Multiple sequence alignment - TraesCS7A01G251500

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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 TraesCS7A01G251500 chr7A 100.000 2622 0 0 1 2622 235470182 235467561 0 4843
1 TraesCS7A01G251500 chr7D 94.224 2666 87 15 1 2622 220980463 220977821 0 4008
2 TraesCS7A01G251500 chr7B 93.910 1724 56 16 931 2622 175998712 176000418 0 2556
3 TraesCS7A01G251500 chr7B 94.356 939 40 4 1 936 175996266 175997194 0 1428


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 TraesCS7A01G251500 chr7A 235467561 235470182 2621 True 4843 4843 100.000 1 2622 1 chr7A.!!$R1 2621
1 TraesCS7A01G251500 chr7D 220977821 220980463 2642 True 4008 4008 94.224 1 2622 1 chr7D.!!$R1 2621
2 TraesCS7A01G251500 chr7B 175996266 176000418 4152 False 1992 2556 94.133 1 2622 2 chr7B.!!$F1 2621

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
829 839 0.296056 CAGCGAGCGAACGAAGATTC 59.704 55.0 5.91 0.0 35.09 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2510 4080 0.550914 ACTGAAGGTGCCTCCAAACA 59.449 50.0 0.0 0.0 39.02 2.83 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
390 391 4.452733 GACGGGTGCGGGAGGAAG 62.453 72.222 0.00 0.00 0.00 3.46
652 653 3.838271 CGCAGGCCGCCTCTTCTA 61.838 66.667 9.68 0.00 37.30 2.10
732 736 3.050339 CAATGGTGGTGGTGGTGC 58.950 61.111 0.00 0.00 0.00 5.01
733 737 2.597217 AATGGTGGTGGTGGTGCG 60.597 61.111 0.00 0.00 0.00 5.34
734 738 3.126703 AATGGTGGTGGTGGTGCGA 62.127 57.895 0.00 0.00 0.00 5.10
755 765 3.822192 CGACGGCATGGAGGACGA 61.822 66.667 0.00 0.00 43.61 4.20
756 766 2.202756 GACGGCATGGAGGACGAC 60.203 66.667 0.00 0.00 43.61 4.34
789 799 1.337071 TCTCGCGAAGAGTGTTGACTT 59.663 47.619 11.33 0.00 46.86 3.01
803 813 2.433868 TGACTTGAGGCGACTTGTAC 57.566 50.000 0.00 0.00 44.43 2.90
804 814 1.961394 TGACTTGAGGCGACTTGTACT 59.039 47.619 0.00 0.00 44.43 2.73
807 817 3.418995 ACTTGAGGCGACTTGTACTAGA 58.581 45.455 11.43 0.00 44.43 2.43
808 818 3.825014 ACTTGAGGCGACTTGTACTAGAA 59.175 43.478 11.43 0.00 44.43 2.10
809 819 4.082679 ACTTGAGGCGACTTGTACTAGAAG 60.083 45.833 11.43 5.01 44.43 2.85
810 820 2.163815 TGAGGCGACTTGTACTAGAAGC 59.836 50.000 11.43 13.91 44.43 3.86
811 821 2.163815 GAGGCGACTTGTACTAGAAGCA 59.836 50.000 21.26 0.00 44.43 3.91
812 822 2.164624 AGGCGACTTGTACTAGAAGCAG 59.835 50.000 21.26 6.70 37.44 4.24
813 823 1.921230 GCGACTTGTACTAGAAGCAGC 59.079 52.381 11.43 4.10 0.00 5.25
814 824 2.177977 CGACTTGTACTAGAAGCAGCG 58.822 52.381 11.43 0.54 0.00 5.18
829 839 0.296056 CAGCGAGCGAACGAAGATTC 59.704 55.000 5.91 0.00 35.09 2.52
889 899 1.360551 CGGTAGTGATCTGGCCGAG 59.639 63.158 0.00 0.00 41.98 4.63
960 2493 1.034356 TCCCTCGCGATTTTATCCGA 58.966 50.000 10.36 0.00 33.30 4.55
986 2519 4.767255 GTGGTGAGGCGAGGCTGG 62.767 72.222 3.24 0.00 0.00 4.85
998 2531 1.539869 AGGCTGGGCAAGGAAGAGA 60.540 57.895 0.00 0.00 0.00 3.10
