Multiple sequence alignment - TraesCS4A01G246700

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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 TraesCS4A01G246700 chr4A 100.000 2800 0 0 1 2800 557664145 557661346 0.000000e+00 5171
1 TraesCS4A01G246700 chr4A 97.858 2801 59 1 1 2800 554698174 554700974 0.000000e+00 4839
2 TraesCS4A01G246700 chr1D 92.720 2857 130 26 1 2800 96036115 96033280 0.000000e+00 4052
3 TraesCS4A01G246700 chr1D 91.358 2858 142 29 1 2800 64335920 64338730 0.000000e+00 3812
4 TraesCS4A01G246700 chr1D 92.403 2330 115 16 524 2800 439404020 439406340 0.000000e+00 3265
5 TraesCS4A01G246700 chr7D 91.282 2856 150 32 1 2800 600062939 600065751 0.000000e+00 3803
6 TraesCS4A01G246700 chr6A 91.126 2851 170 31 4 2800 121725555 121722734 0.000000e+00 3786
7 TraesCS4A01G246700 chr3B 90.753 2509 148 25 341 2800 734914114 734911641 0.000000e+00 3271
8 TraesCS4A01G246700 chr3B 87.239 2398 179 40 368 2681 774402758 774405112 0.000000e+00 2615
9 TraesCS4A01G246700 chr3A 88.218 2402 166 30 468 2800 714788224 714790577 0.000000e+00 2760
10 TraesCS4A01G246700 chr3A 89.650 2029 121 27 280 2241 638855302 638853296 0.000000e+00 2501
11 TraesCS4A01G246700 chr3A 88.419 1986 118 26 883 2800 607845898 607847839 0.000000e+00 2290
12 TraesCS4A01G246700 chr1B 91.531 2031 100 17 524 2503 596176023 596178032 0.000000e+00 2732
13 TraesCS4A01G246700 chr1B 93.128 422 24 2 1 418 596175558 596175978 5.130000e-172 614
14 TraesCS4A01G246700 chr4D 94.611 1633 58 11 1 1606 42333873 42335502 0.000000e+00 2501
15 TraesCS4A01G246700 chr7B 93.551 1473 76 3 1 1455 6998569 7000040 0.000000e+00 2176
16 TraesCS4A01G246700 chr7B 89.392 1348 107 12 1486 2800 7000041 7001385 0.000000e+00 1664
17 TraesCS4A01G246700 chr2B 87.078 1749 104 38 526 2215 755329850 755331535 0.000000e+00 1866
18 TraesCS4A01G246700 chr3D 89.898 1376 60 17 857 2169 579688196 579689555 0.000000e+00 1698
19 TraesCS4A01G246700 chr2A 85.577 1671 148 38 1164 2800 749651368 749652979 0.000000e+00 1664
20 TraesCS4A01G246700 chr6D 92.498 1133 65 6 1 1129 68973814 68974930 0.000000e+00 1604


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 TraesCS4A01G246700 chr4A 557661346 557664145 2799 True 5171 5171 100.0000 1 2800 1 chr4A.!!$R1 2799
1 TraesCS4A01G246700 chr4A 554698174 554700974 2800 False 4839 4839 97.8580 1 2800 1 chr4A.!!$F1 2799
2 TraesCS4A01G246700 chr1D 96033280 96036115 2835 True 4052 4052 92.7200 1 2800 1 chr1D.!!$R1 2799
3 TraesCS4A01G246700 chr1D 64335920 64338730 2810 False 3812 3812 91.3580 1 2800 1 chr1D.!!$F1 2799
4 TraesCS4A01G246700 chr1D 439404020 439406340 2320 False 3265 3265 92.4030 524 2800 1 chr1D.!!$F2 2276
5 TraesCS4A01G246700 chr7D 600062939 600065751 2812 False 3803 3803 91.2820 1 2800 1 chr7D.!!$F1 2799
6 TraesCS4A01G246700 chr6A 121722734 121725555 2821 True 3786 3786 91.1260 4 2800 1 chr6A.!!$R1 2796
7 TraesCS4A01G246700 chr3B 734911641 734914114 2473 True 3271 3271 90.7530 341 2800 1 chr3B.!!$R1 2459
8 TraesCS4A01G246700 chr3B 774402758 774405112 2354 False 2615 2615 87.2390 368 2681 1 chr3B.!!$F1 2313
9 TraesCS4A01G246700 chr3A 714788224 714790577 2353 False 2760 2760 88.2180 468 2800 1 chr3A.!!$F2 2332
10 TraesCS4A01G246700 chr3A 638853296 638855302 2006 True 2501 2501 89.6500 280 2241 1 chr3A.!!$R1 1961
11 TraesCS4A01G246700 chr3A 607845898 607847839 1941 False 2290 2290 88.4190 883 2800 1 chr3A.!!$F1 1917
12 TraesCS4A01G246700 chr1B 596175558 596178032 2474 False 1673 2732 92.3295 1 2503 2 chr1B.!!$F1 2502
13 TraesCS4A01G246700 chr4D 42333873 42335502 1629 False 2501 2501 94.6110 1 1606 1 chr4D.!!$F1 1605
14 TraesCS4A01G246700 chr7B 6998569 7001385 2816 False 1920 2176 91.4715 1 2800 2 chr7B.!!$F1 2799
15 TraesCS4A01G246700 chr2B 755329850 755331535 1685 False 1866 1866 87.0780 526 2215 1 chr2B.!!$F1 1689
16 TraesCS4A01G246700 chr3D 579688196 579689555 1359 False 1698 1698 89.8980 857 2169 1 chr3D.!!$F1 1312
17 TraesCS4A01G246700 chr2A 749651368 749652979 1611 False 1664 1664 85.5770 1164 2800 1 chr2A.!!$F1 1636
18 TraesCS4A01G246700 chr6D 68973814 68974930 1116 False 1604 1604 92.4980 1 1129 1 chr6D.!!$F1 1128

