Multiple sequence alignment - TraesCS2A01G293100

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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 TraesCS2A01G293100 chr2A 100.000 3065 0 0 1 3065 504285608 504282544 0.000000e+00 5661
1 TraesCS2A01G293100 chr7D 95.611 1367 53 3 1702 3065 535843214 535844576 0.000000e+00 2185
2 TraesCS2A01G293100 chr7D 95.332 814 25 3 892 1705 535842348 535843148 0.000000e+00 1280
3 TraesCS2A01G293100 chr5B 91.249 1337 106 7 1716 3047 540296200 540297530 0.000000e+00 1810
4 TraesCS2A01G293100 chr5B 89.461 816 84 2 889 1704 503742510 503743323 0.000000e+00 1029
5 TraesCS2A01G293100 chr6D 94.643 1120 53 3 1705 2821 138966677 138965562 0.000000e+00 1729
6 TraesCS2A01G293100 chr6D 94.717 814 43 0 892 1705 138967559 138966746 0.000000e+00 1266
7 TraesCS2A01G293100 chr3B 87.826 1380 155 9 1694 3065 573989402 573990776 0.000000e+00 1605
8 TraesCS2A01G293100 chr3B 88.821 814 90 1 892 1705 573988534 573989346 0.000000e+00 998
9 TraesCS2A01G293100 chr1D 94.057 1060 56 4 2009 3065 479325388 479324333 0.000000e+00 1602
10 TraesCS2A01G293100 chr1D 94.349 814 45 1 892 1705 479333928 479333116 0.000000e+00 1247
11 TraesCS2A01G293100 chr6B 87.620 1357 154 8 1702 3050 63781824 63783174 0.000000e+00 1563
12 TraesCS2A01G293100 chr6B 87.745 816 97 3 891 1705 63780945 63781758 0.000000e+00 950
13 TraesCS2A01G293100 chr3D 86.862 1332 164 4 1705 3033 284855563 284854240 0.000000e+00 1480
14 TraesCS2A01G293100 chr3D 88.329 814 94 1 892 1705 284856444 284855632 0.000000e+00 976
15 TraesCS2A01G293100 chr7B 84.465 1384 198 11 1692 3065 443314815 443316191 0.000000e+00 1349
16 TraesCS2A01G293100 chr7B 84.287 821 121 8 889 1705 443313945 443314761 0.000000e+00 795
17 TraesCS2A01G293100 chr1A 84.298 1382 201 10 1692 3065 386776375 386775002 0.000000e+00 1336
18 TraesCS2A01G293100 chr2D 91.629 896 45 15 1 886 373220802 373221677 0.000000e+00 1212
19 TraesCS2A01G293100 chr7A 92.383 814 43 1 892 1705 580651247 580652041 0.000000e+00 1142
20 TraesCS2A01G293100 chr2B 88.859 754 32 18 3 748 442790853 442791562 0.000000e+00 880
21 TraesCS2A01G293100 chr2B 86.087 115 6 5 772 886 442791631 442791735 6.940000e-22 115


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 TraesCS2A01G293100 chr2A 504282544 504285608 3064 True 5661.0 5661 100.0000 1 3065 1 chr2A.!!$R1 3064
1 TraesCS2A01G293100 chr7D 535842348 535844576 2228 False 1732.5 2185 95.4715 892 3065 2 chr7D.!!$F1 2173
