Multiple sequence alignment - TraesCS7A01G237600

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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 TraesCS7A01G237600 chr7A 100.000 2255 0 0 1 2255 211277027 211274773 0 4165
1 TraesCS7A01G237600 chr7A 97.662 1711 39 1 546 2255 60149559 60147849 0 2937
2 TraesCS7A01G237600 chr7A 97.814 549 12 0 1 549 120826861 120826313 0 948
3 TraesCS7A01G237600 chr7A 97.632 549 13 0 1 549 120923851 120923303 0 942
4 TraesCS7A01G237600 chr1D 98.071 1711 31 2 546 2255 141314407 141312698 0 2976
5 TraesCS7A01G237600 chr2B 98.013 1711 32 2 546 2255 799246700 799248409 0 2970
6 TraesCS7A01G237600 chr7B 97.897 1712 34 1 546 2255 644466171 644467882 0 2961
7 TraesCS7A01G237600 chrUn 97.838 1711 36 1 546 2255 225926981 225928691 0 2953
8 TraesCS7A01G237600 chr3A 97.838 1711 36 1 546 2255 633109982 633111692 0 2953
9 TraesCS7A01G237600 chr1B 97.604 1711 40 1 546 2255 672477889 672479599 0 2931
10 TraesCS7A01G237600 chr1B 97.488 1712 40 3 546 2255 638701938 638700228 0 2920
11 TraesCS7A01G237600 chr4B 97.193 1710 48 0 546 2255 209078789 209077080 0 2892
12 TraesCS7A01G237600 chr7D 97.996 549 10 1 1 549 382012173 382011626 0 952
13 TraesCS7A01G237600 chr5B 97.814 549 12 0 1 549 713044222 713043674 0 948
14 TraesCS7A01G237600 chr5A 97.814 549 12 0 1 549 16621281 16620733 0 948
15 TraesCS7A01G237600 chr2D 97.814 549 12 0 1 549 17965197 17964649 0 948
16 TraesCS7A01G237600 chr3B 97.814 549 11 1 1 549 201633815 201633268 0 946
17 TraesCS7A01G237600 chr2A 97.806 547 12 0 1 547 735174791 735175337 0 944
18 TraesCS7A01G237600 chr6B 97.632 549 13 0 1 549 525680156 525680704 0 942


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 TraesCS7A01G237600 chr7A 211274773 211277027 2254 True 4165 4165 100.000 1 2255 1 chr7A.!!$R4 2254
1 TraesCS7A01G237600 chr7A 60147849 60149559 1710 True 2937 2937 97.662 546 2255 1 chr7A.!!$R1 1709
2 TraesCS7A01G237600 chr7A 120826313 120826861 548 True 948 948 97.814 1 549 1 chr7A.!!$R2 548
3 TraesCS7A01G237600 chr7A 120923303 120923851 548 True 942 942 97.632 1 549 1 chr7A.!!$R3 548
4 TraesCS7A01G237600 chr1D 141312698 141314407 1709 True 2976 2976 98.071 546 2255 1 chr1D.!!$R1 1709
5 TraesCS7A01G237600 chr2B 799246700 799248409 1709 False 2970 2970 98.013 546 2255 1 chr2B.!!$F1 1709
6 TraesCS7A01G237600 chr7B 644466171 644467882 1711 False 2961 2961 97.897 546 2255 1 chr7B.!!$F1 1709
7 TraesCS7A01G237600 chrUn 225926981 225928691 1710 False 2953 2953 97.838 546 2255 1 chrUn.!!$F1 1709
8 TraesCS7A01G237600 chr3A 633109982 633111692 1710 False 2953 2953 97.838 546 2255 1 chr3A.!!$F1 1709
