Multiple sequence alignment - TraesCS5A01G452800

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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 TraesCS5A01G452800 chr5A 100.000 2530 0 0 1 2530 634358837 634356308 0.000000e+00 4673
1 TraesCS5A01G452800 chr5A 88.270 2566 227 36 1 2529 635244671 635247199 0.000000e+00 3003
2 TraesCS5A01G452800 chr5A 88.304 2565 219 38 1 2529 634990933 634988414 0.000000e+00 3000
3 TraesCS5A01G452800 chr5A 88.946 1755 182 10 16 1764 638380823 638382571 0.000000e+00 2156
4 TraesCS5A01G452800 chr5A 86.338 527 61 8 2008 2529 638334274 638333754 4.720000e-157 564
5 TraesCS5A01G452800 chr5B 92.058 2531 161 14 1 2529 637216462 637213970 0.000000e+00 3524
6 TraesCS5A01G452800 chr5B 88.762 2536 223 37 7 2529 637783968 637781482 0.000000e+00 3048
7 TraesCS5A01G452800 chr5B 88.674 2534 223 37 7 2529 637805134 637802654 0.000000e+00 3031
8 TraesCS5A01G452800 chr5B 88.676 2190 200 26 12 2193 637729951 637727802 0.000000e+00 2627
9 TraesCS5A01G452800 chr5D 91.604 2537 196 14 1 2529 507519212 507516685 0.000000e+00 3489
10 TraesCS5A01G452800 chr5D 93.384 1829 97 17 705 2529 506739544 506737736 0.000000e+00 2686
11 TraesCS5A01G452800 chr5D 93.338 1306 68 10 1227 2529 506703339 506702050 0.000000e+00 1912
12 TraesCS5A01G452800 chr5D 93.305 926 59 3 1 925 506704260 506703337 0.000000e+00 1363
13 TraesCS5A01G452800 chr5D 92.672 696 50 1 1 695 506740220 506739525 0.000000e+00 1002


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 TraesCS5A01G452800 chr5A 634356308 634358837 2529 True 4673.0 4673 100.0000 1 2530 1 chr5A.!!$R1 2529
1 TraesCS5A01G452800 chr5A 635244671 635247199 2528 False 3003.0 3003 88.2700 1 2529 1 chr5A.!!$F1 2528
2 TraesCS5A01G452800 chr5A 634988414 634990933 2519 True 3000.0 3000 88.3040 1 2529 1 chr5A.!!$R2 2528
3 TraesCS5A01G452800 chr5A 638380823 638382571 1748 False 2156.0 2156 88.9460 16 1764 1 chr5A.!!$F2 1748
4 TraesCS5A01G452800 chr5A 638333754 638334274 520 True 564.0 564 86.3380 2008 2529 1 chr5A.!!$R3 521
5 TraesCS5A01G452800 chr5B 637213970 637216462 2492 True 3524.0 3524 92.0580 1 2529 1 chr5B.!!$R1 2528
6 TraesCS5A01G452800 chr5B 637781482 637783968 2486 True 3048.0 3048 88.7620 7 2529 1 chr5B.!!$R3 2522
7 TraesCS5A01G452800 chr5B 637802654 637805134 2480 True 3031.0 3031 88.6740 7 2529 1 chr5B.!!$R4 2522
8 TraesCS5A01G452800 chr5B 637727802 637729951 2149 True 2627.0 2627 88.6760 12 2193 1 chr5B.!!$R2 2181
9 TraesCS5A01G452800 chr5D 507516685 507519212 2527 True 3489.0 3489 91.6040 1 2529 1 chr5D.!!$R1 2528
10 TraesCS5A01G452800 chr5D 506737736 506740220 2484 True 1844.0 2686 93.0280 1 2529 2 chr5D.!!$R3 2528
11 TraesCS5A01G452800 chr5D 506702050 506704260 2210 True 1637.5 1912 93.3215 1 2529 2 chr5D.!!$R2 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
325 329 0.752009 CTGGCCATGAGCTGCATCTT 60.752 55.0 5.51 0.0 43.05 2.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1871 1926 0.396001 AAGTACCTCCGAGCCTCTCC 60.396 60.0 0.0 0.0 0.0 3.71 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
