Multiple sequence alignment - TraesCS7A01G523300

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 TraesCS7A01G523300 chr7A 100.000 2563 0 0 1 2563 706003652 706001090 0.000000e+00 4734
1 TraesCS7A01G523300 chr7A 94.639 2052 67 5 1 2029 705969386 705967355 0.000000e+00 3140
2 TraesCS7A01G523300 chr7A 91.877 714 47 8 1304 2007 705938981 705938269 0.000000e+00 987
3 TraesCS7A01G523300 chr7A 88.797 607 54 5 707 1311 705939614 705939020 0.000000e+00 732
4 TraesCS7A01G523300 chr7A 94.479 163 7 2 2033 2194 83174313 83174474 1.520000e-62 250
5 TraesCS7A01G523300 chr7A 93.902 164 8 2 2032 2194 55542959 55542797 1.970000e-61 246
6 TraesCS7A01G523300 chr7A 93.413 167 9 2 2029 2194 731730531 731730696 1.970000e-61 246
7 TraesCS7A01G523300 chr7A 84.821 112 15 2 414 524 577062093 577062203 7.500000e-21 111
8 TraesCS7A01G523300 chr5D 95.786 1495 56 3 544 2032 19747672 19746179 0.000000e+00 2405
9 TraesCS7A01G523300 chr5D 89.173 508 29 3 1 483 19763703 19763197 6.060000e-171 610
10 TraesCS7A01G523300 chr5D 95.263 380 18 0 2184 2563 198401160 198400781 1.010000e-168 603
11 TraesCS7A01G523300 chr5D 94.960 377 19 0 2187 2563 198338007 198337631 2.200000e-165 592
12 TraesCS7A01G523300 chr7B 88.692 1521 129 20 524 2013 705465982 705464474 0.000000e+00 1816
13 TraesCS7A01G523300 chr7B 90.160 1250 93 8 1 1225 705520028 705518784 0.000000e+00 1600
14 TraesCS7A01G523300 chr7B 94.510 765 37 3 1272 2032 705518785 705518022 0.000000e+00 1175
15 TraesCS7A01G523300 chr7B 85.811 148 15 6 1 145 436740939 436741083 4.420000e-33 152
16 TraesCS7A01G523300 chrUn 91.165 1313 90 13 707 2008 92847086 92848383 0.000000e+00 1759
17 TraesCS7A01G523300 chrUn 83.585 463 62 6 71 524 209972855 209972398 3.050000e-114 422
18 TraesCS7A01G523300 chrUn 81.166 223 39 2 303 524 477238913 477238693 2.620000e-40 176
19 TraesCS7A01G523300 chrUn 86.806 144 18 1 560 703 311695285 311695427 2.640000e-35 159
20 TraesCS7A01G523300 chr2B 88.368 533 32 11 2032 2563 524358903 524358400 4.690000e-172 614
21 TraesCS7A01G523300 chr4A 95.225 377 18 0 2187 2563 236200554 236200178 4.720000e-167 597
22 TraesCS7A01G523300 chr4A 94.695 377 20 0 2187 2563 67946744 67946368 1.020000e-163 586
23 TraesCS7A01G523300 chr4A 94.695 377 20 0 2187 2563 186440692 186440316 1.020000e-163 586
24 TraesCS7A01G523300 chr4A 87.194 531 40 15 2033 2563 16399758 16400260 1.710000e-161 579
25 TraesCS7A01G523300 chr2A 94.737 380 20 0 2184 2563 180337060 180337439 2.200000e-165 592
26 TraesCS7A01G523300 chr2A 92.326 417 25 5 2152 2563 773776136 773775722 1.020000e-163 586
27 TraesCS7A01G523300 chr2A 84.568 162 11 12 1 155 17833771 17833925 5.710000e-32 148
