Multiple sequence alignment - TraesCS5A01G512600

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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 TraesCS5A01G512600 chr5A 100.000 1427 0 0 844 2270 676814146 676815572 0.000000e+00 2636.0
1 TraesCS5A01G512600 chr5A 91.096 876 45 6 873 1716 573791703 573792577 0.000000e+00 1155.0
2 TraesCS5A01G512600 chr5A 100.000 402 0 0 1 402 676813303 676813704 0.000000e+00 743.0
3 TraesCS5A01G512600 chr5A 89.455 275 18 3 1878 2142 573792864 573793137 1.000000e-88 337.0
4 TraesCS5A01G512600 chr7A 96.322 1305 38 6 845 2142 58358647 58359948 0.000000e+00 2135.0
5 TraesCS5A01G512600 chr7A 95.720 701 27 1 873 1573 735979271 735978574 0.000000e+00 1125.0
6 TraesCS5A01G512600 chr7A 92.857 588 35 5 1558 2142 735978188 735977605 0.000000e+00 846.0
7 TraesCS5A01G512600 chr7A 96.278 403 14 1 1 402 58358143 58358545 0.000000e+00 660.0
8 TraesCS5A01G512600 chr7A 93.069 404 26 2 1 402 735979837 735979434 6.980000e-165 590.0
9 TraesCS5A01G512600 chr7A 97.163 141 3 1 2130 2270 58359977 58360116 1.050000e-58 237.0
10 TraesCS5A01G512600 chr7A 93.836 146 9 0 2124 2269 201971013 201971158 1.060000e-53 220.0
11 TraesCS5A01G512600 chr1A 93.005 915 50 6 873 1782 564251612 564252517 0.000000e+00 1323.0
12 TraesCS5A01G512600 chr1A 94.813 694 36 0 873 1566 564260334 564259641 0.000000e+00 1083.0
13 TraesCS5A01G512600 chr1A 94.118 408 18 2 1 402 588666129 588665722 1.150000e-172 616.0
14 TraesCS5A01G512600 chr1A 93.069 404 26 2 1 402 564251046 564251449 6.980000e-165 590.0
15 TraesCS5A01G512600 chr1A 86.519 497 42 7 1798 2270 515249936 515249441 7.180000e-145 523.0
16 TraesCS5A01G512600 chr1A 96.429 196 7 0 1947 2142 564252935 564253130 7.820000e-85 324.0
17 TraesCS5A01G512600 chr1A 95.918 196 8 0 1947 2142 564258690 564258495 3.640000e-83 318.0
18 TraesCS5A01G512600 chr1A 96.528 144 5 0 2127 2270 564258468 564258325 2.910000e-59 239.0
19 TraesCS5A01G512600 chr1A 97.080 137 4 0 2134 2270 564253164 564253300 4.880000e-57 231.0
20 TraesCS5A01G512600 chr3A 94.256 853 34 7 881 1722 702487635 702486787 0.000000e+00 1290.0
21 TraesCS5A01G512600 chr3A 95.519 781 25 7 873 1651 737722514 737721742 0.000000e+00 1240.0
22 TraesCS5A01G512600 chr3A 93.711 636 30 7 1514 2142 737721390 737720758 0.000000e+00 944.0
23 TraesCS5A01G512600 chr3A 94.059 404 22 2 1 402 737723085 737722682 1.490000e-171 612.0
24 TraesCS5A01G512600 chr3A 93.317 404 25 2 1 402 702488209 702487806 1.500000e-166 595.0
25 TraesCS5A01G512600 chr3A 96.350 137 5 0 2134 2270 702486221 702486085 2.270000e-55 226.0
26 TraesCS5A01G512600 chr4A 95.379 779 31 3 873 1650 29434926 29435700 0.000000e+00 1234.0
27 TraesCS5A01G512600 chr4A 94.228 589 23 9 1560 2142 29436149 29436732 0.000000e+00 889.0
28 TraesCS5A01G512600 chr4A 94.015 401 22 2 4 402 556010686 556010286 6.930000e-170 606.0
29 TraesCS5A01G512600 chr4A 94.149 188 10 1 1955 2142 556009077 556008891 3.690000e-73 285.0
30 TraesCS5A01G512600 chr4A 97.080 137 3 1 2134 2270 29436767 29436902 1.750000e-56 230.0
31 TraesCS5A01G512600 chr2A 96.180 733 23 2 873 1603 52604814 52604085 0.000000e+00 1194.0
32 TraesCS5A01G512600 chr2A 92.320 625 26 10 1524 2142 52603740 52603132 0.000000e+00 869.0
33 TraesCS5A01G512600 chr2A 96.241 399 13 2 1 397 52605361 52604963 0.000000e+00 652.0
34 TraesCS5A01G512600 chr2A 94.307 404 21 2 1 402 161588606 161588203 3.200000e-173 617.0
35 TraesCS5A01G512600 chr2A 95.213 188 8 1 1955 2142 161586961 161586775 1.700000e-76 296.0
36 TraesCS5A01G512600 chr2A 96.377 138 5 0 2133 2270 767475835 767475698 6.310000e-56 228.0
37 TraesCS5A01G512600 chr2A 96.324 136 4 1 2135 2270 52603097 52602963 2.930000e-54 222.0
38 TraesCS5A01G512600 chr2A 95.833 48 2 0 1836 1883 52603377 52603330 6.720000e-11 78.7


