Multiple sequence alignment - TraesCS5A01G349200

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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 TraesCS5A01G349200 chr5A 100.000 2255 0 0 1 2255 552382456 552380202 0.000000e+00 4165.0
1 TraesCS5A01G349200 chr7A 97.815 1510 23 4 1 1505 32948559 32947055 0.000000e+00 2597.0
2 TraesCS5A01G349200 chr7A 86.922 1254 89 25 246 1498 17458535 17459714 0.000000e+00 1338.0
3 TraesCS5A01G349200 chr3A 97.732 1499 26 6 1 1498 479688744 479690235 0.000000e+00 2573.0
4 TraesCS5A01G349200 chr6A 97.597 1498 30 2 1 1498 594278372 594279863 0.000000e+00 2562.0
5 TraesCS5A01G349200 chr6D 93.484 1151 50 10 350 1498 25493859 25494986 0.000000e+00 1687.0
6 TraesCS5A01G349200 chr6D 93.253 1156 52 11 350 1503 413024132 413025263 0.000000e+00 1679.0
7 TraesCS5A01G349200 chr6D 89.061 1289 81 24 1 1280 462350987 462352224 0.000000e+00 1544.0
8 TraesCS5A01G349200 chr6D 94.412 340 7 5 1 332 25493374 25493709 1.540000e-141 512.0
9 TraesCS5A01G349200 chr6D 94.611 334 12 3 1 332 413023657 413023986 1.540000e-141 512.0
10 TraesCS5A01G349200 chr5D 93.397 1151 51 10 350 1498 485921523 485920396 0.000000e+00 1681.0
11 TraesCS5A01G349200 chr5D 87.092 1255 87 26 245 1498 450171090 450169910 0.000000e+00 1351.0
12 TraesCS5A01G349200 chr5D 93.955 761 31 7 1501 2255 437085758 437085007 0.000000e+00 1136.0
13 TraesCS5A01G349200 chr4D 93.310 1151 52 10 350 1498 506094805 506095932 0.000000e+00 1676.0
14 TraesCS5A01G349200 chr4D 94.412 340 7 5 1 332 506094321 506094656 1.540000e-141 512.0
15 TraesCS5A01G349200 chr4D 80.657 274 45 5 1985 2255 465904368 465904100 2.940000e-49 206.0
16 TraesCS5A01G349200 chr4D 79.487 273 50 4 1985 2255 50226433 50226701 2.960000e-44 189.0
17 TraesCS5A01G349200 chr1A 86.614 1255 93 27 246 1499 249376329 249375149 0.000000e+00 1317.0
18 TraesCS5A01G349200 chr6B 93.014 730 34 4 595 1322 124059969 124060683 0.000000e+00 1050.0
19 TraesCS5A01G349200 chr6B 92.105 380 16 5 1 379 124059576 124059942 7.140000e-145 523.0
20 TraesCS5A01G349200 chr6B 90.588 170 14 2 1331 1499 124062608 124062776 8.110000e-55 224.0
21 TraesCS5A01G349200 chr4A 93.158 380 19 4 1 379 648979530 648979903 3.270000e-153 551.0
22 TraesCS5A01G349200 chr7B 93.773 273 10 3 1984 2254 491196790 491197057 9.700000e-109 403.0
23 TraesCS5A01G349200 chr2B 92.727 275 12 4 1984 2255 379116875 379117144 7.550000e-105 390.0
24 TraesCS5A01G349200 chr2B 93.056 144 7 2 402 543 759994554 759994412 8.160000e-50 207.0
