Multiple sequence alignment - TraesCS1A01G172200

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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 TraesCS1A01G172200 chr1A 100.000 2965 0 0 1 2965 307734535 307737499 0 5476
1 TraesCS1A01G172200 chr1A 94.817 2971 144 8 1 2965 221267064 221264098 0 4625
2 TraesCS1A01G172200 chr2A 96.370 2975 95 11 1 2965 313167063 313164092 0 4883
3 TraesCS1A01G172200 chr3A 95.923 2968 113 6 4 2965 197672371 197669406 0 4804
4 TraesCS1A01G172200 chr3A 94.480 2971 156 5 1 2965 309534600 309531632 0 4571
5 TraesCS1A01G172200 chr6A 95.797 2974 112 8 1 2965 387304369 387301400 0 4787
6 TraesCS1A01G172200 chr4D 95.491 2972 126 6 1 2965 396674292 396677262 0 4739
7 TraesCS1A01G172200 chr5D 95.259 2974 130 7 1 2965 107866529 107863558 0 4700


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 TraesCS1A01G172200 chr1A 307734535 307737499 2964 False 5476 5476 100.000 1 2965 1 chr1A.!!$F1 2964
1 TraesCS1A01G172200 chr1A 221264098 221267064 2966 True 4625 4625 94.817 1 2965 1 chr1A.!!$R1 2964
2 TraesCS1A01G172200 chr2A 313164092 313167063 2971 True 4883 4883 96.370 1 2965 1 chr2A.!!$R1 2964
3 TraesCS1A01G172200 chr3A 197669406 197672371 2965 True 4804 4804 95.923 4 2965 1 chr3A.!!$R1 2961
4 TraesCS1A01G172200 chr3A 309531632 309534600 2968 True 4571 4571 94.480 1 2965 1 chr3A.!!$R2 2964
5 TraesCS1A01G172200 chr6A 387301400 387304369 2969 True 4787 4787 95.797 1 2965 1 chr6A.!!$R1 2964
6 TraesCS1A01G172200 chr4D 396674292 396677262 2970 False 4739 4739 95.491 1 2965 1 chr4D.!!$F1 2964
7 TraesCS1A01G172200 chr5D 107863558 107866529 2971 True 4700 4700 95.259 1 2965 1 chr5D.!!$R1 2964

