Multiple sequence alignment - TraesCS5A01G127100

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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 TraesCS5A01G127100 chr5A 100.000 3027 0 0 1 3027 282588934 282585908 0.000000e+00 5590
1 TraesCS5A01G127100 chr5B 96.266 2678 55 14 1 2654 230249515 230246859 0.000000e+00 4349
2 TraesCS5A01G127100 chr5B 97.613 377 5 2 2655 3027 230246810 230246434 0.000000e+00 643
3 TraesCS5A01G127100 chr5B 94.118 85 5 0 582 666 36727196 36727280 2.450000e-26 130
4 TraesCS5A01G127100 chr5D 96.214 2641 55 10 1 2611 214920668 214918043 0.000000e+00 4281
5 TraesCS5A01G127100 chr5D 97.241 435 8 2 2597 3027 214918088 214917654 0.000000e+00 734
6 TraesCS5A01G127100 chr2D 87.830 3147 201 63 22 3027 567476249 567479354 0.000000e+00 3522
7 TraesCS5A01G127100 chr2D 95.652 46 2 0 2597 2642 567478876 567478921 1.160000e-09 75
8 TraesCS5A01G127100 chr2B 88.604 2729 177 55 22 2642 680192919 680195621 0.000000e+00 3193
9 TraesCS5A01G127100 chr2B 82.143 504 35 12 2565 3027 680195572 680196061 6.120000e-102 381
10 TraesCS5A01G127100 chr2A 87.202 2391 173 46 731 3027 706994904 706997255 0.000000e+00 2597
11 TraesCS5A01G127100 chr2A 92.272 427 19 6 321 733 706994352 706994778 7.230000e-166 593
12 TraesCS5A01G127100 chr2A 89.459 351 22 8 22 359 706994007 706994355 2.160000e-116 429
13 TraesCS5A01G127100 chr2A 97.727 44 0 1 2598 2641 706996785 706996827 1.160000e-09 75
14 TraesCS5A01G127100 chrUn 97.613 377 5 2 2655 3027 476965435 476965811 0.000000e+00 643
15 TraesCS5A01G127100 chr4B 83.417 597 69 21 847 1431 135211254 135211832 7.430000e-146 527
16 TraesCS5A01G127100 chr4B 87.943 141 11 3 531 666 135210867 135211006 8.680000e-36 161
17 TraesCS5A01G127100 chr4D 82.833 600 74 20 847 1431 95780931 95781516 7.490000e-141 510
18 TraesCS5A01G127100 chr4D 87.943 141 11 3 531 666 95780563 95780702 8.680000e-36 161
19 TraesCS5A01G127100 chr4A 82.529 601 73 21 850 1431 483951563 483950976 1.620000e-137 499
20 TraesCS5A01G127100 chr4A 87.591 137 10 4 536 666 483951949 483951814 5.230000e-33 152
21 TraesCS5A01G127100 chr3D 81.550 271 43 5 1097 1362 362069952 362069684 1.830000e-52 217


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 TraesCS5A01G127100 chr5A 282585908 282588934 3026 True 5590.0 5590 100.0000 1 3027 1 chr5A.!!$R1 3026
1 TraesCS5A01G127100 chr5B 230246434 230249515 3081 True 2496.0 4349 96.9395 1 3027 2 chr5B.!!$R1 3026
2 TraesCS5A01G127100 chr5D 214917654 214920668 3014 True 2507.5 4281 96.7275 1 3027 2 chr5D.!!$R1 3026
