Multiple sequence alignment - TraesCS4D01G167000

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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 TraesCS4D01G167000 chr4D 100.000 2610 0 0 1 2610 285094155 285096764 0 4820
1 TraesCS4D01G167000 chr4D 95.411 2615 115 5 1 2610 123656012 123653398 0 4159
2 TraesCS4D01G167000 chr4D 95.373 2615 116 5 1 2610 123509313 123506699 0 4154
3 TraesCS4D01G167000 chr4D 95.302 2618 113 9 1 2610 123738810 123736195 0 4145
4 TraesCS4D01G167000 chr7D 95.224 2617 115 8 1 2610 579028568 579031181 0 4132
5 TraesCS4D01G167000 chr6D 95.031 2616 123 7 1 2610 108466552 108469166 0 4104
6 TraesCS4D01G167000 chr6D 94.205 1484 79 5 1 1478 57920022 57921504 0 2257
7 TraesCS4D01G167000 chrUn 92.433 2630 159 24 1 2610 221549578 221546969 0 3718
8 TraesCS4D01G167000 chrUn 92.393 2629 162 23 1 2610 186192576 186189967 0 3712
9 TraesCS4D01G167000 chr7B 92.097 2632 165 26 1 2610 743004902 743007512 0 3668
10 TraesCS4D01G167000 chr7A 91.629 2628 174 24 1 2610 120879296 120881895 0 3592
11 TraesCS4D01G167000 chr7A 94.258 1463 79 5 1 1459 211291149 211292610 0 2231
12 TraesCS4D01G167000 chr3B 94.054 1480 84 4 1 1478 730160375 730161852 0 2242
13 TraesCS4D01G167000 chr5A 94.266 1465 78 4 1 1459 534932638 534934102 0 2235


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 TraesCS4D01G167000 chr4D 285094155 285096764 2609 False 4820 4820 100.000 1 2610 1 chr4D.!!$F1 2609
1 TraesCS4D01G167000 chr4D 123653398 123656012 2614 True 4159 4159 95.411 1 2610 1 chr4D.!!$R2 2609
2 TraesCS4D01G167000 chr4D 123506699 123509313 2614 True 4154 4154 95.373 1 2610 1 chr4D.!!$R1 2609
3 TraesCS4D01G167000 chr4D 123736195 123738810 2615 True 4145 4145 95.302 1 2610 1 chr4D.!!$R3 2609
4 TraesCS4D01G167000 chr7D 579028568 579031181 2613 False 4132 4132 95.224 1 2610 1 chr7D.!!$F1 2609
5 TraesCS4D01G167000 chr6D 108466552 108469166 2614 False 4104 4104 95.031 1 2610 1 chr6D.!!$F2 2609
6 TraesCS4D01G167000 chr6D 57920022 57921504 1482 False 2257 2257 94.205 1 1478 1 chr6D.!!$F1 1477
7 TraesCS4D01G167000 chrUn 221546969 221549578 2609 True 3718 3718 92.433 1 2610 1 chrUn.!!$R2 2609
8 TraesCS4D01G167000 chrUn 186189967 186192576 2609 True 3712 3712 92.393 1 2610 1 chrUn.!!$R1 2609
9 TraesCS4D01G167000 chr7B 743004902 743007512 2610 False 3668 3668 92.097 1 2610 1 chr7B.!!$F1 2609