25 TraesCS5A01G349200 chr1D 83.838 198 30 1 1499 1694 123704780 123704583 1.060000e-43 187.0
26 TraesCS5A01G349200 chr1D 85.965 57 2 5 2161 2216 363104824 363104875 3.130000e-04 56.5
27 TraesCS5A01G349200 chr1B 89.130 92 8 2 1699 1789 390839219 390839309 1.830000e-21 113.0


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 TraesCS5A01G349200 chr5A 552380202 552382456 2254 True 4165.0 4165 100.000000 1 2255 1 chr5A.!!$R1 2254
1 TraesCS5A01G349200 chr7A 32947055 32948559 1504 True 2597.0 2597 97.815000 1 1505 1 chr7A.!!$R1 1504
2 TraesCS5A01G349200 chr7A 17458535 17459714 1179 False 1338.0 1338 86.922000 246 1498 1 chr7A.!!$F1 1252
3 TraesCS5A01G349200 chr3A 479688744 479690235 1491 False 2573.0 2573 97.732000 1 1498 1 chr3A.!!$F1 1497
4 TraesCS5A01G349200 chr6A 594278372 594279863 1491 False 2562.0 2562 97.597000 1 1498 1 chr6A.!!$F1 1497
5 TraesCS5A01G349200 chr6D 462350987 462352224 1237 False 1544.0 1544 89.061000 1 1280 1 chr6D.!!$F1 1279
6 TraesCS5A01G349200 chr6D 25493374 25494986 1612 False 1099.5 1687 93.948000 1 1498 2 chr6D.!!$F2 1497
7 TraesCS5A01G349200 chr6D 413023657 413025263 1606 False 1095.5 1679 93.932000 1 1503 2 chr6D.!!$F3 1502
8 TraesCS5A01G349200 chr5D 485920396 485921523 1127 True 1681.0 1681 93.397000 350 1498 1 chr5D.!!$R3 1148
9 TraesCS5A01G349200 chr5D 450169910 450171090 1180 True 1351.0 1351 87.092000 245 1498 1 chr5D.!!$R2 1253
10 TraesCS5A01G349200 chr5D 437085007 437085758 751 True 1136.0 1136 93.955000 1501 2255 1 chr5D.!!$R1 754
11 TraesCS5A01G349200 chr4D 506094321 506095932 1611 False 1094.0 1676 93.861000 1 1498 2 chr4D.!!$F2 1497
12 TraesCS5A01G349200 chr1A 249375149 249376329 1180 True 1317.0 1317 86.614000 246 1499 1 chr1A.!!$R1 1253
13 TraesCS5A01G349200 chr6B 124059576 124062776 3200 False 599.0 1050 91.902333 1 1499 3 chr6B.!!$F1 1498

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
841 1004 7.912773 GGAGAACTTGAAGCTTTTATGCTAATC 59.087 37.037 0.0 0.0 43.24 1.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1808 3898 0.45541 GCTCAAAAGCCACACACACA 59.545 50.0 0.0 0.0 43.1 3.72 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
43 45 9.869844 ATTTAATCTTTTCTTATGAAGCGATCG 57.130 29.630 11.69 11.69 33.28 3.69
841 1004 7.912773 GGAGAACTTGAAGCTTTTATGCTAATC 59.087 37.037 0.00 0.00 43.24 1.75
1027 1199 2.681064 CTGTTGGGGGCCATGGTG 60.681 66.667 14.67 0.00 31.53 4.17
1422 3510 8.776470 CCGTAATTTTAGTTTTGTAACTCCTCA 58.224 33.333 0.00 0.00 43.45 3.86
