Multiple sequence alignment - TraesCS2B01G361500

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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 TraesCS2B01G361500 chr2B 100.000 3859 0 0 1 3859 514553050 514549192 0 7127
1 TraesCS2B01G361500 chr2B 95.859 3864 131 8 1 3859 123382169 123386008 0 6222
2 TraesCS2B01G361500 chr2B 95.234 3504 138 15 361 3859 35778468 35774989 0 5518
3 TraesCS2B01G361500 chr4B 96.609 3863 95 15 1 3859 173393420 173389590 0 6375
4 TraesCS2B01G361500 chr4B 95.938 3865 120 13 1 3859 89440493 89436660 0 6233
5 TraesCS2B01G361500 chr4B 95.806 3839 132 17 1 3831 629506241 629510058 0 6170
6 TraesCS2B01G361500 chr4B 95.626 3864 128 13 1 3859 199607601 199611428 0 6161
7 TraesCS2B01G361500 chr4B 95.215 3866 144 14 1 3859 30501929 30505760 0 6076
8 TraesCS2B01G361500 chr3B 96.301 3866 115 11 1 3859 646354832 646358676 0 6322
9 TraesCS2B01G361500 chr3B 96.065 3863 125 12 1 3857 656109232 656105391 0 6266
10 TraesCS2B01G361500 chr3B 94.391 3227 133 9 636 3859 281592073 281588892 0 4913
11 TraesCS2B01G361500 chr7B 96.144 3812 113 10 52 3859 192829159 192825378 0 6194
12 TraesCS2B01G361500 chr7B 95.732 3866 129 11 1 3859 330126037 330129873 0 6192
13 TraesCS2B01G361500 chr5B 95.525 3866 145 14 1 3859 519961574 519957730 0 6156
14 TraesCS2B01G361500 chr5B 96.109 2416 62 13 1456 3859 358455054 358452659 0 3912
15 TraesCS2B01G361500 chr1B 95.497 3864 143 13 1 3859 575067001 575063164 0 6143
16 TraesCS2B01G361500 chr1B 93.856 3890 188 30 1 3859 84522058 84518189 0 5812


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 TraesCS2B01G361500 chr2B 514549192 514553050 3858 True 7127 7127 100.000 1 3859 1 chr2B.!!$R2 3858
1 TraesCS2B01G361500 chr2B 123382169 123386008 3839 False 6222 6222 95.859 1 3859 1 chr2B.!!$F1 3858
2 TraesCS2B01G361500 chr2B 35774989 35778468 3479 True 5518 5518 95.234 361 3859 1 chr2B.!!$R1 3498
3 TraesCS2B01G361500 chr4B 173389590 173393420 3830 True 6375 6375 96.609 1 3859 1 chr4B.!!$R2 3858
4 TraesCS2B01G361500 chr4B 89436660 89440493 3833 True 6233 6233 95.938 1 3859 1 chr4B.!!$R1 3858
5 TraesCS2B01G361500 chr4B 629506241 629510058 3817 False 6170 6170 95.806 1 3831 1 chr4B.!!$F3 3830
6 TraesCS2B01G361500 chr4B 199607601 199611428 3827 False 6161 6161 95.626 1 3859 1 chr4B.!!$F2 3858
7 TraesCS2B01G361500 chr4B 30501929 30505760 3831 False 6076 6076 95.215 1 3859 1 chr4B.!!$F1 3858
8 TraesCS2B01G361500 chr3B 646354832 646358676 3844 False 6322 6322 96.301 1 3859 1 chr3B.!!$F1 3858
9 TraesCS2B01G361500 chr3B 656105391 656109232 3841 True 6266 6266 96.065 1 3857 1 chr3B.!!$R2 3856
10 TraesCS2B01G361500 chr3B 281588892 281592073 3181 True 4913 4913 94.391 636 3859 1 chr3B.!!$R1 3223
11 TraesCS2B01G361500 chr7B 192825378 192829159 3781 True 6194 6194 96.144 52 3859 1 chr7B.!!$R1 3807
12 TraesCS2B01G361500 chr7B 330126037 330129873 3836 False 6192 6192 95.732 1 3859 1 chr7B.!!$F1 3858
