Multiple sequence alignment - TraesCS1B01G214300

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 TraesCS1B01G214300 chr1B 100.000 2880 0 0 1 2880 389088837 389091716 0.000000e+00 5319.0
1 TraesCS1B01G214300 chr1B 95.760 2052 66 14 1 2038 389006625 389008669 0.000000e+00 3288.0
2 TraesCS1B01G214300 chr1B 91.282 585 40 9 1 578 319161911 319161331 0.000000e+00 787.0
3 TraesCS1B01G214300 chr1B 92.096 544 35 7 1 540 118173242 118173781 0.000000e+00 760.0
4 TraesCS1B01G214300 chr1A 93.838 2337 69 27 591 2880 358174586 358176894 0.000000e+00 3448.0
5 TraesCS1B01G214300 chr1A 94.409 1574 60 14 591 2150 358151112 358152671 0.000000e+00 2394.0
6 TraesCS1B01G214300 chr1D 96.972 1321 33 2 591 1911 286749702 286751015 0.000000e+00 2211.0
7 TraesCS1B01G214300 chr1D 96.017 929 26 10 1956 2880 286751018 286751939 0.000000e+00 1500.0
8 TraesCS1B01G214300 chrUn 93.846 585 28 6 1 578 347152999 347152416 0.000000e+00 874.0
9 TraesCS1B01G214300 chr5D 93.139 583 32 7 1 578 554386888 554387467 0.000000e+00 848.0
10 TraesCS1B01G214300 chr5D 92.991 585 31 8 1 578 92442736 92442155 0.000000e+00 845.0
11 TraesCS1B01G214300 chr2D 92.905 592 29 10 1 584 648655023 648655609 0.000000e+00 848.0
12 TraesCS1B01G214300 chr2B 90.206 582 47 8 1 578 407148466 407149041 0.000000e+00 750.0
13 TraesCS1B01G214300 chr2B 89.555 584 49 8 1 578 407103152 407103729 0.000000e+00 730.0
14 TraesCS1B01G214300 chr3D 73.944 284 70 4 1404 1685 157443216 157442935 8.440000e-21 111.0
15 TraesCS1B01G214300 chr3D 76.879 173 36 4 1404 1574 157540411 157540241 8.500000e-16 95.3
16 TraesCS1B01G214300 chr3A 73.611 288 67 8 1404 1685 170811851 170812135 5.080000e-18 102.0
17 TraesCS1B01G214300 chr5B 77.844 167 33 3 1403 1567 700997744 700997908 1.830000e-17 100.0
18 TraesCS1B01G214300 chr4B 86.022 93 13 0 1404 1496 547205193 547205285 1.830000e-17 100.0
19 TraesCS1B01G214300 chr4A 84.946 93 14 0 1404 1496 26413652 26413560 8.500000e-16 95.3


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 TraesCS1B01G214300 chr1B 389088837 389091716 2879 False 5319.0 5319 100.0000 1 2880 1 chr1B.!!$F3 2879
1 TraesCS1B01G214300 chr1B 389006625 389008669 2044 False 3288.0 3288 95.7600 1 2038 1 chr1B.!!$F2 2037
2 TraesCS1B01G214300 chr1B 319161331 319161911 580 True 787.0 787 91.2820 1 578 1 chr1B.!!$R1 577
3 TraesCS1B01G214300 chr1B 118173242 118173781 539 False 760.0 760 92.0960 1 540 1 chr1B.!!$F1 539
4 TraesCS1B01G214300 chr1A 358174586 358176894 2308 False 3448.0 3448 93.8380 591 2880 1 chr1A.!!$F2 2289
5 TraesCS1B01G214300 chr1A 358151112 358152671 1559 False 2394.0 2394 94.4090 591 2150 1 chr1A.!!$F1 1559
6 TraesCS1B01G214300 chr1D 286749702 286751939 2237 False 1855.5 2211 96.4945 591 2880 2 chr1D.!!$F1 2289
7 TraesCS1B01G214300 chrUn 347152416 347152999 583 True 874.0 874 93.8460 1 578 1 chrUn.!!$R1 577
8 TraesCS1B01G214300 chr5D 554386888 554387467 579 False 848.0 848 93.1390 1 578 1 chr5D.!!$F1 577
9 TraesCS1B01G214300 chr5D 92442155 92442736 581 True 845.0 845 92.9910 1 578 1 chr5D.!!$R1 577
10 TraesCS1B01G214300 chr2D 648655023 648655609 586 False 848.0 848 92.9050 1 584 1 chr2D.!!$F1 583
11 TraesCS1B01G214300 chr2B 407148466 407149041 575 False 750.0 750 90.2060 1 578 1 chr2B.!!$F2 577
12 TraesCS1B01G214300 chr2B 407103152 407103729 577 False 730.0 730 89.5550 1 578 1 chr2B.!!$F1 577

