Multiple sequence alignment - TraesCS7B01G414000

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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 TraesCS7B01G414000 chr7B 100.000 4716 0 0 1 4716 681953024 681957739 0 8709
1 TraesCS7B01G414000 chr7B 96.286 4712 158 11 1 4696 695576178 695571468 0 7716
2 TraesCS7B01G414000 chr3B 96.838 4712 131 7 1 4696 817686344 817691053 0 7860
3 TraesCS7B01G414000 chr3B 96.688 3955 116 4 756 4696 817710255 817714208 0 6564
4 TraesCS7B01G414000 chr3B 96.892 2703 78 4 1995 4696 784350889 784348192 0 4521
5 TraesCS7B01G414000 chr6B 96.350 4712 154 7 1 4696 83866045 83870754 0 7733
6 TraesCS7B01G414000 chr6A 96.326 4709 155 9 1 4693 307922647 307917941 0 7721
7 TraesCS7B01G414000 chr7A 96.318 4698 158 6 1 4683 395513524 395518221 0 7703
8 TraesCS7B01G414000 chr5A 96.066 4702 142 7 1 4687 213046758 213051431 0 7618
9 TraesCS7B01G414000 chr5A 96.694 3932 116 3 776 4693 631069218 631065287 0 6529
10 TraesCS7B01G414000 chr1A 95.654 4717 154 15 1 4693 236391029 236395718 0 7528
11 TraesCS7B01G414000 chr2A 96.640 3274 91 4 1433 4693 290319739 290323006 0 5419
12 TraesCS7B01G414000 chr2A 95.836 1393 54 4 1 1391 290318352 290319742 0 2248
13 TraesCS7B01G414000 chrUn 95.545 2671 94 7 1 2653 87506300 87503637 0 4250
14 TraesCS7B01G414000 chrUn 95.509 2672 91 8 1 2653 87516122 87513461 0 4242


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 TraesCS7B01G414000 chr7B 681953024 681957739 4715 False 8709.0 8709 100.000 1 4716 1 chr7B.!!$F1 4715
1 TraesCS7B01G414000 chr7B 695571468 695576178 4710 True 7716.0 7716 96.286 1 4696 1 chr7B.!!$R1 4695
2 TraesCS7B01G414000 chr3B 817686344 817691053 4709 False 7860.0 7860 96.838 1 4696 1 chr3B.!!$F1 4695
3 TraesCS7B01G414000 chr3B 817710255 817714208 3953 False 6564.0 6564 96.688 756 4696 1 chr3B.!!$F2 3940
4 TraesCS7B01G414000 chr3B 784348192 784350889 2697 True 4521.0 4521 96.892 1995 4696 1 chr3B.!!$R1 2701
5 TraesCS7B01G414000 chr6B 83866045 83870754 4709 False 7733.0 7733 96.350 1 4696 1 chr6B.!!$F1 4695
6 TraesCS7B01G414000 chr6A 307917941 307922647 4706 True 7721.0 7721 96.326 1 4693 1 chr6A.!!$R1 4692
7 TraesCS7B01G414000 chr7A 395513524 395518221 4697 False 7703.0 7703 96.318 1 4683 1 chr7A.!!$F1 4682
8 TraesCS7B01G414000 chr5A 213046758 213051431 4673 False 7618.0 7618 96.066 1 4687 1 chr5A.!!$F1 4686
9 TraesCS7B01G414000 chr5A 631065287 631069218 3931 True 6529.0 6529 96.694 776 4693 1 chr5A.!!$R1 3917
10 TraesCS7B01G414000 chr1A 236391029 236395718 4689 False 7528.0 7528 95.654 1 4693 1 chr1A.!!$F1 4692
