Multiple sequence alignment - TraesCS1B01G311300

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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 TraesCS1B01G311300 chr1B 100.000 2855 0 0 1 2855 534668503 534665649 0.000000e+00 5273.0
1 TraesCS1B01G311300 chr1B 95.455 44 2 0 757 800 443999174 443999217 1.420000e-08 71.3
2 TraesCS1B01G311300 chr1D 95.814 2532 88 9 336 2855 398978476 398975951 0.000000e+00 4072.0
3 TraesCS1B01G311300 chr1D 94.030 201 6 3 1 196 398978806 398978607 1.660000e-77 300.0
4 TraesCS1B01G311300 chr1A 95.446 1691 66 4 1166 2855 495704325 495702645 0.000000e+00 2686.0
5 TraesCS1B01G311300 chr1A 89.264 1127 67 30 1 1097 495705429 495704327 0.000000e+00 1362.0
6 TraesCS1B01G311300 chr7D 86.667 60 3 1 748 807 256187577 256187631 8.540000e-06 62.1
7 TraesCS1B01G311300 chr6A 93.023 43 1 2 707 748 34560247 34560206 8.540000e-06 62.1
8 TraesCS1B01G311300 chr4D 91.111 45 4 0 710 754 368007030 368007074 8.540000e-06 62.1
9 TraesCS1B01G311300 chrUn 97.059 34 0 1 707 740 470506527 470506495 3.970000e-04 56.5
10 TraesCS1B01G311300 chr6B 96.970 33 1 0 778 810 559287132 559287164 3.970000e-04 56.5
11 TraesCS1B01G311300 chr6B 100.000 28 0 0 780 807 501774016 501774043 5.000000e-03 52.8
12 TraesCS1B01G311300 chr6D 100.000 28 0 0 780 807 321773496 321773469 5.000000e-03 52.8
13 TraesCS1B01G311300 chr2B 100.000 28 0 0 703 730 120562149 120562176 5.000000e-03 52.8


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 TraesCS1B01G311300 chr1B 534665649 534668503 2854 True 5273 5273 100.000 1 2855 1 chr1B.!!$R1 2854
1 TraesCS1B01G311300 chr1D 398975951 398978806 2855 True 2186 4072 94.922 1 2855 2 chr1D.!!$R1 2854
2 TraesCS1B01G311300 chr1A 495702645 495705429 2784 True 2024 2686 92.355 1 2855 2 chr1A.!!$R1 2854

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
499 547 0.370273 CGCTATCGTGCAGACAAACC 59.63 55.0 0.0 0.0 0.0 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1886 1948 0.179048 CAATGGAGGCCGTGCTCATA 60.179 55.0 0.0 0.0 0.0 2.15 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
115 116 2.743183 CGCGGGGAAATCTGAATCTTCT 60.743 50.000 0.00 0.00 0.00 2.85
155 159 2.119495 TCAGGAGGAACATAGGCTTCC 58.881 52.381 0.00 0.00 37.99 3.46
165 169 0.621571 ATAGGCTTCCTGGTCCTGCA 60.622 55.000 12.72 0.00 34.61 4.41
188 200 7.356641 CACAAGGTATGTATCTATGTGCATC 57.643 40.000 0.00 0.00 41.46 3.91
189 201 7.157347 CACAAGGTATGTATCTATGTGCATCT 58.843 38.462 0.00 0.00 41.46 2.90
190 202 7.658982 CACAAGGTATGTATCTATGTGCATCTT 59.341 37.037 0.00 0.00 41.46 2.40
191 203 7.875041 ACAAGGTATGTATCTATGTGCATCTTC 59.125 37.037 0.00 0.00 41.63 2.87
