Multiple sequence alignment - TraesCS4A01G279100

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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 TraesCS4A01G279100 chr4A 100.000 2669 0 0 1 2669 586683725 586681057 0.000000e+00 4929.0
1 TraesCS4A01G279100 chr4A 97.689 1601 33 3 468 2065 456437665 456436066 0.000000e+00 2748.0
2 TraesCS4A01G279100 chr4A 86.478 1590 136 48 704 2253 586700172 586698622 0.000000e+00 1672.0
3 TraesCS4A01G279100 chr4A 87.251 1153 105 22 557 1692 456450398 456449271 0.000000e+00 1277.0
4 TraesCS4A01G279100 chr4A 98.053 565 10 1 2061 2625 456420488 456419925 0.000000e+00 981.0
5 TraesCS4A01G279100 chr4A 95.672 439 10 2 7 444 456443779 456443349 0.000000e+00 697.0
6 TraesCS4A01G279100 chr4A 92.021 188 13 2 554 741 586700368 586700183 2.040000e-66 263.0
7 TraesCS4A01G279100 chr4A 97.619 42 0 1 440 481 456437726 456437686 1.330000e-08 71.3
8 TraesCS4A01G279100 chr4B 85.405 2768 249 72 3 2669 24744745 24747458 0.000000e+00 2730.0
9 TraesCS4A01G279100 chr4B 87.218 1815 157 35 552 2331 24759013 24760787 0.000000e+00 1997.0
10 TraesCS4A01G279100 chr4B 86.782 1445 135 33 539 1964 24741208 24742615 0.000000e+00 1559.0
11 TraesCS4A01G279100 chr4B 86.807 379 33 9 18 381 24758340 24758716 8.900000e-110 407.0
12 TraesCS4A01G279100 chr4B 91.954 174 11 3 156 329 24739504 24739674 9.550000e-60 241.0
13 TraesCS4A01G279100 chr3B 86.642 2171 203 43 539 2669 452717389 452715266 0.000000e+00 2322.0
14 TraesCS4A01G279100 chr3B 82.278 474 30 22 18 471 452717927 452717488 7.020000e-96 361.0
15 TraesCS4A01G279100 chr4D 88.711 1816 146 33 557 2341 14914191 14915978 0.000000e+00 2163.0
16 TraesCS4A01G279100 chr4D 87.113 1614 139 37 753 2313 14862557 14864154 0.000000e+00 1764.0
17 TraesCS4A01G279100 chr4D 85.613 1689 166 38 687 2340 14851054 14852700 0.000000e+00 1701.0
18 TraesCS4A01G279100 chr4D 86.587 1506 139 37 539 2004 14460202 14458720 0.000000e+00 1604.0
19 TraesCS4A01G279100 chr4D 86.671 1448 141 30 539 1960 14908930 14910351 0.000000e+00 1557.0
20 TraesCS4A01G279100 chr4D 87.084 782 64 14 1702 2465 14433509 14432747 0.000000e+00 850.0
21 TraesCS4A01G279100 chr4D 92.705 329 17 3 2341 2669 14918974 14919295 4.020000e-128 468.0
22 TraesCS4A01G279100 chr4D 84.114 491 35 22 18 471 14908113 14908597 4.080000e-118 435.0
23 TraesCS4A01G279100 chr4D 85.894 397 33 9 18 393 14460936 14460542 4.140000e-108 401.0
24 TraesCS4A01G279100 chr4D 84.225 355 26 12 40 367 14913426 14913777 4.290000e-83 318.0
25 TraesCS4A01G279100 chr4D 82.984 382 27 19 539 893 14895785 14896155 7.170000e-81 311.0
26 TraesCS4A01G279100 chr4D 95.699 186 8 0 554 739 14850871 14851056 1.550000e-77 300.0
27 TraesCS4A01G279100 chr4D 84.790 309 16 9 18 321 14867160 14867442 5.630000e-72 281.0


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 TraesCS4A01G279100 chr4A 586681057 586683725 2668 True 4929.00 4929 100.0000 1 2669 1 chr4A.!!$R4 2668
1 TraesCS4A01G279100 chr4A 456436066 456437726 1660 True 1409.65 2748 97.6540 440 2065 2 chr4A.!!$R5 1625
2 TraesCS4A01G279100 chr4A 456449271 456450398 1127 True 1277.00 1277 87.2510 557 1692 1 chr4A.!!$R3 1135
3 TraesCS4A01G279100 chr4A 456419925 456420488 563 True 981.00 981 98.0530 2061 2625 1 chr4A.!!$R1 564
4 TraesCS4A01G279100 chr4A 586698622 586700368 1746 True 967.50 1672 89.2495 554 2253 2 chr4A.!!$R6 1699
5 TraesCS4A01G279100 chr4B 24739504 24747458 7954 False 1510.00 2730 88.0470 3 2669 3 chr4B.!!$F1 2666
6 TraesCS4A01G279100 chr4B 24758340 24760787 2447 False 1202.00 1997 87.0125 18 2331 2 chr4B.!!$F2 2313
7 TraesCS4A01G279100 chr3B 452715266 452717927 2661 True 1341.50 2322 84.4600 18 2669 2 chr3B.!!$R1 2651
8 TraesCS4A01G279100 chr4D 14862557 14867442 4885 False 1022.50 1764 85.9515 18 2313 2 chr4D.!!$F3 2295
9 TraesCS4A01G279100 chr4D 14458720 14460936 2216 True 1002.50 1604 86.2405 18 2004 2 chr4D.!!$R2 1986
10 TraesCS4A01G279100 chr4D 14850871 14852700 1829 False 1000.50 1701 90.6560 554 2340 2 chr4D.!!$F2 1786
11 TraesCS4A01G279100 chr4D 14908113 14919295 11182 False 988.20 2163 87.2852 18 2669 5 chr4D.!!$F4 2651
12 TraesCS4A01G279100 chr4D 14432747 14433509 762 True 850.00 850 87.0840 1702 2465 1 chr4D.!!$R1 763

