Multiple sequence alignment - TraesCS7D01G180300

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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 TraesCS7D01G180300 chr7D 100.000 3205 0 0 1 3205 133491063 133494267 0.000000e+00 5919.0
1 TraesCS7D01G180300 chr7D 99.438 3205 16 2 1 3205 133613435 133610233 0.000000e+00 5818.0
2 TraesCS7D01G180300 chr7D 93.836 1314 67 10 928 2236 133827095 133828399 0.000000e+00 1965.0
3 TraesCS7D01G180300 chr7D 92.523 107 7 1 2246 2352 133828445 133828550 5.540000e-33 152.0
4 TraesCS7D01G180300 chr7A 92.321 2266 134 22 1 2244 132412722 132410475 0.000000e+00 3184.0
5 TraesCS7D01G180300 chr7A 93.619 1332 65 9 928 2240 132618875 132620205 0.000000e+00 1971.0
6 TraesCS7D01G180300 chr7A 92.523 107 7 1 2246 2352 132620245 132620350 5.540000e-33 152.0
7 TraesCS7D01G180300 chr7B 93.610 1565 70 10 600 2152 94811397 94809851 0.000000e+00 2309.0
8 TraesCS7D01G180300 chr7B 94.100 1322 64 8 937 2248 95046571 95045254 0.000000e+00 1997.0
9 TraesCS7D01G180300 chr7B 85.885 418 53 5 329 744 94932979 94932566 1.060000e-119 440.0
10 TraesCS7D01G180300 chr7B 92.245 245 18 1 986 1230 94922136 94921893 2.370000e-91 346.0
11 TraesCS7D01G180300 chr7B 83.462 260 31 5 743 992 94932748 94932491 6.910000e-57 231.0
12 TraesCS7D01G180300 chr7B 85.167 209 30 1 1 209 186813833 186814040 2.500000e-51 213.0
13 TraesCS7D01G180300 chr7B 93.750 112 6 1 2241 2352 94808828 94808718 1.980000e-37 167.0
14 TraesCS7D01G180300 chr7B 96.923 65 2 0 2152 2216 94809322 94809258 3.380000e-20 110.0
15 TraesCS7D01G180300 chrUn 100.000 1174 0 0 1138 2311 429907488 429906315 0.000000e+00 2169.0
16 TraesCS7D01G180300 chrUn 90.909 121 11 0 2391 2511 41586492 41586612 2.560000e-36 163.0
17 TraesCS7D01G180300 chr2D 96.324 816 25 4 2392 3205 599214428 599215240 0.000000e+00 1336.0
18 TraesCS7D01G180300 chr2A 92.857 700 36 10 2514 3205 105546179 105546872 0.000000e+00 1003.0
19 TraesCS7D01G180300 chr2A 90.123 567 42 10 2648 3205 49424218 49424779 0.000000e+00 725.0
20 TraesCS7D01G180300 chr2A 94.215 121 7 0 2393 2513 44088429 44088309 5.460000e-43 185.0
21 TraesCS7D01G180300 chr6D 91.810 696 52 4 2513 3205 12662044 12661351 0.000000e+00 965.0
22 TraesCS7D01G180300 chr3A 87.893 826 70 17 2392 3205 651595073 651594266 0.000000e+00 944.0
23 TraesCS7D01G180300 chr3A 92.683 123 9 0 2391 2513 555406354 555406232 9.140000e-41 178.0
24 TraesCS7D01G180300 chr3A 78.995 219 37 7 31 248 466039089 466039299 1.200000e-29 141.0
25 TraesCS7D01G180300 chr5B 90.636 566 42 7 2648 3205 517547561 517548123 0.000000e+00 741.0
26 TraesCS7D01G180300 chr5B 92.623 122 9 0 2392 2513 459417373 459417494 3.290000e-40 176.0
27 TraesCS7D01G180300 chr5B 91.597 119 10 0 2392 2510 655020120 655020002 7.110000e-37 165.0
28 TraesCS7D01G180300 chr5B 76.577 222 45 3 31 251 513378630 513378415 7.270000e-22 115.0
29 TraesCS7D01G180300 chr4A 90.747 562 41 11 2646 3203 538896146 538896700 0.000000e+00 739.0
30 TraesCS7D01G180300 chr3B 89.912 565 42 12 2646 3203 776951198 776950642 0.000000e+00 713.0
31 TraesCS7D01G180300 chr6B 80.828 845 135 11 1201 2042 611500191 611501011 3.490000e-179 638.0
32 TraesCS7D01G180300 chr6A 80.896 848 129 16 1201 2042 553055019 553055839 3.490000e-179 638.0
33 TraesCS7D01G180300 chr5A 94.215 121 7 0 2393 2513 34693940 34693820 5.460000e-43 185.0
34 TraesCS7D01G180300 chr5A 91.304 69 6 0 2514 2582 38034190 38034258 9.470000e-16 95.3
35 TraesCS7D01G180300 chr2B 91.057 123 9 2 2392 2513 752853848 752853727 7.110000e-37 165.0
36 TraesCS7D01G180300 chr3D 97.674 43 0 1 2352 2393 466382165 466382123 4.430000e-09 73.1