1088 2621 2.514592 CCAGGCATTGGCGTCGAT 60.515 61.111 4.38 0.00 40.87 3.59
1095 2628 1.518572 ATTGGCGTCGATCGTGTCC 60.519 57.895 15.94 14.03 42.13 4.02
1222 2755 3.895232 TGGAGGTTAGCATCTCTCAAC 57.105 47.619 0.00 0.00 0.00 3.18
1249 2782 3.683564 GCAGTGATCCATGACCATCTGAA 60.684 47.826 0.00 0.00 0.00 3.02
1275 2808 3.877559 TCAAGTTATGCACCTGATCCTG 58.122 45.455 0.00 0.00 0.00 3.86
1468 3001 2.217510 AGGCCGTGAGTTCTCTCTTA 57.782 50.000 0.00 0.00 40.98 2.10
1496 3030 6.327626 TCTCCTACCTTAATTTCCATCCTCTG 59.672 42.308 0.00 0.00 0.00 3.35
1537 3077 1.301874 CAACCGGCGTCCCTTGTTA 60.302 57.895 6.01 0.00 0.00 2.41
1603 3143 5.279657 GGTCTACAGATGCATCACATATCCA 60.280 44.000 27.81 1.83 39.84 3.41
1695 3235 1.066858 TGCTGCTTCTTCTACCTTCCG 60.067 52.381 0.00 0.00 0.00 4.30
1724 3264 3.647824 GCTGACTGCAGTGTGGAC 58.352 61.111 27.27 10.06 44.17 4.02
1807 3347 6.860023 GCTCCATTGTCAATGAATGTTATAGC 59.140 38.462 24.31 14.86 41.46 2.97
1844 3384 6.150140 CAGGAAAAACTTCTCTGATTACCAGG 59.850 42.308 0.00 0.00 43.12 4.45
2084 3626 0.098200 CGCGATCAGGTAAGTCGTCA 59.902 55.000 0.00 0.00 37.66 4.35
2404 3972 2.544698 CCGTTCGGCCGTTGGAAAA 61.545 57.895 27.15 7.98 0.00 2.29
2497 4065 4.991776 TGATTAGGGTGTGAAATTGACCA 58.008 39.130 0.00 0.00 0.00 4.02
2499 4067 6.015918 TGATTAGGGTGTGAAATTGACCATT 58.984 36.000 0.00 0.00 0.00 3.16
2500 4068 5.720371 TTAGGGTGTGAAATTGACCATTG 57.280 39.130 0.00 0.00 0.00 2.82
2510 4080 5.010922 TGAAATTGACCATTGCTTGCTTAGT 59.989 36.000 0.00 0.00 0.00 2.24
2588 4159 1.818060 CGGAATTTGGTCATGAGGCAA 59.182 47.619 0.00 0.00 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 4.778143 GTGGACCGGGAGCGCAAT 62.778 66.667 11.47 0.00 0.00 3.56
144 145 2.046023 TTCCTCGTCCTCGCCGTA 60.046 61.111 0.00 0.00 36.96 4.02
148 149 1.446272 CCAAGTTCCTCGTCCTCGC 60.446 63.158 0.00 0.00 36.96 5.03
249 250 1.446272 CACCCTCGTCGGCTTCTTC 60.446 63.158 0.00 0.00 0.00 2.87
390 391 4.475135 GCCTCCCTCAACTCCCGC 62.475 72.222 0.00 0.00 0.00 6.13
695 699 0.820871 CCTTGTCCTCCTCCTCTTCG 59.179 60.000 0.00 0.00 0.00 3.79
698 702 0.178891 TTGCCTTGTCCTCCTCCTCT 60.179 55.000 0.00 0.00 0.00 3.69
732 736 4.470170 TCCATGCCGTCGTCGTCG 62.470 66.667 4.87 4.87 38.55 5.12
733 737 2.579787 CTCCATGCCGTCGTCGTC 60.580 66.667 0.71 0.00 35.01 4.20
734 738 4.129737 CCTCCATGCCGTCGTCGT 62.130 66.667 0.71 0.00 35.01 4.34
772 782 1.453524 CTCAAGTCAACACTCTTCGCG 59.546 52.381 0.00 0.00 29.93 5.87
774 784 1.795286 GCCTCAAGTCAACACTCTTCG 59.205 52.381 0.00 0.00 29.93 3.79
789 799 2.163815 GCTTCTAGTACAAGTCGCCTCA 59.836 50.000 0.00 0.00 0.00 3.86
803 813 1.467556 CGTTCGCTCGCTGCTTCTAG 61.468 60.000 0.00 0.00 40.11 2.43
804 814 1.514228 CGTTCGCTCGCTGCTTCTA 60.514 57.895 0.00 0.00 40.11 2.10
807 817 2.355837 TTCGTTCGCTCGCTGCTT 60.356 55.556 0.00 0.00 40.11 3.91
808 818 2.549611 ATCTTCGTTCGCTCGCTGCT 62.550 55.000 0.00 0.00 40.11 4.24
