Multiple sequence alignment - TraesCS7A01G432700

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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 TraesCS7A01G432700 chr7A 100.000 4648 0 0 1 4648 626868439 626873086 0 8584
1 TraesCS7A01G432700 chr7A 98.220 1236 22 0 3413 4648 49822502 49823737 0 2161
2 TraesCS7A01G432700 chr5A 98.352 1760 27 2 1653 3412 147656126 147654369 0 3088
3 TraesCS7A01G432700 chr5A 98.181 1759 31 1 1653 3411 545792282 545794039 0 3070
4 TraesCS7A01G432700 chr5A 97.399 1653 38 3 1 1653 562123502 562121855 0 2809
5 TraesCS7A01G432700 chr5A 95.003 1581 65 5 78 1653 40241795 40240224 0 2470
6 TraesCS7A01G432700 chr5A 92.303 1611 89 14 78 1653 310017706 310019316 0 2255
7 TraesCS7A01G432700 chr5A 98.626 1237 17 0 3412 4648 687970811 687972047 0 2191
8 TraesCS7A01G432700 chr5A 98.545 1237 17 1 3412 4648 562121860 562120625 0 2183
9 TraesCS7A01G432700 chr5A 98.139 1236 23 0 3413 4648 511207645 511208880 0 2156
10 TraesCS7A01G432700 chr5A 97.453 589 13 1 1 589 687969096 687969682 0 1003
11 TraesCS7A01G432700 chr4A 98.182 1760 30 2 1652 3411 67746629 67748386 0 3072
12 TraesCS7A01G432700 chr4A 98.124 1759 31 2 1653 3411 6968312 6966556 0 3064
13 TraesCS7A01G432700 chr4A 98.222 1237 21 1 3412 4648 499027 497792 0 2161
14 TraesCS7A01G432700 chr6A 98.126 1761 31 2 1652 3411 85809835 85808076 0 3068
15 TraesCS7A01G432700 chr6A 98.068 1760 32 2 1652 3411 167160162 167161919 0 3061
16 TraesCS7A01G432700 chr6A 98.302 1237 20 1 3412 4648 553571408 553570173 0 2167
17 TraesCS7A01G432700 chr2A 98.126 1761 30 2 1653 3411 679819673 679821432 0 3066
18 TraesCS7A01G432700 chr2A 98.126 1761 28 2 1651 3411 567717971 567719726 0 3064
19 TraesCS7A01G432700 chr2A 98.545 1237 18 0 3412 4648 5148965 5150201 0 2185
20 TraesCS7A01G432700 chr2A 98.141 1237 21 1 3412 4648 303637064 303635830 0 2156
21 TraesCS7A01G432700 chr3A 98.068 1760 32 2 1652 3411 659152330 659150573 0 3061
22 TraesCS7A01G432700 chr3A 92.339 496 31 3 78 567 604765174 604765668 0 699
23 TraesCS7A01G432700 chr1A 96.379 1657 54 3 1 1653 16224479 16226133 0 2723
24 TraesCS7A01G432700 chr1A 98.301 1236 21 0 3412 4647 16219531 16220766 0 2167
25 TraesCS7A01G432700 chr5D 96.025 1585 52 4 78 1653 437728764 437727182 0 2567
26 TraesCS7A01G432700 chr2D 95.846 1589 49 7 78 1653 104542176 104540592 0 2553
27 TraesCS7A01G432700 chr2D 95.349 1591 57 7 78 1653 165663652 165665240 0 2512
28 TraesCS7A01G432700 chr2B 95.696 1278 43 6 383 1653 563765620 563766892 0 2045
29 TraesCS7A01G432700 chr2B 95.462 1278 46 6 383 1653 106932675 106933947 0 2028
30 TraesCS7A01G432700 chr6B 95.540 1278 45 6 383 1653 21617339 21616067 0 2034


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 TraesCS7A01G432700 chr7A 626868439 626873086 4647 False 8584 8584 100.0000 1 4648 1 chr7A.!!$F2 4647
1 TraesCS7A01G432700 chr7A 49822502 49823737 1235 False 2161 2161 98.2200 3413 4648 1 chr7A.!!$F1 1235