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 TraesCS7D01G180300 chr7D 133491063 133494267 3204 False 5919.0 5919 100.0000 1 3205 1 chr7D.!!$F1 3204
1 TraesCS7D01G180300 chr7D 133610233 133613435 3202 True 5818.0 5818 99.4380 1 3205 1 chr7D.!!$R1 3204
2 TraesCS7D01G180300 chr7D 133827095 133828550 1455 False 1058.5 1965 93.1795 928 2352 2 chr7D.!!$F2 1424
3 TraesCS7D01G180300 chr7A 132410475 132412722 2247 True 3184.0 3184 92.3210 1 2244 1 chr7A.!!$R1 2243
4 TraesCS7D01G180300 chr7A 132618875 132620350 1475 False 1061.5 1971 93.0710 928 2352 2 chr7A.!!$F1 1424
5 TraesCS7D01G180300 chr7B 95045254 95046571 1317 True 1997.0 1997 94.1000 937 2248 1 chr7B.!!$R2 1311
6 TraesCS7D01G180300 chr7B 94808718 94811397 2679 True 862.0 2309 94.7610 600 2352 3 chr7B.!!$R3 1752
7 TraesCS7D01G180300 chrUn 429906315 429907488 1173 True 2169.0 2169 100.0000 1138 2311 1 chrUn.!!$R1 1173
8 TraesCS7D01G180300 chr2D 599214428 599215240 812 False 1336.0 1336 96.3240 2392 3205 1 chr2D.!!$F1 813
9 TraesCS7D01G180300 chr2A 105546179 105546872 693 False 1003.0 1003 92.8570 2514 3205 1 chr2A.!!$F2 691
10 TraesCS7D01G180300 chr2A 49424218 49424779 561 False 725.0 725 90.1230 2648 3205 1 chr2A.!!$F1 557
11 TraesCS7D01G180300 chr6D 12661351 12662044 693 True 965.0 965 91.8100 2513 3205 1 chr6D.!!$R1 692
12 TraesCS7D01G180300 chr3A 651594266 651595073 807 True 944.0 944 87.8930 2392 3205 1 chr3A.!!$R2 813
13 TraesCS7D01G180300 chr5B 517547561 517548123 562 False 741.0 741 90.6360 2648 3205 1 chr5B.!!$F2 557
14 TraesCS7D01G180300 chr4A 538896146 538896700 554 False 739.0 739 90.7470 2646 3203 1 chr4A.!!$F1 557
15 TraesCS7D01G180300 chr3B 776950642 776951198 556 True 713.0 713 89.9120 2646 3203 1 chr3B.!!$R1 557
16 TraesCS7D01G180300 chr6B 611500191 611501011 820 False 638.0 638 80.8280 1201 2042 1 chr6B.!!$F1 841
17 TraesCS7D01G180300 chr6A 553055019 553055839 820 False 638.0 638 80.8960 1201 2042 1 chr6A.!!$F1 841

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
502 517 2.348411 ATTTTCTAGGACGGCCCATG 57.652 50.0 1.76 0.0 37.41 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2390 3418 2.286872 TCCGGTAAAAACGAGTTTGCA 58.713 42.857 0.0 0.0 32.36 4.08 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
174 175 4.980805 GTGTTCGCACCTCGGGCA 62.981 66.667 0.00 0.0 42.08 5.36
502 517 2.348411 ATTTTCTAGGACGGCCCATG 57.652 50.000 1.76 0.0 37.41 3.66
572 587 5.628797 TCACTGGACAATGGCTAATGATA 57.371 39.130 0.00 0.0 0.00 2.15
819 835 2.367567 AGACTAACGGTTCACCACATGT 59.632 45.455 0.00 0.0 35.14 3.21
859 875 3.262686 GGGAACGAATCGAGCGGC 61.263 66.667 10.55 0.0 0.00 6.53
2311 3339 4.505922 GTGGTGAAGCTTATCTCATCTTCG 59.494 45.833 0.00 0.0 38.14 3.79
2390 3418 4.575973 GCGCCATGCTCCCATCCT 62.576 66.667 0.00 0.0 41.73 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 2.331893 CGCGGGAGGTCATTTGCAA 61.332 57.895 0.00 0.0 0.00 4.08
502 517 1.145803 GTGTGTTGTTCGGGCTAGAC 58.854 55.000 0.00 0.0 0.00 2.59
572 587 2.294449 TGAGTGACTGCTAGGTGAGT 57.706 50.000 0.00 0.0 0.00 3.41
819 835 0.179009 AGCTCACTTTTGCCTGCTGA 60.179 50.000 0.00 0.0 0.00 4.26
878 894 0.460284 CCGCAATTCTAGAGCACCGT 60.460 55.000 3.66 0.0 0.00 4.83
2390 3418 2.286872 TCCGGTAAAAACGAGTTTGCA 58.713 42.857 0.00 0.0 32.36 4.08


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

AutoCloner maintained by Alex Coulton.