2 TraesCS2A01G293100 chr5B 540296200 540297530 1330 False 1810.0 1810 91.2490 1716 3047 1 chr5B.!!$F2 1331
3 TraesCS2A01G293100 chr5B 503742510 503743323 813 False 1029.0 1029 89.4610 889 1704 1 chr5B.!!$F1 815
4 TraesCS2A01G293100 chr6D 138965562 138967559 1997 True 1497.5 1729 94.6800 892 2821 2 chr6D.!!$R1 1929
5 TraesCS2A01G293100 chr3B 573988534 573990776 2242 False 1301.5 1605 88.3235 892 3065 2 chr3B.!!$F1 2173
6 TraesCS2A01G293100 chr1D 479324333 479325388 1055 True 1602.0 1602 94.0570 2009 3065 1 chr1D.!!$R1 1056
7 TraesCS2A01G293100 chr1D 479333116 479333928 812 True 1247.0 1247 94.3490 892 1705 1 chr1D.!!$R2 813
8 TraesCS2A01G293100 chr6B 63780945 63783174 2229 False 1256.5 1563 87.6825 891 3050 2 chr6B.!!$F1 2159
9 TraesCS2A01G293100 chr3D 284854240 284856444 2204 True 1228.0 1480 87.5955 892 3033 2 chr3D.!!$R1 2141
10 TraesCS2A01G293100 chr7B 443313945 443316191 2246 False 1072.0 1349 84.3760 889 3065 2 chr7B.!!$F1 2176
11 TraesCS2A01G293100 chr1A 386775002 386776375 1373 True 1336.0 1336 84.2980 1692 3065 1 chr1A.!!$R1 1373
12 TraesCS2A01G293100 chr2D 373220802 373221677 875 False 1212.0 1212 91.6290 1 886 1 chr2D.!!$F1 885
13 TraesCS2A01G293100 chr7A 580651247 580652041 794 False 1142.0 1142 92.3830 892 1705 1 chr7A.!!$F1 813
14 TraesCS2A01G293100 chr2B 442790853 442791735 882 False 497.5 880 87.4730 3 886 2 chr2B.!!$F1 883

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
697 715 0.313672 GATCTGACGCTAGGCTGGAG 59.686 60.0 0.43 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2065 2217 1.684248 GGCAGTTCCATGAGAGGCAAT 60.684 52.381 0.0 0.0 34.01 3.56 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
45 46 6.257630 GCCTTTGCATCTTTTGTTGTCTTTAA 59.742 34.615 0.00 0.00 37.47 1.52
46 47 7.621102 CCTTTGCATCTTTTGTTGTCTTTAAC 58.379 34.615 0.00 0.00 0.00 2.01
217 222 4.095483 GTGAAATACCTCTGGCATGTCTTG 59.905 45.833 0.00 0.00 0.00 3.02
234 239 2.236893 TCTTGCAGTGCTCATATGGACA 59.763 45.455 17.60 0.00 0.00 4.02
262 267 3.340814 ACTTGATGATTTCTCCGTGCT 57.659 42.857 0.00 0.00 0.00 4.40
289 294 1.938577 CCATTGTCCTCTCGAAGCATG 59.061 52.381 0.00 0.00 0.00 4.06
334 339 5.659440 TTCCCCTGAAATGAAGTAAATGC 57.341 39.130 0.00 0.00 0.00 3.56
336 341 3.181487 CCCCTGAAATGAAGTAAATGCGG 60.181 47.826 0.00 0.00 0.00 5.69
393 398 4.637534 TGTATTCTTCTTCATTCAGCCAGC 59.362 41.667 0.00 0.00 0.00 4.85
