Multiple sequence alignment - TraesCS6D01G181300

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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 TraesCS6D01G181300 chr6D 100.000 2615 0 0 1 2615 204715396 204712782 0 4830
1 TraesCS6D01G181300 chr6D 93.311 2631 158 8 1 2615 214608836 214611464 0 3868
2 TraesCS6D01G181300 chr6D 93.237 2632 152 13 1 2612 7670626 7673251 0 3851
3 TraesCS6D01G181300 chr6D 92.998 2628 162 8 1 2612 192349306 192351927 0 3814
4 TraesCS6D01G181300 chr6D 92.746 2633 154 19 1 2615 220615391 220612778 0 3770
5 TraesCS6D01G181300 chr6D 92.334 2648 164 20 1 2615 226678825 226676184 0 3729
6 TraesCS6D01G181300 chr1D 93.389 2632 154 12 1 2615 56492795 56495423 0 3879
7 TraesCS6D01G181300 chr1D 91.213 2481 174 23 156 2615 128564758 128562301 0 3334
8 TraesCS6D01G181300 chr2D 92.448 2635 160 18 1 2615 280568714 280566099 0 3727
9 TraesCS6D01G181300 chr2D 90.323 2511 215 18 125 2615 283611615 283614117 0 3265
10 TraesCS6D01G181300 chr5D 92.372 2635 162 15 1 2615 298983213 298980598 0 3716
11 TraesCS6D01G181300 chr5D 92.024 2633 189 12 1 2615 155336748 155334119 0 3679
12 TraesCS6D01G181300 chr5D 93.909 2430 131 7 202 2615 532049489 532047061 0 3651
13 TraesCS6D01G181300 chr3D 91.645 2633 183 18 3 2615 239735183 239737798 0 3609
14 TraesCS6D01G181300 chr4D 92.826 2091 129 12 540 2614 464287989 464290074 0 3011
15 TraesCS6D01G181300 chr7D 92.579 1873 113 11 1 1855 139135943 139134079 0 2665
16 TraesCS6D01G181300 chr7D 83.873 1885 229 43 8 1839 310053825 310051963 0 1727
17 TraesCS6D01G181300 chr7B 82.188 2504 372 49 156 2612 382473025 382470549 0 2085
18 TraesCS6D01G181300 chr4A 80.355 1746 267 49 123 1823 347189711 347187997 0 1254
19 TraesCS6D01G181300 chr5B 81.227 1598 236 42 156 1711 216255214 216253639 0 1230
20 TraesCS6D01G181300 chr5B 82.050 1493 208 43 156 1606 177945635 177947109 0 1218
21 TraesCS6D01G181300 chr5B 80.610 1475 195 55 156 1593 161615553 161614133 0 1055
22 TraesCS6D01G181300 chr4B 81.836 1514 205 45 156 1625 338608855 338610342 0 1208
23 TraesCS6D01G181300 chr4B 79.232 1719 258 58 158 1831 346481829 346483493 0 1105


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 TraesCS6D01G181300 chr6D 204712782 204715396 2614 True 4830 4830 100.000 1 2615 1 chr6D.!!$R1 2614
1 TraesCS6D01G181300 chr6D 214608836 214611464 2628 False 3868 3868 93.311 1 2615 1 chr6D.!!$F3 2614
2 TraesCS6D01G181300 chr6D 7670626 7673251 2625 False 3851 3851 93.237 1 2612 1 chr6D.!!$F1 2611
