Multiple sequence alignment - TraesCS6D01G019300

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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 TraesCS6D01G019300 chr6D 100.000 2443 0 0 1 2443 7748794 7746352 0.000000e+00 4512.0
1 TraesCS6D01G019300 chr6D 88.522 1089 84 14 632 1715 7867361 7868413 0.000000e+00 1280.0
2 TraesCS6D01G019300 chr6D 90.943 265 16 4 2181 2443 461526207 461526465 1.390000e-92 350.0
3 TraesCS6D01G019300 chr6D 92.593 108 8 0 2069 2176 7740286 7740393 3.250000e-34 156.0
4 TraesCS6D01G019300 chr6D 96.610 59 2 0 572 630 61766590 61766532 5.560000e-17 99.0
5 TraesCS6D01G019300 chr6A 96.042 2451 48 12 1 2443 8011760 8009351 0.000000e+00 3943.0
6 TraesCS6D01G019300 chr6A 88.218 696 41 14 1038 1715 8165695 8166367 0.000000e+00 793.0
7 TraesCS6D01G019300 chr6A 87.391 230 21 8 825 1051 8163946 8164170 8.670000e-65 257.0
8 TraesCS6D01G019300 chr6A 87.879 198 9 3 632 829 8149431 8149613 4.090000e-53 219.0
9 TraesCS6D01G019300 chr6A 92.593 108 8 0 2069 2176 8002595 8002702 3.250000e-34 156.0
10 TraesCS6D01G019300 chr6B 94.801 1481 46 9 307 1773 14462321 14460858 0.000000e+00 2279.0
11 TraesCS6D01G019300 chr6B 88.869 1096 78 19 632 1714 14411995 14410931 0.000000e+00 1308.0
12 TraesCS6D01G019300 chr6B 91.729 399 17 4 1789 2179 14460874 14460484 7.690000e-150 540.0
13 TraesCS6D01G019300 chr6B 86.059 373 45 2 827 1198 14457043 14456677 6.330000e-106 394.0
14 TraesCS6D01G019300 chr6B 85.185 378 41 7 1251 1615 14456685 14456310 8.250000e-100 374.0
15 TraesCS6D01G019300 chr5A 85.475 358 45 6 1715 2070 688280385 688280033 1.380000e-97 366.0
16 TraesCS6D01G019300 chr5A 85.165 364 45 9 1711 2070 675524911 675525269 4.960000e-97 364.0
17 TraesCS6D01G019300 chr5A 83.774 265 39 4 883 1144 423030289 423030552 5.220000e-62 248.0
18 TraesCS6D01G019300 chr7D 84.916 358 49 5 1715 2070 3848207 3848561 8.310000e-95 357.0
19 TraesCS6D01G019300 chr7D 89.404 151 15 1 2169 2318 113120843 113120993 3.210000e-44 189.0
20 TraesCS6D01G019300 chr7D 89.726 146 15 0 2171 2316 436458611 436458466 1.150000e-43 187.0
21 TraesCS6D01G019300 chr7D 90.441 136 13 0 2183 2318 88182910 88182775 1.930000e-41 180.0
22 TraesCS6D01G019300 chr4A 84.789 355 51 3 1718 2070 741183007 741182654 1.070000e-93 353.0
23 TraesCS6D01G019300 chr4A 92.647 68 4 1 570 636 7123658 7123725 2.000000e-16 97.1
24 TraesCS6D01G019300 chr7A 83.565 359 53 5 1715 2070 3837010 3837365 5.040000e-87 331.0
25 TraesCS6D01G019300 chr1A 76.023 684 126 26 889 1566 110160439 110159788 1.090000e-83 320.0
26 TraesCS6D01G019300 chr1A 80.716 363 58 7 1716 2070 12684068 12683710 3.100000e-69 272.0
27 TraesCS6D01G019300 chr7B 80.716 363 58 7 1716 2070 192783589 192783231 3.100000e-69 272.0
28 TraesCS6D01G019300 chr7B 90.580 138 13 0 2181 2318 22536358 22536495 1.490000e-42 183.0
29 TraesCS6D01G019300 chr7B 91.429 70 6 0 564 633 746618738 746618669 2.000000e-16 97.1
30 TraesCS6D01G019300 chr2D 93.478 138 9 0 2181 2318 10907134 10907271 3.180000e-49 206.0
31 TraesCS6D01G019300 chr2D 91.241 137 12 0 2182 2318 492073305 492073441 1.150000e-43 187.0
32 TraesCS6D01G019300 chr1D 80.682 264 41 8 889 1150 107614537 107614282 1.920000e-46 196.0
33 TraesCS6D01G019300 chr1D 90.000 80 7 1 559 637 466009061 466009140 4.300000e-18 102.0
34 TraesCS6D01G019300 chr5D 90.580 138 11 1 2181 2316 484701566 484701703 5.370000e-42 182.0
35 TraesCS6D01G019300 chr1B 79.333 150 20 10 489 636 4640709 4640569 7.190000e-16 95.3
36 TraesCS6D01G019300 chr5B 93.548 62 4 0 569 630 482410977 482410916 2.590000e-15 93.5
37 TraesCS6D01G019300 chr3B 92.308 65 5 0 566 630 478330221 478330285 2.590000e-15 93.5


