Multiple sequence alignment - TraesCS4D01G118400

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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 TraesCS4D01G118400 chr4D 100.000 2888 0 0 1 2888 98944038 98946925 0.000000e+00 5334.0
1 TraesCS4D01G118400 chr4D 97.727 44 1 0 424 467 508345703 508345660 3.090000e-10 76.8
2 TraesCS4D01G118400 chr4B 96.359 2911 53 15 1 2888 140920395 140923275 0.000000e+00 4739.0
3 TraesCS4D01G118400 chr4A 92.146 2279 152 10 623 2888 477023081 477020817 0.000000e+00 3192.0
4 TraesCS4D01G118400 chr4A 80.614 521 69 19 126 623 477023620 477023109 9.770000e-100 374.0
5 TraesCS4D01G118400 chr1D 94.444 54 0 3 414 464 24780801 24780748 2.390000e-11 80.5
6 TraesCS4D01G118400 chr3B 88.889 63 5 2 414 475 187335716 187335777 3.090000e-10 76.8
7 TraesCS4D01G118400 chr3B 94.000 50 2 1 414 462 700318966 700318917 1.110000e-09 75.0
8 TraesCS4D01G118400 chr3B 92.453 53 1 3 412 461 552477343 552477395 3.990000e-09 73.1
9 TraesCS4D01G118400 chr2A 94.231 52 0 2 424 475 753776405 753776357 3.090000e-10 76.8
10 TraesCS4D01G118400 chr2A 92.453 53 1 3 412 461 608635516 608635568 3.990000e-09 73.1
11 TraesCS4D01G118400 chr7B 94.118 51 0 3 414 461 462238695 462238745 1.110000e-09 75.0
12 TraesCS4D01G118400 chr7B 92.157 51 3 1 425 475 697558540 697558491 1.440000e-08 71.3


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 TraesCS4D01G118400 chr4D 98944038 98946925 2887 False 5334 5334 100.000 1 2888 1 chr4D.!!$F1 2887
1 TraesCS4D01G118400 chr4B 140920395 140923275 2880 False 4739 4739 96.359 1 2888 1 chr4B.!!$F1 2887
2 TraesCS4D01G118400 chr4A 477020817 477023620 2803 True 1783 3192 86.380 126 2888 2 chr4A.!!$R1 2762

