Multiple sequence alignment - TraesCS4A01G132400

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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 TraesCS4A01G132400 chr4A 100.000 2237 0 0 1 2237 178372152 178374388 0.000000e+00 4132
1 TraesCS4A01G132400 chr4A 94.595 148 8 0 1 148 527578518 527578371 1.730000e-56 230
2 TraesCS4A01G132400 chr4D 91.289 2273 114 36 1 2237 301955348 301953124 0.000000e+00 3024
3 TraesCS4A01G132400 chr4B 91.906 1112 59 11 506 1600 376426422 376425325 0.000000e+00 1526
4 TraesCS4A01G132400 chr4B 87.624 404 23 6 1 378 376426823 376426421 5.670000e-121 444
5 TraesCS4A01G132400 chr4B 89.385 179 8 3 2043 2210 376425110 376424932 4.840000e-52 215
6 TraesCS4A01G132400 chr6A 80.669 538 72 19 850 1363 67646413 67646942 2.690000e-104 388
7 TraesCS4A01G132400 chr6B 96.622 148 5 0 1 148 578014884 578015031 1.720000e-61 246
8 TraesCS4A01G132400 chr6B 94.595 148 8 0 1 148 101245330 101245183 1.730000e-56 230
9 TraesCS4A01G132400 chr6B 80.370 270 39 9 850 1108 123915404 123915670 2.270000e-45 193
10 TraesCS4A01G132400 chr3B 95.862 145 6 0 4 148 52857586 52857442 3.710000e-58 235
11 TraesCS4A01G132400 chr3A 95.270 148 7 0 1 148 486214558 486214411 3.710000e-58 235
12 TraesCS4A01G132400 chr2B 95.862 145 6 0 1 145 182355559 182355703 3.710000e-58 235
13 TraesCS4A01G132400 chr1B 95.270 148 7 0 1 148 83210717 83210570 3.710000e-58 235
14 TraesCS4A01G132400 chr1B 95.172 145 7 0 1 145 188443776 188443920 1.730000e-56 230
15 TraesCS4A01G132400 chr3D 95.139 144 7 0 1 144 75769078 75768935 6.210000e-56 228


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 TraesCS4A01G132400 chr4A 178372152 178374388 2236 False 4132.000000 4132 100.000000 1 2237 1 chr4A.!!$F1 2236
1 TraesCS4A01G132400 chr4D 301953124 301955348 2224 True 3024.000000 3024 91.289000 1 2237 1 chr4D.!!$R1 2236
2 TraesCS4A01G132400 chr4B 376424932 376426823 1891 True 728.333333 1526 89.638333 1 2210 3 chr4B.!!$R1 2209
3 TraesCS4A01G132400 chr6A 67646413 67646942 529 False 388.000000 388 80.669000 850 1363 1 chr6A.!!$F1 513

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
546 575 0.252375 AAATGGGCCCTGTGCTTCAT 60.252 50.0 25.7 1.42 40.92 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1438 1509 0.24912 TGGTAGCGCAAGTGCATACT 59.751 50.0 11.47 0.28 42.21 2.12 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
