Multiple sequence alignment - TraesCS2D01G560300

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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 TraesCS2D01G560300 chr2D 100.000 2677 0 0 1 2677 633238369 633235693 0.000000e+00 4944.0
1 TraesCS2D01G560300 chr2D 97.651 2682 58 4 1 2677 633260205 633257524 0.000000e+00 4599.0
2 TraesCS2D01G560300 chr2D 97.551 2450 54 4 233 2677 633287327 633284879 0.000000e+00 4187.0
3 TraesCS2D01G560300 chr2D 91.393 1034 45 19 855 1860 633297549 633298566 0.000000e+00 1376.0
4 TraesCS2D01G560300 chr2D 82.731 249 14 13 2455 2677 633295422 633295667 7.560000e-46 195.0
5 TraesCS2D01G560300 chr2D 82.379 227 27 7 9 229 523159371 523159152 4.550000e-43 185.0
6 TraesCS2D01G560300 chr6D 89.347 995 48 16 897 1860 20475331 20474364 0.000000e+00 1197.0
7 TraesCS2D01G560300 chr6D 82.590 942 77 26 898 1788 18984429 18985334 0.000000e+00 750.0
8 TraesCS2D01G560300 chr6D 80.606 660 75 20 1948 2566 414791821 414791174 6.750000e-126 460.0
9 TraesCS2D01G560300 chr5B 86.171 969 63 34 929 1854 647879603 647878663 0.000000e+00 981.0
10 TraesCS2D01G560300 chr5B 83.929 616 66 19 7 618 65090920 65091506 2.330000e-155 558.0
11 TraesCS2D01G560300 chr4A 94.518 529 29 0 1066 1594 639977521 639978049 0.000000e+00 817.0
12 TraesCS2D01G560300 chr2B 89.024 574 35 9 1307 1860 776645527 776644962 0.000000e+00 686.0
13 TraesCS2D01G560300 chr2B 85.714 469 39 19 858 1316 776645998 776645548 1.120000e-128 470.0
14 TraesCS2D01G560300 chr2B 84.337 415 36 14 2159 2547 776422269 776422680 1.950000e-101 379.0
15 TraesCS2D01G560300 chr2B 90.909 220 15 2 2349 2566 776554311 776554095 9.380000e-75 291.0
16 TraesCS2D01G560300 chr2B 80.631 222 14 13 2484 2677 776587730 776587510 7.720000e-31 145.0
17 TraesCS2D01G560300 chr2B 94.737 57 3 0 2621 2677 776554078 776554022 3.670000e-14 89.8
18 TraesCS2D01G560300 chr5D 88.193 559 44 9 1309 1854 515039418 515038869 0.000000e+00 647.0
19 TraesCS2D01G560300 chr5D 94.792 288 15 0 1307 1594 515094060 515093773 1.460000e-122 449.0
20 TraesCS2D01G560300 chr5D 96.787 249 4 2 1061 1309 515094335 515094091 1.920000e-111 412.0
21 TraesCS2D01G560300 chr5A 88.619 536 39 9 1309 1829 643311808 643311280 1.350000e-177 632.0
22 TraesCS2D01G560300 chr5A 86.345 476 27 25 855 1309 643312299 643311841 4.010000e-133 484.0
23 TraesCS2D01G560300 chr5A 86.715 414 36 7 206 613 653007064 653006664 2.450000e-120 442.0
24 TraesCS2D01G560300 chr5A 86.111 360 29 9 1484 1829 643311065 643310713 4.210000e-98 368.0
25 TraesCS2D01G560300 chr5A 84.211 380 38 9 1484 1849 643310498 643310127 1.530000e-92 350.0
26 TraesCS2D01G560300 chr1A 89.663 416 33 7 206 614 508570402 508569990 3.050000e-144 521.0
27 TraesCS2D01G560300 chr1A 92.308 130 8 2 13 140 508570538 508570409 1.640000e-42 183.0
28 TraesCS2D01G560300 chr7A 88.753 409 39 4 206 608 510498954 510498547 6.660000e-136 494.0
29 TraesCS2D01G560300 chr7A 88.122 362 30 11 1310 1663 151327856 151327500 4.120000e-113 418.0
30 TraesCS2D01G560300 chr2A 83.424 549 55 13 2052 2566 459096526 459095980 6.700000e-131 477.0
31 TraesCS2D01G560300 chr6A 80.466 686 77 23 1925 2566 559862857 559862185 3.120000e-129 472.0
32 TraesCS2D01G560300 chr3B 87.429 350 32 5 967 1316 496853857 496853520 2.500000e-105 392.0
33 TraesCS2D01G560300 chr6B 80.000 595 65 33 2014 2566 625378402 625377820 8.990000e-105 390.0
34 TraesCS2D01G560300 chr4B 87.552 241 24 2 2070 2310 66609109 66609343 9.440000e-70 274.0


