Multiple sequence alignment - TraesCS3D01G510800

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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 TraesCS3D01G510800 chr3D 100.000 2675 0 0 1 2675 595738175 595740849 0.000000e+00 4940
1 TraesCS3D01G510800 chr3D 88.903 1568 123 24 277 1813 595704611 595706158 0.000000e+00 1884
2 TraesCS3D01G510800 chr3D 89.192 1027 102 6 748 1768 595674232 595675255 0.000000e+00 1273
3 TraesCS3D01G510800 chr3D 87.887 1065 105 12 770 1825 595302940 595303989 0.000000e+00 1230
4 TraesCS3D01G510800 chr3D 87.682 893 97 9 942 1830 595286611 595285728 0.000000e+00 1027
5 TraesCS3D01G510800 chr3D 87.026 501 36 8 277 758 595673595 595674085 3.030000e-149 538
6 TraesCS3D01G510800 chr3D 80.508 472 34 31 479 909 595287060 595286606 2.590000e-80 309
7 TraesCS3D01G510800 chr3D 82.703 370 40 13 425 772 595302393 595302760 9.300000e-80 307
8 TraesCS3D01G510800 chr3D 88.172 186 21 1 1992 2177 595304173 595304357 1.250000e-53 220
9 TraesCS3D01G510800 chr3D 88.506 174 20 0 267 440 595287240 595287067 7.500000e-51 211
10 TraesCS3D01G510800 chr3D 81.928 249 33 4 1930 2174 595675410 595675650 1.620000e-47 200
11 TraesCS3D01G510800 chr3D 87.770 139 9 1 101 231 595301608 595301746 3.570000e-34 156
12 TraesCS3D01G510800 chr3D 86.111 144 17 2 2282 2423 595304770 595304912 4.610000e-33 152
13 TraesCS3D01G510800 chr3A 94.706 2720 75 17 1 2675 726514785 726517480 0.000000e+00 4161
14 TraesCS3D01G510800 chr3A 90.586 1211 95 13 585 1784 726457920 726459122 0.000000e+00 1587
15 TraesCS3D01G510800 chr3A 84.021 1333 131 48 479 1768 726411270 726409977 0.000000e+00 1206
16 TraesCS3D01G510800 chr3A 83.857 446 28 12 112 535 726457491 726457914 4.180000e-103 385
17 TraesCS3D01G510800 chr3A 88.506 174 20 0 267 440 726411450 726411277 7.500000e-51 211
18 TraesCS3D01G510800 chr3A 80.702 228 27 9 2198 2412 726862730 726862507 7.660000e-36 161
19 TraesCS3D01G510800 chr3B 91.297 1218 80 12 460 1655 798686144 798687357 0.000000e+00 1639
20 TraesCS3D01G510800 chr3B 91.351 1029 73 12 808 1827 798648155 798649176 0.000000e+00 1393
21 TraesCS3D01G510800 chr3B 84.766 663 50 23 87 726 798647327 798647961 3.780000e-173 617
22 TraesCS3D01G510800 chr3B 92.453 371 16 2 1804 2174 798689892 798690250 1.100000e-143 520
23 TraesCS3D01G510800 chr1A 91.250 80 5 1 101 178 37142806 37142885 1.010000e-19 108
24 TraesCS3D01G510800 chr1A 90.000 80 6 1 101 178 37009136 37009215 4.710000e-18 102


