Multiple sequence alignment - TraesCS2B01G529600

Loading Multiple Alignment...

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 TraesCS2B01G529600 chr2B 100.000 2748 0 0 543 3290 724554439 724551692 0.000000e+00 5075.0
1 TraesCS2B01G529600 chr2B 100.000 258 0 0 1 258 724554981 724554724 8.260000e-131 477.0
2 TraesCS2B01G529600 chr2D 96.917 2757 69 9 543 3290 596125428 596122679 0.000000e+00 4606.0
3 TraesCS2B01G529600 chr2D 84.884 258 7 7 1 258 596125832 596125607 7.100000e-57 231.0
4 TraesCS2B01G529600 chr2A 96.719 2743 79 4 559 3290 729778372 729775630 0.000000e+00 4556.0
5 TraesCS2B01G529600 chr2A 85.878 262 5 8 3 258 729778947 729778712 1.960000e-62 250.0
6 TraesCS2B01G529600 chr3A 80.974 431 54 17 1872 2292 501487287 501487699 1.910000e-82 316.0
7 TraesCS2B01G529600 chr7B 90.865 208 17 2 2276 2482 361656456 361656662 8.990000e-71 278.0
8 TraesCS2B01G529600 chr6D 95.238 42 2 0 1900 1941 221565580 221565621 2.120000e-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 TraesCS2B01G529600 chr2B 724551692 724554981 3289 True 2776.0 5075 100.0000 1 3290 2 chr2B.!!$R1 3289
1 TraesCS2B01G529600 chr2D 596122679 596125832 3153 True 2418.5 4606 90.9005 1 3290 2 chr2D.!!$R1 3289
2 TraesCS2B01G529600 chr2A 729775630 729778947 3317 True 2403.0 4556 91.2985 3 3290 2 chr2A.!!$R1 3287

