Multiple sequence alignment - TraesCS2A01G458500

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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 TraesCS2A01G458500 chr2A 100.000 2402 0 0 1 2402 705995917 705993516 0.000000e+00 4436
1 TraesCS2A01G458500 chr2A 99.381 485 3 0 1830 2314 36933302 36932818 0.000000e+00 880
2 TraesCS2A01G458500 chr2A 78.621 1001 164 32 371 1355 673513874 673512908 3.390000e-173 617
3 TraesCS2A01G458500 chr2A 78.221 877 153 24 548 1410 673957411 673956559 5.880000e-146 527
4 TraesCS2A01G458500 chr2A 97.403 77 1 1 2326 2402 36932847 36932772 1.940000e-26 130
5 TraesCS2A01G458500 chr2A 97.260 73 2 0 1606 1678 36933375 36933303 9.020000e-25 124
6 TraesCS2A01G458500 chr2B 90.035 1425 82 19 203 1579 678008218 678006806 0.000000e+00 1790
7 TraesCS2A01G458500 chr2B 89.335 1444 78 25 83 1462 677963266 677964697 0.000000e+00 1744
8 TraesCS2A01G458500 chr2B 79.021 1001 161 25 371 1355 628208657 628207690 7.240000e-180 640
9 TraesCS2A01G458500 chr2B 78.848 851 153 15 506 1354 628398057 628397232 1.260000e-152 549
10 TraesCS2A01G458500 chr2D 90.607 1203 57 24 1 1157 565744458 565743266 0.000000e+00 1544
11 TraesCS2A01G458500 chr2D 89.124 708 39 12 930 1603 565687919 565687216 0.000000e+00 846
12 TraesCS2A01G458500 chr2D 79.920 1001 152 30 371 1355 529013677 529012710 0.000000e+00 689
13 TraesCS2A01G458500 chr2D 90.147 477 30 6 1140 1603 565742925 565742453 2.640000e-169 604
14 TraesCS2A01G458500 chr2D 79.655 870 141 20 548 1404 529036878 529036032 5.720000e-166 593
15 TraesCS2A01G458500 chr6A 97.740 708 15 1 1607 2314 60427880 60427174 0.000000e+00 1218
16 TraesCS2A01G458500 chr6A 84.347 658 91 10 1607 2258 162913034 162912383 3.370000e-178 634
17 TraesCS2A01G458500 chr6A 97.403 77 1 1 2326 2402 60427203 60427128 1.940000e-26 130
18 TraesCS2A01G458500 chr7A 97.207 716 17 3 1601 2314 419012512 419013226 0.000000e+00 1208
19 TraesCS2A01G458500 chr7A 97.403 77 1 1 2326 2402 419013197 419013272 1.940000e-26 130
20 TraesCS2A01G458500 chr6B 86.072 359 41 7 1607 1958 664306269 664306625 6.270000e-101 377
21 TraesCS2A01G458500 chr6B 92.547 161 10 2 1969 2128 664307766 664307925 1.860000e-56 230


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 TraesCS2A01G458500 chr2A 705993516 705995917 2401 True 4436.0 4436 100.000000 1 2402 1 chr2A.!!$R3 2401
1 TraesCS2A01G458500 chr2A 673512908 673513874 966 True 617.0 617 78.621000 371 1355 1 chr2A.!!$R1 984
2 TraesCS2A01G458500 chr2A 673956559 673957411 852 True 527.0 527 78.221000 548 1410 1 chr2A.!!$R2 862
3 TraesCS2A01G458500 chr2A 36932772 36933375 603 True 378.0 880 98.014667 1606 2402 3 chr2A.!!$R4 796
4 TraesCS2A01G458500 chr2B 678006806 678008218 1412 True 1790.0 1790 90.035000 203 1579 1 chr2B.!!$R3 1376
5 TraesCS2A01G458500 chr2B 677963266 677964697 1431 False 1744.0 1744 89.335000 83 1462 1 chr2B.!!$F1 1379
