Multiple sequence alignment - TraesCS7A01G409000

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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 TraesCS7A01G409000 chr7A 100.000 3822 0 0 1 3822 595103772 595107593 0 7059
1 TraesCS7A01G409000 chr7A 95.723 1707 65 8 454 2159 67381690 67379991 0 2741
2 TraesCS7A01G409000 chr7A 95.380 1710 68 11 454 2159 67145384 67143682 0 2710
3 TraesCS7A01G409000 chr7A 94.782 1744 78 8 2082 3820 699087680 699085945 0 2704
4 TraesCS7A01G409000 chr7A 86.312 884 82 23 1845 2713 678425014 678424155 0 926
5 TraesCS7A01G409000 chr7A 95.011 441 19 3 1 438 699089895 699089455 0 689
6 TraesCS7A01G409000 chr2A 94.413 3401 135 25 449 3820 127162408 127165782 0 5177
7 TraesCS7A01G409000 chr2A 95.126 1744 73 10 2082 3820 560674417 560672681 0 2739
8 TraesCS7A01G409000 chr2A 94.991 1737 73 10 454 2180 560676006 560674274 0 2713
9 TraesCS7A01G409000 chr2A 94.934 1737 70 14 449 2180 206084561 206086284 0 2704
10 TraesCS7A01G409000 chr2A 87.516 1554 139 32 1189 2713 651447734 651449261 0 1744
11 TraesCS7A01G409000 chr2A 96.355 439 15 1 1 438 560676611 560676173 0 721
12 TraesCS7A01G409000 chr2A 95.692 441 16 3 1 438 127161808 127162248 0 706
13 TraesCS7A01G409000 chr5A 94.395 3372 133 29 455 3820 482760848 482757527 0 5129
14 TraesCS7A01G409000 chr5A 87.170 1551 149 28 1189 2713 52393096 52391570 0 1716
15 TraesCS7A01G409000 chr5A 95.900 439 17 1 1 438 591677473 591677911 0 710
16 TraesCS7A01G409000 chr3B 89.656 3316 287 44 529 3820 448319341 448322624 0 4172
17 TraesCS7A01G409000 chr4B 89.551 3321 291 42 529 3820 546146507 546149800 0 4159
18 TraesCS7A01G409000 chr1A 95.154 2538 84 14 1291 3820 399818381 399815875 0 3969
19 TraesCS7A01G409000 chr1A 95.000 440 20 2 1 438 399819778 399819339 0 689
20 TraesCS7A01G409000 chr3A 95.214 1755 72 12 454 2205 164756367 164754622 0 2765
21 TraesCS7A01G409000 chr3A 95.121 1742 77 7 2082 3820 164754787 164753051 0 2739
22 TraesCS7A01G409000 chr3A 96.583 439 14 1 1 438 164756972 164756534 0 726
23 TraesCS7A01G409000 chr6A 95.358 1745 66 14 2082 3820 22754722 22752987 0 2760
24 TraesCS7A01G409000 chr6A 95.123 1743 68 11 2082 3820 54972562 54970833 0 2732
25 TraesCS7A01G409000 chr6A 94.536 1757 81 15 454 2205 54974143 54972397 0 2699
26 TraesCS7A01G409000 chr6A 96.355 439 15 1 1 438 22756908 22756470 0 721
27 TraesCS7A01G409000 chr6A 95.444 439 19 1 1 438 54974748 54974310 0 699
28 TraesCS7A01G409000 chr4A 94.384 1745 86 10 2082 3820 516671190 516669452 0 2669
29 TraesCS7A01G409000 chr4A 94.785 441 20 3 1 438 516682094 516681654 0 684


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 TraesCS7A01G409000 chr7A 595103772 595107593 3821 False 7059.000000 7059 100.000000 1 3822 1 chr7A.!!$F1 3821
