Multiple sequence alignment - TraesCS2B01G511500

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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 TraesCS2B01G511500 chr2B 100.000 2372 0 0 1 2372 707413524 707411153 0.000000e+00 4381
1 TraesCS2B01G511500 chr2B 92.897 1253 49 17 1 1216 550485483 550486732 0.000000e+00 1784
2 TraesCS2B01G511500 chr2B 86.842 760 61 17 1645 2372 550487486 550488238 0.000000e+00 813
3 TraesCS2B01G511500 chr2B 89.085 623 22 12 1262 1839 550486730 550487351 0.000000e+00 732
4 TraesCS2B01G511500 chr2B 84.718 746 72 22 54 776 121648614 121649340 0.000000e+00 708
5 TraesCS2B01G511500 chr2B 83.333 144 6 3 1658 1792 550487450 550487584 1.490000e-22 117
6 TraesCS2B01G511500 chr5B 94.432 1850 66 12 15 1830 545152140 545150294 0.000000e+00 2811
7 TraesCS2B01G511500 chr5B 89.850 1596 81 19 310 1828 403761261 403762852 0.000000e+00 1975
8 TraesCS2B01G511500 chr5B 89.712 243 15 3 1669 1910 403763487 403763720 3.830000e-78 302
9 TraesCS2B01G511500 chr5B 91.979 187 13 2 1645 1830 545150392 545150207 6.500000e-66 261
10 TraesCS2B01G511500 chr4B 94.475 1828 65 20 15 1830 67034481 67032678 0.000000e+00 2784
11 TraesCS2B01G511500 chr4B 94.311 1828 68 20 15 1830 66972488 66970685 0.000000e+00 2767
12 TraesCS2B01G511500 chr4B 94.201 1828 71 19 15 1830 66867857 66866053 0.000000e+00 2756
13 TraesCS2B01G511500 chr4B 93.757 1842 80 19 1 1830 66999380 66997562 0.000000e+00 2732
14 TraesCS2B01G511500 chr4B 93.490 1828 65 20 15 1830 66898418 66896633 0.000000e+00 2667
15 TraesCS2B01G511500 chr4B 93.478 1150 43 15 693 1830 66927177 66926048 0.000000e+00 1679
16 TraesCS2B01G511500 chr4B 94.290 683 25 10 15 697 66927812 66927144 0.000000e+00 1033
17 TraesCS2B01G511500 chr4B 94.989 459 12 1 1925 2372 66865799 66865341 0.000000e+00 710
18 TraesCS2B01G511500 chr4B 94.118 459 16 1 1925 2372 66896388 66895930 0.000000e+00 688
19 TraesCS2B01G511500 chr4B 94.118 459 16 1 1925 2372 66925794 66925336 0.000000e+00 688
20 TraesCS2B01G511500 chr4B 93.900 459 16 2 1925 2372 66970478 66970021 0.000000e+00 682
21 TraesCS2B01G511500 chr4B 93.900 459 17 1 1925 2372 67032066 67031608 0.000000e+00 682
22 TraesCS2B01G511500 chr4B 93.682 459 18 1 1925 2372 66997009 66996551 0.000000e+00 676
23 TraesCS2B01G511500 chr4B 91.500 200 13 4 1643 1839 66896647 66896449 3.000000e-69 272
24 TraesCS2B01G511500 chr4B 93.514 185 9 3 1645 1827 66925972 66925789 3.000000e-69 272
25 TraesCS2B01G511500 chr4B 91.414 198 13 4 1645 1839 66970784 66970588 3.890000e-68 268
