Multiple sequence alignment - TraesCS5A01G048700

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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 TraesCS5A01G048700 chr5A 100.000 2390 0 0 1 2390 44947605 44945216 0 4414
1 TraesCS5A01G048700 chr5D 93.317 2394 127 22 1 2389 56124502 56122137 0 3504
2 TraesCS5A01G048700 chr5B 93.349 1744 77 11 650 2390 58893513 58891806 0 2542
3 TraesCS5A01G048700 chr5B 95.559 608 22 1 1 603 58894114 58893507 0 968


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 TraesCS5A01G048700 chr5A 44945216 44947605 2389 True 4414 4414 100.000 1 2390 1 chr5A.!!$R1 2389
1 TraesCS5A01G048700 chr5D 56122137 56124502 2365 True 3504 3504 93.317 1 2389 1 chr5D.!!$R1 2388
2 TraesCS5A01G048700 chr5B 58891806 58894114 2308 True 1755 2542 94.454 1 2390 2 chr5B.!!$R1 2389

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
107 108 0.320771 AGCTTCGTCGGTGCTGAAAT 60.321 50.0 11.04 0.0 35.54 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1644 1658 0.108472 TTCATGAGTGCTCAGGCTCG 60.108 55.0 8.76 0.0 43.61 5.03 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
22 23 2.472695 TTAGCATCTTGGCGACTGTT 57.527 45.000 0.00 0.00 39.27 3.16
107 108 0.320771 AGCTTCGTCGGTGCTGAAAT 60.321 50.000 11.04 0.00 35.54 2.17
186 187 0.392706 GCCTGGGAAAAACAAGTGGG 59.607 55.000 0.00 0.00 0.00 4.61
187 188 1.047801 CCTGGGAAAAACAAGTGGGG 58.952 55.000 0.00 0.00 0.00 4.96
284 285 3.885297 CCTTTTGACTTCTCTTTGCAGGA 59.115 43.478 0.00 0.00 0.00 3.86
320 321 7.244166 AGATCTCTCATAAATCGCTGTTTTG 57.756 36.000 0.00 0.00 0.00 2.44
358 359 9.467258 CAGGTGCATATAATAATTGGACAAAAG 57.533 33.333 0.00 0.00 33.87 2.27
438 444 6.697019 ACATTTTCAGAAACAAATCCAGAACG 59.303 34.615 0.00 0.00 0.00 3.95
502 508 5.755849 AGCTGGCAGTACTACCAAAAATAT 58.244 37.500 15.80 0.00 34.96 1.28
628 637 6.813649 AGTATATTATGCGCATCTACTTGTGG 59.186 38.462 29.11 0.00 0.00 4.17
679 688 6.155221 ACATAGTAGGTATATGTCTGGCATGG 59.845 42.308 4.74 0.00 39.13 3.66
682 691 4.357918 AGGTATATGTCTGGCATGGTTC 57.642 45.455 4.74 0.00 38.47 3.62
700 709 4.080919 TGGTTCTCATGGTCTAATGTGGAG 60.081 45.833 0.00 0.00 0.00 3.86
707 716 4.142609 TGGTCTAATGTGGAGCATCTTC 57.857 45.455 0.00 0.00 36.67 2.87
708 717 3.126831 GGTCTAATGTGGAGCATCTTCG 58.873 50.000 0.00 0.00 36.67 3.79
729 738 7.611855 TCTTCGATCTATCATAGCTGTATTCCA 59.388 37.037 0.00 0.00 0.00 3.53
1302 1315 0.954452 CCCTTGTGCTCCAGTCAAAC 59.046 55.000 0.00 0.00 0.00 2.93
1379 1393 6.599244 TCTGAGAATGAATTTACCAGCGATTT 59.401 34.615 0.00 0.00 0.00 2.17
