Multiple sequence alignment - TraesCS4A01G161500

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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 TraesCS4A01G161500 chr4A 100.000 2341 0 0 1 2341 350237932 350240272 0 4324
1 TraesCS4A01G161500 chr7D 96.633 2346 71 6 3 2341 382087951 382090295 0 3888
2 TraesCS4A01G161500 chr7D 96.254 2349 74 8 3 2341 626713043 626710699 0 3838
3 TraesCS4A01G161500 chr7A 96.514 2352 67 8 3 2341 638509518 638507169 0 3875
4 TraesCS4A01G161500 chr7A 96.344 2352 70 10 3 2341 708243773 708246121 0 3853
5 TraesCS4A01G161500 chr6B 96.429 2352 70 8 3 2341 596603712 596601362 0 3866
6 TraesCS4A01G161500 chrUn 96.344 2352 72 9 3 2341 171006433 171008783 0 3855
7 TraesCS4A01G161500 chr4D 96.334 2346 75 8 4 2341 123399672 123402014 0 3845
8 TraesCS4A01G161500 chr1B 96.213 2350 76 9 3 2341 672539371 672541718 0 3834
9 TraesCS4A01G161500 chr1A 96.244 2343 80 7 3 2341 94665784 94663446 0 3832


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 TraesCS4A01G161500 chr4A 350237932 350240272 2340 False 4324 4324 100.000 1 2341 1 chr4A.!!$F1 2340
1 TraesCS4A01G161500 chr7D 382087951 382090295 2344 False 3888 3888 96.633 3 2341 1 chr7D.!!$F1 2338
2 TraesCS4A01G161500 chr7D 626710699 626713043 2344 True 3838 3838 96.254 3 2341 1 chr7D.!!$R1 2338
3 TraesCS4A01G161500 chr7A 638507169 638509518 2349 True 3875 3875 96.514 3 2341 1 chr7A.!!$R1 2338
4 TraesCS4A01G161500 chr7A 708243773 708246121 2348 False 3853 3853 96.344 3 2341 1 chr7A.!!$F1 2338
5 TraesCS4A01G161500 chr6B 596601362 596603712 2350 True 3866 3866 96.429 3 2341 1 chr6B.!!$R1 2338
6 TraesCS4A01G161500 chrUn 171006433 171008783 2350 False 3855 3855 96.344 3 2341 1 chrUn.!!$F1 2338
7 TraesCS4A01G161500 chr4D 123399672 123402014 2342 False 3845 3845 96.334 4 2341 1 chr4D.!!$F1 2337
8 TraesCS4A01G161500 chr1B 672539371 672541718 2347 False 3834 3834 96.213 3 2341 1 chr1B.!!$F1 2338
9 TraesCS4A01G161500 chr1A 94663446 94665784 2338 True 3832 3832 96.244 3 2341 1 chr1A.!!$R1 2338