33 34 3.974719 TCAGTGCCCATGCCTTTATTAA 58.025 40.909 0.00 0.00 36.33 1.40
65 75 8.484214 AATCTGTGCTGAGTTTATATAGAGGA 57.516 34.615 0.00 0.00 0.00 3.71
179 197 4.724279 AACAACCATCAAAGTCTAGGGT 57.276 40.909 0.00 0.00 0.00 4.34
180 198 5.836024 AACAACCATCAAAGTCTAGGGTA 57.164 39.130 0.00 0.00 0.00 3.69
185 204 7.827729 ACAACCATCAAAGTCTAGGGTATTAAC 59.172 37.037 0.00 0.00 0.00 2.01
224 244 7.489435 TCAAGACTGATAGTAAGCTTGAATTCG 59.511 37.037 9.86 1.50 36.14 3.34
243 263 2.095110 TCGATAAGCCGAAACGAACAGA 60.095 45.455 0.00 0.00 35.42 3.41
289 317 5.462729 GGCTTCTCGCTACCTTAGTTTATTC 59.537 44.000 0.00 0.00 39.13 1.75
293 321 5.601313 TCTCGCTACCTTAGTTTATTCCCAT 59.399 40.000 0.00 0.00 0.00 4.00
327 355 4.503910 AGCCTGTTTTTGGAACTTCAAAC 58.496 39.130 0.00 0.00 36.49 2.93
359 387 5.776716 ACCAGTCAAACATCCATCTGATTTT 59.223 36.000 0.00 0.00 0.00 1.82
411 439 2.799126 TGCCTGGATTGTAATTCGGT 57.201 45.000 0.00 0.00 0.00 4.69
430 459 3.616560 CGGTCTGCTCTAGCCTTTTTGTA 60.617 47.826 0.00 0.00 41.18 2.41
459 488 8.084985 TGTGAACAATTGAGTCCTACCATATA 57.915 34.615 13.59 0.00 0.00 0.86
487 516 8.547967 TCTTCATTGTTACCAATCTCAGTTAC 57.452 34.615 0.00 0.00 39.28 2.50
545 574 0.471591 AAAATGGGCCCTGTGCTTCA 60.472 50.000 25.70 0.00 40.92 3.02
546 575 0.252375 AAATGGGCCCTGTGCTTCAT 60.252 50.000 25.70 1.42 40.92 2.57
548 577 2.036256 GGGCCCTGTGCTTCATGT 59.964 61.111 17.04 0.00 40.92 3.21
560 589 0.753111 CTTCATGTTAGGCCTGCCCC 60.753 60.000 17.99 0.16 36.58 5.80
561 590 1.214305 TTCATGTTAGGCCTGCCCCT 61.214 55.000 17.99 0.00 39.05 4.79
571 600 2.363795 CTGCCCCTCTGGTACGGA 60.364 66.667 0.00 0.00 44.24 4.69
589 618 1.152546 AACCCTGGTTTGCAGTCCC 60.153 57.895 0.00 0.00 34.22 4.46
602 631 0.698238 CAGTCCCTGGATTGTTCCCA 59.302 55.000 0.00 0.00 41.83 4.37
650 680 4.237018 TCCCTAGTTGTTCATATACCCCC 58.763 47.826 0.00 0.00 0.00 5.40
668 698 3.490348 CCCCAGTGTGAATTTCTCAGTT 58.510 45.455 6.15 0.00 33.60 3.16
672 702 4.741676 CCAGTGTGAATTTCTCAGTTTTGC 59.258 41.667 6.15 0.00 33.60 3.68
703 734 4.574674 TTCCTAGTGATGGTTTGCTCAT 57.425 40.909 0.00 0.00 0.00 2.90
819 851 2.785269 TGGGCCTGATGGAAGTCATAAT 59.215 45.455 4.53 0.00 35.97 1.28
849 881 7.554835 TGTGTTAGTGTATTTTCTTGTCCAGTT 59.445 33.333 0.00 0.00 0.00 3.16
891 923 8.206325 AGATGATGTTACTTTGCTATGTTGAG 57.794 34.615 0.00 0.00 0.00 3.02