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
473 5808 1.153765 TGCGTTGCAGATCGAGGAG 60.154 57.895 11.11 0.0 33.32 3.69 F
477 5812 2.123342 CGTTGCAGATCGAGGAGAATC 58.877 52.381 0.00 0.0 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1500 12737 0.904865 AGGAGACGACCATGGAAGCA 60.905 55.000 21.47 0.0 0.00 3.91 R
1737 12976 2.231235 TGCACGTCTTCTGCTGAGAATA 59.769 45.455 0.00 0.0 37.58 1.75 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
74 5314 3.179443 AGAAAGTCTGACTCGCAACAA 57.821 42.857 11.31 0.00 0.00 2.83
80 5322 2.397413 CTGACTCGCAACAACCCCCT 62.397 60.000 0.00 0.00 0.00 4.79
99 5341 2.287788 CCTGTTGATTGCCACTGACAAC 60.288 50.000 0.00 0.00 40.44 3.32
108 5350 2.499289 TGCCACTGACAACCATGTTTTT 59.501 40.909 0.00 0.00 40.74 1.94
134 5380 2.320587 CGCTGGCGCCATATCTTCC 61.321 63.158 32.87 11.11 0.00 3.46
135 5381 2.320587 GCTGGCGCCATATCTTCCG 61.321 63.158 32.87 17.01 0.00 4.30
294 5548 5.107989 CGATCGAGAAGAGAAACGAAACAAA 60.108 40.000 10.26 0.00 38.22 2.83
296 5550 6.032722 TCGAGAAGAGAAACGAAACAAAAG 57.967 37.500 0.00 0.00 0.00 2.27
335 5616 1.380785 CGGAGCCAGGGTAGGTACA 60.381 63.158 0.00 0.00 0.00 2.90
342 5630 3.070576 GGGTAGGTACACCGCGGT 61.071 66.667 28.70 28.70 39.69 5.68
355 5650 2.665603 GCGGTCAGAAGCTTCCCT 59.334 61.111 22.81 2.23 0.00 4.20
367 5662 2.704572 AGCTTCCCTTTTCTGACGATG 58.295 47.619 0.00 0.00 0.00 3.84
368 5663 2.303022 AGCTTCCCTTTTCTGACGATGA 59.697 45.455 0.00 0.00 0.00 2.92
398 5699 2.973155 GCGCTAGCAAACGTTAGTAG 57.027 50.000 16.45 4.23 44.35 2.57
422 5723 3.376859 AGATGTCTCTTCAGCGAGTACAG 59.623 47.826 0.00 0.00 32.83 2.74
425 5726 3.189495 TGTCTCTTCAGCGAGTACAGAAG 59.811 47.826 0.00 0.00 38.98 2.85
473 5808 1.153765 TGCGTTGCAGATCGAGGAG 60.154 57.895 11.11 0.00 33.32 3.69
477 5812 2.123342 CGTTGCAGATCGAGGAGAATC 58.877 52.381 0.00 0.00 0.00 2.52
983 12209 3.019564 CCCTAGCTAAGCTTGTTGCATT 58.980 45.455 9.86 0.00 45.94 3.56
984 12210 3.445096 CCCTAGCTAAGCTTGTTGCATTT 59.555 43.478 9.86 0.00 45.94 2.32
985 12211 4.418392 CCTAGCTAAGCTTGTTGCATTTG 58.582 43.478 9.86 3.22 45.94 2.32
986 12212 4.082571 CCTAGCTAAGCTTGTTGCATTTGT 60.083 41.667 9.86 0.00 45.94 2.83
2006 13262 7.769220 AGCAATCTCGAAATCATTCAGAAAAT 58.231 30.769 0.00 0.00 35.15 1.82
2086 13346 4.986659 AGCAATCTCAAGAATGTGCAAAAC 59.013 37.500 13.08 0.00 34.71 2.43
2145 13414 0.685131 ACATGGATCCACCGTCCGTA 60.685 55.000 18.99 0.00 42.61 4.02
2264 13559 4.693532 TGGCTCGCCACTTAGTTG 57.306 55.556 6.52 0.00 41.89 3.16
2289 13586 2.187946 GACCTCCATGCTCACCCG 59.812 66.667 0.00 0.00 0.00 5.28
2374 19229 7.486407 TTCTCTATATGGATCTGCTGCAATA 57.514 36.000 3.02 0.00 0.00 1.90
2574 19431 1.972660 GATGGAGGGAGTGGGTTCGG 61.973 65.000 0.00 0.00 0.00 4.30
