Multiple sequence alignment - TraesCS1A01G091900

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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 TraesCS1A01G091900 chr1A 100.000 2537 0 0 1 2537 84483185 84485721 0.000000e+00 4686.0
1 TraesCS1A01G091900 chr1A 98.375 1785 10 3 757 2537 84621153 84622922 0.000000e+00 3118.0
2 TraesCS1A01G091900 chr1A 94.681 846 25 6 21 848 84055299 84056142 0.000000e+00 1295.0
3 TraesCS1A01G091900 chr1A 97.450 745 17 2 1 744 84620426 84621169 0.000000e+00 1269.0
4 TraesCS1A01G091900 chr1A 95.098 714 35 0 861 1574 84796399 84795686 0.000000e+00 1125.0
5 TraesCS1A01G091900 chr1A 94.958 714 36 0 861 1574 85006283 85005570 0.000000e+00 1120.0
6 TraesCS1A01G091900 chr1A 88.636 220 15 5 1941 2160 84795492 84795283 2.500000e-65 259.0
7 TraesCS1A01G091900 chr1A 93.233 133 7 1 668 798 84616129 84616261 7.160000e-46 195.0
8 TraesCS1A01G091900 chr1A 82.474 97 10 6 757 849 84796891 84796798 7.520000e-11 78.7
9 TraesCS1A01G091900 chr1A 93.750 48 2 1 2342 2388 84795174 84795127 1.260000e-08 71.3
10 TraesCS1A01G091900 chr1A 92.683 41 3 0 808 848 85006719 85006679 2.730000e-05 60.2
11 TraesCS1A01G091900 chr3B 93.118 1148 61 8 861 2008 535705308 535704179 0.000000e+00 1666.0
12 TraesCS1A01G091900 chr3B 86.222 675 49 24 1503 2160 535555786 535555139 0.000000e+00 691.0
13 TraesCS1A01G091900 chr3B 79.950 404 53 21 285 664 535709190 535708791 3.220000e-69 272.0
14 TraesCS1A01G091900 chr1D 91.885 1220 52 18 861 2066 87903957 87905143 0.000000e+00 1661.0
15 TraesCS1A01G091900 chr1D 89.286 1232 70 21 1241 2455 88215120 88216306 0.000000e+00 1487.0
16 TraesCS1A01G091900 chr1D 91.432 887 55 7 861 1731 88282287 88281406 0.000000e+00 1197.0
17 TraesCS1A01G091900 chr1D 89.782 597 41 11 1141 1723 88243854 88243264 0.000000e+00 747.0
18 TraesCS1A01G091900 chr1D 84.615 481 29 15 1638 2103 87909280 87909730 1.080000e-118 436.0
19 TraesCS1A01G091900 chr1D 81.156 398 54 16 285 663 88184339 88184734 1.480000e-77 300.0
20 TraesCS1A01G091900 chr1D 90.278 216 21 0 1941 2156 88243199 88242984 1.490000e-72 283.0
21 TraesCS1A01G091900 chr1D 81.283 187 16 7 576 744 88244693 88244508 1.580000e-27 134.0
22 TraesCS1A01G091900 chr1D 89.320 103 11 0 2106 2208 87905144 87905246 2.050000e-26 130.0
23 TraesCS1A01G091900 chr1D 95.588 68 1 2 2471 2537 88216395 88216461 9.600000e-20 108.0
24 TraesCS1A01G091900 chr1D 86.667 105 1 5 757 848 87903435 87903539 1.240000e-18 104.0
25 TraesCS1A01G091900 chr1D 84.762 105 2 4 757 847 88208099 88208203 2.690000e-15 93.5
26 TraesCS1A01G091900 chr1D 84.112 107 1 8 757 849 88244524 88244420 3.480000e-14 89.8
27 TraesCS1A01G091900 chr1D 84.112 107 1 8 757 849 88282792 88282688 3.480000e-14 89.8
28 TraesCS1A01G091900 chr1D 93.750 48 2 1 2342 2388 88242873 88242826 1.260000e-08 71.3
29 TraesCS1A01G091900 chr1B 90.580 1104 75 12 861 1950 142037792 142038880 0.000000e+00 1435.0
30 TraesCS1A01G091900 chr1B 93.578 763 49 0 861 1623 142094052 142094814 0.000000e+00 1138.0
31 TraesCS1A01G091900 chr1B 94.545 715 39 0 861 1575 141845283 141845997 0.000000e+00 1105.0
32 TraesCS1A01G091900 chr1B 89.474 893 50 19 861 1731 142134211 142133341 0.000000e+00 1088.0
33 TraesCS1A01G091900 chr1B 85.919 838 66 23 1629 2455 142102573 142103369 0.000000e+00 846.0
34 TraesCS1A01G091900 chr1B 89.020 255 25 1 1946 2200 141846199 141846450 1.890000e-81 313.0
35 TraesCS1A01G091900 chr1B 81.454 399 49 22 285 664 141844223 141844615 1.140000e-78 303.0
36 TraesCS1A01G091900 chr1B 81.644 365 51 14 285 636 142025884 142026245 3.190000e-74 289.0
37 TraesCS1A01G091900 chr1B 80.874 366 53 15 285 636 142092991 142093353 3.220000e-69 272.0
38 TraesCS1A01G091900 chr1B 93.506 77 5 0 668 744 142026370 142026446 5.740000e-22 115.0
39 TraesCS1A01G091900 chr1B 93.506 77 5 0 668 744 142134777 142134701 5.740000e-22 115.0
40 TraesCS1A01G091900 chr1B 86.408 103 14 0 2106 2208 142038969 142039071 2.060000e-21 113.0
41 TraesCS1A01G091900 chr1B 93.421 76 3 1 669 744 141844709 141844782 7.420000e-21 111.0
42 TraesCS1A01G091900 chr1B 93.506 77 1 2 668 744 142037219 142037291 7.420000e-21 111.0
43 TraesCS1A01G091900 chr1B 93.506 77 1 2 668 744 142093479 142093551 7.420000e-21 111.0
44 TraesCS1A01G091900 chr1B 83.178 107 2 9 757 849 142134717 142134613 1.620000e-12 84.2
45 TraesCS1A01G091900 chr1B 93.750 48 2 1 2342 2388 142132949 142132902 1.260000e-08 71.3
46 TraesCS1A01G091900 chr4D 91.695 879 53 10 866 1731 464797687 464796816 0.000000e+00 1201.0
47 TraesCS1A01G091900 chr4D 86.120 317 37 7 301 611 464798668 464798353 4.040000e-88 335.0
48 TraesCS1A01G091900 chr5A 81.776 214 33 6 401 609 19221882 19222094 9.330000e-40 174.0