9 TraesCS7A01G237600 chr1B 672477889 672479599 1710 False 2931 2931 97.604 546 2255 1 chr1B.!!$F1 1709
10 TraesCS7A01G237600 chr1B 638700228 638701938 1710 True 2920 2920 97.488 546 2255 1 chr1B.!!$R1 1709
11 TraesCS7A01G237600 chr4B 209077080 209078789 1709 True 2892 2892 97.193 546 2255 1 chr4B.!!$R1 1709
12 TraesCS7A01G237600 chr7D 382011626 382012173 547 True 952 952 97.996 1 549 1 chr7D.!!$R1 548
13 TraesCS7A01G237600 chr5B 713043674 713044222 548 True 948 948 97.814 1 549 1 chr5B.!!$R1 548
14 TraesCS7A01G237600 chr5A 16620733 16621281 548 True 948 948 97.814 1 549 1 chr5A.!!$R1 548
15 TraesCS7A01G237600 chr2D 17964649 17965197 548 True 948 948 97.814 1 549 1 chr2D.!!$R1 548
16 TraesCS7A01G237600 chr3B 201633268 201633815 547 True 946 946 97.814 1 549 1 chr3B.!!$R1 548
17 TraesCS7A01G237600 chr2A 735174791 735175337 546 False 944 944 97.806 1 547 1 chr2A.!!$F1 546
18 TraesCS7A01G237600 chr6B 525680156 525680704 548 False 942 942 97.632 1 549 1 chr6B.!!$F1 548

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
362 363 0.968901 TAGTGACAAGGGCCGACGAT 60.969 55.0 0.0 0.0 0.0 3.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1635 1639 0.179043 TCAAAACTACAGGGCGTGCA 60.179 50.0 7.17 0.0 0.0 4.57 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
163 164 3.082579 GCTCGGCAGAGGGTTCGAT 62.083 63.158 15.89 0.00 44.51 3.59
181 182 6.261603 GGTTCGATAATAGGGTAGGGTTTTTG 59.738 42.308 0.00 0.00 0.00 2.44
345 346 5.582665 GGAAAAGACAAGCATAGTGGTCTAG 59.417 44.000 0.00 0.00 39.55 2.43
362 363 0.968901 TAGTGACAAGGGCCGACGAT 60.969 55.000 0.00 0.00 0.00 3.73
368 369 3.031417 AAGGGCCGACGATGGAAGG 62.031 63.158 0.00 0.00 0.00 3.46
693 694 6.863126 GCAATTTAAGTAGAAAGCTTGCTTCA 59.137 34.615 13.52 0.00 34.05 3.02
837 838 5.305128 AGTTTGCCAAAGGATTTCTCATTCA 59.695 36.000 0.00 0.00 35.03 2.57
922 925 2.610438 ATTTCATTGCTGTGGGTCCT 57.390 45.000 0.00 0.00 0.00 3.85
1160 1163 5.329399 TGGCCTATCTTCTTTAAAAAGCCA 58.671 37.500 3.32 0.00 43.97 4.75
1229 1233 9.337396 GAAAAGAAAATCTTACCATTTTTGGGT 57.663 29.630 0.00 0.00 35.27 4.51
1232 1236 6.492087 AGAAAATCTTACCATTTTTGGGTCGA 59.508 34.615 0.00 0.00 39.85 4.20
1267 1271 6.854578 TCCATTTCCTGAACCTAAACCTAAA 58.145 36.000 0.00 0.00 0.00 1.85
1347 1351 6.127083 GGCTCAAATCCCTTTTTCATATCCAA 60.127 38.462 0.00 0.00 0.00 3.53
1378 1382 6.576313 GCTTTAGGTACGCTTTAGTTTGAAAC 59.424 38.462 0.00 0.00 0.00 2.78
1400 1404 5.930135 ACCATTAAAGATATGCTCGACCTT 58.070 37.500 0.00 0.00 0.00 3.50
1417 1421 4.331717 CGACCTTGTTTATGTCCATGGTAC 59.668 45.833 12.58 9.37 38.72 3.34
