Multiple sequence alignment - TraesCS6A01G317100

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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 TraesCS6A01G317100 chr6A 100.000 2534 0 0 1 2534 553434727 553432194 0.000000e+00 4680.0
1 TraesCS6A01G317100 chr6A 96.692 2539 72 8 1 2534 553396473 553393942 0.000000e+00 4213.0
2 TraesCS6A01G317100 chr6A 94.532 2542 83 28 1 2534 553461679 553459186 0.000000e+00 3873.0
3 TraesCS6A01G317100 chr6A 92.518 2192 143 17 355 2534 553559526 553557344 0.000000e+00 3120.0
4 TraesCS6A01G317100 chr6A 96.355 1701 57 3 63 1760 568279977 568278279 0.000000e+00 2793.0
5 TraesCS6A01G317100 chr6A 91.145 1423 113 11 355 1771 568271422 568270007 0.000000e+00 1917.0
6 TraesCS6A01G317100 chr6A 90.864 1423 117 11 355 1771 553388091 553386676 0.000000e+00 1895.0
7 TraesCS6A01G317100 chr6A 90.801 1424 116 13 355 1771 553426318 553424903 0.000000e+00 1890.0
8 TraesCS6A01G317100 chr6A 90.246 1425 123 13 355 1771 553453332 553451916 0.000000e+00 1847.0
9 TraesCS6A01G317100 chr6A 91.572 1317 99 10 355 1667 568294984 568293676 0.000000e+00 1807.0
10 TraesCS6A01G317100 chr6A 95.077 711 19 4 1826 2534 568277983 568277287 0.000000e+00 1105.0
11 TraesCS6A01G317100 chr6A 97.218 647 18 0 1 647 553525634 553524988 0.000000e+00 1096.0
12 TraesCS6A01G317100 chr6A 95.659 668 25 3 1869 2534 568307718 568307053 0.000000e+00 1070.0
13 TraesCS6A01G317100 chr6A 94.502 582 29 3 1955 2534 553473626 553473046 0.000000e+00 894.0
14 TraesCS6A01G317100 chr6A 96.970 66 1 1 1 65 568291859 568291794 2.670000e-20 110.0
15 TraesCS6A01G317100 chr6B 93.664 584 33 4 34 614 639145370 639144788 0.000000e+00 870.0
16 TraesCS6A01G317100 chr2D 86.467 569 58 14 1977 2533 390062869 390063430 7.750000e-170 606.0
17 TraesCS6A01G317100 chr2D 85.996 557 62 10 1987 2533 280921748 280922298 1.310000e-162 582.0
18 TraesCS6A01G317100 chr3D 86.219 566 63 12 1977 2533 373796277 373795718 1.300000e-167 599.0
19 TraesCS6A01G317100 chr1A 96.970 33 1 0 1738 1770 138710344 138710376 3.520000e-04 56.5


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 TraesCS6A01G317100 chr6A 553432194 553434727 2533 True 4680.0 4680 100.000 1 2534 1 chr6A.!!$R4 2533
1 TraesCS6A01G317100 chr6A 553393942 553396473 2531 True 4213.0 4213 96.692 1 2534 1 chr6A.!!$R2 2533
2 TraesCS6A01G317100 chr6A 553459186 553461679 2493 True 3873.0 3873 94.532 1 2534 1 chr6A.!!$R6 2533
3 TraesCS6A01G317100 chr6A 553557344 553559526 2182 True 3120.0 3120 92.518 355 2534 1 chr6A.!!$R9 2179
4 TraesCS6A01G317100 chr6A 568277287 568279977 2690 True 1949.0 2793 95.716 63 2534 2 chr6A.!!$R12 2471
5 TraesCS6A01G317100 chr6A 568270007 568271422 1415 True 1917.0 1917 91.145 355 1771 1 chr6A.!!$R10 1416
6 TraesCS6A01G317100 chr6A 553386676 553388091 1415 True 1895.0 1895 90.864 355 1771 1 chr6A.!!$R1 1416
7 TraesCS6A01G317100 chr6A 553424903 553426318 1415 True 1890.0 1890 90.801 355 1771 1 chr6A.!!$R3 1416
8 TraesCS6A01G317100 chr6A 553451916 553453332 1416 True 1847.0 1847 90.246 355 1771 1 chr6A.!!$R5 1416
9 TraesCS6A01G317100 chr6A 553524988 553525634 646 True 1096.0 1096 97.218 1 647 1 chr6A.!!$R8 646
10 TraesCS6A01G317100 chr6A 568307053 568307718 665 True 1070.0 1070 95.659 1869 2534 1 chr6A.!!$R11 665
11 TraesCS6A01G317100 chr6A 568291794 568294984 3190 True 958.5 1807 94.271 1 1667 2 chr6A.!!$R13 1666
12 TraesCS6A01G317100 chr6A 553473046 553473626 580 True 894.0 894 94.502 1955 2534 1 chr6A.!!$R7 579
13 TraesCS6A01G317100 chr6B 639144788 639145370 582 True 870.0 870 93.664 34 614 1 chr6B.!!$R1 580
14 TraesCS6A01G317100 chr2D 390062869 390063430 561 False 606.0 606 86.467 1977 2533 1 chr2D.!!$F2 556
15 TraesCS6A01G317100 chr2D 280921748 280922298 550 False 582.0 582 85.996 1987 2533 1 chr2D.!!$F1 546
16 TraesCS6A01G317100 chr3D 373795718 373796277 559 True 599.0 599 86.219 1977 2533 1 chr3D.!!$R1 556