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 TraesCS1A01G091900 chr1A 84483185 84485721 2536 False 4686.000000 4686 100.000000 1 2537 1 chr1A.!!$F2 2536
1 TraesCS1A01G091900 chr1A 84620426 84622922 2496 False 2193.500000 3118 97.912500 1 2537 2 chr1A.!!$F4 2536
2 TraesCS1A01G091900 chr1A 84055299 84056142 843 False 1295.000000 1295 94.681000 21 848 1 chr1A.!!$F1 827
3 TraesCS1A01G091900 chr1A 85005570 85006719 1149 True 590.100000 1120 93.820500 808 1574 2 chr1A.!!$R2 766
4 TraesCS1A01G091900 chr1A 84795127 84796891 1764 True 383.500000 1125 89.989500 757 2388 4 chr1A.!!$R1 1631
5 TraesCS1A01G091900 chr3B 535704179 535709190 5011 True 969.000000 1666 86.534000 285 2008 2 chr3B.!!$R2 1723
6 TraesCS1A01G091900 chr3B 535555139 535555786 647 True 691.000000 691 86.222000 1503 2160 1 chr3B.!!$R1 657
7 TraesCS1A01G091900 chr1D 88215120 88216461 1341 False 797.500000 1487 92.437000 1241 2537 2 chr1D.!!$F5 1296
8 TraesCS1A01G091900 chr1D 88281406 88282792 1386 True 643.400000 1197 87.772000 757 1731 2 chr1D.!!$R2 974
9 TraesCS1A01G091900 chr1D 87903435 87905246 1811 False 631.666667 1661 89.290667 757 2208 3 chr1D.!!$F4 1451
10 TraesCS1A01G091900 chr1D 88242826 88244693 1867 True 265.020000 747 87.841000 576 2388 5 chr1D.!!$R1 1812
11 TraesCS1A01G091900 chr1B 142102573 142103369 796 False 846.000000 846 85.919000 1629 2455 1 chr1B.!!$F1 826
12 TraesCS1A01G091900 chr1B 142037219 142039071 1852 False 553.000000 1435 90.164667 668 2208 3 chr1B.!!$F4 1540
13 TraesCS1A01G091900 chr1B 142092991 142094814 1823 False 507.000000 1138 89.319333 285 1623 3 chr1B.!!$F5 1338
14 TraesCS1A01G091900 chr1B 141844223 141846450 2227 False 458.000000 1105 89.610000 285 2200 4 chr1B.!!$F2 1915
15 TraesCS1A01G091900 chr1B 142132902 142134777 1875 True 339.625000 1088 89.977000 668 2388 4 chr1B.!!$R1 1720
16 TraesCS1A01G091900 chr1B 142025884 142026446 562 False 202.000000 289 87.575000 285 744 2 chr1B.!!$F3 459
17 TraesCS1A01G091900 chr4D 464796816 464798668 1852 True 768.000000 1201 88.907500 301 1731 2 chr4D.!!$R1 1430