10 TraesCS4D01G167000 chr7A 120879296 120881895 2599 False 3592 3592 91.629 1 2610 1 chr7A.!!$F1 2609
11 TraesCS4D01G167000 chr7A 211291149 211292610 1461 False 2231 2231 94.258 1 1459 1 chr7A.!!$F2 1458
12 TraesCS4D01G167000 chr3B 730160375 730161852 1477 False 2242 2242 94.054 1 1478 1 chr3B.!!$F1 1477
13 TraesCS4D01G167000 chr5A 534932638 534934102 1464 False 2235 2235 94.266 1 1459 1 chr5A.!!$F1 1458

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
427 430 1.743996 AAGCTTCTCGAAAGCATCCC 58.256 50.0 24.35 5.15 45.3 3.85 F
1055 1067 0.532115 ATTCAGGAATTTGTGGCGCC 59.468 50.0 22.73 22.73 0.0 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1330 1346 0.947660 TGCTCGTGCTCAGCTCTTTG 60.948 55.000 11.19 0.0 40.48 2.77 R
2429 2458 1.005037 CTGCGGTGAAGTAGGCACA 60.005 57.895 0.00 0.0 37.99 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
71 72 4.647853 AGGGGTGGTTTTCTGTTTACTTTC 59.352 41.667 0.00 0.00 0.00 2.62
119 120 4.758674 CAGAACCTCACAATCATCAGTGTT 59.241 41.667 0.00 0.00 37.07 3.32
149 152 8.253113 AGTTTCATGATGAATATTGGTTTCACC 58.747 33.333 8.90 0.00 36.11 4.02
167 170 6.811253 TTCACCTTTTATTGCTTACGTGAT 57.189 33.333 0.00 0.00 0.00 3.06
188 191 8.183536 CGTGATGAAATATCAATTTGGAACTCA 58.816 33.333 0.00 0.00 39.49 3.41
259 262 4.773323 AGAAAGCGAAGAAAAAGGATGG 57.227 40.909 0.00 0.00 0.00 3.51
271 274 2.834638 AAGGATGGTGCTATGGCTTT 57.165 45.000 1.68 0.00 39.59 3.51
288 291 3.068732 GGCTTTCTTGTGGCTCTTTCTTT 59.931 43.478 0.00 0.00 0.00 2.52
304 307 7.119846 GCTCTTTCTTTTATTGGCTAGTCTCAA 59.880 37.037 0.00 0.00 0.00 3.02
417 420 6.796705 TTAGGTAAAAGGAAAAGCTTCTCG 57.203 37.500 0.00 0.00 0.00 4.04
427 430 1.743996 AAGCTTCTCGAAAGCATCCC 58.256 50.000 24.35 5.15 45.30 3.85
448 451 6.464222 TCCCGAAATATCATAGAATGGTGAC 58.536 40.000 0.00 0.00 0.00 3.67
476 479 2.434336 CACCTTCACGGGAATCATCCTA 59.566 50.000 0.00 0.00 45.77 2.94
540 543 8.265165 AGTTCCCGAAACTTGATTTAGTATTC 57.735 34.615 0.00 0.00 46.26 1.75
551 554 9.442047 ACTTGATTTAGTATTCAGGTTCTTCTG 57.558 33.333 0.00 0.00 28.89 3.02
557 560 6.187727 AGTATTCAGGTTCTTCTGTTCCAA 57.812 37.500 0.00 0.00 36.25 3.53
612 616 2.334023 GGCCCCTCTCTGATAAGTCAT 58.666 52.381 0.00 0.00 32.98 3.06
619 623 5.521735 CCCTCTCTGATAAGTCATGTTTTCG 59.478 44.000 0.00 0.00 32.98 3.46
