Multiple sequence alignment - TraesCS6A01G029500

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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 TraesCS6A01G029500 chr6A 100.000 3041 0 0 1 3041 15490867 15487827 0.000000e+00 5616.0
1 TraesCS6A01G029500 chr4A 96.040 1414 44 3 572 1985 86178363 86176962 0.000000e+00 2290.0
2 TraesCS6A01G029500 chr4A 96.562 669 15 3 2380 3041 86176298 86175631 0.000000e+00 1101.0
3 TraesCS6A01G029500 chr4A 93.333 375 12 4 2021 2382 86176709 86176335 2.670000e-150 542.0
4 TraesCS6A01G029500 chr4A 91.946 149 6 1 420 568 86178673 86178531 1.430000e-48 204.0
5 TraesCS6A01G029500 chr4A 97.826 46 1 0 1980 2025 86176952 86176907 2.510000e-11 80.5
6 TraesCS6A01G029500 chr3B 89.718 1420 132 8 566 1985 222766548 222767953 0.000000e+00 1801.0
7 TraesCS6A01G029500 chr3B 91.278 493 42 1 2377 2868 222777498 222777990 0.000000e+00 671.0
8 TraesCS6A01G029500 chr3B 89.431 369 26 2 2021 2376 222777090 222777458 1.290000e-123 453.0
9 TraesCS6A01G029500 chr3B 95.146 103 5 0 2939 3041 222784227 222784329 2.430000e-36 163.0
10 TraesCS6A01G029500 chr3B 84.354 147 17 2 422 568 222766043 222766183 4.090000e-29 139.0
11 TraesCS6A01G029500 chr3B 90.323 62 3 2 417 478 416530843 416530785 9.040000e-11 78.7
12 TraesCS6A01G029500 chr6B 89.366 1420 124 5 566 1985 633004039 633002647 0.000000e+00 1760.0
13 TraesCS6A01G029500 chr6B 91.403 663 56 1 2380 3041 633001983 633001321 0.000000e+00 907.0
14 TraesCS6A01G029500 chr6B 88.076 369 31 3 2021 2376 633002394 633002026 2.800000e-115 425.0
15 TraesCS6A01G029500 chr7B 88.557 1407 146 7 583 1985 564739074 564740469 0.000000e+00 1692.0
16 TraesCS6A01G029500 chr7B 89.881 672 67 1 2371 3041 564741124 564741795 0.000000e+00 863.0
17 TraesCS6A01G029500 chr7B 85.095 369 42 3 2021 2376 564740722 564741090 6.200000e-97 364.0
18 TraesCS6A01G029500 chr7B 83.660 153 20 4 417 568 564738435 564738583 4.090000e-29 139.0
19 TraesCS6A01G029500 chr1B 86.510 1401 167 12 581 1977 198545684 198544302 0.000000e+00 1520.0
20 TraesCS6A01G029500 chr1B 89.873 474 44 4 2570 3041 198491875 198491404 9.320000e-170 606.0
21 TraesCS6A01G029500 chr1B 81.622 370 55 3 2023 2379 198544039 198543670 8.250000e-76 294.0
22 TraesCS6A01G029500 chr6D 86.129 1413 158 16 581 1993 151503530 151502156 0.000000e+00 1489.0
23 TraesCS6A01G029500 chr6D 88.369 662 73 4 2382 3041 151501496 151500837 0.000000e+00 793.0
24 TraesCS6A01G029500 chr6D 97.416 387 10 0 1 387 14230654 14230268 0.000000e+00 660.0
25 TraesCS6A01G029500 chr6D 82.320 362 51 5 2031 2379 151501899 151501538 4.930000e-78 302.0
26 TraesCS6A01G029500 chr6D 100.000 28 0 0 382 409 14229687 14229660 5.000000e-03 52.8
27 TraesCS6A01G029500 chr3A 95.885 729 30 0 1257 1985 75455772 75455044 0.000000e+00 1181.0
28 TraesCS6A01G029500 chr3A 95.516 669 19 3 2380 3041 75454380 75453716 0.000000e+00 1059.0
29 TraesCS6A01G029500 chr3A 94.400 375 8 2 2021 2382 75454791 75454417 5.690000e-157 564.0
30 TraesCS6A01G029500 chr3A 97.826 46 1 0 1980 2025 75455034 75454989 2.510000e-11 80.5
31 TraesCS6A01G029500 chr4D 79.879 661 114 15 2382 3033 150890546 150891196 1.650000e-127 466.0
32 TraesCS6A01G029500 chr2A 76.301 173 38 2 704 876 87699897 87700066 4.180000e-14 89.8
33 TraesCS6A01G029500 chr5D 90.323 62 3 2 417 478 12325180 12325122 9.040000e-11 78.7
34 TraesCS6A01G029500 chr7D 93.750 48 2 1 429 475 387925990 387926037 1.510000e-08 71.3
35 TraesCS6A01G029500 chr7D 91.304 46 3 1 434 478 186504450 186504405 9.100000e-06 62.1
36 TraesCS6A01G029500 chr5A 95.455 44 1 1 432 475 267953461 267953419 5.440000e-08 69.4
37 TraesCS6A01G029500 chr5B 87.719 57 4 1 425 478 137059419 137059363 2.530000e-06 63.9