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 TraesCS6D01G019300 chr6D 7746352 7748794 2442 True 4512.00 4512 100.0000 1 2443 1 chr6D.!!$R1 2442
1 TraesCS6D01G019300 chr6D 7867361 7868413 1052 False 1280.00 1280 88.5220 632 1715 1 chr6D.!!$F2 1083
2 TraesCS6D01G019300 chr6A 8009351 8011760 2409 True 3943.00 3943 96.0420 1 2443 1 chr6A.!!$R1 2442
3 TraesCS6D01G019300 chr6A 8163946 8166367 2421 False 525.00 793 87.8045 825 1715 2 chr6A.!!$F3 890
4 TraesCS6D01G019300 chr6B 14410931 14411995 1064 True 1308.00 1308 88.8690 632 1714 1 chr6B.!!$R1 1082
5 TraesCS6D01G019300 chr6B 14456310 14462321 6011 True 896.75 2279 89.4435 307 2179 4 chr6B.!!$R2 1872
6 TraesCS6D01G019300 chr1A 110159788 110160439 651 True 320.00 320 76.0230 889 1566 1 chr1A.!!$R2 677

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
180 181 1.571215 CCGGTAACAACACGAAGGCC 61.571 60.0 0.0 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1868 3443 0.472471 TCATTTATGGAGGGACCGGC 59.528 55.0 0.0 0.0 42.61 6.13 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
180 181 1.571215 CCGGTAACAACACGAAGGCC 61.571 60.000 0.00 0.00 0.00 5.19
274 278 4.001652 TGGTTCGTTGTTTGTGTTAGTCA 58.998 39.130 0.00 0.00 0.00 3.41
554 568 4.342665 GCGGGTGGATTTATTTTTGGGATA 59.657 41.667 0.00 0.00 0.00 2.59
582 596 5.489997 TGGGCTGATATAGGATGACATCATT 59.510 40.000 17.08 7.26 36.57 2.57
898 914 8.856490 ATACATTAATTCAACGCCAAAGATTC 57.144 30.769 0.00 0.00 0.00 2.52
901 917 3.747099 ATTCAACGCCAAAGATTCGAG 57.253 42.857 0.00 0.00 0.00 4.04
1193 2748 8.786826 ATCAGTTACCTTCATTCGTATTCAAA 57.213 30.769 0.00 0.00 0.00 2.69
1286 2855 0.950836 TTCGTGCATGTTGGGACTTG 59.049 50.000 5.68 0.00 34.87 3.16
1685 3257 3.712091 ATCCAAGTCGAGGAATCGTAC 57.288 47.619 0.00 0.00 38.93 3.67
1915 3490 3.356290 AGCTTGAAAACAACTCACACCT 58.644 40.909 0.00 0.00 0.00 4.00
2025 3606 4.083862 GAGTGGACCGGTGCCCTC 62.084 72.222 21.62 21.62 0.00 4.30
2369 6964 0.951040 CTGCAGAAACCGGTCCAGAC 60.951 60.000 8.04 0.00 0.00 3.51
2370 6965 1.070786 GCAGAAACCGGTCCAGACA 59.929 57.895 8.04 0.00 0.00 3.41
2372 6967 1.442769 CAGAAACCGGTCCAGACATG 58.557 55.000 8.04 0.00 0.00 3.21
2373 6968 1.001974 CAGAAACCGGTCCAGACATGA 59.998 52.381 8.04 0.00 0.00 3.07
2386 6981 2.926200 CAGACATGAGATCCAACGACAC 59.074 50.000 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
163 164 0.535553 TGGGCCTTCGTGTTGTTACC 60.536 55.000 4.53 0.00 0.00 2.85
274 278 4.289672 TCTTTCTTTACTGCCCATCTTCCT 59.710 41.667 0.00 0.00 0.00 3.36