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 TraesCS2D01G560300 chr2D 633235693 633238369 2676 True 4944.0 4944 100.0000 1 2677 1 chr2D.!!$R2 2676
1 TraesCS2D01G560300 chr2D 633257524 633260205 2681 True 4599.0 4599 97.6510 1 2677 1 chr2D.!!$R3 2676
2 TraesCS2D01G560300 chr2D 633284879 633287327 2448 True 4187.0 4187 97.5510 233 2677 1 chr2D.!!$R4 2444
3 TraesCS2D01G560300 chr2D 633295422 633298566 3144 False 785.5 1376 87.0620 855 2677 2 chr2D.!!$F1 1822
4 TraesCS2D01G560300 chr6D 20474364 20475331 967 True 1197.0 1197 89.3470 897 1860 1 chr6D.!!$R1 963
5 TraesCS2D01G560300 chr6D 18984429 18985334 905 False 750.0 750 82.5900 898 1788 1 chr6D.!!$F1 890
6 TraesCS2D01G560300 chr6D 414791174 414791821 647 True 460.0 460 80.6060 1948 2566 1 chr6D.!!$R2 618
7 TraesCS2D01G560300 chr5B 647878663 647879603 940 True 981.0 981 86.1710 929 1854 1 chr5B.!!$R1 925
8 TraesCS2D01G560300 chr5B 65090920 65091506 586 False 558.0 558 83.9290 7 618 1 chr5B.!!$F1 611
9 TraesCS2D01G560300 chr4A 639977521 639978049 528 False 817.0 817 94.5180 1066 1594 1 chr4A.!!$F1 528
10 TraesCS2D01G560300 chr2B 776644962 776645998 1036 True 578.0 686 87.3690 858 1860 2 chr2B.!!$R3 1002
11 TraesCS2D01G560300 chr5D 515038869 515039418 549 True 647.0 647 88.1930 1309 1854 1 chr5D.!!$R1 545
12 TraesCS2D01G560300 chr5D 515093773 515094335 562 True 430.5 449 95.7895 1061 1594 2 chr5D.!!$R2 533
13 TraesCS2D01G560300 chr5A 643310127 643312299 2172 True 458.5 632 86.3215 855 1849 4 chr5A.!!$R2 994
14 TraesCS2D01G560300 chr1A 508569990 508570538 548 True 352.0 521 90.9855 13 614 2 chr1A.!!$R1 601
15 TraesCS2D01G560300 chr2A 459095980 459096526 546 True 477.0 477 83.4240 2052 2566 1 chr2A.!!$R1 514
16 TraesCS2D01G560300 chr6A 559862185 559862857 672 True 472.0 472 80.4660 1925 2566 1 chr6A.!!$R1 641
17 TraesCS2D01G560300 chr6B 625377820 625378402 582 True 390.0 390 80.0000 2014 2566 1 chr6B.!!$R1 552

