Multiple sequence alignment - TraesCS4A01G182200

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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 TraesCS4A01G182200 chr4A 100.000 2456 0 0 1 2456 457567303 457569758 0.000000e+00 4536.0
1 TraesCS4A01G182200 chr4A 99.072 1509 12 1 1 1507 456335313 456336821 0.000000e+00 2708.0
2 TraesCS4A01G182200 chr4A 98.119 957 12 4 1502 2456 713515675 713516627 0.000000e+00 1663.0
3 TraesCS4A01G182200 chr4A 84.579 629 77 10 882 1507 456293850 456294461 7.510000e-170 606.0
4 TraesCS4A01G182200 chr4B 93.778 1318 61 12 202 1507 179750346 179751654 0.000000e+00 1960.0
5 TraesCS4A01G182200 chr4B 96.653 956 22 5 1508 2456 96269686 96268734 0.000000e+00 1580.0
6 TraesCS4A01G182200 chr4B 87.174 499 55 6 1009 1507 179842567 179842078 2.130000e-155 558.0
7 TraesCS4A01G182200 chr4B 94.203 207 11 1 7 213 179749894 179750099 5.100000e-82 315.0
8 TraesCS4A01G182200 chr4D 94.918 1220 47 10 298 1510 117663748 117662537 0.000000e+00 1895.0
9 TraesCS4A01G182200 chr4D 88.978 499 49 4 1009 1507 117706361 117705869 1.610000e-171 612.0
10 TraesCS4A01G182200 chr4D 93.870 261 13 1 2 262 117664004 117663747 8.230000e-105 390.0
11 TraesCS4A01G182200 chr4D 79.839 124 21 4 204 324 470797380 470797502 1.210000e-13 87.9
12 TraesCS4A01G182200 chr4D 92.453 53 3 1 259 311 379776490 379776541 9.420000e-10 75.0
13 TraesCS4A01G182200 chr3A 99.370 953 5 1 1504 2456 371159537 371158586 0.000000e+00 1725.0
14 TraesCS4A01G182200 chr1B 97.053 950 25 2 1508 2456 7370686 7369739 0.000000e+00 1596.0
15 TraesCS4A01G182200 chr1B 77.273 616 91 26 1506 2087 207853757 207854357 1.420000e-82 316.0
16 TraesCS4A01G182200 chr5B 95.474 950 27 6 1508 2456 534992476 534991542 0.000000e+00 1502.0
17 TraesCS4A01G182200 chr6D 91.693 951 51 9 1506 2455 448570262 448571185 0.000000e+00 1293.0
18 TraesCS4A01G182200 chrUn 90.986 588 29 9 1556 2135 112560770 112561341 0.000000e+00 771.0
19 TraesCS4A01G182200 chrUn 94.406 286 8 5 2171 2456 112561344 112561621 1.350000e-117 433.0
20 TraesCS4A01G182200 chrUn 88.496 113 12 1 239 350 287774911 287775023 4.260000e-28 135.0
21 TraesCS4A01G182200 chrUn 88.496 113 12 1 239 350 297964067 297964179 4.260000e-28 135.0
22 TraesCS4A01G182200 chr7B 82.614 880 109 33 1563 2425 64842867 64843719 0.000000e+00 737.0
23 TraesCS4A01G182200 chr7B 83.333 576 75 10 903 1470 700630470 700629908 1.680000e-141 512.0
24 TraesCS4A01G182200 chr1A 87.958 573 31 14 1540 2101 507755370 507754825 2.060000e-180 641.0
25 TraesCS4A01G182200 chr7D 81.422 689 95 19 831 1504 611445297 611444627 1.290000e-147 532.0
26 TraesCS4A01G182200 chr7D 81.975 638 78 14 843 1471 611459241 611458632 7.840000e-140 507.0
27 TraesCS4A01G182200 chr7A 81.599 663 81 17 860 1507 701428408 701427772 6.060000e-141 510.0
28 TraesCS4A01G182200 chr6B 77.336 578 87 18 1506 2052 715311510 715310946 3.970000e-78 302.0
29 TraesCS4A01G182200 chr2B 84.034 119 15 2 235 350 109955446 109955329 7.180000e-21 111.0