26 TraesCS2B01G511500 chr4B 92.513 187 12 2 1645 1830 66926059 66925874 1.400000e-67 267
27 TraesCS2B01G511500 chr4B 92.553 188 11 3 1645 1830 66926147 66925961 1.400000e-67 267
28 TraesCS2B01G511500 chr4B 91.935 186 15 0 1645 1830 66866064 66865879 6.500000e-66 261
29 TraesCS2B01G511500 chr4B 92.021 188 12 3 1645 1830 66866152 66865966 6.500000e-66 261
30 TraesCS2B01G511500 chr1A 88.323 1079 70 27 512 1538 582355376 582354302 0.000000e+00 1243
31 TraesCS2B01G511500 chr1A 83.240 358 34 13 1645 1979 582353746 582353392 2.960000e-79 305
32 TraesCS2B01G511500 chr1B 88.347 738 51 15 1658 2372 641877341 641878066 0.000000e+00 854
33 TraesCS2B01G511500 chr1B 82.849 723 79 24 1669 2372 274855480 274856176 7.250000e-170 606
34 TraesCS2B01G511500 chr1B 86.842 304 35 5 1533 1832 631972068 631971766 3.780000e-88 335
35 TraesCS2B01G511500 chr6A 86.575 730 54 18 1669 2372 610057328 610058039 0.000000e+00 765
36 TraesCS2B01G511500 chr4A 85.450 756 67 15 1645 2372 14841088 14841828 0.000000e+00 747
37 TraesCS2B01G511500 chr2D 82.902 772 79 23 1645 2372 531355934 531356696 0.000000e+00 645
38 TraesCS2B01G511500 chr3B 83.333 726 70 29 1669 2372 79975988 79975292 7.200000e-175 623
39 TraesCS2B01G511500 chr7B 83.172 517 42 23 1871 2372 372042791 372043277 4.680000e-117 431
40 TraesCS2B01G511500 chr7B 82.205 517 47 24 1871 2372 51057492 51057006 1.020000e-108 403
41 TraesCS2B01G511500 chr7B 79.932 294 37 13 1690 1981 372042557 372042830 1.860000e-46 196
42 TraesCS2B01G511500 chr7D 92.661 109 8 0 1871 1979 161533731 161533623 8.780000e-35 158


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 TraesCS2B01G511500 chr2B 707411153 707413524 2371 True 4381.0 4381 100.000000 1 2372 1 chr2B.!!$R1 2371
1 TraesCS2B01G511500 chr2B 550485483 550488238 2755 False 861.5 1784 88.039250 1 2372 4 chr2B.!!$F2 2371
2 TraesCS2B01G511500 chr2B 121648614 121649340 726 False 708.0 708 84.718000 54 776 1 chr2B.!!$F1 722
3 TraesCS2B01G511500 chr5B 545150207 545152140 1933 True 1536.0 2811 93.205500 15 1830 2 chr5B.!!$R1 1815
4 TraesCS2B01G511500 chr5B 403761261 403763720 2459 False 1138.5 1975 89.781000 310 1910 2 chr5B.!!$F1 1600
5 TraesCS2B01G511500 chr4B 67031608 67034481 2873 True 1733.0 2784 94.187500 15 2372 2 chr4B.!!$R6 2357
6 TraesCS2B01G511500 chr4B 66996551 66999380 2829 True 1704.0 2732 93.719500 1 2372 2 chr4B.!!$R5 2371
7 TraesCS2B01G511500 chr4B 66970021 66972488 2467 True 1239.0 2767 93.208333 15 2372 3 chr4B.!!$R4 2357
8 TraesCS2B01G511500 chr4B 66895930 66898418 2488 True 1209.0 2667 93.036000 15 2372 3 chr4B.!!$R2 2357