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
664 681 0.393820 CTGCTTGTTGTTTGGCCCAT 59.606 50.000 0.0 0.0 0.0 4.00 F
761 778 1.296715 GCATCTCCGTCTGGTGGTT 59.703 57.895 0.0 0.0 36.3 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1871 1892 0.667487 TCAGCTTCGCTCTTTCCACG 60.667 55.000 0.0 0.0 36.40 4.94 R
2391 2415 1.003545 CGGAGTATTTTCATGCAGCCG 60.004 52.381 0.0 0.0 32.12 5.52 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
153 159 7.838079 AAAGTTGGGCATGCATATATTTCTA 57.162 32.000 21.36 0.00 0.00 2.10
191 199 7.339721 GGGAAAAGATAAGAAACCTAAGGGAAG 59.660 40.741 0.00 0.00 36.25 3.46
261 269 3.878778 AGCATAGAGTGAAAGCCGAAAT 58.121 40.909 0.00 0.00 0.00 2.17
338 350 8.932791 GTTGTCTCTCTTGATAAAAATCGGTTA 58.067 33.333 0.00 0.00 0.00 2.85
601 618 5.677178 CGTGTCTGTTTTCTTTTAGAAGCAC 59.323 40.000 0.00 0.00 35.37 4.40
664 681 0.393820 CTGCTTGTTGTTTGGCCCAT 59.606 50.000 0.00 0.00 0.00 4.00
727 744 4.073201 CAGGCATAGGTCCCCTGT 57.927 61.111 4.19 0.00 40.92 4.00
761 778 1.296715 GCATCTCCGTCTGGTGGTT 59.703 57.895 0.00 0.00 36.30 3.67
899 918 3.006217 GGCAACTCCTTTCATTTTCAGCT 59.994 43.478 0.00 0.00 0.00 4.24
950 969 2.918131 GCACGATGTTTTCTGCCTGTTC 60.918 50.000 0.00 0.00 0.00 3.18
1083 1103 3.866066 GCTCTAATGAAGCTGTGGACACA 60.866 47.826 4.92 4.92 39.32 3.72
1088 1108 3.502164 AAGCTGTGGACACAAGCTT 57.498 47.368 23.67 23.67 43.75 3.74
1130 1150 2.355513 GCTCTGATGAAGGTGTGGACAT 60.356 50.000 0.00 0.00 0.00 3.06
1171 1191 1.912971 AGCAGCTCTGATGATGGCA 59.087 52.632 0.29 0.00 0.00 4.92
1270 1290 4.311606 TCTGTACTTTAGTCATTTGCGCA 58.688 39.130 5.66 5.66 0.00 6.09
1284 1304 1.665599 GCGCATATGGGCCATTTGC 60.666 57.895 37.07 37.07 46.68 3.68
1312 1332 5.439721 TGAATTATTGAGGCATGTGCTACT 58.560 37.500 4.84 0.00 41.70 2.57
1328 1348 7.658179 TGTGCTACTGTATGAAGAAAAAGAG 57.342 36.000 0.00 0.00 0.00 2.85
1525 1545 1.511850 TGATGTCAAAGTGTGCTCGG 58.488 50.000 0.00 0.00 0.00 4.63
1631 1651 1.339438 GGCAGAGAATGGTGAGAAGCA 60.339 52.381 0.00 0.00 0.00 3.91
1871 1892 1.009829 CACATAACTGGAGCCGCTTC 58.990 55.000 0.00 0.00 0.00 3.86
2191 2214 1.458588 GGGTTTGTTGGGCCAAGGA 60.459 57.895 21.62 8.43 0.00 3.36
2200 2223 1.606601 GGGCCAAGGAAACCAGGAC 60.607 63.158 4.39 0.00 0.00 3.85
2309 2332 4.619760 GCTTTTGCCTAACGTTGTAATTCC 59.380 41.667 11.99 0.00 40.15 3.01
2494 2518 2.356382 CGTTGTTGCTTGGGTTTACAGA 59.644 45.455 0.00 0.00 0.00 3.41
2537 2561 4.327087 ACGCTCTTTTTGCACTTCTTTTTG 59.673 37.500 0.00 0.00 0.00 2.44
2555 2579 4.740922 CAGCCACCCTGCATACAA 57.259 55.556 0.00 0.00 34.21 2.41
2655 2679 0.322456 CCTGCGATTTCTGGGTCCAA 60.322 55.000 0.00 0.00 0.00 3.53
2760 2784 4.222336 TCAGGTGTTGGAACCAATTCATT 58.778 39.130 9.53 0.00 43.20 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 59 6.571150 GCCAACTTTGCTTTCTCATCATACTT 60.571 38.462 0.00 0.00 0.00 2.24
617 634 7.365295 CCAGCCCAGTAAACCTTAAATACTCTA 60.365 40.741 0.00 0.00 0.00 2.43
727 744 3.309296 AGATGCCGAGGAAGAGGAATAA 58.691 45.455 0.00 0.00 0.00 1.40
761 778 1.618837 CGTCTCTCAAGGAAGGGTTCA 59.381 52.381 0.00 0.00 0.00 3.18
899 918 2.497675 GACAGCAATGGAGTAGGAGTCA 59.502 50.000 0.00 0.00 0.00 3.41
1066 1086 1.610522 GCTTGTGTCCACAGCTTCATT 59.389 47.619 11.88 0.00 42.94 2.57
1075 1095 3.550842 GGTTCATCAAAGCTTGTGTCCAC 60.551 47.826 0.00 0.00 32.48 4.02
1083 1103 0.889186 ACGCGGGTTCATCAAAGCTT 60.889 50.000 12.47 0.00 35.64 3.74
1088 1108 0.671163 GGTGTACGCGGGTTCATCAA 60.671 55.000 15.98 0.00 0.00 2.57
1130 1150 1.219124 GCCCGTTCATCAGAGCTCA 59.781 57.895 17.77 0.00 0.00 4.26
1171 1191 3.607741 CTTCATCAGAGCTTGTGTCCAT 58.392 45.455 0.00 0.00 0.00 3.41
1233 1253 6.992063 AAGTACAGATCATGACCACATTTC 57.008 37.500 0.00 0.00 34.15 2.17
1242 1262 7.010460 CGCAAATGACTAAAGTACAGATCATGA 59.990 37.037 0.00 0.00 0.00 3.07
1270 1290 3.106054 TCAACAAGCAAATGGCCCATAT 58.894 40.909 0.00 0.00 46.50 1.78
1284 1304 5.290158 GCACATGCCTCAATAATTCAACAAG 59.710 40.000 0.00 0.00 34.31 3.16
1312 1332 6.533730 TCTGAAGCCTCTTTTTCTTCATACA 58.466 36.000 4.63 0.00 43.36 2.29
1328 1348 1.471684 CCTTGCATGTCTTCTGAAGCC 59.528 52.381 12.54 1.64 0.00 4.35
1525 1545 2.815478 ACATAGCAGCTAAGACGCTTC 58.185 47.619 11.66 0.00 38.41 3.86
1695 1716 8.754080 AGTAGAGAAGTACTACAAGCATTCAAT 58.246 33.333 0.00 0.00 41.56 2.57
1871 1892 0.667487 TCAGCTTCGCTCTTTCCACG 60.667 55.000 0.00 0.00 36.40 4.94
2129 2152 7.254117 CGACTGAACATTACTAAACATAGGCAG 60.254 40.741 0.00 0.00 0.00 4.85
2200 2223 4.298332 ACATTACTGCCAAAAGAAAAGCG 58.702 39.130 0.00 0.00 0.00 4.68
2309 2332 8.427012 TGTACGCTTAATTACTTTAGACAAACG 58.573 33.333 0.00 0.00 0.00 3.60
2391 2415 1.003545 CGGAGTATTTTCATGCAGCCG 60.004 52.381 0.00 0.00 32.12 5.52
2494 2518 2.127271 TGTTCGACCATGGCAATGAT 57.873 45.000 13.04 0.00 35.67 2.45
2555 2579 3.450457 TCTTTGACCAACCAACAAAGCAT 59.550 39.130 0.00 0.00 45.41 3.79
2605 2629 7.170489 GGAACTACTAGGTAAAACACTCACAAC 59.830 40.741 0.00 0.00 0.00 3.32
2709 2733 1.154093 CAGTTCAATGGCAGCGCAG 60.154 57.895 11.47 1.31 0.00 5.18
2760 2784 4.360951 AACAAGTTTCAGGAACCCGATA 57.639 40.909 0.00 0.00 39.13 2.92


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

AutoCloner maintained by Alex Coulton.