Multiple sequence alignment - TraesCS4B01G151000

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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 TraesCS4B01G151000 chr4B 100.000 2246 0 0 1 2246 239620479 239622724 0.000000e+00 4148.0
1 TraesCS4B01G151000 chr4B 96.616 2246 73 3 1 2246 240016198 240013956 0.000000e+00 3723.0
2 TraesCS4B01G151000 chr3A 94.417 1236 59 2 1 1227 433764530 433765764 0.000000e+00 1892.0
3 TraesCS4B01G151000 chr3A 92.632 1235 81 2 1 1225 575149671 575150905 0.000000e+00 1768.0
4 TraesCS4B01G151000 chr3A 87.302 63 0 1 2160 2214 730070095 730070033 5.180000e-07 65.8
5 TraesCS4B01G151000 chr7B 94.008 1235 63 4 1 1226 365876216 365874984 0.000000e+00 1860.0
6 TraesCS4B01G151000 chr7B 92.045 616 37 6 1234 1845 658576787 658576180 0.000000e+00 856.0
7 TraesCS4B01G151000 chr7B 92.045 616 37 6 1234 1845 658687106 658686499 0.000000e+00 856.0
8 TraesCS4B01G151000 chr4D 93.937 1237 63 4 1 1227 210026558 210025324 0.000000e+00 1858.0
9 TraesCS4B01G151000 chr1B 93.431 1233 72 2 1 1224 40282516 40283748 0.000000e+00 1820.0
10 TraesCS4B01G151000 chr5A 91.754 1237 89 7 1 1225 173529042 173527807 0.000000e+00 1707.0
11 TraesCS4B01G151000 chr5A 92.786 804 47 6 1 793 683756640 683755837 0.000000e+00 1153.0
12 TraesCS4B01G151000 chr5A 93.793 435 27 0 791 1225 683752375 683751941 0.000000e+00 654.0
13 TraesCS4B01G151000 chr5B 94.383 819 37 4 1 810 415416744 415415926 0.000000e+00 1249.0
14 TraesCS4B01G151000 chr5B 94.759 477 24 1 1770 2245 599243130 599242654 0.000000e+00 741.0
15 TraesCS4B01G151000 chr5D 91.170 906 61 11 1 890 68971077 68971979 0.000000e+00 1212.0
16 TraesCS4B01G151000 chr4A 89.789 901 72 11 1 890 292710043 292709152 0.000000e+00 1136.0
17 TraesCS4B01G151000 chr4A 92.058 617 35 6 1234 1845 664564527 664565134 0.000000e+00 856.0
18 TraesCS4B01G151000 chr7A 95.958 569 23 0 659 1227 617960339 617959771 0.000000e+00 924.0
19 TraesCS4B01G151000 chr7A 97.222 36 1 0 610 645 458388920 458388955 6.700000e-06 62.1
20 TraesCS4B01G151000 chr3B 92.220 617 35 5 1234 1845 673561259 673561867 0.000000e+00 861.0
21 TraesCS4B01G151000 chr3B 75.984 254 38 10 1980 2214 808015136 808014887 2.360000e-20 110.0
22 TraesCS4B01G151000 chrUn 92.058 617 35 6 1234 1845 49051120 49051727 0.000000e+00 856.0
23 TraesCS4B01G151000 chrUn 92.058 617 35 6 1234 1845 49054914 49055521 0.000000e+00 856.0
24 TraesCS4B01G151000 chrUn 92.058 617 35 6 1234 1845 49106606 49107213 0.000000e+00 856.0
25 TraesCS4B01G151000 chrUn 92.045 616 37 6 1234 1845 307452866 307452259 0.000000e+00 856.0
26 TraesCS4B01G151000 chr3D 82.909 275 27 10 1980 2240 600652447 600652179 1.740000e-56 230.0
27 TraesCS4B01G151000 chr3D 91.089 101 8 1 1882 1981 600652581 600652481 3.890000e-28 135.0