13 TraesCS2B01G361500 chr5B 519957730 519961574 3844 True 6156 6156 95.525 1 3859 1 chr5B.!!$R2 3858
14 TraesCS2B01G361500 chr5B 358452659 358455054 2395 True 3912 3912 96.109 1456 3859 1 chr5B.!!$R1 2403
15 TraesCS2B01G361500 chr1B 575063164 575067001 3837 True 6143 6143 95.497 1 3859 1 chr1B.!!$R2 3858
16 TraesCS2B01G361500 chr1B 84518189 84522058 3869 True 5812 5812 93.856 1 3859 1 chr1B.!!$R1 3858

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
946 976 0.539438 TGCCGCTTCCATTTCCACTT 60.539 50.0 0.00 0.0 0.0 3.16 F
2455 2501 0.108585 AAGCGCCTCAAAGACTTCCA 59.891 50.0 2.29 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2681 2728 0.111639 GGCTGTTCCCCCACAGTTTA 59.888 55.000 2.95 0.0 45.31 2.01 R
3275 3341 1.549170 TCCTCGGCTGAAACTTAGTCC 59.451 52.381 0.00 0.0 0.00 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
158 159 7.224753 TGACAAGTTCAACTACTAAAGCTCAAG 59.775 37.037 0.00 0.00 0.00 3.02
267 270 4.692523 AAATAATCTCAAACCCCCACCT 57.307 40.909 0.00 0.00 0.00 4.00
572 579 9.988815 CACTAGTGTATAAAGGCTTCAATAGAT 57.011 33.333 20.81 8.33 33.13 1.98
655 679 2.234168 CAAAATGCCATCATCACCACCA 59.766 45.455 0.00 0.00 31.27 4.17
721 745 7.011109 GCTTGACAAGACTAGTTAGTTCAACAA 59.989 37.037 19.51 0.00 39.81 2.83
760 784 2.354805 GGATGGTTAGTTCTTCCACGCT 60.355 50.000 0.00 0.00 33.91 5.07
899 929 9.533253 CTGCAAAAATACCCCATTTTCTTATAG 57.467 33.333 0.00 0.00 44.37 1.31
946 976 0.539438 TGCCGCTTCCATTTCCACTT 60.539 50.000 0.00 0.00 0.00 3.16
956 986 3.066064 TCCATTTCCACTTCACACAAACG 59.934 43.478 0.00 0.00 0.00 3.60
961 991 1.946768 CCACTTCACACAAACGTCCAT 59.053 47.619 0.00 0.00 0.00 3.41
1003 1033 2.721167 CGTCGGAGGAAGGCCATGA 61.721 63.158 5.01 0.00 36.29 3.07
1117 1147 0.250295 CACCAGAACGCTCAAAGGGA 60.250 55.000 0.00 0.00 31.91 4.20
1194 1224 1.741732 GCCAACGAGATGATGAGCAGT 60.742 52.381 0.00 0.00 0.00 4.40
1233 1263 3.386768 GGCTTGTATCCGAGCTTCATA 57.613 47.619 0.00 0.00 45.90 2.15
1239 1269 3.821600 TGTATCCGAGCTTCATAGGAGTC 59.178 47.826 0.00 0.00 36.08 3.36
1844 1877 9.838975 TTAAGTTACATGCATTTCAGTTACATG 57.161 29.630 0.00 0.00 42.92 3.21
1845 1878 6.324819 AGTTACATGCATTTCAGTTACATGC 58.675 36.000 0.00 0.00 41.38 4.06
1863 1896 4.202101 ACATGCATTTCCGAAACTGTGAAA 60.202 37.500 0.00 0.00 33.00 2.69
2175 2213 7.373778 TGAATCAAGCAGTGCATATATCATC 57.626 36.000 19.20 5.64 0.00 2.92
2213 2251 8.985315 ATGATTCTCTAATTTGGTGAAGCATA 57.015 30.769 19.80 2.43 39.66 3.14
2455 2501 0.108585 AAGCGCCTCAAAGACTTCCA 59.891 50.000 2.29 0.00 0.00 3.53
2481 2527 6.015434 GTGGGAGGAGAAATTGTACACATTTT 60.015 38.462 13.58 7.18 33.65 1.82
2681 2728 3.848975 AGAAGATGAACAGGGAAGACCAT 59.151 43.478 0.00 0.00 43.89 3.55
2925 2979 7.500892 TGTGTGTCCTTAGTATTGTTGTTTCAT 59.499 33.333 0.00 0.00 0.00 2.57
3087 3144 7.596494 TCATCCATGATTTGAAGTTGAAACTC 58.404 34.615 0.00 0.00 38.57 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
