Multiple sequence alignment - TraesCS1D01G055800

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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 TraesCS1D01G055800 chr1D 100.000 2664 0 0 1 2664 36837644 36834981 0.000000e+00 4920
1 TraesCS1D01G055800 chr1B 92.196 2691 142 37 1 2664 56885069 56882420 0.000000e+00 3744
2 TraesCS1D01G055800 chr1A 93.770 2472 104 29 1 2450 36273079 36270636 0.000000e+00 3666
3 TraesCS1D01G055800 chr1A 95.918 147 6 0 2518 2664 36270605 36270459 3.430000e-59 239


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 TraesCS1D01G055800 chr1D 36834981 36837644 2663 True 4920.0 4920 100.000 1 2664 1 chr1D.!!$R1 2663
1 TraesCS1D01G055800 chr1B 56882420 56885069 2649 True 3744.0 3744 92.196 1 2664 1 chr1B.!!$R1 2663
2 TraesCS1D01G055800 chr1A 36270459 36273079 2620 True 1952.5 3666 94.844 1 2664 2 chr1A.!!$R1 2663

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
724 726 4.20395 CAGCGTGCTGTTTGTTACTTTA 57.796 40.909 13.62 0.0 39.1 1.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2402 2435 0.460284 GGATCAGCCGCTTCTTCGAA 60.46 55.0 0.0 0.0 0.0 3.71 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
135 136 7.919385 ATAAAATATGAAAAGCATGACCCCT 57.081 32.000 0.00 0.00 37.87 4.79
171 172 5.824097 TGGGAAGAACAGTTTTACCTTGTAC 59.176 40.000 9.57 0.00 0.00 2.90
252 253 9.331282 AGAACATGAGGAACTTATAAGCATTAC 57.669 33.333 12.54 1.39 41.55 1.89
320 322 4.730966 CCTGAATGGTAGCTACTCCTAGA 58.269 47.826 22.74 3.34 0.00 2.43
724 726 4.203950 CAGCGTGCTGTTTGTTACTTTA 57.796 40.909 13.62 0.00 39.10 1.85
821 824 6.137794 TCAAGCATCTAGTGAAGCTAGTAC 57.862 41.667 0.00 0.00 45.13 2.73
879 882 9.817365 CTATATGGTCTTGAAAATTCTAATGCG 57.183 33.333 0.00 0.00 0.00 4.73
943 946 9.307121 CTCAATGTTAAAGATTAGTCGAGATGT 57.693 33.333 0.00 0.00 0.00 3.06
981 984 4.776743 CAAAATATTCCGATGCCTTCTCG 58.223 43.478 0.00 0.00 35.92 4.04
1035 1038 1.114627 ATACTGCAGCGATGACCTGA 58.885 50.000 15.27 0.00 32.03 3.86
1058 1061 5.363979 AACAAGAGAAATTTTCGAGCTCC 57.636 39.130 8.47 0.00 34.02 4.70
1062 1065 3.009584 AGAGAAATTTTCGAGCTCCCCTT 59.990 43.478 8.47 0.00 34.02 3.95
1097 1112 9.821662 AACAGTGAAGTATTACTAAAATTTCGC 57.178 29.630 0.00 0.00 0.00 4.70
1103 1118 9.221775 GAAGTATTACTAAAATTTCGCCACATG 57.778 33.333 0.00 0.00 0.00 3.21
1126 1141 4.133820 CACATGTAAAGACTCACCACCAA 58.866 43.478 0.00 0.00 0.00 3.67
