Multiple sequence alignment - TraesCS4B01G159000

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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 TraesCS4B01G159000 chr4B 100.000 2111 0 0 1 2111 308684036 308681926 0 3899
1 TraesCS4B01G159000 chr4B 95.756 589 23 2 1 588 327772689 327772102 0 948
2 TraesCS4B01G159000 chr1A 95.528 1543 46 12 589 2111 554458789 554460328 0 2446
3 TraesCS4B01G159000 chr2B 95.244 1535 53 12 589 2111 474900664 474902190 0 2412
4 TraesCS4B01G159000 chr1D 94.974 1532 61 9 589 2108 254417387 254418914 0 2388
5 TraesCS4B01G159000 chr1D 93.730 1547 67 12 589 2111 51877752 51876212 0 2292
6 TraesCS4B01G159000 chr6D 94.182 1547 56 17 589 2111 45511248 45509712 0 2327
7 TraesCS4B01G159000 chr5D 93.955 1555 59 16 589 2111 503287621 503289172 0 2318
8 TraesCS4B01G159000 chr5D 93.459 1544 63 18 589 2107 6180624 6179094 0 2257
9 TraesCS4B01G159000 chr5D 94.557 1378 48 9 589 1940 512416164 512414788 0 2104
10 TraesCS4B01G159000 chr5A 93.815 1536 70 15 589 2111 607199769 607198246 0 2287
11 TraesCS4B01G159000 chr7B 93.599 1531 74 14 589 2107 105256275 105254757 0 2263
12 TraesCS4B01G159000 chr7B 95.756 589 23 2 1 588 293816565 293817152 0 948
13 TraesCS4B01G159000 chrUn 95.770 591 23 2 1 590 116558450 116557861 0 952
14 TraesCS4B01G159000 chrUn 95.616 593 25 1 1 593 165063915 165064506 0 950
15 TraesCS4B01G159000 chrUn 95.756 589 23 2 1 588 46912437 46913024 0 948
16 TraesCS4B01G159000 chrUn 95.756 589 24 1 1 588 120438135 120438723 0 948
17 TraesCS4B01G159000 chrUn 95.608 592 23 3 1 591 464439447 464438858 0 946
18 TraesCS4B01G159000 chr6B 95.756 589 23 2 1 588 379278030 379277443 0 948
19 TraesCS4B01G159000 chr3A 95.756 589 23 2 1 588 320676879 320677466 0 948


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 TraesCS4B01G159000 chr4B 308681926 308684036 2110 True 3899 3899 100.000 1 2111 1 chr4B.!!$R1 2110
1 TraesCS4B01G159000 chr4B 327772102 327772689 587 True 948 948 95.756 1 588 1 chr4B.!!$R2 587
2 TraesCS4B01G159000 chr1A 554458789 554460328 1539 False 2446 2446 95.528 589 2111 1 chr1A.!!$F1 1522
3 TraesCS4B01G159000 chr2B 474900664 474902190 1526 False 2412 2412 95.244 589 2111 1 chr2B.!!$F1 1522
4 TraesCS4B01G159000 chr1D 254417387 254418914 1527 False 2388 2388 94.974 589 2108 1 chr1D.!!$F1 1519
5 TraesCS4B01G159000 chr1D 51876212 51877752 1540 True 2292 2292 93.730 589 2111 1 chr1D.!!$R1 1522
6 TraesCS4B01G159000 chr6D 45509712 45511248 1536 True 2327 2327 94.182 589 2111 1 chr6D.!!$R1 1522
7 TraesCS4B01G159000 chr5D 503287621 503289172 1551 False 2318 2318 93.955 589 2111 1 chr5D.!!$F1 1522
8 TraesCS4B01G159000 chr5D 6179094 6180624 1530 True 2257 2257 93.459 589 2107 1 chr5D.!!$R1 1518
9 TraesCS4B01G159000 chr5D 512414788 512416164 1376 True 2104 2104 94.557 589 1940 1 chr5D.!!$R2 1351
10 TraesCS4B01G159000 chr5A 607198246 607199769 1523 True 2287 2287 93.815 589 2111 1 chr5A.!!$R1 1522
11 TraesCS4B01G159000 chr7B 105254757 105256275 1518 True 2263 2263 93.599 589 2107 1 chr7B.!!$R1 1518
12 TraesCS4B01G159000 chr7B 293816565 293817152 587 False 948 948 95.756 1 588 1 chr7B.!!$F1 587
13 TraesCS4B01G159000 chrUn 116557861 116558450 589 True 952 952 95.770 1 590 1 chrUn.!!$R1 589
14 TraesCS4B01G159000 chrUn 165063915 165064506 591 False 950 950 95.616 1 593 1 chrUn.!!$F3 592
15 TraesCS4B01G159000 chrUn 46912437 46913024 587 False 948 948 95.756 1 588 1 chrUn.!!$F1 587
16 TraesCS4B01G159000 chrUn 120438135 120438723 588 False 948 948 95.756 1 588 1 chrUn.!!$F2 587
17 TraesCS4B01G159000 chrUn 464438858 464439447 589 True 946 946 95.608 1 591 1 chrUn.!!$R2 590
18 TraesCS4B01G159000 chr6B 379277443 379278030 587 True 948 948 95.756 1 588 1 chr6B.!!$R1 587
19 TraesCS4B01G159000 chr3A 320676879 320677466 587 False 948 948 95.756 1 588 1 chr3A.!!$F1 587

