Multiple sequence alignment - TraesCS2D01G181800

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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 TraesCS2D01G181800 chr2D 100.000 3126 0 0 1 3126 126787714 126790839 0.000000e+00 5773
1 TraesCS2D01G181800 chr4D 95.523 3127 134 5 1 3126 57543568 57546689 0.000000e+00 4994
2 TraesCS2D01G181800 chr4D 77.727 880 169 25 2116 2981 449449810 449448944 5.980000e-142 514
3 TraesCS2D01G181800 chr4B 93.612 3131 179 15 1 3126 423960677 423957563 0.000000e+00 4654
4 TraesCS2D01G181800 chr4B 75.453 827 189 13 1001 1821 208147041 208147859 1.050000e-104 390
5 TraesCS2D01G181800 chr4A 93.227 3130 201 11 1 3126 346764698 346767820 0.000000e+00 4595
6 TraesCS2D01G181800 chr7B 93.069 3131 196 11 1 3126 479578451 479575337 0.000000e+00 4560
7 TraesCS2D01G181800 chr5A 90.604 3129 272 13 1 3115 616102398 616105518 0.000000e+00 4130
8 TraesCS2D01G181800 chr5A 90.476 3129 280 10 1 3115 293565375 293562251 0.000000e+00 4111
9 TraesCS2D01G181800 chr6D 85.514 3141 424 26 4 3126 216719637 216716510 0.000000e+00 3251
10 TraesCS2D01G181800 chr6B 91.895 1937 149 7 1193 3126 12181612 12183543 0.000000e+00 2700
11 TraesCS2D01G181800 chr7D 93.633 267 17 0 2730 2996 581836281 581836547 1.750000e-107 399


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 TraesCS2D01G181800 chr2D 126787714 126790839 3125 False 5773 5773 100.000 1 3126 1 chr2D.!!$F1 3125
1 TraesCS2D01G181800 chr4D 57543568 57546689 3121 False 4994 4994 95.523 1 3126 1 chr4D.!!$F1 3125
2 TraesCS2D01G181800 chr4D 449448944 449449810 866 True 514 514 77.727 2116 2981 1 chr4D.!!$R1 865
3 TraesCS2D01G181800 chr4B 423957563 423960677 3114 True 4654 4654 93.612 1 3126 1 chr4B.!!$R1 3125
4 TraesCS2D01G181800 chr4B 208147041 208147859 818 False 390 390 75.453 1001 1821 1 chr4B.!!$F1 820
5 TraesCS2D01G181800 chr4A 346764698 346767820 3122 False 4595 4595 93.227 1 3126 1 chr4A.!!$F1 3125
6 TraesCS2D01G181800 chr7B 479575337 479578451 3114 True 4560 4560 93.069 1 3126 1 chr7B.!!$R1 3125
7 TraesCS2D01G181800 chr5A 616102398 616105518 3120 False 4130 4130 90.604 1 3115 1 chr5A.!!$F1 3114
8 TraesCS2D01G181800 chr5A 293562251 293565375 3124 True 4111 4111 90.476 1 3115 1 chr5A.!!$R1 3114
9 TraesCS2D01G181800 chr6D 216716510 216719637 3127 True 3251 3251 85.514 4 3126 1 chr6D.!!$R1 3122
10 TraesCS2D01G181800 chr6B 12181612 12183543 1931 False 2700 2700 91.895 1193 3126 1 chr6B.!!$F1 1933

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
735 739 1.170919 CGACAGACGTATCCCCCGAT 61.171 60.0 0.0 0.0 37.22 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2350 2390 0.618981 CTGGGTAGGGTTTGAGGTCC 59.381 60.0 0.0 0.0 0.0 4.46 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