64 65 5.755409 TTATAACGCATCATATCCCACCT 57.245 39.130 0.00 0.00 0.00 4.00
121 123 2.844946 TGTCGCCAATGTTCTTCTTCA 58.155 42.857 0.00 0.00 0.00 3.02
139 141 3.350992 TCATATCCACCCTCCATCACT 57.649 47.619 0.00 0.00 0.00 3.41
146 148 1.135915 CACCCTCCATCACTTCTCTCG 59.864 57.143 0.00 0.00 0.00 4.04
159 161 1.557099 TCTCTCGTGCTACCCAACAT 58.443 50.000 0.00 0.00 0.00 2.71
160 162 1.204704 TCTCTCGTGCTACCCAACATG 59.795 52.381 0.00 0.00 0.00 3.21
302 306 2.272923 TCGTGAAGGCGATGGAGAA 58.727 52.632 0.00 0.00 35.83 2.87
325 329 0.752009 CTGGCCATGAGCTGCATCTT 60.752 55.000 5.51 0.00 43.05 2.40
369 373 8.871629 ATAACACAACATAATCAGGGTACAAA 57.128 30.769 0.00 0.00 0.00 2.83
490 497 3.841255 AGCCTTAGCCTTCATATCCCTAC 59.159 47.826 0.00 0.00 41.25 3.18
505 512 7.570982 TCATATCCCTACTCCATCCTTTGTTTA 59.429 37.037 0.00 0.00 0.00 2.01
661 669 7.161404 TGACATCCATGTTTATGCCTCTATAC 58.839 38.462 0.00 0.00 41.95 1.47
666 676 8.201242 TCCATGTTTATGCCTCTATACATACA 57.799 34.615 0.00 0.00 32.79 2.29
675 685 5.221904 TGCCTCTATACATACATGTTGCCAT 60.222 40.000 2.30 2.94 41.97 4.40
1020 1062 2.761213 GCATCCAAGGCCCAAGGG 60.761 66.667 0.00 0.00 38.57 3.95
1158 1200 2.239907 AGTTGACCTATTCCTTGAGGGC 59.760 50.000 0.00 0.00 41.80 5.19
1229 1271 0.908198 CCTGAGGTGCTTAGCTTCCT 59.092 55.000 17.64 17.64 36.66 3.36
1291 1334 9.513906 TGTATTGATTTGAACATAAGTCCTTGA 57.486 29.630 0.00 0.00 0.00 3.02
1461 1504 3.582208 TGATATTTTTGTGCCCAAGCCTT 59.418 39.130 0.00 0.00 38.69 4.35
1574 1617 6.258160 CGATGGACGAAATATTTTTCTGCTT 58.742 36.000 1.43 0.00 45.77 3.91
1580 1623 7.857885 GGACGAAATATTTTTCTGCTTATGGAG 59.142 37.037 1.43 0.00 39.30 3.86
1606 1649 9.520204 GCTATGTTTTCTTATGTATGCATTGTT 57.480 29.630 3.54 0.00 36.58 2.83
1617 1660 7.636259 ATGTATGCATTGTTGTGTTGTTTAC 57.364 32.000 3.54 0.00 29.54 2.01
1690 1733 6.352016 TCTAAGCAAGAAGAACATGAGACT 57.648 37.500 0.00 0.00 0.00 3.24
1699 1742 7.346751 AGAAGAACATGAGACTCTATCCTTC 57.653 40.000 0.00 9.66 0.00 3.46
1871 1926 6.534793 GGGTATGTTTTGCATAATTTGTCAGG 59.465 38.462 0.00 0.00 41.29 3.86
1897 1952 2.957006 GGCTCGGAGGTACTTGAGATTA 59.043 50.000 7.20 0.00 41.69 1.75
1964 2019 8.325421 TGAAGTATGTCCTTGCGTTTATAAAA 57.675 30.769 0.00 0.00 0.00 1.52
1970 2025 5.766174 TGTCCTTGCGTTTATAAAACTCCTT 59.234 36.000 0.00 0.00 0.00 3.36
2060 2115 0.749049 CGCCTCTCTCACATGATCCA 59.251 55.000 0.00 0.00 0.00 3.41
2072 2127 5.850614 TCACATGATCCACTACATCATCAG 58.149 41.667 0.00 0.00 38.67 2.90
2116 2172 6.730977 CCTTCCCTAATCCTACATCCATTCTA 59.269 42.308 0.00 0.00 0.00 2.10
2125 2181 7.559335 TCCTACATCCATTCTATTGTGCTAT 57.441 36.000 0.00 0.00 0.00 2.97
2159 2215 0.455464 TGTCGTCGCATAAGTCACCG 60.455 55.000 0.00 0.00 0.00 4.94
2184 2241 3.429492 TGGCTTTCCAAAGATGTGCATA 58.571 40.909 3.11 0.00 39.99 3.14
2245 2307 7.110043 TCATTTGCCATATTTATGTGAGCAA 57.890 32.000 7.97 7.97 35.28 3.91
2317 2379 1.295915 ATATGCCTCCCCTTTGCCCA 61.296 55.000 0.00 0.00 0.00 5.36
2355 2417 0.892755 TACTCAGGGTACAAGGCACG 59.107 55.000 0.00 0.00 0.00 5.34