401 406 1.379576 ATTCAGCCAGCTCCTTGCC 60.380 57.895 0.00 0.00 44.23 4.52
409 414 1.386533 CAGCTCCTTGCCTGGTATTG 58.613 55.000 0.00 0.00 44.23 1.90
422 427 3.118592 CCTGGTATTGTCTCCAGTCCTTC 60.119 52.174 9.79 0.00 46.79 3.46
432 437 0.951040 CCAGTCCTTCTGAACCGTGC 60.951 60.000 0.00 0.00 46.27 5.34
433 438 0.951040 CAGTCCTTCTGAACCGTGCC 60.951 60.000 0.00 0.00 46.27 5.01
434 439 1.070786 GTCCTTCTGAACCGTGCCA 59.929 57.895 0.00 0.00 0.00 4.92
439 444 2.419990 CCTTCTGAACCGTGCCATCATA 60.420 50.000 0.00 0.00 0.00 2.15
440 445 3.470709 CTTCTGAACCGTGCCATCATAT 58.529 45.455 0.00 0.00 0.00 1.78
578 583 3.461061 GACATTGAGATCGGCATCTTGA 58.539 45.455 0.00 0.00 39.71 3.02
697 715 0.313672 GATCTGACGCTAGGCTGGAG 59.686 60.000 0.43 0.00 0.00 3.86
713 731 1.003580 TGGAGAGCATTGTGGGAGAAC 59.996 52.381 0.00 0.00 0.00 3.01
736 754 4.085055 CGTAACACTTGCTGACTTGTACAG 60.085 45.833 0.00 0.00 38.27 2.74
756 774 4.937620 ACAGCATTGTACGATCTCACATTT 59.062 37.500 0.00 0.00 35.25 2.32
758 776 4.937620 AGCATTGTACGATCTCACATTTGT 59.062 37.500 0.00 0.00 0.00 2.83
759 777 6.035975 CAGCATTGTACGATCTCACATTTGTA 59.964 38.462 0.00 0.00 0.00 2.41
760 778 6.036083 AGCATTGTACGATCTCACATTTGTAC 59.964 38.462 0.00 0.00 34.32 2.90
761 779 6.036083 GCATTGTACGATCTCACATTTGTACT 59.964 38.462 0.00 0.00 34.70 2.73
794 864 5.565592 ACCATCATTTCAGTACGTACGTA 57.434 39.130 23.60 23.60 0.00 3.57
795 865 5.953183 ACCATCATTTCAGTACGTACGTAA 58.047 37.500 28.34 15.72 31.86 3.18
832 903 9.474313 AGCCTTTGGATTATTCTTGTATTTGTA 57.526 29.630 0.00 0.00 0.00 2.41
842 913 9.860650 TTATTCTTGTATTTGTATGTATGGCCT 57.139 29.630 3.32 0.00 0.00 5.19
865 936 7.201688 GCCTTTTTGAATTTGGAAAAGCAACTA 60.202 33.333 12.62 0.00 38.44 2.24
875 946 9.995003 ATTTGGAAAAGCAACTAATTGATAACA 57.005 25.926 0.00 0.00 38.15 2.41
1176 1248 1.529244 GGTGAAGTGGTTGCTGGCT 60.529 57.895 0.00 0.00 0.00 4.75
1309 1381 1.522668 TGTGGCTGAATTTGAGTCCG 58.477 50.000 0.00 0.00 0.00 4.79
1503 1576 3.184628 CCTCCCAATAGCCAGGATGATA 58.815 50.000 0.00 0.00 39.69 2.15
1551 1624 1.207329 GATCACAACGGAGGCTACCTT 59.793 52.381 0.00 0.00 31.76 3.50
1563 1636 4.262981 GGAGGCTACCTTCGAGATAGAGTA 60.263 50.000 0.00 0.00 31.76 2.59
1585 1658 2.372504 TCGGTGGAGGTCAATAAACCAA 59.627 45.455 0.00 0.00 42.12 3.67
1587 1660 3.128589 CGGTGGAGGTCAATAAACCAATG 59.871 47.826 0.00 0.00 42.12 2.82
1635 1708 3.196685 CGAGGAGAAAGAAGGTGGATTCT 59.803 47.826 0.00 0.00 41.31 2.40
1928 2080 2.223386 TGCTTCTTACGGCAACACAAAC 60.223 45.455 0.00 0.00 35.40 2.93
