Multiple sequence alignment - TraesCS3A01G506100

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 TraesCS3A01G506100 chr3A 100.000 2499 0 0 1 2499 727905081 727902583 0.000000e+00 4615
1 TraesCS3A01G506100 chr4A 92.800 2500 139 17 1 2469 45263356 45265845 0.000000e+00 3581
2 TraesCS3A01G506100 chr4A 89.287 2315 215 27 1 2299 279452654 279454951 0.000000e+00 2870
3 TraesCS3A01G506100 chr5A 92.246 2502 149 19 4 2474 232660981 232663468 0.000000e+00 3504
4 TraesCS3A01G506100 chr5A 92.819 2075 107 16 458 2499 398745394 398743329 0.000000e+00 2968
5 TraesCS3A01G506100 chr2A 91.673 2534 166 27 1 2499 490628585 490631108 0.000000e+00 3469
6 TraesCS3A01G506100 chr2A 84.833 389 55 4 2114 2499 121074844 121075231 3.010000e-104 388
7 TraesCS3A01G506100 chr6A 90.766 2534 180 30 1 2499 401500570 401498056 0.000000e+00 3334
8 TraesCS3A01G506100 chr6A 89.643 2520 209 31 1 2489 178095995 178093497 0.000000e+00 3160
9 TraesCS3A01G506100 chr1A 90.415 2504 217 21 1 2499 252751410 252753895 0.000000e+00 3273
10 TraesCS3A01G506100 chr4D 87.698 2528 242 46 1 2489 179916674 179919171 0.000000e+00 2881
11 TraesCS3A01G506100 chr2D 87.624 2513 258 44 1 2495 554138632 554136155 0.000000e+00 2868
12 TraesCS3A01G506100 chr1D 89.792 2214 194 26 1 2202 110914111 110916304 0.000000e+00 2808
13 TraesCS3A01G506100 chr1D 88.281 384 40 5 2118 2499 110916266 110916646 2.930000e-124 455
14 TraesCS3A01G506100 chr7A 89.062 384 39 3 2118 2499 206734460 206734078 8.090000e-130 473
15 TraesCS3A01G506100 chr6B 86.732 407 50 4 2096 2499 670220829 670220424 1.360000e-122 449


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 TraesCS3A01G506100 chr3A 727902583 727905081 2498 True 4615.0 4615 100.0000 1 2499 1 chr3A.!!$R1 2498
1 TraesCS3A01G506100 chr4A 45263356 45265845 2489 False 3581.0 3581 92.8000 1 2469 1 chr4A.!!$F1 2468
2 TraesCS3A01G506100 chr4A 279452654 279454951 2297 False 2870.0 2870 89.2870 1 2299 1 chr4A.!!$F2 2298
3 TraesCS3A01G506100 chr5A 232660981 232663468 2487 False 3504.0 3504 92.2460 4 2474 1 chr5A.!!$F1 2470
4 TraesCS3A01G506100 chr5A 398743329 398745394 2065 True 2968.0 2968 92.8190 458 2499 1 chr5A.!!$R1 2041
5 TraesCS3A01G506100 chr2A 490628585 490631108 2523 False 3469.0 3469 91.6730 1 2499 1 chr2A.!!$F2 2498
6 TraesCS3A01G506100 chr6A 401498056 401500570 2514 True 3334.0 3334 90.7660 1 2499 1 chr6A.!!$R2 2498
7 TraesCS3A01G506100 chr6A 178093497 178095995 2498 True 3160.0 3160 89.6430 1 2489 1 chr6A.!!$R1 2488
8 TraesCS3A01G506100 chr1A 252751410 252753895 2485 False 3273.0 3273 90.4150 1 2499 1 chr1A.!!$F1 2498
9 TraesCS3A01G506100 chr4D 179916674 179919171 2497 False 2881.0 2881 87.6980 1 2489 1 chr4D.!!$F1 2488
10 TraesCS3A01G506100 chr2D 554136155 554138632 2477 True 2868.0 2868 87.6240 1 2495 1 chr2D.!!$R1 2494
11 TraesCS3A01G506100 chr1D 110914111 110916646 2535 False 1631.5 2808 89.0365 1 2499 2 chr1D.!!$F1 2498