2614 19471 4.994852 GGTGAATGTAACTACTTCAGTGCA 59.005 41.667 0.00 0.00 37.63 4.57
2636 19493 1.067212 ACTCGTGACTTGTTTCTCGCT 59.933 47.619 0.00 0.00 33.54 4.93
2652 19509 2.301505 GCTGCTACGCGATGTGAAT 58.698 52.632 15.93 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 5255 2.421751 CTCCAGTCTCCGGAGTAAGA 57.578 55.000 30.17 20.22 44.35 2.10
74 5314 1.228862 GTGGCAATCAACAGGGGGT 60.229 57.895 0.00 0.00 0.00 4.95
80 5322 1.680735 GGTTGTCAGTGGCAATCAACA 59.319 47.619 15.85 8.32 39.71 3.33
99 5341 3.001127 CCAGCGAAACAACAAAAACATGG 59.999 43.478 0.00 0.00 0.00 3.66
108 5350 3.959975 GGCGCCAGCGAAACAACA 61.960 61.111 24.80 0.00 46.35 3.33
134 5380 6.075415 CCTTGCACTTTAAATATTCGATTGCG 60.075 38.462 0.00 0.00 39.35 4.85
135 5381 6.972328 TCCTTGCACTTTAAATATTCGATTGC 59.028 34.615 0.00 0.00 0.00 3.56
211 5463 3.118531 AGGGATTCTCATTGGCTACTGT 58.881 45.455 0.00 0.00 0.00 3.55
212 5464 3.853355 AGGGATTCTCATTGGCTACTG 57.147 47.619 0.00 0.00 0.00 2.74
268 5522 3.386613 TCGTTTCTCTTCTCGATCGAC 57.613 47.619 15.15 0.36 0.00 4.20
294 5548 5.126384 CGGTCTCTCTCAAATAGTTCTCCTT 59.874 44.000 0.00 0.00 0.00 3.36
296 5550 4.202070 CCGGTCTCTCTCAAATAGTTCTCC 60.202 50.000 0.00 0.00 0.00 3.71
335 5616 2.048127 GAAGCTTCTGACCGCGGT 60.048 61.111 34.89 34.89 0.00 5.68
355 5650 6.512253 GCATAGCATGATTCATCGTCAGAAAA 60.512 38.462 0.00 0.00 0.00 2.29
396 5697 2.357323 CTCGCTGAAGAGACATCTGCTA 59.643 50.000 0.00 0.00 40.57 3.49
397 5698 1.134753 CTCGCTGAAGAGACATCTGCT 59.865 52.381 0.00 0.00 40.57 4.24
398 5699 1.135141 ACTCGCTGAAGAGACATCTGC 60.135 52.381 7.43 0.00 40.57 4.26
422 5723 2.199236 CCGCCGGTTTATCTGTACTTC 58.801 52.381 1.90 0.00 0.00 3.01
425 5726 1.156034 GGCCGCCGGTTTATCTGTAC 61.156 60.000 4.45 0.00 0.00 2.90
473 5808 3.896648 TTCAACCGAACTTGCTGATTC 57.103 42.857 0.00 0.00 0.00 2.52
477 5812 3.243035 TGTCATTTCAACCGAACTTGCTG 60.243 43.478 0.00 0.00 0.00 4.41
1357 12594 2.158986 CGAGGAGCTCACCTTTCATCAT 60.159 50.000 17.19 0.00 40.73 2.45
1500 12737 0.904865 AGGAGACGACCATGGAAGCA 60.905 55.000 21.47 0.00 0.00 3.91
1737 12976 2.231235 TGCACGTCTTCTGCTGAGAATA 59.769 45.455 0.00 0.00 37.58 1.75
1812 13057 4.141620 GGATCTGAAGGCTAAACCATGAGA 60.142 45.833 0.00 0.00 43.14 3.27
2006 13262 8.710835 TGTATTCACGTAATTTTGAGAGCATA 57.289 30.769 0.00 0.00 0.00 3.14
2086 13346 5.766150 TGGTAGAAAAACCACTCATGTTG 57.234 39.130 0.00 0.00 44.68 3.33
2374 19229 3.264193 TGACACTAGAAGACCCATTGCAT 59.736 43.478 0.00 0.00 0.00 3.96
2574 19431 2.690497 TCACCTCGGATCAAGATCTGAC 59.310 50.000 15.72 0.00 45.50 3.51
2614 19471 2.284417 GCGAGAAACAAGTCACGAGTTT 59.716 45.455 0.92 0.92 38.10 2.66


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

AutoCloner maintained by Alex Coulton.