Multiple sequence alignment - TraesCS5B01G241500

Loading Multiple Alignment...

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 TraesCS5B01G241500 chr5B 100.000 3158 0 0 1 3158 421498445 421501602 0.000000e+00 5832.0
1 TraesCS5B01G241500 chr5A 94.507 1966 61 14 917 2865 456099974 456098039 0.000000e+00 2988.0
2 TraesCS5B01G241500 chr5A 89.879 494 31 6 394 870 456104005 456103514 4.480000e-173 617.0
3 TraesCS5B01G241500 chr5D 94.118 1836 56 18 905 2732 356636714 356638505 0.000000e+00 2745.0
4 TraesCS5B01G241500 chr5D 95.200 125 6 0 2743 2867 356639517 356639641 6.910000e-47 198.0
5 TraesCS5B01G241500 chr5D 87.248 149 13 1 2868 3010 375171733 375171881 7.010000e-37 165.0
6 TraesCS5B01G241500 chr5D 85.276 163 15 5 2862 3017 375164631 375164791 3.260000e-35 159.0
7 TraesCS5B01G241500 chr6B 76.386 1317 284 20 985 2292 52981060 52979762 0.000000e+00 684.0
8 TraesCS5B01G241500 chr6B 76.763 1205 253 21 997 2189 62389795 62390984 0.000000e+00 649.0
9 TraesCS5B01G241500 chr6B 76.331 1183 259 16 985 2158 52568258 52567088 5.790000e-172 614.0
10 TraesCS5B01G241500 chr6B 75.896 1228 255 34 983 2189 53077159 53075952 9.760000e-165 590.0
11 TraesCS5B01G241500 chr6B 75.853 1172 264 14 995 2158 16429001 16430161 2.110000e-161 579.0
12 TraesCS5B01G241500 chr6B 75.242 1240 275 23 963 2185 53062549 53061325 7.650000e-156 560.0
13 TraesCS5B01G241500 chr6B 75.126 1186 254 33 999 2166 670533459 670532297 4.670000e-143 518.0
14 TraesCS5B01G241500 chr6B 78.278 778 147 18 1521 2287 16339500 16340266 6.130000e-132 481.0
15 TraesCS5B01G241500 chr6B 76.744 774 174 6 1418 2189 15219322 15218553 8.090000e-116 427.0
16 TraesCS5B01G241500 chr6A 77.660 1128 212 29 993 2102 9336035 9337140 0.000000e+00 651.0
17 TraesCS5B01G241500 chr6A 76.159 1208 241 20 999 2183 18732376 18733559 2.710000e-165 592.0
18 TraesCS5B01G241500 chr6D 76.777 1210 247 22 997 2183 18001615 18000417 0.000000e+00 647.0
19 TraesCS5B01G241500 chr6D 76.409 1153 249 19 997 2136 16775747 16774605 4.510000e-168 601.0
20 TraesCS5B01G241500 chr6D 95.294 85 4 0 3052 3136 459281086 459281002 5.490000e-28 135.0
21 TraesCS5B01G241500 chr1B 76.697 1090 230 20 1116 2192 27678003 27676925 4.540000e-163 584.0
22 TraesCS5B01G241500 chr1B 74.490 1372 309 37 984 2337 662153016 662154364 9.890000e-155 556.0
23 TraesCS5B01G241500 chr1A 76.083 1154 241 28 999 2137 589248496 589247363 1.270000e-158 569.0
24 TraesCS5B01G241500 chr1A 85.906 149 14 3 2868 3010 498800914 498801061 5.460000e-33 152.0
25 TraesCS5B01G241500 chr7A 96.970 297 3 1 2868 3158 692900718 692901014 7.870000e-136 494.0
26 TraesCS5B01G241500 chr2A 85.953 299 36 4 2865 3158 696279544 696279841 6.580000e-82 315.0
27 TraesCS5B01G241500 chr2A 85.522 297 36 5 2868 3158 20273381 20273086 1.420000e-78 303.0
28 TraesCS5B01G241500 chr2A 85.475 179 16 7 2868 3038 690320023 690320199 9.000000e-41 178.0
29 TraesCS5B01G241500 chr3D 87.931 174 19 2 2867 3038 590161450 590161277 1.480000e-48 204.0
30 TraesCS5B01G241500 chrUn 80.672 238 37 6 2108 2344 42220936 42220707 3.240000e-40 176.0
31 TraesCS5B01G241500 chr4B 87.919 149 12 1 2868 3010 106494318 106494466 1.510000e-38 171.0
32 TraesCS5B01G241500 chr4A 100.000 33 0 0 777 809 676910386 676910418 9.460000e-06 62.1