898 930 4.655963 ACTTTGCTATGTTGAGTCCATGT 58.344 39.130 0.00 0.00 0.00 3.21
930 966 9.941664 GAATTGTCTATTGGTTCAGTTATGATG 57.058 33.333 0.00 0.00 34.73 3.07
931 967 7.864108 TTGTCTATTGGTTCAGTTATGATGG 57.136 36.000 0.00 0.00 34.73 3.51
939 985 4.323485 GGTTCAGTTATGATGGTCTGGTGA 60.323 45.833 0.00 0.00 34.73 4.02
962 1008 3.417101 TGGTGGCACATAAGTACCAAAG 58.583 45.455 20.82 0.00 42.73 2.77
1336 1405 2.560504 TGTTCACGCTGACTTGAATGT 58.439 42.857 0.00 0.00 36.56 2.71
1337 1406 2.287644 TGTTCACGCTGACTTGAATGTG 59.712 45.455 0.00 0.00 36.56 3.21
1338 1407 1.511850 TCACGCTGACTTGAATGTGG 58.488 50.000 0.00 0.00 0.00 4.17
1438 1509 1.702401 TCTGTTGCTATTGGTGTGGGA 59.298 47.619 0.00 0.00 0.00 4.37
1457 1528 0.249120 AGTATGCACTTGCGCTACCA 59.751 50.000 9.73 0.00 45.83 3.25
1503 1574 6.255020 AGTCTAATTTAAACATCGGTACTGCG 59.745 38.462 0.00 0.00 0.00 5.18
1505 1576 5.616488 AATTTAAACATCGGTACTGCGTT 57.384 34.783 0.00 0.12 0.00 4.84
1513 1584 1.000827 TCGGTACTGCGTTCGGTTAAA 60.001 47.619 0.00 0.00 33.08 1.52
1572 1643 5.010213 AGTTTTGCCTTATTTGCCGTCTTAA 59.990 36.000 0.00 0.00 0.00 1.85
1585 1656 6.176975 TGCCGTCTTAATTGTTGATTGTAG 57.823 37.500 0.00 0.00 0.00 2.74
1586 1657 5.703592 TGCCGTCTTAATTGTTGATTGTAGT 59.296 36.000 0.00 0.00 0.00 2.73
1587 1658 6.874664 TGCCGTCTTAATTGTTGATTGTAGTA 59.125 34.615 0.00 0.00 0.00 1.82
1641 1712 5.231265 AGTCTCTTGTTTTCGGTTGTTTC 57.769 39.130 0.00 0.00 0.00 2.78
1651 1722 2.993937 TCGGTTGTTTCTGTGAAGGTT 58.006 42.857 0.00 0.00 0.00 3.50
1779 1853 3.894759 AGGATGATTGACCCATTCACAG 58.105 45.455 0.00 0.00 32.26 3.66
1803 1877 1.832883 TGTGTTGCAAGTTGGACAGT 58.167 45.000 0.00 0.00 0.00 3.55
1808 1882 1.388547 TGCAAGTTGGACAGTGGTTC 58.611 50.000 4.75 0.00 0.00 3.62
1839 1913 4.488126 TTGTCAGACAAAAGTATGCTGC 57.512 40.909 13.90 0.00 34.76 5.25
1840 1914 3.743521 TGTCAGACAAAAGTATGCTGCT 58.256 40.909 0.00 0.00 0.00 4.24
1841 1915 3.499537 TGTCAGACAAAAGTATGCTGCTG 59.500 43.478 0.00 0.00 0.00 4.41
1878 1952 7.701539 TGTGTTCCTTTATTCACATGCTTAT 57.298 32.000 0.00 0.00 36.17 1.73
1883 1957 9.503427 GTTCCTTTATTCACATGCTTATTACAC 57.497 33.333 0.00 0.00 0.00 2.90
1884 1958 9.461312 TTCCTTTATTCACATGCTTATTACACT 57.539 29.630 0.00 0.00 0.00 3.55
1885 1959 9.461312 TCCTTTATTCACATGCTTATTACACTT 57.539 29.630 0.00 0.00 0.00 3.16
1925 1999 9.920946 ATTAGTGTTGTATTTTGATCTGGGTAT 57.079 29.630 0.00 0.00 0.00 2.73