11 TraesCS7B01G414000 chr2A 290318352 290323006 4654 False 3833.5 5419 96.238 1 4693 2 chr2A.!!$F1 4692
12 TraesCS7B01G414000 chrUn 87503637 87506300 2663 True 4250.0 4250 95.545 1 2653 1 chrUn.!!$R1 2652
13 TraesCS7B01G414000 chrUn 87513461 87516122 2661 True 4242.0 4242 95.509 1 2653 1 chrUn.!!$R2 2652

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
947 956 0.787084 TCTCCTCCTCACCTCACCTT 59.213 55.000 0.00 0.0 0.00 3.50 F
1448 1512 0.682209 TACCCTTCTTCGCGCCTAGT 60.682 55.000 0.00 0.0 0.00 2.57 F
2022 2098 1.002662 ATGCCTCCTCTGCTCTCCA 59.997 57.895 0.00 0.0 0.00 3.86 F
3086 3171 1.548357 GGAGGAGGAGCTCAAGCACA 61.548 60.000 17.19 0.0 45.16 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2074 2151 0.478072 TTGGCACTCACAGGGTTGAT 59.522 50.000 0.00 0.0 0.00 2.57 R
3086 3171 1.152756 GTGGTGCCTCTTGGTGGTT 60.153 57.895 0.00 0.0 35.27 3.67 R
3501 3614 2.175499 ACAGGGCATGGTATTACAGCAT 59.825 45.455 3.46 0.0 46.29 3.79 R
4334 4448 0.527565 CATAAGTGGGTTGCACTGGC 59.472 55.000 0.00 0.0 41.68 4.85 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
55 56 3.318557 GGAGCAAACTACGAGGTAGCTAT 59.681 47.826 0.00 0.00 39.51 2.97
56 57 4.291783 GAGCAAACTACGAGGTAGCTATG 58.708 47.826 0.00 0.00 39.51 2.23
440 447 7.476540 TGATTTAGCACCTTACTTCTAGTCA 57.523 36.000 0.00 0.00 0.00 3.41
535 542 2.545113 CGGATCGTGGATAATCACCGTT 60.545 50.000 0.00 0.00 34.36 4.44
720 729 3.260100 CTGTTGCCCACCCCCTCT 61.260 66.667 0.00 0.00 0.00 3.69
764 773 2.659063 CCTCACCATCGAGCCCACA 61.659 63.158 0.00 0.00 0.00 4.17
804 813 4.473520 CTCGCCCGCAACCCTCAT 62.474 66.667 0.00 0.00 0.00 2.90
908 917 3.400054 GCACCGGTAAGCCCCTCT 61.400 66.667 6.87 0.00 0.00 3.69
947 956 0.787084 TCTCCTCCTCACCTCACCTT 59.213 55.000 0.00 0.00 0.00 3.50
1101 1119 1.764054 CCGCCTCCTCCAGATCCTT 60.764 63.158 0.00 0.00 0.00 3.36
1283 1301 6.183360 GGTGGTATTAAGAGCTGATGGAACTA 60.183 42.308 0.00 0.00 0.00 2.24
1317 1335 3.288964 GAGTAGTACAGCTTGGCCTCTA 58.711 50.000 3.32 0.00 0.00 2.43
1448 1512 0.682209 TACCCTTCTTCGCGCCTAGT 60.682 55.000 0.00 0.00 0.00 2.57
1792 1856 5.420725 TGGACATGCAGTTAGTCTGTATT 57.579 39.130 10.06 0.00 44.78 1.89
1806 1870 5.411781 AGTCTGTATTTGTCTTAGCGAAGG 58.588 41.667 6.73 0.00 33.09 3.46
2022 2098 1.002662 ATGCCTCCTCTGCTCTCCA 59.997 57.895 0.00 0.00 0.00 3.86
2037 2113 1.612146 TCCAGGCTCGGACCAATCA 60.612 57.895 2.10 0.00 0.00 2.57
2074 2151 2.882761 ACGCACGTCTCCTGCTATTATA 59.117 45.455 0.00 0.00 32.03 0.98
2611 2696 4.050553 CAATGTACAACCTGTTTGCTTGG 58.949 43.478 0.00 0.00 39.01 3.61
2778 2863 6.323739 ACATTAGTTTGTCACCTTGTTTCCAT 59.676 34.615 0.00 0.00 0.00 3.41
2788 2873 4.016444 ACCTTGTTTCCATTGATACGCAT 58.984 39.130 0.00 0.00 0.00 4.73