618 620 1.224592 GGATCACAGCCCGTGGAAT 59.775 57.895 4.19 0.00 46.36 3.01
651 653 3.104512 TCAAATTCTTCTCGGGCTAGGA 58.895 45.455 0.00 0.00 0.00 2.94
735 739 1.170919 CGACAGACGTATCCCCCGAT 61.171 60.000 0.00 0.00 37.22 4.18
765 769 1.404986 CGTTTCTGTTCCCGATGCCTA 60.405 52.381 0.00 0.00 0.00 3.93
783 787 3.764434 GCCTAGGACCTGATCATTATCGA 59.236 47.826 14.75 0.00 34.60 3.59
916 920 2.106511 GCCCCTCCTCTTATATTGCACA 59.893 50.000 0.00 0.00 0.00 4.57
1061 1065 1.181098 GGCACCACCATTGTTGCTCT 61.181 55.000 0.00 0.00 38.86 4.09
1149 1162 3.683937 GCCATTGCCACGCTGGTT 61.684 61.111 6.02 0.00 40.46 3.67
1380 1393 4.611807 CGAGGACTGAACTATCGTAGCATC 60.612 50.000 0.00 0.00 0.00 3.91
1605 1619 5.563592 TCTTGATGATATTGGCTATGGTGG 58.436 41.667 0.00 0.00 0.00 4.61
1617 1631 3.181445 GGCTATGGTGGTTCATGGACATA 60.181 47.826 6.44 0.00 34.30 2.29
1717 1731 2.044650 CACCCTCTGCCCCATGTG 60.045 66.667 0.00 0.00 0.00 3.21
1914 1931 3.076621 CTGACAATGCTCCAGCTGTTAA 58.923 45.455 13.81 0.00 42.66 2.01
1941 1958 0.466922 GCTCCCCATATTGCTGCTGT 60.467 55.000 0.00 0.00 0.00 4.40
1981 1998 7.226325 CCTGTGATTAAGGATCTGAATCTCAAC 59.774 40.741 14.52 7.91 36.91 3.18
1985 2002 4.543590 AAGGATCTGAATCTCAACGTGT 57.456 40.909 0.00 0.00 32.12 4.49
2019 2045 1.251251 GTTCAAGTTGATGCTGCCCT 58.749 50.000 6.36 0.00 0.00 5.19
2028 2054 1.020437 GATGCTGCCCTTGTAGAAGC 58.980 55.000 0.00 0.00 0.00 3.86
2134 2160 6.238842 GCCAGCATGAACTATAATGACAATGT 60.239 38.462 0.00 0.00 39.69 2.71
2137 2163 9.049523 CAGCATGAACTATAATGACAATGTAGT 57.950 33.333 0.00 0.00 39.69 2.73
2167 2193 3.679389 AGGAATCTCAAACGCAGAACAT 58.321 40.909 0.00 0.00 0.00 2.71
2243 2269 1.826385 ACCTTGCTGCCTACAATGAC 58.174 50.000 0.00 0.00 0.00 3.06
2284 2310 5.237882 TGGTGAGGCCAACATTGTTAATGT 61.238 41.667 5.01 1.55 45.94 2.71
2286 2312 7.963512 TGGTGAGGCCAACATTGTTAATGTAC 61.964 42.308 5.01 1.47 45.57 2.90
2340 2373 0.807496 GGCCAGACAGAAGTGCATTC 59.193 55.000 0.00 0.00 38.28 2.67
2442 2488 1.603455 GCAGCCACCAGTAAGCCAA 60.603 57.895 0.00 0.00 0.00 4.52
2665 2713 5.597806 GATGCCATCATCATTGACAAACAT 58.402 37.500 0.00 0.00 46.44 2.71
2672 2720 1.617850 TCATTGACAAACATGCCCCAC 59.382 47.619 0.00 0.00 0.00 4.61
2703 2752 4.770010 TGAAATTCCAATCAACACCCTACC 59.230 41.667 0.00 0.00 0.00 3.18
2854 2903 8.699749 CATTTTAGAACCTTTTCATCGTTTTCC 58.300 33.333 0.00 0.00 33.72 3.13
2982 3031 9.777297 ATTGCAGTAGGATTTGTTTTGTTTATT 57.223 25.926 0.00 0.00 0.00 1.40
3051 3100 3.990318 ATGATCATGATTGCAGCACAG 57.010 42.857 10.14 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
