Multiple sequence alignment - TraesCS4A01G467300

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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 TraesCS4A01G467300 chr4A 100.000 2810 0 0 1 2810 729653496 729656305 0.000000e+00 5190.0
1 TraesCS4A01G467300 chr4A 92.322 2084 142 6 3 2081 729797856 729799926 0.000000e+00 2946.0
2 TraesCS4A01G467300 chr4A 91.105 1765 141 11 429 2185 729151967 729153723 0.000000e+00 2375.0
3 TraesCS4A01G467300 chr4A 89.363 1335 114 17 584 1913 729213131 729214442 0.000000e+00 1653.0
4 TraesCS4A01G467300 chr4A 91.992 949 72 3 1281 2226 729120520 729119573 0.000000e+00 1328.0
5 TraesCS4A01G467300 chr4A 94.672 732 37 2 1496 2226 729921293 729922023 0.000000e+00 1134.0
6 TraesCS4A01G467300 chr4A 88.857 700 61 6 679 1367 729857232 729857925 0.000000e+00 845.0
7 TraesCS4A01G467300 chr4A 92.599 581 29 5 2244 2810 648753568 648754148 0.000000e+00 822.0
8 TraesCS4A01G467300 chr4A 90.709 592 42 4 695 1286 730007204 730006626 0.000000e+00 776.0
9 TraesCS4A01G467300 chr4A 88.158 608 45 11 633 1217 729920318 729920921 0.000000e+00 699.0
10 TraesCS4A01G467300 chr4A 90.270 370 29 5 3 372 729151376 729151738 7.040000e-131 477.0
11 TraesCS4A01G467300 chr4A 90.881 329 23 4 38 366 729212686 729213007 4.300000e-118 435.0
12 TraesCS4A01G467300 chr4A 88.509 322 23 4 1906 2224 729214771 729215081 7.350000e-101 377.0
13 TraesCS4A01G467300 chr4A 87.153 288 26 5 369 647 729904238 729904523 1.620000e-82 316.0
14 TraesCS4A01G467300 chr4A 92.500 200 11 2 3 202 729903656 729903851 1.650000e-72 283.0
15 TraesCS4A01G467300 chr4A 98.876 89 1 0 3 91 729857128 729857216 2.900000e-35 159.0
16 TraesCS4A01G467300 chr4A 100.000 28 0 0 736 763 729857212 729857239 5.000000e-03 52.8
17 TraesCS4A01G467300 chr7D 95.546 2133 72 8 1 2133 10056020 10058129 0.000000e+00 3391.0
18 TraesCS4A01G467300 chr7D 94.286 70 2 1 2159 2226 10058129 10058198 3.830000e-19 106.0
19 TraesCS4A01G467300 chr7A 89.608 2040 182 18 200 2211 9684196 9682159 0.000000e+00 2566.0
20 TraesCS4A01G467300 chr7A 90.495 1536 111 12 699 2226 9363816 9365324 0.000000e+00 1995.0
21 TraesCS4A01G467300 chr7A 91.622 370 29 1 3 372 9507723 9508090 6.940000e-141 510.0
22 TraesCS4A01G467300 chr7A 93.007 286 19 1 3 288 9684880 9684596 1.560000e-112 416.0
23 TraesCS4A01G467300 chr7A 82.203 354 35 13 362 710 9362146 9362476 2.130000e-71 279.0
24 TraesCS4A01G467300 chr7A 91.489 188 12 1 369 552 9508145 9508332 3.590000e-64 255.0
25 TraesCS4A01G467300 chr7A 96.875 32 0 1 105 136 9684257 9684227 5.000000e-03 52.8
26 TraesCS4A01G467300 chr1D 93.226 561 34 3 2253 2810 363730894 363731453 0.000000e+00 822.0
27 TraesCS4A01G467300 chr1B 92.281 583 29 9 2244 2810 538198636 538199218 0.000000e+00 813.0
28 TraesCS4A01G467300 chr1B 90.385 572 43 6 2248 2810 589226583 589227151 0.000000e+00 741.0
29 TraesCS4A01G467300 chr6B 92.123 584 30 5 2243 2810 348693907 348693324 0.000000e+00 809.0
