Multiple sequence alignment - TraesCS4A01G107500

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 TraesCS4A01G107500 chr4A 100.000 2276 0 0 1 2276 124243379 124245654 0.000000e+00 4204.0
1 TraesCS4A01G107500 chr4A 87.419 1391 119 41 925 2276 279052882 279051509 0.000000e+00 1548.0
2 TraesCS4A01G107500 chr2A 96.450 1352 37 4 925 2276 361775439 361776779 0.000000e+00 2220.0
3 TraesCS4A01G107500 chr2A 95.772 1348 41 6 925 2272 361754178 361755509 0.000000e+00 2159.0
4 TraesCS4A01G107500 chr2A 96.034 933 37 0 1 933 361753140 361754072 0.000000e+00 1519.0
5 TraesCS4A01G107500 chr2A 96.129 930 36 0 1 930 361774401 361775330 0.000000e+00 1519.0
6 TraesCS4A01G107500 chr2A 92.584 863 54 9 1 860 261452026 261452881 0.000000e+00 1230.0
7 TraesCS4A01G107500 chr2A 82.918 281 34 12 1966 2242 296077547 296077277 8.120000e-60 241.0
8 TraesCS4A01G107500 chr2A 92.029 138 9 2 794 931 45502875 45503010 2.310000e-45 193.0
9 TraesCS4A01G107500 chr2A 91.667 48 4 0 1375 1422 78479005 78478958 1.460000e-07 67.6
10 TraesCS4A01G107500 chr5A 95.938 1354 43 4 925 2276 109701960 109703303 0.000000e+00 2185.0
11 TraesCS4A01G107500 chr5A 95.492 1353 52 4 925 2276 109693827 109695171 0.000000e+00 2152.0
12 TraesCS4A01G107500 chr5A 95.820 933 39 0 1 933 109700922 109701854 0.000000e+00 1507.0
13 TraesCS4A01G107500 chr5A 95.391 933 42 1 1 933 109692790 109693721 0.000000e+00 1483.0
14 TraesCS4A01G107500 chr7A 95.488 1352 50 4 925 2276 328648635 328649975 0.000000e+00 2148.0
15 TraesCS4A01G107500 chr7A 95.344 1353 51 5 925 2276 328640697 328642038 0.000000e+00 2139.0
16 TraesCS4A01G107500 chr7A 94.962 933 47 0 1 933 328639659 328640591 0.000000e+00 1463.0
17 TraesCS4A01G107500 chr3A 95.270 1353 49 4 925 2276 360369978 360371316 0.000000e+00 2130.0
18 TraesCS4A01G107500 chr3A 95.192 1352 55 4 925 2276 360361738 360363079 0.000000e+00 2128.0
19 TraesCS4A01G107500 chr3A 94.962 933 47 0 1 933 360360700 360361632 0.000000e+00 1463.0
20 TraesCS4A01G107500 chr3A 94.844 931 48 0 1 931 360368940 360369870 0.000000e+00 1454.0
21 TraesCS4A01G107500 chr6A 93.255 934 58 5 1 933 351855790 351854861 0.000000e+00 1371.0


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 TraesCS4A01G107500 chr4A 124243379 124245654 2275 False 4204.0 4204 100.0000 1 2276 1 chr4A.!!$F1 2275
1 TraesCS4A01G107500 chr4A 279051509 279052882 1373 True 1548.0 1548 87.4190 925 2276 1 chr4A.!!$R1 1351
2 TraesCS4A01G107500 chr2A 361774401 361776779 2378 False 1869.5 2220 96.2895 1 2276 2 chr2A.!!$F4 2275
3 TraesCS4A01G107500 chr2A 361753140 361755509 2369 False 1839.0 2159 95.9030 1 2272 2 chr2A.!!$F3 2271
4 TraesCS4A01G107500 chr2A 261452026 261452881 855 False 1230.0 1230 92.5840 1 860 1 chr2A.!!$F2 859
5 TraesCS4A01G107500 chr5A 109700922 109703303 2381 False 1846.0 2185 95.8790 1 2276 2 chr5A.!!$F2 2275
6 TraesCS4A01G107500 chr5A 109692790 109695171 2381 False 1817.5 2152 95.4415 1 2276 2 chr5A.!!$F1 2275
7 TraesCS4A01G107500 chr7A 328648635 328649975 1340 False 2148.0 2148 95.4880 925 2276 1 chr7A.!!$F1 1351
8 TraesCS4A01G107500 chr7A 328639659 328642038 2379 False 1801.0 2139 95.1530 1 2276 2 chr7A.!!$F2 2275
9 TraesCS4A01G107500 chr3A 360360700 360363079 2379 False 1795.5 2128 95.0770 1 2276 2 chr3A.!!$F1 2275
10 TraesCS4A01G107500 chr3A 360368940 360371316 2376 False 1792.0 2130 95.0570 1 2276 2 chr3A.!!$F2 2275
11 TraesCS4A01G107500 chr6A 351854861 351855790 929 True 1371.0 1371 93.2550 1 933 1 chr6A.!!$R1 932

