Multiple sequence alignment - TraesCS1A01G074500

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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 TraesCS1A01G074500 chr1A 100.000 2951 0 0 1 2951 58021910 58024860 0.000000e+00 5450.0
1 TraesCS1A01G074500 chr1A 98.855 2445 27 1 1 2445 58026930 58024487 0.000000e+00 4359.0
2 TraesCS1A01G074500 chr1A 94.055 1026 34 10 1551 2574 487468228 487469228 0.000000e+00 1531.0
3 TraesCS1A01G074500 chr1A 98.667 375 4 1 2578 2951 58024354 58023980 0.000000e+00 664.0
4 TraesCS1A01G074500 chr1A 92.982 342 12 5 2611 2951 487469079 487468749 3.420000e-134 488.0
5 TraesCS1A01G074500 chr1A 97.059 34 0 1 653 685 487467998 487468031 4.110000e-04 56.5
6 TraesCS1A01G074500 chr3B 98.912 2574 28 0 1 2574 607815406 607817979 0.000000e+00 4599.0
7 TraesCS1A01G074500 chr3B 95.650 2575 92 8 1 2574 821050175 821052730 0.000000e+00 4117.0
8 TraesCS1A01G074500 chr3B 98.667 375 4 1 2578 2951 607817850 607817476 0.000000e+00 664.0
9 TraesCS1A01G074500 chr3B 92.021 376 17 6 2578 2951 821052601 821052237 1.570000e-142 516.0
10 TraesCS1A01G074500 chr7A 98.718 2574 31 1 1 2574 706441235 706443806 0.000000e+00 4569.0
11 TraesCS1A01G074500 chr7A 98.524 2574 38 0 1 2574 694028332 694030905 0.000000e+00 4543.0
12 TraesCS1A01G074500 chr7A 98.667 375 4 1 2578 2951 694030776 694030402 0.000000e+00 664.0
13 TraesCS1A01G074500 chr7A 97.884 378 7 1 2575 2951 706443680 706443303 0.000000e+00 652.0
14 TraesCS1A01G074500 chr7B 98.252 2574 41 1 1 2574 581347458 581344889 0.000000e+00 4501.0
15 TraesCS1A01G074500 chr7B 95.579 2149 82 6 427 2574 297120954 297118818 0.000000e+00 3430.0
16 TraesCS1A01G074500 chr7B 96.970 429 12 1 1 429 297141651 297141224 0.000000e+00 719.0
17 TraesCS1A01G074500 chr7B 97.619 378 8 1 2575 2951 581345015 581345392 0.000000e+00 647.0
18 TraesCS1A01G074500 chr7B 91.557 379 18 5 2575 2951 297118944 297119310 7.300000e-141 510.0
19 TraesCS1A01G074500 chr1B 93.330 2039 121 5 1 2032 499020604 499018574 0.000000e+00 2998.0
20 TraesCS1A01G074500 chr6B 85.474 1900 204 38 696 2573 654600210 654602059 0.000000e+00 1914.0
21 TraesCS1A01G074500 chrUn 93.713 1193 44 8 1361 2547 94940007 94938840 0.000000e+00 1759.0
22 TraesCS1A01G074500 chrUn 92.105 342 14 6 2611 2951 94938963 94939292 1.240000e-128 470.0
23 TraesCS1A01G074500 chr5B 94.639 1026 28 10 1551 2574 491653972 491652972 0.000000e+00 1565.0
24 TraesCS1A01G074500 chr5B 92.982 342 12 5 2611 2951 491653121 491653451 3.420000e-134 488.0
25 TraesCS1A01G074500 chr4D 89.864 1026 90 9 698 1720 506088862 506087848 0.000000e+00 1306.0
26 TraesCS1A01G074500 chr4D 91.468 586 40 3 54 630 506089458 506088874 0.000000e+00 797.0
27 TraesCS1A01G074500 chr4D 93.333 255 10 1 2320 2574 366217973 366218220 1.290000e-98 370.0
28 TraesCS1A01G074500 chr4D 87.302 126 8 2 2578 2702 366218091 366217973 1.430000e-28 137.0


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 TraesCS1A01G074500 chr1A 58021910 58024860 2950 False 5450.00 5450 100.000 1 2951 1 chr1A.!!$F1 2950
1 TraesCS1A01G074500 chr1A 58023980 58026930 2950 True 2511.50 4359 98.761 1 2951 2 chr1A.!!$R2 2950
2 TraesCS1A01G074500 chr1A 487467998 487469228 1230 False 793.75 1531 95.557 653 2574 2 chr1A.!!$F2 1921
3 TraesCS1A01G074500 chr3B 607815406 607817979 2573 False 4599.00 4599 98.912 1 2574 1 chr3B.!!$F1 2573
4 TraesCS1A01G074500 chr3B 821050175 821052730 2555 False 4117.00 4117 95.650 1 2574 1 chr3B.!!$F2 2573
5 TraesCS1A01G074500 chr7A 706441235 706443806 2571 False 4569.00 4569 98.718 1 2574 1 chr7A.!!$F2 2573
6 TraesCS1A01G074500 chr7A 694028332 694030905 2573 False 4543.00 4543 98.524 1 2574 1 chr7A.!!$F1 2573
7 TraesCS1A01G074500 chr7B 581344889 581347458 2569 True 4501.00 4501 98.252 1 2574 1 chr7B.!!$R3 2573
8 TraesCS1A01G074500 chr7B 297118818 297120954 2136 True 3430.00 3430 95.579 427 2574 1 chr7B.!!$R1 2147
9 TraesCS1A01G074500 chr1B 499018574 499020604 2030 True 2998.00 2998 93.330 1 2032 1 chr1B.!!$R1 2031
10 TraesCS1A01G074500 chr6B 654600210 654602059 1849 False 1914.00 1914 85.474 696 2573 1 chr6B.!!$F1 1877
11 TraesCS1A01G074500 chrUn 94938840 94940007 1167 True 1759.00 1759 93.713 1361 2547 1 chrUn.!!$R1 1186
12 TraesCS1A01G074500 chr5B 491652972 491653972 1000 True 1565.00 1565 94.639 1551 2574 1 chr5B.!!$R1 1023
13 TraesCS1A01G074500 chr4D 506087848 506089458 1610 True 1051.50 1306 90.666 54 1720 2 chr4D.!!$R2 1666