3 TraesCS5A01G127100 chr2D 567476249 567479354 3105 False 1798.5 3522 91.7410 22 3027 2 chr2D.!!$F1 3005
4 TraesCS5A01G127100 chr2B 680192919 680196061 3142 False 1787.0 3193 85.3735 22 3027 2 chr2B.!!$F1 3005
5 TraesCS5A01G127100 chr2A 706994007 706997255 3248 False 923.5 2597 91.6650 22 3027 4 chr2A.!!$F1 3005
6 TraesCS5A01G127100 chr4B 135210867 135211832 965 False 344.0 527 85.6800 531 1431 2 chr4B.!!$F1 900
7 TraesCS5A01G127100 chr4D 95780563 95781516 953 False 335.5 510 85.3880 531 1431 2 chr4D.!!$F1 900
8 TraesCS5A01G127100 chr4A 483950976 483951949 973 True 325.5 499 85.0600 536 1431 2 chr4A.!!$R1 895

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
785 1081 0.320374 TGCACCAAGTCCTCCTTACG 59.680 55.0 0.00 0.0 0.0 3.18 F
786 1082 0.320697 GCACCAAGTCCTCCTTACGT 59.679 55.0 0.00 0.0 0.0 3.57 F
1714 2088 1.098050 GGTGAATTCTTGCAGGCGAT 58.902 50.0 7.05 0.0 0.0 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1714 2088 1.886585 GTCTGCCTCTCTCTGCGAA 59.113 57.895 0.00 0.00 0.00 4.70 R
1836 2210 2.182537 GGTGGGTGTAGCCGTACG 59.817 66.667 8.69 8.69 38.44 3.67 R
2861 3453 1.270147 ACGTAAAACTTCTGCCGAGCT 60.270 47.619 0.00 0.00 0.00 4.09 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 66 0.888619 GTTACTTTGCTTGGAGGGCC 59.111 55.000 0.00 0.00 0.00 5.80
175 181 3.075884 CTCGGGCTAGAGTACTCCATAC 58.924 54.545 19.38 7.85 33.75 2.39
232 255 5.240891 TCAGATGTCACATCTCAAAAGACC 58.759 41.667 17.98 0.00 33.32 3.85
387 458 8.537049 TGTTGGAAATTGCATTTCTGAATAAG 57.463 30.769 16.14 0.00 46.03 1.73
446 530 2.254546 TGGATGTCCAACACAGACAC 57.745 50.000 0.00 0.00 46.43 3.67
447 531 1.488393 TGGATGTCCAACACAGACACA 59.512 47.619 0.00 0.00 46.43 3.72
448 532 2.146342 GGATGTCCAACACAGACACAG 58.854 52.381 0.00 0.00 46.43 3.66
670 775 5.280062 CCTGATCATTCCTCATCAGCTACAT 60.280 44.000 0.00 0.00 43.27 2.29
785 1081 0.320374 TGCACCAAGTCCTCCTTACG 59.680 55.000 0.00 0.00 0.00 3.18
786 1082 0.320697 GCACCAAGTCCTCCTTACGT 59.679 55.000 0.00 0.00 0.00 3.57
1363 1721 3.338126 GACGCCGGAGACATCGTGT 62.338 63.158 13.83 0.00 37.92 4.49
1675 2041 3.591196 TGCATGTGCTGAAAATTACCC 57.409 42.857 6.55 0.00 42.66 3.69
1714 2088 1.098050 GGTGAATTCTTGCAGGCGAT 58.902 50.000 7.05 0.00 0.00 4.58
2034 2415 4.891756 CAGGGGCAGTTCATAAAGATGATT 59.108 41.667 0.00 0.00 41.77 2.57
2035 2416 5.361857 CAGGGGCAGTTCATAAAGATGATTT 59.638 40.000 0.00 0.00 41.77 2.17
2039 2420 6.351286 GGGCAGTTCATAAAGATGATTTGGTT 60.351 38.462 0.00 0.00 41.77 3.67
2122 2517 1.697432 CTACCCTGGACCAAGTGACAA 59.303 52.381 7.02 0.00 0.00 3.18
2327 2729 1.705186 TCAGGTTGAAAAGGAGAGGGG 59.295 52.381 0.00 0.00 0.00 4.79
