Multiple sequence alignment - TraesCS7D01G162900

Loading Multiple Alignment...

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 TraesCS7D01G162900 chr7D 100.000 4496 0 0 1 4496 112839596 112835101 0.000000e+00 8303.0
1 TraesCS7D01G162900 chr7D 86.541 795 96 11 3 792 112920979 112920191 0.000000e+00 865.0
2 TraesCS7D01G162900 chr7D 89.474 475 44 6 3 473 112892311 112891839 2.990000e-166 595.0
3 TraesCS7D01G162900 chr7D 81.846 325 53 6 470 792 112879979 112879659 7.410000e-68 268.0
4 TraesCS7D01G162900 chr7A 95.283 4516 159 19 3 4496 118188456 118183973 0.000000e+00 7110.0
5 TraesCS7D01G162900 chr7A 81.583 581 91 10 3 572 727345744 727346319 2.450000e-127 466.0
6 TraesCS7D01G162900 chr7A 81.067 581 93 11 3 572 727353061 727353635 8.870000e-122 448.0
7 TraesCS7D01G162900 chr7A 80.105 573 100 12 3 569 104810918 104811482 9.000000e-112 414.0
8 TraesCS7D01G162900 chr7A 91.103 281 20 4 4217 4496 694112149 694111873 4.250000e-100 375.0
9 TraesCS7D01G162900 chr7B 95.729 3278 106 12 936 4183 72314393 72311120 0.000000e+00 5247.0
10 TraesCS7D01G162900 chr7B 89.231 260 26 2 4184 4441 683030302 683030043 1.560000e-84 324.0
11 TraesCS7D01G162900 chr7B 82.500 80 12 2 4217 4295 308688605 308688527 8.070000e-08 69.4
12 TraesCS7D01G162900 chr7B 78.788 99 15 6 4184 4280 616619157 616619251 1.350000e-05 62.1
13 TraesCS7D01G162900 chr2A 81.788 593 92 11 3 584 333712928 333713515 2.430000e-132 483.0
14 TraesCS7D01G162900 chr2A 80.640 594 97 12 3 584 364473458 364472871 1.150000e-120 444.0
15 TraesCS7D01G162900 chr3A 81.619 593 93 9 3 584 550401390 550400803 1.130000e-130 477.0
16 TraesCS7D01G162900 chr3A 94.643 168 7 1 4007 4172 38712018 38712185 4.460000e-65 259.0
17 TraesCS7D01G162900 chr3A 95.152 165 6 1 4010 4172 187898745 187898581 4.460000e-65 259.0
18 TraesCS7D01G162900 chr6A 81.756 581 90 11 3 572 250719165 250719740 5.260000e-129 472.0
19 TraesCS7D01G162900 chr6A 81.113 593 96 11 3 584 34295361 34294774 1.140000e-125 460.0
20 TraesCS7D01G162900 chr6A 94.643 168 7 1 4007 4172 601624045 601624212 4.460000e-65 259.0
21 TraesCS7D01G162900 chr2D 81.724 580 90 8 3 571 330491404 330491978 1.890000e-128 470.0
22 TraesCS7D01G162900 chr1A 81.282 593 95 11 3 584 216451717 216451130 2.450000e-127 466.0
23 TraesCS7D01G162900 chr1A 95.152 165 6 1 4010 4172 109013304 109013140 4.460000e-65 259.0
24 TraesCS7D01G162900 chr4D 80.607 593 99 10 3 584 423867017 423867604 1.150000e-120 444.0