28 TraesCS7A01G523300 chr1D 83.437 483 67 7 50 524 344753359 344752882 1.090000e-118 436
29 TraesCS7A01G523300 chr1D 82.729 469 59 13 71 524 344738246 344737785 5.140000e-107 398
30 TraesCS7A01G523300 chr1D 88.356 146 16 1 561 706 118824260 118824116 9.430000e-40 174
31 TraesCS7A01G523300 chr1D 79.399 233 38 10 296 523 483531737 483531510 3.410000e-34 156
32 TraesCS7A01G523300 chr3D 81.489 470 46 19 70 523 540248242 540247798 5.250000e-92 348
33 TraesCS7A01G523300 chr6A 95.122 164 6 2 2032 2194 319196807 319196969 9.100000e-65 257
34 TraesCS7A01G523300 chr6A 94.512 164 5 4 2033 2194 595577702 595577863 1.520000e-62 250
35 TraesCS7A01G523300 chr6A 92.814 167 11 1 2032 2197 395641947 395642113 9.160000e-60 241
36 TraesCS7A01G523300 chr1A 95.000 160 7 1 2032 2190 122433818 122433977 1.520000e-62 250
37 TraesCS7A01G523300 chr1A 96.471 85 3 0 1 85 496422986 496422902 9.560000e-30 141
38 TraesCS7A01G523300 chr6D 93.413 167 9 2 2029 2194 158937568 158937403 1.970000e-61 246
39 TraesCS7A01G523300 chr6D 93.413 167 8 3 2029 2194 272002472 272002636 7.080000e-61 244
40 TraesCS7A01G523300 chr1B 78.611 360 55 12 121 458 465845341 465845700 4.290000e-53 219
41 TraesCS7A01G523300 chr1B 85.526 152 20 1 555 706 446082478 446082627 9.490000e-35 158
42 TraesCS7A01G523300 chr3A 81.707 246 26 13 1 244 708742091 708742319 1.210000e-43 187
43 TraesCS7A01G523300 chr3B 81.223 229 21 18 1 213 763349803 763349581 5.670000e-37 165
44 TraesCS7A01G523300 chr3B 87.234 141 18 0 561 701 454024011 454023871 7.340000e-36 161
45 TraesCS7A01G523300 chr3B 86.395 147 18 2 561 706 665261323 665261468 2.640000e-35 159
46 TraesCS7A01G523300 chr6B 82.941 170 27 2 537 706 151812948 151813115 4.420000e-33 152
47 TraesCS7A01G523300 chr6B 98.667 75 1 0 2 76 7191653 7191727 1.600000e-27 134
48 TraesCS7A01G523300 chr6B 98.667 75 1 0 2 76 7233734 7233808 1.600000e-27 134
49 TraesCS7A01G523300 chr6B 92.045 88 7 0 1 88 6804292 6804205 9.630000e-25 124


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 TraesCS7A01G523300 chr7A 706001090 706003652 2562 True 4734.0 4734 100.000 1 2563 1 chr7A.!!$R3 2562
1 TraesCS7A01G523300 chr7A 705967355 705969386 2031 True 3140.0 3140 94.639 1 2029 1 chr7A.!!$R2 2028
2 TraesCS7A01G523300 chr7A 705938269 705939614 1345 True 859.5 987 90.337 707 2007 2 chr7A.!!$R4 1300
3 TraesCS7A01G523300 chr5D 19746179 19747672 1493 True 2405.0 2405 95.786 544 2032 1 chr5D.!!$R1 1488
4 TraesCS7A01G523300 chr5D 19763197 19763703 506 True 610.0 610 89.173 1 483 1 chr5D.!!$R2 482
5 TraesCS7A01G523300 chr7B 705464474 705465982 1508 True 1816.0 1816 88.692 524 2013 1 chr7B.!!$R1 1489
