Multiple sequence alignment - TraesCS3A01G304000

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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 TraesCS3A01G304000 chr3A 100.000 2225 0 0 1 2225 539298093 539300317 0.000000e+00 4109.0
1 TraesCS3A01G304000 chr3A 94.126 1379 70 5 850 2225 620783860 620782490 0.000000e+00 2087.0
2 TraesCS3A01G304000 chr3A 94.103 1238 60 5 991 2225 535554882 535553655 0.000000e+00 1869.0
3 TraesCS3A01G304000 chr1A 95.235 1637 62 7 592 2225 86564681 86563058 0.000000e+00 2577.0
4 TraesCS3A01G304000 chr1A 93.750 608 24 3 1 595 86565347 86564741 0.000000e+00 900.0
5 TraesCS3A01G304000 chr7A 94.078 1638 84 6 592 2225 352831795 352830167 0.000000e+00 2475.0
6 TraesCS3A01G304000 chr7A 94.167 600 32 2 1 600 352832447 352831851 0.000000e+00 911.0
7 TraesCS3A01G304000 chr6A 92.988 1583 77 5 646 2225 291223697 291222146 0.000000e+00 2278.0
8 TraesCS3A01G304000 chr6A 93.939 132 7 1 469 600 419204881 419204751 4.850000e-47 198.0
9 TraesCS3A01G304000 chr5D 94.634 1379 62 5 850 2225 309717865 309716496 0.000000e+00 2126.0
10 TraesCS3A01G304000 chr5D 89.202 426 22 9 155 562 436821976 436821557 5.480000e-141 510.0
11 TraesCS3A01G304000 chr5D 93.182 44 1 2 592 635 436821442 436821401 1.840000e-06 63.9
12 TraesCS3A01G304000 chr2D 94.054 1379 72 4 850 2225 648400411 648399040 0.000000e+00 2084.0
13 TraesCS3A01G304000 chr2D 93.785 177 10 1 646 821 295488298 295488122 4.710000e-67 265.0
14 TraesCS3A01G304000 chr4A 93.691 1379 77 4 850 2225 67424822 67423451 0.000000e+00 2056.0
15 TraesCS3A01G304000 chr4A 93.687 1299 69 7 643 1938 75131034 75132322 0.000000e+00 1932.0
16 TraesCS3A01G304000 chr4A 93.457 1238 70 4 991 2225 559211605 559210376 0.000000e+00 1827.0
17 TraesCS3A01G304000 chr4A 92.701 137 9 1 464 600 559211865 559211730 1.740000e-46 196.0
18 TraesCS3A01G304000 chr5A 92.966 1379 85 6 850 2225 104950817 104949448 0.000000e+00 1999.0
19 TraesCS3A01G304000 chr5A 93.296 1238 73 4 991 2225 37110510 37111740 0.000000e+00 1818.0
20 TraesCS3A01G304000 chr5A 85.714 301 15 4 155 437 552076413 552076123 2.160000e-75 292.0
21 TraesCS3A01G304000 chr5A 94.118 51 1 2 324 372 37110204 37110254 2.370000e-10 76.8
22 TraesCS3A01G304000 chr5A 92.593 54 2 2 324 375 546857361 546857308 2.370000e-10 76.8
23 TraesCS3A01G304000 chr2B 93.700 1238 68 3 991 2225 87814122 87815352 0.000000e+00 1845.0
24 TraesCS3A01G304000 chr5B 92.105 418 23 6 155 562 530972203 530971786 4.120000e-162 580.0
25 TraesCS3A01G304000 chr5B 91.429 420 23 6 155 562 530611407 530611825 4.150000e-157 564.0
26 TraesCS3A01G304000 chr5B 96.599 147 3 2 8 154 530611144 530611288 2.210000e-60 243.0
27 TraesCS3A01G304000 chr5B 94.805 154 7 1 7 160 530972464 530972312 2.860000e-59 239.0
28 TraesCS3A01G304000 chr5B 93.939 132 7 1 469 600 535528017 535527887 4.850000e-47 198.0
