Multiple sequence alignment - TraesCS3B01G564600

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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 TraesCS3B01G564600 chr3B 100.000 2672 0 0 1 2672 797589469 797592140 0 4935
1 TraesCS3B01G564600 chr5A 98.096 2678 41 5 1 2669 19245368 19248044 0 4654
2 TraesCS3B01G564600 chr7D 98.094 2676 43 4 1 2669 382053552 382050878 0 4652
3 TraesCS3B01G564600 chr7D 97.907 2676 48 4 1 2669 203503472 203500798 0 4625
4 TraesCS3B01G564600 chr7D 97.870 2676 49 4 1 2669 381927474 381924800 0 4619
5 TraesCS3B01G564600 chr7B 98.016 2672 50 3 1 2669 742992915 742990244 0 4638
6 TraesCS3B01G564600 chr7B 97.980 2673 49 4 1 2669 716875311 716877982 0 4632
7 TraesCS3B01G564600 chr7A 98.016 2672 49 4 1 2669 60282782 60280112 0 4638
8 TraesCS3B01G564600 chr1A 98.016 2672 49 4 1 2669 498687758 498690428 0 4638
9 TraesCS3B01G564600 chrUn 97.868 2673 52 4 1 2669 186204951 186207622 0 4615


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 TraesCS3B01G564600 chr3B 797589469 797592140 2671 False 4935 4935 100.000 1 2672 1 chr3B.!!$F1 2671
1 TraesCS3B01G564600 chr5A 19245368 19248044 2676 False 4654 4654 98.096 1 2669 1 chr5A.!!$F1 2668
2 TraesCS3B01G564600 chr7D 382050878 382053552 2674 True 4652 4652 98.094 1 2669 1 chr7D.!!$R3 2668
3 TraesCS3B01G564600 chr7D 203500798 203503472 2674 True 4625 4625 97.907 1 2669 1 chr7D.!!$R1 2668
4 TraesCS3B01G564600 chr7D 381924800 381927474 2674 True 4619 4619 97.870 1 2669 1 chr7D.!!$R2 2668
5 TraesCS3B01G564600 chr7B 742990244 742992915 2671 True 4638 4638 98.016 1 2669 1 chr7B.!!$R1 2668
6 TraesCS3B01G564600 chr7B 716875311 716877982 2671 False 4632 4632 97.980 1 2669 1 chr7B.!!$F1 2668
7 TraesCS3B01G564600 chr7A 60280112 60282782 2670 True 4638 4638 98.016 1 2669 1 chr7A.!!$R1 2668
8 TraesCS3B01G564600 chr1A 498687758 498690428 2670 False 4638 4638 98.016 1 2669 1 chr1A.!!$F1 2668
9 TraesCS3B01G564600 chrUn 186204951 186207622 2671 False 4615 4615 97.868 1 2669 1 chrUn.!!$F1 2668