2382 2446 4.021192 CCACCAAATAGTGAAGTGGCAAAT 60.021 41.667 0.00 0.00 41.38 2.32
2407 2471 5.533112 AGGAAAGAGATCCATTCTACTCCA 58.467 41.667 11.26 0.00 42.27 3.86
2529 2593 5.812652 TCCATGTTTTACAAACACGAGTTC 58.187 37.500 4.21 0.00 36.84 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 1.985159 TGGGTAGGTGGGATATGATGC 59.015 52.381 0.00 0.00 0.00 3.91
54 55 1.297141 AGTGGTGGGTAGGTGGGATAT 59.703 52.381 0.00 0.00 0.00 1.63
64 65 0.892755 GTGTCGATCAGTGGTGGGTA 59.107 55.000 0.00 0.00 0.00 3.69
121 123 3.906846 GAGAAGTGATGGAGGGTGGATAT 59.093 47.826 0.00 0.00 0.00 1.63
139 141 1.334160 TGTTGGGTAGCACGAGAGAA 58.666 50.000 0.00 0.00 0.00 2.87
146 148 2.052104 GGGGCATGTTGGGTAGCAC 61.052 63.158 0.00 0.00 0.00 4.40
159 161 4.160439 CGCTTCTATATTGATAGAGGGGCA 59.840 45.833 7.78 0.00 43.25 5.36
160 162 4.442192 CCGCTTCTATATTGATAGAGGGGC 60.442 50.000 12.74 9.45 45.71 5.80
369 373 0.892358 CTGCTTGGTGATGGTGTGCT 60.892 55.000 0.00 0.00 0.00 4.40
406 410 4.901250 AGGAGGAAGAGAATGGAGATCTTC 59.099 45.833 0.00 0.00 45.30 2.87
490 497 9.933723 AAAAAGATTGATAAACAAAGGATGGAG 57.066 29.630 0.00 0.00 42.03 3.86
520 527 6.280855 ACAAAAACTATAAAGGGTGGATGC 57.719 37.500 0.00 0.00 0.00 3.91
628 636 3.648339 AACATGGATGTCAACACAAGC 57.352 42.857 0.00 0.00 40.80 4.01
1020 1062 0.036858 GTGCCTTCACAGAGGAGGAC 60.037 60.000 0.00 0.00 42.66 3.85
1461 1504 3.165875 ACTCGAGATCCTGAACCTTGAA 58.834 45.455 21.68 0.00 0.00 2.69
1574 1617 9.219603 GCATACATAAGAAAACATAGCTCCATA 57.780 33.333 0.00 0.00 0.00 2.74
1580 1623 9.520204 AACAATGCATACATAAGAAAACATAGC 57.480 29.630 0.00 0.00 34.62 2.97
1606 1649 7.148641 ACAACACAATGAAAGTAAACAACACA 58.851 30.769 0.00 0.00 0.00 3.72
1654 1697 5.522456 TCTTGCTTAGAACGAACGAACTTA 58.478 37.500 0.14 0.00 0.00 2.24
1699 1742 6.873997 AGCAATATATCAATGCCATGGAATG 58.126 36.000 18.40 10.72 46.21 2.67
1832 1885 7.574217 GCAAAACATACCCTCGATTAAAGTTGA 60.574 37.037 0.00 0.00 0.00 3.18
1871 1926 0.396001 AAGTACCTCCGAGCCTCTCC 60.396 60.000 0.00 0.00 0.00 3.71
2060 2115 3.445450 ACGAAGAGCACTGATGATGTAGT 59.555 43.478 0.00 0.00 0.00 2.73
2072 2127 1.086634 GCTGATGGGACGAAGAGCAC 61.087 60.000 0.00 0.00 0.00 4.40
2116 2172 1.949525 GGATGCGTTGGATAGCACAAT 59.050 47.619 0.00 0.00 46.83 2.71
2125 2181 0.953471 CGACAAAGGGATGCGTTGGA 60.953 55.000 0.59 0.00 0.00 3.53
2159 2215 4.098349 TGCACATCTTTGGAAAGCCATATC 59.902 41.667 0.00 0.00 45.46 1.63
2210 2269 7.383156 AATATGGCAAATGAAATTGGGAGAT 57.617 32.000 0.00 0.00 36.10 2.75
2211 2270 6.811634 AATATGGCAAATGAAATTGGGAGA 57.188 33.333 0.00 0.00 36.10 3.71
2212 2271 8.995220 CATAAATATGGCAAATGAAATTGGGAG 58.005 33.333 0.00 0.00 36.10 4.30
2219 2281 7.554211 TGCTCACATAAATATGGCAAATGAAA 58.446 30.769 5.48 0.00 38.00 2.69
2317 2379 7.310671 CCTGAGTATGCCATGGTACTTATACAT 60.311 40.741 14.67 7.96 31.61 2.29
2355 2417 3.689649 CCACTTCACTATTTGGTGGTAGC 59.310 47.826 0.00 0.00 41.52 3.58
2382 2446 5.600484 GGAGTAGAATGGATCTCTTTCCTCA 59.400 44.000 0.00 0.00 39.71 3.86


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

AutoCloner maintained by Alex Coulton.