3 TraesCS6D01G181300 chr6D 192349306 192351927 2621 False 3814 3814 92.998 1 2612 1 chr6D.!!$F2 2611
4 TraesCS6D01G181300 chr6D 220612778 220615391 2613 True 3770 3770 92.746 1 2615 1 chr6D.!!$R2 2614
5 TraesCS6D01G181300 chr6D 226676184 226678825 2641 True 3729 3729 92.334 1 2615 1 chr6D.!!$R3 2614
6 TraesCS6D01G181300 chr1D 56492795 56495423 2628 False 3879 3879 93.389 1 2615 1 chr1D.!!$F1 2614
7 TraesCS6D01G181300 chr1D 128562301 128564758 2457 True 3334 3334 91.213 156 2615 1 chr1D.!!$R1 2459
8 TraesCS6D01G181300 chr2D 280566099 280568714 2615 True 3727 3727 92.448 1 2615 1 chr2D.!!$R1 2614
9 TraesCS6D01G181300 chr2D 283611615 283614117 2502 False 3265 3265 90.323 125 2615 1 chr2D.!!$F1 2490
10 TraesCS6D01G181300 chr5D 298980598 298983213 2615 True 3716 3716 92.372 1 2615 1 chr5D.!!$R2 2614
11 TraesCS6D01G181300 chr5D 155334119 155336748 2629 True 3679 3679 92.024 1 2615 1 chr5D.!!$R1 2614
12 TraesCS6D01G181300 chr5D 532047061 532049489 2428 True 3651 3651 93.909 202 2615 1 chr5D.!!$R3 2413
13 TraesCS6D01G181300 chr3D 239735183 239737798 2615 False 3609 3609 91.645 3 2615 1 chr3D.!!$F1 2612
14 TraesCS6D01G181300 chr4D 464287989 464290074 2085 False 3011 3011 92.826 540 2614 1 chr4D.!!$F1 2074
15 TraesCS6D01G181300 chr7D 139134079 139135943 1864 True 2665 2665 92.579 1 1855 1 chr7D.!!$R1 1854
16 TraesCS6D01G181300 chr7D 310051963 310053825 1862 True 1727 1727 83.873 8 1839 1 chr7D.!!$R2 1831
17 TraesCS6D01G181300 chr7B 382470549 382473025 2476 True 2085 2085 82.188 156 2612 1 chr7B.!!$R1 2456
18 TraesCS6D01G181300 chr4A 347187997 347189711 1714 True 1254 1254 80.355 123 1823 1 chr4A.!!$R1 1700
19 TraesCS6D01G181300 chr5B 216253639 216255214 1575 True 1230 1230 81.227 156 1711 1 chr5B.!!$R2 1555
20 TraesCS6D01G181300 chr5B 177945635 177947109 1474 False 1218 1218 82.050 156 1606 1 chr5B.!!$F1 1450
21 TraesCS6D01G181300 chr5B 161614133 161615553 1420 True 1055 1055 80.610 156 1593 1 chr5B.!!$R1 1437
22 TraesCS6D01G181300 chr4B 338608855 338610342 1487 False 1208 1208 81.836 156 1625 1 chr4B.!!$F1 1469
23 TraesCS6D01G181300 chr4B 346481829 346483493 1664 False 1105 1105 79.232 158 1831 1 chr4B.!!$F2 1673

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
699 750 2.640826 ACGACCCCACCTATCTTTTTGA 59.359 45.455 0.0 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1865 2062 1.051812 GGGGTCGAGGATGATGATGT 58.948 55.0 0.0 0.0 0.0 3.06 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