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
24 25 0.463474 GATGAGCAGAGGAGGCCAAC 60.463 60.000 5.01 0.00 0.0 3.77 F
27 28 0.463474 GAGCAGAGGAGGCCAACATC 60.463 60.000 5.01 5.96 0.0 3.06 F
29 30 1.028868 GCAGAGGAGGCCAACATCAC 61.029 60.000 5.01 0.00 0.0 3.06 F
31 32 1.077429 GAGGAGGCCAACATCACCC 60.077 63.158 5.01 0.00 0.0 4.61 F
32 33 1.852157 AGGAGGCCAACATCACCCA 60.852 57.895 5.01 0.00 0.0 4.51 F
38 40 1.948508 CCAACATCACCCACACACG 59.051 57.895 0.00 0.00 0.0 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1203 1270 0.243907 TGAGCTTCTGCGACAGGTAC 59.756 55.000 6.95 0.00 45.42 3.34 R
2025 2092 0.526524 CTCGTCGAACATCAGCTCCC 60.527 60.000 0.00 0.00 0.00 4.30 R
2041 2108 0.453390 GCCCCTTTTCTTGCATCTCG 59.547 55.000 0.00 0.00 0.00 4.04 R
2156 2223 7.877612 TCAAGTGTTGACTTCTGCTATCATTTA 59.122 33.333 0.00 0.00 40.68 1.40 R
2202 2269 0.657840 GGTTTAGCTGCATGGCTACG 59.342 55.000 7.14 0.00 43.40 3.51 R
2339 2412 3.138839 TGAATGTACATCAGATGGGGCAT 59.861 43.478 15.13 11.81 33.60 4.40 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
23 24 0.619832 AGATGAGCAGAGGAGGCCAA 60.620 55.000 5.01 0.00 0.00 4.52
24 25 0.463474 GATGAGCAGAGGAGGCCAAC 60.463 60.000 5.01 0.00 0.00 3.77
25 26 1.203441 ATGAGCAGAGGAGGCCAACA 61.203 55.000 5.01 0.00 0.00 3.33
26 27 1.203441 TGAGCAGAGGAGGCCAACAT 61.203 55.000 5.01 0.00 0.00 2.71
27 28 0.463474 GAGCAGAGGAGGCCAACATC 60.463 60.000 5.01 5.96 0.00 3.06
28 29 1.203441 AGCAGAGGAGGCCAACATCA 61.203 55.000 5.01 0.00 0.00 3.07
29 30 1.028868 GCAGAGGAGGCCAACATCAC 61.029 60.000 5.01 0.00 0.00 3.06
31 32 1.077429 GAGGAGGCCAACATCACCC 60.077 63.158 5.01 0.00 0.00 4.61
32 33 1.852157 AGGAGGCCAACATCACCCA 60.852 57.895 5.01 0.00 0.00 4.51
38 40 1.948508 CCAACATCACCCACACACG 59.051 57.895 0.00 0.00 0.00 4.49
99 105 2.351924 AAAAGGCCTGCTGGTTCGGA 62.352 55.000 5.69 0.00 35.27 4.55
100 106 3.553095 AAGGCCTGCTGGTTCGGAC 62.553 63.158 5.69 0.00 35.27 4.79
735 801 2.438434 CTAGGGTTTGGCCGGCAG 60.438 66.667 30.85 10.59 38.44 4.85
1203 1270 3.429960 GGTACTTCGGCTACTTAAGTGGG 60.430 52.174 18.56 11.49 35.23 4.61
1464 1531 2.320781 CAAGGATCGAGGTCTATGGGT 58.679 52.381 0.00 0.00 0.00 4.51
1495 1562 4.125703 AGATCATCAGTTGAAAGATCGGC 58.874 43.478 15.88 0.00 40.99 5.54
1602 1669 2.881513 TGGCGCATTAAGTTCACTTGAA 59.118 40.909 10.83 0.00 37.40 2.69
1758 1825 4.451096 GCTCAAATGTCGAAAAGTCCTGTA 59.549 41.667 0.00 0.00 0.00 2.74
1814 1881 5.104259 AGTGTAGGTGGATCAAGGAAATC 57.896 43.478 0.00 0.00 0.00 2.17
2025 2092 8.777865 TGATTAGGTCATCTGTTGAGTTAAAG 57.222 34.615 0.00 0.00 34.17 1.85
2041 2108 2.100605 AAAGGGAGCTGATGTTCGAC 57.899 50.000 0.00 0.00 0.00 4.20
2156 2223 3.136077 AGCAGTGGACAATCAGATGCTAT 59.864 43.478 0.00 0.00 38.40 2.97
2202 2269 4.127907 TGATCTCTGCTCATGATTTCAGC 58.872 43.478 12.35 6.05 0.00 4.26
2339 2412 8.572185 TGAAATTTTGTCCGATGTATTTCTTCA 58.428 29.630 0.00 0.00 34.64 3.02
2804 2878 5.959583 ATATTTCTCTTTTCTCCCTCGGT 57.040 39.130 0.00 0.00 0.00 4.69
3047 3125 2.372504 TCCGGTACAATTCCAGTTCCAA 59.627 45.455 0.00 0.00 0.00 3.53
3066 3144 4.892934 TCCAAATAATTGCATGTAGGGACC 59.107 41.667 0.00 0.00 35.10 4.46
3095 3173 5.449304 AGTTTACCGAATTTTGAAGAAGCG 58.551 37.500 0.00 0.00 0.00 4.68
3101 3179 2.882742 ATTTTGAAGAAGCGACGCTC 57.117 45.000 24.69 16.14 38.25 5.03
3118 3196 0.902531 CTCACGGTACCTGAATGGGT 59.097 55.000 10.90 0.00 42.86 4.51
3128 3206 2.311542 ACCTGAATGGGTGCATTTCCTA 59.688 45.455 0.00 0.00 41.11 2.94