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
908 911 0.321653 GGTCTTGGCATCGGACTTGT 60.322 55.0 12.88 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1851 1998 2.249844 ATGTTTTGTTCGACCGGACT 57.75 45.0 9.46 0.0 0.0 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
270 273 2.277591 CCGGGTGTCCCACGAGTTA 61.278 63.158 5.64 0.0 45.83 2.24
300 303 3.541711 GAAACGAGTGACAATTTGGACG 58.458 45.455 0.78 0.0 0.00 4.79
452 455 3.755378 GGTAGTGGAAGTAGTCGTTCTCA 59.245 47.826 0.00 0.0 0.00 3.27
456 459 4.341520 AGTGGAAGTAGTCGTTCTCACTTT 59.658 41.667 0.00 0.0 34.49 2.66
544 547 3.181493 GGTCGACGGTACATGTTCTGTAT 60.181 47.826 16.00 0.0 42.21 2.29
709 712 1.081641 GTCTCGGTTCTTGCGACGA 60.082 57.895 0.00 0.0 0.00 4.20
908 911 0.321653 GGTCTTGGCATCGGACTTGT 60.322 55.000 12.88 0.0 0.00 3.16
1016 1133 1.693640 CCATGGAGGCAGGAAGGTT 59.306 57.895 5.56 0.0 0.00 3.50
1604 1740 0.398318 GCTAGATGGGCCTAGGGTTG 59.602 60.000 11.72 0.0 37.27 3.77
1797 1944 2.498885 AGGAAAGGATTTTGAGCATGGC 59.501 45.455 0.00 0.0 39.27 4.40
1868 2015 3.409851 AAAAGTCCGGTCGAACAAAAC 57.590 42.857 0.00 0.0 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
196 199 1.267806 CGCACACTTCTCCTTTGCATT 59.732 47.619 0.00 0.0 32.51 3.56
270 273 0.387929 TCACTCGTTTCCTTGTCGCT 59.612 50.000 0.00 0.0 0.00 4.93
300 303 0.799534 GATGCTCATGTTTGCACCGC 60.800 55.000 11.51 3.6 42.26 5.68
452 455 4.202223 ACGGAGTGTGAACATCTACAAAGT 60.202 41.667 0.00 0.0 42.51 2.66
456 459 3.442625 CCTACGGAGTGTGAACATCTACA 59.557 47.826 0.00 0.0 45.73 2.74
483 486 2.026905 GCAAGTTCCTTGTTGACCCCA 61.027 52.381 5.92 0.0 42.77 4.96
544 547 3.099619 CTACCGCCGCTCGAACGTA 62.100 63.158 7.52 0.0 41.67 3.57
576 579 1.731720 GACGTGTACGACCTACTCCT 58.268 55.000 11.79 0.0 43.02 3.69
709 712 4.159135 CCCACTACGACCTTGTACAACTAT 59.841 45.833 3.59 0.0 0.00 2.12
908 911 2.063015 ATGGTTCTGTCCCAACGCCA 62.063 55.000 0.00 0.0 35.14 5.69
1016 1133 3.214123 CCGATCCCCAGCGTCGTA 61.214 66.667 0.00 0.0 33.77 3.43
1068 1185 2.187946 CCGCTCGCTCCCTTCATT 59.812 61.111 0.00 0.0 0.00 2.57
1332 1451 3.148084 CCAAGTCCCTGTGTCCGT 58.852 61.111 0.00 0.0 0.00 4.69
1413 1532 2.444706 CCTCGATCCTCCCTGCCA 60.445 66.667 0.00 0.0 0.00 4.92
1604 1740 1.984570 GGCCAGCCTTTTCCCTTCC 60.985 63.158 0.00 0.0 0.00 3.46
1663 1800 2.042261 ATCCCTAGGCCCAACCGT 59.958 61.111 2.05 0.0 46.52 4.83
1763 1909 5.616975 ATCCTTTCCTTAACCCTCCTTTT 57.383 39.130 0.00 0.0 0.00 2.27
1764 1910 5.616975 AATCCTTTCCTTAACCCTCCTTT 57.383 39.130 0.00 0.0 0.00 3.11
1765 1911 5.616975 AAATCCTTTCCTTAACCCTCCTT 57.383 39.130 0.00 0.0 0.00 3.36
1766 1912 5.075900 TCAAAATCCTTTCCTTAACCCTCCT 59.924 40.000 0.00 0.0 0.00 3.69
1797 1944 7.845617 TTTTGTGAGTTCGGAAAAATTATCG 57.154 32.000 0.00 0.0 0.00 2.92
1851 1998 2.249844 ATGTTTTGTTCGACCGGACT 57.750 45.000 9.46 0.0 0.00 3.85
1852 1999 3.242804 TGAAATGTTTTGTTCGACCGGAC 60.243 43.478 9.46 0.0 0.00 4.79
1853 2000 2.943690 TGAAATGTTTTGTTCGACCGGA 59.056 40.909 9.46 0.0 0.00 5.14
2191 2355 8.523915 TGTCTTCTTGCCATTATGTCATTAAT 57.476 30.769 0.00 0.0 0.00 1.40
2192 2356 7.936496 TGTCTTCTTGCCATTATGTCATTAA 57.064 32.000 0.00 0.0 0.00 1.40
2193 2357 7.774625 TCATGTCTTCTTGCCATTATGTCATTA 59.225 33.333 0.00 0.0 0.00 1.90


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

AutoCloner maintained by Alex Coulton.