30 TraesCS4A01G467300 chr5D 92.361 576 30 5 2249 2810 241110408 241110983 0.000000e+00 808.0
31 TraesCS4A01G467300 chr5D 90.138 578 41 8 2249 2810 428472224 428471647 0.000000e+00 737.0
32 TraesCS4A01G467300 chr5B 91.508 577 33 6 2247 2810 248920613 248920040 0.000000e+00 780.0
33 TraesCS4A01G467300 chr5B 90.189 581 32 8 2243 2810 148989153 148988585 0.000000e+00 734.0
34 TraesCS4A01G467300 chr7B 91.577 558 47 0 2253 2810 450282865 450283422 0.000000e+00 771.0
35 TraesCS4A01G467300 chr3D 90.941 574 40 5 2249 2810 3965541 3964968 0.000000e+00 761.0
36 TraesCS4A01G467300 chr2D 78.500 1200 202 37 610 1796 564475911 564477067 0.000000e+00 736.0
37 TraesCS4A01G467300 chr2D 80.947 950 152 18 858 1796 564438276 564439207 0.000000e+00 725.0
38 TraesCS4A01G467300 chrUn 88.756 418 34 5 2243 2647 318020591 318021008 1.500000e-137 499.0
39 TraesCS4A01G467300 chrUn 88.756 418 34 5 2243 2647 421370849 421371266 1.500000e-137 499.0


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 TraesCS4A01G467300 chr4A 729653496 729656305 2809 False 5190.000000 5190 100.000000 1 2810 1 chr4A.!!$F2 2809
1 TraesCS4A01G467300 chr4A 729797856 729799926 2070 False 2946.000000 2946 92.322000 3 2081 1 chr4A.!!$F3 2078
2 TraesCS4A01G467300 chr4A 729151376 729153723 2347 False 1426.000000 2375 90.687500 3 2185 2 chr4A.!!$F4 2182
3 TraesCS4A01G467300 chr4A 729119573 729120520 947 True 1328.000000 1328 91.992000 1281 2226 1 chr4A.!!$R1 945
4 TraesCS4A01G467300 chr4A 729920318 729922023 1705 False 916.500000 1134 91.415000 633 2226 2 chr4A.!!$F8 1593
5 TraesCS4A01G467300 chr4A 648753568 648754148 580 False 822.000000 822 92.599000 2244 2810 1 chr4A.!!$F1 566
6 TraesCS4A01G467300 chr4A 729212686 729215081 2395 False 821.666667 1653 89.584333 38 2224 3 chr4A.!!$F5 2186
7 TraesCS4A01G467300 chr4A 730006626 730007204 578 True 776.000000 776 90.709000 695 1286 1 chr4A.!!$R2 591
8 TraesCS4A01G467300 chr4A 729857128 729857925 797 False 352.266667 845 95.911000 3 1367 3 chr4A.!!$F6 1364
9 TraesCS4A01G467300 chr4A 729903656 729904523 867 False 299.500000 316 89.826500 3 647 2 chr4A.!!$F7 644
10 TraesCS4A01G467300 chr7D 10056020 10058198 2178 False 1748.500000 3391 94.916000 1 2226 2 chr7D.!!$F1 2225
11 TraesCS4A01G467300 chr7A 9362146 9365324 3178 False 1137.000000 1995 86.349000 362 2226 2 chr7A.!!$F1 1864
12 TraesCS4A01G467300 chr7A 9682159 9684880 2721 True 1011.600000 2566 93.163333 3 2211 3 chr7A.!!$R1 2208
13 TraesCS4A01G467300 chr7A 9507723 9508332 609 False 382.500000 510 91.555500 3 552 2 chr7A.!!$F2 549
14 TraesCS4A01G467300 chr1D 363730894 363731453 559 False 822.000000 822 93.226000 2253 2810 1 chr1D.!!$F1 557
15 TraesCS4A01G467300 chr1B 538198636 538199218 582 False 813.000000 813 92.281000 2244 2810 1 chr1B.!!$F1 566
16 TraesCS4A01G467300 chr1B 589226583 589227151 568 False 741.000000 741 90.385000 2248 2810 1 chr1B.!!$F2 562