25 TraesCS7D01G162900 chr4D 81.192 537 84 10 58 584 233090742 233091271 2.500000e-112 416.0
26 TraesCS7D01G162900 chr4B 89.836 305 27 3 4184 4485 368110897 368111200 5.450000e-104 388.0
27 TraesCS7D01G162900 chr4B 92.339 248 15 3 4250 4496 368110519 368110275 2.570000e-92 350.0
28 TraesCS7D01G162900 chr5A 95.152 165 6 1 4010 4172 19029942 19029778 4.460000e-65 259.0
29 TraesCS7D01G162900 chr5A 94.643 168 7 2 4007 4172 320375666 320375833 4.460000e-65 259.0
30 TraesCS7D01G162900 chr4A 95.152 165 6 1 4010 4172 607647842 607647678 4.460000e-65 259.0
31 TraesCS7D01G162900 chr1D 83.036 224 32 6 4184 4405 347204946 347205165 9.860000e-47 198.0
32 TraesCS7D01G162900 chr2B 80.488 123 19 5 4184 4304 96944470 96944589 6.190000e-14 89.8
33 TraesCS7D01G162900 chr2B 80.435 92 16 2 4205 4295 691909297 691909207 8.070000e-08 69.4


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 TraesCS7D01G162900 chr7D 112835101 112839596 4495 True 8303 8303 100.000 1 4496 1 chr7D.!!$R1 4495
1 TraesCS7D01G162900 chr7D 112920191 112920979 788 True 865 865 86.541 3 792 1 chr7D.!!$R4 789
2 TraesCS7D01G162900 chr7A 118183973 118188456 4483 True 7110 7110 95.283 3 4496 1 chr7A.!!$R1 4493
3 TraesCS7D01G162900 chr7A 727345744 727346319 575 False 466 466 81.583 3 572 1 chr7A.!!$F2 569
4 TraesCS7D01G162900 chr7A 727353061 727353635 574 False 448 448 81.067 3 572 1 chr7A.!!$F3 569
5 TraesCS7D01G162900 chr7A 104810918 104811482 564 False 414 414 80.105 3 569 1 chr7A.!!$F1 566
6 TraesCS7D01G162900 chr7B 72311120 72314393 3273 True 5247 5247 95.729 936 4183 1 chr7B.!!$R1 3247
7 TraesCS7D01G162900 chr2A 333712928 333713515 587 False 483 483 81.788 3 584 1 chr2A.!!$F1 581
8 TraesCS7D01G162900 chr2A 364472871 364473458 587 True 444 444 80.640 3 584 1 chr2A.!!$R1 581
9 TraesCS7D01G162900 chr3A 550400803 550401390 587 True 477 477 81.619 3 584 1 chr3A.!!$R2 581
10 TraesCS7D01G162900 chr6A 250719165 250719740 575 False 472 472 81.756 3 572 1 chr6A.!!$F1 569
11 TraesCS7D01G162900 chr6A 34294774 34295361 587 True 460 460 81.113 3 584 1 chr6A.!!$R1 581
12 TraesCS7D01G162900 chr2D 330491404 330491978 574 False 470 470 81.724 3 571 1 chr2D.!!$F1 568
13 TraesCS7D01G162900 chr1A 216451130 216451717 587 True 466 466 81.282 3 584 1 chr1A.!!$R2 581
14 TraesCS7D01G162900 chr4D 423867017 423867604 587 False 444 444 80.607 3 584 1 chr4D.!!$F2 581