6 TraesCS7A01G523300 chr7B 705518022 705520028 2006 True 1387.5 1600 92.335 1 2032 2 chr7B.!!$R2 2031
7 TraesCS7A01G523300 chrUn 92847086 92848383 1297 False 1759.0 1759 91.165 707 2008 1 chrUn.!!$F1 1301
8 TraesCS7A01G523300 chr2B 524358400 524358903 503 True 614.0 614 88.368 2032 2563 1 chr2B.!!$R1 531
9 TraesCS7A01G523300 chr4A 16399758 16400260 502 False 579.0 579 87.194 2033 2563 1 chr4A.!!$F1 530

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
332 366 1.649815 CAGTGGCGCGGTTTAACAA 59.35 52.632 8.83 0.0 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2136 2266 0.546122 TATGGGCATGGGTGTCAGTC 59.454 55.0 0.0 0.0 0.0 3.51 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
32 33 4.944962 TGAGTTATGTGCTACAATGTGC 57.055 40.909 0.00 0.00 0.00 4.57
170 197 8.812513 AATTGAGGAGTTGTTATGATGATGAA 57.187 30.769 0.00 0.00 0.00 2.57
274 307 9.931210 CTATCTCAAAATTTAATAACGGGTGTC 57.069 33.333 0.00 0.00 0.00 3.67
332 366 1.649815 CAGTGGCGCGGTTTAACAA 59.350 52.632 8.83 0.00 0.00 2.83
342 376 2.912345 GCGGTTTAACAATTTACCAGCG 59.088 45.455 0.00 0.00 0.00 5.18
397 431 5.276868 CGCGCTACTGCTATTTCAAATTACT 60.277 40.000 5.56 0.00 36.97 2.24
471 505 2.207229 AGTAGCGTGTCCACCAGCA 61.207 57.895 0.00 0.00 0.00 4.41
624 659 7.878477 ACATACAAAGCAAAATGAGTGAATG 57.122 32.000 0.00 0.00 0.00 2.67
810 856 9.191995 GAGATTTAATGTTCACCACGAATTTTT 57.808 29.630 0.00 0.00 35.63 1.94
884 930 4.712829 TCCTGACTAATATTTCGTCACCCA 59.287 41.667 13.26 2.37 34.32 4.51
1014 1060 1.003118 GTGGGCATGGAGAAGTACACA 59.997 52.381 0.00 0.00 0.00 3.72
1035 1081 2.035449 AGAACGTGTGCAGTTACTAGCA 59.965 45.455 5.62 5.62 38.65 3.49
1118 1168 8.629986 CGATATATGATGAAAAATTGTTTCCGC 58.370 33.333 0.00 0.00 0.00 5.54
1237 1292 7.327275 GCCATTTGTTCGTTGTTGTTTCATATA 59.673 33.333 0.00 0.00 0.00 0.86
1699 1814 2.985957 GGGCACCGTTGTAACCTATA 57.014 50.000 0.00 0.00 40.86 1.31
1745 1860 9.445878 ACTTATCATGAGGATTATTAGCATGTG 57.554 33.333 0.09 0.00 37.98 3.21
2047 2176 1.145531 CCATGTAGGGATGGCAATGGA 59.854 52.381 6.29 0.00 36.69 3.41
2058 2187 2.712384 TGGCAATGGATAGGGTATGGA 58.288 47.619 0.00 0.00 0.00 3.41
2065 2194 2.179645 TGGATAGGGTATGGACGGGTAA 59.820 50.000 0.00 0.00 0.00 2.85
2069 2198 2.554563 AGGGTATGGACGGGTAAAACT 58.445 47.619 0.00 0.00 0.00 2.66
2102 2231 4.644685 CCAAACCCATACCCATAGAAACTG 59.355 45.833 0.00 0.00 0.00 3.16
2116 2246 6.317893 CCATAGAAACTGTTTATACCCACCAC 59.682 42.308 9.54 0.00 0.00 4.16
2131 2261 2.025416 CCACCACTTCAATACCCATGGA 60.025 50.000 15.22 0.00 0.00 3.41
2136 2266 6.881065 CACCACTTCAATACCCATGGATATAG 59.119 42.308 15.22 2.78 0.00 1.31
2199 2329 3.943269 TGGGTATCCATCTGGTATCCT 57.057 47.619 0.00 0.00 38.32 3.24