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
708 713 1.481871 CTACGAAGGGGTTAGGAGCA 58.518 55.000 0.00 0.0 0.0 4.26 F
1067 1072 1.361543 ACTGGACAGGGGTAAGCTCTA 59.638 52.381 4.14 0.0 0.0 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1669 1680 0.179233 CTGCGCGCGATCGTATACTA 60.179 55.0 37.18 2.45 38.14 1.82 R
2521 2532 1.324005 CCCTCTCCCTCGGACTCAAC 61.324 65.0 0.00 0.00 0.00 3.18 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
26 27 3.466836 AGGCTTTGGTTATACCTGGGTA 58.533 45.455 1.70 1.70 39.58 3.69
389 393 5.186992 TGATGAGTAAGATCGAACAAGGGAA 59.813 40.000 0.00 0.00 0.00 3.97
477 481 6.256539 CGATCCATTGGTTCATATAGAATCCG 59.743 42.308 13.00 0.00 36.48 4.18
588 593 2.225142 ACTAACAGCTGAGTCCTCTCCA 60.225 50.000 23.35 0.00 39.75 3.86
684 689 6.516860 GCAGGTTCGGATCACTTACTATACAT 60.517 42.308 0.00 0.00 0.00 2.29
708 713 1.481871 CTACGAAGGGGTTAGGAGCA 58.518 55.000 0.00 0.00 0.00 4.26
720 725 4.098501 GGGTTAGGAGCATTTTCAAGATGG 59.901 45.833 0.00 0.00 0.00 3.51
744 749 5.637104 TCTTTCTTTGTCGAGACGAAAAG 57.363 39.130 7.27 8.64 37.72 2.27
1067 1072 1.361543 ACTGGACAGGGGTAAGCTCTA 59.638 52.381 4.14 0.00 0.00 2.43
1159 1169 2.365617 CAGTGCTTCGGGTACTATGGAT 59.634 50.000 0.00 0.00 38.80 3.41
1175 1185 2.705148 TGGATCCTCTGCCATCCATTA 58.295 47.619 14.23 0.00 43.11 1.90
1199 1209 1.741770 GAGCCGTTTCATGAGCGGT 60.742 57.895 29.00 20.47 46.41 5.68
1249 1260 7.656412 TCAAAGGTTTCATGAAATCGAAATCA 58.344 30.769 23.05 6.04 36.56 2.57
1410 1421 1.611936 GCTTCTCCCCCACACTTCTTC 60.612 57.143 0.00 0.00 0.00 2.87
1417 1428 3.140144 TCCCCCACACTTCTTCATTTCTT 59.860 43.478 0.00 0.00 0.00 2.52
1531 1542 2.158445 TCCCAACGAAAATGGAAAGGGA 60.158 45.455 0.00 0.00 40.56 4.20
1933 1944 2.380571 AAACCTTCCGGCCACCCAAT 62.381 55.000 2.24 0.00 0.00 3.16
1964 1975 2.613133 CGCTAGTCACTACTCCCACTAC 59.387 54.545 0.00 0.00 37.15 2.73
1998 2009 1.680651 CCCATAACCCAAAGCGGCA 60.681 57.895 1.45 0.00 0.00 5.69
2369 2380 7.186021 CAATGCTGCAGAAAAAGAAGATTTT 57.814 32.000 20.43 0.00 35.29 1.82
2465 2476 1.347707 AGAAAGGAATGCTGTCACCGA 59.652 47.619 0.00 0.00 0.00 4.69
2521 2532 8.310382 CCCACATATATAGAGTCAAAAGAGAGG 58.690 40.741 0.00 0.00 0.00 3.69
2669 2681 2.413453 GCTCTCTGAACCGAACATGAAC 59.587 50.000 0.00 0.00 0.00 3.18
2670 2682 3.653344 CTCTCTGAACCGAACATGAACA 58.347 45.455 0.00 0.00 0.00 3.18
2671 2683 4.248859 CTCTCTGAACCGAACATGAACAT 58.751 43.478 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 1.334869 CACCAGAAACTTCGCTTTGCT 59.665 47.619 0.00 0.00 0.00 3.91
71 72 2.180159 ATACGGGCGTGCTTCCTTGT 62.180 55.000 0.00 0.00 0.00 3.16
260 264 2.517650 AGCGAGATAGGCTTTACTGC 57.482 50.000 0.00 0.00 37.50 4.40
389 393 7.465900 TTACTTCATCCTTTCCATATCCCTT 57.534 36.000 0.00 0.00 0.00 3.95
588 593 1.679032 GGCAACTATCTCCTGCGGTTT 60.679 52.381 0.00 0.00 36.93 3.27
657 662 1.207329 GTAAGTGATCCGAACCTGCCT 59.793 52.381 0.00 0.00 0.00 4.75
708 713 7.649306 CGACAAAGAAAGAACCATCTTGAAAAT 59.351 33.333 0.00 0.00 45.19 1.82
720 725 5.385396 TTTCGTCTCGACAAAGAAAGAAC 57.615 39.130 0.00 0.00 34.89 3.01
744 749 5.907866 TTTAATCGAAAAGATGGGTTCCC 57.092 39.130 0.12 0.12 40.02 3.97
946 951 1.413808 GGGGAGAGAGTGGAGCCTATT 60.414 57.143 0.00 0.00 0.00 1.73
997 1002 2.361438 GTCGACTCGTTATCCCCATCTT 59.639 50.000 8.70 0.00 0.00 2.40
1067 1072 4.943705 CCACACTTGGCTCTACACATTTAT 59.056 41.667 0.00 0.00 35.56 1.40
1159 1169 1.141657 GCTGTAATGGATGGCAGAGGA 59.858 52.381 0.00 0.00 0.00 3.71
1410 1421 0.811281 GGAAGGGGCACGAAGAAATG 59.189 55.000 0.00 0.00 0.00 2.32
1417 1428 4.776322 CATGCGGAAGGGGCACGA 62.776 66.667 0.00 0.00 44.23 4.35
1643 1654 1.302993 CCCCGTCGGTTGTTGGAAT 60.303 57.895 11.06 0.00 0.00 3.01
1669 1680 0.179233 CTGCGCGCGATCGTATACTA 60.179 55.000 37.18 2.45 38.14 1.82
1927 1938 3.965347 ACTAGCGTTATAGGTCATTGGGT 59.035 43.478 0.00 0.00 0.00 4.51
1933 1944 5.678583 AGTAGTGACTAGCGTTATAGGTCA 58.321 41.667 0.00 0.00 32.65 4.02
1984 1995 1.338655 GTTCTTTGCCGCTTTGGGTTA 59.661 47.619 0.00 0.00 38.63 2.85
2046 2057 4.506288 TCCATTACAATGTTCTCATACGCG 59.494 41.667 3.53 3.53 34.60 6.01
2369 2380 5.632902 GCTTCCTATGGGGGTACATTACAAA 60.633 44.000 0.00 0.00 35.33 2.83
2521 2532 1.324005 CCCTCTCCCTCGGACTCAAC 61.324 65.000 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.