1927 2001 8.281212 AGTGTTGTATTTTGATCTGGGTATTC 57.719 34.615 0.00 0.00 0.00 1.75
1928 2002 7.065803 AGTGTTGTATTTTGATCTGGGTATTCG 59.934 37.037 0.00 0.00 0.00 3.34
1932 2006 5.695851 ATTTTGATCTGGGTATTCGCATC 57.304 39.130 0.00 0.00 36.01 3.91
1961 2035 3.558505 CTGCGACTGTTTTCTTGAATGG 58.441 45.455 0.00 0.00 0.00 3.16
1964 2038 4.097135 TGCGACTGTTTTCTTGAATGGAAA 59.903 37.500 0.00 0.00 0.00 3.13
2001 2075 1.853963 TCTGGCACCTTCCTCTAGTC 58.146 55.000 0.00 0.00 0.00 2.59
2075 2150 5.881447 ACGTGTGTATCTGTACATTCTCTC 58.119 41.667 0.00 0.00 42.43 3.20
2076 2151 5.414765 ACGTGTGTATCTGTACATTCTCTCA 59.585 40.000 0.00 0.00 42.43 3.27
2077 2152 6.072119 ACGTGTGTATCTGTACATTCTCTCAA 60.072 38.462 0.00 0.00 42.43 3.02
2078 2153 6.470556 CGTGTGTATCTGTACATTCTCTCAAG 59.529 42.308 0.00 0.00 42.43 3.02
2135 2218 4.029418 CGTACAAATTTCTTTGCATGAGCG 59.971 41.667 0.00 0.00 44.63 5.03
2170 2259 6.037172 GCTAACATTATTATATCCAGGCCACG 59.963 42.308 5.01 0.00 0.00 4.94
2207 2296 8.891671 AGTATGTAGTAGTAGTAGAAGCAGTC 57.108 38.462 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 54 6.704493 TGCCGTTGTCATTCCTCTATATAAAC 59.296 38.462 0.00 0.00 0.00 2.01
63 73 0.521735 GGTCTTGCCGTTGTCATTCC 59.478 55.000 0.00 0.00 0.00 3.01
65 75 1.234615 CGGGTCTTGCCGTTGTCATT 61.235 55.000 0.00 0.00 38.44 2.57
160 178 7.282450 GGTTAATACCCTAGACTTTGATGGTTG 59.718 40.741 0.00 0.00 38.60 3.77
161 179 7.037153 TGGTTAATACCCTAGACTTTGATGGTT 60.037 37.037 0.00 0.00 44.35 3.67
179 197 6.017440 GTCTTGAGTGTGCAAAGTGGTTAATA 60.017 38.462 0.00 0.00 0.00 0.98
180 198 4.887071 TCTTGAGTGTGCAAAGTGGTTAAT 59.113 37.500 0.00 0.00 0.00 1.40
185 204 2.032550 CAGTCTTGAGTGTGCAAAGTGG 59.967 50.000 0.00 0.00 0.00 4.00
224 244 4.657075 TTTCTGTTCGTTTCGGCTTATC 57.343 40.909 0.00 0.00 0.00 1.75
250 270 4.134563 GAGAAGCCCTGACAAACTGTTTA 58.865 43.478 5.31 0.00 0.00 2.01
256 276 1.869690 GCGAGAAGCCCTGACAAAC 59.130 57.895 0.00 0.00 40.81 2.93
289 317 3.244561 ACAGGCTTATGGATTACGATGGG 60.245 47.826 0.00 0.00 0.00 4.00
293 321 5.124776 CCAAAAACAGGCTTATGGATTACGA 59.875 40.000 0.00 0.00 0.00 3.43
327 355 1.530655 GTTTGACTGGTGGTGGGGG 60.531 63.158 0.00 0.00 0.00 5.40
359 387 1.816224 GCTTACCGGCAAAAGGAATCA 59.184 47.619 0.00 0.00 0.00 2.57
411 439 3.941483 GCATACAAAAAGGCTAGAGCAGA 59.059 43.478 3.54 0.00 44.36 4.26
430 459 3.759581 AGGACTCAATTGTTCACAGCAT 58.240 40.909 5.13 0.00 0.00 3.79