6 TraesCS2A01G458500 chr2B 628207690 628208657 967 True 640.0 640 79.021000 371 1355 1 chr2B.!!$R1 984
7 TraesCS2A01G458500 chr2B 628397232 628398057 825 True 549.0 549 78.848000 506 1354 1 chr2B.!!$R2 848
8 TraesCS2A01G458500 chr2D 565742453 565744458 2005 True 1074.0 1544 90.377000 1 1603 2 chr2D.!!$R4 1602
9 TraesCS2A01G458500 chr2D 565687216 565687919 703 True 846.0 846 89.124000 930 1603 1 chr2D.!!$R3 673
10 TraesCS2A01G458500 chr2D 529012710 529013677 967 True 689.0 689 79.920000 371 1355 1 chr2D.!!$R1 984
11 TraesCS2A01G458500 chr2D 529036032 529036878 846 True 593.0 593 79.655000 548 1404 1 chr2D.!!$R2 856
12 TraesCS2A01G458500 chr6A 60427128 60427880 752 True 674.0 1218 97.571500 1607 2402 2 chr6A.!!$R2 795
13 TraesCS2A01G458500 chr6A 162912383 162913034 651 True 634.0 634 84.347000 1607 2258 1 chr6A.!!$R1 651
14 TraesCS2A01G458500 chr7A 419012512 419013272 760 False 669.0 1208 97.305000 1601 2402 2 chr7A.!!$F1 801
15 TraesCS2A01G458500 chr6B 664306269 664307925 1656 False 303.5 377 89.309500 1607 2128 2 chr6B.!!$F1 521

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
124 126 0.036388 TCAGGAATTCAGGACACGGC 60.036 55.0 7.93 0.0 0.00 5.68 F
1206 1641 0.393944 AGACCGTGATGACCTCGCTA 60.394 55.0 0.00 0.0 31.89 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1269 1704 0.523072 CCAGTTCCGTTGCATCCAAG 59.477 55.0 0.00 0.00 0.00 3.61 R
2345 3951 0.387878 GTATCCATCGAGCTCTGGCG 60.388 60.0 15.57 1.68 44.37 5.69 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
124 126 0.036388 TCAGGAATTCAGGACACGGC 60.036 55.000 7.93 0.00 0.00 5.68
175 177 2.412770 GCGCACCAAAAATGGAAAGATG 59.587 45.455 0.30 0.00 0.00 2.90
177 179 3.401182 GCACCAAAAATGGAAAGATGCA 58.599 40.909 1.10 0.00 0.00 3.96
193 195 4.015084 AGATGCAAGTTTCAGGAAGGATG 58.985 43.478 0.00 0.00 0.00 3.51
271 284 1.455959 CCCCGGAACAAACCCAACA 60.456 57.895 0.73 0.00 0.00 3.33
272 285 1.737201 CCCGGAACAAACCCAACAC 59.263 57.895 0.73 0.00 0.00 3.32
273 286 1.737201 CCGGAACAAACCCAACACC 59.263 57.895 0.00 0.00 0.00 4.16
274 287 1.737201 CGGAACAAACCCAACACCC 59.263 57.895 0.00 0.00 0.00 4.61
275 288 1.038130 CGGAACAAACCCAACACCCA 61.038 55.000 0.00 0.00 0.00 4.51
276 289 1.196012 GGAACAAACCCAACACCCAA 58.804 50.000 0.00 0.00 0.00 4.12
309 323 1.147824 AAGCGATCATGGGGAGCAG 59.852 57.895 0.00 0.00 0.00 4.24
493 531 2.892640 CAGATCCAGTTCCGCCGA 59.107 61.111 0.00 0.00 0.00 5.54
628 678 3.071459 GCACACGATGGCGAAGACG 62.071 63.158 0.00 0.00 41.59 4.18
641 691 1.528400 CGAAGACGCACGAGTTCGATA 60.528 52.381 19.38 0.00 43.50 2.92
689 739 0.753262 CTACCGGTTCATGGAGAGGG 59.247 60.000 15.04 0.00 0.00 4.30
995 1072 1.731700 CGGGTCGTATCACCGTCAT 59.268 57.895 0.00 0.00 42.53 3.06
1180 1615 6.372659 TGAAAGCATCCTCTGTAAGAACATTC 59.627 38.462 0.00 0.00 46.34 2.67
1201 1636 0.396435 TGCAAAGACCGTGATGACCT 59.604 50.000 0.00 0.00 0.00 3.85
1206 1641 0.393944 AGACCGTGATGACCTCGCTA 60.394 55.000 0.00 0.00 31.89 4.26
