Multiple sequence alignment - TraesCS4A01G142900

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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 TraesCS4A01G142900 chr4A 100.000 2459 0 0 1 2459 232104806 232102348 0.000000e+00 4542.0
1 TraesCS4A01G142900 chr4A 96.201 1711 59 3 755 2459 254605298 254607008 0.000000e+00 2795.0
2 TraesCS4A01G142900 chr4A 94.577 756 41 0 1 756 612498787 612499542 0.000000e+00 1170.0
3 TraesCS4A01G142900 chr4A 95.378 238 9 1 2220 2457 257851974 257851739 6.420000e-101 377.0
4 TraesCS4A01G142900 chr4A 95.378 238 7 1 1992 2225 257861240 257861003 2.310000e-100 375.0
5 TraesCS4A01G142900 chr4A 86.667 90 8 4 1552 1637 536090324 536090235 2.010000e-16 97.1
6 TraesCS4A01G142900 chr1B 91.354 1226 71 11 755 1964 318979559 318978353 0.000000e+00 1644.0
7 TraesCS4A01G142900 chr1B 92.479 944 52 6 1036 1964 320735990 320736929 0.000000e+00 1332.0
8 TraesCS4A01G142900 chr1B 90.504 674 59 5 1 673 355090298 355090967 0.000000e+00 885.0
9 TraesCS4A01G142900 chr1B 93.014 501 26 6 1964 2459 318978178 318977682 0.000000e+00 723.0
10 TraesCS4A01G142900 chr1B 92.659 504 26 6 1964 2459 320737103 320737603 0.000000e+00 715.0
11 TraesCS4A01G142900 chr1B 93.774 257 15 1 755 1010 320714559 320714815 3.840000e-103 385.0
12 TraesCS4A01G142900 chr1B 93.671 79 2 1 2204 2279 672545600 672545522 5.560000e-22 115.0
13 TraesCS4A01G142900 chr5A 89.920 1131 103 8 755 1877 400066132 400067259 0.000000e+00 1447.0
14 TraesCS4A01G142900 chr5A 90.504 674 60 4 1 673 33900137 33900807 0.000000e+00 887.0
15 TraesCS4A01G142900 chr5A 85.259 251 25 7 1964 2203 400067584 400067833 5.250000e-62 248.0
16 TraesCS4A01G142900 chr5A 92.045 88 6 1 1877 1964 400067326 400067412 3.320000e-24 122.0
17 TraesCS4A01G142900 chr5A 94.286 35 1 1 1969 2002 93643258 93643224 4.000000e-03 52.8
18 TraesCS4A01G142900 chr1D 94.974 776 21 10 755 1516 104025488 104026259 0.000000e+00 1201.0
19 TraesCS4A01G142900 chr1D 94.800 500 22 1 1964 2459 104031485 104031984 0.000000e+00 776.0
20 TraesCS4A01G142900 chr1D 95.815 454 18 1 1511 1964 104030859 104031311 0.000000e+00 732.0
21 TraesCS4A01G142900 chr1A 93.783 756 46 1 1 756 577181916 577182670 0.000000e+00 1134.0
22 TraesCS4A01G142900 chr1A 90.950 674 55 5 1 673 118768262 118767594 0.000000e+00 902.0
23 TraesCS4A01G142900 chr6B 91.138 756 61 5 1 755 664683313 664684063 0.000000e+00 1020.0
24 TraesCS4A01G142900 chr5B 90.323 775 57 10 1 763 548054534 548055302 0.000000e+00 1000.0
25 TraesCS4A01G142900 chr5B 90.504 674 60 4 1 673 440229882 440229212 0.000000e+00 887.0
26 TraesCS4A01G142900 chr5B 86.813 273 20 8 494 755 548050033 548050300 8.600000e-75 291.0
