Multiple sequence alignment - TraesCS5A01G094700

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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 TraesCS5A01G094700 chr5A 100.000 1870 0 0 1 1870 131787223 131785354 0.000000e+00 3454
1 TraesCS5A01G094700 chr5A 100.000 158 0 0 2155 2312 131785069 131784912 2.250000e-75 292
2 TraesCS5A01G094700 chr5D 91.467 1922 104 35 1 1870 120889701 120887788 0.000000e+00 2586
3 TraesCS5A01G094700 chr5D 85.119 168 11 8 2155 2312 120887725 120887562 2.380000e-35 159
4 TraesCS5A01G094700 chr5B 94.378 1583 50 15 89 1664 134025814 134024264 0.000000e+00 2394
5 TraesCS5A01G094700 chr5B 88.462 156 9 6 2158 2312 134023957 134023810 1.830000e-41 180


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 TraesCS5A01G094700 chr5A 131784912 131787223 2311 True 1873.0 3454 100.000 1 2312 2 chr5A.!!$R1 2311
1 TraesCS5A01G094700 chr5D 120887562 120889701 2139 True 1372.5 2586 88.293 1 2312 2 chr5D.!!$R1 2311
2 TraesCS5A01G094700 chr5B 134023810 134025814 2004 True 1287.0 2394 91.420 89 2312 2 chr5B.!!$R1 2223