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 TraesCS6A01G029500 chr6A 15487827 15490867 3040 True 5616.000000 5616 100.00000 1 3041 1 chr6A.!!$R1 3040
1 TraesCS6A01G029500 chr4A 86175631 86178673 3042 True 843.500000 2290 95.14140 420 3041 5 chr4A.!!$R1 2621
2 TraesCS6A01G029500 chr3B 222766043 222767953 1910 False 970.000000 1801 87.03600 422 1985 2 chr3B.!!$F2 1563
3 TraesCS6A01G029500 chr3B 222777090 222777990 900 False 562.000000 671 90.35450 2021 2868 2 chr3B.!!$F3 847
4 TraesCS6A01G029500 chr6B 633001321 633004039 2718 True 1030.666667 1760 89.61500 566 3041 3 chr6B.!!$R1 2475
5 TraesCS6A01G029500 chr7B 564738435 564741795 3360 False 764.500000 1692 86.79825 417 3041 4 chr7B.!!$F1 2624
6 TraesCS6A01G029500 chr1B 198543670 198545684 2014 True 907.000000 1520 84.06600 581 2379 2 chr1B.!!$R2 1798
7 TraesCS6A01G029500 chr6D 151500837 151503530 2693 True 861.333333 1489 85.60600 581 3041 3 chr6D.!!$R2 2460
8 TraesCS6A01G029500 chr6D 14229660 14230654 994 True 356.400000 660 98.70800 1 409 2 chr6D.!!$R1 408
9 TraesCS6A01G029500 chr3A 75453716 75455772 2056 True 721.125000 1181 95.90675 1257 3041 4 chr3A.!!$R1 1784
10 TraesCS6A01G029500 chr4D 150890546 150891196 650 False 466.000000 466 79.87900 2382 3033 1 chr4D.!!$F1 651

