Multiple sequence alignment - TraesCS7D01G238600

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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 TraesCS7D01G238600 chr7D 100.000 3725 0 0 1 3725 203512224 203515948 0 6879
1 TraesCS7D01G238600 chr7D 99.081 2830 23 2 3 2830 381961529 381958701 0 5079
2 TraesCS7D01G238600 chr7D 99.011 2830 25 2 3 2830 382062310 382065138 0 5068
3 TraesCS7D01G238600 chr7D 98.905 2832 25 5 3 2830 626685604 626682775 0 5053
4 TraesCS7D01G238600 chr6D 99.081 2830 23 2 3 2830 124529754 124532582 0 5079
5 TraesCS7D01G238600 chrUn 98.906 2833 24 6 3 2830 189404714 189407544 0 5053
6 TraesCS7D01G238600 chrUn 98.988 889 9 0 2837 3725 225927837 225928725 0 1592
7 TraesCS7D01G238600 chr7B 98.905 2831 27 3 3 2830 644461075 644463904 0 5053
8 TraesCS7D01G238600 chr7B 99.325 889 6 0 2837 3725 644467028 644467916 0 1609
9 TraesCS7D01G238600 chr1D 98.869 2830 27 4 3 2830 141319501 141316675 0 5044
10 TraesCS7D01G238600 chr1D 99.325 889 6 0 2837 3725 141313552 141312664 0 1609
11 TraesCS7D01G238600 chr3A 98.587 2830 36 3 3 2830 633104889 633107716 0 5001
12 TraesCS7D01G238600 chr3A 98.875 889 10 0 2837 3725 633110838 633111726 0 1587
13 TraesCS7D01G238600 chr1B 98.518 2834 35 4 3 2830 668811531 668808699 0 4994
14 TraesCS7D01G238600 chr1B 98.539 890 11 2 2837 3725 638701082 638700194 0 1570
15 TraesCS7D01G238600 chr2B 99.213 889 7 0 2837 3725 799247555 799248443 0 1604
16 TraesCS7D01G238600 chr4D 99.100 889 8 0 2837 3725 123716013 123716901 0 1598
17 TraesCS7D01G238600 chr7A 98.988 889 9 0 2837 3725 60148703 60147815 0 1592
18 TraesCS7D01G238600 chr6B 98.538 889 13 0 2837 3725 306996406 306995518 0 1570


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 TraesCS7D01G238600 chr7D 203512224 203515948 3724 False 6879.0 6879 100.000 1 3725 1 chr7D.!!$F1 3724
1 TraesCS7D01G238600 chr7D 381958701 381961529 2828 True 5079.0 5079 99.081 3 2830 1 chr7D.!!$R1 2827
2 TraesCS7D01G238600 chr7D 382062310 382065138 2828 False 5068.0 5068 99.011 3 2830 1 chr7D.!!$F2 2827
3 TraesCS7D01G238600 chr7D 626682775 626685604 2829 True 5053.0 5053 98.905 3 2830 1 chr7D.!!$R2 2827
4 TraesCS7D01G238600 chr6D 124529754 124532582 2828 False 5079.0 5079 99.081 3 2830 1 chr6D.!!$F1 2827
5 TraesCS7D01G238600 chrUn 189404714 189407544 2830 False 5053.0 5053 98.906 3 2830 1 chrUn.!!$F1 2827
6 TraesCS7D01G238600 chrUn 225927837 225928725 888 False 1592.0 1592 98.988 2837 3725 1 chrUn.!!$F2 888
7 TraesCS7D01G238600 chr7B 644461075 644467916 6841 False 3331.0 5053 99.115 3 3725 2 chr7B.!!$F1 3722
8 TraesCS7D01G238600 chr1D 141312664 141319501 6837 True 3326.5 5044 99.097 3 3725 2 chr1D.!!$R1 3722
9 TraesCS7D01G238600 chr3A 633104889 633111726 6837 False 3294.0 5001 98.731 3 3725 2 chr3A.!!$F1 3722
10 TraesCS7D01G238600 chr1B 668808699 668811531 2832 True 4994.0 4994 98.518 3 2830 1 chr1B.!!$R2 2827
11 TraesCS7D01G238600 chr1B 638700194 638701082 888 True 1570.0 1570 98.539 2837 3725 1 chr1B.!!$R1 888
12 TraesCS7D01G238600 chr2B 799247555 799248443 888 False 1604.0 1604 99.213 2837 3725 1 chr2B.!!$F1 888
13 TraesCS7D01G238600 chr4D 123716013 123716901 888 False 1598.0 1598 99.100 2837 3725 1 chr4D.!!$F1 888
14 TraesCS7D01G238600 chr7A 60147815 60148703 888 True 1592.0 1592 98.988 2837 3725 1 chr7A.!!$R1 888
15 TraesCS7D01G238600 chr6B 306995518 306996406 888 True 1570.0 1570 98.538 2837 3725 1 chr6B.!!$R1 888