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
222 230 0.609131 AACCACATTGGCCTTCGGAG 60.609 55.000 3.32 0.0 42.67 4.63 F
423 440 1.341531 CCTTTCAGTCGACACAGGACT 59.658 52.381 19.50 0.0 45.26 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1228 1305 0.169009 GCTGTGAAAACCGCATCTCC 59.831 55.000 0.00 0.00 34.34 3.71 R
1960 2053 1.133407 GCTTGGGTCTCGAGTAGTGAG 59.867 57.143 13.13 7.77 34.72 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
107 108 6.558394 TGGTAATGAGATCTCCATGGTAATCA 59.442 38.462 20.03 16.29 0.00 2.57
115 116 7.256399 AGATCTCCATGGTAATCATAGGGTAA 58.744 38.462 22.62 0.00 34.12 2.85
116 117 7.739444 AGATCTCCATGGTAATCATAGGGTAAA 59.261 37.037 22.62 0.00 34.12 2.01
117 118 7.888514 TCTCCATGGTAATCATAGGGTAAAT 57.111 36.000 12.58 0.00 34.12 1.40
213 221 1.468520 CCGCTCTAACAACCACATTGG 59.531 52.381 0.00 0.00 43.20 3.16
222 230 0.609131 AACCACATTGGCCTTCGGAG 60.609 55.000 3.32 0.00 42.67 4.63
254 262 4.422073 TGCTCCATGAACCGATAATCTT 57.578 40.909 0.00 0.00 0.00 2.40
292 302 1.795768 ATATATGCCGCTTGTGGACG 58.204 50.000 4.17 0.00 0.00 4.79
306 316 2.035442 GGACGGAAGCAAGCCTCAC 61.035 63.158 0.00 0.00 0.00 3.51
308 318 1.569479 GACGGAAGCAAGCCTCACAC 61.569 60.000 0.00 0.00 0.00 3.82
423 440 1.341531 CCTTTCAGTCGACACAGGACT 59.658 52.381 19.50 0.00 45.26 3.85
428 445 1.399714 AGTCGACACAGGACTGTCAA 58.600 50.000 19.50 0.00 42.87 3.18
430 447 2.167693 AGTCGACACAGGACTGTCAAAA 59.832 45.455 19.50 0.00 42.87 2.44
453 470 3.720949 CGTCTTACATTATGGGACGGA 57.279 47.619 20.50 2.30 43.69 4.69
454 471 3.639538 CGTCTTACATTATGGGACGGAG 58.360 50.000 20.50 2.74 43.69 4.63
455 472 3.552273 CGTCTTACATTATGGGACGGAGG 60.552 52.174 20.50 5.87 43.69 4.30
456 473 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
730 806 5.337554 CAGTGCATTCCTGTGTTATTCATG 58.662 41.667 0.00 0.00 0.00 3.07
965 1042 1.648568 AGGTCTCATCCTCCTCTTCCA 59.351 52.381 0.00 0.00 31.32 3.53
1228 1305 0.378962 GTCGTGGATCCAGAGACTCG 59.621 60.000 29.39 22.19 34.29 4.18
1440 1533 1.932511 GCAGAGATGAGTAGCTTGTGC 59.067 52.381 0.00 0.00 40.05 4.57
1569 1662 2.026542 AGAAGCAGATGAACTCATGGCA 60.027 45.455 12.78 0.00 36.57 4.92
1870 1963 9.653516 AAGATAAGAGATTTCTCATAGTCCTGA 57.346 33.333 10.07 0.00 45.21 3.86
1886 1979 8.542926 CATAGTCCTGAATGACATATGGGATTA 58.457 37.037 7.80 3.99 37.73 1.75
1918 2011 2.930040 AGAAACATACTGGACGCATTCG 59.070 45.455 0.00 0.00 42.43 3.34
1960 2053 5.163982 GCACGTGAAGGAAGTAAAGTCATAC 60.164 44.000 22.23 0.00 0.00 2.39
2524 2622 7.041098 GGAACATACATCATACCTGAACCATTC 60.041 40.741 0.00 0.00 34.37 2.67
2564 2662 7.776618 TTCTTATCTTCTGGTGAGTACTTCA 57.223 36.000 0.00 0.00 0.00 3.02
2596 2694 4.644103 AAGAAGCGAATTTGATGATGGG 57.356 40.909 0.00 0.00 0.00 4.00
2869 2973 3.588842 ACCTTGAGATCCATGTTGAGGAA 59.411 43.478 0.00 0.00 38.93 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
107 108 3.290710 CAGGTTGCAGCATTTACCCTAT 58.709 45.455 10.65 0.00 0.00 2.57
170 178 4.358851 CGACTTCAGAGTTCAGATCATCC 58.641 47.826 0.00 0.00 35.88 3.51
222 230 1.742831 TCATGGAGCATTTTACACCGC 59.257 47.619 0.00 0.00 0.00 5.68