1269 1704 1.820519 TGCATTCAGTTCATTGCCTCC 59.179 47.619 0.00 0.00 34.20 4.30
1302 1737 3.062763 GGAACTGGATGATGTGATAGCG 58.937 50.000 0.00 0.00 0.00 4.26
1355 1790 5.744666 TCTCCTTTGGTTTTAGTTGAACG 57.255 39.130 0.00 0.00 0.00 3.95
1462 1914 1.395635 TAGTAGGCTCGATCGGCAAA 58.604 50.000 23.67 12.22 0.00 3.68
1472 1924 2.875933 TCGATCGGCAAACAAAGTCTTT 59.124 40.909 16.41 0.00 0.00 2.52
1543 2012 5.996513 AGTACTTCTCTAACGAGTGTCTTGA 59.003 40.000 0.00 0.00 38.45 3.02
1603 2072 9.443323 AAGTAGTTTTGTTTTGCCAACTATTTT 57.557 25.926 0.00 0.00 34.92 1.82
1678 2147 2.202932 GAGCGCGTGTGGATCCAT 60.203 61.111 19.62 0.00 0.00 3.41
1679 2148 2.512286 AGCGCGTGTGGATCCATG 60.512 61.111 19.62 12.25 0.00 3.66
1681 2150 2.512286 CGCGTGTGGATCCATGCT 60.512 61.111 19.62 0.00 43.62 3.79
1682 2151 2.108514 CGCGTGTGGATCCATGCTT 61.109 57.895 19.62 0.00 43.62 3.91
1684 2153 1.308069 GCGTGTGGATCCATGCTTGT 61.308 55.000 19.62 0.00 42.73 3.16
1685 2154 0.448990 CGTGTGGATCCATGCTTGTG 59.551 55.000 19.62 0.25 0.00 3.33
1686 2155 1.538047 GTGTGGATCCATGCTTGTGT 58.462 50.000 19.62 0.00 0.00 3.72
1728 2197 2.037367 CTCTCCGACCCCACCTCA 59.963 66.667 0.00 0.00 0.00 3.86
1744 2213 5.070001 CCACCTCACATCTTTTCCTAAACA 58.930 41.667 0.00 0.00 0.00 2.83
1781 2250 4.620723 ACAGAGACCATTCCTACCATACA 58.379 43.478 0.00 0.00 0.00 2.29
2014 3620 3.456380 AGGTATGCTCAAACCCATTGT 57.544 42.857 0.00 0.00 40.11 2.71
2053 3659 3.511699 TGTTCCTCAACGATTCATCTCG 58.488 45.455 0.00 0.00 44.14 4.04
2317 3923 4.749310 CAACGCCAGAGCTCCGCT 62.749 66.667 18.35 1.91 43.88 5.52
2333 3939 4.749310 CTCGCCAACGCCAGAGCT 62.749 66.667 0.00 0.00 39.84 4.09
2334 3940 4.742201 TCGCCAACGCCAGAGCTC 62.742 66.667 5.27 5.27 39.84 4.09
2338 3944 4.749310 CAACGCCAGAGCTCCGCT 62.749 66.667 18.35 1.91 43.88 5.52
2354 3960 4.749310 CTCGCCAACGCCAGAGCT 62.749 66.667 0.00 0.00 39.84 4.09
2355 3961 4.742201 TCGCCAACGCCAGAGCTC 62.742 66.667 5.27 5.27 39.84 4.09
2398 4004 1.741770 GAATGCTTGGAGTCGCCGT 60.742 57.895 0.00 0.00 40.66 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 1.770294 AGTCTACCTGGCTAGCTGTC 58.230 55.000 15.72 0.00 0.00 3.51
65 66 1.827969 CAAGTCTACCTGGCTAGCTGT 59.172 52.381 15.72 11.95 0.00 4.40
124 126 1.394917 CAGAAATCGCAAAGTCCTCGG 59.605 52.381 0.00 0.00 0.00 4.63
175 177 3.149196 TCACATCCTTCCTGAAACTTGC 58.851 45.455 0.00 0.00 0.00 4.01
177 179 4.256920 CGATCACATCCTTCCTGAAACTT 58.743 43.478 0.00 0.00 0.00 2.66
193 195 4.934989 GGGTTGGACTCCGATCAC 57.065 61.111 0.00 0.00 0.00 3.06
221 233 0.680618 TTTTGTAGGAAGGCGACGGA 59.319 50.000 0.00 0.00 0.00 4.69
493 531 2.414824 CGCGTAGTCTTTGAGAAGCTCT 60.415 50.000 0.00 0.00 32.75 4.09
622 672 1.838943 GTATCGAACTCGTGCGTCTTC 59.161 52.381 0.00 0.00 40.80 2.87
628 678 2.228914 GCCGGTATCGAACTCGTGC 61.229 63.158 1.90 0.00 40.80 5.34
641 691 2.668550 GAAACTCTTGCCGCCGGT 60.669 61.111 4.45 0.00 0.00 5.28
689 739 4.615834 CGACGCCTCTAGCTCGCC 62.616 72.222 0.00 0.00 40.39 5.54