2832 2917 5.655488 CTTTTCTGATCGACAGTATCAGGT 58.345 41.667 11.91 0.00 46.81 4.00
2842 2927 5.122869 TCGACAGTATCAGGTAGTAACACAC 59.877 44.000 0.00 0.00 0.00 3.82
3027 3112 3.397955 ACCCATGGTCTTGTTCCTTTACT 59.602 43.478 11.73 0.00 0.00 2.24
3086 3171 1.548357 GGAGGAGGAGCTCAAGCACA 61.548 60.000 17.19 0.00 45.16 4.57
3410 3523 2.840066 CGGCAGCGTCTCCTCTAGG 61.840 68.421 0.00 0.00 0.00 3.02
3484 3597 2.092538 CGGTGAGTCCTTCTCCTACCTA 60.093 54.545 0.00 0.00 42.12 3.08
3501 3614 5.045213 CCTACCTATAGCTCCATCTCTGAGA 60.045 48.000 10.23 10.23 31.26 3.27
3561 3674 3.333029 TTAGTCTGTGCTTGCTATGCA 57.667 42.857 0.00 0.00 38.19 3.96
3774 3887 9.985730 ATCTTATGACACACAATCAATTTTTGT 57.014 25.926 0.00 0.00 37.79 2.83
3977 4090 8.834749 AAGGAGTTGAGTATTAAGTGAACTTC 57.165 34.615 0.00 0.00 33.27 3.01
4119 4232 4.455877 CCTAAGAAAGTTGGAAGTGCGAAT 59.544 41.667 0.00 0.00 0.00 3.34
4171 4284 4.810790 GCTACTCAGCAAAGAGTTGTCTA 58.189 43.478 11.00 0.00 46.26 2.59
4442 4556 5.010012 GTGGGACCAGCTCCAAAATATATTG 59.990 44.000 0.00 0.00 41.63 1.90
4641 4756 2.281692 ACATCAGCTTGCCACGCA 60.282 55.556 0.00 0.00 36.47 5.24
4689 4804 1.944024 CTAGTGACCAAAACGCCACAA 59.056 47.619 0.00 0.00 32.35 3.33
4696 4811 2.959707 ACCAAAACGCCACAATAGGAAA 59.040 40.909 0.00 0.00 0.00 3.13
4697 4812 3.576550 ACCAAAACGCCACAATAGGAAAT 59.423 39.130 0.00 0.00 0.00 2.17
4698 4813 4.767928 ACCAAAACGCCACAATAGGAAATA 59.232 37.500 0.00 0.00 0.00 1.40
4699 4814 5.105917 ACCAAAACGCCACAATAGGAAATAG 60.106 40.000 0.00 0.00 0.00 1.73
4700 4815 5.105917 CCAAAACGCCACAATAGGAAATAGT 60.106 40.000 0.00 0.00 0.00 2.12
4701 4816 5.813080 AAACGCCACAATAGGAAATAGTC 57.187 39.130 0.00 0.00 0.00 2.59
4702 4817 4.481368 ACGCCACAATAGGAAATAGTCA 57.519 40.909 0.00 0.00 0.00 3.41
4703 4818 4.442706 ACGCCACAATAGGAAATAGTCAG 58.557 43.478 0.00 0.00 0.00 3.51
4704 4819 4.081087 ACGCCACAATAGGAAATAGTCAGT 60.081 41.667 0.00 0.00 0.00 3.41
4705 4820 4.876107 CGCCACAATAGGAAATAGTCAGTT 59.124 41.667 0.00 0.00 0.00 3.16
4706 4821 5.354234 CGCCACAATAGGAAATAGTCAGTTT 59.646 40.000 0.00 0.00 0.00 2.66
4707 4822 6.537301 CGCCACAATAGGAAATAGTCAGTTTA 59.463 38.462 0.00 0.00 0.00 2.01
4708 4823 7.465513 CGCCACAATAGGAAATAGTCAGTTTAC 60.466 40.741 0.00 0.00 0.00 2.01
4709 4824 7.465513 GCCACAATAGGAAATAGTCAGTTTACG 60.466 40.741 0.00 0.00 0.00 3.18
4710 4825 7.762615 CCACAATAGGAAATAGTCAGTTTACGA 59.237 37.037 0.00 0.00 0.00 3.43
4711 4826 8.592998 CACAATAGGAAATAGTCAGTTTACGAC 58.407 37.037 0.00 0.00 0.00 4.34
4712 4827 7.763071 ACAATAGGAAATAGTCAGTTTACGACC 59.237 37.037 0.00 0.00 33.70 4.79