642 648 5.835151 CGAAACGAAAAGCAAATGACAAATG 59.165 36.000 0.00 0.00 0.00 2.32
679 685 3.700538 TCTCCACTACCCGCTTTACTAA 58.299 45.455 0.00 0.00 0.00 2.24
815 825 7.648142 TCAATCTTTTTAGTTCGTGCTTCATT 58.352 30.769 0.00 0.00 0.00 2.57
828 838 2.174360 GCTTCATTGGCTCCTCCTTTT 58.826 47.619 0.00 0.00 35.26 2.27
917 928 5.654603 TTTGAGTCTTTACGAGCAGGATA 57.345 39.130 0.00 0.00 0.00 2.59
918 929 5.854010 TTGAGTCTTTACGAGCAGGATAT 57.146 39.130 0.00 0.00 0.00 1.63
930 941 3.330701 GAGCAGGATATGGGATGGGTTAA 59.669 47.826 0.00 0.00 0.00 2.01
940 951 5.004361 TGGGATGGGTTAAGTTCATTCAA 57.996 39.130 0.00 0.00 0.00 2.69
948 959 5.506649 GGGTTAAGTTCATTCAAAACGAGCA 60.507 40.000 0.00 0.00 0.00 4.26
1025 1037 5.181748 GGAAGAAAAGCTCTCTTCTATGCA 58.818 41.667 25.97 0.00 45.42 3.96
1027 1039 6.150140 GGAAGAAAAGCTCTCTTCTATGCAAA 59.850 38.462 25.97 0.00 45.42 3.68
1055 1067 0.532115 ATTCAGGAATTTGTGGCGCC 59.468 50.000 22.73 22.73 0.00 6.53
1070 1082 2.500098 TGGCGCCTTATCAAAGAGTAGT 59.500 45.455 29.70 0.00 34.37 2.73
1072 1084 3.430374 GGCGCCTTATCAAAGAGTAGTGA 60.430 47.826 22.15 0.00 34.37 3.41
1161 1177 5.504665 CGCAACTGATTCTTTCACTGTTCTT 60.505 40.000 0.00 0.00 0.00 2.52
1183 1199 5.330455 TCAAGCGTCTTATCAAGATCTGT 57.670 39.130 0.00 0.00 40.18 3.41
1222 1238 6.603201 AGGATCCATTTTCTTTCGAAATGCTA 59.397 34.615 15.82 0.00 38.81 3.49
1284 1300 1.003233 GAGGTGCCTGGAAGTGGAC 60.003 63.158 0.00 0.00 0.00 4.02
1330 1346 1.163554 CAAGAGCAAGGCAAGTCTCC 58.836 55.000 0.00 0.00 0.00 3.71
1447 1473 0.405585 CTTTTCTCTTCCAGCCCCCA 59.594 55.000 0.00 0.00 0.00 4.96
1569 1595 8.466617 TCTTCTCTACTAACCACAAGGATATC 57.533 38.462 0.00 0.00 38.69 1.63
1580 1606 3.005261 CACAAGGATATCGGGACTCTCTG 59.995 52.174 0.00 0.00 0.00 3.35
1591 1617 3.056536 CGGGACTCTCTGTTTCATCTTCA 60.057 47.826 0.00 0.00 0.00 3.02
1632 1658 1.136305 GGCACATGCTTCTCCGTACTA 59.864 52.381 3.48 0.00 41.70 1.82
1637 1663 5.352284 CACATGCTTCTCCGTACTAATTCT 58.648 41.667 0.00 0.00 0.00 2.40
1658 1684 1.342672 ATGGAATTAGCCCGACCCGT 61.343 55.000 0.00 0.00 0.00 5.28
1686 1712 6.465948 TCAAATTTTTGGTGGGAATCATCAG 58.534 36.000 3.38 0.00 37.84 2.90
1726 1753 3.196007 CGGCTCACGCTTTTTAATGAA 57.804 42.857 0.00 0.00 36.09 2.57
1750 1777 1.301423 TTTATGGTTATGCCGGCGAC 58.699 50.000 23.90 19.53 41.21 5.19
1785 1812 5.793030 TGGTAATTGGTTTGTTCCGATTT 57.207 34.783 3.92 0.00 40.72 2.17
