Multiple sequence alignment - TraesCS4B01G244600

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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 TraesCS4B01G244600 chr4B 100.000 3389 0 0 1 3389 506322438 506325826 0.000000e+00 6259.0
1 TraesCS4B01G244600 chr4A 93.918 3206 112 36 228 3389 64567548 64570714 0.000000e+00 4763.0
2 TraesCS4B01G244600 chr4D 94.043 2770 113 29 639 3389 409480541 409477805 0.000000e+00 4154.0
3 TraesCS4B01G244600 chr4D 86.838 661 61 8 1 651 409481234 409480590 0.000000e+00 715.0
4 TraesCS4B01G244600 chr3D 85.714 84 11 1 97 179 520707580 520707663 1.680000e-13 87.9
5 TraesCS4B01G244600 chr3D 81.928 83 15 0 97 179 611294300 611294382 1.690000e-08 71.3
6 TraesCS4B01G244600 chr1D 81.481 108 16 4 75 179 319431704 319431810 6.030000e-13 86.1
7 TraesCS4B01G244600 chr1D 83.333 78 12 1 103 179 448557699 448557622 1.690000e-08 71.3
8 TraesCS4B01G244600 chr5A 78.014 141 23 8 43 179 625702437 625702573 7.790000e-12 82.4
9 TraesCS4B01G244600 chr7B 83.544 79 12 1 102 179 709795885 709795963 4.690000e-09 73.1
10 TraesCS4B01G244600 chr5B 78.899 109 17 5 75 179 633142676 633142782 6.070000e-08 69.4
11 TraesCS4B01G244600 chr5D 82.278 79 13 1 102 179 42015452 42015530 2.180000e-07 67.6


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 TraesCS4B01G244600 chr4B 506322438 506325826 3388 False 6259.0 6259 100.0000 1 3389 1 chr4B.!!$F1 3388
1 TraesCS4B01G244600 chr4A 64567548 64570714 3166 False 4763.0 4763 93.9180 228 3389 1 chr4A.!!$F1 3161
2 TraesCS4B01G244600 chr4D 409477805 409481234 3429 True 2434.5 4154 90.4405 1 3389 2 chr4D.!!$R1 3388

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
680 756 0.041833 TGGGAGACTAGCTTGGCTCT 59.958 55.0 26.87 9.25 40.44 4.09 F
872 949 0.312102 GCCTGTCAAGCCAGTTTGTC 59.688 55.0 0.00 0.00 0.00 3.18 F
1900 1997 0.109039 TAGTACGTGCATTGCAGCGA 60.109 50.0 27.89 15.52 40.08 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1900 1997 0.039326 AGACTACTAGGCGGGTGTGT 59.961 55.0 0.00 0.00 0.00 3.72 R
1904 2001 0.324460 AAGCAGACTACTAGGCGGGT 60.324 55.0 0.00 0.00 28.03 5.28 R
3199 3331 0.545548 GGAGACCAGGTCCTTGTCCT 60.546 60.0 16.72 7.03 32.18 3.85 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
31 32 4.162690 CTACTGGCGGGCCACCTC 62.163 72.222 12.67 0.00 41.89 3.85
33 34 3.305619 TACTGGCGGGCCACCTCTA 62.306 63.158 12.67 0.00 41.89 2.43
40 41 1.051812 CGGGCCACCTCTATCAGAAT 58.948 55.000 4.39 0.00 33.28 2.40