2 TraesCS7A01G432700 chr5A 147654369 147656126 1757 True 3088 3088 98.3520 1653 3412 1 chr5A.!!$R2 1759
3 TraesCS7A01G432700 chr5A 545792282 545794039 1757 False 3070 3070 98.1810 1653 3411 1 chr5A.!!$F3 1758
4 TraesCS7A01G432700 chr5A 562120625 562123502 2877 True 2496 2809 97.9720 1 4648 2 chr5A.!!$R3 4647
5 TraesCS7A01G432700 chr5A 40240224 40241795 1571 True 2470 2470 95.0030 78 1653 1 chr5A.!!$R1 1575
6 TraesCS7A01G432700 chr5A 310017706 310019316 1610 False 2255 2255 92.3030 78 1653 1 chr5A.!!$F1 1575
7 TraesCS7A01G432700 chr5A 511207645 511208880 1235 False 2156 2156 98.1390 3413 4648 1 chr5A.!!$F2 1235
8 TraesCS7A01G432700 chr5A 687969096 687972047 2951 False 1597 2191 98.0395 1 4648 2 chr5A.!!$F4 4647
9 TraesCS7A01G432700 chr4A 67746629 67748386 1757 False 3072 3072 98.1820 1652 3411 1 chr4A.!!$F1 1759
10 TraesCS7A01G432700 chr4A 6966556 6968312 1756 True 3064 3064 98.1240 1653 3411 1 chr4A.!!$R2 1758
11 TraesCS7A01G432700 chr4A 497792 499027 1235 True 2161 2161 98.2220 3412 4648 1 chr4A.!!$R1 1236
12 TraesCS7A01G432700 chr6A 85808076 85809835 1759 True 3068 3068 98.1260 1652 3411 1 chr6A.!!$R1 1759
13 TraesCS7A01G432700 chr6A 167160162 167161919 1757 False 3061 3061 98.0680 1652 3411 1 chr6A.!!$F1 1759
14 TraesCS7A01G432700 chr6A 553570173 553571408 1235 True 2167 2167 98.3020 3412 4648 1 chr6A.!!$R2 1236
15 TraesCS7A01G432700 chr2A 679819673 679821432 1759 False 3066 3066 98.1260 1653 3411 1 chr2A.!!$F3 1758
16 TraesCS7A01G432700 chr2A 567717971 567719726 1755 False 3064 3064 98.1260 1651 3411 1 chr2A.!!$F2 1760
17 TraesCS7A01G432700 chr2A 5148965 5150201 1236 False 2185 2185 98.5450 3412 4648 1 chr2A.!!$F1 1236
18 TraesCS7A01G432700 chr2A 303635830 303637064 1234 True 2156 2156 98.1410 3412 4648 1 chr2A.!!$R1 1236
19 TraesCS7A01G432700 chr3A 659150573 659152330 1757 True 3061 3061 98.0680 1652 3411 1 chr3A.!!$R1 1759
20 TraesCS7A01G432700 chr1A 16219531 16226133 6602 False 2445 2723 97.3400 1 4647 2 chr1A.!!$F1 4646
21 TraesCS7A01G432700 chr5D 437727182 437728764 1582 True 2567 2567 96.0250 78 1653 1 chr5D.!!$R1 1575
22 TraesCS7A01G432700 chr2D 104540592 104542176 1584 True 2553 2553 95.8460 78 1653 1 chr2D.!!$R1 1575
23 TraesCS7A01G432700 chr2D 165663652 165665240 1588 False 2512 2512 95.3490 78 1653 1 chr2D.!!$F1 1575
24 TraesCS7A01G432700 chr2B 563765620 563766892 1272 False 2045 2045 95.6960 383 1653 1 chr2B.!!$F2 1270
25 TraesCS7A01G432700 chr2B 106932675 106933947 1272 False 2028 2028 95.4620 383 1653 1 chr2B.!!$F1 1270
26 TraesCS7A01G432700 chr6B 21616067 21617339 1272 True 2034 2034 95.5400 383 1653 1 chr6B.!!$R1 1270

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
289 5241 1.745489 GGACCTCCACGGCAATGAC 60.745 63.158 0.0 0.0 35.61 3.06 F
1138 6200 0.321122 GCCATCCCAGCCTTCTATCG 60.321 60.000 0.0 0.0 0.00 2.92 F
2406 7478 0.392998 GCATGTCAGTCCCACCGAAT 60.393 55.000 0.0 0.0 0.00 3.34 F