29 TraesCS3A01G304000 chr5B 91.489 47 2 2 589 635 530611938 530611982 1.840000e-06 63.9
30 TraesCS3A01G304000 chr2A 94.697 132 6 1 469 600 607534489 607534359 1.040000e-48 204.0
31 TraesCS3A01G304000 chr2A 92.593 54 2 2 324 375 607534542 607534489 2.370000e-10 76.8
32 TraesCS3A01G304000 chr4D 91.964 112 8 1 723 833 299342861 299342972 2.960000e-34 156.0
33 TraesCS3A01G304000 chr4D 96.154 78 3 0 643 720 299342614 299342691 6.450000e-26 128.0
34 TraesCS3A01G304000 chr7D 91.071 112 9 1 723 833 149102065 149102176 1.380000e-32 150.0
35 TraesCS3A01G304000 chr7D 96.154 78 3 0 643 720 149101818 149101895 6.450000e-26 128.0


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 TraesCS3A01G304000 chr3A 539298093 539300317 2224 False 4109.00 4109 100.000000 1 2225 1 chr3A.!!$F1 2224
1 TraesCS3A01G304000 chr3A 620782490 620783860 1370 True 2087.00 2087 94.126000 850 2225 1 chr3A.!!$R2 1375
2 TraesCS3A01G304000 chr3A 535553655 535554882 1227 True 1869.00 1869 94.103000 991 2225 1 chr3A.!!$R1 1234
3 TraesCS3A01G304000 chr1A 86563058 86565347 2289 True 1738.50 2577 94.492500 1 2225 2 chr1A.!!$R1 2224
4 TraesCS3A01G304000 chr7A 352830167 352832447 2280 True 1693.00 2475 94.122500 1 2225 2 chr7A.!!$R1 2224
5 TraesCS3A01G304000 chr6A 291222146 291223697 1551 True 2278.00 2278 92.988000 646 2225 1 chr6A.!!$R1 1579
6 TraesCS3A01G304000 chr5D 309716496 309717865 1369 True 2126.00 2126 94.634000 850 2225 1 chr5D.!!$R1 1375
7 TraesCS3A01G304000 chr5D 436821401 436821976 575 True 286.95 510 91.192000 155 635 2 chr5D.!!$R2 480
8 TraesCS3A01G304000 chr2D 648399040 648400411 1371 True 2084.00 2084 94.054000 850 2225 1 chr2D.!!$R2 1375
9 TraesCS3A01G304000 chr4A 67423451 67424822 1371 True 2056.00 2056 93.691000 850 2225 1 chr4A.!!$R1 1375
10 TraesCS3A01G304000 chr4A 75131034 75132322 1288 False 1932.00 1932 93.687000 643 1938 1 chr4A.!!$F1 1295
11 TraesCS3A01G304000 chr4A 559210376 559211865 1489 True 1011.50 1827 93.079000 464 2225 2 chr4A.!!$R2 1761
12 TraesCS3A01G304000 chr5A 104949448 104950817 1369 True 1999.00 1999 92.966000 850 2225 1 chr5A.!!$R1 1375
13 TraesCS3A01G304000 chr5A 37110204 37111740 1536 False 947.40 1818 93.707000 324 2225 2 chr5A.!!$F1 1901
14 TraesCS3A01G304000 chr2B 87814122 87815352 1230 False 1845.00 1845 93.700000 991 2225 1 chr2B.!!$F1 1234
15 TraesCS3A01G304000 chr5B 530971786 530972464 678 True 409.50 580 93.455000 7 562 2 chr5B.!!$R2 555
16 TraesCS3A01G304000 chr5B 530611144 530611982 838 False 290.30 564 93.172333 8 635 3 chr5B.!!$F1 627

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
720 980 3.07233 TGCATGTTCAGAGTTTGGGACTA 59.928 43.478 0.0 0.0 39.19 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1636 1902 0.464373 ATCGCATAGCTTGTGTGGGG 60.464 55.0 11.09 0.0 37.14 4.96 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