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 TraesCS3D01G510800 chr3D 595738175 595740849 2674 False 4940.000000 4940 100.000000 1 2675 1 chr3D.!!$F2 2674
1 TraesCS3D01G510800 chr3D 595704611 595706158 1547 False 1884.000000 1884 88.903000 277 1813 1 chr3D.!!$F1 1536
2 TraesCS3D01G510800 chr3D 595673595 595675650 2055 False 670.333333 1273 86.048667 277 2174 3 chr3D.!!$F4 1897
3 TraesCS3D01G510800 chr3D 595285728 595287240 1512 True 515.666667 1027 85.565333 267 1830 3 chr3D.!!$R1 1563
4 TraesCS3D01G510800 chr3D 595301608 595304912 3304 False 413.000000 1230 86.528600 101 2423 5 chr3D.!!$F3 2322
5 TraesCS3D01G510800 chr3A 726514785 726517480 2695 False 4161.000000 4161 94.706000 1 2675 1 chr3A.!!$F1 2674
6 TraesCS3D01G510800 chr3A 726457491 726459122 1631 False 986.000000 1587 87.221500 112 1784 2 chr3A.!!$F2 1672
7 TraesCS3D01G510800 chr3A 726409977 726411450 1473 True 708.500000 1206 86.263500 267 1768 2 chr3A.!!$R2 1501
8 TraesCS3D01G510800 chr3B 798686144 798690250 4106 False 1079.500000 1639 91.875000 460 2174 2 chr3B.!!$F2 1714
9 TraesCS3D01G510800 chr3B 798647327 798649176 1849 False 1005.000000 1393 88.058500 87 1827 2 chr3B.!!$F1 1740

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
245 259 0.319728 CCCATGCCTCTGATACTCCG 59.68 60.0 0.0 0.0 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1707 5179 1.270826 GAAGGAAGGCTCCAGCAAAAC 59.729 52.381 0.03 0.0 45.24 2.43 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
55 56 5.739161 CGTAAGGCTGCATATTCTGTTTTTC 59.261 40.000 0.50 0.00 0.00 2.29
72 73 3.469008 TTTCGGTTATGATCGATGCCT 57.531 42.857 0.54 0.00 35.25 4.75
73 74 3.469008 TTCGGTTATGATCGATGCCTT 57.531 42.857 0.54 0.00 35.25 4.35
206 220 2.422597 TGCTGTCTGTACCAATTTCCG 58.577 47.619 0.00 0.00 0.00 4.30
241 255 1.475751 CCACACCCATGCCTCTGATAC 60.476 57.143 0.00 0.00 0.00 2.24
242 256 1.487976 CACACCCATGCCTCTGATACT 59.512 52.381 0.00 0.00 0.00 2.12
243 257 1.765314 ACACCCATGCCTCTGATACTC 59.235 52.381 0.00 0.00 0.00 2.59
244 258 1.071385 CACCCATGCCTCTGATACTCC 59.929 57.143 0.00 0.00 0.00 3.85
245 259 0.319728 CCCATGCCTCTGATACTCCG 59.680 60.000 0.00 0.00 0.00 4.63
246 260 1.043816 CCATGCCTCTGATACTCCGT 58.956 55.000 0.00 0.00 0.00 4.69
247 261 2.239400 CCATGCCTCTGATACTCCGTA 58.761 52.381 0.00 0.00 0.00 4.02
401 740 2.071540 TCAGTGAATCTTTGCTCGCTG 58.928 47.619 6.34 6.34 46.77 5.18
415 754 3.439825 TGCTCGCTGCTCAAATTCATAAA 59.560 39.130 0.00 0.00 43.37 1.40
