Multiple sequence alignment - TraesCS4A01G278900

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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 TraesCS4A01G278900 chr4A 100.000 2684 0 0 1 2684 586502902 586500219 0.000000e+00 4957
1 TraesCS4A01G278900 chr4A 82.835 903 131 16 990 1886 456455932 456455048 0.000000e+00 787
2 TraesCS4A01G278900 chr4A 81.681 928 151 13 992 1918 586682734 586681825 0.000000e+00 754
3 TraesCS4A01G278900 chr4D 90.199 1959 118 45 753 2684 14936039 14937950 0.000000e+00 2486
4 TraesCS4A01G278900 chr4D 82.705 902 133 15 990 1886 14857907 14858790 0.000000e+00 780
5 TraesCS4A01G278900 chr4D 81.417 974 156 20 990 1954 14862800 14863757 0.000000e+00 773
6 TraesCS4A01G278900 chr4D 81.134 970 166 12 990 1954 14914617 14915574 0.000000e+00 761
7 TraesCS4A01G278900 chr4D 86.692 263 34 1 186 448 14934372 14934633 9.400000e-75 291
8 TraesCS4A01G278900 chr2A 98.707 1315 16 1 621 1934 196207959 196206645 0.000000e+00 2333
9 TraesCS4A01G278900 chr2A 98.138 752 9 3 1937 2684 196202161 196201411 0.000000e+00 1306
10 TraesCS4A01G278900 chr2A 98.929 560 6 0 1 560 196208884 196208325 0.000000e+00 1002
11 TraesCS4A01G278900 chr4B 88.450 1368 96 32 1254 2598 24919381 24918053 0.000000e+00 1594
12 TraesCS4A01G278900 chr4B 82.309 944 139 21 990 1925 24741634 24742557 0.000000e+00 793


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 TraesCS4A01G278900 chr4A 586500219 586502902 2683 True 4957.0 4957 100.0000 1 2684 1 chr4A.!!$R2 2683
1 TraesCS4A01G278900 chr4A 456455048 456455932 884 True 787.0 787 82.8350 990 1886 1 chr4A.!!$R1 896
2 TraesCS4A01G278900 chr4A 586681825 586682734 909 True 754.0 754 81.6810 992 1918 1 chr4A.!!$R3 926
3 TraesCS4A01G278900 chr4D 14934372 14937950 3578 False 1388.5 2486 88.4455 186 2684 2 chr4D.!!$F4 2498
4 TraesCS4A01G278900 chr4D 14857907 14858790 883 False 780.0 780 82.7050 990 1886 1 chr4D.!!$F1 896
5 TraesCS4A01G278900 chr4D 14862800 14863757 957 False 773.0 773 81.4170 990 1954 1 chr4D.!!$F2 964
6 TraesCS4A01G278900 chr4D 14914617 14915574 957 False 761.0 761 81.1340 990 1954 1 chr4D.!!$F3 964
7 TraesCS4A01G278900 chr2A 196206645 196208884 2239 True 1667.5 2333 98.8180 1 1934 2 chr2A.!!$R2 1933
8 TraesCS4A01G278900 chr2A 196201411 196202161 750 True 1306.0 1306 98.1380 1937 2684 1 chr2A.!!$R1 747
9 TraesCS4A01G278900 chr4B 24918053 24919381 1328 True 1594.0 1594 88.4500 1254 2598 1 chr4B.!!$R1 1344
10 TraesCS4A01G278900 chr4B 24741634 24742557 923 False 793.0 793 82.3090 990 1925 1 chr4B.!!$F1 935

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
613 638 0.037232 AAGGGTAGCAACGACTCTGC 60.037 55.0 0.0 0.0 40.24 4.26 F
615 640 1.014564 GGGTAGCAACGACTCTGCAC 61.015 60.0 0.0 0.0 42.48 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1500 2655 0.106268 AGACAAACATGGTGGCCACA 60.106 50.0 35.78 22.39 35.8 4.17 R