26 27 2.955607 GTTTCCTAACGTGTTTCGGG 57.044 50.000 0.00 0.00 44.69 5.14
97 100 4.764172 AGGACTACTACGAACGATACACT 58.236 43.478 0.14 0.00 0.00 3.55
383 414 6.073440 GTTTGTCAAGCATTGCATGAGAAAAT 60.073 34.615 29.04 0.00 45.58 1.82
418 449 6.348498 ACAAAGAGCCAAACAAGCTTTTAAT 58.652 32.000 0.00 0.00 41.75 1.40
475 508 8.028938 AGCAAGAACCATAACATCATAAAACAC 58.971 33.333 0.00 0.00 0.00 3.32
476 509 7.812191 GCAAGAACCATAACATCATAAAACACA 59.188 33.333 0.00 0.00 0.00 3.72
514 550 5.067023 TCGATCTTGGATCATATCATCGGAG 59.933 44.000 8.04 0.00 34.31 4.63
688 739 4.572571 TGGTTGCACGACCCCACC 62.573 66.667 5.11 0.00 39.01 4.61
699 750 2.640826 ACGACCCCACCTATCTTTTTGA 59.359 45.455 0.00 0.00 0.00 2.69
1049 1117 1.543802 ACTCTTCCTCGAGCAAGACAG 59.456 52.381 14.90 9.04 34.35 3.51
1143 1222 0.107703 GCATCGACAATCTCCCACCA 60.108 55.000 0.00 0.00 0.00 4.17
1278 1369 3.005554 TCTTCTACCACTTCGTCCTACG 58.994 50.000 0.00 0.00 44.19 3.51
1299 1390 0.680280 AAGAAGGAGCCGCTCGAGTA 60.680 55.000 15.13 0.00 0.00 2.59
1382 1473 1.073216 CGCGTCAAGATCGTCAAGCT 61.073 55.000 0.00 0.00 0.00 3.74
1467 1613 1.726865 CACAAGCACAAGAACGGCA 59.273 52.632 0.00 0.00 0.00 5.69
1596 1742 2.860293 CGCAACGTGCCTTTCGAT 59.140 55.556 0.00 0.00 41.12 3.59
1711 1866 0.388649 GTGCATCGTCACGTTCCTCT 60.389 55.000 0.00 0.00 0.00 3.69
1712 1876 0.109272 TGCATCGTCACGTTCCTCTC 60.109 55.000 0.00 0.00 0.00 3.20
1743 1907 1.374252 GCGCCTCCTCAAGTTCGAA 60.374 57.895 0.00 0.00 0.00 3.71
1826 1990 3.821306 GGTTGACAACCCTCCTTGT 57.179 52.632 24.53 0.00 46.12 3.16
1899 2099 2.549992 CGACCCCAACACAATGAAGAGA 60.550 50.000 0.00 0.00 0.00 3.10
1910 2110 4.862574 CACAATGAAGAGAAACGATACGGA 59.137 41.667 0.00 0.00 0.00 4.69
1931 2131 2.584835 AGCTAAAGTTCACCATGCCA 57.415 45.000 0.00 0.00 0.00 4.92
2230 2442 0.668535 AAACAAGGAACCAAGAGCGC 59.331 50.000 0.00 0.00 0.00 5.92
2291 2503 1.398390 GCCAATGTCACGGAAGATGAC 59.602 52.381 0.00 0.00 45.58 3.06
2314 2526 4.434330 CGAGAAAACTATGGCACGTTTCTC 60.434 45.833 21.95 21.95 32.60 2.87
2322 2534 1.153353 GGCACGTTTCTCGAATGGAA 58.847 50.000 0.00 0.00 42.86 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 1.812571 TGTCGAACCGTCCCTAAGTAC 59.187 52.381 0.00 0.00 0.00 2.73
97 100 5.496556 CAAGGTGAGGTTGATACCACAATA 58.503 41.667 0.00 0.00 44.94 1.90
291 316 7.687388 AGAGATGATACCAAGATATGCAACAT 58.313 34.615 0.00 0.00 0.00 2.71
418 449 6.294731 GCTCTTTGCTTATCTTTCCCTTTTGA 60.295 38.462 0.00 0.00 38.95 2.69
470 503 9.436957 AGATCGAGTATAACAATCTTTGTGTTT 57.563 29.630 0.00 0.00 44.59 2.83