1 TraesCS7A01G409000 chr7A 67379991 67381690 1699 True 2741.000000 2741 95.723000 454 2159 1 chr7A.!!$R2 1705
2 TraesCS7A01G409000 chr7A 67143682 67145384 1702 True 2710.000000 2710 95.380000 454 2159 1 chr7A.!!$R1 1705
3 TraesCS7A01G409000 chr7A 699085945 699089895 3950 True 1696.500000 2704 94.896500 1 3820 2 chr7A.!!$R4 3819
4 TraesCS7A01G409000 chr7A 678424155 678425014 859 True 926.000000 926 86.312000 1845 2713 1 chr7A.!!$R3 868
5 TraesCS7A01G409000 chr2A 127161808 127165782 3974 False 2941.500000 5177 95.052500 1 3820 2 chr2A.!!$F3 3819
6 TraesCS7A01G409000 chr2A 206084561 206086284 1723 False 2704.000000 2704 94.934000 449 2180 1 chr2A.!!$F1 1731
7 TraesCS7A01G409000 chr2A 560672681 560676611 3930 True 2057.666667 2739 95.490667 1 3820 3 chr2A.!!$R1 3819
8 TraesCS7A01G409000 chr2A 651447734 651449261 1527 False 1744.000000 1744 87.516000 1189 2713 1 chr2A.!!$F2 1524
9 TraesCS7A01G409000 chr5A 482757527 482760848 3321 True 5129.000000 5129 94.395000 455 3820 1 chr5A.!!$R2 3365
10 TraesCS7A01G409000 chr5A 52391570 52393096 1526 True 1716.000000 1716 87.170000 1189 2713 1 chr5A.!!$R1 1524
11 TraesCS7A01G409000 chr3B 448319341 448322624 3283 False 4172.000000 4172 89.656000 529 3820 1 chr3B.!!$F1 3291
12 TraesCS7A01G409000 chr4B 546146507 546149800 3293 False 4159.000000 4159 89.551000 529 3820 1 chr4B.!!$F1 3291
13 TraesCS7A01G409000 chr1A 399815875 399819778 3903 True 2329.000000 3969 95.077000 1 3820 2 chr1A.!!$R1 3819
14 TraesCS7A01G409000 chr3A 164753051 164756972 3921 True 2076.666667 2765 95.639333 1 3820 3 chr3A.!!$R1 3819
15 TraesCS7A01G409000 chr6A 54970833 54974748 3915 True 2043.333333 2732 95.034333 1 3820 3 chr6A.!!$R2 3819
16 TraesCS7A01G409000 chr6A 22752987 22756908 3921 True 1740.500000 2760 95.856500 1 3820 2 chr6A.!!$R1 3819
17 TraesCS7A01G409000 chr4A 516669452 516671190 1738 True 2669.000000 2669 94.384000 2082 3820 1 chr4A.!!$R1 1738

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
527 687 4.923281 TGACTTGTGATATCTGAACACACG 59.077 41.667 3.98 13.02 42.8 4.49 F
1551 1764 1.449726 AAGCGTTGTTCCCCCGTTTC 61.450 55.000 0.00 0.00 0.0 2.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2433 2853 0.521291 GCAAACTTGTGCATAGGCGA 59.479 50.0 0.0 0.0 44.29 5.54 R
3321 3761 0.042188 CACCTGCACGAACTTCAACG 60.042 55.0 0.0 0.0 0.00 4.10 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
362 367 5.278266 GCAGTTTCAGTAACCAATTGCACTA 60.278 40.000 0.00 0.00 37.46 2.74
449 491 7.380602 GCAATAGACTATGAATGTGGCAAATTC 59.619 37.037 21.16 21.16 35.10 2.17
450 492 8.407832 CAATAGACTATGAATGTGGCAAATTCA 58.592 33.333 29.86 29.86 45.46 2.57
527 687 4.923281 TGACTTGTGATATCTGAACACACG 59.077 41.667 3.98 13.02 42.80 4.49
