Multiple sequence alignment - TraesCS1D01G453300

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 TraesCS1D01G453300 chr1D 100.000 2491 0 0 1 2491 494305863 494308353 0.000000e+00 4601
1 TraesCS1D01G453300 chr1D 85.968 1240 125 35 855 2057 494349617 494350844 0.000000e+00 1280
2 TraesCS1D01G453300 chr1D 83.062 738 83 24 934 1643 493782611 493781888 1.260000e-177 632
3 TraesCS1D01G453300 chr1A 95.666 2492 60 18 18 2491 592924130 592926591 0.000000e+00 3960
4 TraesCS1D01G453300 chr1A 86.895 1137 107 30 787 1889 592994122 592995250 0.000000e+00 1236
5 TraesCS1D01G453300 chr1A 83.154 742 79 29 934 1643 592100244 592099517 9.720000e-179 636
6 TraesCS1D01G453300 chr1A 85.106 517 63 4 933 1447 592852019 592852523 1.320000e-142 516
7 TraesCS1D01G453300 chr1A 81.835 534 43 36 30 541 592992980 592993481 1.390000e-107 399
8 TraesCS1D01G453300 chrUn 92.568 1830 79 21 640 2457 290639177 290637393 0.000000e+00 2573
9 TraesCS1D01G453300 chrUn 92.568 1830 79 21 640 2457 290644902 290643118 0.000000e+00 2573
10 TraesCS1D01G453300 chrUn 92.568 1830 79 21 640 2457 320337287 320339071 0.000000e+00 2573
11 TraesCS1D01G453300 chrUn 92.224 643 31 12 18 651 290639858 290639226 0.000000e+00 893
12 TraesCS1D01G453300 chrUn 92.224 643 31 12 18 651 290645583 290644951 0.000000e+00 893
13 TraesCS1D01G453300 chrUn 92.224 643 31 12 18 651 320336606 320337238 0.000000e+00 893
14 TraesCS1D01G453300 chr1B 86.133 1298 134 30 795 2057 687531275 687532561 0.000000e+00 1358


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 TraesCS1D01G453300 chr1D 494305863 494308353 2490 False 4601.0 4601 100.000 1 2491 1 chr1D.!!$F1 2490
1 TraesCS1D01G453300 chr1D 494349617 494350844 1227 False 1280.0 1280 85.968 855 2057 1 chr1D.!!$F2 1202
2 TraesCS1D01G453300 chr1D 493781888 493782611 723 True 632.0 632 83.062 934 1643 1 chr1D.!!$R1 709
3 TraesCS1D01G453300 chr1A 592924130 592926591 2461 False 3960.0 3960 95.666 18 2491 1 chr1A.!!$F2 2473
4 TraesCS1D01G453300 chr1A 592992980 592995250 2270 False 817.5 1236 84.365 30 1889 2 chr1A.!!$F3 1859
5 TraesCS1D01G453300 chr1A 592099517 592100244 727 True 636.0 636 83.154 934 1643 1 chr1A.!!$R1 709
6 TraesCS1D01G453300 chr1A 592852019 592852523 504 False 516.0 516 85.106 933 1447 1 chr1A.!!$F1 514
7 TraesCS1D01G453300 chrUn 290637393 290645583 8190 True 1733.0 2573 92.396 18 2457 4 chrUn.!!$R1 2439
8 TraesCS1D01G453300 chrUn 320336606 320339071 2465 False 1733.0 2573 92.396 18 2457 2 chrUn.!!$F1 2439
9 TraesCS1D01G453300 chr1B 687531275 687532561 1286 False 1358.0 1358 86.133 795 2057 1 chr1B.!!$F1 1262