475 508 8.648557 TCCAAGATCGAGTATAACAATCTTTG 57.351 34.615 0.00 0.00 35.15 2.77
476 509 9.482627 GATCCAAGATCGAGTATAACAATCTTT 57.517 33.333 0.00 0.00 35.15 2.52
485 518 8.778358 CGATGATATGATCCAAGATCGAGTATA 58.222 37.037 0.00 0.00 35.02 1.47
514 550 5.583854 CCCAAGTATGCTCTATGTATGATGC 59.416 44.000 0.00 0.00 0.00 3.91
688 739 6.136071 CGGAAACACACACTCAAAAAGATAG 58.864 40.000 0.00 0.00 0.00 2.08
699 750 1.207570 TGGTACACGGAAACACACACT 59.792 47.619 0.00 0.00 0.00 3.55
925 985 3.244561 ACCTTGACCGATGTTGAAGATGT 60.245 43.478 0.00 0.00 0.00 3.06
1049 1117 3.025866 ACGTAGTTGTTCGGATCGC 57.974 52.632 0.00 0.00 37.78 4.58
1278 1369 3.191539 CGAGCGGCTCCTTCTTGC 61.192 66.667 23.36 0.00 0.00 4.01
1299 1390 2.614446 CGGTGTCGTCGGAGTGTCT 61.614 63.158 0.00 0.00 0.00 3.41
1324 1415 0.815734 CGATGTCGGGGTACTTGAGT 59.184 55.000 0.00 0.00 35.37 3.41
1382 1473 2.563620 TGTGTGTAGAGGATTGCGGTTA 59.436 45.455 0.00 0.00 0.00 2.85
1467 1613 1.088306 TCTTGTTGGCGTTGACGTTT 58.912 45.000 5.36 0.00 42.22 3.60
1530 1676 1.745232 TGTTCTTGTCGTTGTGCCTT 58.255 45.000 0.00 0.00 0.00 4.35
1590 1736 2.601314 CGGCGTGACTTGAATATCGAAA 59.399 45.455 0.00 0.00 0.00 3.46
1596 1742 1.470285 GGCTACGGCGTGACTTGAATA 60.470 52.381 24.86 0.00 39.81 1.75
1711 1866 1.447838 GGCGCTTGTCGATCTTGGA 60.448 57.895 7.64 0.00 41.67 3.53
1712 1876 1.424493 GAGGCGCTTGTCGATCTTGG 61.424 60.000 7.64 0.00 41.67 3.61
1743 1907 4.825422 TCTCGATGAACTTGATGCTCTTT 58.175 39.130 0.00 0.00 0.00 2.52
1824 1988 5.414144 TGACAAACTCATGTTGTTCTTGACA 59.586 36.000 2.12 5.04 36.39 3.58
1826 1990 6.507958 TTGACAAACTCATGTTGTTCTTGA 57.492 33.333 2.12 0.00 36.39 3.02
1865 2062 1.051812 GGGGTCGAGGATGATGATGT 58.948 55.000 0.00 0.00 0.00 3.06
1899 2099 5.697633 TGAACTTTAGCTTTCCGTATCGTTT 59.302 36.000 0.00 0.00 0.00 3.60
1910 2110 3.230134 TGGCATGGTGAACTTTAGCTTT 58.770 40.909 0.00 0.00 0.00 3.51
1931 2131 3.319122 GGTCATTGCTTCCAGTGAACTTT 59.681 43.478 0.00 0.00 40.91 2.66
2230 2442 6.936279 TCCATTTCCTTGTAGTACTCTTCAG 58.064 40.000 0.00 0.00 0.00 3.02
2291 2503 3.432252 AGAAACGTGCCATAGTTTTCTCG 59.568 43.478 0.00 0.00 40.24 4.04
2314 2526 7.605309 TCTTGATAGGATGATTGATTCCATTCG 59.395 37.037 0.00 0.00 34.27 3.34
2322 2534 6.817641 GCGATCTTCTTGATAGGATGATTGAT 59.182 38.462 0.00 0.00 35.14 2.57
2406 2618 2.101750 TGAAGTCGTCTTGTACTTGCCA 59.898 45.455 0.00 0.00 36.10 4.92


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

AutoCloner maintained by Alex Coulton.