Multiple sequence alignment - TraesCS5A01G228600

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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 TraesCS5A01G228600 chr5A 100.000 3248 0 0 1 3248 444597654 444594407 0.000000 5999.0
1 TraesCS5A01G228600 chr5D 94.823 3284 119 22 1 3248 347275217 347278485 0.000000 5075.0
2 TraesCS5A01G228600 chr5B 91.807 1843 84 30 35 1840 403857615 403855803 0.000000 2505.0
3 TraesCS5A01G228600 chr5B 95.968 496 20 0 1879 2374 403855825 403855330 0.000000 806.0
4 TraesCS5A01G228600 chr5B 100.000 30 0 0 1841 1870 403855840 403855811 0.000453 56.5


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 TraesCS5A01G228600 chr5A 444594407 444597654 3247 True 5999.0 5999 100.000 1 3248 1 chr5A.!!$R1 3247
1 TraesCS5A01G228600 chr5D 347275217 347278485 3268 False 5075.0 5075 94.823 1 3248 1 chr5D.!!$F1 3247
2 TraesCS5A01G228600 chr5B 403855330 403857615 2285 True 1122.5 2505 95.925 35 2374 3 chr5B.!!$R1 2339

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
653 668 0.316937 CGTGCACGCATTTGACAACT 60.317 50.0 28.16 0.0 0.0 3.16 F
1106 1150 0.244994 AGCAGTCGAGGCAGTACAAG 59.755 55.0 11.19 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1974 2025 0.321919 GAGCCATCCTTGCACTGACA 60.322 55.0 0.0 0.0 0.0 3.58 R
2832 2883 0.168128 GCTGTCGTATTTGCCGCTTT 59.832 50.0 0.0 0.0 0.0 3.51 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
182 185 4.155826 TGTTCGCAGCAAAAGTAGCATATT 59.844 37.500 0.00 0.00 0.00 1.28
183 186 4.277257 TCGCAGCAAAAGTAGCATATTG 57.723 40.909 0.00 0.00 0.00 1.90
184 187 2.785477 CGCAGCAAAAGTAGCATATTGC 59.215 45.455 1.31 1.31 46.43 3.56
224 227 1.318576 GGGTTTTGACACCAGACCAG 58.681 55.000 0.00 0.00 38.79 4.00
426 432 9.118236 GTGTTCTTTGTTTTCTATTAGCACATC 57.882 33.333 0.00 0.00 0.00 3.06
447 453 9.472361 CACATCCTAATTTTGATGATGGAAATC 57.528 33.333 18.48 0.00 40.64 2.17
456 462 9.713684 ATTTTGATGATGGAAATCTAAAGGGTA 57.286 29.630 0.00 0.00 34.07 3.69
653 668 0.316937 CGTGCACGCATTTGACAACT 60.317 50.000 28.16 0.00 0.00 3.16
726 747 8.284945 AGCACATCACATACATTGAAGTTTAT 57.715 30.769 0.00 0.00 0.00 1.40
734 755 4.701956 ACATTGAAGTTTATCCCAAGCG 57.298 40.909 0.00 0.00 0.00 4.68
738 759 1.327764 GAAGTTTATCCCAAGCGCTCG 59.672 52.381 12.06 0.00 0.00 5.03