691 872 5.012664 TGAGTTGCCACATCTTAGGTTTCTA 59.987 40.000 0.00 0.00 0.00 2.10
694 875 5.235850 TGCCACATCTTAGGTTTCTACAA 57.764 39.130 0.00 0.00 0.00 2.41
841 1030 6.183359 GCCACATTTATGTTTTCGACAATCAC 60.183 38.462 0.00 0.00 42.62 3.06
1046 1252 6.473758 ACGATGATGATGATTTCATGGATCT 58.526 36.000 0.00 0.00 45.29 2.75
1178 1386 8.070171 CAGTCGTCTGTCATGAACTAAAATTTT 58.930 33.333 8.75 8.75 36.97 1.82
1216 1424 4.241590 GGCAACAACTGATCATTTGTCA 57.758 40.909 26.02 0.00 33.83 3.58
1551 1764 1.449726 AAGCGTTGTTCCCCCGTTTC 61.450 55.000 0.00 0.00 0.00 2.78
1566 1779 1.880027 CGTTTCTTTCCTGGGTTGGAG 59.120 52.381 0.00 0.00 37.43 3.86
1885 2109 1.730446 GCAGGCGAAACTGAAAGATGC 60.730 52.381 6.41 0.00 40.97 3.91
1908 2132 5.088739 CGAAGAACATGAATTGGTGTAAGC 58.911 41.667 0.00 0.00 0.00 3.09
1917 2141 2.284754 TTGGTGTAAGCTCATTGCCA 57.715 45.000 0.00 0.00 44.23 4.92
2163 2506 6.904463 TCATATTATGATTGCAACTGCCAT 57.096 33.333 0.00 6.02 35.63 4.40
2164 2507 6.916440 TCATATTATGATTGCAACTGCCATC 58.084 36.000 0.00 8.45 41.83 3.51
2167 2510 2.951457 TGATTGCAACTGCCATCATG 57.049 45.000 12.94 0.00 44.82 3.07
2168 2511 2.448453 TGATTGCAACTGCCATCATGA 58.552 42.857 12.94 0.00 44.82 3.07
2169 2512 2.164827 TGATTGCAACTGCCATCATGAC 59.835 45.455 12.94 0.00 44.82 3.06
2170 2513 1.618487 TTGCAACTGCCATCATGACA 58.382 45.000 0.00 0.00 41.18 3.58
2171 2514 1.618487 TGCAACTGCCATCATGACAA 58.382 45.000 0.00 0.00 41.18 3.18
2172 2515 2.172679 TGCAACTGCCATCATGACAAT 58.827 42.857 0.00 0.00 41.18 2.71
2173 2516 3.354467 TGCAACTGCCATCATGACAATA 58.646 40.909 0.00 0.00 41.18 1.90
2174 2517 3.955551 TGCAACTGCCATCATGACAATAT 59.044 39.130 0.00 0.00 41.18 1.28
2175 2518 4.202070 TGCAACTGCCATCATGACAATATG 60.202 41.667 0.00 0.00 41.18 1.78
2176 2519 4.794981 GCAACTGCCATCATGACAATATGG 60.795 45.833 12.85 12.85 42.59 2.74
2715 3146 6.310467 TCTGTCATTCGTGCTGAAACTTATAC 59.690 38.462 0.00 0.00 40.71 1.47
2755 3188 5.379757 GTTGTTTTCTGCAACACATGAAG 57.620 39.130 0.00 0.00 43.91 3.02
2877 3314 2.224281 GGGGGCCTCAAAACTTTGAAAG 60.224 50.000 4.16 2.89 45.61 2.62
3194 3634 4.514585 AACTGGTTGCCGTGGCCA 62.515 61.111 0.00 0.00 41.09 5.36
3300 3740 1.601903 GACATGGAGAACGTGCAACAA 59.398 47.619 0.00 0.00 39.81 2.83
3310 3750 0.586319 CGTGCAACAAGACACCGATT 59.414 50.000 0.00 0.00 35.74 3.34
3321 3761 5.351465 ACAAGACACCGATTATGATGAACAC 59.649 40.000 0.00 0.00 0.00 3.32
3653 4098 5.925506 TGTTTCCTCCATCTTATACGTGA 57.074 39.130 0.00 0.00 0.00 4.35
3720 4165 1.033202 AACGCCAACCCGTGTTTCTT 61.033 50.000 0.00 0.00 41.90 2.52
3820 4265 1.530771 GGGATCCTGTCATGCTGCT 59.469 57.895 12.58 0.00 0.00 4.24
3821 4266 0.761187 GGGATCCTGTCATGCTGCTA 59.239 55.000 12.58 0.00 0.00 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 4.824537 TGTTTGCCTTCATACTGCAGTTTA 59.175 37.500 27.06 8.50 36.21 2.01