2338 2743 0.560688 GGAGAGGGGGTGAGAGAGAT 59.439 60.000 0.00 0.00 0.00 2.75
2879 3471 3.898517 AAAGCTCGGCAGAAGTTTTAC 57.101 42.857 0.00 0.00 0.00 2.01
2963 3558 3.198853 GGTCTAAGAGGCAAGTTCCAGAT 59.801 47.826 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 1.333619 CTGGTTTTGGTTGGACTCACG 59.666 52.381 0.00 0.00 0.00 4.35
64 66 2.632996 TGACCACCTGTTAAGAGGACAG 59.367 50.000 24.66 14.07 43.19 3.51
156 162 2.814919 CAGTATGGAGTACTCTAGCCCG 59.185 54.545 21.88 3.80 41.73 6.13
175 181 6.293298 GGCTGTGTGCTCTTATTATCATTCAG 60.293 42.308 0.00 0.00 42.39 3.02
232 255 0.035056 CTTGTTCAGGGCAGTAGGGG 60.035 60.000 0.00 0.00 0.00 4.79
387 458 1.856265 CGGTGCAAGAAAGTCCTGGC 61.856 60.000 0.00 0.00 33.71 4.85
444 528 2.903350 TGGTGCTGCAGTGCTGTG 60.903 61.111 21.31 10.67 0.00 3.66
445 529 2.593725 CTGGTGCTGCAGTGCTGT 60.594 61.111 21.31 0.00 0.00 4.40
446 530 1.449726 TTTCTGGTGCTGCAGTGCTG 61.450 55.000 17.60 17.27 0.00 4.41
447 531 1.152902 TTTCTGGTGCTGCAGTGCT 60.153 52.632 17.60 0.00 0.00 4.40
448 532 1.008079 GTTTCTGGTGCTGCAGTGC 60.008 57.895 16.64 8.58 0.00 4.40
1363 1721 2.882876 GCGCACCCTCTCGAAGTA 59.117 61.111 0.30 0.00 0.00 2.24
1606 1964 3.125316 GCTTTGTTCTTGATTGCTGCAA 58.875 40.909 18.43 18.43 0.00 4.08
1675 2041 3.133003 ACCGGAGAATGGTGTAAGAGATG 59.867 47.826 9.46 0.00 38.60 2.90
1714 2088 1.886585 GTCTGCCTCTCTCTGCGAA 59.113 57.895 0.00 0.00 0.00 4.70
1836 2210 2.182537 GGTGGGTGTAGCCGTACG 59.817 66.667 8.69 8.69 38.44 3.67
2009 2390 3.350219 TCTTTATGAACTGCCCCTGTC 57.650 47.619 0.00 0.00 0.00 3.51
2034 2415 3.321682 CCTCAAGAATGGCTTCAAACCAA 59.678 43.478 0.00 0.00 41.49 3.67
2035 2416 2.892852 CCTCAAGAATGGCTTCAAACCA 59.107 45.455 0.00 0.00 42.61 3.67
2039 2420 3.267812 AGGATCCTCAAGAATGGCTTCAA 59.732 43.478 9.02 0.00 33.60 2.69
2122 2517 3.575687 CCTTCAAAGGGTCAATTCAAGCT 59.424 43.478 0.50 0.00 42.66 3.74
2327 2729 3.181423 ACCATCCCTCTATCTCTCTCACC 60.181 52.174 0.00 0.00 0.00 4.02
2389 2798 7.601508 CACTACATACAGATGACACATGCATAT 59.398 37.037 0.00 0.00 36.48 1.78
2394 2803 5.052481 CCCACTACATACAGATGACACATG 58.948 45.833 0.00 0.00 36.48 3.21
2569 3009 6.003326 TGAGAAGTTAAGGTGAATGCATTGA 58.997 36.000 18.59 5.30 0.00 2.57
2599 3039 5.513233 AGAAGGTAAGGTGAATGCATTGAT 58.487 37.500 18.59 0.00 0.00 2.57
2861 3453 1.270147 ACGTAAAACTTCTGCCGAGCT 60.270 47.619 0.00 0.00 0.00 4.09
2879 3471 1.518056 ATTGAGCCCACTTGCACACG 61.518 55.000 0.00 0.00 31.47 4.49
2912 3504 7.215719 ACTTAGCCATCCTTTTTCTTTGTAC 57.784 36.000 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.