Multiple sequence alignment - TraesCS5A01G254700

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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 TraesCS5A01G254700 chr5A 100.000 3759 0 0 1 3759 470244253 470240495 0.000000e+00 6942.0
1 TraesCS5A01G254700 chr5A 99.169 1805 15 0 1955 3759 470227168 470225364 0.000000e+00 3251.0
2 TraesCS5A01G254700 chr5D 92.278 2098 131 17 1 2080 368367365 368365281 0.000000e+00 2948.0
3 TraesCS5A01G254700 chr5D 92.692 1683 108 9 2090 3759 368365305 368363625 0.000000e+00 2412.0
4 TraesCS5A01G254700 chr5D 97.222 36 1 0 2048 2083 374322714 374322679 1.130000e-05 62.1
5 TraesCS5A01G254700 chr5B 91.556 2108 133 25 1 2080 436284613 436282523 0.000000e+00 2865.0
6 TraesCS5A01G254700 chr5B 91.392 1545 118 6 2093 3634 436282545 436281013 0.000000e+00 2102.0
7 TraesCS5A01G254700 chr5B 97.297 37 1 0 2047 2083 436282632 436282596 3.130000e-06 63.9
8 TraesCS5A01G254700 chr1D 83.196 1095 154 23 856 1933 627004 625923 0.000000e+00 976.0
9 TraesCS5A01G254700 chr1D 80.299 1269 188 43 836 2087 470447 471670 0.000000e+00 902.0
10 TraesCS5A01G254700 chr1D 80.639 971 160 23 2094 3050 625821 624865 0.000000e+00 726.0
11 TraesCS5A01G254700 chr1D 83.941 741 102 15 2094 2820 471641 472378 0.000000e+00 693.0
12 TraesCS5A01G254700 chr1D 77.606 777 133 29 1 749 628228 627465 2.070000e-117 433.0
13 TraesCS5A01G254700 chr1A 81.785 1109 171 23 839 1933 3464418 3463327 0.000000e+00 900.0
14 TraesCS5A01G254700 chr1A 81.142 1103 181 26 842 1933 2550491 2551577 0.000000e+00 859.0
15 TraesCS5A01G254700 chr1A 80.776 1108 179 23 842 1934 2849077 2850165 0.000000e+00 835.0
16 TraesCS5A01G254700 chr1B 80.397 1107 184 24 842 1934 3575988 3574901 0.000000e+00 811.0
17 TraesCS5A01G254700 chr1B 84.663 802 103 13 839 1631 4522764 4521974 0.000000e+00 782.0
18 TraesCS5A01G254700 chr1B 79.286 1149 191 40 2094 3212 4207612 4208743 0.000000e+00 760.0
19 TraesCS5A01G254700 chr1B 79.852 541 87 17 1 528 4523923 4523392 3.540000e-100 375.0
20 TraesCS5A01G254700 chr1B 79.664 536 86 17 1 525 4205023 4205546 7.670000e-97 364.0
21 TraesCS5A01G254700 chr1B 79.151 542 88 20 1 528 4814508 4813978 5.970000e-93 351.0
22 TraesCS5A01G254700 chr2A 86.964 560 69 4 2239 2796 766328001 766328558 8.860000e-176 627.0
23 TraesCS5A01G254700 chr2D 86.275 561 71 5 2239 2796 641067445 641068002 4.150000e-169 604.0
24 TraesCS5A01G254700 chr2B 85.336 566 74 6 2239 2801 800188023 800187464 9.050000e-161 577.0
25 TraesCS5A01G254700 chrUn 82.749 371 53 3 3388 3748 229253832 229254201 1.680000e-83 320.0
26 TraesCS5A01G254700 chr6B 88.889 54 5 1 2030 2083 343035222 343035170 8.720000e-07 65.8
27 TraesCS5A01G254700 chr6A 100.000 35 0 0 2049 2083 297639049 297639083 8.720000e-07 65.8
28 TraesCS5A01G254700 chr7A 100.000 31 0 0 2053 2083 282366560 282366590 1.460000e-04 58.4