1787 1814 6.583562 TGGTAATTGGTTTGTTCCGATTTTT 58.416 32.000 3.92 0.00 40.72 1.94
1884 1911 6.651975 TCCTATTAAGCTCAGCCTTAGTAC 57.348 41.667 0.00 0.00 0.00 2.73
1926 1953 2.429610 TGAACAGTCTATCCGCCCTTAC 59.570 50.000 0.00 0.00 0.00 2.34
1958 1985 0.463474 GCCATTCTGGAGGAGCAGTC 60.463 60.000 0.00 0.00 40.96 3.51
1973 2000 4.795278 GGAGCAGTCGATTTAGCAATTTTG 59.205 41.667 0.00 0.00 0.00 2.44
2139 2167 0.968901 ATCACTTCCGGTACTGGCGA 60.969 55.000 16.58 9.76 0.00 5.54
2142 2170 2.283388 TTCCGGTACTGGCGAGGT 60.283 61.111 16.58 0.00 0.00 3.85
2143 2171 1.885163 CTTCCGGTACTGGCGAGGTT 61.885 60.000 16.58 0.00 0.00 3.50
2160 2188 8.832521 TGGCGAGGTTAATTACAATGTTATTAG 58.167 33.333 5.22 0.00 0.00 1.73
2239 2268 7.961326 ATTATACCAGCATCTCTTTTGGTTT 57.039 32.000 0.00 0.00 40.94 3.27
2264 2293 4.899457 TCGGTCATCCAGAGGTGTATATTT 59.101 41.667 0.00 0.00 0.00 1.40
2274 2303 6.769822 CCAGAGGTGTATATTTTCATTCTGCT 59.230 38.462 0.00 0.00 32.30 4.24
2408 2437 7.573710 AGTTTGGGCTCATCATATGTTTACTA 58.426 34.615 1.90 0.00 0.00 1.82
2451 2480 0.105039 GCCTACTTCACCGCAGCTAT 59.895 55.000 0.00 0.00 0.00 2.97
2472 2501 2.374170 TCATGATCATAGCTGTGCCCAT 59.626 45.455 8.15 8.35 0.00 4.00
2527 2556 3.386726 TGTGGGGAGGTTCGATACAATAG 59.613 47.826 0.00 0.00 0.00 1.73
2594 2623 2.503869 AGGAGGGCTCACTGGAATAT 57.496 50.000 0.00 0.00 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 5.008613 TCAACATTCTTTCCACAGCAACTAC 59.991 40.000 0.00 0.00 0.00 2.73
71 72 1.402259 AGAGACGACGTAGGCTGATTG 59.598 52.381 9.45 0.00 0.00 2.67
212 215 6.014242 TCAACAATGTGAATCTACCTCACTCT 60.014 38.462 4.74 0.00 43.03 3.24
259 262 1.135286 GCCACAAGAAAGCCATAGCAC 60.135 52.381 0.00 0.00 43.56 4.40
271 274 5.278957 GCCAATAAAAGAAAGAGCCACAAGA 60.279 40.000 0.00 0.00 0.00 3.02
288 291 5.357742 TCATGCTTGAGACTAGCCAATAA 57.642 39.130 0.00 0.00 37.85 1.40
304 307 8.587608 TCCAAAAGAAATTGAAACTATCATGCT 58.412 29.630 0.00 0.00 38.03 3.79
417 420 7.672983 TTCTATGATATTTCGGGATGCTTTC 57.327 36.000 0.00 0.00 0.00 2.62
427 430 6.156519 TCGGTCACCATTCTATGATATTTCG 58.843 40.000 0.00 0.00 0.00 3.46
448 451 4.814900 CCGTGAAGGTGATCTCGG 57.185 61.111 3.78 3.78 46.16 4.63
476 479 0.417035 TCCCTTCCCCCAATTTGCAT 59.583 50.000 0.00 0.00 0.00 3.96
530 533 8.383175 TGGAACAGAAGAACCTGAATACTAAAT 58.617 33.333 0.00 0.00 37.59 1.40