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
881 896 1.003003 TGCATCTGACATTCGTTGGGA 59.997 47.619 0.0 0.0 0.0 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1897 1923 0.250901 AGCAGGGCTCGACAAAACAT 60.251 50.0 0.0 0.0 30.62 2.71 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
28 29 1.068127 TCGAAATTACCTCTAGCCCGC 59.932 52.381 0.00 0.00 0.00 6.13
92 93 1.205893 GCACTTCGAAGGTCTGGAGAT 59.794 52.381 27.86 1.65 0.00 2.75
110 111 2.021639 AGATCCTCCTTGAGATTCCCCA 60.022 50.000 0.00 0.00 0.00 4.96
122 123 4.079443 TGAGATTCCCCATTTACCGGAAAT 60.079 41.667 9.46 7.28 39.07 2.17
148 149 1.112113 CGCAGGTCCTTCCTTAGCTA 58.888 55.000 0.00 0.00 45.67 3.32
151 152 2.436173 GCAGGTCCTTCCTTAGCTACAT 59.564 50.000 0.00 0.00 45.67 2.29
204 215 1.722034 GATCCATCCCAGAGTAGCCA 58.278 55.000 0.00 0.00 0.00 4.75
495 506 2.347490 GCAAACGGGAGGCTCTCA 59.653 61.111 15.97 0.00 31.08 3.27
515 526 4.191544 TCAAAAAGACGATAGAGGCCATG 58.808 43.478 5.01 0.00 41.38 3.66
530 541 1.275856 GCCATGTTGAAATGCCAAGGA 59.724 47.619 0.00 0.00 0.00 3.36
560 571 2.506644 AGACTCCCTAGCGTCTCTACTT 59.493 50.000 2.78 0.00 35.72 2.24
587 598 1.043116 AATGCGATCTCGAGGACCCA 61.043 55.000 13.56 6.13 43.02 4.51
640 652 3.023832 AGGATGGTTAGGGCGATTTTTG 58.976 45.455 0.00 0.00 0.00 2.44
815 827 1.815003 CTTCAATGGGGTGTGCTCTTC 59.185 52.381 0.00 0.00 0.00 2.87
853 868 6.604171 TGCCAATATGATCTTAATGAGGTGT 58.396 36.000 5.47 0.00 0.00 4.16
881 896 1.003003 TGCATCTGACATTCGTTGGGA 59.997 47.619 0.00 0.00 0.00 4.37
990 1008 1.757699 GGAGAAGGGTAGCCTAGTGTG 59.242 57.143 15.26 0.00 0.00 3.82
1021 1039 4.747529 ACCGCGGCGAACCCTTAC 62.748 66.667 28.58 0.00 0.00 2.34
1193 1214 1.612442 GTCCACTCTAGGGGGTGCA 60.612 63.158 0.00 0.00 32.68 4.57
1255 1276 1.652947 GGGGAAGTGAAGAGTACCCA 58.347 55.000 0.00 0.00 39.10 4.51
1267 1288 2.000447 GAGTACCCAACGACATTCAGC 59.000 52.381 0.00 0.00 0.00 4.26
1285 1306 3.134623 TCAGCGATGAATGTAGACCCATT 59.865 43.478 0.00 0.00 37.74 3.16
1322 1343 2.122954 GGTCCTGGGAGAGGTGGT 59.877 66.667 0.00 0.00 43.37 4.16
1351 1372 2.254737 CTGAGCTGAGGGAAGCCAGG 62.255 65.000 0.00 0.00 44.68 4.45
1365 1386 1.630369 AGCCAGGCAATTGAGTCACTA 59.370 47.619 15.80 0.00 0.00 2.74
1432 1453 1.021968 ATTGCGAAATACGGCTTCCC 58.978 50.000 0.00 0.00 42.83 3.97
1463 1484 1.955458 TTTCAACAAGGGGGCTGGGT 61.955 55.000 0.00 0.00 0.00 4.51
1490 1511 1.136305 CCTTCATAGAAAGGCGACCGA 59.864 52.381 0.00 0.00 39.47 4.69
1511 1532 2.029828 AGCCTAGATTAGATGTTCGCCG 60.030 50.000 0.00 0.00 0.00 6.46
1519 1540 9.355215 CTAGATTAGATGTTCGCCGTTTTATAT 57.645 33.333 0.00 0.00 0.00 0.86
1688 1714 1.320344 CCGAACCTCTGATCGACCCA 61.320 60.000 1.01 0.00 41.43 4.51
1810 1836 5.427036 AAATGAAATACGAACAACCACGT 57.573 34.783 0.00 0.00 44.72 4.49
1897 1923 4.883585 AGGACGACGTACCATGATACTTTA 59.116 41.667 6.59 0.00 0.00 1.85
1922 1948 1.295423 GTCGAGCCCTGCTTTGGTA 59.705 57.895 0.00 0.00 39.88 3.25
1941 1967 6.073447 TGGTATCTGGTTTGATGGTTGTAT 57.927 37.500 0.00 0.00 0.00 2.29
2047 2074 1.201181 CTTCTCCGCTATGATCTCCCG 59.799 57.143 0.00 0.00 0.00 5.14
2064 2091 6.390048 TCTCCCGAGTAGTTCATATAGGAT 57.610 41.667 0.00 0.00 0.00 3.24
2251 2279 2.496070 CCCACAGAAATACGACCTCTCA 59.504 50.000 0.00 0.00 0.00 3.27
2315 2344 6.728089 AATTTGGAAACATTGGGCAATTTT 57.272 29.167 0.00 0.00 42.32 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.588373 GGCTAGAGGTAATTTCGATGATCTTC 59.412 42.308 0.00 0.00 0.00 2.87