323 327 1.725641 TATCTTTCTGCGCCACACAG 58.274 50.000 4.18 0.00 36.44 3.66
554 568 3.584848 GTCATCCTATATCAGCCCACCTT 59.415 47.826 0.00 0.00 0.00 3.50
676 692 5.449177 CCTGGTTTTTAGATTGAGGCGAATC 60.449 44.000 4.62 4.62 33.21 2.52
716 732 7.228308 CCAAAGATGTATCATCCTCCTTTTCTC 59.772 40.741 6.18 0.00 0.00 2.87
898 914 6.204301 TCGTTTATATAGAGGGACAAGACTCG 59.796 42.308 0.00 0.00 38.72 4.18
901 917 7.274603 AGTCGTTTATATAGAGGGACAAGAC 57.725 40.000 6.99 0.00 0.00 3.01
1148 2703 7.453393 ACTGATCAATACTTGAGAGGACAAAA 58.547 34.615 0.00 0.00 43.98 2.44
1149 2704 7.009179 ACTGATCAATACTTGAGAGGACAAA 57.991 36.000 0.00 0.00 43.98 2.83
1150 2705 6.611613 ACTGATCAATACTTGAGAGGACAA 57.388 37.500 0.00 0.00 43.98 3.18
1151 2706 6.611613 AACTGATCAATACTTGAGAGGACA 57.388 37.500 0.00 0.00 43.98 4.02
1193 2748 6.892658 TGTTAACTAAACAGGTGCAATGAT 57.107 33.333 7.22 0.00 43.22 2.45
1286 2855 4.617959 CAAGTTCAATCCATGATCCATGC 58.382 43.478 0.00 0.00 40.20 4.06
1861 3436 2.997897 GAGGGACCGGCTGTCAGT 60.998 66.667 11.25 0.00 46.38 3.41
1862 3437 3.775654 GGAGGGACCGGCTGTCAG 61.776 72.222 11.25 0.00 46.38 3.51
1863 3438 2.523740 TATGGAGGGACCGGCTGTCA 62.524 60.000 11.25 0.00 46.38 3.58
1864 3439 1.335132 TTATGGAGGGACCGGCTGTC 61.335 60.000 0.00 0.00 43.67 3.51
1866 3441 0.474184 ATTTATGGAGGGACCGGCTG 59.526 55.000 0.00 0.00 42.61 4.85
1867 3442 0.474184 CATTTATGGAGGGACCGGCT 59.526 55.000 0.00 0.00 42.61 5.52
1868 3443 0.472471 TCATTTATGGAGGGACCGGC 59.528 55.000 0.00 0.00 42.61 6.13
1869 3444 2.371841 TCATCATTTATGGAGGGACCGG 59.628 50.000 0.00 0.00 42.61 5.28
1870 3445 3.403038 GTCATCATTTATGGAGGGACCG 58.597 50.000 0.00 0.00 42.61 4.79
1915 3490 4.097286 GCCGGCCTAATATTTGAGACAAAA 59.903 41.667 18.11 0.00 0.00 2.44
2025 3606 4.899239 GCTGGGATGACGAGGGCG 62.899 72.222 0.00 0.00 44.79 6.13
2138 3720 1.771255 AGGTTTCAGCCTTCAGACTGT 59.229 47.619 1.59 0.00 34.71 3.55
2141 3723 4.837972 AGAATAGGTTTCAGCCTTCAGAC 58.162 43.478 0.00 0.00 39.94 3.51
2193 6701 7.172532 TGGACGGCTCATATTATTTTGATGTAC 59.827 37.037 0.00 0.00 0.00 2.90
2369 6964 2.278026 TCGTGTCGTTGGATCTCATG 57.722 50.000 0.00 0.00 0.00 3.07
2370 6965 3.190079 CAATCGTGTCGTTGGATCTCAT 58.810 45.455 0.00 0.00 0.00 2.90
2372 6967 2.607187 ACAATCGTGTCGTTGGATCTC 58.393 47.619 0.00 0.00 29.49 2.75
2373 6968 2.743636 ACAATCGTGTCGTTGGATCT 57.256 45.000 0.00 0.00 29.49 2.75
2386 6981 4.238761 ACCCATCGACTATGTACAATCG 57.761 45.455 17.00 17.00 33.34 3.34


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

AutoCloner maintained by Alex Coulton.