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
185 200 3.202906 TGTGAAACTAGTGCACCTTGAC 58.797 45.455 14.63 7.17 38.04 3.18 F
1077 1618 2.747460 TCCTCCATGCTGCGCAAC 60.747 61.111 13.05 7.98 43.62 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1364 1924 0.176910 TGGCGTTATCATCAGCGGAA 59.823 50.0 0.0 0.0 0.0 4.30 R
2135 8485 0.179032 TCACAACATTGACCTGGCGT 60.179 50.0 0.0 0.0 0.0 5.68 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
58 69 6.800072 AAGCTCTAAGGTTCATAGCTACTT 57.200 37.500 0.00 0.00 42.49 2.24
94 105 6.566197 TTCTGCCTTCTTCATTTTTCTCTC 57.434 37.500 0.00 0.00 0.00 3.20
98 109 5.352569 TGCCTTCTTCATTTTTCTCTCGATC 59.647 40.000 0.00 0.00 0.00 3.69
185 200 3.202906 TGTGAAACTAGTGCACCTTGAC 58.797 45.455 14.63 7.17 38.04 3.18
259 278 4.289238 TGCATCCATTTTTGCCATTTCT 57.711 36.364 0.00 0.00 38.08 2.52
405 441 5.277857 AGTACACCATAGGCTCACATAAC 57.722 43.478 0.00 0.00 0.00 1.89
508 547 5.385198 TGTTTCTTTTGTCCTCATAGGCTT 58.615 37.500 0.00 0.00 34.61 4.35
541 583 9.853921 GCAATCTACAATTTTCTTTTTCTTGTG 57.146 29.630 0.00 0.00 32.66 3.33
551 593 5.612725 TCTTTTTCTTGTGCCCTCATTTT 57.387 34.783 0.00 0.00 0.00 1.82
1003 1541 6.760298 CAGTTCTTTTAGCTAGCTGATCATGA 59.240 38.462 27.68 13.87 0.00 3.07
1077 1618 2.747460 TCCTCCATGCTGCGCAAC 60.747 61.111 13.05 7.98 43.62 4.17
1291 1843 5.006746 GTCACCTCATCGACACAATATTTCC 59.993 44.000 0.00 0.00 32.24 3.13
1364 1924 0.902531 ATGTGAAGATCGTCGGGGTT 59.097 50.000 4.15 0.00 0.00 4.11
1460 7745 2.103771 TGAGATTCTGCAGCCTATGGTC 59.896 50.000 9.47 0.00 0.00 4.02
1681 7995 8.963725 ACAATTATATGCATGGGATTGATGTAG 58.036 33.333 24.86 8.62 0.00 2.74
1921 8266 6.772360 TTAATCACAAAAGATATGCCAGCA 57.228 33.333 0.00 0.00 0.00 4.41
1923 8268 5.864418 ATCACAAAAGATATGCCAGCAAT 57.136 34.783 0.00 0.00 0.00 3.56
2135 8485 4.019411 TGCTCATGAGTTTACCCAGATGAA 60.019 41.667 23.38 0.00 0.00 2.57
2299 8650 6.458888 GGCTCTTCCAACTTAATCAATACAGC 60.459 42.308 0.00 0.00 34.01 4.40
2309 8660 2.871096 TCAATACAGCCCCGAGTTTT 57.129 45.000 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.949397 TCTGTTGCTTGCAGCTTGAG 59.051 50.000 10.50 0.89 42.97 3.02
1 2 1.612676 ATCTGTTGCTTGCAGCTTGA 58.387 45.000 10.50 8.91 42.97 3.02
2 3 2.227149 TGTATCTGTTGCTTGCAGCTTG 59.773 45.455 10.50 4.40 42.97 4.01
3 4 2.507484 TGTATCTGTTGCTTGCAGCTT 58.493 42.857 10.50 0.00 42.97 3.74
4 5 2.189594 TGTATCTGTTGCTTGCAGCT 57.810 45.000 10.50 0.00 42.97 4.24
5 6 2.223433 GGATGTATCTGTTGCTTGCAGC 60.223 50.000 2.51 2.51 42.82 5.25
6 7 3.276857 AGGATGTATCTGTTGCTTGCAG 58.723 45.455 0.00 0.00 35.43 4.41