15 TraesCS7D01G162900 chr4D 233090742 233091271 529 False 416 416 81.192 58 584 1 chr4D.!!$F1 526

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
751 765 0.321034 GGCGGTTTACGGGTCTCTTT 60.321 55.0 0.0 0.0 44.51 2.52 F
870 893 0.675083 TTGCTCTAACCACCGTTCGA 59.325 50.0 0.0 0.0 33.17 3.71 F
2195 2222 1.125711 AACCACGGGCAGGTAGAAGT 61.126 55.0 0.0 0.0 38.76 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2281 2308 1.547372 GTTTGGCTTCACATCCTGCAT 59.453 47.619 0.0 0.0 0.00 3.96 R
3150 3177 9.853555 CACAATCCATTTACAAAAGCAGTATAA 57.146 29.630 0.0 0.0 0.00 0.98 R
4313 4370 0.179189 GCGCACCATGCTAGTCAAAC 60.179 55.000 0.3 0.0 42.25 2.93 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
48 49 5.917541 GTAGACACGATGAAACTCCAAAA 57.082 39.130 0.00 0.00 0.00 2.44
50 51 5.613358 AGACACGATGAAACTCCAAAATC 57.387 39.130 0.00 0.00 0.00 2.17
55 56 5.399301 CACGATGAAACTCCAAAATCAACAC 59.601 40.000 0.00 0.00 0.00 3.32
119 120 1.272490 AGAGAATCAACTTGACGCCGA 59.728 47.619 0.00 0.00 37.82 5.54
128 130 1.732259 ACTTGACGCCGAATAGCAAAG 59.268 47.619 0.00 0.00 0.00 2.77
160 162 7.096271 GCATAGAAATCATCAACACTAGAGTCG 60.096 40.741 0.00 0.00 0.00 4.18
280 291 4.293662 AGGCCTAGGAACTCAAAGAAAG 57.706 45.455 14.75 0.00 41.75 2.62
304 315 5.488341 ACTGAAACAGAACACTACAAGTGT 58.512 37.500 6.88 6.88 46.72 3.55
476 488 1.258982 GCAACCTGATTAGCATCGACG 59.741 52.381 0.00 0.00 31.08 5.12
572 585 2.816411 AGAACACCCCAGAGACGAATA 58.184 47.619 0.00 0.00 0.00 1.75
574 587 2.233305 ACACCCCAGAGACGAATACT 57.767 50.000 0.00 0.00 0.00 2.12
575 588 1.825474 ACACCCCAGAGACGAATACTG 59.175 52.381 0.00 0.00 0.00 2.74
594 607 1.373590 GCGCATATGGTTTCGGTGGT 61.374 55.000 0.30 0.00 0.00 4.16
635 648 0.826715 CTGGAGGGAGAGCGATTTGA 59.173 55.000 0.00 0.00 0.00 2.69
636 649 1.208052 CTGGAGGGAGAGCGATTTGAA 59.792 52.381 0.00 0.00 0.00 2.69
637 650 1.208052 TGGAGGGAGAGCGATTTGAAG 59.792 52.381 0.00 0.00 0.00 3.02
659 672 0.960364 GGAGAAGGTGAAATGCGGCA 60.960 55.000 4.58 4.58 0.00 5.69
678 691 4.702831 GGCAGAGGAGGATAAGAGAAAAG 58.297 47.826 0.00 0.00 0.00 2.27
680 693 4.407296 GCAGAGGAGGATAAGAGAAAAGGA 59.593 45.833 0.00 0.00 0.00 3.36
681 694 5.453198 GCAGAGGAGGATAAGAGAAAAGGAG 60.453 48.000 0.00 0.00 0.00 3.69
684 697 4.966168 AGGAGGATAAGAGAAAAGGAGGAC 59.034 45.833 0.00 0.00 0.00 3.85
751 765 0.321034 GGCGGTTTACGGGTCTCTTT 60.321 55.000 0.00 0.00 44.51 2.52
794 808 0.680618 TTTTTAGCGGACCTGGTCGA 59.319 50.000 19.98 3.24 32.65 4.20