44 45 2.891580 GGCCACCTCTATCAGAATACGA 59.108 50.000 0.00 0.00 0.00 3.43
48 49 5.241064 GCCACCTCTATCAGAATACGAGTTA 59.759 44.000 0.00 0.00 0.00 2.24
71 72 8.862074 GTTAAAATGTTAACAACGTGAGGTTTT 58.138 29.630 13.23 13.51 45.70 2.43
72 73 7.892778 AAAATGTTAACAACGTGAGGTTTTT 57.107 28.000 13.23 8.43 36.49 1.94
150 152 8.689972 TCTAATAACTTCTTAGAACCCTAACCG 58.310 37.037 0.00 0.00 33.42 4.44
159 161 3.483421 AGAACCCTAACCGAAAAAGTGG 58.517 45.455 0.00 0.00 0.00 4.00
172 174 6.711645 ACCGAAAAAGTGGTAGTTTTATGCTA 59.288 34.615 0.00 0.00 36.50 3.49
225 227 4.634703 TGACGGGTGCGGCATTGT 62.635 61.111 5.72 5.10 0.00 2.71
226 228 4.101790 GACGGGTGCGGCATTGTG 62.102 66.667 5.72 0.00 0.00 3.33
249 251 4.083484 GGGTTCATTTTCAGTACTTCACCG 60.083 45.833 0.00 0.00 0.00 4.94
285 287 4.617959 GCATGAGTATTGAGTAGCCGTTA 58.382 43.478 0.00 0.00 0.00 3.18
592 595 0.807667 GATGTTCAGAGCGCCATCGT 60.808 55.000 2.29 0.00 38.14 3.73
604 615 2.222819 GCGCCATCGTTTTCTTCTACTG 60.223 50.000 0.00 0.00 38.14 2.74
610 621 5.805994 CCATCGTTTTCTTCTACTGGTACTC 59.194 44.000 0.00 0.00 0.00 2.59
615 626 2.641305 TCTTCTACTGGTACTCGCTCC 58.359 52.381 0.00 0.00 0.00 4.70
621 639 0.242825 CTGGTACTCGCTCCGTGAAA 59.757 55.000 0.00 0.00 0.00 2.69
652 728 9.915629 ATAAGAGTGTTTAGACTTCACTACTTG 57.084 33.333 17.18 0.00 41.58 3.16
679 755 0.176910 GTGGGAGACTAGCTTGGCTC 59.823 60.000 21.36 21.36 40.44 4.70
680 756 0.041833 TGGGAGACTAGCTTGGCTCT 59.958 55.000 26.87 9.25 40.44 4.09
717 794 3.006430 CCATCCATGCATGCATACACAAT 59.994 43.478 31.73 17.18 34.91 2.71
718 795 4.502431 CCATCCATGCATGCATACACAATT 60.502 41.667 31.73 6.60 34.91 2.32
719 796 5.279056 CCATCCATGCATGCATACACAATTA 60.279 40.000 31.73 11.84 34.91 1.40
720 797 5.185668 TCCATGCATGCATACACAATTAC 57.814 39.130 31.73 0.00 34.91 1.89
721 798 4.643784 TCCATGCATGCATACACAATTACA 59.356 37.500 31.73 0.00 34.91 2.41
722 799 5.126707 TCCATGCATGCATACACAATTACAA 59.873 36.000 31.73 0.00 34.91 2.41
872 949 0.312102 GCCTGTCAAGCCAGTTTGTC 59.688 55.000 0.00 0.00 0.00 3.18
1054 1134 1.892468 CAGCAGAGCAAGCGAATTTC 58.108 50.000 0.00 0.00 37.01 2.17
1069 1149 0.730265 ATTTCGCGCGCTTAATTGGA 59.270 45.000 30.48 14.26 0.00 3.53
1079 1159 3.797039 CGCTTAATTGGATCCTGAGTGA 58.203 45.455 14.23 0.00 0.00 3.41
1081 1161 4.818546 CGCTTAATTGGATCCTGAGTGAAT 59.181 41.667 14.23 0.00 0.00 2.57
1082 1162 5.277683 CGCTTAATTGGATCCTGAGTGAATG 60.278 44.000 14.23 0.00 0.00 2.67