1390 1404 6.721571 TTACCAGCGATTTAAAGTTCTGAG 57.278 37.500 12.28 7.24 0.00 3.35
1397 1411 8.450964 CAGCGATTTAAAGTTCTGAGGAAAATA 58.549 33.333 7.28 0.00 32.81 1.40
1409 1423 9.411801 GTTCTGAGGAAAATAGAAATTTGGTTC 57.588 33.333 0.00 0.00 35.46 3.62
1433 1447 1.440618 TACCAAAGAGGGTCCTTGCA 58.559 50.000 0.00 0.00 43.89 4.08
1508 1522 4.818417 CAGCCGTGCAGTTTAACG 57.182 55.556 0.00 0.00 39.48 3.18
1580 1594 2.951642 CCTTGTTCCTTGCTTTGACTCA 59.048 45.455 0.00 0.00 0.00 3.41
1638 1652 5.018809 TCTTCAGCTTTCCCTGCATAATTT 58.981 37.500 0.00 0.00 32.87 1.82
1644 1658 4.038042 GCTTTCCCTGCATAATTTAGACCC 59.962 45.833 0.00 0.00 0.00 4.46
1670 1684 3.931468 CCTGAGCACTCATGAAACACTAG 59.069 47.826 0.00 0.00 39.13 2.57
1709 1723 1.070134 TGGTCCAAGTGCTACAGTGAC 59.930 52.381 0.00 0.00 0.00 3.67
1748 1762 2.892784 AGAGTATAACCTGCCGCTTC 57.107 50.000 0.00 0.00 0.00 3.86
1750 1764 1.138266 GAGTATAACCTGCCGCTTCCA 59.862 52.381 0.00 0.00 0.00 3.53
1790 1804 2.939103 GGAGTGACTGATTGGTGCATAC 59.061 50.000 0.00 0.00 0.00 2.39
1791 1805 3.599343 GAGTGACTGATTGGTGCATACA 58.401 45.455 0.00 0.00 0.00 2.29
1793 1807 4.592942 AGTGACTGATTGGTGCATACAAT 58.407 39.130 16.49 16.49 40.98 2.71
1800 1814 7.930217 ACTGATTGGTGCATACAATATGTTAC 58.070 34.615 16.50 6.83 38.57 2.50
1801 1815 6.953843 TGATTGGTGCATACAATATGTTACG 58.046 36.000 16.50 0.00 38.57 3.18
1831 1845 5.192927 AGAGATTGTGGTGTTTGAACTTGA 58.807 37.500 0.00 0.00 0.00 3.02
1846 1860 8.868916 GTTTGAACTTGAAAATGTCAAAGCTTA 58.131 29.630 0.00 0.00 45.67 3.09
1907 1921 0.818040 AAACGCAGCCGAAAGAACCT 60.818 50.000 0.00 0.00 38.29 3.50
2017 2031 8.642432 TGGTATGTCTTAACAGAATAGGATGAG 58.358 37.037 0.00 0.00 39.20 2.90
2022 2036 7.615757 TGTCTTAACAGAATAGGATGAGTCAGA 59.384 37.037 0.00 0.00 0.00 3.27
2072 2086 7.775120 ACAAAAGTTAAATGAGATATGCAGGG 58.225 34.615 0.00 0.00 0.00 4.45
2241 2255 6.455690 AAGAACCTGAGGGTAAAGAAGAAT 57.544 37.500 2.38 0.00 46.67 2.40
2332 2347 9.628500 AAAAACTCACTCTTAAACTTCCTACAT 57.372 29.630 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 2.300967 GGTCAGGCCCTCCATGTCA 61.301 63.158 0.00 0.00 33.74 3.58
107 108 5.186992 TCATCGACAGGACCTTAAAAGATGA 59.813 40.000 15.36 15.36 39.39 2.92
217 218 5.526115 AGCATTGTTTCTTGACATTGTCAG 58.474 37.500 18.27 12.98 43.69 3.51
358 359 8.580720 TCTCATTCTTAGGACATATCTGTTAGC 58.419 37.037 0.00 0.00 35.14 3.09
502 508 7.518188 AGTTTCCTCTCTGTCCTGAAAATTAA 58.482 34.615 0.00 0.00 0.00 1.40
628 637 7.812191 TGCACATGGTTGAACAATTTAGATAAC 59.188 33.333 0.00 0.00 0.00 1.89