618 620 7.541783 CCGAGAAGAATTTGAATTATTGTTGCA 59.458 33.333 1.45 0.00 30.66 4.08
651 653 0.398318 GGCGGCCCATCTCTATTCTT 59.602 55.000 8.12 0.00 0.00 2.52
735 739 3.043713 CAGAAACGCGAGCTGGCA 61.044 61.111 21.16 0.00 0.00 4.92
765 769 6.951198 AGTTAGATCGATAATGATCAGGTCCT 59.049 38.462 0.00 0.00 45.81 3.85
783 787 5.835280 CCTGATTTTATTGGGGCAGTTAGAT 59.165 40.000 0.00 0.00 0.00 1.98
985 989 1.377725 CCATTGGAGGCAAGCTCGT 60.378 57.895 0.00 0.00 0.00 4.18
1143 1156 3.512516 GCGATGCCAGGAACCAGC 61.513 66.667 0.00 0.00 0.00 4.85
1380 1393 6.808008 AACCAGACATCATGAGTAAAAGTG 57.192 37.500 0.09 0.00 0.00 3.16
1532 1546 9.440761 AGGTAAAGTATCAGGATTAATGACTCT 57.559 33.333 0.00 0.00 0.00 3.24
1579 1593 7.362660 CCACCATAGCCAATATCATCAAGATTG 60.363 40.741 0.00 0.00 38.19 2.67
1605 1619 5.250200 TGTAAGTTGGGTATGTCCATGAAC 58.750 41.667 0.00 0.00 36.58 3.18
1617 1631 5.487488 TCTCTGGACATAATGTAAGTTGGGT 59.513 40.000 0.00 0.00 0.00 4.51
1681 1695 2.001269 AGGGTTTCCTCCATCCGGG 61.001 63.158 0.00 0.00 39.80 5.73
1717 1731 0.674269 CATGCCAAAACCCACCATGC 60.674 55.000 0.00 0.00 0.00 4.06
1726 1740 2.450476 AGGACCTCATCATGCCAAAAC 58.550 47.619 0.00 0.00 0.00 2.43
1914 1931 2.754186 GCAATATGGGGAGCCTCATTGT 60.754 50.000 7.28 0.00 0.00 2.71
1941 1958 1.117994 CACAGGAGCAGGAGCATCTA 58.882 55.000 0.00 0.00 45.49 1.98
1981 1998 3.811722 ACATTTGTATCAGCACACACG 57.188 42.857 0.00 0.00 0.00 4.49
1985 2002 6.039159 TCAACTTGAACATTTGTATCAGCACA 59.961 34.615 0.00 0.00 0.00 4.57
2019 2045 0.948678 GGTTTGCACCGCTTCTACAA 59.051 50.000 0.00 0.00 31.60 2.41
2134 2160 4.251103 TGAGATTCCTCACTGGCTACTA 57.749 45.455 0.00 0.00 44.01 1.82
2167 2193 6.472016 TCAGTATTGCCTTCAACAGTGATAA 58.528 36.000 0.00 0.00 34.97 1.75
2284 2310 5.189539 TCAATGTCCATGATCTGACAAGGTA 59.810 40.000 14.34 2.70 44.04 3.08
2286 2312 4.520179 TCAATGTCCATGATCTGACAAGG 58.480 43.478 14.34 10.69 44.04 3.61
2340 2373 1.264288 GTTTGAGGTCCGAAACTGCAG 59.736 52.381 13.48 13.48 0.00 4.41
2350 2390 0.618981 CTGGGTAGGGTTTGAGGTCC 59.381 60.000 0.00 0.00 0.00 4.46
2442 2488 7.133133 TCTTCCTCTTGTTAGTAACTTTGGT 57.867 36.000 14.00 0.00 0.00 3.67
2612 2660 2.666317 CCCCAGGTTGACAGAAACTTT 58.334 47.619 0.00 0.00 0.00 2.66
2672 2720 2.024080 TGATTGGAATTTCAGGAGGGGG 60.024 50.000 0.00 0.00 0.00 5.40
2703 2752 3.499737 GTCCAGTGCCAATCGCCG 61.500 66.667 0.00 0.00 36.24 6.46
2904 2953 9.507329 CCATAGTAGCTCATTATTACAAACCAT 57.493 33.333 0.00 0.00 0.00 3.55
2994 3043 2.151881 TGTGCAACATTTGATGGCAC 57.848 45.000 8.02 8.02 45.67 5.01
3038 3087 1.677942 TTGTGACTGTGCTGCAATCA 58.322 45.000 2.77 6.15 30.11 2.57
3051 3100 1.814394 TCTCATTGGCAGCATTGTGAC 59.186 47.619 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.