1468 3556 1.828660 AGGGTGGATAGACGGCTCG 60.829 63.158 0.00 0.00 0.00 5.03
1499 3587 4.155280 GCCAATCACCGTAACAGTTGTATT 59.845 41.667 0.00 0.00 0.00 1.89
1534 3622 5.727791 GCAGTATTTAGTGTTGGCATTCTCG 60.728 44.000 0.00 0.00 0.00 4.04
1545 3633 1.792949 GGCATTCTCGTATAAGGCACG 59.207 52.381 0.00 0.00 40.72 5.34
1589 3677 7.700505 TCTATGGCGTACATATAAATCCTACG 58.299 38.462 0.00 0.00 41.07 3.51
1612 3700 4.023365 GCCAGCAATATCTTCCAACTGATC 60.023 45.833 0.00 0.00 0.00 2.92
1613 3701 5.128205 CCAGCAATATCTTCCAACTGATCA 58.872 41.667 0.00 0.00 0.00 2.92
1619 3707 2.771089 TCTTCCAACTGATCAGCACAC 58.229 47.619 22.83 0.00 0.00 3.82
1660 3750 4.822350 TGGTTTGACAAAATATCCACGTCA 59.178 37.500 1.27 0.00 34.92 4.35
1713 3803 9.875691 CAATTATACTTATGCCAGCACTATCTA 57.124 33.333 0.00 0.00 0.00 1.98
1748 3838 0.596341 GCGTTGGTTGAAAATGGCGT 60.596 50.000 0.00 0.00 0.00 5.68
1808 3898 7.347508 CTAGTTAAGTGAACTTGTATTGCGT 57.652 36.000 0.00 0.00 46.79 5.24
1809 3899 5.985781 AGTTAAGTGAACTTGTATTGCGTG 58.014 37.500 5.95 0.00 46.79 5.34
1851 3941 1.473965 CGCTGTGGGCTGTATTCAGAT 60.474 52.381 3.14 0.00 43.76 2.90
1868 3958 9.690434 GTATTCAGATTTTATGTCTTCGTGAAC 57.310 33.333 0.00 0.00 0.00 3.18
1878 3968 1.210967 TCTTCGTGAACCTTGGGTGTT 59.789 47.619 0.00 0.00 35.34 3.32
1900 3990 7.434307 GTGTTTCTTTTAACCACTAAAGGCTTC 59.566 37.037 0.00 0.00 33.29 3.86
1918 4008 3.127721 GCTTCAGTCATCTAAAGTTGGGC 59.872 47.826 0.00 0.00 0.00 5.36
1921 4011 4.922206 TCAGTCATCTAAAGTTGGGCAAT 58.078 39.130 0.00 0.00 0.00 3.56
1923 4013 4.701651 CAGTCATCTAAAGTTGGGCAATCA 59.298 41.667 0.00 0.00 0.00 2.57
1935 4025 1.141858 GGGCAATCACCTCCTTCCTAG 59.858 57.143 0.00 0.00 0.00 3.02
1946 4036 8.214721 TCACCTCCTTCCTAGAAATAAAAAGA 57.785 34.615 0.00 0.00 0.00 2.52
2046 4138 0.179032 AGGTTTGTCGTGATGCACCA 60.179 50.000 0.00 0.00 0.00 4.17
2050 4142 0.320050 TTGTCGTGATGCACCAGCTA 59.680 50.000 0.00 0.00 42.74 3.32
2111 4203 8.588290 TTAATGAAGGCCAATGTAACTAATGT 57.412 30.769 5.01 0.00 0.00 2.71
2191 4285 7.335422 AGTGTTGAGAAATCGAGCATATTCTTT 59.665 33.333 0.00 0.00 32.54 2.52
2192 4286 8.604035 GTGTTGAGAAATCGAGCATATTCTTTA 58.396 33.333 0.00 0.00 32.54 1.85
2193 4287 9.161629 TGTTGAGAAATCGAGCATATTCTTTAA 57.838 29.630 0.00 0.00 32.54 1.52
2226 4320 4.046462 CACAAAAGTGAACATGAAGGCTG 58.954 43.478 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 42 3.356529 AAATTTCTGGTGCCTCTCGAT 57.643 42.857 0.00 0.0 0.00 3.59
41 43 2.859165 AAATTTCTGGTGCCTCTCGA 57.141 45.000 0.00 0.0 0.00 4.04