2537 7609 1.937098 ATACCCCTCCACCTCCTCTA 58.063 55.000 0.0 0.0 0.00 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1244 6306 0.991146 AGGTGATGGTGTACATGCCA 59.009 50.000 7.6 7.6 40.72 4.92 R
3043 8115 0.675522 ACGAAGGGTAATGGTTGCGG 60.676 55.000 0.0 0.0 0.00 5.69 R
3543 8618 3.033659 ACCACCAACATTAACCCACAA 57.966 42.857 0.0 0.0 0.00 3.33 R
3756 8831 5.120053 CACACGCATACTAACATCACAAAGA 59.880 40.000 0.0 0.0 0.00 2.52 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
33 4982 4.931601 GCGATGATGGTCATGTGTATATGT 59.068 41.667 0.00 0.00 37.20 2.29
289 5241 1.745489 GGACCTCCACGGCAATGAC 60.745 63.158 0.00 0.00 35.61 3.06
380 5338 2.744166 GCATCAGGAACTCTGCATGCTA 60.744 50.000 20.33 6.18 44.33 3.49
592 5636 7.442969 ACTTCTATGCTACTACTACTACTGCTG 59.557 40.741 0.00 0.00 0.00 4.41
745 5789 9.875708 AATTCTTGGGCAATATATGGTAGTTTA 57.124 29.630 0.00 0.00 0.00 2.01
777 5821 3.152341 GCCCAAGATTAGTATGCTGCAT 58.848 45.455 20.18 20.18 0.00 3.96
850 5895 1.893062 CACCTCACTGGATCTCGCA 59.107 57.895 0.00 0.00 39.71 5.10
1138 6200 0.321122 GCCATCCCAGCCTTCTATCG 60.321 60.000 0.00 0.00 0.00 2.92
1186 6248 2.816411 AGTAGCACCAGTACCTTGCTA 58.184 47.619 13.86 13.86 44.82 3.49
1643 6714 1.556451 TGCATGCTACCTGATGAGTGT 59.444 47.619 20.33 0.00 0.00 3.55
1647 6718 4.437930 GCATGCTACCTGATGAGTGTTTTC 60.438 45.833 11.37 0.00 0.00 2.29
1648 6719 4.623932 TGCTACCTGATGAGTGTTTTCT 57.376 40.909 0.00 0.00 0.00 2.52
1649 6720 4.973168 TGCTACCTGATGAGTGTTTTCTT 58.027 39.130 0.00 0.00 0.00 2.52
1785 6856 1.203001 TGGATGTGAAAGTGGAACCCC 60.203 52.381 0.00 0.00 37.80 4.95
1814 6885 2.424956 GCTAAGGACAAAGGATTGGCTG 59.575 50.000 0.00 0.00 44.51 4.85
2161 7232 4.635324 TGTTTCCCTTTCGTAACTTTTCGT 59.365 37.500 0.00 0.00 0.00 3.85
2265 7337 1.002624 GAGCAAATCGGTCCCACCA 60.003 57.895 0.00 0.00 38.47 4.17
2406 7478 0.392998 GCATGTCAGTCCCACCGAAT 60.393 55.000 0.00 0.00 0.00 3.34
2416 7488 4.341235 CAGTCCCACCGAATATCTCTAACA 59.659 45.833 0.00 0.00 0.00 2.41
2437 7509 6.243216 ACAGTCACTAGGTTTACCTTTTCA 57.757 37.500 6.76 0.00 46.09 2.69
2537 7609 1.937098 ATACCCCTCCACCTCCTCTA 58.063 55.000 0.00 0.00 0.00 2.43
2728 7800 8.789767 AATCCAAATCCTATGAGAGAGAGTTA 57.210 34.615 0.00 0.00 0.00 2.24
2944 8016 2.281484 GCAAGTCCTTCGTGGGCA 60.281 61.111 4.84 0.00 44.59 5.36
2962 8034 2.033738 GCAATGGCCATGGTGGGATAA 61.034 52.381 21.63 0.00 38.19 1.75
2978 8050 4.898861 TGGGATAAACAAGGTTGCTTCTTT 59.101 37.500 0.00 0.00 0.00 2.52
3043 8115 3.462678 GAGCCCTCCGTGGACTCC 61.463 72.222 0.00 0.00 38.35 3.85
3430 8505 9.802039 TCCTACACTTTGTAATATTTCACCTTT 57.198 29.630 0.00 0.00 31.67 3.11
3634 8709 1.746615 GCGGCAAGAAGCTCATGGA 60.747 57.895 0.00 0.00 44.79 3.41
3756 8831 4.175962 TGGTTCCCTTTATTCTCTCCTGT 58.824 43.478 0.00 0.00 0.00 4.00
3867 8942 2.073056 CAGGCGCAATGTGTTGTAGTA 58.927 47.619 10.83 0.00 37.65 1.82
4184 9259 2.254152 TCTGACTATGGTTCCAGCCT 57.746 50.000 0.00 0.00 0.00 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