17 TraesCS4A01G467300 chr6B 348693324 348693907 583 True 809.000000 809 92.123000 2243 2810 1 chr6B.!!$R1 567
18 TraesCS4A01G467300 chr5D 241110408 241110983 575 False 808.000000 808 92.361000 2249 2810 1 chr5D.!!$F1 561
19 TraesCS4A01G467300 chr5D 428471647 428472224 577 True 737.000000 737 90.138000 2249 2810 1 chr5D.!!$R1 561
20 TraesCS4A01G467300 chr5B 248920040 248920613 573 True 780.000000 780 91.508000 2247 2810 1 chr5B.!!$R2 563
21 TraesCS4A01G467300 chr5B 148988585 148989153 568 True 734.000000 734 90.189000 2243 2810 1 chr5B.!!$R1 567
22 TraesCS4A01G467300 chr7B 450282865 450283422 557 False 771.000000 771 91.577000 2253 2810 1 chr7B.!!$F1 557
23 TraesCS4A01G467300 chr3D 3964968 3965541 573 True 761.000000 761 90.941000 2249 2810 1 chr3D.!!$R1 561
24 TraesCS4A01G467300 chr2D 564475911 564477067 1156 False 736.000000 736 78.500000 610 1796 1 chr2D.!!$F2 1186
25 TraesCS4A01G467300 chr2D 564438276 564439207 931 False 725.000000 725 80.947000 858 1796 1 chr2D.!!$F1 938

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
383 1107 0.110056 CATCTTGTTGTCGGCTGTGC 60.11 55.0 0.0 0.0 0.0 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2231 5002 0.623723 GACCCCAGCCAAATCACCTA 59.376 55.0 0.0 0.0 0.0 3.08 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
218 385 5.221621 TGACACCATCAAGTTGTCACTGATA 60.222 40.000 2.11 0.00 35.00 2.15
374 1098 9.507329 AACATATTACTCTGAACATCTTGTTGT 57.493 29.630 0.00 0.00 41.28 3.32
382 1106 1.229428 ACATCTTGTTGTCGGCTGTG 58.771 50.000 0.00 0.00 0.00 3.66
383 1107 0.110056 CATCTTGTTGTCGGCTGTGC 60.110 55.000 0.00 0.00 0.00 4.57
537 1379 3.567164 ACAAGTTCTGCATTGACAAGGAG 59.433 43.478 3.57 2.32 0.00 3.69
641 1487 8.978539 GTTTTCTTCCACCTATCAATGTTTTTC 58.021 33.333 0.00 0.00 0.00 2.29
831 3047 3.637714 GCGTTGTTTCTCCGCAGA 58.362 55.556 0.00 0.00 46.26 4.26
1317 3735 4.015084 CTGATTTCCTGCTCAACATCCTT 58.985 43.478 0.00 0.00 0.00 3.36
1557 3975 3.330275 CGGCAATACCCGCTTAGC 58.670 61.111 0.00 0.00 42.03 3.09
1642 4060 9.934190 GCACATCAAAATTGTTTCAAGTATTTT 57.066 25.926 0.00 0.00 32.14 1.82
1651 4069 9.454859 AATTGTTTCAAGTATTTTTGGTCCAAA 57.545 25.926 13.26 13.26 0.00 3.28
1652 4070 8.485976 TTGTTTCAAGTATTTTTGGTCCAAAG 57.514 30.769 16.47 4.40 34.72 2.77
1684 4102 1.692519 GGCGGTATGTCTACCAAGGAT 59.307 52.381 2.96 0.00 46.80 3.24
1749 4167 4.216411 TCTAGTATTTGCAGGTTCCACC 57.784 45.455 0.00 0.00 38.99 4.61
1764 4182 2.113139 ACCGGCAACTTCACCCAG 59.887 61.111 0.00 0.00 0.00 4.45
1918 4673 2.351157 GCACAACAGTTTCTGCTCCATC 60.351 50.000 5.70 0.00 34.37 3.51
1961 4719 6.713450 GGGAAAGTGAGTATTGTGGAAAGTTA 59.287 38.462 0.00 0.00 0.00 2.24
2227 4998 9.753674 TGGAAGACATATTTTTAAGAGATTGGT 57.246 29.630 0.00 0.00 0.00 3.67
2237 5008 9.753674 ATTTTTAAGAGATTGGTGAATAGGTGA 57.246 29.630 0.00 0.00 0.00 4.02
2238 5009 9.753674 TTTTTAAGAGATTGGTGAATAGGTGAT 57.246 29.630 0.00 0.00 0.00 3.06
2239 5010 9.753674 TTTTAAGAGATTGGTGAATAGGTGATT 57.246 29.630 0.00 0.00 0.00 2.57