679 688 3.873952 GCTCCACATTAGACCATGAGAAC 59.126 47.826 0.00 0.00 0.00 3.01
682 691 3.548745 TGCTCCACATTAGACCATGAG 57.451 47.619 0.00 0.00 0.00 2.90
692 701 3.834489 AGATCGAAGATGCTCCACATT 57.166 42.857 0.00 0.00 45.12 2.71
700 709 5.649557 ACAGCTATGATAGATCGAAGATGC 58.350 41.667 3.13 0.00 45.12 3.91
1224 1237 1.356624 GCATGAAGAAATCCGGCCG 59.643 57.895 21.04 21.04 0.00 6.13
1302 1315 1.048601 ATGCCCACAGTAGTATCCGG 58.951 55.000 0.00 0.00 0.00 5.14
1356 1369 6.757897 AAATCGCTGGTAAATTCATTCTCA 57.242 33.333 0.00 0.00 0.00 3.27
1409 1423 3.721087 AGGACCCTCTTTGGTATGTTG 57.279 47.619 0.00 0.00 39.24 3.33
1433 1447 4.640771 TTATCTGGAGAACAACAGCCTT 57.359 40.909 0.00 0.00 34.76 4.35
1505 1519 3.343617 CATAACCCATCACAACCTCGTT 58.656 45.455 0.00 0.00 0.00 3.85
1508 1522 2.684881 CAGCATAACCCATCACAACCTC 59.315 50.000 0.00 0.00 0.00 3.85
1580 1594 2.292521 TGCCATCAAGGTACTCTCCTCT 60.293 50.000 0.00 0.00 38.49 3.69
1589 1603 4.038642 GGTCAAAAAGTTGCCATCAAGGTA 59.961 41.667 0.00 0.00 40.61 3.08
1638 1652 2.052690 GTGCTCAGGCTCGGGTCTA 61.053 63.158 0.00 0.00 39.59 2.59
1644 1658 0.108472 TTCATGAGTGCTCAGGCTCG 60.108 55.000 8.76 0.00 43.61 5.03
1670 1684 5.863935 GGACCAGCTATCAAAATTCAAACAC 59.136 40.000 0.00 0.00 0.00 3.32
1709 1723 3.130516 TCTTCCTGCTGTAGTGATTACCG 59.869 47.826 0.00 0.00 0.00 4.02
1790 1804 9.273016 ACAATCTCTTTATCCCGTAACATATTG 57.727 33.333 0.00 0.00 0.00 1.90
1791 1805 9.273016 CACAATCTCTTTATCCCGTAACATATT 57.727 33.333 0.00 0.00 0.00 1.28
1793 1807 7.147620 ACCACAATCTCTTTATCCCGTAACATA 60.148 37.037 0.00 0.00 0.00 2.29
1800 1814 3.873910 ACACCACAATCTCTTTATCCCG 58.126 45.455 0.00 0.00 0.00 5.14
1801 1815 5.710099 TCAAACACCACAATCTCTTTATCCC 59.290 40.000 0.00 0.00 0.00 3.85
1831 1845 6.934056 TGCACCATATAAGCTTTGACATTTT 58.066 32.000 3.20 0.00 0.00 1.82
1907 1921 3.130340 GCTCAGGAAACAAACTTGGACAA 59.870 43.478 0.00 0.00 0.00 3.18
2001 2015 6.325028 CCCTTCTGACTCATCCTATTCTGTTA 59.675 42.308 0.00 0.00 0.00 2.41
2017 2031 3.956744 AGCATCCTAAAACCCTTCTGAC 58.043 45.455 0.00 0.00 0.00 3.51
2022 2036 4.657814 TCTGAAGCATCCTAAAACCCTT 57.342 40.909 0.00 0.00 0.00 3.95
2072 2086 5.143376 TGTACAGCAGGACTTAGGTAAAC 57.857 43.478 0.00 0.00 0.00 2.01
2081 2095 2.162681 GCCAAATTGTACAGCAGGACT 58.837 47.619 9.15 0.00 0.00 3.85
2123 2137 2.288666 TGACTTGCTTTCGTTTGCTCT 58.711 42.857 0.00 0.00 0.00 4.09
2158 2172 6.734104 TCTGAAGCTTCTAAGAAGCAAATC 57.266 37.500 26.09 17.14 45.30 2.17


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

AutoCloner maintained by Alex Coulton.