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
54 59 3.834813 TCAGTCATAGCTTCAGTTCAGGT 59.165 43.478 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1883 1916 1.153745 CCTCAGACCTTCGCTTCGG 60.154 63.158 0.0 0.0 0.0 4.3 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
54 59 3.834813 TCAGTCATAGCTTCAGTTCAGGT 59.165 43.478 0.00 0.00 0.00 4.00
311 324 4.207891 ACTGCAACTATCACCTCGATTT 57.792 40.909 0.00 0.00 35.39 2.17
346 359 7.201644 GCTGCTGCTATTACTTCAGATTTGTTA 60.202 37.037 8.53 0.00 36.03 2.41
446 459 6.619801 AAAGTTACGCTCTTCAGTCAAATT 57.380 33.333 0.00 0.00 0.00 1.82
510 524 4.401022 TCCATCCATTGTCTTATGGCATC 58.599 43.478 1.65 0.00 43.94 3.91
1367 1400 2.109181 GCTACCAGATCCGGTGCC 59.891 66.667 11.10 0.00 40.39 5.01
1883 1916 1.202188 GCGCCAACTTCAAATAGGAGC 60.202 52.381 0.00 0.00 37.96 4.70
1905 1938 2.771763 AAGCGAAGGTCTGAGGCACG 62.772 60.000 0.00 0.00 37.06 5.34
1920 1953 2.281761 ACGGCACAAGAAGCAGGG 60.282 61.111 0.00 0.00 0.00 4.45
1983 2018 1.202675 TCGTTGCCCTCTACCGTTTTT 60.203 47.619 0.00 0.00 0.00 1.94
2049 2092 0.955428 CCTGTCCATGTGAACCACGG 60.955 60.000 0.00 0.00 37.14 4.94
2076 2120 0.879090 TGACGCACGACTGATAGTGT 59.121 50.000 0.00 0.00 40.26 3.55
2105 2149 1.453148 GCAGCACGATCAAAGCAAAAC 59.547 47.619 0.00 0.00 0.00 2.43
2125 2169 4.935352 ACATTTGCAGGTTGTATTGTGT 57.065 36.364 0.00 0.00 0.00 3.72
2150 2194 9.888878 GTCTAAAAACACCCTAGTTCAATTAAC 57.111 33.333 0.00 0.00 38.46 2.01
2291 2338 5.543507 AGAAATCGCCTACAGAGAATCAT 57.456 39.130 0.00 0.00 37.82 2.45
2299 2346 7.778083 TCGCCTACAGAGAATCATTAACTTTA 58.222 34.615 0.00 0.00 37.82 1.85
2357 2404 2.207229 GGGTTCAACTGGGTTGCCC 61.207 63.158 9.24 9.24 42.55 5.36
2359 2406 0.759060 GGTTCAACTGGGTTGCCCTT 60.759 55.000 5.73 0.00 45.70 3.95
2360 2407 0.389025 GTTCAACTGGGTTGCCCTTG 59.611 55.000 5.73 3.16 45.70 3.61
2363 2410 4.621087 ACTGGGTTGCCCTTGCCC 62.621 66.667 5.73 0.00 45.70 5.36
2477 2529 5.440610 AGACACAATCAAGGAGTCAAGTTT 58.559 37.500 0.00 0.00 0.00 2.66
2773 2849 7.943079 ACAATGTGAATGGATGATACTGAAA 57.057 32.000 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 7.234355 ACTGAATTTTCCCTCATGTTACTTCT 58.766 34.615 0.00 0.00 0.00 2.85
28 29 6.373774 CCTGAACTGAAGCTATGACTGAATTT 59.626 38.462 0.00 0.00 0.00 1.82
120 127 9.625747 TCATATTAACATGTTTGATGCTTCCTA 57.374 29.630 17.78 0.00 0.00 2.94
1270 1303 1.798234 CGTACCCCGCCGTGATATCA 61.798 60.000 0.00 0.00 0.00 2.15
1367 1400 2.803155 TAGCAGGCCGTGGCTTTCAG 62.803 60.000 21.75 0.00 41.41 3.02
1706 1739 1.303888 CCCAGTTGTGGCTCATGCT 60.304 57.895 0.00 0.00 43.44 3.79
1786 1819 2.047560 GTCAGCCCGGTGGTGTAC 60.048 66.667 17.82 12.44 43.10 2.90
1883 1916 1.153745 CCTCAGACCTTCGCTTCGG 60.154 63.158 0.00 0.00 0.00 4.30
1905 1938 3.376918 GCCCCTGCTTCTTGTGCC 61.377 66.667 0.00 0.00 33.53 5.01
1920 1953 1.934463 CGTTGTCAGTGTCACAGCC 59.066 57.895 5.62 0.00 0.00 4.85
1983 2018 2.806608 AGTAAGGAACGAAGCAACGA 57.193 45.000 9.33 0.00 37.03 3.85
2076 2120 3.038788 TGATCGTGCTGCAGAGTTTTA 57.961 42.857 20.43 0.00 0.00 1.52
2105 2149 5.125100 AGACACAATACAACCTGCAAATG 57.875 39.130 0.00 0.00 0.00 2.32
2150 2194 2.095567 CACCTCTGATTGCACGGAAAAG 60.096 50.000 0.00 0.00 0.00 2.27
2291 2338 4.761227 GGGACGGGTGTTCAATAAAGTTAA 59.239 41.667 0.00 0.00 0.00 2.01
2299 2346 0.481128 AAAGGGGACGGGTGTTCAAT 59.519 50.000 0.00 0.00 0.00 2.57
2357 2404 3.441500 AGAGGTAAAAGAAGGGGCAAG 57.558 47.619 0.00 0.00 0.00 4.01
2359 2406 2.041216 GGAAGAGGTAAAAGAAGGGGCA 59.959 50.000 0.00 0.00 0.00 5.36
2360 2407 2.309162 AGGAAGAGGTAAAAGAAGGGGC 59.691 50.000 0.00 0.00 0.00 5.80
2477 2529 8.052141 TGAATGATGGATGTGTGGATACTTTTA 58.948 33.333 0.00 0.00 37.61 1.52
2773 2849 6.702329 ACAAGATTCTTTCATCCGTTAGTCT 58.298 36.000 0.00 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.