2240 5011 9.753674 TTTAAGAGATTGGTGAATAGGTGATTT 57.246 29.630 0.00 0.00 0.00 2.17
2241 5012 7.636150 AAGAGATTGGTGAATAGGTGATTTG 57.364 36.000 0.00 0.00 0.00 2.32
2245 5016 3.355378 TGGTGAATAGGTGATTTGGCTG 58.645 45.455 0.00 0.00 0.00 4.85
2447 5246 2.023318 CCGATCTAGAAGCGACGGT 58.977 57.895 16.98 0.00 36.38 4.83
2453 5252 0.038526 CTAGAAGCGACGGTGTTGGT 60.039 55.000 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
218 385 7.506328 AAACGCTAAGAGGTAGAACAAATTT 57.494 32.000 0.00 0.00 30.50 1.82
324 990 5.371526 TGACTATGCAATCATCTCCTTTCC 58.628 41.667 0.00 0.00 34.22 3.13
325 991 6.932356 TTGACTATGCAATCATCTCCTTTC 57.068 37.500 0.00 0.00 34.22 2.62
374 1098 1.302366 GAATCATCATGCACAGCCGA 58.698 50.000 0.00 0.00 0.00 5.54
382 1106 1.968493 AGCCAATGGGAATCATCATGC 59.032 47.619 0.00 0.00 34.44 4.06
383 1107 7.061054 AGATATAGCCAATGGGAATCATCATG 58.939 38.462 0.00 0.00 34.44 3.07
641 1487 8.239314 ACAAGCAGAACAATGACATTAACATAG 58.761 33.333 0.00 0.00 0.00 2.23
1317 3735 3.407967 GCCCCATTCTGACCGGGA 61.408 66.667 6.32 0.00 43.21 5.14
1499 3917 2.997980 TGTCGATGCCAATATGGTTGT 58.002 42.857 0.00 0.00 40.46 3.32
1642 4060 1.243342 CGGATGCTGCTTTGGACCAA 61.243 55.000 1.69 1.69 0.00 3.67
1749 4167 2.281761 AGCTGGGTGAAGTTGCCG 60.282 61.111 0.00 0.00 0.00 5.69
1764 4182 4.517285 TCCATGACTTTATCTGGTTCAGC 58.483 43.478 0.00 0.00 31.25 4.26
1845 4264 0.747255 ATCCGACAACTCCATCTCCG 59.253 55.000 0.00 0.00 0.00 4.63
1918 4673 3.636679 TCCCATGAGAGAAGTAGAGGTG 58.363 50.000 0.00 0.00 0.00 4.00
1961 4719 9.809096 CACTCAACACTCTCAATACAATAGTAT 57.191 33.333 0.00 0.00 42.66 2.12
2064 4823 9.459640 GTCCTGTTTAAGTGATTAAAAAGAACC 57.540 33.333 10.78 0.00 34.96 3.62
2226 4997 2.689983 CCCAGCCAAATCACCTATTCAC 59.310 50.000 0.00 0.00 0.00 3.18
2227 4998 2.358090 CCCCAGCCAAATCACCTATTCA 60.358 50.000 0.00 0.00 0.00 2.57
2228 4999 2.310538 CCCCAGCCAAATCACCTATTC 58.689 52.381 0.00 0.00 0.00 1.75
2229 5000 1.645919 ACCCCAGCCAAATCACCTATT 59.354 47.619 0.00 0.00 0.00 1.73
2230 5001 1.215423 GACCCCAGCCAAATCACCTAT 59.785 52.381 0.00 0.00 0.00 2.57
2231 5002 0.623723 GACCCCAGCCAAATCACCTA 59.376 55.000 0.00 0.00 0.00 3.08
2232 5003 1.384191 GACCCCAGCCAAATCACCT 59.616 57.895 0.00 0.00 0.00 4.00
2233 5004 2.046285 CGACCCCAGCCAAATCACC 61.046 63.158 0.00 0.00 0.00 4.02
2234 5005 2.700773 GCGACCCCAGCCAAATCAC 61.701 63.158 0.00 0.00 0.00 3.06
2235 5006 2.361104 GCGACCCCAGCCAAATCA 60.361 61.111 0.00 0.00 0.00 2.57
2298 5080 1.152139 GAGGAGGATGGGCTAGGCT 60.152 63.158 16.80 0.00 0.00 4.58
2447 5246 2.968156 CCGCCGTCGAAACCAACA 60.968 61.111 0.00 0.00 38.10 3.33
2504 5328 3.711059 CTGATCCAGGCCAGCCACC 62.711 68.421 12.03 0.00 38.92 4.61
2506 5330 3.414193 CCTGATCCAGGCCAGCCA 61.414 66.667 12.03 0.00 45.13 4.75
2622 5446 3.322514 GCTACACCTGCCAGAACAA 57.677 52.632 0.00 0.00 0.00 2.83
2647 5471 1.630148 GACGAAGAAGATGACCACCG 58.370 55.000 0.00 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.