2431 3612 5.273944 AGAAGCAAAATCACTTTCGAACAC 58.726 37.5 0.00 0.00 0.0 3.32 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
153 154 0.325296 TCCATACAAGCCCCTCGACT 60.325 55.000 0.00 0.00 0.00 4.18
459 460 2.514510 TATTGCTCGGGCGTGCTCAA 62.515 55.000 1.14 0.00 42.25 3.02
562 566 4.033776 CCTTGCCGCCCCTGAGAA 62.034 66.667 0.00 0.00 0.00 2.87
563 567 2.437359 CTTGCCGCCCCTGAGAAG 60.437 66.667 0.00 0.00 0.00 2.85
564 568 4.722700 TTGCCGCCCCTGAGAAGC 62.723 66.667 0.00 0.00 0.00 3.86
569 594 1.758514 CGCCCCTGAGAAGCCTCTA 60.759 63.158 0.00 0.00 40.10 2.43
570 595 1.826709 GCCCCTGAGAAGCCTCTAC 59.173 63.158 0.00 0.00 40.10 2.59
571 596 1.691195 GCCCCTGAGAAGCCTCTACC 61.691 65.000 0.00 0.00 40.10 3.18
591 616 1.394151 CCCCCTCCTCTCTCCAACT 59.606 63.158 0.00 0.00 0.00 3.16
594 619 0.041833 CCCTCCTCTCTCCAACTCCA 59.958 60.000 0.00 0.00 0.00 3.86
595 620 1.553417 CCCTCCTCTCTCCAACTCCAA 60.553 57.143 0.00 0.00 0.00 3.53
596 621 1.830477 CCTCCTCTCTCCAACTCCAAG 59.170 57.143 0.00 0.00 0.00 3.61
597 622 1.830477 CTCCTCTCTCCAACTCCAAGG 59.170 57.143 0.00 0.00 0.00 3.61
598 623 0.908198 CCTCTCTCCAACTCCAAGGG 59.092 60.000 0.00 0.00 0.00 3.95
599 624 1.650528 CTCTCTCCAACTCCAAGGGT 58.349 55.000 0.00 0.00 0.00 4.34
600 625 2.559931 CCTCTCTCCAACTCCAAGGGTA 60.560 54.545 0.00 0.00 0.00 3.69
601 626 2.763448 CTCTCTCCAACTCCAAGGGTAG 59.237 54.545 0.00 0.00 0.00 3.18
602 627 1.208293 CTCTCCAACTCCAAGGGTAGC 59.792 57.143 0.00 0.00 0.00 3.58
603 628 0.984230 CTCCAACTCCAAGGGTAGCA 59.016 55.000 0.00 0.00 0.00 3.49
604 629 1.351017 CTCCAACTCCAAGGGTAGCAA 59.649 52.381 0.00 0.00 0.00 3.91
605 630 1.073284 TCCAACTCCAAGGGTAGCAAC 59.927 52.381 0.00 0.00 0.00 4.17
606 631 1.156736 CAACTCCAAGGGTAGCAACG 58.843 55.000 0.00 0.00 0.00 4.10
607 632 1.053424 AACTCCAAGGGTAGCAACGA 58.947 50.000 0.00 0.00 0.00 3.85
608 633 0.320697 ACTCCAAGGGTAGCAACGAC 59.679 55.000 0.00 0.00 0.00 4.34
609 634 0.608640 CTCCAAGGGTAGCAACGACT 59.391 55.000 0.00 0.00 0.00 4.18
610 635 0.606604 TCCAAGGGTAGCAACGACTC 59.393 55.000 0.00 0.00 0.00 3.36
611 636 0.608640 CCAAGGGTAGCAACGACTCT 59.391 55.000 0.00 0.00 0.00 3.24
612 637 1.673033 CCAAGGGTAGCAACGACTCTG 60.673 57.143 0.00 0.00 0.00 3.35
613 638 0.037232 AAGGGTAGCAACGACTCTGC 60.037 55.000 0.00 0.00 40.24 4.26
614 639 1.185618 AGGGTAGCAACGACTCTGCA 61.186 55.000 0.00 0.00 42.48 4.41
615 640 1.014564 GGGTAGCAACGACTCTGCAC 61.015 60.000 0.00 0.00 42.48 4.57
616 641 1.014564 GGTAGCAACGACTCTGCACC 61.015 60.000 0.00 0.13 42.48 5.01
617 642 1.014564 GTAGCAACGACTCTGCACCC 61.015 60.000 0.00 0.00 42.48 4.61
618 643 1.468506 TAGCAACGACTCTGCACCCA 61.469 55.000 0.00 0.00 42.48 4.51
619 644 1.672356 GCAACGACTCTGCACCCAT 60.672 57.895 0.00 0.00 39.69 4.00
1500 2655 1.885850 GTTCAACACCGGCGACACT 60.886 57.895 9.30 0.00 0.00 3.55
