Multiple sequence alignment - TraesCS5A01G453600

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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 TraesCS5A01G453600 chr5A 100.000 2529 0 0 1 2529 635244691 635247219 0.000000e+00 4671
1 TraesCS5A01G453600 chr5A 95.138 2530 112 7 1 2529 634990913 634988394 0.000000e+00 3980
2 TraesCS5A01G453600 chr5A 88.192 2566 229 36 1 2529 634358817 634356289 0.000000e+00 2992
3 TraesCS5A01G453600 chr5A 86.723 1770 186 27 1 1755 638380828 638382563 0.000000e+00 1921
4 TraesCS5A01G453600 chr5A 85.741 540 73 4 1991 2527 638334274 638333736 3.650000e-158 568
5 TraesCS5A01G453600 chr5D 90.047 2562 188 40 1 2529 507519192 507516665 0.000000e+00 3256
6 TraesCS5A01G453600 chr5D 90.491 1588 135 11 954 2529 506739299 506737716 0.000000e+00 2082
7 TraesCS5A01G453600 chr5D 90.229 1310 118 5 1229 2529 506703338 506702030 0.000000e+00 1701
8 TraesCS5A01G453600 chr5D 88.324 925 83 19 1 911 506704240 506703327 0.000000e+00 1086
9 TraesCS5A01G453600 chr5D 90.909 264 15 9 694 953 506739532 506739274 1.860000e-91 346
10 TraesCS5A01G453600 chr5B 87.912 2548 234 37 1 2529 637216442 637213950 0.000000e+00 2931
11 TraesCS5A01G453600 chr5B 87.201 2219 182 43 1 2186 637729942 637727793 0.000000e+00 2431
12 TraesCS5A01G453600 chr5B 89.049 1598 135 16 954 2529 637804213 637802634 0.000000e+00 1945
13 TraesCS5A01G453600 chr5B 88.529 1604 138 20 954 2529 637783047 637781462 0.000000e+00 1901
14 TraesCS5A01G453600 chr5B 89.569 882 74 11 1 868 637783954 637783077 0.000000e+00 1103
15 TraesCS5A01G453600 chr5B 89.569 882 74 11 1 868 637805120 637804243 0.000000e+00 1103


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 TraesCS5A01G453600 chr5A 635244691 635247219 2528 False 4671.0 4671 100.0000 1 2529 1 chr5A.!!$F1 2528
1 TraesCS5A01G453600 chr5A 634988394 634990913 2519 True 3980.0 3980 95.1380 1 2529 1 chr5A.!!$R2 2528
2 TraesCS5A01G453600 chr5A 634356289 634358817 2528 True 2992.0 2992 88.1920 1 2529 1 chr5A.!!$R1 2528
3 TraesCS5A01G453600 chr5A 638380828 638382563 1735 False 1921.0 1921 86.7230 1 1755 1 chr5A.!!$F2 1754
4 TraesCS5A01G453600 chr5A 638333736 638334274 538 True 568.0 568 85.7410 1991 2527 1 chr5A.!!$R3 536
5 TraesCS5A01G453600 chr5D 507516665 507519192 2527 True 3256.0 3256 90.0470 1 2529 1 chr5D.!!$R1 2528
6 TraesCS5A01G453600 chr5D 506702030 506704240 2210 True 1393.5 1701 89.2765 1 2529 2 chr5D.!!$R2 2528
7 TraesCS5A01G453600 chr5D 506737716 506739532 1816 True 1214.0 2082 90.7000 694 2529 2 chr5D.!!$R3 1835
8 TraesCS5A01G453600 chr5B 637213950 637216442 2492 True 2931.0 2931 87.9120 1 2529 1 chr5B.!!$R1 2528