487 516 6.582636 TGCTATTTGTAGTATCACTTCAGGG 58.417 40.000 0.00 0.00 27.41 4.45
545 574 1.308216 AGAGGGGCAGGCCTAACAT 60.308 57.895 13.81 0.00 36.10 2.71
546 575 2.124996 AGAGGGGCAGGCCTAACA 59.875 61.111 13.81 0.00 36.10 2.41
548 577 2.189558 TACCAGAGGGGCAGGCCTAA 62.190 60.000 13.81 0.00 42.05 2.69
571 600 1.152546 GGGACTGCAAACCAGGGTT 60.153 57.895 10.35 0.00 46.14 4.11
650 680 5.585390 AGCAAAACTGAGAAATTCACACTG 58.415 37.500 0.00 0.00 0.00 3.66
668 698 6.121776 TCACTAGGAAATAAGGTGAGCAAA 57.878 37.500 0.00 0.00 33.74 3.68
672 702 6.240549 ACCATCACTAGGAAATAAGGTGAG 57.759 41.667 0.00 0.00 39.70 3.51
703 734 1.227527 CGTCGCAGGAATGCCCATA 60.228 57.895 0.00 0.00 37.41 2.74
770 802 8.382030 TGTGGCACTAGAATGTTAATGATATG 57.618 34.615 19.83 0.00 0.00 1.78
806 838 9.330063 CACTAACACATACATTATGACTTCCAT 57.670 33.333 0.00 0.00 39.45 3.41
819 851 8.995220 GGACAAGAAAATACACTAACACATACA 58.005 33.333 0.00 0.00 0.00 2.29
930 966 2.032681 GCCACCAGTCACCAGACC 59.967 66.667 0.00 0.00 46.15 3.85
931 967 1.598130 GTGCCACCAGTCACCAGAC 60.598 63.158 0.00 0.00 45.31 3.51
939 985 2.781681 GGTACTTATGTGCCACCAGT 57.218 50.000 10.48 0.00 46.34 4.00
992 1038 1.555075 TCCACAAGCCCATCTCTGTAC 59.445 52.381 0.00 0.00 0.00 2.90
1167 1217 0.827507 AGGGCATCCGCAAAAACTGT 60.828 50.000 0.00 0.00 41.24 3.55
1268 1330 9.573166 TGATTAGCTTTTACATAATGCTGGTAT 57.427 29.630 0.00 1.03 35.47 2.73
1270 1332 7.880160 TGATTAGCTTTTACATAATGCTGGT 57.120 32.000 0.00 0.00 35.47 4.00
1438 1509 0.249120 TGGTAGCGCAAGTGCATACT 59.751 50.000 11.47 0.28 42.21 2.12
1457 1528 7.114754 AGACTGAACATTTACATGGTGATCAT 58.885 34.615 0.00 0.00 34.27 2.45
1503 1574 6.183360 CCACCAGATAATGTCTTTAACCGAAC 60.183 42.308 0.00 0.00 34.00 3.95
1505 1576 5.424757 CCACCAGATAATGTCTTTAACCGA 58.575 41.667 0.00 0.00 34.00 4.69
1513 1584 3.370953 GGTTCTGCCACCAGATAATGTCT 60.371 47.826 0.00 0.00 46.84 3.41
1539 1610 7.095649 GGCAAATAAGGCAAAACTACAGAAAAG 60.096 37.037 0.00 0.00 0.00 2.27
1585 1656 8.712228 AATGATTCCCAAGGAAAAGGATATAC 57.288 34.615 0.00 0.00 45.41 1.47
1586 1657 9.728100 AAAATGATTCCCAAGGAAAAGGATATA 57.272 29.630 0.00 0.00 45.41 0.86
1587 1658 8.488668 CAAAATGATTCCCAAGGAAAAGGATAT 58.511 33.333 0.00 0.00 45.41 1.63
1662 1733 8.723311 GCACAATGTATACAGTACTAAACCAAA 58.277 33.333 11.91 0.00 0.00 3.28
1663 1734 8.098286 AGCACAATGTATACAGTACTAAACCAA 58.902 33.333 11.91 0.00 0.00 3.67