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
207 208 1.098050 CCCCTCATTTGCTTTCCTCG 58.902 55.0 0.00 0.0 0.00 4.63 F
1070 1101 1.355796 TACGCGATTTGCCTTGACCG 61.356 55.0 15.93 0.0 42.08 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1164 1195 0.608640 AGTGACGGTTCCATGTCTCC 59.391 55.000 0.00 0.0 36.10 3.71 R
2170 2256 2.093869 GCCATGCATGTTCCACTGAATT 60.094 45.455 24.58 0.0 31.98 2.17 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
112 113 6.421202 GGATCAGAACCAGTTGTACGATATTC 59.579 42.308 0.00 0.00 0.00 1.75
118 119 6.282199 ACCAGTTGTACGATATTCTCAAGT 57.718 37.500 0.00 0.00 0.00 3.16
143 144 1.243902 GGAAATGCGAGGTCCAACAA 58.756 50.000 0.00 0.00 0.00 2.83
159 160 3.181477 CCAACAACAAGCACATGAAGGAA 60.181 43.478 0.00 0.00 0.00 3.36
207 208 1.098050 CCCCTCATTTGCTTTCCTCG 58.902 55.000 0.00 0.00 0.00 4.63
220 221 5.120399 TGCTTTCCTCGTTACTTTTCTTCA 58.880 37.500 0.00 0.00 0.00 3.02
369 377 1.799121 GACGTACGTTGACCTCGGC 60.799 63.158 23.70 2.00 0.00 5.54
469 477 3.449018 GCATATGGATATGTCTCCCGACT 59.551 47.826 4.56 0.00 41.63 4.18
497 505 2.559231 TCATGCACTACAACGTGACCTA 59.441 45.455 0.00 0.00 37.06 3.08
512 520 5.104693 ACGTGACCTACAAAATATGGGATGA 60.105 40.000 0.00 0.00 0.00 2.92
584 592 8.795513 TGATTTCAAGCTCACAATGAAGAAATA 58.204 29.630 0.00 0.00 35.36 1.40
683 696 8.436778 TGTGGGCTACATACTATATTTTGTGAT 58.563 33.333 0.00 0.00 33.42 3.06
824 841 8.729805 ACTTCTTTCAATTAAACATGGCAAAA 57.270 26.923 0.00 0.00 0.00 2.44
884 905 3.181507 CCGCTTTGTCATTCATGTACCTG 60.182 47.826 0.00 0.00 0.00 4.00
1070 1101 1.355796 TACGCGATTTGCCTTGACCG 61.356 55.000 15.93 0.00 42.08 4.79
1164 1195 7.439157 TGAATACTTCATCAACAACCTCAAG 57.561 36.000 0.00 0.00 34.08 3.02
1208 1239 4.453480 AAAACTCAAGGGTCCAGATCAA 57.547 40.909 0.00 0.00 0.00 2.57
1429 1471 2.513259 AAAGTGGGAAGGCCGACGA 61.513 57.895 0.00 0.00 46.42 4.20
1456 1498 0.534877 TCGTCACAGCTGCAATGGTT 60.535 50.000 15.27 0.00 0.00 3.67
1507 1552 8.997621 AATTGGTTGATGAATGAAGATTTCAG 57.002 30.769 0.00 0.00 43.98 3.02
1541 1586 6.202937 CAATACACGAGAGTTCATAGAGGAC 58.797 44.000 0.00 0.00 46.40 3.85
1879 1935 3.391965 TGTCTGAAAACATGGCAAATGC 58.608 40.909 0.00 0.00 41.14 3.56
1894 1950 3.304861 GCAAATGCAGTTGATCAGACACA 60.305 43.478 29.48 1.67 41.59 3.72
2049 2111 7.922505 TTTTCACAGTTTGCACATAATACAC 57.077 32.000 0.00 0.00 0.00 2.90
2099 2161 2.494471 ACACGGAAATCTACACGATGGA 59.506 45.455 0.00 0.00 31.20 3.41
2104 2167 3.797256 GGAAATCTACACGATGGAAGACG 59.203 47.826 0.00 0.00 31.20 4.18
2107 2170 1.749063 TCTACACGATGGAAGACGCAT 59.251 47.619 0.00 0.00 0.00 4.73
2112 2175 4.883083 ACACGATGGAAGACGCATTATAT 58.117 39.130 0.00 0.00 0.00 0.86
2153 2216 6.765036 CAGTAGAACTAACATGGCAGATTCAT 59.235 38.462 0.00 0.00 0.00 2.57
2170 2256 1.976404 TCATTGGAAAAGGCATGGCAA 59.024 42.857 22.64 5.96 0.00 4.52
2288 2447 8.868522 TCCAGAGTCATTCTCACATTTTAAAT 57.131 30.769 0.00 0.00 44.98 1.40
2289 2448 9.300681 TCCAGAGTCATTCTCACATTTTAAATT 57.699 29.630 0.00 0.00 44.98 1.82
2290 2449 9.918630 CCAGAGTCATTCTCACATTTTAAATTT 57.081 29.630 0.00 0.00 44.98 1.82
2398 2558 6.393990 TCTTTGCTTTCTTGTGTTTTGCTTA 58.606 32.000 0.00 0.00 0.00 3.09