819 862 7.808672 ACAAATGACATGCAATTACCAATTTG 58.191 30.769 13.40 13.40 0.00 2.32
1061 1105 2.037772 ACAGAGATCCCGCATATTCCAC 59.962 50.000 0.00 0.00 0.00 4.02
1067 1111 1.774254 TCCCGCATATTCCACTTCCAT 59.226 47.619 0.00 0.00 0.00 3.41
1068 1112 2.174639 TCCCGCATATTCCACTTCCATT 59.825 45.455 0.00 0.00 0.00 3.16
1069 1113 2.294233 CCCGCATATTCCACTTCCATTG 59.706 50.000 0.00 0.00 0.00 2.82
1070 1114 3.213506 CCGCATATTCCACTTCCATTGA 58.786 45.455 0.00 0.00 0.00 2.57
1071 1115 3.251729 CCGCATATTCCACTTCCATTGAG 59.748 47.826 0.00 0.00 0.00 3.02
1072 1116 3.251729 CGCATATTCCACTTCCATTGAGG 59.748 47.826 0.00 0.00 39.47 3.86
1106 1150 0.244994 AGCAGTCGAGGCAGTACAAG 59.755 55.000 11.19 0.00 0.00 3.16
1184 1228 4.712337 CCCTCTGTCTAGTTATCACCTTGT 59.288 45.833 0.00 0.00 0.00 3.16
1237 1281 2.942604 TACCCCTCTCAAGTAAGGCT 57.057 50.000 0.00 0.00 0.00 4.58
1241 1285 1.134965 CCCTCTCAAGTAAGGCTCACG 60.135 57.143 0.00 0.00 0.00 4.35
1247 1291 3.682696 TCAAGTAAGGCTCACGTCTCTA 58.317 45.455 0.00 0.00 0.00 2.43
1343 1388 2.523657 TGCCCTTGCAACATGCCA 60.524 55.556 0.00 0.00 46.66 4.92
1361 1406 2.226315 AGTGAGCAGGTGCCATGGA 61.226 57.895 18.40 0.00 43.38 3.41
1368 1413 0.816825 CAGGTGCCATGGATCGAAGG 60.817 60.000 18.40 0.00 0.00 3.46
1456 1501 7.319646 AGTGAGCTTTGTTCTAGACTTCATAG 58.680 38.462 0.00 0.00 0.00 2.23
1497 1542 7.698836 ACAGCAAAATCTTTGTACATGAAAC 57.301 32.000 0.00 0.00 0.00 2.78
1629 1676 4.451900 AGTGATCGTTTCTCAAGTTGGTT 58.548 39.130 2.34 0.00 0.00 3.67
1681 1731 3.505680 TCGGTTACTTCCTGTAGCGTTTA 59.494 43.478 0.00 0.00 33.85 2.01
1730 1780 4.529897 TGTTCATGCTTCATGGAATAGCT 58.470 39.130 6.92 0.00 41.66 3.32
1761 1811 2.521547 AAAGGAGGAAGCTTCATGGG 57.478 50.000 27.02 0.00 0.00 4.00
1803 1853 0.679640 TGGGATTCATGTGGTTCGGC 60.680 55.000 0.00 0.00 0.00 5.54
1817 1867 0.306840 TTCGGCGTACTCAGCTATCG 59.693 55.000 6.85 0.00 34.52 2.92
1955 2006 2.023015 TGGACATGGGTAGAGTGATCCT 60.023 50.000 0.00 0.00 0.00 3.24
1974 2025 2.223829 CCTAGAAGATGACGCGGTGAAT 60.224 50.000 12.47 0.00 0.00 2.57
2057 2108 1.420532 AAGCCACCGGGTTGGAACTA 61.421 55.000 15.11 0.00 42.19 2.24
2068 2119 2.280628 GTTGGAACTAAGCTAGCGCAT 58.719 47.619 11.47 2.38 39.10 4.73
2326 2377 3.648545 ACAGTTCTTCTCCCTAGTGCTTT 59.351 43.478 0.00 0.00 0.00 3.51
2354 2405 1.337823 CCAACGTTGTCTCCCCTACTG 60.338 57.143 25.63 3.15 0.00 2.74