1936 2088 1.403679 CGGCAACACAAACTCCAGAAA 59.596 47.619 0.00 0.00 0.00 2.52
2065 2217 2.037687 CCTGCCCAGCCCAATGAA 59.962 61.111 0.00 0.00 0.00 2.57
2270 2422 0.253044 TTAGTGGTGGCATCAGGCTC 59.747 55.000 0.00 0.00 44.01 4.70
2635 2787 1.675641 GACAATCGGCAGGCAGGTT 60.676 57.895 0.00 0.00 0.00 3.50
2733 2888 6.042093 AGAGACACTTACCTTCTGTTGAATCA 59.958 38.462 0.00 0.00 0.00 2.57
2886 3041 0.620700 AGGCAAATAGAGGTCCGGGT 60.621 55.000 0.00 0.00 0.00 5.28
2910 3065 2.615493 CCAAGGTATTGCGGACTCACTT 60.615 50.000 0.00 0.00 34.91 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
217 222 2.636830 ACTTGTCCATATGAGCACTGC 58.363 47.619 3.65 0.00 0.00 4.40
234 239 8.076178 CACGGAGAAATCATCAAGTTTTTACTT 58.924 33.333 0.00 0.00 0.00 2.24
262 267 1.134367 CGAGAGGACAATGGCGAGTTA 59.866 52.381 0.00 0.00 0.00 2.24
289 294 1.010797 CTCATTATGTGGCGCGCAC 60.011 57.895 34.42 26.87 0.00 5.34
327 332 6.560711 AGATAACAAAATGGACCGCATTTAC 58.439 36.000 0.00 0.00 32.58 2.01
393 398 2.420687 GGAGACAATACCAGGCAAGGAG 60.421 54.545 2.81 0.00 0.00 3.69
409 414 1.067495 CGGTTCAGAAGGACTGGAGAC 60.067 57.143 0.00 0.00 45.76 3.36
422 427 3.879295 AGAAATATGATGGCACGGTTCAG 59.121 43.478 0.00 0.00 0.00 3.02
578 583 3.031736 AGCTTCCACCTACATACATCGT 58.968 45.455 0.00 0.00 0.00 3.73
633 642 2.979177 TCCCCATCCCACGATGTTATA 58.021 47.619 0.00 0.00 43.87 0.98
634 643 1.814429 TCCCCATCCCACGATGTTAT 58.186 50.000 0.00 0.00 43.87 1.89
652 661 7.917505 CCTAAAATGTCAATCAGCCAACTATTC 59.082 37.037 0.00 0.00 0.00 1.75
697 715 2.380084 TACGTTCTCCCACAATGCTC 57.620 50.000 0.00 0.00 0.00 4.26
713 731 3.799963 TGTACAAGTCAGCAAGTGTTACG 59.200 43.478 0.00 0.00 0.00 3.18
736 754 5.221891 ACAAATGTGAGATCGTACAATGC 57.778 39.130 8.76 0.00 0.00 3.56
828 899 7.605691 CCAAATTCAAAAAGGCCATACATACAA 59.394 33.333 5.01 0.00 0.00 2.41
829 900 7.038729 TCCAAATTCAAAAAGGCCATACATACA 60.039 33.333 5.01 0.00 0.00 2.29
832 903 6.371595 TCCAAATTCAAAAAGGCCATACAT 57.628 33.333 5.01 0.00 0.00 2.29
833 904 5.815233 TCCAAATTCAAAAAGGCCATACA 57.185 34.783 5.01 0.00 0.00 2.29
834 905 7.503521 TTTTCCAAATTCAAAAAGGCCATAC 57.496 32.000 5.01 0.00 0.00 2.39
835 906 6.206438 GCTTTTCCAAATTCAAAAAGGCCATA 59.794 34.615 5.01 0.00 39.34 2.74
836 907 5.009911 GCTTTTCCAAATTCAAAAAGGCCAT 59.990 36.000 5.01 0.00 39.34 4.40
837 908 4.337836 GCTTTTCCAAATTCAAAAAGGCCA 59.662 37.500 5.01 0.00 39.34 5.36