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
794 804 4.002267 ACGACATCATTAACACAATGCG 57.998 40.909 0.0 0.0 0.0 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1776 1824 1.564818 AGTGAGATCGTGGGAGGAGTA 59.435 52.381 0.0 0.0 0.0 2.59 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
95 96 7.757526 TCATTAAGTGTTTTGTATTGATCGGG 58.242 34.615 0.00 0.00 0.00 5.14
313 314 5.948742 TCCATCATAGTGTGGACATTACA 57.051 39.130 0.00 0.00 39.51 2.41
672 679 6.263842 TCGTGAGGACAACTCTACTTTTTCTA 59.736 38.462 0.00 0.00 46.72 2.10
721 731 8.210946 TGTAAATCAGAACTACCATGGGATAAG 58.789 37.037 18.09 10.17 0.00 1.73
774 784 7.986085 ACCAAGCATGTATTAATGAGGATAC 57.014 36.000 0.00 0.00 0.00 2.24
776 786 6.873605 CCAAGCATGTATTAATGAGGATACGA 59.126 38.462 0.00 0.00 46.39 3.43
779 789 7.615403 AGCATGTATTAATGAGGATACGACAT 58.385 34.615 0.00 0.00 46.39 3.06
794 804 4.002267 ACGACATCATTAACACAATGCG 57.998 40.909 0.00 0.00 0.00 4.73
979 989 5.758296 TGCTAGCTTTCCCTCAATATAAACG 59.242 40.000 17.23 0.00 0.00 3.60
1034 1044 6.292061 GCAAAATCAACGAACAACATTAGCAA 60.292 34.615 0.00 0.00 0.00 3.91
1279 1291 7.823799 TCTCTATTGTGATTTGTGCACAGATAA 59.176 33.333 21.68 12.92 45.85 1.75
1400 1412 0.403271 AGAGCAGTTGCATGGAAGGT 59.597 50.000 0.00 0.00 45.16 3.50
1432 1444 2.248280 TGTTGCTGCCGAAAGAACTA 57.752 45.000 0.00 0.00 0.00 2.24
1595 1607 4.782019 TTTCCATTGCATCGCTAAAGTT 57.218 36.364 0.00 0.00 0.00 2.66
1776 1824 0.178873 TCTAACAAGACCCCAGGCCT 60.179 55.000 0.00 0.00 0.00 5.19
1867 2145 4.060667 CCGCACCCCAAATCCCCT 62.061 66.667 0.00 0.00 0.00 4.79
1872 2150 1.231018 CACCCCAAATCCCCTCCATA 58.769 55.000 0.00 0.00 0.00 2.74
1942 2220 0.321653 GTCACCGAAGCCACCAGATT 60.322 55.000 0.00 0.00 0.00 2.40
1953 2231 2.066999 ACCAGATTCGGCCCCTCTC 61.067 63.158 0.00 0.00 0.00 3.20
2364 3030 7.323656 GTGTTTGACTAATGGAAACTGAAATCG 59.676 37.037 0.00 0.00 32.01 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 96 9.647797 ACGGGATAGAAATTTTTGGTATTTTTC 57.352 29.630 0.00 0.0 0.00 2.29
313 314 1.289160 TGACAAGGCCTAATGGAGCT 58.711 50.000 5.16 0.0 34.57 4.09
600 606 3.573538 TGCATGAAACTAAGTGTTGCCAT 59.426 39.130 0.00 0.0 39.13 4.40
672 679 1.212935 GCCCTCACCCACACTCATTAT 59.787 52.381 0.00 0.0 0.00 1.28
721 731 8.671384 TGAGCCTATTATACATGTGGTTTAAC 57.329 34.615 9.11 0.0 0.00 2.01
774 784 3.063316 TCCGCATTGTGTTAATGATGTCG 59.937 43.478 3.97 0.0 0.00 4.35
776 786 6.238731 CCTTATCCGCATTGTGTTAATGATGT 60.239 38.462 3.97 0.0 0.00 3.06
779 789 5.432645 TCCTTATCCGCATTGTGTTAATGA 58.567 37.500 3.97 0.0 0.00 2.57
942 952 3.030873 AGCTAGCAGTCTTGGATCTCT 57.969 47.619 18.83 0.0 0.00 3.10
943 953 3.817709 AAGCTAGCAGTCTTGGATCTC 57.182 47.619 18.83 0.0 0.00 2.75
979 989 1.068264 GTTCTTTGCCTAGGTGCTTGC 60.068 52.381 11.31 0.0 0.00 4.01
1034 1044 8.102484 TGGGAGATAGTTAGCTATTCCTTTTT 57.898 34.615 18.29 0.0 37.99 1.94
1116 1126 2.037772 GACATGAGAAGACAGTGGTGGT 59.962 50.000 0.00 0.0 0.00 4.16
1279 1291 2.703536 TCCACAGTTGTACACAGGTCAT 59.296 45.455 0.00 0.0 0.00 3.06
1776 1824 1.564818 AGTGAGATCGTGGGAGGAGTA 59.435 52.381 0.00 0.0 0.00 2.59
1867 2145 4.160439 ACTGCGAGAGACAAAGAATATGGA 59.840 41.667 0.00 0.0 0.00 3.41
1872 2150 2.300152 TGGACTGCGAGAGACAAAGAAT 59.700 45.455 0.00 0.0 0.00 2.40
2392 3058 5.185828 ACCTTTCCTTAGAACAATTCATGCC 59.814 40.000 0.00 0.0 0.00 4.40


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

AutoCloner maintained by Alex Coulton.