192 204 7.789202 AGGTATGTATCTATGTGCATCTTCT 57.211 36.000 0.00 0.00 0.00 2.85
193 205 8.200024 AGGTATGTATCTATGTGCATCTTCTT 57.800 34.615 0.00 0.00 0.00 2.52
194 206 8.654997 AGGTATGTATCTATGTGCATCTTCTTT 58.345 33.333 0.00 0.00 0.00 2.52
195 207 8.930760 GGTATGTATCTATGTGCATCTTCTTTC 58.069 37.037 0.00 0.00 0.00 2.62
196 208 7.976135 ATGTATCTATGTGCATCTTCTTTCC 57.024 36.000 0.00 0.00 0.00 3.13
197 209 6.888105 TGTATCTATGTGCATCTTCTTTCCA 58.112 36.000 0.00 0.00 0.00 3.53
203 215 6.600882 ATGTGCATCTTCTTTCCAATTTCT 57.399 33.333 0.00 0.00 0.00 2.52
251 296 1.407299 GCATGCCGGCTCCATATCATA 60.407 52.381 29.70 2.45 0.00 2.15
257 302 3.201290 CCGGCTCCATATCATAGCATTC 58.799 50.000 0.00 0.00 38.01 2.67
258 303 3.369787 CCGGCTCCATATCATAGCATTCA 60.370 47.826 0.00 0.00 38.01 2.57
259 304 3.869832 CGGCTCCATATCATAGCATTCAG 59.130 47.826 0.00 0.00 38.01 3.02
264 312 7.122353 GGCTCCATATCATAGCATTCAGAAATT 59.878 37.037 0.00 0.00 38.01 1.82
268 316 9.764870 CCATATCATAGCATTCAGAAATTTACG 57.235 33.333 0.00 0.00 0.00 3.18
300 348 4.552166 AAGCAATGTGGTAATCGTATGC 57.448 40.909 0.00 0.00 0.00 3.14
499 547 0.370273 CGCTATCGTGCAGACAAACC 59.630 55.000 0.00 0.00 0.00 3.27
506 554 1.301716 TGCAGACAAACCTCTCGGC 60.302 57.895 0.00 0.00 0.00 5.54
550 598 3.002791 TGACTTGCGGACATCAAATCTC 58.997 45.455 0.00 0.00 0.00 2.75
587 637 5.921408 TCTAAAACAAACAGCACGTTTTTGT 59.079 32.000 4.97 7.99 45.79 2.83
968 1023 1.353358 TCGTCTACCAGAGTCCAGGAA 59.647 52.381 6.25 0.00 0.00 3.36
1112 1167 5.863397 TCTTTATTGCATAGCTTGTGTTTGC 59.137 36.000 0.00 0.00 0.00 3.68
1326 1385 3.688673 GGAGAAGAAAGTGGAAGATGCAG 59.311 47.826 0.00 0.00 0.00 4.41
1390 1449 8.127150 TCATACTCTGGACACAAGGATATATG 57.873 38.462 0.00 0.00 0.00 1.78
1401 1460 3.726557 AGGATATATGGGTGCATGTGG 57.273 47.619 0.00 0.00 0.00 4.17
1433 1492 2.297033 TGGAATTCCTGCAGCTGTTTTC 59.703 45.455 24.73 9.21 36.82 2.29
1445 1504 3.928375 CAGCTGTTTTCATTAACCATGCC 59.072 43.478 5.25 0.00 32.13 4.40
1446 1505 3.577848 AGCTGTTTTCATTAACCATGCCA 59.422 39.130 0.00 0.00 32.13 4.92
1462 1521 2.200067 TGCCAACATTTTTCAACTGCG 58.800 42.857 0.00 0.00 0.00 5.18
1534 1593 0.449388 CTCCTACGTACGCCGAACTT 59.551 55.000 16.72 0.00 40.70 2.66
1576 1635 1.005347 GTTTTCGTGTCTGTGGACGTG 60.005 52.381 0.00 0.00 44.83 4.49
1610 1669 0.802494 ACACAAATGTTCCGCCGATC 59.198 50.000 0.00 0.00 34.46 3.69
1662 1721 8.175069 TGCTCAAACTAAATGTCATTTCGATAC 58.825 33.333 14.07 0.15 33.82 2.24
1738 1800 7.381948 CGACATTCATCTTCTTGAGAGATAAGG 59.618 40.741 0.00 0.00 37.93 2.69
1867 1929 0.038744 AACCTGATGTTCCTGCCTGG 59.961 55.000 0.00 0.00 28.45 4.45