795 809 0.680618 TTTTAGCGGACCTGGTCGAA 59.319 50.000 19.98 8.99 32.65 3.71
797 811 0.896940 TTAGCGGACCTGGTCGAACT 60.897 55.000 19.98 17.70 32.65 3.01
799 813 3.048602 CGGACCTGGTCGAACTGT 58.951 61.111 19.98 0.00 32.65 3.55
829 843 2.973694 TAGTGTCCAGTTAATCCGCC 57.026 50.000 0.00 0.00 0.00 6.13
830 844 1.276622 AGTGTCCAGTTAATCCGCCT 58.723 50.000 0.00 0.00 0.00 5.52
836 850 3.694566 GTCCAGTTAATCCGCCTGAAAAT 59.305 43.478 0.00 0.00 0.00 1.82
844 858 4.193334 GCCTGAAAATCGCGGCCC 62.193 66.667 6.13 0.00 36.56 5.80
870 893 0.675083 TTGCTCTAACCACCGTTCGA 59.325 50.000 0.00 0.00 33.17 3.71
1059 1086 3.558109 CCTCCTTCTTCAAGTCCTTCACC 60.558 52.174 0.00 0.00 0.00 4.02
1080 1107 2.401699 CTGTTCTCCCACAGGCAGCA 62.402 60.000 0.00 0.00 40.60 4.41
1084 1111 3.972971 CTCCCACAGGCAGCAGAGC 62.973 68.421 0.00 0.00 0.00 4.09
1649 1676 1.518133 CGCTCCTGCAGTGCTACTC 60.518 63.158 17.60 1.04 39.64 2.59
1906 1933 3.084039 GAGATGTTTGACAAGATGGCCA 58.916 45.455 8.56 8.56 0.00 5.36
2016 2043 6.874288 ATATTTGAGGTAATGAAGAGCAGC 57.126 37.500 0.00 0.00 0.00 5.25
2130 2157 5.365314 TGAAAATGCTGGGAAGTTAAAACCT 59.635 36.000 0.00 0.00 0.00 3.50
2142 2169 7.881751 GGGAAGTTAAAACCTAGTGATGTTACT 59.118 37.037 0.00 0.00 34.71 2.24
2195 2222 1.125711 AACCACGGGCAGGTAGAAGT 61.126 55.000 0.00 0.00 38.76 3.01
2281 2308 2.073056 GTGCACATGTGTTCGATACCA 58.927 47.619 26.01 10.67 0.00 3.25
3150 3177 5.749462 AGTTGTGCTCCAAATAAGATAGCT 58.251 37.500 0.00 0.00 34.07 3.32
3201 3228 1.271434 TGTGGTCGAGTAGAGACTGCT 60.271 52.381 0.00 0.00 38.58 4.24
3316 3343 8.451748 GGAATACAACTAAAGGATGTGAACTTC 58.548 37.037 0.00 0.00 0.00 3.01
3589 3640 3.515502 TGCTAGCAGATTGTTCCTACTGT 59.484 43.478 14.93 0.00 33.57 3.55
3815 3869 3.765381 TGGTTGCTTCTGAATTGGATGA 58.235 40.909 0.00 0.00 0.00 2.92
3852 3906 7.657352 TTAAATATCCTTTATAGGCCCCAGT 57.343 36.000 0.00 0.00 41.69 4.00
3872 3926 4.623167 CAGTCGTATCCAAGACTTCAAGTG 59.377 45.833 0.00 0.00 44.46 3.16
4343 4400 1.070376 CATGGTGCGCATCGATGTAAG 60.070 52.381 25.47 17.69 0.00 2.34
4350 4407 2.032549 GCGCATCGATGTAAGAAATGCT 60.033 45.455 25.47 0.00 40.37 3.79
4400 4457 4.182744 TTTTTAAGCCAGCCGCCA 57.817 50.000 0.00 0.00 38.78 5.69
4481 4540 5.732247 GCTTACCATGCCGATTTTTAATCGT 60.732 40.000 17.43 4.09 39.67 3.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 4.096382 GTCTTGTCAGGTTGTTGTGTTGAT 59.904 41.667 0.00 0.00 0.00 2.57