292 302 0.819259 TGTGTGTGAGGCTTGCTTCC 60.819 55.000 2.37 0.00 0.00 3.46
306 316 4.031201 GGATCAACGTTTGTTTTGTGTGTG 59.969 41.667 0.00 0.00 35.72 3.82
308 318 4.420168 AGGATCAACGTTTGTTTTGTGTG 58.580 39.130 0.00 0.00 35.72 3.82
428 445 5.122711 CCGTCCCATAATGTAAGACGTTTTT 59.877 40.000 9.63 0.00 46.62 1.94
430 447 4.081531 TCCGTCCCATAATGTAAGACGTTT 60.082 41.667 9.63 0.00 46.62 3.60
432 449 3.025978 TCCGTCCCATAATGTAAGACGT 58.974 45.455 9.63 0.00 46.62 4.34
434 451 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
435 452 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
436 453 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
437 454 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
438 455 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
439 456 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
440 457 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
441 458 2.970640 GTTACTCCCTCCGTCCCATAAT 59.029 50.000 0.00 0.00 0.00 1.28
442 459 2.023695 AGTTACTCCCTCCGTCCCATAA 60.024 50.000 0.00 0.00 0.00 1.90
443 460 1.572415 AGTTACTCCCTCCGTCCCATA 59.428 52.381 0.00 0.00 0.00 2.74
444 461 0.338814 AGTTACTCCCTCCGTCCCAT 59.661 55.000 0.00 0.00 0.00 4.00
445 462 0.613853 CAGTTACTCCCTCCGTCCCA 60.614 60.000 0.00 0.00 0.00 4.37
446 463 0.324091 TCAGTTACTCCCTCCGTCCC 60.324 60.000 0.00 0.00 0.00 4.46
447 464 0.816373 GTCAGTTACTCCCTCCGTCC 59.184 60.000 0.00 0.00 0.00 4.79
448 465 1.836802 AGTCAGTTACTCCCTCCGTC 58.163 55.000 0.00 0.00 30.33 4.79
449 466 2.169330 GAAGTCAGTTACTCCCTCCGT 58.831 52.381 0.00 0.00 37.50 4.69
450 467 2.094649 GTGAAGTCAGTTACTCCCTCCG 60.095 54.545 0.00 0.00 37.50 4.63
451 468 2.234168 GGTGAAGTCAGTTACTCCCTCC 59.766 54.545 0.00 0.00 37.50 4.30
452 469 2.897969 TGGTGAAGTCAGTTACTCCCTC 59.102 50.000 0.00 0.00 37.50 4.30
453 470 2.900546 CTGGTGAAGTCAGTTACTCCCT 59.099 50.000 0.00 0.00 37.50 4.20
454 471 2.897969 TCTGGTGAAGTCAGTTACTCCC 59.102 50.000 0.00 0.00 37.50 4.30
455 472 4.464597 AGATCTGGTGAAGTCAGTTACTCC 59.535 45.833 0.00 0.00 37.50 3.85
456 473 5.652994 AGATCTGGTGAAGTCAGTTACTC 57.347 43.478 0.00 0.00 37.50 2.59
653 725 5.450965 CCCATGTGCAGAAGATAAAATGTCC 60.451 44.000 0.00 0.00 0.00 4.02
709 785 5.314923 ACATGAATAACACAGGAATGCAC 57.685 39.130 0.00 0.00 0.00 4.57
730 806 4.081586 CAGTCAAGTTAGTTAGGAGGGGAC 60.082 50.000 0.00 0.00 0.00 4.46
1228 1305 0.169009 GCTGTGAAAACCGCATCTCC 59.831 55.000 0.00 0.00 34.34 3.71
1400 1493 5.764686 TCTGCAGAAATTCTGTCAAGCTTTA 59.235 36.000 22.28 0.00 45.94 1.85
1815 1908 3.189618 TCTGCCAGCATACTCTTGATG 57.810 47.619 0.00 0.00 32.87 3.07
1886 1979 7.495934 CGTCCAGTATGTTTCTTGATAAATCCT 59.504 37.037 0.00 0.00 0.00 3.24
1918 2011 4.273480 ACGTGCTTGACTAAATGGCATATC 59.727 41.667 0.00 0.00 35.37 1.63
1960 2053 1.133407 GCTTGGGTCTCGAGTAGTGAG 59.867 57.143 13.13 7.77 34.72 3.51
2524 2622 7.244166 AGATAAGAATTCAGCAAGTTCATCG 57.756 36.000 8.44 0.00 0.00 3.84
2729 2827 3.923461 GTCTGAATCAAGTCCGACTTCTG 59.077 47.826 10.98 2.42 36.03 3.02


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

AutoCloner maintained by Alex Coulton.