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
151 152 1.405121 GCCTTGTACGACCTAGGGTTG 60.405 57.143 14.81 4.61 42.54 3.77 F
168 169 2.897326 GGTTGGTTTTAGGATGCCTTGT 59.103 45.455 0.00 0.00 34.61 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1088 1114 1.379977 TCCTCGCGTCCAGGATTCT 60.380 57.895 10.75 0.0 34.91 2.4 R
1861 1917 1.651987 TATGTGTAGCGCAAAGGAGC 58.348 50.000 11.47 0.0 40.48 4.7 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
61 62 4.951254 TGAGTTGTGGACGAAACAATCTA 58.049 39.130 0.00 0.00 39.57 1.98
151 152 1.405121 GCCTTGTACGACCTAGGGTTG 60.405 57.143 14.81 4.61 42.54 3.77
168 169 2.897326 GGTTGGTTTTAGGATGCCTTGT 59.103 45.455 0.00 0.00 34.61 3.16
480 482 3.018856 TCTCGGAGTTGGTTTAGCGATA 58.981 45.455 4.69 0.00 0.00 2.92
857 879 9.700831 ACCCTATTTTTGCTATTGATAAGAGTT 57.299 29.630 0.00 0.00 0.00 3.01
1088 1114 6.043243 GGATTCTTATCTAATGACCCAGGACA 59.957 42.308 0.00 0.00 0.00 4.02
1120 1146 3.181397 CGCGAGGAGTAAAAATTCCGTA 58.819 45.455 0.00 0.00 38.54 4.02
1123 1149 5.555818 CGCGAGGAGTAAAAATTCCGTATTC 60.556 44.000 0.00 0.00 38.54 1.75
1183 1210 3.526019 AGAAAATCCGGGGGTCAGAATTA 59.474 43.478 0.00 0.00 0.00 1.40
1225 1252 0.918983 TGATCCAAGGGAGCGGAAAT 59.081 50.000 0.00 0.00 41.58 2.17
1235 1262 2.106684 GGGAGCGGAAATAGAGGGATTT 59.893 50.000 0.00 0.00 0.00 2.17
1337 1364 3.606687 AGCGAAAGGTTTCCGTGATATT 58.393 40.909 0.00 0.00 40.01 1.28
1343 1370 8.378421 GCGAAAGGTTTCCGTGATATTATATAC 58.622 37.037 0.00 0.00 33.68 1.47
1692 1743 6.593268 AAGTAAGTAGACCTGACTCCTTTC 57.407 41.667 0.00 0.00 33.29 2.62
1935 1997 9.672673 CAGAATCCTCTATTTTAGTTCTTCCAA 57.327 33.333 0.00 0.00 0.00 3.53
1967 2029 4.179133 AGAGAGGGAATGGGAAAAGAAGA 58.821 43.478 0.00 0.00 0.00 2.87
2052 2114 7.816945 ATGCTGAATTCAAAGGTTTATTTCG 57.183 32.000 9.88 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 3.705579 TCCGGACGGATTTTAAGGTGATA 59.294 43.478 9.76 0.00 39.76 2.15
61 62 2.393768 CGGATTCTGCTGCAGCGTT 61.394 57.895 32.11 17.21 45.83 4.84
151 152 2.161609 CGTCACAAGGCATCCTAAAACC 59.838 50.000 0.00 0.00 31.13 3.27
168 169 0.471211 AAGGAGGTGGGAGAACGTCA 60.471 55.000 0.00 0.00 36.82 4.35
230 231 7.432148 ACTAAACAAATCCCAAGGAAAAAGT 57.568 32.000 0.00 0.00 34.34 2.66
397 399 3.973425 AGGTCTATTCCTGCAAGCAATT 58.027 40.909 0.00 0.00 36.35 2.32
480 482 1.597027 ACAACGTTGCGCCTTAGCT 60.597 52.632 27.61 2.12 38.13 3.32
573 576 0.461961 GCTTGTGATAGAGGCGGAGT 59.538 55.000 0.00 0.00 0.00 3.85
575 578 0.461548 CAGCTTGTGATAGAGGCGGA 59.538 55.000 0.00 0.00 0.00 5.54
1088 1114 1.379977 TCCTCGCGTCCAGGATTCT 60.380 57.895 10.75 0.00 34.91 2.40
1146 1173 9.672673 CCCGGATTTTCTCATAGATAAATGTAT 57.327 33.333 0.73 0.00 0.00 2.29
1183 1210 5.799827 TTTGGGACTTTCGAATTGGAAAT 57.200 34.783 14.91 6.79 35.52 2.17
1343 1370 7.275341 TGCAACCATTATTTCTTATTTCTTGCG 59.725 33.333 0.00 0.00 33.44 4.85
1611 1659 6.581171 AGAACCCTTGCTTTCTTGATAAAG 57.419 37.500 0.00 0.00 39.10 1.85
1692 1743 3.815856 ATAGCGGATAGAGGCATCATG 57.184 47.619 0.00 0.00 0.00 3.07
1758 1813 6.198591 CGCGGTCTAAGTCTAAGGAAATAAAG 59.801 42.308 0.00 0.00 0.00 1.85
1842 1898 8.794335 AAGGAGCTACGATTTCTTCTTATTTT 57.206 30.769 0.00 0.00 0.00 1.82
1843 1899 8.669243 CAAAGGAGCTACGATTTCTTCTTATTT 58.331 33.333 0.00 0.00 0.00 1.40
1861 1917 1.651987 TATGTGTAGCGCAAAGGAGC 58.348 50.000 11.47 0.00 40.48 4.70
1935 1997 3.181436 CCATTCCCTCTCTATTGCATGGT 60.181 47.826 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.