941 1015 1.070445 ATGGCGCCATACAGCTCTC 59.930 57.895 39.91 1.98 34.49 3.20
942 1016 1.227764 CATGGCGCCATACAGCTCT 60.228 57.895 39.94 15.97 34.91 4.09
987 1064 2.001357 CTGCATGTCGATGACGGTG 58.999 57.895 0.00 0.00 40.21 4.94
1180 1615 1.131126 GGTCATCACGGTCTTTGCATG 59.869 52.381 0.00 0.00 0.00 4.06
1269 1704 0.523072 CCAGTTCCGTTGCATCCAAG 59.477 55.000 0.00 0.00 0.00 3.61
1302 1737 1.138661 AGCTCAGCATACTCTTGGCTC 59.861 52.381 0.00 0.00 35.27 4.70
1355 1790 3.378427 ACTTTGATTTGCCGAGCCTATTC 59.622 43.478 0.00 0.00 0.00 1.75
1603 2072 5.464389 GCGGAAGTAAAAGGCTTTATCGATA 59.536 40.000 13.77 0.00 29.86 2.92
1604 2073 4.272748 GCGGAAGTAAAAGGCTTTATCGAT 59.727 41.667 13.77 2.16 29.86 3.59
1678 2147 4.182433 TGCGGGTCCACACAAGCA 62.182 61.111 0.00 0.00 35.08 3.91
1679 2148 3.357079 CTGCGGGTCCACACAAGC 61.357 66.667 0.00 0.00 0.00 4.01
1681 2150 4.947147 GGCTGCGGGTCCACACAA 62.947 66.667 0.00 0.00 0.00 3.33
1728 2197 6.207810 TGGCGTATTTGTTTAGGAAAAGATGT 59.792 34.615 0.00 0.00 0.00 3.06
1744 2213 4.443034 GGTCTCTGTATTCCTGGCGTATTT 60.443 45.833 0.00 0.00 0.00 1.40
1781 2250 1.135373 CCGCCGCTCGTATCTGAATAT 60.135 52.381 0.00 0.00 36.19 1.28
2014 3620 7.233144 TGAGGAACAAAGATTTGAATGGATTGA 59.767 33.333 12.07 0.00 40.55 2.57
2316 3922 4.749310 AGCTCTGGCGTTGGCGAG 62.749 66.667 0.00 7.48 45.34 5.03
2317 3923 4.742201 GAGCTCTGGCGTTGGCGA 62.742 66.667 6.43 0.00 44.37 5.54
2337 3943 4.749310 AGCTCTGGCGTTGGCGAG 62.749 66.667 0.00 7.48 45.34 5.03
2338 3944 4.742201 GAGCTCTGGCGTTGGCGA 62.742 66.667 6.43 0.00 44.37 5.54
2340 3946 4.742201 TCGAGCTCTGGCGTTGGC 62.742 66.667 12.85 0.00 44.37 4.52
2341 3947 2.169789 CATCGAGCTCTGGCGTTGG 61.170 63.158 12.85 0.00 44.37 3.77
2342 3948 2.169789 CCATCGAGCTCTGGCGTTG 61.170 63.158 12.85 4.50 44.37 4.10
2343 3949 1.680522 ATCCATCGAGCTCTGGCGTT 61.681 55.000 15.57 2.56 44.37 4.84
2344 3950 0.823769 TATCCATCGAGCTCTGGCGT 60.824 55.000 15.57 9.97 44.37 5.68
2345 3951 0.387878 GTATCCATCGAGCTCTGGCG 60.388 60.000 15.57 1.68 44.37 5.69
2346 3952 0.676184 TGTATCCATCGAGCTCTGGC 59.324 55.000 15.57 4.59 39.06 4.85
2347 3953 1.959985 AGTGTATCCATCGAGCTCTGG 59.040 52.381 14.47 14.47 0.00 3.86
2348 3954 3.379240 CAAGTGTATCCATCGAGCTCTG 58.621 50.000 12.85 3.91 0.00 3.35
2349 3955 2.363680 CCAAGTGTATCCATCGAGCTCT 59.636 50.000 12.85 0.00 0.00 4.09
2350 3956 2.101582 ACCAAGTGTATCCATCGAGCTC 59.898 50.000 2.73 2.73 0.00 4.09
2351 3957 2.101582 GACCAAGTGTATCCATCGAGCT 59.898 50.000 0.00 0.00 0.00 4.09
2352 3958 2.159099 TGACCAAGTGTATCCATCGAGC 60.159 50.000 0.00 0.00 0.00 5.03
2353 3959 3.491619 CCTGACCAAGTGTATCCATCGAG 60.492 52.174 0.00 0.00 0.00 4.04
2354 3960 2.430694 CCTGACCAAGTGTATCCATCGA 59.569 50.000 0.00 0.00 0.00 3.59
2355 3961 2.430694 TCCTGACCAAGTGTATCCATCG 59.569 50.000 0.00 0.00 0.00 3.84


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

AutoCloner maintained by Alex Coulton.