Multiple sequence alignment - TraesCS7D01G442800

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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 TraesCS7D01G442800 chr7D 100.000 3970 0 0 1 3970 562196517 562200486 0.000000e+00 7332
1 TraesCS7D01G442800 chr7D 94.444 3978 190 17 1 3970 524303691 524307645 0.000000e+00 6093
2 TraesCS7D01G442800 chr7D 93.541 3979 221 23 1 3970 524248958 524252909 0.000000e+00 5891
3 TraesCS7D01G442800 chr7D 94.695 3393 164 11 1 3384 524311336 524314721 0.000000e+00 5254
4 TraesCS7D01G442800 chr7D 94.062 421 25 0 3550 3970 524299934 524300354 1.200000e-179 640
5 TraesCS7D01G442800 chr7A 93.449 3969 243 10 9 3970 604260612 604264570 0.000000e+00 5873
6 TraesCS7D01G442800 chr7A 93.465 3963 241 12 1 3956 604249825 604253776 0.000000e+00 5867
7 TraesCS7D01G442800 chr7A 93.236 3977 248 12 1 3970 604255228 604259190 0.000000e+00 5834
8 TraesCS7D01G442800 chr6A 94.587 3399 159 15 1 3384 74148176 74151564 0.000000e+00 5234
9 TraesCS7D01G442800 chr6A 91.432 3805 257 30 1 3781 52290340 52286581 0.000000e+00 5156
10 TraesCS7D01G442800 chr6A 93.946 859 46 3 3113 3970 555445125 555445978 0.000000e+00 1293
11 TraesCS7D01G442800 chr6D 91.983 3667 250 24 317 3964 41624299 41620658 0.000000e+00 5103
12 TraesCS7D01G442800 chr6B 88.278 691 64 7 3284 3963 95514562 95515246 0.000000e+00 811


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 TraesCS7D01G442800 chr7D 562196517 562200486 3969 False 7332.000000 7332 100.000000 1 3970 1 chr7D.!!$F2 3969
1 TraesCS7D01G442800 chr7D 524248958 524252909 3951 False 5891.000000 5891 93.541000 1 3970 1 chr7D.!!$F1 3969
2 TraesCS7D01G442800 chr7D 524299934 524314721 14787 False 3995.666667 6093 94.400333 1 3970 3 chr7D.!!$F3 3969
3 TraesCS7D01G442800 chr7A 604249825 604264570 14745 False 5858.000000 5873 93.383333 1 3970 3 chr7A.!!$F1 3969
4 TraesCS7D01G442800 chr6A 74148176 74151564 3388 False 5234.000000 5234 94.587000 1 3384 1 chr6A.!!$F1 3383
5 TraesCS7D01G442800 chr6A 52286581 52290340 3759 True 5156.000000 5156 91.432000 1 3781 1 chr6A.!!$R1 3780
6 TraesCS7D01G442800 chr6A 555445125 555445978 853 False 1293.000000 1293 93.946000 3113 3970 1 chr6A.!!$F2 857
7 TraesCS7D01G442800 chr6D 41620658 41624299 3641 True 5103.000000 5103 91.983000 317 3964 1 chr6D.!!$R1 3647
8 TraesCS7D01G442800 chr6B 95514562 95515246 684 False 811.000000 811 88.278000 3284 3963 1 chr6B.!!$F1 679