2201 2331 5.568552 TGGGTATCCATCTGGTATCCTAT 57.431 43.478 0.00 0.00 38.32 2.57
2202 2332 6.684241 TGGGTATCCATCTGGTATCCTATA 57.316 41.667 0.00 0.00 38.32 1.31
2203 2333 6.441222 TGGGTATCCATCTGGTATCCTATAC 58.559 44.000 0.00 0.00 38.32 1.47
2204 2334 5.839606 GGGTATCCATCTGGTATCCTATACC 59.160 48.000 8.83 8.83 37.08 2.73
2205 2335 5.839606 GGTATCCATCTGGTATCCTATACCC 59.160 48.000 12.43 0.00 34.22 3.69
2206 2336 5.568552 ATCCATCTGGTATCCTATACCCA 57.431 43.478 12.43 1.54 36.79 4.51
2207 2337 5.363124 TCCATCTGGTATCCTATACCCAA 57.637 43.478 12.43 2.73 36.79 4.12
2208 2338 5.927465 TCCATCTGGTATCCTATACCCAAT 58.073 41.667 12.43 4.64 36.79 3.16
2209 2339 5.726308 TCCATCTGGTATCCTATACCCAATG 59.274 44.000 12.43 13.81 36.79 2.82
2210 2340 5.104360 CCATCTGGTATCCTATACCCAATGG 60.104 48.000 20.89 20.89 39.79 3.16
2230 2360 5.996271 TGGGTATCCATTGGGTACAATAA 57.004 39.130 24.14 6.77 45.24 1.40
2239 2369 8.546083 TCCATTGGGTACAATAAATAGCATTT 57.454 30.769 2.09 0.00 45.24 2.32
2284 2414 8.511465 AAATGAGTTCAAAATTCAAGTGATCG 57.489 30.769 0.00 0.00 30.62 3.69
2287 2417 5.762045 AGTTCAAAATTCAAGTGATCGTGG 58.238 37.500 0.00 0.00 0.00 4.94
2303 2433 5.699915 TGATCGTGGTAGAGTAGTATAGCAC 59.300 44.000 19.78 19.78 42.75 4.40
2321 2451 1.330655 ACGTATGTGGCCTCCTCCAG 61.331 60.000 3.32 0.00 36.67 3.86
2375 2505 3.570212 AGCGGTTGGTGGAAGGCT 61.570 61.111 0.00 0.00 0.00 4.58
2415 2545 2.113986 GGGATTGGGGATCGCTGG 59.886 66.667 9.90 0.00 42.68 4.85
2452 2582 2.085320 GAGTCTGGTAGCGAAGAGTCA 58.915 52.381 10.64 0.00 40.92 3.41
2462 2592 7.722363 TGGTAGCGAAGAGTCAATATTTCATA 58.278 34.615 0.00 0.00 0.00 2.15
2484 2614 7.987458 TCATATTTTTGAGGAGTCACATAGGAC 59.013 37.037 0.00 0.00 38.08 3.85
2552 2682 8.842358 TGACTTGTTTAAGGAATACGAGATTT 57.158 30.769 0.00 0.00 38.26 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
145 170 8.812513 TTCATCATCATAACAACTCCTCAATT 57.187 30.769 0.00 0.00 0.00 2.32
194 227 7.623268 TCATCATAATAACAACTCATCGTCG 57.377 36.000 0.00 0.00 0.00 5.12
342 376 2.678336 AGCTCTATTGTTAAAGCGCACC 59.322 45.455 11.47 0.00 39.72 5.01
397 431 2.097036 TGTTTCTGCCTAGCGCTACTA 58.903 47.619 14.45 1.60 38.78 1.82
416 450 8.824159 ACAACTATCTATTAGCAGTAGCATTG 57.176 34.615 0.00 0.00 45.49 2.82
471 505 4.624125 GCTGGATTTTGAGCTACCAGTAGT 60.624 45.833 0.00 0.00 46.55 2.73
876 922 8.521170 TCCTTCTTATATATAGATGGGTGACG 57.479 38.462 17.31 0.00 37.48 4.35
1014 1060 2.035449 TGCTAGTAACTGCACACGTTCT 59.965 45.455 0.00 0.00 33.94 3.01
1035 1081 3.194542 CGAGAAGAAGAATCCAGAGTGGT 59.805 47.826 0.00 0.00 39.03 4.16
1324 1429 9.853177 CAATACTCCCACCTAGAGAATAAAAAT 57.147 33.333 0.00 0.00 35.27 1.82