838 909 4.337836 TGCTTTTCCAAATTCAAAAAGGCC 59.662 37.500 15.78 0.00 39.34 5.19
839 910 5.497635 TGCTTTTCCAAATTCAAAAAGGC 57.502 34.783 15.78 11.45 39.34 4.35
840 911 7.087409 AGTTGCTTTTCCAAATTCAAAAAGG 57.913 32.000 15.78 4.22 39.34 3.11
875 946 6.408206 CGGGGAAAAAGTAGTCCTCTATGAAT 60.408 42.308 0.00 0.00 31.57 2.57
886 957 3.870538 AGGTTTCGGGGAAAAAGTAGT 57.129 42.857 0.00 0.00 33.14 2.73
887 958 4.259356 CCTAGGTTTCGGGGAAAAAGTAG 58.741 47.826 0.00 0.00 33.14 2.57
1034 1106 4.164294 GGTATTATTCGATCCCGAGTTCG 58.836 47.826 0.00 0.00 46.39 3.95
1131 1203 2.630098 ACCATCCAGACGGTCATCTATG 59.370 50.000 11.27 8.07 0.00 2.23
1309 1381 1.135731 CTCTGTCACGGTCTCGCTC 59.864 63.158 0.00 0.00 40.63 5.03
1503 1576 7.856415 ACTTAGCAATCTGAACCTCTTTATCT 58.144 34.615 0.00 0.00 0.00 1.98
1551 1624 3.306849 CCTCCACCGATACTCTATCTCGA 60.307 52.174 0.00 0.00 34.41 4.04
1556 1629 3.878237 TGACCTCCACCGATACTCTAT 57.122 47.619 0.00 0.00 0.00 1.98
1563 1636 2.574369 TGGTTTATTGACCTCCACCGAT 59.426 45.455 0.00 0.00 40.47 4.18
1585 1658 3.718434 TCAATAAGCACCCATCTCCTCAT 59.282 43.478 0.00 0.00 0.00 2.90
1587 1660 3.845781 TCAATAAGCACCCATCTCCTC 57.154 47.619 0.00 0.00 0.00 3.71
1692 1765 5.343307 TGTTCTCATCAAGATCCGAATGA 57.657 39.130 0.00 0.00 32.82 2.57
1928 2080 5.782893 ACTCGGATCTAGATTTTCTGGAG 57.217 43.478 6.70 9.59 37.41 3.86
1936 2088 4.890581 AGTGCTTGTACTCGGATCTAGATT 59.109 41.667 6.70 0.00 0.00 2.40
2065 2217 1.684248 GGCAGTTCCATGAGAGGCAAT 60.684 52.381 0.00 0.00 34.01 3.56
2265 2417 2.957402 TCATGTGACCAAAAGAGCCT 57.043 45.000 0.00 0.00 0.00 4.58
2270 2422 7.866898 TCAACAATAACATCATGTGACCAAAAG 59.133 33.333 0.00 0.00 0.00 2.27
2314 2466 8.978874 TTTAACAGTAGCATCAATATGTCCAT 57.021 30.769 0.00 0.00 35.38 3.41
2399 2551 6.867816 CCAACTATGATGTCTATCTTCAGCTC 59.132 42.308 0.00 0.00 34.51 4.09
2400 2552 6.740960 GCCAACTATGATGTCTATCTTCAGCT 60.741 42.308 0.00 0.00 34.51 4.24
2401 2553 5.407995 GCCAACTATGATGTCTATCTTCAGC 59.592 44.000 0.00 0.00 34.51 4.26
2402 2554 5.632764 CGCCAACTATGATGTCTATCTTCAG 59.367 44.000 0.00 0.00 34.51 3.02
2635 2787 2.016318 CCTCGCCTTGACATTTGCATA 58.984 47.619 0.00 0.00 0.00 3.14
2733 2888 4.759693 TCCGCTACAACAAAACAATGATCT 59.240 37.500 0.00 0.00 0.00 2.75
2886 3041 1.480954 GAGTCCGCAATACCTTGGAGA 59.519 52.381 0.00 0.00 32.72 3.71
2910 3065 3.616956 AGCGTTTCCTTCAGATGATGA 57.383 42.857 0.00 0.00 35.62 2.92


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

AutoCloner maintained by Alex Coulton.