289 5241 2.743752 CGACCATGTGCAGGCTTCG 61.744 63.158 0.00 0.0 0.00 3.79
380 5338 5.495926 AAGATGATGAGACAAAGGACAGT 57.504 39.130 0.00 0.0 0.00 3.55
567 5549 7.572353 GCAGCAGTAGTAGTAGTAGCATAGAAG 60.572 44.444 0.00 0.0 0.00 2.85
568 5550 6.205076 GCAGCAGTAGTAGTAGTAGCATAGAA 59.795 42.308 0.00 0.0 0.00 2.10
569 5551 5.701750 GCAGCAGTAGTAGTAGTAGCATAGA 59.298 44.000 0.00 0.0 0.00 1.98
589 5633 9.070257 TAATCAGGATTAAATGCAGACAGCAGC 62.070 40.741 0.00 0.0 42.31 5.25
592 5636 5.511234 AATCAGGATTAAATGCAGACAGC 57.489 39.130 0.00 0.0 45.96 4.40
745 5789 0.687354 ATCTTGGGCGTGAAGAGTGT 59.313 50.000 0.00 0.0 33.01 3.55
777 5821 1.313889 ATGGAGTGAGGAGGGAGAGA 58.686 55.000 0.00 0.0 0.00 3.10
838 5883 0.321653 GGGTTTGTGCGAGATCCAGT 60.322 55.000 0.00 0.0 0.00 4.00
850 5895 1.244019 GCAAGATGAGCGGGGTTTGT 61.244 55.000 0.00 0.0 0.00 2.83
1155 6217 1.202663 TGGTGCTACTACCGTGCAAAA 60.203 47.619 0.00 0.0 43.87 2.44
1186 6248 1.057851 TCCCTTCCGTTCCCAACAGT 61.058 55.000 0.00 0.0 0.00 3.55
1244 6306 0.991146 AGGTGATGGTGTACATGCCA 59.009 50.000 7.60 7.6 40.72 4.92
1326 6388 1.135373 GTCGAGGAAGATGAGCGTGAA 60.135 52.381 0.00 0.0 0.00 3.18
1643 6714 6.978080 GGATAGTTGCACTTTCACAAAGAAAA 59.022 34.615 3.00 0.0 45.11 2.29
1647 6718 4.520492 AGGGATAGTTGCACTTTCACAAAG 59.480 41.667 10.06 0.0 44.10 2.77
1648 6719 4.469657 AGGGATAGTTGCACTTTCACAAA 58.530 39.130 10.06 0.0 32.90 2.83
1649 6720 4.098914 AGGGATAGTTGCACTTTCACAA 57.901 40.909 10.06 0.0 32.90 3.33
1723 6794 6.715280 AGCTTTCCTGAAATAGTCATCTTGA 58.285 36.000 0.00 0.0 35.07 3.02
1785 6856 5.964958 TCCTTTGTCCTTAGCATTTTGAG 57.035 39.130 0.00 0.0 0.00 3.02
1814 6885 4.064388 AGAGTCTTGAGCTTTTGAGCTTC 58.936 43.478 2.06 0.0 46.36 3.86
2161 7232 2.736721 CAATTCGCTCTTTCGGTGAGAA 59.263 45.455 0.00 0.0 37.01 2.87
2265 7337 4.202367 CCAGAGAGTTGGTCAGGTAAACTT 60.202 45.833 0.00 0.0 34.37 2.66
2406 7478 8.334734 AGGTAAACCTAGTGACTGTTAGAGATA 58.665 37.037 0.00 0.0 46.48 1.98
2437 7509 0.748450 TCAACAAACTCGGTCGGACT 59.252 50.000 8.23 0.0 0.00 3.85
2537 7609 1.137872 GATGGCTCTCTCCACGAATGT 59.862 52.381 0.00 0.0 39.25 2.71
2728 7800 5.014123 TCAAATGATAGTCTCCCCAACACTT 59.986 40.000 0.00 0.0 0.00 3.16
2944 8016 2.292785 TGTTTATCCCACCATGGCCATT 60.293 45.455 17.92 0.0 35.79 3.16
2962 8034 3.096092 TCCACAAAGAAGCAACCTTGTT 58.904 40.909 0.00 0.0 36.24 2.83
3043 8115 0.675522 ACGAAGGGTAATGGTTGCGG 60.676 55.000 0.00 0.0 0.00 5.69
3430 8505 6.824196 TCAAACCGAATAAACCTATGCATACA 59.176 34.615 1.16 0.0 0.00 2.29
3543 8618 3.033659 ACCACCAACATTAACCCACAA 57.966 42.857 0.00 0.0 0.00 3.33
3756 8831 5.120053 CACACGCATACTAACATCACAAAGA 59.880 40.000 0.00 0.0 0.00 2.52
4184 9259 6.053005 ACAGGACAAAAACTTCGATAGTCAA 58.947 36.000 0.00 0.0 35.54 3.18
4600 9676 1.534717 AAGCCCAACATTGCAGCCT 60.535 52.632 0.00 0.0 0.00 4.58


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

AutoCloner maintained by Alex Coulton.