9 TraesCS2B01G511500 chr4B 66865341 66867857 2516 True 997.0 2756 93.286500 15 2372 4 chr4B.!!$R1 2357
10 TraesCS2B01G511500 chr4B 66925336 66927812 2476 True 701.0 1679 93.411000 15 2372 6 chr4B.!!$R3 2357
11 TraesCS2B01G511500 chr1A 582353392 582355376 1984 True 774.0 1243 85.781500 512 1979 2 chr1A.!!$R1 1467
12 TraesCS2B01G511500 chr1B 641877341 641878066 725 False 854.0 854 88.347000 1658 2372 1 chr1B.!!$F2 714
13 TraesCS2B01G511500 chr1B 274855480 274856176 696 False 606.0 606 82.849000 1669 2372 1 chr1B.!!$F1 703
14 TraesCS2B01G511500 chr6A 610057328 610058039 711 False 765.0 765 86.575000 1669 2372 1 chr6A.!!$F1 703
15 TraesCS2B01G511500 chr4A 14841088 14841828 740 False 747.0 747 85.450000 1645 2372 1 chr4A.!!$F1 727
16 TraesCS2B01G511500 chr2D 531355934 531356696 762 False 645.0 645 82.902000 1645 2372 1 chr2D.!!$F1 727
17 TraesCS2B01G511500 chr3B 79975292 79975988 696 True 623.0 623 83.333000 1669 2372 1 chr3B.!!$R1 703
18 TraesCS2B01G511500 chr7B 372042557 372043277 720 False 313.5 431 81.552000 1690 2372 2 chr7B.!!$F1 682

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
126 150 0.322975 TCTTGCTCCTCTGTCTTGCC 59.677 55.0 0.0 0.0 0.0 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1823 3846 4.072131 CTCTTGTGCCAAAAAGCCTACTA 58.928 43.478 0.0 0.0 0.0 1.82 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
103 127 2.043852 TCGCTCACTCCTCCTCCC 60.044 66.667 0.00 0.0 0.00 4.30
104 128 2.363018 CGCTCACTCCTCCTCCCA 60.363 66.667 0.00 0.0 0.00 4.37
126 150 0.322975 TCTTGCTCCTCTGTCTTGCC 59.677 55.000 0.00 0.0 0.00 4.52
169 218 1.671054 CCACGTCGGCATGGTTTCT 60.671 57.895 0.00 0.0 0.00 2.52
284 339 2.565391 GGTTAGGGTTTGTGATTTGGGG 59.435 50.000 0.00 0.0 0.00 4.96
285 340 3.236047 GTTAGGGTTTGTGATTTGGGGT 58.764 45.455 0.00 0.0 0.00 4.95
455 527 1.065401 CAGAAAGGCGTGTTGCTTTCA 59.935 47.619 11.73 0.0 42.86 2.69
473 545 0.890683 CAAAGGAATCCACACTGGCC 59.109 55.000 0.61 0.0 37.47 5.36
638 711 2.543641 GCAGCATCTTAAAACCATGGC 58.456 47.619 13.04 0.0 0.00 4.40
683 849 0.403655 TGCATGGGTTACTGGAGCAA 59.596 50.000 0.00 0.0 0.00 3.91
854 1034 5.300539 TCAGCTCTGAATGTGAGGATAGTAC 59.699 44.000 0.00 0.0 36.53 2.73
933 1115 4.065789 GTTCAGGAAGTAGAAACTGTGGG 58.934 47.826 0.00 0.0 35.62 4.61
1112 1311 1.939255 GCAGAGCTATGAGAAGTTGGC 59.061 52.381 13.69 0.0 0.00 4.52
1263 1465 6.003326 TGTCATTAGGAACATGAAGCTCAAA 58.997 36.000 0.00 0.0 32.37 2.69
1502 1729 9.599866 TGGTGATGTAATGTAGTAATCTTCAAG 57.400 33.333 0.00 0.0 0.00 3.02
1799 3822 2.897326 GGCATCAAGTAGGGGTTTTTGT 59.103 45.455 0.00 0.0 0.00 2.83
