Multiple sequence alignment - TraesCS6A01G332500

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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 TraesCS6A01G332500 chr6A 100.000 2448 0 0 1 2448 564237627 564240074 0.000000e+00 4521.0
1 TraesCS6A01G332500 chr6A 96.940 2451 66 6 1 2448 564190171 564192615 0.000000e+00 4102.0
2 TraesCS6A01G332500 chr6A 96.582 1726 48 6 680 2400 564132052 564133771 0.000000e+00 2850.0
3 TraesCS6A01G332500 chr6A 97.067 682 19 1 1 681 564224353 564225034 0.000000e+00 1147.0
4 TraesCS6A01G332500 chr6A 96.788 685 21 1 1 684 136819024 136818340 0.000000e+00 1142.0
5 TraesCS6A01G332500 chr6A 96.642 685 22 1 1 684 37859051 37858367 0.000000e+00 1136.0
6 TraesCS6A01G332500 chr6A 96.481 682 23 1 1 681 564168375 564169056 0.000000e+00 1125.0
7 TraesCS6A01G332500 chr6A 84.367 1209 122 41 763 1926 564117558 564118744 0.000000e+00 1123.0
8 TraesCS6A01G332500 chr6A 84.129 775 63 36 884 1646 564259894 564260620 0.000000e+00 695.0
9 TraesCS6A01G332500 chr6A 100.000 44 0 0 2713 2756 564240339 564240382 6.330000e-12 82.4
10 TraesCS6A01G332500 chr6B 90.779 1822 106 18 680 2447 634321516 634323329 0.000000e+00 2377.0
11 TraesCS6A01G332500 chr6B 84.010 1207 112 43 680 1832 634315287 634316466 0.000000e+00 1085.0
12 TraesCS6A01G332500 chr6B 89.718 603 35 13 1047 1646 634329953 634330531 0.000000e+00 745.0
13 TraesCS6A01G332500 chr6D 91.552 1740 78 25 680 2372 420935323 420937040 0.000000e+00 2335.0
14 TraesCS6A01G332500 chr6D 82.729 1297 149 40 680 1926 420898769 420900040 0.000000e+00 1085.0
15 TraesCS6A01G332500 chr6D 86.194 775 60 21 884 1646 420956415 420957154 0.000000e+00 795.0
16 TraesCS6A01G332500 chr6D 95.455 44 2 0 2713 2756 420937045 420937088 1.370000e-08 71.3
17 TraesCS6A01G332500 chr4A 97.214 682 18 1 1 681 257508036 257508717 0.000000e+00 1153.0
18 TraesCS6A01G332500 chr2A 97.214 682 18 1 1 681 739397871 739397190 0.000000e+00 1153.0
19 TraesCS6A01G332500 chr2A 96.779 683 20 2 1 681 161413096 161413778 0.000000e+00 1138.0
20 TraesCS6A01G332500 chr5A 96.642 685 22 1 1 684 316670355 316669671 0.000000e+00 1136.0


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 TraesCS6A01G332500 chr6A 564237627 564240382 2755 False 2301.70 4521 100.0000 1 2756 2 chr6A.!!$F7 2755
1 TraesCS6A01G332500 chr6A 564190171 564192615 2444 False 4102.00 4102 96.9400 1 2448 1 chr6A.!!$F4 2447
2 TraesCS6A01G332500 chr6A 564132052 564133771 1719 False 2850.00 2850 96.5820 680 2400 1 chr6A.!!$F2 1720
3 TraesCS6A01G332500 chr6A 564224353 564225034 681 False 1147.00 1147 97.0670 1 681 1 chr6A.!!$F5 680
4 TraesCS6A01G332500 chr6A 136818340 136819024 684 True 1142.00 1142 96.7880 1 684 1 chr6A.!!$R2 683
5 TraesCS6A01G332500 chr6A 37858367 37859051 684 True 1136.00 1136 96.6420 1 684 1 chr6A.!!$R1 683
6 TraesCS6A01G332500 chr6A 564168375 564169056 681 False 1125.00 1125 96.4810 1 681 1 chr6A.!!$F3 680
7 TraesCS6A01G332500 chr6A 564117558 564118744 1186 False 1123.00 1123 84.3670 763 1926 1 chr6A.!!$F1 1163
8 TraesCS6A01G332500 chr6A 564259894 564260620 726 False 695.00 695 84.1290 884 1646 1 chr6A.!!$F6 762
9 TraesCS6A01G332500 chr6B 634321516 634323329 1813 False 2377.00 2377 90.7790 680 2447 1 chr6B.!!$F2 1767
10 TraesCS6A01G332500 chr6B 634315287 634316466 1179 False 1085.00 1085 84.0100 680 1832 1 chr6B.!!$F1 1152
11 TraesCS6A01G332500 chr6B 634329953 634330531 578 False 745.00 745 89.7180 1047 1646 1 chr6B.!!$F3 599
12 TraesCS6A01G332500 chr6D 420935323 420937088 1765 False 1203.15 2335 93.5035 680 2756 2 chr6D.!!$F3 2076
13 TraesCS6A01G332500 chr6D 420898769 420900040 1271 False 1085.00 1085 82.7290 680 1926 1 chr6D.!!$F1 1246
14 TraesCS6A01G332500 chr6D 420956415 420957154 739 False 795.00 795 86.1940 884 1646 1 chr6D.!!$F2 762
15 TraesCS6A01G332500 chr4A 257508036 257508717 681 False 1153.00 1153 97.2140 1 681 1 chr4A.!!$F1 680
16 TraesCS6A01G332500 chr2A 739397190 739397871 681 True 1153.00 1153 97.2140 1 681 1 chr2A.!!$R1 680
17 TraesCS6A01G332500 chr2A 161413096 161413778 682 False 1138.00 1138 96.7790 1 681 1 chr2A.!!$F1 680
18 TraesCS6A01G332500 chr5A 316669671 316670355 684 True 1136.00 1136 96.6420 1 684 1 chr5A.!!$R1 683