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
222 223 1.959085 GTGGCAATGGTCACCTGTG 59.041 57.895 0.0 0.0 43.89 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2059 2218 1.945394 CTTACATCATCAGCAGCACCC 59.055 52.381 0.0 0.0 0.0 4.61 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
222 223 1.959085 GTGGCAATGGTCACCTGTG 59.041 57.895 0.00 0.00 43.89 3.66
394 401 3.696051 GCAATGATCACCTGCTTTCCTTA 59.304 43.478 19.63 0.00 33.20 2.69
673 684 6.547880 TGTTTTTGTGGAGAATAAGTGGCTTA 59.452 34.615 0.00 0.00 0.00 3.09
1162 1211 9.241317 CTTTGTAATGATATTGGAATTGCTGTC 57.759 33.333 0.00 0.00 0.00 3.51
1355 1447 0.744771 GGAGCCCGACTTTGACCATC 60.745 60.000 0.00 0.00 0.00 3.51
1834 1975 4.062991 ACGACAAACCAGGTGACTTATTC 58.937 43.478 0.00 0.00 40.21 1.75
1897 2038 8.490355 GCTTTCAAATGGTCAGAGTTTAAATTG 58.510 33.333 0.00 0.00 0.00 2.32
1907 2048 7.805071 GGTCAGAGTTTAAATTGTGATCAGTTG 59.195 37.037 14.01 0.00 0.00 3.16
2059 2218 5.334319 TCTTCATTTGCAAATATGACTGCG 58.666 37.500 23.69 9.59 41.63 5.18
2454 2655 1.321743 CTGTCTTGAAGCGCGTATGAC 59.678 52.381 8.43 10.67 0.00 3.06
2470 2671 5.103000 CGTATGACTCGACTGATTTTCCTT 58.897 41.667 0.00 0.00 0.00 3.36
2736 2946 3.105203 CACGTTTTGTGTTCATGGTGAC 58.895 45.455 0.00 0.00 43.88 3.67
2772 2983 0.038983 TACTTGTGCGTGCGCTTCTA 60.039 50.000 17.49 7.09 42.51 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
222 223 6.361748 CCGTATGCGTTAATAGACTAAGGAAC 59.638 42.308 1.69 0.00 36.15 3.62
394 401 8.579850 TTTCTTCCAGTATGCATTGATAAACT 57.420 30.769 3.54 0.00 31.97 2.66
673 684 1.566298 GGAGGCCAGGACATCCACTT 61.566 60.000 5.01 0.00 40.28 3.16
730 741 8.924511 TTGATCTTCATTTCAAGAGGTTAGTT 57.075 30.769 0.00 0.00 35.83 2.24
1013 1035 1.352622 GGGTCCCATGATAGTGGCCA 61.353 60.000 0.00 0.00 37.96 5.36
1162 1211 3.081804 GGACCCCTAAGACATTTGTGTG 58.918 50.000 0.00 0.00 0.00 3.82
1355 1447 5.826737 AGGAATGCAGATCATTACCTTTGAG 59.173 40.000 0.00 0.00 45.31 3.02
1408 1500 5.500234 ACCAAGCTTATATCAGCAACAAGA 58.500 37.500 11.37 0.00 42.84 3.02
1834 1975 3.325870 TGATTTGTAGTCCTGCAACTCG 58.674 45.455 9.63 0.00 37.56 4.18
1907 2048 7.333672 AGGATTCGGTATAAAACAAGTCAGAAC 59.666 37.037 0.00 0.00 0.00 3.01
2059 2218 1.945394 CTTACATCATCAGCAGCACCC 59.055 52.381 0.00 0.00 0.00 4.61
2454 2655 3.929610 GAGGACAAGGAAAATCAGTCGAG 59.070 47.826 0.00 0.00 0.00 4.04
2470 2671 0.599558 AAACGGACGAATCGAGGACA 59.400 50.000 10.55 0.00 0.00 4.02
2730 2940 1.676968 CAGGAACCATCGGTCACCA 59.323 57.895 0.00 0.00 33.12 4.17
2736 2946 0.725117 GTAAACGCAGGAACCATCGG 59.275 55.000 8.86 0.00 0.00 4.18
2772 2983 6.634035 CACGAAACGCATGATCATGAAATAAT 59.366 34.615 34.65 16.84 41.20 1.28


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

AutoCloner maintained by Alex Coulton.