1145 1160 2.490509 CAATGCAACTCTTCTGATGGCA 59.509 45.455 0.00 0.00 0.00 4.92
1162 1177 0.250513 GCAGAGTCTTTCGGGGTCAT 59.749 55.000 0.00 0.00 0.00 3.06
1198 1213 1.298859 GGCTTCACGCTTCCATCGTT 61.299 55.000 0.00 0.00 38.19 3.85
1227 1242 2.434359 GCGGGGTGGAACTCTTCG 60.434 66.667 0.00 0.00 37.58 3.79
1242 1257 1.747924 TCTTCGTCTCCATCTCTGCAG 59.252 52.381 7.63 7.63 0.00 4.41
1441 1469 5.128919 AGCAACTCTAATTAAGCTCATGGG 58.871 41.667 0.00 0.00 0.00 4.00
1448 1476 2.128771 TTAAGCTCATGGGGCTTCAC 57.871 50.000 23.00 0.00 45.45 3.18
1451 1479 1.001641 GCTCATGGGGCTTCACAGT 60.002 57.895 0.00 0.00 0.00 3.55
1457 1485 0.467290 TGGGGCTTCACAGTTTCCAC 60.467 55.000 0.00 0.00 0.00 4.02
1459 1487 1.515521 GGGCTTCACAGTTTCCACCG 61.516 60.000 0.00 0.00 0.00 4.94
1462 1490 1.002792 GCTTCACAGTTTCCACCGAAC 60.003 52.381 0.00 0.00 0.00 3.95
1463 1491 2.561569 CTTCACAGTTTCCACCGAACT 58.438 47.619 0.00 0.00 37.82 3.01
1465 1493 1.760613 TCACAGTTTCCACCGAACTCT 59.239 47.619 0.00 0.00 35.26 3.24
1467 1495 3.385433 TCACAGTTTCCACCGAACTCTAA 59.615 43.478 0.00 0.00 35.26 2.10
1468 1496 4.039973 TCACAGTTTCCACCGAACTCTAAT 59.960 41.667 0.00 0.00 35.26 1.73
1469 1497 4.755123 CACAGTTTCCACCGAACTCTAATT 59.245 41.667 0.00 0.00 35.26 1.40
1470 1498 5.929992 CACAGTTTCCACCGAACTCTAATTA 59.070 40.000 0.00 0.00 35.26 1.40
1474 1504 3.777478 TCCACCGAACTCTAATTAAGCG 58.223 45.455 0.00 0.00 0.00 4.68
1494 1524 1.142097 GGAGGACGCTTGGAGCTAC 59.858 63.158 0.00 0.00 39.60 3.58
1918 1950 1.360393 AAAGCCCAGGAAGACCCACA 61.360 55.000 0.00 0.00 37.41 4.17
2033 2065 1.411787 CCTCCTCCTCATTCGGGTAGT 60.412 57.143 0.00 0.00 0.00 2.73
2034 2066 1.683917 CTCCTCCTCATTCGGGTAGTG 59.316 57.143 0.00 0.00 0.00 2.74
2035 2067 1.006758 TCCTCCTCATTCGGGTAGTGT 59.993 52.381 0.00 0.00 0.00 3.55
2036 2068 1.137086 CCTCCTCATTCGGGTAGTGTG 59.863 57.143 0.00 0.00 0.00 3.82
2037 2069 0.535335 TCCTCATTCGGGTAGTGTGC 59.465 55.000 0.00 0.00 0.00 4.57
2065 2097 0.547954 AGGGTTCCTCTTCCTCCACC 60.548 60.000 0.00 0.00 0.00 4.61
2145 2178 1.129326 CACGATCCGAGGTAATTCGC 58.871 55.000 0.00 0.00 39.19 4.70
2279 2312 2.432119 GGGAGAAGGAGATCCCGAC 58.568 63.158 0.00 0.00 45.63 4.79
2280 2313 0.397254 GGGAGAAGGAGATCCCGACA 60.397 60.000 0.00 0.00 45.63 4.35
2286 2319 2.105128 GAGATCCCGACAGTGGCG 59.895 66.667 12.68 12.68 0.00 5.69
2325 2358 2.125229 CCTCGACCTCGACCTCGA 60.125 66.667 8.88 8.88 44.22 4.04
2328 2361 2.436292 CGACCTCGACCTCGACCT 60.436 66.667 1.47 0.00 44.22 3.85
