Multiple sequence alignment - TraesCS2B01G001200

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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 TraesCS2B01G001200 chr2B 100.000 2402 0 0 1 2402 631838 634239 0.000000e+00 4436.0
1 TraesCS2B01G001200 chr2B 93.353 2407 136 9 1 2402 488701814 488704201 0.000000e+00 3537.0
2 TraesCS2B01G001200 chr2B 89.920 377 34 4 47 422 485685733 485685360 1.290000e-132 483.0
3 TraesCS2B01G001200 chr4A 96.719 2408 69 5 1 2402 622161369 622163772 0.000000e+00 4000.0
4 TraesCS2B01G001200 chr4A 88.854 323 29 3 1978 2295 716535122 716534802 8.050000e-105 390.0
5 TraesCS2B01G001200 chr4A 97.059 34 1 0 2369 2402 726216880 726216913 9.270000e-05 58.4
6 TraesCS2B01G001200 chr1A 96.216 2405 86 5 1 2402 143378964 143376562 0.000000e+00 3932.0
7 TraesCS2B01G001200 chr1A 95.254 1833 83 4 1 1830 480976003 480974172 0.000000e+00 2900.0
8 TraesCS2B01G001200 chr7A 94.142 2407 134 7 1 2402 346769592 346767188 0.000000e+00 3657.0
9 TraesCS2B01G001200 chr3D 96.416 1674 58 1 731 2402 124495014 124493341 0.000000e+00 2758.0
10 TraesCS2B01G001200 chr3D 95.646 735 29 3 1 732 124495796 124495062 0.000000e+00 1177.0
11 TraesCS2B01G001200 chr7B 96.587 586 19 1 1 585 511463902 511463317 0.000000e+00 970.0
12 TraesCS2B01G001200 chr1B 90.451 377 32 4 47 422 200035722 200035349 5.970000e-136 494.0
13 TraesCS2B01G001200 chr1B 88.889 45 5 0 1 45 84414545 84414501 3.340000e-04 56.5
14 TraesCS2B01G001200 chr5A 87.425 334 31 3 1835 2163 208947309 208947636 8.110000e-100 374.0
15 TraesCS2B01G001200 chr5A 86.826 334 35 2 1835 2163 219128348 219128677 4.880000e-97 364.0
16 TraesCS2B01G001200 chr5A 94.000 50 3 0 2353 2402 208947633 208947682 2.560000e-10 76.8
17 TraesCS2B01G001200 chr5A 95.455 44 2 0 2353 2396 219128674 219128717 1.190000e-08 71.3
18 TraesCS2B01G001200 chrUn 88.189 254 24 2 1910 2157 402215522 402215775 5.020000e-77 298.0
19 TraesCS2B01G001200 chrUn 93.220 59 4 0 1850 1908 333864602 333864660 1.180000e-13 87.9
20 TraesCS2B01G001200 chrUn 93.220 59 4 0 1850 1908 388630258 388630316 1.180000e-13 87.9
21 TraesCS2B01G001200 chrUn 94.000 50 3 0 2353 2402 402215831 402215880 2.560000e-10 76.8


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 TraesCS2B01G001200 chr2B 631838 634239 2401 False 4436.0 4436 100.000 1 2402 1 chr2B.!!$F1 2401
1 TraesCS2B01G001200 chr2B 488701814 488704201 2387 False 3537.0 3537 93.353 1 2402 1 chr2B.!!$F2 2401
2 TraesCS2B01G001200 chr4A 622161369 622163772 2403 False 4000.0 4000 96.719 1 2402 1 chr4A.!!$F1 2401
3 TraesCS2B01G001200 chr1A 143376562 143378964 2402 True 3932.0 3932 96.216 1 2402 1 chr1A.!!$R1 2401
4 TraesCS2B01G001200 chr1A 480974172 480976003 1831 True 2900.0 2900 95.254 1 1830 1 chr1A.!!$R2 1829
5 TraesCS2B01G001200 chr7A 346767188 346769592 2404 True 3657.0 3657 94.142 1 2402 1 chr7A.!!$R1 2401
6 TraesCS2B01G001200 chr3D 124493341 124495796 2455 True 1967.5 2758 96.031 1 2402 2 chr3D.!!$R1 2401
7 TraesCS2B01G001200 chr7B 511463317 511463902 585 True 970.0 970 96.587 1 585 1 chr7B.!!$R1 584