540 543 2.561569 ACGTTGGAACAGAAGAACCTG 58.438 47.619 0.00 0.00 42.39 4.00
551 554 7.858583 AGAACTTGAATACTAAACGTTGGAAC 58.141 34.615 0.00 0.00 0.00 3.62
557 560 9.194271 GAAGAGAAGAACTTGAATACTAAACGT 57.806 33.333 0.00 0.00 0.00 3.99
619 623 6.624526 CACATTTGTCATTTGCTTTTCGTTTC 59.375 34.615 0.00 0.00 0.00 2.78
642 648 1.646189 GAGAAGAGCCATCGAACCAC 58.354 55.000 0.00 0.00 0.00 4.16
815 825 2.376518 AGTGATCAAAAAGGAGGAGCCA 59.623 45.455 0.00 0.00 40.02 4.75
828 838 0.614697 TCCGGCAGGAGAGTGATCAA 60.615 55.000 0.00 0.00 42.75 2.57
896 907 5.451937 CCATATCCTGCTCGTAAAGACTCAA 60.452 44.000 0.00 0.00 0.00 3.02
917 928 5.205517 TGAATGAACTTAACCCATCCCAT 57.794 39.130 0.00 0.00 0.00 4.00
918 929 4.666412 TGAATGAACTTAACCCATCCCA 57.334 40.909 0.00 0.00 0.00 4.37
930 941 8.511321 TGTTATTATGCTCGTTTTGAATGAACT 58.489 29.630 0.00 0.00 0.00 3.01
940 951 5.533528 GGGGGTATTGTTATTATGCTCGTTT 59.466 40.000 0.00 0.00 0.00 3.60
948 959 6.391649 TGTCTTCCAGGGGGTATTGTTATTAT 59.608 38.462 0.00 0.00 34.93 1.28
953 964 2.354328 TGTCTTCCAGGGGGTATTGTT 58.646 47.619 0.00 0.00 34.93 2.83
1025 1037 7.658575 CCACAAATTCCTGAATGACATCTTTTT 59.341 33.333 0.00 0.00 0.00 1.94
1027 1039 6.694447 CCACAAATTCCTGAATGACATCTTT 58.306 36.000 0.00 0.00 0.00 2.52
1081 1093 0.395311 ACCAAGTAGGGCTCGATCGA 60.395 55.000 18.32 18.32 43.89 3.59
1161 1177 5.105063 CACAGATCTTGATAAGACGCTTGA 58.895 41.667 0.00 0.00 41.01 3.02
1183 1199 1.415126 GGATCCTCCCTCATTCTCCCA 60.415 57.143 3.84 0.00 0.00 4.37
1330 1346 0.947660 TGCTCGTGCTCAGCTCTTTG 60.948 55.000 11.19 0.00 40.48 2.77
1447 1473 2.353349 AGAGAAAAGAAAGAGGGGCCT 58.647 47.619 0.84 0.00 0.00 5.19
1479 1505 3.593780 ACTTTCCTTATCAAAGAGGGGCT 59.406 43.478 0.00 0.00 35.24 5.19
1526 1552 4.346418 AGAAGAGCCATCGAACCATATTCT 59.654 41.667 0.00 0.00 0.00 2.40
1527 1553 4.636249 AGAAGAGCCATCGAACCATATTC 58.364 43.478 0.00 0.00 0.00 1.75
1569 1595 3.056536 TGAAGATGAAACAGAGAGTCCCG 60.057 47.826 0.00 0.00 0.00 5.14
1580 1606 3.248266 GCAATGGCACTGAAGATGAAAC 58.752 45.455 0.00 0.00 40.72 2.78
1637 1663 1.071071 CGGGTCGGGCTAATTCCATAA 59.929 52.381 0.00 0.00 0.00 1.90
1658 1684 5.244851 TGATTCCCACCAAAAATTTGATCGA 59.755 36.000 7.44 0.00 40.55 3.59
1669 1695 2.905415 AGCTGATGATTCCCACCAAA 57.095 45.000 0.00 0.00 0.00 3.28
1686 1712 9.724839 TGAGCCGTTATTAAAACATTATAAAGC 57.275 29.630 0.00 0.00 0.00 3.51