1664 1735 7.547722 CAGCACAATGTATACAGTACTAAACCA 59.452 37.037 11.91 0.00 0.00 3.67
1665 1736 7.011109 CCAGCACAATGTATACAGTACTAAACC 59.989 40.741 11.91 0.00 0.00 3.27
1666 1737 7.465513 GCCAGCACAATGTATACAGTACTAAAC 60.466 40.741 11.91 0.00 0.00 2.01
1667 1738 6.537301 GCCAGCACAATGTATACAGTACTAAA 59.463 38.462 11.91 0.00 0.00 1.85
1668 1739 6.046593 GCCAGCACAATGTATACAGTACTAA 58.953 40.000 11.91 0.00 0.00 2.24
1708 1782 3.951775 TGAGAAGCTCAGGAAGAGTTC 57.048 47.619 0.00 0.00 46.47 3.01
1779 1853 4.180057 TGTCCAACTTGCAACACAAAATC 58.820 39.130 0.00 0.00 37.96 2.17
1803 1877 1.199327 TGACAAACAAAACGCGAACCA 59.801 42.857 15.93 0.00 0.00 3.67
1808 1882 2.166741 TGTCTGACAAACAAAACGCG 57.833 45.000 8.27 3.53 0.00 6.01
1835 1909 0.316204 AAAATCCTGTGTGCAGCAGC 59.684 50.000 11.57 0.00 41.26 5.25
1836 1910 1.338973 ACAAAATCCTGTGTGCAGCAG 59.661 47.619 0.00 10.38 41.26 4.24
1837 1911 1.067364 CACAAAATCCTGTGTGCAGCA 59.933 47.619 0.00 0.00 41.52 4.41
1838 1912 1.774639 CACAAAATCCTGTGTGCAGC 58.225 50.000 0.00 0.00 41.52 5.25
1857 1931 9.503427 GTGTAATAAGCATGTGAATAAAGGAAC 57.497 33.333 0.00 0.00 0.00 3.62
1883 1957 9.915629 ACAACACTAATTACAAGACTAGAGAAG 57.084 33.333 0.00 0.00 0.00 2.85
1902 1976 7.065803 CGAATACCCAGATCAAAATACAACACT 59.934 37.037 0.00 0.00 0.00 3.55
1917 1991 4.631131 CTGTTATGATGCGAATACCCAGA 58.369 43.478 0.00 0.00 0.00 3.86
1928 2002 1.004185 CAGTCGCAGCTGTTATGATGC 60.004 52.381 16.64 0.00 44.76 3.91
1961 2035 8.131731 GCCAGATGAGTAAATGTCCTAATTTTC 58.868 37.037 0.00 0.00 32.16 2.29
1964 2038 6.543831 GTGCCAGATGAGTAAATGTCCTAATT 59.456 38.462 0.00 0.00 0.00 1.40
2001 2075 4.156008 GTGGGTATGTTAAGGTTCAGCTTG 59.844 45.833 1.40 0.00 0.00 4.01
2075 2150 1.068474 GAATGCAGCTTGCTTGCTTG 58.932 50.000 14.43 0.52 45.31 4.01
2076 2151 0.677288 TGAATGCAGCTTGCTTGCTT 59.323 45.000 14.43 8.28 45.31 3.91
2077 2152 0.895530 ATGAATGCAGCTTGCTTGCT 59.104 45.000 14.43 0.00 45.31 3.91
2078 2153 1.393539 CAATGAATGCAGCTTGCTTGC 59.606 47.619 9.12 9.09 45.31 4.01
2135 2218 9.250624 GATATAATAATGTTAGCATCCGTCCTC 57.749 37.037 0.00 0.00 33.50 3.71
2170 2259 7.571080 ACTACTACATACTAAGAGAGGCAAC 57.429 40.000 0.00 0.00 0.00 4.17
2207 2296 2.554032 CCTCACCTTAACCAAAGTGCAG 59.446 50.000 0.00 0.00 32.89 4.41


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

AutoCloner maintained by Alex Coulton.