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
72 73 0.645868 GAGCAACATACGAACTCCGC 59.354 55.0 0.0 0.0 43.32 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1665 1713 0.3199 TGCTCTTGACGAGGTTCTGC 60.32 55.0 0.0 0.0 40.25 4.26 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 6.142320 GCACTTAAGTAATTATGCGCATTTCC 59.858 38.462 30.42 8.83 0.00 3.13
36 37 0.735632 GCGCATTTCCGGCATCAAAA 60.736 50.000 0.30 0.00 0.00 2.44
46 47 4.277476 TCCGGCATCAAAAGGATACAAAT 58.723 39.130 0.00 0.00 41.41 2.32
62 63 9.797642 AGGATACAAATCATAATGAGCAACATA 57.202 29.630 0.00 0.00 37.35 2.29
66 67 7.984391 ACAAATCATAATGAGCAACATACGAA 58.016 30.769 0.00 0.00 38.38 3.85
67 68 7.910162 ACAAATCATAATGAGCAACATACGAAC 59.090 33.333 0.00 0.00 38.38 3.95
70 71 5.753438 TCATAATGAGCAACATACGAACTCC 59.247 40.000 0.00 0.00 38.38 3.85
72 73 0.645868 GAGCAACATACGAACTCCGC 59.354 55.000 0.00 0.00 43.32 5.54
80 81 4.604976 ACATACGAACTCCGCATAACTAC 58.395 43.478 0.00 0.00 43.32 2.73
113 114 4.943705 AGTCAAACACAAACAGTCTGACAT 59.056 37.500 10.88 0.00 35.39 3.06
169 175 6.683974 ATAGGACCGAAATTTGATGTTGAG 57.316 37.500 0.00 0.00 0.00 3.02
222 228 1.956477 ACATGCGAGCCTTCTTTGTTT 59.044 42.857 0.00 0.00 0.00 2.83
223 229 3.058293 CACATGCGAGCCTTCTTTGTTTA 60.058 43.478 0.00 0.00 0.00 2.01
565 571 5.707411 ACGTACAGTATCGTTAATTTGGC 57.293 39.130 0.00 0.00 36.93 4.52
587 593 4.003788 CCCGTCGTTGTCCCAGCT 62.004 66.667 0.00 0.00 0.00 4.24
637 643 4.141959 TGACTGATCTCGTCAATATTGCCA 60.142 41.667 10.76 0.00 38.36 4.92
657 668 2.102749 CGCACATGGCCAAATCCG 59.897 61.111 10.96 7.23 40.31 4.18
711 726 2.328319 AGCCAGATGAGAGATTCCTCC 58.672 52.381 0.00 0.00 40.30 4.30
848 868 3.214328 CAGCGCTATAAAAGGAACCCAT 58.786 45.455 10.99 0.00 0.00 4.00
854 874 6.053005 CGCTATAAAAGGAACCCATTGACTA 58.947 40.000 0.00 0.00 0.00 2.59
910 930 4.332543 CACAACAGAAGCACAAACTACTCA 59.667 41.667 0.00 0.00 0.00 3.41
975 995 1.192146 ACCAGCTTGCCTCGAGGTTA 61.192 55.000 31.43 18.73 37.57 2.85
1116 1139 1.476891 GACCTCGGTGTCAATGCTCTA 59.523 52.381 0.00 0.00 35.29 2.43
1149 1172 0.413037 ACCATGATCCCAAGGGCAAA 59.587 50.000 0.00 0.00 35.55 3.68
1321 1344 0.475906 ATGGCTGTAGAGGGCATTCC 59.524 55.000 0.00 0.00 45.50 3.01
1325 1348 1.745141 GCTGTAGAGGGCATTCCACAG 60.745 57.143 10.78 10.78 39.04 3.66
1351 1374 4.711846 TCAATATAGTCGGAGGGATGGATG 59.288 45.833 0.00 0.00 0.00 3.51
1419 1442 5.502544 CGAAGAGTGTGGAAGACAAGTTTTC 60.503 44.000 0.00 0.00 35.91 2.29
1497 1522 7.054124 AGTCCTACTCTGACAACAAATTTTGA 58.946 34.615 15.81 0.00 35.15 2.69
1523 1571 9.862371 AATCACTATATGTAGTAAGCTATGTGC 57.138 33.333 1.36 0.00 39.12 4.57
1524 1572 8.404107 TCACTATATGTAGTAAGCTATGTGCA 57.596 34.615 1.36 0.00 40.70 4.57
1529 1577 5.097742 TGTAGTAAGCTATGTGCATGGTT 57.902 39.130 0.00 0.00 45.94 3.67
1665 1713 9.559732 TCTGTATGGAGTGTCAATTATTTATGG 57.440 33.333 0.00 0.00 0.00 2.74
1667 1715 7.777440 TGTATGGAGTGTCAATTATTTATGGCA 59.223 33.333 0.00 0.00 0.00 4.92
1686 1761 1.998315 CAGAACCTCGTCAAGAGCATG 59.002 52.381 0.00 0.00 45.54 4.06
1738 1813 7.961283 GGAAGAAAGAATGACACGGTTTATAAC 59.039 37.037 0.00 0.00 0.00 1.89
1802 1886 4.202101 TGTCGGTTTGGTCGTAGTTCTTTA 60.202 41.667 0.00 0.00 0.00 1.85
2208 2294 5.533112 TCCCTCTATTCTCACTCTCCATTT 58.467 41.667 0.00 0.00 0.00 2.32
2230 2326 6.599986 TTCCTAGGTTATCTCCTCTCTCTT 57.400 41.667 9.08 0.00 38.86 2.85
2244 2340 1.339610 CTCTCTTCCATGCCCTACTCG 59.660 57.143 0.00 0.00 0.00 4.18
2293 2389 1.676006 CTGACCGGCCAAAACATATCC 59.324 52.381 0.00 0.00 0.00 2.59
2296 2392 1.283613 ACCGGCCAAAACATATCCTCA 59.716 47.619 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.287308 TGCCGGAAATGCGCATAATTAC 60.287 45.455 25.61 15.15 0.00 1.89