1700 5172 0.676466 TGGCCTGCCATTCAGTAACG 60.676 55.000 6.80 0.00 41.89 3.18
1707 5179 4.466828 CTGCCATTCAGTAACGAGTTTTG 58.533 43.478 0.00 0.00 38.02 2.44
1872 5379 8.761497 TGTTAATGTCTCGAGTAGTTCTTTTTG 58.239 33.333 13.13 0.00 0.00 2.44
1964 5497 2.882761 ACCGACAAAAAGCCTCCTTTAC 59.117 45.455 0.00 0.00 40.30 2.01
2010 5543 1.065998 ACCCAGCGCGGTTAATTTCTA 60.066 47.619 8.73 0.00 29.19 2.10
2143 5676 5.046376 ACCACATGAATGTCACATGAGTAGA 60.046 40.000 13.54 0.00 45.22 2.59
2196 5759 1.072505 GTCCTCAACGAAAGGGGCA 59.927 57.895 0.00 0.00 34.46 5.36
2248 5811 5.272283 AGGTGTTAGTTGTATATGACCCG 57.728 43.478 0.00 0.00 0.00 5.28
2249 5812 4.713321 AGGTGTTAGTTGTATATGACCCGT 59.287 41.667 0.00 0.00 0.00 5.28
2255 5818 2.870411 GTTGTATATGACCCGTTCAGCC 59.130 50.000 0.00 0.00 37.77 4.85
2278 5841 0.788383 ATGGAGCATTGGGGGCATAT 59.212 50.000 0.00 0.00 0.00 1.78
2334 6176 2.452505 GGTGGCAGCATTTAGGGTTTA 58.547 47.619 12.58 0.00 0.00 2.01
2352 6194 4.101898 GGTTTAAAGGTGGATGGGTGTTTT 59.898 41.667 0.00 0.00 0.00 2.43
2431 6273 0.317519 GCAACTGGTACAACGCCAAC 60.318 55.000 0.00 0.00 38.70 3.77
2436 6278 1.280444 GGTACAACGCCAACGGTTG 59.720 57.895 13.86 13.86 46.04 3.77
2473 6324 8.963277 TCAGTTTCTATAAGGATAGGTAGGGTA 58.037 37.037 0.00 0.00 36.45 3.69
2494 6345 8.004801 AGGGTATAGGGATAAAGATTGTTTTGG 58.995 37.037 0.00 0.00 0.00 3.28
2519 6370 7.650104 GGTCAAATTTGAACAAACGGAGAATAA 59.350 33.333 27.51 0.00 44.23 1.40
2561 6412 6.833041 TGAGGTGTTAAACATTGTAGGAAGA 58.167 36.000 0.00 0.00 0.00 2.87
2562 6413 6.934645 TGAGGTGTTAAACATTGTAGGAAGAG 59.065 38.462 0.00 0.00 0.00 2.85
2563 6414 5.705905 AGGTGTTAAACATTGTAGGAAGAGC 59.294 40.000 0.00 0.00 0.00 4.09
2565 6416 6.348540 GGTGTTAAACATTGTAGGAAGAGCTG 60.349 42.308 0.00 0.00 0.00 4.24
2592 6449 3.823304 TGCAAAAGGCCAAAAACAGTTTT 59.177 34.783 5.01 5.37 43.89 2.43
2593 6450 4.279420 TGCAAAAGGCCAAAAACAGTTTTT 59.721 33.333 16.87 16.87 43.89 1.94
2620 6477 7.317390 TGGAGTGAAAAGGTGTTTAGAAAAAC 58.683 34.615 0.00 0.00 44.40 2.43
2635 6492 2.770164 AAAACAGTCCCTCTCATCCG 57.230 50.000 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 6.148150 CAGCCTTACGAACTAAATTAACACCA 59.852 38.462 0.00 0.00 0.00 4.17
55 56 4.552166 AAAAAGGCATCGATCATAACCG 57.448 40.909 0.00 0.00 0.00 4.44
206 220 2.677524 TGGCATGCTGGGTTGAGC 60.678 61.111 18.92 0.00 39.62 4.26
375 714 4.212004 CGAGCAAAGATTCACTGAAACAGA 59.788 41.667 5.76 0.00 35.18 3.41