2384 2435 2.030007 GCTGCCAATAGCTTGTTGTTCA 60.030 45.455 0.00 0.00 44.23 3.18
2394 2445 4.769688 AGCTTGTTGTTCATCCATCGATA 58.230 39.130 0.00 0.00 0.00 2.92
2395 2446 5.371526 AGCTTGTTGTTCATCCATCGATAT 58.628 37.500 0.00 0.00 0.00 1.63
2438 2489 2.703409 CACTAACCATCGCTGCGC 59.297 61.111 18.65 0.00 0.00 6.09
2461 2512 0.325933 CCACTGATGCCACCTTCTCA 59.674 55.000 0.00 0.00 0.00 3.27
2484 2535 0.842467 ACCCCTAGCAGCAGTTTCCT 60.842 55.000 0.00 0.00 0.00 3.36
2494 2545 1.227823 CAGTTTCCTGCGGGTGTCA 60.228 57.895 12.43 0.00 0.00 3.58
2549 2600 4.137543 TGCCTTTTCTTCCTCTTCTTCAC 58.862 43.478 0.00 0.00 0.00 3.18
2578 2629 4.169508 CTCACTTGAGTTGTATGTCTCCG 58.830 47.826 0.00 0.00 37.40 4.63
2579 2630 3.572682 TCACTTGAGTTGTATGTCTCCGT 59.427 43.478 0.00 0.00 0.00 4.69
2601 2652 2.288825 CCGCCCTACAATCATACGTCAT 60.289 50.000 0.00 0.00 0.00 3.06
2614 2665 2.949451 ACGTCATTGAATCTCTCGCT 57.051 45.000 0.00 0.00 0.00 4.93
2621 2672 7.491372 ACGTCATTGAATCTCTCGCTTATTAAA 59.509 33.333 0.00 0.00 0.00 1.52
2746 2797 5.945155 ACGAGCTCAAAACTGTAACAAAAA 58.055 33.333 15.40 0.00 0.00 1.94
2784 2835 5.508320 CCAATAAAACCGCAACCTAGTTTGT 60.508 40.000 1.71 0.00 34.12 2.83
2832 2883 2.643551 GAGTGCCTATTTGCTGCCTTA 58.356 47.619 0.00 0.00 0.00 2.69
2904 2955 6.423905 GTGGCGACTTAAGCAATCTATTATCA 59.576 38.462 1.29 0.00 36.08 2.15
3137 3188 7.499895 TCGTATATGTGGGAATATATGCTCGTA 59.500 37.037 0.00 0.00 34.22 3.43
3169 3220 9.906660 TTAAAAGCGTCATGTATTTCAAGAAAT 57.093 25.926 12.21 12.21 42.95 2.17
3241 3292 5.639506 AGTATGTGAGCACAACTAACATCAC 59.360 40.000 7.46 0.00 46.16 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.126343 AGTGGACACGTTTTGAAACAGAC 59.874 43.478 7.32 0.37 38.81 3.51
183 186 1.527034 TGGTGAGTGCAAGAGAATGC 58.473 50.000 0.00 0.00 46.58 3.56
184 187 3.119602 CCAATGGTGAGTGCAAGAGAATG 60.120 47.826 0.00 0.00 0.00 2.67
185 188 3.087031 CCAATGGTGAGTGCAAGAGAAT 58.913 45.455 0.00 0.00 0.00 2.40
186 189 2.507484 CCAATGGTGAGTGCAAGAGAA 58.493 47.619 0.00 0.00 0.00 2.87
187 190 1.271543 CCCAATGGTGAGTGCAAGAGA 60.272 52.381 0.00 0.00 0.00 3.10
188 191 1.171308 CCCAATGGTGAGTGCAAGAG 58.829 55.000 0.00 0.00 0.00 2.85
189 192 0.478072 ACCCAATGGTGAGTGCAAGA 59.522 50.000 0.00 0.00 45.58 3.02
224 227 1.480954 TCTATTCGGAGCCCTTCACAC 59.519 52.381 0.00 0.00 0.00 3.82
