Multiple sequence alignment - TraesCS6B01G105600

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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 TraesCS6B01G105600 chr6B 100.000 4038 0 0 1 4038 85666548 85670585 0.000000e+00 7457
1 TraesCS6B01G105600 chr6B 94.626 1470 66 11 1 1458 42180199 42178731 0.000000e+00 2265
2 TraesCS6B01G105600 chr7B 97.241 4059 89 13 1 4038 300045246 300049302 0.000000e+00 6854
3 TraesCS6B01G105600 chr7B 95.117 3461 144 18 597 4038 19805730 19809184 0.000000e+00 5432
4 TraesCS6B01G105600 chr7B 91.788 1303 91 11 597 1888 192832811 192831514 0.000000e+00 1799
5 TraesCS6B01G105600 chr4B 96.919 4057 102 15 1 4038 434983545 434987597 0.000000e+00 6778
6 TraesCS6B01G105600 chr3B 96.796 4058 106 15 1 4038 545968847 545964794 0.000000e+00 6752
7 TraesCS6B01G105600 chr3B 96.451 4057 110 17 1 4038 151818818 151814777 0.000000e+00 6663
8 TraesCS6B01G105600 chr3B 93.777 1864 89 12 49 1888 151822490 151820630 0.000000e+00 2774
9 TraesCS6B01G105600 chr3B 94.619 1468 68 9 1 1458 664729684 664728218 0.000000e+00 2263
10 TraesCS6B01G105600 chr3B 91.776 1301 97 7 597 1888 545971962 545970663 0.000000e+00 1801
11 TraesCS6B01G105600 chr3B 87.262 1311 143 14 597 1888 355966872 355965567 0.000000e+00 1474
12 TraesCS6B01G105600 chr3B 81.296 941 133 27 597 1519 171435945 171435030 0.000000e+00 723
13 TraesCS6B01G105600 chr3B 80.806 943 138 29 597 1519 310884889 310885808 0.000000e+00 699
14 TraesCS6B01G105600 chr2B 94.394 2408 87 17 1650 4038 514551595 514549217 0.000000e+00 3655
15 TraesCS6B01G105600 chr2B 80.978 941 137 29 597 1519 433375845 433376761 0.000000e+00 708
16 TraesCS6B01G105600 chr2B 80.021 941 142 28 597 1518 515534580 515535493 0.000000e+00 654
17 TraesCS6B01G105600 chr6A 96.569 2157 56 8 1890 4038 158978414 158976268 0.000000e+00 3557
18 TraesCS6B01G105600 chr5A 96.430 2157 63 8 1890 4038 541981948 541984098 0.000000e+00 3544
19 TraesCS6B01G105600 chr5A 96.387 2159 62 9 1890 4038 465659167 465661319 0.000000e+00 3541
20 TraesCS6B01G105600 chr5A 91.872 1378 75 20 1 1362 142248019 142246663 0.000000e+00 1890
21 TraesCS6B01G105600 chr2A 96.387 2159 62 10 1890 4038 284804964 284807116 0.000000e+00 3541
22 TraesCS6B01G105600 chr2A 93.033 1378 61 18 1 1362 685100611 685099253 0.000000e+00 1980
23 TraesCS6B01G105600 chr2A 92.572 552 25 8 1 537 384171183 384170633 0.000000e+00 778
24 TraesCS6B01G105600 chr1B 94.320 1479 62 12 1 1458 84522054 84520577 0.000000e+00 2246
25 TraesCS6B01G105600 chr1A 93.396 1378 56 18 1 1362 70942059 70940701 0.000000e+00 2008
26 TraesCS6B01G105600 chr3A 91.257 1384 80 23 1 1362 417397295 417398659 0.000000e+00 1847
27 TraesCS6B01G105600 chr4A 82.549 1318 185 29 597 1889 278180678 278179381 0.000000e+00 1118
28 TraesCS6B01G105600 chr7A 83.824 748 99 17 1153 1889 616374610 616375346 0.000000e+00 691
29 TraesCS6B01G105600 chr7A 82.602 638 92 12 1175 1803 469511526 469512153 2.740000e-151 545


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 TraesCS6B01G105600 chr6B 85666548 85670585 4037 False 7457.0 7457 100.000 1 4038 1 chr6B.!!$F1 4037