809 819 1.687494 AATCTTCGTTCGCTCGCTGC 61.687 55.000 0.00 0.00 38.57 5.25
810 820 0.296056 GAATCTTCGTTCGCTCGCTG 59.704 55.000 0.00 0.00 0.00 5.18
811 821 0.171455 AGAATCTTCGTTCGCTCGCT 59.829 50.000 0.00 0.00 33.36 4.93
812 822 0.296056 CAGAATCTTCGTTCGCTCGC 59.704 55.000 0.00 0.00 33.36 5.03
813 823 0.296056 GCAGAATCTTCGTTCGCTCG 59.704 55.000 0.00 0.00 33.36 5.03
814 824 0.296056 CGCAGAATCTTCGTTCGCTC 59.704 55.000 0.00 0.00 33.36 5.03
840 850 0.957395 ACCGCAAAGCCTGACATCTG 60.957 55.000 0.00 0.00 0.00 2.90
841 851 0.250901 AACCGCAAAGCCTGACATCT 60.251 50.000 0.00 0.00 0.00 2.90
909 919 1.369321 GATCCCGCCTCTGACATCC 59.631 63.158 0.00 0.00 0.00 3.51
911 921 0.692419 AAGGATCCCGCCTCTGACAT 60.692 55.000 8.55 0.00 37.26 3.06
936 2469 3.463944 GATAAAATCGCGAGGGAAAGGA 58.536 45.455 16.66 0.00 0.00 3.36
960 2493 3.953775 CCTCACCACCGCACCCTT 61.954 66.667 0.00 0.00 0.00 3.95
986 2519 1.475682 CAGCCATTTCTCTTCCTTGCC 59.524 52.381 0.00 0.00 0.00 4.52
998 2531 2.043625 CACCACTGCACAGCCATTT 58.956 52.632 0.00 0.00 0.00 2.32
1073 2606 2.586079 CGATCGACGCCAATGCCT 60.586 61.111 10.26 0.00 34.51 4.75
1088 2621 3.371063 GCCGAGACAGGGACACGA 61.371 66.667 0.00 0.00 0.00 4.35
1222 2755 0.531532 GTCATGGATCACTGCGAGGG 60.532 60.000 0.00 0.00 0.00 4.30
1249 2782 4.623932 TCAGGTGCATAACTTGAACTCT 57.376 40.909 0.00 0.00 41.55 3.24
1275 2808 3.671702 GCAGGTGAGAATTGTTAGCTTGC 60.672 47.826 0.00 1.84 0.00 4.01
1468 3001 8.119062 AGGATGGAAATTAAGGTAGGAGAAAT 57.881 34.615 0.00 0.00 0.00 2.17
1537 3077 2.573083 CCCGGCCTGCAACAACAAT 61.573 57.895 0.00 0.00 0.00 2.71
1603 3143 2.868583 CGATCATGATTCGGTGCTTTCT 59.131 45.455 10.14 0.00 0.00 2.52
1695 3235 1.094073 CAGTCAGCAGGGCAGCATAC 61.094 60.000 0.00 1.73 36.85 2.39
1724 3264 1.269621 ACACTGAAGGAAGACGAACGG 60.270 52.381 0.00 0.00 0.00 4.44
1807 3347 3.571401 AGTTTTTCCTGATGACCAAGCTG 59.429 43.478 0.00 0.00 0.00 4.24
1887 3427 3.235157 GCACAATTGCTCTATTGCCAA 57.765 42.857 5.05 0.00 46.17 4.52
1960 3500 0.745845 CCCTGATGTTTGAGAGGCGG 60.746 60.000 0.00 0.00 0.00 6.13
1961 3501 1.372087 GCCCTGATGTTTGAGAGGCG 61.372 60.000 0.00 0.00 0.00 5.52
1962 3502 1.372087 CGCCCTGATGTTTGAGAGGC 61.372 60.000 0.00 0.00 35.55 4.70
1963 3503 1.372087 GCGCCCTGATGTTTGAGAGG 61.372 60.000 0.00 0.00 0.00 3.69
2084 3626 1.204941 GCACCATACGACTTCCTCACT 59.795 52.381 0.00 0.00 0.00 3.41
2153 3695 3.423154 GCCGTTGTTGAGCTCCCG 61.423 66.667 12.15 5.63 0.00 5.14
2404 3972 0.551131 AGGGTCTTGGCCTTGAGGAT 60.551 55.000 3.32 0.00 37.39 3.24
2497 4065 3.256631 CCTCCAAACACTAAGCAAGCAAT 59.743 43.478 0.00 0.00 0.00 3.56
2499 4067 2.229792 CCTCCAAACACTAAGCAAGCA 58.770 47.619 0.00 0.00 0.00 3.91
2500 4068 1.068264 GCCTCCAAACACTAAGCAAGC 60.068 52.381 0.00 0.00 0.00 4.01
2510 4080 0.550914 ACTGAAGGTGCCTCCAAACA 59.449 50.000 0.00 0.00 39.02 2.83
2588 4159 1.344438 TCTGACTTGCACCGATTCTGT 59.656 47.619 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.