307 313 5.011635 TCCTGCTGTTTTAGTACTGATGTCA 59.988 40.000 5.39 0.00 0.00 3.58
464 471 9.535878 TTTTATTTTCATCTGTACCAACCAAAC 57.464 29.630 0.00 0.00 0.00 2.93
572 579 7.660617 TCCGTGTGGATGTTTAAGTATTGTTTA 59.339 33.333 0.00 0.00 40.17 2.01
655 679 1.069765 CCCACTTGCACGTCTCTGT 59.930 57.895 0.00 0.00 0.00 3.41
899 929 1.827399 TTGTGGGAACGAGGGAGAGC 61.827 60.000 0.00 0.00 0.00 4.09
956 986 2.737039 GCTTTGGAGAGAGACGATGGAC 60.737 54.545 0.00 0.00 0.00 4.02
961 991 0.541998 TGGGCTTTGGAGAGAGACGA 60.542 55.000 0.00 0.00 0.00 4.20
1117 1147 1.377725 CCTTGCCGTGGAGCTCAAT 60.378 57.895 17.19 0.00 0.00 2.57
1194 1224 1.045350 CGCCTCCCTTCATCCTGAGA 61.045 60.000 0.00 0.00 0.00 3.27
1233 1263 2.093106 GTGTACTCCACATCGACTCCT 58.907 52.381 0.00 0.00 43.92 3.69
1836 1869 4.518970 ACAGTTTCGGAAATGCATGTAACT 59.481 37.500 3.26 0.00 34.34 2.24
1837 1870 4.616802 CACAGTTTCGGAAATGCATGTAAC 59.383 41.667 3.26 0.00 34.34 2.50
1838 1871 4.517075 TCACAGTTTCGGAAATGCATGTAA 59.483 37.500 3.26 0.00 34.34 2.41
1839 1872 4.068599 TCACAGTTTCGGAAATGCATGTA 58.931 39.130 3.26 0.00 34.34 2.29
1840 1873 2.884012 TCACAGTTTCGGAAATGCATGT 59.116 40.909 3.26 0.00 34.34 3.21
1841 1874 3.557577 TCACAGTTTCGGAAATGCATG 57.442 42.857 3.26 6.46 34.34 4.06
1842 1875 4.582701 TTTCACAGTTTCGGAAATGCAT 57.417 36.364 3.26 0.00 34.34 3.96
1843 1876 4.297510 CATTTCACAGTTTCGGAAATGCA 58.702 39.130 3.26 0.00 46.03 3.96
1844 1877 4.891277 CATTTCACAGTTTCGGAAATGC 57.109 40.909 3.26 0.00 46.03 3.56
1846 1879 5.982890 ATCCATTTCACAGTTTCGGAAAT 57.017 34.783 6.43 0.00 40.76 2.17
1847 1880 5.068460 ACAATCCATTTCACAGTTTCGGAAA 59.932 36.000 0.00 0.00 35.27 3.13
1848 1881 4.582656 ACAATCCATTTCACAGTTTCGGAA 59.417 37.500 0.00 0.00 0.00 4.30
1849 1882 4.141287 ACAATCCATTTCACAGTTTCGGA 58.859 39.130 0.00 0.00 0.00 4.55
1850 1883 4.503741 ACAATCCATTTCACAGTTTCGG 57.496 40.909 0.00 0.00 0.00 4.30
1863 1896 5.263599 TGCTAATCTGGTGAAACAATCCAT 58.736 37.500 0.00 0.00 39.98 3.41
1906 1941 8.851541 AATTTGGTGCATAAATTTCAGAACAT 57.148 26.923 15.01 0.00 34.93 2.71
2175 2213 8.879342 ATTAGAGAATCATTTTACCAGAGTCG 57.121 34.615 0.00 0.00 37.82 4.18
2213 2251 2.939103 GCTATCTTCGTTGCTTCACCAT 59.061 45.455 0.00 0.00 0.00 3.55
2455 2501 3.650942 TGTGTACAATTTCTCCTCCCACT 59.349 43.478 0.00 0.00 0.00 4.00
2481 2527 1.761784 ACCTGCAATGCTGAAACCAAA 59.238 42.857 13.76 0.00 0.00 3.28
2497 2543 3.181367 GCATCCGCTTGTCACCTG 58.819 61.111 0.00 0.00 34.30 4.00
2681 2728 0.111639 GGCTGTTCCCCCACAGTTTA 59.888 55.000 2.95 0.00 45.31 2.01
2925 2979 9.388346 CAACATAACGAAAGCAAACTACAAATA 57.612 29.630 0.00 0.00 0.00 1.40
3087 3144 4.465512 GTTGCGTGGCAGCCATCG 62.466 66.667 19.75 22.49 40.61 3.84
3275 3341 1.549170 TCCTCGGCTGAAACTTAGTCC 59.451 52.381 0.00 0.00 0.00 3.85
3424 3490 2.676632 ACCGTGTGTTCAACTGTACA 57.323 45.000 0.00 0.00 0.00 2.90
3661 3734 6.811170 TGTTGTGTTTCTTGTGATTTTTCTCC 59.189 34.615 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.