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
126 127 3.316071 TTGCAACACATGGCCTATTTG 57.684 42.857 3.32 2.01 0.0 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2026 5690 8.602424 TCTTCCTTGGACTTCACATCTATTTAA 58.398 33.333 0.0 0.0 0.0 1.52 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
93 94 7.639113 AACAATGTGGTTTTTCAGTAAGAGA 57.361 32.000 0.00 0.00 0.00 3.10
126 127 3.316071 TTGCAACACATGGCCTATTTG 57.684 42.857 3.32 2.01 0.00 2.32
197 199 6.385759 TGAATGCAAGGGTACTATTTCTCCTA 59.614 38.462 0.00 0.00 0.00 2.94
749 918 3.452466 CGTCACCCGCGTAAATTTAAA 57.548 42.857 4.92 0.00 0.00 1.52
750 919 3.808095 CGTCACCCGCGTAAATTTAAAA 58.192 40.909 4.92 0.00 0.00 1.52
751 920 4.217497 CGTCACCCGCGTAAATTTAAAAA 58.783 39.130 4.92 0.00 0.00 1.94
854 1084 3.690460 ACAGCCTCGATCCTCAAAATTT 58.310 40.909 0.00 0.00 0.00 1.82
856 1086 5.253330 ACAGCCTCGATCCTCAAAATTTTA 58.747 37.500 2.44 0.00 0.00 1.52
857 1087 5.888161 ACAGCCTCGATCCTCAAAATTTTAT 59.112 36.000 2.44 0.00 0.00 1.40
859 1089 7.556275 ACAGCCTCGATCCTCAAAATTTTATAA 59.444 33.333 2.44 0.00 0.00 0.98
1770 5289 0.175760 TCCTGATGGCGTGCTAGAAC 59.824 55.000 0.00 0.00 0.00 3.01
1900 5455 5.809001 TGATAAGCTTCTGAATCTGGTTGT 58.191 37.500 0.00 0.00 0.00 3.32
2026 5690 7.443272 TGAGAAAATCGATGTTGATGCATAGAT 59.557 33.333 5.31 0.00 40.97 1.98
2357 6041 1.332195 CTCCGGTCTCATCATGGCTA 58.668 55.000 0.00 0.00 0.00 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 6.238759 GCACTCTCTTACTGAAAAACCACATT 60.239 38.462 0.00 0.00 0.00 2.71
93 94 3.866379 TTGCAATGGGAGCCGCACT 62.866 57.895 0.00 0.00 33.29 4.40
126 127 1.066002 CCATCATCAATTGCCACGACC 59.934 52.381 0.00 0.00 0.00 4.79
640 683 5.540400 TCTCTCTCTTTTTGGTTCCGTTA 57.460 39.130 0.00 0.00 0.00 3.18
854 1084 8.933807 AGATCTCGATAATCGACTCGTTTATAA 58.066 33.333 12.61 6.00 44.82 0.98
856 1086 7.367159 AGATCTCGATAATCGACTCGTTTAT 57.633 36.000 12.52 12.52 44.82 1.40
857 1087 6.782298 AGATCTCGATAATCGACTCGTTTA 57.218 37.500 12.00 4.79 44.82 2.01
859 1089 5.444983 CAAGATCTCGATAATCGACTCGTT 58.555 41.667 12.00 0.00 44.82 3.85
2026 5690 8.602424 TCTTCCTTGGACTTCACATCTATTTAA 58.398 33.333 0.00 0.00 0.00 1.52
2357 6041 4.248058 GCATTGCAATGGAAGTAAAGCTT 58.752 39.130 34.23 0.00 37.21 3.74


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

AutoCloner maintained by Alex Coulton.