3265 3343 6.018262 GTGAGCTATCGTTGCCATTTACAATA 60.018 38.462 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 1.891919 GTGCGTGTGTGGGTGATGT 60.892 57.895 0.00 0.00 0.00 3.06
24 25 1.891449 TGTGCGTGTGTGGGTGATG 60.891 57.895 0.00 0.00 0.00 3.07
25 26 1.891919 GTGTGCGTGTGTGGGTGAT 60.892 57.895 0.00 0.00 0.00 3.06
26 27 2.512745 GTGTGCGTGTGTGGGTGA 60.513 61.111 0.00 0.00 0.00 4.02
27 28 3.582120 GGTGTGCGTGTGTGGGTG 61.582 66.667 0.00 0.00 0.00 4.61
28 29 4.868116 GGGTGTGCGTGTGTGGGT 62.868 66.667 0.00 0.00 0.00 4.51
29 30 4.866224 TGGGTGTGCGTGTGTGGG 62.866 66.667 0.00 0.00 0.00 4.61
31 32 3.935872 CGTGGGTGTGCGTGTGTG 61.936 66.667 0.00 0.00 0.00 3.82
123 129 2.410687 CCGAGAGAAGCGAGGCAGA 61.411 63.158 0.00 0.00 0.00 4.26
124 130 2.103934 CCGAGAGAAGCGAGGCAG 59.896 66.667 0.00 0.00 0.00 4.85
125 131 4.135153 GCCGAGAGAAGCGAGGCA 62.135 66.667 0.00 0.00 46.48 4.75
127 133 2.411290 GAGCCGAGAGAAGCGAGG 59.589 66.667 0.00 0.00 0.00 4.63
128 134 1.781025 ATCGAGCCGAGAGAAGCGAG 61.781 60.000 3.76 0.00 39.91 5.03
212 218 2.048603 AATCTCGGCTTGGGCTTGC 61.049 57.895 0.00 0.00 38.73 4.01
213 219 1.805254 CAATCTCGGCTTGGGCTTG 59.195 57.895 0.00 0.00 38.73 4.01
214 220 2.048603 GCAATCTCGGCTTGGGCTT 61.049 57.895 0.00 0.00 38.73 4.35
215 221 2.439156 GCAATCTCGGCTTGGGCT 60.439 61.111 0.00 0.00 38.73 5.19
216 222 3.880846 CGCAATCTCGGCTTGGGC 61.881 66.667 0.00 0.00 37.82 5.36
1041 1108 4.943252 AGCTGCCGCTGCTGTTGT 62.943 61.111 22.45 0.00 46.86 3.32
1182 1249 3.194329 ACCCACTTAAGTAGCCGAAGTAC 59.806 47.826 8.04 0.00 32.22 2.73
1197 1264 0.830444 TCTGCGACAGGTACCCACTT 60.830 55.000 8.74 0.00 31.51 3.16
1203 1270 0.243907 TGAGCTTCTGCGACAGGTAC 59.756 55.000 6.95 0.00 45.42 3.34
1233 1300 4.978083 AAGCAGGCACATCTTATCAAAG 57.022 40.909 0.00 0.00 0.00 2.77
1464 1531 2.484742 ACTGATGATCTTGCAGTGCA 57.515 45.000 15.37 15.37 41.02 4.57
1495 1562 3.181463 CCATTTGGGCCCATATGTTTCAG 60.181 47.826 37.80 25.36 34.88 3.02
1602 1669 5.551233 TGAAAAGACACCGATCTCTTCAAT 58.449 37.500 0.00 0.00 33.67 2.57
1814 1881 1.665679 CATTAACTGCTGGCGGTAGTG 59.334 52.381 18.05 1.62 39.91 2.74
1845 1912 2.676839 CTCATAACAGCTGCTGAAGTGG 59.323 50.000 34.28 18.66 35.18 4.00
2025 2092 0.526524 CTCGTCGAACATCAGCTCCC 60.527 60.000 0.00 0.00 0.00 4.30
2041 2108 0.453390 GCCCCTTTTCTTGCATCTCG 59.547 55.000 0.00 0.00 0.00 4.04
2156 2223 7.877612 TCAAGTGTTGACTTCTGCTATCATTTA 59.122 33.333 0.00 0.00 40.68 1.40
2202 2269 0.657840 GGTTTAGCTGCATGGCTACG 59.342 55.000 7.14 0.00 43.40 3.51
2339 2412 3.138839 TGAATGTACATCAGATGGGGCAT 59.861 43.478 15.13 11.81 33.60 4.40
2547 2620 4.468510 AGTCGGGACTTATGGATGTAACAA 59.531 41.667 0.00 0.00 38.83 2.83
2804 2878 2.092968 GCCCTGAACAGACACATGGATA 60.093 50.000 3.19 0.00 0.00 2.59
2906 2983 2.100749 AGAACCGCGATCATGATACACA 59.899 45.455 8.23 0.00 0.00 3.72
3010 3088 4.301072 ACCGGAGATTTCTTTCCATTCA 57.699 40.909 9.46 0.00 32.87 2.57
3014 3092 4.627284 TTGTACCGGAGATTTCTTTCCA 57.373 40.909 9.46 0.00 32.87 3.53
3047 3125 4.342092 GCAAGGTCCCTACATGCAATTATT 59.658 41.667 0.00 0.00 38.89 1.40
3066 3144 7.581476 TCTTCAAAATTCGGTAAACTAGCAAG 58.419 34.615 0.00 0.00 0.00 4.01
3095 3173 0.172803 ATTCAGGTACCGTGAGCGTC 59.827 55.000 6.18 0.00 36.15 5.19
3101 3179 1.024579 GCACCCATTCAGGTACCGTG 61.025 60.000 6.18 7.82 38.39 4.94
3118 3196 6.063404 TGCATCTATCAACATAGGAAATGCA 58.937 36.000 10.53 10.53 37.74 3.96


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

AutoCloner maintained by Alex Coulton.