27 TraesCS4A01G142900 chr3A 90.504 674 60 4 1 673 8126842 8127512 0.000000e+00 887.0
28 TraesCS4A01G142900 chr3B 90.370 675 59 6 1 673 25498838 25498168 0.000000e+00 881.0
29 TraesCS4A01G142900 chrUn 93.421 228 15 0 1737 1964 480131499 480131726 3.030000e-89 339.0
30 TraesCS4A01G142900 chrUn 93.671 79 2 1 2204 2279 171012611 171012533 5.560000e-22 115.0
31 TraesCS4A01G142900 chr2B 84.000 350 36 9 1532 1876 218085948 218086282 3.950000e-83 318.0
32 TraesCS4A01G142900 chr2B 84.000 350 36 9 1532 1876 218088092 218088426 3.950000e-83 318.0
33 TraesCS4A01G142900 chr2B 90.909 88 8 0 1877 1964 218086333 218086420 4.300000e-23 119.0
34 TraesCS4A01G142900 chr2B 90.909 88 8 0 1877 1964 218088477 218088564 4.300000e-23 119.0
35 TraesCS4A01G142900 chr2B 90.909 88 8 0 1877 1964 218090617 218090704 4.300000e-23 119.0
36 TraesCS4A01G142900 chr2B 93.671 79 2 1 2204 2279 391149127 391149049 5.560000e-22 115.0
37 TraesCS4A01G142900 chr7B 93.671 79 2 1 2204 2279 54044853 54044931 5.560000e-22 115.0
38 TraesCS4A01G142900 chr3D 86.207 58 5 3 1963 2019 375885774 375885829 2.640000e-05 60.2
39 TraesCS4A01G142900 chr7A 94.286 35 1 1 1969 2002 584990442 584990408 4.000000e-03 52.8
40 TraesCS4A01G142900 chr2D 94.286 35 1 1 1969 2002 304089109 304089075 4.000000e-03 52.8
41 TraesCS4A01G142900 chr2D 94.286 35 1 1 1969 2002 304193613 304193647 4.000000e-03 52.8


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 TraesCS4A01G142900 chr4A 232102348 232104806 2458 True 4542.000000 4542 100.000000 1 2459 1 chr4A.!!$R1 2458
1 TraesCS4A01G142900 chr4A 254605298 254607008 1710 False 2795.000000 2795 96.201000 755 2459 1 chr4A.!!$F1 1704
2 TraesCS4A01G142900 chr4A 612498787 612499542 755 False 1170.000000 1170 94.577000 1 756 1 chr4A.!!$F2 755
3 TraesCS4A01G142900 chr1B 318977682 318979559 1877 True 1183.500000 1644 92.184000 755 2459 2 chr1B.!!$R2 1704
4 TraesCS4A01G142900 chr1B 320735990 320737603 1613 False 1023.500000 1332 92.569000 1036 2459 2 chr1B.!!$F3 1423
5 TraesCS4A01G142900 chr1B 355090298 355090967 669 False 885.000000 885 90.504000 1 673 1 chr1B.!!$F2 672
6 TraesCS4A01G142900 chr5A 33900137 33900807 670 False 887.000000 887 90.504000 1 673 1 chr5A.!!$F1 672
7 TraesCS4A01G142900 chr5A 400066132 400067833 1701 False 605.666667 1447 89.074667 755 2203 3 chr5A.!!$F2 1448
8 TraesCS4A01G142900 chr1D 104025488 104026259 771 False 1201.000000 1201 94.974000 755 1516 1 chr1D.!!$F1 761
9 TraesCS4A01G142900 chr1D 104030859 104031984 1125 False 754.000000 776 95.307500 1511 2459 2 chr1D.!!$F2 948