1 TraesCS6B01G105600 chr6B 42178731 42180199 1468 True 2265.0 2265 94.626 1 1458 1 chr6B.!!$R1 1457
2 TraesCS6B01G105600 chr7B 300045246 300049302 4056 False 6854.0 6854 97.241 1 4038 1 chr7B.!!$F2 4037
3 TraesCS6B01G105600 chr7B 19805730 19809184 3454 False 5432.0 5432 95.117 597 4038 1 chr7B.!!$F1 3441
4 TraesCS6B01G105600 chr7B 192831514 192832811 1297 True 1799.0 1799 91.788 597 1888 1 chr7B.!!$R1 1291
5 TraesCS6B01G105600 chr4B 434983545 434987597 4052 False 6778.0 6778 96.919 1 4038 1 chr4B.!!$F1 4037
6 TraesCS6B01G105600 chr3B 151814777 151822490 7713 True 4718.5 6663 95.114 1 4038 2 chr3B.!!$R4 4037
7 TraesCS6B01G105600 chr3B 545964794 545971962 7168 True 4276.5 6752 94.286 1 4038 2 chr3B.!!$R5 4037
8 TraesCS6B01G105600 chr3B 664728218 664729684 1466 True 2263.0 2263 94.619 1 1458 1 chr3B.!!$R3 1457
9 TraesCS6B01G105600 chr3B 355965567 355966872 1305 True 1474.0 1474 87.262 597 1888 1 chr3B.!!$R2 1291
10 TraesCS6B01G105600 chr3B 171435030 171435945 915 True 723.0 723 81.296 597 1519 1 chr3B.!!$R1 922
11 TraesCS6B01G105600 chr3B 310884889 310885808 919 False 699.0 699 80.806 597 1519 1 chr3B.!!$F1 922
12 TraesCS6B01G105600 chr2B 514549217 514551595 2378 True 3655.0 3655 94.394 1650 4038 1 chr2B.!!$R1 2388
13 TraesCS6B01G105600 chr2B 433375845 433376761 916 False 708.0 708 80.978 597 1519 1 chr2B.!!$F1 922
14 TraesCS6B01G105600 chr2B 515534580 515535493 913 False 654.0 654 80.021 597 1518 1 chr2B.!!$F2 921
15 TraesCS6B01G105600 chr6A 158976268 158978414 2146 True 3557.0 3557 96.569 1890 4038 1 chr6A.!!$R1 2148
16 TraesCS6B01G105600 chr5A 541981948 541984098 2150 False 3544.0 3544 96.430 1890 4038 1 chr5A.!!$F2 2148
17 TraesCS6B01G105600 chr5A 465659167 465661319 2152 False 3541.0 3541 96.387 1890 4038 1 chr5A.!!$F1 2148
18 TraesCS6B01G105600 chr5A 142246663 142248019 1356 True 1890.0 1890 91.872 1 1362 1 chr5A.!!$R1 1361
19 TraesCS6B01G105600 chr2A 284804964 284807116 2152 False 3541.0 3541 96.387 1890 4038 1 chr2A.!!$F1 2148
20 TraesCS6B01G105600 chr2A 685099253 685100611 1358 True 1980.0 1980 93.033 1 1362 1 chr2A.!!$R2 1361
21 TraesCS6B01G105600 chr2A 384170633 384171183 550 True 778.0 778 92.572 1 537 1 chr2A.!!$R1 536
22 TraesCS6B01G105600 chr1B 84520577 84522054 1477 True 2246.0 2246 94.320 1 1458 1 chr1B.!!$R1 1457
23 TraesCS6B01G105600 chr1A 70940701 70942059 1358 True 2008.0 2008 93.396 1 1362 1 chr1A.!!$R1 1361
24 TraesCS6B01G105600 chr3A 417397295 417398659 1364 False 1847.0 1847 91.257 1 1362 1 chr3A.!!$F1 1361
25 TraesCS6B01G105600 chr4A 278179381 278180678 1297 True 1118.0 1118 82.549 597 1889 1 chr4A.!!$R1 1292
26 TraesCS6B01G105600 chr7A 616374610 616375346 736 False 691.0 691 83.824 1153 1889 1 chr7A.!!$F2 736
27 TraesCS6B01G105600 chr7A 469511526 469512153 627 False 545.0 545 82.602 1175 1803 1 chr7A.!!$F1 628

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
355 3487 0.313672 GCCACTCGCACCAAAAATCA 59.686 50.000 0.0 0.0 37.47 2.57 F
509 3656 0.400213 CAACAACTCCCAGGGCACTA 59.600 55.000 0.0 0.0 0.00 2.74 F
1367 8264 5.692115 TGGTGAGCAATCCTACTCATTTA 57.308 39.130 0.0 0.0 44.29 1.40 F