1 2 6.459923 GGCTAGAGGTAATTTCGATGATCTT 58.540 40.000 0.00 0.00 0.00 2.40
28 29 2.914289 GATGACCCCCTCTGGCTG 59.086 66.667 0.00 0.00 0.00 4.85
43 44 1.964373 GGGTTGGCGTTGTGTCGAT 60.964 57.895 0.00 0.00 0.00 3.59
92 93 2.594536 ATGGGGAATCTCAAGGAGGA 57.405 50.000 0.00 0.00 0.00 3.71
110 111 1.480789 GGGTGGCATTTCCGGTAAAT 58.519 50.000 0.00 3.63 38.36 1.40
148 149 2.621668 GGGCTTGCTCCCTTTCTTATGT 60.622 50.000 2.57 0.00 43.13 2.29
151 152 0.331616 GGGGCTTGCTCCCTTTCTTA 59.668 55.000 0.00 0.00 45.80 2.10
173 184 1.694696 GGATGGATCGAGGTTTAGGCT 59.305 52.381 0.00 0.00 0.00 4.58
349 360 2.633657 CGAACGCTTGCAGTTGCT 59.366 55.556 5.62 0.00 42.66 3.91
433 444 2.107204 AGAGACAAAAGCAGTCCCACAT 59.893 45.455 0.00 0.00 36.68 3.21
495 506 4.222124 ACATGGCCTCTATCGTCTTTTT 57.778 40.909 3.32 0.00 0.00 1.94
515 526 2.416747 GGCTTTCCTTGGCATTTCAAC 58.583 47.619 0.00 0.00 0.00 3.18
530 541 1.280457 CTAGGGAGTCTGTGGGCTTT 58.720 55.000 0.00 0.00 0.00 3.51
560 571 3.490933 CCTCGAGATCGCATTTTAGGTCA 60.491 47.826 15.71 0.00 39.60 4.02
662 674 7.177878 AGAAGTCATGGAAGTGTGGATAAATT 58.822 34.615 0.00 0.00 0.00 1.82
807 819 5.522097 GCATACTCTCCTAAAAGAAGAGCAC 59.478 44.000 0.00 0.00 0.00 4.40
815 827 9.160496 GATCATATTGGCATACTCTCCTAAAAG 57.840 37.037 0.00 0.00 0.00 2.27
853 868 0.040058 ATGTCAGATGCAAAGCCCCA 59.960 50.000 0.00 0.00 0.00 4.96
881 896 2.529312 GGGCTCCCGTAGAGGAAAT 58.471 57.895 2.29 0.00 45.00 2.17
990 1008 0.725784 CGCGGTTCATTGTTGTGCTC 60.726 55.000 0.00 0.00 0.00 4.26
997 1015 2.666862 TTCGCCGCGGTTCATTGT 60.667 55.556 28.70 0.00 0.00 2.71
1097 1115 3.689161 CACTTTCCCGTATGAGCATTTGA 59.311 43.478 0.00 0.00 0.00 2.69
1099 1117 3.950397 TCACTTTCCCGTATGAGCATTT 58.050 40.909 0.00 0.00 0.00 2.32
1193 1214 0.608130 TAATCTGCGCAGGTGTGTCT 59.392 50.000 35.36 17.07 0.00 3.41
1207 1228 4.525487 TCTTGTAACCGTCACCTGTAATCT 59.475 41.667 0.00 0.00 0.00 2.40
1267 1288 3.141398 CCCAATGGGTCTACATTCATCG 58.859 50.000 10.91 0.00 38.94 3.84
1285 1306 0.404040 GGAATGATTATCCCCGCCCA 59.596 55.000 0.00 0.00 0.00 5.36
1322 1343 0.964700 CTCAGCTCAGACTGGTGTCA 59.035 55.000 1.81 0.00 45.20 3.58
1351 1372 4.464112 GGTCGTTTTAGTGACTCAATTGC 58.536 43.478 0.00 0.00 35.45 3.56
1365 1386 2.668550 GCCTCCTGCGGTCGTTTT 60.669 61.111 0.00 0.00 0.00 2.43
1432 1453 7.500141 CCCCCTTGTTGAAATTTGGATATTAG 58.500 38.462 0.00 0.00 0.00 1.73
1463 1484 2.632377 CCTTTCTATGAAGGCGAGCAA 58.368 47.619 0.00 0.00 39.75 3.91
1490 1511 2.029828 CGGCGAACATCTAATCTAGGCT 60.030 50.000 0.00 0.00 0.00 4.58
1519 1540 7.447510 CCCCCTTTACCTTCTCTTTCTATTA 57.552 40.000 0.00 0.00 0.00 0.98
1713 1739 7.222000 ACTTACTGAATCTCGTCTTTCTCTT 57.778 36.000 0.00 0.00 0.00 2.85
1784 1810 6.302313 CGTGGTTGTTCGTATTTCATTTTCTC 59.698 38.462 0.00 0.00 0.00 2.87
1810 1836 9.295825 ACATTCAAGTCAATCTATTACAACCAA 57.704 29.630 0.00 0.00 0.00 3.67
1825 1851 4.454678 AGCAAGAAGACACATTCAAGTCA 58.545 39.130 0.00 0.00 37.23 3.41
1897 1923 0.250901 AGCAGGGCTCGACAAAACAT 60.251 50.000 0.00 0.00 30.62 2.71
1922 1948 4.158394 GCACATACAACCATCAAACCAGAT 59.842 41.667 0.00 0.00 0.00 2.90
1941 1967 4.396790 GGAATGTACCGGATTTTTAGCACA 59.603 41.667 9.46 0.00 0.00 4.57
2064 2091 7.011389 CACGAATAGGAATGAAACAGCAATAGA 59.989 37.037 0.00 0.00 0.00 1.98
2315 2344 7.293073 ACCAGACGGAATAGTAGGTATAAAGA 58.707 38.462 0.00 0.00 32.88 2.52


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

AutoCloner maintained by Alex Coulton.