50 51 3.440173 AGTCTTGTCAGGTTGTTGTGTTG 59.560 43.478 0.00 0.00 0.00 3.33
55 56 1.334869 GCCAGTCTTGTCAGGTTGTTG 59.665 52.381 0.00 0.00 0.00 3.33
119 120 9.123902 TGATTTCTATGCACATACTTTGCTATT 57.876 29.630 0.00 0.00 40.86 1.73
128 130 7.923888 AGTGTTGATGATTTCTATGCACATAC 58.076 34.615 0.00 0.00 0.00 2.39
160 162 3.224324 CCATGAGCATGCCAGGGC 61.224 66.667 21.35 2.62 37.49 5.19
280 291 6.037423 CACTTGTAGTGTTCTGTTTCAGTC 57.963 41.667 0.00 0.00 41.19 3.51
304 315 1.807142 TCGTGTTGTTGTTGCTGTTCA 59.193 42.857 0.00 0.00 0.00 3.18
476 488 1.885871 GATGCCACTGGTTCTTGCC 59.114 57.895 0.00 0.00 0.00 4.52
539 552 3.561313 GGGGTGTTCTTTCTGGCAAGATA 60.561 47.826 0.00 0.00 32.69 1.98
541 554 1.478654 GGGGTGTTCTTTCTGGCAAGA 60.479 52.381 0.00 0.00 0.00 3.02
572 585 0.392461 ACCGAAACCATATGCGCAGT 60.392 50.000 18.32 4.97 0.00 4.40
574 587 1.372838 CCACCGAAACCATATGCGCA 61.373 55.000 14.96 14.96 0.00 6.09
575 588 1.355210 CCACCGAAACCATATGCGC 59.645 57.895 0.00 0.00 0.00 6.09
594 607 0.243365 TAGTTTTCCGGCGAGCGTAA 59.757 50.000 9.30 0.00 0.00 3.18
635 648 2.165998 GCATTTCACCTTCTCCAGCTT 58.834 47.619 0.00 0.00 0.00 3.74
636 649 1.831580 GCATTTCACCTTCTCCAGCT 58.168 50.000 0.00 0.00 0.00 4.24
637 650 0.449388 CGCATTTCACCTTCTCCAGC 59.551 55.000 0.00 0.00 0.00 4.85
659 672 5.042979 TCCTCCTTTTCTCTTATCCTCCTCT 60.043 44.000 0.00 0.00 0.00 3.69
678 691 0.321387 GTTTCAGGTTCCCGTCCTCC 60.321 60.000 0.00 0.00 32.37 4.30
680 693 0.108019 GTGTTTCAGGTTCCCGTCCT 59.892 55.000 0.00 0.00 35.45 3.85
681 694 1.226030 CGTGTTTCAGGTTCCCGTCC 61.226 60.000 0.00 0.00 0.00 4.79
684 697 1.519408 AATCGTGTTTCAGGTTCCCG 58.481 50.000 0.00 0.00 0.00 5.14
693 706 1.347221 CGGCGCCTAATCGTGTTTC 59.653 57.895 26.68 0.00 0.00 2.78
703 716 0.664761 GCGATATATACCGGCGCCTA 59.335 55.000 26.68 11.87 41.65 3.93
751 765 0.871057 CCGGCCCGTAAAACGTTTAA 59.129 50.000 15.03 0.00 40.58 1.52
806 820 4.456566 GGCGGATTAACTGGACACTAAAAA 59.543 41.667 0.00 0.00 0.00 1.94
807 821 4.004982 GGCGGATTAACTGGACACTAAAA 58.995 43.478 0.00 0.00 0.00 1.52
808 822 3.262405 AGGCGGATTAACTGGACACTAAA 59.738 43.478 0.00 0.00 0.00 1.85
809 823 2.835764 AGGCGGATTAACTGGACACTAA 59.164 45.455 0.00 0.00 0.00 2.24
810 824 2.167693 CAGGCGGATTAACTGGACACTA 59.832 50.000 0.00 0.00 0.00 2.74
821 835 0.934496 CGCGATTTTCAGGCGGATTA 59.066 50.000 0.00 0.00 45.69 1.75
829 843 3.876198 CCGGGCCGCGATTTTCAG 61.876 66.667 23.20 0.00 0.00 3.02