9 TraesCS5A01G453600 chr5B 637727793 637729942 2149 True 2431.0 2431 87.2010 1 2186 1 chr5B.!!$R2 2185
10 TraesCS5A01G453600 chr5B 637802634 637805120 2486 True 1524.0 1945 89.3090 1 2529 2 chr5B.!!$R4 2528
11 TraesCS5A01G453600 chr5B 637781462 637783954 2492 True 1502.0 1901 89.0490 1 2529 2 chr5B.!!$R3 2528

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
55 60 0.694105 ATCCCACCCACCGATGATCA 60.694 55.000 0.0 0.0 0.0 2.92 F
85 90 1.268899 CCCGATATTCTACTTCGCCGT 59.731 52.381 0.0 0.0 0.0 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1350 1372 1.208706 TTCCCCCATAGCACGAATCA 58.791 50.0 0.0 0.0 0.0 2.57 R
1696 1719 2.028420 TGTCAATGCCTCGGAATCAG 57.972 50.0 0.0 0.0 0.0 2.90 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
49 54 1.200519 CTTCTTATCCCACCCACCGA 58.799 55.000 0.00 0.00 0.00 4.69
55 60 0.694105 ATCCCACCCACCGATGATCA 60.694 55.000 0.00 0.00 0.00 2.92
72 77 3.245766 TGATCATCACTCTCCCCCGATAT 60.246 47.826 0.00 0.00 0.00 1.63
85 90 1.268899 CCCGATATTCTACTTCGCCGT 59.731 52.381 0.00 0.00 0.00 5.68
99 106 1.586154 CGCCGTTGCTTCTTCCCATT 61.586 55.000 0.00 0.00 34.43 3.16
144 151 3.958798 GCTACTCAACACACCCCTCTATA 59.041 47.826 0.00 0.00 0.00 1.31
267 274 3.676873 GCGGATTTTTGCATCATGAAGGT 60.677 43.478 0.00 0.00 0.00 3.50
271 278 7.424803 CGGATTTTTGCATCATGAAGGTAATA 58.575 34.615 0.00 0.00 0.00 0.98
282 289 7.855784 TCATGAAGGTAATAGAGATTGGCTA 57.144 36.000 0.00 0.00 0.00 3.93
408 415 3.640967 CTCCATTCTCTTCCTCCTCGAAT 59.359 47.826 0.00 0.00 0.00 3.34
436 443 2.520120 TCCTCCATCTCCTCCACTGTAT 59.480 50.000 0.00 0.00 0.00 2.29
470 480 7.348274 CCTTAGCCTTCATATCCCTATTCCATA 59.652 40.741 0.00 0.00 0.00 2.74
491 502 8.504005 TCCATACTTTGTTTCTCGATCTTTTTC 58.496 33.333 0.00 0.00 0.00 2.29
569 580 9.381038 ACAAGAGGTGAGGTTATATATGTGTAT 57.619 33.333 0.00 0.00 0.00 2.29
645 657 8.188799 TGTTTATGCCTCTCTATATATACGTGC 58.811 37.037 0.00 0.00 0.00 5.34
654 668 7.035612 TCTCTATATATACGTGCTGCCATTTG 58.964 38.462 0.00 0.00 0.00 2.32
1038 1058 2.713708 AGGATCCTCCTTTATGAAGGCC 59.286 50.000 9.02 6.58 46.91 5.19
1301 1323 7.639113 ACATGAGTCCTTGTTTTAAGTTTGA 57.361 32.000 0.00 0.00 0.00 2.69
1350 1372 4.582656 TGTTGCTTAACAGGCAGTTGTAAT 59.417 37.500 5.44 0.00 41.50 1.89
1696 1719 0.824759 AGAACATGAGACGCTACCCC 59.175 55.000 0.00 0.00 0.00 4.95
1714 1737 1.303309 CCTGATTCCGAGGCATTGAC 58.697 55.000 0.00 0.00 0.00 3.18
1721 1744 6.295249 TGATTCCGAGGCATTGACATATTTA 58.705 36.000 0.00 0.00 0.00 1.40
1725 1748 6.061441 TCCGAGGCATTGACATATTTATTGT 58.939 36.000 0.00 0.00 0.00 2.71
1765 1814 2.353208 GGGCGCAATGTTTTGTCCATTA 60.353 45.455 10.83 0.00 35.17 1.90
1871 1922 2.826488 AGGAGAGAGGCTCAAAGCTAA 58.174 47.619 18.26 0.00 45.81 3.09