1886 1948 2.568956 TGGCAGTCAATAGAGCTTCAGT 59.431 45.455 0.00 0.00 0.00 3.41
1888 1950 4.406972 TGGCAGTCAATAGAGCTTCAGTAT 59.593 41.667 0.00 0.00 0.00 2.12
1906 1968 2.045926 GAGCACGGCCTCCATTGT 60.046 61.111 0.00 0.00 0.00 2.71
2071 2133 3.261580 CTGTCCATATGAACTCGCACAA 58.738 45.455 3.65 0.00 0.00 3.33
2211 2275 5.068636 CAGGACAGAATTTATGGGATGGAG 58.931 45.833 0.00 0.00 0.00 3.86
2248 2312 0.749454 ATGCAGGGGTTTGATCGCTC 60.749 55.000 0.00 0.00 0.00 5.03
2255 2319 1.533731 GGGTTTGATCGCTCGTTCAAA 59.466 47.619 18.73 18.73 39.81 2.69
2260 2324 3.297830 TGATCGCTCGTTCAAAGAAGA 57.702 42.857 1.07 0.00 0.00 2.87
2453 2520 1.142748 GATCTGCAGGTCGGGTCTG 59.857 63.158 12.06 0.00 35.49 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
165 169 7.308450 AGATGCACATAGATACATACCTTGT 57.692 36.000 0.00 0.00 42.62 3.16
175 179 8.985315 AATTGGAAAGAAGATGCACATAGATA 57.015 30.769 0.00 0.00 0.00 1.98
178 190 7.769220 AGAAATTGGAAAGAAGATGCACATAG 58.231 34.615 0.00 0.00 0.00 2.23
182 194 7.115947 CAGAAAGAAATTGGAAAGAAGATGCAC 59.884 37.037 0.00 0.00 0.00 4.57
185 197 7.376615 AGCAGAAAGAAATTGGAAAGAAGATG 58.623 34.615 0.00 0.00 0.00 2.90
186 198 7.450944 AGAGCAGAAAGAAATTGGAAAGAAGAT 59.549 33.333 0.00 0.00 0.00 2.40
187 199 6.774656 AGAGCAGAAAGAAATTGGAAAGAAGA 59.225 34.615 0.00 0.00 0.00 2.87
188 200 6.979465 AGAGCAGAAAGAAATTGGAAAGAAG 58.021 36.000 0.00 0.00 0.00 2.85
189 201 6.547141 TGAGAGCAGAAAGAAATTGGAAAGAA 59.453 34.615 0.00 0.00 0.00 2.52
190 202 6.064060 TGAGAGCAGAAAGAAATTGGAAAGA 58.936 36.000 0.00 0.00 0.00 2.52
191 203 6.323203 TGAGAGCAGAAAGAAATTGGAAAG 57.677 37.500 0.00 0.00 0.00 2.62
192 204 6.096705 TGTTGAGAGCAGAAAGAAATTGGAAA 59.903 34.615 0.00 0.00 0.00 3.13
193 205 5.593909 TGTTGAGAGCAGAAAGAAATTGGAA 59.406 36.000 0.00 0.00 0.00 3.53
194 206 5.132502 TGTTGAGAGCAGAAAGAAATTGGA 58.867 37.500 0.00 0.00 0.00 3.53
195 207 5.443185 TGTTGAGAGCAGAAAGAAATTGG 57.557 39.130 0.00 0.00 0.00 3.16
196 208 6.921857 ACATTGTTGAGAGCAGAAAGAAATTG 59.078 34.615 0.00 0.00 0.00 2.32
197 209 7.047460 ACATTGTTGAGAGCAGAAAGAAATT 57.953 32.000 0.00 0.00 0.00 1.82
203 215 5.129634 TGGTTACATTGTTGAGAGCAGAAA 58.870 37.500 0.00 0.00 0.00 2.52
264 312 8.364894 ACCACATTGCTTAGATGTATATCGTAA 58.635 33.333 0.00 0.00 38.38 3.18
316 364 8.533569 AAGGAAATGAACTTTTCTTGACCTAA 57.466 30.769 11.10 0.00 40.52 2.69
325 373 3.977427 ACGCCAAGGAAATGAACTTTTC 58.023 40.909 0.00 0.00 35.34 2.29
499 547 2.805099 GCAAATCCAATAGAGCCGAGAG 59.195 50.000 0.00 0.00 0.00 3.20
506 554 2.643551 ACCACGGCAAATCCAATAGAG 58.356 47.619 0.00 0.00 34.01 2.43