2489 2649 1.299316 CTGGGTTTGTGTGCTTGCG 60.299 57.895 0.00 0.00 0.00 4.85
2492 2652 0.387239 GGGTTTGTGTGCTTGCGATC 60.387 55.000 0.00 0.00 0.00 3.69
2494 2654 0.310543 GTTTGTGTGCTTGCGATCCA 59.689 50.000 0.00 0.00 0.00 3.41
2495 2655 1.068333 GTTTGTGTGCTTGCGATCCAT 60.068 47.619 0.00 0.00 0.00 3.41
2496 2656 2.106477 TTGTGTGCTTGCGATCCATA 57.894 45.000 0.00 0.00 0.00 2.74
2497 2657 2.330440 TGTGTGCTTGCGATCCATAT 57.670 45.000 0.00 0.00 0.00 1.78
2498 2658 2.212652 TGTGTGCTTGCGATCCATATC 58.787 47.619 0.00 0.00 0.00 1.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
112 113 2.030893 TCGCATTTCCAAAGCACTTGAG 60.031 45.455 0.38 0.00 37.17 3.02
118 119 0.881118 GACCTCGCATTTCCAAAGCA 59.119 50.000 0.00 0.00 0.00 3.91
143 144 3.213206 TCAGTTCCTTCATGTGCTTGT 57.787 42.857 0.00 0.00 0.00 3.16
159 160 2.806244 GTGTGGTCATTACGCTTTCAGT 59.194 45.455 0.00 0.00 0.00 3.41
303 311 6.475504 TCTGTCCAAACATGAGTTGTATGAT 58.524 36.000 0.00 0.00 37.68 2.45
311 319 3.576078 TGGTTCTGTCCAAACATGAGT 57.424 42.857 0.00 0.00 34.13 3.41
369 377 0.171231 TCACAGACTCGGCAAGATCG 59.829 55.000 0.00 0.00 0.00 3.69
446 454 3.440127 TCGGGAGACATATCCATATGCA 58.560 45.455 6.49 0.00 42.98 3.96
469 477 5.467063 TCACGTTGTAGTGCATGATTGTTTA 59.533 36.000 0.00 0.00 41.61 2.01
497 505 6.322201 GTGGAAGTCATCATCCCATATTTTGT 59.678 38.462 0.00 0.00 34.68 2.83
512 520 3.828451 CAGGATTTTGTGGTGGAAGTCAT 59.172 43.478 0.00 0.00 0.00 3.06
584 592 5.649831 GCAAAGAAGGAAGGAATACTCACAT 59.350 40.000 0.00 0.00 0.00 3.21
674 687 7.037438 GCCACATGAAACATCTATCACAAAAT 58.963 34.615 0.00 0.00 0.00 1.82
683 696 3.191162 GCTGTTGCCACATGAAACATCTA 59.809 43.478 0.00 0.00 33.60 1.98
824 841 3.088532 TGAGCCCGCAAAGAATGTTTAT 58.911 40.909 0.00 0.00 0.00 1.40
863 880 3.436704 ACAGGTACATGAATGACAAAGCG 59.563 43.478 15.54 0.00 0.00 4.68
983 1014 0.744414 CATGGGGAACAGTACCTGCG 60.744 60.000 0.00 0.00 34.37 5.18
1070 1101 2.686405 ACCTCAAAACGTTGGTTCTTCC 59.314 45.455 0.00 0.00 34.62 3.46
1164 1195 0.608640 AGTGACGGTTCCATGTCTCC 59.391 55.000 0.00 0.00 36.10 3.71
1208 1239 5.050091 GCGACATACTCGATTGGAAAATGAT 60.050 40.000 0.00 0.00 46.14 2.45
1281 1315 2.850568 AGGGTTTAGGGATTGGTGTAGG 59.149 50.000 0.00 0.00 0.00 3.18
1386 1428 5.048083 GCAAGGTATTCCAACATGTGAAAGA 60.048 40.000 0.00 0.00 35.89 2.52
1456 1498 4.633175 TGTGTATTTTACGGAGCTCAACA 58.367 39.130 17.19 3.52 0.00 3.33
1507 1552 0.668096 TCGTGTATTGGACCGTGTGC 60.668 55.000 0.00 0.00 0.00 4.57
1541 1586 0.662619 TGTTGGCTTTCTTGACAGCG 59.337 50.000 3.17 0.00 36.85 5.18
1810 1864 4.584325 ACTAGTACTACCAACCACGAACAA 59.416 41.667 0.00 0.00 0.00 2.83
1879 1935 5.532557 TCACTAACTGTGTCTGATCAACTG 58.467 41.667 0.00 0.00 46.27 3.16
2099 2161 8.737168 ATGCCATGTTATATATAATGCGTCTT 57.263 30.769 8.40 0.00 0.00 3.01
2153 2216 3.181447 TGAATTTGCCATGCCTTTTCCAA 60.181 39.130 0.00 0.00 0.00 3.53
2170 2256 2.093869 GCCATGCATGTTCCACTGAATT 60.094 45.455 24.58 0.00 31.98 2.17
2398 2558 6.605119 AGATACAAATCGGGATTGGAGATTT 58.395 36.000 2.85 0.00 43.04 2.17


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

AutoCloner maintained by Alex Coulton.