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
939 4718 0.605589 AAGTTGGCTTCCCTACGCAC 60.606 55.000 0.0 0.0 41.06 5.34 F
1654 5436 1.381327 TACTTCGGGGAGCCTCAGG 60.381 63.158 0.0 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1827 5609 1.215382 CTCTTCGATGACCACGCCA 59.785 57.895 0.0 0.0 0.0 5.69 R
3145 6937 0.534203 TGAAAGAAACCGGCTCGCTT 60.534 50.000 0.0 0.0 0.0 4.68 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
95 3855 6.897259 TTGAAATCCCGAATTAGTCTTACG 57.103 37.500 0.00 0.0 0.00 3.18
591 4359 9.971922 AATATAAAGCAATCCATAAACAGAAGC 57.028 29.630 0.00 0.0 0.00 3.86
592 4360 5.990120 AAAGCAATCCATAAACAGAAGCT 57.010 34.783 0.00 0.0 0.00 3.74
593 4361 5.990120 AAGCAATCCATAAACAGAAGCTT 57.010 34.783 0.00 0.0 35.23 3.74
594 4362 5.990120 AGCAATCCATAAACAGAAGCTTT 57.010 34.783 0.00 0.0 0.00 3.51
595 4363 6.350629 AGCAATCCATAAACAGAAGCTTTT 57.649 33.333 0.00 0.0 0.00 2.27
596 4364 6.762333 AGCAATCCATAAACAGAAGCTTTTT 58.238 32.000 0.00 0.0 0.00 1.94
631 4401 9.295825 TGTTTTGACTATGTTTGGATAGACAAT 57.704 29.630 0.00 0.0 39.04 2.71
757 4531 6.988622 AAATACATTTGAAATGCCATGTGG 57.011 33.333 17.19 0.0 32.15 4.17
766 4540 4.525874 TGAAATGCCATGTGGTAAATGTGA 59.474 37.500 0.35 0.0 37.57 3.58
771 4545 6.788598 TGCCATGTGGTAAATGTGATAAAT 57.211 33.333 0.35 0.0 37.57 1.40
913 4692 3.709633 ATGGGCAGAGCAGCACGA 61.710 61.111 0.00 0.0 42.06 4.35
939 4718 0.605589 AAGTTGGCTTCCCTACGCAC 60.606 55.000 0.00 0.0 41.06 5.34
973 4752 2.047274 TACCTCGCAAGCCTGTGC 60.047 61.111 0.00 0.0 41.32 4.57
974 4753 2.786539 CTACCTCGCAAGCCTGTGCA 62.787 60.000 5.58 0.0 45.19 4.57
1087 4866 2.747855 CCAAGAGCAAGGTCCGCC 60.748 66.667 0.00 0.0 0.00 6.13
1654 5436 1.381327 TACTTCGGGGAGCCTCAGG 60.381 63.158 0.00 0.0 0.00 3.86
1827 5609 4.655963 ACACAAAAGTGGATAGACTGCAT 58.344 39.130 0.38 0.0 0.00 3.96
1829 5611 4.012374 ACAAAAGTGGATAGACTGCATGG 58.988 43.478 0.00 0.0 0.00 3.66
1872 5654 2.664851 CAGTGGAACAGCGGCGAA 60.665 61.111 12.98 0.0 41.80 4.70
1917 5699 2.061773 CTTGACGTTCTCATCACGCTT 58.938 47.619 0.00 0.0 41.53 4.68
2035 5817 5.187772 GGTTCAAGGGCCTAGATTGAATTTT 59.812 40.000 18.61 0.0 42.88 1.82
2843 6626 1.556911 CTACATGGCTTCACCTGGACT 59.443 52.381 0.00 0.0 40.22 3.85
3145 6937 2.351111 GGTTTTGTCCGTTTCACGTACA 59.649 45.455 0.00 0.0 38.65 2.90
3552 18159 2.840038 AGTGAGGTATGCAATGAGGACA 59.160 45.455 0.00 0.0 0.00 4.02
3564 18171 4.572389 GCAATGAGGACACATATTTCGAGT 59.428 41.667 0.00 0.0 0.00 4.18
3617 18233 7.866729 TGAAAGCAATACAGACACGATTAAAA 58.133 30.769 0.00 0.0 0.00 1.52
3646 18262 3.593442 TTATGGGCCAATGGAACTAGG 57.407 47.619 11.89 0.0 0.00 3.02
3651 18267 2.100197 GGCCAATGGAACTAGGGAAAC 58.900 52.381 2.05 0.0 0.00 2.78
3739 18355 5.598417 ACTATTATGGGCCAATGGAAGAAAC 59.402 40.000 11.89 0.0 0.00 2.78
3806 18422 2.871096 AATTAAAGGACTCGTGGGCA 57.129 45.000 0.00 0.0 0.00 5.36
3854 18470 2.439507 GAGAAGCAGATGGATGGGGTAA 59.560 50.000 0.00 0.0 0.00 2.85