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
807 816 0.319641 GGTTCCATAGGCGACGGATC 60.32 60.0 0.0 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2447 5121 1.581149 AGGTTATGCTCCTCTAGGGGT 59.419 52.381 8.98 0.0 38.19 4.95 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
618 627 8.567948 GGTTTAAATCAGACTTCACTCATTTGA 58.432 33.333 0.00 0.00 0.00 2.69
807 816 0.319641 GGTTCCATAGGCGACGGATC 60.320 60.000 0.00 0.00 0.00 3.36
931 2217 1.259609 ATGGAAACGAGTACGACCCA 58.740 50.000 0.00 0.00 42.66 4.51
1170 2488 2.611971 CGGTGAGGAATTTCAGGTCGAA 60.612 50.000 0.00 0.00 0.00 3.71
1218 2536 1.115326 TCCGCCACATGATCGAGGAT 61.115 55.000 0.00 0.00 0.00 3.24
1333 2738 1.215673 CCAGCTCCTCCACCTCTACTA 59.784 57.143 0.00 0.00 0.00 1.82
1367 2772 1.038130 GCCGAGGACCTGAAGAGCTA 61.038 60.000 0.00 0.00 0.00 3.32
1630 3668 7.361799 GGCACTATTTCGTTGAATTACTCCTTT 60.362 37.037 0.00 0.00 0.00 3.11
1631 3669 8.662141 GCACTATTTCGTTGAATTACTCCTTTA 58.338 33.333 0.00 0.00 0.00 1.85
1812 3872 4.196193 TGAAATAGCCTTATTGTGTCCGG 58.804 43.478 0.00 0.00 30.00 5.14
1855 4485 2.598637 TGCGAAAGATCTGTCGAAATCG 59.401 45.455 34.29 17.57 39.64 3.34
1904 4534 3.130516 AGCAGCATTTGTCAGAATCATGG 59.869 43.478 0.00 0.00 0.00 3.66
2038 4670 3.429141 CCCAGAACTGCAGCAGCG 61.429 66.667 23.05 8.42 46.23 5.18
2093 4735 5.843421 ACTTCTTCCTGATGATACTAGGCAT 59.157 40.000 0.00 0.00 0.00 4.40
2124 4766 1.005275 AGGAGATGCGCCGATCATG 60.005 57.895 4.18 0.00 0.00 3.07
2133 4775 2.176273 GCCGATCATGAGCGCAAGT 61.176 57.895 27.11 0.00 39.12 3.16
2447 5121 8.090788 ACCAGCAGATAAATAAGAGAAAGGTA 57.909 34.615 0.00 0.00 0.00 3.08
2453 5127 9.155785 CAGATAAATAAGAGAAAGGTACCCCTA 57.844 37.037 8.74 0.00 41.56 3.53
2578 5252 4.614946 ACTGACTTCCGTGTTAGTACAAC 58.385 43.478 0.00 0.00 35.47 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
931 2217 2.116125 GCTGCCTTGGGTGGACTT 59.884 61.111 0.00 0.0 0.00 3.01
1359 2764 0.382515 AGTCGGCGTCATAGCTCTTC 59.617 55.000 6.85 0.0 37.29 2.87
1512 2963 7.869800 AGTCATTCTTGATGTTGAAAGTCTTC 58.130 34.615 0.00 0.0 37.06 2.87
1648 3688 9.817809 TCTTCTTGCATAATACGAAGTCTAAAT 57.182 29.630 0.00 0.0 43.93 1.40
1855 4485 1.623359 GCTGAGACTCGTGACATCAC 58.377 55.000 1.70 1.7 43.15 3.06
1887 4517 4.713824 AGCACCATGATTCTGACAAATG 57.286 40.909 0.00 0.0 0.00 2.32
2038 4670 7.587037 TTTAATGGGAGATCATTGGTGATTC 57.413 36.000 0.00 0.0 44.96 2.52
2093 4735 2.754552 GCATCTCCTGTTTGTTATGGCA 59.245 45.455 0.00 0.0 0.00 4.92
2133 4775 2.434884 GCTAGGCGTGCTTGCAGA 60.435 61.111 0.00 0.0 36.28 4.26
2447 5121 1.581149 AGGTTATGCTCCTCTAGGGGT 59.419 52.381 8.98 0.0 38.19 4.95
2624 5298 7.610305 GGAATATGAACTCCAACCACTAAGAAA 59.390 37.037 0.00 0.0 0.00 2.52


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

AutoCloner maintained by Alex Coulton.