10 TraesCS4A01G142900 chr1A 577181916 577182670 754 False 1134.000000 1134 93.783000 1 756 1 chr1A.!!$F1 755
11 TraesCS4A01G142900 chr1A 118767594 118768262 668 True 902.000000 902 90.950000 1 673 1 chr1A.!!$R1 672
12 TraesCS4A01G142900 chr6B 664683313 664684063 750 False 1020.000000 1020 91.138000 1 755 1 chr6B.!!$F1 754
13 TraesCS4A01G142900 chr5B 548054534 548055302 768 False 1000.000000 1000 90.323000 1 763 1 chr5B.!!$F2 762
14 TraesCS4A01G142900 chr5B 440229212 440229882 670 True 887.000000 887 90.504000 1 673 1 chr5B.!!$R1 672
15 TraesCS4A01G142900 chr3A 8126842 8127512 670 False 887.000000 887 90.504000 1 673 1 chr3A.!!$F1 672
16 TraesCS4A01G142900 chr3B 25498168 25498838 670 True 881.000000 881 90.370000 1 673 1 chr3B.!!$R1 672

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
294 296 0.184933 TTGGTGGTGAGGAACTTGGG 59.815 55.0 0.0 0.0 41.55 4.12 F
533 535 0.462789 AAACGTCTCAACCTCGGTGT 59.537 50.0 0.0 0.0 0.00 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1226 1240 1.058748 CATTACCAGCGCGTTCGTG 59.941 57.895 8.43 0.01 38.14 4.35 R
2359 2658 0.384309 TACAGCCGACGAGCTTATGG 59.616 55.000 7.92 1.27 42.61 2.74 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
18 19 1.302033 GGCCACGCATATGGGAGAG 60.302 63.158 25.04 13.69 40.43 3.20
83 84 3.188460 GGCCGTGCGAATATTATTGACAT 59.812 43.478 0.00 0.00 0.00 3.06
95 96 2.306341 ATTGACATGGCTCAGAGACG 57.694 50.000 0.00 0.00 0.00 4.18
199 201 0.762461 GGGTGCTGAGGAGATAGCCT 60.762 60.000 0.00 0.00 42.17 4.58
294 296 0.184933 TTGGTGGTGAGGAACTTGGG 59.815 55.000 0.00 0.00 41.55 4.12
410 412 1.980765 TCAGCTTCTCCATGACTTGGT 59.019 47.619 7.22 0.00 46.52 3.67
533 535 0.462789 AAACGTCTCAACCTCGGTGT 59.537 50.000 0.00 0.00 0.00 4.16
831 843 9.494271 TTGAGTCTTTTAGCATATGTGGATATC 57.506 33.333 4.29 0.00 0.00 1.63
998 1012 4.469657 TGTGGGAAGCTTTTTGTAGTCAT 58.530 39.130 0.00 0.00 0.00 3.06
1111 1125 3.617284 CAAGGTAAGTTCCCGCCTATTT 58.383 45.455 0.00 0.00 0.00 1.40
1169 1183 4.818534 TCAAGTTGTGAAGTGAAGCATC 57.181 40.909 2.11 0.00 31.51 3.91
1524 1563 7.503902 TGCTGACAGACACTATCTCAGTATATT 59.496 37.037 6.65 0.00 34.41 1.28
1625 1666 9.685828 CTTAGATTCACTGGATAAGCTACTAAC 57.314 37.037 0.00 0.00 0.00 2.34
1752 1794 5.125100 TCTTGTGGCATTGATTGACTTTC 57.875 39.130 0.00 0.00 32.91 2.62
1831 1873 4.989168 AGAAGAGCTTGTAACGTTACTTGG 59.011 41.667 32.10 23.16 34.77 3.61
1845 1887 1.223187 ACTTGGCTTACCGTTGAACG 58.777 50.000 11.30 11.30 42.11 3.95
2065 2356 7.490657 AGTAGTAATGTGGATAACCTTGTGA 57.509 36.000 0.00 0.00 37.04 3.58
2359 2658 5.946942 TCCATCTAGATCATATTGAGGCC 57.053 43.478 1.03 0.00 0.00 5.19