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 TraesCS5A01G512600 chr5A 676813303 676815572 2269 False 1689.500000 2636 100.000000 1 2270 2 chr5A.!!$F2 2269
1 TraesCS5A01G512600 chr5A 573791703 573793137 1434 False 746.000000 1155 90.275500 873 2142 2 chr5A.!!$F1 1269
2 TraesCS5A01G512600 chr7A 58358143 58360116 1973 False 1010.666667 2135 96.587667 1 2270 3 chr7A.!!$F2 2269
3 TraesCS5A01G512600 chr7A 735977605 735979837 2232 True 853.666667 1125 93.882000 1 2142 3 chr7A.!!$R1 2141
4 TraesCS5A01G512600 chr1A 564251046 564253300 2254 False 617.000000 1323 94.895750 1 2270 4 chr1A.!!$F1 2269
5 TraesCS5A01G512600 chr1A 564258325 564260334 2009 True 546.666667 1083 95.753000 873 2270 3 chr1A.!!$R3 1397
6 TraesCS5A01G512600 chr3A 737720758 737723085 2327 True 932.000000 1240 94.429667 1 2142 3 chr3A.!!$R2 2141
7 TraesCS5A01G512600 chr3A 702486085 702488209 2124 True 703.666667 1290 94.641000 1 2270 3 chr3A.!!$R1 2269
8 TraesCS5A01G512600 chr4A 29434926 29436902 1976 False 784.333333 1234 95.562333 873 2270 3 chr4A.!!$F1 1397
9 TraesCS5A01G512600 chr4A 556008891 556010686 1795 True 445.500000 606 94.082000 4 2142 2 chr4A.!!$R1 2138
10 TraesCS5A01G512600 chr2A 52602963 52605361 2398 True 603.140000 1194 95.379600 1 2270 5 chr2A.!!$R2 2269
11 TraesCS5A01G512600 chr2A 161586775 161588606 1831 True 456.500000 617 94.760000 1 2142 2 chr2A.!!$R3 2141

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
1224 1305 0.179156 ACGACAACGATAACGGCGAT 60.179 50.0 16.62 3.59 44.46 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2104 4138 9.069078 CAATGCAAAGTCAACTCACATTATTAG 57.931 33.333 0.0 0.0 0.0 1.73 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
1224 1305 0.179156 ACGACAACGATAACGGCGAT 60.179 50.000 16.62 3.59 44.46 4.58
1445 1526 8.563732 TGAACAATCAAGTGTTGAAATCGATAA 58.436 29.630 0.00 0.00 43.95 1.75
1814 3808 3.067684 AGCCTATTTAAACTGGTGCGT 57.932 42.857 9.27 0.00 0.00 5.24
1975 3997 3.916438 TAGTGGGCCGCTGGAAGGA 62.916 63.158 29.35 5.26 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
189 190 3.643554 GTTGGGGCGTACTGGGGT 61.644 66.667 0.00 0.00 0.00 4.95
1006 1057 4.129737 GAGCGCCGTCAGGTAGCA 62.130 66.667 2.29 0.00 42.67 3.49
1790 3535 4.857037 CGCACCAGTTTAAATAGGCTTTTC 59.143 41.667 0.00 0.00 0.00 2.29
1795 3540 2.731027 GCACGCACCAGTTTAAATAGGC 60.731 50.000 8.36 1.01 0.00 3.93
2104 4138 9.069078 CAATGCAAAGTCAACTCACATTATTAG 57.931 33.333 0.00 0.00 0.00 1.73


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

AutoCloner maintained by Alex Coulton.