1875 4093 5.583457 TCACAAGAGTAGCAACATCATCATG 59.417 40.000 0.00 0.0 35.92 3.07
2005 4415 6.388619 ACCAGAACCTAAGTTGGTCATTAT 57.611 37.500 0.00 0.0 39.83 1.28
2018 4428 7.913789 AGTTGGTCATTATAGTACCAGAACAA 58.086 34.615 0.00 0.0 43.82 2.83
2222 4635 1.891150 CTCCCTTTGCAGCAGTTGAAT 59.109 47.619 0.00 0.0 0.00 2.57
2223 4636 1.614903 TCCCTTTGCAGCAGTTGAATG 59.385 47.619 0.00 0.0 0.00 2.67
2257 4706 1.503542 CTTACCCTTTGCAGCAGCG 59.496 57.895 0.00 0.0 46.23 5.18
2296 4751 1.407437 GGTGCAGTGGTAGAAGATGGG 60.407 57.143 0.00 0.0 0.00 4.00
2307 4768 1.918957 AGAAGATGGGGTCCTCTTTGG 59.081 52.381 0.00 0.0 31.99 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 74 1.374560 GAGAGCAGCGAGACAGAGTA 58.625 55.000 0.00 0.00 0.00 2.59
103 127 3.001414 CAAGACAGAGGAGCAAGACATG 58.999 50.000 0.00 0.00 0.00 3.21
104 128 2.614987 GCAAGACAGAGGAGCAAGACAT 60.615 50.000 0.00 0.00 0.00 3.06
159 208 1.098050 ATCGCTCCAAGAAACCATGC 58.902 50.000 0.00 0.00 0.00 4.06
169 218 0.757561 TATCGGACCCATCGCTCCAA 60.758 55.000 0.00 0.00 0.00 3.53
213 262 0.735632 GTCGTCAGAAGCTGAGCTGG 60.736 60.000 8.16 0.58 41.46 4.85
455 527 0.609131 CGGCCAGTGTGGATTCCTTT 60.609 55.000 2.24 0.00 40.96 3.11
473 545 0.040067 GCACAGCAAAGAAACCTCCG 60.040 55.000 0.00 0.00 0.00 4.63
638 711 5.957842 TCTAACTTAACAATGTTGCCAGG 57.042 39.130 9.15 0.00 0.00 4.45
683 849 2.610438 AACCCATGCATCCTTTGTCT 57.390 45.000 0.00 0.00 0.00 3.41
779 945 6.952773 TGCTAGTTAAACAATGTTGTCCTT 57.047 33.333 0.00 0.00 41.31 3.36
961 1160 1.144708 TGCATTCTCAAGGGTGTTGGA 59.855 47.619 0.00 0.00 0.00 3.53
1009 1208 5.816777 CCTCATTCATGTCTCTCTTCCTTTC 59.183 44.000 0.00 0.00 0.00 2.62
1014 1213 7.862512 ATTTTCCTCATTCATGTCTCTCTTC 57.137 36.000 0.00 0.00 0.00 2.87
1112 1311 5.474532 TCCAAAAGTCCATTGACATCTTCAG 59.525 40.000 0.00 0.00 44.33 3.02
1263 1465 6.405538 CAAATTCTTCCTCTCTTCAGCTAGT 58.594 40.000 0.00 0.00 0.00 2.57
1823 3846 4.072131 CTCTTGTGCCAAAAAGCCTACTA 58.928 43.478 0.00 0.00 0.00 1.82
2005 4415 8.154203 TGATCATCAAGTTTTGTTCTGGTACTA 58.846 33.333 0.00 0.00 0.00 1.82
2018 4428 6.506500 GATGACCAAGTGATCATCAAGTTT 57.493 37.500 10.30 0.00 46.98 2.66
2222 4635 0.395862 AAGGCTCGAGCTACTAGGCA 60.396 55.000 34.46 0.00 38.88 4.75
2223 4636 1.267533 GTAAGGCTCGAGCTACTAGGC 59.732 57.143 34.46 17.44 41.70 3.93
2257 4706 3.624861 CACCATCAACAAGATCTGCTACC 59.375 47.826 0.00 0.00 33.72 3.18
2296 4751 0.890996 CAGCACCACCAAAGAGGACC 60.891 60.000 0.00 0.00 41.22 4.46


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

AutoCloner maintained by Alex Coulton.