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 TraesCS4B01G151000 chr4B 239620479 239622724 2245 False 4148.0 4148 100.0000 1 2246 1 chr4B.!!$F1 2245
1 TraesCS4B01G151000 chr4B 240013956 240016198 2242 True 3723.0 3723 96.6160 1 2246 1 chr4B.!!$R1 2245
2 TraesCS4B01G151000 chr3A 433764530 433765764 1234 False 1892.0 1892 94.4170 1 1227 1 chr3A.!!$F1 1226
3 TraesCS4B01G151000 chr3A 575149671 575150905 1234 False 1768.0 1768 92.6320 1 1225 1 chr3A.!!$F2 1224
4 TraesCS4B01G151000 chr7B 365874984 365876216 1232 True 1860.0 1860 94.0080 1 1226 1 chr7B.!!$R1 1225
5 TraesCS4B01G151000 chr7B 658576180 658576787 607 True 856.0 856 92.0450 1234 1845 1 chr7B.!!$R2 611
6 TraesCS4B01G151000 chr7B 658686499 658687106 607 True 856.0 856 92.0450 1234 1845 1 chr7B.!!$R3 611
7 TraesCS4B01G151000 chr4D 210025324 210026558 1234 True 1858.0 1858 93.9370 1 1227 1 chr4D.!!$R1 1226
8 TraesCS4B01G151000 chr1B 40282516 40283748 1232 False 1820.0 1820 93.4310 1 1224 1 chr1B.!!$F1 1223
9 TraesCS4B01G151000 chr5A 173527807 173529042 1235 True 1707.0 1707 91.7540 1 1225 1 chr5A.!!$R1 1224
10 TraesCS4B01G151000 chr5A 683751941 683756640 4699 True 903.5 1153 93.2895 1 1225 2 chr5A.!!$R2 1224
11 TraesCS4B01G151000 chr5B 415415926 415416744 818 True 1249.0 1249 94.3830 1 810 1 chr5B.!!$R1 809
12 TraesCS4B01G151000 chr5D 68971077 68971979 902 False 1212.0 1212 91.1700 1 890 1 chr5D.!!$F1 889
13 TraesCS4B01G151000 chr4A 292709152 292710043 891 True 1136.0 1136 89.7890 1 890 1 chr4A.!!$R1 889
14 TraesCS4B01G151000 chr4A 664564527 664565134 607 False 856.0 856 92.0580 1234 1845 1 chr4A.!!$F1 611
15 TraesCS4B01G151000 chr7A 617959771 617960339 568 True 924.0 924 95.9580 659 1227 1 chr7A.!!$R1 568
16 TraesCS4B01G151000 chr3B 673561259 673561867 608 False 861.0 861 92.2200 1234 1845 1 chr3B.!!$F1 611
17 TraesCS4B01G151000 chrUn 49051120 49055521 4401 False 856.0 856 92.0580 1234 1845 2 chrUn.!!$F2 611
18 TraesCS4B01G151000 chrUn 49106606 49107213 607 False 856.0 856 92.0580 1234 1845 1 chrUn.!!$F1 611
19 TraesCS4B01G151000 chrUn 307452259 307452866 607 True 856.0 856 92.0450 1234 1845 1 chrUn.!!$R1 611