1083 1163 5.824624 GCTTAATTGGATCCTGAGTGAATGA 59.175 40.000 14.23 0.00 0.00 2.57
1084 1164 6.017275 GCTTAATTGGATCCTGAGTGAATGAG 60.017 42.308 14.23 6.45 0.00 2.90
1114 1198 0.538057 TGAAAAGGAGGCAGCTGTGG 60.538 55.000 16.64 0.00 0.00 4.17
1115 1199 0.538287 GAAAAGGAGGCAGCTGTGGT 60.538 55.000 16.64 0.00 0.00 4.16
1192 1282 4.585216 TTCCACCCCTCCCCGTGT 62.585 66.667 0.00 0.00 0.00 4.49
1273 1363 3.532155 ACGGCGCTCATCCTCTCC 61.532 66.667 6.90 0.00 0.00 3.71
1286 1376 4.772231 TCTCCCCGTTCCCCGAGG 62.772 72.222 0.00 0.00 39.56 4.63
1675 1768 1.738099 CGGCGTCTCCTTCAAGGTG 60.738 63.158 2.50 0.28 36.53 4.00
1870 1963 1.086067 CCTCACAGCAGGTACGCATG 61.086 60.000 0.00 0.00 0.00 4.06
1883 1980 1.302366 ACGCATGCATCACCATGTAG 58.698 50.000 19.57 0.00 43.46 2.74
1884 1981 1.302366 CGCATGCATCACCATGTAGT 58.698 50.000 19.57 0.00 43.46 2.73
1900 1997 0.109039 TAGTACGTGCATTGCAGCGA 60.109 50.000 27.89 15.52 40.08 4.93
1904 2001 2.638719 GTGCATTGCAGCGACACA 59.361 55.556 12.53 0.00 40.08 3.72
2194 2295 3.531207 CAGGAGGAGATCGCCGCA 61.531 66.667 19.97 0.00 40.51 5.69
2247 2348 3.434319 CATGCTCCGCGGCAACTT 61.434 61.111 23.51 7.37 45.68 2.66
2264 2365 8.221766 GCGGCAACTTTATAAATCATACTACTC 58.778 37.037 0.00 0.00 0.00 2.59
2265 2366 9.256477 CGGCAACTTTATAAATCATACTACTCA 57.744 33.333 0.00 0.00 0.00 3.41
2332 2459 3.065233 TCAATCGAGGATTTCATTTGCCG 59.935 43.478 0.00 0.00 28.87 5.69
3086 3218 2.981909 GGCAAGCTGCTGCACTCA 60.982 61.111 18.42 0.00 44.28 3.41
3384 3516 2.919856 ACCAGACGCTGCACCTCT 60.920 61.111 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 8.124586 TCACGTTGTTAACATTTTAACTCGTA 57.875 30.769 23.29 15.50 45.59 3.43
44 45 7.324354 ACCTCACGTTGTTAACATTTTAACT 57.676 32.000 9.56 0.00 45.15 2.24
48 49 7.892778 AAAAACCTCACGTTGTTAACATTTT 57.107 28.000 9.56 7.67 29.54 1.82
127 129 7.486407 TCGGTTAGGGTTCTAAGAAGTTATT 57.514 36.000 0.00 0.00 36.27 1.40
128 130 7.486407 TTCGGTTAGGGTTCTAAGAAGTTAT 57.514 36.000 0.00 0.00 36.27 1.89
130 132 5.813513 TTCGGTTAGGGTTCTAAGAAGTT 57.186 39.130 0.00 0.00 36.27 2.66
144 146 7.536281 GCATAAAACTACCACTTTTTCGGTTAG 59.464 37.037 0.00 0.00 36.69 2.34
187 189 7.984050 CCGTCAGATTAAGCTATTCCATCATAT 59.016 37.037 0.00 0.00 0.00 1.78
190 192 5.511373 CCCGTCAGATTAAGCTATTCCATCA 60.511 44.000 0.00 0.00 0.00 3.07
191 193 4.932200 CCCGTCAGATTAAGCTATTCCATC 59.068 45.833 0.00 0.00 0.00 3.51
195 197 3.495001 GCACCCGTCAGATTAAGCTATTC 59.505 47.826 0.00 0.00 0.00 1.75