46 47 5.931724 TCTGATGCGTAACTTTTCTCATTGA 59.068 36.000 0.00 0.00 0.00 2.57
72 73 5.578157 ACAAACTGTAGGGAGTGGTATTT 57.422 39.130 0.00 0.00 0.00 1.40
191 310 5.234972 CCAATGTTTTCTTTCCTTTCTGCAC 59.765 40.000 0.00 0.00 0.00 4.57
405 554 7.520119 TGTTCGTCATTTACATCACATACTC 57.480 36.000 0.00 0.00 0.00 2.59
431 580 3.299050 CAGCGGACTGTTTACCACA 57.701 52.632 0.00 0.00 39.22 4.17
490 639 6.978080 CACCATGGTTACTTTGCCATAATAAC 59.022 38.462 16.84 0.00 43.05 1.89
518 667 5.311265 GGATGATTGTTGAGATATGAGGCA 58.689 41.667 0.00 0.00 0.00 4.75
576 771 3.419264 AATGTCGGCATACGTACGTTA 57.581 42.857 27.92 12.76 44.69 3.18
720 980 3.072330 TGCATGTTCAGAGTTTGGGACTA 59.928 43.478 0.00 0.00 39.19 2.59
786 1046 7.309990 CCTTGATGTTGGTTGGTCTATTTTGAT 60.310 37.037 0.00 0.00 0.00 2.57
865 1125 9.226606 ACATGCATTAACTTTTACTGCTACTAA 57.773 29.630 0.00 0.00 34.02 2.24
926 1186 4.308458 CCACGCACCAAGGACGGA 62.308 66.667 10.11 0.00 0.00 4.69
976 1237 4.452795 ACCGATCGATCAGTCACTATAGTG 59.547 45.833 24.37 24.37 46.91 2.74
1134 1395 2.101415 CGTAGATGGTGATCTCAAGGCA 59.899 50.000 0.00 0.00 39.76 4.75
1185 1446 2.859165 CCAAGTTTGGGACTAGCAGA 57.141 50.000 2.87 0.00 44.70 4.26
1222 1483 1.747355 CAGAGGCTTGCCGATCAATTT 59.253 47.619 5.95 0.00 33.57 1.82
1253 1514 4.502962 TGCAGGAAAAGGTTTTTGTTGAG 58.497 39.130 0.00 0.00 0.00 3.02
1281 1544 7.287061 TGAAAAGAAAACCATCTGAAGGTCTA 58.713 34.615 4.87 0.00 38.76 2.59
1309 1572 8.183830 TGTGTTTGATGAAAAAGTTTGTCATC 57.816 30.769 30.22 30.22 45.19 2.92
1360 1623 5.355630 GCTGAGATCCCCTTTCTTAAGTTTC 59.644 44.000 1.63 0.00 0.00 2.78
1378 1641 2.342406 TCAAGATCCCCACCTTCAGA 57.658 50.000 0.00 0.00 0.00 3.27
1403 1666 2.429610 GGATTGACTCAATGCAGCCAAT 59.570 45.455 16.19 0.00 40.91 3.16
1505 1768 9.944376 AGTAGAGCTACAAAATTTGTATTCTCA 57.056 29.630 28.80 20.05 44.46 3.27
1562 1828 3.359033 ACTTTGGCTACATGTGCATCAT 58.641 40.909 9.11 0.00 37.22 2.45
1563 1829 3.765511 ACTTTGGCTACATGTGCATCATT 59.234 39.130 9.11 0.00 34.09 2.57
1574 1840 5.304871 ACATGTGCATCATTGCCCATTATAA 59.695 36.000 0.00 0.00 43.29 0.98
1636 1902 2.681097 GCAGAAGTGAAGTATCCCCACC 60.681 54.545 0.00 0.00 0.00 4.61
1637 1903 2.092914 CAGAAGTGAAGTATCCCCACCC 60.093 54.545 0.00 0.00 0.00 4.61
1638 1904 1.212195 GAAGTGAAGTATCCCCACCCC 59.788 57.143 0.00 0.00 0.00 4.95
1639 1905 0.623617 AGTGAAGTATCCCCACCCCC 60.624 60.000 0.00 0.00 0.00 5.40
1640 1906 0.917333 GTGAAGTATCCCCACCCCCA 60.917 60.000 0.00 0.00 0.00 4.96
1641 1907 0.917333 TGAAGTATCCCCACCCCCAC 60.917 60.000 0.00 0.00 0.00 4.61
1733 1999 6.472016 TCACTTTGACACTAGATAATGCCAA 58.528 36.000 0.00 0.00 0.00 4.52
1987 2254 3.002791 CGTGCAAAGAAAGGCATCTCTA 58.997 45.455 0.00 0.00 42.75 2.43
2016 2283 2.443255 ACCAACCAGATGGAACTCAACT 59.557 45.455 5.72 0.00 43.54 3.16
2051 2318 6.735678 TGTAGATGCATTGACGTACAAATT 57.264 33.333 0.00 0.00 42.03 1.82
2064 2331 6.422701 TGACGTACAAATTTGTTCTCACTAGG 59.577 38.462 27.66 15.55 42.35 3.02