7 8 3.273434 GAGGATGTATCTGTTGCTTGCA 58.727 45.455 0.00 0.00 0.00 4.08
8 9 2.615912 GGAGGATGTATCTGTTGCTTGC 59.384 50.000 0.00 0.00 0.00 4.01
9 10 3.624861 GTGGAGGATGTATCTGTTGCTTG 59.375 47.826 0.00 0.00 0.00 4.01
10 11 3.370953 GGTGGAGGATGTATCTGTTGCTT 60.371 47.826 0.00 0.00 0.00 3.91
11 12 2.171448 GGTGGAGGATGTATCTGTTGCT 59.829 50.000 0.00 0.00 0.00 3.91
12 13 2.092968 TGGTGGAGGATGTATCTGTTGC 60.093 50.000 0.00 0.00 0.00 4.17
13 14 3.912496 TGGTGGAGGATGTATCTGTTG 57.088 47.619 0.00 0.00 0.00 3.33
14 15 5.455326 GCTTATGGTGGAGGATGTATCTGTT 60.455 44.000 0.00 0.00 0.00 3.16
15 16 4.040952 GCTTATGGTGGAGGATGTATCTGT 59.959 45.833 0.00 0.00 0.00 3.41
16 17 4.285517 AGCTTATGGTGGAGGATGTATCTG 59.714 45.833 0.00 0.00 0.00 2.90
58 69 2.057922 AGGCAGAAACAGAGGAAGGAA 58.942 47.619 0.00 0.00 0.00 3.36
94 105 1.723542 GTAGAAGATGCATGGCGATCG 59.276 52.381 11.69 11.69 0.00 3.69
98 109 3.377346 ACTAGTAGAAGATGCATGGCG 57.623 47.619 2.46 0.00 0.00 5.69
185 200 3.441222 TGTGCTGCATAGATCAAAACCTG 59.559 43.478 5.27 0.00 0.00 4.00
259 278 5.443955 CGAAAAAGCAAAGAACGCAAGAAAA 60.444 36.000 0.00 0.00 43.62 2.29
405 441 8.171164 AGAGAAAAGGAACAAAAGAACATAGG 57.829 34.615 0.00 0.00 0.00 2.57
581 623 1.392589 ACCACCAGTGCAACAAGAAG 58.607 50.000 0.00 0.00 41.43 2.85
778 955 2.402564 TGAGGGGAAGAGATGGTGATC 58.597 52.381 0.00 0.00 0.00 2.92
1003 1541 1.064166 CAATGCCTTGAGGGAGGATGT 60.064 52.381 0.00 0.00 39.50 3.06
1077 1618 0.460987 GGGTGATCTCGCAGTGGAAG 60.461 60.000 6.94 0.00 0.00 3.46
1291 1843 2.095567 GCCTGTCAAGCAACATGTACAG 60.096 50.000 14.59 14.59 35.29 2.74
1364 1924 0.176910 TGGCGTTATCATCAGCGGAA 59.823 50.000 0.00 0.00 0.00 4.30
1460 7745 3.008375 TCTTCTTGTTGATGACCTCCTGG 59.992 47.826 0.00 0.00 39.83 4.45
1681 7995 6.803154 AAATTAACAGGAAGTGCTACAGAC 57.197 37.500 0.00 0.00 0.00 3.51
1763 8097 6.892658 ATTATCAAACACTTGTTGGTAGCA 57.107 33.333 0.00 0.00 38.44 3.49
1921 8266 5.736951 TCCACCGGAAAATTCAAATGATT 57.263 34.783 9.46 0.00 0.00 2.57
1952 8298 2.228822 ACAGTCCATTTGAAATCACGCC 59.771 45.455 0.00 0.00 0.00 5.68
2135 8485 0.179032 TCACAACATTGACCTGGCGT 60.179 50.000 0.00 0.00 0.00 5.68
2233 8583 3.820467 CCAGCAAACTACCATCAACTGAA 59.180 43.478 0.00 0.00 0.00 3.02
2309 8660 1.548269 CTGGATGGCCGCCTTTAAAAA 59.452 47.619 11.61 0.00 36.79 1.94
2366 8720 9.533253 AAGTGAGAACCTTTTCATGTATTTTTG 57.467 29.630 0.00 0.00 33.72 2.44
2381 8735 1.900486 CTCGGGGTAAAGTGAGAACCT 59.100 52.381 0.00 0.00 33.59 3.50
2385 8739 2.893215 TCTCTCGGGGTAAAGTGAGA 57.107 50.000 0.00 0.00 35.47 3.27


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

AutoCloner maintained by Alex Coulton.