Multiple sequence alignment - TraesCS1A01G235700

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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 TraesCS1A01G235700 chr1A 100.000 3881 0 0 1 3881 417390226 417386346 0.000000e+00 7167.0
1 TraesCS1A01G235700 chr1A 84.819 1851 246 25 1069 2900 406582997 406584831 0.000000e+00 1829.0
2 TraesCS1A01G235700 chr1A 84.333 1851 255 25 1069 2900 425257516 425255682 0.000000e+00 1779.0
3 TraesCS1A01G235700 chr1A 84.168 1857 248 26 1069 2906 407517753 407515924 0.000000e+00 1759.0
4 TraesCS1A01G235700 chr1A 84.063 1851 258 25 1069 2900 421638386 421640218 0.000000e+00 1749.0
5 TraesCS1A01G235700 chr1A 100.000 478 0 0 591 1068 417395294 417394817 0.000000e+00 883.0
6 TraesCS1A01G235700 chr1A 96.875 32 1 0 2962 2993 419025120 419025151 2.000000e-03 54.7
7 TraesCS1A01G235700 chr1D 97.403 2811 65 6 1069 3874 328445579 328442772 0.000000e+00 4780.0
8 TraesCS1A01G235700 chr1D 84.935 1852 242 24 1069 2900 322381401 322383235 0.000000e+00 1840.0
9 TraesCS1A01G235700 chr1D 83.858 1809 249 26 1069 2865 323636896 323638673 0.000000e+00 1683.0
10 TraesCS1A01G235700 chr1D 85.600 375 47 6 3045 3413 325503731 325503358 1.690000e-103 387.0
11 TraesCS1A01G235700 chr1D 92.949 156 11 0 1069 1224 325504082 325503927 1.080000e-55 228.0
12 TraesCS1A01G235700 chr1D 81.890 127 13 5 2886 3002 325492503 325492377 8.870000e-17 99.0
13 TraesCS1A01G235700 chr1B 97.163 2326 64 2 1069 3392 442620621 442618296 0.000000e+00 3928.0
14 TraesCS1A01G235700 chr1B 97.200 2214 58 3 1672 3881 442551746 442549533 0.000000e+00 3742.0
15 TraesCS1A01G235700 chr1B 90.783 1801 158 8 1069 2865 326927087 326925291 0.000000e+00 2399.0
16 TraesCS1A01G235700 chr1B 84.557 1852 249 25 1069 2900 435361044 435362878 0.000000e+00 1801.0
17 TraesCS1A01G235700 chr1B 84.762 315 42 6 3045 3357 326925128 326924818 1.050000e-80 311.0
18 TraesCS1A01G235700 chr1B 91.026 156 14 0 1069 1224 437860537 437860382 1.090000e-50 211.0
19 TraesCS1A01G235700 chr1B 84.615 104 6 5 2909 3002 437835063 437834960 1.150000e-15 95.3
20 TraesCS1A01G235700 chr1B 94.737 38 2 0 2965 3002 437861415 437861378 4.190000e-05 60.2
21 TraesCS1A01G235700 chr7A 99.345 1069 5 2 1 1068 62271966 62270899 0.000000e+00 1934.0
22 TraesCS1A01G235700 chr7A 99.581 477 2 0 592 1068 62277032 62276556 0.000000e+00 870.0
23 TraesCS1A01G235700 chr5B 98.976 1074 8 2 1 1072 464176980 464178052 0.000000e+00 1919.0
24 TraesCS1A01G235700 chr2B 98.048 1076 11 3 1 1070 26516060 26514989 0.000000e+00 1862.0
25 TraesCS1A01G235700 chr2B 96.562 960 19 5 1 952 9690228 9691181 0.000000e+00 1578.0
26 TraesCS1A01G235700 chr5A 97.868 1079 12 5 1 1069 616555389 616556466 0.000000e+00 1855.0
27 TraesCS1A01G235700 chr5A 98.680 606 8 0 464 1069 437164264 437163659 0.000000e+00 1075.0
28 TraesCS1A01G235700 chrUn 99.303 1004 5 2 66 1068 358863993 358864995 0.000000e+00 1814.0
29 TraesCS1A01G235700 chrUn 97.287 1069 6 4 1 1068 81893270 81892224 0.000000e+00 1792.0
30 TraesCS1A01G235700 chr4B 96.881 1090 11 6 1 1069 14040644 14039557 0.000000e+00 1803.0
31 TraesCS1A01G235700 chr4B 96.774 1085 12 5 4 1068 646961012 646959931 0.000000e+00 1788.0