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 TraesCS5A01G254700 chr5A 470240495 470244253 3758 True 6942.000000 6942 100.000000 1 3759 1 chr5A.!!$R2 3758
1 TraesCS5A01G254700 chr5A 470225364 470227168 1804 True 3251.000000 3251 99.169000 1955 3759 1 chr5A.!!$R1 1804
2 TraesCS5A01G254700 chr5D 368363625 368367365 3740 True 2680.000000 2948 92.485000 1 3759 2 chr5D.!!$R2 3758
3 TraesCS5A01G254700 chr5B 436281013 436284613 3600 True 1676.966667 2865 93.415000 1 3634 3 chr5B.!!$R1 3633
4 TraesCS5A01G254700 chr1D 470447 472378 1931 False 797.500000 902 82.120000 836 2820 2 chr1D.!!$F1 1984
5 TraesCS5A01G254700 chr1D 624865 628228 3363 True 711.666667 976 80.480333 1 3050 3 chr1D.!!$R1 3049
6 TraesCS5A01G254700 chr1A 3463327 3464418 1091 True 900.000000 900 81.785000 839 1933 1 chr1A.!!$R1 1094
7 TraesCS5A01G254700 chr1A 2550491 2551577 1086 False 859.000000 859 81.142000 842 1933 1 chr1A.!!$F1 1091
8 TraesCS5A01G254700 chr1A 2849077 2850165 1088 False 835.000000 835 80.776000 842 1934 1 chr1A.!!$F2 1092
9 TraesCS5A01G254700 chr1B 3574901 3575988 1087 True 811.000000 811 80.397000 842 1934 1 chr1B.!!$R1 1092
10 TraesCS5A01G254700 chr1B 4521974 4523923 1949 True 578.500000 782 82.257500 1 1631 2 chr1B.!!$R3 1630
11 TraesCS5A01G254700 chr1B 4205023 4208743 3720 False 562.000000 760 79.475000 1 3212 2 chr1B.!!$F1 3211
12 TraesCS5A01G254700 chr1B 4813978 4814508 530 True 351.000000 351 79.151000 1 528 1 chr1B.!!$R2 527
13 TraesCS5A01G254700 chr2A 766328001 766328558 557 False 627.000000 627 86.964000 2239 2796 1 chr2A.!!$F1 557
14 TraesCS5A01G254700 chr2D 641067445 641068002 557 False 604.000000 604 86.275000 2239 2796 1 chr2D.!!$F1 557
15 TraesCS5A01G254700 chr2B 800187464 800188023 559 True 577.000000 577 85.336000 2239 2801 1 chr2B.!!$R1 562