2329 2362 2.462782 CGACCTCGACCTCGACCTC 61.463 68.421 1.47 0.00 44.22 3.85
2330 2363 2.436292 ACCTCGACCTCGACCTCG 60.436 66.667 0.00 1.30 44.22 4.63
2331 2364 3.878519 CCTCGACCTCGACCTCGC 61.879 72.222 2.68 0.00 44.22 5.03
2332 2365 3.878519 CTCGACCTCGACCTCGCC 61.879 72.222 2.68 0.00 44.22 5.54
2458 2491 2.203015 CCATAAGGTGGGGTCGCG 60.203 66.667 0.00 0.00 44.79 5.87
2460 2493 3.081409 ATAAGGTGGGGTCGCGCT 61.081 61.111 5.56 0.00 0.00 5.92
2461 2494 3.090219 ATAAGGTGGGGTCGCGCTC 62.090 63.158 5.56 0.00 0.00 5.03
2474 2507 3.080121 CGCTCCTGGCTTCTCCCT 61.080 66.667 0.00 0.00 39.13 4.20
2574 2607 1.765904 TGTGGGTGAGCTGAAGTGTTA 59.234 47.619 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
147 148 4.862371 ACAAGGTAAAACTGTTCTTCCCA 58.138 39.130 0.00 0.00 0.00 4.37
151 152 7.043565 TCTTCGTACAAGGTAAAACTGTTCTT 58.956 34.615 0.00 0.00 0.00 2.52
171 172 2.287849 TGCGATCCTGCTATTCTCTTCG 60.288 50.000 0.00 0.00 35.36 3.79
210 211 6.054941 TCATGTTCTGTAGAGTTTTGAAGCA 58.945 36.000 0.00 0.00 0.00 3.91
259 260 9.775854 CCATGTTGCCATTATTATTTTTATCCA 57.224 29.630 0.00 0.00 0.00 3.41
320 322 3.814842 TCTTTCGTGCAGTGTTGATCATT 59.185 39.130 0.00 0.00 0.00 2.57
646 648 2.737252 GCTACTTTGCTTAGTTGCGACT 59.263 45.455 12.27 12.27 37.20 4.18
648 650 2.761559 TGCTACTTTGCTTAGTTGCGA 58.238 42.857 15.69 6.85 45.70 5.10
706 708 6.630045 GGTTAGTTAAAGTAACAAACAGCACG 59.370 38.462 6.65 0.00 41.07 5.34
708 710 6.829811 AGGGTTAGTTAAAGTAACAAACAGCA 59.170 34.615 6.65 0.00 41.07 4.41
709 711 7.012610 TGAGGGTTAGTTAAAGTAACAAACAGC 59.987 37.037 6.65 0.00 41.07 4.40
713 715 8.442374 AGGATGAGGGTTAGTTAAAGTAACAAA 58.558 33.333 6.65 0.00 41.07 2.83
724 726 8.159229 ACTAACAAATAGGATGAGGGTTAGTT 57.841 34.615 0.00 0.00 43.91 2.24
879 882 0.476771 TGGAGGTGTGGTTCCTTTCC 59.523 55.000 0.00 0.00 35.20 3.13
943 946 2.869101 TTTGCAGGGTGTGTGCTATA 57.131 45.000 0.00 0.00 41.78 1.31
981 984 1.452108 CGCCTTGAAGGATGGGGTC 60.452 63.158 16.93 0.00 37.67 4.46
1017 1020 0.894835 TTCAGGTCATCGCTGCAGTA 59.105 50.000 16.64 4.31 0.00 2.74
1035 1038 5.278512 GGGAGCTCGAAAATTTCTCTTGTTT 60.279 40.000 7.83 0.00 0.00 2.83
1058 1061 2.023673 TCACTGTTTGTGCTGAAAGGG 58.976 47.619 0.00 0.00 45.81 3.95
1062 1065 6.765989 AGTAATACTTCACTGTTTGTGCTGAA 59.234 34.615 0.00 0.00 45.81 3.02
1080 1083 7.376530 GCATGTGGCGAAATTTTAGTAATAC 57.623 36.000 0.00 0.00 0.00 1.89