2112 2379 2.305927 TCCAAGTGAGGAAGAATGGGAC 59.694 50.000 0.00 0.00 33.93 4.46
2212 2479 8.826710 CAACTTCACATAAGTTTCTGTCAGTTA 58.173 33.333 0.00 0.00 38.32 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 3.908103 ACCACTCCCTACAGTTTGTACAT 59.092 43.478 0.00 0.00 0.00 2.29
450 599 3.758023 CCATGGTGAAGCTACAATGTGAA 59.242 43.478 2.57 0.00 31.35 3.18
467 616 7.106439 TGTTATTATGGCAAAGTAACCATGG 57.894 36.000 11.19 11.19 46.20 3.66
490 639 7.094334 CCTCATATCTCAACAATCATCCCAATG 60.094 40.741 0.00 0.00 0.00 2.82
596 791 6.169557 TGTATAACGGTCCAGAGCATTAAT 57.830 37.500 0.00 0.00 0.00 1.40
865 1125 6.099845 AGGTGCAAGCAGGTTAATACTAGTAT 59.900 38.462 9.71 9.71 36.26 2.12
997 1258 2.756907 ACCCTCTGATGTAGACATGCT 58.243 47.619 0.00 0.00 36.57 3.79
1134 1395 2.154462 GCTCCACAGTATTTGCACACT 58.846 47.619 0.00 0.00 0.00 3.55
1185 1446 3.181436 CCTCTGCAATATGGGTCCTCAAT 60.181 47.826 0.00 0.00 0.00 2.57
1222 1483 1.004745 CCTTTTCCTGCAAGCCTCCTA 59.995 52.381 0.00 0.00 0.00 2.94
1253 1514 5.636543 CCTTCAGATGGTTTTCTTTTCATGC 59.363 40.000 0.00 0.00 0.00 4.06
1281 1544 8.997323 TGACAAACTTTTTCATCAAACACAAAT 58.003 25.926 0.00 0.00 0.00 2.32
1309 1572 3.436704 ACGCAATACTTGACCATGAGTTG 59.563 43.478 0.00 0.00 0.00 3.16
1360 1623 1.630369 TGTCTGAAGGTGGGGATCTTG 59.370 52.381 0.00 0.00 0.00 3.02
1378 1641 2.426024 GCTGCATTGAGTCAATCCATGT 59.574 45.455 15.60 0.00 34.31 3.21
1403 1666 3.314080 GTGACGACCCTTGATTTGAAACA 59.686 43.478 0.00 0.00 0.00 2.83
1436 1699 5.699915 CCCTTATACATCTTCACTGCATCAG 59.300 44.000 0.00 0.00 37.52 2.90
1505 1768 7.448161 TCCACATGTCAGATGTTAAGAAAATGT 59.552 33.333 0.00 0.00 0.00 2.71
1562 1828 5.929058 TTCTGCATTGTTATAATGGGCAA 57.071 34.783 4.00 0.00 0.00 4.52
1563 1829 6.097981 TGAATTCTGCATTGTTATAATGGGCA 59.902 34.615 7.05 0.00 0.00 5.36
1574 1840 9.453572 TCTTCTTATAGTTGAATTCTGCATTGT 57.546 29.630 7.05 0.00 0.00 2.71
1636 1902 0.464373 ATCGCATAGCTTGTGTGGGG 60.464 55.000 11.09 0.00 37.14 4.96
1637 1903 2.138320 CTATCGCATAGCTTGTGTGGG 58.862 52.381 11.09 5.89 37.14 4.61
1638 1904 3.097877 TCTATCGCATAGCTTGTGTGG 57.902 47.619 11.09 0.93 37.14 4.17
1639 1905 4.363138 TCTTCTATCGCATAGCTTGTGTG 58.637 43.478 0.00 0.00 37.14 3.82
1640 1906 4.655762 TCTTCTATCGCATAGCTTGTGT 57.344 40.909 0.00 0.00 37.14 3.72
1641 1907 5.284864 TCTTCTTCTATCGCATAGCTTGTG 58.715 41.667 0.00 0.00 37.17 3.33
1733 1999 8.213679 ACTCCTCACATGCATTAGTATTATTGT 58.786 33.333 0.00 0.00 0.00 2.71
1987 2254 4.860802 TCCATCTGGTTGGTGTATCAAT 57.139 40.909 0.00 0.00 38.01 2.57
2051 2318 4.901197 TTGGCATACCTAGTGAGAACAA 57.099 40.909 0.00 0.00 36.63 2.83
2090 2357 3.054065 GTCCCATTCTTCCTCACTTGGAT 60.054 47.826 0.00 0.00 35.83 3.41
2112 2379 7.922811 AGAAACTCACAAATAGCTTTTTCCTTG 59.077 33.333 0.00 0.00 0.00 3.61


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

AutoCloner maintained by Alex Coulton.