507 516 7.969536 ATTCTTCTGTATGGATACCAAATCG 57.030 36.000 0.00 0.00 36.95 3.34
702 722 7.645340 GGATAAACTTCAATGTATGTGATGTGC 59.355 37.037 0.00 0.00 34.60 4.57
734 755 1.726791 CGAGAGAGATAGAGAGCGAGC 59.273 57.143 0.00 0.00 0.00 5.03
738 759 4.893424 ACAAACGAGAGAGATAGAGAGC 57.107 45.455 0.00 0.00 0.00 4.09
745 788 4.238514 GTGCAACTACAAACGAGAGAGAT 58.761 43.478 0.00 0.00 0.00 2.75
819 862 2.797156 CCACATCTCATCGATCCGTTTC 59.203 50.000 0.00 0.00 0.00 2.78
1061 1105 3.754965 TCAACCTCAACCTCAATGGAAG 58.245 45.455 0.00 0.00 39.71 3.46
1067 1111 1.518367 ACCCTCAACCTCAACCTCAA 58.482 50.000 0.00 0.00 0.00 3.02
1068 1112 2.257207 CTACCCTCAACCTCAACCTCA 58.743 52.381 0.00 0.00 0.00 3.86
1069 1113 1.066071 GCTACCCTCAACCTCAACCTC 60.066 57.143 0.00 0.00 0.00 3.85
1070 1114 0.984995 GCTACCCTCAACCTCAACCT 59.015 55.000 0.00 0.00 0.00 3.50
1071 1115 0.690762 TGCTACCCTCAACCTCAACC 59.309 55.000 0.00 0.00 0.00 3.77
1072 1116 1.348036 ACTGCTACCCTCAACCTCAAC 59.652 52.381 0.00 0.00 0.00 3.18
1106 1150 7.517575 GCTGTTAAGTTCTCTTCTCTTGAACAC 60.518 40.741 0.00 0.00 41.56 3.32
1184 1228 4.079253 GGAACCAAGAAGTAGAATGCCAA 58.921 43.478 0.00 0.00 0.00 4.52
1237 1281 4.761975 ACCAGTTTTTGTTAGAGACGTGA 58.238 39.130 0.00 0.00 0.00 4.35
1241 1285 7.215085 TCTTAGGACCAGTTTTTGTTAGAGAC 58.785 38.462 0.00 0.00 0.00 3.36
1247 1291 6.379988 ACAACATCTTAGGACCAGTTTTTGTT 59.620 34.615 0.00 0.00 0.00 2.83
1343 1388 1.569030 ATCCATGGCACCTGCTCACT 61.569 55.000 6.96 0.00 41.70 3.41
1368 1413 3.487372 ACCTTTGGCTTAGGAGTGTTTC 58.513 45.455 11.61 0.00 36.58 2.78
1410 1455 5.943416 CACTACCATACATCTTTTCCACCAA 59.057 40.000 0.00 0.00 0.00 3.67
1411 1456 5.249622 TCACTACCATACATCTTTTCCACCA 59.750 40.000 0.00 0.00 0.00 4.17
1456 1501 3.572255 TGCTGTAAACACCCTTCAAATCC 59.428 43.478 0.00 0.00 0.00 3.01
1629 1676 4.962362 TCACAGAATCTCTATAGGTGCCAA 59.038 41.667 0.00 0.00 0.00 4.52
1647 1694 5.238650 AGGAAGTAACCGAAACAATTCACAG 59.761 40.000 0.00 0.00 35.15 3.66
1681 1731 2.880890 GTTGCACTCTCCACACTTTGAT 59.119 45.455 0.00 0.00 0.00 2.57
1761 1811 8.831550 CCCAAAGAACTAACAAATCTAGCTATC 58.168 37.037 0.00 0.00 0.00 2.08
1803 1853 5.093457 TCAAACTTTCGATAGCTGAGTACG 58.907 41.667 2.50 0.00 0.00 3.67
1817 1867 6.907212 CGCTGTATCACCATAATCAAACTTTC 59.093 38.462 0.00 0.00 0.00 2.62