1516 1520 1.339727 GGTCGTTTAGCAGTTCCCCAT 60.340 52.381 0.00 0.00 0.00 4.00
1529 1533 0.253347 TCCCCATCCAGCTTTCTCCT 60.253 55.000 0.00 0.00 0.00 3.69
1635 1639 2.678336 GCTGAAAAGCCGTAGTGCTAAT 59.322 45.455 0.00 0.00 41.80 1.73
1656 1660 1.539827 GCACGCCCTGTAGTTTTGAAT 59.460 47.619 0.00 0.00 0.00 2.57
1817 1821 6.574269 GCACCTATTGTTAAGGCTTGGAAAAT 60.574 38.462 10.69 7.89 37.67 1.82
1849 1853 1.283321 GGCTCCCTTCCTTCACTGAAT 59.717 52.381 0.00 0.00 0.00 2.57
1870 1874 0.037734 GATTCACCCGGGTCCAAACT 59.962 55.000 27.51 5.32 0.00 2.66
2007 2012 4.692475 CCTTTCGTTCGGGCCGGT 62.692 66.667 27.98 0.00 0.00 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 6.628644 AGCAACTTATCCTAAGGTCTCTTT 57.371 37.500 0.00 0.00 34.59 2.52
163 164 4.535692 ACCGTCAAAAACCCTACCCTATTA 59.464 41.667 0.00 0.00 0.00 0.98
345 346 2.100631 CATCGTCGGCCCTTGTCAC 61.101 63.158 0.00 0.00 0.00 3.67
362 363 2.678934 CTCCGTCCCGACCTTCCA 60.679 66.667 0.00 0.00 0.00 3.53
693 694 6.766944 CAGCTTTAGTTGAATGATCTGATCCT 59.233 38.462 14.71 2.36 0.00 3.24
922 925 4.314961 ACAATCTTATTCGAGCACACACA 58.685 39.130 0.00 0.00 0.00 3.72
1071 1074 2.714250 ACAACCTGAATACCAAGGGACA 59.286 45.455 0.00 0.00 0.00 4.02
1160 1163 8.887036 AAAGTTTTGCGAAATCCTTATCTTTT 57.113 26.923 1.61 0.00 0.00 2.27
1213 1216 4.658063 ACATCGACCCAAAAATGGTAAGA 58.342 39.130 0.00 0.00 35.85 2.10
1347 1351 1.221021 GCGTACCTAAAGCCTGCCT 59.779 57.895 0.00 0.00 0.00 4.75
1378 1382 5.760253 ACAAGGTCGAGCATATCTTTAATGG 59.240 40.000 18.15 0.00 0.00 3.16
1400 1404 4.080807 ACGATGGTACCATGGACATAAACA 60.081 41.667 35.31 7.35 36.70 2.83
1417 1421 5.698089 TGATAGTAGAAGGTACGTACGATGG 59.302 44.000 24.41 0.00 0.00 3.51
1516 1520 1.924731 TTCTCGAGGAGAAAGCTGGA 58.075 50.000 13.56 0.00 44.37 3.86
1529 1533 1.924731 TCTCAGGAAGGCTTTCTCGA 58.075 50.000 4.67 6.32 33.68 4.04
1635 1639 0.179043 TCAAAACTACAGGGCGTGCA 60.179 50.000 7.17 0.00 0.00 4.57
1656 1660 2.069273 GCTCGCTGCTGTCTTTTTAGA 58.931 47.619 0.00 0.00 38.95 2.10
1794 1798 6.154534 GGATTTTCCAAGCCTTAACAATAGGT 59.845 38.462 0.00 0.00 35.36 3.08
1817 1821 3.522343 GGAAGGGAGCCTAAACTTAAGGA 59.478 47.826 7.53 0.00 36.08 3.36
1849 1853 0.478942 TTTGGACCCGGGTGAATCAA 59.521 50.000 36.01 24.84 0.00 2.57
1915 1919 1.694150 CGGGGCTCTCTCCAATCATTA 59.306 52.381 0.00 0.00 0.00 1.90
2007 2012 1.362932 GATAGATCAGGGCCCCTCCTA 59.637 57.143 21.43 15.30 34.92 2.94
2046 2052 0.783850 AAAAGGGGGAGCAAAGCCTA 59.216 50.000 0.00 0.00 0.00 3.93
2172 2178 1.275291 GTGTCTGGAAACTCGGGATCA 59.725 52.381 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.