3947 18563 3.243704 CCACACCCACGAAACATGAAATT 60.244 43.478 0.00 0.0 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
136 3901 1.608055 CATGTGTGTGAGGGAAAGCA 58.392 50.000 0.00 0.00 0.00 3.91
187 3953 3.862402 CGACGGAGCGCGTACTCT 61.862 66.667 8.43 0.00 36.87 3.24
189 3955 3.657835 GAACGACGGAGCGCGTACT 62.658 63.158 8.43 0.00 38.21 2.73
572 4340 5.990120 AAAGCTTCTGTTTATGGATTGCT 57.010 34.783 0.00 0.00 0.00 3.91
726 4500 9.887629 TGGCATTTCAAATGTATTTATGTTGAT 57.112 25.926 11.80 0.00 0.00 2.57
731 4505 8.552865 CCACATGGCATTTCAAATGTATTTATG 58.447 33.333 11.80 10.77 32.15 1.90
757 4531 9.454585 CATGTGTGGATCATTTATCACATTTAC 57.545 33.333 5.97 0.00 42.15 2.01
771 4545 7.803487 AGATATATTCCTCATGTGTGGATCA 57.197 36.000 4.79 0.00 37.52 2.92
861 4640 5.776716 CCCCTCTTTATATGTTACCTCGGTA 59.223 44.000 0.00 0.00 0.00 4.02
864 4643 5.539193 AGACCCCTCTTTATATGTTACCTCG 59.461 44.000 0.00 0.00 0.00 4.63
913 4692 1.133356 AGGGAAGCCAACTTTGCTCTT 60.133 47.619 0.00 0.00 38.34 2.85
939 4718 2.434702 AGGTAGCTTCCCTTGTTATCGG 59.565 50.000 5.64 0.00 0.00 4.18
973 4752 1.164662 ACTGCTGCTTGCTGAGTGTG 61.165 55.000 13.76 0.00 42.27 3.82
974 4753 0.883814 GACTGCTGCTTGCTGAGTGT 60.884 55.000 13.76 0.00 42.27 3.55
1116 4895 4.016706 CCCGGCGGAAGTGGAAGT 62.017 66.667 30.79 0.00 0.00 3.01
1534 5313 0.982673 GACGTTGAAGATGACGACCG 59.017 55.000 2.69 0.00 41.53 4.79
1538 5317 0.109458 TCCCGACGTTGAAGATGACG 60.109 55.000 3.74 0.00 44.34 4.35
1608 5390 1.143183 GAAGACAAGCCGGCGGATA 59.857 57.895 33.44 0.00 0.00 2.59
1827 5609 1.215382 CTCTTCGATGACCACGCCA 59.785 57.895 0.00 0.00 0.00 5.69
1829 5611 2.508891 CGCTCTTCGATGACCACGC 61.509 63.158 0.00 0.00 41.67 5.34
2035 5817 3.609853 GACTATGAGGCAATTGGTCACA 58.390 45.455 7.72 0.00 0.00 3.58
2843 6626 2.751688 GACACCCCAGCCGGTTTA 59.248 61.111 1.90 0.00 32.17 2.01
2864 6647 3.491619 GCTTGGACTCGCTGAGATTGATA 60.492 47.826 11.64 0.00 33.32 2.15
3066 6857 1.950909 ACGAAACAAAGCGGGATGAAA 59.049 42.857 0.00 0.00 0.00 2.69
3145 6937 0.534203 TGAAAGAAACCGGCTCGCTT 60.534 50.000 0.00 0.00 0.00 4.68
3552 18159 6.922407 CAGATCTGATCACACTCGAAATATGT 59.078 38.462 18.34 0.00 0.00 2.29
3564 18171 4.279420 CCCGTAATCTCAGATCTGATCACA 59.721 45.833 25.30 10.53 39.13 3.58
3617 18233 3.899360 CCATTGGCCCATAATCACAGATT 59.101 43.478 0.00 0.00 0.00 2.40
3646 18262 6.659824 TCTCAGATATTTAGTTGGGGTTTCC 58.340 40.000 0.00 0.00 0.00 3.13
3739 18355 5.108254 GCTTGCAAGTTTAATCACGTCTTTG 60.108 40.000 26.55 0.00 0.00 2.77
3846 18462 0.335019 GCCTCCTTGGTTTACCCCAT 59.665 55.000 0.00 0.00 38.35 4.00
3854 18470 3.181423 TGTCCTTAAATGCCTCCTTGGTT 60.181 43.478 0.00 0.00 38.35 3.67
3931 18547 5.101628 CACCCATAATTTCATGTTTCGTGG 58.898 41.667 0.00 0.00 0.00 4.94
3947 18563 1.142965 CGGCGTGTCATCACCCATA 59.857 57.895 0.00 0.00 41.09 2.74


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

AutoCloner maintained by Alex Coulton.