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
118 119 0.984230 CCTTGCTACCTCACCTTGGA 59.016 55.0 0.00 0.0 0.00 3.53 F
1026 1441 0.110486 ACACCGAGCCAGGACAATTT 59.890 50.0 1.68 0.0 34.73 1.82 F
1506 2191 0.692476 ATGTACCTGCAAGTGGAGCA 59.308 50.0 0.00 0.0 40.19 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1506 2191 0.825010 CTTGTCCAGGCACCAGCTTT 60.825 55.000 0.00 0.00 41.70 3.51 R
1909 2620 1.811778 TCTATCCATGGAGCCTTGCT 58.188 50.000 21.33 3.62 43.88 3.91 R
3203 3949 1.692762 CCCCATCGGCCCTATATAGCT 60.693 57.143 4.04 0.00 0.00 3.32 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
41 42 4.280677 TCATTGGAAGGAACACAATTCACC 59.719 41.667 0.00 0.00 32.89 4.02
118 119 0.984230 CCTTGCTACCTCACCTTGGA 59.016 55.000 0.00 0.00 0.00 3.53
133 134 5.128663 TCACCTTGGATGAATCAATAGACGA 59.871 40.000 0.00 0.00 0.00 4.20
135 136 5.363868 ACCTTGGATGAATCAATAGACGAGA 59.636 40.000 0.00 0.00 0.00 4.04
147 148 6.997655 TCAATAGACGAGAATGGCAATCTAT 58.002 36.000 4.78 0.00 32.12 1.98
149 150 8.585018 TCAATAGACGAGAATGGCAATCTATAA 58.415 33.333 4.78 0.00 30.92 0.98
228 232 6.550843 TGCCTGTTTGTTTATGTATTCATCG 58.449 36.000 0.00 0.00 35.70 3.84
401 415 2.955614 GCTAACTAGCCGTGAACTCAA 58.044 47.619 0.00 0.00 43.39 3.02
823 1236 3.434940 ACTAGAAACGGGGCTGAAAAT 57.565 42.857 0.00 0.00 0.00 1.82
830 1244 6.627243 AGAAACGGGGCTGAAAATTAAATAC 58.373 36.000 0.00 0.00 0.00 1.89
1026 1441 0.110486 ACACCGAGCCAGGACAATTT 59.890 50.000 1.68 0.00 34.73 1.82
1172 1587 6.982141 GGATTCCACGTACAAACATATCACTA 59.018 38.462 0.00 0.00 0.00 2.74
1211 1626 9.555727 TCAAATGCTTTTGAGTAAACTACTAGT 57.444 29.630 20.42 0.00 44.81 2.57
1481 2166 1.531149 GTGCTACAACTCACAATGCGT 59.469 47.619 0.00 0.00 33.63 5.24
1506 2191 0.692476 ATGTACCTGCAAGTGGAGCA 59.308 50.000 0.00 0.00 40.19 4.26
1904 2614 7.335422 AGTTATGAGGACATGAATGACTTGTTC 59.665 37.037 0.00 0.00 37.08 3.18
2417 3145 1.909302 CTGGAGATTGGGTGGTGTACT 59.091 52.381 0.00 0.00 0.00 2.73
2619 3347 8.311836 CCACATTAAGAACTACAACTCTAAGGA 58.688 37.037 0.00 0.00 0.00 3.36
3203 3949 6.896860 ACAAACATGAAGATTTCCATATGGGA 59.103 34.615 21.78 10.84 46.61 4.37
3396 4143 2.280797 GCCCGAGTGCACTTGTCA 60.281 61.111 28.38 0.00 0.00 3.58
3600 4347 1.202976 ACAAGGAGGTGCAGATTGCTT 60.203 47.619 2.48 0.00 45.31 3.91
3685 4441 6.317140 TGAAATGGAATTCTCTGGAAGATTCG 59.683 38.462 5.23 0.00 37.90 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 7.537596 TTGTGTTCCTTCCAATGAAACATAT 57.462 32.000 0.00 0.00 0.00 1.78
13 14 5.867903 TTGTGTTCCTTCCAATGAAACAT 57.132 34.783 0.00 0.00 0.00 2.71
118 119 5.614308 TGCCATTCTCGTCTATTGATTCAT 58.386 37.500 0.00 0.00 0.00 2.57
133 134 9.803507 TCTCATTCATTTATAGATTGCCATTCT 57.196 29.630 0.00 0.00 0.00 2.40
208 210 8.458052 AGAATGCGATGAATACATAAACAAACA 58.542 29.630 0.00 0.00 36.82 2.83
212 214 6.912051 GCAAGAATGCGATGAATACATAAACA 59.088 34.615 0.00 0.00 43.83 2.83
295 302 7.979537 CCTAAATTTTAGTTGGGAACATAAGCC 59.020 37.037 13.68 0.00 42.32 4.35
392 406 8.968242 GTTCTGTAAATGGAAATTTGAGTTCAC 58.032 33.333 0.00 0.00 0.00 3.18
399 413 7.209475 AGTGGTGTTCTGTAAATGGAAATTTG 58.791 34.615 0.00 0.00 0.00 2.32
401 415 6.777580 AGAGTGGTGTTCTGTAAATGGAAATT 59.222 34.615 0.00 0.00 0.00 1.82
534 587 7.701539 ACAAGCATTCCAAATCTAACACATA 57.298 32.000 0.00 0.00 0.00 2.29
861 1275 2.041620 ACCAGCCATTTACAGTGTGGAT 59.958 45.455 5.88 0.00 34.94 3.41
1026 1441 2.779755 TTTCAGCTCGAAGGCCATAA 57.220 45.000 5.01 0.00 34.32 1.90
1172 1587 6.670695 AAAGCATTTGAGTTTACCAGGATT 57.329 33.333 0.00 0.00 36.60 3.01
1210 1625 8.502387 TGCAAGCAAAACCAAATTATGAAATAC 58.498 29.630 0.00 0.00 0.00 1.89
1211 1626 8.613060 TGCAAGCAAAACCAAATTATGAAATA 57.387 26.923 0.00 0.00 0.00 1.40
1212 1627 7.444792 TCTGCAAGCAAAACCAAATTATGAAAT 59.555 29.630 0.00 0.00 0.00 2.17
1481 2166 2.172505 CCACTTGCAGGTACATATCCCA 59.827 50.000 0.00 0.00 0.00 4.37
1506 2191 0.825010 CTTGTCCAGGCACCAGCTTT 60.825 55.000 0.00 0.00 41.70 3.51
1801 2510 6.262720 ACTCGGAGAATACCTATGTAGTTCAC 59.737 42.308 12.86 0.00 34.09 3.18
1909 2620 1.811778 TCTATCCATGGAGCCTTGCT 58.188 50.000 21.33 3.62 43.88 3.91
2417 3145 9.859427 GAATGATGGTTTTTCTAAATCATGACA 57.141 29.630 0.00 0.00 43.43 3.58
2619 3347 3.071457 CCAAAAGGGGTCAAAAGCTTGAT 59.929 43.478 0.00 0.00 43.39 2.57
3203 3949 1.692762 CCCCATCGGCCCTATATAGCT 60.693 57.143 4.04 0.00 0.00 3.32
3396 4143 3.995199 TGTCGAACTCTTTGATCTTGCT 58.005 40.909 0.00 0.00 0.00 3.91
3600 4347 2.204291 AAGGGACCAGGGATGCCA 60.204 61.111 5.86 0.00 0.00 4.92
3685 4441 0.745845 AACATCCGCTCATGGCTCAC 60.746 55.000 0.00 0.00 39.13 3.51


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

AutoCloner maintained by Alex Coulton.