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
427 441 1.064685 GTGGTAGGGGGAAATCACTGG 60.065 57.143 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1626 1695 0.978146 GGAGCAGTAAGGAGGGAGCA 60.978 60.0 0.0 0.0 0.0 4.26 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
31 34 1.818785 GTCTGGAGCAGCAGCATCC 60.819 63.158 3.17 8.14 45.49 3.51
101 106 9.237846 GTAAGCTTCTGAAATGTAAATTATGCC 57.762 33.333 0.00 0.00 0.00 4.40
227 239 7.874016 TCTCGGTTTAAATACTGTGAGCTTAAA 59.126 33.333 0.00 0.00 0.00 1.52
228 240 8.556213 TCGGTTTAAATACTGTGAGCTTAAAT 57.444 30.769 0.00 0.00 0.00 1.40
229 241 9.656040 TCGGTTTAAATACTGTGAGCTTAAATA 57.344 29.630 0.00 0.00 0.00 1.40
302 314 9.495754 GATAATCTAAACTGCACATTCTGAAAC 57.504 33.333 0.00 0.00 0.00 2.78
427 441 1.064685 GTGGTAGGGGGAAATCACTGG 60.065 57.143 0.00 0.00 0.00 4.00
709 723 4.033358 CCACGCTGCTTAGATTGTCTAAAG 59.967 45.833 0.00 0.00 38.38 1.85
811 875 8.685838 TTTATTTCCTAACTGTGCACTTAGTT 57.314 30.769 21.89 21.89 40.09 2.24
812 876 9.781633 TTTATTTCCTAACTGTGCACTTAGTTA 57.218 29.630 21.80 21.80 38.11 2.24
1383 1451 9.582431 CAAAGATCATGCTTTTCTTTATGTCAT 57.418 29.630 10.43 0.00 37.55 3.06
1464 1532 5.183904 GCAATCTTTAGGAACTGGACATGTT 59.816 40.000 0.00 0.00 41.52 2.71
1506 1574 7.498900 CCTGTGCTTATACCATGATTTTGTCTA 59.501 37.037 0.00 0.00 0.00 2.59
1608 1677 1.051812 CTATTCCATCGCCCCTCACT 58.948 55.000 0.00 0.00 0.00 3.41
1612 1681 2.063979 CCATCGCCCCTCACTGGTA 61.064 63.158 0.00 0.00 0.00 3.25
1626 1695 0.914417 CTGGTACCCCACTCCCACAT 60.914 60.000 10.07 0.00 35.17 3.21
1736 1805 2.151881 TGGTGCTAACGAAAACGCTA 57.848 45.000 0.00 0.00 0.00 4.26
1749 1818 3.141488 CGCTACCTCCTCGCCACT 61.141 66.667 0.00 0.00 0.00 4.00
1750 1819 1.822613 CGCTACCTCCTCGCCACTA 60.823 63.158 0.00 0.00 0.00 2.74
2076 2145 2.044650 TGCTCCATTCTGGCAGCC 60.045 61.111 10.34 3.66 37.47 4.85
2097 2166 2.352814 CGTGAATCTCGGGACAGTTCTT 60.353 50.000 0.00 0.00 0.00 2.52
2146 2215 3.737559 TGGTGTTATCTGCCCATTCTT 57.262 42.857 0.00 0.00 0.00 2.52
2213 2284 3.934457 ATTGTTTGTTTCACGGATCCC 57.066 42.857 6.06 0.00 0.00 3.85
2326 2397 1.149133 AAATCCCACCCTCCTTGCCT 61.149 55.000 0.00 0.00 0.00 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 34 0.321671 TGAGAAGGAAGGAAGGTGCG 59.678 55.000 0.00 0.00 0.00 5.34
34 37 2.418669 TGGTTGAGAAGGAAGGAAGGT 58.581 47.619 0.00 0.00 0.00 3.50
227 239 4.332819 GCACGACAATTTAGCTCCTGTTAT 59.667 41.667 0.00 0.00 0.00 1.89
228 240 3.682858 GCACGACAATTTAGCTCCTGTTA 59.317 43.478 0.00 0.00 0.00 2.41
229 241 2.484264 GCACGACAATTTAGCTCCTGTT 59.516 45.455 0.00 0.00 0.00 3.16
230 242 2.076863 GCACGACAATTTAGCTCCTGT 58.923 47.619 0.00 0.00 0.00 4.00
302 314 3.306364 CCGAGGGCAAGAGTCCAATATAG 60.306 52.174 0.00 0.00 43.99 1.31
427 441 8.968242 CAAATAGAAGTTTTAGTTTCCAACTGC 58.032 33.333 0.00 0.00 42.84 4.40
591 605 7.083858 GCTATTGTTGTAGCAAGACAAAATGA 58.916 34.615 1.32 0.00 45.03 2.57
798 862 7.426456 CGAATTTTATGCTAACTAAGTGCACAG 59.574 37.037 21.04 11.28 39.63 3.66
812 876 9.450807 GAAATATGTGCTAACGAATTTTATGCT 57.549 29.630 0.00 0.00 0.00 3.79
859 923 6.183360 CCAAAATGGAAAAAGGATGCAAACAA 60.183 34.615 0.00 0.00 40.96 2.83
1137 1201 0.465705 CAGGATAAGCGGCCTTCAGA 59.534 55.000 0.00 0.00 32.47 3.27
1388 1456 5.634896 CCATTGGAATTTAGAGCATATCGC 58.365 41.667 0.00 0.00 42.91 4.58
1464 1532 3.370527 GCACAGGGGTTCTTATAGAGCAA 60.371 47.826 0.00 0.00 0.00 3.91
1612 1681 2.532715 AGCATGTGGGAGTGGGGT 60.533 61.111 0.00 0.00 0.00 4.95
1626 1695 0.978146 GGAGCAGTAAGGAGGGAGCA 60.978 60.000 0.00 0.00 0.00 4.26
1949 2018 7.026562 TGAACTTGCAAAATATACATTGGTCG 58.973 34.615 0.00 0.00 0.00 4.79
1996 2065 4.557690 CACAGTATGCAGTGTACGTACTTC 59.442 45.833 25.12 17.59 42.53 3.01
2076 2145 1.202582 AGAACTGTCCCGAGATTCACG 59.797 52.381 0.00 0.00 0.00 4.35
2097 2166 1.851304 GGATTGATCCAAGGCCACAA 58.149 50.000 5.01 1.72 46.38 3.33


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

AutoCloner maintained by Alex Coulton.