1103 1118 2.484264 GGTGGTGAGTCTTTACATGTGC 59.516 50.000 9.11 0.00 0.00 4.57
1126 1141 2.026542 TCTGCCATCAGAAGAGTTGCAT 60.027 45.455 0.00 0.00 45.69 3.96
1145 1160 0.250513 GCATGACCCCGAAAGACTCT 59.749 55.000 0.00 0.00 0.00 3.24
1214 1229 0.966920 TGGAGACGAAGAGTTCCACC 59.033 55.000 0.00 0.00 36.12 4.61
1227 1242 3.244146 ACATATGCTGCAGAGATGGAGAC 60.244 47.826 20.43 0.00 0.00 3.36
1242 1257 2.615912 GCTTCCTCTTGTGGACATATGC 59.384 50.000 1.58 0.00 35.58 3.14
1414 1436 6.727824 TGAGCTTAATTAGAGTTGCTTGAC 57.272 37.500 0.00 0.00 0.00 3.18
1423 1445 4.363991 AGCCCCATGAGCTTAATTAGAG 57.636 45.455 4.53 0.00 37.24 2.43
1441 1469 0.534203 TCGGTGGAAACTGTGAAGCC 60.534 55.000 0.00 0.00 0.00 4.35
1448 1476 6.402226 GCTTAATTAGAGTTCGGTGGAAACTG 60.402 42.308 0.00 0.00 33.05 3.16
1451 1479 4.628333 CGCTTAATTAGAGTTCGGTGGAAA 59.372 41.667 0.00 0.00 33.05 3.13
1457 1485 1.521423 CCGCGCTTAATTAGAGTTCGG 59.479 52.381 5.56 11.21 0.00 4.30
1459 1487 2.795470 CCTCCGCGCTTAATTAGAGTTC 59.205 50.000 5.56 0.00 0.00 3.01
1462 1490 2.395654 GTCCTCCGCGCTTAATTAGAG 58.604 52.381 5.56 0.00 0.00 2.43
1463 1491 1.268896 CGTCCTCCGCGCTTAATTAGA 60.269 52.381 5.56 0.00 0.00 2.10
1465 1493 3.261441 CGTCCTCCGCGCTTAATTA 57.739 52.632 5.56 0.00 0.00 1.40
1684 1714 3.453679 GTTCCTCCGCGCCTCTCT 61.454 66.667 0.00 0.00 0.00 3.10
1966 1998 5.047660 CGAGGAATTAGTAGCAGAGCCTAAT 60.048 44.000 0.00 0.00 33.86 1.73
2033 2065 2.715532 GAACCCTCGAGCACAGCACA 62.716 60.000 6.99 0.00 0.00 4.57
2034 2066 2.029844 GAACCCTCGAGCACAGCAC 61.030 63.158 6.99 0.00 0.00 4.40
2035 2067 2.343758 GAACCCTCGAGCACAGCA 59.656 61.111 6.99 0.00 0.00 4.41
2036 2068 2.435059 GGAACCCTCGAGCACAGC 60.435 66.667 6.99 0.00 0.00 4.40
2037 2069 1.216710 GAGGAACCCTCGAGCACAG 59.783 63.158 6.99 0.00 41.08 3.66
2186 2219 3.444916 GATTACAGCGAGAAATCGACCA 58.555 45.455 1.17 0.00 34.64 4.02
2402 2435 0.460284 GGATCAGCCGCTTCTTCGAA 60.460 55.000 0.00 0.00 0.00 3.71
2458 2491 2.588989 CAGGGAGAAGCCAGGAGC 59.411 66.667 0.00 0.00 44.25 4.70
2460 2493 1.613630 GACCAGGGAGAAGCCAGGA 60.614 63.158 0.00 0.00 38.95 3.86
2461 2494 2.674220 GGACCAGGGAGAAGCCAGG 61.674 68.421 0.00 0.00 38.95 4.45
2462 2495 1.908340 CTGGACCAGGGAGAAGCCAG 61.908 65.000 14.26 0.00 38.95 4.85
2463 2496 1.920325 CTGGACCAGGGAGAAGCCA 60.920 63.158 14.26 0.00 38.95 4.75
2474 2507 1.274167 GATAACACACGTCCTGGACCA 59.726 52.381 20.68 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.