362 367 3.354948 TGTGCAGATTAGTTGCCATCT 57.645 42.857 0.00 0.00 40.81 2.90
392 398 9.326489 AGAATATACTATCCAAGTGGCAATAGA 57.674 33.333 9.52 0.64 39.39 1.98
449 491 7.254050 CCGTACAATGAATTTGCCACATTTATG 60.254 37.037 0.00 0.00 39.03 1.90
450 492 6.756074 CCGTACAATGAATTTGCCACATTTAT 59.244 34.615 0.00 0.00 39.03 1.40
451 493 6.096036 CCGTACAATGAATTTGCCACATTTA 58.904 36.000 0.00 0.00 39.03 1.40
452 494 4.928615 CCGTACAATGAATTTGCCACATTT 59.071 37.500 0.00 0.00 39.03 2.32
527 687 2.102252 TGAACAACCTGAAATTGCCACC 59.898 45.455 0.00 0.00 0.00 4.61
573 751 9.311916 GCCATGTTAAAATGCAACATAGAATTA 57.688 29.630 0.00 0.00 43.11 1.40
580 758 6.821031 AATTGCCATGTTAAAATGCAACAT 57.179 29.167 14.00 0.00 45.23 2.71
691 872 5.835280 AGAAAGTCACAAAATCCTCCATTGT 59.165 36.000 0.00 0.00 37.76 2.71
694 875 6.983906 AAAGAAAGTCACAAAATCCTCCAT 57.016 33.333 0.00 0.00 0.00 3.41
1046 1252 1.195442 TGCCCGATTCCACTGTGGTA 61.195 55.000 25.15 17.33 39.03 3.25
1054 1260 1.002624 GTCCAGTTGCCCGATTCCA 60.003 57.895 0.00 0.00 0.00 3.53
1178 1386 4.582240 TGTTGCCATGTTTTCACTGTCATA 59.418 37.500 0.00 0.00 0.00 2.15
1551 1764 0.771127 TGGACTCCAACCCAGGAAAG 59.229 55.000 0.00 0.00 37.20 2.62
1566 1779 3.165498 GACGTGTTCGGCATGGAC 58.835 61.111 0.00 0.00 45.53 4.02
1624 1837 9.014297 CATGAGTAGTTCCATCTTAAAAACCTT 57.986 33.333 0.00 0.00 0.00 3.50
1885 2109 5.088739 GCTTACACCAATTCATGTTCTTCG 58.911 41.667 0.00 0.00 0.00 3.79
1908 2132 1.250328 TGCAGGAAGTTGGCAATGAG 58.750 50.000 1.92 0.00 34.05 2.90
2152 2495 1.618487 TTGTCATGATGGCAGTTGCA 58.382 45.000 0.00 0.00 44.36 4.08
2160 2503 4.688879 GCAATTGCCATATTGTCATGATGG 59.311 41.667 20.06 7.77 42.65 3.51
2161 2504 5.839262 GCAATTGCCATATTGTCATGATG 57.161 39.130 20.06 0.00 37.72 3.07
2433 2853 0.521291 GCAAACTTGTGCATAGGCGA 59.479 50.000 0.00 0.00 44.29 5.54
2511 2932 5.777732 ACCTGCAGTTTTCCATATTTGGTAA 59.222 36.000 13.81 0.00 44.06 2.85
2755 3188 5.174395 AGAATGATGAACACTGACTAGCAC 58.826 41.667 0.00 0.00 0.00 4.40
2877 3314 1.741770 GAGTGCACGTCCATCCACC 60.742 63.158 12.01 0.00 0.00 4.61
3194 3634 5.542635 TCTTGGGAACTGTTGTAGTCATACT 59.457 40.000 0.00 0.00 39.18 2.12
3300 3740 4.112634 CGTGTTCATCATAATCGGTGTCT 58.887 43.478 0.00 0.00 0.00 3.41
3310 3750 4.986034 ACGAACTTCAACGTGTTCATCATA 59.014 37.500 14.53 0.00 41.67 2.15
3321 3761 0.042188 CACCTGCACGAACTTCAACG 60.042 55.000 0.00 0.00 0.00 4.10
3564 4008 6.041511 GCAAAAACAAATGCAAAAAGGGATT 58.958 32.000 0.00 0.00 42.12 3.01
3653 4098 2.345244 CCAGCTGTCGCCTCACTT 59.655 61.111 13.81 0.00 36.60 3.16
3720 4165 1.305201 GCACCTTTGTTCAACCGAGA 58.695 50.000 0.00 0.00 0.00 4.04


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

AutoCloner maintained by Alex Coulton.