTCTTTTAAAAACAAAAATCCTG 57.623 29.630 1.66 0.00 0.00 3.86
2851 16730 4.690748 CGTGTCATATTCAGTCCAGTGTTT 59.309 41.667 0.00 0.00 0.00 2.83
2854 16733 5.700832 TGTCATATTCAGTCCAGTGTTTGAC 59.299 40.000 0.00 0.00 0.00 3.18
3099 16988 4.314440 GTCCGTGCTGGTGCCTCA 62.314 66.667 0.00 0.00 39.52 3.86
3173 17062 8.737175 TGTAACTCTAGAATGAATTCTACACGT 58.263 33.333 7.05 4.32 44.80 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
692 1225 1.409412 CGAAGTGAACGAGGAGTGTG 58.591 55.000 0.00 0.00 0.00 3.82
1555 2127 3.113322 CGTAACCATCGTCATCATCGTT 58.887 45.455 0.00 0.00 0.00 3.85
1577 2161 0.603569 ATCAACCGCTCTGACGAACT 59.396 50.000 0.00 0.00 34.06 3.01
1596 2180 3.036091 CCCGGTTTTGGAGGAGTAGATA 58.964 50.000 0.00 0.00 0.00 1.98
1605 2189 2.676471 CAGGCCCCGGTTTTGGAG 60.676 66.667 0.00 0.00 0.00 3.86
1866 7816 6.804295 CCCAGATCGAGAGTTTATAAAGATCG 59.196 42.308 15.42 15.42 38.32 3.69
1929 7879 1.545841 TCAGATACCTGACGCTGTGT 58.454 50.000 0.00 0.00 44.01 3.72
1977 7927 3.066342 CGACAATATGGTACTCGTGTCCT 59.934 47.826 0.00 0.00 33.43 3.85
2115 15922 4.916424 ACATAAGGAAGATAGGGCTCCATT 59.084 41.667 0.00 0.00 0.00 3.16
2225 16032 3.485463 TTACTTGGGCCCTATGATTCG 57.515 47.619 25.70 4.70 0.00 3.34
2236 16052 2.856222 AGCTGCTGATATTACTTGGGC 58.144 47.619 0.00 0.00 0.00 5.36
2267 16084 2.618241 AGCAACGCAACATCAGAAAGAA 59.382 40.909 0.00 0.00 0.00 2.52
2346 16164 8.322091 AGCTAGTGTCACTAAATTAACTGGAAT 58.678 33.333 13.63 0.00 29.00 3.01
2458 16305 5.463061 CACAACAATCTGGAAATCACAAACC 59.537 40.000 0.00 0.00 0.00 3.27
2528 16376 7.141363 GCACAAAAAGTCTCAACATAGAACAT 58.859 34.615 0.00 0.00 0.00 2.71
2703 16553 5.118286 CAGGAGCACAGGATTTTTGTTTTT 58.882 37.500 0.00 0.00 0.00 1.94
2704 16554 4.162131 ACAGGAGCACAGGATTTTTGTTTT 59.838 37.500 0.00 0.00 0.00 2.43
2705 16555 3.706086 ACAGGAGCACAGGATTTTTGTTT 59.294 39.130 0.00 0.00 0.00 2.83
2706 16556 3.299503 ACAGGAGCACAGGATTTTTGTT 58.700 40.909 0.00 0.00 0.00 2.83
2707 16557 2.887152 GACAGGAGCACAGGATTTTTGT 59.113 45.455 0.00 0.00 0.00 2.83
2708 16558 2.886523 TGACAGGAGCACAGGATTTTTG 59.113 45.455 0.00 0.00 0.00 2.44
2718 16568 3.988379 TTTCAACATTGACAGGAGCAC 57.012 42.857 0.00 0.00 36.83 4.40
2851 16730 5.562298 AGTTTAGTTTCAGGCTTAGGTCA 57.438 39.130 0.00 0.00 0.00 4.02
2854 16733 7.039313 ACAAAAGTTTAGTTTCAGGCTTAGG 57.961 36.000 0.00 0.00 0.00 2.69
3086 16975 2.359230 GACCTGAGGCACCAGCAC 60.359 66.667 0.00 0.00 44.61 4.40
3099 16988 9.185680 GTCTGTTATTTAATAACCATTGGACCT 57.814 33.333 20.83 0.00 43.42 3.85


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

AutoCloner maintained by Alex Coulton.