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
435 439 5.899547 TCCTTCATCTTCTTATGAGTAGCCA 59.100 40.000 0.0 0.0 37.2 4.75 F
1663 1679 3.317603 TCGATGAACAGCAGATTGACA 57.682 42.857 0.0 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1916 1932 1.196808 GCAGCGTTCCATTCTTTTCGA 59.803 47.619 0.0 0.0 0.00 3.71 R
2830 2846 0.248054 CATGGACATAAACGCCACGC 60.248 55.000 0.0 0.0 33.93 5.34 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
292 293 6.536582 GCAGCATTCTCAGATTACTTGACTTA 59.463 38.462 0.00 0.0 0.00 2.24
365 369 6.125719 AGTCTGAGAGAAGGCTTTTTCTTTT 58.874 36.000 14.05 0.0 37.53 2.27
435 439 5.899547 TCCTTCATCTTCTTATGAGTAGCCA 59.100 40.000 0.00 0.0 37.20 4.75
628 633 9.740710 AGCTAAATGACAATCTTAACCTACTTT 57.259 29.630 0.00 0.0 0.00 2.66
705 710 7.458170 TGAGTTATCTTTTAGTTCTCTCCCCTT 59.542 37.037 0.00 0.0 0.00 3.95
1438 1454 3.463944 CAGTTGTACACTCCCTTCGTTT 58.536 45.455 0.00 0.0 30.92 3.60
1663 1679 3.317603 TCGATGAACAGCAGATTGACA 57.682 42.857 0.00 0.0 0.00 3.58
1706 1722 7.079451 TGTTTTTCTCTCCTTTCCTATCAGT 57.921 36.000 0.00 0.0 0.00 3.41
1977 1993 4.220821 GTCGGATCCCATATAAGAAGCTCA 59.779 45.833 6.06 0.0 0.00 4.26
2485 2501 3.073356 AGGAACCTTTTCAATACGGTCCA 59.927 43.478 0.00 0.0 32.80 4.02
2557 2573 5.480422 AGATTTTTATGGCGGTTCTTCCTTT 59.520 36.000 0.00 0.0 0.00 3.11
2830 2846 1.156645 GCGCTGCTGGATACTTCTGG 61.157 60.000 0.00 0.0 37.61 3.86
2831 2847 1.156645 CGCTGCTGGATACTTCTGGC 61.157 60.000 0.00 0.0 37.61 4.85
2832 2848 1.156645 GCTGCTGGATACTTCTGGCG 61.157 60.000 0.00 0.0 37.61 5.69
2833 2849 0.176680 CTGCTGGATACTTCTGGCGT 59.823 55.000 0.00 0.0 37.61 5.68
2834 2850 0.108186 TGCTGGATACTTCTGGCGTG 60.108 55.000 0.00 0.0 37.61 5.34
2835 2851 0.811616 GCTGGATACTTCTGGCGTGG 60.812 60.000 0.00 0.0 37.61 4.94
2893 6029 5.736951 ACTATCAACCAGATGAGATAGGC 57.263 43.478 11.59 0.0 42.53 3.93
3287 6423 2.567615 GCTCCCTTCCTTCACTGAACTA 59.432 50.000 0.00 0.0 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
292 293 3.943671 TCTCTCCTCTAAGCTAGCAGT 57.056 47.619 18.83 6.84 0.00 4.40
375 379 4.721274 TGATCACCCCTCTGATTTGTGATA 59.279 41.667 12.91 4.00 44.33 2.15
435 439 2.203998 CTGAGGACCCCCTGTGGT 60.204 66.667 0.00 0.00 44.53 4.16
628 633 7.386851 CACAGTTTCTTAAGGATCCTGTAAGA 58.613 38.462 26.23 26.23 35.16 2.10
705 710 3.330701 ACTCTTTCCTATCCACTTTGCCA 59.669 43.478 0.00 0.00 0.00 4.92
1090 1098 2.512485 CACCAAAATGCAAGTGCTGA 57.488 45.000 4.69 0.00 42.66 4.26
1206 1218 3.963374 TGATTAGACCATGTCCCTGAGAG 59.037 47.826 0.00 0.00 32.18 3.20
1438 1454 3.394274 TCAGAATCAACAAGGGTTCTCCA 59.606 43.478 0.00 0.00 38.24 3.86
1663 1679 1.544691 CAAAGCAATGCCAAGAGCTCT 59.455 47.619 11.45 11.45 44.23 4.09
1706 1722 3.064207 CGAACAAAAGGATCGGAACTCA 58.936 45.455 0.00 0.00 38.05 3.41
1916 1932 1.196808 GCAGCGTTCCATTCTTTTCGA 59.803 47.619 0.00 0.00 0.00 3.71
1977 1993 5.556915 TGTTTGAATGATCGGGTAAAGAGT 58.443 37.500 0.00 0.00 0.00 3.24
2347 2363 1.261619 CCGAGGCATAAAAGACGCATC 59.738 52.381 0.00 0.00 33.34 3.91
2485 2501 1.195115 TGAACGGGAGCTAGCAATCT 58.805 50.000 18.83 0.00 0.00 2.40
2830 2846 0.248054 CATGGACATAAACGCCACGC 60.248 55.000 0.00 0.00 33.93 5.34
2831 2847 0.376852 CCATGGACATAAACGCCACG 59.623 55.000 5.56 0.00 33.93 4.94
2832 2848 1.459450 ACCATGGACATAAACGCCAC 58.541 50.000 21.47 0.00 33.93 5.01
2833 2849 3.118223 TGATACCATGGACATAAACGCCA 60.118 43.478 21.47 1.67 35.91 5.69
2834 2850 3.472652 TGATACCATGGACATAAACGCC 58.527 45.455 21.47 0.00 0.00 5.68
2835 2851 4.143115 CGATGATACCATGGACATAAACGC 60.143 45.833 21.47 7.59 32.09 4.84
2893 6029 5.929415 GAGACTAACTCTGACCTTTCAAAGG 59.071 44.000 15.22 15.22 46.48 3.11
2911 6047 7.015001 ACGACCTAAAAGAAAAAGAGGAGACTA 59.985 37.037 0.00 0.00 44.43 2.59
3082 6218 6.035843 TGCTGTCTTTTTAGCTTCAAAACTG 58.964 36.000 0.00 0.00 40.52 3.16
3287 6423 0.541063 GGTTTGGACCCGGGTGAATT 60.541 55.000 36.01 5.17 40.25 2.17


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

AutoCloner maintained by Alex Coulton.