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
650 660 2.134789 AGGCTGATGTTGATGGGTTC 57.865 50.000 0.0 0.0 0.0 3.62 F
956 973 3.195825 CGTGAGAGGACTATTTTCTGGGT 59.804 47.826 0.0 0.0 0.0 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1585 1632 0.108992 TTACCAACTCGGCTAGTGCG 60.109 55.0 0.00 0.0 38.88 5.34 R
2898 3092 2.143876 ACTTGGCCAGAACTTGTGTT 57.856 45.0 5.11 0.0 39.42 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
650 660 2.134789 AGGCTGATGTTGATGGGTTC 57.865 50.000 0.00 0.0 0.00 3.62
956 973 3.195825 CGTGAGAGGACTATTTTCTGGGT 59.804 47.826 0.00 0.0 0.00 4.51
994 1011 6.112927 AGTTTATGTTGGATTGGTGCATTT 57.887 33.333 0.00 0.0 0.00 2.32
1371 1391 5.782893 AGTTCTACTATGAGATGCAGGAC 57.217 43.478 0.00 0.0 0.00 3.85
1666 1714 5.047847 CACTAAGAACCAAGAGTCGTTTCA 58.952 41.667 0.00 0.0 0.00 2.69
1783 1831 5.755409 TGCTAGTTTATGGAAGAGGTTGA 57.245 39.130 0.00 0.0 0.00 3.18
1788 1836 5.561679 AGTTTATGGAAGAGGTTGAAGGAC 58.438 41.667 0.00 0.0 0.00 3.85
2005 2058 4.020543 AGTTGGCAACCTGTGAAGTTTAA 58.979 39.130 25.81 0.0 0.00 1.52
2122 2207 1.680338 ACTTGGCCAGAACTTGTGTC 58.320 50.000 5.11 0.0 0.00 3.67
2446 2537 5.292101 CCAAACGCAAACCATAACTTTTTGA 59.708 36.000 0.00 0.0 32.91 2.69
2619 2813 0.106918 TTTCTGCCACGGTTTCCTGT 60.107 50.000 0.00 0.0 0.00 4.00
2827 3021 9.761504 TTCAAAATGCAAACTCATAATCAAGAA 57.238 25.926 0.00 0.0 0.00 2.52
2898 3092 9.481340 GTCAAGTGATAGTCATTCATAGCAATA 57.519 33.333 0.00 0.0 0.00 1.90
2932 3126 6.016610 TCTGGCCAAGTTACATTAAAGTGTTC 60.017 38.462 7.01 0.0 33.62 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
650 660 7.219484 ACAGACTGAATGGAACCTAAAATTG 57.781 36.000 10.08 0.00 0.00 2.32
819 836 5.412286 GGCAAATAAGCATGAAACAACCAAT 59.588 36.000 0.00 0.00 35.83 3.16
950 967 2.550175 TGGTCTGATCATCAACCCAGA 58.450 47.619 15.63 0.00 31.20 3.86
956 973 7.094248 CCAACATAAACTTGGTCTGATCATCAA 60.094 37.037 0.00 1.16 34.50 2.57
994 1011 6.429692 CCCGCATATTGTTCCTTCATGTATTA 59.570 38.462 0.00 0.00 0.00 0.98
1585 1632 0.108992 TTACCAACTCGGCTAGTGCG 60.109 55.000 0.00 0.00 38.88 5.34
1666 1714 2.237143 TGATTTCTTCAGCGGACTCCAT 59.763 45.455 0.00 0.00 0.00 3.41
1783 1831 2.308866 CTGTGGTAATTGGGAGGTCCTT 59.691 50.000 0.00 0.00 36.20 3.36
1788 1836 3.931907 TGATCTGTGGTAATTGGGAGG 57.068 47.619 0.00 0.00 0.00 4.30
2005 2058 7.234577 TCCTAAATACCAAAAGTTGCCATCTTT 59.765 33.333 0.00 0.00 36.81 2.52
2122 2207 8.281194 GTCAAGTGATAGTCATTCATAGCAATG 58.719 37.037 0.00 0.00 35.39 2.82
2619 2813 3.695830 GGTGATTCTAACCACCTGTGA 57.304 47.619 0.00 0.00 46.94 3.58
2827 3021 9.601217 ACTTGCACGTATCTATCTTATTTTCTT 57.399 29.630 0.00 0.00 0.00 2.52
2898 3092 2.143876 ACTTGGCCAGAACTTGTGTT 57.856 45.000 5.11 0.00 39.42 3.32


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

AutoCloner maintained by Alex Coulton.