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
564 1151 1.379176 CTCGTCAGGGCTCTCCTCA 60.379 63.158 0.0 0.0 46.12 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2434 4007 1.079612 CGTCTCCATGCAGAGCACA 60.08 57.895 0.0 0.0 43.04 4.57 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
28 29 3.050275 GGGACGACAACAGCAGCC 61.050 66.667 0.00 0.00 0.00 4.85
30 31 3.414700 GACGACAACAGCAGCCCG 61.415 66.667 0.00 0.00 0.00 6.13
62 63 3.326006 GCACCATCTCCCATCTGATCTAA 59.674 47.826 0.00 0.00 0.00 2.10
85 86 3.434299 CCGACCGCAAAAACTTACTGTAT 59.566 43.478 0.00 0.00 0.00 2.29
139 140 3.911365 TGCATGAATTCGTTTGCTTTACG 59.089 39.130 21.21 0.00 40.23 3.18
189 190 3.023119 TCAAGCACTCAAGCCTTTTGAA 58.977 40.909 0.00 0.00 34.23 2.69
203 204 5.945784 AGCCTTTTGAATTATCTGCACTGTA 59.054 36.000 0.00 0.00 0.00 2.74
207 208 8.246180 CCTTTTGAATTATCTGCACTGTACAAT 58.754 33.333 0.00 0.00 0.00 2.71
339 340 5.808540 TCAGTCGATATTTTTCCACTAACCG 59.191 40.000 0.00 0.00 0.00 4.44
418 1005 4.425578 TGATCAGCGATCAAGGCG 57.574 55.556 15.66 0.00 44.70 5.52
564 1151 1.379176 CTCGTCAGGGCTCTCCTCA 60.379 63.158 0.00 0.00 46.12 3.86
643 1706 4.021925 GCCCTGCCTTCCAGTCGT 62.022 66.667 0.00 0.00 40.06 4.34
655 1718 2.152699 CAGTCGTGACGCCGTCATC 61.153 63.158 24.10 15.97 44.63 2.92
1104 2185 3.064987 CTCCGTCCCGTTCATCGCT 62.065 63.158 0.00 0.00 38.35 4.93
1501 2582 4.069232 CTGTCTCGCTTCGGGGCA 62.069 66.667 0.00 0.00 40.60 5.36
1718 2811 3.827898 GGAGGAGGGCAGTCGTCG 61.828 72.222 0.00 0.00 33.06 5.12
1726 2819 4.738345 GCAGTCGTCGTCGTCGCT 62.738 66.667 7.01 5.22 38.33 4.93
1796 2889 1.463214 TTCTGGGGGAGCCAGAACA 60.463 57.895 0.92 0.00 45.61 3.18
1914 3016 3.134127 GACAGGCATTCGGGTGGC 61.134 66.667 6.44 6.44 44.31 5.01
1954 3056 1.460689 TCGGGAGGTTCAGGTGGTT 60.461 57.895 0.00 0.00 0.00 3.67
2434 4007 0.464373 CGGTGCAGGCTAATGTGGAT 60.464 55.000 0.00 0.00 0.00 3.41
2451 4024 1.297664 GATGTGCTCTGCATGGAGAC 58.702 55.000 13.58 10.79 41.91 3.36
2591 4170 3.853330 CGAAGCATGCGACCACCG 61.853 66.667 13.01 7.00 42.52 4.94
2610 4190 0.107508 GGCAGCAGCAAGTCCTCATA 60.108 55.000 2.65 0.00 44.61 2.15
2662 4242 3.034635 GTGATCTCTGAGGAAGCCCTTA 58.965 50.000 4.59 0.00 44.53 2.69
2723 4303 1.827789 ACATTGCCGCTGTGTTGGT 60.828 52.632 0.00 0.00 0.00 3.67
2919 4499 3.013219 TGCAGTGTTTCAAGTAGTTGCA 58.987 40.909 5.35 0.00 37.91 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 1.600485 CAGTAAGTTTTTGCGGTCGGT 59.400 47.619 0.00 0.00 0.00 4.69
139 140 7.118724 TGTACGATAACAACAAAAACTCGAAC 58.881 34.615 0.00 0.00 0.00 3.95
339 340 5.448632 CCGATGCTTTGACCAGGTAATAAAC 60.449 44.000 0.00 0.00 0.00 2.01
367 368 2.102578 GATGCACCAGCCCAAAAGTAT 58.897 47.619 0.00 0.00 41.13 2.12
409 996 0.031994 GAGGAGAGAGCGCCTTGATC 59.968 60.000 2.29 0.00 45.01 2.92
410 997 0.396974 AGAGGAGAGAGCGCCTTGAT 60.397 55.000 2.29 0.00 45.01 2.57
411 998 0.613292 AAGAGGAGAGAGCGCCTTGA 60.613 55.000 2.29 0.00 45.01 3.02
412 999 0.179113 GAAGAGGAGAGAGCGCCTTG 60.179 60.000 2.29 0.00 45.01 3.61
413 1000 1.662438 CGAAGAGGAGAGAGCGCCTT 61.662 60.000 2.29 0.00 45.01 4.35
415 1002 2.411290 CGAAGAGGAGAGAGCGCC 59.589 66.667 2.29 0.00 0.00 6.53
416 1003 2.278531 GCGAAGAGGAGAGAGCGC 60.279 66.667 0.00 0.00 37.60 5.92
417 1004 1.063972 CAGCGAAGAGGAGAGAGCG 59.936 63.158 0.00 0.00 0.00 5.03
418 1005 1.226945 GCAGCGAAGAGGAGAGAGC 60.227 63.158 0.00 0.00 0.00 4.09
419 1006 1.063972 CGCAGCGAAGAGGAGAGAG 59.936 63.158 9.98 0.00 0.00 3.20
420 1007 3.191836 CGCAGCGAAGAGGAGAGA 58.808 61.111 9.98 0.00 0.00 3.10
643 1706 2.885113 CTGGAGATGACGGCGTCA 59.115 61.111 40.35 40.35 46.90 4.35
1796 2889 1.504912 CACCTCCTGATCATCCACCT 58.495 55.000 0.00 0.00 0.00 4.00
1855 2957 4.137872 GTCATTCCCCGACGGCGA 62.138 66.667 15.16 1.74 40.82 5.54
1954 3056 2.828868 GACCATGGAGGCCGCATA 59.171 61.111 21.47 0.00 43.14 3.14
2378 3951 1.382522 GACATCGGTGTGCATGGAAT 58.617 50.000 5.76 0.00 39.09 3.01
2434 4007 1.079612 CGTCTCCATGCAGAGCACA 60.080 57.895 0.00 0.00 43.04 4.57
2591 4170 0.107508 TATGAGGACTTGCTGCTGCC 60.108 55.000 13.47 0.00 38.71 4.85
2662 4242 2.818432 AGAACAAGTCGACGTACATCCT 59.182 45.455 10.46 0.26 0.00 3.24
2723 4303 1.384525 CGACTCCCAACCAAACAACA 58.615 50.000 0.00 0.00 0.00 3.33
2748 4328 1.668294 CTCCTCCATAAGCGGCGAT 59.332 57.895 12.98 0.00 0.00 4.58


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

AutoCloner maintained by Alex Coulton.