1955 2006 2.165641 ACATTCACCGCGTCATCTTCTA 59.834 45.455 4.92 0.00 0.00 2.10
1974 2025 0.321919 GAGCCATCCTTGCACTGACA 60.322 55.000 0.00 0.00 0.00 3.58
2057 2108 4.241555 CCCGGGATGCGCTAGCTT 62.242 66.667 18.48 0.00 45.42 3.74
2068 2119 0.768622 ATGAAAGTTGTGACCCGGGA 59.231 50.000 32.02 1.07 0.00 5.14
2241 2292 5.918576 GCCACGCCCAACTTTTATTAATATC 59.081 40.000 0.00 0.00 0.00 1.63
2326 2377 0.834612 AGACAACGTTGGGTGGAAGA 59.165 50.000 30.34 0.00 0.00 2.87
2384 2435 6.767423 TCAATGACAACAACATATCGATGGAT 59.233 34.615 8.54 0.00 37.39 3.41
2394 2445 6.949352 AAGAGAAGTCAATGACAACAACAT 57.051 33.333 16.38 0.00 34.60 2.71
2395 2446 7.520453 GCATAAGAGAAGTCAATGACAACAACA 60.520 37.037 16.38 0.00 34.60 3.33
2438 2489 2.361610 GGTGGCATCAGTGGTGGG 60.362 66.667 5.34 0.00 0.00 4.61
2461 2512 0.916358 AACTGCTGCTAGGGGTGGAT 60.916 55.000 0.00 0.00 0.00 3.41
2484 2535 1.801771 CGACTAAAATTGACACCCGCA 59.198 47.619 0.00 0.00 0.00 5.69
2527 2578 4.137543 GTGAAGAAGAGGAAGAAAAGGCA 58.862 43.478 0.00 0.00 0.00 4.75
2559 2610 3.056749 GGACGGAGACATACAACTCAAGT 60.057 47.826 0.00 0.00 35.17 3.16
2578 2629 1.068127 ACGTATGATTGTAGGGCGGAC 59.932 52.381 0.00 0.00 0.00 4.79
2579 2630 1.338973 GACGTATGATTGTAGGGCGGA 59.661 52.381 0.00 0.00 0.00 5.54
2601 2652 7.915293 TGGTTTTAATAAGCGAGAGATTCAA 57.085 32.000 0.00 0.00 39.99 2.69
2659 2710 8.754991 TCTGGTTTTGTTCACTAATCCTTTAA 57.245 30.769 3.82 0.00 0.00 1.52
2680 2731 7.678947 ACTAATCTTTGTCATCAAGTTCTGG 57.321 36.000 0.00 0.00 34.88 3.86
2724 2775 5.053286 CGTTTTTGTTACAGTTTTGAGCTCG 60.053 40.000 9.64 0.00 0.00 5.03
2746 2797 0.611200 TATTGGCCACTAGTGTGCGT 59.389 50.000 21.18 14.34 42.54 5.24
2784 2835 5.534654 ACCTTGATGCAGTTTGCTACTTAAA 59.465 36.000 2.48 0.00 45.31 1.52
2832 2883 0.168128 GCTGTCGTATTTGCCGCTTT 59.832 50.000 0.00 0.00 0.00 3.51
2844 2895 3.414136 TTGGGGCAGTTGCTGTCGT 62.414 57.895 3.88 0.00 36.90 4.34
3054 3105 9.762933 ACATGAATAGTTATTTTTGTTTGCAGT 57.237 25.926 0.00 0.00 0.00 4.40
3137 3188 8.892723 TGAAATACATGACGCTTTTAAGATCAT 58.107 29.630 0.00 0.00 35.21 2.45
3169 3220 9.774413 TTGTTTTCACCTTTTGTTACCTTTTTA 57.226 25.926 0.00 0.00 0.00 1.52
3212 3263 6.154534 TGTTAGTTGTGCTCACATACTAGGAT 59.845 38.462 16.58 0.00 41.52 3.24


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

AutoCloner maintained by Alex Coulton.