401 740 4.722194 TGTGCGAGTTTATGAATTTGAGC 58.278 39.130 0.00 0.00 0.00 4.26
415 754 2.941453 ACAACGATCTATGTGCGAGT 57.059 45.000 0.00 0.00 0.00 4.18
502 1006 9.840427 TGCTGTTTCTTGCTAAATATAAACTTC 57.160 29.630 0.00 0.00 0.00 3.01
897 1938 5.485708 ACAATTCCAGGTAGTAGAAAGAGCT 59.514 40.000 0.00 0.00 0.00 4.09
1505 2555 3.370978 CACCTTGACATTGTCGATGGTAC 59.629 47.826 20.21 0.00 40.21 3.34
1700 5172 2.101415 AGGCTCCAGCAAAACAAAACTC 59.899 45.455 0.03 0.00 44.36 3.01
1707 5179 1.270826 GAAGGAAGGCTCCAGCAAAAC 59.729 52.381 0.03 0.00 45.24 2.43
1872 5379 2.696187 GACCCAGGGACTCTTGATAGAC 59.304 54.545 14.54 0.00 34.60 2.59
1964 5497 5.702670 TGCAGACAGGAAAGAAATGAGTAAG 59.297 40.000 0.00 0.00 0.00 2.34
2143 5676 5.184892 ACTCCTATTTGCAGTCCTGATTT 57.815 39.130 0.00 0.00 0.00 2.17
2248 5811 0.682209 ATGCTCCATGGTGGCTGAAC 60.682 55.000 24.47 6.88 37.47 3.18
2249 5812 0.040058 AATGCTCCATGGTGGCTGAA 59.960 50.000 24.47 11.58 37.47 3.02
2255 5818 1.759299 CCCCCAATGCTCCATGGTG 60.759 63.158 12.58 10.95 0.00 4.17
2334 6176 2.046292 CCAAAACACCCATCCACCTTT 58.954 47.619 0.00 0.00 0.00 3.11
2416 6258 1.161563 AACCGTTGGCGTTGTACCAG 61.162 55.000 0.00 0.00 38.73 4.00
2431 6273 2.358737 GACACCAGAGCCCAACCG 60.359 66.667 0.00 0.00 0.00 4.44
2436 6278 0.398318 AGAAACTGACACCAGAGCCC 59.602 55.000 0.00 0.00 43.02 5.19
2473 6324 8.893563 TTGACCAAAACAATCTTTATCCCTAT 57.106 30.769 0.00 0.00 0.00 2.57
2494 6345 8.568732 TTATTCTCCGTTTGTTCAAATTTGAC 57.431 30.769 20.35 15.10 36.83 3.18
2511 6362 5.104318 AGAGTCACCCCTGAAATTATTCTCC 60.104 44.000 0.00 0.00 36.48 3.71
2513 6364 6.394345 AAGAGTCACCCCTGAAATTATTCT 57.606 37.500 0.00 0.00 36.48 2.40
2519 6370 3.245052 CCTCAAAGAGTCACCCCTGAAAT 60.245 47.826 0.00 0.00 0.00 2.17
2561 6412 1.466851 GGCCTTTTGCAAGTCCAGCT 61.467 55.000 0.00 0.00 43.89 4.24
2562 6413 1.005748 GGCCTTTTGCAAGTCCAGC 60.006 57.895 0.00 0.00 43.89 4.85
2563 6414 0.752054 TTGGCCTTTTGCAAGTCCAG 59.248 50.000 3.32 0.00 39.25 3.86
2565 6416 2.323968 TTTTGGCCTTTTGCAAGTCC 57.676 45.000 3.32 0.41 43.89 3.85
2592 6449 7.469537 TTCTAAACACCTTTTCACTCCAAAA 57.530 32.000 0.00 0.00 0.00 2.44
2593 6450 7.469537 TTTCTAAACACCTTTTCACTCCAAA 57.530 32.000 0.00 0.00 0.00 3.28
2609 6466 6.149640 GGATGAGAGGGACTGTTTTTCTAAAC 59.850 42.308 0.00 0.00 41.55 2.01
2620 6477 1.028905 GAGACGGATGAGAGGGACTG 58.971 60.000 0.00 0.00 41.55 3.51


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

AutoCloner maintained by Alex Coulton.