2703 9630 4.625800 GCGGATGCTGGAGAAGTT 57.374 55.556 0.0 0.0 38.39 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1409 8307 8.547894 GTTGGGAAACAAGTGTGATTAAATTTC 58.452 33.333 0.0 0.0 40.38 2.17 R
1764 8671 9.859427 AAATGTTGTATGTTCTTCATTGGTATG 57.141 29.630 0.0 0.0 37.91 2.39 R
2886 9813 2.159476 GCGTACGTGATGAGGTTGTCTA 60.159 50.000 17.9 0.0 0.00 2.59 R
3873 10812 5.122239 TGTCTTCTGTTGTGTTTCTTGTGAG 59.878 40.000 0.0 0.0 0.00 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
316 3439 9.495572 TTCAAACATACATACAACATCAGTACA 57.504 29.630 0.00 0.00 0.00 2.90
349 3481 3.555324 TCAGGCCACTCGCACCAA 61.555 61.111 5.01 0.00 40.31 3.67
350 3482 2.594303 CAGGCCACTCGCACCAAA 60.594 61.111 5.01 0.00 40.31 3.28
351 3483 2.192861 CAGGCCACTCGCACCAAAA 61.193 57.895 5.01 0.00 40.31 2.44
352 3484 1.454847 AGGCCACTCGCACCAAAAA 60.455 52.632 5.01 0.00 40.31 1.94
353 3485 0.827507 AGGCCACTCGCACCAAAAAT 60.828 50.000 5.01 0.00 40.31 1.82
354 3486 0.388520 GGCCACTCGCACCAAAAATC 60.389 55.000 0.00 0.00 40.31 2.17
355 3487 0.313672 GCCACTCGCACCAAAAATCA 59.686 50.000 0.00 0.00 37.47 2.57
356 3488 1.666888 GCCACTCGCACCAAAAATCAG 60.667 52.381 0.00 0.00 37.47 2.90
358 3490 2.034558 CCACTCGCACCAAAAATCAGTT 59.965 45.455 0.00 0.00 0.00 3.16
359 3491 3.300009 CACTCGCACCAAAAATCAGTTC 58.700 45.455 0.00 0.00 0.00 3.01
509 3656 0.400213 CAACAACTCCCAGGGCACTA 59.600 55.000 0.00 0.00 0.00 2.74
1367 8264 5.692115 TGGTGAGCAATCCTACTCATTTA 57.308 39.130 0.00 0.00 44.29 1.40
1372 8270 5.903010 TGAGCAATCCTACTCATTTACCCTA 59.097 40.000 0.00 0.00 37.99 3.53
1570 8476 8.131100 GCGGAAGATTAAATTCTGAATTGATCA 58.869 33.333 25.47 0.00 35.45 2.92
1653 8559 9.736023 AAAAAGATGTTTCTGAACTTGATGTAC 57.264 29.630 0.00 0.00 36.70 2.90
2138 9062 8.846943 TTTCTGAACTTCATGAACTAGCATAA 57.153 30.769 3.38 0.00 0.00 1.90
2703 9630 4.625800 GCGGATGCTGGAGAAGTT 57.374 55.556 0.00 0.00 38.39 2.66
3208 10135 5.216566 TCAAGTACATCGTTTGCTTATGC 57.783 39.130 0.00 0.00 40.20 3.14
3420 10355 5.476945 TCTCAGTACAGCTTAGACATGAACA 59.523 40.000 0.00 0.00 0.00 3.18
3514 10450 7.119262 CCGAGGACAACATTCAGTACTAAAAAT 59.881 37.037 0.00 0.00 0.00 1.82
3688 10626 1.157585 GAACGGGAAGCTTCAGTTCC 58.842 55.000 33.71 23.72 42.57 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
316 3439 2.787994 CCTGACTGATCCTGCTGTTTT 58.212 47.619 0.00 0.00 0.00 2.43
1409 8307 8.547894 GTTGGGAAACAAGTGTGATTAAATTTC 58.452 33.333 0.00 0.00 40.38 2.17
1764 8671 9.859427 AAATGTTGTATGTTCTTCATTGGTATG 57.141 29.630 0.00 0.00 37.91 2.39
2138 9062 9.926158 CTATACTAGTGCATCAAGATCAGAATT 57.074 33.333 5.39 0.00 0.00 2.17
2886 9813 2.159476 GCGTACGTGATGAGGTTGTCTA 60.159 50.000 17.90 0.00 0.00 2.59
3208 10135 2.228822 AGCTAGCAAATTTGTTGGACGG 59.771 45.455 19.98 6.15 0.00 4.79
3688 10626 5.699458 AGTACGTCACTGTTTTAAGGAATGG 59.301 40.000 0.00 0.00 35.62 3.16
3766 10704 6.953101 TGTTTGGTATAATCCTAGCACTTGA 58.047 36.000 0.00 0.00 0.00 3.02
3858 10797 7.447374 TTCTTGTGAGTTTTCTCTTTTGTCA 57.553 32.000 0.00 0.00 46.30 3.58
3873 10812 5.122239 TGTCTTCTGTTGTGTTTCTTGTGAG 59.878 40.000 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.