1750 1777 5.130350 ACCAATTACCAAATCCACCTATCG 58.870 41.667 0.00 0.00 0.00 2.92
1785 1812 3.243704 GCCATGTCAGTTGCACCTAAAAA 60.244 43.478 0.00 0.00 0.00 1.94
1787 1814 1.885887 GCCATGTCAGTTGCACCTAAA 59.114 47.619 0.00 0.00 0.00 1.85
1788 1815 1.202867 TGCCATGTCAGTTGCACCTAA 60.203 47.619 0.00 0.00 0.00 2.69
1899 1926 2.893637 CGGATAGACTGTTCACCCAAG 58.106 52.381 0.00 0.00 0.00 3.61
1900 1927 1.066430 GCGGATAGACTGTTCACCCAA 60.066 52.381 0.00 0.00 0.00 4.12
1907 1934 1.407979 CGTAAGGGCGGATAGACTGTT 59.592 52.381 0.00 0.00 0.00 3.16
1926 1953 2.872245 CAGAATGGCTGGTAATACCACG 59.128 50.000 8.27 6.31 44.79 4.94
1958 1985 8.180267 AGATGAAGACTCAAAATTGCTAAATCG 58.820 33.333 0.00 0.00 34.49 3.34
1973 2000 7.113658 TGAAATACCTGGTAGATGAAGACTC 57.886 40.000 12.78 0.00 0.00 3.36
1986 2013 8.971073 AGAACCTAAAATTGATGAAATACCTGG 58.029 33.333 0.00 0.00 0.00 4.45
2024 2051 6.091577 GTCCACACATGTCGAACATAATTGTA 59.908 38.462 0.00 0.00 36.53 2.41
2029 2056 3.007506 AGGTCCACACATGTCGAACATAA 59.992 43.478 0.00 0.00 36.53 1.90
2033 2060 1.148310 CAGGTCCACACATGTCGAAC 58.852 55.000 0.00 0.00 29.27 3.95
2037 2064 2.086869 CATTCCAGGTCCACACATGTC 58.913 52.381 0.00 0.00 32.08 3.06
2043 2070 2.092968 GCATAGTCATTCCAGGTCCACA 60.093 50.000 0.00 0.00 0.00 4.17
2089 2116 3.539604 AGGAATGCTGTCACTAGAATGC 58.460 45.455 0.00 0.00 0.00 3.56
2091 2118 6.552445 AAGTAGGAATGCTGTCACTAGAAT 57.448 37.500 0.00 0.00 0.00 2.40
2139 2167 8.967664 TCGGCTAATAACATTGTAATTAACCT 57.032 30.769 0.00 0.00 0.00 3.50
2160 2188 6.514063 AGGTTGTATTAAAGTCTCTATCGGC 58.486 40.000 0.00 0.00 0.00 5.54
2239 2268 1.348064 ACACCTCTGGATGACCGAAA 58.652 50.000 0.00 0.00 39.42 3.46
2264 2293 6.855763 AATACCAAATCCAAGCAGAATGAA 57.144 33.333 0.00 0.00 39.69 2.57
2360 2389 7.793036 ACTAGAAATCCAAGAACACCTATACC 58.207 38.462 0.00 0.00 0.00 2.73
2408 2437 3.093717 CGTATCAACGTCTAAGCCCAT 57.906 47.619 0.00 0.00 44.21 4.00
2429 2458 1.005037 CTGCGGTGAAGTAGGCACA 60.005 57.895 0.00 0.00 37.99 4.57
2451 2480 1.770061 TGGGCACAGCTATGATCATGA 59.230 47.619 18.72 0.00 0.00 3.07
2472 2501 9.109393 CGATCCAACTAAAGATTTTGATTCCTA 57.891 33.333 0.00 0.00 0.00 2.94
2527 2556 5.296748 ACAGCAAATAACATGGGTGTTTTC 58.703 37.500 0.00 0.00 46.07 2.29


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

AutoCloner maintained by Alex Coulton.