844 858 1.080093 TGGTTAGAGCAACTCGCCG 60.080 57.895 0.00 0.00 44.04 6.46
853 876 3.031660 CTCGAACGGTGGTTAGAGC 57.968 57.895 4.57 0.00 44.90 4.09
870 893 1.205893 GTCGCTTGAAGATGGGACTCT 59.794 52.381 0.00 0.00 41.13 3.24
902 929 4.231439 GTGGACTCTCGAGTTTTTCTCTC 58.769 47.826 13.13 0.00 42.66 3.20
1035 1062 3.325135 TGAAGGACTTGAAGAAGGAGGAC 59.675 47.826 0.00 0.00 32.95 3.85
1059 1086 0.604780 CTGCCTGTGGGAGAACAGTG 60.605 60.000 0.00 0.00 44.17 3.66
1649 1676 2.898920 ATCTGGACGGCCTGCATTGG 62.899 60.000 9.82 0.00 33.46 3.16
1677 1704 2.766313 CTCATCCTTTGGAACACGTCA 58.234 47.619 0.00 0.00 39.29 4.35
1755 1782 3.015145 CCGTCCACCTTCCCCCAT 61.015 66.667 0.00 0.00 0.00 4.00
1842 1869 2.102925 CTGTTTTGCAAACCCATGGACT 59.897 45.455 15.22 0.00 0.00 3.85
1906 1933 6.332630 GCAAATCAGCAACATAACCATAAGT 58.667 36.000 0.00 0.00 0.00 2.24
1972 1999 5.738619 ATTTTCACCGCCTTTCCTATTTT 57.261 34.783 0.00 0.00 0.00 1.82
2130 2157 5.715434 TGTACAGTGCAGTAACATCACTA 57.285 39.130 0.00 0.00 38.85 2.74
2142 2169 3.207265 AGAACCACATTGTACAGTGCA 57.793 42.857 17.45 0.00 34.48 4.57
2195 2222 3.769300 TGAGGTGAGCAACTGATAAGCTA 59.231 43.478 0.00 0.00 39.02 3.32
2281 2308 1.547372 GTTTGGCTTCACATCCTGCAT 59.453 47.619 0.00 0.00 0.00 3.96
3150 3177 9.853555 CACAATCCATTTACAAAAGCAGTATAA 57.146 29.630 0.00 0.00 0.00 0.98
3201 3228 5.913946 TCATCTCCTCATAGTAGGTCAGA 57.086 43.478 0.00 0.00 37.91 3.27
3316 3343 4.517075 GTCCCTTTGAAGAACCTCTTTCAG 59.483 45.833 0.00 0.00 36.73 3.02
3589 3640 4.150897 ACCTTGAGAAAGTAGTTGCACA 57.849 40.909 0.00 0.00 0.00 4.57
3708 3759 6.882140 CCAACAATTAACATACAGGACCTACA 59.118 38.462 0.00 0.00 0.00 2.74
3852 3906 4.866508 ACACTTGAAGTCTTGGATACGA 57.133 40.909 0.00 0.00 42.51 3.43
3872 3926 9.997482 ACAATTACATACGGTATTTGAATCAAC 57.003 29.630 14.16 0.00 42.10 3.18
4008 4062 6.405278 TCGATGCTCTAAACATAATCTCCA 57.595 37.500 0.00 0.00 0.00 3.86
4179 4236 0.667993 TGTTGCCAAACACAGCTAGC 59.332 50.000 6.62 6.62 41.41 3.42
4208 4265 9.511144 CTGTAGTTTTTCAATACTTCGGTTTTT 57.489 29.630 0.00 0.00 0.00 1.94
4313 4370 0.179189 GCGCACCATGCTAGTCAAAC 60.179 55.000 0.30 0.00 42.25 2.93
4400 4457 2.616376 TCAACTACTGTTTGCACGCAAT 59.384 40.909 5.11 0.00 35.70 3.56
4405 4462 5.522460 TGAACTAGTCAACTACTGTTTGCAC 59.478 40.000 0.00 0.00 39.39 4.57
4413 4470 4.261909 CCGTTGGTGAACTAGTCAACTACT 60.262 45.833 17.95 0.00 44.60 2.57


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

AutoCloner maintained by Alex Coulton.