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 TraesCS1A01G235700 chr1A 417386346 417390226 3880 True 7167.0 7167 100.0000 1 3881 1 chr1A.!!$R2 3880
1 TraesCS1A01G235700 chr1A 406582997 406584831 1834 False 1829.0 1829 84.8190 1069 2900 1 chr1A.!!$F1 1831
2 TraesCS1A01G235700 chr1A 425255682 425257516 1834 True 1779.0 1779 84.3330 1069 2900 1 chr1A.!!$R4 1831
3 TraesCS1A01G235700 chr1A 407515924 407517753 1829 True 1759.0 1759 84.1680 1069 2906 1 chr1A.!!$R1 1837
4 TraesCS1A01G235700 chr1A 421638386 421640218 1832 False 1749.0 1749 84.0630 1069 2900 1 chr1A.!!$F3 1831
5 TraesCS1A01G235700 chr1D 328442772 328445579 2807 True 4780.0 4780 97.4030 1069 3874 1 chr1D.!!$R2 2805
6 TraesCS1A01G235700 chr1D 322381401 322383235 1834 False 1840.0 1840 84.9350 1069 2900 1 chr1D.!!$F1 1831
7 TraesCS1A01G235700 chr1D 323636896 323638673 1777 False 1683.0 1683 83.8580 1069 2865 1 chr1D.!!$F2 1796
8 TraesCS1A01G235700 chr1D 325503358 325504082 724 True 307.5 387 89.2745 1069 3413 2 chr1D.!!$R3 2344
9 TraesCS1A01G235700 chr1B 442618296 442620621 2325 True 3928.0 3928 97.1630 1069 3392 1 chr1B.!!$R3 2323
10 TraesCS1A01G235700 chr1B 442549533 442551746 2213 True 3742.0 3742 97.2000 1672 3881 1 chr1B.!!$R2 2209
11 TraesCS1A01G235700 chr1B 435361044 435362878 1834 False 1801.0 1801 84.5570 1069 2900 1 chr1B.!!$F1 1831
12 TraesCS1A01G235700 chr1B 326924818 326927087 2269 True 1355.0 2399 87.7725 1069 3357 2 chr1B.!!$R4 2288
13 TraesCS1A01G235700 chr7A 62270899 62271966 1067 True 1934.0 1934 99.3450 1 1068 1 chr7A.!!$R1 1067
14 TraesCS1A01G235700 chr5B 464176980 464178052 1072 False 1919.0 1919 98.9760 1 1072 1 chr5B.!!$F1 1071
15 TraesCS1A01G235700 chr2B 26514989 26516060 1071 True 1862.0 1862 98.0480 1 1070 1 chr2B.!!$R1 1069
16 TraesCS1A01G235700 chr2B 9690228 9691181 953 False 1578.0 1578 96.5620 1 952 1 chr2B.!!$F1 951
17 TraesCS1A01G235700 chr5A 616555389 616556466 1077 False 1855.0 1855 97.8680 1 1069 1 chr5A.!!$F1 1068
18 TraesCS1A01G235700 chr5A 437163659 437164264 605 True 1075.0 1075 98.6800 464 1069 1 chr5A.!!$R1 605
19 TraesCS1A01G235700 chrUn 358863993 358864995 1002 False 1814.0 1814 99.3030 66 1068 1 chrUn.!!$F1 1002
20 TraesCS1A01G235700 chrUn 81892224 81893270 1046 True 1792.0 1792 97.2870 1 1068 1 chrUn.!!$R1 1067
21 TraesCS1A01G235700 chr4B 14039557 14040644 1087 True 1803.0 1803 96.8810 1 1069 1 chr4B.!!$R1 1068
22 TraesCS1A01G235700 chr4B 646959931 646961012 1081 True 1788.0 1788 96.7740 4 1068 1 chr4B.!!$R2 1064