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
582 602 0.31179 AAAGCACTTGCACCATGACG 59.688 50.0 3.62 0.0 45.16 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2045 9334 0.321021 CAGAGCCTCACAGAGCTTGT 59.679 55.0 0.0 0.0 40.11 3.16 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
543 553 5.596772 ACCCTAAAGAAAGTAGCAAGCAAAA 59.403 36.000 0.00 0.00 0.00 2.44
582 602 0.311790 AAAGCACTTGCACCATGACG 59.688 50.000 3.62 0.00 45.16 4.35
852 4338 7.991647 AACTATAGCTAAAGGAAGGGTAAGT 57.008 36.000 0.00 0.00 0.00 2.24
949 4436 6.375455 AGCATAAGTAACCACCAAAATCTCTG 59.625 38.462 0.00 0.00 0.00 3.35
1098 4586 1.234821 GTGTTGCCCATCTCGAACAA 58.765 50.000 0.00 0.00 30.43 2.83
1155 4643 1.040646 CCCTTGAGCTACCGCATCTA 58.959 55.000 0.00 0.00 39.10 1.98
1246 4734 3.367910 GCTTCACGAGAGGAAGAAGTGAT 60.368 47.826 6.35 0.00 43.46 3.06
1321 8603 4.704833 GGTCAGCGGCAGGAGCAA 62.705 66.667 15.79 0.00 44.61 3.91
1324 8606 2.670934 CAGCGGCAGGAGCAACTT 60.671 61.111 1.45 0.00 44.61 2.66
1401 8683 4.248842 TACCATCATGCGCCCCCG 62.249 66.667 4.18 0.00 37.57 5.73
1669 8951 2.365293 GACCTTGCACCAAGACCATTTT 59.635 45.455 6.54 0.00 43.42 1.82
1748 9032 8.798859 AAATAAGAGACAGTGCAAGATGTTAT 57.201 30.769 0.00 0.00 0.00 1.89
1944 9233 9.182933 CAGAAGTGTAGTACTCAAACTAAGAAC 57.817 37.037 0.00 0.00 39.18 3.01
1957 9246 4.640789 ACTAAGAACAGCATAGAGACCG 57.359 45.455 0.00 0.00 0.00 4.79
2041 9330 9.088512 CAGTAAAAGTATCAACTACATCAGGAC 57.911 37.037 0.00 0.00 33.75 3.85
2045 9334 7.482169 AAGTATCAACTACATCAGGACTCAA 57.518 36.000 0.00 0.00 33.75 3.02
2050 9339 3.931578 ACTACATCAGGACTCAACAAGC 58.068 45.455 0.00 0.00 0.00 4.01
2054 9343 2.827800 TCAGGACTCAACAAGCTCTG 57.172 50.000 0.00 0.00 32.62 3.35
2074 9363 2.767960 TGTGAGGCTCTGCTATCATCAA 59.232 45.455 16.72 0.00 30.25 2.57
2097 9386 2.019984 GAGCATTGTTGGGATCCTCAC 58.980 52.381 12.58 9.21 0.00 3.51
2098 9387 1.355381 AGCATTGTTGGGATCCTCACA 59.645 47.619 12.58 11.83 0.00 3.58
2101 9390 2.401583 TTGTTGGGATCCTCACATCG 57.598 50.000 12.58 0.00 24.99 3.84
2115 9404 2.935849 TCACATCGGATTCCAATTGTCG 59.064 45.455 4.43 0.99 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
131 133 8.038351 TGTGATTGCAGTAGTATTTACTTGCTA 58.962 33.333 12.96 7.92 39.54 3.49
468 478 8.644216 ACACGGGAGTTATGTATACAAATCATA 58.356 33.333 10.14 0.00 44.67 2.15
582 602 0.034089 ATACCCAGGTCAAGCTTGCC 60.034 55.000 21.99 23.26 0.00 4.52
949 4436 8.113173 AGGTCTCTAGTTAATGATCGGTATTC 57.887 38.462 0.00 0.00 0.00 1.75
1155 4643 2.203337 TTTGCTGCCTCGCCTTGT 60.203 55.556 0.00 0.00 0.00 3.16
1162 4650 3.192001 TGATTCTTCATGTTTGCTGCCTC 59.808 43.478 0.00 0.00 0.00 4.70
1246 4734 4.709886 TGGTGAGACAATTTCCTCGATCTA 59.290 41.667 0.00 0.00 32.30 1.98
1292 8574 0.035458 CGCTGACCCTCCTCAACTTT 59.965 55.000 0.00 0.00 0.00 2.66
1568 8850 6.515272 ACAGAAATATGTTGTGGTTCCATC 57.485 37.500 0.00 0.00 0.00 3.51
1570 8852 6.774673 TCTACAGAAATATGTTGTGGTTCCA 58.225 36.000 0.00 0.00 34.56 3.53
1653 8935 5.184864 CAGGTATAAAAATGGTCTTGGTGCA 59.815 40.000 0.00 0.00 0.00 4.57
1669 8951 6.094881 GCTTTTTGCACCATACTCAGGTATAA 59.905 38.462 0.00 0.00 42.31 0.98
1748 9032 2.751259 CTGCTTGCCTCATTCAGCTTAA 59.249 45.455 0.00 0.00 0.00 1.85
1872 9161 4.127171 GGTTAGCACTCAACTTCTGTTCA 58.873 43.478 0.00 0.00 33.52 3.18
1918 9207 9.182933 GTTCTTAGTTTGAGTACTACACTTCTG 57.817 37.037 0.00 0.00 37.72 3.02
1926 9215 9.239551 TCTATGCTGTTCTTAGTTTGAGTACTA 57.760 33.333 0.00 0.00 0.00 1.82
1944 9233 2.659897 GCGGCGGTCTCTATGCTG 60.660 66.667 9.78 0.00 38.04 4.41
1957 9246 1.860676 TTCGTAATCCAGTATGCGGC 58.139 50.000 0.00 0.00 31.97 6.53
2041 9330 1.155042 GCCTCACAGAGCTTGTTGAG 58.845 55.000 10.85 10.85 38.16 3.02
2045 9334 0.321021 CAGAGCCTCACAGAGCTTGT 59.679 55.000 0.00 0.00 40.11 3.16
2050 9339 2.030371 TGATAGCAGAGCCTCACAGAG 58.970 52.381 0.00 0.00 0.00 3.35
2054 9343 3.069300 TCTTGATGATAGCAGAGCCTCAC 59.931 47.826 0.00 0.00 0.00 3.51
2074 9363 2.172293 GAGGATCCCAACAATGCTCTCT 59.828 50.000 8.55 0.00 38.25 3.10
2097 9386 1.002468 GGCGACAATTGGAATCCGATG 60.002 52.381 10.83 0.00 0.00 3.84
2098 9387 1.308998 GGCGACAATTGGAATCCGAT 58.691 50.000 10.83 0.00 0.00 4.18
2101 9390 1.091537 TTCGGCGACAATTGGAATCC 58.908 50.000 10.16 4.50 0.00 3.01
2166 9455 7.195646 ACATGTTGAACAACTACACAAATCTG 58.804 34.615 16.70 0.00 41.67 2.90
2168 9457 7.985634 AACATGTTGAACAACTACACAAATC 57.014 32.000 11.07 0.00 41.67 2.17


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

AutoCloner maintained by Alex Coulton.