587 637 7.821359 CAGAAATATGAACAAGAAGAGACCAGA 59.179 37.037 0.00 0.00 0.00 3.86
777 827 8.964772 GTACTACTCCCTCTGTAAAGAAATACA 58.035 37.037 0.00 0.00 34.72 2.29
778 828 8.964772 TGTACTACTCCCTCTGTAAAGAAATAC 58.035 37.037 0.00 0.00 0.00 1.89
779 829 9.710818 ATGTACTACTCCCTCTGTAAAGAAATA 57.289 33.333 0.00 0.00 0.00 1.40
780 830 8.611051 ATGTACTACTCCCTCTGTAAAGAAAT 57.389 34.615 0.00 0.00 0.00 2.17
1039 1094 4.460382 AGTTGCCAGTTGTAAATGAGATGG 59.540 41.667 0.00 0.00 0.00 3.51
1112 1167 0.652592 GCACTACGTAGCATGGCAAG 59.347 55.000 22.40 0.00 0.00 4.01
1141 1196 2.749621 GGCCTTACAATCAGTTGACCAG 59.250 50.000 0.00 0.00 38.71 4.00
1154 1209 0.251608 GGCTTCCTTTGGGCCTTACA 60.252 55.000 4.53 0.00 42.31 2.41
1259 1318 2.906389 AGTCACATTCCCAGAGCTGTAA 59.094 45.455 0.00 0.00 0.00 2.41
1326 1385 2.989422 ACTGTTTTATTGGCGTCAGC 57.011 45.000 0.00 0.00 44.18 4.26
1390 1449 1.470996 TTGGAAAGCCACATGCACCC 61.471 55.000 0.00 0.00 45.94 4.61
1425 1484 3.924144 TGGCATGGTTAATGAAAACAGC 58.076 40.909 0.00 0.00 38.46 4.40
1433 1492 6.798315 TGAAAAATGTTGGCATGGTTAATG 57.202 33.333 0.00 0.00 39.49 1.90
1445 1504 2.347846 GCTGCGCAGTTGAAAAATGTTG 60.348 45.455 35.80 9.19 45.01 3.33
1446 1505 1.860326 GCTGCGCAGTTGAAAAATGTT 59.140 42.857 35.80 0.00 45.01 2.71
1462 1521 3.120121 CGCTGAATTTTACAACAAGCTGC 59.880 43.478 0.00 0.00 0.00 5.25
1534 1593 4.761739 ACAAGATCGGAATGCTTCAAAGAA 59.238 37.500 0.00 0.00 0.00 2.52
1576 1635 0.881118 TGTGTACCGGTAGTTCGTCC 59.119 55.000 16.41 1.42 0.00 4.79
1610 1669 7.246674 TCGCTCAAAGCTAAATTAGTAATGG 57.753 36.000 1.68 0.00 39.60 3.16
1738 1800 0.820871 ACCAGCTTGTCGATCTCCTC 59.179 55.000 0.00 0.00 0.00 3.71
1818 1880 4.915667 TCGAAAGACTGTTTACTCATGACG 59.084 41.667 0.00 0.00 33.31 4.35
1867 1929 5.595885 TCATACTGAAGCTCTATTGACTGC 58.404 41.667 0.00 0.00 0.00 4.40
1886 1948 0.179048 CAATGGAGGCCGTGCTCATA 60.179 55.000 0.00 0.00 0.00 2.15
1888 1950 2.046023 CAATGGAGGCCGTGCTCA 60.046 61.111 0.00 0.00 0.00 4.26
1906 1968 0.540454 CTCTTGCTGATGCTCCCAGA 59.460 55.000 0.00 0.00 40.48 3.86
2071 2133 7.867403 GGTGTCAATCAATCAGTACATTGTTTT 59.133 33.333 0.00 0.00 35.56 2.43
2248 2312 6.951256 TGATATGTCTGTCTTCTTTGAACG 57.049 37.500 0.00 0.00 0.00 3.95
2255 2319 9.911788 ACCAAATAATTGATATGTCTGTCTTCT 57.088 29.630 0.00 0.00 38.94 2.85
2260 2324 7.776969 AGCTCACCAAATAATTGATATGTCTGT 59.223 33.333 0.00 0.00 38.94 3.41
2321 2388 0.620700 ACCCCTATTTCCTGCTCGGT 60.621 55.000 0.00 0.00 0.00 4.69
2386 2453 1.302285 CTGGCCACCAAGCTCATCT 59.698 57.895 0.00 0.00 30.80 2.90


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

AutoCloner maintained by Alex Coulton.