2422 2722 9.734620 CTCATTAGTTTCACTTCAATGTTTCAA 57.265 29.630 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 0.252284 ATCGGTCACCACCTTCCTCT 60.252 55.000 0.00 0.00 41.17 3.69
18 19 0.676782 CCAATCGGTCACCACCTTCC 60.677 60.000 0.00 0.00 41.17 3.46
83 84 3.443925 CTCGCCGTCTCTGAGCCA 61.444 66.667 0.00 0.00 0.00 4.75
95 96 0.733150 GCAGGTATGTTTTCCTCGCC 59.267 55.000 0.00 0.00 30.91 5.54
322 324 3.508840 GGCGCAGGAATGTTCGGG 61.509 66.667 10.83 0.00 0.00 5.14
328 330 2.515523 CTCAGGGGCGCAGGAATG 60.516 66.667 10.83 0.00 0.00 2.67
364 366 0.537188 CCAACTATGTCCTCTGGCGT 59.463 55.000 0.00 0.00 0.00 5.68
410 412 2.583441 CCCAGACCAACCTCAGCGA 61.583 63.158 0.00 0.00 0.00 4.93
533 535 3.321648 ATGCAGCACGTCCCCTCA 61.322 61.111 0.00 0.00 0.00 3.86
685 697 1.340399 TGAGCCGCATCAGGAATCCT 61.340 55.000 0.00 0.00 0.00 3.24
689 701 0.252761 TCATTGAGCCGCATCAGGAA 59.747 50.000 0.00 0.00 0.00 3.36
734 746 6.371809 ACATGTTAAACAACATCTTGTCGT 57.628 33.333 0.00 0.00 39.88 4.34
735 747 8.775220 TTTACATGTTAAACAACATCTTGTCG 57.225 30.769 2.30 0.00 39.88 4.35
946 959 8.157476 AGACTTAGAAGCAAAGAAAATCCACTA 58.843 33.333 0.00 0.00 0.00 2.74
998 1012 2.749706 TTTGCCCCGTGTCGCCATTA 62.750 55.000 0.00 0.00 0.00 1.90
1034 1048 2.254737 ATCAGCAGGCTCTCCAGTGC 62.255 60.000 0.00 0.00 34.68 4.40
1169 1183 5.983720 CCAACCAGAGTTCTACATATTACCG 59.016 44.000 0.00 0.00 32.45 4.02
1226 1240 1.058748 CATTACCAGCGCGTTCGTG 59.941 57.895 8.43 0.01 38.14 4.35
1405 1443 9.255304 GTTCTGCAATTTTAAAGTTGTGGAATA 57.745 29.630 20.48 6.67 0.00 1.75
1529 1568 8.044908 ACCAACAACGACACCTATTAGATAAAT 58.955 33.333 0.00 0.00 0.00 1.40
1673 1715 8.529476 GGGAACTTCTTAACAAGTATGAGACTA 58.471 37.037 0.00 0.00 37.44 2.59
1688 1730 5.740290 ATCTGAAACTCGGGAACTTCTTA 57.260 39.130 0.00 0.00 0.00 2.10
1740 1782 4.452825 TGGTTGTACCGAAAGTCAATCAA 58.547 39.130 0.00 0.00 42.58 2.57
1746 1788 6.529477 GTCTAACTATGGTTGTACCGAAAGTC 59.471 42.308 4.47 0.00 42.58 3.01
1752 1794 6.334989 TCATTGTCTAACTATGGTTGTACCG 58.665 40.000 4.47 0.00 42.58 4.02
1831 1873 2.742954 ACAAACGTTCAACGGTAAGC 57.257 45.000 15.74 0.00 42.91 3.09
1946 2055 6.426587 ACTTTGTATGCATACCCATTCTTCT 58.573 36.000 29.36 4.22 32.33 2.85
1996 2280 2.833631 ACAAGAACGGACCGAGAAAT 57.166 45.000 23.38 0.42 0.00 2.17
2065 2356 8.423349 TGACAATTTGAAAGGTGAAAAGATCAT 58.577 29.630 2.79 0.00 40.97 2.45
2359 2658 0.384309 TACAGCCGACGAGCTTATGG 59.616 55.000 7.92 1.27 42.61 2.74
2419 2719 7.610865 ACTTCACAACAAGGAAGAAAAATTGA 58.389 30.769 8.25 0.00 42.39 2.57
2422 2722 6.265577 CGACTTCACAACAAGGAAGAAAAAT 58.734 36.000 8.25 0.00 42.39 1.82


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

AutoCloner maintained by Alex Coulton.