15 16 1.665264 TTGATGCCGGAAATGCGCAT 61.665 50.000 19.28 19.28 45.62 4.73
17 18 0.735632 TTTTGATGCCGGAAATGCGC 60.736 50.000 5.05 0.00 0.00 6.09
18 19 1.270971 CTTTTGATGCCGGAAATGCG 58.729 50.000 5.05 0.00 0.00 4.73
22 23 3.691575 TGTATCCTTTTGATGCCGGAAA 58.308 40.909 5.05 0.00 35.40 3.13
26 27 5.247507 TGATTTGTATCCTTTTGATGCCG 57.752 39.130 0.00 0.00 35.40 5.69
36 37 8.701908 ATGTTGCTCATTATGATTTGTATCCT 57.298 30.769 0.00 0.00 32.08 3.24
46 47 5.753438 GGAGTTCGTATGTTGCTCATTATGA 59.247 40.000 0.00 0.00 37.91 2.15
55 56 1.006832 ATGCGGAGTTCGTATGTTGC 58.993 50.000 0.00 0.00 42.38 4.17
62 63 1.820519 TGGTAGTTATGCGGAGTTCGT 59.179 47.619 0.00 0.00 41.72 3.85
66 67 2.240493 GCATGGTAGTTATGCGGAGT 57.760 50.000 0.00 0.00 41.16 3.85
72 73 4.252878 TGACTGTGTGCATGGTAGTTATG 58.747 43.478 0.00 0.00 0.00 1.90
80 81 1.404748 TGTGTTTGACTGTGTGCATGG 59.595 47.619 0.00 0.00 0.00 3.66
207 213 7.762382 AGGAAAATATAAACAAAGAAGGCTCG 58.238 34.615 0.00 0.00 0.00 5.03
565 571 1.743995 GGGACAACGACGGGGAATG 60.744 63.158 0.00 0.00 0.00 2.67
587 593 2.296752 CTGCATGTTGTCCCACAATTCA 59.703 45.455 0.00 0.00 40.59 2.57
637 643 3.340953 GATTTGGCCATGTGCGCGT 62.341 57.895 6.09 0.00 42.61 6.01
657 668 1.745653 GGGCCATCTACTTTTCTGCAC 59.254 52.381 4.39 0.00 0.00 4.57
711 726 6.366332 GGAATATTAGCTTGTGTCGACCTATG 59.634 42.308 14.12 5.48 0.00 2.23
848 868 4.359434 TGGTTTGGTAGCATGTAGTCAA 57.641 40.909 0.00 0.00 0.00 3.18
854 874 1.357420 TGGGATGGTTTGGTAGCATGT 59.643 47.619 0.00 0.00 44.68 3.21
910 930 4.877251 CGTACTCCTAGCTAGAGAACTTGT 59.123 45.833 22.70 12.76 35.27 3.16
951 971 2.611473 CCTCGAGGCAAGCTGGTATATG 60.611 54.545 20.67 0.00 0.00 1.78
954 974 0.978146 ACCTCGAGGCAAGCTGGTAT 60.978 55.000 31.56 4.57 39.32 2.73
955 975 1.192146 AACCTCGAGGCAAGCTGGTA 61.192 55.000 31.56 0.00 39.32 3.25
975 995 1.051812 CCCCCTGACGCTAGATCAAT 58.948 55.000 0.00 0.00 0.00 2.57
1149 1172 1.832167 GAGCGCCCTCTCCATCTCT 60.832 63.158 2.29 0.00 35.16 3.10
1321 1344 3.005897 CCTCCGACTATATTGACCCTGTG 59.994 52.174 0.00 0.00 0.00 3.66
1325 1348 2.885616 TCCCTCCGACTATATTGACCC 58.114 52.381 0.00 0.00 0.00 4.46
1351 1374 2.233186 ACCGGAGTTAGGCTCTGTAAAC 59.767 50.000 9.46 0.00 46.65 2.01
1497 1522 9.862371 GCACATAGCTTACTACATATAGTGATT 57.138 33.333 0.00 0.00 40.18 2.57
1523 1571 7.627088 GCAACCTAGCTATATGCATAAACCATG 60.627 40.741 11.13 3.23 45.94 3.66
1524 1572 6.375455 GCAACCTAGCTATATGCATAAACCAT 59.625 38.462 11.13 0.00 45.94 3.55
1529 1577 7.522073 GCAAAAGCAACCTAGCTATATGCATAA 60.522 37.037 20.79 0.00 45.89 1.90
1628 1676 9.190317 TGACACTCCATACAGATATATATCCAC 57.810 37.037 17.44 0.00 33.17 4.02
1639 1687 9.559732 CCATAAATAATTGACACTCCATACAGA 57.440 33.333 0.00 0.00 0.00 3.41
1640 1688 8.292448 GCCATAAATAATTGACACTCCATACAG 58.708 37.037 0.00 0.00 0.00 2.74
1641 1689 7.777440 TGCCATAAATAATTGACACTCCATACA 59.223 33.333 0.00 0.00 0.00 2.29
1642 1690 8.165239 TGCCATAAATAATTGACACTCCATAC 57.835 34.615 0.00 0.00 0.00 2.39
1664 1712 1.016653 GCTCTTGACGAGGTTCTGCC 61.017 60.000 0.00 0.00 40.25 4.85
1665 1713 0.319900 TGCTCTTGACGAGGTTCTGC 60.320 55.000 0.00 0.00 40.25 4.26
1667 1715 1.895798 TCATGCTCTTGACGAGGTTCT 59.104 47.619 0.00 0.00 40.25 3.01
1686 1761 4.711399 TGAATCACTGGGATCATCACATC 58.289 43.478 0.00 0.00 34.28 3.06
2178 2264 9.315363 GGAGAGTGAGAATAGAGGGATTTATAA 57.685 37.037 0.00 0.00 0.00 0.98
2208 2294 5.073965 GGAAGAGAGAGGAGATAACCTAGGA 59.926 48.000 17.98 0.00 40.73 2.94
2244 2340 7.201947 CCAACTAACCCTATAGTAGTGTTACCC 60.202 44.444 0.00 0.00 35.09 3.69


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

AutoCloner maintained by Alex Coulton.