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
657 659 1.389106 GCCGTACACTAACTTTGAGCG 59.611 52.381 0.0 0.0 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2298 2431 0.250513 AGAAGACAACCGATGAGGCC 59.749 55.0 0.0 0.0 46.52 5.19 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
338 340 2.028385 AGACCGCGTCTTCACCTTATTT 60.028 45.455 4.92 0.00 40.28 1.40
613 615 6.349777 GGAATTCTCTCTCAAAGACTTCGAGA 60.350 42.308 5.74 5.74 34.80 4.04
657 659 1.389106 GCCGTACACTAACTTTGAGCG 59.611 52.381 0.00 0.00 0.00 5.03
754 757 8.242053 ACATCATTGAAGCAACATAAGAAGAAG 58.758 33.333 0.00 0.00 0.00 2.85
908 934 7.872483 CCAGGTGCTTACTGTGATTAAAAATTT 59.128 33.333 0.00 0.00 34.16 1.82
1390 1464 1.202842 TCATACGCGTCCCTATCTCCA 60.203 52.381 18.63 0.00 0.00 3.86
1533 1618 2.357517 GGTGGACCAGTGCGACAG 60.358 66.667 0.00 0.00 35.64 3.51
1534 1619 2.734591 GTGGACCAGTGCGACAGA 59.265 61.111 0.00 0.00 0.00 3.41
1535 1620 1.293498 GTGGACCAGTGCGACAGAT 59.707 57.895 0.00 0.00 0.00 2.90
2042 2149 6.579666 AACGGTCCCTTAAATTTAACTTCC 57.420 37.500 6.54 6.59 0.00 3.46
2267 2400 3.241530 ACTTGCGGTCAGGCCTCA 61.242 61.111 0.00 0.00 34.25 3.86
2268 2401 2.270205 CTTGCGGTCAGGCCTCAT 59.730 61.111 0.00 0.00 31.16 2.90
2269 2402 1.817099 CTTGCGGTCAGGCCTCATC 60.817 63.158 0.00 0.00 31.16 2.92
2270 2403 3.664025 TTGCGGTCAGGCCTCATCG 62.664 63.158 4.26 4.26 31.16 3.84
2336 2469 2.026542 TCTTGTAGAGCTCGTAGACCCA 60.027 50.000 8.37 0.00 0.00 4.51
2348 2481 1.572689 TAGACCCAGAGCTCCTCGGT 61.573 60.000 10.93 13.35 35.36 4.69
2376 2509 2.356382 CTCTAGATGTTTCGCTCGGAGT 59.644 50.000 6.90 0.00 0.00 3.85
2400 2533 4.470602 AGACCATGTACACCTCATCGATA 58.529 43.478 0.00 0.00 0.00 2.92
2436 2569 1.745320 GCTCGAAGGCCTCCCGATTA 61.745 60.000 24.51 8.41 35.76 1.75
2742 2875 3.503827 TGTCAATATCTTCGCACGACT 57.496 42.857 0.00 0.00 0.00 4.18
2743 2876 4.625972 TGTCAATATCTTCGCACGACTA 57.374 40.909 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
613 615 1.202758 TGTCGTTTGAGAGCAACCCAT 60.203 47.619 0.00 0.00 32.79 4.00
908 934 3.924114 TCATCGCCTTCCCTTAATCAA 57.076 42.857 0.00 0.00 0.00 2.57
1242 1311 2.507102 CCACGTCGCGCAGAAGAT 60.507 61.111 18.05 4.25 32.54 2.40
1390 1464 7.724490 TTCCTTATACAGATCATCCATCGAT 57.276 36.000 0.00 0.00 36.50 3.59
1728 1822 2.350964 GGTTGCGTTTTATTCTTGCCGA 60.351 45.455 0.00 0.00 0.00 5.54
1775 1869 2.662857 GCGCTGCATGCCTCGATA 60.663 61.111 26.05 3.13 38.78 2.92
1952 2056 3.391799 GGGCCTAAATTTAAGGGACCA 57.608 47.619 19.20 0.00 45.95 4.02
2079 2192 4.646945 TGCTACCTTTGTGTTTGAATCCAA 59.353 37.500 0.00 0.00 0.00 3.53
2269 2402 1.364171 GTGGGGAGGTCGATGATCG 59.636 63.158 8.83 8.83 42.10 3.69
2270 2403 1.749033 GGTGGGGAGGTCGATGATC 59.251 63.158 0.00 0.00 0.00 2.92
2298 2431 0.250513 AGAAGACAACCGATGAGGCC 59.749 55.000 0.00 0.00 46.52 5.19
2336 2469 2.351657 TCGTCACCGAGGAGCTCT 59.648 61.111 14.64 0.00 38.40 4.09
2348 2481 2.478031 GCGAAACATCTAGAGCTCGTCA 60.478 50.000 8.37 0.00 0.00 4.35
2359 2492 0.888619 TCACTCCGAGCGAAACATCT 59.111 50.000 0.00 0.00 0.00 2.90
2376 2509 2.427095 CGATGAGGTGTACATGGTCTCA 59.573 50.000 17.26 17.26 38.59 3.27
2400 2533 3.061848 CAAATTGAGGCCCCGCGT 61.062 61.111 4.92 0.00 0.00 6.01
2412 2545 0.681243 GGGAGGCCTTCGAGCAAATT 60.681 55.000 6.77 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.