2431 3612 1.531423 AGCTTCTGCATGAGTGGTTG 58.469 50.000 0.00 0.00 42.74 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
153 154 3.007074 TGCGTATCCCAGAGTTGTTGTAA 59.993 43.478 0.00 0.00 0.00 2.41
459 460 5.529791 CACGTCCGAGTAATATTTCATCCT 58.470 41.667 0.00 0.00 0.00 3.24
576 601 1.830477 CTTGGAGTTGGAGAGAGGAGG 59.170 57.143 0.00 0.00 0.00 4.30
577 602 1.830477 CCTTGGAGTTGGAGAGAGGAG 59.170 57.143 0.00 0.00 0.00 3.69
578 603 1.553417 CCCTTGGAGTTGGAGAGAGGA 60.553 57.143 0.00 0.00 0.00 3.71
580 605 1.650528 ACCCTTGGAGTTGGAGAGAG 58.349 55.000 0.00 0.00 0.00 3.20
587 612 1.156736 CGTTGCTACCCTTGGAGTTG 58.843 55.000 0.00 0.00 0.00 3.16
591 616 0.606604 GAGTCGTTGCTACCCTTGGA 59.393 55.000 0.00 0.00 0.00 3.53
594 619 0.037232 GCAGAGTCGTTGCTACCCTT 60.037 55.000 0.00 0.00 38.51 3.95
595 620 1.185618 TGCAGAGTCGTTGCTACCCT 61.186 55.000 6.00 0.00 42.02 4.34
596 621 1.014564 GTGCAGAGTCGTTGCTACCC 61.015 60.000 6.00 0.00 42.02 3.69
597 622 1.014564 GGTGCAGAGTCGTTGCTACC 61.015 60.000 6.00 7.69 42.02 3.18
598 623 1.014564 GGGTGCAGAGTCGTTGCTAC 61.015 60.000 6.00 3.21 42.02 3.58
599 624 1.292223 GGGTGCAGAGTCGTTGCTA 59.708 57.895 6.00 0.00 42.02 3.49
600 625 2.031163 GGGTGCAGAGTCGTTGCT 59.969 61.111 6.00 0.00 42.02 3.91
601 626 1.672356 ATGGGTGCAGAGTCGTTGC 60.672 57.895 0.00 0.00 41.86 4.17
602 627 0.320683 TCATGGGTGCAGAGTCGTTG 60.321 55.000 0.00 0.00 0.00 4.10
603 628 0.320771 GTCATGGGTGCAGAGTCGTT 60.321 55.000 0.00 0.00 0.00 3.85
604 629 1.293498 GTCATGGGTGCAGAGTCGT 59.707 57.895 0.00 0.00 0.00 4.34
605 630 1.016130 GTGTCATGGGTGCAGAGTCG 61.016 60.000 0.00 0.00 0.00 4.18
606 631 1.016130 CGTGTCATGGGTGCAGAGTC 61.016 60.000 0.00 0.00 0.00 3.36
607 632 1.004560 CGTGTCATGGGTGCAGAGT 60.005 57.895 0.00 0.00 0.00 3.24
608 633 0.320683 TTCGTGTCATGGGTGCAGAG 60.321 55.000 0.00 0.00 0.00 3.35
609 634 0.602638 GTTCGTGTCATGGGTGCAGA 60.603 55.000 0.00 0.00 0.00 4.26
610 635 0.884259 TGTTCGTGTCATGGGTGCAG 60.884 55.000 0.00 0.00 0.00 4.41
611 636 0.464554 TTGTTCGTGTCATGGGTGCA 60.465 50.000 0.00 0.00 0.00 4.57
612 637 0.881118 ATTGTTCGTGTCATGGGTGC 59.119 50.000 0.00 0.00 0.00 5.01
613 638 2.150390 TGATTGTTCGTGTCATGGGTG 58.850 47.619 0.00 0.00 0.00 4.61
614 639 2.552315 GTTGATTGTTCGTGTCATGGGT 59.448 45.455 0.00 0.00 0.00 4.51
615 640 2.095263 GGTTGATTGTTCGTGTCATGGG 60.095 50.000 0.00 0.00 0.00 4.00
616 641 2.095263 GGGTTGATTGTTCGTGTCATGG 60.095 50.000 0.00 0.00 0.00 3.66
617 642 2.813754 AGGGTTGATTGTTCGTGTCATG 59.186 45.455 0.00 0.00 0.00 3.07
618 643 3.074412 GAGGGTTGATTGTTCGTGTCAT 58.926 45.455 0.00 0.00 0.00 3.06
619 644 2.489971 GAGGGTTGATTGTTCGTGTCA 58.510 47.619 0.00 0.00 0.00 3.58
1500 2655 0.106268 AGACAAACATGGTGGCCACA 60.106 50.000 35.78 22.39 35.80 4.17
2431 3612 5.273944 AGAAGCAAAATCACTTTCGAACAC 58.726 37.500 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.