4713 4828 4.741342 AGGAAATAGTCAGTTTACGACCG 58.259 43.478 0.00 0.00 33.70 4.79
4714 4829 4.219288 AGGAAATAGTCAGTTTACGACCGT 59.781 41.667 0.00 0.00 33.70 4.83
4715 4830 4.560427 GGAAATAGTCAGTTTACGACCGTC 59.440 45.833 0.00 0.00 33.70 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 1.477295 AGCTACCTCGTAGTTTGCTCC 59.523 52.381 0.00 0.00 38.30 4.70
434 441 9.716507 CCATTTAAATTGGTCGTAATTGACTAG 57.283 33.333 0.00 0.00 38.91 2.57
804 813 2.652095 CCGAAACCCTAGCCACGGA 61.652 63.158 0.00 0.00 42.40 4.69
908 917 1.395635 TAGTGCGCGAATAAGGAGGA 58.604 50.000 12.10 0.00 0.00 3.71
1113 1131 3.307906 TTGACGACGGTGAGGGGG 61.308 66.667 0.00 0.00 0.00 5.40
1127 1145 1.525077 GCGTGGTTCCAGGTGTTGA 60.525 57.895 12.15 0.00 0.00 3.18
1283 1301 2.678934 TACTCGCTTCCGGGCACT 60.679 61.111 0.00 0.00 38.95 4.40
1317 1335 5.544176 TCTGATCAAAGAAGGAAGTACAGGT 59.456 40.000 0.00 0.00 0.00 4.00
1792 1856 2.143122 CTTGTGCCTTCGCTAAGACAA 58.857 47.619 0.00 2.75 34.37 3.18
1806 1870 5.466728 TCATTGTAACAGTCTTCTCTTGTGC 59.533 40.000 0.00 0.00 0.00 4.57
2022 2098 1.901085 GAGTGATTGGTCCGAGCCT 59.099 57.895 0.00 0.00 0.00 4.58
2074 2151 0.478072 TTGGCACTCACAGGGTTGAT 59.522 50.000 0.00 0.00 0.00 2.57
2740 2825 5.073965 ACAAACTAATGTTCCAGGGAGGTAA 59.926 40.000 0.00 0.00 39.02 2.85
2778 2863 6.200808 CAGCAAACAATATCATGCGTATCAA 58.799 36.000 0.00 0.00 43.39 2.57
2788 2873 5.840243 AGCATAAGCAGCAAACAATATCA 57.160 34.783 0.00 0.00 45.49 2.15
2832 2917 7.928307 ACCGAGACTAATTAGTGTGTTACTA 57.072 36.000 22.68 0.00 40.89 1.82
2842 2927 9.582431 TGATTTCAAGTAACCGAGACTAATTAG 57.418 33.333 11.05 11.05 0.00 1.73
3027 3112 2.229792 GCAGGACAAACAAGACCATGA 58.770 47.619 0.00 0.00 0.00 3.07
3086 3171 1.152756 GTGGTGCCTCTTGGTGGTT 60.153 57.895 0.00 0.00 35.27 3.67
3501 3614 2.175499 ACAGGGCATGGTATTACAGCAT 59.825 45.455 3.46 0.00 46.29 3.79
3561 3674 6.605119 AGCTAATTAGGCTCCAATACACAAT 58.395 36.000 14.28 0.00 34.70 2.71
3813 3926 3.102972 AGAGAGCCAGCAAACTAGATGA 58.897 45.455 0.00 0.00 0.00 2.92
3816 3929 2.232452 GTGAGAGAGCCAGCAAACTAGA 59.768 50.000 0.00 0.00 0.00 2.43
3977 4090 9.831737 CATACAGAAATTGTTTCCAGTTAGAAG 57.168 33.333 0.00 0.00 41.29 2.85
4054 4167 7.133133 AGAGGAACCAAGTAAAGAAGTTACA 57.867 36.000 0.00 0.00 44.03 2.41
4119 4232 1.454276 CTTCGCGCTTTTCTTCACGTA 59.546 47.619 5.56 0.00 0.00 3.57
4310 4424 3.587061 AGGTTCCCATCTCACACACAATA 59.413 43.478 0.00 0.00 0.00 1.90
4334 4448 0.527565 CATAAGTGGGTTGCACTGGC 59.472 55.000 0.00 0.00 41.68 4.85
4689 4804 6.096001 ACGGTCGTAAACTGACTATTTCCTAT 59.904 38.462 0.00 0.00 37.71 2.57


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

AutoCloner maintained by Alex Coulton.