1915 1966 8.726650 TTCGTGAGACATTGATTTTTAACATG 57.273 30.769 0.00 0.00 41.84 3.21
2086 2138 3.137360 GTCCCATCAGCCTTTCCTAATCT 59.863 47.826 0.00 0.00 0.00 2.40
2135 2187 1.593006 CATCCCTTTGTCGTCGCATAC 59.407 52.381 0.00 0.00 0.00 2.39
2216 2278 8.133024 TCCCCATATTCATTTGCCATATTTAC 57.867 34.615 0.00 0.00 0.00 2.01
2248 2310 2.827921 AGTGGAGGATTTTTGCATGGTC 59.172 45.455 0.00 0.00 0.00 4.02
2346 2409 2.028130 CAAGGCACACTACCACCAAAA 58.972 47.619 0.00 0.00 0.00 2.44
2412 2475 8.839310 TTTAGCTCCATTATAAGATCTTGCTC 57.161 34.615 18.47 0.00 0.00 4.26
2422 2485 1.484240 AGATCTTGCTCCAGCCTACAC 59.516 52.381 0.00 0.00 41.18 2.90
2427 2490 0.618680 TGCTCCAGCCTACACATCCT 60.619 55.000 0.00 0.00 41.18 3.24
2520 2583 7.687941 ACAAACATGAGTTTATAAGAGGTGG 57.312 36.000 0.00 0.00 45.80 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 54 1.133041 TCGGGGGAGAGTGATGATCAT 60.133 52.381 8.25 8.25 0.00 2.45
55 60 3.551635 AGAATATCGGGGGAGAGTGAT 57.448 47.619 0.00 0.00 0.00 3.06
85 90 1.428912 AGGGTGAATGGGAAGAAGCAA 59.571 47.619 0.00 0.00 0.00 3.91
99 106 0.712979 AGAGAGGTGATGGAGGGTGA 59.287 55.000 0.00 0.00 0.00 4.02
408 415 1.758514 GGAGATGGAGGACGAGGCA 60.759 63.158 0.00 0.00 0.00 4.75
436 443 5.012148 GGATATGAAGGCTAAGGCTAGAACA 59.988 44.000 0.00 0.00 37.50 3.18
470 480 6.693315 TGGAAAAAGATCGAGAAACAAAGT 57.307 33.333 0.00 0.00 0.00 2.66
491 502 8.977412 ACAAAAACTATAAAGGGTGGATAATGG 58.023 33.333 0.00 0.00 0.00 3.16
1038 1058 2.104111 TGTGGTGTCCTCAACAACTAGG 59.896 50.000 0.00 0.00 46.41 3.02
1181 1201 4.669866 ATGATGGGCATGTCCTTATCAT 57.330 40.909 20.93 20.93 40.69 2.45
1207 1227 1.552792 GAAGCTAAGCACCTCAGGACT 59.447 52.381 0.00 0.00 0.00 3.85
1350 1372 1.208706 TTCCCCCATAGCACGAATCA 58.791 50.000 0.00 0.00 0.00 2.57
1696 1719 2.028420 TGTCAATGCCTCGGAATCAG 57.972 50.000 0.00 0.00 0.00 2.90
1721 1744 6.208599 CCCTATTTATATTGGTGCCGAACAAT 59.791 38.462 0.00 0.00 40.21 2.71
1725 1748 4.076394 GCCCTATTTATATTGGTGCCGAA 58.924 43.478 0.00 0.00 0.00 4.30
1871 1922 8.864069 TCACGAAATGTTAAAACAATGTCAAT 57.136 26.923 0.00 0.00 43.03 2.57
1915 1966 4.968788 CGCAAGGACGTACTTTAGAGTATC 59.031 45.833 11.26 0.00 40.33 2.24
2086 2138 4.262036 GGTAGCACGAGATAATGGATGTGA 60.262 45.833 0.00 0.00 0.00 3.58
2135 2187 6.700960 TCTTTGGAAATGCAATATTTATGGCG 59.299 34.615 0.00 0.00 35.34 5.69
2216 2278 2.575993 CTCCACTCTCTGCCCACG 59.424 66.667 0.00 0.00 0.00 4.94
2248 2310 1.466167 CAACGAATCTGCACCTCCTTG 59.534 52.381 0.00 0.00 0.00 3.61
2346 2409 1.407437 CCTCCTTTGCCGCTTCACTAT 60.407 52.381 0.00 0.00 0.00 2.12
2412 2475 4.780815 TGAAATAAGGATGTGTAGGCTGG 58.219 43.478 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.