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
795 816 1.893137 TGTAGCAGACACGAAGGATGT 59.107 47.619 0.00 0.00 31.20 3.06 F
1567 1614 0.469917 TGCAGTAGCTAAGGGCATCC 59.530 55.000 10.24 0.00 44.79 3.51 F
2318 2386 0.177373 TGGTCTGCTGCTGCTATCAG 59.823 55.000 17.00 5.76 43.16 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2067 2135 0.108138 GAGATGGACGGACACCAAGG 60.108 60.000 0.0 0.0 40.93 3.61 R
2833 2901 1.286880 GCACAACATGGGTCACTGC 59.713 57.895 0.0 0.0 0.00 4.40 R
3698 3800 2.420642 CATGCCACTCCATATTCCTCG 58.579 52.381 0.0 0.0 0.00 4.63 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
795 816 1.893137 TGTAGCAGACACGAAGGATGT 59.107 47.619 0.00 0.00 31.20 3.06
1327 1374 2.486548 GCTGGGAACTTTGTCAGTGGTA 60.487 50.000 0.00 0.00 35.12 3.25
1567 1614 0.469917 TGCAGTAGCTAAGGGCATCC 59.530 55.000 10.24 0.00 44.79 3.51
1594 1641 1.387295 GGCTGCAGCTGGGAATAACC 61.387 60.000 35.82 13.26 41.70 2.85
1893 1952 1.224075 CCGACATCAGTGGCATCATC 58.776 55.000 0.00 0.00 30.50 2.92
1928 1987 4.881850 GGCTGGTGTAGTGCTAATAAACAT 59.118 41.667 0.00 0.00 0.00 2.71
2054 2122 2.372264 AGCCAGTGCCAAAGTCATATG 58.628 47.619 0.00 0.00 38.69 1.78
2067 2135 5.869753 AAGTCATATGCAAGAACACTGTC 57.130 39.130 0.00 0.00 0.00 3.51
2110 2178 1.227380 GTCGCGGCATTCTCATCCT 60.227 57.895 5.47 0.00 0.00 3.24
2211 2279 1.386533 CACTCACCATGCTTGGATCC 58.613 55.000 24.48 4.20 46.92 3.36
2215 2283 2.308722 ACCATGCTTGGATCCGGGT 61.309 57.895 24.48 0.00 46.92 5.28
2226 2294 1.697432 GGATCCGGGTCATTCCACATA 59.303 52.381 18.43 0.00 38.11 2.29
2247 2315 1.573108 AATCAGGGACGTCCATGTCT 58.427 50.000 39.20 27.93 46.97 3.41
2318 2386 0.177373 TGGTCTGCTGCTGCTATCAG 59.823 55.000 17.00 5.76 43.16 2.90
2559 2627 2.432444 CCGAGGTTGTCCTGCAAAATA 58.568 47.619 0.00 0.00 45.24 1.40
2634 2702 0.249911 AGACAAGGCCGTTCACAGTC 60.250 55.000 0.00 0.00 0.00 3.51
2642 2710 1.878102 GCCGTTCACAGTCCACAGAAT 60.878 52.381 0.00 0.00 0.00 2.40
2694 2762 7.039434 TCCATATACACACTGAAGATGGAGATC 60.039 40.741 0.00 0.00 37.14 2.75
2833 2901 0.955919 GGGAAGTTTGAGCTGGGTCG 60.956 60.000 0.00 0.00 0.00 4.79
3031 3129 2.622942 CCACACATACACTGCCAGTTTT 59.377 45.455 0.00 0.00 0.00 2.43
3043 3141 4.588528 ACTGCCAGTTTTTGATGTGGTATT 59.411 37.500 0.00 0.00 32.20 1.89
3264 3363 2.323599 TCTGATGAGGGATGTGCCTAG 58.676 52.381 0.00 0.00 36.66 3.02
3698 3800 2.224314 GTGCTTGTTCTTGCTAGTGACC 59.776 50.000 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1567 1614 2.667536 AGCTGCAGCCACGACAAG 60.668 61.111 34.39 0.00 43.38 3.16
1594 1641 3.574284 TGCAAGAAATGATTTGGGTCG 57.426 42.857 0.00 0.00 0.00 4.79
2054 2122 1.334869 CACCAAGGACAGTGTTCTTGC 59.665 52.381 31.37 4.65 45.09 4.01
2067 2135 0.108138 GAGATGGACGGACACCAAGG 60.108 60.000 0.00 0.00 40.93 3.61
2211 2279 4.036734 CCTGATTTTATGTGGAATGACCCG 59.963 45.833 0.00 0.00 38.00 5.28
2215 2283 4.881273 CGTCCCTGATTTTATGTGGAATGA 59.119 41.667 0.00 0.00 0.00 2.57
2226 2294 2.305927 AGACATGGACGTCCCTGATTTT 59.694 45.455 36.86 20.38 36.52 1.82
2318 2386 1.078143 GTGGTGAGGATGGCTGACC 60.078 63.158 0.00 0.00 0.00 4.02
2559 2627 2.912956 TGCTTCAGGTATCTTGGGAAGT 59.087 45.455 0.00 0.00 37.77 3.01
2642 2710 2.122167 GGGCCCACGTTTGTCACAA 61.122 57.895 19.95 0.00 0.00 3.33
2694 2762 2.009774 CGCACTGTAAGAGATTTGGGG 58.990 52.381 0.00 0.00 37.43 4.96
2833 2901 1.286880 GCACAACATGGGTCACTGC 59.713 57.895 0.00 0.00 0.00 4.40
3085 3183 7.012327 ACCTGTTGAACCAAATGATATGATACG 59.988 37.037 0.00 0.00 0.00 3.06
3106 3204 4.943705 CCATGTAGATGTAAGCAAACCTGT 59.056 41.667 0.00 0.00 0.00 4.00
3264 3363 6.654793 TCAGTTAAACACAACCATTTTTGC 57.345 33.333 0.00 0.00 0.00 3.68
3698 3800 2.420642 CATGCCACTCCATATTCCTCG 58.579 52.381 0.00 0.00 0.00 4.63
3761 3865 3.396260 TTTTGTTACTCGGGTGGAGAG 57.604 47.619 0.00 0.00 46.23 3.20


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

AutoCloner maintained by Alex Coulton.