1745 1860 6.367422 ACGAGAGATTGAAGTTGTGAAGATTC 59.633 38.462 0.00 0.00 0.00 2.52
1887 2002 3.685139 TTGTTGGTCTCATGAGAGTCC 57.315 47.619 25.76 22.74 46.37 3.85
2047 2176 4.301205 AGTTTTACCCGTCCATACCCTAT 58.699 43.478 0.00 0.00 0.00 2.57
2058 2187 3.008375 GGGTAGAAGGAAGTTTTACCCGT 59.992 47.826 7.55 0.00 42.78 5.28
2065 2194 3.205733 TGGGTTTGGGTAGAAGGAAGTTT 59.794 43.478 0.00 0.00 0.00 2.66
2069 2198 3.267551 GGTATGGGTTTGGGTAGAAGGAA 59.732 47.826 0.00 0.00 0.00 3.36
2102 2231 5.591472 GGGTATTGAAGTGGTGGGTATAAAC 59.409 44.000 0.00 0.00 0.00 2.01
2116 2246 8.037758 GTCAGTCTATATCCATGGGTATTGAAG 58.962 40.741 24.94 20.51 0.00 3.02
2131 2261 2.639839 GGGCATGGGTGTCAGTCTATAT 59.360 50.000 0.00 0.00 0.00 0.86
2136 2266 0.546122 TATGGGCATGGGTGTCAGTC 59.454 55.000 0.00 0.00 0.00 3.51
2189 2319 4.435137 CCCATTGGGTATAGGATACCAGA 58.565 47.826 14.10 5.59 38.25 3.86
2190 2320 4.844349 CCCATTGGGTATAGGATACCAG 57.156 50.000 14.10 4.53 38.25 4.00
2209 2339 7.122204 GCTATTTATTGTACCCAATGGATACCC 59.878 40.741 0.49 0.00 41.37 3.69
2210 2340 7.668052 TGCTATTTATTGTACCCAATGGATACC 59.332 37.037 0.49 0.00 41.37 2.73
2211 2341 8.630054 TGCTATTTATTGTACCCAATGGATAC 57.370 34.615 0.00 0.00 41.37 2.24
2212 2342 9.821240 AATGCTATTTATTGTACCCAATGGATA 57.179 29.630 0.00 0.00 41.37 2.59
2213 2343 8.725606 AATGCTATTTATTGTACCCAATGGAT 57.274 30.769 0.00 0.00 41.37 3.41
2214 2344 8.546083 AAATGCTATTTATTGTACCCAATGGA 57.454 30.769 0.00 0.00 41.37 3.41
2258 2388 8.971321 CGATCACTTGAATTTTGAACTCATTTT 58.029 29.630 0.00 0.00 0.00 1.82
2265 2395 5.519722 ACCACGATCACTTGAATTTTGAAC 58.480 37.500 0.00 0.00 0.00 3.18
2284 2414 6.426328 ACATACGTGCTATACTACTCTACCAC 59.574 42.308 0.00 0.00 0.00 4.16
2287 2417 6.620303 GCCACATACGTGCTATACTACTCTAC 60.620 46.154 0.00 0.00 42.17 2.59
2303 2433 1.330655 ACTGGAGGAGGCCACATACG 61.331 60.000 5.01 0.00 33.52 3.06
2321 2451 4.785453 CTCCAAGAGGCCGCCCAC 62.785 72.222 5.55 0.42 33.74 4.61
2331 2461 1.273495 ACTCCTCTGATGCCTCCAAGA 60.273 52.381 0.00 0.00 0.00 3.02
2346 2476 0.176680 CAACCGCTGCTCATACTCCT 59.823 55.000 0.00 0.00 0.00 3.69
2375 2505 1.904865 ACCGCCTTCCACTACGTCA 60.905 57.895 0.00 0.00 0.00 4.35
2400 2530 0.397941 TGATCCAGCGATCCCCAATC 59.602 55.000 0.00 0.00 43.82 2.67
2415 2545 5.049818 CCAGACTCTTGTCAAACACTTGATC 60.050 44.000 0.00 0.00 43.39 2.92
2419 2549 4.222124 ACCAGACTCTTGTCAAACACTT 57.778 40.909 0.00 0.00 45.20 3.16
2426 2556 1.905637 TCGCTACCAGACTCTTGTCA 58.094 50.000 0.00 0.00 45.20 3.58
2462 2592 5.178797 CGTCCTATGTGACTCCTCAAAAAT 58.821 41.667 0.00 0.00 32.97 1.82
2484 2614 1.299468 GCTCGCCACTCCTCATACG 60.299 63.158 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.