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 TraesCS4A01G182200 chr4A 457567303 457569758 2455 False 4536.0 4536 100.0000 1 2456 1 chr4A.!!$F3 2455
1 TraesCS4A01G182200 chr4A 456335313 456336821 1508 False 2708.0 2708 99.0720 1 1507 1 chr4A.!!$F2 1506
2 TraesCS4A01G182200 chr4A 713515675 713516627 952 False 1663.0 1663 98.1190 1502 2456 1 chr4A.!!$F4 954
3 TraesCS4A01G182200 chr4A 456293850 456294461 611 False 606.0 606 84.5790 882 1507 1 chr4A.!!$F1 625
4 TraesCS4A01G182200 chr4B 96268734 96269686 952 True 1580.0 1580 96.6530 1508 2456 1 chr4B.!!$R1 948
5 TraesCS4A01G182200 chr4B 179749894 179751654 1760 False 1137.5 1960 93.9905 7 1507 2 chr4B.!!$F1 1500
6 TraesCS4A01G182200 chr4D 117662537 117664004 1467 True 1142.5 1895 94.3940 2 1510 2 chr4D.!!$R2 1508
7 TraesCS4A01G182200 chr3A 371158586 371159537 951 True 1725.0 1725 99.3700 1504 2456 1 chr3A.!!$R1 952
8 TraesCS4A01G182200 chr1B 7369739 7370686 947 True 1596.0 1596 97.0530 1508 2456 1 chr1B.!!$R1 948
9 TraesCS4A01G182200 chr1B 207853757 207854357 600 False 316.0 316 77.2730 1506 2087 1 chr1B.!!$F1 581
10 TraesCS4A01G182200 chr5B 534991542 534992476 934 True 1502.0 1502 95.4740 1508 2456 1 chr5B.!!$R1 948
11 TraesCS4A01G182200 chr6D 448570262 448571185 923 False 1293.0 1293 91.6930 1506 2455 1 chr6D.!!$F1 949
12 TraesCS4A01G182200 chrUn 112560770 112561621 851 False 602.0 771 92.6960 1556 2456 2 chrUn.!!$F3 900
13 TraesCS4A01G182200 chr7B 64842867 64843719 852 False 737.0 737 82.6140 1563 2425 1 chr7B.!!$F1 862
14 TraesCS4A01G182200 chr7B 700629908 700630470 562 True 512.0 512 83.3330 903 1470 1 chr7B.!!$R1 567
15 TraesCS4A01G182200 chr1A 507754825 507755370 545 True 641.0 641 87.9580 1540 2101 1 chr1A.!!$R1 561
16 TraesCS4A01G182200 chr7D 611444627 611445297 670 True 532.0 532 81.4220 831 1504 1 chr7D.!!$R1 673
17 TraesCS4A01G182200 chr7D 611458632 611459241 609 True 507.0 507 81.9750 843 1471 1 chr7D.!!$R2 628
18 TraesCS4A01G182200 chr7A 701427772 701428408 636 True 510.0 510 81.5990 860 1507 1 chr7A.!!$R1 647
19 TraesCS4A01G182200 chr6B 715310946 715311510 564 True 302.0 302 77.3360 1506 2052 1 chr6B.!!$R1 546

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
935 1236 0.323178 CAAGCTGCCAGATCCCAACT 60.323 55.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2187 2576 0.683973 CAGAGCTGGAACTGGTGAGT 59.316 55.0 0.0 0.0 38.32 3.41 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
410 681 1.203758 TCGTGCGTCAATGGTGATAGT 59.796 47.619 0.00 0.0 35.80 2.12
935 1236 0.323178 CAAGCTGCCAGATCCCAACT 60.323 55.000 0.00 0.0 0.00 3.16
936 1237 1.065199 CAAGCTGCCAGATCCCAACTA 60.065 52.381 0.00 0.0 0.00 2.24
937 1238 0.835941 AGCTGCCAGATCCCAACTAG 59.164 55.000 0.00 0.0 0.00 2.57
938 1239 0.817229 GCTGCCAGATCCCAACTAGC 60.817 60.000 0.00 0.0 0.00 3.42
1053 1359 1.153823 CTTCGACAAGGACGGCGAT 60.154 57.895 16.62 0.0 32.38 4.58
1301 1625 2.181021 GGAAGCCACGACGACGAT 59.819 61.111 15.32 0.0 42.66 3.73
1475 1800 4.210331 TGATCATCGACTCTCTTCATGGA 58.790 43.478 0.00 0.0 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
364 628 3.800440 GCGAAAATGCTACGCCTAC 57.200 52.632 0.00 0.00 45.35 3.18
1053 1359 4.980805 GACGCGGACACCTTGCCA 62.981 66.667 12.47 0.00 0.00 4.92
1301 1625 1.299850 CTCGCCGGCGTAATCATCA 60.300 57.895 44.16 24.29 40.74 3.07
2187 2576 0.683973 CAGAGCTGGAACTGGTGAGT 59.316 55.000 0.00 0.00 38.32 3.41


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

AutoCloner maintained by Alex Coulton.