42 44 4.695455 TCTTAAAATTTCTGGTGCCTCTCG 59.305 41.667 0.00 0.0 0.00 4.04
43 45 5.473504 TGTCTTAAAATTTCTGGTGCCTCTC 59.526 40.000 0.00 0.0 0.00 3.20
841 1004 0.989602 AAGGTAAACCCCCTCTTCCG 59.010 55.000 0.00 0.0 36.42 4.30
1027 1199 1.265905 CCACTGCCGTTGTTTACCTTC 59.734 52.381 0.00 0.0 0.00 3.46
1288 1460 0.392998 GGTGCCCACATCGAACTCAT 60.393 55.000 0.00 0.0 0.00 2.90
1308 1480 5.975693 AAATTCATCACACAATAACCCGT 57.024 34.783 0.00 0.0 0.00 5.28
1422 3510 6.380274 TCTGACGGTGAGAAAATAGGAGTTAT 59.620 38.462 0.00 0.0 0.00 1.89
1468 3556 4.142859 TGTTACGGTGATTGGCGATTTTAC 60.143 41.667 0.00 0.0 0.00 2.01
1513 3601 5.796350 ACGAGAATGCCAACACTAAATAC 57.204 39.130 0.00 0.0 0.00 1.89
1514 3602 9.256477 CTTATACGAGAATGCCAACACTAAATA 57.744 33.333 0.00 0.0 0.00 1.40
1523 3611 3.202906 GTGCCTTATACGAGAATGCCAA 58.797 45.455 0.00 0.0 0.00 4.52
1526 3614 2.739292 TCGTGCCTTATACGAGAATGC 58.261 47.619 0.00 0.0 44.65 3.56
1534 3622 4.990257 TCTAGTGTTGTCGTGCCTTATAC 58.010 43.478 0.00 0.0 0.00 1.47
1589 3677 3.282021 TCAGTTGGAAGATATTGCTGGC 58.718 45.455 0.00 0.0 0.00 4.85
1612 3700 0.322816 ATGTGGGCCTAAGTGTGCTG 60.323 55.000 4.53 0.0 0.00 4.41
1613 3701 1.285280 TATGTGGGCCTAAGTGTGCT 58.715 50.000 4.53 0.0 0.00 4.40
1641 3731 4.068599 TGCTGACGTGGATATTTTGTCAA 58.931 39.130 0.00 0.0 38.91 3.18
1660 3750 4.350816 TGCCAGATTTATATGGGTAGTGCT 59.649 41.667 5.61 0.0 39.51 4.40
1729 3819 0.596341 ACGCCATTTTCAACCAACGC 60.596 50.000 0.00 0.0 0.00 4.84
1807 3897 1.798813 GCTCAAAAGCCACACACACAC 60.799 52.381 0.00 0.0 43.10 3.82
1808 3898 0.455410 GCTCAAAAGCCACACACACA 59.545 50.000 0.00 0.0 43.10 3.72
1809 3899 3.256620 GCTCAAAAGCCACACACAC 57.743 52.632 0.00 0.0 43.10 3.82
1851 3941 4.517453 CCCAAGGTTCACGAAGACATAAAA 59.483 41.667 0.00 0.0 0.00 1.52
1868 3958 4.404394 AGTGGTTAAAAGAAACACCCAAGG 59.596 41.667 1.95 0.0 0.00 3.61
1878 3968 6.831868 ACTGAAGCCTTTAGTGGTTAAAAGAA 59.168 34.615 0.46 0.0 35.19 2.52
1900 3990 4.701651 TGATTGCCCAACTTTAGATGACTG 59.298 41.667 0.00 0.0 0.00 3.51
1918 4008 8.807948 TTTTATTTCTAGGAAGGAGGTGATTG 57.192 34.615 0.00 0.0 0.00 2.67
1921 4011 8.214721 TCTTTTTATTTCTAGGAAGGAGGTGA 57.785 34.615 0.00 0.0 0.00 4.02
1992 4084 3.341823 CTCACCACTAGCTTCTGCATTT 58.658 45.455 0.00 0.0 42.74 2.32
2046 4138 9.177608 TCAGCAAATAACAGATTTGTAATAGCT 57.822 29.630 10.73 0.0 40.19 3.32
2111 4203 5.483937 TCCAGGATAGACTTTAAGCAGACAA 59.516 40.000 0.00 0.0 0.00 3.18


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

AutoCloner maintained by Alex Coulton.