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 TraesCS5B01G241500 chr5B 421498445 421501602 3157 False 5832.0 5832 100.000 1 3158 1 chr5B.!!$F1 3157
1 TraesCS5B01G241500 chr5A 456098039 456104005 5966 True 1802.5 2988 92.193 394 2865 2 chr5A.!!$R1 2471
2 TraesCS5B01G241500 chr5D 356636714 356639641 2927 False 1471.5 2745 94.659 905 2867 2 chr5D.!!$F3 1962
3 TraesCS5B01G241500 chr6B 52979762 52981060 1298 True 684.0 684 76.386 985 2292 1 chr6B.!!$R3 1307
4 TraesCS5B01G241500 chr6B 62389795 62390984 1189 False 649.0 649 76.763 997 2189 1 chr6B.!!$F3 1192
5 TraesCS5B01G241500 chr6B 52567088 52568258 1170 True 614.0 614 76.331 985 2158 1 chr6B.!!$R2 1173
6 TraesCS5B01G241500 chr6B 53075952 53077159 1207 True 590.0 590 75.896 983 2189 1 chr6B.!!$R5 1206
7 TraesCS5B01G241500 chr6B 16429001 16430161 1160 False 579.0 579 75.853 995 2158 1 chr6B.!!$F2 1163
8 TraesCS5B01G241500 chr6B 53061325 53062549 1224 True 560.0 560 75.242 963 2185 1 chr6B.!!$R4 1222
9 TraesCS5B01G241500 chr6B 670532297 670533459 1162 True 518.0 518 75.126 999 2166 1 chr6B.!!$R6 1167
10 TraesCS5B01G241500 chr6B 16339500 16340266 766 False 481.0 481 78.278 1521 2287 1 chr6B.!!$F1 766
11 TraesCS5B01G241500 chr6B 15218553 15219322 769 True 427.0 427 76.744 1418 2189 1 chr6B.!!$R1 771
12 TraesCS5B01G241500 chr6A 9336035 9337140 1105 False 651.0 651 77.660 993 2102 1 chr6A.!!$F1 1109
13 TraesCS5B01G241500 chr6A 18732376 18733559 1183 False 592.0 592 76.159 999 2183 1 chr6A.!!$F2 1184
14 TraesCS5B01G241500 chr6D 18000417 18001615 1198 True 647.0 647 76.777 997 2183 1 chr6D.!!$R2 1186
15 TraesCS5B01G241500 chr6D 16774605 16775747 1142 True 601.0 601 76.409 997 2136 1 chr6D.!!$R1 1139
16 TraesCS5B01G241500 chr1B 27676925 27678003 1078 True 584.0 584 76.697 1116 2192 1 chr1B.!!$R1 1076
17 TraesCS5B01G241500 chr1B 662153016 662154364 1348 False 556.0 556 74.490 984 2337 1 chr1B.!!$F1 1353
18 TraesCS5B01G241500 chr1A 589247363 589248496 1133 True 569.0 569 76.083 999 2137 1 chr1A.!!$R1 1138


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
264 265 0.032678 CGAGGCAGCAGATACGGAAT 59.967 55.0 0.00 0.0 0.00 3.01 F
363 364 0.098376 GAACGCGTCCTAGTCATCGT 59.902 55.0 14.44 0.0 0.00 3.73 F
591 592 0.108138 GTATGAGCGCTTCAGGTGGT 60.108 55.0 13.26 0.0 39.68 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1293 4855 0.322816 AGAGTAACCGCGGGTCAGTA 60.323 55.000 31.76 4.12 33.12 2.74 R
1519 5087 0.472471 ACCACCTTGTCGATGTTGGT 59.528 50.000 0.00 0.00 0.00 3.67 R
2517 6096 1.480137 AGGACTCAGACATAGCAGTGC 59.520 52.381 7.13 7.13 0.00 4.40 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)



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

AutoCloner maintained by Alex Coulton.