225 227 4.825085 GGTGAAGTACTGAAAATGAACCCA 59.175 41.667 0.00 0.00 0.00 4.51
226 228 4.083484 CGGTGAAGTACTGAAAATGAACCC 60.083 45.833 0.00 0.00 37.93 4.11
285 287 5.814705 GTGACTTAGCTTGCAAGATAGATGT 59.185 40.000 30.39 23.77 0.00 3.06
349 351 7.496920 ACGCCATTATTATGTATCATCATGGAG 59.503 37.037 0.00 0.00 0.00 3.86
592 595 4.082354 GGAGCGAGTACCAGTAGAAGAAAA 60.082 45.833 0.00 0.00 0.00 2.29
604 615 1.787012 TTTTTCACGGAGCGAGTACC 58.213 50.000 0.00 0.00 0.00 3.34
652 728 4.479786 AGCTAGTCTCCCACTTCAAATC 57.520 45.455 0.00 0.00 36.43 2.17
717 794 0.531090 ACACGAGCCGCAGTTTGTAA 60.531 50.000 0.00 0.00 0.00 2.41
718 795 0.314618 TACACGAGCCGCAGTTTGTA 59.685 50.000 0.00 0.00 0.00 2.41
719 796 1.068417 TACACGAGCCGCAGTTTGT 59.932 52.632 0.00 0.00 0.00 2.83
720 797 0.944311 AGTACACGAGCCGCAGTTTG 60.944 55.000 0.00 0.00 0.00 2.93
721 798 0.666577 GAGTACACGAGCCGCAGTTT 60.667 55.000 0.00 0.00 0.00 2.66
722 799 1.080705 GAGTACACGAGCCGCAGTT 60.081 57.895 0.00 0.00 0.00 3.16
872 949 5.297278 AGAAAGGCTAGTACAGTACGAGATG 59.703 44.000 21.47 6.19 33.88 2.90
1054 1134 1.082756 GGATCCAATTAAGCGCGCG 60.083 57.895 28.44 28.44 0.00 6.86
1069 1149 1.202510 GCGCTCTCATTCACTCAGGAT 60.203 52.381 0.00 0.00 0.00 3.24
1114 1198 0.728129 TGACGACGTGCTCGATCAAC 60.728 55.000 16.04 6.30 46.14 3.18
1115 1199 0.170339 ATGACGACGTGCTCGATCAA 59.830 50.000 16.04 0.00 46.14 2.57
1192 1282 1.511305 GCTCTGCACGTAGTAGGCA 59.489 57.895 0.00 0.00 41.61 4.75
1675 1768 4.660938 AACCGCTCCACCTTGCCC 62.661 66.667 0.00 0.00 0.00 5.36
1870 1963 1.593006 GCACGTACTACATGGTGATGC 59.407 52.381 0.00 0.00 32.14 3.91
1883 1980 1.225745 GTCGCTGCAATGCACGTAC 60.226 57.895 22.08 16.79 35.70 3.67
1884 1981 1.666234 TGTCGCTGCAATGCACGTA 60.666 52.632 22.08 13.83 35.70 3.57
1900 1997 0.039326 AGACTACTAGGCGGGTGTGT 59.961 55.000 0.00 0.00 0.00 3.72
1904 2001 0.324460 AAGCAGACTACTAGGCGGGT 60.324 55.000 0.00 0.00 28.03 5.28
2104 2205 3.437795 CCACGCGGTACCGAGACT 61.438 66.667 39.18 19.24 41.57 3.24
2407 2534 6.288294 ACTCAGTAGACAATTTGCACAAGTA 58.712 36.000 0.00 0.00 0.00 2.24
2504 2636 2.474526 CCATCGAGTGCTTAAACGCTTG 60.475 50.000 0.89 0.89 33.57 4.01
3007 3139 2.391724 GACCAAGGTGGCCTCGTTCA 62.392 60.000 9.68 0.00 42.67 3.18
3194 3326 3.073228 CAGGTCCTTGTCCTGGAGA 57.927 57.895 0.00 0.00 46.03 3.71
3199 3331 0.545548 GGAGACCAGGTCCTTGTCCT 60.546 60.000 16.72 7.03 32.18 3.85


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

AutoCloner maintained by Alex Coulton.